Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015672.1 Corchorus capsularis cultivar CVL-1 contig15693, 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: 50864
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:81 original size:26 final size:26
Alignment explanation
Indices: 47--114 Score: 93
Period size: 26 Copynumber: 2.6 Consensus size: 26
37 TACTGAGTTT
*
47 ATTATTTTATGTTTAATTAGTATCTA
1 ATTAGTTTATGTTTAATTAGTATCTA
*
73 ATTAGTTTAT-TATTAATTAGTATTTA
1 ATTAGTTTATGT-TTAATTAGTATCTA
*
99 ATTAGTTTATGATTAA
1 ATTAGTTTATGTTTAA
115 AATGAAGGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
25 1 0.03
26 36 0.97
ACGTcount: A:0.34, C:0.01, G:0.09, T:0.56
Consensus pattern (26 bp):
ATTAGTTTATGTTTAATTAGTATCTA
Found at i:91 original size:15 final size:15
Alignment explanation
Indices: 71--114 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
61 AATTAGTATC
71 TAATTAGTTTATTAT
1 TAATTAGTTTATTAT
86 TAATTAG--TA-T-T
1 TAATTAGTTTATTAT
*
97 TAATTAGTTTATGAT
1 TAATTAGTTTATTAT
112 TAA
1 TAA
115 AATGAAGGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 8
0.73 0.03 0.24
Matches are distributed among these distances:
11 8 0.33
12 1 0.04
13 4 0.17
15 11 0.46
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (15 bp):
TAATTAGTTTATTAT
Found at i:162 original size:24 final size:25
Alignment explanation
Indices: 123--182 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 25
113 AAAATGAAGG
*
123 AAAATGAA-TTTGAAG-ATTTGTTA
1 AAAATGAAGTTTGAAGAAGTTGTTA
146 AAAATGAAGTTTGAAGAAGTTGTTA
1 AAAATGAAGTTTGAAGAAGTTGTTA
* *
171 GAAATTAAGTTT
1 AAAATGAAGTTT
183 AGAGTTTGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
23 8 0.25
24 7 0.22
25 17 0.53
ACGTcount: A:0.43, C:0.00, G:0.20, T:0.37
Consensus pattern (25 bp):
AAAATGAAGTTTGAAGAAGTTGTTA
Found at i:294 original size:21 final size:21
Alignment explanation
Indices: 253--296 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
243 CAAAAGTGTA
**
253 AAAAGGGGGACGGTATTTAGC
1 AAAAGGGGGACGGTAAATAGC
274 AAAAGAGGGG-CGGTAAATAGC
1 AAAAG-GGGGACGGTAAATAGC
295 AA
1 AA
297 TTCAGTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.41, C:0.09, G:0.36, T:0.14
Consensus pattern (21 bp):
AAAAGGGGGACGGTAAATAGC
Found at i:1770 original size:28 final size:29
Alignment explanation
Indices: 1713--1771 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
1703 ATTGTGCGGT
* **
1713 AAAAGAAATTATAATTTTTTTTTTATAATA
1 AAAAGAAATTATAA-TATTTTAATATAATA
1743 AAAAGAAATTATAA-ATTTTAATATAATA
1 AAAAGAAATTATAATATTTTAATATAATA
1771 A
1 A
1772 TAATATATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.42
Consensus pattern (29 bp):
AAAAGAAATTATAATATTTTAATATAATA
Found at i:1772 original size:31 final size:30
Alignment explanation
Indices: 1713--1774 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
1703 ATTGTGCGGT
** * *
1713 AAAAGAAATTATAATTTTTTTTTTATAATA
1 AAAAGAAATTATAATTTTAATATAATAATA
1743 AAAAGAAATTATAAATTTTAATATAATAATA
1 AAAAGAAATTAT-AATTTTAATATAATAATA
1774 A
1 A
1775 TATATTTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 12 0.44
31 15 0.56
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (30 bp):
AAAAGAAATTATAATTTTAATATAATAATA
Found at i:1905 original size:2 final size:2
Alignment explanation
Indices: 1893--1950 Score: 80
Period size: 2 Copynumber: 28.5 Consensus size: 2
1883 AGTTTAGACT
* * *
1893 TA TA TA GTA TA TA TA TA GA TA TA GA TA TA GA TA TA 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
1936 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
1951 TGCCTCTAGG
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
2 47 0.96
3 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (2 bp):
TA
Found at i:4610 original size:11 final size:11
Alignment explanation
Indices: 4594--4626 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
4584 AAAATTACCG
4594 AGTGTACCACA
1 AGTGTACCACA
4605 AGTGTA-CACA
1 AGTGTACCACA
*
4615 GGTGTACCACA
1 AGTGTACCACA
4626 A
1 A
4627 CAGGTTTACT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.18
Consensus pattern (11 bp):
AGTGTACCACA
Found at i:8104 original size:11 final size:11
Alignment explanation
Indices: 8088--8113 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
8078 GTAAGTACCA
8088 GAAACATCAAG
1 GAAACATCAAG
8099 GAAACATCAAG
1 GAAACATCAAG
8110 GAAA
1 GAAA
8114 TTGACCAATT
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:0.58, C:0.15, G:0.19, T:0.08
Consensus pattern (11 bp):
GAAACATCAAG
Found at i:9398 original size:12 final size:12
Alignment explanation
Indices: 9381--9406 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
9371 TAAAAGGGAA
9381 TTTCCTTGATGT
1 TTTCCTTGATGT
9393 TTTCCTTGATGT
1 TTTCCTTGATGT
9405 TT
1 TT
9407 CTGGTTCTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.15, G:0.15, T:0.62
Consensus pattern (12 bp):
TTTCCTTGATGT
Found at i:17826 original size:32 final size:31
Alignment explanation
Indices: 17743--17826 Score: 109
Period size: 31 Copynumber: 2.7 Consensus size: 31
17733 TTGCCTCATA
17743 AACTT-CAAA-TCAGGACATTTTCCCCCTTG
1 AACTTCCAAATTCAGGACATTTTCCCCCTTG
* **
17772 AACTTCCAAATTCAGGATATTTTGTCCCTTG
1 AACTTCCAAATTCAGGACATTTTCCCCCTTG
*
17803 AACTTCCCAAATTCAAGACATTTT
1 AACTT-CCAAATTCAGGACATTTT
17827 ACCTCTAACG
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
29 5 0.11
30 4 0.09
31 22 0.47
32 16 0.34
ACGTcount: A:0.30, C:0.26, G:0.10, T:0.35
Consensus pattern (31 bp):
AACTTCCAAATTCAGGACATTTTCCCCCTTG
Found at i:19562 original size:17 final size:18
Alignment explanation
Indices: 19540--19573 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
19530 GAATCGGAAG
*
19540 AGAAGG-AGAAGTGTAAA
1 AGAAGGAAGAAGGGTAAA
19557 AGAAGGAAGAAGGGTAA
1 AGAAGGAAGAAGGGTAA
19574 TGCTTTGAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.53, C:0.00, G:0.38, T:0.09
Consensus pattern (18 bp):
AGAAGGAAGAAGGGTAAA
Found at i:21770 original size:83 final size:82
Alignment explanation
Indices: 21678--21840 Score: 272
Period size: 83 Copynumber: 2.0 Consensus size: 82
21668 AAAGCTCTTG
* *
21678 AAATTAAATAATGATAAATTATATTTATTTACAAAAGCACGAAAGCGACAGGAAAATGAAGCTAG
1 AAATTAAATAATGATAAATTATATTTATTTACAAAAGCACGAAAACGACAAGAAAATGAA-CTAG
* *
21743 AGCTTTATTAGGCACACT
65 AACGTTATTAGGCACACT
*
21761 AAATTAAATAATGATAAATTATATTTATTTACAAAAGCATGAAAACGACAAGAAAATGAACTAGA
1 AAATTAAATAATGATAAATTATATTTATTTACAAAAGCACGAAAACGACAAGAAAATGAACTAGA
21826 ACGTTATTAGGCACA
66 ACGTTATTAGGCACA
21841 TTAATTTTGT
Statistics
Matches: 75, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
82 18 0.24
83 57 0.76
ACGTcount: A:0.48, C:0.11, G:0.14, T:0.26
Consensus pattern (82 bp):
AAATTAAATAATGATAAATTATATTTATTTACAAAAGCACGAAAACGACAAGAAAATGAACTAGA
ACGTTATTAGGCACACT
Found at i:23900 original size:543 final size:545
Alignment explanation
Indices: 22829--23907 Score: 1932
Period size: 543 Copynumber: 2.0 Consensus size: 545
22819 CGGTTCCATA
* *
22829 TGGGCTCCAATTTCTGCTGACGTTGCTACGTTTAGCTGACTTGTAAAAGGCACGTCAGCCAAGGT
1 TGGGCTCCAATTTCTGCTGACGTGGCTACGTTTAGCTGACTTGTAAAAGCCACGTCAGCCAAGGT
22894 AAGTCCCACTCAACTAAAAAAAAGGAAAAATAAATTGGAAAAAAGAAAAAGAAAATAAATTTCGT
66 AAGTCCCACTCAACTAAAAAAAAGGAAAAATAAATTGGAAAAAAGAAAAAGAAAATAAATTTCGT
*
22959 TAAATCAAAACAGAAATTTTTTTATAATAATTTTTTTATTATTAAAATAAAGAAAAAAAAACAAA
131 TAAATCAAAACAGAAAATTTTTTATAATAATTTTTTTATTATTAAAATAAAGAAAAAAAAACAAA
* *
23024 AACAATAGCTAAGAATTAAAAACGAAAAAATGAGAATCAAAACCAAAAATCTCAAATCCTTTTTT
196 AACAATAGCTAAGAATTAAAAACGAAAAAATGAGAATCAAAACCAAAAATCTCAAATCCTCTCTT
* *
23089 TCTCCTTCTTCAACCAATTTGCCCATGTTTCCCTTCAACACTTCGTTTTTCTTCCCTCCCAATCA
261 TCTCCTTCTTCAACCAATTTGCCCATGTTTCCCCTCAACACTTCGTTTCTCTTCCCTCCCAATCA
* *
23154 CATGTTCAAGTAACTCCTAGTCTCATCATGAATCCTTAAACTTAAGCTTCCTCTCATTTTCTTCG
326 CATGTTCAAGTAACTCCTACTCTCATCATGAATCCTTAAACTCAAGCTTCCTCTCATTTTCTTCG
* *
23219 AACATTTAACCAAATTAAACAGAAATTGCAAAATTCACCTTGAGACTAGATAATAGCTTTTGTTT
391 AACATTTAACCAAATTAAACAGAAATTGCAAAATTCACCTTCAGACTAGATAATAACTTTTGTTT
* *
23284 TCTTTCCGGCAACACCAACAAAACCAAAATCAAATAATTTTCTTCTTCCTTCCTTTTTTTCAGAA
456 TCTTTCCGCCAACACCAACAAAACCAAAATCAAATAATTTTCTTCTTCCTTCCTTTTTTCCAGAA
23349 AATCAACCCACTTTGGTGTTTCGTC
521 AATCAACCCACTTTGGTGTTTCGTC
23374 TGGGCTCCAATTTTCTGCTGACGTGGCTACGTTTAGCTGACTTGTAAAAGCCACGTCAGCCAAGG
1 TGGGCTCCAA-TTTCTGCTGACGTGGCTACGTTTAGCTGACTTGTAAAAGCCACGTCAGCCAAGG
**
23439 TGGGTCCCACTCAACTAAAAAAAAGGAAAAATAAATTGGAAAAAAGAAAAAGAAAATAAATTTCG
65 TAAGTCCCACTCAACTAAAAAAAAGGAAAAATAAATTGGAAAAAAGAAAAAGAAAATAAATTTCG
* *
23504 TTAAATCAAAACATAAAATTTTTTATAATAATTTTTTTATTATTAAAAT-AAG-AAAAAACA-AA
130 TTAAATCAAAACAGAAAATTTTTTATAATAATTTTTTTATTATTAAAATAAAGAAAAAAAAACAA
*
23566 AAACAATAGCTAAGAATT-AAAACGAAAAAATGAGAATCAAAACCAAAAATCTCAAGTCCTCTCT
195 AAACAATAGCTAAGAATTAAAAACGAAAAAATGAGAATCAAAACCAAAAATCTCAAATCCTCTCT
23630 TTCTCCTTCTTCAACCAATTTGCCCATGTTTCCCCTCAACACTTCGTTTCTCTTCCCTCCCAATC
260 TTCTCCTTCTTCAACCAATTTGCCCATGTTTCCCCTCAACACTTCGTTTCTCTTCCCTCCCAATC
*
23695 ACATGTTCAAGTAACTCCTACTCTCATCATGAATCCTTAAACTCAAGCTTCCCTTTCATTTTCTT
325 ACATGTTCAAGTAACTCCTACTCTCATCATGAATCCTTAAACTCAAGCTT-CCTCTCATTTTCTT
*
23760 CGAACATTTAACCAAATTAAACATAAATTGCAAAATTCACCTTCAGACTAGATAATAACTTTTGT
389 CGAACATTTAACCAAATTAAACAGAAATTGCAAAATTCACCTTCAGACTAGATAATAACTTTTGT
23825 TTTCTTTCCGCCAACACCAACAAAACCAAAATCAAATAATTTTCTTCTTCCTTCCTTTTTTCCAG
454 TTTCTTTCCGCCAACACCAACAAAACCAAAATCAAATAATTTTCTTCTTCCTTCCTTTTTTCCAG
23890 AAAATCAACCCACTTTGG
519 AAAATCAACCCACTTTGG
23908 CTTAATCCTC
Statistics
Matches: 512, Mismatches: 20, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
542 154 0.30
543 176 0.34
544 7 0.01
545 13 0.03
546 162 0.32
ACGTcount: A:0.38, C:0.22, G:0.10, T:0.31
Consensus pattern (545 bp):
TGGGCTCCAATTTCTGCTGACGTGGCTACGTTTAGCTGACTTGTAAAAGCCACGTCAGCCAAGGT
AAGTCCCACTCAACTAAAAAAAAGGAAAAATAAATTGGAAAAAAGAAAAAGAAAATAAATTTCGT
TAAATCAAAACAGAAAATTTTTTATAATAATTTTTTTATTATTAAAATAAAGAAAAAAAAACAAA
AACAATAGCTAAGAATTAAAAACGAAAAAATGAGAATCAAAACCAAAAATCTCAAATCCTCTCTT
TCTCCTTCTTCAACCAATTTGCCCATGTTTCCCCTCAACACTTCGTTTCTCTTCCCTCCCAATCA
CATGTTCAAGTAACTCCTACTCTCATCATGAATCCTTAAACTCAAGCTTCCTCTCATTTTCTTCG
AACATTTAACCAAATTAAACAGAAATTGCAAAATTCACCTTCAGACTAGATAATAACTTTTGTTT
TCTTTCCGCCAACACCAACAAAACCAAAATCAAATAATTTTCTTCTTCCTTCCTTTTTTCCAGAA
AATCAACCCACTTTGGTGTTTCGTC
Found at i:25116 original size:21 final size:21
Alignment explanation
Indices: 25090--25133 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
25080 TTTAACTGGA
25090 TTGCTAAACACCGCCCCATTT
1 TTGCTAAACACCGCCCCATTT
**
25111 TTGCTATTCACCGCCCCATTT
1 TTGCTAAACACCGCCCCATTT
25132 TT
1 TT
25134 TATGCTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.36, G:0.09, T:0.36
Consensus pattern (21 bp):
TTGCTAAACACCGCCCCATTT
Found at i:25518 original size:32 final size:32
Alignment explanation
Indices: 25482--25606 Score: 214
Period size: 32 Copynumber: 3.9 Consensus size: 32
25472 CGTCCCACCG
25482 GGGCGGCCTGCCGTGGCGAAGCCGCCCCATGA
1 GGGCGGCCTGCCGTGGCGAAGCCGCCCCATGA
* * *
25514 GGGCGGCTTGCCGTGGCGAAGCCACCGCATGA
1 GGGCGGCCTGCCGTGGCGAAGCCGCCCCATGA
*
25546 GGGCGGCCTGCCGTGGTGAAGCCGCCCCATGA
1 GGGCGGCCTGCCGTGGCGAAGCCGCCCCATGA
25578 GGGCGGCCTGCCGTGGCGAAGCCGCCCCA
1 GGGCGGCCTGCCGTGGCGAAGCCGCCCCA
25607 GTGGGGAGGC
Statistics
Matches: 85, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 85 1.00
ACGTcount: A:0.13, C:0.36, G:0.41, T:0.10
Consensus pattern (32 bp):
GGGCGGCCTGCCGTGGCGAAGCCGCCCCATGA
Found at i:25639 original size:33 final size:33
Alignment explanation
Indices: 25588--25684 Score: 90
Period size: 33 Copynumber: 2.9 Consensus size: 33
25578 GGGCGGCCTG
* *
25588 CCGTGGC-GAAGCCGCCCCAGTGGGGAGGCTCCG
1 CCGTGGCTG-AGCCTCCCCAGTGGGGAGGCTCCA
* **
25621 CCGTGGTTGAGCCTCCCCAGTGGATAGGCTCCA
1 CCGTGGCTGAGCCTCCCCAGTGGGGAGGCTCCA
* * *
25654 TCGTGGCTGAACCGT-CCTAGTGGGGAGGCTC
1 CCGTGGCTGAGCC-TCCCCAGTGGGGAGGCTC
25685 AGTGTAAAAG
Statistics
Matches: 51, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
33 49 0.96
34 2 0.04
ACGTcount: A:0.13, C:0.32, G:0.37, T:0.18
Consensus pattern (33 bp):
CCGTGGCTGAGCCTCCCCAGTGGGGAGGCTCCA
Found at i:26913 original size:7 final size:7
Alignment explanation
Indices: 26903--26967 Score: 76
Period size: 7 Copynumber: 9.0 Consensus size: 7
26893 AATAGATAGG
26903 AGTAGAT
1 AGTAGAT
*
26910 AGTAGAC
1 AGTAGAT
26917 AGATAGAT
1 AG-TAGAT
*
26925 GGTAGAT
1 AGTAGAT
26932 AGTAGAT
1 AGTAGAT
*
26939 TGTAGAT
1 AGTAGAT
*
26946 ATCTAGAT
1 A-GTAGAT
26954 AGTAGAT
1 AGTAGAT
26961 AGTAGAT
1 AGTAGAT
26968 TACAAATTAT
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
7 37 0.77
8 11 0.23
ACGTcount: A:0.40, C:0.03, G:0.28, T:0.29
Consensus pattern (7 bp):
AGTAGAT
Found at i:26929 original size:15 final size:14
Alignment explanation
Indices: 26903--26967 Score: 58
Period size: 15 Copynumber: 4.5 Consensus size: 14
26893 AATAGATAGG
26903 AGTAGATAGTAGAC
1 AGTAGATAGTAGAC
* *
26917 AGATAGATGGTAGAT
1 AG-TAGATAGTAGAC
* *
26932 AGTAGATTGTAGAT
1 AGTAGATAGTAGAC
* *
26946 ATCTAGATAGTAGAT
1 A-GTAGATAGTAGAC
26961 AGTAGAT
1 AGTAGAT
26968 TACAAATTAT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
14 19 0.44
15 24 0.56
ACGTcount: A:0.40, C:0.03, G:0.28, T:0.29
Consensus pattern (14 bp):
AGTAGATAGTAGAC
Found at i:26936 original size:29 final size:29
Alignment explanation
Indices: 26903--26967 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
26893 AATAGATAGG
*
26903 AGTAGATAGTAGACAGATAGATGGTAGAT
1 AGTAGATAGTAGACAGATAGATAGTAGAT
* * **
26932 AGTAGATTGTAGATATCTAGATAGTAGAT
1 AGTAGATAGTAGACAGATAGATAGTAGAT
26961 AGTAGAT
1 AGTAGAT
26968 TACAAATTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.40, C:0.03, G:0.28, T:0.29
Consensus pattern (29 bp):
AGTAGATAGTAGACAGATAGATAGTAGAT
Found at i:28293 original size:12 final size:12
Alignment explanation
Indices: 28276--28301 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
28266 ACGTTTATAT
28276 GACACGAAACAC
1 GACACGAAACAC
28288 GACACGAAACAC
1 GACACGAAACAC
28300 GA
1 GA
28302 ATTGTCAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.31, G:0.19, T:0.00
Consensus pattern (12 bp):
GACACGAAACAC
Found at i:29741 original size:21 final size:21
Alignment explanation
Indices: 29698--29741 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
29688 AATATGGGGG
*
29698 TTGCTAAATACCGCCCTAGTT
1 TTGCTAAATACCGCCCCAGTT
* *
29719 TTGCTAAATATCGCCCCATTT
1 TTGCTAAATACCGCCCCAGTT
29740 TT
1 TT
29742 TACACTTTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.27, G:0.11, T:0.39
Consensus pattern (21 bp):
TTGCTAAATACCGCCCCAGTT
Found at i:29863 original size:33 final size:32
Alignment explanation
Indices: 29826--29938 Score: 138
Period size: 32 Copynumber: 3.5 Consensus size: 32
29816 GTCGGAGCCT
* *
29826 CCCCACTGGGGCGACTTCACCATGGGCAGGCCG
1 CCCCACTGGGGCGGCTTCACCA-CGGCAGGCCG
* *
29859 CCCCACTGGGGCGGCTTCTCCACGGCAAGCCG
1 CCCCACTGGGGCGGCTTCACCACGGCAGGCCG
*
29891 CCCTCA-TGGGGCGGCTTCGCCACGGCAGGCCG
1 CCC-CACTGGGGCGGCTTCACCACGGCAGGCCG
**
29923 CCCCGGTGGGGCGGCT
1 CCCCACTGGGGCGGCT
29939 AGACCAAATT
Statistics
Matches: 71, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
31 1 0.01
32 48 0.68
33 22 0.31
ACGTcount: A:0.11, C:0.41, G:0.36, T:0.12
Consensus pattern (32 bp):
CCCCACTGGGGCGGCTTCACCACGGCAGGCCG
Found at i:31438 original size:2 final size:2
Alignment explanation
Indices: 31431--31463 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
31421 AATCTGAGTG
31431 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
31464 CTCTTTGTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31538 original size:47 final size:48
Alignment explanation
Indices: 31469--31562 Score: 172
Period size: 47 Copynumber: 2.0 Consensus size: 48
31459 ATATACTCTT
*
31469 TGTTTGTTGCATGTATTAGCTTTAGAATTACTACGGTTA-CCCGAGTC
1 TGTTTGTTGCATATATTAGCTTTAGAATTACTACGGTTATCCCGAGTC
31516 TGTTTGTTGCATATATTAGCTTTAGAATTACTACGGTTATCCCGAGT
1 TGTTTGTTGCATATATTAGCTTTAGAATTACTACGGTTATCCCGAGT
31563 AGCAGATACC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
47 38 0.84
48 7 0.16
ACGTcount: A:0.22, C:0.16, G:0.20, T:0.41
Consensus pattern (48 bp):
TGTTTGTTGCATATATTAGCTTTAGAATTACTACGGTTATCCCGAGTC
Found at i:32765 original size:3 final size:3
Alignment explanation
Indices: 32757--32798 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
32747 TTAACGTATA
32757 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
32799 GCTATTAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:34558 original size:27 final size:27
Alignment explanation
Indices: 34520--34576 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
34510 ATTCTATTAA
34520 GTAGAAGGACTCAACTGACACCAAATT
1 GTAGAAGGACTCAACTGACACCAAATT
34547 GTAGAAGGACTCAACTGACACCAAATT
1 GTAGAAGGACTCAACTGACACCAAATT
34574 GTA
1 GTA
34577 AGTAGAGGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.19
Consensus pattern (27 bp):
GTAGAAGGACTCAACTGACACCAAATT
Found at i:37927 original size:3 final size:3
Alignment explanation
Indices: 37913--37960 Score: 87
Period size: 3 Copynumber: 15.7 Consensus size: 3
37903 TTTAATATTT
37913 TAA TATA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
37959 TA
1 TA
37961 TATTGTATTT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:39904 original size:14 final size:14
Alignment explanation
Indices: 39885--39916 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
39875 TTTGATCCTT
39885 AATTATATAAAAAA
1 AATTATATAAAAAA
*
39899 AATTATATAAAATA
1 AATTATATAAAAAA
39913 AATT
1 AATT
39917 TTTAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTATATAAAAAA
Found at i:40433 original size:2 final size:2
Alignment explanation
Indices: 40426--40461 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
40416 AGCTAGGTGG
40426 TA 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 TA
40462 AAATACCCCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:41165 original size:28 final size:28
Alignment explanation
Indices: 41133--41189 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
41123 TCCTTCTGTC
41133 CCATAATATAAGTCCATTTTAATCGAAT
1 CCATAATATAAGTCCATTTTAATCGAAT
41161 CCATAATATAAGTCCATTTTAATCGAAT
1 CCATAATATAAGTCCATTTTAATCGAAT
41189 C
1 C
41190 ACAAAGTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.39, C:0.19, G:0.07, T:0.35
Consensus pattern (28 bp):
CCATAATATAAGTCCATTTTAATCGAAT
Found at i:43249 original size:3 final size:3
Alignment explanation
Indices: 43241--43270 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
43231 GCTTAAGAGC
43241 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
43271 TGATTTACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:46833 original size:163 final size:163
Alignment explanation
Indices: 46558--46890 Score: 648
Period size: 163 Copynumber: 2.0 Consensus size: 163
46548 TGGAAGATCT
*
46558 GGAAGGATAAGTCCGAATCAAAACATGTTGCCTCAAATGGATAGGTATACCCCAAATAAAAATAA
1 GGAATGATAAGTCCGAATCAAAACATGTTGCCTCAAATGGATAGGTATACCCCAAATAAAAATAA
46623 GACATTTGAAGAAATCCATGATAATGTTAGACTACCTGTGAATAATCAGTCTAATCAGAATAGAA
66 GACATTTGAAGAAATCCATGATAATGTTAGACTACCTGTGAATAATCAGTCTAATCAGAATAGAA
46688 GTGTTGCAGAGGCCTGGGGGCAAACTTAGCCTA
131 GTGTTGCAGAGGCCTGGGGGCAAACTTAGCCTA
46721 GGAATGATAAGTCCGAATCAAAACATGTTGCCTCAAATGGATAGGTATACCCCAAATAAAAATAA
1 GGAATGATAAGTCCGAATCAAAACATGTTGCCTCAAATGGATAGGTATACCCCAAATAAAAATAA
46786 GACATTTGAAGAAATCCATGATAATGTTAGACTACCTGTGAATAATCAGTCTAATCAGAATAGAA
66 GACATTTGAAGAAATCCATGATAATGTTAGACTACCTGTGAATAATCAGTCTAATCAGAATAGAA
*
46851 GTGTTGCAGAGGCCTGGGGGCAAACTTAGCTTA
131 GTGTTGCAGAGGCCTGGGGGCAAACTTAGCCTA
46884 GGAATGA
1 GGAATGA
46891 AGTTAATGTT
Statistics
Matches: 168, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
163 168 1.00
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.24
Consensus pattern (163 bp):
GGAATGATAAGTCCGAATCAAAACATGTTGCCTCAAATGGATAGGTATACCCCAAATAAAAATAA
GACATTTGAAGAAATCCATGATAATGTTAGACTACCTGTGAATAATCAGTCTAATCAGAATAGAA
GTGTTGCAGAGGCCTGGGGGCAAACTTAGCCTA
Found at i:49385 original size:14 final size:14
Alignment explanation
Indices: 49366--49399 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
49356 GCATATTAAC
49366 TTTAGTCCATTTAG
1 TTTAGTCCATTTAG
49380 TTTAGTCCATTTAG
1 TTTAGTCCATTTAG
*
49394 ATTAGT
1 TTTAGT
49400 ATCATAGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.12, G:0.15, T:0.50
Consensus pattern (14 bp):
TTTAGTCCATTTAG
Found at i:49576 original size:20 final size:20
Alignment explanation
Indices: 49540--49578 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
49530 AAATACAAGG
*
49540 CATTTGATTTAGGAATTGGA
1 CATTTGATTTAGAAATTGGA
49560 CATTTGATTT-GCAAATTGG
1 CATTTGATTTAG-AAATTGG
49579 TGCTCTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.28, C:0.08, G:0.23, T:0.41
Consensus pattern (20 bp):
CATTTGATTTAGAAATTGGA
Done.