Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold396
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: 560635
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 4 of 4
Found at i:473504 original size:18 final size:18
Alignment explanation
Indices: 473439--473506 Score: 64
Period size: 21 Copynumber: 3.5 Consensus size: 18
473429 TAATAAAAAA
473439 ATTAAATATATTTTTATATT
1 ATTAAATAT-TTTTTA-ATT
* * *
473459 AATATATATTTTATAATT
1 ATTAAATATTTTTTAATT
473477 AAATTTAAATATTTTTTAATT
1 --A-TTAAATATTTTTTAATT
473498 ATTAAATAT
1 ATTAAATAT
473507 GTTGAGTTGA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
18 11 0.28
19 6 0.15
20 8 0.21
21 14 0.36
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTAAATATTTTTTAATT
Found at i:474003 original size:18 final size:17
Alignment explanation
Indices: 473981--474024 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
473971 AAATTAGTAT
473981 ATATTTTAATTTTTAAA
1 ATATTTTAATTTTTAAA
* *
473998 ATTATTTTTATTTTTTAA
1 A-TATTTTAATTTTTAAA
474016 ATATTTTAA
1 ATATTTTAA
474025 AAAATATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
ATATTTTAATTTTTAAA
Found at i:474937 original size:15 final size:16
Alignment explanation
Indices: 474912--474941 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
474902 TTTAGATAAG
474912 ATTAGATTTATTTATA
1 ATTAGATTTATTTATA
474928 ATTA-ATTTATTTAT
1 ATTAGATTTATTTAT
474942 TTGATTTGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (16 bp):
ATTAGATTTATTTATA
Found at i:477610 original size:15 final size:16
Alignment explanation
Indices: 477586--477624 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
477576 AAACTCTAAA
*
477586 TATTTTAAAT-AAGTT
1 TATTTAAAATAAAGTT
477601 TATTTAAAATAAAGTT
1 TATTTAAAATAAAGTT
477617 TA-TTAAAA
1 TATTTAAAA
477625 AATACAACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 15 0.68
16 7 0.32
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (16 bp):
TATTTAAAATAAAGTT
Found at i:477625 original size:16 final size:15
Alignment explanation
Indices: 477592--477625 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
477582 TAAATATTTT
*
477592 AAATAAGTTTATTTA
1 AAATAAGTTTATTAA
477607 AAATAAAGTTTATTAA
1 AAAT-AAGTTTATTAA
477623 AAA
1 AAA
477626 ATACAACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (15 bp):
AAATAAGTTTATTAA
Found at i:478400 original size:22 final size:21
Alignment explanation
Indices: 478362--478403 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
478352 TAATTTTATT
478362 TAAATTTAATTATAAAATATA
1 TAAATTTAATTATAAAATATA
* *
478383 TAAATTTTATTTTAAAA-ATA
1 TAAATTTAATTATAAAATATA
478403 T
1 T
478404 TTTTAATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TAAATTTAATTATAAAATATA
Found at i:479846 original size:23 final size:24
Alignment explanation
Indices: 479820--479866 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
479810 TTTTATCATA
*
479820 TTATAATTAAATT-TTTTAAAAAT
1 TTATAATTAAATTAATTTAAAAAT
* *
479843 TTATATTTATATTAATTTAAAAAT
1 TTATAATTAAATTAATTTAAAAAT
479867 ATTTATATAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
TTATAATTAAATTAATTTAAAAAT
Found at i:480920 original size:25 final size:25
Alignment explanation
Indices: 480864--480926 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
480854 AATTTGATGT
* *
480864 AAAAA-ATAATATGAGTATAACAAA
1 AAAAATATAATATAAATATAACAAA
*
480888 AAAAATATAATATAAATATAATAAA
1 AAAAATATAATATAAATATAACAAA
*
480913 AAATATATGAATAT
1 AAAAATAT-AATAT
480927 TTTAAATTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 5 0.15
25 23 0.70
26 5 0.15
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.27
Consensus pattern (25 bp):
AAAAATATAATATAAATATAACAAA
Found at i:480940 original size:39 final size:39
Alignment explanation
Indices: 480897--480988 Score: 116
Period size: 39 Copynumber: 2.3 Consensus size: 39
480887 AAAAAATATA
480897 ATATAAATATAATAAAAAATATATGAAT-ATTTTAAA-TTT
1 ATATAAATATAAT-AAAAAT-TATGAATAATTTTAAATTTT
* *
480936 ATATAATAATATAATATAAATTATTAATAATTTTAAATTTT
1 ATAT-A-AATATAATAAAAATTATGAATAATTTTAAATTTT
480977 ATATAAATATAA
1 ATATAAATATAA
480989 AATATTTTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
39 17 0.36
40 15 0.32
41 15 0.32
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (39 bp):
ATATAAATATAATAAAAATTATGAATAATTTTAAATTTT
Found at i:480985 original size:21 final size:21
Alignment explanation
Indices: 480916--480985 Score: 53
Period size: 21 Copynumber: 3.5 Consensus size: 21
480906 TAATAAAAAA
*
480916 TATATGAAT-ATTTTAAATTT
1 TATATAAATAATTTTAAATTT
*
480936 ATATAATAATATAA-TATAAA--T
1 -TAT-ATAA-ATAATTTTAAATTT
480957 TAT-T-AATAATTTTAAATTT
1 TATATAAATAATTTTAAATTT
480976 TATATAAATA
1 TATATAAATA
480986 TAAAATATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 16
0.67 0.05 0.28
Matches are distributed among these distances:
16 4 0.11
17 6 0.16
18 1 0.03
19 4 0.11
20 4 0.11
21 8 0.21
22 3 0.08
23 7 0.18
24 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (21 bp):
TATATAAATAATTTTAAATTT
Found at i:480993 original size:41 final size:40
Alignment explanation
Indices: 480897--480993 Score: 112
Period size: 41 Copynumber: 2.4 Consensus size: 40
480887 AAAAAATATA
480897 ATATAAATATAATAA-A-AAATATATGAATATTTTAAATTT
1 ATATAAATATAA-AATATAAATATATGAATATTTTAAATTT
* *
480936 ATAT-AATAATATAATATAAAT-TATTAATAATTTTAAATTTT
1 ATATAAAT-ATAAAATATAAATATATGAAT-ATTTTAAA-TTT
480977 ATATAAATATAAAATAT
1 ATATAAATATAAAATAT
480994 TTTAAATATT
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
38 5 0.10
39 14 0.29
40 12 0.24
41 15 0.31
42 3 0.06
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (40 bp):
ATATAAATATAAAATATAAATATATGAATATTTTAAATTT
Found at i:481005 original size:27 final size:27
Alignment explanation
Indices: 480943--481104 Score: 103
Period size: 24 Copynumber: 6.1 Consensus size: 27
480933 TTTATATAAT
* *
480943 AATATAATATAAAT-TATTAATAATTTTA
1 AATATTATATAAATATA-AAAT-ATTTTA
*
480971 AATTTTATATAAATATAAAATATTTTA
1 AATATTATATAAATATAAAATATTTTA
*
480998 AATATTAT-TATAATAT--AATA-TATA
1 AATATTATATA-AATATAAAATATTTTA
481022 AATATTATATAAATA-AATAA-AGTTTTA
1 AATATTATATAAATATAA-AATA-TTTTA
*
481049 AATA-TA-A-AAATATAAAATACTTTA
1 AATATTATATAAATATAAAATATTTTA
* * *
481073 ATTATCT-TCTTAATATATAAAAAATTTTA
1 AATAT-TAT-ATAA-ATATAAAATATTTTA
481102 AAT
1 AAT
481105 TAAATTACCA
Statistics
Matches: 106, Mismatches: 12, Indels: 31
0.71 0.08 0.21
Matches are distributed among these distances:
24 29 0.27
25 11 0.10
26 7 0.07
27 25 0.24
28 17 0.16
29 17 0.16
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.44
Consensus pattern (27 bp):
AATATTATATAAATATAAAATATTTTA
Found at i:481030 original size:11 final size:11
Alignment explanation
Indices: 480890--481036 Score: 67
Period size: 11 Copynumber: 14.5 Consensus size: 11
480880 ATAACAAAAA
*
480890 AAATATAATAT
1 AAATATTATAT
480901 AAATA-TA-AT
1 AAATATTATAT
* *
480910 AAAAAATATAT
1 AAATATTATAT
*
480921 GAATATT-T-T
1 AAATATTATAT
480930 AAAT-TTATAT
1 AAATATTATAT
*
480940 -AATAATATAAT
1 AAATATTAT-AT
480951 ATAA-ATTAT-T
1 A-AATATTATAT
480961 -AATAATT-T-T
1 AAAT-ATTATAT
*
480970 AAATTTTATAT
1 AAATATTATAT
480981 -AA-A-TATA-
1 AAATATTATAT
480988 AAATATT-T-T
1 AAATATTATAT
480997 AAATATTATTAT
1 AAATATTA-TAT
*
481009 AATATAATATAT
1 AA-ATATTATAT
481021 AAATATTATAT
1 AAATATTATAT
481032 AAATA
1 AAATA
481037 AATAAAGTTT
Statistics
Matches: 103, Mismatches: 12, Indels: 42
0.66 0.08 0.27
Matches are distributed among these distances:
8 10 0.10
9 27 0.26
10 19 0.18
11 28 0.27
12 12 0.12
13 7 0.07
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.44
Consensus pattern (11 bp):
AAATATTATAT
Found at i:481031 original size:13 final size:13
Alignment explanation
Indices: 480996--481032 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
480986 TAAAATATTT
480996 TAAATATTAT-TA
1 TAAATATTATATA
*
481008 T-AATATAATATA
1 TAAATATTATATA
481020 TAAATATTATATA
1 TAAATATTATATA
481033 AATAAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
11 7 0.33
12 4 0.19
13 10 0.48
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TAAATATTATATA
Found at i:481066 original size:75 final size:70
Alignment explanation
Indices: 480894--481073 Score: 178
Period size: 67 Copynumber: 2.6 Consensus size: 70
480884 CAAAAAAAAT
* *
480894 ATAAT-ATAAA-TATAATA-AAAAATATATGAATATTTTAAATTTATATAATAATATAATATAAA
1 ATAATAATAAATTTTAATATAAAAATATA-AAATATTTTAAATTTATATAATAATATAATATAAA
*
480956 TTATTA
65 ATATTA
**
480962 ATAATTTTAAATTTT-ATAT--AAATATAAAATATTTTAAATATTAT-T-ATAATATAATATATA
1 ATAATAATAAATTTTAATATAAAAATATAAAATATTTTAAAT-TTATATAATAATATAATATA-A
481022 AATATTA
64 AATATTA
*
481029 TATAAATAAATAAAGTTTTAAATATAAAAATATAAAATACTTTAA
1 -AT-AAT-AATAAA-TTTT-AATATAAAAATATAAAATATTTTAA
481074 TTATCTTCTT
Statistics
Matches: 92, Mismatches: 7, Indels: 19
0.78 0.06 0.16
Matches are distributed among these distances:
66 13 0.14
67 20 0.22
68 18 0.20
69 10 0.11
70 6 0.07
71 4 0.04
73 4 0.04
75 17 0.18
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (70 bp):
ATAATAATAAATTTTAATATAAAAATATAAAATATTTTAAATTTATATAATAATATAATATAAAA
TATTA
Found at i:482421 original size:13 final size:13
Alignment explanation
Indices: 482405--482438 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
482395 TTTATGTTAT
*
482405 TTTTATATTATAA
1 TTTTATATTAAAA
*
482418 TTTTATTTTAAAA
1 TTTTATATTAAAA
482431 TTTTATAT
1 TTTTATAT
482439 ATTTATATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
TTTTATATTAAAA
Found at i:482452 original size:19 final size:19
Alignment explanation
Indices: 482428--482483 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
482418 TTTTATTTTA
482428 AAATTTTATATATTTATAT
1 AAATTTTATATATTTATAT
482447 AAATTTTGATGATA-TTA-AT
1 AAATTTT-AT-ATATTTATAT
*
482466 AATTTTTATTATATTTAT
1 AAATTTTA-TATATTTAT
482484 TTTGTATAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
18 4 0.13
19 19 0.61
20 5 0.16
21 3 0.10
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (19 bp):
AAATTTTATATATTTATAT
Found at i:482531 original size:10 final size:11
Alignment explanation
Indices: 482501--482532 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
482491 AAATTAATTT
482501 TTATATTTT-A
1 TTATATTTTAA
482511 TTATATTTTAA
1 TTATATTTTAA
482522 TTAT-TTTTAA
1 TTATATTTTAA
482532 T
1 T
482533 GTTAATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 16 0.76
11 5 0.24
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTATATTTTAA
Found at i:483738 original size:6 final size:6
Alignment explanation
Indices: 483724--483755 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
483714 AATTAGTTTT
*
483724 TTATGA TTATAA TTATAA TTATAA TTATAA TT
1 TTATAA TTATAA TTATAA TTATAA TTATAA TT
483756 GTTATATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (6 bp):
TTATAA
Found at i:488006 original size:17 final size:17
Alignment explanation
Indices: 487984--488025 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
487974 TAAATAATTA
487984 ATTTAAT-GAATTTAAAT
1 ATTTAATAG-ATTTAAAT
*
488001 ATTTAATAGATTTTAAT
1 ATTTAATAGATTTAAAT
488018 ATTTAATA
1 ATTTAATA
488026 TATATTATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 22 0.96
18 1 0.04
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (17 bp):
ATTTAATAGATTTAAAT
Found at i:488037 original size:17 final size:17
Alignment explanation
Indices: 487998--488040 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
487988 AATGAATTTA
*
487998 AATATTTAATAGATTTT
1 AATATTTAATAGATATT
*
488015 AATATTTAATATATATT
1 AATATTTAATAGATATT
*
488032 ATTATTTAA
1 AATATTTAA
488041 ATTGAATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (17 bp):
AATATTTAATAGATATT
Found at i:488643 original size:2 final size:2
Alignment explanation
Indices: 488638--488664 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
488628 ATATATATAT
488638 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
488665 ACATCTGAGT
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:490804 original size:15 final size:15
Alignment explanation
Indices: 490781--490811 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
490771 CGACTCATAT
*
490781 ATATGTATATATTTA
1 ATATATATATATTTA
490796 ATATATATATATTTA
1 ATATATATATATTTA
490811 A
1 A
490812 AATTTAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (15 bp):
ATATATATATATTTA
Found at i:492028 original size:21 final size:21
Alignment explanation
Indices: 492004--492044 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
491994 TTATATGATA
492004 ATTTAAAATATATAATATATC
1 ATTTAAAATATATAATATATC
* *
492025 ATTTATATTATATAATATAT
1 ATTTAAAATATATAATATAT
492045 AACTATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
ATTTAAAATATATAATATATC
Found at i:492076 original size:21 final size:21
Alignment explanation
Indices: 492012--492076 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
492002 TAATTTAAAA
* *
492012 TATATAATATAT-CATTTATAT
1 TATATAATATATAAATATAT-T
* *
492033 TATATAATATATAACTATTTT
1 TATATAATATATAAATATATT
492054 TATATAATAATATAAATA-ATT
1 TATATAAT-ATATAAATATATT
492075 TA
1 TA
492077 AATTTTAAAC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 25 0.69
22 11 0.31
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (21 bp):
TATATAATATATAAATATATT
Found at i:492166 original size:21 final size:21
Alignment explanation
Indices: 492141--492186 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
492131 TTTTATTATT
492141 TTAATTGTGAAATATT-TTTAA
1 TTAATT-TGAAATATTATTTAA
* *
492162 TTAATTTTAAATTTTATTTAA
1 TTAATTTGAAATATTATTTAA
492183 TTAA
1 TTAA
492187 ATTAATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (21 bp):
TTAATTTGAAATATTATTTAA
Found at i:493422 original size:47 final size:47
Alignment explanation
Indices: 493370--493463 Score: 143
Period size: 47 Copynumber: 2.0 Consensus size: 47
493360 TATATAAAAT
* *
493370 TTAATACTAAACTCAATGACGTAAAATATAAATTACTTTGATTTTAA
1 TTAATACTAAACTCAATAACGTAAAATATAAATTACATTGATTTTAA
* * *
493417 TTAATACTAAATTCAGTAACTTAAAATATAAATTACATTGATTTTAA
1 TTAATACTAAACTCAATAACGTAAAATATAAATTACATTGATTTTAA
493464 CACTAAAGCT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.39
Consensus pattern (47 bp):
TTAATACTAAACTCAATAACGTAAAATATAAATTACATTGATTTTAA
Found at i:493504 original size:21 final size:21
Alignment explanation
Indices: 493478--493524 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
493468 AAAGCTATAG
493478 ATATAATATAAAAAT-ATAAAA
1 ATATAA-ATAAAAATGATAAAA
* *
493499 ATATAAATAAATATGATATAA
1 ATATAAATAAAAATGATAAAA
493520 ATATA
1 ATATA
493525 TTAATATGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (21 bp):
ATATAAATAAAAATGATAAAA
Found at i:494837 original size:21 final size:21
Alignment explanation
Indices: 494813--494856 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
494803 ATTTTATAAA
494813 TTTAAAATTAAAATTTTAATT
1 TTTAAAATTAAAATTTTAATT
* ** *
494834 TTTATAATTTTAATTTTTATT
1 TTTAAAATTAAAATTTTAATT
494855 TT
1 TT
494857 CAAATTATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTAAAATTAAAATTTTAATT
Found at i:494844 original size:15 final size:15
Alignment explanation
Indices: 494824--494853 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
494814 TTAAAATTAA
494824 AATTTTAATTTTTAT
1 AATTTTAATTTTTAT
494839 AATTTTAATTTTTAT
1 AATTTTAATTTTTAT
494854 TTTCAAATTA
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
AATTTTAATTTTTAT
Found at i:494862 original size:20 final size:21
Alignment explanation
Indices: 494818--494867 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
494808 ATAAATTTAA
* *
494818 AATTAAAATTTTAATTTTTAT
1 AATTATAATTTTAATTTTCAT
* *
494839 AATTTTAATTTTTATTTTCA-
1 AATTATAATTTTAATTTTCAT
494859 AATTATAAT
1 AATTATAAT
494868 CTCGACTATA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
AATTATAATTTTAATTTTCAT
Found at i:495060 original size:24 final size:27
Alignment explanation
Indices: 495028--495079 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 27
495018 TAAAATTTTT
495028 AATATAAAAAATATCAT-AAT-TTAAA
1 AATATAAAAAATATCATAAATATTAAA
*
495053 AATA-AAAAAATATTATAAATATTAAA
1 AATATAAAAAATATCATAAATATTAAA
495079 A
1 A
495080 TTTAATCTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 11 0.46
25 7 0.29
26 6 0.25
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (27 bp):
AATATAAAAAATATCATAAATATTAAA
Found at i:495373 original size:15 final size:14
Alignment explanation
Indices: 495344--495386 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
495334 TACAGTGGTT
495344 ATATATTTTATTATA
1 ATATATTTTA-TATA
*
495359 TTATAGTTTTATATA
1 ATATA-TTTTATATA
*
495374 AAATATTTTATAT
1 ATATATTTTATAT
495387 TTTTATAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 8 0.33
15 11 0.46
16 5 0.21
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (14 bp):
ATATATTTTATATA
Found at i:495393 original size:20 final size:20
Alignment explanation
Indices: 495359--495406 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 20
495349 TTTTATTATA
495359 TTATAGTTTTATATAAAATATT
1 TTATA-TTTTATATAAAA-ATT
495381 TTATATTTT-TATAAAAATT
1 TTATATTTTATATAAAAATT
495400 TTGATAT
1 TT-ATAT
495407 ATCTATGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.20
20 11 0.44
21 4 0.16
22 5 0.20
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (20 bp):
TTATATTTTATATAAAAATT
Found at i:495408 original size:22 final size:22
Alignment explanation
Indices: 495359--495406 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
495349 TTTTATTATA
*
495359 TTATAGTTTTATATAAAATATT
1 TTATATTTTTATATAAAATATT
495381 TTATATTTTTATA-AAAAT-TT
1 TTATATTTTTATATAAAATATT
*
495401 TGATAT
1 TTATAT
495407 ATCTATGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 7 0.29
21 5 0.21
22 12 0.50
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (22 bp):
TTATATTTTTATATAAAATATT
Found at i:495460 original size:11 final size:11
Alignment explanation
Indices: 495444--495480 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
495434 AAAATATTTA
495444 TATATTTATAT
1 TATATTTATAT
495455 TATATTTATA-
1 TATATTTATAT
*
495465 -ATTTTTATAT
1 TATATTTATAT
495475 TATATT
1 TATATT
495481 ATTTTTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
9 8 0.36
11 14 0.64
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TATATTTATAT
Found at i:495462 original size:28 final size:25
Alignment explanation
Indices: 495431--495482 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
495421 TTATATAAAT
495431 TTTAAAATATTTATATATTTATATTATA
1 TTTAAAAT-TTT-TATA-TTATATTATA
*
495459 TTTATAATTTTTATATTATATTAT
1 TTTAAAATTTTTATATTATATTAT
495483 TTTTTAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 9 0.39
26 4 0.17
27 3 0.13
28 7 0.30
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (25 bp):
TTTAAAATTTTTATATTATATTATA
Found at i:495473 original size:20 final size:19
Alignment explanation
Indices: 495437--495510 Score: 75
Period size: 19 Copynumber: 4.0 Consensus size: 19
495427 AAATTTTAAA
495437 ATATTTATATATTTATATT
1 ATATTTATATATTTATATT
*
495456 ATATTTATAATTTTTATATT
1 ATATTTAT-ATATTTATATT
*
495476 ATA-TTAT-TTTTTA-ATT
1 ATATTTATATATTTATATT
*
495492 ATTATTTTTATATTT-TATT
1 A-TATTTATATATTTATATT
495511 CGTATCTTTA
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
16 4 0.09
17 8 0.17
18 3 0.06
19 19 0.40
20 13 0.28
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
ATATTTATATATTTATATT
Found at i:495502 original size:25 final size:25
Alignment explanation
Indices: 495448--495510 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
495438 TATTTATATA
*
495448 TTTATATTATATTTATAATTTTTAT
1 TTTATATTATATTTATAATTATTAT
* *
495473 ATTATATTAT-TTTTTAATTATTATT
1 TTTATATTATATTTATAATTATTA-T
*
495498 TTTATATTTTATT
1 TTTATATTATATT
495511 CGTATCTTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
24 11 0.35
25 18 0.58
26 2 0.06
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (25 bp):
TTTATATTATATTTATAATTATTAT
Found at i:495510 original size:16 final size:15
Alignment explanation
Indices: 495454--495506 Score: 72
Period size: 15 Copynumber: 3.5 Consensus size: 15
495444 TATATTTATA
*
495454 TTATATTTATAATTT
1 TTATATTTATTATTT
495469 TTATATTATATTATTT
1 TTATATT-TATTATTT
*
495485 TT-TAATTATTATTT
1 TTATATTTATTATTT
495499 TTATATTT
1 TTATATTT
495507 TATTCGTATC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
14 10 0.30
15 14 0.42
16 9 0.27
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTATATTTATTATTT
Found at i:504980 original size:20 final size:19
Alignment explanation
Indices: 504957--504994 Score: 67
Period size: 19 Copynumber: 1.9 Consensus size: 19
504947 AAATAGATAT
504957 TTTTTTTGTAAATTCTTTAG
1 TTTTTTT-TAAATTCTTTAG
504977 TTTTTTTTAAATTCTTTA
1 TTTTTTTTAAATTCTTTA
504995 AATAAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.68
Consensus pattern (19 bp):
TTTTTTTTAAATTCTTTAG
Found at i:505273 original size:14 final size:14
Alignment explanation
Indices: 505254--505281 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
505244 TGTGGGGGAA
505254 AAAAATAAAATTTT
1 AAAAATAAAATTTT
505268 AAAAATAAAATTTT
1 AAAAATAAAATTTT
505282 TTAAAAGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AAAAATAAAATTTT
Found at i:505282 original size:15 final size:15
Alignment explanation
Indices: 505254--505287 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
505244 TGTGGGGGAA
505254 AAAAATAAAA-TTTT
1 AAAAATAAAATTTTT
505268 AAAAATAAAATTTTTT
1 AAAAATAAAA-TTTTT
505284 AAAA
1 AAAA
505288 GATTATTAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 10 0.56
16 8 0.44
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
AAAAATAAAATTTTT
Found at i:506062 original size:31 final size:34
Alignment explanation
Indices: 505979--506062 Score: 93
Period size: 36 Copynumber: 2.5 Consensus size: 34
505969 TCTTAACATG
505979 AATTATAATTTTAATAATAATTTTTTAATTTAAATTT
1 AATTATAATTTTAA-AATAATTTTTTAATTT--ATTT
* *
506016 AATTATAAATATAAAATAATTTTTTAA-TT-TTT
1 AATTATAATTTTAAAATAATTTTTTAATTTATTT
*
506048 AA-TATTATTTTAAAA
1 AATTATAATTTTAAAA
506063 AATAAAATAA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
31 10 0.24
32 5 0.12
35 2 0.05
36 13 0.31
37 12 0.29
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (34 bp):
AATTATAATTTTAAAATAATTTTTTAATTTATTT
Found at i:506068 original size:38 final size:36
Alignment explanation
Indices: 505994--506072 Score: 97
Period size: 38 Copynumber: 2.1 Consensus size: 36
505984 TAATTTTAAT
*
505994 AATAATTTTTTAATTTAAATTTAATTATAAATATAA
1 AATAATTTTTTAATTTAAATTTAATTATAAAAATAA
* *
506030 AATAATTTTTTAATTTTTAATATT-ATTTTAAAAAATAA
1 AATAATTTTTTAA-TTTAAAT-TTAATTAT-AAAAATAA
506068 AATAA
1 AATAA
506073 AATTCGAATC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
36 13 0.35
37 10 0.27
38 14 0.38
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (36 bp):
AATAATTTTTTAATTTAAATTTAATTATAAAAATAA
Found at i:508991 original size:93 final size:92
Alignment explanation
Indices: 508858--509111 Score: 260
Period size: 93 Copynumber: 2.7 Consensus size: 92
508848 GACCTTAAAT
** *
508858 TTTCTCACGCTAAGCTGTAATGGTTGATTGGAAACCTTTCTGTTGCATGAACATGCTATGTCGAA
1 TTTCTCACATTAAGCTGTAATGGTTGATTGTAAACCTTTCTGTTGCATGAACATGCTATGTCGAA
* * * **
508923 GTCTTATATGGTA-ATTAGAGCTCA-AATT
66 GTCATAAATGATAGATTA-A-C-CATAAGG
* * * * * * * * *
508951 TTTTTCAGATTAAGCTGTAATGGTTGATTGTAAACTTTTCTTTTACATGAGCATGCAATATCATA
1 TTTCTCACATTAAGCTGTAATGGTTGATTGTAAACCTTTCTGTTGCATGAACATGCTATGTC-GA
* *
509016 AGGCATAAATGATAGTTTAACCATAAGG
65 AGTCATAAATGATAGATTAACCATAAGG
* * *
509044 TTTCTCACATTAAGCTGTAATAGTTGATTGTAAACCTTTCTGTTGCATAAATATGCTATGTCGAA
1 TTTCTCACATTAAGCTGTAATGGTTGATTGTAAACCTTTCTGTTGCATGAACATGCTATGTCGAA
509109 GTC
66 GTC
509112 CTACATGAGC
Statistics
Matches: 126, Mismatches: 32, Indels: 7
0.76 0.19 0.04
Matches are distributed among these distances:
92 6 0.05
93 105 0.83
94 12 0.10
95 3 0.02
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.38
Consensus pattern (92 bp):
TTTCTCACATTAAGCTGTAATGGTTGATTGTAAACCTTTCTGTTGCATGAACATGCTATGTCGAA
GTCATAAATGATAGATTAACCATAAGG
Found at i:509956 original size:27 final size:27
Alignment explanation
Indices: 509926--509980 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
509916 GGGCACAAAG
509926 CCTGGGGCGCCTCTGTATATTTTGAAA
1 CCTGGGGCGCCTCTGTATATTTTGAAA
509953 CCTGGGGCGCCTCTGTATATTTTGAAA
1 CCTGGGGCGCCTCTGTATATTTTGAAA
509980 C
1 C
509981 AACTTACGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.18, C:0.24, G:0.25, T:0.33
Consensus pattern (27 bp):
CCTGGGGCGCCTCTGTATATTTTGAAA
Found at i:510253 original size:15 final size:15
Alignment explanation
Indices: 510235--510266 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
510225 ATATTATTTT
*
510235 TACGTATTATAATTA
1 TACGTATAATAATTA
510250 TACGTATAATAATTA
1 TACGTATAATAATTA
510265 TA
1 TA
510267 AATTTTGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (15 bp):
TACGTATAATAATTA
Found at i:510948 original size:81 final size:82
Alignment explanation
Indices: 510851--511015 Score: 224
Period size: 82 Copynumber: 2.0 Consensus size: 82
510841 AATAAAATTT
* *
510851 ATATAATATAAATTATTATTAAAATATT-TTTTTCAGCCTTTTTAATGATAATTTTGACAGCTTT
1 ATATAATATAAATTATTATCAAAATATTCTTTTTCAGCCATTTTAATGATAATTTTGACAGCTTT
*
510915 TCTGGATTTTGATGTTG
66 TCTGGATTTTGAGGTTG
* * ** * * * *
510932 ATATTATATAAATTATTGTCAAAATATTCTTTTTGGGGCATTTTGATGATAATTTTGAGATCTTT
1 ATATAATATAAATTATTATCAAAATATTCTTTTTCAGCCATTTTAATGATAATTTTGACAGCTTT
510997 TCTGGATTTTGAGGTTG
66 TCTGGATTTTGAGGTTG
511014 AT
1 AT
511016 GATACTTTAG
Statistics
Matches: 72, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
81 25 0.35
82 47 0.65
ACGTcount: A:0.29, C:0.07, G:0.15, T:0.50
Consensus pattern (82 bp):
ATATAATATAAATTATTATCAAAATATTCTTTTTCAGCCATTTTAATGATAATTTTGACAGCTTT
TCTGGATTTTGAGGTTG
Found at i:512713 original size:3 final size:3
Alignment explanation
Indices: 512705--512741 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
512695 GTTGTAAAAT
512705 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
512742 TAACTATGGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:516144 original size:18 final size:17
Alignment explanation
Indices: 516113--516146 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
516103 GTTAACGTAT
*
516113 TAAAATTTATAAATATA
1 TAAAATTTAAAAATATA
516130 TAAATATTTAAAAATAT
1 TAAA-ATTTAAAAATAT
516147 TTATAATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAAATTTAAAAATATA
Found at i:517755 original size:54 final size:54
Alignment explanation
Indices: 517718--517913 Score: 266
Period size: 54 Copynumber: 3.6 Consensus size: 54
517708 TCCTCCGGAG
* * *
517718 TTTGGATCAGGTTATGGACGGAGACCCGAGTACGAGCAGCCTCCACCGCCTGAA
1 TTTGGATCCGGGTATGGACGGAGACCCGAATACGAGCAGCCTCCACCGCCTGAA
* * *
517772 CTTGGATCTGGGTATGGACGGAGACCCGAATATGAGCAGCCTCCACCGCCTGAA
1 TTTGGATCCGGGTATGGACGGAGACCCGAATACGAGCAGCCTCCACCGCCTGAA
* * * * *
517826 TTTGGATCCGGATATGGACGGAGACCAGAATATGAACAGCCTCCGCCGCCTGAA
1 TTTGGATCCGGGTATGGACGGAGACCCGAATACGAGCAGCCTCCACCGCCTGAA
* * *
517880 TTTGGATCCGGGTATGGCCGGAAACCCGAGTACG
1 TTTGGATCCGGGTATGGACGGAGACCCGAATACG
517914 CAGAACAAGA
Statistics
Matches: 125, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 125 1.00
ACGTcount: A:0.24, C:0.27, G:0.30, T:0.19
Consensus pattern (54 bp):
TTTGGATCCGGGTATGGACGGAGACCCGAATACGAGCAGCCTCCACCGCCTGAA
Found at i:517830 original size:108 final size:108
Alignment explanation
Indices: 517676--517908 Score: 286
Period size: 108 Copynumber: 2.2 Consensus size: 108
517666 TGAATCTGGT
* * * * * * * *
517676 TATGGCCGAAAACCTGAATTTGAGCAGCCGCCTCCTCCGGAGTTTGGATCAGGTTATGGACGGAG
1 TATGGACGGAAACCCGAATATGAGCAGCCGCCACCGCCGGAATTTGGATCAGGATATGGACGGAG
* * * *
517741 ACCCGAGTACGAGCAGCCTCCACCGCCTGAACTTGGATCTGGG
66 ACCAGAATACGAACAGCCTCCACCGCCTGAACTTGGATCCGGG
* * * *
517784 TATGGACGGAGACCCGAATATGAGCAGCCTCCACCGCCTGAATTTGGATCCGGATATGGACGGAG
1 TATGGACGGAAACCCGAATATGAGCAGCCGCCACCGCCGGAATTTGGATCAGGATATGGACGGAG
* * *
517849 ACCAGAATATGAACAGCCTCCGCCGCCTGAATTTGGATCCGGG
66 ACCAGAATACGAACAGCCTCCACCGCCTGAACTTGGATCCGGG
*
517892 TATGGCCGGAAACCCGA
1 TATGGACGGAAACCCGA
517909 GTACGCAGAA
Statistics
Matches: 104, Mismatches: 21, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
108 104 1.00
ACGTcount: A:0.24, C:0.27, G:0.29, T:0.19
Consensus pattern (108 bp):
TATGGACGGAAACCCGAATATGAGCAGCCGCCACCGCCGGAATTTGGATCAGGATATGGACGGAG
ACCAGAATACGAACAGCCTCCACCGCCTGAACTTGGATCCGGG
Found at i:518833 original size:19 final size:18
Alignment explanation
Indices: 518797--518834 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
518787 AAAAAAAAAA
*
518797 TATTATTTAAACTTATTT
1 TATTATTTAAAATTATTT
518815 TATTATTTAAAAATTATTT
1 TATTATTT-AAAATTATTT
518834 T
1 T
518835 TATAATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (18 bp):
TATTATTTAAAATTATTT
Found at i:522158 original size:86 final size:87
Alignment explanation
Indices: 522065--522248 Score: 352
Period size: 87 Copynumber: 2.1 Consensus size: 87
522055 TTTAAAATTG
522065 AAAAATATTTTAATTTTTATTAT-ATATAATATTCAAAATCTATTTTTTGTCTGATTCGAATTAT
1 AAAAATATTTTAATTTTTATTATAATATAATATTCAAAATCTATTTTTTGTCTGATTCGAATTAT
522129 ATATTATATAGTTTATTATATA
66 ATATTATATAGTTTATTATATA
*
522151 AAAAATATTTTATTTTTTATTATAATATAATATTCAAAATCTATTTTTTGTCTGATTCGAATTAT
1 AAAAATATTTTAATTTTTATTATAATATAATATTCAAAATCTATTTTTTGTCTGATTCGAATTAT
522216 ATATTATATAGTTTATTATATA
66 ATATTATATAGTTTATTATATA
522238 AAAAATATTTT
1 AAAAATATTTT
522249 TTTATTTTTA
Statistics
Matches: 96, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
86 22 0.23
87 74 0.77
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.52
Consensus pattern (87 bp):
AAAAATATTTTAATTTTTATTATAATATAATATTCAAAATCTATTTTTTGTCTGATTCGAATTAT
ATATTATATAGTTTATTATATA
Found at i:522366 original size:29 final size:30
Alignment explanation
Indices: 522311--522367 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
522301 TTATTAGTTA
* * * *
522311 ATATTAAATTTATGTTATTTTATTTTTTAT
1 ATATAAAATTTATGTTATATAAATTTTTAT
522341 ATATAAAATTTAT-TTATATAAATTTTT
1 ATATAAAATTTATGTTATATAAATTTTT
522368 GAGACATGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 11 0.48
30 12 0.52
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (30 bp):
ATATAAAATTTATGTTATATAAATTTTTAT
Found at i:523991 original size:42 final size:42
Alignment explanation
Indices: 523944--524038 Score: 172
Period size: 42 Copynumber: 2.3 Consensus size: 42
523934 GCCACATGAG
523944 GTGGCGATTTCCTAACTTCAAGTTGGGAAATCACCATTTAAA
1 GTGGCGATTTCCTAACTTCAAGTTGGGAAATCACCATTTAAA
*
523986 GTGGCGATTTCCTAATTTCAAGTTGGGAAATCACCATTTAAA
1 GTGGCGATTTCCTAACTTCAAGTTGGGAAATCACCATTTAAA
*
524028 GTGACGATTTC
1 GTGGCGATTTC
524039 ACAACACGAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (42 bp):
GTGGCGATTTCCTAACTTCAAGTTGGGAAATCACCATTTAAA
Found at i:524024 original size:21 final size:21
Alignment explanation
Indices: 523963--524029 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
523953 TCCTAACTTC
523963 AAGTTGGGAAATCACCATTTA
1 AAGTTGGGAAATCACCATTTA
** * *
523984 AAG-TGGCGATTTC-CTAATTTC
1 AAGTTGG-GAAATCAC-CATTTA
524005 AAGTTGGGAAATCACCATTTA
1 AAGTTGGGAAATCACCATTTA
524026 AAGT
1 AAGT
524030 GACGATTTCA
Statistics
Matches: 34, Mismatches: 8, Indels: 8
0.68 0.16 0.16
Matches are distributed among these distances:
20 4 0.12
21 26 0.76
22 4 0.12
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.31
Consensus pattern (21 bp):
AAGTTGGGAAATCACCATTTA
Found at i:524225 original size:39 final size:39
Alignment explanation
Indices: 524181--524332 Score: 121
Period size: 39 Copynumber: 3.9 Consensus size: 39
524171 ATAAAATCTA
* *
524181 AAAGATATGGGTAATATATAAATTTTTTATTATATTTTG
1 AAAGATATGAGTAATATATAAATTTTTTATTAAATTTTG
* * * *
524220 AAAGATATTAGTAAT-TATAGATTATTTATTAGAA-TTTA
1 AAAGATATGAGTAATATATAAATTTTTTATTA-AATTTTG
* * * * * * *
524258 AAAAATGTAACTAATATATAAAATTTTTGTTCAAATTCTG
1 AAAGATATGAGTAATATATAAATTTTTTATT-AAATTTTG
* *
524298 -AAGATATGATTAATATATAAATTTTATTTTTAAAT
1 AAAGATATGAGTAATATATAAATTTT-TTATTAAAT
524333 AAATATAATA
Statistics
Matches: 86, Mismatches: 22, Indels: 10
0.73 0.19 0.08
Matches are distributed among these distances:
38 28 0.33
39 51 0.59
40 7 0.08
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.45
Consensus pattern (39 bp):
AAAGATATGAGTAATATATAAATTTTTTATTAAATTTTG
Found at i:524664 original size:91 final size:92
Alignment explanation
Indices: 524505--524814 Score: 477
Period size: 92 Copynumber: 3.4 Consensus size: 92
524495 AATAAATGTG
*
524505 ATTATATCTGAGAATCAGA-T-TTTTTTAT--AAAAAGAGAAAAGTTGATTGATTGTAAATGTCA
1 ATTATATCTGAGAATCAGATTCTTTTTTATAGAAAAAAAGAAAAGTTGATTGATTGTAAATGTCA
* *
524566 AACTGTAAAAATTAGACTAATGCATGA
66 GACTGTAAAGATTAGACTAATGCATGA
524593 ATTATATCTGAGAATCAGATT-TTTTTTATAGAAAAAAAGAAAAGTTGATTGATTGTAAATGTCA
1 ATTATATCTGAGAATCAGATTCTTTTTTATAGAAAAAAAGAAAAGTTGATTGATTGTAAATGTCA
* *
524657 GATTGTAATGATTAGACTAATGCATGA
66 GACTGTAAAGATTAGACTAATGCATGA
* * *
524684 ATTATATGTAAGAATCAGATTCTTTTTTATAGAAAAAAAGAAAACTTGATTGATTGTAAATGTCA
1 ATTATATCTGAGAATCAGATTCTTTTTTATAGAAAAAAAGAAAAGTTGATTGATTGTAAATGTCA
* * *
524749 GACTGCAAGGATTAAACTAATGCATGA
66 GACTGTAAAGATTAGACTAATGCATGA
*
524776 ATTATATTTGAGAATCAGATTCTTTTTTATAGAAAAAAA
1 ATTATATCTGAGAATCAGATTCTTTTTTATAGAAAAAAA
524815 AGACTACAAG
Statistics
Matches: 204, Mismatches: 14, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
88 19 0.09
89 9 0.04
91 74 0.36
92 102 0.50
ACGTcount: A:0.42, C:0.07, G:0.16, T:0.35
Consensus pattern (92 bp):
ATTATATCTGAGAATCAGATTCTTTTTTATAGAAAAAAAGAAAAGTTGATTGATTGTAAATGTCA
GACTGTAAAGATTAGACTAATGCATGA
Found at i:524955 original size:158 final size:158
Alignment explanation
Indices: 524666--524969 Score: 396
Period size: 158 Copynumber: 1.9 Consensus size: 158
524656 AGATTGTAAT
** *
524666 GATTAGACTAATGCATGAATTATATGTAAGAATCAGATTCTTTTTTATAGAAAAAAAGAAAACTT
1 GATTAGACTAATGCATGAATTATACCTAAGAATCAGATTCTTTTTGATAGAAAAAAAGAAAACTT
* * * * * * *
524731 GATTGATTGTAAATGTCAGACTGCAAGGATTAAACTAATGCATGAATTATATTTGAGAATCAGAT
66 GATTGATTATAAATATCACACTGCAAAGATTAAACTAATACATAAATTATATTTGAAAATCAGAT
* *
524796 TCTTTTTTATAGAAAAAAAAGACTACAAG
131 TCCTTTTGATA-AAAAAAAAGACTACAAG
* * * * *
524825 GATTAGACTAATGCATGAATTGTACCTGAGAATCAGATTCTTTTTGGTA-AAATCAAA-AAAAGT
1 GATTAGACTAATGCATGAATTATACCTAAGAATCAGATTCTTTTTGATAGAAA-AAAAGAAAACT
* * *
524888 TGATTGATTATAAGTATCACACTGCAAAGATTAAACTAGTACATAAATTATATTTGAAAATTAGA
65 TGATTGATTATAAATATCACACTGCAAAGATTAAACTAATACATAAATTATATTTGAAAATCAGA
524953 TTCCTTTTGATAAAAAA
130 TTCCTTTTGATAAAAAA
524970 GCTTGTAAAT
Statistics
Matches: 124, Mismatches: 20, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
157 5 0.04
158 73 0.59
159 46 0.37
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (158 bp):
GATTAGACTAATGCATGAATTATACCTAAGAATCAGATTCTTTTTGATAGAAAAAAAGAAAACTT
GATTGATTATAAATATCACACTGCAAAGATTAAACTAATACATAAATTATATTTGAAAATCAGAT
TCCTTTTGATAAAAAAAAAGACTACAAG
Found at i:530214 original size:22 final size:21
Alignment explanation
Indices: 530140--530214 Score: 62
Period size: 22 Copynumber: 3.4 Consensus size: 21
530130 AAATTTTTAC
* *
530140 AAATAGAAATAAATAATAATTC
1 AAATA-AAATTAATAATAATTA
* * *
530162 TAATCAAATTAATATTATAAATA
1 AAATAAAATTAATA--ATAATTA
530185 AAAT-AAATTAATAATAACTTA
1 AAATAAAATTAATAATAA-TTA
530206 AAATAAAAT
1 AAATAAAAT
530215 AACTTTAAAC
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
20 4 0.10
21 14 0.33
22 16 0.38
23 8 0.19
ACGTcount: A:0.63, C:0.04, G:0.01, T:0.32
Consensus pattern (21 bp):
AAATAAAATTAATAATAATTA
Found at i:530535 original size:22 final size:22
Alignment explanation
Indices: 530504--530555 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
530494 CCCGTGATTT
*
530504 TTTTTTTAATTTAA-ATTTAAAA
1 TTTTTATAA-TTAATATTTAAAA
*
530526 TTTTTATAATTAATATTTTAAA
1 TTTTTATAATTAATATTTAAAA
*
530548 TTTATATA
1 TTTTTATA
530556 TAATAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 4 0.15
22 22 0.85
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTTTATAATTAATATTTAAAA
Found at i:530585 original size:22 final size:21
Alignment explanation
Indices: 530556--530615 Score: 68
Period size: 22 Copynumber: 2.9 Consensus size: 21
530546 AATTTATATA
*
530556 TAAT-AAAATAAAAATTAATT
1 TAATAAAAAAAAAAATTAATT
*
530576 TAATAAAAAAATTAAATTAATT
1 TAATAAAAAAA-AAAATTAATT
* *
530598 TTATAAATAAAAAAATTA
1 TAATAAAAAAAAAAATTA
530616 TACTTTAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
20 4 0.12
21 11 0.33
22 18 0.55
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
TAATAAAAAAAAAAATTAATT
Found at i:530801 original size:36 final size:35
Alignment explanation
Indices: 530712--530802 Score: 91
Period size: 36 Copynumber: 2.6 Consensus size: 35
530702 CAAATCATAC
*
530712 ATTAATTTTTTAAAATT--TAATTAAATATTATTT
1 ATTAAATTTTTAAAATTAATAATTAAATATTATTT
* *
530745 -TT-TATTTTATAAAAAATAATAATTAATATATTATTT
1 ATTAAATTTT-T-AAAATTAATAATTAA-ATATTATTT
*
530781 ATTAAATTTTTAAATTTAATAA
1 ATTAAATTTTTAAAATTAATAA
530803 ATTTATACAT
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
31 4 0.09
32 3 0.07
33 5 0.11
35 7 0.16
36 18 0.40
37 3 0.07
38 5 0.11
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (35 bp):
ATTAAATTTTTAAAATTAATAATTAAATATTATTT
Found at i:537500 original size:30 final size:30
Alignment explanation
Indices: 537466--537554 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 30
537456 AAAGTAAATT
** *
537466 TTAAGAGTTTATTTGAATTTAAATTAAAAA
1 TTAAGAGTTTATTTGAATGCAAAATAAAAA
* * *
537496 TTAAGGGTTAATTTGAGTGCAAAATAAAAA
1 TTAAGAGTTTATTTGAATGCAAAATAAAAA
* *
537526 TTAAAAATTTATTTGAATGC--AATAAAAA
1 TTAAGAGTTTATTTGAATGCAAAATAAAAA
537554 T
1 T
537555 ATAATAAGTT
Statistics
Matches: 48, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
28 9 0.19
30 39 0.81
ACGTcount: A:0.48, C:0.02, G:0.12, T:0.37
Consensus pattern (30 bp):
TTAAGAGTTTATTTGAATGCAAAATAAAAA
Found at i:537871 original size:33 final size:33
Alignment explanation
Indices: 537832--537900 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
537822 GAAAAGATCT
*
537832 TATCTTTATATTTATATTTAAATATATATCAAA
1 TATCTTTATATCTATATTTAAATATATATCAAA
* *
537865 TATCTTTATATCTATATTTGAATATATATCGAA
1 TATCTTTATATCTATATTTAAATATATATCAAA
537898 TAT
1 TAT
537901 AAATATCAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.39, C:0.07, G:0.03, T:0.51
Consensus pattern (33 bp):
TATCTTTATATCTATATTTAAATATATATCAAA
Found at i:537912 original size:13 final size:13
Alignment explanation
Indices: 537890--537919 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
537880 ATTTGAATAT
*
537890 ATATCGAATATAA
1 ATATCAAATATAA
537903 ATATCAAATATAA
1 ATATCAAATATAA
537916 ATAT
1 ATAT
537920 TTTAAGATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (13 bp):
ATATCAAATATAA
Found at i:538865 original size:23 final size:23
Alignment explanation
Indices: 538831--538876 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
538821 CAAATTTTTT
* **
538831 TCAAACTTCTTACCTGGACCCGA
1 TCAAACTCCTTACCCAGACCCGA
538854 TCAAACTCCTTACCCAGACCCGA
1 TCAAACTCCTTACCCAGACCCGA
538877 CCGAGCTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.28, C:0.39, G:0.11, T:0.22
Consensus pattern (23 bp):
TCAAACTCCTTACCCAGACCCGA
Found at i:542962 original size:12 final size:12
Alignment explanation
Indices: 542935--542984 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
542925 TTTTATATAT
542935 ATTATATTCATAAA
1 ATTATATT--TAAA
542949 ATTATATTTAAA
1 ATTATATTTAAA
542961 A-T-TA--TAAA
1 ATTATATTTAAA
542969 ATTATATTTAAA
1 ATTATATTTAAA
542981 ATTA
1 ATTA
542985 GCTTAACCAG
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
8 5 0.16
9 1 0.03
10 4 0.12
11 1 0.03
12 13 0.41
14 8 0.25
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (12 bp):
ATTATATTTAAA
Found at i:542969 original size:20 final size:20
Alignment explanation
Indices: 542944--542984 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
542934 TATTATATTC
542944 ATAAAATTATATTTAAAATT
1 ATAAAATTATATTTAAAATT
542964 ATAAAATTATATTTAAAATT
1 ATAAAATTATATTTAAAATT
542984 A
1 A
542985 GCTTAACCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
ATAAAATTATATTTAAAATT
Found at i:544337 original size:13 final size:13
Alignment explanation
Indices: 544319--544345 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
544309 AAATACAACG
544319 TACAATTAGTCGA
1 TACAATTAGTCGA
544332 TACAATTAGTCGA
1 TACAATTAGTCGA
544345 T
1 T
544346 TACCGATGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (13 bp):
TACAATTAGTCGA
Found at i:545436 original size:22 final size:22
Alignment explanation
Indices: 545408--545456 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
545398 ACCAAATACA
545408 TCACCTAACACACCTAACATTC
1 TCACCTAACACACCTAACATTC
545430 TCACCTAACACACCTAACATTC
1 TCACCTAACACACCTAACATTC
545452 TCACC
1 TCACC
545457 AAATACATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.35, C:0.43, G:0.00, T:0.22
Consensus pattern (22 bp):
TCACCTAACACACCTAACATTC
Found at i:545465 original size:56 final size:55
Alignment explanation
Indices: 545380--545504 Score: 214
Period size: 56 Copynumber: 2.3 Consensus size: 55
545370 ATATACATGT
545380 TAACACACCTAACATCTCACCAAATACATCACCTAACACACCTAACATTCTCACC
1 TAACACACCTAACATCTCACCAAATACATCACCTAACACACCTAACATTCTCACC
545435 TAACACACCTAACATTCTCACCAAATACATCACCTAACACACCTAACATTCTCACC
1 TAACACACCTAACA-TCTCACCAAATACATCACCTAACACACCTAACATTCTCACC
* * *
545491 AAATACACTTAACA
1 TAACACACCTAACA
545505 AAGAAATTAA
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
55 14 0.21
56 52 0.79
ACGTcount: A:0.42, C:0.38, G:0.00, T:0.21
Consensus pattern (55 bp):
TAACACACCTAACATCTCACCAAATACATCACCTAACACACCTAACATTCTCACC
Found at i:545472 original size:34 final size:34
Alignment explanation
Indices: 545430--545497 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
545420 CCTAACATTC
545430 TCACCTAACACACCTAACATTCTCACCAAATACA
1 TCACCTAACACACCTAACATTCTCACCAAATACA
545464 TCACCTAACACACCTAACATTCTCACCAAATACA
1 TCACCTAACACACCTAACATTCTCACCAAATACA
545498 CTTAACAAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.41, C:0.38, G:0.00, T:0.21
Consensus pattern (34 bp):
TCACCTAACACACCTAACATTCTCACCAAATACA
Found at i:550232 original size:22 final size:22
Alignment explanation
Indices: 550202--550332 Score: 94
Period size: 22 Copynumber: 5.9 Consensus size: 22
550192 ACCAAATACA
*
550202 TCACTTAACACACCTAACATTC
1 TCACCTAACACACCTAACATTC
550224 TCACCTAACACACCTAACATTC
1 TCACCTAACACACCTAACATTC
*
550246 TCACCAAACACATCACCTAACA---
1 TCACC-TA-ACA-CACCTAACATTC
*
550268 -CACCTAACATTCTCACC-AA-ATAC
1 TCACCTAACA----CACCTAACATTC
550291 ATCACCTAACACACCTAACATTC
1 -TCACCTAACACACCTAACATTC
* * *
550314 TCACCAAATACACTTAACA
1 TCACCTAACACACCTAACA
550333 AAGAAATTAA
Statistics
Matches: 89, Mismatches: 7, Indels: 26
0.73 0.06 0.21
Matches are distributed among these distances:
19 3 0.03
20 2 0.02
21 10 0.11
22 49 0.55
23 4 0.04
24 3 0.03
25 18 0.20
ACGTcount: A:0.40, C:0.38, G:0.00, T:0.21
Consensus pattern (22 bp):
TCACCTAACACACCTAACATTC
Found at i:550259 original size:56 final size:56
Alignment explanation
Indices: 550173--550284 Score: 206
Period size: 56 Copynumber: 2.0 Consensus size: 56
550163 ATATACATGT
* *
550173 TAACACACCTAACATTCTCACCAAATACATCACTTAACACACCTAACATTCTCACC
1 TAACACACCTAACATTCTCACCAAACACATCACCTAACACACCTAACATTCTCACC
550229 TAACACACCTAACATTCTCACCAAACACATCACCTAACACACCTAACATTCTCACC
1 TAACACACCTAACATTCTCACCAAACACATCACCTAACACACCTAACATTCTCACC
550285 AAATACATCA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.39, C:0.39, G:0.00, T:0.21
Consensus pattern (56 bp):
TAACACACCTAACATTCTCACCAAACACATCACCTAACACACCTAACATTCTCACC
Found at i:550322 original size:34 final size:34
Alignment explanation
Indices: 550224--550325 Score: 195
Period size: 34 Copynumber: 3.0 Consensus size: 34
550214 CCTAACATTC
*
550224 TCACCTAACACACCTAACATTCTCACCAAACACA
1 TCACCTAACACACCTAACATTCTCACCAAATACA
550258 TCACCTAACACACCTAACATTCTCACCAAATACA
1 TCACCTAACACACCTAACATTCTCACCAAATACA
550292 TCACCTAACACACCTAACATTCTCACCAAATACA
1 TCACCTAACACACCTAACATTCTCACCAAATACA
550326 CTTAACAAAG
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
34 67 1.00
ACGTcount: A:0.41, C:0.39, G:0.00, T:0.20
Consensus pattern (34 bp):
TCACCTAACACACCTAACATTCTCACCAAATACA
Found at i:551495 original size:16 final size:16
Alignment explanation
Indices: 551474--551524 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
551464 AAAAATTAAT
551474 AATATATTTAAATATA
1 AATATATTTAAATATA
551490 AATATA--TAATATCATA
1 AATATATTTAA-AT-ATA
*
551506 AATATAATTTCAATATA
1 AATAT-ATTTAAATATA
551523 AA
1 AA
551525 AATTAATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
14 3 0.10
15 2 0.07
16 14 0.48
17 6 0.21
18 2 0.07
19 2 0.07
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (16 bp):
AATATATTTAAATATA
Found at i:551496 original size:18 final size:19
Alignment explanation
Indices: 551451--551497 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
551441 ATTATATTCA
*
551451 AAATTTATATTATAAAAAT
1 AAATATATATTATAAAAAT
* *
551470 TAATAATATATT-TAAATAT
1 AAAT-ATATATTATAAAAAT
551489 AAATATATA
1 AAATATATA
551498 ATATCATAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 5 0.22
19 12 0.52
20 6 0.26
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
AAATATATATTATAAAAAT
Found at i:551522 original size:11 final size:11
Alignment explanation
Indices: 551506--551548 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
551496 TAATATCATA
*
551506 AATATAATTTC
1 AATATAAATTC
551517 AATATAAAAATT-
1 AATAT--AAATTC
551529 AATATAAATTC
1 AATATAAATTC
551540 AATATAAAT
1 AATATAAAT
551549 ATAAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 5 0.18
11 14 0.50
12 5 0.18
13 4 0.14
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (11 bp):
AATATAAATTC
Found at i:551549 original size:29 final size:29
Alignment explanation
Indices: 551461--551557 Score: 85
Period size: 29 Copynumber: 3.3 Consensus size: 29
551451 AAATTTATAT
*
551461 TATAAAAATTAATAATATATTTAAATATAAA
1 TATAAAAATTAATAATA-AATT-AATATAAA
* * * *
551492 TAT-ATAA-T-ATCATAAATATAATTTCAA
1 TATAAAAATTAATAATAAAT-TAATATAAA
551519 TATAAAAATTAAT-ATAAATTCAATATAAA
1 TATAAAAATTAATAATAAATT-AATATAAA
551548 TATAAAAATT
1 TATAAAAATT
551558 TTAAAATCTA
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
27 11 0.21
28 10 0.19
29 24 0.45
30 5 0.09
31 3 0.06
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (29 bp):
TATAAAAATTAATAATAAATTAATATAAA
Found at i:551907 original size:12 final size:12
Alignment explanation
Indices: 551887--551920 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
551877 AAGGTTACAT
*
551887 AGTTGCTAATAA
1 AGTTTCTAATAA
*
551899 AGTTTCTAATTA
1 AGTTTCTAATAA
551911 AGTTTCTAAT
1 AGTTTCTAAT
551921 GATAACTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (12 bp):
AGTTTCTAATAA
Found at i:552219 original size:2 final size:2
Alignment explanation
Indices: 552212--552255 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
552202 GTTGATACAA
*
552212 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
552254 AT
1 AT
552256 CACATGTCCA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:553262 original size:21 final size:21
Alignment explanation
Indices: 553238--553277 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
553228 AATTAAAAAA
553238 ATAAAACAAAAAAAATATAAT
1 ATAAAACAAAAAAAATATAAT
* *
553259 ATAAAATAAAAAATATATA
1 ATAAAACAAAAAAAATATA
553278 TATGAAGATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.23
Consensus pattern (21 bp):
ATAAAACAAAAAAAATATAAT
Found at i:553545 original size:3 final size:3
Alignment explanation
Indices: 553539--553569 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
553529 AGAAATTTAA
553539 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
553570 TGATCAGACG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:554351 original size:3 final size:3
Alignment explanation
Indices: 554345--554374 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
554335 TTTCATGATG
*
554345 ATT ATT ATT ATA ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
554375 GATTGCCTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:554551 original size:2 final size:2
Alignment explanation
Indices: 554544--554583 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
554534 ATGTATAGCA
554544 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
554584 GTTCAATGCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:554644 original size:2 final size:2
Alignment explanation
Indices: 554637--554680 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
554627 GAAGCTTTTC
554637 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
554679 AT
1 AT
554681 TCCCAATAGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:554919 original size:24 final size:22
Alignment explanation
Indices: 554892--554945 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 22
554882 TACATATATG
554892 TATTATATTA-ATTATTTTTAAATA
1 TATTATATTATATTATTTTT---TA
*
554916 TATTA-AATATATTATTTTTTA
1 TATTATATTATATTATTTTTTA
554937 TATTATATT
1 TATTATATT
554946 TAAAATTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 7 0.27
22 2 0.08
23 3 0.12
24 14 0.54
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TATTATATTATATTATTTTTTA
Found at i:554953 original size:24 final size:24
Alignment explanation
Indices: 554900--554956 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
554890 TGTATTATAT
554900 TAATTA-TTTTTAAATATATTAAA
1 TAATTATTTTTTAAATATATTAAA
* *
554923 TATATTATTTTTTATATTATATTTAA
1 TA-ATTATTTTTTA-AATATATTAAA
554949 -AATTATTT
1 TAATTATTT
554957 AATTTATTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
23 2 0.07
24 11 0.38
25 7 0.24
26 9 0.31
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
TAATTATTTTTTAAATATATTAAA
Found at i:559239 original size:10 final size:10
Alignment explanation
Indices: 559224--559262 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
559214 ATGACACAAT
559224 TTATTTTATG
1 TTATTTTATG
559234 TTATTTTATG
1 TTATTTTATG
559244 TTATTCTTAT-
1 TTATT-TTATG
*
559254 TTATATTAT
1 TTATTTTAT
559263 TATCGTTGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
9 4 0.15
10 19 0.70
11 4 0.15
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.69
Consensus pattern (10 bp):
TTATTTTATG
Done.