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 2 of 7
Found at i:574 original size:18 final size:18
Alignment explanation
Indices: 505--572 Score: 120
Period size: 18 Copynumber: 3.8 Consensus size: 18
495 CCCCCCGGCC
505 GCCGAATACACGCCCGCT
1 GCCGAATACACGCCCGCT
523 GCCGAATACACGCCCGCT
1 GCCGAATACACGCCCGCT
541 GCCGAATACACGCCCGCT
1 GCCGAATACACGCCCGCT
*
559 GCCGAGTACA-GCCC
1 GCCGAATACACGCCC
573 CGAACCGGAG
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
17 4 0.08
18 45 0.92
ACGTcount: A:0.22, C:0.44, G:0.24, T:0.10
Consensus pattern (18 bp):
GCCGAATACACGCCCGCT
Found at i:2077 original size:22 final size:22
Alignment explanation
Indices: 2045--2087 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
2035 TTTTGTGCCT
*
2045 TGTGGATTCCTCGAGGAATCCC
1 TGTGGAGTCCTCGAGGAATCCC
2067 TGTGGAGTCCTCGAGGAATCC
1 TGTGGAGTCCTCGAGGAATCC
2088 ACCGGTTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.19, C:0.26, G:0.30, T:0.26
Consensus pattern (22 bp):
TGTGGAGTCCTCGAGGAATCCC
Found at i:12624 original size:24 final size:24
Alignment explanation
Indices: 12582--12658 Score: 118
Period size: 24 Copynumber: 3.2 Consensus size: 24
12572 CGGCCAGCAG
* * *
12582 CAGGGCGGCCAGGCGCAGGGCCAA
1 CAGGGCGGTCAGCCACAGGGCCAA
12606 CAGGGCGGTCAGCCACAGGGCCAA
1 CAGGGCGGTCAGCCACAGGGCCAA
*
12630 CAGGGTGGTCAGCCACAGGGCCAA
1 CAGGGCGGTCAGCCACAGGGCCAA
12654 CAGGG
1 CAGGG
12659 TGGCCAGGCG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.23, C:0.31, G:0.42, T:0.04
Consensus pattern (24 bp):
CAGGGCGGTCAGCCACAGGGCCAA
Found at i:12659 original size:24 final size:24
Alignment explanation
Indices: 12597--12661 Score: 121
Period size: 24 Copynumber: 2.7 Consensus size: 24
12587 CGGCCAGGCG
*
12597 CAGGGCCAACAGGGCGGTCAGCCA
1 CAGGGCCAACAGGGTGGTCAGCCA
12621 CAGGGCCAACAGGGTGGTCAGCCA
1 CAGGGCCAACAGGGTGGTCAGCCA
12645 CAGGGCCAACAGGGTGG
1 CAGGGCCAACAGGGTGG
12662 CCAGGCGCAG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.25, C:0.29, G:0.40, T:0.06
Consensus pattern (24 bp):
CAGGGCCAACAGGGTGGTCAGCCA
Found at i:33999 original size:21 final size:21
Alignment explanation
Indices: 33974--34019 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
33964 CGACGAGGTG
33974 AAGGCCCGCCC-CGCGGCGAAC
1 AAGG-CCGCCCGCGCGGCGAAC
*
33995 AAGGCTGCCCGCGCGGCGAAC
1 AAGGCCGCCCGCGCGGCGAAC
34016 AAGG
1 AAGG
34020 GCCAGGGCGC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.22, C:0.39, G:0.37, T:0.02
Consensus pattern (21 bp):
AAGGCCGCCCGCGCGGCGAAC
Found at i:34004 original size:24 final size:21
Alignment explanation
Indices: 33981--34019 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
33971 GTGAAGGCCC
33981 GCCC-CGCGGCGAACAAGGCT
1 GCCCGCGCGGCGAACAAGGCT
34001 GCCCGCGCGGCGAACAAGG
1 GCCCGCGCGGCGAACAAGG
34020 GCCAGGGCGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.21, C:0.38, G:0.38, T:0.03
Consensus pattern (21 bp):
GCCCGCGCGGCGAACAAGGCT
Found at i:39933 original size:18 final size:18
Alignment explanation
Indices: 39912--39953 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
39902 CGGCGGCGGG
39912 GGTGGCACCGGCGGTTCC
1 GGTGGCACCGGCGGTTCC
** *
39930 GGTGGGTCCGGGGGTTCC
1 GGTGGCACCGGCGGTTCC
39948 GGTGGC
1 GGTGGC
39954 GGTGGTGGCG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.02, C:0.26, G:0.52, T:0.19
Consensus pattern (18 bp):
GGTGGCACCGGCGGTTCC
Found at i:63164 original size:18 final size:18
Alignment explanation
Indices: 63137--63182 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
63127 GGTCGGCCGG
* **
63137 GCCGTCGTGGTCGGTTCC
1 GCCGTGGTGGTCGGCGCC
*
63155 GGCGTGGTGGTCGGCGCC
1 GCCGTGGTGGTCGGCGCC
63173 GCCGTGGTGG
1 GCCGTGGTGG
63183 GTTCCGGCGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.00, C:0.28, G:0.50, T:0.22
Consensus pattern (18 bp):
GCCGTGGTGGTCGGCGCC
Found at i:63167 original size:36 final size:35
Alignment explanation
Indices: 63127--63240 Score: 119
Period size: 36 Copynumber: 3.3 Consensus size: 35
63117 GCTGCGTCCG
*
63127 GGTCGGCCGGGCCGTCGTGGTCGGTTCCGGCGTGGT
1 GGTCGG-CGGGCCGTCGTGGTCGGTTCCGGCGTCGT
* *
63163 GGTCGGC--GCCGCCGTGGTGGGTTCCGGCGTCGT
1 GGTCGGCGGGCCGTCGTGGTCGGTTCCGGCGTCGT
*
63196 CGTCGGCGGTTG-CGTCGTGGTCGGTTCCGGC-TCGCT
1 GGTCGGCGG--GCCGTCGTGGTCGGTTCCGGCGTCG-T
*
63232 GGTCTGCGG
1 GGTCGGCGG
63241 CGGAGGCGGC
Statistics
Matches: 65, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
33 29 0.45
35 4 0.06
36 31 0.48
37 1 0.02
ACGTcount: A:0.00, C:0.29, G:0.47, T:0.24
Consensus pattern (35 bp):
GGTCGGCGGGCCGTCGTGGTCGGTTCCGGCGTCGT
Found at i:63186 original size:33 final size:33
Alignment explanation
Indices: 63137--63226 Score: 99
Period size: 33 Copynumber: 2.6 Consensus size: 33
63127 GGTCGGCCGG
* * *
63137 GCCGTCGTGGTCGGTTCCGGCGTGGTGGTCGGC
1 GCCGCCGTGGTCGGTTCCGGCGTCGTCGTCGGC
*
63170 GCCGCCGTGGTGGGTTCCGGCGTCGTCGTCGGC
1 GCCGCCGTGGTCGGTTCCGGCGTCGTCGTCGGC
* *
63203 GGTTGCGTCGTGGTCGGTTCCGGC
1 -G--CCGCCGTGGTCGGTTCCGGC
63227 TCGCTGGTCT
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
33 29 0.62
34 1 0.02
36 17 0.36
ACGTcount: A:0.00, C:0.29, G:0.47, T:0.24
Consensus pattern (33 bp):
GCCGCCGTGGTCGGTTCCGGCGTCGTCGTCGGC
Found at i:68181 original size:14 final size:13
Alignment explanation
Indices: 68162--68195 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
68152 TTGGCCGGTG
*
68162 GCGGCGGCTCGGCC
1 GCGGCGGCCCGG-C
68176 GCGGCGGCCCGGC
1 GCGGCGGCCCGGC
68189 GCGGCGG
1 GCGGCGG
68196 GGTGGCCCGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.00, C:0.41, G:0.56, T:0.03
Consensus pattern (13 bp):
GCGGCGGCCCGGC
Found at i:70015 original size:18 final size:20
Alignment explanation
Indices: 69975--70018 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
69965 GGGCGCCGAA
69975 TAGCCGGGCTGCTGCTGACCG
1 TAGCCGGGCTGCTGCTGA-CG
*
69996 TAGCCGGGCTGTTGC-G-CG
1 TAGCCGGGCTGCTGCTGACG
70014 TAGCC
1 TAGCC
70019 CTGGCCGTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 7 0.32
20 1 0.05
21 14 0.64
ACGTcount: A:0.09, C:0.32, G:0.39, T:0.20
Consensus pattern (20 bp):
TAGCCGGGCTGCTGCTGACG
Found at i:70152 original size:15 final size:15
Alignment explanation
Indices: 70109--70235 Score: 76
Period size: 15 Copynumber: 8.3 Consensus size: 15
70099 CCTGCCTGCC
70109 GCCCTGCTGGCCGTA
1 GCCCTGCTGGCCGTA
* * *
70124 ACCCGGTTGGCCGTA
1 GCCCTGCTGGCCGTA
*
70139 GCCCTGCTGACCGTA
1 GCCCTGCTGGCCGTA
** *
70154 GCCGGGCTCGG-CATA
1 GCCCTGCT-GGCCGTA
* **
70169 GCCCTGGTCACCGTA
1 GCCCTGCTGGCCGTA
70184 GCCGGGCTGCTGGCCGTA
1 GCC---CTGCTGGCCGTA
* * *
70202 ACCCGGCTGGTCGTA
1 GCCCTGCTGGCCGTA
**
70217 GCCGGGCTGGCCGTA
1 GCCCTGCTGGCCGTA
70232 GCCC
1 GCCC
70236 GCACCCTGCT
Statistics
Matches: 80, Mismatches: 27, Indels: 10
0.68 0.23 0.09
Matches are distributed among these distances:
15 68 0.85
16 1 0.01
18 11 0.14
ACGTcount: A:0.10, C:0.37, G:0.35, T:0.17
Consensus pattern (15 bp):
GCCCTGCTGGCCGTA
Found at i:70247 original size:36 final size:35
Alignment explanation
Indices: 70202--70271 Score: 95
Period size: 36 Copynumber: 2.0 Consensus size: 35
70192 GCTGGCCGTA
* * *
70202 ACCCGGCTGGTCGTAGCCGGGCTGGCCGTAGCCCGC
1 ACCCGGCTGGCCGTACCCGGGCTCGCCGTA-CCCGC
*
70238 ACCCTGCTGGCCGTACCCGGGCTCGCCGTACCCG
1 ACCCGGCTGGCCGTACCCGGGCTCGCCGTACCCG
70272 GGCTGCCCGT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 4 0.13
36 26 0.87
ACGTcount: A:0.09, C:0.43, G:0.34, T:0.14
Consensus pattern (35 bp):
ACCCGGCTGGCCGTACCCGGGCTCGCCGTACCCGC
Found at i:70267 original size:15 final size:15
Alignment explanation
Indices: 70247--70275 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
70237 CACCCTGCTG
70247 GCCGTACCCGGGCTC
1 GCCGTACCCGGGCTC
70262 GCCGTACCCGGGCT
1 GCCGTACCCGGGCT
70276 GCCCGTAACC
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:0.07, C:0.45, G:0.34, T:0.14
Consensus pattern (15 bp):
GCCGTACCCGGGCTC
Found at i:70281 original size:15 final size:15
Alignment explanation
Indices: 70243--70282 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
70233 CCCGCACCCT
*
70243 GCTGGCCGTACCCGG
1 GCTGCCCGTACCCGG
70258 GCT-CGCCGTACCCGG
1 GCTGC-CCGTACCCGG
70273 GCTGCCCGTA
1 GCTGCCCGTA
70283 ACCCTGATCG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 21 0.95
16 1 0.05
ACGTcount: A:0.07, C:0.42, G:0.35, T:0.15
Consensus pattern (15 bp):
GCTGCCCGTACCCGG
Found at i:70387 original size:15 final size:15
Alignment explanation
Indices: 70315--70394 Score: 54
Period size: 15 Copynumber: 5.1 Consensus size: 15
70305 TGGCCGCCCT
*
70315 GCTGGTCGTAGCCGG
1 GCTGGCCGTAGCCGG
* *
70330 GCTCGCCGTACCCCGG
1 GCTGGCCGTA-GCCGG
* *
70346 CCT-GCCGTAGCCGCCCT
1 GCTGGCCGTAGCCG---G
*
70363 GCTGGTCGTAGCCGG
1 GCTGGCCGTAGCCGG
*
70378 GCTGGCCGTACCCGG
1 GCTGGCCGTAGCCGG
70393 GC
1 GC
70395 GCGCCCTGCT
Statistics
Matches: 49, Mismatches: 11, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
14 3 0.06
15 29 0.59
16 6 0.12
17 2 0.04
18 9 0.18
ACGTcount: A:0.06, C:0.40, G:0.38, T:0.16
Consensus pattern (15 bp):
GCTGGCCGTAGCCGG
Found at i:71503 original size:17 final size:17
Alignment explanation
Indices: 71481--71513 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
71471 GCTTCTCGCT
71481 TGTGGCTGCCTCGGTGG
1 TGTGGCTGCCTCGGTGG
71498 TGTGGCTGCCTCGGTG
1 TGTGGCTGCCTCGGTG
71514 TCGGGGCCGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.00, C:0.24, G:0.45, T:0.30
Consensus pattern (17 bp):
TGTGGCTGCCTCGGTGG
Found at i:73220 original size:18 final size:18
Alignment explanation
Indices: 73199--73233 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
73189 GCGATCTCGG
* *
73199 CGCTGGCCGCGGTGCTGA
1 CGCTGCCCGCGCTGCTGA
73217 CGCTGCCCGCGCTGCTG
1 CGCTGCCCGCGCTGCTG
73234 GCCGTGCTCG
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:0.03, C:0.40, G:0.40, T:0.17
Consensus pattern (18 bp):
CGCTGCCCGCGCTGCTGA
Found at i:77151 original size:78 final size:78
Alignment explanation
Indices: 77018--77280 Score: 492
Period size: 78 Copynumber: 3.4 Consensus size: 78
77008 GGCTGCTGCG
* *
77018 CACCGCCTGAGCGGGTCAGCGGCCGGAGGCGGTAGCGCAGCGTCACCACGCAGGCCGCCCCGCTC
1 CACCGCCTGAGCGGGTCAGCGGCCGGAGGCGGTAGCGCAGCGTGACCACGTAGGCCGCCCCGCTC
77083 AGGCGAGATGTGA
66 AGGCGAGATGTGA
77096 CACCGCCTGAGCGGGTCAGCGGCCGGAGGCGGTAGCGCAGCGTGACCACGTAGGCCGCCCCGCTC
1 CACCGCCTGAGCGGGTCAGCGGCCGGAGGCGGTAGCGCAGCGTGACCACGTAGGCCGCCCCGCTC
77161 AGGCGAGATGTGA
66 AGGCGAGATGTGA
77174 CACCGCCTGAGCGGGTCAGCGGCCGGAGGCGGTAGCGCAGCGTGACCACGTAGGCCGCCCCGCTC
1 CACCGCCTGAGCGGGTCAGCGGCCGGAGGCGGTAGCGCAGCGTGACCACGTAGGCCGCCCCGCTC
77239 AGGCGAGATGTGA
66 AGGCGAGATGTGA
77252 CACC-CTCTGAGCGGGTCAGCGGCCGGAGG
1 CACCGC-CTGAGCGGGTCAGCGGCCGGAGG
77281 TGCCGCCTTC
Statistics
Matches: 182, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
77 1 0.01
78 181 0.99
ACGTcount: A:0.16, C:0.34, G:0.40, T:0.10
Consensus pattern (78 bp):
CACCGCCTGAGCGGGTCAGCGGCCGGAGGCGGTAGCGCAGCGTGACCACGTAGGCCGCCCCGCTC
AGGCGAGATGTGA
Found at i:77872 original size:15 final size:15
Alignment explanation
Indices: 77852--77884 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
77842 CGAGCCGGGT
77852 GCCCGCGCCGACGCG
1 GCCCGCGCCGACGCG
77867 GCCCGCGCCGACGCG
1 GCCCGCGCCGACGCG
77882 GCC
1 GCC
77885 GCTGTCGAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.06, C:0.55, G:0.39, T:0.00
Consensus pattern (15 bp):
GCCCGCGCCGACGCG
Found at i:81614 original size:16 final size:16
Alignment explanation
Indices: 81593--81626 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
81583 CGGAGTTCCG
*
81593 TCTCGCAGCGGGAAGA
1 TCTCGCAGCAGGAAGA
81609 TCTCGCAGCAGGAAGA
1 TCTCGCAGCAGGAAGA
81625 TC
1 TC
81627 CGGTGGCCGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.26, C:0.26, G:0.32, T:0.15
Consensus pattern (16 bp):
TCTCGCAGCAGGAAGA
Found at i:93133 original size:27 final size:27
Alignment explanation
Indices: 93095--93176 Score: 119
Period size: 27 Copynumber: 3.0 Consensus size: 27
93085 CTCGGACCGG
93095 ACGGCGGCTGATCGCCCGGCGCGCCGT
1 ACGGCGGCTGATCGCCCGGCGCGCCGT
*
93122 ACGGCGGCTGATCGCCGGGCGCGCCGT
1 ACGGCGGCTGATCGCCCGGCGCGCCGT
* ** *
93149 ACGGCGGTTGGCCACCCGGCGCGCCGT
1 ACGGCGGCTGATCGCCCGGCGCGCCGT
93176 A
1 A
93177 GGACTGGCCG
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.09, C:0.39, G:0.41, T:0.11
Consensus pattern (27 bp):
ACGGCGGCTGATCGCCCGGCGCGCCGT
Found at i:93701 original size:27 final size:27
Alignment explanation
Indices: 93624--93695 Score: 90
Period size: 27 Copynumber: 2.7 Consensus size: 27
93614 GGGTCAGTGA
* *
93624 CCGTACGGCGGCTGTCCGCCGTGCCCG
1 CCGTACGGCGGTTGTCCGCCGGGCCCG
* * * *
93651 CCATAGGGCGGTTGGCCGCCGGGCGCG
1 CCGTACGGCGGTTGTCCGCCGGGCCCG
93678 CCGTACGGCGGTTGTCCG
1 CCGTACGGCGGTTGTCCG
93696 TAGGGCTGTT
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.06, C:0.38, G:0.42, T:0.15
Consensus pattern (27 bp):
CCGTACGGCGGTTGTCCGCCGGGCCCG
Found at i:93706 original size:15 final size:15
Alignment explanation
Indices: 93677--93721 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
93667 CGCCGGGCGC
93677 GCCGTACGGCGGTTG
1 GCCGTACGGCGGTTG
* * *
93692 TCCGTAGGGCTGTTG
1 GCCGTACGGCGGTTG
*
93707 GCCGTACAGCGGTTG
1 GCCGTACGGCGGTTG
93722 CTCGCCGGTC
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.09, C:0.24, G:0.42, T:0.24
Consensus pattern (15 bp):
GCCGTACGGCGGTTG
Found at i:93751 original size:15 final size:15
Alignment explanation
Indices: 93731--93771 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
93721 GCTCGCCGGT
*
93731 CTGCCCGTATG-GCGC
1 CTGCCCGTACGCG-GC
93746 CTGCCCGTACGCGGC
1 CTGCCCGTACGCGGC
93761 CTGCCCGTACG
1 CTGCCCGTACG
93772 GGAGTTGGCC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 23 0.96
16 1 0.04
ACGTcount: A:0.07, C:0.44, G:0.32, T:0.17
Consensus pattern (15 bp):
CTGCCCGTACGCGGC
Found at i:94003 original size:22 final size:22
Alignment explanation
Indices: 93960--94003 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
93950 CCGCTTGGCC
* *
93960 AGGTGTTCGATCGCCTGCGCGT
1 AGGTGTCCGATCGCCAGCGCGT
93982 AGGTGTCCGA-CGCCAGCAGCGT
1 AGGTGTCCGATCGCCAGC-GCGT
94004 GTCCGGGCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.14, C:0.30, G:0.36, T:0.20
Consensus pattern (22 bp):
AGGTGTCCGATCGCCAGCGCGT
Found at i:96694 original size:30 final size:27
Alignment explanation
Indices: 96639--96695 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 27
96629 CGCGGTAGGT
* *
96639 CACCGCCGCCTTGCCGCTGGGCGCGAA
1 CACCACCGCCTTGCCGCCGGGCGCGAA
96666 CACCACCGCCTTGTCGCGCCGGGTCGCGAA
1 CACCACCGCCTTG-C-CGCCGGG-CGCGAA
96696 GTAGCCCAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 12 0.48
28 1 0.04
29 6 0.24
30 6 0.24
ACGTcount: A:0.12, C:0.44, G:0.32, T:0.12
Consensus pattern (27 bp):
CACCACCGCCTTGCCGCCGGGCGCGAA
Found at i:109890 original size:17 final size:18
Alignment explanation
Indices: 109857--109891 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
109847 CGAGACCATC
*
109857 CGCATGGACGGCGCGCTG
1 CGCATGGACGCCGCGCTG
109875 CGCATGG-CGCCGCGCTG
1 CGCATGGACGCCGCGCTG
109892 ATCTCTCGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.09, C:0.37, G:0.43, T:0.11
Consensus pattern (18 bp):
CGCATGGACGCCGCGCTG
Found at i:111540 original size:16 final size:17
Alignment explanation
Indices: 111486--111553 Score: 111
Period size: 17 Copynumber: 4.0 Consensus size: 17
111476 CGGGGCGGCC
111486 GTTGCCCGTTTTCGTGG
1 GTTGCCCGTTTTCGTGG
*
111503 GTTGCCCGTTTCCGTGG
1 GTTGCCCGTTTTCGTGG
111520 GTTGCCCGTTTTCGT-G
1 GTTGCCCGTTTTCGTGG
111536 GTTGCCCGTTTTCCGTGG
1 GTTGCCCGTTTT-CGTGG
111554 ATTCAGAGAA
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
16 13 0.28
17 33 0.70
18 1 0.02
ACGTcount: A:0.00, C:0.26, G:0.34, T:0.40
Consensus pattern (17 bp):
GTTGCCCGTTTTCGTGG
Found at i:115014 original size:15 final size:15
Alignment explanation
Indices: 114994--115024 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
114984 GACGACGCCG
114994 GGGTGACCGAGGATC
1 GGGTGACCGAGGATC
115009 GGGTGACCGAGGATC
1 GGGTGACCGAGGATC
115024 G
1 G
115025 ACAGATCGCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.48, T:0.13
Consensus pattern (15 bp):
GGGTGACCGAGGATC
Found at i:115651 original size:15 final size:15
Alignment explanation
Indices: 115631--115660 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
115621 CGGCGGCGCG
115631 GCCACCACCGTCGGC
1 GCCACCACCGTCGGC
*
115646 GCCACCGCCGTCGGC
1 GCCACCACCGTCGGC
115661 CCCTCGGTGA
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:0.10, C:0.53, G:0.30, T:0.07
Consensus pattern (15 bp):
GCCACCACCGTCGGC
Found at i:119257 original size:39 final size:39
Alignment explanation
Indices: 119214--119295 Score: 94
Period size: 39 Copynumber: 2.1 Consensus size: 39
119204 CGCTTGCGGC
*
119214 GCGGGCGCGG-CGGCCGCGGCGCCGGGTCGCGCCTGCGCG
1 GCGGG-GCGGCCGGCCGCGGCGCCGGGGCGCGCCTGCGCG
* * * * *
119253 GCGGGGCGGCCGGCGGTGGTGGCGGGGCGTGCCTGCGCG
1 GCGGGGCGGCCGGCCGCGGCGCCGGGGCGCGCCTGCGCG
119292 GCGG
1 GCGG
119296 CCGGTGCGCG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
38 4 0.11
39 32 0.89
ACGTcount: A:0.00, C:0.34, G:0.59, T:0.07
Consensus pattern (39 bp):
GCGGGGCGGCCGGCCGCGGCGCCGGGGCGCGCCTGCGCG
Found at i:123535 original size:18 final size:18
Alignment explanation
Indices: 123504--123554 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
123494 GACCGCCGAT
*
123504 GATCCGATGGGCTGAGCA
1 GATCCGACGGGCTGAGCA
* *
123522 GATTCGACGGGCTGAGCG
1 GATCCGACGGGCTGAGCA
123540 GATCCGACGGGCTGA
1 GATCCGACGGGCTGA
123555 TCGGCCGCGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.20, C:0.24, G:0.41, T:0.16
Consensus pattern (18 bp):
GATCCGACGGGCTGAGCA
Found at i:124798 original size:15 final size:15
Alignment explanation
Indices: 124774--124804 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
124764 GCCCCCATGA
*
124774 CGGCGGCCGGGGCCG
1 CGGCGACCGGGGCCG
124789 CGGCGACCGGGGCCG
1 CGGCGACCGGGGCCG
124804 C
1 C
124805 CGGTGCGGCG
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:0.03, C:0.42, G:0.55, T:0.00
Consensus pattern (15 bp):
CGGCGACCGGGGCCG
Found at i:127531 original size:15 final size:15
Alignment explanation
Indices: 127511--127540 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
127501 GCTGCGGTGT
127511 CTGGGACACATCATC
1 CTGGGACACATCATC
127526 CTGGGACACATCATC
1 CTGGGACACATCATC
127541 GGAGGACATC
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:0.27, C:0.33, G:0.20, T:0.20
Consensus pattern (15 bp):
CTGGGACACATCATC
Found at i:128932 original size:15 final size:15
Alignment explanation
Indices: 128912--128947 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
128902 GCCTGACCGA
128912 CGGACACTCGAGCGG
1 CGGACACTCGAGCGG
128927 CGGACACTCGAGCGG
1 CGGACACTCGAGCGG
128942 CGGACA
1 CGGACA
128948 ATAGCCGAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.22, C:0.33, G:0.39, T:0.06
Consensus pattern (15 bp):
CGGACACTCGAGCGG
Found at i:131621 original size:18 final size:18
Alignment explanation
Indices: 131587--131621 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
131577 CCGAGCCGGT
*
131587 GGTGCCCGGTCACCCGCC
1 GGTGCCCGGTCAACCGCC
*
131605 GGTGCCCGGTGAACCGC
1 GGTGCCCGGTCAACCGC
131622 GCGCCGCCGA
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:0.09, C:0.43, G:0.37, T:0.11
Consensus pattern (18 bp):
GGTGCCCGGTCAACCGCC
Found at i:152280 original size:21 final size:21
Alignment explanation
Indices: 152254--152298 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
152244 GATGGTTCCT
152254 CGGTGTTCGGTGTCGCCCCGG
1 CGGTGTTCGGTGTCGCCCCGG
152275 CGGTGTTCGGTGTCGCCCCGG
1 CGGTGTTCGGTGTCGCCCCGG
152296 CGG
1 CGG
152299 CGGTGTTCGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.44, T:0.22
Consensus pattern (21 bp):
CGGTGTTCGGTGTCGCCCCGG
Found at i:152304 original size:24 final size:22
Alignment explanation
Indices: 152254--152314 Score: 88
Period size: 24 Copynumber: 2.7 Consensus size: 22
152244 GATGGTTCCT
152254 CGGTGTTCGGTGTCG-CCCCGG
1 CGGTGTTCGGTGTCGCCCCCGG
152275 CGGTGTTCGGTGTCGCCCCGGCGG
1 CGGTGTTCGGTGTCGCCCC--CGG
*
152299 CGGTGTTCGATGTCGC
1 CGGTGTTCGGTGTCGC
152315 GGAAGCGGTG
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.07
Matches are distributed among these distances:
21 15 0.42
22 3 0.08
24 18 0.50
ACGTcount: A:0.02, C:0.31, G:0.43, T:0.25
Consensus pattern (22 bp):
CGGTGTTCGGTGTCGCCCCCGG
Found at i:152305 original size:45 final size:45
Alignment explanation
Indices: 152254--152341 Score: 113
Period size: 45 Copynumber: 2.0 Consensus size: 45
152244 GATGGTTCCT
* ** *
152254 CGGTGTTCGGTGTCGCCCCGGCGGTGTTCGGTGTCGCCCCGGCGG
1 CGGTGTTCGATGTCGCCCAAGCGGTGTTCGATGTCGCCCCGGCGG
** *
152299 CGGTGTTCGATGTCGCGGAAGCGGTGTTCGATGTCGCCGCGGC
1 CGGTGTTCGATGTCGCCCAAGCGGTGTTCGATGTCGCCCCGGC
152342 CGCGTCGAGG
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.05, C:0.30, G:0.43, T:0.23
Consensus pattern (45 bp):
CGGTGTTCGATGTCGCCCAAGCGGTGTTCGATGTCGCCCCGGCGG
Found at i:152339 original size:24 final size:22
Alignment explanation
Indices: 152254--152340 Score: 81
Period size: 21 Copynumber: 4.0 Consensus size: 22
152244 GATGGTTCCT
* *
152254 CGGTGTTCGGTGTCGCC-CCGG
1 CGGTGTTCGATGTCGCCGCGGG
* *
152275 CGGTGTTCGGTGTCGCCCCGGCGG
1 CGGTGTTCGATGTCGCCGC-G-GG
*
152299 CGGTGTTCGATGTCG-CG-GAAG
1 CGGTGTTCGATGTCGCCGCG-GG
152320 CGGTGTTCGATGTCGCCGCGG
1 CGGTGTTCGATGTCGCCGCGG
152341 CCGCGTCGAG
Statistics
Matches: 55, Mismatches: 6, Indels: 9
0.79 0.09 0.13
Matches are distributed among these distances:
21 34 0.62
22 3 0.05
23 2 0.04
24 16 0.29
ACGTcount: A:0.05, C:0.29, G:0.44, T:0.23
Consensus pattern (22 bp):
CGGTGTTCGATGTCGCCGCGGG
Found at i:153109 original size:15 final size:15
Alignment explanation
Indices: 153089--153117 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
153079 AGCTGGTCAA
153089 GTGGTAAGACCAATC
1 GTGGTAAGACCAATC
153104 GTGGTAAGACCAAT
1 GTGGTAAGACCAAT
153118 TGCTCGGCGA
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:0.34, C:0.17, G:0.28, T:0.21
Consensus pattern (15 bp):
GTGGTAAGACCAATC
Found at i:162219 original size:6 final size:6
Alignment explanation
Indices: 162167--162205 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
162157 CAGGCTCGTT
162167 CGGAGC CGGAGC CGGAGC CGGAGC CGGAGC CGGAGC CGG
1 CGGAGC CGGAGC CGGAGC CGGAGC CGGAGC CGGAGC CGG
162206 GGAGGCCGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.15, C:0.33, G:0.51, T:0.00
Consensus pattern (6 bp):
CGGAGC
Found at i:165860 original size:15 final size:15
Alignment explanation
Indices: 165840--165899 Score: 75
Period size: 15 Copynumber: 4.0 Consensus size: 15
165830 TTGGACACCC
165840 TGCCCACGGAGACGG
1 TGCCCACGGAGACGG
*
165855 TGCCCACGGAGACTG
1 TGCCCACGGAGACGG
* * *
165870 TGCCCTCAGAGACCG
1 TGCCCACGGAGACGG
*
165885 TGCCCTCGGAGACGG
1 TGCCCACGGAGACGG
165900 CGCCTTCGGA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 39 1.00
ACGTcount: A:0.18, C:0.35, G:0.35, T:0.12
Consensus pattern (15 bp):
TGCCCACGGAGACGG
Found at i:165916 original size:30 final size:30
Alignment explanation
Indices: 165848--165919 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 30
165838 CCTGCCCACG
* * *
165848 GAGACGGTGCCCACGGAGACTGTGCCCTCA
1 GAGACCGTGCCCACGGAGACGGCGCCCTCA
* * *
165878 GAGACCGTGCCCTCGGAGACGGCGCCTTCG
1 GAGACCGTGCCCACGGAGACGGCGCCCTCA
*
165908 GAGTCCGTGCCC
1 GAGACCGTGCCC
165920 CCGGGAACCG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.15, C:0.36, G:0.35, T:0.14
Consensus pattern (30 bp):
GAGACCGTGCCCACGGAGACGGCGCCCTCA
Found at i:176574 original size:79 final size:79
Alignment explanation
Indices: 176438--176608 Score: 324
Period size: 79 Copynumber: 2.2 Consensus size: 79
176428 ATCGGCTGAG
* *
176438 CCGGCTCGGGCGCGTCGGATACCGCCTGAGCCGGGTCAGCGGCCGGAGGCGGTAGCGCAGCGTCA
1 CCGGCTCGGGCGCGTCGGACACCGCCTGAGCCGGGTCAGCGGCCGGAGGCGGCAGCGCAGCGTCA
176503 CCACGGAGGCCGCC
66 CCACGGAGGCCGCC
176517 CCGGCTCGGGCGCGTCGGACACCGCCTGAGCCGGGTCAGCGGCCGGAGGCGGCAGCGCAGCGTCA
1 CCGGCTCGGGCGCGTCGGACACCGCCTGAGCCGGGTCAGCGGCCGGAGGCGGCAGCGCAGCGTCA
176582 CCACGGAGGCCGCC
66 CCACGGAGGCCGCC
176596 CCGGCTCGGGCGC
1 CCGGCTCGGGCGC
176609 AAATGGATAC
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
79 90 1.00
ACGTcount: A:0.12, C:0.39, G:0.42, T:0.08
Consensus pattern (79 bp):
CCGGCTCGGGCGCGTCGGACACCGCCTGAGCCGGGTCAGCGGCCGGAGGCGGCAGCGCAGCGTCA
CCACGGAGGCCGCC
Found at i:186573 original size:15 final size:15
Alignment explanation
Indices: 186555--186587 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
186545 CCCCGGCGGC
*
186555 CGAGGGCGCCGTGGG
1 CGAGGCCGCCGTGGG
186570 CGAGGCCGCCGTGGG
1 CGAGGCCGCCGTGGG
186585 CGA
1 CGA
186588 CGGTCCGCGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.09, C:0.30, G:0.55, T:0.06
Consensus pattern (15 bp):
CGAGGCCGCCGTGGG
Found at i:193427 original size:79 final size:80
Alignment explanation
Indices: 193291--193467 Score: 320
Period size: 79 Copynumber: 2.2 Consensus size: 80
193281 CCCGATCGGT
**
193291 CTGACCCCGCTCAGGCTGTGTTTGATTTCGCCCGAGCGGGGGCGGCCTGCGTGGTGATGCTGCGC
1 CTGACCCCGCTCAGGCTGTGTCGGATTTCGCCCGAGCGGGGGCGGCCTGCGTGGTGATGCTGCGC
193356 TGCCGCCTCCGGCCG
66 TGCCGCCTCCGGCCG
*
193371 CTGA-CCCGCTCAGGCTGTGTCGGATTTCGCCTGAGCGGGGGCGGCCTGCGTGGTGATGCTGCGC
1 CTGACCCCGCTCAGGCTGTGTCGGATTTCGCCCGAGCGGGGGCGGCCTGCGTGGTGATGCTGCGC
193435 TGCCGCCTCCGGCCG
66 TGCCGCCTCCGGCCG
193450 CTGACCCCGCTCAGGCTG
1 CTGACCCCGCTCAGGCTG
193468 CTCAGGCGAG
Statistics
Matches: 93, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
79 76 0.82
80 17 0.18
ACGTcount: A:0.07, C:0.36, G:0.37, T:0.20
Consensus pattern (80 bp):
CTGACCCCGCTCAGGCTGTGTCGGATTTCGCCCGAGCGGGGGCGGCCTGCGTGGTGATGCTGCGC
TGCCGCCTCCGGCCG
Found at i:212338 original size:30 final size:30
Alignment explanation
Indices: 212304--212364 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
212294 CAGCACGGAT
*
212304 CCGAACGCCGCCGGTA-GTGACGCCGCCGCG
1 CCGAACGCCGCCGGCACG-GACGCCGCCGCG
212334 CCGAACGCCGCCGGCACGGACGCCGCCGCG
1 CCGAACGCCGCCGGCACGGACGCCGCCGCG
212364 C
1 C
212365 GGCGCGGCAC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.13, C:0.48, G:0.36, T:0.03
Consensus pattern (30 bp):
CCGAACGCCGCCGGCACGGACGCCGCCGCG
Found at i:212341 original size:15 final size:16
Alignment explanation
Indices: 212323--212364 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 16
212313 GCCGGTAGTG
212323 ACGCCGCCGCGC-CGA
1 ACGCCGCCGCGCACGA
*
212338 ACGCCGCCG-GCACGG
1 ACGCCGCCGCGCACGA
212353 ACGCCGCCGCGC
1 ACGCCGCCGCGC
212365 GGCGCGGCAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 2 0.08
15 20 0.83
16 2 0.08
ACGTcount: A:0.12, C:0.52, G:0.36, T:0.00
Consensus pattern (16 bp):
ACGCCGCCGCGCACGA
Found at i:221320 original size:18 final size:20
Alignment explanation
Indices: 221299--221336 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
221289 CGATGCTGTC
221299 GCGGAA-GA-CGCCGAGGAA
1 GCGGAACGATCGCCGAGGAA
221317 GCGGAACGGATCGCCGAGGA
1 GCGGAAC-GATCGCCGAGGA
221337 TCTCGCCCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.35
20 2 0.12
21 9 0.53
ACGTcount: A:0.29, C:0.24, G:0.45, T:0.03
Consensus pattern (20 bp):
GCGGAACGATCGCCGAGGAA
Found at i:222448 original size:15 final size:15
Alignment explanation
Indices: 222430--222461 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
222420 CGACCGTCGC
222430 CGGGTCGGTGATCGT
1 CGGGTCGGTGATCGT
*
222445 CGGGTCGGTGGTCGT
1 CGGGTCGGTGATCGT
222460 CG
1 CG
222462 CCGAGTCGGC
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:0.03, C:0.22, G:0.50, T:0.25
Consensus pattern (15 bp):
CGGGTCGGTGATCGT
Found at i:222526 original size:12 final size:12
Alignment explanation
Indices: 222512--222556 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
222502 GGTGGATGTG
*
222512 GTGCCGGACGTG
1 GTGCCGGACGTC
222524 GTGCCGGACGTC
1 GTGCCGGACGTC
*
222536 GTGTCGGACGTC
1 GTGCCGGACGTC
*
222548 GTGTCGGAC
1 GTGCCGGAC
222557 TCGGAATCGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.09, C:0.27, G:0.44, T:0.20
Consensus pattern (12 bp):
GTGCCGGACGTC
Found at i:242414 original size:15 final size:15
Alignment explanation
Indices: 242391--242421 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
242381 GCAGCGGTGA
242391 GGCGGCGGTGAGGTC
1 GGCGGCGGTGAGGTC
*
242406 GGCGTCGGTGAGGTC
1 GGCGGCGGTGAGGTC
242421 G
1 G
242422 CGCACGGTCT
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:0.06, C:0.19, G:0.58, T:0.16
Consensus pattern (15 bp):
GGCGGCGGTGAGGTC
Found at i:246159 original size:18 final size:18
Alignment explanation
Indices: 246136--246173 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
246126 GGCCTGGCCG
246136 AGCGCATCTGATCAGTCC
1 AGCGCATCTGATCAGTCC
*
246154 AGCGCATCTGCTCAGTCC
1 AGCGCATCTGATCAGTCC
246172 AG
1 AG
246174 TGCGGTGAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.21, C:0.34, G:0.24, T:0.21
Consensus pattern (18 bp):
AGCGCATCTGATCAGTCC
Found at i:252719 original size:9 final size:9
Alignment explanation
Indices: 252705--252733 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
252695 CCCCTATGCA
252705 TGAGCCGAC
1 TGAGCCGAC
252714 TGAGCCGAC
1 TGAGCCGAC
252723 TGAGCCGAC
1 TGAGCCGAC
252732 TG
1 TG
252734 GACGTGACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.21, C:0.31, G:0.34, T:0.14
Consensus pattern (9 bp):
TGAGCCGAC
Found at i:256041 original size:9 final size:9
Alignment explanation
Indices: 256029--256058 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
256019 GGCCTATGCA
256029 TGGCCCAAC
1 TGGCCCAAC
256038 TGGCCCAAC
1 TGGCCCAAC
256047 TGGCCCAAC
1 TGGCCCAAC
256056 TGG
1 TGG
256059 AGCTGACCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.20, C:0.40, G:0.27, T:0.13
Consensus pattern (9 bp):
TGGCCCAAC
Found at i:257053 original size:15 final size:15
Alignment explanation
Indices: 257027--257102 Score: 59
Period size: 15 Copynumber: 5.8 Consensus size: 15
257017 GGTGGGCTCG
257027 GTCGATGCTCGAGCAA
1 GTCGA-GCTCGAGCAA
257043 GTCGAGCTCGAG--A
1 GTCGAGCTCGAGCAA
257056 -T-G-GC-CGAGCAA
1 GTCGAGCTCGAGCAA
257067 GTCGAGCTCGAG--A
1 GTCGAGCTCGAGCAA
257080 -T-G-GC-CGAGCAA
1 GTCGAGCTCGAGCAA
257091 GTCGAGCTCGAG
1 GTCGAGCTCGAG
257103 ATGGCCGGCC
Statistics
Matches: 48, Mismatches: 0, Indels: 25
0.66 0.00 0.34
Matches are distributed among these distances:
9 8 0.17
10 4 0.08
11 4 0.08
12 4 0.08
13 4 0.08
14 4 0.08
15 15 0.31
16 5 0.10
ACGTcount: A:0.24, C:0.25, G:0.37, T:0.14
Consensus pattern (15 bp):
GTCGAGCTCGAGCAA
Found at i:257063 original size:24 final size:24
Alignment explanation
Indices: 257036--257109 Score: 148
Period size: 24 Copynumber: 3.1 Consensus size: 24
257026 GGTCGATGCT
257036 CGAGCAAGTCGAGCTCGAGATGGC
1 CGAGCAAGTCGAGCTCGAGATGGC
257060 CGAGCAAGTCGAGCTCGAGATGGC
1 CGAGCAAGTCGAGCTCGAGATGGC
257084 CGAGCAAGTCGAGCTCGAGATGGC
1 CGAGCAAGTCGAGCTCGAGATGGC
257108 CG
1 CG
257110 GCCGGGACAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.24, C:0.26, G:0.38, T:0.12
Consensus pattern (24 bp):
CGAGCAAGTCGAGCTCGAGATGGC
Found at i:258616 original size:26 final size:26
Alignment explanation
Indices: 258572--258629 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
258562 TGCCAGCCCC
*
258572 GGTCTCGAGGGGACCTTCAACATGAA
1 GGTCTCGAGGAGACCTTCAACATGAA
* *
258598 GGTCTCGAGGAGACGTTCAACTTGAA
1 GGTCTCGAGGAGACCTTCAACATGAA
*
258624 CGTCTC
1 GGTCTC
258630 CCCCTCGGCC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.22
Consensus pattern (26 bp):
GGTCTCGAGGAGACCTTCAACATGAA
Found at i:258911 original size:24 final size:24
Alignment explanation
Indices: 258884--258934 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
258874 AGCAAGTCAG
*
258884 TCGGCCATCTCGAGCTCGACTTGC
1 TCGGCCATCCCGAGCTCGACTTGC
*
258908 TCGGCCATCCCGGGCTCGACTTGC
1 TCGGCCATCCCGAGCTCGACTTGC
258932 TCG
1 TCG
258935 AGCATCGACC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.10, C:0.39, G:0.27, T:0.24
Consensus pattern (24 bp):
TCGGCCATCCCGAGCTCGACTTGC
Found at i:266024 original size:16 final size:17
Alignment explanation
Indices: 266003--266036 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
265993 GCGCGGCGGT
266003 GAGCGG-CACCAGGATC
1 GAGCGGACACCAGGATC
266019 GAGCGGAACACCAGGATC
1 GAGCGG-ACACCAGGATC
266037 AGCAGCAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
18 10 0.62
ACGTcount: A:0.29, C:0.29, G:0.35, T:0.06
Consensus pattern (17 bp):
GAGCGGACACCAGGATC
Found at i:268616 original size:17 final size:17
Alignment explanation
Indices: 268594--268628 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
268584 ATAGCCGACA
268594 CCGCCGATACGCAACAC
1 CCGCCGATACGCAACAC
268611 CCGCCGATACGCAACAC
1 CCGCCGATACGCAACAC
268628 C
1 C
268629 TCAGGAGCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.49, G:0.17, T:0.06
Consensus pattern (17 bp):
CCGCCGATACGCAACAC
Found at i:275227 original size:15 final size:15
Alignment explanation
Indices: 275186--275227 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
275176 GTACCCCCAG
* *
275186 CAGCCCCCGCAATAC
1 CAGCCGCCGCAGTAC
*
275201 CAGCAGCCGCAGTAC
1 CAGCCGCCGCAGTAC
275216 CAGCCGCCGCAG
1 CAGCCGCCGCAG
275228 CCGCAGTACC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.24, C:0.48, G:0.24, T:0.05
Consensus pattern (15 bp):
CAGCCGCCGCAGTAC
Found at i:276164 original size:18 final size:18
Alignment explanation
Indices: 276150--276230 Score: 117
Period size: 18 Copynumber: 4.5 Consensus size: 18
276140 GCTGCTGTTC
276150 GCCGTACTGCGGCTGCTG
1 GCCGTACTGCGGCTGCTG
*
276168 GCCGTACTGGGGCTGCTG
1 GCCGTACTGCGGCTGCTG
** *
276186 GCCGTAGGGCGGCTGCTC
1 GCCGTACTGCGGCTGCTG
*
276204 GCCGTACTGGGGCTGCTG
1 GCCGTACTGCGGCTGCTG
276222 GCCGTACTG
1 GCCGTACTG
276231 AGGCGGTTGC
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 54 1.00
ACGTcount: A:0.06, C:0.31, G:0.42, T:0.21
Consensus pattern (18 bp):
GCCGTACTGCGGCTGCTG
Found at i:276198 original size:36 final size:36
Alignment explanation
Indices: 276158--276227 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
276148 TCGCCGTACT
*
276158 GCGGCTGCTGGCCGTACTGGGGCTGCTGGCCGTAGG
1 GCGGCTGCTCGCCGTACTGGGGCTGCTGGCCGTAGG
276194 GCGGCTGCTCGCCGTACTGGGGCTGCTGGCCGTA
1 GCGGCTGCTCGCCGTACTGGGGCTGCTGGCCGTA
276228 CTGAGGCGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.06, C:0.30, G:0.44, T:0.20
Consensus pattern (36 bp):
GCGGCTGCTCGCCGTACTGGGGCTGCTGGCCGTAGG
Found at i:286329 original size:78 final size:78
Alignment explanation
Indices: 286200--286413 Score: 401
Period size: 78 Copynumber: 2.7 Consensus size: 78
286190 GGTCGGGTAG
*
286200 GGGGCGCCCTGCGTGGTGACGCTGCGCTGCCGACTCCGGGCGCTGACCCGCTCAGGCTGTGTTTG
1 GGGGCGCCCTGCGTGGTGACGCTGCGCTGCCGCCTCCGGGCGCTGACCCGCTCAGGCTGTGTTTG
*
286265 TTTGTGCCTGAGT
66 TTTGTGCCTGAGC
286278 GGGGCGCCCTGCGTGGTGACGCTGCGCTGCCGCCTCCGGGCGCTGACCCGCTCAGGCTGTGTTTG
1 GGGGCGCCCTGCGTGGTGACGCTGCGCTGCCGCCTCCGGGCGCTGACCCGCTCAGGCTGTGTTTG
286343 TTTGTGCCTGAGC
66 TTTGTGCCTGAGC
286356 GGGGCGCCCTGCGTGGTGACGCTGCGCTGCCGCCTCCGGGGCGCTGACCCGCTCAGGC
1 GGGGCGCCCTGCGTGGTGACGCTGCGCTGCCGCCTCC-GGGCGCTGACCCGCTCAGGC
286414 GACGCAGAAC
Statistics
Matches: 133, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
78 113 0.85
79 20 0.15
ACGTcount: A:0.06, C:0.34, G:0.39, T:0.21
Consensus pattern (78 bp):
GGGGCGCCCTGCGTGGTGACGCTGCGCTGCCGCCTCCGGGCGCTGACCCGCTCAGGCTGTGTTTG
TTTGTGCCTGAGC
Found at i:297621 original size:21 final size:21
Alignment explanation
Indices: 297597--297639 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
297587 CCCCGCCAGC
* *
297597 CCCGGCTTCGCGGCCAACCTG
1 CCCGCCTTCCCGGCCAACCTG
297618 CCCGCCTTCCCGGCCAACCTG
1 CCCGCCTTCCCGGCCAACCTG
297639 C
1 C
297640 GCAAGCAGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.53, G:0.23, T:0.14
Consensus pattern (21 bp):
CCCGCCTTCCCGGCCAACCTG
Found at i:309254 original size:18 final size:18
Alignment explanation
Indices: 309231--309267 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
309221 CCGGTCGGCA
309231 CCGCACCGTAGGCGGGCG
1 CCGCACCGTAGGCGGGCG
*
309249 CCGCACCGTGGGCGGGCG
1 CCGCACCGTAGGCGGGCG
309267 C
1 C
309268 TGTGACGTGG
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:0.08, C:0.41, G:0.46, T:0.05
Consensus pattern (18 bp):
CCGCACCGTAGGCGGGCG
Found at i:309276 original size:18 final size:18
Alignment explanation
Indices: 309255--309299 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
309245 GGCGCCGCAC
309255 CGTGGGCGGGCGCTGTGA
1 CGTGGGCGGGCGCTGTGA
* *
309273 CGTGGGC-GGCGTTGTGC
1 CGTGGGCGGGCGCTGTGA
309290 CGTGGGCGGG
1 CGTGGGCGGG
309300 TGTTGCCCCG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 15 0.62
18 9 0.38
ACGTcount: A:0.02, C:0.22, G:0.58, T:0.18
Consensus pattern (18 bp):
CGTGGGCGGGCGCTGTGA
Found at i:322119 original size:24 final size:24
Alignment explanation
Indices: 322083--322153 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 24
322073 GAATGCCCGG
*
322083 GCGGCATGT-GCGGCTGCCCGTACT
1 GCGGC-TGTGGCGGCTGCCCGAACT
322107 GCGGCTGTGGCGGCTGCCCGAACT
1 GCGGCTGTGGCGGCTGCCCGAACT
322131 GCGGC--TGG-GGCTGCCCGAACT
1 GCGGCTGTGGCGGCTGCCCGAACT
322152 GC
1 GC
322154 TGCGGCGGCT
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
21 15 0.33
22 3 0.07
23 3 0.07
24 24 0.53
ACGTcount: A:0.08, C:0.34, G:0.41, T:0.17
Consensus pattern (24 bp):
GCGGCTGTGGCGGCTGCCCGAACT
Found at i:322156 original size:24 final size:24
Alignment explanation
Indices: 322094--322179 Score: 69
Period size: 21 Copynumber: 3.8 Consensus size: 24
322084 CGGCATGTGC
* * *
322094 GGCTGCCCGTACTGCGGCTG-TGG
1 GGCTGCCCGAACTGCTGCGGCTGG
322117 CGGCTGCCCGAA---CTGCGGCTGG
1 -GGCTGCCCGAACTGCTGCGGCTGG
322139 GGCTGCCCGAACTGCTGCGGC---
1 GGCTGCCCGAACTGCTGCGGCTGG
* *
322160 GGCTGGCCGTACTGCTGCGG
1 GGCTGCCCGAACTGCTGCGG
322180 TCCACCCGGC
Statistics
Matches: 53, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
21 33 0.62
22 3 0.06
24 17 0.32
ACGTcount: A:0.07, C:0.34, G:0.42, T:0.17
Consensus pattern (24 bp):
GGCTGCCCGAACTGCTGCGGCTGG
Found at i:322175 original size:21 final size:21
Alignment explanation
Indices: 322110--322179 Score: 88
Period size: 21 Copynumber: 3.3 Consensus size: 21
322100 CCGTACTGCG
*
322110 GCTGTGGCGGCTGCCCGAACT
1 GCTGCGGCGGCTGCCCGAACT
*
322131 GCGGCTGG-GGCTGCCCGAACT
1 GCTGC-GGCGGCTGCCCGAACT
* *
322152 GCTGCGGCGGCTGGCCGTACT
1 GCTGCGGCGGCTGCCCGAACT
322173 GCTGCGG
1 GCTGCGG
322180 TCCACCCGGC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
20 2 0.05
21 38 0.90
22 2 0.05
ACGTcount: A:0.07, C:0.33, G:0.43, T:0.17
Consensus pattern (21 bp):
GCTGCGGCGGCTGCCCGAACT
Found at i:361961 original size:24 final size:24
Alignment explanation
Indices: 361934--361982 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
361924 CGCCCAGCAC
361934 ACCAGC-CCGCCCTCGGCGTGCCCG
1 ACCAGCACCG-CCTCGGCGTGCCCG
* *
361958 ACCAGCACCGCCTCGGTGTGGCCG
1 ACCAGCACCGCCTCGGCGTGCCCG
361982 A
1 A
361983 GCGCCCGGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 19 0.86
25 3 0.14
ACGTcount: A:0.12, C:0.47, G:0.31, T:0.10
Consensus pattern (24 bp):
ACCAGCACCGCCTCGGCGTGCCCG
Found at i:374012 original size:27 final size:27
Alignment explanation
Indices: 373970--374161 Score: 233
Period size: 27 Copynumber: 7.1 Consensus size: 27
373960 TCTGCCTTCC
* *
373970 GTCTCGGCACTGGCCACAACACCGGAG
1 GTCTCGGCACCGGCCACAACGCCGGAG
* *
373997 GTCGCGGCACCGGCCACAACGCCGGGG
1 GTCTCGGCACCGGCCACAACGCCGGAG
*
374024 GTCTCGGCACC-GCCGACAACGCCGGGG
1 GTCTCGGCACCGGCC-ACAACGCCGGAG
374051 GTCTCGGCACCGGCCACAACGCCGGAG
1 GTCTCGGCACCGGCCACAACGCCGGAG
* * * *
374078 GTCTTGGCGCCGGCCACAGCACCGGAG
1 GTCTCGGCACCGGCCACAACGCCGGAG
* *
374105 GTCGCGGCACCGGCCACAACGCCGGGG
1 GTCTCGGCACCGGCCACAACGCCGGAG
* * * *
374132 GTCTTGGCGCCGGCCACGACACCGGAG
1 GTCTCGGCACCGGCCACAACGCCGGAG
374159 GTC
1 GTC
374162 GCGCTCGACG
Statistics
Matches: 141, Mismatches: 22, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
26 3 0.02
27 135 0.96
28 3 0.02
ACGTcount: A:0.16, C:0.39, G:0.36, T:0.08
Consensus pattern (27 bp):
GTCTCGGCACCGGCCACAACGCCGGAG
Found at i:374028 original size:54 final size:54
Alignment explanation
Indices: 373970--374164 Score: 275
Period size: 54 Copynumber: 3.6 Consensus size: 54
373960 TCTGCCTTCC
*
373970 GTCTCGGCACTGGCCACAACACCGGAGGTCGCGGCACCGGCCACAACGCCGGGG
1 GTCTCGGCACCGGCCACAACACCGGAGGTCGCGGCACCGGCCACAACGCCGGGG
* * * *
374024 GTCTCGGCACC-GCCGACAACGCCGGGGGTCTCGGCACCGGCCACAACGCCGGAG
1 GTCTCGGCACCGGCC-ACAACACCGGAGGTCGCGGCACCGGCCACAACGCCGGGG
* * *
374078 GTCTTGGCGCCGGCCACAGCACCGGAGGTCGCGGCACCGGCCACAACGCCGGGG
1 GTCTCGGCACCGGCCACAACACCGGAGGTCGCGGCACCGGCCACAACGCCGGGG
* * *
374132 GTCTTGGCGCCGGCCACGACACCGGAGGTCGCG
1 GTCTCGGCACCGGCCACAACACCGGAGGTCGCG
374165 CTCGACGGGG
Statistics
Matches: 125, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
53 3 0.02
54 119 0.95
55 3 0.02
ACGTcount: A:0.16, C:0.39, G:0.37, T:0.08
Consensus pattern (54 bp):
GTCTCGGCACCGGCCACAACACCGGAGGTCGCGGCACCGGCCACAACGCCGGGG
Found at i:374113 original size:81 final size:81
Alignment explanation
Indices: 373970--374164 Score: 266
Period size: 81 Copynumber: 2.4 Consensus size: 81
373960 TCTGCCTTCC
* * * *
373970 GTCTCGGCACTGGCCACAACACCGGAGGTCGCGGCACCGGCCACAACGCCGGGGGTCTCGGCACC
1 GTCTCGGCACCGGCCACAACACCGGAGGTCGCGGCACCGGCCACAACACCGGAGGTCGCGGCACC
374035 -GCCGACAACGCCGGGG
66 GGCC-ACAACGCCGGGG
* ** * *
374051 GTCTCGGCACCGGCCACAACGCCGGAGGTCTTGGCGCCGGCCACAGCACCGGAGGTCGCGGCACC
1 GTCTCGGCACCGGCCACAACACCGGAGGTCGCGGCACCGGCCACAACACCGGAGGTCGCGGCACC
374116 GGCCACAACGCCGGGG
66 GGCCACAACGCCGGGG
* * *
374132 GTCTTGGCGCCGGCCACGACACCGGAGGTCGCG
1 GTCTCGGCACCGGCCACAACACCGGAGGTCGCG
374165 CTCGACGGGG
Statistics
Matches: 98, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
81 95 0.97
82 3 0.03
ACGTcount: A:0.16, C:0.39, G:0.37, T:0.08
Consensus pattern (81 bp):
GTCTCGGCACCGGCCACAACACCGGAGGTCGCGGCACCGGCCACAACACCGGAGGTCGCGGCACC
GGCCACAACGCCGGGG
Found at i:375019 original size:16 final size:16
Alignment explanation
Indices: 375017--375163 Score: 71
Period size: 17 Copynumber: 8.8 Consensus size: 16
375007 GTGGTCCAGC
375017 GGCCCAGCGGCCCGGT
1 GGCCCAGCGGCCCGGT
*
375033 GGCCTCAGCGGCCGGGT
1 GGCC-CAGCGGCCCGGT
* *
375050 GGTCCAGTGGCCCGGT
1 GGCCCAGCGGCCCGGT
* * *
375066 AGGCCATAGCGGCTCAGT
1 -GGCC-CAGCGGCCCGGT
* ** *
375084 GGCCATAGCGGCCTAGC
1 GGCC-CAGCGGCCCGGT
*
375101 GG-CCATTGTGGCCCGGT
1 GGCCCA--GCGGCCCGGT
* * *
375118 GGCCATAGCGGCCCAGC
1 GGCC-CAGCGGCCCGGT
* *
375135 GGCCCAGCGGCCCAGC
1 GGCCCAGCGGCCCGGT
*
375151 GGCCCAGCAGCCC
1 GGCCCAGCGGCCC
375164 AGCAGCGGCC
Statistics
Matches: 101, Mismatches: 23, Indels: 14
0.73 0.17 0.10
Matches are distributed among these distances:
15 1 0.01
16 38 0.38
17 52 0.51
18 9 0.09
19 1 0.01
ACGTcount: A:0.12, C:0.38, G:0.39, T:0.11
Consensus pattern (16 bp):
GGCCCAGCGGCCCGGT
Found at i:375027 original size:24 final size:25
Alignment explanation
Indices: 374995--375045 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
374985 GCCCGGTGGC
* *
374995 CCCAACGGCCGGGTGGTC-CAGCGG
1 CCCAACGGCCCGGTGGCCTCAGCGG
*
375019 CCCAGCGGCCCGGTGGCCTCAGCGG
1 CCCAACGGCCCGGTGGCCTCAGCGG
375044 CC
1 CC
375046 GGGTGGTCCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 15 0.65
25 8 0.35
ACGTcount: A:0.10, C:0.43, G:0.39, T:0.08
Consensus pattern (25 bp):
CCCAACGGCCCGGTGGCCTCAGCGG
Found at i:375031 original size:41 final size:41
Alignment explanation
Indices: 374983--375062 Score: 133
Period size: 41 Copynumber: 2.0 Consensus size: 41
374973 CAGTGACCAA
374983 CGGCCCGGTGGCCCCAACGGCCGGGTGGTCCAGCGGCCCAG
1 CGGCCCGGTGGCCCCAACGGCCGGGTGGTCCAGCGGCCCAG
* * *
375024 CGGCCCGGTGGCCTCAGCGGCCGGGTGGTCCAGTGGCCC
1 CGGCCCGGTGGCCCCAACGGCCGGGTGGTCCAGCGGCCC
375063 GGTAGGCCAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.07, C:0.40, G:0.42, T:0.10
Consensus pattern (41 bp):
CGGCCCGGTGGCCCCAACGGCCGGGTGGTCCAGCGGCCCAG
Found at i:375086 original size:26 final size:25
Alignment explanation
Indices: 375053--375139 Score: 74
Period size: 25 Copynumber: 3.4 Consensus size: 25
375043 GCCGGGTGGT
375053 CCAGTGGCCCGGTAGGCCATAGCGG
1 CCAGTGGCCCGGTAGGCCATAGCGG
*
375078 CTCAGTGG-CC-ATAGCGGCC-TAGCGG
1 C-CAGTGGCCCGGTA--GGCCATAGCGG
375103 CCATTGTGGCCCGGT-GGCCATAGCGG
1 CCA--GTGGCCCGGTAGGCCATAGCGG
*
375129 CCCAGCGGCCC
1 -CCAGTGGCCC
375140 AGCGGCCCAG
Statistics
Matches: 50, Mismatches: 3, Indels: 18
0.70 0.04 0.25
Matches are distributed among these distances:
24 4 0.08
25 20 0.40
26 20 0.40
27 5 0.10
28 1 0.02
ACGTcount: A:0.14, C:0.36, G:0.37, T:0.14
Consensus pattern (25 bp):
CCAGTGGCCCGGTAGGCCATAGCGG
Found at i:375104 original size:17 final size:17
Alignment explanation
Indices: 375067--375154 Score: 97
Period size: 17 Copynumber: 5.2 Consensus size: 17
375057 TGGCCCGGTA
* *
375067 GGCCATAGCGGCTCAGT
1 GGCCATAGCGGCCCAGC
*
375084 GGCCATAGCGGCCTAGC
1 GGCCATAGCGGCCCAGC
* * * *
375101 GGCCATTGTGGCCCGGT
1 GGCCATAGCGGCCCAGC
375118 GGCCATAGCGGCCCAGC
1 GGCCATAGCGGCCCAGC
*
375135 GGCC-CAGCGGCCCAGC
1 GGCCATAGCGGCCCAGC
375151 GGCC
1 GGCC
375155 CAGCAGCCCA
Statistics
Matches: 58, Mismatches: 13, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
16 15 0.26
17 43 0.74
ACGTcount: A:0.14, C:0.38, G:0.38, T:0.11
Consensus pattern (17 bp):
GGCCATAGCGGCCCAGC
Found at i:375135 original size:8 final size:8
Alignment explanation
Indices: 375124--375190 Score: 80
Period size: 8 Copynumber: 8.0 Consensus size: 8
375114 CGGTGGCCAT
375124 AGCGGCCC
1 AGCGGCCC
375132 AGCGGCCC
1 AGCGGCCC
375140 AGCGGCCC
1 AGCGGCCC
375148 AGCGGCCC
1 AGCGGCCC
*
375156 AGCAGCCCAGC
1 AGC-GGCC--C
375167 AGCGGCCC
1 AGCGGCCC
* *
375175 AGCGACCT
1 AGCGGCCC
375183 AGCGGCCC
1 AGCGGCCC
375191 GGTGGCACGT
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
8 40 0.80
9 3 0.06
10 3 0.06
11 4 0.08
ACGTcount: A:0.16, C:0.48, G:0.34, T:0.01
Consensus pattern (8 bp):
AGCGGCCC
Found at i:375190 original size:27 final size:27
Alignment explanation
Indices: 375139--375190 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
375129 CCCAGCGGCC
*
375139 CAGCGGCCCAGCGGCCCAGCAGCCCAG
1 CAGCGGCCCAGCGACCCAGCAGCCCAG
* *
375166 CAGCGGCCCAGCGACCTAGCGGCCC
1 CAGCGGCCCAGCGACCCAGCAGCCC
375191 GGTGGCACGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.17, C:0.48, G:0.33, T:0.02
Consensus pattern (27 bp):
CAGCGGCCCAGCGACCCAGCAGCCCAG
Found at i:382655 original size:15 final size:15
Alignment explanation
Indices: 382637--382719 Score: 76
Period size: 15 Copynumber: 5.5 Consensus size: 15
382627 CGCCGCCAAG
*
382637 AAGACCACCGCGACC
1 AAGACGACCGCGACC
*
382652 AAGACGGCCGCGACC
1 AAGACGACCGCGACC
* *
382667 AAGACGGCGGCGACC
1 AAGACGACCGCGACC
* * **
382682 AAGACCACGGCGAAG
1 AAGACGACCGCGACC
**
382697 AAGACGACCGCGAAG
1 AAGACGACCGCGACC
382712 AAGACGAC
1 AAGACGAC
382720 GGCCGCGAAG
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 59 1.00
ACGTcount: A:0.35, C:0.34, G:0.31, T:0.00
Consensus pattern (15 bp):
AAGACGACCGCGACC
Found at i:382705 original size:18 final size:16
Alignment explanation
Indices: 382691--382731 Score: 57
Period size: 15 Copynumber: 2.5 Consensus size: 16
382681 CAAGACCACG
382691 GCGAAGAAGACGA-CC
1 GCGAAGAAGACGACCC
382706 GCGAAGAAGACGACGGCC
1 GCGAAGAAGACGAC--CC
382724 GCGAAGAA
1 GCGAAGAA
382732 AACCGCGGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 13 0.57
18 10 0.43
ACGTcount: A:0.39, C:0.24, G:0.37, T:0.00
Consensus pattern (16 bp):
GCGAAGAAGACGACCC
Found at i:382716 original size:45 final size:45
Alignment explanation
Indices: 382637--382722 Score: 109
Period size: 45 Copynumber: 1.9 Consensus size: 45
382627 CGCCGCCAAG
* * * *
382637 AAGACCACCGCGACCAAGACGGCCGCGACCAAGACGGCGGCGACC
1 AAGACCACCGCGAACAAGACGACCGCGAACAAGACGACGGCGACC
* * *
382682 AAGACCACGGCGAAGAAGACGACCGCGAAGAAGACGACGGC
1 AAGACCACCGCGAACAAGACGACCGCGAACAAGACGACGGC
382723 CGCGAAGAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 34 1.00
ACGTcount: A:0.34, C:0.34, G:0.33, T:0.00
Consensus pattern (45 bp):
AAGACCACCGCGAACAAGACGACCGCGAACAAGACGACGGCGACC
Found at i:382741 original size:18 final size:18
Alignment explanation
Indices: 382699--382734 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
382689 CGGCGAAGAA
* *
382699 GACGACCGCGAAGAAGAC
1 GACGGCCGCGAAGAAAAC
382717 GACGGCCGCGAAGAAAAC
1 GACGGCCGCGAAGAAAAC
382735 CGCGGCCAAG
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:0.39, C:0.28, G:0.33, T:0.00
Consensus pattern (18 bp):
GACGGCCGCGAAGAAAAC
Found at i:390602 original size:15 final size:15
Alignment explanation
Indices: 390574--390614 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
390564 CGCTATCTGG
390574 TGTTCT-GA-GCGCA
1 TGTTCTCGACGCGCA
390587 TGTTCTCGACGCGCA
1 TGTTCTCGACGCGCA
*
390602 TGTCCTCGACGCG
1 TGTTCTCGACGCG
390615 GCGCCCGACA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 6 0.24
14 2 0.08
15 17 0.68
ACGTcount: A:0.12, C:0.32, G:0.29, T:0.27
Consensus pattern (15 bp):
TGTTCTCGACGCGCA
Found at i:391998 original size:17 final size:17
Alignment explanation
Indices: 391979--392038 Score: 84
Period size: 17 Copynumber: 3.5 Consensus size: 17
391969 GAATTTGTCG
*
391979 CCCATCAGCACTTCTCG
1 CCCATCAGCACTTCTCA
391996 CCCATCAGCACTTCTCA
1 CCCATCAGCACTTCTCA
* *
392013 CCCCTCACCACTTCTCA
1 CCCATCAGCACTTCTCA
*
392030 CCCCTCAGC
1 CCCATCAGC
392039 GCTCGCATCC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.18, C:0.53, G:0.07, T:0.22
Consensus pattern (17 bp):
CCCATCAGCACTTCTCA
Found at i:396158 original size:13 final size:13
Alignment explanation
Indices: 396136--396175 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
396126 CGGGACGTGG
*
396136 CCGGTGAGCAGGC
1 CCGGTCAGCAGGC
396149 CCGGTCAGCAGGC
1 CCGGTCAGCAGGC
*
396162 CCGGTCAGGAGGC
1 CCGGTCAGCAGGC
396175 C
1 C
396176 GAGGCGACCG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.15, C:0.35, G:0.42, T:0.07
Consensus pattern (13 bp):
CCGGTCAGCAGGC
Found at i:409946 original size:22 final size:21
Alignment explanation
Indices: 409899--409946 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
409889 GGTGCGCGGA
*
409899 TCGGGGGCGGCGACCGTGGTG
1 TCGGGGGCGGCGACCGTGGCG
*
409920 TCGGGCGGCGGCGGAGCGTGGCG
1 TCGGG-GGCGGC-GACCGTGGCG
409943 -CGGG
1 TCGGG
409947 TCCGGTGCGG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 5 0.22
22 10 0.43
23 8 0.35
ACGTcount: A:0.04, C:0.25, G:0.60, T:0.10
Consensus pattern (21 bp):
TCGGGGGCGGCGACCGTGGCG
Found at i:424203 original size:18 final size:20
Alignment explanation
Indices: 424152--424198 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 20
424142 GCGAATGCTT
*
424152 CCGCCACAGGATCGAATCCCG
1 CCGCCAC-GGGTCGAATCCCG
424173 CCGCCAGCGGGTCGAATCCCG
1 CCGCCA-CGGGTCGAATCCCG
424194 CCGCC
1 CCGCC
424199 GGGTCCAGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.17, C:0.47, G:0.28, T:0.09
Consensus pattern (20 bp):
CCGCCACGGGTCGAATCCCG
Found at i:424215 original size:21 final size:21
Alignment explanation
Indices: 424191--424239 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
424181 GGGTCGAATC
424191 CCGCCGCCGGGTCCAGCACTG
1 CCGCCGCCGGGTCCAGCACTG
424212 CCGCCGCCGGGTCCAGCACTG
1 CCGCCGCCGGGTCCAGCACTG
424233 CCGCCGC
1 CCGCCGC
424240 GCGTACGGGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.08, C:0.51, G:0.33, T:0.08
Consensus pattern (21 bp):
CCGCCGCCGGGTCCAGCACTG
Found at i:424490 original size:54 final size:54
Alignment explanation
Indices: 424359--424496 Score: 136
Period size: 54 Copynumber: 2.5 Consensus size: 54
424349 GCCGCGGGTT
** * * *
424359 CGGGTGCCACCGGTTCCGGCACGGCCGCTGGTTCCGGTGTGGCGACCGGTCCAGG
1 CGGG-GCCACCGGTTCCGGCGTGGCCGCTGATCCCGGTGTGCCGACCGGTCCAGG
* * * * * *
424414 CAGGGCGACTGGTACCGACGTGGCCGCTGATCCCGGTGTGCCCG-CCGCTTCC-GG
1 CGGGGCCACCGGTTCCGGCGTGGCCGCTGATCCCGGTGTG-CCGACCG-GTCCAGG
424468 CGGGGCCACCGGTTCCGGCGTGGCCGCTG
1 CGGGGCCACCGGTTCCGGCGTGGCCGCTG
424497 CTTCGGGCGC
Statistics
Matches: 65, Mismatches: 16, Indels: 5
0.76 0.19 0.06
Matches are distributed among these distances:
54 57 0.88
55 8 0.12
ACGTcount: A:0.07, C:0.36, G:0.41, T:0.16
Consensus pattern (54 bp):
CGGGGCCACCGGTTCCGGCGTGGCCGCTGATCCCGGTGTGCCGACCGGTCCAGG
Found at i:440618 original size:17 final size:17
Alignment explanation
Indices: 440596--440631 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
440586 GAGCACCCGG
440596 CGATCGGGTGCGAATGT
1 CGATCGGGTGCGAATGT
440613 CGATCGGGTGCGAATGT
1 CGATCGGGTGCGAATGT
440630 CG
1 CG
440632 TTGCCGGGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.17, C:0.19, G:0.42, T:0.22
Consensus pattern (17 bp):
CGATCGGGTGCGAATGT
Found at i:441244 original size:11 final size:12
Alignment explanation
Indices: 441230--441267 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
441220 GGCGCCGGTT
441230 CGGCGGGGGTC-
1 CGGCGGGGGTCG
*
441241 CGGCGCGGGTCG
1 CGGCGGGGGTCG
*
441253 CGGCGGGGCTCG
1 CGGCGGGGGTCG
441265 CGG
1 CGG
441268 TCGTGCCGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.00, C:0.32, G:0.61, T:0.08
Consensus pattern (12 bp):
CGGCGGGGGTCG
Found at i:443248 original size:18 final size:18
Alignment explanation
Indices: 443225--443282 Score: 89
Period size: 18 Copynumber: 3.2 Consensus size: 18
443215 GAAAGCGCCC
443225 TGCCGACGAGAAGAGCGG
1 TGCCGACGAGAAGAGCGG
*
443243 TGCCGACGAGAAGAACGG
1 TGCCGACGAGAAGAGCGG
*
443261 TGCCGACGAGAAAGGGCGG
1 TGCCGACGAG-AAGAGCGG
443280 TGC
1 TGC
443283 GGTCCGGGGA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 27 0.75
19 9 0.25
ACGTcount: A:0.28, C:0.22, G:0.43, T:0.07
Consensus pattern (18 bp):
TGCCGACGAGAAGAGCGG
Found at i:446494 original size:12 final size:12
Alignment explanation
Indices: 446477--446510 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
446467 CCGCCGCCGT
446477 CGCCCACCTGCG
1 CGCCCACCTGCG
446489 CGCCCACCTGCG
1 CGCCCACCTGCG
446501 CGCCCACCTG
1 CGCCCACCTG
446511 TCGATCCGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.09, C:0.59, G:0.24, T:0.09
Consensus pattern (12 bp):
CGCCCACCTGCG
Found at i:509158 original size:15 final size:15
Alignment explanation
Indices: 509140--509177 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
509130 CCGGTGCGTG
509140 GTGGACC-GTGCCTTC
1 GTGGACCGGT-CCTTC
509155 GTGGACCGGTCCTTC
1 GTGGACCGGTCCTTC
*
509170 GTGCACCG
1 GTGGACCG
509178 CCCCACGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 19 0.90
16 2 0.10
ACGTcount: A:0.08, C:0.34, G:0.34, T:0.24
Consensus pattern (15 bp):
GTGGACCGGTCCTTC
Found at i:528163 original size:27 final size:27
Alignment explanation
Indices: 528147--528201 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
528137 GGCCGGGTCG
528147 CTCCGCCAACTCGACCGGTGCCGGGAA
1 CTCCGCCAACTCGACCGGTGCCGGGAA
* * *
528174 CTCCGCCAACTCCAACGGCGCCGGGAA
1 CTCCGCCAACTCGACCGGTGCCGGGAA
528201 C
1 C
528202 CAGACGGGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.20, C:0.44, G:0.27, T:0.09
Consensus pattern (27 bp):
CTCCGCCAACTCGACCGGTGCCGGGAA
Found at i:528646 original size:33 final size:33
Alignment explanation
Indices: 528609--528679 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 33
528599 TCGGCGCCGT
*
528609 CCTCGGCACCGGGTCGGCCGGG-CT-GGGCCTCGG
1 CCTCGGCACCGGCTCGG-CGGGTCTCGGG-CTCGG
528642 CCTCGGCACCGGCTCGGCGGGTCTCGGGCTCGG
1 CCTCGGCACCGGCTCGGCGGGTCTCGGGCTCGG
528675 CCTCG
1 CCTCG
528680 CGACGGGTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
32 4 0.11
33 28 0.80
34 3 0.09
ACGTcount: A:0.03, C:0.41, G:0.42, T:0.14
Consensus pattern (33 bp):
CCTCGGCACCGGCTCGGCGGGTCTCGGGCTCGG
Found at i:528758 original size:15 final size:14
Alignment explanation
Indices: 528740--528841 Score: 60
Period size: 15 Copynumber: 6.9 Consensus size: 14
528730 GGTGCCGCGC
528740 TCGGTTCCGCGGCGG
1 TCGGTTCCGCGGC-G
* *
528755 TCGGCTCGGCAGGCG
1 TCGGTTCCGC-GGCG
*
528770 TCGGTTCCGCCGCCG
1 TCGGTTCCG-CGGCG
*
528785 TCGGTTCCGCCGGGG
1 TCGGTTCCG-CGGCG
* *
528800 TGGGTTCGGCGGGCG
1 TCGGTTCCGC-GGCG
* * *
528815 TCGGCTCGGCCGGTG
1 TCGGTTCCG-CGGCG
*
528830 TCGGATCCGCGG
1 TCGGTTCCGCGG
528842 GTGTCGGTCT
Statistics
Matches: 68, Mismatches: 15, Indels: 9
0.74 0.16 0.10
Matches are distributed among these distances:
14 4 0.06
15 59 0.87
16 5 0.07
ACGTcount: A:0.02, C:0.33, G:0.46, T:0.19
Consensus pattern (14 bp):
TCGGTTCCGCGGCG
Found at i:528774 original size:30 final size:30
Alignment explanation
Indices: 528740--528860 Score: 109
Period size: 30 Copynumber: 4.0 Consensus size: 30
528730 GGTGCCGCGC
*
528740 TCGGTTCCGC-GGCGGTCGGCTCGGCAGGCG
1 TCGGTTCCGCGGGC-GTCGGCTCGGCCGGCG
* * * * *
528770 TCGGTTCCGCCGCCGTCGGTTCCGCCGGGG
1 TCGGTTCCGCGGGCGTCGGCTCGGCCGGCG
* * *
528800 TGGGTTCGGCGGGCGTCGGCTCGGCCGGTG
1 TCGGTTCCGCGGGCGTCGGCTCGGCCGGCG
* *
528830 TCGGATCCGCGGGTGTCGGTCTCGGCTCGGC
1 TCGGTTCCGCGGGCGTCGG-CTCGGC-CGGC
528861 CGGTGCCGGT
Statistics
Matches: 71, Mismatches: 17, Indels: 4
0.77 0.18 0.04
Matches are distributed among these distances:
30 60 0.85
31 8 0.11
32 3 0.04
ACGTcount: A:0.02, C:0.33, G:0.45, T:0.20
Consensus pattern (30 bp):
TCGGTTCCGCGGGCGTCGGCTCGGCCGGCG
Found at i:528782 original size:45 final size:45
Alignment explanation
Indices: 528740--528855 Score: 119
Period size: 45 Copynumber: 2.6 Consensus size: 45
528730 GGTGCCGCGC
528740 TCGGTTCCG-CGGCGGTCGGCTCGGCAGGCGTCGGTTCCGCCGCCG
1 TCGGTTCCGCCGG-GGTCGGCTCGGCAGGCGTCGGTTCCGCCGCCG
* * * * * **
528785 TCGGTTCCGCCGGGGTGGGTTCGGCGGGCGTCGGCTCGGCCGGTG
1 TCGGTTCCGCCGGGGTCGGCTCGGCAGGCGTCGGTTCCGCCGCCG
*
528830 TCGGATCCG-CGGGTGTCGGTCTCGGC
1 TCGGTTCCGCCGGG-GTCGG-CTCGGC
528856 TCGGCCGGTG
Statistics
Matches: 58, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
44 4 0.07
45 46 0.79
46 8 0.14
ACGTcount: A:0.02, C:0.33, G:0.46, T:0.20
Consensus pattern (45 bp):
TCGGTTCCGCCGGGGTCGGCTCGGCAGGCGTCGGTTCCGCCGCCG
Found at i:528864 original size:15 final size:15
Alignment explanation
Indices: 528846--528892 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
528836 CCGCGGGTGT
528846 CGGTCTCGGCTCGGC
1 CGGTCTCGGCTCGGC
*
528861 CGGTGC-CGGTTCGGC
1 CGGT-CTCGGCTCGGC
*
528876 CGGACTCGGCTCGGC
1 CGGTCTCGGCTCGGC
528891 CG
1 CG
528893 CGGTGGGTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 1 0.04
15 25 0.93
16 1 0.04
ACGTcount: A:0.02, C:0.38, G:0.43, T:0.17
Consensus pattern (15 bp):
CGGTCTCGGCTCGGC
Found at i:528914 original size:30 final size:29
Alignment explanation
Indices: 528850--528907 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 29
528840 GGGTGTCGGT
528850 CTCGGCTCGGCCGGTGCCGGTTCGGCCGGA
1 CTCGGCTCGGCCGGTG-CGGTTCGGCCGGA
528880 CTCGGCTCGGCCGCGGTG-GGTTCGGCCG
1 CTCGGCTCGG-C-CGGTGCGGTTCGGCCG
528908 CGCTCGGTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 20 0.77
31 1 0.04
32 5 0.19
ACGTcount: A:0.02, C:0.36, G:0.45, T:0.17
Consensus pattern (29 bp):
CTCGGCTCGGCCGGTGCGGTTCGGCCGGA
Found at i:528916 original size:15 final size:15
Alignment explanation
Indices: 528867--528917 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
528857 CGGCCGGTGC
528867 CGGTTCGGCCG-GACT
1 CGGTTCGGCCGCG-CT
* *
528882 CGGCTCGGCCGCGGT
1 CGGTTCGGCCGCGCT
*
528897 GGGTTCGGCCGCGCT
1 CGGTTCGGCCGCGCT
528912 CGGTTC
1 CGGTTC
528918 CGCCTCACCG
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
15 28 0.97
16 1 0.03
ACGTcount: A:0.02, C:0.35, G:0.43, T:0.20
Consensus pattern (15 bp):
CGGTTCGGCCGCGCT
Found at i:529117 original size:27 final size:26
Alignment explanation
Indices: 529083--529139 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
529073 CGATCGCCGT
**
529083 CGCCGCACCGGAGGCGCCCGCACCCG
1 CGCCGCACCCCAGGCGCCCGCACCCG
529109 CGCCGGCACCCCAGGCGCCCGC-CCC-
1 CGCC-GCACCCCAGGCGCCCGCACCCG
529134 CGCCGC
1 CGCCGC
529140 GCCGTCGGCC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 2 0.07
25 4 0.14
26 7 0.25
27 15 0.54
ACGTcount: A:0.09, C:0.60, G:0.32, T:0.00
Consensus pattern (26 bp):
CGCCGCACCCCAGGCGCCCGCACCCG
Found at i:547201 original size:20 final size:20
Alignment explanation
Indices: 547168--547216 Score: 75
Period size: 18 Copynumber: 2.5 Consensus size: 20
547158 GTTCCGGTGG
*
547168 GGGCCGAGCCGTGTGTGT--
1 GGGCGGAGCCGTGTGTGTGC
547186 GGGCGGAGCCGTGTGTGTGC
1 GGGCGGAGCCGTGTGTGTGC
547206 GGGCGGAGCCG
1 GGGCGGAGCCG
547217 AGGGCTCAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 17 0.61
20 11 0.39
ACGTcount: A:0.06, C:0.22, G:0.55, T:0.16
Consensus pattern (20 bp):
GGGCGGAGCCGTGTGTGTGC
Found at i:550851 original size:14 final size:14
Alignment explanation
Indices: 550832--550864 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
550822 CGGCGTCCGC
550832 GCTGACCGAACTCG
1 GCTGACCGAACTCG
550846 GCTGACCGAACTCG
1 GCTGACCGAACTCG
550860 GCTGA
1 GCTGA
550865 GCGGATCGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.21, C:0.33, G:0.30, T:0.15
Consensus pattern (14 bp):
GCTGACCGAACTCG
Found at i:553062 original size:24 final size:22
Alignment explanation
Indices: 553017--553063 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 22
553007 GCGGCTTCAC
553017 CAGGACCGCGACGGTGCTGGTG
1 CAGGACCGCGACGGTGCTGGTG
553039 CAGGCACCGCGCAGCGGT-CTGGTG
1 CAGG-ACCGCG-A-CGGTGCTGGTG
553063 C
1 C
553064 TCGACCCCGA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 4 0.18
23 6 0.27
24 8 0.36
25 4 0.18
ACGTcount: A:0.13, C:0.32, G:0.43, T:0.13
Consensus pattern (22 bp):
CAGGACCGCGACGGTGCTGGTG
Found at i:560262 original size:18 final size:18
Alignment explanation
Indices: 560254--560321 Score: 100
Period size: 18 Copynumber: 3.8 Consensus size: 18
560244 CGATGCCGCG
* *
560254 GGTTCGACCAAGGCTGCG
1 GGTTCGACCGAGGCTGCC
*
560272 GGTTCGACGGAGGCTGCC
1 GGTTCGACCGAGGCTGCC
*
560290 GGTTCGACCCAGGCTGCC
1 GGTTCGACCGAGGCTGCC
560308 GGTTCGACCGAGGC
1 GGTTCGACCGAGGC
560322 CGTGGGGCAG
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.13, C:0.31, G:0.40, T:0.16
Consensus pattern (18 bp):
GGTTCGACCGAGGCTGCC
Found at i:560337 original size:18 final size:18
Alignment explanation
Indices: 560315--560362 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
560305 GCCGGTTCGA
*
560315 CCGAGGCCGTGGGGCAGAG
1 CCGAGGCCGCGGGGCAG-G
*
560334 -CGAGGCCGCGGGGGAGG
1 CCGAGGCCGCGGGGCAGG
560351 CCGAGGCCGCGG
1 CCGAGGCCGCGG
560363 AGGCGGTGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 1 0.04
18 25 0.96
ACGTcount: A:0.12, C:0.29, G:0.56, T:0.02
Consensus pattern (18 bp):
CCGAGGCCGCGGGGCAGG
Found at i:560460 original size:15 final size:16
Alignment explanation
Indices: 560416--560462 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 16
560406 CAGCCTGGCC
*
560416 AAGTCCGGTTTGTCG-
1 AAGTCCGGTCTGTCGA
* *
560431 AAGTCCGGCCCGTCGA
1 AAGTCCGGTCTGTCGA
560447 AAG-CCGGTCTGTCGA
1 AAGTCCGGTCTGTCGA
560462 A
1 A
560463 GGACGGGCCG
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 23 0.88
16 3 0.12
ACGTcount: A:0.19, C:0.28, G:0.32, T:0.21
Consensus pattern (16 bp):
AAGTCCGGTCTGTCGA
Found at i:568369 original size:20 final size:22
Alignment explanation
Indices: 568346--568387 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
568336 GGGCCCTGGC
568346 GCGGCT-CGGCG-ACAGCGCGG
1 GCGGCTACGGCGCACAGCGCGG
*
568366 GCGGCTACGGCGCACTGCGCGG
1 GCGGCTACGGCGCACAGCGCGG
568388 CGTCGCGCGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.32
21 5 0.26
22 8 0.42
ACGTcount: A:0.10, C:0.36, G:0.48, T:0.07
Consensus pattern (22 bp):
GCGGCTACGGCGCACAGCGCGG
Found at i:569785 original size:22 final size:23
Alignment explanation
Indices: 569760--569803 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
569750 CTGCGAACGG
*
569760 CGGGTGAACGGG-CCCGTCCGGC
1 CGGGCGAACGGGACCCGTCCGGC
*
569782 CGGGCGAACGGGAGCCGTCCGG
1 CGGGCGAACGGGACCCGTCCGG
569804 AAGGCCGATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.11, C:0.34, G:0.48, T:0.07
Consensus pattern (23 bp):
CGGGCGAACGGGACCCGTCCGGC
Found at i:585107 original size:77 final size:77
Alignment explanation
Indices: 584984--585242 Score: 443
Period size: 77 Copynumber: 3.4 Consensus size: 77
584974 GCTCGTCACC
584984 GCCTGACC-GGTCAGCGGCCGGAGGCGGTAGCGGAGCGTGACCACGCAGGCCGCCCCGGGCGGGC
1 GCCTGACCGGGTCAGCGGCCGGAGGCGGTAGCGGAGCGTGACCACGCAGGCCGCCCCGGGCGGGC
*
585048 GCATCGGATACC
66 GCATCGGATACA
* *
585060 GCCTGACCGGGTCAGCGGCCGGAGGCGGTAGCGGAGCGTCACCACGCAGGCCGCCCCGGTCGGGC
1 GCCTGACCGGGTCAGCGGCCGGAGGCGGTAGCGGAGCGTGACCACGCAGGCCGCCCCGGGCGGGC
*
585125 GCAAAT-GG-CACA
66 GC--ATCGGATACA
585137 GCCTGACCGGGTCAGCGGCCGGAGGCGGTAGCGGAGCGTGACCACGCAGGCCGCCCCGGGCGGGC
1 GCCTGACCGGGTCAGCGGCCGGAGGCGGTAGCGGAGCGTGACCACGCAGGCCGCCCCGGGCGGGC
585202 GCATCGGATACA
66 GCATCGGATACA
585214 GCCTGACCGGGTCAGCGGCCGGAGGCGGT
1 GCCTGACCGGGTCAGCGGCCGGAGGCGGT
585243 GGTCTCTACC
Statistics
Matches: 171, Mismatches: 7, Indels: 9
0.91 0.04 0.05
Matches are distributed among these distances:
75 2 0.01
76 10 0.06
77 155 0.91
78 2 0.01
79 2 0.01
ACGTcount: A:0.15, C:0.34, G:0.42, T:0.08
Consensus pattern (77 bp):
GCCTGACCGGGTCAGCGGCCGGAGGCGGTAGCGGAGCGTGACCACGCAGGCCGCCCCGGGCGGGC
GCATCGGATACA
Found at i:586998 original size:17 final size:17
Alignment explanation
Indices: 586966--586999 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
586956 CGGCGTCCGA
* *
586966 ATTGTCCGGTGGGTGCC
1 ATTGTCCGGCGAGTGCC
586983 ATTGTCCGGCGAGTGCC
1 ATTGTCCGGCGAGTGCC
587000 GGTCGGGTGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.09, C:0.26, G:0.38, T:0.26
Consensus pattern (17 bp):
ATTGTCCGGCGAGTGCC
Done.