Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021014.1 Corchorus olitorius cultivar O-4 contig21047, 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: 79800
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:4732 original size:28 final size:29
Alignment explanation
Indices: 4673--4737 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 29
4663 ATTATGTTAA
* *
4673 AAAATCTTTCAAAAATTATTTTTAAATAT
1 AAAATATTTTAAAAATTATTTTTAAATAT
* *
4702 AAATTATTTTAAAAA-TATTTTT-CATATT
1 AAAATATTTTAAAAATTATTTTTAAATA-T
4730 AAAATATT
1 AAAATATT
4738 GCTTAAATTC
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
27 3 0.10
28 15 0.50
29 12 0.40
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (29 bp):
AAAATATTTTAAAAATTATTTTTAAATAT
Found at i:5487 original size:55 final size:55
Alignment explanation
Indices: 5402--5593 Score: 221
Period size: 60 Copynumber: 3.5 Consensus size: 55
5392 CAGGTTGTTT
*
5402 AAGCCGCCCTTTGCGGGTTTTCAACTTGAACCTCACTTTTTTTTTTTTTGCAGTTC
1 AAGCCACCCTTT-CGGGTTTTCAACTTGAACCTCACTTTTTTTTTTTTTGCAGTTC
*
5458 AAGCCACCCTTTCGGGTTTTCAACTTGAACCTCACCTTTTTTTTTTCTTTTTTGCAGTAC
1 AAGCCACCCTTTCGGGTTTTCAACTTGAACCTCA-C---TTTTTTT-TTTTTTGCAGTTC
* * * *
5518 AAGCCACCCTTTCGGGTTTTCAAGTTG-A-C-C-CTTTTTTTTTTTGTGCGGTTT
1 AAGCCACCCTTTCGGGTTTTCAACTTGAACCTCACTTTTTTTTTTTTTGCAGTTC
* * *
5569 GAGCCGCCCTTTCGGGTTTTTAACT
1 AAGCCACCCTTTCGGGTTTTCAACT
5594 CAAACCTCTC
Statistics
Matches: 120, Mismatches: 11, Indels: 15
0.82 0.08 0.10
Matches are distributed among these distances:
51 30 0.25
52 7 0.06
55 23 0.19
56 12 0.10
57 1 0.01
58 1 0.01
59 8 0.07
60 38 0.32
ACGTcount: A:0.14, C:0.25, G:0.17, T:0.44
Consensus pattern (55 bp):
AAGCCACCCTTTCGGGTTTTCAACTTGAACCTCACTTTTTTTTTTTTTGCAGTTC
Found at i:5614 original size:111 final size:115
Alignment explanation
Indices: 5402--5618 Score: 264
Period size: 111 Copynumber: 1.9 Consensus size: 115
5392 CAGGTTGTTT
* *
5402 AAGCCGCCCTTTGCGGGTTTTCAACTTGAACCTCACTTTTTTTTTTTTTGCAGTTCAAGCCACCC
1 AAGCCACCCTTTGCGGGTTTTCAACTTGAACCTCACTTTTTTTTTTTGTGCAGTTCAAGCCACCC
** * * *
5467 TTTCGGGTTTTCAACTTGAACCTCACCTTTTTTTTTTCTTTTTTGCAGTAC
66 TTTCGGGTTTTCAACTCAAACCTCACCCTCTCTTTTT-TTTTTTGCAGTAC
* * ** *
5518 AAGCCACCCTTT-CGGGTTTTCAAGTTG-A-C-C-CTTTTTTTTTTTGTGCGGTTTGAGCCGCCC
1 AAGCCACCCTTTGCGGGTTTTCAACTTGAACCTCACTTTTTTTTTTTGTGCAGTTCAAGCCACCC
* *
5578 TTTCGGGTTTTTAACTCAAACCTCTCCCTCTCTTTTTTTTT
66 TTTCGGGTTTTCAACTCAAACCTCACCCTCTCTTTTTTTTT
5619 CAATTTTTCA
Statistics
Matches: 87, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
110 4 0.05
111 55 0.63
112 1 0.01
113 1 0.01
114 1 0.01
115 14 0.16
116 11 0.13
ACGTcount: A:0.14, C:0.26, G:0.15, T:0.45
Consensus pattern (115 bp):
AAGCCACCCTTTGCGGGTTTTCAACTTGAACCTCACTTTTTTTTTTTGTGCAGTTCAAGCCACCC
TTTCGGGTTTTCAACTCAAACCTCACCCTCTCTTTTTTTTTTTGCAGTAC
Found at i:5701 original size:15 final size:15
Alignment explanation
Indices: 5660--5703 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
5650 TAACGACTCC
5660 TAATTTTATCAAAA-
1 TAATTTTATCAAAAG
*
5674 TCATTTT-TCCAAAAG
1 TAATTTTAT-CAAAAG
5689 TAATTTTATCAAAAG
1 TAATTTTATCAAAAG
5704 AAAATATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
13 1 0.04
14 11 0.44
15 12 0.48
16 1 0.04
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (15 bp):
TAATTTTATCAAAAG
Found at i:8480 original size:18 final size:17
Alignment explanation
Indices: 8453--8487 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
8443 CTTAGACATC
8453 TCCTTCATTCTTCTTTGT
1 TCCTTCATTCTT-TTTGT
*
8471 TCCTTGATTCTTTTTGT
1 TCCTTCATTCTTTTTGT
8488 CGGTTGCACC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.06, C:0.23, G:0.09, T:0.63
Consensus pattern (17 bp):
TCCTTCATTCTTTTTGT
Found at i:10083 original size:22 final size:23
Alignment explanation
Indices: 10055--10097 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
10045 TACTTGGATC
*
10055 TCCATTGATGATCA-TTCAAGCT
1 TCCATTGAAGATCATTTCAAGCT
10077 TCCATTGAAGATCATTTCAAG
1 TCCATTGAAGATCATTTCAAG
10098 AATTGAAGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (23 bp):
TCCATTGAAGATCATTTCAAGCT
Found at i:15349 original size:25 final size:25
Alignment explanation
Indices: 15312--15359 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
15302 ATTGTTGGGG
*
15312 ATCCCCACTTAAGCACAAATCAATT
1 ATCCCCACCTAAGCACAAATCAATT
*
15337 ATCCCCACCTAAGCAGAAATCAA
1 ATCCCCACCTAAGCACAAATCAA
15360 ATAAATAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.42, C:0.33, G:0.06, T:0.19
Consensus pattern (25 bp):
ATCCCCACCTAAGCACAAATCAATT
Found at i:19571 original size:21 final size:22
Alignment explanation
Indices: 19547--19592 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
19537 GTTCCTATGC
* *
19547 TTTTCACTAT-TTTTATGTGTA
1 TTTTAACTATATTTTATGAGTA
*
19568 TTTTAACTCTATTTTATGAGTA
1 TTTTAACTATATTTTATGAGTA
19590 TTT
1 TTT
19593 GTGTTTTTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.22, C:0.09, G:0.09, T:0.61
Consensus pattern (22 bp):
TTTTAACTATATTTTATGAGTA
Found at i:19762 original size:30 final size:30
Alignment explanation
Indices: 19726--19805 Score: 146
Period size: 30 Copynumber: 2.7 Consensus size: 30
19716 CGAAGTTCGT
19726 GATTTGAAGACTTATTGAAGATAATTTGGA
1 GATTTGAAGACTTATTGAAGATAATTTGGA
19756 GATTTGAAGACTTATTGAAGATAATTTGGA
1 GATTTGAAGACTTATTGAAGATAATTTGGA
19786 GATTTGAAGAC-T-TTGAAGAT
1 GATTTGAAGACTTATTGAAGAT
19806 TTATTCCAAG
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
28 8 0.16
29 1 0.02
30 41 0.82
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.36
Consensus pattern (30 bp):
GATTTGAAGACTTATTGAAGATAATTTGGA
Found at i:33561 original size:66 final size:65
Alignment explanation
Indices: 33223--33578 Score: 297
Period size: 66 Copynumber: 5.4 Consensus size: 65
33213 CTTTTCACCA
* * * * * *
33223 AAAGGGTA-TTTTGGTAAT-CAAAAGTGAACTCAAATGCAAAAATGACAAAATTGACCCTTTGAC
1 AAAGGGTATTTTTGGAAATAGAAAACTAAACTCAAATGC-AAAA-GACAAAAATGACCCTTCGAC
33286 CG
64 CG
* * * * * *** * *
33288 AAAGGGTATTTTGGGAAA-AGTAAACT-AACTTGGATATGGAAAAGTTGAAATTGGCCCTTCGAC
1 AAAGGGTATTTTTGGAAATAGAAAACTAAAC-T-CAAATGCAAAAGACAAAAATGACCCTTCGAC
33351 CG
64 CG
* * * ** * *
33353 AAAGGGCATTTTTGGAAAAAGAAAGTACTAAACTTAGGTACAAAAGACAAAAACGACCCTTCGAC
1 AAAGGGTATTTTTGGAAATAGAAA--ACTAAACTCAAATGCAAAAGACAAAAATGACCCTTCGAC
33418 CG
64 CG
** * *
33420 AAAGGGTATTTTTAAAAATAGAAAATACTAAACTTAAATGCAAGAAGACAAAAACGACCCTTCGA
1 AAAGGGTATTTTTGGAAATAG-AAA-ACTAAACTCAAATGCAA-AAGACAAAAATGACCCTTCGA
33485 CCG
63 CCG
* * * *
33488 AAAGGGTATTTTTGGAAATAGAAAAGTAAAGTCAAATGCAAAAGGACGAAAATGACCCTTCGACG
1 AAAGGGTATTTTTGGAAATAGAAAACTAAACTCAAATGCAAAA-GACAAAAATGACCCTTCGACC
33553 G
65 G
**
33554 AAAGGGTATTTCCGGAAATAGAAAA
1 AAAGGGTATTTTTGGAAATAGAAAA
33579 TAGAGCTTAT
Statistics
Matches: 236, Mismatches: 44, Indels: 21
0.78 0.15 0.07
Matches are distributed among these distances:
65 46 0.19
66 76 0.32
67 61 0.26
68 50 0.21
69 3 0.01
ACGTcount: A:0.43, C:0.14, G:0.21, T:0.22
Consensus pattern (65 bp):
AAAGGGTATTTTTGGAAATAGAAAACTAAACTCAAATGCAAAAGACAAAAATGACCCTTCGACCG
Found at i:43893 original size:20 final size:22
Alignment explanation
Indices: 43868--43908 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
43858 GAAGAGTATG
43868 TGGTTAACCAT-C-ATCTTACA
1 TGGTTAACCATACGATCTTACA
*
43888 TGGTTAGCCATACGATCTTAC
1 TGGTTAACCATACGATCTTAC
43909 CAAGTCCAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 1 0.06
22 7 0.39
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.34
Consensus pattern (22 bp):
TGGTTAACCATACGATCTTACA
Found at i:45202 original size:21 final size:21
Alignment explanation
Indices: 45173--45213 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
45163 GAAAGCAAAA
* *
45173 CACAGTCCCTCACCTGACGTC
1 CACACTCCCTCACATGACGTC
45194 CACACTCCCTCACATGACGT
1 CACACTCCCTCACATGACGT
45214 GACCTGACAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.22, C:0.46, G:0.12, T:0.20
Consensus pattern (21 bp):
CACACTCCCTCACATGACGTC
Found at i:45900 original size:60 final size:60
Alignment explanation
Indices: 45806--45953 Score: 199
Period size: 60 Copynumber: 2.5 Consensus size: 60
45796 CAAAAAGGCC
* * * * * *
45806 TAATTTGTCTATTTTTTATAAGTTGAAGTATGCAATTGA-AAATTTTGGAAGTTCATGGGT
1 TAATTTGTCTATTTTTTAAAAGTTCAAGTATGCAATTGACAAA-TTTGGAAATCCATAGAT
* *
45866 TAATTTGTCTAGTTTTTAAAAGTTCAAGTGTGCAATTGACAAATTTGGAAATCCATAGAT
1 TAATTTGTCTATTTTTTAAAAGTTCAAGTATGCAATTGACAAATTTGGAAATCCATAGAT
*
45926 TAATTTGTCTATTTTTTACAAGTTCAAG
1 TAATTTGTCTATTTTTTAAAAGTTCAAG
45954 GACCAAATTG
Statistics
Matches: 77, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
60 74 0.96
61 3 0.04
ACGTcount: A:0.32, C:0.08, G:0.17, T:0.43
Consensus pattern (60 bp):
TAATTTGTCTATTTTTTAAAAGTTCAAGTATGCAATTGACAAATTTGGAAATCCATAGAT
Found at i:51630 original size:9 final size:8
Alignment explanation
Indices: 51603--51632 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
51593 TCAATACATG
51603 CAAAATTT
1 CAAAATTT
51611 CAAAATTT
1 CAAAATTT
51619 CAAAATTTT
1 CAAAA-TTT
51628 CAAAA
1 CAAAA
51633 AAATTATGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.33
Consensus pattern (8 bp):
CAAAATTT
Found at i:62369 original size:18 final size:18
Alignment explanation
Indices: 62329--62365 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
62319 TTCATAGCTC
*
62329 CACAATATCAGGTCGGGT
1 CACAATATCAGGCCGGGT
62347 CACAAT-TCAGGCCGGGT
1 CACAATATCAGGCCGGGT
62364 CA
1 CA
62366 ACAAGAATCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (18 bp):
CACAATATCAGGCCGGGT
Found at i:66873 original size:43 final size:43
Alignment explanation
Indices: 66807--66891 Score: 152
Period size: 43 Copynumber: 2.0 Consensus size: 43
66797 TAAATAACCG
*
66807 GGAAAATAAATTGAATAAAGGAAAACTACAAGTTTTTGAACTA
1 GGAAAATAAATTGAAGAAAGGAAAACTACAAGTTTTTGAACTA
*
66850 GGAATATAAATTGAAGAAAGGAAAACTACAAGTTTTTGAACT
1 GGAAAATAAATTGAAGAAAGGAAAACTACAAGTTTTTGAACT
66892 GAAAATTTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.49, C:0.07, G:0.18, T:0.26
Consensus pattern (43 bp):
GGAAAATAAATTGAAGAAAGGAAAACTACAAGTTTTTGAACTA
Found at i:66928 original size:52 final size:52
Alignment explanation
Indices: 66856--66954 Score: 171
Period size: 52 Copynumber: 1.9 Consensus size: 52
66846 ACTAGGAATA
*
66856 TAAATTGAAGAAAGGAAAACTACAAGTTTTTGAACTGAAAATTTAAGGAAAT
1 TAAATTGAAGAAAGGAAAACTACAAGTTTTTAAACTGAAAATTTAAGGAAAT
* *
66908 TAAATTGAATAAAGGCAAACTACAAGTTTTTAAACTGAAAATTTAAG
1 TAAATTGAAGAAAGGAAAACTACAAGTTTTTAAACTGAAAATTTAAG
66955 AATAAATTGT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 44 1.00
ACGTcount: A:0.49, C:0.07, G:0.15, T:0.28
Consensus pattern (52 bp):
TAAATTGAAGAAAGGAAAACTACAAGTTTTTAAACTGAAAATTTAAGGAAAT
Found at i:67082 original size:78 final size:78
Alignment explanation
Indices: 67000--67153 Score: 281
Period size: 78 Copynumber: 2.0 Consensus size: 78
66990 CTTCATGCTG
67000 AACATGATGTTCACAACTACTAAAAAATTGCTTTAAGAACTGCTCCACCACTCGAATATTGCTCT
1 AACATGATGTTCACAACTACTAAAAAATTGCTTTAAGAACTGCTCCACCACTCGAATATTGCTCT
*
67065 CGAAGTTGGCTTC
66 CGAAATTGGCTTC
* *
67078 AACATGATGTTCACAACTACTGAAAAATTGCTTTAAGAATTGCTCCACCACTCGAATATTGCTCT
1 AACATGATGTTCACAACTACTAAAAAATTGCTTTAAGAACTGCTCCACCACTCGAATATTGCTCT
67143 CGAAATTGGCT
66 CGAAATTGGCT
67154 GGAAATTTAC
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 73 1.00
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.30
Consensus pattern (78 bp):
AACATGATGTTCACAACTACTAAAAAATTGCTTTAAGAACTGCTCCACCACTCGAATATTGCTCT
CGAAATTGGCTTC
Found at i:70647 original size:42 final size:43
Alignment explanation
Indices: 70602--70685 Score: 141
Period size: 45 Copynumber: 1.9 Consensus size: 43
70592 CTAAATTTTA
70602 CTCCATCTCTAGATAATCCATCAAAATAAAGCTAATATTCTACTC
1 CTCCATCTCTAGATAATCCATCAAAATAAAGCTAATATTCTA--C
*
70647 CTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATT
1 CTCCATCTCTAGATAATCCATCAAAATAAAGCTAATATT
70686 AATTGTTGCT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.39, C:0.24, G:0.05, T:0.32
Consensus pattern (43 bp):
CTCCATCTCTAGATAATCCATCAAAATAAAGCTAATATTCTAC
Found at i:71882 original size:131 final size:130
Alignment explanation
Indices: 71655--71906 Score: 373
Period size: 131 Copynumber: 1.9 Consensus size: 130
71645 CATTGTTTAA
* *
71655 ACTTTTATAATTTTACTCAACTAAAAACTCTATTTTTATTCACTTAAATCTAATATCTTTATAAC
1 ACTTTTATAATTTTACTCAACTAAAAACTCTATTTTTATTCAATTAAATCTAATATCCTTATAAC
*
71720 TATTTAATTTTTACCATTTTACTATTCTAATTAAAAACTTATATATATTAGAATTTTTTAAATAT
66 TATTTAATTTTTACCATTTTACTATTCTAATTAAAAACTTAGATATATTAGAATTTTTTAAATAT
* * * * * *
71785 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTTGTTTAATTAAATTTTATATCCTTATAC
1 ACTTTTATAATTTTACTCAACTAAAAACTCTA-TTTTTATTCAATTAAATCTAATATCCTTATAA
*
71850 CTAATTT-ATTTTTATCATTTTACTAATT-TAATTAAAAACTTAGATATATTAGAATTT
65 CT-ATTTAATTTTTACCATTTTACT-ATTCTAATTAAAAACTTAGATATATTAGAATTT
71907 GGATAAATGA
Statistics
Matches: 109, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
130 31 0.28
131 71 0.65
132 7 0.06
ACGTcount: A:0.37, C:0.12, G:0.02, T:0.50
Consensus pattern (130 bp):
ACTTTTATAATTTTACTCAACTAAAAACTCTATTTTTATTCAATTAAATCTAATATCCTTATAAC
TATTTAATTTTTACCATTTTACTATTCTAATTAAAAACTTAGATATATTAGAATTTTTTAAATAT
Found at i:74129 original size:68 final size:67
Alignment explanation
Indices: 73990--74263 Score: 404
Period size: 67 Copynumber: 4.0 Consensus size: 67
73980 ATAAAAACTC
*
73990 TATAATTTTCATGGAGACGAGATAATGAAAAAGAAAAAACTATGTTTCTTCAAAAAGGAAAAGTC
1 TATAATTTTCATGGAGACAAGATAATGAAAAAGAAAAAACTATGTTTCTTCAAAAAGGAAAAGTC
74055 AA
66 AA
*
74057 TATAATTTTCATGGAGACGAGATAATGAAAAAGAAAAAAACTATGTTTCTTCAAAAAGGAAAAGT
1 TATAATTTTCATGGAGACAAGATAATGAAAAAG-AAAAAACTATGTTTCTTCAAAAAGGAAAAGT
74122 CAA
65 CAA
*
74125 TATAATTTTCATGGAGACAAGATAATGAACAAGAAAAAACTATGTTTCTTCAAAAAGGAAAAGTC
1 TATAATTTTCATGGAGACAAGATAATGAAAAAGAAAAAACTATGTTTCTTCAAAAAGGAAAAGTC
74190 AAAA
66 --AA
* * * * * *
74194 TATAATTTTCATGGAGCCAAGATTAAAAAGAAAAGGAAAGAACCATGTTTCTTCAGAAAGGAAAA
1 TATAATTTTCATGGAGACAAGA-T--AATGAAAAAGAAAAAACTATGTTTCTTCAAAAAGGAAAA
*
74259 CTCAA
63 GTCAA
74264 AATATGGTTG
Statistics
Matches: 191, Mismatches: 10, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
67 65 0.34
68 65 0.34
69 23 0.12
70 3 0.02
72 35 0.18
ACGTcount: A:0.49, C:0.10, G:0.16, T:0.24
Consensus pattern (67 bp):
TATAATTTTCATGGAGACAAGATAATGAAAAAGAAAAAACTATGTTTCTTCAAAAAGGAAAAGTC
AA
Found at i:75873 original size:10 final size:10
Alignment explanation
Indices: 75858--75888 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
75848 CAGAAACCAA
75858 ACATATATAT
1 ACATATATAT
75868 ACATATATAT
1 ACATATATAT
75878 ACATATATAT
1 ACATATATAT
75888 A
1 A
75889 TATAGTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.39
Consensus pattern (10 bp):
ACATATATAT
Found at i:77979 original size:26 final size:26
Alignment explanation
Indices: 77943--77995 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
77933 CCGGTTAGAC
77943 TAGGGGATCGGACCGATTTTGATCGG
1 TAGGGGATCGGACCGATTTTGATCGG
77969 TAGGGGATCGGACCGATTTTGATCGG
1 TAGGGGATCGGACCGATTTTGATCGG
77995 T
1 T
77996 TTTAGACATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.19, C:0.15, G:0.38, T:0.28
Consensus pattern (26 bp):
TAGGGGATCGGACCGATTTTGATCGG
Found at i:79005 original size:45 final size:45
Alignment explanation
Indices: 78954--79080 Score: 227
Period size: 45 Copynumber: 2.8 Consensus size: 45
78944 AATTCTACTT
78954 CATCTCTAGGTAATTCATCAAAATAAAGCTAATATTATACTCCTC
1 CATCTCTAGGTAATTCATCAAAATAAAGCTAATATTATACTCCTC
* *
78999 CATCTCTAGGTAATTCATCAAAATAAAGATAATATTCTACTCCTC
1 CATCTCTAGGTAATTCATCAAAATAAAGCTAATATTATACTCCTC
*
79044 CATCTCTAGGTAATTCATCAAAATAAACCTAATATTA
1 CATCTCTAGGTAATTCATCAAAATAAAGCTAATATTA
79081 ATTGTTGCTT
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 77 1.00
ACGTcount: A:0.39, C:0.21, G:0.06, T:0.33
Consensus pattern (45 bp):
CATCTCTAGGTAATTCATCAAAATAAAGCTAATATTATACTCCTC
Done.