Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold551
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: 32502
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Found at i:12713 original size:32 final size:32
Alignment explanation
Indices: 12672--12736 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
12662 AAGATGAGGG
*
12672 CAAAGGTGAACATGGCTCAATGGAGAGCCGAT
1 CAAAGGTGAACACGGCTCAATGGAGAGCCGAT
12704 CAAAGGTGAACACGGCTCAATGGAGAGCCGAT
1 CAAAGGTGAACACGGCTCAATGGAGAGCCGAT
12736 C
1 C
12737 GTAATATTGG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.34, C:0.22, G:0.31, T:0.14
Consensus pattern (32 bp):
CAAAGGTGAACACGGCTCAATGGAGAGCCGAT
Found at i:18243 original size:30 final size:31
Alignment explanation
Indices: 18204--18302 Score: 116
Period size: 31 Copynumber: 3.3 Consensus size: 31
18194 TTCGAGTCAA
*
18204 GACTAAAATTTTA-AAACTTGAAAAGTATAGG
1 GACT-AAATTTGATAAACTTGAAAAGTATAGG
* * *
18235 GATTAAATTTGATCAATTTGAAAAGTATAGG
1 GACTAAATTTGATAAACTTGAAAAGTATAGG
18266 GACTAAATTTGATCAAA-TT--AAAGTATAGG
1 GACTAAATTTGAT-AAACTTGAAAAGTATAGG
18295 GACTAAAT
1 GACTAAAT
18303 ACAGCACTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
29 18 0.30
30 7 0.12
31 33 0.55
32 2 0.03
ACGTcount: A:0.45, C:0.06, G:0.17, T:0.31
Consensus pattern (31 bp):
GACTAAATTTGATAAACTTGAAAAGTATAGG
Found at i:18257 original size:31 final size:31
Alignment explanation
Indices: 18221--18302 Score: 132
Period size: 31 Copynumber: 2.7 Consensus size: 31
18211 ATTTTAAAAC
* *
18221 TTGAAAAGTATAGGGATTAAATTTGATCAAT
1 TTGAAAAGTATAGGGACTAAATTTGATCAAA
18252 TTGAAAAGTATAGGGACTAAATTTGATCAAA
1 TTGAAAAGTATAGGGACTAAATTTGATCAAA
18283 TT--AAAGTATAGGGACTAAAT
1 TTGAAAAGTATAGGGACTAAAT
18303 ACAGCACTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
29 18 0.37
31 31 0.63
ACGTcount: A:0.44, C:0.05, G:0.20, T:0.32
Consensus pattern (31 bp):
TTGAAAAGTATAGGGACTAAATTTGATCAAA
Found at i:20456 original size:23 final size:23
Alignment explanation
Indices: 20426--20471 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
20416 CTTGGTTTGG
20426 GTTCCCAATCTCATCAACCAAGT
1 GTTCCCAATCTCATCAACCAAGT
20449 GTTCCCAATCTCATCAACCAAGT
1 GTTCCCAATCTCATCAACCAAGT
20472 CATTCGTAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.35, G:0.09, T:0.26
Consensus pattern (23 bp):
GTTCCCAATCTCATCAACCAAGT
Found at i:24735 original size:37 final size:37
Alignment explanation
Indices: 24674--24819 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
24664 TACGTATGAT
* *
24674 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
24709 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
24746 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
24783 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
24820 TAAAGCTATC
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 9 0.09
36 3 0.03
37 92 0.88
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:24836 original size:46 final size:46
Alignment explanation
Indices: 24783--25005 Score: 257
Period size: 52 Copynumber: 4.6 Consensus size: 46
24773 TAAGTGTAGC
* *
24783 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTAT
* * *
24829 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTAT
*
24875 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCAAAGCTAT
* *
24927 CACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCAAAGCTAT
*
24979 CACTTATCACTTTATCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
25006 AGTACTCAAA
Statistics
Matches: 161, Mismatches: 9, Indels: 14
0.88 0.05 0.08
Matches are distributed among these distances:
46 68 0.42
49 1 0.01
50 1 0.01
51 3 0.02
52 88 0.55
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTAT
Found at i:24902 original size:52 final size:52
Alignment explanation
Indices: 24826--24999 Score: 267
Period size: 52 Copynumber: 3.3 Consensus size: 52
24816 TAGCTAAAGC
* * *
24826 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
24879 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
* ** *
24931 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
24983 TATCACTTTATCACTTG
1 TATCACTTT-TCACTTG
25000 ATCAGAAGTA
Statistics
Matches: 112, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
52 94 0.84
53 18 0.16
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.36
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
Found at i:24971 original size:98 final size:98
Alignment explanation
Indices: 24782--25005 Score: 244
Period size: 98 Copynumber: 2.3 Consensus size: 98
24772 ATAAGTGTAG
* * * *
24782 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTC
1 CCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTGCCAC
*
24847 TTGATCAGATAAGTATAGCCGAAGCTATCA-CTTA
66 TTGATCAGATAAGTATAGCCGAAGCTA-AAGC-TA
* * *
24881 TCACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTT-CCAC
1 CCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTGCCAC
* * *
24944 TTG-TCACTTGATCAG-ATAAG-TGTAGCTAAAGCTA
66 TTGATCA---GATAAGTAT-AGCCGAAGCTAAAGCTA
*
24978 CCACTTATCACTTTATCACTTGATCAGA
1 CCACTTATCACTTTGTCACTTGATCAGA
25006 AGTACTCAAA
Statistics
Matches: 105, Mismatches: 14, Indels: 13
0.80 0.11 0.10
Matches are distributed among these distances:
96 3 0.03
97 17 0.16
98 69 0.66
99 16 0.15
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (98 bp):
CCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTGCCAC
TTGATCAGATAAGTATAGCCGAAGCTAAAGCTA
Found at i:28397 original size:39 final size:37
Alignment explanation
Indices: 28330--28422 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 37
28320 ACCAGAATGG
* *
28330 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGA
* *
28369 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGA
* *
28406 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
28423 AATCTATCCG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 19 0.41
38 2 0.04
39 22 0.48
40 3 0.07
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGAAAGTTGA
Found at i:28786 original size:3 final size:3
Alignment explanation
Indices: 28778--28822 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
28768 ATTCCCACTC
* * * *
28778 ATA ATA ATA ATA ATA CTA ATA ATA ATA CTA ATA CTA ATA TTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
28823 CTTACCTCAC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:28823 original size:18 final size:18
Alignment explanation
Indices: 28778--28824 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
28768 ATTCCCACTC
*
28778 ATAATAATAATAATACTA
1 ATAATAATACTAATACTA
28796 ATAATAATACTAATACTA
1 ATAATAATACTAATACTA
*
28814 ATATTAATACT
1 ATAATAATACT
28825 TACCTCACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (18 bp):
ATAATAATACTAATACTA
Found at i:28824 original size:12 final size:12
Alignment explanation
Indices: 28782--28822 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
28772 CCACTCATAA
28782 TAATAATAATAC
1 TAATAATAATAC
28794 TAATAATAATAC
1 TAATAATAATAC
* *
28806 TAATACTAATAT
1 TAATAATAATAC
28818 TAATA
1 TAATA
28823 CTTACCTCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (12 bp):
TAATAATAATAC
Found at i:29562 original size:20 final size:20
Alignment explanation
Indices: 29528--29567 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
29518 TTCTATTCTG
*
29528 TTTCTTTTCTGTTTTGTTTC
1 TTTCTTTTCTGTTTTATTTC
29548 TTTCTTTTTCT-TTTTATTTC
1 TTTC-TTTTCTGTTTTATTTC
29568 CTTTTATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.03, C:0.15, G:0.05, T:0.78
Consensus pattern (20 bp):
TTTCTTTTCTGTTTTATTTC
Found at i:29734 original size:31 final size:28
Alignment explanation
Indices: 29698--29765 Score: 73
Period size: 31 Copynumber: 2.3 Consensus size: 28
29688 TTGTCTTTAT
**
29698 TTAATTTATTTCTTAATATAATATTTATAA
1 TTAATTTATTTAATAATAT-A-ATTTATAA
* *
29728 TGTAATTAATTTAATAATATACTTTATAA
1 T-TAATTTATTTAATAATATAATTTATAA
29757 TTAATTTAT
1 TTAATTTAT
29766 ATATTTATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
28 7 0.22
29 8 0.25
30 2 0.06
31 15 0.47
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.54
Consensus pattern (28 bp):
TTAATTTATTTAATAATATAATTTATAA
Found at i:29782 original size:21 final size:20
Alignment explanation
Indices: 29744--29782 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
29734 TAATTTAATA
*
29744 ATATACTTTATAATTAATTT
1 ATATACTTTATAAATAATTT
*
29764 ATATATTTATATAAATAAT
1 ATATACTT-TATAAATAAT
29783 AATATAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATACTTTATAAATAATTT
Done.