Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1247
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: 25904
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.31
Found at i:1728 original size:40 final size:40
Alignment explanation
Indices: 1644--1866 Score: 287
Period size: 40 Copynumber: 5.7 Consensus size: 40
1634 TTGAATGATG
* * * *
1644 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
1684 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
1724 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
1763 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
1803 TCCGGGTTAAGTCCCGAAGGCA-TT-TGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
1842 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
1867 AACGAGTAGC
Statistics
Matches: 163, Mismatches: 13, Indels: 14
0.86 0.07 0.07
Matches are distributed among these distances:
38 31 0.19
39 41 0.25
40 83 0.51
41 8 0.05
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:1780 original size:79 final size:80
Alignment explanation
Indices: 1644--1866 Score: 287
Period size: 79 Copynumber: 2.8 Consensus size: 80
1634 TTGAATGATG
* * * * *
1644 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGCTAAG-TCCCGAAGGCAT
*
1707 TTGTGCGAGATACTAAT
64 TTGTGCGAGATACTAAA
*
1724 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTT
*
1788 GTGCGAGTTACTAAA
66 GTGCGAGATACTAAA
* *
1803 TCCGGGTTAAGTCCCGAAGGCA-TT-TGCGAGTTACTATAA-CCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGCTAAGTCCCGAAGGCATT
1865 TG
65 TG
1867 AACGAGTAGC
Statistics
Matches: 128, Mismatches: 11, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
78 36 0.28
79 64 0.50
80 28 0.22
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTT
GTGCGAGATACTAAA
Found at i:9832 original size:40 final size:40
Alignment explanation
Indices: 9594--9818 Score: 305
Period size: 40 Copynumber: 5.7 Consensus size: 40
9584 TTGAATGATG
* * * *
9594 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
9634 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
9674 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
9713 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
9753 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
9794 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
9819 AACGAGTAGC
Statistics
Matches: 167, Mismatches: 13, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
39 35 0.21
40 122 0.73
41 10 0.06
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:9840 original size:119 final size:119
Alignment explanation
Indices: 9594--9851 Score: 301
Period size: 119 Copynumber: 2.2 Consensus size: 119
9584 TTGAATGATG
* *
9594 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
* **
9659 GTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
66 GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAAA
* * * **
9713 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* * *
9776 TTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATA
64 TTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-CTAAA
* *
9833 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
9852 TACGTGATTT
Statistics
Matches: 119, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
118 3 0.03
119 84 0.71
120 32 0.27
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAAA
Found at i:13004 original size:40 final size:40
Alignment explanation
Indices: 12912--13163 Score: 385
Period size: 39 Copynumber: 6.5 Consensus size: 40
12902 GGATTGATAC
* *
12912 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-AT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
12951 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
12991 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
13030 CCGGGCTAAGTCCCGAAGGCATTTGTGC-AGTTACTATA-
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
13068 CC-GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
13107 CCGGGCTAAGTCCCGAAGGCATTTGAGCTAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
*
13147 CC-GGCTAAAT-CCGAAGG
1 CCGGGCTAAGTCCCGAAGG
13164 TACTTGGTTT
Statistics
Matches: 202, Mismatches: 6, Indels: 11
0.92 0.03 0.05
Matches are distributed among these distances:
37 25 0.12
38 29 0.14
39 74 0.37
40 74 0.37
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:13145 original size:116 final size:119
Alignment explanation
Indices: 12912--13163 Score: 392
Period size: 116 Copynumber: 2.2 Consensus size: 119
12902 GGATTGATAC
12912 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATCCGGGCTAAGTCCCGAAGGCATTTGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATCCGGGCTAAGTCCCGAAGGCATTTGT
* *
12977 GCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-
66 GCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTTACTATAT
*
13030 CCGGGCTAAGTCCCGAAGGCATTTGTGC-AGTTACT-ATACC-GGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAAT-CCGGGCTAAGTCCCGAAGGCATTTG
*
13092 TGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTGAGCTAG-TAGCTATAT
65 TGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTTA-CTATAT
*
13147 CC-GGCTAAAT-CCGAAGG
1 CCGGGCTAAGTCCCGAAGG
13164 TACTTGGTTT
Statistics
Matches: 126, Mismatches: 5, Indels: 9
0.90 0.04 0.06
Matches are distributed among these distances:
115 9 0.07
116 79 0.63
117 10 0.08
118 28 0.22
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.25
Consensus pattern (119 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATCCGGGCTAAGTCCCGAAGGCATTTGT
GCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTTACTATAT
Found at i:19547 original size:11 final size:11
Alignment explanation
Indices: 19531--19555 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
19521 GTGACTAGAC
19531 AAAAAAAAAAG
1 AAAAAAAAAAG
19542 AAAAAAAAAAG
1 AAAAAAAAAAG
19553 AAA
1 AAA
19556 GTGTGTTCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:20304 original size:85 final size:85
Alignment explanation
Indices: 20194--20372 Score: 349
Period size: 85 Copynumber: 2.1 Consensus size: 85
20184 GGCCGGCCAT
20194 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAC
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAC
20259 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
*
20279 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAC
20344 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
20364 GAGCATGGG
1 GAGCATGGG
20373 CAATAAAATA
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 93 1.00
ACGTcount: A:0.38, C:0.09, G:0.27, T:0.26
Consensus pattern (85 bp):
GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAC
GTAAGGATTAATAAAATAAA
Found at i:21637 original size:39 final size:40
Alignment explanation
Indices: 21536--21719 Score: 225
Period size: 40 Copynumber: 4.7 Consensus size: 40
21526 TCGAATGATG
* * *
21536 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACAATA
*
21576 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAT-
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTAC-AATA
*
21616 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACAA-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACAATA
* *
21654 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACAATA
* *
21694 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
21720 AACGAGTAGC
Statistics
Matches: 125, Mismatches: 12, Indels: 14
0.83 0.08 0.09
Matches are distributed among these distances:
38 12 0.10
39 46 0.37
40 57 0.46
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACAATA
Found at i:21671 original size:78 final size:81
Alignment explanation
Indices: 21536--21717 Score: 232
Period size: 78 Copynumber: 2.3 Consensus size: 81
21526 TCGAATGATG
* *
21536 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
21600 TGTGCGAGTTACTA-A
66 TGTGCGAGTTACTATA
* * **
21615 TTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTA-CAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
21676 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGTTACTATA
* *
21694 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
21718 TGAACGAGTA
Statistics
Matches: 90, Mismatches: 8, Indels: 9
0.84 0.07 0.08
Matches are distributed among these distances:
77 1 0.01
78 46 0.51
79 26 0.29
80 17 0.19
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGTTACTATA
Found at i:24143 original size:40 final size:40
Alignment explanation
Indices: 24088--24335 Score: 351
Period size: 40 Copynumber: 6.2 Consensus size: 40
24078 GGATTGATAC
*
24088 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTACTATAA
*
24127 TCCGGGCTAAGTCCCGAAGGCATTTGTG-TGAGTTACTATAT
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGTTACTATAA
* *
24168 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATCA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTACTATAA
*
24208 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTACTATCA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTACTATAA
* * *
24248 CCAGGCTAAGTCCCAAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTACTATAA
* *
24288 CCGGGCTAAGTCCCGAAGGCATTTGAGCTAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTA-CTATAA
24328 CC-GGCTAA
1 CCGGGCTAA
24336 ACTCCAAGGT
Statistics
Matches: 189, Mismatches: 15, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
39 9 0.05
40 179 0.95
41 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTACTATAA
Done.