Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2094
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: 30911
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Found at i:846 original size:21 final size:21
Alignment explanation
Indices: 786--846 Score: 54
Period size: 20 Copynumber: 2.9 Consensus size: 21
776 TTCATTAAAA
*
786 TTTAAGTAAATAATTATTAAAGT
1 TTTAAGT-AA-AATTATAAAAGT
*
809 TTTAAGTAATATT-TAAAAGT
1 TTTAAGTAAAATTATAAAAGT
*
829 TTT-TGATAAAATTATAAA
1 TTTAAG-TAAAATTATAAA
847 TTTTAGTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
19 1 0.03
20 15 0.47
21 7 0.22
22 2 0.06
23 7 0.22
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (21 bp):
TTTAAGTAAAATTATAAAAGT
Found at i:1532 original size:7 final size:8
Alignment explanation
Indices: 1517--1578 Score: 58
Period size: 8 Copynumber: 8.1 Consensus size: 8
1507 ACCCTTGACA
1517 CCCTAAAC
1 CCCTAAAC
1525 CCCT-AAC
1 CCCTAAAC
*
1532 CCTTAAAC
1 CCCTAAAC
*
1540 CCTTAAAC
1 CCCTAAAC
*
1548 CCTTAAA-
1 CCCTAAAC
*
1555 CCCTTAAC
1 CCCTAAAC
*
1563 CTCT-AAC
1 CCCTAAAC
1570 CCCTAAAC
1 CCCTAAAC
1578 C
1 C
1579 TCAATCCCAA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
7 17 0.37
8 29 0.63
ACGTcount: A:0.34, C:0.45, G:0.00, T:0.21
Consensus pattern (8 bp):
CCCTAAAC
Found at i:1533 original size:23 final size:21
Alignment explanation
Indices: 1507--1575 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 21
1497 TAACTTGAGT
1507 ACCCTTGACACCCTAAACCCCTA
1 ACCCTT-A-ACCCTAAACCCCTA
*
1530 ACCCTTAAACCCTTAAACCCTTAA
1 ACCCTT-AACCC-TAAACCCCT-A
1554 ACCCTTAACCTCT-AACCCCTA
1 ACCCTTAACC-CTAAACCCCTA
1575 A
1 A
1576 ACCTCAATCC
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
21 2 0.05
22 10 0.25
23 20 0.50
24 8 0.20
ACGTcount: A:0.33, C:0.43, G:0.01, T:0.22
Consensus pattern (21 bp):
ACCCTTAACCCTAAACCCCTA
Found at i:1550 original size:16 final size:16
Alignment explanation
Indices: 1516--1561 Score: 69
Period size: 16 Copynumber: 3.0 Consensus size: 16
1506 TACCCTTGAC
*
1516 ACCC-TAAACCCCT-A
1 ACCCTTAAACCCTTAA
1530 ACCCTTAAACCCTTAA
1 ACCCTTAAACCCTTAA
1546 ACCCTTAAACCCTTAA
1 ACCCTTAAACCCTTAA
1562 CCTCTAACCC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
14 4 0.14
15 8 0.28
16 17 0.59
ACGTcount: A:0.37, C:0.41, G:0.00, T:0.22
Consensus pattern (16 bp):
ACCCTTAAACCCTTAA
Found at i:1578 original size:15 final size:15
Alignment explanation
Indices: 1522--1580 Score: 50
Period size: 15 Copynumber: 3.9 Consensus size: 15
1512 TGACACCCTA
*
1522 AACCCCTAACCCT-T
1 AACCCCTAAACCTCT
*
1536 AAACCCTTAAACC-CTT
1 -AACCCCTAAACCTC-T
* *
1552 AAACCCTTAACCTCT
1 AACCCCTAAACCTCT
1567 AACCCCTAAACCTC
1 AACCCCTAAACCTC
1581 AATCCCAACC
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
15 32 0.94
16 2 0.06
ACGTcount: A:0.34, C:0.44, G:0.00, T:0.22
Consensus pattern (15 bp):
AACCCCTAAACCTCT
Found at i:1910 original size:63 final size:62
Alignment explanation
Indices: 1842--1964 Score: 192
Period size: 63 Copynumber: 2.0 Consensus size: 62
1832 ACCCCAACCT
* *
1842 TAAACATTATTTAATATATAAATTAAAAAATACTAATTAAACTAAATCTTAAACCCTAACCCC
1 TAAACATTATTTAATATATAAATTAAAAAACACTAATTAAACTAAA-CCTAAACCCTAACCCC
* * *
1905 TAAACATTATTTAATATATAAATTAAAATACACTAATTAATCTAAACCTAAACTCTAACC
1 TAAACATTATTTAATATATAAATTAAAAAACACTAATTAAACTAAACCTAAACCCTAACC
1965 TAACACCAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
62 12 0.22
63 43 0.78
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (62 bp):
TAAACATTATTTAATATATAAATTAAAAAACACTAATTAAACTAAACCTAAACCCTAACCCC
Found at i:2080 original size:14 final size:15
Alignment explanation
Indices: 2057--2089 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2047 CTTAAATTAG
2057 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
*
2071 AATCCGTAATTCCAT
1 AATCCCTAATTCCAT
2086 AATC
1 AATC
2090 TATAAACCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.36, C:0.30, G:0.03, T:0.30
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:2562 original size:41 final size:40
Alignment explanation
Indices: 2472--2772 Score: 232
Period size: 41 Copynumber: 7.4 Consensus size: 40
2462 TAAAATGTTG
* * *
2472 AAAAAGCGCCGCTAAA-ATCTCGGAGCATTAGCAGTGCTTTCCC
1 AAAAA-CGCCGCTAAAGATCT--GAGCATTAGCGGCGCTTT-TC
* *
2515 AAAAACGCCGCTAAAGATCTGAGTACTAGCGGCGCTTTTC
1 AAAAACGCCGCTAAAGATCTGAGCATTAGCGGCGCTTTTC
* * * * *
2555 TATAAACGCCGCTAAAGATTTGAGCA-TCGCGGCGATTTGGC
1 -AAAAACGCCGCTAAAGATCTGAGCATTAGCGGCGCTTT-TC
* * * * *
2596 -AAAACGCCGATAAAAGATCTG-GCACTAGCAGCACTTCTAC
1 AAAAACGCCGCT-AAAGATCTGAGCATTAGCGGCGCTT-TTC
* * * *
2636 AGAAATGCCGCTAAATATCTGAGCATTACCGGCGCTTTTCC
1 AAAAACGCCGCTAAAGATCTGAGCATTAGCGGCGCTTTT-C
* * * * *
2677 AAAAACGCTGTTAAAGATCTAAGCATTAGCGGCGCTTATG
1 AAAAACGCCGCTAAAGATCTGAGCATTAGCGGCGCTTTTC
* * *
2717 AAAAACGCCGCTAAAGATCTGGGAATTAGCGGCGCTTTTTT
1 AAAAACGCCGCTAAAGATCTGAGCATTAGCGGCGC-TTTTC
*
2758 TAAAACGCCGCTAAA
1 AAAAACGCCGCTAAA
2773 TCCCCGAAAG
Statistics
Matches: 203, Mismatches: 45, Indels: 22
0.75 0.17 0.08
Matches are distributed among these distances:
39 12 0.06
40 66 0.33
41 106 0.52
42 10 0.05
43 9 0.04
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.23
Consensus pattern (40 bp):
AAAAACGCCGCTAAAGATCTGAGCATTAGCGGCGCTTTTC
Found at i:2727 original size:81 final size:80
Alignment explanation
Indices: 2470--2755 Score: 222
Period size: 81 Copynumber: 3.5 Consensus size: 80
2460 GATAAAATGT
* * * * *
2470 TGAAAAAGCGCCGCTAAA-ATCTCGGAGCATTAGCAGTGCTTTCCCAAAAACGCCGCTAAAGATC
1 TGAAAAA-CGCCGCTAAAGATCT--GAGCATTACCGGCGCTTTTCCAAAAACGCCGTTAAAGATC
* *
2534 TGAGTACTAGCGGCGCTTT
63 T-AGCACTAGCGGCGCTTA
* * * * ** *
2553 TCTATAAACGCCGCTAAAGATTTGAGCA-T-CGCGGCGATTTGGC-AAAACGCCGATAAAAGATC
1 T-GAAAAACGCCGCTAAAGATCTGAGCATTAC-CGGCGCTTTTCCAAAAACGCCG-TTAAAGATC
* * * *
2615 TGGCACTAGCAGCACTTC
63 TAGCACTAGCGGCGCTTA
* * *
2633 T-ACAGAAATGCCGCTAAATATCTGAGCATTACCGGCGCTTTTCCAAAAACGCTGTTAAAGATCT
1 TGA-A-AAACGCCGCTAAAGATCTGAGCATTACCGGCGCTTTTCCAAAAACGCCGTTAAAGATCT
*
2697 AAGCATTAGCGGCGCTTA
64 -AGCACTAGCGGCGCTTA
* * *
2715 TGAAAAACGCCGCTAAAGATCTGGGAATTAGCGGCGCTTTT
1 TGAAAAACGCCGCTAAAGATCTGAGCATTACCGGCGCTTTT
2756 TTTAAAACGC
Statistics
Matches: 157, Mismatches: 35, Indels: 24
0.73 0.16 0.11
Matches are distributed among these distances:
78 1 0.01
80 42 0.27
81 67 0.43
82 28 0.18
83 12 0.08
84 7 0.04
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.23
Consensus pattern (80 bp):
TGAAAAACGCCGCTAAAGATCTGAGCATTACCGGCGCTTTTCCAAAAACGCCGTTAAAGATCTAG
CACTAGCGGCGCTTA
Found at i:2733 original size:121 final size:121
Alignment explanation
Indices: 2521--2738 Score: 278
Period size: 121 Copynumber: 1.8 Consensus size: 121
2511 TCCCAAAAAC
* * * * * * *
2521 GCCGCTAAAGATCTGAGTACTAGCGGCGCTTTTCTATAAACGCCGCTAAAGATTTGAGCATCGCG
1 GCCGCTAAAGATCTGAGCACTACCGGCGCTTTTCCAAAAACGCCGCTAAAGATCTAAGCATAGCG
*
2586 GCGATTTGGCAAAACGCCGATAAAAGATCTGGCACTAGCAGCACTTCTACAGAAAT
66 GCGATTTGGAAAAACGCCGATAAAAGATCTGGCACTAGCAGCACTTCTACAGAAAT
* * * *
2642 GCCGCTAAATATCTGAGCATTACCGGCGCTTTTCCAAAAACGCTGTTAAAGATCTAAGCATTAGC
1 GCCGCTAAAGATCTGAGCACTACCGGCGCTTTTCCAAAAACGCCGCTAAAGATCTAAGCA-TAGC
* *
2707 GGCGCTTAT-GAAAAACGCCGCT-AAAGATCTGG
65 GGCGATT-TGGAAAAACGCCGATAAAAGATCTGG
2739 GAATTAGCGG
Statistics
Matches: 81, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
121 60 0.74
122 20 0.25
123 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.23
Consensus pattern (121 bp):
GCCGCTAAAGATCTGAGCACTACCGGCGCTTTTCCAAAAACGCCGCTAAAGATCTAAGCATAGCG
GCGATTTGGAAAAACGCCGATAAAAGATCTGGCACTAGCAGCACTTCTACAGAAAT
Found at i:4551 original size:20 final size:20
Alignment explanation
Indices: 4526--4575 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
4516 GGCTTAAAAA
4526 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
4546 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
4563 GTGGTAGTGGATT
1 TTGGTAGTGGATT
4576 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:9190 original size:20 final size:20
Alignment explanation
Indices: 9165--9214 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
9155 TGGCTTAAAA
9165 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
9185 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
9202 GTGGTAGTGGATT
1 TTGGTAGTGGATT
9215 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Done.