Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014082.1 Corchorus capsularis cultivar CVL-1 contig14103, 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: 71971
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:1819 original size:24 final size:25
Alignment explanation
Indices: 1780--1831 Score: 79
Period size: 24 Copynumber: 2.1 Consensus size: 25
1770 GCCACCGTAA
* *
1780 ACAAGCTTGCACAGGATTGAAATTC
1 ACAAGCTTGCAAAGGATTGAAACTC
1805 ACAAGC-TGCAAAGGATTGAAACTC
1 ACAAGCTTGCAAAGGATTGAAACTC
1829 ACA
1 ACA
1832 TGTACTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 19 0.76
25 6 0.24
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.19
Consensus pattern (25 bp):
ACAAGCTTGCAAAGGATTGAAACTC
Found at i:10101 original size:3 final size:3
Alignment explanation
Indices: 10095--10134 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
10085 TATTATATTT
10095 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
10135 CAACGAGATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:11030 original size:11 final size:11
Alignment explanation
Indices: 11014--11049 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
11004 ATTTATTCAT
11014 TATTAATTA-A
1 TATTAATTAGA
11024 CTATTAATTAGA
1 -TATTAATTAGA
11036 TATTAATTAGA
1 TATTAATTAGA
11047 TAT
1 TAT
11050 ATAGTATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 23 0.96
12 1 0.04
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (11 bp):
TATTAATTAGA
Found at i:12298 original size:17 final size:17
Alignment explanation
Indices: 12276--12310 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
12266 TAAGGGGAAG
12276 AAGAAAGAAGA-AAAAGA
1 AAGAAA-AAGAGAAAAGA
12293 AAGAAAAAGAGAAAAGA
1 AAGAAAAAGAGAAAAGA
12310 A
1 A
12311 TTCAGTGGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (17 bp):
AAGAAAAAGAGAAAAGA
Found at i:26741 original size:18 final size:19
Alignment explanation
Indices: 26718--26755 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
26708 CCACCCATTC
26718 TCTCTCCTTT-CTCTTCTA
1 TCTCTCCTTTACTCTTCTA
26736 TCTCTCCTTTACTCTTCTA
1 TCTCTCCTTTACTCTTCTA
26755 T
1 T
26756 GGTTTCAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.08, C:0.37, G:0.00, T:0.55
Consensus pattern (19 bp):
TCTCTCCTTTACTCTTCTA
Found at i:27761 original size:31 final size:32
Alignment explanation
Indices: 27721--27781 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
27711 GGGTTCGGGT
*
27721 TTAAGTCAGG-TCATGTTGAATTTGGGTCAGA
1 TTAAGTCAGGTTCAGGTTGAATTTGGGTCAGA
* *
27752 TTAATTCAGGTTCGGGTTGAATTTGGGTCA
1 TTAAGTCAGGTTCAGGTTGAATTTGGGTCA
27782 TGTTGATTCG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 9 0.35
32 17 0.65
ACGTcount: A:0.23, C:0.10, G:0.30, T:0.38
Consensus pattern (32 bp):
TTAAGTCAGGTTCAGGTTGAATTTGGGTCAGA
Found at i:27772 original size:32 final size:32
Alignment explanation
Indices: 27735--27811 Score: 102
Period size: 32 Copynumber: 2.4 Consensus size: 32
27725 GTCAGGTCAT
27735 GTTGAATTTGGGTCA-GATTAATTCAGGTTCGG
1 GTTGAATTTGGGTCATG-TTAATTCAGGTTCGG
* *
27767 GTTGAATTTGGGTCATGTTGATTCGGGTTCGG
1 GTTGAATTTGGGTCATGTTAATTCAGGTTCGG
* *
27799 GTTCAGTTTGGGT
1 GTTGAATTTGGGT
27812 TTTGGCCAGA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
32 39 0.98
33 1 0.03
ACGTcount: A:0.16, C:0.09, G:0.35, T:0.40
Consensus pattern (32 bp):
GTTGAATTTGGGTCATGTTAATTCAGGTTCGG
Found at i:36199 original size:18 final size:19
Alignment explanation
Indices: 36142--36199 Score: 55
Period size: 24 Copynumber: 2.8 Consensus size: 19
36132 TATTAATTGT
36142 TAAATTAAATTAAGTGTAA
1 TAAATTAAATTAAGTGTAA
*
36161 TAAAAACTTATTAACTAAGTGTAA
1 T--AAA-TTA--AATTAAGTGTAA
36185 T-AATTAAATTAAGTG
1 TAAATTAAATTAAGTG
36200 AATGATTGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 11
0.71 0.04 0.24
Matches are distributed among these distances:
18 8 0.25
19 1 0.03
20 3 0.09
21 5 0.16
22 3 0.09
24 12 0.38
ACGTcount: A:0.50, C:0.03, G:0.10, T:0.36
Consensus pattern (19 bp):
TAAATTAAATTAAGTGTAA
Found at i:37468 original size:14 final size:14
Alignment explanation
Indices: 37449--37475 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
37439 CAAAATTACC
37449 CTTACTTAATAAAA
1 CTTACTTAATAAAA
37463 CTTACTTAATAAA
1 CTTACTTAATAAA
37476 CTAATAGAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (14 bp):
CTTACTTAATAAAA
Found at i:37590 original size:18 final size:19
Alignment explanation
Indices: 37562--37600 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
37552 AGATACAATA
37562 TTTATAATAA-TTATTATTT
1 TTTATAATAATTTA-TATTT
37581 TTTA-AATAATTTATATTT
1 TTTATAATAATTTATATTT
37599 TT
1 TT
37601 ACTTCTTTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTATAATAATTTATATTT
Found at i:38286 original size:6 final size:6
Alignment explanation
Indices: 38275--38301 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
38265 TTTCGAAGGC
38275 TTTGGT TTTGGT TTTGGT TTTGGT TTT
1 TTTGGT TTTGGT TTTGGT TTTGGT TTT
38302 AAGGAGCTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.30, T:0.70
Consensus pattern (6 bp):
TTTGGT
Found at i:39169 original size:16 final size:16
Alignment explanation
Indices: 39139--39193 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
39129 TCATACGTGT
* *
39139 CTCGGGTCACAGGTCA
1 CTCGGGTTACGGGTCA
39155 CTCGGGTTACGGGTCA
1 CTCGGGTTACGGGTCA
* * *
39171 TTTGGATTACGGGTCA
1 CTCGGGTTACGGGTCA
*
39187 TTCGGGT
1 CTCGGGT
39194 CATCTAGGTT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.15, C:0.22, G:0.35, T:0.29
Consensus pattern (16 bp):
CTCGGGTTACGGGTCA
Found at i:46841 original size:21 final size:22
Alignment explanation
Indices: 46817--46863 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
46807 ATTATCAAGA
* *
46817 AATATTA-AATATTCTAGGGAT
1 AATATTAGAATATACTAGAGAT
46838 AATA-TAGAATATACTAGAGAT
1 AATATTAGAATATACTAGAGAT
46859 AATAT
1 AATAT
46864 GATTCCCTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.49, C:0.04, G:0.13, T:0.34
Consensus pattern (22 bp):
AATATTAGAATATACTAGAGAT
Found at i:51052 original size:2 final size:2
Alignment explanation
Indices: 51040--51073 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
51030 TTTTTAGTTG
*
51040 CT CT GCT CT CT CT CT CT TT CT CT CT CT CT CT CT C
1 CT CT -CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
51074 AGTCTCACTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.00, C:0.47, G:0.03, T:0.50
Consensus pattern (2 bp):
CT
Found at i:55405 original size:25 final size:24
Alignment explanation
Indices: 55371--55419 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 24
55361 TATGGTCTGT
55371 TAGATTGTTCATTTTCAAGCCCAA
1 TAGATTGTTCATTTTCAAGCCCAA
55395 TAGATTTGTTCATTTTCAAGCCCAA
1 TAGA-TTGTTCATTTTCAAGCCCAA
55420 AGAGGATTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 4 0.17
25 20 0.83
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (24 bp):
TAGATTGTTCATTTTCAAGCCCAA
Found at i:61358 original size:22 final size:22
Alignment explanation
Indices: 61330--61438 Score: 79
Period size: 22 Copynumber: 5.1 Consensus size: 22
61320 ATTATACTAT
*
61330 TTTTGATGATGTCCTTATGAAA
1 TTTTGATAATGTCCTTATGAAA
*
61352 TTTTGATAATCTTCC-TATGAAA
1 TTTTGATAAT-GTCCTTATGAAA
* *
61374 TTATGATAAT-TACATTAT----
1 TTTTGATAATGT-CCTTATGAAA
* * *
61392 TTTTTATGACGTCCTTATGAAA
1 TTTTGATAATGTCCTTATGAAA
61414 TTTTGATAATGTTCC-TATGAAA
1 TTTTGATAATG-TCCTTATGAAA
61436 TTT
1 TTT
61439 CAATAACGAT
Statistics
Matches: 66, Mismatches: 12, Indels: 18
0.69 0.12 0.19
Matches are distributed among these distances:
18 11 0.17
19 1 0.02
20 1 0.02
21 1 0.02
22 46 0.70
23 6 0.09
ACGTcount: A:0.30, C:0.10, G:0.12, T:0.48
Consensus pattern (22 bp):
TTTTGATAATGTCCTTATGAAA
Found at i:61380 original size:62 final size:62
Alignment explanation
Indices: 61283--61437 Score: 238
Period size: 62 Copynumber: 2.5 Consensus size: 62
61273 GAAATATTCA
* * * * *
61283 TATGAAATTATGATAACCTTCCTATTAAATTATGATAATTATACTATTTTTGATGATGTCCT
1 TATGAAATTTTGATAATCTTCCTATGAAATTATGATAATTACACTATTTTTGATGACGTCCT
* *
61345 TATGAAATTTTGATAATCTTCCTATGAAATTATGATAATTACATTATTTTTTATGACGTCCT
1 TATGAAATTTTGATAATCTTCCTATGAAATTATGATAATTACACTATTTTTGATGACGTCCT
*
61407 TATGAAATTTTGATAATGTTCCTATGAAATT
1 TATGAAATTTTGATAATCTTCCTATGAAATT
61438 TCAATAACGA
Statistics
Matches: 85, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
62 85 1.00
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.46
Consensus pattern (62 bp):
TATGAAATTTTGATAATCTTCCTATGAAATTATGATAATTACACTATTTTTGATGACGTCCT
Found at i:61510 original size:24 final size:22
Alignment explanation
Indices: 61465--61510 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
61455 GAATTTCGAG
*
61465 AACCTTCTTATAATTTTTTTAA
1 AACCTTCTTATAATTTTGTTAA
61487 AACCTTCTTATGAAATTTTGTTAA
1 AACCTTCTTAT--AATTTTGTTAA
61511 CCTCCCTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 11 0.52
24 10 0.48
ACGTcount: A:0.33, C:0.13, G:0.04, T:0.50
Consensus pattern (22 bp):
AACCTTCTTATAATTTTGTTAA
Found at i:61587 original size:22 final size:22
Alignment explanation
Indices: 61539--61943 Score: 167
Period size: 22 Copynumber: 18.7 Consensus size: 22
61529 AAGGCCTCAC
* *
61539 TATGAAATTTTGATAACTTCCA
1 TATGAAATTTTGATAACCTACA
*
61561 AATGAAATTTTGATAACCTACA
1 TATGAAATTTTGATAACCTACA
* * * *
61583 TATGATATATTGATAATC-ACGT
1 TATGAAATTTTGATAACCTAC-A
* ** * *
61605 TATGAAAATTAAAAAACCTCCA
1 TATGAAATTTTGATAACCTACA
* * *
61627 TATG-AATTGTCAGTAATC-ACA
1 TATGAAATTTTGA-TAACCTACA
* * *
61648 CTCTTAAATTTTGATAA-TTACA
1 -TATGAAATTTTGATAACCTACA
* *
61670 CTATGAAATTATGATAACCT-CGT
1 -TATGAAATTTTGATAACCTAC-A
* *
61693 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTACA
* ** * *
61715 TATAAAATTTTGATAAATTTCCC
1 TATGAAATTTTGAT-AACCTACA
* * *
61738 TATAAAATTTTGATAACCTCCT
1 TATGAAATTTTGATAACCTACA
*
61760 TATGAAATCTTGATAA-CTAC-
1 TATGAAATTTTGATAACCTACA
* * *
61780 ----AAATTTTGATAATCTCCC
1 TATGAAATTTTGATAACCTACA
**
61798 TATGATTTTTTGATAACCT-CA
1 TATGAAATTTTGATAACCTACA
* * * *
61819 TTATG-AATTTTGTTAATCTCCC
1 -TATGAAATTTTGATAACCTACA
* * *
61841 TATGAAATTTTGATCTACATGC-
1 TATGAAATTTTGAT-AACCTACA
*
61863 TATGAAATTTTGATAACCCT-CT
1 TATGAAATTTTGATAA-CCTACA
* *
61885 TATGAAATTTTGA-AAACTAAA
1 TATGAAATTTTGATAACCTACA
***
61906 CTATGAAATTTTGATAACCTTTG
1 -TATGAAATTTTGATAACCTACA
61929 TATGAAATTTTGATA
1 TATGAAATTTTGATA
61944 TCCTCCCTGA
Statistics
Matches: 287, Mismatches: 71, Indels: 50
0.70 0.17 0.12
Matches are distributed among these distances:
16 11 0.04
17 3 0.01
20 2 0.01
21 30 0.10
22 206 0.72
23 35 0.12
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTACA
Found at i:61587 original size:44 final size:43
Alignment explanation
Indices: 61539--61943 Score: 190
Period size: 44 Copynumber: 9.3 Consensus size: 43
61529 AAGGCCTCAC
* *
61539 TATGAAATTTTGATAACTTCCAAATGAAATTTTGATAACCTACA
1 TATGAAATTTTGATAAC-TCCATATGAAATTTTGATAACCTCCA
* * * * ** *
61583 TATGATATATTGATAA-TCACGTTATGAAAATTAAAAAACCTCCA
1 TATGAAATTTTGATAACTC-C-ATATGAAATTTTGATAACCTCCA
* * * * * *
61627 TATG-AATTGTCAGTAA-TCACACTCTTAAATTTTGATAA-TTACA
1 TATGAAATTTTGA-TAACTC-CA-TATGAAATTTTGATAACCTCCA
* **
61670 CTATGAAATTATGATAACCTCGTTATGAAATTTTGATAACCTTCC-
1 -TATGAAATTTTGATAA-CTCCATATGAAATTTTGATAACC-TCCA
* * * * *
61715 TATAAAATTTTGATAAATTTCCCTATAAAATTTTGATAACCTCCT
1 TATGAAATTTTGAT-AA-CTCCATATGAAATTTTGATAACCTCCA
* * * *
61760 TATGAAATCTTGATAA---C-TA-CAAATTTTGATAATCTCCC
1 TATGAAATTTTGATAACTCCATATGAAATTTTGATAACCTCCA
** * * *
61798 TATGATTTTTTGATAAC-CTCATTATG-AATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACTC-CA-TATGAAATTTTGATAACCTCCA
* * *
61841 TATGAAATTTTGATCTACATGC-TATGAAATTTTGATAACC-CTCT
1 TATGAAATTTTGAT-AAC-TCCATATGAAATTTTGATAACCTC-CA
* ** ***
61885 TATGAAATTTTGAAAACTAAACTATGAAATTTTGATAACCTTTG
1 TATGAAATTTTGATAACTCCA-TATGAAATTTTGATAACCTCCA
61929 TATGAAATTTTGATA
1 TATGAAATTTTGATA
61944 TCCTCCCTGA
Statistics
Matches: 273, Mismatches: 62, Indels: 52
0.71 0.16 0.13
Matches are distributed among these distances:
38 29 0.11
39 2 0.01
40 1 0.00
41 1 0.00
42 3 0.01
43 45 0.16
44 148 0.54
45 40 0.15
46 4 0.01
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (43 bp):
TATGAAATTTTGATAACTCCATATGAAATTTTGATAACCTCCA
Found at i:62089 original size:22 final size:22
Alignment explanation
Indices: 62038--62166 Score: 134
Period size: 22 Copynumber: 5.9 Consensus size: 22
62028 TCCCCAGAAA
* * * *
62038 TATGAAATTTTGGTAATCACAT
1 TATGAAATTTTGATAACCTCTT
62060 T-TGAAATTTTGATAACCTCTT
1 TATGAAATTTTGATAACCTCTT
*
62081 TATGAAATTTTGATAACCTCTC
1 TATGAAATTTTGATAACCTCTT
* * * *
62103 TATAAAATTTTGTTGACCCCTT
1 TATGAAATTTTGATAACCTCTT
* * *
62125 TATGAAATTTTGATAATCACAT
1 TATGAAATTTTGATAACCTCTT
*
62147 TATGTAATTTTGATAACCTC
1 TATGAAATTTTGATAACCTC
62167 GCTTTAAAAT
Statistics
Matches: 87, Mismatches: 19, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
21 17 0.20
22 70 0.80
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCTT
Found at i:62156 original size:44 final size:44
Alignment explanation
Indices: 62038--62181 Score: 161
Period size: 44 Copynumber: 3.3 Consensus size: 44
62028 TCCCCAGAAA
* *
62038 TATGAAATTTTGGTAATCACATT-TGAAATTTTGATAACCTCTT
1 TATGAAATTTTGATAATCACATTATGAAATTTTGATAACCCCTT
* * * * *
62081 TATGAAATTTTGATAACCTC-TCTATAAAATTTTGTTGACCCCTT
1 TATGAAATTTTGATAATCACAT-TATGAAATTTTGATAACCCCTT
*
62125 TATGAAATTTTGATAATCACATTATGTAATTTTGATAACCTCGCTT
1 TATGAAATTTTGATAATCACATTATGAAATTTTGATAACC-C-CTT
62171 TA--AAATTTTGA
1 TATGAAATTTTGA
62182 AATTGGACCA
Statistics
Matches: 83, Mismatches: 13, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
42 1 0.01
43 18 0.22
44 57 0.69
45 2 0.02
46 5 0.06
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (44 bp):
TATGAAATTTTGATAATCACATTATGAAATTTTGATAACCCCTT
Found at i:62177 original size:22 final size:21
Alignment explanation
Indices: 62063--62181 Score: 89
Period size: 22 Copynumber: 5.4 Consensus size: 21
62053 ATCACATTTG
62063 AAATTTTGATAACCT-CTTTA
1 AAATTTTGATAACCTCCTTTA
*
62083 TGAAATTTTGATAACCTCTCTATA
1 --AAATTTTGATAACCTC-CTTTA
* *
62107 AAATTTTGTTGACC-CCTTTA
1 AAATTTTGATAACCTCCTTTA
* * * *
62127 TGAAATTTTGATAATCACATTATG
1 --AAATTTTGATAACCTCCTT-TA
*
62151 TAATTTTGATAACCTCGCTTTA
1 AAATTTTGATAACCTC-CTTTA
62173 AAATTTTGA
1 AAATTTTGA
62182 AATTGGACCA
Statistics
Matches: 75, Mismatches: 15, Indels: 14
0.72 0.14 0.13
Matches are distributed among these distances:
20 4 0.05
21 1 0.01
22 60 0.80
23 5 0.07
24 5 0.07
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (21 bp):
AAATTTTGATAACCTCCTTTA
Found at i:62486 original size:32 final size:32
Alignment explanation
Indices: 62450--62516 Score: 93
Period size: 31 Copynumber: 2.1 Consensus size: 32
62440 TTAGTAATGG
62450 CAATTTAGAAATATGTTATTAAAAA-AAGGATA
1 CAATTTAGAAATATGTT-TTAAAAATAAGGATA
* *
62482 CAA-TTGGAAATATGTTTTAAAAATAAGGGTA
1 CAATTTAGAAATATGTTTTAAAAATAAGGATA
62513 CAAT
1 CAAT
62517 CGGAAAACAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 7 0.23
31 21 0.68
32 3 0.10
ACGTcount: A:0.49, C:0.04, G:0.15, T:0.31
Consensus pattern (32 bp):
CAATTTAGAAATATGTTTTAAAAATAAGGATA
Found at i:62495 original size:31 final size:31
Alignment explanation
Indices: 62457--62522 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
62447 TGGCAATTTA
*
62457 GAAATATGTTATTAAAAA-AAGGATACAATTG
1 GAAATATGTT-TTAAAAATAAGGATACAATCG
*
62488 GAAATATGTTTTAAAAATAAGGGTACAATCG
1 GAAATATGTTTTAAAAATAAGGATACAATCG
62519 GAAA
1 GAAA
62523 ACATAAAGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 7 0.22
31 25 0.78
ACGTcount: A:0.50, C:0.05, G:0.18, T:0.27
Consensus pattern (31 bp):
GAAATATGTTTTAAAAATAAGGATACAATCG
Found at i:67379 original size:18 final size:18
Alignment explanation
Indices: 67356--67402 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
67346 TAACCTCCTT
**
67356 CATTGGTAGCAGGATTGG
1 CATTGGTAGCAGGATTAA
*
67374 CATTGGTAGCAGTATTAA
1 CATTGGTAGCAGGATTAA
67392 CATTGGTAGCA
1 CATTGGTAGCA
67403 CCATTAACCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.28, C:0.13, G:0.30, T:0.30
Consensus pattern (18 bp):
CATTGGTAGCAGGATTAA
Found at i:67408 original size:18 final size:18
Alignment explanation
Indices: 67374--67410 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
67364 GCAGGATTGG
**
67374 CATTGGTAGCAGTATTAA
1 CATTGGTAGCACCATTAA
67392 CATTGGTAGCACCATTAA
1 CATTGGTAGCACCATTAA
67410 C
1 C
67411 CAAAGTCACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (18 bp):
CATTGGTAGCACCATTAA
Found at i:68027 original size:29 final size:28
Alignment explanation
Indices: 67993--68049 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
67983 TAACTATCCA
*
67993 TTTTGGAACAAATTGGCACTTGAACTTTT
1 TTTTGGAACAAATTGCCACTT-AACTTTT
* *
68022 TTTTGGGACAAATTGCCCCTTAACTTTT
1 TTTTGGAACAAATTGCCACTTAACTTTT
68050 AAAAACGAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 7 0.28
29 18 0.72
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.42
Consensus pattern (28 bp):
TTTTGGAACAAATTGCCACTTAACTTTT
Found at i:68795 original size:28 final size:27
Alignment explanation
Indices: 68741--68796 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
68731 TCTCGTTTTT
* *
68741 AAAAATTAAGGGATCAATTTATCCAAA
1 AAAAATTAAGAGACCAATTTATCCAAA
* *
68768 AAAAATTAAGAGACCAATTTGTCCCAA
1 AAAAATTAAGAGACCAATTTATCCAAA
68795 AA
1 AA
68797 TGTATAGTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.52, C:0.14, G:0.11, T:0.23
Consensus pattern (27 bp):
AAAAATTAAGAGACCAATTTATCCAAA
Found at i:71826 original size:14 final size:15
Alignment explanation
Indices: 71797--71840 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
71787 CGTCCCACTT
*
71797 TTTACACTTTTGCCC
1 TTTACACTTTTACCC
71812 TTTAC-CTTTTACCC
1 TTTACACTTTTACCC
71826 TTTTTACACTTTTAC
1 --TTTACACTTTTAC
71841 ACTGAGCCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 8 0.32
15 5 0.20
16 5 0.20
17 7 0.28
ACGTcount: A:0.16, C:0.30, G:0.02, T:0.52
Consensus pattern (15 bp):
TTTACACTTTTACCC
Done.