Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015589.1 Corchorus olitorius cultivar O-4 contig15622, 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: 93389
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:2745 original size:2 final size:2
Alignment explanation
Indices: 2735--2774 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
2725 TCTTGTGTGA
*
2735 AG AG GG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2775 CTTGAATTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
AG
Found at i:6991 original size:16 final size:16
Alignment explanation
Indices: 6970--7005 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
6960 ATATCTTTTA
6970 ATTTTTTGATTTTTCC
1 ATTTTTTGATTTTTCC
6986 ATTTTTTGATTTTTCC
1 ATTTTTTGATTTTTCC
7002 -TTTT
1 ATTTT
7006 CTTCTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.11, C:0.11, G:0.06, T:0.72
Consensus pattern (16 bp):
ATTTTTTGATTTTTCC
Found at i:7022 original size:23 final size:24
Alignment explanation
Indices: 6987--7034 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
6977 GATTTTTCCA
*
6987 TTTTTTGATTTTTCCTTTTCTTCTT
1 TTTTTTGA-TTTTCATTTTCTTCTT
*
7012 TTTTTTG-TTTTCATTTTTTTCTT
1 TTTTTTGATTTTCATTTTCTTCTT
7035 CAACTTTGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 14 0.67
25 7 0.33
ACGTcount: A:0.04, C:0.12, G:0.04, T:0.79
Consensus pattern (24 bp):
TTTTTTGATTTTCATTTTCTTCTT
Found at i:11556 original size:2 final size:2
Alignment explanation
Indices: 11549--11574 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
11539 TTCAAAACAT
11549 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
11575 CACACACACA
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:11579 original size:2 final size:2
Alignment explanation
Indices: 11574--11608 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
11564 ATATATATAT
11574 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
11609 TATACAAAGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:15388 original size:17 final size:17
Alignment explanation
Indices: 15366--15417 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 17
15356 AACTCTCATT
15366 TTTTTTTTATTTTTCTC
1 TTTTTTTTATTTTTCTC
*
15383 TTTTTTGCTATTTTTCT-
1 TTTTTT-TTATTTTTCTC
**
15400 TTTCTCCTTATTTTTCTC
1 TTT-TTTTTATTTTTCTC
15418 CTCTTCCACC
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
17 18 0.64
18 10 0.36
ACGTcount: A:0.06, C:0.17, G:0.02, T:0.75
Consensus pattern (17 bp):
TTTTTTTTATTTTTCTC
Found at i:15388 original size:18 final size:18
Alignment explanation
Indices: 15365--15417 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
15355 CAACTCTCAT
*
15365 TTTTTTTTTATTTTTCTC
1 TTTTTTCTTATTTTTCTC
15383 TTTTTTGC-TATTTTTCT-
1 TTTTTT-CTTATTTTTCTC
* *
15400 TTTCTCCTTATTTTTCTC
1 TTTTTTCTTATTTTTCTC
15418 CTCTTCCACC
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 1 0.03
17 13 0.45
18 15 0.52
ACGTcount: A:0.06, C:0.17, G:0.02, T:0.75
Consensus pattern (18 bp):
TTTTTTCTTATTTTTCTC
Found at i:20853 original size:13 final size:13
Alignment explanation
Indices: 20835--20860 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20825 ATGTGGCAAT
20835 TTTTTTATTTTTA
1 TTTTTTATTTTTA
20848 TTTTTTATTTTTA
1 TTTTTTATTTTTA
20861 CAAAATTTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTTATTTTTA
Found at i:23398 original size:65 final size:66
Alignment explanation
Indices: 23322--23448 Score: 211
Period size: 65 Copynumber: 1.9 Consensus size: 66
23312 GGGCTGAGAC
*
23322 AAACTAAATAGAGTTCTAAGAAAAAGGGGAATTAAAGTAGTAACTG-AAATTTAAAAAGGGACAA
1 AAACTAAATAGAGTTCTAAGAAAAAGGAGAATTAAAGTAGTAACTGTAAATTTAAAAAGGGACAA
23386 T
66 T
* * *
23387 AAACTAAATAGAGTTGTAAGGAAAAGGAGAATTAAAGTGGTAACTGTAAATTTAAAAAGGGA
1 AAACTAAATAGAGTTCTAAGAAAAAGGAGAATTAAAGTAGTAACTGTAAATTTAAAAAGGGA
23449 TTCATTTGTC
Statistics
Matches: 57, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
65 42 0.74
66 15 0.26
ACGTcount: A:0.51, C:0.05, G:0.22, T:0.22
Consensus pattern (66 bp):
AAACTAAATAGAGTTCTAAGAAAAAGGAGAATTAAAGTAGTAACTGTAAATTTAAAAAGGGACAA
T
Found at i:24695 original size:21 final size:21
Alignment explanation
Indices: 24658--24697 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
24648 ACTGCCCAGC
*
24658 TGGGTCTTAAGGCAAACCACA
1 TGGGTCTCAAGGCAAACCACA
24679 TGGGTGCTCAAGG-AAACCA
1 TGGGT-CTCAAGGCAAACCA
24698 TGTGGGCGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.33, C:0.23, G:0.28, T:0.17
Consensus pattern (21 bp):
TGGGTCTCAAGGCAAACCACA
Found at i:30336 original size:24 final size:25
Alignment explanation
Indices: 30290--30338 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
30280 ATTGTAGTAT
*
30290 TTATTTATCTTGTTGCTTAATTTTA
1 TTATTTATCTTGTTGATTAATTTTA
* *
30315 TTATTT-TCTTGTTTATTTATTTTA
1 TTATTTATCTTGTTGATTAATTTTA
30339 ATTGTTCACT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.18, C:0.06, G:0.06, T:0.69
Consensus pattern (25 bp):
TTATTTATCTTGTTGATTAATTTTA
Found at i:31171 original size:22 final size:22
Alignment explanation
Indices: 31143--31188 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
31133 AAAATCTCCT
31143 AATTCAACC-TCTGGAGAGGTCG
1 AATTCAACCTTC-GGAGAGGTCG
* *
31165 AATTCAATCTTCGTAGAGGTCG
1 AATTCAACCTTCGGAGAGGTCG
31187 AA
1 AA
31189 ACAACAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 19 0.90
23 2 0.10
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (22 bp):
AATTCAACCTTCGGAGAGGTCG
Found at i:34740 original size:16 final size:16
Alignment explanation
Indices: 34715--34748 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
34705 GTTGCTTAAT
34715 TTTATTATTTTT-TTG
1 TTTATTATTTTTATTG
34730 TTTATTTATTTTTATTG
1 TTTA-TTATTTTTATTG
34747 TT
1 TT
34749 CACTTAATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 8 0.47
17 5 0.29
ACGTcount: A:0.15, C:0.00, G:0.06, T:0.79
Consensus pattern (16 bp):
TTTATTATTTTTATTG
Found at i:41277 original size:220 final size:221
Alignment explanation
Indices: 40885--41285 Score: 653
Period size: 220 Copynumber: 1.8 Consensus size: 221
40875 TTTAGTTACC
* *
40885 AGGGAAATTACTAAAAAGCCAAATTGAGGATTAATGTGGTGCCACCTTTTGGCTTTTTTTGGTCT
1 AGGGAAATTACTAAAAAGCCAAATTGAGGATTAATGTGGTGCCACCTTTAGGCTTTTTTTGGACT
* *
40950 TTTCTCACTTTTCGGATGACTAAAAAGCCCCTCTATGAGTTTCCCCCTTTCCTTTTCCTGCTACC
66 TTTCTCACTTTTCGGATGACTAAAAAGCCCCTCTATGAGTTTCCCCCCTTCATTTTCCTGCTACC
* * **
41015 TTTTTTTGTAATTACTCATTTCACTTCCTTAATTGCTTTTAATTAATGTTTCTCCCCCATTTCCT
131 CTTTTTTGTAATTACCCATTTCACTTCCCAAATTGCTTTTAATTAATGTTTCTCCCCCATTTCCT
41080 TTTTTCCTCTCACCAACTCAGTAGCA
196 TTTTTCCTCTCACCAACTCAGTAGCA
* * *
41106 AGGGTAATTACT-AAAGGCCAAATTGAGGATTAATGTTGTGCCACCTTTAGGCTTTTTTTGGACT
1 AGGGAAATTACTAAAAAGCCAAATTGAGGATTAATGTGGTGCCACCTTTAGGCTTTTTTTGGACT
*
41170 TTTCTCACTTTTTGGATGACTAAAAAGCCCCTAC-ATGAGTTTCCCCCCTTCATTTTCCTGCTAC
66 TTTCTCACTTTTCGGATGACTAAAAAGCCCCT-CTATGAGTTTCCCCCCTTCATTTTCCTGCTAC
* *
41234 CCTTTTTTGTAATTACCCATTTCCCTTCCCAAATTGTTTTTAATTAATGTTT
130 CCTTTTTTGTAATTACCCATTTCACTTCCCAAATTGCTTTTAATTAATGTTT
41286 AAGGCTTTTA
Statistics
Matches: 165, Mismatches: 14, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
220 153 0.93
221 12 0.07
ACGTcount: A:0.22, C:0.24, G:0.13, T:0.41
Consensus pattern (221 bp):
AGGGAAATTACTAAAAAGCCAAATTGAGGATTAATGTGGTGCCACCTTTAGGCTTTTTTTGGACT
TTTCTCACTTTTCGGATGACTAAAAAGCCCCTCTATGAGTTTCCCCCCTTCATTTTCCTGCTACC
CTTTTTTGTAATTACCCATTTCACTTCCCAAATTGCTTTTAATTAATGTTTCTCCCCCATTTCCT
TTTTTCCTCTCACCAACTCAGTAGCA
Found at i:47052 original size:28 final size:28
Alignment explanation
Indices: 46998--47058 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
46988 AAAAATTAGT
*
46998 GTTTTACCCTAAGAATGAGTAAATTACC
1 GTTTTACCCTAAGAATGAGTAAATTACA
*
47026 GTTTTACCCTTAGAA-G-GTTAAATTTACA
1 GTTTTACCCTAAGAATGAG-TAAA-TTACA
47054 GTTTT
1 GTTTT
47059 GCCCATTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 1 0.03
27 5 0.17
28 23 0.79
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (28 bp):
GTTTTACCCTAAGAATGAGTAAATTACA
Found at i:47893 original size:28 final size:29
Alignment explanation
Indices: 47853--47909 Score: 107
Period size: 28 Copynumber: 2.0 Consensus size: 29
47843 GTAGTTATTG
47853 GTCCTTTTTAATGTTTAAGTTGGTCCCAT
1 GTCCTTTTTAATGTTTAAGTTGGTCCCAT
47882 GTCC-TTTTAATGTTTAAGTTGGTCCCAT
1 GTCCTTTTTAATGTTTAAGTTGGTCCCAT
47910 ATTTGCTTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 24 0.86
29 4 0.14
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.47
Consensus pattern (29 bp):
GTCCTTTTTAATGTTTAAGTTGGTCCCAT
Found at i:48176 original size:13 final size:13
Alignment explanation
Indices: 48158--48183 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
48148 TAACATTTGT
48158 CTTTGTTTTACAG
1 CTTTGTTTTACAG
48171 CTTTGTTTTACAG
1 CTTTGTTTTACAG
48184 TCTATATAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.54
Consensus pattern (13 bp):
CTTTGTTTTACAG
Found at i:50677 original size:18 final size:17
Alignment explanation
Indices: 50649--50683 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
50639 TAATAAGAGG
50649 AAAAGAAAGAAAAAGGA
1 AAAAGAAAGAAAAAGGA
50666 AAAAGAAAAGAAAAAGGA
1 AAAAG-AAAGAAAAAGGA
50684 TAGGATTAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (17 bp):
AAAAGAAAGAAAAAGGA
Found at i:53968 original size:40 final size:39
Alignment explanation
Indices: 53923--54015 Score: 98
Period size: 40 Copynumber: 2.4 Consensus size: 39
53913 TTAATACCTG
* *
53923 GTGGATTAAAGGCTTGA-AAGAGTAACACCTGGCCTTTTTA
1 GTGGATTAAAGGCTTGATAA-AGCAACACCTGG-ATTTTTA
* * *
53963 GTGGATAAAATGCTTGATAAAGCCACACCTGGATTTTTA
1 GTGGATTAAAGGCTTGATAAAGCAACACCTGGATTTTTA
**
54002 GTAAATTAAAGGCT
1 GTGGATTAAAGGCT
54016 GGAATTTAAT
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
39 16 0.37
40 25 0.58
41 2 0.05
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (39 bp):
GTGGATTAAAGGCTTGATAAAGCAACACCTGGATTTTTA
Found at i:59075 original size:62 final size:58
Alignment explanation
Indices: 58998--59110 Score: 172
Period size: 62 Copynumber: 1.9 Consensus size: 58
58988 CAATATTAGC
58998 TTCAAGGGTCAAATGACTTGATCTTGAACTTGATGACAATTTGAGAGTTTGATTTGATTTGG
1 TTCAAGGGTCAAATGACTTGATCTTGAA-TTGATGAC---TTGAGAGTTTGATTTGATTTGG
* *
59060 TTCAAGGGTCGAATGACTTGATCTTGAATTGATGACTTGGGAGTTTGATTT
1 TTCAAGGGTCAAATGACTTGATCTTGAATTGATGACTTGAGAGTTTGATTT
59111 TATTCGAGGG
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
58 14 0.29
61 8 0.16
62 27 0.55
ACGTcount: A:0.26, C:0.10, G:0.26, T:0.39
Consensus pattern (58 bp):
TTCAAGGGTCAAATGACTTGATCTTGAATTGATGACTTGAGAGTTTGATTTGATTTGG
Found at i:59329 original size:44 final size:44
Alignment explanation
Indices: 59280--59450 Score: 281
Period size: 44 Copynumber: 3.9 Consensus size: 44
59270 TTCTCCTTGG
*
59280 ATCTTCTTTGATAATAATCCTCCACATATGTGGATCTTCTTTCA
1 ATCTTCTTTGATAATAATCCTCCACATACGTGGATCTTCTTTCA
* *
59324 ATCTTCTTTGAT-ATAATCTTCCACATACGTGGATCTTCTTTTA
1 ATCTTCTTTGATAATAATCCTCCACATACGTGGATCTTCTTTCA
* *
59367 GTCTTCTTTGATAATAATCCTCCACATACGTGGATCCTCTTTCA
1 ATCTTCTTTGATAATAATCCTCCACATACGTGGATCTTCTTTCA
*
59411 ATCTTCTTTGATAATAATCCTCCACATACATGGATCTTCT
1 ATCTTCTTTGATAATAATCCTCCACATACGTGGATCTTCT
59451 GGAGATTTTT
Statistics
Matches: 116, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
43 39 0.34
44 77 0.66
ACGTcount: A:0.25, C:0.24, G:0.09, T:0.42
Consensus pattern (44 bp):
ATCTTCTTTGATAATAATCCTCCACATACGTGGATCTTCTTTCA
Found at i:61700 original size:73 final size:73
Alignment explanation
Indices: 61596--61742 Score: 260
Period size: 73 Copynumber: 2.0 Consensus size: 73
61586 AAAAAACTAT
* *
61596 CCATTTGAGAAAAAAAAACTTATTGTGCCAAAAAAGAAACAACCATTAACTACCTATTTAAACAT
1 CCATTTGAGAAAAAAAAACTTATTGTACCAAAAAAAAAACAACCATTAACTACCTATTTAAACAT
61661 -AACTAAC
66 AAACTAAC
61668 CCATTTGAGAAAAAAAAAACTTATTGTACCAAAAAAAAAACAACCATTAACTACCTATTTAAACA
1 CCATTTGAG-AAAAAAAAACTTATTGTACCAAAAAAAAAACAACCATTAACTACCTATTTAAACA
61733 TAAACTAAC
65 TAAACTAAC
61742 C
1 C
61743 TTTTAATATA
Statistics
Matches: 71, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
72 9 0.13
73 54 0.76
74 8 0.11
ACGTcount: A:0.52, C:0.20, G:0.05, T:0.23
Consensus pattern (73 bp):
CCATTTGAGAAAAAAAAACTTATTGTACCAAAAAAAAAACAACCATTAACTACCTATTTAAACAT
AAACTAAC
Found at i:61894 original size:65 final size:65
Alignment explanation
Indices: 61786--61916 Score: 176
Period size: 65 Copynumber: 2.0 Consensus size: 65
61776 AGTGGTTTTA
* * * *
61786 ATTAGTATCTAAAAGCAACAGAATTGATTGATTCTAGTGGAAACAGATTGACAGAATAATAGGCT
1 ATTAGTATCTAAAAGCAACAGAATTGATAGATTCTAGTAGAAACAGACTGACAGAATAATAAGCT
* *
61851 ATTAGTATTTACAAA-CAACAGAATTGACTAG-TTCTAGTAGAAACAGACTGACGGAATAATAAG
1 ATTAGTATCTA-AAAGCAACAGAATTGA-TAGATTCTAGTAGAAACAGACTGACAGAATAATAAG
61914 CT
64 CT
61916 A
1 A
61917 CTCTTCTGGG
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
65 53 0.91
66 5 0.09
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (65 bp):
ATTAGTATCTAAAAGCAACAGAATTGATAGATTCTAGTAGAAACAGACTGACAGAATAATAAGCT
Found at i:65326 original size:74 final size:73
Alignment explanation
Indices: 65203--65350 Score: 235
Period size: 74 Copynumber: 2.0 Consensus size: 73
65193 AAAAATATAT
* *
65203 CCATTTGAGGAAAAAAAAACTTATTGTGCCAAAAAAGAAACTACCATTAACTACCTATTTAAATA
1 CCATTTGAGGAAAAAAAAACTTATGGTGCCAAAAAAGAAACTACCATTAACTACCTATTTAAACA
65268 TAACTAAC
66 TAACTAAC
* *
65276 CCATTTGAGAAGAAAAAAAATCTTATGGTGCCAAAAAA-AAACTATCATTAACTACCTATTTAAA
1 CCATTTGAG--GAAAAAAAAACTTATGGTGCCAAAAAAGAAACTACCATTAACTACCTATTTAAA
65340 CATAACTAAC
64 CATAACTAAC
65350 C
1 C
65351 TTTTAATATA
Statistics
Matches: 69, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
73 9 0.13
74 35 0.51
75 25 0.36
ACGTcount: A:0.48, C:0.18, G:0.08, T:0.26
Consensus pattern (73 bp):
CCATTTGAGGAAAAAAAAACTTATGGTGCCAAAAAAGAAACTACCATTAACTACCTATTTAAACA
TAACTAAC
Found at i:65448 original size:33 final size:33
Alignment explanation
Indices: 65411--65508 Score: 96
Period size: 33 Copynumber: 3.1 Consensus size: 33
65401 TCTAAAAGCA
65411 ACAGAATTGACTAATTCTAGTGGAAACAGACTG
1 ACAGAATTGACTAATTCTAGTGGAAACAGACTG
* * **** * *
65444 ACAGAATAGGCT-A-T-TAGTATTTACAAAC-A
1 ACAGAATTGACTAATTCTAGTGGAAACAGACTG
65473 ACAGAATTGACTAATTCTAGTGGAAACAGACTG
1 ACAGAATTGACTAATTCTAGTGGAAACAGACTG
65506 ACA
1 ACA
65509 AAATAATAAG
Statistics
Matches: 45, Mismatches: 16, Indels: 8
0.65 0.23 0.12
Matches are distributed among these distances:
29 10 0.22
30 10 0.22
31 2 0.04
32 10 0.22
33 13 0.29
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.24
Consensus pattern (33 bp):
ACAGAATTGACTAATTCTAGTGGAAACAGACTG
Found at i:65491 original size:62 final size:62
Alignment explanation
Indices: 65394--65513 Score: 206
Period size: 62 Copynumber: 1.9 Consensus size: 62
65384 AGTGGTTTTA
*
65394 ATTAGTATCTAAAAGCAACAGAATTGACTAATTCTAGTGGAAACAGACTGACAGAATAGGCT
1 ATTAGTATCTAAAAGCAACAGAATTGACTAATTCTAGTGGAAACAGACTGACAAAATAGGCT
*
65456 ATTAGTATTTACAAA-CAACAGAATTGACTAATTCTAGTGGAAACAGACTGACAAAATA
1 ATTAGTATCTA-AAAGCAACAGAATTGACTAATTCTAGTGGAAACAGACTGACAAAATA
65514 ATAAGCCACA
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
62 52 0.95
63 3 0.05
ACGTcount: A:0.44, C:0.14, G:0.17, T:0.25
Consensus pattern (62 bp):
ATTAGTATCTAAAAGCAACAGAATTGACTAATTCTAGTGGAAACAGACTGACAAAATAGGCT
Found at i:67251 original size:21 final size:21
Alignment explanation
Indices: 67225--67266 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
67215 ATATATGATC
*
67225 CAATTCCGATCGCCATAGATG
1 CAATTCCGATCACCATAGATG
67246 CAATTCCGATCACCATAGATG
1 CAATTCCGATCACCATAGATG
67267 ATTAAGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.24
Consensus pattern (21 bp):
CAATTCCGATCACCATAGATG
Found at i:71912 original size:40 final size:39
Alignment explanation
Indices: 71868--71957 Score: 96
Period size: 40 Copynumber: 2.2 Consensus size: 39
71858 ATGATTTCTA
71868 AAATCAGGGA-TCAAATTGCACAAAT-AACAA-ATAAAATCTT
1 AAATCAGGGACTC--ATTGCACAAATCAA-AAGATAAAATC-T
*
71908 AAATCTAGGGACTCATTGCACAAATCAAAAGATAACATCT
1 AAATC-AGGGACTCATTGCACAAATCAAAAGATAAAATCT
71948 AAGATCAGGG
1 AA-ATCAGGG
71958 GGCACATTGA
Statistics
Matches: 44, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
40 25 0.57
41 17 0.39
42 2 0.05
ACGTcount: A:0.48, C:0.17, G:0.14, T:0.21
Consensus pattern (39 bp):
AAATCAGGGACTCATTGCACAAATCAAAAGATAAAATCT
Found at i:81735 original size:148 final size:148
Alignment explanation
Indices: 81467--81764 Score: 578
Period size: 148 Copynumber: 2.0 Consensus size: 148
81457 GTTTCTTATG
*
81467 CTTTCCAAAGTGTTGTGTAATATATCAAAACCACAAAGATTCACCACATGAAGCGATTCCGAAAT
1 CTTTCCAAAGTGTTGTGTAATATATCAAAACCACAAAGATTCACCACATGAAGCGATTCCGAAAG
*
81532 TAATCAAAGGATAACATTGTTTTCTGAGTTTTGTTTGTTTCGGGTTTGATGTATTTACAAAATAA
66 TAATCAAAGGATAACATTGTTTTCTGAGTTGTGTTTGTTTCGGGTTTGATGTATTTACAAAATAA
81597 CTTTCCGATTTTCAATAA
131 CTTTCCGATTTTCAATAA
81615 CTTTCCAAAGTGTTGTGTAATATATCAAAACCACAAAGATTCACCACATGAAGCGATTCCGAAAG
1 CTTTCCAAAGTGTTGTGTAATATATCAAAACCACAAAGATTCACCACATGAAGCGATTCCGAAAG
81680 TAATCAAAGGATAACATTGTTTTCTGAGTTGTGTTTGTTTCGGGTTTGATGTATTTACAAAATAA
66 TAATCAAAGGATAACATTGTTTTCTGAGTTGTGTTTGTTTCGGGTTTGATGTATTTACAAAATAA
81745 CTTTCCGATTTTCAATAA
131 CTTTCCGATTTTCAATAA
81763 CT
1 CT
81765 CAAGCGCTTG
Statistics
Matches: 148, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
148 148 1.00
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (148 bp):
CTTTCCAAAGTGTTGTGTAATATATCAAAACCACAAAGATTCACCACATGAAGCGATTCCGAAAG
TAATCAAAGGATAACATTGTTTTCTGAGTTGTGTTTGTTTCGGGTTTGATGTATTTACAAAATAA
CTTTCCGATTTTCAATAA
Found at i:82375 original size:71 final size:72
Alignment explanation
Indices: 82292--82436 Score: 211
Period size: 73 Copynumber: 2.0 Consensus size: 72
82282 AAAAAACTAT
* * * * *
82292 CCATTTGGGAAAAGAAAACTTATTGTGC-CAAAAAAAAACTACCATTAACTACCTATTTAAACAT
1 CCATTTGAGAAAAAAAAACTTATTGTGCAAAAAAAAAAACAACCATTAACTACCTATTCAAACAT
82356 AACTAAC
66 AACTAAC
* *
82363 CCATTTGAGAAAAAAAAACTTATTGTGCAAAAAAAAAAAACAACCATTAACTATCTATTCACACA
1 CCATTTGAGAAAAAAAAACTTATTGTGC-AAAAAAAAAAACAACCATTAACTACCTATTCAAACA
82428 TAACTAAC
65 TAACTAAC
82436 C
1 C
82437 TTTTAATATA
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
71 26 0.40
73 39 0.60
ACGTcount: A:0.49, C:0.20, G:0.07, T:0.24
Consensus pattern (72 bp):
CCATTTGAGAAAAAAAAACTTATTGTGCAAAAAAAAAAACAACCATTAACTACCTATTCAAACAT
AACTAAC
Found at i:86721 original size:2 final size:2
Alignment explanation
Indices: 86714--86741 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
86704 TAATTTTATC
86714 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
86742 TGATAACAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.