Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 75 of 204
Found at i:23483769 original size:16 final size:16
Alignment explanation
Indices: 23483748--23483778 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
23483738 TATATTTTTT
23483748 ATAAAAATCGTAAAAA
1 ATAAAAATCGTAAAAA
*
23483764 ATAAAAATTGTAAAA
1 ATAAAAATCGTAAAA
23483779 TTTTATAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.03, G:0.06, T:0.23
Consensus pattern (16 bp):
ATAAAAATCGTAAAAA
Found at i:23484628 original size:9 final size:9
Alignment explanation
Indices: 23484593--23484660 Score: 70
Period size: 9 Copynumber: 7.7 Consensus size: 9
23484583 ACTATATAAA
23484593 ATTTTATAT
1 ATTTTATAT
*
23484602 ATTTCATAT
1 ATTTTATAT
23484611 ATTTCTATAT
1 ATTT-TATAT
23484621 ATTTTATA-
1 ATTTTATAT
*
23484629 ATTTT-TAAG
1 ATTTTAT-AT
23484638 ATTTTATAT
1 ATTTTATAT
23484647 -TTTTATAT
1 ATTTTATAT
*
23484655 TTTTTA
1 ATTTTA
23484661 CGATTATTAT
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
7 1 0.02
8 14 0.27
9 27 0.53
10 9 0.18
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (9 bp):
ATTTTATAT
Found at i:23484628 original size:17 final size:17
Alignment explanation
Indices: 23484594--23484660 Score: 73
Period size: 17 Copynumber: 3.8 Consensus size: 17
23484584 CTATATAAAA
23484594 TTTTATATATTTCATATAT
1 TTTTATATATTT--TATAT
*
23484613 TTCTATATATTTTATAAT
1 TTTTATATATTTTAT-AT
*
23484631 TTTTA-AGATTTTATAT
1 TTTTATATATTTTATAT
*
23484647 TTTTATATTTTTTA
1 TTTTATATATTTTA
23484661 CGATTATTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
16 7 0.17
17 17 0.41
18 6 0.15
19 11 0.27
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (17 bp):
TTTTATATATTTTATAT
Found at i:23484645 original size:26 final size:25
Alignment explanation
Indices: 23484611--23484687 Score: 100
Period size: 26 Copynumber: 3.0 Consensus size: 25
23484601 TATTTCATAT
23484611 ATTTCTATATATTTTATAATTTTTAAG
1 ATTT-TATAT-TTTTATAATTTTTAAG
* *
23484638 ATTTTATATTTTTATATTTTTTACG
1 ATTTTATATTTTTATAATTTTTAAG
*
23484663 ATTATTATATTTTTCTAATTTTTAA
1 ATT-TTATATTTTTATAATTTTTAA
23484688 TAAAATTTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
25 17 0.39
26 23 0.52
27 4 0.09
ACGTcount: A:0.30, C:0.04, G:0.03, T:0.64
Consensus pattern (25 bp):
ATTTTATATTTTTATAATTTTTAAG
Found at i:23484899 original size:87 final size:86
Alignment explanation
Indices: 23484791--23485006 Score: 283
Period size: 87 Copynumber: 2.5 Consensus size: 86
23484781 ATAAAAGCAA
* *
23484791 GGGCTTAATTGCTTTTCTTGAAAAAGTTTGAGGGTATTTTTGATGTC-CTTTGAAAGTTCAAGTA
1 GGGCTTAATTACTTTTTTTGAAAAAGTTTGAGGGTATTTTTGATG-CACTTTGAAAGTTCAAGTA
* *
23484855 CCCAATTGAGTGCAAAAAAAAAG
65 ACCAAATGAGTGC-AAAAAAAAG
* ** *
23484878 GGGCTTAATTACTTTTTTTG-AAAAGATTTGAGAGCCTTTTTGATGCATTTTGAAAGTTCAAGTA
1 GGGCTTAATTACTTTTTTTGAAAAAG-TTTGAGGGTATTTTTGATGCACTTTGAAAGTTCAAGTA
23484942 ACCAAATGAGTGCAAAAAAAAG
65 ACCAAATGAGTGCAAAAAAAAG
* * *
23484964 GGGTTTAATTACTTTTTTGTGAAAAAATTTGAGGGTTTTTTTG
1 GGGCTTAATTACTTTTTT-TGAAAAAGTTTGAGGGTATTTTTG
23485007 CACCCTTAAA
Statistics
Matches: 112, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
86 32 0.29
87 76 0.68
88 4 0.04
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (86 bp):
GGGCTTAATTACTTTTTTTGAAAAAGTTTGAGGGTATTTTTGATGCACTTTGAAAGTTCAAGTAA
CCAAATGAGTGCAAAAAAAAG
Found at i:23486731 original size:2 final size:2
Alignment explanation
Indices: 23486724--23486754 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
23486714 CAAATCAAAC
23486724 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
23486755 TACTAGAGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:23487749 original size:24 final size:24
Alignment explanation
Indices: 23487717--23487770 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
23487707 ATGAGATACT
*
23487717 GACCTTTTCGTTGATATCCTTTTC
1 GACCTTTTCATTGATATCCTTTTC
*
23487741 GACCTTTTCATTTATATCCTTTTC
1 GACCTTTTCATTGATATCCTTTTC
*
23487765 AACCTT
1 GACCTT
23487771 CTTTAATGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.17, C:0.26, G:0.07, T:0.50
Consensus pattern (24 bp):
GACCTTTTCATTGATATCCTTTTC
Found at i:23508614 original size:25 final size:26
Alignment explanation
Indices: 23508560--23508614 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 26
23508550 AAAATTTATT
23508560 TTAAAATTAAAAAAAATTATTTTAAAA
1 TTAAAATTAAAAAAAATTA-TTTAAAA
*
23508587 --AAATTTAAAAAAAA-T-TTTAAAA
1 TTAAAATTAAAAAAAATTATTTAAAA
23508609 TTAAAA
1 TTAAAA
23508615 ATATTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 7
0.73 0.06 0.21
Matches are distributed among these distances:
22 7 0.29
24 4 0.17
25 13 0.54
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (26 bp):
TTAAAATTAAAAAAAATTATTTAAAA
Found at i:23508625 original size:11 final size:11
Alignment explanation
Indices: 23508578--23508608 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
23508568 AAAAAAAATT
23508578 ATTTTAAAAAA
1 ATTTTAAAAAA
*
23508589 ATTTAAAAAAA
1 ATTTTAAAAAA
23508600 ATTTTAAAA
1 ATTTTAAAA
23508609 TTAAAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
ATTTTAAAAAA
Found at i:23508654 original size:18 final size:17
Alignment explanation
Indices: 23508594--23508635 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
23508584 AAAAAATTTA
23508594 AAAAAAATTTTAAAATT
1 AAAAAAATTTTAAAATT
*
23508611 AAAAATATTTTAAAATT
1 AAAAAAATTTTAAAATT
23508628 AAAAAAAT
1 AAAAAAAT
23508636 AAAAAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAAAAATTTTAAAATT
Found at i:23508659 original size:36 final size:39
Alignment explanation
Indices: 23508612--23508687 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 39
23508602 TTTAAAATTA
23508612 AAAATATTTTAAAATT-AAAAAAATAAAA-AAA-ATATTT
1 AAAATATTTT-AAATTGAAAAAAATAAAATAAATATATTT
*
23508649 AAAATA-TTTAAATTGAAAAAATTAAAATAAATATATTT
1 AAAATATTTTAAATTGAAAAAAATAAAATAAATATATTT
23508687 A
1 A
23508688 TTATATCGGC
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
35 5 0.14
36 14 0.40
37 9 0.26
38 7 0.20
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (39 bp):
AAAATATTTTAAATTGAAAAAAATAAAATAAATATATTT
Found at i:23513599 original size:22 final size:21
Alignment explanation
Indices: 23513571--23513624 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 21
23513561 GTTCGTGTAA
23513571 TTAAATTGTATATTTATATGTT
1 TTAAATTGTATA-TTATATGTT
*
23513593 TTAAATTG-A-ATTATTTGTT
1 TTAAATTGTATATTATATGTT
*
23513612 TGTGAATTGTATA
1 T-TAAATTGTATA
23513625 ATTGCCATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
19 9 0.33
20 7 0.26
21 2 0.07
22 9 0.33
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.56
Consensus pattern (21 bp):
TTAAATTGTATATTATATGTT
Found at i:23515019 original size:16 final size:17
Alignment explanation
Indices: 23514998--23515032 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
23514988 AATTAAATTA
23514998 AATTAAATAA-TTTCTC
1 AATTAAATAATTTTCTC
23515014 AATTAAATAATTTTCTC
1 AATTAAATAATTTTCTC
23515031 AA
1 AA
23515033 CCCAATTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (17 bp):
AATTAAATAATTTTCTC
Found at i:23529858 original size:20 final size:20
Alignment explanation
Indices: 23529835--23529881 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
23529825 TTATAAATTT
23529835 TAAAAAGTCAAAATAATA-TA
1 TAAAAAGTCAAAA-AATATTA
**
23529855 TAAAAA-TTGAAAAATATTA
1 TAAAAAGTCAAAAAATATTA
23529874 TAAAAAGT
1 TAAAAAGT
23529882 ACTTAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 4 0.17
19 12 0.52
20 7 0.30
ACGTcount: A:0.64, C:0.02, G:0.06, T:0.28
Consensus pattern (20 bp):
TAAAAAGTCAAAAAATATTA
Found at i:23530746 original size:27 final size:25
Alignment explanation
Indices: 23530677--23530747 Score: 67
Period size: 27 Copynumber: 2.8 Consensus size: 25
23530667 TAGTTTATAA
23530677 TATATTTAT-AT-TAAATATTAAAC
1 TATATTTATGATATAAATATTAAAC
* *
23530700 T-TATTTTATGTTATATAATAGTTAAAG
1 TATA-TTTATGATATA-AATA-TTAAAC
23530727 TATATTTATGATAATAAATAT
1 TATATTTATGAT-ATAAATAT
23530748 ATATTTATCA
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
22 2 0.05
23 6 0.16
24 1 0.03
25 2 0.05
26 5 0.13
27 17 0.45
28 5 0.13
ACGTcount: A:0.44, C:0.01, G:0.06, T:0.49
Consensus pattern (25 bp):
TATATTTATGATATAAATATTAAAC
Found at i:23538943 original size:28 final size:28
Alignment explanation
Indices: 23538904--23538960 Score: 66
Period size: 28 Copynumber: 2.0 Consensus size: 28
23538894 AAATATTTTG
23538904 TAATAATCAATG-TT-ATATATAAACTTAA
1 TAATAATCAATGCTTAAT-TA-AAACTTAA
23538932 TAATAGAT-AATGCTTAATTAAAACTTAA
1 TAATA-ATCAATGCTTAATTAAAACTTAA
23538960 T
1 T
23538961 TAAATTACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
28 18 0.69
29 6 0.23
30 2 0.08
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.39
Consensus pattern (28 bp):
TAATAATCAATGCTTAATTAAAACTTAA
Found at i:23543231 original size:3 final size:3
Alignment explanation
Indices: 23543223--23543263 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
23543213 GGATAAACTA
23543223 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -TT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
23543264 CCATCTCATA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:23548603 original size:30 final size:28
Alignment explanation
Indices: 23548567--23548632 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 28
23548557 AATTATAAAC
* *
23548567 AAATTATACAAAATATATAAATTTATTTCA
1 AAATTATAAAAAATAT-TAAATTTA-TTAA
23548597 AAATTATTAAAAAATATTAAATTTATTAA
1 AAATTA-TAAAAAATATTAAATTTATTAA
23548626 AAATTAT
1 AAATTAT
23548633 TATTATTACC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 1 0.03
29 9 0.27
30 14 0.42
31 9 0.27
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (28 bp):
AAATTATAAAAAATATTAAATTTATTAA
Found at i:23548632 original size:10 final size:10
Alignment explanation
Indices: 23548596--23548634 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
23548586 AATTTATTTC
23548596 AAAATTATTA
1 AAAATTATTA
*
23548606 AAAAATATT-
1 AAAATTATTA
*
23548615 AAATTTATTA
1 AAAATTATTA
23548625 AAAATTATTA
1 AAAATTATTA
23548635 TTATTACCAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
9 7 0.29
10 17 0.71
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
AAAATTATTA
Found at i:23548638 original size:16 final size:17
Alignment explanation
Indices: 23548598--23548640 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 17
23548588 TTTATTTCAA
23548598 AATTATTAAAAAATATT
1 AATTATTAAAAAATATT
*
23548615 AAATTTATTAAAAATTATT
1 -AA-TTATTAAAAAATATT
23548634 -ATTATTA
1 AATTATTA
23548641 CCATTTGTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 6 0.26
17 1 0.04
18 2 0.09
19 14 0.61
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AATTATTAAAAAATATT
Found at i:23551515 original size:25 final size:24
Alignment explanation
Indices: 23551479--23551535 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 24
23551469 GTAACCAATT
*
23551479 TCAGCTCTTATGAGCTTACCGTTAC
1 TCAGCT-TTATGAGCTTACCATTAC
*
23551504 TCAGCTTGTATGAGCTTACCATTAT
1 TCAGCTT-TATGAGCTTACCATTAC
23551529 TCAGCTT
1 TCAGCTT
23551536 AGAGGAGCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 1 0.03
25 28 0.97
ACGTcount: A:0.21, C:0.25, G:0.16, T:0.39
Consensus pattern (24 bp):
TCAGCTTTATGAGCTTACCATTAC
Found at i:23551543 original size:25 final size:25
Alignment explanation
Indices: 23551490--23551547 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
23551480 CAGCTCTTAT
* *
23551490 GAGCTTACCGTTACTCAGCTTGTAT
1 GAGCTTACCATTACTCAGCTTGTAG
*
23551515 GAGCTTACCATTATTCAGCTTAG-AG
1 GAGCTTACCATTACTCAGCTT-GTAG
23551540 GAGCTTAC
1 GAGCTTAC
23551548 TGTTTATCGC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 28 0.97
26 1 0.03
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.33
Consensus pattern (25 bp):
GAGCTTACCATTACTCAGCTTGTAG
Found at i:23553611 original size:69 final size:68
Alignment explanation
Indices: 23553500--23553637 Score: 213
Period size: 69 Copynumber: 2.0 Consensus size: 68
23553490 TTAACACTTG
* *
23553500 TTATGGAAAACTTTTAATATTCTAAGTTTTTCTTTGTAATTTAGTTTTTAGTTTTTAGTTTTTTT
1 TTATGGAAAACTTTTAATATTCTAAGTTTTTCTTTGTAATTTAATTTTTAGTTTTT-GTTTCTTT
*
23553565 TTCT
65 CTCT
* * *
23553569 TTATGGACAGCTTTTGATATTCTAAGTTTTTCTTTGTAATTTAATTTTTAGTTTTTGTTTCTTTC
1 TTATGGAAAACTTTTAATATTCTAAGTTTTTCTTTGTAATTTAATTTTTAGTTTTTGTTTCTTTC
23553634 TCT
66 TCT
23553637 T
1 T
23553638 AAGGTTTAGA
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
68 11 0.17
69 52 0.83
ACGTcount: A:0.20, C:0.08, G:0.11, T:0.62
Consensus pattern (68 bp):
TTATGGAAAACTTTTAATATTCTAAGTTTTTCTTTGTAATTTAATTTTTAGTTTTTGTTTCTTTC
TCT
Found at i:23563003 original size:76 final size:76
Alignment explanation
Indices: 23562877--23563028 Score: 304
Period size: 76 Copynumber: 2.0 Consensus size: 76
23562867 TCCATTCAAA
23562877 GCACAATTAAACACACTCAAAACATGCCAAAACAATCATCCTAGGTGCCTAACCAATGTACCCTC
1 GCACAATTAAACACACTCAAAACATGCCAAAACAATCATCCTAGGTGCCTAACCAATGTACCCTC
23562942 ATTGGTACCAC
66 ATTGGTACCAC
23562953 GCACAATTAAACACACTCAAAACATGCCAAAACAATCATCCTAGGTGCCTAACCAATGTACCCTC
1 GCACAATTAAACACACTCAAAACATGCCAAAACAATCATCCTAGGTGCCTAACCAATGTACCCTC
23563018 ATTGGTACCAC
66 ATTGGTACCAC
23563029 ATTTATATCA
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 76 1.00
ACGTcount: A:0.38, C:0.32, G:0.11, T:0.20
Consensus pattern (76 bp):
GCACAATTAAACACACTCAAAACATGCCAAAACAATCATCCTAGGTGCCTAACCAATGTACCCTC
ATTGGTACCAC
Found at i:23568252 original size:14 final size:12
Alignment explanation
Indices: 23568226--23568266 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 12
23568216 TATTTTATAG
23568226 TTTTTAAAATTT
1 TTTTTAAAATTT
*
23568238 TTTATATATAATTT
1 TTT-T-TAAAATTT
23568252 TTTTTAAAATTT
1 TTTTTAAAATTT
23568264 TTT
1 TTT
23568267 GAGATGTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 13 0.52
13 2 0.08
14 10 0.40
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTTTAAAATTT
Found at i:23573657 original size:12 final size:12
Alignment explanation
Indices: 23573640--23573668 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
23573630 TAGAAAATGA
23573640 ATGTATTAAAAT
1 ATGTATTAAAAT
23573652 ATGTATTAAAAT
1 ATGTATTAAAAT
23573664 ATGTA
1 ATGTA
23573669 GGTATGCATA
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:0.48, C:0.00, G:0.10, T:0.41
Consensus pattern (12 bp):
ATGTATTAAAAT
Found at i:23573878 original size:13 final size:13
Alignment explanation
Indices: 23573860--23573884 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23573850 AAATAAAATG
23573860 AATAAGTATATAT
1 AATAAGTATATAT
23573873 AATAAGTATATA
1 AATAAGTATATA
23573885 AAAACTAAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (13 bp):
AATAAGTATATAT
Found at i:23573893 original size:15 final size:14
Alignment explanation
Indices: 23573860--23573906 Score: 51
Period size: 15 Copynumber: 3.4 Consensus size: 14
23573850 AAATAAAATG
*
23573860 AATAAGTATAT-AT
1 AATAAGTATATAAA
23573873 AATAAGTATATAAA
1 AATAAGTATATAAA
* *
23573887 AACTAAGAAAATAAA
1 AA-TAAGTATATAAA
23573902 AATAA
1 AATAA
23573907 AGAAAAATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
13 11 0.38
14 6 0.21
15 12 0.41
ACGTcount: A:0.66, C:0.02, G:0.06, T:0.26
Consensus pattern (14 bp):
AATAAGTATATAAA
Found at i:23574123 original size:28 final size:29
Alignment explanation
Indices: 23574092--23574147 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
23574082 TGGTATCGCA
*
23574092 TAACTGTG-ATGAAAAAC-TAAAAATGGGT
1 TAACT-TGAATGAAAAACGAAAAAATGGGT
*
23574120 TAACTTGAATTAAAAACGAAAAAATGGG
1 TAACTTGAATGAAAAACGAAAAAATGGG
23574148 GCGAATTTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 2 0.08
28 13 0.54
29 9 0.38
ACGTcount: A:0.50, C:0.07, G:0.20, T:0.23
Consensus pattern (29 bp):
TAACTTGAATGAAAAACGAAAAAATGGGT
Found at i:23576191 original size:89 final size:89
Alignment explanation
Indices: 23575812--23576172 Score: 650
Period size: 89 Copynumber: 4.1 Consensus size: 89
23575802 CACCATCTTT
*
23575812 GATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTACTATCTTTGATCTA
1 GATCTGCTTTCTTGGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTACTATCTTTGATCTA
23575877 CTTCACGCCAATACATGAAGACAA
66 CTTCACGCCAATACATGAAGACAA
* *
23575901 GATCTGCTTTCTTGGATCTACTTCGCCACTAGTATGGGAAGACAAGATCTGCTATCTTTGATCTA
1 GATCTGCTTTCTTGGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTACTATCTTTGATCTA
*
23575966 CTTCATGCCAATACATGAAGACAA
66 CTTCACGCCAATACATGAAGACAA
23575990 GATCTGCTTTCTTGGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTACTATCTTTGATCTA
1 GATCTGCTTTCTTGGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTACTATCTTTGATCTA
23576055 CTTCACGCCAATACATGAAGACAA
66 CTTCACGCCAATACATGAAGACAA
* *
23576079 GATCCGCTTTCTTGGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTA
1 GATCTGCTTTCTTGGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTACTATCTTTGATCTA
*
23576144 CTTCACGCCAATACATGGAGACAA
66 CTTCACGCCAATACATGAAGACAA
*
23576168 TATCT
1 GATCT
23576173 ATTGTATTTG
Statistics
Matches: 260, Mismatches: 12, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
89 260 1.00
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (89 bp):
GATCTGCTTTCTTGGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTACTATCTTTGATCTA
CTTCACGCCAATACATGAAGACAA
Found at i:23576213 original size:222 final size:222
Alignment explanation
Indices: 23575893--23576413 Score: 731
Period size: 222 Copynumber: 2.3 Consensus size: 222
23575883 GCCAATACAT
* * * * *
23575893 GAAGACAAGATCTGCTTTCTTGGATCTACTT--CGCCACTAGTATGGGAAGACAAGATCTGCTAT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATA-CAT-GG-AGACAAGATCTGTTAT
* *
23575956 CTTTGATCTACTTCATGCCAATACATGAAGACAAGATCTGCTTTCTTGGATCTACTTCGCCACCA
63 CTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCA
*
23576021 GTATGGGAAGACAAGATCTACTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCCGC
128 GTATGGGAAGACAAGATCTACTATATTTGATCTACTTCACGCCAATACATGAAGACAAGATCCGC
*
23576086 TTTCTTGGATCTACTTCGCCACCAGTATGG
193 TTTCTTCGATCTACTTCGCCACCAGTATGG
* * * *
23576116 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGGAGACAATATCTATTGTATT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGGAGACAAGATCTGTTATCTT
* * * *
23576181 TGATCTACTTCACGCCGATACATGAAGACAAGATCTGTTTTTTTCGATCTGCTTCGCCACCAGTA
66 TGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTA
* * * * * *
23576246 TGGGAAGACAATATCTATTGTATTTGATCTACTTCACGCCGATACATGAAGACAAGATCTGTTTT
131 TGGGAAGACAAGATCTACTATATTTGATCTACTTCACGCCAATACATGAAGACAAGATCCGCTTT
* *
23576311 TTTCGATCTGCTTCGCCACCAGTATGG
196 CTTCGATCTACTTCGCCACCAGTATGG
* * * * *
23576338 GAAGACAAGATCTGGTATCTTTGGTCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGGAGACAAGATCTGTTATCTT
23576403 TGATCTACTTC
66 TGATCTACTTC
23576414 GCCACCAGTA
Statistics
Matches: 263, Mismatches: 33, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
222 223 0.85
223 31 0.12
224 2 0.01
225 7 0.03
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (222 bp):
GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGGAGACAAGATCTGTTATCTT
TGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTA
TGGGAAGACAAGATCTACTATATTTGATCTACTTCACGCCAATACATGAAGACAAGATCCGCTTT
CTTCGATCTACTTCGCCACCAGTATGG
Found at i:23576255 original size:178 final size:176
Alignment explanation
Indices: 23575849--23576437 Score: 521
Period size: 178 Copynumber: 3.3 Consensus size: 176
23575839 ACCAGTATGG
* * * * * * ** *
23575849 GAAGACAAGATCTACTATCTTTGATCTACTTC-ACGCCAATACATGAAGACAAGATCTGCTTTCT
1 GAAGACAAGATCT-GTTTTTTTGATCTACTTCGCCACCAGTACGGGAAGACAAGATCCGCTTTCT
* *
23575913 TGGATCTACTTCGCCACTAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCATGCCAAT
65 TGGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAAT
* * * * * ***
23575978 ACATGAAGACAAGATCTGCTTTCTTGGATCTACTTCGCCACCAGTATGG
130 ACATGGAGACAAGATCT-ATTTCTTTGATCTACTTC-ACGCCAGTACAT
* * * * * * **
23576027 GAAGACAAGATCTACTATCTTTGATCTACTTC-ACGCCAATACATGAAGACAAGATCCGCTTTCT
1 GAAGACAAGATCT-GTTTTTTTGATCTACTTCGCCACCAGTACGGGAAGACAAGATCCGCTTTCT
23576091 TGGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAAT
65 TGGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAAT
* *
23576156 ACATGGAGACAATATCTATTGTATTTGATCTACTTCACGCC-GATACAT
130 ACATGGAGACAAGATCTATT-TCTTTGATCTACTTCACGCCAG-TACAT
* * * ** *
23576204 GAAGACAAGATCTGTTTTTTTCGATCTGCTTCGCCACCAGTATGGGAAGACAATAT-CTATTGTA
1 GAAGACAAGATCTGTTTTTTT-GATCTACTTCGCCACCAGTACGGGAAGACAAGATCCGCTT-TC
* * * *** * * *
23576268 TTTGATCTACTTC-ACGCC-GATACATGAAGACAAGATCTG-TTTTTTTCGATCTGCTT--CGCC
64 TTGGATCTACTTCGCCACCAG-TATGGGAAGACAAGATCTGCTATCTTT-GATCTACTTCACGCC
** * * * *
23576328 ACCAGTATGGGAAGACAAGATCTGGTATCTTTGGTCTACTTCACGCCAGTACAT
127 AATA-CAT-GG-AGACAAGATCT-ATTTCTTTGATCTACTTCACGCCAGTACAT
*
23576382 GAAGACAAGATCTGTTTTCTTTGATCTACTTCGCCACCAGTAGGGGAAGACAAGAT
1 GAAGACAAGATCTGTTTT-TTTGATCTACTTCGCCACCAGTACGGGAAGACAAGAT
23576438 TTGGTATCTT
Statistics
Matches: 351, Mismatches: 47, Indels: 26
0.83 0.11 0.06
Matches are distributed among these distances:
175 6 0.02
176 14 0.04
177 61 0.17
178 265 0.75
179 5 0.01
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (176 bp):
GAAGACAAGATCTGTTTTTTTGATCTACTTCGCCACCAGTACGGGAAGACAAGATCCGCTTTCTT
GGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATA
CATGGAGACAAGATCTATTTCTTTGATCTACTTCACGCCAGTACAT
Found at i:23576431 original size:311 final size:311
Alignment explanation
Indices: 23575868--23576471 Score: 956
Period size: 311 Copynumber: 1.9 Consensus size: 311
23575858 ATCTACTATC
* *
23575868 TTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTGGATCTACTTCGCCACTAG
1 TTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAG
* * *
23575933 TATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCATGCCAATACATGAAGACAAGATCTGCT
66 TATGGGAAGACAAGATCTACTATATTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCT
*
23575998 TTCTTGGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTACTATCTTTGATCTACTTCACGC
131 TTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTACTATCTTTGATCTACTTCACGC
*
23576063 CAATACATGAAGACAAGATCCGCTTTCTTGGATCTACTTCGCCACCAGTATGGGAAGACAAGATC
196 CAATACATGAAGACAAGATCCGCTTTCTTGGATCTACTTCGCCACCAGTAGGGGAAGACAAGATC
23576128 TGCTATCTTTGATCTACTTCACGCCAATACATGGAGACAATATCTATTGTA
261 TGCTATCTTTGATCTACTTCACGCCAATACATGGAGACAATATCTATTGTA
* * * *
23576179 TTTGATCTACTTCACGCCGATACATGAAGACAAGATCTGTTTTTTTCGATCTGCTTCGCCACCAG
1 TTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAG
* * * * *
23576244 TATGGGAAGACAATATCTATTGTATTTGATCTACTTCACGCCGATACATGAAGACAAGATCTGTT
66 TATGGGAAGACAAGATCTACTATATTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCT
* * ** *
23576309 TTTTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGGTATCTTTGGTCTACTTCACGC
131 TTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTACTATCTTTGATCTACTTCACGC
* * * * *
23576374 CAGTACATGAAGACAAGATCTGTTTTCTTTGATCTACTTCGCCACCAGTAGGGGAAGACAAGATT
196 CAATACATGAAGACAAGATCCGCTTTCTTGGATCTACTTCGCCACCAGTAGGGGAAGACAAGATC
* *
23576439 TGGTATCTTTGATCTACTTCACGCCAGTACATG
261 TGCTATCTTTGATCTACTTCACGCCAATACATG
23576472 AAGATATGAT
Statistics
Matches: 265, Mismatches: 28, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
311 265 1.00
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.31
Consensus pattern (311 bp):
TTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAG
TATGGGAAGACAAGATCTACTATATTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCT
TTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTACTATCTTTGATCTACTTCACGC
CAATACATGAAGACAAGATCCGCTTTCTTGGATCTACTTCGCCACCAGTAGGGGAAGACAAGATC
TGCTATCTTTGATCTACTTCACGCCAATACATGGAGACAATATCTATTGTA
Found at i:23576499 original size:222 final size:222
Alignment explanation
Indices: 23575893--23576574 Score: 606
Period size: 222 Copynumber: 3.1 Consensus size: 222
23575883 GCCAATACAT
* * * * ** *
23575893 GAAGACAAGATCTGCTTTCTTGGATCTACTT--CGCCACTAGTATGGGAAGACAAGATCTGCTAT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATA-CAT--GAAGACAAGATCTATTGT
* ** * * * * *
23575956 CTTTGATCTACTTCATGCCAATACATGAAGACAAGATCTGCTTTC-TTGGATCTACTTCGCCACC
63 ATTTGATCTACTTCACACCGATACAGGAAGACAAGATCTG-TATCTTTCGATCTACTTCGACACC
** * * * *
23576020 AGTATGGGAAGACAAGATCTACTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCCG
127 AGTACAGGAAGACAATATCCATTGTCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCCG
*
23576085 CTTTCTTGGATCTACTTCGCCACCAGTATGG
192 CTTTCTTCGATCTACTTCGCCACCAGTATGG
* *
23576116 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGGAGACAATATCTATTGTATT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTATTGTATT
* * * * * *
23576181 TGATCTACTTCACGCCGATACATGAAGACAAGATCTGTTTTTTTCGATCTGCTTCGCCACCAGTA
66 TGATCTACTTCACACCGATACAGGAAGACAAGATCTGTATCTTTCGATCTACTTCGACACCAGTA
** * * * * *
23576246 TGGGAAGACAATATCTATTGTATTTGATCTACTTCACGCCGATACATGAAGACAAGATCTGTTTT
131 CAGGAAGACAATATCCATTGTCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCCGCTTT
* *
23576311 TTTCGATCTGCTTCGCCACCAGTATGG
196 CTTCGATCTACTTCGCCACCAGTATGG
* * * * * *
23576338 GAAGACAAGATCTGGTATCTTTGGTCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTATTGTATT
* ** * *
23576403 TGATCTACTTCGCCACC-AGTAGGGGAAGACAAGATTTGGTATCTTT-GATCTACTTC-ACGCCA
66 TGATCTACTTC-ACACCGA-TACAGGAAGACAAGATCT-GTATCTTTCGATCTACTTCGACACCA
* * * * * * * * *** *
23576465 GTACATGAAGA-TATGATCCGTTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCT
128 GTACAGGAAGACAAT-ATCCATTGTCTTTGATCTACTTC-ACGCCAATACATGAAGACAAGATCC
* * * * * *
23576529 G-TATATTCGATCCACTTCGCTACCAATATAG
191 GCTTTCTTCGATCTACTTCGCCACCAGTATGG
*
23576560 GAAGACAGGATCTGC
1 GAAGACAAGATCTGC
23576575 CGCTTTTCAA
Statistics
Matches: 382, Mismatches: 69, Indels: 17
0.82 0.15 0.04
Matches are distributed among these distances:
221 5 0.01
222 288 0.75
223 74 0.19
224 8 0.02
225 7 0.02
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.31
Consensus pattern (222 bp):
GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTATTGTATT
TGATCTACTTCACACCGATACAGGAAGACAAGATCTGTATCTTTCGATCTACTTCGACACCAGTA
CAGGAAGACAATATCCATTGTCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCCGCTTT
CTTCGATCTACTTCGCCACCAGTATGG
Found at i:23576499 original size:311 final size:311
Alignment explanation
Indices: 23575866--23576572 Score: 950
Period size: 311 Copynumber: 2.3 Consensus size: 311
23575856 AGATCTACTA
* *
23575866 TCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTGGATCTACTTCGCCACT
1 TCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACC
* * *
23575931 AGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCATGCCAATACATGAAGACAAGATCTG
66 AGTATGGGAAGACAAGATCTACTATATTTGATCTACTTCACGCCAATACATGAAGACAAGATCTG
*
23575996 CTTTCTTGGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTACTATCTTTGATCTACTTCAC
131 CTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTACTATCTTTGATCTACTTCAC
*
23576061 GCCAATACATGAAGACAAGATCCGCTTTCTTGGATCTACTTCGCCACCAGTATGGGAAGACAAGA
196 GCCAATACATGAAGACAAGATCCGCTTTCTTGGATCTACTTCGCCACCAGTAGGGGAAGACAAGA
* *
23576126 TCTGCTATCTTTGATCTACTTCACGCCAATACATGGAGACAATATCTATTG
261 TCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAATATCCATTG
* * * * *
23576177 TATTTGATCTACTTCACGCCGATACATGAAGACAAGATCTGTTTTTTTCGATCTGCTTCGCCACC
1 TCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACC
* * * *
23576242 AGTATGGGAAGACAATATCTATTGTATTTGATCTACTTCACGCCGATACATGAAGACAAGATCTG
66 AGTATGGGAAGACAAGATCTACTATATTTGATCTACTTCACGCCAATACATGAAGACAAGATCTG
* * * ** *
23576307 TTTTTTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGGTATCTTTGGTCTACTTCAC
131 CTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTACTATCTTTGATCTACTTCAC
* * * *
23576372 GCCAGTACATGAAGACAAGATCTGTTTTCTTTGATCTACTTCGCCACCAGTAGGGGAAGACAAGA
196 GCCAATACATGAAGACAAGATCCGCTTTCTTGGATCTACTTCGCCACCAGTAGGGGAAGACAAGA
* * * * * *
23576437 TTTGGTATCTTTGATCTACTTCACGCCAGTACATGAAGA-TATGATCCGTTT
261 TCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAT-ATCCATTG
* * * * *** * * * *
23576488 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTG-TATATTCGATCCACTTCGCTAC
1 TCTTTGATCTACTTC-ACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCAC
* * *
23576552 CAATATAGGAAGACAGGATCT
65 CAGTATGGGAAGACAAGATCT
23576573 GCCGCTTTTC
Statistics
Matches: 342, Mismatches: 52, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
310 2 0.01
311 321 0.94
312 19 0.06
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (311 bp):
TCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACC
AGTATGGGAAGACAAGATCTACTATATTTGATCTACTTCACGCCAATACATGAAGACAAGATCTG
CTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTACTATCTTTGATCTACTTCAC
GCCAATACATGAAGACAAGATCCGCTTTCTTGGATCTACTTCGCCACCAGTAGGGGAAGACAAGA
TCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAATATCCATTG
Found at i:23576564 original size:89 final size:89
Alignment explanation
Indices: 23576177--23576573 Score: 526
Period size: 89 Copynumber: 4.5 Consensus size: 89
23576167 ATATCTATTG
* * *
23576177 TATTTGATCTACTTCACGCCGATACATGAAGACAAGATCTGTTTTTTTCGATCTGCTTCGCCACC
1 TATTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACC
* ** *
23576242 AGTATGGGAAGACAATATCTATTG
66 AGTATGGGAAGACAAGATCTGGTA
* * *
23576266 TATTTGATCTACTTCACGCCGATACATGAAGACAAGATCTGTTTTTTTCGATCTGCTTCGCCACC
1 TATTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACC
23576331 AGTATGGGAAGACAAGATCTGGTA
66 AGTATGGGAAGACAAGATCTGGTA
* * * *
23576355 TCTTTGGTCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTTGATCTACTTCGCCACC
1 TATTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACC
* *
23576420 AGTAGGGGAAGACAAGATTTGGTA
66 AGTATGGGAAGACAAGATCTGGTA
* * * * *
23576444 TCTTTGATCTACTTCACGCCAGTACATGAAGATATGATCCGTTTTCTTCGATCTACTTCGCCACC
1 TATTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACC
23576509 AGTATGGGAAGACAAGATCT-GTA
66 AGTATGGGAAGACAAGATCTGGTA
* * * * * * *
23576532 TATTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTG
1 TATTTGATCTACTTCAC-GCCAATACATGAAGACAAGATCTG
23576574 CCGCTTTTCA
Statistics
Matches: 276, Mismatches: 31, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
88 16 0.06
89 260 0.94
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.31
Consensus pattern (89 bp):
TATTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACC
AGTATGGGAAGACAAGATCTGGTA
Found at i:23577863 original size:48 final size:50
Alignment explanation
Indices: 23577811--23577914 Score: 115
Period size: 50 Copynumber: 2.1 Consensus size: 50
23577801 CTTTGCGAGT
* * *
23577811 TTTCACCTTAGCCTCTC-CATTTTTTT-ACTC-AAGGCTCCCTTTGTAGGG
1 TTTCACCCTAGCCTCTCTCATTTTTTTGACTCGAA-GCGCCCTTTGTAGGC
** **
23577859 TTTCACCCTAGTTTCTCTTTTTTTTTTGACTCGAAGCGCCCTTTGTAGGC
1 TTTCACCCTAGCCTCTCTCATTTTTTTGACTCGAAGCGCCCTTTGTAGGC
23577909 TTTCAC
1 TTTCAC
23577915 ATTGGTCCCA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
48 14 0.30
49 7 0.15
50 23 0.50
51 2 0.04
ACGTcount: A:0.13, C:0.28, G:0.14, T:0.44
Consensus pattern (50 bp):
TTTCACCCTAGCCTCTCTCATTTTTTTGACTCGAAGCGCCCTTTGTAGGC
Found at i:23584470 original size:45 final size:45
Alignment explanation
Indices: 23584405--23584556 Score: 198
Period size: 45 Copynumber: 3.4 Consensus size: 45
23584395 CACCATCTTT
* *
23584405 GATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAA
1 GATCTGCTATCTTTGATCTACTTCGCCACCAGTATGGGAAGACAA
* * * * ***
23584450 GATCTACTATCTTTGATCTACTTC-ACGCCAATACATGAAGACAA
1 GATCTGCTATCTTTGATCTACTTCGCCACCAGTATGGGAAGACAA
* *
23584494 GATCTGCTTTCTTGGATCTACTTCGCCACCAGTATGGGAAGACAA
1 GATCTGCTATCTTTGATCTACTTCGCCACCAGTATGGGAAGACAA
23584539 GATCTGCTATCTTTGATC
1 GATCTGCTATCTTTGATC
23584557 NNNNNNNNNN
Statistics
Matches: 86, Mismatches: 20, Indels: 2
0.80 0.19 0.02
Matches are distributed among these distances:
44 35 0.41
45 51 0.59
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (45 bp):
GATCTGCTATCTTTGATCTACTTCGCCACCAGTATGGGAAGACAA
Found at i:23585148 original size:44 final size:44
Alignment explanation
Indices: 23585098--23585181 Score: 123
Period size: 44 Copynumber: 1.9 Consensus size: 44
23585088 ATCCGTTTTC
* * *
23585098 TTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGTATA
1 TTCGATCCACTTCGCCACCAATATAGGAAGACAAGATCTGTATA
* *
23585142 TTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTG
1 TTCGATCCACTTCGCCACCAATATAGGAAGACAAGATCTG
23585182 CCGCTTTTCA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 35 1.00
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (44 bp):
TTCGATCCACTTCGCCACCAATATAGGAAGACAAGATCTGTATA
Found at i:23589142 original size:22 final size:22
Alignment explanation
Indices: 23589064--23589136 Score: 101
Period size: 22 Copynumber: 3.3 Consensus size: 22
23589054 GCATCATGTT
**
23589064 TAACGTACTAAGCTCTCATGTT
1 TAACGTACTAAGCTCTCATGGC
* * *
23589086 TAACGAACTAAACCCTCATGGC
1 TAACGTACTAAGCTCTCATGGC
23589108 TAACGTACTAAGCTCTCATGGC
1 TAACGTACTAAGCTCTCATGGC
23589130 TAACGTA
1 TAACGTA
23589137 TAAAGCAGAT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.27
Consensus pattern (22 bp):
TAACGTACTAAGCTCTCATGGC
Found at i:23590996 original size:12 final size:12
Alignment explanation
Indices: 23590979--23591007 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
23590969 TAGAAAATGA
23590979 ATGTATTAAAAT
1 ATGTATTAAAAT
23590991 ATGTATTAAAAT
1 ATGTATTAAAAT
23591003 ATGTA
1 ATGTA
23591008 GGTATGCATA
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:0.48, C:0.00, G:0.10, T:0.41
Consensus pattern (12 bp):
ATGTATTAAAAT
Found at i:23591215 original size:13 final size:13
Alignment explanation
Indices: 23591197--23591221 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23591187 AAATAAAATG
23591197 AATAAGTATATAT
1 AATAAGTATATAT
23591210 AATAAGTATATA
1 AATAAGTATATA
23591222 AAAACTAAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (13 bp):
AATAAGTATATAT
Found at i:23591230 original size:15 final size:14
Alignment explanation
Indices: 23591197--23591243 Score: 51
Period size: 15 Copynumber: 3.4 Consensus size: 14
23591187 AAATAAAATG
*
23591197 AATAAGTATAT-AT
1 AATAAGTATATAAA
23591210 AATAAGTATATAAA
1 AATAAGTATATAAA
* *
23591224 AACTAAGAAAATAAA
1 AA-TAAGTATATAAA
23591239 AATAA
1 AATAA
23591244 AGAAAAATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
13 11 0.38
14 6 0.21
15 12 0.41
ACGTcount: A:0.66, C:0.02, G:0.06, T:0.26
Consensus pattern (14 bp):
AATAAGTATATAAA
Found at i:23591460 original size:28 final size:29
Alignment explanation
Indices: 23591429--23591484 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
23591419 TGGTACCGCA
*
23591429 TAACTGTG-ATGAAAAAC-TAAAAATGGGT
1 TAACT-TGAATGAAAAACGAAAAAATGGGT
*
23591457 TAACTTGAATTAAAAACGAAAAAATGGG
1 TAACTTGAATGAAAAACGAAAAAATGGG
23591485 GCGAATTTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 2 0.08
28 13 0.54
29 9 0.38
ACGTcount: A:0.50, C:0.07, G:0.20, T:0.23
Consensus pattern (29 bp):
TAACTTGAATGAAAAACGAAAAAATGGGT
Found at i:23610370 original size:27 final size:27
Alignment explanation
Indices: 23610318--23610370 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
23610308 AAAATATGAA
* *
23610318 AAATTATACAAATGATATACTTTAATC
1 AAATTATACAAATGATATAATATAATC
*
23610345 AAATTATACAATTGAT-TAAATATAAT
1 AAATTATACAAATGATAT-AATATAAT
23610371 ACACTATACA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 1 0.05
27 21 0.95
ACGTcount: A:0.51, C:0.08, G:0.04, T:0.38
Consensus pattern (27 bp):
AAATTATACAAATGATATAATATAATC
Found at i:23610495 original size:47 final size:46
Alignment explanation
Indices: 23610442--23610631 Score: 208
Period size: 47 Copynumber: 4.1 Consensus size: 46
23610432 AATTTAATAT
*
23610442 GAAAAAACGTAAATTAAAATAGAAAGAAAGATAATTTAAATGAAATGA
1 GAAAAAA-TTAAATTAAAAT-GAAAGAAAGATAATTTAAATGAAATGA
* * * *
23610490 GAAAAAATTCAATGT-AAATGGAA-AAA-ATGATTTAAATAAAATGA
1 GAAAAAATTAAAT-TAAAATGAAAGAAAGATAATTTAAATGAAATGA
* * *
23610534 GAAAAAAATTAAATTAAAATGGGAAGATAGATAATTTAAATGAAATCA
1 G-AAAAAATTAAATTAAAAT-GAAAGAAAGATAATTTAAATGAAATGA
* *
23610582 GAAAAAATTAAATTTAAATGAAAAAAAAGATAATTTAAATGAAATG-
1 GAAAAAATTAAATTAAAATG-AAAGAAAGATAATTTAAATGAAATGA
23610628 GAAA
1 GAAA
23610632 TGAAAATTGA
Statistics
Matches: 120, Mismatches: 15, Indels: 16
0.79 0.10 0.11
Matches are distributed among these distances:
44 18 0.15
45 18 0.15
46 12 0.10
47 48 0.40
48 24 0.20
ACGTcount: A:0.61, C:0.02, G:0.14, T:0.24
Consensus pattern (46 bp):
GAAAAAATTAAATTAAAATGAAAGAAAGATAATTTAAATGAAATGA
Found at i:23610498 original size:21 final size:21
Alignment explanation
Indices: 23610474--23610609 Score: 80
Period size: 21 Copynumber: 6.1 Consensus size: 21
23610464 AAAGAAAGAT
23610474 AATTTAAATGAAATGAGAAAA
1 AATTTAAATGAAATGAGAAAA
*
23610495 AA-TTCAATGTAAATG-GAAAAA
1 AATTTAAATG-AAATGAG-AAAA
*
23610516 ATGATTTAAATAAAATGAGAAAA
1 A--ATTTAAATGAAATGAGAAAA
* * *
23610539 AAATTAAATTAAAATGGGAAGATAGAT
1 AATTTAAA-TGAAAT--G-AGA-A-AA
*
23610566 AATTTAAATGAAATCAGAAAA
1 AATTTAAATGAAATGAGAAAA
* *
23610587 AA-TTAAATTTAAATGAAAAAA
1 AATTTAAA-TGAAATGAGAAAA
23610608 AA
1 AA
23610610 GATAATTTAA
Statistics
Matches: 90, Mismatches: 12, Indels: 26
0.70 0.09 0.20
Matches are distributed among these distances:
20 12 0.13
21 33 0.37
22 7 0.08
23 14 0.16
24 7 0.08
25 3 0.03
26 6 0.07
27 8 0.09
ACGTcount: A:0.61, C:0.01, G:0.12, T:0.25
Consensus pattern (21 bp):
AATTTAAATGAAATGAGAAAA
Found at i:23610503 original size:20 final size:20
Alignment explanation
Indices: 23610480--23610517 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
23610470 AGATAATTTA
23610480 AATG-AAATGAGAAAAAATTC
1 AATGTAAATG-GAAAAAATTC
23610500 AATGTAAATGGAAAAAAT
1 AATGTAAATGGAAAAAAT
23610518 GATTTAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.61, C:0.03, G:0.16, T:0.21
Consensus pattern (20 bp):
AATGTAAATGGAAAAAATTC
Found at i:23610579 original size:26 final size:24
Alignment explanation
Indices: 23610470--23610676 Score: 99
Period size: 23 Copynumber: 9.0 Consensus size: 24
23610460 ATAGAAAGAA
23610470 AGATAATTTAAATGAAAT-GAGAA-
1 AGATAATTTAAATGAAATGGA-AAT
*
23610493 A-A-AA-TTCAATGTAAATGGAAA-
1 AGATAATTTAAATG-AAATGGAAAT
* * *
23610514 AAATGATTTAAATAAAATGAGAAA-
1 AGATAATTTAAATGAAATG-GAAAT
*
23610538 A-A-AA-TTAAATTAAAATGGGAAGAT
1 AGATAATTTAAA-TGAAAT-GGAA-AT
*
23610562 AGATAATTTAAATGAAATCAGAAA-
1 AGATAATTTAAATGAAAT-GGAAAT
* *
23610586 AAATTAAATTTAAATGAAA---AAAA
1 AGA-T-AATTTAAATGAAATGGAAAT
23610609 AGATAATTTAAATGAAATGGAAAT
1 AGATAATTTAAATGAAATGGAAAT
* *
23610633 -GAAAATTGAAATGAAATGGAAAT
1 AGATAATTTAAATGAAATGGAAAT
* *
23610656 ACA-AA-TGAAATGAAAT-GAAAT
1 AGATAATTTAAATGAAATGGAAAT
23610677 GGAAGAAATG
Statistics
Matches: 150, Mismatches: 14, Indels: 42
0.73 0.07 0.20
Matches are distributed among these distances:
20 6 0.04
21 32 0.21
22 29 0.19
23 35 0.23
24 17 0.11
25 3 0.02
26 23 0.15
27 5 0.03
ACGTcount: A:0.59, C:0.01, G:0.14, T:0.25
Consensus pattern (24 bp):
AGATAATTTAAATGAAATGGAAAT
Found at i:23610636 original size:5 final size:5
Alignment explanation
Indices: 23610618--23610699 Score: 94
Period size: 5 Copynumber: 15.6 Consensus size: 5
23610608 AAGATAATTT
*
23610618 AAATG AAATGG AAATG AAAATTG AAATG AAATGG AAATAC AAATG AAATG
1 AAATG AAAT-G AAATG -AAA-TG AAATG AAAT-G AAAT-G AAATG AAATG
*
23610668 AAATG AAATG GAA-G AAATG AAATG AAATG AAA
1 AAATG AAATG AAATG AAATG AAATG AAATG AAA
23610700 AAAAAGGTGA
Statistics
Matches: 67, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
4 3 0.04
5 42 0.63
6 20 0.30
7 2 0.03
ACGTcount: A:0.60, C:0.01, G:0.21, T:0.18
Consensus pattern (5 bp):
AAATG
Found at i:23610655 original size:29 final size:26
Alignment explanation
Indices: 23610618--23610699 Score: 102
Period size: 24 Copynumber: 3.3 Consensus size: 26
23610608 AAGATAATTT
*
23610618 AAATGAAATGGAAATG-AA--AATTG
1 AAATGAAATGGAAATGAAATGAAATG
*
23610641 AAATGAAATGGAAATACAAATGAAATG
1 AAATGAAATGGAAAT-GAAATGAAATG
23610668 AAATGAAATGG-AA-GAAATGAAATG
1 AAATGAAATGGAAATGAAATGAAATG
23610692 AAATGAAA
1 AAATGAAA
23610700 AAAAAGGTGA
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
23 15 0.29
24 18 0.35
25 2 0.04
26 2 0.04
27 15 0.29
ACGTcount: A:0.60, C:0.01, G:0.21, T:0.18
Consensus pattern (26 bp):
AAATGAAATGGAAATGAAATGAAATG
Found at i:23610668 original size:92 final size:92
Alignment explanation
Indices: 23610442--23610703 Score: 221
Period size: 92 Copynumber: 2.8 Consensus size: 92
23610432 AATTTAATAT
** * * * * * * *
23610442 GAAAAAACGTAAATTAAAATAGAAAGAAAGATAATTTAAATGAAATGAGAAAAAATTCAATGTAA
1 GAAAAAAATTAAATTAAAATGGGAAGATACATAATTGAAATGAAATCAGAAAAAATTAAATGTAA
* *
23610507 ATGGAAAAAATGATTTAAATAAAATGA
66 ATGAAAAAAATAATTTAAATAAAATGA
* * *
23610534 GAAAAAAATTAAATTAAAATGGGAAGATAGATAATTTAAATGAAATCAGAAAAAATTAAATTTAA
1 GAAAAAAATTAAATTAAAATGGGAAGATACATAATTGAAATGAAATCAGAAAAAATTAAATGTAA
*
23610599 ATGAAAAAAAAGATAATTTAAATGAAATG-
66 ATG--AAAAAA-ATAATTTAAATAAAATGA
* * * * *
23610628 GAAATGAAAATTGAAA-TGAAAT-GGAA-ATACAAATGAAATGAAATGAAAT-GGAAGAAATGAA
1 GAAA--AAAATT-AAATTAAAATGGGAAGATAC--AT-AATTGAAATGAAATCAGAAAAAATTAA
23610689 ATG-AAATGAAAAAAA
60 ATGTAAATGAAAAAAA
23610704 AGGTGAAATG
Statistics
Matches: 142, Mismatches: 19, Indels: 18
0.79 0.11 0.10
Matches are distributed among these distances:
92 61 0.43
93 6 0.04
94 12 0.08
95 24 0.17
96 24 0.17
97 15 0.11
ACGTcount: A:0.61, C:0.02, G:0.15, T:0.22
Consensus pattern (92 bp):
GAAAAAAATTAAATTAAAATGGGAAGATACATAATTGAAATGAAATCAGAAAAAATTAAATGTAA
ATGAAAAAAATAATTTAAATAAAATGA
Found at i:23611009 original size:22 final size:25
Alignment explanation
Indices: 23610966--23611014 Score: 68
Period size: 22 Copynumber: 2.1 Consensus size: 25
23610956 GACTACTTCT
23610966 AATTGATATAAAAAAATATGAAATG
1 AATTGATATAAAAAAATATGAAATG
*
23610991 AATTGA-A-AAAAAAAT-TGAATTG
1 AATTGATATAAAAAAATATGAAATG
23611013 AA
1 AA
23611015 AAAAGATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 8 0.35
23 8 0.35
24 1 0.04
25 6 0.26
ACGTcount: A:0.61, C:0.00, G:0.12, T:0.27
Consensus pattern (25 bp):
AATTGATATAAAAAAATATGAAATG
Found at i:23611108 original size:17 final size:19
Alignment explanation
Indices: 23611073--23611112 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
23611063 TGTATATTAG
*
23611073 GAAAAAAATAAATTTAAAT
1 GAAAAAAATAAATTGAAAT
23611092 GAAAAAAAT-AA-TGAAAT
1 GAAAAAAATAAATTGAAAT
23611109 GAAA
1 GAAA
23611113 TGTTAAATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 9 0.45
18 2 0.10
19 9 0.45
ACGTcount: A:0.70, C:0.00, G:0.10, T:0.20
Consensus pattern (19 bp):
GAAAAAAATAAATTGAAAT
Found at i:23611111 original size:5 final size:5
Alignment explanation
Indices: 23611101--23611379 Score: 61
Period size: 5 Copynumber: 51.4 Consensus size: 5
23611091 TGAAAAAAAT
* * *
23611101 AATGA AATGA AATGTTA AATGAA ATATGA ATATAA AATGA AATGTA ATTTGT
1 AATGA AATGA AATG--A AATG-A A-ATGA A-ATGA AATGA AATG-A A-ATGA
*
23611153 AATGA ATATGA AATGTTA AATGA ATATGA AATGA AATGA AACG- -ATGA
1 AATGA A-ATGA AATG--A AATGA A-ATGA AATGA AATGA AATGA AATGA
* * * * *
23611200 TTATGA AATGG AATGA AAGTTTA AATGAA AAT-A AATTATA AATTTA AATGA
1 -AATGA AATGA AATGA AA--TGA AATG-A AATGA AA-T-GA AA-TGA AATGA
** * **
23611251 AAACA AA--A ACTGA AATGAA AAAAA AATTGA AATGAGA AAT-A AAT-A
1 AATGA AATGA AATGA AATG-A AATGA AA-TGA AAT--GA AATGA AATGA
* ** *
23611296 AATTTA AATGGA AAAAA AAT-A AATTA AATGA AATGGA AATGTA AATGA
1 AA-TGA AAT-GA AATGA AATGA AATGA AATGA AAT-GA AATG-A AATGA
*
23611344 AATGGA AATGGA AATGGA AATGGA AATGA AACGA AA
1 AAT-GA AAT-GA AAT-GA AAT-GA AATGA AATGA AA
23611380 AAAATAAAAA
Statistics
Matches: 214, Mismatches: 29, Indels: 62
0.70 0.10 0.20
Matches are distributed among these distances:
3 4 0.02
4 14 0.07
5 88 0.41
6 79 0.37
7 29 0.14
ACGTcount: A:0.57, C:0.01, G:0.16, T:0.25
Consensus pattern (5 bp):
AATGA
Found at i:23611140 original size:35 final size:35
Alignment explanation
Indices: 23611101--23611252 Score: 109
Period size: 35 Copynumber: 4.3 Consensus size: 35
23611091 TGAAAAAAAT
23611101 AATGAAATGAAATGTTAAATGAAATATGAATATAA
1 AATGAAATGAAATGTTAAATGAAATATGAATATAA
* * * *
23611136 AATGAAATGTAAT-TTGTAATG-AATATGAAATGTTA
1 AATGAAATGAAATGTT-AAATGAAATATG-AATATAA
* * *
23611171 AATGAATATGAAATG--AAATGAAACGATGATTATGA
1 AATGAA-ATGAAATGTTAAATGAAA-TATGAATATAA
* *
23611206 AATGGAATGAAA-GTTTAAATGAAA-ATAAATTATAA
1 AATGAAATGAAATG-TTAAATGAAATATGAA-TATAA
* *
23611241 ATTTAAATGAAA
1 AATGAAATGAAA
23611253 ACAAAAACTG
Statistics
Matches: 90, Mismatches: 17, Indels: 20
0.71 0.13 0.16
Matches are distributed among these distances:
33 1 0.01
34 21 0.23
35 51 0.57
36 17 0.19
ACGTcount: A:0.53, C:0.01, G:0.16, T:0.30
Consensus pattern (35 bp):
AATGAAATGAAATGTTAAATGAAATATGAATATAA
Found at i:23611176 original size:18 final size:18
Alignment explanation
Indices: 23611101--23611185 Score: 88
Period size: 18 Copynumber: 4.8 Consensus size: 18
23611091 TGAAAAAAAT
23611101 AATGAA-ATGAAATGTTA
1 AATGAATATGAAATGTTA
* *
23611118 AATGAAATATG-AATATAA
1 AATG-AATATGAAATGTTA
* *
23611136 AATGAA-ATGTAAT-TTGT
1 AATGAATATGAAATGTT-A
23611153 AATGAATATGAAATGTTA
1 AATGAATATGAAATGTTA
23611171 AATGAATATGAAATG
1 AATGAATATGAAATG
23611186 AAATGAAACG
Statistics
Matches: 56, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
16 4 0.07
17 15 0.27
18 32 0.57
19 5 0.09
ACGTcount: A:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (18 bp):
AATGAATATGAAATGTTA
Found at i:23611199 original size:24 final size:24
Alignment explanation
Indices: 23611172--23611217 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
23611162 GAAATGTTAA
23611172 ATGAATATGAAATGAAATGAAACG
1 ATGAATATGAAATGAAATGAAACG
* *
23611196 ATGATTATGAAATGGAATGAAA
1 ATGAATATGAAATGAAATGAAA
23611218 GTTTAAATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.52, C:0.02, G:0.22, T:0.24
Consensus pattern (24 bp):
ATGAATATGAAATGAAATGAAACG
Found at i:23611224 original size:52 final size:51
Alignment explanation
Indices: 23611101--23611228 Score: 152
Period size: 52 Copynumber: 2.5 Consensus size: 51
23611091 TGAAAAAAAT
* *
23611101 AATGAAATGAAATGTTAAATGAAATATGAATATAAAATGAAATGTAATTTGT
1 AATGAAATGAAATGTTAAATG-AATATGAATATAAAATGAAACGTAATTTGA
* *
23611153 AATGAATATGAAATGTTAAATGAATATGAA-ATGAAATGAAACGATGATTATGA
1 AATGAA-ATGAAATGTTAAATGAATATGAATATAAAATGAAACG-TAATT-TGA
*
23611206 AATGGAATGAAA-GTTTAAATGAA
1 AATGAAATGAAATG-TTAAATGAA
23611229 AATAAATTAT
Statistics
Matches: 67, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
51 12 0.18
52 33 0.49
53 22 0.33
ACGTcount: A:0.52, C:0.01, G:0.18, T:0.30
Consensus pattern (51 bp):
AATGAAATGAAATGTTAAATGAATATGAATATAAAATGAAACGTAATTTGA
Found at i:23611268 original size:18 final size:17
Alignment explanation
Indices: 23611245--23611285 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
23611235 TTATAAATTT
23611245 AAATGAAAACAAAAACTG
1 AAATGAAAA-AAAAACTG
*
23611263 AAATGAAAAAAAAATTG
1 AAATGAAAAAAAAACTG
23611280 AAATGA
1 AAATGA
23611286 GAAATAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.68, C:0.05, G:0.12, T:0.15
Consensus pattern (17 bp):
AAATGAAAAAAAAACTG
Found at i:23611281 original size:17 final size:17
Alignment explanation
Indices: 23611239--23611315 Score: 73
Period size: 18 Copynumber: 4.2 Consensus size: 17
23611229 AATAAATTAT
*
23611239 AAATTTAAATGAAAACAA
1 AAATTGAAATGAAAA-AA
*
23611257 AAACTGAAATGAAAAAA
1 AAATTGAAATGAAAAAA
23611274 AAATTGAAATGAGAAATAAA
1 AAATTGAAAT--GAAA-AAA
* *
23611294 TAAATTTAAATGGAAAAA
1 -AAATTGAAATGAAAAAA
23611312 AAAT
1 AAAT
23611316 AAATTAAATG
Statistics
Matches: 50, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
17 15 0.30
18 16 0.32
19 7 0.14
20 3 0.06
21 9 0.18
ACGTcount: A:0.66, C:0.03, G:0.10, T:0.21
Consensus pattern (17 bp):
AAATTGAAATGAAAAAA
Found at i:23611319 original size:25 final size:25
Alignment explanation
Indices: 23611287--23611334 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
23611277 TTGAAATGAG
*
23611287 AAATAAA-TAAATTTAAATGGAAAAA
1 AAATAAATTAAA-TGAAATGGAAAAA
23611312 AAATAAATTAAATGAAATGGAAA
1 AAATAAATTAAATGAAATGGAAA
23611335 TGTAAATGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.67, C:0.00, G:0.10, T:0.23
Consensus pattern (25 bp):
AAATAAATTAAATGAAATGGAAAAA
Found at i:23611322 original size:20 final size:21
Alignment explanation
Indices: 23611268--23611325 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
23611258 AACTGAAATG
23611268 AAAAAA-AAATTGAAAT-GAGA
1 AAAAAATAAATT-AAATGGAGA
*
23611288 AATAAATAAATTTAAATGGA-A
1 AAAAAATAAA-TTAAATGGAGA
23611309 AAAAAATAAATTAAATG
1 AAAAAATAAATTAAATG
23611326 AAATGGAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 12 0.36
21 17 0.52
22 4 0.12
ACGTcount: A:0.67, C:0.00, G:0.10, T:0.22
Consensus pattern (21 bp):
AAAAAATAAATTAAATGGAGA
Found at i:23611336 original size:6 final size:6
Alignment explanation
Indices: 23611321--23611371 Score: 79
Period size: 6 Copynumber: 8.8 Consensus size: 6
23611311 AAAATAAATT
*
23611321 AAAT-G AAATGG AAATGT AAAT-G AAATGG AAATGG AAATGG AAATGG
1 AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG
23611367 AAATG
1 AAATG
23611372 AAACGAAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
5 8 0.19
6 34 0.81
ACGTcount: A:0.53, C:0.00, G:0.27, T:0.20
Consensus pattern (6 bp):
AAATGG
Found at i:23611342 original size:17 final size:17
Alignment explanation
Indices: 23611316--23611371 Score: 87
Period size: 17 Copynumber: 3.3 Consensus size: 17
23611306 GAAAAAAAAT
23611316 AAAT-TAAATGAAATGG
1 AAATGTAAATGAAATGG
23611332 AAATGTAAATGAAATGG
1 AAATGTAAATGAAATGG
*
23611349 AAATGGAAATGGAAATGG
1 AAATGTAAAT-GAAATGG
23611367 AAATG
1 AAATG
23611372 AAACGAAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
16 4 0.11
17 21 0.57
18 12 0.32
ACGTcount: A:0.54, C:0.00, G:0.25, T:0.21
Consensus pattern (17 bp):
AAATGTAAATGAAATGG
Found at i:23613079 original size:20 final size:20
Alignment explanation
Indices: 23613050--23613090 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
23613040 ATAAGCTGTT
23613050 ACACAACCCTCAATAAACAA
1 ACACAACCCTCAATAAACAA
*
23613070 ACACAGCCCTCAATAAACAA
1 ACACAACCCTCAATAAACAA
23613090 A
1 A
23613091 ATTTAATACC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.54, C:0.34, G:0.02, T:0.10
Consensus pattern (20 bp):
ACACAACCCTCAATAAACAA
Found at i:23616692 original size:90 final size:90
Alignment explanation
Indices: 23616598--23616827 Score: 372
Period size: 90 Copynumber: 2.6 Consensus size: 90
23616588 TACAGATTAA
* **
23616598 ATTAAATTTACAGATACAAAAAGGTACAAACATTCTAAGAAATTAATACACGAAAATATAAAAAT
1 ATTAAATTTACAGATATAAAAAAATACAAACATTCTAAGAAATTAATACACGAAAATATAAAAAT
* *
23616663 GAAACCTTAAATCCTAGACAACTAT
66 GAAACCTTAAATCCTAAACAACTAC
* *
23616688 ATTAAATTTATAGATATAAAAAAATACAAATATTCTAAGAAATTAATACACGAAAATATAAAAAT
1 ATTAAATTTACAGATATAAAAAAATACAAACATTCTAAGAAATTAATACACGAAAATATAAAAAT
*
23616753 GAAACCTTAAATCCTAAACAAGTAC
66 GAAACCTTAAATCCTAAACAACTAC
23616778 ATTAAATTTACAGATATAAAAAAATACAAACATTCTAAAGAAA-TAATACA
1 ATTAAATTTACAGATATAAAAAAATACAAACATTCT-AAGAAATTAATACA
23616828 ATTATTTTGA
Statistics
Matches: 129, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
90 123 0.95
91 6 0.05
ACGTcount: A:0.56, C:0.12, G:0.06, T:0.26
Consensus pattern (90 bp):
ATTAAATTTACAGATATAAAAAAATACAAACATTCTAAGAAATTAATACACGAAAATATAAAAAT
GAAACCTTAAATCCTAAACAACTAC
Found at i:23622628 original size:13 final size:13
Alignment explanation
Indices: 23622610--23622644 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
23622600 ATTAATTTAA
23622610 AAAAATAACTATG
1 AAAAATAACTATG
23622623 AAAAATAACTATG
1 AAAAATAACTATG
23622636 AAAAATAAC
1 AAAAATAAC
23622645 CCTACTATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.66, C:0.09, G:0.06, T:0.20
Consensus pattern (13 bp):
AAAAATAACTATG
Found at i:23623213 original size:31 final size:31
Alignment explanation
Indices: 23623167--23623252 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 31
23623157 TTAACAACTC
* * *
23623167 AATAACTAAATTAAAATTTTTTGAATAGTTTA
1 AATAATTAAATTAAAATTTTTTAAATA-ATTA
*
23623199 AA-AATTTAAA-TAAAAATTTTTAAATAATTA
1 AATAA-TTAAATTAAAATTTTTTAAATAATTA
*
23623229 AATAATTAAATTATAATTTTTTAA
1 AATAATTAAATTAAAATTTTTTAA
23623253 TTAAGTAACC
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
30 10 0.22
31 29 0.64
32 6 0.13
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.44
Consensus pattern (31 bp):
AATAATTAAATTAAAATTTTTTAAATAATTA
Found at i:23624481 original size:14 final size:14
Alignment explanation
Indices: 23624464--23624505 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
23624454 ATTATTAAAA
*
23624464 TAAAATTATAGTAT
1 TAAAATTATATTAT
*
23624478 T-AAATT-TTTTAT
1 TAAAATTATATTAT
23624490 TAAAATTATATTAT
1 TAAAATTATATTAT
23624504 TA
1 TA
23624506 GAGATTAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
12 5 0.22
13 10 0.43
14 8 0.35
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (14 bp):
TAAAATTATATTAT
Found at i:23626263 original size:20 final size:19
Alignment explanation
Indices: 23626238--23626284 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 19
23626228 ATTAATTATT
23626238 TATAAAATTTAATTAGAATA
1 TATAAAATTTAATTA-AATA
* * *
23626258 TATAAACTATATTTAAATA
1 TATAAAATTTAATTAAATA
23626277 TA-AAAATT
1 TATAAAATT
23626285 AAATATTTGT
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
18 4 0.18
19 6 0.27
20 12 0.55
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (19 bp):
TATAAAATTTAATTAAATA
Found at i:23628544 original size:13 final size:13
Alignment explanation
Indices: 23628502--23628551 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
23628492 GCTAAAGCAA
23628502 AGTAGAGCAAAGC
1 AGTAGAGCAAAGC
*
23628515 AGCAGAGGCACAA--
1 AGTAGA-GCA-AAGC
23628528 AGTAGAGCAAAGC
1 AGTAGAGCAAAGC
*
23628541 AGTAAAGCAAA
1 AGTAGAGCAAA
23628552 AGAGGCATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
11 2 0.07
12 3 0.10
13 20 0.67
14 3 0.10
15 2 0.07
ACGTcount: A:0.50, C:0.16, G:0.28, T:0.06
Consensus pattern (13 bp):
AGTAGAGCAAAGC
Found at i:23633459 original size:13 final size:13
Alignment explanation
Indices: 23633441--23633467 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
23633431 GTTTGTAACA
23633441 GAAAATGGCAGGT
1 GAAAATGGCAGGT
23633454 GAAAATGGCAGGT
1 GAAAATGGCAGGT
23633467 G
1 G
23633468 TTACGTTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.41, T:0.15
Consensus pattern (13 bp):
GAAAATGGCAGGT
Found at i:23638750 original size:51 final size:50
Alignment explanation
Indices: 23638688--23638802 Score: 128
Period size: 51 Copynumber: 2.3 Consensus size: 50
23638678 TTATAAAACT
* *
23638688 TATATATATATAAAATACA-TAATGCATTTATGAAAACAATGAAAATATA-AA
1 TATATA-ATATAAAATACATTAATGCATTTA-CAAAAAAAT-AAAATATATAA
* *
23638739 TATATACATATAAAATATATTCATGCATTTACAAAAAAATAAAATATATAA
1 TATATA-ATATAAAATACATTAATGCATTTACAAAAAAATAAAATATATAA
*
23638790 -GTATAATATAAAA
1 TATATAATATAAAA
23638803 CGTGGAAAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
49 8 0.14
50 12 0.21
51 26 0.46
52 10 0.18
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.32
Consensus pattern (50 bp):
TATATAATATAAAATACATTAATGCATTTACAAAAAAATAAAATATATAA
Found at i:23639360 original size:19 final size:21
Alignment explanation
Indices: 23639322--23639360 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
23639312 CTTTTTTTGA
*
23639322 AATCGTAAATAAGTAAAAAAT
1 AATCGTAAATAAGAAAAAAAT
23639343 AATCG-AAA-AAGAAAAAAA
1 AATCGTAAATAAGAAAAAAA
23639361 AAAGAAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.69, C:0.05, G:0.10, T:0.15
Consensus pattern (21 bp):
AATCGTAAATAAGAAAAAAAT
Found at i:23639641 original size:21 final size:21
Alignment explanation
Indices: 23639564--23639634 Score: 133
Period size: 21 Copynumber: 3.4 Consensus size: 21
23639554 AATCATATCT
*
23639564 TCTAAGATTGTATATATCATA
1 TCTAAGATTGCATATATCATA
23639585 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATATCATA
23639606 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATATCATA
23639627 TCTAAGAT
1 TCTAAGAT
23639635 CGTATATCCT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39
Consensus pattern (21 bp):
TCTAAGATTGCATATATCATA
Found at i:23640028 original size:44 final size:44
Alignment explanation
Indices: 23639952--23640067 Score: 146
Period size: 44 Copynumber: 2.7 Consensus size: 44
23639942 CTCTAATCCA
* * * * * *
23639952 CTCCACTACAACTT-AGGGAGACAGGATTTGTTTATTTAGTCTG
1 CTCCACTGCAACTTCAGGAAGATAAGACTTGTTTACTTAGTCTG
23639995 C-CTCACTGCAACTTCAGGAAGATAAGACTTGTTTACTTAGTCTG
1 CTC-CACTGCAACTTCAGGAAGATAAGACTTGTTTACTTAGTCTG
*
23640039 CTCCACTGCAACTTCAGGGAGATAAGACT
1 CTCCACTGCAACTTCAGGAAGATAAGACT
23640068 AGACGCGATC
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
42 1 0.02
43 11 0.17
44 50 0.79
45 1 0.02
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (44 bp):
CTCCACTGCAACTTCAGGAAGATAAGACTTGTTTACTTAGTCTG
Found at i:23640315 original size:210 final size:213
Alignment explanation
Indices: 23639989--23640416 Score: 628
Period size: 210 Copynumber: 2.0 Consensus size: 213
23639979 TTGTTTATTT
* * *
23639989 AGTCTGCCTCACTGCAACTTCAGGAAGATAAGACTTGTTTACTTAGTCTGCTCCACTGCAACTTC
1 AGTCTACCTCACTGCAACTTCAGGAAGATAAGACTTGCTTACTGAGTCTGCTCCACT---A-TTC
*
23640054 AGGGAGATAAGACTAGACGCGATCAGCTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTGA
62 AGGGAGATAAGACTAGACGCGATCAGCTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTAA
* ** * * *
23640119 TCTGCTCCACTGTAACTTCAGGGAGATAGGATTATTGGCTCTAATATGCTCCACTGCAACTTCAG
127 TCCGCTCCACTACAACTTCAAGGAGATACGATTATCGGCTCTAATATGCTCCACTGCAACTTCAG
23640184 GGAGATAAGATTTGCCATCTTC
192 GGAGATAAGATTTGCCATCTTC
* *
23640206 AGTCTACCTCACTGCAACTTCAGGAGGATAAGACTTGCTTGCTGAGTCTGCT-CACT-TT-AGGG
1 AGTCTACCTCACTGCAACTTCAGGAAGATAAGACTTGCTTACTGAGTCTGCTCCACTATTCAGGG
* * *
23640268 AGATAAGATTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTAATCCG
66 AGATAAGACTAGACGCGATCAGCTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTAATCCG
* * *
23640333 CTCTACTACAACTTCAAGGAGATACGATTATCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAG
131 CTCCACTACAACTTCAAGGAGATACGATTATCGGCTCTAATATGCTCCACTGCAACTTCAGGGAG
*
23640398 ATAATATTTGCCATCTTC
196 ATAAGATTTGCCATCTTC
23640416 A
1 A
23640417 ACCTACTCCG
Statistics
Matches: 192, Mismatches: 19, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
210 139 0.72
211 2 0.01
216 4 0.02
217 47 0.24
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.29
Consensus pattern (213 bp):
AGTCTACCTCACTGCAACTTCAGGAAGATAAGACTTGCTTACTGAGTCTGCTCCACTATTCAGGG
AGATAAGACTAGACGCGATCAGCTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTAATCCG
CTCCACTACAACTTCAAGGAGATACGATTATCGGCTCTAATATGCTCCACTGCAACTTCAGGGAG
ATAAGATTTGCCATCTTC
Found at i:23640355 original size:44 final size:44
Alignment explanation
Indices: 23640289--23640401 Score: 115
Period size: 44 Copynumber: 2.6 Consensus size: 44
23640279 GATGCGATCT
*
23640289 GCTCT-CTGCAACTTC-AGAGAGATAAGATCCA-AGGTTTTAATCC
1 GCTCTACTGCAACTTCAAG-GAGATAAGAT-CATAGGCTTTAATCC
* * * * *
23640332 GCTCTACTACAACTTCAAGGAGATACGATTATCGGCTTTAATCT
1 GCTCTACTGCAACTTCAAGGAGATAAGATCATAGGCTTTAATCC
* *
23640376 GCTCCACTGCAACTTCAGGGAGATAA
1 GCTCTACTGCAACTTCAAGGAGATAA
23640402 TATTTGCCAT
Statistics
Matches: 57, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
43 6 0.11
44 49 0.86
45 2 0.04
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (44 bp):
GCTCTACTGCAACTTCAAGGAGATAAGATCATAGGCTTTAATCC
Found at i:23640558 original size:132 final size:132
Alignment explanation
Indices: 23640372--23640975 Score: 934
Period size: 132 Copynumber: 4.6 Consensus size: 132
23640362 ATCGGCTTTA
* ** * * * *
23640372 ATCTGCTCCACTGCAACTTCAGGGAGATAATATTTGCCATCTTCAACCTACTCCGCTGCTGCTCA
1 ATCTGCTCCACTACTGCTT-AGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCA
* *
23640437 GGGAGATAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTACCGTCT
65 GGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCT
*
23640502 TTG
130 TCG
* *
23640505 ATCTGCTCTACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAG
* *
23640570 GGAGACAAGGCTTGGTGGCTTAAATCTGCTTTCCACTATCTTGGAAAGATAAGATTTGCTGTCTT
66 GGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTT
23640635 CG
131 CG
*
23640637 ATCTGCTCCACTACTGCTTAGGGAGATAGGATCT---A----CAACCTACTCCGCTGCTGCTCAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAG
* *
23640695 AGAGACAAGGCTTTGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTT
66 GGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTT
*
23640760 TG
131 CG
* *
23640762 ATCTACTCCACTACTGCTTAGGGAGATAAGATCTACAATATTCAACCTACTCCGCTGCTGCTCAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAG
* *
23640827 GGAGACAATGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAATATAAGATTTGCCGTCTT
66 GGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTT
23640892 CG
131 CG
* *
23640894 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGTTGCTCAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAG
23640959 GGAGACAAGGCTTGGTG
66 GGAGACAAGGCTTGGTG
23640976 TTTCACCGAT
Statistics
Matches: 430, Mismatches: 34, Indels: 15
0.90 0.07 0.03
Matches are distributed among these distances:
125 116 0.27
128 1 0.00
129 1 0.00
132 297 0.69
133 15 0.03
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.30
Consensus pattern (132 bp):
ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAG
GGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTT
CG
Found at i:23640721 original size:257 final size:257
Alignment explanation
Indices: 23640410--23640931 Score: 918
Period size: 257 Copynumber: 2.0 Consensus size: 257
23640400 AATATTTGCC
* * *
23640410 ATCTTCAACCTACTCCGCTGCTGCTCAGGGAGATAAGGCTTGGTGGCTTAAATCTGCTTCCCACT
1 ATCTACAACCTACTCCGCTGCTGCTCAGAGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACT
* *
23640475 ATCTTGGAAAGATAAGATTTACCGTCTTTGATCTGCTCTACTACTGCTTAGGGAGATAAGATCTA
66 ATCTTGGAAAGATAAGATTTACCGTCTTTGATCTACTCCACTACTGCTTAGGGAGATAAGATCTA
* * *
23640540 CAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTTCCA
131 CAATATTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCA
* *
23640605 CTATCTTGGAAAGATAAGATTTGCTGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAGG
196 CTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAG
*
23640667 ATCTACAACCTACTCCGCTGCTGCTCAGAGAGACAAGGCTTTGTGGCTTAAATCTGCTTCCCACT
1 ATCTACAACCTACTCCGCTGCTGCTCAGAGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACT
*
23640732 ATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTACTCCACTACTGCTTAGGGAGATAAGATCTA
66 ATCTTGGAAAGATAAGATTTACCGTCTTTGATCTACTCCACTACTGCTTAGGGAGATAAGATCTA
*
23640797 CAATATTCAACCTACTCCGCTGCTGCTCAGGGAGACAATGCTTGGTGGCTTAAATCTGCTTCCCA
131 CAATATTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCA
*
23640862 CTATCTTGGAAATATAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAG
196 CTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAG
23640924 ATCTACAA
1 ATCTACAA
23640932 TCTTCAACCT
Statistics
Matches: 251, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
257 251 1.00
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.30
Consensus pattern (257 bp):
ATCTACAACCTACTCCGCTGCTGCTCAGAGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACT
ATCTTGGAAAGATAAGATTTACCGTCTTTGATCTACTCCACTACTGCTTAGGGAGATAAGATCTA
CAATATTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCA
CTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAG
Found at i:23642232 original size:11 final size:11
Alignment explanation
Indices: 23642200--23642234 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
23642190 CTCATTTTGC
23642200 TTTTCTTTTCCT
1 TTTTCTTTT-CT
23642212 TTTTC-TTTCT
1 TTTTCTTTTCT
23642222 TTTTCTTTTCT
1 TTTTCTTTTCT
23642233 TT
1 TT
23642235 CTTTCTCTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 7 0.32
11 10 0.45
12 5 0.23
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTCTTTTCT
Found at i:23642232 original size:15 final size:15
Alignment explanation
Indices: 23642201--23642256 Score: 60
Period size: 16 Copynumber: 3.6 Consensus size: 15
23642191 TCATTTTGCT
*
23642201 TTTCTTTTCCTTTTTC
1 TTTCTTTTTC-TTTTC
23642217 TTTCTTTTTCTTTTC
1 TTTCTTTTTCTTTTC
23642232 TTTCTTTCTCTCTTTT-
1 TTTCTTT-T-TCTTTTC
*
23642248 TTTGTTTTT
1 TTTCTTTTT
23642257 GAAAAATTTG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
14 1 0.03
15 13 0.36
16 16 0.44
17 6 0.17
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (15 bp):
TTTCTTTTTCTTTTC
Found at i:23642245 original size:27 final size:26
Alignment explanation
Indices: 23642194--23642256 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 26
23642184 TGGCCTCTCA
23642194 TTTTGCTTTTCTTTTCCTTTTTCTTT
1 TTTTGCTTTTCTTTTCCTTTTTCTTT
*
23642220 CTTTTTCTTTTC-TTT-CTTTCTCTCTTT
1 -TTTTGCTTTTCTTTTCCTTT-T-TCTTT
*
23642247 TTTTGTTTTT
1 TTTTGCTTTT
23642257 GAAAAATTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
25 4 0.13
26 12 0.39
27 15 0.48
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.78
Consensus pattern (26 bp):
TTTTGCTTTTCTTTTCCTTTTTCTTT
Found at i:23647521 original size:21 final size:21
Alignment explanation
Indices: 23647495--23647535 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
23647485 TTTCCCTCTC
23647495 TTGTAATTATCTAGTCATTTA
1 TTGTAATTATCTAGTCATTTA
23647516 TTGTAATTATCTAGTCATTT
1 TTGTAATTATCTAGTCATTT
23647536 CAAACCTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.10, G:0.10, T:0.54
Consensus pattern (21 bp):
TTGTAATTATCTAGTCATTTA
Found at i:23652407 original size:23 final size:24
Alignment explanation
Indices: 23652376--23652422 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
23652366 AAACATATGC
23652376 TCTTCTCTTCTTC-TTCTTCTTTT
1 TCTTCTCTTCTTCTTTCTTCTTTT
* * *
23652399 TCTTTTCTTTTTCTTTTTTCTTTT
1 TCTTCTCTTCTTCTTTCTTCTTTT
23652423 CTTGTTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (24 bp):
TCTTCTCTTCTTCTTTCTTCTTTT
Found at i:23652414 original size:11 final size:11
Alignment explanation
Indices: 23652376--23652425 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
23652366 AAACATATGC
* *
23652376 TCTTCTCTTCT
1 TCTTTTCTTTT
23652387 TCTTCTTCTTTT
1 TCTT-TTCTTTT
23652399 TCTTTTCTTTT
1 TCTTTTCTTTT
*
23652410 TCTTTTTTCTTT
1 TCTTTTCT-TTT
23652422 TCTT
1 TCTT
23652426 GTTTTTTCAC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
11 18 0.53
12 16 0.47
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (11 bp):
TCTTTTCTTTT
Found at i:23654661 original size:25 final size:25
Alignment explanation
Indices: 23654608--23654662 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
23654598 TAATTAGTAT
* * *
23654608 AAAATATTAATAATTCAATAAATTG
1 AAAATATTAATAATTAAATAAAATC
23654633 AAAA-ATTAAATAATTAAATAAAATC
1 AAAATATT-AATAATTAAATAAAATC
23654658 AAAAT
1 AAAAT
23654663 TTAGGAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
24 3 0.12
25 22 0.88
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.31
Consensus pattern (25 bp):
AAAATATTAATAATTAAATAAAATC
Found at i:23655428 original size:16 final size:15
Alignment explanation
Indices: 23655398--23655436 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
23655388 TATGCAAAGT
* *
23655398 TAATAATAATTAATA
1 TAATTATAATAAATA
23655413 TATATTATAATAAATA
1 TA-ATTATAATAAATA
23655429 TAATTATA
1 TAATTATA
23655437 TACTAGTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TAATTATAATAAATA
Found at i:23661180 original size:71 final size:71
Alignment explanation
Indices: 23661030--23661208 Score: 195
Period size: 71 Copynumber: 2.5 Consensus size: 71
23661020 TGAACTTTAT
** * *
23661030 TCGATGTTGCTCACTCAAGCTATTGAGAATCCACAA-AATGTGTTGGATCTCAGCTATCGATAAG
1 TCGATGTTGCTCACTCAAGCTATCAAGAATCCACAACAATGTGTTGAATCTCAGCCATCGATAA-
23661094 GTATAATG
65 G-ATAATG
* * * * *
23661102 -CGGTGTTGTTCACTCAAGCTATCAAGAATCCGCAACACT-TGTTGAATCTCAGCCATCGTTAA-
1 TCGATGTTGCTCACTCAAGCTATCAAGAATCCACAACAATGTGTTGAATCTCAGCCATCGATAAG
23661164 ATAATG
66 ATAATG
* *
23661170 ACTCGATGTTGCTCACTCAAGTTGTCAAGAATCCACAAC
1 --TCGATGTTGCTCACTCAAGCTATCAAGAATCCACAAC
23661209 TTAAGTTGTA
Statistics
Matches: 89, Mismatches: 14, Indels: 9
0.79 0.12 0.08
Matches are distributed among these distances:
68 6 0.07
71 81 0.91
72 2 0.02
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.29
Consensus pattern (71 bp):
TCGATGTTGCTCACTCAAGCTATCAAGAATCCACAACAATGTGTTGAATCTCAGCCATCGATAAG
ATAATG
Found at i:23663901 original size:28 final size:28
Alignment explanation
Indices: 23663849--23663902 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
23663839 TTCTTTTGGT
* *
23663849 ATTTTTGCCTAAAATATTTTTTTTAACA
1 ATTTTTCCCTAAAATATTTCTTTTAACA
23663877 ATTTTTCCCTAAAATCA-TTCTTTTAA
1 ATTTTTCCCTAAAAT-ATTTCTTTTAA
23663903 AAAATTGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 22 0.96
29 1 0.04
ACGTcount: A:0.31, C:0.15, G:0.02, T:0.52
Consensus pattern (28 bp):
ATTTTTCCCTAAAATATTTCTTTTAACA
Found at i:23663947 original size:13 final size:15
Alignment explanation
Indices: 23663929--23663974 Score: 51
Period size: 18 Copynumber: 3.0 Consensus size: 15
23663919 AAATAAACAC
23663929 AATA-TTTATAA-AA
1 AATATTTTATAATAA
23663942 AATATTTTATAATAAAA
1 AATATTTTATAAT--AA
23663959 TAATATTTTATAATAA
1 -AATATTTTATAATAA
23663975 GTTATGTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
13 4 0.14
14 7 0.25
16 2 0.07
17 2 0.07
18 13 0.46
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AATATTTTATAATAA
Found at i:23663965 original size:18 final size:17
Alignment explanation
Indices: 23663936--23663974 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 17
23663926 CACAATATTT
23663936 ATAAAAAATATTTTATA
1 ATAAAAAATATTTTATA
23663953 ATAAAATAATATTTTATA
1 ATAAAA-AATATTTTATA
23663971 ATAA
1 ATAA
23663975 GTTATGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATAAAAAATATTTTATA
Found at i:23670218 original size:25 final size:26
Alignment explanation
Indices: 23670190--23670239 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
23670180 CTCATTCATC
*
23670190 CTCTCTTTCTT-CGTTTTTAGTTTCT
1 CTCTCTTTCTTGCATTTTTAGTTTCT
*
23670215 CTCTCTTTCTTGCATTTTTTGTTTC
1 CTCTCTTTCTTGCATTTTTAGTTTC
23670240 AAACATTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 11 0.50
26 11 0.50
ACGTcount: A:0.04, C:0.24, G:0.08, T:0.64
Consensus pattern (26 bp):
CTCTCTTTCTTGCATTTTTAGTTTCT
Found at i:23671475 original size:29 final size:30
Alignment explanation
Indices: 23671438--23671494 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
23671428 TTCAAGCCTT
*
23671438 GGGGAAAAA-TATAATTATGCAAAAGTTTA
1 GGGGAAAAATTATAATTATGAAAAAGTTTA
* * *
23671467 GGGGTAAAATTGTAATTTTGAAAAAGTT
1 GGGGAAAAATTATAATTATGAAAAAGTT
23671495 AGAGTCGAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 8 0.35
30 15 0.65
ACGTcount: A:0.44, C:0.02, G:0.23, T:0.32
Consensus pattern (30 bp):
GGGGAAAAATTATAATTATGAAAAAGTTTA
Found at i:23671906 original size:50 final size:50
Alignment explanation
Indices: 23671831--23672073 Score: 351
Period size: 50 Copynumber: 4.8 Consensus size: 50
23671821 ATTTGGGTAA
* *
23671831 AGAGGTTCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGGTG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* *
23671881 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* *
23671931 AGAGGTCCCATGTAAGAGCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
23671981 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
23672031 AGTACATCCCATGTAAGACCATGTCTGGGTCATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
23672074 TGTCATTATC
Statistics
Matches: 173, Mismatches: 19, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
50 140 0.81
51 33 0.19
ACGTcount: A:0.24, C:0.23, G:0.32, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:23676368 original size:38 final size:39
Alignment explanation
Indices: 23676317--23676392 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 39
23676307 TAACATCTTT
*
23676317 TTTTTTCTTTATCTATTATTATAAA-TTCATTAAAACTA
1 TTTTTTCTTTATCTATTATTATAAACATCATTAAAACTA
*
23676355 TTTTTTCTTTATCTATTGTTATAAACATCATTAAAACT
1 TTTTTTCTTTATCTATTATTATAAACATCATTAAAACT
23676393 TAAGGGAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
38 24 0.69
39 11 0.31
ACGTcount: A:0.33, C:0.12, G:0.01, T:0.54
Consensus pattern (39 bp):
TTTTTTCTTTATCTATTATTATAAACATCATTAAAACTA
Found at i:23680714 original size:19 final size:19
Alignment explanation
Indices: 23680690--23680726 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
23680680 ATTAAGATAT
23680690 AAATAATAAAAAATTATGA
1 AAATAATAAAAAATTATGA
23680709 AAATAATAAAAAATTATG
1 AAATAATAAAAAATTATG
23680727 TAACGCCCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (19 bp):
AAATAATAAAAAATTATGA
Found at i:23687656 original size:20 final size:20
Alignment explanation
Indices: 23687612--23687739 Score: 96
Period size: 20 Copynumber: 6.3 Consensus size: 20
23687602 ACCACACCAA
* * *
23687612 AGGCATCAAAGATGCATACAA
1 AGGCACCAAAG-TGCAAACAG
*
23687633 AGGCACCGAAGTGCAAACAG
1 AGGCACCAAAGTGCAAACAG
* *
23687653 AGGCA-AAAATGTGCAATCAG
1 AGGCACCAAA-GTGCAAACAG
* *
23687673 AGGCACCAGAGTGCAAATAG
1 AGGCACCAAAGTGCAAACAG
** ***
23687693 AAACACCAAAGTGTTTACAG
1 AGGCACCAAAGTGCAAACAG
*
23687713 AGGCACCAAAGTGCAAATAG
1 AGGCACCAAAGTGCAAACAG
*
23687733 AAGCACC
1 AGGCACC
23687740 GTAGTGCAAT
Statistics
Matches: 80, Mismatches: 25, Indels: 5
0.73 0.23 0.05
Matches are distributed among these distances:
19 2 0.03
20 67 0.84
21 11 0.14
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (20 bp):
AGGCACCAAAGTGCAAACAG
Found at i:23693835 original size:19 final size:19
Alignment explanation
Indices: 23693811--23693849 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
23693801 CAGGAAGAAA
23693811 TATGTTAGTCAGTGGTATC
1 TATGTTAGTCAGTGGTATC
23693830 TATGTTAGTCAGTGGTATC
1 TATGTTAGTCAGTGGTATC
23693849 T
1 T
23693850 CGACAAAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.21, C:0.10, G:0.26, T:0.44
Consensus pattern (19 bp):
TATGTTAGTCAGTGGTATC
Found at i:23704922 original size:52 final size:52
Alignment explanation
Indices: 23704865--23704965 Score: 143
Period size: 52 Copynumber: 1.9 Consensus size: 52
23704855 ACCAACTAGT
* *
23704865 AAAATATTCATAAAAATGAAACAAAAACTG-T-AGGACTTAAAACTAAAAATAA
1 AAAATATTCACAAAAATAAAACAAAAA-TGATAAGG-CTTAAAACTAAAAATAA
*
23704917 AAAATATTCACCAAAATAAAACAAAAATGATAAGGCTTAAAACTAAAAA
1 AAAATATTCACAAAAATAAAACAAAAATGATAAGGCTTAAAACTAAAAA
23704966 ATGAAACAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
51 2 0.05
52 39 0.89
53 3 0.07
ACGTcount: A:0.62, C:0.11, G:0.07, T:0.20
Consensus pattern (52 bp):
AAAATATTCACAAAAATAAAACAAAAATGATAAGGCTTAAAACTAAAAATAA
Found at i:23704973 original size:34 final size:34
Alignment explanation
Indices: 23704929--23705056 Score: 114
Period size: 34 Copynumber: 3.7 Consensus size: 34
23704919 AATATTCACC
* *
23704929 AAAATAAAACAAAAATGATAAGGCTTAAAACTAA
1 AAAATAAAACAAAAATAATAAGACTTAAAACTAA
* *
23704963 AAAATGAAACAAAAATAATAAGACTTAAAACTCTA
1 AAAATAAAACAAAAATAATAAGACTTAAAACT-AA
* ** ** *
23704998 ACAGCAGAAACACTACTAATAAGACTTAAAACTAA
1 AAAATA-AAACAAAAATAATAAGACTTAAAACTAA
* *
23705033 AAAATGGAAA-AAAAATTATAAGAC
1 AAAAT-AAAACAAAAATAATAAGAC
23705057 CTATAATTAA
Statistics
Matches: 71, Mismatches: 20, Indels: 6
0.73 0.21 0.06
Matches are distributed among these distances:
34 39 0.55
35 9 0.13
36 23 0.32
ACGTcount: A:0.62, C:0.12, G:0.09, T:0.18
Consensus pattern (34 bp):
AAAATAAAACAAAAATAATAAGACTTAAAACTAA
Found at i:23705093 original size:40 final size:41
Alignment explanation
Indices: 23705043--23705128 Score: 111
Period size: 40 Copynumber: 2.1 Consensus size: 41
23705033 AAAATGGAAA
* *
23705043 AAAAATTATAAGACCTATAATTAATAATACAAAATATTCAC
1 AAAAATTATAAAACCTATAATTAACAATACAAAATATTCAC
** * *
23705084 AAAAA-TATAAAATTTATAATTAACACTACAAAATATTTAC
1 AAAAATTATAAAACCTATAATTAACAATACAAAATATTCAC
23705124 AAAAA
1 AAAAA
23705129 ATCAGATAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
40 34 0.87
41 5 0.13
ACGTcount: A:0.59, C:0.10, G:0.01, T:0.29
Consensus pattern (41 bp):
AAAAATTATAAAACCTATAATTAACAATACAAAATATTCAC
Found at i:23707359 original size:2 final size:2
Alignment explanation
Indices: 23707352--23707405 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
23707342 ACAATTATGA
*
23707352 AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23707394 AT AT AT AT AT AT
1 AT AT AT AT AT AT
23707406 TTCAATGTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:23712830 original size:16 final size:16
Alignment explanation
Indices: 23712811--23712860 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
23712801 GAGAGAATGG
23712811 AAAAAGAAAAGAAAAA
1 AAAAAGAAAAGAAAAA
* *
23712827 AAAAAGTAAAGTTAAAA
1 AAAAAGAAAAG-AAAAA
*
23712844 AAACAGAAAAGAAAAA
1 AAAAAGAAAAGAAAAA
23712860 A
1 A
23712861 TTTAAATTGC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
16 15 0.54
17 13 0.46
ACGTcount: A:0.80, C:0.02, G:0.12, T:0.06
Consensus pattern (16 bp):
AAAAAGAAAAGAAAAA
Found at i:23712854 original size:17 final size:15
Alignment explanation
Indices: 23712811--23712860 Score: 55
Period size: 17 Copynumber: 3.1 Consensus size: 15
23712801 GAGAGAATGG
23712811 AAAAAGAAAAGAAAAA
1 AAAAAGAAAAG-AAAA
*
23712827 AAAAAGTAAAGTTAAAA
1 AAAAAGAAAAG--AAAA
*
23712844 AAACAGAAAAGAAAA
1 AAAAAGAAAAGAAAA
23712859 AA
1 AA
23712861 TTTAAATTGC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 6 0.21
16 10 0.34
17 13 0.45
ACGTcount: A:0.80, C:0.02, G:0.12, T:0.06
Consensus pattern (15 bp):
AAAAAGAAAAGAAAA
Found at i:23716374 original size:32 final size:32
Alignment explanation
Indices: 23716333--23716395 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
23716323 ACACAATTAT
*
23716333 ATGCTAGTTTTCTCAACTTTAAAGATCTCCCA
1 ATGCTAGTTTTATCAACTTTAAAGATCTCCCA
*
23716365 ATGCTAGTTTTATCAATTTTAAAGATCTCCC
1 ATGCTAGTTTTATCAACTTTAAAGATCTCCC
23716396 GTGTACATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.40
Consensus pattern (32 bp):
ATGCTAGTTTTATCAACTTTAAAGATCTCCCA
Found at i:23720476 original size:34 final size:32
Alignment explanation
Indices: 23720428--23720510 Score: 87
Period size: 33 Copynumber: 2.5 Consensus size: 32
23720418 AGAAACTATG
* * *
23720428 ATTTCTAACACATATTCTAAGTCTATATTG-ACCA
1 ATTTCTAACTCATATTCT-A-TATAT-TTGAACAA
*
23720462 ATTTCTAACTCATATTTCTATATGTTTGAACAA
1 ATTTCTAACTCATA-TTCTATATATTTGAACAA
23720495 ATTTCTAACTCATATT
1 ATTTCTAACTCATATT
23720511 TCAATATCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
32 5 0.12
33 20 0.47
34 14 0.33
35 4 0.09
ACGTcount: A:0.34, C:0.18, G:0.05, T:0.43
Consensus pattern (32 bp):
ATTTCTAACTCATATTCTATATATTTGAACAA
Found at i:23721130 original size:18 final size:18
Alignment explanation
Indices: 23721099--23721146 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
23721089 TGTTGTTCGT
*
23721099 TTTCAAAACATTATTC-A
1 TTTCAAAACGTTATTCAA
*
23721116 TTTACAAATCGTTATTCAA
1 TTT-CAAAACGTTATTCAA
23721135 TTTCAAAACGTT
1 TTTCAAAACGTT
23721147 TTCTTATTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 3 0.12
18 19 0.73
19 4 0.15
ACGTcount: A:0.38, C:0.17, G:0.04, T:0.42
Consensus pattern (18 bp):
TTTCAAAACGTTATTCAA
Found at i:23730782 original size:24 final size:24
Alignment explanation
Indices: 23730750--23730798 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
23730740 ATTTGTTGAG
23730750 TATGACTCCTATTTCAGTCAAATT
1 TATGACTCCTATTTCAGTCAAATT
23730774 TATGACTCCTATTTCAGTCAAATT
1 TATGACTCCTATTTCAGTCAAATT
23730798 T
1 T
23730799 GAGAAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.29, C:0.20, G:0.08, T:0.43
Consensus pattern (24 bp):
TATGACTCCTATTTCAGTCAAATT
Found at i:23738080 original size:19 final size:19
Alignment explanation
Indices: 23738056--23738094 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
23738046 AAAAACAAAT
23738056 TAACATAAATGATCTAAAA
1 TAACATAAATGATCTAAAA
*
23738075 TAACATAAATTATCTAAAA
1 TAACATAAATGATCTAAAA
23738094 T
1 T
23738095 TAAGACAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.56, C:0.10, G:0.03, T:0.31
Consensus pattern (19 bp):
TAACATAAATGATCTAAAA
Found at i:23746874 original size:20 final size:20
Alignment explanation
Indices: 23746851--23746920 Score: 63
Period size: 20 Copynumber: 3.3 Consensus size: 20
23746841 TCAAAAAGGG
23746851 AAATAATAAAAAGAAAACTT
1 AAATAATAAAAAGAAAACTT
23746871 AAATAAATGAAATAA-ATAAGACATT
1 AAAT-AAT-AAA-AAGA-AA-AC-TT
*
23746896 -GATAATAAAAAGAAAACTT
1 AAATAATAAAAAGAAAACTT
23746915 AAATAA
1 AAATAA
23746921 ATGAAATAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 16
0.69 0.03 0.28
Matches are distributed among these distances:
19 2 0.05
20 10 0.25
21 7 0.17
22 8 0.20
23 7 0.17
24 4 0.10
25 2 0.05
ACGTcount: A:0.67, C:0.04, G:0.07, T:0.21
Consensus pattern (20 bp):
AAATAATAAAAAGAAAACTT
Found at i:23746903 original size:44 final size:44
Alignment explanation
Indices: 23746853--23746941 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
23746843 AAAAAGGGAA
23746853 ATAATAAAAAGAAAACTTAAATAAATGAAATAAATAAGACATTG
1 ATAATAAAAAGAAAACTTAAATAAATGAAATAAATAAGACATTG
23746897 ATAATAAAAAGAAAACTTAAATAAATGAAATAAATAAGACATTG
1 ATAATAAAAAGAAAACTTAAATAAATGAAATAAATAAGACATTG
23746941 A
1 A
23746942 CATGATGATG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.64, C:0.04, G:0.09, T:0.22
Consensus pattern (44 bp):
ATAATAAAAAGAAAACTTAAATAAATGAAATAAATAAGACATTG
Found at i:23748184 original size:146 final size:146
Alignment explanation
Indices: 23747678--23748271 Score: 814
Period size: 146 Copynumber: 4.1 Consensus size: 146
23747668 CAAAGTTTTC
* * *
23747678 TTTAGAAAAATCACTACTTTTCTTAAAAATCAAAACTTTATTTCGAAATAGTTGAAAAAGATCAA
1 TTTAAAAAAATCACTATTTTTCTTAAAAATCAAAACTTTATTTCGAAATAGTTGAAAAAGATAAA
* * *
23747743 ATTTTGTTTTAAAATTTTAAACTTTTCATTTAAAATGACTAAAAAATATATTTTTATTTTTAAAA
66 ATTTTGTTTTAAAATTGTAAACTTTTCCTTTAAAATGACTAAAAAATAGATTTTTATTTTTAAAA
23747808 ATCTAAACTTTCTC-T
131 ATCTAAACTTTCTCTT
* * * * *
23747823 TTTAAAAAAATCACTCTTTTTATTAAAAATCAAAATTTTATTTCGAAATAGTTGAAAAACAT-CA
1 TTTAAAAAAATCACTATTTTTCTTAAAAATCAAAACTTTATTTCGAAATAGTTGAAAAAGATAAA
*
23747887 ATTTT-TTTT--AATT-TAATA-TTTTCCTTTAAAATGACTAAAAACAT--CTTTTTATTTTTAA
66 ATTTTGTTTTAAAATTGTAA-ACTTTTCCTTTAAAATGACTAAAAA-ATAGATTTTTATTTTTAA
23747945 AAATCTAAACTTTCTCTT
129 AAATCTAAACTTTCTCTT
* * *
23747963 TTAAAAAAAATAATCACTATTTTTCTTAAAAATCAAAGCTTTATTTTGAAATAGTTGAAAAAGAT
1 TT--TAAAAA-AATCACTATTTTTCTTAAAAATCAAAACTTTATTTCGAAATAGTTGAAAAAGAT
*
23748028 CAAAATTTTGTTTTAAAATTGTAAACATTTCCTTTAAAATGACTAAAAACA-A-ATTTTTATTTT
63 -AAAATTTTGTTTTAAAATTGTAAACTTTTCCTTTAAAATGACTAAAAA-ATAGATTTTTATTTT
* *
23748091 TAAAAATATAAAATTTCTCTT
126 TAAAAATCTAAACTTTCTCTT
23748112 TTTAAAAAAATCACTATTTTTCTTAAAAATCAAAACTTTATTTCGAAATAGTTGAAAAAGATTAA
1 TTTAAAAAAATCACTATTTTTCTTAAAAATCAAAACTTTATTTCGAAATAGTTGAAAAAGA-TAA
* * * *
23748177 AACTTTGTTTTAAAAATGTAAGCCTTTCCTTTAAAATGACTAAAGAAATAGATTTTTATTTTTAA
65 AATTTTGTTTTAAAATTGTAAACTTTTCCTTTAAAATGACTAAA-AAATAGATTTTTATTTTTAA
23748242 AAATCTAAACTTTCTCTTT
129 AAATCTAAACTTTCTC-TT
23748261 TTTGAAAAAAA
1 TTT-AAAAAAA
23748272 AAATCAAAAA
Statistics
Matches: 399, Mismatches: 30, Indels: 35
0.86 0.06 0.08
Matches are distributed among these distances:
139 29 0.07
140 28 0.07
141 7 0.02
142 5 0.01
143 52 0.13
144 6 0.02
145 62 0.16
146 98 0.25
147 9 0.02
148 33 0.08
149 63 0.16
150 7 0.02
ACGTcount: A:0.43, C:0.10, G:0.05, T:0.42
Consensus pattern (146 bp):
TTTAAAAAAATCACTATTTTTCTTAAAAATCAAAACTTTATTTCGAAATAGTTGAAAAAGATAAA
ATTTTGTTTTAAAATTGTAAACTTTTCCTTTAAAATGACTAAAAAATAGATTTTTATTTTTAAAA
ATCTAAACTTTCTCTT
Found at i:23748601 original size:3 final size:3
Alignment explanation
Indices: 23748595--23748658 Score: 56
Period size: 3 Copynumber: 21.0 Consensus size: 3
23748585 TAAAGAAAAA
* * * * * *
23748595 AAT AAT AAT GAT ATTT AAT AAT AAT AAT AAT AGT AGT AGT AGT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
23748641 GAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT
23748659 TTGGGCCTTT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
3 50 0.96
4 2 0.04
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:23749171 original size:42 final size:42
Alignment explanation
Indices: 23749111--23749285 Score: 244
Period size: 42 Copynumber: 4.2 Consensus size: 42
23749101 ATATACACTA
* *
23749111 CAATTAAAAGTAAATGGACCTCCACATCT-GGCCTTCTAAATG
1 CAATGAAAAGTAAATGGACCTCCACACCTGGGCC-TCTAAATG
* *
23749153 CAATGAAAGGTAAATGGACCTCCACACCTGGGCCTTTAAATG
1 CAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATG
*
23749195 CAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATA
1 CAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATG
* ** *
23749237 CAATGAAAAGTAAGTGGACCTCCACATTTGGGCCCCTAAATG
1 CAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATG
*
23749279 TAATGAA
1 CAATGAA
23749286 TGCTTTCCTT
Statistics
Matches: 119, Mismatches: 13, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
42 115 0.97
43 4 0.03
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.22
Consensus pattern (42 bp):
CAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATG
Found at i:23749677 original size:2 final size:2
Alignment explanation
Indices: 23749670--23749713 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
23749660 AATTTAGTTC
23749670 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
23749712 CT
1 CT
23749714 GTTGTTGTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:23760589 original size:16 final size:15
Alignment explanation
Indices: 23760570--23760608 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
23760560 CGTTCTCCTC
23760570 TTTCTTTTTCTTTTGT
1 TTTCTTTTTCTTTT-T
*
23760586 TTTCTTTTTGTTTTT
1 TTTCTTTTTCTTTTT
23760601 TCTTCTTT
1 T-TTCTTT
23760609 CCTTTTTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 2 0.10
16 19 0.90
ACGTcount: A:0.00, C:0.13, G:0.05, T:0.82
Consensus pattern (15 bp):
TTTCTTTTTCTTTTT
Found at i:23765430 original size:151 final size:149
Alignment explanation
Indices: 23765125--23765454 Score: 455
Period size: 151 Copynumber: 2.2 Consensus size: 149
23765115 AAAATCAAAA
* * * * * *
23765125 TTTTCTTTAAAAAATCACTACTTTTGTTAAAATTCAGAGCTTTATTTCGAAATAGTTGAAAAGGA
1 TTTTTTTTAAAAAATCACTACTTTTCTTAAAAATCAAAACTTTATTTCGAAATAGTTGAAAACGA
* *
23765190 TCAAAACTTTGTTTTAGAATTTTAAACTTTTCCTTTAAATGACTAAAAATCATATTTTTATTTTT
66 TCAAAACTTTGTTTTAGAAATTTAAACTTTTCCTTTAAATGACTAAAAAACATATTTTTATTTTT
23765255 AAAAATCTAAACTTTCTCTT
131 AAAAATCTAAACTTTCTC-T
* *
23765275 TTTTTTTTAAAAAAATCGCTATTTTTCTTAAAAATCAAAACTTTATTTCGAAATAGTTGAAAACG
1 TTTTTTTT-AAAAAATCACTACTTTTCTTAAAAATCAAAACTTTATTTCGAAATAGTTGAAAACG
* *
23765340 ATCAATACTTTGTTTT-GAAAATTTAAACTTTTTCTTTTAAAATGACTAAAAAACATATTTTTAT
65 ATCAAAACTTTGTTTTAG-AAATTTAAAC-TTTTCCTTT-AAATGACTAAAAAACATATTTTTAT
23765404 TTTTAAAAATCTAAACTTTCTCT
127 TTTTAAAAATCTAAACTTTCTCT
** **
23765427 TTTTTGAATAAAAAATCAAAACTTTTCT
1 TTTTT-TTTAAAAAATCACTACTTTTCT
23765455 CAAGATCAAG
Statistics
Matches: 157, Mismatches: 18, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
150 8 0.05
151 73 0.46
152 29 0.18
153 47 0.30
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.45
Consensus pattern (149 bp):
TTTTTTTTAAAAAATCACTACTTTTCTTAAAAATCAAAACTTTATTTCGAAATAGTTGAAAACGA
TCAAAACTTTGTTTTAGAAATTTAAACTTTTCCTTTAAATGACTAAAAAACATATTTTTATTTTT
AAAAATCTAAACTTTCTCT
Found at i:23768853 original size:22 final size:22
Alignment explanation
Indices: 23768823--23768865 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
23768813 ACACCAAAAC
*
23768823 AGGCTTTTAGCGGCGCTTTTTT
1 AGGCCTTTAGCGGCGCTTTTTT
23768845 AGGCCTTTAGCGGCGCTTTTT
1 AGGCCTTTAGCGGCGCTTTTT
23768866 AGCGCCGCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.09, C:0.21, G:0.28, T:0.42
Consensus pattern (22 bp):
AGGCCTTTAGCGGCGCTTTTTT
Done.