Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011393.1 Corchorus capsularis cultivar CVL-1 contig11414, 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: 80228
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3466 original size:32 final size:32
Alignment explanation
Indices: 3418--3832 Score: 282
Period size: 36 Copynumber: 12.5 Consensus size: 32
3408 TAAACTAAAG
*
3418 AAGTAAAAGAA--AATCAGTAGAAAGGAGTGA
1 AAGTAAAAGAAGTAATCAGTAGAAAGGAGTAA
* *
3448 AAGTAAGAGAAGTAATCAGTAGAAGAAAAAGAGTAA
1 AAGTAAAAGAAGTAATCAGT---AG-AAAGGAGTAA
* *
3484 AAGTAAAAGGAGTAATCAGTGGAAGTAAAGGAGTGA
1 AAGTAAAAGAAGTAATCAGT---AG-AAAGGAGTAA
*
3520 AAGTAAAAGAAGTAATCAGTAGAAATAAAAGAGTAA
1 AAGTAAAAGAAGTAATCAGTAG----AAAGGAGTAA
* *
3556 AAGTAAAAGAAGTAATCAGAAAAAGGAAAAGAGTAA
1 AAGTAAAAGAAGTAATCAG---TA-GAAAGGAGTAA
* *
3592 AAGTAAGAGAAGTAATCAGTAGAAGTAAAGGAGTAC
1 AAGTAAAAGAAGTAATCAGT---AG-AAAGGAGTAA
* **
3628 AAGTAAAAGAAGTAATTAGCATAATGAAGTAAAAGT-A
1 AAGTAAAAGAAGTAATCAG--T-A-GAA--AGGAGTAA
* * *
3665 AAGTAAAAGAGGTAATCAGCAGAGTA-GAGTAA
1 AAGTAAAAGAAGTAATCAGTAGA-AAGGAGTAA
3697 AAGTAAAAGAAGTAATCAGTAG-AAGGAAGTAA
1 AAGTAAAAGAAGTAATCAGTAGAAAGG-AGTAA
*
3729 GAGTAAAAGAAGTAATCAGTA-AAA-GAGTAA
1 AAGTAAAAGAAGTAATCAGTAGAAAGGAGTAA
3759 AAG-----GAAGTAATCAGTAGAAAGGAGTAA
1 AAGTAAAAGAAGTAATCAGTAGAAAGGAGTAA
* *
3786 AAG-AAGAAAAAGTAATCAGCA-AAATGGAGTAA
1 AAGTAA-AAGAAGTAATCAGTAGAAA-GGAGTAA
*
3818 AAGTAAAAGGAGTAA
1 AAGTAAAAGAAGTAA
3833 AAGGGGTAAA
Statistics
Matches: 313, Mismatches: 36, Indels: 70
0.75 0.09 0.17
Matches are distributed among these distances:
25 13 0.04
26 3 0.01
27 9 0.03
30 18 0.06
31 8 0.03
32 84 0.27
33 6 0.02
34 1 0.00
35 3 0.01
36 143 0.46
37 18 0.06
38 5 0.02
39 1 0.00
40 1 0.00
ACGTcount: A:0.56, C:0.04, G:0.25, T:0.15
Consensus pattern (32 bp):
AAGTAAAAGAAGTAATCAGTAGAAAGGAGTAA
Found at i:3498 original size:36 final size:36
Alignment explanation
Indices: 3442--3754 Score: 306
Period size: 36 Copynumber: 8.9 Consensus size: 36
3432 CAGTAGAAAG
* *
3442 GAGTGAAAGTAAGAGAAGTAATCAGTAGAAGAAAAA
1 GAGTAAAAGTAAAAGAAGTAATCAGTAGAAGAAAAA
* * * *
3478 GAGTAAAAGTAAAAGGAGTAATCAGTGGAAGTAAAG
1 GAGTAAAAGTAAAAGAAGTAATCAGTAGAAGAAAAA
*
3514 GAGTGAAAGTAAAAGAAGTAATCAGTAGAA-ATAAAA
1 GAGTAAAAGTAAAAGAAGTAATCAGTAGAAGA-AAAA
* * *
3550 GAGTAAAAGTAAAAGAAGTAATCAGAAAAAGGAAAA
1 GAGTAAAAGTAAAAGAAGTAATCAGTAGAAGAAAAA
* * *
3586 GAGTAAAAGTAAGAGAAGTAATCAGTAGAAGTAAAG
1 GAGTAAAAGTAAAAGAAGTAATCAGTAGAAGAAAAA
* * * *
3622 GAGTACAAGTAAAAGAAGTAATTAGCATAATGAAGTAAA
1 GAGTAAAAGTAAAAGAAGTAATCAGTAGAA-GAA--AAA
* * *
3661 -AGT-AAAGTAAAAGAGGTAATCAGCAG-AG---TA
1 GAGTAAAAGTAAAAGAAGTAATCAGTAGAAGAAAAA
*
3691 GAGTAAAAGTAAAAGAAGTAATCAGTAGAAG---GA
1 GAGTAAAAGTAAAAGAAGTAATCAGTAGAAGAAAAA
* *
3724 -AGTAAGAGTAAAAGAAGTAATCAGTAAAAGA
1 GAGTAAAAGTAAAAGAAGTAATCAGTAGAAGA
3755 GTAAAAGGAA
Statistics
Matches: 231, Mismatches: 37, Indels: 21
0.80 0.13 0.07
Matches are distributed among these distances:
30 1 0.00
31 3 0.01
32 49 0.21
33 3 0.01
35 1 0.00
36 148 0.64
37 21 0.09
38 3 0.01
39 2 0.01
ACGTcount: A:0.55, C:0.04, G:0.25, T:0.16
Consensus pattern (36 bp):
GAGTAAAAGTAAAAGAAGTAATCAGTAGAAGAAAAA
Found at i:3749 original size:16 final size:16
Alignment explanation
Indices: 3698--3758 Score: 81
Period size: 16 Copynumber: 3.9 Consensus size: 16
3688 GTAGAGTAAA
3698 AGTAAAAGAAGTAATC
1 AGTAAAAGAAGTAATC
* *
3714 AGTAGAAGGAAGTAA-G
1 AGTA-AAAGAAGTAATC
3730 AGTAAAAGAAGTAATC
1 AGTAAAAGAAGTAATC
3746 AGTAAAAG-AGTAA
1 AGTAAAAGAAGTAA
3759 AAGGAAGTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
15 14 0.36
16 16 0.41
17 9 0.23
ACGTcount: A:0.56, C:0.03, G:0.25, T:0.16
Consensus pattern (16 bp):
AGTAAAAGAAGTAATC
Found at i:3765 original size:25 final size:26
Alignment explanation
Indices: 3727--3788 Score: 101
Period size: 25 Copynumber: 2.4 Consensus size: 26
3717 AGAAGGAAGT
3727 AAGAGTAAAA-GAAGTAATCAGTA-A
1 AAGAGTAAAAGGAAGTAATCAGTAGA
3751 AAGAGTAAAAGGAAGTAATCAGTAGA
1 AAGAGTAAAAGGAAGTAATCAGTAGA
3777 AAGGAGTAAAAG
1 AA-GAGTAAAAG
3789 AAGAAAAAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
24 10 0.29
25 13 0.37
26 3 0.09
27 9 0.26
ACGTcount: A:0.56, C:0.03, G:0.26, T:0.15
Consensus pattern (26 bp):
AAGAGTAAAAGGAAGTAATCAGTAGA
Found at i:3774 original size:57 final size:58
Alignment explanation
Indices: 3698--3820 Score: 164
Period size: 57 Copynumber: 2.1 Consensus size: 58
3688 GTAGAGTAAA
* * *
3698 AGTAAAA-GAAGTAATCAGTAG-AAGGAAGTAAGAGTAA-AAGAAGTAATCAGTAAAA-G
1 AGTAAAAGGAAGTAATCAGTAGAAAGG-AGTAAAAG-AAGAAAAAGTAATCAGCAAAAGG
3754 AGTAAAAGGAAGTAATCAGTAGAAAGGAGTAAAAGAAGAAAAAGTAATCAGCAAAATGG
1 AGTAAAAGGAAGTAATCAGTAGAAAGGAGTAAAAGAAGAAAAAGTAATCAGCAAAA-GG
3813 AGTAAAAG
1 AGTAAAAG
3821 TAAAAGGAGT
Statistics
Matches: 59, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
56 9 0.15
57 37 0.63
58 4 0.07
59 9 0.15
ACGTcount: A:0.56, C:0.04, G:0.25, T:0.15
Consensus pattern (58 bp):
AGTAAAAGGAAGTAATCAGTAGAAAGGAGTAAAAGAAGAAAAAGTAATCAGCAAAAGG
Found at i:3784 original size:17 final size:15
Alignment explanation
Indices: 3754--3835 Score: 58
Period size: 15 Copynumber: 5.1 Consensus size: 15
3744 TCAGTAAAAG
*
3754 AGTAAAAGGAAGTAATC
1 AGTAAAAGG-AGTAA-A
3771 AGTAGAAAGGAGTAAA
1 AGTA-AAAGGAGTAAA
** *
3787 AG-AAGAAAAAGTAATC
1 AGTAA-AAGGAGTAA-A
*
3803 AGCAAAATGGAGTAAA
1 AGTAAAA-GGAGTAAA
3819 AGTAAAAGGAGTAAA
1 AGTAAAAGGAGTAAA
3834 AG
1 AG
3836 GGGTAAACAG
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
14 1 0.02
15 18 0.35
16 12 0.23
17 16 0.31
18 5 0.10
ACGTcount: A:0.57, C:0.04, G:0.26, T:0.13
Consensus pattern (15 bp):
AGTAAAAGGAGTAAA
Found at i:3784 original size:89 final size:88
Alignment explanation
Indices: 3666--3832 Score: 205
Period size: 89 Copynumber: 1.9 Consensus size: 88
3656 GTAAAAGTAA
* * * * *
3666 AGTAAAAGAGGTAATCAGCAGAGTAGAGTAAAAGTAA-AAGAAGTAATCAGTAGAA-GGAAGTAA
1 AGTAAAAGAAGTAATCAGCAGAGAAGAGTAAAAG-AAGAAAAAGTAATCAGCAAAATGG-AGTAA
*
3729 GAGTAAAAGAAGTAATCAGTAAAAG
64 AAGTAAAAGAAGTAATCAGTAAAAG
*
3754 AGTAAAAGGAAGTAATCAGTAGA-AAGGAGTAAAAGAAGAAAAAGTAATCAGCAAAATGGAGTAA
1 AGTAAAA-GAAGTAATCAGCAGAGAA-GAGTAAAAGAAGAAAAAGTAATCAGCAAAATGGAGTAA
*
3818 AAGTAAAAGGAGTAA
64 AAGTAAAAGAAGTAA
3833 AAGGGGTAAA
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
88 10 0.15
89 55 0.82
90 2 0.03
ACGTcount: A:0.55, C:0.04, G:0.26, T:0.15
Consensus pattern (88 bp):
AGTAAAAGAAGTAATCAGCAGAGAAGAGTAAAAGAAGAAAAAGTAATCAGCAAAATGGAGTAAAA
GTAAAAGAAGTAATCAGTAAAAG
Found at i:3935 original size:17 final size:17
Alignment explanation
Indices: 3909--3942 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3899 ATAGTATTAA
*
3909 TTAGCTTAATTCGGGGT
1 TTAGCCTAATTCGGGGT
3926 TTAGCCTAATTCGGGGT
1 TTAGCCTAATTCGGGGT
3943 AATTGAGTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.15, G:0.29, T:0.38
Consensus pattern (17 bp):
TTAGCCTAATTCGGGGT
Found at i:5229 original size:22 final size:22
Alignment explanation
Indices: 5204--5612 Score: 210
Period size: 22 Copynumber: 18.4 Consensus size: 22
5194 AAAATATTCA
*
5204 TATGAAATTATGATAACCTCTC
1 TATGAAATTTTGATAACCTCTC
* *
5226 TATGAAATTTTTG-TAATCACAT-
1 TATGAAA-TTTTGATAACCTC-TC
* * *
5248 TTTGAAAATTTGATAACCTCTT
1 TATGAAATTTTGATAACCTCTC
*
5270 TATGAAATTTTGATAACCTCTT
1 TATGAAATTTTGATAACCTCTC
* * * *
5292 TATAAAATTTTGTTGACCCCTC
1 TATGAAATTTTGATAACCTCTC
* *
5314 TATGAAATTTTGATAATCACAT-
1 TATGAAATTTTGATAACCTC-TC
* *
5336 TATGTAATTTTGATAACCTCGC
1 TATGAAATTTTGATAACCTCTC
* ** *
5358 TTTGAAATTTTGATAACAACAC
1 TATGAAATTTTGATAACCTCTC
*
5380 TATGAAATTTTGATAATCT-TC
1 TATGAAATTTTGATAACCTCTC
*
5401 ATAT-AAATTTTGATAATCCGATCTT
1 -TATGAAATTTTGATAA-CC--TCTC
* * * *
5426 TTTGAAATTTCGATAATCACTC
1 TATGAAATTTTGATAACCTCTC
* *
5448 TAAGAGA-TTTGATAACCT-TC
1 TATGAAATTTTGATAACCTCTC
* * * *
5468 TATCAAATTTTGGTACTCCTTATC
1 TATGAAATTTTGATA-ACC-TCTC
* *
5492 AAATTGAGACTTTT-ATAACCT-TC
1 -TA-TGA-AATTTTGATAACCTCTC
* * * *
5515 ATATGAAGTTTTAATAACCACAC
1 -TATGAAATTTTGATAACCTCTC
* *
5538 TATAAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTCTC
* *
5560 AATGAAATATT-AGTAACCTC-C
1 TATGAAATTTTGA-TAACCTCTC
* * *
5581 TAATGAAATTTTGTTAACCACAC
1 T-ATGAAATTTTGATAACCTCTC
5604 TATGAAATT
1 TATGAAATT
5613 CGTATAATCC
Statistics
Matches: 290, Mismatches: 72, Indels: 50
0.70 0.17 0.12
Matches are distributed among these distances:
20 6 0.02
21 39 0.13
22 200 0.69
23 14 0.05
24 7 0.02
25 15 0.05
26 4 0.01
27 5 0.02
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCTC
Found at i:7353 original size:48 final size:47
Alignment explanation
Indices: 7282--7379 Score: 169
Period size: 48 Copynumber: 2.1 Consensus size: 47
7272 TATAATTTTC
*
7282 ATTTTATTTATAATCAAGTTTTTAATTGATAAATTTTTTTGGTACATA
1 ATTTTATTTATAATCAAGTTTTTAATTGA-AAATTTCTTTGGTACATA
*
7330 ATTTTATTTATAATCAAGTTTTTAATTGACAATTTCTTTGGTACATA
1 ATTTTATTTATAATCAAGTTTTTAATTGAAAATTTCTTTGGTACATA
7377 ATT
1 ATT
7380 GATAAATTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
47 19 0.40
48 29 0.60
ACGTcount: A:0.33, C:0.06, G:0.08, T:0.53
Consensus pattern (47 bp):
ATTTTATTTATAATCAAGTTTTTAATTGAAAATTTCTTTGGTACATA
Found at i:9920 original size:31 final size:31
Alignment explanation
Indices: 9794--9930 Score: 139
Period size: 31 Copynumber: 4.4 Consensus size: 31
9784 ATGTCCAATG
* * * * *
9794 TGGCATGCCATGTGTACTAAACAGTGACACG
1 TGGCATGCCACGTGTACCAAAAAGTGACGCA
* * *
9825 TGTCACGTCACGTGTACCAAAAAGTGACGCA
1 TGGCATGCCACGTGTACCAAAAAGTGACGCA
* * *
9856 TGTCACGCCACGTATACCAAAAAGTGACGCA
1 TGGCATGCCACGTGTACCAAAAAGTGACGCA
* * **
9887 TGGCATGTCACGTGTACCAGAAAGTGATACA
1 TGGCATGCCACGTGTACCAAAAAGTGACGCA
9918 TGGCATGCCACGT
1 TGGCATGCCACGT
9931 ACATAAAAAG
Statistics
Matches: 88, Mismatches: 18, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 88 1.00
ACGTcount: A:0.31, C:0.25, G:0.24, T:0.20
Consensus pattern (31 bp):
TGGCATGCCACGTGTACCAAAAAGTGACGCA
Found at i:11294 original size:24 final size:24
Alignment explanation
Indices: 11243--11294 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
11233 AAATTGTTCG
* * *
11243 ATGATGTAAGAATTATTCGACGCT
1 ATGATGTAAGAATTACTCCACGCC
*
11267 ATGATGTAAGAATTACTCCATGCC
1 ATGATGTAAGAATTACTCCACGCC
11291 ATGA
1 ATGA
11295 CGTGAACTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (24 bp):
ATGATGTAAGAATTACTCCACGCC
Found at i:12573 original size:4 final size:4
Alignment explanation
Indices: 12564--12589 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
12554 TACCTAATAC
12564 TAGA TAGA TAGA TAGA TAGA TAGA TA
1 TAGA TAGA TAGA TAGA TAGA TAGA TA
12590 AAAGTTGGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.23, T:0.27
Consensus pattern (4 bp):
TAGA
Found at i:12691 original size:42 final size:42
Alignment explanation
Indices: 12630--12714 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 42
12620 TGGCATAAAG
* *
12630 TTTGATTTGTTCTTATTAATGTATGCTAAAAAAACGAATATA
1 TTTGATTTGTTCTCATTAATGTATGCCAAAAAAACGAATATA
*
12672 TTTGATTTGTTCTCGTTAATGTATGCCAAAAAAACGAATATA
1 TTTGATTTGTTCTCATTAATGTATGCCAAAAAAACGAATATA
12714 T
1 T
12715 ATAGAGAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.41
Consensus pattern (42 bp):
TTTGATTTGTTCTCATTAATGTATGCCAAAAAAACGAATATA
Found at i:14831 original size:6 final size:6
Alignment explanation
Indices: 14820--14844 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
14810 ATCACTCATC
14820 AAGAGG AAGAGG AAGAGG AAGAGG A
1 AAGAGG AAGAGG AAGAGG AAGAGG A
14845 CTCCTCAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (6 bp):
AAGAGG
Found at i:17019 original size:13 final size:13
Alignment explanation
Indices: 17001--17027 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
16991 CACCATACAT
17001 ATTGAATTGAAGG
1 ATTGAATTGAAGG
17014 ATTGAATTGAAGG
1 ATTGAATTGAAGG
17027 A
1 A
17028 ATCCGATGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.30, T:0.30
Consensus pattern (13 bp):
ATTGAATTGAAGG
Found at i:19332 original size:15 final size:16
Alignment explanation
Indices: 19307--19337 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
19297 TAATGATGCT
19307 ACTCAAGAGGAAGAGG
1 ACTCAAGAGGAAGAGG
19323 ACTC-AGAGGAAGAGG
1 ACTCAAGAGGAAGAGG
19338 CCTACTGTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.42, C:0.13, G:0.39, T:0.06
Consensus pattern (16 bp):
ACTCAAGAGGAAGAGG
Found at i:37052 original size:31 final size:31
Alignment explanation
Indices: 37014--37078 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
37004 AACTGAACTA
37014 ACTCAAACATCCAAGATCTAAAGATCTGGAG
1 ACTCAAACATCCAAGATCTAAAGATCTGGAG
37045 ACTCAAACATCCAAGATCTAAAGATCTGGAG
1 ACTCAAACATCCAAGATCTAAAGATCTGGAG
37076 ACT
1 ACT
37079 GATAACCCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.42, C:0.23, G:0.15, T:0.20
Consensus pattern (31 bp):
ACTCAAACATCCAAGATCTAAAGATCTGGAG
Found at i:69235 original size:15 final size:15
Alignment explanation
Indices: 69215--69246 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
69205 TCAATTGATT
69215 AAAGTTTCAAACCAA
1 AAAGTTTCAAACCAA
69230 AAAGTTTCAAACCAA
1 AAAGTTTCAAACCAA
69245 AA
1 AA
69247 TTAAGAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.56, C:0.19, G:0.06, T:0.19
Consensus pattern (15 bp):
AAAGTTTCAAACCAA
Found at i:69454 original size:21 final size:22
Alignment explanation
Indices: 69407--69455 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 22
69397 ACACGTGTAT
69407 CAATACCTAATCAAGATATTAGC
1 CAATACCTAATCAAGATA-TAGC
*
69430 CAATACCTAATCAAGATA-GGC
1 CAATACCTAATCAAGATATAGC
69451 CAATA
1 CAATA
69456 ATCTATAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 7 0.28
23 18 0.72
ACGTcount: A:0.45, C:0.22, G:0.10, T:0.22
Consensus pattern (22 bp):
CAATACCTAATCAAGATATAGC
Found at i:73639 original size:20 final size:19
Alignment explanation
Indices: 73606--73645 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
73596 GAAATAGATT
*
73606 ATATTGCCATTAATTTCACC
1 ATATTGCCAGTAATTT-ACC
*
73626 ATATTTCCAGTAATTTACC
1 ATATTGCCAGTAATTTACC
73645 A
1 A
73646 ACAATTTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.33, C:0.23, G:0.05, T:0.40
Consensus pattern (19 bp):
ATATTGCCAGTAATTTACC
Found at i:74188 original size:14 final size:14
Alignment explanation
Indices: 74171--74199 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
74161 TGTTGTTTAC
74171 CCCTTGGTCGAACT
1 CCCTTGGTCGAACT
74185 CCCTTGGTCGAACT
1 CCCTTGGTCGAACT
74199 C
1 C
74200 TTCCCCTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.38, G:0.21, T:0.28
Consensus pattern (14 bp):
CCCTTGGTCGAACT
Found at i:76935 original size:12 final size:12
Alignment explanation
Indices: 76918--76942 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
76908 TTGATGATAA
76918 TAATAATTATAT
1 TAATAATTATAT
76930 TAATAATTATAT
1 TAATAATTATAT
76942 T
1 T
76943 CTATGGAATC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TAATAATTATAT
Done.