Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008691.1 Corchorus capsularis cultivar CVL-1 contig08712, 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: 88453
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:1722 original size:19 final size:18
Alignment explanation
Indices: 1690--1734 Score: 65
Period size: 19 Copynumber: 2.5 Consensus size: 18
1680 CATTTTCCAT
1690 TTTCTCTT-TTTTTTTTC
1 TTTCTCTTCTTTTTTTTC
1707 TTTCTCTTCTTCTTTTTTC
1 TTTCTCTTCTT-TTTTTTC
*
1726 TTTTTCTTC
1 TTTCTCTTC
1735 AATTTTTGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 8 0.32
18 2 0.08
19 15 0.60
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTCTCTTCTTTTTTTTC
Found at i:1741 original size:19 final size:18
Alignment explanation
Indices: 1690--1741 Score: 52
Period size: 19 Copynumber: 2.9 Consensus size: 18
1680 CATTTTCCAT
*
1690 TTTCTCTT-TTTTTTTTC
1 TTTCTCTTCATTTTTTTC
*
1707 TTTCTCTTCTTCTTTTTTC
1 TTTCTCTTCAT-TTTTTTC
* *
1726 TTTTTCTTCAATTTTT
1 TTTCTCTTCATTTTTT
1742 GATCTAAACA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
17 8 0.27
18 7 0.23
19 15 0.50
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTCTCTTCATTTTTTTC
Found at i:5992 original size:27 final size:27
Alignment explanation
Indices: 5961--6015 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
5951 CCTAATGCCA
*
5961 TGTGATCTAAATTAAATATTCTAAAAC
1 TGTGAACTAAATTAAATATTCTAAAAC
5988 TGTGAACTAAATTAAATATTCTAAAAC
1 TGTGAACTAAATTAAATATTCTAAAAC
6015 T
1 T
6016 TAAATAATGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.36
Consensus pattern (27 bp):
TGTGAACTAAATTAAATATTCTAAAAC
Found at i:12009 original size:156 final size:157
Alignment explanation
Indices: 11724--12029 Score: 596
Period size: 156 Copynumber: 2.0 Consensus size: 157
11714 AATGCCACGC
11724 AGCTCTCCAGGCCAAATCTGTGAAATTTTGAACAATGTCAAGCTCAAATCAGAATATAGAAAATA
1 AGCTCTCCAGGCCAAATCTGTGAAATTTTGAACAATGTCAAGCTCAAATCAGAATATAGAAAATA
*
11789 TAATTTATAAATCAGTATTGTTTCATGTCTTAAAAAATTAGCCCAACCTGCATTTCTAGCCTGAG
66 TAATTTATAAATCAATATTGTTTCATGTCTTAAAAAATTAGCCCAACCTGCATTTCTAGCCTGAG
11854 AGATATCTGATTCTGCCTTAAAAACGT
131 AGATATCTGATTCTGCCTTAAAAACGT
11881 AGCTCTCCAGGCCAAATCTGTGAAATTTTGAA-AATGTCAAGCTCAAATCAGAATATAGAAAATA
1 AGCTCTCCAGGCCAAATCTGTGAAATTTTGAACAATGTCAAGCTCAAATCAGAATATAGAAAATA
11945 TAATTTATAAATCAATATTGTTTCATGTCTTAAAAAATTAGCCCAACCTGCATTTCTAGCCTGAG
66 TAATTTATAAATCAATATTGTTTCATGTCTTAAAAAATTAGCCCAACCTGCATTTCTAGCCTGAG
12010 AGATATCTGATTCTGCCTTA
131 AGATATCTGATTCTGCCTTA
12030 GAAATGTAAG
Statistics
Matches: 148, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
156 116 0.78
157 32 0.22
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (157 bp):
AGCTCTCCAGGCCAAATCTGTGAAATTTTGAACAATGTCAAGCTCAAATCAGAATATAGAAAATA
TAATTTATAAATCAATATTGTTTCATGTCTTAAAAAATTAGCCCAACCTGCATTTCTAGCCTGAG
AGATATCTGATTCTGCCTTAAAAACGT
Found at i:32183 original size:32 final size:31
Alignment explanation
Indices: 32147--32239 Score: 91
Period size: 32 Copynumber: 2.9 Consensus size: 31
32137 GCAAAATAAG
32147 GGCACTTTATGAA-ACAAACGCCCCTAAATAGT
1 GGCACTTTA-GAAGA-AAACGCCCCTAAATAGT
* * * *
32179 GGCACATAAGGAAGAAAATGCCCCTACATAGT
1 GGCACTTTA-GAAGAAAACGCCCCTAAATAGT
*
32211 GGCAATTTAGTAAGAAAACG-CCCTAAATA
1 GGCACTTTAG-AAGAAAACGCCCCTAAATA
32240 ATGGAATTTA
Statistics
Matches: 49, Mismatches: 10, Indels: 5
0.77 0.16 0.08
Matches are distributed among these distances:
31 9 0.18
32 39 0.80
33 1 0.02
ACGTcount: A:0.41, C:0.22, G:0.18, T:0.19
Consensus pattern (31 bp):
GGCACTTTAGAAGAAAACGCCCCTAAATAGT
Found at i:33984 original size:5 final size:5
Alignment explanation
Indices: 33974--34006 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
33964 CTCAAGTTCT
33974 TTTTA TTTTA TTTTA TTTTA TTTTA -TTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
34007 CTCAATAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:37928 original size:124 final size:125
Alignment explanation
Indices: 37700--38191 Score: 443
Period size: 124 Copynumber: 3.9 Consensus size: 125
37690 TCCAGTAGTG
* * * * * *
37700 AAACATCGCTAAAAAATACTATATCGACATTTGCAAATGTCGTAGCAACTTATTCACATCATTTG
1 AAACATCGCTAAAAAATACTATACCGACGTTTGCAAATGTCGAAACAAGTTAATCACATCATTTG
* * *
37765 TTTTCAACGTATTCCGACATTTGTAAACGTTGATTTAGATATTATATTGTGACATTTATT
66 ATTTCAACGTATTCCGACATTTGTAAGCGTTGATATAGATATTATATTGTGACATTTATT
* * * * *
37825 AAACATCGCTACAAAATATTATACCTACGTTTGCAAATGTCGAAACAAGTTAAT-ATATCTTTTG
1 AAACATCGCTAAAAAATACTATACCGACGTTTGCAAATGTCGAAACAAGTTAATCACATCATTTG
* * * ** * *
37889 ATTTCAACATATTCCGACATTTGTAAGCGTTGGTATAGATATCATA-CATGAGATTTATA
66 ATTTCAACGTATTCCGACATTTGTAAGCGTTGATATAGATATTATATTGTGACATTTATT
** ** * * * * *
37948 AAATGTCGGAAAAAAAATACTAGATCGACGTTTGCAAATGTAGGAACAAGTTATTCACATCATTT
1 AAACATC-GCTAAAAAATACTATACCGACGTTTGCAAATGTCGAAACAAGTTAATCACATCATTT
* * * *
38013 GTTTTCGACGTATTCCGACATTTGTAAGTGTTGCTATATATATATATATATATATTATATCGTGA
65 GATTTCAACGTATTCCGACATTTGTAAGCGTTG--------ATATAGATAT-TA-TAT-T-GTGA
38078 CATTTATT
118 CATTTATT
* * * * * *
38086 AAAAATCGCCACAAAATATTATACCTACGTTTGCAAATGTC-AGAACAAGTTAAT-ATATCATTT
1 AAACATCGCTAAAAAATACTATACCGACGTTTGCAAATGTCGA-AACAAGTTAATCACATCATTT
* * *
38149 GATTTCAACGTATTCTGACATTTGTAAGCATTGATATATATAT
65 GATTTCAACGTATTCCGACATTTGTAAGCGTTGATATAGATAT
38192 CATACCATGA
Statistics
Matches: 287, Mismatches: 64, Indels: 29
0.76 0.17 0.08
Matches are distributed among these distances:
123 14 0.05
124 85 0.30
125 81 0.28
128 10 0.03
133 8 0.03
134 1 0.00
135 2 0.01
136 36 0.13
137 36 0.13
138 14 0.05
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.37
Consensus pattern (125 bp):
AAACATCGCTAAAAAATACTATACCGACGTTTGCAAATGTCGAAACAAGTTAATCACATCATTTG
ATTTCAACGTATTCCGACATTTGTAAGCGTTGATATAGATATTATATTGTGACATTTATT
Found at i:39601 original size:12 final size:12
Alignment explanation
Indices: 39572--39605 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
39562 AACATTTAAC
*
39572 TAATTTCAATAA
1 TAATTTCAAAAA
39584 -AATTTCAAAAA
1 TAATTTCAAAAA
39595 TAATTTCAAAA
1 TAATTTCAAAA
39606 TAAAAGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (12 bp):
TAATTTCAAAAA
Found at i:40039 original size:13 final size:13
Alignment explanation
Indices: 40021--40054 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
40011 TTAAAAGTAC
40021 TAAAAATTTGTAA
1 TAAAAATTTGTAA
**
40034 TAAAAATTTGTTG
1 TAAAAATTTGTAA
40047 TAAAAATT
1 TAAAAATT
40055 AACGTGTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (13 bp):
TAAAAATTTGTAA
Found at i:42803 original size:3 final size:3
Alignment explanation
Indices: 42795--42820 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
42785 ATTACATTAC
42795 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
42821 CATTTTGGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:43712 original size:24 final size:22
Alignment explanation
Indices: 43680--43724 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
43670 CATTCAAAAA
*
43680 AATCATTTCCAGACTAGCAAGTTC
1 AATCATTT-CAGAC-AGAAAGTTC
*
43704 AATCTTTTCAGACAGAAAGTT
1 AATCATTTCAGACAGAAAGTT
43725 AGAGTTTGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 7 0.37
23 5 0.26
24 7 0.37
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (22 bp):
AATCATTTCAGACAGAAAGTTC
Found at i:46392 original size:20 final size:20
Alignment explanation
Indices: 46367--46404 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
46357 CGAGTTCCCT
46367 TCTTTGGAGTAACTTTCACA
1 TCTTTGGAGTAACTTTCACA
46387 TCTTTGGAGTAACTTTCA
1 TCTTTGGAGTAACTTTCA
46405 TTGCCAGCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.42
Consensus pattern (20 bp):
TCTTTGGAGTAACTTTCACA
Found at i:52535 original size:21 final size:22
Alignment explanation
Indices: 52488--52535 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
52478 GTTCCAGCCA
**
52488 TCATTG-CCTTCTTCTTTTTCT
1 TCATTGTCCTTCTTCTGATTCT
52509 TC-TTGTCCTTCTTCTGATTC-
1 TCATTGTCCTTCTTCTGATTCT
52529 TCATTGT
1 TCATTGT
52536 TGTTCAATGG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.06, C:0.27, G:0.08, T:0.58
Consensus pattern (22 bp):
TCATTGTCCTTCTTCTGATTCT
Found at i:55380 original size:12 final size:12
Alignment explanation
Indices: 55365--55389 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
55355 TAAATTGAAG
55365 AATTAATTATTA
1 AATTAATTATTA
55377 AATTAATTATTA
1 AATTAATTATTA
55389 A
1 A
55390 GTAGCAACTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AATTAATTATTA
Found at i:55928 original size:15 final size:16
Alignment explanation
Indices: 55901--55930 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
55891 CACATAGAAC
55901 AATTAATTTCTATTAT
1 AATTAATTTCTATTAT
55917 AATTAA-TTCTATTA
1 AATTAATTTCTATTA
55931 AGAAGGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (16 bp):
AATTAATTTCTATTAT
Found at i:57233 original size:11 final size:11
Alignment explanation
Indices: 57212--57247 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
57202 TAGCAAGCTC
*
57212 AACTAAAACTA
1 AACTAACACTA
*
57223 AACTCACACTA
1 AACTAACACTA
57234 AACTAACACTA
1 AACTAACACTA
57245 AAC
1 AAC
57248 CTAAAACATG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.56, C:0.28, G:0.00, T:0.17
Consensus pattern (11 bp):
AACTAACACTA
Found at i:57964 original size:17 final size:17
Alignment explanation
Indices: 57942--57974 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
57932 TTCCATTTAT
57942 TTTTTCACTTTT-TTTTC
1 TTTTTCA-TTTTCTTTTC
57959 TTTTTCATTTTCTTTT
1 TTTTTCATTTTCTTTT
57975 TTTATTTTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTCATTTTCTTTTC
Found at i:58722 original size:26 final size:27
Alignment explanation
Indices: 58693--58745 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
58683 AATGCAATGC
58693 ATGCAAACA-AAA-AGAAAATGAAAAAT
1 ATGCAAACATAAACA-AAAATGAAAAAT
*
58719 ATGCAAACATAAACAAAAATGCAAAAT
1 ATGCAAACATAAACAAAAATGAAAAAT
58746 TTTTTTACCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 9 0.38
27 14 0.58
28 1 0.04
ACGTcount: A:0.66, C:0.11, G:0.09, T:0.13
Consensus pattern (27 bp):
ATGCAAACATAAACAAAAATGAAAAAT
Found at i:60356 original size:15 final size:16
Alignment explanation
Indices: 60331--60360 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
60321 CACAGAGAAC
60331 AATTAAATTCTATTAT
1 AATTAAATTCTATTAT
60347 AATT-AATTCTATTA
1 AATTAAATTCTATTA
60361 AGAAGGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (16 bp):
AATTAAATTCTATTAT
Found at i:66703 original size:15 final size:15
Alignment explanation
Indices: 66677--66714 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
66667 CATTATAACT
66677 TGTTTTGTTATTTAC
1 TGTTTTGTTATTTAC
*
66692 TGTTTTGTTATTTGC
1 TGTTTTGTTATTTAC
66707 TGATTTTG
1 TG-TTTTG
66715 AGTGTGGCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 16 0.76
16 5 0.24
ACGTcount: A:0.11, C:0.05, G:0.18, T:0.66
Consensus pattern (15 bp):
TGTTTTGTTATTTAC
Found at i:72597 original size:14 final size:13
Alignment explanation
Indices: 72583--72618 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
72573 ACTTTTAATA
72583 AAATGTTTTTTAT
1 AAATGTTTTTTAT
*
72596 AAATGATTTTTATT
1 AAATGTTTTTTA-T
72610 AAATGTTTT
1 AAATGTTTT
72619 GGGTGCATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.58
Consensus pattern (13 bp):
AAATGTTTTTTAT
Found at i:81886 original size:16 final size:16
Alignment explanation
Indices: 81860--81994 Score: 114
Period size: 16 Copynumber: 8.6 Consensus size: 16
81850 CATGCAGTTT
*
81860 TTTCAGGTCATTCGGG
1 TTTCGGGTCATTCGGG
* *
81876 TTTTGGGTCA-TCTAGG
1 TTTCGGGTCATTC-GGG
*
81892 -TTCGGGTTA-TCGGG
1 TTTCGGGTCATTCGGG
** * *
81906 CCTCGGGTCGTTTGGG
1 TTTCGGGTCATTCGGG
* *
81922 TCTCGGGTCATACGGG
1 TTTCGGGTCATTCGGG
81938 TTTCGGGTCATTCGGG
1 TTTCGGGTCATTCGGG
* *
81954 TCTCGGGTCATTCAGG
1 TTTCGGGTCATTCGGG
*
81970 TTCCGGGTCATTCGGG
1 TTTCGGGTCATTCGGG
*
81986 TCTCGGGTC
1 TTTCGGGTC
81995 TACCGGGTCT
Statistics
Matches: 93, Mismatches: 23, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
14 2 0.02
15 17 0.18
16 74 0.80
ACGTcount: A:0.08, C:0.21, G:0.36, T:0.34
Consensus pattern (16 bp):
TTTCGGGTCATTCGGG
Found at i:81937 original size:9 final size:9
Alignment explanation
Indices: 81924--81987 Score: 59
Period size: 9 Copynumber: 7.8 Consensus size: 9
81914 CGTTTGGGTC
81924 TCGGGTCAT
1 TCGGGTCAT
*
81933 ACGGGT--T
1 TCGGGTCAT
81940 TCGGGTCAT
1 TCGGGTCAT
81949 TCGGGTC--
1 TCGGGTCAT
81956 TCGGGTCAT
1 TCGGGTCAT
*
81965 TCAGGT--T
1 TCGGGTCAT
*
81972 CCGGGTCAT
1 TCGGGTCAT
81981 TCGGGTC
1 TCGGGTC
81988 TCGGGTCTAC
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
7 18 0.42
9 25 0.58
ACGTcount: A:0.09, C:0.23, G:0.36, T:0.31
Consensus pattern (9 bp):
TCGGGTCAT
Found at i:82001 original size:16 final size:16
Alignment explanation
Indices: 81919--82009 Score: 55
Period size: 16 Copynumber: 5.7 Consensus size: 16
81909 CGGGTCGTTT
81919 GGGTCTCGGGTCATA-C
1 GGGTCTCGGGTC-TACC
* *
81935 GGGTTTCGGGTC-ATTC
1 GGGTCTCGGGTCTA-CC
* *
81951 GGGTCTCGGGTCATTCA
1 GGGTCTCGGGTC-TACC
* *
81968 GGTTC-CGGGTC-ATTC
1 GGGTCTCGGGTCTA-CC
81983 GGGTCTCGGGTCTACC
1 GGGTCTCGGGTCTACC
*
81999 GGGTCTTGGGT
1 GGGTCTCGGGT
82010 TGGGCGGGTT
Statistics
Matches: 56, Mismatches: 12, Indels: 14
0.68 0.15 0.17
Matches are distributed among these distances:
14 1 0.02
15 4 0.07
16 46 0.82
17 5 0.09
ACGTcount: A:0.08, C:0.23, G:0.38, T:0.31
Consensus pattern (16 bp):
GGGTCTCGGGTCTACC
Found at i:82479 original size:21 final size:21
Alignment explanation
Indices: 82454--82501 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
82444 TAGCGAATTT
82454 ATAATAGGTAAAATCATAACA
1 ATAATAGGTAAAATCATAACA
* *
82475 ATAATTGGTAAAATTATAACA
1 ATAATAGGTAAAATCATAACA
82496 ATAATA
1 ATAATA
82502 TAAATTGTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.56, C:0.06, G:0.08, T:0.29
Consensus pattern (21 bp):
ATAATAGGTAAAATCATAACA
Found at i:82643 original size:32 final size:32
Alignment explanation
Indices: 82605--82678 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 32
82595 TCGGGTTAAT
* * * *
82605 GTCTCGGGTTATTTGGGTTTCGGGTCATAC-GA
1 GTCTCGGGTCATTCGGGTTACGGATCAT-CTGA
*
82637 GTCTCGGGTCATTCGGGTTACGGATCATCTGG
1 GTCTCGGGTCATTCGGGTTACGGATCATCTGA
82669 GTCTCGGGTC
1 GTCTCGGGTC
82679 GTTTACTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
31 1 0.03
32 35 0.97
ACGTcount: A:0.11, C:0.20, G:0.35, T:0.34
Consensus pattern (32 bp):
GTCTCGGGTCATTCGGGTTACGGATCATCTGA
Found at i:84945 original size:14 final size:13
Alignment explanation
Indices: 84926--84987 Score: 61
Period size: 14 Copynumber: 4.5 Consensus size: 13
84916 TATAATAATA
*
84926 AAATAACAATTACT
1 AAATAA-AAATACT
84940 AAATAAAAATACT
1 AAATAAAAATACT
*
84953 AAATAAAATAATAAT
1 AAAT-AAA-AATACT
*
84968 AAAAATAAAATACT
1 AAATA-AAAATACT
84982 AAATAA
1 AAATAA
84988 TAACACTCTA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
13 11 0.28
14 19 0.47
15 10 0.25
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.24
Consensus pattern (13 bp):
AAATAAAAATACT
Found at i:84971 original size:24 final size:23
Alignment explanation
Indices: 84913--84990 Score: 70
Period size: 24 Copynumber: 3.3 Consensus size: 23
84903 ACTCTGAAAT
* *
84913 TAAT-ATAATAATAAAATAACAAT
1 TAATAATAAAAATAAAAT-ACAAA
*
84936 TACTAAATAAAAATACTAAATA-AAA
1 TAAT-AATAAAAATA--AAATACAAA
84961 TAATAATAAAAATAAAATACTAAA
1 TAATAATAAAAATAAAATAC-AAA
84985 TAATAA
1 TAATAA
84991 CACTCTATAA
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
22 5 0.11
23 3 0.07
24 19 0.42
25 13 0.29
26 1 0.02
27 4 0.09
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (23 bp):
TAATAATAAAAATAAAATACAAA
Found at i:84983 original size:29 final size:32
Alignment explanation
Indices: 84922--84987 Score: 93
Period size: 29 Copynumber: 2.2 Consensus size: 32
84912 TTAATATAAT
*
84922 AATAAAATAACAATTACTAAATAAAAATACTA
1 AATAAAATAACAATTACAAAATAAAAATACTA
*
84954 AATAAAATAATAA-TA-AAAAT-AAAATACTA
1 AATAAAATAACAATTACAAAATAAAAATACTA
84983 AATAA
1 AATAA
84988 TAACACTCTA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
29 14 0.44
30 4 0.12
31 2 0.06
32 12 0.38
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.24
Consensus pattern (32 bp):
AATAAAATAACAATTACAAAATAAAAATACTA
Found at i:87253 original size:2 final size:2
Alignment explanation
Indices: 87246--87273 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
87236 GGATTCCTGC
87246 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
87274 TATGCAAAAT
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.