Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020108.1 Corchorus olitorius cultivar O-4 contig20141, 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: 106890
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:4543 original size:21 final size:22
Alignment explanation
Indices: 4517--4592 Score: 93
Period size: 21 Copynumber: 3.5 Consensus size: 22
4507 TCTCACAGAG
*
4517 AGGTTATCAAAA-ATCATAGGA
1 AGGTTATCAAAATTTCATAGGA
4538 AGGTTA-CAAAATTTCATAGGA
1 AGGTTATCAAAATTTCATAGGA
* **
4559 AGGTTTATTAAAATTTCATAGTT
1 AGG-TTATCAAAATTTCATAGGA
4582 AGGTTATCAAA
1 AGGTTATCAAA
4593 GTTTAATATT
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.11
21 17 0.36
22 10 0.21
23 15 0.32
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.33
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATAGGA
Found at i:4617 original size:29 final size:29
Alignment explanation
Indices: 4566--4621 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
4556 GGAAGGTTTA
* **
4566 TTAAAATTTCATAGTTAGGTTATCAAAGT
1 TTAAAATTTCATAGGTAAATTATCAAAGT
*
4595 TTAATATTTCATAGGTAAATTATCAAA
1 TTAAAATTTCATAGGTAAATTATCAAA
4622 ATTTCATAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.41
Consensus pattern (29 bp):
TTAAAATTTCATAGGTAAATTATCAAAGT
Found at i:4639 original size:22 final size:22
Alignment explanation
Indices: 4613--4668 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 22
4603 TCATAGGTAA
*
4613 ATTATCAAAATTTCATAACG-TG
1 ATTATCAAAATTTAATAA-GTTG
*
4635 GTTATCAAAATTTAATAAGTTG
1 ATTATCAAAATTTAATAAGTTG
4657 ATTATCAAAATT
1 ATTATCAAAATT
4669 ACTTAAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
21 1 0.03
22 29 0.97
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (22 bp):
ATTATCAAAATTTAATAAGTTG
Found at i:4802 original size:2 final size:2
Alignment explanation
Indices: 4759--4793 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4749 AAACTATTAA
4759 AT 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 AT A
4794 ACTTATATAA
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:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5100 original size:31 final size:31
Alignment explanation
Indices: 5029--5100 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 31
5019 GTCTATCAGC
*
5029 TTTTAATTTGTTTAATTTAAGACTTTCATTT
1 TTTTAATTTGTTTAATTTAAGACTTTAATTT
*
5060 TAATT-ATTTGTTTAATTTAATG-C-TTAATTT
1 T-TTTAATTTGTTTAATTTAA-GACTTTAATTT
5090 ATTTTAATTTG
1 -TTTTAATTTG
5101 CAATAATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
30 8 0.24
31 23 0.68
32 3 0.09
ACGTcount: A:0.28, C:0.04, G:0.07, T:0.61
Consensus pattern (31 bp):
TTTTAATTTGTTTAATTTAAGACTTTAATTT
Found at i:5390 original size:13 final size:12
Alignment explanation
Indices: 5354--5400 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
5344 TCAATCTTTA
*
5354 TATATATTGATAA
1 TATATATT-ATAT
*
5367 TA-ATGTTATAT
1 TATATATTATAT
5378 TATATTATTATAT
1 TATA-TATTATAT
5391 TATATATTAT
1 TATATATTAT
5401 CAATAAACTT
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:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (12 bp):
TATATATTATAT
Found at i:6569 original size:75 final size:75
Alignment explanation
Indices: 6484--6626 Score: 225
Period size: 75 Copynumber: 1.9 Consensus size: 75
6474 ATATTTTATT
*
6484 ATATTTTAATAATGACATAATTAAAATACATTTTGATAA-AGACAATTTAGAAATATATTTGAAA
1 ATATTTTAATAATGACATAATTAAAATACATTTTGATAATA-ACAATATAGAAATATATTTGAAA
6548 AAAAGTACACG
65 AAAAGTACACG
* * * *
6559 ATATTTTAATAATGACCTAATTCAAATATATTTTGATAATAACACTATAGAAATATATTTGAAAA
1 ATATTTTAATAATGACATAATTAAAATACATTTTGATAATAACAATATAGAAATATATTTGAAAA
6624 AAA
66 AAA
6627 AAATTAATAA
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
75 61 0.98
76 1 0.02
ACGTcount: A:0.50, C:0.07, G:0.08, T:0.35
Consensus pattern (75 bp):
ATATTTTAATAATGACATAATTAAAATACATTTTGATAATAACAATATAGAAATATATTTGAAAA
AAAGTACACG
Found at i:6655 original size:11 final size:11
Alignment explanation
Indices: 6641--6665 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
6631 TAATAATGAC
6641 ATAATTAAAAA
1 ATAATTAAAAA
6652 ATAATTAAAAA
1 ATAATTAAAAA
6663 ATA
1 ATA
6666 TTTTGATACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
ATAATTAAAAA
Found at i:8710 original size:11 final size:11
Alignment explanation
Indices: 8693--8724 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
8683 ACAGCGCAAT
8693 AAAAACAAAAC
1 AAAAACAAAAC
*
8704 GAAAACAAAAC
1 AAAAACAAAAC
8715 AAAAACAAAA
1 AAAAACAAAA
8725 AACAGAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.81, C:0.16, G:0.03, T:0.00
Consensus pattern (11 bp):
AAAAACAAAAC
Found at i:23715 original size:15 final size:15
Alignment explanation
Indices: 23683--23721 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
23673 GTTGGATGCA
* * *
23683 GCTTGTTTTGATGTT
1 GCTTGGTTTGAGGAT
23698 GCTTGGTTTGAGGAT
1 GCTTGGTTTGAGGAT
23713 GCTTGGTTT
1 GCTTGGTTT
23722 AATGTGGATG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.08, C:0.08, G:0.33, T:0.51
Consensus pattern (15 bp):
GCTTGGTTTGAGGAT
Found at i:25978 original size:15 final size:15
Alignment explanation
Indices: 25960--26014 Score: 74
Period size: 15 Copynumber: 3.7 Consensus size: 15
25950 CCGATATGAG
*
25960 GAATCCACACTATCA
1 GAATCCACATTATCA
*
25975 GAATCCATATTATCA
1 GAATCCACATTATCA
*
25990 GAATCCCCATTATCA
1 GAATCCACATTATCA
*
26005 GGATCCACAT
1 GAATCCACAT
26015 CCTCAACTTG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.36, C:0.29, G:0.09, T:0.25
Consensus pattern (15 bp):
GAATCCACATTATCA
Found at i:26206 original size:18 final size:18
Alignment explanation
Indices: 26183--26228 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
26173 TTATTGTCAG
*
26183 CATTCTCAGCTTGCTCAC
1 CATTCTCACCTTGCTCAC
*
26201 CATTCTCACCTTGCTGAC
1 CATTCTCACCTTGCTCAC
26219 CATTCTCACC
1 CATTCTCACC
26229 ATCATTCGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.17, C:0.41, G:0.09, T:0.33
Consensus pattern (18 bp):
CATTCTCACCTTGCTCAC
Found at i:28034 original size:7 final size:7
Alignment explanation
Indices: 28022--28048 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
28012 CCCTCTGAAA
28022 AAAAAAT
1 AAAAAAT
28029 AAAAAAT
1 AAAAAAT
28036 AAAAAAT
1 AAAAAAT
28043 AAAAAA
1 AAAAAA
28049 CTTCGTGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (7 bp):
AAAAAAT
Found at i:31040 original size:21 final size:22
Alignment explanation
Indices: 31014--31057 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
31004 AAGCAGCGAT
31014 GTTA-GGCTTAGAGAAGGT-GAA
1 GTTAGGGCTTAG-GAAGGTAGAA
31035 GTTAGGGCTTAGGAAGGTAGAA
1 GTTAGGGCTTAGGAAGGTAGAA
31057 G
1 G
31058 AACCAGAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.32, C:0.05, G:0.41, T:0.23
Consensus pattern (22 bp):
GTTAGGGCTTAGGAAGGTAGAA
Found at i:32417 original size:52 final size:52
Alignment explanation
Indices: 32358--32563 Score: 313
Period size: 52 Copynumber: 4.0 Consensus size: 52
32348 TCCTTCTAAG
* * * *
32358 TTTTCAAAATGGGAAAGTTCCCATCATGTTTTCAACGTGTTCAATTTAGGTT
1 TTTTCAAAGTGGGAAAGTTCCCATCAGGTTTTCAAAGTGTTCAATTTAGGTC
* *
32410 TTTTCAAAGTGGGGAAGTTCCCATCAGGTTTTCAATGTGTTCAATTTAGGTC
1 TTTTCAAAGTGGGAAAGTTCCCATCAGGTTTTCAAAGTGTTCAATTTAGGTC
* * *
32462 TTTTCAAAGTGGGGAAGTTCCCATCAAGTTTTCAAAATGTTCAATTTAGGTC
1 TTTTCAAAGTGGGAAAGTTCCCATCAGGTTTTCAAAGTGTTCAATTTAGGTC
* *
32514 TTTTCAAAGTGGGAAAGTTCCCATCAGGTTATCAAAGCGTTCAATTTAGG
1 TTTTCAAAGTGGGAAAGTTCCCATCAGGTTTTCAAAGTGTTCAATTTAGG
32564 GAAGGTTCCC
Statistics
Matches: 141, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 141 1.00
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (52 bp):
TTTTCAAAGTGGGAAAGTTCCCATCAGGTTTTCAAAGTGTTCAATTTAGGTC
Found at i:32664 original size:37 final size:37
Alignment explanation
Indices: 32618--32699 Score: 119
Period size: 37 Copynumber: 2.2 Consensus size: 37
32608 GGGGGGGGGG
* *
32618 AAGATCCCGCTAGTTTTAGTTTTGTCTTAAGAAGGGA
1 AAGATCCCGCTAGTTTTACTTTCGTCTTAAGAAGGGA
* * *
32655 AAGATCCCGCTAGTTTTACTTTCGTTTTAGGATGGGA
1 AAGATCCCGCTAGTTTTACTTTCGTCTTAAGAAGGGA
32692 AAGATCCC
1 AAGATCCC
32700 ATCAAACAAC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (37 bp):
AAGATCCCGCTAGTTTTACTTTCGTCTTAAGAAGGGA
Found at i:38713 original size:63 final size:63
Alignment explanation
Indices: 38634--38757 Score: 203
Period size: 63 Copynumber: 2.0 Consensus size: 63
38624 TCTTTAGGAC
38634 AAAATTAATAGCTTATGATTTAATCTTCACTTAATTTAAAACAACAGATTGGGTCACGTGCAA
1 AAAATTAATAGCTTATGATTTAATCTTCACTTAATTTAAAACAACAGATTGGGTCACGTGCAA
* * * * *
38697 AAAATTAGTAGCTTATGATTTTATCTTCATTTAATTTAAAAGAACAGATTGGGTTACGTGC
1 AAAATTAATAGCTTATGATTTAATCTTCACTTAATTTAAAACAACAGATTGGGTCACGTGC
38758 GTTGCACGTG
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 56 1.00
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (63 bp):
AAAATTAATAGCTTATGATTTAATCTTCACTTAATTTAAAACAACAGATTGGGTCACGTGCAA
Found at i:40609 original size:25 final size:26
Alignment explanation
Indices: 40571--40620 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
40561 TGTTAATGGA
40571 TTTTCCTAGAAGAATTAGG-TTTTAC
1 TTTTCCTAGAAGAATTAGGATTTTAC
**
40596 TTTTCCTATTAGAATTAGGATTTTA
1 TTTTCCTAGAAGAATTAGGATTTTA
40621 GTCAAGTGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.28, C:0.10, G:0.14, T:0.48
Consensus pattern (26 bp):
TTTTCCTAGAAGAATTAGGATTTTAC
Found at i:41613 original size:13 final size:13
Alignment explanation
Indices: 41595--41622 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
41585 GGTTTGCAAG
41595 AAGTGCTTTTTAA
1 AAGTGCTTTTTAA
41608 AAGTGCTTTTTAA
1 AAGTGCTTTTTAA
41621 AA
1 AA
41623 TTTGGGTAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (13 bp):
AAGTGCTTTTTAA
Found at i:42252 original size:13 final size:13
Alignment explanation
Indices: 42234--42259 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
42224 GATTTTAATG
42234 TTTATGGATTTTC
1 TTTATGGATTTTC
42247 TTTATGGATTTTC
1 TTTATGGATTTTC
42260 CCAGAAGGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.08, G:0.15, T:0.62
Consensus pattern (13 bp):
TTTATGGATTTTC
Found at i:45430 original size:6 final size:6
Alignment explanation
Indices: 45419--45460 Score: 77
Period size: 6 Copynumber: 7.2 Consensus size: 6
45409 CAAAAATTAA
45419 TTATTT TTATTT TTATTT TTATTT TTATTT TTA-TT TTATTT T
1 TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT T
45461 CAAAGAAAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 5 0.14
6 30 0.86
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TTATTT
Found at i:47469 original size:15 final size:15
Alignment explanation
Indices: 47449--47479 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
47439 AAGAAAGTGG
*
47449 AATAAAATTAAAAAA
1 AATAAAAATAAAAAA
47464 AATAAAAATAAAAAA
1 AATAAAAATAAAAAA
47479 A
1 A
47480 CAAGAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (15 bp):
AATAAAAATAAAAAA
Found at i:56188 original size:2 final size:2
Alignment explanation
Indices: 56181--56213 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
56171 TACTATTTAG
56181 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
56214 CCTTTTTAAC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:56559 original size:13 final size:14
Alignment explanation
Indices: 56541--56570 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
56531 ATTTTTTCCC
56541 TTTTTATCTTTT-T
1 TTTTTATCTTTTCT
56554 TTTTTATCTTTTCT
1 TTTTTATCTTTTCT
56568 TTT
1 TTT
56571 ATCAATTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTATCTTTTCT
Found at i:56928 original size:56 final size:56
Alignment explanation
Indices: 56837--56947 Score: 179
Period size: 56 Copynumber: 2.0 Consensus size: 56
56827 TCTTCTTCCT
* *
56837 TATAGCTAATCCTTATCTTTCCCGCAACCAAAATTTCTGAATGATTCCTTAAGATC
1 TATAACTAATCCTTAACTTTCCCGCAACCAAAATTTCTGAATGATTCCTTAAGATC
*
56893 TATAACTAATCCTTAACTTTCCC-CTAACCAAAATTTCTGAATGGTTCCTTAAGAT
1 TATAACTAATCCTTAACTTTCCCGC-AACCAAAATTTCTGAATGATTCCTTAAGAT
56948 TATTAAAAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
55 1 0.02
56 50 0.98
ACGTcount: A:0.32, C:0.24, G:0.08, T:0.36
Consensus pattern (56 bp):
TATAACTAATCCTTAACTTTCCCGCAACCAAAATTTCTGAATGATTCCTTAAGATC
Found at i:57310 original size:25 final size:25
Alignment explanation
Indices: 57276--57324 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
57266 TGTTGGTTTG
57276 TAGAGACCGAGCGAGAGTGCTCAAA
1 TAGAGACCGAGCGAGAGTGCTCAAA
57301 TAGAGACCGAGCGAGAGTGCTCAA
1 TAGAGACCGAGCGAGAGTGCTCAA
57325 GATTATTTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.35, C:0.20, G:0.33, T:0.12
Consensus pattern (25 bp):
TAGAGACCGAGCGAGAGTGCTCAAA
Found at i:58167 original size:21 final size:21
Alignment explanation
Indices: 58132--58173 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
58122 TATGGGTGTG
*
58132 TGTGATTGTTTGGTTTGGTAGA
1 TGTGATTGATTGGTTT-GTAGA
58154 TGTGA-TGATTGGTTTGTAGA
1 TGTGATTGATTGGTTTGTAGA
58174 GACCGAGCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 9 0.47
22 5 0.26
ACGTcount: A:0.17, C:0.00, G:0.36, T:0.48
Consensus pattern (21 bp):
TGTGATTGATTGGTTTGTAGA
Found at i:58945 original size:51 final size:51
Alignment explanation
Indices: 58887--58984 Score: 196
Period size: 51 Copynumber: 1.9 Consensus size: 51
58877 TTAGATATTT
58887 AATATTACACGTGTTATGATCTCAGTATGGACTGGCCTCTCCAGTCCATAA
1 AATATTACACGTGTTATGATCTCAGTATGGACTGGCCTCTCCAGTCCATAA
58938 AATATTACACGTGTTATGATCTCAGTATGGACTGGCCTCTCCAGTCC
1 AATATTACACGTGTTATGATCTCAGTATGGACTGGCCTCTCCAGTCC
58985 TTTTTATGGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (51 bp):
AATATTACACGTGTTATGATCTCAGTATGGACTGGCCTCTCCAGTCCATAA
Found at i:75652 original size:17 final size:17
Alignment explanation
Indices: 75606--75652 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
75596 AACACATCCA
*
75606 TTTTATTGG-TAGACAT
1 TTTTTTTGGTTAGACAT
* *
75622 TTTAATTTGTTTAGACAT
1 TTT-TTTTGGTTAGACAT
75640 TTTTTTTGGTTAG
1 TTTTTTTGGTTAG
75653 TTTTGCATTG
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
16 3 0.12
17 11 0.46
18 10 0.42
ACGTcount: A:0.21, C:0.04, G:0.17, T:0.57
Consensus pattern (17 bp):
TTTTTTTGGTTAGACAT
Found at i:79080 original size:10 final size:10
Alignment explanation
Indices: 79065--79109 Score: 65
Period size: 10 Copynumber: 4.6 Consensus size: 10
79055 CAAATTTGAA
79065 GAAAAAAAAT
1 GAAAAAAAAT
*
79075 GAAAAAGAA-
1 GAAAAAAAAT
79084 GAAAAAAAAT
1 GAAAAAAAAT
*
79094 GAAAAAAAAG
1 GAAAAAAAAT
79104 GAAAAA
1 GAAAAA
79110 TCAGAAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
9 8 0.26
10 23 0.74
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (10 bp):
GAAAAAAAAT
Found at i:79086 original size:19 final size:19
Alignment explanation
Indices: 79062--79109 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
79052 GGTCAAATTT
79062 GAAGAAAAAAAATGAAAAA
1 GAAGAAAAAAAATGAAAAA
79081 GAAGAAAAAAAATGAAAAA
1 GAAGAAAAAAAATGAAAAA
*
79100 AAAGGAAAAA
1 GAA-GAAAAA
79110 TCAGAAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 21 0.78
20 6 0.22
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (19 bp):
GAAGAAAAAAAATGAAAAA
Found at i:79169 original size:22 final size:21
Alignment explanation
Indices: 79140--79193 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
79130 ATAAAATGTG
*
79140 TTTTCAAAAATTGTTTTTCTT-
1 TTTTCAAAAATTG-TTCTCTTA
*
79161 TTTCTCAAATA-TGTTCTCTTA
1 TTT-TCAAAAATTGTTCTCTTA
79182 TTTTCAAAAATT
1 TTTTCAAAAATT
79194 TAAGAAAAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
20 12 0.44
21 9 0.33
22 6 0.22
ACGTcount: A:0.28, C:0.13, G:0.04, T:0.56
Consensus pattern (21 bp):
TTTTCAAAAATTGTTCTCTTA
Found at i:80806 original size:20 final size:19
Alignment explanation
Indices: 80769--80815 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
80759 TGATATAATT
*
80769 AAAAGAAAAAAGAAAGAAG
1 AAAAGAAAAAAAAAAGAAG
80788 AAAAGAAAAGAAAAAAGAAG
1 AAAAGAAAA-AAAAAAGAAG
*
80808 AAAGGAAA
1 AAAAGAAA
80816 GAATCATGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (19 bp):
AAAAGAAAAAAAAAAGAAG
Found at i:82778 original size:22 final size:22
Alignment explanation
Indices: 82752--82813 Score: 106
Period size: 22 Copynumber: 2.8 Consensus size: 22
82742 AGCCGACGAT
82752 GGCGCTGCAAGCTAGGTGGAGC
1 GGCGCTGCAAGCTAGGTGGAGC
* *
82774 GGCGCTGCAAGCTAGGCGGAGT
1 GGCGCTGCAAGCTAGGTGGAGC
82796 GGCGCTGCAAGCTAGGTG
1 GGCGCTGCAAGCTAGGTG
82814 AGGCGGTGCA
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:0.18, C:0.23, G:0.45, T:0.15
Consensus pattern (22 bp):
GGCGCTGCAAGCTAGGTGGAGC
Found at i:83920 original size:53 final size:53
Alignment explanation
Indices: 83862--84023 Score: 202
Period size: 53 Copynumber: 3.1 Consensus size: 53
83852 TCAAGTCTTC
* * *
83862 AAAGTATTCAATTTAACTCTTTTTCAAGTCGGGAAGGTTCCCATCAGTTTTCA
1 AAAGTATTCAATTTAACTCTTCTTCAAATCGGGAAAGTTCCCATCAGTTTTCA
* * * *
83915 AAAGTATTCCATCTAGCTCTTCTTCAAATCGGGAAAGTTCCCATCAATTTTC-
1 AAAGTATTCAATTTAACTCTTCTTCAAATCGGGAAAGTTCCCATCAGTTTTCA
* * *
83967 AAAGTATTCAATTTCAC-CAGTCTTCAAATTGGGAAAGTTCCCATCCAGTTTTCA
1 AAAGTATTCAATTTAACTC-TTCTTCAAATCGGGAAAGTTCCCAT-CAGTTTTCA
84021 AAA
1 AAA
84024 TTGTCAAATT
Statistics
Matches: 92, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
51 1 0.01
52 36 0.39
53 52 0.57
54 3 0.03
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.35
Consensus pattern (53 bp):
AAAGTATTCAATTTAACTCTTCTTCAAATCGGGAAAGTTCCCATCAGTTTTCA
Found at i:84075 original size:35 final size:36
Alignment explanation
Indices: 83989--84266 Score: 282
Period size: 35 Copynumber: 7.7 Consensus size: 36
83979 TTCACCAGTC
* *
83989 TTCAAATTGGGAAAGTTCCCATCCAGTTTTCAAAATT
1 TTCAAATTGGGAAAGTTCCCATCCAGTTTT-TAAGTT
*
84026 GTCAAATTGGGAAAGTTCCCA-CCAGTTTTTAAGTT
1 TTCAAATTGGGAAAGTTCCCATCCAGTTTTTAAGTT
* *
84061 TTTAAATTGGGAAAGTTCCCA-CCAGTTTTTAAATT
1 TTCAAATTGGGAAAGTTCCCATCCAGTTTTTAAGTT
* * * *
84096 TTTAAATTGGAAAAGTTCTCA-CCAGTCTTTAAGTT
1 TTCAAATTGGGAAAGTTCCCATCCAGTTTTTAAGTT
* *
84131 TTCAAATTGGGAAAGTTCACATTCAGTTTTTAAAGTT
1 TTCAAATTGGGAAAGTTCCCATCCAGTTTTT-AAGTT
* *
84168 TTTAAATTGGGAAAGTTCCCATCAAG-TTTT-AGTT
1 TTCAAATTGGGAAAGTTCCCATCCAGTTTTTAAGTT
* * *
84202 TTCAATTTAGGGAGAGTTCCCGTCATTTTCAG-TTTT-AGTT
1 TTCAAATT-GGGAAAGTT-CC--CA--TCCAGTTTTTAAGTT
*
84242 TTCAAAGTGGGAAAGTTCCCATCCA
1 TTCAAATTGGGAAAGTTCCCATCCA
84267 AAACATTTTC
Statistics
Matches: 205, Mismatches: 28, Indels: 19
0.81 0.11 0.08
Matches are distributed among these distances:
34 13 0.06
35 93 0.45
36 23 0.11
37 47 0.23
38 4 0.02
39 8 0.04
40 17 0.08
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.38
Consensus pattern (36 bp):
TTCAAATTGGGAAAGTTCCCATCCAGTTTTTAAGTT
Found at i:84220 original size:107 final size:105
Alignment explanation
Indices: 83989--84197 Score: 285
Period size: 107 Copynumber: 1.9 Consensus size: 105
83979 TTCACCAGTC
* * * * *
83989 TTCAAATTGGGAAAGTTCCCATCCAGT-TTTCAAAATTGTCAAATTGGGAAAGTTCCCACCAGTT
1 TTCAAATTGGAAAAGTTCTCA-CCAGTCTTT--AAGTTTTCAAATTGGGAAAGTTCACACCAGTT
*
84053 TTTAAGTTTTTAAATTGGGAAAGTTCCCACCAGTTTTTAAATT
63 TTTAAGTTTTTAAATTGGGAAAGTTCCCACAAGTTTTTAAATT
* *
84096 TTTAAATTGGAAAAGTTCTCACCAGTCTTTAAGTTTTCAAATTGGGAAAGTTCACATTCAGTTTT
1 TTCAAATTGGAAAAGTTCTCACCAGTCTTTAAGTTTTCAAATTGGGAAAGTTCACA-CCAGTTTT
84161 TAAAGTTTTTAAATTGGGAAAGTTCCCATCAAGTTTT
65 T-AAGTTTTTAAATTGGGAAAGTTCCCA-CAAGTTTT
84198 AGTTTTCAAT
Statistics
Matches: 90, Mismatches: 8, Indels: 7
0.86 0.08 0.07
Matches are distributed among these distances:
105 23 0.26
106 13 0.14
107 47 0.52
108 7 0.08
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (105 bp):
TTCAAATTGGAAAAGTTCTCACCAGTCTTTAAGTTTTCAAATTGGGAAAGTTCACACCAGTTTTT
AAGTTTTTAAATTGGGAAAGTTCCCACAAGTTTTTAAATT
Found at i:86695 original size:13 final size:11
Alignment explanation
Indices: 86669--86710 Score: 50
Period size: 10 Copynumber: 3.7 Consensus size: 11
86659 ATAAAAAAAT
86669 GAAAAAATAAA
1 GAAAAAATAAA
86680 GAAAAGAATGAAA
1 GAAAA-AAT-AAA
*
86693 GAAAAAA-AAT
1 GAAAAAATAAA
86703 GAAAAAAT
1 GAAAAAAT
86711 GAAAATAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
10 9 0.33
11 5 0.19
12 5 0.19
13 8 0.30
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (11 bp):
GAAAAAATAAA
Found at i:87128 original size:12 final size:11
Alignment explanation
Indices: 87094--87186 Score: 73
Period size: 12 Copynumber: 8.0 Consensus size: 11
87084 GAAATTCAAT
87094 CAAAAACAAAAA
1 CAAAAA-AAAAA
87106 -AAATATAAAAAA
1 CAAA-A-AAAAAA
87118 CAAAAACAAAAA
1 CAAAAA-AAAAA
87130 CAAAAAAAATAA
1 CAAAAAAAA-AA
*
87142 -AAAATAAAAA
1 CAAAAAAAAAA
*
87152 TAAAAATAAAAA
1 CAAAAA-AAAAA
* *
87164 TAAAAAAAAAT
1 CAAAAAAAAAA
87175 CAATAAAAAAAA
1 CAA-AAAAAAAA
87187 TCAACTCGAA
Statistics
Matches: 68, Mismatches: 5, Indels: 16
0.76 0.06 0.18
Matches are distributed among these distances:
10 2 0.03
11 24 0.35
12 38 0.56
13 4 0.06
ACGTcount: A:0.84, C:0.06, G:0.00, T:0.10
Consensus pattern (11 bp):
CAAAAAAAAAA
Found at i:87130 original size:30 final size:29
Alignment explanation
Indices: 87094--87186 Score: 102
Period size: 29 Copynumber: 3.2 Consensus size: 29
87084 GAAATTCAAT
87094 CAAAAACAAAAAAAATATAAAAAACAAAAA
1 CAAAAACAAAAAAAA-ATAAAAAACAAAAA
*
87124 CAAAAAC-AAAAAAAATAAAAAATAAAAA
1 CAAAAACAAAAAAAAATAAAAAACAAAAA
* * *
87152 TAAAAATAAAAATAAAA-AAAAATCAATAAA
1 CAAAAACAAAAA-AAAATAAAAAACAA-AAA
87182 -AAAAA
1 CAAAAA
87187 TCAACTCGAA
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
28 18 0.33
29 23 0.42
30 14 0.25
ACGTcount: A:0.84, C:0.06, G:0.00, T:0.10
Consensus pattern (29 bp):
CAAAAACAAAAAAAAATAAAAAACAAAAA
Found at i:87143 original size:28 final size:28
Alignment explanation
Indices: 87094--87186 Score: 100
Period size: 28 Copynumber: 3.2 Consensus size: 28
87084 GAAATTCAAT
87094 CAAAAACAAAAAAAATATAAAAAACAAAAA
1 CAAAAAC-AAAAAAA-ATAAAAAACAAAAA
*
87124 CAAAAACAAAAAAAATAAAAAATAAAAA
1 CAAAAACAAAAAAAATAAAAAACAAAAA
* *
87152 TAAAAATAAAAATAAA-AAAAAATCAATAAA
1 CAAAAACAAAAA-AAATAAAAAA-CAA-AAA
87182 -AAAAA
1 CAAAAA
87187 TCAACTCGAA
Statistics
Matches: 56, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
28 29 0.52
29 17 0.30
30 10 0.18
ACGTcount: A:0.84, C:0.06, G:0.00, T:0.10
Consensus pattern (28 bp):
CAAAAACAAAAAAAATAAAAAACAAAAA
Found at i:87174 original size:35 final size:34
Alignment explanation
Indices: 87096--87173 Score: 95
Period size: 34 Copynumber: 2.3 Consensus size: 34
87086 AATTCAATCA
* * *
87096 AAAACAAAAAAAATATAAAAAACAAAAACAAAAAC
1 AAAA-AAAAAAAAAATAAAAAATAAAAATAAAAAC
*
87131 AAAAAAAATAAAAAAT-AAAAATAAAAATAAAAAT
1 AAAAAAAA-AAAAAATAAAAAATAAAAATAAAAAC
87165 AAAAAAAAA
1 AAAAAAAAA
87174 TCAATAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
33 1 0.03
34 27 0.71
35 10 0.26
ACGTcount: A:0.86, C:0.05, G:0.00, T:0.09
Consensus pattern (34 bp):
AAAAAAAAAAAAAATAAAAAATAAAAATAAAAAC
Found at i:87186 original size:1 final size:1
Alignment explanation
Indices: 87095--87173 Score: 59
Period size: 1 Copynumber: 79.0 Consensus size: 1
87085 AAATTCAATC
* * * * * * * * * *
87095 AAAAACAAAAAAAATATAAAAAACAAAAACAAAAACAAAAAAAATAAAAAATAAAAATAAAAATA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
87160 AAAATAAAAAAAAA
1 AAAAAAAAAAAAAA
87174 TCAATAAAAA
Statistics
Matches: 56, Mismatches: 22, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 56 1.00
ACGTcount: A:0.86, C:0.05, G:0.00, T:0.09
Consensus pattern (1 bp):
A
Found at i:87190 original size:13 final size:12
Alignment explanation
Indices: 87095--87186 Score: 64
Period size: 13 Copynumber: 7.4 Consensus size: 12
87085 AAATTCAATC
87095 AAAAACAA-AAA
1 AAAAACAATAAA
* * *
87106 AAATATAAAAAA
1 AAAAACAATAAA
87118 CAAAAACAA-AAA
1 -AAAAACAATAAA
*
87130 CAAAAAAAATAAA
1 -AAAAACAATAAA
*
87143 AAATAAAAATAAA
1 AAA-AACAATAAA
87156 AATAAA-AATAAAA
1 AA-AAACAAT-AAA
87169 AAAAATCAATAAA
1 AAAAA-CAATAAA
87182 AAAAA
1 AAAAA
87187 TCAACTCGAA
Statistics
Matches: 68, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
11 6 0.09
12 23 0.34
13 35 0.51
14 4 0.06
ACGTcount: A:0.85, C:0.05, G:0.00, T:0.10
Consensus pattern (12 bp):
AAAAACAATAAA
Found at i:88552 original size:169 final size:167
Alignment explanation
Indices: 88272--88877 Score: 820
Period size: 169 Copynumber: 3.7 Consensus size: 167
88262 TTCCATATAC
88272 GTTAAGTTTAAAATCCTTGGTCAAGGTCTCTATTCAGAGTTTACATTGATAAGTCCTCCGGGCAC
1 GTTAAGTTTAAAATCCTTGGTCAAGGTCTCTATTCAGAGTTTACATTGATAAGTCCTCCGGGCAC
* *
88337 AAATTCAGAAACCTTCGGGTATTAATTCTGATAAGTCCTTCGGGCAATTGATAAAACCTCTGGGT
66 AAATTCAGAAACCTCCGGGTATTAATTCTGATAAGTCCTCCGGGCAATTGATAAAACCTCTGGGT
88402 ACCATTTCATTTCATCAAGTTTTTCATCAAAAATTCAT
131 ACCATTTCATTTCATCAAGTTTTTCATC-AAAATTCAT
* *
88440 GCTTAAGTTTAAAATCCTTGGTCAAGGTCTCTATTCAGAGTTTATATTGATAAGTCCTCCAGGCA
1 G-TTAAGTTTAAAATCCTTGGTCAAGGTCTCTATTCAGAGTTTACATTGATAAGTCCTCCGGGCA
* * * *
88505 AAAATTCAGAAACCTCCGGGTATTAATTCCGATAAGTCCTCCGGGCAATCGGTAAAACCTCTGGG
65 CAAATTCAGAAACCTCCGGGTATTAATTCTGATAAGTCCTCCGGGCAATTGATAAAACCTCTGGG
* *
88570 TACCATTTCATTTCATAAAG--TTT--TC----GT-AT
130 TACCATTTCATTTCATCAAGTTTTTCATCAAAATTCAT
* * * * * * *
88599 -TTAAGTTTAAGATCCTTGTTTAAGGTCTCAATTCA-AGGTTTGCATTGGTAAGTCCTCCGAGCA
1 GTTAAGTTTAAAATCCTTGGTCAAGGTCTCTATTCAGA-GTTTACATTGATAAGTCCTCCGGGCA
* * **
88662 CAAATTCAGAAACCTCTGGGTATTAATTTTGATAAGTCCTCCGGGCAATTGATAAAACCTCCAGG
65 CAAATTCAGAAACCTCCGGGTATTAATTCTGATAAGTCCTCCGGGCAATTGATAAAACCTCTGGG
* * *
88727 TACCATTTGATTTCATCAAGTTTGTCACCAAAAGTTCAT
130 TACCATTTCATTTCATCAAGTTTTTCATCAAAA-TTCAT
* * * *
88766 GTTTAAGTTTAAAATCCTTGGTTAAGGTCTCTTTTCAGAGTTTGCATTGGTAAGTCCTCCGGGCA
1 G-TTAAGTTTAAAATCCTTGGTCAAGGTCTCTATTCAGAGTTTACATTGATAAGTCCTCCGGGCA
* *
88831 CAAGTTTAGAAACCTCCGGGTATTAATTCTGATAAGTCCTCCGGGCA
65 CAAATTCAGAAACCTCCGGGTATTAATTCTGATAAGTCCTCCGGGCA
88878 TCTCATATTT
Statistics
Matches: 382, Mismatches: 41, Indels: 29
0.85 0.09 0.06
Matches are distributed among these distances:
156 1 0.00
157 127 0.33
159 4 0.01
160 1 0.00
161 1 0.00
165 2 0.01
166 1 0.00
167 5 0.01
168 1 0.00
169 238 0.62
170 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (167 bp):
GTTAAGTTTAAAATCCTTGGTCAAGGTCTCTATTCAGAGTTTACATTGATAAGTCCTCCGGGCAC
AAATTCAGAAACCTCCGGGTATTAATTCTGATAAGTCCTCCGGGCAATTGATAAAACCTCTGGGT
ACCATTTCATTTCATCAAGTTTTTCATCAAAATTCAT
Found at i:88867 original size:326 final size:326
Alignment explanation
Indices: 88273--88877 Score: 944
Period size: 326 Copynumber: 1.9 Consensus size: 326
88263 TCCATATACG
* *
88273 TTAAGTTTAAAATCCTTGGTCAAGGTCTCTATTCAGAGTTTACATTGATAAGTCCTCCGGGCACA
1 TTAAGTTTAAAATCCTTGGTCAAGGTCTCAATTCAGAGTTTACATTGATAAGTCCTCCGAGCACA
* **
88338 AATTCAGAAACCTTCGGGTATTAATTCTGATAAGTCCTTCGGGCAATTGATAAAACCTCTGGGTA
66 AATTCAGAAACCTTCGGGTATTAATTCTGATAAGTCCTCCGGGCAATTGATAAAACCTCCAGGTA
* *
88403 CCATTTCATTTCATCAAGTTTTTCATCAAAAATTCATGCTTAAGTTTAAAATCCTTGGTCAAGGT
131 CCATTTCATTTCATCAAGTTTGTCACCAAAAATTCATGCTTAAGTTTAAAATCCTTGGTCAAGGT
*
88468 CTCTATTCAGAGTTTATATTGATAAGTCCTCCAGGCAAAAATTCAGAAACCTCCGGGTATTAATT
196 CTCTATTCAGAGTTTACATTGATAAGTCCTCCAGGCAAAAATTCAGAAACCTCCGGGTATTAATT
88533 CCGATAAGTCCTCCGGGCAATCGGTAAAACCTCTGGGTACCATTTCATTTCATAAAGTTTTCGTA
261 CCGATAAGTCCTCCGGGCAATCGGTAAAACCTCTGGGTACCATTTCATTTCATAAAGTTTTCGTA
88598 T
326 T
* * * * *
88599 TTAAGTTTAAGATCCTTGTTTAAGGTCTCAATTCA-AGGTTTGCATTGGTAAGTCCTCCGAGCAC
1 TTAAGTTTAAAATCCTTGGTCAAGGTCTCAATTCAGA-GTTTACATTGATAAGTCCTCCGAGCAC
*
88663 AAATTCAGAAACC-TCTGGGTATTAATTTTGATAAGTCCTCCGGGCAATTGATAAAACCTCCAGG
65 AAATTCAGAAACCTTC-GGGTATTAATTCTGATAAGTCCTCCGGGCAATTGATAAAACCTCCAGG
* * * *
88727 TACCATTTGATTTCATCAAGTTTGTCACCAAAAGTTCATGTTTAAGTTTAAAATCCTTGGTTAAG
129 TACCATTTCATTTCATCAAGTTTGTCACCAAAAATTCATGCTTAAGTTTAAAATCCTTGGTCAAG
* * * * * * *
88792 GTCTCTTTTCAGAGTTTGCATTGGTAAGTCCTCCGGGCACAAGTTTAGAAACCTCCGGGTATTAA
194 GTCTCTATTCAGAGTTTACATTGATAAGTCCTCCAGGCAAAAATTCAGAAACCTCCGGGTATTAA
*
88857 TTCTGATAAGTCCTCCGGGCA
259 TTCCGATAAGTCCTCCGGGCA
88878 TCTCATATTT
Statistics
Matches: 251, Mismatches: 26, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
325 3 0.01
326 248 0.99
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (326 bp):
TTAAGTTTAAAATCCTTGGTCAAGGTCTCAATTCAGAGTTTACATTGATAAGTCCTCCGAGCACA
AATTCAGAAACCTTCGGGTATTAATTCTGATAAGTCCTCCGGGCAATTGATAAAACCTCCAGGTA
CCATTTCATTTCATCAAGTTTGTCACCAAAAATTCATGCTTAAGTTTAAAATCCTTGGTCAAGGT
CTCTATTCAGAGTTTACATTGATAAGTCCTCCAGGCAAAAATTCAGAAACCTCCGGGTATTAATT
CCGATAAGTCCTCCGGGCAATCGGTAAAACCTCTGGGTACCATTTCATTTCATAAAGTTTTCGTA
T
Found at i:89134 original size:30 final size:30
Alignment explanation
Indices: 89132--89290 Score: 266
Period size: 30 Copynumber: 5.3 Consensus size: 30
89122 TCATTGCGTT
* *
89132 ATTGGTTTATTTTGATCCTGGTTTAGGATC
1 ATTGCTTTATTTTAATCCTGGTTTAGGATC
*
89162 ATTGCTTTATTTTAATCATGGTTTAGGATC
1 ATTGCTTTATTTTAATCCTGGTTTAGGATC
*
89192 ATTGCCTTATTTTAATCCTGGTTTAGGATC
1 ATTGCTTTATTTTAATCCTGGTTTAGGATC
*
89222 ATTGC-GTATTTTAATCCTGGTTTAGGATC
1 ATTGCTTTATTTTAATCCTGGTTTAGGATC
89251 ATTGCTTTATTTTAATCCTGGTTTAGGATC
1 ATTGCTTTATTTTAATCCTGGTTTAGGATC
89281 ATTGCTTTAT
1 ATTGCTTTAT
89291 CAGTTTATTT
Statistics
Matches: 121, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
29 28 0.23
30 93 0.77
ACGTcount: A:0.20, C:0.13, G:0.18, T:0.49
Consensus pattern (30 bp):
ATTGCTTTATTTTAATCCTGGTTTAGGATC
Found at i:89172 original size:38 final size:38
Alignment explanation
Indices: 88908--89172 Score: 406
Period size: 38 Copynumber: 7.0 Consensus size: 38
88898 CTTCTACTTT
* *
88908 GTTTATTTCGATCCTGGTTTAGGATCATTACTTT-TTCA
1 GTTTATTTCGATCCTGGTTTAGGATCATTGCTTTATT-G
*
88946 GTTTATTTCGATCCTGGTTTAGGATCATTGCGTTATTG
1 GTTTATTTCGATCCTGGTTTAGGATCATTGCTTTATTG
* **
88984 GTTTATTTCGATCCTGGTTTAGGATCATAGCTTTGCTG
1 GTTTATTTCGATCCTGGTTTAGGATCATTGCTTTATTG
**
89022 GTTTATTTCGATCCTGGTTTAGGATCATTGCTTTGCTG
1 GTTTATTTCGATCCTGGTTTAGGATCATTGCTTTATTG
**
89060 GTTTATTTCGATCCTGGTTTAGGATCATTGCTTTATCA
1 GTTTATTTCGATCCTGGTTTAGGATCATTGCTTTATTG
*
89098 GTTTATTTCGATCCTGGTTTAGGATCATTGCGTTATTG
1 GTTTATTTCGATCCTGGTTTAGGATCATTGCTTTATTG
*
89136 GTTTATTTTGATCCTGGTTTAGGATCATTGCTTTATT
1 GTTTATTTCGATCCTGGTTTAGGATCATTGCTTTATT
89173 TTAATCATGG
Statistics
Matches: 209, Mismatches: 17, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
38 207 0.99
39 2 0.01
ACGTcount: A:0.16, C:0.14, G:0.21, T:0.48
Consensus pattern (38 bp):
GTTTATTTCGATCCTGGTTTAGGATCATTGCTTTATTG
Found at i:89261 original size:59 final size:60
Alignment explanation
Indices: 89132--89286 Score: 258
Period size: 59 Copynumber: 2.6 Consensus size: 60
89122 TCATTGCGTT
* * *
89132 ATTGGTTTATTTTGATCCTGGTTTAGGATCATTGCTTTATTTTAATCATGGTTTAGGATC
1 ATTGCTTTATTTTAATCCTGGTTTAGGATCATTGCTGTATTTTAATCATGGTTTAGGATC
* *
89192 ATTGCCTTATTTTAATCCTGGTTTAGGATCATTGC-GTATTTTAATCCTGGTTTAGGATC
1 ATTGCTTTATTTTAATCCTGGTTTAGGATCATTGCTGTATTTTAATCATGGTTTAGGATC
89251 ATTGCTTTATTTTAATCCTGGTTTAGGATCATTGCT
1 ATTGCTTTATTTTAATCCTGGTTTAGGATCATTGCT
89287 TTATCAGTTT
Statistics
Matches: 88, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
59 56 0.64
60 32 0.36
ACGTcount: A:0.20, C:0.13, G:0.19, T:0.48
Consensus pattern (60 bp):
ATTGCTTTATTTTAATCCTGGTTTAGGATCATTGCTGTATTTTAATCATGGTTTAGGATC
Found at i:89307 original size:38 final size:38
Alignment explanation
Indices: 89256--89549 Score: 148
Period size: 38 Copynumber: 8.2 Consensus size: 38
89246 GGATCATTGC
*
89256 TTTATTTTAATCCTGGTTTAGGATCATTGCTTTATCAG
1 TTTATTTCAATCCTGGTTTAGGATCATTGCTTTATCAG
*
89294 TTTATTTCAATCCTGGTTTAGGAT-ATGTACTTTATC--
1 TTTATTTCAATCCTGGTTTAGGATCAT-TGCTTTATCAG
* * *
89330 --CATTTCAATCCTGGTTTAAGATCATTGCTTCATCAG
1 TTTATTTCAATCCTGGTTTAGGATCATTGCTTTATCAG
* * * * * *
89366 -----TT-AATCCCGATGTAGGATTATTGCATTATGAG
1 TTTATTTCAATCCTGGTTTAGGATCATTGCTTTATCAG
* * * *
89398 TTAATTTCAATCCTGATTTAGGATTATTAC-TT-T-AG
1 TTTATTTCAATCCTGGTTTAGGATCATTGCTTTATCAG
* *
89433 TTTATTTGAAT-C----TT--GCTCATTG-TTTCATCAG
1 TTTATTTCAATCCTGGTTTAGGATCATTGCTTT-ATCAG
* * * * *
89464 TTATATTTCAGTCATGATTTAGCATTATTGCTTTATCAG
1 TT-TATTTCAATCCTGGTTTAGGATCATTGCTTTATCAG
* * * *
89503 TTTTACTTCGATCTTGGTTCAGGATCATTGC-TTATCAG
1 -TTTATTTCAATCCTGGTTTAGGATCATTGCTTTATCAG
*
89541 TTAATTTCA
1 TTTATTTCA
89550 TAATCATATT
Statistics
Matches: 193, Mismatches: 39, Indels: 49
0.69 0.14 0.17
Matches are distributed among these distances:
28 7 0.04
30 3 0.02
31 4 0.02
32 29 0.15
33 2 0.01
34 28 0.15
35 13 0.07
36 1 0.01
37 14 0.07
38 57 0.30
39 30 0.16
40 5 0.03
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.47
Consensus pattern (38 bp):
TTTATTTCAATCCTGGTTTAGGATCATTGCTTTATCAG
Found at i:89365 original size:72 final size:68
Alignment explanation
Indices: 89228--89367 Score: 192
Period size: 72 Copynumber: 2.0 Consensus size: 68
89218 GATCATTGCG
* * * *
89228 TATTTTAATCCTGGTTTAGGATCATTGCTTTATTTTAATCCTGGTTTAGGATCATTGCTTTATCA
1 TATTTCAATCCTGGTTTAGGATCATTACTTTATTTTAATCCTGGTTTAAGATCATTGCTTCATCA
89293 GTT
66 GTT
89296 TATTTCAATCCTGGTTTAGGAT-ATGTACTTTATCCATTTCAATCCTGGTTTAAGATCATTGCTT
1 TATTTCAATCCTGGTTTAGGATCAT-TACTTTAT---TTT-AATCCTGGTTTAAGATCATTGCTT
89360 CATCAGTT
61 CATCAGTT
89368 AATCCCGATG
Statistics
Matches: 63, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
67 2 0.03
68 28 0.44
71 3 0.05
72 30 0.48
ACGTcount: A:0.22, C:0.16, G:0.15, T:0.47
Consensus pattern (68 bp):
TATTTCAATCCTGGTTTAGGATCATTACTTTATTTTAATCCTGGTTTAAGATCATTGCTTCATCA
GTT
Found at i:89405 original size:104 final size:102
Alignment explanation
Indices: 89229--89431 Score: 264
Period size: 104 Copynumber: 2.0 Consensus size: 102
89219 ATCATTGCGT
* * * * * * * *
89229 ATTTTAATCCTGGTTTAGGATCATTGCTTTATTTTAATCCTGGTTTAGGATCATTGCTTTATCAG
1 ATTTCAATCCTGGTTTAAGATCATTGCTTCATGTTAATCCCGATGTAGGATCATTGCATTATCAG
* *
89294 TTTATTTCAATCCTGGTTTAGGA-TATGTACTTTATCC
66 TTAATTTCAATCCTGATTTAGGATTAT-TACTTTATCC
* *
89331 ATTTCAATCCTGGTTTAAGATCATTGCTTCATCAGTTAATCCCGATGTAGGATTATTGCATTATG
1 ATTTCAATCCTGGTTTAAGATCATTGCTTCAT--GTTAATCCCGATGTAGGATCATTGCATTATC
89396 AGTTAATTTCAATCCTGATTTAGGATTATTACTTTA
64 AGTTAATTTCAATCCTGATTTAGGATTATTACTTTA
89432 GTTTATTTGA
Statistics
Matches: 86, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
102 29 0.34
104 54 0.63
105 3 0.03
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.45
Consensus pattern (102 bp):
ATTTCAATCCTGGTTTAAGATCATTGCTTCATGTTAATCCCGATGTAGGATCATTGCATTATCAG
TTAATTTCAATCCTGATTTAGGATTATTACTTTATCC
Found at i:89600 original size:40 final size:38
Alignment explanation
Indices: 89520--89617 Score: 97
Period size: 40 Copynumber: 2.4 Consensus size: 38
89510 TCGATCTTGG
*
89520 TTCAGGATCATTGCTTATCAGTTAATTTCATAATCATA
1 TTCAGGATCATTGCTTATCAGTTAATTTCAGAATCATA
** * * *
89558 TTCAGGATTGTTGCTTTCATCAGTTAGTTTCAGGATCCTA
1 TTCAGGATCATTGC-TT-ATCAGTTAATTTCAGAATCATA
89598 TTCGAGGATCTATTTGCTTA
1 TTC-AGGATC-A-TTGCTTA
89618 AAATTTCATC
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
38 12 0.26
39 2 0.04
40 21 0.45
41 6 0.13
42 2 0.04
43 4 0.09
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.43
Consensus pattern (38 bp):
TTCAGGATCATTGCTTATCAGTTAATTTCAGAATCATA
Found at i:90092 original size:17 final size:17
Alignment explanation
Indices: 90044--90092 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
90034 ATAGCACATC
90044 CATTTTA-TTGG-TAGA
1 CATTTTATTTGGTTAGA
*
90059 CATTTTAATTTGTTTAGA
1 CATTTT-ATTTGGTTAGA
90077 CATTTTATTTGGTTAG
1 CATTTTATTTGGTTAG
90093 TTTTGCATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 6 0.21
16 1 0.03
17 12 0.41
18 10 0.34
ACGTcount: A:0.24, C:0.06, G:0.16, T:0.53
Consensus pattern (17 bp):
CATTTTATTTGGTTAGA
Found at i:105969 original size:33 final size:33
Alignment explanation
Indices: 105927--105997 Score: 142
Period size: 33 Copynumber: 2.2 Consensus size: 33
105917 TTAAGGGTTG
105927 TAATTTTATTTTCATTTTTATGGATACTTATAT
1 TAATTTTATTTTCATTTTTATGGATACTTATAT
105960 TAATTTTATTTTCATTTTTATGGATACTTATAT
1 TAATTTTATTTTCATTTTTATGGATACTTATAT
105993 TAATT
1 TAATT
105998 AATTTATAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.61
Consensus pattern (33 bp):
TAATTTTATTTTCATTTTTATGGATACTTATAT
Found at i:106010 original size:33 final size:33
Alignment explanation
Indices: 105927--106010 Score: 116
Period size: 33 Copynumber: 2.5 Consensus size: 33
105917 TTAAGGGTTG
* *
105927 TAATTTTATTTTCATTTTTATGGATACTTATAT
1 TAATTTAATTTTAATTTTTATGGATACTTATAT
* *
105960 TAATTTTATTTTCATTTTTATGGATACTTATAT
1 TAATTTAATTTTAATTTTTATGGATACTTATAT
105993 TAA-TTAATTTATAATTTT
1 TAATTTAATTT-TAATTTT
106011 AGTTGATGTA
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
32 6 0.12
33 42 0.88
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.61
Consensus pattern (33 bp):
TAATTTAATTTTAATTTTTATGGATACTTATAT
Done.