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 38 of 193
Found at i:11688845 original size:10 final size:10
Alignment explanation
Indices: 11688832--11688932 Score: 66
Period size: 10 Copynumber: 10.3 Consensus size: 10
11688822 ATTTATAGAG
11688832 TTTTATAATT
1 TTTTATAATT
11688842 TTTT-T-ATAT
1 TTTTATAAT-T
* *
11688851 TTCTAT-ATA
1 TTTTATAATT
11688860 TTTTATAATT
1 TTTTATAATT
* ***
11688870 TTTTTTACGA
1 TTTTATAATT
*
11688880 TTTTACAATT
1 TTTTATAATT
*
11688890 TTTTATATTT
1 TTTTATAATT
*
11688900 TTTTATGA-T
1 TTTTATAATT
11688909 TTTTATAATTT
1 TTTTATAA-TT
*
11688920 TTTTCTAATT
1 TTTTATAATT
11688930 TTT
1 TTT
11688933 AATATTTAAT
Statistics
Matches: 67, Mismatches: 19, Indels: 10
0.70 0.20 0.10
Matches are distributed among these distances:
8 2 0.03
9 18 0.27
10 39 0.58
11 8 0.12
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.69
Consensus pattern (10 bp):
TTTTATAATT
Found at i:11688903 original size:20 final size:20
Alignment explanation
Indices: 11688880--11688939 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
11688870 TTTTTTACGA
11688880 TTTTACAATTTTTTATATTT
1 TTTTACAATTTTTTATATTT
**
11688900 TTTTATGA-TTTTTATAATTT
1 TTTTACAATTTTTTAT-ATTT
*
11688920 TTTT-CTAATTTTTAATATTT
1 TTTTAC-AATTTTTTATATTT
11688940 AATTTTTTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
19 7 0.22
20 19 0.59
21 6 0.19
ACGTcount: A:0.25, C:0.03, G:0.02, T:0.70
Consensus pattern (20 bp):
TTTTACAATTTTTTATATTT
Found at i:11688921 original size:28 final size:29
Alignment explanation
Indices: 11688800--11688921 Score: 101
Period size: 29 Copynumber: 4.2 Consensus size: 29
11688790 ATTTCTTTAC
* * *
11688800 ATTTTGTATAATTTTCTTACGA-ATTTATA
1 ATTTT-TATAATTTTTTTATGATTTTTATA
* *
11688829 GAGTTTTATAATTTTTTTAT-ATTTCTAT-
1 -ATTTTTATAATTTTTTTATGATTTTTATA
* *
11688857 ATATTTTATAATTTTTTTTACGA-TTTTACA
1 AT-TTTTATAA-TTTTTTTATGATTTTTATA
11688887 ATTTTT-TATATTTTTTTATGATTTTTATA
1 ATTTTTATA-ATTTTTTTATGATTTTTATA
11688916 ATTTTT
1 ATTTTT
11688922 TTCTAATTTT
Statistics
Matches: 74, Mismatches: 11, Indels: 15
0.74 0.11 0.15
Matches are distributed among these distances:
27 1 0.01
28 21 0.28
29 45 0.61
30 7 0.09
ACGTcount: A:0.27, C:0.04, G:0.05, T:0.64
Consensus pattern (29 bp):
ATTTTTATAATTTTTTTATGATTTTTATA
Found at i:11690751 original size:90 final size:88
Alignment explanation
Indices: 11690657--11690833 Score: 228
Period size: 90 Copynumber: 2.0 Consensus size: 88
11690647 ATCTTTTTTT
* * * * * *
11690657 TTTTTTTTGCATTTATTTGGCTATTTAAACTTTCAAAATGCATCAAAAAAAGCCCTCAAATCTTT
1 TTTTTTTTGCACTCAATTGGATACTTAAACTTTCAAAATGCATCAAAAAAA-CCCTCAAACCTTT
11690722 TCAAAAAAAAGCAATTAAGCCCCTA
65 TCAAAAAAAA-CAATTAAGCCCCTA
* * * * *
11690747 TTTTTTTTGCACTCAATTGGATACTTGAACTTTCAAAATGCATCAAAAAGATCTTTAAACCTTTT
1 TTTTTTTTGCACTCAATTGGATACTTAAACTTTCAAAATGCATCAAAAAAACCCTCAAACCTTTT
*
11690812 CAAATAAAACAATTAAGCCCCT
66 CAAAAAAAACAATTAAGCCCCT
11690834 GCTTTTATTA
Statistics
Matches: 75, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
88 13 0.17
89 18 0.24
90 44 0.59
ACGTcount: A:0.37, C:0.19, G:0.08, T:0.36
Consensus pattern (88 bp):
TTTTTTTTGCACTCAATTGGATACTTAAACTTTCAAAATGCATCAAAAAAACCCTCAAACCTTTT
CAAAAAAAACAATTAAGCCCCTA
Found at i:11690918 original size:28 final size:26
Alignment explanation
Indices: 11690867--11690939 Score: 74
Period size: 28 Copynumber: 2.7 Consensus size: 26
11690857 ATTATAAAAA
* * *
11690867 TTAAAATCAATAAAAGTTATAAATATT
1 TTAAAATTAATAAAAATT-CAAATATT
*
11690894 ATTAAATTTTAATAAAAATTCAAATATT
1 -TTAAA-ATTAATAAAAATTCAAATATT
*
11690922 TTAAAATTATTAAAAATT
1 TTAAAATTAATAAAAATT
11690940 AGAAATATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
26 11 0.29
27 5 0.13
28 12 0.32
29 10 0.26
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (26 bp):
TTAAAATTAATAAAAATTCAAATATT
Found at i:11691029 original size:29 final size:29
Alignment explanation
Indices: 11690939--11691029 Score: 78
Period size: 28 Copynumber: 3.1 Consensus size: 29
11690929 TATTAAAAAT
* * *
11690939 TAGAAATATATATATAAAATTTATAATTTTA
1 TAGAAATATA-A-AAAAAATATAAAATTTTA
* * *
11690970 TA-ATTATAGTAAAAAAATTATAAAA-TATA
1 TAGA-AATA-TAAAAAAAATATAAAATTTTA
11690999 TAGAAATATAAAAAAAATATAAAATTTTA
1 TAGAAATATAAAAAAAATATAAAATTTTA
11691028 TA
1 TA
11691030 AAGTCGTAAG
Statistics
Matches: 47, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
28 15 0.32
29 13 0.28
30 11 0.23
31 6 0.13
32 2 0.04
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.37
Consensus pattern (29 bp):
TAGAAATATAAAAAAAATATAAAATTTTA
Found at i:11691063 original size:21 final size:21
Alignment explanation
Indices: 11691019--11691091 Score: 59
Period size: 19 Copynumber: 3.7 Consensus size: 21
11691009 AAAAAAATAT
* *
11691019 AAAATTTTATAAAGTCGTAAG
1 AAAATTATATAAAATCGTAAG
11691040 AAAATTATATAAAAT-GTAATG
1 AAAATTATATAAAATCGTAA-G
**
11691061 -AAA-TATA-AATTTCGTAA-
1 AAAATTATATAAAATCGTAAG
11691078 AAAATTATA-AAAAT
1 AAAATTATATAAAAT
11691092 TATCGTACCA
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
18 6 0.14
19 15 0.36
20 7 0.17
21 14 0.33
ACGTcount: A:0.56, C:0.03, G:0.08, T:0.33
Consensus pattern (21 bp):
AAAATTATATAAAATCGTAAG
Found at i:11691535 original size:82 final size:81
Alignment explanation
Indices: 11691367--11691557 Score: 206
Period size: 83 Copynumber: 2.3 Consensus size: 81
11691357 AGAACAGGGG
*** *
11691367 CTTAATTGCTTTTTTGAAAAATTTTGAGGGTCATTTTTATGCATTTTAAAAGTTCAAATACCCAA
1 CTTAATTGCTTTTTT-AAAAATTTTGAGAACCATTTTTATGCATTTTAAAAGCTCAAATACCCAA
* *
11691432 TTGTGTAAAAAAAATGGA
65 TTGAGTAAAAAAAA-GAA
* * * * *
11691450 CTTAATTGCTTTTTTAAAAATTTTGAGAACCTTTTTTTATGTATTTTGAAAA-CTCAAGTGCTCA
1 CTTAATTGCTTTTTTAAAAATTTTGAGAACC-ATTTTTATGCATTTT-AAAAGCTCAAATACCCA
11691514 ATTGAGTATAAAAAAA-AA
64 ATTGAGTA-AAAAAAAGAA
**
11691532 CTTAATTAATTTTTTAAAAATTTTGA
1 CTTAATTGCTTTTTTAAAAATTTTGA
11691558 AGATTTTTAC
Statistics
Matches: 92, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
82 38 0.41
83 43 0.47
84 11 0.12
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.42
Consensus pattern (81 bp):
CTTAATTGCTTTTTTAAAAATTTTGAGAACCATTTTTATGCATTTTAAAAGCTCAAATACCCAAT
TGAGTAAAAAAAAGAA
Found at i:11697035 original size:187 final size:189
Alignment explanation
Indices: 11696717--11697277 Score: 876
Period size: 187 Copynumber: 3.0 Consensus size: 189
11696707 AAAAAGACGG
** * *
11696717 AACCAAATTAGTGAAAAAAATTAAGTAAGAATAGATGATTTAAGTAGAGCAAATCTGCATTTAGA
1 AACCAAATTAGTGAAAAAAA-CGAGTAAGAATAGATGATTTAAGTAGAGCAAATCTGCAATGAGA
* *
11696782 ACAGAGATCTTCAACATCAACTAAACAGCTTAATGCATTTCTCTTCACATTGATCTACTCTTACC
65 ACAGAGATCTTCAACATCAACTAAACAGCTTAACGCATTTCTCTTCACATTGATCTACTATTACC
* *
11696847 TAAAATCAAACATGAAATTCTCACTCTTTATCAGGAAACAAACAAAC-A-A-TAAACACT
130 TAAAATCAAACATGAAATCCTCACTCTTTCTCAGGAAACAAACAAACAACACTAAACACT
* * *
11696904 AACCAAATTAGTGAAAAGAAACGAGTAAGACTAGAAGATTTAAGTAGAGCAAATCTGCAACGAGA
1 AACCAAATTAGTGAAAA-AAACGAGTAAGAATAGATGATTTAAGTAGAGCAAATCTGCAATGAGA
* * *
11696969 ACGGAGATCTTCAACATCAAGTAAACATCTTAACGCATTTCTCTTCACATTGATCTACTATTACC
65 ACAGAGATCTTCAACATCAACTAAACAGCTTAACGCATTTCTCTTCACATTGATCTACTATTACC
11697034 TAAAATCAAACATGAAATCCTCACTCTTTCTCAGGAAACAAACAAACAATAAACACTAAACACT
130 TAAAATCAAACATGAAATCCTCACTCTTTCTCAGGAAACAAACAAAC----AACACTAAACACT
* * * *
11697098 AACCAAAGTAGTGAAAAAAAGGAGTAAGAATAGATTATTTAAGTAGAGCACATCTGCAATGAGAA
1 AACCAAATTAGTGAAAAAAACGAGTAAGAATAGATGATTTAAGTAGAGCAAATCTGCAATGAGAA
11697163 CAGAGATCTTCAACATCAACTAAACAGCTTAACGCATTTCTCTTCACATTGATCTACTATTACCT
66 CAGAGATCTTCAACATCAACTAAACAGCTTAACGCATTTCTCTTCACATTGATCTACTATTACCT
*
11697228 AAAATCAAACATGAAATCCTCACTCTTTCTCAGGAAACAAACAAGCAACA
131 AAAATCAAACATGAAATCCTCACTCTTTCTCAGGAAACAAACAAACAACA
11697278 ATTTATTTTC
Statistics
Matches: 341, Mismatches: 25, Indels: 14
0.90 0.07 0.04
Matches are distributed among these distances:
187 159 0.47
188 3 0.01
189 4 0.01
192 1 0.00
193 150 0.44
194 24 0.07
ACGTcount: A:0.43, C:0.20, G:0.12, T:0.25
Consensus pattern (189 bp):
AACCAAATTAGTGAAAAAAACGAGTAAGAATAGATGATTTAAGTAGAGCAAATCTGCAATGAGAA
CAGAGATCTTCAACATCAACTAAACAGCTTAACGCATTTCTCTTCACATTGATCTACTATTACCT
AAAATCAAACATGAAATCCTCACTCTTTCTCAGGAAACAAACAAACAACACTAAACACT
Found at i:11697799 original size:11 final size:12
Alignment explanation
Indices: 11697777--11697801 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
11697767 ACTAATTCTC
11697777 TTTTTACTTTTT
1 TTTTTACTTTTT
11697789 TTTTTACTTTTT
1 TTTTTACTTTTT
11697801 T
1 T
11697802 CCTAACTTAT
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:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTTACTTTTT
Found at i:11698245 original size:33 final size:33
Alignment explanation
Indices: 11698166--11698248 Score: 112
Period size: 33 Copynumber: 2.5 Consensus size: 33
11698156 TATTTTGGTC
** *
11698166 ATTACGAAAGTGTACTTATATTATTTGTGAGCT
1 ATTACGAAAGTGTTTTTATATTATTTGAGAGCT
* *
11698199 ATTACGAAAGTGTTTTTATATTATTTGAGGGTT
1 ATTACGAAAGTGTTTTTATATTATTTGAGAGCT
*
11698232 ATTATGAAAGTGTTTTT
1 ATTACGAAAGTGTTTTT
11698249 TTGTAATTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.29, C:0.05, G:0.19, T:0.47
Consensus pattern (33 bp):
ATTACGAAAGTGTTTTTATATTATTTGAGAGCT
Found at i:11700266 original size:31 final size:29
Alignment explanation
Indices: 11700207--11700268 Score: 79
Period size: 31 Copynumber: 2.1 Consensus size: 29
11700197 ATTTAGACCT
* *
11700207 TTAAAAGCTAAAAAAAATTTTTGGACCCC
1 TTAAAAACTAAAAAAAATTTTTGAACCCC
*
11700236 TTAAAAACTAGAAAACAATATTTTGAACCCC
1 TTAAAAACTA-AAAAAAAT-TTTTGAACCCC
11700267 TT
1 TT
11700269 TCAGCCAAGG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 9 0.32
30 7 0.25
31 12 0.43
ACGTcount: A:0.45, C:0.18, G:0.08, T:0.29
Consensus pattern (29 bp):
TTAAAAACTAAAAAAAATTTTTGAACCCC
Found at i:11701616 original size:43 final size:43
Alignment explanation
Indices: 11701569--11701654 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 43
11701559 CACTTATTAC
* * * *
11701569 AAATTGTTTATACTTTTAATTTTATAGTCAATCCTTTTTATAT
1 AAATTATTTATAATTTTAATTTTATAATCAACCCTTTTTATAT
*
11701612 AAATTATTTATAATTTTGATTTTATAATCAACCCTTTTTATAT
1 AAATTATTTATAATTTTAATTTTATAATCAACCCTTTTTATAT
11701655 TAATCTCATT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.33, C:0.09, G:0.03, T:0.55
Consensus pattern (43 bp):
AAATTATTTATAATTTTAATTTTATAATCAACCCTTTTTATAT
Found at i:11706376 original size:23 final size:24
Alignment explanation
Indices: 11706348--11706392 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
11706338 AGATTTTTTT
11706348 TATAAAAG-AATATT-AAAAATAAA
1 TATAAAAGTAAT-TTGAAAAATAAA
11706371 TATAAAAGTAATTTGAAAAATA
1 TATAAAAGTAATTTGAAAAATA
11706393 GATTAATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (24 bp):
TATAAAAGTAATTTGAAAAATAAA
Found at i:11712284 original size:19 final size:22
Alignment explanation
Indices: 11712260--11712307 Score: 66
Period size: 19 Copynumber: 2.3 Consensus size: 22
11712250 TCAGGATAAT
*
11712260 AAAATAATT-TAATA-ATA-TA
1 AAAATAATTAAAATATATATTA
11712279 AAAATAATTAAAATATATATTA
1 AAAATAATTAAAATATATATTA
11712301 AAAATAA
1 AAAATAA
11712308 AAAAAAAGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 9 0.36
20 4 0.16
21 3 0.12
22 9 0.36
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
AAAATAATTAAAATATATATTA
Found at i:11712313 original size:22 final size:20
Alignment explanation
Indices: 11712270--11712313 Score: 52
Period size: 22 Copynumber: 2.1 Consensus size: 20
11712260 AAAATAATTT
**
11712270 AATAATATAAAAATAATTAA
1 AATAATATAAAAATAAAAAA
11712290 AATATATATTAAAAATAAAAAA
1 AATA-ATA-TAAAAATAAAAAA
11712312 AA
1 AA
11712314 AGTTTAATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 3 0.15
22 13 0.65
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (20 bp):
AATAATATAAAAATAAAAAA
Found at i:11715783 original size:8 final size:7
Alignment explanation
Indices: 11715755--11715779 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
11715745 ATGGCTCTGG
11715755 TTTTGTT
1 TTTTGTT
11715762 TTTTGTT
1 TTTTGTT
11715769 TTTTGTT
1 TTTTGTT
11715776 TTTT
1 TTTT
11715780 TGTTCCTTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (7 bp):
TTTTGTT
Found at i:11717603 original size:19 final size:19
Alignment explanation
Indices: 11717549--11717605 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
11717539 CAAAATAATC
*
11717549 AAAATAATTTTCAAAAATTG
1 AAAATAATTTT-AAAAATTA
*
11717569 AAAATAATTTTTAAAATTA
1 AAAATAATTTTAAAAATTA
11717588 AAAAT-ATTTATAAAAATT
1 AAAATAATTT-TAAAAATT
11717606 CTAAAAATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 4 0.12
19 18 0.55
20 11 0.33
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (19 bp):
AAAATAATTTTAAAAATTA
Found at i:11717660 original size:22 final size:20
Alignment explanation
Indices: 11717549--11717679 Score: 61
Period size: 20 Copynumber: 6.2 Consensus size: 20
11717539 CAAAATAATC
** *
11717549 AAAATAATTTTCAAAAATTG
1 AAAATAATTTAAAAAAATTA
**
11717569 AAAATAATTT-TTAAAATTA
1 AAAATAATTTAAAAAAATTA
*
11717588 AAAAT-ATTTATAAAAATTCTA
1 AAAATAATTTA-AAAAAAT-TA
*
11717609 AAAATTTGTATTGTTAAAAAAATTA
1 AAAA----TAAT-TTAAAAAAATTA
* **
11717634 TAAATTTTTTAAAAAAATCTAA
1 AAAATAATTTAAAAAAAT-T-A
*
11717656 AAAATAATTT-AAAAATTTA
1 AAAATAATTTAAAAAAATTA
11717675 AAAAT
1 AAAAT
11717680 TTTATAAAAT
Statistics
Matches: 86, Mismatches: 14, Indels: 23
0.70 0.11 0.19
Matches are distributed among these distances:
18 4 0.05
19 17 0.20
20 25 0.29
21 16 0.19
22 8 0.09
25 6 0.07
26 7 0.08
27 3 0.03
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (20 bp):
AAAATAATTTAAAAAAATTA
Found at i:11719555 original size:24 final size:23
Alignment explanation
Indices: 11719514--11719561 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
11719504 CAACAAAAAA
11719514 TAAAAATAAAAAATATATCAAAT
1 TAAAAATAAAAAATATATCAAAT
*
11719537 TAAAATATAAAATAA-ATATTAAAT
1 TAAAA-ATAAAA-AATATATCAAAT
11719561 T
1 T
11719562 TTAACATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 5 0.23
24 15 0.68
25 2 0.09
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (23 bp):
TAAAAATAAAAAATATATCAAAT
Found at i:11719640 original size:75 final size:73
Alignment explanation
Indices: 11719521--11719667 Score: 231
Period size: 75 Copynumber: 2.0 Consensus size: 73
11719511 AAATAAAAAT
* *
11719521 AAAAAATATATCAAATTAAAATATAAAATAAATATTAAATTTTAACATAATCCACTAATAATTAC
1 AAAAAAAATATCAAATTAAAATATAAAATAAATATTAAAATTTAACATAATCCACTAATAATTAC
*
11719586 TCAAAAGA
66 CCAAAAGA
* *
11719594 AAAAAAAATATCAAATTAAAATATAAAAAATAAATATTAAAATTTAACATATTCTACTAATAATT
1 AAAAAAAATATCAAATTAAAATAT--AAAATAAATATTAAAATTTAACATAATCCACTAATAATT
11719659 ACCCAAAAG
64 ACCCAAAAG
11719668 CTAATCTTTA
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
73 23 0.34
75 44 0.66
ACGTcount: A:0.60, C:0.10, G:0.01, T:0.29
Consensus pattern (73 bp):
AAAAAAAATATCAAATTAAAATATAAAATAAATATTAAAATTTAACATAATCCACTAATAATTAC
CCAAAAGA
Found at i:11725586 original size:6 final size:7
Alignment explanation
Indices: 11725556--11725585 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
11725546 CTTATTTATC
11725556 TTTT-AT
1 TTTTCAT
11725562 TTTTCAT
1 TTTTCAT
11725569 TTTTCAT
1 TTTTCAT
11725576 TTTTCAT
1 TTTTCAT
11725583 TTT
1 TTT
11725586 CCTTTCTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.17
7 19 0.83
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTCAT
Found at i:11733348 original size:26 final size:25
Alignment explanation
Indices: 11733318--11733374 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
11733308 TCTAAATGCT
*
11733318 CCGTTTAACTTAAAAC-CTAAAGCACA
1 CCGTTTAA-TTAAAACAC-AAAACACA
* *
11733344 CCGTTTTATTTAAACACAAAACACA
1 CCGTTTAATTAAAACACAAAACACA
11733369 CCGTTT
1 CCGTTT
11733375 TCTACTTCTG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 19 0.70
26 8 0.30
ACGTcount: A:0.39, C:0.26, G:0.07, T:0.28
Consensus pattern (25 bp):
CCGTTTAATTAAAACACAAAACACA
Found at i:11737618 original size:28 final size:28
Alignment explanation
Indices: 11737578--11737808 Score: 193
Period size: 28 Copynumber: 8.2 Consensus size: 28
11737568 AGCTCGTGCG
* * *
11737578 GACTCTTTCTTGAAAGATAGTTCATACA
1 GACTCTTGCTTGAAAGATAGTCCATGCA
*
11737606 GACTCTTGCTTGAATGATAGTCCATGCA
1 GACTCTTGCTTGAAAGATAGTCCATGCA
* * ** *
11737634 GACTCCTACTTG-AAGAATAGTCTTTGCG
1 GACTCTTGCTTGAAAG-ATAGTCCATGCA
* * * *
11737662 GACTCTTGTTTAAAAGATAGTTCATG-T
1 GACTCTTGCTTGAAAGATAGTCCATGCA
*
11737689 GAACTCTTGCTTGAATA-ATAGTCTATGC-
1 G-ACTCTTGCTTGAA-AGATAGTCCATGCA
* * *
11737717 GAACTCTTACTTTAAAGATAGTCCATGTA
1 G-ACTCTTGCTTGAAAGATAGTCCATGCA
**
11737746 GACTCTTGCTTG-AAGAATAGTCCATGTG
1 GACTCTTGCTTGAAAG-ATAGTCCATGCA
*
11737774 GAGTCTTGCTTGAAAGATAGTCCATGCA
1 GACTCTTGCTTGAAAGATAGTCCATGCA
*
11737802 AACTCTT
1 GACTCTT
11737809 ATATGGCAAA
Statistics
Matches: 160, Mismatches: 34, Indels: 18
0.75 0.16 0.08
Matches are distributed among these distances:
27 7 0.04
28 145 0.91
29 8 0.05
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (28 bp):
GACTCTTGCTTGAAAGATAGTCCATGCA
Found at i:11737666 original size:56 final size:56
Alignment explanation
Indices: 11737606--11737808 Score: 237
Period size: 56 Copynumber: 3.6 Consensus size: 56
11737596 AGTTCATACA
* * * *
11737606 GACTCTTGCTTGAATGATAGTCCATGCAGACTCCTACTTGAAGAATAGTCTTTGCG
1 GACTCTTGCTTGAAAGATAGTCCATGCAGACTCTTGCTTGAAGAATAGTCTATGCG
* * * * *
11737662 GACTCTTGTTTAAAAGATAGTTCATG-TGAACTCTTGCTTGAATAATAGTCTATGCG
1 GACTCTTGCTTGAAAGATAGTCCATGCAG-ACTCTTGCTTGAAGAATAGTCTATGCG
* * * * * *
11737718 AACTCTTACTTTAAAGATAGTCCATGTAGACTCTTGCTTGAAGAATAGTCCATGTG
1 GACTCTTGCTTGAAAGATAGTCCATGCAGACTCTTGCTTGAAGAATAGTCTATGCG
* *
11737774 GAGTCTTGCTTGAAAGATAGTCCATGCAAACTCTT
1 GACTCTTGCTTGAAAGATAGTCCATGCAGACTCTT
11737809 ATATGGCAAA
Statistics
Matches: 121, Mismatches: 24, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
55 1 0.01
56 119 0.98
57 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (56 bp):
GACTCTTGCTTGAAAGATAGTCCATGCAGACTCTTGCTTGAAGAATAGTCTATGCG
Found at i:11737728 original size:84 final size:82
Alignment explanation
Indices: 11737574--11737809 Score: 219
Period size: 84 Copynumber: 2.8 Consensus size: 82
11737564 GATTAGCTCG
** *
11737574 TGCGGACTCTT-TCTTGAAAGATAGTTCAT-ACAGACTCTTGCTTGAATGATAGTCCATGCAGAC
1 TGCGGACTCTTGT-TT-AAAGATAGTTCATGTGA-ACTCTTGCTTGAATAATAGTCCATGCA-AC
* **
11737637 TCCTACTTG-AAGAATAGTCTT
62 TCTTACTTGAAAG-ATAGTCCA
*
11737658 TGCGGACTCTTGTTTAAAAGATAGTTCATGTGAACTCTTGCTTGAATAATAGTCTATGCGAACTC
1 TGCGGACTCTTGTTT-AAAGATAGTTCATGTGAACTCTTGCTTGAATAATAGTCCATGC-AACTC
*
11737723 TTACTTTAAAGATAGTCCA
64 TTACTTGAAAGATAGTCCA
** * * * * *
11737742 TGTAGACTCTTGCTTGAAGAATAGTCCATGTGGAGTCTTGCTTGAA-AGATAGTCCATGCAAACT
1 TGCGGACTCTTGTTTAAAG-ATAGTTCATGTGAACTCTTGCTTGAATA-ATAGTCCATGC-AACT
11737806 CTTA
63 CTTA
11737810 TATGGCAAAG
Statistics
Matches: 128, Mismatches: 18, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
83 4 0.03
84 118 0.92
85 6 0.05
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.34
Consensus pattern (82 bp):
TGCGGACTCTTGTTTAAAGATAGTTCATGTGAACTCTTGCTTGAATAATAGTCCATGCAACTCTT
ACTTGAAAGATAGTCCA
Found at i:11740818 original size:14 final size:14
Alignment explanation
Indices: 11740799--11740826 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
11740789 TGATTTATGC
11740799 TTAAATATTAATGT
1 TTAAATATTAATGT
11740813 TTAAATATTAATGT
1 TTAAATATTAATGT
11740827 GATTTATGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
TTAAATATTAATGT
Found at i:11740826 original size:37 final size:38
Alignment explanation
Indices: 11740776--11740896 Score: 154
Period size: 37 Copynumber: 3.0 Consensus size: 38
11740766 ATATCTATAC
11740776 TTAAATATTAATGTGATTTATGCTTAAATATTAATGT-
1 TTAAATATTAATGTGATTTATGCTTAAATATTAATGTG
11740813 TTAAATATTAATGTGATTTATGCTTAAATATTAAGATGATTTG
1 TTAAATATTAATGTGATTTATGCTTAAATATT-A-ATG---TG
*
11740856 TGCTCAAATATTAAGGTGATTTATGCTTAAATATTAATGTG
1 T--T-AAATATTAATGTGATTTATGCTTAAATATTAATGTG
11740897 ATTTGTGTTT
Statistics
Matches: 74, Mismatches: 1, Indels: 14
0.83 0.01 0.16
Matches are distributed among these distances:
37 32 0.43
38 1 0.01
39 3 0.04
41 2 0.03
42 1 0.01
43 1 0.01
44 3 0.04
45 2 0.03
46 29 0.39
ACGTcount: A:0.36, C:0.04, G:0.14, T:0.45
Consensus pattern (38 bp):
TTAAATATTAATGTGATTTATGCTTAAATATTAATGTG
Found at i:11740839 original size:23 final size:23
Alignment explanation
Indices: 11740813--11740955 Score: 173
Period size: 23 Copynumber: 6.2 Consensus size: 23
11740803 ATATTAATGT
11740813 TTAAATATTAATGTGATTTATGC
1 TTAAATATTAATGTGATTTATGC
*
11740836 TTAAATATTAA-GATGATTTGTGC
1 TTAAATATTAATG-TGATTTATGC
* *
11740859 TCAAATATTAAGGTGATTTATGC
1 TTAAATATTAATGTGATTTATGC
* *
11740882 TTAAATATTAATGTGATTTGTGT
1 TTAAATATTAATGTGATTTATGC
** * *
11740905 TTAAATATTGTTATGATTTATGA
1 TTAAATATTAATGTGATTTATGC
11740928 TTAAATATTAATGTGA-TTATCGC
1 TTAAATATTAATGTGATTTAT-GC
11740951 TTAAA
1 TTAAA
11740956 GAATTAAGAT
Statistics
Matches: 101, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
22 5 0.05
23 95 0.94
24 1 0.01
ACGTcount: A:0.35, C:0.04, G:0.15, T:0.46
Consensus pattern (23 bp):
TTAAATATTAATGTGATTTATGC
Found at i:11741075 original size:36 final size:36
Alignment explanation
Indices: 11741025--11741138 Score: 160
Period size: 36 Copynumber: 3.2 Consensus size: 36
11741015 TCATGTCTGT
*
11741025 TGTGAAAATGAATATGTGAGTATGTTCTTCATGCCA
1 TGTGACAATGAATATGTGAGTATGTTCTTCATGCCA
*
11741061 TGTGACAATAAATATGT-AGGTATGTTCTTCATGCCA
1 TGTGACAATGAATATGTGA-GTATGTTCTTCATGCCA
* *
11741097 TGTGACAGA-GAATATGTGAGTATATTCTTCATGACA
1 TGTGACA-ATGAATATGTGAGTATGTTCTTCATGCCA
11741133 TGTGAC
1 TGTGAC
11741139 TGATTATATT
Statistics
Matches: 70, Mismatches: 5, Indels: 6
0.86 0.06 0.07
Matches are distributed among these distances:
35 1 0.01
36 67 0.96
37 2 0.03
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.35
Consensus pattern (36 bp):
TGTGACAATGAATATGTGAGTATGTTCTTCATGCCA
Found at i:11745782 original size:12 final size:12
Alignment explanation
Indices: 11745757--11745794 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
11745747 TGCAAATGAA
11745757 TCATTTCTCATTT
1 TCATTTC-CATTT
11745770 TCATTTCCATTT
1 TCATTTCCATTT
*
11745782 TCATTCCCATTT
1 TCATTTCCATTT
11745794 T
1 T
11745795 TTAATAAACC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 17 0.71
13 7 0.29
ACGTcount: A:0.16, C:0.26, G:0.00, T:0.58
Consensus pattern (12 bp):
TCATTTCCATTT
Found at i:11754568 original size:17 final size:17
Alignment explanation
Indices: 11754546--11754580 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
11754536 TACCAAAAAG
11754546 AAAATATCATACCACCA
1 AAAATATCATACCACCA
11754563 AAAATATCATACCACCA
1 AAAATATCATACCACCA
11754580 A
1 A
11754581 TCATAAGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.54, C:0.29, G:0.00, T:0.17
Consensus pattern (17 bp):
AAAATATCATACCACCA
Found at i:11756831 original size:6 final size:6
Alignment explanation
Indices: 11756820--11756844 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
11756810 GAGCCTTGTA
11756820 TATGTG TATGTG TATGTG TATGTG T
1 TATGTG TATGTG TATGTG TATGTG T
11756845 GTATACTTGA
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:0.00, G:0.32, T:0.52
Consensus pattern (6 bp):
TATGTG
Found at i:11762864 original size:39 final size:39
Alignment explanation
Indices: 11762821--11762900 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
11762811 TTTATATGTG
11762821 TAAATTGATTTAATTACATGATTTAATAGGAAAACTGAT
1 TAAATTGATTTAATTACATGATTTAATAGGAAAACTGAT
11762860 TAAATTGATTTAATTACATGATTTAATAGGAAAACTGAT
1 TAAATTGATTTAATTACATGATTTAATAGGAAAACTGAT
11762899 TA
1 TA
11762901 TTTATTGTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.44, C:0.05, G:0.12, T:0.39
Consensus pattern (39 bp):
TAAATTGATTTAATTACATGATTTAATAGGAAAACTGAT
Found at i:11763268 original size:42 final size:42
Alignment explanation
Indices: 11763157--11763268 Score: 163
Period size: 42 Copynumber: 2.7 Consensus size: 42
11763147 GAGGATAAAT
* *
11763157 TTAAA-GAAGAATCATGTCTCAGAATGAAAATGAGAATATGA
1 TTAAAGGAAGAATCATGTCTCGGAATGAGAATGAGAATATGA
* *
11763198 TTAAAGGAAGAATCATGTCTCGGGATGAGAATGAGAATGTGA
1 TTAAAGGAAGAATCATGTCTCGGAATGAGAATGAGAATATGA
* *
11763240 TTAAAGGAAGACTCATGACTCGGAATGAG
1 TTAAAGGAAGAATCATGTCTCGGAATGAG
11763269 CGTGGGATTT
Statistics
Matches: 63, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
41 5 0.08
42 58 0.92
ACGTcount: A:0.42, C:0.09, G:0.26, T:0.23
Consensus pattern (42 bp):
TTAAAGGAAGAATCATGTCTCGGAATGAGAATGAGAATATGA
Found at i:11771339 original size:29 final size:29
Alignment explanation
Indices: 11771297--11771360 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 29
11771287 GAAAAGTACT
* *
11771297 AATTAATTCTTTTCTTTGCGGGAATTTAG
1 AATTAATTATTTTCTTTGCAGGAATTTAG
11771326 AATTAATTATTTTCTTTGCAGGAATTTAG
1 AATTAATTATTTTCTTTGCAGGAATTTAG
11771355 -ATTAAT
1 AATTAAT
11771361 ATACTTCGCC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
28 6 0.18
29 27 0.82
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.48
Consensus pattern (29 bp):
AATTAATTATTTTCTTTGCAGGAATTTAG
Found at i:11773383 original size:17 final size:17
Alignment explanation
Indices: 11773352--11773403 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
11773342 TATTTTGTAT
* *
11773352 TAAATTAATTATGATTC
1 TAAATTATTTGTGATTC
*
11773369 TAAATTATTTGTGATTT
1 TAAATTATTTGTGATTC
*
11773386 TATATTATACTTGTGATT
1 TAAATTAT--TTGTGATT
11773404 GTAATTATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
17 21 0.72
19 8 0.28
ACGTcount: A:0.33, C:0.04, G:0.10, T:0.54
Consensus pattern (17 bp):
TAAATTATTTGTGATTC
Found at i:11773401 original size:19 final size:18
Alignment explanation
Indices: 11773377--11773412 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
11773367 TCTAAATTAT
*
11773377 TTGTGATTTTATATTATAC
1 TTGTGATTGTA-ATTATAC
11773396 TTGTGATTGTAATTATA
1 TTGTGATTGTAATTATA
11773413 AAAATTCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.28, C:0.03, G:0.14, T:0.56
Consensus pattern (18 bp):
TTGTGATTGTAATTATAC
Found at i:11786131 original size:20 final size:20
Alignment explanation
Indices: 11786106--11786144 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
11786096 CACGTATCAG
*
11786106 ACATAAAGCATATTTAAAAC
1 ACATAAAGCAAATTTAAAAC
*
11786126 ACATAAATCAAATTTAAAA
1 ACATAAAGCAAATTTAAAA
11786145 TTCATCTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.59, C:0.13, G:0.03, T:0.26
Consensus pattern (20 bp):
ACATAAAGCAAATTTAAAAC
Found at i:11787295 original size:24 final size:24
Alignment explanation
Indices: 11787262--11787317 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
11787252 ATTTGAGAAA
*
11787262 TAATT-TTTCAGTTAAACTCAGTT
1 TAATTGTTTCAATTAAACTCAGTT
* *
11787285 TAATTGTTTCAATTAAATTCTGTT
1 TAATTGTTTCAATTAAACTCAGTT
*
11787309 TATTTGTTT
1 TAATTGTTT
11787318 AAGTCAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 5 0.18
24 23 0.82
ACGTcount: A:0.27, C:0.09, G:0.09, T:0.55
Consensus pattern (24 bp):
TAATTGTTTCAATTAAACTCAGTT
Found at i:11787326 original size:24 final size:24
Alignment explanation
Indices: 11787282--11787329 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
11787272 GTTAAACTCA
*
11787282 GTTTAATTGTTTCAATTAAATTCT
1 GTTTAATTGTTTCAATCAAATTCT
*
11787306 GTTTATTTGTTT-AAGTCAAATTCT
1 GTTTAATTGTTTCAA-TCAAATTCT
11787330 TATTAGCCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 19 0.90
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.54
Consensus pattern (24 bp):
GTTTAATTGTTTCAATCAAATTCT
Found at i:11787459 original size:28 final size:28
Alignment explanation
Indices: 11787419--11787475 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
11787409 CACTTATTAG
*
11787419 ATATACCCATTAAAGTTGAGAACTCCTA
1 ATATACCCATTAAAGTTGAAAACTCCTA
11787447 ATATACCCATTAAAGTTGAAAACTCCTA
1 ATATACCCATTAAAGTTGAAAACTCCTA
11787475 A
1 A
11787476 CACTTTTGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.28
Consensus pattern (28 bp):
ATATACCCATTAAAGTTGAAAACTCCTA
Found at i:11789303 original size:24 final size:24
Alignment explanation
Indices: 11789275--11789361 Score: 113
Period size: 24 Copynumber: 3.6 Consensus size: 24
11789265 AGAAATAATC
*
11789275 TTTCAGTTAAACTCTATTTAATTG
1 TTTCAGTTAAACTCTATTTATTTG
*
11789299 TTTCAGTTAAAC-CCAGTTTATTTG
1 TTTCAGTTAAACTCTA-TTTATTTG
*
11789323 TTTCAATTAAACTCTATTTATTTG
1 TTTCAGTTAAACTCTATTTATTTG
* *
11789347 TTTGAGTCAAACTCT
1 TTTCAGTTAAACTCT
11789362 TATTAGTCTA
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
23 2 0.04
24 50 0.93
25 2 0.04
ACGTcount: A:0.28, C:0.15, G:0.09, T:0.48
Consensus pattern (24 bp):
TTTCAGTTAAACTCTATTTATTTG
Found at i:11798499 original size:18 final size:18
Alignment explanation
Indices: 11798457--11798500 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
11798447 TAAATATAGA
11798457 TTTAAAAAATAAATTTGG
1 TTTAAAAAATAAATTTGG
* *
11798475 ATGAAAAAATAAAGTTT-G
1 TTTAAAAAATAAA-TTTGG
11798493 TTTAAAAA
1 TTTAAAAA
11798501 CGAATTTAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
18 18 0.86
19 3 0.14
ACGTcount: A:0.55, C:0.00, G:0.11, T:0.34
Consensus pattern (18 bp):
TTTAAAAAATAAATTTGG
Found at i:11798777 original size:23 final size:21
Alignment explanation
Indices: 11798744--11798801 Score: 66
Period size: 23 Copynumber: 2.7 Consensus size: 21
11798734 AAGTATATAT
11798744 ATTTTTAAAAT-TTTATTTTTA
1 ATTTTTAAAATATTTA-TTTTA
11798765 ATTTATTAGAAATATTTATTTTA
1 ATTT-TTA-AAATATTTATTTTA
*
11798788 ATTTTT-TAATATTT
1 ATTTTTAAAATATTT
11798802 TTCATGTATT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
20 7 0.21
21 4 0.12
22 5 0.15
23 13 0.39
24 4 0.12
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
ATTTTTAAAATATTTATTTTA
Found at i:11802110 original size:22 final size:22
Alignment explanation
Indices: 11802084--11802126 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
11802074 GTATGCAAAA
11802084 TTCAACAAATGTGAGTTTTGGC
1 TTCAACAAATGTGAGTTTTGGC
* * *
11802106 TTCAAGAAGTGTGATTTTTGG
1 TTCAACAAATGTGAGTTTTGG
11802127 GCAATGTGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.09, G:0.26, T:0.40
Consensus pattern (22 bp):
TTCAACAAATGTGAGTTTTGGC
Found at i:11809333 original size:17 final size:17
Alignment explanation
Indices: 11809311--11809349 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
11809301 ACATGCGCTC
*
11809311 TTGTACGAGATATGTGA
1 TTGTACGAGATAAGTGA
11809328 TTGTACGAGATAAGTGA
1 TTGTACGAGATAAGTGA
11809345 TTGTA
1 TTGTA
11809350 TGGAGATGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.31, C:0.05, G:0.28, T:0.36
Consensus pattern (17 bp):
TTGTACGAGATAAGTGA
Found at i:11817842 original size:27 final size:29
Alignment explanation
Indices: 11817774--11817842 Score: 79
Period size: 27 Copynumber: 2.4 Consensus size: 29
11817764 TTTTTGTTAG
* *
11817774 AAGGAACGCCTTTGTGGTGAGACTACGTAA
1 AAGGAAAGCC-TTGTGGCGAGACTACGTAA
* *
11817804 AAGGACACCCTTGTGGCGAGACT-C-TAA
1 AAGGAAAGCCTTGTGGCGAGACTACGTAA
11817831 AAGGAAAGCCTT
1 AAGGAAAGCCTT
11817843 TGTGATTATC
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
27 13 0.39
28 1 0.03
29 12 0.36
30 7 0.21
ACGTcount: A:0.32, C:0.20, G:0.28, T:0.20
Consensus pattern (29 bp):
AAGGAAAGCCTTGTGGCGAGACTACGTAA
Found at i:11819540 original size:14 final size:14
Alignment explanation
Indices: 11819521--11819549 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
11819511 CTTGCTCCTC
11819521 TCGTGTTAGCGCAA
1 TCGTGTTAGCGCAA
11819535 TCGTGTTAGCGCAA
1 TCGTGTTAGCGCAA
11819549 T
1 T
11819550 ACGCTTGCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.31
Consensus pattern (14 bp):
TCGTGTTAGCGCAA
Found at i:11820061 original size:19 final size:19
Alignment explanation
Indices: 11820034--11820071 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
11820024 AAAACAAATT
11820034 AATGAGCAACAAAAGTGGG
1 AATGAGCAACAAAAGTGGG
* *
11820053 AATGGGCAACAAACGTGGG
1 AATGAGCAACAAAAGTGGG
11820072 TTATGCCCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.42, C:0.13, G:0.34, T:0.11
Consensus pattern (19 bp):
AATGAGCAACAAAAGTGGG
Found at i:11829674 original size:217 final size:217
Alignment explanation
Indices: 11829299--11829733 Score: 807
Period size: 217 Copynumber: 2.0 Consensus size: 217
11829289 ATTTGTAAGG
*
11829299 GGTAATCAATGCATCGGCACTGCTATGAAAATGGGATCGTTTTGGTCTGGGGTGCAAACCAGATA
1 GGTAATCAATGCACCGGCACTGCTATGAAAATGGGATCGTTTTGGTCTGGGGTGCAAACCAGATA
11829364 TGAAAGAAAAGAAGAAAAAGATTGAAAGGAAGCGAGAAACGAGAAAAGCACGACTGGCTTAGGGA
66 TGAAAGAAAAGAAGAAAAAGATTGAAAGGAAGCGAGAAACGAGAAAAGCACGACTGGCTTAGGGA
* *
11829429 GAGATCAAGTGGGAGCTAATGATCTTTCCCCACATATCAAAGACTTTCGTTTTCGGTGGAATGAG
131 GAGATCAAGTGGGAGCTAATGATCTTTCCCCACATATCAAAAACTTTCGTTTCCGGTGGAATGAG
11829494 GATTGAAGAAGAGAAGAAGAGT
196 GATTGAAGAAGAGAAGAAGAGT
*
11829516 GGTAATCAATGCACCGGTACTGCTATGAAAATGGGATCGTTTTGGTCTGGGGTGCAAACCAGATA
1 GGTAATCAATGCACCGGCACTGCTATGAAAATGGGATCGTTTTGGTCTGGGGTGCAAACCAGATA
* *
11829581 TGAAAGAAAAGAAGAAAGAGATTGAAAGGAAGCGAGAAACGAGAAAAGCACGACTGGCTTGGGGA
66 TGAAAGAAAAGAAGAAAAAGATTGAAAGGAAGCGAGAAACGAGAAAAGCACGACTGGCTTAGGGA
*
11829646 GAGATCAAGTGGGAGCTAATGATCTTTCCCTACATATCAAAAACTTTCGTTTCCGGTGGAATGAG
131 GAGATCAAGTGGGAGCTAATGATCTTTCCCCACATATCAAAAACTTTCGTTTCCGGTGGAATGAG
11829711 GATTGAAGAAGAGAAGAAGAGT
196 GATTGAAGAAGAGAAGAAGAGT
11829733 G
1 G
11829734 AAAGAGTTAC
Statistics
Matches: 211, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
217 211 1.00
ACGTcount: A:0.37, C:0.13, G:0.29, T:0.21
Consensus pattern (217 bp):
GGTAATCAATGCACCGGCACTGCTATGAAAATGGGATCGTTTTGGTCTGGGGTGCAAACCAGATA
TGAAAGAAAAGAAGAAAAAGATTGAAAGGAAGCGAGAAACGAGAAAAGCACGACTGGCTTAGGGA
GAGATCAAGTGGGAGCTAATGATCTTTCCCCACATATCAAAAACTTTCGTTTCCGGTGGAATGAG
GATTGAAGAAGAGAAGAAGAGT
Found at i:11834390 original size:21 final size:21
Alignment explanation
Indices: 11834364--11834409 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
11834354 TAATGGAGGG
11834364 GAACGTTTGAGTCGCAACGGC
1 GAACGTTTGAGTCGCAACGGC
11834385 GAACGTTTGAGTCGCAACGGC
1 GAACGTTTGAGTCGCAACGGC
11834406 GAAC
1 GAAC
11834410 CTTGTACCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.26, C:0.24, G:0.33, T:0.17
Consensus pattern (21 bp):
GAACGTTTGAGTCGCAACGGC
Found at i:11834549 original size:49 final size:50
Alignment explanation
Indices: 11834397--11834888 Score: 319
Period size: 49 Copynumber: 10.0 Consensus size: 50
11834387 ACGTTTGAGT
* * *
11834397 CGCAACGGCGAACCTTGTACCTCAG-AGACACGAAAGGAAATATTTAAGC
1 CGCAACGGCGAACCTTGTACCTCAGAAGACATGAAGGGAAAGATTTAAGC
** * * * * *
11834446 CGCAACGGCGAATCC-AATACCGCA-AAGATAATGGAGGGAAAGGTTTAAGT
1 CGCAACGGCGAA-CCTTGTACCTCAGAAGA-CATGAAGGGAAAGATTTAAGC
*
11834496 CGCAATGGCGAACCTTGTACCTCAGAAG-CATGAAGGGAAAGATTTAAGC
1 CGCAACGGCGAACCTTGTACCTCAGAAGACATGAAGGGAAAGATTTAAGC
* * * *
11834545 CGCAACGGCGTA--TTCAGTACCAC-GAAGATATGAAGGGAAAAATTTAAGC
1 CGCAACGGCGAACCTT--GTACCTCAGAAGACATGAAGGGAAAGATTTAAGC
* * * * * * *
11834594 CGCAACGACGAATCC-AGTACCGC-GAAGATATAAAGGGAAAGGTTTAAGT
1 CGCAACGGCGAA-CCTTGTACCTCAGAAGACATGAAGGGAAAGATTTAAGC
* * * * *
11834643 CGTAATGGCGAACCTTGTACCTTAGAAG-CGTGAAGGAAAAGATTTAAGC
1 CGCAACGGCGAACCTTGTACCTCAGAAGACATGAAGGGAAAGATTTAAGC
* * ** * * * * * * *
11834692 CGTAACTGTAAATCTTGTACCAC-GAAGATATAAATGGAAAGCTTTAAGT
1 CGCAACGGCGAACCTTGTACCTCAGAAGACATGAAGGGAAAGATTTAAGC
* ** *
11834741 CGCAACGACGGGCCTTGTACCTCAGAAG-CATGAAGGAAAAGATTTAAGC
1 CGCAACGGCGAACCTTGTACCTCAGAAGACATGAAGGGAAAGATTTAAGC
* * * * * * ** * *
11834790 TGCAATGGCAAATCTAGTACCTCA-AAGATACAAAGGGAAAGGTTTAAGT
1 CGCAACGGCGAACCTTGTACCTCAGAAGACATGAAGGGAAAGATTTAAGC
* * * * * *
11834839 CGCAACGGTGAGCCTTGTACCTTAGAA-TCATGAAAGGAAAAATTTAAGC
1 CGCAACGGCGAACCTTGTACCTCAGAAGACATGAAGGGAAAGATTTAAGC
11834888 C
1 C
11834889 ATAATGGGGA
Statistics
Matches: 324, Mismatches: 102, Indels: 34
0.70 0.22 0.07
Matches are distributed among these distances:
47 2 0.01
48 13 0.04
49 263 0.81
50 43 0.13
51 3 0.01
ACGTcount: A:0.37, C:0.19, G:0.24, T:0.20
Consensus pattern (50 bp):
CGCAACGGCGAACCTTGTACCTCAGAAGACATGAAGGGAAAGATTTAAGC
Found at i:11834573 original size:99 final size:98
Alignment explanation
Indices: 11834389--11834605 Score: 274
Period size: 99 Copynumber: 2.2 Consensus size: 98
11834379 AACGGCGAAC
* *
11834389 GTTTGAGTCGCAACGGCGAACCTTGTACCTCAGAGACACGAAAGGAAATATTTAAGCCGCAACGG
1 GTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAGACACGAAAGGAAAGATTTAAGCCGCAACGG
* * *
11834454 CGAATCCAATACCGCAAAGATAATGGAGGGAAAG
66 CGAATCCAATACCACAAAGAT-ATGAAGGGAAAA
* * *
11834488 GTTTAAGTCGCAATGGCGAACCTTGTACCTCAGA-AGCATGAAGGGAAAGATTTAAGCCGCAACG
1 GTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAGA-CACGAAAGGAAAGATTTAAGCCGCAACG
* * * *
11834552 GCGTATTCAGTACCACGAAGATATGAAGGGAAAA
65 GCGAATCCAATACCACAAAGATATGAAGGGAAAA
* * *
11834586 ATTTAAGCCGCAACGACGAA
1 GTTTAAGTCGCAACGGCGAA
11834606 TCCAGTACCG
Statistics
Matches: 101, Mismatches: 16, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
98 27 0.27
99 74 0.73
ACGTcount: A:0.36, C:0.20, G:0.26, T:0.18
Consensus pattern (98 bp):
GTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAGACACGAAAGGAAAGATTTAAGCCGCAACGG
CGAATCCAATACCACAAAGATATGAAGGGAAAA
Found at i:11834631 original size:98 final size:99
Alignment explanation
Indices: 11834397--11834641 Score: 230
Period size: 99 Copynumber: 2.5 Consensus size: 99
11834387 ACGTTTGAGT
* * * * *
11834397 CGCAACGGCGAACCTTGTACCTCAG-AGACACGAAA-GGAAATATTTAAGCCGCAACGGCGAATC
1 CGCAACGACGAACCTAGTACCGCAGAAG-CA-TAAAGGGAAAGATTTAAGCCGCAACGGCGAATC
* * ** *
11834460 CAATACCGCAAAGATAATGGAGGGAAAGGTTTAAGT
64 CAATACCACAAAGATAATGAAGGGAAAAATTTAAGC
* * * * * * *
11834496 CGCAATGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGTATTCA
1 CGCAACGACGAACCTAGTACCGCAGAAGCATAAAGGGAAAGATTTAAGCCGCAACGGCGAATCCA
* *
11834561 GTACCACGAAGAT-ATGAAGGGAAAAATTTAAGC
66 ATACCACAAAGATAATGAAGGGAAAAATTTAAGC
* *
11834594 CGCAACGACGAATCC-AGTACCGC-GAAGATATAAAGGGAAAGGTTTAAG
1 CGCAACGACGAA-CCTAGTACCGCAGAAG-CATAAAGGGAAAGATTTAAG
11834642 TCGTAATGGC
Statistics
Matches: 122, Mismatches: 20, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
97 4 0.03
98 51 0.42
99 65 0.53
100 2 0.02
ACGTcount: A:0.38, C:0.20, G:0.26, T:0.17
Consensus pattern (99 bp):
CGCAACGACGAACCTAGTACCGCAGAAGCATAAAGGGAAAGATTTAAGCCGCAACGGCGAATCCA
ATACCACAAAGATAATGAAGGGAAAAATTTAAGC
Found at i:11834685 original size:147 final size:148
Alignment explanation
Indices: 11834432--11834750 Score: 428
Period size: 147 Copynumber: 2.2 Consensus size: 148
11834422 AGACACGAAA
* * **
11834432 GGAAATATTTAAGCCGCAACGGCGAATCCAATACCGCAAAGATAATGGAGGGAAAGGTTTAAGTC
1 GGAAAAATTTAAGCCGCAACGACGAATCCAATACCGCAAAGATAATAAAGGGAAAGGTTTAAGTC
* *
11834497 GCAATGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGT-ATTC-
66 GCAATGGCGAACCTTGTACCTCAGAAGCATGAAGGAAAAGATTTAAGCCGCAAC--CGTAAATCT
*
11834560 AGTACCACGAAGATATGAAG
129 AGTACCACGAAGATATAAAG
* *
11834580 GGAAAAATTTAAGCCGCAACGACGAATCCAGTACCGCGAAGAT-ATAAAGGGAAAGGTTTAAGTC
1 GGAAAAATTTAAGCCGCAACGACGAATCCAATACCGCAAAGATAATAAAGGGAAAGGTTTAAGTC
* * * * * *
11834644 GTAATGGCGAACCTTGTACCTTAGAAGCGTGAAGGAAAAGATTTAAGCCGTAACTGTAAATCTTG
66 GCAATGGCGAACCTTGTACCTCAGAAGCATGAAGGAAAAGATTTAAGCCGCAACCGTAAATCTAG
*
11834709 TACCACGAAGATATAAAT
131 TACCACGAAGATATAAAG
** *
11834727 GGAAAGCTTTAAGTCGCAACGACG
1 GGAAAAATTTAAGCCGCAACGACG
11834751 GGCCTTGTAC
Statistics
Matches: 150, Mismatches: 19, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
145 2 0.01
146 3 0.02
147 106 0.71
148 39 0.26
ACGTcount: A:0.37, C:0.18, G:0.25, T:0.20
Consensus pattern (148 bp):
GGAAAAATTTAAGCCGCAACGACGAATCCAATACCGCAAAGATAATAAAGGGAAAGGTTTAAGTC
GCAATGGCGAACCTTGTACCTCAGAAGCATGAAGGAAAAGATTTAAGCCGCAACCGTAAATCTAG
TACCACGAAGATATAAAG
Found at i:11834787 original size:147 final size:146
Alignment explanation
Indices: 11834432--11834813 Score: 376
Period size: 147 Copynumber: 2.6 Consensus size: 146
11834422 AGACACGAAA
* * * * * * ** *
11834432 GGAAATATTTAAGCCGCAACGGCGAATCCAATACCGCAAAGATAATGGAGGGAAAGGTTTAAGTC
1 GGAAAAATTTAAGCCGCAACGACGAAGCCAGTACCGCGAAGA-CATAAAGGAAAAGGTTTAAGTC
* *
11834497 GCAATGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGTATTCAG
65 GCAATGGCGAACCTTGTACCTCAGAAGCATGAAGGAAAAGATTTAAGCCGCAAC-GCGTAATCAG
*
11834562 TACCACGAAGATATGAAG
129 TACCACGAAGATATAAAG
* * *
11834580 GGAAAAATTTAAGCCGCAACGACGAATCCAGTACCGCGAAGATATAAAGGGAAAGGTTTAAGTCG
1 GGAAAAATTTAAGCCGCAACGACGAAGCCAGTACCGCGAAGACATAAAGGAAAAGGTTTAAGTCG
* * * * * *
11834645 TAATGGCGAACCTTGTACCTTAGAAGCGTGAAGGAAAAGATTTAAGCCGTAAC-TGTAAATCTTG
66 CAATGGCGAACCTTGTACCTCAGAAGCATGAAGGAAAAGATTTAAGCCGCAACGCGT-AATC-AG
*
11834709 TACCACGAAGATATAAAT
129 TACCACGAAGATATAAAG
** * * * * * *
11834727 GGAAAGCTTTAAGTCGCAACGACG-GGCCTTGTACCTCAGAAG-CATGAAGGAAAAGATTTAAG-
1 GGAAAAATTTAAGCCGCAACGACGAAGCC-AGTACCGC-GAAGACATAAAGGAAAAGGTTTAAGT
* * *
11834789 CTGCAATGGCAAATCTAGTACCTCA
64 C-GCAATGGCGAACCTTGTACCTCA
11834814 AAGATACAAA
Statistics
Matches: 196, Mismatches: 33, Indels: 11
0.82 0.14 0.05
Matches are distributed among these distances:
145 2 0.01
146 6 0.03
147 146 0.74
148 42 0.21
ACGTcount: A:0.37, C:0.18, G:0.25, T:0.20
Consensus pattern (146 bp):
GGAAAAATTTAAGCCGCAACGACGAAGCCAGTACCGCGAAGACATAAAGGAAAAGGTTTAAGTCG
CAATGGCGAACCTTGTACCTCAGAAGCATGAAGGAAAAGATTTAAGCCGCAACGCGTAATCAGTA
CCACGAAGATATAAAG
Found at i:11834895 original size:98 final size:98
Alignment explanation
Indices: 11834574--11834912 Score: 378
Period size: 98 Copynumber: 3.5 Consensus size: 98
11834564 CCACGAAGAT
* * * * *
11834574 ATGAAGGGAAAA-ATTTAAGCCGCAACGACGAATCCAGTACCGCGAAGATATAAAGGGAAAGGTT
1 ATGAA-GGAAAAGATTTAAGCCGCAATGGCAAATCTAGTACCACGAAGATATAAAGGGAAAGGTT
* * *
11834638 TAAGTCGTAATGGCGAACCTTGTACCTTAGAAGC
65 TAAGTCGCAACGGCGAGCCTTGTACCTTAGAAGC
* * * * * *
11834672 GTGAAGGAAAAGATTTAAGCCGTAACT-GTAAATCTTGTACCACGAAGATATAAATGGAAAGCTT
1 ATGAAGGAAAAGATTTAAGCCGCAA-TGGCAAATCTAGTACCACGAAGATATAAAGGGAAAGGTT
* * *
11834736 TAAGTCGCAACGACGGGCCTTGTACCTCAGAAGC
65 TAAGTCGCAACGGCGAGCCTTGTACCTTAGAAGC
* * * *
11834770 ATGAAGGAAAAGATTTAAGCTGCAATGGCAAATCTAGTACCTCAAAGATACAAAGGGAAAGGTTT
1 ATGAAGGAAAAGATTTAAGCCGCAATGGCAAATCTAGTACCACGAAGATATAAAGGGAAAGGTTT
* *
11834835 AAGTCGCAACGGTGAGCCTTGTACCTTAGAATC
66 AAGTCGCAACGGCGAGCCTTGTACCTTAGAAGC
** ** *
11834868 ATGAAAGGAAAA-ATTTAAGCCATAATGGGGAATTTAGTACCACGA
1 ATG-AAGGAAAAGATTTAAGCCGCAATGGCAAATCTAGTACCACGA
11834913 TGACATTGTA
Statistics
Matches: 197, Mismatches: 40, Indels: 8
0.80 0.16 0.03
Matches are distributed among these distances:
97 7 0.04
98 182 0.92
99 8 0.04
ACGTcount: A:0.38, C:0.17, G:0.24, T:0.22
Consensus pattern (98 bp):
ATGAAGGAAAAGATTTAAGCCGCAATGGCAAATCTAGTACCACGAAGATATAAAGGGAAAGGTTT
AAGTCGCAACGGCGAGCCTTGTACCTTAGAAGC
Found at i:11836734 original size:642 final size:642
Alignment explanation
Indices: 11835511--11836797 Score: 2538
Period size: 642 Copynumber: 2.0 Consensus size: 642
11835501 TACACCCAAA
11835511 CCCATATGAAAACCCTAATTTGAATAGGTTCTGCTCCAGCCGCCACATGCCACTTCAGCATCGCC
1 CCCATATGAAAACCCTAATTTGAATAGGTTCTGCTCCAGCCGCCACATGCCACTTCAGCATCGCC
11835576 ATGTCATCACCGCGTCAGCGCCACATCATTACCATGTCAGTCACGTGACCCCTCAGTGTCTGACC
66 ATGTCATCACCGCGTCAGCGCCACATCATTACCATGTCAGTCACGTGACCCCTCAGTGTCTGACC
*
11835641 GTTGACTTCTCGACTTCTGTAACTGCTCGGCTCCCAAAAACGTCTCTGCCCAATGATCAACCCTC
131 ATTGACTTCTCGACTTCTGTAACTGCTCGGCTCCCAAAAACGTCTCTGCCCAATGATCAACCCTC
11835706 TGCCCGAAGCAACCTGCTGCCGCCCTTGCACCAAAATGGCCATGGCACTCTCCCCGGCGTCGGCT
196 TGCCCGAAGCAACCTGCTGCCGCCCTTGCACCAAAATGGCCATGGCACTCTCCCCGGCGTCGGCT
11835771 TTGATCGTAGGAGACCCCCATCACCAGCGTGAAAATGAACCTGCAAGAAAGAAACAACAAAGAAC
261 TTGATCGTAGGAGACCCCCATCACCAGCGTGAAAATGAACCTGCAAGAAAGAAACAACAAAGAAC
11835836 AACAGAGAAAGAATACAGAGGACAAAAAAACAGTATCTCTATAATTTTTGATGGCTATAAAAGCC
326 AACAGAGAAAGAATACAGAGGACAAAAAAACAGTATCTCTATAATTTTTGATGGCTATAAAAGCC
11835901 ATCGCAAAATCTGTAAAATAACACACGAAGGGAATACAAAAAAGCAAAATAAAATACAAGCAAAG
391 ATCGCAAAATCTGTAAAATAACACACGAAGGGAATACAAAAAAGCAAAATAAAATACAAGCAAAG
11835966 TTTCAAATAGCGATCGAGGGAAGCCAATAGACAACCAGTCAAATCATGAAGGTAGTTTTATTTTT
456 TTTCAAATAGCGATCGAGGGAAGCCAATAGACAACCAGTCAAATCATGAAGGTAGTTTTATTTTT
11836031 GTTACTTACATATTGTTTATTTATTTTCAAAGCATAAAGACGAATAAAAAATAATAAATAAAAAA
521 GTTACTTACATATTGTTTATTTATTTTCAAAGCATAAAGACGAATAAAAAATAATAAATAAAAAA
11836096 GGGGTTAAAAGGGCATACCTCGATTCGAAACGCTGTCGCTGGAGCCATTGACTGAAT
586 GGGGTTAAAAGGGCATACCTCGATTCGAAACGCTGTCGCTGGAGCCATTGACTGAAT
11836153 CCCATATGAAAACCCTAATTTGAATAGGTTCTGCTCCAGCCGCCACATGCCACTTCAGCATCGCC
1 CCCATATGAAAACCCTAATTTGAATAGGTTCTGCTCCAGCCGCCACATGCCACTTCAGCATCGCC
*
11836218 ATGTCATCGCCGCGTCAGCGCCACATCATTACCATGTCAGTCACGTGACCCCTCAGTGTCTGACC
66 ATGTCATCACCGCGTCAGCGCCACATCATTACCATGTCAGTCACGTGACCCCTCAGTGTCTGACC
*
11836283 ATTGACTTCTCGACTTCTGTAACTGCTCGGCTCCCAAAAACGTCTCTGCCCAATGATCGACCCTC
131 ATTGACTTCTCGACTTCTGTAACTGCTCGGCTCCCAAAAACGTCTCTGCCCAATGATCAACCCTC
*
11836348 TGCTCGAAGCAACCTGCTGCCGCCCTTGCACCAAAATGGCCATGGCACTCTCCCCGGCGTCGGCT
196 TGCCCGAAGCAACCTGCTGCCGCCCTTGCACCAAAATGGCCATGGCACTCTCCCCGGCGTCGGCT
11836413 TTGATCGTAGGAGACCCCCATCACCAGCGTGAAAATGAACCTGCAAGAAAGAAACAACAAAGAAC
261 TTGATCGTAGGAGACCCCCATCACCAGCGTGAAAATGAACCTGCAAGAAAGAAACAACAAAGAAC
11836478 AACAGAGAAAGAATACAGAGGACAAAAAAACAGTATCTCTATAATTTTTGATGGCTATAAAAGCC
326 AACAGAGAAAGAATACAGAGGACAAAAAAACAGTATCTCTATAATTTTTGATGGCTATAAAAGCC
11836543 ATCGCAAAATCTGTAAAATAACACACGAAGGGAATACAAAAAAGCAAAATAAAATACAAGCAAAG
391 ATCGCAAAATCTGTAAAATAACACACGAAGGGAATACAAAAAAGCAAAATAAAATACAAGCAAAG
11836608 TTTCAAATAGCGATCGAGGGAAGCCAATAGACAACCAGTCAAATCATGAAGGTAGTTTTATTTTT
456 TTTCAAATAGCGATCGAGGGAAGCCAATAGACAACCAGTCAAATCATGAAGGTAGTTTTATTTTT
11836673 GTTACTTACATATTGTTTATTTATTTTCAAAGCATAAAGACGAATAAAAAATAATAAATAAAAAA
521 GTTACTTACATATTGTTTATTTATTTTCAAAGCATAAAGACGAATAAAAAATAATAAATAAAAAA
11836738 GGGGTTAAAAGGGCATACCTCGATTCGAAACGCTGTCGCTGGAGCCATTGACTGAAT
586 GGGGTTAAAAGGGCATACCTCGATTCGAAACGCTGTCGCTGGAGCCATTGACTGAAT
11836795 CCC
1 CCC
11836798 TTTCGAACAT
Statistics
Matches: 641, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
642 641 1.00
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (642 bp):
CCCATATGAAAACCCTAATTTGAATAGGTTCTGCTCCAGCCGCCACATGCCACTTCAGCATCGCC
ATGTCATCACCGCGTCAGCGCCACATCATTACCATGTCAGTCACGTGACCCCTCAGTGTCTGACC
ATTGACTTCTCGACTTCTGTAACTGCTCGGCTCCCAAAAACGTCTCTGCCCAATGATCAACCCTC
TGCCCGAAGCAACCTGCTGCCGCCCTTGCACCAAAATGGCCATGGCACTCTCCCCGGCGTCGGCT
TTGATCGTAGGAGACCCCCATCACCAGCGTGAAAATGAACCTGCAAGAAAGAAACAACAAAGAAC
AACAGAGAAAGAATACAGAGGACAAAAAAACAGTATCTCTATAATTTTTGATGGCTATAAAAGCC
ATCGCAAAATCTGTAAAATAACACACGAAGGGAATACAAAAAAGCAAAATAAAATACAAGCAAAG
TTTCAAATAGCGATCGAGGGAAGCCAATAGACAACCAGTCAAATCATGAAGGTAGTTTTATTTTT
GTTACTTACATATTGTTTATTTATTTTCAAAGCATAAAGACGAATAAAAAATAATAAATAAAAAA
GGGGTTAAAAGGGCATACCTCGATTCGAAACGCTGTCGCTGGAGCCATTGACTGAAT
Found at i:11845583 original size:13 final size:15
Alignment explanation
Indices: 11845554--11845586 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
11845544 GGTGAAGAAA
11845554 ATAAATATTTGATAT
1 ATAAATATTTGATAT
11845569 ATAAATA-TT-ATAT
1 ATAAATATTTGATAT
11845582 ATAAA
1 ATAAA
11845587 GAAAAATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.50
14 2 0.11
15 7 0.39
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (15 bp):
ATAAATATTTGATAT
Found at i:11845671 original size:2 final size:2
Alignment explanation
Indices: 11845660--11845691 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
11845650 ATATCAATTT
11845660 TA TA -A TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11845692 ATTGACAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11846926 original size:14 final size:14
Alignment explanation
Indices: 11846907--11846951 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
11846897 TGGGATGAAA
11846907 ATAAATTTTTAATT
1 ATAAATTTTTAATT
11846921 ATAAATTTAATTAATT
1 ATAAATTT--TTAATT
* *
11846937 AAAAATTTTAAATT
1 ATAAATTTTTAATT
11846951 A
1 A
11846952 ATTACAACTG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 14 0.52
16 13 0.48
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
ATAAATTTTTAATT
Found at i:11862207 original size:27 final size:27
Alignment explanation
Indices: 11862166--11862282 Score: 105
Period size: 27 Copynumber: 4.3 Consensus size: 27
11862156 TTAAGAGATT
*
11862166 TTTTTTTTAATTTTTAAGGGGTCCAAA
1 TTTTTTTTAACTTTTAAGGGGTCCAAA
*
11862193 TTTTTTTTAACTTTTACA--GGT-CAAT
1 TTTTTTTTAACTTTTA-AGGGGTCCAAA
* *
11862218 TTTTTTATTAACTTTTAAGGGCTCTTAAA
1 TTTTTT-TTAACTTTTAAGGGGTC-CAAA
** ** *
11862247 TTTTTTTTAGTTTTTAAGGTTTCAAAA
1 TTTTTTTTAACTTTTAAGGGGTCCAAA
11862274 TTTTTTTTA
1 TTTTTTTTA
11862283 CCAACTTTTA
Statistics
Matches: 74, Mismatches: 10, Indels: 12
0.77 0.10 0.12
Matches are distributed among these distances:
25 10 0.14
26 13 0.18
27 29 0.39
28 14 0.19
29 8 0.11
ACGTcount: A:0.25, C:0.08, G:0.10, T:0.57
Consensus pattern (27 bp):
TTTTTTTTAACTTTTAAGGGGTCCAAA
Found at i:11865900 original size:19 final size:19
Alignment explanation
Indices: 11865864--11865916 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 19
11865854 TATGTTTATT
11865864 ATTTATATTATTGAATTAA
1 ATTTATATTATTGAATTAA
*
11865883 ATTTCATATT-TTGTATT--
1 ATTT-ATATTATTGAATTAA
*
11865900 ATTTATTTTATTGAATT
1 ATTTATATTATTGAATT
11865917 GTTTAATCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 4 0.14
17 10 0.34
19 10 0.34
20 5 0.17
ACGTcount: A:0.32, C:0.02, G:0.06, T:0.60
Consensus pattern (19 bp):
ATTTATATTATTGAATTAA
Found at i:11875728 original size:7 final size:7
Alignment explanation
Indices: 11875716--11875761 Score: 85
Period size: 7 Copynumber: 6.7 Consensus size: 7
11875706 AAGTTTTTCT
11875716 CCCTTCC
1 CCCTTCC
11875723 CCCTTCC
1 CCCTTCC
11875730 CCCTTCC
1 CCCTTCC
11875737 CCCTTCC
1 CCCTTCC
11875744 CCCTT-C
1 CCCTTCC
11875750 CCCTTCC
1 CCCTTCC
11875757 CCCTT
1 CCCTT
11875762 TCTCCTACAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
6 6 0.16
7 32 0.84
ACGTcount: A:0.00, C:0.70, G:0.00, T:0.30
Consensus pattern (7 bp):
CCCTTCC
Found at i:11875740 original size:21 final size:20
Alignment explanation
Indices: 11875716--11875761 Score: 83
Period size: 20 Copynumber: 2.2 Consensus size: 20
11875706 AAGTTTTTCT
11875716 CCCTTCCCCCTTCCCCCTTCC
1 CCCTTCCCCCTT-CCCCTTCC
11875737 CCCTTCCCCCTTCCCCTTCC
1 CCCTTCCCCCTTCCCCTTCC
11875757 CCCTT
1 CCCTT
11875762 TCTCCTACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.00, C:0.70, G:0.00, T:0.30
Consensus pattern (20 bp):
CCCTTCCCCCTTCCCCTTCC
Found at i:11880331 original size:50 final size:50
Alignment explanation
Indices: 11880178--11880346 Score: 173
Period size: 50 Copynumber: 3.4 Consensus size: 50
11880168 ACCATTCTTT
* * * * * * * *
11880178 AGCTTCAGGAGTATAAGATTCGTCTTTGCGGCTTTAATTTGTCCCTCTAC
1 AGCTTTAGGTGTATGAGATTCGCCATTGCGGCTTCAATCTATCCCTCTAC
* *
11880228 A-CTTTAGGTGTATGAGATTCGCCATTGCGGCTTCAATC-AGCCCCTTTAC
1 AGCTTTAGGTGTATGAGATTCGCCATTGCGGCTTCAATCTA-TCCCTCTAC
* * * *
11880277 AGCTTTGGGTGTATGAGATTTGCCATTGCGGCTTCAATCTATTCCTCTAT
1 AGCTTTAGGTGTATGAGATTCGCCATTGCGGCTTCAATCTATCCCTCTAC
*
11880327 AGCTTTAGG-GTATAAGATTC
1 AGCTTTAGGTGTATGAGATTC
11880347 ATTGTTTTGT
Statistics
Matches: 97, Mismatches: 19, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
49 47 0.48
50 49 0.51
51 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (50 bp):
AGCTTTAGGTGTATGAGATTCGCCATTGCGGCTTCAATCTATCCCTCTAC
Found at i:11884391 original size:16 final size:15
Alignment explanation
Indices: 11884360--11884409 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
11884350 TTATCATAAA
11884360 TTTT-TTTTTCTTCT
1 TTTTCTTTTTCTTCT
11884374 TTTTCTTTTTCTTCCT
1 TTTTCTTTTTCTT-CT
*
11884390 TTTTCTCATTT-TTCT
1 TTTTCT-TTTTCTTCT
11884405 TTTTC
1 TTTTC
11884410 AAATGATTGA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
14 4 0.12
15 15 0.47
16 10 0.31
17 3 0.09
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTCTTTTTCTTCT
Found at i:11901674 original size:70 final size:67
Alignment explanation
Indices: 11901544--11901675 Score: 165
Period size: 70 Copynumber: 1.9 Consensus size: 67
11901534 TAAATAATAA
* * * * *
11901544 AATGGTTTTGCCTTTTAACTTAATGGGTAAATATTTATCAAAATGACATAATTTTACCTTTTAAC
1 AATGGTTTTGACTTTTAACTTAAAGAGTAAACATTTATCAAAACGACATAATTTTACCTTTTAAC
11901609 TT
66 TT
* * *
11901611 AATGGTTTTGACTTTTAACTTTAGAAAGAGTAAACATTTATCAAAACGACGTAGTTTTGCCTTTT
1 AATGGTTTTGACTTTTAAC-TT--AAAGAGTAAACATTTATCAAAACGACATAATTTTACCTTTT
11901676 CATATTTGGA
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
67 18 0.33
68 2 0.04
70 34 0.63
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.42
Consensus pattern (67 bp):
AATGGTTTTGACTTTTAACTTAAAGAGTAAACATTTATCAAAACGACATAATTTTACCTTTTAAC
TT
Found at i:11904241 original size:12 final size:12
Alignment explanation
Indices: 11904224--11904262 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
11904214 ACAAATATGT
11904224 AAATAAAAAATA
1 AAATAAAAAATA
11904236 AAATAAAAAATA
1 AAATAAAAAATA
*
11904248 ATAACAAACAAATA
1 A-AATAAA-AAATA
11904262 A
1 A
11904263 TAAATTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 13 0.54
13 5 0.21
14 6 0.25
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.15
Consensus pattern (12 bp):
AAATAAAAAATA
Found at i:11906757 original size:30 final size:29
Alignment explanation
Indices: 11906723--11906832 Score: 132
Period size: 30 Copynumber: 3.7 Consensus size: 29
11906713 ATTGAAAATT
*
11906723 AAAATTATTTAATAATTTTATTATTTCAAA
1 AAAATAATTTAATAATTTTA-TATTTCAAA
11906753 AAAATAATTTTAATAATTTTATATTTC-AA
1 AAAATAA-TTTAATAATTTTATATTTCAAA
* * *
11906782 AAAATAATTTAAAAAAATTTATATTTTAAA
1 AAAATAATTT-AATAATTTTATATTTCAAA
*
11906812 AAAATATTTTTAATAATTTTA
1 AAAATA-ATTTAATAATTTTA
11906833 AAATCATTTG
Statistics
Matches: 69, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
28 3 0.04
29 22 0.32
30 28 0.41
31 16 0.23
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (29 bp):
AAAATAATTTAATAATTTTATATTTCAAA
Found at i:11906802 original size:29 final size:29
Alignment explanation
Indices: 11906739--11906814 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
11906729 ATTTAATAAT
* * *
11906739 TTTATTATTTCAAAAAAATAATTTTAATAAT
1 TTTA-TATTTC-AAAAAATAATTTAAAAAAA
11906770 TTTATATTTCAAAAAATAATTTAAAAAAA
1 TTTATATTTCAAAAAATAATTTAAAAAAA
*
11906799 TTTATATTTTAAAAAA
1 TTTATATTTCAAAAAA
11906815 ATATTTTTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 31 0.76
30 6 0.15
31 4 0.10
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (29 bp):
TTTATATTTCAAAAAATAATTTAAAAAAA
Found at i:11907126 original size:4 final size:4
Alignment explanation
Indices: 11907117--11907169 Score: 52
Period size: 4 Copynumber: 12.2 Consensus size: 4
11907107 AAATAAAGGA
* *
11907117 AAAT AAAT AAAT AAAAT AAAT AAAT AAAT ATATAT ATAT ATAT AAAT AGAAT
1 AAAT AAAT AAAT -AAAT AAAT AAAT AAAT A-A-AT AAAT AAAT AAAT A-AAT
11907169 A
1 A
11907170 CCTTGAGCAA
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
4 31 0.72
5 9 0.21
6 3 0.07
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (4 bp):
AAAT
Found at i:11907134 original size:13 final size:13
Alignment explanation
Indices: 11907116--11907144 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
11907106 GAAATAAAGG
11907116 AAAATAAATAAAT
1 AAAATAAATAAAT
11907129 AAAATAAATAAAT
1 AAAATAAATAAAT
11907142 AAA
1 AAA
11907145 TATATATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (13 bp):
AAAATAAATAAAT
Found at i:11912363 original size:119 final size:120
Alignment explanation
Indices: 11912135--11912373 Score: 392
Period size: 119 Copynumber: 2.0 Consensus size: 120
11912125 ATTTCTCTCG
* *
11912135 TTCTTCATCTTTTTCAGTAGCTTGAAGAAGAAGTACCCATGGAAGGTTTTGCATGAAGCATACTT
1 TTCTTCATATTTTTCAGTAGCTCGAAGAAGAAGTACCCATGGAAGGTTTTGCATGAAGCATACTT
* *
11912200 CATAAGGATGAAGCTGGAAAAGTAGGGAAACCAACAAGCGGGTAAGGTTCTTAAC
66 CATAAGGAGGAAGCTGGAAAAGTAGGAAAACCAACAAGCGGGTAAGGTTCTTAAC
* *
11912255 TTCTTCATATTTTTGA-TAGCTCGAAGAAGGAGTACCCATGGAAGGTTTTGCATGAAGCATACTT
1 TTCTTCATATTTTTCAGTAGCTCGAAGAAGAAGTACCCATGGAAGGTTTTGCATGAAGCATACTT
*
11912319 CATTAA-GAGGAAGCTGGAAAAGTAGGAAAACCAACAAGTGGGTAAGGTTCTTAAC
66 CA-TAAGGAGGAAGCTGGAAAAGTAGGAAAACCAACAAGCGGGTAAGGTTCTTAAC
11912374 CCTTCTGTGA
Statistics
Matches: 111, Mismatches: 7, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
119 94 0.85
120 17 0.15
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (120 bp):
TTCTTCATATTTTTCAGTAGCTCGAAGAAGAAGTACCCATGGAAGGTTTTGCATGAAGCATACTT
CATAAGGAGGAAGCTGGAAAAGTAGGAAAACCAACAAGCGGGTAAGGTTCTTAAC
Found at i:11913019 original size:51 final size:51
Alignment explanation
Indices: 11912910--11913030 Score: 120
Period size: 51 Copynumber: 2.4 Consensus size: 51
11912900 ATATACAGTG
* * * * * *
11912910 TAAGACTATAGATAAAAGAAGCTATGACAATCTGGTATAAGGTAAATGGCG
1 TAAGACCATAGATGAAAGAAGCTATGACAATATGGTATAAGATAAATAGCA
* * **
11912961 TAGGACCATAGATGAAAGAGGCTATGACAATATGGTATGAA-ATACGTAGCA
1 TAAGACCATAGATGAAAGAAGCTATGACAATATGGTAT-AAGATAAATAGCA
11913012 TAAGACCAT-GTATGAAAGA
1 TAAGACCATAG-ATGAAAGA
11913031 TTTCATGACA
Statistics
Matches: 57, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
50 1 0.02
51 54 0.95
52 2 0.04
ACGTcount: A:0.43, C:0.11, G:0.24, T:0.22
Consensus pattern (51 bp):
TAAGACCATAGATGAAAGAAGCTATGACAATATGGTATAAGATAAATAGCA
Found at i:11913356 original size:33 final size:33
Alignment explanation
Indices: 11913313--11913394 Score: 101
Period size: 33 Copynumber: 2.5 Consensus size: 33
11913303 ATAGCCCATT
* ** *
11913313 GGGATAGTAAACATAGAACATATAAAGTCTGTC
1 GGGATAGTAAACATAGAAAATATAAAACCCGTC
* * *
11913346 GGGACAGTAAACACAAAAAATATAAAACCCGTC
1 GGGATAGTAAACATAGAAAATATAAAACCCGTC
11913379 GGGATAGTAAACATAG
1 GGGATAGTAAACATAG
11913395 GATGAGTCCG
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.46, C:0.15, G:0.21, T:0.18
Consensus pattern (33 bp):
GGGATAGTAAACATAGAAAATATAAAACCCGTC
Found at i:11914789 original size:20 final size:23
Alignment explanation
Indices: 11914764--11914804 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
11914754 ACTGCTCATC
11914764 TATCA-TT-ATTC-ATCTTTTAT
1 TATCATTTCATTCAATCTTTTAT
11914784 TATCATTTCATTCAATCTTTT
1 TATCATTTCATTCAATCTTTT
11914805 TTAATAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 2 0.11
22 4 0.22
23 7 0.39
ACGTcount: A:0.24, C:0.17, G:0.00, T:0.59
Consensus pattern (23 bp):
TATCATTTCATTCAATCTTTTAT
Found at i:11919404 original size:381 final size:381
Alignment explanation
Indices: 11918701--11919465 Score: 1530
Period size: 381 Copynumber: 2.0 Consensus size: 381
11918691 TAGGAATGAT
11918701 TATGGTTTTCTCCGAAATGGAGAAGTGGAATCATTTGGAAATGAATGTAGATTTCTAATCTTATA
1 TATGGTTTTCTCCGAAATGGAGAAGTGGAATCATTTGGAAATGAATGTAGATTTCTAATCTTATA
11918766 TAGGATTACTTAAAAAATGATGGAAGAATGAGTTTATGTTTTTGGACTGTTATTGAAGCCCGAAA
66 TAGGATTACTTAAAAAATGATGGAAGAATGAGTTTATGTTTTTGGACTGTTATTGAAGCCCGAAA
11918831 AAGAAAATAAACCATTCGATCATAGTGAACATGTTGCGTTGTGACATATTAAACAAATTTTCTCG
131 AAGAAAATAAACCATTCGATCATAGTGAACATGTTGCGTTGTGACATATTAAACAAATTTTCTCG
11918896 AAATATTGAACAAATGTTCTTGATGATCTCTTTTGTTGTTGTAGGACCTTTGAAAGATGATATTT
196 AAATATTGAACAAATGTTCTTGATGATCTCTTTTGTTGTTGTAGGACCTTTGAAAGATGATATTT
11918961 ATACCTTCTAATTGATTTTCAACCATTGTGGTTATTGAGAAAGTAAATAGAGCCATTTGAATGAA
261 ATACCTTCTAATTGATTTTCAACCATTGTGGTTATTGAGAAAGTAAATAGAGCCATTTGAATGAA
11919026 AACACCAATTCATTTAATTCACCTGCAACAAAAGGTATCGATACTTTTTTTACGAG
326 AACACCAATTCATTTAATTCACCTGCAACAAAAGGTATCGATACTTTTTTTACGAG
11919082 TATGGTTTTCTCCGAAATGGAGAAGTGGAATCATTTGGAAATGAATGTAGATTTCTAATCTTATA
1 TATGGTTTTCTCCGAAATGGAGAAGTGGAATCATTTGGAAATGAATGTAGATTTCTAATCTTATA
11919147 TAGGATTACTTAAAAAATGATGGAAGAATGAGTTTATGTTTTTGGACTGTTATTGAAGCCCGAAA
66 TAGGATTACTTAAAAAATGATGGAAGAATGAGTTTATGTTTTTGGACTGTTATTGAAGCCCGAAA
11919212 AAGAAAATAAACCATTCGATCATAGTGAACATGTTGCGTTGTGACATATTAAACAAATTTTCTCG
131 AAGAAAATAAACCATTCGATCATAGTGAACATGTTGCGTTGTGACATATTAAACAAATTTTCTCG
11919277 AAATATTGAACAAATGTTCTTGATGATCTCTTTTGTTGTTGTAGGACCTTTGAAAGATGATATTT
196 AAATATTGAACAAATGTTCTTGATGATCTCTTTTGTTGTTGTAGGACCTTTGAAAGATGATATTT
11919342 ATACCTTCTAATTGATTTTCAACCATTGTGGTTATTGAGAAAGTAAATAGAGCCATTTGAATGAA
261 ATACCTTCTAATTGATTTTCAACCATTGTGGTTATTGAGAAAGTAAATAGAGCCATTTGAATGAA
11919407 AACACCAATTCATTTAATTCACCTGCAACAAAAGGTATCGATACTTTTTTTACGAG
326 AACACCAATTCATTTAATTCACCTGCAACAAAAGGTATCGATACTTTTTTTACGAG
11919463 TAT
1 TAT
11919466 CGATCATATT
Statistics
Matches: 384, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
381 384 1.00
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (381 bp):
TATGGTTTTCTCCGAAATGGAGAAGTGGAATCATTTGGAAATGAATGTAGATTTCTAATCTTATA
TAGGATTACTTAAAAAATGATGGAAGAATGAGTTTATGTTTTTGGACTGTTATTGAAGCCCGAAA
AAGAAAATAAACCATTCGATCATAGTGAACATGTTGCGTTGTGACATATTAAACAAATTTTCTCG
AAATATTGAACAAATGTTCTTGATGATCTCTTTTGTTGTTGTAGGACCTTTGAAAGATGATATTT
ATACCTTCTAATTGATTTTCAACCATTGTGGTTATTGAGAAAGTAAATAGAGCCATTTGAATGAA
AACACCAATTCATTTAATTCACCTGCAACAAAAGGTATCGATACTTTTTTTACGAG
Found at i:11919586 original size:21 final size:21
Alignment explanation
Indices: 11919552--11919593 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
11919542 ATACATGATA
**
11919552 AAAGGTATTGATACATTTTGT
1 AAAGGTATCAATACATTTTGT
*
11919573 AAAGGTATCAATACTTTTTGT
1 AAAGGTATCAATACATTTTGT
11919594 GTTTGCTTGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (21 bp):
AAAGGTATCAATACATTTTGT
Found at i:11921751 original size:19 final size:20
Alignment explanation
Indices: 11921723--11921760 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
11921713 ATTAAAAAGT
11921723 AAAATAATTT-TCAAAAATTC
1 AAAATAATTTAT-AAAAATTC
11921743 AAAAT-ATTTATAAAAATT
1 AAAATAATTTATAAAAATT
11921761 TTAAAATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAATAATTTATAAAAATTC
Found at i:11921766 original size:20 final size:20
Alignment explanation
Indices: 11921722--11921767 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
11921712 AATTAAAAAG
11921722 TAAAATAATTTTCAAAAATT
1 TAAAATAATTTTCAAAAATT
*
11921742 CAAAAT-ATTTAT-AAAAATTT
1 TAAAATAATTT-TCAAAAA-TT
11921762 TAAAAT
1 TAAAAT
11921768 TTCATTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (20 bp):
TAAAATAATTTTCAAAAATT
Found at i:11928019 original size:4 final size:4
Alignment explanation
Indices: 11928012--11928041 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
11928002 ATTCAAATAA
11928012 ATTT ATTT ATTT ATTT ATTT ATTT AATTT A
1 ATTT ATTT ATTT ATTT ATTT ATTT -ATTT A
11928042 CTAAGCTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (4 bp):
ATTT
Found at i:11931888 original size:73 final size:72
Alignment explanation
Indices: 11931716--11931913 Score: 236
Period size: 73 Copynumber: 2.7 Consensus size: 72
11931706 TTTAAAAGTT
* * * ***
11931716 CAAAAACAGTAAGTTACACGGCCTGGACACACGGGCGTGTGTCAGACCATGTGGATATTTTGTTT
1 CAAAAACAGTAAGTTACACGGCCTGGACACACGGGCGTGTGCCAGACCGTGTGCATACCGTGTTT
*
11931781 GTGGAAT
66 GTGGAAA
* * *
11931788 CAGAAACAGTGAGTTACACGGGCTGGACACACGGGCGTGTGCCAGACCGTGTGCTCATACCGT-T
1 CAAAAACAGTAAGTTACACGGCCTGGACACACGGGCGTGTGCCAGACCGTGTG--CATACCGTGT
*
11931852 TTGTGTAAA
64 TTGTGGAAA
* ** *
11931861 CAAAAACAATAAGTTACACGGTTTGGACACACGGGCGTGTCCCAGACCGTGTG
1 CAAAAACAGTAAGTTACACGGCCTGGACACACGGGCGTGTGCCAGACCGTGTG
11931914 ACACACACTG
Statistics
Matches: 107, Mismatches: 17, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
72 48 0.45
73 55 0.51
74 4 0.04
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.23
Consensus pattern (72 bp):
CAAAAACAGTAAGTTACACGGCCTGGACACACGGGCGTGTGCCAGACCGTGTGCATACCGTGTTT
GTGGAAA
Found at i:11932096 original size:39 final size:38
Alignment explanation
Indices: 11932003--11932149 Score: 125
Period size: 39 Copynumber: 3.8 Consensus size: 38
11931993 GTTATCAAAT
11932003 TACTGAACTGGCAGTGACACTGTAAACACTAAAATACAA
1 TACTGAACTGGCAGTGACACTGTAAACACT-AAATACAA
* * * * *
11932042 CATTGAACTGACAGTGACATTGTAAACAGCGT-AATACTA
1 TACTGAACTGGCAGTGACACTGTAAACA-C-TAAATACAA
* * ** *
11932081 TACTGAGCTGGCAGTGACACTATAAACACTATGTAGCTA
1 TACTGAACTGGCAGTGACACTGTAAACACTAAATA-CAA
* * * *
11932120 TATTGAACTAGTAGTGACACTATAAACACT
1 TACTGAACTGGCAGTGACACTGTAAACACT
11932150 GCGATGCTAT
Statistics
Matches: 87, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
37 1 0.01
38 3 0.03
39 81 0.93
40 1 0.01
41 1 0.01
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.25
Consensus pattern (38 bp):
TACTGAACTGGCAGTGACACTGTAAACACTAAATACAA
Found at i:11935991 original size:37 final size:38
Alignment explanation
Indices: 11935932--11936010 Score: 88
Period size: 37 Copynumber: 2.1 Consensus size: 38
11935922 TTCGAAGATA
** *
11935932 TAAAGTGATACCCAGTGTCTCATC-AGCCTAGCCGAAG
1 TAAAGTGATACCCAGTACCTCATCGAACCTAGCCGAAG
* * * *
11935969 TAAAGTGGTATCCAGTACCTCATCGAATCTATCCGAAG
1 TAAAGTGATACCCAGTACCTCATCGAACCTAGCCGAAG
11936007 TAAA
1 TAAA
11936011 ATAATGACAC
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
37 20 0.59
38 14 0.41
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (38 bp):
TAAAGTGATACCCAGTACCTCATCGAACCTAGCCGAAG
Found at i:11936160 original size:18 final size:18
Alignment explanation
Indices: 11936137--11936173 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
11936127 ACAATTCATA
11936137 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* *
11936155 TCACTTTCACTTTCAATT
1 TCACTTTCAATTCCAATT
11936173 T
1 T
11936174 TGATCACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:11946068 original size:11 final size:11
Alignment explanation
Indices: 11946049--11946081 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
11946039 TTAGGATATT
11946049 ATTTATATTTA
1 ATTTATATTTA
*
11946060 ATTTGTATTTA
1 ATTTATATTTA
11946071 ATTTATATTTA
1 ATTTATATTTA
11946082 TCTTTTTAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (11 bp):
ATTTATATTTA
Found at i:11952433 original size:3 final size:3
Alignment explanation
Indices: 11952425--11952463 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
11952415 AGGAAACCCA
*
11952425 ATT ATT ATT ATT ATT ATT ATT ATT CTT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
11952464 TAATTTTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:11955692 original size:11 final size:11
Alignment explanation
Indices: 11955673--11955705 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
11955663 TTAGGATATT
11955673 ATTTATATTTA
1 ATTTATATTTA
*
11955684 ATTTGTATTTA
1 ATTTATATTTA
11955695 ATTTATATTTA
1 ATTTATATTTA
11955706 TCTTTTTAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (11 bp):
ATTTATATTTA
Found at i:11955733 original size:14 final size:14
Alignment explanation
Indices: 11955696--11955725 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
11955686 TTGTATTTAA
*
11955696 TTTATATTTATCTT
1 TTTAGATTTATCTT
11955710 TTTAGATTTATCTT
1 TTTAGATTTATCTT
11955724 TT
1 TT
11955726 AGAGTTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.20, C:0.07, G:0.03, T:0.70
Consensus pattern (14 bp):
TTTAGATTTATCTT
Found at i:11958445 original size:39 final size:39
Alignment explanation
Indices: 11958387--11958557 Score: 184
Period size: 39 Copynumber: 4.4 Consensus size: 39
11958377 GACACTGTAA
* *
11958387 ACACTGTAAACACTTCAATATAACACTGAACTGGCAGTG
1 ACACTGTAAACACTGCAATACAACACTGAACTGGCAGTG
11958426 ACACTGTAAACACTGCAATACAACACTGAACTGGCAGTG
1 ACACTGTAAACACTGCAATACAACACTGAACTGGCAGTG
* * * * * **
11958465 GCACTGTAAATACCGTAATACAAAACTGAGTTGGCAGTG
1 ACACTGTAAACACTGCAATACAACACTGAACTGGCAGTG
* * * *
11958504 ACACTGTAAACACT--ATGTAGCTATATTGAACTGGCAGTG
1 ACACTGTAAACACTGCA-ATA-CAACACTGAACTGGCAGTG
*
11958543 ACACTTTAAACACTG
1 ACACTGTAAACACTG
11958558 AAATGCTATT
Statistics
Matches: 110, Mismatches: 19, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
37 1 0.01
38 2 0.02
39 107 0.97
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.23
Consensus pattern (39 bp):
ACACTGTAAACACTGCAATACAACACTGAACTGGCAGTG
Found at i:11958577 original size:39 final size:39
Alignment explanation
Indices: 11958413--11958593 Score: 131
Period size: 39 Copynumber: 4.6 Consensus size: 39
11958403 AATATAACAC
* * * *
11958413 TGAACTGGCAGTGACACTGTAAACACTGCAATA-CAACAC
1 TGAACTGGCAGTGACACTGTAAACACT-AAATAGCTATAT
* * * * *
11958452 TGAACTGGCAGTGGCACTGTAAATACCGT-AATA-CAAAAC
1 TGAACTGGCAGTGACACTGTAAACA-C-TAAATAGCTATAT
** **
11958491 TGAGTTGGCAGTGACACTGTAAACACTATGTAGCTATAT
1 TGAACTGGCAGTGACACTGTAAACACTAAATAGCTATAT
*
11958530 TGAACTGGCAGTGACACTTTAAACACTGAAAT-GCTAT-T
1 TGAACTGGCAGTGACACTGTAAACACT-AAATAGCTATAT
*
11958568 TCGATCTGGC-GATGACACTGTAAACA
1 T-GAACTGGCAG-TGACACTGTAAACA
11958594 TCGCATGGTT
Statistics
Matches: 116, Mismatches: 19, Indels: 14
0.78 0.13 0.09
Matches are distributed among these distances:
37 1 0.01
38 6 0.05
39 105 0.91
40 3 0.03
41 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.24
Consensus pattern (39 bp):
TGAACTGGCAGTGACACTGTAAACACTAAATAGCTATAT
Found at i:11960300 original size:80 final size:80
Alignment explanation
Indices: 11960192--11960343 Score: 207
Period size: 80 Copynumber: 1.9 Consensus size: 80
11960182 CCAAAAATAA
* * * ** * * *
11960192 TATTATTTTAATAACTTTAATGTTAAATTTAATTTAATATTTTTCTTGAT-GGTATTTTATTAAT
1 TATTAATTTAATAAATTTAATATTAAATTTAAACTAATATTTATCTTGATAAGTATTATATTAAT
11960256 TTAATATAAATATTC
66 TTAATATAAATATTC
*
11960271 TATTAATTTAATAAGATTTAATATTAAATTTAAACTAATATTTATCTTGATAATTATTATATTAA
1 TATTAATTTAATAA-ATTTAATATTAAATTTAAACTAATATTTATCTTGATAAGTATTATATTAA
11960336 TTTAATAT
65 TTTAATAT
11960344 TAAAGTAATT
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
79 13 0.21
80 31 0.50
81 18 0.29
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.53
Consensus pattern (80 bp):
TATTAATTTAATAAATTTAATATTAAATTTAAACTAATATTTATCTTGATAAGTATTATATTAAT
TTAATATAAATATTC
Found at i:11960361 original size:80 final size:79
Alignment explanation
Indices: 11960193--11960362 Score: 191
Period size: 80 Copynumber: 2.1 Consensus size: 79
11960183 CAAAAATAAT
* * * ** * * *
11960193 ATTATTTTAATAACTTTAATGTTAAATTTAATTTAATATTTTTCTTGATGGTATTTTATTAATTT
1 ATTAATTTAATAAATTTAATATTAAATTTAAACTAATATTTATCTTGATAGTATTATATTAATTT
* *
11960258 AATATAAATATTCT
66 AATATAAATAGTCA
*
11960272 ATTAATTTAATAAGATTTAATATTAAATTTAAACTAATATTTATCTTGATAATTATTATATTAAT
1 ATTAATTTAATAA-ATTTAATATTAAATTTAAACTAATATTTATCTTGAT-AGTATTATATTAAT
*
11960337 TTAATATTAA-AGT-A
64 TTAATATAAATAGTCA
11960351 ATTAAGTTTAAT
1 ATTAA-TTTAAT
11960363 TATAATTGAA
Statistics
Matches: 76, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
79 17 0.22
80 39 0.51
81 20 0.26
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.52
Consensus pattern (79 bp):
ATTAATTTAATAAATTTAATATTAAATTTAAACTAATATTTATCTTGATAGTATTATATTAATTT
AATATAAATAGTCA
Found at i:11960476 original size:127 final size:130
Alignment explanation
Indices: 11960271--11960510 Score: 360
Period size: 127 Copynumber: 1.9 Consensus size: 130
11960261 ATAAATATTC
11960271 TATTAATTTAATAAGATTTAATATTAAATTTAAACTAATATTTATCTTGATAATTATTATATTAA
1 TATTAATTTAATAAGATTTAATATTAAATTTAAACTAATATTTATCTTGATAATTATTATATTAA
*
11960336 TTTAATATTAAAGTAATTAAGTTTAATTATAATTGAACTCTCTAAACTCTCCTTATATAGAGAGA
66 TTTAATATTAAAGTAATTAAGTTTAATTATAATTAAACTCTCTAAACTCTCCTTATATAGAGAGA
* * * * ** *
11960401 TATTATTTTAATAA-CTTTAGTATTTAATTTAATTTAATATTT-TCTTGATAATT-TTTTATTAA
1 TATTAATTTAATAAGATTTAATATTAAATTTAAACTAATATTTATCTTGATAATTATTATATTAA
* * *
11960463 TTTAATATTAAAGTGATTAAGTTTAATTATAGTTAAACTCTTTAAACT
66 TTTAATATTAAAGTAATTAAGTTTAATTATAATTAAACTCTCTAAACT
11960511 TTCCCAATAT
Statistics
Matches: 99, Mismatches: 11, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
127 52 0.53
128 11 0.11
129 23 0.23
130 13 0.13
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.49
Consensus pattern (130 bp):
TATTAATTTAATAAGATTTAATATTAAATTTAAACTAATATTTATCTTGATAATTATTATATTAA
TTTAATATTAAAGTAATTAAGTTTAATTATAATTAAACTCTCTAAACTCTCCTTATATAGAGAGA
Found at i:11970900 original size:21 final size:21
Alignment explanation
Indices: 11970876--11970928 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
11970866 CCTGTAACTT
*
11970876 CTATCGATATAAGCATACAAA
1 CTATCGATACAAGCATACAAA
*
11970897 CTATCGATACAAGCATATAAA
1 CTATCGATACAAGCATACAAA
*
11970918 CTACCGATACA
1 CTATCGATACA
11970929 TCAATACTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.45, C:0.23, G:0.09, T:0.23
Consensus pattern (21 bp):
CTATCGATACAAGCATACAAA
Found at i:11988682 original size:21 final size:21
Alignment explanation
Indices: 11988658--11988708 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
11988648 ATAATAGCAT
11988658 AATCCAAATATAAAGTTTAGA
1 AATCCAAATATAAAGTTTAGA
* *
11988679 AATCCAAACATAAAGTTTATA
1 AATCCAAATATAAAGTTTAGA
11988700 AATCCAAAT
1 AATCCAAAT
11988709 TATATAATCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.53, C:0.14, G:0.06, T:0.27
Consensus pattern (21 bp):
AATCCAAATATAAAGTTTAGA
Found at i:11988725 original size:13 final size:13
Alignment explanation
Indices: 11988695--11988727 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
11988685 AACATAAAGT
11988695 TTATAAATCCAAA
1 TTATAAATCCAAA
11988708 TTATATAATCCAAA
1 TTATA-AATCCAAA
11988722 -TATAAA
1 TTATAAA
11988728 ACTTTAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 2 0.11
13 9 0.47
14 8 0.42
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (13 bp):
TTATAAATCCAAA
Found at i:11991200 original size:61 final size:61
Alignment explanation
Indices: 11991088--11991246 Score: 171
Period size: 61 Copynumber: 2.6 Consensus size: 61
11991078 ATCTTATAAT
* * * *
11991088 ATTTACACATTCTATCAATTT-GATCCTTAA-TAT-AAAAATTCAACAAATTTAGCCCTCAAT
1 ATTTACAAAATCTGTCAATTTAG-TCC-TAACTATAAAAAATTCAACAAATTTAGCCCTCAAC
* * * * * *
11991148 ATTTACAAAATTTGTCATTTTAGTTCTAATTATAAAAAATTCAATAAATTTAGCCCTCGAC
1 ATTTACAAAATCTGTCAATTTAGTCCTAACTATAAAAAATTCAACAAATTTAGCCCTCAAC
* *
11991209 ATTTATAAAATCTGTCAATTTAGTCCTAACTCTAAAAA
1 ATTTACAAAATCTGTCAATTTAGTCCTAACTATAAAAA
11991247 TTAAAAAATA
Statistics
Matches: 81, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
59 3 0.04
60 21 0.26
61 57 0.70
ACGTcount: A:0.40, C:0.17, G:0.05, T:0.38
Consensus pattern (61 bp):
ATTTACAAAATCTGTCAATTTAGTCCTAACTATAAAAAATTCAACAAATTTAGCCCTCAAC
Found at i:11992334 original size:17 final size:17
Alignment explanation
Indices: 11992309--11992342 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
11992299 ATGTGAGGTA
*
11992309 ATATATATAAAACAAAT
1 ATATATATAAAAAAAAT
*
11992326 ATATTTATAAAAAAAAT
1 ATATATATAAAAAAAAT
11992343 TAAAAAATCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (17 bp):
ATATATATAAAAAAAAT
Found at i:11996919 original size:24 final size:24
Alignment explanation
Indices: 11996891--11996938 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
11996881 TATACCAATA
11996891 ATGCAAATCAAATTGATTAAGAAC
1 ATGCAAATCAAATTGATTAAGAAC
11996915 ATGCAAATCAAATTGATTAAGAAC
1 ATGCAAATCAAATTGATTAAGAAC
11996939 TACCCCAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.25
Consensus pattern (24 bp):
ATGCAAATCAAATTGATTAAGAAC
Found at i:11998737 original size:2 final size:2
Alignment explanation
Indices: 11998730--11998768 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
11998720 AGAATTATTA
11998730 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11998769 ACCTTATTAA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11999503 original size:6 final size:6
Alignment explanation
Indices: 11999492--11999516 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
11999482 ATTTTAATAA
11999492 AATTAT AATTAT AATTAT AATTAT A
1 AATTAT AATTAT AATTAT AATTAT A
11999517 TTAGTACTTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
AATTAT
Found at i:12007675 original size:39 final size:38
Alignment explanation
Indices: 12007632--12007749 Score: 128
Period size: 39 Copynumber: 3.0 Consensus size: 38
12007622 AACACTGCGG
12007632 TGCAATACTAAGCTGACGGTAACACTGTAAATATCGTAA
1 TGCAATACTAA-CTGACGGTAACACTGTAAATATCGTAA
* * *
12007671 TGCAATACTAAACTAACGATAACATTGTAAATATCGTAA
1 TGCAATACT-AACTGACGGTAACACTGTAAATATCGTAA
* * * * * *
12007710 TGTAGTACTGAACTGATGGTGACACTGTAAACACCGTAA
1 TGCAATACT-AACTGACGGTAACACTGTAAATATCGTAA
12007749 T
1 T
12007750 ACTATACCGA
Statistics
Matches: 65, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
39 63 0.97
40 2 0.03
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.27
Consensus pattern (38 bp):
TGCAATACTAACTGACGGTAACACTGTAAATATCGTAA
Found at i:12009653 original size:13 final size:12
Alignment explanation
Indices: 12009617--12009656 Score: 55
Period size: 11 Copynumber: 3.3 Consensus size: 12
12009607 GATATGAGTA
12009617 AAAAAATTATAT
1 AAAAAATTATAT
*
12009629 AATAAATT-TAT
1 AAAAAATTATAT
12009640 AAAAAATTGATAT
1 AAAAAATT-ATAT
12009653 AAAA
1 AAAA
12009657 TTAATTAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 10 0.42
12 7 0.29
13 7 0.29
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (12 bp):
AAAAAATTATAT
Found at i:12011939 original size:245 final size:239
Alignment explanation
Indices: 12011439--12012041 Score: 652
Period size: 245 Copynumber: 2.5 Consensus size: 239
12011429 TTCACCGTCT
* * *
12011439 GTTC-GTGGAATTTGGTTTTCCATTTCGGACTGTATTTAAGGGGAAAAATAGGATCGTAGAATTC
1 GTTCTGTGGAATTTGGTTTTTCATTTCGGATTGTATTT-AGGGGAAAAAAAGGATCGTAGAA-TC
* * *
12011503 TAAATTTATATTCAATTAAATCAGCCTAACATTTTTGTTAATAATTGTTTTTAATATAGTTTCGT
64 TAAATTTATATTCAATTAAATCAGCCTAACATTTTTGTTAATTATTG--TTT-ACATA-TTCCGT
* * * *
12011568 AGCTAACAAATTGATTAATCTGAATTATTATTTATTTTGCGAAATTTGATAAAAAATTATGTTGC
125 ACCTAACAAATTGATTAATCTGAATTATTATTTATTTTGCAAAAATTGATAAAAAATTAGGTTGC
* * *
12011633 TTTTTCTTTGTCTTCATTTTTGTTTCTCAATTGTTAATTCCAATGCGCTA
190 TTTTTCTTTGCCTTCATTTTTGTTTCTCAATTATTAATTCCAATGCGCCA
* * **
12011683 GTTCT-TGGAATTAGGTTTTTCATTTC-GAGTTGTATATAGGGGAAAAGAAAATATCGTAGAATC
1 GTTCTGTGGAATTTGGTTTTTCATTTCGGA-TTGTATTTAGGGGAAAA-AAAGGATCGTAGAATC
* * * *
12011746 TAAATTTATAATAAATTATATCAGACTAAC-TTTTTGTTAATTATTGTTT-CAT-TTCCGTACCT
64 TAAATTTATATTCAATTAAATCAGCCTAACATTTTTGTTAATTATTGTTTACATATTCCGTACCT
**
12011808 AACAAATTGATTAATCTGAATAACTTATTTATTATTTATTTTGCAAAAAATTGAT-AACGATTAG
129 AACAAATTGATTAATCTG----A---A-TTATTATTTATTTTGC-AAAAATTGATAAAAAATTAG
* * *
12011872 GTTGTTTTTTTCTTTGCCGTT-ATTTTT-TCTTCTCAATTATTAGTTTCC-CTGCGCCA
185 GTTG-CTTTTTCTTTGCC-TTCATTTTTGT-TTCTCAATTATTA-ATTCCAATGCGCCA
* *
12011928 GTT-TGTGGAATTTGGTTTTTCATTTTGGATTGTATTTAGGGGGAAAAAATAGGATCGTGGAATC
1 GTTCTGTGGAATTTGGTTTTTCATTTCGGATTGTATTTA-GGGGAAAAAA-AGGATCGTAGAATC
* *
12011992 AAAATTTATATTCAATTAAATCAGCCTAACTTTTTTGTTAATTATTGTTT
64 TAAATTTATATTCAATTAAATCAGCCTAACATTTTTGTTAATTATTGTTT
12012042 GTTTCTAATC
Statistics
Matches: 301, Mismatches: 37, Indels: 39
0.80 0.10 0.10
Matches are distributed among these distances:
236 26 0.09
238 2 0.01
240 4 0.01
242 15 0.05
243 40 0.13
244 68 0.23
245 75 0.25
246 52 0.17
247 19 0.06
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.45
Consensus pattern (239 bp):
GTTCTGTGGAATTTGGTTTTTCATTTCGGATTGTATTTAGGGGAAAAAAAGGATCGTAGAATCTA
AATTTATATTCAATTAAATCAGCCTAACATTTTTGTTAATTATTGTTTACATATTCCGTACCTAA
CAAATTGATTAATCTGAATTATTATTTATTTTGCAAAAATTGATAAAAAATTAGGTTGCTTTTTC
TTTGCCTTCATTTTTGTTTCTCAATTATTAATTCCAATGCGCCA
Found at i:12017982 original size:16 final size:16
Alignment explanation
Indices: 12017963--12018002 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
12017953 ATTGAATATG
*
12017963 GTTGTAATGAAATACA
1 GTTGTAATGAAATAAA
12017979 GTTGTAATGAAATAAA
1 GTTGTAATGAAATAAA
*
12017995 GTCGTAAT
1 GTTGTAAT
12018003 CAGTAATTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.42, C:0.05, G:0.20, T:0.33
Consensus pattern (16 bp):
GTTGTAATGAAATAAA
Found at i:12018242 original size:60 final size:63
Alignment explanation
Indices: 12018172--12018307 Score: 206
Period size: 60 Copynumber: 2.2 Consensus size: 63
12018162 TTATTAAATA
* *
12018172 TAATAGGATTATTATTAAATATAATTTAATAAA-AATAAT-ATAAATAATTTAATTA-TATTT
1 TAATATGATTATTATTAAATATAATTTAATAAATAATAATAATAAATAATTTAATAACTATTT
* *
12018232 TAATATGATTATTATTAAATATAATTTAATAAATAATAATAATATATAATTTAATAACTTTTT
1 TAATATGATTATTATTAAATATAATTTAATAAATAATAATAATAAATAATTTAATAACTATTT
*
12018295 TAATATAATTATT
1 TAATATGATTATT
12018308 TTTATATTAA
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
60 32 0.47
61 6 0.09
62 14 0.21
63 16 0.24
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (63 bp):
TAATATGATTATTATTAAATATAATTTAATAAATAATAATAATAAATAATTTAATAACTATTT
Found at i:12020639 original size:32 final size:33
Alignment explanation
Indices: 12020596--12020671 Score: 138
Period size: 32 Copynumber: 2.4 Consensus size: 33
12020586 CTTAAAAATT
12020596 TTAA-TTTTTTTGTGCATCTTTTAGATTTTATA
1 TTAATTTTTTTTGTGCATCTTTTAGATTTTATA
12020628 TT-ATTTTTTTTGTGCATCTTTTAGATTTTATA
1 TTAATTTTTTTTGTGCATCTTTTAGATTTTATA
12020660 TTAATTTTTTTT
1 TTAATTTTTTTT
12020672 AAAATGTCAA
Statistics
Matches: 42, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
31 1 0.02
32 32 0.76
33 9 0.21
ACGTcount: A:0.20, C:0.05, G:0.08, T:0.67
Consensus pattern (33 bp):
TTAATTTTTTTTGTGCATCTTTTAGATTTTATA
Found at i:12030009 original size:35 final size:35
Alignment explanation
Indices: 12029960--12030039 Score: 142
Period size: 35 Copynumber: 2.3 Consensus size: 35
12029950 ATTCCATAAT
* *
12029960 CTTTATATTTTATATCTGTTTTAGTTCTTTTTTTC
1 CTTTAAATTATATATCTGTTTTAGTTCTTTTTTTC
12029995 CTTTAAATTATATATCTGTTTTAGTTCTTTTTTTC
1 CTTTAAATTATATATCTGTTTTAGTTCTTTTTTTC
12030030 CTTTAAATTA
1 CTTTAAATTA
12030040 ACTCAATCAC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.20, C:0.11, G:0.05, T:0.64
Consensus pattern (35 bp):
CTTTAAATTATATATCTGTTTTAGTTCTTTTTTTC
Found at i:12030195 original size:30 final size:30
Alignment explanation
Indices: 12030161--12030217 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
12030151 AAATTAATCG
* *
12030161 ATCAATTAAGTTGTTTTAAGTTCAAGTTAA
1 ATCAATTAAATTATTTTAAGTTCAAGTTAA
12030191 ATCAATTAAATTATTTTAAGTTCAAGT
1 ATCAATTAAATTATTTTAAGTTCAAGT
12030218 AGAGATTCAA
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:0.39, C:0.07, G:0.11, T:0.44
Consensus pattern (30 bp):
ATCAATTAAATTATTTTAAGTTCAAGTTAA
Found at i:12030582 original size:83 final size:83
Alignment explanation
Indices: 12030481--12030635 Score: 283
Period size: 83 Copynumber: 1.9 Consensus size: 83
12030471 TTAAAAAATT
12030481 AACTGAATTTCATATTTTTGTGGATTTAAATATTTGATGGATAATATTAATTCAAATTTAGTACT
1 AACTGAATTTCATATTTTTGTGGATTTAAATATTTGATGGATAATATTAATTCAAATTTAGTACT
*
12030546 GTATATAAAAAATTAACA
66 GAATATAAAAAATTAACA
* *
12030564 AACTTAATTTCATATTTTTGTGGATTTAAATATTTGATGGATAATATTAATTCAAATTTAGTATT
1 AACTGAATTTCATATTTTTGTGGATTTAAATATTTGATGGATAATATTAATTCAAATTTAGTACT
12030629 GAATATA
66 GAATATA
12030636 TTACTTAGAT
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 69 1.00
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.45
Consensus pattern (83 bp):
AACTGAATTTCATATTTTTGTGGATTTAAATATTTGATGGATAATATTAATTCAAATTTAGTACT
GAATATAAAAAATTAACA
Found at i:12034709 original size:20 final size:19
Alignment explanation
Indices: 12034681--12034734 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
12034671 AGTCTTCAAG
12034681 GTATCGGTAGAAGTGGAGTT
1 GTAT-GGTAGAAGTGGAGTT
*
12034701 GTATAGGTAGAAGTTGAGTT
1 GTAT-GGTAGAAGTGGAGTT
*
12034721 CTACTGGTAGAAGT
1 GTA-TGGTAGAAGT
12034735 CACACTGGAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.28, C:0.06, G:0.35, T:0.31
Consensus pattern (19 bp):
GTATGGTAGAAGTGGAGTT
Found at i:12040105 original size:19 final size:20
Alignment explanation
Indices: 12040081--12040120 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
12040071 ATTTTAATTT
12040081 TAAAATATAAAA-ATAAAAA
1 TAAAATATAAAATATAAAAA
12040100 TAAAATATAAAATATAAAAA
1 TAAAATATAAAATATAAAAA
12040120 T
1 T
12040121 TATTTTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (20 bp):
TAAAATATAAAATATAAAAA
Found at i:12040979 original size:33 final size:34
Alignment explanation
Indices: 12040952--12041018 Score: 120
Period size: 33 Copynumber: 2.0 Consensus size: 34
12040942 TAAAAATTTT
12040952 AAAATTATAAATCAATACAATGAT-AAAATTACA
1 AAAATTATAAATCAATACAATGATAAAAATTACA
12040985 AAAATTATAAATCAATACAATGAT-AAAATTACA
1 AAAATTATAAATCAATACAATGATAAAAATTACA
12041018 A
1 A
12041019 TTTAACTCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.61, C:0.09, G:0.03, T:0.27
Consensus pattern (34 bp):
AAAATTATAAATCAATACAATGATAAAAATTACA
Found at i:12040980 original size:17 final size:17
Alignment explanation
Indices: 12040960--12041013 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
12040950 TTAAAATTAT
12040960 AAATCAATACAATGATA
1 AAATCAATACAATGATA
*
12040977 AAATTACAA-A-AATTAT-
1 AAA-T-CAATACAATGATA
12040993 AAATCAATACAATGATA
1 AAATCAATACAATGATA
12041010 AAAT
1 AAAT
12041014 TACAATTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
14 3 0.10
15 2 0.07
16 8 0.27
17 12 0.40
18 2 0.07
19 3 0.10
ACGTcount: A:0.61, C:0.09, G:0.04, T:0.26
Consensus pattern (17 bp):
AAATCAATACAATGATA
Found at i:12041010 original size:16 final size:16
Alignment explanation
Indices: 12040958--12041011 Score: 58
Period size: 16 Copynumber: 3.3 Consensus size: 16
12040948 TTTTAAAATT
12040958 ATAAATCAATACAATG
1 ATAAATCAATACAATG
*
12040974 ATAAAATTACAA-A-AATT
1 AT-AAA-T-CAATACAATG
12040991 ATAAATCAATACAATG
1 ATAAATCAATACAATG
12041007 ATAAA
1 ATAAA
12041012 ATTACAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
14 3 0.10
15 2 0.06
16 13 0.42
17 8 0.26
18 2 0.06
19 3 0.10
ACGTcount: A:0.61, C:0.09, G:0.04, T:0.26
Consensus pattern (16 bp):
ATAAATCAATACAATG
Found at i:12045059 original size:7 final size:7
Alignment explanation
Indices: 12045047--12045074 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
12045037 AAGGTGGACG
12045047 AGGGAAA
1 AGGGAAA
12045054 AGGGAAA
1 AGGGAAA
12045061 AGGGAAA
1 AGGGAAA
12045068 AGGGAAA
1 AGGGAAA
12045075 GGTGTTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (7 bp):
AGGGAAA
Found at i:12048887 original size:55 final size:55
Alignment explanation
Indices: 12048803--12048915 Score: 208
Period size: 55 Copynumber: 2.1 Consensus size: 55
12048793 TTGCCTCAGC
*
12048803 TCAGCTGTAGACGAACGAAGCAACTCAGTATTAGAATCATCTCTCGGCCCATCGA
1 TCAGCTCTAGACGAACGAAGCAACTCAGTATTAGAATCATCTCTCGGCCCATCGA
*
12048858 TCAGCTCTAGACGAACGAAGCAACTCAGTATTAGAATCATTTCTCGGCCCATCGA
1 TCAGCTCTAGACGAACGAAGCAACTCAGTATTAGAATCATCTCTCGGCCCATCGA
12048913 TCA
1 TCA
12048916 AACTGTCAAT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (55 bp):
TCAGCTCTAGACGAACGAAGCAACTCAGTATTAGAATCATCTCTCGGCCCATCGA
Done.