Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold524
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: 92980
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.32
Warning! 5065 characters in sequence are not A, C, G, or T
Found at i:2779 original size:20 final size:20
Alignment explanation
Indices: 2754--2794 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
2744 AATTTTCGCG
2754 TTTATTTATATAATT-TATTT
1 TTTATTTATAT-ATTATATTT
2774 TTTATTTATATATTATATTT
1 TTTATTTATATATTATATTT
2794 T
1 T
2795 ATAATATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTATTTATATATTATATTT
Found at i:7605 original size:13 final size:11
Alignment explanation
Indices: 7571--7627 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 11
7561 GAGCTGCCAT
7571 GAAAGAAACAGA
1 GAAAGAAA-AGA
7583 GAAAGAAAAGA
1 GAAAGAAAAGA
7594 GACAATGAAAAGA
1 GA-AA-GAAAAGA
*
7607 AAAAGAAGAAGA
1 GAAAGAA-AAGA
7619 -AGAAGAAAA
1 GA-AAGAAAA
7628 TGCTAAATAA
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
11 11 0.28
12 21 0.52
13 8 0.20
ACGTcount: A:0.70, C:0.04, G:0.25, T:0.02
Consensus pattern (11 bp):
GAAAGAAAAGA
Found at i:15309 original size:29 final size:30
Alignment explanation
Indices: 15253--15311 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
15243 AAATTGAATT
*
15253 AAATTAAAATTGTATGTATAAAATTACACA
1 AAATTAAAATTGTATATATAAAATTACACA
*
15283 AAATTAAAATT-TATATATAACATTACACA
1 AAATTAAAATTGTATATATAAAATTACACA
15312 TTAGACTACA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 16 0.59
30 11 0.41
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.34
Consensus pattern (30 bp):
AAATTAAAATTGTATATATAAAATTACACA
Found at i:28115 original size:26 final size:28
Alignment explanation
Indices: 28061--28121 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
28051 TATTATCAAG
* *
28061 AATTTTATGAAATTATATATTATTATTA
1 AATTATATGAAATAATATATTATTATTA
*
28089 AATTATATGTAATAATA-ATTATT-TTA
1 AATTATATGAAATAATATATTATTATTA
28115 AATTATA
1 AATTATA
28122 CAAATTCATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (28 bp):
AATTATATGAAATAATATATTATTATTA
Found at i:28322 original size:15 final size:15
Alignment explanation
Indices: 28287--28338 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
28277 TTAAGAATTT
*
28287 TATTAAATTAT-ATA
1 TATTTAATTATAATA
28301 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
28315 TATTTAATAATAAT-
1 TATTTAATTATAATA
28329 TATGTTAATT
1 TAT-TTAATT
28339 TATATTTTAN
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:28747 original size:16 final size:16
Alignment explanation
Indices: 28728--28779 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
28718 GATTTGCTAT
* * *
28728 TACACATCTATTCCAT
1 TACACCTCTAATCCAA
28744 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
28760 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
28776 TACA
1 TACA
28780 GCGAACCAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.37, C:0.35, G:0.00, T:0.29
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:33166 original size:37 final size:37
Alignment explanation
Indices: 33116--33192 Score: 136
Period size: 37 Copynumber: 2.1 Consensus size: 37
33106 TTTTCTCTAG
*
33116 CCTTTTATCTAATTCTAATTTCATTAATGTTATTATT
1 CCTTTTATCTAATTCTAATTTCATTAATATTATTATT
*
33153 CCTTTTATCTAATTCTAATTTTATTAATATTATTATT
1 CCTTTTATCTAATTCTAATTTCATTAATATTATTATT
33190 CCT
1 CCT
33193 GTGAATATGT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.27, C:0.14, G:0.01, T:0.57
Consensus pattern (37 bp):
CCTTTTATCTAATTCTAATTTCATTAATATTATTATT
Found at i:33566 original size:32 final size:33
Alignment explanation
Indices: 33520--33597 Score: 124
Period size: 32 Copynumber: 2.4 Consensus size: 33
33510 TATTCGATCA
*
33520 TTTTAAATAATTTCAAAGTATATAATCTAA-TCC
1 TTTTTAAT-ATTTCAAAGTATATAATCTAATTCC
33553 TTTTTAATATTTCAAAGTATATAATCTAATTCC
1 TTTTTAATATTTCAAAGTATATAATCTAATTCC
33586 -TTTTAATATTTC
1 TTTTTAATATTTC
33598 GAGTGGGATA
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
32 33 0.77
33 10 0.23
ACGTcount: A:0.37, C:0.12, G:0.03, T:0.49
Consensus pattern (33 bp):
TTTTTAATATTTCAAAGTATATAATCTAATTCC
Found at i:42849 original size:149 final size:149
Alignment explanation
Indices: 42579--42880 Score: 604
Period size: 149 Copynumber: 2.0 Consensus size: 149
42569 TTAGTAGCAG
42579 ACTCTTATCATGCCAATACATAGTAAACCAGGTTATTTCAAGAGAACCATTCAACTAATCCAGAC
1 ACTCTTATCATGCCAATACATAGTAAACCAGGTTATTTCAAGAGAACCATTCAACTAATCCAGAC
42644 ATTGCATCAATAAAAGAACAATGTGATCAGCATATCAAAATAGAAGCCAAGATTATACCGAATGT
66 ATTGCATCAATAAAAGAACAATGTGATCAGCATATCAAAATAGAAGCCAAGATTATACCGAATGT
42709 AGAAAGCTGGCAAATGGAA
131 AGAAAGCTGGCAAATGGAA
42728 ACTCTTATCATGCCAATACATAGTAAACCAGGTTATTTCAAGAGAACCATTCAACTAATCCAGAC
1 ACTCTTATCATGCCAATACATAGTAAACCAGGTTATTTCAAGAGAACCATTCAACTAATCCAGAC
42793 ATTGCATCAATAAAAGAACAATGTGATCAGCATATCAAAATAGAAGCCAAGATTATACCGAATGT
66 ATTGCATCAATAAAAGAACAATGTGATCAGCATATCAAAATAGAAGCCAAGATTATACCGAATGT
42858 AGAAAGCTGGCAAATGGAA
131 AGAAAGCTGGCAAATGGAA
42877 ACTC
1 ACTC
42881 CGCGAGTGAC
Statistics
Matches: 153, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
149 153 1.00
ACGTcount: A:0.43, C:0.19, G:0.15, T:0.23
Consensus pattern (149 bp):
ACTCTTATCATGCCAATACATAGTAAACCAGGTTATTTCAAGAGAACCATTCAACTAATCCAGAC
ATTGCATCAATAAAAGAACAATGTGATCAGCATATCAAAATAGAAGCCAAGATTATACCGAATGT
AGAAAGCTGGCAAATGGAA
Found at i:53161 original size:6 final size:6
Alignment explanation
Indices: 53150--53210 Score: 106
Period size: 6 Copynumber: 10.3 Consensus size: 6
53140 TTTTATCTAC
*
53150 TTTTAT TTTTAT TTTTAT TTTTAT TTTTA- TTTTAA TTTTAT TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
53197 TTTTAT TTTTAT TT
1 TTTTAT TTTTAT TT
53211 AGAGTTTTCT
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
5 5 0.09
6 48 0.91
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTAT
Found at i:53201 original size:29 final size:29
Alignment explanation
Indices: 53150--53210 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
53140 TTTTATCTAC
*
53150 TTTTATTTTTATTTTTATTTTTATTTTTA
1 TTTTAATTTTATTTTTATTTTTATTTTTA
53179 TTTTAATTTTATTTTTATTTTTATTTTTA
1 TTTTAATTTTATTTTTATTTTTATTTTTA
53208 TTT
1 TTT
53211 AGAGTTTTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (29 bp):
TTTTAATTTTATTTTTATTTTTATTTTTA
Found at i:54002 original size:13 final size:13
Alignment explanation
Indices: 53984--54008 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53974 AACAAGCTGC
53984 TTTTAGCTTAAAT
1 TTTTAGCTTAAAT
53997 TTTTAGCTTAAA
1 TTTTAGCTTAAA
54009 GCACTTATGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (13 bp):
TTTTAGCTTAAAT
Found at i:54370 original size:15 final size:13
Alignment explanation
Indices: 54342--54366 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54332 TAAATTAAAA
54342 TTTTCAAAATCAT
1 TTTTCAAAATCAT
54355 TTTTCAAAATCA
1 TTTTCAAAATCA
54367 CATTTCCAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTTCAAAATCAT
Found at i:72146 original size:95 final size:97
Alignment explanation
Indices: 71972--72163 Score: 370
Period size: 95 Copynumber: 2.0 Consensus size: 97
71962 TTGAAATTGT
71972 TATTAATGTAGGATAACGTGAGTTTGATGAAATGTATTATATTTTTATTTAAAGATTAAGAAGAT
1 TATTAATGTAGGATAACGTGAGTTTGATGAAATGTATTATATTTTTATTTAAAGATTAAGAAGAT
72037 AATTATGAGTAATTTTAAATATTAT-ATAAAA
66 AATTATGAGTAATTTTAAATATTATAATAAAA
72068 TATTAATGTA-GATAACGTGAGTTTGATGAAATGTATTATATTTTTATTTAAAGATTAAGAAGAT
1 TATTAATGTAGGATAACGTGAGTTTGATGAAATGTATTATATTTTTATTTAAAGATTAAGAAGAT
72132 AATTATGAGTAATTTTAAATATTATAATAAAA
66 AATTATGAGTAATTTTAAATATTATAATAAAA
72164 ATAAATATTC
Statistics
Matches: 95, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
95 79 0.83
96 16 0.17
ACGTcount: A:0.43, C:0.01, G:0.14, T:0.42
Consensus pattern (97 bp):
TATTAATGTAGGATAACGTGAGTTTGATGAAATGTATTATATTTTTATTTAAAGATTAAGAAGAT
AATTATGAGTAATTTTAAATATTATAATAAAA
Found at i:72210 original size:4 final size:4
Alignment explanation
Indices: 72201--72226 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
72191 TTTAATGTTT
72201 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
72227 AGTTATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:76436 original size:51 final size:51
Alignment explanation
Indices: 76381--76537 Score: 137
Period size: 51 Copynumber: 3.2 Consensus size: 51
76371 AAATATACAT
76381 AAATATTTATTACTCGCATTATGAAGTGGTATAAATCTAATATATATTTAA
1 AAATATTTATTACTCGCATTATGAAGTGGTATAAATCTAATATATATTTAA
* * ** * *** * ** **
76432 AAATATTT-TT-TTC-C-TCAAAAAATAAAAT-AATTTTTTATA-AAATACA
1 AAATATTTATTACTCGCATTATGAAGTGGTATAAATCTAATATATATTTA-A
76478 TAAATATTTATTACTCGCATTATGAAGTGGTATAAATCTAATATATATTTAA
1 -AAATATTTATTACTCGCATTATGAAGTGGTATAAATCTAATATATATTTAA
76530 AAATATTT
1 AAATATTT
76538 TTTTCCTCAA
Statistics
Matches: 72, Mismatches: 26, Indels: 16
0.63 0.23 0.14
Matches are distributed among these distances:
45 3 0.04
46 9 0.12
47 15 0.21
48 3 0.04
49 4 0.06
50 3 0.04
51 23 0.32
52 9 0.12
53 3 0.04
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (51 bp):
AAATATTTATTACTCGCATTATGAAGTGGTATAAATCTAATATATATTTAA
Found at i:76497 original size:98 final size:99
Alignment explanation
Indices: 76359--76569 Score: 397
Period size: 98 Copynumber: 2.1 Consensus size: 99
76349 TATCGTTTTC
76359 AAATTTTTTATAAAATATACATAAATATTTATTACTCGCATTATGAAGTGGTATAAATCTAATAT
1 AAATTTTTTAT-AAATATACATAAATATTTATTACTCGCATTATGAAGTGGTATAAATCTAATAT
76424 ATATTTAAAAATATTTTTTTCCTCAAAAAATAAAA
65 ATATTTAAAAATATTTTTTTCCTCAAAAAATAAAA
*
76459 TAATTTTTTATAAA-ATACATAAATATTTATTACTCGCATTATGAAGTGGTATAAATCTAATATA
1 AAATTTTTTATAAATATACATAAATATTTATTACTCGCATTATGAAGTGGTATAAATCTAATATA
76523 TATTTAAAAATATTTTTTTCCTCAAAAAATAAAA
66 TATTTAAAAATATTTTTTTCCTCAAAAAATAAAA
76557 AAATTTTTTATAA
1 AAATTTTTTATAA
76570 GTGTGTTATT
Statistics
Matches: 109, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
98 96 0.88
99 3 0.03
100 10 0.09
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (99 bp):
AAATTTTTTATAAATATACATAAATATTTATTACTCGCATTATGAAGTGGTATAAATCTAATATA
TATTTAAAAATATTTTTTTCCTCAAAAAATAAAA
Found at i:90492 original size:15 final size:15
Alignment explanation
Indices: 90475--90534 Score: 93
Period size: 15 Copynumber: 4.0 Consensus size: 15
90465 GAGCAGGTTT
* *
90475 TGGAGAAGCACCTCT
1 TGGAGAAGCAACTCG
90490 TGGAGAAGCAACTCG
1 TGGAGAAGCAACTCG
90505 TGGAGAAGCAACTCG
1 TGGAGAAGCAACTCG
*
90520 TGGAGAAGCAGCTCG
1 TGGAGAAGCAACTCG
90535 AGGGGGTGGA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 42 1.00
ACGTcount: A:0.30, C:0.22, G:0.33, T:0.15
Consensus pattern (15 bp):
TGGAGAAGCAACTCG
Found at i:90591 original size:18 final size:18
Alignment explanation
Indices: 90557--90605 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 18
90547 TGGAGGTGGT
90557 GAAGCAGCTC-T--AGGG
1 GAAGCAGCTCGTGGAGGG
*
90572 GATGCAGCTCGTGGAGGG
1 GAAGCAGCTCGTGGAGGG
*
90590 GAAGCAGCTCTTGGAG
1 GAAGCAGCTCGTGGAG
90606 AAGCAACCCT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 9 0.32
16 1 0.04
18 18 0.64
ACGTcount: A:0.22, C:0.18, G:0.43, T:0.16
Consensus pattern (18 bp):
GAAGCAGCTCGTGGAGGG
Found at i:90620 original size:15 final size:15
Alignment explanation
Indices: 90602--90636 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
90592 AGCAGCTCTT
90602 GGAGAAGCAACCCTA
1 GGAGAAGCAACCCTA
* *
90617 GGAGAGGCAACCCTC
1 GGAGAAGCAACCCTA
90632 GGAGA
1 GGAGA
90637 TGGACCCTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.34, C:0.26, G:0.34, T:0.06
Consensus pattern (15 bp):
GGAGAAGCAACCCTA
Done.