Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold516
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: 56519
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Found at i:4995 original size:40 final size:39
Alignment explanation
Indices: 4826--5047 Score: 200
Period size: 39 Copynumber: 5.6 Consensus size: 39
4816 TTGAATGCTG
* * * * * *
4826 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAA
** * *
4866 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAGT
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGTTACTAA-A
* *
4906 TCCGGGTTAAG-CCCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGTTACTAAA
*
4945 TCCGGGTTAAGT-CCGAAGGCATTCGTGCGAGTTAATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTT-ACTAAA
*
4985 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* * *
5024 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
5048 TGAACGAGGA
Statistics
Matches: 152, Mismatches: 20, Indels: 21
0.79 0.10 0.11
Matches are distributed among these distances:
38 3 0.02
39 73 0.48
40 58 0.38
41 18 0.12
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:5067 original size:79 final size:80
Alignment explanation
Indices: 4906--5082 Score: 191
Period size: 79 Copynumber: 2.2 Consensus size: 80
4896 AGATACAAGT
* * *
4906 TCCGGGTTAAG-CCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCGAAGGCATTCG
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCGAAGGCATTCG
** * *
4970 TGCGAGTTAATTAAA
66 AACGAGTGAACTAAA
* * * *
4985 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGT-CCGAAGGCATTC
* *
5049 GAACGAG-GAGCTATA
65 GAACGAGTGAACTAAA
*
5064 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
5083 TATGTGATTT
Statistics
Matches: 82, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
78 15 0.18
79 43 0.52
80 24 0.29
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCGAAGGCATTCG
AACGAGTGAACTAAA
Found at i:8599 original size:79 final size:79
Alignment explanation
Indices: 8441--8662 Score: 231
Period size: 79 Copynumber: 2.8 Consensus size: 79
8431 GAATGATGTC
* * * * * *
8441 CGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACCATATCCGGACTAAGAT-CCGAAGGCATT
1 CGGGCTAAGTACCGAAGGCAATTGTGCGAGA-T-ACTATAACCGGGCTAAG-TCCCGAAGGCATT
8503 TGTGCGAGATACTAATT
63 TGTGCGAGATACTAATT
* *
8520 CCGGGCTAAG-ACCGAAGGCATTTGTGCGAGATACTA-ATTCCGGGCTAAG-CCCGAAGGCATTT
1 -CGGGCTAAGTACCGAAGGCAATTGTGCGAGATACTATA-ACCGGGCTAAGTCCCGAAGGCATTT
*
8582 GTGCGAGTTACTGAATT
64 GTGCGAGATACT-AATT
* * * *
8599 CGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAACCGGGCTATGTCCCGAAGGCATTTG
1 CGGGCTAAGTACCGAAGGCAATTGTGCGAGATACTATAACCGGGCTAAGTCCCGAAGGCATTTG
8663 AACGAGTAGC
Statistics
Matches: 123, Mismatches: 11, Indels: 16
0.82 0.07 0.11
Matches are distributed among these distances:
78 32 0.26
79 57 0.46
80 33 0.27
81 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (79 bp):
CGGGCTAAGTACCGAAGGCAATTGTGCGAGATACTATAACCGGGCTAAGTCCCGAAGGCATTTGT
GCGAGATACTAATT
Found at i:8669 original size:40 final size:39
Alignment explanation
Indices: 8439--8662 Score: 240
Period size: 40 Copynumber: 5.6 Consensus size: 39
8429 TTGAATGATG
* * *
8439 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CAT
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAT
* * *
8478 ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAT
* *
8519 TCCGGGCTAAGACCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAT
8558 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTGAAT
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACT-AAT
* *
8598 T-CGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACT-AT
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAT
* *
8636 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAG-CCCGAAGGCATTTG
8663 AACGAGTAGC
Statistics
Matches: 161, Mismatches: 17, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
38 2 0.01
39 69 0.43
40 81 0.50
41 9 0.06
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:8684 original size:79 final size:79
Alignment explanation
Indices: 8492--8695 Score: 188
Period size: 79 Copynumber: 2.6 Consensus size: 79
8482 GGACTAAGAT
** * * *
8492 CCGAAGGCATTTGTGCGAGATACT-AATTCCGGGCTAAGA--CCGAAGGCATTTGTGCGAGATAC
1 CCGAAGGCATTTGAACGAGTTACTGAATTCC-GGTTAA-ATCCCGAAGGCAATTGTGCGAGATAC
*
8554 TAATTCCGGGCTAAGC
64 TAATACCGGGCTAAGC
** * * *
8570 CCGAAGGCATTTGTGCGAGTTACTGAATTCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACT-
1 CCGAAGGCATTTGAACGAGTTACTGAATTCCGGTTAAATCCCGAAGGCAATTGTGCGAGATACTA
*
8634 ATAACCGGGCTATGTC
66 AT-ACCGGGCTAAG-C
*
8650 CCGAAGGCATTTGAACGAG-TAGCT--ATATCCGGTTAAATTCCGAAGG
1 CCGAAGGCATTTGAACGAGTTA-CTGAAT-TCCGGTTAAATCCCGAAGG
8696 TACGTGATTT
Statistics
Matches: 106, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
78 32 0.30
79 54 0.51
80 20 0.19
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGAACGAGTTACTGAATTCCGGTTAAATCCCGAAGGCAATTGTGCGAGATACTA
ATACCGGGCTAAGC
Found at i:10879 original size:30 final size:30
Alignment explanation
Indices: 10838--10894 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
10828 AAAATCATAT
10838 TTTGGCAAAATTACAATTTTGCCCCTAAAC
1 TTTGGCAAAATTACAATTTTGCCCCTAAAC
* *
10868 TTTGTCAAAATTACATTTTTGCCCCTA
1 TTTGGCAAAATTACAATTTTGCCCCTA
10895 CACTCGTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.30, C:0.23, G:0.09, T:0.39
Consensus pattern (30 bp):
TTTGGCAAAATTACAATTTTGCCCCTAAAC
Found at i:18883 original size:28 final size:28
Alignment explanation
Indices: 18851--18978 Score: 177
Period size: 29 Copynumber: 4.5 Consensus size: 28
18841 ATAGTAAGTC
*
18851 CGCACACTTAGTGTTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
18879 CGCACACTTAGTGCTTACATAATCAAACT
1 CGCACACTTAGTGC-TATATAATCAAACT
18908 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * *
18936 TGCACACTTAGTGCTAT-TCAATTTAAACC
1 CGCACACTTAGTGCTATAT-AA-TCAAACT
18965 CGCACACTTAGTGC
1 CGCACACTTAGTGC
18979 CAATCTCATG
Statistics
Matches: 90, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
27 1 0.01
28 44 0.49
29 45 0.50
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:18941 original size:57 final size:57
Alignment explanation
Indices: 18850--18978 Score: 188
Period size: 57 Copynumber: 2.3 Consensus size: 57
18840 TATAGTAAGT
*
18850 CCGCACACTTAGTGTTATATAATCAAACTCGCACACTTAGTGCT-TACATAATCAAAC
1 CCGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATACA-AATCAAAC
* * * * *
18907 TCGCACACTTAGTGCTATATAATCAAACTTGCACACTTAGTGCTATTCAATTTAAAC
1 CCGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATACAAATCAAAC
18964 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
18979 CAATCTCATG
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
57 61 0.95
58 3 0.05
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29
Consensus pattern (57 bp):
CCGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATACAAATCAAAC
Found at i:31518 original size:20 final size:20
Alignment explanation
Indices: 31477--31521 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
31467 TGAAAGTGCT
*
31477 AAAGAAAAGAAAATCGAGAA
1 AAAGAAAAGAAAATCGAAAA
*
31497 AAAGAAAGGAAAAAT-GAAAA
1 AAAGAAAAG-AAAATCGAAAA
31517 AAAGA
1 AAAGA
31522 GTGAAAAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.73, C:0.02, G:0.20, T:0.04
Consensus pattern (20 bp):
AAAGAAAAGAAAATCGAAAA
Found at i:31556 original size:14 final size:14
Alignment explanation
Indices: 31510--31561 Score: 56
Period size: 13 Copynumber: 3.9 Consensus size: 14
31500 GAAAGGAAAA
31510 ATGAAAA-AAAGAG
1 ATGAAAAGAAAGAG
** *
31523 -TGAAAAGATCGTG
1 ATGAAAAGAAAGAG
31536 A-GAAAAGAAAGAG
1 ATGAAAAGAAAGAG
31549 ATGAAAAGAAAGA
1 ATGAAAAGAAAGA
31562 AAAAGAGTGT
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
12 6 0.20
13 13 0.43
14 11 0.37
ACGTcount: A:0.62, C:0.02, G:0.27, T:0.10
Consensus pattern (14 bp):
ATGAAAAGAAAGAG
Found at i:33704 original size:48 final size:48
Alignment explanation
Indices: 33633--33757 Score: 198
Period size: 48 Copynumber: 2.6 Consensus size: 48
33623 AAGTGCAAAC
*
33633 ATCATGGCCTGAAGCCAACTCAATGTATCTCGCACCCGAAGTACCAAT
1 ATCATGGCCTGAAGCCAACTCAATGTATCTCGAACCCGAAGTACCAAT
* * *
33681 ATCATGG-CTCGAAGCCAACTCAATGTATGTCGAACTCGAAGTGCCAAT
1 ATCATGGCCT-GAAGCCAACTCAATGTATCTCGAACCCGAAGTACCAAT
33729 ATCATGGCCTGAAGCCAACTCAATGTATC
1 ATCATGGCCTGAAGCCAACTCAATGTATC
33758 ACATATACTG
Statistics
Matches: 70, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
47 2 0.03
48 66 0.94
49 2 0.03
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.22
Consensus pattern (48 bp):
ATCATGGCCTGAAGCCAACTCAATGTATCTCGAACCCGAAGTACCAAT
Found at i:42634 original size:5 final size:6
Alignment explanation
Indices: 42617--42644 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
42607 TGAGGATTAA
42617 GTGGGG GTGGGG GTGGGG GTGGGG GTGG
1 GTGGGG GTGGGG GTGGGG GTGGGG GTGG
42645 AGGTTTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.82, T:0.18
Consensus pattern (6 bp):
GTGGGG
Found at i:44026 original size:12 final size:12
Alignment explanation
Indices: 44009--44033 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43999 CAAAATCCCT
44009 ATACACATTTAC
1 ATACACATTTAC
44021 ATACACATTTAC
1 ATACACATTTAC
44033 A
1 A
44034 ATTTCAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (12 bp):
ATACACATTTAC
Found at i:47351 original size:27 final size:27
Alignment explanation
Indices: 47293--47352 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 27
47283 ATACATCTCA
*
47293 TAGGGGCATATCAGTCATTTTACCATG
1 TAGGGGCATATCAGTCATTTTACAATG
*
47320 TAGGGGCATTTCAGTCATTTTATCAATG
1 TAGGGGCATATCAGTCATTTTA-CAATG
47348 -AGGGG
1 TAGGGG
47353 GTCTAGGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 26 0.87
28 4 0.13
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33
Consensus pattern (27 bp):
TAGGGGCATATCAGTCATTTTACAATG
Found at i:49746 original size:79 final size:82
Alignment explanation
Indices: 49635--49819 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 82
49625 GCTACTCGTT
* * *
49635 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
49698 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
49715 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
49778 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
49795 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
49820 CATCATTCAA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.59
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:49819 original size:40 final size:40
Alignment explanation
Indices: 49616--49819 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
49606 CGGAATTTAA
** *
49616 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
49656 CCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
49696 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
49735 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
49775 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
49815 CCGGA
1 CCGGA
49820 CATCATTCAA
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.24
40 92 0.66
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Done.