Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
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: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 122 of 125
Found at i:38564978 original size:101 final size:100
Alignment explanation
Indices: 38564719--38565132 Score: 431
Period size: 100 Copynumber: 4.1 Consensus size: 100
38564709 GGATCATCAA
* * *
38564719 TTTTTTATTTT-AATTTTCATTTCGAACTCTTAGTTAAGC-TATCGTCGCTTTTGATTTTCATTT
1 TTTTTT-TTTTCAATTTTCATTTCGAACTCTCAGTTAAGCTTATCGTAGCATTTGATTTTCATTT
* *
38564782 CTTTATATGCCGGATCTTCAATTTTTTTATTTCTCTC
65 CTTTATATGCCGGATCTTCAA-ATTTTTATTTCTCTG
** * * * * *
38564819 TTTTCTTTTTGAAAATTTCACTTCGAACACTTACTTAAGCTTATCGTAGCATTTGATTTTCATTT
1 TTTT-TTTTTTCAATTTTCATTTCGAACTCTCAGTTAAGCTTATCGTAGCATTTGATTTTCATTT
* * *
38564884 CTTAATATGGCGGATCTTCAAATTTTTGTTTCTCTG
65 CTTTATATGCCGGATCTTCAAATTTTTATTTCTCTG
* * * *
38564920 TTTTTTTTTTCATTTTTCATTTTGAACTCTCAGTTAAAGCTTATCATAGCAGTTGA-TTTCATTT
1 TTTTTTTTTTCAATTTTCATTTCGAACTCTCAGTT-AAGCTTATCGTAGCATTTGATTTTCATTT
* * **
38564984 CTTTACATGGCACATCTTCAAATTTTTATTTCTCTG
65 CTTTATATGCCGGATCTTCAAATTTTTATTTCTCTG
* * * *
38565020 CTGTTATTTTTTTCCA-TTTCGAAGTTCGAACTCTCTGTTAACCTTATCGTAGCATTTGATTTTC
1 -T-TT-TTTTTTTCAATTTTC--ATTTCGAACTCTCAGTTAAGCTTATCGTAGCATTTGATTTTC
* * * * *
38565084 ATTTCCTCATATGCCGGCTCTTCAAATTTTCATTTCTTTG
61 ATTTCTTTATATGCCGGATCTTCAAATTTTTATTTCTCTG
38565124 TTTTTTTTT
1 TTTTTTTTT
38565133 AAAGCTAAAA
Statistics
Matches: 259, Mismatches: 45, Indels: 19
0.80 0.14 0.06
Matches are distributed among these distances:
100 68 0.26
101 67 0.26
102 49 0.19
103 26 0.10
104 49 0.19
ACGTcount: A:0.20, C:0.18, G:0.10, T:0.52
Consensus pattern (100 bp):
TTTTTTTTTTCAATTTTCATTTCGAACTCTCAGTTAAGCTTATCGTAGCATTTGATTTTCATTTC
TTTATATGCCGGATCTTCAAATTTTTATTTCTCTG
Found at i:38575741 original size:44 final size:45
Alignment explanation
Indices: 38575672--38575764 Score: 125
Period size: 44 Copynumber: 2.1 Consensus size: 45
38575662 TATAGAAAAC
* * * *
38575672 TAAACCCACAAGGATTAATAACAGAATTTGGCCATTTTTAGCAT-
1 TAAACCCACAAGGACTAATAACAGAACTTGACCATTTTAAGCATA
* *
38575716 TAAATCCACAAGGACTAATAGCAGAACTTGACCATTTTAAGCATA
1 TAAACCCACAAGGACTAATAACAGAACTTGACCATTTTAAGCATA
38575761 TAAA
1 TAAA
38575765 GAGGATTTGC
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 38 0.90
45 4 0.10
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.27
Consensus pattern (45 bp):
TAAACCCACAAGGACTAATAACAGAACTTGACCATTTTAAGCATA
Found at i:38575938 original size:44 final size:44
Alignment explanation
Indices: 38575875--38575961 Score: 156
Period size: 44 Copynumber: 2.0 Consensus size: 44
38575865 TACAGAAAAC
* *
38575875 TAAATCCACAAGGATTAATAGCAGAATTTGAGCATTTTTAGCAT
1 TAAATCCACAAGGACTAATAGCAGAATTTGACCATTTTTAGCAT
38575919 TAAATCCACAAGGACTAATAGCAGAATTTGACCATTTTTAGCA
1 TAAATCCACAAGGACTAATAGCAGAATTTGACCATTTTTAGCA
38575962 ATATAAGAGG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.30
Consensus pattern (44 bp):
TAAATCCACAAGGACTAATAGCAGAATTTGACCATTTTTAGCAT
Found at i:38581762 original size:32 final size:32
Alignment explanation
Indices: 38581711--38581771 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
38581701 TACTGTATTA
**
38581711 ATGGGCTGGGTTTGGGTAAAAGTATCATGGAT
1 ATGGGCTGAATTTGGGTAAAAGTATCATGGAT
*
38581743 ATGGGCTGAATTTGTGTAAAAGTATCATG
1 ATGGGCTGAATTTGGGTAAAAGTATCATG
38581772 AATGTTTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.28, C:0.07, G:0.33, T:0.33
Consensus pattern (32 bp):
ATGGGCTGAATTTGGGTAAAAGTATCATGGAT
Found at i:38591343 original size:15 final size:15
Alignment explanation
Indices: 38591323--38591352 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
38591313 ACGAAAACAC
38591323 AAGAGAAGTATCGAT
1 AAGAGAAGTATCGAT
*
38591338 AAGAGAGGTATCGAT
1 AAGAGAAGTATCGAT
38591353 GTGCTATGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.30, T:0.20
Consensus pattern (15 bp):
AAGAGAAGTATCGAT
Found at i:38593408 original size:95 final size:93
Alignment explanation
Indices: 38593229--38593561 Score: 329
Period size: 95 Copynumber: 3.5 Consensus size: 93
38593219 CAAATTATGA
* * * * * * *
38593229 TACTATGCTCAATTTTGGATATATAATAAGAAAAGCGAGTTAATACTAAAGAAATTAAACAAGGT
1 TACTATGCTCAA-TTTGGATGTATAATAAGAAAAACGAGTTAAAAGTGATGAAATTAAACAAGTT
*
38593294 TTTTTGGTTAAATTATGATTTTAGTCCGTC
65 TTTTTGGTTAAATTATGATTTT-GTCCCTC
* * *
38593324 TATTATGCTCTAATTTGGATGTAAAATAAAGAAAAACAAGTTAAAAGTGATGAAATTAAACAA-T
1 TACTATGCTC-AATTTGGATGTATAAT-AAGAAAAACGAGTTAAAAGTGATGAAATTAAACAAGT
*
38593388 TTTTTTGGTTAAATTCTGATTTTGGTCCCTC
64 TTTTTTGGTTAAATTATGATTTT-GTCCCTC
* * * * * *
38593419 AACTATGCTC---TT-CATTGTATAATAAGAAATACGACTTACAAGTGATG-AACTAAACAAGTT
1 TACTATGCTCAATTTGGA-TGTATAATAAGAAAAACGAGTTAAAAGTGATGAAATTAAACAAG-T
*
38593479 TTTTTTGGTGTTAAATTAT-AGTTTTGATCCTTC
64 TTTTTT-G-GTTAAATTATGA-TTTTG-TCCCTC
*
38593512 TACCATGCTCAAATTTGGATGTATAATAAGAAAAACGAGTTAAAAGTGAT
1 TACTATGCTC-AATTTGGATGTATAATAAGAAAAACGAGTTAAAAGTGAT
38593562 CAAACGAATT
Statistics
Matches: 194, Mismatches: 30, Indels: 26
0.78 0.12 0.10
Matches are distributed among these distances:
89 9 0.05
90 21 0.11
91 16 0.08
92 3 0.02
93 26 0.13
95 57 0.29
96 31 0.16
97 30 0.15
98 1 0.01
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.37
Consensus pattern (93 bp):
TACTATGCTCAATTTGGATGTATAATAAGAAAAACGAGTTAAAAGTGATGAAATTAAACAAGTTT
TTTTGGTTAAATTATGATTTTGTCCCTC
Found at i:38593619 original size:2 final size:2
Alignment explanation
Indices: 38593612--38593652 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
38593602 CATAATTATA
38593612 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
38593653 CCAAATCGTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:38600327 original size:21 final size:21
Alignment explanation
Indices: 38600303--38600344 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
38600293 AAATATATGT
38600303 TCAAAT-AACTACAAAGTATAA
1 TCAAATCAA-TACAAAGTATAA
*
38600324 TCAAATCAATATAAAGTATAA
1 TCAAATCAATACAAAGTATAA
38600345 ATTGATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.57, C:0.12, G:0.05, T:0.26
Consensus pattern (21 bp):
TCAAATCAATACAAAGTATAA
Found at i:38603614 original size:31 final size:31
Alignment explanation
Indices: 38603579--38603642 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
38603569 GGTCATTCAA
*
38603579 CATTGAACTATTTAAAAATTTTCATTTAAGT
1 CATTGAACTATTCAAAAATTTTCATTTAAGT
* * *
38603610 CATTGAACTATTCGAAAGTTTTTATTTAAGT
1 CATTGAACTATTCAAAAATTTTCATTTAAGT
38603641 CA
1 CA
38603643 CTAGACTGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.44
Consensus pattern (31 bp):
CATTGAACTATTCAAAAATTTTCATTTAAGT
Found at i:38605374 original size:15 final size:15
Alignment explanation
Indices: 38605356--38605386 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
38605346 ATTATCCAAA
38605356 TCTGTTTTATTTTTG
1 TCTGTTTTATTTTTG
38605371 TCTGTTTTATTTTTG
1 TCTGTTTTATTTTTG
38605386 T
1 T
38605387 AAGTTTGACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.06, G:0.13, T:0.74
Consensus pattern (15 bp):
TCTGTTTTATTTTTG
Found at i:38605392 original size:15 final size:15
Alignment explanation
Indices: 38605359--38605392 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
38605349 ATCCAAATCT
**
38605359 GTTTTATTTTTGTCT
1 GTTTTATTTTTGTAA
38605374 GTTTTATTTTTGTAA
1 GTTTTATTTTTGTAA
38605389 GTTT
1 GTTT
38605393 GACTCATCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.03, G:0.15, T:0.71
Consensus pattern (15 bp):
GTTTTATTTTTGTAA
Found at i:38618608 original size:15 final size:14
Alignment explanation
Indices: 38618569--38618610 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
38618559 AAACAAAACC
38618569 TTGTTTTTGTTCTGT
1 TTGTTTTTGTT-TGT
38618584 TT-TGTTTTGTTTGT
1 TTGT-TTTTGTTTGT
38618598 TTGTTTGTTGTTT
1 TTGTTT-TTGTTT
38618611 TAATGGTGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
14 8 0.33
15 16 0.67
ACGTcount: A:0.00, C:0.02, G:0.21, T:0.76
Consensus pattern (14 bp):
TTGTTTTTGTTTGT
Found at i:38619214 original size:71 final size:71
Alignment explanation
Indices: 38619097--38619238 Score: 207
Period size: 71 Copynumber: 2.0 Consensus size: 71
38619087 ACTAGCATGT
*
38619097 ATGTTAAGGCTTGAACTCAAGATCTTAGTATATAGAAGATCCCGAGTGAACTATGGTACTACTTG
1 ATGTTAAGGCTTGAACTCAAGACCTTAGTATATAGAAGATCCCGAGTGAACTATGGTACTACTTG
38619162 AGCTAG
66 AGCTAG
* * * *
38619168 ATGTTAAGGCTT-AAGCTCAAGACCTCTAGTAT-TAGAGGTTCTCGAGTGAACTATGGTACTATT
1 ATGTTAAGGCTTGAA-CTCAAGACCT-TAGTATATAGAAGATCCCGAGTGAACTATGGTACTACT
38619231 TGAGCTAG
64 TGAGCTAG
38619239 TTTGTTGAAT
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
70 2 0.03
71 56 0.88
72 6 0.09
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.31
Consensus pattern (71 bp):
ATGTTAAGGCTTGAACTCAAGACCTTAGTATATAGAAGATCCCGAGTGAACTATGGTACTACTTG
AGCTAG
Found at i:38622209 original size:174 final size:178
Alignment explanation
Indices: 38622025--38622352 Score: 443
Period size: 174 Copynumber: 1.8 Consensus size: 178
38622015 TCTTTTGTCA
*
38622025 ATGCATGCATGCATGTCATTTGGTTTTCT-TGGA-TTCTGTACGGTTCCCGGGATATGATTCTCC
1 ATGCATGCATGCATGTCATTT-GTTTTCTATGGATTTC-GTACGGTTCCCGGGATATGATCCTCC
* * **
38622088 AAGAAACCTCC-AA-ATGCATGCATG-G-CTGTATATATGTGTTTATGTATGTTATTTGGATTTT
64 AAGAAACCTCCAAACATGCATGCATGAGTATGTATATATGTGTTTATGTATGTCATTCAGATTTT
* *
38622149 GTATGGTTCCCGTTTGTTAATGTGTTCATCTTTTGTCAATGTATGTATGT
129 GAATGGTTCCCGTTTGTCAATGTGTTCATCTTTTGTCAATGTATGTATGT
* * * *
38622199 ATGCATGCATGCATGTCATTTGTTTTTTATGGATTTCGTATGGTTCCTGGGATATGGTCCTCCAA
1 ATGCATGCATGCATGTCATTTGTTTTCTATGGATTTCGTACGGTTCCCGGGATATGATCCTCCAA
*
38622264 GAACCCTCCAAAAGCATGCATGCATGCATGTATGTATATATGTGTTTATGTATGTCATTCAGATT
66 GAAACCTCC-AAA-CATGCATGCATG-A-GTATGTATATATGTGTTTATGTATGTCATTCAGATT
*
38622329 TTGAATGGTTCCCTTTTGTCAATG
127 TTGAATGGTTCCCGTTTGTCAATG
38622353 CATACATGCA
Statistics
Matches: 131, Mismatches: 13, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
173 6 0.05
174 57 0.44
175 3 0.02
176 2 0.02
178 11 0.08
181 1 0.01
182 51 0.39
ACGTcount: A:0.21, C:0.16, G:0.21, T:0.41
Consensus pattern (178 bp):
ATGCATGCATGCATGTCATTTGTTTTCTATGGATTTCGTACGGTTCCCGGGATATGATCCTCCAA
GAAACCTCCAAACATGCATGCATGAGTATGTATATATGTGTTTATGTATGTCATTCAGATTTTGA
ATGGTTCCCGTTTGTCAATGTGTTCATCTTTTGTCAATGTATGTATGT
Found at i:38630509 original size:14 final size:15
Alignment explanation
Indices: 38630490--38630518 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
38630480 ATTAACCCAA
38630490 TGATTC-AATATCTT
1 TGATTCTAATATCTT
38630504 TGATTCTAATATCTT
1 TGATTCTAATATCTT
38630519 CTTCCCGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.28, C:0.14, G:0.07, T:0.52
Consensus pattern (15 bp):
TGATTCTAATATCTT
Found at i:38634069 original size:21 final size:21
Alignment explanation
Indices: 38634031--38634070 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
38634021 TCACAAGCCG
38634031 AGTATCGAGCTTGAGCTTGAT
1 AGTATCGAGCTTGAGCTTGAT
38634052 AGTATTCGAGCTTG-GCTTG
1 AGTA-TCGAGCTTGAGCTTG
38634071 GTTCGATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.20, C:0.15, G:0.30, T:0.35
Consensus pattern (21 bp):
AGTATCGAGCTTGAGCTTGAT
Found at i:38641701 original size:31 final size:29
Alignment explanation
Indices: 38641626--38641702 Score: 75
Period size: 31 Copynumber: 2.5 Consensus size: 29
38641616 ACTTGAGTTT
*
38641626 TTTTTGTTGCAATTAGGTACCTAAGTTTGA
1 TTTTTGTT-CAATTAGGTACCTAACTTTGA
*
38641656 TTTTAATGTTCAATTTGGTACCTAAACTTT-A
1 TTTT--TGTTCAATTAGGTACCT-AACTTTGA
38641687 TTGTTTGTTCCAATTA
1 TT-TTTGTT-CAATTA
38641703 AGTGTCTTTG
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
30 8 0.21
31 20 0.51
32 11 0.28
ACGTcount: A:0.25, C:0.12, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTTTGTTCAATTAGGTACCTAACTTTGA
Found at i:38642853 original size:30 final size:31
Alignment explanation
Indices: 38642802--38642861 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
38642792 TTTAAAATTT
*
38642802 AAATAATAAATTTTTTGTTATAAT-TTTTTA
1 AAATAATAAATTATTTGTTATAATATTTTTA
38642832 AAATATATAAATTATTT-TTATAATATTTTT
1 AAATA-ATAAATTATTTGTTATAATATTTTT
38642862 TAAGATTTAG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 12 0.44
31 15 0.56
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (31 bp):
AAATAATAAATTATTTGTTATAATATTTTTA
Found at i:38645001 original size:22 final size:22
Alignment explanation
Indices: 38644971--38645013 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
38644961 CTTACATACA
*
38644971 TATACACGTATGTTTATATATG
1 TATACACGTATGTATATATATG
*
38644993 TATATACGTATGTATATATAT
1 TATACACGTATGTATATATAT
38645014 ATAATTTATT
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:0.35, C:0.07, G:0.12, T:0.47
Consensus pattern (22 bp):
TATACACGTATGTATATATATG
Found at i:38646649 original size:29 final size:30
Alignment explanation
Indices: 38646617--38646698 Score: 94
Period size: 30 Copynumber: 2.8 Consensus size: 30
38646607 TAAACCCTTC
* *
38646617 AAATTTTGAATTTTTTACTTAAACCT-CAA
1 AAATTTTAAATTTTTTAATTAAACCTACAA
** * *
38646646 AAATTTTAAAAATTCTAAATAAACCTACAA
1 AAATTTTAAATTTTTTAATTAAACCTACAA
*
38646676 AAGTTTTAAATTTTTTAATTAAA
1 AAATTTTAAATTTTTTAATTAAA
38646699 TCCTTTAAAT
Statistics
Matches: 41, Mismatches: 11, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
29 20 0.49
30 21 0.51
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.41
Consensus pattern (30 bp):
AAATTTTAAATTTTTTAATTAAACCTACAA
Found at i:38647757 original size:18 final size:16
Alignment explanation
Indices: 38647724--38647759 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
38647714 TTTTTTTTCT
38647724 AATTAAAATAGAAATC
1 AATTAAAATAGAAATC
38647740 AATTACAAATATGAAATC
1 AATTA-AAATA-GAAATC
38647758 AA
1 AA
38647760 GGAACTACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.28
17 5 0.28
18 8 0.44
ACGTcount: A:0.61, C:0.08, G:0.06, T:0.25
Consensus pattern (16 bp):
AATTAAAATAGAAATC
Found at i:38650538 original size:23 final size:23
Alignment explanation
Indices: 38650508--38650581 Score: 87
Period size: 23 Copynumber: 3.2 Consensus size: 23
38650498 CTAGCGCGCT
38650508 TACTGTTTCGCATTTCGTGTGCC
1 TACTGTTTCGCATTTCGTGTGCC
*
38650531 TACTGTTTCGCACTTT-GTGTGCT
1 TACTGTTTCGCA-TTTCGTGTGCC
* * **
38650554 TACTATTTCACACCTCGTGTGCC
1 TACTGTTTCGCATTTCGTGTGCC
38650577 TACTG
1 TACTG
38650582 ATTTGTGCTA
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
22 1 0.02
23 38 0.90
24 3 0.07
ACGTcount: A:0.12, C:0.27, G:0.19, T:0.42
Consensus pattern (23 bp):
TACTGTTTCGCATTTCGTGTGCC
Found at i:38650642 original size:23 final size:23
Alignment explanation
Indices: 38650597--38650649 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
38650587 TGCTATGTGC
*
38650597 GCCTACT-GATTGCACTGTCTGT
1 GCCTACTGGATTGCACTGACTGT
*
38650619 GCCTACTGGATTGCACTGAGTGT
1 GCCTACTGGATTGCACTGACTGT
*
38650642 GCTTACTG
1 GCCTACTG
38650650 TTAAGTACTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 7 0.26
23 20 0.74
ACGTcount: A:0.15, C:0.25, G:0.26, T:0.34
Consensus pattern (23 bp):
GCCTACTGGATTGCACTGACTGT
Found at i:38658630 original size:20 final size:20
Alignment explanation
Indices: 38658605--38658643 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
38658595 AAAAAACAAA
38658605 AAATAAATCAAAT-ATATATG
1 AAATAAAT-AAATAATATATG
38658625 AAATAAATAAATAATATAT
1 AAATAAATAAATAATATAT
38658644 ATAGCAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (20 bp):
AAATAAATAAATAATATATG
Found at i:38658652 original size:24 final size:25
Alignment explanation
Indices: 38658601--38658652 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
38658591 TTTAAAAAAA
38658601 CAAA-AAATAAATCAAATATATATG
1 CAAATAAATAAATCAAATATATATG
38658625 -AAATAAATAAAT--AATATATATAG
1 CAAATAAATAAATCAAATATATAT-G
38658648 CAAAT
1 CAAAT
38658653 TTTATAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
22 9 0.36
23 4 0.16
24 12 0.48
ACGTcount: A:0.63, C:0.06, G:0.04, T:0.27
Consensus pattern (25 bp):
CAAATAAATAAATCAAATATATATG
Found at i:38672368 original size:30 final size:31
Alignment explanation
Indices: 38672334--38672394 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
38672324 AAAATATTAT
* * *
38672334 TTAAG-CCTCCAAAATTTTTGAGAATTATAA
1 TTAAGTCCTACAAAAGTTTTGACAATTATAA
*
38672364 TTAAGTCCTATAAAAGTTTTGACAATTATAA
1 TTAAGTCCTACAAAAGTTTTGACAATTATAA
38672395 CTAAACCTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 5 0.19
31 21 0.81
ACGTcount: A:0.41, C:0.11, G:0.10, T:0.38
Consensus pattern (31 bp):
TTAAGTCCTACAAAAGTTTTGACAATTATAA
Found at i:38672445 original size:24 final size:24
Alignment explanation
Indices: 38672400--38672445 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
38672390 TATAACTAAA
* *
38672400 CCTTGAATTTTTTTTGAGAATTCT
1 CCTTGAATTTTTTTTCAAAATTCT
38672424 CCTT-AATTTTTTTTCCAAAATT
1 CCTTGAATTTTTTTT-CAAAATT
38672446 TTCAATTAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.24, C:0.15, G:0.07, T:0.54
Consensus pattern (24 bp):
CCTTGAATTTTTTTTCAAAATTCT
Found at i:38676355 original size:4 final size:4
Alignment explanation
Indices: 38676346--38676374 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
38676336 TCATGACTTA
38676346 ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
38676375 CATATATATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:38678615 original size:18 final size:19
Alignment explanation
Indices: 38678592--38678634 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
38678582 ATTACAGGTA
38678592 TCTAAATTA-TATCTAAAT
1 TCTAAATTAGTATCTAAAT
*
38678610 TCTAAATTAGTCTCTAAAT
1 TCTAAATTAGTATCTAAAT
*
38678629 TTTAAA
1 TCTAAA
38678635 AAACATTCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.42, C:0.12, G:0.02, T:0.44
Consensus pattern (19 bp):
TCTAAATTAGTATCTAAAT
Found at i:38679255 original size:36 final size:36
Alignment explanation
Indices: 38679208--38679281 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
38679198 TGGTGATTTG
38679208 CTAATGGGAATCAACATGGCAGTTAAGTAGCTATTC
1 CTAATGGGAATCAACATGGCAGTTAAGTAGCTATTC
38679244 CTAATGGGAATCAACATGGCAGTTAAGTAGCTATTC
1 CTAATGGGAATCAACATGGCAGTTAAGTAGCTATTC
38679280 CT
1 CT
38679282 CAAATATATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (36 bp):
CTAATGGGAATCAACATGGCAGTTAAGTAGCTATTC
Found at i:38686892 original size:108 final size:110
Alignment explanation
Indices: 38686730--38687173 Score: 368
Period size: 108 Copynumber: 3.9 Consensus size: 110
38686720 GTTATTGGCT
* *
38686730 TTTTATGATCAATCAGGTTTGAGTTC-AGGTTAATCGGATTGGATTCTAGAGTTCAGGTCAGTTT
1 TTTTATGATCAATCAGGTTTGAGTTCGA-GTTAATCGGATTGAATTCTTG-GTTCAGGTCAGTTT
*
38686794 GGTCAATCCAAGTTCAAATCATTTCTGGTTTGGATCATTTT-A-TC-
64 GGTCAATCCAAGTTCAAATAATTTCTGGTTTGGATCATTTTCAGTCG
* *
38686838 TTTTATGATCAATCAGGTTTGAGTTCGAGTTAATCGGATTGAATTCTTGTGTTCAAGTCAGTTCG
1 TTTTATGATCAATCAGGTTTGAGTTCGAGTTAATCGGATTGAATTCTTG-GTTCAGGTCAGTTTG
38686903 GTCAATCCAAGTTCAAATAATTTCTGG-TTGGATCATTTTCAGGTTCGGG
65 GTCAATCCAAGTTCAAATAATTTCTGGTTTGGATCATTTTCA-G-TC--G
** * * * ** *
38686952 TTATTGACTTTTC-ATCGGGTTTGAGTTCGAGTTAATCAGATTCAATTCTTGACTAAGGTCA-TT
1 TT-TT-A-TGATCAATCAGGTTTGAGTTCGAGTTAATCGGATTGAATTCTTGGTTCAGGTCAGTT
* * * *
38687015 TCGGTCAATCCCAGTTCAAATTACTTCTGGTTTGAATCATTTTCAGGTTCG
63 T-GGTCAATCCAAGTTCAAATAATTTCTGGTTTGGATCATTTTCA-G-TCG
** ** ** * *
38687066 GGTTATTGACTTTTTATC-GAGTTTGAGTTC-AGGCCAATTGGATTGGATTCTTGGGTTCAGGTC
1 TTTTA-TGA---TCAATCAG-GTTTGAGTTCGA-GTTAATCGGATTGAATTCTT-GGTTCAGGTC
* * * *
38687129 A-TTTCGGTCAATCCAAGTTCAAATCATTTTTAGTTTGGATTATTT
59 AGTTT-GGTCAATCCAAGTTCAAATAATTTCTGGTTTGGATCATTT
38687174 CAAGTTCGGG
Statistics
Matches: 274, Mismatches: 42, Indels: 31
0.79 0.12 0.09
Matches are distributed among these distances:
107 12 0.04
108 85 0.31
109 1 0.00
111 2 0.01
112 2 0.01
113 2 0.01
114 5 0.02
115 36 0.13
116 81 0.30
117 48 0.18
ACGTcount: A:0.23, C:0.15, G:0.21, T:0.41
Consensus pattern (110 bp):
TTTTATGATCAATCAGGTTTGAGTTCGAGTTAATCGGATTGAATTCTTGGTTCAGGTCAGTTTGG
TCAATCCAAGTTCAAATAATTTCTGGTTTGGATCATTTTCAGTCG
Found at i:38687057 original size:116 final size:116
Alignment explanation
Indices: 38686853--38687188 Score: 419
Period size: 116 Copynumber: 2.9 Consensus size: 116
38686843 TGATCAATCA
*
38686853 GGTTTGAGTTCGAGTTAATCGGATTGAATTCTTGTGTTCAA-GTCAGTTCGGTCAATCCAAGTTC
1 GGTTTGAGTTCGAGTTAATCGGATTGAATTCTTG-GTT-AAGGTCATTTCGGTCAATCCAAGTTC
38686917 AAATAATTTCTGG-TTGGATCATTTTCAGGTTCGGGTTATTGACTTTTCATCG
64 AAATAATTTCTGGTTTGGATCATTTTCAGGTTCGGGTTATTGACTTTTCATCG
* * ** *
38686969 GGTTTGAGTTCGAGTTAATCAGATTCAATTCTTGACTAAGGTCATTTCGGTCAATCCCAGTTCAA
1 GGTTTGAGTTCGAGTTAATCGGATTGAATTCTTGGTTAAGGTCATTTCGGTCAATCCAAGTTCAA
* * * *
38687034 ATTACTTCTGGTTTGAATCATTTTCAGGTTCGGGTTATTGACTTTTTATCG
66 ATAATTTCTGGTTTGGATCATTTTCAGGTTCGGGTTATTGACTTTTCATCG
* ** * * *
38687085 AGTTTGAGTTC-AGGCCAATTGGATTGGATTCTTGGGTTCAGGTCATTTCGGTCAATCCAAGTTC
1 GGTTTGAGTTCGA-GTTAATCGGATTGAATTCTT-GGTTAAGGTCATTTCGGTCAATCCAAGTTC
* * * * *
38687149 AAATCATTTTTAGTTTGGATTA-TTTCAAGTTCGGGTTATT
64 AAATAATTTCTGGTTTGGATCATTTTCAGGTTCGGGTTATT
38687189 AATTTTTTAT
Statistics
Matches: 188, Mismatches: 28, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
114 2 0.01
115 34 0.18
116 110 0.59
117 42 0.22
ACGTcount: A:0.22, C:0.15, G:0.22, T:0.41
Consensus pattern (116 bp):
GGTTTGAGTTCGAGTTAATCGGATTGAATTCTTGGTTAAGGTCATTTCGGTCAATCCAAGTTCAA
ATAATTTCTGGTTTGGATCATTTTCAGGTTCGGGTTATTGACTTTTCATCG
Found at i:38687092 original size:232 final size:226
Alignment explanation
Indices: 38686624--38687188 Score: 576
Period size: 232 Copynumber: 2.5 Consensus size: 226
38686614 AATCATTTCC
* * *
38686624 GGTTTGAGTTCAAGTTAAT--ATTGGATTCTCGTGTTCAGGTCAGTTTGGTCAATCCAAGTTCGA
1 GGTTTGAGTTC-AGTTAATGGATTGGATTCTTGTGTTCAGGTCAGTTCGGTCAATCCAAGTTCAA
* *
38686687 ATCATTTCTGATTTGGATCATTTTCAGGTTTGGGTTATTGGCTTTTTATGATCAATCAGGTTTGA
65 ATCATTTCTG-TTTGGATCATTTTCAGGTTCGGGTTATTGAC--TTTAT-ATCAATCAGGTTTGA
* ** * * *
38686752 GTTCAGGTTAATCGGATTGGATTCTAGAGTTCAGGTCAGTTTGGTCAATCCAAGTTCAAATCATT
126 GTTCAGGTTAATCAGATTCAATTCTAGAGCTAAGGTCAGTTTGGTCAATCCAAGTTCAAATCACT
* **
38686817 TCTGGTTTGGATCATTTTATCTTTTATGATCAATCA
191 TCTGGTTTGAATCATTTTATCGGTTATGATCAATCA
* *
38686853 GGTTTGAGTTCGAGTTAATCGGATTGAATTCTTGTGTTCAAGTCAGTTCGGTCAATCCAAGTTCA
1 GGTTTGAGTTC-AGTTAAT-GGATTGGATTCTTGTGTTCAGGTCAGTTCGGTCAATCCAAGTTCA
* * *
38686918 AATAATTTCTGGTTGGATCATTTTCAGGTTCGGGTTATTGAC-TT-T-TC-ATCGGGTTTGAGTT
64 AATCATTTCTGTTTGGATCATTTTCAGGTTCGGGTTATTGACTTTATATCAATCAGGTTTGAGTT
* * *
38686979 C-GAGTTAATCAGATTCAATTCTTGA-CTAAGGTCA-TTTCGGTCAATCCCAGTTCAAATTACTT
129 CAG-GTTAATCAGATTCAATTCTAGAGCTAAGGTCAGTTT-GGTCAATCCAAGTTCAAATCACTT
**
38687041 CTGGTTTGAATCATTTTCAGGTTCGGGTTATTGACTTTTTATC-
192 CTGGTTTGAATCATTTT-A---TC-GGTTA-TGA---TCAATCA
** * *
38687084 GAGTTTGAGTTCAGGCCAATTGGATTGGATTCTTGGGTTCAGGTCATTTCGGTCAATCCAAGTTC
1 G-GTTTGAGTTCA-GTTAA-TGGATTGGATTCTTGTGTTCAGGTCAGTTCGGTCAATCCAAGTTC
* * *
38687149 AAATCATTTTTAGTTTGGATTA-TTTCAAGTTCGGGTTATT
63 AAATCATTTCT-GTTTGGATCATTTTCAGGTTCGGGTTATT
38687189 AATTTTTTAT
Statistics
Matches: 282, Mismatches: 36, Indels: 33
0.80 0.10 0.09
Matches are distributed among these distances:
222 3 0.01
223 45 0.16
224 33 0.12
225 2 0.01
227 3 0.01
228 5 0.02
229 21 0.07
231 30 0.11
232 131 0.46
233 9 0.03
ACGTcount: A:0.22, C:0.14, G:0.22, T:0.41
Consensus pattern (226 bp):
GGTTTGAGTTCAGTTAATGGATTGGATTCTTGTGTTCAGGTCAGTTCGGTCAATCCAAGTTCAAA
TCATTTCTGTTTGGATCATTTTCAGGTTCGGGTTATTGACTTTATATCAATCAGGTTTGAGTTCA
GGTTAATCAGATTCAATTCTAGAGCTAAGGTCAGTTTGGTCAATCCAAGTTCAAATCACTTCTGG
TTTGAATCATTTTATCGGTTATGATCAATCA
Found at i:38691973 original size:6 final size:6
Alignment explanation
Indices: 38691952--38691987 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
38691942 TCCTCCACGC
* *
38691952 CCTCTA CCCCTA CCTCTC CCTCTA CCTCTA CCTCTA
1 CCTCTA CCTCTA CCTCTA CCTCTA CCTCTA CCTCTA
38691988 TTAGCTGATC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.14, C:0.56, G:0.00, T:0.31
Consensus pattern (6 bp):
CCTCTA
Found at i:38691974 original size:18 final size:18
Alignment explanation
Indices: 38691951--38691986 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
38691941 TTCCTCCACG
38691951 CCCTCTACCCCTACCTCT
1 CCCTCTACCCCTACCTCT
*
38691969 CCCTCTACCTCTACCTCT
1 CCCTCTACCCCTACCTCT
38691987 ATTAGCTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.58, G:0.00, T:0.31
Consensus pattern (18 bp):
CCCTCTACCCCTACCTCT
Found at i:38693415 original size:31 final size:32
Alignment explanation
Indices: 38693379--38693448 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 32
38693369 ATGATTATTA
** *
38693379 AACTATTTGAAAGT-TTTTATTTAAGTCGTTG
1 AACTATTCAAAAGTCTTTTATTTAAGTCATTG
38693410 AACTATTCAAAAGTCTTTTATTTAAGTCATTG
1 AACTATTCAAAAGTCTTTTATTTAAGTCATTG
*
38693442 GACTATT
1 AACTATT
38693449 AAGTTTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 12 0.35
32 22 0.65
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.46
Consensus pattern (32 bp):
AACTATTCAAAAGTCTTTTATTTAAGTCATTG
Found at i:38697071 original size:30 final size:30
Alignment explanation
Indices: 38696967--38697071 Score: 76
Period size: 30 Copynumber: 3.5 Consensus size: 30
38696957 TAATATAATT
* *
38696967 TTTGGTACTTGAACTTGATACTTTTTT-TAA
1 TTTGGTACCTAAACTTGATA-TTTTTTCTAA
* *
38696997 TTTGGTACCTAAA-TT--T-TTTTTGGACCCAA
1 TTTGGTACCTAAACTTGATATTTTT---TCTAA
* * *
38697026 TTTCGTATCTGAACTTGATATTTTTTCTAA
1 TTTGGTACCTAAACTTGATATTTTTTCTAA
38697056 TTTGGTACCTAAACTT
1 TTTGGTACCTAAACTT
38697072 TTTTTTAAAA
Statistics
Matches: 55, Mismatches: 12, Indels: 16
0.66 0.14 0.19
Matches are distributed among these distances:
25 5 0.09
27 1 0.02
29 14 0.25
30 29 0.53
32 1 0.02
33 5 0.09
ACGTcount: A:0.24, C:0.14, G:0.12, T:0.50
Consensus pattern (30 bp):
TTTGGTACCTAAACTTGATATTTTTTCTAA
Found at i:38703124 original size:20 final size:20
Alignment explanation
Indices: 38703099--38703138 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
38703089 TGTGGTTTAA
38703099 ACTTTAAAGTGAAAGACGGT
1 ACTTTAAAGTGAAAGACGGT
38703119 ACTTTAAAGTGAAAGACGGT
1 ACTTTAAAGTGAAAGACGGT
38703139 CATAAAGCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.25, T:0.25
Consensus pattern (20 bp):
ACTTTAAAGTGAAAGACGGT
Found at i:38703352 original size:15 final size:14
Alignment explanation
Indices: 38703334--38703375 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 14
38703324 GATCTTCCTC
38703334 TTCTTCCTCGTTCTT
1 TTCTTCCTC-TTCTT
38703349 TTCTTCCTCTTC--
1 TTCTTCCTCTTCTT
*
38703361 TTCTTCATCTTCTT
1 TTCTTCCTCTTCTT
38703375 T
1 T
38703376 GGGAGGATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
12 11 0.46
14 4 0.17
15 9 0.38
ACGTcount: A:0.02, C:0.33, G:0.02, T:0.62
Consensus pattern (14 bp):
TTCTTCCTCTTCTT
Found at i:38706987 original size:15 final size:16
Alignment explanation
Indices: 38706967--38706999 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
38706957 ATGTCGTCAT
38706967 TTGAAAT-TAAAAAAA
1 TTGAAATATAAAAAAA
*
38706982 TTGAAATATAAATAAA
1 TTGAAATATAAAAAAA
38706998 TT
1 TT
38707000 TTATTTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (16 bp):
TTGAAATATAAAAAAA
Found at i:38709796 original size:6 final size:6
Alignment explanation
Indices: 38709760--38709807 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 6
38709750 TATTTGAGAT
* * *
38709760 TTTTAA TATTTAA GTTTGA TTTTAA TGTTAA TTTTAA TATTTAA TTTT
1 TTTTAA T-TTTAA TTTTAA TTTTAA TTTTAA TTTTAA T-TTTAA TTTT
38709808 TTTAATTTGA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
6 23 0.68
7 11 0.32
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.62
Consensus pattern (6 bp):
TTTTAA
Found at i:38710376 original size:123 final size:125
Alignment explanation
Indices: 38710222--38710453 Score: 310
Period size: 124 Copynumber: 1.9 Consensus size: 125
38710212 TTTGTGATTC
* ** *
38710222 TATGGCATTTTTAAGAAGATTACTTGTTTAAAATTGGAAATTAAGGAAGTTAATTTCTCTTT-TC
1 TATGGCATTTTCAAGAAGATTACTTGTTTAAAATTGGAAACAAAGGAAGTTAATTGCTCTTTGT-
38710286 TTT-GATTTCATGGAAAACCCAAATTGACTTCA-TATATGAAAGCCGCAATAGGTATGGGCT
65 TTTAGATTTCATGGAAAACCCAAATTGACTT-ATTATATGAAAGCCGCAATAGGTATGGGCT
* * *
38710346 TATGGCATTTTCACG-AGATTTCTTGTTTAAAATTGGAGACAAAGGAAGTTAATTGCTCTTTGTT
1 TATGGCATTTTCAAGAAGATTACTTGTTTAAAATTGGAAACAAAGGAAGTTAATTGCTCTTTGTT
* *** *
38710410 TTAGCTTTCATGGAAATTTCAAATTGACTTATTATTTGAAAGCC
66 TTAGATTTCATGGAAAACCCAAATTGACTTATTATATGAAAGCC
38710454 TCATTAGCTC
Statistics
Matches: 93, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
123 45 0.48
124 48 0.52
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.39
Consensus pattern (125 bp):
TATGGCATTTTCAAGAAGATTACTTGTTTAAAATTGGAAACAAAGGAAGTTAATTGCTCTTTGTT
TTAGATTTCATGGAAAACCCAAATTGACTTATTATATGAAAGCCGCAATAGGTATGGGCT
Found at i:38714249 original size:41 final size:41
Alignment explanation
Indices: 38714187--38714268 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
38714177 CATATGGCAA
* *
38714187 ATATTGTATAATTGTTCGGTTTTCTGCAATTTTTTCCATTC
1 ATATTGTATAATTGTTAGGTTTTCCGCAATTTTTTCCATTC
*
38714228 ATATTGTATAATTGTTAGGTTTTCCGTAATTTTTTCCATTC
1 ATATTGTATAATTGTTAGGTTTTCCGCAATTTTTTCCATTC
38714269 TTCTGTGTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.21, C:0.13, G:0.12, T:0.54
Consensus pattern (41 bp):
ATATTGTATAATTGTTAGGTTTTCCGCAATTTTTTCCATTC
Found at i:38716960 original size:22 final size:23
Alignment explanation
Indices: 38716918--38716961 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
38716908 AATTATTTTA
38716918 TTTGATAATACTAAATTTTAATT
1 TTTGATAATACTAAATTTTAATT
* *
38716941 TTTGATATTACT-TATTTTAAT
1 TTTGATAATACTAAATTTTAAT
38716962 GTGAATAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.57
Consensus pattern (23 bp):
TTTGATAATACTAAATTTTAATT
Found at i:38718512 original size:28 final size:27
Alignment explanation
Indices: 38718472--38718525 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 27
38718462 AACTTGACAC
*
38718472 TTTTTCTTAATTTGGTACTTAAACTTT
1 TTTTTCTTAATTTGGTACTCAAACTTT
*
38718499 TTTTTGTTCAATTTGGTACTCAAACTT
1 TTTTTCTT-AATTTGGTACTCAAACTT
38718526 GACACTGTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 7 0.29
28 17 0.71
ACGTcount: A:0.22, C:0.13, G:0.09, T:0.56
Consensus pattern (27 bp):
TTTTTCTTAATTTGGTACTCAAACTTT
Found at i:38718855 original size:31 final size:30
Alignment explanation
Indices: 38718814--38718927 Score: 90
Period size: 31 Copynumber: 3.8 Consensus size: 30
38718804 TAAAAAAAAC
38718814 TTAGGTACCAAATTAGGAAAAAATGCCAAGT
1 TTAGGTACCAAATTAGGAAAAAATG-CAAGT
* * **
38718845 TTGGGTACCAAATTGGGTCCAAAA---AAGT
1 TTAGGTACCAAATTAGG-AAAAAATGCAAGT
*
38718873 TTAGGTACCAAATTAAGAAAAAATGTCAAGT
1 TTAGGTACCAAATTAGGAAAAAATG-CAAGT
* * * *
38718904 TCAAGCACCAAATTGGGTAAAAAA
1 TTAGGTACCAAATTAGG-AAAAAA
38718928 AAATTAGGTA
Statistics
Matches: 63, Mismatches: 14, Indels: 11
0.72 0.16 0.12
Matches are distributed among these distances:
27 4 0.06
28 18 0.29
31 31 0.49
32 10 0.16
ACGTcount: A:0.45, C:0.13, G:0.19, T:0.23
Consensus pattern (30 bp):
TTAGGTACCAAATTAGGAAAAAATGCAAGT
Found at i:38718937 original size:58 final size:58
Alignment explanation
Indices: 38718804--38718973 Score: 207
Period size: 59 Copynumber: 2.9 Consensus size: 58
38718794 AAATTGAATC
* * * **
38718804 TAAAAAAAACTTAGGTACCAAATTAGGAAAAAATGCCAAGTTTGGGTACCAAATTGGG
1 TAAAAAAAAATTAGGTACCAAATTAAGAAAAAATGTCAAGTTCAGGTACCAAATTGGG
* ** * *
38718862 TCCAAAAAAGTTTAGGTACCAAATTAAGAAAAAATGTCAAGTTCAAGCACCAAATTGGG
1 T-AAAAAAAAATTAGGTACCAAATTAAGAAAAAATGTCAAGTTCAGGTACCAAATTGGG
* * *
38718921 TAAAAAAAAATTAGGTACTAAATTAA-AAAAAGTATCAAGTTCAGGTACCAAAT
1 TAAAAAAAAATTAGGTACCAAATTAAGAAAAAATGTCAAGTTCAGGTACCAAAT
38718974 GTTATATTAA
Statistics
Matches: 94, Mismatches: 17, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
57 23 0.24
58 22 0.23
59 49 0.52
ACGTcount: A:0.48, C:0.12, G:0.16, T:0.23
Consensus pattern (58 bp):
TAAAAAAAAATTAGGTACCAAATTAAGAAAAAATGTCAAGTTCAGGTACCAAATTGGG
Found at i:38719250 original size:6 final size:6
Alignment explanation
Indices: 38719239--38719263 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
38719229 GGTTTTGAAT
38719239 TTTAAA TTTAAA TTTAAA TTTAAA T
1 TTTAAA TTTAAA TTTAAA TTTAAA T
38719264 AAAGTTTAAA
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):
TTTAAA
Found at i:38721729 original size:15 final size:12
Alignment explanation
Indices: 38721695--38721719 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
38721685 CCAGTAGTAA
38721695 CCCCTTCTGCTG
1 CCCCTTCTGCTG
38721707 CCCCTTCTGCTG
1 CCCCTTCTGCTG
38721719 C
1 C
38721720 TCCGTCTTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.52, G:0.16, T:0.32
Consensus pattern (12 bp):
CCCCTTCTGCTG
Found at i:38723688 original size:26 final size:28
Alignment explanation
Indices: 38723642--38723697 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 28
38723632 TCAATTTGTG
*
38723642 TTTTAAAATTTTCAAAGTCATTTC-AAA
1 TTTTAAAATTCTCAAAGTCATTTCTAAA
38723669 TTTTAAAATTCTCAAA-TCATTTCTAAA
1 TTTTAAAATTCTCAAAGTCATTTCTAAA
38723696 TT
1 TT
38723698 CGAATCATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 7 0.26
27 20 0.74
ACGTcount: A:0.39, C:0.12, G:0.02, T:0.46
Consensus pattern (28 bp):
TTTTAAAATTCTCAAAGTCATTTCTAAA
Found at i:38726150 original size:29 final size:29
Alignment explanation
Indices: 38726117--38726172 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
38726107 TTTAGTGACC
* *
38726117 GGATCAAATTAATCCCTTTATTATTAAAT
1 GGATCAAATTAATCCCTATACTATTAAAT
* *
38726146 GGATCAATTTAATTCCTATACTATTAA
1 GGATCAAATTAATCCCTATACTATTAA
38726173 GAAAAATCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (29 bp):
GGATCAAATTAATCCCTATACTATTAAAT
Found at i:38731821 original size:17 final size:17
Alignment explanation
Indices: 38731785--38731823 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
38731775 TAAATAAATT
*
38731785 ATTATATGAAAAATATA
1 ATTATATGAAAAATAAA
38731802 ATTATAT-AAAAATTAAA
1 ATTATATGAAAAA-TAAA
38731819 ATTAT
1 ATTAT
38731824 TTATTTTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
ATTATATGAAAAATAAA
Found at i:38733226 original size:12 final size:12
Alignment explanation
Indices: 38733209--38733238 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
38733199 AACGAATCAT
38733209 GATGATCATGAC
1 GATGATCATGAC
*
38733221 GATGATCATGAT
1 GATGATCATGAC
38733233 GATGAT
1 GATGAT
38733239 GATAATAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.27, T:0.30
Consensus pattern (12 bp):
GATGATCATGAC
Found at i:38738300 original size:12 final size:12
Alignment explanation
Indices: 38738285--38738310 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
38738275 CTAGGGGGCT
38738285 GACAAGGGCCCC
1 GACAAGGGCCCC
38738297 GACAAGGGCCCC
1 GACAAGGGCCCC
38738309 GA
1 GA
38738311 TCTCCCTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.38, G:0.35, T:0.00
Consensus pattern (12 bp):
GACAAGGGCCCC
Found at i:38740404 original size:25 final size:26
Alignment explanation
Indices: 38740369--38740417 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
38740359 TACTATGTTG
* *
38740369 TATATTTTAAATAAACTTA-AAAATA
1 TATATTGTAAATAAAATTAGAAAATA
38740394 TATATTGTAAATAAAATTAGAAAA
1 TATATTGTAAATAAAATTAGAAAA
38740418 AAAGAAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (26 bp):
TATATTGTAAATAAAATTAGAAAATA
Found at i:38740912 original size:14 final size:14
Alignment explanation
Indices: 38740882--38740912 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
38740872 CCGCTTATAG
*
38740882 AAACGCAGGAAATA
1 AAACGCAGGAAAAA
38740896 AAACGCAGGAAAAA
1 AAACGCAGGAAAAA
38740910 AAA
1 AAA
38740913 AAAAAACTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.65, C:0.13, G:0.19, T:0.03
Consensus pattern (14 bp):
AAACGCAGGAAAAA
Found at i:38746578 original size:104 final size:104
Alignment explanation
Indices: 38746391--38746605 Score: 360
Period size: 104 Copynumber: 2.1 Consensus size: 104
38746381 TAGTTTCTCA
*
38746391 TTTGTAATTTGATATAATGTCATTGCAAAGTTCATCCTCAACCTATTATTTGATTCTGAATATTG
1 TTTGAAATTTGATATAATGTCATTGCAAAGTTCATCCTCAACCTATTATTTGATTCTGAATATTG
*
38746456 TTTAGGAACCATTGTTTCATGGAAAATGTCTTTCGCATT
66 TTTAGGAACCATTGTTTCATGGAAAATGTCTTTCACATT
*
38746495 TTTGAAATTTGATATAATGTCATTGCAAAGTTCATCCTCAATCTATTATTTGATTCCT-AATATT
1 TTTGAAATTTGATATAATGTCATTGCAAAGTTCATCCTCAACCTATTATTTGATT-CTGAATATT
* * *
38746559 TTTTAGGAACCATTTTTTCATGGAAAATGTTTTTCACATT
65 GTTTAGGAACCATTGTTTCATGGAAAATGTCTTTCACATT
38746599 TTTGAAA
1 TTTGAAA
38746606 GCATTAGATA
Statistics
Matches: 104, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
104 102 0.98
105 2 0.02
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.45
Consensus pattern (104 bp):
TTTGAAATTTGATATAATGTCATTGCAAAGTTCATCCTCAACCTATTATTTGATTCTGAATATTG
TTTAGGAACCATTGTTTCATGGAAAATGTCTTTCACATT
Found at i:38748321 original size:23 final size:21
Alignment explanation
Indices: 38748283--38748341 Score: 64
Period size: 23 Copynumber: 2.7 Consensus size: 21
38748273 GCTTCTGGGC
* *
38748283 TTTCTTTGTTTCTGTTTCTAT
1 TTTCTTTGTTTATGTTTCAAT
38748304 TTTCTTTTGTTTGATGTTTCAAT
1 TTTC-TTTGTTT-ATGTTTCAAT
*
38748327 TTTGCTTGGTTTATG
1 TTT-CTTTGTTTATG
38748342 GGCCCTTGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
21 4 0.12
22 10 0.31
23 17 0.53
24 1 0.03
ACGTcount: A:0.08, C:0.10, G:0.15, T:0.66
Consensus pattern (21 bp):
TTTCTTTGTTTATGTTTCAAT
Found at i:38751247 original size:11 final size:12
Alignment explanation
Indices: 38751219--38751246 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
38751209 CGAGGAAAAG
38751219 AAAAACAATACA
1 AAAAACAATACA
38751231 AAAAACAATACA
1 AAAAACAATACA
38751243 AAAA
1 AAAA
38751247 CCAAACGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.79, C:0.14, G:0.00, T:0.07
Consensus pattern (12 bp):
AAAAACAATACA
Found at i:38756561 original size:27 final size:26
Alignment explanation
Indices: 38756530--38756590 Score: 68
Period size: 28 Copynumber: 2.3 Consensus size: 26
38756520 AGTAATTATC
*
38756530 TAAAAAAATTGAAAGAAAAAGAACAA
1 TAAAAAAATTGAAAGAAAAAAAACAA
***
38756556 TTAAAATCTTTTGAAAGAAAAAAAACAA
1 -TAAAA-AAATTGAAAGAAAAAAAACAA
38756584 TAAAAAA
1 TAAAAAA
38756591 CTTAAATTTA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
27 10 0.37
28 17 0.63
ACGTcount: A:0.69, C:0.05, G:0.08, T:0.18
Consensus pattern (26 bp):
TAAAAAAATTGAAAGAAAAAAAACAA
Found at i:38760600 original size:205 final size:205
Alignment explanation
Indices: 38760230--38760767 Score: 636
Period size: 205 Copynumber: 2.6 Consensus size: 205
38760220 AAGAACAGAG
* * * * *
38760230 ACAAGTTTTTAAACATTCAACACACCATATTCCAATGCATAGATGACAATCAAAGATGGATATAG
1 ACAAGTTCTTAAACATTCAAGACACCATATTCCAATACATAGATGACAATCAAAGATGAATACAG
* * * *
38760295 ATAAAAATCCAAGAGCGAAAACAAGATTTTAAGCATTCAACACACCATATTTCAATGCATTGATC
66 ATAAAAATCCAAGAGCAAAAACAAGATTTTAAACATTCAACACACCATATTTCAATACATAGATC
* * * * *
38760360 TAGTATGCAAAAATTATAACAAATAATTTAATAAGTCGACGAACAAAAATGAACATAGATCCAAA
131 TAGTATGCAAAAATTAGAACAAATAATTAAATAAGTCGACAAACAAAAACGAACATAGACCCAAA
38760425 TTC-AAAACAA
196 TTCAAAAAC-A
* * * *
38760435 ACAAGTTCTTAAACATTCAAGACACTATAGTT-CGATACATAGATGACAAACAAAGATGAATGCA
1 ACAAGTTCTTAAACATTCAAGACACCATA-TTCCAATACATAGATGACAATCAAAGATGAATACA
* * *** *
38760499 GGA-CAAAATCCACGAGCAAAAATGTGATTTTAAACATTCAACACACCATATTTCGATACATAGA
65 -GATAAAAATCCAAGAGCAAAAACAAGATTTTAAACATTCAACACACCATATTTCAATACATAGA
* * * *
38760563 TCTAGTATGCAAAATTTAGAACACATAATTAAATAAGTCGACAAACAAAGACGAATATAGACCCA
129 TCTAGTATGCAAAAATTAGAACAAATAATTAAATAAGTCGACAAACAAAAACGAACATAGACCCA
38760628 AATTCAAAAACA
194 AATTCAAAAACA
* *
38760640 AGAAGTTCTTAAACATTCAAGACACCATATTCCAATACATAGATGACAATCAAAGATGAAAACTA
1 ACAAGTTCTTAAACATTCAAGACACCATATTCCAATACATAGATGACAATCAAAGATGAATAC-A
* * * * ** *
38760705 -ATCAAAATCCAAGAACTACAATAACAAG-TTCTAAAACACTCAACATGCCATATTACAATACAT
65 GATAAAAATCCAAGAGC-A-AA-AACAAGATT-TTAAACATTCAACACACCATATTTCAATACAT
38760768 TCAAAACCAA
Statistics
Matches: 278, Mismatches: 45, Indels: 17
0.82 0.13 0.05
Matches are distributed among these distances:
204 3 0.01
205 231 0.83
206 11 0.04
207 4 0.01
208 29 0.10
ACGTcount: A:0.48, C:0.18, G:0.11, T:0.23
Consensus pattern (205 bp):
ACAAGTTCTTAAACATTCAAGACACCATATTCCAATACATAGATGACAATCAAAGATGAATACAG
ATAAAAATCCAAGAGCAAAAACAAGATTTTAAACATTCAACACACCATATTTCAATACATAGATC
TAGTATGCAAAAATTAGAACAAATAATTAAATAAGTCGACAAACAAAAACGAACATAGACCCAAA
TTCAAAAACA
Found at i:38760812 original size:61 final size:64
Alignment explanation
Indices: 38760738--38760864 Score: 161
Period size: 64 Copynumber: 2.0 Consensus size: 64
38760728 ACAAGTTCTA
* * *
38760738 AAACACTCAACAT-GCCATATTACAATACATT-CAAAACCAATTCAGAAATGG-CTTGAAACCC
1 AAACACTCAACATGGACATAGTACAATACATTAAAAAACCAATTCAGAAATGGACTTGAAACCC
* * * *
38760799 AAACACTCAACATGGAGATAGTACAATACATTAAAAAAAGCAATTTAGAAATGGATTTGAAACCC
1 AAACACTCAACATGGACATAGTACAATACATT-AAAAAACCAATTCAGAAATGGACTTGAAACCC
38760864 A
1 A
38760865 CTTGTGGTTC
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
61 13 0.24
62 15 0.27
64 17 0.31
65 10 0.18
ACGTcount: A:0.47, C:0.20, G:0.11, T:0.21
Consensus pattern (64 bp):
AAACACTCAACATGGACATAGTACAATACATTAAAAAACCAATTCAGAAATGGACTTGAAACCC
Found at i:38761464 original size:21 final size:20
Alignment explanation
Indices: 38761438--38761476 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
38761428 CCTTGCCTTG
38761438 TCTTTTTTATTTTTATTTTTA
1 TCTTTTTT-TTTTTATTTTTA
*
38761459 TCTTTTTTTTTTTGTTTT
1 TCTTTTTTTTTTTATTTT
38761477 AAGGTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.08, C:0.05, G:0.03, T:0.85
Consensus pattern (20 bp):
TCTTTTTTTTTTTATTTTTA
Found at i:38761589 original size:30 final size:30
Alignment explanation
Indices: 38761555--38761621 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
38761545 ATTACAAAAT
* * *
38761555 AGTCATTAAATTATTCAAAAATTTTATTTA
1 AGTCACTAAACTATTCAAAAACTTTATTTA
* *
38761585 AGTCACTGAACTATTCAAAAGCTTTATTTA
1 AGTCACTAAACTATTCAAAAACTTTATTTA
38761615 AGTCACT
1 AGTCACT
38761622 GCACTGTTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.39, C:0.13, G:0.07, T:0.40
Consensus pattern (30 bp):
AGTCACTAAACTATTCAAAAACTTTATTTA
Found at i:38761622 original size:30 final size:30
Alignment explanation
Indices: 38761566--38761622 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
38761556 GTCATTAAAT
*
38761566 TATTCAAAAATTTTATTTAAGTCACTGAAC
1 TATTCAAAAACTTTATTTAAGTCACTGAAC
*
38761596 TATTCAAAAGCTTTATTTAAGTCACTG
1 TATTCAAAAACTTTATTTAAGTCACTG
38761623 CACTGTTAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (30 bp):
TATTCAAAAACTTTATTTAAGTCACTGAAC
Found at i:38762530 original size:29 final size:31
Alignment explanation
Indices: 38762469--38762531 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
38762459 TCAAATTTTG
***
38762469 ATTTTTTTTATAAATATATATATATTTGGTA
1 ATTTTTTTTATAAATATATATATATTACATA
*
38762500 ATTTTTTTTATAAATATAT-TA-GTTACATA
1 ATTTTTTTTATAAATATATATATATTACATA
38762529 ATT
1 ATT
38762532 ATGTTTTCAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 7 0.25
30 2 0.07
31 19 0.68
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.57
Consensus pattern (31 bp):
ATTTTTTTTATAAATATATATATATTACATA
Found at i:38764204 original size:15 final size:16
Alignment explanation
Indices: 38764169--38764223 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 16
38764159 GACGACGGTG
38764169 ATAAGAAGAGTAAAA-A
1 ATAAGAAGAG-AAAAGA
38764185 A-AAGAA-AGAAAAGA
1 ATAAGAAGAGAAAAGA
*
38764199 ATAAGAAGGAGAAGAAGG
1 ATAAGAA-GAGAA-AAGA
38764217 ATAAGAA
1 ATAAGAA
38764224 AAAGAATAGC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
13 4 0.12
14 4 0.12
15 10 0.30
16 1 0.03
17 4 0.12
18 10 0.30
ACGTcount: A:0.67, C:0.00, G:0.25, T:0.07
Consensus pattern (16 bp):
ATAAGAAGAGAAAAGA
Found at i:38764213 original size:24 final size:24
Alignment explanation
Indices: 38764186--38764248 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 24
38764176 GAGTAAAAAA
*
38764186 AAGAAAGAAAAGAATAAGAAGGAG-
1 AAGAAAGAAAAGAAAAAGAA-GAGC
* * *
38764210 AAGAAGGATAAGAAAAAGAATAGC
1 AAGAAAGAAAAGAAAAAGAAGAGC
38764234 AAGAAAGAAAA-AAAA
1 AAGAAAGAAAAGAAAA
38764249 TACGATGAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
23 6 0.19
24 26 0.81
ACGTcount: A:0.70, C:0.02, G:0.24, T:0.05
Consensus pattern (24 bp):
AAGAAAGAAAAGAAAAAGAAGAGC
Found at i:38767007 original size:58 final size:58
Alignment explanation
Indices: 38766943--38767059 Score: 225
Period size: 58 Copynumber: 2.0 Consensus size: 58
38766933 CGAATTGATT
*
38766943 TGTATTAATTTAATCTATTTAATCTCTATTTAATGAAAAAAATCAAAGTTTCACTACA
1 TGTATTAATTTAATCTATTTAATCTCTATTAAATGAAAAAAATCAAAGTTTCACTACA
38767001 TGTATTAATTTAATCTATTTAATCTCTATTAAATGAAAAAAATCAAAGTTTCACTACA
1 TGTATTAATTTAATCTATTTAATCTCTATTAAATGAAAAAAATCAAAGTTTCACTACA
38767059 T
1 T
38767060 ATGAACCACA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.42, C:0.12, G:0.05, T:0.41
Consensus pattern (58 bp):
TGTATTAATTTAATCTATTTAATCTCTATTAAATGAAAAAAATCAAAGTTTCACTACA
Found at i:38768135 original size:15 final size:15
Alignment explanation
Indices: 38768100--38768175 Score: 50
Period size: 15 Copynumber: 4.9 Consensus size: 15
38768090 GACAACGGTG
38768100 ATAAGAAGAGTAAAA-A
1 ATAAGAA-AG-AAAAGA
38768116 A-AAGAAAGAAAAGA
1 ATAAGAAAGAAAAGA
*
38768130 ATAAGAAGGAGAAGAAGG
1 ATAAGAA--AGAA-AAGA
38768148 ATAAGAAA-AAGAAGA
1 ATAAGAAAGAA-AAGA
**
38768163 GCAAGAAAGAAAA
1 ATAAGAAAGAAAA
38768176 AAAATACGAT
Statistics
Matches: 50, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
13 4 0.08
14 4 0.08
15 24 0.48
16 4 0.08
17 4 0.08
18 10 0.20
ACGTcount: A:0.68, C:0.01, G:0.25, T:0.05
Consensus pattern (15 bp):
ATAAGAAAGAAAAGA
Found at i:38768144 original size:24 final size:24
Alignment explanation
Indices: 38768117--38768179 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 24
38768107 GAGTAAAAAA
*
38768117 AAGAAAGAAAAGAATAAGAAGGAG-
1 AAGAAAGAAAAGAAAAAGAA-GAGC
* *
38768141 AAGAAGGATAAGAAAAAGAAGAGC
1 AAGAAAGAAAAGAAAAAGAAGAGC
38768165 AAGAAAGAAAA-AAAA
1 AAGAAAGAAAAGAAAA
38768180 TACGATGAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
23 7 0.21
24 26 0.79
ACGTcount: A:0.70, C:0.02, G:0.25, T:0.03
Consensus pattern (24 bp):
AAGAAAGAAAAGAAAAAGAAGAGC
Found at i:38768160 original size:18 final size:18
Alignment explanation
Indices: 38768120--38768162 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
38768110 TAAAAAAAAG
38768120 AAAGAA-AAGAATAAGAA
1 AAAGAAGAAGAATAAGAA
** *
38768137 GGAGAAGAAGGATAAGAA
1 AAAGAAGAAGAATAAGAA
38768155 AAAGAAGA
1 AAAGAAGA
38768163 GCAAGAAAGA
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.67, C:0.00, G:0.28, T:0.05
Consensus pattern (18 bp):
AAAGAAGAAGAATAAGAA
Found at i:38773357 original size:24 final size:23
Alignment explanation
Indices: 38773330--38773395 Score: 69
Period size: 24 Copynumber: 2.8 Consensus size: 23
38773320 AAGAGTAAAA
*
38773330 AGAATAAAGAAAAGAATAAGAAGG
1 AGAAGAAAGAAAAGAATAAGAA-G
* * *
38773354 AGAAGAAGGATAAGAAAAAGAAG
1 AGAAGAAAGAAAAGAATAAGAAG
*
38773377 AGCAAGAAAGAAAAAAATA
1 AG-AAGAAAGAAAAGAATA
38773396 CGATGAAAGT
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
23 3 0.09
24 30 0.91
ACGTcount: A:0.68, C:0.02, G:0.24, T:0.06
Consensus pattern (23 bp):
AGAAGAAAGAAAAGAATAAGAAG
Found at i:38773375 original size:18 final size:18
Alignment explanation
Indices: 38773329--38773377 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
38773319 GAAGAGTAAA
38773329 AAGAATAAAGAA-AAGAAT
1 AAGAA-AAAGAAGAAGAAT
** *
38773347 AAGAAGGAGAAGAAGGAT
1 AAGAAAAAGAAGAAGAAT
38773365 AAGAAAAAGAAGA
1 AAGAAAAAGAAGA
38773378 GCAAGAAAGA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
17 4 0.16
18 21 0.84
ACGTcount: A:0.67, C:0.00, G:0.27, T:0.06
Consensus pattern (18 bp):
AAGAAAAAGAAGAAGAAT
Found at i:38775631 original size:22 final size:21
Alignment explanation
Indices: 38775594--38775634 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
38775584 ATTTTTTAAA
38775594 ATATAATATAATTATAAAAAT
1 ATATAATATAATTATAAAAAT
38775615 ATATGAATATTAA-TATAAAA
1 ATAT-AATA-TAATTATAAAA
38775635 TTATTTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.22
22 11 0.61
23 3 0.17
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (21 bp):
ATATAATATAATTATAAAAAT
Found at i:38775841 original size:19 final size:19
Alignment explanation
Indices: 38775817--38775855 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
38775807 TATGCTCCCT
38775817 AAATTTA-GGAATCAGTTTA
1 AAATTTATGGAAT-AGTTTA
*
38775836 AAATTTATGTAATAGTTTA
1 AAATTTATGGAATAGTTTA
38775855 A
1 A
38775856 TTACATTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.44, C:0.03, G:0.13, T:0.41
Consensus pattern (19 bp):
AAATTTATGGAATAGTTTA
Found at i:38776031 original size:53 final size:53
Alignment explanation
Indices: 38775948--38776054 Score: 169
Period size: 53 Copynumber: 2.0 Consensus size: 53
38775938 TGGATTAAAG
* * ** *
38775948 TTGTTCATGGGCTAGGTCGAGGCTCGAATTAGAAATGAAATTTCAAGTTCGGC
1 TTGTTCATGGGCTAGATCGAGGCTCAAATTAGAAAAAAAAATTCAAGTTCGGC
38776001 TTGTTCATGGGCTAGATCGAGGCTCAAATTAGAAAAAAAAATTCAAGTTCGGC
1 TTGTTCATGGGCTAGATCGAGGCTCAAATTAGAAAAAAAAATTCAAGTTCGGC
38776054 T
1 T
38776055 CGCCCTATCC
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (53 bp):
TTGTTCATGGGCTAGATCGAGGCTCAAATTAGAAAAAAAAATTCAAGTTCGGC
Found at i:38785312 original size:8 final size:8
Alignment explanation
Indices: 38785301--38785325 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
38785291 TTAATTAATG
38785301 ATATTTAA
1 ATATTTAA
38785309 ATATTTAA
1 ATATTTAA
38785317 ATATTTAA
1 ATATTTAA
38785325 A
1 A
38785326 AGAGAGTGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
ATATTTAA
Found at i:38797908 original size:26 final size:26
Alignment explanation
Indices: 38797860--38797911 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
38797850 ATAATTTTTA
* *
38797860 GAGATTAAATTAAAATTTTACTATTT
1 GAGATTAAATTAAAACTTCACTATTT
**
38797886 GAGATTAAATTGTAACTTCACTATTT
1 GAGATTAAATTAAAACTTCACTATTT
38797912 ACTATCATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.44
Consensus pattern (26 bp):
GAGATTAAATTAAAACTTCACTATTT
Found at i:38801568 original size:16 final size:16
Alignment explanation
Indices: 38801547--38801580 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
38801537 AAAATAATTT
38801547 AAATTTAATTAAATGA
1 AAATTTAATTAAATGA
*
38801563 AAATTTAATTCAATGA
1 AAATTTAATTAAATGA
38801579 AA
1 AA
38801581 CCACACTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.35
Consensus pattern (16 bp):
AAATTTAATTAAATGA
Found at i:38802451 original size:12 final size:12
Alignment explanation
Indices: 38802434--38802458 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
38802424 AATCGTAAAA
38802434 ATAAAATTTAAT
1 ATAAAATTTAAT
38802446 ATAAAATTTAAT
1 ATAAAATTTAAT
38802458 A
1 A
38802459 AATTAAGATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
ATAAAATTTAAT
Found at i:38803997 original size:21 final size:24
Alignment explanation
Indices: 38803959--38804004 Score: 62
Period size: 21 Copynumber: 2.0 Consensus size: 24
38803949 AAAGATATAT
*
38803959 ATAATTATTAAATATTAAATAAAA
1 ATAATTATTAAATATTAAAAAAAA
38803983 ATAATTA-T-AAT-TTAAAAAAAA
1 ATAATTATTAAATATTAAAAAAAA
38804004 A
1 A
38804005 AAAATTGTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 10 0.48
22 3 0.14
23 1 0.05
24 7 0.33
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (24 bp):
ATAATTATTAAATATTAAAAAAAA
Found at i:38805403 original size:22 final size:22
Alignment explanation
Indices: 38805349--38805403 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
38805339 ATTATAATAG
*
38805349 AGTTAACATTTAATGTTTAAAA
1 AGTTAATATTTAATGTTTAAAA
** *
38805371 AAAT-ATAATTTATTGTTTAAAA
1 AGTTAAT-ATTTAATGTTTAAAA
38805393 AGTTAATATTT
1 AGTTAATATTT
38805404 TGAAGTTTTA
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
21 1 0.04
22 22 0.88
23 2 0.08
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (22 bp):
AGTTAATATTTAATGTTTAAAA
Found at i:38814262 original size:24 final size:24
Alignment explanation
Indices: 38814235--38814292 Score: 82
Period size: 24 Copynumber: 2.4 Consensus size: 24
38814225 GAGAATGTAT
38814235 GTTTATGCTCG-TCAGCCACTATAC
1 GTTTATGCTCGCT-AGCCACTATAC
38814259 GTTTATGCTCGCTAGCCACTATAC
1 GTTTATGCTCGCTAGCCACTATAC
* *
38814283 CTCTATGCTC
1 GTTTATGCTC
38814293 ACGAATTAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
24 30 0.97
25 1 0.03
ACGTcount: A:0.19, C:0.31, G:0.16, T:0.34
Consensus pattern (24 bp):
GTTTATGCTCGCTAGCCACTATAC
Found at i:38816599 original size:8 final size:8
Alignment explanation
Indices: 38816586--38816610 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
38816576 CCACTCTCTT
38816586 TTTAAATA
1 TTTAAATA
38816594 TTTAAATA
1 TTTAAATA
38816602 TTTAAATA
1 TTTAAATA
38816610 T
1 T
38816611 CATTAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
TTTAAATA
Found at i:38818571 original size:17 final size:17
Alignment explanation
Indices: 38818544--38818595 Score: 77
Period size: 17 Copynumber: 3.1 Consensus size: 17
38818534 GACCCAACTG
*
38818544 AATTTAAATTTATTTTA
1 AATTTAAATTTATTTAA
* *
38818561 AGTTTATATTTATTTAA
1 AATTTAAATTTATTTAA
38818578 AATTTAAATTTATTTAA
1 AATTTAAATTTATTTAA
38818595 A
1 A
38818596 TTAATAATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
AATTTAAATTTATTTAA
Found at i:38824178 original size:11 final size:11
Alignment explanation
Indices: 38824162--38824205 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
38824152 TCAACGTGTT
*
38824162 AAAAAAAGAGA
1 AAAAAAAAAGA
38824173 AAAAAAAAAGA
1 AAAAAAAAAGA
* *
38824184 AAAACAAAACA
1 AAAAAAAAAGA
38824195 AATAAAAAAAG
1 AA-AAAAAAAG
38824206 GCCAAGATAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
11 21 0.78
12 6 0.22
ACGTcount: A:0.84, C:0.05, G:0.09, T:0.02
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:38826777 original size:25 final size:25
Alignment explanation
Indices: 38826749--38826800 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
38826739 ATTTTATTTA
38826749 AATATAAA-TATAAAATT-TGAAACTC
1 AATATAAACT-TAAAATTAT-AAACTC
38826774 AATATAAACTTAAAATTATAAACTC
1 AATATAAACTTAAAATTATAAACTC
38826799 AA
1 AA
38826801 ACTTCAACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 23 0.92
26 2 0.08
ACGTcount: A:0.58, C:0.10, G:0.02, T:0.31
Consensus pattern (25 bp):
AATATAAACTTAAAATTATAAACTC
Found at i:38827062 original size:18 final size:18
Alignment explanation
Indices: 38827039--38827089 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
38827029 TAAAAAAATA
38827039 ATAATAAAATTAAATATT
1 ATAATAAAATTAAATATT
* *
38827057 ATAATAATATTGTAATA-T
1 ATAATAAAATT-AAATATT
38827075 A-AA-AAAATTAAATAT
1 ATAATAAAATTAAATAT
38827090 ATTATATTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
15 4 0.15
16 5 0.19
17 2 0.07
18 12 0.44
19 4 0.15
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (18 bp):
ATAATAAAATTAAATATT
Found at i:38830351 original size:19 final size:19
Alignment explanation
Indices: 38830302--38830353 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
38830292 GAAAGAAAAT
38830302 AAAGAGAGAAA-AGAAAAGG
1 AAAGAGAGAAATA-AAAAGG
**
38830321 AAAG-TTGAAATAAAAAGG
1 AAAGAGAGAAATAAAAAGG
38830339 AAAGAGAGAAATAAA
1 AAAGAGAGAAATAAA
38830354 TAATTAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
18 14 0.52
19 13 0.48
ACGTcount: A:0.67, C:0.00, G:0.25, T:0.08
Consensus pattern (19 bp):
AAAGAGAGAAATAAAAAGG
Found at i:38841523 original size:3 final size:3
Alignment explanation
Indices: 38841515--38841551 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
38841505 ACACGTGTTT
38841515 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
38841552 TACTATTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:38842878 original size:22 final size:23
Alignment explanation
Indices: 38842853--38842895 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
38842843 AACTTTCAAG
38842853 AATCTACAAT-AATATCAATTCT
1 AATCTACAATAAATATCAATTCT
*
38842875 AATCTACAATAAATATTAATT
1 AATCTACAATAAATATCAATT
38842896 AAAGGAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (23 bp):
AATCTACAATAAATATCAATTCT
Found at i:38850116 original size:16 final size:16
Alignment explanation
Indices: 38850097--38850138 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
38850087 ATCATTTTAG
38850097 GTTTATATAATTTTGA
1 GTTTATATAATTTTGA
* *
38850113 GTTTAAATTATTTTGA
1 GTTTATATAATTTTGA
*
38850129 ATTTAT-TAAT
1 GTTTATATAAT
38850139 CGAATTTTTT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
15 3 0.14
16 18 0.86
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (16 bp):
GTTTATATAATTTTGA
Found at i:38854950 original size:21 final size:24
Alignment explanation
Indices: 38854917--38854973 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 24
38854907 TGTAATTTGT
*
38854917 AATTTGATTATTTATT-AAAG-T-A
1 AATTT-ATAATTTATTAAAAGATGA
*
38854939 AATTTATAATTTTTTAAAAGATGA
1 AATTTATAATTTATTAAAAGATGA
38854963 AA-TTATAATTT
1 AATTTATAATTT
38854974 TTTTATATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
21 8 0.27
22 9 0.30
23 10 0.33
24 3 0.10
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (24 bp):
AATTTATAATTTATTAAAAGATGA
Found at i:38855302 original size:30 final size:31
Alignment explanation
Indices: 38855247--38855312 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 31
38855237 AATACTTTAT
*
38855247 ATTTTTATAATTTTTAAAAGATTAAATTA-A
1 ATTTTTATAATTTTTAAAAGATTAAAGTACA
*
38855277 ATTTTTATAATTTTTAGTAAG-TTAAAGTACA
1 ATTTTTATAATTTTTA-AAAGATTAAAGTACA
38855308 ATTTT
1 ATTTT
38855313 ATTTTTAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
30 23 0.72
31 9 0.28
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.52
Consensus pattern (31 bp):
ATTTTTATAATTTTTAAAAGATTAAAGTACA
Found at i:38862266 original size:101 final size:102
Alignment explanation
Indices: 38861965--38862491 Score: 261
Period size: 105 Copynumber: 5.2 Consensus size: 102
38861955 GATACCCTTG
* * * * **
38861965 ACTAACGCTATATGTAAAGCAAAA-GAA-AGATAAAGAA-AGGAAGG-TGCCATCAATATTGATA
1 ACTAAGGCTATATGTAAAGCAAAAGGAAGAGA-AAAGAAGAAGAGGGATACCATCAATATCAATA
*** * * * ** *
38862026 TTTTAATATCTGTTAAAT-TCATAATTACTATACCGTTA
65 TCCAAATATTTGTTAAATCT-ACAATTACGATACATTTT
** * * *
38862064 ACTAAAACTATATGTAAAGCAAAAAGAAGAG-AAA-AA-AA-AGGG-T-CTATCAATATCGATAT
1 ACTAAGGCTATATGTAAAGCAAAAGGAAGAGAAAAGAAGAAGAGGGATACCATCAATATCAATAT
* * * * * * *
38862123 TCTAATGTCTATTAAAT-TCACAATCAC-A-ATATTCTT
66 CCAAATATTTGTTAAATCT-ACAATTACGATACATT-TT
* * *
38862159 AACTAAGGCTATATGTAAATCAAAAAAGG-AGAGAAATGAATAA-AGGGATACCATCAATATCAA
1 -ACTAAGGCTATATGTAAAGC--AAAAGGAAGAGAAAAGAAGAAGAGGGATACCATCAATATCAA
38862222 TATCCAAAT-TTTGTTAAATCTACAATTACGATACATTTT
63 TATCCAAATATTTGTTAAATCTACAATTACGATACATTTT
* * * *
38862261 ACTAAGGTTATATGTAAAGCAAAAGGAAGAGAAAAGAAGAAGAGGGGTATCATCAATATCGATAT
1 ACTAAGGCTATATGTAAAGCAAAAGGAAGAGAAAAGAAGAAGAGGGATACCATCAATATCAATAT
* * * ** *
38862326 TCTAATATTTGTTAAATATTATGCAAACACGATATC-TTTA
66 CCAAATATTTGTTAAAT-CTA--CAATTACGATA-CATTTT
* * * * * **
38862366 ACTAAAGCAATATGTAAAGCAAGAAAGAA-AGAAAAG-AGAAGAGAGGCTACTATCAATATTGAT
1 ACTAAGGCTATATGTAAAGCAA-AAGGAAGAGAAAAGAAGAAGAG-GGATACCATCAATATCAAT
* * * * * * * * *
38862429 ATTCTAATATCTGATAAATCCATAATTATGATA-ACCTTA
64 ATCCAAATATTTGTTAAATCTACAATTACGATACA-TTTT
38862468 ACTAAGGCTAT-TCGTAAAGCAAAA
1 ACTAAGGCTATAT-GTAAAGCAAAA
38862492 AAGAAAGGAA
Statistics
Matches: 342, Mismatches: 60, Indels: 50
0.76 0.13 0.11
Matches are distributed among these distances:
94 2 0.01
95 2 0.01
96 53 0.15
97 8 0.02
98 10 0.03
99 33 0.10
100 21 0.06
101 63 0.18
102 60 0.18
103 6 0.02
104 8 0.02
105 70 0.20
106 6 0.02
ACGTcount: A:0.46, C:0.12, G:0.14, T:0.28
Consensus pattern (102 bp):
ACTAAGGCTATATGTAAAGCAAAAGGAAGAGAAAAGAAGAAGAGGGATACCATCAATATCAATAT
CCAAATATTTGTTAAATCTACAATTACGATACATTTT
Found at i:38862379 original size:105 final size:101
Alignment explanation
Indices: 38861965--38862544 Score: 392
Period size: 101 Copynumber: 5.8 Consensus size: 101
38861955 GATACCCTTG
* * ** *
38861965 ACTAACGCTATATGTAAAGC-AAAAGAA-AG-ATA-AAGAAAGGAAGGTGCCATCAATATTGATA
1 ACTAAAGCTATATGTAAAGCAAAAAGAAGAGAAAAGAAGAAAGG--GGTATCATCAATATCGATA
* * * * * * *
38862026 TTTTAATATCTGTTAAATTCATAATTACTATACCGTTA
64 TTCTAATATCTGTTAAATTTACAATCACGATATCTTTA
* *
38862064 ACTAAAACTATATGTAAAGCAAAAAGAAGAG-AAA-AA-AAA-GGGTCT-ATCAATATCGATATT
1 ACTAAAGCTATATGTAAAGCAAAAAGAAGAGAAAAGAAGAAAGGGGTATCATCAATATCGATATT
* * * *
38862124 CTAATGTCTATTAAATTCACAATCACAATAT-TCTTA
66 CTAATATCTGTTAAATTTACAATCACGATATCT-TTA
* * * * * * * *
38862160 ACTAAGGCTATATGTAAATCAAAAAAGGAGAGAAATGAATAAAGGGATACCATCAATATCAATAT
1 ACTAAAGCTATATGTAAAGC-AAAAAGAAGAGAAAAGAAGAAAGGGGTATCATCAATATCGATAT
* * * * * *
38862225 CCAAAT-TTTGTTAAATCTACAATTACGATA-CATTTT
65 TCTAATATCTGTTAAATTTACAATCACGATATC-TTTA
* * *
38862261 ACTAAGGTTATATGTAAAGCAAAAGGAAGAGAAAAGAAGAAGAGGGGTATCATCAATATCGATAT
1 ACTAAAGCTATATGTAAAGCAAAAAGAAGAGAAAAGAAGAA-AGGGGTATCATCAATATCGATAT
* *
38862326 TCTAATATTTGTTAAATATTATGCAAACACGATATCTTTA
65 TCTAATATCTGTTAAAT-TTA--CAATCACGATATCTTTA
* * *
38862366 ACTAAAGCAATATGTAAAGCAAGAAAGAA-AGAAAAG-AGAAGAGAGGCTA-CTATCAATATTGA
1 ACTAAAGCTATATGTAAAGCAA-AAAGAAGAGAAAAGAAGAA-AG-GGGTATC-ATCAATATCGA
* ** * * * * *
38862428 TATTCTAATATCTGATAAATCCATAATTATGATAACCTTA
62 TATTCTAATATCTGTTAAATTTACAATCACGATATCTTTA
* * * *
38862468 ACTAAGGCTAT-TCGTAAAGCAAAAAAGAA-AGGAAA-AAGAAA---GTACCATTAATATCGATA
1 ACTAAAGCTATAT-GTAAAGC-AAAAAGAAGAGAAAAGAAGAAAGGGGTATCATCAATATCGATA
* *
38862527 TTTTAATATCTATTAAAT
64 TTCTAATATCTGTTAAAT
38862545 CCGGAATCAC
Statistics
Matches: 385, Mismatches: 72, Indels: 50
0.76 0.14 0.10
Matches are distributed among these distances:
96 58 0.15
97 41 0.11
98 3 0.01
99 21 0.05
100 30 0.08
101 73 0.19
102 70 0.18
103 4 0.01
104 9 0.02
105 70 0.18
106 6 0.02
ACGTcount: A:0.46, C:0.12, G:0.14, T:0.28
Consensus pattern (101 bp):
ACTAAAGCTATATGTAAAGCAAAAAGAAGAGAAAAGAAGAAAGGGGTATCATCAATATCGATATT
CTAATATCTGTTAAATTTACAATCACGATATCTTTA
Found at i:38864008 original size:21 final size:20
Alignment explanation
Indices: 38863965--38864009 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
38863955 TGATAGGACA
* * *
38863965 AAAAGAAAAGGAAATGAATG
1 AAAAGAAAAGAAAAAGAAAG
38863985 AAAAGAAATAGAAAAAGAAAG
1 AAAAGAAA-AGAAAAAGAAAG
38864006 AAAA
1 AAAA
38864010 TTATTTTTCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (20 bp):
AAAAGAAAAGAAAAAGAAAG
Found at i:38866729 original size:31 final size:31
Alignment explanation
Indices: 38866691--38866765 Score: 123
Period size: 31 Copynumber: 2.4 Consensus size: 31
38866681 TTTTATCCAT
38866691 TTTGGTACTTAAACTTAACACTTTTTTATAA
1 TTTGGTACTTAAACTTAACACTTTTTTATAA
* *
38866722 TTTGGTACTTAAACTTGACACTTTTTTTTAA
1 TTTGGTACTTAAACTTAACACTTTTTTATAA
*
38866753 GTTGGTACTTAAA
1 TTTGGTACTTAAA
38866766 ACTTTTTGGG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.29, C:0.12, G:0.11, T:0.48
Consensus pattern (31 bp):
TTTGGTACTTAAACTTAACACTTTTTTATAA
Found at i:38867001 original size:4 final size:4
Alignment explanation
Indices: 38866992--38867024 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
38866982 TTTAGTTTTA
*
38866992 ATTT ATTT ATTT ATTT ATTT ATTT ATTA ATTT A
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT A
38867025 AAATAATGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (4 bp):
ATTT
Found at i:38870433 original size:25 final size:24
Alignment explanation
Indices: 38870405--38870475 Score: 61
Period size: 25 Copynumber: 2.8 Consensus size: 24
38870395 GTTTTAAAAT
38870405 TTATTTATAATTAATTATTATCTAA
1 TTATTTATAATTAATTATTA-CTAA
* * * *
38870430 TTATGTTAAAATAAAATTATTAGTAT
1 TTAT-TTATAAT-TAATTATTACTAA
*
38870456 TTATTTATAAATACATTATT
1 TTATTTATAATTA-ATTATT
38870476 TTTTTCTGTT
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
24 1 0.03
25 15 0.42
26 12 0.33
27 8 0.22
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (24 bp):
TTATTTATAATTAATTATTACTAA
Found at i:38870695 original size:31 final size:30
Alignment explanation
Indices: 38870648--38870718 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
38870638 ACTATAAAAA
*
38870648 TAATCACTT-TTGTTTGACTCAAGTTACATTT
1 TAATCACTTATTGTTTGA--AAAGTTACATTT
*
38870679 TAGTCACTTATT-TTTGAAAAGTTACATTT
1 TAATCACTTATTGTTTGAAAAGTTACATTT
38870708 TAATCACTTAT
1 TAATCACTTAT
38870719 GTTATTATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 21 0.58
31 13 0.36
32 2 0.06
ACGTcount: A:0.30, C:0.14, G:0.08, T:0.48
Consensus pattern (30 bp):
TAATCACTTATTGTTTGAAAAGTTACATTT
Found at i:38871325 original size:18 final size:18
Alignment explanation
Indices: 38871304--38871339 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
38871294 GTTTTAGGGT
*
38871304 TTAAATTTTTTTAATTAA
1 TTAAATTTATTTAATTAA
38871322 TTAAATTTATTTAATTAA
1 TTAAATTTATTTAATTAA
38871340 AAATATATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTAAATTTATTTAATTAA
Found at i:38872142 original size:87 final size:87
Alignment explanation
Indices: 38871968--38872148 Score: 215
Period size: 86 Copynumber: 2.1 Consensus size: 87
38871958 TTAATATAAT
* * * *
38871968 ATTTGGTACGTGAACTTGACACATTTTCCTAATTTGGTACTTAAACTTTTTTGGTCCAATTTGGT
1 ATTTGGTACCTAAACTTGA-ACATTTT-CTAAGTTGGTACTTAAACTTTTTGGGTCCAATTTGGT
38872033 ACTCAAACTTGATACTTTTTTCTTA
64 ACTCAAACTTGATACTTTTTTC-TA
*
38872058 ATTTGGTACCTAAACTTG-ACATTTT-TAAGTTGGTACTTAAACTTTTTAGGGTCTAATTTGGT-
1 ATTTGGTACCTAAACTTGAACATTTTCTAAGTTGGTACTTAAACTTTTT-GGGTCCAATTTGGTA
* * **
38872120 CCCTGAACTTGATTTTTTTTTCTA
65 CTC-AAACTTGATACTTTTTTCTA
38872144 ATTTG
1 ATTTG
38872149 ATATCTAATA
Statistics
Matches: 80, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
86 30 0.38
87 27 0.34
88 7 0.09
90 16 0.20
ACGTcount: A:0.24, C:0.15, G:0.14, T:0.47
Consensus pattern (87 bp):
ATTTGGTACCTAAACTTGAACATTTTCTAAGTTGGTACTTAAACTTTTTGGGTCCAATTTGGTAC
TCAAACTTGATACTTTTTTCTA
Found at i:38872461 original size:60 final size:59
Alignment explanation
Indices: 38872306--38872461 Score: 145
Period size: 60 Copynumber: 2.6 Consensus size: 59
38872296 TAAATTTAGA
**
38872306 TACCAAATTGAAT-TAAAAAAAGCTTAGGTACCAAATTAGAAAAAAATACCAAGTTAAGG
1 TACCAAATTG-ATCTAAAAAAAATTTAGGTACCAAATTAGAAAAAAATACCAAGTTAAGG
* * * * * * * * **
38872365 TACCATATTGGGTCCAAAAAAGATTTTGGTATCAAATTAGGAAAAATTATTAAGTTCAA-G
1 TACCAAATT-GATCTAAAAAAAATTTAGGTACCAAATTAGAAAAAAATACCAAGTT-AAGG
*
38872425 TACCAAATTAGATCTAAAAAAAATTTAGATACCAAAT
1 TACCAAATT-GATCTAAAAAAAATTTAGGTACCAAAT
38872462 ATTATAATGC
Statistics
Matches: 74, Mismatches: 20, Indels: 5
0.75 0.20 0.05
Matches are distributed among these distances:
59 9 0.12
60 63 0.85
61 2 0.03
ACGTcount: A:0.49, C:0.12, G:0.13, T:0.27
Consensus pattern (59 bp):
TACCAAATTGATCTAAAAAAAATTTAGGTACCAAATTAGAAAAAAATACCAAGTTAAGG
Found at i:38875200 original size:16 final size:16
Alignment explanation
Indices: 38875179--38875211 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
38875169 TTAAAGTTCG
*
38875179 AAATGTGTTAATCTCA
1 AAATGTGCTAATCTCA
38875195 AAATGTGCTAATCTCA
1 AAATGTGCTAATCTCA
38875211 A
1 A
38875212 TCTAAACAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.33
Consensus pattern (16 bp):
AAATGTGCTAATCTCA
Found at i:38876507 original size:16 final size:17
Alignment explanation
Indices: 38876469--38876501 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
38876459 ATTTCATCTT
*
38876469 TAATTTTTTATAATTTA
1 TAATATTTTATAATTTA
38876486 TAATATTTTA-AATTTA
1 TAATATTTTATAATTTA
38876502 ATATATAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TAATATTTTATAATTTA
Found at i:38877215 original size:29 final size:28
Alignment explanation
Indices: 38877173--38877246 Score: 80
Period size: 29 Copynumber: 2.5 Consensus size: 28
38877163 AAATTTTAAA
38877173 TTAATAAATATAAAA-TTAATTTTAA-CTTT
1 TTAA-AAATATAAAATTTAA-TTTAATC-TT
38877202 TTAAAAATAATAAAATTTAATTTAATCTT
1 TTAAAAAT-ATAAAATTTAATTTAATCTT
*
38877231 TTAAAATCTATAAAAT
1 TTAAAA-ATATAAAAT
38877247 ATGAGTTATT
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
28 4 0.10
29 30 0.75
30 6 0.15
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (28 bp):
TTAAAAATATAAAATTTAATTTAATCTT
Found at i:38878675 original size:28 final size:30
Alignment explanation
Indices: 38878635--38878694 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
38878625 AACCAGACTC
38878635 TAAAAAAAAAC-TT-AATAGTCTAGTAACT
1 TAAAAAAAAACTTTCAATAGTCTAGTAACT
* *
38878663 TAAATAAAAACTTTCGAATAGTCTAGTGACT
1 TAAAAAAAAACTTTC-AATAGTCTAGTAACT
38878694 T
1 T
38878695 GAATGATAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 10 0.37
29 2 0.07
31 15 0.56
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.32
Consensus pattern (30 bp):
TAAAAAAAAACTTTCAATAGTCTAGTAACT
Found at i:38879237 original size:14 final size:15
Alignment explanation
Indices: 38879194--38879240 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
38879184 TTTATTTAAA
*
38879194 TAATTT-ATATTATTT
1 TAATTTAATATT-TAT
38879209 TAATTTAATATTTAT
1 TAATTTAATATTTAT
*
38879224 TAATTTTA-ATTTAT
1 TAATTTAATATTTAT
38879238 TAA
1 TAA
38879241 AATTTTAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 9 0.31
15 15 0.52
16 5 0.17
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TAATTTAATATTTAT
Found at i:38881104 original size:6 final size:6
Alignment explanation
Indices: 38881093--38881126 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
38881083 CCCATCTCCG
38881093 CCGCCT CCGCCT CCGCCT CCGCCT CCGCCT CCGC
1 CCGCCT CCGCCT CCGCCT CCGCCT CCGCCT CCGC
38881127 TTCCTGTCAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.68, G:0.18, T:0.15
Consensus pattern (6 bp):
CCGCCT
Found at i:38887818 original size:30 final size:30
Alignment explanation
Indices: 38887784--38887843 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
38887774 CAAATATATT
* *
38887784 GACATGATCAAACAACTACAACTTAGAACC
1 GACATAATAAAACAACTACAACTTAGAACC
* **
38887814 GACATAATAAAACAATTACTTCTTAGAACC
1 GACATAATAAAACAACTACAACTTAGAACC
38887844 AAGCCAAAAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.47, C:0.23, G:0.08, T:0.22
Consensus pattern (30 bp):
GACATAATAAAACAACTACAACTTAGAACC
Found at i:38891575 original size:81 final size:81
Alignment explanation
Indices: 38891439--38891605 Score: 219
Period size: 81 Copynumber: 2.1 Consensus size: 81
38891429 AAAAACTACC
* ** * * * *
38891439 ATTATCTGTTTGTTGATTCAAGTTTGTTGTTCGGAATTTGTTCTGGGGCAAATCTTGCATGCCGA
1 ATTATCTGTTTGTTGATTCAAGTTTGTCGTTCGGAATCGGTTCCGGGACAAATCTTGCATACCAA
* *
38891504 GAAACTAGTTCTTTTT
66 GAAACTAATTATTTTT
* *
38891520 GTTATCTGTTTGTTGATTCAAGTTTGTCGTTCGGAATCCGGTTCCGGGAC-AATCTTTCATACCA
1 ATTATCTGTTTGTTGATTCAAGTTTGTCGTTCGGAAT-CGGTTCCGGGACAAATCTTGCATACCA
38891584 AGAAACTAATTATTTTT
65 AGAAACTAATTATTTTT
38891601 ATTAT
1 ATTAT
38891606 GTTACATATA
Statistics
Matches: 73, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
81 65 0.89
82 8 0.11
ACGTcount: A:0.22, C:0.15, G:0.20, T:0.43
Consensus pattern (81 bp):
ATTATCTGTTTGTTGATTCAAGTTTGTCGTTCGGAATCGGTTCCGGGACAAATCTTGCATACCAA
GAAACTAATTATTTTT
Found at i:38911103 original size:140 final size:141
Alignment explanation
Indices: 38910882--38911203 Score: 330
Period size: 140 Copynumber: 2.3 Consensus size: 141
38910872 TTAGGCAGTA
* * ** * * *
38910882 GACTCGACCTGTTAAATGTTACCACTTTGAACTAACTTACCTAAGTTCTGGTTTCGCTGCTACCT
1 GACTC-ACCTGTTAAATGTCACCACTTTGAACCAACTTAGATAAGTTCCGGTTTCGCAGCTACCC
* * *
38910947 ATAAATAGATATGGATATCTAAGACATGA-TCTTAC-CTGTGCATCATCACTACTGCCCT-TATT
65 ATAAACAGATATGGATATCTAAGACATGACTCTT-CTCTGTGCATCATCACCACTG-ACTGTATT
* *
38911009 GTTTTCTGGCTCTG
128 GTTTTCCGGCTCCG
* * * *
38911023 TACTCACCTGTTAAATGTCACCTCTTTGGACCAACTTAGATAAGTTCCGCG-TTCGCAGCTTCCC
1 GACTCACCTGTTAAATGTCACCACTTTGAACCAACTTAGATAAGTTCCG-GTTTCGCAGCTACCC
* * *** *
38911087 ATATACAGATGA-GGATATCTTATTTATGACTCTTCTCTGTGCATCATCACCACTGATTGTATTG
65 ATAAACAGAT-ATGGATATCTAAGACATGACTCTTCTCTGTGCATCATCACCACTGACTGTATTG
38911151 TTTTCCGGCTCCG
129 TTTTCCGGCTCCG
* * *
38911164 GACTTGACCTGTTACACGTCACCACTTTGAACCAACTTAG
1 GAC-TCACCTGTTAAATGTCACCACTTTGAACCAACTTAG
38911204 CAATGTTCTG
Statistics
Matches: 147, Mismatches: 28, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
140 70 0.48
141 46 0.31
142 31 0.21
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.35
Consensus pattern (141 bp):
GACTCACCTGTTAAATGTCACCACTTTGAACCAACTTAGATAAGTTCCGGTTTCGCAGCTACCCA
TAAACAGATATGGATATCTAAGACATGACTCTTCTCTGTGCATCATCACCACTGACTGTATTGTT
TTCCGGCTCCG
Found at i:38915484 original size:118 final size:116
Alignment explanation
Indices: 38915276--38915516 Score: 358
Period size: 118 Copynumber: 2.1 Consensus size: 116
38915266 TCCATATGAA
* * *
38915276 AAAATAAAAAATAAACCAATCTAAATTGAATTGTCATAAATAATTCAAAAAATCCAGTAGAACTA
1 AAAATAAAAAATAAACCAATCTAAATCGAATTATCATAAATAATTCAAAAAATCCAATAGAACTA
*
38915341 ACCAAATTTAACCCCAAAACATATATATTAATATTGGTGAACATTCATTATTT
66 ACAAAATTTAACCCC-AAA-ATATATATTAATATTGGTGAACATTCATTATTT
* * * *
38915394 AAAATAAAAAATAAATCAATCTAAATCGAATTATGATAAATAATTCAAAAAATCCAATTGTACTA
1 AAAATAAAAAATAAACCAATCTAAATCGAATTATCATAAATAATTCAAAAAATCCAATAGAACTA
* *
38915459 ACAAAATTT-ATCTCAAACATATATATTAATATTGGTGAACATTCATTATTT
66 ACAAAATTTAACCCCAAA-ATATATATTAATATTGGTGAACATTCATTATTT
38915510 AAAATAA
1 AAAATAA
38915517 GGGAAGTTAT
Statistics
Matches: 113, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
116 44 0.39
117 3 0.03
118 66 0.58
ACGTcount: A:0.51, C:0.12, G:0.05, T:0.31
Consensus pattern (116 bp):
AAAATAAAAAATAAACCAATCTAAATCGAATTATCATAAATAATTCAAAAAATCCAATAGAACTA
ACAAAATTTAACCCCAAAATATATATTAATATTGGTGAACATTCATTATTT
Found at i:38922436 original size:19 final size:18
Alignment explanation
Indices: 38922412--38922448 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
38922402 AATCTCATTA
*
38922412 TTAATTTGAAAGTTAAAAT
1 TTAATTT-AAAATTAAAAT
38922431 TTAATTTAAAATTAAAAT
1 TTAATTTAAAATTAAAAT
38922449 AAAAATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.43
Consensus pattern (18 bp):
TTAATTTAAAATTAAAAT
Found at i:38922762 original size:16 final size:16
Alignment explanation
Indices: 38922741--38922774 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
38922731 TCTATTTAAA
*
38922741 AATTGTATATTAAATC
1 AATTGTACATTAAATC
38922757 AATTGTACATTAAATC
1 AATTGTACATTAAATC
38922773 AA
1 AA
38922775 AGAACAATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.38
Consensus pattern (16 bp):
AATTGTACATTAAATC
Found at i:38929974 original size:20 final size:20
Alignment explanation
Indices: 38929928--38929975 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
38929918 AATTAGTTAT
*
38929928 ATAAAATATTTTTTTTATTA
1 ATAAAATATTTTTTTAATTA
*
38929948 ATTAAATATTTTTTTAATTTA
1 ATAAAATATTTTTTTAA-TTA
38929969 A-AAAATA
1 ATAAAATA
38929976 GATCGATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 20 0.83
21 4 0.17
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
ATAAAATATTTTTTTAATTA
Found at i:38930146 original size:25 final size:26
Alignment explanation
Indices: 38930100--38930155 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
38930090 CATCATACTT
38930100 AAGCAACAACTCCAATACATTT-CCA
1 AAGCAACAACTCCAATACATTTGCCA
* *
38930125 AAGCAACAACTCC-ATAAGATTTGCTA
1 AAGCAACAACTCCAAT-ACATTTGCCA
38930151 AAGCA
1 AAGCA
38930156 TTTACATCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 2 0.07
25 18 0.67
26 7 0.26
ACGTcount: A:0.45, C:0.27, G:0.09, T:0.20
Consensus pattern (26 bp):
AAGCAACAACTCCAATACATTTGCCA
Found at i:38930394 original size:23 final size:24
Alignment explanation
Indices: 38930328--38930396 Score: 65
Period size: 23 Copynumber: 2.9 Consensus size: 24
38930318 TTTGACGAAA
38930328 ATTATAAATGTTG-ATAAAATAATT
1 ATTATAAAT-TTGTATAAAATAATT
* *
38930352 A-TATCAAATTT-TAATGAAAT-TTT
1 ATTAT-AAATTTGT-ATAAAATAATT
38930375 ATTATAAATTTGTATAAAATAA
1 ATTATAAATTTGTATAAAATAA
38930397 ACTCTAAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 12
0.69 0.08 0.24
Matches are distributed among these distances:
23 20 0.57
24 15 0.43
ACGTcount: A:0.49, C:0.01, G:0.06, T:0.43
Consensus pattern (24 bp):
ATTATAAATTTGTATAAAATAATT
Done.