Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022036.1 Corchorus olitorius cultivar O-4 contig22069, 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: 84809
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:569 original size:21 final size:21
Alignment explanation
Indices: 543--602 Score: 93
Period size: 21 Copynumber: 2.9 Consensus size: 21
533 TGAGCAAGTT
543 GGATATGATGCGGACTCAACA
1 GGATATGATGCGGACTCAACA
564 GGATATGATGCGGACTCAACA
1 GGATATGATGCGGACTCAACA
* * *
585 AGATACGATGCGGGCTCA
1 GGATATGATGCGGACTCA
603 GCAAGGCGAC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.32, C:0.20, G:0.30, T:0.18
Consensus pattern (21 bp):
GGATATGATGCGGACTCAACA
Found at i:6677 original size:9 final size:9
Alignment explanation
Indices: 6663--6691 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
6653 GAATATGCTA
6663 AAGAGTGCC
1 AAGAGTGCC
6672 AAGAGTGCC
1 AAGAGTGCC
6681 AAGAGTGCC
1 AAGAGTGCC
6690 AA
1 AA
6692 AAGCATGGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.38, C:0.21, G:0.31, T:0.10
Consensus pattern (9 bp):
AAGAGTGCC
Found at i:8354 original size:36 final size:36
Alignment explanation
Indices: 8308--8391 Score: 150
Period size: 36 Copynumber: 2.3 Consensus size: 36
8298 AAGCACCTCT
8308 ATCATCATCTTCCTCACCGCCTTCACTATCACCCCC
1 ATCATCATCTTCCTCACCGCCTTCACTATCACCCCC
* *
8344 ATCATCATCTTCCTCACTGCCTTCACTATCACCCTC
1 ATCATCATCTTCCTCACCGCCTTCACTATCACCCCC
8380 ATCATCATCTTC
1 ATCATCATCTTC
8392 TTCTTCCTCC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.20, C:0.45, G:0.02, T:0.32
Consensus pattern (36 bp):
ATCATCATCTTCCTCACCGCCTTCACTATCACCCCC
Found at i:12257 original size:110 final size:111
Alignment explanation
Indices: 11957--12301 Score: 647
Period size: 111 Copynumber: 3.1 Consensus size: 111
11947 CCCTAGGATG
11957 TTGATCACCCAAGGAAGGTTGTTTGATCACCCTAAGCCATTACAAGGGTGACGCCACCCAGCTTT
1 TTGATCACCCAAGGAAGGTTGTTTGATCACCCTAAGCCATTACAAGGGTGACGCCACCCAGCTTT
*
12022 GGTCTAGTGGCATCATTTTCAATATATGAAGCGTGCGGCAATGTGC
66 GGTCTAGTGGCATCGTTTTCAATATATGAAGCGTGCGGCAATGTGC
*
12068 TTGATCACCCAAGGAAGGTTGTTTGATCACCCTAAGCCATTATAAGGGTGACGCCACCCAGCTTT
1 TTGATCACCCAAGGAAGGTTGTTTGATCACCCTAAGCCATTACAAGGGTGACGCCACCCAGCTTT
*
12133 GGTCTAGTGGCATCGTTTTCAATATATGAAGCGTGTGGCAATGTGC
66 GGTCTAGTGGCATCGTTTTCAATATATGAAGCGTGCGGCAATGTGC
12179 TTGATCACCC-AGGAAGGTTGTTTGATCACCCTAAGCCATTACAAGGGTGACGCCACCCAGCTTT
1 TTGATCACCCAAGGAAGGTTGTTTGATCACCCTAAGCCATTACAAGGGTGACGCCACCCAGCTTT
*
12243 GGTCTTGTGGCATCGTTTTCAATATATGAAGCGTGCGGCAATGTGC
66 GGTCTAGTGGCATCGTTTTCAATATATGAAGCGTGCGGCAATGTGC
12289 TTGATCACCCAAG
1 TTGATCACCCAAG
12302 TAATAATGAT
Statistics
Matches: 227, Mismatches: 6, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
110 107 0.47
111 120 0.53
ACGTcount: A:0.24, C:0.23, G:0.25, T:0.28
Consensus pattern (111 bp):
TTGATCACCCAAGGAAGGTTGTTTGATCACCCTAAGCCATTACAAGGGTGACGCCACCCAGCTTT
GGTCTAGTGGCATCGTTTTCAATATATGAAGCGTGCGGCAATGTGC
Found at i:15484 original size:13 final size:13
Alignment explanation
Indices: 15466--15491 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
15456 AAGGTAACAA
15466 CAAAAATCATCAC
1 CAAAAATCATCAC
15479 CAAAAATCATCAC
1 CAAAAATCATCAC
15492 TCATGCCAAG
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:0.54, C:0.31, G:0.00, T:0.15
Consensus pattern (13 bp):
CAAAAATCATCAC
Found at i:30248 original size:19 final size:20
Alignment explanation
Indices: 30197--30248 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 20
30187 ATGTGGTGTT
30197 TTTAATAA-TAATTATTCAA
1 TTTAATAATTAATTATTCAA
** *
30216 TAAAATAATT-ATTATT-TA
1 TTTAATAATTAATTATTCAA
30234 TTTAATAATTAATTA
1 TTTAATAATTAATTA
30249 ATTTCAGCCC
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
18 9 0.35
19 16 0.62
20 1 0.04
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTAATAATTAATTATTCAA
Found at i:30685 original size:29 final size:29
Alignment explanation
Indices: 30653--30709 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
30643 CTCATAATCC
30653 AGCAAAAGTTATTAACCAGCTCTCATCTA
1 AGCAAAAGTTATTAACCAGCTCTCATCTA
30682 AGCAAAAGTTATTAACCAGCTCTCATCT
1 AGCAAAAGTTATTAACCAGCTCTCATCT
30710 CATGTCTCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.37, C:0.25, G:0.11, T:0.28
Consensus pattern (29 bp):
AGCAAAAGTTATTAACCAGCTCTCATCTA
Found at i:33575 original size:11 final size:11
Alignment explanation
Indices: 33559--33584 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
33549 AGATAATTTC
33559 TTTTCTTCTAG
1 TTTTCTTCTAG
33570 TTTTCTTCTAG
1 TTTTCTTCTAG
33581 TTTT
1 TTTT
33585 TTAGGGCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:34711 original size:33 final size:35
Alignment explanation
Indices: 34674--34740 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 35
34664 TGCATTTTTC
*
34674 TTTTTCTCTGCGT-TTT-ATTCTGAAAAAAAAATA
1 TTTTTCTCTGCGTCTTTAATTCTAAAAAAAAAATA
* *
34707 TTTTTCTTTGCGTCTTTAATTTTAAAAAAAAAAT
1 TTTTTCTCTGCGTCTTTAATTCTAAAAAAAAAAT
34741 TGTGTTGTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 12 0.41
34 3 0.10
35 14 0.48
ACGTcount: A:0.34, C:0.10, G:0.07, T:0.48
Consensus pattern (35 bp):
TTTTTCTCTGCGTCTTTAATTCTAAAAAAAAAATA
Found at i:36835 original size:6 final size:6
Alignment explanation
Indices: 36814--36847 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
36804 AACATGTTAA
**
36814 TTTTCT TTTTAG TTTTCT TTTTCT TTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTT
36848 AGGATTTCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.03, C:0.12, G:0.03, T:0.82
Consensus pattern (6 bp):
TTTTCT
Found at i:47370 original size:41 final size:41
Alignment explanation
Indices: 47322--47400 Score: 149
Period size: 41 Copynumber: 1.9 Consensus size: 41
47312 ATTAAATTTA
*
47322 GCATCAACCCCTAATTTAAAATTAAAGGAGGGATTTACCCC
1 GCATCAACCCCTAATTTAAAATTAAAGGAGGAATTTACCCC
47363 GCATCAACCCCTAATTTAAAATTAAAGGAGGAATTTAC
1 GCATCAACCCCTAATTTAAAATTAAAGGAGGAATTTAC
47401 GTGGTAAATC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.39, C:0.22, G:0.14, T:0.25
Consensus pattern (41 bp):
GCATCAACCCCTAATTTAAAATTAAAGGAGGAATTTACCCC
Found at i:49639 original size:22 final size:22
Alignment explanation
Indices: 49611--49656 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
49601 TTTTGCTTTT
*
49611 GAGTTTAGCATGAAGGAAAGGA
1 GAGTTTAGCATGAAGGAAAAGA
49633 GAGTTTAGCATGAAGGAAAAGA
1 GAGTTTAGCATGAAGGAAAAGA
49655 GA
1 GA
49657 TGTTGGTGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.43, C:0.04, G:0.35, T:0.17
Consensus pattern (22 bp):
GAGTTTAGCATGAAGGAAAAGA
Found at i:51433 original size:17 final size:17
Alignment explanation
Indices: 51406--51459 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
51396 AACCCATCTA
*
51406 ATCTTTGATCACCAGTG
1 ATCTTAGATCACCAGTG
51423 ATCTT-GCATCACTC-GTG
1 ATCTTAG-ATCAC-CAGTG
*
51440 ATCTTAGATCACTAGTG
1 ATCTTAGATCACCAGTG
51457 ATC
1 ATC
51460 CGGGGGGTGA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
16 1 0.03
17 29 0.91
18 2 0.06
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.35
Consensus pattern (17 bp):
ATCTTAGATCACCAGTG
Found at i:51716 original size:30 final size:28
Alignment explanation
Indices: 51680--51743 Score: 92
Period size: 30 Copynumber: 2.2 Consensus size: 28
51670 TTTATAAAAG
*
51680 TATTTATTGCATATTAAATAAATATTCTAA
1 TATTTATTACATATT-AATAAATATT-TAA
51710 TATTTATTACATATTAATAAATATTTAA
1 TATTTATTACATATTAATAAATATTTAA
*
51738 AATTTA
1 TATTTA
51744 AATATTATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 8 0.25
29 10 0.31
30 14 0.44
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (28 bp):
TATTTATTACATATTAATAAATATTTAA
Found at i:51748 original size:25 final size:28
Alignment explanation
Indices: 51689--51750 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
51679 GTATTTATTG
*
51689 CATATTAAATAAATATTCTAATATTTATTA
1 CATATT-AATAAATATTCTAAAATTTA-TA
51719 CATATTAATAAATATT-TAAAATTTA-A
1 CATATTAATAAATATTCTAAAATTTATA
51745 -ATATTA
1 CATATTA
51751 TTTGAAATGA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
25 6 0.19
26 1 0.03
28 8 0.26
29 10 0.32
30 6 0.19
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (28 bp):
CATATTAATAAATATTCTAAAATTTATA
Found at i:51824 original size:11 final size:11
Alignment explanation
Indices: 51801--51861 Score: 56
Period size: 11 Copynumber: 5.5 Consensus size: 11
51791 AATCTTAATT
51801 AACGAAC-ATA
1 AACGAACTATA
*
51811 AACGAGCTATA
1 AACGAACTATA
51822 AAC-AACCTATTA
1 AACGAA-CTA-TA
*
51834 AACGAACAATA
1 AACGAACTATA
51845 AACGAAC-ACTA
1 AACGAACTA-TA
51856 AACGAA
1 AACGAA
51862 TATTAATTGA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
10 8 0.19
11 26 0.60
12 7 0.16
13 2 0.05
ACGTcount: A:0.56, C:0.21, G:0.10, T:0.13
Consensus pattern (11 bp):
AACGAACTATA
Found at i:52591 original size:16 final size:16
Alignment explanation
Indices: 52572--52613 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
52562 CCGTCCGAAT
*
52572 CCGAACCCGAAATTAC
1 CCGAACCCGAAAATAC
52588 CCGAACCCGAAAATAC
1 CCGAACCCGAAAATAC
52604 CCGAACCCGA
1 CCGAACCCGA
52614 GGCAGTCCGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.38, C:0.40, G:0.14, T:0.07
Consensus pattern (16 bp):
CCGAACCCGAAAATAC
Found at i:52842 original size:14 final size:14
Alignment explanation
Indices: 52823--52870 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 14
52813 GCTAAACTAC
52823 TAAATATATATAAT
1 TAAATATATATAAT
52837 TAAATATATATATAT
1 TAAATATATATA-AT
*
52852 ATAACT-TATATAACT
1 -TAAATATATATAA-T
52867 TAAA
1 TAAA
52871 GCAAAAGATT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
14 16 0.55
15 9 0.31
16 4 0.14
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (14 bp):
TAAATATATATAAT
Found at i:53450 original size:13 final size:12
Alignment explanation
Indices: 53414--53460 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
53404 TCAATCTTTA
*
53414 TATATATTGATAA
1 TATATATT-ATAT
*
53427 TA-ATGTTATAT
1 TATATATTATAT
53438 TATATTATTATAT
1 TATA-TATTATAT
53451 TATATATTAT
1 TATATATTAT
53461 CAATAAACTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 5 0.17
12 11 0.38
13 13 0.45
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (12 bp):
TATATATTATAT
Found at i:53639 original size:17 final size:17
Alignment explanation
Indices: 53593--53642 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 17
53583 CAAACTTGAG
*
53593 CCCGA-ACCCGACCCGA
1 CCCGAGACCCAACCCGA
* *
53609 CCCGAGCCCCAACCCTA
1 CCCGAGACCCAACCCGA
*
53626 CCCGAGACCGAACCCGA
1 CCCGAGACCCAACCCGA
53643 AAATACCCAA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
16 5 0.19
17 22 0.81
ACGTcount: A:0.26, C:0.54, G:0.18, T:0.02
Consensus pattern (17 bp):
CCCGAGACCCAACCCGA
Found at i:53670 original size:15 final size:15
Alignment explanation
Indices: 53633--53673 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
53623 CTACCCGAGA
53633 CCGAACCCGAAAATAC
1 CCGAACCCG-AAATAC
* *
53649 CCAAACCCGAAGTAC
1 CCGAACCCGAAATAC
53664 CCGAACCCGA
1 CCGAACCCGA
53674 GCCCGCCCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.39, C:0.41, G:0.15, T:0.05
Consensus pattern (15 bp):
CCGAACCCGAAATAC
Found at i:55769 original size:168 final size:172
Alignment explanation
Indices: 55491--55956 Score: 537
Period size: 178 Copynumber: 2.7 Consensus size: 172
55481 AGTGGTCTAT
* * * * * * * *
55491 TTAATATTATATAATTTTTGCTCCGGATATCCGATCAAGATGATTCAAGTGTCTATTAAAACGTT
1 TTAATATTACATAACTTTTGCACCAGATGTCCGATTAAGGTGATTCAAGTGTCTATTAAAAGGTT
55556 GTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTAAATTTAATGTTTCAAG-T-AT-C-C
66 GTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTAAATTTAATGTTTCAAGATAATCCTC
* *
55617 AAAAAAATTAGTTGTTTCGGTTAACATGAATGGACGGTCCAC
131 AAAAAAATTAGTTGTTTCGGTTAACAGGAATGGACCGTCCAC
* * * * *
55659 TTAATATTACATAACTTTTGCTCCAGATGT-CTACTTGAGGTGATTCAATTGTCTCTTAAAAGGT
1 TTAATATTACATAACTTTTGCACCAGATGTCCGA-TTAAGGTGATTCAAGTGTCTATTAAAAGGT
* * * *
55723 TGTTCCATGATCTATAACTTTCATAAAGGACTCAAAAACTAAATTTATTGTTTCAAGTATAAAAA
65 TGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTAAATTTAATGTTTCAAG-AT----A
* *** *
55788 ATCCTTCCAAAAAATTAGTTGTTTCGGTTATTGGGAATGGACCGTTCAC
125 ATCC-TCAAAAAAATTAGTTGTTTCGGTTAACAGGAATGGACCGTCCAC
* * *
55837 TTAATATTACATAATTTTTGCACCAGATGTCCGATTAAGGTGATTCAAGTATCTGTTAAAAGGTT
1 TTAATATTACATAACTTTTGCACCAGATGTCCGATTAAGGTGATTCAAGTGTCTATTAAAAGGTT
* * * * * *
55902 GTTTCGTGATCTACAACTTTCATGAAGGACTTGAAAGCTAAATTTGATATTTCAA
66 GTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTAAATTTAATGTTTCAA
55957 ACACCAAAAA
Statistics
Matches: 247, Mismatches: 39, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
167 2 0.01
168 103 0.42
170 1 0.00
175 2 0.01
176 1 0.00
178 136 0.55
179 2 0.01
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Consensus pattern (172 bp):
TTAATATTACATAACTTTTGCACCAGATGTCCGATTAAGGTGATTCAAGTGTCTATTAAAAGGTT
GTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTAAATTTAATGTTTCAAGATAATCCTC
AAAAAAATTAGTTGTTTCGGTTAACAGGAATGGACCGTCCAC
Found at i:58665 original size:33 final size:33
Alignment explanation
Indices: 58623--58689 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
58613 TGTATGGGTA
58623 GAGGTAGAAGATATTTTTTCCATCAAACAATAT
1 GAGGTAGAAGATATTTTTTCCATCAAACAATAT
58656 GAGGTAGAAGATATTTTTTCCATCAAACAATAT
1 GAGGTAGAAGATATTTTTTCCATCAAACAATAT
58689 G
1 G
58690 TGATATTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (33 bp):
GAGGTAGAAGATATTTTTTCCATCAAACAATAT
Found at i:68766 original size:14 final size:14
Alignment explanation
Indices: 68747--68789 Score: 77
Period size: 14 Copynumber: 3.1 Consensus size: 14
68737 CTCGGGGGAG
68747 ACAGACAGCTACAT
1 ACAGACAGCTACAT
*
68761 ACAGACTGCTACAT
1 ACAGACAGCTACAT
68775 ACAGACAGCTACAT
1 ACAGACAGCTACAT
68789 A
1 A
68790 ATTACGTGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.42, C:0.28, G:0.14, T:0.16
Consensus pattern (14 bp):
ACAGACAGCTACAT
Found at i:69037 original size:30 final size:30
Alignment explanation
Indices: 69001--69060 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
68991 CCGCACCCTG
69001 ACAGTTCCAACATAGTGCTATCATGTAGAT
1 ACAGTTCCAACATAGTGCTATCATGTAGAT
69031 ACAGTTCCAACATAGTGCTATCATGTAGAT
1 ACAGTTCCAACATAGTGCTATCATGTAGAT
69061 TGGGTGGCTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (30 bp):
ACAGTTCCAACATAGTGCTATCATGTAGAT
Found at i:74460 original size:51 final size:51
Alignment explanation
Indices: 74358--74460 Score: 127
Period size: 51 Copynumber: 2.0 Consensus size: 51
74348 CGTTCTTCAA
* * **
74358 TATTTCCTTGTTTCAATCTTGTCTCCGGACAAAAGAACACTCTTTTAGTGT
1 TATTCCCTTGTTTCAATCTTGTCTCCGGACAAAAGAACACTCGTACAGTGT
* * *
74409 TATTCCCTTGTTTCAATCTTGTTTCCGGACATAAGGACACT-GTACACGTGT
1 TATTCCCTTGTTTCAATCTTGTCTCCGGACAAAAGAACACTCGTACA-GTGT
74460 T
1 T
74461 TCTTTCTCAG
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
50 2 0.05
51 42 0.95
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.40
Consensus pattern (51 bp):
TATTCCCTTGTTTCAATCTTGTCTCCGGACAAAAGAACACTCGTACAGTGT
Found at i:82408 original size:17 final size:17
Alignment explanation
Indices: 82386--82418 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
82376 ATTAGTAAAG
82386 TTGTTACACC-AGATAAT
1 TTGTTAC-CCTAGATAAT
82403 TTGTTACCCTAGATAA
1 TTGTTACCCTAGATAA
82419 CTCTACGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.36
Consensus pattern (17 bp):
TTGTTACCCTAGATAAT
Found at i:83561 original size:21 final size:21
Alignment explanation
Indices: 83524--83597 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 21
83514 CCAAAAAGGG
83524 AAAAGAAAA-ATATAAAGGAAAT
1 AAAAGAAAAGA-A-AAAGGAAAT
*
83546 AAAAGAAAAGAAAAAGGAAGAA
1 AAAAGAAAAGAAAAAGGAA-AT
*
83568 AAAAAAAGAAGGAAATAAGGAAAT
1 AAAAGAA-AA-GAAA-AAGGAAAT
*
83592 TAAAGA
1 AAAAGA
83598 TTTATTTGGA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
21 7 0.17
22 17 0.40
23 3 0.07
24 9 0.21
25 6 0.14
ACGTcount: A:0.73, C:0.00, G:0.19, T:0.08
Consensus pattern (21 bp):
AAAAGAAAAGAAAAAGGAAAT
Done.