Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013536.1 Corchorus capsularis cultivar CVL-1 contig13557, 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: 169640
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:447 original size:109 final size:109
Alignment explanation
Indices: 276--571 Score: 441
Period size: 109 Copynumber: 2.7 Consensus size: 109
266 TAAATTAAAA
** *
276 TGGTAAAAATAAAAAAAATTATATAAAATATT-GAATTTAATTAAATGAAAATAGAGTTTTTAGT
1 TGGTAAAAAT-AAAGTAATTATA-AAGATATTAG-ATTTAATTAAATGAAAATAGAGTTTTTAGT
* *
340 AGAATAAAGTTGTATATTAGAAAAATTTTTAATATATCCAAATTTTT
63 AGAATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
387 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGA
1 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGA
*
452 ATAAAATTGTATATTAGAAAAAATTTTAGTATATCCAAATTTTT
66 ATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
* *
496 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTTAATTGAATAAAAATAGAGTTTCTA
1 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAA-TT-A---AATGAAAATAGAGTTTTTA
561 GTAGAATAAAA
61 GTAGAATAAAA
572 CTATAATAGT
Statistics
Matches: 171, Mismatches: 8, Indels: 9
0.91 0.04 0.05
Matches are distributed among these distances:
109 119 0.70
110 13 0.08
111 11 0.06
114 28 0.16
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.38
Consensus pattern (109 bp):
TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGA
ATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
Found at i:670 original size:2 final size:2
Alignment explanation
Indices: 663--705 Score: 59
Period size: 2 Copynumber: 21.0 Consensus size: 2
653 CTAGTACTTT
* *
663 TA TA TA TA GTA TA GA TA TA TA TA TA TA TA TA TA CA TA TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
706 ATGCATTTAC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (2 bp):
TA
Found at i:1069 original size:24 final size:25
Alignment explanation
Indices: 1037--1086 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
1027 GAATTTCAAC
**
1037 AAAAAAAAAAG-TCATACCTCAAAG
1 AAAAAAAAAAGTTCATAAATCAAAG
1061 AAAAAAAAAAGTTCATAAATCAAAG
1 AAAAAAAAAAGTTCATAAATCAAAG
1086 A
1 A
1087 CTAAAGTAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 11 0.48
25 12 0.52
ACGTcount: A:0.66, C:0.12, G:0.08, T:0.14
Consensus pattern (25 bp):
AAAAAAAAAAGTTCATAAATCAAAG
Found at i:7652 original size:2 final size:2
Alignment explanation
Indices: 7640--7673 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
7630 TTATAATTAT
7640 TA TA T- TA TA TA TA TA TA TA TA TA TA TA CTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
7674 GTAATTTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 27 0.90
3 2 0.07
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8000 original size:14 final size:14
Alignment explanation
Indices: 7977--8012 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
7967 TATCACTTTA
7977 TATG-ATGTAATTT
1 TATGAATGTAATTT
7990 TATGAATGTAATTT
1 TATGAATGTAATTT
8004 TATGAATGT
1 TATGAATGT
8013 TTTGCAGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 4 0.18
14 18 0.82
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (14 bp):
TATGAATGTAATTT
Found at i:17751 original size:2 final size:2
Alignment explanation
Indices: 17746--17782 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
17736 AGCTTAGTGC
17746 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17783 TGATGAATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:21821 original size:21 final size:22
Alignment explanation
Indices: 21738--21843 Score: 94
Period size: 22 Copynumber: 4.9 Consensus size: 22
21728 TCGCTATATT
*
21738 ATTTTGATAACC-TCCCTAAGAA
1 ATTTTGATAACCAT-CCTATGAA
* * *
21760 ATTATGATAAAC-TCTCTGTGAA
1 ATTTTGATAACCATC-CTATGAA
*
21782 ACTTTGATAACCA-CACTATGAA
1 ATTTTGATAACCATC-CTATGAA
21804 ATTTTGAT-ACCATCCTATGAA
1 ATTTTGATAACCATCCTATGAA
* *
21825 ATTTTAATAACCATACTAT
1 ATTTTGATAACCATCCTAT
21844 ATAAAATTAT
Statistics
Matches: 68, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
21 19 0.28
22 49 0.72
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.35
Consensus pattern (22 bp):
ATTTTGATAACCATCCTATGAA
Found at i:21872 original size:22 final size:22
Alignment explanation
Indices: 21742--21874 Score: 85
Period size: 22 Copynumber: 6.0 Consensus size: 22
21732 TATATTATTT
** *
21742 TGATAACCTCCCTAAGAAATTA
1 TGATAACCTCTATATGAAATTA
* * *
21764 TGATAAACTCTCTGTGAAACTT-
1 TGATAACCTCTATATGAAA-TTA
* *
21786 TGATAACCAC-ACTATGAAATTT
1 TGATAACCTCTA-TATGAAATTA
* *
21808 TGAT-ACCATC-CTATGAAATTT
1 TGATAACC-TCTATATGAAATTA
* *
21829 TAATAACCATACTATATAAAATTA
1 TGATAACC-T-CTATATGAAATTA
21853 TGATAACCTCTATATGAAATTA
1 TGATAACCTCTATATGAAATTA
21875 ACTTTGATGA
Statistics
Matches: 88, Mismatches: 16, Indels: 14
0.75 0.14 0.12
Matches are distributed among these distances:
21 18 0.20
22 51 0.58
23 4 0.05
24 15 0.17
ACGTcount: A:0.41, C:0.17, G:0.08, T:0.34
Consensus pattern (22 bp):
TGATAACCTCTATATGAAATTA
Found at i:21966 original size:22 final size:22
Alignment explanation
Indices: 21938--21979 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
21928 GATTTGGTAC
21938 ACTATGAAATTTGGATAACCAT
1 ACTATGAAATTTGGATAACCAT
* *
21960 ACTATGAACTTTTGATAACC
1 ACTATGAAATTTGGATAACC
21980 TCGACCGTAC
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:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (22 bp):
ACTATGAAATTTGGATAACCAT
Found at i:22077 original size:22 final size:23
Alignment explanation
Indices: 22052--22106 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
22042 GAATATCTTC
**
22052 TATAAAATTTTTG-TAACTGCAT
1 TATAAAATTTTTGATAACCACAT
22074 TATAAAA-TTTTGATAACCACAT
1 TATAAAATTTTTGATAACCACAT
*
22096 TATGAAATTTT
1 TATAAAATTTT
22107 GGTAGCCACA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 5 0.18
22 20 0.71
23 3 0.11
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (23 bp):
TATAAAATTTTTGATAACCACAT
Found at i:22107 original size:22 final size:22
Alignment explanation
Indices: 22071--22127 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
22061 TTTGTAACTG
*
22071 CATTATAAAATTTTGATAACCA
1 CATTATGAAATTTTGATAACCA
* *
22093 CATTATGAAATTTTGGTAGCCA
1 CATTATGAAATTTTGATAACCA
*
22115 CACTATGAAATTT
1 CATTATGAAATTT
22128 CAATAATCTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.37
Consensus pattern (22 bp):
CATTATGAAATTTTGATAACCA
Found at i:23921 original size:17 final size:17
Alignment explanation
Indices: 23899--23935 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
23889 GTTATCCAGC
23899 ACCTCATGATACCTAGT
1 ACCTCATGATACCTAGT
* *
23916 ACCTCATGCTACCTGGT
1 ACCTCATGATACCTAGT
23933 ACC
1 ACC
23936 ATGAGGGGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.24, C:0.35, G:0.14, T:0.27
Consensus pattern (17 bp):
ACCTCATGATACCTAGT
Found at i:25089 original size:30 final size:30
Alignment explanation
Indices: 25033--25089 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
25023 ATATTAACTT
* *
25033 AAACTACATAATTTGTGTATCGCCAAAAAA
1 AAACTACATAATTTGTGTAGCACCAAAAAA
25063 AAACTACATAATTTGTG-AGCAACCAAA
1 AAACTACATAATTTGTGTAGC-ACCAAA
25090 GAGGTCGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 2 0.08
30 22 0.92
ACGTcount: A:0.47, C:0.18, G:0.11, T:0.25
Consensus pattern (30 bp):
AAACTACATAATTTGTGTAGCACCAAAAAA
Found at i:34487 original size:2 final size:2
Alignment explanation
Indices: 34480--34520 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
34470 GTGCGTCAAC
34480 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
34521 AGAGAGAGAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.00, G:0.51, T:0.49
Consensus pattern (2 bp):
GT
Found at i:39835 original size:15 final size:16
Alignment explanation
Indices: 39815--39864 Score: 68
Period size: 15 Copynumber: 3.1 Consensus size: 16
39805 ACTCAATTAA
39815 ATTTATATAT-TTATT
1 ATTTATATATGTTATT
39830 ATTTATATATGGTATATT
1 ATTTATATAT-GT-TATT
39848 A-TTATATATGTTATT
1 ATTTATATATGTTATT
39863 AT
1 AT
39865 ATATTTGATT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
15 15 0.48
16 2 0.06
17 9 0.29
18 5 0.16
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (16 bp):
ATTTATATATGTTATT
Found at i:39919 original size:2 final size:2
Alignment explanation
Indices: 39912--39936 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
39902 ACATCCTAGT
39912 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
39937 TTAATATTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:41840 original size:13 final size:13
Alignment explanation
Indices: 41822--41855 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
41812 TAGAGCATTC
**
41822 ATTTTTTTTTGTA
1 ATTTTTTTTTAAA
41835 ATTTTTTTTTAAA
1 ATTTTTTTTTAAA
41848 ATTTTTTT
1 ATTTTTTT
41856 GGGATTCATT
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:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (13 bp):
ATTTTTTTTTAAA
Found at i:53896 original size:16 final size:16
Alignment explanation
Indices: 53875--53911 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
53865 AATGCACCAA
*
53875 AGTAACCGACATGCAT
1 AGTAACCGACAGGCAT
*
53891 AGTAACCGATAGGCAT
1 AGTAACCGACAGGCAT
53907 AGTAA
1 AGTAA
53912 TAAAGAAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.41, C:0.19, G:0.22, T:0.19
Consensus pattern (16 bp):
AGTAACCGACAGGCAT
Found at i:58558 original size:18 final size:19
Alignment explanation
Indices: 58522--58561 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
58512 TTGTTAACCA
58522 AATTATAATTATCTTGTAT
1 AATTATAATTATCTTGTAT
58541 AATTATAATTAT-TTGTAT
1 AATTATAATTATCTTGTAT
58559 AAT
1 AAT
58562 CATAGACTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.53
Consensus pattern (19 bp):
AATTATAATTATCTTGTAT
Found at i:63817 original size:24 final size:24
Alignment explanation
Indices: 63788--63858 Score: 79
Period size: 24 Copynumber: 3.0 Consensus size: 24
63778 CAGACACCAA
* * *
63788 CTCCTTCTTCTCTTCCTTCTTCTC
1 CTCCTTCTTCTCCTCCTCCTCCTC
*
63812 TTCCTTCTTCTCCTCCTCCTCCTC
1 CTCCTTCTTCTCCTCCTCCTCCTC
* * *
63836 CTCCTTCTCCTTCTTCTCCTCCT
1 CTCCTTCTTCTCCTCCTCCTCCT
63859 TGGGGGTAGG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (24 bp):
CTCCTTCTTCTCCTCCTCCTCCTC
Found at i:63825 original size:9 final size:9
Alignment explanation
Indices: 63788--63855 Score: 50
Period size: 9 Copynumber: 7.6 Consensus size: 9
63778 CAGACACCAA
63788 CTCCTTCTT
1 CTCCTTCTT
63797 CT-CTTCCTT
1 CTCCTT-CTT
*
63806 CTTC-TCTT
1 CTCCTTCTT
* *
63814 CCTTCTTCTC
1 -CTCCTTCTT
* *
63824 CTCCTCCTC
1 CTCCTTCTT
*
63833 CTCCTCCTT
1 CTCCTTCTT
63842 CTCCTTCTT
1 CTCCTTCTT
63851 CTCCT
1 CTCCT
63856 CCTTGGGGGT
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
8 6 0.12
9 40 0.80
10 4 0.08
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (9 bp):
CTCCTTCTT
Found at i:63845 original size:12 final size:12
Alignment explanation
Indices: 63788--63858 Score: 67
Period size: 12 Copynumber: 6.2 Consensus size: 12
63778 CAGACACCAA
*
63788 CTCCTTCTTCTC
1 CTCCTTCTCCTC
* *
63800 TTCCTTCTTCTC
1 CTCCTTCTCCTC
* *
63812 TTCCTTCTTCTC
1 CTCCTTCTCCTC
*
63824 CTCCTCCTCCTC
1 CTCCTTCTCCTC
63836 CTCCTTCTCCT-
1 CTCCTTCTCCTC
63847 -T-CTTCTCCTC
1 CTCCTTCTCCTC
63857 CT
1 CT
63859 TGGGGGTAGG
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
9 8 0.15
10 1 0.02
11 1 0.02
12 42 0.81
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (12 bp):
CTCCTTCTCCTC
Found at i:63859 original size:12 final size:12
Alignment explanation
Indices: 63788--63843 Score: 76
Period size: 12 Copynumber: 4.7 Consensus size: 12
63778 CAGACACCAA
63788 CTCCTTCTTCTC
1 CTCCTTCTTCTC
*
63800 TTCCTTCTTCTC
1 CTCCTTCTTCTC
*
63812 TTCCTTCTTCTC
1 CTCCTTCTTCTC
* *
63824 CTCCTCCTCCTC
1 CTCCTTCTTCTC
63836 CTCCTTCT
1 CTCCTTCT
63844 CCTTCTTCTC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 39 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (12 bp):
CTCCTTCTTCTC
Found at i:65353 original size:7 final size:7
Alignment explanation
Indices: 65333--65369 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
65323 GAGAGAGTGA
65333 GAGTG-G
1 GAGTGTG
65339 GAGTGTG
1 GAGTGTG
*
65346 GGGTGTG
1 GAGTGTG
65353 GAGTGTG
1 GAGTGTG
65360 GAGTGTG
1 GAGTGTG
65367 GAG
1 GAG
65370 GGAAATGTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
6 5 0.18
7 23 0.82
ACGTcount: A:0.14, C:0.00, G:0.62, T:0.24
Consensus pattern (7 bp):
GAGTGTG
Found at i:72426 original size:14 final size:14
Alignment explanation
Indices: 72407--72434 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
72397 CGTCTAACAA
72407 TTCAAACTAAGGGT
1 TTCAAACTAAGGGT
72421 TTCAAACTAAGGGT
1 TTCAAACTAAGGGT
72435 ACCATTCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (14 bp):
TTCAAACTAAGGGT
Found at i:77166 original size:11 final size:11
Alignment explanation
Indices: 77150--77185 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
77140 CCATTATACT
77150 ATATCTAATTA
1 ATATCTAATTA
77161 ATATCTAATTA
1 ATATCTAATTA
77172 ATAGT-TAATTA
1 ATA-TCTAATTA
77183 ATA
1 ATA
77186 ATGAATAAAT
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:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (11 bp):
ATATCTAATTA
Found at i:78325 original size:9 final size:10
Alignment explanation
Indices: 78312--78346 Score: 52
Period size: 10 Copynumber: 3.3 Consensus size: 10
78302 GTTTAAAATA
78312 AAAAAAAAAC
1 AAAAAAAAAC
78322 AAAAAAAAAC
1 AAAAAAAAAC
78332 AAACAAACAAAC
1 AAA-AAA-AAAC
78344 AAA
1 AAA
78347 TTTGCCGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 13 0.57
11 3 0.13
12 7 0.30
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:78669 original size:2 final size:2
Alignment explanation
Indices: 78664--78692 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
78654 ATATTATCAG
78664 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
78693 TATCAATAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:82325 original size:60 final size:60
Alignment explanation
Indices: 82247--82409 Score: 247
Period size: 60 Copynumber: 2.7 Consensus size: 60
82237 GCGTGAGACA
* * * *
82247 GACCCTTATTTGAACATTTTGGTAAATGTTAGGCCCTTATTTGGCCAAATTCAAAGAT-G
1 GACCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
* *
82306 GAGCCCTTATTTGAGCATTTTAGCAAACGTTAGGCCCTTATTTAGCCAAATTAAAAGATCG
1 GA-CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
*
82367 GACCCTAATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
1 GACCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
82410 AGCAATTAGC
Statistics
Matches: 93, Mismatches: 9, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
59 2 0.02
60 88 0.95
61 3 0.03
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (60 bp):
GACCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
Found at i:82346 original size:31 final size:30
Alignment explanation
Indices: 82249--82413 Score: 108
Period size: 31 Copynumber: 5.5 Consensus size: 30
82239 GTGAGACAGA
* * *
82249 CCCTTATTTGAACATTTTGGTAAATGTTAGG
1 CCCTTATTTGAGCATTTTAGCAAA-GTTAGG
** * *
82280 CCCTTATTTG-GCCAAATT--CAAAGATGGAG
1 CCCTTATTTGAG-CATTTTAGCAAAGTTAG-G
82309 CCCTTATTTGAGCATTTTAGCAAACGTTAGG
1 CCCTTATTTGAGCATTTTAGCAAA-GTTAGG
** * *
82340 CCCTTATTT-AGCCAAATTA--AAAGATCGG
1 CCCTTATTTGAG-CATTTTAGCAAAGTTAGG
* *
82368 ACCCTAATTTGAGCATTTTGGCAAACGTTAGG
1 -CCCTTATTTGAGCATTTTAGCAAA-GTTAGG
82400 CCCTTATTTGAGCA
1 CCCTTATTTGAGCA
82414 ATTAGCCTTA
Statistics
Matches: 101, Mismatches: 21, Indels: 24
0.69 0.14 0.16
Matches are distributed among these distances:
28 7 0.07
29 33 0.33
30 5 0.05
31 49 0.49
32 7 0.07
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.33
Consensus pattern (30 bp):
CCCTTATTTGAGCATTTTAGCAAAGTTAGG
Found at i:90056 original size:10 final size:10
Alignment explanation
Indices: 90041--90081 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
90031 AAGAGAGGAG
90041 CTTTTTCTTT
1 CTTTTTCTTT
*
90051 CTTTTTCTCT
1 CTTTTTCTTT
*
90061 CCTTTTCTTTT
1 CTTTTTC-TTT
90072 CTTTTTCTTT
1 CTTTTTCTTT
90082 TTCTTCTTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
10 18 0.69
11 8 0.31
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (10 bp):
CTTTTTCTTT
Found at i:92642 original size:30 final size:28
Alignment explanation
Indices: 92566--92649 Score: 87
Period size: 28 Copynumber: 2.9 Consensus size: 28
92556 TGGCACATGA
* * * *
92566 CCTTTTTTACATGTGGCGTGCCATGTGT
1 CCTTTTGTACATGTGGCATGCCACGTGG
*
92594 CCTTTTGTACACGTGGCATGCCACGTGG
1 CCTTTTGTACATGTGGCATGCCACGTGG
* *
92622 CCTTTTTGATATATGTGGCATACCACGT
1 CC-TTTTG-TACATGTGGCATGCCACGT
92650 CGGATGCCCG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
28 25 0.54
29 5 0.11
30 16 0.35
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.37
Consensus pattern (28 bp):
CCTTTTGTACATGTGGCATGCCACGTGG
Found at i:93338 original size:23 final size:23
Alignment explanation
Indices: 93308--93354 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
93298 TCCATCTCTT
93308 AAACCCCAACATTCAACAAAAAA
1 AAACCCCAACATTCAACAAAAAA
* *
93331 AAACCCCAACATTCAGCCAAAAA
1 AAACCCCAACATTCAACAAAAAA
93354 A
1 A
93355 TTTGAGGCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.57, C:0.32, G:0.02, T:0.09
Consensus pattern (23 bp):
AAACCCCAACATTCAACAAAAAA
Found at i:94843 original size:11 final size:11
Alignment explanation
Indices: 94800--94837 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
94790 TTCCTATATA
*
94800 AAATAAATTAT
1 AAATTAATTAT
94811 CAAA-TAATTAT
1 -AAATTAATTAT
94822 AAATTAATTAT
1 AAATTAATTAT
94833 AAATT
1 AAATT
94838 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:102992 original size:21 final size:21
Alignment explanation
Indices: 102967--103012 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
102957 CGAGCTTGAC
*
102967 GAAGACGAAGTTGA-AGATGAA
1 GAAGACGAAGGTGATA-ATGAA
*
102988 GAAGACGATGGTGATAATGAA
1 GAAGACGAAGGTGATAATGAA
103009 GAAG
1 GAAG
103013 CACGTTGCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.46, C:0.04, G:0.35, T:0.15
Consensus pattern (21 bp):
GAAGACGAAGGTGATAATGAA
Found at i:103344 original size:18 final size:17
Alignment explanation
Indices: 103321--103382 Score: 61
Period size: 18 Copynumber: 3.5 Consensus size: 17
103311 CGCCTTGTTG
103321 TGATCTTTATTTTCTTTC
1 TGATCTTTATTTT-TTTC
* *
103339 TGATCTTTCATCTGTTTC
1 TGATCTTT-ATTTTTTTC
* *
103357 TGATCATTGTTGTTTTTC
1 TGATCTTTATT-TTTTTC
103375 TGATCTTT
1 TGATCTTT
103383 CTCTTCGTTT
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
17 1 0.03
18 31 0.89
19 3 0.09
ACGTcount: A:0.11, C:0.16, G:0.11, T:0.61
Consensus pattern (17 bp):
TGATCTTTATTTTTTTC
Found at i:112113 original size:21 final size:21
Alignment explanation
Indices: 112087--112128 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
112077 TTTATCATAA
112087 ATTAATATCTCAAAGTTTTTT
1 ATTAATATCTCAAAGTTTTTT
*
112108 ATTAATATCTTAAAGTTTTTT
1 ATTAATATCTCAAAGTTTTTT
112129 TTTTTTGAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (21 bp):
ATTAATATCTCAAAGTTTTTT
Found at i:113188 original size:96 final size:94
Alignment explanation
Indices: 113041--113230 Score: 344
Period size: 96 Copynumber: 2.0 Consensus size: 94
113031 AAAAGAAGAG
*
113041 AGAGAGAGAGAGAGAGCAGCAGCAGCAACATGACCTTATTTGCCTATAAGTCTCACTAACGCTGT
1 AGAGAGAGAGAGAGAGCAGCAGCAGCAACATGACCTCATTTGCCTATAAGTCTCACTAACGCTGT
113106 CAATATATACATGTTAAAAAACCCACCAAT
66 CAATATATACATGTTAAAAAA-CCACCAAT
113136 AGAGAGAGAGAGAGCAGCAGCAGCAGCAACATGACCTCATTTGCCTATAAGTCTCACTAACGCTG
1 AGAGAGAGAGAGAG-AGCAGCAGCAGCAACATGACCTCATTTGCCTATAAGTCTCACTAACGCTG
*
113201 TCAATATATATATGTTAAAAAACCACCAAT
65 TCAATATATACATGTTAAAAAACCACCAAT
113231 CCTTTCACCA
Statistics
Matches: 92, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
95 22 0.24
96 70 0.76
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (94 bp):
AGAGAGAGAGAGAGAGCAGCAGCAGCAACATGACCTCATTTGCCTATAAGTCTCACTAACGCTGT
CAATATATACATGTTAAAAAACCACCAAT
Found at i:120376 original size:18 final size:18
Alignment explanation
Indices: 120353--120390 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
120343 AGGCGGTGGC
120353 GGAGGAGGTG-TCGGAGGA
1 GGAGGAGGTGCT-GGAGGA
120371 GGAGGAGGTGCTGGAGGA
1 GGAGGAGGTGCTGGAGGA
120389 GG
1 GG
120391 CTAAAAGGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 18 0.95
19 1 0.05
ACGTcount: A:0.21, C:0.05, G:0.63, T:0.11
Consensus pattern (18 bp):
GGAGGAGGTGCTGGAGGA
Found at i:124395 original size:23 final size:22
Alignment explanation
Indices: 124359--124423 Score: 67
Period size: 23 Copynumber: 2.9 Consensus size: 22
124349 GAAGACCTCA
*
124359 ATATGAAATTTTGATAACCAAC
1 ATATGAAATATTGATAACCAAC
* * **
124381 ACTATGAGATGTTGATAACCTCC
1 A-TATGAAATATTGATAACCAAC
*
124404 ATATGATATATTGATAACCA
1 ATATGAAATATTGATAACCA
124424 CTTTATAAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
22 17 0.49
23 18 0.51
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.32
Consensus pattern (22 bp):
ATATGAAATATTGATAACCAAC
Found at i:124417 original size:22 final size:22
Alignment explanation
Indices: 124316--124422 Score: 72
Period size: 22 Copynumber: 4.8 Consensus size: 22
124306 TTAACTTTCT
* * *
124316 TATGAAATTTTGTTAACCTCCC
1 TATGAAATATTGATAACCTCCA
* * * *
124338 TAAGGAATTTTGA-AGACCTCAA
1 TATGAAATATTGATA-ACCTCCA
* **
124360 TATGAAATTTTGATAACCAACA
1 TATGAAATATTGATAACCTCCA
* *
124382 CTATGAGATGTTGATAACCTCCA
1 -TATGAAATATTGATAACCTCCA
*
124405 TATGATATATTGATAACC
1 TATGAAATATTGATAACC
124423 ACTTTATAAA
Statistics
Matches: 66, Mismatches: 16, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
21 1 0.02
22 46 0.70
23 19 0.29
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (22 bp):
TATGAAATATTGATAACCTCCA
Found at i:124506 original size:22 final size:21
Alignment explanation
Indices: 124476--124524 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
124466 TACACTGTAA
*
124476 AAATTTGATAATCACACTATG
1 AAATTTGATAACCACACTATG
* *
124497 AAATTGTGATAACCTCGCTATG
1 AAATT-TGATAACCACACTATG
124519 AAATTT
1 AAATTT
124525 TAATAAATCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 6 0.25
22 18 0.75
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (21 bp):
AAATTTGATAACCACACTATG
Found at i:124545 original size:23 final size:23
Alignment explanation
Indices: 124507--124576 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
124497 AAATTGTGAT
* *
124507 AACCTCGCTATGAAATTTTAATA
1 AACCTCCCTATAAAATTTTAATA
* *
124530 AATCTTCCTATAAAATTTTAATA
1 AACCTCCCTATAAAATTTTAATA
*
124553 AACCTCCCTATAAAATTTTGATA
1 AACCTCCCTATAAAATTTTAATA
124576 A
1 A
124577 CTTTCTTATG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.41, C:0.17, G:0.04, T:0.37
Consensus pattern (23 bp):
AACCTCCCTATAAAATTTTAATA
Found at i:124654 original size:22 final size:21
Alignment explanation
Indices: 124603--124767 Score: 109
Period size: 22 Copynumber: 7.5 Consensus size: 21
124593 TGATAACTAC
* *
124603 AAATTTTGATAAGCTCCCTATG
1 AAATTTTGATAACCT-CATATG
** *
124625 ATTTTTTGATTACCTCATTATG
1 AAATTTTGATAACCTCA-TATG
* * *
124647 AAAATTTGCTAATCTCCATATG
1 AAATTTTGATAACCT-CATATG
* *
124669 AAATTTTGATCTACAT-ACTATG
1 AAATTTTGAT-AACCTCA-TATG
*
124691 AAATTTTGATAACCCTCTTATG
1 AAATTTTGATAA-CCTCATATG
* *
124713 AAATTTTGA-AAACTAAACTATG
1 AAATTTTGATAACCT-CA-TATG
*
124735 AAAATTTGATAACCTTCATATG
1 AAATTTTGATAACC-TCATATG
124757 AAATTTTGATA
1 AAATTTTGATA
124768 TTCTCACTGA
Statistics
Matches: 107, Mismatches: 26, Indels: 20
0.70 0.17 0.13
Matches are distributed among these distances:
20 2 0.02
21 5 0.05
22 91 0.85
23 8 0.07
24 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (21 bp):
AAATTTTGATAACCTCATATG
Found at i:124676 original size:44 final size:42
Alignment explanation
Indices: 124607--124766 Score: 133
Period size: 44 Copynumber: 3.6 Consensus size: 42
124597 AACTACAAAT
* ** *
124607 TTTGATAAGCTCCCTATGATTTTTTGATTACCTCATTATGAAAA
1 TTTGATAA-CTCCATATGAAATTTTGATTACCT-ACTATGAAAA
* * *
124651 TTTGCTAATCTCCATATGAAATTTTGATCTACATACTATGAAAT
1 TTTGATAA-CTCCATATGAAATTTTGAT-TACCTACTATGAAAA
* * * *
124695 TTTGATAACCCTCTTATGAAATTTTGA-AAACTAAACTATGAAAA
1 TTTGATAACTC-CATATGAAATTTTGATTACCT--ACTATGAAAA
*
124739 TTTGATAACCTTCATATGAAATTTTGAT
1 TTTGATAA-CTCCATATGAAATTTTGAT
124767 ATTCTCACTG
Statistics
Matches: 92, Mismatches: 18, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
42 2 0.02
43 2 0.02
44 83 0.90
45 5 0.05
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (42 bp):
TTTGATAACTCCATATGAAATTTTGATTACCTACTATGAAAA
Found at i:124830 original size:19 final size:19
Alignment explanation
Indices: 124758--124824 Score: 98
Period size: 19 Copynumber: 3.5 Consensus size: 19
124748 CTTCATATGA
* *
124758 AATTTTGATATTCTCACTG
1 AATTTTGATATCCTCCCTG
124777 AATTTTGATATCCTCCCTG
1 AATTTTGATATCCTCCCTG
*
124796 AATTTTGGTATCCTCCCTG
1 AATTTTGATATCCTCCCTG
124815 AAATTTTGAT
1 -AATTTTGAT
124825 TACTCCATCA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
19 35 0.81
20 8 0.19
ACGTcount: A:0.24, C:0.19, G:0.12, T:0.45
Consensus pattern (19 bp):
AATTTTGATATCCTCCCTG
Found at i:124955 original size:22 final size:22
Alignment explanation
Indices: 124930--125112 Score: 139
Period size: 22 Copynumber: 8.4 Consensus size: 22
124920 AATCACATTT
*
124930 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
*
124952 TGAAATTTTGATAACATCTTTA
1 TGAAATTTTGATAACCTCTTTA
* * * * *
124974 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTCTTTA
* * *
124996 TGAAATTTTGATAATCACATTA
1 TGAAATTTTGATAACCTCTTTA
* *
125018 TGTAATTTTGATAACCTCGCTT-
1 TGAAATTTTGATAACCTC-TTTA
125040 TGAAATTTTGATAACAC-C---A
1 TGAAATTTTGATAAC-CTCTTTA
125059 TGAAATTTTGATAA--TCTTCATA
1 TGAAATTTTGATAACCTCTT--TA
125081 T-AAATTTTGATAATCCTATCTTTA
1 TGAAATTTTGATAA-CC--TCTTTA
125105 TGAAATTT
1 TGAAATTT
125113 CAATAATCAC
Statistics
Matches: 126, Mismatches: 20, Indels: 27
0.73 0.12 0.16
Matches are distributed among these distances:
17 1 0.01
19 14 0.11
21 12 0.10
22 83 0.66
23 3 0.02
24 3 0.02
25 6 0.05
26 4 0.03
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.43
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTTTA
Found at i:124956 original size:44 final size:44
Alignment explanation
Indices: 124906--125053 Score: 144
Period size: 44 Copynumber: 3.4 Consensus size: 44
124896 GAAATACCAC
124906 TATGAAATTTTTG-TAATCACATTTTGAAAATTTGATAACCTCTT
1 TATGAAA-TTTTGATAATCACATTTTGAAAATTTGATAACCTCTT
* * * *
124950 TATGAAATTTTGATAA-CATC-TTTAT-AAAATTTTGTTGACCCCTC
1 TATGAAATTTTGATAATCA-CATTT-TGAAAA-TTTGATAACCTCTT
* * * *
124994 TATGAAATTTTGATAATCACATTATGTAATTTTGATAACCTCGCT
1 TATGAAATTTTGATAATCACATTTTGAAAATTTGATAACCTC-TT
125039 T-TGAAATTTTGATAA
1 TATGAAATTTTGATAA
125054 CACCATGAAA
Statistics
Matches: 84, Mismatches: 12, Indels: 16
0.75 0.11 0.14
Matches are distributed among these distances:
43 14 0.17
44 63 0.75
45 7 0.08
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (44 bp):
TATGAAATTTTGATAATCACATTTTGAAAATTTGATAACCTCTT
Found at i:125019 original size:66 final size:63
Alignment explanation
Indices: 124930--125112 Score: 174
Period size: 66 Copynumber: 2.8 Consensus size: 63
124920 AATCACATTT
* * * * * * *
124930 TGAAAATTTGATAACCTCTTTATGAAATTTTGATAACATCTTTATAAAATTTTGTTGACCCCTCT
1 TGAAATTTTGATAATCTCATTATGAAATTTTGATAACATCTTTATGAAATTTTGAT-AACAC-C-
124995 A
63 A
* * * *
124996 TGAAATTTTGATAATCACATTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAACACCA
1 TGAAATTTTGATAATCTCATTATGAAATTTTGATAACATC-TTTATGAAATTTTGATAACACCA
125059 TGAAATTTTGATAATCTTCA-TAT-AAATTTTGATAATCCTATCTTTATGAAATTT
1 TGAAATTTTGATAATC-TCATTATGAAATTTTGATAA--C-ATCTTTATGAAATTT
125113 CAATAATCAC
Statistics
Matches: 96, Mismatches: 15, Indels: 13
0.77 0.12 0.10
Matches are distributed among these distances:
62 11 0.11
63 20 0.21
64 6 0.06
65 13 0.14
66 44 0.46
67 2 0.02
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.43
Consensus pattern (63 bp):
TGAAATTTTGATAATCTCATTATGAAATTTTGATAACATCTTTATGAAATTTTGATAACACCA
Found at i:125208 original size:22 final size:21
Alignment explanation
Indices: 125179--125254 Score: 57
Period size: 22 Copynumber: 3.5 Consensus size: 21
125169 AAATTGAGAC
125179 TTTT-ATAACCTTCATATGAAA
1 TTTTGATAACCTTC-TATGAAA
* * *
125200 TTTTGATAACCTCCCGATGAAG
1 TTTTGATAACCT-TCTATGAAA
*
125222 TATT-AGTAACCTTCTAATGAAA
1 TTTTGA-TAACCTTCT-ATGAAA
*
125244 TTTTGCTAACC
1 TTTTGATAACC
125255 ACACTTTGAA
Statistics
Matches: 41, Mismatches: 9, Indels: 9
0.69 0.15 0.15
Matches are distributed among these distances:
21 6 0.15
22 34 0.83
23 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (21 bp):
TTTTGATAACCTTCTATGAAA
Found at i:125414 original size:22 final size:22
Alignment explanation
Indices: 125331--125517 Score: 146
Period size: 22 Copynumber: 8.4 Consensus size: 22
125321 TTGTGATAAT
*
125331 TAACCACCCTATGAAATTTTGAA
1 TAACCACACTATGAAATTTTG-A
* * *
125354 TAACTA-ACCTAAGAAATTTTAA
1 TAACCACA-CTATGAAATTTTGA
** *
125376 TAACCTGATGCTATGAAATTTTGG
1 TAACC--ACACTATGAAATTTTGA
* *
125400 TAACCACTCTATGAAATTTTGG
1 TAACCACACTATGAAATTTTGA
* *
125422 TAACTACACTATGAAATTTTGG
1 TAACCACACTATGAAATTTTGA
*
125444 TAACCACACTATGGAATTTTGA
1 TAACCACACTATGAAATTTTGA
* * * *
125466 TAACCTC-CTCATGGAATTATAA
1 TAACCACACT-ATGAAATTTTGA
*
125488 TAACCATC-TTATGAAATTTTGA
1 TAACCA-CACTATGAAATTTTGA
125510 TAACCACA
1 TAACCACA
125518 TAGAGACAAG
Statistics
Matches: 133, Mismatches: 24, Indels: 15
0.77 0.14 0.09
Matches are distributed among these distances:
21 3 0.02
22 95 0.71
23 18 0.14
24 17 0.13
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (22 bp):
TAACCACACTATGAAATTTTGA
Found at i:125821 original size:32 final size:33
Alignment explanation
Indices: 125793--125859 Score: 86
Period size: 32 Copynumber: 2.1 Consensus size: 33
125783 GGCAATTTAG
125793 AAATAT-ATTTTAAAAA-AAGGGGTACAATTGA
1 AAATATGATTTTAAAAATAAGGGGTACAATTGA
* *
125824 AAATATGTTTTTAAAAATAA-GGGTATAATCTGA
1 AAATATGATTTTAAAAATAAGGGGTACAAT-TGA
125857 AAA
1 AAA
125860 CATAAAGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 6 0.19
32 17 0.55
33 8 0.26
ACGTcount: A:0.51, C:0.03, G:0.15, T:0.31
Consensus pattern (33 bp):
AAATATGATTTTAAAAATAAGGGGTACAATTGA
Found at i:133203 original size:25 final size:25
Alignment explanation
Indices: 133169--133218 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
133159 TCTTTAGCTC
133169 ATGTTGTTCCATCGGGGATAACTTG
1 ATGTTGTTCCATCGGGGATAACTTG
133194 ATGTTGTTCCATCGGGGATAACTTG
1 ATGTTGTTCCATCGGGGATAACTTG
133219 GTTCGAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.20, C:0.16, G:0.28, T:0.36
Consensus pattern (25 bp):
ATGTTGTTCCATCGGGGATAACTTG
Found at i:134444 original size:21 final size:20
Alignment explanation
Indices: 134402--134449 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
134392 AAAGAAAATC
*
134402 AATATAATAATAATTAATTT
1 AATATAATAATAATTAACTT
134422 AATAGTAATAATAA-TAACCTT
1 AATA-TAATAATAATTAA-CTT
134443 AAT-TAAT
1 AATATAAT
134450 CAAATACTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 4 0.16
20 7 0.28
21 14 0.56
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (20 bp):
AATATAATAATAATTAACTT
Found at i:139582 original size:63 final size:62
Alignment explanation
Indices: 139484--139608 Score: 214
Period size: 63 Copynumber: 2.0 Consensus size: 62
139474 CCAAAGGTAT
139484 GGCTTAGTTCTATGGATTTAACAGATCTAAGTTATTGTTTCAAGTAAATGAAGGTTGCTTTA
1 GGCTTAGTTCTATGGATTTAACAGATCTAAGTTATTGTTTCAAGTAAATGAAGGTTGCTTTA
* * *
139546 GGCTTTGTTCTATGGAATTTAAGAGATCTAAGTTATTGTTTCAAGTAAATGAAGGTTGGTTTA
1 GGCTTAGTTCTATGG-ATTTAACAGATCTAAGTTATTGTTTCAAGTAAATGAAGGTTGCTTTA
139609 CTCACCTATG
Statistics
Matches: 59, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
62 14 0.24
63 45 0.76
ACGTcount: A:0.29, C:0.08, G:0.22, T:0.41
Consensus pattern (62 bp):
GGCTTAGTTCTATGGATTTAACAGATCTAAGTTATTGTTTCAAGTAAATGAAGGTTGCTTTA
Found at i:144926 original size:12 final size:12
Alignment explanation
Indices: 144907--144940 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
144897 TACAATATTC
144907 TATTTTTTTTAA
1 TATTTTTTTTAA
* *
144919 TGTTTTTTATAA
1 TATTTTTTTTAA
144931 TATTTTTTTT
1 TATTTTTTTT
144941 GGTATAAAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (12 bp):
TATTTTTTTTAA
Found at i:150061 original size:29 final size:29
Alignment explanation
Indices: 150019--150074 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
150009 ATGGAATTCT
150019 AGTAATCATATTATTTTTCCTCACTACAA
1 AGTAATCATATTATTTTTCCTCACTACAA
150048 AGTAATCATATTATTTTTCCTCACTAC
1 AGTAATCATATTATTTTTCCTCACTAC
150075 TAATTTAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.32, C:0.21, G:0.04, T:0.43
Consensus pattern (29 bp):
AGTAATCATATTATTTTTCCTCACTACAA
Found at i:161380 original size:18 final size:18
Alignment explanation
Indices: 161357--161391 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
161347 ACAAAAATTG
161357 AAATTGTTCATAAACAAA
1 AAATTGTTCATAAACAAA
*
161375 AAATTGTTCATGAACAA
1 AAATTGTTCATAAACAA
161392 TGTAATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (18 bp):
AAATTGTTCATAAACAAA
Found at i:162310 original size:28 final size:28
Alignment explanation
Indices: 162279--162336 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
162269 CTAGCAGACA
162279 ATTCACAAGGCAGAGATATACACAAAGT
1 ATTCACAAGGCAGAGATATACACAAAGT
*
162307 ATTCACAATGCAGAGATATACACAAAGT
1 ATTCACAAGGCAGAGATATACACAAAGT
162335 AT
1 AT
162337 CCTCGACTCC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.47, C:0.17, G:0.16, T:0.21
Consensus pattern (28 bp):
ATTCACAAGGCAGAGATATACACAAAGT
Found at i:163040 original size:2 final size:2
Alignment explanation
Indices: 163033--163074 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
163023 TAGGTTTTAG
163033 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
163073 TA
1 TA
163075 ATCTATACTA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:163373 original size:23 final size:22
Alignment explanation
Indices: 163326--163383 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
163316 ATATTATTTT
*
163326 TATAATTTTTATGAATAATATA
1 TATAATTATTATGAATAATATA
* *
163348 TATTATTATTATTAATATATATA
1 TATAATTATTATGAATA-ATATA
163371 TATAATTA-TATGA
1 TATAATTATTATGA
163384 TAAACGAACG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
22 18 0.60
23 12 0.40
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (22 bp):
TATAATTATTATGAATAATATA
Found at i:163914 original size:23 final size:23
Alignment explanation
Indices: 163883--163932 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
163873 GTTCAAGCTT
* *
163883 TGTC-TATCATCTCTCCTCCTTA
1 TGTCTTATCATCCCTCCTCATTA
163905 TGTCTTATCATCCCTCCTCATTA
1 TGTCTTATCATCCCTCCTCATTA
163928 TGTCT
1 TGTCT
163933 AGAAAATGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 4 0.16
23 21 0.84
ACGTcount: A:0.14, C:0.34, G:0.06, T:0.46
Consensus pattern (23 bp):
TGTCTTATCATCCCTCCTCATTA
Found at i:164440 original size:203 final size:203
Alignment explanation
Indices: 164198--164806 Score: 863
Period size: 203 Copynumber: 3.0 Consensus size: 203
164188 TGGGGGGAGG
* *
164198 GGGGTGATGGGGGTTGCTTGAGGAAGGCAAGGAAACCATTGAAGACAAAGCCGTTGAAGGCACAC
1 GGGGTGAAGAGGGTTGCTTGAGGAAGGCAAGGAAACCATTGAAGACAAAGCCGTTGAAGGCACAC
* * *
164263 CACCCGGATAAACACTAGATGGACCGGGGAGGTCACCGGGATAAAATCTACATGAGAAACATACA
66 CACCCGGATAAACACTAGATGGACCAGGGAGGTCAACAGGATAAAATCTACATGAGAAACATACA
*
164328 TATGAGAATACATGACAAGCAAGAGAATAAAAACTTATGAAAGGGTAAAGGATGAAATAGGAAAA
131 TATGAGAATACATGACAAGCAAGAGAA-AAAAACTTATGAAAGGGTAAAGGATGAAACAGGAAAA
164393 ACTTACCCA
195 ACTTACCCA
* * * *
164402 -GGGTGAAGAGGGTTACTTGAGGATGGCAAGGCAACCATTGAAGACAAAGCCATTGAAGGCACAC
1 GGGGTGAAGAGGGTTGCTTGAGGAAGGCAAGGAAACCATTGAAGACAAAGCCGTTGAAGGCACAC
** ** * *
164466 CAATCAAATAAACACTAGATGGACCAGGGAGGTCAACAAGATAAAACCTACATGAG--A-ATACA
66 CACCCGGATAAACACTAGATGGACCAGGGAGGTCAACAGGATAAAATCTACATGAGAAACATACA
* * *
164528 TATGAGAATATATGACAAGCAAGAGAAAACAACTTATGAGAGGGTAAAGGATGAAACAGGAAAAA
131 TATGAGAATACATGACAAGCAAGAGAAAAAAACTTATGAAAGGGTAAAGGATGAAACAGGAAAAA
164593 CTTACGCAAACA
196 CTTAC-C---CA
* *
164605 TGGGGTGAAGAGGGTTGCTTGAGAAAGACAAGGAAACCATTGAAGACAAA-CTCGTTGAAGGCAC
1 -GGGGTGAAGAGGGTTGCTTGAGGAAGGCAAGGAAACCATTGAAGACAAAGC-CGTTGAAGGCAC
* *
164669 ACCACCCGGATAAACATTAGATGGACCAGGGAGGTCAACAGGATAAAATCTACATCAGAAACATA
64 ACCACCCGGATAAACACTAGATGGACCAGGGAGGTCAACAGGATAAAATCTACATGAGAAACATA
* * * *
164734 CATATGAG-ATACATGACGAGCAAGAG-AAAAAACTTATGAAAGGGTAAAGGTTGAAGCAGAAAA
129 CATATGAGAATACATGACAAGCAAGAGAAAAAAACTTATGAAAGGGTAAAGGATGAAACAGGAAA
164797 AACTTACCCA
194 AACTTACCCA
164807 AAGGGGGGAT
Statistics
Matches: 355, Mismatches: 40, Indels: 22
0.85 0.10 0.05
Matches are distributed among these distances:
199 40 0.11
200 32 0.09
201 1 0.00
202 2 0.01
203 107 0.30
204 1 0.00
205 105 0.30
206 39 0.11
207 17 0.05
208 11 0.03
ACGTcount: A:0.43, C:0.16, G:0.25, T:0.16
Consensus pattern (203 bp):
GGGGTGAAGAGGGTTGCTTGAGGAAGGCAAGGAAACCATTGAAGACAAAGCCGTTGAAGGCACAC
CACCCGGATAAACACTAGATGGACCAGGGAGGTCAACAGGATAAAATCTACATGAGAAACATACA
TATGAGAATACATGACAAGCAAGAGAAAAAAACTTATGAAAGGGTAAAGGATGAAACAGGAAAAA
CTTACCCA
Found at i:168749 original size:11 final size:11
Alignment explanation
Indices: 168733--168767 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
168723 TTGACAGCGC
168733 AACAAAAACAA
1 AACAAAAACAA
*
168744 AACAAAAACGA
1 AACAAAAACAA
168755 AACAAAAACAA
1 AACAAAAACAA
168766 AA
1 AA
168768 AACAGAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.80, C:0.17, G:0.03, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Done.