Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2925
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: 69976
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Found at i:6734 original size:27 final size:26
Alignment explanation
Indices: 6625--6820 Score: 242
Period size: 27 Copynumber: 7.6 Consensus size: 26
6615 ATATTAAGTC
* * *
6625 CGCACACTCAGTGCTATATAATAACT
1 CGCACACTTAGTGCTACATAACAACT
* *
6651 CGCACACTT-GTACTATATAATCAACT
1 CGCACACTTAGTGCTACATAA-CAACT
*
6677 CGCACACTTAGTGCTACAT-A-AGCT
1 CGCACACTTAGTGCTACATAACAACT
6701 CGCACACTTAGTGCTACATAACAAGCT
1 CGCACACTTAGTGCTACATAACAA-CT
6728 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAA-CAA-CT
*
6756 CGCACACTTAGTGC-ACATATCAACT
1 CGCACACTTAGTGCTACATAACAACT
6781 CG--CACTTAGTGCTACATAATCAACT
1 CGCACACTTAGTGCTACATAA-CAACT
6806 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
6821 GTACAATTTA
Statistics
Matches: 151, Mismatches: 9, Indels: 19
0.84 0.05 0.11
Matches are distributed among these distances:
23 10 0.07
24 27 0.18
25 22 0.15
26 26 0.17
27 46 0.30
28 20 0.13
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.26
Consensus pattern (26 bp):
CGCACACTTAGTGCTACATAACAACT
Found at i:6736 original size:51 final size:52
Alignment explanation
Indices: 6625--6820 Score: 251
Period size: 51 Copynumber: 3.8 Consensus size: 52
6615 ATATTAAGTC
* * * *
6625 CGCACACTCAGTGCTATATAATAACTCGCACACTT-GTACTATATAATCAACT
1 CGCACACTTAGTGCTACATAATAACTCGCACACTTAGTGCTACATAA-CAACT
*
6677 CGCACACTTAGTGCTACAT-A-AGCTCGCACACTTAGTGCTACATAACAAGCT
1 CGCACACTTAGTGCTACATAATAACTCGCACACTTAGTGCTACATAACAA-CT
*
6728 CGCACACTTAGTGCTACATAATCAAGCTCGCACACTTAGTGC-ACATATCAACT
1 CGCACACTTAGTGCTACATAAT-AA-CTCGCACACTTAGTGCTACATAACAACT
6781 CG--CACTTAGTGCTACATAATCAACTCGCACACTTAGTGCT
1 CGCACACTTAGTGCTACATAAT-AACTCGCACACTTAGTGCT
6821 GTACAATTTA
Statistics
Matches: 130, Mismatches: 7, Indels: 15
0.86 0.05 0.10
Matches are distributed among these distances:
50 31 0.24
51 52 0.40
52 18 0.14
53 4 0.03
54 9 0.07
55 16 0.12
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.26
Consensus pattern (52 bp):
CGCACACTTAGTGCTACATAATAACTCGCACACTTAGTGCTACATAACAACT
Found at i:6787 original size:78 final size:76
Alignment explanation
Indices: 6628--6820 Score: 257
Period size: 78 Copynumber: 2.5 Consensus size: 76
6618 TTAAGTCCGC
* * * * *
6628 ACACTCAGTGCTATATAATAACTCGCACACTT-GTACTATATAATCAACTCGCACACTTAGTGCT
1 ACACTTAGTGCTACATAACAACTCGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCT
*
6692 ACATAAGCTCG
66 ACATAAACTCG
6703 CACACTTAGTGCTACATAACAAGCTCGCACACTTAGTGCTACATAATCAAGCTCGCACACTTAGT
1 -ACACTTAGTGCTACATAACAA-CTCGCACACTTAGTGCTACATAATCAA-CTCGCACACTTAGT
6768 GC-ACATATCAACTCG
63 GCTACATA--AACTCG
6783 -CACTTAGTGCTACATAATCAACTCGCACACTTAGTGCT
1 ACACTTAGTGCTACATAA-CAACTCGCACACTTAGTGCT
6821 GTACAATTTA
Statistics
Matches: 105, Mismatches: 6, Indels: 10
0.87 0.05 0.08
Matches are distributed among these distances:
76 18 0.17
77 11 0.10
78 52 0.50
79 19 0.18
80 5 0.05
ACGTcount: A:0.32, C:0.28, G:0.13, T:0.26
Consensus pattern (76 bp):
ACACTTAGTGCTACATAACAACTCGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCT
ACATAAACTCG
Found at i:8796 original size:21 final size:21
Alignment explanation
Indices: 8767--8807 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
8757 AACTTCTCTC
*
8767 CTAAGTATATTATTTACATAA
1 CTAAATATATTATTTACATAA
8788 CTAAATATATTATTTACATA
1 CTAAATATATTATTTACATA
8808 GTTAACATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (21 bp):
CTAAATATATTATTTACATAA
Found at i:9462 original size:21 final size:20
Alignment explanation
Indices: 9423--9462 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
9413 TATGTATGGG
*
9423 TTTTGAAGTTTGATGATAGA
1 TTTTGAAGGTTGATGATAGA
*
9443 TTTTGAATGGTTGTTGATAG
1 TTTTGAA-GGTTGATGATAG
9463 TCAAATAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.25, C:0.00, G:0.28, T:0.47
Consensus pattern (20 bp):
TTTTGAAGGTTGATGATAGA
Found at i:35542 original size:24 final size:24
Alignment explanation
Indices: 35505--35683 Score: 313
Period size: 24 Copynumber: 7.4 Consensus size: 24
35495 CTGGAGCCCT
*
35505 AGCCTCTTTTAATAACTGGGGCAAA
1 AGCC-CTTTTAATAACTGGGGCATA
35530 AGCCCTTTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
* *
35554 AGCCCTTTTGATAATTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
35578 AGCCCTTTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
35602 AGCCCTTTTTAATAACTGGGGCATA
1 AGCCC-TTTTAATAACTGGGGCATA
35627 AGCCCTTTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
35651 AGCCCTTTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
35675 AGCCCTTTT
1 AGCCCTTTT
35684 GCACTTCCTC
Statistics
Matches: 148, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
24 120 0.81
25 28 0.19
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (24 bp):
AGCCCTTTTAATAACTGGGGCATA
Found at i:35635 original size:73 final size:73
Alignment explanation
Indices: 35505--35683 Score: 315
Period size: 73 Copynumber: 2.5 Consensus size: 73
35495 CTGGAGCCCT
* * *
35505 AGCCTCTTTTAATAACTGGGGCAAAAGCCC-TTTTAATAACTGGGGCATAAGCCCTTTTGATAAT
1 AGCC-CTTTTAATAACTGGGGCATAAGCCCTTTTTAATAACTGGGGCATAAGCCCTTTTAATAAC
35569 TGGGGCATA
65 TGGGGCATA
35578 AGCCCTTTTAATAACTGGGGCATAAGCCCTTTTTAATAACTGGGGCATAAGCCCTTTTAATAACT
1 AGCCCTTTTAATAACTGGGGCATAAGCCCTTTTTAATAACTGGGGCATAAGCCCTTTTAATAACT
35643 GGGGCATA
66 GGGGCATA
35651 AGCCCTTTTAATAACTGGGGCATAAGCCCTTTT
1 AGCCCTTTTAATAACTGGGGCATAAGCCCTTTT
35684 GCACTTCCTC
Statistics
Matches: 102, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
72 24 0.24
73 78 0.76
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (73 bp):
AGCCCTTTTAATAACTGGGGCATAAGCCCTTTTTAATAACTGGGGCATAAGCCCTTTTAATAACT
GGGGCATA
Found at i:35758 original size:20 final size:20
Alignment explanation
Indices: 35733--35799 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
35723 TTATGAATAC
35733 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
35753 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
* *
35773 GTCGTGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
35793 ATTATGT
1 ATCATGT
35800 TTATCAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.37
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:38670 original size:30 final size:30
Alignment explanation
Indices: 38616--38672 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
38606 GAGAAAACAA
**
38616 AATAAAGAAATCCAAGATTGAGAAACCTAG
1 AATAAAGAAATCCAAGATAAAGAAACCTAG
38646 AATAAAGAAATCC-AGAATAAAGAAACC
1 AATAAAGAAATCCAAG-ATAAAGAAACC
38673 CAAGATAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 2 0.08
30 22 0.92
ACGTcount: A:0.58, C:0.14, G:0.14, T:0.14
Consensus pattern (30 bp):
AATAAAGAAATCCAAGATAAAGAAACCTAG
Found at i:38680 original size:15 final size:16
Alignment explanation
Indices: 38616--38677 Score: 67
Period size: 15 Copynumber: 4.1 Consensus size: 16
38606 GAGAAAACAA
38616 AATAAAGAAATCCAAG
1 AATAAAGAAATCCAAG
** *
38632 -ATTGAGAAA-CCTAG
1 AATAAAGAAATCCAAG
38646 AATAAAGAAATCC-AG
1 AATAAAGAAATCCAAG
*
38661 AATAAAGAAACCCAAG
1 AATAAAGAAATCCAAG
38677 A
1 A
38678 TAAGATACTA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
14 4 0.11
15 28 0.76
16 5 0.14
ACGTcount: A:0.58, C:0.15, G:0.15, T:0.13
Consensus pattern (16 bp):
AATAAAGAAATCCAAG
Found at i:48573 original size:26 final size:26
Alignment explanation
Indices: 48543--48621 Score: 69
Period size: 26 Copynumber: 3.1 Consensus size: 26
48533 ATTATAAAAT
48543 AAAAAGAGATTGAGAGAATAAAGAAC
1 AAAAAGAGATTGAGAGAATAAAGAAC
* *
48569 AAAAA-A-ATT-ATGATG-TTATAA-AAT
1 AAAAAGAGATTGA-GA-GAATA-AAGAAC
*
48593 AAAGAGAGATTGAGAGAATAAAGAAC
1 AAAAAGAGATTGAGAGAATAAAGAAC
48619 AAA
1 AAA
48622 GGAAATATGA
Statistics
Matches: 40, Mismatches: 5, Indels: 16
0.66 0.08 0.26
Matches are distributed among these distances:
23 1 0.03
24 13 0.32
25 8 0.20
26 17 0.43
27 1 0.03
ACGTcount: A:0.61, C:0.03, G:0.19, T:0.18
Consensus pattern (26 bp):
AAAAAGAGATTGAGAGAATAAAGAAC
Found at i:54971 original size:6 final size:7
Alignment explanation
Indices: 54943--54973 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
54933 CTAAGAAAAT
54943 AACATAA
1 AACATAA
54950 AACATAA
1 AACATAA
54957 AACATAA
1 AACATAA
54964 AA-ATAA
1 AACATAA
54970 AACA
1 AACA
54974 AATAAACTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.74, C:0.13, G:0.00, T:0.13
Consensus pattern (7 bp):
AACATAA
Found at i:57094 original size:17 final size:17
Alignment explanation
Indices: 57072--57116 Score: 90
Period size: 17 Copynumber: 2.6 Consensus size: 17
57062 AATGGGCCGT
57072 GTGAGCCCCACGGGATC
1 GTGAGCCCCACGGGATC
57089 GTGAGCCCCACGGGATC
1 GTGAGCCCCACGGGATC
57106 GTGAGCCCCAC
1 GTGAGCCCCAC
57117 AAGGGTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.18, C:0.38, G:0.33, T:0.11
Consensus pattern (17 bp):
GTGAGCCCCACGGGATC
Found at i:62713 original size:40 final size:40
Alignment explanation
Indices: 62669--62856 Score: 299
Period size: 40 Copynumber: 4.7 Consensus size: 40
62659 GCTACTTGCT
*
62669 CAAATTCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
62709 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGTA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
62749 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* * * *
62789 CAAATGCCTTCGGG-TTTAGCCCGG-AATTAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
62828 CAAATGCCTTCGGGACTTAGCCCGGTTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
62857 CATCCGAATA
Statistics
Matches: 136, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
38 1 0.01
39 33 0.24
40 101 0.74
41 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.27
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:65090 original size:93 final size:93
Alignment explanation
Indices: 64978--65149 Score: 310
Period size: 93 Copynumber: 1.8 Consensus size: 93
64968 CGCCCATAAG
*
64978 CGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCATCCATAAGTGAACTCGGACTCAACTC
1 CGAACTCGGACTCAACTCAACGAGCTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTC
65042 AACGAGTTCGGATGCCTAGTTACATCTCA
65 AACGAGTTCGGATGCCTAGTTACATCTCA
*
65071 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
65136 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
65150 TCAATCATCC
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
92 2 0.03
93 74 0.97
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:65144 original size:46 final size:46
Alignment explanation
Indices: 64971--65146 Score: 209
Period size: 46 Copynumber: 3.8 Consensus size: 46
64961 TGTAACCCGC
* *
64971 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTC-GGACATTCGCAT
* *
65017 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
65067 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
65110 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
65147 TGCTCAATCA
Statistics
Matches: 111, Mismatches: 9, Indels: 20
0.79 0.06 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 4 0.04
46 61 0.55
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Done.