Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1964
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: 27219
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.30
Found at i:873 original size:56 final size:56
Alignment explanation
Indices: 787--906 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
777 ACAAGGGATG
787 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
843 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
899 ATGGGCAA
1 ATGGGCAA
907 TAAACTAATA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:2121 original size:40 final size:40
Alignment explanation
Indices: 2031--2294 Score: 331
Period size: 40 Copynumber: 6.7 Consensus size: 40
2021 TCGAATGATG
* * * *
2031 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * * *
2071 TCCAGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
2111 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
2150 TCTGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
2189 TCCGGGTTAAGTCCCGAAGGTATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
2229 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
2270 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
2295 AACGAGTAGC
Statistics
Matches: 197, Mismatches: 21, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
39 70 0.36
40 117 0.59
41 10 0.05
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:2316 original size:79 final size:78
Alignment explanation
Indices: 2031--2327 Score: 332
Period size: 79 Copynumber: 3.8 Consensus size: 78
2021 TCGAATGATG
* * * * **
2031 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCAGACTAAGAT-CCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCC-GGTTAAG-TCCCGAAGGCAT
*
2094 TTGTGCGAGATACTAA
63 TTGTGCGAGTTACTAA
* *
2110 TTCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAATCTGGGTTAAGTCCCGAAGGCATT
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATC-CGGTTAAGTCCCGAAGGCATT
2174 TGTGCGAGTTACTAA
64 TGTGCGAGTTACTAA
* *
2189 TCCGGGTTAAGTCCCGAAGGTATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCC-GGTTAAGTCCCGAAGGCATTT
2254 GTGCGAGTTACTATA
65 GTGCGAGTTACTA-A
* * ** * * *
2269 ACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATATCCGGTTAAATTCCGAAGG
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTAAATCCGGTTAAGTCCCGAAGG
2328 TACGTGATTT
Statistics
Matches: 188, Mismatches: 22, Indels: 15
0.84 0.10 0.07
Matches are distributed among these distances:
78 11 0.06
79 126 0.67
80 51 0.27
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (78 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGTTAAGTCCCGAAGGCATTTG
TGCGAGTTACTAA
Found at i:9331 original size:40 final size:40
Alignment explanation
Indices: 9257--9440 Score: 234
Period size: 40 Copynumber: 4.7 Consensus size: 40
9247 GCTACTCGTT
*
9257 CAAATGCCTTC-GGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
9296 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
9336 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
9376 CCAATGCCTTC-GGATCTTAGTCCGGATAT-GTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
9416 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
9441 CATCATTCGA
Statistics
Matches: 130, Mismatches: 10, Indels: 10
0.87 0.07 0.07
Matches are distributed among these distances:
39 34 0.26
40 94 0.72
41 2 0.02
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:10609 original size:48 final size:53
Alignment explanation
Indices: 10557--10667 Score: 144
Period size: 48 Copynumber: 2.2 Consensus size: 53
10547 TATTAGTTTA
10557 TTGCCCATGCTTCTT-TTTT-TTTCCCATT-C-AC-ACATGTTTCATGACA-TT
1 TTGCCCATGCTTCTTATTTTATTTCCCATTACAACAACATG-TTCATGACAGTT
*
10605 TTGCCCATGCTTCTTATTTTATTTTCCATTAACAACAACATGTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTCCCATT-ACAACAACATGTTCATGACA-GTT
10660 TTGCCCAT
1 TTGCCCAT
10668 CATCCCTTGT
Statistics
Matches: 54, Mismatches: 1, Indels: 9
0.84 0.02 0.14
Matches are distributed among these distances:
48 15 0.28
49 4 0.07
50 8 0.15
52 1 0.02
53 11 0.20
54 5 0.09
55 10 0.19
ACGTcount: A:0.21, C:0.25, G:0.09, T:0.45
Consensus pattern (53 bp):
TTGCCCATGCTTCTTATTTTATTTCCCATTACAACAACATGTTCATGACAGTT
Found at i:17170 original size:78 final size:81
Alignment explanation
Indices: 17029--17210 Score: 223
Period size: 78 Copynumber: 2.3 Consensus size: 81
17019 TACTCGTTCA
* *
17029 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGA
* *
17093 TTTAGTAAC-TCGCACC
66 TATAGTAACTTAGCA-C
**
17109 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGT-ACTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
* *
17170 ATATGGTCACTTAGCAC
65 ATATAGTAACTTAGCAC
*
17187 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
17211 CATCATTCGA
Statistics
Matches: 89, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
77 3 0.03
78 45 0.51
79 28 0.31
80 13 0.15
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:17210 original size:40 final size:40
Alignment explanation
Indices: 17008--17210 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
16998 CGGAATTTAA
** *
17008 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
17048 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
17088 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
17127 CCGGA-ATTAGT-ACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
17166 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
17206 CCGGA
1 CCGGA
17211 CATCATTCGA
Statistics
Matches: 140, Mismatches: 15, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
37 2 0.01
38 17 0.12
39 28 0.20
40 82 0.59
41 11 0.08
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:18440 original size:55 final size:56
Alignment explanation
Indices: 18339--18457 Score: 231
Period size: 55 Copynumber: 2.1 Consensus size: 56
18329 TATTAGTTTA
18339 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
18395 TTGCCCATGCTTCTTATTTTATT-TTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
18450 TTGCCCAT
1 TTGCCCAT
18458 CATCCCTTGT
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
55 40 0.63
56 23 0.37
ACGTcount: A:0.23, C:0.24, G:0.09, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:24994 original size:79 final size:81
Alignment explanation
Indices: 24885--25067 Score: 232
Period size: 79 Copynumber: 2.3 Consensus size: 81
24875 TACTCGTTCA
* *
24885 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
24948 ATTTAGTAAC-TCGCACC
65 ATATAGTAACTTAGCA-C
**
24965 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
* *
25028 TATGGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
25044 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
25068 CATCATTCGA
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 59 0.66
80 28 0.31
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:25067 original size:40 final size:40
Alignment explanation
Indices: 24864--25067 Score: 238
Period size: 40 Copynumber: 5.1 Consensus size: 40
24854 CGGAATTTAA
** *
24864 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
24904 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
24944 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
24983 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
25023 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
25063 CCGGA
1 CCGGA
25068 CATCATTCGA
Statistics
Matches: 141, Mismatches: 16, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.23
40 94 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:26262 original size:56 final size:56
Alignment explanation
Indices: 26195--26314 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
26185 TATTAGTTTA
26195 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
26251 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
26307 TTGCCCAT
1 TTGCCCAT
26315 CATCCCTTGT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Done.