Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008346.1 Corchorus capsularis cultivar CVL-1 contig08367, 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: 60620
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:683 original size:23 final size:23
Alignment explanation
Indices: 653--708 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
643 TTCGGGTATT
* *
653 TTCGGGTTC-GGGCTTGGATCGGG
1 TTCGGGTTCAGGCCCTGG-TCGGG
676 TTCGGGTTCAGGCCCTGGTCGGG
1 TTCGGGTTCAGGCCCTGGTCGGG
*
699 TTTGGGTTCA
1 TTCGGGTTCA
709 CTTTCGATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 23 0.79
24 6 0.21
ACGTcount: A:0.05, C:0.20, G:0.43, T:0.32
Consensus pattern (23 bp):
TTCGGGTTCAGGCCCTGGTCGGG
Found at i:3775 original size:11 final size:10
Alignment explanation
Indices: 3757--3790 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
3747 AATTGTTTTC
3757 AAATCTTCAA
1 AAATCTTCAA
3767 AATATCTTCAA
1 AA-ATCTTCAA
3778 GAAATCTTCAA
1 -AAATCTTCAA
3789 AA
1 AA
3791 CATGAACTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.29
Consensus pattern (10 bp):
AAATCTTCAA
Found at i:3960 original size:21 final size:21
Alignment explanation
Indices: 3921--3959 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
3911 TGCAAAATAG
3921 GGTAAAAACACATATAAAAGT
1 GGTAAAAACACATATAAAAGT
*
3942 GGTAAAAA-ATATATAAAA
1 GGTAAAAACACATATAAAA
3960 ATAACTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.62, C:0.05, G:0.13, T:0.21
Consensus pattern (21 bp):
GGTAAAAACACATATAAAAGT
Found at i:8088 original size:23 final size:23
Alignment explanation
Indices: 8058--8104 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
8048 TGGAGGAAGA
8058 GGGTTAGTGGTGACTGTTTTGAT
1 GGGTTAGTGGTGACTGTTTTGAT
8081 GGGTTAGTGGTGACTGTTTTGAT
1 GGGTTAGTGGTGACTGTTTTGAT
8104 G
1 G
8105 CAATTTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.13, C:0.04, G:0.40, T:0.43
Consensus pattern (23 bp):
GGGTTAGTGGTGACTGTTTTGAT
Found at i:14734 original size:22 final size:23
Alignment explanation
Indices: 14693--14744 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 23
14683 AATTGTTTTC
*
14693 TTAA-TTAGTATTTTAGTTTAGT
1 TTAATTTAGTATTTTAGTTTACT
14715 TTAATTTAGT-TTTT-GCTTTACT
1 TTAATTTAGTATTTTAG-TTTACT
*
14737 TTTATTTA
1 TTAATTTA
14745 ATTGCTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 1 0.04
22 20 0.77
23 5 0.19
ACGTcount: A:0.23, C:0.04, G:0.10, T:0.63
Consensus pattern (23 bp):
TTAATTTAGTATTTTAGTTTACT
Found at i:29424 original size:2 final size:2
Alignment explanation
Indices: 29417--29450 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
29407 ATTAATAATC
29417 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
29451 CTAGTCGTTA
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:30378 original size:151 final size:151
Alignment explanation
Indices: 30200--30507 Score: 535
Period size: 151 Copynumber: 2.0 Consensus size: 151
30190 GGTCAATCAC
* *
30200 AATAACCTTTTAAATTAAAACGGTAAAAATAAAATAGTTATAAAAATTTTGAATTTAATTAAATG
1 AATAAACTTTTAAATTAAAACGGTAAAAATAAAATAGTTATAAAAATATTGAATTTAATTAAATG
* *
30265 AAAATAGAGTTTTTAGTATAATCAAACTATATATTAAAAAATTTTAATATATCCAAGTTTTTAAT
66 AAAATAGAGTTTTTAGTAGAATCAAACTATATATTAAAAAATTTTAATATATCCAAGTTCTTAAT
30330 GAAAAATAGTAAAATGGTAAA
131 GAAAAATAGTAAAATGGTAAA
* * * *
30351 AATAAACTTTTAAATTGAAATGTTAAAAATAAAATAGTTTTAAAAATATTGAATTTAATTAAATG
1 AATAAACTTTTAAATTAAAACGGTAAAAATAAAATAGTTATAAAAATATTGAATTTAATTAAATG
*
30416 AAAATAGAGTTTTTAGTAGAATCAAACTATATATTAAAAAATTTTAATATATCTAAGTTCTTAAT
66 AAAATAGAGTTTTTAGTAGAATCAAACTATATATTAAAAAATTTTAATATATCCAAGTTCTTAAT
30481 GAAAAATAGTAAAATGGTAAA
131 GAAAAATAGTAAAATGGTAAA
30502 AATAAA
1 AATAAA
30508 GTAATTATAA
Statistics
Matches: 148, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
151 148 1.00
ACGTcount: A:0.52, C:0.04, G:0.09, T:0.36
Consensus pattern (151 bp):
AATAAACTTTTAAATTAAAACGGTAAAAATAAAATAGTTATAAAAATATTGAATTTAATTAAATG
AAAATAGAGTTTTTAGTAGAATCAAACTATATATTAAAAAATTTTAATATATCCAAGTTCTTAAT
GAAAAATAGTAAAATGGTAAA
Found at i:36509 original size:29 final size:30
Alignment explanation
Indices: 36476--36552 Score: 93
Period size: 29 Copynumber: 2.6 Consensus size: 30
36466 AGGGTCATCC
*
36476 AGGGGTATTTTGATCATTTTCACATCTA-G
1 AGGGGTATTTTGGTCATTTTCACATCTAGG
* ** *
36505 AGGGGCATTTTGGTCATTTTTGCATTTAGG
1 AGGGGTATTTTGGTCATTTTCACATCTAGG
*
36535 GGGGGTATTTTGGTCATT
1 AGGGGTATTTTGGTCATT
36553 CTTAATCTAC
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 23 0.57
30 17 0.43
ACGTcount: A:0.18, C:0.10, G:0.29, T:0.43
Consensus pattern (30 bp):
AGGGGTATTTTGGTCATTTTCACATCTAGG
Found at i:39864 original size:40 final size:39
Alignment explanation
Indices: 39820--39950 Score: 104
Period size: 40 Copynumber: 3.3 Consensus size: 39
39810 AAAAGTAGTA
39820 AATCAGTAAATCTGTAATTAAGAGTCAAGGTAAAGGGATT
1 AATCAGTAAATCTGTAATTAAGAGTCAA-GTAAAGGGATT
* * * * * * *
39860 AATCAGTAAAT-TCATAATTAAAAAAG-GAAGCAAAAGTAGT
1 AATCAGTAAATCT-GTAATT--AAGAGTCAAGTAAAGGGATT
* * * *
39900 AATCAGTAGATCAGTAATTAAGAGTCAAAGTAAAGAGATA
1 AATCAGTAAATCTGTAATTAAGAGTC-AAGTAAAGGGATT
39940 AATCAGTAAAT
1 AATCAGTAAAT
39951 TGATAAGAGG
Statistics
Matches: 66, Mismatches: 19, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
38 4 0.06
39 1 0.02
40 55 0.83
41 2 0.03
42 4 0.06
ACGTcount: A:0.50, C:0.08, G:0.18, T:0.24
Consensus pattern (39 bp):
AATCAGTAAATCTGTAATTAAGAGTCAAGTAAAGGGATT
Found at i:39922 original size:80 final size:81
Alignment explanation
Indices: 39802--39956 Score: 240
Period size: 80 Copynumber: 1.9 Consensus size: 81
39792 TAAAAGGAGT
* * * * *
39802 AAGGAAGTAAAAGTAGTAAATCAGTAAATCTGTAATTAAGAGTCAAGGTAAAGGGATTAATCAGT
1 AAGGAAGCAAAAGTAGTAAATCAGTAAATCAGTAATTAAGAGTCAAAGTAAAGAGATAAATCAGT
39867 AAATTCATAATTAAAA
66 AAATTCATAATTAAAA
*
39883 AAGGAAGCAAAAGTAGT-AATCAGTAGATCAGTAATTAAGAGTCAAAGTAAAGAGATAAATCAGT
1 AAGGAAGCAAAAGTAGTAAATCAGTAAATCAGTAATTAAGAGTCAAAGTAAAGAGATAAATCAGT
*
39947 AAATTGATAA
66 AAATTCATAA
39957 GAGGAAGTAA
Statistics
Matches: 67, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
80 51 0.76
81 16 0.24
ACGTcount: A:0.50, C:0.06, G:0.19, T:0.24
Consensus pattern (81 bp):
AAGGAAGCAAAAGTAGTAAATCAGTAAATCAGTAATTAAGAGTCAAAGTAAAGAGATAAATCAGT
AAATTCATAATTAAAA
Found at i:39999 original size:32 final size:32
Alignment explanation
Indices: 39909--40032 Score: 99
Period size: 32 Copynumber: 3.8 Consensus size: 32
39899 TAATCAGTAG
**** *
39909 ATCAGTAATTAAGAGTCAAAGT-AAAGAGATAA
1 ATCAGTAATTAAGAAAGGAAGTAAAAGAG-TTA
* * *
39941 ATCAGTAAATTGATAAGAGGAAGTAAAATTAG-TA
1 ATCAGT-AATTAAGAA-AGGAAGTAAAA-GAGTTA
*
39975 ATCAGTAATTAAGAAAGGAAGTAAAAGGGTTA
1 ATCAGTAATTAAGAAAGGAAGTAAAAGAGTTA
* *
40007 ATTAGCAATTAAGAAAGGAAGTAAAA
1 ATCAGTAATTAAGAAAGGAAGTAAAA
40033 AGGACTGATC
Statistics
Matches: 73, Mismatches: 14, Indels: 10
0.75 0.14 0.10
Matches are distributed among these distances:
31 1 0.01
32 43 0.59
33 13 0.18
34 11 0.15
35 3 0.04
36 2 0.03
ACGTcount: A:0.52, C:0.04, G:0.21, T:0.23
Consensus pattern (32 bp):
ATCAGTAATTAAGAAAGGAAGTAAAAGAGTTA
Found at i:40248 original size:35 final size:35
Alignment explanation
Indices: 40209--40393 Score: 194
Period size: 35 Copynumber: 5.5 Consensus size: 35
40199 GAGGAAAATG
*
40209 GTAAAGAGTAATCAGTAAAGAGAAAA-GAGAAAAAA
1 GTAAAGAGTAATCAGTAAAGAGAAAATG-GTAAAAA
*
40244 GTAAAGAGTAATCAGTAAAGAGGAAAATGGTAAAGA
1 GTAAAGAGTAATCAGTAAAGA-GAAAATGGTAAAAA
* *
40280 GTATAGAGTAATTAGTAAAGAGAAAA--G-----A
1 GTAAAGAGTAATCAGTAAAGAGAAAATGGTAAAAA
40308 GTAAAGAGTAATCAGT-AAGA-AAAATGGTAAAAA
1 GTAAAGAGTAATCAGTAAAGAGAAAATGGTAAAAA
* *
40341 GTAAAAAGTAATCAGTAAAG-GAAAAATGGTAAAGA
1 GTAAAGAGTAATCAGTAAAGAG-AAAATGGTAAAAA
* *
40376 GTAAAGAATAGTCAGTAA
1 GTAAAGAGTAATCAGTAA
40394 GGAGTAATTA
Statistics
Matches: 127, Mismatches: 11, Indels: 24
0.78 0.07 0.15
Matches are distributed among these distances:
26 4 0.03
27 4 0.03
28 16 0.13
33 17 0.13
34 3 0.02
35 53 0.42
36 29 0.23
37 1 0.01
ACGTcount: A:0.56, C:0.03, G:0.24, T:0.17
Consensus pattern (35 bp):
GTAAAGAGTAATCAGTAAAGAGAAAATGGTAAAAA
Found at i:40250 original size:64 final size:64
Alignment explanation
Indices: 40182--40379 Score: 262
Period size: 64 Copynumber: 3.1 Consensus size: 64
40172 GTAAGGGGTA
* ** *
40182 AAAGAGTAATCAGTAAAGAGGAAAATGGTAAAGAGTAATCAGTAAAGAGAAAAGAGAAAAAAGT
1 AAAGAGTAATCAGTAAAGAGGAAAATGGTAAAGAGTAATAAGTAATCAGTAAAGAGAAAAAAGT
* *
40246 AAAGAGTAATCAGTAAAGAGGAAAATGGTAAAGAGT-ATAGAGTAATTAGTAAAGAGAAAAGAGT
1 AAAGAGTAATCAGTAAAGAGGAAAATGGTAAAGAGTAATA-AGTAATCAGTAAAGAGAAAAAAGT
* * *
40310 AAAGAGTAATCAGT-AAGA--AAAATGGTAAAAAGTAAAAAGTAATCAGTAAAG-GAAAAATGGT
1 AAAGAGTAATCAGTAAAGAGGAAAATGGTAAAGAGTAATAAGTAATCAGTAAAGAGAAAAA-AGT
40371 AAAGAGTAA
1 AAAGAGTAA
40380 AGAATAGTCA
Statistics
Matches: 121, Mismatches: 10, Indels: 9
0.86 0.07 0.06
Matches are distributed among these distances:
60 5 0.04
61 38 0.31
62 2 0.02
63 6 0.05
64 70 0.58
ACGTcount: A:0.57, C:0.03, G:0.24, T:0.17
Consensus pattern (64 bp):
AAAGAGTAATCAGTAAAGAGGAAAATGGTAAAGAGTAATAAGTAATCAGTAAAGAGAAAAAAGT
Found at i:40253 original size:7 final size:7
Alignment explanation
Indices: 40182--40318 Score: 89
Period size: 7 Copynumber: 19.3 Consensus size: 7
40172 GTAAGGGGTA
40182 AAAGAGT
1 AAAGAGT
**
40189 AATCAGT
1 AAAGAGT
*
40196 AAAGAGG
1 AAAGAGT
40203 AAA-ATGGT
1 AAAGA--GT
40211 AAAGAGT
1 AAAGAGT
**
40218 AATCAGT
1 AAAGAGT
*
40225 AAAGAGA
1 AAAGAGT
*
40232 AAAGAGA
1 AAAGAGT
*
40239 AAAAAGT
1 AAAGAGT
40246 AAAGAGT
1 AAAGAGT
**
40253 AATCAGT
1 AAAGAGT
*
40260 AAAGAGG
1 AAAGAGT
40267 AAA-ATGGT
1 AAAGA--GT
40275 AAAGAGT
1 AAAGAGT
*
40282 ATAGAGT
1 AAAGAGT
**
40289 AATTAGT
1 AAAGAGT
*
40296 AAAGAGA
1 AAAGAGT
40303 AAAGAGT
1 AAAGAGT
40310 AAAGAGT
1 AAAGAGT
40317 AA
1 AA
40319 TCAGTAAGAA
Statistics
Matches: 96, Mismatches: 28, Indels: 12
0.71 0.21 0.09
Matches are distributed among these distances:
6 2 0.02
7 84 0.88
8 8 0.08
9 2 0.02
ACGTcount: A:0.56, C:0.02, G:0.26, T:0.16
Consensus pattern (7 bp):
AAAGAGT
Found at i:40465 original size:86 final size:85
Alignment explanation
Indices: 40307--40501 Score: 231
Period size: 86 Copynumber: 2.3 Consensus size: 85
40297 AAGAGAAAAG
* * * ** *
40307 AGTAAAGAGTAATCAGT-AAGA--AAAATGGTAAAAAGTAAAAAGTAATCAGTAAAGGAAAAATG
1 AGTAAGGAGTAATTAGTAAAGAGTAAAATGATAAAAAAAAAAAAGTAATCAGTAAAAGAAAAATG
*
40369 GTAAAGAGTAAAGAAT-AGTC
66 GTAAAAAGTAAAGAATGA-TC
*
40389 AGTAAGGAGTAATTAGTAAAGAGTAAAATGATAAAAAAAAAAAGAGTAATCAGTAAAAGAAGAAT
1 AGTAAGGAGTAATTAGTAAAGAGTAAAATGATAAAAAAAAAAA-AGTAATCAGTAAAAGAAAAAT
*
40454 GGTAAAAAGTAAAGAGTGATC
65 GGTAAAAAGTAAAGAATGATC
40475 AGTAAAGGAAG-AA-TAGTAAAGAGTAAA
1 AGT-AAGG-AGTAATTAGTAAAGAGTAAA
40502 GGGTAATCAG
Statistics
Matches: 97, Mismatches: 9, Indels: 10
0.84 0.08 0.09
Matches are distributed among these distances:
82 15 0.15
83 4 0.04
85 16 0.16
86 53 0.55
87 7 0.07
88 2 0.02
ACGTcount: A:0.57, C:0.03, G:0.23, T:0.18
Consensus pattern (85 bp):
AGTAAGGAGTAATTAGTAAAGAGTAAAATGATAAAAAAAAAAAAGTAATCAGTAAAAGAAAAATG
GTAAAAAGTAAAGAATGATC
Found at i:40466 original size:121 final size:119
Alignment explanation
Indices: 40310--40529 Score: 323
Period size: 121 Copynumber: 1.8 Consensus size: 119
40300 AGAAAAGAGT
*
40310 AAAGAGTAATCAGTAAGAAAAATGGTAAAAAGTAAAAAGTAATCAGTAAAGGAAAAATGGTAAAG
1 AAAGAGTAATCAGTAAGAAAAATGGTAAAAAGTAAAAAGTAATCAGTAAAGGAAAAATAGTAAAG
* * * *
40375 AGTAAAGAATAGTCAGTAAGGAGTAATTAGTAAAGAGTAAAATGATAAAAAAAA
66 AGTAAAGAATAATCAGTAAAGAGAAAATAGTAAAGAGTAAAATGATAAAAAAAA
* * * *
40429 AAAGAGTAATCAGTAAAAGAAGAATGGTAAAAAGTAAAGAGTGATCAGTAAAGGAAGAATAGTAA
1 AAAGAGTAATCAGT--AAGAAAAATGGTAAAAAGTAAAAAGTAATCAGTAAAGGAAAAATAGTAA
**
40494 AGAGTAAAGGGTAATCAGTAAAGAGAAAATAGTAAA
64 AGAGTAAAGAATAATCAGTAAAGAGAAAATAGTAAA
40530 AGGTAATCAG
Statistics
Matches: 88, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
119 14 0.16
121 74 0.84
ACGTcount: A:0.57, C:0.03, G:0.23, T:0.18
Consensus pattern (119 bp):
AAAGAGTAATCAGTAAGAAAAATGGTAAAAAGTAAAAAGTAATCAGTAAAGGAAAAATAGTAAAG
AGTAAAGAATAATCAGTAAAGAGAAAATAGTAAAGAGTAAAATGATAAAAAAAA
Found at i:40468 original size:35 final size:35
Alignment explanation
Indices: 40389--40535 Score: 147
Period size: 35 Copynumber: 4.1 Consensus size: 35
40379 AAGAATAGTC
* *
40389 AGTAAGGAGTAATTAGTAAAGAGTAAAAT-GATAAAAA
1 AGTAAAGAGTAATCAGTAAAGAG-AAAATAG-T-AAAA
** *
40426 AAAAAAGAGTAATCAGTAAA-AGAAGAATGGTAAAA
1 AGTAAAGAGTAATCAGTAAAGAGAA-AATAGTAAAA
* *
40461 AGTAAAGAGTGATCAGTAAAG-GAAGAATAGTAAAG
1 AGTAAAGAGTAATCAGTAAAGAGAA-AATAGTAAAA
*
40496 AGTAAAGGGTAATCAGTAAAGAGAAAATAGTAAAA
1 AGTAAAGAGTAATCAGTAAAGAGAAAATAGTAAAA
*
40531 GGTAA
1 AGTAA
40536 TCAGTAAAAA
Statistics
Matches: 93, Mismatches: 13, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
35 67 0.72
36 9 0.10
37 17 0.18
ACGTcount: A:0.56, C:0.02, G:0.24, T:0.18
Consensus pattern (35 bp):
AGTAAAGAGTAATCAGTAAAGAGAAAATAGTAAAA
Found at i:40513 original size:21 final size:21
Alignment explanation
Indices: 40489--40742 Score: 169
Period size: 21 Copynumber: 11.6 Consensus size: 21
40479 AAGGAAGAAT
*
40489 AGTAAAGAGTAAAGGGTAATC
1 AGTAAAGAGTAAATGGTAATC
*
40510 AGTAAAGAGAAAATAGTAAAAGGTAATC
1 AGTAAAGAG-------TAAATGGTAATC
* * *
40538 AGTAAAAAAT-AATGATAATC
1 AGTAAAGAGTAAATGGTAATC
*
40558 AGTAAATG-GTAAATTAGTAATC
1 AGTAAA-GAGTAAA-TGGTAATC
*
40580 AGT-AAGAGCAAAATGGTAATC
1 AGTAAAGAG-TAAATGGTAATC
* * *
40601 AGT-GAGGGCAAAATGGTAATC
1 AGTAAAGAG-TAAATGGTAATC
40622 AGTAAAGAGTAAAATGGTAATC
1 AGTAAAGAGT-AAATGGTAATC
* *
40644 AGTAAAAAGTAAGAAGGTAATC
1 AGTAAAGAGTAA-ATGGTAATC
*
40666 AGTAAAGAGTAAAATAGTAATC
1 AGTAAAGAGT-AAATGGTAATC
* *
40688 AGT-AAGAGCAAAATGGTAATT
1 AGTAAAGAG-TAAATGGTAATC
*
40709 AGT-AAGAGTAAAATAGTAATC
1 AGTAAAGAGT-AAATGGTAATC
*
40730 AATAAAGAGTAAA
1 AGTAAAGAGTAAA
40743 AGGTGATCGG
Statistics
Matches: 186, Mismatches: 28, Indels: 38
0.74 0.11 0.15
Matches are distributed among these distances:
20 16 0.09
21 82 0.44
22 68 0.37
23 2 0.01
28 18 0.10
ACGTcount: A:0.52, C:0.05, G:0.22, T:0.22
Consensus pattern (21 bp):
AGTAAAGAGTAAATGGTAATC
Found at i:40544 original size:14 final size:14
Alignment explanation
Indices: 40496--40544 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
40486 AATAGTAAAG
*
40496 AGTAAAGGGTAATC
1 AGTAAAAGGTAATC
**
40510 AGTAAAGAGAAAAT-
1 AGTAAA-AGGTAATC
40524 AGTAAAAGGTAATC
1 AGTAAAAGGTAATC
40538 AGTAAAA
1 AGTAAAA
40545 AATAATGATA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
13 5 0.18
14 19 0.68
15 4 0.14
ACGTcount: A:0.55, C:0.04, G:0.22, T:0.18
Consensus pattern (14 bp):
AGTAAAAGGTAATC
Found at i:40581 original size:22 final size:22
Alignment explanation
Indices: 40553--40743 Score: 196
Period size: 21 Copynumber: 8.9 Consensus size: 22
40543 AAAATAATGA
*
40553 TAATCAGTAAATG-GTAAATTAG
1 TAATCAGTAAA-GAGTAAAATAG
* *
40575 TAATCAGT-AAGAGCAAAATGG
1 TAATCAGTAAAGAGTAAAATAG
* * * *
40596 TAATCAGT-GAGGGCAAAATGG
1 TAATCAGTAAAGAGTAAAATAG
*
40617 TAATCAGTAAAGAGTAAAATGG
1 TAATCAGTAAAGAGTAAAATAG
* *
40639 TAATCAGTAAAAAGTAAGAA-GG
1 TAATCAGTAAAGAGTAA-AATAG
40661 TAATCAGTAAAGAGTAAAATAG
1 TAATCAGTAAAGAGTAAAATAG
* *
40683 TAATCAGT-AAGAGCAAAATGG
1 TAATCAGTAAAGAGTAAAATAG
*
40704 TAATTAGT-AAGAGTAAAATAG
1 TAATCAGTAAAGAGTAAAATAG
*
40725 TAATCAATAAAGAGTAAAA
1 TAATCAGTAAAGAGTAAAA
40744 GGTGATCGGT
Statistics
Matches: 146, Mismatches: 18, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
20 1 0.01
21 72 0.49
22 71 0.49
23 2 0.01
ACGTcount: A:0.50, C:0.06, G:0.21, T:0.23
Consensus pattern (22 bp):
TAATCAGTAAAGAGTAAAATAG
Found at i:40684 original size:108 final size:105
Alignment explanation
Indices: 40524--40746 Score: 315
Period size: 108 Copynumber: 2.1 Consensus size: 105
40514 AAGAGAAAAT
*
40524 AGTAAAAGGTAATCAGTAAAAAATAATGATAATCAGTAAATGGTAAATTAGTAATCAGTAAGAGC
1 AGTAAAAGGTAATCAGTAAAAAATAATGATAATCAGTAAATGGTAAAATAGTAATCAGTAAGAGC
* * * *
40589 AAAATGGTAATCAGTGAGGGCAAAATGGTAATCAGTAAAG
66 AAAATGGTAATCAGTAAGAGCAAAATAGTAATCAATAAAG
*
40629 AGTAAAATGGTAATCAGTAAAAAGTAA-GAAGGTAATCAGTAAA-GAGTAAAATAGTAATCAGTA
1 AGTAAAA-GGTAATCAGTAAAAAATAATG-A--TAATCAGTAAATG-GTAAAATAGTAATCAGTA
* *
40692 AGAGCAAAATGGTAATTAGTAAGAGTAAAATAGTAATCAATAAAG
61 AGAGCAAAATGGTAATCAGTAAGAGCAAAATAGTAATCAATAAAG
40737 AGTAAAAGGT
1 AGTAAAAGGT
40747 GATCGGTGAT
Statistics
Matches: 105, Mismatches: 8, Indels: 8
0.87 0.07 0.07
Matches are distributed among these distances:
105 8 0.08
106 19 0.18
107 4 0.04
108 74 0.70
ACGTcount: A:0.51, C:0.05, G:0.22, T:0.22
Consensus pattern (105 bp):
AGTAAAAGGTAATCAGTAAAAAATAATGATAATCAGTAAATGGTAAAATAGTAATCAGTAAGAGC
AAAATGGTAATCAGTAAGAGCAAAATAGTAATCAATAAAG
Found at i:42564 original size:50 final size:50
Alignment explanation
Indices: 42505--42606 Score: 186
Period size: 50 Copynumber: 2.0 Consensus size: 50
42495 GTTGAAGATG
* *
42505 CCACCTGGGAATGCTTGTTTACACCCCAGCAGAAATATCCTTTGTTCAAT
1 CCACCTGGGAATGCCTGTTTACACCCCAGCAGAAATATCCTCTGTTCAAT
42555 CCACCTGGGAATGCCTGTTTACACCCCAGCAGAAATATCCTCTGTTCAAT
1 CCACCTGGGAATGCCTGTTTACACCCCAGCAGAAATATCCTCTGTTCAAT
42605 CC
1 CC
42607 TTGAGGACAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.25, C:0.31, G:0.16, T:0.27
Consensus pattern (50 bp):
CCACCTGGGAATGCCTGTTTACACCCCAGCAGAAATATCCTCTGTTCAAT
Found at i:43268 original size:62 final size:62
Alignment explanation
Indices: 43167--43293 Score: 245
Period size: 62 Copynumber: 2.0 Consensus size: 62
43157 TATTATAATC
43167 AAACCTATCCAAGAAATGCAATCCCGCGGGCTGCATTCCTTACAGTTGTCCCTTAAAATTCA
1 AAACCTATCCAAGAAATGCAATCCCGCGGGCTGCATTCCTTACAGTTGTCCCTTAAAATTCA
*
43229 AAACCTATCCAAGAAATGCAATCCCGCGGGCTGCGTTCCTTACAGTTGTCCCTTAAAATTCA
1 AAACCTATCCAAGAAATGCAATCCCGCGGGCTGCATTCCTTACAGTTGTCCCTTAAAATTCA
43291 AAA
1 AAA
43294 TCCAAGCGGA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.25
Consensus pattern (62 bp):
AAACCTATCCAAGAAATGCAATCCCGCGGGCTGCATTCCTTACAGTTGTCCCTTAAAATTCA
Found at i:52217 original size:37 final size:39
Alignment explanation
Indices: 52165--52242 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 39
52155 TTATATGCTA
* * *
52165 GATCAACATACATGTCTTTTCATATAGACATAACTTTAT
1 GATCAACATACATGTCTTTCCAAATAGACATAACTGTAT
52204 GATCAA-A-ACATGTCTTTCCAAATAGACATAACTGTAT
1 GATCAACATACATGTCTTTCCAAATAGACATAACTGTAT
52241 GA
1 GA
52243 ATAATTAACA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 29 0.81
38 1 0.03
39 6 0.17
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.33
Consensus pattern (39 bp):
GATCAACATACATGTCTTTCCAAATAGACATAACTGTAT
Found at i:54967 original size:30 final size:31
Alignment explanation
Indices: 54913--54977 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
54903 AACTTTATGT
* * *
54913 TTTCCGATTATACCCTTATTTTTAAAATATA
1 TTTCCAATTATACCCCTATTTTTAAAACATA
*
54944 TTTCCAATTGTACCCCT-TTTTTAAAACATA
1 TTTCCAATTATACCCCTATTTTTAAAACATA
54974 TTTC
1 TTTC
54978 TAAATTGTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 16 0.53
31 14 0.47
ACGTcount: A:0.29, C:0.20, G:0.03, T:0.48
Consensus pattern (31 bp):
TTTCCAATTATACCCCTATTTTTAAAACATA
Found at i:57369 original size:27 final size:26
Alignment explanation
Indices: 57311--57361 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
57301 CTTAAGATGT
*
57311 TAAAATTACATATTTGCCCCTGACAG
1 TAAAATTACATATTTGCCCCTAACAG
57337 TGAAAATTACAGT-TTTGCCCCTAAC
1 T-AAAATTACA-TATTTGCCCCTAAC
57362 GGCTAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 1 0.05
27 20 0.91
28 1 0.05
ACGTcount: A:0.33, C:0.24, G:0.12, T:0.31
Consensus pattern (26 bp):
TAAAATTACATATTTGCCCCTAACAG
Found at i:58276 original size:16 final size:17
Alignment explanation
Indices: 58244--58278 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
58234 TTACTAATTG
58244 TTTTATTATAACTTGTT
1 TTTTATTATAACTTGTT
*
58261 TTTTTTTATAAC-TGTT
1 TTTTATTATAACTTGTT
58277 TT
1 TT
58279 GGTTGTGAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.20, C:0.06, G:0.06, T:0.69
Consensus pattern (17 bp):
TTTTATTATAACTTGTT
Found at i:60287 original size:196 final size:198
Alignment explanation
Indices: 59871--60620 Score: 960
Period size: 198 Copynumber: 3.8 Consensus size: 198
59861 AATCACTTTA
* * * *
59871 TATAATCTTTCTTATAGGATTATTATATAATACACTTTTCAGTGTAAATTTTACACTCC-TAAGC
1 TATAATTTTTCTTATAGGATTATTATACAATACAC-TGTCAGTGTAAATTTTAGACTCCATAAGC
*
59935 GGGTTAAGAAGTTGACACATACCCCATTTCATAATCAATTAAATATTTAATATTAATACATATTC
65 GGGTTAAGAAGTTGA-ACATACCTCATTTCATAATCAATTAAATATTTAATATTAATACATATTC
** * * * * * **
60000 ATTAA-GGGACACATGTCAACCTTTAAACCCTGCACATGCAATCTGCT-AAATCGACTGACATTG
129 CCTAAGGGGACACATGTCAACCCTTAAACCCGGCACGTGCAGTCTGCTAAAATCCACTGACGGTG
60063 TATAG
194 TATAG
* * * *
60068 TATAATTTTTCTTATAAGATTATTATACAATCCACTGTCAGTATAAATTTTGGACTCCATAAGCG
1 TATAATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAATTTTAGACTCCATAAGCG
* *
60133 GGTTAAGAAGTTG-ACATACC-CATTTCATAATTAATTCAATATTTAATATTAATACAATATTCC
66 GGTTAAGAAGTTGAACATACCTCATTTCATAATCAATTAAATATTTAATATTAATAC-ATATTCC
* *
60196 CTAAGGGGACACATGTCAACCCTTAAACCTC-GCACGTGCTGTTTGCTAAAATCCACTGACGGTG
130 CTAAGGGGACACATGTCAACCCTTAAACC-CGGCACGTGCAGTCTGCTAAAATCCACTGACGGTG
60260 TATTA-
194 TA-TAG
* * * * * * * *
60265 TATAATTTTT-TTATATGATTATTATACAACACGCTGTCAATTTGAATTTTAAACTCTATAAGCG
1 TATAATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAATTTTAGACTCCATAAGCG
* **
60329 GGTTAAGAAGTTGACACATACCTCATTTCATCATCAATTAAATAGATAATATTAATACATATTCC
66 GGTTAAGAAGTTGA-ACATACCTCATTTCATAATCAATTAAATATTTAATATTAATACATATTCC
* * * *
60394 CTAAAGGAACACATGTCAACCC-TAAACCCGGCACGTGCAGTCTGCTAAACTCCACTTACGGTGT
130 CTAAGGGGACACATGTCAACCCTTAAACCCGGCACGTGCAGTCTGCTAAAATCCACTGACGGTGT
60458 ATAG
195 ATAG
* * * * *
60462 TATAATTTTTCTTATAGGATTATTATACAATAAACTTTCAGTGTAAATTTTGGTCTCCATAAGCT
1 TATAATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAATTTTAGACTCCATAAGCG
* *
60527 GGTTAAGAAGTTGACACATACCTCATTTCATAATTAATTAAATATTTAATATTAATACATATTTC
66 GGTTAAGAAGTTGA-ACATACCTCATTTCATAATCAATTAAATATTTAATATTAATACATATTCC
* *
60592 TTAAGGGGCCACATGTCAACCCTTAAACC
130 CTAAGGGGACACATGTCAACCCTTAAACC
Statistics
Matches: 477, Mismatches: 63, Indels: 24
0.85 0.11 0.04
Matches are distributed among these distances:
194 33 0.07
195 16 0.03
196 114 0.24
197 123 0.26
198 155 0.32
199 36 0.08
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (198 bp):
TATAATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAATTTTAGACTCCATAAGCG
GGTTAAGAAGTTGAACATACCTCATTTCATAATCAATTAAATATTTAATATTAATACATATTCCC
TAAGGGGACACATGTCAACCCTTAAACCCGGCACGTGCAGTCTGCTAAAATCCACTGACGGTGTA
TAG
Done.