Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3677
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: 27800
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Found at i:438 original size:14 final size:15
Alignment explanation
Indices: 409--439 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
399 TAAGTGGAAA
409 AAATATGGGCCATTT
1 AAATATGGGCCATTT
424 AAATATGGG-CATTT
1 AAATATGGGCCATTT
438 AA
1 AA
440 TTAAGTGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.32
Consensus pattern (15 bp):
AAATATGGGCCATTT
Found at i:6268 original size:14 final size:14
Alignment explanation
Indices: 6236--6277 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
6226 CATGAGTCTT
6236 TAAAAATAAATAGAAA
1 TAAAAATAAA-A-AAA
*
6252 TAAAAGTAAAAAAA
1 TAAAAATAAAAAAA
6266 TAAAAATAAAAA
1 TAAAAATAAAAA
6278 TAAAACGAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 14 0.58
15 1 0.04
16 9 0.38
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.17
Consensus pattern (14 bp):
TAAAAATAAAAAAA
Found at i:6272 original size:20 final size:21
Alignment explanation
Indices: 6238--6282 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
6228 TGAGTCTTTA
* *
6238 AAAATAAATAGAAATAAAAGT
1 AAAATAAATAAAAATAAAAAT
6259 AAAA-AAATAAAAATAAAAAT
1 AAAATAAATAAAAATAAAAAT
6279 AAAA
1 AAAA
6283 CGAGTTTGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (21 bp):
AAAATAAATAAAAATAAAAAT
Found at i:9992 original size:14 final size:14
Alignment explanation
Indices: 9969--10004 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
9959 AAGTGCTCAT
9969 ACAT-TATAAAATC
1 ACATATATAAAATC
9982 ACATATATAAAATC
1 ACATATATAAAATC
9996 ACATATATA
1 ACATATATA
10005 TCATACCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 4 0.18
14 18 0.82
ACGTcount: A:0.56, C:0.14, G:0.00, T:0.31
Consensus pattern (14 bp):
ACATATATAAAATC
Found at i:12184 original size:12 final size:12
Alignment explanation
Indices: 12154--12184 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
12144 TATCATCCTG
12154 TAAATATTAAAA
1 TAAATATTAAAA
12166 T-AATATTAAAA
1 TAAATATTAAAA
12177 TAAATATT
1 TAAATATT
12185 TCAATGTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
TAAATATTAAAA
Found at i:12421 original size:30 final size:30
Alignment explanation
Indices: 12386--12451 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
12376 ACCCTAGGGG
12386 ACACACGGCCATGTACCAAGGCCACGTGTC
1 ACACACGGCCATGTACCAAGGCCACGTGTC
* *
12416 ACACACGGCCGTGTACCAAGGCCATGTGTC
1 ACACACGGCCATGTACCAAGGCCACGTGTC
12446 ACACAC
1 ACACAC
12452 AGTTGAGCCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.27, C:0.36, G:0.23, T:0.14
Consensus pattern (30 bp):
ACACACGGCCATGTACCAAGGCCACGTGTC
Found at i:16445 original size:39 final size:40
Alignment explanation
Indices: 16368--16514 Score: 120
Period size: 40 Copynumber: 3.7 Consensus size: 40
16358 TAGCTCCTCG
* * *
16368 TTCAAGTGCCTTCGGGACATAGCCCGG-TTATAGTAACTCA
1 TTCAA-TGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
* *
16408 TTCAATGCCTTCGGGACTTAACCCGGATTTTA-AAACTCG
1 TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** * * * *
16447 CACGAATGCCTTCGGGACTTAACCCGGAAT-TAGTATCTCG
1 TTC-AATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** *
16487 CACAAAGGCCTTCGGGACTTAACCCGGA
1 TTC-AATGCCTTCGGGACTTAACCCGGA
16515 ATTAATAACT
Statistics
Matches: 92, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
39 27 0.29
40 65 0.71
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
Found at i:16525 original size:80 final size:80
Alignment explanation
Indices: 16414--16594 Score: 219
Period size: 80 Copynumber: 2.3 Consensus size: 80
16404 CTCATTCAAT
* * *
16414 GCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGA-AT
1 GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTC-GGATCTTAACCCGGATA-
*
16477 TAGT-A-TCTCGCACAAA
64 TAGTCACT-TAGCACAAA
**
16493 GGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATACCTTCGGATCTTAGTCCGGATA
1 -GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATACCTTCGGATCTTAACCCGGATA
16557 TAGTCACTTAGCACAAA
64 TAGTCACTTAGCACAAA
*
16574 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
16595 CAGCATTCAA
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 7 0.08
80 71 0.80
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTCGGATCTTAACCCGGATATA
GTCACTTAGCACAAA
Found at i:16554 original size:40 final size:40
Alignment explanation
Indices: 16411--16594 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
16401 TAACTCATTC
* *
16411 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
16451 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
16491 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
* ** * * *
16531 AATACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
16572 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
16595 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
39 8 0.07
40 103 0.84
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:25398 original size:59 final size:59
Alignment explanation
Indices: 25306--25478 Score: 197
Period size: 59 Copynumber: 2.9 Consensus size: 59
25296 AAATCAAGCT
* * **
25306 GTTACAATCCCTTTTCATAATCGATAGCCGAAGCTATCCTTTTTCATAATTCGATGGTC
1 GTTACCATCCCTTTTCATAATCAATAGCCGAAGCTATCCCCTTTCATAATTCGATGGTC
* *
25365 GTTACCATCCCTTTTCATAATCAATAGCTGAAGCTATCCCCTTTCATAATTCGATGGTT
1 GTTACCATCCCTTTTCATAATCAATAGCCGAAGCTATCCCCTTTCATAATTCGATGGTC
* * * * * * *
25424 GTCACCATCCCCATTTTCATAGTCGATGGTCGTA-CTATCCCTTTTCATAA-TCGAT
1 GTTACCAT-CCC-TTTTCATAATCAATAGCCGAAGCTATCCCCTTTCATAATTCGAT
25479 AGCTGGAACT
Statistics
Matches: 98, Mismatches: 14, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
59 65 0.66
60 18 0.18
61 15 0.15
ACGTcount: A:0.24, C:0.26, G:0.13, T:0.37
Consensus pattern (59 bp):
GTTACCATCCCTTTTCATAATCAATAGCCGAAGCTATCCCCTTTCATAATTCGATGGTC
Found at i:25452 original size:31 final size:28
Alignment explanation
Indices: 25312--25478 Score: 129
Period size: 29 Copynumber: 5.7 Consensus size: 28
25302 AGCTGTTACA
* * * *
25312 ATCCCTTTTCATAATCGATAGCCGAAGCT
1 ATCCCTTTTCATAATCGATGGTCGTA-CC
*
25341 ATCCTTTTTCATAATTCGATGGTCGTTACC
1 ATCCCTTTTCATAA-TCGATGGTCG-TACC
* * * *
25371 ATCCCTTTTCATAATCAATAG-CTGAAGCT
1 ATCCCTTTTCATAATCGATGGTC-GTA-CC
* *
25400 ATCCCCTTTCATAATTCGATGGTTGTCACC
1 ATCCCTTTTCATAA-TCGATGGTCGT-ACC
* *
25430 ATCCCCATTTTCATAGTCGATGGTCGTACT
1 AT-CCC-TTTTCATAATCGATGGTCGTACC
25460 ATCCCTTTTCATAATCGAT
1 ATCCCTTTTCATAATCGAT
25479 AGCTGGAACT
Statistics
Matches: 108, Mismatches: 21, Indels: 19
0.73 0.14 0.13
Matches are distributed among these distances:
28 15 0.14
29 36 0.33
30 35 0.32
31 15 0.14
32 7 0.06
ACGTcount: A:0.24, C:0.26, G:0.13, T:0.37
Consensus pattern (28 bp):
ATCCCTTTTCATAATCGATGGTCGTACC
Found at i:25499 original size:29 final size:29
Alignment explanation
Indices: 25312--25500 Score: 125
Period size: 29 Copynumber: 6.4 Consensus size: 29
25302 AGCTGTTACA
*
25312 ATCCCTTTTCATAATCGATAGC-CGAAGCT
1 ATCCCTTTTCATAATCGATAGCTGGAA-CT
* * ** *
25341 ATCCTTTTTCATAATTCGAT-GGTCGTTACC
1 ATCCCTTTTCATAA-TCGATAGCT-GGAACT
*
25371 ATCCCTTTTCATAATCAATAGCT-GAAGCT
1 ATCCCTTTTCATAATCGATAGCTGGAA-CT
* * * ** *
25400 ATCCCCTTTCATAATTCGATGGTTGTCACC
1 ATCCCTTTTCATAA-TCGATAGCTGGAACT
* * * *
25430 ATCCCCATTTTCATAGTCGAT-GGTCGTACT
1 AT-CCC-TTTTCATAATCGATAGCTGGAACT
25460 ATCCCTTTTCATAATCGATAGCTGGAACT
1 ATCCCTTTTCATAATCGATAGCTGGAACT
*
25489 ATCTCTTTTCAT
1 ATCCCTTTTCAT
25501 TGGTCAATCA
Statistics
Matches: 119, Mismatches: 31, Indels: 20
0.70 0.18 0.12
Matches are distributed among these distances:
28 14 0.12
29 52 0.44
30 36 0.30
31 10 0.08
32 7 0.06
ACGTcount: A:0.24, C:0.26, G:0.13, T:0.38
Consensus pattern (29 bp):
ATCCCTTTTCATAATCGATAGCTGGAACT
Found at i:25515 original size:89 final size:91
Alignment explanation
Indices: 25346--25515 Score: 211
Period size: 89 Copynumber: 1.9 Consensus size: 91
25336 AAGCTATCCT
*
25346 TTTTCATAATTCGATGGTCGTTACCATCCCTTTTCATAATCAATAGCTGAAGCTATCCCCTTTCA
1 TTTTCATAAGTCGATGGTCGTTACCATCCCTTTTCATAATCAATAGCTGAAGCTATCCCCTTTCA
* * **
25411 TAATTCGATGGTTGTCACCATCCCCA
66 TAAGTCAATCATTGTCACCATCCCCA
* * * *
25437 TTTTCAT-AGTCGATGGTCG-TACTATCCCTTTTCATAATCGATAGCTGGAA-CTATCTCTTTTC
1 TTTTCATAAGTCGATGGTCGTTACCATCCCTTTTCATAATCAATAGCT-GAAGCTATCCCCTTTC
**
25499 ATTGGTCAATCATTGTC
65 ATAAGTCAATCATTGTC
25516 GATACGTTGT
Statistics
Matches: 67, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
89 46 0.69
90 14 0.21
91 7 0.10
ACGTcount: A:0.23, C:0.25, G:0.14, T:0.39
Consensus pattern (91 bp):
TTTTCATAAGTCGATGGTCGTTACCATCCCTTTTCATAATCAATAGCTGAAGCTATCCCCTTTCA
TAAGTCAATCATTGTCACCATCCCCA
Done.