Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010616.1 Corchorus capsularis cultivar CVL-1 contig10637, 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: 83192
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:310 original size:32 final size:32
Alignment explanation
Indices: 269--363 Score: 100
Period size: 32 Copynumber: 3.0 Consensus size: 32
259 GGTAATGGTA
* *
269 TGATCCTGAATTCTAAATTCTGATTTCTGATT
1 TGATTCTGAATTCTAAATTCTGATTTATGATT
* * * * *
301 TGATTCTGAATTCTAAGTTCTAACTTATAACT
1 TGATTCTGAATTCTAAATTCTGATTTATGATT
* * *
333 TGTTTCTGAATTCTAATTTCTGATTTGTGAT
1 TGATTCTGAATTCTAAATTCTGATTTATGAT
364 GTGAAGTCAT
Statistics
Matches: 49, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.25, C:0.14, G:0.13, T:0.48
Consensus pattern (32 bp):
TGATTCTGAATTCTAAATTCTGATTTATGATT
Found at i:409 original size:19 final size:19
Alignment explanation
Indices: 385--447 Score: 73
Period size: 19 Copynumber: 3.6 Consensus size: 19
375 AACTTATGCT
385 AATTCTGATTTGTGAAGTG
1 AATTCTGATTTGTGAAGTG
*
404 AATTCTGATTTCTG-A-T-
1 AATTCTGATTTGTGAAGTG
420 --TTCTGATTTGTGAAGTG
1 AATTCTGATTTGTGAAGTG
*
437 AATTCTAATTT
1 AATTCTGATTT
448 CTGATTTGTG
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
14 11 0.31
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 21 0.58
ACGTcount: A:0.25, C:0.08, G:0.19, T:0.48
Consensus pattern (19 bp):
AATTCTGATTTGTGAAGTG
Found at i:429 original size:33 final size:33
Alignment explanation
Indices: 387--515 Score: 133
Period size: 33 Copynumber: 4.0 Consensus size: 33
377 CTTATGCTAA
387 TTCTGATTTGTGAAGTGAATTCTGATTTCTGAT
1 TTCTGATTTGTGAAGTGAATTCTGATTTCTGAT
*
420 TTCTGATTTGTGAAGTGAATTCTAATTTCTGAT
1 TTCTGATTTGTGAAGTGAATTCTGATTTCTGAT
* * * * * *
453 TTGTGA--AGTGAAGT-CATTAACTTA-TGCT-AA
1 TTCTGATTTGTGAAGTGAATT--CTGATTTCTGAT
*
483 TTCTGATTTGTGAAGTGAATTCTGAATTCTGAT
1 TTCTGATTTGTGAAGTGAATTCTGATTTCTGAT
516 GCATTTGCTT
Statistics
Matches: 76, Mismatches: 13, Indels: 14
0.74 0.13 0.14
Matches are distributed among these distances:
30 9 0.12
31 13 0.17
32 13 0.17
33 41 0.54
ACGTcount: A:0.26, C:0.09, G:0.20, T:0.45
Consensus pattern (33 bp):
TTCTGATTTGTGAAGTGAATTCTGATTTCTGAT
Found at i:442 original size:26 final size:26
Alignment explanation
Indices: 413--464 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
403 GAATTCTGAT
*
413 TTCTGATTTCTGATTTGTGAAGTGAA
1 TTCTAATTTCTGATTTGTGAAGTGAA
439 TTCTAATTTCTGATTTGTGAAGTGAA
1 TTCTAATTTCTGATTTGTGAAGTGAA
465 GTCATTAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.25, C:0.08, G:0.21, T:0.46
Consensus pattern (26 bp):
TTCTAATTTCTGATTTGTGAAGTGAA
Found at i:453 original size:96 final size:96
Alignment explanation
Indices: 339--515 Score: 336
Period size: 96 Copynumber: 1.8 Consensus size: 96
329 AACTTGTTTC
*
339 TGAATTCTAATTTCTGATTTGTGATGTGAAGTCATTAACTTATGCTAATTCTGATTTGTGAAGTG
1 TGAATTCTAATTTCTGATTTGTGAAGTGAAGTCATTAACTTATGCTAATTCTGATTTGTGAAGTG
*
404 AATTCTGATTTCTGATTTCTGATTTGTGAAG
66 AATTCTGAATTCTGATTTCTGATTTGTGAAG
435 TGAATTCTAATTTCTGATTTGTGAAGTGAAGTCATTAACTTATGCTAATTCTGATTTGTGAAGTG
1 TGAATTCTAATTTCTGATTTGTGAAGTGAAGTCATTAACTTATGCTAATTCTGATTTGTGAAGTG
500 AATTCTGAATTCTGAT
66 AATTCTGAATTCTGAT
516 GCATTTGCTT
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
96 79 1.00
ACGTcount: A:0.27, C:0.10, G:0.19, T:0.45
Consensus pattern (96 bp):
TGAATTCTAATTTCTGATTTGTGAAGTGAAGTCATTAACTTATGCTAATTCTGATTTGTGAAGTG
AATTCTGAATTCTGATTTCTGATTTGTGAAG
Found at i:2390 original size:2 final size:2
Alignment explanation
Indices: 2383--2412 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2373 ATATTCAAGA
2383 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2413 CTCATAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3813 original size:19 final size:18
Alignment explanation
Indices: 3784--3819 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
3774 TTTAAAAGAA
*
3784 CAAATAAATTCTTGAAAG
1 CAAATAAATTCTAGAAAG
3802 CAAATCAAATTCTAGAAA
1 CAAAT-AAATTCTAGAAA
3820 CTGATATAAA
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:0.53, C:0.14, G:0.08, T:0.25
Consensus pattern (18 bp):
CAAATAAATTCTAGAAAG
Found at i:8754 original size:16 final size:16
Alignment explanation
Indices: 8733--8763 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
8723 CCTTACAGTT
*
8733 ATCTGTATATGAAGTA
1 ATCTGTAAATGAAGTA
8749 ATCTGTAAATGAAGT
1 ATCTGTAAATGAAGT
8764 TGTATTTTGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.35
Consensus pattern (16 bp):
ATCTGTAAATGAAGTA
Found at i:12366 original size:22 final size:21
Alignment explanation
Indices: 12341--12404 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 21
12331 ACTATTTCTT
*
12341 ATAACGTCCTTATGAAATTTTG
1 ATAACGTCC-TATGAAATTTTA
*
12363 ATAATCTTCCTATGAAATTTTA
1 ATAA-CGTCCTATGAAATTTTA
* *
12385 ATAACGATACTATGGAATTT
1 ATAACG-TCCTATGAAATTT
12405 CGAGAACCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 1 0.03
22 30 0.86
23 4 0.11
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.41
Consensus pattern (21 bp):
ATAACGTCCTATGAAATTTTA
Found at i:12373 original size:60 final size:60
Alignment explanation
Indices: 12229--12373 Score: 193
Period size: 60 Copynumber: 2.4 Consensus size: 60
12219 GAAATATTCA
* * * * *
12229 TACGAAATTGTGATAATCTTCCCATTAAATTATGATAATTATACTATTTTTTATGACGTCCT
1 TACGAAATTTTGATAATCTT-CC-TGAAATTATGATAATTACACTATTTCTTATAACGTCCT
*
12291 TACAAAATTTTGATAA-CATTCCTGAAATTATGATAATTACACTATTTCTTATAACGTCCT
1 TACGAAATTTTGATAATC-TTCCTGAAATTATGATAATTACACTATTTCTTATAACGTCCT
*
12351 TATGAAATTTTGATAATCTTCCT
1 TACGAAATTTTGATAATCTTCCT
12374 ATGAAATTTT
Statistics
Matches: 73, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
60 53 0.73
61 4 0.05
62 16 0.22
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.43
Consensus pattern (60 bp):
TACGAAATTTTGATAATCTTCCTGAAATTATGATAATTACACTATTTCTTATAACGTCCT
Found at i:12452 original size:22 final size:22
Alignment explanation
Indices: 12349--12888 Score: 161
Period size: 22 Copynumber: 24.8 Consensus size: 22
12339 TTATAACGTC
*
12349 CTTATGAAATTTTGATAATCTT
1 CTTATGAAATTTTGATAACCTT
* * * *
12371 CCTATGAAATTTTAATAACGATA
1 CTTATGAAATTTTGATAAC-CTT
* * *
12394 C-TATGGAATTTCGAGAACCTT
1 CTTATGAAATTTTGATAACCTT
* **
12415 TTTAT--AATTTTTTTAACCTT
1 CTTATGAAATTTTGATAACCTT
* *
12435 CTTATGAAATTTTGTTAACCTC
1 CTTATGAAATTTTGATAACCTT
* * * *
12457 CCTAAGGAATTTTGA-AGATC-T
1 CTTATGAAATTTTGATA-ACCTT
* **
12478 CACTATGAAATTTTGATAACCAA
1 C-TTATGAAATTTTGATAACCTT
* *
12501 CATTAT-AAGATGTTGATAACCTC
1 C-TTATGAA-ATTTTGATAACCTT
* * **
12524 CATAT-AATATATTGATAACAAT
1 CTTATGAA-ATTTTGATAACCTT
* * * * *
12546 GTTATGAAAATTTAAAAACCTC
1 CTTATGAAATTTTGATAACCTT
* * * *
12568 CATATG-AATTGTCAGTAATCAC-A
1 CTTATGAAATTTTGA-TAA-C-CTT
* * *
12591 C-TCTGAAATTTTGATAATC-A
1 CTTATGAAATTTTGATAACCTT
*
12611 CGTTATGAAATTGTGATAACC-T
1 C-TTATGAAATTTTGATAACCTT
* * *
12633 CGCTATGGAATTTTGATAAATCTT
1 C-TTATGAAATTTTGAT-AACCTT
* * * *
12657 CCTATAAAATTTTGATAAATCTC
1 CTTATGAAATTTTGAT-AACCTT
* * *
12680 CCTATAAAATTTTGATAACCTC
1 CTTATGAAATTTTGATAACCTT
* *
12702 CTTATGGAATCTTGATAA----
1 CTTATGAAATTTTGATAACCTT
* *
12720 C-TA-CAAATTTTGATAACCTC
1 CTTATGAAATTTTGATAACCTT
* **
12740 CCTATGATTTTTTGATAACC-T
1 CTTATGAAATTTTGATAACCTT
* * *
12761 CATTATGAAATTTTGTTAATCTC
1 C-TTATGAAATTTTGATAACCTT
* * * *
12784 CCTATGAAATTTTGATCTACATA
1 CTTATGAAATTTTGAT-AACCTT
*
12807 C-TATGAAATTTTGATAACCCT
1 CTTATGAAATTTTGATAACCTT
* *
12828 CTTATGAAATTTTGA-AAACTAAA
1 CTTATGAAATTTTGATAACCT--T
*
12851 C-TATGAAATTTTAATAACCTT
1 CTTATGAAATTTTGATAACCTT
*
12872 CATATGAAATTTTGATA
1 CTTATGAAATTTTGATA
12889 TCCTCCCTGA
Statistics
Matches: 381, Mismatches: 105, Indels: 64
0.69 0.19 0.12
Matches are distributed among these distances:
16 10 0.03
17 2 0.01
18 1 0.00
20 19 0.05
21 18 0.05
22 251 0.66
23 77 0.20
24 3 0.01
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (22 bp):
CTTATGAAATTTTGATAACCTT
Found at i:12667 original size:23 final size:23
Alignment explanation
Indices: 12641--12697 Score: 105
Period size: 23 Copynumber: 2.5 Consensus size: 23
12631 CTCGCTATGG
*
12641 AATTTTGATAAATCTTCCTATAA
1 AATTTTGATAAATCTCCCTATAA
12664 AATTTTGATAAATCTCCCTATAA
1 AATTTTGATAAATCTCCCTATAA
12687 AATTTTGATAA
1 AATTTTGATAA
12698 CCTCCTTATG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.42
Consensus pattern (23 bp):
AATTTTGATAAATCTCCCTATAA
Found at i:13062 original size:22 final size:22
Alignment explanation
Indices: 13019--13066 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
13009 ATTTTGAAAA
* *
13019 TTTGATAACCTCTTTATGAAAT
1 TTTGATAACCTCTCTATCAAAT
13041 TTTGATAACCTCTCTATCAAAT
1 TTTGATAACCTCTCTATCAAAT
13063 TTTG
1 TTTG
13067 TTGTCCAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.29, C:0.17, G:0.08, T:0.46
Consensus pattern (22 bp):
TTTGATAACCTCTCTATCAAAT
Found at i:13272 original size:37 final size:38
Alignment explanation
Indices: 13192--13278 Score: 113
Period size: 38 Copynumber: 2.3 Consensus size: 38
13182 CAAATAGATC
* *
13192 ATTGGAGACGAAGACAAAAAGCAAAATTAAATACAACG
1 ATTGGAAACAAAGACAAAAAGCAAAATTAAATACAACG
* * **
13230 ATTGGAAACAAAGATAAAAGGCAAAATTAAATAGGACG
1 ATTGGAAACAAAGACAAAAAGCAAAATTAAATACAACG
13268 -TTGGAAACAAA
1 ATTGGAAACAAA
13279 AAGCCAAATT
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
37 11 0.26
38 32 0.74
ACGTcount: A:0.55, C:0.10, G:0.20, T:0.15
Consensus pattern (38 bp):
ATTGGAAACAAAGACAAAAAGCAAAATTAAATACAACG
Found at i:13446 original size:30 final size:32
Alignment explanation
Indices: 13401--13466 Score: 100
Period size: 31 Copynumber: 2.1 Consensus size: 32
13391 TGGCGATTTA
* *
13401 GAAATATGTTTTTAAAAA-AAGGGTACAATTG
1 GAAATATGTTTTTAAAAATAAGGATACAATCG
13432 GAAATATG-TTTTAAAAATAAGGATACAATCG
1 GAAATATGTTTTTAAAAATAAGGATACAATCG
13463 GAAA
1 GAAA
13467 ACATAAAGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 9 0.28
31 23 0.72
ACGTcount: A:0.48, C:0.05, G:0.18, T:0.29
Consensus pattern (32 bp):
GAAATATGTTTTTAAAAATAAGGATACAATCG
Found at i:15386 original size:22 final size:22
Alignment explanation
Indices: 15361--15944 Score: 244
Period size: 22 Copynumber: 26.7 Consensus size: 22
15351 ATGATCCCAT
15361 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* *** *
15383 TATGAAATTTTAATAATGATAC
1 TATGAAATTTTGATAACCTTCC
* * * **
15405 TATGGAATTTCGAGAACCTTTT
1 TATGAAATTTTGATAACCTTCC
** *
15427 TAT-AAATTTTTTTAACCTTCT
1 TATGAAATTTTGATAACCTTCC
* * *
15448 TATGAAATTTTGTTACCCTCCC
1 TATGAAATTTTGATAACCTTCC
* * *
15470 TAAGGAATTTTGA-AGACC-TCAA
1 TATGAAATTTTGATA-ACCTTC-C
15492 TATGAAATTTTGATAA-CTTCC
1 TATGAAATTTTGATAACCTTCC
**
15513 TAATGAAATTTTGATAACCAACAC
1 T-ATGAAATTTTGATAACCTTC-C
* *
15537 TATGAGATGTTGATAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* * *
15558 ATATGATATATTGATAACC-ACGC
1 -TATGAAATTTTGATAACCTTC-C
*
15581 TATGAAAATTTT-AAAACC-TCC
1 TATG-AAATTTTGATAACCTTCC
* *
15602 ATATG-AATTGTT-AGTAATC-ACAC
1 -TATGAAATT-TTGA-TAACCTTC-C
* * * *
15625 TCTGAAATTTTGATAATCATAC
1 TATGAAATTTTGATAACCTTCC
15647 TATGAAATTGTGGTGATAACC-TCGC
1 TATGAAATT-T--TGATAACCTTC-C
*
15672 TATGAAATTTTGATAAATCTTCC
1 TATGAAATTTTGAT-AACCTTCC
* ** *
15695 TATAAAATTTTGATAAAAATCCC
1 TATGAAATTTTGAT-AACCTTCC
* * * *
15718 TATAAAATTTTGTTAACTTTCT
1 TATGAAATTTTGATAACCTTCC
*
15740 TATGAAATCTTGATAA-----C
1 TATGAAATTTTGATAACCTTCC
*
15757 TA-CAAATTTTGATAACC-TCTC
1 TATGAAATTTTGATAACCTTC-C
** *
15778 TATGATTTTTTGATAACC-TCAT
1 TATGAAATTTTGATAACCTTC-C
* * *
15800 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTTCC
* * * *
15822 TATGAGATTTTGATCTA-CATAC
1 TATGAAATTTTGAT-AACCTTCC
* *
15844 TATGAAATTTTGATAACCCTCT
1 TATGAAATTTTGATAACCTTCC
* * **
15866 TATAAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-TCC
*
15888 TATGAAATTTTGATAACCTTCA
1 TATGAAATTTTGATAACCTTCC
*
15910 TATGAAATTTTGATATCC-TCC
1 TATGAAATTTTGATAACCTTCC
*
15931 -CTGAAATTTTGATA
1 TATGAAATTTTGATA
15945 TCCTCTCTGA
Statistics
Matches: 421, Mismatches: 106, Indels: 72
0.70 0.18 0.12
Matches are distributed among these distances:
16 11 0.03
17 2 0.00
20 17 0.04
21 33 0.08
22 262 0.62
23 73 0.17
24 6 0.01
25 17 0.04
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:15702 original size:23 final size:22
Alignment explanation
Indices: 15671--15755 Score: 80
Period size: 23 Copynumber: 3.8 Consensus size: 22
15661 GATAACCTCG
*
15671 CTATGAAATTTTGATAAATCTTC
1 CTATAAAATTTTGATAAAT-TTC
* *
15694 CTATAAAATTTTGATAAAAATCC
1 CTATAAAATTTTGAT-AAATTTC
* *
15717 CTATAAAATTTTGTTAACTTTC
1 CTATAAAATTTTGATAAATTTC
* * *
15739 TTATGAAATCTTGATAA
1 CTATAAAATTTTGATAA
15756 CTACAAATTT
Statistics
Matches: 50, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
22 17 0.34
23 30 0.60
24 3 0.06
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42
Consensus pattern (22 bp):
CTATAAAATTTTGATAAATTTC
Found at i:15937 original size:20 final size:20
Alignment explanation
Indices: 15912--15955 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
15902 AACCTTCATA
15912 TGAAATTTTGATATCCTCCC
1 TGAAATTTTGATATCCTCCC
*
15932 TGAAATTTTGATATCCTCTC
1 TGAAATTTTGATATCCTCCC
15952 TGAA
1 TGAA
15956 TTTATTACTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.41
Consensus pattern (20 bp):
TGAAATTTTGATATCCTCCC
Found at i:17435 original size:22 final size:22
Alignment explanation
Indices: 17410--17644 Score: 126
Period size: 22 Copynumber: 10.8 Consensus size: 22
17400 ACTTATCAAC
17410 AACCTCTTTATGAAATTTTGAT
1 AACCTCTTTATGAAATTTTGAT
*
17432 AACCTCTTTATGAAATTTTGTT
1 AACCTCTTTATGAAATTTTGAT
* * * **
17454 GATCC-CTCTATGAAACTCAGAT
1 -AACCTCTTTATGAAATTTTGAT
* * * * *
17476 AATCACATTATGTAACTTTGAT
1 AACCTCTTTATGAAATTTTGAT
*
17498 AACCTCGCTT-TGAAATTTTGAT
1 AACCTC-TTTATGAAATTTTGAT
** **
17520 AACAACACTATGAAATTTTGAT
1 AACCTCTTTATGAAATTTTGAT
*
17542 AATCT-TCTTAT-AAATTTTGAT
1 AACCTCT-TTATGAAATTTTGAT
* *
17563 AATCTGATCTTTATGAAATTTCGAT
1 AA-C--CTCTTTATGAAATTTTGAT
* * * *
17588 AATCACTCTATGAGA-TTTGAT
1 AACCTCTTTATGAAATTTTGAT
* *
17609 AACCT-TCTATCAAATTTTGAT
1 AACCTCTTTATGAAATTTTGAT
*
17630 -A-CTCCTTATGAAATT
1 AACCTCTTTATGAAATT
17645 GAGACTTTTA
Statistics
Matches: 157, Mismatches: 44, Indels: 26
0.69 0.19 0.11
Matches are distributed among these distances:
19 2 0.01
20 16 0.10
21 29 0.18
22 88 0.56
23 5 0.03
24 5 0.03
25 12 0.08
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (22 bp):
AACCTCTTTATGAAATTTTGAT
Found at i:17679 original size:22 final size:23
Alignment explanation
Indices: 17669--17760 Score: 70
Period size: 22 Copynumber: 4.2 Consensus size: 23
17659 CTTCATATGG
17669 AATTTTGATAACC-ACACTATAA
1 AATTTTGATAACCTACACTATAA
* *
17691 AATTTTGATAACCT-CCCCATAA
1 AATTTTGATAACCTACACTATAA
* *
17713 AATATT-AGTAACCT-C-CTAATGA
1 AATTTTGA-TAACCTACACT-ATAA
* *
17735 AATTTTGTTAACC-ACACTATGA
1 AATTTTGATAACCTACACTATAA
17757 AATT
1 AATT
17761 CTTATAATCT
Statistics
Matches: 57, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
21 2 0.04
22 53 0.93
23 2 0.04
ACGTcount: A:0.40, C:0.20, G:0.07, T:0.34
Consensus pattern (23 bp):
AATTTTGATAACCTACACTATAA
Found at i:17776 original size:22 final size:22
Alignment explanation
Indices: 17664--17792 Score: 66
Period size: 22 Copynumber: 5.9 Consensus size: 22
17654 ATAACCTTCA
* * * *
17664 TATGGAATTTTGATAACCACAC
1 TATGAAATTTTGATAATCTCGC
* * *
17686 TATAAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAATCTCGC
* * * *
17708 CATAAAATATT-AGTAACCTC-C
1 TATGAAATTTTGA-TAATCTCGC
* * * *
17729 TAATGAAATTTTGTTAACCACAC
1 T-ATGAAATTTTGATAATCTCGC
17752 TATGAAATTCTT-ATAATCTCGC
1 TATGAAATT-TTGATAATCTCGC
*
17774 TATGACATTTTGATAATCT
1 TATGAAATTTTGATAATCT
17793 TTTTAATAAT
Statistics
Matches: 85, Mismatches: 16, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
21 4 0.05
22 77 0.91
23 4 0.05
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.36
Consensus pattern (22 bp):
TATGAAATTTTGATAATCTCGC
Found at i:17889 original size:24 final size:22
Alignment explanation
Indices: 17825--17986 Score: 89
Period size: 22 Copynumber: 7.3 Consensus size: 22
17815 TTGTGATAAT
*
17825 TAACC-ACCTTATGAAATTTCAA
1 TAACCAACC-TATGAAATTTTAA
*
17847 TAACCAACCTAAGAAATTTTAA
1 TAACCAACCTATGAAATTTTAA
* * **
17869 TAACCTGATCGTATGAAATTTTGG
1 TAACC--AACCTATGAAATTTTAA
***
17893 TAACC-ACACTATGAAATTTCGG
1 TAACCAAC-CTATGAAATTTTAA
*
17915 TAACC-ACACTATGAAATTTTGA
1 TAACCAAC-CTATGAAATTTTAA
* * *
17937 TAACC-GCCTCATGGAATTATAA
1 TAACCAACCT-ATGAAATTTTAA
* * * *
17959 TAACCATCTTTTGAAATTTTGA
1 TAACCAACCTATGAAATTTTAA
17981 TAACCA
1 TAACCA
17987 CATAGAGACA
Statistics
Matches: 112, Mismatches: 22, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
21 3 0.03
22 87 0.78
23 5 0.04
24 17 0.15
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.32
Consensus pattern (22 bp):
TAACCAACCTATGAAATTTTAA
Found at i:17908 original size:22 final size:22
Alignment explanation
Indices: 17880--17941 Score: 106
Period size: 22 Copynumber: 2.8 Consensus size: 22
17870 AACCTGATCG
17880 TATGAAATTTTGGTAACCACAC
1 TATGAAATTTTGGTAACCACAC
*
17902 TATGAAATTTCGGTAACCACAC
1 TATGAAATTTTGGTAACCACAC
*
17924 TATGAAATTTTGATAACC
1 TATGAAATTTTGGTAACC
17942 GCCTCATGGA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (22 bp):
TATGAAATTTTGGTAACCACAC
Found at i:18089 original size:178 final size:178
Alignment explanation
Indices: 17888--18243 Score: 662
Period size: 178 Copynumber: 2.0 Consensus size: 178
17878 CGTATGAAAT
17888 TTTGGTAACCACACTATGAAATTTCGGTAACCACACTATGAAATTTTGATAACCGCCTCATGGAA
1 TTTGGTAACCACACTATGAAATTTCGGTAACCACACTATGAAATTTTGATAACCGCCTCATGGAA
*
17953 TTATAATAACCATCTTTTGAAATTTTGATAACCACATAGAGACAAGAAAATCAAAATCATAATAG
66 TTATAATAACCATCTTATGAAATTTTGATAACCACATAGAGACAAGAAAATCAAAATCATAATAG
18018 CATCTACTCTTCTAACTCAACAA-TTTCCAATTGAAC-AAAGTGAATGCG
131 CATCTACTCTTCT-ACTCAACAATTTTCC-ATTGAACAAAAGTGAATGCG
18066 TTTGGTAACCACACTATGAAATTTCGGTAACCACACTATGAAATTTTGATAACCGCCTCATGGAA
1 TTTGGTAACCACACTATGAAATTTCGGTAACCACACTATGAAATTTTGATAACCGCCTCATGGAA
*
18131 TTATAATAACCATCTTATGAAATTTTGATAACCACATAGAGACAAGAAAATCAAGATCATAATAG
66 TTATAATAACCATCTTATGAAATTTTGATAACCACATAGAGACAAGAAAATCAAAATCATAATAG
18196 CATCTACTCTTCTACTCAACAATTTTCCATTGAACAAAAGTGAATGCG
131 CATCTACTCTTCTACTCAACAATTTTCCATTGAACAAAAGTGAATGCG
18244 GCAAAACATT
Statistics
Matches: 174, Mismatches: 2, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
177 16 0.09
178 158 0.91
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.29
Consensus pattern (178 bp):
TTTGGTAACCACACTATGAAATTTCGGTAACCACACTATGAAATTTTGATAACCGCCTCATGGAA
TTATAATAACCATCTTATGAAATTTTGATAACCACATAGAGACAAGAAAATCAAAATCATAATAG
CATCTACTCTTCTACTCAACAATTTTCCATTGAACAAAAGTGAATGCG
Found at i:18118 original size:22 final size:22
Alignment explanation
Indices: 18066--18166 Score: 98
Period size: 22 Copynumber: 4.6 Consensus size: 22
18056 AGTGAATGCG
*
18066 TTTGGTAACCACACTATGAAAT
1 TTTGATAACCACACTATGAAAT
* *
18088 TTCGGTAACCACACTATGAAAT
1 TTTGATAACCACACTATGAAAT
* *
18110 TTTGATAACCGC-CTCATGGAAT
1 TTTGATAACCACACT-ATGAAAT
* * *
18132 TATAATAACCATC-TTATGAAAT
1 TTTGATAACCA-CACTATGAAAT
18154 TTTGATAACCACA
1 TTTGATAACCACA
18167 TAGAGACAAG
Statistics
Matches: 64, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
21 3 0.05
22 59 0.92
23 2 0.03
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.32
Consensus pattern (22 bp):
TTTGATAACCACACTATGAAAT
Found at i:18596 original size:119 final size:119
Alignment explanation
Indices: 18416--18651 Score: 325
Period size: 118 Copynumber: 2.0 Consensus size: 119
18406 CAATTTGACA
* *
18416 AACTTATAATTCGGTTTAAATTGAAATTTTTAATTAATTTTTAAATAATAAATAATAATAA-T-A
1 AACTTATAATTCGATCTAAATTGAAATTTTTAATTAATTTTTAAATAATAAATAATAATAAGTCA
* * *
18479 ATTTAGAAATATATTTGGAAAAAAGGATGCAATCGGAAAACATAAAGT-TTCCCAT
66 ATTTAGAAATATAATT-G-AAAAAGGATACAATCGGAAAACAAAAAGTGTTCCCAT
* **
18534 AACTTATAATTCGATCTAAATTGAAATTTTATAATTAATTTTTAAGTAATAAATTTTAATAATGT
1 AACTTATAATTCGATCTAAATTGAAATTTT-TAATTAATTTTTAAATAATAAATAATAATAA-GT
* *
18599 CAATTTAGAAATCTAATTGAAAAAGGGTACAATCGGAAAACAAAAAGTGTTCC
64 CAATTTAGAAATATAATTGAAAAAGGATACAATCGGAAAACAAAAAGTGTTCC
18652 ATTTTTTGTA
Statistics
Matches: 103, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
118 28 0.27
119 28 0.27
120 26 0.25
121 6 0.06
122 15 0.15
ACGTcount: A:0.46, C:0.08, G:0.11, T:0.36
Consensus pattern (119 bp):
AACTTATAATTCGATCTAAATTGAAATTTTTAATTAATTTTTAAATAATAAATAATAATAAGTCA
ATTTAGAAATATAATTGAAAAAGGATACAATCGGAAAACAAAAAGTGTTCCCAT
Found at i:19566 original size:14 final size:14
Alignment explanation
Indices: 19547--19574 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
19537 AGACAAAAGA
19547 CAAAATTAAATAGG
1 CAAAATTAAATAGG
19561 CAAAATTAAATAGG
1 CAAAATTAAATAGG
19575 ATGTTGGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.14, T:0.21
Consensus pattern (14 bp):
CAAAATTAAATAGG
Found at i:19741 original size:32 final size:32
Alignment explanation
Indices: 19705--19771 Score: 84
Period size: 31 Copynumber: 2.1 Consensus size: 32
19695 TTATTAAAGG
*
19705 CAATTTAGAAATATGTTTTTAAAAA-AAGGATA
1 CAATTTAGAAATAT-ATTTTAAAAATAAGGATA
* *
19737 CAA-TTGGAAATATATTTTAAAAATAAGGGTA
1 CAATTTAGAAATATATTTTAAAAATAAGGATA
19768 CAAT
1 CAAT
19772 CAGAAAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
30 9 0.30
31 18 0.60
32 3 0.10
ACGTcount: A:0.49, C:0.04, G:0.13, T:0.33
Consensus pattern (32 bp):
CAATTTAGAAATATATTTTAAAAATAAGGATA
Found at i:19747 original size:31 final size:31
Alignment explanation
Indices: 19712--19771 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
19702 AGGCAATTTA
*
19712 GAAATATGTTTTTAAAAA-AAGGATACAATTG
1 GAAATAT-ATTTTAAAAATAAGGATACAATTG
*
19743 GAAATATATTTTAAAAATAAGGGTACAAT
1 GAAATATATTTTAAAAATAAGGATACAAT
19772 CAGAAAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 9 0.35
31 17 0.65
ACGTcount: A:0.50, C:0.03, G:0.15, T:0.32
Consensus pattern (31 bp):
GAAATATATTTTAAAAATAAGGATACAATTG
Found at i:23758 original size:23 final size:23
Alignment explanation
Indices: 23732--23779 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
23722 AAACAATAAT
23732 TAAGCTTATATTTATATTAAATC
1 TAAGCTTATATTTATATTAAATC
23755 TAAGCTTATATTTATATTAAATC
1 TAAGCTTATATTTATATTAAATC
23778 TA
1 TA
23780 TTTATTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.40, C:0.08, G:0.04, T:0.48
Consensus pattern (23 bp):
TAAGCTTATATTTATATTAAATC
Found at i:25103 original size:13 final size:13
Alignment explanation
Indices: 25087--25115 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
25077 TTCAATACAT
25087 TAATTTCATGATA
1 TAATTTCATGATA
25100 TAATTTCATGATA
1 TAATTTCATGATA
25113 TAA
1 TAA
25116 CTTGATATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (13 bp):
TAATTTCATGATA
Found at i:25488 original size:21 final size:22
Alignment explanation
Indices: 25464--25504 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
25454 CCGCCCCAAG
*
25464 AGGGCGGCTTA-CCATGGCTCA
1 AGGGCGGCTTAGCCACGGCTCA
25485 AGGGCGGCTTAGCCACGGCT
1 AGGGCGGCTTAGCCACGGCT
25505 GTGCCGCCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.17, C:0.29, G:0.37, T:0.17
Consensus pattern (22 bp):
AGGGCGGCTTAGCCACGGCTCA
Found at i:31309 original size:29 final size:29
Alignment explanation
Indices: 31266--31323 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
31256 TCTAGTTTAA
* *
31266 ACAGGTCTCAGATTCGACACTTTGTGTAC
1 ACAGGTCTCAAATTCGACACTTTATGTAC
31295 ACAGGTCTCAAATTCGACACTTTATGTAC
1 ACAGGTCTCAAATTCGACACTTTATGTAC
31324 GTAGCTGCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (29 bp):
ACAGGTCTCAAATTCGACACTTTATGTAC
Found at i:51757 original size:117 final size:118
Alignment explanation
Indices: 51544--51762 Score: 334
Period size: 117 Copynumber: 1.9 Consensus size: 118
51534 TTTCCCCCAC
* * *
51544 TATTCTTTGCTATTAGTTGAATTAATTGATAGAGAAACTTAGAAACTTATATATGCTTAACTTTG
1 TATTCTTTGCTATTAGTTGAATTAATTGAGAGAGAAACTTAGAAACTTATACATGCTTAACCTTG
*
51609 ACTTGCAGTAACATTTCAAATCATCTTTTGTCAACCATTTCCCCACTATTCAA
66 ACTTGCAATAACATTTCAAATCATCTTTTGTCAACCATTTCCCCACTATTCAA
* *
51662 TATTCTTTGCTATTAGTTGAATTAATTGAGCGAGAAACTTA-AATCTTATACATGCTTAACCTTG
1 TATTCTTTGCTATTAGTTGAATTAATTGAGAGAGAAACTTAGAAACTTATACATGCTTAACCTTG
* * *
51726 TCTTGCAATAATC-TTTCAAATTATCTTTTGTCCACCA
66 ACTTGCAATAA-CATTTCAAATCATCTTTTGTCAACCA
51763 ATCACTCCAA
Statistics
Matches: 91, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
117 51 0.56
118 40 0.44
ACGTcount: A:0.31, C:0.18, G:0.11, T:0.41
Consensus pattern (118 bp):
TATTCTTTGCTATTAGTTGAATTAATTGAGAGAGAAACTTAGAAACTTATACATGCTTAACCTTG
ACTTGCAATAACATTTCAAATCATCTTTTGTCAACCATTTCCCCACTATTCAA
Found at i:53363 original size:21 final size:21
Alignment explanation
Indices: 53338--53404 Score: 71
Period size: 24 Copynumber: 3.0 Consensus size: 21
53328 TTTGTTTATA
53338 TTTTTAACGGTTAATCAAGTAG
1 TTTTT-ACGGTTAATCAAGTAG
* * *
53360 TTTTGTTCTGGTTAAAGCAAGTAT
1 TTTT-TAC-GGTT-AATCAAGTAG
53384 TTTTTACGGTTAATCAAGTAG
1 TTTTTACGGTTAATCAAGTAG
53405 CTAAATGATT
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
21 8 0.22
22 9 0.25
23 7 0.19
24 12 0.33
ACGTcount: A:0.28, C:0.09, G:0.19, T:0.43
Consensus pattern (21 bp):
TTTTTACGGTTAATCAAGTAG
Found at i:53830 original size:69 final size:69
Alignment explanation
Indices: 53713--53849 Score: 152
Period size: 69 Copynumber: 2.0 Consensus size: 69
53703 GTTAAGATAC
* ** * *
53713 TAAGTTAACTAAGTTAAGCTAATTATATACTTTCAAATTTGTTAATT-AACTAAAACAGTAAGTT
1 TAAGTTAACTAAGTTAAGCTAATTAAATACTTAAAAATTTCTGAATTAAACTAAAACAGTAAGTT
53777 AAGA
66 AAGA
* * * *
53781 TAAGCTTAGCTAAGTTAAGCTAATTAAATAC-TAAAAATTTCTGGCATTAAAAGTAAAATAGTAA
1 TAAG-TTAACTAAGTTAAGCTAATTAAATACTTAAAAATTTCT-GAATT-AAACTAAAACAGTAA
53845 GTTAA
63 GTTAA
53850 TAAGCCTTCA
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
68 12 0.21
69 27 0.48
71 17 0.30
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.34
Consensus pattern (69 bp):
TAAGTTAACTAAGTTAAGCTAATTAAATACTTAAAAATTTCTGAATTAAACTAAAACAGTAAGTT
AAGA
Found at i:53899 original size:20 final size:20
Alignment explanation
Indices: 53865--53929 Score: 85
Period size: 20 Copynumber: 3.2 Consensus size: 20
53855 CTTCAAACTG
53865 CTTCAATAAGTCTTAATAACC
1 CTTC-ATAAGTCTTAATAACC
* *
53886 CTTCATAAGACTTAATAAAC
1 CTTCATAAGTCTTAATAACC
* *
53906 CTTTATAAGTGTTAATAACC
1 CTTCATAAGTCTTAATAACC
53926 CTTC
1 CTTC
53930 CAAAATTTGG
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
20 33 0.89
21 4 0.11
ACGTcount: A:0.37, C:0.22, G:0.06, T:0.35
Consensus pattern (20 bp):
CTTCATAAGTCTTAATAACC
Found at i:60173 original size:15 final size:15
Alignment explanation
Indices: 60155--60198 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
60145 TTAGGGTTTA
60155 GGGTTTTGGAATTTG
1 GGGTTTTGGAATTTG
*
60170 GGGTTTTCGAATTTG
1 GGGTTTTGGAATTTG
*
60185 GGATTTTGG-ATTTG
1 GGGTTTTGGAATTTG
60199 CAATTTGGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 5 0.19
15 21 0.81
ACGTcount: A:0.14, C:0.02, G:0.36, T:0.48
Consensus pattern (15 bp):
GGGTTTTGGAATTTG
Found at i:61146 original size:19 final size:20
Alignment explanation
Indices: 61100--61147 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 20
61090 TGTGGCACGC
*
61100 CACATGTACCAAAAAGTCGTGC
1 CACATGTACCAAAAA--CGTGA
61122 CACATGTACCAAAAA-GTGA
1 CACATGTACCAAAAACGTGA
61141 CACATGT
1 CACATGT
61148 CACGCCATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 10 0.40
22 15 0.60
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CACATGTACCAAAAACGTGA
Found at i:61152 original size:53 final size:53
Alignment explanation
Indices: 61067--61169 Score: 152
Period size: 53 Copynumber: 1.9 Consensus size: 53
61057 GACGTGGCAC
* **
61067 GCCACGTGTACCAAAAAGTGACATGTGGCACGCCACATGTACCAAAAAGTCGT
1 GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGTCGT
* **
61120 GCCACATGTACCAAAAAGTGACACATGTCACGCCATGTGTACCAAAAAGT
1 GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGT
61170 GACACGTGGC
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 44 1.00
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.17
Consensus pattern (53 bp):
GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGTCGT
Found at i:61197 original size:31 final size:31
Alignment explanation
Indices: 61119--61216 Score: 117
Period size: 31 Copynumber: 3.2 Consensus size: 31
61109 CAAAAAGTCG
* *
61119 TGCCACATGTACCAAAAAGTGACACATGTCA
1 TGCCACATGTACCAAAAAGTGACACGTGGCA
* **
61150 CGCCATGTGTACCAAAAAGTGACACGTGGCA
1 TGCCACATGTACCAAAAAGTGACACGTGGCA
** *
61181 TGCCACATGTTTCAAAAA-TGGCACGTGGCA
1 TGCCACATGTACCAAAAAGTGACACGTGGCA
61211 TGCCAC
1 TGCCAC
61217 GTGCACAAAA
Statistics
Matches: 56, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
30 17 0.30
31 39 0.70
ACGTcount: A:0.33, C:0.27, G:0.21, T:0.19
Consensus pattern (31 bp):
TGCCACATGTACCAAAAAGTGACACGTGGCA
Found at i:62685 original size:34 final size:34
Alignment explanation
Indices: 62640--62704 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
62630 TAAACCCCTA
*
62640 AACAAACAAAGCTAAACCCAGAAATCATTTTCAC
1 AACAAACAAAGCTAAACCCAGAAATAATTTTCAC
* *
62674 AACAAAGAAAGCTAAATCCAGAAATAATTTT
1 AACAAACAAAGCTAAACCCAGAAATAATTTT
62705 GAAATACCCT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.52, C:0.20, G:0.08, T:0.20
Consensus pattern (34 bp):
AACAAACAAAGCTAAACCCAGAAATAATTTTCAC
Found at i:64816 original size:117 final size:122
Alignment explanation
Indices: 64616--64843 Score: 394
Period size: 117 Copynumber: 1.9 Consensus size: 122
64606 GTCACAGTGC
*
64616 TGAGGGATCTCGGGTGATAGGTTCTGATTCTGATAGTAGAGGGACGAATTTGTAGAAAAAAAAAT
1 TGAGGGATCTCGGGTGATAGGTTCTGA-T-TGATAGTAGAGGGACCAATTTGTAGAAAAAAAAAT
64681 TACAAGAACCAAAATCAACATTTGGTATAGTACAAGGACCACTCGGCAGTGCACTGACG
64 TACAAGAACCAAAATCAACATTTGGTATAGTACAAGGACCACTCGGCAGTGCACTGACG
64740 TGAGGGATCTCGGGTGATAGGTTCTGA-T-A-A-TAGAGGGACCAATTTGTAG-AAAAAAAATTA
1 TGAGGGATCTCGGGTGATAGGTTCTGATTGATAGTAGAGGGACCAATTTGTAGAAAAAAAAATTA
64800 CAAGAACCAAAATCAACATTTGGTATAGTACAAGGACCACTCGG
66 CAAGAACCAAAATCAACATTTGGTATAGTACAAGGACCACTCGG
64844 GGACTTTTAC
Statistics
Matches: 103, Mismatches: 1, Indels: 7
0.93 0.01 0.06
Matches are distributed among these distances:
117 55 0.53
118 18 0.17
119 1 0.01
120 1 0.01
121 1 0.01
124 27 0.26
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.23
Consensus pattern (122 bp):
TGAGGGATCTCGGGTGATAGGTTCTGATTGATAGTAGAGGGACCAATTTGTAGAAAAAAAAATTA
CAAGAACCAAAATCAACATTTGGTATAGTACAAGGACCACTCGGCAGTGCACTGACG
Found at i:72919 original size:81 final size:81
Alignment explanation
Indices: 72791--72943 Score: 216
Period size: 81 Copynumber: 1.9 Consensus size: 81
72781 CCTCCAGAAC
**
72791 ATCAAATTGCTGCTGCAGTCTTTTCATCTGCTCCTGCAAGGCTTGAATCTCCACCCTCCTCCTTT
1 ATCAAATTGCTGCTGCAGTCTTTTCATCTGCTCCTGCAAGGCTTGAATCTCCACCCTCAGCCTTT
*
72856 CAGTTTCAACCAGATT
66 CAATTTCAACCAGATT
* * * * * * *
72872 ATCAAGTTTCTGCTGCAGTGTTTTCATCTGCTCCTTCAGGGTTTGAATCTCCACGCTCAGCCTTT
1 ATCAAATTGCTGCTGCAGTCTTTTCATCTGCTCCTGCAAGGCTTGAATCTCCACCCTCAGCCTTT
72937 CAATTTC
66 CAATTTC
72944 CAGTGACCAT
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
81 62 1.00
ACGTcount: A:0.18, C:0.30, G:0.15, T:0.37
Consensus pattern (81 bp):
ATCAAATTGCTGCTGCAGTCTTTTCATCTGCTCCTGCAAGGCTTGAATCTCCACCCTCAGCCTTT
CAATTTCAACCAGATT
Found at i:73719 original size:22 final size:22
Alignment explanation
Indices: 73672--73721 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
73662 TAAATTAACT
*
73672 AATTAAAACTAATAAACTAAGC
1 AATTAAAACTAATAAACTAAGA
* *
73694 AATTAAATACTAATTAATTAA-A
1 AATTAAA-ACTAATAAACTAAGA
73716 AATTAA
1 AATTAA
73722 TTTTTTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 13 0.54
23 11 0.46
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.30
Consensus pattern (22 bp):
AATTAAAACTAATAAACTAAGA
Found at i:77321 original size:12 final size:12
Alignment explanation
Indices: 77304--77332 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
77294 CAATTAACTA
77304 AATTATATATAT
1 AATTATATATAT
77316 AATTATATATAT
1 AATTATATATAT
77328 AATTA
1 AATTA
77333 AAGATAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AATTATATATAT
Found at i:77510 original size:20 final size:21
Alignment explanation
Indices: 77473--77513 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
77463 AACCCGTTAA
*
77473 TTAAAGCGTGTCACTCGTGTC
1 TTAAAGCGTGTCAATCGTGTC
*
77494 TTAAA-CGTGTTAATCGTGTC
1 TTAAAGCGTGTCAATCGTGTC
77514 AAGACACGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.37
Consensus pattern (21 bp):
TTAAAGCGTGTCAATCGTGTC
Found at i:77573 original size:42 final size:43
Alignment explanation
Indices: 77503--77585 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 43
77493 CTTAAACGTG
77503 TTAATCGTGTCAAGACACGATTACGACACGAAACACAATAATC
1 TTAATCGTGTCAAGACACGATTACGACACGAAACACAATAATC
* * *
77546 TTAATCGTGTC-CGACACGATT-CAGACACGAGACACGATAA
1 TTAATCGTGTCAAGACACGATTAC-GACACGAAACACAATAA
77586 GCCAAACACA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
41 1 0.03
42 24 0.67
43 11 0.31
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (43 bp):
TTAATCGTGTCAAGACACGATTACGACACGAAACACAATAATC
Found at i:78261 original size:20 final size:21
Alignment explanation
Indices: 78238--78280 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
78228 TAATCGTGTC
*
78238 AAGACACGATTAATACG-TTT
1 AAGACACGAGTAATACGATTT
*
78258 AAGACACGAGTGATACGATTT
1 AAGACACGAGTAATACGATTT
78279 AA
1 AA
78281 TTAACGTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.26
Consensus pattern (21 bp):
AAGACACGAGTAATACGATTT
Found at i:78438 original size:12 final size:12
Alignment explanation
Indices: 78421--78446 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
78411 CAATTATCTT
78421 TAATTATATATA
1 TAATTATATATA
78433 TAATTATATATA
1 TAATTATATATA
78445 TA
1 TA
78447 GTTTAGTTAA
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:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TAATTATATATA
Found at i:81640 original size:9 final size:9
Alignment explanation
Indices: 81626--81652 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
81616 AATTTCAAAT
81626 CTCCACTGC
1 CTCCACTGC
81635 CTCCACTGC
1 CTCCACTGC
81644 CTCCACTGC
1 CTCCACTGC
81653 TATAGATTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.11, C:0.56, G:0.11, T:0.22
Consensus pattern (9 bp):
CTCCACTGC
Found at i:82793 original size:15 final size:16
Alignment explanation
Indices: 82770--82864 Score: 93
Period size: 16 Copynumber: 6.0 Consensus size: 16
82760 AACTCGTCTG
*
82770 AACCTGAACCC-AAAA
1 AACCCGAACCCGAAAA
82785 AACCCGAACCCGAAAA
1 AACCCGAACCCGAAAA
*** *
82801 AGTTCAAACCCGAAAA
1 AACCCGAACCCGAAAA
82817 AACCCGAACCCGAAAA
1 AACCCGAACCCGAAAA
* * *
82833 AGCTCAAACCCGAAAA
1 AACCCGAACCCGAAAA
* *
82849 AACTCGAATCCGAAAA
1 AACCCGAACCCGAAAA
82865 TTTATGAAAA
Statistics
Matches: 64, Mismatches: 15, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
15 10 0.16
16 54 0.84
ACGTcount: A:0.51, C:0.32, G:0.12, T:0.06
Consensus pattern (16 bp):
AACCCGAACCCGAAAA
Found at i:82822 original size:32 final size:32
Alignment explanation
Indices: 82776--82864 Score: 144
Period size: 32 Copynumber: 2.8 Consensus size: 32
82766 TCTGAACCTG
*
82776 AACCC-AAAAAACCCGAACCCGAAAAAGTTCA
1 AACCCGAAAAAACCCGAACCCGAAAAAGCTCA
82807 AACCCGAAAAAACCCGAACCCGAAAAAGCTCA
1 AACCCGAAAAAACCCGAACCCGAAAAAGCTCA
* *
82839 AACCCGAAAAAACTCGAATCCGAAAA
1 AACCCGAAAAAACCCGAACCCGAAAA
82865 TTTATGAAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
31 5 0.09
32 49 0.91
ACGTcount: A:0.52, C:0.31, G:0.11, T:0.06
Consensus pattern (32 bp):
AACCCGAAAAAACCCGAACCCGAAAAAGCTCA
Found at i:83074 original size:15 final size:15
Alignment explanation
Indices: 83024--83104 Score: 108
Period size: 16 Copynumber: 5.2 Consensus size: 15
83014 CCCGAATCCG
83024 AATTAACCTGACCCA
1 AATTAACCTGACCCA
* *
83039 AATTTAACCCGAACCCG
1 AA-TTAACCTG-ACCCA
83056 AATTAACCTGACCCA
1 AATTAACCTGACCCA
*
83071 AATTAACCCGAACCCA
1 AATTAACCTG-ACCCA
83087 AATTAACCTGACCCA
1 AATTAACCTGACCCA
83102 AAT
1 AAT
83105 CCAATCCAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
15 23 0.40
16 28 0.49
17 6 0.11
ACGTcount: A:0.41, C:0.33, G:0.07, T:0.19
Consensus pattern (15 bp):
AATTAACCTGACCCA
Found at i:83080 original size:31 final size:31
Alignment explanation
Indices: 83012--83104 Score: 159
Period size: 31 Copynumber: 3.0 Consensus size: 31
83002 ACCCAAACAG
*
83012 AACCCGAATCCGAATTAACCTGACCCAAATTT
1 AACCCGAACCCGAATTAACCTGACCCAAA-TT
83044 AACCCGAACCCGAATTAACCTGACCCAAATT
1 AACCCGAACCCGAATTAACCTGACCCAAATT
*
83075 AACCCGAACCCAAATTAACCTGACCCAAAT
1 AACCCGAACCCGAATTAACCTGACCCAAAT
83105 CCAATCCAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
31 31 0.53
32 28 0.47
ACGTcount: A:0.40, C:0.34, G:0.09, T:0.17
Consensus pattern (31 bp):
AACCCGAACCCGAATTAACCTGACCCAAATT
Done.