Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A10
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: 110302803
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1825971 characters in sequence are not A, C, G, or T
File 2 of 343
Found at i:439742 original size:15 final size:16
Alignment explanation
Indices: 439722--439758 Score: 67
Period size: 15 Copynumber: 2.4 Consensus size: 16
439712 GGTACTTGAT
439722 GAATAATGAAGAATC-
1 GAATAATGAAGAATCG
439737 GAATAATGAAGAATCG
1 GAATAATGAAGAATCG
439753 GAATAA
1 GAATAA
439759 CATAGACCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.54, C:0.05, G:0.22, T:0.19
Consensus pattern (16 bp):
GAATAATGAAGAATCG
Found at i:442474 original size:11 final size:11
Alignment explanation
Indices: 442390--442496 Score: 60
Period size: 11 Copynumber: 9.8 Consensus size: 11
442380 GCAACTTAAC
442390 AATAAAATACAT
1 AATAAAATA-AT
* *
442402 -TTAAAATAGT
1 AATAAAATAAT
* *
442412 AGTAAAATCAAC
1 AATAAAAT-AAT
442424 AATAAAATAAT
1 AATAAAATAAT
* * *
442435 AATTATACAAT
1 AATAAAATAAT
*
442446 -ATCTAAATAAT
1 AAT-AAAATAAT
442457 AAT--AATAAT
1 AATAAAATAAT
442466 AATAAAATAAT
1 AATAAAATAAT
** *
442477 AGCAACATAAT
1 AATAAAATAAT
442488 AATAAAATA
1 AATAAAATA
442497 TACTAAACAA
Statistics
Matches: 71, Mismatches: 18, Indels: 13
0.70 0.18 0.13
Matches are distributed among these distances:
9 9 0.13
10 3 0.04
11 49 0.69
12 10 0.14
ACGTcount: A:0.63, C:0.07, G:0.03, T:0.28
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:443230 original size:60 final size:60
Alignment explanation
Indices: 443152--443304 Score: 150
Period size: 60 Copynumber: 2.5 Consensus size: 60
443142 ATTAAATGTG
* ** * *
443152 CCAATTTAAATCAAAAAGCCAAGTTT-AGGTACCGAATCAAACCAAAA-TAAACTTTAGATA
1 CCAAATTAAATCTTAAAGCCAA-TTTCAAGTACCGAATCAAA-CAAAAGAAAACTTTAGATA
* * * *
443212 TCAAATTAAATCTTAAAGCCAATTTCAAGTACCTAATTAGACAAAAGAAAACTTTAGATA
1 CCAAATTAAATCTTAAAGCCAATTTCAAGTACCGAATCAAACAAAAGAAAACTTTAGATA
* * *
443272 CCAATTTAAA-CTTTAAAGCCAAATACAAGTACC
1 CCAAATTAAATC-TTAAAGCCAATTTCAAGTACC
443305 AAAATGTATA
Statistics
Matches: 77, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
59 9 0.12
60 68 0.88
ACGTcount: A:0.48, C:0.18, G:0.08, T:0.25
Consensus pattern (60 bp):
CCAAATTAAATCTTAAAGCCAATTTCAAGTACCGAATCAAACAAAAGAAAACTTTAGATA
Found at i:445763 original size:34 final size:34
Alignment explanation
Indices: 445715--445780 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
445705 ATCTTATCTG
* *
445715 GCATTATCAATGGTGATTTAATGTTTTTTTTTTA
1 GCATGATCAATGGTGATTTAATGTTGTTTTTTTA
445749 GCATGATCAATGGTGATTTAATGTTGTTTTTT
1 GCATGATCAATGGTGATTTAATGTTGTTTTTT
445781 CCACCCTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.23, C:0.06, G:0.18, T:0.53
Consensus pattern (34 bp):
GCATGATCAATGGTGATTTAATGTTGTTTTTTTA
Found at i:448714 original size:16 final size:16
Alignment explanation
Indices: 448693--448732 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
448683 AGAAAGTCTT
448693 TTTAAAAATAAATTTA
1 TTTAAAAATAAATTTA
**
448709 TTT-AAAATATTTTTA
1 TTTAAAAATAAATTTA
448724 TTTAAAAAT
1 TTTAAAAAT
448733 TTGGTAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTTAAAAATAAATTTA
Found at i:457558 original size:35 final size:35
Alignment explanation
Indices: 457519--457589 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
457509 TTAAAAAATA
457519 ATTAAAATTTAGAAAAATTTTAAAAAAACCAGTTC
1 ATTAAAATTTAGAAAAATTTTAAAAAAACCAGTTC
*
457554 ATTAAAATTTAGAAAAATTTTAAAAAAATCAGTTC
1 ATTAAAATTTAGAAAAATTTTAAAAAAACCAGTTC
457589 A
1 A
457590 ATCGGTTCCA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.55, C:0.07, G:0.06, T:0.32
Consensus pattern (35 bp):
ATTAAAATTTAGAAAAATTTTAAAAAAACCAGTTC
Found at i:461044 original size:19 final size:19
Alignment explanation
Indices: 461020--461057 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
461010 ACCCTGATTG
*
461020 TCTTCCACAAATGTTTTGA
1 TCTTCCACAAATGTCTTGA
*
461039 TCTTCCACGAATGTCTTGA
1 TCTTCCACAAATGTCTTGA
461058 CATTAGGCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.13, T:0.39
Consensus pattern (19 bp):
TCTTCCACAAATGTCTTGA
Found at i:473196 original size:12 final size:12
Alignment explanation
Indices: 473179--473203 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
473169 AGCAAACCAG
473179 GAAATTTGCTTC
1 GAAATTTGCTTC
473191 GAAATTTGCTTC
1 GAAATTTGCTTC
473203 G
1 G
473204 TAAAAAGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (12 bp):
GAAATTTGCTTC
Found at i:490614 original size:11 final size:11
Alignment explanation
Indices: 490598--490630 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
490588 ATTTTAAATA
490598 ATTTAATAATT
1 ATTTAATAATT
490609 ATTTAATAATT
1 ATTTAATAATT
*
490620 TTTTAA-AATT
1 ATTTAATAATT
490630 A
1 A
490631 AGTGACTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 4 0.20
11 16 0.80
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
ATTTAATAATT
Found at i:495096 original size:22 final size:22
Alignment explanation
Indices: 495080--495125 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
495070 TATAAGTACA
495080 ATTAGGATTAATAATAAATAAT
1 ATTAGGATTAATAATAAATAAT
495102 ATTAGGATTAATAATAAATAAT
1 ATTAGGATTAATAATAAATAAT
495124 AT
1 AT
495126 ATATTTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.37
Consensus pattern (22 bp):
ATTAGGATTAATAATAAATAAT
Found at i:495145 original size:15 final size:16
Alignment explanation
Indices: 495115--495160 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
495105 AGGATTAATA
495115 ATAAATAA-TATATATT
1 ATAAATAATTAT-TATT
495131 -TAAATAATTATTATT
1 ATAAATAATTATTATT
* *
495146 ATAATTAATCATTAT
1 ATAAATAATTATTAT
495161 AAAAGACGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 11 0.42
16 15 0.58
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (16 bp):
ATAAATAATTATTATT
Found at i:495349 original size:30 final size:31
Alignment explanation
Indices: 495309--495370 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
495299 TATTAAATTC
* * *
495309 AAATTTAATAATTTAGTGAC-TTAAATAAAA
1 AAATTAAATAATTCAATGACTTTAAATAAAA
*
495339 AAATTAAATAATTCAATGACTTTAAATGAAA
1 AAATTAAATAATTCAATGACTTTAAATAAAA
495370 A
1 A
495371 TCTTCAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 17 0.63
31 10 0.37
ACGTcount: A:0.55, C:0.05, G:0.06, T:0.34
Consensus pattern (31 bp):
AAATTAAATAATTCAATGACTTTAAATAAAA
Found at i:502873 original size:23 final size:22
Alignment explanation
Indices: 502830--502873 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
502820 TTCAATTGTT
* **
502830 TTTTTTTTGGTGATATTGTTTG
1 TTTTTTTTGGTGAGAAAGTTTG
502852 TTTTTTTTGGTTGAGAAAGTTT
1 TTTTTTTTGG-TGAGAAAGTTT
502874 TGATATTTGG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.14, C:0.00, G:0.23, T:0.64
Consensus pattern (22 bp):
TTTTTTTTGGTGAGAAAGTTTG
Found at i:510088 original size:45 final size:45
Alignment explanation
Indices: 510024--510113 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
510014 AAAAAAAGGT
510024 GAGGAATGATATAGTAAATTTCTTTAAATTGTTCTTCATGAGTTA
1 GAGGAATGATATAGTAAATTTCTTTAAATTGTTCTTCATGAGTTA
510069 GAGGAATGATATAGTAAATTTCTTTAAATTGTTCTTCATGAGTTA
1 GAGGAATGATATAGTAAATTTCTTTAAATTGTTCTTCATGAGTTA
510114 ATATTTAGGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.42
Consensus pattern (45 bp):
GAGGAATGATATAGTAAATTTCTTTAAATTGTTCTTCATGAGTTA
Found at i:518137 original size:3 final size:3
Alignment explanation
Indices: 518129--518167 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
518119 TTTAGGGAAC
*
518129 TAT TAT TAT TAT TAT TAT TAT TAT TGT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
518168 CAGGGGCGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:520715 original size:16 final size:16
Alignment explanation
Indices: 520694--520725 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
520684 ACCAAGGAGA
*
520694 AATTCATGCACGTAAG
1 AATTCATGCACATAAG
520710 AATTCATGCACATAAG
1 AATTCATGCACATAAG
520726 TTATGCTGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.25
Consensus pattern (16 bp):
AATTCATGCACATAAG
Found at i:535307 original size:12 final size:12
Alignment explanation
Indices: 535290--535314 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
535280 GGTGTTCAGT
535290 CGGTTAACCGAC
1 CGGTTAACCGAC
535302 CGGTTAACCGAC
1 CGGTTAACCGAC
535314 C
1 C
535315 CGAAATTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:535489 original size:9 final size:9
Alignment explanation
Indices: 535475--535584 Score: 157
Period size: 9 Copynumber: 11.6 Consensus size: 9
535465 TTTGGTTAAA
535475 AATTACCCG
1 AATTACCCG
535484 AATTACCCG
1 AATTACCCG
535493 AATTACCCG
1 AATTACCCG
*
535502 ACTTACCCG
1 AATTACCCG
535511 AATTACCCG
1 AATTACCCG
535520 AATTACCCG
1 AATTACCCG
535529 AAAATTACCCG
1 --AATTACCCG
535540 AAAATTACCCG
1 --AATTACCCG
535551 AATTACCCG
1 AATTACCCG
535560 AAAATTACCCG
1 --AATTACCCG
535571 AATTACCCG
1 AATTACCCG
535580 AATTA
1 AATTA
535585 AATCACTACA
Statistics
Matches: 95, Mismatches: 2, Indels: 8
0.90 0.02 0.08
Matches are distributed among these distances:
9 66 0.69
11 29 0.31
ACGTcount: A:0.37, C:0.31, G:0.10, T:0.22
Consensus pattern (9 bp):
AATTACCCG
Found at i:535613 original size:17 final size:17
Alignment explanation
Indices: 535591--535651 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
535581 ATTAAATCAC
535591 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
** * *
535608 TACATAAATCTTTGAATCAC
1 TACAT-AA--TTAAAAACAT
*
535628 TACATAATTAAAAATAT
1 TACATAATTAAAAACAT
535645 TACATAA
1 TACATAA
535652 GTCTTTGAAT
Statistics
Matches: 32, Mismatches: 9, Indels: 6
0.68 0.19 0.13
Matches are distributed among these distances:
17 17 0.53
18 2 0.06
19 2 0.06
20 11 0.34
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (17 bp):
TACATAATTAAAAACAT
Found at i:535633 original size:20 final size:20
Alignment explanation
Indices: 535608--535671 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 20
535598 TTAAAAACAT
535608 TACATAAATCTTTGAATCAC
1 TACATAAATCTTTGAATCAC
*** *
535628 TACAT-AAT-TAAAAAT-AT
1 TACATAAATCTTTGAATCAC
*
535645 TACATAAGTCTTTGAATCAC
1 TACATAAATCTTTGAATCAC
535665 TACATAA
1 TACATAA
535672 TTAAAAATAT
Statistics
Matches: 32, Mismatches: 9, Indels: 6
0.68 0.19 0.13
Matches are distributed among these distances:
17 6 0.19
18 6 0.19
19 7 0.22
20 13 0.41
ACGTcount: A:0.45, C:0.16, G:0.05, T:0.34
Consensus pattern (20 bp):
TACATAAATCTTTGAATCAC
Found at i:535691 original size:37 final size:37
Alignment explanation
Indices: 535585--535697 Score: 192
Period size: 37 Copynumber: 3.1 Consensus size: 37
535575 ACCCGAATTA
* *
535585 AATCACTACATAATTAAAAACATTACATAAATCTTTG
1 AATCACTACATAATTAAAAATATTACATAAGTCTTTG
535622 AATCACTACATAATTAAAAATATTACATAAGTCTTTG
1 AATCACTACATAATTAAAAATATTACATAAGTCTTTG
*
535659 AATCACTACATAATTAAAAATATTACACAAGTC-TTG
1 AATCACTACATAATTAAAAATATTACATAAGTCTTTG
535695 AAT
1 AAT
535698 TAAAACATAA
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
36 6 0.08
37 67 0.92
ACGTcount: A:0.48, C:0.15, G:0.04, T:0.33
Consensus pattern (37 bp):
AATCACTACATAATTAAAAATATTACATAAGTCTTTG
Found at i:535765 original size:24 final size:24
Alignment explanation
Indices: 535738--535796 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
535728 ATTCTCCATT
*
535738 TATATCCATTTCATCTTTCCAAAA
1 TATATCCATTTCATCTCTCCAAAA
*
535762 TATATTCATTTCATCTCTCCAAAA
1 TATATCCATTTCATCTCTCCAAAA
*
535786 TATCTCCATTT
1 TATATCCATTT
535797 GCATTAAACC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.31, C:0.25, G:0.00, T:0.44
Consensus pattern (24 bp):
TATATCCATTTCATCTCTCCAAAA
Found at i:538879 original size:16 final size:16
Alignment explanation
Indices: 538858--538891 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
538848 TTTTTTTTCT
*
538858 TACATTAATTATAATA
1 TACATTAATTACAATA
538874 TACATTAATTACAATA
1 TACATTAATTACAATA
538890 TA
1 TA
538892 TTCAATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (16 bp):
TACATTAATTACAATA
Found at i:539813 original size:16 final size:17
Alignment explanation
Indices: 539792--539832 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
539782 GCCTAAGAGA
539792 AAATTGGGCT-GGATTT
1 AAATTGGGCTGGGATTT
*
539808 AAATTGGGCTGGGTTTT
1 AAATTGGGCTGGGATTT
539825 AAATTGGG
1 AAATTGGG
539833 AGGGAGTAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.24, C:0.05, G:0.34, T:0.37
Consensus pattern (17 bp):
AAATTGGGCTGGGATTT
Found at i:552029 original size:15 final size:15
Alignment explanation
Indices: 551981--552030 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
551971 TTTATCAAAT
551981 TTATATTGATTGAAA
1 TTATATTGATTGAAA
* * *
551996 TCATTTTGATTGAAT
1 TTATATTGATTGAAA
552011 TTATATTGATTGAAA
1 TTATATTGATTGAAA
552026 TTATA
1 TTATA
552031 ATATATATAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.36, C:0.02, G:0.12, T:0.50
Consensus pattern (15 bp):
TTATATTGATTGAAA
Found at i:552558 original size:23 final size:23
Alignment explanation
Indices: 552519--552585 Score: 107
Period size: 23 Copynumber: 2.9 Consensus size: 23
552509 GAGGATTTAT
*
552519 AATATTCCGAGTGTGTTTGGGTTG
1 AATATTCTG-GTGTGTTTGGGTTG
552543 AATATTCTGGTGTGTTTGGGTTG
1 AATATTCTGGTGTGTTTGGGTTG
*
552566 GATATTCTGGTGTGTTTGGG
1 AATATTCTGGTGTGTTTGGG
552586 AGGAATCCAC
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
23 33 0.80
24 8 0.20
ACGTcount: A:0.13, C:0.06, G:0.36, T:0.45
Consensus pattern (23 bp):
AATATTCTGGTGTGTTTGGGTTG
Found at i:552711 original size:18 final size:19
Alignment explanation
Indices: 552690--552730 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
552680 AATGAAATGA
552690 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
552708 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
552727 GAAA
1 GAAA
552731 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:561051 original size:17 final size:17
Alignment explanation
Indices: 561029--561063 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
561019 CAAATATTAA
561029 ATTATTTA-TATAGTTTT
1 ATTATTTATTATA-TTTT
561046 ATTATTTATTATATTTT
1 ATTATTTATTATATTTT
561063 A
1 A
561064 AAATTTTGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (17 bp):
ATTATTTATTATATTTT
Found at i:563021 original size:41 final size:40
Alignment explanation
Indices: 562960--563045 Score: 136
Period size: 41 Copynumber: 2.1 Consensus size: 40
562950 TTTCCATTAA
562960 TTAATTATTGCAGTTAGATGACGGTTAACTAGCTGCATCAG
1 TTAATTATTGCAGTTAGATGACGGTTAACTAGCTG-ATCAG
* * *
563001 TTAATTATTGCAGTTGGATGATGGTTAACTAGCTGATGAG
1 TTAATTATTGCAGTTAGATGACGGTTAACTAGCTGATCAG
563041 TTAAT
1 TTAAT
563046 GACTGTCCCT
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
40 9 0.21
41 33 0.79
ACGTcount: A:0.29, C:0.10, G:0.23, T:0.37
Consensus pattern (40 bp):
TTAATTATTGCAGTTAGATGACGGTTAACTAGCTGATCAG
Found at i:563521 original size:29 final size:27
Alignment explanation
Indices: 563479--563537 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 27
563469 CTCTACTGTA
563479 AAAGTCAAGTCA-TTTCTATAATTAATTTT
1 AAAGTCAAGTCATTTTC-ATAATT--TTTT
*
563508 AAAGTTAAGTCATTTTCATAATTTTTT
1 AAAGTCAAGTCATTTTCATAATTTTTT
563535 AAA
1 AAA
563538 CTTAGAGGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 7 0.25
29 17 0.61
30 4 0.14
ACGTcount: A:0.39, C:0.08, G:0.07, T:0.46
Consensus pattern (27 bp):
AAAGTCAAGTCATTTTCATAATTTTTT
Found at i:571089 original size:18 final size:18
Alignment explanation
Indices: 571068--571118 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
571058 TTTATCATAT
571068 TAATAATTTTTTTTATAG
1 TAATAATTTTTTTTATAG
*
571086 TAATTCA-TTTTTTTA-AG
1 TAA-TAATTTTTTTTATAG
*
571103 TAA-AATTTTTTATATA
1 TAATAATTTTTTTTATA
571119 AATTTATAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
15 1 0.04
16 7 0.26
17 6 0.22
18 11 0.41
19 2 0.07
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (18 bp):
TAATAATTTTTTTTATAG
Found at i:575543 original size:51 final size:51
Alignment explanation
Indices: 575467--575563 Score: 185
Period size: 51 Copynumber: 1.9 Consensus size: 51
575457 ATTTTATAGG
*
575467 AAACTTAAATACATTTGAGAAGCTACCTATCCTATTAGCCCCTAGTCTATA
1 AAACTTAAATACATTTGAGAAGCTACCCATCCTATTAGCCCCTAGTCTATA
575518 AAACTTAAATACATTTGAGAAGCTACCCATCCTATTAGCCCCTAGT
1 AAACTTAAATACATTTGAGAAGCTACCCATCCTATTAGCCCCTAGT
575564 TTGAATTTGT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.35, C:0.25, G:0.10, T:0.30
Consensus pattern (51 bp):
AAACTTAAATACATTTGAGAAGCTACCCATCCTATTAGCCCCTAGTCTATA
Found at i:578470 original size:31 final size:30
Alignment explanation
Indices: 578396--578473 Score: 77
Period size: 31 Copynumber: 2.5 Consensus size: 30
578386 TTATATTTAG
* *
578396 TTTTAATGTTTAATTTAGTAATTGAGGTTT
1 TTTTAATGTTTAATTTAGTAATTGAGATTA
** *
578426 TTTTTGTGTTTTAATTT-GATATTTGAGATTGA
1 TTTTAATG-TTTAATTTAG-TAATTGAGATT-A
578458 TTTTAATGTTTAATTT
1 TTTTAATGTTTAATTT
578474 TTATTTAAGT
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
30 7 0.18
31 25 0.66
32 6 0.16
ACGTcount: A:0.24, C:0.00, G:0.15, T:0.60
Consensus pattern (30 bp):
TTTTAATGTTTAATTTAGTAATTGAGATTA
Found at i:581144 original size:30 final size:30
Alignment explanation
Indices: 581108--581169 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
581098 AGGGGGAGGC
*
581108 GGCATTCCAGGGCGTGGGGGTGGTGGAGCA
1 GGCATTCCAGGGCGTGGGGGTGGTGGACCA
*
581138 GGCATTCCAGGGCGTGGTGGTGGTGGACCA
1 GGCATTCCAGGGCGTGGGGGTGGTGGACCA
581168 GG
1 GG
581170 AGGTCCTCTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.13, C:0.18, G:0.52, T:0.18
Consensus pattern (30 bp):
GGCATTCCAGGGCGTGGGGGTGGTGGACCA
Found at i:583196 original size:5 final size:5
Alignment explanation
Indices: 583186--583214 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
583176 TATAAGATAT
583186 ATAAA ATAAA AT-AA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
583215 TATAGTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
ATAAA
Found at i:583203 original size:14 final size:14
Alignment explanation
Indices: 583186--583216 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
583176 TATAAGATAT
583186 ATAAAATAAAATAA
1 ATAAAATAAAATAA
583200 ATAAAATAAAATAA
1 ATAAAATAAAATAA
583214 ATA
1 ATA
583217 TAGTTATACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
ATAAAATAAAATAA
Found at i:583216 original size:9 final size:10
Alignment explanation
Indices: 583186--583214 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
583176 TATAAGATAT
583186 ATAAAATAAA
1 ATAAAATAAA
583196 AT-AAATAAA
1 ATAAAATAAA
583205 ATAAAATAAA
1 ATAAAATAAA
583215 TATAGTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (10 bp):
ATAAAATAAA
Found at i:588648 original size:31 final size:31
Alignment explanation
Indices: 588606--588679 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
588596 AAAAAATAAC
* *
588606 AAATTGGCTCTTTTAAAAAGGTCGATGGTTA
1 AAATTGACTCTTTTAAAAAGGTCGATGGTCA
* * *
588637 AAATTGACTCTTTTTAAAATGTTGATGGTCA
1 AAATTGACTCTTTTAAAAAGGTCGATGGTCA
*
588668 AAATGGACTCTT
1 AAATTGACTCTT
588680 CGTAAAAGAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.38
Consensus pattern (31 bp):
AAATTGACTCTTTTAAAAAGGTCGATGGTCA
Found at i:592387 original size:12 final size:12
Alignment explanation
Indices: 592370--592396 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
592360 CCGCCCCCTC
592370 CTCCACCTCCAT
1 CTCCACCTCCAT
592382 CTCCACCTCCAT
1 CTCCACCTCCAT
592394 CTC
1 CTC
592397 GGAAGTTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.59, G:0.00, T:0.26
Consensus pattern (12 bp):
CTCCACCTCCAT
Found at i:594470 original size:21 final size:21
Alignment explanation
Indices: 594435--594482 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 21
594425 AGGTCTAAAT
594435 TATTTATACAATATG-TGCACATA
1 TATTTATA-AATATGAT-CA-ATA
594458 TATTTAT-AATATGATCAATA
1 TATTTATAAATATGATCAATA
594478 TATTT
1 TATTT
594483 TAGAAATGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 8 0.33
21 8 0.33
22 1 0.04
23 7 0.29
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.46
Consensus pattern (21 bp):
TATTTATAAATATGATCAATA
Found at i:600984 original size:12 final size:12
Alignment explanation
Indices: 600967--600997 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
600957 AATTCTCATA
600967 AATTATTAATAT
1 AATTATTAATAT
600979 AATTATTAATAT
1 AATTATTAATAT
600991 AA-TATTA
1 AATTATTA
600998 TTTTATGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.26
12 14 0.74
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AATTATTAATAT
Found at i:608998 original size:2 final size:2
Alignment explanation
Indices: 608991--609015 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
608981 TAAATCAAAG
608991 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
609016 CTTTAATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:624976 original size:29 final size:27
Alignment explanation
Indices: 624943--625009 Score: 71
Period size: 30 Copynumber: 2.3 Consensus size: 27
624933 ATTATTAATA
*
624943 TATATATATTTGAACTACAATTAAAATT
1 TATATATATTTGAA-TAAAATTAAAATT
* *
624971 TCATATACATAATTGCATAAAATTAAAATT
1 T-ATAT--ATATTTGAATAAAATTAAAATT
625001 TATATATAT
1 TATATATAT
625010 CAAATTGTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
27 3 0.09
28 1 0.03
29 8 0.25
30 13 0.41
31 7 0.22
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.42
Consensus pattern (27 bp):
TATATATATTTGAATAAAATTAAAATT
Found at i:627791 original size:14 final size:15
Alignment explanation
Indices: 627760--627794 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
627750 AAATTTTAAG
627760 AAAAATGAATATTGT
1 AAAAATGAATATTGT
*
627775 AAAAATGGATATT-T
1 AAAAATGAATATTGT
627789 AAAAAT
1 AAAAAT
627795 TTTAATTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.31
Consensus pattern (15 bp):
AAAAATGAATATTGT
Found at i:635680 original size:22 final size:23
Alignment explanation
Indices: 635654--635702 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
635644 ATTAAAAAGA
* *
635654 TAAAA-TTATATTTTTATTATCG
1 TAAAAGTTACATTTTTACTATCG
635676 TAAAAGTTACATTTTTACTATCG
1 TAAAAGTTACATTTTTACTATCG
635699 TAAA
1 TAAA
635703 GTTTGCAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.39, C:0.08, G:0.06, T:0.47
Consensus pattern (23 bp):
TAAAAGTTACATTTTTACTATCG
Found at i:644339 original size:25 final size:25
Alignment explanation
Indices: 644278--644339 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
644268 TTTGCTTGAA
*
644278 AATTTATATGATAGGAAAATCGTATG
1 AATTTA-ATGATAGGAAAATCGTATC
** * **
644304 AAAATATTGATAGGAAAATTTTATC
1 AATTTAATGATAGGAAAATCGTATC
644329 AATTTAATGAT
1 AATTTAATGAT
644340 TAGTTAGAAA
Statistics
Matches: 27, Mismatches: 9, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
25 23 0.85
26 4 0.15
ACGTcount: A:0.45, C:0.03, G:0.15, T:0.37
Consensus pattern (25 bp):
AATTTAATGATAGGAAAATCGTATC
Found at i:649647 original size:49 final size:50
Alignment explanation
Indices: 649529--649775 Score: 257
Period size: 49 Copynumber: 4.8 Consensus size: 50
649519 GATAATAACA
* * * ** * *
649529 TGCCAAAGCCATGTCCCTGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
649580 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGA-CTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
649629 TGCCAACGCCATGTCCCAGACATGGTCTTACA-TGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
649678 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
649733 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
649776 TTACCCAAAT
Statistics
Matches: 166, Mismatches: 21, Indels: 13
0.83 0.10 0.06
Matches are distributed among these distances:
48 4 0.02
49 77 0.46
50 9 0.05
51 32 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:649702 original size:98 final size:104
Alignment explanation
Indices: 649528--649768 Score: 325
Period size: 98 Copynumber: 2.3 Consensus size: 104
649518 TGATAATAAC
* **
649528 ATGCCAAAGCCATGTCCCTGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACAT-GGATCCTCTCGTGATGGTGCCCATGCCATG
* *
649593 TCCCAGACATGGTCTTATAGGGGA-CTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
649629 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGA-CCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGATCCTCTCGTGAT-GGTGCCCATGCCATG
649691 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
*
649733 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGG
649769 GATCTCTTTA
Statistics
Matches: 124, Mismatches: 8, Indels: 12
0.86 0.06 0.08
Matches are distributed among these distances:
97 1 0.01
98 44 0.35
99 8 0.06
100 31 0.25
102 3 0.02
103 1 0.01
104 2 0.02
105 34 0.27
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGATCCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:649891 original size:13 final size:13
Alignment explanation
Indices: 649870--649901 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
649860 ACTCGGATCA
*
649870 TCATCAAATAAAT
1 TCATAAAATAAAT
649883 TCATAAAATAAAT
1 TCATAAAATAAAT
649896 TCATAA
1 TCATAA
649902 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:650147 original size:30 final size:30
Alignment explanation
Indices: 650113--650170 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
650103 CCTCGACTCT
*
650113 AACTTTTTCAAAATTACAATTTTACCCCTA
1 AACTTTTACAAAATTACAATTTTACCCCTA
* * *
650143 AACTTTTACATAATTACATTTTTTCCCC
1 AACTTTTACAAAATTACAATTTTACCCC
650171 AAGGCTCGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.33, C:0.24, G:0.00, T:0.43
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTACCCCTA
Found at i:657231 original size:50 final size:50
Alignment explanation
Indices: 657107--657355 Score: 284
Period size: 50 Copynumber: 4.8 Consensus size: 50
657097 GATAATAACA
* * ** * *
657107 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
657158 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
657208 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
657258 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
657313 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
657356 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 21, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.54
51 33 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:657285 original size:100 final size:104
Alignment explanation
Indices: 657106--657355 Score: 357
Period size: 100 Copynumber: 2.4 Consensus size: 104
657096 TGATAATAAC
**
657106 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
657171 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
657208 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
657271 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
657313 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
657356 TTACCCAAAT
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:657471 original size:13 final size:13
Alignment explanation
Indices: 657450--657481 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
657440 GCTTGGATCA
*
657450 TCATCAAATAAAT
1 TCATAAAATAAAT
657463 TCATAAAATAAAT
1 TCATAAAATAAAT
657476 TCATAA
1 TCATAA
657482 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:657728 original size:30 final size:30
Alignment explanation
Indices: 657693--657750 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
657683 CCTCGACTCT
*
657693 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
657723 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
657751 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:665707 original size:26 final size:26
Alignment explanation
Indices: 665678--665737 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 26
665668 CACTATATTC
665678 TCAATTCAATTACAATTTT-CACATTT
1 TCAATTCAATT-CAATTTTCCACATTT
* *
665704 TCAATTCAA-TCATTTTTCCACCTTT
1 TCAATTCAATTCAATTTTCCACATTT
665729 TCAA-TCAAT
1 TCAATTCAAT
665738 ATTATTTCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
24 10 0.33
25 11 0.37
26 9 0.30
ACGTcount: A:0.32, C:0.23, G:0.00, T:0.45
Consensus pattern (26 bp):
TCAATTCAATTCAATTTTCCACATTT
Found at i:686174 original size:3 final size:3
Alignment explanation
Indices: 686166--686194 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
686156 TTATTGCTTT
686166 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
686195 TAATTCATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:687535 original size:13 final size:15
Alignment explanation
Indices: 687507--687536 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
687497 ACCTCCCAAA
687507 ATAAAAAATTTATAT
1 ATAAAAAATTTATAT
687522 ATAAAAAATTTATAT
1 ATAAAAAATTTATAT
687537 TTTAATCTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
ATAAAAAATTTATAT
Found at i:694637 original size:6 final size:6
Alignment explanation
Indices: 694628--694696 Score: 61
Period size: 6 Copynumber: 11.5 Consensus size: 6
694618 CCTCCTTATA
* * *
694628 TCTATC TCTATGC -CTA-C TCCTATC TCTGTC CCTATC TCTATC CCTATC
1 TCTATC TCTAT-C TCTATC T-CTATC TCTATC TCTATC TCTATC TCTATC
* *
694676 CCTATC CCTATC TCTATC TCT
1 TCTATC TCTATC TCTATC TCT
694697 GTCCCTCTTA
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
4 1 0.02
6 49 0.92
7 3 0.06
ACGTcount: A:0.14, C:0.41, G:0.03, T:0.42
Consensus pattern (6 bp):
TCTATC
Found at i:694652 original size:18 final size:17
Alignment explanation
Indices: 694629--694737 Score: 84
Period size: 18 Copynumber: 6.4 Consensus size: 17
694619 CTCCTTATAT
*
694629 CTATCTCTATGCCTACTC
1 CTATCTCTATCCCTA-TC
*
694647 CTATCTCTGTCCCTATC
1 CTATCTCTATCCCTATC
*
694664 TCTATCCCTATCCCTATCC
1 -CTATCTCTATCCCTAT-C
* *
694683 CTATCTCTATCTCTGTC
1 CTATCTCTATCCCTATC
*
694700 C-CTCT-TATCCCTATCC
1 CTATCTCTATCCCTAT-C
694716 CTATC-CTTAT-CCT-TC
1 CTATCTC-TATCCCTATC
694731 CTATCTC
1 CTATCTC
694738 GCATCTCCAT
Statistics
Matches: 73, Mismatches: 11, Indels: 16
0.73 0.11 0.16
Matches are distributed among these distances:
15 13 0.18
16 7 0.10
17 9 0.12
18 43 0.59
19 1 0.01
ACGTcount: A:0.14, C:0.42, G:0.03, T:0.41
Consensus pattern (17 bp):
CTATCTCTATCCCTATC
Found at i:694661 original size:12 final size:12
Alignment explanation
Indices: 694646--694737 Score: 82
Period size: 12 Copynumber: 7.7 Consensus size: 12
694636 TATGCCTACT
*
694646 CCTATCTCTGTC
1 CCTATCTCTATC
694658 CCTATCTCTATC
1 CCTATCTCTATC
*
694670 CCTATCCCTATC
1 CCTATCTCTATC
694682 CCTATCTCTATC
1 CCTATCTCTATC
* *
694694 TCTGTCCCTCTTATC
1 CCTAT--CTC-TATC
*
694709 CCTATCCCTATC
1 CCTATCTCTATC
*
694721 CTTATC-CT-T-
1 CCTATCTCTATC
694730 CCTATCTC
1 CCTATCTC
694738 GCATCTCCAT
Statistics
Matches: 66, Mismatches: 10, Indels: 10
0.77 0.12 0.12
Matches are distributed among these distances:
9 5 0.08
10 2 0.03
11 2 0.03
12 45 0.68
13 2 0.03
14 3 0.05
15 7 0.11
ACGTcount: A:0.13, C:0.43, G:0.02, T:0.41
Consensus pattern (12 bp):
CCTATCTCTATC
Found at i:696791 original size:29 final size:30
Alignment explanation
Indices: 696719--696800 Score: 96
Period size: 29 Copynumber: 2.7 Consensus size: 30
696709 TTTTTGAGAT
696719 TTTATTAAAATAATATAAAAGATAAAATTAA
1 TTTATTAAAATAATAT-AAAGATAAAATTAA
* * *
696750 TTTTTTTAAATAATAT-AAGTTATAAATT-A
1 TTTATTAAAATAATATAAAGATA-AAATTAA
696779 TTTATTAAAATAATATGAAAGA
1 TTTATTAAAATAATAT-AAAGA
696801 ACAATAATTT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
29 20 0.48
30 5 0.12
31 17 0.40
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (30 bp):
TTTATTAAAATAATATAAAGATAAAATTAA
Found at i:696810 original size:29 final size:28
Alignment explanation
Indices: 696719--696810 Score: 80
Period size: 29 Copynumber: 3.1 Consensus size: 28
696709 TTTTTGAGAT
696719 TTTATTAAAATAATATAAAAGATAAAATTAA
1 TTTATTAAAATAATAT-AAAGAT-AAA-TAA
* * *
696750 TTTTTTTAAATAATAT-AAGTTATAAATTA
1 TTTATTAAAATAATATAAAG--ATAAATAA
696779 TTTATTAAAATAATATGAAAGA-ACAATAA
1 TTTATTAAAATAATAT-AAAGATA-AATAA
696808 TTT
1 TTT
696811 TAGGTGTCGC
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
28 1 0.02
29 27 0.54
30 3 0.06
31 19 0.38
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.41
Consensus pattern (28 bp):
TTTATTAAAATAATATAAAGATAAATAA
Found at i:708156 original size:30 final size:29
Alignment explanation
Indices: 708098--708156 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
708088 AATATCAAAA
* *
708098 TTATACATGAATTTTGTTTTTATACAATT
1 TTATACATGAATTTTGATTTGATACAATT
* *
708127 TTATATATGAAATTTTGATTTGATCCAATT
1 TTATACATG-AATTTTGATTTGATACAATT
708157 CTCACAAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 8 0.32
30 17 0.68
ACGTcount: A:0.32, C:0.07, G:0.08, T:0.53
Consensus pattern (29 bp):
TTATACATGAATTTTGATTTGATACAATT
Found at i:714540 original size:13 final size:14
Alignment explanation
Indices: 714516--714549 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
714506 AAACAGCATT
*
714516 AGAAGGTTTATGGA
1 AGAAGATTTATGGA
714530 A-AAGATTTATGGA
1 AGAAGATTTATGGA
714543 AGAAGAT
1 AGAAGAT
714550 ACTCCGCTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.44, C:0.00, G:0.29, T:0.26
Consensus pattern (14 bp):
AGAAGATTTATGGA
Found at i:721385 original size:4 final size:4
Alignment explanation
Indices: 721376--721405 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
721366 AATGATGAAA
721376 TCCC TCCC TCCC TCCC TCCC TCCC TCCC TC
1 TCCC TCCC TCCC TCCC TCCC TCCC TCCC TC
721406 TCTCTCTCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.00, C:0.73, G:0.00, T:0.27
Consensus pattern (4 bp):
TCCC
Found at i:722686 original size:84 final size:84
Alignment explanation
Indices: 722576--722924 Score: 376
Period size: 84 Copynumber: 4.2 Consensus size: 84
722566 ACTTTGGGCC
*
722576 CTTCAACAGCCTTCTT-AT--TTTCTTCTGCAATCTTCCTTTGC-TCTTCTGCTTTAGCCATCT-
1 CTTCAACAGCCTTCTTCATAGTTTCTTCTGCAATCTTCCTCTGCTTC-TCTGCTTTAGCCATCTC
**
722636 CAATATCAGCTTGTTTTCTTA
65 CAA-ATCAGCACGTTTTCTTA
* * * *
722657 CTTCAACCGCCTTCTTCAT-GTTTTCTTCTGCAATCTTCCTTTGCTTCACTGCTTCAGCCATCTC
1 CTTCAACAGCCTTCTTCATAG-TTTCTTCTGCAATCTTCCTCTGCTTCTCTGCTTTAGCCATCTC
*
722721 TAAATCAGCACGTTTTC-TA
65 CAAATCAGCACGTTTTCTTA
*
722740 TCTTCAACAGCCTTCTTCTTAGTTTCTT-TAGCAATCTTCCTCTGCTTCTCTGCTTTAGCCATCT
1 -CTTCAACAGCCTTCTTCATAGTTTCTTCT-GCAATCTTCCTCTGCTTCTCTGCTTTAGCCATCT
* *
722804 CCAAATCAGCACATTTTCTTT
64 CCAAATCAGCACGTTTTCTTA
* * * * ** *
722825 CATCAACAGCCTTTTTCTTAGTTTCTTCTGCACTCTTCCTCAAC-TCGCTTGCTTTAGCCATCTC
1 CTTCAACAGCCTTCTTCATAGTTTCTTCTGCAATCTTCCTCTGCTTCTC-TGCTTTAGCCATCTC
* *
722889 CAAATC-GACAAGTTTTCTTT
65 CAAATCAG-CACGTTTTCTTA
*
722909 CTTCAACTGCCTTCTT
1 CTTCAACAGCCTTCTT
722925 TTTCTCTTCT
Statistics
Matches: 231, Mismatches: 25, Indels: 21
0.83 0.09 0.08
Matches are distributed among these distances:
81 15 0.06
82 2 0.01
83 7 0.03
84 200 0.87
85 7 0.03
ACGTcount: A:0.17, C:0.31, G:0.09, T:0.43
Consensus pattern (84 bp):
CTTCAACAGCCTTCTTCATAGTTTCTTCTGCAATCTTCCTCTGCTTCTCTGCTTTAGCCATCTCC
AAATCAGCACGTTTTCTTA
Found at i:723819 original size:12 final size:12
Alignment explanation
Indices: 723802--723827 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
723792 ATACATTATG
723802 AAAATATTGTAA
1 AAAATATTGTAA
723814 AAAATATTGTAA
1 AAAATATTGTAA
723826 AA
1 AA
723828 TATGCTTCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (12 bp):
AAAATATTGTAA
Found at i:732313 original size:22 final size:23
Alignment explanation
Indices: 732279--732322 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
732269 AAAAAAATTA
*
732279 TAAAATTACTA-TTGAATTATTT
1 TAAAATTACTATTTAAATTATTT
**
732301 TAAAATTTTTATTTAAATTATT
1 TAAAATTACTATTTAAATTATT
732323 AAAATTCTCT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (23 bp):
TAAAATTACTATTTAAATTATTT
Found at i:732479 original size:30 final size:31
Alignment explanation
Indices: 732443--732516 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 31
732433 ATAACCTATA
* * *
732443 TTTTTATAATTTTTTAAAATATTAAAT-TAT
1 TTTTTATTATTTTTTAAAAAATTAAATAAAT
*
732473 TTTTTATTA-GTTTTAAAAAATTAAATAAAT
1 TTTTTATTATTTTTTAAAAAATTAAATAAAT
732503 TTTTTATTATTTTT
1 TTTTTATTATTTTT
732517 AGGGGTCAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
29 15 0.41
30 19 0.51
31 3 0.08
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (31 bp):
TTTTTATTATTTTTTAAAAAATTAAATAAAT
Found at i:754678 original size:4 final size:4
Alignment explanation
Indices: 754669--754695 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
754659 TCAATACGTG
754669 CATA CATA CATA CATA CATA CATA CAT
1 CATA CATA CATA CATA CATA CATA CAT
754696 GCATGTATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (4 bp):
CATA
Found at i:756100 original size:29 final size:28
Alignment explanation
Indices: 756042--756129 Score: 79
Period size: 29 Copynumber: 3.0 Consensus size: 28
756032 TCTATTTGGT
*
756042 ATATAAACTTTGATTT-ACTGTAATTATAC
1 ATATAAACTTTGATTTGA-T-TAATTGTAC
*
756071 ATATAAACTTTGATTTGGTTCAATTGTAC
1 ATATAAACTTTGATTTGATT-AATTGTAC
* *
756100 ACATAAAATTTTGATCTTGATTTAATTGTA
1 ATAT-AAACTTTGAT-TTGA-TTAATTGTA
756130 AACAATTTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
28 1 0.02
29 27 0.55
30 9 0.18
31 10 0.20
32 2 0.04
ACGTcount: A:0.35, C:0.09, G:0.10, T:0.45
Consensus pattern (28 bp):
ATATAAACTTTGATTTGATTAATTGTAC
Found at i:756127 original size:31 final size:31
Alignment explanation
Indices: 756069--756129 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
756059 CTGTAATTAT
*
756069 ACATATAAACTTTGATTTGGTTCAATTGTAC
1 ACATATAAACTTTGATTTGATTCAATTGTAC
* *
756100 ACATA-AAATTTTGATCTTGATTTAATTGTA
1 ACATATAAACTTTGAT-TTGATTCAATTGTA
756130 AACAATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 9 0.35
31 17 0.65
ACGTcount: A:0.34, C:0.10, G:0.11, T:0.44
Consensus pattern (31 bp):
ACATATAAACTTTGATTTGATTCAATTGTAC
Found at i:756486 original size:26 final size:26
Alignment explanation
Indices: 756450--756502 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
756440 TTTACATCAT
756450 TAAAGGTGCTCATGGATCGAATTAGA
1 TAAAGGTGCTCATGGATCGAATTAGA
756476 TAAAGGTGCTCATGGATCGAATTAGA
1 TAAAGGTGCTCATGGATCGAATTAGA
756502 T
1 T
756503 CAAGATTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.28
Consensus pattern (26 bp):
TAAAGGTGCTCATGGATCGAATTAGA
Found at i:760492 original size:28 final size:28
Alignment explanation
Indices: 760452--760510 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
760442 ATAACTCGTT
760452 CTTAATTCTTAAATAAAAAGATAATACG
1 CTTAATTCTTAAATAAAAAGATAATACG
*
760480 CTTAATTCTTAAATAAAAGGATAATACG
1 CTTAATTCTTAAATAAAAAGATAATACG
760508 CTT
1 CTT
760511 CCTCGCAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.46, C:0.12, G:0.08, T:0.34
Consensus pattern (28 bp):
CTTAATTCTTAAATAAAAAGATAATACG
Found at i:762775 original size:11 final size:11
Alignment explanation
Indices: 762750--762808 Score: 54
Period size: 11 Copynumber: 5.7 Consensus size: 11
762740 AAAGAAGCCG
762750 AGAAGCCGA-A
1 AGAAGCCGAGA
*
762760 AGAAGCTGAGA
1 AGAAGCCGAGA
762771 AGAAGCCG-GA
1 AGAAGCCGAGA
* *
762781 A-AAACCCA-A
1 AGAAGCCGAGA
*
762790 AGAAGCTGAGA
1 AGAAGCCGAGA
762801 AGAAGCCG
1 AGAAGCCG
762809 GAAAAACCCA
Statistics
Matches: 37, Mismatches: 8, Indels: 7
0.71 0.15 0.13
Matches are distributed among these distances:
9 6 0.16
10 15 0.41
11 16 0.43
ACGTcount: A:0.47, C:0.19, G:0.31, T:0.03
Consensus pattern (11 bp):
AGAAGCCGAGA
Found at i:762794 original size:30 final size:30
Alignment explanation
Indices: 762741--762853 Score: 174
Period size: 30 Copynumber: 3.8 Consensus size: 30
762731 GACAAACCTA
* * *
762741 AAGAAGCC-GAGAAGCCGAAAGAAGCTGAG
1 AAGAAGCCGGAAAAACCCAAAGAAGCTGAG
762770 AAGAAGCCGGAAAAACCCAAAGAAGCTGAG
1 AAGAAGCCGGAAAAACCCAAAGAAGCTGAG
**
762800 AAGAAGCCGGAAAAACCCAAAGATCCTGAG
1 AAGAAGCCGGAAAAACCCAAAGAAGCTGAG
762830 AAGAAGCCGGAAAAACCCAAAGAA
1 AAGAAGCCGGAAAAACCCAAAGAA
762854 CCTGCTCCTG
Statistics
Matches: 77, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
29 8 0.10
30 69 0.90
ACGTcount: A:0.50, C:0.20, G:0.27, T:0.04
Consensus pattern (30 bp):
AAGAAGCCGGAAAAACCCAAAGAAGCTGAG
Found at i:762912 original size:69 final size:69
Alignment explanation
Indices: 762826--762978 Score: 288
Period size: 69 Copynumber: 2.2 Consensus size: 69
762816 CCAAAGATCC
* *
762826 TGAGAAGAAGCCGGAAAAACCCAAAGAACCTGCTCCTGGGAAGAGACCGCCAAAGCCCAAAGACG
1 TGAGACGAAACCGGAAAAACCCAAAGAACCTGCTCCTGGGAAGAGACCGCCAAAGCCCAAAGACG
762891 GTGG
66 GTGG
762895 TGAGACGAAACCGGAAAAACCCAAAGAACCTGCTCCTGGGAAGAGACCGCCAAAGCCCAAAGACG
1 TGAGACGAAACCGGAAAAACCCAAAGAACCTGCTCCTGGGAAGAGACCGCCAAAGCCCAAAGACG
762960 GTGG
66 GTGG
762964 TGAGACGAAACCGGA
1 TGAGACGAAACCGGA
762979 TATACCTAGA
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
69 82 1.00
ACGTcount: A:0.38, C:0.26, G:0.29, T:0.07
Consensus pattern (69 bp):
TGAGACGAAACCGGAAAAACCCAAAGAACCTGCTCCTGGGAAGAGACCGCCAAAGCCCAAAGACG
GTGG
Found at i:762921 original size:33 final size:33
Alignment explanation
Indices: 762881--762978 Score: 88
Period size: 36 Copynumber: 2.9 Consensus size: 33
762871 ACCGCCAAAG
762881 CCCAAAGACGGTGGTGAGACGAAACCGGAAAAA
1 CCCAAAGACGGTGGTGAGACGAAACCGGAAAAA
* ** * * * ** *
762914 CCCAAAGAACCTGCTCCTGGGAAGAGACCGCCAAAG
1 CCCAAAG-A-C-GGTGGTGAGACGAAACCGGAAAAA
762950 CCCAAAGACGGTGGTGAGACGAAACCGGA
1 CCCAAAGACGGTGGTGAGACGAAACCGGA
762979 TATACCTAGA
Statistics
Matches: 45, Mismatches: 17, Indels: 6
0.66 0.25 0.09
Matches are distributed among these distances:
33 19 0.42
34 2 0.04
35 2 0.04
36 22 0.49
ACGTcount: A:0.37, C:0.27, G:0.30, T:0.07
Consensus pattern (33 bp):
CCCAAAGACGGTGGTGAGACGAAACCGGAAAAA
Found at i:762955 original size:36 final size:36
Alignment explanation
Indices: 762845--762957 Score: 124
Period size: 36 Copynumber: 3.2 Consensus size: 36
762835 GCCGGAAAAA
762845 CCCAAAGAACCTGCTCCTGGGAAGAGACCGCCAAAG
1 CCCAAAGAACCTGCTCCTGGGAAGAGACCGCCAAAG
* ** * * * ** *
762881 CCCAAAG-A-C-GGTGGTGAGACGAAACCGGAAAAA
1 CCCAAAGAACCTGCTCCTGGGAAGAGACCGCCAAAG
762914 CCCAAAGAACCTGCTCCTGGGAAGAGACCGCCAAAG
1 CCCAAAGAACCTGCTCCTGGGAAGAGACCGCCAAAG
762950 CCCAAAGA
1 CCCAAAGA
762958 CGGTGGTGAG
Statistics
Matches: 56, Mismatches: 18, Indels: 6
0.70 0.22 0.08
Matches are distributed among these distances:
33 22 0.39
34 2 0.04
35 2 0.04
36 30 0.54
ACGTcount: A:0.37, C:0.30, G:0.26, T:0.07
Consensus pattern (36 bp):
CCCAAAGAACCTGCTCCTGGGAAGAGACCGCCAAAG
Found at i:765782 original size:24 final size:23
Alignment explanation
Indices: 765744--765793 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
765734 TTAATATATG
* *
765744 AAATATAAATTTTAAATATTTTT
1 AAATATAAATATTAAATATTTAT
*
765767 AAATAATAAATATTAATTATTTAT
1 AAAT-ATAAATATTAAATATTTAT
765791 AAA
1 AAA
765794 ATTTAAAGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
AAATATAAATATTAAATATTTAT
Found at i:765847 original size:21 final size:21
Alignment explanation
Indices: 765821--765860 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
765811 AAACTATATT
765821 TTAAATATTTA-AATATAATCA
1 TTAAATATTTATAAT-TAATCA
765842 TTAAATATTTATAATTAAT
1 TTAAATATTTATAATTAAT
765861 ATTTTAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (21 bp):
TTAAATATTTATAATTAATCA
Found at i:765866 original size:14 final size:14
Alignment explanation
Indices: 765845--765893 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 14
765835 ATAATCATTA
765845 AATA-TTTATAATT
1 AATATTTTATAATT
*
765858 AATATTTTA-AA-A
1 AATATTTTATAATT
*
765870 AATATTTTTTAATT
1 AATATTTTATAATT
765884 AATAATTTTA
1 AAT-ATTTTA
765894 ATAAATTTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
12 8 0.29
13 8 0.29
14 7 0.25
15 5 0.18
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
AATATTTTATAATT
Found at i:765882 original size:26 final size:26
Alignment explanation
Indices: 765844--765899 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
765834 TATAATCATT
765844 AAATATTTATAATTAAT-ATTTTAAA
1 AAATATTTATAATTAATAATTTTAAA
* *
765869 AAATATTTTTTAATTAATAATTTTAAT
1 AAATA-TTTATAATTAATAATTTTAAA
765896 AAAT
1 AAAT
765900 TTGTACTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 5 0.19
26 11 0.41
27 11 0.41
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
AAATATTTATAATTAATAATTTTAAA
Found at i:772920 original size:243 final size:243
Alignment explanation
Indices: 772492--772976 Score: 880
Period size: 243 Copynumber: 2.0 Consensus size: 243
772482 CAGACGAAGC
772492 AGGAACACTCCTGCCCATCTTGTCCTGGTCTTCTCTGATGGCCTTGTCAGGTGCCCTCCTCTCAG
1 AGGAACACTCCTGCCCATCTTGTCCTGGTCTTCTCTGATGGCCTTGTCAGGTGCCCTCCTCTCAG
* *
772557 CTTGAGCCTGTTCAAAATTACAATTCATAGGTGCTGCAGGAACACCCTTTTCCTTCCTTACATCC
66 CTTGAGCCCGTTCAAAATTACAATTCATAGATGCTGCAGGAACACCCTTTTCCTTCCTTACATCC
*
772622 CCTTCAGCACCTTCAGTACTTAAACTTTTAGCTGCTGCCATGAAAGATACTAATCTCTCAGCAAC
131 CCTTCAGCACCTTCAGCACTTAAACTTTTAGCTGCTGCCATGAAAGATACTAATCTCTCAGCAAC
*
772687 TTCTAAGGCTTTAGGGAGGGAATCAGCAACAGTAGCTGTCAAATCAGA
196 TTCTAAGGCTTTAGGGAGGGAATCAGCAACAGAAGCTGTCAAATCAGA
** *
772735 AGGAACACTCCTGTTCATCTTGTCCTGGTCTTCTCTGATGGCCTTGTCAGGTTCCCTCCTCTCAG
1 AGGAACACTCCTGCCCATCTTGTCCTGGTCTTCTCTGATGGCCTTGTCAGGTGCCCTCCTCTCAG
772800 CTTGAGCCCGTTCAAAATTACAATTCATAGATGCTGCAGGAACACCCTTTTCCTTCCTTACATCC
66 CTTGAGCCCGTTCAAAATTACAATTCATAGATGCTGCAGGAACACCCTTTTCCTTCCTTACATCC
*
772865 CCTTCAGCACCTTCAGCACTTAAACTTTTAGCTGCTTCCATGAAAGATACTAATCTCTCAGCAAC
131 CCTTCAGCACCTTCAGCACTTAAACTTTTAGCTGCTGCCATGAAAGATACTAATCTCTCAGCAAC
* *
772930 TTCTAAGGCTTTAGGGAGGGGATCAGTAACAGAAGCTGTCAAATCAG
196 TTCTAAGGCTTTAGGGAGGGAATCAGCAACAGAAGCTGTCAAATCAG
772977 CAACACTTGA
Statistics
Matches: 232, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
243 232 1.00
ACGTcount: A:0.24, C:0.28, G:0.18, T:0.30
Consensus pattern (243 bp):
AGGAACACTCCTGCCCATCTTGTCCTGGTCTTCTCTGATGGCCTTGTCAGGTGCCCTCCTCTCAG
CTTGAGCCCGTTCAAAATTACAATTCATAGATGCTGCAGGAACACCCTTTTCCTTCCTTACATCC
CCTTCAGCACCTTCAGCACTTAAACTTTTAGCTGCTGCCATGAAAGATACTAATCTCTCAGCAAC
TTCTAAGGCTTTAGGGAGGGAATCAGCAACAGAAGCTGTCAAATCAGA
Found at i:776545 original size:14 final size:14
Alignment explanation
Indices: 776526--776565 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
776516 TTGATTGGCA
776526 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
776540 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
776554 GGAAAATGTTTT
1 GTAAAATGTTTT
776566 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:776574 original size:20 final size:20
Alignment explanation
Indices: 776549--776588 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
776539 CGTAAAATGA
*
776549 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
776569 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
776589 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:776578 original size:34 final size:35
Alignment explanation
Indices: 776534--776600 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
776524 CAGTAAAATG
*
776534 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
776568 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
776601 CTAGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:776712 original size:20 final size:20
Alignment explanation
Indices: 776687--776725 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
776677 GTTTTTACAT
776687 ATATTAATAAATTTATATAC
1 ATATTAATAAATTTATATAC
*
776707 ATATTAATAAATTTTTATA
1 ATATTAATAAATTTATATA
776726 TTTTAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATTAATAAATTTATATAC
Found at i:776785 original size:15 final size:15
Alignment explanation
Indices: 776756--776808 Score: 52
Period size: 17 Copynumber: 3.2 Consensus size: 15
776746 TATTGCAATG
*
776756 ATTTATTTATAAATAA
1 ATTT-TTTATTAATAA
776772 ATTTTTTATTAATAAA
1 ATTTTTTATTAAT-AA
776788 AGTTTTTTATCTAATTAA
1 A-TTTTTTAT-TAA-TAA
776806 ATT
1 ATT
776809 CCAAATGTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
15 8 0.25
16 7 0.22
17 10 0.31
18 6 0.19
19 1 0.03
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (15 bp):
ATTTTTTATTAATAA
Found at i:776999 original size:14 final size:14
Alignment explanation
Indices: 776980--777019 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
776970 TTGATTGCCA
776980 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
776994 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
777008 GGAAAATGTTTT
1 GTAAAATGTTTT
777020 ACTTTTCTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:779859 original size:18 final size:18
Alignment explanation
Indices: 779838--779888 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
779828 AGGAATGAAG
779838 GAAGGGAGAAGAATGGAT
1 GAAGGGAGAAGAATGGAT
*** *
779856 GAAGGGAGCTTACTGGAT
1 GAAGGGAGAAGAATGGAT
779874 GAAGGGAGAAGAATG
1 GAAGGGAGAAGAATG
779889 CCTGAGAGCT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.39, C:0.04, G:0.43, T:0.14
Consensus pattern (18 bp):
GAAGGGAGAAGAATGGAT
Found at i:795743 original size:6 final size:6
Alignment explanation
Indices: 795734--795760 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
795724 CAGTCTCAAG
795734 CTCGGA CTCGGA CTCGGA CTCGGA CTC
1 CTCGGA CTCGGA CTCGGA CTCGGA CTC
795761 AGTCGTTGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.37, G:0.30, T:0.19
Consensus pattern (6 bp):
CTCGGA
Found at i:817097 original size:33 final size:33
Alignment explanation
Indices: 817050--817141 Score: 100
Period size: 33 Copynumber: 2.8 Consensus size: 33
817040 TTAATGAGAA
* *
817050 TTTCAAAAAAAATTGAGGAAGCTTAATT-GAATT
1 TTTCAAAAAAAATTGAGG-AGCCTAATTAAAATT
*
817083 TTTCAAAAAGAATTGAGGAGCCTAATTAAAATT
1 TTTCAAAAAAAATTGAGGAGCCTAATTAAAATT
*
817116 TTT-AGAAAAAAAGTT-AAGAGCCTAAT
1 TTTCA-AAAAAAA-TTGAGGAGCCTAAT
817142 GAGTTTATTT
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
32 9 0.18
33 40 0.78
34 2 0.04
ACGTcount: A:0.47, C:0.08, G:0.15, T:0.30
Consensus pattern (33 bp):
TTTCAAAAAAAATTGAGGAGCCTAATTAAAATT
Found at i:823743 original size:141 final size:144
Alignment explanation
Indices: 823586--823931 Score: 403
Period size: 145 Copynumber: 2.4 Consensus size: 144
823576 TAAATGGGGT
* * *
823586 AAAATACAATCTTACTCCTAATCTAAGGGCATCCATGGTACTTTTACCAATTAAAGGTGTATATA
1 AAAATGCAATCATACTCCTAATCTAAGGGCATCTATGGTACTTTTACCAATTAAAGGTGTATATA
* ** * * *
823651 TATAT-T-C-AAACACCTTTAATTGCTCTTTGATATAATGTATAGTA-ACTAATTTGAACATTTT
66 TATATATACTAAACACCTTTAATTGCCCTTTGATATAAAATACA-AAGACTAATTTAAACATTTT
*
823712 TTTAATAGATCGGTC
130 TTTAATAGATCGGCC
* * * * * *
823727 AAAATGCAATCCTACTCCTACTCTAAAGGTATCTATGGTACTTTTACCAATTAGAGGTATATATA
1 AAAATGCAATCATACTCCTAATCTAAGGGCATCTATGGTACTTTTACCAATTAAAGGTGTATATA
* * * * *
823792 TATATATACTTACACACTTTTAATTGCCCTTTTATTTAAAATACAAAGATTAATTTAAACATTTT
66 TATATATAC-TAAACACCTTTAATTGCCCTTTGATATAAAATACAAAGACTAATTTAAACATTTT
*
823857 TTTAATAGATTGGCC
130 TTTAATAGATCGGCC
* * * * *
823872 AAAATGCAATAATGCTCCTAATTTAAGGGCAGCTATGGTACTTTTACCAATTAAACGTGT
1 AAAATGCAATCATACTCCTAATCTAAGGGCATCTATGGTACTTTTACCAATTAAAGGTGT
823932 GTGAATACAT
Statistics
Matches: 168, Mismatches: 32, Indels: 6
0.82 0.16 0.03
Matches are distributed among these distances:
141 62 0.37
142 1 0.01
143 1 0.01
144 1 0.01
145 103 0.61
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (144 bp):
AAAATGCAATCATACTCCTAATCTAAGGGCATCTATGGTACTTTTACCAATTAAAGGTGTATATA
TATATATACTAAACACCTTTAATTGCCCTTTGATATAAAATACAAAGACTAATTTAAACATTTTT
TTAATAGATCGGCC
Found at i:833517 original size:182 final size:181
Alignment explanation
Indices: 832884--833601 Score: 819
Period size: 182 Copynumber: 4.0 Consensus size: 181
832874 TTCCATTACT
* * * * * * * *
832884 TTTCTCCTTTACTGACACAAACAAATACATAAATAGATTACTTTCATCAACTTAACCTGATTTTT
1 TTTCTCCTTT-CTGAGACAAATATATACATAAATGGACTATTTTCATCAATTTAACCTGAATTTT
* *
832949 AACACTCCATTAAGCTTAATATTAGCTGCAATTCACAGCTTCTTGGTTAATTGCAGTTTGCTTCT
65 AACACTCCATTAAGCTTAATATTAGCTGCAATTCACAGCTTCTTGATTAATTGCAATTTGCTTCT
* * * * *
833014 AAAAAAGAAACTTAACTGACTGAAGCCTGATTATAACATGTAATACTTCAAC
130 AAGAAAGAAACTAAACTGACCGAAGCCTGATTACAACATGTGATACTTCAAC
* *
833066 TTTCTCCTTTTCTGAGACAAATATATACATGAATGGACTATTTTCATCAAATTAACCTGACA-TT
1 TTTCTCC-TTTCTGAGACAAATATATACATAAATGGACTATTTTCATCAATTTAACCTGA-ATTT
* * * * *
833130 TAACCCTCCATTAAGCTTAATA-TAGCTGCAATTCGCAGCTTCTTGATTAATAGCAA-TTGGTCA
64 TAACACTCCATTAAGCTTAATATTAGCTGCAATTCACAGCTTCTTGATTAATTGCAATTTGCT-T
* * * *
833193 CT-GGAAAAGAAACTAAACTGACCGAAGCCTGGTTACAACATTTGATACTTGAA-
128 CTAAG-AAAGAAACTAAACTGACCGAAGCCTGATTACAACATGTGATACTTCAAC
* * *
833246 -TCCT-C-TTCTGAGACAAATATGA-ACATAAATGGACTATTTTCATCAATTTAATCTGACTTTT
1 TTTCTCCTTTCTGAGACAAATAT-ATACATAAATGGACTATTTTCATCAATTTAACCTGAATTTT
* **
833307 AACACTCCATTGAGCTTAATATTAGCTGCAATTCACAGCTTCTTGATTGGTTGCAATTTGCTTCT
65 AACACTCCATTAAGCTTAATATTAGCTGCAATTCACAGCTTCTTGATTAATTGCAATTTGCTTCT
* * *
833372 AAGAAAGAAACTAAACTGACTGAAGCCTGATGACAACATGTGATACATCAAC
130 AAGAAAGAAACTAAACTGACCGAAGCCTGATTACAACATGTGATACTTCAAC
* * * ** *
833424 TTTCTCCTTTCCTAAGACAAATATATACATAAACGGATTATTTTTGTCAATTTAA-CTCAATTTC
1 TTTCTCCTTT-CTGAGACAAATATATACATAAATGGACTATTTTCATCAATTTAACCTGAATTT-
* ** * * * *
833488 TAACACTCCATCAAGCTTAATATTAGCTGCAATTTGCATCTTCTTGATGAATTTCAAATTGCTTC
64 TAACACTCCATTAAGCTTAATATTAGCTGCAATTCACAGCTTCTTGATTAATTGCAATTTGCTT-
* * *
833553 CTAA-AAAGAAACTAAACTAACCGAAGACTGATTACAACACGTGATACTT
128 CTAAGAAAGAAACTAAACTGACCGAAGCCTGATTACAACATGTGATACTT
833602 AATCCATAAT
Statistics
Matches: 450, Mismatches: 69, Indels: 34
0.81 0.12 0.06
Matches are distributed among these distances:
176 68 0.15
177 75 0.17
178 6 0.01
179 6 0.01
180 5 0.01
181 82 0.18
182 201 0.45
183 7 0.02
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.34
Consensus pattern (181 bp):
TTTCTCCTTTCTGAGACAAATATATACATAAATGGACTATTTTCATCAATTTAACCTGAATTTTA
ACACTCCATTAAGCTTAATATTAGCTGCAATTCACAGCTTCTTGATTAATTGCAATTTGCTTCTA
AGAAAGAAACTAAACTGACCGAAGCCTGATTACAACATGTGATACTTCAAC
Found at i:834256 original size:16 final size:16
Alignment explanation
Indices: 834212--834261 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
834202 ATTAAAATGG
834212 TAAAATTTT-AATTTA
1 TAAAATTTTAAATTTA
**
834227 -AGTATTTTATAATTTA
1 TAAAATTTTA-AATTTA
*
834243 TAAAATTTTAAATTAA
1 TAAAATTTTAAATTTA
834259 TAA
1 TAA
834262 TAATAAAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
14 6 0.22
16 14 0.52
17 7 0.26
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (16 bp):
TAAAATTTTAAATTTA
Found at i:834280 original size:22 final size:23
Alignment explanation
Indices: 834229--834281 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 23
834219 TTAATTTAAG
* *
834229 TATTTT-ATAATTTATAAAATTT
1 TATTTTAATAATTAATAAAATTA
**
834251 TAAATTAATAA-TAATAAAATTA
1 TATTTTAATAATTAATAAAATTA
834273 TATTTTAAT
1 TATTTTAAT
834282 TTTTTTAAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TATTTTAATAATTAATAAAATTA
Found at i:834288 original size:53 final size:51
Alignment explanation
Indices: 834212--834326 Score: 122
Period size: 53 Copynumber: 2.2 Consensus size: 51
834202 ATTAAAATGG
* * * *
834212 TAAAATTTTAATTTAAGTATTTTATAATTTATAAAATTTTAAATTAATAATAA
1 TAAAATTATAATTTAAGTATTTTAAAAATAATAAAA-TTTAAATTAATAAT-A
* * * * * *
834265 TAAAATTATATTTTAATTTTTTTAAAAATAATAAAATTTAATTTAATCATT
1 TAAAATTATAATTTAAGTATTTTAAAAATAATAAAATTTAAATTAATAATA
834316 TAAAATTATAA
1 TAAAATTATAA
834327 ATATATAAAC
Statistics
Matches: 51, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
51 10 0.20
52 12 0.24
53 29 0.57
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.49
Consensus pattern (51 bp):
TAAAATTATAATTTAAGTATTTTAAAAATAATAAAATTTAAATTAATAATA
Found at i:834320 original size:28 final size:30
Alignment explanation
Indices: 834255--834327 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 30
834245 AAATTTTAAA
* **
834255 TTAATAATAATAAAATTATATTTTAATTTTT
1 TTAA-AATAATAAAATTATAATTTAATTCAT
834286 TTAAAAATAATAAAATT-TAATTTAA-TCAT
1 TT-AAAATAATAAAATTATAATTTAATTCAT
*
834315 TTAAAATTATAAA
1 TTAAAATAATAAA
834328 TATATAAACT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
28 10 0.27
29 4 0.11
30 7 0.19
31 14 0.38
32 2 0.05
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (30 bp):
TTAAAATAATAAAATTATAATTTAATTCAT
Found at i:841249 original size:2 final size:2
Alignment explanation
Indices: 841242--841273 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
841232 TTCTTTTTGT
841242 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
841274 GATTGGAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:842508 original size:22 final size:20
Alignment explanation
Indices: 842467--842509 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 20
842457 TTTGATAAAA
*
842467 AAATAGAGACAATTATAATT
1 AAATAGAGACAATTAGAATT
842487 AAATAGAGACAATATTAGAATT
1 AAATAGAGAC-A-ATTAGAATT
842509 A
1 A
842510 GATAATATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
21 1 0.05
22 9 0.45
ACGTcount: A:0.56, C:0.05, G:0.12, T:0.28
Consensus pattern (20 bp):
AAATAGAGACAATTAGAATT
Found at i:855308 original size:27 final size:26
Alignment explanation
Indices: 855262--855318 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
855252 ATTTGAAAAT
*
855262 TTTTATTTAATCCTTAAACTTTTAAA
1 TTTTATTTAATCCTTAAACTGTTAAA
*
855288 TTTTATTTAAGTCAC-TGAACTGTTAAA
1 TTTTATTTAA-TC-CTTAAACTGTTAAA
855315 TTTT
1 TTTT
855319 TTCTTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 10 0.37
27 16 0.59
28 1 0.04
ACGTcount: A:0.32, C:0.11, G:0.05, T:0.53
Consensus pattern (26 bp):
TTTTATTTAATCCTTAAACTGTTAAA
Found at i:858983 original size:10 final size:12
Alignment explanation
Indices: 858957--858986 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
858947 AATAGTGTTT
858957 TATTTATAAATA
1 TATTTATAAATA
858969 TATTTATAAATA
1 TATTTATAAATA
858981 T-TTTAT
1 TATTTAT
858987 TGTTAAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.28
12 13 0.72
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
TATTTATAAATA
Found at i:859817 original size:20 final size:20
Alignment explanation
Indices: 859781--859820 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
859771 TTAATATATA
*
859781 TAATGAATTTAATTTTAAAT
1 TAATGAATTTAAGTTTAAAT
859801 TAATCGAATTT-AGTTTAAAT
1 TAAT-GAATTTAAGTTTAAAT
859821 AGTTAACTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.47
Consensus pattern (20 bp):
TAATGAATTTAAGTTTAAAT
Found at i:860430 original size:37 final size:37
Alignment explanation
Indices: 860339--860421 Score: 152
Period size: 37 Copynumber: 2.3 Consensus size: 37
860329 TTAAAAAATG
860339 AAATTA-A-TAATATTTATTTTATTTTATTTCAATTA
1 AAATTATATTAATATTTATTTTATTTTATTTCAATTA
860374 AAATTATATTAATATTTATTTTATTTTATTTCAATTA
1 AAATTATATTAATATTTATTTTATTTTATTTCAATTA
860411 AAATTATATTA
1 AAATTATATTA
860422 TCTTTTATTA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
35 6 0.13
36 1 0.02
37 39 0.85
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (37 bp):
AAATTATATTAATATTTATTTTATTTTATTTCAATTA
Found at i:860920 original size:26 final size:26
Alignment explanation
Indices: 860891--860946 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
860881 TTTGAATCAA
*
860891 ATTTGAA-TAAAATTTAACATTTTAAC
1 ATTTGAAGTAAAACTTAA-ATTTTAAC
* *
860917 ATTTTAAGTTAAACTTAAATTTTAAC
1 ATTTGAAGTAAAACTTAAATTTTAAC
860943 ATTT
1 ATTT
860947 TTATCTGAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 18 0.69
27 8 0.31
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (26 bp):
ATTTGAAGTAAAACTTAAATTTTAAC
Found at i:877269 original size:138 final size:137
Alignment explanation
Indices: 876867--877259 Score: 355
Period size: 136 Copynumber: 2.9 Consensus size: 137
876857 CCTTGTAGTC
* * * * * * * * * *
876867 TGACTTACTATTACACTCAATTGCTATATGTCCGTTTTATGGTCCACGAAGAGTAATTTTTTC-A
1 TGACATACCATTACACCCAATTACTCTATATCCATTTTACGGTCCACGAAGAGAAATCTTTTCGA
* * ** * *
876931 AGGTTATGATTGTTTCTCTCTACAATATTATATACAAGTTTGAACTTGAGGTCACTCCTCGAAAG
66 AGGTTATGATTGTTTCTCTCAACAATATTATATGCAAGTTTGAACAAGAGTTCACTCCTCGAGAG
*
876996 TATTACG
131 TATAACG
** * * * *
877003 TGAGTTACCATTACATCCAATTGCTCTATGTCCA--TTACAGTCCACGAAGA-ATAATCTTTTTC
1 TGACATACCATTACACCCAATTACTCTATATCCATTTTACGGTCCACGAAGAGA-AATC-TTTTC
* * * * * * * *
877065 GAGGGTTATGATTGTTTCTCTCAACTATATTATCTGCAAGGTTTAAATAAGATTTCCCTCGTCGA
64 GAAGGTTATGATTGTTTCTCTCAACAATATTATATGCAA-GTTTGAACAAGAGTTCACTCCTCGA
* *
877130 GAGTGTAATG
128 GAGTATAACG
* **
877140 TGACATACTATTACACCCAATTACTCTATATTTATTTTACGGTCCACGAAGAGAAATCTTTTCGA
1 TGACATACCATTACACCCAATTACTCTATATCCATTTTACGGTCCACGAAGAGAAATCTTTTCGA
* * *
877205 AGGTTATAGA-TGTTTTTCCCAACAATATTATATGCAATGTTTGAACCAGAGTTCA
66 AGGTTAT-GATTGTTTCTCTCAACAATATTATATGCAA-GTTTGAACAAGAGTTCA
877260 TTTTTCGAGA
Statistics
Matches: 202, Mismatches: 47, Indels: 14
0.77 0.18 0.05
Matches are distributed among these distances:
134 17 0.08
135 5 0.02
136 61 0.30
137 49 0.24
138 48 0.24
139 21 0.10
140 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.37
Consensus pattern (137 bp):
TGACATACCATTACACCCAATTACTCTATATCCATTTTACGGTCCACGAAGAGAAATCTTTTCGA
AGGTTATGATTGTTTCTCTCAACAATATTATATGCAAGTTTGAACAAGAGTTCACTCCTCGAGAG
TATAACG
Found at i:877439 original size:36 final size:36
Alignment explanation
Indices: 877392--877470 Score: 140
Period size: 36 Copynumber: 2.2 Consensus size: 36
877382 AATATATGAT
*
877392 TTGTGATTATAGTACTTGTTGTCAATGCATCATACC
1 TTGTGATTATAGTACTTATTGTCAATGCATCATACC
877428 TTGTGATTATAGTACTTATTGTCAATGCATCATACC
1 TTGTGATTATAGTACTTATTGTCAATGCATCATACC
*
877464 ATGTGAT
1 TTGTGAT
877471 CTCTTATATG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.42
Consensus pattern (36 bp):
TTGTGATTATAGTACTTATTGTCAATGCATCATACC
Found at i:879569 original size:20 final size:21
Alignment explanation
Indices: 879544--879585 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
879534 AATTTTTTAA
879544 TTATTTTAAAT-ATAAAATAT
1 TTATTTTAAATCATAAAATAT
*
879564 TTATTTTATATCATAAAATAT
1 TTATTTTAAATCATAAAATAT
879585 T
1 T
879586 AAAATTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
TTATTTTAAATCATAAAATAT
Found at i:884571 original size:6 final size:7
Alignment explanation
Indices: 884520--884571 Score: 52
Period size: 7 Copynumber: 7.4 Consensus size: 7
884510 TAATATCTAG
884520 ATTT-AA
1 ATTTAAA
*
884526 ATTGAAA
1 ATTTAAA
*
884533 TTTTAAA
1 ATTTAAA
884540 ATTTAAA
1 ATTTAAA
884547 ATTTAAA
1 ATTTAAA
*
884554 AGTATAAA
1 A-TTTAAA
*
884562 AATTAAA
1 ATTTAAA
884569 ATT
1 ATT
884572 GATCAATTCG
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
6 3 0.08
7 27 0.75
8 6 0.17
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (7 bp):
ATTTAAA
Found at i:889734 original size:182 final size:182
Alignment explanation
Indices: 889427--889791 Score: 721
Period size: 182 Copynumber: 2.0 Consensus size: 182
889417 ACTTTGCTCA
889427 AAATTAGGATTTAATTTTTATACTTAAATTTGATATAAATTGATCCTTTACAATTATAATGTTAG
1 AAATTAGGATTTAATTTTTATACTTAAATTTGATATAAATTGATCCTTTACAATTATAATGTTAG
*
889492 TAGTATACTTATTCATAGGTCAAACTAATAATCCAAACTCCATAATTTATTCGAAACTTGAGAGA
66 TAGTATACTTATTCATAGGTCAAACTAATAATCCAAACTCCATAATTTATTCAAAACTTGAGAGA
889557 ATTATGAAATATTAAGTCTGAAAAATAAGTTAAGCAGATAGTATAAATATGT
131 ATTATGAAATATTAAGTCTGAAAAATAAGTTAAGCAGATAGTATAAATATGT
889609 AAATTAGGATTTAATTTTTATACTTAAATTTGATATAAATTGATCCTTTACAATTATAATGTTAG
1 AAATTAGGATTTAATTTTTATACTTAAATTTGATATAAATTGATCCTTTACAATTATAATGTTAG
889674 TAGTATACTTATTCATAGGTCAAACTAATAATCCAAACTCCATAATTTATTCAAAACTTGAGAGA
66 TAGTATACTTATTCATAGGTCAAACTAATAATCCAAACTCCATAATTTATTCAAAACTTGAGAGA
889739 ATTATGAAATATTAAGTCTGAAAAATAAGTTAAGCAGATAGTATAAATATGT
131 ATTATGAAATATTAAGTCTGAAAAATAAGTTAAGCAGATAGTATAAATATGT
889791 A
1 A
889792 TTGATCCTAT
Statistics
Matches: 182, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
182 182 1.00
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.37
Consensus pattern (182 bp):
AAATTAGGATTTAATTTTTATACTTAAATTTGATATAAATTGATCCTTTACAATTATAATGTTAG
TAGTATACTTATTCATAGGTCAAACTAATAATCCAAACTCCATAATTTATTCAAAACTTGAGAGA
ATTATGAAATATTAAGTCTGAAAAATAAGTTAAGCAGATAGTATAAATATGT
Found at i:892729 original size:26 final size:27
Alignment explanation
Indices: 892679--892732 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
892669 CTGGAAACCA
892679 ACACAGAAGAAGAATGAACACTAAAATC
1 ACACAGAAGAAGAA-GAACACTAAAATC
892707 ACACAGAAGAAGAA-AATCA-TAAAATC
1 ACACAGAAGAAGAAGAA-CACTAAAATC
892733 TCTATTTAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 9 0.36
27 2 0.08
28 14 0.56
ACGTcount: A:0.59, C:0.17, G:0.13, T:0.11
Consensus pattern (27 bp):
ACACAGAAGAAGAAGAACACTAAAATC
Found at i:893747 original size:17 final size:17
Alignment explanation
Indices: 893721--893775 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
893711 ATATCAAATA
*
893721 TAATAAAAATATAATTT
1 TAATATAAATATAATTT
*
893738 TAATATAAATATTTAATTA
1 TAATATAAATA--TAATTT
893757 T-AT-TAAATATAAATTT
1 TAATATAAATAT-AATTT
893773 TAA
1 TAA
893776 ATAGATTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 1 0.03
16 5 0.16
17 17 0.55
18 2 0.06
19 6 0.19
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TAATATAAATATAATTT
Found at i:893783 original size:22 final size:24
Alignment explanation
Indices: 893738--893821 Score: 73
Period size: 26 Copynumber: 3.4 Consensus size: 24
893728 AATATAATTT
* *
893738 TAATATAAATATTTAATTATATTA
1 TAATATAAATATTTAAATAGATTA
893762 -AATATAAAT-TTTAAATAGATTA
1 TAATATAAATATTTAAATAGATTA
* **
893784 TAAAATAAAAATAAGTAAATAAGAGTTA
1 T--AATATAAATATTTAAAT-AGA-TTA
893812 TAATATAAAT
1 TAATATAAAT
893822 TTATCACTAT
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
22 11 0.23
23 9 0.19
25 8 0.17
26 13 0.27
27 3 0.06
28 4 0.08
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (24 bp):
TAATATAAATATTTAAATAGATTA
Found at i:893791 original size:23 final size:23
Alignment explanation
Indices: 893742--893792 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
893732 TAATTTTAAT
* * *
893742 ATAAATATTTAATTATATTAAAT
1 ATAAATATTTAAATAGATTAAAA
893765 ATAAAT-TTTAAATAGATTATAAA
1 ATAAATATTTAAATAGATTA-AAA
893788 ATAAA
1 ATAAA
893793 AATAAGTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (23 bp):
ATAAATATTTAAATAGATTAAAA
Found at i:896961 original size:2 final size:2
Alignment explanation
Indices: 896956--897023 Score: 118
Period size: 2 Copynumber: 34.0 Consensus size: 2
896946 AGCGTATATA
* *
896956 TG TG TG TA TG TG TG CG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
896998 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
897024 ATATACTTTA
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.01, C:0.01, G:0.49, T:0.49
Consensus pattern (2 bp):
TG
Found at i:902047 original size:11 final size:13
Alignment explanation
Indices: 902020--902051 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
902010 TTCAACAATT
902020 AATTTTTAGTCTC
1 AATTTTTAGTCTC
902033 AATTTTTA-T-TC
1 AATTTTTAGTCTC
902044 AATTTTTA
1 AATTTTTA
902052 AATAGTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 10 0.53
12 1 0.05
13 8 0.42
ACGTcount: A:0.28, C:0.09, G:0.03, T:0.59
Consensus pattern (13 bp):
AATTTTTAGTCTC
Found at i:913868 original size:142 final size:143
Alignment explanation
Indices: 913607--913887 Score: 485
Period size: 142 Copynumber: 2.0 Consensus size: 143
913597 CCAGATAAAT
* *
913607 TAATTATAACTAATAGTTAATTATTGTGGTTTGCTTGTATATGGAACCTAATGAACTTGGTTACG
1 TAATAATAACTAATAGTTAATTATTGTGGTTTGATTGTATATGGAACCTAATGAACTTGGTTACG
*
913672 TGGTTTAATGTTTGTTTGAATACTTAAGTTTCATTAATGATTAATTGTTTGATCTC-TAAGGAGC
66 TGGTTTAATGTTTGTTTGAATACTTAACTTTCATTAATGATTAATTGTTTGATCTCTTAAGGAGC
913736 TCTTTGAGTCCTG
131 TCTTTGAGTCCTG
* *
913749 TAATAATAACTAATAAG-TAATTATTGTGGTTTGATTGTATGTGGAACCTAATGAACTTGGTTAT
1 TAATAATAACTAAT-AGTTAATTATTGTGGTTTGATTGTATATGGAACCTAATGAACTTGGTTAC
*
913813 GTGGTTTAATGTTTGTTTGAATACTTAACTTTCATTAGTGATTAATTGTTTGATCTCTTAAGGAG
65 GTGGTTTAATGTTTGTTTGAATACTTAACTTTCATTAATGATTAATTGTTTGATCTCTTAAGGAG
913878 CTCTTTGAGT
130 CTCTTTGAGT
913888 TCCCTAATAA
Statistics
Matches: 131, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
142 112 0.85
143 19 0.15
ACGTcount: A:0.27, C:0.09, G:0.19, T:0.44
Consensus pattern (143 bp):
TAATAATAACTAATAGTTAATTATTGTGGTTTGATTGTATATGGAACCTAATGAACTTGGTTACG
TGGTTTAATGTTTGTTTGAATACTTAACTTTCATTAATGATTAATTGTTTGATCTCTTAAGGAGC
TCTTTGAGTCCTG
Found at i:919477 original size:21 final size:21
Alignment explanation
Indices: 919453--919493 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
919443 TATTGAGAAA
919453 TATTTATTT-TAATATTTTTAG
1 TATTT-TTTATAATATTTTTAG
*
919474 TATTTTTTATTATATTTTTA
1 TATTTTTTATAATATTTTTA
919494 AAACTTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (21 bp):
TATTTTTTATAATATTTTTAG
Found at i:919916 original size:34 final size:33
Alignment explanation
Indices: 919873--919972 Score: 107
Period size: 34 Copynumber: 3.0 Consensus size: 33
919863 TGTTATTTTC
**
919873 AAAATATATATAATTTTTATTTGTATAATAATTT
1 AAAA-ATATATAAAATTTATTTGTATAATAATTT
*
919907 AACAAATATATAAAATTTATTAT-TATAAAAATTAT
1 AA-AAATATATAAAATTTATT-TGTATAATAATT-T
*
919942 AAAAATA-A-AAAATTTATTCGTATAATAATTT
1 AAAAATATATAAAATTTATTTGTATAATAATTT
919973 TTATTATAGA
Statistics
Matches: 57, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
31 1 0.02
32 19 0.33
33 1 0.02
34 30 0.53
35 6 0.11
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (33 bp):
AAAAATATATAAAATTTATTTGTATAATAATTT
Done.