Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014227.1 Corchorus capsularis cultivar CVL-1 contig14248, 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: 26976
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32
Found at i:10 original size:2 final size:2
Alignment explanation
Indices: 4--35 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1 TGC
4 AT AT 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 AT AT
36 CTTTCTACTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:895 original size:21 final size:22
Alignment explanation
Indices: 849--898 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
839 AAATAATGTC
*
849 CGTAGCAAATGTAAATAAAGCG
1 CGTAGCAAATGCAAATAAAGCG
*
871 CGTAGCAAATGCAAAT-AAGCT
1 CGTAGCAAATGCAAATAAAGCG
892 CGTAGCA
1 CGTAGCA
899 TATAGGAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 11 0.42
22 15 0.58
ACGTcount: A:0.42, C:0.18, G:0.22, T:0.18
Consensus pattern (22 bp):
CGTAGCAAATGCAAATAAAGCG
Found at i:1331 original size:26 final size:26
Alignment explanation
Indices: 1295--1344 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
1285 TGCCTACAAA
1295 TGCCCAATGCTCCCACACTCATATAC
1 TGCCCAATGCTCCCACACTCATATAC
1321 TGCCCAATGCTCCCACACTCATAT
1 TGCCCAATGCTCCCACACTCATAT
1345 CGGTTTGTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.26, C:0.42, G:0.08, T:0.24
Consensus pattern (26 bp):
TGCCCAATGCTCCCACACTCATATAC
Found at i:3546 original size:13 final size:13
Alignment explanation
Indices: 3528--3611 Score: 53
Period size: 13 Copynumber: 6.1 Consensus size: 13
3518 AATATCTAAA
3528 AAACTGAATTCAG
1 AAACTGAATTCAG
*
3541 AAACTGAAATCAG
1 AAACTGAATTCAG
*
3554 AATCTGATTTCATTTCAG
1 AAACTGA----A-TTCAG
*
3572 AAACTGATTTCAG
1 AAACTGAATTCAG
**
3585 ATTCTGAAATT-AG
1 AAACTG-AATTCAG
*
3598 AAACTGAAATCAG
1 AAACTGAATTCAG
3611 A
1 A
3612 CTTATTTCAA
Statistics
Matches: 53, Mismatches: 11, Indels: 14
0.68 0.14 0.18
Matches are distributed among these distances:
12 3 0.06
13 36 0.68
14 3 0.06
17 1 0.02
18 10 0.19
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (13 bp):
AAACTGAATTCAG
Found at i:3699 original size:22 final size:23
Alignment explanation
Indices: 3671--3724 Score: 83
Period size: 22 Copynumber: 2.4 Consensus size: 23
3661 AACAATAAGA
*
3671 AAAAAACAGCAAGTTTGAGG-GG
1 AAAAAACAGCAACTTTGAGGCGG
*
3693 AAAAAACAGCGACTTTGAGGCGG
1 AAAAAACAGCAACTTTGAGGCGG
3716 AAAAAACAG
1 AAAAAACAG
3725 AATCTGTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 18 0.62
23 11 0.38
ACGTcount: A:0.48, C:0.13, G:0.28, T:0.11
Consensus pattern (23 bp):
AAAAAACAGCAACTTTGAGGCGG
Found at i:4479 original size:12 final size:12
Alignment explanation
Indices: 4448--4491 Score: 52
Period size: 12 Copynumber: 3.4 Consensus size: 12
4438 ATCATCTTCC
4448 TCTTCCTCATCTAAT
1 TCTTCCTCA-CT--T
4463 TCTTCCTCACTT
1 TCTTCCTCACTT
*
4475 TCTTCCCCACTT
1 TCTTCCTCACTT
4487 TCTTC
1 TCTTC
4492 TCCCTCTTCC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 17 0.61
14 2 0.07
15 9 0.32
ACGTcount: A:0.11, C:0.41, G:0.00, T:0.48
Consensus pattern (12 bp):
TCTTCCTCACTT
Found at i:10635 original size:74 final size:73
Alignment explanation
Indices: 10557--10712 Score: 251
Period size: 74 Copynumber: 2.1 Consensus size: 73
10547 TAGTCCTTTC
* *
10557 ACACTTTTCAGG-TGACTAAAAAGCCCCTCTATGAGTTTCCCCTATTCCTTTTCCTTCTACCCTT
1 ACACTTTTC-GGATGACTAAAAAGCCCATCTATGAGTTTCCCCCATTCCTTTTCCTTCTACCC-T
10621 TTTCGTAATT
64 TTTCGTAATT
*
10631 ACACTTTTCGGATGACTAAAAAGCCCATTTATGAGTTTCCCCCATTCCTTTTCCTTCTACCCTTT
1 ACACTTTTCGGATGACTAAAAAGCCCATCTATGAGTTTCCCCCATTCCTTTTCCTTCTACCCTTT
10696 TCGTAATT
66 TCGTAATT
*
10704 ACACATTTC
1 ACACTTTTC
10713 CCTTCCTTAA
Statistics
Matches: 77, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
73 21 0.27
74 56 0.73
ACGTcount: A:0.22, C:0.29, G:0.09, T:0.40
Consensus pattern (73 bp):
ACACTTTTCGGATGACTAAAAAGCCCATCTATGAGTTTCCCCCATTCCTTTTCCTTCTACCCTTT
TCGTAATT
Found at i:15005 original size:32 final size:31
Alignment explanation
Indices: 14935--15007 Score: 92
Period size: 32 Copynumber: 2.3 Consensus size: 31
14925 TAAAAGTAGC
* *
14935 AATCAATAATTAAGGGTCAAAGTAAAAGGGT
1 AATCAGTAATTAAGAGTCAAAGTAAAAGGGT
* *
14966 AAGTCAGTAATTAAGAGTCAAGGTAAAAGGATT
1 AA-TCAGTAATTAAGAGTCAAAGTAAAAGG-GT
14999 AATCAGTAA
1 AATCAGTAA
15008 ATTGATAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
31 2 0.06
32 31 0.86
33 3 0.08
ACGTcount: A:0.48, C:0.07, G:0.22, T:0.23
Consensus pattern (31 bp):
AATCAGTAATTAAGAGTCAAAGTAAAAGGGT
Found at i:15119 original size:29 final size:30
Alignment explanation
Indices: 15074--15133 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
15064 GGATAAAATA
15074 AAAAAAAAAGAAGAAGAAGAAGTAATCAGT
1 AAAAAAAAAGAAGAAGAAGAAGTAATCAGT
* * *
15104 AAAAAGAAAGAA-AAGAGGAAGTGATCAGT
1 AAAAAAAAAGAAGAAGAAGAAGTAATCAGT
15133 A
1 A
15134 GAATGGAGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 16 0.59
30 11 0.41
ACGTcount: A:0.63, C:0.03, G:0.23, T:0.10
Consensus pattern (30 bp):
AAAAAAAAAGAAGAAGAAGAAGTAATCAGT
Found at i:15253 original size:111 final size:111
Alignment explanation
Indices: 15138--15349 Score: 361
Period size: 111 Copynumber: 1.9 Consensus size: 111
15128 TCAGTAGAAT
* * *
15138 GGAGTGAAAGTAAAAGAAGTAATCAGTAAAAGCCAAAGAGCAAAAGTAAGAGAAGTAATCAGAAA
1 GGAGTAAAAGTAAAAGAAGTAATCAGTAAAAGCAAAAGAGCAAAAGTAAAAGAAGTAATCAGAAA
15203 AATGGTAATCAAGAGAAGTAATCAGTAGAAGAAGTAGTCAGCAAAA
66 AATGGTAATCAAGAGAAGTAATCAGTAGAAGAAGTAGTCAGCAAAA
* * *
15249 GGAGTAAAAGTAAAAGAGGTAATCAGTAAAAGTAAAAGAGCAAAAGTAAAAGAAGTAATCAGATA
1 GGAGTAAAAGTAAAAGAAGTAATCAGTAAAAGCAAAAGAGCAAAAGTAAAAGAAGTAATCAGAAA
*
15314 AATGGTAATCAAGAGAAGTAATCAGTAGAAGGAGTA
66 AATGGTAATCAAGAGAAGTAATCAGTAGAAGAAGTA
15350 AAAGTAAAAA
Statistics
Matches: 94, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
111 94 1.00
ACGTcount: A:0.53, C:0.07, G:0.25, T:0.16
Consensus pattern (111 bp):
GGAGTAAAAGTAAAAGAAGTAATCAGTAAAAGCAAAAGAGCAAAAGTAAAAGAAGTAATCAGAAA
AATGGTAATCAAGAGAAGTAATCAGTAGAAGAAGTAGTCAGCAAAA
Found at i:15307 original size:36 final size:38
Alignment explanation
Indices: 15245--15315 Score: 110
Period size: 36 Copynumber: 1.9 Consensus size: 38
15235 AGTAGTCAGC
* *
15245 AAAAGGAGTAAAAGTAAAAGAGGTAATCAG-TAAAAGT
1 AAAAGGAGCAAAAGTAAAAGAAGTAATCAGATAAAAGT
15282 AAAA-GAGCAAAAGTAAAAGAAGTAATCAGATAAA
1 AAAAGGAGCAAAAGTAAAAGAAGTAATCAGATAAA
15316 TGGTAATCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 23 0.74
37 8 0.26
ACGTcount: A:0.61, C:0.04, G:0.21, T:0.14
Consensus pattern (38 bp):
AAAAGGAGCAAAAGTAAAAGAAGTAATCAGATAAAAGT
Found at i:15365 original size:44 final size:45
Alignment explanation
Indices: 15313--15452 Score: 128
Period size: 44 Copynumber: 3.0 Consensus size: 45
15303 GTAATCAGAT
15313 AAATGGTAATCAAGAGAAGTAATCAGTAGAAGGAGTAAAAGTAAA
1 AAATGGTAATCAAGAGAAGTAATCAGTAGAAGGAGTAAAAGTAAA
* *
15358 AAA-GGTAATC-AGTAAAAGTAAT-AG-AGCAA-AAGTAAAAAAGTAATCAGAA
1 AAATGGTAATCAAG-AGAAGTAATCAGTAG-AAGGAGT--AAAAG---T-A-AA
* *
15407 AAATGGTAATCAAGAGTAGTAATCAGTAAAAGGAGTAAAAGTAAA
1 AAATGGTAATCAAGAGAAGTAATCAGTAGAAGGAGTAAAAGTAAA
15452 A
1 A
15453 GTAAAAGAAG
Statistics
Matches: 75, Mismatches: 6, Indels: 28
0.69 0.06 0.26
Matches are distributed among these distances:
42 5 0.07
43 6 0.08
44 20 0.27
45 6 0.08
46 1 0.01
47 2 0.03
48 1 0.01
49 5 0.07
50 19 0.25
51 6 0.08
52 4 0.05
ACGTcount: A:0.56, C:0.05, G:0.21, T:0.18
Consensus pattern (45 bp):
AAATGGTAATCAAGAGAAGTAATCAGTAGAAGGAGTAAAAGTAAA
Found at i:15372 original size:111 final size:111
Alignment explanation
Indices: 15139--15375 Score: 334
Period size: 111 Copynumber: 2.1 Consensus size: 111
15129 CAGTAGAATG
* * *
15139 GAGTGAAAGTAAAAGAAGTAATCAGTAAAAGCCAAAGAGCAAAAGTAAGAGAAGTAATCAGAAAA
1 GAGTAAAAGTAAAAGAAGTAATCAGTAAAAGCAAAAGAGCAAAAGTAAAAGAAGTAATCAGAAAA
** * *
15204 ATGGTAATCAAGAGAAGTAATCAGTAGAAGAAGTAGTCAGCAAAAG
66 ATGGTAATCAAGAGAAGTAATCAGTAGAAGAAGTAGAAAGAAAAAA
* * *
15250 GAGTAAAAGTAAAAGAGGTAATCAGTAAAAGTAAAAGAGCAAAAGTAAAAGAAGTAATCAGATAA
1 GAGTAAAAGTAAAAGAAGTAATCAGTAAAAGCAAAAGAGCAAAAGTAAAAGAAGTAATCAGAAAA
*
15315 ATGGTAATCAAGAGAAGTAATCAGTAGAAGGAGTA-AAAGTAAAAAA
66 ATGGTAATCAAGAGAAGTAATCAGTAGAAGAAGTAGAAAG-AAAAAA
*
15361 G-GTAATCAGTAAAAG
1 GAGTAA-AAGTAAAAG
15376 TAATAGAGCA
Statistics
Matches: 112, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
110 6 0.05
111 106 0.95
ACGTcount: A:0.54, C:0.06, G:0.24, T:0.16
Consensus pattern (111 bp):
GAGTAAAAGTAAAAGAAGTAATCAGTAAAAGCAAAAGAGCAAAAGTAAAAGAAGTAATCAGAAAA
ATGGTAATCAAGAGAAGTAATCAGTAGAAGAAGTAGAAAGAAAAAA
Found at i:15448 original size:94 final size:94
Alignment explanation
Indices: 15232--15520 Score: 418
Period size: 95 Copynumber: 3.0 Consensus size: 94
15222 AATCAGTAGA
* * *
15232 AGAAGTAGTCAGCAAAAGGAGTAAAAGTAAAAGAGGTAATCAGTAAAAGTAAAAGAGCAAAAGTA
1 AGAAGTAATCAGTAAAAGGAGTAAAAGTAAAAAAGGTAATCAGTAAAAGT-AAAGAGCAAAAGTA
*
15297 AAAGAAGTAATCAGATAAATGGTAATCAAG
65 AAAGAAGTAATCAGAAAAATGGTAATCAAG
*
15327 AGAAGTAATCAGTAGAAGGAGTAAAAGTAAAAAAGGTAATCAGTAAAAGTAATAGAGCAAAAGTA
1 AGAAGTAATCAGTAAAAGGAGTAAAAGTAAAAAAGGTAATCAGTAAAAGTAA-AGAGCAAAAGTA
15392 AAA-AAGTAATCAGAAAAATGGTAATCAAG
65 AAAGAAGTAATCAGAAAAATGGTAATCAAG
* *
15421 AGTAGTAATCAGTAAAAGGAGTAAAAGTAAAAGTAAAAGAAGTAATCAGTAAAAGCCAAAGAGCA
1 AGAAGTAATCAGTAAAAGGAGTAAAAGT--AA--AAAAG--GTAATCAGTAAAAG-TAAAGAGCA
15486 AAAGTAAAAGAAGTAATCAGAAAAAATGGTAATCA
59 AAAGTAAAAGAAGTAATCAG-AAAAATGGTAATCA
15521 GTAAAGAGTA
Statistics
Matches: 176, Mismatches: 8, Indels: 13
0.89 0.04 0.07
Matches are distributed among these distances:
94 53 0.30
95 61 0.35
96 2 0.01
98 5 0.03
100 29 0.16
101 12 0.07
102 14 0.08
ACGTcount: A:0.56, C:0.06, G:0.21, T:0.16
Consensus pattern (94 bp):
AGAAGTAATCAGTAAAAGGAGTAAAAGTAAAAAAGGTAATCAGTAAAAGTAAAGAGCAAAAGTAA
AAGAAGTAATCAGAAAAATGGTAATCAAG
Found at i:15456 original size:21 final size:21
Alignment explanation
Indices: 15431--15495 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
15421 AGTAGTAATC
15431 AGTAAAAGGAGTAAAAGTAAA
1 AGTAAAAGGAGTAAAAGTAAA
* *
15452 AGTAAAAGAAGTAATCAGTAAA
1 AGTAAAAGGAGTAA-AAGTAAA
** *
15474 AGCCAAA-GAGCAAAAGTAAA
1 AGTAAAAGGAGTAAAAGTAAA
15494 AG
1 AG
15496 AAGTAATCAG
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
20 8 0.22
21 17 0.47
22 11 0.31
ACGTcount: A:0.60, C:0.06, G:0.22, T:0.12
Consensus pattern (21 bp):
AGTAAAAGGAGTAAAAGTAAA
Found at i:15465 original size:37 final size:36
Alignment explanation
Indices: 15424--15510 Score: 113
Period size: 36 Copynumber: 2.4 Consensus size: 36
15414 AATCAAGAGT
* *
15424 AGTAATCAGTAAAAG-GAGTAAAAGTAAAAGTAAAAGA
1 AGTAATCAGTAAAAGCCA--AAAAGCAAAAGTAAAAGA
*
15461 AGTAATCAGTAAAAGCCAAAGAGCAAAAGTAAAAGA
1 AGTAATCAGTAAAAGCCAAAAAGCAAAAGTAAAAGA
*
15497 AGTAATCAGAAAAA
1 AGTAATCAGTAAAA
15511 ATGGTAATCA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
36 29 0.64
37 15 0.33
38 1 0.02
ACGTcount: A:0.60, C:0.07, G:0.20, T:0.14
Consensus pattern (36 bp):
AGTAATCAGTAAAAGCCAAAAAGCAAAAGTAAAAGA
Found at i:15595 original size:20 final size:20
Alignment explanation
Indices: 15572--15640 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
15562 CAAAGAGTAA
* *
15572 AGTAAAAATAATCATTAAGG
1 AGTAAAAATAATCAGTAAAG
** *
15592 AGTAATGATAATCAGTAAAA
1 AGTAAAAATAATCAGTAAAG
15612 AGTAAAAAAGTAATCAGTAAAG
1 AGT-AAAAA-TAATCAGTAAAG
15634 AGTAAAA
1 AGTAAAA
15641 TGGTAAAATG
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
20 18 0.46
21 7 0.18
22 14 0.36
ACGTcount: A:0.58, C:0.04, G:0.16, T:0.22
Consensus pattern (20 bp):
AGTAAAAATAATCAGTAAAG
Found at i:15693 original size:32 final size:33
Alignment explanation
Indices: 15630--15705 Score: 111
Period size: 32 Copynumber: 2.3 Consensus size: 33
15620 AGTAATCAGT
15630 AAAGAGTAAAATGGTAAAATGGTAACCAAATTC
1 AAAGAGTAAAATGGTAAAATGGTAACCAAATTC
**
15663 AAAGAGTAAAAT-G-ACAAATGGTAATTAAATTC
1 AAAGAGTAAAATGGTA-AAATGGTAACCAAATTC
15695 AAAGAGTAAAA
1 AAAGAGTAAAA
15706 GTAGTAATTA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
31 1 0.03
32 27 0.68
33 12 0.30
ACGTcount: A:0.55, C:0.07, G:0.17, T:0.21
Consensus pattern (33 bp):
AAAGAGTAAAATGGTAAAATGGTAACCAAATTC
Found at i:15712 original size:26 final size:26
Alignment explanation
Indices: 15678--15739 Score: 99
Period size: 26 Copynumber: 2.4 Consensus size: 26
15668 GTAAAATGAC
*
15678 AAATGGTAATTAAATTCAA-AGAGTA
1 AAATAGTAATTAAATTCAAGAGAGTA
15703 AAAGTAGTAATTAAATTCAAGAGAGTA
1 AAA-TAGTAATTAAATTCAAGAGAGTA
15730 AAATAGTAAT
1 AAATAGTAAT
15740 CAGTAAAGAG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
25 3 0.09
26 22 0.65
27 9 0.26
ACGTcount: A:0.53, C:0.03, G:0.16, T:0.27
Consensus pattern (26 bp):
AAATAGTAATTAAATTCAAGAGAGTA
Found at i:15774 original size:22 final size:22
Alignment explanation
Indices: 15724--15768 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
15714 TAAATTCAAG
15724 AGAGTAAAATAGTAATCAGTAA
1 AGAGTAAAATAGTAATCAGTAA
15746 AGAGTAAAATAGTAATCAGTAA
1 AGAGTAAAATAGTAATCAGTAA
15768 A
1 A
15769 AGGTAATCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (22 bp):
AGAGTAAAATAGTAATCAGTAA
Found at i:15790 original size:35 final size:36
Alignment explanation
Indices: 15726--15842 Score: 137
Period size: 42 Copynumber: 3.1 Consensus size: 36
15716 AATTCAAGAG
*
15726 AGTAAAATAGTAATCAGTAAAGAGTAAAATAGTAATC
1 AGTAAAATGGTAATCAGT-AAGAGTAAAATAGTAATC
*
15763 AGTAAAA-GGTAATCAGTAAGAGTAAAATAATAATC
1 AGTAAAATGGTAATCAGTAAGAGTAAAATAGTAATC
*
15798 AGTAAGAGCAAAATGGTAATTAGTAAGAGTAAAATAGTAATC
1 AGT------AAAATGGTAATCAGTAAGAGTAAAATAGTAATC
15840 AGT
1 AGT
15843 GAAGAGTAAA
Statistics
Matches: 69, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
35 20 0.29
36 9 0.13
37 7 0.10
41 4 0.06
42 29 0.42
ACGTcount: A:0.52, C:0.05, G:0.19, T:0.24
Consensus pattern (36 bp):
AGTAAAATGGTAATCAGTAAGAGTAAAATAGTAATC
Found at i:15865 original size:21 final size:21
Alignment explanation
Indices: 15763--15863 Score: 125
Period size: 21 Copynumber: 4.9 Consensus size: 21
15753 AATAGTAATC
15763 AGTAAAA-GGTAATCAGTAAG
1 AGTAAAATGGTAATCAGTAAG
**
15783 AGTAAAATAATAATCAGTAAG
1 AGTAAAATGGTAATCAGTAAG
* *
15804 AGCAAAATGGTAATTAGTAAG
1 AGTAAAATGGTAATCAGTAAG
*
15825 AGTAAAATAGTAATCAGTGAAG
1 AGTAAAATGGTAATCAGT-AAG
*
15847 AGTAAAA-GGTGATCAGT
1 AGTAAAATGGTAATCAGT
15864 GATTCAAAGA
Statistics
Matches: 68, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
20 7 0.10
21 51 0.75
22 10 0.15
ACGTcount: A:0.50, C:0.05, G:0.23, T:0.23
Consensus pattern (21 bp):
AGTAAAATGGTAATCAGTAAG
Found at i:19908 original size:19 final size:18
Alignment explanation
Indices: 19867--19908 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
19857 TTATATATAA
*
19867 AAATTGATAATGCTCATT
1 AAATTGATAATGCTCACT
19885 AAATTGATAAAATGCT-ACT
1 AAATTGAT--AATGCTCACT
19904 AAATT
1 AAATT
19909 TATTAAAGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 8 0.38
19 7 0.33
20 6 0.29
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.36
Consensus pattern (18 bp):
AAATTGATAATGCTCACT
Found at i:21290 original size:31 final size:31
Alignment explanation
Indices: 21255--21381 Score: 77
Period size: 31 Copynumber: 4.2 Consensus size: 31
21245 ACTATATTGA
21255 GAGAAGAGTTGGAAACTTGGAATGAGAGTGG
1 GAGAAGAGTTGGAAACTTGGAATGAGAGTGG
* ** **
21286 GAGAATTAGGGGGGCACTTGAGGAA-GA-A-TGG
1 GAGAA-GAGTTGGAAACTT--GGAATGAGAGTGG
* * * * *
21317 GAGAAGAGTTGGAATAC--AGACT-ATATTGA
1 GAGAAGAGTTGGAA-ACTTGGAATGAGAGTGG
*
21346 GAGAAGAGTTGGAAACTTGGAATGAGAGAGG
1 GAGAAGAGTTGGAAACTTGGAATGAGAGTGG
21377 GAGAA
1 GAGAA
21382 TGGGAGGGGG
Statistics
Matches: 67, Mismatches: 19, Indels: 20
0.63 0.18 0.19
Matches are distributed among these distances:
27 3 0.04
28 3 0.04
29 16 0.24
30 7 0.10
31 23 0.34
32 9 0.13
33 2 0.03
34 4 0.06
ACGTcount: A:0.38, C:0.05, G:0.39, T:0.18
Consensus pattern (31 bp):
GAGAAGAGTTGGAAACTTGGAATGAGAGTGG
Found at i:21363 original size:91 final size:91
Alignment explanation
Indices: 21208--21382 Score: 323
Period size: 91 Copynumber: 1.9 Consensus size: 91
21198 CAGCACCAGT
21208 GCACTTGAGGAAGAATGGGAGAAGAATAGGAATACAGACTATATTGAGAGAAGAGTTGGAAACTT
1 GCACTTGAGGAAGAATGGGAGAAGAATAGGAATACAGACTATATTGAGAGAAGAGTTGGAAACTT
*
21273 GGAATGAGAGTGGGAGAATTAGGGGG
66 GGAATGAGAGAGGGAGAATTAGGGGG
* *
21299 GCACTTGAGGAAGAATGGGAGAAGAGTTGGAATACAGACTATATTGAGAGAAGAGTTGGAAACTT
1 GCACTTGAGGAAGAATGGGAGAAGAATAGGAATACAGACTATATTGAGAGAAGAGTTGGAAACTT
21364 GGAATGAGAGAGGGAGAAT
66 GGAATGAGAGAGGGAGAAT
21383 GGGAGGGGGG
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
91 81 1.00
ACGTcount: A:0.39, C:0.06, G:0.37, T:0.19
Consensus pattern (91 bp):
GCACTTGAGGAAGAATGGGAGAAGAATAGGAATACAGACTATATTGAGAGAAGAGTTGGAAACTT
GGAATGAGAGAGGGAGAATTAGGGGG
Found at i:22471 original size:21 final size:21
Alignment explanation
Indices: 22434--22473 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
22424 TTCTTAATAC
*
22434 TAACATTTTTTATAACCTTTA
1 TAACATTTTTTACAACCTTTA
22455 TAAC-TTTTTTAGCAACCTT
1 TAACATTTTTTA-CAACCTT
22474 AAAGAAGAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.30, C:0.17, G:0.03, T:0.50
Consensus pattern (21 bp):
TAACATTTTTTACAACCTTTA
Found at i:23762 original size:46 final size:44
Alignment explanation
Indices: 23706--23800 Score: 120
Period size: 44 Copynumber: 2.1 Consensus size: 44
23696 ATATCCCTAA
*
23706 GGGCATTTCTCTCTCCCCAAAGTCCCCAAACACAATT-ATAACACAG
1 GGGCAATTCTC-CT-CCCAAAGTCCCCAAACAC-ATTCATAACACAG
* *
23752 GGGCAATTCTCCTTCCAAAGTCCTCAAACACATTCATAACACAG
1 GGGCAATTCTCCTCCCAAAGTCCCCAAACACATTCATAACACAG
*
23796 AGGCA
1 GGGCA
23801 TCTATATTAA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
43 3 0.07
44 29 0.66
45 2 0.05
46 10 0.23
ACGTcount: A:0.34, C:0.33, G:0.13, T:0.21
Consensus pattern (44 bp):
GGGCAATTCTCCTCCCAAAGTCCCCAAACACATTCATAACACAG
Done.