Tandem Repeats Finder Program written by:
Gary Benson
Department of Biomathematical Sciences
Mount Sinai School of Medicine
Version 4.00
Sequence: NFA 2003-09-04
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 6021225
ACGTcount: A:0.15, C:0.35, G:0.35, T:0.15
File 6 of 7
Found at i:3427646 original size:20 final size:21
Alignment explanation
Indices: 3427611--3427658 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
3427601 ATCACCGGGT
*
3427611 CGGCGACCGCCCCGGC-CAGCA
1 CGGCGGCCGCCCCGGCGCAG-A
3427632 CGGCGGCCG-CCCGGCGCAGA
1 CGGCGGCCGCCCCGGCGCAGA
3427652 CGGCGGC
1 CGGCGGC
3427659 GGATGATCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.10, C:0.48, G:0.42, T:0.00
Consensus pattern (21 bp):
CGGCGGCCGCCCCGGCGCAGA
Found at i:3428679 original size:76 final size:76
Alignment explanation
Indices: 3428594--3428767 Score: 287
Period size: 76 Copynumber: 2.3 Consensus size: 76
3428584 GACAGCACAG
3428594 CGCTCAGGCGGTGCCTGTCCGCCCGACCGGGGCGGCCTCCATGGTCACACTGCGCTACCACCTCC
1 CGCTCAGGCGGTGCCTGTCCGCCCGACCGGGGCGGCCTCCATGGTCACACTGCGCTACCACCTCC
3428659 GGCCGCTGACC
66 GGCCGCTGACC
* * * * *
3428670 CGCTCAGGCGGTGCCTGTTCGCCTGAGCGGGGCGGCCTCCATGGTCACGCTGCGCTACCGCCTCC
1 CGCTCAGGCGGTGCCTGTCCGCCCGACCGGGGCGGCCTCCATGGTCACACTGCGCTACCACCTCC
3428735 GGCCGCTGACC
66 GGCCGCTGACC
3428746 CGCTCAGGCGGTGGCCTG-CCGC
1 CGCTCAGGCGGT-GCCTGTCCGC
3428768 TTGGGCAGCT
Statistics
Matches: 91, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
76 86 0.95
77 5 0.05
ACGTcount: A:0.09, C:0.43, G:0.33, T:0.16
Consensus pattern (76 bp):
CGCTCAGGCGGTGCCTGTCCGCCCGACCGGGGCGGCCTCCATGGTCACACTGCGCTACCACCTCC
GGCCGCTGACC
Found at i:3433279 original size:18 final size:18
Alignment explanation
Indices: 3433256--3433291 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
3433246 GATACTCAGA
3433256 TTGATGTCACCGGGCTCG
1 TTGATGTCACCGGGCTCG
3433274 TTGATGTCACCGGGCTCG
1 TTGATGTCACCGGGCTCG
3433292 GCATCGCGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.28, G:0.33, T:0.28
Consensus pattern (18 bp):
TTGATGTCACCGGGCTCG
Found at i:3445014 original size:16 final size:16
Alignment explanation
Indices: 3444995--3445025 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
3444985 CACGGGCCGT
3444995 GCGACACACGACGACA
1 GCGACACACGACGACA
3445011 GCGACACACGACGAC
1 GCGACACACGACGAC
3445026 GTGGAGTGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.39, G:0.26, T:0.00
Consensus pattern (16 bp):
GCGACACACGACGACA
Found at i:3481080 original size:15 final size:16
Alignment explanation
Indices: 3481054--3481087 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
3481044 TGTTCGCCGA
3481054 GCCCGAGCACGCGCGC
1 GCCCGAGCACGCGCGC
*
3481070 GCCCG-GCACGCGCTC
1 GCCCGAGCACGCGCGC
3481085 GCC
1 GCC
3481088 GAGGTCTACG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.09, C:0.53, G:0.35, T:0.03
Consensus pattern (16 bp):
GCCCGAGCACGCGCGC
Found at i:3626625 original size:12 final size:12
Alignment explanation
Indices: 3626608--3626636 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
3626598 AATAGCGAGA
3626608 ACTCGTCACAGC
1 ACTCGTCACAGC
3626620 ACTCGTCACAGC
1 ACTCGTCACAGC
3626632 ACTCG
1 ACTCG
3626637 ACGCCGCGCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.24, C:0.41, G:0.17, T:0.17
Consensus pattern (12 bp):
ACTCGTCACAGC
Found at i:3630691 original size:15 final size:15
Alignment explanation
Indices: 3630671--3630703 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
3630661 TCACCGCGCG
3630671 CGCCGACG-GCCTGCA
1 CGCCGACGTG-CTGCA
3630686 CGCCGACGTGCTGCA
1 CGCCGACGTGCTGCA
3630701 CGC
1 CGC
3630704 GGTCCGCTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 16 0.94
16 1 0.06
ACGTcount: A:0.12, C:0.45, G:0.33, T:0.09
Consensus pattern (15 bp):
CGCCGACGTGCTGCA
Found at i:3634162 original size:15 final size:15
Alignment explanation
Indices: 3634138--3634167 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3634128 CGCGACCGAC
*
3634138 CAGCCGGCGCCCGCG
1 CAGCCCGCGCCCGCG
3634153 CAGCCCGCGCCCGCG
1 CAGCCCGCGCCCGCG
3634168 GACCGCTGCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.57, G:0.37, T:0.00
Consensus pattern (15 bp):
CAGCCCGCGCCCGCG
Found at i:3653470 original size:11 final size:11
Alignment explanation
Indices: 3653454--3653479 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3653444 ACCGGCCGGA
3653454 CTGATACGGCC
1 CTGATACGGCC
3653465 CTGATACGGCC
1 CTGATACGGCC
3653476 CTGA
1 CTGA
3653480 CACACCCACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.19, C:0.35, G:0.27, T:0.19
Consensus pattern (11 bp):
CTGATACGGCC
Found at i:3677270 original size:22 final size:23
Alignment explanation
Indices: 3677222--3677270 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 23
3677212 CCGAAGTCGG
3677222 GCGCGCCGCAGACGTGCGCGACC
1 GCGCGCCGCAGACGTGCGCGACC
3677245 -CGCGCC-CAGACCGTGCGCG-CC
1 GCGCGCCGCAGA-CGTGCGCGACC
3677266 GCGCG
1 GCGCG
3677271 GAATTTCGCG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
21 6 0.25
22 18 0.75
ACGTcount: A:0.10, C:0.47, G:0.39, T:0.04
Consensus pattern (23 bp):
GCGCGCCGCAGACGTGCGCGACC
Found at i:3682686 original size:15 final size:15
Alignment explanation
Indices: 3682676--3682711 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
3682666 GTGACAGTCG
3682676 CTCCGGCGACATCTA
1 CTCCGGCGACATCTA
*
3682691 CTCCGGCGACATCTT
1 CTCCGGCGACATCTA
3682706 CTCCGG
1 CTCCGG
3682712 ACATGCCAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.14, C:0.42, G:0.22, T:0.22
Consensus pattern (15 bp):
CTCCGGCGACATCTA
Found at i:3684865 original size:22 final size:21
Alignment explanation
Indices: 3684840--3684885 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
3684830 TGTACAGCTC
3684840 GCCGC-CGTCGGCGGGCGGACCG
1 GCCGCGCGTCGGC-GGC-GACCG
3684862 GCCGCGGCGTCGGCGGCGACCG
1 GCCGC-GCGTCGGCGGCGACCG
3684884 GC
1 GC
3684886 ACCGAGTGCG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 12 0.55
23 3 0.14
24 7 0.32
ACGTcount: A:0.04, C:0.41, G:0.50, T:0.04
Consensus pattern (21 bp):
GCCGCGCGTCGGCGGCGACCG
Found at i:3689249 original size:15 final size:15
Alignment explanation
Indices: 3689229--3689286 Score: 98
Period size: 15 Copynumber: 3.9 Consensus size: 15
3689219 CCTGACCCTG
*
3689229 CTGACCCGGCTGACC
1 CTGACCCGGCTGGCC
3689244 CTGACCCGGCTGGCC
1 CTGACCCGGCTGGCC
*
3689259 CTGACCCTGCTGGCC
1 CTGACCCGGCTGGCC
3689274 CTGACCCGGCTGG
1 CTGACCCGGCTGG
3689287 GCGGGCGGCT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 40 1.00
ACGTcount: A:0.09, C:0.45, G:0.31, T:0.16
Consensus pattern (15 bp):
CTGACCCGGCTGGCC
Found at i:3691064 original size:15 final size:14
Alignment explanation
Indices: 3691046--3691091 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
3691036 CGCGTTCGCG
*
3691046 GGCGGCCTGGTCGGC
1 GGCGGCC-GGGCGGC
3691061 GGCGGCGCGGGCGGC
1 GGCGGC-CGGGCGGC
3691076 GGCGGCCGCGGCGGC
1 GGCGGCCG-GGCGGC
3691091 G
1 G
3691092 ACCCGGATCG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 2 0.07
15 25 0.89
16 1 0.04
ACGTcount: A:0.00, C:0.35, G:0.61, T:0.04
Consensus pattern (14 bp):
GGCGGCCGGGCGGC
Found at i:3697857 original size:21 final size:21
Alignment explanation
Indices: 3697833--3697877 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3697823 CACGTTGATG
*
3697833 GGCGCGCTCGGCCT-CGGCTTC
1 GGCGCGCTCGACCTGCGGC-TC
*
3697854 GGCGTGCTCGACCTGCGGCTC
1 GGCGCGCTCGACCTGCGGCTC
3697875 GGC
1 GGC
3697878 CTCGACGGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.02, C:0.40, G:0.40, T:0.18
Consensus pattern (21 bp):
GGCGCGCTCGACCTGCGGCTC
Found at i:3700117 original size:16 final size:17
Alignment explanation
Indices: 3700082--3700141 Score: 65
Period size: 16 Copynumber: 3.7 Consensus size: 17
3700072 CCCAGTCTCA
3700082 CGAACCGGCAG-C-CTC
1 CGAACCGGCAGTCGCTC
*
3700097 ACGAACCGGCA-TCGTTC
1 -CGAACCGGCAGTCGCTC
*
3700114 CGAA-CGGCAGTGGCTC
1 CGAACCGGCAGTCGCTC
3700130 CGAACCGGCAGT
1 CGAACCGGCAGT
3700142 GTAAGAACTG
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
15 5 0.14
16 23 0.62
17 9 0.24
ACGTcount: A:0.22, C:0.37, G:0.30, T:0.12
Consensus pattern (17 bp):
CGAACCGGCAGTCGCTC
Found at i:3703064 original size:24 final size:24
Alignment explanation
Indices: 3703032--3703122 Score: 69
Period size: 24 Copynumber: 3.7 Consensus size: 24
3703022 TCGGGTGGCA
3703032 CCGCGAAGAAGACGGCCAAGGCGC
1 CCGCGAAGAAGACGGCCAAGGCGC
** *
3703056 CCGCGAAGAA-AGCCACCAAGGCGG
1 CCGCGAAGAAGA-CGGCCAAGGCGC
* * *
3703080 CGGCGAAGAAAACGGCCGAGAAGC-C
1 CCGCGAAGAAGACGGCC-A-AGGCGC
3703105 CGCGGCGAAGAAGACGGC
1 C-C-GCGAAGAAGACGGC
3703123 GAAGAAGACC
Statistics
Matches: 51, Mismatches: 10, Indels: 9
0.73 0.14 0.13
Matches are distributed among these distances:
23 1 0.02
24 31 0.61
25 3 0.06
26 3 0.06
27 13 0.25
ACGTcount: A:0.32, C:0.31, G:0.37, T:0.00
Consensus pattern (24 bp):
CCGCGAAGAAGACGGCCAAGGCGC
Found at i:3703122 original size:12 final size:12
Alignment explanation
Indices: 3703107--3703131 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3703097 GAGAAGCCCG
3703107 CGGCGAAGAAGA
1 CGGCGAAGAAGA
3703119 CGGCGAAGAAGA
1 CGGCGAAGAAGA
3703131 C
1 C
3703132 CGCCGCCCGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.20, G:0.40, T:0.00
Consensus pattern (12 bp):
CGGCGAAGAAGA
Found at i:3703128 original size:27 final size:27
Alignment explanation
Indices: 3703079--3703134 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
3703069 CACCAAGGCG
*
3703079 GCGGCGAAGAAAACGGCCGAGAAGCCC
1 GCGGCGAAGAAAACGGCCGAGAAGACC
*
3703106 GCGGCGAAGAAGACGG-CGAAGAAGACC
1 GCGGCGAAGAAAACGGCCG-AGAAGACC
3703133 GC
1 GC
3703135 CGCCCGCAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 2 0.08
27 24 0.92
ACGTcount: A:0.34, C:0.27, G:0.39, T:0.00
Consensus pattern (27 bp):
GCGGCGAAGAAAACGGCCGAGAAGACC
Found at i:3726375 original size:16 final size:15
Alignment explanation
Indices: 3726337--3726422 Score: 66
Period size: 15 Copynumber: 5.6 Consensus size: 15
3726327 CGGGCCGGCG
* *
3726337 CATTCCAGGGCGGCT
1 CATTCCAGAGCGGAT
*
3726352 CGTTCCAGAGACGGAT
1 CATTCCAGAG-CGGAT
* *
3726368 CCTTCCAGAGCGGCT
1 CATTCCAGAGCGGAT
**
3726383 CATTCCAGAGCCGCTT
1 CATTCCAGAG-CGGAT
3726399 CATTCCAGAGCCGG-T
1 CATTCCAGAG-CGGAT
*
3726414 TATTCCAGA
1 CATTCCAGA
3726423 TCGATGACGA
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
15 30 0.51
16 29 0.49
ACGTcount: A:0.20, C:0.33, G:0.26, T:0.22
Consensus pattern (15 bp):
CATTCCAGAGCGGAT
Found at i:3726405 original size:31 final size:31
Alignment explanation
Indices: 3726337--3726422 Score: 93
Period size: 31 Copynumber: 2.8 Consensus size: 31
3726327 CGGGCCGGCG
* * *
3726337 CATTCCAGGGCGGCTCGTTCCAGAGACGGAT
1 CATTCCAGAGCGGCTCATTCCAGAGACGCAT
* * *
3726368 CCTTCCAGAGCGGCTCATTCCAGAGCCGCTT
1 CATTCCAGAGCGGCTCATTCCAGAGACGCAT
*
3726399 CATTCCAGAGCCGG-TTATTCCAGA
1 CATTCCAGAG-CGGCTCATTCCAGA
3726423 TCGATGACGA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
31 43 0.93
32 3 0.07
ACGTcount: A:0.20, C:0.33, G:0.26, T:0.22
Consensus pattern (31 bp):
CATTCCAGAGCGGCTCATTCCAGAGACGCAT
Found at i:3734946 original size:21 final size:22
Alignment explanation
Indices: 3734906--3734946 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
3734896 GCATCCCGCA
*
3734906 CCGGCGCCCACCGCCGCCGATT
1 CCGGCGCCCACCGCCACCGATT
*
3734928 CCGGCG-CCAGCGCCACCGA
1 CCGGCGCCCACCGCCACCGA
3734947 CCGCTTCAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.12, C:0.54, G:0.29, T:0.05
Consensus pattern (22 bp):
CCGGCGCCCACCGCCACCGATT
Found at i:3739664 original size:12 final size:12
Alignment explanation
Indices: 3739647--3739676 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
3739637 CCGGGGCCGC
3739647 CACCGCGTCGGG
1 CACCGCGTCGGG
3739659 CACCGCGTCGGG
1 CACCGCGTCGGG
3739671 CACCGC
1 CACCGC
3739677 CACCGCGCGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.10, C:0.47, G:0.37, T:0.07
Consensus pattern (12 bp):
CACCGCGTCGGG
Found at i:3747200 original size:15 final size:15
Alignment explanation
Indices: 3747180--3747211 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
3747170 ACCCGAGCAG
3747180 CGACATCCGGAACCC
1 CGACATCCGGAACCC
3747195 CGACATCCGGAACCC
1 CGACATCCGGAACCC
3747210 CG
1 CG
3747212 TCCGTTCGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.47, G:0.22, T:0.06
Consensus pattern (15 bp):
CGACATCCGGAACCC
Found at i:3794938 original size:9 final size:9
Alignment explanation
Indices: 3794924--3794950 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
3794914 TGGCGCGGTG
3794924 CAGCAGCAC
1 CAGCAGCAC
3794933 CAGCAGCAC
1 CAGCAGCAC
3794942 CAGCAGCAC
1 CAGCAGCAC
3794951 GCTGGTGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.44, G:0.22, T:0.00
Consensus pattern (9 bp):
CAGCAGCAC
Found at i:3797212 original size:16 final size:16
Alignment explanation
Indices: 3797193--3797235 Score: 86
Period size: 16 Copynumber: 2.7 Consensus size: 16
3797183 CCGGCTCCCG
3797193 AACGAACCGGCGCGGA
1 AACGAACCGGCGCGGA
3797209 AACGAACCGGCGCGGA
1 AACGAACCGGCGCGGA
3797225 AACGAACCGGC
1 AACGAACCGGC
3797236 CCGGCATCGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.33, C:0.33, G:0.35, T:0.00
Consensus pattern (16 bp):
AACGAACCGGCGCGGA
Found at i:3848306 original size:15 final size:15
Alignment explanation
Indices: 3848286--3848314 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3848276 GCGGGCGCAG
3848286 CCGGCGCGCTCGCGC
1 CCGGCGCGCTCGCGC
3848301 CCGGCGCGCTCGCG
1 CCGGCGCGCTCGCG
3848315 GGCGCGCACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.52, G:0.41, T:0.07
Consensus pattern (15 bp):
CCGGCGCGCTCGCGC
Found at i:3866308 original size:14 final size:16
Alignment explanation
Indices: 3866289--3866321 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3866279 CGCGCCGTGC
3866289 ACCG-CCCCGA-CGCG
1 ACCGCCCCCGACCGCG
3866303 ACCGCCCCCGACCGCG
1 ACCGCCCCCGACCGCG
3866319 ACC
1 ACC
3866322 CCGGCACCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 6 0.35
16 7 0.41
ACGTcount: A:0.15, C:0.61, G:0.24, T:0.00
Consensus pattern (16 bp):
ACCGCCCCCGACCGCG
Found at i:3871670 original size:15 final size:15
Alignment explanation
Indices: 3871646--3871680 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
3871636 GGCGTTCGCC
*
3871646 GGGGCGGACGCGACA
1 GGGGCCGACGCGACA
*
3871661 GGGGCCGACGCGACG
1 GGGGCCGACGCGACA
3871676 GGGGC
1 GGGGC
3871681 GGCCGCCTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.14, C:0.29, G:0.57, T:0.00
Consensus pattern (15 bp):
GGGGCCGACGCGACA
Found at i:3876487 original size:24 final size:24
Alignment explanation
Indices: 3876460--3876506 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
3876450 GTTCTCCGCG
*
3876460 GCCGAGCTGGTCGGCGTC-ATCGAC
1 GCCGAGCTGGACGGC-TCGATCGAC
*
3876484 GCCGCGCTGGACGGCTCGATCGA
1 GCCGAGCTGGACGGCTCGATCGA
3876507 GGAACTCGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.13, C:0.34, G:0.38, T:0.15
Consensus pattern (24 bp):
GCCGAGCTGGACGGCTCGATCGAC
Found at i:3879490 original size:22 final size:23
Alignment explanation
Indices: 3879440--3879495 Score: 69
Period size: 25 Copynumber: 2.4 Consensus size: 23
3879430 CGCACACGCC
*
3879440 ACCGCACCCGTGGTGCGCATCAGCC
1 ACCGCACCCGTGGTGCG-A-CAGCA
3879465 ACCGCACCCGTGGTGCG-CAGCA
1 ACCGCACCCGTGGTGCGACAGCA
*
3879487 ACCGTACCC
1 ACCGCACCC
3879496 CGCGGGTGCG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 12 0.41
25 17 0.59
ACGTcount: A:0.18, C:0.45, G:0.27, T:0.11
Consensus pattern (23 bp):
ACCGCACCCGTGGTGCGACAGCA
Found at i:3881874 original size:15 final size:15
Alignment explanation
Indices: 3881854--3881889 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
3881844 TGGTTCTGCG
*
3881854 CCACCACCCGCCGCA
1 CCACCAACCGCCGCA
3881869 CCACCAACCGCCGCA
1 CCACCAACCGCCGCA
3881884 CCACCA
1 CCACCA
3881890 TTCGTCCACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.25, C:0.64, G:0.11, T:0.00
Consensus pattern (15 bp):
CCACCAACCGCCGCA
Found at i:3910876 original size:15 final size:15
Alignment explanation
Indices: 3910836--3910882 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
3910826 GTGCCGGTGC
3910836 GGTGGCGGGCGC-GG
1 GGTGGCGGGCGCGGG
*
3910850 GCTCGGCGGGCGCGGG
1 GGT-GGCGGGCGCGGG
*
3910866 GGTGGCCGGCGCCGGG
1 GGTGGCGGGCG-CGGG
3910882 G
1 G
3910883 CGGGCTGCGC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 2 0.07
15 16 0.59
16 9 0.33
ACGTcount: A:0.00, C:0.28, G:0.66, T:0.06
Consensus pattern (15 bp):
GGTGGCGGGCGCGGG
Found at i:3914941 original size:15 final size:15
Alignment explanation
Indices: 3914917--3914950 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
3914907 TCGGTGTAGC
3914917 GCCG-CTTGGCCTCG
1 GCCGCCTTGGCCTCG
3914931 GCCGCCTTGGCCTCG
1 GCCGCCTTGGCCTCG
3914946 GCCGC
1 GCCGC
3914951 GGCCATCCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.00, C:0.47, G:0.35, T:0.18
Consensus pattern (15 bp):
GCCGCCTTGGCCTCG
Found at i:3917552 original size:78 final size:78
Alignment explanation
Indices: 3917423--3917596 Score: 321
Period size: 78 Copynumber: 2.2 Consensus size: 78
3917413 GCGCCCGTCC
* *
3917423 ACCCGCTCAGTCGGTATCGACCTGCGCCTGAGCGGGACGGCCTCCGTGGTCACGCTCCGCTGCCA
1 ACCCGCTCAGTCGGTGTCCACCTGCGCCTGAGCGGGACGGCCTCCGTGGTCACGCTCCGCTGCCA
3917488 ACTCCGGCCGCTG
66 ACTCCGGCCGCTG
*
3917501 ACCCGCTCAGTCGGTGTCCACCTGCGCCTGAGCGGGACGGCCTCCGTGGTCACGCTCCGCTGCCG
1 ACCCGCTCAGTCGGTGTCCACCTGCGCCTGAGCGGGACGGCCTCCGTGGTCACGCTCCGCTGCCA
3917566 ACTCCGGCCGCTG
66 ACTCCGGCCGCTG
3917579 ACCCGCTCAGTCGGTGTC
1 ACCCGCTCAGTCGGTGTC
3917597 GAGCTGGGCG
Statistics
Matches: 93, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 93 1.00
ACGTcount: A:0.10, C:0.41, G:0.31, T:0.17
Consensus pattern (78 bp):
ACCCGCTCAGTCGGTGTCCACCTGCGCCTGAGCGGGACGGCCTCCGTGGTCACGCTCCGCTGCCA
ACTCCGGCCGCTG
Found at i:3926509 original size:18 final size:18
Alignment explanation
Indices: 3926486--3926520 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3926476 GCGTCGTCCT
*
3926486 GGGTCATGCCGCGCACCC
1 GGGTCAGGCCGCGCACCC
*
3926504 GGGTCAGGCCGTGCACC
1 GGGTCAGGCCGCGCACC
3926521 ACGCCGGACT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.11, C:0.40, G:0.37, T:0.11
Consensus pattern (18 bp):
GGGTCAGGCCGCGCACCC
Found at i:3933607 original size:27 final size:27
Alignment explanation
Indices: 3933565--3933676 Score: 197
Period size: 27 Copynumber: 4.1 Consensus size: 27
3933555 CTGCTGTCCG
*
3933565 GGCAGGTTCACGCACTCGCCGCGACGAT
1 GGCA-GTTCACACACTCGCCGCGACGAT
3933593 GGCAGTTCACACACTCGCCGCGACGAT
1 GGCAGTTCACACACTCGCCGCGACGAT
*
3933620 GGCAGTTCACACACTCGCCGCAACGAT
1 GGCAGTTCACACACTCGCCGCGACGAT
3933647 GGCAGTTCACACACTCGCCGCGACGAT
1 GGCAGTTCACACACTCGCCGCGACGAT
3933674 GGC
1 GGC
3933677 GACGAGCGGC
Statistics
Matches: 81, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
27 77 0.95
28 4 0.05
ACGTcount: A:0.21, C:0.37, G:0.28, T:0.14
Consensus pattern (27 bp):
GGCAGTTCACACACTCGCCGCGACGAT
Found at i:3937739 original size:24 final size:23
Alignment explanation
Indices: 3937712--3937889 Score: 91
Period size: 24 Copynumber: 7.4 Consensus size: 23
3937702 CCGGATCGAT
3937712 CGCACAGCACAGCGCAGGCACTGC
1 CGCACA-CACAGCGCAGGCACTGC
* * *
3937736 CGCAC-CACA-CGCCACCGAATCGGC
1 CGCACACACAGCG-CA-GGCA-CTGC
*
3937760 CGCGCAACACAGCGCAGGCACTGC
1 CGCAC-ACACAGCGCAGGCACTGC
* * *
3937784 CGCAC-CACA-CGCCACCGAATCGGC
1 CGCACACACAGCG-CA-GGCA-CTGC
*
3937808 CGCGCAACACAGCGCAGGCACTGC
1 CGCAC-ACACAGCGCAGGCACTGC
*
3937832 CGCAC-CACA-CGCCACCGG-ATCGGC
1 CGCACACACAGCG-CA--GGCA-CTGC
3937856 CGCACAGCACAGCGCAGGCACTGC
1 CGCACA-CACAGCGCAGGCACTGC
3937880 CGCACCACAC
1 CGCA-CACAC
3937890 GCCACCGATT
Statistics
Matches: 115, Mismatches: 18, Indels: 42
0.66 0.10 0.24
Matches are distributed among these distances:
21 6 0.05
22 18 0.16
23 5 0.04
24 55 0.48
25 7 0.06
26 18 0.16
27 6 0.05
ACGTcount: A:0.25, C:0.46, G:0.25, T:0.04
Consensus pattern (23 bp):
CGCACACACAGCGCAGGCACTGC
Found at i:3937743 original size:48 final size:48
Alignment explanation
Indices: 3937646--3937918 Score: 336
Period size: 48 Copynumber: 5.7 Consensus size: 48
3937636 CGACCGGAGA
* * * * * *
3937646 ACACGGCACCGGACCGACCGGC-CAGCACAGCGCGGGCGTCAG-CGGACC
1 ACACGCCACCGGATCGACC-GCACAGCACAGCGCAGGC-ACTGCCGCACC
* *
3937694 ACACGGCACCGGATCGATCGCACAGCACAGCGCAGGCACTGCCGCACC
1 ACACGCCACCGGATCGACCGCACAGCACAGCGCAGGCACTGCCGCACC
* * * *
3937742 ACACGCCACCGAATCGGCCGCGCAACACAGCGCAGGCACTGCCGCACC
1 ACACGCCACCGGATCGACCGCACAGCACAGCGCAGGCACTGCCGCACC
* * * *
3937790 ACACGCCACCGAATCGGCCGCGCAACACAGCGCAGGCACTGCCGCACC
1 ACACGCCACCGGATCGACCGCACAGCACAGCGCAGGCACTGCCGCACC
*
3937838 ACACGCCACCGGATCGGCCGCACAGCACAGCGCAGGCACTGCCGCACC
1 ACACGCCACCGGATCGACCGCACAGCACAGCGCAGGCACTGCCGCACC
*
3937886 ACACGCCACC-GATTCGACCGGACAGCACAGCGC
1 ACACGCCACCGGA-TCGACCGCACAGCACAGCGC
3937919 GAGCGTCACC
Statistics
Matches: 205, Mismatches: 17, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
47 6 0.03
48 199 0.97
ACGTcount: A:0.24, C:0.44, G:0.27, T:0.04
Consensus pattern (48 bp):
ACACGCCACCGGATCGACCGCACAGCACAGCGCAGGCACTGCCGCACC
Found at i:3938608 original size:21 final size:20
Alignment explanation
Indices: 3938583--3938621 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
3938573 GGCCGAGAGG
*
3938583 GCCGACGCACACGACACGGCA
1 GCCGAAGCACACG-CACGGCA
*
3938604 GCCGAAGGACACGCACGG
1 GCCGAAGCACACGCACGG
3938622 ACCGAGCCAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.28, C:0.38, G:0.33, T:0.00
Consensus pattern (20 bp):
GCCGAAGCACACGCACGGCA
Found at i:3942082 original size:12 final size:12
Alignment explanation
Indices: 3942065--3942089 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3942055 ATGACGGACC
3942065 AGCGCGACCACG
1 AGCGCGACCACG
3942077 AGCGCGACCACG
1 AGCGCGACCACG
3942089 A
1 A
3942090 CCACGCCGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.40, G:0.32, T:0.00
Consensus pattern (12 bp):
AGCGCGACCACG
Found at i:3953856 original size:15 final size:15
Alignment explanation
Indices: 3953836--3953864 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3953826 TCATGAGCGT
3953836 GGTGCTGCGCAACTC
1 GGTGCTGCGCAACTC
3953851 GGTGCTGCGCAACT
1 GGTGCTGCGCAACT
3953865 GGCCCGCCTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.31, G:0.34, T:0.21
Consensus pattern (15 bp):
GGTGCTGCGCAACTC
Found at i:3971239 original size:18 final size:18
Alignment explanation
Indices: 3971216--3971250 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
3971206 GGGGCAGCAC
3971216 CACCGGCAGCGGATCGCG
1 CACCGGCAGCGGATCGCG
3971234 CACCGGCAGCGGATCGC
1 CACCGGCAGCGGATCGC
3971251 TGCCGCGCCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.40, G:0.37, T:0.06
Consensus pattern (18 bp):
CACCGGCAGCGGATCGCG
Found at i:3971801 original size:15 final size:15
Alignment explanation
Indices: 3971781--3971839 Score: 91
Period size: 15 Copynumber: 3.9 Consensus size: 15
3971771 GGCCACCTCG
3971781 TCGTAGGCGTCGTCT
1 TCGTAGGCGTCGTCT
3971796 TCGTAGGCGTCGTCT
1 TCGTAGGCGTCGTCT
*
3971811 TCGTAGGTGTCGTCT
1 TCGTAGGCGTCGTCT
* *
3971826 CCGTAGGTGTCGTC
1 TCGTAGGCGTCGTC
3971840 GTAAGCCTCG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 42 1.00
ACGTcount: A:0.07, C:0.25, G:0.34, T:0.34
Consensus pattern (15 bp):
TCGTAGGCGTCGTCT
Found at i:3975702 original size:15 final size:16
Alignment explanation
Indices: 3975679--3975711 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
3975669 ATCAAGATCG
3975679 CGACACCGCA-GCCGT
1 CGACACCGCACGCCGT
*
3975694 CGACCCCGCACGCCGT
1 CGACACCGCACGCCGT
3975710 CG
1 CG
3975712 CCGACGCGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.15, C:0.52, G:0.27, T:0.06
Consensus pattern (16 bp):
CGACACCGCACGCCGT
Found at i:3976669 original size:15 final size:14
Alignment explanation
Indices: 3976649--3976752 Score: 100
Period size: 15 Copynumber: 7.0 Consensus size: 14
3976639 CGCAAGGCTG
3976649 CCGCCAAGAAGGCC
1 CCGCCAAGAAGGCC
3976663 CCGGCCAAGAAGGCC
1 CC-GCCAAGAAGGCC
* *
3976678 GCAGCGAAGAAGGCAC
1 -CCGCCAAGAAGGC-C
3976694 CCGCCAAGAAGGCC
1 CCGCCAAGAAGGCC
*
3976708 GCGGCCAAGAAGGCGC
1 -CCGCCAAGAAGGC-C
* *
3976724 CTGCGAAGAAGGCC
1 CCGCCAAGAAGGCC
*
3976738 ACCACCAAGAAGGCC
1 -CCGCCAAGAAGGCC
3976753 GGCCCCGACG
Statistics
Matches: 74, Mismatches: 10, Indels: 11
0.78 0.11 0.12
Matches are distributed among these distances:
14 4 0.05
15 67 0.91
16 3 0.04
ACGTcount: A:0.31, C:0.36, G:0.33, T:0.01
Consensus pattern (14 bp):
CCGCCAAGAAGGCC
Found at i:3976688 original size:30 final size:29
Alignment explanation
Indices: 3976651--3976752 Score: 116
Period size: 30 Copynumber: 3.4 Consensus size: 29
3976641 CAAGGCTGCC
3976651 GCCAAGAAGGCCCCGGCCAAGAAGGCCGCA
1 GCCAAGAAGGCCCC-GCCAAGAAGGCCGCA
* *
3976681 GCGAAGAAGGCACCCGCCAAGAAGGCCGCG
1 GCCAAGAAGGC-CCCGCCAAGAAGGCCGCA
* * *
3976711 GCCAAGAAGGCGCCTGCGAAGAAGGCCACCA
1 GCCAAGAAGGC-CCCGCCAAGAAGGCC-GCA
3976742 -CCAAGAAGGCC
1 GCCAAGAAGGCC
3976753 GGCCCCGACG
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
29 1 0.02
30 57 0.92
31 4 0.06
ACGTcount: A:0.31, C:0.34, G:0.33, T:0.01
Consensus pattern (29 bp):
GCCAAGAAGGCCCCGCCAAGAAGGCCGCA
Found at i:3976691 original size:45 final size:45
Alignment explanation
Indices: 3976649--3976752 Score: 147
Period size: 45 Copynumber: 2.3 Consensus size: 45
3976639 CGCAAGGCTG
*
3976649 CCGCCAAGAAGGCCCCGGCCAAGAAGGC-CGCAGCGAAGAAGGCAC
1 CCGCCAAGAAGGCCCCGGCCAAGAAGGCGC-CAGCGAAGAAGGCAA
* * *
3976694 CCGCCAAGAAGGCCGCGGCCAAGAAGGCGCCTGCGAAGAAGGCCA
1 CCGCCAAGAAGGCCCCGGCCAAGAAGGCGCCAGCGAAGAAGGCAA
*
3976739 CCACCAAGAAGGCC
1 CCGCCAAGAAGGCC
3976753 GGCCCCGACG
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
45 52 0.98
46 1 0.02
ACGTcount: A:0.31, C:0.36, G:0.33, T:0.01
Consensus pattern (45 bp):
CCGCCAAGAAGGCCCCGGCCAAGAAGGCGCCAGCGAAGAAGGCAA
Found at i:3993768 original size:18 final size:19
Alignment explanation
Indices: 3993745--3993780 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
3993735 GCGTTCTTTC
3993745 GTCTC-GGGCCACGTCTCG
1 GTCTCGGGGCCACGTCTCG
3993763 GTCTCGGGGCCACGTCTC
1 GTCTCGGGGCCACGTCTC
3993781 AGGCGGGATC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.06, C:0.39, G:0.33, T:0.22
Consensus pattern (19 bp):
GTCTCGGGGCCACGTCTCG
Found at i:4002118 original size:21 final size:22
Alignment explanation
Indices: 4002079--4002119 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
4002069 CGGTGACGGT
*
4002079 GCCGCCGCAGGCGGCGAGCATC
1 GCCGCCGCAGCCGGCGAGCATC
*
4002101 GCCG-CGCAGCCGGTGAGCA
1 GCCGCCGCAGCCGGCGAGCA
4002120 GCAGGCCGCG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.15, C:0.39, G:0.41, T:0.05
Consensus pattern (22 bp):
GCCGCCGCAGCCGGCGAGCATC
Found at i:4021571 original size:23 final size:23
Alignment explanation
Indices: 4021541--4021618 Score: 156
Period size: 23 Copynumber: 3.4 Consensus size: 23
4021531 AAAGGCCATC
4021541 GCCGCGGTCCGGCGCTGAACCGA
1 GCCGCGGTCCGGCGCTGAACCGA
4021564 GCCGCGGTCCGGCGCTGAACCGA
1 GCCGCGGTCCGGCGCTGAACCGA
4021587 GCCGCGGTCCGGCGCTGAACCGA
1 GCCGCGGTCCGGCGCTGAACCGA
4021610 GCCGCGGTC
1 GCCGCGGTC
4021619 TGCCGCCGAG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.12, C:0.40, G:0.40, T:0.09
Consensus pattern (23 bp):
GCCGCGGTCCGGCGCTGAACCGA
Found at i:4034479 original size:24 final size:23
Alignment explanation
Indices: 4034452--4034497 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
4034442 CGTTGACGAC
4034452 CGTCGCCTGGCG-GCTCGGCCATGT
1 CGTCGCC-GGCGTGCTC-GCCATGT
*
4034476 CGTCGTCGGCGTGCTCGCCATG
1 CGTCGCCGGCGTGCTCGCCATG
4034498 CGCAACGCCG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.04, C:0.37, G:0.37, T:0.22
Consensus pattern (23 bp):
CGTCGCCGGCGTGCTCGCCATGT
Found at i:4042177 original size:16 final size:16
Alignment explanation
Indices: 4042155--4042216 Score: 79
Period size: 16 Copynumber: 3.9 Consensus size: 16
4042145 CCTGGGCTGA
4042155 GCGGATTCAGGCGGGC
1 GCGGATTCAGGCGGGC
*
4042171 ACGGATTCAGGCGGGC
1 GCGGATTCAGGCGGGC
* * *
4042187 GCGGGTTCGGGCGGGT
1 GCGGATTCAGGCGGGC
*
4042203 GCGGGTTCAGGCGG
1 GCGGATTCAGGCGG
4042217 TGCGACGGCG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.10, C:0.23, G:0.53, T:0.15
Consensus pattern (16 bp):
GCGGATTCAGGCGGGC
Found at i:4050005 original size:15 final size:15
Alignment explanation
Indices: 4049985--4050015 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4049975 TTCGTGAACT
*
4049985 CGATGTCCGTCCCGC
1 CGATGTCCGTCACGC
4050000 CGATGTCCGTCACGC
1 CGATGTCCGTCACGC
4050015 C
1 C
4050016 TGTGGTCTCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.10, C:0.45, G:0.26, T:0.19
Consensus pattern (15 bp):
CGATGTCCGTCACGC
Found at i:4070049 original size:15 final size:15
Alignment explanation
Indices: 4070025--4070073 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 15
4070015 GGTTTTTCGT
*
4070025 CGCCAATGCTCGTCG
1 CGCCACTGCTCGTCG
4070040 CGCCACTGCTCGTCG
1 CGCCACTGCTCGTCG
* *
4070055 CGCTACGGCTCGTTCG
1 CGCCACTGCTCG-TCG
4070071 CGC
1 CGC
4070074 TACAACTTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
15 24 0.80
16 6 0.20
ACGTcount: A:0.08, C:0.43, G:0.29, T:0.20
Consensus pattern (15 bp):
CGCCACTGCTCGTCG
Found at i:4070073 original size:16 final size:15
Alignment explanation
Indices: 4070032--4070076 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
4070022 CGTCGCCAAT
* *
4070032 GCTCGTCGCGCCACT
1 GCTCGTCGCGCTACG
4070047 GCTCGTCGCGCTACG
1 GCTCGTCGCGCTACG
4070062 GCTCGTTCGCGCTAC
1 GCTCG-TCGCGCTAC
4070077 AACTTGTCGA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 18 0.67
16 9 0.33
ACGTcount: A:0.07, C:0.42, G:0.29, T:0.22
Consensus pattern (15 bp):
GCTCGTCGCGCTACG
Found at i:4081820 original size:13 final size:13
Alignment explanation
Indices: 4081804--4081833 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
4081794 CCGCATCCAC
*
4081804 CGACCGCGGGCCG
1 CGACCGCGGCCCG
4081817 CGACCGCGGCCCG
1 CGACCGCGGCCCG
4081830 CGAC
1 CGAC
4081834 AGACTTCATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.10, C:0.50, G:0.40, T:0.00
Consensus pattern (13 bp):
CGACCGCGGCCCG
Found at i:4081906 original size:15 final size:15
Alignment explanation
Indices: 4081886--4081915 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4081876 GGCGTCGCTG
*
4081886 GCCCTCGCCGTGACC
1 GCCCTCGCCCTGACC
4081901 GCCCTCGCCCTGACC
1 GCCCTCGCCCTGACC
4081916 CTCGGAGCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.57, G:0.23, T:0.13
Consensus pattern (15 bp):
GCCCTCGCCCTGACC
Found at i:4082447 original size:21 final size:21
Alignment explanation
Indices: 4082421--4082464 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
4082411 TGAGCCCGCA
4082421 GCCGTGAC-AGAGGGCCGGGAG
1 GCCGTGACGA-AGGGCCGGGAG
4082442 GCCGTGACGAAGGGCCGGGAG
1 GCCGTGACGAAGGGCCGGGAG
4082463 GC
1 GC
4082465 ATGCCTCCCG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.18, C:0.25, G:0.52, T:0.05
Consensus pattern (21 bp):
GCCGTGACGAAGGGCCGGGAG
Found at i:4084442 original size:12 final size:12
Alignment explanation
Indices: 4084412--4084460 Score: 64
Period size: 12 Copynumber: 4.2 Consensus size: 12
4084402 GCTCCCGCCG
*
4084412 GGCCGG-TCGGC
1 GGCCGGTTCCGC
4084423 GGCCGGTTCCGC
1 GGCCGGTTCCGC
* *
4084435 GGCGGGTTCGGC
1 GGCCGGTTCCGC
4084447 GGCCGGTTCCGC
1 GGCCGGTTCCGC
4084459 GG
1 GG
4084461 GCCGTGCCGA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
11 6 0.19
12 26 0.81
ACGTcount: A:0.00, C:0.35, G:0.51, T:0.14
Consensus pattern (12 bp):
GGCCGGTTCCGC
Found at i:4087466 original size:77 final size:78
Alignment explanation
Indices: 4087339--4087515 Score: 268
Period size: 77 Copynumber: 2.3 Consensus size: 78
4087329 ACCGACACGA
*
4087339 CCGGCCGCCGACCCGCTCAGGCTCAGTCCGAATTCGCCTGAGCGCGGCGGCCTCCACGGCCACAC
1 CCGGCCGCTGACCCGCTCAGGCTCAGTCCGAATTCGCCTGAGCGCGGCGGCCTCCACGGCCACAC
4087404 T-CCGCTACCCCT
66 TCCCGCTACCCCT
* * * *
4087416 CCGGCCGCTGACCCGCTCAGGCTGAG-CCGGATTGGGCCTGAGCGCGGCGGCCTCCACGGCCACG
1 CCGGCCGCTGACCCGCTCAGGCTCAGTCCGAATT-CGCCTGAGCGCGGCGGCCTCCACGGCCACA
*
4087480 CTCCCGCTACCGCT
65 CTCCCGCTACCCCT
*
4087494 ACGGCCGCTGACCCGCTCAGGC
1 CCGGCCGCTGACCCGCTCAGGC
4087516 GGTGACCGTG
Statistics
Matches: 91, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
76 6 0.07
77 54 0.59
78 31 0.34
ACGTcount: A:0.12, C:0.46, G:0.30, T:0.12
Consensus pattern (78 bp):
CCGGCCGCTGACCCGCTCAGGCTCAGTCCGAATTCGCCTGAGCGCGGCGGCCTCCACGGCCACAC
TCCCGCTACCCCT
Found at i:4091444 original size:23 final size:24
Alignment explanation
Indices: 4091418--4091467 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
4091408 CTCGATACGA
4091418 CTTTGTGCG-ATTTTGCGCGCAAC
1 CTTTGTGCGTATTTTGCGCGCAAC
* * *
4091441 CTTTGTGGGTCTTTTGCGCGGAAC
1 CTTTGTGCGTATTTTGCGCGCAAC
4091465 CTT
1 CTT
4091468 GTGGGCCACA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.10, C:0.24, G:0.28, T:0.38
Consensus pattern (24 bp):
CTTTGTGCGTATTTTGCGCGCAAC
Found at i:4091469 original size:23 final size:24
Alignment explanation
Indices: 4091428--4091472 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
4091418 CTTTGTGCGA
4091428 TTTTGCGCGCAACCTTTGTGGGTC
1 TTTTGCGCGCAACCTTTGTGGGTC
*
4091452 TTTTGCGCGGAACC-TTGTGGG
1 TTTTGCGCGCAACCTTTGTGGG
4091473 CCACAGGCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.09, C:0.22, G:0.33, T:0.36
Consensus pattern (24 bp):
TTTTGCGCGCAACCTTTGTGGGTC
Found at i:4159800 original size:17 final size:15
Alignment explanation
Indices: 4159763--4159803 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
4159753 GCCTTCTTGG
4159763 TTGG-GGTGGGCTTT
1 TTGGTGGTGGGCTTT
4159777 TTGGTGGTGGGCTTCT
1 TTGGTGGTGGGCTT-T
4159793 TCTGGTGGTGG
1 T-TGGTGGTGG
4159804 TCGTAGTCGG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.17
15 9 0.38
16 2 0.08
17 9 0.38
ACGTcount: A:0.00, C:0.10, G:0.49, T:0.41
Consensus pattern (15 bp):
TTGGTGGTGGGCTTT
Found at i:4178821 original size:19 final size:19
Alignment explanation
Indices: 4178797--4178836 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
4178787 ACCATCAGCT
4178797 TTGCGAGGTCGTCACGGCG
1 TTGCGAGGTCGTCACGGCG
4178816 TTGCGAGGTCGTCACGGCG
1 TTGCGAGGTCGTCACGGCG
4178835 TT
1 TT
4178837 TGCTCGTGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (19 bp):
TTGCGAGGTCGTCACGGCG
Found at i:4216220 original size:27 final size:27
Alignment explanation
Indices: 4216167--4216226 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
4216157 GACGCGGCGT
* *
4216167 GCGCTGCGGCATCGCACCCGGGTTCGG
1 GCGCGGCGGCATCGCACCCGGGCTCGG
*
4216194 GCGCGGCGGCATCG-AGCCGGGGCTCGG
1 GCGCGGCGGCATCGCA-CCCGGGCTCGG
*
4216221 CCGCGG
1 GCGCGG
4216227 ACCACCCGGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 1 0.04
27 27 0.96
ACGTcount: A:0.07, C:0.37, G:0.47, T:0.10
Consensus pattern (27 bp):
GCGCGGCGGCATCGCACCCGGGCTCGG
Found at i:4216312 original size:27 final size:27
Alignment explanation
Indices: 4216281--4216346 Score: 100
Period size: 27 Copynumber: 2.4 Consensus size: 27
4216271 CCGGCGTGGC
4216281 GCCGGGACGCGG-CGCACCCTG-GCCGGG
1 GCCGGGACGCGGAC-CACCCTGCG-CGGG
4216308 GCCGGGACGCGGACCACCCTGCGCGGG
1 GCCGGGACGCGGACCACCCTGCGCGGG
4216335 GCCGGGACGCGG
1 GCCGGGACGCGG
4216347 GCCGCCGGGC
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
27 35 0.95
28 2 0.05
ACGTcount: A:0.09, C:0.39, G:0.48, T:0.03
Consensus pattern (27 bp):
GCCGGGACGCGGACCACCCTGCGCGGG
Found at i:4216361 original size:27 final size:26
Alignment explanation
Indices: 4216281--4216361 Score: 74
Period size: 27 Copynumber: 3.0 Consensus size: 26
4216271 CCGGCGTGGC
*
4216281 GCCGGGACGCGGCGCACCCTGG-CCGGG
1 GCCGGGACGCGG-GC-CCCCGGCCCGGG
* * *
4216308 GCCGGGACGCGGACCACCCTGCGCGGG
1 GCCGGGACGCGGGCC-CCCGGCCCGGG
*
4216335 GCCGGGACGCGGGCCGCCGGGCCCGGG
1 GCCGGGACGCGGGCC-CCCGGCCCGGG
4216362 ACGGGCCGCC
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
25 1 0.02
26 4 0.09
27 38 0.88
ACGTcount: A:0.07, C:0.41, G:0.49, T:0.02
Consensus pattern (26 bp):
GCCGGGACGCGGGCCCCCGGCCCGGG
Found at i:4225678 original size:82 final size:83
Alignment explanation
Indices: 4225411--4225691 Score: 510
Period size: 83 Copynumber: 3.4 Consensus size: 83
4225401 AGGTGGTCGG
* * *
4225411 CCGCTTCTGAGCCGGGTCAGCGGCGGGAGGCGGCAGCGGAGCGTCACCCACGGAGGCCGCCCCGG
1 CCGCCTCTGAGCCGGGTCAGCGGCCGGAGCCGGCAGCGGAGCGTCACCCACGGAGGCCGCCCCGG
4225476 CTCAGGGCACATCGGACA
66 CTCAGGGCACATCGGACA
4225494 CCGCCTCTGAGCCGGGTCAGCGGCCGGAGCCGGCAGCGGAGCGTCACCCACGGAGGCCGCCCCGG
1 CCGCCTCTGAGCCGGGTCAGCGGCCGGAGCCGGCAGCGGAGCGTCACCCACGGAGGCCGCCCCGG
4225559 CTCAGGGCACATCGGACA
66 CTCAGGGCACATCGGACA
4225577 CCGCCTCTGAGCCGGGTCAGCGGCCGGAGCCGGCAGCGGAGCGTCA-CCACGGAGGCCGCCCCGG
1 CCGCCTCTGAGCCGGGTCAGCGGCCGGAGCCGGCAGCGGAGCGTCACCCACGGAGGCCGCCCCGG
* *
4225641 CTCAGAGCACGTCGGACA
66 CTCAGGGCACATCGGACA
4225659 CCGCCTCTGAGCCGGGTCAGCGGCCGGAGCCGG
1 CCGCCTCTGAGCCGGGTCAGCGGCCGGAGCCGG
4225692 GTCAGCTCCG
Statistics
Matches: 193, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
82 67 0.35
83 126 0.65
ACGTcount: A:0.15, C:0.38, G:0.39, T:0.08
Consensus pattern (83 bp):
CCGCCTCTGAGCCGGGTCAGCGGCCGGAGCCGGCAGCGGAGCGTCACCCACGGAGGCCGCCCCGG
CTCAGGGCACATCGGACA
Found at i:4229865 original size:18 final size:18
Alignment explanation
Indices: 4229844--4229879 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
4229834 ACGAATGGGA
4229844 TTGAGGACACGATGAGCG
1 TTGAGGACACGATGAGCG
4229862 TTGAGGACACGATGAGCG
1 TTGAGGACACGATGAGCG
4229880 CAGCCACGCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.17, G:0.39, T:0.17
Consensus pattern (18 bp):
TTGAGGACACGATGAGCG
Found at i:4233738 original size:78 final size:78
Alignment explanation
Indices: 4233609--4233881 Score: 501
Period size: 78 Copynumber: 3.5 Consensus size: 78
4233599 CGGGCGGCCA
4233609 GCTGCGCTACCACCTCCGGCCGCTGACACGCTCAGGCGGTGTCTGATTCTGCCTGAGCGGGGCGG
1 GCTGCGCTACCACCTCCGGCCGCTGACACGCTCAGGCGGTGTCTGATTCTGCCTGAGCGGGGCGG
*
4233674 CCTCCATGGTGAC
66 CCTCCGTGGTGAC
* *
4233687 GCTGCGCTACCACCTCCGCCCGCTGACCCGCTCAGGCGGTGTCTGATTCTGCCTGAGCGGGGCGG
1 GCTGCGCTACCACCTCCGGCCGCTGACACGCTCAGGCGGTGTCTGATTCTGCCTGAGCGGGGCGG
4233752 CCTCCGTGGTGAC
66 CCTCCGTGGTGAC
*
4233765 GCTGCGCTACCGCCTCCGGCCGCTGACACGCTCAGGCGGTGTCTGATTCTGCCTGAGCGGGGCGG
1 GCTGCGCTACCACCTCCGGCCGCTGACACGCTCAGGCGGTGTCTGATTCTGCCTGAGCGGGGCGG
4233830 CCTCCGTGGTGAC
66 CCTCCGTGGTGAC
*
4233843 GCTGCGCTACCGCCTCCGGCCGCTGACACGCTCAGGCGG
1 GCTGCGCTACCACCTCCGGCCGCTGACACGCTCAGGCGG
4233882 CGCGCGGCGA
Statistics
Matches: 189, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 189 1.00
ACGTcount: A:0.10, C:0.38, G:0.34, T:0.18
Consensus pattern (78 bp):
GCTGCGCTACCACCTCCGGCCGCTGACACGCTCAGGCGGTGTCTGATTCTGCCTGAGCGGGGCGG
CCTCCGTGGTGAC
Found at i:4236549 original size:9 final size:9
Alignment explanation
Indices: 4236535--4236567 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
4236525 CCGTCCGGCA
4236535 GACGGCTCG
1 GACGGCTCG
4236544 GACGGCTCG
1 GACGGCTCG
*
4236553 GACGGCTCA
1 GACGGCTCG
4236562 GACGGC
1 GACGGC
4236568 GGAACCGACC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.15, C:0.33, G:0.42, T:0.09
Consensus pattern (9 bp):
GACGGCTCG
Found at i:4245211 original size:14 final size:14
Alignment explanation
Indices: 4245192--4245221 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
4245182 GGGCATCGTC
4245192 TTGTTCACCATCAG
1 TTGTTCACCATCAG
4245206 TTGTTCACCATCAG
1 TTGTTCACCATCAG
4245220 TT
1 TT
4245222 CGGACTCCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.27, G:0.13, T:0.40
Consensus pattern (14 bp):
TTGTTCACCATCAG
Found at i:4255591 original size:15 final size:16
Alignment explanation
Indices: 4255571--4255601 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4255561 ACGGCCTGAG
4255571 GCCCCT-GGGAGGGCA
1 GCCCCTGGGGAGGGCA
4255586 GCCCCTGGGGAGGGCA
1 GCCCCTGGGGAGGGCA
4255602 TAGCGGCTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.13, C:0.32, G:0.48, T:0.06
Consensus pattern (16 bp):
GCCCCTGGGGAGGGCA
Found at i:4261762 original size:18 final size:18
Alignment explanation
Indices: 4261719--4261755 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
4261709 CGCCCCGCCT
*
4261719 CGCGACGAACACCGCACC
1 CGCGCCGAACACCGCACC
4261737 CGCGCCGAACACCGCACC
1 CGCGCCGAACACCGCACC
4261755 C
1 C
4261756 AGCCCGAGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.54, G:0.22, T:0.00
Consensus pattern (18 bp):
CGCGCCGAACACCGCACC
Found at i:4271312 original size:15 final size:15
Alignment explanation
Indices: 4271292--4271325 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
4271282 GCGCCCGTCG
*
4271292 CCGCACCCTTCTTTC
1 CCGCACCCTTCTTCC
4271307 CCGCACCCTTCTTCC
1 CCGCACCCTTCTTCC
4271322 CCGC
1 CCGC
4271326 GGCCTGTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.06, C:0.59, G:0.09, T:0.26
Consensus pattern (15 bp):
CCGCACCCTTCTTCC
Found at i:4271339 original size:15 final size:15
Alignment explanation
Indices: 4271321--4271354 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
4271311 ACCCTTCTTC
4271321 CCCGCGGCCTGTTTT
1 CCCGCGGCCTGTTTT
4271336 CCCGCGGCCTGTTTT
1 CCCGCGGCCTGTTTT
4271351 CCCG
1 CCCG
4271355 TGGATTTCGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.00, C:0.44, G:0.26, T:0.29
Consensus pattern (15 bp):
CCCGCGGCCTGTTTT
Found at i:4281329 original size:18 final size:18
Alignment explanation
Indices: 4281306--4281341 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
4281296 TCGGCCCGGG
4281306 ACGAACAGGCACCACCGC
1 ACGAACAGGCACCACCGC
4281324 ACGAACAGGCACCACCGC
1 ACGAACAGGCACCACCGC
4281342 GACAGGCCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.44, G:0.22, T:0.00
Consensus pattern (18 bp):
ACGAACAGGCACCACCGC
Found at i:4281346 original size:15 final size:17
Alignment explanation
Indices: 4281305--4281348 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
4281295 GTCGGCCCGG
4281305 GACGAACAGGCACCACC
1 GACGAACAGGCACCACC
4281322 GCACGAACAGGCACCACC
1 G-ACGAACAGGCACCACC
4281340 G-CG-ACAGGC
1 GACGAACAGGC
4281349 CAGGAGACCA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 6 0.23
16 2 0.08
17 1 0.04
18 17 0.65
ACGTcount: A:0.32, C:0.41, G:0.27, T:0.00
Consensus pattern (17 bp):
GACGAACAGGCACCACC
Found at i:4288172 original size:15 final size:15
Alignment explanation
Indices: 4288134--4288175 Score: 75
Period size: 15 Copynumber: 2.8 Consensus size: 15
4288124 GATGCCCCCG
*
4288134 CCGCCGCCATCCGCA
1 CCGCCGCCGTCCGCA
4288149 CCGCCGCCGTCCGCA
1 CCGCCGCCGTCCGCA
4288164 CCGCCGCCGTCC
1 CCGCCGCCGTCC
4288176 ACGTCGCCGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.07, C:0.62, G:0.24, T:0.07
Consensus pattern (15 bp):
CCGCCGCCGTCCGCA
Found at i:4288185 original size:18 final size:18
Alignment explanation
Indices: 4288164--4288206 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
4288154 GCCGTCCGCA
* *
4288164 CCGCCGCCGTCCACGTCG
1 CCGCCCCCGACCACGTCG
*
4288182 CCGCCCCCGACCTCGTCG
1 CCGCCCCCGACCACGTCG
*
4288200 CCTCCCC
1 CCGCCCC
4288207 GGGTCCCCGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.05, C:0.63, G:0.21, T:0.12
Consensus pattern (18 bp):
CCGCCCCCGACCACGTCG
Found at i:4288313 original size:18 final size:18
Alignment explanation
Indices: 4288195--4288307 Score: 208
Period size: 18 Copynumber: 6.2 Consensus size: 18
4288185 CCCCCGACCT
*
4288195 CGTCGCCTCCCCGGGTCCC
1 CGTCACCTCCCC-GGTCCC
4288214 CGTCACCTCCCCGGTCCC
1 CGTCACCTCCCCGGTCCC
4288232 CGTCACCTCCCCGGTCCC
1 CGTCACCTCCCCGGTCCC
4288250 CGTCACCTCCCCGGTCCC
1 CGTCACCTCCCCGGTCCC
4288268 CGTCACCTCCCCGGTCCC
1 CGTCACCTCCCCGGTCCC
4288286 CGTCACCTCCCCGGTCCC
1 CGTCACCTCCCCGGTCCC
4288304 CGTC
1 CGTC
4288308 GACTCCGCTG
Statistics
Matches: 93, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
18 82 0.88
19 11 0.12
ACGTcount: A:0.04, C:0.60, G:0.19, T:0.17
Consensus pattern (18 bp):
CGTCACCTCCCCGGTCCC
Found at i:4288531 original size:21 final size:21
Alignment explanation
Indices: 4288493--4288532 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
4288483 ACCGCCCCCG
* *
4288493 CGCCGCGGTCGCCATCGCCAT
1 CGCCGCGGCCACCATCGCCAT
*
4288514 CGCCGCGGCCACCTTCGCC
1 CGCCGCGGCCACCATCGCC
4288533 GCCGCAGGCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.07, C:0.53, G:0.28, T:0.12
Consensus pattern (21 bp):
CGCCGCGGCCACCATCGCCAT
Found at i:4288632 original size:114 final size:114
Alignment explanation
Indices: 4288415--4288632 Score: 287
Period size: 114 Copynumber: 1.9 Consensus size: 114
4288405 CCGCCGTTCC
* * *
4288415 CGCCGCCGACGGCGCTGTCACCGGATTCGTCACCCCTGTCCCCCACGCTGCTGCGGGCTGCATCC
1 CGCCGCCGACGGCACTGTCACCGAATTCCTCACCCCTGTCCCCCACGCTGCTGCGGGCTGCATCC
* * * *
4288480 GAGACCGCCCCCGCGCCGCGGTCGCCATCGCCATCGCCGCGGCCACCTT
66 GAGACCGCCCCCGCACCGCGGCCGCCATCACCACCGCCGCGGCCACCTT
* * *
4288529 CGCCGCCG-CAGGCACTGTCACCGAATTCCTCGCTCCTGTCCCCCACGCTGCTGCGGGCTGCATG
1 CGCCGCCGAC-GGCACTGTCACCGAATTCCTCACCCCTGTCCCCCACGCTGCTGCGGGCTGCATC
* * *
4288593 CGAGACTGCCCCGGCACCGTC-GCCGCCGTCACCACCGCCG
65 CGAGACCGCCCCCGCACCG-CGGCCGCCATCACCACCGCCG
4288633 TTGCCGTAGC
Statistics
Matches: 89, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
113 1 0.01
114 87 0.98
115 1 0.01
ACGTcount: A:0.11, C:0.48, G:0.28, T:0.14
Consensus pattern (114 bp):
CGCCGCCGACGGCACTGTCACCGAATTCCTCACCCCTGTCCCCCACGCTGCTGCGGGCTGCATCC
GAGACCGCCCCCGCACCGCGGCCGCCATCACCACCGCCGCGGCCACCTT
Found at i:4301368 original size:18 final size:18
Alignment explanation
Indices: 4301345--4301380 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
4301335 GGCTGGGTTT
4301345 GCTGCCGTAATCCACAGC
1 GCTGCCGTAATCCACAGC
**
4301363 GCTGCCGTCGTCCACAGC
1 GCTGCCGTAATCCACAGC
4301381 CGTCGGGCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.42, G:0.25, T:0.17
Consensus pattern (18 bp):
GCTGCCGTAATCCACAGC
Found at i:4306777 original size:13 final size:12
Alignment explanation
Indices: 4306752--4306797 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
4306742 TTGGAGATGT
4306752 CGGGCATCCCGG
1 CGGGCATCCCGG
4306764 CGGGCATCCC--
1 CGGGCATCCCGG
*
4306774 C-GGCATTCCGG
1 CGGGCATCCCGG
4306785 CGGGCATGCCCGG
1 CGGGCAT-CCCGG
4306798 GAATCCGCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
9 7 0.25
10 1 0.04
11 1 0.04
12 15 0.54
13 4 0.14
ACGTcount: A:0.09, C:0.41, G:0.39, T:0.11
Consensus pattern (12 bp):
CGGGCATCCCGG
Found at i:4306784 original size:21 final size:21
Alignment explanation
Indices: 4306754--4306797 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
4306744 GGAGATGTCG
4306754 GGCATCCCGGCGGGCATCCCC
1 GGCATCCCGGCGGGCATCCCC
* *
4306775 GGCATTCCGGCGGGCATGCCC
1 GGCATCCCGGCGGGCATCCCC
4306796 GG
1 GG
4306798 GAATCCGCCG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.09, C:0.41, G:0.39, T:0.11
Consensus pattern (21 bp):
GGCATCCCGGCGGGCATCCCC
Found at i:4306804 original size:21 final size:21
Alignment explanation
Indices: 4306760--4306804 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
4306750 GTCGGGCATC
*
4306760 CCGGCGGGCATCCCCGGCATT
1 CCGGCGGGCATCCCCGGCAAT
* *
4306781 CCGGCGGGCATGCCCGGGAAT
1 CCGGCGGGCATCCCCGGCAAT
4306802 CCG
1 CCG
4306805 CCGCGCACCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.11, C:0.40, G:0.38, T:0.11
Consensus pattern (21 bp):
CCGGCGGGCATCCCCGGCAAT
Found at i:4306851 original size:9 final size:9
Alignment explanation
Indices: 4306837--4306864 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
4306827 GGCCGCGACC
4306837 GCCCTTCTT
1 GCCCTTCTT
4306846 GCCCTTCTT
1 GCCCTTCTT
4306855 GCCCTTCTT
1 GCCCTTCTT
4306864 G
1 G
4306865 GCGTTGCGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.00, C:0.43, G:0.14, T:0.43
Consensus pattern (9 bp):
GCCCTTCTT
Found at i:4314288 original size:15 final size:15
Alignment explanation
Indices: 4314268--4314334 Score: 98
Period size: 15 Copynumber: 4.5 Consensus size: 15
4314258 TGCCGGCGTG
4314268 TCGGTGGGCGCGGTA
1 TCGGTGGGCGCGGTA
4314283 TCGGTGGGCGCGGTA
1 TCGGTGGGCGCGGTA
* * *
4314298 TGGGTGGGCGCCGTG
1 TCGGTGGGCGCGGTA
*
4314313 TCGGTGGGCGCGGTG
1 TCGGTGGGCGCGGTA
4314328 TCGGTGG
1 TCGGTGG
4314335 CCGGTGCCGT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 47 1.00
ACGTcount: A:0.03, C:0.19, G:0.57, T:0.21
Consensus pattern (15 bp):
TCGGTGGGCGCGGTA
Found at i:4316995 original size:21 final size:21
Alignment explanation
Indices: 4316969--4317008 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
4316959 GTGCCGCTGG
4316969 GCGGCGACGA-GTTCGGCCTTC
1 GCGGCGACGATG-TCGGCCTTC
*
4316990 GCGGCGTCGATGTCGGCCT
1 GCGGCGACGATGTCGGCCT
4317009 GGATCTCGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.07, C:0.33, G:0.40, T:0.20
Consensus pattern (21 bp):
GCGGCGACGATGTCGGCCTTC
Found at i:4317980 original size:24 final size:24
Alignment explanation
Indices: 4317931--4317981 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
4317921 CGGCGGCGAT
*
4317931 CTCCACCGCCTCGCGCAGTTCCGC
1 CTCCACCGCCTCGCGCAGGTCCGC
* *
4317955 CTCCTCCGCCTCGACGC-GGTCGGC
1 CTCCACCGCCTCG-CGCAGGTCCGC
4317979 CTC
1 CTC
4317982 GGCCTCCAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 20 0.87
25 3 0.13
ACGTcount: A:0.06, C:0.53, G:0.24, T:0.18
Consensus pattern (24 bp):
CTCCACCGCCTCGCGCAGGTCCGC
Found at i:4321059 original size:30 final size:30
Alignment explanation
Indices: 4321011--4321069 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
4321001 CTCCATCTTC
* *
4321011 CACAGGGTGGATCTTCCACAATGGAATGTT
1 CACAGGGTGCATCCTCCACAATGGAATGTT
* **
4321041 CACAGTGTGCATCCTCCACTGTGGAATGT
1 CACAGGGTGCATCCTCCACAATGGAATGT
4321070 CAATGCCGTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.27
Consensus pattern (30 bp):
CACAGGGTGCATCCTCCACAATGGAATGTT
Found at i:4327684 original size:27 final size:26
Alignment explanation
Indices: 4327653--4327706 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 26
4327643 GCGTGCCGAA
4327653 CTGGCCGA-CGCCTACGACGAGCCGCGC
1 CTGGCCGAGCGCCTACG-CGAG-CGCGC
*
4327680 CTGGCCGAGCGCCTGCGCGAGCGCGC
1 CTGGCCGAGCGCCTACGCGAGCGCGC
4327706 C
1 C
4327707 GCGGAGCTGC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 6 0.24
27 12 0.48
28 7 0.28
ACGTcount: A:0.11, C:0.44, G:0.37, T:0.07
Consensus pattern (26 bp):
CTGGCCGAGCGCCTACGCGAGCGCGC
Found at i:4337431 original size:18 final size:18
Alignment explanation
Indices: 4337390--4337433 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
4337380 CCTCGATGGT
*
4337390 GCCGATGGTGTCGCCCGC
1 GCCGACGGTGTCGCCCGC
*
4337408 -CGCGACGGTGTCGCCCTC
1 GC-CGACGGTGTCGCCCGC
4337426 GCCGACGG
1 GCCGACGG
4337434 CCAGGGTCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 1 0.05
18 20 0.91
19 1 0.05
ACGTcount: A:0.07, C:0.41, G:0.39, T:0.14
Consensus pattern (18 bp):
GCCGACGGTGTCGCCCGC
Found at i:4354391 original size:15 final size:17
Alignment explanation
Indices: 4354347--4354392 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 17
4354337 GCGCACTACA
4354347 CGCCGCCCGCGCGGCCGT
1 CGCCGCCCGCGC-GCCGT
**
4354365 CGCCGCGTGCGC-CCG-
1 CGCCGCCCGCGCGCCGT
4354380 CGCCGCCCGCGCG
1 CGCCGCCCGCGCG
4354393 GTGTGACCCC
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
15 10 0.43
16 3 0.13
18 10 0.43
ACGTcount: A:0.00, C:0.57, G:0.39, T:0.04
Consensus pattern (17 bp):
CGCCGCCCGCGCGCCGT
Found at i:4360684 original size:15 final size:15
Alignment explanation
Indices: 4360666--4360718 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 15
4360656 GCGGGCGCCT
4360666 TCTTCGCGGCCGTGG
1 TCTTCGCGGCCGTGG
4360681 TCTTCTTGGCGGCCGTGG
1 TCTTC---GCGGCCGTGG
*
4360699 CCTTCGTC-GCCGTGG
1 TCTTCG-CGGCCGTGG
4360714 TCTTC
1 TCTTC
4360719 TTGGCGGCGG
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
15 17 0.53
16 1 0.03
18 14 0.44
ACGTcount: A:0.00, C:0.34, G:0.34, T:0.32
Consensus pattern (15 bp):
TCTTCGCGGCCGTGG
Found at i:4360685 original size:18 final size:18
Alignment explanation
Indices: 4360664--4360732 Score: 74
Period size: 18 Copynumber: 4.0 Consensus size: 18
4360654 TCGCGGGCGC
4360664 CTTCTTCGCGGCCGTGGT
1 CTTCTTCGCGGCCGTGGT
*
4360682 CTTCTTGGCGGCCGTGG-
1 CTTCTTCGCGGCCGTGGT
4360699 C--CTTCGTC-GCCGTGGT
1 CTTCTTCG-CGGCCGTGGT
* *
4360715 CTTCTTGGCGGCGGTGGT
1 CTTCTTCGCGGCCGTGGT
4360733 GGTCTTCTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
15 11 0.26
16 2 0.05
17 2 0.05
18 27 0.64
ACGTcount: A:0.00, C:0.30, G:0.38, T:0.32
Consensus pattern (18 bp):
CTTCTTCGCGGCCGTGGT
Found at i:4360735 original size:21 final size:21
Alignment explanation
Indices: 4360710--4360752 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
4360700 CTTCGTCGCC
*
4360710 GTGGTCTTCTTGGCGGCGGTG
1 GTGGTCTTCTTGGCCGCGGTG
4360731 GTGGTCTTCTTGGCCGCGGTG
1 GTGGTCTTCTTGGCCGCGGTG
4360752 G
1 G
4360753 CCTTGGTCGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.00, C:0.21, G:0.47, T:0.33
Consensus pattern (21 bp):
GTGGTCTTCTTGGCCGCGGTG
Found at i:4360770 original size:15 final size:15
Alignment explanation
Indices: 4360752--4360794 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
4360742 GGCCGCGGTG
*
4360752 GCCTTGGTCGCCGAC
1 GCCTTGGTCGCCGAA
4360767 GCCTTGGTCGCCGAA
1 GCCTTGGTCGCCGAA
*
4360782 GCCTTGGTGGCCG
1 GCCTTGGTCGCCG
4360795 TCGTCTTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.07, C:0.35, G:0.37, T:0.21
Consensus pattern (15 bp):
GCCTTGGTCGCCGAA
Found at i:4360939 original size:15 final size:15
Alignment explanation
Indices: 4360919--4360950 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
4360909 TGGCCGTGGT
4360919 GGTCTTCTTGGCGGC
1 GGTCTTCTTGGCGGC
4360934 GGTCTTCTTGGCGGC
1 GGTCTTCTTGGCGGC
4360949 GG
1 GG
4360951 CCGTGGTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.25, G:0.44, T:0.31
Consensus pattern (15 bp):
GGTCTTCTTGGCGGC
Found at i:4360944 original size:36 final size:36
Alignment explanation
Indices: 4360880--4360981 Score: 111
Period size: 36 Copynumber: 2.9 Consensus size: 36
4360870 GGGCCTTGGT
* * *
4360880 CGCCGTCGTCTTCTTGGCGG-GGGC--CTTGGTGGC
1 CGCCGTGGTCTTCTTGGCGGCGGTCTTCTTGGCGGC
**
4360913 CGTGGTGGTCTTCTTGGCGGCGGTCTTCTTGGCGGC
1 CGCCGTGGTCTTCTTGGCGGCGGTCTTCTTGGCGGC
* * *
4360949 GGCCGTGGTCTTCTTGGCCGCCGTCTTCTTGGC
1 CGCCGTGGTCTTCTTGGCGGCGGTCTTCTTGGC
4360982 CGCCACAGGG
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
33 17 0.30
34 3 0.05
36 36 0.64
ACGTcount: A:0.00, C:0.29, G:0.39, T:0.31
Consensus pattern (36 bp):
CGCCGTGGTCTTCTTGGCGGCGGTCTTCTTGGCGGC
Found at i:4360967 original size:15 final size:15
Alignment explanation
Indices: 4360956--4360985 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
4360946 GGCGGCCGTG
4360956 GTCTTCTTGGCCGCC
1 GTCTTCTTGGCCGCC
4360971 GTCTTCTTGGCCGCC
1 GTCTTCTTGGCCGCC
4360986 ACAGGGGCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.40, G:0.27, T:0.33
Consensus pattern (15 bp):
GTCTTCTTGGCCGCC
Found at i:4373418 original size:20 final size:21
Alignment explanation
Indices: 4373393--4373433 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
4373383 GCAGTTCCGT
4373393 AGATACAGAAAGG-CCCGCAC
1 AGATACAGAAAGGCCCCGCAC
4373413 AGATACAGAAAGGCCCCGCAC
1 AGATACAGAAAGGCCCCGCAC
4373434 CGACCGGTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.39, C:0.32, G:0.24, T:0.05
Consensus pattern (21 bp):
AGATACAGAAAGGCCCCGCAC
Found at i:4373472 original size:15 final size:15
Alignment explanation
Indices: 4373452--4373517 Score: 69
Period size: 15 Copynumber: 4.1 Consensus size: 15
4373442 GCGGGGCCTT
4373452 GTTCAACGCCTCAGC
1 GTTCAACGCCTCAGC
4373467 GTTCAATGCCCGCCTCAGC
1 GTTCAA----CGCCTCAGC
* * *
4373486 GTTCAATGCGTCGGC
1 GTTCAACGCCTCAGC
4373501 GTTCAACGCCTCAGC
1 GTTCAACGCCTCAGC
4373516 GT
1 GT
4373518 GATCAGCCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
15 26 0.63
19 15 0.37
ACGTcount: A:0.17, C:0.36, G:0.24, T:0.23
Consensus pattern (15 bp):
GTTCAACGCCTCAGC
Found at i:4373482 original size:19 final size:19
Alignment explanation
Indices: 4373458--4373494 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
4373448 CCTTGTTCAA
4373458 CGCCTCAGCGTTCAATGCC
1 CGCCTCAGCGTTCAATGCC
4373477 CGCCTCAGCGTTCAATGC
1 CGCCTCAGCGTTCAATGC
4373495 GTCGGCGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.16, C:0.41, G:0.22, T:0.22
Consensus pattern (19 bp):
CGCCTCAGCGTTCAATGCC
Found at i:4381842 original size:18 final size:18
Alignment explanation
Indices: 4381819--4381859 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 18
4381809 ATTCCCCGCG
*
4381819 CACCGGCAGCGGCGAGGA
1 CACCGGCAGCGGCGACGA
4381837 CACC-G--GCGGCGACGA
1 CACCGGCAGCGGCGACGA
4381852 CACCGGCA
1 CACCGGCA
4381860 AGAGCGACAC
Statistics
Matches: 19, Mismatches: 1, Indels: 6
0.73 0.04 0.23
Matches are distributed among these distances:
15 13 0.68
16 1 0.05
17 1 0.05
18 4 0.21
ACGTcount: A:0.22, C:0.39, G:0.39, T:0.00
Consensus pattern (18 bp):
CACCGGCAGCGGCGACGA
Found at i:4381847 original size:15 final size:15
Alignment explanation
Indices: 4381827--4381858 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
4381817 CGCACCGGCA
*
4381827 GCGGCGAGGACACCG
1 GCGGCGACGACACCG
4381842 GCGGCGACGACACCG
1 GCGGCGACGACACCG
4381857 GC
1 GC
4381859 AAGAGCGACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.38, G:0.44, T:0.00
Consensus pattern (15 bp):
GCGGCGACGACACCG
Found at i:4401309 original size:18 final size:18
Alignment explanation
Indices: 4401286--4401320 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
4401276 GTGTACCGGG
4401286 TGGCGCCGGTCGAGGCGC
1 TGGCGCCGGTCGAGGCGC
4401304 TGGCGCCGGTCGAGGCG
1 TGGCGCCGGTCGAGGCG
4401321 AGCGGCGGCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.06, C:0.31, G:0.51, T:0.11
Consensus pattern (18 bp):
TGGCGCCGGTCGAGGCGC
Found at i:4404177 original size:24 final size:24
Alignment explanation
Indices: 4404083--4404186 Score: 66
Period size: 24 Copynumber: 4.3 Consensus size: 24
4404073 CGGCGTCGGG
* * *
4404083 GCGGGCTGGGCGGGACCGCCCGGT
1 GCGGGCTGAGCGGGAACGCCCGGC
* *
4404107 GCAGGCTGAGC-GGAGACGTCCGGC
1 GCGGGCTGAGCGGGA-ACGCCCGGC
* ** * * *
4404131 CCGACCTCACCGGGAACACCCGGC
1 GCGGGCTGAGCGGGAACGCCCGGC
* *
4404155 GCGGGCTGAGCGGGAACGGCCGGT
1 GCGGGCTGAGCGGGAACGCCCGGC
*
4404179 GCGTGCTG
1 GCGGGCTG
4404187 GTCCGCGGCA
Statistics
Matches: 56, Mismatches: 22, Indels: 4
0.68 0.27 0.05
Matches are distributed among these distances:
23 3 0.05
24 50 0.89
25 3 0.05
ACGTcount: A:0.12, C:0.34, G:0.45, T:0.09
Consensus pattern (24 bp):
GCGGGCTGAGCGGGAACGCCCGGC
Found at i:4404270 original size:24 final size:24
Alignment explanation
Indices: 4404243--4404441 Score: 148
Period size: 24 Copynumber: 8.3 Consensus size: 24
4404233 TGAACGGGAG
*
4404243 CACCAGGCACAGGCTGGGCCGGAA
1 CACCCGGCACAGGCTGGGCCGGAA
* * *
4404267 CACCCGGAACAGGCTGGCCCGAAA
1 CACCCGGCACAGGCTGGGCCGGAA
** *
4404291 CACCTAGCGCAGGCT-GGCCGGAA
1 CACCCGGCACAGGCTGGGCCGGAA
*** * *
4404314 GCGGGCGGCGCAGGCTGAGCCGGAA
1 -CACCCGGCACAGGCTGGGCCGGAA
*
4404339 CACCCGGCACAGGCTGAGCCGGAA
1 CACCCGGCACAGGCTGGGCCGGAA
* * * *
4404363 CACCCGACGCAAGCTGGCCCGGAA
1 CACCCGGCACAGGCTGGGCCGGAA
* * * * *
4404387 CACCCGGCGCGGGCTGAGCGGGAC
1 CACCCGGCACAGGCTGGGCCGGAA
* * **
4404411 CGCCCGGCGCAGGCTGACCCGGAA
1 CACCCGGCACAGGCTGGGCCGGAA
4404435 CACCCGG
1 CACCCGG
4404442 AGCCGGACCG
Statistics
Matches: 135, Mismatches: 38, Indels: 4
0.76 0.21 0.02
Matches are distributed among these distances:
23 6 0.04
24 122 0.90
25 7 0.05
ACGTcount: A:0.21, C:0.37, G:0.37, T:0.05
Consensus pattern (24 bp):
CACCCGGCACAGGCTGGGCCGGAA
Found at i:4404351 original size:72 final size:72
Alignment explanation
Indices: 4404252--4404438 Score: 200
Period size: 72 Copynumber: 2.6 Consensus size: 72
4404242 GCACCAGGCA
* * * *
4404252 CAGGCTGGGCCGGAACACCCGGAACAGGCTGGCCCGAAACACCTAG-CGCAGGCTGG-CCGGAAG
1 CAGGCTGAGCCGGAACACCCGGCACAGGCTGGCCCGGAACACC-AGACGCAAGCTGGCCCGGAA-
***
4404315 CGGGCGGCG
64 CACCCGGCG
*
4404324 CAGGCTGAGCCGGAACACCCGGCACAGGCTGAG-CCGGAACACCCGACGCAAGCTGGCCCGGAAC
1 CAGGCTGAGCCGGAACACCCGGCACAGGCTG-GCCCGGAACACCAGACGCAAGCTGGCCCGGAAC
4404388 ACCCGGCG
65 ACCCGGCG
* * * * * *
4404396 CGGGCTGAGCGGGACCGCCCGGCGCAGGCTGACCCGGAACACC
1 CAGGCTGAGCCGGAACACCCGGCACAGGCTGGCCCGGAACACC
4404439 CGGAGCCGGA
Statistics
Matches: 97, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
71 1 0.01
72 89 0.92
73 7 0.07
ACGTcount: A:0.21, C:0.37, G:0.37, T:0.05
Consensus pattern (72 bp):
CAGGCTGAGCCGGAACACCCGGCACAGGCTGGCCCGGAACACCAGACGCAAGCTGGCCCGGAACA
CCCGGCG
Found at i:4404385 original size:48 final size:48
Alignment explanation
Indices: 4404243--4404441 Score: 179
Period size: 48 Copynumber: 4.1 Consensus size: 48
4404233 TGAACGGGAG
* * * *
4404243 CACCAGGCACAGGCTGGGCCGGAACACCCGGA-ACAGGCTGGCCCGAAA
1 CACCCGGCACAGGCTGAGCCGGAACACCC-GACGCAGGCTGGCCCGGAA
** * *** *
4404291 CACCTAGCGCAGGCTG-GCCGGAAGCGGGCGGCGCAGGCTGAG-CCGGAA
1 CACCCGGCACAGGCTGAGCCGGAA-CACCCGACGCAGGCTG-GCCCGGAA
*
4404339 CACCCGGCACAGGCTGAGCCGGAACACCCGACGCAAGCTGGCCCGGAA
1 CACCCGGCACAGGCTGAGCCGGAACACCCGACGCAGGCTGGCCCGGAA
* * * * * * *
4404387 CACCCGGCGCGGGCTGAGCGGGACCGCCCGGCGCAGGCTGACCCGGAA
1 CACCCGGCACAGGCTGAGCCGGAACACCCGACGCAGGCTGGCCCGGAA
4404435 CACCCGG
1 CACCCGG
4404442 AGCCGGACCG
Statistics
Matches: 121, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
47 9 0.07
48 104 0.86
49 8 0.07
ACGTcount: A:0.21, C:0.37, G:0.37, T:0.05
Consensus pattern (48 bp):
CACCCGGCACAGGCTGAGCCGGAACACCCGACGCAGGCTGGCCCGGAA
Found at i:4405682 original size:20 final size:20
Alignment explanation
Indices: 4405646--4405683 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
4405636 TTTCGCAGGC
*
4405646 GCGCGGATGCGTGCCGGGCG
1 GCGCGGATGCGTACCGGGCG
4405666 GCGC-GATGCCGTACCGGG
1 GCGCGGATG-CGTACCGGG
4405684 GCAGCACGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.08, C:0.32, G:0.50, T:0.11
Consensus pattern (20 bp):
GCGCGGATGCGTACCGGGCG
Found at i:4407406 original size:18 final size:18
Alignment explanation
Indices: 4407385--4407421 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
4407375 ACGGCAGAAT
4407385 CCGGCGCGACCGATGCGG
1 CCGGCGCGACCGATGCGG
4407403 CCGGCGCGACCGATGCGG
1 CCGGCGCGACCGATGCGG
4407421 C
1 C
4407422 GGGCACGGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.11, C:0.41, G:0.43, T:0.05
Consensus pattern (18 bp):
CCGGCGCGACCGATGCGG
Found at i:4413521 original size:22 final size:22
Alignment explanation
Indices: 4413495--4413559 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
4413485 CCCGGGCTCG
4413495 TCGACACCGCCGCCCAGGCCCA
1 TCGACACCGCCGCCCAGGCCCA
*
4413517 TCGACACCGCCTCCCAGGCCCA
1 TCGACACCGCCGCCCAGGCCCA
4413539 TCGACACCGACCG-CCAGGCCC
1 TCGACACCG-CCGCCCAGGCCC
4413560 GTCAACACAG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
22 38 0.95
23 2 0.05
ACGTcount: A:0.18, C:0.54, G:0.22, T:0.06
Consensus pattern (22 bp):
TCGACACCGCCGCCCAGGCCCA
Found at i:4413529 original size:44 final size:44
Alignment explanation
Indices: 4413479--4413576 Score: 126
Period size: 44 Copynumber: 2.2 Consensus size: 44
4413469 CCCGACATCG
* * *
4413479 CAGCCTCCCGGGCTCGTCGACACCG-CCGCCCAGGCCCATCGACA
1 CAGCCTCCCGGGCCCATCGACACCGACCG-CCAGGCCCATCAACA
* * *
4413523 CCGCCTCCCAGGCCCATCGACACCGACCGCCAGGCCCGTCAACA
1 CAGCCTCCCGGGCCCATCGACACCGACCGCCAGGCCCATCAACA
4413567 CAGCCTCCCG
1 CAGCCTCCCG
4413577 TCGGCCGCCA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
44 42 0.93
45 3 0.07
ACGTcount: A:0.17, C:0.52, G:0.22, T:0.08
Consensus pattern (44 bp):
CAGCCTCCCGGGCCCATCGACACCGACCGCCAGGCCCATCAACA
Found at i:4414430 original size:16 final size:16
Alignment explanation
Indices: 4414409--4414473 Score: 85
Period size: 16 Copynumber: 4.1 Consensus size: 16
4414399 GTCCTCGGCT
4414409 GAGCGGACGATTCGCC
1 GAGCGGACGATTCGCC
*
4414425 GAGCGGACGATTCGCT
1 GAGCGGACGATTCGCC
* * *
4414441 GAGCGGACGAGTCTCT
1 GAGCGGACGATTCGCC
*
4414457 GGGCGGACGATTCGCC
1 GAGCGGACGATTCGCC
4414473 G
1 G
4414474 TCAGTCCAGC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 42 1.00
ACGTcount: A:0.17, C:0.28, G:0.40, T:0.15
Consensus pattern (16 bp):
GAGCGGACGATTCGCC
Found at i:4414442 original size:32 final size:32
Alignment explanation
Indices: 4414406--4414471 Score: 96
Period size: 32 Copynumber: 2.1 Consensus size: 32
4414396 ACCGTCCTCG
*
4414406 GCTGAGCGGACGATTCGCCGAGCGGACGATTC
1 GCTGAGCGGACGAGTCGCCGAGCGGACGATTC
* * *
4414438 GCTGAGCGGACGAGTCTCTGGGCGGACGATTC
1 GCTGAGCGGACGAGTCGCCGAGCGGACGATTC
4414470 GC
1 GC
4414472 CGTCAGTCCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.17, C:0.27, G:0.39, T:0.17
Consensus pattern (32 bp):
GCTGAGCGGACGAGTCGCCGAGCGGACGATTC
Found at i:4452123 original size:15 final size:15
Alignment explanation
Indices: 4452103--4452136 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
4452093 GACATCGCCG
4452103 CGACGACGGGCGGCA
1 CGACGACGGGCGGCA
*
4452118 CGACGACGGGCGGCG
1 CGACGACGGGCGGCA
4452133 CGAC
1 CGAC
4452137 ATCCACCTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.18, C:0.35, G:0.47, T:0.00
Consensus pattern (15 bp):
CGACGACGGGCGGCA
Done.