Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold251
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: 39569
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:5083 original size:34 final size:34
Alignment explanation
Indices: 5032--5104 Score: 80
Period size: 34 Copynumber: 2.1 Consensus size: 34
5022 CGCTCGAAGC
5032 CTGCGGGACTTAGCCGGACATATT-TCC-GCACTAG
1 CTGCGGGACTTAGCCGG--ATATTATCCAGCACTAG
*
5066 CTGC-GGACTTAATCCGGATATTAATCCAGCACTAG
1 CTGCGGGACTT-AGCCGGATATT-ATCCAGCACTAG
5101 CTGC
1 CTGC
5105 AGACCGTCAG
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
32 5 0.15
33 6 0.18
34 12 0.35
35 11 0.32
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.25
Consensus pattern (34 bp):
CTGCGGGACTTAGCCGGATATTATCCAGCACTAG
Found at i:9759 original size:12 final size:12
Alignment explanation
Indices: 9708--9763 Score: 53
Period size: 12 Copynumber: 4.7 Consensus size: 12
9698 TTTCTTTTGT
9708 TTCTTTTTCTAAC
1 TTCTTTTTC-AAC
* *
9721 TT-ATTTTC-TC
1 TTCTTTTTCAAC
9731 TTCTTTCTTCAAC
1 TTCTTT-TTCAAC
*
9744 TTCTTTTTCAAT
1 TTCTTTTTCAAC
9756 TTCTTTTT
1 TTCTTTTT
9764 GTTTCACATT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
10 3 0.09
11 2 0.06
12 21 0.60
13 9 0.26
ACGTcount: A:0.12, C:0.21, G:0.00, T:0.66
Consensus pattern (12 bp):
TTCTTTTTCAAC
Found at i:14157 original size:33 final size:33
Alignment explanation
Indices: 14120--14190 Score: 90
Period size: 33 Copynumber: 2.2 Consensus size: 33
14110 CTCAGCCCTC
**
14120 ATCAG-AATTAATTGGGCCTAGCCCATTCTCAAA
1 ATCAGTAA-TAATTGGGCCTAGCCCATTAACAAA
* *
14153 ATCAGTAATAGTTGGGCTTAGCCCATTAACAAA
1 ATCAGTAATAATTGGGCCTAGCCCATTAACAAA
14186 ATCAG
1 ATCAG
14191 GTGGACCTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 31 0.94
34 2 0.06
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (33 bp):
ATCAGTAATAATTGGGCCTAGCCCATTAACAAA
Found at i:14651 original size:27 final size:27
Alignment explanation
Indices: 14621--14711 Score: 94
Period size: 27 Copynumber: 3.4 Consensus size: 27
14611 AGGCATAATC
* *
14621 GTCATTCTACCATATAGGAGCATTACG
1 GTCATTTTACCATACAGGAGCATTACG
* * * *
14648 GTCATTTTACCCTACAGGGGTATTATG
1 GTCATTTTACCATACAGGAGCATTACG
*
14675 GTCATTTTACCATACAAGG-GTATTACG
1 GTCATTTTACCATAC-AGGAGCATTACG
*
14702 GTCTTTTTAC
1 GTCATTTTAC
14712 ACTACCAAGG
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
27 51 0.94
28 3 0.06
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (27 bp):
GTCATTTTACCATACAGGAGCATTACG
Found at i:14721 original size:28 final size:26
Alignment explanation
Indices: 14642--14725 Score: 98
Period size: 27 Copynumber: 3.1 Consensus size: 26
14632 ATATAGGAGC
*
14642 ATTACGGTCATTTTACCCTACAGGGGT
1 ATTACGGTCATTTTA-CCTACAAGGGT
*
14669 ATTATGGTCATTTTACCATACAAGGGT
1 ATTACGGTCATTTTACC-TACAAGGGT
*
14696 ATTACGGTCTTTTTACACTACCAA-GGT
1 ATTACGGTCATTTTAC-CTA-CAAGGGT
14723 ATT
1 ATT
14726 TTAGTAATTT
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
26 2 0.04
27 44 0.88
28 4 0.08
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (26 bp):
ATTACGGTCATTTTACCTACAAGGGT
Found at i:14752 original size:27 final size:27
Alignment explanation
Indices: 14722--14848 Score: 114
Period size: 27 Copynumber: 4.7 Consensus size: 27
14712 ACTACCAAGG
* *
14722 TATTTTAGTAATTTTATGAACTAGGGC
1 TATTTTGGTAATTTTATAAACTAGGGC
* * * *
14749 TATTTTGGTAATTTTCTAAATTGGGGG
1 TATTTTGGTAATTTTATAAACTAGGGC
* *
14776 TATTTTGGTAATTTT-TCAAACCAGGGG
1 TATTTTGGTAATTTTAT-AAACTAGGGC
* * * *
14803 TATTTCGATAATTTTTTAAACTAGGGG
1 TATTTTGGTAATTTTATAAACTAGGGC
*
14830 TATTTCGGTAATTTT-TAAA
1 TATTTTGGTAATTTTATAAA
14849 ATCGAGGGTA
Statistics
Matches: 85, Mismatches: 13, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
26 5 0.06
27 79 0.93
28 1 0.01
ACGTcount: A:0.28, C:0.07, G:0.20, T:0.46
Consensus pattern (27 bp):
TATTTTGGTAATTTTATAAACTAGGGC
Found at i:14778 original size:54 final size:54
Alignment explanation
Indices: 14720--14871 Score: 155
Period size: 54 Copynumber: 2.8 Consensus size: 54
14710 ACACTACCAA
* * * * * * *
14720 GGTATTTTAGTAATTTTAT-GAACTAGGGCTATTTTGGTAATTTTCTAAATTGGG
1 GGTATTTTGGTAATTTT-TCAAACCAGGGCTATTTCGATAATTTTCTAAACTAGG
* *
14774 GGTATTTTGGTAATTTTTCAAACCAGGGGTATTTCGATAATTTTTTAAACTAGG
1 GGTATTTTGGTAATTTTTCAAACCAGGGCTATTTCGATAATTTTCTAAACTAGG
* * * *
14828 GGTATTTCGGTAATTTTTAAAATCGAGGG-TATTTCGTTAATTTT
1 GGTATTTTGGTAATTTTTCAAA-CCAGGGCTATTTCGATAATTTT
14872 GCAATGCGGA
Statistics
Matches: 83, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
53 1 0.01
54 77 0.93
55 5 0.06
ACGTcount: A:0.26, C:0.07, G:0.21, T:0.45
Consensus pattern (54 bp):
GGTATTTTGGTAATTTTTCAAACCAGGGCTATTTCGATAATTTTCTAAACTAGG
Found at i:14806 original size:81 final size:81
Alignment explanation
Indices: 14720--14871 Score: 191
Period size: 81 Copynumber: 1.9 Consensus size: 81
14710 ACACTACCAA
* * * * *
14720 GGTATTTTAG-TAATTTTATGAACTAGGGCTATTTTGGTAATTTTCT-AAATTGGGGGTATTTTG
1 GGTA-TTTAGATAATTTTATAAACTAGGGCTATTTCGGTAATTTT-TAAAATCGAGGGTATTTCG
14783 GTAATTTTTCAAACCAGG
64 GTAATTTTTCAAACCAGG
* * * *
14801 GGTATTTCGATAATTTTTTAAACTAGGGGTATTTCGGTAATTTTTAAAATCGAGGGTATTTCGTT
1 GGTATTTAGATAATTTTATAAACTAGGGCTATTTCGGTAATTTTTAAAATCGAGGGTATTTCGGT
14866 AATTTT
66 AATTTT
14872 GCAATGCGGA
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
80 5 0.08
81 55 0.92
ACGTcount: A:0.26, C:0.07, G:0.21, T:0.45
Consensus pattern (81 bp):
GGTATTTAGATAATTTTATAAACTAGGGCTATTTCGGTAATTTTTAAAATCGAGGGTATTTCGGT
AATTTTTCAAACCAGG
Found at i:14857 original size:27 final size:25
Alignment explanation
Indices: 14720--14871 Score: 106
Period size: 27 Copynumber: 5.7 Consensus size: 25
14710 ACACTACCAA
** * *
14720 GGTATTTTAGTAATTTTATGAACTAG
1 GGTATTTCGGTAATTTT-TAAACGAG
* * *
14746 GGCTATTTTGGTAATTTTCTAAATTGGG
1 GG-TATTTCGGTAATTTT-TAAA-CGAG
* *
14774 GGTATTTTGGTAATTTTTCAAACCAGG
1 GGTATTTCGGTAATTTTT-AAACGA-G
* *
14801 GGTATTTCGATAATTTTTTAAACTAGG
1 GGTATTTCGGTAA-TTTTTAAACGA-G
14828 GGTATTTCGGTAATTTTTAAAATCGAG
1 GGTATTTCGGTAATTTTT-AAA-CGAG
*
14855 GGTATTTCGTTAATTTT
1 GGTATTTCGGTAATTTT
14872 GCAATGCGGA
Statistics
Matches: 104, Mismatches: 15, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
26 8 0.08
27 86 0.83
28 10 0.10
ACGTcount: A:0.26, C:0.07, G:0.21, T:0.45
Consensus pattern (25 bp):
GGTATTTCGGTAATTTTTAAACGAG
Found at i:24787 original size:27 final size:27
Alignment explanation
Indices: 24749--24896 Score: 181
Period size: 27 Copynumber: 5.5 Consensus size: 27
24739 CAATTTAATG
**
24749 AAATGACTGTTTTGCCCTTATGGGGTA
1 AAATGACTGTTTTGCCCTTATATGGTA
* *
24776 AAATGACTGTTTTGCCCTCATAAGGTA
1 AAATGACTGTTTTGCCCTTATATGGTA
* *
24803 AAATGACTATTTTGCCCTTATGTGGTA
1 AAATGACTGTTTTGCCCTTATATGGTA
* * *
24830 AAATGATTGTTTTACCCTCAT-TGGTA
1 AAATGACTGTTTTGCCCTTATATGGTA
*
24856 AAATGACTATTTTGCCCTTATATGGTA
1 AAATGACTGTTTTGCCCTTATATGGTA
* *
24883 AGATGATTGTTTTG
1 AAATGACTGTTTTG
24897 TCCTATGTGA
Statistics
Matches: 102, Mismatches: 18, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
26 22 0.22
27 80 0.78
ACGTcount: A:0.26, C:0.14, G:0.20, T:0.40
Consensus pattern (27 bp):
AAATGACTGTTTTGCCCTTATATGGTA
Found at i:24882 original size:53 final size:54
Alignment explanation
Indices: 24749--24895 Score: 224
Period size: 54 Copynumber: 2.7 Consensus size: 54
24739 CAATTTAATG
* * * *
24749 AAATGACTGTTTTGCCCTTATGGGGTAAAATGACTGTTTTGCCCTCATAAGGTA
1 AAATGACTATTTTGCCCTTATGTGGTAAAATGATTGTTTTACCCTCATAAGGTA
*
24803 AAATGACTATTTTGCCCTTATGTGGTAAAATGATTGTTTTACCCTCAT-TGGTA
1 AAATGACTATTTTGCCCTTATGTGGTAAAATGATTGTTTTACCCTCATAAGGTA
* *
24856 AAATGACTATTTTGCCCTTATATGGTAAGATGATTGTTTT
1 AAATGACTATTTTGCCCTTATGTGGTAAAATGATTGTTTT
24896 GTCCTATGTG
Statistics
Matches: 86, Mismatches: 7, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
53 42 0.49
54 44 0.51
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.40
Consensus pattern (54 bp):
AAATGACTATTTTGCCCTTATGTGGTAAAATGATTGTTTTACCCTCATAAGGTA
Found at i:30424 original size:39 final size:39
Alignment explanation
Indices: 30349--30425 Score: 95
Period size: 39 Copynumber: 2.0 Consensus size: 39
30339 TTTCTCTATG
*
30349 CTATTACATATCTATTCGATTCAATCAAACACAATAATA
1 CTATTACATATCTATTCCATTCAATCAAACACAATAATA
* *
30388 CTATTACACT-TCTATTCCATTACATTCAACCA-AATAAT
1 CTATTACA-TATCTATTCCATT-CAATCAAACACAATAAT
30426 TGAATTACTA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
39 24 0.73
40 9 0.27
ACGTcount: A:0.40, C:0.23, G:0.01, T:0.35
Consensus pattern (39 bp):
CTATTACATATCTATTCCATTCAATCAAACACAATAATA
Found at i:30457 original size:16 final size:16
Alignment explanation
Indices: 30436--30482 Score: 76
Period size: 16 Copynumber: 2.9 Consensus size: 16
30426 TGAATTACTA
30436 ATTACAGCCCTATTCC
1 ATTACAGCCCTATTCC
* *
30452 ATTACAGCTCTATTTC
1 ATTACAGCCCTATTCC
30468 ATTACAGCCCTATTC
1 ATTACAGCCCTATTC
30483 TATTCTAGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.26, C:0.32, G:0.06, T:0.36
Consensus pattern (16 bp):
ATTACAGCCCTATTCC
Found at i:30604 original size:43 final size:42
Alignment explanation
Indices: 30526--30606 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
30516 CTGAGATTAT
* *
30526 GTGTAAGACCATATCTGGGATATGGCATCGATACGAGACTTC
1 GTGTAAGACCATAGCTAGGATATGGCATCGATACGAGACTTC
* *
30568 GTGTAAGACCATAGCTAGGTTATTGGCATTGATACGAGA
1 GTGTAAGACCATAGCTAGGATA-TGGCATCGATACGAGA
30607 TTACATATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
42 19 0.56
43 15 0.44
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (42 bp):
GTGTAAGACCATAGCTAGGATATGGCATCGATACGAGACTTC
Found at i:30632 original size:43 final size:43
Alignment explanation
Indices: 30529--30633 Score: 124
Period size: 43 Copynumber: 2.5 Consensus size: 43
30519 AGATTATGTG
* * *
30529 TAAGACCATATCTGGGATA-TGGCATCGATACGAGACTTCGTG
1 TAAGACCATATCTGGGTTATTGGCATCGATACGAGACTTCATA
* * *
30571 TAAGACCATAGCTAGGTTATTGGCATTGATACGAGA-TTACATA
1 TAAGACCATATCTGGGTTATTGGCATCGATACGAGACTT-CATA
*
30614 TAAGACCATCTCTGGGTTAT
1 TAAGACCATATCTGGGTTAT
30634 GGTATTGGTA
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
42 18 0.35
43 34 0.65
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (43 bp):
TAAGACCATATCTGGGTTATTGGCATCGATACGAGACTTCATA
Found at i:33313 original size:43 final size:42
Alignment explanation
Indices: 33217--33316 Score: 103
Period size: 42 Copynumber: 2.4 Consensus size: 42
33207 GACTTATGAT
* * *
33217 TTACATGTAAGACCATGTCTTGGACATCGGCATCATATTTAA
1 TTACATGTAAGACCATGCCTGGGACATCGGCACCATATTTAA
* * * * *
33259 TTTCATTTAAGACCCTGCCTGGGATAGT-GGCACCGATATTTGA
1 TTACATGTAAGACCATGCCTGGGACA-TCGGCACC-ATATTTAA
33302 TTACATGTAAGACCA
1 TTACATGTAAGACCA
33317 CGTATAGGAC
Statistics
Matches: 45, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
42 25 0.56
43 20 0.44
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (42 bp):
TTACATGTAAGACCATGCCTGGGACATCGGCACCATATTTAA
Found at i:38492 original size:6 final size:7
Alignment explanation
Indices: 38477--38507 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
38467 CATTAAGTGA
38477 TTTTATT
1 TTTTATT
38484 TTTTATT
1 TTTTATT
38491 TTTTATT
1 TTTTATT
*
38498 TTTTGTT
1 TTTTATT
38505 TTT
1 TTT
38508 GTCCAAGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.10, C:0.00, G:0.03, T:0.87
Consensus pattern (7 bp):
TTTTATT
Done.