Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold64
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: 7997333
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 95991 characters in sequence are not A, C, G, or T
File 17 of 45
Found at i:3165134 original size:29 final size:29
Alignment explanation
Indices: 3165089--3165144 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
3165079 TTTTAATTTT
* *
3165089 TTTATATTTTTAAATAATTATATTTTATA
1 TTTATATTTTAAAATAAATATATTTTATA
*
3165118 TTTATA-TTTAAATATAAATATTTTTTA
1 TTTATATTTTAAA-ATAAATATATTTTA
3165145 AAAAAATAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 5 0.22
29 18 0.78
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (29 bp):
TTTATATTTTAAAATAAATATATTTTATA
Found at i:3169022 original size:17 final size:18
Alignment explanation
Indices: 3169002--3169036 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
3168992 TATTTTTACG
3169002 TTTTTA-AATTTTA-AAT
1 TTTTTATAATTTTATAAT
3169018 TTTTTATAATTTTATAAT
1 TTTTTATAATTTTATAAT
3169036 T
1 T
3169037 AAATTTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 7 0.41
18 4 0.24
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTTTATAATTTTATAAT
Found at i:3170977 original size:4 final size:4
Alignment explanation
Indices: 3170970--3171000 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
3170960 TACTGCTAAC
3170970 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAA
3171001 TTAATTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:3171409 original size:18 final size:20
Alignment explanation
Indices: 3171372--3171438 Score: 65
Period size: 18 Copynumber: 3.6 Consensus size: 20
3171362 ATTTTAATGT
*
3171372 ATTATAATTATATT--TAAA
1 ATTATTATTATATTAATAAA
*
3171390 A-TATT-TTATATTTATAAA
1 ATTATTATTATATTAATAAA
3171408 ATTATTATTATATTAAT-AA
1 ATTATTATTATATTAATAAA
*
3171427 TTTA-TATTATAT
1 ATTATTATTATAT
3171439 AAAATTAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
16 7 0.17
17 3 0.07
18 14 0.33
19 9 0.21
20 9 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
ATTATTATTATATTAATAAA
Found at i:3171419 original size:36 final size:34
Alignment explanation
Indices: 3171372--3171445 Score: 96
Period size: 33 Copynumber: 2.1 Consensus size: 34
3171362 ATTTTAATGT
*
3171372 ATTATAATTATATTTAAAATATTTTATATT-TATAAA
1 ATTATAATTATA-TT--AATAATTTATATTATATAAA
*
3171408 ATTATTATTATATTAATAATTTATATTATATAAA
1 ATTATAATTATATTAATAATTTATATTATATAAA
3171442 ATTA
1 ATTA
3171446 AAATATTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
33 12 0.34
34 10 0.29
35 2 0.06
36 11 0.31
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (34 bp):
ATTATAATTATATTAATAATTTATATTATATAAA
Found at i:3171463 original size:34 final size:33
Alignment explanation
Indices: 3171389--3171465 Score: 86
Period size: 33 Copynumber: 2.3 Consensus size: 33
3171379 TTATATTTAA
* * *
3171389 AATATTTTATATTTATAAAATTATTATTATATT
1 AATAATTTATATTTATAAAATTATAAATATATT
3171422 AATAATTTATATTATATAAAATTA-AAATAT-TT
1 AATAATTTATATT-TATAAAATTATAAATATATT
3171454 ATATAAATTTAT
1 A-AT-AATTTAT
3171466 TAAAATTTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
32 3 0.08
33 18 0.47
34 17 0.45
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (33 bp):
AATAATTTATATTTATAAAATTATAAATATATT
Found at i:3171479 original size:24 final size:22
Alignment explanation
Indices: 3171417--3171479 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 22
3171407 AATTATTATT
3171417 ATATTAATAATTTATATTATATAA
1 ATATTAA-AATTTA-ATTATATAA
*
3171441 A-ATTAAAA--TATTTATATAA
1 ATATTAAAATTTAATTATATAA
3171460 ATTTATTAAAATTTAATTAT
1 A--TATTAAAATTTAATTAT
3171480 TTTTATATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
19 9 0.28
20 2 0.06
22 9 0.28
23 5 0.16
24 7 0.22
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATATTAAAATTTAATTATATAA
Found at i:3171513 original size:12 final size:11
Alignment explanation
Indices: 3171471--3171514 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
3171461 TTTATTAAAA
3171471 TTTA-ATTATT
1 TTTATATTATT
3171481 TTTATATTATT
1 TTTATATTATT
3171492 TTTATAATTATAT
1 TTTAT-ATTAT-T
*
3171505 TTAATATTAT
1 TTTATATTAT
3171515 CAAATATAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
10 4 0.13
11 11 0.37
12 10 0.33
13 5 0.17
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TTTATATTATT
Found at i:3171790 original size:5 final size:5
Alignment explanation
Indices: 3171780--3171833 Score: 72
Period size: 5 Copynumber: 10.4 Consensus size: 5
3171770 GTCATGGATG
* *
3171780 AATAA AATAA AATAA AATAA AATAA AATAA TAATAC AATAAA AATAT AATAA
1 AATAA AATAA AATAA AATAA AATAA AATAA -AATAA AAT-AA AATAA AATAA
3171832 AA
1 AA
3171834 AAATAGATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
5 35 0.81
6 8 0.19
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (5 bp):
AATAA
Found at i:3171834 original size:11 final size:11
Alignment explanation
Indices: 3171780--3171834 Score: 69
Period size: 11 Copynumber: 5.2 Consensus size: 11
3171770 GTCATGGATG
3171780 AATAAAAT-AA
1 AATAAAATAAA
3171790 AATAAAAT-AA
1 AATAAAATAAA
*
3171800 AATAAAATAAT
1 AATAAAATAAA
*
3171811 AATACAATAAA
1 AATAAAATAAA
*
3171822 AATATAATAAA
1 AATAAAATAAA
3171833 AA
1 AA
3171835 AATAGATATT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
10 18 0.45
11 22 0.55
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (11 bp):
AATAAAATAAA
Found at i:3172340 original size:28 final size:30
Alignment explanation
Indices: 3172276--3172340 Score: 70
Period size: 28 Copynumber: 2.4 Consensus size: 30
3172266 ATATTAGTAT
3172276 TATTTAT--TTTTATATAAATTTGATACGA
1 TATTTATAATTTTATATAAATTTGATACGA
* *
3172304 TA-TTA-AATTTTATTTAAATTT-AT-CTA
1 TATTTATAATTTTATATAAATTTGATACGA
3172330 TATTTATAATT
1 TATTTATAATT
3172341 AAGTGATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
26 4 0.13
27 8 0.26
28 19 0.61
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.57
Consensus pattern (30 bp):
TATTTATAATTTTATATAAATTTGATACGA
Found at i:3172533 original size:19 final size:19
Alignment explanation
Indices: 3172490--3172533 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
3172480 ATATCGTATT
3172490 TTTTATTTAAAATATTATA
1 TTTTATTTAAAATATTATA
*
3172509 TATTTATTT-AAATTTTAATA
1 T-TTTATTTAAAATATT-ATA
3172529 TTTTA
1 TTTTA
3172534 ATTATTTACA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTTATTTAAAATATTATA
Found at i:3172582 original size:13 final size:13
Alignment explanation
Indices: 3172564--3172609 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
3172554 AAAAATATAT
3172564 TTATTTATTAATA
1 TTATTTATTAATA
* *
3172577 TTATTTATTTATT
1 TTATTTATTAATA
3172590 TTATTT-TTAA-A
1 TTATTTATTAATA
3172601 TTATATTAT
1 TTAT-TTAT
3172610 ATCATATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
11 4 0.15
12 5 0.19
13 18 0.67
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TTATTTATTAATA
Found at i:3172583 original size:17 final size:16
Alignment explanation
Indices: 3172557--3172589 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
3172547 TATAAATAAA
3172557 AATATATTTATTTATT
1 AATATATTTATTTATT
3172573 AATATTATTTATTTATT
1 AATA-TATTTATTTATT
3172590 TTATTTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
AATATATTTATTTATT
Found at i:3175063 original size:41 final size:41
Alignment explanation
Indices: 3175006--3175087 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
3174996 AATACCTGTG
* *
3175006 ATTTAAGTGGTTGTTATAAGAATATGAGACATTGTTCCTTT
1 ATTTAAATGGTTGTTATAACAATATGAGACATTGTTCCTTT
*
3175047 ATTTAAATGGTTGTTATAACAATCTGAGACATTGTTCCTTT
1 ATTTAAATGGTTGTTATAACAATATGAGACATTGTTCCTTT
3175088 CTCCTTCCCC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.29, C:0.10, G:0.17, T:0.44
Consensus pattern (41 bp):
ATTTAAATGGTTGTTATAACAATATGAGACATTGTTCCTTT
Found at i:3177781 original size:2 final size:2
Alignment explanation
Indices: 3177774--3177806 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3177764 CATACTATTT
3177774 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3177807 CTTAAACTTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3178663 original size:17 final size:17
Alignment explanation
Indices: 3178614--3178690 Score: 58
Period size: 17 Copynumber: 4.8 Consensus size: 17
3178604 TGAAAGTAAA
3178614 AATA-TATTATAAATATT
1 AATATTATT-TAAATATT
* *
3178631 AA-A--ATTAAAATTTT
1 AATATTATTTAAATATT
3178645 AATATTATTTAAATATT
1 AATATTATTTAAATATT
* *
3178662 AATATTAATTATATA-T
1 AATATTATTTAAATATT
*
3178678 AA-ATTAATTAAAT
1 AATATTATTTAAAT
3178691 TAAATTTTAA
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
14 8 0.16
15 14 0.28
16 4 0.08
17 24 0.48
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AATATTATTTAAATATT
Found at i:3180084 original size:3 final size:3
Alignment explanation
Indices: 3180059--3180110 Score: 77
Period size: 3 Copynumber: 17.0 Consensus size: 3
3180049 CACAACATGA
* *
3180059 AAT AAT AGT AAT AAA AAT AAAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT
3180105 AAT AAT
1 AAT AAT
3180111 GGCTAAAGTT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3180345 original size:27 final size:27
Alignment explanation
Indices: 3180302--3180368 Score: 68
Period size: 27 Copynumber: 2.6 Consensus size: 27
3180292 CAATTTTTAT
* *
3180302 TTTTTAAAATAT--TTATATATGAT-A
1 TTTTTAAAATATAAATATAAATGATAA
*
3180326 TATTTTAAAATATAAATATAAATTATAA
1 T-TTTTAAAATATAAATATAAATGATAA
*
3180354 TTTTTTAAATATAAA
1 TTTTTAAAATATAAA
3180369 AAAATTTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
24 1 0.03
25 11 0.31
27 21 0.60
28 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (27 bp):
TTTTTAAAATATAAATATAAATGATAA
Found at i:3180352 original size:25 final size:26
Alignment explanation
Indices: 3180298--3180368 Score: 65
Period size: 25 Copynumber: 2.7 Consensus size: 26
3180288 TGATCAATTT
* ** *
3180298 TTATTTTTTAAAATATTTATATATGA
1 TTATATTTTAAAATATAAATATATAA
3180324 -TATATTTTAAAATATAAATATA-AA
1 TTATATTTTAAAATATAAATATATAA
*
3180348 TTATAATTTTTTAAATATAAA
1 TTAT-A-TTTTAAAATATAAA
3180369 AAAATTTAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
24 1 0.03
25 22 0.59
26 1 0.03
27 13 0.35
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (26 bp):
TTATATTTTAAAATATAAATATATAA
Found at i:3181332 original size:10 final size:10
Alignment explanation
Indices: 3181317--3181373 Score: 57
Period size: 10 Copynumber: 5.9 Consensus size: 10
3181307 ATGTACGATA
3181317 AAAATATATT
1 AAAATATATT
3181327 AAAATATA-T
1 AAAATATATT
*
3181336 AAATATAAATT
1 AAA-ATATATT
3181347 -AAATATA-T
1 AAAATATATT
*
3181355 AAAATTTATT
1 AAAATATATT
*
3181365 GAAATATAT
1 AAAATATAT
3181374 AATATTGAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
8 1 0.03
9 14 0.37
10 22 0.58
11 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (10 bp):
AAAATATATT
Found at i:3181352 original size:19 final size:19
Alignment explanation
Indices: 3181317--3181375 Score: 75
Period size: 19 Copynumber: 3.1 Consensus size: 19
3181307 ATGTACGATA
3181317 AAAATATATTAAAATATAT
1 AAAATATATTAAAATATAT
*
3181336 AAATATAAATT-AAATATAT
1 AAA-ATATATTAAAATATAT
* *
3181355 AAAATTTATTGAAATATAT
1 AAAATATATTAAAATATAT
3181374 AA
1 AA
3181376 TATTGAATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
18 5 0.14
19 24 0.69
20 6 0.17
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (19 bp):
AAAATATATTAAAATATAT
Found at i:3181422 original size:43 final size:43
Alignment explanation
Indices: 3181329--3181444 Score: 121
Period size: 43 Copynumber: 2.7 Consensus size: 43
3181319 AATATATTAA
* *
3181329 AATATATAAATATAAATTA-AATATATAAAATTTATTGAAATATAT
1 AATAT-TAAATAT-AATTATAATATAT-AATTTTATAGAAATATAT
* *
3181374 AATATTGAATAATAA-TAT-ATATCATAATTTTATAGATATATAT
1 AATATTAAAT-ATAATTATAATAT-ATAATTTTATAGAAATATAT
*
3181417 TATATTAAATATAATTATAATATATAAT
1 AATATTAAATATAATTATAATATATAAT
3181445 AATTAATTAA
Statistics
Matches: 60, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
42 4 0.07
43 37 0.62
44 12 0.20
45 7 0.12
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (43 bp):
AATATTAAATATAATTATAATATATAATTTTATAGAAATATAT
Found at i:3181442 original size:7 final size:7
Alignment explanation
Indices: 3181367--3181475 Score: 56
Period size: 7 Copynumber: 16.0 Consensus size: 7
3181357 AATTTATTGA
3181367 AATATAT
1 AATATAT
3181374 AATAT-T
1 AATATAT
3181380 GAATA-AT
1 -AATATAT
3181387 AATATAT
1 AATATAT
3181394 -ATCATA-
1 AAT-ATAT
* *
3181400 ATTTTAT
1 AATATAT
3181407 AGATATAT
1 A-ATATAT
*
3181415 ATTATATT
1 AATATA-T
3181423 AA-ATAT
1 AATATAT
3181429 AAT-TAT
1 AATATAT
3181435 AATATAT
1 AATATAT
3181442 AATA-ATT
1 AATATA-T
3181449 AAT-TAAT
1 AATAT-AT
*
3181456 AAGAT-T
1 AATATAT
3181462 AATATAT
1 AATATAT
*
3181469 TATATAT
1 AATATAT
3181476 GGTGTGATGT
Statistics
Matches: 78, Mismatches: 9, Indels: 30
0.67 0.08 0.26
Matches are distributed among these distances:
6 24 0.31
7 45 0.58
8 9 0.12
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (7 bp):
AATATAT
Found at i:3181443 original size:13 final size:14
Alignment explanation
Indices: 3181382--3181444 Score: 56
Period size: 15 Copynumber: 4.4 Consensus size: 14
3181372 ATAATATTGA
*
3181382 ATAATAATATATAT
1 ATAATTATATATAT
* *
3181396 CATAATTTTATAGAT
1 -ATAATTATATATAT
*
3181411 ATATATTATATTAAAT
1 ATA-ATTATA-TATAT
3181427 ATAATTATA-ATAT
1 ATAATTATATATAT
3181440 ATAAT
1 ATAAT
3181445 AATTAATTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
13 8 0.20
14 3 0.08
15 22 0.55
16 7 0.17
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (14 bp):
ATAATTATATATAT
Found at i:3181464 original size:20 final size:21
Alignment explanation
Indices: 3181428--3181470 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
3181418 ATATTAAATA
*
3181428 TAATTATAATATATAATA-AT
1 TAATTATAAGATATAATATAT
3181448 TAATTAATAAGAT-TAATATAT
1 TAATT-ATAAGATATAATATAT
3181469 TA
1 TA
3181471 TATATGGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
TAATTATAAGATATAATATAT
Found at i:3182166 original size:29 final size:31
Alignment explanation
Indices: 3182134--3182216 Score: 84
Period size: 29 Copynumber: 2.7 Consensus size: 31
3182124 ATTATTCTAT
* *
3182134 TATTTAAGTAATTATTTATATT-TTTATT-A
1 TATTTAAATAATTATTTATATTATTGATTAA
* *
3182163 TATTCAAATAAATATTTAT-TTATTGATTAA
1 TATTTAAATAATTATTTATATTATTGATTAA
3182193 TATTTGAAAT-ATTAATTTATATTA
1 TATTT-AAATAATT-ATTTATATTA
3182217 AAAACTTATT
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
28 2 0.05
29 21 0.49
30 7 0.16
31 10 0.23
32 3 0.07
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (31 bp):
TATTTAAATAATTATTTATATTATTGATTAA
Found at i:3182243 original size:23 final size:23
Alignment explanation
Indices: 3182213--3182266 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
3182203 ATTAATTTAT
*
3182213 ATTAAAAACTTATTTAAATATAA
1 ATTAAAAAATTATTTAAATATAA
*
3182236 ATTAAAAAATTATTTTAATATAA
1 ATTAAAAAATTATTTAAATATAA
*
3182259 CTTAAAAA
1 ATTAAAAA
3182267 TAAAAAACAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (23 bp):
ATTAAAAAATTATTTAAATATAA
Found at i:3182252 original size:24 final size:22
Alignment explanation
Indices: 3182204--3182266 Score: 72
Period size: 23 Copynumber: 2.8 Consensus size: 22
3182194 ATTTGAAATA
* * *
3182204 TTAATTTATATTAAAAACTTAT
1 TTAATATAAATTAAAAAATTAT
3182226 TTAAATATAAATTAAAAAATTATT
1 TT-AATATAAATTAAAAAATTA-T
*
3182250 TTAATATAACTTAAAAA
1 TTAATATAAATTAAAAA
3182267 TAAAAAACAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
22 2 0.06
23 30 0.86
24 3 0.09
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (22 bp):
TTAATATAAATTAAAAAATTAT
Found at i:3185801 original size:30 final size:28
Alignment explanation
Indices: 3185767--3185856 Score: 83
Period size: 30 Copynumber: 3.0 Consensus size: 28
3185757 TTTGGATTTT
*
3185767 TATTTTTTATATCATAATATTATATTATTA
1 TATTTTTTAAAT-ATAATATT-TATTATTA
* *
3185797 TATTTTTTAAATAAAAAAATTTTATT-TTA
1 TATTTTTTAAAT-ATAATA-TTTATTATTA
*
3185826 TATTTTTGTACATATAATATTTAATTATTA
1 TATTTTT-TAAATATAATATTT-ATTATTA
3185856 T
1 T
3185857 GTTATTATAC
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
28 3 0.06
29 17 0.35
30 27 0.55
31 2 0.04
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.58
Consensus pattern (28 bp):
TATTTTTTAAATATAATATTTATTATTA
Found at i:3186728 original size:18 final size:18
Alignment explanation
Indices: 3186701--3186737 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3186691 ATCTTTAATT
*
3186701 ATAAAATTTTATTTTTTA
1 ATAAAATTTTATTCTTTA
*
3186719 ATAAATTTTTATTCTTTA
1 ATAAAATTTTATTCTTTA
3186737 A
1 A
3186738 ATATTAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (18 bp):
ATAAAATTTTATTCTTTA
Found at i:3187069 original size:17 final size:17
Alignment explanation
Indices: 3187049--3187081 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3187039 AATAAAAATA
3187049 TATATCAAATA-TAATTT
1 TATAT-AAATACTAATTT
3187066 TATATAAATACTAATT
1 TATATAAATACTAATT
3187082 AAATAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (17 bp):
TATATAAATACTAATTT
Found at i:3187074 original size:38 final size:40
Alignment explanation
Indices: 3187000--3187074 Score: 93
Period size: 40 Copynumber: 1.9 Consensus size: 40
3186990 AGCAATAAAT
* * *
3187000 ATAAAAATATATATAATTAATAAATTATTTTTTAAATTTA
1 ATAAAAATATATATAAATAATAAATTATTATATAAATTTA
3187040 ATAAAAATATATATCAAAT-AT-AATT-TTATATAAAT
1 ATAAAAATATATAT-AAATAATAAATTATTATATAAAT
3187075 ACTAATTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
38 8 0.26
39 4 0.13
40 16 0.52
41 3 0.10
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (40 bp):
ATAAAAATATATATAAATAATAAATTATTATATAAATTTA
Found at i:3188833 original size:22 final size:21
Alignment explanation
Indices: 3188795--3188891 Score: 72
Period size: 22 Copynumber: 4.4 Consensus size: 21
3188785 ATTTAAACTT
3188795 AAATTTAAAT-AATAATATAA
1 AAATTTAAATAAATAATATAA
3188815 AAATTTATAATAAATAATA-AA
1 AAATTTA-AATAAATAATATAA
* *
3188836 TAAATTTAAATTTAATATTCATATA
1 -AAATTTAAA-TAAATAAT-ATA-A
* *
3188861 AATTTTAATAATAAAAAATATAA
1 AAATTT-A-AATAAATAATATAA
*
3188884 ATATTTAA
1 AAATTTAA
3188892 TTTACTTTCA
Statistics
Matches: 60, Mismatches: 8, Indels: 17
0.71 0.09 0.20
Matches are distributed among these distances:
20 7 0.12
21 8 0.13
22 21 0.35
23 6 0.10
24 9 0.15
25 7 0.12
26 2 0.03
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (21 bp):
AAATTTAAATAAATAATATAA
Found at i:3188872 original size:47 final size:48
Alignment explanation
Indices: 3188788--3188880 Score: 118
Period size: 47 Copynumber: 2.0 Consensus size: 48
3188778 TTATTTAATT
*
3188788 TAAACTTAAATTTAAATAATAATATAAAAATTTATAATAAATAATAAA
1 TAAACTTAAATTTAAATAATAATATAAAAATTTATAATAAAAAATAAA
* * * *
3188836 TAAATTTAAATTT-AATATTCATAT-AAATTTTAATAATAAAAAATA
1 TAAACTTAAATTTAAATAATAATATAAAAATTT-ATAATAAAAAATA
3188881 TAAATATTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
46 6 0.15
47 21 0.54
48 12 0.31
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (48 bp):
TAAACTTAAATTTAAATAATAATATAAAAATTTATAATAAAAAATAAA
Found at i:3193562 original size:2 final size:2
Alignment explanation
Indices: 3193555--3193586 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3193545 CTACAATTAC
*
3193555 AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3193587 TGCATCAACC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3194903 original size:90 final size:90
Alignment explanation
Indices: 3194722--3194894 Score: 271
Period size: 90 Copynumber: 1.9 Consensus size: 90
3194712 TATTAATGAA
* * *
3194722 ATTAAATGATTGTCACGATCTACTGAAACATATTTAAAATTTAAGATAATATTTTAATATTGTTA
1 ATTAAATGATTATCACAATCTACTAAAACATATTTAAAATTTAAGATAATATTTTAATATTGTTA
3194787 TATGAATTTTAAAAAGTTTTTAATC
66 TATGAATTTTAAAAAGTTTTTAATC
* *
3194812 ATTAAATGATTATTACAATCTATTAAAACATATTTAAAATTTAAGATAATATTTTTAATATT-TT
1 ATTAAATGATTATCACAATCTACTAAAACATATTTAAAATTTAAGATAATA-TTTTAATATTGTT
3194876 -TATGAATTTTAAAAA-TTTT
65 ATATGAATTTTAAAAAGTTTT
3194895 ATTGATCATG
Statistics
Matches: 77, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
88 4 0.05
89 15 0.19
90 48 0.62
91 10 0.13
ACGTcount: A:0.43, C:0.05, G:0.06, T:0.46
Consensus pattern (90 bp):
ATTAAATGATTATCACAATCTACTAAAACATATTTAAAATTTAAGATAATATTTTAATATTGTTA
TATGAATTTTAAAAAGTTTTTAATC
Found at i:3198069 original size:29 final size:29
Alignment explanation
Indices: 3198027--3198086 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
3198017 AGTTTGGAGT
*
3198027 TTGGATTAAATTGATGGCTCATTTAGCAA
1 TTGGATTAAATTGATGGCTCATTTAACAA
3198056 TTGGATTAAATTGATGGCTCATTTAACAA
1 TTGGATTAAATTGATGGCTCATTTAACAA
3198085 TT
1 TT
3198087 TAAAAAATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.40
Consensus pattern (29 bp):
TTGGATTAAATTGATGGCTCATTTAACAA
Found at i:3198117 original size:19 final size:19
Alignment explanation
Indices: 3198093--3198138 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
3198083 AATTTAAAAA
3198093 ATATTAAAATATTAAT-TTT
1 ATATTAAAAT-TTAATATTT
*
3198112 ATATTAATATTTAATATTT
1 ATATTAAAATTTAATATTT
3198131 ATAATTAA
1 AT-ATTAA
3198139 TTTAATTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 5 0.21
19 14 0.58
20 5 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
ATATTAAAATTTAATATTT
Found at i:3198128 original size:13 final size:13
Alignment explanation
Indices: 3198100--3198144 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 13
3198090 AAAATATTAA
3198100 AATATTAAT-TTT
1 AATATTAATATTT
3198112 -ATATTAATATTT
1 AATATTAATATTT
* *
3198124 AATATTTATAATT
1 AATATTAATATTT
3198137 AAT-TTAAT
1 AATATTAAT
3198145 TAAAAATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
11 8 0.29
12 7 0.25
13 13 0.46
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
AATATTAATATTT
Found at i:3200465 original size:16 final size:16
Alignment explanation
Indices: 3200446--3200479 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3200436 ATAATTTTTT
* *
3200446 ATTTAAATTAAATTAA
1 ATTTAAAATAAATCAA
3200462 ATTTAAAATAAATCAA
1 ATTTAAAATAAATCAA
3200478 AT
1 AT
3200480 AAATAATTCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (16 bp):
ATTTAAAATAAATCAA
Found at i:3203372 original size:11 final size:11
Alignment explanation
Indices: 3203358--3203396 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
3203348 TGCATTTTAT
3203358 TTATTAAAATA
1 TTATTAAAATA
*
3203369 TTATTAAATTA
1 TTATTAAAATA
3203380 -T-TTAAAATA
1 TTATTAAAATA
3203389 TTATTAAA
1 TTATTAAA
3203397 TTTAATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
9 7 0.29
10 2 0.08
11 15 0.62
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
TTATTAAAATA
Found at i:3203415 original size:23 final size:20
Alignment explanation
Indices: 3203361--3203398 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
3203351 ATTTTATTTA
3203361 TTAAAATATTATTAAATTAT
1 TTAAAATATTATTAAATTAT
3203381 TTAAAATATTATTAAATT
1 TTAAAATATTATTAAATT
3203399 TAATTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTAAAATATTATTAAATTAT
Found at i:3204798 original size:20 final size:20
Alignment explanation
Indices: 3204761--3204798 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3204751 TACTCTTATC
*
3204761 TTTTAAAATTTTTGCAAACT
1 TTTTAAAATTTCTGCAAACT
3204781 TTTTAAGAATTTCT-CAAA
1 TTTTAA-AATTTCTGCAAA
3204799 TATAGATGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.37, C:0.11, G:0.05, T:0.47
Consensus pattern (20 bp):
TTTTAAAATTTCTGCAAACT
Found at i:3209134 original size:24 final size:24
Alignment explanation
Indices: 3209107--3209152 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
3209097 TAAGTCACTG
* *
3209107 TATTATATTATTTTTTTAATTAAA
1 TATTATATGAATTTTTTAATTAAA
* *
3209131 TATTTTATGAATTTTTTCATTA
1 TATTATATGAATTTTTTAATTA
3209153 TAAAAAAGTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (24 bp):
TATTATATGAATTTTTTAATTAAA
Found at i:3210079 original size:2 final size:2
Alignment explanation
Indices: 3210072--3210099 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3210062 TCCCCAAGGA
3210072 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
3210100 TTCAAAAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3216963 original size:17 final size:17
Alignment explanation
Indices: 3216909--3216996 Score: 83
Period size: 17 Copynumber: 5.1 Consensus size: 17
3216899 TTTAATTTGT
3216909 ATATATAATA-AATATAA
1 ATATATAATATAATAT-A
*
3216926 ATAAATAAT-TAAT-TA
1 ATATATAATATAATATA
*
3216941 AAATATAATATAATATA
1 ATATATAATATAATATA
* *
3216958 ATATATAATATATTAAA
1 ATATATAATATAATATA
3216975 ATTTATATAATATGAATATA
1 A--TATATAATAT-AATATA
3216995 AT
1 AT
3216997 TTTTTTTAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
15 8 0.14
16 5 0.09
17 28 0.49
18 1 0.02
19 10 0.18
20 5 0.09
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (17 bp):
ATATATAATATAATATA
Found at i:3216966 original size:32 final size:33
Alignment explanation
Indices: 3216911--3216994 Score: 104
Period size: 32 Copynumber: 2.6 Consensus size: 33
3216901 TAATTTGTAT
*
3216911 ATATAATA-AATATAAATAAATAAT-TAATTAAA
1 ATATAATATAATATAAATATATAATAT-ATTAAA
3216943 ATATAATATAATAT-AATATATAATATATTAAA
1 ATATAATATAATATAAATATATAATATATTAAA
* *
3216975 AT-TTATATAATATGAATATA
1 ATATAATATAATATAAATATA
3216995 ATTTTTTTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
31 10 0.21
32 31 0.66
33 6 0.13
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (33 bp):
ATATAATATAATATAAATATATAATATATTAAA
Found at i:3218095 original size:22 final size:22
Alignment explanation
Indices: 3218069--3218110 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
3218059 TATTTTTATT
3218069 TAAAT-TTAATTATAAAAATATA
1 TAAATATTAA-TATAAAAATATA
3218091 TAAATATTAATATAAAAATA
1 TAAATATTAATATAAAAATA
3218111 AAATTTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATA
Found at i:3218122 original size:20 final size:22
Alignment explanation
Indices: 3218069--3218123 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
3218059 TATTTTTATT
3218069 TAAA-TTTAATTATAAAAATATA
1 TAAATTTTAA-TATAAAAATATA
*
3218091 TAAATATTAATATAAAAATA-A
1 TAAATTTTAATATAAAAATATA
*
3218112 -AATTTTTAATAT
1 TAAATTTTAATAT
3218124 TTTAATATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 10 0.34
21 1 0.03
22 14 0.48
23 4 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TAAATTTTAATATAAAAATATA
Found at i:3218143 original size:21 final size:20
Alignment explanation
Indices: 3218118--3218160 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 20
3218108 ATAAAATTTT
3218118 TAAT-ATTTTAATATATTTAAA
1 TAATAATTTTAAT-TA-TTAAA
3218139 TAATAAATTTTAATTATTAAA
1 TAAT-AATTTTAATTATTAAA
3218160 T
1 T
3218161 CAAACGAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 10 0.50
22 2 0.10
23 8 0.40
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TAATAATTTTAATTATTAAA
Found at i:3221661 original size:19 final size:19
Alignment explanation
Indices: 3221613--3221666 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
3221603 AAGCTAGGCA
3221613 GGTTTAGGGTTCATATCCT
1 GGTTTAGGGTTCATATCCT
** *
3221632 -AATTGGAGGTTCATATCCT
1 GGTTTAG-GGTTCATATCCT
3221651 GGTTTAGGGTTCATAT
1 GGTTTAGGGTTCATAT
3221667 TATAGGTTTC
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
18 3 0.11
19 21 0.78
20 3 0.11
ACGTcount: A:0.20, C:0.13, G:0.26, T:0.41
Consensus pattern (19 bp):
GGTTTAGGGTTCATATCCT
Found at i:3222078 original size:26 final size:27
Alignment explanation
Indices: 3222048--3222106 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 27
3222038 CTAAATCGAG
3222048 TTAAATTAAATTTAA-TATTTT-AAATT
1 TTAAATTAAATTTAAGT-TTTTAAAATT
**
3222074 TTAAATTTTATTTAAGTTTTTAAAATT
1 TTAAATTAAATTTAAGTTTTTAAAATT
*
3222101 ATAAAT
1 TTAAAT
3222107 AGTAATTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 17 0.61
27 11 0.39
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (27 bp):
TTAAATTAAATTTAAGTTTTTAAAATT
Found at i:3223002 original size:30 final size:30
Alignment explanation
Indices: 3222955--3223033 Score: 103
Period size: 29 Copynumber: 2.7 Consensus size: 30
3222945 TTAAACTAAC
3222955 ATAAAAATAATAATTTTATTAA-TATTTTAA
1 ATAAAAA-AATAATTTTATTAATTATTTTAA
*
3222985 ATAATAAAATAAATTTTA--AATTATTTTAA
1 ATAAAAAAAT-AATTTTATTAATTATTTTAA
3223014 ATAAAAAAATAATTTT-TTAA
1 ATAAAAAAATAATTTTATTAA
3223034 ACCGAGTTTC
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
28 8 0.19
29 22 0.51
30 13 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (30 bp):
ATAAAAAAATAATTTTATTAATTATTTTAA
Found at i:3226483 original size:23 final size:23
Alignment explanation
Indices: 3226457--3226515 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
3226447 TATTAATTTA
* *
3226457 AATTATTTTAATATTATTTTTTT
1 AATTATTTTAATATTATTTATAT
*
3226480 AATTATTAATAATA-TATTTATAT
1 AATTATT-TTAATATTATTTATAT
3226503 AA--ATTTTAATATT
1 AATTATTTTAATATT
3226516 TAATAACAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
20 5 0.17
21 4 0.13
23 16 0.53
24 5 0.17
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
AATTATTTTAATATTATTTATAT
Found at i:3226511 original size:30 final size:30
Alignment explanation
Indices: 3226476--3226539 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 30
3226466 AATATTATTT
* *
3226476 TTTTAAT-TATTAATAA-TATATTTATATAAA
1 TTTTAATAT-TTAATAACAATA-TTAAATAAA
3226506 TTTTAATATTTAATAACAATATTAAATAAA
1 TTTTAATATTTAATAACAATATTAAATAAA
3226536 TTTT
1 TTTT
3226540 TTATATTCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 26 0.87
31 4 0.13
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (30 bp):
TTTTAATATTTAATAACAATATTAAATAAA
Found at i:3226558 original size:30 final size:30
Alignment explanation
Indices: 3226476--3226559 Score: 77
Period size: 30 Copynumber: 2.8 Consensus size: 30
3226466 AATATTATTT
*
3226476 TTTTAATTATT-AAT-AATATATTTATATAAA
1 TTTTAA-TATTCAATAAATATA-TTAAATAAA
*
3226506 TTTTAATATTTAATAACA-ATATTAAATAAA
1 TTTTAATATTCAATAA-ATATATTAAATAAA
*
3226536 TTTTTTATATTCAA-AAATATATTA
1 -TTTTAATATTCAATAAATATATTA
3226560 TATTTATTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
29 5 0.11
30 25 0.54
31 15 0.33
32 1 0.02
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (30 bp):
TTTTAATATTCAATAAATATATTAAATAAA
Found at i:3231329 original size:6 final size:5
Alignment explanation
Indices: 3231299--3231418 Score: 55
Period size: 5 Copynumber: 22.8 Consensus size: 5
3231289 AATTGGGTGC
* * *
3231299 AATAT AAAAA AATAAT AATAT AATAT GAATAT -ATAT AATTT AAATTAT
1 AATAT AATAT AAT-AT AATAT AATAT -AATAT AATAT AATAT -AA-TAT
* * * * * *
3231347 AACTAT ATTAA AAT-T TATAT AAATAT AAAAT ATTTT AAATAT AATTAT
1 AA-TAT AATAT AATAT AATAT -AATAT AATAT AATAT -AATAT AA-TAT
* *
3231395 AATAT AATAA AATAT AATAA AATA
1 AATAT AATAT AATAT AATAT AATA
3231419 ACACCATAAG
Statistics
Matches: 84, Mismatches: 22, Indels: 18
0.68 0.18 0.15
Matches are distributed among these distances:
4 6 0.07
5 47 0.56
6 29 0.35
7 2 0.02
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (5 bp):
AATAT
Found at i:3233880 original size:14 final size:14
Alignment explanation
Indices: 3233854--3233886 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
3233844 AATATGAAAA
3233854 AAAATTATAAATTTT
1 AAAATTATAAA-TTT
3233869 AAAATT-TAAATTT
1 AAAATTATAAATTT
3233882 AAAAT
1 AAAAT
3233887 CAATTAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.44
14 4 0.22
15 6 0.33
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
AAAATTATAAATTT
Found at i:3236072 original size:25 final size:27
Alignment explanation
Indices: 3236044--3236097 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
3236034 TTTTTATTCG
3236044 TATTTAAT-ATTTTTTAAA-ATATAAA
1 TATTTAATAATTTTTTAAATATATAAA
3236069 TATTTAATAAAATTTTTTAAATATATAAA
1 TATTTAAT--AATTTTTTAAATATATAAA
3236098 AAATTAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 8 0.32
28 10 0.40
29 7 0.28
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (27 bp):
TATTTAATAATTTTTTAAATATATAAA
Found at i:3236104 original size:29 final size:28
Alignment explanation
Indices: 3236052--3236109 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
3236042 CGTATTTAAT
* * *
3236052 ATTTTTTAAAATATAAATATTTAATAAA
1 ATTTTTTAAAATATAAAAAATTAAAAAA
3236080 ATTTTTTAAATATATAAAAAATTAAAAAA
1 ATTTTTTAAA-ATATAAAAAATTAAAAAA
3236109 A
1 A
3236110 ATAAAAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 10 0.38
29 16 0.62
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (28 bp):
ATTTTTTAAAATATAAAAAATTAAAAAA
Found at i:3237862 original size:12 final size:12
Alignment explanation
Indices: 3237845--3237878 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
3237835 CGGCAGATAA
3237845 GAAAAACAGAAG
1 GAAAAACAGAAG
3237857 GAAAAA-AGAAG
1 GAAAAACAGAAG
*
3237868 AAAAAACAGAA
1 GAAAAACAGAA
3237879 AAGAAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.74, C:0.06, G:0.21, T:0.00
Consensus pattern (12 bp):
GAAAAACAGAAG
Found at i:3238070 original size:3 final size:3
Alignment explanation
Indices: 3238064--3238097 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
3238054 CAACAACAAC
3238064 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
3238098 TATTCCTGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3240262 original size:29 final size:30
Alignment explanation
Indices: 3240204--3240264 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
3240194 ATTTAAGTTA
* *
3240204 ATATTTATTTGTTTAAAATGAAATATATTT
1 ATATTTATTTATTTAAAATGAAATAAATTT
*
3240234 ATATTTATTTATTT-AAATTAAATAAATTT
1 ATATTTATTTATTTAAAATGAAATAAATTT
3240263 AT
1 AT
3240265 TTAAAACATC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 15 0.54
30 13 0.46
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (30 bp):
ATATTTATTTATTTAAAATGAAATAAATTT
Found at i:3240305 original size:12 final size:12
Alignment explanation
Indices: 3240288--3240344 Score: 57
Period size: 12 Copynumber: 5.0 Consensus size: 12
3240278 AATATACCAT
3240288 TAAATATATTTA
1 TAAATATATTTA
*
3240300 TGAATA-A-TTA
1 TAAATATATTTA
*
3240310 AAAATATATTTA
1 TAAATATATTTA
**
3240322 TAAATA-ATAAA
1 TAAATATATTTA
3240333 TAAATATATTTA
1 TAAATATATTTA
3240345 AATAAATGAA
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
10 7 0.21
11 11 0.32
12 16 0.47
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (12 bp):
TAAATATATTTA
Found at i:3240311 original size:20 final size:20
Alignment explanation
Indices: 3240286--3240381 Score: 70
Period size: 22 Copynumber: 4.5 Consensus size: 20
3240276 TGAATATACC
*
3240286 ATTAAATATATTTATGAATA
1 ATTAAATATATTTATAAATA
3240306 ATTAAAAATATATTTATAAATA
1 ATT--AAATATATTTATAAATA
3240328 ATAAATAAATATATTTAAATAAATGA
1 AT---TAAATATATTT--ATAAAT-A
* *
3240354 A-TAAATATATCTATTAAT-
1 ATTAAATATATTTATAAATA
*
3240372 TTTAAATATA
1 ATTAAATATA
3240382 AAATAATAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 19
0.73 0.05 0.22
Matches are distributed among these distances:
19 8 0.13
20 8 0.13
22 28 0.44
23 10 0.16
25 7 0.11
26 2 0.03
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.42
Consensus pattern (20 bp):
ATTAAATATATTTATAAATA
Found at i:3240317 original size:22 final size:23
Alignment explanation
Indices: 3240288--3240363 Score: 95
Period size: 22 Copynumber: 3.4 Consensus size: 23
3240278 AATATACCAT
* *
3240288 TAAATATATTTATGAATAATTAA
1 TAAATATATTTATAAATAATAAA
3240311 -AAATATATTTATAAATAATAAA
1 TAAATATATTTATAAATAATAAA
*
3240333 TAAATATA-TT-TAAATAAATGAA
1 TAAATATATTTATAAAT-AATAAA
3240355 TAAATATAT
1 TAAATATAT
3240364 CTATTAATTT
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
21 5 0.11
22 35 0.74
23 7 0.15
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (23 bp):
TAAATATATTTATAAATAATAAA
Found at i:3240435 original size:37 final size:38
Alignment explanation
Indices: 3240337--3240435 Score: 93
Period size: 37 Copynumber: 2.7 Consensus size: 38
3240327 AATAAATAAA
* *
3240337 TATATT-TAAATAAAT-GAATAA-ATATATCTATTAAT
1 TATATTATAAATAAATAAAATAATAAATATCTATTAAT
* * *
3240372 TTTAAATATAAA-ATAATAAAA-CATAAATAT-TATTAAT
1 TAT-ATTATAAATA-AATAAAATAATAAATATCTATTAAT
3240409 TATATTATAAATAAATAAAATAATAAA
1 TATATTATAAATAAATAAAATAATAAA
3240436 AATAATTTTA
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
35 2 0.04
36 17 0.35
37 23 0.47
38 7 0.14
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.38
Consensus pattern (38 bp):
TATATTATAAATAAATAAAATAATAAATATCTATTAAT
Found at i:3240475 original size:10 final size:10
Alignment explanation
Indices: 3240460--3240498 Score: 51
Period size: 10 Copynumber: 3.6 Consensus size: 10
3240450 CGAATATAAT
3240460 TAATTTTAAA
1 TAATTTTAAA
3240470 TAATTTATTAAA
1 TAA-TT-TTAAA
3240482 TAAATTTTAAA
1 T-AATTTTAAA
3240493 TAATTT
1 TAATTT
3240499 ATTTATTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 8 0.31
11 8 0.31
12 8 0.31
13 2 0.08
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (10 bp):
TAATTTTAAA
Found at i:3240482 original size:12 final size:12
Alignment explanation
Indices: 3240465--3240501 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
3240455 ATAATTAATT
3240465 TTAAATAATTTA
1 TTAAATAATTTA
*
3240477 TTAAATAAATT-
1 TTAAATAATTTA
3240488 TTAAATAATTTA
1 TTAAATAATTTA
3240500 TT
1 TT
3240502 TATTTATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 10 0.45
12 12 0.55
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
TTAAATAATTTA
Found at i:3240493 original size:11 final size:11
Alignment explanation
Indices: 3240461--3240495 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
3240451 GAATATAATT
3240461 AATTTTAAATA
1 AATTTTAAATA
*
3240472 ATTTATTAAATA
1 AATT-TTAAATA
3240484 AATTTTAAATA
1 AATTTTAAATA
3240495 A
1 A
3240496 TTTATTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
AATTTTAAATA
Found at i:3240514 original size:30 final size:30
Alignment explanation
Indices: 3240472--3240533 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
3240462 ATTTTAAATA
3240472 ATTTATTAAATAAATTTTA-AATAATTTATTT
1 ATTTATTAAATAAATTTTATAAT--TTTATTT
3240503 ATTTA-TAAATAAATTTTATAATTTTATTT
1 ATTTATTAAATAAATTTTATAATTTTATTT
3240532 AT
1 AT
3240534 ATTTATTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
29 9 0.30
30 13 0.43
31 8 0.27
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (30 bp):
ATTTATTAAATAAATTTTATAATTTTATTT
Found at i:3240826 original size:6 final size:6
Alignment explanation
Indices: 3240815--3240881 Score: 50
Period size: 6 Copynumber: 11.2 Consensus size: 6
3240805 ATTATTAATT
* *
3240815 TATTTA TATTTA -ATTAA TTTTTAA TATTTA TA-TT- TATTTA TATTTA
1 TATTTA TATTTA TATTTA TATTT-A TATTTA TATTTA TATTTA TATTTA
* *
3240861 TAAATTA TAATTTA AATTTA T
1 T-ATTTA T-ATTTA TATTTA T
3240882 TTAAATTTAT
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
4 2 0.04
5 8 0.17
6 23 0.48
7 15 0.31
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (6 bp):
TATTTA
Found at i:3240847 original size:24 final size:25
Alignment explanation
Indices: 3240815--3240884 Score: 76
Period size: 24 Copynumber: 2.9 Consensus size: 25
3240805 ATTATTAATT
*
3240815 TATTTATATTTAATTA-ATTTTTAA
1 TATTTATATTTAATTATATTTATAA
*
3240839 TATTTATATTTATTTATATTTATAA
1 TATTTATATTTAATTATATTTATAA
3240864 -A-TTATAATTTAAATT-TATTTA
1 TATTTAT-ATTT-AATTATATTTA
3240885 AATTTATTCA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
23 4 0.10
24 26 0.65
25 10 0.25
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (25 bp):
TATTTATATTTAATTATATTTATAA
Found at i:3240854 original size:10 final size:10
Alignment explanation
Indices: 3240812--3240914 Score: 62
Period size: 10 Copynumber: 10.9 Consensus size: 10
3240802 TATATTATTA
3240812 ATTTATTTAT
1 ATTTATTTAT
*
3240822 ATTTAATTA-
1 ATTTATTTAT
3240831 A-TT-TTTA-
1 ATTTATTTAT
3240838 A--TATTTAT
1 ATTTATTTAT
3240846 ATTTATTTAT
1 ATTTATTTAT
*
3240856 ATTTA--TAA
1 ATTTATTTAT
*
3240864 ATTATAATTTAA
1 ATT-T-ATTTAT
*
3240876 ATTTATTTAA
1 ATTTATTTAT
*
3240886 ATTTATTCAT
1 ATTTATTTAT
*
3240896 ATTATATTTTT
1 ATT-TATTTAT
3240907 ATTT-TTTA
1 ATTTATTTA
3240915 AAATATATAT
Statistics
Matches: 76, Mismatches: 8, Indels: 19
0.74 0.08 0.18
Matches are distributed among these distances:
6 1 0.01
7 8 0.11
8 8 0.11
9 5 0.07
10 39 0.51
11 9 0.12
12 6 0.08
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (10 bp):
ATTTATTTAT
Found at i:3240874 original size:30 final size:32
Alignment explanation
Indices: 3240811--3240891 Score: 94
Period size: 30 Copynumber: 2.5 Consensus size: 32
3240801 ATATATTATT
* *
3240811 AATTTATTTATATTTAATTAATTTTTAATATTTA
1 AATTTATTTATATTT-A-TAAATTATAATATTTA
*
3240845 TATTTATTTATATTTATAAATTAT-A-ATTTA
1 AATTTATTTATATTTATAAATTATAATATTTA
*
3240875 AATTTATTTAAATTTAT
1 AATTTATTTATATTTAT
3240892 TCATATTATA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
30 20 0.48
31 1 0.02
32 6 0.14
33 1 0.02
34 14 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (32 bp):
AATTTATTTATATTTATAAATTATAATATTTA
Found at i:3240910 original size:21 final size:22
Alignment explanation
Indices: 3240879--3240933 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
3240869 AATTTAAATT
* * *
3240879 TATTTAAATTTATTCATAT-TA
1 TATTTTAATTTATTAAAATATA
* *
3240900 TATTTTTATTTTTTAAAATATA
1 TATTTTAATTTATTAAAATATA
3240922 TATTTTAATTTA
1 TATTTTAATTTA
3240934 ATTTTTTAAA
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
21 14 0.54
22 12 0.46
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTTTAATTTATTAAAATATA
Found at i:3240924 original size:27 final size:26
Alignment explanation
Indices: 3240894--3240959 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 26
3240884 AAATTTATTC
3240894 ATATTATATTTTTATTTTTTAAAATAT
1 ATATTATATTTTTATTTTTTAAAAT-T
* * *
3240921 ATATTTTAATTTAATTTTTTAAAATT
1 ATATTATATTTTTATTTTTTAAAATT
*
3240947 A-AATATATTTTTA
1 ATATTATATTTTTA
3240960 ATAAATTTTT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
25 8 0.25
26 2 0.06
27 22 0.69
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (26 bp):
ATATTATATTTTTATTTTTTAAAATT
Found at i:3240955 original size:30 final size:27
Alignment explanation
Indices: 3240907--3240970 Score: 76
Period size: 30 Copynumber: 2.3 Consensus size: 27
3240897 TTATATTTTT
*
3240907 ATTTTTTAAAATATATA-TTTTAATTTA
1 ATTTTTTAAAATATATATTTTTAA-TAA
3240934 ATTTTTTAAAATTAAATATATTTTTAATAA
1 ATTTTTTAAAA-T--ATATATTTTTAATAA
3240964 ATTTTTT
1 ATTTTTT
3240971 CATTACTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
27 11 0.34
28 1 0.03
30 14 0.44
31 6 0.19
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (27 bp):
ATTTTTTAAAATATATATTTTTAATAA
Found at i:3247404 original size:21 final size:21
Alignment explanation
Indices: 3247377--3247427 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
3247367 TTGAATACGC
3247377 TTATTTTTT--ATTTTAAAAA
1 TTATTTTTTAAATTTTAAAAA
*
3247396 TTATTTTTTAAATTTTAAATA
1 TTATTTTTTAAATTTTAAAAA
3247417 TTATTTTTTAA
1 TTATTTTTTAA
3247428 CGATATAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 9 0.31
21 20 0.69
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TTATTTTTTAAATTTTAAAAA
Found at i:3247813 original size:2 final size:2
Alignment explanation
Indices: 3247806--3247843 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3247796 TATCTTAGAA
3247806 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
3247844 GATAAGTGCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3248492 original size:21 final size:23
Alignment explanation
Indices: 3248468--3248515 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
3248458 AAATTACCCA
3248468 TTTTAC-TAAAAAAAATA-TCAT
1 TTTTACTTAAAAAAAATATTCAT
* *
3248489 TTTTACTTGAAAAAACTATTCAT
1 TTTTACTTAAAAAAAATATTCAT
3248512 TTTT
1 TTTT
3248516 TTAATTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 6 0.26
22 9 0.39
23 8 0.35
ACGTcount: A:0.42, C:0.10, G:0.02, T:0.46
Consensus pattern (23 bp):
TTTTACTTAAAAAAAATATTCAT
Found at i:3250210 original size:24 final size:24
Alignment explanation
Indices: 3250178--3250238 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
3250168 ATGGTAATCT
*
3250178 TTTTACCTGACTGAAGATGCTGAG
1 TTTTCCCTGACTGAAGATGCTGAG
* *
3250202 TTTTCCCTGACCGAAGATGCTGGG
1 TTTTCCCTGACTGAAGATGCTGAG
* *
3250226 GTTTCCCTAACTG
1 TTTTCCCTGACTG
3250239 GAGCTCGAAC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.20, C:0.23, G:0.25, T:0.33
Consensus pattern (24 bp):
TTTTCCCTGACTGAAGATGCTGAG
Found at i:3253204 original size:2 final size:2
Alignment explanation
Indices: 3253197--3253234 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3253187 TACAGGGAAA
3253197 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
3253235 GTTTGACGGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3259871 original size:32 final size:31
Alignment explanation
Indices: 3259830--3259904 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 31
3259820 TAAATAAATT
*
3259830 ATTTCATTAAAATAAAAATTATTTATATTTTTA
1 ATTT-ATTAAAATAAAAATT-TATATATTTTTA
* *
3259863 ATTTATTAATAATATATATTTATATATTTTTA
1 ATTTATTAA-AATAAAAATTTATATATTTTTA
*
3259895 ATGTATTAAA
1 ATTTATTAAA
3259905 TACAACTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
31 1 0.03
32 24 0.65
33 12 0.32
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (31 bp):
ATTTATTAAAATAAAAATTTATATATTTTTA
Found at i:3269975 original size:2 final size:2
Alignment explanation
Indices: 3269968--3269998 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3269958 ATCTCTTTTG
3269968 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3269999 GAAAATGTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3270964 original size:9 final size:9
Alignment explanation
Indices: 3270958--3271004 Score: 58
Period size: 9 Copynumber: 4.8 Consensus size: 9
3270948 TAACTTAATA
3270958 AATTTAAAAT
1 AATTT-AAAT
3270968 AATTTAAAT
1 AATTTAAAT
3270977 AATTTAAATTT
1 AATTTAAA--T
3270988 AATTTTAAAT
1 AA-TTTAAAT
3270998 AATTTAA
1 AATTTAA
3271005 CATTTTGACA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
9 17 0.50
10 8 0.24
11 3 0.09
12 6 0.18
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
AATTTAAAT
Found at i:3270974 original size:19 final size:19
Alignment explanation
Indices: 3270947--3271004 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 19
3270937 AATAAAGTTT
3270947 ATAACTT-AATAAATTTAAA
1 ATAACTTAAAT-AATTTAAA
*
3270966 ATAATTTAAATAATTTAAA
1 ATAACTTAAATAATTTAAA
* *
3270985 TTTAATTTTAAATAATTTAA
1 -ATAA-CTTAAATAATTTAA
3271005 CATTTTGACA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.41
20 6 0.18
21 14 0.41
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (19 bp):
ATAACTTAAATAATTTAAA
Found at i:3270992 original size:30 final size:30
Alignment explanation
Indices: 3270958--3271040 Score: 98
Period size: 30 Copynumber: 2.7 Consensus size: 30
3270948 TAACTTAATA
3270958 AATTTAAAATAATTTAAATAATTT-A-AATTT
1 AATTTAAAATAATTTAAAT--TTTGACAATTT
*
3270988 AATTTTAAATAATTTAACATTTTGACAATTT
1 AATTTAAAATAATTTAA-ATTTTGACAATTT
* *
3271019 AAATTAAAATAACTTAAATTTT
1 AATTTAAAATAATTTAAATTTT
3271041 TTTCAACTTG
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
29 3 0.07
30 22 0.48
31 21 0.46
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (30 bp):
AATTTAAAATAATTTAAATTTTGACAATTT
Found at i:3270996 original size:21 final size:20
Alignment explanation
Indices: 3270958--3271009 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
3270948 TAACTTAATA
*
3270958 AATTTAAA-ATAATTTAAAT
1 AATTTAAATTTAATTTAAAT
3270977 AATTTAAATTTAATTTTAAAT
1 AATTTAAATTTAA-TTTAAAT
3270998 AATTTAACATTT
1 AATTTAA-ATTT
3271010 TGACAATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 8 0.28
20 3 0.10
21 14 0.48
22 4 0.14
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
AATTTAAATTTAATTTAAAT
Found at i:3271957 original size:23 final size:23
Alignment explanation
Indices: 3271931--3272013 Score: 64
Period size: 24 Copynumber: 3.6 Consensus size: 23
3271921 TTAATTTGAA
3271931 AATTTAAAATTATTTTTATAAAT
1 AATTTAAAATTATTTTTATAAAT
* *
3271954 AATTAAAAAAATATTTTTATATTAAT
1 AATT-TAAAATTATTTTTATA--AAT
* *
3271980 AA-TT-ATA-TATTTTTATAATT
1 AATTTAAAATTATTTTTATAAAT
* *
3272000 AAATTAAATTTATT
1 AATTTAAAATTATT
3272014 AATAAATAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
20 4 0.09
21 2 0.04
22 11 0.23
23 10 0.21
24 14 0.30
25 1 0.02
26 5 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AATTTAAAATTATTTTTATAAAT
Found at i:3271968 original size:24 final size:25
Alignment explanation
Indices: 3271936--3271984 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
3271926 TTGAAAATTT
*
3271936 AAAATTATTTTTATA-AATAATTAA
1 AAAAATATTTTTATATAATAATTAA
3271960 AAAAATATTTTTATATTAATAATTA
1 AAAAATATTTTTATA-TAATAATTA
3271985 TATATTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 14 0.64
26 8 0.36
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
AAAAATATTTTTATATAATAATTAA
Found at i:3272009 original size:26 final size:25
Alignment explanation
Indices: 3271941--3272009 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 25
3271931 AATTTAAAAT
* *
3271941 TATTTTTATAAATAATTAAA-AAAA
1 TATTTTTATAATTAATTAAATTAAA
*
3271965 TATTTTTAT-ATTAA-T-AATTATA
1 TATTTTTATAATTAATTAAATTAAA
3271987 TATTTTTATAATTAAATTAAATT
1 TATTTTTATAATT-AATTAAATT
3272010 TATTAATAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
21 2 0.05
22 12 0.32
23 7 0.19
24 11 0.30
25 1 0.03
26 4 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
TATTTTTATAATTAATTAAATTAAA
Found at i:3272243 original size:23 final size:22
Alignment explanation
Indices: 3272217--3272267 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
3272207 AAATATTGTA
3272217 AATATTATATAAAAATATAATAT
1 AATATTATATAAAAATATAA-AT
* * *
3272240 AATATGATATGAATATATAAAT
1 AATATTATATAAAAATATAAAT
3272262 AA-ATTA
1 AATATTA
3272268 AAATTTATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 3 0.12
22 4 0.17
23 17 0.71
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (22 bp):
AATATTATATAAAAATATAAAT
Found at i:3272294 original size:21 final size:22
Alignment explanation
Indices: 3272252--3272294 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
3272242 TATGATATGA
*
3272252 ATATATAAATAAATTAAAATTT
1 ATATATAAATAAATAAAAATTT
3272274 ATATA-AAAT-AATAAAATATTT
1 ATATATAAATAAATAAAA-ATTT
3272295 TAAATGCTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 6 0.32
21 8 0.42
22 5 0.26
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
ATATATAAATAAATAAAAATTT
Found at i:3272338 original size:15 final size:16
Alignment explanation
Indices: 3272315--3272352 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
3272305 TATACATGAT
3272315 AATATTAAATAAATAA
1 AATATTAAATAAATAA
*
3272331 AATA-TAAATACATAA
1 AATATTAAATAAATAA
*
3272346 ATTATTA
1 AATATTA
3272353 GATTTAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (16 bp):
AATATTAAATAAATAA
Found at i:3273469 original size:35 final size:36
Alignment explanation
Indices: 3273400--3273471 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 36
3273390 TTAAGTGATT
* ** *
3273400 GAGAGGTTCTATCTTAGCTTTTGAAAAAGATAGGGA
1 GAGAGATTCTATCTTAGCTCGTGAAAAAAATAGGGA
3273436 GAGAGATTCTATCTTAGCTCGT-AAAAAAATAGGGA
1 GAGAGATTCTATCTTAGCTCGTGAAAAAAATAGGGA
3273471 G
1 G
3273472 GTTTCTATCT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 13 0.41
36 19 0.59
ACGTcount: A:0.36, C:0.10, G:0.26, T:0.28
Consensus pattern (36 bp):
GAGAGATTCTATCTTAGCTCGTGAAAAAAATAGGGA
Found at i:3273483 original size:32 final size:34
Alignment explanation
Indices: 3273400--3273485 Score: 104
Period size: 35 Copynumber: 2.5 Consensus size: 34
3273390 TTAAGTGATT
** *
3273400 GAGAGGTTCTATCTTAGCTTTTGAAAAAGATAGG
1 GAGAGGTTCTATCTTAGCTCGTGAAAAAAATAGG
3273434 GAGAGAGATTCTATCTTAGCTCGT-AAAAAAATAGG
1 GAGAG-G-TTCTATCTTAGCTCGTGAAAAAAATAGG
*
3273469 GAG-GTTTCTATCTTAGC
1 GAGAGGTTCTATCTTAGC
3273486 CTTGAAAGAT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
32 12 0.26
34 6 0.13
35 14 0.30
36 14 0.30
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.31
Consensus pattern (34 bp):
GAGAGGTTCTATCTTAGCTCGTGAAAAAAATAGG
Found at i:3279302 original size:2 final size:2
Alignment explanation
Indices: 3279297--3279324 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3279287 CTGATCACAC
3279297 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
3279325 GAGTGTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3282074 original size:2 final size:2
Alignment explanation
Indices: 3282067--3282107 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3282057 AAAAGGCAAA
3282067 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
3282108 ACATGTATTA
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:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3283638 original size:31 final size:31
Alignment explanation
Indices: 3283601--3283673 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
3283591 AAGTATAATT
*
3283601 TTTTTAGAATAAAAGT-CATTTATCTCTTAAA
1 TTTTTAGAA-AAAAATACATTTATCTCTTAAA
* *
3283632 TTTTTAGAAAAAAATATATTTATCTCTTTAA
1 TTTTTAGAAAAAAATACATTTATCTCTTAAA
*
3283663 TATTTA-AAAAA
1 TTTTTAGAAAAA
3283674 TATTTATTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 10 0.27
31 27 0.73
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (31 bp):
TTTTTAGAAAAAAATACATTTATCTCTTAAA
Found at i:3284828 original size:6 final size:6
Alignment explanation
Indices: 3284817--3284843 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
3284807 AAAATATTTT
3284817 AAATAA AAATAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAATAA AAATAA AAA
3284844 ATTGATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:3286138 original size:17 final size:16
Alignment explanation
Indices: 3286118--3286149 Score: 55
Period size: 16 Copynumber: 1.9 Consensus size: 16
3286108 ATTTAAAATA
3286118 ATTTTATAATAAAAAAC
1 ATTTTA-AATAAAAAAC
3286135 ATTTTAAATAAAAAA
1 ATTTTAAATAAAAAA
3286150 TAAATAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (16 bp):
ATTTTAAATAAAAAAC
Found at i:3286312 original size:21 final size:21
Alignment explanation
Indices: 3286273--3286315 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
3286263 AAATCTTAAA
*
3286273 AAAATAAATAAAATTATTTTC
1 AAAATAAATAAAATGATTTTC
3286294 AAAATCAAATAAAA-GATTTTC
1 AAAAT-AAATAAAATGATTTTC
3286315 A
1 A
3286316 TCCATAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (21 bp):
AAAATAAATAAAATGATTTTC
Found at i:3299014 original size:15 final size:15
Alignment explanation
Indices: 3298994--3299022 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3298984 AAATCTCGAT
3298994 TCATTATTATTATTA
1 TCATTATTATTATTA
3299009 TCATTATTATTATT
1 TCATTATTATTATT
3299023 TCAATATTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (15 bp):
TCATTATTATTATTA
Found at i:3306588 original size:20 final size:21
Alignment explanation
Indices: 3306522--3306590 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
3306512 TCACTTCGTT
3306522 TCTTTTTGTCCAAGTTACTTC
1 TCTTTTTGTCCAAGTTACTTC
*
3306543 TCTTTTTGTCCAAGTTGCTTC
1 TCTTTTTGTCCAAGTTACTTC
* * *
3306564 TCTTTTTGTCTAACTCACTTC
1 TCTTTTTGTCCAAGTTACTTC
3306585 -CTTTTT
1 TCTTTTT
3306591 TCTTTGTGAG
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 6 0.14
21 37 0.86
ACGTcount: A:0.12, C:0.25, G:0.09, T:0.55
Consensus pattern (21 bp):
TCTTTTTGTCCAAGTTACTTC
Found at i:3306943 original size:27 final size:27
Alignment explanation
Indices: 3306905--3306957 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
3306895 TCACTAACTA
3306905 ATACTAATCTAATACTAATAGAATAGT
1 ATACTAATCTAATACTAATAGAATAGT
3306932 ATACTAATCTAATACTAATAGAATAG
1 ATACTAATCTAATACTAATAGAATAG
3306958 AAAAAATAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.49, C:0.11, G:0.08, T:0.32
Consensus pattern (27 bp):
ATACTAATCTAATACTAATAGAATAGT
Found at i:3306944 original size:5 final size:6
Alignment explanation
Indices: 3306901--3306951 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
3306891 GGGATCACTA
* *
3306901 ACTAAT ACTAAT -CTAAT ACTAAT A-GAAT AGT-AT ACTAAT -CTAAT
1 ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT
3306945 ACTAAT A
1 ACTAAT A
3306952 GAATAGAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
5 18 0.47
6 20 0.53
ACGTcount: A:0.49, C:0.14, G:0.04, T:0.33
Consensus pattern (6 bp):
ACTAAT
Found at i:3306967 original size:14 final size:14
Alignment explanation
Indices: 3306948--3306975 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3306938 ATCTAATACT
3306948 AATAGAATAGAAAA
1 AATAGAATAGAAAA
3306962 AATAGAATAGAAAA
1 AATAGAATAGAAAA
3306976 TACTAATATA
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:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (14 bp):
AATAGAATAGAAAA
Found at i:3308853 original size:25 final size:26
Alignment explanation
Indices: 3308804--3308856 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
3308794 ACAATGCGAG
*
3308804 TAATTTATATTTTATATTATTAAATT
1 TAATTTATATTTTATATTATAAAATT
3308830 TAATATTA-ATTTT-TATTATAAAATT
1 TAAT-TTATATTTTATATTATAAAATT
3308855 TA
1 TA
3308857 CAATAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 13 0.52
26 9 0.36
27 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (26 bp):
TAATTTATATTTTATATTATAAAATT
Found at i:3309654 original size:26 final size:27
Alignment explanation
Indices: 3309620--3309671 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
3309610 GAAATATAAA
3309620 TTTGATCATAT-TA-TCTCAATTTTATTG
1 TTTGATCAT-TCTACTC-CAATTTTATTG
3309647 TTTG-TCATTCTACTCCAATTTTATT
1 TTTGATCATTCTACTCCAATTTTATT
3309672 AAATTTAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
25 1 0.04
26 16 0.70
27 6 0.26
ACGTcount: A:0.23, C:0.15, G:0.06, T:0.56
Consensus pattern (27 bp):
TTTGATCATTCTACTCCAATTTTATTG
Found at i:3310607 original size:30 final size:29
Alignment explanation
Indices: 3310544--3310610 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 29
3310534 ATATAATAAT
*
3310544 TTATATATAAATTAATTAAATATCAATTTA
1 TTAT-TATAAATTAATTAAATATCAATTCA
* * *
3310574 TTATTATAAATTGAGTTAAATCTCGATTCA
1 TTATTATAAATT-AATTAAATATCAATTCA
3310604 TTATTAT
1 TTATTAT
3310611 TAATAAATAG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 8 0.25
30 24 0.75
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.48
Consensus pattern (29 bp):
TTATTATAAATTAATTAAATATCAATTCA
Found at i:3313761 original size:24 final size:24
Alignment explanation
Indices: 3313733--3313778 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
3313723 AATAAAAATT
3313733 AGCCACCAATTTTGACAAACAACA
1 AGCCACCAATTTTGACAAACAACA
* * *
3313757 AGCCACCATTTTTTACATACAA
1 AGCCACCAATTTTGACAAACAA
3313779 AAATAACCAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.41, C:0.28, G:0.07, T:0.24
Consensus pattern (24 bp):
AGCCACCAATTTTGACAAACAACA
Found at i:3313804 original size:28 final size:28
Alignment explanation
Indices: 3313773--3313836 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
3313763 CATTTTTTAC
3313773 ATACAAA-AATAACCACCATATTTGACAA
1 ATACAAAGAA-AACCACCATATTTGACAA
* *
3313801 ATACAAAGGAAACCATCATATTTGACAA
1 ATACAAAGAAAACCACCATATTTGACAA
3313829 ATACAAAG
1 ATACAAAG
3313837 GGTGGCATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
28 32 0.97
29 1 0.03
ACGTcount: A:0.53, C:0.19, G:0.08, T:0.20
Consensus pattern (28 bp):
ATACAAAGAAAACCACCATATTTGACAA
Found at i:3313837 original size:28 final size:28
Alignment explanation
Indices: 3313783--3313837 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
3313773 ATACAAAAAT
3313783 AACCACCATATTTGACAAATACAAAGGA
1 AACCACCATATTTGACAAATACAAAGGA
*
3313811 AACCATCATATTTGACAAATACAAAGG
1 AACCACCATATTTGACAAATACAAAGG
3313838 GTGGCATTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.49, C:0.20, G:0.11, T:0.20
Consensus pattern (28 bp):
AACCACCATATTTGACAAATACAAAGGA
Found at i:3315771 original size:21 final size:22
Alignment explanation
Indices: 3315733--3315778 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
3315723 ATCTGTTGAA
* **
3315733 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
3315754 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
3315776 ACT
1 ACT
3315779 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:3321374 original size:6 final size:6
Alignment explanation
Indices: 3321363--3321394 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
3321353 TTCTCAAATG
3321363 CAGACA CAGACA CAGACA CAGACA CAGACA CA
1 CAGACA CAGACA CAGACA CAGACA CAGACA CA
3321395 TAGGGATGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.34, G:0.16, T:0.00
Consensus pattern (6 bp):
CAGACA
Found at i:3322011 original size:14 final size:15
Alignment explanation
Indices: 3321971--3322011 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
3321961 ATTTTTTCCA
3321971 TTTATATTTTTTAAT
1 TTTATATTTTTTAAT
*
3321986 TCTATATTTTTT-AT
1 TTTATATTTTTTAAT
*
3322000 TTTATCTTTTTT
1 TTTATATTTTTT
3322012 TTTGGGTGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTATATTTTTTAAT
Found at i:3322954 original size:19 final size:19
Alignment explanation
Indices: 3322921--3322982 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 19
3322911 TAAATATAAA
3322921 TATATTAATT-T-TTTAAT
1 TATATTAATTATATTTAAT
*
3322938 TATATTAATTATATTTAAA
1 TATATTAATTATATTTAAT
*
3322957 TATATTATATCATA-TTAAT
1 TATATTA-ATTATATTTAAT
3322976 TATATTA
1 TATATTA
3322983 TTTTTATATT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
17 10 0.26
18 1 0.03
19 23 0.59
20 5 0.13
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
TATATTAATTATATTTAAT
Found at i:3322960 original size:10 final size:10
Alignment explanation
Indices: 3322920--3322981 Score: 53
Period size: 9 Copynumber: 6.5 Consensus size: 10
3322910 TTAAATATAA
3322920 ATATATTAATT
1 ATAT-TTAATT
3322931 -T-TTTAATT
1 ATATTTAATT
3322939 ATA-TTAATT
1 ATATTTAATT
*
3322948 ATATTTAAAT
1 ATATTTAATT
*
3322958 ATA-TTATATC
1 ATATTTA-ATT
3322968 ATA-TTAATT
1 ATATTTAATT
3322977 ATATT
1 ATATT
3322982 ATTTTTATAT
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
8 6 0.14
9 19 0.45
10 17 0.40
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (10 bp):
ATATTTAATT
Done.