Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold132
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: 2458301
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 25 characters in sequence are not A, C, G, or T
File 3 of 15
Found at i:433196 original size:2 final size:2
Alignment explanation
Indices: 433189--433215 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
433179 GCAAAAAGGA
433189 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
433216 GTGATGCCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:434629 original size:5 final size:5
Alignment explanation
Indices: 434619--434686 Score: 50
Period size: 5 Copynumber: 13.2 Consensus size: 5
434609 TGCAACTTTA
* * *
434619 AATAT AATAT AAT-T -ATAT AATAT AAAAAT AATTAA AATTT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT -AATAT AA-TAT AATAT AATAT AATAT
*
434669 AAAAAT AATAT AAATAT A
1 -AATAT AATAT -AATAT A
434687 TCAAATTTAA
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
3 2 0.04
4 2 0.04
5 29 0.59
6 16 0.33
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
AATAT
Found at i:434711 original size:27 final size:25
Alignment explanation
Indices: 434617--434715 Score: 94
Period size: 27 Copynumber: 3.8 Consensus size: 25
434607 TATGCAACTT
*
434617 TAAATATAATATAAT-TATATAATA
1 TAAAAATAATATAATATATATAATA
* *
434641 TAAAAATAATTAAAATTTAATATAATA
1 TAAAAATAA-TATAATAT-ATATAATA
*
434668 TAAAAATAATATAA-ATATATCAAATT
1 TAAAAATAATATAATATATAT--AATA
434694 TAAAATATAATTATAATATATA
1 TAAAA-ATAA-TATAATATATA
434716 AAAATTATAA
Statistics
Matches: 62, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
24 12 0.19
25 6 0.10
26 13 0.21
27 21 0.34
28 5 0.08
29 5 0.08
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (25 bp):
TAAAAATAATATAATATATATAATA
Found at i:435576 original size:6 final size:6
Alignment explanation
Indices: 435565--435589 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
435555 AAGAGATGGT
435565 GGTGGC GGTGGC GGTGGC GGTGGC G
1 GGTGGC GGTGGC GGTGGC GGTGGC G
435590 AAGAGAGGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.68, T:0.16
Consensus pattern (6 bp):
GGTGGC
Found at i:435923 original size:21 final size:20
Alignment explanation
Indices: 435864--435924 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 20
435854 ATTTTTATAA
435864 TTAAATTAAATAAAATTTTAAT
1 TTAAATT-AA-AAAATTTTAAT
* *
435886 AT-AAGTAAAATAATTTTAAT
1 TTAAATTAAAA-AATTTTAAT
435906 TTAAATTATAAAAATTTTA
1 TTAAATTA-AAAAATTTTA
435925 TGTTAAGTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
19 2 0.06
20 12 0.38
21 14 0.44
22 4 0.12
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
TTAAATTAAAAAATTTTAAT
Found at i:436631 original size:3 final size:3
Alignment explanation
Indices: 436625--436660 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
436615 CATAAAAAAA
*
436625 TAT TAT TAT TAT TAT TAT TTT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
436661 AAAACGACTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:440555 original size:14 final size:14
Alignment explanation
Indices: 440536--440588 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
440526 ACTTTCCATT
440536 AAAAATAGAAAATA
1 AAAAATAGAAAATA
*
440550 AAAAATA-AAATTA
1 AAAAATAGAAAATA
440563 AAAAA-AGAAGAGA-A
1 AAAAATAGAA-A-ATA
440577 AAAAAT-GAAAAT
1 AAAAATAGAAAAT
440589 TCTTTATCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 11
0.71 0.04 0.24
Matches are distributed among these distances:
12 2 0.06
13 13 0.41
14 17 0.53
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.13
Consensus pattern (14 bp):
AAAAATAGAAAATA
Found at i:440563 original size:26 final size:28
Alignment explanation
Indices: 440533--440589 Score: 75
Period size: 26 Copynumber: 2.1 Consensus size: 28
440523 TTGACTTTCC
*
440533 ATTAAAAATAGAA-A-ATAAAAAAT-AAA
1 ATTAAAAAAAGAAGAGA-AAAAAATGAAA
440559 ATTAAAAAAAGAAGAGAAAAAAATGAAA
1 ATTAAAAAAAGAAGAGAAAAAAATGAAA
440587 ATT
1 ATT
440590 CTTTATCCAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 12 0.44
27 8 0.30
28 7 0.26
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.18
Consensus pattern (28 bp):
ATTAAAAAAAGAAGAGAAAAAAATGAAA
Found at i:440726 original size:2 final size:2
Alignment explanation
Indices: 440719--440751 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
440709 AGAAGAAACA
440719 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
440752 TCTTTGGCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:441843 original size:6 final size:6
Alignment explanation
Indices: 441812--441837 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
441802 ATCATTCTTG
441812 TTTGTT TTTGTT TTTGTT TTTGTT TT
1 TTTGTT TTTGTT TTTGTT TTTGTT TT
441838 CTTTTTTGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (6 bp):
TTTGTT
Found at i:446534 original size:34 final size:37
Alignment explanation
Indices: 446481--446587 Score: 103
Period size: 39 Copynumber: 2.9 Consensus size: 37
446471 TTAAATAATT
* *
446481 TATTTTATTAATTAAAAATTTTAATACATTATT-TTTA
1 TATTTTATTAATT-AAAATTTAAATAAATTATTATTTA
*
446518 TATTTTA-TAATT-AAATTTAAATAAATTATTATTTT
1 TATTTTATTAATTAAAATTTAAATAAATTATTATTTA
** * *
446553 TATTAAATAAATTAATTAATTAAAATAAATTATTA
1 TATTTTATTAATTAA--AATTTAAATAAATTATTA
446588 AATTTTATAT
Statistics
Matches: 58, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
34 16 0.28
35 8 0.14
36 9 0.16
37 8 0.14
39 17 0.29
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (37 bp):
TATTTTATTAATTAAAATTTAAATAAATTATTATTTA
Found at i:446546 original size:21 final size:20
Alignment explanation
Indices: 446522--446585 Score: 60
Period size: 21 Copynumber: 3.2 Consensus size: 20
446512 TTTTTATATT
446522 TTATAATTAAATTTAAATAAA
1 TTATAATT-AATTTAAATAAA
* **
446543 TTATTATTTTTATTAAATAAA
1 TTATAATTAAT-TTAAATAAA
*
446564 -T-TAATTAATTAAAATAAA
1 TTATAATTAATTTAAATAAA
446582 TTAT
1 TTAT
446586 TAAATTTTAT
Statistics
Matches: 33, Mismatches: 7, Indels: 7
0.70 0.15 0.15
Matches are distributed among these distances:
18 8 0.24
19 6 0.18
20 3 0.09
21 16 0.48
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TTATAATTAATTTAAATAAA
Found at i:446554 original size:18 final size:18
Alignment explanation
Indices: 446527--446592 Score: 53
Period size: 18 Copynumber: 3.5 Consensus size: 18
446517 ATATTTTATA
*
446527 ATTAAATTTAAATAAATT
1 ATTATATTTAAATAAATT
*
446545 ATTATTTTTATTAAATAAATT
1 ATTA--TAT-TTAAATAAATT
*
446566 AATTA-ATTAAAATAAATT
1 -ATTATATTTAAATAAATT
*
446584 ATTAAATTT
1 ATTATATTT
446593 TATATTTAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
17 4 0.11
18 17 0.45
19 1 0.03
20 1 0.03
21 11 0.29
22 4 0.11
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
ATTATATTTAAATAAATT
Found at i:447056 original size:13 final size:13
Alignment explanation
Indices: 446999--447058 Score: 54
Period size: 14 Copynumber: 4.5 Consensus size: 13
446989 TAAATTAAAA
446999 AAATAATA-TATT
1 AAATAATATTATT
*
447011 AAAT-ATAATTTTTT
1 AAATAAT-A-TTATT
447025 AAA-AATATTATCAT
1 AAATAATATTAT--T
447039 AAATAATATTATT
1 AAATAATATTATT
447052 AAATAAT
1 AAATAAT
447059 GATGAATATT
Statistics
Matches: 39, Mismatches: 2, Indels: 13
0.72 0.04 0.24
Matches are distributed among these distances:
11 2 0.05
12 8 0.21
13 9 0.23
14 12 0.31
15 8 0.21
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (13 bp):
AAATAATATTATT
Found at i:447307 original size:20 final size:19
Alignment explanation
Indices: 447282--447328 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 19
447272 GGTAAATGAG
447282 ATTTTTATAATTAAT-TTTTA
1 ATTTTTATAA--AATATTTTA
447302 ATTTTTA-AAAATATTTTA
1 ATTTTTATAAAATATTTTA
447320 ATTATTTAT
1 ATT-TTTAT
447329 TTTCGTGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
17 3 0.12
18 8 0.33
19 6 0.25
20 7 0.29
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTTTTATAAAATATTTTA
Found at i:447687 original size:11 final size:11
Alignment explanation
Indices: 447671--447719 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
447661 ATAAATATTA
447671 AATTTTAAAAT
1 AATTTTAAAAT
*
447682 AATTTTTAAAT
1 AATTTTAAAAT
*
447693 AATTTATTTAAAT
1 AA-TT-TTAAAAT
447706 AATTTTAAAA-
1 AATTTTAAAAT
447716 AATT
1 AATT
447720 AATTATTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
10 4 0.12
11 17 0.50
12 4 0.12
13 9 0.26
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
AATTTTAAAAT
Found at i:447704 original size:13 final size:12
Alignment explanation
Indices: 447673--447711 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
447663 AAATATTAAA
*
447673 TTTTAAAATAA-
1 TTTTTAAATAAT
447684 TTTTTAAATAAT
1 TTTTTAAATAAT
447696 TTATTTAAATAAT
1 TT-TTTAAATAAT
447709 TTT
1 TTT
447712 AAAAAATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 10 0.40
12 3 0.12
13 12 0.48
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
TTTTTAAATAAT
Found at i:453444 original size:18 final size:19
Alignment explanation
Indices: 453401--453444 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
453391 TTAATCTTCG
453401 ATTAAAT-TTAAAAAATTT
1 ATTAAATATTAAAAAATTT
* *
453419 ATTTAATATTTAAAAATTT
1 ATTAAATATTAAAAAATTT
453438 -TTAAATA
1 ATTAAATA
453445 AAAATATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
ATTAAATATTAAAAAATTT
Found at i:453461 original size:19 final size:20
Alignment explanation
Indices: 453437--453495 Score: 59
Period size: 19 Copynumber: 3.0 Consensus size: 20
453427 TTTAAAAATT
453437 TTTAAATAAAAATA-TTAAA
1 TTTAAATAAAAATATTTAAA
*
453456 TTTAAA-AAATATATTTAAA
1 TTTAAATAAAAATATTTAAA
** *
453475 TAAAAATAAAATTAATTTAAA
1 TTTAAATAAAAAT-ATTTAAA
453496 AACAGATTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
18 6 0.19
19 15 0.47
20 4 0.12
21 7 0.22
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
TTTAAATAAAAATATTTAAA
Found at i:453478 original size:32 final size:30
Alignment explanation
Indices: 453421--453482 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 30
453411 AAAAATTTAT
453421 TTAATATTTAAAAATTTTTAAATAAAAATA
1 TTAATATTTAAAAATTTTTAAATAAAAATA
453451 TTAA-ATTTAAAAAATATATTTAAATAAAAATA
1 TTAATATTT-AAAAAT-T-TTTAAATAAAAATA
453483 AAATTAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
29 4 0.14
30 10 0.34
31 1 0.03
32 14 0.48
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (30 bp):
TTAATATTTAAAAATTTTTAAATAAAAATA
Found at i:454031 original size:2 final size:2
Alignment explanation
Indices: 454024--454053 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
454014 AAATGTAAAG
454024 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
454054 TATTTGAGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:454116 original size:13 final size:13
Alignment explanation
Indices: 454095--454135 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
454085 ACACATTTTT
454095 AAAATATTAATAA
1 AAAATATTAATAA
*
454108 AAGATATTAATAA
1 AAAATATTAATAA
454121 ATAAATA-TAATAA
1 A-AAATATTAATAA
454134 AA
1 AA
454136 TTTATTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 1 0.04
13 20 0.80
14 4 0.16
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.29
Consensus pattern (13 bp):
AAAATATTAATAA
Found at i:454141 original size:26 final size:27
Alignment explanation
Indices: 454096--454149 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
454086 CACATTTTTA
454096 AAATATTAATAAAAGATATTAATAAAT
1 AAATATTAATAAAAGATATTAATAAAT
** *
454123 AAATA-TAATAAAATTTATTATTAAAT
1 AAATATTAATAAAAGATATTAATAAAT
454149 A
1 A
454150 TAATGAGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 19 0.79
27 5 0.21
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (27 bp):
AAATATTAATAAAAGATATTAATAAAT
Found at i:455367 original size:2 final size:2
Alignment explanation
Indices: 455360--455390 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
455350 TTAAGATACC
455360 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
455391 ACCAAATCGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:456260 original size:30 final size:29
Alignment explanation
Indices: 456211--456284 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 29
456201 AAACACATTA
* * *
456211 ATTAAAATACTGTTAATATTTAAATAAATT
1 ATTAAAATAATATT-ATATTAAAATAAATT
*
456241 ATTAATAATAATATTATATTAAAATAAGTT
1 ATTAA-AATAATATTATATTAAAATAAATT
*
456271 ATTAAAATATTATT
1 ATTAAAATAATATT
456285 TAATCAGTGA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
29 8 0.21
30 23 0.61
31 7 0.18
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (29 bp):
ATTAAAATAATATTATATTAAAATAAATT
Found at i:456497 original size:18 final size:19
Alignment explanation
Indices: 456468--456528 Score: 63
Period size: 18 Copynumber: 3.2 Consensus size: 19
456458 ATTTTTAAAA
*
456468 TTAATAAAAAATTATATTT
1 TTAATAAAAAATAATATTT
*
456487 TTAAT-AAAAATAATATTA
1 TTAATAAAAAATAATATTT
456505 TT-ATAAATATAATAATAGTTT
1 TTAATAAA-A-AATAATA-TTT
456526 TTA
1 TTA
456529 TTATTATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
17 2 0.06
18 15 0.44
19 6 0.18
20 7 0.21
21 4 0.12
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (19 bp):
TTAATAAAAAATAATATTT
Found at i:456738 original size:31 final size:31
Alignment explanation
Indices: 456697--456759 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
456687 TTATCTAATT
*
456697 ATTAAGGGTTATAATCATCTAAGTATTTTAA
1 ATTAAAGGTTATAATCATCTAAGTATTTTAA
*
456728 ATTAAAGGTTATAATCATCTAATTATTTTAA
1 ATTAAAGGTTATAATCATCTAAGTATTTTAA
456759 A
1 A
456760 ATTTTAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.41, C:0.06, G:0.10, T:0.43
Consensus pattern (31 bp):
ATTAAAGGTTATAATCATCTAAGTATTTTAA
Found at i:456773 original size:22 final size:22
Alignment explanation
Indices: 456747--456831 Score: 65
Period size: 22 Copynumber: 4.0 Consensus size: 22
456737 TATAATCATC
456747 TAATTATTTTAAAATTTTAATT
1 TAATTATTTTAAAATTTTAATT
** *
456769 TAATTAGGTTATAATTGTCTAA-T
1 TAATTATTTTAAAATT-T-TAATT
456792 T-A-T-TTTTAAAA--TTAATT
1 TAATTATTTTAAAATTTTAATT
*
456809 ATAATTATTTTAAATTTTTAATT
1 -TAATTATTTTAAAATTTTAATT
456832 ATTTTAATTT
Statistics
Matches: 47, Mismatches: 7, Indels: 17
0.66 0.10 0.24
Matches are distributed among these distances:
16 3 0.06
17 2 0.04
18 1 0.02
19 1 0.02
20 6 0.13
21 8 0.17
22 14 0.30
23 9 0.19
24 3 0.06
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (22 bp):
TAATTATTTTAAAATTTTAATT
Found at i:456780 original size:41 final size:40
Alignment explanation
Indices: 456721--456804 Score: 116
Period size: 41 Copynumber: 2.1 Consensus size: 40
456711 TCATCTAAGT
456721 ATTTTAAATTAAAGGTTATAATCATCTAATTA-TTTTAAA
1 ATTTTAAATTAAAGGTTATAATCATCTAATTATTTTTAAA
* **
456760 ATTTTAATTTAATTAGGTTATAATTGTCTAATTATTTTTAAA
1 ATTTTAAATTAA--AGGTTATAATCATCTAATTATTTTTAAA
456802 ATT
1 ATT
456805 AATTATAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
39 11 0.28
41 18 0.46
42 10 0.26
ACGTcount: A:0.39, C:0.04, G:0.06, T:0.51
Consensus pattern (40 bp):
ATTTTAAATTAAAGGTTATAATCATCTAATTATTTTTAAA
Found at i:456814 original size:41 final size:40
Alignment explanation
Indices: 456733--456836 Score: 115
Period size: 41 Copynumber: 2.6 Consensus size: 40
456723 TTTAAATTAA
*
456733 AGGTTATAATCATCTAATTA-TTTTAAAATTTTAATTTAATT
1 AGGTTATAAT-TTCTAATTATTTTTAAAA-TTTAATTTAATT
456774 AGGTTATAATTGTCTAATTATTTTTAAAA-TTAATTATAATT
1 AGGTTATAATT-TCTAATTATTTTTAAAATTTAATT-TAATT
** *
456815 ATTTTA-AATTTTTAATTATTTT
1 AGGTTATAATTTCTAATTATTTT
456837 AATTTGCTAA
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
39 11 0.20
40 10 0.18
41 27 0.48
42 8 0.14
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.55
Consensus pattern (40 bp):
AGGTTATAATTTCTAATTATTTTTAAAATTTAATTTAATT
Found at i:456992 original size:38 final size:38
Alignment explanation
Indices: 456901--456993 Score: 100
Period size: 39 Copynumber: 2.4 Consensus size: 38
456891 TAAATAATAA
*
456901 TAATATAAAATTTTAAAATAATTAGACGATTACAACTCT
1 TAAT-TAAAATTTAAAAATAATTAGACGATTACAACTCT
* * *
456940 TAATTTAAATTTTAAAAATAATTATACGATTATAA-T-T
1 TAA-TTAAAATTTAAAAATAATTAGACGATTACAACTCT
456977 TAAATTAAAAGTTTAAA
1 T-AATTAAAA-TTTAAA
456994 TTAAATATTT
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
37 7 0.15
38 9 0.20
39 29 0.63
40 1 0.02
ACGTcount: A:0.51, C:0.05, G:0.04, T:0.40
Consensus pattern (38 bp):
TAATTAAAATTTAAAAATAATTAGACGATTACAACTCT
Found at i:457165 original size:27 final size:30
Alignment explanation
Indices: 457103--457170 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 30
457093 TATTGTATTT
* *
457103 ATATAATATTATTAATTTAAAAATATACTA
1 ATATAATAATATTAATTAAAAAATATACTA
*
457133 ACATAATAATA-TAATTAAAAAATAT-C-A
1 ATATAATAATATTAATTAAAAAATATACTA
457160 ATATAATAATA
1 ATATAATAATA
457171 ATTTTAATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
27 11 0.32
28 1 0.03
29 13 0.38
30 9 0.26
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (30 bp):
ATATAATAATATTAATTAAAAAATATACTA
Found at i:457169 original size:30 final size:30
Alignment explanation
Indices: 457105--457179 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
457095 TTGTATTTAT
* * *
457105 ATAATATTATTAATTTAAAAATATACTAAC
1 ATAATAATATTAATTAAAAAATATAATAAC
457135 ATAATAATA-TAATTAAAAAATATCAATATA-
1 ATAATAATATTAATTAAAAAATAT-AATA-AC
*
457165 ATAATAATTTTAATT
1 ATAATAATATTAATT
457180 TTAATAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
29 13 0.34
30 19 0.50
31 6 0.16
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (30 bp):
ATAATAATATTAATTAAAAAATATAATAAC
Found at i:457255 original size:32 final size:33
Alignment explanation
Indices: 457219--457287 Score: 88
Period size: 32 Copynumber: 2.1 Consensus size: 33
457209 TAATTCTATT
457219 TAAAAATTATTAAAACATTTAA-TGATTTTAA-G
1 TAAAAATTATT-AAACATTTAAGTGATTTTAATG
* * *
457251 TAAAATTTATTAATCTTTTAAGTGATTTTAATG
1 TAAAAATTATTAAACATTTAAGTGATTTTAATG
457284 TAAA
1 TAAA
457288 TTTGTTAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 8 0.25
32 19 0.59
33 5 0.16
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (33 bp):
TAAAAATTATTAAACATTTAAGTGATTTTAATG
Found at i:457289 original size:32 final size:31
Alignment explanation
Indices: 457236--457311 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 31
457226 TATTAAAACA
457236 TTTAATGATTTTAAGTAAAATTTATTAATCT
1 TTTAATGATTTTAAGTAAAATTTATTAATCT
*
457267 TTTAAGTGATTTTAATGT-AAATTTGTTAAT-T
1 TTTAA-TGATTTTAA-GTAAAATTTATTAATCT
457298 AATTTAATGATTTT
1 --TTTAATGATTTT
457312 TTATGAATCA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
31 6 0.15
32 27 0.68
33 7 0.17
ACGTcount: A:0.36, C:0.01, G:0.09, T:0.54
Consensus pattern (31 bp):
TTTAATGATTTTAAGTAAAATTTATTAATCT
Found at i:457358 original size:16 final size:16
Alignment explanation
Indices: 457325--457368 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
457315 TGAATCAAAA
457325 TAATATTATTTT--AT
1 TAATATTATTTTAAAT
457339 TAAT-TTCATTTTAAAT
1 TAATATT-ATTTTAAAT
457355 TAATATTATTTTAA
1 TAATATTATTTTAA
457369 TAATTTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 2 0.08
14 9 0.35
16 13 0.50
17 2 0.08
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATATTATTTTAAAT
Found at i:457557 original size:7 final size:7
Alignment explanation
Indices: 457549--457581 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
457539 AGTTTCAAAT
*
457549 TTAAAAT
1 TTAAAAA
457556 TTAAAAA
1 TTAAAAA
457563 TTAAAAA
1 TTAAAAA
457570 TT-AAAA
1 TTAAAAA
457576 TTAAAA
1 TTAAAA
457582 GTTCTTAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (7 bp):
TTAAAAA
Found at i:457857 original size:17 final size:18
Alignment explanation
Indices: 457811--457849 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
457801 GGTGGTTAAT
* *
457811 TAGATATATATATATATA
1 TAGATATTTTTATATATA
457829 TAGATATTTTTATAATATA
1 TAGATATTTTTAT-ATATA
457848 TA
1 TA
457850 TTTTTTTAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (18 bp):
TAGATATTTTTATATATA
Found at i:470240 original size:19 final size:19
Alignment explanation
Indices: 470216--470254 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
470206 TTTCACATAC
* *
470216 ACAGTAACTGTATATGTGA
1 ACAGTAACTATATACGTGA
*
470235 ACAGTACCTATATACGTGA
1 ACAGTAACTATATACGTGA
470254 A
1 A
470255 TAGTGCCTCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.28
Consensus pattern (19 bp):
ACAGTAACTATATACGTGA
Found at i:470572 original size:50 final size:50
Alignment explanation
Indices: 470503--470659 Score: 201
Period size: 50 Copynumber: 3.2 Consensus size: 50
470493 TTGCTTAGAA
*
470503 TCAACAATTACGATCACCTCTCTCTATTGTCAAAGGTTAATGAAGAATAG
1 TCAATAATTACGATCACCTCTCTCTATTGTCAAAGGTTAATGAAGAATAG
* * ** *
470553 -CTAATAATTACGATTACCTCTCTTTATTGTCAAA-GTTGGTGAAAAATAG
1 TC-AATAATTACGATCACCTCTCTCTATTGTCAAAGGTTAATGAAGAATAG
* * * *
470602 TCAACAATTACGACCACCTCTCTCGAATGTCAAAGGTTAATGAAGAATAG
1 TCAATAATTACGATCACCTCTCTCTATTGTCAAAGGTTAATGAAGAATAG
470652 TCAATAAT
1 TCAATAAT
470660 GGTAATACCT
Statistics
Matches: 88, Mismatches: 16, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
49 39 0.44
50 49 0.56
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Consensus pattern (50 bp):
TCAATAATTACGATCACCTCTCTCTATTGTCAAAGGTTAATGAAGAATAG
Found at i:472805 original size:20 final size:17
Alignment explanation
Indices: 472774--472821 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 17
472764 TAAAAAAATT
472774 ATTAAT-TATTATAATTA
1 ATTAATATATTATAA-TA
472791 ATATAATGATATTATAATA
1 AT-TAAT-ATATTATAATA
472810 ATTAATATATTA
1 ATTAATATATTA
472822 ACAAATCTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
17 8 0.29
18 8 0.29
19 4 0.14
20 8 0.29
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (17 bp):
ATTAATATATTATAATA
Found at i:473642 original size:21 final size:20
Alignment explanation
Indices: 473608--473646 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
473598 CACATTTTTA
*
473608 TCTAAATGTATCGATACATT
1 TCTAAATATATCGATACATT
473628 TCTAGAATATATCGATACA
1 TCTA-AATATATCGATACA
473647 AGGTCTCAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.36
Consensus pattern (20 bp):
TCTAAATATATCGATACATT
Found at i:482575 original size:15 final size:16
Alignment explanation
Indices: 482545--482578 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
482535 ATTATTTGAG
482545 TTTAAATTAATAAATTA
1 TTTAAATT-ATAAATTA
482562 TTTAAATT-TAAATTA
1 TTTAAATTATAAATTA
482577 TT
1 TT
482579 GAATTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTAAATTATAAATTA
Found at i:482583 original size:23 final size:23
Alignment explanation
Indices: 482532--482576 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
482522 ATTGATATTT
* *
482532 TAAATTATTTGAGTTTAAATTAA
1 TAAATTATTTAAATTTAAATTAA
482555 TAAATTATTTAAATTTAAATTA
1 TAAATTATTTAAATTTAAATTA
482577 TTGAATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (23 bp):
TAAATTATTTAAATTTAAATTAA
Found at i:487966 original size:24 final size:24
Alignment explanation
Indices: 487939--487990 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
487929 TTAATTCCTT
* *
487939 TTCTTTAATCTTTCCCTTTTTGGA
1 TTCTCTAATCCTTCCCTTTTTGGA
** *
487963 TTCTCTCTTCCTTCCTTTTTTGGA
1 TTCTCTAATCCTTCCCTTTTTGGA
487987 TTCT
1 TTCT
487991 ATGCTACATG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.08, C:0.25, G:0.08, T:0.60
Consensus pattern (24 bp):
TTCTCTAATCCTTCCCTTTTTGGA
Found at i:488659 original size:23 final size:25
Alignment explanation
Indices: 488632--488693 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 25
488622 AAAAATGATG
488632 TAAATATTATATAAAATA-ATA-AT
1 TAAATATTATATAAAATATATATAT
*
488655 TAAATAAAATAATATAAAATATATATAT
1 TAAAT---ATTATATAAAATATATATAT
488683 TAAATATTATA
1 TAAATATTATA
488694 ACATGAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
23 5 0.16
25 5 0.16
26 12 0.38
27 3 0.09
28 7 0.22
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (25 bp):
TAAATATTATATAAAATATATATAT
Found at i:488661 original size:16 final size:16
Alignment explanation
Indices: 488637--488668 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
488627 TGATGTAAAT
*
488637 ATTATATAAAATAATA
1 ATTAAATAAAATAATA
488653 ATTAAATAAAATAATA
1 ATTAAATAAAATAATA
488669 TAAAATATAT
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
ATTAAATAAAATAATA
Found at i:494758 original size:15 final size:14
Alignment explanation
Indices: 494738--494769 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
494728 GTTTTGCATA
494738 AGAAAATTCCATCCT
1 AGAAAATTCCAT-CT
494753 AGAAAATTCCATCT
1 AGAAAATTCCATCT
494767 AGA
1 AGA
494770 TGCTTATAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.44, C:0.22, G:0.09, T:0.25
Consensus pattern (14 bp):
AGAAAATTCCATCT
Found at i:505809 original size:2 final size:2
Alignment explanation
Indices: 505802--505832 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
505792 TCAACCACCA
505802 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
505833 AAATTACTAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:507372 original size:4 final size:4
Alignment explanation
Indices: 507363--507390 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
507353 GTAAACAAAG
507363 ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC
507391 CTTGAGTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:507700 original size:3 final size:3
Alignment explanation
Indices: 507692--507716 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
507682 AAGAGAAGGA
507692 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
507717 CTTACCTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:509297 original size:19 final size:20
Alignment explanation
Indices: 509262--509299 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
509252 TTATTGATTA
*
509262 AATATAAATTATTATTTAAT
1 AATAAAAATTATTATTTAAT
509282 AATAAAAATT-TTATTTAA
1 AATAAAAATTATTATTTAA
509300 ATTTAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AATAAAAATTATTATTTAAT
Found at i:509377 original size:19 final size:20
Alignment explanation
Indices: 509322--509386 Score: 66
Period size: 17 Copynumber: 3.4 Consensus size: 20
509312 ATATAAATTT
*
509322 TAATATAAATAATTTTTAATA
1 TAATTTAAATAA-TTTTAATA
*
509343 TTATTTAAATAA---TAATA
1 TAATTTAAATAATTTTAATA
*
509360 TAATTTAAA-AATTTTAATT
1 TAATTTAAATAATTTTAATA
509379 TAATTTAA
1 TAATTTAA
509387 TTTAATTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
16 2 0.05
17 13 0.35
19 12 0.32
21 10 0.27
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TAATTTAAATAATTTTAATA
Found at i:509380 original size:5 final size:5
Alignment explanation
Indices: 509372--509396 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
509362 ATTTAAAAAT
509372 TTTAA TTTAA TTTAA TTTAA TTTAA
1 TTTAA TTTAA TTTAA TTTAA TTTAA
509397 ATAAAACTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTTAA
Found at i:510524 original size:23 final size:23
Alignment explanation
Indices: 510479--510539 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
510469 TACAATTATG
510479 TAATAT-AAAT-TGATAAAAAAA
1 TAATATAAAATATGATAAAAAAA
510500 TAAT-TAAAATATGATATAAAAAA
1 TAATATAAAATATGATA-AAAAAA
510523 TAATAT-AAATAT-ATAAA
1 TAATATAAAATATGATAAA
510540 TATATCAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
20 1 0.03
21 10 0.28
22 8 0.22
23 16 0.44
24 1 0.03
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (23 bp):
TAATATAAAATATGATAAAAAAA
Found at i:510579 original size:32 final size:33
Alignment explanation
Indices: 510522--510590 Score: 113
Period size: 32 Copynumber: 2.1 Consensus size: 33
510512 GATATAAAAA
*
510522 ATAATATAAATATATAAATATATCAAATTTTAT
1 ATAATATAAATATATAAATATATCAAAATTTAT
*
510555 ATAATATAAAT-TATTAATATATCAAAATTTAT
1 ATAATATAAATATATAAATATATCAAAATTTAT
510587 ATAA
1 ATAA
510591 AATATATAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 23 0.68
33 11 0.32
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (33 bp):
ATAATATAAATATATAAATATATCAAAATTTAT
Found at i:514224 original size:13 final size:13
Alignment explanation
Indices: 514196--514229 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
514186 TTTTATACTC
*
514196 ATTAAA-ATATAT
1 ATTAAATATAAAT
514208 ATTAAATATAAAT
1 ATTAAATATAAAT
514221 ATTAAATAT
1 ATTAAATAT
514230 GTATTATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 6 0.30
13 14 0.70
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
ATTAAATATAAAT
Found at i:515675 original size:2 final size:2
Alignment explanation
Indices: 515668--515699 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
515658 AAATCAAAAT
515668 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
515700 TATATATATA
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:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:515704 original size:2 final size:2
Alignment explanation
Indices: 515699--515733 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
515689 ACACACACAC
515699 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
515734 GTTAGTTCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:519059 original size:5 final size:5
Alignment explanation
Indices: 519014--519067 Score: 54
Period size: 5 Copynumber: 10.4 Consensus size: 5
519004 TTAATAAATG
* * * *
519014 TTATA TTTATA TTATT TTAATA TTAAA TTTTA TTATT TTATA TTATA TTATA
1 TTATA -TTATA TTATA TT-ATA TTATA TTATA TTATA TTATA TTATA TTATA
519066 TT
1 TT
519068 TATAATTATC
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
5 30 0.77
6 9 0.23
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (5 bp):
TTATA
Found at i:520886 original size:18 final size:18
Alignment explanation
Indices: 520855--520907 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
520845 ATAAAATTAA
* *
520855 TTAAT-TTTTTTATATCT
1 TTAATATTTTATATATAT
520872 TT-ATAATTTTATATATAT
1 TTAAT-ATTTTATATATAT
520890 TTAATATTTTA-ATATAT
1 TTAATATTTTATATATAT
520907 T
1 T
520908 AATTATTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
16 2 0.06
17 9 0.29
18 18 0.58
19 2 0.06
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (18 bp):
TTAATATTTTATATATAT
Found at i:529592 original size:22 final size:21
Alignment explanation
Indices: 529567--529619 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
529557 ATTATATTTT
529567 TTTAAATTAATATTTAATAAAA
1 TTTAAATTAATATTT-ATAAAA
* *
529589 TTTAAATTTTATATTTTTAAAA
1 TTTAAA-TTAATATTTATAAAA
529611 TTTATAATT
1 TTTA-AATT
529620 TTTTTATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 17 0.63
23 10 0.37
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTAAATTAATATTTATAAAA
Found at i:529611 original size:16 final size:16
Alignment explanation
Indices: 529589--529622 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
529579 TTTAATAAAA
*
529589 TTTAAATTTTAT-ATT
1 TTTAAAATTTATAATT
529604 TTTAAAATTTATAATT
1 TTTAAAATTTATAATT
529620 TTT
1 TTT
529623 TTATTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTAAAATTTATAATT
Found at i:536650 original size:11 final size:11
Alignment explanation
Indices: 536615--536674 Score: 63
Period size: 11 Copynumber: 5.6 Consensus size: 11
536605 GTATTGATAT
536615 TATTTTT-TTA
1 TATTTTTATTA
* *
536625 TA-TTATATCA
1 TATTTTTATTA
536635 TATTTTTATTA
1 TATTTTTATTA
*
536646 TATTTTGATTA
1 TATTTTTATTA
536657 T-TTTTATATTA
1 TATTTT-TATTA
536668 TATTTTT
1 TATTTTT
536675 TTCAAAATTA
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
9 3 0.08
10 10 0.25
11 23 0.57
12 4 0.10
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.70
Consensus pattern (11 bp):
TATTTTTATTA
Found at i:537460 original size:2 final size:2
Alignment explanation
Indices: 537453--537493 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
537443 ACACGCTAGA
537453 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
537494 ATTTGCAATC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:538596 original size:24 final size:26
Alignment explanation
Indices: 538545--538602 Score: 93
Period size: 24 Copynumber: 2.3 Consensus size: 26
538535 TGGGTGGCTA
*
538545 GTCAACAAAAGCCACCCTTTGTGTTT
1 GTCAACAAAAGCCACCCTATGTGTTT
538571 GTCAACAAAAGCCA-CC-ATGTGTTT
1 GTCAACAAAAGCCACCCTATGTGTTT
538595 GTCAACAA
1 GTCAACAA
538603 TGGTGGTTAC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 15 0.48
25 2 0.06
26 14 0.45
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.26
Consensus pattern (26 bp):
GTCAACAAAAGCCACCCTATGTGTTT
Found at i:538631 original size:27 final size:27
Alignment explanation
Indices: 538592--538657 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
538582 CCACCATGTG
*
538592 TTTGTCAACAATGGTGGTTACTTTGTA
1 TTTGTCAAAAATGGTGGTTACTTTGTA
* * *
538619 TTTGTCAAAAATGGTGGTTCCTTTTTG
1 TTTGTCAAAAATGGTGGTTACTTTGTA
538646 TTTGTCAAAAAT
1 TTTGTCAAAAAT
538658 TATGGCTTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.24, C:0.11, G:0.20, T:0.45
Consensus pattern (27 bp):
TTTGTCAAAAATGGTGGTTACTTTGTA
Found at i:538687 original size:24 final size:24
Alignment explanation
Indices: 538619--538688 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 24
538609 TTACTTTGTA
* *
538619 TTTGTCAAAAATGGTGGTTCCTTTTTG
1 TTTGTCAAAATTGGTGG---CTTGTTG
*
538646 TTTGTCAAAAATT-ATGGCTTGTTG
1 TTTGTC-AAAATTGGTGGCTTGTTG
538670 TTTGTCAAAATTGGTGGCT
1 TTTGTCAAAATTGGTGGCT
538689 AATTTTTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
23 6 0.16
24 17 0.46
27 9 0.24
28 5 0.14
ACGTcount: A:0.21, C:0.10, G:0.23, T:0.46
Consensus pattern (24 bp):
TTTGTCAAAATTGGTGGCTTGTTG
Found at i:544819 original size:34 final size:33
Alignment explanation
Indices: 544773--544838 Score: 96
Period size: 34 Copynumber: 2.0 Consensus size: 33
544763 GATGCTTCTA
*
544773 AAAATTATTTGTATTTGTTATCACATATATTTT
1 AAAATTATTTGTACTTGTTATCACATATATTTT
* *
544806 AAAATTTTATTGTACTTGTTATCACATGTATTT
1 AAAATTAT-TTGTACTTGTTATCACATATATTT
544839 ATATGTGAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 7 0.24
34 22 0.76
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.53
Consensus pattern (33 bp):
AAAATTATTTGTACTTGTTATCACATATATTTT
Found at i:548140 original size:21 final size:21
Alignment explanation
Indices: 548116--548178 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 21
548106 GCCCTCAATT
* *
548116 TCTGCAACTAAGGCTGTCACA
1 TCTGCAACTAAGCCTGTAACA
* * *
548137 TCTGCAGCAAAGCCTGTAATA
1 TCTGCAACTAAGCCTGTAACA
* * *
548158 TCTGGAACTAAGTCTGCAACA
1 TCTGCAACTAAGCCTGTAACA
548179 AAACCTGTAG
Statistics
Matches: 31, Mismatches: 11, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (21 bp):
TCTGCAACTAAGCCTGTAACA
Found at i:551373 original size:19 final size:19
Alignment explanation
Indices: 551349--551389 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
551339 GTCCCAAAAC
*
551349 TCCAAGTCCTGAGATCATT
1 TCCAAGTCCTGAAATCATT
551368 TCCAAGTCCTGAAATCATT
1 TCCAAGTCCTGAAATCATT
551387 TCC
1 TCC
551390 CTAGCAAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.27, C:0.29, G:0.12, T:0.32
Consensus pattern (19 bp):
TCCAAGTCCTGAAATCATT
Found at i:551699 original size:48 final size:48
Alignment explanation
Indices: 551628--551723 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
551618 ATGACTGGCA
551628 AAACATGATACTAGTAACAAGAGTAGCAAGATGCTCTTAAGATAGTTT
1 AAACATGATACTAGTAACAAGAGTAGCAAGATGCTCTTAAGATAGTTT
551676 AAACATGATACTAGTAACAAGAGTAGCAAGATGCTCTTAAGATAGTTT
1 AAACATGATACTAGTAACAAGAGTAGCAAGATGCTCTTAAGATAGTTT
551724 TGATTACAGA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (48 bp):
AAACATGATACTAGTAACAAGAGTAGCAAGATGCTCTTAAGATAGTTT
Found at i:555434 original size:23 final size:24
Alignment explanation
Indices: 555400--555449 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
555390 AAATTTTAAT
555400 AATTTATATTTTAAAATATAAA-A
1 AATTTATATTTTAAAATATAAATA
* *
555423 AATTTA-ATTTTTATAATTTAAATA
1 AATTTATA-TTTTAAAATATAAATA
555447 AAT
1 AAT
555450 ATAACTATCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 1 0.04
23 18 0.78
24 4 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
AATTTATATTTTAAAATATAAATA
Found at i:555528 original size:22 final size:25
Alignment explanation
Indices: 555474--555529 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 25
555464 AATAGTCAAA
555474 TAATAAATATAAGTAAAATATATATT
1 TAAT-AATATAAGTAAAATATATATT
555500 T-AT--TATAAGTAAAA-A-AT-TT
1 TAATAATATAAGTAAAATATATATT
555519 TAATAATATAA
1 TAATAATATAA
555530 AATTTAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
19 3 0.11
20 4 0.15
21 1 0.04
22 16 0.59
25 2 0.07
26 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (25 bp):
TAATAATATAAGTAAAATATATATT
Found at i:557301 original size:11 final size:10
Alignment explanation
Indices: 557263--557309 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
557253 AGTTCTTAGT
*
557263 ATTTTTTTTA
1 ATTTTTTATA
* *
557273 ATTTTTCAAA
1 ATTTTTTATA
557283 ATTTTTTATA
1 ATTTTTTATA
*
557293 ATTTATT-TA
1 ATTTTTTATA
557302 ATTTTTTA
1 ATTTTTTA
557310 GATGAGAACT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
9 8 0.28
10 21 0.72
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (10 bp):
ATTTTTTATA
Found at i:557585 original size:11 final size:12
Alignment explanation
Indices: 557555--557584 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
557545 GTTACTTTTA
*
557555 TTTTTTTAATTT
1 TTTTTTTGATTT
557567 TTTTTTTGATTT
1 TTTTTTTGATTT
557579 TTTTTT
1 TTTTTT
557585 GTTTGGTAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.10, C:0.00, G:0.03, T:0.87
Consensus pattern (12 bp):
TTTTTTTGATTT
Found at i:558914 original size:16 final size:17
Alignment explanation
Indices: 558880--558920 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
558870 CTGAAAAATG
558880 TATTTTTTTATTAGTGT
1 TATTTTTTTATTAGTGT
558897 TATTTTTTTGA-TAG-GT
1 TATTTTTTT-ATTAGTGT
558913 TATTTTTT
1 TATTTTTT
558921 GTTTTTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 10 0.43
17 12 0.52
18 1 0.04
ACGTcount: A:0.17, C:0.00, G:0.12, T:0.71
Consensus pattern (17 bp):
TATTTTTTTATTAGTGT
Found at i:561570 original size:89 final size:89
Alignment explanation
Indices: 561422--561735 Score: 333
Period size: 89 Copynumber: 3.5 Consensus size: 89
561412 GATCTAATAA
* * * * * * *
561422 AATAAAATTCTTGAAACTCGAAAGATGTAACAGATGCATGTAGATATCATATTCTTTTTGACACG
1 AATAAAATTCTTAAAACTCGAAAAATATAACAGATGCATGTAGGTATCAAATTCCTTTTGATACG
*
561487 ACGAAAAATATTTAACTAATATC-T
66 ACGAAAAATATTTAACTAAT-GCAT
* * * * *
561511 AATAAAATTCTTAAAACCCGAAAGATGTAACAGATGCATGTGGGTATCAAATTCCTTTTGATACT
1 AATAAAATTCTTAAAACTCGAAAAATATAACAGATGCATGTAGGTATCAAATTCCTTTTGATACG
*
561576 ACGAAAAATATTTAACTAATGCTT
66 ACGAAAAATATTTAACTAATGCAT
* * * * * * * * * *
561600 AATAAAATTCTTGAAACTTGAAAAATATGATAGTTACATGTGGGTATCAGATTCCTTCTGATATG
1 AATAAAATTCTTAAAACTCGAAAAATATAACAGATGCATGTAGGTATCAAATTCCTTTTGATACG
* * *
561665 ATGAAAAGTATTTGACTAATGCAT
66 ACGAAAAATATTTAACTAATGCAT
* * * *
561689 AATAAATTTTTTAAAACTCGAAAAATATTACAGATGCACGTAGGTAT
1 AATAAAATTCTTAAAACTCGAAAAATATAACAGATGCATGTAGGTAT
561736 GAGATTTTTG
Statistics
Matches: 188, Mismatches: 36, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
88 1 0.01
89 187 0.99
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (89 bp):
AATAAAATTCTTAAAACTCGAAAAATATAACAGATGCATGTAGGTATCAAATTCCTTTTGATACG
ACGAAAAATATTTAACTAATGCAT
Found at i:562874 original size:16 final size:15
Alignment explanation
Indices: 562848--562877 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
562838 TTGATAAAAT
562848 AATTTATTTAAATTA
1 AATTTATTTAAATTA
562863 AATTTGATTTAAATT
1 AATTT-ATTTAAATT
562878 TAAAATTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
AATTTATTTAAATTA
Found at i:563072 original size:16 final size:16
Alignment explanation
Indices: 563000--563065 Score: 71
Period size: 16 Copynumber: 4.1 Consensus size: 16
562990 GATCATAAAC
563000 TTAAAATAAATT-AAAA
1 TTAAAAT-AATTAAAAA
* * * *
563016 TAAAAATAATTTATAT
1 TTAAAATAATTAAAAA
563032 TTAAAATAATTAAAAA
1 TTAAAATAATTAAAAA
563048 TTAAAATAATTCAAAAA
1 TTAAAATAATT-AAAAA
563065 T
1 T
563066 AATATAAAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
15 4 0.10
16 31 0.76
17 6 0.15
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (16 bp):
TTAAAATAATTAAAAA
Found at i:563786 original size:13 final size:14
Alignment explanation
Indices: 563755--563788 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
563745 TCAAAACAAG
*
563755 AAAAGAAATAGTAA
1 AAAAGAAAAAGTAA
563769 AAAAGAAAAAG-AA
1 AAAAGAAAAAGTAA
563782 AAAAGAA
1 AAAAGAA
563789 GTCGATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.47
14 10 0.53
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (14 bp):
AAAAGAAAAAGTAA
Found at i:564219 original size:5 final size:5
Alignment explanation
Indices: 564209--564233 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
564199 AGTGGAGGAA
564209 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
564234 TGAAGAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:568785 original size:3 final size:3
Alignment explanation
Indices: 568777--568825 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
568767 GGGCTTGTTC
568777 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
568825 T
1 T
568826 GTCTCATCTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:569143 original size:13 final size:13
Alignment explanation
Indices: 569125--569151 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
569115 AGATACGAAA
569125 ATTTATGTGGTTC
1 ATTTATGTGGTTC
569138 ATTTATGTGGTTC
1 ATTTATGTGGTTC
569151 A
1 A
569152 GCTTTTAAAT
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:0.19, C:0.07, G:0.22, T:0.52
Consensus pattern (13 bp):
ATTTATGTGGTTC
Found at i:580340 original size:21 final size:22
Alignment explanation
Indices: 580302--580347 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
580292 ATCTGTTGAA
* **
580302 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
580323 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
580345 ACT
1 ACT
580348 TGTCTGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:582825 original size:20 final size:20
Alignment explanation
Indices: 582800--582838 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
582790 AAGAATTGAA
582800 GAGAGATACAAGAGAGGGAT
1 GAGAGATACAAGAGAGGGAT
**
582820 GAGAGATACTTGAGAGGGA
1 GAGAGATACAAGAGAGGGA
582839 GGAGGGAGCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.05, G:0.41, T:0.13
Consensus pattern (20 bp):
GAGAGATACAAGAGAGGGAT
Found at i:582970 original size:28 final size:27
Alignment explanation
Indices: 582927--582992 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
582917 AGCCTCAATA
* * *
582927 TTTGACAAATATAAAAGAAACCATCATT
1 TTTGACAAACACAAAA-AAACCATAATT
* * *
582955 TTTTACAAACACAAAATAATCATAATT
1 TTTGACAAACACAAAAAAACCATAATT
582982 TTTGACAAACA
1 TTTGACAAACA
582993 AATAGGTGAC
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
27 18 0.58
28 13 0.42
ACGTcount: A:0.50, C:0.15, G:0.05, T:0.30
Consensus pattern (27 bp):
TTTGACAAACACAAAAAAACCATAATT
Found at i:590970 original size:22 final size:24
Alignment explanation
Indices: 590941--590988 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
590931 TTTCTTTTTG
*
590941 AAAA-ATATATTAAAAAAAGATTT
1 AAAATATATATGAAAAAAAGATTT
*
590964 AAAATATATATGAAAAAAATATTT
1 AAAATATATATGAAAAAAAGATTT
590988 A
1 A
590989 CTACGCTATC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (24 bp):
AAAATATATATGAAAAAAAGATTT
Found at i:591425 original size:19 final size:18
Alignment explanation
Indices: 591403--591447 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
591393 ATATATAAAA
591403 ATATTAAAAATATATTTTT
1 ATATTAAAAATATA-TTTT
*
591422 ATATT-AATATATATTTT
1 ATATTAAAAATATATTTT
591439 ATAATTAAA
1 AT-ATTAAA
591448 TTTAAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 6 0.26
18 10 0.43
19 7 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATATTAAAAATATATTTT
Found at i:591445 original size:18 final size:16
Alignment explanation
Indices: 591411--591446 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 16
591401 AAATATTAAA
591411 AATATATTTTTATATT
1 AATATATTTTTATATT
591427 AATATATATTTTATAATT
1 AATATAT-TTTTAT-ATT
591445 AA
1 AA
591447 ATTTAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
17 6 0.33
18 5 0.28
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
AATATATTTTTATATT
Found at i:591511 original size:23 final size:25
Alignment explanation
Indices: 591466--591512 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
591456 ATATTATTAT
591466 ATTTAATAAATAATAATTTAAATCA
1 ATTTAATAAATAATAATTTAAATCA
591491 ATTTAAGTAAA-AA-AA-TTAAATC
1 ATTTAA-TAAATAATAATTTAAATC
591513 TAAATAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 7 0.33
24 2 0.10
25 8 0.38
26 4 0.19
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.36
Consensus pattern (25 bp):
ATTTAATAAATAATAATTTAAATCA
Found at i:596757 original size:12 final size:12
Alignment explanation
Indices: 596737--596771 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
596727 TTTGGATAAC
*
596737 AAAAAAAAAAAT
1 AAAATAAAAAAT
596749 AAAATAAAAAAT
1 AAAATAAAAAAT
596761 AAAATAAAAAA
1 AAAATAAAAAA
596772 ACCAAAAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (12 bp):
AAAATAAAAAAT
Found at i:596759 original size:17 final size:17
Alignment explanation
Indices: 596737--596769 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
596727 TTTGGATAAC
596737 AAAAAAAAAAATAAAAT
1 AAAAAAAAAAATAAAAT
*
596754 AAAAAATAAAATAAAA
1 AAAAAAAAAAATAAAA
596770 AAACCAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (17 bp):
AAAAAAAAAAATAAAAT
Found at i:597463 original size:34 final size:33
Alignment explanation
Indices: 597415--597633 Score: 244
Period size: 34 Copynumber: 6.5 Consensus size: 33
597405 TGGTAAAAAC
*
597415 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
* *
597448 CTACCATTTAGTCAACAATGGTAAGCC-ACAAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
597482 CACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** * *
597516 TTCTCATTTAATCAACAAAGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * *
597550 CTCCCATTTAGTCAACAATGGCAAACC-ACCAAAT
1 C-ACCATTTAATCAACAATGG-TAACCTACCAAAT
*
597584 CACTCATTTAATCAACAATGGTAAACTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
597618 CACCATTTAATCAACA
1 CACCATTTAATCAACA
597634 GTTCTCCCAC
Statistics
Matches: 156, Mismatches: 21, Indels: 18
0.80 0.11 0.09
Matches are distributed among these distances:
33 21 0.13
34 129 0.83
35 6 0.04
ACGTcount: A:0.42, C:0.26, G:0.08, T:0.25
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:597531 original size:68 final size:68
Alignment explanation
Indices: 597417--597633 Score: 285
Period size: 68 Copynumber: 3.2 Consensus size: 68
597407 GTAAAAACCA
* * * *
597417 CCATTTAATCAACAATGGCAACCTACCAAATCTAC-CATTTAGTCAACAATGGTAAGCCACAAAA
1 CCATTTAATCAACAATGGCAAACTACCAAAT-TACTCATTTAATCAACAATGGTAAGCTACCAAA
597481 TCAC
65 TCAC
* * * * *
597485 CCATTTAATCAATAATGGTAAGCTACCAAATTTCTCATTTAATCAACAAAGGTAAGCTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTACTCATTTAATCAACAATGGTAAGCTACCAAAT
*
597550 CTC
66 CAC
* * * *
597553 CCATTTAGTCAACAATGGCAAACCACCAAATCACTCATTTAATCAACAATGGTAAACTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTACTCATTTAATCAACAATGGTAAGCTACCAAAT
597618 CA-
66 CAC
597620 CCATTTAATCAACA
1 CCATTTAATCAACA
597634 GTTCTCCCAC
Statistics
Matches: 128, Mismatches: 20, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
67 15 0.12
68 113 0.88
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (68 bp):
CCATTTAATCAACAATGGCAAACTACCAAATTACTCATTTAATCAACAATGGTAAGCTACCAAAT
CAC
Found at i:597560 original size:102 final size:101
Alignment explanation
Indices: 597415--597633 Score: 321
Period size: 102 Copynumber: 2.2 Consensus size: 101
597405 TGGTAAAAAC
* * *
597415 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACAAA
1 CACCATTTAATCAACAAAGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACAAA
* *
597480 ATCACCCATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
** * * * *
597516 TTCTCATTTAATCAACAAAGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCA
1 CAC-CATTTAATCAACAAAGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACAA
*
597581 AATCACTCATTTAATCAACAATGGTAAACTACCAAAT
65 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
597618 CACCATTTAATCAACA
1 CACCATTTAATCAACA
597634 GTTCTCCCAC
Statistics
Matches: 103, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
101 14 0.14
102 89 0.86
ACGTcount: A:0.42, C:0.26, G:0.08, T:0.25
Consensus pattern (101 bp):
CACCATTTAATCAACAAAGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACAAA
ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:602089 original size:34 final size:33
Alignment explanation
Indices: 602041--602259 Score: 235
Period size: 34 Copynumber: 6.5 Consensus size: 33
602031 TGGTAAAAAC
*
602041 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
*
602074 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* * *
602108 CACCCATTTAATCAATAATGGTAAGCTATCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** *
602142 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * *
602176 CTCTCATTTAGTCAACAATGGCAAACC-ACCAAAT
1 CAC-CATTTAATCAACAATGG-TAACCTACCAAAT
* * *
602210 CATCCATTTAATTAACAATAGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
602244 CACCATTTAATCAACA
1 CACCATTTAATCAACA
602260 GAAAAAAATA
Statistics
Matches: 157, Mismatches: 21, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
33 20 0.13
34 131 0.83
35 6 0.04
ACGTcount: A:0.41, C:0.25, G:0.07, T:0.26
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:602157 original size:68 final size:68
Alignment explanation
Indices: 602043--602259 Score: 267
Period size: 68 Copynumber: 3.2 Consensus size: 68
602033 GTAAAAACCA
* * * *
602043 CCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATCTTCCATTTAATCAACAATGGTAAGCTACCAAAT
602108 CAC
66 CAC
* * * *
602111 CCATTTAATCAATAATGGTAAGCTATCAAAT-TTCTCATTTAATCAACAATGGTAAGCTACCAAA
1 CCATTTAATCAACAATGGCAAACTACCAAATCTTC-CATTTAATCAACAATGGTAAGCTACCAAA
*
602175 TCTC
65 TCAC
* * * * * * *
602179 TCATTTAGTCAACAATGGCAAACCACCAAATCATCCATTTAATTAACAATAGTAAACTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATCTTCCATTTAATCAACAATGGTAAGCTACCAAAT
602244 CA-
66 CAC
602246 CCATTTAATCAACA
1 CCATTTAATCAACA
602260 GAAAAAAATA
Statistics
Matches: 125, Mismatches: 22, Indels: 5
0.82 0.14 0.03
Matches are distributed among these distances:
67 14 0.11
68 109 0.87
69 2 0.02
ACGTcount: A:0.41, C:0.25, G:0.07, T:0.27
Consensus pattern (68 bp):
CCATTTAATCAACAATGGCAAACTACCAAATCTTCCATTTAATCAACAATGGTAAGCTACCAAAT
CAC
Found at i:602220 original size:102 final size:101
Alignment explanation
Indices: 602041--602259 Score: 305
Period size: 102 Copynumber: 2.2 Consensus size: 101
602031 TGGTAAAAAC
* *
602041 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
* * * *
602106 ATCACCCATTTAATCAATAATGGTAAGCTATCAAAT
66 ATCACCCATTTAATCAACAATAGTAAACTACCAAAT
** * *
602142 TTCTCATTTAATCAACAATGGTAAGCTACCAAATCT-CTCATTTAGTCAACAATGGCAAACCACC
1 CAC-CATTTAATCAACAATGGCAACCTACCAAATCTAC-CATTTAGTCAACAATGGCAAACCACC
* *
602206 AAATCATCCATTTAATTAACAATAGTAAACTACCAAAT
64 AAATCACCCATTTAATCAACAATAGTAAACTACCAAAT
602244 CACCATTTAATCAACA
1 CACCATTTAATCAACA
602260 GAAAAAAATA
Statistics
Matches: 102, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
101 15 0.15
102 87 0.85
ACGTcount: A:0.41, C:0.25, G:0.07, T:0.26
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAACAATAGTAAACTACCAAAT
Found at i:606109 original size:18 final size:18
Alignment explanation
Indices: 606083--606134 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
606073 ATATATTCGT
*
606083 ATATATTTATTTTATTTTG
1 ATAT-TTTATTTTATTTTA
*
606102 ATATTTTATTATATTTTA
1 ATATTTTATTTTATTTTA
*
606120 ATTATTTTATATTAT
1 A-TATTTTATTTTAT
606135 ATAATCATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 13 0.46
19 15 0.54
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (18 bp):
ATATTTTATTTTATTTTA
Found at i:615473 original size:23 final size:23
Alignment explanation
Indices: 615425--615475 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
615415 TTTTATTTTG
*
615425 AAATAAAAATAATTGTAATTTAA
1 AAATAAAAATAATTATAATTTAA
615448 AAATAAAAA-AATTATAAATATTAA
1 AAATAAAAATAATTAT-AAT-TTAA
615472 AAAT
1 AAAT
615476 CAAATTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 5 0.20
23 12 0.48
24 8 0.32
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (23 bp):
AAATAAAAATAATTATAATTTAA
Found at i:616114 original size:17 final size:17
Alignment explanation
Indices: 616081--616112 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
616071 GAATTAATTA
616081 TGAAATTAAAACTAAAG
1 TGAAATTAAAACTAAAG
616098 TGAAATTAAAA-TAAA
1 TGAAATTAAAACTAAA
616113 AGATTAGGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.62, C:0.03, G:0.09, T:0.25
Consensus pattern (17 bp):
TGAAATTAAAACTAAAG
Found at i:616402 original size:30 final size:30
Alignment explanation
Indices: 616357--616421 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
616347 TTATAAAAAA
*
616357 TTAAATATAAGATAAAATATAAAAT-AATAT
1 TTAAAAATAAGAT-AAATATAAAATGAATAT
* *
616387 TTAAAAATAATATAAATATAATATGAATAT
1 TTAAAAATAAGATAAATATAAAATGAATAT
*
616417 ATAAA
1 TTAAA
616422 TATTTTATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (30 bp):
TTAAAAATAAGATAAATATAAAATGAATAT
Found at i:616407 original size:11 final size:11
Alignment explanation
Indices: 616360--616417 Score: 55
Period size: 11 Copynumber: 5.1 Consensus size: 11
616350 TAAAAAATTA
*
616360 AATATAAGATAA
1 AATATAA-ATAT
616372 AATATAAA-AT
1 AATATAAATAT
*
616382 AATATTTAAAAAT
1 AATA--TAAATAT
616395 AATATAAATAT
1 AATATAAATAT
*
616406 AATATGAATAT
1 AATATAAATAT
616417 A
1 A
616418 TAAATATTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
10 5 0.12
11 18 0.45
12 11 0.28
13 6 0.15
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (11 bp):
AATATAAATAT
Found at i:616471 original size:20 final size:20
Alignment explanation
Indices: 616414--616471 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 20
616404 ATAATATGAA
*
616414 TATATAAATATTTTATATTAT
1 TATATAAATATTTAATATT-T
*
616435 TA-AT-AA-A-TTAA-AATT
1 TATATAAATATTTAATATTT
616450 TATATAAATATTTAATATTT
1 TATATAAATATTTAATATTT
616470 TA
1 TA
616472 AATATTATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 11
0.67 0.07 0.26
Matches are distributed among these distances:
15 3 0.10
16 4 0.14
17 5 0.17
18 2 0.07
19 6 0.21
20 7 0.24
21 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TATATAAATATTTAATATTT
Found at i:616689 original size:12 final size:12
Alignment explanation
Indices: 616672--616708 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
616662 GAATTACATT
616672 AGCAAGAGAGAG
1 AGCAAGAGAGAG
616684 AGCAAGAGAGAG
1 AGCAAGAGAGAG
616696 AG--AGAGAGAG
1 AGCAAGAGAGAG
616706 AGC
1 AGC
616709 TGAGCTGCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.42
12 14 0.58
ACGTcount: A:0.49, C:0.08, G:0.43, T:0.00
Consensus pattern (12 bp):
AGCAAGAGAGAG
Found at i:616883 original size:15 final size:17
Alignment explanation
Indices: 616865--616901 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
616855 TTTTATTTTT
*
616865 TAAATTTTAAT-T-AAA
1 TAAATTTAAATATAAAA
616880 TAAATTTAAATATAAAA
1 TAAATTTAAATATAAAA
616897 TAAAT
1 TAAAT
616902 GATTGAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 10 0.53
16 1 0.05
17 8 0.42
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAATTTAAATATAAAA
Found at i:618104 original size:17 final size:18
Alignment explanation
Indices: 618052--618120 Score: 65
Period size: 17 Copynumber: 3.9 Consensus size: 18
618042 AGCTTCTTAG
*
618052 TTATTATAATATATGTAAA
1 TTATTA-AATATATATAAA
618071 -TA-TAAATATAATATAAA
1 TTATTAAATAT-ATATAAA
618088 TTATTAAATATAT-TAAAA
1 TTATTAAATATATAT-AAA
*
618106 TT-TTAAATTTATATA
1 TTATTAAATATATATA
618121 TTATTTTTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
16 5 0.12
17 19 0.44
18 12 0.28
19 7 0.16
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (18 bp):
TTATTAAATATATATAAA
Found at i:619777 original size:16 final size:16
Alignment explanation
Indices: 619756--619787 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
619746 TATCAATTGG
619756 ACGAATCAAATTAATT
1 ACGAATCAAATTAATT
619772 ACGAATCAAATTAATT
1 ACGAATCAAATTAATT
619788 TAATTTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.12, G:0.06, T:0.31
Consensus pattern (16 bp):
ACGAATCAAATTAATT
Found at i:625873 original size:101 final size:101
Alignment explanation
Indices: 625698--625904 Score: 405
Period size: 101 Copynumber: 2.0 Consensus size: 101
625688 TTTATTAGAC
*
625698 TTTTGCGATTGAAAGAGTGATTAGCAATTTGACTTGATGTTATGTTGCATTTGTAAATATATTTG
1 TTTTGCGATTGAAAGAGTGATTAGCAATGTGACTTGATGTTATGTTGCATTTGTAAATATATTTG
625763 GGATTGTCTTTGCTGCCAGCACGTTCCATAGTGTTG
66 GGATTGTCTTTGCTGCCAGCACGTTCCATAGTGTTG
625799 TTTTGCGATTGAAAGAGTGATTAGCAATGTGACTTGATGTTATGTTGCATTTGTAAATATATTTG
1 TTTTGCGATTGAAAGAGTGATTAGCAATGTGACTTGATGTTATGTTGCATTTGTAAATATATTTG
625864 GGATTGTCTTTGCTGCCAGCACGTTCCATAGTGTTG
66 GGATTGTCTTTGCTGCCAGCACGTTCCATAGTGTTG
625900 TTTTG
1 TTTTG
625905 GTTCTGGTTT
Statistics
Matches: 105, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
101 105 1.00
ACGTcount: A:0.22, C:0.12, G:0.24, T:0.42
Consensus pattern (101 bp):
TTTTGCGATTGAAAGAGTGATTAGCAATGTGACTTGATGTTATGTTGCATTTGTAAATATATTTG
GGATTGTCTTTGCTGCCAGCACGTTCCATAGTGTTG
Found at i:627143 original size:32 final size:32
Alignment explanation
Indices: 627107--627169 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
627097 ATGTATCGTT
*
627107 AAATATTTAATATGATTTTAT-GAGATCTAGTC
1 AAATATTCAATATGATTTTATAG-GATCTAGTC
627139 AAATATTCAATATGATTTTATAGGATCTAGT
1 AAATATTCAATATGATTTTATAGGATCTAGT
627170 TTCATTCAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 28 0.97
33 1 0.03
ACGTcount: A:0.38, C:0.06, G:0.13, T:0.43
Consensus pattern (32 bp):
AAATATTCAATATGATTTTATAGGATCTAGTC
Found at i:627283 original size:63 final size:64
Alignment explanation
Indices: 627182--627312 Score: 203
Period size: 63 Copynumber: 2.0 Consensus size: 64
627172 CATTCAAGTT
627182 ACAGATTTTAGCCAATAGGAAGAATCTTCTTATCAATCTAAAGATCATTTGGATT-TCATTAGTA
1 ACAGATTTTAGCCAAT---AAGAATCTTCTTATCAATCTAAAGATCATTTGGATTAT-ATTAGTA
627246 ATG
62 ATG
*
627249 ACAGATTTTAGCCAAT-AGAATCTTTTTATCAATCTAAAGATCATTTGGATTATATTAGTAATG
1 ACAGATTTTAGCCAATAAGAATCTTCTTATCAATCTAAAGATCATTTGGATTATATTAGTAATG
627312 A
1 A
627313 GGATTTAAAA
Statistics
Matches: 62, Mismatches: 1, Indels: 6
0.90 0.01 0.09
Matches are distributed among these distances:
63 45 0.73
64 1 0.02
67 16 0.26
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (64 bp):
ACAGATTTTAGCCAATAAGAATCTTCTTATCAATCTAAAGATCATTTGGATTATATTAGTAATG
Found at i:627585 original size:76 final size:77
Alignment explanation
Indices: 627505--627662 Score: 185
Period size: 79 Copynumber: 2.0 Consensus size: 77
627495 ATGAATAATT
* * * * * * *
627505 ATCTGTTTTTAGAAGAAATTAGAGA-A-TTTTTTGAGAATCTTATAAGATTCGTTCGTTCTTTTT
1 ATCTGTTTCTAGAAGAAATCA-AAATATTTTTTTGACAATCTTACAAGATTCATTCGTTCTCTTT
*
627568 TCTTTGATAGATG
65 TCTTTGATAAATG
* *
627581 ATCTGTTTCTGGAAGAAATCAAAATTATTTTTTTTGACAATCTTGCAAGATTCATTCGTTCTCTT
1 ATCTGTTTCTAGAAGAAATCAAAA-TA-TTTTTTTGACAATCTTACAAGATTCATTCGTTCTCTT
627646 TTCTTTGATAAATG
64 TTCTTTGATAAATG
627660 ATC
1 ATC
627663 AGAACTTTAT
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
75 2 0.03
76 18 0.26
77 1 0.01
79 47 0.69
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.46
Consensus pattern (77 bp):
ATCTGTTTCTAGAAGAAATCAAAATATTTTTTTGACAATCTTACAAGATTCATTCGTTCTCTTTT
CTTTGATAAATG
Found at i:630085 original size:33 final size:35
Alignment explanation
Indices: 630043--630126 Score: 109
Period size: 36 Copynumber: 2.4 Consensus size: 35
630033 AACTATATTA
630043 AAGTGCATGCATA-A-TCCTAAAAAAAAAAAAATT
1 AAGTGCATGCATATATTCCTAAAAAAAAAAAAATT
* ** *
630076 AAGTTCATGCATAATATTTTTAAAAAAAGAAAAATT
1 AAGTGCATGCAT-ATATTCCTAAAAAAAAAAAAATT
630112 AAGTGCATGCATATA
1 AAGTGCATGCATATA
630127 ATAATTATAA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
33 11 0.26
34 1 0.02
35 4 0.09
36 27 0.63
ACGTcount: A:0.52, C:0.10, G:0.11, T:0.27
Consensus pattern (35 bp):
AAGTGCATGCATATATTCCTAAAAAAAAAAAAATT
Found at i:634673 original size:4 final size:4
Alignment explanation
Indices: 634657--634689 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
634647 AAATAGACAA
634657 AAAT AAA- AAAT AAAT AAAT AAAT AAAT -AAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
634690 AATATTGATC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
3 6 0.22
4 21 0.78
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:634675 original size:8 final size:8
Alignment explanation
Indices: 634657--634689 Score: 52
Period size: 7 Copynumber: 4.4 Consensus size: 8
634647 AAATAGACAA
634657 AAATAAA-
1 AAATAAAT
634664 AAATAAAT
1 AAATAAAT
634672 AAATAAAT
1 AAATAAAT
634680 AAAT-AAT
1 AAATAAAT
634687 AAA
1 AAA
634690 AATATTGATC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 13 0.52
8 12 0.48
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (8 bp):
AAATAAAT
Found at i:637421 original size:24 final size:23
Alignment explanation
Indices: 637335--637421 Score: 53
Period size: 24 Copynumber: 3.9 Consensus size: 23
637325 ATATACTATG
* *
637335 TATATTTATTAAATCTATT-GTAT
1 TATATTT-TTAAATATATTATTAT
*
637358 TAGTGATGTTTAAATATATTA-TAT
1 TA-T-ATTTTTAAATATATTATTAT
637382 TATATATTTT---T-T-TTATTAT
1 TATAT-TTTTAAATATATTATTAT
637401 TATATTTATTAAATATATTAT
1 TATATTT-TTAAATATATTAT
637422 ATTTTACCAT
Statistics
Matches: 50, Mismatches: 3, Indels: 21
0.68 0.04 0.28
Matches are distributed among these distances:
18 5 0.10
19 11 0.22
20 1 0.02
22 3 0.06
23 7 0.14
24 20 0.40
25 3 0.06
ACGTcount: A:0.36, C:0.01, G:0.05, T:0.59
Consensus pattern (23 bp):
TATATTTTTAAATATATTATTAT
Found at i:644212 original size:21 final size:21
Alignment explanation
Indices: 644187--644228 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
644177 CCCAATTATG
644187 TGGAAATATACAATTTTTAGC
1 TGGAAATATACAATTTTTAGC
644208 TGGAAATATACAATTTTTAGC
1 TGGAAATATACAATTTTTAGC
644229 CAAAAATATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (21 bp):
TGGAAATATACAATTTTTAGC
Found at i:644235 original size:21 final size:21
Alignment explanation
Indices: 644190--644237 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
644180 AATTATGTGG
***
644190 AAATATACAATTTTTAGCTGG
1 AAATATACAATTTTTAGCCAA
644211 AAATATACAATTTTTAGCCAA
1 AAATATACAATTTTTAGCCAA
644232 AAATAT
1 AAATAT
644238 CAGATCCCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.35
Consensus pattern (21 bp):
AAATATACAATTTTTAGCCAA
Found at i:648167 original size:31 final size:31
Alignment explanation
Indices: 648129--648194 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
648119 CATAGATGAG
648129 TTACCTTGCAATCTTAAACTAATGAACTCAA
1 TTACCTTGCAATCTTAAACTAATGAACTCAA
* *
648160 TTACCTTGCAATCTTAAACTGATGAACTTAA
1 TTACCTTGCAATCTTAAACTAATGAACTCAA
648191 TTAC
1 TTAC
648195 TTTGAACCGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.36, C:0.21, G:0.08, T:0.35
Consensus pattern (31 bp):
TTACCTTGCAATCTTAAACTAATGAACTCAA
Done.