Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold810
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: 31479
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Found at i:780 original size:35 final size:34
Alignment explanation
Indices: 683--781 Score: 108
Period size: 35 Copynumber: 2.9 Consensus size: 34
673 CTTAAGATTA
*
683 ACCTTTACATGATGAATAGACAAAATGCAAATCG
1 ACCTTTACATGATGAATCGACAAAATGCAAATCG
* * * * * *
717 AACTTTAAATGATGAACCGTCGATAATGCAAATTG
1 ACCTTTACATGATGAATCGAC-AAAATGCAAATCG
*
752 ACCTTTACATGATGAATCGCCAAGAATGCA
1 ACCTTTACATGATGAATCGACAA-AATGCA
782 TATCAAACTT
Statistics
Matches: 51, Mismatches: 12, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
34 17 0.33
35 34 0.67
ACGTcount: A:0.40, C:0.18, G:0.16, T:0.25
Consensus pattern (34 bp):
ACCTTTACATGATGAATCGACAAAATGCAAATCG
Found at i:1717 original size:89 final size:91
Alignment explanation
Indices: 1560--1743 Score: 345
Period size: 89 Copynumber: 2.0 Consensus size: 91
1550 CAATATATCG
1560 ATATTATATGAAAATTTTCACTATGAACAAGCTTTTTTCTCCAAATTATCATAATTTCACCTTCA
1 ATATTATATGAAAATTTTCACTATGAACAAGCTTTTTTCTCCAAATTATCATAATTTCACCTTCA
1625 TAGTGGCCTTAGATCACTTCATAATC
66 TAGTGGCCTTAGATCACTTCATAATC
*
1651 ATATTATATGAAAATTTTCACTAT-AACAAGC-TTTTTCTCCAAATTATCATAATTTCACCTTTA
1 ATATTATATGAAAATTTTCACTATGAACAAGCTTTTTTCTCCAAATTATCATAATTTCACCTTCA
1714 TAGTGGCCTTAGATCACTTCATAATC
66 TAGTGGCCTTAGATCACTTCATAATC
1740 ATAT
1 ATAT
1744 AAGACGTCGT
Statistics
Matches: 92, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
89 61 0.66
90 7 0.08
91 24 0.26
ACGTcount: A:0.34, C:0.19, G:0.07, T:0.40
Consensus pattern (91 bp):
ATATTATATGAAAATTTTCACTATGAACAAGCTTTTTTCTCCAAATTATCATAATTTCACCTTCA
TAGTGGCCTTAGATCACTTCATAATC
Found at i:2379 original size:13 final size:13
Alignment explanation
Indices: 2361--2387 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2351 ACATCATGCT
2361 TTGTATCGATACA
1 TTGTATCGATACA
2374 TTGTATCGATACA
1 TTGTATCGATACA
2387 T
1 T
2388 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2396 original size:19 final size:19
Alignment explanation
Indices: 2371--2427 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
2361 TTGTATCGAT
*
2371 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
* *
2390 TCATTGTATCGATATATGG
1 ACATTGTATCGATACATGG
*
2409 ACAATTTTATCGATACATG
1 AC-ATTGTATCGATACATG
2428 AAACTGGCAG
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.39
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:10761 original size:105 final size:104
Alignment explanation
Indices: 10585--10783 Score: 316
Period size: 105 Copynumber: 1.9 Consensus size: 104
10575 ATCTAAGGGA
10585 AGAAAATCTGATTATCAAGGGGGAGAAATTTTTTGTAAAATTTTTTTTAACTAGAGCCTTAATTA
1 AGAAAATCTGATTATCAAGGGGGAGAAATTTTTTG-AAAATTTTTTTTAACTAGAGCCTTAATTA
10650 TTCTATAAA-GAAGGA-GACAAATGAAACTTTTATGAAGGGGG
65 TTCTATAAATG--GGAGGA-AAATGAAACTTTTATGAAGGGGG
10691 AGAAAATCTGATTATCAAGGGGGAGAAATTTTTATG-AAATTTTTTTTAA-TGAGAGCCTTAATT
1 AGAAAATCTGATTATCAAGGGGGAGAAATTTTT-TGAAAATTTTTTTTAACT-AGAGCCTTAATT
10754 ATTCTATAAATGGGAGGAAAATGAAACTTT
64 ATTCTATAAATGGGAGGAAAATGAAACTTT
10784 GATATCTAAA
Statistics
Matches: 89, Mismatches: 0, Indels: 10
0.90 0.00 0.10
Matches are distributed among these distances:
104 16 0.18
105 37 0.42
106 34 0.38
107 2 0.02
ACGTcount: A:0.39, C:0.07, G:0.20, T:0.34
Consensus pattern (104 bp):
AGAAAATCTGATTATCAAGGGGGAGAAATTTTTTGAAAATTTTTTTTAACTAGAGCCTTAATTAT
TCTATAAATGGGAGGAAAATGAAACTTTTATGAAGGGGG
Found at i:11328 original size:13 final size:13
Alignment explanation
Indices: 11310--11334 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11300 CATCATGCTT
11310 TGTATCGATACAA
1 TGTATCGATACAA
11323 TGTATCGATACA
1 TGTATCGATACA
11335 TGTTCATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:11331 original size:33 final size:32
Alignment explanation
Indices: 11289--11353 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
11279 ACATACGCAG
*
11289 ATGTATCGATACATCATGCTTTGTATCGATACA
1 ATGTATCGATACAT-ATGCATTGTATCGATACA
* *
11322 ATGTATCGATACATGTTCATTGTATCGATACA
1 ATGTATCGATACATATGCATTGTATCGATACA
11354 TGAAACTAGC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.52
33 14 0.48
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (32 bp):
ATGTATCGATACATATGCATTGTATCGATACA
Found at i:11409 original size:20 final size:20
Alignment explanation
Indices: 11384--11437 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
11374 CTACCATTGT
*
11384 TTGTATCGATACATGGT-ACA
1 TTGTATCGATACATGATGA-A
11404 TTGTATCGATACATGATGAA
1 TTGTATCGATACATGATGAA
11424 TTGTATCGATACAT
1 TTGTATCGATACAT
11438 TACTTCTAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (20 bp):
TTGTATCGATACATGATGAA
Found at i:15086 original size:15 final size:15
Alignment explanation
Indices: 15062--15102 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
15052 AATAAATCAA
15062 AAATTGTTGAAAATG
1 AAATTGTTGAAAATG
* *
15077 AAATTCTTGAAAATT
1 AAATTGTTGAAAATG
15092 AAATTGTTGAA
1 AAATTGTTGAA
15103 CTAGAAAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.46, C:0.02, G:0.15, T:0.37
Consensus pattern (15 bp):
AAATTGTTGAAAATG
Found at i:17202 original size:20 final size:20
Alignment explanation
Indices: 17177--17215 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
17167 TTTTCCAAAT
**
17177 GTTTTATGTTGATTTTCTTA
1 GTTTTATGTAAATTTTCTTA
17197 GTTTTATGTAAATTTTCTT
1 GTTTTATGTAAATTTTCTT
17216 CATGTATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.05, G:0.13, T:0.64
Consensus pattern (20 bp):
GTTTTATGTAAATTTTCTTA
Found at i:17344 original size:47 final size:47
Alignment explanation
Indices: 17291--17393 Score: 179
Period size: 47 Copynumber: 2.2 Consensus size: 47
17281 AGCATGATAC
17291 ATGCATTTTATGGTATCCATACATTATTTATCATGATTTACATATCT
1 ATGCATTTTATGGTATCCATACATTATTTATCATGATTTACATATCT
* *
17338 ATGCATTTTATGGTATCCATGCATTATTTATCATGATTTACATGTCT
1 ATGCATTTTATGGTATCCATACATTATTTATCATGATTTACATATCT
*
17385 ATGTATTTT
1 ATGCATTTT
17394 CCATGAATAT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 53 1.00
ACGTcount: A:0.27, C:0.14, G:0.11, T:0.49
Consensus pattern (47 bp):
ATGCATTTTATGGTATCCATACATTATTTATCATGATTTACATATCT
Found at i:17359 original size:18 final size:18
Alignment explanation
Indices: 17290--17362 Score: 52
Period size: 18 Copynumber: 4.4 Consensus size: 18
17280 GAGCATGATA
17290 CATGCATTTTATGGTATC
1 CATGCATTTTATGGTATC
* *
17308 CATACA--TTAT-TTAT-
1 CATGCATTTTATGGTATC
**
17322 CATG-A-TTTA-CATATC
1 CATGCATTTTATGGTATC
*
17337 TATGCATTTTATGGTATC
1 CATGCATTTTATGGTATC
17355 CATGCATT
1 CATGCATT
17363 ATTTATCATG
Statistics
Matches: 41, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
13 1 0.02
14 9 0.22
15 6 0.15
16 5 0.12
17 4 0.10
18 16 0.39
ACGTcount: A:0.27, C:0.16, G:0.11, T:0.45
Consensus pattern (18 bp):
CATGCATTTTATGGTATC
Found at i:17700 original size:37 final size:39
Alignment explanation
Indices: 17622--17709 Score: 94
Period size: 38 Copynumber: 2.3 Consensus size: 39
17612 ATCTTGCAAC
* *
17622 TTTCAT-ACAGTTCTATGTTATTTTCCATGATTAAGGTAT
1 TTTCATGACA-TTCTATGTCATTTTCCATGATAAAGGTAT
* *
17661 TTT-ATGTCATTCTA-GTCATTTTTCATGACTAAAGG-AT
1 TTTCATGACATTCTATGTCATTTTCCATGA-TAAAGGTAT
17698 TTTCATGACATT
1 TTTCATGACATT
17710 TCATGCATTC
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
37 17 0.41
38 19 0.46
39 5 0.12
ACGTcount: A:0.26, C:0.14, G:0.12, T:0.48
Consensus pattern (39 bp):
TTTCATGACATTCTATGTCATTTTCCATGATAAAGGTAT
Found at i:20970 original size:41 final size:40
Alignment explanation
Indices: 20904--20983 Score: 115
Period size: 41 Copynumber: 2.0 Consensus size: 40
20894 AGTAGTCATT
*
20904 ACAATTTCATTTGAAAAATTTTGTATAATGTTTTATAGAC
1 ACAATTTCATTTGAAAAATTTTGTATAATGTTATATAGAC
* **
20944 ACAATTTCGTTTGTAAACTTTTTGTATAATGTTATATAGA
1 ACAATTTCATTTG-AAAAATTTTGTATAATGTTATATAGA
20984 ATGCACCTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
40 12 0.34
41 23 0.66
ACGTcount: A:0.35, C:0.07, G:0.11, T:0.46
Consensus pattern (40 bp):
ACAATTTCATTTGAAAAATTTTGTATAATGTTATATAGAC
Found at i:21343 original size:26 final size:27
Alignment explanation
Indices: 21288--21348 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 27
21278 ATTATTTTTT
* *
21288 ATTTTAA-AATATAACTTTAAGACAAT
1 ATTTTAATAATATAACTTTAAAACAAA
* *
21314 ATTTTAATAATAT-ATTTTAAAATAAA
1 ATTTTAATAATATAACTTTAAAACAAA
*
21340 ATTTCAATA
1 ATTTTAATA
21349 TTTATTTAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
26 24 0.83
27 5 0.17
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.43
Consensus pattern (27 bp):
ATTTTAATAATATAACTTTAAAACAAA
Found at i:21755 original size:32 final size:33
Alignment explanation
Indices: 21695--21758 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
21685 TACACCCAGA
* *
21695 TGTATTGATATATATTGCTTAGTATCGATACAT
1 TGTATTGATACATATTGCATAGTATCGATACAT
*
21728 TGTATTGATACATGTT-CATAGTATCGATACA
1 TGTATTGATACATATTGCATAGTATCGATACA
21759 CCTTGAAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.31, C:0.11, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATTGATACATATTGCATAGTATCGATACAT
Found at i:29690 original size:33 final size:33
Alignment explanation
Indices: 29648--29712 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
29638 TACCACTGTT
* * *
29648 TGTATCGATACATGGCGCATTGTATTGATACAA
1 TGTATCGATACATGACGAATTGTATCGATACAA
*
29681 TGTATCGATACATGATGAATTGTATCGATACA
1 TGTATCGATACATGACGAATTGTATCGATACA
29713 TTGCTTCAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (33 bp):
TGTATCGATACATGACGAATTGTATCGATACAA
Done.