Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012634.1 Corchorus capsularis cultivar CVL-1 contig12655, 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: 70459
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--97 Score: 187
Period size: 2 Copynumber: 49.0 Consensus size: 2
1 TC TC TC T- TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
42 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
84 TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC
98 CTTCTCTTGC
Statistics
Matches: 94, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 93 0.99
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1555 original size:12 final size:12
Alignment explanation
Indices: 1538--1562 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1528 GGCCATGTTT
1538 GGAGGTGACAGC
1 GGAGGTGACAGC
1550 GGAGGTGACAGC
1 GGAGGTGACAGC
1562 G
1 G
1563 ATGATGAAGA
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:0.24, C:0.16, G:0.52, T:0.08
Consensus pattern (12 bp):
GGAGGTGACAGC
Found at i:2239 original size:67 final size:67
Alignment explanation
Indices: 2131--2264 Score: 268
Period size: 67 Copynumber: 2.0 Consensus size: 67
2121 AGAAACAGAA
2131 GGAGGAGCGGGGAGGCCATCCTTATCGAGAATGAAAACCAGAGGGAAAGGGGGTTGAAAAACCCG
1 GGAGGAGCGGGGAGGCCATCCTTATCGAGAATGAAAACCAGAGGGAAAGGGGGTTGAAAAACCCG
2196 AC
66 AC
2198 GGAGGAGCGGGGAGGCCATCCTTATCGAGAATGAAAACCAGAGGGAAAGGGGGTTGAAAAACCCG
1 GGAGGAGCGGGGAGGCCATCCTTATCGAGAATGAAAACCAGAGGGAAAGGGGGTTGAAAAACCCG
2263 AC
66 AC
2265 CTAAGGGGCA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.34, C:0.18, G:0.37, T:0.10
Consensus pattern (67 bp):
GGAGGAGCGGGGAGGCCATCCTTATCGAGAATGAAAACCAGAGGGAAAGGGGGTTGAAAAACCCG
AC
Found at i:8007 original size:19 final size:20
Alignment explanation
Indices: 7983--8022 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
7973 GCAAAACAAC
7983 ACAAAGA-GAGAAAAGGAAA
1 ACAAAGAGGAGAAAAGGAAA
*
8002 ACAAAGAGGGGAAAAGGAAA
1 ACAAAGAGGAGAAAAGGAAA
8022 A
1 A
8023 GGTGGGGGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.65, C:0.05, G:0.30, T:0.00
Consensus pattern (20 bp):
ACAAAGAGGAGAAAAGGAAA
Found at i:15643 original size:26 final size:26
Alignment explanation
Indices: 15598--15648 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
15588 ATGTTTGCCT
*
15598 CATCAATTTTCTACCATCTAGTGTAC
1 CATCAATTTTCTACCATCTAATGTAC
* *
15624 CATCAATTTTCTATCGTCTAATGTA
1 CATCAATTTTCTACCATCTAATGTA
15649 TCCCACTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.27, C:0.24, G:0.08, T:0.41
Consensus pattern (26 bp):
CATCAATTTTCTACCATCTAATGTAC
Found at i:25007 original size:141 final size:142
Alignment explanation
Indices: 24773--25050 Score: 407
Period size: 141 Copynumber: 2.0 Consensus size: 142
24763 ATGACCAACG
* *
24773 CTTTCGTCACTATTATCTATAATTATAGTGTCAAAAAATGTCGTCGCAAAAGAGCAAGTATAATG
1 CTTTCGTCACTATTATCAATAATTATAGTGTCAAAAAATGTCGTCACAAAAGAGCAAGTATAATG
* *
24838 ACAACTTATATAGTCACTATTAGGGTTTCTTCTATCGACATAATTGCCATTAATAGATATAGTTA
66 ACAACTTATATAGTCACTATTAGGGTTTCTTCTATCAACATAATTGCCATTAATAGATACAGTTA
24903 TTGTGTCAATCC
131 TTGTGTCAATCC
* **
24915 CTTTCGTCACTATTATCAATAATTATAGTGTC-AAAAATTTCGTCACAAAAGATTACA-TATAAT
1 CTTTCGTCACTATTATCAATAATTATAGTGTCAAAAAATGTCGTCACAAAAGAGCA-AGTATAAT
* * * * * * *
24978 GACAACTTATATTGTCACTCTTAGTGTTTCTTGTGTCAACATAATTGTCATTATTAGATACAGTT
65 GACAACTTATATAGTCACTATTAGGGTTTCTTCTATCAACATAATTGCCATTAATAGATACAGTT
25043 ATTGTGTC
130 ATTGTGTC
25051 GATGATGTCG
Statistics
Matches: 121, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
141 89 0.74
142 32 0.26
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (142 bp):
CTTTCGTCACTATTATCAATAATTATAGTGTCAAAAAATGTCGTCACAAAAGAGCAAGTATAATG
ACAACTTATATAGTCACTATTAGGGTTTCTTCTATCAACATAATTGCCATTAATAGATACAGTTA
TTGTGTCAATCC
Found at i:27196 original size:24 final size:24
Alignment explanation
Indices: 27144--27214 Score: 115
Period size: 24 Copynumber: 2.9 Consensus size: 24
27134 GGTCATATAG
*
27144 GGGCATTTTGGTCATTTTTGCACTAA
1 GGGCATTTTGGTCA--TTTACACTAA
27170 GGGCATTTTGGTCATTTACACTAA
1 GGGCATTTTGGTCATTTACACTAA
27194 GGGCATTTTGGTCATTTACAC
1 GGGCATTTTGGTCATTTACAC
27215 ATTTAGGGGG
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
24 30 0.68
26 14 0.32
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.39
Consensus pattern (24 bp):
GGGCATTTTGGTCATTTACACTAA
Found at i:31419 original size:13 final size:14
Alignment explanation
Indices: 31401--31429 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
31391 ATAATTGGAC
31401 TTTGCATTCAT-CA
1 TTTGCATTCATGCA
31414 TTTGCATTCATGCA
1 TTTGCATTCATGCA
31428 TT
1 TT
31430 GAGTAGAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.21, C:0.21, G:0.10, T:0.48
Consensus pattern (14 bp):
TTTGCATTCATGCA
Found at i:33995 original size:21 final size:21
Alignment explanation
Indices: 33969--34021 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
33959 GCACTGGAGT
* * *
33969 ACATGGGTCGCGAGGCAAACC
1 ACATGGGGCGCCAAGCAAACC
33990 ACATGGGGCGCCAAGCAAACC
1 ACATGGGGCGCCAAGCAAACC
34011 ACAT-GGGCGCC
1 ACATGGGGCGCC
34022 CAGCGCTAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 7 0.24
21 22 0.76
ACGTcount: A:0.28, C:0.32, G:0.32, T:0.08
Consensus pattern (21 bp):
ACATGGGGCGCCAAGCAAACC
Found at i:38889 original size:18 final size:18
Alignment explanation
Indices: 38866--38902 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
38856 TAAACAATTA
38866 AAATATCCTCAGTTTTCC
1 AAATATCCTCAGTTTTCC
38884 AAATATCCTCAGTTTTCC
1 AAATATCCTCAGTTTTCC
38902 A
1 A
38903 GGTAACTGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.27, G:0.05, T:0.38
Consensus pattern (18 bp):
AAATATCCTCAGTTTTCC
Found at i:45943 original size:2 final size:2
Alignment explanation
Indices: 45936--45961 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
45926 TTGTTGTGAT
45936 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
45962 ATGTCCTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:46048 original size:32 final size:31
Alignment explanation
Indices: 45994--46065 Score: 74
Period size: 32 Copynumber: 2.3 Consensus size: 31
45984 TTTAGAAAGC
* **
45994 GACACTTTGTTCTATTACCTTTCTTTTTTTGG
1 GACACTTTGTCCTATTACCTTTC-AATTTTGG
*
46026 GACACTTTGTCCCT-TTAGCTTTCAATTTTGG
1 GACACTTTGT-CCTATTACCTTTCAATTTTGG
*
46057 GACAATTTG
1 GACACTTTG
46066 ATACAAATGG
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
31 14 0.41
32 18 0.53
33 2 0.06
ACGTcount: A:0.17, C:0.19, G:0.15, T:0.49
Consensus pattern (31 bp):
GACACTTTGTCCTATTACCTTTCAATTTTGG
Found at i:49445 original size:34 final size:34
Alignment explanation
Indices: 49407--49472 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
49397 AATGCAAAAT
49407 CGCAGAAAAATGCAAATCCAACTTGTGCAATGCG
1 CGCAGAAAAATGCAAATCCAACTTGTGCAATGCG
*
49441 CGCAGAAAAATGCAAATCCATCTTGTGCAATG
1 CGCAGAAAAATGCAAATCCAACTTGTGCAATG
49473 TCTAAGTGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.20
Consensus pattern (34 bp):
CGCAGAAAAATGCAAATCCAACTTGTGCAATGCG
Found at i:49726 original size:27 final size:27
Alignment explanation
Indices: 49681--49755 Score: 96
Period size: 27 Copynumber: 2.8 Consensus size: 27
49671 AAGTGAACTT
* * *
49681 AAAATGACCATAATACCCCTAAATGCA
1 AAAATGACCAAAATGCCCCTAAACGCA
* **
49708 AAAATGACCAAAATGCCCCTGAACGTG
1 AAAATGACCAAAATGCCCCTAAACGCA
49735 AAAATGACCAAAATGCCCCTA
1 AAAATGACCAAAATGCCCCTA
49756 TGTGACCCTA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.45, C:0.27, G:0.12, T:0.16
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTAAACGCA
Found at i:50796 original size:23 final size:26
Alignment explanation
Indices: 50770--50820 Score: 65
Period size: 24 Copynumber: 2.1 Consensus size: 26
50760 AATTAGGGAT
50770 TTAAAAT-AACT-AATGAAA-AGCAA
1 TTAAAATAAACTAAATGAAAGAGCAA
*
50793 TT-AAATAAAGTAAATGAAAGAGCAA
1 TTAAAATAAACTAAATGAAAGAGCAA
50818 TTA
1 TTA
50821 TTTAAAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
22 4 0.17
23 5 0.22
24 7 0.30
25 7 0.30
ACGTcount: A:0.59, C:0.06, G:0.12, T:0.24
Consensus pattern (26 bp):
TTAAAATAAACTAAATGAAAGAGCAA
Found at i:51845 original size:27 final size:28
Alignment explanation
Indices: 51804--51864 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 28
51794 CATCTTTTAA
51804 TTTTCTAATTTTTTCCTTTT-TT-TTCAT
1 TTTTCTAATTTTTT-CTTTTCTTCTTCAT
*
51831 TTTTCTAGA-TTTTTCTTTTCTTCTTCTT
1 TTTTCTA-ATTTTTTCTTTTCTTCTTCAT
51859 TTTTCT
1 TTTTCT
51865 TCTTCTCTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 5 0.17
27 14 0.47
28 11 0.37
ACGTcount: A:0.08, C:0.16, G:0.02, T:0.74
Consensus pattern (28 bp):
TTTTCTAATTTTTTCTTTTCTTCTTCAT
Found at i:51860 original size:16 final size:14
Alignment explanation
Indices: 51841--51891 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 14
51831 TTTTCTAGAT
51841 TTTTCTTTTCTTCTTC
1 TTTT-TTTTCTTC-TC
51857 TTTTTTCTTCTTCTC
1 TTTTTT-TTCTTCTC
51872 TTTTTTTTC--CT-
1 TTTTTTTTCTTCTC
51883 TTTTTTTTC
1 TTTTTTTTC
51892 AAATCTTGAC
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
11 9 0.26
12 2 0.06
14 3 0.09
15 10 0.29
16 10 0.29
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTTTTTCTTCTC
Found at i:51861 original size:18 final size:16
Alignment explanation
Indices: 51814--51885 Score: 58
Period size: 18 Copynumber: 4.2 Consensus size: 16
51804 TTTTCTAATT
51814 TTTTC-CTTTTTTTTC
1 TTTTCTCTTTTTTTTC
**
51829 ATTTT-TCTAGATTTTTC
1 -TTTTCTCT-TTTTTTTC
51846 TTTTCTTCTTCTTTTTTC
1 TTTTC-TCTT-TTTTTTC
51864 TTCTTCTCTTTTTTTTCC
1 TT-TTCTCTTTTTTTT-C
51882 TTTT
1 TTTT
51886 TTTTTCAAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
16 10 0.22
17 14 0.31
18 18 0.40
19 3 0.07
ACGTcount: A:0.04, C:0.19, G:0.01, T:0.75
Consensus pattern (16 bp):
TTTTCTCTTTTTTTTC
Found at i:51864 original size:13 final size:13
Alignment explanation
Indices: 51846--51891 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
51836 TAGATTTTTC
51846 TTTTCTTCTTCTT
1 TTTTCTTCTTCTT
51859 TTTTCTTCTTCTCT
1 TTTTCTTCTTCT-T
* *
51873 TTTTTTTCCTTTTT
1 TTTTCTT-CTTCTT
51887 TTTTC
1 TTTTC
51892 AAATCTTGAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 12 0.43
14 12 0.43
15 4 0.14
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTCTTCTTCTT
Found at i:57581 original size:25 final size:24
Alignment explanation
Indices: 57549--57607 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 24
57539 CCCGCCCGAT
57549 CCGAGACCCGACGAACCC-G-TGAC
1 CCGAGACCCGAC-AACCCAGATGAC
57572 CCGAATGACCCG-CAACCCAGATGAC
1 CCG-A-GACCCGACAACCCAGATGAC
57597 CCGAGACCCGA
1 CCGAGACCCGA
57608 ATTACCCGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
23 14 0.45
24 4 0.13
25 13 0.42
ACGTcount: A:0.29, C:0.42, G:0.24, T:0.05
Consensus pattern (24 bp):
CCGAGACCCGACAACCCAGATGAC
Found at i:57582 original size:16 final size:16
Alignment explanation
Indices: 57570--57680 Score: 109
Period size: 16 Copynumber: 6.9 Consensus size: 16
57560 CGAACCCGTG
*
57570 ACCCGAATGACCCGCA
1 ACCCGAATGACCCGAA
*
57586 ACCC-AGATGACCCGAG
1 ACCCGA-ATGACCCGAA
* *
57602 ACCCGAATTACCCGTA
1 ACCCGAATGACCCGAA
*
57618 ATCC-AGATGACCCGAA
1 ACCCGA-ATGACCCGAA
* *
57634 ACCCGAATGACGCGAG
1 ACCCGAATGACCCGAA
*
57650 ACCCGTATGACCCGAA
1 ACCCGAATGACCCGAA
*
57666 ACCCGAATAACCCGA
1 ACCCGAATGACCCGA
57681 GACATTAATC
Statistics
Matches: 75, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
15 2 0.03
16 71 0.95
17 2 0.03
ACGTcount: A:0.33, C:0.37, G:0.20, T:0.10
Consensus pattern (16 bp):
ACCCGAATGACCCGAA
Found at i:57599 original size:32 final size:31
Alignment explanation
Indices: 57570--57680 Score: 134
Period size: 32 Copynumber: 3.5 Consensus size: 31
57560 CGAACCCGTG
*
57570 ACCCGAATGACCCGCAACCCAGATGACCCGAG
1 ACCCGAATGACCCG-AACCCAGATGACCCGAA
* *
57602 ACCCGAATTACCCGTAATCCAGATGACCCGAA
1 ACCCGAATGACCCG-AACCCAGATGACCCGAA
*
57634 ACCCGAATGACGCGAGACCC-GTATGACCCGAA
1 ACCCGAATGACCCGA-ACCCAG-ATGACCCGAA
*
57666 ACCCGAATAACCCGA
1 ACCCGAATGACCCGA
57681 GACATTAATC
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
31 2 0.03
32 66 0.97
ACGTcount: A:0.33, C:0.37, G:0.20, T:0.10
Consensus pattern (31 bp):
ACCCGAATGACCCGAACCCAGATGACCCGAA
Found at i:57615 original size:48 final size:48
Alignment explanation
Indices: 57549--57680 Score: 133
Period size: 48 Copynumber: 2.8 Consensus size: 48
57539 CCCGCCCGAT
** * *
57549 CCGAGACCCGACGAACCCGTGACCCGAATGACCCGCAACCC-AGATGAC
1 CCGAGACCCGAATAACCCGTAACCCGAATGACCCGAAACCCGA-ATGAC
* *
57597 CCGAGACCCGAATTACCCGTAATCC-AGATGACCCGAAACCCGAATGAC
1 CCGAGACCCGAATAACCCGTAACCCGA-ATGACCCGAAACCCGAATGAC
* * * * *
57645 GCGAGACCCGTATGACCCGAAACCCGAATAACCCGA
1 CCGAGACCCGAATAACCCGTAACCCGAATGACCCGA
57681 GACATTAATC
Statistics
Matches: 69, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
47 1 0.01
48 66 0.96
49 2 0.03
ACGTcount: A:0.32, C:0.38, G:0.21, T:0.09
Consensus pattern (48 bp):
CCGAGACCCGAATAACCCGTAACCCGAATGACCCGAAACCCGAATGAC
Found at i:57814 original size:21 final size:21
Alignment explanation
Indices: 57789--57835 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
57779 TACAATTTAT
57789 ATTATTGTAATAATTTTACCA
1 ATTATTGTAATAATTTTACCA
* * *
57810 ATTATTGTTATGATTTTACCT
1 ATTATTGTAATAATTTTACCA
57831 ATTAT
1 ATTAT
57836 AAATTGACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.32, C:0.09, G:0.06, T:0.53
Consensus pattern (21 bp):
ATTATTGTAATAATTTTACCA
Found at i:58431 original size:16 final size:16
Alignment explanation
Indices: 58307--58432 Score: 85
Period size: 16 Copynumber: 7.9 Consensus size: 16
58297 GACCTAAGAT
*
58307 CCGAATGACCCGGAAC
1 CCGAATGACCCGAAAC
* ** *
58323 GCGAATGACTTGAGAC
1 CCGAATGACCCGAAAC
* * *
58339 CCAAATAACTCGAAAC
1 CCGAATGACCCGAAAC
* *
58355 CCGTATGACCCGAGAC
1 CCGAATGACCCGAAAC
* * *
58371 CCGAACGACCCGAGAT
1 CCGAATGACCCGAAAC
*
58387 CCGAATAACCCG-AA-
1 CCGAATGACCCGAAAC
*
58401 CCTAGATGACCCGAAAC
1 CCGA-ATGACCCGAAAC
*
58418 CCGAATGATCCGAAA
1 CCGAATGACCCGAAA
58433 AAACTGCATG
Statistics
Matches: 82, Mismatches: 25, Indels: 6
0.73 0.22 0.05
Matches are distributed among these distances:
14 3 0.04
15 8 0.10
16 68 0.83
17 3 0.04
ACGTcount: A:0.36, C:0.33, G:0.21, T:0.11
Consensus pattern (16 bp):
CCGAATGACCCGAAAC
Found at i:60457 original size:52 final size:51
Alignment explanation
Indices: 60343--60464 Score: 163
Period size: 52 Copynumber: 2.4 Consensus size: 51
60333 AAAATGTTGT
* * * *
60343 TTGAATGTTTTGAAAACTTGATGGGAACTTTCCACTTTGAAATGACCTAAA
1 TTGAATGCTTTGAAAACTTAATGGGAACTTTCCACTTTGAAAAGACATAAA
** **
60394 TTGAACACTTTGAAAACTTAATGGGAACTTTCCCACTTTGAAAAGGGATAAA
1 TTGAATGCTTTGAAAACTTAATGGGAACTTT-CCACTTTGAAAAGACATAAA
60446 TTGAATGCTTTGAAAACTT
1 TTGAATGCTTTGAAAACTT
60465 TGAATGAAAT
Statistics
Matches: 60, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
51 27 0.45
52 33 0.55
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (51 bp):
TTGAATGCTTTGAAAACTTAATGGGAACTTTCCACTTTGAAAAGACATAAA
Found at i:62138 original size:6 final size:6
Alignment explanation
Indices: 62125--62156 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
62115 AAAGCAAAAC
62125 AAAT-T AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAATCT AAA
62157 GCAGATTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (6 bp):
AAATCT
Found at i:67091 original size:13 final size:13
Alignment explanation
Indices: 67073--67113 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
67063 AATCTAAATC
* *
67073 TAAAGCAGATTAA
1 TAAAGCAAACTAA
67086 TAAAGCAAACTAA
1 TAAAGCAAACTAA
67099 TAAAGCAAAC-AA
1 TAAAGCAAACTAA
67111 TAA
1 TAA
67114 TTATAAAGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
12 5 0.19
13 21 0.81
ACGTcount: A:0.61, C:0.12, G:0.10, T:0.17
Consensus pattern (13 bp):
TAAAGCAAACTAA
Done.