Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold168
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: 2098754
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
File 5 of 16
Found at i:487397 original size:5 final size:5
Alignment explanation
Indices: 487382--487430 Score: 62
Period size: 5 Copynumber: 9.4 Consensus size: 5
487372 ATAAATAATT
* *
487382 AATATA AATAA AATAA AATAA AATAA AATAA TAATAT AATTA AATAA AA
1 AATA-A AATAA AATAA AATAA AATAA AATAA -AATAA AATAA AATAA AA
487431 AATTAATTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
5 30 0.79
6 8 0.21
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (5 bp):
AATAA
Found at i:487437 original size:21 final size:20
Alignment explanation
Indices: 487372--487433 Score: 65
Period size: 21 Copynumber: 3.1 Consensus size: 20
487362 TTTATTAATT
*
487372 ATAA-ATAATTAATATAAATA
1 ATAATATAATTAA-ATAAAAA
* *
487392 A-AATAAAATAAAATAAAATA
1 ATAATATAATTAAATAAAA-A
487412 ATAATATAATTAAATAAAAA
1 ATAATATAATTAAATAAAAA
487432 AT
1 AT
487434 TAATTTTTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
19 7 0.21
20 12 0.35
21 15 0.44
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (20 bp):
ATAATATAATTAAATAAAAA
Found at i:487850 original size:16 final size:15
Alignment explanation
Indices: 487780--487865 Score: 57
Period size: 16 Copynumber: 5.4 Consensus size: 15
487770 ATAATATTAT
487780 TTTAAATATTATATAA
1 TTTAAATATTA-ATAA
** *
487796 AATAAATTATTAATTTA
1 TTTAAA-TATTAA-TAA
*
487813 TTAAAAT-TTATATAAA
1 TTTAAATATTA-AT-AA
*
487829 TATAAATATGTAATAA
1 TTTAAATAT-TAATAA
*
487845 TTTAAATATTAATTA
1 TTTAAATATTAATAA
487860 TTTAAA
1 TTTAAA
487866 AAATTTATTA
Statistics
Matches: 53, Mismatches: 11, Indels: 13
0.69 0.14 0.17
Matches are distributed among these distances:
15 15 0.28
16 23 0.43
17 13 0.25
18 2 0.04
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (15 bp):
TTTAAATATTAATAA
Found at i:487850 original size:33 final size:32
Alignment explanation
Indices: 487764--487855 Score: 82
Period size: 33 Copynumber: 2.8 Consensus size: 32
487754 AAATTAATTA
*
487764 AAATATATAATATTATTTTAAATATTATATAAAAT
1 AAATAT-TAATA--ATTTAAAATATTATATAAAAT
*
487799 AAATTATTAAT-TTATTAAAAT-TTATATAAATAT
1 AAA-TATTAATAAT-TTAAAATATTATATAAA-AT
487832 AAATATGTAATAATTT-AAATATTA
1 AAATAT-TAATAATTTAAAATATTA
487856 ATTATTTAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 14
0.74 0.05 0.22
Matches are distributed among these distances:
32 17 0.35
33 20 0.42
34 1 0.02
35 7 0.15
36 3 0.06
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (32 bp):
AAATATTAATAATTTAAAATATTATATAAAAT
Found at i:487862 original size:15 final size:16
Alignment explanation
Indices: 487831--487865 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
487821 TATATAAATA
487831 TAAATATGTAATAATT
1 TAAATATGTAATAATT
*
487847 TAAATAT-TAATTATT
1 TAAATATGTAATAATT
487862 TAAA
1 TAAA
487866 AAATTTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (16 bp):
TAAATATGTAATAATT
Found at i:487998 original size:36 final size:36
Alignment explanation
Indices: 487908--488033 Score: 96
Period size: 36 Copynumber: 3.3 Consensus size: 36
487898 TAATATAAAC
487908 AAATATTTTTATTTATAAA-TTAAATTATTTATTCAATTTAA
1 AAATATTTTTA--TATAAATTTAAATTA---ATTCAATTT-A
**
487949 TATAATAAATTTATATAAATTTAAATTAATTCAATTTA
1 -A-AATATTTTTATATAAATTTAAATTAATTCAATTTA
* **
487987 AAATATTTTTATTTAAATTT-AATT-ATAAAATATATA
1 AAATATTTTTATATAAATTTAAATTAATTCAAT-T-TA
488023 AAATATTTTTA
1 AAATATTTTTA
488034 AAATTTTTAT
Statistics
Matches: 73, Mismatches: 7, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
34 5 0.07
35 5 0.07
36 29 0.40
37 1 0.01
38 1 0.01
39 9 0.12
41 6 0.08
42 9 0.12
43 8 0.11
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (36 bp):
AAATATTTTTATATAAATTTAAATTAATTCAATTTA
Found at i:489566 original size:15 final size:16
Alignment explanation
Indices: 489548--489606 Score: 57
Period size: 17 Copynumber: 3.6 Consensus size: 16
489538 AAAATTTAAT
489548 AATATAAATTAATA-A
1 AATATAAATTAATATA
*
489563 AATATTAAATTTTATATA
1 AATA-TAAA-TTAATATA
**
489581 AATATATTTTAAATATA
1 AATATAAATT-AATATA
489598 AATATAAAT
1 AATATAAAT
489607 ATGTATGAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
15 4 0.12
16 6 0.18
17 19 0.56
18 5 0.15
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AATATAAATTAATATA
Found at i:489620 original size:23 final size:24
Alignment explanation
Indices: 489576--489625 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
489566 ATTAAATTTT
* *
489576 ATATAAATATATTTTAAATATA-A
1 ATATAAATATATATGAAATATATA
* *
489599 ATATAAATATGTATGAATTATATA
1 ATATAAATATATATGAAATATATA
489623 ATA
1 ATA
489626 ATTGTTAGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
23 18 0.82
24 4 0.18
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (24 bp):
ATATAAATATATATGAAATATATA
Found at i:490178 original size:17 final size:17
Alignment explanation
Indices: 490138--490179 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
490128 TAAAAATAAT
*
490138 TATATTGATATTAAATA
1 TATATTTATATTAAATA
**
490155 TATATTTATATTTTATA
1 TATATTTATATTAAATA
490172 TATATTTA
1 TATATTTA
490180 AATAATATAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
TATATTTATATTAAATA
Found at i:492485 original size:21 final size:22
Alignment explanation
Indices: 492434--492493 Score: 54
Period size: 21 Copynumber: 2.8 Consensus size: 22
492424 TTATTTAAAA
* *
492434 AATATTAAAAAATATTTTTATGT
1 AATA-TAAAAATTATTTATATGT
*
492457 AA-AAAAAAATTATTTATAT-T
1 AATATAAAAATTATTTATATGT
492477 AATAT-AAAATTAATTTA
1 AATATAAAAATT-ATTTA
492494 ATTTTATATA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
20 9 0.29
21 19 0.61
22 1 0.03
23 2 0.06
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
AATATAAAAATTATTTATATGT
Found at i:494245 original size:33 final size:32
Alignment explanation
Indices: 494115--494245 Score: 78
Period size: 33 Copynumber: 4.2 Consensus size: 32
494105 AGTATAAGGG
494115 TAAATATATCAATTCAAAAGATAAAGATAATTT
1 TAAATATATCAATT-AAAAGATAAAGATAATTT
* * * *
494148 TAAACCAT-TTACTTAAATAGA-AAATA-AATTT
1 TAAA-TATATCAATTAAA-AGATAAAGATAATTT
* * * ***
494179 ATAAAT-TAT--ATT-TAATATAAATATAAGGG
1 -TAAATATATCAATTAAAAGATAAAGATAATTT
494208 TAAATATATCAATTCAAAAGATAAAGATAATTT
1 TAAATATATCAATT-AAAAGATAAAGATAATTT
494241 TAAAT
1 TAAAT
494246 CTTAAAATTT
Statistics
Matches: 70, Mismatches: 17, Indels: 22
0.64 0.16 0.20
Matches are distributed among these distances:
27 2 0.03
28 11 0.16
29 7 0.10
30 1 0.01
31 9 0.13
32 11 0.16
33 27 0.39
34 2 0.03
ACGTcount: A:0.53, C:0.05, G:0.06, T:0.35
Consensus pattern (32 bp):
TAAATATATCAATTAAAAGATAAAGATAATTT
Found at i:494407 original size:226 final size:226
Alignment explanation
Indices: 494013--494427 Score: 803
Period size: 226 Copynumber: 1.8 Consensus size: 226
494003 CAAATATGAA
494013 TTTAAATCTTAAAATTTTTTTGGATCTTAAGATTTGTGACCAAATTTACTCTTAAATTAAAATAT
1 TTTAAATCTTAAAATTTTTTTGGATCTTAAGATTTGTGACCAAATTTACTCTTAAATTAAAATAT
*
494078 TTATGGCAAGTTTATTTTAAAATTAAAAGTATAAGGGTAAATATATCAATTCAAAAGATAAAGAT
66 TTATGACAAGTTTATTTTAAAATTAAAAGTATAAGGGTAAATATATCAATTCAAAAGATAAAGAT
*
494143 AATTTTAAACCATTTACTTAAATAGAAAATAAATTTATAAATTATATTTAATATAAATATAAGGG
131 AATTTTAAACCATTTACTTAAATAGAAAATAAATTTATAAATTATATTTAATAAAAATATAAGGG
494208 TAAATATATCAATTCAAAAGATAAAGATAAT
196 TAAATATATCAATTCAAAAGATAAAGATAAT
494239 TTTAAATCTTAAAATTTTTTTGGATCTTAAGATTTGTGACCAAATTTACTCTTAAATTAAAATAT
1 TTTAAATCTTAAAATTTTTTTGGATCTTAAGATTTGTGACCAAATTTACTCTTAAATTAAAATAT
494304 TTATGACAAGTTTATTTTAAAATTAAAAGTATAAGGGTAAATATATCAATTCAAAAGATAAAGAT
66 TTATGACAAGTTTATTTTAAAATTAAAAGTATAAGGGTAAATATATCAATTCAAAAGATAAAGAT
*
494369 AATTTTAAACCATTTGCTTAAATAGAAAATAAATTTATAAATTATATTTAATAAAAATA
131 AATTTTAAACCATTTACTTAAATAGAAAATAAATTTATAAATTATATTTAATAAAAATA
494428 ATCCTTGATT
Statistics
Matches: 186, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
226 186 1.00
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.39
Consensus pattern (226 bp):
TTTAAATCTTAAAATTTTTTTGGATCTTAAGATTTGTGACCAAATTTACTCTTAAATTAAAATAT
TTATGACAAGTTTATTTTAAAATTAAAAGTATAAGGGTAAATATATCAATTCAAAAGATAAAGAT
AATTTTAAACCATTTACTTAAATAGAAAATAAATTTATAAATTATATTTAATAAAAATATAAGGG
TAAATATATCAATTCAAAAGATAAAGATAAT
Found at i:494639 original size:22 final size:21
Alignment explanation
Indices: 494608--494654 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
494598 ATAATATTAA
494608 AAATTT-TAT-TTTTAT-ATT
1 AAATTTATATATTTTATAATT
494626 AATATTTATATATTTTATAATT
1 AA-ATTTATATATTTTATAATT
494648 AAATTTA
1 AAATTTA
494655 AATAAAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 2 0.08
19 4 0.16
20 3 0.12
21 11 0.44
22 5 0.20
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
AAATTTATATATTTTATAATT
Found at i:494692 original size:20 final size:20
Alignment explanation
Indices: 494651--494691 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
494641 TATAATTAAA
494651 TTTAAATAAAATATATATTT
1 TTTAAATAAAATATATATTT
*
494671 TTTAATTAAAAT-T-TATTT
1 TTTAAATAAAATATATATTT
494689 TTT
1 TTT
494692 TGGATCTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
19 1 0.05
20 11 0.55
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTAAATAAAATATATATTT
Found at i:495348 original size:73 final size:74
Alignment explanation
Indices: 495153--495445 Score: 435
Period size: 74 Copynumber: 4.0 Consensus size: 74
495143 TTGCTTCACA
* *
495153 ATTAATGGGGCTTTAGAATAGCCAATGAATTGATTGAAAGTGTTTATTACTATAAAGAGATAAAT
1 ATTAATGGGGCTTTAGAAAAGCCAATGAATTGATTGAAAGTGTTTATTACTATAAAAAGATAAAT
*
495218 AAAATTATT
66 AAAATTATG
* *
495227 ATTAATGGGGCTTTAGAAAAAGCCAATGAATTAATTGGAAGTGTTTATTACTATAAAAAGATAAA
1 ATTAATGGGGCTTTAG-AAAAGCCAATGAATTGATTGAAAGTGTTTATTACTATAAAAAGATAAA
495292 -AAAATTATG
65 TAAAATTATG
* * * *
495301 ATAAATGGGGTTTTAGAAAAGCCAATGAATTGATTGGAAGTGCTTATTACTATAAAAAGATAAAT
1 ATTAATGGGGCTTTAGAAAAGCCAATGAATTGATTGAAAGTGTTTATTACTATAAAAAGATAAAT
495366 AAAATTATG
66 AAAATTATG
* * ** * *
495375 ATTAATGGGGTTTTAGGAAAGTTAATGAATTGATTGAAAATGTTTATTATTATAAAAAGATAAAT
1 ATTAATGGGGCTTTAGAAAAGCCAATGAATTGATTGAAAGTGTTTATTACTATAAAAAGATAAAT
495440 AAAATT
66 AAAATT
495446 TTGTGTAAAA
Statistics
Matches: 200, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
73 46 0.23
74 110 0.55
75 44 0.22
ACGTcount: A:0.44, C:0.04, G:0.18, T:0.34
Consensus pattern (74 bp):
ATTAATGGGGCTTTAGAAAAGCCAATGAATTGATTGAAAGTGTTTATTACTATAAAAAGATAAAT
AAAATTATG
Found at i:495642 original size:2 final size:2
Alignment explanation
Indices: 495635--495680 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
495625 AACACTTGAT
* * *
495635 TA TA TA TA TA TA TA TA -A TT TA TA TA TA TG TA TA TA TA TC TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
495676 TA TA T
1 TA TA T
495681 CACACTTTCA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:502846 original size:18 final size:18
Alignment explanation
Indices: 502825--502920 Score: 54
Period size: 18 Copynumber: 5.2 Consensus size: 18
502815 TATTTTAAAT
*
502825 TATTTAAAAATATTTTTA
1 TATTTAAAAATATATTTA
**
502843 TA-TTAATATTTATAATTTA
1 TATTTAA-AAATAT-ATTTA
* *
502862 -ATTTAAATAAAATTTTTAA
1 TATTTAAA-AATATATTT-A
502881 TATTTAAATAATA-ATTTA
1 TATTTAAA-AATATATTTA
* *
502899 AATTTAAAATATATATATA
1 TATTTAAAA-ATATATTTA
502918 TAT
1 TAT
502921 ATTCAAGTTT
Statistics
Matches: 58, Mismatches: 12, Indels: 15
0.68 0.14 0.18
Matches are distributed among these distances:
17 5 0.09
18 22 0.38
19 20 0.34
20 11 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TATTTAAAAATATATTTA
Found at i:502847 original size:31 final size:31
Alignment explanation
Indices: 502783--502884 Score: 75
Period size: 31 Copynumber: 3.1 Consensus size: 31
502773 TTGGCATATA
* *
502783 ATTATTTT-GATTAGTTT-AAAAT-TTTATTTT
1 ATTATTTTAAATTA-TTTAAAAATATTT-TTAT
502813 ATTATTTTAAATTATTTAAAAATATTTTTAT
1 ATTATTTTAAATTATTTAAAAATATTTTTAT
*
502844 ATTAATATTTATAATTTAATTTAAATAAAATTTTTAAT
1 ATT-AT-TTTA-AA-TT-ATTTAAA-AATATTTTT-AT
502882 ATT
1 ATT
502885 TAAATAATAA
Statistics
Matches: 59, Mismatches: 3, Indels: 12
0.80 0.04 0.16
Matches are distributed among these distances:
30 11 0.19
31 15 0.25
32 5 0.08
33 4 0.07
34 2 0.03
35 2 0.03
36 7 0.12
37 8 0.14
38 5 0.08
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (31 bp):
ATTATTTTAAATTATTTAAAAATATTTTTAT
Found at i:502853 original size:34 final size:37
Alignment explanation
Indices: 502799--502884 Score: 99
Period size: 34 Copynumber: 2.4 Consensus size: 37
502789 TTGATTAGTT
* *
502799 TAAAA-TTTTATTTTATTATTT-TAAATT-ATTTAAA
1 TAAAATTTTTATATTAATATTTATAAATTAATTTAAA
* *
502833 -AATATTTTTATATTAATATTTATAATTTAATTTAAA
1 TAAAATTTTTATATTAATATTTATAAATTAATTTAAA
502869 TAAAATTTTTAATATT
1 TAAAATTTTT-ATATT
502885 TAAATAATAA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
33 3 0.07
34 14 0.33
35 5 0.12
36 7 0.17
37 8 0.19
38 5 0.12
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (37 bp):
TAAAATTTTTATATTAATATTTATAAATTAATTTAAA
Found at i:502909 original size:19 final size:18
Alignment explanation
Indices: 502854--502906 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
502844 ATTAATATTT
502854 ATAATTT-AATTTAAATA
1 ATAATTTAAATTTAAATA
502871 A-AATTTTTAATATTTAAATA
1 ATAA--TTTAA-ATTTAAATA
502891 ATAATTTAAATTTAAA
1 ATAATTTAAATTTAAA
502907 ATATATATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
16 2 0.06
17 1 0.03
18 10 0.32
19 6 0.19
20 10 0.32
21 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATAATTTAAATTTAAATA
Found at i:503868 original size:18 final size:18
Alignment explanation
Indices: 503819--503894 Score: 60
Period size: 16 Copynumber: 4.6 Consensus size: 18
503809 AAAAACACAT
*
503819 TATAAATAT-ATATTTTA
1 TATAAATATAAAATTTTA
503836 TAT-AATAT-AAA--TTA
1 TATAAATATAAAATTTTA
*
503850 T-TAATATATCAAATTTTA
1 TATAA-ATATAAAATTTTA
*
503868 TATAAATATAAAATATT-
1 TATAAATATAAAATTTTA
503885 T-TAAATATAA
1 TATAAATATAA
503895 TTATAATTTA
Statistics
Matches: 50, Mismatches: 3, Indels: 13
0.76 0.05 0.20
Matches are distributed among these distances:
13 1 0.02
14 5 0.10
15 4 0.08
16 19 0.38
17 4 0.08
18 14 0.28
19 3 0.06
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (18 bp):
TATAAATATAAAATTTTA
Found at i:504256 original size:16 final size:15
Alignment explanation
Indices: 504231--504265 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
504221 TCAGTACAGA
*
504231 TCTCATCTTCTCGATC
1 TCTCACCTTCTC-ATC
504247 TCTCACCTTCTCATC
1 TCTCACCTTCTCATC
504262 TCTC
1 TCTC
504266 TCTCTTTCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.11, C:0.43, G:0.03, T:0.43
Consensus pattern (15 bp):
TCTCACCTTCTCATC
Found at i:510485 original size:25 final size:25
Alignment explanation
Indices: 510470--510522 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
510460 ATATATATAT
510470 ATATAATTTAAATATAAATAAAAAA
1 ATATAATTTAAATATAAATAAAAAA
*
510495 ATATAATTTTTAAATA-ATATAAAAAA
1 ATATAA--TTTAAATATAAATAAAAAA
510521 AT
1 AT
510523 TTTAAAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 6 0.24
26 11 0.44
27 8 0.32
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (25 bp):
ATATAATTTAAATATAAATAAAAAA
Found at i:510704 original size:34 final size:34
Alignment explanation
Indices: 510640--510822 Score: 269
Period size: 34 Copynumber: 5.4 Consensus size: 34
510630 GGGTAGCAAC
* *
510640 TGTTGATTAAAT-GGTGATTTGGTAGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* *
510673 TGTTGACTAAATGGGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
510707 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
510741 TGTTGATTAAATGGGTGATTTGGTGGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
510775 TGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
510809 TGTTGATTAAATGG
1 TGTTGATTAAATGG
510823 TGGTTTTTAC
Statistics
Matches: 134, Mismatches: 15, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
33 11 0.08
34 123 0.92
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:510815 original size:102 final size:101
Alignment explanation
Indices: 510640--510822 Score: 321
Period size: 102 Copynumber: 1.8 Consensus size: 101
510630 GGGTAGCAAC
510640 TGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1 TGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
510705 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
66 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * * *
510741 TGTTGATTAAATGGGTGATTTGGTGGTTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTTGC
1 TGTTGATTAAAT-GGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTAC
510806 CATTGTTGATTAAATGG
65 CATTGTTGATTAAATGG
510823 TGGTTTTTAC
Statistics
Matches: 77, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
101 12 0.16
102 65 0.84
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (101 bp):
TGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:511183 original size:19 final size:19
Alignment explanation
Indices: 511127--511189 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
511117 TGGTTGTCGA
**
511127 GGTACTATTCACGTATATA
1 GGTACTATTCACGTATACG
511146 GGTACTATTCACGTATACG
1 GGTACTATTCACGTATACG
*
511165 GGTACTATTCAAGTATACG
1 GGTACTATTCACGTATACG
*
511184 GTTACT
1 GGTACT
511190 GTACACGTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (19 bp):
GGTACTATTCACGTATACG
Found at i:515321 original size:34 final size:34
Alignment explanation
Indices: 515255--515439 Score: 264
Period size: 34 Copynumber: 5.5 Consensus size: 34
515245 AAGTGGGAGA
* *
515255 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
515288 ATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
515322 ATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
515356 ATTGTTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
515390 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
515424 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
515440 TGGTTTTTAC
Statistics
Matches: 134, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
33 13 0.10
34 121 0.90
ACGTcount: A:0.25, C:0.08, G:0.28, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:515430 original size:102 final size:101
Alignment explanation
Indices: 515255--515439 Score: 325
Period size: 102 Copynumber: 1.8 Consensus size: 101
515245 AAGTGGGAGA
515255 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTA
1 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTA
515320 CCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
66 CCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
* * *
515356 ATTGTTGATTAAATGGGTGATTTGGTGGTTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTT
1 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTT
*
515421 GCCATTGTTGATTAAATGG
65 ACCATTGTTGATTAAATGG
515440 TGGTTTTTAC
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
101 14 0.18
102 65 0.82
ACGTcount: A:0.25, C:0.08, G:0.28, T:0.40
Consensus pattern (101 bp):
ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTA
CCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
Found at i:519619 original size:27 final size:28
Alignment explanation
Indices: 519595--519672 Score: 88
Period size: 27 Copynumber: 2.8 Consensus size: 28
519585 ATTCATATTA
519595 ATTTAAAAAATTTATATATTTATATCAT
1 ATTTAAAAAATTTATATATTTATATCAT
**
519623 ATTT-ATTAATTT-TATATTATATATCAT
1 ATTTAAAAAATTTATATATT-TATATCAT
* *
519650 ATTTAAAATAATATATAAATTTA
1 ATTTAAAA-AATTTATATATTTA
519673 AACACATTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
26 6 0.15
27 18 0.45
28 5 0.12
29 6 0.15
30 5 0.12
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (28 bp):
ATTTAAAAAATTTATATATTTATATCAT
Found at i:519854 original size:18 final size:18
Alignment explanation
Indices: 519831--519899 Score: 63
Period size: 18 Copynumber: 3.9 Consensus size: 18
519821 TTAATAATAA
519831 TTTAATATAAAAATAAAT
1 TTTAATATAAAAATAAAT
** *
519849 TTTAATATTTAAATAATT
1 TTTAATATAAAAATAAAT
*
519867 TTTAA-A-AAAAAT-TAT
1 TTTAATATAAAAATAAAT
*
519882 TTTAAATATTAAAATAAA
1 TTT-AATATAAAAATAAA
519900 CTAAAAAAAT
Statistics
Matches: 38, Mismatches: 9, Indels: 7
0.70 0.17 0.13
Matches are distributed among these distances:
15 4 0.11
16 6 0.16
17 2 0.05
18 25 0.66
19 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TTTAATATAAAAATAAAT
Found at i:519877 original size:34 final size:36
Alignment explanation
Indices: 519814--519898 Score: 90
Period size: 34 Copynumber: 2.4 Consensus size: 36
519804 AATATTTTTA
519814 TTTAA-ATTT-AATAATAATTTAATATAAAAATAAAT
1 TTTAATATTTAAATAATAATTTAATATAAAAAT-AAT
* *
519849 TTTAATATTTAAATAAT-TTTTAA-A-AAAAATTAT
1 TTTAATATTTAAATAATAATTTAATATAAAAATAAT
*
519882 TTTAAATATTAAAATAA
1 TTT-AATATTTAAATAA
519899 ACTAAAAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
33 5 0.11
34 18 0.41
35 6 0.14
36 9 0.20
37 6 0.14
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (36 bp):
TTTAATATTTAAATAATAATTTAATATAAAAATAAT
Found at i:520789 original size:2 final size:2
Alignment explanation
Indices: 520782--520857 Score: 143
Period size: 2 Copynumber: 38.0 Consensus size: 2
520772 TATTTTTGTT
*
520782 TC TC TC TC TC TC TC TC TC TC GC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
520824 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
520858 ACCTTAATTA
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.00, C:0.50, G:0.01, T:0.49
Consensus pattern (2 bp):
TC
Found at i:528147 original size:20 final size:20
Alignment explanation
Indices: 528122--528165 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
528112 AATTTAAATC
528122 AACTCAAATCAAATTTATAA
1 AACTCAAATCAAATTTATAA
528142 AACTCAAATCAAATTTATAA
1 AACTCAAATCAAATTTATAA
528162 AACT
1 AACT
528166 TCGTGACTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.30
Consensus pattern (20 bp):
AACTCAAATCAAATTTATAA
Found at i:528326 original size:25 final size:25
Alignment explanation
Indices: 528295--528346 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
528285 ATTCGAAATT
*
528295 AAATTTATAAAATATTATTAATTAA
1 AAATTTATAAAATACTATTAATTAA
528320 AAATTTATAAAATACTATTAATTAA
1 AAATTTATAAAATACTATTAATTAA
528345 AA
1 AA
528347 GTGATTGCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (25 bp):
AAATTTATAAAATACTATTAATTAA
Found at i:529061 original size:5 final size:5
Alignment explanation
Indices: 529051--529080 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
529041 CTATATATAA
*
529051 ATATT ATATT ATTTT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT
529081 TTGGAAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (5 bp):
ATATT
Found at i:534092 original size:21 final size:22
Alignment explanation
Indices: 534066--534111 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
534056 TAGGATCATA
*
534066 TTAAATTAATTTAATA-CTAAT
1 TTAAATTAACTTAATATCTAAT
*
534087 TTAAATTAACTTAATATTTAAT
1 TTAAATTAACTTAATATCTAAT
534109 TTA
1 TTA
534112 TAAATAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (22 bp):
TTAAATTAACTTAATATCTAAT
Found at i:534139 original size:24 final size:23
Alignment explanation
Indices: 534066--534145 Score: 67
Period size: 24 Copynumber: 3.4 Consensus size: 23
534056 TAGGATCATA
* *
534066 TTAAATTAATTTAATA-CTAA-T
1 TTAAATAAATTTAATATTTAATT
* *
534087 TTAAATTAACTTAATATTTAATT
1 TTAAATAAATTTAATATTTAATT
534110 TATAAATAAATTTATATATTT-ATT
1 T-TAAATAAATTTA-ATATTTAATT
534134 ATTAAATCAAAT
1 -TTAAAT-AAAT
534146 CAAATTTGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
21 15 0.31
22 3 0.06
23 2 0.04
24 18 0.37
25 11 0.22
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (23 bp):
TTAAATAAATTTAATATTTAATT
Found at i:534744 original size:20 final size:20
Alignment explanation
Indices: 534719--534765 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
534709 TATTTATATA
*
534719 ATAAAAAATTAAAT-TTAATT
1 ATAAAAAATAAAATATTAA-T
*
534739 ATAAAATATAAAATATTAAT
1 ATAAAAAATAAAATATTAAT
534759 ATAAAAA
1 ATAAAAA
534766 TAATTTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
ATAAAAAATAAAATATTAAT
Found at i:534799 original size:18 final size:18
Alignment explanation
Indices: 534773--534813 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
534763 AAATAATTTT
534773 TTTAAATA-TAAATATAAA
1 TTTAAATATTAAAT-TAAA
*
534791 TTTATATATTAAATTAAA
1 TTTAAATATTAAATTAAA
534809 TTTAA
1 TTTAA
534814 TAAAAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TTTAAATATTAAATTAAA
Found at i:539589 original size:11 final size:10
Alignment explanation
Indices: 539571--539616 Score: 51
Period size: 11 Copynumber: 4.6 Consensus size: 10
539561 TAAAATATTT
*
539571 TAAATATAAT
1 TAAATATAAA
539581 TATAATATAAA
1 TA-AATATAAA
539592 TAAATAT--A
1 TAAATATAAA
539600 TAAATATAAAA
1 TAAATAT-AAA
539611 TAAATA
1 TAAATA
539617 CATAAATCAT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
8 8 0.26
10 7 0.23
11 16 0.52
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (10 bp):
TAAATATAAA
Found at i:539630 original size:27 final size:27
Alignment explanation
Indices: 539557--539638 Score: 78
Period size: 27 Copynumber: 3.0 Consensus size: 27
539547 AATTTGTATA
* * *
539557 AATATAAA-ATATTTTAAATATAATTAT
1 AATATAAATAAATATTAAATATAA-AAT
539584 AATATAAATAAATATATAAATATAAAAT
1 AATATAAATAAATAT-TAAATATAAAAT
* *
539612 AA-ATACATAAATCATTAAATCTAAAAT
1 AATATAAATAAAT-ATTAAATATAAAAT
539639 GAATTTGGGT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
27 28 0.60
28 10 0.21
29 9 0.19
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (27 bp):
AATATAAATAAATATTAAATATAAAAT
Found at i:540402 original size:13 final size:13
Alignment explanation
Indices: 540384--540417 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
540374 AATTAAAATT
*
540384 TTAATTAATTTAA
1 TTAATTAATTAAA
*
540397 TTAATTGATTAAA
1 TTAATTAATTAAA
540410 TTAATTAA
1 TTAATTAA
540418 AATAATTTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (13 bp):
TTAATTAATTAAA
Found at i:544869 original size:30 final size:30
Alignment explanation
Indices: 544835--544902 Score: 127
Period size: 30 Copynumber: 2.3 Consensus size: 30
544825 GACGTAAATA
544835 GGGAGACCTGCTCCTGCTTCTACGATTTCT
1 GGGAGACCTGCTCCTGCTTCTACGATTTCT
544865 GGGAGACCTGCTCCTGCTTCTACGATTTCT
1 GGGAGACCTGCTCCTGCTTCTACGATTTCT
*
544895 AGGAGACC
1 GGGAGACC
544903 AGCTGAAACA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.16, C:0.29, G:0.25, T:0.29
Consensus pattern (30 bp):
GGGAGACCTGCTCCTGCTTCTACGATTTCT
Found at i:547178 original size:24 final size:24
Alignment explanation
Indices: 547137--547201 Score: 78
Period size: 24 Copynumber: 2.7 Consensus size: 24
547127 TGAAAAAACA
* *
547137 GTAGAGGTGGAAGGTGGAGGAGATG
1 GTAGAGGTGG-TGGTGGAGAAGATG
547162 GTAGA-GTAGGTGGTGGAGAAGATG
1 GTAGAGGT-GGTGGTGGAGAAGATG
*
547186 GTGGAGGTGGTGGTGG
1 GTAGAGGTGGTGGTGG
547202 TGGAAGGGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
24 26 0.74
25 9 0.26
ACGTcount: A:0.23, C:0.00, G:0.57, T:0.20
Consensus pattern (24 bp):
GTAGAGGTGGTGGTGGAGAAGATG
Found at i:547187 original size:12 final size:12
Alignment explanation
Indices: 547149--547191 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
547139 AGAGGTGGAA
*
547149 GGTGGAGGAGAT
1 GGTGGAGAAGAT
* * *
547161 GGTAGAGTAGGT
1 GGTGGAGAAGAT
547173 GGTGGAGAAGAT
1 GGTGGAGAAGAT
547185 GGTGGAG
1 GGTGGAG
547192 GTGGTGGTGG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.26, C:0.00, G:0.56, T:0.19
Consensus pattern (12 bp):
GGTGGAGAAGAT
Found at i:549063 original size:15 final size:17
Alignment explanation
Indices: 549035--549066 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
549025 TAATTTTATT
549035 TATATTTAATTATAAAA
1 TATATTTAATTATAAAA
549052 TATA-TTAA-TATAAAA
1 TATATTTAATTATAAAA
549067 ATAATATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 4 0.27
17 4 0.27
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TATATTTAATTATAAAA
Found at i:549091 original size:19 final size:18
Alignment explanation
Indices: 549043--549091 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
549033 TTTATATTTA
549043 ATTATAAAATATATTAAT
1 ATTATAAAATATATTAAT
* * *
549061 ATAAAAATAATATTTTAAT
1 ATTATAA-AATATATTAAT
549080 ATTTATAAAATA
1 A-TTATAAAATA
549092 ATAAAATAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
18 5 0.21
19 15 0.62
20 4 0.17
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATTATAAAATATATTAAT
Found at i:549266 original size:18 final size:19
Alignment explanation
Indices: 549202--549268 Score: 54
Period size: 17 Copynumber: 3.7 Consensus size: 19
549192 TAAATAAAAA
549202 TTATTAATTTAAA-TAATT
1 TTATTAATTTAAATTAATT
* *
549220 TAATTAAATTAAAATTTAA-T
1 TTATT-AATTTAAA-TTAATT
*
549240 TTA--ATTTTAAATTAATT
1 TTATTAATTTAAATTAATT
549257 TTATT-ATTTAAA
1 TTATTAATTTAAA
549269 GGATTAAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
16 4 0.11
17 10 0.27
18 10 0.27
19 7 0.19
20 3 0.08
21 3 0.08
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TTATTAATTTAAATTAATT
Found at i:549575 original size:19 final size:20
Alignment explanation
Indices: 549553--549590 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
549543 AAAATATATT
*
549553 ATTT-TTAAAATATTAAATA
1 ATTTATTAAAATATAAAATA
549572 ATTTATTAAAATATAAAAT
1 ATTTATTAAAATATAAAAT
549591 TAAAAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTTATTAAAATATAAAATA
Found at i:550966 original size:291 final size:291
Alignment explanation
Indices: 550442--551021 Score: 1040
Period size: 291 Copynumber: 2.0 Consensus size: 291
550432 TTTTAAAAAT
*
550442 TGATGTATTCTTTATTAAATTGCATTTCTTTCGGGTTTCAAAGCATGAAGTGGGAGAATCGCGCT
1 TGATGTATTCTTTATTAAATTGCATTTCTTTCGGGTTTCAAAGCATGAAGTGGGAGAATCGCACT
*
550507 GTATTATCGGTGGGGTTTTATTTGATCTAAAATGTAGTTAGGTCCATTTCAGAAAACTTTTTTTT
66 GTATTATCGGTGGGGTTTTATTTGATCTAAAATGCAGTTAGGTCCATTTCAGAAAACTTTTTTTT
*
550572 CTTTTTTTTGTTGTAGTTTCTGTAAACATTGCTTCAATTTTGATAGCGGAATTAAAATTTGGAAA
131 CTTTTTTTTGTTGTAGTTTCTGCAAACATTGCTTCAATTTTGATAGCGGAATTAAAATTTGGAAA
*
550637 TCGTACATAGTAATGAGCTATGTTTCCTGTATTGAGGTGACTCTTGGGTGAAT-TTCGAATACGA
196 TCGTACATAGTAATGAGCTATGTTGCCTGTATTGAGGTGACTCTTGGGTGAATGTT-GAATACGA
550701 ATATGTGTCTGACATGATATACGCTTTTTTAA
260 ATATGTGTCTGACATGATATACGCTTTTTTAA
550733 TGATGTATTCTTTATTAAATTGCATTTCTTTCGGGTTTCAAAGCATGAAGTGGGAGAATCGCACT
1 TGATGTATTCTTTATTAAATTGCATTTCTTTCGGGTTTCAAAGCATGAAGTGGGAGAATCGCACT
550798 GTATTATCGGTGGGGTTTTATTTGATCTAAAATGCAGTTAGGTCCATTTCAGAAAACTTTTTTTT
66 GTATTATCGGTGGGGTTTTATTTGATCTAAAATGCAGTTAGGTCCATTTCAGAAAACTTTTTTTT
* *
550863 -TCTTTTTTTGTT-TCGGTTTCTGCAAACATTGCTTCAATTTTGATAGTGGAATTAAAATTTGGA
131 CT-TTTTTTTGTTGT-AGTTTCTGCAAACATTGCTTCAATTTTGATAGCGGAATTAAAATTTGGA
*
550926 AATCGTACATGGTAATGAGCTATGTTGCCTGTATTGAGGTGACTCTTGGGTGAATGTTGAATACG
194 AATCGTACATAGTAATGAGCTATGTTGCCTGTATTGAGGTGACTCTTGGGTGAATGTTGAATACG
*
550991 AATATGTGTCTGACATGGTATACGCTTTTTT
259 AATATGTGTCTGACATGATATACGCTTTTTT
551022 TATATTTTTT
Statistics
Matches: 278, Mismatches: 8, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
290 2 0.01
291 274 0.99
292 2 0.01
ACGTcount: A:0.25, C:0.12, G:0.21, T:0.42
Consensus pattern (291 bp):
TGATGTATTCTTTATTAAATTGCATTTCTTTCGGGTTTCAAAGCATGAAGTGGGAGAATCGCACT
GTATTATCGGTGGGGTTTTATTTGATCTAAAATGCAGTTAGGTCCATTTCAGAAAACTTTTTTTT
CTTTTTTTTGTTGTAGTTTCTGCAAACATTGCTTCAATTTTGATAGCGGAATTAAAATTTGGAAA
TCGTACATAGTAATGAGCTATGTTGCCTGTATTGAGGTGACTCTTGGGTGAATGTTGAATACGAA
TATGTGTCTGACATGATATACGCTTTTTTAA
Found at i:552995 original size:2 final size:2
Alignment explanation
Indices: 552988--553033 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
552978 TCTTAAATGT
* *
552988 CA CA CA CA CG CA CA GA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
553030 CA CA
1 CA CA
553034 TATATATATA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.48, G:0.04, T:0.00
Consensus pattern (2 bp):
CA
Found at i:553038 original size:2 final size:2
Alignment explanation
Indices: 553033--553057 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
553023 ACACACACAC
553033 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
553058 AAGTGCTACG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:559505 original size:16 final size:16
Alignment explanation
Indices: 559484--559515 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
559474 AGAAAGGGAA
559484 TTCTTTTTTTTCTTTT
1 TTCTTTTTTTTCTTTT
*
559500 TTCTTTTTTTTGTTTT
1 TTCTTTTTTTTCTTTT
559516 GGGTTTGGGG
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:0.00, C:0.09, G:0.03, T:0.88
Consensus pattern (16 bp):
TTCTTTTTTTTCTTTT
Found at i:560734 original size:2 final size:2
Alignment explanation
Indices: 560727--560772 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
560717 CTCCATCTCC
560727 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
560769 AT AT
1 AT AT
560773 TTTATCACAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:560940 original size:28 final size:29
Alignment explanation
Indices: 560907--560975 Score: 88
Period size: 28 Copynumber: 2.4 Consensus size: 29
560897 TTTAAACCTG
*
560907 TTAAATTTATTTAT-TATTTAAAATAATA
1 TTAAATATATTTATATATTTAAAATAATA
** *
560935 TTAAATATAAATATATATTTAATATAATA
1 TTAAATATATTTATATATTTAAAATAATA
560964 -TAAATATATTTA
1 TTAAATATATTTA
560976 GTTTTTTTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 21 0.62
29 13 0.38
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (29 bp):
TTAAATATATTTATATATTTAAAATAATA
Found at i:560945 original size:17 final size:17
Alignment explanation
Indices: 560925--560966 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
560915 ATTTATTATT
560925 TAAAATAATATTAAATA
1 TAAAATAATATTAAATA
*
560942 T-AAATATATATTTAATA
1 TAAAATA-ATATTAAATA
*
560959 TAATATAA
1 TAAAATAA
560967 ATATATTTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
16 5 0.24
17 12 0.57
18 4 0.19
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAAATAATATTAAATA
Found at i:561795 original size:11 final size:11
Alignment explanation
Indices: 561758--561874 Score: 64
Period size: 11 Copynumber: 10.5 Consensus size: 11
561748 TAATTACATG
*
561758 AATATAATATG
1 AATATAATATA
* *
561769 TATAAAATATTAA
1 AATATAATA-T-A
561782 AATATAATATA
1 AATATAATATA
* *
561793 AATATATTTTTA
1 AATATA-ATATA
*
561805 AA-ATTTATATA
1 AATA-TAATATA
561816 AATATAA-A-A
1 AATATAATATA
*
561825 TAT-TAATATA
1 AATATAATATA
*
561835 ATTATAATA-A
1 AATATAATATA
561845 AATAATATATATA
1 AAT-ATA-ATATA
*
561858 AATATGATATA
1 AATATAATATA
561869 AATATA
1 AATATA
561875 TAAATTATCA
Statistics
Matches: 78, Mismatches: 17, Indels: 22
0.67 0.15 0.19
Matches are distributed among these distances:
8 3 0.04
9 4 0.05
10 6 0.08
11 40 0.51
12 14 0.18
13 11 0.14
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (11 bp):
AATATAATATA
Found at i:561795 original size:19 final size:19
Alignment explanation
Indices: 561773--561862 Score: 58
Period size: 21 Copynumber: 4.3 Consensus size: 19
561763 AATATGTATA
561773 AAATATTAAAATATAATAT
1 AAATATTAAAATATAATAT
*
561792 AAATATATTTTTAAAAT-TTATAT
1 -AA-ATA---TTAAAATATAATAT
561815 AAATA-TAAAATATTAATAT
1 AAATATTAAAATA-TAATAT
*
561834 AATTATAATAAAATAATATATAT
1 AA--ATATTAAAAT-ATA-ATAT
561857 AAATAT
1 AAATAT
561863 GATATAAATA
Statistics
Matches: 56, Mismatches: 3, Indels: 21
0.70 0.04 0.26
Matches are distributed among these distances:
17 6 0.11
19 7 0.12
20 2 0.04
21 12 0.21
22 10 0.18
23 12 0.21
24 7 0.12
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AAATATTAAAATATAATAT
Found at i:561820 original size:34 final size:38
Alignment explanation
Indices: 561781--561875 Score: 99
Period size: 42 Copynumber: 2.5 Consensus size: 38
561771 TAAAATATTA
*
561781 AAATATAATATAAATATATT-T-TTAAAAT-T-TATAT
1 AAATATAATATAAATATATTATAATAAAATATATATAT
*
561815 AAATATAAAATATTAATATAATTATAATAAAATAATATATAT
1 AAATAT--AATATAAATAT-ATTATAATAAAAT-ATATATAT
*
561857 AAATATGATATAAATATAT
1 AAATATAATATAAATATAT
561876 AAATTATCAA
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
34 6 0.12
36 10 0.20
37 3 0.06
38 1 0.02
39 8 0.16
40 9 0.18
41 1 0.02
42 11 0.22
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (38 bp):
AAATATAATATAAATATATTATAATAAAATATATATAT
Found at i:561856 original size:42 final size:42
Alignment explanation
Indices: 561761--561862 Score: 109
Period size: 42 Copynumber: 2.4 Consensus size: 42
561751 TTACATGAAT
* * **
561761 ATAATATGTATAAAATATTAAAATATAATATAAATATATTTTTA
1 ATAATATATAT-AAATA-TAAAATATAATATAAATATATATAAA
* *
561805 A-AATTTATATAAATATAAAATATTAATATAATTATA-ATAAA
1 ATAATATATATAAATATAAAATA-TAATATAAATATATATAAA
561846 ATAATATATATAAATAT
1 ATAATATATATAAATAT
561863 GATATAAATA
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
41 10 0.20
42 31 0.63
43 7 0.14
44 1 0.02
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (42 bp):
ATAATATATATAAATATAAAATATAATATAAATATATATAAA
Found at i:561875 original size:19 final size:18
Alignment explanation
Indices: 561759--561879 Score: 62
Period size: 17 Copynumber: 6.9 Consensus size: 18
561749 AATTACATGA
*
561759 ATATAATATGTATAAA-AT
1 ATATAA-ATATATAAATAT
561777 AT-TAAA-ATAT-AATAT
1 ATATAAATATATAAATAT
* * * * *
561792 AAATATATTTTTAAAATTT
1 ATATAAATATAT-AAATAT
561811 ATATAAATATA-AAATAT
1 ATATAAATATATAAATAT
561828 -TAATATAAT-TAT-AATA-
1 AT-ATA-AATATATAAATAT
*
561844 AAATAATATATATAAATAT
1 ATATAA-ATATATAAATAT
561863 GATATAAATATATAAAT
1 -ATATAAATATATAAAT
561880 TATCAACGTA
Statistics
Matches: 76, Mismatches: 13, Indels: 27
0.66 0.11 0.23
Matches are distributed among these distances:
14 2 0.03
15 7 0.09
16 10 0.13
17 22 0.29
18 9 0.12
19 21 0.28
20 5 0.07
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
ATATAAATATATAAATAT
Found at i:561875 original size:23 final size:23
Alignment explanation
Indices: 561764--561876 Score: 73
Period size: 23 Copynumber: 5.2 Consensus size: 23
561754 CATGAATATA
* *
561764 ATATGTATAAA-ATATTA-AAAT
1 ATATATATAAATATAATATAAAT
* *
561785 ATA-ATATAAATATATTTTTAAA-
1 ATATATATAAATATA-ATATAAAT
* *
561807 ATTTATATAAATATAA-A-ATAT
1 ATATATATAAATATAATATAAAT
*
561828 -TA-ATATAATTATAATA-AAAT
1 ATATATATAAATATAATATAAAT
*
561848 AATATATATAAATATGATATAAAT
1 -ATATATATAAATATAATATAAAT
561872 ATATA
1 ATATA
561877 AATTATCAAC
Statistics
Matches: 71, Mismatches: 11, Indels: 18
0.71 0.11 0.18
Matches are distributed among these distances:
19 11 0.15
20 13 0.18
21 6 0.08
22 6 0.08
23 31 0.44
24 4 0.06
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (23 bp):
ATATATATAAATATAATATAAAT
Found at i:563016 original size:19 final size:18
Alignment explanation
Indices: 562994--563036 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
562984 ATATCAAATA
562994 TTAAAATAGTTAATATTTT
1 TTAAAAT-GTTAATATTTT
* *
563013 TTAAAATTTTAATTTTTT
1 TTAAAATGTTAATATTTT
563031 TTAAAA
1 TTAAAA
563037 AATTTATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (18 bp):
TTAAAATGTTAATATTTT
Found at i:563048 original size:18 final size:18
Alignment explanation
Indices: 563003--563048 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
562993 ATTAAAATAG
*
563003 TTAATATTTTTTAAAATT
1 TTAATATTTTTTAAAAAT
*
563021 TTAATTTTTTTTAAAAAAT
1 TTAATATTTTTT-AAAAAT
563040 TT-ATATTTT
1 TTAATATTTT
563049 AATATTTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 17 0.71
19 7 0.29
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTAATATTTTTTAAAAAT
Found at i:563055 original size:14 final size:14
Alignment explanation
Indices: 563038--563067 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
563028 TTTTTAAAAA
*
563038 ATTTATATTTTAAT
1 ATTTATATTTAAAT
563052 ATTTATATTTAAAT
1 ATTTATATTTAAAT
563066 AT
1 AT
563068 ATATCAAATA
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
ATTTATATTTAAAT
Found at i:563124 original size:13 final size:13
Alignment explanation
Indices: 563106--563131 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
563096 AATATAATAA
563106 AGCAAAGCACCAT
1 AGCAAAGCACCAT
563119 AGCAAAGCACCAT
1 AGCAAAGCACCAT
563132 CTTTAGATGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (13 bp):
AGCAAAGCACCAT
Found at i:567261 original size:2 final size:2
Alignment explanation
Indices: 567254--567281 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
567244 ATTATAGTTG
567254 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
567282 TGTTACAAAG
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:567870 original size:2 final size:2
Alignment explanation
Indices: 567863--567906 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
567853 GCTTAAGTTC
567863 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
567905 AT
1 AT
567907 GTCGCTCTGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:568322 original size:2 final size:2
Alignment explanation
Indices: 568315--568355 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
568305 TTCACCATAA
568315 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
568356 GAGAGAGAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:568360 original size:2 final size:2
Alignment explanation
Indices: 568355--568384 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
568345 ATATATATAT
568355 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
568385 GTGGTTTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:569194 original size:21 final size:21
Alignment explanation
Indices: 569168--569215 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
569158 TTAATCACAT
569168 CAAAACTG-AACCAAATTCAAA
1 CAAAACTGAAACCAAA-TCAAA
**
569189 CAAAACTGAAATGAAATCAAA
1 CAAAACTGAAACCAAATCAAA
569210 CAAAAC
1 CAAAAC
569216 ACTAAGTTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 19 0.79
22 5 0.21
ACGTcount: A:0.60, C:0.21, G:0.06, T:0.12
Consensus pattern (21 bp):
CAAAACTGAAACCAAATCAAA
Found at i:570757 original size:17 final size:18
Alignment explanation
Indices: 570733--570783 Score: 63
Period size: 17 Copynumber: 3.0 Consensus size: 18
570723 ATTTTAAAAA
*
570733 ATATATATATAAATTATT
1 ATATATATATAAAATATT
570751 A-ATATAT-TAAAAT-TT
1 ATATATATATAAAATATT
*
570766 ATATAAATATAAAATATT
1 ATATATATATAAAATATT
570784 TTAAGATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
15 3 0.11
16 10 0.36
17 12 0.43
18 3 0.11
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
ATATATATATAAAATATT
Found at i:570781 original size:27 final size:27
Alignment explanation
Indices: 570738--570831 Score: 81
Period size: 27 Copynumber: 3.6 Consensus size: 27
570728 AAAAAATATA
*
570738 TATATAAAT-TATTAATATATTAAAATT
1 TATATAAATATA-AAATATATTAAAATT
* *
570765 TATATAAATATAAAATATTTTAAGA-T
1 TATATAAATATAAAATATATTAAAATT
*
570791 TATGATATA-ATAAAATATA-T-AAATAT
1 TAT-ATAAATATAAAATATATTAAAAT-T
*
570817 GATATAAATATAAAA
1 TATATAAATATAAAA
570832 ATTTTTAAGT
Statistics
Matches: 54, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
24 2 0.04
25 5 0.09
26 22 0.41
27 23 0.43
28 2 0.04
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.40
Consensus pattern (27 bp):
TATATAAATATAAAATATATTAAAATT
Found at i:570829 original size:26 final size:29
Alignment explanation
Indices: 570766--570831 Score: 81
Period size: 26 Copynumber: 2.5 Consensus size: 29
570756 ATTAAAATTT
*
570766 ATATAAATATAAAATATTTTAAGATTATG
1 ATATAAATATAAAATATTATAAGATTATG
570795 ATAT--A-ATAAAATA-TATAA-A-TATG
1 ATATAAATATAAAATATTATAAGATTATG
570818 ATATAAATATAAAA
1 ATATAAATATAAAA
570832 ATTTTTAAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
23 8 0.24
24 1 0.03
25 5 0.15
26 14 0.42
27 1 0.03
29 4 0.12
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (29 bp):
ATATAAATATAAAATATTATAAGATTATG
Found at i:578205 original size:2 final size:2
Alignment explanation
Indices: 578200--578224 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
578190 CTCTCTGCTT
578200 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 T
578225 GTATGTATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:578376 original size:2 final size:2
Alignment explanation
Indices: 578369--578398 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
578359 TTTTAATTTC
578369 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
578399 CTTTCTGTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:579702 original size:17 final size:17
Alignment explanation
Indices: 579682--579725 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
579672 AATATAATAC
579682 ATATAAAAT-AATAAAAT
1 ATATAAAATAAAT-AAAT
*
579699 ATATAACATAAATAAAT
1 ATATAAAATAAATAAAT
579716 ATATTAAAAT
1 ATA-TAAAAT
579726 GTATAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (17 bp):
ATATAAAATAAATAAAT
Found at i:579760 original size:18 final size:17
Alignment explanation
Indices: 579737--579789 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 17
579727 TATAAAAAAT
579737 AATTTATTAATATATTAA
1 AATTTATTAA-ATATTAA
579755 AATTTATATAAATA-TAA
1 AATTTAT-TAAATATTAA
579772 AATATT-TTAAAATATTAA
1 AAT-TTATT-AAATATTAA
579790 TATAATATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
16 1 0.03
17 12 0.39
18 15 0.48
19 3 0.10
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AATTTATTAAATATTAA
Found at i:579768 original size:20 final size:20
Alignment explanation
Indices: 579710--579770 Score: 57
Period size: 18 Copynumber: 3.5 Consensus size: 20
579700 TATAACATAA
*
579710 ATAAATATATTAAAATGTAT
1 ATAAATATATTAAAATTTAT
579730 A-AAA-A-A-T--AATTTAT
1 ATAAATATATTAAAATTTAT
579744 -T-AATATATTAAAATTTAT
1 ATAAATATATTAAAATTTAT
579762 ATAAATATA
1 ATAAATATA
579771 AAATATTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 16
0.65 0.02 0.33
Matches are distributed among these distances:
13 2 0.06
14 7 0.22
15 1 0.03
16 2 0.06
17 1 0.03
18 8 0.25
19 4 0.12
20 7 0.22
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (20 bp):
ATAAATATATTAAAATTTAT
Found at i:579775 original size:27 final size:28
Alignment explanation
Indices: 579682--579822 Score: 91
Period size: 29 Copynumber: 5.0 Consensus size: 28
579672 AATATAATAC
*
579682 ATATAAAATA-A-TAAAATATATAACATA
1 ATATAAAATATATTAAAATAT-TAATATA
* *
579709 A-AT-AAATATATTAAAATGTATAAAAAATA
1 ATATAAAATATATTAAAA--TAT-TAATATA
* *
579738 ATTTATTAATATATTAAAAT-TT-ATATAA
1 ATATA-AAATATATTAAAATATTAATAT-A
*
579766 ATATAAAATATTTTAAAATATTAATATA
1 ATATAAAATATATTAAAATATTAATATA
*
579794 ATATAATAA-ATTATAAAAATA-TAATATA
1 ATATAA-AATA-TATTAAAATATTAATATA
579822 A
1 A
579823 AAATATAAAT
Statistics
Matches: 91, Mismatches: 11, Indels: 23
0.73 0.09 0.18
Matches are distributed among these distances:
25 5 0.05
26 3 0.03
27 21 0.23
28 23 0.25
29 25 0.27
30 2 0.02
32 12 0.13
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.38
Consensus pattern (28 bp):
ATATAAAATATATTAAAATATTAATATA
Found at i:579780 original size:20 final size:19
Alignment explanation
Indices: 579727--579778 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 19
579717 TATTAAAATG
*
579727 TATAAAAAATAATTTATTAA
1 TATATAAAAT-ATTTATTAA
*
579747 TATATTAAA-ATTTATATAA
1 TATATAAAATATTTAT-TAA
579766 -ATATAAAATATTT
1 TATATAAAATATTT
579779 TAAAATATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 13 0.48
19 7 0.26
20 7 0.26
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TATATAAAATATTTATTAA
Found at i:579810 original size:28 final size:28
Alignment explanation
Indices: 579752--579835 Score: 79
Period size: 28 Copynumber: 3.0 Consensus size: 28
579742 ATTAATATAT
*
579752 TAAAAT-TT-ATATAAATATAA-AATATTT
1 TAAAATATTAATAT-AATATAATAA-ATTA
579779 TAAAATATTAATATAATATAATAAATTA
1 TAAAATATTAATATAATATAATAAATTA
*
579807 TAAAA-ATATAATATAA-AAATATAAATTA
1 TAAAATAT-TAATATAATATA-ATAAATTA
579835 T
1 T
579836 TATATGACGA
Statistics
Matches: 50, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
27 10 0.20
28 34 0.68
29 6 0.12
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (28 bp):
TAAAATATTAATATAATATAATAAATTA
Found at i:579821 original size:13 final size:13
Alignment explanation
Indices: 579780--579830 Score: 59
Period size: 13 Copynumber: 3.7 Consensus size: 13
579770 AAAATATTTT
579780 AAAATATTAATATA
1 AAAATA-TAATATA
579794 ATATAATA-AATTATA
1 A-A-AATATAA-TATA
579809 AAAATATAATATA
1 AAAATATAATATA
579822 AAAATATAA
1 AAAATATAA
579831 ATTATTATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
13 17 0.52
14 6 0.18
15 6 0.18
16 4 0.12
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
AAAATATAATATA
Found at i:579839 original size:23 final size:25
Alignment explanation
Indices: 579785--579839 Score: 73
Period size: 23 Copynumber: 2.4 Consensus size: 25
579775 ATTTTAAAAT
579785 ATTAATATAATATAATAAATTATAA
1 ATTAATATAATATAATAAATTATAA
579810 A--AATATAATATAA-AAA-TATAA
1 ATTAATATAATATAATAAATTATAA
*
579831 ATTATTATA
1 ATTAATATA
579840 TGACGAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 6 0.22
22 3 0.11
23 17 0.63
25 1 0.04
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (25 bp):
ATTAATATAATATAATAAATTATAA
Found at i:580100 original size:16 final size:17
Alignment explanation
Indices: 579983--580127 Score: 78
Period size: 16 Copynumber: 8.8 Consensus size: 17
579973 ATGGAAGGAA
579983 AATATAAAAT-TT-TAT
1 AATATAAAATATTATAT
*
579998 AATATTAAATAGGATTATAT
1 AATA-TAAA-A-TATTATAT
* *
580018 GAATATAAAATA-AATAA
1 -AATATAAAATATTATAT
*
580035 AATAATTAAAATATAATAT
1 AAT-A-TAAAATATTATAT
* *
580054 GATAT-AAATA-TGTAT
1 AATATAAAATATTATAT
*
580069 -A-GTAAAAT-TTATAT
1 AATATAAAATATTATAT
*
580083 AATATAAATTATTA-AT
1 AATATAAAATATTATAT
580099 AAT-TAAAAT-TTATAT
1 AATATAAAATATTATAT
580114 AAATATAAAATATT
1 -AATATAAAATATT
580128 TTAAATACTA
Statistics
Matches: 99, Mismatches: 13, Indels: 33
0.68 0.09 0.23
Matches are distributed among these distances:
13 1 0.01
14 12 0.12
15 15 0.15
16 25 0.25
17 15 0.15
18 11 0.11
19 9 0.09
20 7 0.07
21 4 0.04
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (17 bp):
AATATAAAATATTATAT
Found at i:580109 original size:31 final size:30
Alignment explanation
Indices: 580020--580127 Score: 105
Period size: 30 Copynumber: 3.5 Consensus size: 30
580010 GATTATATGA
* * *
580020 ATATAAAATAAATA-AAATAATTAAAATATA
1 ATATAATATAAATATTAATAATTAAAAT-TT
* *
580050 ATATGATATAAATATGT-AT-AGTAAAATTT
1 ATATAATATAAATAT-TAATAATTAAAATTT
580079 ATATAATATAAATTATTAATAATTAAAATTT
1 ATATAATATAAA-TATTAATAATTAAAATTT
580110 ATATAAATATAAAATATT
1 ATAT-AATAT-AAATATT
580128 TTAAATACTA
Statistics
Matches: 64, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
29 13 0.20
30 24 0.38
31 15 0.23
32 9 0.14
33 3 0.05
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (30 bp):
ATATAATATAAATATTAATAATTAAAATTT
Found at i:580775 original size:17 final size:17
Alignment explanation
Indices: 580753--580787 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
580743 ATTAATCAAA
580753 TTAAAAA-TTAAATATTT
1 TTAAAAATTTAAA-ATTT
580770 TTAAAAATTTAAAATTT
1 TTAAAAATTTAAAATTT
580787 T
1 T
580788 ATGATAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TTAAAAATTTAAAATTT
Found at i:588914 original size:23 final size:23
Alignment explanation
Indices: 588887--588930 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
588877 AATTATATTT
*
588887 TTTTATAATTTAATATTTAAAAA
1 TTTTATAATTAAATATTTAAAAA
588910 TTTTATAATTAAATATTTAAA
1 TTTTATAATTAAATATTTAAA
588931 TTTTATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTTATAATTAAATATTTAAAAA
Found at i:591481 original size:15 final size:16
Alignment explanation
Indices: 591461--591511 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
591451 ATTCCTATTG
*
591461 AAAAAAGTTTAAGTTA
1 AAAAAAGCTTAAGTTA
*
591477 AAAAAAGCTTAGGTTA
1 AAAAAAGCTTAAGTTA
591493 AAAAAAG--TAAGTTTA
1 AAAAAAGCTTAAG-TTA
591508 AAAA
1 AAAA
591512 GTGTATTGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
14 3 0.10
15 7 0.23
16 21 0.68
ACGTcount: A:0.59, C:0.02, G:0.14, T:0.25
Consensus pattern (16 bp):
AAAAAAGCTTAAGTTA
Found at i:591482 original size:16 final size:16
Alignment explanation
Indices: 591461--591500 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
591451 ATTCCTATTG
591461 AAAAAAGTTTAAGTTA
1 AAAAAAGTTTAAGTTA
* *
591477 AAAAAAGCTTAGGTTA
1 AAAAAAGTTTAAGTTA
591493 AAAAAAGT
1 AAAAAAGT
591501 AAGTTTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.57, C:0.03, G:0.15, T:0.25
Consensus pattern (16 bp):
AAAAAAGTTTAAGTTA
Found at i:591687 original size:23 final size:22
Alignment explanation
Indices: 591631--591688 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
591621 TCATTTCATT
591631 TAAAAATTA-ATTTTTAAATTA
1 TAAAAATTATATTTTTAAATTA
* *
591652 TAAAAATTTTATTTTTTAATTA
1 TAAAAATTATATTTTTAAATTA
*
591674 TATAATATTATATTT
1 TA-AAAATTATATTT
591689 ATTATAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 8 0.26
22 13 0.42
23 10 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TAAAAATTATATTTTTAAATTA
Found at i:591927 original size:10 final size:10
Alignment explanation
Indices: 591904--591956 Score: 70
Period size: 10 Copynumber: 5.2 Consensus size: 10
591894 TGTTACGGAT
591904 TTTAAATAAAA
1 TTTAAAT-AAA
**
591915 TTTTTATAAA
1 TTTAAATAAA
591925 TTTAAATAAA
1 TTTAAATAAA
*
591935 TTTAAAAAAA
1 TTTAAATAAA
591945 TTTAAATAAA
1 TTTAAATAAA
591955 TT
1 TT
591957 AAACTTTTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
10 31 0.86
11 5 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
TTTAAATAAA
Found at i:592898 original size:21 final size:21
Alignment explanation
Indices: 592863--592904 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
592853 GACTGATACA
592863 TTAAAATAAAATTTTAAATATT
1 TTAAAATAAAATTTT-AATATT
*
592885 TTAAAA-ATAATTTTAATATT
1 TTAAAATAAAATTTTAATATT
592905 AAATAACTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.32
21 7 0.37
22 6 0.32
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TTAAAATAAAATTTTAATATT
Found at i:593177 original size:104 final size:104
Alignment explanation
Indices: 593060--593273 Score: 410
Period size: 104 Copynumber: 2.1 Consensus size: 104
593050 TTTTTTACTG
593060 ATTCTTCTTTATATAATATAATATAAACCATCTTATTTATATTATTTTTATATCATACCTAAATA
1 ATTCTTCTTTATATAATATAATATAAACCATCTTATTTATATTATTTTTATATCATACCTAAATA
*
593125 AAAAAAAGGCACACTTTCTAACAAATCAAATTGGTCGAT
66 AAAAAAAGACACACTTTCTAACAAATCAAATTGGTCGAT
*
593164 ATTCTTCTTTATATAATATAATATAAATCATCTTATTTATATTATTTTTATATCATACCTAAATA
1 ATTCTTCTTTATATAATATAATATAAACCATCTTATTTATATTATTTTTATATCATACCTAAATA
593229 AAAAAAAGACACACTTTCTAACAAATCAAATTGGTCGAT
66 AAAAAAAGACACACTTTCTAACAAATCAAATTGGTCGAT
593268 ATTCTT
1 ATTCTT
593274 TGCTTTCTGC
Statistics
Matches: 108, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
104 108 1.00
ACGTcount: A:0.41, C:0.14, G:0.04, T:0.41
Consensus pattern (104 bp):
ATTCTTCTTTATATAATATAATATAAACCATCTTATTTATATTATTTTTATATCATACCTAAATA
AAAAAAAGACACACTTTCTAACAAATCAAATTGGTCGAT
Found at i:593375 original size:4 final size:4
Alignment explanation
Indices: 593366--593397 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
593356 CACAGCATTG
593366 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT
593398 ATTTATTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
CTTT
Found at i:593931 original size:19 final size:20
Alignment explanation
Indices: 593902--593939 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
593892 TTAAACATGA
*
593902 TAAAAATATAAAAATATTCT
1 TAAAAATATAAAAAAATTCT
593922 TAAAAA-ATAAAAAAATTC
1 TAAAAATATAAAAAAATTC
593940 AGAGATTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (20 bp):
TAAAAATATAAAAAAATTCT
Found at i:594211 original size:22 final size:21
Alignment explanation
Indices: 594164--594207 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
594154 AAAATATTTT
*
594164 TATTTAAATTTAATTACAAAA
1 TATTTAAATTTAATTAAAAAA
594185 TATTTAAATATTAA-TAAAAAA
1 TATTTAAAT-TTAATTAAAAAA
594206 TA
1 TA
594208 ATTTTTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
TATTTAAATTTAATTAAAAAA
Found at i:594812 original size:21 final size:20
Alignment explanation
Indices: 594770--594818 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
594760 TATAAATAAT
* *
594770 AAAATATATTTATATTTATA
1 AAAATATAATTATATATATA
594790 AAAATATAATTATAATATATA
1 AAAATATAATTAT-ATATATA
594811 AAAATATA
1 AAAATATA
594819 CCAATAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 12 0.46
21 14 0.54
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAATATAATTATATATATA
Found at i:594825 original size:21 final size:21
Alignment explanation
Indices: 594786--594825 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
594776 TATTTATATT
**
594786 TATAAAAATATAATTATAATA
1 TATAAAAATATAACAATAATA
*
594807 TATAAAAATATACCAATAA
1 TATAAAAATATAACAATAA
594826 AATACGATTA
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:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (21 bp):
TATAAAAATATAACAATAATA
Found at i:595025 original size:34 final size:34
Alignment explanation
Indices: 594973--595038 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
594963 TATTTTATGA
* * *
594973 AAAAAATTATTTAATTATT-TTTATAATTTTTTTT
1 AAAAAATAATATAATTATTATATAT-ATTTTTTTT
*
595007 AAAAAATAATATATTTATTATATATATTTTTT
1 AAAAAATAATATAATTATTATATATATTTTTT
595039 CAATATAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 23 0.85
35 4 0.15
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (34 bp):
AAAAAATAATATAATTATTATATATATTTTTTTT
Found at i:595053 original size:31 final size:29
Alignment explanation
Indices: 594984--595054 Score: 72
Period size: 31 Copynumber: 2.3 Consensus size: 29
594974 AAAAATTATT
*
594984 TAATTATTTTTATAATTTTTTTTAAAAAA
1 TAATTATTTTTATAATTTTTTTCAAAAAA
* *
595013 TAATATATTTATTATATATATTTTTTCAATATA
1 TAAT-TATTT-TTATA-AT-TTTTTTCAAAAAA
595046 -AATTATTTT
1 TAATTATTTT
595055 AATAGATTCG
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
29 4 0.11
30 6 0.17
31 10 0.29
32 5 0.14
33 10 0.29
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (29 bp):
TAATTATTTTTATAATTTTTTTCAAAAAA
Found at i:595425 original size:28 final size:30
Alignment explanation
Indices: 595394--595456 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 30
595384 TAATTTCTTT
*
595394 ATTTAAGTCGC-ATTTTTTT-ATATTTTTA
1 ATTTAAGTCACAATTTTTTTAATATTTTTA
* *
595422 ATTT-ATTCACAATTTTTTTAATTTTTTTA
1 ATTTAAGTCACAATTTTTTTAATATTTTTA
595451 ATTTAA
1 ATTTAA
595457 AAAAATTACA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 4 0.14
28 12 0.41
29 12 0.41
30 1 0.03
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.62
Consensus pattern (30 bp):
ATTTAAGTCACAATTTTTTTAATATTTTTA
Found at i:596748 original size:19 final size:19
Alignment explanation
Indices: 596713--596770 Score: 50
Period size: 19 Copynumber: 3.1 Consensus size: 19
596703 ATTCCCAATA
*
596713 AAATTTAT-TGATAATTTAT
1 AAATTTATATTAT-ATTTAT
596732 AAATTTATATTATATTTGAT
1 AAATTTATATTATATTT-AT
* *
596752 ATATTT-TATTTTA-TTAT
1 AAATTTATATTATATTTAT
596769 AA
1 AA
596771 TCATATTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
17 3 0.09
18 2 0.06
19 18 0.55
20 10 0.30
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (19 bp):
AAATTTATATTATATTTAT
Found at i:596804 original size:19 final size:21
Alignment explanation
Indices: 596759--596816 Score: 70
Period size: 19 Copynumber: 2.9 Consensus size: 21
596749 GATATATTTT
*
596759 ATTTTATTATAATCATATTTAA
1 ATTTT-TTATAATCATATATAA
596781 ATTTTTTATAATCA-ATAT-A
1 ATTTTTTATAATCATATATAA
596800 ATTTTTTAT-AT-ATATAT
1 ATTTTTTATAATCATATAT
596817 TAATAACTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
17 1 0.03
18 6 0.18
19 10 0.29
20 3 0.09
21 9 0.26
22 5 0.15
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTTTTTATAATCATATATAA
Found at i:597248 original size:20 final size:20
Alignment explanation
Indices: 597189--597250 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
597179 TAATTAAATT
*
597189 TTAATAAAAATA-ATTTTTAA
1 TTAATAAAAATATA-TTTAAA
* * *
597209 TTATTAAATAT-TAATGTAAA
1 TTAATAAAAATAT-ATTTAAA
597229 TTAATAAAAATATATTTAAA
1 TTAATAAAAATATATTTAAA
597249 TT
1 TT
597251 TTAATTTAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
20 30 0.94
21 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
TTAATAAAAATATATTTAAA
Found at i:598177 original size:36 final size:34
Alignment explanation
Indices: 598111--598186 Score: 86
Period size: 35 Copynumber: 2.2 Consensus size: 34
598101 TGAACTCCTC
* *
598111 ATATA-ATTATATAATAAATATTAATTTTATATTT
1 ATATATATCATATAATAAATATTAATATTATA-TT
598145 ATATATATCATATAA-AGAATATATAATATTATATT
1 ATATATATCATATAATA-AATAT-TAATATTATATT
598180 ATA-ATAT
1 ATATATAT
598187 TAAAAATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
34 10 0.27
35 18 0.49
36 9 0.24
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (34 bp):
ATATATATCATATAATAAATATTAATATTATATT
Found at i:598206 original size:27 final size:28
Alignment explanation
Indices: 598176--598246 Score: 78
Period size: 27 Copynumber: 2.6 Consensus size: 28
598166 TATAATATTA
598176 TATTATAATATTAAAAATATAA-TAAAT
1 TATTATAATATTAAAAATATAATTAAAT
* *
598203 TATT-T-ATATTTTAAAATTTAATTAAAT
1 TATTATAATA-TTAAAAATATAATTAAAT
598230 TATTA-AATTATTAAAAA
1 TATTATAA-TATTAAAAA
598247 ATTTTAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
25 3 0.08
26 11 0.31
27 13 0.36
28 7 0.19
29 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (28 bp):
TATTATAATATTAAAAATATAATTAAAT
Found at i:598609 original size:21 final size:21
Alignment explanation
Indices: 598565--598622 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
598555 TTTAAAAATT
598565 TTATAAAATT-TA-TTATCAA
1 TTATAAAATTATATTTATCAA
*
598584 ATATAATAATTATATTTAT-AA
1 TTATAA-AATTATATTTATCAA
*
598605 TTATAAAAATTATTTTTA
1 TTAT-AAAATTATATTTA
598623 ATGATTTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
19 5 0.16
20 4 0.12
21 17 0.53
22 6 0.19
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
TTATAAAATTATATTTATCAA
Found at i:598894 original size:21 final size:19
Alignment explanation
Indices: 598861--598900 Score: 62
Period size: 21 Copynumber: 2.0 Consensus size: 19
598851 ACTTTTTTTA
598861 AATATTTATATTTAAATTT
1 AATATTTATATTTAAATTT
598880 AATATTTTAATATTTAAATTT
1 AATA-TTT-ATATTTAAATTT
598901 TTTTAATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.21
20 3 0.16
21 12 0.63
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
AATATTTATATTTAAATTT
Found at i:598902 original size:15 final size:14
Alignment explanation
Indices: 598856--598901 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
598846 TAATTACTTT
*
598856 TTTTAAATATTTATA
1 TTTTAAAT-TTAATA
598871 -TTTAAATTTAATA
1 TTTTAAATTTAATA
598884 TTTTAATATTTAA-A
1 TTTTAA-ATTTAATA
598898 TTTT
1 TTTT
598902 TTTAATAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 5 0.18
14 17 0.61
15 6 0.21
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TTTTAAATTTAATA
Found at i:598998 original size:17 final size:17
Alignment explanation
Indices: 598976--599025 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
598966 TTTTTTACGC
598976 ATTTAAAAATTAATTTA
1 ATTTAAAAATTAATTTA
*
598993 ATTTAATAATT-ATTT-
1 ATTTAAAAATTAATTTA
599008 -TTTAAAAATTAATATTA
1 ATTTAAAAATTAAT-TTA
599025 A
1 A
599026 ATAATTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
14 9 0.33
15 2 0.07
16 6 0.22
17 10 0.37
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTAAAAATTAATTTA
Found at i:599100 original size:2 final size:2
Alignment explanation
Indices: 599089--599120 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
599079 ATTGCGAACT
599089 TA TA -A 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
599121 GAAAAGGTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:599427 original size:12 final size:12
Alignment explanation
Indices: 599394--599432 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
599384 TCATTTCAAA
599394 TTTAAATAATTTAT
1 TTTAAATAA-TT-T
*
599408 TTTTAATAATTT
1 TTTAAATAATTT
599420 TTTAAATAATTT
1 TTTAAATAATTT
599432 T
1 T
599433 AAAAAATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 13 0.57
13 2 0.09
14 8 0.35
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTAAATAATTT
Found at i:599695 original size:13 final size:13
Alignment explanation
Indices: 599677--599703 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
599667 TAAGTACATA
599677 AAATTAAAATTTT
1 AAATTAAAATTTT
599690 AAATTAAAATTTT
1 AAATTAAAATTTT
599703 A
1 A
599704 TAAATTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATTAAAATTTT
Found at i:599753 original size:21 final size:21
Alignment explanation
Indices: 599701--599757 Score: 62
Period size: 23 Copynumber: 2.6 Consensus size: 21
599691 AATTAAAATT
599701 TTATAAATTTAAATAAATATGAA
1 TTAT-AATTTAAATAAATAT-AA
599724 TTATAATTTAATATAAATAT-A
1 TTATAATTTAA-ATAAATATAA
* *
599745 TTTTTATTTAAAT
1 TTATAATTTAAAT
599758 TTAATAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 2 0.06
21 10 0.32
22 7 0.23
23 12 0.39
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
TTATAATTTAAATAAATATAA
Found at i:599783 original size:20 final size:19
Alignment explanation
Indices: 599753--599805 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 19
599743 TATTTTTATT
599753 TAAATTTAATAAAAAAATA
1 TAAATTTAATAAAAAAATA
*
599772 TAAATATTAATATAAAAATA
1 TAAAT-TTAATAAAAAAATA
599792 TAATATTTTAATAA
1 TAA-A-TTTAATAA
599806 TATAATTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 5 0.17
20 16 0.55
21 7 0.24
22 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAATTTAATAAAAAAATA
Found at i:604791 original size:25 final size:25
Alignment explanation
Indices: 604746--604813 Score: 63
Period size: 25 Copynumber: 2.8 Consensus size: 25
604736 TTATTCATTG
* *
604746 AAATAATT-TATC-TATCAATTAAAT
1 AAATTATTATATCTTATTAATT-AAT
604770 AAACTT-TTATAT-TTATTAATTAAT
1 AAA-TTATTATATCTTATTAATTAAT
604794 AAATTAGTTATATCTTATTA
1 AAATTA-TTATATCTTATTA
604814 TGTAGTAAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
23 2 0.06
24 11 0.31
25 17 0.47
26 6 0.17
ACGTcount: A:0.44, C:0.06, G:0.01, T:0.49
Consensus pattern (25 bp):
AAATTATTATATCTTATTAATTAAT
Found at i:606943 original size:20 final size:20
Alignment explanation
Indices: 606920--606957 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
606910 AAACAATCTC
*
606920 AAAAAAAACCCAGAAAAAGA
1 AAAAAAAACCAAGAAAAAGA
606940 AAAAAAAACCAAGAAAAA
1 AAAAAAAACCAAGAAAAA
606958 TAACAGCGAA
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:0.79, C:0.13, G:0.08, T:0.00
Consensus pattern (20 bp):
AAAAAAAACCAAGAAAAAGA
Found at i:607630 original size:16 final size:17
Alignment explanation
Indices: 607609--607641 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
607599 TAAAATTAAG
607609 TAAAT-AATTTAATTTT
1 TAAATAAATTTAATTTT
*
607625 TAAATAAATTTTATTTT
1 TAAATAAATTTAATTTT
607642 ATTTTATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TAAATAAATTTAATTTT
Found at i:607725 original size:20 final size:18
Alignment explanation
Indices: 607698--607742 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
607688 AATTAGATTT
*
607698 AAATATATATTTGTA-AAA
1 AAATAAATATTT-TATAAA
*
607716 ATATAAATATTTTATAAA
1 AAATAAATATTTTATAAA
607734 AAATAAATA
1 AAATAAATA
607743 ATTAAATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 2 0.09
18 21 0.91
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (18 bp):
AAATAAATATTTTATAAA
Done.