Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold65
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: 3097370
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.31
Warning! 315397 characters in sequence are not A, C, G, or T
File 3 of 17
Found at i:430201 original size:21 final size:21
Alignment explanation
Indices: 430176--430231 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 21
430166 TTTTTTAAAT
*
430176 TTTAATAAATATAAATTATTA
1 TTTAATAAATATAAAATATTA
*
430197 TTTAATAATTA-AAAATATTA
1 TTTAATAAATATAAAATATTA
*
430217 TTTTATAAAT-TAAAA
1 TTTAATAAATATAAAA
430232 ATTTTCCAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 20 0.67
21 10 0.33
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TTTAATAAATATAAAATATTA
Found at i:430217 original size:20 final size:20
Alignment explanation
Indices: 430176--430233 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 20
430166 TTTTTTAAAT
* *
430176 TTTAATAAATATAAATTATTA
1 TTTAATAATTA-AAAATATTA
430197 TTTAATAATTAAAAATATTA
1 TTTAATAATTAAAAATATTA
*
430217 TTTTATAAATTAAAAAT
1 TTTAAT-AATTAAAAAT
430234 TTTCCAAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 13 0.39
21 20 0.61
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TTTAATAATTAAAAATATTA
Found at i:430903 original size:28 final size:29
Alignment explanation
Indices: 430867--430922 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
430857 TTAAATTATT
*
430867 ATTTTATTAATAAAA-AT-ATTTTATTTAG
1 ATTTAATT-ATAAAATATAATTTTATTTAG
*
430895 ATTTAATTATAAAATATAATTTTTTTTA
1 ATTTAATTATAAAATATAATTTTATTTA
430923 ATATATTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 6 0.25
28 9 0.38
29 9 0.38
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (29 bp):
ATTTAATTATAAAATATAATTTTATTTAG
Found at i:431048 original size:20 final size:18
Alignment explanation
Indices: 431006--431065 Score: 57
Period size: 20 Copynumber: 3.1 Consensus size: 18
430996 TTATCGTTCA
431006 AATTTAAATTAATTTAAT
1 AATTTAAATTAATTTAAT
* *
431024 TATTTAAAATTAAATTTGAT
1 AATTT-AAATT-AATTTAAT
*
431044 AATTTTAAATATAATTAAAT
1 AA-TTTAAAT-TAATTTAAT
431064 AA
1 AA
431066 ATATAATATA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
18 4 0.12
19 5 0.15
20 20 0.61
21 4 0.12
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
AATTTAAATTAATTTAAT
Found at i:431068 original size:14 final size:14
Alignment explanation
Indices: 431049--431090 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
431039 TTGATAATTT
431049 TAAATATAATTAAA
1 TAAATATAATTAAA
*
431063 TAAATATAATATATA
1 TAAATATAAT-TAAA
431078 TAAA-ATAATTAAA
1 TAAATATAATTAAA
431091 ATATGATATG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 3 0.12
14 15 0.60
15 7 0.28
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
TAAATATAATTAAA
Found at i:431176 original size:33 final size:32
Alignment explanation
Indices: 431118--431218 Score: 88
Period size: 32 Copynumber: 3.2 Consensus size: 32
431108 TATAAATTTT
* *
431118 AAAATTTATATAATATAAATGATTTATATATC
1 AAAATTAATATAATATAAATGATTTAAATATC
431150 AAAATTAATATAAATATTAAAT-ATTTAAATAT-
1 AAAATTAATAT-AATA-TAAATGATTTAAATATC
* *
431182 -AATTATAATATAATA-AAAT-ATATAAATAT-
1 AAAAT-TAATATAATATAAATGATTTAAATATC
431211 ATAAATTA
1 A-AAATTA
431219 TTAGTTGTAT
Statistics
Matches: 59, Mismatches: 5, Indels: 12
0.78 0.07 0.16
Matches are distributed among these distances:
29 13 0.22
30 2 0.03
31 10 0.17
32 16 0.27
33 13 0.22
34 5 0.08
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (32 bp):
AAAATTAATATAATATAAATGATTTAAATATC
Found at i:431215 original size:8 final size:8
Alignment explanation
Indices: 431157--431216 Score: 59
Period size: 8 Copynumber: 7.0 Consensus size: 8
431147 ATCAAAATTA
431157 ATATAAAT
1 ATATAAAT
431165 AT-TAAAT
1 ATATAAAT
*
431172 ATTTAAAT
1 ATATAAAT
431180 ATAATTATAAT
1 AT-A-TA-AAT
431191 ATAATAAAAT
1 AT-AT-AAAT
431201 ATATAAAT
1 ATATAAAT
431209 ATATAAAT
1 ATATAAAT
431217 TATTAGTTGT
Statistics
Matches: 46, Mismatches: 1, Indels: 10
0.81 0.02 0.18
Matches are distributed among these distances:
7 7 0.15
8 21 0.46
9 2 0.04
10 8 0.17
11 8 0.17
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
ATATAAAT
Found at i:431437 original size:3 final size:3
Alignment explanation
Indices: 431429--431467 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
431419 TCAATTTGAG
431429 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
431468 CACTTAATCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:432922 original size:14 final size:14
Alignment explanation
Indices: 432903--432931 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
432893 TTTATTAAAC
432903 AATAAAATAATTAA
1 AATAAAATAATTAA
432917 AATAAAATAATTAA
1 AATAAAATAATTAA
432931 A
1 A
432932 TAAGTCATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
AATAAAATAATTAA
Found at i:433518 original size:16 final size:16
Alignment explanation
Indices: 433491--433541 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
433481 TATATAATAA
433491 TAATAATATATTATATT
1 TAATAAT-TATTATATT
* * *
433508 TATTATTTATTAAATT
1 TAATAATTATTATATT
433524 TAATAATTATTTATATT
1 TAATAATTA-TTATATT
433541 T
1 T
433542 TTTAAAATTT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
16 15 0.56
17 12 0.44
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATAATTATTATATT
Found at i:434874 original size:6 final size:6
Alignment explanation
Indices: 434844--434894 Score: 57
Period size: 6 Copynumber: 8.2 Consensus size: 6
434834 TTGAAAATCA
* * *
434844 TAAATTT TAAATTT TAAATT CAAATT TAAATT TAAGTC TAAATT TAAATT
1 TAAA-TT TAAA-TT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
434894 T
1 T
434895 CCAAATATAA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
6 27 0.71
7 11 0.29
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (6 bp):
TAAATT
Found at i:435398 original size:20 final size:20
Alignment explanation
Indices: 435375--435447 Score: 59
Period size: 18 Copynumber: 4.0 Consensus size: 20
435365 AATAATATAA
435375 ATATATATAAAATATT-AA-
1 ATATATATAAAATATTAAAT
*
435393 ATATATA-AAAAT-TTATAT
1 ATATATATAAAATATTAAAT
* * *
435411 AAATATATAATATTTTAAAT
1 ATATATATAAAATATTAAAT
*
435431 AT-TAT-TATAATATTAAA
1 ATATATATAAAATATTAAA
435448 ATAATAAAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
16 2 0.05
17 6 0.14
18 22 0.51
19 7 0.16
20 6 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
ATATATATAAAATATTAAAT
Found at i:435410 original size:14 final size:16
Alignment explanation
Indices: 435375--435450 Score: 54
Period size: 16 Copynumber: 4.9 Consensus size: 16
435365 AATAATATAA
435375 ATATATATAAAATATT
1 ATATATATAAAATATT
*
435391 AAATATATAAAA-ATT
1 ATATATATAAAATATT
*
435406 -TATATA-AATATA-T
1 ATATATATAAAATATT
* *
435419 A-ATATTTTAAATATT
1 ATATATATAAAATATT
435434 ATTATAATATTAAAATA
1 A-TAT-ATA-TAAAATA
435451 ATAAAAACAG
Statistics
Matches: 44, Mismatches: 8, Indels: 13
0.68 0.12 0.20
Matches are distributed among these distances:
13 8 0.18
14 10 0.23
15 5 0.11
16 11 0.25
17 2 0.05
18 2 0.05
19 6 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATATATAAAATATT
Found at i:443608 original size:23 final size:23
Alignment explanation
Indices: 443582--443628 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
443572 GGGTGAAAGG
443582 AATATGCCTGGCTAATGATTGAC
1 AATATGCCTGGCTAATGATTGAC
443605 AATATGCCTGGCTAATGATTGAC
1 AATATGCCTGGCTAATGATTGAC
443628 A
1 A
443629 CATTCCTAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (23 bp):
AATATGCCTGGCTAATGATTGAC
Found at i:444237 original size:2 final size:2
Alignment explanation
Indices: 444230--444256 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
444220 CTTAAAAGCA
444230 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
444257 GATAATCACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:444748 original size:2 final size:2
Alignment explanation
Indices: 444741--444793 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
444731 AAATAAAACA
*
444741 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG GG 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 AG
444783 AG AG AG AG AG A
1 AG AG AG AG AG A
444794 AACTCACAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:445751 original size:2 final size:2
Alignment explanation
Indices: 445744--445778 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
445734 AGAAATGAGA
445744 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
445779 GTATTATTGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:447149 original size:13 final size:13
Alignment explanation
Indices: 447133--447166 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
447123 ATTTGATATT
447133 AAAATTTAA-AATA
1 AAAATTTAATAA-A
447146 AAAATTTAATAAA
1 AAAATTTAATAAA
447159 AAAATTTA
1 AAAATTTA
447167 TTTTTAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 18 0.90
14 2 0.10
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAATTTAATAAA
Found at i:447675 original size:16 final size:16
Alignment explanation
Indices: 447656--447720 Score: 64
Period size: 16 Copynumber: 4.2 Consensus size: 16
447646 AAAAAAATTA
447656 ATAATTATAATTT-TTT
1 ATAATTAT-ATTTATTT
447672 ATAATT-TATTTATTT
1 ATAATTATATTTATTT
* * *
447687 -TTATTATAATTAATT
1 ATAATTATATTTATTT
*
447702 ATAATAATATTTATTT
1 ATAATTATATTTATTT
447718 ATA
1 ATA
447721 TTCGTATAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
14 8 0.21
15 11 0.28
16 20 0.51
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
ATAATTATATTTATTT
Found at i:447695 original size:30 final size:31
Alignment explanation
Indices: 447659--447722 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 31
447649 AAAATTAATA
** * *
447659 ATTATAATTTTTTATAAT-TTATTTATTTTT
1 ATTATAATTAATTATAATAATATTTATTTAT
447689 ATTATAATTAATTATAATAATATTTATTTAT
1 ATTATAATTAATTATAATAATATTTATTTAT
447720 ATT
1 ATT
447723 CGTATAAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 16 0.55
31 13 0.45
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (31 bp):
ATTATAATTAATTATAATAATATTTATTTAT
Found at i:447702 original size:10 final size:10
Alignment explanation
Indices: 447659--447706 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
447649 AAAATTAATA
447659 ATTATAATTT
1 ATTATAATTT
*
447669 TTTATAATTT
1 ATTATAATTT
*
447679 ATT-TATTTTT
1 ATTATA-ATTT
*
447689 ATTATAATTA
1 ATTATAATTT
447699 ATTATAAT
1 ATTATAAT
447707 AATATTTATT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
9 2 0.06
10 27 0.87
11 2 0.06
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
ATTATAATTT
Found at i:453586 original size:32 final size:31
Alignment explanation
Indices: 453550--453654 Score: 117
Period size: 32 Copynumber: 3.4 Consensus size: 31
453540 TAATGATTTG
453550 TCAAATTTATAAGTAATTTTATCTAATATTCA
1 TCAAATTTATAAGTAATTTTATCTAATATT-A
* *
453582 TCAAATTTACAAGTAATTTTATTTAATATTTA
1 TCAAATTTATAAGTAATTTTATCTAATA-TTA
* * *
453614 TTAAATTTATGAA-TAATTATGTC-AAT-TTA
1 TCAAATTTAT-AAGTAATTTTATCTAATATTA
453643 TCAAATTTATAA
1 TCAAATTTATAA
453655 TCAATATCAA
Statistics
Matches: 63, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
28 2 0.03
29 12 0.19
31 3 0.05
32 42 0.67
33 4 0.06
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.48
Consensus pattern (31 bp):
TCAAATTTATAAGTAATTTTATCTAATATTA
Found at i:454396 original size:38 final size:39
Alignment explanation
Indices: 454311--454390 Score: 97
Period size: 43 Copynumber: 1.9 Consensus size: 39
454301 ATTAAATTTG
*
454311 ATGAATAATTTAATTTGTAAATGGATTGTAATCTACATATAAA
1 ATGAATAATTTAATTTGTAAATAGATTGTAATCTAC----AAA
* *
454354 ATGAATAATTTAATTTTTGAATAGATTGTAATCTACA
1 ATGAATAATTTAATTTGTAAATAGATTGTAATCTACA
454391 CATGAAACGA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
39 1 0.03
43 33 0.97
ACGTcount: A:0.42, C:0.05, G:0.11, T:0.41
Consensus pattern (39 bp):
ATGAATAATTTAATTTGTAAATAGATTGTAATCTACAAA
Found at i:454569 original size:3 final size:3
Alignment explanation
Indices: 454561--454593 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
454551 AAACTTAGTA
454561 TAT TAT TAT TAT TAT TAT T-T TCAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT
454594 AATATAGAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 24 0.86
4 2 0.07
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:455229 original size:22 final size:22
Alignment explanation
Indices: 455201--455243 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
455191 AAAAATTAAA
455201 TAAATAAT-TATATATATTTTAT
1 TAAATAATATATAT-TATTTTAT
455223 TAAATAATATATATTATTTTA
1 TAAATAATATATATTATTTTA
455244 AATTAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TAAATAATATATATTATTTTAT
Found at i:455234 original size:19 final size:19
Alignment explanation
Indices: 455210--455246 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
455200 ATAAATAATT
455210 ATATATATT-TTATTAAATA
1 ATATATATTATT-TTAAATA
455229 ATATATATTATTTTAAAT
1 ATATATATTATTTTAAAT
455247 TAAAAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
ATATATATTATTTTAAATA
Found at i:459041 original size:23 final size:22
Alignment explanation
Indices: 459002--459048 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
458992 AAATTAAAGA
* *
459002 AATTGATATTTAGTTTAATTAT
1 AATTGATATTTAATTTAATCAT
*
459024 AATTGGATGTTTAATTTAATCAT
1 AATT-GATATTTAATTTAATCAT
459047 AA
1 AA
459049 ATGTGTATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.38, C:0.02, G:0.11, T:0.49
Consensus pattern (22 bp):
AATTGATATTTAATTTAATCAT
Found at i:459211 original size:17 final size:17
Alignment explanation
Indices: 459189--459225 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
459179 TGTTACCAAG
*
459189 ATTAAAAATATATATAT
1 ATTAAAAATAAATATAT
*
459206 ATTAAATATAAATATAT
1 ATTAAAAATAAATATAT
459223 ATT
1 ATT
459226 TTATATGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATTAAAAATAAATATAT
Found at i:459222 original size:19 final size:19
Alignment explanation
Indices: 459198--459298 Score: 55
Period size: 19 Copynumber: 5.2 Consensus size: 19
459188 GATTAAAAAT
459198 ATATATATATTAAATATAA
1 ATATATATATTAAATATAA
* *
459217 ATATATATTTTATATGA-AA
1 ATATATATATTAAAT-ATAA
* * *
459236 ATATTTA-ATTTAATTTTAA
1 ATATATATA-TTAAATATAA
* **
459255 TATTATATAATATT-TATATTT
1 -A-TATAT-ATATTAAATATAA
*
459276 ATTTATATATTAAATATAA
1 ATATATATATTAAATATAA
459295 ATAT
1 ATAT
459299 TTAAAAATCA
Statistics
Matches: 56, Mismatches: 18, Indels: 16
0.62 0.20 0.18
Matches are distributed among these distances:
18 5 0.09
19 38 0.68
20 3 0.05
21 6 0.11
22 3 0.05
23 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (19 bp):
ATATATATATTAAATATAA
Found at i:459268 original size:28 final size:29
Alignment explanation
Indices: 459234--459302 Score: 81
Period size: 28 Copynumber: 2.3 Consensus size: 29
459224 TTTTATATGA
459234 AAATATTTAATTTAATTT-TAATATT-ATAT
1 AAATATTTAATTT-ATTTAT-ATATTAATAT
459263 -AATATTTATATTTATTTATATATTAAATAT
1 AAATATTTA-ATTTATTTATATATT-AATAT
459293 AAATATTTAA
1 AAATATTTAA
459303 AAATCAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
28 17 0.49
29 5 0.14
30 5 0.14
31 8 0.23
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (29 bp):
AAATATTTAATTTATTTATATATTAATAT
Found at i:463153 original size:15 final size:13
Alignment explanation
Indices: 463134--463168 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
463124 ATTCACATCA
463134 ATTTTTTTAATTT
1 ATTTTTTTAATTT
*
463147 AATTTTTTAATTT
1 ATTTTTTTAATTT
463160 ATTTATTTT
1 ATTT-TTTT
463169 TAATATTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 15 0.79
14 4 0.21
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
ATTTTTTTAATTT
Found at i:465162 original size:26 final size:23
Alignment explanation
Indices: 465126--465172 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 23
465116 TGTGAAATTT
*
465126 TTTTTCTTGACTGGCGTGAAGCTG
1 TTTTTCTTGACAGG-GTGAAGCTG
465150 TTTTTCTGATGACAGGGTGAAGC
1 TTTTTCT--TGACAGGGTGAAGC
465173 GCGGTCGAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 7 0.35
25 7 0.35
26 6 0.30
ACGTcount: A:0.17, C:0.15, G:0.30, T:0.38
Consensus pattern (23 bp):
TTTTTCTTGACAGGGTGAAGCTG
Found at i:469475 original size:13 final size:13
Alignment explanation
Indices: 469457--469488 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
469447 TTCAATTTTT
469457 CTCCCCCTCCCCC
1 CTCCCCCTCCCCC
469470 CTCCCCC-CCCCC
1 CTCCCCCTCCCCC
469482 C-CCCCCT
1 CTCCCCCT
469489 TCTCTCTCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 6 0.33
13 7 0.39
ACGTcount: A:0.00, C:0.88, G:0.00, T:0.12
Consensus pattern (13 bp):
CTCCCCCTCCCCC
Found at i:469494 original size:2 final size:2
Alignment explanation
Indices: 469489--469522 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
469479 CCCCCCCCCT
*
469489 TC TC TC TC TC TC TC TC TC TC TC TC TC TC CC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
469523 ACAAAACAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
TC
Found at i:470223 original size:13 final size:14
Alignment explanation
Indices: 470205--470233 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
470195 AAAAAATTAT
470205 AAAATTAT-AATAA
1 AAAATTATAAATAA
470218 AAAATTATAAATAA
1 AAAATTATAAATAA
470232 AA
1 AA
470234 TATTCTCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
AAAATTATAAATAA
Found at i:471311 original size:16 final size:17
Alignment explanation
Indices: 471286--471321 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
471276 TACATTAAAC
*
471286 ATAAATTTAATTAAAAA
1 ATAAATTTAAATAAAAA
471303 ATAAA-TTAAATAAAAA
1 ATAAATTTAAATAAAAA
471319 ATA
1 ATA
471322 TACATAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
ATAAATTTAAATAAAAA
Found at i:482778 original size:26 final size:22
Alignment explanation
Indices: 482742--482789 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 22
482732 ATTATTTTAT
482742 ATTTTTTAATAATTTAATTAAAAA
1 ATTTTTTAATAATTT--TTAAAAA
482766 ATTTCTTTAAATAATTTTTAAAAA
1 ATTT-TTT-AATAATTTTTAAAAA
482790 TCAATTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 11 0.50
25 3 0.14
26 8 0.36
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (22 bp):
ATTTTTTAATAATTTTTAAAAA
Found at i:483714 original size:2 final size:2
Alignment explanation
Indices: 483707--483753 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
483697 CTGCAAAAGA
* *
483707 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT AT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
483749 AT AT A
1 AT AT A
483754 AACAAAATTG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:485266 original size:31 final size:31
Alignment explanation
Indices: 485231--485304 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
485221 TAAGCCAAAT
485231 TAAATTTAATTTGAATTTGATT-GATGGTTAA
1 TAAATTTAATTTGAATTTGATTAG-TGGTTAA
* *
485262 TAAATTTAATTTGGATTTGGTTAGTGGTTAA
1 TAAATTTAATTTGAATTTGATTAGTGGTTAA
* *
485293 CAAATTCAATTT
1 TAAATTTAATTT
485305 TGATTTAACT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
31 37 0.97
32 1 0.03
ACGTcount: A:0.34, C:0.03, G:0.16, T:0.47
Consensus pattern (31 bp):
TAAATTTAATTTGAATTTGATTAGTGGTTAA
Found at i:486893 original size:15 final size:15
Alignment explanation
Indices: 486864--486923 Score: 61
Period size: 15 Copynumber: 4.1 Consensus size: 15
486854 AAAAAATAAA
**
486864 ATATTTAATTTTTTT
1 ATATTTAATAATTTT
486879 ATATTTAATAATTTT
1 ATATTTAATAATTTT
* *
486894 AAATTTTA-AATTTT
1 ATATTTAATAATTTT
486908 AATATTT-ATAATTTT
1 -ATATTTAATAATTTT
486923 A
1 A
486924 AAATATAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
14 8 0.21
15 30 0.79
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
ATATTTAATAATTTT
Found at i:486900 original size:7 final size:7
Alignment explanation
Indices: 486888--486925 Score: 51
Period size: 7 Copynumber: 5.3 Consensus size: 7
486878 TATATTTAAT
486888 AATTTTA
1 AATTTTA
486895 AATTTTA
1 AATTTTA
486902 AATTTT-
1 AATTTTA
486908 AATATTTA
1 AAT-TTTA
486916 TAATTTTA
1 -AATTTTA
486924 AA
1 AA
486926 ATATAATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
6 3 0.11
7 18 0.64
8 4 0.14
9 3 0.11
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (7 bp):
AATTTTA
Found at i:486936 original size:29 final size:30
Alignment explanation
Indices: 486873--486936 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 30
486863 AATATTTAAT
* * *
486873 TTTTTTATATTTAATAATTTTAAATTTTAA
1 TTTTTAATATTTAATAATTTTAAAATATAA
*
486903 ATTTTAATATTT-ATAATTTTAAAATATAA
1 TTTTTAATATTTAATAATTTTAAAATATAA
486932 TTTTT
1 TTTTT
486937 GATCATATTA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 19 0.66
30 10 0.34
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (30 bp):
TTTTTAATATTTAATAATTTTAAAATATAA
Found at i:489969 original size:15 final size:16
Alignment explanation
Indices: 489949--489990 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
489939 TCATCACCCC
489949 AAATTTATAAAAT-TT
1 AAATTTATAAAATATT
*
489964 AAATTTATTAAATATT
1 AAATTTATAAAATATT
*
489980 ATATTT-TAAAA
1 AAATTTATAAAA
489991 ATAATTATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 16 0.70
16 7 0.30
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AAATTTATAAAATATT
Found at i:490696 original size:18 final size:18
Alignment explanation
Indices: 490642--490702 Score: 65
Period size: 18 Copynumber: 3.4 Consensus size: 18
490632 TTTATTTAAA
*
490642 TTTAATTATAAAAT-ATAT
1 TTTAA-TATAAAATAATTT
*
490660 ATTAATA-AAAATAATTT
1 TTTAATATAAAATAATTT
490677 TTTAATATAAAATTAA-TT
1 TTTAATATAAAA-TAATTT
490695 TTTAATAT
1 TTTAATAT
490703 TTTAATATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
16 5 0.14
17 11 0.30
18 18 0.49
19 3 0.08
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTAATATAAAATAATTT
Found at i:490767 original size:18 final size:17
Alignment explanation
Indices: 490739--490772 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
490729 AGTTATCGAA
490739 TTAAATTAAATTTTAAT
1 TTAAATTAAATTTTAAT
490756 TTAAACTTAAATTTTAA
1 TTAAA-TTAAATTTTAA
490773 ATTATTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAAATTAAATTTTAAT
Found at i:491309 original size:2 final size:2
Alignment explanation
Indices: 491302--491340 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
491292 ATTGGAATAC
*
491302 AT AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
491341 CTTACACATG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:491804 original size:35 final size:35
Alignment explanation
Indices: 491764--491833 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
491754 CACATTAGAA
491764 ACAAAGTCCAGAATCATAATTTTGTCAATTAGATT
1 ACAAAGTCCAGAATCATAATTTTGTCAATTAGATT
491799 ACAAAGTCCAGAATCATAATTTTGTCAATTAGATT
1 ACAAAGTCCAGAATCATAATTTTGTCAATTAGATT
491834 TCAATTGCAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.34
Consensus pattern (35 bp):
ACAAAGTCCAGAATCATAATTTTGTCAATTAGATT
Found at i:500636 original size:2 final size:2
Alignment explanation
Indices: 500631--500667 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
500621 ACACACACAC
500631 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
500668 ATTTTAAAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:501163 original size:10 final size:8
Alignment explanation
Indices: 501138--501190 Score: 54
Period size: 8 Copynumber: 6.6 Consensus size: 8
501128 TGAGCGCATC
501138 ATAAATAT
1 ATAAATAT
501146 ATAAATAT
1 ATAAATAT
*
501154 ATCAATAT
1 ATAAATAT
* *
501162 ATATATAAA
1 ATAAAT-AT
501171 ATAAAT-T
1 ATAAATAT
*
501178 ATTAATAT
1 ATAAATAT
501186 ATAAA
1 ATAAA
501191 AATTATATAA
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
7 5 0.14
8 24 0.69
9 6 0.17
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (8 bp):
ATAAATAT
Found at i:504140 original size:4 final size:4
Alignment explanation
Indices: 504133--504157 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
504123 AAAAAATGGA
504133 AAAG AAAG AAAG AAAG AAAG AAAG A
1 AAAG AAAG AAAG AAAG AAAG AAAG A
504158 TGGGGGAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:505506 original size:21 final size:21
Alignment explanation
Indices: 505482--505521 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
505472 AAAAGTGGTA
505482 ATATAAAAAATTTATTTAATT
1 ATATAAAAAATTTATTTAATT
** *
505503 ATATTTAATATTTATTTAA
1 ATATAAAAAATTTATTTAA
505522 ATAAAAATAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATATAAAAAATTTATTTAATT
Found at i:506086 original size:28 final size:28
Alignment explanation
Indices: 506028--506083 Score: 78
Period size: 30 Copynumber: 2.0 Consensus size: 28
506018 AATTAAATAA
*
506028 AATTAATTTATTTTTAAAAATTTAATTT
1 AATTAATTTATTATTAAAAATTTAATTT
506056 AATTAATTTAAATTATTAAAAA-TTAATT
1 AATTAATTT--ATTATTAAAAATTTAATT
506084 AATATGCACA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 9 0.36
29 6 0.24
30 10 0.40
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (28 bp):
AATTAATTTATTATTAAAAATTTAATTT
Found at i:514511 original size:2 final size:2
Alignment explanation
Indices: 514499--514528 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
514489 AATTCATAAA
*
514499 AT AT GT 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
514529 TTTCCCTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:514613 original size:13 final size:14
Alignment explanation
Indices: 514595--514623 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
514585 AATTCTGCCT
514595 AAAAAAT-ATATTA
1 AAAAAATCATATTA
514608 AAAAAATCATATTA
1 AAAAAATCATATTA
514622 AA
1 AA
514624 TTTTGGATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (14 bp):
AAAAAATCATATTA
Found at i:515137 original size:16 final size:16
Alignment explanation
Indices: 515116--515147 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
515106 TAATTGACTC
*
515116 AAATTTAAAATTATTT
1 AAATTTAAAATAATTT
515132 AAATTTAAAATAATTT
1 AAATTTAAAATAATTT
515148 GTATCTGACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AAATTTAAAATAATTT
Found at i:518765 original size:2 final size:2
Alignment explanation
Indices: 518760--518788 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
518750 ATATATATAT
518760 AG 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 AG A
518789 TTATGGGGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:520523 original size:2 final size:2
Alignment explanation
Indices: 520516--520542 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
520506 AGCTGTACCA
520516 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
520543 TTCACTAAGC
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:534698 original size:17 final size:17
Alignment explanation
Indices: 534676--534711 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
534666 TAAGTTAATT
534676 TTTATTTAAA-ATAATAA
1 TTTATTTAAATATAA-AA
534693 TTTATTTAAATATAAAA
1 TTTATTTAAATATAAAA
534710 TT
1 TT
534712 AAAAGATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTATTTAAATATAAAA
Found at i:537842 original size:17 final size:19
Alignment explanation
Indices: 537822--537863 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
537812 AATTAAATTA
537822 AATA-AGTAAAAATTAT-T
1 AATATAGTAAAAATTATAT
* *
537839 AATATATTAAAATTTATAT
1 AATATAGTAAAAATTATAT
537858 AATATA
1 AATATA
537864 TATTATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 4 0.19
18 10 0.48
19 7 0.33
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (19 bp):
AATATAGTAAAAATTATAT
Found at i:537862 original size:19 final size:18
Alignment explanation
Indices: 537828--537864 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
537818 ATTAAATAAG
537828 TAAAAATTATTAATATAT
1 TAAAAATTATTAATATAT
*
537846 TAAAATTTATATAATATAT
1 TAAAAATTAT-TAATATAT
537865 ATTATATATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TAAAAATTATTAATATAT
Found at i:537878 original size:28 final size:29
Alignment explanation
Indices: 537828--537894 Score: 95
Period size: 28 Copynumber: 2.4 Consensus size: 29
537818 ATTAAATAAG
*
537828 TAAAA-AT-TATTAATATATTAAAATTTA
1 TAAAATATATATTAATATATCAAAATTTA
*
537855 TATAATATATATT-ATATATCAAAATTTA
1 TAAAATATATATTAATATATCAAAATTTA
537883 TAAAATATATAT
1 TAAAATATATAT
537895 AAAAGATGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
27 4 0.11
28 27 0.77
29 4 0.11
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (29 bp):
TAAAATATATATTAATATATCAAAATTTA
Found at i:537961 original size:17 final size:19
Alignment explanation
Indices: 537929--537967 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
537919 ATTTTATTAA
537929 ATTTAATAAAAATTAAT-T
1 ATTTAATAAAAATTAATAT
*
537947 ATTTAA-AATAATTAATAT
1 ATTTAATAAAAATTAATAT
537965 ATT
1 ATT
537968 ATGATGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
ATTTAATAAAAATTAATAT
Found at i:538660 original size:18 final size:18
Alignment explanation
Indices: 538637--538769 Score: 67
Period size: 18 Copynumber: 7.8 Consensus size: 18
538627 AAATATAATT
538637 ATATAAATATAATATATA
1 ATATAAATATAATATATA
538655 ATATAAATAT-ATAT-T-
1 ATATAAATATAATATATA
* *
538670 -T-TAAA-AT-TTATATC
1 ATATAAATATAATATATA
538684 ATATAAATTATTAATATAT-
1 ATATAAA-TA-TAATATATA
*
538703 -TA-AAAT-TGATATA-A
1 ATATAAATATAATATATA
*
538717 ATATAAAATATATTATATA
1 ATAT-AAATATAATATATA
* *
538736 AAATTAGAATATAATA-AAA
1 ATA-TA-AATATAATATATA
538755 TATATAAATATAATA
1 -ATATAAATATAATA
538770 AAAATATATG
Statistics
Matches: 89, Mismatches: 9, Indels: 34
0.67 0.07 0.26
Matches are distributed among these distances:
12 5 0.06
13 5 0.06
14 7 0.08
15 3 0.03
16 6 0.07
17 11 0.12
18 27 0.30
19 9 0.10
20 16 0.18
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.41
Consensus pattern (18 bp):
ATATAAATATAATATATA
Found at i:538662 original size:32 final size:33
Alignment explanation
Indices: 538626--538760 Score: 130
Period size: 32 Copynumber: 4.3 Consensus size: 33
538616 TTAATGATTT
538626 TAAATATA-ATTATAT-AAATATAATATATAATA
1 TAAATATATATTATATAAAAT-TAATATATAATA
*
538658 TAAATATATATT-T-TAAAATT--TATATCATA
1 TAAATATATATTATATAAAATTAATATATAATA
* *
538687 TAAAT-TATTAATATATTAAAATTGATATA-AATA
1 TAAATATA-TATTATA-TAAAATTAATATATAATA
538720 TAAA-ATATATTATATAAAATTAGA-ATATAATA
1 TAAATATATATTATATAAAATTA-ATATATAATA
538752 -AAATATATA
1 TAAATATATA
538761 AATATAATAA
Statistics
Matches: 86, Mismatches: 5, Indels: 24
0.75 0.04 0.21
Matches are distributed among these distances:
28 2 0.02
29 16 0.19
30 1 0.01
31 15 0.17
32 36 0.42
33 12 0.14
34 4 0.05
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (33 bp):
TAAATATATATTATATAAAATTAATATATAATA
Found at i:538674 original size:13 final size:13
Alignment explanation
Indices: 538628--538767 Score: 67
Period size: 13 Copynumber: 10.5 Consensus size: 13
538618 AATGATTTTA
*
538628 AATATAATTATAT
1 AATATAAATATAT
538641 AA-ATATAATATAT
1 AATATA-AATATAT
538654 AATATAAATATAT
1 AATATAAATATAT
* *
538667 ATTTTAAAATTTATAT
1 AATAT-AAA--TATAT
*
538683 CATATAAAT-TATT
1 AATATAAATATA-T
*
538696 AATATATTAAAAT-T
1 AATATA--AATATAT
* *
538710 GATATAAATATAA
1 AATATAAATATAT
*
538723 AATAT-ATTATAT
1 AATATAAATATAT
* *
538735 AAAATTAGA-ATAT
1 AATA-TAAATATAT
538748 AATA-AAATATAT
1 AATATAAATATAT
538760 AAATATAA
1 -AATATAA
538768 TAAAAATATA
Statistics
Matches: 93, Mismatches: 19, Indels: 29
0.66 0.13 0.21
Matches are distributed among these distances:
11 2 0.02
12 21 0.23
13 43 0.46
14 14 0.15
15 5 0.05
16 8 0.09
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (13 bp):
AATATAAATATAT
Found at i:538729 original size:47 final size:45
Alignment explanation
Indices: 538650--538767 Score: 123
Period size: 47 Copynumber: 2.5 Consensus size: 45
538640 TAAATATAAT
* * *
538650 ATATAATATAAATATAT-ATTTTAAAATTTATATCATAT-AAATTATTA
1 ATATAATA-AAATATATAAATATAAAA--TATATCATATAAAATTA-GA
* *
538697 ATATATTAAAATTGATATAAATATAAAATATATTATATAAAATTAGA
1 ATATAATAAAA-T-ATATAAATATAAAATATATCATATAAAATTAGA
538744 ATATAATAAAATATATAAATATAA
1 ATATAATAAAATATATAAATATAA
538768 TAAAAATATA
Statistics
Matches: 61, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
45 12 0.20
46 4 0.07
47 28 0.46
48 10 0.16
49 7 0.11
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.41
Consensus pattern (45 bp):
ATATAATAAAATATATAAATATAAAATATATCATATAAAATTAGA
Found at i:538788 original size:36 final size:36
Alignment explanation
Indices: 538715--538791 Score: 97
Period size: 36 Copynumber: 2.1 Consensus size: 36
538705 AAATTGATAT
538715 AAATATAAAATATATTATATAAAATTAGAATATAATA
1 AAATATAAAATATA-TATATAAAATTAGAATATAATA
538752 AAATATATAAATATA-ATA-AAAATATATGAATA-AATA
1 AAATATA-AAATATATATATAAAAT-TA-GAATATAATA
538788 AAAT
1 AAAT
538792 TGGATAAGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
35 5 0.14
36 13 0.35
37 12 0.32
38 7 0.19
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (36 bp):
AAATATAAAATATATATATAAAATTAGAATATAATA
Found at i:538791 original size:17 final size:18
Alignment explanation
Indices: 538733--538791 Score: 79
Period size: 19 Copynumber: 3.4 Consensus size: 18
538723 AATATATTAT
538733 ATAAAAT-TA-GAATATA
1 ATAAAATATATGAATATA
*
538749 ATAAAATATATAAATATA
1 ATAAAATATATGAATATA
538767 ATAAAAATATATGAATA-A
1 AT-AAAATATATGAATATA
538785 ATAAAAT
1 ATAAAAT
538792 TGGATAAGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
16 7 0.18
17 7 0.18
18 11 0.29
19 13 0.34
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (18 bp):
ATAAAATATATGAATATA
Found at i:539141 original size:5 final size:5
Alignment explanation
Indices: 539133--539166 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
539123 TAAAAAAAAA
*
539133 TTATT TTATT TTATT TTATTT TTTTT TTATT TTA
1 TTATT TTATT TTATT TTA-TT TTATT TTATT TTA
539167 AGAAAGTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 22 0.85
6 4 0.15
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTATT
Found at i:539160 original size:16 final size:16
Alignment explanation
Indices: 539136--539166 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
539126 AAAAAAATTA
539136 TTTTATTTTATTTTAT
1 TTTTATTTTATTTTAT
*
539152 TTTTTTTTTATTTTA
1 TTTTATTTTATTTTA
539167 AGAAAGTGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTATTTTATTTTAT
Found at i:539300 original size:18 final size:19
Alignment explanation
Indices: 539259--539301 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
539249 ATTTTTTTTG
*
539259 AATTCAATAAAAAATAATA
1 AATTAAATAAAAAATAATA
* *
539278 TATTAAATACAAAA-AATA
1 AATTAAATAAAAAATAATA
539296 AATTAA
1 AATTAA
539302 TGATAATTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (19 bp):
AATTAAATAAAAAATAATA
Found at i:539687 original size:26 final size:26
Alignment explanation
Indices: 539658--539742 Score: 84
Period size: 26 Copynumber: 3.3 Consensus size: 26
539648 TTGAGACAAA
* *
539658 ATTAATGTCACTAAAGTTATTTAATC
1 ATTAATGTCACTAAAGTTGTTTAAAC
* * * *
539684 ATTAATGATC-C-AAAGATGCTCACAAA
1 ATTAATG-TCACTAAAGTTGTTTA-AAC
539710 ATTAATGTCACTAAAGTTGTTTAAAC
1 ATTAATGTCACTAAAGTTGTTTAAAC
539736 ATTAATG
1 ATTAATG
539743 ATCCAAGGAT
Statistics
Matches: 45, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
25 9 0.20
26 26 0.58
27 10 0.22
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.35
Consensus pattern (26 bp):
ATTAATGTCACTAAAGTTGTTTAAAC
Found at i:539715 original size:52 final size:52
Alignment explanation
Indices: 539653--539755 Score: 179
Period size: 52 Copynumber: 2.0 Consensus size: 52
539643 AGTTGTTGAG
*
539653 ACAAAATTAATGTCACTAAAGTTATTTAATCATTAATGATCCAAAGATGCTC
1 ACAAAATTAATGTCACTAAAGTTATTTAAACATTAATGATCCAAAGATGCTC
* *
539705 ACAAAATTAATGTCACTAAAGTTGTTTAAACATTAATGATCCAAGGATGCT
1 ACAAAATTAATGTCACTAAAGTTATTTAAACATTAATGATCCAAAGATGCT
539756 GTCAATTCCA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.32
Consensus pattern (52 bp):
ACAAAATTAATGTCACTAAAGTTATTTAAACATTAATGATCCAAAGATGCTC
Found at i:539836 original size:17 final size:17
Alignment explanation
Indices: 539814--539882 Score: 54
Period size: 16 Copynumber: 4.0 Consensus size: 17
539804 TATTTAAAAT
539814 ATTTTATATTTATATAA
1 ATTTTATATTTATATAA
*
539831 ATTTTA-ATATA-ATAA
1 ATTTTATATTTATATAA
* *
539846 TAATTTATA-TTATCTAAA
1 -ATTTTATATTTATAT-AA
539864 ATTTTATATATTTATATAA
1 A-TTT-TATATTTATATAA
539883 TATCATATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
15 4 0.10
16 11 0.28
17 9 0.23
18 4 0.10
19 6 0.15
20 5 0.13
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATATTTATATAA
Found at i:539854 original size:33 final size:34
Alignment explanation
Indices: 539811--539874 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 34
539801 AATTATTTAA
*
539811 AATATTTTATATT-TATATAAATTTTA-ATATAAT
1 AATAATTTATATTATATA-AAATTTTATATATAAT
*
539844 AATAATTTATATTATCTAAAATTTTATATAT
1 AATAATTTATATTATATAAAATTTTATATAT
539875 TTATATAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
33 20 0.74
34 7 0.26
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (34 bp):
AATAATTTATATTATATAAAATTTTATATATAAT
Found at i:539876 original size:25 final size:25
Alignment explanation
Indices: 539848--539932 Score: 72
Period size: 25 Copynumber: 3.6 Consensus size: 25
539838 TATAATAATA
* *
539848 ATTTATATTATCTAAAATTTTATAT
1 ATTTATATAATATAAAATTTTATAT
* *
539873 ATTTATATAATATCATATTTTATAT
1 ATTTATATAATATAAAATTTTATAT
* *
539898 ATTT-TTTAAT-T---ATTTTTTAT
1 ATTTATATAATATAAAATTTTATAT
*
539918 ATTTATATTATATAA
1 ATTTATATAATATAA
539933 TTATATTGTA
Statistics
Matches: 48, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
20 12 0.25
21 4 0.08
22 1 0.02
23 1 0.02
24 5 0.10
25 25 0.52
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (25 bp):
ATTTATATAATATAAAATTTTATAT
Found at i:539910 original size:52 final size:51
Alignment explanation
Indices: 539785--539910 Score: 123
Period size: 52 Copynumber: 2.5 Consensus size: 51
539775 TGTGTTTTAT
* * **
539785 TATTTTAT-TATATTATAATTATTTAAAATATTTTATATTTATATAAATTT
1 TATTTTATATATATTTTAATTATCTAAAATATTTTATATTTATATAAATCA
* * *
539835 TAATATA-ATAATAATTTATATTATCTAAAAT-TTTATATATTTATATAATATCA
1 TATTTTATAT-ATATTTTA-ATTATCTAAAATATTT-TATATTTATATAA-ATCA
*
539888 TATTTTATATATTTTTTAATTAT
1 TATTTTATATATATTTTAATTAT
539911 TTTTTATATT
Statistics
Matches: 59, Mismatches: 11, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
50 6 0.10
51 9 0.15
52 29 0.49
53 13 0.22
54 2 0.03
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (51 bp):
TATTTTATATATATTTTAATTATCTAAAATATTTTATATTTATATAAATCA
Found at i:539931 original size:13 final size:13
Alignment explanation
Indices: 539904--539946 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
539894 ATATATTTTT
* *
539904 TAATTATTTTTTA
1 TAATTATATTATA
*
539917 TATTTATATTATA
1 TAATTATATTATA
*
539930 TAATTATATTGTA
1 TAATTATATTATA
539943 TAAT
1 TAAT
539947 ATAAATTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (13 bp):
TAATTATATTATA
Found at i:539938 original size:19 final size:19
Alignment explanation
Indices: 539914--539953 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
539904 TAATTATTTT
*
539914 TTATATT-TATATTATATAA
1 TTATATTGTATAATATA-AA
539933 TTATATTGTATAATATAAA
1 TTATATTGTATAATATAAA
539952 TT
1 TT
539954 TAATTAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (19 bp):
TTATATTGTATAATATAAA
Found at i:539944 original size:26 final size:26
Alignment explanation
Indices: 539895--539944 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
539885 TCATATTTTA
* * * *
539895 TATATTTTTTAATTATTTTTTATATT
1 TATATTATATAATTATATTGTATATT
539921 TATATTATATAATTATATTGTATA
1 TATATTATATAATTATATTGTATA
539945 ATATAAATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (26 bp):
TATATTATATAATTATATTGTATATT
Found at i:540836 original size:20 final size:20
Alignment explanation
Indices: 540813--540850 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
540803 ATATTGTTAG
540813 TAAAAATAATAATTTTATAT
1 TAAAAATAATAATTTTATAT
*
540833 TAAATATAATAATTTTAT
1 TAAAAATAATAATTTTAT
540851 TCATAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TAAAAATAATAATTTTATAT
Found at i:540851 original size:18 final size:18
Alignment explanation
Indices: 540799--540851 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 18
540789 TAAGATTCGT
*
540799 TAATATATTGTTAGTAAAAA
1 TAATA-ATT-TTATTAAAAA
*
540819 TAATAATTTTATATTAAATA
1 TAATAA-TTT-TATTAAAAA
540839 TAATAATTTTATT
1 TAATAATTTTATT
540852 CATAATTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
18 4 0.14
19 5 0.17
20 20 0.69
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (18 bp):
TAATAATTTTATTAAAAA
Found at i:541432 original size:23 final size:26
Alignment explanation
Indices: 541377--541432 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 26
541367 TATTAATTAT
541377 TTTTAATTTAATATTATAAAAATATA
1 TTTTAATTTAATATTATAAAAATATA
*
541403 TTATAATTT-AT-TTA-AAAACATA-A
1 TTTTAATTTAATATTATAAAA-ATATA
541426 TTTTAAT
1 TTTTAAT
541433 ATATATAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 11 0.41
24 6 0.22
25 2 0.07
26 8 0.30
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (26 bp):
TTTTAATTTAATATTATAAAAATATA
Found at i:541442 original size:15 final size:17
Alignment explanation
Indices: 541422--541454 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
541412 ATTTAAAAAC
541422 ATAA-TTTT-AATATAT
1 ATAATTTTTCAATATAT
541437 ATAATTTTTCAATATAT
1 ATAATTTTTCAATATAT
541454 A
1 A
541455 ATATAATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 4 0.25
17 8 0.50
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (17 bp):
ATAATTTTTCAATATAT
Found at i:542800 original size:2 final size:2
Alignment explanation
Indices: 542793--542830 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
542783 TTACATTAAT
542793 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
542831 CTTTTACTAA
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):
TA
Found at i:548786 original size:26 final size:26
Alignment explanation
Indices: 548757--548809 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
548747 ACCCACTCAT
548757 ACTTTTTTGGACATAAAACTGATTTA
1 ACTTTTTTGGACATAAAACTGATTTA
548783 ACTTTTTTGGACATAAAACTGATTTA
1 ACTTTTTTGGACATAAAACTGATTTA
548809 A
1 A
548810 GTCATTGGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (26 bp):
ACTTTTTTGGACATAAAACTGATTTA
Found at i:549068 original size:20 final size:18
Alignment explanation
Indices: 549053--549126 Score: 57
Period size: 20 Copynumber: 4.1 Consensus size: 18
549043 GGTATTTTAA
549053 TTTAATTTCGTATATTTT
1 TTTAATTTCGTATATTTT
*
549071 TTATAA-ATC--ATATTATT
1 TT-TAATTTCGTATATT-TT
**
549088 TTT-ATTTCGGGTATTTT
1 TTTAATTTCGTATATTTT
549105 AATTTAATTTCGTATATTTT
1 --TTTAATTTCGTATATTTT
549125 TT
1 TT
549127 ATAAATCATA
Statistics
Matches: 43, Mismatches: 5, Indels: 16
0.67 0.08 0.25
Matches are distributed among these distances:
15 1 0.02
16 8 0.19
17 6 0.14
18 10 0.23
19 6 0.14
20 12 0.28
ACGTcount: A:0.26, C:0.05, G:0.07, T:0.62
Consensus pattern (18 bp):
TTTAATTTCGTATATTTT
Found at i:549103 original size:54 final size:54
Alignment explanation
Indices: 549039--549148 Score: 220
Period size: 54 Copynumber: 2.0 Consensus size: 54
549029 CACGCTTCGC
549039 TTCGGGTATTTTAATTTAATTTCGTATATTTTTTATAAATCATATTATTTTTAT
1 TTCGGGTATTTTAATTTAATTTCGTATATTTTTTATAAATCATATTATTTTTAT
549093 TTCGGGTATTTTAATTTAATTTCGTATATTTTTTATAAATCATATTATTTTTAT
1 TTCGGGTATTTTAATTTAATTTCGTATATTTTTTATAAATCATATTATTTTTAT
549147 TT
1 TT
549149 AAGTTTGTGG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.27, C:0.05, G:0.07, T:0.60
Consensus pattern (54 bp):
TTCGGGTATTTTAATTTAATTTCGTATATTTTTTATAAATCATATTATTTTTAT
Found at i:550498 original size:17 final size:17
Alignment explanation
Indices: 550476--550513 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
550466 TACAAATATA
550476 ATTACAT-ATTTATAAAT
1 ATTACATAATTTAT-AAT
550493 ATTACATAAATTTATAAT
1 ATTACAT-AATTTATAAT
550511 ATT
1 ATT
550514 TTAAATAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.37
18 6 0.32
19 6 0.32
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (17 bp):
ATTACATAATTTATAAT
Found at i:550655 original size:24 final size:24
Alignment explanation
Indices: 550587--550656 Score: 77
Period size: 26 Copynumber: 2.7 Consensus size: 24
550577 AAATATACAT
550587 AAAATAAAATAAATTATTAATATGTCA
1 AAAATAAAA-AAA-TA-TAATATGTCA
* *
550614 AAAATATACAAAAATATAATATTTTA
1 AAAATA-A-AAAAATATAATATGTCA
550640 AAAATAAAAAAATATAA
1 AAAATAAAAAAATATAA
550657 ATACAAACAT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
24 10 0.26
25 1 0.03
26 14 0.36
27 8 0.21
28 4 0.10
29 2 0.05
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (24 bp):
AAAATAAAAAAATATAATATGTCA
Found at i:550708 original size:16 final size:16
Alignment explanation
Indices: 550689--550723 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
550679 ATAATTTTTT
550689 TTTTCTTCTTTCTTTC
1 TTTTCTTCTTTCTTTC
*
550705 TTTTTTTCTTTCTTTC
1 TTTTCTTCTTTCTTTC
550721 TTT
1 TTT
550724 CCCACTACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTCTTCTTTCTTTC
Found at i:550716 original size:4 final size:4
Alignment explanation
Indices: 550690--550724 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
550680 TAATTTTTTT
*
550690 TTTC -TTC TTTC TTTC TTTT TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
550725 CCACTACATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 3 0.11
4 25 0.89
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:550855 original size:20 final size:20
Alignment explanation
Indices: 550823--550932 Score: 77
Period size: 20 Copynumber: 5.4 Consensus size: 20
550813 ATATTATCAT
550823 TATAATAAAAAATAATTAAAA
1 TATAAT-AAAAATAATTAAAA
550844 TATAATAAAAAT-A--AAAA
1 TATAATAAAAATAATTAAAA
* *
550861 TATAATATTAAATACTTTAAAA
1 TATAATA-AAAATA-ATTAAAA
* * *
550883 TTTATATAATATTAATTATAAA
1 TATA-ATAAAAATAATTA-AAA
550905 TAT-ATAAAAAT-ATATATAAA
1 TATAATAAAAATAAT-TA-AAA
550925 TATAATAA
1 TATAATAA
550933 TATTTTAAAT
Statistics
Matches: 70, Mismatches: 10, Indels: 18
0.71 0.10 0.18
Matches are distributed among these distances:
17 11 0.16
18 4 0.06
19 3 0.04
20 21 0.30
21 13 0.19
22 15 0.21
23 3 0.04
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (20 bp):
TATAATAAAAATAATTAAAA
Found at i:550867 original size:11 final size:11
Alignment explanation
Indices: 550823--550856 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
550813 ATATTATCAT
550823 TATAATAAAAA
1 TATAATAAAAA
*
550834 -ATAATTAAAA
1 TATAATAAAAA
550844 TATAATAAAAA
1 TATAATAAAAA
550855 TA
1 TA
550857 AAAATATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
TATAATAAAAA
Found at i:550940 original size:60 final size:58
Alignment explanation
Indices: 550835--550964 Score: 144
Period size: 60 Copynumber: 2.3 Consensus size: 58
550825 TAATAAAAAA
* *
550835 TAATTAAAATATAATAAAAATAAAAATATAATATTAAATACTTTAAAATTTATATAATAT
1 TAATTAAAATATAATAAAAATAAAAATATAATATAAAATACTTT-AAATAT-TATAATAT
* * *
550895 TAATTATAAATAT-ATAAAAATATATATA-AATATAATAATATTTTAAATATTATAATAT
1 TAATTA-AAATATAATAAAAATAAAAATATAATATAA-AATACTTTAAATATTATAATAT
550953 T--TT-AAATATAAT
1 TAATTAAAATATAAT
550965 TATAATTTGA
Statistics
Matches: 62, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
54 6 0.10
55 2 0.03
56 2 0.03
58 9 0.15
59 11 0.18
60 26 0.42
61 6 0.10
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.42
Consensus pattern (58 bp):
TAATTAAAATATAATAAAAATAAAAATATAATATAAAATACTTTAAATATTATAATAT
Found at i:550951 original size:8 final size:9
Alignment explanation
Indices: 550897--550961 Score: 62
Period size: 10 Copynumber: 7.2 Consensus size: 9
550887 TATAATATTA
550897 ATTATAAAT
1 ATTATAAAT
*
550906 ATATAAAAAT
1 AT-TATAAAT
550916 ATATATAAAT
1 AT-TATAAAT
*
550926 ATAAT-AAT
1 ATTATAAAT
*
550934 ATTTTAAAT
1 ATTATAAAT
550943 ATTAT-AAT
1 ATTATAAAT
*
550951 ATTTTAAAT
1 ATTATAAAT
550960 AT
1 AT
550962 AATTATAATT
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
8 13 0.28
9 16 0.35
10 17 0.37
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
ATTATAAAT
Found at i:550980 original size:20 final size:17
Alignment explanation
Indices: 550906--550964 Score: 82
Period size: 17 Copynumber: 3.4 Consensus size: 17
550896 AATTATAAAT
* *
550906 ATATAAAAATATATATAA
1 ATATAATAATAT-TTTAA
550924 ATATAATAATATTTTAA
1 ATATAATAATATTTTAA
*
550941 ATATTATAATATTTTAA
1 ATATAATAATATTTTAA
550958 ATATAAT
1 ATATAAT
550965 TATAATTTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
17 26 0.70
18 11 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATATAATAATATTTTAA
Found at i:552455 original size:21 final size:21
Alignment explanation
Indices: 552409--552456 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
552399 ATATTTAAAA
552409 ATATAATATAAAAATAAATAC
1 ATATAATATAAAAATAAATAC
* * **
552430 GTATAATATAAATATACGTAC
1 ATATAATATAAAAATAAATAC
552451 ATATAA
1 ATATAA
552457 AAATATATAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.58, C:0.06, G:0.04, T:0.31
Consensus pattern (21 bp):
ATATAATATAAAAATAAATAC
Found at i:552509 original size:32 final size:30
Alignment explanation
Indices: 552472--552542 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 30
552462 TATATTAAAT
*
552472 AAAATA-AATTATTAATATATAAAAAATATATA
1 AAAATATAA-TATT-ATAAATAAAAAATA-ATA
*
552504 AAAATATAATATTTTAAATAAAAAATAATA
1 AAAATATAATATTATAAATAAAAAATAATA
*
552534 CAAATATAA
1 AAAATATAA
552543 ACAAATAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 11 0.31
31 12 0.34
32 10 0.29
33 2 0.06
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.32
Consensus pattern (30 bp):
AAAATATAATATTATAAATAAAAAATAATA
Found at i:552540 original size:51 final size:47
Alignment explanation
Indices: 552451--552549 Score: 110
Period size: 51 Copynumber: 2.0 Consensus size: 47
552441 ATATACGTAC
* **
552451 ATATAAAAATATATATTAAATAAAATAAATTATTAATATATAAAAAAT
1 ATATAAAAATATATATTAAATAAAATAAAATACAAATATA-AAAAAAT
*
552499 ATATAAAAATATAATATTTTAAATAAAA-AATAATACAAATATAAACAAAT
1 ATATAAAAATAT-ATA--TTAAATAAAATAA-AATACAAATATAAAAAAAT
552549 A
1 A
552550 AATTTTTTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
48 12 0.28
49 3 0.07
50 9 0.21
51 19 0.44
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (47 bp):
ATATAAAAATATATATTAAATAAAATAAAATACAAATATAAAAAAAT
Found at i:552606 original size:17 final size:18
Alignment explanation
Indices: 552568--552606 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
552558 TCTCTTCTTT
* *
552568 CTTTTGTTCCTTTTTCTT
1 CTTTTGTTCCTTTCTCTC
552586 CTTTT-TTCCTTTCTCTC
1 CTTTTGTTCCTTTCTCTC
552603 CTTT
1 CTTT
552607 CCTTTTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.00, C:0.28, G:0.03, T:0.69
Consensus pattern (18 bp):
CTTTTGTTCCTTTCTCTC
Found at i:552613 original size:22 final size:20
Alignment explanation
Indices: 552556--552614 Score: 61
Period size: 22 Copynumber: 2.9 Consensus size: 20
552546 AATAAATTTT
552556 TTTCTCTTCTTTCTTTTGTTCC
1 TTTCTC-TCTTTCTTTT-TTCC
552578 TTT-T-TC-TTCTTTTTTCC
1 TTTCTCTCTTTCTTTTTTCC
552595 TTTCTCTCCTTTCCTTTTTT
1 TTTCTCT-CTTT-CTTTTTT
552615 TTTCTTTCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
17 7 0.22
18 8 0.25
19 3 0.09
20 1 0.03
21 3 0.09
22 10 0.31
ACGTcount: A:0.00, C:0.27, G:0.02, T:0.71
Consensus pattern (20 bp):
TTTCTCTCTTTCTTTTTTCC
Found at i:554599 original size:19 final size:19
Alignment explanation
Indices: 554575--554623 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 19
554565 AAAACTTCTT
554575 ATTTTAAAAATAATTATTA
1 ATTTTAAAAATAATTATTA
** * * *
554594 ATTTTATTATTTATTATTT
1 ATTTTAAAAATAATTATTA
554613 ATTTTAAAAAT
1 ATTTTAAAAAT
554624 CAAATTAAAA
Statistics
Matches: 22, Mismatches: 8, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTTTAAAAATAATTATTA
Found at i:554953 original size:4 final size:4
Alignment explanation
Indices: 554946--554976 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
554936 ATAAAGTCCT
554946 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTA
554977 TCGTTTCAAC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:555251 original size:24 final size:25
Alignment explanation
Indices: 555202--555256 Score: 78
Period size: 24 Copynumber: 2.2 Consensus size: 25
555192 TCAATAATTT
*
555202 TAAATATAATTACATAAATATAATA
1 TAAAAATAATTACATAAATATAATA
555227 TAAAAATAATTA-A-AATATATAATA
1 TAAAAATAATTACATAA-ATATAATA
555251 TAAAAA
1 TAAAAA
555257 ATATTTTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 2 0.07
24 15 0.54
25 11 0.39
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (25 bp):
TAAAAATAATTACATAAATATAATA
Found at i:555260 original size:14 final size:13
Alignment explanation
Indices: 555203--555260 Score: 57
Period size: 14 Copynumber: 4.5 Consensus size: 13
555193 CAATAATTTT
*
555203 AAATATAATTACAT
1 AAATATAATTA-AA
*
555217 AAATATAA-TATA
1 AAATATAATTAAA
555229 AAA-ATAATTAAA
1 AAATATAATTAAA
*
555241 ATATATAATATAAA
1 AAATATAAT-TAAA
555255 AAATAT
1 AAATAT
555261 TTTATAATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
11 4 0.11
12 8 0.22
13 7 0.19
14 17 0.47
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (13 bp):
AAATATAATTAAA
Found at i:564679 original size:23 final size:23
Alignment explanation
Indices: 564649--564696 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
564639 AGAGTTTCTA
564649 CTTATTTCCTAGAACGGGTAAGC
1 CTTATTTCCTAGAACGGGTAAGC
*
564672 CTTATTTCCTAGACCGGGTAAGC
1 CTTATTTCCTAGAACGGGTAAGC
564695 CT
1 CT
564697 GCGCTATGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.31
Consensus pattern (23 bp):
CTTATTTCCTAGAACGGGTAAGC
Found at i:567608 original size:8 final size:7
Alignment explanation
Indices: 567581--567605 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
567571 CCTTACGTCA
567581 TTTTAAT
1 TTTTAAT
567588 TTTTAAT
1 TTTTAAT
567595 TTTTAAT
1 TTTTAAT
567602 TTTT
1 TTTT
567606 TAAATATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTAAT
Found at i:567782 original size:21 final size:21
Alignment explanation
Indices: 567744--567788 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
567734 AAATTATGAT
* *
567744 TTTTTAAATATATAAAATAAA
1 TTTTTAAAAAAATAAAATAAA
* *
567765 TTTTTAAAAAAATTAAATACA
1 TTTTTAAAAAAATAAAATAAA
567786 TTT
1 TTT
567789 ATATCAAATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
TTTTTAAAAAAATAAAATAAA
Found at i:568248 original size:141 final size:136
Alignment explanation
Indices: 568039--568310 Score: 309
Period size: 141 Copynumber: 2.0 Consensus size: 136
568029 AATTTTTTAT
* *
568039 AATATGAATTAATCTTTATTTATTATTTTTTATTAACCTTGAAGTCCTAATTAATGCATAATTTC
1 AATATGAACTAATCTTTATTTATTATTTTTTAATAACCTTGAAG-CCTAATTAATGCATAATTTC
* * * *
568104 TTAATATTGATATGTATTTTTTATTATTAACTAATTTTTAATTTAAGTTTAT-TTAATGATTTTT
65 TTAATA-TG-TAT-T-TTTATTAATATTAACT-ATTTTTAATCTAAGTTTATATTAATGATTTTC
568168 TTATTAGATGAA
125 TTATTAGATGAA
* ** * *
568180 AATATTAACTAATCTTTATTTATTATTTTCTTAATAATTTTGAAG-CTTATTGAT-C-TAAATTT
1 AATATGAACTAATCTTTATTTATTATTTT-TTAATAACCTTGAAGCCTAATTAATGCAT-AA-TT
* *
568242 TCCTTAATATGTATTTTTATTAATATTAACTATTTTTAATCTAAGTTTCTATTAATTATTTTCTT
63 T-CTTAATATGTATTTTTATTAATATTAACTATTTTTAATCTAAGTTTATATTAATGATTTTCTT
568307 ATTA
127 ATTA
568311 TGTTAAGATT
Statistics
Matches: 113, Mismatches: 13, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
136 17 0.15
137 30 0.27
138 2 0.02
139 6 0.05
140 12 0.11
141 34 0.30
142 12 0.11
ACGTcount: A:0.33, C:0.07, G:0.06, T:0.55
Consensus pattern (136 bp):
AATATGAACTAATCTTTATTTATTATTTTTTAATAACCTTGAAGCCTAATTAATGCATAATTTCT
TAATATGTATTTTTATTAATATTAACTATTTTTAATCTAAGTTTATATTAATGATTTTCTTATTA
GATGAA
Found at i:572654 original size:2 final size:2
Alignment explanation
Indices: 572649--572685 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
572639 ATCCTGGAGG
572649 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
572686 GGTAGAAGGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:573964 original size:2 final size:2
Alignment explanation
Indices: 573957--573982 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
573947 CAAGAGCCTG
573957 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
573983 ACAAGCTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:590815 original size:50 final size:48
Alignment explanation
Indices: 590760--590854 Score: 163
Period size: 50 Copynumber: 1.9 Consensus size: 48
590750 GGAGGGTCGG
590760 AGAAGCTCGTGAGCTTCTTGATGAGATGAGAAGAAGGGGAATCAAACTGA
1 AGAAGCTCGTGAGCTTCTTGATGAGATGAG-A-AAGGGGAATCAAACTGA
*
590810 AGAAGCTCGTTAGCTTCTTGATGAGATGAGAAAGGGGAATCAAAC
1 AGAAGCTCGTGAGCTTCTTGATGAGATGAGAAAGGGGAATCAAAC
590855 CTGATCACAT
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
48 14 0.32
49 1 0.02
50 29 0.66
ACGTcount: A:0.36, C:0.13, G:0.31, T:0.21
Consensus pattern (48 bp):
AGAAGCTCGTGAGCTTCTTGATGAGATGAGAAAGGGGAATCAAACTGA
Found at i:594400 original size:13 final size:14
Alignment explanation
Indices: 594362--594406 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
594352 TTAAGAATAA
594362 TTAATAATTATTTT
1 TTAATAATTATTTT
*
594376 TAAATGAATTATTTT
1 TTAAT-AATTATTTT
594391 TTAA-AATTATATTT
1 TTAATAATTAT-TTT
594405 TT
1 TT
594407 TTAAAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 6 0.22
14 9 0.33
15 12 0.44
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (14 bp):
TTAATAATTATTTT
Found at i:596407 original size:18 final size:20
Alignment explanation
Indices: 596381--596417 Score: 51
Period size: 18 Copynumber: 1.9 Consensus size: 20
596371 ATATATATTA
596381 AAAAATTAT-TAAA-ATATC
1 AAAAATTATATAAATATATC
*
596399 AAAATTTATATAAATATAT
1 AAAAATTATATAAATATAT
596418 AATATTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 8 0.50
19 4 0.25
20 4 0.25
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAAATTATATAAATATATC
Found at i:596493 original size:17 final size:18
Alignment explanation
Indices: 596471--596517 Score: 71
Period size: 17 Copynumber: 2.7 Consensus size: 18
596461 ATATTAATAC
596471 ATAAAAAATTATA-TAAA
1 ATAAAAAATTATAGTAAA
596488 ATAAAAAATTA-AGTAAA
1 ATAAAAAATTATAGTAAA
596505 ATTAAAAAATTAT
1 A-TAAAAAATTAT
596518 CACGTGATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 1 0.04
17 16 0.59
18 10 0.37
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (18 bp):
ATAAAAAATTATAGTAAA
Found at i:597351 original size:25 final size:26
Alignment explanation
Indices: 597323--597378 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 26
597313 TTTTGTTCAT
* * *
597323 TTTATTTTTTATTAATTATTTTA-AA
1 TTTATTTTTTATAAAATATATTATAA
597348 TTTA-TTTTTATAAAATATATTATAA
1 TTTATTTTTTATAAAATATATTATAA
597373 TTTATT
1 TTTATT
597379 AATAGATATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
24 15 0.58
25 10 0.38
26 1 0.04
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (26 bp):
TTTATTTTTTATAAAATATATTATAA
Found at i:598298 original size:2 final size:2
Alignment explanation
Indices: 598291--598318 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
598281 ATGAATTAAA
598291 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
598319 TCTATCGACA
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:599139 original size:14 final size:14
Alignment explanation
Indices: 599122--599151 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
599112 TTTTAAAAAA
599122 TAAAATTTAATATT
1 TAAAATTTAATATT
*
599136 TAAATTTTAATATT
1 TAAAATTTAATATT
599150 TA
1 TA
599152 TATATATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TAAAATTTAATATT
Found at i:599967 original size:2 final size:2
Alignment explanation
Indices: 599960--600000 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
599950 AGGATTATGA
599960 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
600001 AGCTCCTTCG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.