Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007590.1 Corchorus capsularis cultivar CVL-1 contig07611, 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: 148724
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:1423 original size:30 final size:31
Alignment explanation
Indices: 1389--1556 Score: 204
Period size: 30 Copynumber: 5.6 Consensus size: 31
1379 TGAGGTAAAG
*
1389 GTTAATGAAGA-AGAGTCTGAGAGAGTGGAA
1 GTTAATGAAGATGGAGTCTGAGAGAGTGGAA
* * *
1419 GTTAATGAA-ATTGAGTCTGAGAGACTGGAG
1 GTTAATGAAGATGGAGTCTGAGAGAGTGGAA
*
1449 GTCAATG-AGATGGAGTCTGAGAGAGTGGAA
1 GTTAATGAAGATGGAGTCTGAGAGAGTGGAA
* *
1479 ATTAATGAA-ATGGAGTCTGAGAGAGTGGAG
1 GTTAATGAAGATGGAGTCTGAGAGAGTGGAA
* *
1509 GTTAATGTA-ATGGAGTCTGATAGAGTGGAA
1 GTTAATGAAGATGGAGTCTGAGAGAGTGGAA
*
1539 ATTAATGAA-ATGGAGTCT
1 GTTAATGAAGATGGAGTCT
1557 CTGACAGTTA
Statistics
Matches: 119, Mismatches: 16, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
29 2 0.02
30 116 0.97
31 1 0.01
ACGTcount: A:0.36, C:0.05, G:0.35, T:0.25
Consensus pattern (31 bp):
GTTAATGAAGATGGAGTCTGAGAGAGTGGAA
Found at i:1485 original size:60 final size:60
Alignment explanation
Indices: 1401--1556 Score: 251
Period size: 60 Copynumber: 2.6 Consensus size: 60
1391 TAATGAAGAA
* *
1401 GAGTCTGAGAGAGTGGAAGTTAATGAAATTGAGTCTGAGAGACTGGAGGTCAATG-AGATG
1 GAGTCTGAGAGAGTGGAAATTAATGAAATGGAGTCTGAGAGACTGGAGGTCAATGTA-ATG
* *
1461 GAGTCTGAGAGAGTGGAAATTAATGAAATGGAGTCTGAGAGAGTGGAGGTTAATGTAATG
1 GAGTCTGAGAGAGTGGAAATTAATGAAATGGAGTCTGAGAGACTGGAGGTCAATGTAATG
*
1521 GAGTCTGATAGAGTGGAAATTAATGAAATGGAGTCT
1 GAGTCTGAGAGAGTGGAAATTAATGAAATGGAGTCT
1557 CTGACAGTTA
Statistics
Matches: 90, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
60 89 0.99
61 1 0.01
ACGTcount: A:0.35, C:0.05, G:0.35, T:0.25
Consensus pattern (60 bp):
GAGTCTGAGAGAGTGGAAATTAATGAAATGGAGTCTGAGAGACTGGAGGTCAATGTAATG
Found at i:1688 original size:96 final size:96
Alignment explanation
Indices: 1503--1729 Score: 303
Period size: 96 Copynumber: 2.4 Consensus size: 96
1493 GTCTGAGAGA
* * * * *
1503 GTGGAGGTTAATGTAATGGAGTCTGATAGAGTGGAAATTAATGAAATGGAGTCTCTGACAGTTAA
1 GTGGAAGTTAATGAAATTGAGTCTGAGAGAGTGGAAATTAATGAAATGGAGTCTCCGACAGTTAA
*
1568 GCTCAATAGGGAGGCTGATTTGGATTCAGAT
66 GCTCAATAGGGAGGCTGATATGGATTCAGAT
* * * ** * * * *
1599 GTGGGA-TTCAATGAAATTGAGTCTGAGAGAGTGGCAGTTAATGTGATTGAGTCTCCGAGATTTG
1 GTGGAAGTT-AATGAAATTGAGTCTGAGAGAGTGGAAATTAATGAAATGGAGTCTCCGACAGTTA
1663 AGCTCAATAGGGAGGCTGATATGGATTCAGAT
65 AGCTCAATAGGGAGGCTGATATGGATTCAGAT
1695 GTGGAAGTTAATGAAATTGAGTCTGAGAGAGTGGA
1 GTGGAAGTTAATGAAATTGAGTCTGAGAGAGTGGA
1730 GGTCAATGAA
Statistics
Matches: 112, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
95 2 0.02
96 108 0.96
97 2 0.02
ACGTcount: A:0.30, C:0.08, G:0.33, T:0.29
Consensus pattern (96 bp):
GTGGAAGTTAATGAAATTGAGTCTGAGAGAGTGGAAATTAATGAAATGGAGTCTCCGACAGTTAA
GCTCAATAGGGAGGCTGATATGGATTCAGAT
Found at i:1738 original size:30 final size:30
Alignment explanation
Indices: 1695--1838 Score: 180
Period size: 30 Copynumber: 4.8 Consensus size: 30
1685 GGATTCAGAT
*
1695 GTGGAAGTTAATGAAATTGAGTCTGAGAGA
1 GTGGAGGTTAATGAAATTGAGTCTGAGAGA
* *** *
1725 GTGGAGGTCAATGAAAAACAGTCAGAGAGA
1 GTGGAGGTTAATGAAATTGAGTCTGAGAGA
* *
1755 GTGGAAGTTGATGAAATTGAGTCTGAGAGA
1 GTGGAGGTTAATGAAATTGAGTCTGAGAGA
* *
1785 GGGGAGGTTAATGAAATTGAGTCTGGGAGA
1 GTGGAGGTTAATGAAATTGAGTCTGAGAGA
* *
1815 GTGGAGGTTAATGTAATGGAGTCT
1 GTGGAGGTTAATGAAATTGAGTCT
1839 CTGAAAGTTG
Statistics
Matches: 94, Mismatches: 20, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 94 1.00
ACGTcount: A:0.34, C:0.05, G:0.37, T:0.24
Consensus pattern (30 bp):
GTGGAGGTTAATGAAATTGAGTCTGAGAGA
Found at i:9569 original size:30 final size:30
Alignment explanation
Indices: 9503--9582 Score: 92
Period size: 30 Copynumber: 2.6 Consensus size: 30
9493 ATTAATTCAT
*
9503 AAAAATTAGAAAACATTTTTTTTTAGAGAAAG
1 AAAAATTAGAAAACA--TTTTTTGAGAGAAAG
*
9535 AAAAATTAGAAAACATTTTTTGAGGGAATA-
1 AAAAATTAGAAAACATTTTTTGAGAGAA-AG
9565 AAAAA-TAGAAAACTATTT
1 AAAAATTAGAAAAC-ATTT
9583 GAACTAGTAA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
29 8 0.18
30 20 0.45
31 1 0.02
32 15 0.34
ACGTcount: A:0.53, C:0.04, G:0.12, T:0.31
Consensus pattern (30 bp):
AAAAATTAGAAAACATTTTTTGAGAGAAAG
Found at i:9808 original size:18 final size:19
Alignment explanation
Indices: 9772--9820 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
9762 ACCGTGAGAG
9772 AAGAACAAA-AAAAACAAAA
1 AAGAA-AAAGAAAAACAAAA
*
9791 ATGAAAAAGAAAAA-AAAA
1 AAGAAAAAGAAAAACAAAA
*
9809 AAGAGAAAGAAA
1 AAGAAAAAGAAA
9821 CAAGAGAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 17 0.65
19 9 0.35
ACGTcount: A:0.82, C:0.04, G:0.12, T:0.02
Consensus pattern (19 bp):
AAGAAAAAGAAAAACAAAA
Found at i:11976 original size:25 final size:25
Alignment explanation
Indices: 11927--11977 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
11917 TTAGTAGAAT
*
11927 AATTGTAAAAGTTTATTTCTAAAAA
1 AATTGTAAAAGTATATTTCTAAAAA
11952 AATTGTAAAAGAATATATTT-TAAAAA
1 AATTGTAAAAG--TATATTTCTAAAAA
11978 TTCTAATATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 11 0.48
26 6 0.26
27 6 0.26
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.37
Consensus pattern (25 bp):
AATTGTAAAAGTATATTTCTAAAAA
Found at i:15690 original size:29 final size:29
Alignment explanation
Indices: 15625--15690 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 29
15615 GAAAATGACA
* * *
15625 TATTTGGCCAAAATTAAGAGTTCATGAGT
1 TATTTGACCAAAATTAAAAGTTCAAGAGT
*
15654 GATATTGACCAAAA-TAAAAGTTCAAGAGCT
1 TAT-TTGACCAAAATTAAAAGTTCAAGAG-T
15684 TATTTGA
1 TATTTGA
15691 TCGTTGAAGG
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
29 18 0.60
30 12 0.40
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (29 bp):
TATTTGACCAAAATTAAAAGTTCAAGAGT
Found at i:16624 original size:2 final size:2
Alignment explanation
Indices: 16617--16679 Score: 52
Period size: 2 Copynumber: 35.5 Consensus size: 2
16607 CCGTGTAGTA
*
16617 AT AT AT AT A- AT -T AA AT AT AT AT -T AT AT AT A- AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
16654 -T AG AT AT AT AT A- AT A- AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16680 ATTATTAAAC
Statistics
Matches: 49, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
1 8 0.16
2 41 0.84
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:16652 original size:19 final size:19
Alignment explanation
Indices: 16618--16676 Score: 75
Period size: 19 Copynumber: 3.0 Consensus size: 19
16608 CGTGTAGTAA
16618 TATATATAATTAAATATATAT
1 TATATATAA-T-AATATATAT
*
16639 TATATATAATAATAT-TAGA
1 TATATATAATAATATATA-T
16658 TATATATAATAATATATAT
1 TATATATAATAATATATAT
16677 ATAATTATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
18 2 0.06
19 20 0.59
20 3 0.09
21 9 0.26
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (19 bp):
TATATATAATAATATATAT
Found at i:21707 original size:33 final size:35
Alignment explanation
Indices: 21670--21748 Score: 81
Period size: 41 Copynumber: 2.1 Consensus size: 35
21660 GTTCTACCTG
21670 TCATCAA-TGC-CATGAAAAGTTACTACCATATAT
1 TCATCAAGTGCACATGAAAAGTTACTACCATATAT
*
21703 TCATCCAAGCAAGTTCATCATGAAAAGTTACTACCATATAT
1 TCAT-----CAAGTGCA-CATGAAAAGTTACTACCATATAT
21744 TCATC
1 TCATC
21749 CAAGCAAGTT
Statistics
Matches: 37, Mismatches: 1, Indels: 13
0.73 0.02 0.25
Matches are distributed among these distances:
33 4 0.11
36 1 0.03
38 3 0.08
39 2 0.05
41 27 0.73
ACGTcount: A:0.38, C:0.23, G:0.09, T:0.30
Consensus pattern (35 bp):
TCATCAAGTGCACATGAAAAGTTACTACCATATAT
Found at i:21737 original size:41 final size:41
Alignment explanation
Indices: 21680--21766 Score: 174
Period size: 41 Copynumber: 2.1 Consensus size: 41
21670 TCATCAATGC
21680 CATGAAAAGTTACTACCATATATTCATCCAAGCAAGTTCAT
1 CATGAAAAGTTACTACCATATATTCATCCAAGCAAGTTCAT
21721 CATGAAAAGTTACTACCATATATTCATCCAAGCAAGTTCAT
1 CATGAAAAGTTACTACCATATATTCATCCAAGCAAGTTCAT
21762 CATGA
1 CATGA
21767 GTCATGACAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.39, C:0.22, G:0.10, T:0.29
Consensus pattern (41 bp):
CATGAAAAGTTACTACCATATATTCATCCAAGCAAGTTCAT
Found at i:25047 original size:11 final size:11
Alignment explanation
Indices: 25033--25072 Score: 71
Period size: 11 Copynumber: 3.6 Consensus size: 11
25023 AAAAATAATT
25033 AGAAAATGAAA
1 AGAAAATGAAA
*
25044 AGAAAATGAAG
1 AGAAAATGAAA
25055 AGAAAATGAAA
1 AGAAAATGAAA
25066 AGAAAAT
1 AGAAAAT
25073 TGCAAACATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.70, C:0.00, G:0.20, T:0.10
Consensus pattern (11 bp):
AGAAAATGAAA
Found at i:41357 original size:28 final size:28
Alignment explanation
Indices: 41317--41373 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
41307 TCAATAGACT
41317 TAGAAAAACTTATCTTA-TATATGGTATA
1 TAGAAAAACTTATC-TAGTATATGGTATA
*
41345 TAGAAAACCTTATCTAGTATATGGTATA
1 TAGAAAAACTTATCTAGTATATGGTATA
41373 T
1 T
41374 CAGCATAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 2 0.07
28 25 0.93
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.39
Consensus pattern (28 bp):
TAGAAAAACTTATCTAGTATATGGTATA
Found at i:44032 original size:18 final size:18
Alignment explanation
Indices: 44002--44037 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
43992 ATAATAATAA
44002 TAATAAATACTAATTAAT
1 TAATAAATACTAATTAAT
44020 TAATATAAT-CTAATTAAT
1 TAATA-AATACTAATTAAT
44038 GATTCATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.82
19 3 0.18
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (18 bp):
TAATAAATACTAATTAAT
Found at i:51709 original size:19 final size:18
Alignment explanation
Indices: 51681--51722 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
51671 TCTCGCTTGT
*
51681 TTTTTCCCCTTGATGCTCTG
1 TTTTTCCCCTT--TGATCTG
51701 TTTTT-CCCTTTGATCTG
1 TTTTTCCCCTTTGATCTG
51718 TTTTT
1 TTTTT
51723 TAAACAGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 11 0.52
19 5 0.24
20 5 0.24
ACGTcount: A:0.05, C:0.24, G:0.12, T:0.60
Consensus pattern (18 bp):
TTTTTCCCCTTTGATCTG
Found at i:51723 original size:19 final size:20
Alignment explanation
Indices: 51680--51723 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
51670 TTCTCGCTTG
51680 TTTTTTCCCCTTGATGCTCT
1 TTTTTTCCCCTTGATGCTCT
* * *
51700 GTTTTTCCCTTTGAT-CTGT
1 TTTTTTCCCCTTGATGCTCT
51719 TTTTT
1 TTTTT
51724 AAACAGAATG
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.05, C:0.23, G:0.11, T:0.61
Consensus pattern (20 bp):
TTTTTTCCCCTTGATGCTCT
Found at i:57022 original size:6 final size:6
Alignment explanation
Indices: 57011--57035 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
57001 CAAAACTATG
57011 ACAAAT ACAAAT ACAAAT ACAAAT A
1 ACAAAT ACAAAT ACAAAT ACAAAT A
57036 TGAAAGTAGT
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:0.68, C:0.16, G:0.00, T:0.16
Consensus pattern (6 bp):
ACAAAT
Found at i:58604 original size:22 final size:22
Alignment explanation
Indices: 58579--58620 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
58569 AAATGAAGTA
58579 TTCATACGAAATTATGATAACG
1 TTCATACGAAATTATGATAACG
**
58601 TTCATATTAAATTATGATAA
1 TTCATACGAAATTATGATAA
58621 TTACACTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.38
Consensus pattern (22 bp):
TTCATACGAAATTATGATAACG
Found at i:58657 original size:22 final size:21
Alignment explanation
Indices: 58630--58738 Score: 89
Period size: 22 Copynumber: 5.1 Consensus size: 21
58620 ATTACACTAT
*
58630 TTTTGATAACGTCCTTATGAAA
1 TTTTGATAACTTCC-TATGAAA
58652 TTTTGATAACCTTCCTATGAAA
1 TTTTGATAA-CTTCCTATGAAA
* * * *
58674 TTATGATAA-TTACAAT--AT
1 TTTTGATAACTTCCTATGAAA
* * *
58692 TTTTTATGACGTCCTTATGAAA
1 TTTTGATAACTTCC-TATGAAA
58714 TTTTGATAACATTCCTATGAAA
1 TTTTGATAAC-TTCCTATGAAA
58736 TTT
1 TTT
58739 CAATAATGAT
Statistics
Matches: 66, Mismatches: 15, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
18 7 0.11
19 2 0.03
20 7 0.11
22 43 0.65
23 7 0.11
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (21 bp):
TTTTGATAACTTCCTATGAAA
Found at i:58745 original size:62 final size:62
Alignment explanation
Indices: 58586--58737 Score: 232
Period size: 62 Copynumber: 2.5 Consensus size: 62
58576 GTATTCATAC
* * * * *
58586 GAAATTATGATAACGTTCATATTAAATTATGATAATTACACTATTTTTGATAACGTCCTTAT
1 GAAATTTTGATAACATTCCTATGAAATTATGATAATTACAATATTTTTGATAACGTCCTTAT
* * *
58648 GAAATTTTGATAACCTTCCTATGAAATTATGATAATTACAATATTTTTTATGACGTCCTTAT
1 GAAATTTTGATAACATTCCTATGAAATTATGATAATTACAATATTTTTGATAACGTCCTTAT
58710 GAAATTTTGATAACATTCCTATGAAATT
1 GAAATTTTGATAACATTCCTATGAAATT
58738 TCAATAATGA
Statistics
Matches: 82, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
62 82 1.00
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.42
Consensus pattern (62 bp):
GAAATTTTGATAACATTCCTATGAAATTATGATAATTACAATATTTTTGATAACGTCCTTAT
Found at i:58808 original size:24 final size:23
Alignment explanation
Indices: 58765--58810 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
58755 GAATTTCGAG
*
58765 AACCTTTTTATAAATTTTGTTTT
1 AACCTTCTTATAAATTTTGTTTT
58788 AACCTTCTTATGAAATTTTGTTT
1 AACCTTCTTAT-AAATTTTGTTT
58811 ACCTCCCTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.26, C:0.11, G:0.07, T:0.57
Consensus pattern (23 bp):
AACCTTCTTATAAATTTTGTTTT
Found at i:58836 original size:22 final size:22
Alignment explanation
Indices: 58811--58852 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
58801 AATTTTGTTT
* *
58811 ACCTCCCTAAGGAATTTTGAAG
1 ACCTCACTAAGAAATTTTGAAG
*
58833 ACCTCACTATGAAATTTTGA
1 ACCTCACTAAGAAATTTTGA
58853 TAACCAACAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.31
Consensus pattern (22 bp):
ACCTCACTAAGAAATTTTGAAG
Found at i:59025 original size:23 final size:22
Alignment explanation
Indices: 58953--59157 Score: 154
Period size: 22 Copynumber: 9.5 Consensus size: 22
58943 AATCACACTC
* * *
58953 TGAAATTTTTATAATCACACTA
1 TGAAATTTTGATAATCTCCCTA
* * *
58975 TGAAATTGTGATAACCTCGCTA
1 TGAAATTTTGATAATCTCCCTA
58997 TGAAATTTTGATAAATCTCCCTA
1 TGAAATTTTGAT-AATCTCCCTA
* *
59020 TAAAATTCTGATAAATCTCCCTA
1 TGAAATTTTGAT-AATCTCCCTA
* * *
59043 TAAAATTTTGATAACCTCCTTA
1 TGAAATTTTGATAATCTCCCTA
*
59065 TGAAATCTTGATAA-----CTA
1 TGAAATTTTGATAATCTCCCTA
* *
59082 -CAAA-TTTGATAACCTCCCTA
1 TGAAATTTTGATAATCTCCCTA
** * **
59102 TGATTTTTTGATAACCTCATTA
1 TGAAATTTTGATAATCTCCCTA
* *
59124 TGAGATTTTGTTAATCTCCCTA
1 TGAAATTTTGATAATCTCCCTA
59146 TGAAATTTTGAT
1 TGAAATTTTGAT
59158 TTACATATAT
Statistics
Matches: 144, Mismatches: 31, Indels: 16
0.75 0.16 0.08
Matches are distributed among these distances:
15 7 0.05
16 3 0.02
17 2 0.01
20 3 0.02
21 1 0.01
22 88 0.61
23 40 0.28
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (22 bp):
TGAAATTTTGATAATCTCCCTA
Found at i:59026 original size:45 final size:46
Alignment explanation
Indices: 58953--59056 Score: 122
Period size: 46 Copynumber: 2.3 Consensus size: 46
58943 AATCACACTC
* * * *
58953 TGAAATTTTTAT-AATCACACTATGAAATTGTGAT-AACCTCGCTA
1 TGAAATTTTGATAAATCACACTATAAAATTCTGATAAACCTCCCTA
* * *
58997 TGAAATTTTGATAAATCTCCCTATAAAATTCTGATAAATCTCCCTA
1 TGAAATTTTGATAAATCACACTATAAAATTCTGATAAACCTCCCTA
*
59043 TAAAATTTTGATAA
1 TGAAATTTTGATAA
59057 CCTCCTTATG
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
44 11 0.22
45 18 0.36
46 21 0.42
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (46 bp):
TGAAATTTTGATAAATCACACTATAAAATTCTGATAAACCTCCCTA
Found at i:59318 original size:22 final size:22
Alignment explanation
Indices: 59285--59412 Score: 80
Period size: 22 Copynumber: 5.8 Consensus size: 22
59275 GAAGTACCAC
*
59285 TATGAAATTTTGGTAATCACATT
1 TATGAAATTTTGGTAACCAC-TT
* * *
59308 T-TGAAAATTTGATAACCTCTT
1 TATGAAATTTTGGTAACCACTT
* *
59329 TATGAAATTTTGGTAACCGCTC
1 TATGAAATTTTGGTAACCACTT
* * * *
59351 TATAAAATTTTGTTGACC-CATC
1 TATGAAATTTTGGTAACCAC-TT
** * *
59373 TATGAAATTTTAATAATCACAT
1 TATGAAATTTTGGTAACCACTT
* *
59395 TATGTAATTTTGATAACC
1 TATGAAATTTTGGTAACC
59413 TTGCTTTGAA
Statistics
Matches: 81, Mismatches: 21, Indels: 7
0.74 0.19 0.06
Matches are distributed among these distances:
21 4 0.05
22 75 0.93
23 2 0.02
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.41
Consensus pattern (22 bp):
TATGAAATTTTGGTAACCACTT
Found at i:59580 original size:37 final size:37
Alignment explanation
Indices: 59493--59586 Score: 116
Period size: 38 Copynumber: 2.5 Consensus size: 37
59483 CTAAGCTCGG
* * *
59493 ATAGGACGTTGGAGACGAAGACAAAAAGCAAAATTAA
1 ATAGGACGTTGGAAACAAAGACAAAAAGAAAAATTAA
** * *
59530 ATATAATGATTGGAAACAAAGACAAAAGGAAAAATTAA
1 ATAGGACG-TTGGAAACAAAGACAAAAAGAAAAATTAA
59568 ATAGGACGTTGGAAACAAA
1 ATAGGACGTTGGAAACAAA
59587 AAGTTAAATT
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
37 16 0.35
38 30 0.65
ACGTcount: A:0.54, C:0.09, G:0.21, T:0.16
Consensus pattern (37 bp):
ATAGGACGTTGGAAACAAAGACAAAAAGAAAAATTAA
Found at i:64257 original size:28 final size:28
Alignment explanation
Indices: 64217--64272 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
64207 GCTTCTATAA
*
64217 TTCCCTTTCTGATTCTAATGCATTTATG
1 TTCCCTTTCTGATTCTAATGCATGTATG
64245 TTCCCTTTCTGATTCTAATGCATGTATG
1 TTCCCTTTCTGATTCTAATGCATGTATG
64273 GATTGTTATC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.18, C:0.21, G:0.12, T:0.48
Consensus pattern (28 bp):
TTCCCTTTCTGATTCTAATGCATGTATG
Found at i:83659 original size:15 final size:16
Alignment explanation
Indices: 83637--83674 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
83627 CGCTCAAATG
83637 TCGGGTC-ATTTGGGT
1 TCGGGTCAATTTGGGT
* *
83652 TTGGGTCAATTTTGGT
1 TCGGGTCAATTTGGGT
83668 TCGGGTC
1 TCGGGTC
83675 CTTATCAGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.08, C:0.13, G:0.37, T:0.42
Consensus pattern (16 bp):
TCGGGTCAATTTGGGT
Found at i:95180 original size:2 final size:2
Alignment explanation
Indices: 95173--95204 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
95163 GAAATAAAGC
95173 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
95205 TCTCTTTAAT
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:97403 original size:39 final size:39
Alignment explanation
Indices: 97349--97453 Score: 201
Period size: 39 Copynumber: 2.7 Consensus size: 39
97339 GATGGTTGCT
97349 CCTTTATAAGATGCAGCACCGCGCTCTGCCTTCTTTTTC
1 CCTTTATAAGATGCAGCACCGCGCTCTGCCTTCTTTTTC
97388 CCTTTATAAGATGCAGCACCGCGCTCTGCCTTCTTTTTC
1 CCTTTATAAGATGCAGCACCGCGCTCTGCCTTCTTTTTC
*
97427 CCTTTACAAGATGCAGCACCGCGCTCT
1 CCTTTATAAGATGCAGCACCGCGCTCT
97454 TTGTTTAGAA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 65 1.00
ACGTcount: A:0.17, C:0.34, G:0.16, T:0.32
Consensus pattern (39 bp):
CCTTTATAAGATGCAGCACCGCGCTCTGCCTTCTTTTTC
Found at i:106256 original size:11 final size:11
Alignment explanation
Indices: 106223--106248 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
106213 TCTATCACTT
106223 AGAAAAAAAAA
1 AGAAAAAAAAA
106234 AGAAAAAAAAA
1 AGAAAAAAAAA
106245 AGAA
1 AGAA
106249 GAAGAAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (11 bp):
AGAAAAAAAAA
Found at i:133375 original size:2 final size:2
Alignment explanation
Indices: 133368--133396 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
133358 TTATACAAAA
133368 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
133397 ATGGAATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:144634 original size:3 final size:3
Alignment explanation
Indices: 144626--144653 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
144616 AACTAATTTC
144626 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
144654 CAGTCTAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:146387 original size:17 final size:17
Alignment explanation
Indices: 146351--146387 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
146341 AAATTAAATC
146351 AAAATAAATTGTAATAA
1 AAAATAAATTGTAATAA
*
146368 AAAATTAAATTTTAATAA
1 AAAA-TAAATTGTAATAA
146386 AA
1 AA
146388 TTTACAAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (17 bp):
AAAATAAATTGTAATAA
Found at i:148678 original size:2 final size:2
Alignment explanation
Indices: 148671--148723 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
148661 GTATAGAGGA
148671 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
148713 AG AG AG AG AG A
1 AG AG AG AG AG A
148724 C
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Done.