Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 11 of 193
Found at i:3951909 original size:60 final size:59
Alignment explanation
Indices: 3951836--3952249 Score: 346
Period size: 60 Copynumber: 7.0 Consensus size: 59
3951826 GGGAAAGTTG
* *
3951836 GTGTCGACCATTGCATGGCCAACACAAAAAAAATTGATCTTTTATCAGATAAAAAAAGAA
1 GTGTCGACCATTGCATGGCCAACACAAAAAAATTTGATTTTTTATCAGA-AAAAAAAGAA
* * * * *
3951896 GTGTCGACCATTGCATGGCCAACACAAAAAAA-ATAATTTTTTACCAGATAAAAAAGGAG
1 GTGTCGACCATTGCATGGCCAACACAAAAAAATTTGATTTTTTATCAGA-AAAAAAAGAA
* **
3951955 GTGTCGACCATTGCATGGCCAACACCAAAAAAATTTGAATTTTTTATCAG-AAAAAAGGGG
1 GTGTCGACCATTGCATGGCCAACA-CAAAAAAATTTG-ATTTTTTATCAGAAAAAAAAGAA
** * * **
3952015 GTGTCGGTCATGGCATGGCCAACAC-AAAAAATTTGATTTTTTATTCAG-ATAAAAAGGG
1 GTGTCGACCATTGCATGGCCAACACAAAAAAATTTGATTTTTTA-TCAGAAAAAAAAGAA
* * * * *
3952073 GTGTC-AGCCATGGCATAGTCAACACCAAAAAATTTGATTTTTTTTATCAG-ACAAAAAGAA
1 GTGTCGA-CCATTGCATGGCCAACACAAAAAAATTTGA--TTTTTTATCAGAAAAAAAAGAA
** * * * * *
3952133 GGTGTCGACCA-TGCAATGGCCAACACCTAAAAATTTTATTTTTTATCTGACAAAAAGGGA
1 -GTGTCGACCATTGC-ATGGCCAACACAAAAAAATTTGATTTTTTATCAGAAAAAAAAGAA
* * * * *
3952193 GTGTCGGCCATGGCATAGCCAACACCCAAAAAAA----ATTTTTTGTCAGATAAAAAAGAA
1 GTGTCGACCATTGCATGGCCAACA--CAAAAAAATTTGATTTTTTATCAGAAAAAAAAGAA
3952250 TTTTTTTTTA
Statistics
Matches: 297, Mismatches: 42, Indels: 33
0.80 0.11 0.09
Matches are distributed among these distances:
57 26 0.09
58 42 0.14
59 85 0.29
60 91 0.31
61 41 0.14
62 12 0.04
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.25
Consensus pattern (59 bp):
GTGTCGACCATTGCATGGCCAACACAAAAAAATTTGATTTTTTATCAGAAAAAAAAGAA
Found at i:3951959 original size:59 final size:59
Alignment explanation
Indices: 3951835--3952247 Score: 378
Period size: 59 Copynumber: 7.0 Consensus size: 59
3951825 AGGGAAAGTT
* * *
3951835 GGTGTCGACCATTGCATGGCCAACACAAAAAAAATTGATCTTTTATCAGATAAAAAAAGA
1 GGTGTCGACCATTGCATGGCCAACAC-AAAAAAATTAATTTTTTATCAGATAAAAAAGGA
* * *
3951895 AGTGTCGACCATTGCATGGCCAACACAAAAAAAATAATTTTTTACCAGATAAAAAAGGA
1 GGTGTCGACCATTGCATGGCCAACACAAAAAAATTAATTTTTTATCAGATAAAAAAGGA
*
3951954 GGTGTCGACCATTGCATGGCCAACACCAAAAAAATTTGAATTTTTTATCAG--AAAAAAGGG
1 GGTGTCGACCATTGCATGGCCAACA-CAAAAAAA-TT-AATTTTTTATCAGATAAAAAAGGA
** * * *
3952014 GGTGTCGGTCATGGCATGGCCAACACAAAAAATTTGATTTTTTATTCAGAT-AAAAAGG-
1 GGTGTCGACCATTGCATGGCCAACACAAAAAAATTAATTTTTTA-TCAGATAAAAAAGGA
* * * * * * *
3952072 GGTGTC-AGCCATGGCATAGTCAACACCAAAAAATTTGATTTTTTTTATCAGA-CAAAAAGAA
1 GGTGTCGA-CCATTGCATGGCCAACA-CAAAAAAATT-A-ATTTTTTATCAGATAAAAAAGGA
* * * * * *
3952133 GGTGTCGACCA-TGCAATGGCCAACACCTAAAAATTTTATTTTTTATCTGACAAAAAGGGA
1 GGTGTCGACCATTGC-ATGGCCAACA-CAAAAAAATTAATTTTTTATCAGATAAAAAAGGA
* * * * *
3952193 -GTGTCGGCCATGGCATAGCCAACACCCAAAAAA--AATTTTTTGTCAGATAAAAAAG
1 GGTGTCGACCATTGCATGGCCAACA-CAAAAAAATTAATTTTTTATCAGATAAAAAAG
3952248 AATTTTTTTT
Statistics
Matches: 295, Mismatches: 42, Indels: 35
0.79 0.11 0.09
Matches are distributed among these distances:
57 25 0.08
58 26 0.09
59 112 0.38
60 84 0.28
61 35 0.12
62 13 0.04
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.25
Consensus pattern (59 bp):
GGTGTCGACCATTGCATGGCCAACACAAAAAAATTAATTTTTTATCAGATAAAAAAGGA
Found at i:3951985 original size:119 final size:117
Alignment explanation
Indices: 3951835--3952249 Score: 423
Period size: 119 Copynumber: 3.5 Consensus size: 117
3951825 AGGGAAAGTT
* * * *
3951835 GGTGTCGACCATTGCATGGCCAACACAAAAAAAATTGATCTTTTATCAGATAAAAAAAGAAGTGT
1 GGTGTCGACCATGGCATAGCCAACACCAAAAAAATTGATTTTTTATCAG--AAAAAAAGAAGTGT
** *
3951900 CGACCATTGCATGGCCAACACAAAAAAAATAATTTTTTACCAGATAAAAAAGGA
64 CGACCATTGCATGGCCAACACAAAAAATTTAATTTTTTATCAGATAAAAAAGGA
* * * **
3951954 GGTGTCGACCATTGCATGGCCAACACCAAAAAAATTTGAATTTTTTATCAGAAAAAAGGGGGTGT
1 GGTGTCGACCATGGCATAGCCAACACCAAAAAAA-TTG-ATTTTTTATCAGAAAAAAAGAAGTGT
** * *
3952019 CGGTCATGGCATGGCCAACACAAAAAATTTGATTTTTTATTCAGAT-AAAAAGG-
64 CGACCATTGCATGGCCAACACAAAAAATTTAATTTTTTA-TCAGATAAAAAAGGA
* * *
3952072 GGTGTC-AGCCATGGCATAGTCAACACCAAAAAATTTGATTTTTTTTATCAGACAAAAAGAAGGT
1 GGTGTCGA-CCATGGCATAGCCAACACCAAAAAAATTGA--TTTTTTATCAGAAAAAAAGAA-GT
* * * * *
3952136 GTCGACCA-TGCAATGGCCAACACCTAAAAATTTTATTTTTTATCTGACAAAAAGGGA
62 GTCGACCATTGC-ATGGCCAACA-CAAAAAATTTAATTTTTTATCAGATAAAAAAGGA
* *
3952193 -GTGTCGGCCATGGCATAGCCAACACCCAAAAAAA---ATTTTTTGTCAGATAAAAAAGAA
1 GGTGTCGACCATGGCATAGCCAACA-CCAAAAAAATTGATTTTTTATCAGA-AAAAAAGAA
3952250 TTTTTTTTTA
Statistics
Matches: 249, Mismatches: 33, Indels: 30
0.80 0.11 0.10
Matches are distributed among these distances:
116 12 0.05
117 12 0.05
118 48 0.19
119 106 0.43
120 52 0.21
121 19 0.08
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.25
Consensus pattern (117 bp):
GGTGTCGACCATGGCATAGCCAACACCAAAAAAATTGATTTTTTATCAGAAAAAAAGAAGTGTCG
ACCATTGCATGGCCAACACAAAAAATTTAATTTTTTATCAGATAAAAAAGGA
Found at i:3953190 original size:8 final size:9
Alignment explanation
Indices: 3953159--3953188 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
3953149 TTAGGGCTCC
3953159 TTTTATTTT
1 TTTTATTTT
3953168 TTTTATTTT
1 TTTTATTTT
3953177 TTTTATTTT
1 TTTTATTTT
3953186 TTT
1 TTT
3953189 ATGTCTGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTTATTTT
Found at i:3960653 original size:23 final size:23
Alignment explanation
Indices: 3960627--3960673 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
3960617 AGAAAAAACC
* *
3960627 AGAATAACCGTGCTAATAAGCAG
1 AGAAAAACCATGCTAATAAGCAG
*
3960650 AGAAAAACTATGCTAATAAGCAG
1 AGAAAAACCATGCTAATAAGCAG
3960673 A
1 A
3960674 CAATCAGATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.49, C:0.15, G:0.19, T:0.17
Consensus pattern (23 bp):
AGAAAAACCATGCTAATAAGCAG
Found at i:3961393 original size:21 final size:21
Alignment explanation
Indices: 3961369--3961417 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
3961359 CAATAACTAC
** *
3961369 AAAATAAAATTAATCAAATAT
1 AAAATAAAAAAAATCAAAAAT
* *
3961390 AAAAGAAAAAAAATTAAAAAT
1 AAAATAAAAAAAATCAAAAAT
3961411 AAAATAA
1 AAAATAA
3961418 TCCAAAATAA
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:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (21 bp):
AAAATAAAAAAAATCAAAAAT
Found at i:3965030 original size:15 final size:16
Alignment explanation
Indices: 3965012--3965041 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3965002 TTCTAAAATT
3965012 TTGGGTT-ATTTTGGA
1 TTGGGTTAATTTTGGA
3965027 TTGGGTTAATTTTGG
1 TTGGGTTAATTTTGG
3965042 CATCGGGTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.13, C:0.00, G:0.33, T:0.53
Consensus pattern (16 bp):
TTGGGTTAATTTTGGA
Found at i:3965633 original size:28 final size:27
Alignment explanation
Indices: 3965587--3965655 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 27
3965577 TTCACTATTT
* *
3965587 TAAATATAAATATTTATTATTAAAGTACA
1 TAAATATAAA-ATTAATTA-TAAAGTAAA
*
3965616 -AAATATTAAAATTAATTATAAATTAAA
1 TAAATA-TAAAATTAATTATAAAGTAAA
3965643 TAAATATAAAATT
1 TAAATATAAAATT
3965656 CGGTTGGATT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
27 14 0.40
28 17 0.49
29 4 0.11
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (27 bp):
TAAATATAAAATTAATTATAAAGTAAA
Found at i:3976546 original size:18 final size:18
Alignment explanation
Indices: 3976515--3976552 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
3976505 TCACGGTTCT
3976515 TTTTTACTAAATTATAATA
1 TTTTTACTAAATTAT-ATA
*
3976534 TTTTTA-TATATTATATA
1 TTTTTACTAAATTATATA
3976551 TT
1 TT
3976553 GAAATGGGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 7 0.39
19 6 0.33
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTTTACTAAATTATATA
Found at i:3980388 original size:20 final size:20
Alignment explanation
Indices: 3980352--3980396 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
3980342 TCATTAAGCT
*
3980352 TTAATTAATCTCTTTTAATC
1 TTAATTAATCTCATTTAATC
*
3980372 TTAATTAAGTCT-ATTTACTC
1 TTAATTAA-TCTCATTTAATC
3980392 TTAAT
1 TTAAT
3980397 ACAAATCATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 19 0.86
21 3 0.14
ACGTcount: A:0.31, C:0.13, G:0.02, T:0.53
Consensus pattern (20 bp):
TTAATTAATCTCATTTAATC
Found at i:3987903 original size:28 final size:27
Alignment explanation
Indices: 3987871--3987930 Score: 84
Period size: 28 Copynumber: 2.2 Consensus size: 27
3987861 AATGGAGTTC
* * *
3987871 CACATATAAGATAGTCCTAGCAGACTT
1 CACATATAAGATAATACTAGAAGACTT
3987898 CTACATATAAGATAATACTAGAAGACTT
1 C-ACATATAAGATAATACTAGAAGACTT
3987926 CACAT
1 CACAT
3987931 CTTTCATAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 5 0.17
28 24 0.83
ACGTcount: A:0.42, C:0.20, G:0.12, T:0.27
Consensus pattern (27 bp):
CACATATAAGATAATACTAGAAGACTT
Found at i:3989425 original size:16 final size:16
Alignment explanation
Indices: 3989404--3989436 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3989394 TGATGATTTT
*
3989404 AATGTTAAAGGACTAA
1 AATGTTAAAGGAATAA
3989420 AATGTTAAAGGAATAA
1 AATGTTAAAGGAATAA
3989436 A
1 A
3989437 TTTGTAAGGA
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:0.55, C:0.03, G:0.18, T:0.24
Consensus pattern (16 bp):
AATGTTAAAGGAATAA
Found at i:3989873 original size:18 final size:16
Alignment explanation
Indices: 3989850--3989885 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
3989840 CTTAGTAAAT
3989850 ATTAAATTGAGGAATGAA
1 ATTAAATTGA--AATGAA
3989868 ATTAAATTGAAATGAA
1 ATTAAATTGAAATGAA
3989884 AT
1 AT
3989886 GGTATTGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
18 10 0.56
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (16 bp):
ATTAAATTGAAATGAA
Found at i:3990609 original size:52 final size:52
Alignment explanation
Indices: 3990426--3990593 Score: 275
Period size: 52 Copynumber: 3.2 Consensus size: 52
3990416 TAAATGCAAA
* * *
3990426 AGGTCCGATGACTATGTGTCATTGTGAGTATATGAATCCTTTACAGATTATA
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
3990478 AGGTCCGATGACTATGTGTCAT-GTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* *
3990529 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTTCGGATTTTG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
*
3990581 AGGTCAGATGACT
1 AGGTCCGATGACT
3990594 CCGTATCATC
Statistics
Matches: 110, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
51 49 0.45
52 61 0.55
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
Found at i:3994177 original size:52 final size:52
Alignment explanation
Indices: 3994108--3994396 Score: 384
Period size: 52 Copynumber: 5.5 Consensus size: 52
3994098 AAATGAAAAA
* * *
3994108 AAGGTCCAATGATTAAGTGTCATCGTGAGTACATGAATCCTTCACAGATTAT
1 AAGGTCCGATGACTAAGTGTCATCGTGAGTACATGAATCCTTCACGGATTAT
*
3994160 AAGGTCCGATGACTAAGTGTCATCGTGAGTACATGAATCCTTTACGGATTAT
1 AAGGTCCGATGACTAAGTGTCATCGTGAGTACATGAATCCTTCACGGATTAT
3994212 AAGGTCCGATGACTAAGTGTCATCGTGAGTACATGAATCCTTTACGGACGGATTAT
1 AAGGTCCGATGACTAAGTGTCATCGTGAGTACATGAATCC-TT-C--ACGGATTAT
* *
3994268 AAAGTCTGATGACTAAGTGTCATCGTGAGTACATGAATCCTTCACGGATTAT
1 AAGGTCCGATGACTAAGTGTCATCGTGAGTACATGAATCCTTCACGGATTAT
* * * * * **
3994320 AAGGTCTGATGACTAAGTGTCATCGTGACTATATGAATTCCTTTACGAAACA-
1 AAGGTCCGATGACTAAGTGTCATCGTGAGTACATGAA-TCCTTCACGGATTAT
3994372 AGAGGTCCGATGACTATA-TGTCATC
1 A-AGGTCCGATGACTA-AGTGTCATC
3994397 ATAAGTATTA
Statistics
Matches: 215, Mismatches: 15, Indels: 13
0.88 0.06 0.05
Matches are distributed among these distances:
52 132 0.61
53 32 0.15
54 2 0.01
55 2 0.01
56 47 0.22
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (52 bp):
AAGGTCCGATGACTAAGTGTCATCGTGAGTACATGAATCCTTCACGGATTAT
Found at i:3994302 original size:108 final size:107
Alignment explanation
Indices: 3994108--3994367 Score: 400
Period size: 108 Copynumber: 2.4 Consensus size: 107
3994098 AAATGAAAAA
* * *
3994108 AAGGTCCAATGATTAAGTGTCATCGTGAGTACATGAATCC-TT-C-ACAGATTATAAGGTCCGAT
1 AAGGTCCGATGACTAAGTGTCATCGTGAGTACATGAATCCTTTACGACAGATTATAAAGTCCGAT
*
3994170 GACTAAGTGTCATCGTGAGTACATGAATCCTTTACGGATTAT
66 GACTAAGTGTCATCGTGAGTACATGAATCCTTCACGGATTAT
* *
3994212 AAGGTCCGATGACTAAGTGTCATCGTGAGTACATGAATCCTTTACGGACGGATTATAAAGTCTGA
1 AAGGTCCGATGACTAAGTGTCATCGTGAGTACATGAATCCTTTAC-GACAGATTATAAAGTCCGA
3994277 TGACTAAGTGTCATCGTGAGTACATGAATCCTTCACGGATTAT
65 TGACTAAGTGTCATCGTGAGTACATGAATCCTTCACGGATTAT
* * *
3994320 AAGGTCTGATGACTAAGTGTCATCGTGACTATATGAATTCCTTTACGA
1 AAGGTCCGATGACTAAGTGTCATCGTGAGTACATGAA-TCCTTTACGA
3994368 AACAAGAGGT
Statistics
Matches: 142, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
104 38 0.27
105 2 0.01
106 1 0.01
108 93 0.65
109 8 0.06
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (107 bp):
AAGGTCCGATGACTAAGTGTCATCGTGAGTACATGAATCCTTTACGACAGATTATAAAGTCCGAT
GACTAAGTGTCATCGTGAGTACATGAATCCTTCACGGATTAT
Found at i:3994412 original size:108 final size:105
Alignment explanation
Indices: 3994108--3994403 Score: 325
Period size: 108 Copynumber: 2.8 Consensus size: 105
3994098 AAATGAAAAA
* * * * * *
3994108 AAGGTCCAATGATTAAGTGTCATCGTGAGTACATGAATCCTTCAC--AGATTATAAGGTCCGATG
1 AAGGTCCGATGACTAAGTGTCATCGTGACTACATGAATCCTTTACGGAGA-TACAAAGTCCGATG
* * *
3994171 ACTAAGTGTCATCGTGAGTACATGAATCCTTTACGGATTAT
65 ACTAAGTGTCATCATGAGTAAATGAATCCTTCACGGATTAT
* * *
3994212 AAGGTCCGATGACTAAGTGTCATCGTGAGTACATGAATCCTTTACGGACGGATTATAAAGTCTGA
1 AAGGTCCGATGACTAAGTGTCATCGTGACTACATGAATCCTTTACGGA--GA-TACAAAGTCCGA
* *
3994277 TGACTAAGTGTCATCGTGAGTACATGAATCCTTCACGGATTAT
63 TGACTAAGTGTCATCATGAGTAAATGAATCCTTCACGGATTAT
* *
3994320 AAGGTCTGATGACTAAGTGTCATCGTGACTATATGAATTCCTTTAC-GA-A-ACAAGAGGTCCGA
1 AAGGTCCGATGACTAAGTGTCATCGTGACTACATGAA-TCCTTTACGGAGATACAA-A-GTCCGA
*
3994382 TGACTATA-TGTCATCATAAGTA
63 TGACTA-AGTGTCATCATGAGTA
3994404 TTAAATGAAA
Statistics
Matches: 171, Mismatches: 13, Indels: 15
0.86 0.07 0.08
Matches are distributed among these distances:
103 3 0.02
104 43 0.25
105 24 0.14
106 2 0.01
108 91 0.53
109 8 0.05
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (105 bp):
AAGGTCCGATGACTAAGTGTCATCGTGACTACATGAATCCTTTACGGAGATACAAAGTCCGATGA
CTAAGTGTCATCATGAGTAAATGAATCCTTCACGGATTAT
Found at i:3996257 original size:19 final size:20
Alignment explanation
Indices: 3996234--3996285 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
3996224 AAAAAATATA
*
3996234 AATTTTGAATTTTTATAAAT
1 AATTTTGAATTTTTAAAAAT
3996254 -ATTTTGAA-TTTTAAAAAT
1 AATTTTGAATTTTTAAAAAT
*
3996272 AATTTTAAATTTTT
1 AATTTTGAATTTTT
3996286 TTGTAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 9 0.32
19 15 0.54
20 4 0.14
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (20 bp):
AATTTTGAATTTTTAAAAAT
Found at i:3996264 original size:46 final size:45
Alignment explanation
Indices: 3996179--3996265 Score: 115
Period size: 45 Copynumber: 1.9 Consensus size: 45
3996169 ATTATTTTAG
* *
3996179 AAAAAATTAAAATTTTAACTTTTTTATATATTTTTAATTTTTTTT
1 AAAAAATTAAAATTTTAACTTTTTTAAATATTTTGAATTTTTTTT
3996224 AAAAAA-TATAAATTTTGAA-TTTTTATAAATATTTTGAATTTT
1 AAAAAATTA-AAATTTT-AACTTTTT-TAAATATTTTGAATTTT
3996266 AAAAATAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
44 2 0.05
45 18 0.49
46 17 0.46
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.55
Consensus pattern (45 bp):
AAAAAATTAAAATTTTAACTTTTTTAAATATTTTGAATTTTTTTT
Found at i:3996562 original size:12 final size:12
Alignment explanation
Indices: 3996547--3996576 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
3996537 ATTTATTCTC
3996547 TTTTT-CTTTAT
1 TTTTTCCTTTAT
3996558 TTTTTCCTTTAT
1 TTTTTCCTTTAT
3996570 TTTTTCC
1 TTTTTCC
3996577 CTCTCTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.28
12 13 0.72
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTTCCTTTAT
Found at i:4004724 original size:29 final size:29
Alignment explanation
Indices: 4004674--4004734 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
4004664 TTCGGATCTT
** * *
4004674 TTATAAAAATATTATTAAAAATTAATTAA
1 TTATAAAAATAGAATGAAAAATAAATTAA
*
4004703 TTATAAAAATAGAATGATAAATAAATTAA
1 TTATAAAAATAGAATGAAAAATAAATTAA
4004732 TTA
1 TTA
4004735 CGAAAATAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (29 bp):
TTATAAAAATAGAATGAAAAATAAATTAA
Found at i:4013493 original size:5 final size:5
Alignment explanation
Indices: 4013483--4013513 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
4013473 ATTGGGGCTC
4013483 ATGCT ATGCT ATGCT ATGCT ATGCT ATGCT A
1 ATGCT ATGCT ATGCT ATGCT ATGCT ATGCT A
4013514 ATACAATAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (5 bp):
ATGCT
Found at i:4018245 original size:40 final size:40
Alignment explanation
Indices: 4018169--4018277 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 40
4018159 CAAAAAACAT
* * * *
4018169 CGCAAAAGGTAAAAGCAATAGTGGCGTTTTTGCATAAACGT
1 CGCAAAAGGTAAAA-CAATAGCGGCGTTTCTACATAAACGC
* * *
4018210 TGTAAAAGGTAAAACAATAGCGGTGTTTCTACATAAACGC
1 CGCAAAAGGTAAAACAATAGCGGCGTTTCTACATAAACGC
* *
4018250 CGCAAAAGATAAAGCAATAGCGGCGTTT
1 CGCAAAAGGTAAAACAATAGCGGCGTTT
4018278 ATAGAAAAAA
Statistics
Matches: 56, Mismatches: 12, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
40 44 0.79
41 12 0.21
ACGTcount: A:0.39, C:0.16, G:0.23, T:0.23
Consensus pattern (40 bp):
CGCAAAAGGTAAAACAATAGCGGCGTTTCTACATAAACGC
Found at i:4018338 original size:41 final size:41
Alignment explanation
Indices: 4018291--4018543 Score: 163
Period size: 41 Copynumber: 6.2 Consensus size: 41
4018281 GAAAAAACGT
*
4018291 CGCTAAAGGTCAGAGCATTAGCGGCATTGATTAGAAACCGC
1 CGCTAAAGGTCAGAGCATTAGCGGCATTGATGAGAAACCGC
* * ** * **
4018332 CGCTAAATGTTAGAGCATTAGCGGGGTTTATGAGAAAGTGC
1 CGCTAAAGGTCAGAGCATTAGCGGCATTGATGAGAAACCGC
* ** * **
4018373 CGCTAAAGGTCAGAGCATTAGTGGTGTTTATG-GAAAAGAGC
1 CGCTAAAGGTCAGAGCATTAGCGGCATTGATGAG-AAACCGC
* * * * * * ** *
4018414 CGTTAAAGGTCATCA-CACTAGTGACATTTATGAGAAAGTGT
1 CGCTAAAGGTCA-GAGCATTAGCGGCATTGATGAGAAACCGC
* * * *
4018455 CGCTAAAGGTCAGAGCATTAGCGGCATTTATGGGAAAGCGT
1 CGCTAAAGGTCAGAGCATTAGCGGCATTGATGAGAAACCGC
* * * *
4018496 CGCTAAAGATTAAAGCATTAGCGG-AGTTTG-TGAGAAAGCGC
1 CGCTAAAGGTCAGAGCATTAGCGGCA--TTGATGAGAAACCGC
4018537 CGCTAAA
1 CGCTAAA
4018544 TATCAAAAAA
Statistics
Matches: 172, Mismatches: 34, Indels: 12
0.79 0.16 0.06
Matches are distributed among these distances:
40 3 0.02
41 165 0.96
42 4 0.02
ACGTcount: A:0.32, C:0.16, G:0.28, T:0.24
Consensus pattern (41 bp):
CGCTAAAGGTCAGAGCATTAGCGGCATTGATGAGAAACCGC
Found at i:4018377 original size:82 final size:81
Alignment explanation
Indices: 4018247--4018543 Score: 258
Period size: 82 Copynumber: 3.6 Consensus size: 81
4018237 TCTACATAAA
* * * * * ** *
4018247 CGCCGCAAAAGATAAAGCAATAGCGGCGTTTATAGAAAAAACGTCGCTAAAGGTCAGAGCATTAG
1 CGCCGCTAAAGTTAAAGCATTAGCGGAGTTTAT-GAGAAAGTGCCGCTAAAGGTCAGAGCATTAG
* * *
4018312 CGGCATTGATTAGAAAC
65 CGGCATTTATTGGAAAG
* *
4018329 CGCCGCTAAATGTTAGAGCATTAGCGGGGTTTATGAGAAAGTGCCGCTAAAGGTCAGAGCATTAG
1 CGCCGCTAAA-GTTAAAGCATTAGCGGAGTTTATGAGAAAGTGCCGCTAAAGGTCAGAGCATTAG
* **
4018394 TGGTGTTTA-TGGAAAAG
65 CGGCATTTATTGG-AAAG
* * * * * * * *
4018411 AGCCGTTAAAGGTCATCA-CACTAG-TGACATTTATGAGAAAGTGTCGCTAAAGGTCAGAGCATT
1 CGCCGCTAAA-GTTA-AAGCATTAGCGGA-GTTTATGAGAAAGTGCCGCTAAAGGTCAGAGCATT
*
4018474 AGCGGCATTTATGGGAAAG
63 AGCGGCATTTATTGGAAAG
* * *
4018493 CGTCGCTAAAGATTAAAGCATTAGCGGAGTTTGTGAGAAAGCGCCGCTAAA
1 CGCCGCTAAAG-TTAAAGCATTAGCGGAGTTTATGAGAAAGTGCCGCTAAA
4018544 TATCAAAAAA
Statistics
Matches: 167, Mismatches: 40, Indels: 16
0.75 0.18 0.07
Matches are distributed among these distances:
81 5 0.03
82 138 0.83
83 24 0.14
ACGTcount: A:0.34, C:0.16, G:0.28, T:0.23
Consensus pattern (81 bp):
CGCCGCTAAAGTTAAAGCATTAGCGGAGTTTATGAGAAAGTGCCGCTAAAGGTCAGAGCATTAGC
GGCATTTATTGGAAAG
Found at i:4024774 original size:13 final size:13
Alignment explanation
Indices: 4024756--4024786 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
4024746 ACTCAAATAA
4024756 AAAATATTAAACT
1 AAAATATTAAACT
*
4024769 AAAATATTAATCT
1 AAAATATTAAACT
4024782 AAAAT
1 AAAAT
4024787 TTGGATTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAATATTAAACT
Found at i:4025114 original size:95 final size:98
Alignment explanation
Indices: 4024947--4025139 Score: 284
Period size: 95 Copynumber: 2.0 Consensus size: 98
4024937 ATATTTATCT
*
4024947 TTGGATTGGTGAAACTTAAACTAACATAGTACTTTAGGCTTTTGTGAAATCGTCCTTTCATTTAT
1 TTGGATTGGTGAAACTTAAACT-ACATAGTACTTTAGGCTTTTGTGAAATCATCCTTTCATTTAT
*
4025012 ATAGAGTCAATATCTCAACCATTTTCTCAAGCTG
65 ATAGAGTCAATATCTCAACAATTTTCTCAAGCTG
* * **
4025046 TTGGATTGGTGAAACTT-AA-T-CTTAGTATTTTAGGCTTTTGTGAGTTCATCCTTTCATTTATA
1 TTGGATTGGTGAAACTTAAACTACATAGTACTTTAGGCTTTTGTGAAATCATCCTTTCATTTATA
* *
4025108 TAGAGTCGATGTCTCAACAATTTTCTCAAGCT
66 TAGAGTCAATATCTCAACAATTTTCTCAAGCT
4025140 TTTGAGAGGT
Statistics
Matches: 86, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
95 66 0.77
97 1 0.01
98 2 0.02
99 17 0.20
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (98 bp):
TTGGATTGGTGAAACTTAAACTACATAGTACTTTAGGCTTTTGTGAAATCATCCTTTCATTTATA
TAGAGTCAATATCTCAACAATTTTCTCAAGCTG
Found at i:4035110 original size:20 final size:20
Alignment explanation
Indices: 4035085--4035123 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
4035075 TTCGAATATA
*
4035085 TTAATTTTAATTCTTTTATG
1 TTAATTTTAATTATTTTATG
4035105 TTAATTTTAATTATTTTAT
1 TTAATTTTAATTATTTTAT
4035124 ATAAAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (20 bp):
TTAATTTTAATTATTTTATG
Found at i:4066497 original size:7 final size:8
Alignment explanation
Indices: 4066482--4066511 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
4066472 TGTCAACTAG
4066482 ATAAAAAA
1 ATAAAAAA
4066490 ATAAAAAA
1 ATAAAAAA
4066498 ATAAAAAA
1 ATAAAAAA
4066506 ATAAAA
1 ATAAAA
4066512 TTACTTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (8 bp):
ATAAAAAA
Found at i:4066633 original size:11 final size:11
Alignment explanation
Indices: 4066608--4066692 Score: 50
Period size: 11 Copynumber: 7.6 Consensus size: 11
4066598 TAAAAACCAT
*
4066608 AAAAATTTAGGA
1 AAAAATTTA-TA
4066620 AAAAATTTAT-
1 AAAAATTTATA
4066630 AAAAA-TTATA
1 AAAAATTTATA
* * *
4066640 AGAAATTAATT
1 AAAAATTTATA
*
4066651 AAAAATATATA
1 AAAAATTTATA
*
4066662 ATAATTAAATTAT-
1 A-AA--AATTTATA
*
4066675 AAAATTTTATA
1 AAAAATTTATA
4066686 AAAAATT
1 AAAAATT
4066693 AATTTTATAA
Statistics
Matches: 54, Mismatches: 13, Indels: 13
0.68 0.16 0.16
Matches are distributed among these distances:
9 4 0.07
10 14 0.26
11 17 0.31
12 13 0.24
13 1 0.02
14 5 0.09
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (11 bp):
AAAAATTTATA
Found at i:4066653 original size:21 final size:20
Alignment explanation
Indices: 4066620--4066696 Score: 66
Period size: 21 Copynumber: 3.5 Consensus size: 20
4066610 AAATTTAGGA
*
4066620 AAAAATTTA-TAAAAATTAT
1 AAAAATTAATTAAAAATTAT
4066639 AAGAAATTAATTAAAAATATAT
1 AA-AAATTAATTAAAAAT-TAT
*
4066661 AATAATTAAATTATAAAATTTTAT
1 AAAAATT-AATTA-AAAA--TTAT
4066685 AAAAAATTAATT
1 -AAAAATTAATT
4066697 TTATAATTGA
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
19 2 0.04
20 6 0.13
21 11 0.23
22 10 0.21
23 4 0.09
24 7 0.15
25 7 0.15
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (20 bp):
AAAAATTAATTAAAAATTAT
Found at i:4066852 original size:18 final size:19
Alignment explanation
Indices: 4066829--4066874 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
4066819 AAAAAATGTT
*
4066829 TTTTTATAAATTT-TATTA
1 TTTTTATAAATTTATAATA
*
4066847 TTTTTAATTAATTTATAATA
1 TTTTT-ATAAATTTATAATA
4066867 TTTTTATA
1 TTTTTATA
4066875 TATTCTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 5 0.22
19 9 0.39
20 9 0.39
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTTTATAAATTTATAATA
Found at i:4066915 original size:10 final size:9
Alignment explanation
Indices: 4066829--4066943 Score: 56
Period size: 9 Copynumber: 12.4 Consensus size: 9
4066819 AAAAAATGTT
4066829 TTTTTATAA
1 TTTTTATAA
* *
4066838 ATTTTATTA
1 TTTTTATAA
4066847 TTTTTAATTAA
1 TTTTT-A-TAA
*
4066858 TTTATA-ATA
1 TTTTTATA-A
4066867 TTTTTATATA
1 TTTTTATA-A
*
4066877 TTCTTA-AA
1 TTTTTATAA
** *
4066885 AATATATAA
1 TTTTTATAA
* *
4066894 TTTTGATGAT
1 TTTTTAT-AA
4066904 TTTTTATAA
1 TTTTTATAA
*
4066913 TTTTTGTAA
1 TTTTTATAA
*
4066922 CTTTTTAT-G
1 -TTTTTATAA
4066931 TTTTTATAA
1 TTTTTATAA
4066940 TTTT
1 TTTT
4066944 AGAACGCATC
Statistics
Matches: 76, Mismatches: 22, Indels: 16
0.67 0.19 0.14
Matches are distributed among these distances:
8 11 0.14
9 36 0.47
10 23 0.30
11 6 0.08
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (9 bp):
TTTTTATAA
Found at i:4068330 original size:12 final size:12
Alignment explanation
Indices: 4068313--4068346 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
4068303 CGGCAAACCA
4068313 CAACAACAACAG
1 CAACAACAACAG
4068325 CAACAACAACAG
1 CAACAACAACAG
*
4068337 CAACAGCAAC
1 CAACAACAAC
4068347 GGGAACATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.56, C:0.35, G:0.09, T:0.00
Consensus pattern (12 bp):
CAACAACAACAG
Found at i:4069925 original size:26 final size:26
Alignment explanation
Indices: 4069896--4069948 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
4069886 ATATTCTTAA
4069896 CTTAGTAAGTGAGATTGAGATTTTAT
1 CTTAGTAAGTGAGATTGAGATTTTAT
*
4069922 CTTAGTAAGTGGGATTGAGATTTTAT
1 CTTAGTAAGTGAGATTGAGATTTTAT
4069948 C
1 C
4069949 AGGTGTCCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.28, C:0.06, G:0.25, T:0.42
Consensus pattern (26 bp):
CTTAGTAAGTGAGATTGAGATTTTAT
Found at i:4072409 original size:11 final size:11
Alignment explanation
Indices: 4072393--4072425 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
4072383 TCTTTACAGT
4072393 GAAAGAAGTTG
1 GAAAGAAGTTG
4072404 GAAAGAAGTTG
1 GAAAGAAGTTG
4072415 GAAAGAAGTTG
1 GAAAGAAGTTG
4072426 TTAATAATAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.45, C:0.00, G:0.36, T:0.18
Consensus pattern (11 bp):
GAAAGAAGTTG
Found at i:4080933 original size:30 final size:31
Alignment explanation
Indices: 4080899--4080957 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
4080889 TTGTGTATAA
* *
4080899 AATTATAC-TAAAATCAAAATTTATATATCG
1 AATTACACATAAAATCAAAATTGATATATCG
* *
4080929 AATTACACATTAAATCAAAGTTGATATAT
1 AATTACACATAAAATCAAAATTGATATAT
4080958 AATTTTTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 7 0.29
31 17 0.71
ACGTcount: A:0.49, C:0.10, G:0.05, T:0.36
Consensus pattern (31 bp):
AATTACACATAAAATCAAAATTGATATATCG
Found at i:4084072 original size:32 final size:32
Alignment explanation
Indices: 4084036--4084096 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
4084026 TCATGAACTT
*
4084036 ATAAATTAATTACTTGAATTTAATAACTCGTG
1 ATAAATTAATTAATTGAATTTAATAACTCGTG
* *
4084068 ATAAATTAATTAATTTAATTTGATAACTC
1 ATAAATTAATTAATTGAATTTAATAACTC
4084097 AAATTGATTA
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:0.43, C:0.08, G:0.07, T:0.43
Consensus pattern (32 bp):
ATAAATTAATTAATTGAATTTAATAACTCGTG
Found at i:4085962 original size:23 final size:23
Alignment explanation
Indices: 4085934--4085980 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
4085924 AGGAGTTAAA
4085934 TTTTCAAAATA-AAAATTTACGTT
1 TTTTCAAAATATAAAATTTA-GTT
* *
4085957 TTTTCAATATATATAATTTAGTT
1 TTTTCAAAATATAAAATTTAGTT
4085980 T
1 T
4085981 GTGTTAGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.51
Consensus pattern (23 bp):
TTTTCAAAATATAAAATTTAGTT
Found at i:4088595 original size:14 final size:13
Alignment explanation
Indices: 4088562--4088613 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
4088552 CAATTTAAAT
*
4088562 AATATTTTTTTAA
1 AATATTTATTTAA
4088575 AATTATTTATTATAA
1 AA-TATTTATT-TAA
*
4088590 AATATTAATTTAA
1 AATATTTATTTAA
*
4088603 AATATATATTT
1 AATATTTATTT
4088614 TATTATTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
13 14 0.42
14 14 0.42
15 5 0.15
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AATATTTATTTAA
Found at i:4101095 original size:27 final size:28
Alignment explanation
Indices: 4101051--4101104 Score: 76
Period size: 27 Copynumber: 1.9 Consensus size: 28
4101041 AATTAATCTG
4101051 AAATTAAATAATTGAAGT-TCATAGTAA
1 AAATTAAATAATTGAAGTATCATAGTAA
4101078 AAATTAAATTAATT-AAGTCATCATAGT
1 AAATTAAA-TAATTGAAGT-ATCATAGT
4101105 TTTATAAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 12 0.50
28 5 0.21
29 7 0.29
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.35
Consensus pattern (28 bp):
AAATTAAATAATTGAAGTATCATAGTAA
Found at i:4103984 original size:50 final size:50
Alignment explanation
Indices: 4103909--4104007 Score: 162
Period size: 50 Copynumber: 2.0 Consensus size: 50
4103899 TTCAGTATTC
* *
4103909 TGACTTCTGATATATAAAACATAAGGAAGAATCCGTTTTGTTGGTAAAAT
1 TGACTTCTGATATATAAAACATAAGGAAGAATACATTTTGTTGGTAAAAT
* *
4103959 TGACTTCTGGTATATAAAACATAAGGAAGGATACATTTTGTTGGTAAAA
1 TGACTTCTGATATATAAAACATAAGGAAGAATACATTTTGTTGGTAAAA
4104008 AACTGACTTC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.33
Consensus pattern (50 bp):
TGACTTCTGATATATAAAACATAAGGAAGAATACATTTTGTTGGTAAAAT
Found at i:4116065 original size:18 final size:19
Alignment explanation
Indices: 4116031--4116066 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
4116021 TATCCAATTC
*
4116031 TTTTTTTTTTTATATTTTG
1 TTTTTTTTTCTATATTTTG
4116050 TTTTTTTTTCTA-ATTTT
1 TTTTTTTTTCTATATTTT
4116067 TATCTGTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.11, C:0.03, G:0.03, T:0.83
Consensus pattern (19 bp):
TTTTTTTTTCTATATTTTG
Found at i:4116449 original size:35 final size:36
Alignment explanation
Indices: 4116397--4116468 Score: 119
Period size: 35 Copynumber: 2.0 Consensus size: 36
4116387 ACTCGACGTA
4116397 TTTTGCTGGTCTAATGTTTCCTTA-TTTTCTCTTTG
1 TTTTGCTGGTCTAATGTTTCCTTATTTTTCTCTTTG
* *
4116432 TTTTGCTGGTTTGATGTTTCCTTATTTTTCTCTTTG
1 TTTTGCTGGTCTAATGTTTCCTTATTTTTCTCTTTG
4116468 T
1 T
4116469 CTTGTTATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
35 22 0.65
36 12 0.35
ACGTcount: A:0.07, C:0.15, G:0.15, T:0.62
Consensus pattern (36 bp):
TTTTGCTGGTCTAATGTTTCCTTATTTTTCTCTTTG
Found at i:4120060 original size:29 final size:29
Alignment explanation
Indices: 4119994--4120135 Score: 115
Period size: 29 Copynumber: 4.8 Consensus size: 29
4119984 CCTTAAATTA
** *
4119994 TCCAAAAATTGTATTTTGACCCCT-AAACT
1 TCCAAAAATTACATTTTTA-CCCTAAAACT
*
4120023 TCTCTAAAATTACATTTTTACCCTAAAACT
1 TC-CAAAAATTACATTTTTACCCTAAAACT
* * * *
4120053 TCGAAAAAATATATTTTTAACCTCAAAACT
1 TCCAAAAATTACATTTTTACCCT-AAAACT
** * * * *
4120083 TTTAGAAAATTGCATTTTAACCCCAAAAAT
1 TCCA-AAAATTACATTTTTACCCTAAAACT
4120113 TCCAAAAATTACATTTTTACCCT
1 TCCAAAAATTACATTTTTACCCT
4120136 CGAATGTCCA
Statistics
Matches: 86, Mismatches: 23, Indels: 8
0.74 0.20 0.07
Matches are distributed among these distances:
29 38 0.44
30 35 0.41
31 13 0.15
ACGTcount: A:0.39, C:0.21, G:0.04, T:0.36
Consensus pattern (29 bp):
TCCAAAAATTACATTTTTACCCTAAAACT
Found at i:4120145 original size:29 final size:29
Alignment explanation
Indices: 4120113--4120218 Score: 83
Period size: 29 Copynumber: 3.6 Consensus size: 29
4120103 CCCCAAAAAT
4120113 TCCAAAAATT-ACATTTTTACCCTCGAATG
1 TCCAAAAATTCA-ATTTTTACCCTCGAATG
* * * *
4120142 TCCAACAATTCAATTTTTGATCC-CGATTCT
1 TCCAAAAATTCAATTTTT-ACCCTCGAAT-G
* * * *
4120172 TCTAAAAATTACCA-TTTTACCCTCGGACG
1 TCCAAAAATT-CAATTTTTACCCTCGAATG
4120201 TCCAAAAATTCAATTTTT
1 TCCAAAAATTCAATTTTT
4120219 GATCCTGATT
Statistics
Matches: 57, Mismatches: 14, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
28 2 0.04
29 35 0.61
30 18 0.32
31 2 0.04
ACGTcount: A:0.32, C:0.25, G:0.07, T:0.37
Consensus pattern (29 bp):
TCCAAAAATTCAATTTTTACCCTCGAATG
Found at i:4120181 original size:59 final size:60
Alignment explanation
Indices: 4120116--4120325 Score: 207
Period size: 59 Copynumber: 3.6 Consensus size: 60
4120106 CAAAAATTCC
* *
4120116 AAAAATTA-CATTTTTACCCTCGAATGTCCAACAATTCAATTTTTGATCCCGATTCTTCT
1 AAAAATTACCATTTTTACCCTCGAACGTCCAAAAATTCAATTTTTGATCCCGATTCTTCT
* * *
4120175 AAAAATTACCA-TTTTACCCTCGGACGTCCAAAAATTCAATTTTTGATCCTGATTTTTCT
1 AAAAATTACCATTTTTACCCTCGAACGTCCAAAAATTCAATTTTTGATCCCGATTCTTCT
* * * ** * * * * *
4120234 AAAAATTACCA-TTTTACTCTCGGACTTTTAAAATTTC-ATTTTTAACCCCAAATT-TTCC
1 AAAAATTACCATTTTTACCCTCGAACGTCCAAAAATTCAATTTTTGATCCC-GATTCTTCT
**
4120292 AAAAATTACCATTTTGCCCCTCGAGA-GTCCAAAA
1 AAAAATTACCATTTTTACCCTCGA-ACGTCCAAAA
4120326 TTACTATTTT
Statistics
Matches: 125, Mismatches: 22, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
58 23 0.18
59 99 0.79
60 3 0.02
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.37
Consensus pattern (60 bp):
AAAAATTACCATTTTTACCCTCGAACGTCCAAAAATTCAATTTTTGATCCCGATTCTTCT
Found at i:4132073 original size:92 final size:92
Alignment explanation
Indices: 4131911--4132565 Score: 1123
Period size: 92 Copynumber: 7.1 Consensus size: 92
4131901 TTCTACAGGT
*
4131911 TTCAAACATCAATTCTTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
1 TTCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
*
4131976 GAAGTTGTAGTAATAGCAAGATGAAGC
66 GAAGTTGTAGTAAGAGCAAGATGAAGC
* * *
4132003 TTCGAACATCAACTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAACAAGTCTTTATCTCTCT
1 TTCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
* *
4132068 AAAGTTGTAGTAAGAGTAAGATGAAGC
66 GAAGTTGTAGTAAGAGCAAGATGAAGC
*
4132095 TTCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGACAGCAAGTCTTTATCTCTCT
1 TTCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
4132160 GAAGTTGTAGTAAGAGCAAGATGAAGC
66 GAAGTTGTAGTAAGAGCAAGATGAAGC
*
4132187 TTCAAACATCAACTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
1 TTCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
4132252 GAAGTTGTAGTAAGAGCAAGATGAAGC
66 GAAGTTGTAGTAAGAGCAAGATGAAGC
* *
4132279 TTCGAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAACAAGTCTTTATCTCTCT
1 TTCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
* *
4132344 GAAGTTGTAATAAGAGCAAAATGAAGC
66 GAAGTTGTAGTAAGAGCAAGATGAAGC
* *
4132371 TTCAAACATCAACTCCTATCCTCTTGAAGTTGCAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
1 TTCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
*
4132436 GAAGTTGTAGTAAGAGCAAGATGAAGT
66 GAAGTTGTAGTAAGAGCAAGATGAAGC
*
4132463 TTCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTATCT
1 TTCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
**
4132528 GAAGTTACAGTAAGAGCAAGATGAAGC
66 GAAGTTGTAGTAAGAGCAAGATGAAGC
*
4132555 CTC-AACATCAA
1 TTCAAACATCAA
4132566 ACCCTATTTT
Statistics
Matches: 529, Mismatches: 34, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
91 8 0.02
92 521 0.98
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (92 bp):
TTCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
GAAGTTGTAGTAAGAGCAAGATGAAGC
Found at i:4134663 original size:29 final size:29
Alignment explanation
Indices: 4134594--4134729 Score: 96
Period size: 29 Copynumber: 4.7 Consensus size: 29
4134584 AAACTTTTGG
* *** *
4134594 AAAATTACATTTTAACCTTAAAAATTCCA
1 AAAATTCCATTTTAACCCCGAAACTTCCA
* * *
4134623 AAAAATACATTTT-GCCACCG-AACTTCCA
1 AAAATTCCATTTTAACC-CCGAAACTTCCA
*
4134651 AAAATTCCAATTTTAACCTCGAAACTTCCA
1 AAAATTCC-ATTTTAACCCCGAAACTTCCA
* * * **
4134681 AAAATTCTATTTTGACCCCAAAACTTTTA
1 AAAATTCCATTTTAACCCCGAAACTTCCA
*
4134710 AAAATTACCATTTTACCCCC
1 AAAATT-CCATTTTAACCCC
4134730 TGATGTCCAA
Statistics
Matches: 83, Mismatches: 19, Indels: 9
0.75 0.17 0.08
Matches are distributed among these distances:
28 15 0.18
29 41 0.49
30 27 0.33
ACGTcount: A:0.40, C:0.25, G:0.03, T:0.32
Consensus pattern (29 bp):
AAAATTCCATTTTAACCCCGAAACTTCCA
Found at i:4134753 original size:59 final size:58
Alignment explanation
Indices: 4134677--4134810 Score: 144
Period size: 59 Copynumber: 2.3 Consensus size: 58
4134667 CCTCGAAACT
*
4134677 TCCAAAAATTCTATTTTGACCCCAAAACTTTTAAAAATTACCATTTTACCCCCTG-ATG
1 TCCAAAAATTCTATTTTGACCCCAAAACTTCTAAAAATTACCATTTTA-CCCCTGAATG
* * * *** **
4134735 TCCAAAAATTTTGTTTTTGATCTTGATTCTTCTAAAAATTACCATTTTACCCCTGAATG
1 TCCAAAAATTCT-ATTTTGACCCCAAAACTTCTAAAAATTACCATTTTACCCCTGAATG
* *
4134794 TCCAAAAAATCAATTTT
1 TCCAAAAATTCTATTTT
4134811 TGATCCTGAT
Statistics
Matches: 61, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
58 21 0.34
59 40 0.66
ACGTcount: A:0.34, C:0.22, G:0.06, T:0.39
Consensus pattern (58 bp):
TCCAAAAATTCTATTTTGACCCCAAAACTTCTAAAAATTACCATTTTACCCCTGAATG
Found at i:4134811 original size:59 final size:58
Alignment explanation
Indices: 4134708--4134845 Score: 195
Period size: 59 Copynumber: 2.3 Consensus size: 58
4134698 CCAAAACTTT
* *** *
4134708 TAAAAATTACCATTTTACCCCCTGATGTCCAAAAATTTTGTTTTTGATCTTGATTCTTC
1 TAAAAATTACCATTTTA-CCCCTGATGTCCAAAAAATCAATTTTTGATCCTGATTCTTC
*
4134767 TAAAAATTACCATTTTACCCCTGAATGTCCAAAAAATCAATTTTTGATCCTGATTTTTC
1 TAAAAATTACCATTTTACCCCTG-ATGTCCAAAAAATCAATTTTTGATCCTGATTCTTC
*
4134826 TAAAAATTACCGTTTTACCC
1 TAAAAATTACCATTTTACCC
4134846 TCGGACTTCT
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
58 6 0.08
59 65 0.92
ACGTcount: A:0.31, C:0.21, G:0.07, T:0.41
Consensus pattern (58 bp):
TAAAAATTACCATTTTACCCCTGATGTCCAAAAAATCAATTTTTGATCCTGATTCTTC
Found at i:4140220 original size:15 final size:15
Alignment explanation
Indices: 4140200--4140230 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4140190 TTCATATAAA
*
4140200 TTAAAAAATTTTAAC
1 TTAAAAAATTCTAAC
4140215 TTAAAAAATTCTAAC
1 TTAAAAAATTCTAAC
4140230 T
1 T
4140231 ATTAATTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.39
Consensus pattern (15 bp):
TTAAAAAATTCTAAC
Found at i:4146531 original size:27 final size:29
Alignment explanation
Indices: 4146476--4146531 Score: 80
Period size: 27 Copynumber: 2.0 Consensus size: 29
4146466 TTATCCAAAT
4146476 AATATAAAAATAATAATTAATTACAAAAA
1 AATATAAAAATAATAATTAATTACAAAAA
* *
4146505 AATATGAAAAT-AT-ATTAATTACGAAAA
1 AATATAAAAATAATAATTAATTACAAAAA
4146532 TAGGTATTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 13 0.52
28 2 0.08
29 10 0.40
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.29
Consensus pattern (29 bp):
AATATAAAAATAATAATTAATTACAAAAA
Found at i:4147256 original size:25 final size:28
Alignment explanation
Indices: 4147228--4147286 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
4147218 AATAAATACT
4147228 TATTTTT-GTAATTAA-TA-TATATTTA
1 TATTTTTCGTAATTAATTATTATATTTA
*
4147253 TATTTTTTTCGTAATTAATTATTATTTTTA
1 TA--TTTTTCGTAATTAATTATTATATTTA
4147283 TATT
1 TATT
4147287 ATTTAAGTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
25 2 0.07
27 5 0.18
28 10 0.36
29 2 0.07
30 9 0.32
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (28 bp):
TATTTTTCGTAATTAATTATTATATTTA
Found at i:4147266 original size:28 final size:29
Alignment explanation
Indices: 4147230--4147286 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
4147220 TAAATACTTA
4147230 TTTTTGTAATTAA-TA-TATATTTATATT
1 TTTTTGTAATTAATTATTATATTTATATT
*
4147257 TTTTTCGTAATTAATTATTATTTTTATATT
1 TTTTT-GTAATTAATTATTATATTTATATT
4147287 ATTTAAGTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 5 0.19
28 8 0.31
29 2 0.08
30 11 0.42
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.65
Consensus pattern (29 bp):
TTTTTGTAATTAATTATTATATTTATATT
Found at i:4148542 original size:21 final size:20
Alignment explanation
Indices: 4148509--4148548 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
4148499 GAGAGTTTAC
4148509 AAATCAAAATATAATCAAACA
1 AAATCAAAATAT-ATCAAACA
**
4148530 AAATCAACGTATATCAAAC
1 AAATCAAAATATATCAAAC
4148549 CGCAGAGGCG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.60, C:0.17, G:0.03, T:0.20
Consensus pattern (20 bp):
AAATCAAAATATATCAAACA
Found at i:4149096 original size:36 final size:36
Alignment explanation
Indices: 4149018--4149096 Score: 88
Period size: 36 Copynumber: 2.2 Consensus size: 36
4149008 GTGCTAAGTT
* *
4149018 ATATAATTTTTTATAATATGTAACTTAAATCAAAATA
1 ATATAA-TATTTATAATATGTAACTTAAATCAAAAAA
* **
4149055 ATATAATATTTATAATATTTAACTTTCAT-AAAAAA
1 ATATAATATTTATAATATGTAACTTAAATCAAAAAA
4149090 ATTATAA
1 A-TATAA
4149097 ATAGTTCAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
35 6 0.17
36 24 0.67
37 6 0.17
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (36 bp):
ATATAATATTTATAATATGTAACTTAAATCAAAAAA
Found at i:4158173 original size:109 final size:109
Alignment explanation
Indices: 4157982--4158212 Score: 356
Period size: 109 Copynumber: 2.1 Consensus size: 109
4157972 CAAAAGACAC
* * * * * *
4157982 TGTAAGTGGCTTTGCACTTCTACAGTGGTTTGAGGAGCCATCATCTTCTGTGGTTAATTTATTGC
1 TGTAAGCGGTTTTGCACTTCTACAGTGGTTTGAAGAGCCACCATCTTCTGTGGTTAACTTATTAC
*
4158047 TGACTAATTGCAAAGCTTCCATGCAATTCAGTTTGAGGGTTTGA
66 TGACTAATTGCAAAGCTTCCATGCAATTCAATTTGAGGGTTTGA
* *
4158091 TGTAAGCGGTTTTGCACTTCTACAGTGGTTTTAAGAGCCACCATCTTTTGTGGTTAACTTATTAC
1 TGTAAGCGGTTTTGCACTTCTACAGTGGTTTGAAGAGCCACCATCTTCTGTGGTTAACTTATTAC
*
4158156 TGGCTAATTGCAAAGCTTCCATGCAATTCAATTTGAGGGTTTGA
66 TGACTAATTGCAAAGCTTCCATGCAATTCAATTTGAGGGTTTGA
*
4158200 TGTAATC-GTTTTG
1 TGTAAGCGGTTTTG
4158213 TGCTTTTTTT
Statistics
Matches: 111, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
108 6 0.05
109 105 0.95
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.39
Consensus pattern (109 bp):
TGTAAGCGGTTTTGCACTTCTACAGTGGTTTGAAGAGCCACCATCTTCTGTGGTTAACTTATTAC
TGACTAATTGCAAAGCTTCCATGCAATTCAATTTGAGGGTTTGA
Found at i:4160683 original size:24 final size:25
Alignment explanation
Indices: 4160615--4160687 Score: 94
Period size: 25 Copynumber: 3.0 Consensus size: 25
4160605 TTTGGGGTCC
* **
4160615 AATTTGGTACCCGACTCTTTTTTTT
1 AATTTGGTACCTGAAGCTTTTTTTT
**
4160640 AATTTGGTACCTGACTCTTTTTTTT
1 AATTTGGTACCTGAAGCTTTTTTTT
4160665 AATTTGGTACCT-AAGCTTTTTTT
1 AATTTGGTACCTGAAGCTTTTTTT
4160688 AAGGTTCGAT
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
24 9 0.20
25 36 0.80
ACGTcount: A:0.18, C:0.16, G:0.12, T:0.53
Consensus pattern (25 bp):
AATTTGGTACCTGAAGCTTTTTTTT
Found at i:4160687 original size:25 final size:25
Alignment explanation
Indices: 4160615--4160676 Score: 115
Period size: 25 Copynumber: 2.5 Consensus size: 25
4160605 TTTGGGGTCC
*
4160615 AATTTGGTACCCGACTCTTTTTTTT
1 AATTTGGTACCTGACTCTTTTTTTT
4160640 AATTTGGTACCTGACTCTTTTTTTT
1 AATTTGGTACCTGACTCTTTTTTTT
4160665 AATTTGGTACCT
1 AATTTGGTACCT
4160677 AAGCTTTTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.18, C:0.18, G:0.13, T:0.52
Consensus pattern (25 bp):
AATTTGGTACCTGACTCTTTTTTTT
Found at i:4166875 original size:21 final size:21
Alignment explanation
Indices: 4166851--4166904 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
4166841 CCTGTACTAG
4166851 TTCTACCGATACAAG-CATGAT
1 TTCTACCGATACAAGTCATG-T
*
4166872 TTCTACTGATACAAGTCATGT
1 TTCTACCGATACAAGTCATGT
**
4166893 AACTACCGATAC
1 TTCTACCGATAC
4166905 CAAAAACTCC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 24 0.86
22 4 0.14
ACGTcount: A:0.33, C:0.24, G:0.13, T:0.30
Consensus pattern (21 bp):
TTCTACCGATACAAGTCATGT
Found at i:4168685 original size:22 final size:23
Alignment explanation
Indices: 4168660--4168706 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 23
4168650 GACTTTCATC
4168660 ATTAAGCTTTAATTAA-TC-ATTT
1 ATTAAGC-TTAATTAATTCTATTT
*
4168682 ATTAATCTTAATTAATTCTATTT
1 ATTAAGCTTAATTAATTCTATTT
4168705 AT
1 AT
4168707 ACTTAATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 8 0.36
22 8 0.36
23 6 0.27
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.53
Consensus pattern (23 bp):
ATTAAGCTTAATTAATTCTATTT
Found at i:4173813 original size:18 final size:18
Alignment explanation
Indices: 4173764--4173815 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
4173754 TTTTGAATAA
*
4173764 TTTTATA-TATTTTTATT
1 TTTTATATTATTATTATT
* *
4173781 TTTTA-ATAAAATATTATT
1 TTTTATAT-TATTATTATT
4173799 TTTTATATTATTATTAT
1 TTTTATATTATTATTAT
4173816 GAAATTAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
16 1 0.04
17 5 0.19
18 19 0.70
19 2 0.07
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTATATTATTATTATT
Found at i:4174035 original size:16 final size:17
Alignment explanation
Indices: 4173999--4174035 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
4173989 TACTAATATT
*
4173999 AAAAATAAAAATTTATG
1 AAAAATAAAAATTTATA
4174016 AAAAATAAAAATTTA-A
1 AAAAATAAAAATTTATA
4174032 AAAA
1 AAAA
4174036 TTACTAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (17 bp):
AAAAATAAAAATTTATA
Found at i:4175114 original size:20 final size:21
Alignment explanation
Indices: 4175089--4175131 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
4175079 TACCTCAAAC
* *
4175089 CCCCAAACATTTTTACT-TTT
1 CCCCAAAAACTTTTACTCTTT
4175109 CCCCAAAAACTTTTACTCTTT
1 CCCCAAAAACTTTTACTCTTT
4175130 CC
1 CC
4175132 TACTTTCCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.26, C:0.35, G:0.00, T:0.40
Consensus pattern (21 bp):
CCCCAAAAACTTTTACTCTTT
Found at i:4175420 original size:171 final size:171
Alignment explanation
Indices: 4175106--4175425 Score: 423
Period size: 171 Copynumber: 1.9 Consensus size: 171
4175096 CATTTTTACT
** * *
4175106 TTTCCCCAAAAACTTTTACTCTTTCCTACTTTCCCTCAAAACTTTTACTCTCCTCTCATCTCAGC
1 TTTCCCCAAAAACTTTTACTCCCTCCTACTTTCCCTCAAAACTTTTACTCCCCTCTCATCCCAGC
* * * ** *
4175171 TCCAATCTACCTCAAACTCATTTCCCTCCAATTTTTTTTTAAATATTTTCCCTCCAATATTTTAC
66 TCCAATCTACCCCAAACTCATTCCCCCCCAATTTTTTTAAAAATATTTTCCCTCCAAAATTTTAC
4175236 TCTTCCCATTTACT-TTCCCTAAAAATCCTCAAAACTTTTTA
131 TC-TCCCATTTACTCTTCCCTAAAAATCCTCAAAACTTTTTA
* *
4175277 TTTCCCC-AAAACTTTTATTCCCTCCTACTTTTCCTCTAAAACTTTTACTCCCCTCTCATCCCA-
1 TTTCCCCAAAAACTTTTACTCCCTCCTACTTTCCCTC-AAAACTTTTACTCCCCTCTCATCCCAG
* * *
4175340 CTCCTCATCTACCCCAAACTCATTCCCCCCTCAATTTTTTTAAAAATATTTTTCCTTCAAAATTT
65 CTCC-AATCTACCCCAAACTCATTCCCCCC-CAATTTTTTTAAAAATATTTTCCCTCCAAAATTT
*
4175405 TACTC-CCTTATTTACTCTTCC
128 TACTCTCC-CATTTACTCTTCC
4175426 TCAAAATTTT
Statistics
Matches: 128, Mismatches: 16, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
170 31 0.24
171 59 0.46
172 38 0.30
ACGTcount: A:0.24, C:0.34, G:0.00, T:0.42
Consensus pattern (171 bp):
TTTCCCCAAAAACTTTTACTCCCTCCTACTTTCCCTCAAAACTTTTACTCCCCTCTCATCCCAGC
TCCAATCTACCCCAAACTCATTCCCCCCCAATTTTTTTAAAAATATTTTCCCTCCAAAATTTTAC
TCTCCCATTTACTCTTCCCTAAAAATCCTCAAAACTTTTTA
Found at i:4175744 original size:18 final size:18
Alignment explanation
Indices: 4175721--4175791 Score: 56
Period size: 18 Copynumber: 3.9 Consensus size: 18
4175711 CAATTTCATA
4175721 TTTTATATTTAAAATAAT
1 TTTTATATTTAAAATAAT
**
4175739 TTTTAT-TAAAAAATCACAT
1 TTTTATATTTAAAAT-A-AT
* * *
4175758 TTTTACATTTAATATATT
1 TTTTATATTTAAAATAAT
4175776 TTTTA-ATTTTAAAATA
1 TTTTATA-TTTAAAATA
4175792 CATAGTGACA
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
17 7 0.17
18 21 0.51
19 8 0.20
20 5 0.12
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTTATATTTAAAATAAT
Found at i:4186044 original size:2 final size:2
Alignment explanation
Indices: 4186037--4186076 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
4186027 TAACACTTTA
4186037 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
4186077 GAGCGGGATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4190847 original size:21 final size:19
Alignment explanation
Indices: 4190823--4190863 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
4190813 CTCTACAACT
4190823 AAAATTCTAAGAATGTAAAAA
1 AAAATTC-AAGAAT-TAAAAA
*
4190844 AAAATTCAATAATTAAAAA
1 AAAATTCAAGAATTAAAAA
4190863 A
1 A
4190864 TATATATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 5 0.26
21 7 0.37
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (19 bp):
AAAATTCAAGAATTAAAAA
Found at i:4193463 original size:29 final size:29
Alignment explanation
Indices: 4193417--4193472 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
4193407 ATAAATTTAA
* * * *
4193417 ATTTTTATCATATTATTATTTCATATTAC
1 ATTTATATCACATAATTATATCATATTAC
4193446 ATTTATATCACATAATTATATCATATT
1 ATTTATATCACATAATTATATCATATT
4193473 CGAAATTTAT
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:0.36, C:0.11, G:0.00, T:0.54
Consensus pattern (29 bp):
ATTTATATCACATAATTATATCATATTAC
Found at i:4198060 original size:187 final size:188
Alignment explanation
Indices: 4197744--4198118 Score: 540
Period size: 187 Copynumber: 2.0 Consensus size: 188
4197734 CCAAATTTAA
*
4197744 AAAAATTGTCAAGCTAAGAACCAAAATAGACATCTTTGACAGGTACAATTACTATAGAGTTCGAT
1 AAAAATTGTCAAGCTAAGAACCAAAATAGACATCTTTGACAGGTACAATTACTATAGAGTTCAAT
* * * * * *
4197809 GGTAAGATTGATGAATTTAATTTTTATTATTCGTTAGAACATCCTAGTGAAGTGTCCAAGGTATG
66 AGTAAGACTGATGAATTTAATATTTATGATTCATTAGAACATCCCAGTGAAGTGTCCAAGGTATG
* * **
4197874 CATTGAGGATACG-GTTCTAAGACACGAGATTCTTTGAACTTACATGATGAAATTAGG
131 CAATGAGGATACGAATTCTAAGACACGAGATTCTTTGAACTTACACAATGAAATTAGG
4197931 AAAAATTGTCAAGCTAAGAACCAAAATAGACATCTTTGAC-GGATACAATTACTAT-GAAGTTCA
1 AAAAATTGTCAAGCTAAGAACCAAAATAGACATCTTTGACAGG-TACAATTACTATAG-AGTTCA
* * *
4197994 ATAGTAAGGCTGATGAATTTAATATTTATGGTTCATTAGAACATCCCAGTGAAGTGTCCGAGGTA
64 ATAGTAAGACTGATGAATTTAATATTTATGATTCATTAGAACATCCCAGTGAAGTGTCCAAGGTA
* *
4198059 TGCAATGAGGATACGATTAATTTTGAGACACGAGATTCTTTGAACTTACACAATGAAATT
129 TGCAATGAGGATACG---AATTCTAAGACACGAGATTCTTTGAACTTACACAATGAAATT
4198119 GAATCAATTC
Statistics
Matches: 166, Mismatches: 16, Indels: 8
0.87 0.08 0.04
Matches are distributed among these distances:
186 3 0.02
187 127 0.77
191 36 0.22
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (188 bp):
AAAAATTGTCAAGCTAAGAACCAAAATAGACATCTTTGACAGGTACAATTACTATAGAGTTCAAT
AGTAAGACTGATGAATTTAATATTTATGATTCATTAGAACATCCCAGTGAAGTGTCCAAGGTATG
CAATGAGGATACGAATTCTAAGACACGAGATTCTTTGAACTTACACAATGAAATTAGG
Found at i:4200598 original size:17 final size:17
Alignment explanation
Indices: 4200560--4200601 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
4200550 GGAAAAAGTA
*
4200560 GTTACAAGAATATGAAAT
1 GTTA-AAGAATATGAAAG
4200578 GTTAAAGAATAT-AGAAG
1 GTTAAAGAATATGA-AAG
4200595 GTTAAAG
1 GTTAAAG
4200602 GTCAAGGGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 17 0.77
18 4 0.18
ACGTcount: A:0.50, C:0.02, G:0.21, T:0.26
Consensus pattern (17 bp):
GTTAAAGAATATGAAAG
Found at i:4202854 original size:14 final size:14
Alignment explanation
Indices: 4202835--4202875 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
4202825 TTAAAACTAG
*
4202835 TTATTTTTAAGATT
1 TTATTTTTAAAATT
4202849 TTATTTTATAAAATT
1 TTATTTT-TAAAATT
*
4202864 TTAGTTTTAAAA
1 TTATTTTTAAAA
4202876 AACTTTCACA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (14 bp):
TTATTTTTAAAATT
Found at i:4202866 original size:15 final size:15
Alignment explanation
Indices: 4202835--4202876 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
4202825 TTAAAACTAG
*
4202835 TTATTTT-TAAGATT
1 TTATTTTATAAAATT
4202849 TTATTTTATAAAATT
1 TTATTTTATAAAATT
4202864 TTAGTTTTA-AAAA
1 TTA-TTTTATAAAA
4202877 ACTTTCACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 7 0.28
15 13 0.52
16 5 0.20
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (15 bp):
TTATTTTATAAAATT
Found at i:4203237 original size:15 final size:14
Alignment explanation
Indices: 4203196--4203246 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 14
4203186 ATTTTGGTTA
4203196 TTAAAATTAATTATTT
1 TTAAAATT--TTATTT
*
4203212 TTAAGATTTTATTT
1 TTAAAATTTTATTT
4203226 TATAAAATTTTATTT
1 T-TAAAATTTTATTT
4203241 TTAAAA
1 TTAAAA
4203247 AACTTTTACA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 12 0.38
15 13 0.41
16 7 0.22
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (14 bp):
TTAAAATTTTATTT
Found at i:4206927 original size:19 final size:19
Alignment explanation
Indices: 4206903--4206939 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
4206893 AGTTTTTATT
*
4206903 TTTAATTTTTTTATTAATG
1 TTTAATGTTTTTATTAATG
4206922 TTTAATGTTTTTATTAAT
1 TTTAATGTTTTTATTAAT
4206940 ATTAGTTATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (19 bp):
TTTAATGTTTTTATTAATG
Found at i:4207403 original size:20 final size:20
Alignment explanation
Indices: 4207353--4207404 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
4207343 ATAATTTTTT
*
4207353 AAAATTATAAAAATTATTAA
1 AAAATTATAAAAAGTATTAA
4207373 AAAA-TAGTAAAAAGTA-TAA
1 AAAATTA-TAAAAAGTATTAA
4207392 AAATATTATAAAA
1 AAA-ATTATAAAA
4207405 TAATCAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
19 8 0.29
20 18 0.64
21 2 0.07
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (20 bp):
AAAATTATAAAAAGTATTAA
Found at i:4207406 original size:10 final size:9
Alignment explanation
Indices: 4207353--4207395 Score: 50
Period size: 10 Copynumber: 4.6 Consensus size: 9
4207343 ATAATTTTTT
4207353 AAAATTATA
1 AAAATTATA
4207362 AAAATTATTA
1 AAAATTA-TA
*
4207372 AAAAATAGTA
1 AAAATTA-TA
*
4207382 AAAAGTATA
1 AAAATTATA
4207391 AAAAT
1 AAAAT
4207396 ATTATAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
9 13 0.45
10 16 0.55
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (9 bp):
AAAATTATA
Found at i:4207486 original size:2 final size:2
Alignment explanation
Indices: 4207481--4207519 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
4207471 TCAAAACTAT
4207481 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
4207520 GGATTATAAT
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:4207628 original size:20 final size:19
Alignment explanation
Indices: 4207599--4207636 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
4207589 ATCAATATGT
*
4207599 TATATATTATACGATATAA
1 TATATATTATACAATATAA
4207618 TATAGTATTATACAATATA
1 TATA-TATTATACAATATA
4207637 GGAGTAAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (19 bp):
TATATATTATACAATATAA
Found at i:4208810 original size:13 final size:11
Alignment explanation
Indices: 4208744--4208803 Score: 67
Period size: 11 Copynumber: 5.9 Consensus size: 11
4208734 CCACATCAAC
*
4208744 AAATGATTTTA
1 AAATTATTTTA
4208755 AAATTA--TTA
1 AAATTATTTTA
4208764 AAATTATTTTA
1 AAATTATTTTA
*
4208775 AAA--A-TATA
1 AAATTATTTTA
4208783 AAATTATTTTA
1 AAATTATTTTA
4208794 AAATTATTTT
1 AAATTATTTT
4208804 TTAAAATATA
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
8 6 0.15
9 10 0.24
10 1 0.02
11 24 0.59
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (11 bp):
AAATTATTTTA
Found at i:4208813 original size:31 final size:30
Alignment explanation
Indices: 4208753--4208830 Score: 115
Period size: 31 Copynumber: 2.6 Consensus size: 30
4208743 CAAATGATTT
4208753 TAAAATTA--TTAAAATTATTTTAAAAATA
1 TAAAATTATTTTAAAATTATTTTAAAAATA
*
4208781 TAAAATTATTTTAAAATTATTTTTTAAAATA
1 TAAAATTATTTTAAAATTA-TTTTAAAAATA
4208812 TAAAATTATTTTAATAATT
1 TAAAATTATTTTAA-AATT
4208831 TAATCATCAT
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
28 8 0.18
30 9 0.20
31 24 0.53
32 4 0.09
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (30 bp):
TAAAATTATTTTAAAATTATTTTAAAAATA
Found at i:4209594 original size:96 final size:97
Alignment explanation
Indices: 4209407--4209601 Score: 257
Period size: 96 Copynumber: 2.0 Consensus size: 97
4209397 TTCCTAAGAA
* * * * * *
4209407 ATGAGATTGAAATAGAGAACCTTGAAGGGTTAGAAGAGTGATGGAAGAAGAATAAGTCATGGTTT
1 ATGAGATTAAAATAAAGAACCTTGAAAGGTTAGAAGAATGAT-G-AGAAGAAAAAGCCATGGTTT
*
4209472 GATTCAGAATCCAAGTGAAGAAGTAGCCATGGTT
64 GATTCAAAATCCAAGTGAAGAAGTAGCCATGGTT
* * *
4209506 ATGAGATTAAAATAAAGAACCTTGAAAGGTTGGGAGAATGAT-AGAAGAAAAAGCCATGGTTTGG
1 ATGAGATTAAAATAAAGAACCTTGAAAGGTTAGAAGAATGATGAGAAGAAAAAGCCATGGTTTGA
* *
4209570 TTCAAAATCTAAGTGGAGAAGTAGCCATGGTT
66 TTCAAAATCCAAGTGAAGAAGTAGCCATGGTT
4209602 TGGTTCAAAA
Statistics
Matches: 84, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
96 48 0.57
99 36 0.43
ACGTcount: A:0.39, C:0.08, G:0.28, T:0.24
Consensus pattern (97 bp):
ATGAGATTAAAATAAAGAACCTTGAAAGGTTAGAAGAATGATGAGAAGAAAAAGCCATGGTTTGA
TTCAAAATCCAAGTGAAGAAGTAGCCATGGTT
Found at i:4209718 original size:14 final size:14
Alignment explanation
Indices: 4209699--4209752 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
4209689 GATGAAATTG
4209699 GGAAAGAAATAATA
1 GGAAAGAAATAATA
*
4209713 GGAAAGAAGATGAAATTG
1 GGAAAGAA-AT--AA-TA
4209731 GGAAAGAAATAATA
1 GGAAAGAAATAATA
*
4209745 AGAAAGAA
1 GGAAAGAA
4209753 GATGAAATTG
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
14 16 0.48
15 4 0.12
17 4 0.12
18 9 0.27
ACGTcount: A:0.61, C:0.00, G:0.26, T:0.13
Consensus pattern (14 bp):
GGAAAGAAATAATA
Found at i:4209720 original size:32 final size:32
Alignment explanation
Indices: 4209684--4209762 Score: 149
Period size: 32 Copynumber: 2.5 Consensus size: 32
4209674 AAAAGTGAGG
*
4209684 AAGAAGATGAAATTGGGAAAGAAATAATAGGA
1 AAGAAGATGAAATTGGGAAAGAAATAATAAGA
4209716 AAGAAGATGAAATTGGGAAAGAAATAATAAGA
1 AAGAAGATGAAATTGGGAAAGAAATAATAAGA
4209748 AAGAAGATGAAATTG
1 AAGAAGATGAAATTG
4209763 AAAATTAAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.57, C:0.00, G:0.27, T:0.16
Consensus pattern (32 bp):
AAGAAGATGAAATTGGGAAAGAAATAATAAGA
Found at i:4209795 original size:11 final size:11
Alignment explanation
Indices: 4209779--4209817 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
4209769 AAAATGATTT
4209779 AATAATTTTAA
1 AATAATTTTAA
4209790 AATAATTTT--
1 AATAATTTTAA
4209799 AATAATTTTAA
1 AATAATTTTAA
*
4209810 AATCATTT
1 AATAATTT
4209818 ACTGACGTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 9 0.36
11 16 0.64
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (11 bp):
AATAATTTTAA
Found at i:4209801 original size:20 final size:20
Alignment explanation
Indices: 4209767--4209817 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
4209757 AAATTGAAAA
*
4209767 TTAAAATGA-TTTAATAATT
1 TTAAAATAATTTTAATAATT
4209786 TTAAAATAATTTTAATAATT
1 TTAAAATAATTTTAATAATT
*
4209806 TTAAAATCATTT
1 TTAAAATAATTT
4209818 ACTGACGTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 8 0.28
20 21 0.72
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (20 bp):
TTAAAATAATTTTAATAATT
Found at i:4209802 original size:9 final size:9
Alignment explanation
Indices: 4209776--4209809 Score: 50
Period size: 9 Copynumber: 3.6 Consensus size: 9
4209766 ATTAAAATGA
4209776 TTTAATAAT
1 TTTAATAAT
4209785 TTTAAAATAAT
1 TTT--AATAAT
4209796 TTTAATAAT
1 TTTAATAAT
4209805 TTTAA
1 TTTAA
4209810 AATCATTTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 14 0.61
11 9 0.39
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (9 bp):
TTTAATAAT
Found at i:4219534 original size:2 final size:2
Alignment explanation
Indices: 4219527--4219559 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
4219517 ACACATCCAT
*
4219527 TA TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4219560 TTAATATGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:4221968 original size:28 final size:27
Alignment explanation
Indices: 4221934--4221989 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 27
4221924 TATACATATT
*
4221934 TATAATTTTATCATTTTTAGAGTTAAAA
1 TATAATTTTATCATTATTA-AGTTAAAA
*
4221962 TATAATTTTATCATTATTAATTTAAAA
1 TATAATTTTATCATTATTAAGTTAAAA
4221989 T
1 T
4221990 TTTATAAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 8 0.31
28 18 0.69
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.52
Consensus pattern (27 bp):
TATAATTTTATCATTATTAAGTTAAAA
Found at i:4223856 original size:33 final size:32
Alignment explanation
Indices: 4223819--4223886 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
4223809 AAAATTAAAT
*
4223819 AAATAAAAAAATGTATAAAT-TTTTTAAATATTA
1 AAATAAAAAAA--TATAAATATTTTTAAAAATTA
* *
4223852 AAATAATATAATATAAATATTTTTAAAAATTA
1 AAATAAAAAAATATAAATATTTTTAAAAATTA
4223884 AAA
1 AAA
4223887 AAATATAGGC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 7 0.23
32 15 0.48
33 9 0.29
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (32 bp):
AAATAAAAAAATATAAATATTTTTAAAAATTA
Found at i:4223869 original size:31 final size:32
Alignment explanation
Indices: 4223832--4223893 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
4223822 TAAAAAAATG
* *
4223832 TATAAAT-TTTTTAAATATTAAAATAATATAA
1 TATAAATATTTTTAAAAATTAAAAAAATATAA
4223863 TATAAATATTTTTAAAAATTAAAAAAATATA
1 TATAAATATTTTTAAAAATTAAAAAAATATA
4223894 GGCCGGCCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
31 7 0.25
32 21 0.75
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (32 bp):
TATAAATATTTTTAAAAATTAAAAAAATATAA
Found at i:4248348 original size:23 final size:22
Alignment explanation
Indices: 4248322--4248364 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
4248312 ATCCCTTTCC
*
4248322 AGAATTAAATTATATATTTTGAA
1 AGAATTAAAATATA-ATTTTGAA
4248345 AGAATTAAAATATAATTTTG
1 AGAATTAAAATATAATTTTG
4248365 TTTTTCACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (22 bp):
AGAATTAAAATATAATTTTGAA
Found at i:4254442 original size:2 final size:2
Alignment explanation
Indices: 4254435--4254460 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4254425 ATCAACTTTC
4254435 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
4254461 GCATGTTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4257300 original size:3 final size:3
Alignment explanation
Indices: 4257294--4257325 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
4257284 ACCAGCGTCT
*
4257294 TCA TCA TCA TCA TCA TCA TCA TCA CCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
4257326 CTCGTCACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.38, G:0.00, T:0.31
Consensus pattern (3 bp):
TCA
Found at i:4258699 original size:6 final size:6
Alignment explanation
Indices: 4258688--4258733 Score: 83
Period size: 6 Copynumber: 7.7 Consensus size: 6
4258678 GGGCTTCACT
*
4258688 TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC CCTTCC TCTT
1 TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTT
4258734 GTTCTACTTC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (6 bp):
TCTTCC
Found at i:4261732 original size:2 final size:2
Alignment explanation
Indices: 4261725--4261756 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
4261715 AGCAAACAGC
*
4261725 GA GA GA GA AA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
4261757 ATGAGTGTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4262108 original size:11 final size:12
Alignment explanation
Indices: 4262084--4262113 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
4262074 CTATTATTAC
4262084 TTTTAATGTGAT
1 TTTTAATGTGAT
4262096 TTTTAATGT-AT
1 TTTTAATGTGAT
4262107 TTTTAAT
1 TTTTAAT
4262114 AATTATTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.50
12 9 0.50
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (12 bp):
TTTTAATGTGAT
Found at i:4269022 original size:31 final size:30
Alignment explanation
Indices: 4268986--4269054 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 30
4268976 GAAAAAAATT
*
4268986 AATAATCTAGTGATTTAAATAAAAATATTTA
1 AATAAT-TAGTGATTTAAACAAAAATATTTA
* * * *
4269017 AATAATTCAGTAACTTAAACGAAAATTTTTA
1 AATAATT-AGTGATTTAAACAAAAATATTTA
4269048 AATAATT
1 AATAATT
4269055 TAATGATTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 1 0.03
31 31 0.97
ACGTcount: A:0.51, C:0.06, G:0.06, T:0.38
Consensus pattern (30 bp):
AATAATTAGTGATTTAAACAAAAATATTTA
Found at i:4269938 original size:15 final size:15
Alignment explanation
Indices: 4269918--4269947 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4269908 CCCGCGAAAT
*
4269918 CTACACCGAGGAAGA
1 CTACACCGAAGAAGA
4269933 CTACACCGAAGAAGA
1 CTACACCGAAGAAGA
4269948 ATGGAATGAA
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:0.27, G:0.23, T:0.07
Consensus pattern (15 bp):
CTACACCGAAGAAGA
Found at i:4283573 original size:14 final size:15
Alignment explanation
Indices: 4283537--4283587 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
4283527 ACAAAATATT
4283537 AACATAAATAATTAA
1 AACATAAATAATTAA
* * *
4283552 AACGTAAA-ATTTCA
1 AACATAAATAATTAA
*
4283566 AACATAAATAACTAA
1 AACATAAATAATTAA
*
4283581 AATATAA
1 AACATAA
4283588 TCTGATACAA
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
14 11 0.41
15 16 0.59
ACGTcount: A:0.63, C:0.10, G:0.02, T:0.25
Consensus pattern (15 bp):
AACATAAATAATTAA
Found at i:4284274 original size:6 final size:6
Alignment explanation
Indices: 4284263--4284287 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
4284253 ATAAAAGAGT
4284263 GTGGCA GTGGCA GTGGCA GTGGCA G
1 GTGGCA GTGGCA GTGGCA GTGGCA G
4284288 AGGTGATGAT
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:0.16, C:0.16, G:0.52, T:0.16
Consensus pattern (6 bp):
GTGGCA
Found at i:4291069 original size:16 final size:15
Alignment explanation
Indices: 4291022--4291069 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 15
4291012 GGTTTGACTC
* *
4291022 ATTTTTAAATTTATA
1 ATTTTTATATTTATT
4291037 ATGTTTTATATTATATT
1 AT-TTTTATATT-TATT
4291054 ATTTTTATATATTATT
1 ATTTTTATAT-TTATT
4291070 TAATTTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
15 2 0.07
16 20 0.71
17 6 0.21
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (15 bp):
ATTTTTATATTTATT
Found at i:4291404 original size:23 final size:21
Alignment explanation
Indices: 4291356--4291405 Score: 55
Period size: 23 Copynumber: 2.3 Consensus size: 21
4291346 ATGAAAAATG
*
4291356 TATAAAATTATTAAATAATAA
1 TATAAAATTATTAAAAAATAA
* *
4291377 AATAAATATTTTTAAAAAAATAA
1 TATAAA-ATTATT-AAAAAATAA
4291400 TATAAA
1 TATAAA
4291406 CAGATCTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 5 0.22
22 5 0.22
23 13 0.57
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
TATAAAATTATTAAAAAATAA
Found at i:4292075 original size:24 final size:24
Alignment explanation
Indices: 4292014--4292076 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
4292004 TAGAGTAATA
* *
4292014 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
*
4292038 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
4292062 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
4292077 GATTATTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.51, C:0.11, G:0.14, T:0.24
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:4294032 original size:24 final size:24
Alignment explanation
Indices: 4294004--4294062 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
4293994 TAGAGTAATA
* *
4294004 AGAGTTTGACTCAAATAAATAAAC
1 AGAGTTTAACTCAAACAAATAAAC
* *
4294028 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTCAAACAAATAAAC
*
4294052 AGAATTTAACT
1 AGAGTTTAACT
4294063 GAAAGATTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.51, C:0.10, G:0.12, T:0.27
Consensus pattern (24 bp):
AGAGTTTAACTCAAACAAATAAAC
Found at i:4294065 original size:24 final size:24
Alignment explanation
Indices: 4294020--4294066 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
4294010 TGACTCAAAT
* *
4294020 AAATAAACAGAGTTTAATTGAAAC
1 AAATAAACAGAATTTAACTGAAAC
4294044 AAATAAACAGAATTTAACTGAAA
1 AAATAAACAGAATTTAACTGAAA
4294067 GATTATTTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.57, C:0.09, G:0.11, T:0.23
Consensus pattern (24 bp):
AAATAAACAGAATTTAACTGAAAC
Found at i:4294352 original size:23 final size:23
Alignment explanation
Indices: 4294287--4294354 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 23
4294277 TATAAAAATT
*
4294287 TAAATTA-ATTT-ATTTTTTATGAA
1 TAAATTATATTTAAATTTTTA--AA
4294310 T-AATTATA-TTAAATTATTTAAA
1 TAAATTATATTTAAATT-TTTAAA
*
4294332 TAAATTATATTTAAGTTTTTAAA
1 TAAATTATATTTAAATTTTTAAA
4294355 AGATTTTATG
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
22 10 0.26
23 18 0.47
24 10 0.26
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (23 bp):
TAAATTATATTTAAATTTTTAAA
Found at i:4307956 original size:11 final size:11
Alignment explanation
Indices: 4307900--4307949 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
4307890 ATATTCAAAT
*
4307900 AATAACAACAA
1 AATAATAACAA
*
4307911 AATAACAACAA
1 AATAATAACAA
* * *
4307922 TATAATAGCGA
1 AATAATAACAA
4307933 AATAATAACAA
1 AATAATAACAA
4307944 AATAAT
1 AATAAT
4307950 GAAAAAAATG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 32 1.00
ACGTcount: A:0.66, C:0.12, G:0.04, T:0.18
Consensus pattern (11 bp):
AATAATAACAA
Found at i:4308234 original size:39 final size:38
Alignment explanation
Indices: 4308177--4308332 Score: 127
Period size: 39 Copynumber: 4.1 Consensus size: 38
4308167 AACTTTAAGA
4308177 TGATCTATTCAATTATTTTTTAGAATTGAATTGTAAAAT
1 TGATCTATTCAA-TATTTTTTAGAATTGAATTGTAAAAT
* ** * * *
4308216 TGATCTATTCGATCATTTTGCAAAATAGAATTGTAAGAT
1 TGATCTATTCAAT-ATTTTTTAGAATTGAATTGTAAAAT
* * * ***
4308255 TCATGTATTCGATA-TTTTTAGAATTG-ATTAGTAGGGT
1 TGATCTATTCAATATTTTTTAGAATTGAATT-GTAAAAT
* * * *
4308292 TGATTTATTCAATATTTTTTAGAATTAAATTGCAAAGT
1 TGATCTATTCAATATTTTTTAGAATTGAATTGTAAAAT
4308330 TGA
1 TGA
4308333 CGTATTGGAT
Statistics
Matches: 92, Mismatches: 21, Indels: 9
0.75 0.17 0.07
Matches are distributed among these distances:
36 3 0.03
37 24 0.26
38 20 0.22
39 45 0.49
ACGTcount: A:0.34, C:0.06, G:0.15, T:0.45
Consensus pattern (38 bp):
TGATCTATTCAATATTTTTTAGAATTGAATTGTAAAAT
Found at i:4308800 original size:16 final size:17
Alignment explanation
Indices: 4308763--4308800 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
4308753 AGTTCATAAT
4308763 ATTT-TATATTATGTTA
1 ATTTATATATTATGTTA
4308779 ACTTTATATATTATG-TA
1 A-TTTATATATTATGTTA
4308796 ATTTA
1 ATTTA
4308801 AAATACATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 5 0.25
17 6 0.30
18 9 0.45
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (17 bp):
ATTTATATATTATGTTA
Found at i:4308917 original size:16 final size:16
Alignment explanation
Indices: 4308898--4308945 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
4308888 TAATTTCAAT
4308898 AAATTAAAAATATATA
1 AAATTAAAAATATATA
*
4308914 AAATTATTAAATAT-TA
1 AAATTA-AAAATATATA
* *
4308930 AAATAAAAAAAATATA
1 AAATTAAAAATATATA
4308946 TATATAGATG
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 5 0.19
16 15 0.58
17 6 0.23
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AAATTAAAAATATATA
Found at i:4319357 original size:14 final size:14
Alignment explanation
Indices: 4319318--4319363 Score: 65
Period size: 14 Copynumber: 3.2 Consensus size: 14
4319308 TAAATATTAA
4319318 ATATATTAAAAATT
1 ATATATTAAAAATT
* *
4319332 ATAAATTCAAAAAAT
1 ATATATT-AAAAATT
4319347 ATATATTAAAAATT
1 ATATATTAAAAATT
4319361 ATA
1 ATA
4319364 AATAATGTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 15 0.56
15 12 0.44
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (14 bp):
ATATATTAAAAATT
Found at i:4319657 original size:19 final size:19
Alignment explanation
Indices: 4319615--4319654 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
4319605 AAAATGAAAT
*
4319615 TAATATTTTTTTGACATCA
1 TAATATTTTTTTAACATCA
4319634 TAATATTTTTTTAAC-TCA
1 TAATATTTTTTTAACATCA
4319652 TAA
1 TAA
4319655 ATAGAAGGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (19 bp):
TAATATTTTTTTAACATCA
Found at i:4321374 original size:11 final size:11
Alignment explanation
Indices: 4321360--4321386 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
4321350 GTTCGTGAAT
4321360 CGTTCATATAA
1 CGTTCATATAA
4321371 CGTTCATATAA
1 CGTTCATATAA
4321382 CGTTC
1 CGTTC
4321387 GTTTACTAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (11 bp):
CGTTCATATAA
Found at i:4325233 original size:22 final size:22
Alignment explanation
Indices: 4325208--4325249 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
4325198 CCTCAAATCC
*
4325208 AAACCTTAAATCTTGAATCTTA
1 AAACCTCAAATCTTGAATCTTA
4325230 AAACCTCAAATCTTGAATCT
1 AAACCTCAAATCTTGAATCT
4325250 CGAACCCACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.21, G:0.05, T:0.33
Consensus pattern (22 bp):
AAACCTCAAATCTTGAATCTTA
Found at i:4325355 original size:28 final size:27
Alignment explanation
Indices: 4325295--4325356 Score: 70
Period size: 28 Copynumber: 2.3 Consensus size: 27
4325285 ATTTTGATCC
* *
4325295 TAAATTTTGAATCCAAATCCTAAATCT
1 TAAACTTTGAATCCAAATCCTAAACCT
* *
4325322 TAAACTTTGAAATCCGAATCCTGAACCT
1 TAAACTTTG-AATCCAAATCCTAAACCT
*
4325350 TGAACTT
1 TAAACTT
4325357 GAGGTGAAGA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 8 0.28
28 21 0.72
ACGTcount: A:0.37, C:0.21, G:0.08, T:0.34
Consensus pattern (27 bp):
TAAACTTTGAATCCAAATCCTAAACCT
Found at i:4326782 original size:29 final size:29
Alignment explanation
Indices: 4326750--4326976 Score: 105
Period size: 29 Copynumber: 7.8 Consensus size: 29
4326740 TTTGACTTTC
*
4326750 GGGGGCAAAAATGGAATTTTGGTGAAACT
1 GGGGGTAAAAATGGAATTTTGGTGAAACT
* * *
4326779 GGGGTTAAAAATGGGATTTT-G-GAAAGTT
1 GGGGGTAAAAATGGAATTTTGGTGAAA-CT
** *
4326807 TAGGG-ATAAAATGGTAATTTTTGGTGAAACC
1 GGGGGTA-AAAATGG-AA-TTTTGGTGAAACT
* **
4326838 GGGGTTAAAAATGGAATTTTGG-GAAGTTT
1 GGGGGTAAAAATGGAATTTTGGTGAA-ACT
* **
4326867 GGGGGT-AAAATGGTAATTTTTG-GAAGTTTT
1 GGGGGTAAAAATGG-AATTTTGGTGAA--ACT
* **
4326897 GGGGTTAAAAATGGAATTTTGG-GAAGTTT
1 GGGGGTAAAAATGGAATTTTGGTGAA-ACT
* *
4326926 AGGGGT-AAAATGGTAATTTTTGGT-AAA-A
1 GGGGGTAAAAATGG-AA-TTTTGGTGAAACT
*
4326954 GCGGGGTTAAAATGGAATTTTGG
1 G-GGGGTAAAAATGGAATTTTGG
4326977 AAAGTTCGGG
Statistics
Matches: 155, Mismatches: 27, Indels: 33
0.72 0.13 0.15
Matches are distributed among these distances:
27 5 0.03
28 34 0.22
29 55 0.35
30 39 0.25
31 17 0.11
32 5 0.03
ACGTcount: A:0.32, C:0.02, G:0.33, T:0.33
Consensus pattern (29 bp):
GGGGGTAAAAATGGAATTTTGGTGAAACT
Found at i:4326842 original size:59 final size:59
Alignment explanation
Indices: 4326757--4326982 Score: 300
Period size: 59 Copynumber: 3.9 Consensus size: 59
4326747 TTCGGGGGCA
* * *
4326757 AAAATGG-AA-TTTTGGTGAAACTGGGGTTAAAAATGGGATTTTGGAAAGTTTAGGGAT
1 AAAATGGTAATTTTTGGTGAAACCGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
* *
4326814 AAAATGGTAATTTTTGGTGAAACCGGGGTTAAAAATGGAATTTTGGGAAGTTTGGGGGT
1 AAAATGGTAATTTTTGGTGAAACCGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
*** *
4326873 AAAATGGTAATTTTT-G-GAAGTTTTGGGGTTAAAAATGGAATTTTGGGAAGTTTAGGGGT
1 AAAATGGTAATTTTTGGTGAA--ACCGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
* *
4326932 AAAATGGTAATTTTTGGTAAAAGCGGGGTT-AAAATGGAATTTTGGAAAGTT
1 AAAATGGTAATTTTTGGTGAAACCGGGGTTAAAAATGGAATTTTGGAAAGTT
4326983 CGGGGACTAG
Statistics
Matches: 149, Mismatches: 14, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
57 10 0.07
58 23 0.15
59 113 0.76
60 1 0.01
61 2 0.01
ACGTcount: A:0.33, C:0.02, G:0.31, T:0.34
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGTGAAACCGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
Found at i:4326847 original size:30 final size:29
Alignment explanation
Indices: 4326757--4326987 Score: 147
Period size: 30 Copynumber: 7.9 Consensus size: 29
4326747 TTCGGGGGCA
**
4326757 AAAATGGAA-TTTTGGTGAAACT-GGGGTT
1 AAAATGGAATTTTTGG-GAAGTTCGGGGTT
* * ** *
4326785 AAAAATGGGA-TTTTGGAAAGTTTAGGGAT
1 -AAAATGGAATTTTTGGGAAGTTCGGGGTT
**
4326814 AAAATGGTAATTTTTGGTGAA-ACCGGGGTT
1 AAAATGG-AATTTTTGG-GAAGTTCGGGGTT
* *
4326844 AAAAATGGAA-TTTTGGGAAGTTTGGGGGT
1 -AAAATGGAATTTTTGGGAAGTTCGGGGTT
*
4326873 AAAATGGTAATTTTT-GGAAGTTTTGGGGTT
1 AAAATGG-AATTTTTGGGAAG-TTCGGGGTT
*
4326903 AAAAATGGAA-TTTTGGGAAGTTTAGGGG-T
1 -AAAATGGAATTTTTGGGAAG-TTCGGGGTT
* ***
4326932 AAAATGGTAATTTTTGGTAAAAGCGGGGTT
1 AAAATGG-AATTTTTGGGAAGTTCGGGGTT
*
4326962 AAAATGGAA-TTTTGGAAAGTTCGGGG
1 AAAATGGAATTTTTGGGAAGTTCGGGG
4326988 ACTAGAGAGC
Statistics
Matches: 160, Mismatches: 28, Indels: 29
0.74 0.13 0.13
Matches are distributed among these distances:
28 40 0.25
29 50 0.31
30 54 0.34
31 16 0.10
ACGTcount: A:0.32, C:0.02, G:0.32, T:0.33
Consensus pattern (29 bp):
AAAATGGAATTTTTGGGAAGTTCGGGGTT
Done.