Tandem Repeats Finder Program written by:
Gary Benson
Department of Biomathematical Sciences
Mount Sinai School of Medicine
Version 4.00
Sequence: pNF1 2003-09-03
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: 184026
ACGTcount: A:0.16, C:0.33, G:0.34, T:0.17
Found at i:13808 original size:19 final size:19
Alignment explanation
Indices: 13784--13820 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
13774 AGGTGTATGC
13784 GCTGGTGAAGCGGTGGCGG
1 GCTGGTGAAGCGGTGGCGG
* *
13803 GCTGGTGAGGGGGTGGCG
1 GCTGGTGAAGCGGTGGCG
13821 TCGGATCTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.08, C:0.14, G:0.62, T:0.16
Consensus pattern (19 bp):
GCTGGTGAAGCGGTGGCGG
Found at i:36046 original size:22 final size:22
Alignment explanation
Indices: 36021--36062 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
36011 GACGAGTCCA
36021 CACTGAAGAG-GACTTCGAAAAT
1 CACTGAAG-GTGACTTCGAAAAT
36043 CACTGAAGGTGACTTCGAAA
1 CACTGAAGGTGACTTCGAAA
36063 CGTGACATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.38, C:0.19, G:0.24, T:0.19
Consensus pattern (22 bp):
CACTGAAGGTGACTTCGAAAAT
Found at i:72597 original size:9 final size:9
Alignment explanation
Indices: 72585--72626 Score: 84
Period size: 9 Copynumber: 4.7 Consensus size: 9
72575 GTGGCTGGCG
72585 GCGTCGATC
1 GCGTCGATC
72594 GCGTCGATC
1 GCGTCGATC
72603 GCGTCGATC
1 GCGTCGATC
72612 GCGTCGATC
1 GCGTCGATC
72621 GCGTCG
1 GCGTCG
72627 CGATCGTGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 33 1.00
ACGTcount: A:0.10, C:0.33, G:0.36, T:0.21
Consensus pattern (9 bp):
GCGTCGATC
Found at i:88475 original size:16 final size:16
Alignment explanation
Indices: 88454--88485 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
88444 CGCTTATTAC
88454 GAGGTGTTGCAGTCCA
1 GAGGTGTTGCAGTCCA
88470 GAGGTGTTGCAGTCCA
1 GAGGTGTTGCAGTCCA
88486 AGGGGGACCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.38, T:0.25
Consensus pattern (16 bp):
GAGGTGTTGCAGTCCA
Found at i:89717 original size:15 final size:15
Alignment explanation
Indices: 89676--89722 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
89666 CGTGGAGGAA
**
89676 CCGCCCATGGCCATG
1 CCGCCCATGTTCATG
*
89691 CCG-CCGTGGTTCATG
1 CCGCCCAT-GTTCATG
89706 CCGCCCATGTTCATG
1 CCGCCCATGTTCATG
89721 CC
1 CC
89723 CGACATGCCT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 3 0.12
15 20 0.77
16 3 0.12
ACGTcount: A:0.11, C:0.43, G:0.26, T:0.21
Consensus pattern (15 bp):
CCGCCCATGTTCATG
Found at i:103043 original size:18 final size:18
Alignment explanation
Indices: 103020--103054 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
103010 GTCTGGGTGA
103020 CCGCGGCCGCACTGGTCG
1 CCGCGGCCGCACTGGTCG
103038 CCGCGGCCGCACTGGTC
1 CCGCGGCCGCACTGGTC
103055 ACCAGCTCCC
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:0.46, G:0.37, T:0.11
Consensus pattern (18 bp):
CCGCGGCCGCACTGGTCG
Found at i:104779 original size:21 final size:21
Alignment explanation
Indices: 104755--104795 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
104745 GGTCGGCGTG
104755 GCGGCTCAGTTC-GGCGATGTC
1 GCGG-TCAGTTCGGGCGATGTC
*
104776 GCGGTCGGTTCGGGCGATGT
1 GCGGTCAGTTCGGGCGATGT
104796 TGGCGCAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.07, C:0.24, G:0.44, T:0.24
Consensus pattern (21 bp):
GCGGTCAGTTCGGGCGATGTC
Found at i:123885 original size:14 final size:14
Alignment explanation
Indices: 123866--123894 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
123856 ACCTCCACGG
123866 GTGCTTATGAATCT
1 GTGCTTATGAATCT
123880 GTGCTTATGAATCT
1 GTGCTTATGAATCT
123894 G
1 G
123895 ATGGAGCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.14, G:0.24, T:0.41
Consensus pattern (14 bp):
GTGCTTATGAATCT
Found at i:164760 original size:15 final size:15
Alignment explanation
Indices: 164742--164795 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 15
164732 AGCGGCACCC
164742 GCCGCTCCGGCAGCT
1 GCCGCTCCGGCAGCT
* * * *
164757 GCCGATCCGCCACCC
1 GCCGCTCCGGCAGCT
*
164772 GCCGCTCCGGCGGCT
1 GCCGCTCCGGCAGCT
164787 GCCGCTCCG
1 GCCGCTCCG
164796 CCTCCTGCCG
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.06, C:0.52, G:0.31, T:0.11
Consensus pattern (15 bp):
GCCGCTCCGGCAGCT
Found at i:164773 original size:30 final size:30
Alignment explanation
Indices: 164737--164806 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
164727 GTGGCAGCGG
164737 CACCCGCCGCTCCGGCAGCTGCCGATCCGC
1 CACCCGCCGCTCCGGCAGCTGCCGATCCGC
* *
164767 CACCCGCCGCTCCGGCGGCTGCCGCTCCGC
1 CACCCGCCGCTCCGGCAGCTGCCGATCCGC
* *
164797 CTCCTGCCGC
1 CACCCGCCGC
164807 GGGCCCGGCC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.06, C:0.56, G:0.27, T:0.11
Consensus pattern (30 bp):
CACCCGCCGCTCCGGCAGCTGCCGATCCGC
Found at i:164803 original size:15 final size:15
Alignment explanation
Indices: 164737--164806 Score: 59
Period size: 15 Copynumber: 4.7 Consensus size: 15
164727 GTGGCAGCGG
* *
164737 CACCCGCCGCTCCGG
1 CACCTGCCGCTCCGC
* *
164752 CAGCTGCCGATCCGC
1 CACCTGCCGCTCCGC
* *
164767 CACCCGCCGCTCCGG
1 CACCTGCCGCTCCGC
**
164782 CGGCTGCCGCTCCGC
1 CACCTGCCGCTCCGC
*
164797 CTCCTGCCGC
1 CACCTGCCGC
164807 GGGCCCGGCC
Statistics
Matches: 41, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
15 41 1.00
ACGTcount: A:0.06, C:0.56, G:0.27, T:0.11
Consensus pattern (15 bp):
CACCTGCCGCTCCGC
Found at i:165124 original size:12 final size:12
Alignment explanation
Indices: 165107--165134 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
165097 ACCCATCACC
165107 CCCGGCGGACGT
1 CCCGGCGGACGT
165119 CCCGGCGGACGT
1 CCCGGCGGACGT
165131 CCCG
1 CCCG
165135 CCCCCGCCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.46, G:0.39, T:0.07
Consensus pattern (12 bp):
CCCGGCGGACGT
Found at i:172006 original size:12 final size:12
Alignment explanation
Indices: 171989--172021 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
171979 GTTGCGGACT
171989 TCGCCGCCGACG
1 TCGCCGCCGACG
172001 TCGCCGCCGACG
1 TCGCCGCCGACG
*
172013 TCGTCGCCG
1 TCGCCGCCG
172022 GGGTCGATCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.06, C:0.48, G:0.33, T:0.12
Consensus pattern (12 bp):
TCGCCGCCGACG
Done.