Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_696
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: 50778
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Found at i:3773 original size:16 final size:16
Alignment explanation
Indices: 3752--3819 Score: 118
Period size: 16 Copynumber: 4.2 Consensus size: 16
3742 GATTTGCTAT
3752 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
3768 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
3784 TACACTTCTAATCCAA
1 TACACCTCTAATCCAA
*
3800 TACATCTCTAATCCAA
1 TACACCTCTAATCCAA
3816 TACA
1 TACA
3820 GCGAACCAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.38, C:0.34, G:0.00, T:0.28
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:6809 original size:39 final size:40
Alignment explanation
Indices: 6605--6827 Score: 236
Period size: 40 Copynumber: 5.6 Consensus size: 40
6595 TTGAATGCTG
* * * * * *
6605 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTACTAAA
** * * *
6645 TCCGGACTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAA
*
6685 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
**
6725 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* *
6765 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* * *
6804 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
6828 TGAACGAGGA
Statistics
Matches: 161, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
39 35 0.22
40 118 0.73
41 8 0.05
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
Found at i:6847 original size:79 final size:80
Alignment explanation
Indices: 6680--6862 Score: 226
Period size: 79 Copynumber: 2.3 Consensus size: 80
6670 GTGCGAGATA
* * *
6680 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
** **
6745 CATTCGTGCGAGTTG
66 CATTCGAACGAGGAG
* * * *
6760 TTAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
*
6824 CATTTGAACGAGGAG
66 CATTCGAACGAGGAG
* *
6839 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
6863 TACGTGATTT
Statistics
Matches: 87, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
78 14 0.16
79 46 0.53
80 27 0.31
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
CATTCGAACGAGGAG
Found at i:14657 original size:39 final size:40
Alignment explanation
Indices: 14454--14675 Score: 236
Period size: 40 Copynumber: 5.6 Consensus size: 40
14444 TTGAATGCTG
* * * * *
14454 TCCGGGCTAAGTCCCGAAGGC-TT-GTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTACTAAA
** * * *
14493 TCCGGACTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAA
*
14533 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
**
14573 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* *
14613 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* * *
14652 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
14676 TGAACGAGGA
Statistics
Matches: 160, Mismatches: 19, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
39 53 0.33
40 103 0.64
41 4 0.03
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
Found at i:14695 original size:79 final size:80
Alignment explanation
Indices: 14528--14709 Score: 217
Period size: 79 Copynumber: 2.3 Consensus size: 80
14518 GTGCGAGATA
* * *
14528 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
** **
14593 CATTCGTGCGAGTTG
66 CATTCGAACGAGGAG
* * * *
14608 TTAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
*
14672 CATTTGAACGAGGAG
66 CATTCGAACGAGGAG
* *
14687 CTATATCC--GTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
14710 TACGTGATTT
Statistics
Matches: 86, Mismatches: 16, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
77 13 0.15
79 46 0.53
80 27 0.31
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
CATTCGAACGAGGAG
Found at i:17138 original size:15 final size:15
Alignment explanation
Indices: 17120--17172 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 15
17110 AATTATCTAT
17120 AAACATATTAACTAA
1 AAACATATTAACTAA
*
17135 AAACAATAATTATCTATA
1 AAAC-AT-ATTAACTA-A
17153 AAA-ATATTAACTAA
1 AAACATATTAACTAA
17167 AGAACA
1 A-AACA
17173 ATAATATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
14 2 0.06
15 13 0.42
16 5 0.16
17 7 0.23
18 4 0.13
ACGTcount: A:0.60, C:0.11, G:0.02, T:0.26
Consensus pattern (15 bp):
AAACATATTAACTAA
Found at i:17140 original size:32 final size:33
Alignment explanation
Indices: 17104--17177 Score: 132
Period size: 32 Copynumber: 2.3 Consensus size: 33
17094 ATGTGCATTC
*
17104 AACAATAATTATCTATAAACATATTAACTAAA-
1 AACAATAATTATCTATAAAAATATTAACTAAAG
17136 AACAATAATTATCTATAAAAATATTAACTAAAG
1 AACAATAATTATCTATAAAAATATTAACTAAAG
17169 AACAATAAT
1 AACAATAAT
17178 ATAAAATTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
32 31 0.77
33 9 0.22
ACGTcount: A:0.58, C:0.11, G:0.01, T:0.30
Consensus pattern (33 bp):
AACAATAATTATCTATAAAAATATTAACTAAAG
Found at i:17156 original size:19 final size:19
Alignment explanation
Indices: 17104--17156 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 19
17094 ATGTGCATTC
17104 AACAATAATTATCTAT--A
1 AACAATAATTATCTATAAA
*
17121 AAC-AT-ATTAAC--TAAA
1 AACAATAATTATCTATAAA
17136 AACAATAATTATCTATAAA
1 AACAATAATTATCTATAAA
17155 AA
1 AA
17157 TATTAACTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 10
0.70 0.05 0.25
Matches are distributed among these distances:
13 1 0.04
15 9 0.32
16 4 0.14
17 8 0.29
19 6 0.21
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.30
Consensus pattern (19 bp):
AACAATAATTATCTATAAA
Found at i:19108 original size:28 final size:28
Alignment explanation
Indices: 19062--19136 Score: 78
Period size: 28 Copynumber: 2.7 Consensus size: 28
19052 CAAACCATAC
** * * *
19062 ATTTTGATTTTTAAATTTTAATTTTAGT
1 ATTTTGATTTTCCATTTTTAATTTGAGA
*
19090 TTTTTGATTTTCCATTTTTAATTTGAGA
1 ATTTTGATTTTCCATTTTTAATTTGAGA
* *
19118 AGTTTGATTTTGCATTTTT
1 ATTTTGATTTTCCATTTTT
19137 TTAATATTTT
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.23, C:0.04, G:0.11, T:0.63
Consensus pattern (28 bp):
ATTTTGATTTTCCATTTTTAATTTGAGA
Found at i:24535 original size:34 final size:34
Alignment explanation
Indices: 24497--24574 Score: 95
Period size: 34 Copynumber: 2.3 Consensus size: 34
24487 CACATTATAA
24497 TGCATCATTTTAAACATCATATT-TAGTTTCATAT
1 TGCATCATTTTAAACATCAT-TTCTAGTTTCATAT
* * * * *
24531 TGCATCATTGTAGACATCATTTCTTGTTTCCTTT
1 TGCATCATTTTAAACATCATTTCTAGTTTCATAT
24565 TGCATCATTT
1 TGCATCATTT
24575 AGTTTTTTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
33 2 0.05
34 35 0.95
ACGTcount: A:0.24, C:0.18, G:0.09, T:0.49
Consensus pattern (34 bp):
TGCATCATTTTAAACATCATTTCTAGTTTCATAT
Found at i:25526 original size:30 final size:29
Alignment explanation
Indices: 25469--25526 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
25459 GGTTTTGTGG
**
25469 CCACAAGGGTGGCCACACGACTGTGTGCC
1 CCACAAGGGTGGCCACACGACAATGTGCC
* *
25498 CCACATGGGTGGCTCACACGGCAATGTGC
1 CCACAAGGGTGGC-CACACGACAATGTGC
25527 AATTGGGAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 12 0.50
30 12 0.50
ACGTcount: A:0.21, C:0.33, G:0.31, T:0.16
Consensus pattern (29 bp):
CCACAAGGGTGGCCACACGACAATGTGCC
Found at i:28543 original size:68 final size:67
Alignment explanation
Indices: 28471--28620 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
28461 CATCATGTGT
* * * *
28471 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
28533 ATGTAG
62 ATGTAG
** * *
28539 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
28604 AG
66 AG
28606 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
28621 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:33548 original size:28 final size:28
Alignment explanation
Indices: 33504--33570 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
33494 TCTCACTGTA
* *
33504 CGAAATATTCAGAATGACACTTAGTGTG
1 CGAAATATTGAGAATGACACTTAATGTG
*
33532 CGAGATATTGAGAATGACACTTAATGTG
1 CGAAATATTGAGAATGACACTTAATGTG
*
33560 TGAAATATTGA
1 CGAAATATTGA
33571 ATGATTCAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.30
Consensus pattern (28 bp):
CGAAATATTGAGAATGACACTTAATGTG
Found at i:38708 original size:33 final size:32
Alignment explanation
Indices: 38636--38715 Score: 79
Period size: 33 Copynumber: 2.4 Consensus size: 32
38626 CTGTATGGAG
* * *
38636 ATGGGCTAAGACCCACACTGTTACTGATACTGT
1 ATGGGCTAAG-GCCACACTGATACTGAGACTGT
* *
38669 ATTGGGCTAAGGCCACACTGATATTGCGACTGAT
1 A-TGGGCTAAGGCCACACTGATACTGAGACTG-T
*
38703 ATGGGCTTAGGCC
1 ATGGGCTAAGGCC
38716 CAGTTGTGTA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
33 28 0.72
34 11 0.28
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (32 bp):
ATGGGCTAAGGCCACACTGATACTGAGACTGT
Found at i:43693 original size:21 final size:22
Alignment explanation
Indices: 43669--43709 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
43659 CTAGATTAAA
*
43669 AGTACCAAA-ATCCATAAATCT
1 AGTAACAAACATCCATAAATCT
*
43690 AGTAATAAACATCCATAAAT
1 AGTAACAAACATCCATAAAT
43710 ATGCTAAGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.51, C:0.20, G:0.05, T:0.24
Consensus pattern (22 bp):
AGTAACAAACATCCATAAATCT
Found at i:45507 original size:6 final size:6
Alignment explanation
Indices: 45502--45544 Score: 77
Period size: 6 Copynumber: 7.2 Consensus size: 6
45492 AAATTGAAAT
*
45502 AAAAAT AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG A
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG A
45545 TAAGAGGAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:48662 original size:27 final size:27
Alignment explanation
Indices: 48631--48808 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
48621 TAAATTGTAC
48631 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
48658 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
48684 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
48712 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
48740 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
48767 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
48794 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
48809 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:48745 original size:82 final size:81
Alignment explanation
Indices: 48632--48787 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
48622 AAATTGTACA
* *
48632 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
48696 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
48713 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
48778 TGCGAGTTGA
65 TGCGAATTGA
48788 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:48799 original size:82 final size:81
Alignment explanation
Indices: 48628--48808 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
48618 GATTAAATTG
* *
48628 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
48693 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
48709 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
48773 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
48791 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
48809 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Done.