Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010134.1 Corchorus capsularis cultivar CVL-1 contig10155, 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: 61639
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33
Found at i:496 original size:6 final size:6
Alignment explanation
Indices: 485--512 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
475 TATAATCTGC
485 TTTAGA TTTAGA TTTAGA TTTAGA TTTA
1 TTTAGA TTTAGA TTTAGA TTTAGA TTTA
513 TTTTGCTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (6 bp):
TTTAGA
Found at i:4562 original size:30 final size:30
Alignment explanation
Indices: 4526--4627 Score: 95
Period size: 30 Copynumber: 3.4 Consensus size: 30
4516 CTGTGTTATA
*
4526 TGTGTTTGGGGACTTCAGTATAGATGCCTC
1 TGTGTTTAGGGACTTCAGTATAGATGCCTC
* *
4556 TGTGTTTAGGGACTTTAATATAGATGCC-C
1 TGTGTTTAGGGACTTCAGTATAGATGCCTC
* *
4585 TTGTGCTT-GAGGACTTTGATGTA-A-ATGCCTC
1 -TGTGTTTAG-GGAC-TTCA-GTATAGATGCCTC
4616 TGTGTTTAGGGA
1 TGTGTTTAGGGA
4628 TGAATACCCT
Statistics
Matches: 59, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
29 2 0.03
30 49 0.83
31 6 0.10
32 2 0.03
ACGTcount: A:0.20, C:0.14, G:0.28, T:0.38
Consensus pattern (30 bp):
TGTGTTTAGGGACTTCAGTATAGATGCCTC
Found at i:4676 original size:53 final size:53
Alignment explanation
Indices: 4610--4820 Score: 251
Period size: 53 Copynumber: 3.8 Consensus size: 53
4600 TTGATGTAAA
* *
4610 TGCCTCTGTGTTTAGGGATGAATACCCTTGTGGTTGAGGACTTTTGAGAGAGG
1 TGCCTCTGTGTTTAGGGATAAATACCCTTGTGTTTGAGGACTTTTGAGAGAGG
* *
4663 TGCCTCTGTGTTTAGGGATGAATACCCTTGTGTTTGAGGACTTTTGGGAGAGG
1 TGCCTCTGTGTTTAGGGATAAATACCCTTGTGTTTGAGGACTTTTGAGAGAGG
* * * **
4716 TGCCTCTGTGTTTAGGGACTTATAAATGCCCTTGTGTTTGAGGACTTTTAATATAGAAT
1 TGCCTCTGTGTTTAGGG----ATAAATACCCTTGTGTTTGAGGACTTTT--GAGAGAGG
* * *
4775 TGCCTCTATGTTTAGGGACTAAATGCCCTTGTGTTTGAAGACTTTT
1 TGCCTCTGTGTTTAGGGA-TAAATACCCTTGTGTTTGAGGACTTTT
4821 AATTGTTGGG
Statistics
Matches: 140, Mismatches: 11, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
53 68 0.49
55 1 0.01
56 26 0.19
57 26 0.19
59 19 0.14
ACGTcount: A:0.20, C:0.14, G:0.28, T:0.38
Consensus pattern (53 bp):
TGCCTCTGTGTTTAGGGATAAATACCCTTGTGTTTGAGGACTTTTGAGAGAGG
Found at i:4823 original size:56 final size:54
Alignment explanation
Indices: 4579--4821 Score: 244
Period size: 53 Copynumber: 4.5 Consensus size: 54
4569 TTTAATATAG
* * *
4579 ATGCCCTTGTGCTTGAGGACTTTGAT-GTA-AA-TGCCTCTGTGTTTAGGGATGA
1 ATGCCCTTGTGTTTGAGGACTTTTATAG-AGAAGTGCCTCTGTGTTTAGGGATAA
* * * * *
4631 ATACCCTTGTGGTTGAGGACTTTT-GAGAGAGGTGCCTCTGTGTTTAGGGATGA
1 ATGCCCTTGTGTTTGAGGACTTTTATAGAGAAGTGCCTCTGTGTTTAGGGATAA
* ** *
4684 ATACCCTTGTGTTTGAGGACTTTT-GGGAGAGGTGCCTCTGTGTTTAGGGACTTATAA
1 ATGCCCTTGTGTTTGAGGACTTTTATAGAGAAGTGCCTCTGTGTTTAGGG----ATAA
* * *
4741 ATGCCCTTGTGTTTGAGGACTTTTAATATAGAATTGCCTCTATGTTTAGGGACTAA
1 ATGCCCTTGTGTTTGAGGACTTTT-ATAGAGAAGTGCCTCTGTGTTTAGGGA-TAA
*
4797 ATGCCCTTGTGTTTGAAGACTTTTA
1 ATGCCCTTGTGTTTGAGGACTTTTA
4822 ATTGTTGGGT
Statistics
Matches: 165, Mismatches: 16, Indels: 17
0.83 0.08 0.09
Matches are distributed among these distances:
51 1 0.01
52 23 0.14
53 68 0.41
55 2 0.01
56 26 0.16
57 26 0.16
59 19 0.12
ACGTcount: A:0.21, C:0.14, G:0.28, T:0.37
Consensus pattern (54 bp):
ATGCCCTTGTGTTTGAGGACTTTTATAGAGAAGTGCCTCTGTGTTTAGGGATAA
Found at i:5068 original size:2 final size:2
Alignment explanation
Indices: 5063--5095 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5053 AAAAAAGGGA
5063 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
5096 AAAGAAGAGT
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:5785 original size:20 final size:20
Alignment explanation
Indices: 5757--5802 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
5747 ATGGGGCATT
*
5757 TCAATTTAATAGCAGAACAG
1 TCAAGTTAATAGCAGAACAG
*
5777 TCAAGTTAATCGCAGAACAG
1 TCAAGTTAATAGCAGAACAG
*
5797 TTAAGT
1 TCAAGT
5803 GAGTGCAAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.26
Consensus pattern (20 bp):
TCAAGTTAATAGCAGAACAG
Found at i:7221 original size:35 final size:35
Alignment explanation
Indices: 7179--7620 Score: 670
Period size: 35 Copynumber: 12.7 Consensus size: 35
7169 AGTAATAAGT
7179 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
*
7214 AACTTAATTCAGGGTAATTAAGTGAGTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
* * * *
7249 AACTTAATTCTGGGTAATTAAGTCAGTCGGTAATA
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
* *
7284 AACTTAATTCAGGGTAATTAAGTAATTCAATAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
**
7319 AACTTAATTCAGGGTAATTAAGTGGGTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
*
7354 AACTTAATTCAGGGAAATTAAGTAAGTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
* * *
7389 AGCTTAATTCAGGGTAATTAAGTAATTCAATAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
* *
7424 AACTTAATTCAGGGTAATTAAGTAATTCAATAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
7459 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
* *
7494 AACTTAATTCAGGGTAATTAAGTCAGTCAGTAATA
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
* * *
7529 AACGTAATTAAGGGTAATTAAGTAATTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
* * *
7564 AACTTAATTCAGGATAATTAAGTAAGT-AATAAGC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
7598 AACTTAATTCAGGGTAATTAAGT
1 AACTTAATTCAGGGTAATTAAGT
7621 TTAGTAAAAA
Statistics
Matches: 368, Mismatches: 39, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
34 27 0.07
35 341 0.93
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (35 bp):
AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
Found at i:7433 original size:17 final size:17
Alignment explanation
Indices: 7411--7469 Score: 66
Period size: 17 Copynumber: 3.4 Consensus size: 17
7401 GGTAATTAAG
7411 TAATTCAATAATCAACT
1 TAATTCAATAATCAACT
* * *
7428 TAATTCAGGGTAATTAA-G
1 TAATTCA--ATAATCAACT
7446 TAATTCAATAATCAACT
1 TAATTCAATAATCAACT
7463 TAATTCA
1 TAATTCA
7470 GGGTAATTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
16 6 0.18
17 14 0.42
18 7 0.21
19 6 0.18
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.36
Consensus pattern (17 bp):
TAATTCAATAATCAACT
Found at i:8772 original size:25 final size:25
Alignment explanation
Indices: 8743--8792 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
8733 TTCAAAATTG
* * *
8743 TAATTCATAATTATTAATAATTAAA
1 TAATTAATAATAATCAATAATTAAA
8768 TAATTAATAATAATCAATAATTAAA
1 TAATTAATAATAATCAATAATTAAA
8793 AAAAATCTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (25 bp):
TAATTAATAATAATCAATAATTAAA
Found at i:8799 original size:17 final size:17
Alignment explanation
Indices: 8766--8799 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
8756 TTAATAATTA
* *
8766 AATAATTAATAATAATC
1 AATAATTAAAAAAAATC
8783 AATAATTAAAAAAAATC
1 AATAATTAAAAAAAATC
8800 TAAAACAAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (17 bp):
AATAATTAAAAAAAATC
Found at i:8901 original size:13 final size:13
Alignment explanation
Indices: 8885--8909 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
8875 TTACAAAATT
8885 TTAGATCTACAAC
1 TTAGATCTACAAC
8898 TTAGATCTACAA
1 TTAGATCTACAA
8910 AATAACAACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.32
Consensus pattern (13 bp):
TTAGATCTACAAC
Found at i:9745 original size:2 final size:2
Alignment explanation
Indices: 9738--9768 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
9728 ATAGAATCGA
9738 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 A
9769 CTTATTTGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15727 original size:23 final size:23
Alignment explanation
Indices: 15701--15761 Score: 79
Period size: 23 Copynumber: 2.6 Consensus size: 23
15691 AATCTGATGA
15701 GTATTTGAATATTTGGATATTT-G
1 GTATTTGAATATTTGG-TATTTGG
*
15724 GTATTTGGATATTTGGTATTTGG
1 GTATTTGAATATTTGGTATTTGG
15747 GTATGTATGAATATT
1 GTAT-T-TGAATATT
15762 CTAAGTATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 5 0.15
23 20 0.61
24 1 0.03
25 7 0.21
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.51
Consensus pattern (23 bp):
GTATTTGAATATTTGGTATTTGG
Found at i:15730 original size:7 final size:8
Alignment explanation
Indices: 15702--15746 Score: 67
Period size: 8 Copynumber: 5.9 Consensus size: 8
15692 ATCTGATGAG
*
15702 TATTTGAA
1 TATTTGGA
15710 TATTTGGA
1 TATTTGGA
15718 TATTTGG-
1 TATTTGGA
15725 TATTTGGA
1 TATTTGGA
15733 TATTTGG-
1 TATTTGGA
15740 TATTTGG
1 TATTTGG
15747 GTATGTATGA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
7 14 0.40
8 21 0.60
ACGTcount: A:0.22, C:0.00, G:0.24, T:0.53
Consensus pattern (8 bp):
TATTTGGA
Found at i:15730 original size:15 final size:15
Alignment explanation
Indices: 15710--15746 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
15700 AGTATTTGAA
15710 TATTTGGATATTTGG
1 TATTTGGATATTTGG
15725 TATTTGGATATTTGG
1 TATTTGGATATTTGG
15740 TATTTGG
1 TATTTGG
15747 GTATGTATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.27, T:0.54
Consensus pattern (15 bp):
TATTTGGATATTTGG
Found at i:23464 original size:30 final size:31
Alignment explanation
Indices: 23389--23466 Score: 83
Period size: 30 Copynumber: 2.5 Consensus size: 31
23379 CCCTGTGTTA
* *
23389 TATGTGTTTGGGGACTTTAGTATAGATGCCTC
1 TATGTG-TTGAGGACTTTAATATAGATGCCTC
23421 TATGT-TT-AGGGACTTTAATATAGATGCC-C
1 TATGTGTTGA-GGACTTTAATATAGATGCCTC
23450 T-TGTGCTTGAGGACTTT
1 TATGTG-TTGAGGACTTT
23467 GATGTAAATG
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
28 3 0.08
29 2 0.05
30 29 0.73
31 1 0.03
32 5 0.12
ACGTcount: A:0.21, C:0.13, G:0.26, T:0.41
Consensus pattern (31 bp):
TATGTGTTGAGGACTTTAATATAGATGCCTC
Found at i:23625 original size:56 final size:55
Alignment explanation
Indices: 23444--23634 Score: 214
Period size: 56 Copynumber: 3.5 Consensus size: 55
23434 TTTAATATAG
* * * *
23444 ATGCCCTTGTGCTTGAGGAC-TTTGATGTA-AATGTCTCTGTGTTTA-GGA-TGA
1 ATGCCCTTGTGTTTGAGGACTTTTAATGTAGAATGCCTCTGTGTTTAGGGACTAA
* * * *
23495 ATACCCTTGTGTTTGAGGACTTTT--GGGAGAGGTGCCTCTGTGTTTAGGGACTTATAA
1 ATGCCCTTGTGTTTGAGGACTTTTAATGTAGA-ATGCCTCTGTGTTTAGGGAC---TAA
*
23552 ATGCCCTTGTGTTTGAGGACTTTTAATATAGAATTGCCTCTGTGTTTAGGGACTAA
1 ATGCCCTTGTGTTTGAGGACTTTTAATGTAGAA-TGCCTCTGTGTTTAGGGACTAA
23608 ATGCCCTTGTGTTTGAGGACTTTTAAT
1 ATGCCCTTGTGTTTGAGGACTTTTAAT
23635 TGTTGGGTAA
Statistics
Matches: 117, Mismatches: 12, Indels: 17
0.80 0.08 0.12
Matches are distributed among these distances:
50 2 0.02
51 19 0.16
52 16 0.14
53 3 0.03
56 30 0.26
57 25 0.21
59 22 0.19
ACGTcount: A:0.20, C:0.14, G:0.26, T:0.39
Consensus pattern (55 bp):
ATGCCCTTGTGTTTGAGGACTTTTAATGTAGAATGCCTCTGTGTTTAGGGACTAA
Found at i:28466 original size:74 final size:74
Alignment explanation
Indices: 28388--28544 Score: 262
Period size: 74 Copynumber: 2.1 Consensus size: 74
28378 TGGTCTTTTC
* * *
28388 ACACTTTTCAGG-TTACTAAAAAGCCCCTCTATGAGTTTCCCCTATTCCTTTTCCTTCTATCCTT
1 ACACTTTTC-GGATGACTAAAAAGCCCCTCTATGAGTTTCCCCCATTCCTTTTCCTTCTACCCTT
28452 TTTCGTAATT
65 TTTCGTAATT
28462 ACACTTTTCGGATGACTAAAAAGCCCCTCTATGAGTTTCCCCCATTCCTTTTCCTTCTACCCTTT
1 ACACTTTTCGGATGACTAAAAAGCCCCTCTATGAGTTTCCCCCATTCCTTTTCCTTCTACCCTTT
28527 TTCGTAATT
66 TTCGTAATT
*
28536 ACACATTTC
1 ACACTTTTC
28545 CCTTCCTTAA
Statistics
Matches: 78, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
73 2 0.03
74 76 0.97
ACGTcount: A:0.21, C:0.30, G:0.08, T:0.41
Consensus pattern (74 bp):
ACACTTTTCGGATGACTAAAAAGCCCCTCTATGAGTTTCCCCCATTCCTTTTCCTTCTACCCTTT
TTCGTAATT
Found at i:28582 original size:20 final size:21
Alignment explanation
Indices: 28551--28589 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
28541 TTTCCCTTCC
28551 TTAATGGTTTTTAATTAATGT
1 TTAATGGTTTTTAATTAATGT
28572 TTAAT-GTTTTTAATTAAT
1 TTAATGGTTTTTAATTAAT
28590 TGCTTCTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.59
Consensus pattern (21 bp):
TTAATGGTTTTTAATTAATGT
Found at i:30759 original size:1 final size:1
Alignment explanation
Indices: 30753--30779 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
30743 ATTGTGTGAG
30753 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
30780 CATTTCTCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:33065 original size:2 final size:2
Alignment explanation
Indices: 33060--33094 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
33050 AAAAAAAAAA
33060 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
33095 ATTTTTTGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:37134 original size:18 final size:18
Alignment explanation
Indices: 37113--37153 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
37103 CATGTACGGG
37113 TATGACGACTTTGATGGT
1 TATGACGACTTTGATGGT
* *
37131 TATGATGGCTTTGATGGT
1 TATGACGACTTTGATGGT
37149 TATGA
1 TATGA
37154 TAGTGATCTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.22, C:0.07, G:0.29, T:0.41
Consensus pattern (18 bp):
TATGACGACTTTGATGGT
Found at i:39895 original size:4 final size:4
Alignment explanation
Indices: 39886--39937 Score: 54
Period size: 4 Copynumber: 12.8 Consensus size: 4
39876 TTATTACTAC
*
39886 TTAA TTAA TTAA TATAA TTGGA TTAA TTAA TCT-A -TAA TTAA TTAA TTAA
1 TTAA TTAA TTAA T-TAA TT-AA TTAA TTAA T-TAA TTAA TTAA TTAA TTAA
39935 TTA
1 TTA
39938 TGCTTTACTG
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
2 1 0.02
3 1 0.02
4 31 0.76
5 8 0.20
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (4 bp):
TTAA
Found at i:44423 original size:16 final size:15
Alignment explanation
Indices: 44396--44428 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
44386 AACCCAACCC
44396 AAGAAGAGAAGAAGA
1 AAGAAGAGAAGAAGA
44411 AAGAAGAAGAAGAAGA
1 AAGAAG-AGAAGAAGA
44427 AA
1 AA
44429 AAAACAAGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (15 bp):
AAGAAGAGAAGAAGA
Found at i:45444 original size:17 final size:18
Alignment explanation
Indices: 45416--45450 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
45406 CCTCCCCATA
45416 ATACCTAGGTAGTATGAG
1 ATACCTAGGTAGTATGAG
45434 ATACC-AGGTAGTATGAG
1 ATACCTAGGTAGTATGAG
45451 GTGATAGGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.34, C:0.11, G:0.29, T:0.26
Consensus pattern (18 bp):
ATACCTAGGTAGTATGAG
Found at i:47028 original size:3 final size:3
Alignment explanation
Indices: 47020--47122 Score: 145
Period size: 3 Copynumber: 34.7 Consensus size: 3
47010 CCTAATTAAG
47020 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * * *
47068 ATT ATT ATT ATT ATT ATT ATT ACT ACT ACT ACT ACT ATT GTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
47116 A-T ATT AT
1 ATT ATT AT
47123 AGTTATTAAA
Statistics
Matches: 95, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
2 2 0.02
3 93 0.98
ACGTcount: A:0.33, C:0.05, G:0.01, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:51497 original size:167 final size:165
Alignment explanation
Indices: 51220--51704 Score: 628
Period size: 167 Copynumber: 2.9 Consensus size: 165
51210 AACATATGGA
* ** * * ** *
51220 AATTACTAAAAGATCCCCACCCCGGATTTAATGAGGAGCGAGATAACTAATTTTTTTTCGTCTTT
1 AATTAATAAAAGATCCCCACCAAGGA-TTGATGATGAGTTAGAGAACTAA-TTTTTTTCGTCTTT
* * *
51285 TCCCACTTGGCAGATTACTTAAATGTCCTAACTATTAATTCTTGAGGGGATTAAATAACTAGACT
64 TCCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTA-ACT
* *
51350 TTTTGTTCATTTCTCAATTGACTTTAATAGAGTAGTGG
128 TTTTGGTCATTTCTCAATTGACTTGAATAGAGTAGTGG
* * * * * ** *
51388 AATTACTAAAAGATCCCTACCAATGCTTGCTTTTGGAGTTAGAGAACTTATTTTTTTCGTCTTTT
1 AATTAATAAAAGATCCCCACCAAGGATTGATGAT-GAGTTAGAGAACTAATTTTTTTCGTCTTTT
* * * *
51453 CCTACTTGGCAGAATACCTAAATGCCCTAACTTTTGATTCTTGAGGGGATTAAATAAGTAATCTT
65 CCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTAA-CTT
* *
51518 TTTGGTAATTTCTCAATGGACTTGAATAGAGTAGTGG
129 TTTGGTCATTTCTCAATTGACTTGAATAGAGTAGTGG
* * * *
51555 AATTAATAAAAGATCCCCATCAAGGATTGATGATGAGTTAGAGCACTAATCTTTTTCGTCTTTAC
1 AATTAATAAAAGATCCCCACCAAGGATTGATGATGAGTTAGAGAACTAATTTTTTTCGTCTTTTC
*
51620 CTACTTGGCAGATTGCTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTAAACTTT
66 CTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACT-AACTTT
51685 TTGGTCATTTCTCAATTGAC
130 TTGGTCATTTCTCAATTGAC
51705 AAATGACTAA
Statistics
Matches: 270, Mismatches: 44, Indels: 8
0.84 0.14 0.02
Matches are distributed among these distances:
166 103 0.38
167 135 0.50
168 32 0.12
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (165 bp):
AATTAATAAAAGATCCCCACCAAGGATTGATGATGAGTTAGAGAACTAATTTTTTTCGTCTTTTC
CTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTAACTTTT
TGGTCATTTCTCAATTGACTTGAATAGAGTAGTGG
Found at i:51973 original size:9 final size:9
Alignment explanation
Indices: 51959--51988 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
51949 ATTCTCATCT
51959 TATCTTTAA
1 TATCTTTAA
51968 TATCTTTAA
1 TATCTTTAA
51977 TATCTTTAA
1 TATCTTTAA
51986 TAT
1 TAT
51989 AGCAATTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (9 bp):
TATCTTTAA
Found at i:55990 original size:29 final size:27
Alignment explanation
Indices: 55929--55990 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
55919 GGGTGTCATC
55929 CCTT-TGGTATGGGAGACGGAAATCTT
1 CCTTCTGGTATGGGAGACGGAAATCTT
* * *
55955 CCCTCTGGTATGGGTGATGGACAATTCTT
1 CCTTCTGGTATGGGAGACGGA-AA-TCTT
55984 CCTTCTG
1 CCTTCTG
55991 CCTGTCATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 3 0.10
27 14 0.48
28 2 0.07
29 10 0.34
ACGTcount: A:0.18, C:0.21, G:0.27, T:0.34
Consensus pattern (27 bp):
CCTTCTGGTATGGGAGACGGAAATCTT
Found at i:58689 original size:10 final size:10
Alignment explanation
Indices: 58663--58706 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
58653 GTTATTTATT
*
58663 TATTTATTAC
1 TATTTTTTAC
58673 TATTTTTTTAC
1 TA-TTTTTTAC
58684 TATTTTTTAC
1 TATTTTTTAC
*
58694 TATTATTT-C
1 TATTTTTTAC
58703 TATT
1 TATT
58707 AATAATATCA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
9 5 0.16
10 17 0.55
11 9 0.29
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.68
Consensus pattern (10 bp):
TATTTTTTAC
Found at i:59738 original size:178 final size:181
Alignment explanation
Indices: 59398--59763 Score: 542
Period size: 178 Copynumber: 2.0 Consensus size: 181
59388 TATTCTGGAA
* * *
59398 ACAAAATACTTACTGCTTGTTTTATCTGCTTTGTTATATCAGCATGTAACAGCAAGTTGCAAACA
1 ACAAAATACTTACTGCTTCTTTTATATGCTTTGTTATATCAACATGTAACAGCAAGTTGCAAACA
* *
59463 TTGCATGATAACGCCCTAAATTGAACAAATCTGTTAACGTTGTTTGGCTAAAAATTTTAAATTGT
66 TTGCATGATAACGCCC---ACTG---AAATCTGTTAACCTTGTTTGGCTAAAAATTTTAAATTGT
*
59528 CATAAGCAATCAGTTTTTCATTTGACATCAAAGACG-AAATTATGCTTTAACCTTGAG
125 CATAAGCAATCAGTTTTTCATTTGACATCAAAGA-GAAAACTATGCTTTAACCTTGAG
* *
59585 ACAAAATACTTACTGCTTCTTTTATATGCTTTGTTATATCAACTTGTAACAGTAAGTTGCAAACA
1 ACAAAATACTTACTGCTTCTTTTATATGCTTTGTTATATCAACATGTAACAGCAAGTTGCAAACA
* *
59650 TTGCATGATAAC-CCC-CTG-AATCTGTTAACCTTTTTTGGCTTAAAATTTTAAATTGTCATAAG
66 TTGCATGATAACGCCCACTGAAATCTGTTAACCTTGTTTGGCTAAAAATTTTAAATTGTCATAAG
*
59712 CAATTAGTTTTTCATTTGACATCAAAGAGAAAACTATGCTTTAACCTTGAG
131 CAATCAGTTTTTCATTTGACATCAAAGAGAAAACTATGCTTTAACCTTGAG
59763 A
1 A
59764 AGAAAATAAA
Statistics
Matches: 167, Mismatches: 11, Indels: 11
0.88 0.06 0.06
Matches are distributed among these distances:
177 1 0.01
178 89 0.53
182 2 0.01
186 3 0.02
187 72 0.43
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (181 bp):
ACAAAATACTTACTGCTTCTTTTATATGCTTTGTTATATCAACATGTAACAGCAAGTTGCAAACA
TTGCATGATAACGCCCACTGAAATCTGTTAACCTTGTTTGGCTAAAAATTTTAAATTGTCATAAG
CAATCAGTTTTTCATTTGACATCAAAGAGAAAACTATGCTTTAACCTTGAG
Found at i:59823 original size:29 final size:30
Alignment explanation
Indices: 59763--59823 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 30
59753 TAACCTTGAG
59763 AAGAAAATAAAGCTGCAAAAAGAATTCAAAA
1 AAGAAAATAAAGCTGC-AAAAGAATTCAAAA
*
59794 AAGAAAATAGAGCTGC-AAAGAATTCAAAA
1 AAGAAAATAAAGCTGCAAAAGAATTCAAAA
59823 A
1 A
59824 GTATAAGGAG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 14 0.48
31 15 0.52
ACGTcount: A:0.62, C:0.10, G:0.15, T:0.13
Consensus pattern (30 bp):
AAGAAAATAAAGCTGCAAAAGAATTCAAAA
Found at i:60552 original size:186 final size:185
Alignment explanation
Indices: 60235--60571 Score: 541
Period size: 186 Copynumber: 1.8 Consensus size: 185
60225 AAAGAGAAGG
* * * *
60235 AATATCAGCTTGTAACAGCAAGTTGCAAATATTGCATGATAAACCCCTTAATTGTACAAATCTAT
1 AATATCAACTTGTAACAGCAAGTTGCAAACATTGCATGATAAACCCCTTAAATGAACAAATCTAT
*
60300 TAACCTTTTTTGGCTAAAAATTTTAAATTGTCATCATCAATAAGTTTTTCATTTGACATAAAAGA
66 TAACCTTTTTTGGCTAAAAATTTTAAATTGTCATCAGCAATAAGTTTTTCATTTGACATAAAAGA
* *
60365 GGAAATTATGCTTTAACCTTGAGACAAAATACTTACTGCTTCTTTTATCTGCCAA
131 GGAAACTATGATTTAACCTTGAGACAAAATACTTACTGCTTCTTTTATCTGCCAA
60420 AATATCAACTTGTAACAGCAAGTTGCAAAACATTGCATGAT-AACCCCTTGAAATGAACAAATCT
1 AATATCAACTTGTAACAGCAAGTTGC-AAACATTGCATGATAAACCCCTT-AAATGAACAAATCT
* * * * *
60484 GTTAATCTTTTTTGGCTAAAAATTTTAAATTTTCATCAGCAATCAGTTTTTCATTTGACATCAAA
64 ATTAACCTTTTTTGGCTAAAAATTTTAAATTGTCATCAGCAATAAGTTTTTCATTTGACATAAAA
60549 GAGGAAACTATGATTTAACCTTG
129 GAGGAAACTATGATTTAACCTTG
60572 GGAAGAAAAT
Statistics
Matches: 138, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
185 33 0.24
186 105 0.76
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (185 bp):
AATATCAACTTGTAACAGCAAGTTGCAAACATTGCATGATAAACCCCTTAAATGAACAAATCTAT
TAACCTTTTTTGGCTAAAAATTTTAAATTGTCATCAGCAATAAGTTTTTCATTTGACATAAAAGA
GGAAACTATGATTTAACCTTGAGACAAAATACTTACTGCTTCTTTTATCTGCCAA
Found at i:60628 original size:30 final size:31
Alignment explanation
Indices: 60574--60635 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
60564 TAACCTTGGG
60574 AAGAAAATAAAGCTGCAAAAAGAATTCAAAAA
1 AAGAAAATAAAGCTGC-AAAAGAATTCAAAAA
* *
60606 AAGAATATAGAGCTGC-AAAGAATTCAAAAA
1 AAGAAAATAAAGCTGCAAAAGAATTCAAAAA
60636 GTATAAGGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 14 0.50
32 14 0.50
ACGTcount: A:0.61, C:0.10, G:0.15, T:0.15
Consensus pattern (31 bp):
AAGAAAATAAAGCTGCAAAAGAATTCAAAAA
Found at i:61135 original size:29 final size:30
Alignment explanation
Indices: 61074--61135 Score: 99
Period size: 31 Copynumber: 2.1 Consensus size: 30
61064 ATAAAGCTGC
61074 AAAGAAAATAAAGCTGCAAAAAGAATTCAAA
1 AAAGAAAATAAAGCTGC-AAAAGAATTCAAA
*
61105 AAAGAAAATAGAGCTGC-AAAGAATTCAAA
1 AAAGAAAATAAAGCTGCAAAAGAATTCAAA
61134 AA
1 AA
61136 GTATAAGGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 14 0.47
31 16 0.53
ACGTcount: A:0.63, C:0.10, G:0.15, T:0.13
Consensus pattern (30 bp):
AAAGAAAATAAAGCTGCAAAAGAATTCAAA
Done.