Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006862.1 Corchorus capsularis cultivar CVL-1 contig06883, 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: 101262
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:2113 original size:14 final size:13
Alignment explanation
Indices: 2073--2147 Score: 55
Period size: 14 Copynumber: 5.5 Consensus size: 13
2063 ATTCTCAAAA
2073 CAAAAAATGTTTTT
1 CAAAAAATG-TTTT
*
2087 CGAAAAAA--ATTT
1 C-AAAAAATGTTTT
2099 CAAGAAAATGTTTT
1 CAA-AAAATGTTTT
*
2113 CAAAAAAATGACTTT
1 C-AAAAAATG-TTTT
*
2128 CAAAAATGTGTTTT
1 CAAAAA-ATGTTTT
2142 CAAAAA
1 CAAAAA
2148 GGTTTTCAGT
Statistics
Matches: 49, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
11 2 0.04
12 8 0.16
14 25 0.51
15 14 0.29
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.32
Consensus pattern (13 bp):
CAAAAAATGTTTT
Found at i:3958 original size:37 final size:37
Alignment explanation
Indices: 3860--4632 Score: 779
Period size: 37 Copynumber: 20.8 Consensus size: 37
3850 TTCAAGTTTT
* * *
3860 CTGTTTAAGTGTCTTATCAAATCCTTATTTAAGGTCC
1 CTGTTTAGGTTTCTTATCAAATCCTTGTTTAAGGTCC
* * ** * *
3897 CTATTTAGGCGTTTCATAAAAAATCCTTGTTCAAGATCC
1 CTGTTTA-G-GTTTCTTATCAAATCCTTGTTTAAGGTCC
* * *
3936 CTGTTTAGGTTTCTTGTCAAATCCATGTTTAAGGTTC
1 CTGTTTAGGTTTCTTATCAAATCCTTGTTTAAGGTCC
* * * *
3973 ATGTTTAGGTGTCTTATTAAATCCTTATTTAAGGTCC
1 CTGTTTAGGTTTCTTATCAAATCCTTGTTTAAGGTCC
*
4010 CTGTTTAGATTTCTTATCAAATCCTTGTTTAAGGTCC
1 CTGTTTAGGTTTCTTATCAAATCCTTGTTTAAGGTCC
* * * *
4047 CTGTTTAGGTGTCTCATCAAAAT-CTTGTTTAAGATTC
1 CTGTTTAGGTTTCTTATC-AAATCCTTGTTTAAGGTCC
* *
4084 CTGTTTAGATTTCTTATGAAATCCTTGTTTAAGGTCC
1 CTGTTTAGGTTTCTTATCAAATCCTTGTTTAAGGTCC
* * * *
4121 CTGTTTAGGTGTCTCATCAAAAT-CTTGTTTAAGATTC
1 CTGTTTAGGTTTCTTATC-AAATCCTTGTTTAAGGTCC
* * *
4158 ATGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTCT
1 CTGTTTAGGTTTCTTATCAAATCCTTGTTTAAGGTCC
** * * *
4195 CTGTTTAGGAGTCTAATCAAAAT-CTTGTTTAAGATTC
1 CTGTTTAGGTTTCTTATC-AAATCCTTGTTTAAGGTCC
*
4232 CTGTTTAGGTTTCTTATGAAATCCTTGTTTAAGGTCC
1 CTGTTTAGGTTTCTTATCAAATCCTTGTTTAAGGTCC
* * * *
4269 CTGTTTAGGTGTCTCATCAAAAT-CTTGTTTAAGATTC
1 CTGTTTAGGTTTCTTATC-AAATCCTTGTTTAAGGTCC
*
4306 CTGTTTAGGTTTCTTATCAAATCCTTGTGTAAGGTCC
1 CTGTTTAGGTTTCTTATCAAATCCTTGTTTAAGGTCC
* * * * *
4343 CTGTTTAAGTGTCTCATCAAAAT-CTTGTTTAAGATTC
1 CTGTTTAGGTTTCTTATC-AAATCCTTGTTTAAGGTCC
*
4380 CTGTTTAGGTTTCTTATTAAATCCTTGTTTAAGGTCC
1 CTGTTTAGGTTTCTTATCAAATCCTTGTTTAAGGTCC
* ** * *
4417 CTGTTTAGGTGTCTCGTCAAAAT-CTTGTTTAAGATTC
1 CTGTTTAGGTTTCTTATC-AAATCCTTGTTTAAGGTCC
* * *
4454 GTGTTTAGATTTCTTATTAAATCCTTGTTTAAGGTCC
1 CTGTTTAGGTTTCTTATCAAATCCTTGTTTAAGGTCC
* ** * *
4491 CTGTTTAGGTGTCTCGTCAAAAT-CTTGTTTAAGATTC
1 CTGTTTAGGTTTCTTATC-AAATCCTTGTTTAAGGTCC
* * *
4528 CTGTTTAGATTTCTTATTAAATTCTTGTTTAAGGTCC
1 CTGTTTAGGTTTCTTATCAAATCCTTGTTTAAGGTCC
* ** * *
4565 CTGTTTAGGTGTCTCGTCAAAAT-CTTGTTTAAGATTC
1 CTGTTTAGGTTTCTTATC-AAATCCTTGTTTAAGGTCC
*
4602 CTGTTTAGGTTTCTTAACAAATCCTTGTTTA
1 CTGTTTAGGTTTCTTATCAAATCCTTGTTTA
4633 GGTTTCAAAA
Statistics
Matches: 588, Mismatches: 130, Indels: 36
0.78 0.17 0.05
Matches are distributed among these distances:
36 32 0.05
37 495 0.84
38 33 0.06
39 28 0.05
ACGTcount: A:0.23, C:0.16, G:0.16, T:0.45
Consensus pattern (37 bp):
CTGTTTAGGTTTCTTATCAAATCCTTGTTTAAGGTCC
Found at i:3964 original size:24 final size:27
Alignment explanation
Indices: 3922--3971 Score: 70
Period size: 24 Copynumber: 2.0 Consensus size: 27
3912 ATAAAAAATC
*
3922 CTTGTTCAAGATCCCTGTTT-AGGTTT
1 CTTGTTCAAGATCCATGTTTAAGGTTT
3948 CTTG-TCAA-ATCCATGTTTAAGGTT
1 CTTGTTCAAGATCCATGTTTAAGGTT
3972 CATGTTTAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 9 0.41
25 9 0.41
26 4 0.18
ACGTcount: A:0.20, C:0.18, G:0.18, T:0.44
Consensus pattern (27 bp):
CTTGTTCAAGATCCATGTTTAAGGTTT
Found at i:4023 original size:74 final size:74
Alignment explanation
Indices: 3833--4632 Score: 1170
Period size: 74 Copynumber: 10.8 Consensus size: 74
3823 AAAAATTTCA
* * * * * * *
3833 GTCTCATCAAAACCTTGTTCAAGTTTTCTGTTTAAGTGTCTTATCAAATCCTTATTTAAGGTCCC
1 GTCTCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTGTTTAAGGTCCC
* *
3898 TATTTAGGC
66 TGTTTAGGT
* * * * * * *
3907 GTTTCATAAAAAATCCTTGTTCAAGATCCCTGTTTAGGTTTCTTGTCAAATCCATGTTTAAGGTT
1 GTCTCAT-CAAAAT-CTTGTTTAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTGTTTAAGGTC
*
3972 CATGTTTAGGT
64 CCTGTTTAGGT
* * * * * *
3983 GTCTTAT-TAAATCCTTATTTAAGGTCCCTGTTTAGATTTCTTATCAAATCCTTGTTTAAGGTCC
1 GTCTCATCAAAAT-CTTGTTTAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTGTTTAAGGTCC
4047 CTGTTTAGGT
65 CTGTTTAGGT
* *
4057 GTCTCATCAAAATCTTGTTTAAGATTCCTGTTTAGATTTCTTATGAAATCCTTGTTTAAGGTCCC
1 GTCTCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTGTTTAAGGTCCC
4122 TGTTTAGGT
66 TGTTTAGGT
* * *
4131 GTCTCATCAAAATCTTGTTTAAGATTCATGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTCTC
1 GTCTCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTGTTTAAGGTCCC
*
4196 TGTTTAGGA
66 TGTTTAGGT
* *
4205 GTCTAATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTTCTTATGAAATCCTTGTTTAAGGTCCC
1 GTCTCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTGTTTAAGGTCCC
4270 TGTTTAGGT
66 TGTTTAGGT
*
4279 GTCTCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTGTGTAAGGTCCC
1 GTCTCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTGTTTAAGGTCCC
*
4344 TGTTTAAGT
66 TGTTTAGGT
*
4353 GTCTCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTTCTTATTAAATCCTTGTTTAAGGTCCC
1 GTCTCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTGTTTAAGGTCCC
4418 TGTTTAGGT
66 TGTTTAGGT
* * * *
4427 GTCTCGTCAAAATCTTGTTTAAGATTCGTGTTTAGATTTCTTATTAAATCCTTGTTTAAGGTCCC
1 GTCTCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTGTTTAAGGTCCC
4492 TGTTTAGGT
66 TGTTTAGGT
* * * *
4501 GTCTCGTCAAAATCTTGTTTAAGATTCCTGTTTAGATTTCTTATTAAATTCTTGTTTAAGGTCCC
1 GTCTCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTGTTTAAGGTCCC
4566 TGTTTAGGT
66 TGTTTAGGT
* *
4575 GTCTCGTCAAAATCTTGTTTAAGATTCCTGTTTAGGTTTCTTAACAAATCCTTGTTTA
1 GTCTCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTGTTTA
4633 GGTTTCAAAA
Statistics
Matches: 663, Mismatches: 60, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
74 601 0.91
75 8 0.01
76 54 0.08
ACGTcount: A:0.23, C:0.16, G:0.16, T:0.45
Consensus pattern (74 bp):
GTCTCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTGTTTAAGGTCCC
TGTTTAGGT
Found at i:4976 original size:172 final size:171
Alignment explanation
Indices: 4657--4964 Score: 464
Period size: 172 Copynumber: 1.8 Consensus size: 171
4647 TTATTCAAAA
* ***
4657 ATCAAATTTCAAAATCAGCATCTCATAGTTCAAAATTCAAAACCTCCATTTCATGGTTCATTCTT
1 ATCAAAGTTCAAAATCAGCATCTCATAGTTCAAAATTCAAAACCTCCATTTCACAATTCATTCTT
* *
4722 CAAAAATCAAAATTCAAAACTCTCATTTCAGCATTCCATTATTCGAAAATCAAAGTTCAATATTT
66 CAAAAATCAAAATTCAAAACTCTCATTTCAGCATTCCA-TATTCGAAAATCAAAATGCAATATTT
4787 GCATCTTCATTATTCAAAACATGCATTTCAGTATTCCATCCG
130 GCATCTTCATTATTCAAAACATGCATTTCAGTATTCCATCCG
* * * *
4829 ATCAAAGTTCAAAATCAGCATCTCATGGTTCAAAATTCAAAACCTGCATTTCACAATTTATTTTT
1 ATCAAAGTTCAAAATCAGCATCTCATAGTTCAAAATTCAAAACCTCCATTTCACAATTCATTCTT
*
4894 CAAAAGTCAAAATTCAAAACT-TGCATTTCAGCATTCC-T-TTCGAAAATCAAAATGCAA-ATTT
66 CAAAAATCAAAATTCAAAACTCT-CATTTCAGCATTCCATATTCGAAAATCAAAATGCAATATTT
4955 GCAT-TTCATT
130 GCATCTTCATT
4965 TCAAAATTCA
Statistics
Matches: 124, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
167 6 0.05
168 8 0.06
169 17 0.14
170 1 0.01
171 1 0.01
172 91 0.73
ACGTcount: A:0.37, C:0.21, G:0.07, T:0.34
Consensus pattern (171 bp):
ATCAAAGTTCAAAATCAGCATCTCATAGTTCAAAATTCAAAACCTCCATTTCACAATTCATTCTT
CAAAAATCAAAATTCAAAACTCTCATTTCAGCATTCCATATTCGAAAATCAAAATGCAATATTTG
CATCTTCATTATTCAAAACATGCATTTCAGTATTCCATCCG
Found at i:5002 original size:34 final size:34
Alignment explanation
Indices: 4936--5048 Score: 142
Period size: 34 Copynumber: 3.4 Consensus size: 34
4926 ATTCCTTTCG
* * *
4936 AAAA-TCAAAATGC-AAATTTGCATTTCAT-TTC
1 AAAACTCAAAATCCAAAATCTGCATCTCATGTTC
* * *
4967 AAAATTCAAAGTTCAAAATCTGCATCTCATGTTC
1 AAAACTCAAAATCCAAAATCTGCATCTCATGTTC
*
5001 AAAACTCAAAATCCAGAATCTGCATCTCATGTTC
1 AAAACTCAAAATCCAAAATCTGCATCTCATGTTC
5035 AAAACTCAAAATCC
1 AAAACTCAAAATCC
5049 TAATTGTTGT
Statistics
Matches: 71, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
31 4 0.06
32 7 0.10
33 13 0.18
34 47 0.66
ACGTcount: A:0.42, C:0.22, G:0.07, T:0.29
Consensus pattern (34 bp):
AAAACTCAAAATCCAAAATCTGCATCTCATGTTC
Found at i:6332 original size:87 final size:85
Alignment explanation
Indices: 6174--6341 Score: 232
Period size: 87 Copynumber: 1.9 Consensus size: 85
6164 ATTTGAAAAT
* * *
6174 AGAATATTTTCTAAATCTTGCCAAATTGTGGAAGGTTTAGGAGATATTTTAAGAAAATAAATAAA
1 AGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGAAGATA-TTTAAGAAAAGAAATAAA
*
6239 TTATAAAGATTGAATAATAATA
65 TTATAAA-ATTAAATAATAATA
*
6261 AGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGAAGATA-TTAA-AAAAGGAAATAAA
1 AGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGAAGATATTTAAGAAAA-GAAAT-AA
6324 ATTAATAAAATTAAATAA
64 ATT-ATAAAATTAAATAA
6342 GATTGTTAAT
Statistics
Matches: 73, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
84 4 0.05
85 8 0.11
86 13 0.18
87 48 0.66
ACGTcount: A:0.48, C:0.05, G:0.14, T:0.33
Consensus pattern (85 bp):
AGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGAAGATATTTAAGAAAAGAAATAAAT
TATAAAATTAAATAATAATA
Found at i:9577 original size:12 final size:12
Alignment explanation
Indices: 9560--9585 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
9550 TCTCTACCTG
9560 AATTTCTTCACC
1 AATTTCTTCACC
9572 AATTTCTTCACC
1 AATTTCTTCACC
9584 AA
1 AA
9586 AACGTCGACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (12 bp):
AATTTCTTCACC
Found at i:10745 original size:18 final size:18
Alignment explanation
Indices: 10722--10758 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
10712 GAGCATAAGT
*
10722 TCAATTCCATAAGATTGC
1 TCAATTCCACAAGATTGC
*
10740 TCAATTCCACAAGGTTGC
1 TCAATTCCACAAGATTGC
10758 T
1 T
10759 TGGAATATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (18 bp):
TCAATTCCACAAGATTGC
Found at i:17899 original size:9 final size:9
Alignment explanation
Indices: 17887--17911 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
17877 TTTAATAAAA
17887 TATATATAC
1 TATATATAC
17896 TATATATAC
1 TATATATAC
17905 TATATAT
1 TATATAT
17912 TATTTGAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (9 bp):
TATATATAC
Found at i:18725 original size:29 final size:31
Alignment explanation
Indices: 18693--18750 Score: 84
Period size: 29 Copynumber: 1.9 Consensus size: 31
18683 GCAATTTGGG
18693 ATATAACATTAC-AAAA-CAAGCAATTAAAA
1 ATATAACATTACGAAAAGCAAGCAATTAAAA
* *
18722 ATATAACGTTACGAAAAGCGAGCAATTAA
1 ATATAACATTACGAAAAGCAAGCAATTAA
18751 GGATATAGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 11 0.44
30 4 0.16
31 10 0.40
ACGTcount: A:0.55, C:0.14, G:0.10, T:0.21
Consensus pattern (31 bp):
ATATAACATTACGAAAAGCAAGCAATTAAAA
Found at i:18757 original size:31 final size:29
Alignment explanation
Indices: 18691--18757 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 29
18681 ATGCAATTTG
18691 GGATATAACATTACAAAACAAGCAATTAA
1 GGATATAACATTACAAAACAAGCAATTAA
** * *
18720 AAATATAACGTTACGAAAAGCGAGCAATTAA
1 GGATATAACATTAC-AAAA-CAAGCAATTAA
18751 GGATATA
1 GGATATA
18758 GTCAATTAGA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
29 11 0.37
30 4 0.13
31 15 0.50
ACGTcount: A:0.52, C:0.12, G:0.15, T:0.21
Consensus pattern (29 bp):
GGATATAACATTACAAAACAAGCAATTAA
Found at i:19063 original size:17 final size:17
Alignment explanation
Indices: 19041--19074 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
19031 TTCAGAAAAG
19041 AAAATAATTTT-TTTAAA
1 AAAAT-ATTTTATTTAAA
19058 AAAATATTTTATTTAAA
1 AAAATATTTTATTTAAA
19075 TCACTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AAAATATTTTATTTAAA
Found at i:19613 original size:31 final size:32
Alignment explanation
Indices: 19551--19630 Score: 126
Period size: 31 Copynumber: 2.5 Consensus size: 32
19541 TTACAAAACT
*
19551 AGCAATTAAGGATATAACGCTTTTTTTATTTCA
1 AGCAATTAAGGATATAACGC-TTTTTGATTTCA
*
19584 AGCAATTAAGGATATGACG-TTTTTGATTTCA
1 AGCAATTAAGGATATAACGCTTTTTGATTTCA
19615 AGCAATTAAGGATATA
1 AGCAATTAAGGATATA
19631 GTCCGTTAGG
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
31 26 0.59
33 18 0.41
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (32 bp):
AGCAATTAAGGATATAACGCTTTTTGATTTCA
Found at i:23012 original size:23 final size:22
Alignment explanation
Indices: 22980--23022 Score: 77
Period size: 23 Copynumber: 1.9 Consensus size: 22
22970 CATGATATCA
22980 ATATCTACCAATTAAGTACTTG
1 ATATCTACCAATTAAGTACTTG
23002 ATATCATACCAATTAAGTACT
1 ATATC-TACCAATTAAGTACT
23023 CCAAATTGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.40, C:0.19, G:0.07, T:0.35
Consensus pattern (22 bp):
ATATCTACCAATTAAGTACTTG
Found at i:25299 original size:21 final size:21
Alignment explanation
Indices: 25275--25316 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
25265 GGTTCGGTGA
25275 GAGTAAAATTGGTTACTGTAC
1 GAGTAAAATTGGTTACTGTAC
* * *
25296 GAGTTAGATTTGTTACTGTAC
1 GAGTAAAATTGGTTACTGTAC
25317 ATATGAGAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.10, G:0.24, T:0.38
Consensus pattern (21 bp):
GAGTAAAATTGGTTACTGTAC
Found at i:30636 original size:26 final size:27
Alignment explanation
Indices: 30566--30636 Score: 83
Period size: 26 Copynumber: 2.7 Consensus size: 27
30556 GGTGGACTTA
*
30566 AAAATGACCAAAACGCCCCTGAGTGTGC
1 AAAATGACCAAAACG-CCCTGAGTGTCC
* * *
30594 -AAATGACCAGAATGCCCTTAGTG-CC
1 AAAATGACCAAAACGCCCTGAGTGTCC
30619 AAAATGACCAAAACGCCC
1 AAAATGACCAAAACGCCC
30637 CTAGGTGACC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
25 1 0.03
26 23 0.64
27 12 0.33
ACGTcount: A:0.38, C:0.30, G:0.18, T:0.14
Consensus pattern (27 bp):
AAAATGACCAAAACGCCCTGAGTGTCC
Found at i:32351 original size:166 final size:167
Alignment explanation
Indices: 32060--32390 Score: 443
Period size: 166 Copynumber: 2.0 Consensus size: 167
32050 TTAATCTTAA
* * * * ** *
32060 ACTTTAATAGAGTAGTGGAATTACTAAAAGATCCCTACCAAGGCTTGCTTTTGGAGTTAGAGAAC
1 ACTTGAATAGAGTAGTGGAATTAATAAAAGATCCCTACCAAGGATTGATGATGGAGCTAGAGAAC
* * * * *
32125 TTATTTTGTTCGTCTTTTCCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGG
66 TAAATTTGTTCGTCTTTACCTACTTGGCAGAGTACTTAAATGTCCTAACTTTTGATTCTTGAAGG
*
32190 GATTAAATAAATAATCTTTTTGGTCATTTCTCAATGG
131 GATTAAATAAATAAACTTTTTGGTCATTTCTCAATGG
* *
32227 ACTTGAATAGAGTAGTGGAATTAATAAATGATCCGC-ATCAAGGATTGATGAT-GAGCTAGAGAA
1 ACTTGAATAGAGTAGTGGAATTAATAAAAGATCC-CTACCAAGGATTGATGATGGAGCTAGAGAA
* * * *
32290 CTAACATTT-TTCGTCTTTACCTACTTGGCAGAGTACTTAAATTTTCTAATTTTTTATTCTTGAA
65 CTAA-ATTTGTTCGTCTTTACCTACTTGGCAGAGTACTTAAATGTCCTAACTTTTGATTCTTGAA
*
32354 GGGATTAAATAACTAAACTTTTTGGTCATTTCTCAAT
129 GGGATTAAATAAATAAACTTTTTGGTCATTTCTCAAT
32391 TCACAAATGA
Statistics
Matches: 142, Mismatches: 20, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
166 96 0.68
167 45 0.32
168 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (167 bp):
ACTTGAATAGAGTAGTGGAATTAATAAAAGATCCCTACCAAGGATTGATGATGGAGCTAGAGAAC
TAAATTTGTTCGTCTTTACCTACTTGGCAGAGTACTTAAATGTCCTAACTTTTGATTCTTGAAGG
GATTAAATAAATAAACTTTTTGGTCATTTCTCAATGG
Found at i:41454 original size:17 final size:17
Alignment explanation
Indices: 41412--41445 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
41402 GGTTTGCCCC
*
41412 AATTAT-AAAAATTTTT
1 AATTATAAAAAAGTTTT
41428 AATTATAAAAAAGTTTT
1 AATTATAAAAAAGTTTT
41445 A
1 A
41446 TTTTTAAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
AATTATAAAAAAGTTTT
Found at i:41773 original size:18 final size:18
Alignment explanation
Indices: 41750--41807 Score: 77
Period size: 18 Copynumber: 3.4 Consensus size: 18
41740 TCAATGAAAT
41750 TTTTAAACAATACAAACA
1 TTTTAAACAATACAAACA
*
41768 TTTTAAA-AAT-GAAA-A
1 TTTTAAACAATACAAACA
*
41783 TTTTAAACAATACAAACG
1 TTTTAAACAATACAAACA
41801 TTTTAAA
1 TTTTAAA
41808 AACGGACACA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
15 8 0.24
16 6 0.18
17 6 0.18
18 14 0.41
ACGTcount: A:0.53, C:0.10, G:0.03, T:0.33
Consensus pattern (18 bp):
TTTTAAACAATACAAACA
Found at i:41787 original size:33 final size:33
Alignment explanation
Indices: 41742--41809 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
41732 ATAGTTTATC
*
41742 AATGAAATTTTTAAACAATACAAACATTTTAAA
1 AATGAAAATTTTAAACAATACAAACATTTTAAA
*
41775 AATGAAAATTTTAAACAATACAAACGTTTTAAA
1 AATGAAAATTTTAAACAATACAAACATTTTAAA
41808 AA
1 AA
41810 CGGACACATG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.56, C:0.09, G:0.04, T:0.31
Consensus pattern (33 bp):
AATGAAAATTTTAAACAATACAAACATTTTAAA
Found at i:49885 original size:87 final size:87
Alignment explanation
Indices: 49764--49931 Score: 336
Period size: 87 Copynumber: 1.9 Consensus size: 87
49754 GAGCAACTGC
49764 TACAAAGATGATGCAGGGGCTTTCCAGGGGTCGGGTTATTCTCTTGTATATAGAGAAGATGAGAT
1 TACAAAGATGATGCAGGGGCTTTCCAGGGGTCGGGTTATTCTCTTGTATATAGAGAAGATGAGAT
49829 GTATGCCCATATCATTCTCTTG
66 GTATGCCCATATCATTCTCTTG
49851 TACAAAGATGATGCAGGGGCTTTCCAGGGGTCGGGTTATTCTCTTGTATATAGAGAAGATGAGAT
1 TACAAAGATGATGCAGGGGCTTTCCAGGGGTCGGGTTATTCTCTTGTATATAGAGAAGATGAGAT
49916 GTATGCCCATATCATT
66 GTATGCCCATATCATT
49932 TTACGGGGGT
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 81 1.00
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.32
Consensus pattern (87 bp):
TACAAAGATGATGCAGGGGCTTTCCAGGGGTCGGGTTATTCTCTTGTATATAGAGAAGATGAGAT
GTATGCCCATATCATTCTCTTG
Found at i:50004 original size:19 final size:19
Alignment explanation
Indices: 49980--50016 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
49970 ACTGATCTCG
49980 ACTAAAAAACTCGAGCTCA
1 ACTAAAAAACTCGAGCTCA
49999 ACTAAAAAACTCGAGCTC
1 ACTAAAAAACTCGAGCTC
50017 GAGCTCGGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.46, C:0.27, G:0.11, T:0.16
Consensus pattern (19 bp):
ACTAAAAAACTCGAGCTCA
Found at i:50019 original size:6 final size:6
Alignment explanation
Indices: 50008--50055 Score: 66
Period size: 6 Copynumber: 8.3 Consensus size: 6
49998 AACTAAAAAA
50008 CTCGAG CTCGAG CTCG-G CTCGAG CTCGAGG C-CGAG C-CGAG CTCGAG
1 CTCGAG CTCGAG CTCGAG CTCGAG CTCGA-G CTCGAG CTCGAG CTCGAG
50054 CT
1 CT
50056 ACTCGATTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
5 12 0.31
6 25 0.64
7 2 0.05
ACGTcount: A:0.15, C:0.35, G:0.35, T:0.15
Consensus pattern (6 bp):
CTCGAG
Found at i:50030 original size:17 final size:18
Alignment explanation
Indices: 50008--50055 Score: 66
Period size: 17 Copynumber: 2.8 Consensus size: 18
49998 AACTAAAAAA
50008 CTCGAGCTCGAGCTCG-G
1 CTCGAGCTCGAGCTCGAG
50025 CTCGAGCTCGAGGC-CGAG
1 CTCGAGCTCGA-GCTCGAG
50043 C-CGAGCTCGAGCT
1 CTCGAGCTCGAGCT
50056 ACTCGATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 2 0.07
17 22 0.79
18 4 0.14
ACGTcount: A:0.15, C:0.35, G:0.35, T:0.15
Consensus pattern (18 bp):
CTCGAGCTCGAGCTCGAG
Found at i:50042 original size:23 final size:23
Alignment explanation
Indices: 50008--50055 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
49998 AACTAAAAAA
50008 CTCGAGCTCGAGCTCG-GCTCGAG
1 CTCGAGC-CGAGCTCGAGCTCGAG
50031 CTCGAGGCCGAGC-CGAGCTCGAG
1 CTCGA-GCCGAGCTCGAGCTCGAG
50054 CT
1 CT
50056 ACTCGATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 2 0.09
23 19 0.83
24 2 0.09
ACGTcount: A:0.15, C:0.35, G:0.35, T:0.15
Consensus pattern (23 bp):
CTCGAGCCGAGCTCGAGCTCGAG
Found at i:51032 original size:10 final size:10
Alignment explanation
Indices: 51013--51067 Score: 60
Period size: 10 Copynumber: 5.5 Consensus size: 10
51003 AATAGTTATT
51013 TATTTATTAC
1 TATTTATTAC
*
51023 TATTTTTTAC
1 TATTTATTAC
51033 TA-TTATTAC
1 TATTTATTAC
*
51042 TATTTA-TAT
1 TATTTATTAC
51051 TATCATTATTAC
1 TAT--TTATTAC
51063 TATTT
1 TATTT
51068 TTTTCTTATA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
9 13 0.35
10 16 0.43
11 3 0.08
12 5 0.14
ACGTcount: A:0.29, C:0.09, G:0.00, T:0.62
Consensus pattern (10 bp):
TATTTATTAC
Found at i:54653 original size:27 final size:27
Alignment explanation
Indices: 54615--54666 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
54605 AACCCAAGTC
*
54615 AGTCAAGTCAG-TTCTCCATTCAAAGCT
1 AGTCAACTCAGTTTC-CCATTCAAAGCT
54642 AGTCAACTCAGTTTCCCATTCAAAG
1 AGTCAACTCAGTTTCCCATTCAAAG
54667 TTAATTCCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 20 0.87
28 3 0.13
ACGTcount: A:0.31, C:0.27, G:0.13, T:0.29
Consensus pattern (27 bp):
AGTCAACTCAGTTTCCCATTCAAAGCT
Found at i:82286 original size:14 final size:16
Alignment explanation
Indices: 82267--82298 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
82257 AAATAAGCTC
82267 TTGCTTT-TTTTT-TT
1 TTGCTTTCTTTTTCTT
82281 TTGCTTTCTTTTTCTT
1 TTGCTTTCTTTTTCTT
82297 TT
1 TT
82299 TTTTTTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 5 0.31
16 4 0.25
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.81
Consensus pattern (16 bp):
TTGCTTTCTTTTTCTT
Found at i:89799 original size:32 final size:32
Alignment explanation
Indices: 89754--89814 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
89744 ACTATGTCCT
89754 TTTTTAGATGTTCTGGGGTTTTCTTATTTAAG
1 TTTTTAGATGTTCTGGGGTTTTCTTATTTAAG
89786 TTTTTA-ATAGTTCTGGGGTTTTCTTATTT
1 TTTTTAGAT-GTTCTGGGGTTTTCTTATTT
89815 TAGATGACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
31 2 0.07
32 26 0.93
ACGTcount: A:0.15, C:0.07, G:0.20, T:0.59
Consensus pattern (32 bp):
TTTTTAGATGTTCTGGGGTTTTCTTATTTAAG
Found at i:90469 original size:4 final size:4
Alignment explanation
Indices: 90460--90492 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
90450 TTATTCGTCA
*
90460 TTTC TTTC TTTC TTTC TTT- TTTC TTTG TTTC TT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT
90493 GTGTTGCCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (4 bp):
TTTC
Found at i:98581 original size:11 final size:10
Alignment explanation
Indices: 98563--98596 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
98553 AATTGTCTTC
98563 AAATCTTCAA
1 AAATCTTCAA
98573 AATATCTTCAA
1 AA-ATCTTCAA
98584 GAAATCTTCAA
1 -AAATCTTCAA
98595 AA
1 AA
98597 CACGAACTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.29
Consensus pattern (10 bp):
AAATCTTCAA
Found at i:100866 original size:2 final size:2
Alignment explanation
Indices: 100859--100891 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
100849 ATGAATAATG
100859 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
100892 CTAGGTTTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.