Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3198
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 40475
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Found at i:3071 original size:29 final size:28
Alignment explanation
Indices: 3035--3112 Score: 95
Period size: 29 Copynumber: 2.7 Consensus size: 28
3025 TCATGAGATT
*
3035 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA-TAT-CA
*
3065 -GCACTAAGTGTGCGAGTTTAAATATCA
1 GGCACTAAGTGTGCGGGTTTAAATATCA
3092 TGGCACTAAGTGTGCGCGGTT
1 -GGCACTAAGTGTGCG-GGTT
3113 GATTATTAAG
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
27 2 0.05
28 2 0.05
29 35 0.83
30 3 0.07
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.29
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAATATCA
Found at i:5556 original size:168 final size:168
Alignment explanation
Indices: 5278--5613 Score: 663
Period size: 168 Copynumber: 2.0 Consensus size: 168
5268 AGGGGGAGAG
*
5278 TTGTGACACCCCTAATTTGACCCTAGTCGGAAAGCGGTTTCGGGATCGCTAAACCGAGTAACCAA
1 TTGTGACACCCCTAATTTGACCCTAGTCGGAAAGCGGTTTCGGGACCGCTAAACCGAGTAACCAA
5343 ATTATTTGAACATGATATTTATTGTCTAAAATAAATGTGTGAAAATTTTAAGCTTCGATTTAGTA
66 ATTATTTGAACATGATATTTATTGTCTAAAATAAATGTGTGAAAATTTTAAGCTTCGATTTAGTA
5408 AATTTCATGTGAATTTAGTCAATAGGGCTTATGTGTGA
131 AATTTCATGTGAATTTAGTCAATAGGGCTTATGTGTGA
5446 TTGTGACACCCCTAATTTGACCCTAGTCGGAAAGCGGTTTCGGGACCGCTAAACCGAGTAACCAA
1 TTGTGACACCCCTAATTTGACCCTAGTCGGAAAGCGGTTTCGGGACCGCTAAACCGAGTAACCAA
5511 ATTATTTGAACATGATATTTATTGTCTAAAATAAATGTGTGAAAATTTTAAGCTTCGATTTAGTA
66 ATTATTTGAACATGATATTTATTGTCTAAAATAAATGTGTGAAAATTTTAAGCTTCGATTTAGTA
5576 AATTTCATGTGAATTTAGTCAATAGGGCTTATGTGTGA
131 AATTTCATGTGAATTTAGTCAATAGGGCTTATGTGTGA
5614 CATTTTTGAA
Statistics
Matches: 167, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
168 167 1.00
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.34
Consensus pattern (168 bp):
TTGTGACACCCCTAATTTGACCCTAGTCGGAAAGCGGTTTCGGGACCGCTAAACCGAGTAACCAA
ATTATTTGAACATGATATTTATTGTCTAAAATAAATGTGTGAAAATTTTAAGCTTCGATTTAGTA
AATTTCATGTGAATTTAGTCAATAGGGCTTATGTGTGA
Found at i:7940 original size:47 final size:47
Alignment explanation
Indices: 7875--8264 Score: 640
Period size: 47 Copynumber: 8.3 Consensus size: 47
7865 AGACAGTGTA
7875 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
*
7922 TATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
*
7969 TATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
*
8016 TATATATGTGATAAGGCCTAATGGCCGTTGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
* *
8063 TATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
8110 TATATATGT-ATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
8156 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
* * * * * *
8203 TATATATGTGACAGGGCCGAGTGGCCAACT-TGATGGATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGA-TGTGATGAATGTGAAAGTG
* *
8250 CATAAATGTGATAAG
1 TATATATGTGATAAG
8265 TCCCGAAGGG
Statistics
Matches: 321, Mismatches: 20, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
46 45 0.14
47 275 0.86
48 1 0.00
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
Found at i:8159 original size:38 final size:40
Alignment explanation
Indices: 8073--8200 Score: 130
Period size: 46 Copynumber: 2.9 Consensus size: 40
8063 TATATGTGTG
*
8073 ATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGT
1 ATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG-G-----ATGT
8119 ATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGT
1 ATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG-G-----ATGT
8165 GATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
1 -ATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
8201 TGTATATATG
Statistics
Matches: 80, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
46 45 0.56
47 35 0.44
ACGTcount: A:0.34, C:0.09, G:0.29, T:0.28
Consensus pattern (40 bp):
ATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGGATGT
Found at i:8425 original size:37 final size:37
Alignment explanation
Indices: 8383--8461 Score: 106
Period size: 37 Copynumber: 2.1 Consensus size: 37
8373 CCGAGCTCTA
** *
8383 AAGACCCGATGTCTACGTGTGG-GAATTCTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAG-ATTATGTCCGGGT
*
8420 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
8457 AAGAC
1 AAGAC
8462 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 36 0.97
38 1 0.03
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:14005 original size:13 final size:13
Alignment explanation
Indices: 13983--14015 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
13973 AAGGGATTGT
13983 TTAT-TAAACTAA
1 TTATCTAAACTAA
13995 TTATCTAAACTAA
1 TTATCTAAACTAA
*
14008 TTAACTAA
1 TTATCTAA
14016 TTTAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:15273 original size:29 final size:29
Alignment explanation
Indices: 15240--15298 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
15230 TTGCTTGTCC
15240 TCAAGAAAAATTCTCATTTACTGTTAGAA
1 TCAAGAAAAATTCTCATTTACTGTTAGAA
15269 TCAAGAAAAATTCTCATTTACTGTTAGAA
1 TCAAGAAAAATTCTCATTTACTGTTAGAA
15298 T
1 T
15299 TCATTCCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.36
Consensus pattern (29 bp):
TCAAGAAAAATTCTCATTTACTGTTAGAA
Found at i:16981 original size:6 final size:6
Alignment explanation
Indices: 16972--17020 Score: 82
Period size: 6 Copynumber: 8.3 Consensus size: 6
16962 AATAAAATTG
*
16972 AAATGA AAATAA AAATAA AAATAA AAATAA AAATAA AAAT-A AAATAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA
17019 AA
1 AA
17021 TAGAATAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
5 5 0.12
6 36 0.88
ACGTcount: A:0.82, C:0.00, G:0.02, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:18050 original size:21 final size:20
Alignment explanation
Indices: 18026--18070 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
18016 TCGCTTCTCT
*
18026 CACGCCCGTGTGTTATGGTA
1 CACGCCCGTGTATTATGGTA
*
18046 GCACGCCCGTGTATTATTGTA
1 -CACGCCCGTGTATTATGGTA
18067 CACG
1 CACG
18071 GCTGAACAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.29
Consensus pattern (20 bp):
CACGCCCGTGTATTATGGTA
Found at i:21474 original size:13 final size:13
Alignment explanation
Indices: 21452--21484 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
21442 AAGGGTTTGT
21452 TTAT-TAAACTAA
1 TTATCTAAACTAA
21464 TTATCTAAACTAA
1 TTATCTAAACTAA
*
21477 TTAACTAA
1 TTATCTAA
21485 TTTAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:25170 original size:40 final size:40
Alignment explanation
Indices: 25097--25175 Score: 104
Period size: 40 Copynumber: 2.0 Consensus size: 40
25087 ACATATCGGC
* ** *
25097 TAAATATGGCACTTAGTGTGCGGTTCGATATAGCTTTGGA
1 TAAATATGGCACTTAGTGTACAATTCGAGATAGCTTTGGA
* *
25137 TAAATTTGGCACTTAGTGTACAATTTGAGATAGCTTTGG
1 TAAATATGGCACTTAGTGTACAATTCGAGATAGCTTTGG
25176 CTATGTACAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.27, C:0.11, G:0.25, T:0.37
Consensus pattern (40 bp):
TAAATATGGCACTTAGTGTACAATTCGAGATAGCTTTGGA
Found at i:31835 original size:28 final size:28
Alignment explanation
Indices: 31804--31882 Score: 149
Period size: 28 Copynumber: 2.8 Consensus size: 28
31794 AACATCAAAT
31804 ATGGCACTTAGTGTGCGAAATATTGAGA
1 ATGGCACTTAGTGTGCGAAATATTGAGA
*
31832 ATGGCACTTAGTATGCGAAATATTGAGA
1 ATGGCACTTAGTGTGCGAAATATTGAGA
31860 ATGGCACTTAGTGTGCGAAATAT
1 ATGGCACTTAGTGTGCGAAATAT
31883 CGAATGATTC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 49 1.00
ACGTcount: A:0.33, C:0.11, G:0.27, T:0.29
Consensus pattern (28 bp):
ATGGCACTTAGTGTGCGAAATATTGAGA
Done.