Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014288.1 Kokia drynarioides strain JFW-HI SEQ_129322, 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: 137724
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 455 characters in sequence are not A, C, G, or T
Found at i:61 original size:25 final size:26
Alignment explanation
Indices: 14--62 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
4 TTTTATTATT
14 ATTTATATTTAGTTGTTTATTTTGAC
1 ATTTATATTTAGTTGTTTATTTTGAC
*
40 ATTTA-ATTTA-TTGATTTTTTTTG
1 ATTTATATTTAGTTG-TTTATTTTG
63 TTTATTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 3 0.14
25 13 0.62
26 5 0.24
ACGTcount: A:0.22, C:0.02, G:0.10, T:0.65
Consensus pattern (26 bp):
ATTTATATTTAGTTGTTTATTTTGAC
Found at i:5259 original size:24 final size:26
Alignment explanation
Indices: 5232--5279 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
5222 AGAGAAATGT
5232 AAATG-TGATATATGA-A-ATTATGAG
1 AAATGATGA-ATATGAGAGATTATGAG
5256 AAATGATGAATATGAGAGATTATG
1 AAATGATGAATATGAGAGATTATG
5280 CCCAAGTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (26 bp):
AAATGATGAATATGAGAGATTATGAG
Found at i:5374 original size:23 final size:23
Alignment explanation
Indices: 5342--5418 Score: 118
Period size: 23 Copynumber: 3.3 Consensus size: 23
5332 ACGCTAGCAC
*
5342 GCTTATTGTTTCGCACTTCGTGT
1 GCTTACTGTTTCGCACTTCGTGT
5365 GCTTACTGTTTCGCACTTCGTGT
1 GCTTACTGTTTCGCACTTCGTGT
* *
5388 GCTTACTTTTTCGCACCTCGTGT
1 GCTTACTGTTTCGCACTTCGTGT
*
5411 GCCTACTG
1 GCTTACTG
5419 ATTTGCGCTA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.09, C:0.27, G:0.21, T:0.43
Consensus pattern (23 bp):
GCTTACTGTTTCGCACTTCGTGT
Found at i:5478 original size:23 final size:23
Alignment explanation
Indices: 5407--5485 Score: 97
Period size: 23 Copynumber: 3.5 Consensus size: 23
5397 TTCGCACCTC
* * *
5407 GTGTGCCTACTGATTTGCGCTAT
1 GTGTGCCTACTGAATTGCACTGT
* *
5430 GTGCGCCTATTG-ATTGCACTGT
1 GTGTGCCTACTGAATTGCACTGT
5452 GTGTGCCTACTGAATTGCACTGT
1 GTGTGCCTACTGAATTGCACTGT
*
5475 GTGTGCTTACT
1 GTGTGCCTACT
5486 ATTTCCCTAG
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
22 17 0.36
23 30 0.64
ACGTcount: A:0.14, C:0.22, G:0.27, T:0.38
Consensus pattern (23 bp):
GTGTGCCTACTGAATTGCACTGT
Found at i:6040 original size:32 final size:32
Alignment explanation
Indices: 5995--6060 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
5985 TGAAGTCGAG
*
5995 TTCAAGGACCTCTCATCACATCACATTATCCT
1 TTCAAGGACCTCTCATCACATCACATCATCCT
*
6027 TTCAAGGATCTCTCATCACATCACATCATCCT
1 TTCAAGGACCTCTCATCACATCACATCATCCT
6059 TT
1 TT
6061 GGAGAACTCC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.27, C:0.33, G:0.06, T:0.33
Consensus pattern (32 bp):
TTCAAGGACCTCTCATCACATCACATCATCCT
Found at i:8396 original size:16 final size:18
Alignment explanation
Indices: 8357--8390 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
8347 GAAGTTTATA
8357 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
8374 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
8391 AATTTAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:14648 original size:41 final size:40
Alignment explanation
Indices: 14573--14649 Score: 93
Period size: 41 Copynumber: 1.9 Consensus size: 40
14563 ACTATATAAA
**
14573 AAAATTAATAAATAAAAAATTTATAAAATTATTAAATATT
1 AAAATTAATAAATAAAAAATTTATAAAAAAATTAAATATT
* *
14613 AAAA-TAATATAATATAATAATTTTTAAAAAAATTAAA
1 AAAATTAATA-AATA-AAAAATTTATAAAAAAATTAAA
14650 AAATAATATA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
39 5 0.16
40 8 0.26
41 18 0.58
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (40 bp):
AAAATTAATAAATAAAAAATTTATAAAAAAATTAAATATT
Found at i:23625 original size:30 final size:31
Alignment explanation
Indices: 23591--23648 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
23581 TGTTCAATTT
*
23591 TTTAATTACTG-TTTTGTTTCTTTAATTATG
1 TTTAAATACTGTTTTTGTTTCTTTAATTATG
**
23621 TTTAAATGTTGTTTTTGTTTCTTTAATT
1 TTTAAATACTGTTTTTGTTTCTTTAATT
23649 GTCGTTTGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 8 0.33
31 16 0.67
ACGTcount: A:0.19, C:0.05, G:0.10, T:0.66
Consensus pattern (31 bp):
TTTAAATACTGTTTTTGTTTCTTTAATTATG
Found at i:30351 original size:28 final size:27
Alignment explanation
Indices: 30301--30353 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
30291 GTAAATATAT
*
30301 TTTTAATAAAAATAAATTTAATTTTCA
1 TTTTAATAAAAATAAATTAAATTTTCA
30328 TTTTAATTAAAAAT-AATTCAAATTTT
1 TTTTAA-TAAAAATAAATT-AAATTTT
30354 TTTAATGGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 10 0.43
28 13 0.57
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (27 bp):
TTTTAATAAAAATAAATTAAATTTTCA
Found at i:42485 original size:54 final size:54
Alignment explanation
Indices: 42402--42509 Score: 189
Period size: 54 Copynumber: 2.0 Consensus size: 54
42392 AAAGAGAGAA
*
42402 AATCATACACATATATCTTAAAGACAGCTAAGTTTTTCTCCTGTTCACTAAATT
1 AATCATACACATATATCTTAAAGACAGCTAAGTTTTGCTCCTGTTCACTAAATT
* *
42456 AATCATCCACATATATCTTAAAGATAGCTAAGTTTTGCTCCTGTTCACTAAATT
1 AATCATACACATATATCTTAAAGACAGCTAAGTTTTGCTCCTGTTCACTAAATT
42510 CATCTATGGT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.34, C:0.20, G:0.08, T:0.37
Consensus pattern (54 bp):
AATCATACACATATATCTTAAAGACAGCTAAGTTTTGCTCCTGTTCACTAAATT
Found at i:48846 original size:45 final size:44
Alignment explanation
Indices: 48795--48907 Score: 138
Period size: 45 Copynumber: 2.5 Consensus size: 44
48785 GTCTACCATA
*
48795 TTTATGAATCTACATGTATGAGTCCACTATA-CTCATGAATCTTCT
1 TTTATGAAT-TACATGTATGAGTCCACCATATCT-ATGAATCTTCT
* **
48840 TTTATGAATTTGCATGTATGAGTCTGCCATATCTATGAATCTTCT
1 TTTATGAA-TTACATGTATGAGTCCACCATATCTATGAATCTTCT
*
48885 TTTATGAGTTCACATGTATGAGT
1 TTTATGAATT-ACATGTATGAGT
48908 TCGCATATAA
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
44 2 0.03
45 54 0.92
46 3 0.05
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.42
Consensus pattern (44 bp):
TTTATGAATTACATGTATGAGTCCACCATATCTATGAATCTTCT
Found at i:56100 original size:21 final size:21
Alignment explanation
Indices: 56046--56089 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
56036 CTACATCTAC
*
56046 AAATCATACAATTCTCACATT
1 AAATCATCCAATTCTCACATT
56067 AAATCATCCAATTCTCACATT
1 AAATCATCCAATTCTCACATT
56088 AA
1 AA
56090 GTCACATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.43, C:0.25, G:0.00, T:0.32
Consensus pattern (21 bp):
AAATCATCCAATTCTCACATT
Found at i:65822 original size:17 final size:16
Alignment explanation
Indices: 65781--65826 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
65771 GATTCAATAG
*
65781 AACACTAAAAATTCCA
1 AACACAAAAAATTCCA
*
65797 AACACAAAAAATTTCA
1 AACACAAAAAATTCCA
*
65813 AATACTAAAAAATT
1 AACAC-AAAAAATT
65827 GTTTCAGTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 18 0.69
17 8 0.31
ACGTcount: A:0.61, C:0.17, G:0.00, T:0.22
Consensus pattern (16 bp):
AACACAAAAAATTCCA
Found at i:65973 original size:35 final size:35
Alignment explanation
Indices: 65927--65996 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
65917 TTAAAGTCCG
65927 AACAGTAAAATGATAAGGATAACGTCCCTTTCATT
1 AACAGTAAAATGATAAGGATAACGTCCCTTTCATT
*
65962 AACAGTAAAATGATAAGGTTAACGTCCCTTTCATT
1 AACAGTAAAATGATAAGGATAACGTCCCTTTCATT
65997 TTTTGTTTGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (35 bp):
AACAGTAAAATGATAAGGATAACGTCCCTTTCATT
Found at i:67433 original size:26 final size:26
Alignment explanation
Indices: 67397--67447 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
67387 ATTGAGTAGG
*
67397 GACTGATTGTCTTGTCAATGGATATA
1 GACTGATTGTCCTGTCAATGGATATA
*
67423 GACTGGTTGTCCTGTCAATGGATAT
1 GACTGATTGTCCTGTCAATGGATAT
67448 GGAACATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.24, C:0.14, G:0.25, T:0.37
Consensus pattern (26 bp):
GACTGATTGTCCTGTCAATGGATATA
Found at i:68744 original size:27 final size:26
Alignment explanation
Indices: 68679--68746 Score: 66
Period size: 27 Copynumber: 2.5 Consensus size: 26
68669 ATATATTTGA
68679 ATTTTAAATACTTTTTAATTTTAAAAT
1 ATTTTAAATA-TTTTTAATTTTAAAAT
* * *
68706 AATTATATATATTTTTAATTCTTTTAAAT
1 -ATTTTAAATATTTTTAA-T-TTTAAAAT
68735 -TTTTAAATATTT
1 ATTTTAAATATTT
68747 GATGGCATGC
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
27 17 0.52
28 9 0.27
29 7 0.21
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (26 bp):
ATTTTAAATATTTTTAATTTTAAAAT
Found at i:73126 original size:4 final size:4
Alignment explanation
Indices: 73112--73192 Score: 72
Period size: 4 Copynumber: 20.0 Consensus size: 4
73102 ATAAAACATA
* * * *
73112 TATG ATATG TATG TATG TATG TATG TATG TATG AATG AATG CATG AATG
1 TATG -TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * * **
73161 TATG AATG AATG AATG TACA TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG
73193 CCAGTGTAAG
Statistics
Matches: 66, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
4 62 0.94
5 4 0.06
ACGTcount: A:0.35, C:0.02, G:0.23, T:0.40
Consensus pattern (4 bp):
TATG
Found at i:73798 original size:219 final size:220
Alignment explanation
Indices: 73419--73863 Score: 820
Period size: 219 Copynumber: 2.0 Consensus size: 220
73409 ATGTATCAGA
* *
73419 TAACTTTCTTATTTACCTAGTGGCATCAGTTCCTCTATGTGACTCTGATGCTCAGTCTCTATATT
1 TAACTTTCTTATTTACCTAGTGGCATCAGTTCCTCCACGTGACTCTGATGCTCAGTCTCTATATT
* * *
73484 CACCTGGTCTTTGCTTCCGCTACTTTTGACGTCATCATCAACTGTAAGCACAAGGTTGAGATGTA
66 CACCTGGTCTTCGCTTCCGCTACTTTTGACATCATCATCAACTGTAAGCAAAAGGTTGAGATGTA
73549 GTGAAATGTGCATTAGATACAAAACTTTAGTGGTATGCAGTAGTAACCCTGCGATGAATTTTAAA
131 GTGAAATGTGCATTAGATACAAAACTTTAGTGGTATGCAGTAGTAACCCTGCGATGAATTTTAAA
73614 AGAT-AAAGACAGCTCCTACATTGT
196 AGATAAAAGACAGCTCCTACATTGT
**
73638 TAACTTTCTTATTTACCTAGTGGGGTCAGTTCCTCCACGTGACTCTGATGCTCAGTCTCTATATT
1 TAACTTTCTTATTTACCTAGTGGCATCAGTTCCTCCACGTGACTCTGATGCTCAGTCTCTATATT
73703 CACCTGGTCTTCGCTTCCGCTACTTTTGACATCATCATCAACTGTAAGCAAAAGGTTGAGATGTA
66 CACCTGGTCTTCGCTTCCGCTACTTTTGACATCATCATCAACTGTAAGCAAAAGGTTGAGATGTA
73768 GTGAAATGTGCATTAGATACAAAACTTTAGTGGTATGCAGTAGTAACCCTGCGATGAATTTTAAA
131 GTGAAATGTGCATTAGATACAAAACTTTAGTGGTATGCAGTAGTAACCCTGCGATGAATTTTAAA
73833 AGATAAAAGACAGCTCCTACATTGT
196 AGATAAAAGACAGCTCCTACATTGT
73858 TAACTT
1 TAACTT
73864 ACCAGACAGA
Statistics
Matches: 218, Mismatches: 7, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
219 192 0.88
220 26 0.12
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (220 bp):
TAACTTTCTTATTTACCTAGTGGCATCAGTTCCTCCACGTGACTCTGATGCTCAGTCTCTATATT
CACCTGGTCTTCGCTTCCGCTACTTTTGACATCATCATCAACTGTAAGCAAAAGGTTGAGATGTA
GTGAAATGTGCATTAGATACAAAACTTTAGTGGTATGCAGTAGTAACCCTGCGATGAATTTTAAA
AGATAAAAGACAGCTCCTACATTGT
Found at i:75313 original size:14 final size:14
Alignment explanation
Indices: 75294--75323 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
75284 AAGTAGATTG
75294 ACAGTTTGAACCTT
1 ACAGTTTGAACCTT
75308 ACAGTTTGAACCTT
1 ACAGTTTGAACCTT
75322 AC
1 AC
75324 CCATATAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.33
Consensus pattern (14 bp):
ACAGTTTGAACCTT
Found at i:77764 original size:24 final size:24
Alignment explanation
Indices: 77731--77799 Score: 120
Period size: 24 Copynumber: 2.9 Consensus size: 24
77721 ACCCTATAAT
*
77731 ATTACGGGATGGCCATAATGTGAG
1 ATTACAGGATGGCCATAATGTGAG
77755 ATTACAGGATGGCCATAATGTGAG
1 ATTACAGGATGGCCATAATGTGAG
*
77779 ATTACAGGATGGCCAGAATGT
1 ATTACAGGATGGCCATAATGT
77800 TGAAATCCAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.32, C:0.13, G:0.30, T:0.25
Consensus pattern (24 bp):
ATTACAGGATGGCCATAATGTGAG
Found at i:81896 original size:24 final size:24
Alignment explanation
Indices: 81868--81929 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
81858 TAGACTAATA
*
81868 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTCAAACAAATAAAC
* * * *
81892 AGAGTTTAATTGAAATAAATAAAT
1 AGAGTTTAACTCAAACAAATAAAC
81916 AGAGTTTAAC-CAAA
1 AGAGTTTAACTCAAA
81930 AGATTATTTC
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
23 3 0.10
24 28 0.90
ACGTcount: A:0.52, C:0.10, G:0.13, T:0.26
Consensus pattern (24 bp):
AGAGTTTAACTCAAACAAATAAAC
Found at i:83864 original size:24 final size:24
Alignment explanation
Indices: 83836--83894 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
83826 TAGACTAATA
*
83836 AGAGTTTGACTCAAATAAATAAAC
1 AGAGTTTAACTCAAATAAATAAAC
* * *
83860 AGAGTTTAATTGAAATAAATAAAT
1 AGAGTTTAACTCAAATAAATAAAC
*
83884 ATAGTTTAACT
1 AGAGTTTAACT
83895 AAAAGATTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.49, C:0.07, G:0.12, T:0.32
Consensus pattern (24 bp):
AGAGTTTAACTCAAATAAATAAAC
Found at i:88574 original size:30 final size:28
Alignment explanation
Indices: 88523--88595 Score: 92
Period size: 30 Copynumber: 2.5 Consensus size: 28
88513 TACGTTAACA
* *
88523 AGACACCCCTACATTTTCAAGTAGTTCTT
1 AGACACCCCCACATTTCCAAGTAGTTC-T
*
88552 AGACACCCCCCACATTTCCAAGTGGTTCT
1 AGACA-CCCCCACATTTCCAAGTAGTTCT
88581 AGGACACCCCCACAT
1 A-GACACCCCCACAT
88596 GTTCTGTGAT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 16 0.41
30 23 0.59
ACGTcount: A:0.27, C:0.36, G:0.12, T:0.25
Consensus pattern (28 bp):
AGACACCCCCACATTTCCAAGTAGTTCT
Found at i:89370 original size:12 final size:12
Alignment explanation
Indices: 89353--89383 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
89343 GTTGTTTCCT
89353 TTCTTGAAGTCC
1 TTCTTGAAGTCC
89365 TTCTTGAAGTCC
1 TTCTTGAAGTCC
*
89377 TTTTTGA
1 TTCTTGA
89384 CTTCTGCCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.16, C:0.19, G:0.16, T:0.48
Consensus pattern (12 bp):
TTCTTGAAGTCC
Found at i:90898 original size:21 final size:20
Alignment explanation
Indices: 90874--90927 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
90864 GAAATTTAAA
*
90874 ACAACCATAATGATGAGAGTT
1 ACAA-CATAATGAGGAGAGTT
* *
90895 ACAAAACTTATGAGGAGAGTT
1 ACAACA-TAATGAGGAGAGTT
90916 ACAAACATAATG
1 AC-AACATAATG
90928 TTTTGTAGGC
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
20 1 0.04
21 22 0.85
22 3 0.12
ACGTcount: A:0.46, C:0.13, G:0.19, T:0.22
Consensus pattern (20 bp):
ACAACATAATGAGGAGAGTT
Found at i:96316 original size:16 final size:16
Alignment explanation
Indices: 96267--96330 Score: 67
Period size: 16 Copynumber: 4.1 Consensus size: 16
96257 TCAGGTTTTT
**
96267 AAATTTAATTTTTAAA
1 AAATTTAAGATTTAAA
* * *
96283 AATTTTCAGATTTCAA
1 AAATTTAAGATTTAAA
96299 AAATTT-AGATTTAAA
1 AAATTTAAGATTTAAA
*
96314 AAATTTAAAATTTAAA
1 AAATTTAAGATTTAAA
96330 A
1 A
96331 TTTCGTCTAG
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
15 14 0.36
16 25 0.64
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (16 bp):
AAATTTAAGATTTAAA
Found at i:96398 original size:21 final size:21
Alignment explanation
Indices: 96374--96415 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
96364 AAAATCATTT
* *
96374 AATAATTTTATATTTTTAAAA
1 AATAATTTAATAATTTTAAAA
96395 AATAATTTAATAATTTTAAAA
1 AATAATTTAATAATTTTAAAA
96416 TTATTTGTCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
AATAATTTAATAATTTTAAAA
Found at i:97374 original size:2 final size:2
Alignment explanation
Indices: 97369--97412 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
97359 TTATTGATTT
*
97369 TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
97411 TA
1 TA
97413 AAACAAAAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:101679 original size:20 final size:20
Alignment explanation
Indices: 101649--101698 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
101639 ATTAGCATGA
*
101649 TTTATATTAAGTTTAAATAG-G
1 TTTA-ATTAAGATTAAA-AGTG
101670 TTTAATTAAGATTAAAAGTG
1 TTTAATTAAGATTAAAAGTG
*
101690 ATTAATTAA
1 TTTAATTAA
101699 TGCTTAATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 2 0.08
20 20 0.77
21 4 0.15
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (20 bp):
TTTAATTAAGATTAAAAGTG
Found at i:109031 original size:19 final size:19
Alignment explanation
Indices: 108998--109045 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
108988 AAATGATAAA
* *
108998 AATAAAAAAAATAAAACTT
1 AATAAAAATATTAAAACTT
* **
109017 ATTAAAAATATTAAATTTT
1 AATAAAAATATTAAAACTT
109036 AATAAAAATA
1 AATAAAAATA
109046 GAAAATATTT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (19 bp):
AATAAAAATATTAAAACTT
Found at i:109051 original size:19 final size:20
Alignment explanation
Indices: 109019--109057 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
109009 TAAAACTTAT
**
109019 TAAAAATATTAAAT-TTTAA
1 TAAAAATAGAAAATATTTAA
109038 TAAAAATAGAAAATATTTAA
1 TAAAAATAGAAAATATTTAA
109058 ATTTTATCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (20 bp):
TAAAAATAGAAAATATTTAA
Found at i:109053 original size:26 final size:28
Alignment explanation
Indices: 109017--109078 Score: 87
Period size: 27 Copynumber: 2.3 Consensus size: 28
109007 AATAAAACTT
109017 ATTA-AAAATA-TTAAATTTTAAT-AAAA
1 ATTAGAAAATATTTAAATTTT-ATCAAAA
109043 A-TAGAAAATATTTAAATTTTATCAAAA
1 ATTAGAAAATATTTAAATTTTATCAAAA
109070 ATTAGAAAA
1 ATTAGAAAA
109079 AAATTTATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
25 2 0.06
26 9 0.28
27 14 0.44
28 7 0.22
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (28 bp):
ATTAGAAAATATTTAAATTTTATCAAAA
Found at i:109090 original size:10 final size:10
Alignment explanation
Indices: 109077--109149 Score: 51
Period size: 10 Copynumber: 7.3 Consensus size: 10
109067 AAAATTAGAA
109077 AAAAATTTAT
1 AAAAATTTAT
109087 AAAAATTGTA-
1 AAAAATT-TAT
*
109097 AGAAAAATTAT
1 A-AAAATTTAT
*
109108 -AAAATATAT
1 AAAAATTTAT
* * *
109117 AGAAATATAG
1 AAAAATTTAT
*
109127 AAAAAATTAT
1 AAAAATTTAT
*
109137 AAAATTTTAT
1 AAAAATTTAT
109147 AAA
1 AAA
109150 GTTGTAAGAA
Statistics
Matches: 48, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
9 7 0.15
10 34 0.71
11 7 0.15
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (10 bp):
AAAAATTTAT
Found at i:109092 original size:21 final size:21
Alignment explanation
Indices: 109060--109121 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 21
109050 ATATTTAAAT
109060 TTTATCAAAAATTAGAAAAAAA
1 TTTAT-AAAAATTAGAAAAAAA
109082 TTTATAAAAATT-GTAAGAAAAA
1 TTTATAAAAATTAG-AA-AAAAA
109104 -TTATAAAATATATAGAAA
1 TTTATAAAA-AT-TAGAAA
109122 TATAGAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
20 1 0.03
21 17 0.49
22 13 0.37
23 3 0.09
24 1 0.03
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.31
Consensus pattern (21 bp):
TTTATAAAAATTAGAAAAAAA
Found at i:109161 original size:29 final size:28
Alignment explanation
Indices: 109078--109169 Score: 98
Period size: 29 Copynumber: 3.1 Consensus size: 28
109068 AAATTAGAAA
109078 AAAATTTATAAAAATTGTAAGAAAAATTAT
1 AAAATTTAT-AAAATTGTAAG-AAAATTAT
*
109108 AAAATATATAGAAATATAG-AA-AAAATTAT
1 AAAATTTATA-AAAT-T-GTAAGAAAATTAT
*
109137 AAAATTTTATAAAGTTGTAAGAAAATTAT
1 AAAA-TTTATAAAATTGTAAGAAAATTAT
109166 AAAA
1 AAAA
109170 ACTGTAAAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 13
0.77 0.04 0.19
Matches are distributed among these distances:
27 1 0.02
28 3 0.06
29 28 0.53
30 17 0.32
31 3 0.06
32 1 0.02
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.32
Consensus pattern (28 bp):
AAAATTTATAAAATTGTAAGAAAATTAT
Found at i:109180 original size:19 final size:20
Alignment explanation
Indices: 109152--109189 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
109142 TTTATAAAGT
*
109152 TGTAAGAAAATTATAAAAAC
1 TGTAAGAAAAATATAAAAAC
109172 TGTAA-AAAAATATAAAAA
1 TGTAAGAAAAATATAAAAA
109190 AATATAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.66, C:0.03, G:0.08, T:0.24
Consensus pattern (20 bp):
TGTAAGAAAAATATAAAAAC
Found at i:109181 original size:20 final size:19
Alignment explanation
Indices: 109152--109204 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
109142 TTTATAAAGT
*
109152 TGTAAGAAAATTATAAAAAC
1 TGTAA-AAAAATATAAAAAC
*
109172 TGTAAAAAAATATAAAAAAA
1 TGTAAAAAAATAT-AAAAAC
*
109192 TATAAAAAAATAT
1 TGTAAAAAAATAT
109205 TGTACTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 7 0.24
20 22 0.76
ACGTcount: A:0.68, C:0.02, G:0.06, T:0.25
Consensus pattern (19 bp):
TGTAAAAAAATATAAAAAC
Found at i:109187 original size:10 final size:10
Alignment explanation
Indices: 109174--109204 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
109164 ATAAAAACTG
109174 TAAAAAAATA
1 TAAAAAAATA
109184 TAAAAAAATA
1 TAAAAAAATA
109194 TAAAAAAATA
1 TAAAAAAATA
109204 T
1 T
109205 TGTACTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (10 bp):
TAAAAAAATA
Found at i:110940 original size:20 final size:20
Alignment explanation
Indices: 110897--110940 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
110887 GGGGGAAAGT
*
110897 GGGAAAAATAAAAATTTTGA
1 GGGAAAAATAAAAATTTCGA
*
110917 GGGAAAAGTAAAAATGTTCG-
1 GGGAAAAATAAAAAT-TTCGA
110937 GGGA
1 GGGA
110941 TTTGGTGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.48, C:0.02, G:0.30, T:0.20
Consensus pattern (20 bp):
GGGAAAAATAAAAATTTCGA
Found at i:115138 original size:19 final size:18
Alignment explanation
Indices: 115108--115142 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
115098 TTATTATTAG
115108 ACCAATAAAAAAATTCAT
1 ACCAATAAAAAAATTCAT
115126 ACCAATAAAAAAATTCA
1 ACCAATAAAAAAATTCA
115143 ATGTTGGCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.63, C:0.17, G:0.00, T:0.20
Consensus pattern (18 bp):
ACCAATAAAAAAATTCAT
Found at i:115591 original size:374 final size:374
Alignment explanation
Indices: 114902--115651 Score: 1376
Period size: 374 Copynumber: 2.0 Consensus size: 374
114892 AATTAGAGGT
114902 TAATTAGAGGTTAAAATTTTAATAAATTTAATCCTCAACATTAATAAAAAATTAATTTTTAATTT
1 TAATTAGAGGTTAAAATTTTAATAAATTTAATCCTCAACATTAATAAAAAATTAATTTTTAATTT
*
114967 TTAAAAATTTTGTAAAATTATAAAAATTTAAAAATCAAAATTTATCATCTTGTTAATGTTGAGGG
66 TTAAAAAATTTGTAAAATTATAAAAATTTAAAAATCAAAATTTATCATCTTGTTAATGTTGAGGG
* *
115032 CTAAATTTATTAATTTTTTTAGAATTTGAACTAAAATGACTAATTTTGTAAATATTGAAGGTCAA
131 CTAAATTTATTAAATTTTTTAGAATTTGAACTAAAATGACAAATTTTGTAAATATTGAAGGTCAA
*
115097 ATTATTATTAGACCAATAAAAAAATTCATACCAATAAAAAAATTCAATGTTGGCATTTTGGTCAA
196 ATTATTATTAGACCAATAAAAAAATTCAGACCAATAAAAAAATTCAATGTTGGCATTTTGGTCAA
* *
115162 ATTTCACATGTTAACGTTCGGTAATAAAAAAAATTTTGATTTTGATTAGTTTAGTAACGGAAAAA
261 ATTTCACATGTTAACGTTCGGTAACAAAAAAAATTTTGATTTCGATTAGTTTAGTAACGGAAAAA
*
115227 TTAAAAGTTCAGTAACCAAAATAGAACACGGGCAATATTTTAATGATCA
326 TTAAAAGTTCAATAACCAAAATAGAACACGGGCAATATTTTAATGATCA
*
115276 TAATTAGAGGTTAAAATTTTAATAAATTTAATCCTCAACATTAATAAAATATTAATTTTTAATTT
1 TAATTAGAGGTTAAAATTTTAATAAATTTAATCCTCAACATTAATAAAAAATTAATTTTTAATTT
* *
115341 TTAAAAAATTTGTAAAATTATAGAAATTTAAAAATCAAAATTTATCATCTTGTTAATGTTTAGGG
66 TTAAAAAATTTGTAAAATTATAAAAATTTAAAAATCAAAATTTATCATCTTGTTAATGTTGAGGG
115406 CTAAATTTATTAAATTTTTTAGAATTTGAACTAAAATGACAAATTTTGTAAATATTGAAGGTCAA
131 CTAAATTTATTAAATTTTTTAGAATTTGAACTAAAATGACAAATTTTGTAAATATTGAAGGTCAA
* *
115471 ATTATTATTAGACCAATAAAAAAATTCAGATCAATAAAAAAATTCAATGTTTGCATTTTGGTCAA
196 ATTATTATTAGACCAATAAAAAAATTCAGACCAATAAAAAAATTCAATGTTGGCATTTTGGTCAA
115536 ATTTCACATGTTAACGTTCCGGTAACAAAAAAAA-TTTGATTTCGATTAGTTTAGTAACGGAAAA
261 ATTTCACATGTTAACGTT-CGGTAACAAAAAAAATTTTGATTTCGATTAGTTTAGTAACGGAAAA
115600 ATTAAAAGTTCAATAACCAAAATAGAACACGGGCAATATTTTAATGATCA
325 ATTAAAAGTTCAATAACCAAAATAGAACACGGGCAATATTTTAATGATCA
115650 TA
1 TA
115652 TTTATACTTT
Statistics
Matches: 363, Mismatches: 12, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
374 349 0.96
375 14 0.04
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.37
Consensus pattern (374 bp):
TAATTAGAGGTTAAAATTTTAATAAATTTAATCCTCAACATTAATAAAAAATTAATTTTTAATTT
TTAAAAAATTTGTAAAATTATAAAAATTTAAAAATCAAAATTTATCATCTTGTTAATGTTGAGGG
CTAAATTTATTAAATTTTTTAGAATTTGAACTAAAATGACAAATTTTGTAAATATTGAAGGTCAA
ATTATTATTAGACCAATAAAAAAATTCAGACCAATAAAAAAATTCAATGTTGGCATTTTGGTCAA
ATTTCACATGTTAACGTTCGGTAACAAAAAAAATTTTGATTTCGATTAGTTTAGTAACGGAAAAA
TTAAAAGTTCAATAACCAAAATAGAACACGGGCAATATTTTAATGATCA
Found at i:122911 original size:21 final size:22
Alignment explanation
Indices: 122887--122930 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
122877 ATTTAAAGTC
* *
122887 ATTTCAATATTTTTAT-CTTAA
1 ATTTCAACATTTTCATCCTTAA
122908 ATTTCAACATTTTCATCCTTAA
1 ATTTCAACATTTTCATCCTTAA
122930 A
1 A
122931 AAATCAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.34, C:0.16, G:0.00, T:0.50
Consensus pattern (22 bp):
ATTTCAACATTTTCATCCTTAA
Found at i:130495 original size:44 final size:44
Alignment explanation
Indices: 130446--130533 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
130436 TTAAAGGAAA
130446 GATGTTGTGAATATGTGGAAGATGCATGGGTGACCAGTGTTGAG
1 GATGTTGTGAATATGTGGAAGATGCATGGGTGACCAGTGTTGAG
130490 GATGTTGTGAATATGTGGAAGATGCATGGGTGACCAGTGTTGAG
1 GATGTTGTGAATATGTGGAAGATGCATGGGTGACCAGTGTTGAG
130534 AAGTATAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.25, C:0.07, G:0.39, T:0.30
Consensus pattern (44 bp):
GATGTTGTGAATATGTGGAAGATGCATGGGTGACCAGTGTTGAG
Found at i:134001 original size:20 final size:20
Alignment explanation
Indices: 133976--134048 Score: 58
Period size: 20 Copynumber: 3.4 Consensus size: 20
133966 TAGTAGGTAG
133976 TTTAAAAATAAAATATAATT
1 TTTAAAAATAAAATATAATT
* * *
133996 TTTAAAAA-AATTTATTAGTAGGTAG
1 TTTAAAAATAA---AATA-TA-AT-T
134021 TTTAAAAATAAAATATAATT
1 TTTAAAAATAAAATATAATT
134041 TTTAAAAA
1 TTTAAAAA
134049 AATTTCGTTA
Statistics
Matches: 40, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
19 2 0.05
20 16 0.40
21 1 0.03
22 5 0.12
23 5 0.12
24 1 0.03
25 8 0.20
26 2 0.05
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (20 bp):
TTTAAAAATAAAATATAATT
Found at i:134007 original size:45 final size:45
Alignment explanation
Indices: 133952--134053 Score: 204
Period size: 45 Copynumber: 2.3 Consensus size: 45
133942 CTGAATTTAA
133952 TTAAAAAAATTTATTAGTAGGTAGTTTAAAAATAAAATATAATTT
1 TTAAAAAAATTTATTAGTAGGTAGTTTAAAAATAAAATATAATTT
133997 TTAAAAAAATTTATTAGTAGGTAGTTTAAAAATAAAATATAATTT
1 TTAAAAAAATTTATTAGTAGGTAGTTTAAAAATAAAATATAATTT
134042 TTAAAAAAATTT
1 TTAAAAAAATTT
134054 CGTTATTAAT
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:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (45 bp):
TTAAAAAAATTTATTAGTAGGTAGTTTAAAAATAAAATATAATTT
Found at i:134971 original size:92 final size:96
Alignment explanation
Indices: 134800--134991 Score: 227
Period size: 99 Copynumber: 2.0 Consensus size: 96
134790 AAGTACTAAC
134800 AAATTTGATTACGAAATAATTTATAATAATTAAAAATGTTATCTAACAAGTGATAAATATAGATT
1 AAATTTGATTACGAAATAATTTATAATAATTAAAAATGTTATCTAACAAG-GA-AAATATAGATT
* *
134865 CTCTTAAGATATAATTTAAAAGCTAAAAAGACTA
64 CTCTTAAGATATAATTAAAAAACTAAAAA-ACTA
* **
134899 AAATTTGATTAC-AACATAATTTATAAT-ATTAAAAATGTTATCTAGATAA-G-AGGT-TA-A-T
1 AAATTTGATTACGAA-ATAATTTATAATAATTAAAAATGTTATCTA-ACAAGGAAAATATAGATT
* *
134957 CTTTTAAGATATAATTAAAAAATTAAAAAACTA
64 CTCTTAAGATATAATTAAAAAACTAAAAAACTA
134990 AA
1 AA
134992 TATATAGCAT
Statistics
Matches: 84, Mismatches: 7, Indels: 12
0.82 0.07 0.12
Matches are distributed among these distances:
91 6 0.07
92 26 0.31
93 1 0.01
94 2 0.02
95 2 0.02
97 1 0.01
98 19 0.23
99 27 0.32
ACGTcount: A:0.51, C:0.06, G:0.08, T:0.35
Consensus pattern (96 bp):
AAATTTGATTACGAAATAATTTATAATAATTAAAAATGTTATCTAACAAGGAAAATATAGATTCT
CTTAAGATATAATTAAAAAACTAAAAAACTA
Found at i:135731 original size:21 final size:21
Alignment explanation
Indices: 135699--135743 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
135689 AATTAAATTT
135699 TTTATATTTTTATTTTTAAAA
1 TTTATATTTTTATTTTTAAAA
*
135720 TTTA-ATTATTTATTTTTTAAA
1 TTTATATT-TTTATTTTTAAAA
135741 TTT
1 TTT
135744 TAAATTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTATATTTTTATTTTTAAAA
Found at i:135745 original size:22 final size:20
Alignment explanation
Indices: 135698--135746 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 20
135688 AAATTAAATT
135698 TTTTATATTTTTATTTTTAAA
1 TTTTA-ATTTTTATTTTTAAA
*
135719 ATTTAATTATTTATTTTTTAAA
1 TTTTAATT-TTTA-TTTTTAAA
135741 TTTTAA
1 TTTTAA
135747 ATTTAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 3 0.12
21 8 0.33
22 13 0.54
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTAATTTTTATTTTTAAA
Found at i:135748 original size:28 final size:29
Alignment explanation
Indices: 135687--135752 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
135677 ATTATATAAA
* * *
135687 AAAATTAAATTTTTTATATTTTTATTTTT
1 AAAATTTAATTATTTATATTTTTAATTTT
135716 AAAATTTAATTATTTAT-TTTTTAAATTTT
1 AAAATTTAATTATTTATATTTTT-AATTTT
135745 -AAATTTAA
1 AAAATTTAA
135753 AAAAAAAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 13 0.39
29 20 0.61
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (29 bp):
AAAATTTAATTATTTATATTTTTAATTTT
Found at i:137001 original size:17 final size:17
Alignment explanation
Indices: 136979--137052 Score: 112
Period size: 17 Copynumber: 4.4 Consensus size: 17
136969 TTGGAAATTG
*
136979 AATTTATTTTAAAATTA
1 AATTTATTTTAAATTTA
*
136996 AGTTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
*
137013 AATTTATTTGAAATTTA
1 AATTTATTTTAAATTTA
*
137030 AATTTATTATAAATTTA
1 AATTTATTTTAAATTTA
137047 AATTTA
1 AATTTA
137053 AAATGTCATT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 51 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:137028 original size:7 final size:6
Alignment explanation
Indices: 137003--137054 Score: 58
Period size: 6 Copynumber: 9.0 Consensus size: 6
136993 TTAAGTTTAT
137003 TTTAAA TTTAAA TTT--A TTTGAAA TTTAAA TTT--A TTATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TT-TAAA TTTAAA
137049 TTTAAA
1 TTTAAA
137055 ATGTCATTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
4 7 0.17
5 1 0.03
6 25 0.62
7 7 0.17
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:137626 original size:3 final size:3
Alignment explanation
Indices: 137610--137677 Score: 82
Period size: 3 Copynumber: 22.3 Consensus size: 3
137600 AAACGTTTCT
* ** **
137610 TAA TAA TCAT TAA TAA TAA TAA TAA TTG TTT TAA TAA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
137656 TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA T
137678 GAACATGATA
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
3 55 0.96
4 2 0.04
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (3 bp):
TAA
Done.