Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015636.1 Corchorus olitorius cultivar O-4 contig15669, 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: 84135
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:3813 original size:16 final size:17
Alignment explanation
Indices: 3787--3818 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
3777 AGTGCAAATT
3787 AAAATAGAAAAATAAAG
1 AAAATAGAAAAATAAAG
3804 AAAA-AGAAAAATAAA
1 AAAATAGAAAAATAAA
3819 ACGCAATCGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.81, C:0.00, G:0.09, T:0.09
Consensus pattern (17 bp):
AAAATAGAAAAATAAAG
Found at i:4051 original size:12 final size:13
Alignment explanation
Indices: 4029--4058 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
4019 ACTAACAATT
4029 AAAATCAATCAAG
1 AAAATCAATCAAG
4042 AAAA-CAATCAAG
1 AAAATCAATCAAG
4054 AAAAT
1 AAAAT
4059 TAAAGAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.67, C:0.13, G:0.07, T:0.13
Consensus pattern (13 bp):
AAAATCAATCAAG
Found at i:11328 original size:69 final size:70
Alignment explanation
Indices: 11181--11341 Score: 252
Period size: 69 Copynumber: 2.3 Consensus size: 70
11171 CAGATCTTGG
* * *
11181 CCAAGTCCTGTCCAGGACTTGGGCTGTTGAGGAATGCAAAAATACAGGACAAGACTTGGGCAGGA
1 CCAAGTCCTGTCCAGGACTTGTGCTGTTGAGGAACGCAAAAATACAGGACAAGACCTGGGCAGGA
11246 GTTAC
66 GTTAC
* * *
11251 CCAAGTCCTGTCCCGGACTTGTGCTGTTGAGGAGCGC-AAATTACAGGACAAGACCTGGGCAGGA
1 CCAAGTCCTGTCCAGGACTTGTGCTGTTGAGGAACGCAAAAATACAGGACAAGACCTGGGCAGGA
11315 GTTAC
66 GTTAC
*
11320 CCAAGTCCTGTCCAGGAGTTGT
1 CCAAGTCCTGTCCAGGACTTGT
11342 TGCGGGAAAT
Statistics
Matches: 83, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
69 50 0.60
70 33 0.40
ACGTcount: A:0.26, C:0.23, G:0.30, T:0.21
Consensus pattern (70 bp):
CCAAGTCCTGTCCAGGACTTGTGCTGTTGAGGAACGCAAAAATACAGGACAAGACCTGGGCAGGA
GTTAC
Found at i:13947 original size:65 final size:65
Alignment explanation
Indices: 13843--13967 Score: 232
Period size: 65 Copynumber: 1.9 Consensus size: 65
13833 AATTGGTCTT
* *
13843 ACCCATGCATGGGGTACCCTTGGCCTGCCCACGCCTGGGCTAGTGCAGAAAGTTTGAATCGTCCA
1 ACCCATGCATGGGGTACCCTTGGCCTACCCACGCCTGGGCTAGTGCAGAAAGTTGGAATCGTCCA
13908 ACCCATGCATGGGGTACCCTTGGCCTACCCACGCCTGGGCTAGTGCAGAAAGTTGGAATC
1 ACCCATGCATGGGGTACCCTTGGCCTACCCACGCCTGGGCTAGTGCAGAAAGTTGGAATC
13968 AATAGCAAGC
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 58 1.00
ACGTcount: A:0.21, C:0.30, G:0.28, T:0.21
Consensus pattern (65 bp):
ACCCATGCATGGGGTACCCTTGGCCTACCCACGCCTGGGCTAGTGCAGAAAGTTGGAATCGTCCA
Found at i:14183 original size:21 final size:21
Alignment explanation
Indices: 14157--14198 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
14147 GCATCTTAGG
*
14157 CAACTCCGATGAGCTTGAAAC
1 CAACTCCAATGAGCTTGAAAC
14178 CAACTCCAATGAGCTTGAAAC
1 CAACTCCAATGAGCTTGAAAC
14199 TTATTTGTGC
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:0.36, C:0.29, G:0.17, T:0.19
Consensus pattern (21 bp):
CAACTCCAATGAGCTTGAAAC
Found at i:15889 original size:25 final size:25
Alignment explanation
Indices: 15861--15908 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
15851 ACCATCTTAG
*
15861 ATATATGTT-ATTAAATAAATAATAA
1 ATATATGTTAAAT-AATAAATAATAA
*
15886 ATATATTTTAAATAATAAATAAT
1 ATATATGTTAAATAATAAATAAT
15909 GAGTTCAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 18 0.90
26 2 0.10
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (25 bp):
ATATATGTTAAATAATAAATAATAA
Found at i:16177 original size:6 final size:6
Alignment explanation
Indices: 16158--16207 Score: 91
Period size: 6 Copynumber: 8.2 Consensus size: 6
16148 CTTTCAAATA
16158 ATATTT AGTATTT ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT
1 ATATTT A-TATTT ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT
16207 A
1 A
16208 GTATATATAA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
6 37 0.86
7 6 0.14
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (6 bp):
ATATTT
Found at i:17045 original size:1 final size:1
Alignment explanation
Indices: 17039--17063 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
17029 AAATTAGTTT
17039 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
17064 TTACAATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:21134 original size:41 final size:41
Alignment explanation
Indices: 21083--21164 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
21073 AAAGGGACAA
21083 AAAAAGGTTAACCTTTGAAGAAAGGAAATTAAATTAGGGAG
1 AAAAAGGTTAACCTTTGAAGAAAGGAAATTAAATTAGGGAG
*
21124 AAAAAGGTTAACCTTTGAAGAAAGGAAATTAAATTGGGGAG
1 AAAAAGGTTAACCTTTGAAGAAAGGAAATTAAATTAGGGAG
21165 TAGAAGAGGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.48, C:0.05, G:0.26, T:0.22
Consensus pattern (41 bp):
AAAAAGGTTAACCTTTGAAGAAAGGAAATTAAATTAGGGAG
Found at i:21145 original size:20 final size:20
Alignment explanation
Indices: 21083--21146 Score: 51
Period size: 20 Copynumber: 3.1 Consensus size: 20
21073 AAAGGGACAA
21083 AAAAAGGTTAACCTTTGAAG
1 AAAAAGGTTAACCTTTGAAG
* * * *
21103 AAAGGAA-ATTAA-ATTAGGGAG
1 AAA--AAGGTTAACCTT-TGAAG
21124 AAAAAGGTTAACCTTTGAAG
1 AAAAAGGTTAACCTTTGAAG
21144 AAA
1 AAA
21147 GGAAATTAAA
Statistics
Matches: 31, Mismatches: 8, Indels: 10
0.63 0.16 0.20
Matches are distributed among these distances:
19 2 0.06
20 15 0.48
21 12 0.39
22 2 0.06
ACGTcount: A:0.50, C:0.06, G:0.22, T:0.22
Consensus pattern (20 bp):
AAAAAGGTTAACCTTTGAAG
Found at i:21325 original size:24 final size:23
Alignment explanation
Indices: 21298--21349 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
21288 GCCCATCAAC
*
21298 ACAAAAAGAAAAAGCAAAA-AATGA
1 ACAAAAACAAAAA--AAAATAATGA
*
21322 ACAAAACCAAAAAAAAATAATGA
1 ACAAAAACAAAAAAAAATAATGA
21345 ACAAA
1 ACAAA
21350 CCAAATCCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 4 0.16
23 10 0.40
24 11 0.44
ACGTcount: A:0.75, C:0.12, G:0.08, T:0.06
Consensus pattern (23 bp):
ACAAAAACAAAAAAAAATAATGA
Found at i:21327 original size:23 final size:23
Alignment explanation
Indices: 21313--21354 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
21303 AAGAAAAAGC
21313 AAAA-AATGAACAAAACCAAAAA
1 AAAATAATGAACAAAACCAAAAA
21335 AAAATAATGAAC-AAACCAAA
1 AAAATAATGAACAAAACCAAA
21355 TCCACAAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.74, C:0.14, G:0.05, T:0.07
Consensus pattern (23 bp):
AAAATAATGAACAAAACCAAAAA
Found at i:25950 original size:1 final size:1
Alignment explanation
Indices: 25944--25979 Score: 72
Period size: 1 Copynumber: 36.0 Consensus size: 1
25934 AGATGGCGCC
25944 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
25980 GAAGAACATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:27922 original size:16 final size:17
Alignment explanation
Indices: 27893--27932 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
27883 CCAGCACTAG
*
27893 AAAAATCTGAAACCCGA
1 AAAAACCTGAAACCCGA
*
27910 AAAAACCTG-AACCTGA
1 AAAAACCTGAAACCCGA
27926 AAAAACC
1 AAAAACC
27933 CGAATTCAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.55, C:0.25, G:0.10, T:0.10
Consensus pattern (17 bp):
AAAAACCTGAAACCCGA
Found at i:27928 original size:32 final size:32
Alignment explanation
Indices: 27855--27929 Score: 80
Period size: 32 Copynumber: 2.3 Consensus size: 32
27845 CCCGAACCCA
* *
27855 AACCCGAAAAAGCTCAAACCTGAAAAAACCAG
1 AACCTGAAAAAGCTCAAACCCGAAAAAACCAG
* * * *
27887 CA-CTAGAAAAATCTGAAACCCGAAAAAACCTG
1 AACCT-GAAAAAGCTCAAACCCGAAAAAACCAG
27919 AACCTGAAAAA
1 AACCTGAAAAA
27930 ACCCGAATTC
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
31 1 0.03
32 31 0.91
33 2 0.06
ACGTcount: A:0.53, C:0.25, G:0.12, T:0.09
Consensus pattern (32 bp):
AACCTGAAAAAGCTCAAACCCGAAAAAACCAG
Found at i:34874 original size:16 final size:15
Alignment explanation
Indices: 34851--34906 Score: 58
Period size: 16 Copynumber: 3.6 Consensus size: 15
34841 CCGAACCCGA
34851 ACCCAAATTAACCTG
1 ACCCAAATTAACCTG
*
34866 ACCCAAAATTGACCTG
1 ACCC-AAATTAACCTG
* * *
34882 AACTCGAATCAACCTG
1 -ACCCAAATTAACCTG
34898 ACCCAAATT
1 ACCCAAATT
34907 TAACTTGAAC
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
15 10 0.32
16 18 0.58
17 3 0.10
ACGTcount: A:0.39, C:0.32, G:0.09, T:0.20
Consensus pattern (15 bp):
ACCCAAATTAACCTG
Found at i:34937 original size:32 final size:32
Alignment explanation
Indices: 34849--34942 Score: 109
Period size: 32 Copynumber: 2.9 Consensus size: 32
34839 ACCCGAACCC
* * * * *
34849 GAACCCAAATTAACCTGACCCAAAATTGACCT
1 GAACCCGAATCAACCTGACCCAAATTTAACTT
*
34881 GAACTCGAATCAACCTGACCCAAATTTAACTT
1 GAACCCGAATCAACCTGACCCAAATTTAACTT
*
34913 GAACCCGAATCAATCC-GACTCAAATTTAAC
1 GAACCCGAATCAA-CCTGACCCAAATTTAAC
34943 CCAACCTAAC
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
32 51 0.96
33 2 0.04
ACGTcount: A:0.39, C:0.30, G:0.10, T:0.21
Consensus pattern (32 bp):
GAACCCGAATCAACCTGACCCAAATTTAACTT
Found at i:43764 original size:22 final size:23
Alignment explanation
Indices: 43739--43788 Score: 86
Period size: 22 Copynumber: 2.3 Consensus size: 23
43729 ACAGTAGCAT
43739 AATGAAAAT-AAAAAACAATTGC
1 AATGAAAATAAAAAAACAATTGC
43761 AATGAAAATAAAAAAACAATTGC
1 AATGAAAATAAAAAAACAATTGC
43784 -ATGAA
1 AATGAA
43789 GGGAGGTAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 14 0.52
23 13 0.48
ACGTcount: A:0.64, C:0.08, G:0.10, T:0.18
Consensus pattern (23 bp):
AATGAAAATAAAAAAACAATTGC
Found at i:43884 original size:19 final size:19
Alignment explanation
Indices: 43862--43899 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
43852 TCTGAGCAAA
43862 ATCCTAAAATATGGACCAT
1 ATCCTAAAATATGGACCAT
43881 ATCCTAAAATATGGACCAT
1 ATCCTAAAATATGGACCAT
43900 GTATCATGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.21, G:0.11, T:0.26
Consensus pattern (19 bp):
ATCCTAAAATATGGACCAT
Found at i:44096 original size:53 final size:53
Alignment explanation
Indices: 44033--44136 Score: 172
Period size: 53 Copynumber: 2.0 Consensus size: 53
44023 ACTAAAAAAG
44033 CATTTATTGGATAACCAATACTACTAACTAATAGCAAACATTTCTTCATTTAT
1 CATTTATTGGATAACCAATACTACTAACTAATAGCAAACATTTCTTCATTTAT
* * * *
44086 CATTTATTGGATAACCGATACTAGTAACTAATCGTAAACATTTCTTCATTT
1 CATTTATTGGATAACCAATACTACTAACTAATAGCAAACATTTCTTCATTT
44137 TGGTGGTGGG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 47 1.00
ACGTcount: A:0.36, C:0.18, G:0.08, T:0.38
Consensus pattern (53 bp):
CATTTATTGGATAACCAATACTACTAACTAATAGCAAACATTTCTTCATTTAT
Found at i:44645 original size:21 final size:21
Alignment explanation
Indices: 44621--44663 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
44611 ACCAGGTCAG
44621 CACCTAACCCAACTTGACCGA
1 CACCTAACCCAACTTGACCGA
44642 CACCTAACCCAACTTGACCGA
1 CACCTAACCCAACTTGACCGA
44663 C
1 C
44664 TAAAGGAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.44, G:0.09, T:0.14
Consensus pattern (21 bp):
CACCTAACCCAACTTGACCGA
Found at i:45508 original size:31 final size:32
Alignment explanation
Indices: 45473--45545 Score: 114
Period size: 33 Copynumber: 2.3 Consensus size: 32
45463 GGGGTATACT
45473 GTGAATGATTAGCT-AATGGCATACTGTATAA
1 GTGAATGATTAGCTAAATGGCATACTGTATAA
45504 GTGAATGATTAGCTCAAATGGCATACTGTATAA
1 GTGAATGATTAGCT-AAATGGCATACTGTATAA
*
45537 G-GATTGATT
1 GTGAATGATT
45546 TTGATGTATA
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
31 14 0.36
32 7 0.18
33 18 0.46
ACGTcount: A:0.34, C:0.10, G:0.23, T:0.33
Consensus pattern (32 bp):
GTGAATGATTAGCTAAATGGCATACTGTATAA
Found at i:45668 original size:16 final size:16
Alignment explanation
Indices: 45633--45667 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
45623 CAAAAAAATT
45633 AAAATAATTAAAGAAC
1 AAAATAATTAAAGAAC
45649 AAAATAATTAAAG-AC
1 AAAATAATTAAAGAAC
45664 AAAA
1 AAAA
45668 ACAACGAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.17
Consensus pattern (16 bp):
AAAATAATTAAAGAAC
Found at i:46022 original size:22 final size:22
Alignment explanation
Indices: 45994--46037 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
45984 TATATATATA
45994 TATATATATATATCTCACCGAT
1 TATATATATATATCTCACCGAT
46016 TATATATATATATCTCACCGAT
1 TATATATATATATCTCACCGAT
46038 AAATATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.18, G:0.05, T:0.41
Consensus pattern (22 bp):
TATATATATATATCTCACCGAT
Found at i:46026 original size:2 final size:2
Alignment explanation
Indices: 45982--46006 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
45972 AAACTCCGAT
45982 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
46007 CTCACCGATT
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:58690 original size:436 final size:436
Alignment explanation
Indices: 57737--58741 Score: 1162
Period size: 436 Copynumber: 2.3 Consensus size: 436
57727 TTATCAATTG
** * * *
57737 AAATCACAAAATTTCAAAAGTATTTTTTAGAATTGAAACATAAAAATTAGCTTCTGAGTATTTCA
1 AAATCACAAAATTTCGGAAGCATTTTTTAGAATTAAAACATAAAAATTAGCTTTTGAGTATTTCA
* * * * * * * *
57802 AGAAAGTTGTTGATCATAAAATTACCTTTTAATAGACACCTGAATTAAATTAATTGAACAAATAG
66 TGAAAGTTGTAGATCAT-GAATTACCTTTTAATAGACACATGAATCAACTTAATCGGACAAATAG
* *
57867 AACAAAGAAAATAAAAAAAAAATGAAGCGTTAAATCGAGTATGATAGAATTTGTAAAGAACTAAG
130 AACAAAG-AAATAAAAAAAAAATGAAGCGTT-AA-CGAGTAAGATAAAATTTGTAAAGAACTAAG
* * * *
57932 TAGCATAAAATAGAAAAGTATGAGGGTCATTTGATAACTAATTCAAATAAGAAAATATTTCTTAA
192 TAGCATAAAATAGAAAAATATGAGGGCCATTTGATAAATAATCCAAATAAGAAAATATTTCTTAA
* * * * *
57997 TAGATATCTTGAAACATAAAGATTCCCTTTTAAACCCTTCATGAAACTCATAGATCAAATTAACT
257 TAGAGATCTTGAAACATAAAAATTCACATTTAAACCATTCATGAAACTCATAGATCAAATTAACT
* * * * *
58062 TTCGGGTTCTTCATGAAAGTCGTAGATCATACAGTAACCTTTTAACCGACACTTGAATAACTTTA
322 TTCGGGTCCTTCATGAAAGTCGTAAATCATACAATAACCTTTTAACCGACACTTCAATAACTTCA
*** * * * *
58127 ATCGGACATGTGGATCGAAAATTATATGGTATTAAACAGACCAATAATCG
387 ATCGGACATGTGGAGAAAAAATTATACGATATTAAACAGACCAACAATCA
* * * * **
58177 AAA-CGACCAAATTTAGGAAGCATTTTTTTGAATTAAAACATAAAAAATT-GATTTTGAGTCCTT
1 AAATC-ACAAAATTTCGGAAGCATTTTTTAGAATTAAAACAT-AAAAATTAGCTTTTGAGTATTT
** * *
58240 CATGAAAGTTGTAGATCATGAATT-TTTTTTAATAGACGCATAAATCAACTTAATCGGACAAATA
64 CATGAAAGTTGTAGATCATGAATTACCTTTTAATAGACACATGAATCAACTTAATCGGACAAATA
* * * *
58304 GAACAAAG-AATAAAATAAATAAATCTTAA-CGTT-A-GATTAAGATAAAATTTGTAAAGGATTA
129 GAACAAAGAAATAAAA-AAA-AAA--TGAAGCGTTAACGAGTAAGATAAAATTTGTAAAGAACTA
* * * * *
58365 AGTAGTATAAAGTAGAAAAATATGAGGGCCATTTGATAAATAATCCATATAAGAAAATGTTTGTT
190 AGTAGCATAAAATAGAAAAATATGAGGGCCATTTGATAAATAATCCAAATAAGAAAATATTTCTT
* * * *
58430 AATGGAGATCTTGAAGCATAAAAATTCACATTTAAATCATTCATGAAACTCATAGATTAAATTTA
255 AATAGAGATCTTGAAACATAAAAATTCACATTTAAACCATTCATGAAACTCATAGATCAAA-TTA
* * * *
58495 GA-TTTCGTGTCCTTCATGAAAGTCGTAAATCGTGCAATAACCTTTTAACTGACACTTCAATAAC
319 -ACTTTCGGGTCCTTCATGAAAGTCGTAAATCATACAATAACCTTTTAACCGACACTTCAATAAC
** *
58559 TTCAATCGGACATGTGGAGAAAAAATTATACGATATTAAATTGACCAGCAATCA
383 TTCAATCGGACATGTGGAGAAAAAATTATACGATATTAAACAGACCAACAATCA
* * * *
58613 AAATCACAAAATTTCGGAAGCATTTTTTAGAATCAAAATATTAAAATTAGCTTTTGAGTTTTTCA
1 AAATCACAAAATTTCGGAAGCATTTTTTAGAATTAAAACATAAAAATTAGCTTTTGAGTATTTCA
* * ** *
58678 TGAAAATTGTAGATAATGAAATTACCTTTTAATAGACATTTGAATCACCTTAATCGGACAAATA
66 TGAAAGTTGTAGATCATG-AATTACCTTTTAATAGACACATGAATCAACTTAATCGGACAAATA
58742 AAAAAATATA
Statistics
Matches: 469, Mismatches: 84, Indels: 26
0.81 0.15 0.04
Matches are distributed among these distances:
435 136 0.29
436 170 0.36
437 10 0.02
438 75 0.16
439 9 0.02
440 62 0.13
441 7 0.01
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (436 bp):
AAATCACAAAATTTCGGAAGCATTTTTTAGAATTAAAACATAAAAATTAGCTTTTGAGTATTTCA
TGAAAGTTGTAGATCATGAATTACCTTTTAATAGACACATGAATCAACTTAATCGGACAAATAGA
ACAAAGAAATAAAAAAAAAATGAAGCGTTAACGAGTAAGATAAAATTTGTAAAGAACTAAGTAGC
ATAAAATAGAAAAATATGAGGGCCATTTGATAAATAATCCAAATAAGAAAATATTTCTTAATAGA
GATCTTGAAACATAAAAATTCACATTTAAACCATTCATGAAACTCATAGATCAAATTAACTTTCG
GGTCCTTCATGAAAGTCGTAAATCATACAATAACCTTTTAACCGACACTTCAATAACTTCAATCG
GACATGTGGAGAAAAAATTATACGATATTAAACAGACCAACAATCA
Found at i:59016 original size:32 final size:32
Alignment explanation
Indices: 58975--59035 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
58965 TGTAAAACTT
*
58975 TTGAATCGACTATTATACCCTTATTTTTCTAA
1 TTGAATCGACCATTATACCCTTATTTTTCTAA
59007 TTGAATCGACCATTATACCCTTATTTTTC
1 TTGAATCGACCATTATACCCTTATTTTTC
59036 AAACATATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.26, C:0.21, G:0.07, T:0.46
Consensus pattern (32 bp):
TTGAATCGACCATTATACCCTTATTTTTCTAA
Found at i:60495 original size:11 final size:11
Alignment explanation
Indices: 60479--60505 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
60469 CCTCCTATTA
60479 TTATTCTTTAT
1 TTATTCTTTAT
60490 TTATTCTTTAT
1 TTATTCTTTAT
60501 TTATT
1 TTATT
60506 TATTTATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (11 bp):
TTATTCTTTAT
Found at i:60505 original size:15 final size:15
Alignment explanation
Indices: 60485--60531 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
60475 ATTATTATTC
60485 TTTATTTATTCTTTA
1 TTTATTTATTCTTTA
*
60500 TTTATTTATT-TATA
1 TTTATTTATTCTTTA
*
60514 TTTA--TGTTCTTTA
1 TTTATTTATTCTTTA
60527 TTTAT
1 TTTAT
60532 AATTTATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
12 3 0.11
13 7 0.26
14 7 0.26
15 10 0.37
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.72
Consensus pattern (15 bp):
TTTATTTATTCTTTA
Found at i:60509 original size:19 final size:20
Alignment explanation
Indices: 60485--60557 Score: 71
Period size: 19 Copynumber: 3.7 Consensus size: 20
60475 ATTATTATTC
*
60485 TTTATTTATTCTTTAT-TTA
1 TTTATTTATTATTTATGTTA
*
60504 TTTATTTA-TATTTATGTTC
1 TTTATTTATTATTTATGTTA
* *
60523 TTTATTTATAATTTATTATTA
1 TTTATTTATTATTTA-TGTTA
60544 -TTATTATATTATTT
1 TTTATT-TATTATTT
60558 TTGAGACAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
18 6 0.14
19 18 0.41
20 10 0.23
21 10 0.23
ACGTcount: A:0.26, C:0.03, G:0.01, T:0.70
Consensus pattern (20 bp):
TTTATTTATTATTTATGTTA
Found at i:60542 original size:27 final size:26
Alignment explanation
Indices: 60486--60542 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
60476 TTATTATTCT
*
60486 TTATTTATTCTTTATTTATTTATTTA
1 TTATTTATTCTTTATTTATTAATTTA
60512 -TATTTATGTTCTTTATTTA-TAATTTA
1 TTATTTA--TTCTTTATTTATTAATTTA
60538 TTATT
1 TTATT
60543 ATTATTATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 6 0.22
26 6 0.22
27 15 0.56
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.70
Consensus pattern (26 bp):
TTATTTATTCTTTATTTATTAATTTA
Found at i:63119 original size:17 final size:17
Alignment explanation
Indices: 63097--63132 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
63087 AGTCTTCTTC
63097 TTCTTCTAGTTATTTGT
1 TTCTTCTAGTTATTTGT
*
63114 TTCTTCTATTTATTTGT
1 TTCTTCTAGTTATTTGT
63131 TT
1 TT
63133 ACTGAATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.11, C:0.11, G:0.08, T:0.69
Consensus pattern (17 bp):
TTCTTCTAGTTATTTGT
Found at i:65537 original size:16 final size:16
Alignment explanation
Indices: 65516--65546 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
65506 GTTCCTTCCC
65516 TGAACAAGAAAAATGA
1 TGAACAAGAAAAATGA
65532 TGAACAAGAAAAATG
1 TGAACAAGAAAAATG
65547 GAACTAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.61, C:0.06, G:0.19, T:0.13
Consensus pattern (16 bp):
TGAACAAGAAAAATGA
Found at i:65872 original size:17 final size:17
Alignment explanation
Indices: 65850--65884 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
65840 ATTAGCATTT
65850 AGCATAAACATCAAAAG
1 AGCATAAACATCAAAAG
65867 AGCATAAACATCAAAAG
1 AGCATAAACATCAAAAG
65884 A
1 A
65885 AGATATCTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.60, C:0.17, G:0.11, T:0.11
Consensus pattern (17 bp):
AGCATAAACATCAAAAG
Found at i:66150 original size:31 final size:31
Alignment explanation
Indices: 66112--66173 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
66102 GGATCTCATC
*
66112 ATAATCCACATATGATAAATCTATTTTTATG
1 ATAATCCACAAATGATAAATCTATTTTTATG
*
66143 ATAATCCACAAATGGTAAATCTATTTTTATG
1 ATAATCCACAAATGATAAATCTATTTTTATG
66174 TGAGGAAAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.40
Consensus pattern (31 bp):
ATAATCCACAAATGATAAATCTATTTTTATG
Found at i:67777 original size:3 final size:3
Alignment explanation
Indices: 67769--67798 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
67759 ATACAAACTA
67769 ATT ATT ATT ATT ATT ATT ATT ATAT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT AT-T ATT AT
67799 ATACTACTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:71706 original size:2 final size:2
Alignment explanation
Indices: 71699--71732 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
71689 AAACTGTCTT
71699 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
71733 AATTTAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:81473 original size:42 final size:42
Alignment explanation
Indices: 81427--81513 Score: 165
Period size: 42 Copynumber: 2.1 Consensus size: 42
81417 TACATAGCGT
81427 AGTGAATTAGAGATTATCATACACACTTTTAGAGAGAGAGAG
1 AGTGAATTAGAGATTATCATACACACTTTTAGAGAGAGAGAG
*
81469 AGTGAATTAGAGATTATCATACACACTTTTATAGAGAGAGAG
1 AGTGAATTAGAGATTATCATACACACTTTTAGAGAGAGAGAG
81511 AGT
1 AGT
81514 TATAACAACT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.28
Consensus pattern (42 bp):
AGTGAATTAGAGATTATCATACACACTTTTAGAGAGAGAGAG
Done.