Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1022
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: 35321
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Found at i:563 original size:40 final size:40
Alignment explanation
Indices: 474--657 Score: 184
Period size: 40 Copynumber: 4.7 Consensus size: 40
464 TTCGAATATG
* * *
474 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
* *
513 AT-CGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
553 TCCGGGCTAAG--CCGAAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCG-AAGGCATTTGTGCGAGTTACTAAT
*
592 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
631 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
658 AACGAGTAGC
Statistics
Matches: 121, Mismatches: 15, Indels: 16
0.80 0.10 0.11
Matches are distributed among these distances:
38 3 0.02
39 53 0.44
40 62 0.51
41 3 0.02
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:679 original size:79 final size:79
Alignment explanation
Indices: 526--680 Score: 183
Period size: 79 Copynumber: 2.0 Consensus size: 79
516 GGACTAAGAT
* **
526 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCGAAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCGAAAGGCATTGGAACGAGTTACTAA
591 ATCCGGGTTAAGTC
66 ATCCGGGTTAAGTC
* * *
605 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCG-AAGGCATTTGAACGAG-TAG
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG--CCGAAAGGCATTGGAACGAGTTA-
*
667 CTATATCC-GGTTAA
62 CTAAATCCGGGTTAA
681 ATTCCAAGGT
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
78 2 0.03
79 40 0.62
80 20 0.31
81 3 0.05
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCGAAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAGTC
Found at i:7221 original size:85 final size:85
Alignment explanation
Indices: 7078--7256 Score: 358
Period size: 85 Copynumber: 2.1 Consensus size: 85
7068 GGCCGGCCAT
7078 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
7143 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
7163 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
7228 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
7248 GAGCATGGG
1 GAGCATGGG
7257 CAATAAAATA
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 94 1.00
ACGTcount: A:0.38, C:0.08, G:0.27, T:0.26
Consensus pattern (85 bp):
GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
GTAAGGATTAATAAAATAAA
Found at i:8615 original size:40 final size:40
Alignment explanation
Indices: 8424--8608 Score: 209
Period size: 40 Copynumber: 4.7 Consensus size: 40
8414 TCGAATGATG
* * *
8424 TCCGGGCTAAGTCCCGAAGG-ATTTGTG-GTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCG--AGTTACTAAA
* * *
8464 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
8504 TCCAGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
8543 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
8584 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
8609 AACGAGTAGC
Statistics
Matches: 123, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
39 33 0.27
40 79 0.64
41 10 0.08
42 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:8630 original size:79 final size:79
Alignment explanation
Indices: 8477--8631 Score: 190
Period size: 79 Copynumber: 2.0 Consensus size: 79
8467 GGACTAAGAT
* **
8477 CCGAAGGCATTTGTGCGAGATACTAATTCCAGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCAGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
8542 ATCCGGGTTAAGTC
66 ATCCGGGTTAAGTC
* * * *
8556 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCAGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
*
8619 TATATCC-GGTTAA
63 TAAATCCGGGTTAA
8632 ATTCCAAAGG
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
78 2 0.03
79 39 0.60
80 24 0.37
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCAGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAGTC
Found at i:10067 original size:39 final size:39
Alignment explanation
Indices: 10023--10186 Score: 152
Period size: 40 Copynumber: 4.2 Consensus size: 39
10013 CCTTCGGAGT
** * *
10023 TTAGCCAGATATAGCCACTAGCTCAAATGCCTTCAGGAC
1 TTAGCCAGATATAGTAACTAGCACAAATGCCTTCGGGAC
* * *
10062 TTAGCCCGGTTATAGTAACTTGCACAAATGCCTTCGGGAC
1 TTAG-CCAGATATAGTAACTAGCACAAATGCCTTCGGGAC
* * * *
10102 TTAGCCCGGTATAATAACTCGCACAAATGCCTTCGGGAC
1 TTAGCCAGATATAGTAACTAGCACAAATGCCTTCGGGAC
* * *
10141 TTAGCCCGGA-ATTAGTAGCTCA-CACAAATGCCTTCAGGAC
1 TTAG-CCAGATA-TAGTAACT-AGCACAAATGCCTTCGGGAC
10181 TTAGCC
1 TTAGCC
10187 CAGAATTAGT
Statistics
Matches: 104, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
39 42 0.40
40 62 0.60
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.24
Consensus pattern (39 bp):
TTAGCCAGATATAGTAACTAGCACAAATGCCTTCGGGAC
Found at i:10090 original size:40 final size:39
Alignment explanation
Indices: 10046--10207 Score: 207
Period size: 40 Copynumber: 4.1 Consensus size: 39
10036 GCCACTAGCT
*
10046 CAAATGCCTTCAGGACTTAGCCCGGTTATAGTAACTTGCA
1 CAAATGCCTTCAGGACTTAGCCCGG-TATAGTAACTCGCA
* *
10086 CAAATGCCTTCGGGACTTAGCCCGGTATAATAACTCGCA
1 CAAATGCCTTCAGGACTTAGCCCGGTATAGTAACTCGCA
* * * *
10125 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAGCTCACA
1 CAAATGCCTTCAGGACTTAGCCCGGTA-TAGTAACTCGCA
* * *
10165 CAAATGCCTTCAGGACTTAGCCCAGAATTAGTAGCTCGCA
1 CAAATGCCTTCAGGACTTAGCCCGGTA-TAGTAACTCGCA
10205 CAA
1 CAA
10208 CTTAGCCCAG
Statistics
Matches: 111, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
39 38 0.34
40 73 0.66
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.23
Consensus pattern (39 bp):
CAAATGCCTTCAGGACTTAGCCCGGTATAGTAACTCGCA
Found at i:10210 original size:28 final size:28
Alignment explanation
Indices: 10179--10235 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
10169 TGCCTTCAGG
10179 ACTTAGCCCAGAATTAGTAGCTCGCACA
1 ACTTAGCCCAGAATTAGTAGCTCGCACA
10207 ACTTAGCCCAGAATTAGTAGCTCGCACA
1 ACTTAGCCCAGAATTAGTAGCTCGCACA
10235 A
1 A
10236 ATGCCTTCGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.21
Consensus pattern (28 bp):
ACTTAGCCCAGAATTAGTAGCTCGCACA
Found at i:10277 original size:40 final size:40
Alignment explanation
Indices: 10207--10295 Score: 110
Period size: 40 Copynumber: 2.2 Consensus size: 40
10197 AGCTCGCACA
* *
10207 ACTTAGCCCAGAATTAGTAGCTCGCACAAATGCCT-TCGGG
1 ACTTAGCCCAGAATTAGCAGCTAGCACAAAT-CCTCTCGGG
* *
10247 ACTTAGCCCAGAATTAGCCA-CTAGCTCAAATTCTCTCGGG
1 ACTTAGCCCAGAATTAG-CAGCTAGCACAAATCCTCTCGGG
10287 ACTTAGCCC
1 ACTTAGCCC
10296 GGTTATCATC
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
39 2 0.05
40 40 0.93
41 1 0.02
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.24
Consensus pattern (40 bp):
ACTTAGCCCAGAATTAGCAGCTAGCACAAATCCTCTCGGG
Found at i:20495 original size:24 final size:23
Alignment explanation
Indices: 20462--20519 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 23
20452 AGTTGAAAAG
20462 TATAA-AATAAAATAAATAATGATA
1 TATAATAATAAAAT-AAT-ATGATA
*
20486 -ATAATAATAAAATGATATGATA
1 TATAATAATAAAATAATATGATA
20508 TATATATAATAA
1 TATA-ATAATAA
20520 TGTTTGATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
22 6 0.20
23 9 0.30
24 15 0.50
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (23 bp):
TATAATAATAAAATAATATGATA
Found at i:20937 original size:48 final size:48
Alignment explanation
Indices: 20790--20946 Score: 273
Period size: 49 Copynumber: 3.2 Consensus size: 48
20780 CTTACTTTGA
20790 GAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 GAATGTGAAAGTGTATATATATGTGAT-AGGCCTAATGGCCGATGTGAT
20837 GAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCGATGTGAT
1 GAATGTGAAAGTGTATATATATGTGATA-GGCCTAATGGCCGATGTGAT
20886 GAATGTGAAAGTGTATATATATGTGATAGGCCTAATGGCCGATGTGAT
1 GAATGTGAAAGTGTATATATATGTGATAGGCCTAATGGCCGATGTGAT
20934 GAATGTGATAAGT
1 GAATGTGA-AAGT
20947 CCCGAAGGGC
Statistics
Matches: 106, Mismatches: 0, Indels: 6
0.95 0.00 0.05
Matches are distributed among these distances:
47 13 0.12
48 29 0.27
49 64 0.60
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.31
Consensus pattern (48 bp):
GAATGTGAAAGTGTATATATATGTGATAGGCCTAATGGCCGATGTGAT
Found at i:21139 original size:36 final size:37
Alignment explanation
Indices: 21064--21141 Score: 113
Period size: 36 Copynumber: 2.1 Consensus size: 37
21054 CCGAGCTCTA
* * *
21064 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
21101 AAGACCCGATAACTTCGTGT-GAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
21137 AAGAC
1 AAGAC
21142 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 19 0.51
37 18 0.49
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:22682 original size:40 final size:40
Alignment explanation
Indices: 22500--22675 Score: 198
Period size: 40 Copynumber: 4.4 Consensus size: 40
22490 GGGGTGTTAC
* * * *
22500 AGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTA
1 AGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGACTA
* * * *
22540 AGAT-CCGAAGGCATTTGTGCGAGATACTAATTTCGGGCTA
1 AG-TCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTA
**
22580 AG-CCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTA
1 AGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTA
22619 AGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGACTA
1 AGTCCCGAAGGCATTTGTGCGAGTTACTA-AATCCGGACTA
*
22659 TGTCCCGAAGGCATTTG
1 AGTCCCGAAGGCATTTG
22676 AACGAGTAGC
Statistics
Matches: 116, Mismatches: 15, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
39 34 0.29
40 72 0.62
41 10 0.09
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
AGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTA
Found at i:22697 original size:79 final size:79
Alignment explanation
Indices: 22544--22708 Score: 192
Period size: 79 Copynumber: 2.1 Consensus size: 79
22534 GGACTAAGAT
** * **
22544 CCGAAGGCATTTGTGCGAGATACTAATTTCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGACTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
22609 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
22623 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGACTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGACTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
22686 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
22702 CCGAAGG
1 CCGAAGG
22709 TACGTGATTT
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
78 2 0.03
79 46 0.63
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGACTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:30798 original size:79 final size:81
Alignment explanation
Indices: 30662--30846 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
30652 TTGAATGATG
*
30662 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
30726 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
30741 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
30803 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
30821 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
30847 AACGAGTAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:30860 original size:40 final size:40
Alignment explanation
Indices: 30663--30846 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
30653 TGAATGATGT
* * * *
30663 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
30703 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
30743 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
30781 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
30822 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
30847 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:30868 original size:79 final size:79
Alignment explanation
Indices: 30715--30879 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
30705 GGACTAAGAT
* **
30715 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
30780 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
30794 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
30857 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
30873 CCGAAGG
1 CCGAAGG
30880 TACGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.64
80 25 0.33
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Done.