Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1731
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: 61678
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:10683 original size:82 final size:81
Alignment explanation
Indices: 10567--10722 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
10557 AAATTGTACA
* * * *
10567 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTG
1 GCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACG-TGGCACTAAGTG
10631 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
10648 GCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTG
1 GCACTAAGTGTGCGAGTC-AACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTG
*
10713 TGCGAGTTGA
65 TGCGAATTGA
10723 TTGTATAGCA
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 18 0.28
82 47 0.72
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (81 bp):
GCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:10690 original size:55 final size:52
Alignment explanation
Indices: 10566--10719 Score: 175
Period size: 55 Copynumber: 2.9 Consensus size: 52
10556 TAAATTGTAC
* *
10566 AGCACTAAGTGTGCG-ATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATG
1 AGCACTAAGTGTGCGAATT-GACTATGTGGCACTAAGTGTGCG-AGTGAATATG
* * *
10619 ATGCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTCTAACTATG
1 A-GCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGT-GAA-TATG
* * *
10674 TAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTGTGCGAGT
1 -AGCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGT
10720 TGATTGTATA
Statistics
Matches: 86, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
53 3 0.03
54 36 0.42
55 46 0.53
56 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (52 bp):
AGCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGTGAATATG
Found at i:10724 original size:27 final size:27
Alignment explanation
Indices: 10567--10722 Score: 163
Period size: 27 Copynumber: 5.7 Consensus size: 27
10557 AAATTGTACA
*
10567 GCACTAAGTGTGCG-ATTCGACTATGTT
1 GCACTAAGTGTGCGAATT-GACTATGTG
* *
10594 GCACTAAGTGTGCGAAATGAATATGAT-
1 GCACTAAGTGTGCGAATTGACTATG-TG
* *
10621 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAATTGACTATGTG
* * *
10648 GCACTAAGTGTGCGAGTCTAACTATGTA
1 GCACTAAGTGTGCGAAT-TGACTATGTG
* * *
10676 GCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGAATTGACTATGTG
*
10703 GCACTAAGTGTGCGAGTTGA
1 GCACTAAGTGTGCGAATTGA
10723 TTGTATAGCA
Statistics
Matches: 108, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
27 83 0.77
28 25 0.23
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (27 bp):
GCACTAAGTGTGCGAATTGACTATGTG
Found at i:10733 original size:27 final size:27
Alignment explanation
Indices: 10559--10743 Score: 101
Period size: 27 Copynumber: 6.8 Consensus size: 27
10549 GCGGGATTAA
*
10559 ATTGTACAGCACTAAGTGTGCG-ATTCG
1 ATTGTATAGCACTAAGTGTGCGAATT-G
*
10586 ACTATGT-T-GCACTAAGTGTGCGAAATG
1 A-T-TGTATAGCACTAAGTGTGCGAATTG
10613 AATATG-AT-GCACTAAGTGTGCGAATTG
1 -AT-TGTATAGCACTAAGTGTGCGAATTG
*** *** * *
10640 ACCATGCGGCACTAAGTGTGCGAGTCTA
1 ATTGTATAGCACTAAGTGTGCGAAT-TG
* * * *
10668 ACTATGTAGCACTAAGTGTGCGATTTG
1 ATTGTATAGCACTAAGTGTGCGAATTG
*** * *
10695 ATTACGTGGCACTAAGTGTGCGAGTTG
1 ATTGTATAGCACTAAGTGTGCGAATTG
*
10722 ATTGTATAGCACTGAGTGTGCG
1 ATTGTATAGCACTAAGTGTGCG
10744 GGCTCAATAT
Statistics
Matches: 126, Mismatches: 24, Indels: 16
0.76 0.14 0.10
Matches are distributed among these distances:
26 1 0.01
27 96 0.76
28 26 0.21
29 3 0.02
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.29
Consensus pattern (27 bp):
ATTGTATAGCACTAAGTGTGCGAATTG
Found at i:10734 original size:82 final size:81
Alignment explanation
Indices: 10559--10743 Score: 210
Period size: 82 Copynumber: 2.3 Consensus size: 81
10549 GCGGGATTAA
* * * *
10559 ATTGTACAGCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCA
1 ATTGTACAGCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCA
10624 CTAAGTGTGCGAATTG
66 CTAAGTGTGCGAATTG
*** * * ** *
10640 ACCATGCGGCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGG
1 ATTGTACAGCACTAAGTGTGCGAGTC-AACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-G
*
10704 CACTAAGTGTGCGAGTTG
64 CACTAAGTGTGCGAATTG
* *
10722 ATTGTATAGCACTGAGTGTGCG
1 ATTGTACAGCACTAAGTGTGCG
10744 GGCTCAATAT
Statistics
Matches: 82, Mismatches: 20, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
81 21 0.26
82 61 0.74
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
ATTGTACAGCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCA
CTAAGTGTGCGAATTG
Found at i:18753 original size:82 final size:81
Alignment explanation
Indices: 18637--18792 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
18627 AAATTGTACA
* * * *
18637 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTG
1 GCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACG-TGGCACTAAGTG
18701 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
18718 GCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTG
1 GCACTAAGTGTGCGAGTC-AACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTG
*
18783 TGCGAGTTGA
65 TGCGAATTGA
18793 TTGTATAGCA
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 18 0.28
82 47 0.72
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (81 bp):
GCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:18760 original size:55 final size:52
Alignment explanation
Indices: 18636--18789 Score: 175
Period size: 55 Copynumber: 2.9 Consensus size: 52
18626 TAAATTGTAC
* *
18636 AGCACTAAGTGTGCG-ATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATG
1 AGCACTAAGTGTGCGAATT-GACTATGTGGCACTAAGTGTGCG-AGTGAATATG
* * *
18689 ATGCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTCTAACTATG
1 A-GCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGT-GAA-TATG
* * *
18744 TAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTGTGCGAGT
1 -AGCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGT
18790 TGATTGTATA
Statistics
Matches: 86, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
53 3 0.03
54 36 0.42
55 46 0.53
56 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (52 bp):
AGCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGTGAATATG
Found at i:18794 original size:27 final size:27
Alignment explanation
Indices: 18637--18792 Score: 163
Period size: 27 Copynumber: 5.7 Consensus size: 27
18627 AAATTGTACA
*
18637 GCACTAAGTGTGCG-ATTCGACTATGTT
1 GCACTAAGTGTGCGAATT-GACTATGTG
* *
18664 GCACTAAGTGTGCGAAATGAATATGAT-
1 GCACTAAGTGTGCGAATTGACTATG-TG
* *
18691 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAATTGACTATGTG
* * *
18718 GCACTAAGTGTGCGAGTCTAACTATGTA
1 GCACTAAGTGTGCGAAT-TGACTATGTG
* * *
18746 GCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGAATTGACTATGTG
*
18773 GCACTAAGTGTGCGAGTTGA
1 GCACTAAGTGTGCGAATTGA
18793 TTGTATAGCA
Statistics
Matches: 108, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
27 83 0.77
28 25 0.23
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (27 bp):
GCACTAAGTGTGCGAATTGACTATGTG
Found at i:18803 original size:27 final size:27
Alignment explanation
Indices: 18629--18813 Score: 101
Period size: 27 Copynumber: 6.8 Consensus size: 27
18619 GCGGGATTAA
*
18629 ATTGTACAGCACTAAGTGTGCG-ATTCG
1 ATTGTATAGCACTAAGTGTGCGAATT-G
*
18656 ACTATGT-T-GCACTAAGTGTGCGAAATG
1 A-T-TGTATAGCACTAAGTGTGCGAATTG
18683 AATATG-AT-GCACTAAGTGTGCGAATTG
1 -AT-TGTATAGCACTAAGTGTGCGAATTG
*** *** * *
18710 ACCATGCGGCACTAAGTGTGCGAGTCTA
1 ATTGTATAGCACTAAGTGTGCGAAT-TG
* * * *
18738 ACTATGTAGCACTAAGTGTGCGATTTG
1 ATTGTATAGCACTAAGTGTGCGAATTG
*** * *
18765 ATTACGTGGCACTAAGTGTGCGAGTTG
1 ATTGTATAGCACTAAGTGTGCGAATTG
*
18792 ATTGTATAGCACTGAGTGTGCG
1 ATTGTATAGCACTAAGTGTGCG
18814 GGCTCAATAT
Statistics
Matches: 126, Mismatches: 24, Indels: 16
0.76 0.14 0.10
Matches are distributed among these distances:
26 1 0.01
27 96 0.76
28 26 0.21
29 3 0.02
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.29
Consensus pattern (27 bp):
ATTGTATAGCACTAAGTGTGCGAATTG
Found at i:18804 original size:82 final size:81
Alignment explanation
Indices: 18629--18813 Score: 210
Period size: 82 Copynumber: 2.3 Consensus size: 81
18619 GCGGGATTAA
* * * *
18629 ATTGTACAGCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCA
1 ATTGTACAGCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCA
18694 CTAAGTGTGCGAATTG
66 CTAAGTGTGCGAATTG
*** * * ** *
18710 ACCATGCGGCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGG
1 ATTGTACAGCACTAAGTGTGCGAGTC-AACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-G
*
18774 CACTAAGTGTGCGAGTTG
64 CACTAAGTGTGCGAATTG
* *
18792 ATTGTATAGCACTGAGTGTGCG
1 ATTGTACAGCACTAAGTGTGCG
18814 GGCTCAATAT
Statistics
Matches: 82, Mismatches: 20, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
81 21 0.26
82 61 0.74
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
ATTGTACAGCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCA
CTAAGTGTGCGAATTG
Found at i:26400 original size:24 final size:24
Alignment explanation
Indices: 26336--26401 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 24
26326 TATCCATTAA
* *
26336 ATAATCATAA-TAATTATAAAACC
1 ATAATAATAATTAAATATAAAACC
**
26359 ATAATAATAATTTTATATAAAACC
1 ATAATAATAATTAAATATAAAACC
*
26383 ATGATAATAATTAAATATA
1 ATAATAATAATTAAATATA
26402 TATAATACAT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
23 9 0.26
24 26 0.74
ACGTcount: A:0.56, C:0.08, G:0.02, T:0.35
Consensus pattern (24 bp):
ATAATAATAATTAAATATAAAACC
Found at i:34139 original size:17 final size:16
Alignment explanation
Indices: 34100--34142 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
34090 ATTACAAATG
34100 TACCA-ATATAATTTT
1 TACCATATATAATTTT
*
34115 TACACATATATATTTTAT
1 TAC-CATATATAATTT-T
34133 TACCATATAT
1 TACCATATAT
34143 TTATCAACTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 3 0.12
16 2 0.08
17 15 0.62
18 4 0.17
ACGTcount: A:0.40, C:0.14, G:0.00, T:0.47
Consensus pattern (16 bp):
TACCATATATAATTTT
Found at i:34248 original size:24 final size:24
Alignment explanation
Indices: 34184--34249 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 24
34174 TATCCATTAA
* *
34184 ATAATCATAA-TAATTATAAAACC
1 ATAATAATAATTAAATATAAAACC
**
34207 ATAATAATAATTTTATATAAAACC
1 ATAATAATAATTAAATATAAAACC
*
34231 ATGATAATAATTAAATATA
1 ATAATAATAATTAAATATA
34250 TATAATACAT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
23 9 0.26
24 26 0.74
ACGTcount: A:0.56, C:0.08, G:0.02, T:0.35
Consensus pattern (24 bp):
ATAATAATAATTAAATATAAAACC
Found at i:34979 original size:42 final size:42
Alignment explanation
Indices: 34916--35033 Score: 139
Period size: 43 Copynumber: 2.8 Consensus size: 42
34906 GACTTATGAT
* * *
34916 TTACGTGTAAGACCAAGTCTGGGACATTGGCATC-GTATTTGA
1 TTACATGTAAGACC-CGTCTGGGACATTGGCATCAATATTTGA
* * *
34958 TTCCTTGTAAGACCCTGTCTGGGACAGTGGCATCAATATTTGA
1 TTACATGTAAGACCC-GTCTGGGACATTGGCATCAATATTTGA
*
35001 TTACATGTAAGACCACGTCTGGGACGTTGGCAT
1 TTACATGTAAGACC-CGTCTGGGACATTGGCAT
35034 TGTACAAGCT
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
42 29 0.45
43 34 0.53
44 1 0.02
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (42 bp):
TTACATGTAAGACCCGTCTGGGACATTGGCATCAATATTTGA
Found at i:38641 original size:28 final size:28
Alignment explanation
Indices: 38578--38703 Score: 209
Period size: 28 Copynumber: 4.5 Consensus size: 28
38568 ATATTAAGTC
* *
38578 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
38605 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
38633 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAACT
38661 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
38689 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
38704 GTACAATTTA
Statistics
Matches: 94, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
27 22 0.23
28 72 0.77
ACGTcount: A:0.33, C:0.29, G:0.13, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTACATAATCAAACT
Found at i:46705 original size:28 final size:28
Alignment explanation
Indices: 46642--46792 Score: 214
Period size: 28 Copynumber: 5.4 Consensus size: 28
46632 ATATTAAGTC
*
46642 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
46669 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* *
46697 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTATATAATCAAACT
*
46725 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
46753 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
46782 CGCACACTTAG
1 CGCACACTTAG
46793 CGCCAATCTC
Statistics
Matches: 113, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 22 0.19
28 75 0.66
29 16 0.14
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:49082 original size:20 final size:20
Alignment explanation
Indices: 49057--49095 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
49047 TTATAGCGTG
49057 TTTGAGTAGAGCTAGACTTT
1 TTTGAGTAGAGCTAGACTTT
49077 TTTGAGTAGAGCTAGACTT
1 TTTGAGTAGAGCTAGACTT
49096 GGGTTAGACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.26, C:0.10, G:0.26, T:0.38
Consensus pattern (20 bp):
TTTGAGTAGAGCTAGACTTT
Found at i:51072 original size:6 final size:6
Alignment explanation
Indices: 51058--51088 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
51048 AATAAAATTT
51058 AAATAAA AAATAA AAATAA AAATAA AAATAA
1 AAAT-AA AAATAA AAATAA AAATAA AAATAA
51089 TAGTAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 20 0.83
7 4 0.17
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:51095 original size:18 final size:17
Alignment explanation
Indices: 51048--51100 Score: 52
Period size: 18 Copynumber: 3.0 Consensus size: 17
51038 AATAAGACAC
* *
51048 AATAAAATTTAAATAAAA
1 AATAAAAATAAAAT-AAA
51066 AATAAAAATAAAAATAAA
1 AATAAAAAT-AAAATAAA
* *
51084 AATAATAGTAAAATAAA
1 AATAAAAATAAAATAAA
51101 GGGACTCAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
17 8 0.27
18 18 0.60
19 4 0.13
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (17 bp):
AATAAAAATAAAATAAA
Done.