Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010469.1 Corchorus capsularis cultivar CVL-1 contig10490, whole genome shotgun sequence
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: 139682
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:1005 original size:18 final size:18
Alignment explanation
Indices: 982--1018 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
972 GAAATCAATG
*
982 GATGTTAATAGCATTATA
1 GATGTTAATAACATTATA
1000 GATGTTAATAACATTATA
1 GATGTTAATAACATTATA
1018 G
1 G
1019 GGGAGCCAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.05, G:0.16, T:0.38
Consensus pattern (18 bp):
GATGTTAATAACATTATA
Found at i:2263 original size:6 final size:7
Alignment explanation
Indices: 2244--2272 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
2234 AATCCGTGGG
2244 AGAAAAA
1 AGAAAAA
2251 AGAAAAA
1 AGAAAAA
2258 AGAAAAA
1 AGAAAAA
2265 AGAAAAA
1 AGAAAAA
2272 A
1 A
2273 AACCTAGCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (7 bp):
AGAAAAA
Found at i:9483 original size:30 final size:30
Alignment explanation
Indices: 9431--9489 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
9421 TCTGGATGAA
*
9431 CGGAGGAGTTTCAGTCTAGGTCTAGGTCAC
1 CGGAGGAGTTTCAGACTAGGTCTAGGTCAC
* * *
9461 CGGAGGAGTTTCAGAGTCGGTCTGGGTCA
1 CGGAGGAGTTTCAGACTAGGTCTAGGTCA
9490 TTGAGCAGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.19, C:0.19, G:0.37, T:0.25
Consensus pattern (30 bp):
CGGAGGAGTTTCAGACTAGGTCTAGGTCAC
Found at i:10652 original size:23 final size:24
Alignment explanation
Indices: 10626--10673 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
10616 ATTTTATTTC
* * *
10626 TTTTATTTTTTAATA-TTTTTAAA
1 TTTTACTTATTAATACTCTTTAAA
10649 TTTTACTTATTAATACTCTTTAAA
1 TTTTACTTATTAATACTCTTTAAA
10673 T
1 T
10674 ATGATCTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.62
Consensus pattern (24 bp):
TTTTACTTATTAATACTCTTTAAA
Found at i:17306 original size:24 final size:24
Alignment explanation
Indices: 17274--17353 Score: 86
Period size: 24 Copynumber: 3.7 Consensus size: 24
17264 GGAAGGAGAC
17274 TTAAACACATTATCAGCAACCAAG
1 TTAAACACATTATCAGCAACCAAG
*
17298 TTAAACACATTATCA--TA-C---
1 TTAAACACATTATCAGCAACCAAG
*
17316 TTAAATA-A-TATCAGCAACCAAG
1 TTAAACACATTATCAGCAACCAAG
17338 TTAAACACATTATCAG
1 TTAAACACATTATCAG
17354 AATGCATCTT
Statistics
Matches: 44, Mismatches: 4, Indels: 16
0.69 0.06 0.25
Matches are distributed among these distances:
16 5 0.11
17 1 0.02
18 7 0.16
19 1 0.02
21 1 0.02
22 7 0.16
23 1 0.02
24 21 0.48
ACGTcount: A:0.46, C:0.21, G:0.06, T:0.26
Consensus pattern (24 bp):
TTAAACACATTATCAGCAACCAAG
Found at i:19735 original size:2 final size:2
Alignment explanation
Indices: 19728--19757 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
19718 AATATTTTGT
19728 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19758 CACGTTGCGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:22174 original size:24 final size:24
Alignment explanation
Indices: 22116--22165 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
22106 TCTAATTAAA
22116 ATATATTTTTATTTTATCGTAATC
1 ATATATTTTTATTTTATCGTAATC
22140 ATATATTTTTATTTTATCGTAATC
1 ATATATTTTTATTTTATCGTAATC
22164 AT
1 AT
22166 TTCATTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.30, C:0.08, G:0.04, T:0.58
Consensus pattern (24 bp):
ATATATTTTTATTTTATCGTAATC
Found at i:22219 original size:2 final size:2
Alignment explanation
Indices: 22212--22245 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
22202 TTAAGGTTAA
*
22212 AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
22246 TAAAATTTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25518 original size:16 final size:16
Alignment explanation
Indices: 25497--25578 Score: 51
Period size: 16 Copynumber: 5.2 Consensus size: 16
25487 TTTGAGTCAA
25497 GTTAATTCAGGTTTGG
1 GTTAATTCAGGTTTGG
* * *
25513 GTTAATT-TGGGTTAG
1 GTTAATTCAGGTTTGG
* *
25528 GTTAATTCGGGTTCGG
1 GTTAATTCAGGTTTGG
* * *
25544 GTTGAATTTA-GATTAG
1 GTT-AATTCAGGTTTGG
* *
25560 GTTAATTCGGGTTCGG
1 GTTAATTCAGGTTTGG
25576 GTT
1 GTT
25579 CTGTTTGGGT
Statistics
Matches: 46, Mismatches: 17, Indels: 6
0.67 0.25 0.09
Matches are distributed among these distances:
15 16 0.35
16 26 0.57
17 4 0.09
ACGTcount: A:0.18, C:0.06, G:0.33, T:0.43
Consensus pattern (16 bp):
GTTAATTCAGGTTTGG
Found at i:25520 original size:31 final size:32
Alignment explanation
Indices: 25475--25578 Score: 140
Period size: 32 Copynumber: 3.3 Consensus size: 32
25465 CTTGAGTCGA
* * *
25475 GTTCGGGTTGAATTTGAGTCAAGTTAATTCAG
1 GTTCGGGTTGAATTTGAGTTAGGTTAATTCGG
* *
25507 GTTTGGGTT-AATTTGGGTTAGGTTAATTCGG
1 GTTCGGGTTGAATTTGAGTTAGGTTAATTCGG
25538 GTTCGGGTTGAATTT-AGATTAGGTTAATTCGG
1 GTTCGGGTTGAATTTGAG-TTAGGTTAATTCGG
25570 GTTCGGGTT
1 GTTCGGGTT
25579 CTGTTTGGGT
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
31 27 0.43
32 36 0.57
ACGTcount: A:0.19, C:0.07, G:0.33, T:0.41
Consensus pattern (32 bp):
GTTCGGGTTGAATTTGAGTTAGGTTAATTCGG
Found at i:25532 original size:15 final size:15
Alignment explanation
Indices: 25497--25572 Score: 62
Period size: 15 Copynumber: 4.9 Consensus size: 15
25487 TTTGAGTCAA
* *
25497 GTTAATTCAGGTTTGG
1 GTTAATTC-GGGTTAG
*
25513 GTTAATTTGGGTTAG
1 GTTAATTCGGGTTAG
*
25528 GTTAATTCGGGTTCGG
1 GTTAATTCGGGTT-AG
** *
25544 GTTGAATTTAGATTAG
1 GTT-AATTCGGGTTAG
25560 GTTAATTCGGGTT
1 GTTAATTCGGGTT
25573 CGGGTTCTGT
Statistics
Matches: 46, Mismatches: 12, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
15 24 0.52
16 15 0.33
17 7 0.15
ACGTcount: A:0.20, C:0.05, G:0.32, T:0.43
Consensus pattern (15 bp):
GTTAATTCGGGTTAG
Found at i:25745 original size:16 final size:16
Alignment explanation
Indices: 25726--25780 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
25716 TTTTCATAAA
25726 TTTTCGGATTCAGGTT
1 TTTTCGGATTCAGGTT
* *
25742 TTTTCGGGATTGA-GCT
1 TTTTC-GGATTCAGGTT
* *
25758 TTTTCGGGTTCGGGTT
1 TTTTCGGATTCAGGTT
25774 TTTTCGG
1 TTTTCGG
25781 GTTTGAACTT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
15 4 0.13
16 21 0.68
17 6 0.19
ACGTcount: A:0.07, C:0.13, G:0.31, T:0.49
Consensus pattern (16 bp):
TTTTCGGATTCAGGTT
Found at i:25774 original size:32 final size:31
Alignment explanation
Indices: 25726--25846 Score: 145
Period size: 32 Copynumber: 3.8 Consensus size: 31
25716 TTTTCATAAA
* *
25726 TTTTCGGATTCAGGTTTTTTCGGGATTGAGCT
1 TTTTCGGGTTCGGGTTTTTTCGGG-TTGAGCT
*
25758 TTTTCGGGTTCGGGTTTTTTCGGGTTTGAACT
1 TTTTCGGGTTCGGGTTTTTTCGGG-TTGAGCT
* *
25790 TTTTCGGGCTCGTG-TTTTTCGGGTCTGAGCT
1 TTTTCGGGTTCGGGTTTTTTCGGGT-TGAGCT
* *
25821 TTTTCGAGTTCGGGTTTTTCCGGGTT
1 TTTTCGGGTTCGGGTTTTTTCGGGTT
25847 CAGATTCATG
Statistics
Matches: 76, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
30 1 0.01
31 26 0.34
32 49 0.64
ACGTcount: A:0.07, C:0.15, G:0.31, T:0.48
Consensus pattern (31 bp):
TTTTCGGGTTCGGGTTTTTTCGGGTTGAGCT
Found at i:25781 original size:16 final size:16
Alignment explanation
Indices: 25741--25847 Score: 87
Period size: 16 Copynumber: 6.8 Consensus size: 16
25731 GGATTCAGGT
25741 TTTTTCGGGATT-GAGC
1 TTTTTCGGG-TTCGAGC
* *
25757 TTTTTCGGGTTCGGGT
1 TTTTTCGGGTTCGAGC
* *
25773 TTTTTCGGGTTTGAAC
1 TTTTTCGGGTTCGAGC
* *
25789 TTTTTCGGGCTCGTG-
1 TTTTTCGGGTTCGAGC
25804 TTTTTCGGG-TCTGAGC
1 TTTTTCGGGTTC-GAGC
* *
25820 TTTTTCGAGTTCG-GG
1 TTTTTCGGGTTCGAGC
25835 TTTTTCCGGGTTC
1 TTTTT-CGGGTTC
25848 AGATTCATGT
Statistics
Matches: 72, Mismatches: 14, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
14 2 0.03
15 19 0.26
16 49 0.68
17 2 0.03
ACGTcount: A:0.06, C:0.16, G:0.31, T:0.48
Consensus pattern (16 bp):
TTTTTCGGGTTCGAGC
Found at i:31371 original size:16 final size:16
Alignment explanation
Indices: 31350--31381 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
31340 GCAGAACGCA
31350 TGAACCAAACACTTCT
1 TGAACCAAACACTTCT
31366 TGAACCAAACACTTCT
1 TGAACCAAACACTTCT
31382 GCAGCGTGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.31, G:0.06, T:0.25
Consensus pattern (16 bp):
TGAACCAAACACTTCT
Found at i:40720 original size:12 final size:12
Alignment explanation
Indices: 40703--40743 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
40693 TGTGGCCGAA
40703 TGGCCCGTGCGT
1 TGGCCCGTGCGT
40715 TGGCCCGTGCGT
1 TGGCCCGTGCGT
*
40727 T-GCTCCATGCGT
1 TGGC-CCGTGCGT
40739 TGGCC
1 TGGCC
40744 GGTTGCTCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
11 2 0.08
12 22 0.85
13 2 0.08
ACGTcount: A:0.02, C:0.34, G:0.37, T:0.27
Consensus pattern (12 bp):
TGGCCCGTGCGT
Found at i:47108 original size:16 final size:16
Alignment explanation
Indices: 47072--47108 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
47062 ACCCTTAGCC
47072 TAAAACTAGAGAAAAA
1 TAAAACTAGAGAAAAA
* *
47088 CAAAACTAGAGAAAAG
1 TAAAACTAGAGAAAAA
47104 TAAAA
1 TAAAA
47109 GAAGAGAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.68, C:0.08, G:0.14, T:0.11
Consensus pattern (16 bp):
TAAAACTAGAGAAAAA
Found at i:52022 original size:156 final size:155
Alignment explanation
Indices: 51708--52060 Score: 372
Period size: 156 Copynumber: 2.3 Consensus size: 155
51698 GAGCTTCTCA
* **
51708 CCTCAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATGAGCTGAAA
1 CCTCAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTCAAAAAGCTG-AA
* * ** *
51773 CTTTGCCAAGATACTTATAATATTTCCATAAGGCTATGGAAAAAATTCTAAGTAAAACCGAACTC
65 CTTTGCCAAGAGACTTAGAATATCACCATAAAGCTATGGAAAAAATTCTAAGTAAAACCGAACTC
* * * *
51838 CCCTTGATGGTGAACTAGATTTCTCT
130 CCCTAGATAGAGAACTAGATTTCACT
** *
51864 CCTTGAGTTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTC-CAACAAAGCTG-A
1 CCTCAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTCAA-AAAGCTGAA
* * ** *
51927 -TTTTCCACCGGTAGACTTAGGTTATCACCATAAAGCTATGGGAAAAATTCTAAGTAAAACCGAA
65 CTTTGCCA--AG-AGACTTAGAATATCACCATAAAGCTATGGAAAAAATTCTAAGTAAAACCGAA
* * * * *
51991 CT-CTCTAGCATAGAGAAGTTGGTTTGACT
127 CTCCCCTAG-ATAGAGAACTAGATTTCACT
* * *
52020 CCTCAAACTGTCTTTAATTGAAAAACTAGCATAAGTTTTTC
1 CCTCAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTC
52061 GAACTAAGTC
Statistics
Matches: 161, Mismatches: 31, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
153 6 0.04
154 1 0.01
155 7 0.04
156 147 0.91
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.32
Consensus pattern (155 bp):
CCTCAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTCAAAAAGCTGAAC
TTTGCCAAGAGACTTAGAATATCACCATAAAGCTATGGAAAAAATTCTAAGTAAAACCGAACTCC
CCTAGATAGAGAACTAGATTTCACT
Found at i:61338 original size:10 final size:9
Alignment explanation
Indices: 61322--61348 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
61312 TCTGGTCGAA
61322 ATTTTTTTT
1 ATTTTTTTT
61331 ATTTTTTTT
1 ATTTTTTTT
61340 ATTTTTTTT
1 ATTTTTTTT
61349 GATATTTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (9 bp):
ATTTTTTTT
Found at i:62156 original size:21 final size:21
Alignment explanation
Indices: 62130--62178 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
62120 GCACTGGAGG
* * *
62130 ACATGGGTCGCGAGGCAAACC
1 ACATGGGGCGCCAAGCAAACC
*
62151 ACATGGGGCGCCAAGCATACC
1 ACATGGGGCGCCAAGCAAACC
62172 ACATGGG
1 ACATGGG
62179 CCCCCAGCTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.29, C:0.29, G:0.33, T:0.10
Consensus pattern (21 bp):
ACATGGGGCGCCAAGCAAACC
Found at i:68589 original size:4 final size:4
Alignment explanation
Indices: 68580--68639 Score: 93
Period size: 4 Copynumber: 14.2 Consensus size: 4
68570 TTCTAACGCG
68580 CGTA CGTA CGTAA CGTAA CGTAA CGTA CGTA CGTA CGTA CGTA CGTA CGTA
1 CGTA CGTA CGT-A CGT-A CGT-A CGTA CGTA CGTA CGTA CGTA CGTA CGTA
68631 CGTA CGTA C
1 CGTA CGTA C
68640 TACTACTACT
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
4 41 0.75
5 14 0.25
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.23
Consensus pattern (4 bp):
CGTA
Found at i:69397 original size:21 final size:21
Alignment explanation
Indices: 69373--69426 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
69363 AAATACCACC
69373 CAACACCCACCTCAAATCCTT
1 CAACACCCACCTCAAATCCTT
69394 CAACACCCACCTCAAATCCTT
1 CAACACCCACCTCAAATCCTT
69415 CAACACCCACCT
1 CAACACCCACCT
69427 TCATCCAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.33, C:0.50, G:0.00, T:0.17
Consensus pattern (21 bp):
CAACACCCACCTCAAATCCTT
Found at i:72869 original size:21 final size:21
Alignment explanation
Indices: 72843--72891 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
72833 GCACTGGAGG
*
72843 ACATGGGTCG-CAAGGCAAACC
1 ACATGGGGCGCCAA-GCAAACC
*
72864 ACATGGGGCGCCAAGCATACC
1 ACATGGGGCGCCAAGCAAACC
72885 ACATGGG
1 ACATGGG
72892 CCCCCAGCTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 22 0.88
22 3 0.12
ACGTcount: A:0.31, C:0.29, G:0.31, T:0.10
Consensus pattern (21 bp):
ACATGGGGCGCCAAGCAAACC
Found at i:74722 original size:12 final size:12
Alignment explanation
Indices: 74701--74740 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
74691 GTTGTCGCCG
*
74701 GTTGCCCCATGC
1 GTTGCTCCATGC
*
74713 GTTGCTCCATAC
1 GTTGCTCCATGC
*
74725 GATGCTCCATGC
1 GTTGCTCCATGC
74737 GTTG
1 GTTG
74741 GCCAGTCATG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.12, C:0.33, G:0.25, T:0.30
Consensus pattern (12 bp):
GTTGCTCCATGC
Found at i:84141 original size:17 final size:17
Alignment explanation
Indices: 84103--84135 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
84093 TTCATAGTAC
84103 CTAGGTAGTATGAGGTA
1 CTAGGTAGTATGAGGTA
84120 CTAGGTAGTATGAGGT
1 CTAGGTAGTATGAGGT
84136 GATAGGCTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.27, C:0.06, G:0.36, T:0.30
Consensus pattern (17 bp):
CTAGGTAGTATGAGGTA
Found at i:84691 original size:156 final size:156
Alignment explanation
Indices: 84491--84851 Score: 392
Period size: 156 Copynumber: 2.3 Consensus size: 156
84481 CTTCTCACCT
* * *
84491 CAAACTGTCCTTAAACGAAAAACGAGCATAAGTTTTTCATTCTAAGTCTAAATG-AGCTGAAACT
1 CAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTAAACGAAGCTGAAACT
** *
84555 TCACCAAGGT-ACTTAGAATATTTCCAT-AAGACTATGAAAAAAATTCTATGTAAAACCGAACTC
66 TCACC-A-GTAACTTAGAATATCACCATAAAG-CTATGAAAAAAATTCTAAGTAAAACCGAACT-
* * * *
84618 CCCTTG-ATGGTGAACTAGGTTTGTCTCCC
127 CCCTAGCATAGAGAACTAGGTTTGACTCCC
* ** * * ***
84647 TAAGTTGTCTTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTC-CAACGAAGCTGATTTT
1 CAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTAAACGAAGCTGAAACT
* ** *
84711 TCACCAGTAGACTTAGATTATCACCATAAAGCTATGGGAAAAATTCTAAGTAAAACCGAACTCTC
66 TCACCAGTA-ACTTAGAATATCACCATAAAGCTATGAAAAAAATTCTAAGTAAAACCGAACTCCC
* *
84776 TAGCATAGAGAAGTTGGTTTGACTCCC
130 TAGCATAGAGAACTAGGTTTGACTCCC
* *
84803 CAAACTGTCCTTAACTGAAAAACTA-CGATAAGTTTTTCATACTAAGTCT
1 CAAACTGTCCTTAAATGAAAAACTAGC-ATAAGTTTTTCATTCTAAGTCT
84852 GTTTGAGATG
Statistics
Matches: 168, Mismatches: 30, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
154 2 0.01
155 9 0.05
156 154 0.92
157 3 0.02
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (156 bp):
CAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTAAACGAAGCTGAAACT
TCACCAGTAACTTAGAATATCACCATAAAGCTATGAAAAAAATTCTAAGTAAAACCGAACTCCCT
AGCATAGAGAACTAGGTTTGACTCCC
Found at i:86503 original size:23 final size:23
Alignment explanation
Indices: 86446--86508 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 23
86436 AATTAAAATT
86446 AAAAACG-AATTTTTTTTATAAC
1 AAAAACGCAATTTTTTTTATAAC
** *
86468 GCAAACCCTAATTTTTTTTATAGA-
1 AAAAACGC-AATTTTTTTTATA-AC
86492 AAAAACGCAATTTTTTT
1 AAAAACGCAATTTTTTT
86509 AGAAAAAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
22 4 0.12
23 9 0.28
24 18 0.56
25 1 0.03
ACGTcount: A:0.40, C:0.13, G:0.06, T:0.41
Consensus pattern (23 bp):
AAAAACGCAATTTTTTTTATAAC
Found at i:103373 original size:13 final size:13
Alignment explanation
Indices: 103351--103385 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
103341 ATAATTATTG
*
103351 TTTGCATTATTAA
1 TTTGCTTTATTAA
103364 TTTGCTTTATTAA
1 TTTGCTTTATTAA
*
103377 TCTGCTTTA
1 TTTGCTTTA
103386 GATTTAGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.23, C:0.11, G:0.09, T:0.57
Consensus pattern (13 bp):
TTTGCTTTATTAA
Found at i:107146 original size:17 final size:17
Alignment explanation
Indices: 107126--107159 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
107116 ATGGTACCAA
107126 GTAGCATGAGGTACTAG
1 GTAGCATGAGGTACTAG
*
107143 GTAGCATGAGGTGCTAG
1 GTAGCATGAGGTACTAG
107160 ACTGCATCTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.12, G:0.38, T:0.24
Consensus pattern (17 bp):
GTAGCATGAGGTACTAG
Found at i:117252 original size:64 final size:64
Alignment explanation
Indices: 117169--117297 Score: 197
Period size: 64 Copynumber: 2.0 Consensus size: 64
117159 ACCCATCAGC
* **
117169 AACGTTAGTACAAGATGAGTACTTTCATGCCAGAGCAGGTTACGC-ATTCTTTAGGAGTTTCTTT
1 AACGTTAGTACAAGATGAGTACTTCCATGCCAGAGCAGGTTACGCTA-TCTTTACCAGTTTCTTT
* *
117233 AACGTTGGTTCAAGATGAGTACTTCCATGCCAGAGCAGGTTACGCTATCTTTACCAGTTTCTTT
1 AACGTTAGTACAAGATGAGTACTTCCATGCCAGAGCAGGTTACGCTATCTTTACCAGTTTCTTT
117297 A
1 A
117298 TGGCTGTTGT
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
64 58 0.98
65 1 0.02
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (64 bp):
AACGTTAGTACAAGATGAGTACTTCCATGCCAGAGCAGGTTACGCTATCTTTACCAGTTTCTTT
Found at i:122202 original size:14 final size:14
Alignment explanation
Indices: 122180--122209 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
122170 AGACCAAAAC
*
122180 ACTATCCCATCTCT
1 ACTAACCCATCTCT
122194 ACTAACCCATCTCT
1 ACTAACCCATCTCT
122208 AC
1 AC
122210 GGCCATAACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.43, G:0.00, T:0.30
Consensus pattern (14 bp):
ACTAACCCATCTCT
Found at i:129632 original size:7 final size:7
Alignment explanation
Indices: 129620--129659 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
129610 CTTTATAACC
*
129620 TCATAAT
1 TCATAAA
*
129627 TCATAAT
1 TCATAAA
129634 TCATAAA
1 TCATAAA
129641 TCATAAA
1 TCATAAA
129648 TCATAAA
1 TCATAAA
129655 TCATA
1 TCATA
129660 TTTATCATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (7 bp):
TCATAAA
Found at i:131978 original size:2 final size:2
Alignment explanation
Indices: 131971--132011 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
131961 TAAATAATCC
*
131971 TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
132012 CCAAACTCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:137301 original size:17 final size:17
Alignment explanation
Indices: 137279--137314 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
137269 TTGAGCTCAT
137279 TTCTCCTTTCTTCTGGC
1 TTCTCCTTTCTTCTGGC
137296 TTCTCCTTTCTTCTGGC
1 TTCTCCTTTCTTCTGGC
137313 TT
1 TT
137315 TAAACAATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.00, C:0.33, G:0.11, T:0.56
Consensus pattern (17 bp):
TTCTCCTTTCTTCTGGC
Done.