Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1542
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: 32029
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Found at i:3565 original size:27 final size:27
Alignment explanation
Indices: 3534--3711 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
3524 TAAATTGTAC
3534 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
3561 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
3587 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
3615 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
3643 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
3670 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
3697 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
3712 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:3648 original size:82 final size:81
Alignment explanation
Indices: 3535--3690 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
3525 AAATTGTACA
* *
3535 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
3599 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
3616 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
3681 TGCGAGTTGA
65 TGCGAATTGA
3691 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:3702 original size:82 final size:81
Alignment explanation
Indices: 3531--3711 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
3521 GATTAAATTG
* *
3531 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
3596 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
3612 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
3676 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
3694 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
3712 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
Found at i:11618 original size:27 final size:27
Alignment explanation
Indices: 11587--11764 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
11577 TAAATTGTAC
11587 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
11614 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
11640 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
11668 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
11696 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
11723 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
11750 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
11765 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:11701 original size:82 final size:81
Alignment explanation
Indices: 11588--11743 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
11578 AAATTGTACA
* *
11588 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
11652 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
11669 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
11734 TGCGAGTTGA
65 TGCGAATTGA
11744 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:11755 original size:82 final size:81
Alignment explanation
Indices: 11584--11764 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
11574 GATTAAATTG
* *
11584 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
11649 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
11665 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
11729 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
11747 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
11765 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
Found at i:17906 original size:33 final size:33
Alignment explanation
Indices: 17862--17935 Score: 121
Period size: 33 Copynumber: 2.2 Consensus size: 33
17852 GTGATCAACA
**
17862 CAGTATCAGTACAGTCTGGGCCGAAGCCCTATT
1 CAGTATCAGTACAGTCTGGGCAAAAGCCCTATT
*
17895 CAGTATTAGTACAGTCTGGGCAAAAGCCCTATT
1 CAGTATCAGTACAGTCTGGGCAAAAGCCCTATT
17928 CAGTATCA
1 CAGTATCA
17936 CTATAGTGCA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (33 bp):
CAGTATCAGTACAGTCTGGGCAAAAGCCCTATT
Found at i:22561 original size:39 final size:39
Alignment explanation
Indices: 22507--22715 Score: 323
Period size: 39 Copynumber: 5.3 Consensus size: 39
22497 GGACTAAGAT
22507 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGC
1 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGC
22546 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGC
1 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGC
22585 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGC
1 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGC
* * *
22624 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAG-C
* * *
22664 CCGAAGGCATTTGTGCGA-TTACT-ATAACCGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGATACTAAT-TCCGGGCTAAG-C
22703 CCGAAGGCATTTG
1 CCGAAGGCATTTG
22716 AACGAGGAGC
Statistics
Matches: 161, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
38 1 0.01
39 141 0.88
40 19 0.12
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGC
Found at i:22589 original size:78 final size:79
Alignment explanation
Indices: 22456--22715 Score: 329
Period size: 78 Copynumber: 3.3 Consensus size: 79
22446 TTGAATGATG
* * *
22456 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-ATATCCGGACTAAGAT-CCGAAGGCA
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGA-T-ACTAAATCCGGGCTAAG-TCCCGAAGGCA
22516 TTTGTGCGAGATACTAAT
62 TTTGTGCGAGATACTAAT
*
22534 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAG-CCCGAAGGCATTTG
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAATCCGGGCTAAGTCCCGAAGGCATTTG
22598 TGCGAGATACTAAT
66 TGCGAGATACTAAT
* *
22612 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTG
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAATCCGGGCTAAGTCCCGAAGGCATTTG
*
22677 TGCGA-TTACT-AT
66 TGCGAGATACTAAT
* *
22689 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAG-CCCGAAGGCATTTG
22716 AACGAGGAGC
Statistics
Matches: 164, Mismatches: 10, Indels: 15
0.87 0.05 0.08
Matches are distributed among these distances:
77 11 0.07
78 100 0.61
79 52 0.32
80 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (79 bp):
TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAATCCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGATACTAAT
Found at i:30565 original size:39 final size:39
Alignment explanation
Indices: 30479--30685 Score: 296
Period size: 39 Copynumber: 5.3 Consensus size: 39
30469 GGACTAAGAT
30479 CCGAAGGCATTTGTGCGAGATACTAATTCC-GG-TAAGC
1 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGC
30516 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGC
1 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGC
*
30555 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGTTAAGC
1 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGC
* * *
30594 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAG-C
* * *
30634 CCGAAGGCATTTGTGCGA-TTACT-ATAACCGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGATACTAAT-TCCGGGCTAAG-C
30673 CCGAAGGCATTTG
1 CCGAAGGCATTTG
30686 AACGAGGAGC
Statistics
Matches: 159, Mismatches: 7, Indels: 6
0.92 0.04 0.03
Matches are distributed among these distances:
37 30 0.19
38 3 0.02
39 107 0.67
40 19 0.12
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGC
Found at i:30703 original size:79 final size:79
Alignment explanation
Indices: 30479--30718 Score: 253
Period size: 78 Copynumber: 3.1 Consensus size: 79
30469 GGACTAAGAT
* **
30479 CCGAAGGCATTTGTGCGAGATACTAATTCC-GG-TAAGCCCGAAGGCATTTGTGCGAGAT-ACTA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAG-TGACTA
* *
30541 ATTCCGGGCTAAG-C
65 AATCCGGGTTAAGTC
* * ** *
30555 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGTTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
30620 ATCCGGGTTAAGTC
66 ATCCGGGTTAAGTC
* *
30634 CCGAAGGCATTTGTGCGA-TTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-C
* * *
30696 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAGTC
30712 CCGAAGG
1 CCGAAGG
30719 TACGTGATTT
Statistics
Matches: 145, Mismatches: 12, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
76 30 0.21
77 5 0.03
78 66 0.46
79 44 0.30
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
ATCCGGGTTAAGTC
Found at i:30718 original size:118 final size:115
Alignment explanation
Indices: 30473--30691 Score: 298
Period size: 118 Copynumber: 1.9 Consensus size: 115
30463 ATATCCGGAC
*
30473 TAAGATCCGAAGGCATTTGTGCGAGATACTAATTCCGGTAAGCCCGAAGGCATTTGTGCGAGATA
1 TAAG-TCCGAAGGCATTTGTGCGAGATACTAAATCCGGTAAGCCCGAAGGCATTTGTGCGAGATA
* **
30538 CTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAATTCCGGGT
65 CTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGATACTAATTCCGGGT
* * *
30589 TAAGCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-T
1 TAAGTCCGAAGGCATTTGTGCGAGATACTAAATCC-GG-TAAG-CCCGAAGGCATTTGTGCGAGA
*
30653 TACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG
63 TACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAG
30692 GAGCTATATC
Statistics
Matches: 90, Mismatches: 8, Indels: 8
0.85 0.08 0.08
Matches are distributed among these distances:
115 28 0.31
116 8 0.09
117 17 0.19
118 37 0.41
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (115 bp):
TAAGTCCGAAGGCATTTGTGCGAGATACTAAATCCGGTAAGCCCGAAGGCATTTGTGCGAGATAC
TAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGATACTAATTCCGGGT
Done.