Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011343.1 Corchorus capsularis cultivar CVL-1 contig11364, 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: 110073
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:399 original size:27 final size:27
Alignment explanation
Indices: 339--445 Score: 133
Period size: 27 Copynumber: 3.9 Consensus size: 27
329 ATCTTTTAAA
* * *
339 AAAAATGACTAAAATGCCCTCCTGAGTGC
1 AAAAATGACCAAAAT-ACC-CCTGGGTGC
*
368 AAAAATGACCGAAATACCCCTGGGTGC
1 AAAAATGACCAAAATACCCCTGGGTGC
* *
395 GAAAATGACCAAAATGCCCCTGGGTGC
1 AAAAATGACCAAAATACCCCTGGGTGC
*
422 AAAAATGACCAAAATACCCTTGGG
1 AAAAATGACCAAAATACCCCTGGG
446 CGACTCTAAT
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
27 53 0.78
28 2 0.03
29 13 0.19
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.17
Consensus pattern (27 bp):
AAAAATGACCAAAATACCCCTGGGTGC
Found at i:437 original size:54 final size:56
Alignment explanation
Indices: 340--445 Score: 162
Period size: 54 Copynumber: 1.9 Consensus size: 56
330 TCTTTTAAAA
* *
340 AAAATGACTAAAATGCCCTCCTGAGTGCAAAAATGACCGAAATACCCCTGGGTGCG
1 AAAATGACCAAAATGCCCTCCTGAGTGCAAAAATGACCAAAATACCCCTGGGTGCG
* *
396 AAAATGACCAAAATG-CC-CCTGGGTGCAAAAATGACCAAAATACCCTTGGG
1 AAAATGACCAAAATGCCCTCCTGAGTGCAAAAATGACCAAAATACCCCTGGG
446 CGACTCTAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
54 30 0.65
55 2 0.04
56 14 0.30
ACGTcount: A:0.38, C:0.25, G:0.21, T:0.17
Consensus pattern (56 bp):
AAAATGACCAAAATGCCCTCCTGAGTGCAAAAATGACCAAAATACCCCTGGGTGCG
Found at i:2636 original size:87 final size:87
Alignment explanation
Indices: 2545--2709 Score: 305
Period size: 87 Copynumber: 1.9 Consensus size: 87
2535 TCTATTTTTA
2545 TTTAATTAAATCTAATCTCTTTATAACTATTTTATTTTTACCA-TTTTACTATTTTAATTAAAAG
1 TTTAATTAAATCTAATCTCTTTATAACTATTTTATTTTTACCATTTTTACTATTTTAATTAAAA-
2609 AACTTAGATATATTTCAAGATTT
65 AACTTAGATATATTTCAAGATTT
*
2632 TTTAATTAAATCTAATCTCTTTATAACTATTTTATTTTTACCATTTTTACTATTTTAATTACAAA
1 TTTAATTAAATCTAATCTCTTTATAACTATTTTATTTTTACCATTTTTACTATTTTAATTAAAAA
2697 ACTTAGATATATT
66 ACTTAGATATATT
2710 AGAATTTTTT
Statistics
Matches: 76, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
87 57 0.75
88 19 0.25
ACGTcount: A:0.35, C:0.11, G:0.02, T:0.52
Consensus pattern (87 bp):
TTTAATTAAATCTAATCTCTTTATAACTATTTTATTTTTACCATTTTTACTATTTTAATTAAAAA
ACTTAGATATATTTCAAGATTT
Found at i:2734 original size:13 final size:14
Alignment explanation
Indices: 2713--2748 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
2703 ATATATTAGA
2713 ATTTTTTAAATG-T
1 ATTTTTTAAATGAT
*
2726 ATTTCTTAAATGAT
1 ATTTTTTAAATGAT
2740 ATTTTTTAA
1 ATTTTTTAA
2749 CCTTTTACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.33, C:0.03, G:0.06, T:0.58
Consensus pattern (14 bp):
ATTTTTTAAATGAT
Found at i:11514 original size:21 final size:20
Alignment explanation
Indices: 11475--11516 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
11465 TCATTTGCTT
*
11475 ATTGTCTTCAATGCTCTTCA
1 ATTGTCTTCAATGCACTTCA
*
11495 ATTGATCTTCAATGGACTTCA
1 ATTG-TCTTCAATGCACTTCA
11516 A
1 A
11517 ACCTTCAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.40
Consensus pattern (20 bp):
ATTGTCTTCAATGCACTTCA
Found at i:16963 original size:5 final size:6
Alignment explanation
Indices: 16947--16975 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
16937 TTCTGATCGA
16947 ATTTTT ATTTTT A-TTTT ATTTTT ATTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
16976 TGATACTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
ATTTTT
Found at i:16965 original size:11 final size:11
Alignment explanation
Indices: 16949--16974 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
16939 CTGATCGAAT
16949 TTTTATTTTTA
1 TTTTATTTTTA
16960 TTTTATTTTTA
1 TTTTATTTTTA
16971 TTTT
1 TTTT
16975 TTGATACTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:17886 original size:21 final size:20
Alignment explanation
Indices: 17847--17888 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
17837 TCCTTTGCTT
*
17847 ATTGTCTTCAATGCTCTTCA
1 ATTGTCTTCAATGCACTTCA
*
17867 ATTGATCTTCAATGGACTTCA
1 ATTG-TCTTCAATGCACTTCA
17888 A
1 A
17889 ACCTTCAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.40
Consensus pattern (20 bp):
ATTGTCTTCAATGCACTTCA
Found at i:19126 original size:417 final size:417
Alignment explanation
Indices: 18352--19190 Score: 1642
Period size: 417 Copynumber: 2.0 Consensus size: 417
18342 GGAGATGCCA
18352 TTAAGATGCCATTTGATCCTTTGAAGATGACTTAGGTCCGATGACAAGAGTAAGAGCTAAGAAGT
1 TTAAGATGCCATTTGATCCTTTGAAGATGACTTAGGTCCGATGACAAGAGTAAGAGCTAAGAAGT
18417 TCAAAGATGCATTAAGCTTTGTTCGAACTCATCTTGAAGGCTTGAAGTTCATTGAAAATCAATTG
66 TCAAAGATGCATTAAGCTTTGTTCGAACTCATCTTGAAGGCTTGAAGTTCATTGAAAATCAATTG
18482 GGAAGCATTGAAGTCAACATCATCAAGAATATTCCAAACGATTCCAAGCTTTGCACTTTACTTGA
131 GGAAGCATTGAAGTCAACATCATCAAGAATATTCCAAACGATTCCAAGCTTTGCACTTTACTTGA
18547 AATCGTTGAACCCTAGAGCTTGCATTGTGTAATTCGGCCATATGGGCCTTAATTCTAACTTAGCT
196 AATCGTTGAACCCTAGAGCTTGCATTGTGTAATTCGGCCATATGGGCCTTAATTCTAACTTAGCT
18612 TAGCTATTTAATTAGTTTAGATGACATTGGGTTGGGCCTTGTTTGACTAAGTCCAATCCTTACTT
261 TAGCTATTTAATTAGTTTAGATGACATTGGGTTGGGCCTTGTTTGACTAAGTCCAATCCTTACTT
18677 AAATTAGCTATGTATTTACTTTTTCCTAGTAGGACAAGGAGTAGGCTATTTCCTTGATCCTTCCT
326 AAATTAGCTATGTATTTACTTTTTCCTAGTAGGACAAGGAGTAGGCTATTTCCTTGATCCTTCCT
*
18742 TTATATGTAAACCGCCCATAAGGAGGT
391 TTATATGTAAACCGCCCATAAGGAGCT
18769 TTAAGATGCCATTTGATCCTTTGAAGATGACTTAGGTCCGATGACAAGAGTAAGAGCTAAGAAGT
1 TTAAGATGCCATTTGATCCTTTGAAGATGACTTAGGTCCGATGACAAGAGTAAGAGCTAAGAAGT
18834 TCAAAGATGCATTAAGCTTTGTTCGAACTCATCTTGAAGGCTTGAAGTTCATTGAAAATCAATTG
66 TCAAAGATGCATTAAGCTTTGTTCGAACTCATCTTGAAGGCTTGAAGTTCATTGAAAATCAATTG
*
18899 GGAAGCATTGAAGTCAACATCATCAAGAATATTCCCAACGATTCCAAGCTTTGCACTTTACTTGA
131 GGAAGCATTGAAGTCAACATCATCAAGAATATTCCAAACGATTCCAAGCTTTGCACTTTACTTGA
*
18964 AATCGTTGAACCCTAGAGCTTGCATTGTGTAATTCGGCCATATGGGCCTTAATTCTATCTTAGCT
196 AATCGTTGAACCCTAGAGCTTGCATTGTGTAATTCGGCCATATGGGCCTTAATTCTAACTTAGCT
19029 TAGCTATTTAATTAGTTTAGATGACATTGGGTTGGGCCTTGTTTGACTAAGTCCAATCCTTACTT
261 TAGCTATTTAATTAGTTTAGATGACATTGGGTTGGGCCTTGTTTGACTAAGTCCAATCCTTACTT
*
19094 AAATTAGTTATGTATTTACTTTTTCCTAGTAGGACAAGGAGTAGGCTATTTCCTTGATCCTTCCT
326 AAATTAGCTATGTATTTACTTTTTCCTAGTAGGACAAGGAGTAGGCTATTTCCTTGATCCTTCCT
19159 TTATATGTAAACCGCCCATAAGGAGCT
391 TTATATGTAAACCGCCCATAAGGAGCT
19186 TTAAG
1 TTAAG
19191 GGGGTATATG
Statistics
Matches: 418, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
417 418 1.00
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (417 bp):
TTAAGATGCCATTTGATCCTTTGAAGATGACTTAGGTCCGATGACAAGAGTAAGAGCTAAGAAGT
TCAAAGATGCATTAAGCTTTGTTCGAACTCATCTTGAAGGCTTGAAGTTCATTGAAAATCAATTG
GGAAGCATTGAAGTCAACATCATCAAGAATATTCCAAACGATTCCAAGCTTTGCACTTTACTTGA
AATCGTTGAACCCTAGAGCTTGCATTGTGTAATTCGGCCATATGGGCCTTAATTCTAACTTAGCT
TAGCTATTTAATTAGTTTAGATGACATTGGGTTGGGCCTTGTTTGACTAAGTCCAATCCTTACTT
AAATTAGCTATGTATTTACTTTTTCCTAGTAGGACAAGGAGTAGGCTATTTCCTTGATCCTTCCT
TTATATGTAAACCGCCCATAAGGAGCT
Found at i:24122 original size:28 final size:28
Alignment explanation
Indices: 24089--24161 Score: 101
Period size: 28 Copynumber: 2.6 Consensus size: 28
24079 TATCTAAGCC
*
24089 GTATGCCTTTGGGAATTTTACTTAGGCT
1 GTATGCCTTTAGGAATTTTACTTAGGCT
* *
24117 GTATGCCATTATGAATTTTACTTAGGCT
1 GTATGCCTTTAGGAATTTTACTTAGGCT
*
24145 GTTTGCCTTTAGAGAAT
1 GTATGCCTTTAG-GAAT
24162 ACGTGTCGTA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
28 34 0.89
29 4 0.11
ACGTcount: A:0.22, C:0.14, G:0.22, T:0.42
Consensus pattern (28 bp):
GTATGCCTTTAGGAATTTTACTTAGGCT
Found at i:37231 original size:29 final size:30
Alignment explanation
Indices: 37169--37225 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
37159 TTGTGTTATA
* *
37169 TGTGTTTAGGGACTTTAGTATAGATGTCTC
1 TGTGTTTAGGGACTATAGTATAGATGCCTC
*
37199 TGTGTTTAGGGAC-ATAGTATGGATGCC
1 TGTGTTTAGGGACTATAGTATAGATGCC
37226 CTTGTGCTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 11 0.46
30 13 0.54
ACGTcount: A:0.21, C:0.11, G:0.30, T:0.39
Consensus pattern (30 bp):
TGTGTTTAGGGACTATAGTATAGATGCCTC
Found at i:41010 original size:18 final size:19
Alignment explanation
Indices: 40976--41014 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
40966 TGAAGATTTC
40976 TTGAAGATAATTTGAAGAG
1 TTGAAGATAATTTGAAGAG
*
40995 TTGAAGATCA-TTGAAGAG
1 TTGAAGATAATTTGAAGAG
41013 TT
1 TT
41015 ATTTCAAGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.33
Consensus pattern (19 bp):
TTGAAGATAATTTGAAGAG
Found at i:43879 original size:16 final size:15
Alignment explanation
Indices: 43858--43891 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
43848 TAAAGTTTGA
43858 TGGATATTTGAGTATT
1 TGGATATTTG-GTATT
43874 TGGATATTTGGTATT
1 TGGATATTTGGTATT
43889 TGG
1 TGG
43892 GCATGTAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (15 bp):
TGGATATTTGGTATT
Found at i:49763 original size:15 final size:16
Alignment explanation
Indices: 49731--49764 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
49721 AAAGAAGAAT
*
49731 TAAAATTAAATCTAAC
1 TAAAAGTAAATCTAAC
49747 TAAAAGTAAAT-TAAC
1 TAAAAGTAAATCTAAC
49762 TAA
1 TAA
49765 GAAAGCAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.59, C:0.09, G:0.03, T:0.29
Consensus pattern (16 bp):
TAAAAGTAAATCTAAC
Found at i:50292 original size:33 final size:33
Alignment explanation
Indices: 50246--50367 Score: 131
Period size: 33 Copynumber: 3.6 Consensus size: 33
50236 GCGCAACACT
*
50246 GGCCACAAGACCGGCCACGCGACATGGACATGTCC
1 GGCCAC-A-ACCGGCCACGCGACATGGACATGCCC
* *
50281 GGCCATC-ACCGGCCACGCGACATGGACATGGCT
1 GGCCA-CAACCGGCCACGCGACATGGACATGCCC
* ** *
50314 GGCTACAACCGGCCAAACGAC-TCGGCCATGCCC
1 GGCCACAACCGGCCACGCGACAT-GGACATGCCC
50347 GGCCACAACCGGCCACGCGAC
1 GGCCACAACCGGCCACGCGAC
50368 CCTTTGTCTA
Statistics
Matches: 73, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
32 2 0.03
33 65 0.89
35 5 0.07
36 1 0.01
ACGTcount: A:0.24, C:0.40, G:0.28, T:0.08
Consensus pattern (33 bp):
GGCCACAACCGGCCACGCGACATGGACATGCCC
Found at i:52133 original size:19 final size:18
Alignment explanation
Indices: 52100--52135 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
52090 TTGAAATAAT
52100 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
52118 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
52136 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:54368 original size:29 final size:30
Alignment explanation
Indices: 54306--54362 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
54296 TTGTGTTATA
*
54306 TGTGTTTAGGGACTTTAGTATAGATGCCTC
1 TGTGTTTAGGAACTTTAGTATAGATGCCTC
*
54336 TGTGTTTAGGAAC-TTAGTATGGATGCC
1 TGTGTTTAGGAACTTTAGTATAGATGCC
54363 CTTGTGCTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.21, C:0.12, G:0.28, T:0.39
Consensus pattern (30 bp):
TGTGTTTAGGAACTTTAGTATAGATGCCTC
Found at i:54379 original size:29 final size:28
Alignment explanation
Indices: 54306--54379 Score: 69
Period size: 29 Copynumber: 2.5 Consensus size: 28
54296 TTGTGTTATA
*
54306 TGTGTTTAGGGACTTTAGTATAGATGCCTC
1 TGTGTTGA-GGAC-TTAGTATAGATGCCTC
* *
54336 TGTGTTTAGGAACTTAGTATGGATGCC-C
1 TGTGTTGAGG-ACTTAGTATAGATGCCTC
54364 TTGTGCTTGAGGACTT
1 -TGTG-TTGAGGACTT
54380 TGAAAGAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
28 1 0.03
29 23 0.59
30 15 0.38
ACGTcount: A:0.19, C:0.14, G:0.28, T:0.39
Consensus pattern (28 bp):
TGTGTTGAGGACTTAGTATAGATGCCTC
Found at i:54442 original size:30 final size:28
Alignment explanation
Indices: 54406--54507 Score: 86
Period size: 26 Copynumber: 3.5 Consensus size: 28
54396 TTGTGTTATA
*
54406 TGTGTTTGGGGACTTTGATATAGATGCCTC
1 TGTGTTTAGGGACTTT-AT-TAGATGCCTC
*
54436 TGTGTTTAGGGAC-TTATGA-ATGCC-C
1 TGTGTTTAGGGACTTTATTAGATGCCTC
*
54461 TTGTGTTT-GAGGACTTTTAGTGTAGATGTCTC
1 -TGTGTTTAG-GGAC-TTTA-T-TAGATGCCTC
54493 TGTGTTTAGGGACTT
1 TGTGTTTAGGGACTT
54508 ATGAATGCCT
Statistics
Matches: 59, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
25 2 0.03
26 16 0.27
27 1 0.02
28 5 0.08
29 3 0.05
30 15 0.25
31 15 0.25
32 2 0.03
ACGTcount: A:0.17, C:0.12, G:0.29, T:0.42
Consensus pattern (28 bp):
TGTGTTTAGGGACTTTATTAGATGCCTC
Found at i:54465 original size:26 final size:27
Alignment explanation
Indices: 54432--54516 Score: 86
Period size: 26 Copynumber: 3.0 Consensus size: 27
54422 GATATAGATG
54432 CCTCTGTGTTTAGGGACTTATGAATGC
1 CCTCTGTGTTTAGGGACTTATGAATGC
54459 CCT-TGTGTTT-GAGGACTTTTAGTGTAGATG-
1 CCTCTGTGTTTAG-GGAC--TTA-TG-A-ATGC
*
54489 TCTCTGTGTTTAGGGACTTATGAATGC
1 CCTCTGTGTTTAGGGACTTATGAATGC
54516 C
1 C
54517 TGATCGAGCT
Statistics
Matches: 47, Mismatches: 2, Indels: 18
0.70 0.03 0.27
Matches are distributed among these distances:
25 1 0.02
26 14 0.30
27 4 0.09
28 5 0.11
29 5 0.11
30 3 0.06
31 14 0.30
32 1 0.02
ACGTcount: A:0.18, C:0.15, G:0.27, T:0.40
Consensus pattern (27 bp):
CCTCTGTGTTTAGGGACTTATGAATGC
Found at i:54498 original size:57 final size:56
Alignment explanation
Indices: 54406--54516 Score: 177
Period size: 57 Copynumber: 2.0 Consensus size: 56
54396 TTGTGTTATA
*
54406 TGTGTTTGGGGACTTTGATATAGATGCCTCTGTGTTTAGGGACTTATGAATGCCCT
1 TGTGTTTGAGGACTTTGATATAGATGCCTCTGTGTTTAGGGACTTATGAATGCCCT
* * *
54462 TGTGTTTGAGGACTTTTAGTGTAGATGTCTCTGTGTTTAGGGACTTATGAATGCC
1 TGTGTTTGAGGACTTTGA-TATAGATGCCTCTGTGTTTAGGGACTTATGAATGCC
54517 TGATCGAGCT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
56 16 0.32
57 34 0.68
ACGTcount: A:0.18, C:0.13, G:0.29, T:0.41
Consensus pattern (56 bp):
TGTGTTTGAGGACTTTGATATAGATGCCTCTGTGTTTAGGGACTTATGAATGCCCT
Found at i:54506 original size:31 final size:29
Alignment explanation
Indices: 54406--54507 Score: 88
Period size: 31 Copynumber: 3.5 Consensus size: 29
54396 TTGTGTTATA
* * *
54406 TGTGTTTGGGGACTTTGATATAGATGCCTC
1 TGTGTTTAGGGACTTTTATGTAGATG-CTC
*
54436 TGTGTTTAGGGAC--TTATG-A-ATGCCC
1 TGTGTTTAGGGACTTTTATGTAGATGCTC
54461 TTGTGTTT-GAGGACTTTTAGTGTAGATGTCTC
1 -TGTGTTTAG-GGACTTTTA-TGTAGATG-CTC
54493 TGTGTTTAGGGACTT
1 TGTGTTTAGGGACTT
54508 ATGAATGCCT
Statistics
Matches: 58, Mismatches: 5, Indels: 17
0.73 0.06 0.21
Matches are distributed among these distances:
25 3 0.05
26 14 0.24
27 1 0.02
28 6 0.10
29 2 0.03
30 13 0.22
31 16 0.28
32 3 0.05
ACGTcount: A:0.17, C:0.12, G:0.29, T:0.42
Consensus pattern (29 bp):
TGTGTTTAGGGACTTTTATGTAGATGCTC
Found at i:54932 original size:18 final size:18
Alignment explanation
Indices: 54909--54944 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
54899 CCCATATAAC
*
54909 CCTATAATTGGATTTAAA
1 CCTATAATTGGAGTTAAA
54927 CCTATAATTGGAGTTAAA
1 CCTATAATTGGAGTTAAA
54945 ATCCCAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (18 bp):
CCTATAATTGGAGTTAAA
Found at i:56537 original size:20 final size:20
Alignment explanation
Indices: 56509--56559 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
56499 CCGATTTTTC
*
56509 TAAAAAAAAAAAGTTTGCGATT
1 TAAAAAAAAAAA--TTGCGACT
56531 TAAAAAAAAAAATTGCGACT
1 TAAAAAAAAAAATTGCGACT
56551 TAAAAAAAA
1 TAAAAAAAA
56560 TTTAGGGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 16 0.57
22 12 0.43
ACGTcount: A:0.63, C:0.06, G:0.10, T:0.22
Consensus pattern (20 bp):
TAAAAAAAAAAATTGCGACT
Found at i:62514 original size:21 final size:22
Alignment explanation
Indices: 62478--62528 Score: 86
Period size: 21 Copynumber: 2.4 Consensus size: 22
62468 GTGCTTAGGC
62478 ATGGCCGGGACATGCGATGGTG
1 ATGGCCGGGACATGCGATGGTG
*
62500 ATGGTCGGG-CATGCGATGGTG
1 ATGGCCGGGACATGCGATGGTG
62521 ATGGCCGG
1 ATGGCCGG
62529 AAATGTGGCC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 19 0.70
22 8 0.30
ACGTcount: A:0.16, C:0.18, G:0.47, T:0.20
Consensus pattern (22 bp):
ATGGCCGGGACATGCGATGGTG
Found at i:68040 original size:11 final size:9
Alignment explanation
Indices: 68007--68031 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
67997 GGTCGAAATT
68007 TTTTTTTTA
1 TTTTTTTTA
68016 TTTTTTTTA
1 TTTTTTTTA
68025 TTTTTTT
1 TTTTTTT
68032 GATATTTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:68150 original size:11 final size:12
Alignment explanation
Indices: 68126--68152 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
68116 ATTTTCAAAG
68126 TTGCTGATTTTT
1 TTGCTGATTTTT
68138 TTGCTGATTTTT
1 TTGCTGATTTTT
68150 TTG
1 TTG
68153 AATTTTTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.07, G:0.19, T:0.67
Consensus pattern (12 bp):
TTGCTGATTTTT
Found at i:69112 original size:21 final size:22
Alignment explanation
Indices: 69076--69126 Score: 95
Period size: 21 Copynumber: 2.4 Consensus size: 22
69066 GTGCTTAGGC
69076 ATGGCCGGGTCATGCGATGGTG
1 ATGGCCGGGTCATGCGATGGTG
69098 ATGGCCGGG-CATGCGATGGTG
1 ATGGCCGGGTCATGCGATGGTG
69119 ATGGCCGG
1 ATGGCCGG
69127 TCAAGTGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 20 0.69
22 9 0.31
ACGTcount: A:0.14, C:0.20, G:0.47, T:0.20
Consensus pattern (22 bp):
ATGGCCGGGTCATGCGATGGTG
Found at i:81409 original size:33 final size:33
Alignment explanation
Indices: 81331--81414 Score: 87
Period size: 33 Copynumber: 2.5 Consensus size: 33
81321 ACTAGATTCG
* * *
81331 TATCAATCACAAACAACACTTAAAACAGATTTAG
1 TATC-ATCGCAAACAACACTCAAAACAGATTTAC
* * ** *
81365 TGTCATTGCAAACAACACTCAAATTAGGTTTAC
1 TATCATCGCAAACAACACTCAAAACAGATTTAC
81398 TATCATCGCAAACAACA
1 TATCATCGCAAACAACA
81415 TCTAAAATAC
Statistics
Matches: 40, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
33 37 0.93
34 3 0.08
ACGTcount: A:0.44, C:0.23, G:0.08, T:0.25
Consensus pattern (33 bp):
TATCATCGCAAACAACACTCAAAACAGATTTAC
Found at i:86081 original size:30 final size:30
Alignment explanation
Indices: 86047--86141 Score: 112
Period size: 30 Copynumber: 3.3 Consensus size: 30
86037 TCTTGAATTG
86047 ATTCAAAAGGAGTCAAAATATTTGATGTTC
1 ATTCAAAAGGAGTCAAAATATTTGATGTTC
* * *
86077 ATTCAAAAGGTGT----AT-TCTTGA-ATTG
1 ATTCAAAAGGAGTCAAAATAT-TTGATGTTC
86102 ATTCAAAAGGAGTCAAAATATTTGATGTTC
1 ATTCAAAAGGAGTCAAAATATTTGATGTTC
86132 ATTCAAAAGG
1 ATTCAAAAGG
86142 TGTATTCTTG
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
25 15 0.29
26 6 0.12
29 6 0.12
30 25 0.48
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34
Consensus pattern (30 bp):
ATTCAAAAGGAGTCAAAATATTTGATGTTC
Found at i:86092 original size:24 final size:24
Alignment explanation
Indices: 86065--86147 Score: 60
Period size: 25 Copynumber: 3.2 Consensus size: 24
86055 GGAGTCAAAA
86065 TATTTGATGTTCATTCAAAAGGTG
1 TATTTGATGTTCATTCAAAAGGTG
* * *
86089 TATTCTTGA-ATTGATTCAAAAGGAGTCAAAA
1 TA-T-TTGATGTTCATTCAAAA-G-GT----G
86120 TATTTGATGTTCATTCAAAAGGTG
1 TATTTGATGTTCATTCAAAAGGTG
86144 TATT
1 TATT
86148 CTTGAATTGA
Statistics
Matches: 44, Mismatches: 6, Indels: 18
0.65 0.09 0.26
Matches are distributed among these distances:
24 6 0.14
25 11 0.25
26 5 0.11
27 2 0.05
28 2 0.05
29 5 0.11
30 11 0.25
31 2 0.05
ACGTcount: A:0.34, C:0.08, G:0.18, T:0.40
Consensus pattern (24 bp):
TATTTGATGTTCATTCAAAAGGTG
Found at i:86093 original size:55 final size:55
Alignment explanation
Indices: 86032--86174 Score: 277
Period size: 55 Copynumber: 2.6 Consensus size: 55
86022 CAAACTCAAT
86032 TGTATTCTTGAATTGATTCAAAAGGAGTCAAAATATTTGATGTTCATTCAAAAGG
1 TGTATTCTTGAATTGATTCAAAAGGAGTCAAAATATTTGATGTTCATTCAAAAGG
86087 TGTATTCTTGAATTGATTCAAAAGGAGTCAAAATATTTGATGTTCATTCAAAAGG
1 TGTATTCTTGAATTGATTCAAAAGGAGTCAAAATATTTGATGTTCATTCAAAAGG
*
86142 TGTATTCTTGAATTGATTCAAAAGTAGTCAAAA
1 TGTATTCTTGAATTGATTCAAAAGGAGTCAAAA
86175 GAATAGATTC
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
55 87 1.00
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.36
Consensus pattern (55 bp):
TGTATTCTTGAATTGATTCAAAAGGAGTCAAAATATTTGATGTTCATTCAAAAGG
Found at i:86097 original size:26 final size:25
Alignment explanation
Indices: 86074--86165 Score: 87
Period size: 25 Copynumber: 3.5 Consensus size: 25
86064 ATATTTGATG
86074 TTCATTCAAAAGGTGTATTCTTGAA
1 TTCATTCAAAAGGTGTATTCTTGAA
* * *
86099 TTGATTCAAAAGGAGTCAAAATAT-TTGATG
1 TTCATTCAAAAGGTGT----AT-TCTTGA-A
86129 TTCATTCAAAAGGTGTATTCTTGAA
1 TTCATTCAAAAGGTGTATTCTTGAA
*
86154 TTGATTCAAAAG
1 TTCATTCAAAAG
86166 TAGTCAAAAG
Statistics
Matches: 53, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
25 26 0.49
26 6 0.11
29 6 0.11
30 15 0.28
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.37
Consensus pattern (25 bp):
TTCATTCAAAAGGTGTATTCTTGAA
Found at i:86202 original size:23 final size:24
Alignment explanation
Indices: 86156--86203 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
86146 TTCTTGAATT
*
86156 GATTCAAAAGTAGTCAAAAGAATA
1 GATTCAAAAGTAGTCAAAACAATA
86180 GATTCAAAAAG-AG-CAAAACAATA
1 GATTC-AAAAGTAGTCAAAACAATA
86203 G
1 G
86204 GTGAAATAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 10 0.45
24 7 0.32
25 5 0.23
ACGTcount: A:0.56, C:0.10, G:0.17, T:0.17
Consensus pattern (24 bp):
GATTCAAAAGTAGTCAAAACAATA
Found at i:93695 original size:33 final size:33
Alignment explanation
Indices: 93656--93722 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
93646 CAACCATAAT
93656 AAAGGCTAATCTCAATTAAATTCTATTTAACCA
1 AAAGGCTAATCTCAATTAAATTCTATTTAACCA
93689 AAAGGCTAATCTCAATTAAATTCTATTTAACCA
1 AAAGGCTAATCTCAATTAAATTCTATTTAACCA
93722 A
1 A
93723 TCAAACTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.43, C:0.18, G:0.06, T:0.33
Consensus pattern (33 bp):
AAAGGCTAATCTCAATTAAATTCTATTTAACCA
Found at i:94775 original size:43 final size:43
Alignment explanation
Indices: 94726--94809 Score: 143
Period size: 43 Copynumber: 2.0 Consensus size: 43
94716 ACGTCCTATA
94726 TATAACTAAGTTCATGAGCTAGT-CAATAAAATATCCTATAATC
1 TATAACTAAGTTCATGAGCTA-TCCAATAAAATATCCTATAATC
*
94769 TATAACTAAGTTCATGAGCTATCCTATAAAATATCCTATAA
1 TATAACTAAGTTCATGAGCTATCCAATAAAATATCCTATAA
94810 CTAAGTTAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
42 1 0.03
43 38 0.97
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.33
Consensus pattern (43 bp):
TATAACTAAGTTCATGAGCTATCCAATAAAATATCCTATAATC
Found at i:105744 original size:2 final size:2
Alignment explanation
Indices: 105737--105771 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
105727 ATATTCTCAT
105737 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 T
105772 TAAGCAGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.