Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold21
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: 2821038
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.33
Warning! 98422 characters in sequence are not A, C, G, or T
File 3 of 15
Found at i:238113 original size:2 final size:2
Alignment explanation
Indices: 238100--238141 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
238090 TAATATAAAC
*
238100 AT AT AT AA 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
238142 TCAGAGTTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:243743 original size:13 final size:13
Alignment explanation
Indices: 243725--243753 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
243715 TTTATATAAT
243725 ATATAAATCATTA
1 ATATAAATCATTA
243738 ATATAAATCATTA
1 ATATAAATCATTA
243751 ATA
1 ATA
243754 AGTCAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (13 bp):
ATATAAATCATTA
Found at i:247484 original size:9 final size:9
Alignment explanation
Indices: 247470--247512 Score: 59
Period size: 9 Copynumber: 4.6 Consensus size: 9
247460 AAATGAAGAC
247470 AAAAATTAT
1 AAAAATTAT
247479 AAAAATTAT
1 AAAAATTAT
247488 AAAAAATTAAT
1 -AAAAATT-AT
*
247499 AAATATTAT
1 AAAAATTAT
247508 AAAAA
1 AAAAA
247513 CTTAAATTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 15 0.50
10 13 0.43
11 2 0.07
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (9 bp):
AAAAATTAT
Found at i:247492 original size:10 final size:10
Alignment explanation
Indices: 247470--247512 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
247460 AAATGAAGAC
247470 AAAAATTAT-
1 AAAAATTATA
247479 AAAAATTATA
1 AAAAATTATA
247489 AAAAATTA-A
1 AAAAATTATA
*
247498 TAAATATTATA
1 -AAAAATTATA
247509 AAAA
1 AAAA
247513 CTTAAATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
9 10 0.34
10 18 0.62
11 1 0.03
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (10 bp):
AAAAATTATA
Found at i:247493 original size:20 final size:20
Alignment explanation
Indices: 247470--247517 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
247460 AAATGAAGAC
247470 AAAAATT-ATAAAAATTATA
1 AAAAATTAATAAAAATTATA
*
247489 AAAAATTAATAAATATTATA
1 AAAAATTAATAAAAATTATA
*
247509 AAAACTTAA
1 AAAAATTAA
247518 ATTAACAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 7 0.27
20 19 0.73
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAAATTAATAAAAATTATA
Found at i:250720 original size:16 final size:16
Alignment explanation
Indices: 250699--250729 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
250689 AGCTAAACCA
250699 ACAATCATGGTAGCTT
1 ACAATCATGGTAGCTT
250715 ACAATCATGGTAGCT
1 ACAATCATGGTAGCT
250730 CAAGACTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.29
Consensus pattern (16 bp):
ACAATCATGGTAGCTT
Found at i:252047 original size:27 final size:27
Alignment explanation
Indices: 252026--252083 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
252016 TTTAAATATT
*
252026 AAATAAATAAATTTAATATTAAAATAA
1 AAATAAATAAATTAAATATTAAAATAA
*
252053 AAATAAATATATTAAATA--AATAATAA
1 AAATAAATAAATTAAATATTAA-AATAA
252079 AAATA
1 AAATA
252084 TGAATTAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 2 0.07
26 10 0.36
27 16 0.57
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (27 bp):
AAATAAATAAATTAAATATTAAAATAA
Found at i:252064 original size:20 final size:20
Alignment explanation
Indices: 252019--252084 Score: 73
Period size: 20 Copynumber: 3.3 Consensus size: 20
252009 TAAAACTTTT
*
252019 AAATATTAAATAAATAA-ATT
1 AAATATTAAATAAATAATA-A
*
252039 TAATATTAAAATAAA-AATAA
1 AAATATT-AAATAAATAATAA
*
252059 ATATATTAAATAAATAATAA
1 AAATATTAAATAAATAATAA
252079 AAATAT
1 AAATAT
252085 GAATTAATTA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
19 7 0.18
20 23 0.61
21 8 0.21
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAATATTAAATAAATAATAA
Found at i:252198 original size:15 final size:15
Alignment explanation
Indices: 252178--252211 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
252168 ATATTAATAA
252178 TTATTTAATAAATTT
1 TTATTTAATAAATTT
* *
252193 TTATTTAATTATTTT
1 TTATTTAATAAATTT
252208 TTAT
1 TTAT
252212 CAATTCAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TTATTTAATAAATTT
Found at i:252534 original size:18 final size:18
Alignment explanation
Indices: 252511--252547 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
252501 AGATTCGGTT
*
252511 TAAAATAATATTTTTAAA
1 TAAAATAATATATTTAAA
252529 TAAAATAATATATTTAAA
1 TAAAATAATATATTTAAA
252547 T
1 T
252548 TTAATTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAAAATAATATATTTAAA
Found at i:252550 original size:24 final size:22
Alignment explanation
Indices: 252523--252586 Score: 58
Period size: 24 Copynumber: 2.7 Consensus size: 22
252513 AAATAATATT
252523 TTTAAATAAAATAATATATTTAAA
1 TTTAAATAAAATAATATA--TAAA
*
252547 TTTAATTATAAA-AATATATAAA
1 TTTAAATA-AAATAATATATAAA
252569 TATTAATATAAAAATAAT
1 T-TTAA-AT-AAAATAAT
252587 TTTTTAATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
22 5 0.15
23 4 0.12
24 17 0.52
25 7 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
TTTAAATAAAATAATATATAAA
Found at i:252568 original size:22 final size:22
Alignment explanation
Indices: 252538--252584 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
252528 ATAAAATAAT
*
252538 ATATTTAAAT-TTAATTATAAAA
1 ATATATAAATATTAA-TATAAAA
252560 ATATATAAATATTAATATAAAA
1 ATATATAAATATTAATATAAAA
252582 ATA
1 ATA
252585 ATTTTTTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
ATATATAAATATTAATATAAAA
Found at i:252944 original size:20 final size:20
Alignment explanation
Indices: 252921--252958 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
252911 TTCAACGGGT
*
252921 AAAAAATAA-TCAAAAAATA
1 AAAAAAAAACTCAAAAAATA
252940 AAAAAAAAACTCAAAAAAT
1 AAAAAAAAACTCAAAAAAT
252959 CAGACTTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.79, C:0.08, G:0.00, T:0.13
Consensus pattern (20 bp):
AAAAAAAAACTCAAAAAATA
Found at i:253449 original size:21 final size:23
Alignment explanation
Indices: 253425--253475 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
253415 TTTAATAAAA
253425 TTTA-AATTAAATT-T-TTAATTT
1 TTTATAATTAAATTATATT-ATTT
*
253446 TTTATATTTAAATTATATTATTT
1 TTTATAATTAAATTATATTATTT
253469 TTTATAA
1 TTTATAA
253476 ATCTAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 4 0.16
22 8 0.32
23 11 0.44
24 2 0.08
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
TTTATAATTAAATTATATTATTT
Found at i:258865 original size:19 final size:19
Alignment explanation
Indices: 258831--258884 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
258821 ATAATATAAA
*
258831 TATATAAATATTTTAAAATT
1 TATAT-AATATATTAAAATT
*
258851 TATATAATATATTAAATTT
1 TATATAATATATTAAAATT
258870 TATATAA-ATA-TAAAA
1 TATATAATATATTAAAA
258885 AATCAAATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 4 0.13
18 3 0.10
19 19 0.61
20 5 0.16
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TATATAATATATTAAAATT
Found at i:258887 original size:20 final size:20
Alignment explanation
Indices: 258831--258887 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
258821 ATAATATAAA
*
258831 TATATAAATATTTTAAAA-TT
1 TATATAAATA-TATAAAATTT
*
258851 TATAT-AATATATTAAATTT
1 TATATAAATATATAAAATTT
*
258870 TATATAAATATAAAAAAT
1 TATATAAATATATAAAAT
258888 CAAATATAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
18 5 0.16
19 11 0.35
20 15 0.48
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TATATAAATATATAAAATTT
Found at i:258894 original size:20 final size:21
Alignment explanation
Indices: 258871--258916 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
258861 ATTAAATTTT
*
258871 ATATAAATATAAAA-AATCAA
1 ATATAAATATAAAATAATAAA
*
258891 ATATAATTATAAAATAATAAA
1 ATATAAATATAAAATAATAAA
258912 ATATA
1 ATATA
258917 TCAATAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (21 bp):
ATATAAATATAAAATAATAAA
Found at i:260709 original size:12 final size:13
Alignment explanation
Indices: 260663--260722 Score: 52
Period size: 14 Copynumber: 4.6 Consensus size: 13
260653 TGTTATAAAA
260663 AATAATATAAATAT
1 AATAA-ATAAATAT
* * *
260677 TATATATATATAT
1 AATAAATAAATAT
*
260690 ATGTAAATAAATAT
1 A-ATAAATAAATAT
260704 AA-AAAT-AATAT
1 AATAAATAAATAT
260715 AATAAATA
1 AATAAATA
260723 TAGTATGTTA
Statistics
Matches: 35, Mismatches: 8, Indels: 7
0.70 0.16 0.14
Matches are distributed among these distances:
11 7 0.20
12 8 0.23
13 7 0.20
14 13 0.37
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (13 bp):
AATAAATAAATAT
Found at i:260777 original size:17 final size:19
Alignment explanation
Indices: 260757--260798 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
260747 GATGTATTTT
260757 TATTTAA-AA-TTTTAATA
1 TATTTAATAATTTTTAATA
*
260774 TATTTAATAATTTTTATTA
1 TATTTAATAATTTTTAATA
260793 TATTTA
1 TATTTA
260799 TATTTACATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.32
18 2 0.09
19 13 0.59
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TATTTAATAATTTTTAATA
Found at i:263320 original size:19 final size:20
Alignment explanation
Indices: 263296--263342 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 20
263286 TTATTACATC
263296 ATATTAAATTTTTTTA-ATA
1 ATATTAAATTTTTTTATATA
*
263315 ATATT--ATTTTTTTATTTA
1 ATATTAAATTTTTTTATATA
263333 ATAATTAAAT
1 AT-ATTAAAT
263343 CATATAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
17 9 0.39
18 4 0.17
19 8 0.35
21 2 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
ATATTAAATTTTTTTATATA
Found at i:263999 original size:20 final size:20
Alignment explanation
Indices: 263937--263999 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
263927 TTTAAAATTA
263937 AATTAAA-AAATATTTT-TGT
1 AATTAAATAAATATTTTAT-T
* **
263956 AATAAAATAAATAAATTATT
1 AATTAAATAAATATTTTATT
263976 AATTAAATAAATATTTTATT
1 AATTAAATAAATATTTTATT
263996 AATT
1 AATT
264000 TTAAAAAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
19 6 0.17
20 29 0.81
21 1 0.03
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
AATTAAATAAATATTTTATT
Found at i:264059 original size:40 final size:41
Alignment explanation
Indices: 264010--264108 Score: 98
Period size: 40 Copynumber: 2.5 Consensus size: 41
264000 TTAAAAAAAT
* *
264010 TATTAAAAATTATTATAAATGA-TAA-TACTTTTATTTAACA
1 TATTTAAAATTATTATAAATGATTAAGTA-TTATATTTAACA
* * *
264050 TATTTAAAATAATTA-AAATTATTAAGTATTATATTTAATA
1 TATTTAAAATTATTATAAATGATTAAGTATTATATTTAACA
* *
264090 TA-ATAATATTATTATAAAT
1 TATTTAAAATTATTATAAAT
264109 AATATTAATT
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
39 14 0.29
40 32 0.67
41 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (41 bp):
TATTTAAAATTATTATAAATGATTAAGTATTATATTTAACA
Found at i:264678 original size:24 final size:25
Alignment explanation
Indices: 264642--264692 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
264632 TAGGAATGGG
264642 TTAATTATATTTTAAAAT-ATTATT
1 TTAATTATATTTTAAAATAATTATT
* * *
264666 TTAATTATTTTTTCAATTAATTATT
1 TTAATTATATTTTAAAATAATTATT
264691 TT
1 TT
264693 TAATATTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 15 0.65
25 8 0.35
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (25 bp):
TTAATTATATTTTAAAATAATTATT
Found at i:264700 original size:12 final size:13
Alignment explanation
Indices: 264642--264701 Score: 56
Period size: 12 Copynumber: 4.8 Consensus size: 13
264632 TAGGAATGGG
264642 TTAATTA-TATTT
1 TTAATTATTATTT
* *
264654 TAAAATATTA-TT
1 TTAATTATTATTT
264666 TTAATTATT-TTT
1 TTAATTATTATTT
*
264678 TCAATTAATTATTT
1 TTAATT-ATTATTT
264692 TTAA-TATTAT
1 TTAATTATTAT
264702 AAATAATACT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
12 26 0.68
13 6 0.16
14 6 0.16
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (13 bp):
TTAATTATTATTT
Found at i:265352 original size:18 final size:19
Alignment explanation
Indices: 265331--265386 Score: 69
Period size: 18 Copynumber: 2.9 Consensus size: 19
265321 AATTTATACA
265331 TTTTATTATATTTA-ATTT
1 TTTTATTATATTTATATTT
*
265349 TTTTATTATAATTATATTT
1 TTTTATTATATTTATATTT
*
265368 TTGATATTATAATTTATAT
1 TT-TTATTAT-ATTTATAT
265387 AAAATTTTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 13 0.41
19 6 0.19
20 6 0.19
21 7 0.22
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (19 bp):
TTTTATTATATTTATATTT
Found at i:265410 original size:16 final size:17
Alignment explanation
Indices: 265389--265421 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
265379 ATTTATATAA
265389 AATTTTA-GATATTAAT
1 AATTTTATGATATTAAT
*
265405 AATTTTATTATATTAAT
1 AATTTTATGATATTAAT
265422 TTTAAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
AATTTTATGATATTAAT
Found at i:265481 original size:17 final size:17
Alignment explanation
Indices: 265459--265491 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
265449 ATTTATATTA
265459 ATTTTAT-ATAATATTTT
1 ATTTTATGAT-ATATTTT
265476 ATTTTATGATATATTT
1 ATTTTATGATATATTT
265492 CGATTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (17 bp):
ATTTTATGATATATTTT
Found at i:265491 original size:39 final size:39
Alignment explanation
Indices: 265412--265491 Score: 94
Period size: 39 Copynumber: 2.1 Consensus size: 39
265402 AATAATTTTA
* *
265412 TTATATTAATTTTAAAATATTTATTTATTTATATCGTAT
1 TTATATTAATTTTAAAATATTTATATATTTATATCATAT
265451 TTATATTAATTTTATATAATATTT-TAT-TTTATGAT-ATAT
1 TTATATTAATTTTA-A-AATATTTATATATTTAT-ATCATAT
265490 TT
1 TT
265492 CGATTTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
39 24 0.67
40 5 0.14
41 7 0.19
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.61
Consensus pattern (39 bp):
TTATATTAATTTTAAAATATTTATATATTTATATCATAT
Found at i:272396 original size:22 final size:22
Alignment explanation
Indices: 272371--272415 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
272361 GTGATTTTTT
272371 TAAAAA-AATTATTGTATATAAA
1 TAAAAATAATTATTGTAT-TAAA
* *
272393 TAAAAATATTTATTTTATTAAA
1 TAAAAATAATTATTGTATTAAA
272415 T
1 T
272416 GAATTATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
TAAAAATAATTATTGTATTAAA
Found at i:272398 original size:23 final size:22
Alignment explanation
Indices: 272372--272415 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
272362 TGATTTTTTT
272372 AAAAAAATTATTGTATATAAATA
1 AAAAAAATTATTGTAT-TAAATA
* * *
272395 AAAATATTTATTTTATTAAAT
1 AAAAAAATTATTGTATTAAAT
272416 GAATTATAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
AAAAAAATTATTGTATTAAATA
Found at i:272705 original size:5 final size:5
Alignment explanation
Indices: 272672--272703 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
272662 AATAATTAAA
*
272672 AAAAG AAAAG AAAAG AAAAG AAAAG AAGAG AA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AA
272704 GACTTGTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:273006 original size:18 final size:17
Alignment explanation
Indices: 272985--273033 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 17
272975 ATATGATACT
272985 AATTATTAATATATTAAA
1 AATTATTAA-ATATTAAA
273003 AATTATATAAATA-TAAA
1 AATTAT-TAAATATTAAA
273020 AATATATTAAATAT
1 AAT-TATTAAATAT
273034 AATTATAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
17 13 0.46
18 12 0.43
19 3 0.11
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AATTATTAAATATTAAA
Found at i:273043 original size:28 final size:30
Alignment explanation
Indices: 272992--273056 Score: 82
Period size: 28 Copynumber: 2.2 Consensus size: 30
272982 ACTAATTATT
*
272992 AATATATTAAAAATTATATAAATA-TA-AA
1 AATATATTAAAAATAATATAAATATTATAA
*
273020 AATATATTAAATATAAT-TATAATATTATAA
1 AATATATTAAAAATAATATA-AATATTATAA
273050 AATATAT
1 AATATAT
273057 GAACATGATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 2 0.06
28 19 0.59
29 2 0.06
30 9 0.28
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (30 bp):
AATATATTAAAAATAATATAAATATTATAA
Found at i:273048 original size:23 final size:21
Alignment explanation
Indices: 273007--273055 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 21
272997 ATTAAAAATT
273007 ATATAAATATAAAAATATATTAA
1 ATATAAATATAAAAATATA--AA
* * *
273030 ATATAATTATAATATTATAAA
1 ATATAAATATAAAAATATAAA
273051 ATATA
1 ATATA
273056 TGAACATGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 7 0.30
23 16 0.70
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
ATATAAATATAAAAATATAAA
Found at i:273327 original size:17 final size:18
Alignment explanation
Indices: 273288--273329 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
273278 TATTTGAGTA
*
273288 TTTT-TATTTTATTTTAT
1 TTTTATATTTTATATTAT
*
273305 TATTATATTTTA-ATTAT
1 TTTTATATTTTATATTAT
273322 TTTTATAT
1 TTTTATAT
273330 CATGTCATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTATATTTTATATTAT
Found at i:273822 original size:15 final size:15
Alignment explanation
Indices: 273795--273851 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 15
273785 ATAATTTTAT
273795 ATATAAT-TATATAA
1 ATATAATATATATAA
* *
273809 ATATGATATATATAT
1 ATATAATATATATAA
* *
273824 ATATAATATTTAATAC
1 ATATAATATAT-ATAA
273840 ATA-AATATATAT
1 ATATAATATATAT
273852 TTTAAAATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
14 8 0.23
15 21 0.60
16 6 0.17
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (15 bp):
ATATAATATATATAA
Found at i:274083 original size:4 final size:4
Alignment explanation
Indices: 274074--274150 Score: 66
Period size: 4 Copynumber: 19.0 Consensus size: 4
274064 GCTATGAACA
*** * * **
274074 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT CTTT TAAG CTAT GAACA-
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AA-AT
274123 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
274151 CTTCTAAGCT
Statistics
Matches: 58, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
3 1 0.02
4 56 0.97
6 1 0.02
ACGTcount: A:0.66, C:0.04, G:0.03, T:0.27
Consensus pattern (4 bp):
AAAT
Found at i:274117 original size:49 final size:49
Alignment explanation
Indices: 274049--274183 Score: 233
Period size: 45 Copynumber: 2.8 Consensus size: 49
274039 CAAATTCCTA
274049 AAATAAATCTTCTAAGCTATGAACAAAATAAATAAATAAATAAATAAAT
1 AAATAAATCTTCTAAGCTATGAACAAAATAAATAAATAAATAAATAAAT
*
274098 AAATAAATCTTTTAAGCTATGAAC---A-AAATAAATAAATAAATAAAT
1 AAATAAATCTTCTAAGCTATGAACAAAATAAATAAATAAATAAATAAAT
274143 AAATAAATCTTCTAAGCTATGAACAAAATAAATAAATAAAT
1 AAATAAATCTTCTAAGCTATGAACAAAATAAATAAATAAAT
274184 CTTCTAAGCT
Statistics
Matches: 80, Mismatches: 2, Indels: 8
0.89 0.02 0.09
Matches are distributed among these distances:
45 43 0.54
46 1 0.01
48 1 0.01
49 35 0.44
ACGTcount: A:0.60, C:0.08, G:0.04, T:0.27
Consensus pattern (49 bp):
AAATAAATCTTCTAAGCTATGAACAAAATAAATAAATAAATAAATAAAT
Found at i:274177 original size:33 final size:33
Alignment explanation
Indices: 274135--274197 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
274125 ATAAATAAAT
274135 AAATAAATAAATAAATCTTCTAAGCTATGAACA
1 AAATAAATAAATAAATCTTCTAAGCTATGAACA
274168 AAATAAATAAATAAATCTTCTAAGCTATGA
1 AAATAAATAAATAAATCTTCTAAGCTATGA
274198 TGGCTCTGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.54, C:0.11, G:0.06, T:0.29
Consensus pattern (33 bp):
AAATAAATAAATAAATCTTCTAAGCTATGAACA
Found at i:274211 original size:16 final size:16
Alignment explanation
Indices: 274190--274221 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
274180 AAATCTTCTA
274190 AGCTATGATGGCTCTG
1 AGCTATGATGGCTCTG
274206 AGCTATGATGGCTCTG
1 AGCTATGATGGCTCTG
274222 GAAAATTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.31, T:0.31
Consensus pattern (16 bp):
AGCTATGATGGCTCTG
Found at i:274433 original size:24 final size:23
Alignment explanation
Indices: 274406--274450 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
274396 GTGGATTAAA
*
274406 TTAAAAAAATATATATAATTTTAT
1 TTAAAAAAATATA-AAAATTTTAT
**
274430 TTAATTAAATATAAAAATTTT
1 TTAAAAAAATATAAAAATTTT
274451 TTAAATATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 7 0.39
24 11 0.61
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TTAAAAAAATATAAAAATTTTAT
Found at i:274550 original size:16 final size:16
Alignment explanation
Indices: 274508--274552 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 16
274498 AAACATGATA
274508 TATATTCATATTTTTAAT
1 TATATT-ATA-TTTTAAT
*
274526 CATTATTATATTTTAAT
1 TA-TATTATATTTTAAT
274543 TATATTATAT
1 TATATTATAT
274553 AATTATTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 8 0.33
17 8 0.33
18 4 0.17
19 4 0.17
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (16 bp):
TATATTATATTTTAAT
Found at i:274740 original size:17 final size:17
Alignment explanation
Indices: 274707--274739 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
274697 GCCACACTGA
274707 AAATAAAATATAAATAT
1 AAATAAAATATAAATAT
274724 AAAT--AATATAAATAT
1 AAATAAAATATAAATAT
274739 A
1 A
274740 TGTGCAGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.75
17 4 0.25
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
AAATAAAATATAAATAT
Found at i:277468 original size:2 final size:2
Alignment explanation
Indices: 277461--277496 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
277451 AGCCAAAAGC
277461 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
277497 GAAAATGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:280818 original size:22 final size:22
Alignment explanation
Indices: 280767--280823 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
280757 AATGTATATT
280767 TAAATATAAATAT-AAAAAATAA
1 TAAAT-TAAATATAAAAAAATAA
* *
280789 TTATTTAAATATAAAAAAATTAA
1 TAAATTAAATATAAAAAAA-TAA
280812 -AAATTAAATATA
1 TAAATTAAATATA
280824 TTGTATCAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 7 0.24
22 19 0.66
23 3 0.10
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAATTAAATATAAAAAAATAA
Found at i:285305 original size:27 final size:26
Alignment explanation
Indices: 285275--285332 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
285265 TTAATTATTT
285275 AAAAT-TTAAAATTATAAATATAATATA
1 AAAATATTAAAA-TAT-AATATAATATA
*
285302 AAAATAATTAAAATATGATATAATATA
1 AAAAT-ATTAAAATATAATATAATATA
285329 AAAA
1 AAAA
285333 ATAATATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 19 0.68
28 3 0.11
29 6 0.21
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (26 bp):
AAAATATTAAAATATAATATAATATA
Found at i:285313 original size:29 final size:28
Alignment explanation
Indices: 285280--285337 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 28
285270 TATTTAAAAT
285280 TTAAAATTATAAATATAATAT-AAAAATAA
1 TTAAAA-TAT-AATATAATATAAAAAATAA
*
285309 TTAAAATATGATATAATATAAAAAATAA
1 TTAAAATATAATATAATATAAAAAATAA
285337 T
1 T
285338 ATTTATATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 9 0.33
28 12 0.44
29 6 0.22
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (28 bp):
TTAAAATATAATATAATATAAAAAATAA
Found at i:286045 original size:22 final size:24
Alignment explanation
Indices: 286016--286067 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 24
286006 TTATTTAAAT
286016 TTTA-ATAAA-TTAAAAATTAATA
1 TTTATATAAATTTAAAAATTAATA
*
286038 -TTATATAAATTTAAAAATTTATA
1 TTTATATAAATTTAAAAATTAATA
286061 TTTATAT
1 TTTATAT
286068 TTATTATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTATATAAATTTAAAAATTAATA
Found at i:286063 original size:6 final size:6
Alignment explanation
Indices: 286054--286116 Score: 51
Period size: 6 Copynumber: 10.3 Consensus size: 6
286044 AAATTTAAAA
*
286054 ATTTAT ATTTAT ATTTATT ATTATTAT ATGTTAT A-TTAT ATTT-T AATTAT
1 ATTTAT ATTTAT ATTTA-T A-T-TTAT AT-TTAT ATTTAT ATTTAT ATTTAT
*
286104 TTTTAT A-TTAT AT
1 ATTTAT ATTTAT AT
286117 AATTTTATCA
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
5 14 0.30
6 18 0.39
7 8 0.17
8 3 0.07
9 3 0.07
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (6 bp):
ATTTAT
Found at i:286080 original size:15 final size:15
Alignment explanation
Indices: 286062--286141 Score: 67
Period size: 15 Copynumber: 5.2 Consensus size: 15
286052 AAATTTATAT
286062 TTATATTTATTATTA
1 TTATATTTATTATTA
286077 TTATATGTTA-TATTA
1 TTATAT-TTATTATTA
*
286092 -TAT-TTTAATTATTT
1 TTATATTT-ATTATTA
*
286106 TTATATTATATAATTTTA
1 TTATATT-TAT--TATTA
*
286124 TCATATTTATTATTA
1 TTATATTTATTATTA
286139 TTA
1 TTA
286142 ATTATAAAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
12 2 0.04
13 2 0.04
14 7 0.14
15 20 0.39
16 7 0.14
17 4 0.08
18 9 0.18
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (15 bp):
TTATATTTATTATTA
Found at i:286110 original size:29 final size:28
Alignment explanation
Indices: 286056--286111 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
286046 ATTTAAAAAT
286056 TTATATTTATATTTATTATTATTATATG
1 TTATATTTATATTTATTATTATTATATG
*
286084 TTATA-TTATATTTTAATTATTTTTATAT
1 TTATATTTATA-TTT-ATTATTATTATAT
286112 TATATAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 5 0.20
28 8 0.32
29 12 0.48
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (28 bp):
TTATATTTATATTTATTATTATTATATG
Found at i:286183 original size:32 final size:32
Alignment explanation
Indices: 286125--286212 Score: 101
Period size: 32 Copynumber: 2.8 Consensus size: 32
286115 ATAATTTTAT
*
286125 CATATTTATTATTATTAATTATAAAATATAAA
1 CATATTTAATATTATTAATTATAAAATATAAA
*
286157 CATATTTAATATT-TTAATTATAAAA-AT-AT
1 CATATTTAATATTATTAATTATAAAATATAAA
* *
286186 TATATTTAAATATATATTAAATATAAA
1 CATATTT-AATAT-TATTAATTATAAA
286213 TATTAAAATT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
29 7 0.14
30 7 0.14
31 13 0.27
32 22 0.45
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (32 bp):
CATATTTAATATTATTAATTATAAAATATAAA
Found at i:286198 original size:13 final size:13
Alignment explanation
Indices: 286180--286233 Score: 51
Period size: 12 Copynumber: 4.3 Consensus size: 13
286170 TTAATTATAA
286180 AAATATTATATTT
1 AAATATTATATTT
286193 AAATA-TATA-TT
1 AAATATTATATTT
* *
286204 AAATATAAATATTA
1 AAATAT-TATATTT
*
286218 AAAT-TTAAATTT
1 AAATATTATATTT
286230 AAAT
1 AAAT
286234 TTAAAATTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
11 7 0.21
12 12 0.36
13 9 0.27
14 5 0.15
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATATTATATTT
Found at i:286213 original size:17 final size:17
Alignment explanation
Indices: 286165--286215 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
286155 AACATATTTA
* *
286165 ATATTTTAATTATAAA-
1 ATATATTAAATATAAAT
* *
286181 A-ATATTATATTTAAAT
1 ATATATTAAATATAAAT
286197 ATATATTAAATATAAAT
1 ATATATTAAATATAAAT
286214 AT
1 AT
286216 TAAAATTTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
15 10 0.37
16 2 0.07
17 15 0.56
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATATTAAATATAAAT
Found at i:286240 original size:7 final size:7
Alignment explanation
Indices: 286210--286246 Score: 51
Period size: 6 Copynumber: 5.4 Consensus size: 7
286200 TATTAAATAT
286210 AAATATTA
1 AAAT-TTA
286218 AAATTT-
1 AAATTTA
286224 AAATTT-
1 AAATTTA
286230 AAATTTA
1 AAATTTA
286237 AAATTTA
1 AAATTTA
286244 AAA
1 AAA
286247 AATTTTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 12 0.43
7 12 0.43
8 4 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
AAATTTA
Found at i:286240 original size:13 final size:13
Alignment explanation
Indices: 286202--286245 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
286192 TAAATATATA
*
286202 TTAAATATAAATAT
1 TTAAATTTAAA-AT
*
286216 TAAAATTT-AAAT
1 TTAAATTTAAAAT
286228 TTAAATTTAAAAT
1 TTAAATTTAAAAT
286241 TTAAA
1 TTAAA
286246 AAATTTTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
12 9 0.35
13 11 0.42
14 6 0.23
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
TTAAATTTAAAAT
Found at i:286876 original size:17 final size:17
Alignment explanation
Indices: 286846--286909 Score: 53
Period size: 17 Copynumber: 3.6 Consensus size: 17
286836 TATCTTTTTG
286846 TTTTTAGAA-TTTTTATT
1 TTTTTA-AATTTTTTATT
*
286863 TTTTTAAATTTTTTAGAAT
1 TTTTTAAATTTTTT--ATT
286882 TTTTT--ATTTTTTATAT
1 TTTTTAAATTTTTTAT-T
286898 TTTTTGAAATTT
1 TTTTT-AAATTT
286910 GCTTAATTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
15 1 0.03
16 8 0.21
17 18 0.47
19 11 0.29
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (17 bp):
TTTTTAAATTTTTTATT
Found at i:286887 original size:10 final size:9
Alignment explanation
Indices: 286862--286909 Score: 55
Period size: 9 Copynumber: 5.3 Consensus size: 9
286852 GAATTTTTAT
286862 TTTTTTAAA
1 TTTTTTAAA
286871 TTTTTTAGAA
1 TTTTTTA-AA
286881 TTTTTT--A
1 TTTTTTAAA
*
286888 TTTTTTATA
1 TTTTTTAAA
286897 TTTTTTGAAA
1 TTTTTT-AAA
286907 TTT
1 TTT
286910 GCTTAATTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
7 7 0.21
9 14 0.41
10 13 0.38
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (9 bp):
TTTTTTAAA
Found at i:286902 original size:9 final size:9
Alignment explanation
Indices: 286855--286902 Score: 55
Period size: 9 Copynumber: 5.6 Consensus size: 9
286845 GTTTTTAGAA
286855 TTTTTAT-T
1 TTTTTATAT
*
286863 TTTTTAAAT
1 TTTTTATAT
* *
286872 TTTTTAGAA
1 TTTTTATAT
286881 TTTTT-TAT
1 TTTTTATAT
286889 TTTTTATAT
1 TTTTTATAT
286898 TTTTT
1 TTTTT
286903 GAAATTTGCT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
8 12 0.36
9 21 0.64
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (9 bp):
TTTTTATAT
Found at i:286909 original size:26 final size:27
Alignment explanation
Indices: 286846--286902 Score: 91
Period size: 26 Copynumber: 2.2 Consensus size: 27
286836 TATCTTTTTG
286846 TTTTTAGAA-TTTTTATTTTTTTAAAT
1 TTTTTAGAATTTTTTATTTTTTTAAAT
*
286872 TTTTTAGAATTTTTTA-TTTTTTATAT
1 TTTTTAGAATTTTTTATTTTTTTAAAT
286898 TTTTT
1 TTTTT
286903 GAAATTTGCT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 23 0.79
27 6 0.21
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.74
Consensus pattern (27 bp):
TTTTTAGAATTTTTTATTTTTTTAAAT
Found at i:287110 original size:5 final size:5
Alignment explanation
Indices: 287081--287224 Score: 70
Period size: 5 Copynumber: 29.2 Consensus size: 5
287071 TTAATATTCG
*
287081 TATAT TCATAT TATAT T-TA- TATAT TTTAT TATAT TATAAT TATATT
1 TATAT T-ATAT TATAT TATAT TATAT TATAT TATAT TAT-AT TATA-T
* * * * * * *
287127 TAAAA TATTT TATAT T-TAT ATAAAT TTTAA TATAT TA-AT AAT-T TATAT
1 TATAT TATAT TATAT TATAT -TATAT TATAT TATAT TATAT TATAT TATAT
* * * *
287175 TATA- TATAT TTTAA AATAT T-TA- TATATT TATAT CATATT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATA-T TATAT TATA-T TATAT TATAT
287224 T
1 T
287225 TTATAAAATA
Statistics
Matches: 101, Mismatches: 24, Indels: 28
0.66 0.16 0.18
Matches are distributed among these distances:
3 2 0.02
4 21 0.21
5 54 0.53
6 24 0.24
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (5 bp):
TATAT
Found at i:287115 original size:29 final size:30
Alignment explanation
Indices: 287081--287146 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
287071 TTAATATTCG
*
287081 TATATTCAT-ATTATATTT-ATATATTTTAT
1 TATATT-ATAATTATATTTAAAATATTTTAT
287110 TATATTATAATTATATTTAAAATATTTTA-
1 TATATTATAATTATATTTAAAATATTTTAT
287139 TAT-TTATA
1 TATATTATA
287147 TAAATTTTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
28 7 0.21
29 18 0.53
30 9 0.26
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (30 bp):
TATATTATAATTATATTTAAAATATTTTAT
Found at i:287126 original size:40 final size:39
Alignment explanation
Indices: 287081--287228 Score: 101
Period size: 40 Copynumber: 3.7 Consensus size: 39
287071 TTAATATTCG
287081 TATATTCATATTATATTTATATATTTTATTATATTATAAT
1 TATATTCATATTATATTT-TATATTTTATTATATTATAAT
** * *
287121 TATATT--TAAAATATTTTATA-TTTATATAAATTTTAA-
1 TATATTCATATTATATTTTATATTTTAT-TATATTATAAT
* **
287157 TATATTAATAATTTATATTATATATATTTTAAAATATTTATATAT
1 TATATTCAT-A-TTATATT-T-TATATTTTATTATA-TTATA-AT
*
287202 T-TATATCATATT-TATATTATATTTTAT
1 TATAT-TCATATTATATTTTATATTTTAT
287229 AAAATACCAT
Statistics
Matches: 83, Mismatches: 13, Indels: 24
0.69 0.11 0.20
Matches are distributed among these distances:
36 11 0.13
37 12 0.14
38 9 0.11
39 1 0.01
40 20 0.24
41 2 0.02
42 9 0.11
43 10 0.12
44 5 0.06
45 4 0.05
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (39 bp):
TATATTCATATTATATTTTATATTTTATTATATTATAAT
Found at i:287172 original size:33 final size:33
Alignment explanation
Indices: 287130--287207 Score: 104
Period size: 32 Copynumber: 2.4 Consensus size: 33
287120 TTATATTTAA
* *
287130 AATATTTTATATTTATATAAATTTTAATATATT
1 AATAATTTATATTTATATAAATTTTAAAATATT
*
287163 AATAATTTATA-TTATATATATTTTAAAATATT
1 AATAATTTATATTTATATAAATTTTAAAATATT
*
287195 TATATATTTATAT
1 AATA-ATTTATAT
287208 CATATTTATA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
32 22 0.56
33 17 0.44
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (33 bp):
AATAATTTATATTTATATAAATTTTAAAATATT
Found at i:287187 original size:16 final size:16
Alignment explanation
Indices: 287091--287229 Score: 76
Period size: 16 Copynumber: 8.8 Consensus size: 16
287081 TATATTCATA
287091 TTATATT-TATATA-T
1 TTATATTATATATATT
*
287105 TT-TATTATAT-TATAA
1 TTATATTATATATAT-T
*
287120 TTATATT-TAAAATATT
1 TTATATTAT-ATATATT
*
287136 TTATATTTATATAAATT
1 TTATA-TTATATATATT
*
287153 TTA-A-TATATTAATAAT
1 TTATATTATA-T-ATATT
287169 TTATATTATATATATT
1 TTATATTATATATATT
* * *
287185 TTAAAATATTTATATAT
1 TTATATTATATATAT-T
* * *
287202 TTATATCATATTTATA
1 TTATATTATATATATT
*
287218 TTATATTTTATA
1 TTATATTATATA
287230 AAATACCATA
Statistics
Matches: 92, Mismatches: 20, Indels: 24
0.68 0.15 0.18
Matches are distributed among these distances:
13 6 0.07
14 9 0.10
15 4 0.04
16 42 0.46
17 26 0.28
18 5 0.05
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (16 bp):
TTATATTATATATATT
Found at i:287188 original size:24 final size:24
Alignment explanation
Indices: 287156--287207 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
287146 ATAAATTTTA
*
287156 ATATATTAATA-ATTTATATTATAT
1 ATATATTAAAATATTTATA-TATAT
* *
287180 ATATTTTAAAATATTTATATATTT
1 ATATATTAAAATATTTATATATAT
287204 ATAT
1 ATAT
287208 CATATTTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 17 0.71
25 7 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
ATATATTAAAATATTTATATATAT
Found at i:287223 original size:42 final size:40
Alignment explanation
Indices: 287131--287234 Score: 115
Period size: 40 Copynumber: 2.5 Consensus size: 40
287121 TATATTTAAA
*
287131 ATATTTTATATTTATATAAAT-TTTAATATATTAATAATTT
1 ATATTATATATTTATA-AAATATTTAATATATTAATAATTT
*
287171 ATATTATATATATTTTAAAATATTT-ATATATTTATATCATATTT
1 ATATTATATAT-TTATAAAATATTTAATATA-TTA-AT-A-ATTT
287215 ATATTATAT-TTTATAAAATA
1 ATATTATATATTTATAAAATA
287235 CCATATTATA
Statistics
Matches: 55, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
40 19 0.35
41 10 0.18
42 11 0.20
43 2 0.04
44 13 0.24
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (40 bp):
ATATTATATATTTATAAAATATTTAATATATTAATAATTT
Found at i:287590 original size:12 final size:12
Alignment explanation
Indices: 287570--287600 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
287560 TATTAAAAGA
287570 ATAAT-TAAAAT
1 ATAATATAAAAT
287581 ATAATATAAAAT
1 ATAATATAAAAT
287593 ATAATATA
1 ATAATATA
287601 GTATAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.26
12 14 0.74
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
ATAATATAAAAT
Found at i:287600 original size:17 final size:16
Alignment explanation
Indices: 287578--287618 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
287568 GAATAATTAA
287578 AATATAATATAAAATAT
1 AATATAATATAAAA-AT
*
287595 AATATAGTATAAAAAT
1 AATATAATATAAAAAT
287611 AATTATAA
1 AA-TATAA
287619 ATTATGATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (16 bp):
AATATAATATAAAAAT
Found at i:288015 original size:14 final size:14
Alignment explanation
Indices: 287998--288031 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
287988 AAAATTTTTA
*
287998 TTTTTATTTTTCTT
1 TTTTTATTTTTATT
*
288012 TTTTCATTTTTATT
1 TTTTTATTTTTATT
288026 TTTTTA
1 TTTTTA
288032 AAAAATTTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTTTATTTTTATT
Found at i:289222 original size:20 final size:19
Alignment explanation
Indices: 289196--289242 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
289186 GAATAAATAA
* *
289196 AATATTTTTTATATAAATT
1 AATATTTTTTAAAAAAATT
*
289215 AATCATTTATTAAAAAAATT
1 AAT-ATTTTTTAAAAAAATT
289235 AATATTTT
1 AATATTTT
289243 AACTTTTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (19 bp):
AATATTTTTTAAAAAAATT
Found at i:289697 original size:11 final size:12
Alignment explanation
Indices: 289669--289728 Score: 53
Period size: 11 Copynumber: 5.6 Consensus size: 12
289659 TTTATTTAAA
*
289669 ATATTTTATA-T
1 ATATTATATATT
289680 ATA-TATATATT
1 ATATTATATATT
289691 A-ATTATA-A-T
1 ATATTATATATT
289700 ATATT-TATATT
1 ATATTATATATT
*
289711 ATTTTATATATT
1 ATATTATATATT
289723 AT-TTAT
1 ATATTAT
289729 TTTATAATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
9 4 0.10
10 11 0.27
11 18 0.44
12 8 0.20
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
ATATTATATATT
Found at i:289729 original size:16 final size:16
Alignment explanation
Indices: 289683--289734 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
289673 TTTATATATA
* **
289683 TATATATTAATTATAA
1 TATATATTATTTATTT
289699 TATAT-TTATATTATTT
1 TATATATTAT-TTATTT
289715 TATATATTATTTATTT
1 TATATATTATTTATTT
289731 TATA
1 TATA
289735 ATTTTAATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
15 3 0.10
16 24 0.77
17 4 0.13
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TATATATTATTTATTT
Found at i:289752 original size:24 final size:23
Alignment explanation
Indices: 289689--289755 Score: 64
Period size: 24 Copynumber: 2.7 Consensus size: 23
289679 TATATATATA
*
289689 TTAATTATAATATATTTATATTATT
1 TTAATTATAAT-TATTT-TATAATT
*
289714 TT-ATATATTATTTATTTTATAATT
1 TTAAT-TA-TAATTATTTTATAATT
289738 TTAATGTATAATTATTTT
1 TTAAT-TATAATTATTTT
289756 TATTCAAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
24 19 0.54
25 13 0.37
26 3 0.09
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (23 bp):
TTAATTATAATTATTTTATAATT
Found at i:289752 original size:40 final size:41
Alignment explanation
Indices: 289653--289755 Score: 117
Period size: 40 Copynumber: 2.6 Consensus size: 41
289643 CTCTTATCCA
*
289653 TATAATTTTATTTA-AAATATTTTATATATATATATATTAAT
1 TATAATTTTATTTATAATTATTTTATATATATATATATT-AT
* *
289694 TATAA-TATATTTAT-ATTATTTTATATAT-TATTTATT-T
1 TATAATTTTATTTATAATTATTTTATATATATATATATTAT
*
289731 TATAATTTTAATGTATAATTATTTT
1 TATAATTTT-ATTTATAATTATTTT
289756 TATTCAAAAT
Statistics
Matches: 53, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
37 6 0.11
38 2 0.04
39 12 0.23
40 28 0.53
41 5 0.09
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (41 bp):
TATAATTTTATTTATAATTATTTTATATATATATATATTAT
Found at i:289919 original size:21 final size:21
Alignment explanation
Indices: 289895--289958 Score: 56
Period size: 23 Copynumber: 2.9 Consensus size: 21
289885 TATTTTCATT
289895 TATTATAATTATATTTTAAAA
1 TATTATAATTATATTTTAAAA
* * *
289916 TATTTTTATTATTAATTTTAATA
1 TATTATAATTA-T-ATTTTAAAA
*
289939 TATTTATATTTTATATTTTA
1 TA-TTATA-ATTATATTTTA
289959 TTTTAATTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
21 9 0.27
22 1 0.03
23 16 0.48
24 4 0.12
25 3 0.09
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TATTATAATTATATTTTAAAA
Found at i:289950 original size:28 final size:29
Alignment explanation
Indices: 289919--289977 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 29
289909 TTTAAAATAT
289919 TTTTAT-TATTAATTTTAA-TATATTTATA
1 TTTTATAT-TTAATTTTAATTATATTTATA
* *
289947 TTTTATATTTTATTTTAATTATTTTTATA
1 TTTTATATTTAATTTTAATTATATTTATA
289976 TT
1 TT
289978 AAAAATATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 15 0.56
29 12 0.44
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (29 bp):
TTTTATATTTAATTTTAATTATATTTATA
Found at i:289972 original size:15 final size:15
Alignment explanation
Indices: 289930--289979 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
289920 TTTATTATTA
*
289930 ATTTTAATATATTTAT
1 ATTTTAAT-TATTTTT
289946 ATTTT-A-TA-TTTT
1 ATTTTAATTATTTTT
289958 ATTTTAATTATTTTT
1 ATTTTAATTATTTTT
*
289973 ATATTAA
1 ATTTTAA
289980 AAATATAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
12 8 0.28
13 3 0.10
14 2 0.07
15 11 0.38
16 5 0.17
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
ATTTTAATTATTTTT
Found at i:289973 original size:29 final size:29
Alignment explanation
Indices: 289915--289977 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
289905 ATATTTTAAA
289915 ATATTTTTATTATTAATTTTAATATATTT
1 ATATTTTTATTATTAATTTTAATATATTT
*
289944 ATATTTTATATT-TT-ATTTTAATTATTTTT
1 ATATTTT-TATTATTAATTTTAA-TATATTT
289973 ATATT
1 ATATT
289978 AAAAATATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 7 0.23
29 20 0.65
30 4 0.13
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (29 bp):
ATATTTTTATTATTAATTTTAATATATTT
Found at i:292023 original size:31 final size:31
Alignment explanation
Indices: 291953--292029 Score: 79
Period size: 30 Copynumber: 2.5 Consensus size: 31
291943 ATATGTTATC
* * *
291953 ATGTTTTTAAAATA-TTTTTAATGTTTAATT
1 ATGTATTTAAAATATTTTTTAATGATAAATT
*
291983 ATGTTTTTAAAATATTTTTTAAT-ATAAATT
1 ATGTATTTAAAATATTTTTTAATGATAAATT
*
292013 TTGATATTTAAAA-ATTT
1 ATG-TATTTAAAATATTT
292030 ATATTTTGTA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
30 25 0.61
31 16 0.39
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (31 bp):
ATGTATTTAAAATATTTTTTAATGATAAATT
Found at i:292569 original size:2 final size:2
Alignment explanation
Indices: 292564--292596 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
292554 TATACCTCCC
292564 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 A
292597 GAATTATTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:365237 original size:19 final size:18
Alignment explanation
Indices: 365194--365246 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
365184 ATTGTTTATT
*
365194 TAATGATAATTTATTTAA
1 TAATTATAATTTATTTAA
*
365212 TATTTATTAATTTATTT-A
1 TAATTA-TAATTTATTTAA
*
365230 TAAATTATATTTTATTT
1 T-AATTATAATTTATTT
365247 TTATGTTTAC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 15 0.52
19 14 0.48
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (18 bp):
TAATTATAATTTATTTAA
Found at i:365324 original size:17 final size:18
Alignment explanation
Indices: 365295--365328 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
365285 AAATTGTTAA
365295 TATATATATTAATTATTT
1 TATATATATTAATTATTT
365313 TATATA-ATTAATTATT
1 TATATATATTAATTATT
365329 ATTAAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TATATATATTAATTATTT
Found at i:365549 original size:16 final size:16
Alignment explanation
Indices: 365528--365591 Score: 83
Period size: 18 Copynumber: 3.8 Consensus size: 16
365518 ACTTATATAA
365528 TTATATATTTTATTTTT
1 TTATATATTTT-TTTTT
*
365545 TATATATATTTTTTTAT
1 T-TATATATTTTTTTTT
365562 TTATAATTATTTTTTTTT
1 TTAT-A-TATTTTTTTTT
365580 TTATATATTTTT
1 TTATATATTTTT
365592 ATCATATATA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
16 10 0.24
17 8 0.19
18 24 0.57
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (16 bp):
TTATATATTTTTTTTT
Found at i:365585 original size:32 final size:35
Alignment explanation
Indices: 365540--365607 Score: 88
Period size: 32 Copynumber: 2.0 Consensus size: 35
365530 ATATATTTTA
*
365540 TTTTTTATATATAT-TTTTT-T-ATTTATAATTAT
1 TTTTTTATATATATATTTTTATCATATATAATTAT
* *
365572 TTTTTTTTTTATATATTTTTATCATATATAATTAT
1 TTTTTTATATATATATTTTTATCATATATAATTAT
365607 T
1 T
365608 ATATAATTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
32 12 0.40
33 5 0.17
34 1 0.03
35 12 0.40
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.71
Consensus pattern (35 bp):
TTTTTTATATATATATTTTTATCATATATAATTAT
Found at i:366912 original size:8 final size:8
Alignment explanation
Indices: 366892--366929 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
366882 ATAATACTAC
366892 TTTTTCTT
1 TTTTTCTT
*
366900 GTTTTTCCT
1 -TTTTTCTT
366909 TTTTT-TT
1 TTTTTCTT
366916 TTTTTCTT
1 TTTTTCTT
366924 TTTTTC
1 TTTTTC
366930 GCATTTGAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
7 6 0.23
8 13 0.50
9 7 0.27
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.84
Consensus pattern (8 bp):
TTTTTCTT
Found at i:372609 original size:155 final size:159
Alignment explanation
Indices: 372392--372698 Score: 412
Period size: 158 Copynumber: 1.9 Consensus size: 159
372382 AACTAAGTTT
*
372392 AATGATGATGGTGATTTCTTCCTTAACTAGGAGAAAACCAAAATTGTGGGTTCAAGTGGAACTTA
1 AATGATGATGGTGATTTCTTCCTTAACTAGGAGAAAACC-AAATTGCGGGTTCAAGTGGAACTTA
* * *
372457 AATTT-AATCTTA-CCAGGG-AAAGAATGAAACTTTCTTTG-TTTTAAGGAAAACAAGTTATCGA
65 AATTTGAATCTTATCAAGGGTAAAGAATGAAACTTCCTTTGTTTTTAAGGAAAACAAGCTAT-GA
* *
372518 ATAACTCCGTTGTTGTGTTAAAAGTTGGTTC
129 ATAACTCCCTTCTTGTGTTAAAAGTTGGTTC
* * * *
372549 AATGGTGATGGTGGTTATCTTCCTTAACT-GGAAGAAAACC-GA-TGCGGGTTCAGGTGGAACTT
1 AATGATGATGGTGATT-TCTTCCTTAACTAGG-AGAAAACCAAATTGCGGGTTCAAGTGGAACTT
* *
372611 AGATTTGAATCTTATCAAGGGTAAAGAATGAAACTTCCTTTGTTTTTAAGGAAAACAAGCTATTA
64 AAATTTGAATCTTATCAAGGGTAAAGAATGAAACTTCCTTTGTTTTTAAGGAAAACAAGCTATGA
*
372676 ATAGCTCCCTTCTTGTGTTAAAA
129 ATAACTCCCTTCTTGTGTTAAAA
372699 CAGTCTTGTT
Statistics
Matches: 131, Mismatches: 13, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
155 23 0.18
156 8 0.06
157 21 0.16
158 60 0.46
159 19 0.15
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.33
Consensus pattern (159 bp):
AATGATGATGGTGATTTCTTCCTTAACTAGGAGAAAACCAAATTGCGGGTTCAAGTGGAACTTAA
ATTTGAATCTTATCAAGGGTAAAGAATGAAACTTCCTTTGTTTTTAAGGAAAACAAGCTATGAAT
AACTCCCTTCTTGTGTTAAAAGTTGGTTC
Found at i:374874 original size:20 final size:20
Alignment explanation
Indices: 374849--374889 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
374839 ATATTAAGAA
374849 AAAATTAAT-AATAATAATAT
1 AAAATTAATAAATAAT-ATAT
*
374869 AAAATTATTAAATAATATAT
1 AAAATTAATAAATAATATAT
374889 A
1 A
374890 CAAGATAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAATTAATAAATAATATAT
Found at i:377374 original size:32 final size:31
Alignment explanation
Indices: 377338--377409 Score: 99
Period size: 32 Copynumber: 2.3 Consensus size: 31
377328 TTTATTTAAA
377338 ATATTTTATATATATATATATTAATATATTAT
1 ATATTTTATATATATATATATT-ATATATTAT
* * *
377370 ATATTTTATATATTTATATATTATTTATTTT
1 ATATTTTATATATATATATATTATATATTAT
377401 ATAATTTTA
1 AT-ATTTTA
377410 ATGTATAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
31 9 0.25
32 27 0.75
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (31 bp):
ATATTTTATATATATATATATTATATATTAT
Found at i:377409 original size:24 final size:24
Alignment explanation
Indices: 377338--377407 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 24
377328 TTTATTTAAA
* * *
377338 ATATTTTATATA-TATATATATTA
1 ATATATTATATATTTTATATATTT
377361 ATATATTATATATTTTATATATTT
1 ATATATTATATATTTTATATATTT
*
377385 ATATATTATTTATTTTATA-ATTT
1 ATATATTATATATTTTATATATTT
377408 TAATGTATAA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
23 15 0.36
24 27 0.64
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (24 bp):
ATATATTATATATTTTATATATTT
Found at i:377588 original size:21 final size:21
Alignment explanation
Indices: 377564--377627 Score: 56
Period size: 23 Copynumber: 2.9 Consensus size: 21
377554 TATTTTCATT
377564 TATTATAATTATATTTTAAAA
1 TATTATAATTATATTTTAAAA
* * *
377585 TATTTTTATTATTAATTTTAATA
1 TATTATAATTA-T-ATTTTAAAA
*
377608 TATTTATATTTTATATTTTA
1 TA-TTATA-ATTATATTTTA
377628 TTTTAATTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
21 9 0.27
22 1 0.03
23 16 0.48
24 4 0.12
25 3 0.09
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TATTATAATTATATTTTAAAA
Found at i:377619 original size:28 final size:29
Alignment explanation
Indices: 377588--377646 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 29
377578 TTTAAAATAT
377588 TTTTAT-TATTAATTTTAA-TATATTTATA
1 TTTTATAT-TTAATTTTAATTATATTTATA
* *
377616 TTTTATATTTTATTTTAATTATTTTTATA
1 TTTTATATTTAATTTTAATTATATTTATA
377645 TT
1 TT
377647 AAAAATATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 15 0.56
29 12 0.44
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (29 bp):
TTTTATATTTAATTTTAATTATATTTATA
Found at i:377641 original size:15 final size:15
Alignment explanation
Indices: 377599--377648 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
377589 TTTATTATTA
*
377599 ATTTTAATATATTTAT
1 ATTTTAAT-TATTTTT
377615 ATTTT-A-TA-TTTT
1 ATTTTAATTATTTTT
377627 ATTTTAATTATTTTT
1 ATTTTAATTATTTTT
*
377642 ATATTAA
1 ATTTTAA
377649 AAATATAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
12 8 0.28
13 3 0.10
14 2 0.07
15 11 0.38
16 5 0.17
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
ATTTTAATTATTTTT
Found at i:377642 original size:29 final size:29
Alignment explanation
Indices: 377584--377646 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
377574 ATATTTTAAA
377584 ATATTTTTATTATTAATTTTAATATATTT
1 ATATTTTTATTATTAATTTTAATATATTT
*
377613 ATATTTTATATT-TT-ATTTTAATTATTTTT
1 ATATTTT-TATTATTAATTTTAA-TATATTT
377642 ATATT
1 ATATT
377647 AAAAATATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 7 0.23
29 20 0.65
30 4 0.13
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (29 bp):
ATATTTTTATTATTAATTTTAATATATTT
Found at i:379696 original size:31 final size:31
Alignment explanation
Indices: 379631--379702 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 31
379621 TTATCATGTT
* * *
379631 TTTAAAATA-TTTTTAATGTTTAATTGTGTT
1 TTTAAAATATTTTTTAATGATAAATTGTGTA
*
379661 TTTAAAATATTTTTTAAT-ATAAATTTTGATA
1 TTTAAAATATTTTTTAATGATAAATTGTG-TA
379692 TTTAAAA-ATTT
1 TTTAAAATATTT
379703 ATATTTTGTA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
30 20 0.56
31 16 0.44
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.57
Consensus pattern (31 bp):
TTTAAAATATTTTTTAATGATAAATTGTGTA
Found at i:380239 original size:2 final size:2
Alignment explanation
Indices: 380234--380268 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
380224 TATACCTCCC
380234 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
380269 GAATTATTTG
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:384183 original size:17 final size:18
Alignment explanation
Indices: 384158--384208 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
384148 TTTAATATAT
*
384158 AATTATTTTAT-TTTTTA
1 AATTATTTTATATATTTA
*
384175 AATTTTTTTATATATTTA
1 AATTATTTTATATATTTA
384193 AA-TATATTTATATATT
1 AATTAT-TTTATATATT
384209 ATGTATAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
17 12 0.41
18 17 0.59
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
AATTATTTTATATATTTA
Found at i:386705 original size:13 final size:13
Alignment explanation
Indices: 386687--386712 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
386677 CAATTTTTTG
386687 TGTATCGATACAT
1 TGTATCGATACAT
386700 TGTATCGATACAT
1 TGTATCGATACAT
386713 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:386777 original size:21 final size:21
Alignment explanation
Indices: 386751--386826 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
386741 CTGCCAAGAA
*
386751 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
386772 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
386792 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
386813 ATGTATCGATACAT
1 ATGTATCGATACAT
386827 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:386797 original size:20 final size:20
Alignment explanation
Indices: 386772--386844 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
386762 CATCTTTTTT
386772 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
386792 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
386813 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
386833 ATGTATCGATAC
1 ATGTATCGATAC
386845 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:386808 original size:41 final size:41
Alignment explanation
Indices: 386751--386844 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
386741 CTGCCAAGAA
*
386751 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
386792 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
386833 ATGTATCGATAC
1 ATGTATCGATAC
386845 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:387493 original size:31 final size:31
Alignment explanation
Indices: 387458--387522 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
387448 CCCCCGTTTA
387458 ATAAAAAATCTCCCCCTTAATCAAGTAATTC
1 ATAAAAAATCTCCCCCTTAATCAAGTAATTC
387489 ATAAAAAATCTCCCCCTTAATCAAGTAATTC
1 ATAAAAAATCTCCCCCTTAATCAAGTAATTC
387520 ATA
1 ATA
387523 TCAAAATTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.43, C:0.25, G:0.03, T:0.29
Consensus pattern (31 bp):
ATAAAAAATCTCCCCCTTAATCAAGTAATTC
Found at i:389331 original size:13 final size:13
Alignment explanation
Indices: 389313--389351 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
389303 ATAATCACCC
*
389313 TGTATCGATACAG
1 TGTATCGATACAA
389326 TGTATCGATACAA
1 TGTATCGATACAA
389339 TGTATCGATACAA
1 TGTATCGATACAA
389352 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:389362 original size:20 final size:20
Alignment explanation
Indices: 389337--389415 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 20
389327 GTATCGATAC
389337 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
389357 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
*
389382 GATGTATCGATACACAA-AAA
1 AATGTATCGATACA-AAGAAA
*
389402 CATGTATCGATACA
1 AATGTATCGATACA
389416 TTTTGGACAT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
20 32 0.65
25 16 0.33
26 1 0.02
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:391450 original size:15 final size:15
Alignment explanation
Indices: 391430--391460 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
391420 ATTTCGTTTG
*
391430 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
391445 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
391460 G
1 G
391461 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:395534 original size:13 final size:13
Alignment explanation
Indices: 395516--395541 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
395506 CAATTTTTTG
395516 TGTATCGATACAT
1 TGTATCGATACAT
395529 TGTATCGATACAT
1 TGTATCGATACAT
395542 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:395606 original size:21 final size:21
Alignment explanation
Indices: 395580--395655 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
395570 CTGCCAAGAA
*
395580 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
395601 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
395621 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
395642 ATGTATCGATACAT
1 ATGTATCGATACAT
395656 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:395626 original size:20 final size:20
Alignment explanation
Indices: 395601--395673 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
395591 CATCTTTTTT
395601 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
395621 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
395642 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
395662 ATGTATCGATAC
1 ATGTATCGATAC
395674 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:395637 original size:41 final size:41
Alignment explanation
Indices: 395580--395673 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
395570 CTGCCAAGAA
*
395580 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
395621 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
395662 ATGTATCGATAC
1 ATGTATCGATAC
395674 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:396166 original size:50 final size:50
Alignment explanation
Indices: 396103--396264 Score: 189
Period size: 50 Copynumber: 3.2 Consensus size: 50
396093 AGGTGTAAAA
* * *
396103 TAATTGTTGACTATTTTTCATTAATTTTTGACAATTGAGAAAAGTGATCG
1 TAATTGTTGACTATTTTTCAATAATTTTTGACAATAGAGAAAGGTGATCG
* * * * * *
396153 TAATTATTAACTATTTTTTAATAATTTTTGACAATCGAGAGAGGTAATCG
1 TAATTGTTGACTATTTTTCAATAATTTTTGACAATAGAGAAAGGTGATCG
* * * ** *
396203 TAATTGTGGACTATTCTTCACTAACATTTGACAATAGAGAAAGGTGACCG
1 TAATTGTTGACTATTTTTCAATAATTTTTGACAATAGAGAAAGGTGATCG
396253 TAATTGTTGACT
1 TAATTGTTGACT
396265 CTAAGCATCT
Statistics
Matches: 91, Mismatches: 21, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
50 91 1.00
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (50 bp):
TAATTGTTGACTATTTTTCAATAATTTTTGACAATAGAGAAAGGTGATCG
Found at i:404186 original size:2 final size:2
Alignment explanation
Indices: 404179--404213 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
404169 ATTAAAAATA
404179 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
404214 AATCCATTAG
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:405336 original size:36 final size:36
Alignment explanation
Indices: 405286--405564 Score: 274
Period size: 36 Copynumber: 8.0 Consensus size: 36
405276 AAAAAGCAGC
*
405286 TTGGTGCTAACAATGGTACGGGGCCTGGCCGGCCTG
1 TTGGTGCTAGCAATGGTACGGGGCCTGGCCGGCCTG
*
405322 TTGGTGCTAGCAATGGTATGGGG-CTCGGCCGGCCTG
1 TTGGTGCTAGCAATGGTACGGGGCCT-GGCCGGCCTG
*
405358 TTGGTGCTAGCAATGGTATGGGG-CTCGGCCGGCCTG
1 TTGGTGCTAGCAATGGTACGGGGCCT-GGCCGGCCTG
* *
405394 TTGGTGCT---AATGGTACTGGGCCTGGCCGGTCTG
1 TTGGTGCTAGCAATGGTACGGGGCCTGGCCGGCCTG
* * * * *
405427 TTGGTCCTAGCAATGGTACTGGACCTGGTCAGCCTG
1 TTGGTGCTAGCAATGGTACGGGGCCTGGCCGGCCTG
* * * *
405463 TTGGTCCTAGCAATGGTACTGGACCTGGTCGGCC--
1 TTGGTGCTAGCAATGGTACGGGGCCTGGCCGGCCTG
* * *
405497 -TGGTGCTAGCAGTGGTTCGGGGCCTGGTCGGCC--
1 TTGGTGCTAGCAATGGTACGGGGCCTGGCCGGCCTG
* * * *
405530 -TGGTGCTAGCAGTGGTTCCGGGCCTGGTCGGCCTG
1 TTGGTGCTAGCAATGGTACGGGGCCTGGCCGGCCTG
405565 CTAGTCTTAA
Statistics
Matches: 219, Mismatches: 17, Indels: 15
0.87 0.07 0.06
Matches are distributed among these distances:
33 86 0.39
34 2 0.01
35 2 0.01
36 129 0.59
ACGTcount: A:0.11, C:0.24, G:0.39, T:0.26
Consensus pattern (36 bp):
TTGGTGCTAGCAATGGTACGGGGCCTGGCCGGCCTG
Found at i:405496 original size:105 final size:105
Alignment explanation
Indices: 405297--405531 Score: 278
Period size: 105 Copynumber: 2.2 Consensus size: 105
405287 TGGTGCTAAC
* ** *
405297 AATGGTACGGGGCCTGGCCGGCCTGTTGGTGCTAGCAATGGTATGGGGCTCGGCCGGCCTGTTGG
1 AATGGTACGGGGCCTGGCCGGCCTGTTGGTCCTAGCAATGGTATGGACCTCGGCCAGCCTGTTGG
* **
405362 TGCTAGCAATGGTATGGGGCTCGGCCGGCCTGTTGGTGCT
66 TCCTAGCAATGGTATGGACCTCGGCCGGCCTGTTGGTGCT
* * *
405402 AATGGTACTGGGCCTGGCCGGTCTGTTGGTCCTAGCAATGGTACTGGACCT-GGTCAGCCTGTTG
1 AATGGTACGGGGCCTGGCCGGCCTGTTGGTCCTAGCAATGGTA-TGGACCTCGGCCAGCCTGTTG
* * *
405466 GTCCTAGCAATGGTACTGGACCT-GGTCGGCCTGGTGCTAGC-
65 GTCCTAGCAATGGTA-TGGACCTCGGCCGGCCTGTTGGT-GCT
* * *
405507 AGTGGTTCGGGGCCTGGTCGGCCTG
1 AATGGTACGGGGCCTGGCCGGCCTG
405532 GTGCTAGCAG
Statistics
Matches: 109, Mismatches: 18, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
105 97 0.89
106 12 0.11
ACGTcount: A:0.11, C:0.24, G:0.39, T:0.26
Consensus pattern (105 bp):
AATGGTACGGGGCCTGGCCGGCCTGTTGGTCCTAGCAATGGTATGGACCTCGGCCAGCCTGTTGG
TCCTAGCAATGGTATGGACCTCGGCCGGCCTGTTGGTGCT
Found at i:405523 original size:33 final size:33
Alignment explanation
Indices: 405486--405564 Score: 149
Period size: 33 Copynumber: 2.4 Consensus size: 33
405476 TGGTACTGGA
*
405486 CCTGGTCGGCCTGGTGCTAGCAGTGGTTCGGGG
1 CCTGGTCGGCCTGGTGCTAGCAGTGGTTCCGGG
405519 CCTGGTCGGCCTGGTGCTAGCAGTGGTTCCGGG
1 CCTGGTCGGCCTGGTGCTAGCAGTGGTTCCGGG
405552 CCTGGTCGGCCTG
1 CCTGGTCGGCCTG
405565 CTAGTCTTAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.05, C:0.28, G:0.43, T:0.24
Consensus pattern (33 bp):
CCTGGTCGGCCTGGTGCTAGCAGTGGTTCCGGG
Found at i:414604 original size:2 final size:2
Alignment explanation
Indices: 414597--414650 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
414587 GCAAGATACC
*
414597 GA GA GA GA CA GA GA GA 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 GA GA GA GA GA GA GA GA
414639 GA GA GA GA GA GA
1 GA GA GA GA GA GA
414651 AGGTTATGAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.02, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:418427 original size:16 final size:16
Alignment explanation
Indices: 418406--418472 Score: 61
Period size: 16 Copynumber: 4.2 Consensus size: 16
418396 ATAAATATAT
418406 TAAATTTTATATAATA
1 TAAATTTTATATAATA
418422 TAAATTATTA-AT-ATA
1 TAAATT-TTATATAATA
*
418437 TAAAAATTTATATAATA
1 T-AAATTTTATATAATA
418454 TATAATATTT-T-TAATA
1 TA-AAT-TTTATATAATA
418470 TAA
1 TAA
418473 TTATCATATA
Statistics
Matches: 43, Mismatches: 2, Indels: 13
0.74 0.03 0.22
Matches are distributed among these distances:
15 8 0.19
16 22 0.51
17 10 0.23
18 3 0.07
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TAAATTTTATATAATA
Found at i:427148 original size:35 final size:37
Alignment explanation
Indices: 427109--427184 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 37
427099 TATATTTTTT
* *
427109 TAATTTTA-ATTTTTA-ATAATATAAATAATTTAATA
1 TAATTTTATATTTTTATATAATAAAAATAATATAATA
* * *
427144 TAATTTTATTTTTTTATATGATAAAAATTATATAATA
1 TAATTTTATATTTTTATATAATAAAAATAATATAATA
427181 TAAT
1 TAAT
427185 CGAGTTGTGT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
35 8 0.24
36 6 0.18
37 20 0.59
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (37 bp):
TAATTTTATATTTTTATATAATAAAAATAATATAATA
Found at i:428243 original size:27 final size:27
Alignment explanation
Indices: 428224--428307 Score: 86
Period size: 27 Copynumber: 3.2 Consensus size: 27
428214 TTAATTTTAA
428224 AATTTA-ATAAA-TTAAATTTAAATTT
1 AATTTATATAAATTTAAATTTAAATTT
** *
428249 AATTTATATAAATTTAAATAAAAATTA
1 AATTTATATAAATTTAAATTTAAATTT
* *
428276 AATTTA-AGATAATTTAAA-TTAAAATT
1 AATTTATATA-AATTTAAATTTAAATTT
428302 AATTTA
1 AATTTA
428308 AATTTTTTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
25 6 0.12
26 17 0.35
27 25 0.52
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (27 bp):
AATTTATATAAATTTAAATTTAAATTT
Found at i:428246 original size:6 final size:6
Alignment explanation
Indices: 428212--428405 Score: 58
Period size: 6 Copynumber: 33.0 Consensus size: 6
428202 TTATAAACTG
* * *
428212 ATTTAA TTTTAAA ATTTAATA AATTAA ATTTAA ATTT-A ATTT-- ATATAA
1 ATTTAA ATTT-AA ATTT-A-A ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* * *
428260 ATTTAA A-TAAA AATTAA ATTTAA GA--T-A ATTTAA A-TTAA AATT-A
1 ATTTAA ATTTAA ATTTAA ATTTAA -ATTTAA ATTTAA ATTTAA ATTTAA
* * * * *
428303 ATTTAA ATTT-T TTTTAAAA AATTAA ATTTTAA AATTAA AATT-A ATTTAA
1 ATTTAA ATTTAA ATTT--AA ATTTAA A-TTTAA ATTTAA ATTTAA ATTTAA
* * *
428352 ATTT-- TTTTAAAA AATTAA ATTTTAAA ATTTAA A-TT-A ATTTTA ATTTAA
1 ATTTAA ATTT--AA ATTTAA A-TTT-AA ATTTAA ATTTAA ATTTAA ATTTAA
428400 ATTTAA
1 ATTTAA
428406 TTTGATGCCG
Statistics
Matches: 141, Mismatches: 23, Indels: 48
0.67 0.11 0.23
Matches are distributed among these distances:
3 1 0.01
4 9 0.06
5 31 0.22
6 70 0.50
7 19 0.13
8 11 0.08
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.48
Consensus pattern (6 bp):
ATTTAA
Found at i:428260 original size:21 final size:20
Alignment explanation
Indices: 428223--428282 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
428213 TTTAATTTTA
428223 AAATTTAATAAATTAAATTT
1 AAATTTAATAAATTAAATTT
**
428243 AAATTTAATTTATATAAATTT
1 AAATTTAATAAAT-TAAATTT
428264 AAA--TAA-AAATTAAATTT
1 AAATTTAATAAATTAAATTT
428281 AA
1 AA
428283 GATAATTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 9 0.26
18 2 0.06
19 3 0.09
20 11 0.31
21 10 0.29
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
AAATTTAATAAATTAAATTT
Done.