Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012260.1 Corchorus capsularis cultivar CVL-1 contig12281, 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: 73706
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:685 original size:371 final size:372
Alignment explanation
Indices: 1--700 Score: 1384
Period size: 371 Copynumber: 1.9 Consensus size: 372
1 CCAAGGACAATTTGGATGAAGAATGGACCCAATATGTTCATGATTGAAGAGCTTGAAGAGTCAAT
1 CCAAGGACAATTTGGATGAAGAATGGACCCAATATGTTCATGATTGAAGAGCTTGAAGAGTCAAT
66 TTTATCATCATAAGATTGATTTTCAAGAGTTTGAAGCAAAGGAGCAAAGTTGAATTTCAAGACAA
66 TTTATCATCATAAGATTGATTTTCAAGAGTTTGAAGCAAAGGAGCAAAGTTGAATTTCAAGACAA
131 AAAAACATGTCAAGAAGAATCATAGCACTGGAGTACATGGGTTGCGAGGCAAACCACATGGGGCG
131 AAAAACATGTCAAGAAGAATCATAGCACTGGAGTACATGGGTTGCGAGGCAAACCACATGGGGCG
196 CCAAGCATAGCACATGGGCGCCCAACGCTAGTCGAGACATGCCACCAGCAAGCACATGGGCACTG
196 CCAAGCATAGCACATGGGCGCCCAACGCTAGTCGAGACATGCCACCAGCAAGCACATGGGCACTG
261 GCGACATGGGGGCTGAGAGCAACACCCTGGGCGAACAAGCCATCTACATGGGCACCCAGGGGGAG
261 GCGACATGGGGGCTGAGAGCAACACCCTGGGCGAACAAGCCATCTACATGGGCACCCAGGGGGAG
326 TCGGACTTTTTGGAGCCTTTTTGGATGATTATTTACACAAATATTTT
326 TCGGACTTTTTGGAGCCTTTTTGGATGATTATTTACACAAATATTTT
373 CCAAGGACAATTTGGATGAAGAATGGACCCAATATGTTCATGATTGAAGA-CTTGAAGAGTCAAT
1 CCAAGGACAATTTGGATGAAGAATGGACCCAATATGTTCATGATTGAAGAGCTTGAAGAGTCAAT
437 TTTATCATCATAAGATTGATTTTCAAGAGTTTGAAGCAAAGGAGCAAAGTTGAATTTCAAGACAA
66 TTTATCATCATAAGATTGATTTTCAAGAGTTTGAAGCAAAGGAGCAAAGTTGAATTTCAAGACAA
502 AAAAACATGTCAAGAAGAATCATAGCACTGGAGTACATGGGTTGCGAGGCAAACCACATGGGGCG
131 AAAAACATGTCAAGAAGAATCATAGCACTGGAGTACATGGGTTGCGAGGCAAACCACATGGGGCG
567 CCAAGCATAGCACATGGGCGCCCAACGCTAGTCGAGACATGCCACCAGCAAGCACATGGGCACTG
196 CCAAGCATAGCACATGGGCGCCCAACGCTAGTCGAGACATGCCACCAGCAAGCACATGGGCACTG
*
632 GCGACATGGGGGCTGAGAGCAACGCCCTGGGCGAACAAGCCATCTACATGGGCACCCAGGGGGAG
261 GCGACATGGGGGCTGAGAGCAACACCCTGGGCGAACAAGCCATCTACATGGGCACCCAGGGGGAG
697 TCGG
326 TCGG
701 GTTGCAGCCA
Statistics
Matches: 327, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
371 277 0.85
372 50 0.15
ACGTcount: A:0.33, C:0.20, G:0.27, T:0.20
Consensus pattern (372 bp):
CCAAGGACAATTTGGATGAAGAATGGACCCAATATGTTCATGATTGAAGAGCTTGAAGAGTCAAT
TTTATCATCATAAGATTGATTTTCAAGAGTTTGAAGCAAAGGAGCAAAGTTGAATTTCAAGACAA
AAAAACATGTCAAGAAGAATCATAGCACTGGAGTACATGGGTTGCGAGGCAAACCACATGGGGCG
CCAAGCATAGCACATGGGCGCCCAACGCTAGTCGAGACATGCCACCAGCAAGCACATGGGCACTG
GCGACATGGGGGCTGAGAGCAACACCCTGGGCGAACAAGCCATCTACATGGGCACCCAGGGGGAG
TCGGACTTTTTGGAGCCTTTTTGGATGATTATTTACACAAATATTTT
Found at i:3522 original size:31 final size:31
Alignment explanation
Indices: 3451--3532 Score: 94
Period size: 31 Copynumber: 2.6 Consensus size: 31
3441 GTCTATCAAC
*
3451 TTTTAATTTGTTTAATTTAAGGCTTTCATTT
1 TTTTAATTTGTTTAATTTAAGGCTTTAATTT
* * *
3482 TTATGATTTGTTTAATTTAATGC-TTAATTT
1 TTTTAATTTGTTTAATTTAAGGCTTTAATTT
*
3512 GTTTTAATTTGTAATAATTTA
1 -TTTTAATTTGT-TTAATTTA
3533 GTATTAATTA
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
30 6 0.14
31 29 0.69
32 7 0.17
ACGTcount: A:0.27, C:0.04, G:0.10, T:0.60
Consensus pattern (31 bp):
TTTTAATTTGTTTAATTTAAGGCTTTAATTT
Found at i:4057 original size:16 final size:15
Alignment explanation
Indices: 4010--4062 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
4000 ACCCGAGACA
4010 GAACCCGAAAATACCC
1 GAACCC-AAAATACCC
* * *
4026 GAACTCGATATAACCC
1 GAACCCAAAAT-ACCC
4042 GAACCCAAAAATACCC
1 GAACCC-AAAATACCC
4058 GAACC
1 GAACC
4063 TAATTGAACT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
15 3 0.10
16 23 0.79
17 3 0.10
ACGTcount: A:0.43, C:0.36, G:0.11, T:0.09
Consensus pattern (15 bp):
GAACCCAAAATACCC
Found at i:4286 original size:21 final size:19
Alignment explanation
Indices: 4239--4296 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
4229 CTGTTTAGCA
4239 ACTGTACAGATGAGATTAC
1 ACTGTACAGATGAGATTAC
* * *
4258 ATTGTACAGATTAGATTAGGT
1 ACTGTACAGATGAGATTA--C
4279 ACTGTACAGATGAGATTA
1 ACTGTACAGATGAGATTA
4297 TTAGAGCAAC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 16 0.50
21 16 0.50
ACGTcount: A:0.36, C:0.10, G:0.22, T:0.31
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAC
Found at i:6100 original size:39 final size:39
Alignment explanation
Indices: 6055--6130 Score: 125
Period size: 39 Copynumber: 1.9 Consensus size: 39
6045 TTTCACCTCA
* * *
6055 AAAGCAATATCAAATAAATCTTGGTTTGTGTCAAAAGTT
1 AAAGCAATACCAAATAAATCTTGGTTTCTATCAAAAGTT
6094 AAAGCAATACCAAATAAATCTTGGTTTCTATCAAAAG
1 AAAGCAATACCAAATAAATCTTGGTTTCTATCAAAAG
6131 CTAATTTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (39 bp):
AAAGCAATACCAAATAAATCTTGGTTTCTATCAAAAGTT
Found at i:6644 original size:11 final size:10
Alignment explanation
Indices: 6613--6642 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
6603 ACATTTACGG
6613 TAATAAAAAA
1 TAATAAAAAA
6623 TAATAAAAAA
1 TAATAAAAAA
*
6633 TGATAAAAAA
1 TAATAAAAAA
6643 ATTCAGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (10 bp):
TAATAAAAAA
Found at i:6652 original size:20 final size:20
Alignment explanation
Indices: 6628--6683 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
6618 AAAAATAATA
6628 AAAAATGATA-AAAAAATTCAG
1 AAAAA-GATATAAAAAA-TCAG
*
6649 AAAAAGATATTAAAAATCAG
1 AAAAAGATATAAAAAATCAG
*
6669 AAATA-AT-TAAAAAAT
1 AAAAAGATATAAAAAAT
6684 ATTAAATACT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 7 0.23
19 2 0.06
20 12 0.39
21 10 0.32
ACGTcount: A:0.68, C:0.04, G:0.07, T:0.21
Consensus pattern (20 bp):
AAAAAGATATAAAAAATCAG
Found at i:8119 original size:15 final size:14
Alignment explanation
Indices: 8081--8121 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
8071 GAATTACTTA
8081 ATTT-TTTTTAATT
1 ATTTATTTTTAATT
8094 ATTTATATTTTAATT
1 ATTTAT-TTTTAATT
8109 ATTTAATTTTTAA
1 ATTT-ATTTTTAA
8122 GTTCTGAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 4 0.16
14 1 0.04
15 18 0.72
16 2 0.08
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
ATTTATTTTTAATT
Found at i:10996 original size:26 final size:26
Alignment explanation
Indices: 10962--11016 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
10952 TGGATCATCT
*
10962 TTCAATAATT-TCCCAATAACTGGGTC
1 TTCAATAATTCT-CCAATAACTGAGTC
* *
10988 TTCAGTAATTCTCCAATAATTGAGTC
1 TTCAATAATTCTCCAATAACTGAGTC
11014 TTC
1 TTC
11017 TTTGAAAGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 24 0.96
27 1 0.04
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.38
Consensus pattern (26 bp):
TTCAATAATTCTCCAATAACTGAGTC
Found at i:11984 original size:66 final size:63
Alignment explanation
Indices: 11884--12019 Score: 200
Period size: 66 Copynumber: 2.1 Consensus size: 63
11874 TTTTCATTTC
* * *
11884 TTTTTTGTGCTCTAAGTTTTGCCTAAGCCGTCCTTTACAGGATTTTCAACTTAGCGAGCCTCTTT
1 TTTTTTTTGCTCTAACTTTTGCCTAAGCCGTCCTTTACAGAATTTTCAACTTAGCGAG--T-TTT
11949 T
63 T
* *
11950 TTTTTTTTGCTCTAACTTTTGCCTAAGCCGTCCTTTGCAGAATTTTCAACTTATCGAGTTTTT
1 TTTTTTTTGCTCTAACTTTTGCCTAAGCCGTCCTTTACAGAATTTTCAACTTAGCGAGTTTTT
12013 TTTTTTT
1 TTTTTTT
12020 CGGTTGACTG
Statistics
Matches: 65, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
63 11 0.17
64 1 0.02
66 53 0.82
ACGTcount: A:0.16, C:0.21, G:0.14, T:0.49
Consensus pattern (63 bp):
TTTTTTTTGCTCTAACTTTTGCCTAAGCCGTCCTTTACAGAATTTTCAACTTAGCGAGTTTTT
Found at i:13835 original size:5 final size:5
Alignment explanation
Indices: 13825--13850 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
13815 ATTTGAGAAC
13825 TTGAT TTGAT TTGAT TTGAT TTGAT T
1 TTGAT TTGAT TTGAT TTGAT TTGAT T
13851 CAAAGGGTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.62
Consensus pattern (5 bp):
TTGAT
Found at i:14180 original size:26 final size:26
Alignment explanation
Indices: 14146--14200 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
14136 TGGATCTTCT
*
14146 TTCAATAATT-TCCCAATAACTGGGTC
1 TTCAATAATTCT-CCAATAACTGAGTC
* *
14172 TTCAGTAATTCTCCAATAATTGAGTC
1 TTCAATAATTCTCCAATAACTGAGTC
14198 TTC
1 TTC
14201 TTTGAAAGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 24 0.96
27 1 0.04
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.38
Consensus pattern (26 bp):
TTCAATAATTCTCCAATAACTGAGTC
Found at i:14308 original size:16 final size:16
Alignment explanation
Indices: 14287--14321 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
14277 ATCTGAAATA
14287 CTTCAGAGCTTTTCTG
1 CTTCAGAGCTTTTCTG
14303 CTTCAGAGCTTTTCTG
1 CTTCAGAGCTTTTCTG
14319 CTT
1 CTT
14322 TCTAAATTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.11, C:0.26, G:0.17, T:0.46
Consensus pattern (16 bp):
CTTCAGAGCTTTTCTG
Found at i:24227 original size:24 final size:24
Alignment explanation
Indices: 24200--24255 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
24190 GTTATCCACC
*
24200 TTGTTTTCTGCAGGTGCCACTACA
1 TTGTTTTCTACAGGTGCCACTACA
* *
24224 TTGTTTTCTACTGGTGCCGCTACA
1 TTGTTTTCTACAGGTGCCACTACA
24248 TTGTTTTC
1 TTGTTTTC
24256 CTCCCCCTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.45
Consensus pattern (24 bp):
TTGTTTTCTACAGGTGCCACTACA
Found at i:24837 original size:88 final size:87
Alignment explanation
Indices: 24683--24930 Score: 256
Period size: 88 Copynumber: 2.8 Consensus size: 87
24673 GTATAAAAGT
* *
24683 ATTGTATTTATAATTAAGAGGTTCTTAACTGTAATTTTAAGAGTTATTTAATTAAATCTATACAA
1 ATTGTA-TTATAATTAAGAGGTTCTT---T-TCATTTTTAGAGTTATTTAATTAAATCTATACAA
*
24748 TTATTTAACTTATAGTAA-TT-A-TATAAAC
61 TTATTT---TTAGAGTAATTTAATTA-AAAC
*
24776 ATTGTATTCATAATTAAGAGGTTC-TTTCATTTTTAGAGTTATTTAATTAAATATATACAATTAT
1 ATTGTATT-ATAATTAAGAGGTTCTTTTCATTTTTAGAGTTATTTAATTAAATCTATACAATTAT
*
24840 TTTTAGAGTTATTTAATTAAAAC
65 TTTTAGAGTAATTTAATTAAAAC
* **
24863 ATTGTATGTAT--TTAAGAGGTTCTTAATTTCATTTTTAGGGCAATTTAATTAAATCTATACAAT
1 ATTGTAT-TATAATTAAGAGGTTC-T--TTTCATTTTTAGAGTTATTTAATTAAATCTATACAAT
24926 TATTT
62 TATTT
24931 GTAAAATGTA
Statistics
Matches: 137, Mismatches: 9, Indels: 22
0.82 0.05 0.13
Matches are distributed among these distances:
85 18 0.13
86 2 0.01
87 14 0.10
88 40 0.29
89 39 0.28
92 3 0.02
93 21 0.15
ACGTcount: A:0.37, C:0.06, G:0.10, T:0.47
Consensus pattern (87 bp):
ATTGTATTATAATTAAGAGGTTCTTTTCATTTTTAGAGTTATTTAATTAAATCTATACAATTATT
TTTAGAGTAATTTAATTAAAAC
Found at i:24945 original size:16 final size:15
Alignment explanation
Indices: 24924--24980 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 15
24914 AATCTATACA
24924 ATTATTTGTAAAATGT
1 ATTATTTGTAAAA-GT
24940 ATTATTTAGTGTAGAAAGT
1 ATTA-TT--TGTA-AAAGT
24959 ATTATTTGTAAAAAGT
1 ATTATTTGT-AAAAGT
24975 ATTATT
1 ATTATT
24981 ATTCTTTAGC
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
16 18 0.50
17 3 0.08
18 2 0.06
19 10 0.28
20 3 0.08
ACGTcount: A:0.39, C:0.00, G:0.14, T:0.47
Consensus pattern (15 bp):
ATTATTTGTAAAAGT
Found at i:24980 original size:19 final size:19
Alignment explanation
Indices: 24924--24983 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
24914 AATCTATACA
*
24924 ATTATTTGTAAAATGTATT
1 ATTATTTGTAAAAAGTATT
* *
24943 ATT-TAGTGTAGAAAG---T
1 ATTAT-TTGTAAAAAGTATT
24959 ATTATTTGTAAAAAGTATT
1 ATTATTTGTAAAAAGTATT
24978 ATTATT
1 ATTATT
24984 CTTTAGCTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 10
0.67 0.11 0.22
Matches are distributed among these distances:
16 12 0.39
17 1 0.03
18 1 0.03
19 17 0.55
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.48
Consensus pattern (19 bp):
ATTATTTGTAAAAAGTATT
Found at i:26714 original size:42 final size:42
Alignment explanation
Indices: 26655--26736 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 42
26645 AAATGTCAAA
* * *
26655 TGTCAGGCACGGGGTTGTGTCATTCCTAAAATACAGGCACAG
1 TGTCAGGCACAGGGTTGTGCCATTCATAAAATACAGGCACAG
* *
26697 TGTCAGGCACAGGGTTGTGCCGTTCATGAAATACAGGCAC
1 TGTCAGGCACAGGGTTGTGCCATTCATAAAATACAGGCAC
26737 GGAGAACGCC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.26, C:0.22, G:0.29, T:0.23
Consensus pattern (42 bp):
TGTCAGGCACAGGGTTGTGCCATTCATAAAATACAGGCACAG
Found at i:29006 original size:25 final size:25
Alignment explanation
Indices: 28969--29026 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
28959 AAAGAGAAAA
* *
28969 GAAAAGAGGGGAAGGGGGAGAGAAG
1 GAAAAGAGCGGAACGGGGAGAGAAG
* *
28994 GGAAAGAGCGGAACGGGGAGATAAG
1 GAAAAGAGCGGAACGGGGAGAGAAG
29019 GAAAAGAG
1 GAAAAGAG
29027 GGGGAATTGG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.45, C:0.03, G:0.50, T:0.02
Consensus pattern (25 bp):
GAAAAGAGCGGAACGGGGAGAGAAG
Found at i:29408 original size:14 final size:14
Alignment explanation
Indices: 29389--29415 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29379 TAAAAATAAC
29389 AATTATAAACTTTG
1 AATTATAAACTTTG
29403 AATTATAAACTTT
1 AATTATAAACTTT
29416 TTAGCACATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.44
Consensus pattern (14 bp):
AATTATAAACTTTG
Found at i:31284 original size:31 final size:33
Alignment explanation
Indices: 31220--31284 Score: 98
Period size: 35 Copynumber: 2.0 Consensus size: 33
31210 AATCAATTAT
31220 TAACGTTATCGTGTTGTGTCATTTAATTTAGGATC
1 TAACGTTATCGTGTTGTGTCA-TT-ATTTAGGATC
31255 TAACGTTATCGTGTTGTGTCA-T-TTTAGGAT
1 TAACGTTATCGTGTTGTGTCATTATTTAGGAT
31285 ATCAGGCAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
31 8 0.27
33 1 0.03
35 21 0.70
ACGTcount: A:0.22, C:0.11, G:0.22, T:0.46
Consensus pattern (33 bp):
TAACGTTATCGTGTTGTGTCATTATTTAGGATC
Found at i:33272 original size:30 final size:31
Alignment explanation
Indices: 33218--33282 Score: 105
Period size: 30 Copynumber: 2.1 Consensus size: 31
33208 AACTTTATAT
*
33218 TTTCCGATTATACCCTTATTTTTAAAACATA
1 TTTCCAATTATACCCTTATTTTTAAAACATA
*
33249 TTTCCAATTGTACCCTT-TTTTTAAAACATA
1 TTTCCAATTATACCCTTATTTTTAAAACATA
33279 TTTC
1 TTTC
33283 TAAATTGCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 17 0.53
31 15 0.47
ACGTcount: A:0.29, C:0.20, G:0.03, T:0.48
Consensus pattern (31 bp):
TTTCCAATTATACCCTTATTTTTAAAACATA
Found at i:33289 original size:31 final size:31
Alignment explanation
Indices: 33228--33289 Score: 99
Period size: 30 Copynumber: 2.0 Consensus size: 31
33218 TTTCCGATTA
*
33228 TACCCTTATTTTTAAAACATATTTCCAATTG
1 TACCCTTATTTTTAAAACATATTTCAAATTG
33259 TACCCTT-TTTTTAAAACATATTTCTAAATTG
1 TACCCTTATTTTTAAAACATATTTC-AAATTG
33290 CCATTACTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 17 0.59
31 12 0.41
ACGTcount: A:0.32, C:0.18, G:0.03, T:0.47
Consensus pattern (31 bp):
TACCCTTATTTTTAAAACATATTTCAAATTG
Found at i:34349 original size:22 final size:22
Alignment explanation
Indices: 34321--34802 Score: 140
Period size: 22 Copynumber: 21.8 Consensus size: 22
34311 TGTCTGTTCG
34321 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * * *
34343 TGGTTATTATAATTTCACGAGGA
1 TGGTTATCAAAATTTCA-TAAGA
* * *
34366 -GCTTATCAAAATTCCAT-AGCG
1 TGGTTATCAAAATTTCATAAG-A
* * *
34387 TTGTTACCAAAATTTCATATGGA
1 TGGTTATCAAAATTTCATA-AGA
* **
34410 -AGTTATCAAAATTTCATGGGA
1 TGGTTATCAAAATTTCATAAGA
* * *
34431 AGGTTATCAAAATATCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
* *
34453 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAAGA
* ** *
34475 TCAGGTTATTAAAATTTTTTAGGA
1 T--GGTTATCAAAATTTCATAAGA
** **
34499 AAGTTATTGAAATTTCAGT--G-
1 TGGTTATCAAAATTTCA-TAAGA
* *
34519 TGGTTATCAAATTTTCATATGA
1 TGGTTATCAAAATTTCATAAGA
* * * *
34541 AGGTTAT-AAAAGTCTCAATTTTATA
1 TGGTTATCAAAA-TTTC-A--TAAGA
* * * *
34566 AGGAGTACCAAAATTTGAT-AGA
1 TGG-TTATCAAAATTTCATAAGA
* *
34588 AGGTAATC-AAATCTT-AT-AGA
1 TGGTTATCAAAAT-TTCATAAGA
* *
34608 GTGATTATCAGAATTTCATAGAGA
1 -TGGTTATCAAAATTTCATA-AGA
* *
34632 TCAGATTATCAAAATTT-ATAGGA
1 T--GGTTATCAAAATTTCATAAGA
* * *
34655 AGATTATCGAAATTTCATAATG-
1 TGGTTATCAAAATTTCATAA-GA
*
34677 TTGTTATCAAAATTTCA-AAGCA
1 TGGTTATCAAAATTTCATAAG-A
* *
34699 AGGTTATCAAAATTACATAATG-
1 TGGTTATCAAAATTTCATAA-GA
*
34721 TGATTATCAAAATTTCATAGAGA
1 TGGTTATCAAAATTTCATA-AGA
* *
34744 -GGTCA-CAAAATTTTATAGAGA
1 TGGTTATCAAAATTTCATA-AGA
*
34765 -GGTTATCAAAATTTTATAAAGA
1 TGGTTATCAAAATTTCAT-AAGA
*
34787 -GGTTATCAAATTTTCA
1 TGGTTATCAAAATTTCA
34803 AAATGTGATT
Statistics
Matches: 340, Mismatches: 82, Indels: 76
0.68 0.16 0.15
Matches are distributed among these distances:
19 1 0.00
20 23 0.07
21 54 0.16
22 195 0.57
23 15 0.04
24 25 0.07
25 19 0.06
26 4 0.01
27 4 0.01
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:34519 original size:66 final size:65
Alignment explanation
Indices: 34389--34551 Score: 163
Period size: 66 Copynumber: 2.5 Consensus size: 65
34379 CCATAGCGTT
* *
34389 GTTACCAAAATTTCATATGGAAGTTATCAAAATTTCATGGGAAGGTTATCAAAATATCATAGTGT
1 GTTACCAAAATTTCATATGGAAGTTATCAAAATTTCATAGGAAAGTTATCAAAATATCA-AGTGT
34454 G
65 G
* ** ** *
34455 GTTACCAAAATTTCATA-GGATCAGGTTATTAAAATTTTTTAGGAAAGTTATTGAAATTTC-AGT
1 GTTACCAAAATTTCATATGGA--A-GTTATCAAAATTTCATAGGAAAGTTATCAAAATATCAAGT
34518 GTG
63 GTG
* *
34521 GTTATCAAATTTTCATAT-GAAGGTTAT-AAAA
1 GTTACCAAAATTTCATATGGAA-GTTATCAAAA
34552 GTCTCAATTT
Statistics
Matches: 83, Mismatches: 10, Indels: 11
0.80 0.10 0.11
Matches are distributed among these distances:
63 4 0.05
64 7 0.08
65 3 0.04
66 40 0.48
67 1 0.01
68 28 0.34
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (65 bp):
GTTACCAAAATTTCATATGGAAGTTATCAAAATTTCATAGGAAAGTTATCAAAATATCAAGTGTG
Found at i:34640 original size:25 final size:22
Alignment explanation
Indices: 34610--34673 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 22
34600 CTTATAGAGT
34610 GATTATCAGAATTTCATAGAGATCA
1 GATTATCAGAATTTCATAG-GA--A
*
34635 GATTATCAAAATTT-ATAGGAA
1 GATTATCAGAATTTCATAGGAA
34656 GATTATC-GAAATTTCATA
1 GATTATCAG-AATTTCATA
34674 ATGTTGTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
21 13 0.37
22 3 0.09
23 2 0.06
24 4 0.11
25 13 0.37
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.34
Consensus pattern (22 bp):
GATTATCAGAATTTCATAGGAA
Found at i:34754 original size:21 final size:22
Alignment explanation
Indices: 34726--34800 Score: 100
Period size: 21 Copynumber: 3.5 Consensus size: 22
34716 TAATGTGATT
*
34726 ATCAAAATTTCATAGAGAGGTC
1 ATCAAAATTTTATAGAGAGGTC
*
34748 A-CAAAATTTTATAGAGAGGTT
1 ATCAAAATTTTATAGAGAGGTC
* *
34769 ATCAAAATTTTATAAAGAGGTT
1 ATCAAAATTTTATAGAGAGGTC
34791 ATC-AAATTTT
1 ATCAAAATTTT
34801 CAAAATGTGA
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
21 26 0.53
22 23 0.47
ACGTcount: A:0.43, C:0.08, G:0.15, T:0.35
Consensus pattern (22 bp):
ATCAAAATTTTATAGAGAGGTC
Found at i:37429 original size:22 final size:21
Alignment explanation
Indices: 37404--37795 Score: 185
Period size: 22 Copynumber: 18.0 Consensus size: 21
37394 AGTTTAGTTT
37404 TCAAAATTTCATAAGACGGTTA
1 TCAAAATTTCATAAGA-GGTTA
* *
37426 TCAAAATTTCATAGGGAGATTA
1 TCAAAATTTCATA-AGAGGTTA
* *
37448 CCAAAATTTCATAAGGATGTTA
1 TCAAAATTTCATAA-GAGGTTA
*
37470 TCAAAATTT-GT---A-GTTA
1 TCAAAATTTCATAAGAGGTTA
*
37486 TCAAGATTTCATAAGGAGGTTA
1 TCAAAATTTCATAA-GAGGTTA
* * *
37508 TCAAAATTTTATAGGGAAGTTTA
1 TCAAAATTTCATA-AG-AGGTTA
*
37531 TCAAAATTTTATAAGAAGGTTTA
1 TCAAAATTTCATAAG-AGG-TTA
*
37554 TTAAAATTTCATAACGAGGTTA
1 TCAAAATTTCATAA-GAGGTTA
*
37576 TCACAATTTCAT-AGAGTGATTA
1 TCAAAATTTCATAAGAG-G-TTA
* *
37598 TCAAAATTTCA-GAGTGTGATTA
1 TCAAAATTTCATAAGAG-G-TTA
*
37620 -CTAACAA-TTCATACGGAGGTT-
1 TC-AA-AATTTCATA-AGAGGTTA
* * *
37641 TTAAATTTTCATAACATGGTTA
1 TCAAAATTTCATAAGA-GGTTA
* * *
37663 TCAATATATCATATGGAGGTTA
1 TCAAAATTTCATA-AGAGGTTA
* * * *
37685 TCAACATCTCATAGTGTTGGTTA
1 TCAAAATTTCATA-AG-AGGTTA
** *
37708 TCAAAATTTCATTGGGAAGTTA
1 TCAAAATTTCA-TAAGAGGTTA
*
37730 TCAAAATTTCATAGTGAGGTCT-
1 TCAAAATTTCATA-AGAGGT-TA
* * *
37752 TCAAAATTCCTTAGAGAGATTA
1 TCAAAATTTCATA-AGAGGTTA
*
37774 ACAAAATTTCATAAGAAGGTTA
1 TCAAAATTTCATAAG-AGGTTA
37796 AAAAAATTAT
Statistics
Matches: 283, Mismatches: 57, Indels: 60
0.71 0.14 0.15
Matches are distributed among these distances:
16 12 0.04
17 2 0.01
20 5 0.02
21 21 0.07
22 181 0.64
23 58 0.20
24 4 0.01
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (21 bp):
TCAAAATTTCATAAGAGGTTA
Found at i:37495 original size:60 final size:61
Alignment explanation
Indices: 37422--37539 Score: 166
Period size: 60 Copynumber: 2.0 Consensus size: 61
37412 TCATAAGACG
* *
37422 GTTATCAAAATTTCATAGGGAGATTACCAAAATTTCATAAGGATG-TTATCAAAATTTGTA
1 GTTATCAAAATTTCATAAGGAGATTACCAAAATTTCATAAGGAAGTTTATCAAAATTTGTA
* * * * *
37482 GTTATCAAGATTTCATAAGGAGGTTATCAAAATTTTATAGGGAAGTTTATCAAAATTT
1 GTTATCAAAATTTCATAAGGAGATTACCAAAATTTCATAAGGAAGTTTATCAAAATTT
37540 TATAAGAAGG
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
60 38 0.76
61 12 0.24
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.36
Consensus pattern (61 bp):
GTTATCAAAATTTCATAAGGAGATTACCAAAATTTCATAAGGAAGTTTATCAAAATTTGTA
Found at i:37567 original size:23 final size:22
Alignment explanation
Indices: 37404--37880 Score: 172
Period size: 22 Copynumber: 21.9 Consensus size: 22
37394 AGTTTAGTTT
*
37404 TCAAAATTTCATAAGACGGTTA
1 TCAAAATTTCATAAGAAGGTTA
* * *
37426 TCAAAATTTCATAGGGAGATTA
1 TCAAAATTTCATAAGAAGGTTA
* * *
37448 CCAAAATTTCATAAGGATGTTA
1 TCAAAATTTCATAAGAAGGTTA
*
37470 TCAAAA-TT--T--GTA-GTTA
1 TCAAAATTTCATAAGAAGGTTA
* *
37486 TCAAGATTTCATAAGGAGGTTA
1 TCAAAATTTCATAAGAAGGTTA
* * *
37508 TCAAAATTTTATAGGGAAGTTTA
1 TCAAAATTTCATA-AGAAGGTTA
*
37531 TCAAAATTTTATAAGAAGGTTTA
1 TCAAAATTTCATAAGAAGG-TTA
*
37554 TTAAAATTTCATAACG-AGGTTA
1 TCAAAATTTCATAA-GAAGGTTA
*
37576 TCACAATTTCAT-AG-AGTGATTA
1 TCAAAATTTCATAAGAAG-G-TTA
* *
37598 TCAAAATTTCA-GAG-TGTGATTA
1 TCAAAATTTCATAAGAAG-G-TTA
* *
37620 -CTAACAA-TTCATACGGAGGTT-
1 TC-AA-AATTTCATAAGAAGGTTA
* * * *
37641 TTAAATTTTCATAACATGGTTA
1 TCAAAATTTCATAAGAAGGTTA
* * * *
37663 TCAATATATCATATGGAGGTTA
1 TCAAAATTTCATAAGAAGGTTA
* * * **
37685 TCAACATCTCATAGTGTTGGTTA
1 TCAAAATTTCATA-AGAAGGTTA
**
37708 TCAAAATTTCATTGGGAA-GTTA
1 TCAAAATTTCA-TAAGAAGGTTA
*
37730 TCAAAATTTCAT-AGTGAGGTCT-
1 TCAAAATTTCATAAG-AAGGT-TA
* * *
37752 TCAAAA-TTCCTTAGAGAGATTA
1 TCAAAATTTCATAAGA-AGGTTA
*
37774 ACAAAATTTCATAAGAAGGTTA
1 TCAAAATTTCATAAGAAGGTTA
* * * *
37796 -AAAAAATT-ATAAAAAAGGTTC
1 TCAAAATTTCAT-AAGAAGGTTA
** **
37817 TTGAAATTTCAT-AGTATCGTTA
1 TCAAAATTTCATAAG-AAGGTTA
*
37839 TTAAAATTGT-AT-AGAAAGGTTA
1 TCAAAATT-TCATAAG-AAGGTTA
* *
37861 TCAAAATTTAATAAGGAGGT
1 TCAAAATTTCATAAGAAGGT
37881 CATTAAAAAT
Statistics
Matches: 342, Mismatches: 78, Indels: 70
0.70 0.16 0.14
Matches are distributed among these distances:
16 9 0.03
17 4 0.01
19 2 0.01
20 7 0.02
21 42 0.12
22 204 0.60
23 71 0.21
24 3 0.01
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (22 bp):
TCAAAATTTCATAAGAAGGTTA
Found at i:37577 original size:45 final size:45
Alignment explanation
Indices: 37482--37795 Score: 132
Period size: 45 Copynumber: 7.1 Consensus size: 45
37472 AAAATTTGTA
* * * **
37482 GTTATCAAGATTTCATAAGGAGGTTATCAAAATTTTATAGGGAAG
1 GTTATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAACGAAG
* * *
37527 TTTATCAAAATTTTATAAGAAGGTTTATTAAAATTTCATAACG-AG
1 GTTATCAAAATTTCATAAGAAGG-TTATCAAAATTTCATAACGAAG
* * ** *
37572 GTTATCACAATTTCAT-AG-AGTGATTATCAAAATTTCAGAGTG-TG
1 GTTATCAAAATTTCATAAGAAG-G-TTATCAAAATTTCATAACGAAG
* * * * * *
37616 ATTA-CTAACAA-TTCATACGGAGGTT-TTAAATTTTCATAAC-ATG
1 GTTATC-AA-AATTTCATAAGAAGGTTATCAAAATTTCATAACGAAG
* * * * * * ** **
37659 GTTATCAATATATCATATGGAGGTTATCAACATCTCATAGTGTTG
1 GTTATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAACGAAG
** **
37704 GTTATCAAAATTTCATTGGGAA-GTTATCAAAATTTCATAGTG-AG
1 GTTATCAAAATTTCA-TAAGAAGGTTATCAAAATTTCATAACGAAG
* * * *
37748 GTCT-TCAAAA-TTCCTTAGAGAGATTAACAAAATTTCATAA-GAAG
1 GT-TATCAAAATTTCATAAGA-AGGTTATCAAAATTTCATAACGAAG
37792 GTTA
1 GTTA
37796 AAAAAATTAT
Statistics
Matches: 202, Mismatches: 50, Indels: 35
0.70 0.17 0.12
Matches are distributed among these distances:
42 4 0.02
43 38 0.19
44 68 0.34
45 72 0.36
46 20 0.10
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (45 bp):
GTTATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAACGAAG
Found at i:44801 original size:7 final size:7
Alignment explanation
Indices: 44789--44815 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
44779 TAACTCTAAT
44789 AATTCTC
1 AATTCTC
44796 AATTCTC
1 AATTCTC
44803 AATTCTC
1 AATTCTC
44810 AATTCT
1 AATTCT
44816 TCTCCCCCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.26, G:0.00, T:0.44
Consensus pattern (7 bp):
AATTCTC
Found at i:45702 original size:21 final size:21
Alignment explanation
Indices: 45678--45720 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
45668 GTCACCAATG
*
45678 TCAT-TTTCCTTCTCCTTCTGT
1 TCATCTTT-CTTCTCCTGCTGT
*
45699 TCATCTTTCTTCTTCTGCTGT
1 TCATCTTTCTTCTCCTGCTGT
45720 T
1 T
45721 GTTCACCCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.05, C:0.30, G:0.07, T:0.58
Consensus pattern (21 bp):
TCATCTTTCTTCTCCTGCTGT
Found at i:45754 original size:24 final size:25
Alignment explanation
Indices: 45699--45754 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 25
45689 CTCCTTCTGT
*
45699 TCAT-CTTTCTTCTTCTGCTGTTGT
1 TCATCCTTTCTTCTTCTGCTGTTGC
*
45723 TCACCCTTT-TTCTTCTGC-GTTTGC
1 TCATCCTTTCTTCTTCTGCTG-TTGC
45747 TCATCCTT
1 TCATCCTT
45755 CAATTTTTGC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 1 0.04
24 22 0.81
25 4 0.15
ACGTcount: A:0.05, C:0.30, G:0.11, T:0.54
Consensus pattern (25 bp):
TCATCCTTTCTTCTTCTGCTGTTGC
Found at i:58011 original size:22 final size:22
Alignment explanation
Indices: 57986--58029 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
57976 AGGTCGAGTT
57986 CAATATATATTC-TGTCGGTTTC
1 CAATATATATTCGT-TCGGTTTC
58008 CAATATATATTCGTTCGGTTTC
1 CAATATATATTCGTTCGGTTTC
58030 GGTTTCAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.23, C:0.18, G:0.14, T:0.45
Consensus pattern (22 bp):
CAATATATATTCGTTCGGTTTC
Found at i:63813 original size:21 final size:21
Alignment explanation
Indices: 63784--63833 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
63774 GAAGAAGAAA
* *
63784 AAGAAGAAAGTGAGAACGAGG
1 AAGAAGAAAGTGAAAAAGAGG
*
63805 AAGAGGAAAGTGAAAAAGAGG
1 AAGAAGAAAGTGAAAAAGAGG
63826 AAGAAGAA
1 AAGAAGAA
63834 GGAGCTGCTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.58, C:0.02, G:0.36, T:0.04
Consensus pattern (21 bp):
AAGAAGAAAGTGAAAAAGAGG
Found at i:63863 original size:18 final size:18
Alignment explanation
Indices: 63825--63865 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
63815 TGAAAAAGAG
* *
63825 GAAGAAGAAGGAGCTGCT
1 GAAGAAGAAGAAGCTGAT
*
63843 GAAGAAGAAGAATCTGAT
1 GAAGAAGAAGAAGCTGAT
63861 GAAGA
1 GAAGA
63866 GGTTGATGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.46, C:0.07, G:0.34, T:0.12
Consensus pattern (18 bp):
GAAGAAGAAGAAGCTGAT
Done.