Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 102 of 214
Found at i:30113639 original size:9 final size:9
Alignment explanation
Indices: 30113625--30113680 Score: 53
Period size: 9 Copynumber: 6.1 Consensus size: 9
30113615 AAATAAAAAC
30113625 ATTATTAAA
1 ATTATTAAA
30113634 ATTATTAAA
1 ATTATTAAA
30113643 A-TATTAAA
1 ATTATTAAA
30113651 ATTTTATATAAA
1 A--TTAT-TAAA
* *
30113663 CTTATAAAA
1 ATTATTAAA
30113672 ATTA-TAAA
1 ATTATTAAA
30113680 A
1 A
30113681 AATTACAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
8 12 0.31
9 16 0.41
10 4 0.10
11 3 0.08
12 4 0.10
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (9 bp):
ATTATTAAA
Found at i:30113676 original size:19 final size:18
Alignment explanation
Indices: 30113611--30113757 Score: 90
Period size: 19 Copynumber: 7.8 Consensus size: 18
30113601 AAAATGTAAA
30113611 ATAAAAA-TA-AAAACATT
1 ATAAAAATTATAAAAC-TT
*
30113628 ATTAAAATTATTAAAA--T
1 ATAAAAATTA-TAAAACTT
*
30113645 ATTAAAATTTTATATAAACTT
1 A-TAAAA-ATTATA-AAACTT
*
30113666 ATAAAAATTATAAAAAATT
1 ATAAAAATTAT-AAAACTT
* *
30113685 ACAAAAA-AATAATAACTT
1 ATAAAAATTATAA-AACTT
*
30113703 ATAAATATTATAAATACTT
1 ATAAAAATTATAAA-ACTT
30113722 AT-AAAATTATAATAAACTAT
1 ATAAAAATTAT-A-AAACT-T
30113742 ATAAATAATTATAAAA
1 ATAAA-AATTATAAAA
30113758 GATAAAGATA
Statistics
Matches: 101, Mismatches: 12, Indels: 31
0.70 0.08 0.22
Matches are distributed among these distances:
17 10 0.10
18 27 0.27
19 35 0.35
20 18 0.18
21 5 0.05
22 6 0.06
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (18 bp):
ATAAAAATTATAAAACTT
Found at i:30113680 original size:37 final size:37
Alignment explanation
Indices: 30113621--30113757 Score: 118
Period size: 37 Copynumber: 3.6 Consensus size: 37
30113611 ATAAAAATAA
* *
30113621 AAACATTATTAAAATTATTAAAATATTA-AAATTTTATAT
1 AAAC-TTATAAAAATTA-TAAAATATTACAAA-ATTATAT
* **
30113660 AAACTTATAAAAATTATAAAAAATTACAAAAAAATA-
1 AAACTTATAAAAATTATAAAATATTACAAAATTATAT
* *
30113696 ATAACTTATAAATATTAT-AAATACTTATAAAATTATAAT
1 A-AACTTATAAAAATTATAAAATA-TTACAAAATTAT-AT
30113735 AAACTATATAAATAATTATAAAA
1 AAACT-TATAAA-AATTATAAAA
30113758 GATAAAGATA
Statistics
Matches: 79, Mismatches: 11, Indels: 14
0.76 0.11 0.13
Matches are distributed among these distances:
36 5 0.06
37 36 0.46
38 19 0.24
39 11 0.14
40 5 0.06
41 3 0.04
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (37 bp):
AAACTTATAAAAATTATAAAATATTACAAAATTATAT
Found at i:30113681 original size:9 final size:9
Alignment explanation
Indices: 30113611--30113967 Score: 82
Period size: 10 Copynumber: 37.9 Consensus size: 9
30113601 AAAATGTAAA
30113611 ATAAAAA-T
1 ATAAAAATT
30113619 A-AAAACATT
1 ATAAAA-ATT
*
30113628 ATTAAAATT
1 ATAAAAATT
30113637 ATTAAAATATT
1 A-TAAAA-ATT
**
30113648 A-AAATTTT
1 ATAAAAATT
*
30113656 ATATAAACTT
1 ATA-AAAATT
30113666 ATAAAAATT
1 ATAAAAATT
30113675 ATAAAAAATT
1 AT-AAAAATT
* *
30113685 ACAAAAA-A
1 ATAAAAATT
*
30113693 ATAATAACTT
1 ATAA-AAATT
*
30113703 ATAAATATT
1 ATAAAAATT
*
30113712 ATAAATACTT
1 ATAAA-AATT
30113722 AT-AAAATT
1 ATAAAAATT
30113730 ATAATAAACTAT
1 ATAA-AAA-T-T
30113742 ATAAATAATT
1 ATAAA-AATT
30113752 ATAAAAGA-T
1 ATAAAA-ATT
30113761 A-AAGATAATT
1 ATAA-A-AATT
30113771 -TAAATAATT
1 ATAAA-AATT
*
30113780 -T-AAATTT
1 ATAAAAATT
**
30113787 ATTTAAATAT
1 ATAAAAAT-T
30113797 ATAAAAATT
1 ATAAAAATT
*
30113806 ATTAAAAA-A
1 A-TAAAAATT
* **
30113815 ACAAAAAAA
1 ATAAAAATT
*
30113824 ATGGATAATATT
1 AT--A-AAAATT
30113836 ATAAAAACTCT
1 ATAAAAA-T-T
30113847 A-AAAAATT
1 ATAAAAATT
*
30113855 ATCAATAATT
1 AT-AAAAATT
*
30113865 ATAAAACTT
1 ATAAAAATT
**
30113874 ATAAACACAGC
1 ATAAA-A-ATT
30113885 ATAAAAACTT
1 ATAAAAA-TT
30113895 ATTTAAAAA--
1 A--TAAAAATT
30113904 ATCAAAAAGTT
1 AT-AAAAA-TT
* *
30113915 CTAATAATT
1 ATAAAAATT
30113924 ATAAAAA-T
1 ATAAAAATT
*
30113932 ATATAAAATC
1 ATA-AAAATT
30113942 AT-AAAA-T
1 ATAAAAATT
30113949 ATTAAAAATAT
1 A-TAAAAAT-T
30113960 ATAAAAAT
1 ATAAAAAT
30113968 CCATTTATAG
Statistics
Matches: 258, Mismatches: 43, Indels: 94
0.65 0.11 0.24
Matches are distributed among these distances:
7 9 0.03
8 39 0.15
9 86 0.33
10 88 0.34
11 18 0.07
12 18 0.07
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.33
Consensus pattern (9 bp):
ATAAAAATT
Found at i:30113807 original size:19 final size:19
Alignment explanation
Indices: 30113724--30113808 Score: 52
Period size: 19 Copynumber: 4.5 Consensus size: 19
30113714 AAATACTTAT
*
30113724 AAAATTATAATAAACTATATA
1 AAAATTAT-TTAAA-TATATA
*
30113745 AATAATTA--TAAA-AGATA
1 AA-AATTATTTAAATATATA
* * *
30113762 AAGATAATTTAAATA-ATTT
1 AAAATTATTTAAATATA-TA
*
30113781 AAATTTATTTAAATATATA
1 AAAATTATTTAAATATATA
30113800 AAAATTATT
1 AAAATTATT
30113809 AAAAAAACAA
Statistics
Matches: 49, Mismatches: 9, Indels: 14
0.68 0.12 0.19
Matches are distributed among these distances:
16 3 0.06
17 6 0.12
18 5 0.10
19 27 0.55
20 1 0.02
21 2 0.04
22 5 0.10
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (19 bp):
AAAATTATTTAAATATATA
Found at i:30113938 original size:10 final size:10
Alignment explanation
Indices: 30113923--30113967 Score: 53
Period size: 9 Copynumber: 4.9 Consensus size: 10
30113913 TTCTAATAAT
30113923 TATAAAAATA
1 TATAAAAATA
30113933 TAT-AAAAT-
1 TATAAAAATA
*
30113941 CAT-AAAATA
1 TATAAAAATA
30113950 T-TAAAAATA
1 TATAAAAATA
30113959 TATAAAAAT
1 TATAAAAAT
30113968 CCATTTATAG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
8 8 0.27
9 12 0.40
10 10 0.33
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (10 bp):
TATAAAAATA
Found at i:30114485 original size:30 final size:30
Alignment explanation
Indices: 30114451--30114518 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
30114441 ATTATTCTTT
* *
30114451 AAATTTT-TATAATTTATTAGATTTTTATGA
1 AAATTTTATATAATTTATAAG-TTTTTATAA
*
30114481 AAATTTTATATTATTTATAAGTTTTTATAA
1 AAATTTTATATAATTTATAAGTTTTTATAA
*
30114511 AAAATTTA
1 AAATTTTA
30114519 AATATGTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 22 0.67
31 11 0.33
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.54
Consensus pattern (30 bp):
AAATTTTATATAATTTATAAGTTTTTATAA
Found at i:30114634 original size:9 final size:9
Alignment explanation
Indices: 30114437--30114634 Score: 52
Period size: 9 Copynumber: 20.9 Consensus size: 9
30114427 ATAATTTTTA
*
30114437 TTTTATTAT
1 TTTTATAAT
30114446 TCTTTA-AAT
1 T-TTTATAAT
30114455 TTTTATAAT
1 TTTTATAAT
*
30114464 TTATTA-GAT
1 TT-TTATAAT
*
30114473 TTTTATGAAAA
1 TTTTAT--AAT
30114484 TTTTAT-AT
1 TTTTATAAT
30114492 TATTTATAAGT
1 T-TTTATAA-T
*
30114503 TTTTATAAAAA
1 TTTTAT--AAT
*
30114514 ATTTA-AAT
1 TTTTATAAT
* *
30114522 ATGTTAAATAT
1 -TTTTATA-AT
30114533 GTTTTAT-AT
1 -TTTTATAAT
30114542 GTTTTATTAA-
1 -TTTTA-TAAT
30114552 TTTTATAAT
1 TTTTATAAT
30114561 TTATTA-AA-
1 TT-TTATAAT
**
30114569 AATTATAAT
1 TTTTATAAT
*
30114578 TGTTTATCAT
1 T-TTTATAAT
*
30114588 ATTTATAAGT
1 TTTTATAA-T
30114598 TTTTATGAATT
1 TTTTAT-AA-T
* *
30114609 TTTTACAAG
1 TTTTATAAT
*
30114618 TCTTATAAT
1 TTTTATAAT
30114627 TTTTATAA
1 TTTTATAA
30114635 ATTTATACCA
Statistics
Matches: 138, Mismatches: 28, Indels: 46
0.65 0.13 0.22
Matches are distributed among these distances:
7 3 0.02
8 16 0.12
9 57 0.41
10 32 0.23
11 28 0.20
12 2 0.01
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (9 bp):
TTTTATAAT
Found at i:30123756 original size:31 final size:31
Alignment explanation
Indices: 30123707--30123767 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
30123697 TTAGTATAAT
*
30123707 TATATACATGAAACTTTTATTATAATTTAAA
1 TATATACAAGAAACTTTTATTATAATTTAAA
* * * *
30123738 TATATATAAGAAATTTTTATTTTGATTTAA
1 TATATACAAGAAACTTTTATTATAATTTAA
30123768 TTATGCACAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (31 bp):
TATATACAAGAAACTTTTATTATAATTTAAA
Found at i:30124363 original size:32 final size:32
Alignment explanation
Indices: 30124323--30124384 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
30124313 TTTTTTTAAG
* * **
30124323 TTAAATTTAGTCTTTAATTTTTTTTAAAAAAT
1 TTAAATTTAATCATTAACCTTTTTTAAAAAAT
30124355 TTAAATTTAATCATTAACCTTTTTTAAAAA
1 TTAAATTTAATCATTAACCTTTTTTAAAAA
30124385 GAGTCGAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.52
Consensus pattern (32 bp):
TTAAATTTAATCATTAACCTTTTTTAAAAAAT
Found at i:30127666 original size:13 final size:13
Alignment explanation
Indices: 30127648--30127675 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
30127638 TATTGCATTA
30127648 TTTGTTTCGGTTC
1 TTTGTTTCGGTTC
30127661 TTTGTTTCGGTTC
1 TTTGTTTCGGTTC
30127674 TT
1 TT
30127676 GCCTGTATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.00, C:0.14, G:0.21, T:0.64
Consensus pattern (13 bp):
TTTGTTTCGGTTC
Found at i:30129528 original size:13 final size:13
Alignment explanation
Indices: 30129510--30129535 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
30129500 TCTAAATCAG
30129510 AATTATTTTTGAA
1 AATTATTTTTGAA
30129523 AATTATTTTTGAA
1 AATTATTTTTGAA
30129536 CTCAAAAGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (13 bp):
AATTATTTTTGAA
Found at i:30132680 original size:47 final size:47
Alignment explanation
Indices: 30132623--30132768 Score: 126
Period size: 44 Copynumber: 3.2 Consensus size: 47
30132613 ATAAGAACAT
* *
30132623 TTTATTATTAAGAATATTATGAAATTATATATCATTATTAAATTATA
1 TTTAATATTAAGAATATTATGAAATTATATATAATTATTAAATTATA
* * * * *
30132670 TTTAATATT-A-ATTATT-TTAAATTGTATA-AATTCA-TATAATAAAA
1 TTTAATATTAAGAATATTATGAAATTATATATAATT-ATTA-AATTATA
* * * *
30132714 TTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTAT-
1 TTTAATATTAAGAATATTATGAAATTATATATAATTATTAAATTATA
30132760 TTTAA-ATTA
1 TTTAATATTA
30132769 TACAAATTCA
Statistics
Matches: 74, Mismatches: 18, Indels: 16
0.69 0.17 0.15
Matches are distributed among these distances:
43 5 0.07
44 23 0.31
45 9 0.12
46 9 0.12
47 23 0.31
48 5 0.07
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (47 bp):
TTTAATATTAAGAATATTATGAAATTATATATAATTATTAAATTATA
Found at i:30132734 original size:91 final size:90
Alignment explanation
Indices: 30132604--30132768 Score: 260
Period size: 91 Copynumber: 1.8 Consensus size: 90
30132594 TTGATTTTAG
* *
30132604 TAAATTCATATAAGAACATTTTATTATTAAGAATATTATGAAATTATATATCATTATTAAATTAT
1 TAAATTCATATAAGAACAATTTATTATCAAGAATATTATGAAATTATATATCATTATTAAATTAT
30132669 ATTTAATATTAATTATTTTAAATTGTA
66 -TTTAA-ATTAATTATTTTAAATTGTA
* * *
30132696 TAAATTCATATAATAA-AATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTAT
1 TAAATTCATATAAGAACAATTTATTATCAAGAATATTATGAAATTATATATCATTATTAAATTAT
30132760 TTTAAATTA
66 TTTAAATTA
30132769 TACAAATTCA
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
89 4 0.06
90 5 0.07
91 44 0.65
92 15 0.22
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (90 bp):
TAAATTCATATAAGAACAATTTATTATCAAGAATATTATGAAATTATATATCATTATTAAATTAT
TTTAAATTAATTATTTTAAATTGTA
Found at i:30132814 original size:75 final size:73
Alignment explanation
Indices: 30132657--30132795 Score: 215
Period size: 75 Copynumber: 1.9 Consensus size: 73
30132647 TTATATATCA
* * *
30132657 TTATTAAATTATATTTAATATTAATTATTTTAAATTGTATAAATTCATATAATAAAATTTATTAT
1 TTATTAAATTATATTTAATATTAATTATTTTAAATTATACAAATTCATATAAGAAAATTTATTAT
30132722 CAAGAATT
66 CAAGAATT
* *
30132730 TTATGAAATTATATATTATTATTAAATTATTTTAAATTATACAAATTCATATAAGAAAATTTATT
1 TTATTAAATTATAT-TTAATATT-AATTATTTTAAATTATACAAATTCATATAAGAAAATTTATT
30132795 A
64 A
30132796 GTTATAATTA
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
73 13 0.22
74 7 0.12
75 39 0.66
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (73 bp):
TTATTAAATTATATTTAATATTAATTATTTTAAATTATACAAATTCATATAAGAAAATTTATTAT
CAAGAATT
Found at i:30132936 original size:120 final size:120
Alignment explanation
Indices: 30132811--30133347 Score: 936
Period size: 120 Copynumber: 4.5 Consensus size: 120
30132801 AATTATTTTA
* *
30132811 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATCTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT-AAATTATCTTT
30132875 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
30132931 AATTTTATTAAATTATATATTTTAATT-AAATATATTTAATATTAATTAT-TTCAAATTATCTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT-AAATTATCTTT
30132994 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
30133050 AATTTTGTTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATCTTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATCTTTT
30133115 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* * *
30133170 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATCTTTT
30133235 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* * *
30133290 AATTTTATTAAATTATATATTTCAATTATATTATATTTAATAATAATTATGTTTAAAT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATG-TTAAAT
30133348 ATGATTAAAT
Statistics
Matches: 404, Mismatches: 10, Indels: 5
0.96 0.02 0.01
Matches are distributed among these distances:
119 118 0.29
120 279 0.69
121 7 0.02
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATCTTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:30132952 original size:17 final size:17
Alignment explanation
Indices: 30132932--30132965 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
30132922 ATTATTAAGA
30132932 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAA-TATAT
30132949 ATTTTAATTAAATATAT
1 ATTTTAATTAAATATAT
30132966 TTAATATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTTAATTAAATATAT
Found at i:30133077 original size:239 final size:240
Alignment explanation
Indices: 30132811--30133347 Score: 945
Period size: 239 Copynumber: 2.2 Consensus size: 240
30132801 AATTATTTTA
* *
30132811 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATCTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT-AAATTATCTTT
30132875 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATT
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATT
* *
30132940 AAATTATATATTTTAATTA-AATATATTTAATATTAATTAT-TTCAAATTATCTTTTATAGTATC
130 AAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT-AAATTATATTTTATAGTATC
30133003 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
194 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
30133050 AATTTTGTTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATCTTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATCTTTT
30133115 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTA
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTA
*
30133180 AATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGTATCAT
131 AATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTTATAGTATCAT
30133245 ATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
196 ATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* * *
30133290 AATTTTATTAAATTATATATTTCAATTATATTATATTTAATAATAATTATGTTTAAAT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATG-TTAAAT
30133348 ATGATTAAAT
Statistics
Matches: 284, Mismatches: 10, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
239 142 0.50
240 134 0.47
241 8 0.03
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (240 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATCTTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTA
AATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTTATAGTATCAT
ATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:30133210 original size:15 final size:15
Alignment explanation
Indices: 30133175--30133226 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
30133165 TTAAGAATTT
*
30133175 TATTAAATTAT-ATA
1 TATTTAATTATAATA
30133189 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
30133203 TATTTAATAATAAT-
1 TATTTAATTATAATA
30133217 TATGTTAATT
1 TAT-TTAATT
30133227 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:30133567 original size:45 final size:44
Alignment explanation
Indices: 30133484--30133574 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 44
30133474 ACCTCTATTC
*
30133484 CATTCAACCAAACACAAGATTACTCTTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTACTATTACGCCTCTATTCCATTA
* * *
30133528 CATTCAACCAAACA-ATTGATTTGCTATTACGCCTCTATTCTATTA
1 CATTCAACCAAACACA-AGA-TTACTATTACGCCTCTATTCCATTA
30133573 CA
1 CA
30133575 CATCTATTCC
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
43 1 0.02
44 16 0.39
45 24 0.59
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.33
Consensus pattern (44 bp):
CATTCAACCAAACACAAGATTACTATTACGCCTCTATTCCATTA
Found at i:30133572 original size:16 final size:16
Alignment explanation
Indices: 30133551--30133599 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 16
30133541 AATTGATTTG
30133551 CTATTACGCCTCTATT
1 CTATTACGCCTCTATT
* *
30133567 CTATTACACATCTATT
1 CTATTACGCCTCTATT
* *
30133583 CCATTACGGCTCTATT
1 CTATTACGCCTCTATT
30133599 C
1 C
30133600 CAATACAGCG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.22, C:0.31, G:0.06, T:0.41
Consensus pattern (16 bp):
CTATTACGCCTCTATT
Found at i:30135364 original size:14 final size:15
Alignment explanation
Indices: 30135345--30135378 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
30135335 TACAGAATAC
*
30135345 AATAAA-ATATTAAA
1 AATAAATATATAAAA
30135359 AATAAATATATAAAA
1 AATAAATATATAAAA
30135374 AATAA
1 AATAA
30135379 GACAGTGACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AATAAATATATAAAA
Found at i:30140833 original size:25 final size:24
Alignment explanation
Indices: 30140773--30140826 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
30140763 AAGCTCATAT
* *
30140773 GAGCCAATTTCGGGAAGTTCAAGC
1 GAGCCAATATCGGGAAGTTCAAGA
30140797 GAGCCAATATCGGGAAGTTTC-AGA
1 GAGCCAATATCGGGAAG-TTCAAGA
30140821 GAGCCA
1 GAGCCA
30140827 TTAATCGTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 24 0.89
25 3 0.11
ACGTcount: A:0.31, C:0.20, G:0.30, T:0.19
Consensus pattern (24 bp):
GAGCCAATATCGGGAAGTTCAAGA
Found at i:30140896 original size:25 final size:24
Alignment explanation
Indices: 30140839--30140896 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 24
30140829 AATCGTAAAA
*
30140839 CTCATAAGAGCCATAAACGGGAAG
1 CTCATAAGAACCATAAACGGGAAG
** *
30140863 CTCGCAAGAACCATATAATGGGAAG
1 CTCATAAGAACCATA-AACGGGAAG
30140888 CTCATAAGA
1 CTCATAAGA
30140897 GCCAAATATC
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.41, C:0.21, G:0.22, T:0.16
Consensus pattern (24 bp):
CTCATAAGAACCATAAACGGGAAG
Found at i:30148846 original size:6 final size:6
Alignment explanation
Indices: 30148835--30148880 Score: 56
Period size: 6 Copynumber: 7.0 Consensus size: 6
30148825 GCATCAAGCT
30148835 ACCTCC ACCTCC ACCTCC ACCGATCC ACCTCC ACCGGTCC ACCTCC
1 ACCTCC ACCTCC ACCTCC ACC--TCC ACCTCC ACC--TCC ACCTCC
30148881 GGTCCTGCAC
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
6 24 0.67
8 12 0.33
ACGTcount: A:0.17, C:0.61, G:0.07, T:0.15
Consensus pattern (6 bp):
ACCTCC
Found at i:30148863 original size:14 final size:13
Alignment explanation
Indices: 30148835--30148880 Score: 67
Period size: 14 Copynumber: 3.5 Consensus size: 13
30148825 GCATCAAGCT
30148835 ACCTCCACC-TCC
1 ACCTCCACCGTCC
30148847 ACCTCCACCGATCC
1 ACCTCCACCG-TCC
30148861 ACCTCCACCGGTCC
1 ACCTCCACC-GTCC
30148875 ACCTCC
1 ACCTCC
30148881 GGTCCTGCAC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
12 9 0.29
14 21 0.68
15 1 0.03
ACGTcount: A:0.17, C:0.61, G:0.07, T:0.15
Consensus pattern (13 bp):
ACCTCCACCGTCC
Found at i:30150158 original size:32 final size:32
Alignment explanation
Indices: 30150117--30150181 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
30150107 CAATGAGAGT
30150117 ATGGATCAATTTTGATATTGTTATCCTTTAAA
1 ATGGATCAATTTTGATATTGTTATCCTTTAAA
*
30150149 ATGGATCAATTTTGATGTTGTTATCCTTTAAA
1 ATGGATCAATTTTGATATTGTTATCCTTTAAA
30150181 A
1 A
30150182 GCATAAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (32 bp):
ATGGATCAATTTTGATATTGTTATCCTTTAAA
Found at i:30150352 original size:25 final size:25
Alignment explanation
Indices: 30150318--30150369 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
30150308 CTTTTTTAAG
*
30150318 AATTGATTGTTTGTAATTAAATTCA
1 AATTAATTGTTTGTAATTAAATTCA
30150343 AATTAATTGTTTGTAATTAAATTCA
1 AATTAATTGTTTGTAATTAAATTCA
30150368 AA
1 AA
30150370 CAAGTAATCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.40, C:0.04, G:0.10, T:0.46
Consensus pattern (25 bp):
AATTAATTGTTTGTAATTAAATTCA
Found at i:30159973 original size:13 final size:13
Alignment explanation
Indices: 30159956--30160010 Score: 62
Period size: 12 Copynumber: 4.4 Consensus size: 13
30159946 ATTTATTATA
30159956 TTTATTATTT-AT
1 TTTATTATTTAAT
30159968 TGTTA-TATTTAAT
1 T-TTATTATTTAAT
30159981 TTTATTA-TTAAT
1 TTTATTATTTAAT
**
30159993 TAAATTATTTAAT
1 TTTATTATTTAAT
30160006 TTTAT
1 TTTAT
30160011 AAAATATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
12 19 0.54
13 16 0.46
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (13 bp):
TTTATTATTTAAT
Found at i:30164687 original size:30 final size:30
Alignment explanation
Indices: 30164653--30164709 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
30164643 TACATCAGAG
*
30164653 TAGTGGTAGTAGTTGTGTTTAGTAAAAAAT
1 TAGTGGTAGTAGTTGCGTTTAGTAAAAAAT
*
30164683 TAGTGGTAGTAGTTGCGTTTGGTAAAA
1 TAGTGGTAGTAGTTGCGTTTAGTAAAA
30164710 TAATAGATTT
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:0.30, C:0.02, G:0.30, T:0.39
Consensus pattern (30 bp):
TAGTGGTAGTAGTTGCGTTTAGTAAAAAAT
Found at i:30166491 original size:14 final size:14
Alignment explanation
Indices: 30166460--30166508 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
30166450 AGGAAAGAAA
30166460 AAAGAA-AAGGGA-
1 AAAGAAGAAGGGAG
30166472 AGAAGAAGAAGGGAG
1 A-AAGAAGAAGGGAG
* *
30166487 AAAGAAAAAGAGAG
1 AAAGAAGAAGGGAG
30166501 AAA-AAGAA
1 AAAGAAGAA
30166509 AGAAAAAGGA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
12 1 0.03
13 9 0.29
14 20 0.65
15 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (14 bp):
AAAGAAGAAGGGAG
Found at i:30166502 original size:10 final size:10
Alignment explanation
Indices: 30166485--30166516 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
30166475 AGAAGAAGGG
30166485 AGAAAGAAAA
1 AGAAAGAAAA
*
30166495 AGAGAGAAAA
1 AGAAAGAAAA
30166505 AGAAAGAAAA
1 AGAAAGAAAA
30166515 AG
1 AG
30166517 GAAAATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (10 bp):
AGAAAGAAAA
Found at i:30167081 original size:20 final size:20
Alignment explanation
Indices: 30167056--30167093 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
30167046 AAAAATATTC
30167056 AAAAATCCTCGTATTTTAAT
1 AAAAATCCTCGTATTTTAAT
* *
30167076 AAAAATTCTCGTGTTTTA
1 AAAAATCCTCGTATTTTA
30167094 TTAGAATCTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.42
Consensus pattern (20 bp):
AAAAATCCTCGTATTTTAAT
Found at i:30167256 original size:17 final size:17
Alignment explanation
Indices: 30167210--30167258 Score: 71
Period size: 18 Copynumber: 2.8 Consensus size: 17
30167200 TAAAGAAAAA
*
30167210 TCGTGTTTCAAAATTTT
1 TCGTGTTTCAAAATTTC
*
30167227 TCATGTCTTCAAAATTTC
1 TCGTGT-TTCAAAATTTC
30167245 TCGTGTTTCAAAAT
1 TCGTGTTTCAAAAT
30167259 AATGATAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 13 0.46
18 15 0.54
ACGTcount: A:0.27, C:0.16, G:0.10, T:0.47
Consensus pattern (17 bp):
TCGTGTTTCAAAATTTC
Found at i:30167338 original size:16 final size:16
Alignment explanation
Indices: 30167317--30167390 Score: 69
Period size: 17 Copynumber: 4.5 Consensus size: 16
30167307 TCTTTAAAAA
30167317 AAAAATTTCGTGTTTC
1 AAAAATTTCGTGTTTC
** *
30167333 AAAAATTCTCGTGAATA
1 AAAAATT-TCGTGTTTC
*
30167350 AAAAAATTCGTGTTTTC
1 AAAAATTTCGTG-TTTC
*
30167367 AAAAATTCCGGTGTTT-
1 AAAAATTTC-GTGTTTC
30167383 AAAAATTT
1 AAAAATTT
30167391 TTTCGTGTTT
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
16 19 0.42
17 23 0.51
18 3 0.07
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Consensus pattern (16 bp):
AAAAATTTCGTGTTTC
Found at i:30167428 original size:18 final size:19
Alignment explanation
Indices: 30167398--30167655 Score: 120
Period size: 17 Copynumber: 13.9 Consensus size: 19
30167388 TTTTTTCGTG
30167398 TTTTCGTGTTTTCAAAAAA
1 TTTTCGTGTTTTCAAAAAA
30167417 TTCTT-GTG-TTTC-AAAAA
1 TT-TTCGTGTTTTCAAAAAA
30167434 TTTTCGTGTTTTCAAAATTTTCATA
1 TTTTCGTGTTTTCAAAA-----A-A
30167459 TTTTCGTGTTTTCAAAAAAA
1 TTTTCGTGTTTTC-AAAAAA
* *
30167479 TTATCGTGTTTTTTAAAAAAA
1 TTTTCGTG--TTTTCAAAAAA
** *
30167500 AATTCATG-TTT-AAAAAA
1 TTTTCGTGTTTTCAAAAAA
* *
30167517 --TTCATGTTTTC--GAAA
1 TTTTCGTGTTTTCAAAAAA
* *
30167532 TTTTTGTGTTTTC-AAAAT
1 TTTTCGTGTTTTCAAAAAA
30167550 TTTTCGTG---TCAAAAAA
1 TTTTCGTGTTTTCAAAAAA
* * * *
30167566 TTCTCATG-TAT-AGAAAA
1 TTTTCGTGTTTTCAAAAAA
* *
30167583 TTTCCTTGTTTTCAAAACAA
1 TTTTCGTGTTTTCAAAA-AA
*
30167603 -TTCCGTGTTTTCAAAAAA
1 TTTTCGTGTTTTCAAAAAA
* *
30167621 ATTTCGTG-TTTC-GAAAA
1 TTTTCGTGTTTTCAAAAAA
*
30167638 TCTTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
30167656 TTATCATTGT
Statistics
Matches: 185, Mismatches: 27, Indels: 54
0.70 0.10 0.20
Matches are distributed among these distances:
15 11 0.06
16 15 0.08
17 45 0.24
18 33 0.18
19 35 0.19
20 12 0.06
21 11 0.06
22 4 0.02
24 1 0.01
25 14 0.08
26 4 0.02
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (19 bp):
TTTTCGTGTTTTCAAAAAA
Found at i:30167434 original size:17 final size:18
Alignment explanation
Indices: 30167398--30167657 Score: 94
Period size: 18 Copynumber: 14.1 Consensus size: 18
30167388 TTTTTTCGTG
30167398 TTTTCGTGTTTTCAAAAAA
1 TTTTCGTGTTTTC-AAAAA
30167417 TTCTT-GTG-TTTCAAAAA
1 TT-TTCGTGTTTTCAAAAA
30167434 TTTTCGTGTTTTCAAAATTTTCATA
1 TTTTCGTGTTTTC-AAA-----A-A
30167459 TTTTCGTGTTTTCAAAAAAA
1 TTTTCGTGTTTTC--AAAAA
* *
30167479 TTATCGTGTTTTTTAAAAAAA
1 TTTTCGTG--TTTT-CAAAAA
** *
30167500 AATTCATG-TTT-AAAAA
1 TTTTCGTGTTTTCAAAAA
* * *
30167516 -ATTCATGTTTTC-GAAA
1 TTTTCGTGTTTTCAAAAA
* *
30167532 TTTTTGTGTTTTCAAAAT
1 TTTTCGTGTTTTCAAAAA
30167550 TTTTCGTG---TCAAAAAA
1 TTTTCGTGTTTTC-AAAAA
* * *
30167566 TTCTCATG-TAT-AGAAAA
1 TTTTCGTGTTTTCA-AAAA
* *
30167583 TTTCCTTGTTTTCAAAACA
1 TTTTCGTGTTTTCAAAA-A
* *
30167602 ATTCCGTGTTTTCAAAAAA
1 TTTTCGTGTTTTC-AAAAA
* *
30167621 ATTTCGTG-TTTCGAAAA
1 TTTTCGTGTTTTCAAAAA
*
30167638 TCTTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
30167656 TT
1 TT
30167658 ATCATTGTGT
Statistics
Matches: 186, Mismatches: 28, Indels: 55
0.69 0.10 0.20
Matches are distributed among these distances:
15 9 0.05
16 24 0.13
17 38 0.20
18 39 0.21
19 29 0.16
20 14 0.08
21 10 0.05
22 4 0.02
24 1 0.01
25 14 0.08
26 4 0.02
ACGTcount: A:0.32, C:0.12, G:0.10, T:0.46
Consensus pattern (18 bp):
TTTTCGTGTTTTCAAAAA
Found at i:30167438 original size:44 final size:43
Alignment explanation
Indices: 30167356--30167446 Score: 130
Period size: 44 Copynumber: 2.1 Consensus size: 43
30167346 AATAAAAAAA
30167356 TTCGTGTTTTCAAAAATTCCGGTGTTTAAAAATTTTTTCGTGTT
1 TTCGTGTTTTCAAAAATTCCGGTGTTTAAAAA-TTTTTCGTGTT
**
30167400 TTCGTGTTTTCAAAAAATTCTTGTGTTTCAAAAA-TTTTCGTGTT
1 TTCGTGTTTTC-AAAAATTCCGGTGTTT-AAAAATTTTTCGTGTT
30167444 TTC
1 TTC
30167447 AAAATTTTCA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
44 24 0.56
45 14 0.33
46 5 0.12
ACGTcount: A:0.23, C:0.12, G:0.14, T:0.51
Consensus pattern (43 bp):
TTCGTGTTTTCAAAAATTCCGGTGTTTAAAAATTTTTCGTGTT
Found at i:30167455 original size:45 final size:44
Alignment explanation
Indices: 30167362--30167456 Score: 104
Period size: 45 Copynumber: 2.1 Consensus size: 44
30167352 AAAATTCGTG
***
30167362 TTTTC-AAAAATTCCGGTGTTTAAAAATTTTTTCGTGTTTTCGTG
1 TTTTCAAAAAATTCCGGTGTTTAAAAA-TTTTTCGTGTTTTCAAA
**
30167406 TTTTCAAAAAATTCTTGTGTTTCAAAAA-TTTTCGTGTTTTCAAAA
1 TTTTCAAAAAATTCCGGTGTTT-AAAAATTTTTCGTGTTTTC-AAA
30167451 TTTTCA
1 TTTTCA
30167457 TATTTTCGTG
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
44 18 0.42
45 20 0.47
46 5 0.12
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.49
Consensus pattern (44 bp):
TTTTCAAAAAATTCCGGTGTTTAAAAATTTTTCGTGTTTTCAAA
Found at i:30167478 original size:62 final size:62
Alignment explanation
Indices: 30167349--30167489 Score: 164
Period size: 61 Copynumber: 2.3 Consensus size: 62
30167339 TCTCGTGAAT
* * *
30167349 AAAAAAATTCGTGT-TTTCAAAAATTCCGGTGTTTAAAAATTTTTTCGTGTTTTCGTGTTTTC
1 AAAAAAATTCTTGTGTTTCAAAAATTCCGGTGTTTAAAAA-TTTTTCATATTTTCGTGTTTTC
* *
30167411 -AAAAAATTCTTGTGTTTCAAAAATTTTC-GTGTTTTCAAAA-TTTTCATATTTTCGTGTTTTC
1 AAAAAAATTCTTGTGTTTCAAAAA-TTCCGGTG-TTTAAAAATTTTTCATATTTTCGTGTTTTC
* *
30167472 AAAAAAATTATCGTGTTT
1 AAAAAAATTCTTGTGTTT
30167490 TTTAAAAAAA
Statistics
Matches: 68, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
61 31 0.46
62 27 0.40
63 10 0.15
ACGTcount: A:0.30, C:0.11, G:0.12, T:0.48
Consensus pattern (62 bp):
AAAAAAATTCTTGTGTTTCAAAAATTCCGGTGTTTAAAAATTTTTCATATTTTCGTGTTTTC
Found at i:30167509 original size:21 final size:22
Alignment explanation
Indices: 30167467--30167510 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
30167457 TATTTTCGTG
* * *
30167467 TTTTCAAAAAAATTATCGTGTT
1 TTTTAAAAAAAAATATCATGTT
30167489 TTTTAAAAAAAAAT-TCATGTT
1 TTTTAAAAAAAAATATCATGTT
30167510 T
1 T
30167511 AAAAAATTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (22 bp):
TTTTAAAAAAAAATATCATGTT
Found at i:30167533 original size:15 final size:15
Alignment explanation
Indices: 30167496--30167525 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
30167486 GTTTTTTAAA
30167496 AAAAAATTCATGTTT
1 AAAAAATTCATGTTT
30167511 AAAAAATTCATGTTT
1 AAAAAATTCATGTTT
30167526 TCGAAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (15 bp):
AAAAAATTCATGTTT
Found at i:30170856 original size:20 final size:20
Alignment explanation
Indices: 30170831--30170897 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 20
30170821 TTCTACAGGA
30170831 TTTGCACTTCGGTGCCCCTG
1 TTTGCACTTCGGTGCCCCTG
* *
30170851 TTTGCACTTCGATGTCCCTG
1 TTTGCACTTCGGTGCCCCTG
* *
30170871 TTCGCACTACGGTGCCCCTG
1 TTTGCACTTCGGTGCCCCTG
30170891 TTATGCA
1 TT-TGCA
30170898 TATATGATGC
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
20 36 0.92
21 3 0.08
ACGTcount: A:0.10, C:0.33, G:0.22, T:0.34
Consensus pattern (20 bp):
TTTGCACTTCGGTGCCCCTG
Found at i:30171589 original size:29 final size:25
Alignment explanation
Indices: 30171530--30171581 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
30171520 AGCGGTTAAT
30171530 TTACTTCTTACGAGATTACTAAGCA
1 TTACTTCTTACGAGATTACTAAGCA
* *
30171555 TTACTTTTTACGAGCTTACTAAGCA
1 TTACTTCTTACGAGATTACTAAGCA
30171580 TT
1 TT
30171582 CATTACTTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (25 bp):
TTACTTCTTACGAGATTACTAAGCA
Found at i:30175605 original size:46 final size:46
Alignment explanation
Indices: 30175490--30175707 Score: 233
Period size: 46 Copynumber: 4.6 Consensus size: 46
30175480 CTTCAAGAAG
* *
30175490 ATAAGATTCGC-GTCCTTCAGCTTTAATCTACTACAACACTAGGGAA
1 ATAAGATTCGCTG-CCTTCAGCTTTAATCTACTACAACGCCAGGGAA
* * *
30175536 A-AAGATTCGTTGCCTTCAGCTTTAATCTACTGCAATGCCAGGGAA
1 ATAAGATTCGCTGCCTTCAGCTTTAATCTACTACAACGCCAGGGAA
* * * *
30175581 ATAAGATTCGCTGCCTTCAACTTTAATCTATTCCATTGCAATGCCAAGGAAA
1 ATAAGATTCGCTGCCTTCAGCTTTAATCTA---C--TACAACGCC-AGGGAA
* * *
30175633 AAAAGATTCACTGCCTTCAGCTTTAATCTACTACAACGCTAGGGAA
1 ATAAGATTCGCTGCCTTCAGCTTTAATCTACTACAACGCCAGGGAA
* *
30175679 ATAATATTTGCTGCCTTCAGCTTTAATCT
1 ATAAGATTCGCTGCCTTCAGCTTTAATCT
30175708 GTTCCACTGC
Statistics
Matches: 145, Mismatches: 19, Indels: 16
0.81 0.11 0.09
Matches are distributed among these distances:
45 38 0.26
46 58 0.40
47 6 0.04
49 2 0.01
51 9 0.06
52 32 0.22
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (46 bp):
ATAAGATTCGCTGCCTTCAGCTTTAATCTACTACAACGCCAGGGAA
Found at i:30175661 original size:98 final size:97
Alignment explanation
Indices: 30175534--30175738 Score: 286
Period size: 98 Copynumber: 2.1 Consensus size: 97
30175524 AACACTAGGG
** * *
30175534 AAAAAGATTCGTTGCCTTCAGCTTTAATCTACTGCAATGCCAGGGAAATAAGATTCGCTGCCTTC
1 AAAAAGATTCACTGCCTTCAGCTTTAATCTACTACAACGCCAGGGAAATAAGATTCGCTGCCTTC
* *
30175599 AACTTTAATCTATTCCATTGCAATG-CCAAGGAA
66 AACTTTAATCTATTCCACTGCAACGCCCAA--AA
* * *
30175632 AAAAAGATTCACTGCCTTCAGCTTTAATCTACTACAACGCTAGGGAAATAATATTTGCTGCCTTC
1 AAAAAGATTCACTGCCTTCAGCTTTAATCTACTACAACGCCAGGGAAATAAGATTCGCTGCCTTC
* *
30175697 AGCTTTAATCTGTTCCACTGCAACGCCCAAAA
66 AACTTTAATCTATTCCACTGCAACGCCCAAAA
30175729 AAAAAGATTC
1 AAAAAGATTC
30175739 GCCATAATAA
Statistics
Matches: 95, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
97 12 0.13
98 79 0.83
99 4 0.04
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (97 bp):
AAAAAGATTCACTGCCTTCAGCTTTAATCTACTACAACGCCAGGGAAATAAGATTCGCTGCCTTC
AACTTTAATCTATTCCACTGCAACGCCCAAAA
Found at i:30186680 original size:20 final size:20
Alignment explanation
Indices: 30186657--30186694 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
30186647 TTTCATCATC
30186657 TATTTTATAATAA-TATTAGT
1 TATTTTA-AATAACTATTAGT
30186677 TATTTTAAATAACTATTA
1 TATTTTAAATAACTATTA
30186695 TCCTCAACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (20 bp):
TATTTTAAATAACTATTAGT
Found at i:30188051 original size:46 final size:46
Alignment explanation
Indices: 30187950--30188052 Score: 145
Period size: 46 Copynumber: 2.2 Consensus size: 46
30187940 ATAATATCTT
* * *
30187950 ATAATATCCCATTAGAAATCAAATTGTTAAGAGATAATATCCCATA
1 ATAATATCCTATTAGAAATCAAATTGCTAAAAGATAATATCCCATA
* *
30187996 ATAATATCCTATTATG-ATTCAAATTGCTAAAAGATGATATCCCATA
1 ATAATATCCTATTA-GAAATCAAATTGCTAAAAGATAATATCCCATA
30188042 ATAATATCCTA
1 ATAATATCCTA
30188053 ACACCCCCCT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
46 50 0.98
47 1 0.02
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.33
Consensus pattern (46 bp):
ATAATATCCTATTAGAAATCAAATTGCTAAAAGATAATATCCCATA
Found at i:30189429 original size:10 final size:10
Alignment explanation
Indices: 30189414--30189438 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
30189404 GCATCCCATA
30189414 ATAATATCCT
1 ATAATATCCT
30189424 ATAATATCCT
1 ATAATATCCT
30189434 ATAAT
1 ATAAT
30189439 TAGGAATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (10 bp):
ATAATATCCT
Found at i:30190054 original size:20 final size:21
Alignment explanation
Indices: 30190021--30190069 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
30190011 ATTAATTATA
* *
30190021 TTTTATTAAGTGAAAATA-AT
1 TTTTAATAAATGAAAATACAT
*
30190041 TTTTAATAAATGAAATTACAT
1 TTTTAATAAATGAAAATACAT
*
30190062 TTTAAATA
1 TTTTAATA
30190070 TGATTAAAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 15 0.62
21 9 0.38
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (21 bp):
TTTTAATAAATGAAAATACAT
Found at i:30190069 original size:21 final size:19
Alignment explanation
Indices: 30190014--30190066 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 19
30190004 GAATAATATT
* *
30190014 AATTATATTTTATTAAGTGA
1 AATTA-ATTTTAATAAATGA
*
30190034 AAATAATTTTTAATAAATGA
1 AATTAA-TTTTAATAAATGA
30190054 AATTACATTTTAA
1 AATTA-ATTTTAA
30190067 ATATGATTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
19 1 0.04
20 25 0.93
21 1 0.04
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (19 bp):
AATTAATTTTAATAAATGA
Found at i:30193250 original size:15 final size:15
Alignment explanation
Indices: 30193204--30193251 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
30193194 TTGATAAACT
*
30193204 AAAATATTAAGTACTG
1 AAAA-ATTAAGTATTG
*
30193220 AAAAATTAAATATTG
1 AAAAATTAAGTATTG
*
30193235 AAAAATTAAGTGTTG
1 AAAAATTAAGTATTG
30193250 AA
1 AA
30193252 TTTAAGTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
15 24 0.86
16 4 0.14
ACGTcount: A:0.54, C:0.02, G:0.12, T:0.31
Consensus pattern (15 bp):
AAAAATTAAGTATTG
Found at i:30214124 original size:36 final size:36
Alignment explanation
Indices: 30214077--30214147 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
30214067 ACACCGTTAG
* *
30214077 AATTTTAATAACAACTTTTCCTTTCTTTTCAAGATT
1 AATTTTAATAACAACTCTTCCTTTATTTTCAAGATT
*
30214113 AATTTTAATAACAACTCTTCTTTTATTTTCAAGAT
1 AATTTTAATAACAACTCTTCCTTTATTTTCAAGAT
30214148 GGCCAATGCC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.32, C:0.15, G:0.03, T:0.49
Consensus pattern (36 bp):
AATTTTAATAACAACTCTTCCTTTATTTTCAAGATT
Found at i:30217067 original size:55 final size:56
Alignment explanation
Indices: 30216983--30217095 Score: 192
Period size: 55 Copynumber: 2.0 Consensus size: 56
30216973 TAAAAAAATT
30216983 AACTTAATAATTCTTTTACATCGTTACAAT-CCCCAACAATGGTGCCAACAATTTG
1 AACTTAATAATTCTTTTACATCGTTACAATGCCCCAACAATGGTGCCAACAATTTG
**
30217038 AACTTAATAATTCTTTTACATCGTTACAATGGTGCCAACAATGGTGCCAACAATTTG
1 AACTTAATAATTCTTTTACATCGTTACAAT-GCCCCAACAATGGTGCCAACAATTTG
30217095 A
1 A
30217096 CCATGCTATG
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
55 30 0.56
57 24 0.44
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.33
Consensus pattern (56 bp):
AACTTAATAATTCTTTTACATCGTTACAATGCCCCAACAATGGTGCCAACAATTTG
Found at i:30217080 original size:12 final size:12
Alignment explanation
Indices: 30217063--30217091 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
30217053 TTACATCGTT
30217063 ACAATGGTGCCA
1 ACAATGGTGCCA
30217075 ACAATGGTGCCA
1 ACAATGGTGCCA
30217087 ACAAT
1 ACAAT
30217092 TTGACCATGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.17
Consensus pattern (12 bp):
ACAATGGTGCCA
Found at i:30217724 original size:16 final size:15
Alignment explanation
Indices: 30217703--30217732 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
30217693 ATCGAATATC
30217703 AATAAAAACTTAATCA
1 AATAAAAA-TTAATCA
30217719 AATAAAAATTAATC
1 AATAAAAATTAATC
30217733 CATGCAAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.63, C:0.10, G:0.00, T:0.27
Consensus pattern (15 bp):
AATAAAAATTAATCA
Found at i:30219070 original size:27 final size:27
Alignment explanation
Indices: 30219021--30219189 Score: 121
Period size: 27 Copynumber: 6.3 Consensus size: 27
30219011 GGAAGAAACA
* * * *
30219021 CCTTTGTGGCAGTCTTTGTAAAGGAAG
1 CCTTTGTGACAATCTCTATAAAGGAAG
* *
30219048 CCTTTGTGACAATATCTGA-AAAGGGAG
1 CCTTTGTGACAATCTCT-ATAAAGGAAG
* *
30219075 TCTTTGTGACAATCTCTATAATGG-AG
1 CCTTTGTGACAATCTCTATAAAGGAAG
* * *
30219101 -CTTTGTGGCAATATCTATAAAGGATG
1 CCTTTGTGACAATCTCTATAAAGGAAG
* * *
30219127 CCTTTGTGGCGATCTCTATTAAAGAAAG
1 CCTTTGTGACAATCTCTA-TAAAGGAAG
* * *
30219155 CGTTTATGACTATCTCTGA-AAAGGAAG
1 CCTTTGTGACAATCTCT-ATAAAGGAAG
30219182 ACCTTTGT
1 -CCTTTGT
30219190 AGCGCAGTTT
Statistics
Matches: 111, Mismatches: 24, Indels: 13
0.75 0.16 0.09
Matches are distributed among these distances:
25 20 0.18
26 4 0.04
27 61 0.55
28 25 0.23
29 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.33
Consensus pattern (27 bp):
CCTTTGTGACAATCTCTATAAAGGAAG
Found at i:30228953 original size:39 final size:39
Alignment explanation
Indices: 30228909--30229093 Score: 166
Period size: 39 Copynumber: 4.6 Consensus size: 39
30228899 GGCCCATTTT
*
30228909 TATTTTAAAATTTTAGAAAATTAAAAAGTATTTTAAAAA
1 TATTTTAAAATTTTAAAAAATTAAAAAGTATTTTAAAAA
* * *
30228948 TATTTTAAAATATTT-TAAAATTAAAAA--AATTAAAAAA
1 TATTTTAAAAT-TTTAAAAAATTAAAAAGTATTTTAAAAA
30228985 GTATTTTAAAATTATTTTAAATTAAAAAATTAAAAAAGTATTTTAAAAA
1 -TATTTT-AAA--A--TT---TTAAAAAATT-AAAAAGTATTTTAAAAA
* *
30229034 TA-TTTAAAATTTAAAAAAATTAAAAAGTA-TGTAAAAA
1 TATTTTAAAATTTTAAAAAATTAAAAAGTATTTTAAAAA
*
30229071 TATTTTAAAA-TTAAAAAAATTAA
1 TATTTTAAAATTTTAAAAAATTAA
30229094 TATATTTATT
Statistics
Matches: 123, Mismatches: 8, Indels: 32
0.75 0.05 0.20
Matches are distributed among these distances:
37 30 0.24
38 21 0.17
39 34 0.28
40 3 0.02
41 1 0.01
42 3 0.02
43 1 0.01
44 1 0.01
45 2 0.02
46 9 0.07
47 8 0.07
48 2 0.02
49 8 0.07
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.38
Consensus pattern (39 bp):
TATTTTAAAATTTTAAAAAATTAAAAAGTATTTTAAAAA
Found at i:30228959 original size:10 final size:10
Alignment explanation
Indices: 30228932--30228968 Score: 56
Period size: 10 Copynumber: 3.5 Consensus size: 10
30228922 TAGAAAATTA
30228932 AAAAGTATTTT
1 AAAA-TATTTT
30228943 AAAAATATTTT
1 -AAAATATTTT
30228954 AAAATATTTT
1 AAAATATTTT
30228964 AAAAT
1 AAAAT
30228969 TAAAAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 15 0.60
11 6 0.24
12 4 0.16
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (10 bp):
AAAATATTTT
Found at i:30228964 original size:49 final size:49
Alignment explanation
Indices: 30228909--30229005 Score: 151
Period size: 49 Copynumber: 2.0 Consensus size: 49
30228899 GGCCCATTTT
* *
30228909 TATTTTAAAATTTTAGAAAATT-AAAAAGTATTTTAAAAATATTTTAAAA
1 TATTTTAAAA-TTAAAAAAATTAAAAAAGTATTTTAAAAATATTTTAAAA
*
30228958 TATTTTAAAATTAAAAAAATTAAAAAAGTATTTTAAAATTATTTTAAA
1 TATTTTAAAATTAAAAAAATTAAAAAAGTATTTTAAAAATATTTTAAA
30229006 TTAAAAAATT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
48 9 0.20
49 35 0.80
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (49 bp):
TATTTTAAAATTAAAAAAATTAAAAAAGTATTTTAAAAATATTTTAAAA
Found at i:30229008 original size:10 final size:11
Alignment explanation
Indices: 30228932--30228970 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
30228922 TAGAAAATTA
*
30228932 AAAAGTATTTT
1 AAAATTATTTT
*
30228943 AAAAATATTTT
1 AAAATTATTTT
30228954 AAAA-TATTTT
1 AAAATTATTTT
30228964 AAAATTA
1 AAAATTA
30228971 AAAAAATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 10 0.38
11 16 0.62
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (11 bp):
AAAATTATTTT
Found at i:30229012 original size:37 final size:39
Alignment explanation
Indices: 30228909--30229093 Score: 226
Period size: 37 Copynumber: 4.9 Consensus size: 39
30228899 GGCCCATTTT
* * *
30228909 TATTTT-AAAAT-TTTAGAAAATTAAAAAGTATTTTAAAAA-
1 TATTTTAAAAATATTT-TAAAATTAAAAA--AATTAAAAAAG
30228948 TATTTT-AAAATATTTTAAAATTAAAAAAATTAAAAAAG
1 TATTTTAAAAATATTTTAAAATTAAAAAAATTAAAAAAG
*
30228986 TATTTTAAAATTATTTT-AAATT-AAAAAATTAAAAAAG
1 TATTTTAAAAATATTTTAAAATTAAAAAAATTAAAAAAG
30229023 TATTTTAAAAATA-TTTAAAATTTAAAAAAATT-AAAAAG
1 TATTTTAAAAATATTTTAAAA-TTAAAAAAATTAAAAAAG
*
30229061 TA-TGTAAAAATATTTTAAAATTAAAAAAATTAA
1 TATTTTAAAAATATTTTAAAATTAAAAAAATTAA
30229094 TATATTTATT
Statistics
Matches: 132, Mismatches: 6, Indels: 17
0.85 0.04 0.11
Matches are distributed among these distances:
36 3 0.02
37 58 0.44
38 29 0.22
39 39 0.30
40 3 0.02
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.38
Consensus pattern (39 bp):
TATTTTAAAAATATTTTAAAATTAAAAAAATTAAAAAAG
Found at i:30229050 original size:75 final size:75
Alignment explanation
Indices: 30228925--30229093 Score: 211
Period size: 75 Copynumber: 2.2 Consensus size: 75
30228915 AAAATTTTAG
* *
30228925 AAAATTAAAAAGTATTTTAAAAATATTTTAAAATATTTTAAAATT-AAAAAAATTAAAAAAGTAT
1 AAAATTAAAAA--AATTAAAAAATATTTTAAAATATTTTAAAATTAAAAAAAATT-AAAAAGTA-
* *
30228989 TTTAAAATTATTTT
62 TGTAAAAATATTTT
*
30229003 -AAATT-AAAAAATTAAAAAAGTATTTTAAAA-ATATTTAAAATTTAAAAAAATTAAAAAGTATG
1 AAAATTAAAAAAATTAAAAAA-TATTTTAAAATAT-TTTAAAATTAAAAAAAATTAAAAAGTATG
30229065 TAAAAATATTTT
64 TAAAAATATTTT
30229077 AAAATTAAAAAAATTAA
1 AAAATTAAAAAAATTAA
30229094 TATATTTATT
Statistics
Matches: 82, Mismatches: 4, Indels: 12
0.84 0.04 0.12
Matches are distributed among these distances:
74 22 0.27
75 32 0.39
76 23 0.28
77 5 0.06
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (75 bp):
AAAATTAAAAAAATTAAAAAATATTTTAAAATATTTTAAAATTAAAAAAAATTAAAAAGTATGTA
AAAATATTTT
Found at i:30229053 original size:85 final size:85
Alignment explanation
Indices: 30228925--30229083 Score: 227
Period size: 85 Copynumber: 1.9 Consensus size: 85
30228915 AAAATTTTAG
**
30228925 AAAATTAAAAAGTATTTTAAAAATATTTTAAAATATTTTAAAATTAAAAA-AAT-TAAAAAAGTA
1 AAAATTAAAAAGTATTTTAAAAATATTTTAAAATATTAAAAAATTAAAAAGAATGT-AAAAA-TA
30228988 TTTTAAAATTATTTTAAATTAA
64 TTTTAAAATTATTTTAAATTAA
*
30229010 AAAATTAAAAAAGTATTTTAAAAATA-TTTAAAAT-TTAAAAAAATTAAAAAGTATGTAAAAATA
1 AAAATT-AAAAAGTATTTTAAAAATATTTTAAAATATT-AAAAAATTAAAAAGAATGTAAAAATA
30229073 TTTTAAAATTA
64 TTTTAAAATTA
30229084 AAAAAATTAA
Statistics
Matches: 67, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
84 2 0.03
85 38 0.57
86 26 0.39
87 1 0.01
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (85 bp):
AAAATTAAAAAGTATTTTAAAAATATTTTAAAATATTAAAAAATTAAAAAGAATGTAAAAATATT
TTAAAATTATTTTAAATTAA
Found at i:30229080 original size:11 final size:11
Alignment explanation
Indices: 30228929--30229042 Score: 64
Period size: 12 Copynumber: 10.5 Consensus size: 11
30228919 TTTTAGAAAA
30228929 TTAAAAAGTATT
1 TTAAAAA-TATT
30228941 TTAAAAATATT
1 TTAAAAATATT
30228952 TT-AAAATATT
1 TTAAAAATATT
30228962 TT--AAA-A--
1 TTAAAAATATT
*
30228968 TTAAAAA-AAT
1 TTAAAAATATT
*
30228978 TAAAAAAGTATT
1 TTAAAAA-TATT
*
30228990 TTAAAATTATT
1 TTAAAAATATT
* *
30229001 TTAAATTAAAAAAT
1 TT-AA--AAATATT
*
30229015 TAAAAAAGTATT
1 TTAAAAA-TATT
30229027 TTAAAAATA-T
1 TTAAAAATATT
30229037 TTAAAA
1 TTAAAA
30229043 TTTAAAAAAA
Statistics
Matches: 81, Mismatches: 11, Indels: 22
0.71 0.10 0.19
Matches are distributed among these distances:
6 2 0.02
8 5 0.06
9 3 0.04
10 23 0.28
11 17 0.21
12 24 0.30
13 2 0.02
14 5 0.06
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (11 bp):
TTAAAAATATT
Found at i:30240921 original size:43 final size:43
Alignment explanation
Indices: 30240857--30240943 Score: 147
Period size: 43 Copynumber: 2.0 Consensus size: 43
30240847 GGTGAGATTG
* *
30240857 ATTGCCAATAGAATTGCCATGGCAATTTCGGGAAGATGACTTA
1 ATTGCCAACAGAATTGCCATGGCAATTTCGGGAAGATAACTTA
*
30240900 ATTGCCAACAGAATTGTCATGGCAATTTCGGGAAGATAACTTA
1 ATTGCCAACAGAATTGCCATGGCAATTTCGGGAAGATAACTTA
30240943 A
1 A
30240944 CACTTTATCC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (43 bp):
ATTGCCAACAGAATTGCCATGGCAATTTCGGGAAGATAACTTA
Found at i:30241441 original size:25 final size:25
Alignment explanation
Indices: 30241407--30241455 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
30241397 TATTAGGGTG
*
30241407 AATGTTTTATCATCTTTAATGCTCA
1 AATGCTTTATCATCTTTAATGCTCA
30241432 AATGCTTTATCATCTTTAATGCTC
1 AATGCTTTATCATCTTTAATGCTC
30241456 GTGATTTGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.27, C:0.18, G:0.08, T:0.47
Consensus pattern (25 bp):
AATGCTTTATCATCTTTAATGCTCA
Found at i:30247753 original size:41 final size:41
Alignment explanation
Indices: 30247693--30247980 Score: 314
Period size: 41 Copynumber: 7.0 Consensus size: 41
30247683 AAGATTATTG
* ** *
30247693 TGAATTGCACCTATGTGCCCCCGTTTGTACTTCAGTACCCC
1 TGAATTGCACATACATGCCCCCGTTTGTACTTCGGTACCCC
* *
30247734 TAAATTGCACATACATGCCCCCGTTTGTACTTTGGTACCCC
1 TGAATTGCACATACATGCCCCCGTTTGTACTTCGGTACCCC
**
30247775 T-AATTGCACATACATGCCCCTATTTGTACTTCGGTACCCCC
1 TGAATTGCACATACATGCCCCCGTTTGTACTTCGGTA-CCCC
* *** * *
30247816 TGAATTGCACCTATGCGCCCCCGTTTATACGTT-GGTACCCT
1 TGAATTGCACATACATGCCCCCGTTTGTAC-TTCGGTACCCC
* * * *
30247857 TGAATTGCACATACGTGCCCCTGTTTGTACTTTGATACCCC
1 TGAATTGCACATACATGCCCCCGTTTGTACTTCGGTACCCC
* *
30247898 TGAATTGCACATAC--GCTCCCCTATTTGTACTTCGGTACCCT
1 TGAATTGCACATACATGC-CCCC-GTTTGTACTTCGGTACCCC
* *
30247939 TGAATTGCACATACATGCCCCTGTTTGTACTTCGATACCCC
1 TGAATTGCACATACATGCCCCCGTTTGTACTTCGGTACCCC
30247980 T
1 T
30247981 AAATACACTT
Statistics
Matches: 206, Mismatches: 33, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
39 2 0.01
40 37 0.18
41 135 0.66
42 28 0.14
43 4 0.02
ACGTcount: A:0.20, C:0.32, G:0.16, T:0.33
Consensus pattern (41 bp):
TGAATTGCACATACATGCCCCCGTTTGTACTTCGGTACCCC
Found at i:30247854 original size:82 final size:81
Alignment explanation
Indices: 30247693--30247980 Score: 355
Period size: 82 Copynumber: 3.5 Consensus size: 81
30247683 AAGATTATTG
* ** * * **
30247693 TGAATTGCACCTATGTGCCCCCGTTTGTACTTC-AGTACCCCTAAATTGCACATACATGCCCCCG
1 TGAATTGCACATACATGCCCCTGTTTGTACTTCGA-TACCCCTGAATTGCACATACGCGCCCCCG
*
30247757 TTTGTACTTTGGTACCCC
65 TTTGTAC-TTGGTACCCT
* * * *
30247775 T-AATTGCACATACATGCCCCTATTTGTACTTCGGTACCCCCTGAATTGCACCTATGCGCCCCCG
1 TGAATTGCACATACATGCCCCTGTTTGTACTTCGATA-CCCCTGAATTGCACATACGCGCCCCCG
*
30247839 TTTATACGTTGGTACCCT
65 TTTGTAC-TTGGTACCCT
* * * **
30247857 TGAATTGCACATACGTGCCCCTGTTTGTACTTTGATACCCCTGAATTGCACATACGCTCCCCTAT
1 TGAATTGCACATACATGCCCCTGTTTGTACTTCGATACCCCTGAATTGCACATACGCGCCCCCGT
30247922 TTGTACTTCGGTACCCT
66 TTGTACTT-GGTACCCT
30247939 TGAATTGCACATACATGCCCCTGTTTGTACTTCGATACCCCT
1 TGAATTGCACATACATGCCCCTGTTTGTACTTCGATACCCCT
30247981 AAATACACTT
Statistics
Matches: 176, Mismatches: 26, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
81 30 0.17
82 115 0.65
83 31 0.18
ACGTcount: A:0.20, C:0.32, G:0.16, T:0.33
Consensus pattern (81 bp):
TGAATTGCACATACATGCCCCTGTTTGTACTTCGATACCCCTGAATTGCACATACGCGCCCCCGT
TTGTACTTGGTACCCT
Found at i:30247943 original size:123 final size:123
Alignment explanation
Indices: 30247693--30247984 Score: 376
Period size: 123 Copynumber: 2.4 Consensus size: 123
30247683 AAGATTATTG
* *
30247693 TGAATTGCACCTATGTGCCCCCGTTTGTACTTCAGTACCCCTAAATTGCACATACATGCCCCCGT
1 TGAATTGCACCTATGCGCCCCCGTTTATACTTCAGTACCCCTAAATTGCACATACATGCCCCCGT
*
30247758 TTGTACTTTGGTACCCCTAATTGCACATACATGCCCCTATTTGTACTTCGGTACCCCC
66 TTGTACTTTGATACCCCTAATTGCACATACATGCCCCTATTTGTACTTCGGTACCCCC
* * * * *
30247816 TGAATTGCACCTATGCGCCCCCGTTTATACGTT-GGTACCCTTGAATTGCACATACGTGCCCCTG
1 TGAATTGCACCTATGCGCCCCCGTTTATAC-TTCAGTACCCCTAAATTGCACATACATGCCCCCG
* *
30247880 TTTGTACTTTGATACCCCTGAATTGCACATACGCT-CCCCTATTTGTACTTCGGTA-CCCT
65 TTTGTACTTTGATACCCCT-AATTGCACATAC-ATGCCCCTATTTGTACTTCGGTACCCCC
* *** * *
30247939 TGAATTGCACATACATGCCCCTGTTTGTACTTC-GATACCCCTAAAT
1 TGAATTGCACCTATGCGCCCCCGTTTATACTTCAG-TACCCCTAAAT
30247985 ACACTTTTGT
Statistics
Matches: 146, Mismatches: 18, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
122 3 0.02
123 108 0.74
124 34 0.23
125 1 0.01
ACGTcount: A:0.21, C:0.32, G:0.15, T:0.33
Consensus pattern (123 bp):
TGAATTGCACCTATGCGCCCCCGTTTATACTTCAGTACCCCTAAATTGCACATACATGCCCCCGT
TTGTACTTTGATACCCCTAATTGCACATACATGCCCCTATTTGTACTTCGGTACCCCC
Found at i:30270983 original size:31 final size:31
Alignment explanation
Indices: 30270948--30271011 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
30270938 TATCTAAACT
* *
30270948 TTTTTTA-TCCAATTAGGTACCTGAACTTGGC
1 TTTTTTATTCCAATTA-GTACCTAAACTTAGC
30270979 TTTTTTATTCCAATTAGTACCTAAACTTAGC
1 TTTTTTATTCCAATTAGTACCTAAACTTAGC
30271010 TT
1 TT
30271012 CATGGTTCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 22 0.73
32 8 0.27
ACGTcount: A:0.25, C:0.19, G:0.11, T:0.45
Consensus pattern (31 bp):
TTTTTTATTCCAATTAGTACCTAAACTTAGC
Found at i:30275609 original size:82 final size:82
Alignment explanation
Indices: 30275470--30275632 Score: 317
Period size: 82 Copynumber: 2.0 Consensus size: 82
30275460 TTTCATTACA
30275470 AATTTGTAAAGTAAGACAAAATTAAAGATGAAATTTTAATCTTACTTATTTAAATGCTAATTTGA
1 AATTTGTAAAGTAAGACAAAATTAAAGATGAAATTTTAATCTTACTTATTTAAATGCTAATTTGA
30275535 CATATTTTTTTCTAATC
66 CATATTTTTTTCTAATC
*
30275552 AATTTGTAAAGTAAGACAAAATTAAAGATGAAATTTTAATCTTACTTATTTACATGCTAATTTGA
1 AATTTGTAAAGTAAGACAAAATTAAAGATGAAATTTTAATCTTACTTATTTAAATGCTAATTTGA
30275617 CATATTTTTTTCTAAT
66 CATATTTTTTTCTAAT
30275633 TTGACACAGT
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 80 1.00
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.43
Consensus pattern (82 bp):
AATTTGTAAAGTAAGACAAAATTAAAGATGAAATTTTAATCTTACTTATTTAAATGCTAATTTGA
CATATTTTTTTCTAATC
Found at i:30276215 original size:43 final size:43
Alignment explanation
Indices: 30276148--30276232 Score: 152
Period size: 43 Copynumber: 2.0 Consensus size: 43
30276138 ATAGAGAGAA
*
30276148 ATTTGCTATTTGTTTCATTAATCACACACTTATCATATCTTCC
1 ATTTGCTATTTGTTTAATTAATCACACACTTATCATATCTTCC
*
30276191 ATTTGCTATTTGTTTAATTCATCACACACTTATCATATCTTC
1 ATTTGCTATTTGTTTAATTAATCACACACTTATCATATCTTC
30276233 TCCCTTTTCT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.26, C:0.22, G:0.05, T:0.47
Consensus pattern (43 bp):
ATTTGCTATTTGTTTAATTAATCACACACTTATCATATCTTCC
Found at i:30284494 original size:25 final size:26
Alignment explanation
Indices: 30284465--30284541 Score: 95
Period size: 26 Copynumber: 3.0 Consensus size: 26
30284455 ACGAATTTTC
30284465 TCAAAATTTTAAC-AGGGTAAAATTG
1 TCAAAATTTTAACAAGGGTAAAATTG
* * *
30284490 TCAAAACTTTATCAAGGGTTAAATTG
1 TCAAAATTTTAACAAGGGTAAAATTG
*
30284516 TCAGAATTTT-ACAATGGGTAAAATTG
1 TCAAAATTTTAACAA-GGGTAAAATTG
30284542 GGATGAGAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
25 14 0.33
26 29 0.67
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (26 bp):
TCAAAATTTTAACAAGGGTAAAATTG
Found at i:30289039 original size:94 final size:94
Alignment explanation
Indices: 30288878--30289065 Score: 367
Period size: 94 Copynumber: 2.0 Consensus size: 94
30288868 AGGGTTTTAG
*
30288878 ATTCTTCCTCTCCTGACCAGCTAATGCATTAAGAAATACCTACAAAATAGCTAATTATTCATACC
1 ATTCTTCCTCTCCTGAACAGCTAATGCATTAAGAAATACCTACAAAATAGCTAATTATTCATACC
30288943 TCCACTTGCTAATCCCCCCATAGGAGGAT
66 TCCACTTGCTAATCCCCCCATAGGAGGAT
30288972 ATTCTTCCTCTCCTGAACAGCTAATGCATTAAGAAATACCTACAAAATAGCTAATTATTCATACC
1 ATTCTTCCTCTCCTGAACAGCTAATGCATTAAGAAATACCTACAAAATAGCTAATTATTCATACC
30289037 TCCACTTGCTAATCCCCCCATAGGAGGAT
66 TCCACTTGCTAATCCCCCCATAGGAGGAT
30289066 CAGTTCCTCC
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
94 93 1.00
ACGTcount: A:0.32, C:0.28, G:0.11, T:0.29
Consensus pattern (94 bp):
ATTCTTCCTCTCCTGAACAGCTAATGCATTAAGAAATACCTACAAAATAGCTAATTATTCATACC
TCCACTTGCTAATCCCCCCATAGGAGGAT
Found at i:30307580 original size:32 final size:32
Alignment explanation
Indices: 30307506--30307583 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 32
30307496 GCAATGTTTA
* * *
30307506 AATGTAAGACCATAGCTGGGCTATGGCATTTT
1 AATGTAAGACCATAACTGGGCTATGGCACTTG
30307538 AAT-TAAAAGACCATAACTGGG-TATGGCACCTTG
1 AATGT--AAGACCATAACTGGGCTATGGCA-CTTG
30307571 AATGTAAGACCAT
1 AATGTAAGACCAT
30307584 CGTTGGACCA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
31 1 0.03
32 18 0.46
33 19 0.49
34 1 0.03
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.27
Consensus pattern (32 bp):
AATGTAAGACCATAACTGGGCTATGGCACTTG
Found at i:30307652 original size:104 final size:100
Alignment explanation
Indices: 30307475--30307663 Score: 252
Period size: 104 Copynumber: 1.9 Consensus size: 100
30307465 AATTGACGGA
* * * * * *
30307475 TAAGACCATGGTTGGAACATGGCAATGTTTAAATGTAAGACCATAGCTGGGCTATGGCATTTTAA
1 TAAGACCATCGTTGGAACATGGCAATGATAAAATGTAAGACCATAGCTAGGCTATGACATTCTAA
*
30307540 TTAAAAGACCATAACTGGGTATGGCACCTTGAATG
66 TGAAAAGACCATAACTGGGTATGGCACCTTGAATG
*
30307575 TAAGACCATCGTTGGACCATGGCAGTATAGATAAATATGTAAGACCATAGCTAGGCTATGACATT
1 TAAGACCATCGTTGGAACATGGCA--AT-GATAAA-ATGTAAGACCATAGCTAGGCTATGACATT
* *
30307640 CTGATGATAAGACCATAACTGGGT
62 CTAATGAAAAGACCATAACTGGGT
30307664 TATAGCACTA
Statistics
Matches: 75, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
100 22 0.29
102 2 0.03
103 4 0.05
104 47 0.63
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.27
Consensus pattern (100 bp):
TAAGACCATCGTTGGAACATGGCAATGATAAAATGTAAGACCATAGCTAGGCTATGACATTCTAA
TGAAAAGACCATAACTGGGTATGGCACCTTGAATG
Found at i:30309365 original size:20 final size:20
Alignment explanation
Indices: 30309323--30309365 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
30309313 TTTACATGCT
* *
30309323 AATTTGACATATTTTGTTCC
1 AATTTGACATAGTTTGGTCC
* *
30309343 AATTTGACGTAGTTTGGTGC
1 AATTTGACATAGTTTGGTCC
30309363 AAT
1 AAT
30309366 AGAAGAAAAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.26, C:0.12, G:0.19, T:0.44
Consensus pattern (20 bp):
AATTTGACATAGTTTGGTCC
Found at i:30319186 original size:57 final size:57
Alignment explanation
Indices: 30319097--30319265 Score: 216
Period size: 57 Copynumber: 3.0 Consensus size: 57
30319087 AAAATACAAA
* *
30319097 ATCTTAACTAA-ATTAGAATATCAATATTTTAGGTAACTAAT-TTCTTGAGAATCAGTT
1 ATCTTAACTAATA-TAGAATATCAATATTTTAGGTAACTAATCTTC-TAAGAATCAGCT
* * *
30319154 GTCTTAACTAATATAAAATATCAATATTTTAGGTAATTAATCTTCTAAGAATCAGCT
1 ATCTTAACTAATATAGAATATCAATATTTTAGGTAACTAATCTTCTAAGAATCAGCT
** * * *
30319211 ATCTTAACTTGTATAGAATATCATTATTTTAGGTAACTATTCTCCTAAGAATCAG
1 ATCTTAACTAATATAGAATATCAATATTTTAGGTAACTAATCTTCTAAGAATCAG
30319266 GTATATAGTG
Statistics
Matches: 97, Mismatches: 13, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
57 93 0.96
58 4 0.04
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (57 bp):
ATCTTAACTAATATAGAATATCAATATTTTAGGTAACTAATCTTCTAAGAATCAGCT
Found at i:30327641 original size:57 final size:56
Alignment explanation
Indices: 30327554--30327668 Score: 185
Period size: 57 Copynumber: 2.0 Consensus size: 56
30327544 GACATGCAAA
* * *
30327554 ATCTTAACTATATAGAATATCAGTATTTTAGGTAATTAATTTCCTAAGAATCATCT
1 ATCTTAACTATATAGAATATCAGTATTTTAGGTAACTAATTTACTAAGAATCAACT
*
30327610 ATCTTAACTAATATAGAATATCAGTATTTTAGGTAACTAATTTACTATGAATCAACT
1 ATCTTAACT-ATATAGAATATCAGTATTTTAGGTAACTAATTTACTAAGAATCAACT
30327667 AT
1 AT
30327669 ATAGTGTGAT
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
56 9 0.17
57 45 0.83
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.40
Consensus pattern (56 bp):
ATCTTAACTATATAGAATATCAGTATTTTAGGTAACTAATTTACTAAGAATCAACT
Found at i:30334270 original size:23 final size:22
Alignment explanation
Indices: 30334227--30334277 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
30334217 AATTCCTTCA
* *
30334227 AATTAATTTTTATATATTTAAAT
1 AATTTATTTTTAAATATTT-AAT
30334250 AATTTATTTTTAAAT-TATTAAT
1 AATTTATTTTTAAATAT-TTAAT
30334272 AATTTA
1 AATTTA
30334278 GACAAAGATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 10 0.40
23 15 0.60
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
AATTTATTTTTAAATATTTAAT
Found at i:30336058 original size:23 final size:20
Alignment explanation
Indices: 30336009--30336060 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 20
30335999 ATGAATACAC
*
30336009 CAATTTATAATTATATTAGA
1 CAATATATAATTATATTAGA
*
30336029 TAA-ATATAATTATTTATGTAGA
1 CAATATATAATTA--TAT-TAGA
30336051 CAATATATAA
1 CAATATATAA
30336061 ACATAAAATG
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 8 0.32
20 2 0.08
21 3 0.12
22 6 0.24
23 6 0.24
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.42
Consensus pattern (20 bp):
CAATATATAATTATATTAGA
Found at i:30339890 original size:49 final size:50
Alignment explanation
Indices: 30339818--30340003 Score: 205
Period size: 51 Copynumber: 3.7 Consensus size: 50
30339808 GTGAAGTTGC
*
30339818 TAGGTCACGTGTGTAGTACTATGTGCAAGCTACTACG-GTACCGAAATG-A
1 TAGGTCACATGTGTAGTACTATGTGCAAGCTACTACGCGTACCG-AATGAA
* * * **
30339867 TAGGTCACATGTGTAGTACTATGTGCAGGCTATTATGCGTACCGAATAGCT
1 TAGGTCACATGTGTAGTACTATGTGCAAGCTACTACGCGTACCGAAT-GAA
* * * * * *
30339918 TCGATCACGTGTGTAGTACTATGTGCAAGCTACTACGTGTATCGGATGAA
1 TAGGTCACATGTGTAGTACTATGTGCAAGCTACTACGCGTACCGAATGAA
* *
30339968 AATGGTCACATGTGTAGTACTATGTGCAGGCTACTA
1 TA-GGTCACATGTGTAGTACTATGTGCAAGCTACTA
30340004 TGTGAACTGT
Statistics
Matches: 112, Mismatches: 21, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
49 36 0.32
50 8 0.07
51 68 0.61
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.30
Consensus pattern (50 bp):
TAGGTCACATGTGTAGTACTATGTGCAAGCTACTACGCGTACCGAATGAA
Found at i:30349623 original size:25 final size:26
Alignment explanation
Indices: 30349557--30349613 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
30349547 ATCCATCGAA
30349557 TTTTCCTTCTATTCAATCGGGATTTT
1 TTTTCCTTCTATTCAATCGGGATTTT
30349583 TTTTCCTTCTATTCAATCGGGATTTT
1 TTTTCCTTCTATTCAATCGGGATTTT
30349609 TTTTC
1 TTTTC
30349614 TTTTTATCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.14, C:0.19, G:0.11, T:0.56
Consensus pattern (26 bp):
TTTTCCTTCTATTCAATCGGGATTTT
Found at i:30352942 original size:49 final size:49
Alignment explanation
Indices: 30352885--30353029 Score: 209
Period size: 49 Copynumber: 2.9 Consensus size: 49
30352875 TATTTTCTCA
* * *
30352885 ATGCCATAGTCCAACTATGGTCTTACACGTAATCACATATCACATACCG
1 ATGCCATAGCCCAGCTATGGTCTTACACGAAATCACATATCACATACCG
* * *
30352934 ATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATATCACTTACTG
1 ATGCCATAGCCCAGCTATGGTCTTACACGAAATCACATATCACATACCG
*
30352983 ATGCCATAGCCCAGCTATGGCCTTACACGGAAATCACATAATCACAT
1 ATGCCATAGCCCAGCTATGGTCTTACAC-GAAATCACAT-ATCACAT
30353030 TTTCAATTGT
Statistics
Matches: 86, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
49 71 0.83
50 9 0.10
51 6 0.07
ACGTcount: A:0.32, C:0.29, G:0.14, T:0.25
Consensus pattern (49 bp):
ATGCCATAGCCCAGCTATGGTCTTACACGAAATCACATATCACATACCG
Found at i:30356891 original size:16 final size:17
Alignment explanation
Indices: 30356864--30356898 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
30356854 AATAATTAGG
*
30356864 TTGAGAAAATTATTTAA
1 TTGAGAAAATTAATTAA
30356881 TTGAG-AAATTAATTAA
1 TTGAGAAAATTAATTAA
30356897 TT
1 TT
30356899 TAAATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (17 bp):
TTGAGAAAATTAATTAA
Found at i:30358388 original size:12 final size:12
Alignment explanation
Indices: 30358371--30358395 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
30358361 GCGAATCCAA
30358371 ATTAAAATAATT
1 ATTAAAATAATT
30358383 ATTAAAATAATT
1 ATTAAAATAATT
30358395 A
1 A
30358396 AATTACTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
ATTAAAATAATT
Found at i:30362032 original size:6 final size:6
Alignment explanation
Indices: 30362021--30362046 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
30362011 AGATGTAGAG
30362021 CTTCTA CTTCTA CTTCTA CTTCTA CT
1 CTTCTA CTTCTA CTTCTA CTTCTA CT
30362047 CCTAGATCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.35, G:0.00, T:0.50
Consensus pattern (6 bp):
CTTCTA
Found at i:30379005 original size:24 final size:24
Alignment explanation
Indices: 30378978--30379028 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
30378968 GACGATCTAA
30378978 AAGGGAAGGAAAACTAACGAAAGT
1 AAGGGAAGGAAAACTAACGAAAGT
30379002 AAGGGAAGGAAAACTAACGAAAGT
1 AAGGGAAGGAAAACTAACGAAAGT
30379026 AAG
1 AAG
30379029 CATATAGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.55, C:0.08, G:0.29, T:0.08
Consensus pattern (24 bp):
AAGGGAAGGAAAACTAACGAAAGT
Found at i:30380079 original size:27 final size:26
Alignment explanation
Indices: 30380048--30380107 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 26
30380038 ATTATAAATC
30380048 AATAAAGT-ATACATACAAAAATTTTAA
1 AATAAA-TAATACATACAAAAA-TTTAA
* *
30380075 AATAAATAATATATACGAAAATTTAA
1 AATAAATAATACATACAAAAATTTAA
30380101 AATAAAT
1 AATAAAT
30380108 CAAAAATAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
26 13 0.43
27 17 0.57
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (26 bp):
AATAAATAATACATACAAAAATTTAA
Found at i:30381458 original size:9 final size:9
Alignment explanation
Indices: 30381441--30381477 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
30381431 TATAGTTTGA
30381441 TATTCGAAT
1 TATTCGAAT
*
30381450 TATTTGAAT
1 TATTCGAAT
30381459 TATTCGAAT
1 TATTCGAAT
30381468 TATTCGAAT
1 TATTCGAAT
30381477 T
1 T
30381478 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.32, C:0.08, G:0.11, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:30383459 original size:45 final size:45
Alignment explanation
Indices: 30383384--30383515 Score: 124
Period size: 45 Copynumber: 2.9 Consensus size: 45
30383374 ACTTGTAGCG
* * * *
30383384 TCAATTTGCTCCGCCACAACCTGA-AGGAGATAAGATTTGCT-ATCT
1 TCAATCTGCTCCGCTACAACTTCAGA-GAGATAAGATTTGCTGAT-T
* * * * *
30383429 TCAGTCTGCTCCGCTATAACTTCAGAGAGATAAGGTTTGGTGGTT
1 TCAATCTGCTCCGCTACAACTTCAGAGAGATAAGATTTGCTGATT
* * *
30383474 TCAATCTGCTCCTCTGCAACTTCAGGGAGATAAGATTTGCTG
1 TCAATCTGCTCCGCTACAACTTCAGAGAGATAAGATTTGCTG
30383516 TCTGTAGCTT
Statistics
Matches: 69, Mismatches: 16, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
45 67 0.97
46 2 0.03
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (45 bp):
TCAATCTGCTCCGCTACAACTTCAGAGAGATAAGATTTGCTGATT
Found at i:30383702 original size:143 final size:141
Alignment explanation
Indices: 30383407--30383742 Score: 440
Period size: 143 Copynumber: 2.4 Consensus size: 141
30383397 CCACAACCTG
* * * * * *
30383407 AAGGAGATAAGATTTGCTATCTTCAGTCTGCTCCGCTATAACTTCAGAGAGATAAGGTTTGGTGG
1 AAGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGTAACTTCAGGGAGATAAGGTCTGGTGG
* * * * * ** *
30383472 TTTCAATCTGCTCCTCTGCAACTTCAGGGAGATAAGATTTGCTGTCTGTAGCTTTAATTTGTTCC
66 CTTCAATCTGCTCCACTCCAACTTCAGGAAGATAAGATTAGCTAACTGTAGCTTTAATATGTTCC
*
30383537 ACTGCAACGCT
131 ACTGCAACGCC
* * *
30383548 AGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGATGTAACTTTAGGGAGATAAGG-CTGGTGG
1 AAGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGTAACTTCAGGGAGATAAGGTCTGGTGG
*
30383612 CTTCAATCTGCTCCACTCCAACTTTAGGAAGATAAGATTCAGCATAACTTGTAGCTTTAATATGT
66 CTTCAATCTGCTCCACTCCAACTTCAGGAAGATAAGATT-AGC-TAAC-TGTAGCTTTAATATGT
30383677 TCCACTGCAACGCC
128 TCCACTGCAACGCC
* * *
30383691 AAGGAAATAAGATTCGCTGTCTTTAGTTTGCTCCGCTGCAACTTCAGGGAGA
1 AAGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGTAACTTCAGGGAGA
30383743 CTTCTGGAAG
Statistics
Matches: 167, Mismatches: 25, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
140 40 0.24
141 51 0.31
142 2 0.01
143 74 0.44
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (141 bp):
AAGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGTAACTTCAGGGAGATAAGGTCTGGTGG
CTTCAATCTGCTCCACTCCAACTTCAGGAAGATAAGATTAGCTAACTGTAGCTTTAATATGTTCC
ACTGCAACGCC
Found at i:30390690 original size:27 final size:26
Alignment explanation
Indices: 30390659--30390720 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
30390649 ATTATAAATC
30390659 AATAAAGT-ATACATACAAAAATTTTAA
1 AATAAA-TAATACATACAAAAA-TTTAA
* * *
30390686 AATAAATAATATATACGAAAATTTGA
1 AATAAATAATACATACAAAAATTTAA
30390712 AATAAATAA
1 AATAAATAA
30390721 AAAATAGAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 14 0.45
27 17 0.55
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.29
Consensus pattern (26 bp):
AATAAATAATACATACAAAAATTTAA
Found at i:30399094 original size:25 final size:26
Alignment explanation
Indices: 30399065--30399114 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
30399055 CCGTCAGAAA
*
30399065 ATACTCAAG-AAACAACTCGAAAAAC
1 ATACTCAAGAAAACAACTCAAAAAAC
30399090 ATACTCAAGAAAACAACTCAAAAAA
1 ATACTCAAGAAAACAACTCAAAAAA
30399115 TATCATTGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.60, C:0.22, G:0.06, T:0.12
Consensus pattern (26 bp):
ATACTCAAGAAAACAACTCAAAAAAC
Found at i:30399108 original size:13 final size:12
Alignment explanation
Indices: 30399067--30399114 Score: 60
Period size: 12 Copynumber: 3.8 Consensus size: 12
30399057 GTCAGAAAAT
*
30399067 ACTCAAGAAACA
1 ACTCAAAAAACA
*
30399079 ACTCGAAAAACA
1 ACTCAAAAAACA
30399091 TACTCAAGAAAACA
1 -ACTCAA-AAAACA
30399105 ACTCAAAAAA
1 ACTCAAAAAA
30399115 TATCATTGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
12 14 0.45
13 11 0.35
14 6 0.19
ACGTcount: A:0.60, C:0.23, G:0.06, T:0.10
Consensus pattern (12 bp):
ACTCAAAAAACA
Found at i:30407258 original size:11 final size:11
Alignment explanation
Indices: 30407239--30407280 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
30407229 CCTTCAAAAA
30407239 TTCTCTTAAGT
1 TTCTCTTAAGT
*
30407250 TTTTCTTAAGT
1 TTCTCTTAAGT
*
30407261 TCCTCTTAAGT
1 TTCTCTTAAGT
30407272 TTCTCTTAA
1 TTCTCTTAA
30407281 CTCCATTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.19, C:0.19, G:0.07, T:0.55
Consensus pattern (11 bp):
TTCTCTTAAGT
Found at i:30407301 original size:13 final size:13
Alignment explanation
Indices: 30407285--30407319 Score: 63
Period size: 12 Copynumber: 2.8 Consensus size: 13
30407275 TCTTAACTCC
30407285 ATTTTTTAAAATA
1 ATTTTTTAAAATA
30407298 A-TTTTTAAAATA
1 ATTTTTTAAAATA
30407310 ATTTTTTAAA
1 ATTTTTTAAA
30407320 TTTTTTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.57
13 9 0.43
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
ATTTTTTAAAATA
Found at i:30407314 original size:11 final size:12
Alignment explanation
Indices: 30407287--30407329 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
30407277 TTAACTCCAT
30407287 TTTTTAAAATAA
1 TTTTTAAAATAA
30407299 TTTTTAAAATAA
1 TTTTTAAAATAA
* *
30407311 TTTTTTAAAT-T
1 TTTTTAAAATAA
30407322 TTTTTAAA
1 TTTTTAAA
30407330 CTGTAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
11 7 0.25
12 21 0.75
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TTTTTAAAATAA
Found at i:30409133 original size:18 final size:18
Alignment explanation
Indices: 30409107--30409141 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
30409097 AGGTGCGTTT
*
30409107 CCTAGCCCTTATATGTAC
1 CCTAACCCTTATATGTAC
30409125 CCTAACCCTTATATGTA
1 CCTAACCCTTATATGTA
30409142 TCCTTTTCCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.31, G:0.09, T:0.34
Consensus pattern (18 bp):
CCTAACCCTTATATGTAC
Found at i:30409587 original size:44 final size:45
Alignment explanation
Indices: 30409538--30409624 Score: 133
Period size: 44 Copynumber: 2.0 Consensus size: 45
30409528 ATATTTTGAA
*
30409538 TATTTTGATATTATTTTATGTAA-AAGAATAGAAATTT-TTTGAGT
1 TATTTTGATATTATTTGATGTAATAA-AATAGAAATTTATTTGAGT
*
30409582 TATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGA
1 TATTTTGATATTATTTGATGTAATAAAATAGAAATTTATTTGA
30409625 TGTAATAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
44 32 0.82
45 7 0.18
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (45 bp):
TATTTTGATATTATTTGATGTAATAAAATAGAAATTTATTTGAGT
Found at i:30409626 original size:25 final size:25
Alignment explanation
Indices: 30409592--30409754 Score: 196
Period size: 25 Copynumber: 6.7 Consensus size: 25
30409582 TATTTTGATA
30409592 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
30409617 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
* * *
30409642 CTATTTGATGTGATAAAAAAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
*
30409667 TTATTTGATGTAATAAAATAGAAAT
1 TTATTTGATGTAATAAAATAGAAGT
** *
30409692 TT-TTTCGA-GT--T-ATTTTG-A-T
1 TTATTT-GATGTAATAAAATAGAAGT
30409711 ATTATTTGATGTAATAAAATAGAAGT
1 -TTATTTGATGTAATAAAATAGAAGT
30409737 TTATTTGATGTAATAAAA
1 TTATTTGATGTAATAAAA
30409755 ATCCTAACCT
Statistics
Matches: 116, Mismatches: 13, Indels: 18
0.79 0.09 0.12
Matches are distributed among these distances:
19 1 0.01
20 5 0.04
21 8 0.07
22 1 0.01
23 1 0.01
24 8 0.07
25 91 0.78
26 1 0.01
ACGTcount: A:0.42, C:0.01, G:0.15, T:0.42
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:30409802 original size:23 final size:23
Alignment explanation
Indices: 30409750--30410246 Score: 221
Period size: 23 Copynumber: 20.5 Consensus size: 23
30409740 TTTGATGTAA
* *
30409750 TAAAAATCCTAACCTAATTTAAC
1 TAAAAACCCTAACCTAATTTAAT
***
30409773 CCTAAACCCTAACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
30409796 TAAAAACCCTAACCCTAACCTAATTTAAT
1 T--AAA----AACCCTAACCTAATTTAAT
*
30409825 TAAAAACCCTAAACCCT-A---ACT
1 TAAAAACCCT-AA-CCTAATTTAAT
*
30409846 TAAAAACCCTAAACCTTAA-CT--T
1 TAAAAACCCT-AACC-TAATTTAAT
* * *
30409868 TAAAAACCTTAACCTAATTTTAC
1 TAAAAACCCTAACCTAATTTAAT
***
30409891 CCTAAACCCTAACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
30409914 TAAAAACCCTAACCCTAACCTAATTTAAT
1 T--AAA----AACCCTAACCTAATTTAAT
30409943 TAAAAACCCTAACCTTAACCTAATTTAAT
1 TAAAAA--C---CC-TAACCTAATTTAAT
30409972 TAAAAACCTAACCCTAACCTAATTTAAT
1 T--AAA---AACCCTAACCTAATTTAAT
30410000 TAAAAACCCTAAACC----TTAACT
1 TAAAAACCCT-AACCTAATTTAA-T
*
30410021 TAAAAACCCTAAACCTTAA-CT--T
1 TAAAAACCCT-AACC-TAATTTAAT
30410043 TAAAAACCCTAACCTAATTTAACCT
1 TAAAAACCCTAACCTAATTTAA--T
30410068 T--AAACCCTAACCTAATTTAA-
1 TAAAAACCCTAACCTAATTTAAT
*
30410088 TACAAAACCCTACCCTAATTTAAT
1 TA-AAAACCCTAACCTAATTTAAT
30410112 TAAAAACCCTAACCCTAACCTAATTTAAT
1 T--AAA----AACCCTAACCTAATTTAAT
30410141 TAAAAACCCTAACCCTAACCTAATTTAAT
1 T--AAA----AACCCTAACCTAATTTAAT
* **
30410170 TAAAAATCCTAACC--CCTTAACT
1 TAAAAACCCTAACCTAATTTAA-T
*
30410192 TAAAAA-CCTAACC---CTTAACT
1 TAAAAACCCTAACCTAATTTAA-T
*
30410212 TTAAAACCCTAACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
30410235 TAAAAACCCTAA
1 TAAAAACCCTAA
30410247 ACAAAGTTAA
Statistics
Matches: 385, Mismatches: 31, Indels: 116
0.72 0.06 0.22
Matches are distributed among these distances:
20 25 0.06
21 60 0.16
22 29 0.08
23 107 0.28
24 12 0.03
25 11 0.03
26 4 0.01
27 9 0.02
28 17 0.04
29 105 0.27
31 3 0.01
32 1 0.00
34 2 0.01
ACGTcount: A:0.45, C:0.27, G:0.00, T:0.28
Consensus pattern (23 bp):
TAAAAACCCTAACCTAATTTAAT
Found at i:30409850 original size:21 final size:22
Alignment explanation
Indices: 30409824--30409875 Score: 88
Period size: 21 Copynumber: 2.4 Consensus size: 22
30409814 CCTAATTTAA
30409824 TTAAAAACCCTAAACCCTAAC-
1 TTAAAAACCCTAAACCCTAACT
*
30409845 TTAAAAACCCTAAACCTTAACT
1 TTAAAAACCCTAAACCCTAACT
30409867 TTAAAAACC
1 TTAAAAACC
30409876 TTAACCTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 20 0.69
22 9 0.31
ACGTcount: A:0.48, C:0.29, G:0.00, T:0.23
Consensus pattern (22 bp):
TTAAAAACCCTAAACCCTAACT
Found at i:30409999 original size:28 final size:29
Alignment explanation
Indices: 30409770--30410184 Score: 284
Period size: 29 Copynumber: 15.4 Consensus size: 29
30409760 AACCTAATTT
30409770 AACCCTAAACCCTAACCTAATTTAATTAAA
1 AACCCT-AACCCTAACCTAATTTAATTAAA
30409800 AACCCTAACCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
* * ****
30409829 AACCCTAAACCCTAACTTAA--AAACCCTA
1 AACCCT-AACCCTAACCTAATTTAATTAAA
* ** ** *
30409857 AACCTTAACTTTAAAAACCTTAACCTAATT--T
1 AACCCTAACCCT---AACC-TAATTTAATTAAA
*
30409888 TACCCTAAACCCTAACCTAATTTAATTAAA
1 AACCCT-AACCCTAACCTAATTTAATTAAA
30409918 AACCCTAACCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
*
30409947 AACCCTAACCTTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
30409976 AA-CCTAACCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
30410004 AACCCT-A----AACC----TTAACTTAAA
1 AACCCTAACCCTAACCTAATTTAA-TTAAA
* *
30410025 AACCCTAAACCT----TAA-CT--TTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
30410047 AACCCT-A-----ACCTAATTTAACCTT--A
1 AACCCTAACCCTAACCTAATTTAA--TTAAA
30410070 AACCCTAA--C----CTAATTTAA-TACAA
1 AACCCTAACCCTAACCTAATTTAATTA-AA
30410093 AACCCT-A--C---CCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
30410116 AACCCTAACCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
30410145 AACCCTAACCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
*
30410174 AATCCTAACCC
1 AACCCTAACCC
30410185 CTTAACTTAA
Statistics
Matches: 317, Mismatches: 27, Indels: 83
0.74 0.06 0.19
Matches are distributed among these distances:
20 8 0.03
21 13 0.04
22 14 0.04
23 40 0.13
24 8 0.03
25 3 0.01
26 1 0.00
27 4 0.01
28 44 0.14
29 143 0.45
30 26 0.08
31 7 0.02
32 4 0.01
33 2 0.01
ACGTcount: A:0.45, C:0.28, G:0.00, T:0.28
Consensus pattern (29 bp):
AACCCTAACCCTAACCTAATTTAATTAAA
Found at i:30410043 original size:175 final size:170
Alignment explanation
Indices: 30409770--30410233 Score: 747
Period size: 175 Copynumber: 2.7 Consensus size: 170
30409760 AACCTAATTT
30409770 AACCCTAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCT-AACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCT
* * *
30409835 AAACCCTAACTTAAAAACCCTAAACCTTAACTTTAAAAACCTTAACCTAATTTTACCCTAAACCC
65 AAACCTTAACTTAAAAACCCTAAACCTTAACTTTAAAAACCCTAACCTAATTTAACCCTAAACCC
30409900 TAACCTAATTTAATTA-AAAACCCTAACCCTAACCTAATTTAATTAAA
130 TAACCTAATTTAA-TACAAAACCCT-A--C---CCTAATTTAATTAAA
*
30409947 AACCCTAACCTTAACCTAATTTAATTAAAAA-CCTAACCCTAACCTAATTTAATTAAAAACCCTA
1 AACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTA
*
30410011 AACCTTAACTTAAAAACCCTAAACCTTAACTTTAAAAACCCTAACCTAATTTAACCTTAAACCCT
66 AACCTTAACTTAAAAACCCTAAACCTTAACTTTAAAAACCCTAACCTAATTTAACCCTAAACCCT
30410076 AACCTAATTTAATACAAAACCCTACCCTAATTTAATTAAA
131 AACCTAATTTAATACAAAACCCTACCCTAATTTAATTAAA
*
30410116 AACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAATCCTA
1 AACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTA
* *
30410181 ACCCCTTAACTTAAAAA-CCTAACCCTTAACTTT-AAAACCCTAACCTAATTTAA
66 A-ACCTTAACTTAAAAACCCTAAACCTTAACTTTAAAAACCCTAACCTAATTTAA
30410234 TTAAAAACCC
Statistics
Matches: 275, Mismatches: 9, Indels: 14
0.92 0.03 0.05
Matches are distributed among these distances:
169 65 0.24
170 48 0.17
171 14 0.05
172 1 0.00
174 3 0.01
175 114 0.41
176 24 0.09
177 6 0.02
ACGTcount: A:0.44, C:0.28, G:0.00, T:0.28
Consensus pattern (170 bp):
AACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTA
AACCTTAACTTAAAAACCCTAAACCTTAACTTTAAAAACCCTAACCTAATTTAACCCTAAACCCT
AACCTAATTTAATACAAAACCCTACCCTAATTTAATTAAA
Found at i:30410057 original size:21 final size:22
Alignment explanation
Indices: 30409999--30410054 Score: 105
Period size: 21 Copynumber: 2.6 Consensus size: 22
30409989 CCTAATTTAA
30409999 TTAAAAACCCTAAACCTTAAC-
1 TTAAAAACCCTAAACCTTAACT
30410020 TTAAAAACCCTAAACCTTAACT
1 TTAAAAACCCTAAACCTTAACT
30410042 TTAAAAACCCTAA
1 TTAAAAACCCTAA
30410055 CCTAATTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 21 0.62
22 13 0.38
ACGTcount: A:0.48, C:0.27, G:0.00, T:0.25
Consensus pattern (22 bp):
TTAAAAACCCTAAACCTTAACT
Found at i:30410196 original size:21 final size:22
Alignment explanation
Indices: 30410169--30410225 Score: 82
Period size: 21 Copynumber: 2.6 Consensus size: 22
30410159 CCTAATTTAA
30410169 TTAAAAATCCTAACCCCTTAAC-
1 TTAAAAA-CCTAACCCCTTAACT
30410191 TTAAAAACCTAA-CCCTTAACT
1 TTAAAAACCTAACCCCTTAACT
*
30410212 TTAAAACCCTAACC
1 TTAAAAACCTAACC
30410226 TAATTTAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 8 0.25
21 16 0.50
22 8 0.25
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (22 bp):
TTAAAAACCTAACCCCTTAACT
Found at i:30410256 original size:23 final size:23
Alignment explanation
Indices: 30410214--30410257 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
30410204 CCTTAACTTT
* * *
30410214 AAAACCCTAACCTAATTTAATTA
1 AAAACCCTAAACAAAGTTAATTA
30410237 AAAACCCTAAACAAAGTTAAT
1 AAAACCCTAAACAAAGTTAAT
30410258 AATTTTACAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.52, C:0.20, G:0.02, T:0.25
Consensus pattern (23 bp):
AAAACCCTAAACAAAGTTAATTA
Found at i:30410397 original size:116 final size:116
Alignment explanation
Indices: 30410250--30410490 Score: 448
Period size: 116 Copynumber: 2.1 Consensus size: 116
30410240 ACCCTAAACA
*
30410250 AAGTTAATAATTTTACATTCACGTAATGTTAGATTTGGAAAAATGTTTTGACTGCTACTAACAAT
1 AAGTTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGCTACTAACAAT
30410315 TAATAATTTTATATAATTTGATAATTTTACTAACCATTAATACAA-TTTTT
66 TAATAATTTTATATAATTTGATAATTTTACTAACCATTAATACAATTTTTT
*
30410365 AGAGTTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAA
1 A-AGTTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGCTACTAACAA
30410430 TTAATAATTTTATATAATTTGATAATTTTACTAACCATTAATACAATTTTTT
65 TTAATAATTTTATATAATTTGATAATTTTACTAACCATTAATACAATTTTTT
30410482 AAGTTAATA
1 AAGTTAATA
30410491 CAATTTATCA
Statistics
Matches: 122, Mismatches: 2, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
115 1 0.01
116 115 0.94
117 6 0.05
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.43
Consensus pattern (116 bp):
AAGTTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGCTACTAACAAT
TAATAATTTTATATAATTTGATAATTTTACTAACCATTAATACAATTTTTT
Found at i:30410507 original size:17 final size:17
Alignment explanation
Indices: 30410466--30410507 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
30410456 TTTACTAACC
* *
30410466 ATTAATACAATTTTTTA
1 ATTAATACAATTTATCA
30410483 AGTTAATACAATTTATCA
1 A-TTAATACAATTTATCA
30410501 ATTAATA
1 ATTAATA
30410508 ATTGCACAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.45
Consensus pattern (17 bp):
ATTAATACAATTTATCA
Found at i:30413754 original size:125 final size:125
Alignment explanation
Indices: 30413511--30413737 Score: 409
Period size: 125 Copynumber: 1.8 Consensus size: 125
30413501 CCCAAACATG
* *
30413511 CTACTGTAGCAAAAGCGTGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCCCAAATAGCATCCTGC
*
30413576 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAATAATTATTTCTTCTGTGAC
66 TAGAAGCGATTTTATACTATTTGATCAGAAACGTCAAAAAATAATTATTTCTTCTGTGAC
30413636 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCCCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCCCAAATAGCATCCTGC
* *
30413701 TAGAAGTGATTTTATACTATTTGATTAGAAACGTCAA
66 TAGAAGCGATTTTATACTATTTGATCAGAAACGTCAA
30413738 CTCGAAATTA
Statistics
Matches: 97, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
125 97 1.00
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCCCAAATAGCATCCTGC
TAGAAGCGATTTTATACTATTTGATCAGAAACGTCAAAAAATAATTATTTCTTCTGTGAC
Found at i:30424199 original size:7 final size:7
Alignment explanation
Indices: 30424187--30424219 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
30424177 AGAAGTGTCT
30424187 GTTAGTA
1 GTTAGTA
30424194 GTTAGTA
1 GTTAGTA
30424201 GTTAGTA
1 GTTAGTA
30424208 GTTAGTA
1 GTTAGTA
30424215 -TTAGT
1 GTTAGT
30424220 TGTGGTTAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.19
7 21 0.81
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.45
Consensus pattern (7 bp):
GTTAGTA
Found at i:30428284 original size:18 final size:17
Alignment explanation
Indices: 30428261--30428313 Score: 79
Period size: 18 Copynumber: 3.0 Consensus size: 17
30428251 ATATATTATG
*
30428261 ATTTTAGTAAATTCATAT
1 ATTTTATTAAATT-ATAT
30428279 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
30428296 ATTTTTATTAAATTATAT
1 A-TTTTATTAAATTATAT
30428314 TTAATAATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
17 5 0.15
18 28 0.85
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:30428574 original size:16 final size:16
Alignment explanation
Indices: 30428547--30428600 Score: 72
Period size: 16 Copynumber: 3.4 Consensus size: 16
30428537 AGATTTACCT
*
30428547 ATTACACCTCTATTCC
1 ATTACACATCTATTCC
*
30428563 ATTACGCATCTATTCC
1 ATTACACATCTATTCC
* *
30428579 ATTACACCTCTATTTC
1 ATTACACATCTATTCC
30428595 ATTACA
1 ATTACA
30428601 GCGAACCAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.28, C:0.31, G:0.02, T:0.39
Consensus pattern (16 bp):
ATTACACATCTATTCC
Found at i:30429715 original size:19 final size:20
Alignment explanation
Indices: 30429693--30429730 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
30429683 ATTAATGATT
30429693 TAAATT-TGATTA-AATGTTA
1 TAAATTGTG-TTAGAATGTTA
30429712 TAAATTGTGTTAGAATGTT
1 TAAATTGTGTTAGAATGTT
30429731 TCGGTAACTG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (20 bp):
TAAATTGTGTTAGAATGTTA
Found at i:30438509 original size:24 final size:24
Alignment explanation
Indices: 30438473--30438562 Score: 110
Period size: 24 Copynumber: 3.8 Consensus size: 24
30438463 CTCTGAAACA
*
30438473 ATGGAAAGGTTGAAAAGGATAACC
1 ATGGAAAGATTGAAAAGGATAACC
*
30438497 ATGGAAAGATTGAAAAGG-TTACC
1 ATGGAAAGATTGAAAAGGATAACC
* * *
30438520 GATGAAAAGGTCGAAAAGGATAACC
1 -ATGGAAAGATTGAAAAGGATAACC
*
30438545 ATGGAAAGATTGGAAAGG
1 ATGGAAAGATTGAAAAGG
30438563 TTACCAATGA
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
23 4 0.07
24 46 0.85
25 4 0.07
ACGTcount: A:0.46, C:0.08, G:0.30, T:0.17
Consensus pattern (24 bp):
ATGGAAAGATTGAAAAGGATAACC
Found at i:30438576 original size:24 final size:24
Alignment explanation
Indices: 30438484--30438602 Score: 98
Period size: 24 Copynumber: 5.0 Consensus size: 24
30438474 TGGAAAGGTT
* * *
30438484 GAAAAGGATAACC-ATGGAAAGATT
1 GAAAAGG-TTACCAATGAAAAGATC
* *
30438508 GAAAAGGTTACCGATGAAAAGGTC
1 GAAAAGGTTACCAATGAAAAGATC
* * *
30438532 GAAAAGGATAACC-ATGGAAAGATT
1 GAAAAGG-TTACCAATGAAAAGATC
* *
30438556 GGAAAGGTTACCAATGAAAAGGTC
1 GAAAAGGTTACCAATGAAAAGATC
* *
30438580 GAAAATGATACCAATGAAAAGAT
1 GAAAAGGTTACCAATGAAAAGAT
30438603 AAAAAAGGAT
Statistics
Matches: 75, Mismatches: 17, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
23 8 0.11
24 63 0.84
25 4 0.05
ACGTcount: A:0.48, C:0.10, G:0.25, T:0.17
Consensus pattern (24 bp):
GAAAAGGTTACCAATGAAAAGATC
Found at i:30438610 original size:48 final size:48
Alignment explanation
Indices: 30438471--30438602 Score: 194
Period size: 48 Copynumber: 2.8 Consensus size: 48
30438461 ATCTCTGAAA
* *
30438471 CAATGGAAAGGTTGAAAAGGATAACCATGGAAAGATTGAAAAGGTTAC
1 CAATGAAAAGGTCGAAAAGGATAACCATGGAAAGATTGAAAAGGTTAC
* *
30438519 CGATGAAAAGGTCGAAAAGGATAACCATGGAAAGATTGGAAAGGTTAC
1 CAATGAAAAGGTCGAAAAGGATAACCATGGAAAGATTGAAAAGGTTAC
* *
30438567 CAATGAAAAGGTCGAAAATGAT-ACCAATGAAAAGAT
1 CAATGAAAAGGTCGAAAAGGATAACC-ATGGAAAGAT
30438603 AAAAAAGGAT
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
47 3 0.04
48 73 0.96
ACGTcount: A:0.47, C:0.10, G:0.26, T:0.17
Consensus pattern (48 bp):
CAATGAAAAGGTCGAAAAGGATAACCATGGAAAGATTGAAAAGGTTAC
Found at i:30442074 original size:20 final size:18
Alignment explanation
Indices: 30442045--30442081 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 18
30442035 TTGTGTGTTT
30442045 TCTTTTCATTTTAATTTTA
1 TCTTTTCATTTT-ATTTTA
30442064 TCTTGTTCATTTTATTTT
1 TCTT-TTCATTTTATTTT
30442082 CTATTTTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.16, C:0.11, G:0.03, T:0.70
Consensus pattern (18 bp):
TCTTTTCATTTTATTTTA
Done.