Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 114 of 190
Found at i:34607557 original size:41 final size:40
Alignment explanation
Indices: 34607467--34607627 Score: 171
Period size: 41 Copynumber: 3.9 Consensus size: 40
34607457 TCCTACCTTT
* * *
34607467 TGGGTCTTTAGCAGCGTTTTATTAAGAAGCGCCGCTAATGCTG
1 TGGG-CTTTAGCGGCGTTTT-TGAA-AAGCGCCGCTAATGCTA
* *
34607510 TAGGCTTTAGCGGCGTTTTTGAATAAGCGCCGCTAATTCTA
1 TGGGCTTTAGCGGCGTTTTTGAA-AAGCGCCGCTAATGCTA
* *
34607551 TGGGCTTTAGCGGCATTTTTGTAAAAGCGCCGC-AATGCTT
1 TGGGCTTTAGCGGCGTTTTTG-AAAAGCGCCGCTAATGCTA
* *
34607591 TGGCCTTTAGCGGCGCTTTCTAGAAAAGCGCCGCTAA
1 TGGGCTTTAGCGGCG-TTT-TTGAAAAGCGCCGCTAA
34607628 GGACATTTTA
Statistics
Matches: 101, Mismatches: 13, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
40 18 0.18
41 60 0.59
42 20 0.20
43 3 0.03
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.31
Consensus pattern (40 bp):
TGGGCTTTAGCGGCGTTTTTGAAAAGCGCCGCTAATGCTA
Found at i:34607623 original size:82 final size:84
Alignment explanation
Indices: 34607467--34607627 Score: 208
Period size: 82 Copynumber: 1.9 Consensus size: 84
34607457 TCCTACCTTT
* *
34607467 TGGGTCTTTAGCAGCGTTTTATTAAGAAGCGCCGCTAATGCTGTAGGCTTTAGCGGCGTTTTTGA
1 TGGGTCTTTAGCAGCATTTTATTAAGAAGCGCCGCTAATGCTGTAGGCTTTAGCGGCGTTTTAGA
34607532 ATAAGCGCCGCTAATTCTA
66 ATAAGCGCCGCTAATTCTA
* *
34607551 TGGG-CTTTAGCGGCATTTT-TGTAA-AAGCGCCGC-AATGCT-TTGGCCTTTAGCGGCGCTTTC
1 TGGGTCTTTAGCAGCATTTTAT-TAAGAAGCGCCGCTAATGCTGTAGG-CTTTAGCGGCG-TTT-
34607611 TAGAA-AAGCGCCGCTAA
62 TAGAATAAGCGCCGCTAA
34607628 GGACATTTTA
Statistics
Matches: 69, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
80 3 0.04
81 17 0.25
82 25 0.36
83 20 0.29
84 4 0.06
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.31
Consensus pattern (84 bp):
TGGGTCTTTAGCAGCATTTTATTAAGAAGCGCCGCTAATGCTGTAGGCTTTAGCGGCGTTTTAGA
ATAAGCGCCGCTAATTCTA
Found at i:34608349 original size:14 final size:14
Alignment explanation
Indices: 34608330--34608374 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
34608320 TTAATATAAT
* *
34608330 TTAAGGTTTATGGG
1 TTAAGGGTTAGGGG
34608344 TTAAGGGTTAGGGG
1 TTAAGGGTTAGGGG
*
34608358 TTAGGGGTTAGGGG
1 TTAAGGGTTAGGGG
34608372 TTA
1 TTA
34608375 GATGTTAAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.20, C:0.00, G:0.44, T:0.36
Consensus pattern (14 bp):
TTAAGGGTTAGGGG
Found at i:34608381 original size:21 final size:21
Alignment explanation
Indices: 34608341--34608391 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
34608331 TAAGGTTTAT
*
34608341 GGGTTAAGGGTTAGGGGTTAG
1 GGGTTAAGGGTTAGAGGTTAG
* * *
34608362 GGGTTAGGGGTTAGATGTTAA
1 GGGTTAAGGGTTAGAGGTTAG
*
34608383 GAGTTAAGG
1 GGGTTAAGG
34608392 ATTTAGGGTT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.24, C:0.00, G:0.47, T:0.29
Consensus pattern (21 bp):
GGGTTAAGGGTTAGAGGTTAG
Found at i:34608844 original size:20 final size:21
Alignment explanation
Indices: 34608819--34608859 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
34608809 TTAGGGACTA
*
34608819 GGGA-TTATGGTTTAAGGGTT
1 GGGATTTACGGTTTAAGGGTT
*
34608839 GGGATTTACGGTTTAGGGGTT
1 GGGATTTACGGTTTAAGGGTT
34608860 AGGGGTTAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.17, C:0.02, G:0.41, T:0.39
Consensus pattern (21 bp):
GGGATTTACGGTTTAAGGGTT
Found at i:34610456 original size:83 final size:82
Alignment explanation
Indices: 34610242--34610463 Score: 200
Period size: 83 Copynumber: 2.7 Consensus size: 82
34610232 GTGTAATCTA
* * * *
34610242 TTAGTGGCGTTTATGCTAAAAACGCCGC-AATGATGTA-TTAATGTTTTTCAAAACGTCACCGTT
1 TTAGTGGCGTTTTTGCTAAAAACGCCGCAAAT-ATGTATTTAAGGTTCTT-AAAACGGCACCGTT
* *
34610305 TCTCTTCAGGACTTGAAATT
64 TCTATTCAGAACTT-AAATT
** * * * * * *
34610325 TTAGTGGCGTTTTT-CGGGAAAACGCTGGAACTATGGATTAAAGTTTCTTAAAACGGCACCGTTT
1 TTAGTGGCGTTTTTGC-TAAAAACGCCGCAAATATGTATTTAAGGTTCTTAAAACGGCACCGTTT
* * *
34610389 GTATTCAATAAGTT-AATT
65 CTATTC-AGAACTTAAATT
*
34610407 CTTAGTGGCGTTTTTGCTAAAAACGCCGCAAATATATATTTAAGGTTCTTAAAACGG
1 -TTAGTGGCGTTTTTGCTAAAAACGCCGCAAATATGTATTTAAGGTTCTTAAAACGG
34610464 TGCTGTTTCA
Statistics
Matches: 107, Mismatches: 26, Indels: 12
0.74 0.18 0.08
Matches are distributed among these distances:
82 5 0.05
83 88 0.82
84 14 0.13
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (82 bp):
TTAGTGGCGTTTTTGCTAAAAACGCCGCAAATATGTATTTAAGGTTCTTAAAACGGCACCGTTTC
TATTCAGAACTTAAATT
Found at i:34610494 original size:451 final size:451
Alignment explanation
Indices: 34609145--34610495 Score: 2301
Period size: 451 Copynumber: 3.0 Consensus size: 451
34609135 TTGGATATAT
34609145 AGGACCACATTATAA-GAAATAAAAAACATTAGCGGCG-TTGGGTAGAAACGCCGCAACTATGTA
1 AGGACCACATTATAAGGAAA-AAAAAACATTAGCGGCGTTTGGGTAGAAACGCCGCAACTATGTA
*
34609208 CCCATTTTTTTGAAAACGGCGTCGTATCCATTTAGAAATTTAATTTAATTTGTGGCGTTTTTTGG
65 CCCATTTTTTTCAAAACGGCGTCGTATCCATTTAGAAATTTAATTTAATTTGTGGCGTTTTTTGG
* * * *
34609273 GAAAACGCCATAAATATGCATTATAATTTATCAAAACGGCCCCGTTTCAGAAGAGGAGTGTAATT
130 GAAAACGCCATAAATATGTATTATAATTTCTCAAAACGGCACCGTTTCAGAAGAGGAGTGTAATC
* * *
34609338 TATTAGTGGCGTTTATGCTAGAAACGCCGCAAGGATGTATTAATGTTTTTCAAAACGTCACTGTT
195 TATTAGTGGCGTTTATGCTAAAAACGCCGCAATGATGTATTAATGTTTTTCAAAACGTCACCGTT
* * * * * *
34609403 TCACTTCAGGACTTGACATTTTAGTGGCATTTTTCCGGAAAACACCGGAAATATGGATTAAAGTT
260 TCTCTTCAGGACTTGAAATTTTAGTGGCGTTTTTCGGGAAAACGCCGGAACTATGGATTAAAGTT
* * * * * *
34609468 TCTTAAAATGGCATCGTTTCTTTTCAGTAAGTTAATTTTTAGTGGCGTTTTTGCTAAAAACGCCG
325 TCTTAAAACGGCACCGTTTGTATTCAATAAGTTAATTCTTAGTGGCGTTTTTGCTAAAAACGCCG
* * * *
34609533 CAACTATATATTGAAGGTTCTTAAAATGGTGCTGTTTTAGAATTTAATTTTGGCAATTACGC
390 CAAATATATATTGAAGGTTCTTAAAACGGTGCTGTTTCAGAATTTAATTTTGGCAATTATGC
* * *
34609595 AAGACCACATTATAAGGAAAAAAAAACATTAGCAGCGTTTGGGTAGAAACGCCGCAACTATGGAC
1 AGGACCACATTATAAGGAAAAAAAAACATTAGCGGCGTTTGGGTAGAAACGCCGCAACTATGTAC
* *
34609660 CCATTTTTTTCAAAGCGGCATCGTATCCATTTAGAAATTTAATTTAATTTGTGGCGTTTTTTGGG
66 CCATTTTTTTCAAAACGGCGTCGTATCCATTTAGAAATTTAATTTAATTTGTGGCGTTTTTTGGG
34609725 AAAACGCCATAAATATGTATTATAATTTCTCAAAACGGCACCGTTTCAGAAGAGGAGTGTAATCT
131 AAAACGCCATAAATATGTATTATAATTTCTCAAAACGGCACCGTTTCAGAAGAGGAGTGTAATCT
34609790 ATTAGTGGCGTTTATGCTAAAAACGCCGCAATGATGTATTAATGTTTTTCAAAACGTCACCGTTT
196 ATTAGTGGCGTTTATGCTAAAAACGCCGCAATGATGTATTAATGTTTTTCAAAACGTCACCGTTT
*
34609855 CTCTTCAGGACTTGAAATTTTAGTGGCGTTTTTTGGGAAAACGCCGGAACTATGGATTAAAGTTT
261 CTCTTCAGGACTTGAAATTTTAGTGGCGTTTTTCGGGAAAACGCCGGAACTATGGATTAAAGTTT
*
34609920 CTTAAAACGGCACCGTTTGTATTCAATAAGTTAATTCTTAGTGGCGTTTTTGCTAAAAATGCCGC
326 CTTAAAACGGCACCGTTTGTATTCAATAAGTTAATTCTTAGTGGCGTTTTTGCTAAAAACGCCGC
*
34609985 AAATATATATTGAAGGTTCTTAAAACGGTGTTGTTTCAGAATTTAATTTTGGCAATTATGC
391 AAATATATATTGAAGGTTCTTAAAACGGTGCTGTTTCAGAATTTAATTTTGGCAATTATGC
* * * *
34610046 AGGACCACATTATAAGGAAAAAAAAACATTAGCGGCGTTTGAGAAAAAACGCCGCAACTATGTTC
1 AGGACCACATTATAAGGAAAAAAAAACATTAGCGGCGTTTGGGTAGAAACGCCGCAACTATGTAC
* *
34610111 CCATTTTTTTCAAAACGGCGTCGTATCCATCTAGAAATTTAATTTAATTTGTGGCATTTTTTGGG
66 CCATTTTTTTCAAAACGGCGTCGTATCCATTTAGAAATTTAATTTAATTTGTGGCGTTTTTTGGG
* *
34610176 AAAACGCCATAAATATGTATTATAATTTCTCAAAACGGCACTGTTTTAGAAGAGGAGTGTAATCT
131 AAAACGCCATAAATATGTATTATAATTTCTCAAAACGGCACCGTTTCAGAAGAGGAGTGTAATCT
34610241 ATTAGTGGCGTTTATGCTAAAAACGCCGCAATGATGTATTAATGTTTTTCAAAACGTCACCGTTT
196 ATTAGTGGCGTTTATGCTAAAAACGCCGCAATGATGTATTAATGTTTTTCAAAACGTCACCGTTT
*
34610306 CTCTTCAGGACTTGAAATTTTAGTGGCGTTTTTCGGGAAAACGCTGGAACTATGGATTAAAGTTT
261 CTCTTCAGGACTTGAAATTTTAGTGGCGTTTTTCGGGAAAACGCCGGAACTATGGATTAAAGTTT
34610371 CTTAAAACGGCACCGTTTGTATTCAATAAGTTAATTCTTAGTGGCGTTTTTGCTAAAAACGCCGC
326 CTTAAAACGGCACCGTTTGTATTCAATAAGTTAATTCTTAGTGGCGTTTTTGCTAAAAACGCCGC
*
34610436 AAATATATATTTAAGGTTCTTAAAACGGTGCTGTTTCAGAATTTAATTTTGGCAATTATG
391 AAATATATATTGAAGGTTCTTAAAACGGTGCTGTTTCAGAATTTAATTTTGGCAATTATG
34610496 GAAGCAATAG
Statistics
Matches: 849, Mismatches: 50, Indels: 3
0.94 0.06 0.00
Matches are distributed among these distances:
450 30 0.04
451 819 0.96
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.34
Consensus pattern (451 bp):
AGGACCACATTATAAGGAAAAAAAAACATTAGCGGCGTTTGGGTAGAAACGCCGCAACTATGTAC
CCATTTTTTTCAAAACGGCGTCGTATCCATTTAGAAATTTAATTTAATTTGTGGCGTTTTTTGGG
AAAACGCCATAAATATGTATTATAATTTCTCAAAACGGCACCGTTTCAGAAGAGGAGTGTAATCT
ATTAGTGGCGTTTATGCTAAAAACGCCGCAATGATGTATTAATGTTTTTCAAAACGTCACCGTTT
CTCTTCAGGACTTGAAATTTTAGTGGCGTTTTTCGGGAAAACGCCGGAACTATGGATTAAAGTTT
CTTAAAACGGCACCGTTTGTATTCAATAAGTTAATTCTTAGTGGCGTTTTTGCTAAAAACGCCGC
AAATATATATTGAAGGTTCTTAAAACGGTGCTGTTTCAGAATTTAATTTTGGCAATTATGC
Found at i:34611431 original size:12 final size:12
Alignment explanation
Indices: 34611416--34611447 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
34611406 ATTCTTGGAT
34611416 TTTGTTTTCTAG
1 TTTGTTTTCTAG
34611428 TTTGTTTTCTAG
1 TTTGTTTTCTAG
*
34611440 TCTGTTTT
1 TTTGTTTT
34611448 GCGAGATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.06, C:0.09, G:0.16, T:0.69
Consensus pattern (12 bp):
TTTGTTTTCTAG
Found at i:34611652 original size:13 final size:13
Alignment explanation
Indices: 34611634--34611663 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
34611624 AAAGTTGTTA
34611634 AATATTTGATATT
1 AATATTTGATATT
*
34611647 AATATTTGGTATT
1 AATATTTGATATT
34611660 AATA
1 AATA
34611664 ATGAAGTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (13 bp):
AATATTTGATATT
Found at i:34612573 original size:9 final size:9
Alignment explanation
Indices: 34612549--34612758 Score: 140
Period size: 9 Copynumber: 24.3 Consensus size: 9
34612539 TATAAACTTA
34612549 TACATAAACT
1 TACAT-AACT
*
34612559 TGCATAACT
1 TACATAACT
34612568 TACATAA-T
1 TACATAACT
*
34612576 AACATAATAACT
1 TAC---ATAACT
34612588 TACATAA--
1 TACATAACT
* *
34612595 TACATAGCC
1 TACATAACT
34612604 TACATAACT
1 TACATAACT
34612613 TACATAACT
1 TACATAACT
*
34612622 TAAATAACT
1 TACATAACT
34612631 TACATAA--
1 TACATAACT
34612638 TACATAACT
1 TACATAACT
**
34612647 TTGATAACT
1 TACATAACT
* *
34612656 AACATTA--
1 TACATAACT
*
34612663 TACACAACT
1 TACATAACT
34612672 TACATAA--
1 TACATAACT
*
34612679 TACATTACT
1 TACATAACT
* *
34612688 TACTTAACA
1 TACATAACT
* *
34612697 TACATAGCC
1 TACATAACT
34612706 TACATAACT
1 TACATAACT
34612715 TACATAA--
1 TACATAACT
*
34612722 TACACAACT
1 TACATAACT
*
34612731 TACATAGCT
1 TACATAACT
34612740 TACATAA--
1 TACATAACT
34612747 TACATAACT
1 TACATAACT
34612756 TAC
1 TAC
34612759 CCGTGTAATT
Statistics
Matches: 152, Mismatches: 32, Indels: 33
0.70 0.15 0.15
Matches are distributed among these distances:
7 36 0.24
8 3 0.02
9 102 0.67
10 4 0.03
11 4 0.03
12 3 0.02
ACGTcount: A:0.46, C:0.21, G:0.02, T:0.31
Consensus pattern (9 bp):
TACATAACT
Found at i:34612587 original size:20 final size:19
Alignment explanation
Indices: 34612562--34612644 Score: 71
Period size: 20 Copynumber: 4.1 Consensus size: 19
34612552 ATAAACTTGC
34612562 ATAACTTACATAATAACATA
1 ATAACTTACATAAT-ACATA
34612582 ATAACTTACATAATACATAGCCTA
1 ATAACTTACATAATAC--A---TA
*
34612606 CATAACTTACAT-A-ACTTAA
1 -ATAACTTACATAATACAT-A
34612625 ATAACTTACATAATACATA
1 ATAACTTACATAATACATA
34612644 A
1 A
34612645 CTTTGATAAC
Statistics
Matches: 52, Mismatches: 2, Indels: 19
0.71 0.03 0.26
Matches are distributed among these distances:
18 12 0.23
19 6 0.12
20 17 0.33
21 1 0.02
23 2 0.04
24 3 0.06
25 11 0.21
ACGTcount: A:0.51, C:0.18, G:0.01, T:0.30
Consensus pattern (19 bp):
ATAACTTACATAATACATA
Found at i:34612675 original size:84 final size:84
Alignment explanation
Indices: 34612564--34612758 Score: 222
Period size: 84 Copynumber: 2.4 Consensus size: 84
34612554 AAACTTGCAT
* *
34612564 AACTTACATAA-TAACATAAT----AACTTACATAATACA-TAGCCTACATAACTTACATAACTT
1 AACTTACATAACTAACATAATACACAACTTACATAATACATTA-CCTACATAACATACATAACCT
*
34612623 AAATAACTTACATAATACAT
65 AAATAACTTACATAATACAC
** * * * *
34612643 AACTTTGATAACTAACATTATACACAACTTACATAATACATTACTTACTTAACATACATAGCCTA
1 AACTTACATAACTAACATAATACACAACTTACATAATACATTACCTACATAACATACATAACCTA
*
34612708 CATAACTTACATAATACAC
66 AATAACTTACATAATACAC
* * *
34612727 AACTTACATAGCTTACATAATACATAACTTAC
1 AACTTACATAACTAACATAATACACAACTTAC
34612759 CCGTGTAATT
Statistics
Matches: 94, Mismatches: 16, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
79 9 0.10
80 8 0.09
84 75 0.80
85 2 0.02
ACGTcount: A:0.46, C:0.21, G:0.02, T:0.31
Consensus pattern (84 bp):
AACTTACATAACTAACATAATACACAACTTACATAATACATTACCTACATAACATACATAACCTA
AATAACTTACATAATACAC
Found at i:34612758 original size:25 final size:25
Alignment explanation
Indices: 34612548--34612753 Score: 90
Period size: 25 Copynumber: 8.0 Consensus size: 25
34612538 ATATAAACTT
*
34612548 ATACATAAACTTGCATAACTTACATA
1 ATACAT-AACTTACATAACTTACATA
34612574 ATAACATAATAACTTACATAA--TACATA
1 AT-AC---ATAACTTACATAACTTACATA
* *
34612601 GCCTACATAACTTACATAACTTAAATA
1 --ATACATAACTTACATAACTTACATA
**
34612628 ACTTACATAA--TACATAACTTTGATA
1 A--TACATAACTTACATAACTTACATA
* *
34612653 ACTAACATTA--TACACAACTTACATA
1 A-T-ACATAACTTACATAACTTACATA
* * *
34612678 ATACATTACTTACTTAACATACATA
1 ATACATAACTTACATAACTTACATA
* *
34612703 GCCTACATAACTTACATAA--TACACA
1 --ATACATAACTTACATAACTTACATA
*
34612728 ACTTACATAGCTTACATAA--TACATA
1 A--TACATAACTTACATAACTTACATA
34612753 A
1 A
34612754 CTTACCCGTG
Statistics
Matches: 142, Mismatches: 21, Indels: 35
0.72 0.11 0.18
Matches are distributed among these distances:
23 6 0.04
24 2 0.01
25 83 0.58
26 2 0.01
27 34 0.24
28 2 0.01
29 11 0.08
30 2 0.01
ACGTcount: A:0.47, C:0.20, G:0.02, T:0.31
Consensus pattern (25 bp):
ATACATAACTTACATAACTTACATA
Found at i:34618290 original size:66 final size:65
Alignment explanation
Indices: 34618196--34618366 Score: 211
Period size: 66 Copynumber: 2.6 Consensus size: 65
34618186 GATCAAATTA
* * * *
34618196 CACAACTTAAAGCGGAGGCAACATCGAGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCA
1 CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAG-TATGAAGAACTCCA
34618260 G
65 G
* *
34618261 CTACAACTTAAAGCAGATGCAGCAGCGAGAGAATCTGAGGTTCAACGAAAGTATGAAGAACTCCA
1 C-ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCA
34618326 G
65 G
* * *
34618327 CAGTAGCTTAAAGCAGATGC-GACAGCGAGAGAAGCAGAGG
1 CA-CAACTTAAAGCAGATGCAG-CAGCGAGAGAAGCTGAGG
34618367 CTACAGCGAG
Statistics
Matches: 92, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
65 3 0.03
66 85 0.92
67 4 0.04
ACGTcount: A:0.40, C:0.19, G:0.27, T:0.14
Consensus pattern (65 bp):
CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAG
Found at i:34618363 original size:21 final size:21
Alignment explanation
Indices: 34618337--34618428 Score: 123
Period size: 21 Copynumber: 4.4 Consensus size: 21
34618327 CAGTAGCTTA
* *
34618337 AAGCAGATGCGACAGCGAGAG
1 AAGCAGAGGCTACAGCGAGAG
*
34618358 AAGCAGAGGCTACAGCGAGGG
1 AAGCAGAGGCTACAGCGAGAG
34618379 AAGCAGAGGCTACAGCGA-AGG
1 AAGCAGAGGCTACAGCGAGA-G
* *
34618400 AAGTAGAGGCTACAGCGAGGG
1 AAGCAGAGGCTACAGCGAGAG
34618421 AAGCAGAG
1 AAGCAGAG
34618429 CAGCGTAAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
21 62 1.00
ACGTcount: A:0.37, C:0.17, G:0.40, T:0.05
Consensus pattern (21 bp):
AAGCAGAGGCTACAGCGAGAG
Found at i:34618396 original size:42 final size:42
Alignment explanation
Indices: 34618337--34618428 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 42
34618327 CAGTAGCTTA
*
34618337 AAGCAGATGCGACAGCG-AGAGAAGCAGAGGCTACAGCGAGGG
1 AAGCAGAGGCGACAGCGAAG-GAAGCAGAGGCTACAGCGAGGG
* *
34618379 AAGCAGAGGCTACAGCGAAGGAAGTAGAGGCTACAGCGAGGG
1 AAGCAGAGGCGACAGCGAAGGAAGCAGAGGCTACAGCGAGGG
34618421 AAGCAGAG
1 AAGCAGAG
34618429 CAGCGTAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
42 44 0.96
43 2 0.04
ACGTcount: A:0.37, C:0.17, G:0.40, T:0.05
Consensus pattern (42 bp):
AAGCAGAGGCGACAGCGAAGGAAGCAGAGGCTACAGCGAGGG
Found at i:34624644 original size:43 final size:43
Alignment explanation
Indices: 34624570--34624796 Score: 262
Period size: 43 Copynumber: 5.3 Consensus size: 43
34624560 TTTTCGACAA
*
34624570 AAAGCGCCGCTAAAAGATAAGGGTATTTAGCGGCGTTTGTGGAG
1 AAAGCGCCGCT-AAAGATAAGGGTCTTTAGCGGCGTTTGTGGAG
*
34624614 AAAGCGCCGCTAAAGCTAAGGGTCTTTAGCGGCGTTTGTGGAG
1 AAAGCGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGTGGAG
* * * *
34624657 AAAGCGCCGCTAAAGATCAGGTTCTTTAGTGGCGTTTGTGGTG
1 AAAGCGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGTGGAG
* * * * *
34624700 GAAGCGCCGCTATAGATCAA-GGTCTTTTGCGGCGTTTGTTG-T
1 AAAGCGCCGCTAAAGAT-AAGGGTCTTTAGCGGCGTTTGTGGAG
* *** *
34624742 AAAGCGCCGCTAAAGGTCTTGGTCTTCAGCGGCGTTTGTGCGAG
1 AAAGCGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGTG-GAG
34624786 -AAGCGCCGCTA
1 AAAGCGCCGCTA
34624797 TAGACCAACA
Statistics
Matches: 155, Mismatches: 24, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
42 31 0.20
43 112 0.72
44 12 0.08
ACGTcount: A:0.22, C:0.19, G:0.33, T:0.26
Consensus pattern (43 bp):
AAAGCGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGTGGAG
Found at i:34624817 original size:85 final size:85
Alignment explanation
Indices: 34624570--34624821 Score: 267
Period size: 85 Copynumber: 2.9 Consensus size: 85
34624560 TTTTCGACAA
* * * * * *
34624570 AAAGCGCCGCTAAAAGATAAGGGTATTTAGCGGCGTTTGTGGAGAAAGCGCCGCTAAAG-CTAAG
1 AAAGCGCCGCT-AAAGATCAGGTTCTTCAGCGGCGTTTGTGGAG-AAGCGCCGCTATAGACCAA-
34624634 GGTCTTTAGCGGCGTTTGTGGAG
63 GGTCTTTAGCGGCGTTTGTGGAG
* * * *
34624657 AAAGCGCCGCTAAAGATCAGGTTCTTTAGTGGCGTTTGTGGTGGAAGCGCCGCTATAGATCAAGG
1 AAAGCGCCGCTAAAGATCAGGTTCTTCAGCGGCGTTTGTGG-AGAAGCGCCGCTATAGACCAAGG
* * *
34624722 TCTTTTGCGGCGTTTGTTG-T
65 TCTTTAGCGGCGTTTGTGGAG
* * *
34624742 AAAGCGCCGCTAAAGGTCTTGG-TCTTCAGCGGCGTTTGTGCGAGAAGCGCCGCTATAGACCAAC
1 AAAGCGCCGCTAAAGATC-AGGTTCTTCAGCGGCGTTTGTG-GAGAAGCGCCGCTATAGACCAAG
**
34624806 ACCTTTAGCGGCGTTT
64 GTCTTTAGCGGCGTTT
34624822 ATTTCTAAAA
Statistics
Matches: 140, Mismatches: 21, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
85 65 0.46
86 61 0.44
87 14 0.10
ACGTcount: A:0.22, C:0.20, G:0.32, T:0.26
Consensus pattern (85 bp):
AAAGCGCCGCTAAAGATCAGGTTCTTCAGCGGCGTTTGTGGAGAAGCGCCGCTATAGACCAAGGT
CTTTAGCGGCGTTTGTGGAG
Found at i:34624853 original size:34 final size:34
Alignment explanation
Indices: 34624810--34624886 Score: 154
Period size: 34 Copynumber: 2.3 Consensus size: 34
34624800 ACCAACACCT
34624810 TTAGCGGCGTTTATTTCTAAAAACGCCGCTAAAG
1 TTAGCGGCGTTTATTTCTAAAAACGCCGCTAAAG
34624844 TTAGCGGCGTTTATTTCTAAAAACGCCGCTAAAG
1 TTAGCGGCGTTTATTTCTAAAAACGCCGCTAAAG
34624878 TTAGCGGCG
1 TTAGCGGCG
34624887 CAGTCATTAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (34 bp):
TTAGCGGCGTTTATTTCTAAAAACGCCGCTAAAG
Found at i:34625963 original size:41 final size:41
Alignment explanation
Indices: 34625855--34626159 Score: 278
Period size: 41 Copynumber: 7.4 Consensus size: 41
34625845 CGATTATTAA
* * * *
34625855 ACCTTTAGCGGCGTTTTTATTTTAGCGCCGCTAATG-TCCG
1 ACCTTTAGCGGCGTTTTTATCTGAGCGCCACTAATGCTCTG
*
34625895 ATCTTTAGCGGCGTTTTTATCTGAGCGCCACTAATGCTCTG
1 ACCTTTAGCGGCGTTTTTATCTGAGCGCCACTAATGCTCTG
* * * *
34625936 GCCTTTAGCGGCGTTTTTCTCTAAGCGCCGCTAATGCTC-G
1 ACCTTTAGCGGCGTTTTTATCTGAGCGCCACTAATGCTCTG
* * *
34625976 TATCTTTAGTGGCGTTTTTATCTGAGCGCCACTAATTCTCTG
1 -ACCTTTAGCGGCGTTTTTATCTGAGCGCCACTAATGCTCTG
* * * * *
34626018 GCCTTTAGCGGCATTTTTTTCTAAGCGCCGCTAATG-T-TAG
1 ACCTTTAGCGGCGTTTTTATCTGAGCGCCACTAATGCTCT-G
* * *
34626058 TATCTTTAGTGGCGTTTTAATCTGAGCGCCACTAATGCTCTG
1 -ACCTTTAGCGGCGTTTTTATCTGAGCGCCACTAATGCTCTG
* * ** * * * *
34626100 GCTTTTAGCGGCGTTTTATAGGTAAGCGCCGCGAATGCAT-TT
1 ACCTTTAGCGGCGTTTT-TATCTGAGCGCCACTAATGC-TCTG
34626142 ACCTTTAGCGGCGTTTTT
1 ACCTTTAGCGGCGTTTTT
34626160 GCCGAAACGC
Statistics
Matches: 210, Mismatches: 46, Indels: 17
0.77 0.17 0.06
Matches are distributed among these distances:
39 1 0.00
40 35 0.17
41 139 0.66
42 33 0.16
43 2 0.01
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.37
Consensus pattern (41 bp):
ACCTTTAGCGGCGTTTTTATCTGAGCGCCACTAATGCTCTG
Found at i:34626007 original size:82 final size:81
Alignment explanation
Indices: 34625856--34626136 Score: 402
Period size: 82 Copynumber: 3.4 Consensus size: 81
34625846 GATTATTAAA
* * *
34625856 CCTTTAGCGGCGTTTTTATTTTAGCGCCGCTAATGTCCG-ATCTTTAGCGGCGTTTTTATCTGAG
1 CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGT-CGTATCTTTAGTGGCGTTTTTATCTGAG
34625920 CGCCACTAATGCTCTGG
65 CGCCACTAATGCTCTGG
*
34625937 CCTTTAGCGGCGTTTTTCTCTAAGCGCCGCTAATGCTCGTATCTTTAGTGGCGTTTTTATCTGAG
1 CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATG-TCGTATCTTTAGTGGCGTTTTTATCTGAG
*
34626002 CGCCACTAATTCTCTGG
65 CGCCACTAATGCTCTGG
* * * *
34626019 CCTTTAGCGGCATTTTTTTCTAAGCGCCGCTAATGTTAGTATCTTTAGTGGCGTTTTAATCTGAG
1 CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATG-TCGTATCTTTAGTGGCGTTTTTATCTGAG
34626084 CGCCACTAATGCTCTGG
65 CGCCACTAATGCTCTGG
* ** *
34626101 CTTTTAGCGGCGTTTTATAGGTAAGCGCCGCGAATG
1 CCTTTAGCGGCGTTTT-TATCTAAGCGCCGCTAATG
34626137 CATTTACCTT
Statistics
Matches: 180, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
81 34 0.19
82 131 0.73
83 15 0.08
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.37
Consensus pattern (81 bp):
CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGTCGTATCTTTAGTGGCGTTTTTATCTGAGC
GCCACTAATGCTCTGG
Found at i:34626552 original size:2 final size:2
Alignment explanation
Indices: 34626545--34626589 Score: 81
Period size: 2 Copynumber: 22.0 Consensus size: 2
34626535 TTTTTAACTG
34626545 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
34626588 TA
1 TA
34626590 NNNNNNNNNN
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 40 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:34628558 original size:8 final size:10
Alignment explanation
Indices: 34628536--34628572 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
34628526 TATTTTTACT
34628536 TATATATGGA
1 TATATATGGA
*
34628546 TATATATGAA
1 TATATATGGA
34628556 TATATATGGA
1 TATATATGGA
34628566 TATATAT
1 TATATAT
34628573 AGTTATTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (10 bp):
TATATATGGA
Found at i:34629917 original size:11 final size:11
Alignment explanation
Indices: 34629897--34629933 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
34629887 TTATATTTTC
34629897 TAATTTGATTA
1 TAATTTGATTA
*
34629908 TAATTAGATTA
1 TAATTTGATTA
*
34629919 TAATTTCATTA
1 TAATTTGATTA
34629930 TAAT
1 TAAT
34629934 GTTTACTCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (11 bp):
TAATTTGATTA
Found at i:34631543 original size:9 final size:9
Alignment explanation
Indices: 34631529--34631656 Score: 52
Period size: 9 Copynumber: 13.8 Consensus size: 9
34631519 TGTGATATTA
34631529 TACATAAAT
1 TACATAAAT
*
34631538 TACATAACT
1 TACATAAAT
*
34631547 TA-ATTAAT
1 TACATAAAT
*
34631555 TA-AT-ATT
1 TACATAAAT
*
34631562 ATACATAACT
1 -TACATAAAT
34631572 TACATTAATATT
1 TACA-TAA-A-T
34631584 ATACATAAAT
1 -TACATAAAT
*
34631594 TACATAACT
1 TACATAAAT
*
34631603 TA-ATTAAT
1 TACATAAAT
*
34631611 TA-AT-ATT
1 TACATAAAT
*
34631618 ATACATAACT
1 -TACATAAAT
34631628 TACATTAATATT
1 TACA-TAA-A-T
34631640 ATACATAAAT
1 -TACATAAAT
34631650 TACATAA
1 TACATAA
34631657 CTTAATTAAT
Statistics
Matches: 93, Mismatches: 12, Indels: 28
0.70 0.09 0.21
Matches are distributed among these distances:
7 4 0.04
8 20 0.22
9 39 0.42
10 12 0.13
11 2 0.02
12 8 0.09
13 8 0.09
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (9 bp):
TACATAAAT
Found at i:34631566 original size:25 final size:22
Alignment explanation
Indices: 34631538--34631591 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 22
34631528 ATACATAAAT
34631538 TACATAACTTAATTAATTAATATTA
1 TACATAACTT-A--AATTAATATTA
*
34631563 TACATAACTTACATTAATATTA
1 TACATAACTTAAATTAATATTA
34631585 TACATAA
1 TACATAA
34631592 ATTACATAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 17 0.61
24 1 0.04
25 10 0.36
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (22 bp):
TACATAACTTAAATTAATATTA
Found at i:34631581 original size:22 final size:22
Alignment explanation
Indices: 34631548--34631598 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
34631538 TACATAACTT
34631548 AATTA-ATTAATATTATACATA
1 AATTACATTAATATTATACATA
*
34631569 ACTTACATTAATATTATACATA
1 AATTACATTAATATTATACATA
34631591 AATTACAT
1 AATTACAT
34631599 AACTTAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 4 0.15
22 23 0.85
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (22 bp):
AATTACATTAATATTATACATA
Found at i:34631623 original size:25 final size:22
Alignment explanation
Indices: 34631594--34631647 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 22
34631584 ATACATAAAT
34631594 TACATAACTTAATTAATTAATATTA
1 TACATAACTT-A--AATTAATATTA
*
34631619 TACATAACTTACATTAATATTA
1 TACATAACTTAAATTAATATTA
34631641 TACATAA
1 TACATAA
34631648 ATTACATAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 17 0.61
24 1 0.04
25 10 0.36
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (22 bp):
TACATAACTTAAATTAATATTA
Found at i:34631637 original size:22 final size:22
Alignment explanation
Indices: 34631604--34631654 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
34631594 TACATAACTT
34631604 AATTA-ATTAATATTATACATA
1 AATTACATTAATATTATACATA
*
34631625 ACTTACATTAATATTATACATA
1 AATTACATTAATATTATACATA
34631647 AATTACAT
1 AATTACAT
34631655 AACTTAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 4 0.15
22 23 0.85
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (22 bp):
AATTACATTAATATTATACATA
Found at i:34631674 original size:34 final size:35
Alignment explanation
Indices: 34631628--34631720 Score: 120
Period size: 34 Copynumber: 2.7 Consensus size: 35
34631618 ATACATAACT
34631628 TACATTAATATTATACATAAATTACA-TAACTTAAT-
1 TACATTAATATTATACATAAATTACATTAA--TAATA
* *
34631663 TA-ATTAATATTATACATAACTTACATTAATATTA
1 TACATTAATATTATACATAAATTACATTAATAATA
*
34631697 TACATAAATATTATACATAAATTA
1 TACATTAATATTATACATAAATTA
34631721 NNNNNNNNNN
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
33 3 0.06
34 24 0.47
35 24 0.47
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (35 bp):
TACATTAATATTATACATAAATTACATTAATAATA
Found at i:34631679 original size:25 final size:22
Alignment explanation
Indices: 34631650--34631703 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 22
34631640 ATACATAAAT
34631650 TACATAACTTAATTAATTAATATTA
1 TACATAACTT-A--AATTAATATTA
*
34631675 TACATAACTTACATTAATATTA
1 TACATAACTTAAATTAATATTA
34631697 TACATAA
1 TACATAA
34631704 ATATTATACA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 17 0.61
24 1 0.04
25 10 0.36
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (22 bp):
TACATAACTTAAATTAATATTA
Found at i:34631706 original size:13 final size:13
Alignment explanation
Indices: 34631684--34631718 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
34631674 ATACATAACT
*
34631684 TACATTAATATTA
1 TACATAAATATTA
34631697 TACATAAATATTA
1 TACATAAATATTA
34631710 TACATAAAT
1 TACATAAAT
34631719 TANNNNNNNN
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (13 bp):
TACATAAATATTA
Found at i:34631720 original size:56 final size:56
Alignment explanation
Indices: 34631523--34631705 Score: 366
Period size: 56 Copynumber: 3.3 Consensus size: 56
34631513 GGGTGATGTG
34631523 ATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTACATTA
1 ATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTACATTA
34631579 ATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTACATTA
1 ATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTACATTA
34631635 ATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTACATTA
1 ATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTACATTA
34631691 ATATTATACATAAAT
1 ATATTATACATAAAT
34631706 ATTATACATA
Statistics
Matches: 127, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 127 1.00
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (56 bp):
ATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTACATTA
Found at i:34631859 original size:9 final size:9
Alignment explanation
Indices: 34631845--34632012 Score: 94
Period size: 9 Copynumber: 20.2 Consensus size: 9
34631835 ATTAATATTA
34631845 TACATAACT
1 TACATAACT
34631854 TACATAACT
1 TACATAACT
* *
34631863 TACTTAATT
1 TACATAACT
*
34631872 TGCATAA--
1 TACATAACT
*
34631879 TAAATAACT
1 TACATAACT
34631888 TACATAACT
1 TACATAACT
34631897 TACATAA--
1 TACATAACT
34631904 TACATAACT
1 TACATAACT
* *
34631913 TATATGACT
1 TACATAACT
*
34631922 TATATAACT
1 TACATAACT
34631931 TACAT-A--
1 TACATAACT
* *
34631937 -GCATAATT
1 TACATAACT
*
34631945 TTCATAA--
1 TACATAACT
*
34631952 TACACAACT
1 TACATAACT
**
34631961 TACATAGTT
1 TACATAACT
*
34631970 TTCATAA--
1 TACATAACT
*
34631977 TAAATAACT
1 TACATAACT
34631986 TACATAA--
1 TACATAACT
34631993 TACATAACT
1 TACATAACT
*
34632002 TACATAGCT
1 TACATAACT
34632011 TA
1 TA
34632013 ATTATACTTA
Statistics
Matches: 121, Mismatches: 24, Indels: 28
0.70 0.14 0.16
Matches are distributed among these distances:
5 3 0.02
6 1 0.01
7 29 0.24
8 1 0.01
9 87 0.72
ACGTcount: A:0.44, C:0.17, G:0.03, T:0.36
Consensus pattern (9 bp):
TACATAACT
Found at i:34631864 original size:34 final size:34
Alignment explanation
Indices: 34631821--34631904 Score: 105
Period size: 34 Copynumber: 2.5 Consensus size: 34
34631811 NNNNNNNNNN
* * * *
34631821 ACATAACTTAGTTAATTAATATTATACATAACTT
1 ACATAACTTACTTAATTAACATAATAAATAACTT
**
34631855 ACATAACTTACTTAATTTGCATAATAAATAACTT
1 ACATAACTTACTTAATTAACATAATAAATAACTT
*
34631889 ACATAACTTACATAAT
1 ACATAACTTACTTAAT
34631905 ACATAACTTA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.45, C:0.14, G:0.02, T:0.38
Consensus pattern (34 bp):
ACATAACTTACTTAATTAACATAATAAATAACTT
Found at i:34631886 original size:25 final size:25
Alignment explanation
Indices: 34631857--34631999 Score: 98
Period size: 25 Copynumber: 5.9 Consensus size: 25
34631847 CATAACTTAC
* * *
34631857 ATAACTTACTTAATTTGCATAATAA
1 ATAACTTACATAACTTACATAATAA
*
34631882 ATAACTTACATAACTTACATAATAC
1 ATAACTTACATAACTTACATAATAA
* *
34631907 ATAACTTATATGACTT--AT-ATAA
1 ATAACTTACATAACTTACATAATAA
* * * * * *
34631929 CTTACATAGCATAATTTTCATAATAC
1 ATAACTTA-CATAACTTACATAATAA
* ** *
34631955 ACAACTTACATAGTTTTCATAATAA
1 ATAACTTACATAACTTACATAATAA
34631980 ATAACTTACATAA--TACATAA
1 ATAACTTACATAACTTACATAA
34632000 CTTACATAGC
Statistics
Matches: 91, Mismatches: 23, Indels: 10
0.73 0.19 0.08
Matches are distributed among these distances:
22 8 0.09
23 13 0.14
25 63 0.69
26 7 0.08
ACGTcount: A:0.45, C:0.15, G:0.03, T:0.36
Consensus pattern (25 bp):
ATAACTTACATAACTTACATAATAA
Found at i:34631907 original size:16 final size:16
Alignment explanation
Indices: 34631888--34632007 Score: 78
Period size: 16 Copynumber: 7.9 Consensus size: 16
34631878 ATAAATAACT
34631888 TACATAACTTACATAA
1 TACATAACTTACATAA
* *
34631904 TACATAACTTATATGACT
1 TACATAACTTACAT-A-A
*
34631922 TATATAACTTACAT-A
1 TACATAACTTACATAA
* * *
34631937 -GCATAATTTTCATAA
1 TACATAACTTACATAA
* *
34631952 TACACAACTTACATAG
1 TACATAACTTACATAA
34631968 T---T---TT-CATAA
1 TACATAACTTACATAA
*
34631977 TAAATAACTTACATAA
1 TACATAACTTACATAA
34631993 TACATAACTTACATA
1 TACATAACTTACATA
34632008 GCTTAATTAT
Statistics
Matches: 76, Mismatches: 17, Indels: 22
0.66 0.15 0.19
Matches are distributed among these distances:
9 5 0.07
10 2 0.03
12 1 0.01
14 9 0.12
15 3 0.04
16 43 0.57
17 1 0.01
18 12 0.16
ACGTcount: A:0.45, C:0.17, G:0.03, T:0.36
Consensus pattern (16 bp):
TACATAACTTACATAA
Found at i:34631923 original size:34 final size:33
Alignment explanation
Indices: 34631821--34632007 Score: 104
Period size: 34 Copynumber: 5.7 Consensus size: 33
34631811 NNNNNNNNNN
** *
34631821 ACATAACTTAGTTAATTA-ATATTATACATAACTT
1 ACATAACTTACATAATTACATA--ATAAATAACTT
* *
34631855 ACATAACTTACTTAATTTGCATAATAAATAACTT
1 ACATAACTTACATAA-TTACATAATAAATAACTT
* *
34631889 ACATAACTTACATAA-TACATAACTTATATGACTT
1 ACATAACTTACATAATTACATAA--TAAATAACTT
* * **
34631923 ATATAACTTACATAGCA-TA-AT-TTTCATAA--T
1 ACATAACTTACATA--ATTACATAATAAATAACTT
* * *
34631953 ACACAACTTACATAGTTTTCATAATAAATAACTT
1 ACATAACTTACATA-ATTACATAATAAATAACTT
34631987 ACATAA--TACATAACTTACATA
1 ACATAACTTACATAA-TTACATA
34632008 GCTTAATTAT
Statistics
Matches: 118, Mismatches: 23, Indels: 26
0.71 0.14 0.16
Matches are distributed among these distances:
30 14 0.12
31 2 0.02
32 27 0.23
34 65 0.55
35 4 0.03
36 6 0.05
ACGTcount: A:0.45, C:0.16, G:0.03, T:0.37
Consensus pattern (33 bp):
ACATAACTTACATAATTACATAATAAATAACTT
Found at i:34637704 original size:21 final size:21
Alignment explanation
Indices: 34637678--34637722 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
34637668 CAGCAGCTTA
*
34637678 AAGCAGATACGGCAGCAAGAG
1 AAGCAGAGACGGCAGCAAGAG
* *
34637699 AAGCAGAGGCGGCAGCGAGAG
1 AAGCAGAGACGGCAGCAAGAG
34637720 AAG
1 AAG
34637723 AACAGGNNNN
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.40, C:0.18, G:0.40, T:0.02
Consensus pattern (21 bp):
AAGCAGAGACGGCAGCAAGAG
Found at i:34638625 original size:22 final size:22
Alignment explanation
Indices: 34638593--34638635 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
34638583 CTGCGGTGCT
*
34638593 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
*
34638615 AAAAAGTGCCGCTAAAAGCCT
1 AAAAAGCGCCGCTAAAAGCCT
34638636 GTTTTGGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.42, C:0.26, G:0.21, T:0.12
Consensus pattern (22 bp):
AAAAAGCGCCGCTAAAAGCCTA
Found at i:34638771 original size:21 final size:21
Alignment explanation
Indices: 34638747--34638786 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
34638737 AGGCTACATT
34638747 TTTTAA-AATATAATATTAATA
1 TTTTAATAATATAA-ATTAATA
*
34638768 TTTTAATAATGTAAATTAA
1 TTTTAATAATATAAATTAA
34638787 AATACTTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (21 bp):
TTTTAATAATATAAATTAATA
Found at i:34639093 original size:3 final size:3
Alignment explanation
Indices: 34639085--34639109 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
34639075 ATGTGTTAAA
34639085 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
34639110 TATAATTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:34647371 original size:43 final size:43
Alignment explanation
Indices: 34647316--34647397 Score: 114
Period size: 43 Copynumber: 1.9 Consensus size: 43
34647306 CTGGTGAATT
*
34647316 ATTTCAGACTTTATG-TCTAGCAGGCTTCATGCCGGTGTACCGA
1 ATTTCAGACTTTAGGCT-TAGCAGGCTTCATGCCGGTGTACCGA
*
34647359 ATTTCA-AGCTTTAGGCTTAGCAGGCTTCGTGCCGGTGTA
1 ATTTCAGA-CTTTAGGCTTAGCAGGCTTCATGCCGGTGTA
34647398 TCATTTCAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
42 1 0.03
43 33 0.94
44 1 0.03
ACGTcount: A:0.20, C:0.22, G:0.26, T:0.33
Consensus pattern (43 bp):
ATTTCAGACTTTAGGCTTAGCAGGCTTCATGCCGGTGTACCGA
Found at i:34654553 original size:454 final size:453
Alignment explanation
Indices: 34653707--34654609 Score: 1779
Period size: 454 Copynumber: 2.0 Consensus size: 453
34653697 GACGTACCTT
34653707 TATTAGATAAAGCTTATGCTTATCATTTAGCCTTTATCCCGGGTGATTTATGTACTAATATTATT
1 TATTAGATAAAGCTTATGCTTATCATTTAGCCTTTATCCCGGGTGATTTATGTACTAATATTATT
34653772 AGATTTATCCAGCTTTATCTTAGGATAGATTTCGGAGGTTACTTATACATAATTATTATGTTGTT
66 AGATTTATCCAGCTTTATCTTAGGATAGATTTCGGAGGTTACTTATACATAATTATTATGTTGTT
34653837 AAAGATGATTTTATCTCTACTTGGATTGATCTGATATGTTATAAATAGTCAACTATTCACATATG
131 AAAGATGATTTTATCTCTACTTGGATTGATCTGATATGTTATAAATAGTCAACTATTCACATATG
34653902 GAGATTCATCTTCCGGGGTTGCTTGTGTTGCATTTGGTTAATTTATTTGATGTCGACTTTTACTT
196 GAGATTCATCTTCCGGGGTTGCTTGTGTTGCATTTGGTTAATTTATTTGATGTCGACTTTTACTT
34653967 GTATTTTGTATTCTTTTCACAAGTTTTATTGGACAATATTAAACTGTTGTAAGTGAGGTTATTTG
261 GTATTTTGTATTCTTTTCACAAGTTTTATTGGACAATATTAAACTGTTGTAAGTGAGGTTATTTG
34654032 GGCGAGTAGTTGTAACAAGTTGAGACTAGCTATTGGGGCTGCAATTGCTTATTGTGTAAAGATAG
326 GGCGAGTAGTTGTAACAAGTTGAGACTAGCTATTGGGGCTGCAATTGCTTATTGTGTAAAGATAG
34654097 ATTAGGTGTAATACCCTGAAAATTACTACAGTAAGAAAGTAAGATAATATCCTTGATATTAGA
391 ATTAGGTGTAATACCCTGAAAATTACTACAGTAAGAAAGTAAGATAATATCCTTGATATTAGA
*
34654160 TATTAGATAAAGCTTATGCTTATCATTTAGCCTTTATCCCGGGTGATTTATGTGCTAATATTATT
1 TATTAGATAAAGCTTATGCTTATCATTTAGCCTTTATCCCGGGTGATTTATGTACTAATATTATT
*
34654225 AGATTTTATCCAGCTTTATCTTGGGATAGATTTCGGAGGTTACTTATACATAATTATTATGTTGT
66 AGA-TTTATCCAGCTTTATCTTAGGATAGATTTCGGAGGTTACTTATACATAATTATTATGTTGT
34654290 TAAAGATGATTTTATCTCTACTTGGATTGATCTGATATGTTATAAATAGTCAACTATTCACATAT
130 TAAAGATGATTTTATCTCTACTTGGATTGATCTGATATGTTATAAATAGTCAACTATTCACATAT
34654355 GGAGATTCATCTTCCGGGGTTGCTTGTGTTGCATTTGGTTAATTTATTTGATGTCGACTTTTACT
195 GGAGATTCATCTTCCGGGGTTGCTTGTGTTGCATTTGGTTAATTTATTTGATGTCGACTTTTACT
34654420 TGTATTTTGTATTCTTTTCACAAGTTTTATTGGACAATATTAAACTGTTGTAAGTGAGGTTATTT
260 TGTATTTTGTATTCTTTTCACAAGTTTTATTGGACAATATTAAACTGTTGTAAGTGAGGTTATTT
34654485 GGGCGAGTAGTTGTAACAAGTTGAGACTAGCTATTGGGGCTGCAATTGCTTATTGTGTAAAGATA
325 GGGCGAGTAGTTGTAACAAGTTGAGACTAGCTATTGGGGCTGCAATTGCTTATTGTGTAAAGATA
34654550 GATTAGGTGTAATACCCTGAAAATTACTACAGTAAGAAAGTAAGATAATATCCTTGATAT
390 GATTAGGTGTAATACCCTGAAAATTACTACAGTAAGAAAGTAAGATAATATCCTTGATAT
34654610 AGTAAAATAA
Statistics
Matches: 447, Mismatches: 2, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
453 67 0.15
454 380 0.85
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.41
Consensus pattern (453 bp):
TATTAGATAAAGCTTATGCTTATCATTTAGCCTTTATCCCGGGTGATTTATGTACTAATATTATT
AGATTTATCCAGCTTTATCTTAGGATAGATTTCGGAGGTTACTTATACATAATTATTATGTTGTT
AAAGATGATTTTATCTCTACTTGGATTGATCTGATATGTTATAAATAGTCAACTATTCACATATG
GAGATTCATCTTCCGGGGTTGCTTGTGTTGCATTTGGTTAATTTATTTGATGTCGACTTTTACTT
GTATTTTGTATTCTTTTCACAAGTTTTATTGGACAATATTAAACTGTTGTAAGTGAGGTTATTTG
GGCGAGTAGTTGTAACAAGTTGAGACTAGCTATTGGGGCTGCAATTGCTTATTGTGTAAAGATAG
ATTAGGTGTAATACCCTGAAAATTACTACAGTAAGAAAGTAAGATAATATCCTTGATATTAGA
Found at i:34657098 original size:15 final size:16
Alignment explanation
Indices: 34657078--34657111 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
34657068 ACGGATTAGG
34657078 TTTTTATT-TTTCTAT
1 TTTTTATTATTTCTAT
*
34657093 TTTTTATTATTTTTAT
1 TTTTTATTATTTCTAT
34657109 TTT
1 TTT
34657112 CTTCTGTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTTATTATTTCTAT
Found at i:34657956 original size:3 final size:3
Alignment explanation
Indices: 34657865--34657939 Score: 150
Period size: 3 Copynumber: 25.0 Consensus size: 3
34657855 TGTTTCCACC
34657865 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
34657913 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
34657940 TTACTTAATC
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 72 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:34658071 original size:2 final size:2
Alignment explanation
Indices: 34658064--34658102 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
34658054 TAGTATAACT
34658064 TA TA TA 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 TA TA TA T
34658103 TTAACTTCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:34658179 original size:2 final size:2
Alignment explanation
Indices: 34658172--34658202 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
34658162 ATGTTTTTCC
34658172 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34658203 TGAATTGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:34663626 original size:22 final size:22
Alignment explanation
Indices: 34663587--34663631 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
34663577 GGCTGTAATG
*
34663587 AGAATTTCTAGAAATTTT-AAA
1 AGAATTTATAGAAATTTTCAAA
*
34663608 AGAATTTAATAGAATTTTTCAAA
1 AGAATTT-ATAGAAATTTTCAAA
34663631 A
1 A
34663632 ATCCTATGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 9 0.45
23 4 0.20
ACGTcount: A:0.49, C:0.04, G:0.09, T:0.38
Consensus pattern (22 bp):
AGAATTTATAGAAATTTTCAAA
Found at i:34672084 original size:32 final size:31
Alignment explanation
Indices: 34672009--34672105 Score: 124
Period size: 31 Copynumber: 3.0 Consensus size: 31
34671999 CGAACATAAT
34672009 AAATATATATTTTTTATTTTTAAAA-ATATTTTA
1 AAATA-AT-TTTTTTATTTTTAAAATAT-TTTTA
34672042 AAATAATTTTTTTATTTTTAAAATATTTTTA
1 AAATAATTTTTTTATTTTTAAAATATTTTTA
*
34672073 AAATACTTTTTTTAATTTTCTAAAATTATTTTT
1 AAATAATTTTTTT-ATTTT-TAAAA-TATTTTT
34672106 GTGTTTATTT
Statistics
Matches: 59, Mismatches: 1, Indels: 7
0.88 0.01 0.10
Matches are distributed among these distances:
31 33 0.56
32 9 0.15
33 10 0.17
34 7 0.12
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (31 bp):
AAATAATTTTTTTATTTTTAAAATATTTTTA
Found at i:34674547 original size:31 final size:31
Alignment explanation
Indices: 34674512--34674594 Score: 114
Period size: 31 Copynumber: 2.7 Consensus size: 31
34674502 TAGCCAAGTA
* *
34674512 ACTTAAATAAAAACTTTCGAATAATTC-GATG
1 ACTTAAATGAAAACTTTCAAATAATTCAG-TG
*
34674543 ACTTAAATGAAAACTTTCAAATAGTTCAGTG
1 ACTTAAATGAAAACTTTCAAATAATTCAGTG
*
34674574 ACTAAAATGAAAACTTTCAAA
1 ACTTAAATGAAAACTTTCAAA
34674595 CAGTCAGGTG
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
31 46 0.98
32 1 0.02
ACGTcount: A:0.47, C:0.13, G:0.10, T:0.30
Consensus pattern (31 bp):
ACTTAAATGAAAACTTTCAAATAATTCAGTG
Found at i:34680963 original size:16 final size:16
Alignment explanation
Indices: 34680942--34680981 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
34680932 GTTTAGTTCA
*
34680942 CTGTAATCGAATAGAG
1 CTGTAATCGAATAAAG
*
34680958 CTGTAATAGAATAAAG
1 CTGTAATCGAATAAAG
*
34680974 TTGTAATC
1 CTGTAATC
34680982 AGTAATTCAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.30
Consensus pattern (16 bp):
CTGTAATCGAATAAAG
Found at i:34681218 original size:58 final size:58
Alignment explanation
Indices: 34681139--34681262 Score: 178
Period size: 58 Copynumber: 2.1 Consensus size: 58
34681129 TTTTAATAAG
* *
34681139 ATTATTATTAAAAATAATTTAATAAAAATAATAAATAATTTAACCATATT-TTAACATA
1 ATTATTATTAAAAATAATTTAAT-AAAATAATAAATAATTTAACAAAATTCTTAACATA
* * * *
34681197 ATTATTATTAAATATAATTTAATAAAATAATATATAATTTAATAAAATTCTTAATATA
1 ATTATTATTAAAAATAATTTAATAAAATAATAAATAATTTAACAAAATTCTTAACATA
34681255 ATTATTAT
1 ATTATTAT
34681263 ATGAATTAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
57 22 0.37
58 37 0.63
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (58 bp):
ATTATTATTAAAAATAATTTAATAAAATAATAAATAATTTAACAAAATTCTTAACATA
Found at i:34692674 original size:30 final size:30
Alignment explanation
Indices: 34692617--34692675 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
34692607 TTGGGATTGA
* * **
34692617 GAAGACTTGATATCTCGTTCAGGAGCTTGT
1 GAAGACTTGATATCGCATTCAAAAGCTTGT
34692647 GAAGACTTGATATCGCATTCAAAAGCTTG
1 GAAGACTTGATATCGCATTCAAAAGCTTG
34692676 GGATTGAGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.31
Consensus pattern (30 bp):
GAAGACTTGATATCGCATTCAAAAGCTTGT
Found at i:34692687 original size:66 final size:66
Alignment explanation
Indices: 34692571--34692704 Score: 196
Period size: 66 Copynumber: 2.0 Consensus size: 66
34692561 GAGTATGTTT
* ** *
34692571 AGGAACTTGAGAAGACTCGATATCTCATTCAGGATATTGGGATTGAGAAGACTTGATATCTCGTT
1 AGGAACTTGAGAAGACTCGATATCGCATTCAAAAGATTGGGATTGAGAAGACTTGATATCTCGTT
34692636 C
66 C
* * * *
34692637 AGGAGCTTGTGAAGACTTGATATCGCATTCAAAAGCTTGGGATTGAGAAGACTTGATATCTCGTT
1 AGGAACTTGAGAAGACTCGATATCGCATTCAAAAGATTGGGATTGAGAAGACTTGATATCTCGTT
34692702 C
66 C
34692703 AG
1 AG
34692705 AAGCATGGGA
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (66 bp):
AGGAACTTGAGAAGACTCGATATCGCATTCAAAAGATTGGGATTGAGAAGACTTGATATCTCGTT
C
Found at i:34692694 original size:36 final size:36
Alignment explanation
Indices: 34692577--34692714 Score: 144
Period size: 36 Copynumber: 4.0 Consensus size: 36
34692567 GTTTAGGAAC
* * **
34692577 TTGAGAAGACTCGATATCTCATTCAGGATATTGGGA
1 TTGAGAAGACTTGATATCTCATTCAGAAGCTTGGGA
* *
34692613 TTGAGAAGACTTGATATCTCGTTCAGGAGCTT--G-
1 TTGAGAAGACTTGATATCTCATTCAGAAGCTTGGGA
* *
34692646 -T--GAAGACTTGATATCGCATTCAAAAGCTTGGGA
1 TTGAGAAGACTTGATATCTCATTCAGAAGCTTGGGA
* *
34692679 TTGAGAAGACTTGATATCTCGTTCAGAAGCATGGGA
1 TTGAGAAGACTTGATATCTCATTCAGAAGCTTGGGA
34692715 ATATTTGATG
Statistics
Matches: 84, Mismatches: 12, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
30 24 0.29
32 2 0.02
34 2 0.02
36 56 0.67
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (36 bp):
TTGAGAAGACTTGATATCTCATTCAGAAGCTTGGGA
Found at i:34693915 original size:3 final size:3
Alignment explanation
Indices: 34693909--34693949 Score: 73
Period size: 3 Copynumber: 13.3 Consensus size: 3
34693899 CTACTACAAC
34693909 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT ATAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT T
34693950 TTGGTCCCTG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:34694295 original size:19 final size:19
Alignment explanation
Indices: 34694241--34694296 Score: 62
Period size: 18 Copynumber: 2.9 Consensus size: 19
34694231 GTTAAAAAAG
* *
34694241 TTTAATATTTTTTTTTGTTT
1 TTTAA-ATTTTTATTTGATT
34694261 TTTAAATTTTTA-TTGATT
1 TTTAAATTTTTATTTGATT
34694279 TTT-AATTATTTATTTGAT
1 TTTAAATT-TTTATTTGAT
34694297 CATTGTTGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
17 4 0.12
18 12 0.38
19 11 0.34
20 5 0.16
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.71
Consensus pattern (19 bp):
TTTAAATTTTTATTTGATT
Found at i:34697054 original size:16 final size:16
Alignment explanation
Indices: 34697027--34697096 Score: 54
Period size: 17 Copynumber: 4.2 Consensus size: 16
34697017 AAAAAACAGA
*
34697027 AAAATATTAAAATTAT
1 AAAATATAAAAATTAT
34697043 AAAATATAAAAAATTA-
1 AAAATAT-AAAAATTAT
* *
34697059 AAATTGATATAAATTTAT
1 AAAAT-ATA-AAAATTAT
*
34697077 AATATTATAAAAA-TAT
1 AA-AATATAAAAATTAT
34697093 AAAA
1 AAAA
34697097 AATCTAATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
15 1 0.02
16 17 0.39
17 18 0.41
18 5 0.11
19 3 0.07
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (16 bp):
AAAATATAAAAATTAT
Found at i:34697140 original size:35 final size:32
Alignment explanation
Indices: 34697034--34697142 Score: 94
Period size: 35 Copynumber: 3.1 Consensus size: 32
34697024 AGAAAAATAT
* *
34697034 TAAAATTATAAAATATAAAAA-ATTAAAATTGATA
1 TAAATTTATAAATTATAAAAATA-TAAAATT-A-A
34697068 TAAATTTATAATATTATAAAAATATAAAAAATCTAA
1 TAAATTTATAA-ATTATAAAAATAT--AAAAT-TAA
*
34697104 TATATTCTAATAAATTATGAAAAATATAAAATTAA
1 TAAATT-T-ATAAATTAT-AAAAATATAAAATTAA
34697139 TAAA
1 TAAA
34697143 ACATATTTAA
Statistics
Matches: 63, Mismatches: 4, Indels: 15
0.77 0.05 0.18
Matches are distributed among these distances:
34 10 0.16
35 16 0.25
36 12 0.19
37 12 0.19
38 13 0.21
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (32 bp):
TAAATTTATAAATTATAAAAATATAAAATTAA
Found at i:34697164 original size:21 final size:21
Alignment explanation
Indices: 34697123--34697177 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
34697113 ATAAATTATG
34697123 AAAA-ATA-TAAAA-TTAAT-
1 AAAACATATTAAAATTTAATA
*
34697140 AAAACATATTTAAAATTTTATA
1 AAAACATA-TTAAAATTTAATA
*
34697162 AAAACGTATTAAAATT
1 AAAACATATTAAAATT
34697178 CTAAAATCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
17 4 0.13
18 3 0.10
20 5 0.16
21 12 0.39
22 7 0.23
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.35
Consensus pattern (21 bp):
AAAACATATTAAAATTTAATA
Found at i:34697165 original size:38 final size:36
Alignment explanation
Indices: 34697071--34697165 Score: 93
Period size: 38 Copynumber: 2.5 Consensus size: 36
34697061 ATTGATATAA
* ** *
34697071 ATTTATAATATTATAAAAATATAAAAAATCTAATAT
1 ATTTAAAATATTATAAAAATATAAAAAATAAAACAT
34697107 ATTCTAATAA-ATTATGAAAAATATAAAATTAATAAAACAT
1 ATT-TAA-AATATTAT-AAAAATATAAAA--AATAAAACAT
*
34697147 ATTTAAAATTTTATAAAAA
1 ATTTAAAATATTATAAAAA
34697166 CGTATTAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
36 3 0.06
37 7 0.15
38 21 0.44
39 7 0.15
40 10 0.21
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (36 bp):
ATTTAAAATATTATAAAAATATAAAAAATAAAACAT
Found at i:34697210 original size:8 final size:8
Alignment explanation
Indices: 34697197--34697222 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
34697187 TGAAAATTAT
34697197 TAAAAATA
1 TAAAAATA
34697205 TAAAAATA
1 TAAAAATA
34697213 TAAAAATA
1 TAAAAATA
34697221 TA
1 TA
34697223 TCGTTAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (8 bp):
TAAAAATA
Found at i:34697852 original size:9 final size:9
Alignment explanation
Indices: 34697840--34697895 Score: 51
Period size: 10 Copynumber: 6.1 Consensus size: 9
34697830 TTATCTTTAT
34697840 TTTTTATAA
1 TTTTTATAA
34697849 TTTTTTATAA
1 -TTTTTATAA
*
34697859 TTTTTCTAA
1 TTTTTATAA
*
34697868 TTTTT-GAA
1 TTTTTATAA
*
34697876 TTTTTTTAA
1 TTTTTATAA
*
34697885 TGTTTTTTAA
1 T-TTTTATAA
34697895 T
1 T
34697896 AATTTATTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
8 7 0.17
9 16 0.39
10 18 0.44
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.70
Consensus pattern (9 bp):
TTTTTATAA
Found at i:34697853 original size:10 final size:10
Alignment explanation
Indices: 34697838--34697872 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
34697828 TATTATCTTT
34697838 ATTTTTTATA
1 ATTTTTTATA
34697848 ATTTTTTATA
1 ATTTTTTATA
*
34697858 A-TTTTTCTA
1 ATTTTTTATA
34697867 ATTTTT
1 ATTTTT
34697873 GAATTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (10 bp):
ATTTTTTATA
Found at i:34697862 original size:8 final size:9
Alignment explanation
Indices: 34697766--34697895 Score: 61
Period size: 9 Copynumber: 14.0 Consensus size: 9
34697756 TTTAAAAATG
34697766 TTTTATTAA-
1 TTTTA-TAAT
34697775 TTTTATAATT
1 TTTTATAA-T
34697785 TTTTATAAT
1 TTTTATAAT
* *
34697794 ATTTATAGGT
1 TTTTATA-AT
*
34697804 TTATATCAAT
1 TTTTAT-AAT
* *
34697814 TTTAACAAT
1 TTTTATAAT
*
34697823 TTTCAT-AT
1 TTTTATAAT
*
34697831 TATCTT-TATT
1 T-T-TTATAAT
34697841 TTTTATAATT
1 TTTTATAA-T
34697851 TTTTATAAT
1 TTTTATAAT
*
34697860 TTTTCTAAT
1 TTTTATAAT
*
34697869 TTTT-GAAT
1 TTTTATAAT
*
34697877 TTTTTTAAT
1 TTTTATAAT
*
34697886 GTTTTTTAAT
1 -TTTTATAAT
34697896 AATTTATTAT
Statistics
Matches: 94, Mismatches: 16, Indels: 21
0.72 0.12 0.16
Matches are distributed among these distances:
8 15 0.16
9 40 0.43
10 38 0.40
11 1 0.01
ACGTcount: A:0.29, C:0.04, G:0.03, T:0.64
Consensus pattern (9 bp):
TTTTATAAT
Found at i:34697862 original size:19 final size:19
Alignment explanation
Indices: 34697766--34697895 Score: 60
Period size: 19 Copynumber: 6.9 Consensus size: 19
34697756 TTTAAAAATG
34697766 TTTTATTAA-TTTTATAATT
1 TTTTA-TAATTTTTATAATT
* **
34697785 TTTTATAATATTTATAGGT
1 TTTTATAATTTTTATAATT
* * *
34697804 TTATATCAATTTTAACAA-T
1 TTTTAT-AATTTTTATAATT
*
34697823 TTTCAT-ATTATCTT-T-ATT
1 TTTTATAATT-T-TTATAATT
34697841 TTTTATAATTTTTTATAA-T
1 TTTTATAA-TTTTTATAATT
* *
34697860 TTTTCTAATTTTT-GAATT
1 TTTTATAATTTTTATAATT
*
34697878 TTTT-TAATGTTTTTTAAT
1 TTTTATAAT-TTTTATAAT
34697896 AATTTATTAT
Statistics
Matches: 83, Mismatches: 16, Indels: 24
0.67 0.13 0.20
Matches are distributed among these distances:
17 10 0.12
18 26 0.31
19 37 0.45
20 10 0.12
ACGTcount: A:0.29, C:0.04, G:0.03, T:0.64
Consensus pattern (19 bp):
TTTTATAATTTTTATAATT
Found at i:34712411 original size:55 final size:55
Alignment explanation
Indices: 34712351--34712454 Score: 156
Period size: 55 Copynumber: 1.9 Consensus size: 55
34712341 TTATGATCTA
* *
34712351 TTTTTTAGTCACTCAACTATG-AAAATTATAAAATGGTCATTCAACTATTAGTATT
1 TTTTTTA-TCACTCAAATATGAAAAATTATAAAATGGTCACTCAACTATTAGTATT
* *
34712406 TTTTTTATCACTCAAATATGAAAAATTATAGAATGGTCACTCAATTATT
1 TTTTTTATCACTCAAATATGAAAAATTATAAAATGGTCACTCAACTATT
34712455 TAATTTTGTC
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
54 12 0.27
55 32 0.73
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (55 bp):
TTTTTTATCACTCAAATATGAAAAATTATAAAATGGTCACTCAACTATTAGTATT
Found at i:34716531 original size:29 final size:29
Alignment explanation
Indices: 34716499--34716561 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 29
34716489 TCATGTGTAT
* *
34716499 AATTGT-ACTAAATCAAAGTTCATGTATCA
1 AATTGTAACTAAACCAAAGTTCATATAT-A
*
34716528 AATTGTAAATTAAACCAAAGTTCATATATA
1 AATTGT-AACTAAACCAAAGTTCATATATA
34716558 AATT
1 AATT
34716562 TGATATTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 6 0.21
30 5 0.17
31 18 0.62
ACGTcount: A:0.46, C:0.11, G:0.08, T:0.35
Consensus pattern (29 bp):
AATTGTAACTAAACCAAAGTTCATATATA
Found at i:34718181 original size:32 final size:31
Alignment explanation
Indices: 34718115--34718193 Score: 92
Period size: 31 Copynumber: 2.5 Consensus size: 31
34718105 TTTTTTTAGG
* *
34718115 TTTTAAGAG-CCCAAAATTTTTTTTACCAAT
1 TTTTAAGAGACCTAAAATTTTTTTTACCAAC
34718145 TTTTAAGAGACCTAAAATTTTTTTT-CTCAAAC
1 TTTTAAGAGACCTAAAATTTTTTTTAC-C-AAC
34718177 TTTTAA-AGAACCTAAAA
1 TTTTAAGAG-ACCTAAAA
34718194 CTCCATTTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
30 10 0.23
31 17 0.40
32 16 0.37
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.41
Consensus pattern (31 bp):
TTTTAAGAGACCTAAAATTTTTTTTACCAAC
Found at i:34734764 original size:19 final size:19
Alignment explanation
Indices: 34734742--34734790 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
34734732 TTTAAAATTT
34734742 AAAATAATTAAAATTATAAA
1 AAAATAATTAAAATT-TAAA
* *
34734762 AAAATAATTTTATATTT-AA
1 AAAATAA-TTAAAATTTAAA
34734781 AAAATAATTA
1 AAAATAATTA
34734791 CTGACCTGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 2 0.08
19 9 0.36
20 8 0.32
21 6 0.24
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAATAATTAAAATTTAAA
Found at i:34739739 original size:3 final size:3
Alignment explanation
Indices: 34739731--34739778 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
34739721 CAATATGTTT
34739731 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
34739779 CAACTAATTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:34740890 original size:2 final size:2
Alignment explanation
Indices: 34740883--34740925 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
34740873 CCAATACGTT
34740883 TA TA TA TA 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
34740925 T
1 T
34740926 TCCATTCAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:34753934 original size:28 final size:28
Alignment explanation
Indices: 34753894--34753951 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
34753884 AAAAGAAAGA
34753894 ATAAAATCCATTCCTTTTTTGCATCGGT
1 ATAAAATCCATTCCTTTTTTGCATCGGT
34753922 ATAAAATCCATTCCTTTTTTGCATCGGT
1 ATAAAATCCATTCCTTTTTTGCATCGGT
34753950 AT
1 AT
34753952 CTGCCTTATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.26, C:0.21, G:0.10, T:0.43
Consensus pattern (28 bp):
ATAAAATCCATTCCTTTTTTGCATCGGT
Found at i:34761770 original size:25 final size:26
Alignment explanation
Indices: 34761736--34761797 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 26
34761726 CAAACATGTA
* *
34761736 AACGAGAAGCTCT-TTTGAGCCATAT
1 AACGGGAAGCTCTATGTGAGCCATAT
** *
34761761 AACGGGAAGCT-TATGTGAGTTATGT
1 AACGGGAAGCTCTATGTGAGCCATAT
34761786 AACGGGAAGCTC
1 AACGGGAAGCTC
34761798 CGAAGAGCCA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
24 1 0.03
25 29 0.97
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.26
Consensus pattern (26 bp):
AACGGGAAGCTCTATGTGAGCCATAT
Found at i:34761806 original size:50 final size:50
Alignment explanation
Indices: 34761785--34761930 Score: 156
Period size: 50 Copynumber: 2.9 Consensus size: 50
34761775 GTGAGTTATG
34761785 TAACGGGAAGCTCCGAAGAGCCATTAATCGGGAAGCTCATAAGAGCCAGT
1 TAACGGGAAGCTCCGAAGAGCCATTAATCGGGAAGCTCATAAGAGCCAGT
* * * * *
34761835 TATCGGGAAGCTCCGAAGAGCCAATT-ATCGAGAAGCTCACAGGAACCA-T
1 TAACGGGAAGCTCCGAAGAGCC-ATTAATCGGGAAGCTCATAAGAGCCAGT
* * *
34761884 ATAATGGGAAGCT-CGTAAGAGCCA-AATATCGGGACGCTCATAAGAGC
1 -TAACGGGAAGCTCCG-AAGAGCCATTA-ATCGGGAAGCTCATAAGAGC
34761931 TGTGGTGTGT
Statistics
Matches: 78, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
49 4 0.05
50 71 0.91
51 3 0.04
ACGTcount: A:0.35, C:0.22, G:0.27, T:0.16
Consensus pattern (50 bp):
TAACGGGAAGCTCCGAAGAGCCATTAATCGGGAAGCTCATAAGAGCCAGT
Found at i:34761917 original size:25 final size:25
Alignment explanation
Indices: 34761788--34761930 Score: 137
Period size: 25 Copynumber: 5.7 Consensus size: 25
34761778 AGTTATGTAA
**
34761788 CGGGAAGCTCCGAAGAGCC-ATTAAT
1 CGGGAAGCTCATAAGAGCCAATT-AT
*
34761813 CGGGAAGCTCATAAGAGCCAGTTAT
1 CGGGAAGCTCATAAGAGCCAATTAT
**
34761838 CGGGAAGCTCCGAAGAGCCAATTAT
1 CGGGAAGCTCATAAGAGCCAATTAT
* * * * *
34761863 CGAGAAGCTCACAGGAACCATATAAT
1 CGGGAAGCTCATAAGAGCCA-ATTAT
* *
34761889 -GGGAAGCTCGTAAGAGCCAAATAT
1 CGGGAAGCTCATAAGAGCCAATTAT
*
34761913 CGGGACGCTCATAAGAGC
1 CGGGAAGCTCATAAGAGC
34761931 TGTGGTGTGT
Statistics
Matches: 94, Mismatches: 21, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
24 3 0.03
25 85 0.90
26 6 0.06
ACGTcount: A:0.34, C:0.22, G:0.27, T:0.16
Consensus pattern (25 bp):
CGGGAAGCTCATAAGAGCCAATTAT
Found at i:34763189 original size:2 final size:2
Alignment explanation
Indices: 34763182--34763232 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
34763172 AAAATAGACA
34763182 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34763224 AT AT AT AT A
1 AT AT AT AT A
34763233 AGTATCAAGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:34770693 original size:103 final size:103
Alignment explanation
Indices: 34770514--34770710 Score: 274
Period size: 103 Copynumber: 1.9 Consensus size: 103
34770504 TATCAAGACC
* * * *
34770514 GTATCAATACTTTGTAGGTTTTGTGAGAAACATAATGCTATTTTGGTATCGCTTTTAAGAATAGG
1 GTATCAATACTTTGTAGGTTTTGTGAAAAACATAATACCATTTTGGTATCACTTTTAAGAATAGG
34770579 TATCGATAATTCAGAAAATATCGATACTTAATCAAAAG
66 TATCGATAATTCAGAAAATATCGATACTTAATCAAAAG
* *
34770617 GTATCTATACTTAT-TAGGTTTTGTGAAAAACGA-AATACCATTTTGGTATCATTTTTAAGAGA-
1 GTATCAATACTT-TGTAGGTTTTGTGAAAAAC-ATAATACCATTTTGGTATCACTTTTAAGA-AT
* *
34770679 GGGTATCGATAATTCATAAAATATCGATACTT
63 AGGTATCGATAATTCAGAAAATATCGATACTT
34770711 GGCCAAAAAG
Statistics
Matches: 83, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
103 80 0.96
104 3 0.04
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.37
Consensus pattern (103 bp):
GTATCAATACTTTGTAGGTTTTGTGAAAAACATAATACCATTTTGGTATCACTTTTAAGAATAGG
TATCGATAATTCAGAAAATATCGATACTTAATCAAAAG
Found at i:34777630 original size:10 final size:10
Alignment explanation
Indices: 34777574--34777645 Score: 60
Period size: 10 Copynumber: 7.3 Consensus size: 10
34777564 TTCATTTTAG
34777574 AAATTTTTTT
1 AAATTTTTTT
34777584 -AA-TTTTTT
1 AAATTTTTTT
* *
34777592 AACTTTCTTT
1 AAATTTTTTT
* **
34777602 ATATATTCATT
1 AAAT-TTTTTT
34777613 AGAATTTTTTT
1 A-AATTTTTTT
34777624 AAA-TTTTTT
1 AAATTTTTTT
34777633 AAATTTTTTT
1 AAATTTTTTT
34777643 AAA
1 AAA
34777646 AAAATATAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
8 6 0.12
9 12 0.24
10 18 0.37
11 11 0.22
12 2 0.04
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.62
Consensus pattern (10 bp):
AAATTTTTTT
Found at i:34777639 original size:8 final size:9
Alignment explanation
Indices: 34777574--34777641 Score: 55
Period size: 9 Copynumber: 7.0 Consensus size: 9
34777564 TTCATTTTAG
34777574 AAATTTTTT
1 AAATTTTTT
*
34777583 TAATTTTTT
1 AAATTTTTT
*
34777592 AACTTTCTTT
1 AAATTT-TTT
**
34777602 ATATATTCATT
1 A-A-ATTTTTT
34777613 AGAATTTTTTT
1 A-AA-TTTTTT
34777624 AAATTTTTT
1 AAATTTTTT
34777633 AAATTTTTT
1 AAATTTTTT
34777642 TAAAAAAATA
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
9 27 0.59
10 7 0.15
11 10 0.22
12 2 0.04
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.65
Consensus pattern (9 bp):
AAATTTTTT
Found at i:34777732 original size:23 final size:21
Alignment explanation
Indices: 34777664--34777720 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
34777654 AATTCTGGAA
* *
34777664 TTTTAAAAAATTATTTTGAAT
1 TTTTGAAAAATTATTTTAAAT
34777685 TTTTGAAAAATTATTTTAAAT
1 TTTTGAAAAATTATTTTAAAT
34777706 TTTTGAAAAATTATT
1 TTTTGAAAAATTATT
34777721 GTTTACTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (21 bp):
TTTTGAAAAATTATTTTAAAT
Found at i:34783407 original size:2 final size:2
Alignment explanation
Indices: 34783400--34783429 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
34783390 GCGACAAAAC
34783400 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34783430 GAAATACCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34784032 original size:2 final size:2
Alignment explanation
Indices: 34784025--34784053 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
34784015 AGCAAAAAGC
34784025 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 A
34784054 AAATAGAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:34805307 original size:27 final size:27
Alignment explanation
Indices: 34805269--34805351 Score: 114
Period size: 27 Copynumber: 3.1 Consensus size: 27
34805259 ATACATAGTA
* *
34805269 GTGGCGCCTATTTCAGAGGCGCCAATG
1 GTGGTGCCTATTTGAGAGGCGCCAATG
* *
34805296 GTGGTGCCTATTTGAGAGGCGCCATTA
1 GTGGTGCCTATTTGAGAGGCGCCAATG
34805323 GTGGTGCC-ATGTTGAGAGGCGCCAATG
1 GTGGTGCCTAT-TTGAGAGGCGCCAATG
34805350 GT
1 GT
34805352 CTGATTTTTC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
26 2 0.04
27 47 0.96
ACGTcount: A:0.18, C:0.20, G:0.36, T:0.25
Consensus pattern (27 bp):
GTGGTGCCTATTTGAGAGGCGCCAATG
Found at i:34810777 original size:60 final size:60
Alignment explanation
Indices: 34810709--34810830 Score: 183
Period size: 60 Copynumber: 2.0 Consensus size: 60
34810699 ATACTAAACT
* * * *
34810709 AAACACAAAAATTTATAGCTTAATCCTAAATTACTAATAAATTAAGTT-TTAAATAATTAC
1 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAA-TTATAAAATAATTAC
*
34810769 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAATTTAATTATAAAATAATTAC
1 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
34810829 AA
1 AA
34810831 TATTCATACA
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
59 2 0.04
60 54 0.96
ACGTcount: A:0.53, C:0.12, G:0.02, T:0.33
Consensus pattern (60 bp):
AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
Found at i:34810849 original size:21 final size:21
Alignment explanation
Indices: 34810818--34811022 Score: 109
Period size: 21 Copynumber: 9.2 Consensus size: 21
34810808 ATTTAATTAT
34810818 AAAATAATTACAATATTCATAC
1 AAAA-AATTACAATATTCATAC
34810840 AAAAAATTACAATATTACAATATAC
1 AAAAAATTACAATATT-C---ATAC
*
34810865 ATACAAAATTACAAAATTACAATATTC
1 A-A-AAAATTACAATATT-C-ATA--C
34810892 ATACAAAAAAATTACAATATTCATAC
1 --A-AAAA--ATTACAATATTCATAC
34810918 AAAAAATTACAATATTCATAC
1 AAAAAATTACAATATTCATAC
* * *
34810939 --AAAA-TACTA-ATCCAAAAC
1 AAAAAATTACAATATTC-ATAC
* * * * *
34810957 TATAAA-TACAAAATTAATTAT
1 AAAAAATTACAATATTCA-TAC
34810978 AAAATAATTACAATATTCATAC
1 AAAA-AATTACAATATTCATAC
34811000 --AAAATTACAATATTCATAC
1 AAAAAATTACAATATTCATAC
34811019 AAAA
1 AAAA
34811023 TACTAATCCA
Statistics
Matches: 144, Mismatches: 18, Indels: 43
0.70 0.09 0.21
Matches are distributed among these distances:
17 3 0.02
18 7 0.05
19 21 0.15
20 10 0.07
21 35 0.24
22 9 0.06
23 13 0.09
24 1 0.01
25 8 0.06
26 2 0.01
27 16 0.11
28 6 0.04
29 3 0.02
30 10 0.07
ACGTcount: A:0.58, C:0.14, G:0.00, T:0.29
Consensus pattern (21 bp):
AAAAAATTACAATATTCATAC
Found at i:34810875 original size:19 final size:19
Alignment explanation
Indices: 34810823--34811023 Score: 123
Period size: 19 Copynumber: 10.2 Consensus size: 19
34810813 ATTATAAAAT
34810823 AATTACAATATTCATACAAAA
1 AATTACAATATTCATAC--AA
*
34810844 AATTACAATATTACAATA-TA
1 AATTACAATATT-C-ATACAA
* *
34810864 CA-TACAA-AAT--TACAA
1 AATTACAATATTCATACAA
34810879 AATTACAATATTCATACAAAAA
1 AATTACAATATTCATAC---AA
34810901 AATTACAATATTCATACAAAA
1 AATTACAATATTCATAC--AA
34810922 AATTACAATATTCATACAA
1 AATTACAATATTCATACAA
* * *
34810941 AA-TACTA-ATCCAAAACTATA
1 AATTACAATATTC-ATAC-A-A
*
34810961 AA-TACAAAATTAATT-ATAAAA
1 AATTAC--AA-T-ATTCATACAA
34810982 TAATTACAATATTCATACAA
1 -AATTACAATATTCATACAA
34811002 AATTACAATATTCATACAA
1 AATTACAATATTCATACAA
34811021 AAT
1 AAT
34811024 ACTAATCCAA
Statistics
Matches: 145, Mismatches: 14, Indels: 44
0.71 0.07 0.22
Matches are distributed among these distances:
14 2 0.01
15 2 0.01
16 5 0.03
17 5 0.03
18 9 0.06
19 38 0.26
20 14 0.10
21 36 0.25
22 24 0.17
23 8 0.06
25 2 0.01
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (19 bp):
AATTACAATATTCATACAA
Found at i:34810883 original size:27 final size:27
Alignment explanation
Indices: 34810823--34810943 Score: 129
Period size: 27 Copynumber: 4.8 Consensus size: 27
34810813 ATTATAAAAT
34810823 AATTACAATATTCATACAAAAAATTACAA
1 AATTACAATATTCATAC--AAAATTACAA
* *
34810852 TATTACAATATACATACAAAATTACAA
1 AATTACAATATTCATACAAAATTACAA
34810879 AATTACAATATTCATAC--AA--A-AA
1 AATTACAATATTCATACAAAATTACAA
34810901 AATTACAATATTCATAC---A--A-AA
1 AATTACAATATTCATACAAAATTACAA
34810922 AATTACAATATTCATACAAAAT
1 AATTACAATATTCATACAAAAT
34810944 ACTAATCCAA
Statistics
Matches: 84, Mismatches: 4, Indels: 12
0.84 0.04 0.12
Matches are distributed among these distances:
21 21 0.25
22 19 0.23
23 1 0.01
24 1 0.01
25 2 0.02
27 25 0.30
29 15 0.18
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (27 bp):
AATTACAATATTCATACAAAATTACAA
Found at i:34810908 original size:78 final size:78
Alignment explanation
Indices: 34810810--34811013 Score: 245
Period size: 78 Copynumber: 2.6 Consensus size: 78
34810800 TACTAACAAT
* * *
34810810 TTAATTATAAAATAATTACAATATTCATACAAAAAATTACAATATTACAATATAC-ATACAAAAT
1 TTAATTACAAAATAATTACAATATTCATACAAAAAATTACAATATTACAAAATACAATACAAAAC
*
34810874 TACAAAATTACAATA
66 TA-AAAA-TACAAAA
* * *
34810889 TTCA-TACAAAAAAATTACAATATTCATACAAAAAATTACAATATTCATACAAAATACTAATCCA
1 TTAATTACAAAATAATTACAATATTCATACAAAAAATTACAATA-T--TACAAAATAC-AATACA
*
34810953 AAACTATAAATACAAAA
62 AAACTAAAAATACAAAA
*
34810970 TTAATTATAAAATAATTACAATATTCATAC--AAAATTACAATATT
1 TTAATTACAAAATAATTACAATATTCATACAAAAAATTACAATATT
34811014 CATACAAAAT
Statistics
Matches: 108, Mismatches: 11, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
77 1 0.01
78 37 0.34
79 5 0.05
80 12 0.11
81 18 0.17
82 26 0.24
83 9 0.08
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (78 bp):
TTAATTACAAAATAATTACAATATTCATACAAAAAATTACAATATTACAAAATACAATACAAAAC
TAAAAATACAAAA
Found at i:34811040 original size:61 final size:59
Alignment explanation
Indices: 34810874--34811041 Score: 139
Period size: 61 Copynumber: 2.7 Consensus size: 59
34810864 CATACAAAAT
34810874 TACAAAATTACAATATTCATACAAAA-A-AATTACAATATTCATACAAAAAATTACAATATTCA
1 TACAAAATTACAATATTCATACAAAATACAA-T-CAA-ATT-ATA-AAAAAATTACAATATTCA
* * * * *
34810936 TACAAAA-TACTA-ATCCAAAACTATAAATACAAAAT-TAATTATAAAATAATTACAATATTCA
1 TACAAAATTACAATATTC-ATAC-A-AAATAC--AATCAAATTATAAAAAAATTACAATATTCA
*
34810997 TACAAAATTACAATATTCATACAAAATACTAATCCAAACTATAAA
1 TACAAAATTACAATATTCATACAAAATAC-AAT-CAAATTATAAA
34811042 CACTAAATAT
Statistics
Matches: 84, Mismatches: 11, Indels: 23
0.71 0.09 0.19
Matches are distributed among these distances:
59 3 0.04
60 9 0.11
61 40 0.48
62 18 0.21
63 9 0.11
64 2 0.02
66 1 0.01
67 2 0.02
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.29
Consensus pattern (59 bp):
TACAAAATTACAATATTCATACAAAATACAATCAAATTATAAAAAAATTACAATATTCA
Found at i:34811064 original size:80 final size:80
Alignment explanation
Indices: 34810810--34811067 Score: 280
Period size: 80 Copynumber: 3.2 Consensus size: 80
34810800 TACTAACAAT
* *
34810810 TTAATTATAAAATAATTACAATATTCATACAAAAAATTACAATA-T--TACAATATAC--ATACA
1 TTAA-TATAAAATAATTACAATATTCATAC-AAAAATTACAATATTCATACAAAATACTAATCCA
* * * *
34810870 AAATTACAAAATTACAATA
64 AAACTA-TAAA-CACAAAA
* * *
34810889 TTCATACAAAAAAATTACAATATTCATACAAAAAATTACAATATTCATACAAAATACTAATCCAA
1 TTAATATAAAATAATTACAATATTCATAC-AAAAATTACAATATTCATACAAAATACTAATCCAA
*
34810954 AACTATAAATACAAAA
65 AACTATAAACACAAAA
34810970 TTAATTATAAAATAATTACAATATTCATAC-AAAATTACAATATTCATACAAAATACTAATCC-A
1 TTAA-TATAAAATAATTACAATATTCATACAAAAATTACAATATTCATACAAAATACTAATCCAA
*
34811033 AACTATAAACACTAAA
65 AACTATAAACACAAAA
34811049 TATAA-ATAATTAATAATTA
1 T-TAATATAA--AATAATTA
34811068 ATAACAAAAA
Statistics
Matches: 157, Mismatches: 13, Indels: 17
0.84 0.07 0.09
Matches are distributed among these distances:
78 41 0.26
79 20 0.13
80 43 0.27
81 18 0.11
82 26 0.17
83 9 0.06
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (80 bp):
TTAATATAAAATAATTACAATATTCATACAAAAATTACAATATTCATACAAAATACTAATCCAAA
ACTATAAACACAAAA
Found at i:34811154 original size:3 final size:3
Alignment explanation
Indices: 34811148--34811180 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
34811138 CATTACTTTT
34811148 TTC TTC TTC TTC TTC TTC TTC TTC -TC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
34811181 CATTTCTTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:34811375 original size:27 final size:28
Alignment explanation
Indices: 34811316--34811379 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 28
34811306 GAAGGCCACC
* **
34811316 ATTGGCGCCTCCCTATGAGGCATTTTTA
1 ATTGGCGCCTCCATATGAGGCATCATTA
*
34811344 A-TGGCGCCTCTATATGAGGCA-CATTA
1 ATTGGCGCCTCCATATGAGGCATCATTA
34811370 ATTGGCGCCT
1 ATTGGCGCCT
34811380 ACCTGACAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
26 4 0.13
27 26 0.84
28 1 0.03
ACGTcount: A:0.20, C:0.25, G:0.23, T:0.31
Consensus pattern (28 bp):
ATTGGCGCCTCCATATGAGGCATCATTA
Found at i:34811404 original size:5 final size:5
Alignment explanation
Indices: 34811394--34811423 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
34811384 GACAGGCGCC
34811394 ACCCG ACCCG ACCCG ACCCG ACCCG ACCCG
1 ACCCG ACCCG ACCCG ACCCG ACCCG ACCCG
34811424 TTGACCATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.20, C:0.60, G:0.20, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:34812421 original size:6 final size:6
Alignment explanation
Indices: 34812410--34812434 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
34812400 TTATGATGAT
34812410 TAATTA TAATTA TAATTA TAATTA T
1 TAATTA TAATTA TAATTA TAATTA T
34812435 TTGAATATCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TAATTA
Found at i:34813557 original size:23 final size:23
Alignment explanation
Indices: 34813530--34813581 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
34813520 GGATGCCACT
34813530 TTGCATCGAAGTGCCACTAACAC
1 TTGCATCGAAGTGCCACTAACAC
* * *
34813553 TTGCATCGTAGTGTCACTATCAC
1 TTGCATCGAAGTGCCACTAACAC
34813576 TTGCAT
1 TTGCAT
34813582 GCATAGAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.31
Consensus pattern (23 bp):
TTGCATCGAAGTGCCACTAACAC
Found at i:34815398 original size:3 final size:3
Alignment explanation
Indices: 34815390--34815424 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
34815380 ATCAAGAACA
*
34815390 AAT AAT AAT AAT AAT AAT AAG AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
34815425 GATAAATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:34815658 original size:27 final size:24
Alignment explanation
Indices: 34815597--34815658 Score: 72
Period size: 27 Copynumber: 2.4 Consensus size: 24
34815587 AAATTATAAA
34815597 ATATAAAAAAAAATATGTATGTAC
1 ATATAAAAAAAAATATGTATGTAC
34815621 ATATAAGAAAAATATATATGTATGTGA-
1 ATATAA-AAAAA-A-ATATGTATGT-AC
34815648 ATTATAAAAAA
1 A-TATAAAAAA
34815659 TAAAAAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
24 6 0.18
25 5 0.15
26 1 0.03
27 15 0.45
28 6 0.18
ACGTcount: A:0.58, C:0.02, G:0.10, T:0.31
Consensus pattern (24 bp):
ATATAAAAAAAAATATGTATGTAC
Found at i:34819107 original size:125 final size:125
Alignment explanation
Indices: 34818885--34819262 Score: 571
Period size: 125 Copynumber: 3.0 Consensus size: 125
34818875 TCAGGCTTTT
* * *
34818885 TAGGTCCTGGAAGAAATAATTTCGAGTTGACGTTCCTGATCAAATAGTATAAAATCGCTTCTAGC
1 TAGGTCCTGGAAGAAATAATTTCGAGTTGACATTTCTGAGCAAATAGTATAAAATCGCTTCTAGC
* * * *
34818950 AGAATGATGTTTGATAAGAATTTGTGAAATCGCTCCCTCGTGGACGCGCTTTTGCTACAG
66 AGGATGCTATTTGAGAAGAATTTGTGAAATCGCTCCCTCGTGGACGCGCTTTTGCTACAG
* *
34819010 TAGGTCCTGGAAGAAATAATTTTGAGTTGACATTTCTAAGCAAATAGTATAAAATCGCTTCTAGC
1 TAGGTCCTGGAAGAAATAATTTCGAGTTGACATTTCTGAGCAAATAGTATAAAATCGCTTCTAGC
* * *
34819075 AGGATGCTATTTAAGAAGAATTTGTGAAATCGCGCCATCGTGGACGCGCTTTTGCTACAG
66 AGGATGCTATTTGAGAAGAATTTGTGAAATCGCTCCCTCGTGGACGCGCTTTTGCTACAG
* * * * *
34819135 TAGGTCATGGAAGAAATAATTTCGAGTTTACTTTTCTGAGAAAATAGTATAAAATCGCTTCTAGA
1 TAGGTCCTGGAAGAAATAATTTCGAGTTGACATTTCTGAGCAAATAGTATAAAATCGCTTCTAGC
34819200 AGGATGCTATTTGAGAAGAATTTGTGAAA--GCATGCCCTCGTGGACGCGCTTTTGCTACAG
66 AGGATGCTATTTGAGAAGAATTTGTGAAATCGC-T-CCCTCGTGGACGCGCTTTTGCTACAG
34819260 TAG
1 TAG
34819263 CATGTTTGGG
Statistics
Matches: 229, Mismatches: 22, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
123 2 0.01
125 227 0.99
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (125 bp):
TAGGTCCTGGAAGAAATAATTTCGAGTTGACATTTCTGAGCAAATAGTATAAAATCGCTTCTAGC
AGGATGCTATTTGAGAAGAATTTGTGAAATCGCTCCCTCGTGGACGCGCTTTTGCTACAG
Found at i:34822495 original size:22 final size:22
Alignment explanation
Indices: 34822425--34822694 Score: 216
Period size: 23 Copynumber: 12.3 Consensus size: 22
34822415 ATCAAATAAA
*
34822425 TTTAAGTTAAGGG-TTACGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* **
34822446 TTTAAGTTCTA--GTTTAAAGTT
1 TTTAAGTT-AAGGGTTTAGGGTT
* * *
34822467 TTAAAGTTAAGGGTTAAGAGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
34822489 TTTAAGTTAAGGG-TTAAGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
34822510 TTTAAGTTGAGGG-TTA-GGAT
1 TTTAAGTTAAGGGTTTAGGGTT
*
34822530 TTTAAGTTAAGGGTTTGGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
** *
34822552 TTTAA-TTAA-ATTAGTTAGGGGT
1 TTTAAGTTAAGGGT--TTAGGGTT
*
34822574 TTTAAGTTTAAGGGTTTAGGATT
1 TTTAAG-TTAAGGGTTTAGGGTT
**
34822597 TTTAA-TTAAATTAGTTTAGGGTT
1 TTTAAGTT-AA-GGGTTTAGGGTT
*
34822620 TTTAAGTTAAGGGGTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
34822642 TTTAAATTTAAGGGTTTAGGGTT
1 TTT-AAGTTAAGGGTTTAGGGTT
* *
34822665 TTTAATTTTAAGAGTTTAGGGTT
1 TTTAA-GTTAAGGGTTTAGGGTT
34822688 TTTAAGT
1 TTTAAGT
34822695 AATAACTCAA
Statistics
Matches: 199, Mismatches: 34, Indels: 31
0.75 0.13 0.12
Matches are distributed among these distances:
20 18 0.09
21 49 0.25
22 57 0.29
23 68 0.34
24 6 0.03
25 1 0.01
ACGTcount: A:0.27, C:0.01, G:0.26, T:0.46
Consensus pattern (22 bp):
TTTAAGTTAAGGGTTTAGGGTT
Found at i:34822511 original size:43 final size:42
Alignment explanation
Indices: 34822428--34822544 Score: 139
Period size: 43 Copynumber: 2.8 Consensus size: 42
34822418 AAATAAATTT
* * *
34822428 AAGTTAAGGGTTACGGTTTTTAAGTTCTA-GTTTAAAGTTTTA
1 AAGTTAAGGGTTAAGGTTTTTAAGTT-AAGGGTTAAAGTTTTA
* *
34822470 AAGTTAAGGGTTAAGAGTTTTTAAGTTAAGGGTTAAGGTTTTT
1 AAGTTAAGGGTTAAG-GTTTTTAAGTTAAGGGTTAAAGTTTTA
* *
34822513 AAGTTGAGGGTT-AGGATTTTAAGTTAAGGGTT
1 AAGTTAAGGGTTAAGGTTTTTAAGTTAAGGGTT
34822545 TGGGGTTTTT
Statistics
Matches: 66, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
41 17 0.26
42 17 0.26
43 32 0.48
ACGTcount: A:0.29, C:0.02, G:0.27, T:0.42
Consensus pattern (42 bp):
AAGTTAAGGGTTAAGGTTTTTAAGTTAAGGGTTAAAGTTTTA
Found at i:34822589 original size:45 final size:45
Alignment explanation
Indices: 34822529--34822692 Score: 206
Period size: 45 Copynumber: 3.6 Consensus size: 45
34822519 AGGGTTAGGA
* *
34822529 TTTTAAGTTAAGGGTTTGGGGTTTTTAATTAAATTAG-TTAGGGG
1 TTTTAAGTTAAGGGTTTAGGGTTTTTAATTAAATTAGTTTAGGGT
*
34822573 TTTTAAGTTTAAGGGTTTAGGATTTTTAATTAAATTAGTTTAGGGT
1 TTTTAAG-TTAAGGGTTTAGGGTTTTTAATTAAATTAGTTTAGGGT
* * **
34822619 TTTTAAGTTAAGGGGTTAGGGTTTTTAAATTTAA-GGGTTTAGGGT
1 TTTTAAGTTAAGGGTTTAGGGTTTTT-AATTAAATTAGTTTAGGGT
* *
34822664 TTTTAATTTTAAGAGTTTAGGGTTTTTAA
1 TTTTAA-GTTAAGGGTTTAGGGTTTTTAA
34822693 GTAATAACTC
Statistics
Matches: 105, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
44 7 0.07
45 62 0.59
46 36 0.34
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (45 bp):
TTTTAAGTTAAGGGTTTAGGGTTTTTAATTAAATTAGTTTAGGGT
Found at i:34822637 original size:68 final size:66
Alignment explanation
Indices: 34822425--34822694 Score: 252
Period size: 68 Copynumber: 4.1 Consensus size: 66
34822415 ATCAAATAAA
* * * * * *
34822425 TTTAAGTTAAGGGTTACGGTTTTTAAGTTCT-A--GTTTA-AAGTTTTAAAGTTAAGGGTTAAGA
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTT-TAAGGGTTTAGGA-TTTTTAAGTTAAGAGTTTAGG
34822486 GTT
64 GTT
* * * *
34822489 TTTAAGTTAAGGGTTAAGGTTTTTAAG-TTGAGGG-TTAGGA-TTTTAAGTTAAGGGTTTGGGGT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTTAAGGGTTTAGGATTTTTAAGTTAAGAGTTTAGGGT
34822551 T
66 T
** * *
34822552 TTTAA-TTAAATTAGTTAGGGGTTTTAAGTTTAAGGGTTTAGGATTTTTAA-TTAAATTAGTTTA
1 TTTAAGTT-AA-GGGTTAGGGTTTTTAAGTTTAAGGGTTTAGGATTTTTAAGTT-AA-GAGTTTA
34822615 GGGTT
62 GGGTT
* * *
34822620 TTTAAGTTAAGGGGTTAGGGTTTTTAAATTTAAGGGTTTAGGGTTTTTAATTTTAAGAGTTTAGG
1 TTTAAGTTAA-GGGTTAGGGTTTTTAAGTTTAAGGGTTTAGGATTTTTAA-GTTAAGAGTTTAGG
34822685 GTT
64 GTT
34822688 TTTAAGT
1 TTTAAGT
34822695 AATAACTCAA
Statistics
Matches: 171, Mismatches: 21, Indels: 24
0.79 0.10 0.11
Matches are distributed among these distances:
62 3 0.02
63 28 0.16
64 42 0.25
65 8 0.05
66 8 0.05
67 8 0.05
68 68 0.40
69 4 0.02
70 2 0.01
ACGTcount: A:0.27, C:0.01, G:0.26, T:0.46
Consensus pattern (66 bp):
TTTAAGTTAAGGGTTAGGGTTTTTAAGTTTAAGGGTTTAGGATTTTTAAGTTAAGAGTTTAGGGT
T
Found at i:34822898 original size:21 final size:21
Alignment explanation
Indices: 34822860--34822900 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
34822850 TTGTCCAGCT
*
34822860 TCCGGCGGCGGTTGTGGTTCC
1 TCCGGCGGCGGTTCTGGTTCC
34822881 TCCGGCGG-GGATTCTGGTTC
1 TCCGGCGGCGG-TTCTGGTTC
34822901 TTTCGGTACG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.02, C:0.27, G:0.41, T:0.29
Consensus pattern (21 bp):
TCCGGCGGCGGTTCTGGTTCC
Found at i:34823188 original size:18 final size:18
Alignment explanation
Indices: 34823162--34823204 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
34823152 GACTCGGAAA
* *
34823162 AGGAAACATATAAGGGTT
1 AGGAAACATAAAAGGGCT
*
34823180 AGGATACATAAAAGGGCT
1 AGGAAACATAAAAGGGCT
34823198 AGGAAAC
1 AGGAAAC
34823205 GCACCTGGCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.47, C:0.09, G:0.28, T:0.16
Consensus pattern (18 bp):
AGGAAACATAAAAGGGCT
Found at i:34823863 original size:7 final size:7
Alignment explanation
Indices: 34823853--34823878 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
34823843 TTATATACAT
34823853 AATACTA
1 AATACTA
34823860 AATACTA
1 AATACTA
34823867 AATACTA
1 AATACTA
34823874 AATAC
1 AATAC
34823879 CAATCGACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:34824085 original size:20 final size:20
Alignment explanation
Indices: 34824048--34824085 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
34824038 TTTATTTTTA
*
34824048 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
34824068 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
34824086 TATCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:34825086 original size:11 final size:11
Alignment explanation
Indices: 34825072--34825148 Score: 63
Period size: 11 Copynumber: 6.9 Consensus size: 11
34825062 TTAAATGTGG
34825072 ATTTGAGAGAA
1 ATTTGAGAGAA
*
34825083 ATTTG-GAAGGA
1 ATTTGAG-AGAA
34825094 ATTTGAGAGCAA
1 ATTTGAGAG-AA
34825106 A-TTGAGAGGAA
1 ATTTGAGA-GAA
34825117 ATTT-AGAAGAA
1 ATTTGAG-AGAA
*
34825128 A-TTAAGAGGAA
1 ATTTGAGA-GAA
34825139 ATTTGAGAGA
1 ATTTGAGAGA
34825149 GGATTAGTTT
Statistics
Matches: 54, Mismatches: 3, Indels: 18
0.72 0.04 0.24
Matches are distributed among these distances:
10 4 0.07
11 38 0.70
12 12 0.22
ACGTcount: A:0.45, C:0.01, G:0.29, T:0.25
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:34825115 original size:22 final size:22
Alignment explanation
Indices: 34825072--34825148 Score: 88
Period size: 22 Copynumber: 3.5 Consensus size: 22
34825062 TTAAATGTGG
34825072 ATTTGAGAGAAATTTG-GAAGG-A
1 ATTTGAGAGAAA-TTGAG-AGGAA
34825094 ATTTGAGAGCAAATTGAGAGGAA
1 ATTTGAGAG-AAATTGAGAGGAA
*
34825117 ATTT-AGAAGAAATTAAGAGGAA
1 ATTTGAG-AGAAATTGAGAGGAA
34825139 ATTTGAGAGA
1 ATTTGAGAGA
34825149 GGATTAGTTT
Statistics
Matches: 49, Mismatches: 1, Indels: 10
0.82 0.02 0.17
Matches are distributed among these distances:
22 36 0.73
23 13 0.27
ACGTcount: A:0.45, C:0.01, G:0.29, T:0.25
Consensus pattern (22 bp):
ATTTGAGAGAAATTGAGAGGAA
Found at i:34825120 original size:34 final size:34
Alignment explanation
Indices: 34825072--34825147 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 34
34825062 TTAAATGTGG
* * *
34825072 ATTTGAGA-GAAATTTGGAAGGAATTTGAGAGCAA
1 ATTTGAGAGGAAATTTAGAA-GAAATTAAGAGCAA
*
34825106 A-TTGAGAGGAAATTTAGAAGAAATTAAGAGGAA
1 ATTTGAGAGGAAATTTAGAAGAAATTAAGAGCAA
34825139 ATTTGAGAG
1 ATTTGAGAG
34825148 AGGATTAGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
33 18 0.50
34 18 0.50
ACGTcount: A:0.45, C:0.01, G:0.29, T:0.25
Consensus pattern (34 bp):
ATTTGAGAGGAAATTTAGAAGAAATTAAGAGCAA
Found at i:34827684 original size:21 final size:21
Alignment explanation
Indices: 34827636--34827684 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
34827626 TAATATCAAT
* *
34827636 TAATTATAAATACTTAATATT
1 TAATTATAAATAATTAATATA
* * *
34827657 TATTTATAATTAATTATTATA
1 TAATTATAAATAATTAATATA
34827678 TAATTAT
1 TAATTAT
34827685 GTTTAAATAA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (21 bp):
TAATTATAAATAATTAATATA
Found at i:34828313 original size:26 final size:27
Alignment explanation
Indices: 34828252--34828315 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 27
34828242 TTTAGCAATG
34828252 CTTTTAAAAAGTGATTTTGAAAAGTGA
1 CTTTTAAAAAGTGATTTTGAAAAGTGA
* * * *
34828279 CGTGT-AAAAGTGCTTTTGAGAAGTG-
1 CTTTTAAAAAGTGATTTTGAAAAGTGA
*
34828304 TTTTTAAAAAGT
1 CTTTTAAAAAGT
34828316 TTGGTTTAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
25 2 0.07
26 24 0.83
27 3 0.10
ACGTcount: A:0.36, C:0.05, G:0.22, T:0.38
Consensus pattern (27 bp):
CTTTTAAAAAGTGATTTTGAAAAGTGA
Found at i:34833229 original size:9 final size:9
Alignment explanation
Indices: 34833189--34833248 Score: 59
Period size: 9 Copynumber: 6.6 Consensus size: 9
34833179 GGGCGCATAG
34833189 TAAATTTTT
1 TAAATTTTT
34833198 T-AATTTTAT
1 TAAATTTT-T
* *
34833207 CAACTTTTT
1 TAAATTTTT
34833216 ATAAATTTTT
1 -TAAATTTTT
*
34833226 TAAATTCTT
1 TAAATTTTT
*
34833235 AAAATTTTT
1 TAAATTTTT
34833244 TAAAT
1 TAAAT
34833249 AATTTGTTGA
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
8 6 0.15
9 22 0.55
10 12 0.30
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (9 bp):
TAAATTTTT
Found at i:34833242 original size:28 final size:26
Alignment explanation
Indices: 34833189--34833248 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 26
34833179 GGGCGCATAG
*
34833189 TAAATTTTTTAATTTTATCAACTTTTT
1 TAAATTTTTTAATTTTA-CAAATTTTT
34833216 ATAAATTTTTTAAATTCTTA-AAATTTTT
1 -TAAATTTTTT-AATT-TTACAAATTTTT
34833244 TAAAT
1 TAAAT
34833249 AATTTGTTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
27 5 0.17
28 17 0.59
29 4 0.14
30 3 0.10
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (26 bp):
TAAATTTTTTAATTTTACAAATTTTT
Found at i:34834388 original size:16 final size:16
Alignment explanation
Indices: 34834366--34834402 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
34834356 CAATTTTATT
34834366 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
34834383 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
34834398 TAATA
1 TAATA
34834403 TTCATCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:34836492 original size:13 final size:14
Alignment explanation
Indices: 34836472--34836503 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
34836462 TTCAATAAAT
34836472 TAAA-AAAATATTA
1 TAAATAAAATATTA
34836485 -AAATAAAATATTA
1 TAAATAAAATATTA
34836498 TAAATA
1 TAAATA
34836504 TTTTTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 3 0.18
13 9 0.53
14 5 0.29
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
TAAATAAAATATTA
Found at i:34838749 original size:31 final size:31
Alignment explanation
Indices: 34838686--34838751 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
34838676 AAGTTGTGGA
* * *
34838686 TTTAGTCCCTGTATTTTTTGAATTTATCAAT
1 TTTAGTCCCTATACTTTTTGAATTTATAAAT
*
34838717 TTTAGTCTCTATACTTTTTGAATTT-TGAAAT
1 TTTAGTCCCTATACTTTTTGAATTTAT-AAAT
34838748 TTTA
1 TTTA
34838752 ATCTAGGCCA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 1 0.03
31 29 0.97
ACGTcount: A:0.24, C:0.11, G:0.09, T:0.56
Consensus pattern (31 bp):
TTTAGTCCCTATACTTTTTGAATTTATAAAT
Found at i:34844130 original size:25 final size:24
Alignment explanation
Indices: 34844075--34844137 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 24
34844065 TAATTGAATA
**
34844075 TTTAATAATTTTATATATTTTTATT
1 TTTAA-AATTTTATATATAATTATT
*
34844100 TATTAAAATTTTATATATAATTGTCT
1 T-TTAAAATTTTATATATAATTAT-T
*
34844126 TTTAACATTTTA
1 TTTAAAATTTTA
34844138 AATGTTTATA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
25 26 0.81
26 6 0.19
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.60
Consensus pattern (24 bp):
TTTAAAATTTTATATATAATTATT
Found at i:34864587 original size:30 final size:30
Alignment explanation
Indices: 34864523--34864580 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
34864513 TATTTAAGTT
*
34864523 AATTAAGTTATTCGGATCAACTCGAATAAA
1 AATTAAGTTATTAGGATCAACTCGAATAAA
* * *
34864553 AATTAAGTTTTTAGGTTTAACTCGAATA
1 AATTAAGTTATTAGGATCAACTCGAATA
34864581 TGAATTACAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (30 bp):
AATTAAGTTATTAGGATCAACTCGAATAAA
Done.