Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015369.1 Corchorus olitorius cultivar O-4 contig15402, 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: 90083
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:723 original size:22 final size:20
Alignment explanation
Indices: 697--743 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 20
687 AAATTTATAA
*
697 AAATAACGAAAAATCAATATT
1 AAATAACGAAAAACCAA-ATT
718 GAAATAACGAAAAACCAAATT
1 -AAATAACGAAAAACCAAATT
739 AAATA
1 AAATA
744 GTAATCAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 5 0.21
21 3 0.12
22 16 0.67
ACGTcount: A:0.64, C:0.11, G:0.06, T:0.19
Consensus pattern (20 bp):
AAATAACGAAAAACCAAATT
Found at i:11921 original size:21 final size:21
Alignment explanation
Indices: 11881--11921 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
11871 GAGATAGGTA
*
11881 CAGAAATGAAAAGGACAGATT
1 CAGAAATGAAAAGGAAAGATT
11902 CAGAAATGACAAA-GAAAGAT
1 CAGAAATGA-AAAGGAAAGAT
11922 ACATGAATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.56, C:0.10, G:0.22, T:0.12
Consensus pattern (21 bp):
CAGAAATGAAAAGGAAAGATT
Found at i:12673 original size:2 final size:2
Alignment explanation
Indices: 12666--12690 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12656 CAAACTGAAA
12666 GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT G
12691 CAGGTTGAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:27625 original size:2 final size:2
Alignment explanation
Indices: 27620--27649 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
27610 TATATATATA
27620 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
27650 AAATGAAATA
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:34815 original size:19 final size:19
Alignment explanation
Indices: 34791--34831 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
34781 TCAACACATA
34791 ACATAATTTTTGAAGGAGC
1 ACATAATTTTTGAAGGAGC
34810 ACATAATTTTTGAAGGAGC
1 ACATAATTTTTGAAGGAGC
34829 ACA
1 ACA
34832 GAAGATTGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (19 bp):
ACATAATTTTTGAAGGAGC
Found at i:36281 original size:22 final size:22
Alignment explanation
Indices: 36253--36346 Score: 104
Period size: 22 Copynumber: 4.3 Consensus size: 22
36243 ATATAAACCC
*
36253 ATTTTGATAACTACCCTATTAA
1 ATTTTGATAACTACCCTATGAA
*
36275 ATTTTGATAA-TCACGCTATGAA
1 ATTTTGATAACT-ACCCTATGAA
*
36297 ATTTTGATAATTA-CCTATGAA
1 ATTTTGATAACTACCCTATGAA
* *
36318 ATTGTGATAAACT-CCATATGAA
1 ATTTTGAT-AACTACCCTATGAA
36340 ATTTTGA
1 ATTTTGA
36347 CAACCTAACT
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
21 15 0.25
22 45 0.74
23 1 0.02
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (22 bp):
ATTTTGATAACTACCCTATGAA
Found at i:36320 original size:43 final size:44
Alignment explanation
Indices: 36253--36346 Score: 120
Period size: 43 Copynumber: 2.2 Consensus size: 44
36243 ATATAAACCC
* * *
36253 ATTTTGATAACTACCCTATTAAATTTTGATAATCACGC-TATGAA
1 ATTTTGATAACTACCCTATGAAATTGTGATAAACAC-CATATGAA
* *
36297 ATTTTGATAATTA-CCTATGAAATTGTGATAAACTCCATATGAA
1 ATTTTGATAACTACCCTATGAAATTGTGATAAACACCATATGAA
36340 ATTTTGA
1 ATTTTGA
36347 CAACCTAACT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
42 1 0.02
43 31 0.70
44 12 0.27
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (44 bp):
ATTTTGATAACTACCCTATGAAATTGTGATAAACACCATATGAA
Found at i:36389 original size:45 final size:45
Alignment explanation
Indices: 36334--36435 Score: 204
Period size: 45 Copynumber: 2.3 Consensus size: 45
36324 ATAAACTCCA
36334 TATGAAATTTTGACAACCTAACTATAAGATTTTAATAAATCTTCC
1 TATGAAATTTTGACAACCTAACTATAAGATTTTAATAAATCTTCC
36379 TATGAAATTTTGACAACCTAACTATAAGATTTTAATAAATCTTCC
1 TATGAAATTTTGACAACCTAACTATAAGATTTTAATAAATCTTCC
36424 TATGAAATTTTG
1 TATGAAATTTTG
36436 TAACCTTACT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 57 1.00
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.39
Consensus pattern (45 bp):
TATGAAATTTTGACAACCTAACTATAAGATTTTAATAAATCTTCC
Found at i:36410 original size:22 final size:22
Alignment explanation
Indices: 36340--36411 Score: 74
Period size: 22 Copynumber: 3.2 Consensus size: 22
36330 TCCATATGAA
36340 ATTTTGACAACCTAACTATAAG
1 ATTTTGACAACCTAACTATAAG
* * * **
36362 ATTTTAATAAATCTTCCTATGAA-
1 ATTTTGA-CAACCTAACTAT-AAG
36385 ATTTTGACAACCTAACTATAAG
1 ATTTTGACAACCTAACTATAAG
36407 ATTTT
1 ATTTT
36412 AATAAATCTT
Statistics
Matches: 37, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
21 2 0.05
22 19 0.51
23 14 0.38
24 2 0.05
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (22 bp):
ATTTTGACAACCTAACTATAAG
Found at i:36468 original size:21 final size:21
Alignment explanation
Indices: 36253--36468 Score: 55
Period size: 22 Copynumber: 9.9 Consensus size: 21
36243 ATATAAACCC
*
36253 ATTTTGATAA-CTACCCTATTAA
1 ATTTTG-TAACCT-CCCTATGAA
* * *
36275 ATTTTGATAATCACGCTATGAA
1 ATTTTG-TAACCTCCCTATGAA
* *
36297 ATTTTGATAA-TTACCTATGAA
1 ATTTTG-TAACCTCCCTATGAA
* * *
36318 ATTGTGATAAACTCCATATGAA
1 ATTTTG-TAACCTCCCTATGAA
* **
36340 ATTTTGACAACCTAACTAT-AA
1 ATTTTG-TAACCTCCCTATGAA
* * *
36361 GATTTTAATAAATCTTCCTATGAA
1 -ATTTT-GT-AACCTCCCTATGAA
* **
36385 ATTTTGACAACCTAACTAT-AA
1 ATTTTG-TAACCTCCCTATGAA
* * *
36406 GATTTTAATAAATCTTCCTATGAA
1 -ATTTT-GT-AACCTCCCTATGAA
**
36430 ATTTTGTAACCTTACTATG-A
1 ATTTTGTAACCTCCCTATGAA
*
36450 TTTTTGATAACCTCCCTAT
1 ATTTTG-TAACCTCCCTAT
36469 TTAATGGTGT
Statistics
Matches: 144, Mismatches: 38, Indels: 25
0.70 0.18 0.12
Matches are distributed among these distances:
20 6 0.04
21 40 0.28
22 67 0.47
23 27 0.19
24 4 0.03
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.39
Consensus pattern (21 bp):
ATTTTGTAACCTCCCTATGAA
Found at i:36512 original size:31 final size:31
Alignment explanation
Indices: 36466--36526 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 31
36456 ATAACCTCCC
* *
36466 TATTTAATGGTGTTTTT-ATGAGAAACGCCTA
1 TATTTAACGGCGTTTTTGAT-AGAAACGCCTA
36497 TATTTAACGGCGTTTTTGGATAGAAACGCC
1 TATTTAACGGCGTTTTT-GATAGAAACGCC
36527 GCTACTATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 15 0.58
32 9 0.35
33 2 0.08
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38
Consensus pattern (31 bp):
TATTTAACGGCGTTTTTGATAGAAACGCCTA
Found at i:37545 original size:7 final size:7
Alignment explanation
Indices: 37529--37559 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
37519 GGACAAAATT
*
37529 AAAACTA
1 AAAACAA
37536 AAAACAA
1 AAAACAA
37543 AAAACAA
1 AAAACAA
37550 AAAACAA
1 AAAACAA
37557 AAA
1 AAA
37560 TACTAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.84, C:0.13, G:0.00, T:0.03
Consensus pattern (7 bp):
AAAACAA
Found at i:38432 original size:23 final size:22
Alignment explanation
Indices: 38406--38461 Score: 53
Period size: 23 Copynumber: 2.5 Consensus size: 22
38396 AAAAATACAT
38406 TTAAATAAAAA-AAACAAATTTAA
1 TTAAATAAAAATAAACAAA--TAA
38429 TT-AATGAAAAATTAAACAAATAA
1 TTAAAT-AAAAA-TAAACAAATAA
*
38452 ATAAATAAAA
1 TTAAATAAAA
38462 TGAAATTCCA
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
22 3 0.11
23 15 0.54
24 3 0.11
25 7 0.25
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.25
Consensus pattern (22 bp):
TTAAATAAAAATAAACAAATAA
Found at i:40510 original size:17 final size:17
Alignment explanation
Indices: 40487--40520 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
40477 TAATCTTGCC
40487 TTCT-TTTTTC-TTTCT
1 TTCTCTTTTTCTTTTCT
40502 TTCTCTTTTTCTTTTCT
1 TTCTCTTTTTCTTTTCT
40519 TT
1 TT
40521 TTTATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 6 0.35
17 7 0.41
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (17 bp):
TTCTCTTTTTCTTTTCT
Found at i:41023 original size:16 final size:16
Alignment explanation
Indices: 40987--41023 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
40977 TCAAGAATAG
40987 TAAAAACAAAAAAAAA
1 TAAAAACAAAAAAAAA
* *
41003 AAAAAACAAAAAGAAA
1 TAAAAACAAAAAAAAA
41019 TAAAA
1 TAAAA
41024 CGATGCAGAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.86, C:0.05, G:0.03, T:0.05
Consensus pattern (16 bp):
TAAAAACAAAAAAAAA
Found at i:45445 original size:22 final size:22
Alignment explanation
Indices: 45417--45609 Score: 104
Period size: 22 Copynumber: 8.9 Consensus size: 22
45407 ATATAAACCC
*
45417 ATTTTGATAACTACCCTATTAA
1 ATTTTGATAACTACCCTATGAA
*
45439 ATTTTGATAA-TCACGCTATGAA
1 ATTTTGATAACT-ACCCTATGAA
*
45461 ATTTTGATAATTA-CCTATGAA
1 ATTTTGATAACTACCCTATGAA
* *
45482 ATTGTGATAAACT-CCATATGAA
1 ATTTTGAT-AACTACCCTATGAA
* *
45504 ATTTTGACAACCTA-ACTAT-AA
1 ATTTTGATAA-CTACCCTATGAA
* *
45525 GATTTTAATAAATCT-TCCTATGAA
1 -ATTTTGAT-AA-CTACCCTATGAA
45549 ATTTTG-TAACCTTA--CTATG-A
1 ATTTTGATAA-C-TACCCTATGAA
* *
45569 TTTTTGATAACCT-CCCTATGAG
1 ATTTTGATAA-CTACCCTATGAA
*
45591 ATTTTGTTAATCT-CCCTAT
1 ATTTTGATAA-CTACCCTAT
45610 AATTTTTTGA
Statistics
Matches: 134, Mismatches: 21, Indels: 32
0.72 0.11 0.17
Matches are distributed among these distances:
20 7 0.05
21 37 0.28
22 74 0.55
23 14 0.10
24 2 0.01
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.40
Consensus pattern (22 bp):
ATTTTGATAACTACCCTATGAA
Found at i:45484 original size:43 final size:44
Alignment explanation
Indices: 45417--45510 Score: 120
Period size: 43 Copynumber: 2.2 Consensus size: 44
45407 ATATAAACCC
* * *
45417 ATTTTGATAACTACCCTATTAAATTTTGATAATCACGC-TATGAA
1 ATTTTGATAACTACCCTATGAAATTGTGATAAACAC-CATATGAA
* *
45461 ATTTTGATAATTA-CCTATGAAATTGTGATAAACTCCATATGAA
1 ATTTTGATAACTACCCTATGAAATTGTGATAAACACCATATGAA
45504 ATTTTGA
1 ATTTTGA
45511 CAACCTAACT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
42 1 0.02
43 31 0.70
44 12 0.27
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (44 bp):
ATTTTGATAACTACCCTATGAAATTGTGATAAACACCATATGAA
Found at i:45617 original size:22 final size:22
Alignment explanation
Indices: 45569--45619 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
45559 CTTACTATGA
*
45569 TTTTTGATAACCTCCCTATGAG
1 TTTTTGATAACCTCCCTATAAG
* * * *
45591 ATTTTGTTAATCTCCCTATAAT
1 TTTTTGATAACCTCCCTATAAG
45613 TTTTTGA
1 TTTTTGA
45620 ACCTAATTTC
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.24, C:0.18, G:0.10, T:0.49
Consensus pattern (22 bp):
TTTTTGATAACCTCCCTATAAG
Found at i:45918 original size:45 final size:45
Alignment explanation
Indices: 45849--45941 Score: 150
Period size: 45 Copynumber: 2.1 Consensus size: 45
45839 TGCAATCTAA
* *
45849 TCCGGTTTAGCTCTTATAGTATGATTATACGTTTGAAATTTCAAC
1 TCCGGTTTAGCTCTTATAGTATGATTATACGTTTAAAAATTCAAC
* *
45894 TCCGTTTTAGTTCTTATAGTATGATTATACGTTTAAAAATTCAAC
1 TCCGGTTTAGCTCTTATAGTATGATTATACGTTTAAAAATTCAAC
45939 TCC
1 TCC
45942 TTTGAAAAAG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (45 bp):
TCCGGTTTAGCTCTTATAGTATGATTATACGTTTAAAAATTCAAC
Found at i:49898 original size:30 final size:30
Alignment explanation
Indices: 49862--49918 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
49852 ATTTCTTGAT
*
49862 TGAAGATTAATTGAAGATA-ATTTCAAGTCA
1 TGAAGA-TAATTGAAGAAAGATTTCAAGTCA
*
49892 TGAAGATCATTGAAGAAAGATTTCAAG
1 TGAAGATAATTGAAGAAAGATTTCAAG
49919 GCGAAAAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 10 0.42
30 14 0.58
ACGTcount: A:0.44, C:0.07, G:0.19, T:0.30
Consensus pattern (30 bp):
TGAAGATAATTGAAGAAAGATTTCAAGTCA
Found at i:50509 original size:18 final size:19
Alignment explanation
Indices: 50483--50520 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
50473 ATTCTCTTCA
*
50483 TCTATTTTTCT-TCTAGTT
1 TCTAGTTTTCTCTCTAGTT
50501 TCTAGTTTTCTCTCTAGTT
1 TCTAGTTTTCTCTCTAGTT
50520 T
1 T
50521 TAGAAGAGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.11, C:0.18, G:0.08, T:0.63
Consensus pattern (19 bp):
TCTAGTTTTCTCTCTAGTT
Found at i:50509 original size:19 final size:18
Alignment explanation
Indices: 50483--50520 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
50473 ATTCTCTTCA
50483 TCTATTTT-TCTTCTAGTT
1 TCTATTTTCTC-TCTAGTT
50501 TCTAGTTTTCTCTCTAGTT
1 TCTA-TTTTCTCTCTAGTT
50520 T
1 T
50521 TAGAAGAGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
19 12 0.67
20 2 0.11
ACGTcount: A:0.11, C:0.18, G:0.08, T:0.63
Consensus pattern (18 bp):
TCTATTTTCTCTCTAGTT
Found at i:51659 original size:116 final size:116
Alignment explanation
Indices: 51455--51689 Score: 443
Period size: 116 Copynumber: 2.0 Consensus size: 116
51445 GGGATTATCT
51455 TGTGATTTGCTGACGACCGGTCATATATCGATTGATGCAAAAGTTTTTACCGTATGATTATATGA
1 TGTGATTTGCTGACGACCGGTCATATATCGATTGATGCAAAAGTTTTTACCGTATGATTATATGA
*
51520 GAAACACTATTCGAGAACCTTCCACTAATACTGGTAAGACCCCCATCTAGA
66 GAAACACTATCCGAGAACCTTCCACTAATACTGGTAAGACCCCCATCTAGA
*
51571 TGTGATTTGCTGACGACCGGTCATATATCGATTGATGCAAAAGTTTTTACCGTATGATTATATGT
1 TGTGATTTGCTGACGACCGGTCATATATCGATTGATGCAAAAGTTTTTACCGTATGATTATATGA
*
51636 GAAACACTATCCTAGAACCTTCCACTAATACTGGTAAGACCCCCATCTAGA
66 GAAACACTATCCGAGAACCTTCCACTAATACTGGTAAGACCCCCATCTAGA
51687 TGT
1 TGT
51690 TTCAAGCCTA
Statistics
Matches: 116, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
116 116 1.00
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (116 bp):
TGTGATTTGCTGACGACCGGTCATATATCGATTGATGCAAAAGTTTTTACCGTATGATTATATGA
GAAACACTATCCGAGAACCTTCCACTAATACTGGTAAGACCCCCATCTAGA
Found at i:52581 original size:25 final size:25
Alignment explanation
Indices: 52540--52676 Score: 220
Period size: 25 Copynumber: 5.4 Consensus size: 25
52530 TAGCCTATGT
* *
52540 GTTTTCTAAACGCAAGCACAGGCTC
1 GTTTTCCAAACGCAAGCACAGGTTC
* *
52565 GCTTGCCAAACGCAAGCACAGGTTC
1 GTTTTCCAAACGCAAGCACAGGTTC
52590 GTTTTCCAAACGCAAGCACAGGTTC
1 GTTTTCCAAACGCAAGCACAGGTTC
52615 GTTTTCCAAACGCAAGCACAGGTTC
1 GTTTTCCAAACGCAAGCACAGGTTC
*
52640 GTTTTTCCAAACGCAAGCACAGGCTC
1 G-TTTTCCAAACGCAAGCACAGGTTC
52666 GTTTTCCAAAC
1 GTTTTCCAAAC
52677 ACCAGAACAT
Statistics
Matches: 104, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
25 80 0.77
26 24 0.23
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.23
Consensus pattern (25 bp):
GTTTTCCAAACGCAAGCACAGGTTC
Found at i:56923 original size:7 final size:7
Alignment explanation
Indices: 56911--56936 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
56901 CTAATCCGAA
56911 AATCCCC
1 AATCCCC
56918 AATCCCC
1 AATCCCC
56925 AATCCCC
1 AATCCCC
56932 AATCC
1 AATCC
56937 TTTGAAATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.54, G:0.00, T:0.15
Consensus pattern (7 bp):
AATCCCC
Found at i:59551 original size:19 final size:18
Alignment explanation
Indices: 59520--59555 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
59510 ATATGTATAC
59520 TGTATATACTGTATGTAA
1 TGTATATACTGTATGTAA
*
59538 TGTACTATATTGTATGTA
1 TGTA-TATACTGTATGTA
59556 TACATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.31, C:0.06, G:0.17, T:0.47
Consensus pattern (18 bp):
TGTATATACTGTATGTAA
Found at i:64821 original size:29 final size:30
Alignment explanation
Indices: 64764--64839 Score: 97
Period size: 29 Copynumber: 2.7 Consensus size: 30
64754 AGTCATCTAG
64764 GGGGCATTTTGGTCA---TTTTTACATCCA
1 GGGGCATTTTGGTCATTTTTTTTACATCCA
*
64791 GGGGCATTTTGGTCATTTTTTTTAC-TTCA
1 GGGGCATTTTGGTCATTTTTTTTACATCCA
* *
64820 GGGGCACTTTAGTCATTTTT
1 GGGGCATTTTGGTCATTTTT
64840 AATTCATTAC
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
27 15 0.35
29 21 0.49
30 7 0.16
ACGTcount: A:0.16, C:0.16, G:0.22, T:0.46
Consensus pattern (30 bp):
GGGGCATTTTGGTCATTTTTTTTACATCCA
Found at i:68561 original size:15 final size:16
Alignment explanation
Indices: 68541--68571 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
68531 TAATTTAGAG
68541 ATAAAAAAAG-GAAAA
1 ATAAAAAAAGTGAAAA
68556 ATAAAAAAAGTGAAAA
1 ATAAAAAAAGTGAAAA
68572 TCAGAAAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (16 bp):
ATAAAAAAAGTGAAAA
Found at i:72946 original size:5 final size:5
Alignment explanation
Indices: 72936--72998 Score: 126
Period size: 5 Copynumber: 12.6 Consensus size: 5
72926 ATCCCTCCTC
72936 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
72986 TATAT TATAT TAT
1 TATAT TATAT TAT
72999 GTATTGGTTA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 58 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:80911 original size:6 final size:6
Alignment explanation
Indices: 80902--80960 Score: 61
Period size: 6 Copynumber: 10.2 Consensus size: 6
80892 TCGGGTTAAG
* *
80902 TCGGGT TC-GGT CTCGGG- TAGGGT TCGGGT TCGGGG TCGGG- TCGGGT
1 TCGGGT TCGGGT -TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT
*
80948 TCGGGC TCGGGT T
1 TCGGGT TCGGGT T
80961 TGATTTCGAT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
5 12 0.27
6 30 0.68
7 2 0.05
ACGTcount: A:0.02, C:0.19, G:0.51, T:0.29
Consensus pattern (6 bp):
TCGGGT
Found at i:80932 original size:23 final size:23
Alignment explanation
Indices: 80885--80958 Score: 80
Period size: 23 Copynumber: 3.3 Consensus size: 23
80875 TTCGAGTATT
*
80885 TTCGGGCTCGGGTTA-AG-TCGGG
1 TTCGGGCTCGGG-TAGGGTTCGGG
*
80907 TTCGGTCTCGGGTAGGGTTCGGG
1 TTCGGGCTCGGGTAGGGTTCGGG
* *
80930 TTCGGGGTCGGGTCGGGTTCGGG
1 TTCGGGCTCGGGTAGGGTTCGGG
*
80953 CTCGGG
1 TTCGGG
80959 TTTGATTTCG
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
21 2 0.05
22 12 0.27
23 30 0.68
ACGTcount: A:0.04, C:0.19, G:0.50, T:0.27
Consensus pattern (23 bp):
TTCGGGCTCGGGTAGGGTTCGGG
Found at i:80934 original size:17 final size:17
Alignment explanation
Indices: 80904--80952 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
80894 GGGTTAAGTC
80904 GGGTTC-GGTCTCGGGTA
1 GGGTTCGGGT-TCGGGTA
*
80921 GGGTTCGGGTTCGGGGTC
1 GGGTTCGGGTTC-GGGTA
80939 GGG-TCGGGTTCGGG
1 GGGTTCGGGTTCGGG
80953 CTCGGGTTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
16 3 0.10
17 16 0.55
18 10 0.34
ACGTcount: A:0.02, C:0.16, G:0.55, T:0.27
Consensus pattern (17 bp):
GGGTTCGGGTTCGGGTA
Found at i:80957 original size:17 final size:17
Alignment explanation
Indices: 80925--80959 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
80915 CGGGTAGGGT
*
80925 TCGGGTTCGGGGTCGGG
1 TCGGGTTCGGGCTCGGG
80942 TCGGGTTCGGGCTCGGG
1 TCGGGTTCGGGCTCGGG
80959 T
1 T
80960 TTGATTTCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.00, C:0.20, G:0.54, T:0.26
Consensus pattern (17 bp):
TCGGGTTCGGGCTCGGG
Found at i:81108 original size:13 final size:12
Alignment explanation
Indices: 81085--81131 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
81075 AAATTTATTG
81085 ATAATATATAAT
1 ATAATATATAAT
81097 ATAATAATATAAT
1 ATAAT-ATATAAT
* *
81110 ATAACAT-TATT
1 ATAATATATAAT
81121 ATCAATATATA
1 AT-AATATATA
81132 TAAAGATTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 5 0.17
12 11 0.38
13 13 0.45
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40
Consensus pattern (12 bp):
ATAATATATAAT
Found at i:81419 original size:31 final size:31
Alignment explanation
Indices: 81375--81456 Score: 80
Period size: 31 Copynumber: 2.6 Consensus size: 31
81365 TAATCAATTC
* *
81375 TAAATTATTACAAATTAAAACAAAT-TAAG-CAT
1 TAAATTA-AACAAATTAAAA-AAATGAAAGTC-T
*
81407 TAAATTAAACAAA-TAATTAAAATGAAAGTCT
1 TAAATTAAACAAATTAA-AAAAATGAAAGTCT
81438 TAAATTAAACAAATTAAAA
1 TAAATTAAACAAATTAAAA
81457 GTCGATAGAC
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
30 7 0.17
31 24 0.57
32 11 0.26
ACGTcount: A:0.60, C:0.07, G:0.04, T:0.29
Consensus pattern (31 bp):
TAAATTAAACAAATTAAAAAAATGAAAGTCT
Found at i:83274 original size:14 final size:14
Alignment explanation
Indices: 83255--83291 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
83245 CCTTTTAAAT
83255 TAAAATAGTAAAAA
1 TAAAATAGTAAAAA
83269 TAAAAT-GATAAAAA
1 TAAAATAG-TAAAAA
83283 TAAAATAGT
1 TAAAATAGT
83292 TATAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 1 0.05
14 19 0.90
15 1 0.05
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (14 bp):
TAAAATAGTAAAAA
Found at i:88434 original size:31 final size:30
Alignment explanation
Indices: 88396--88456 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
88386 TTTTCTTTGA
88396 TTTTTTTTATACAAAAAAAGCCTAAATTAAT
1 TTTTTTTTATAC-AAAAAAGCCTAAATTAAT
* *
88427 TTTTTTTTCTACTAAAAAGCCTAAATTAAT
1 TTTTTTTTATACAAAAAAGCCTAAATTAAT
88457 GAAGATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 17 0.61
31 11 0.39
ACGTcount: A:0.41, C:0.11, G:0.03, T:0.44
Consensus pattern (30 bp):
TTTTTTTTATACAAAAAAGCCTAAATTAAT
Found at i:88804 original size:16 final size:16
Alignment explanation
Indices: 88783--88822 Score: 64
Period size: 16 Copynumber: 2.5 Consensus size: 16
88773 TATTTTTTGA
88783 TTAAAAAAT-TATTTTT
1 TTAAAAAATATA-TTTT
88799 TTAAAAAATATATTTT
1 TTAAAAAATATATTTT
88815 TTAAAAAA
1 TTAAAAAA
88823 AATTTGGGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 21 0.91
17 2 0.09
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAAAAAATATATTTT
Found at i:89758 original size:31 final size:29
Alignment explanation
Indices: 89692--89759 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 29
89682 TGTGCAAATG
*
89692 GGTCCCTGAAGTGAACTTATTGAGCAATT
1 GGTCCCTGAAGTGAACTTATTAAGCAATT
*
89721 GAGTCCCTGAAGTTG-AGTTAATTAAGCAATT
1 G-GTCCCTGAAG-TGAACTT-ATTAAGCAATT
89752 AGGTCCCT
1 -GGTCCCT
89760 CACCCAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
29 1 0.03
30 13 0.39
31 18 0.55
32 1 0.03
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.31
Consensus pattern (29 bp):
GGTCCCTGAAGTGAACTTATTAAGCAATT
Done.