Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 2 of 206
Found at i:357532 original size:16 final size:17
Alignment explanation
Indices: 357513--357546 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
357503 TGTTTTTGTA
357513 TTCTATTTAAA-ATTTT
1 TTCTATTTAAATATTTT
*
357529 TTCTTTTTAAATATTTT
1 TTCTATTTAAATATTTT
357546 T
1 T
357547 ATGTAAATAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (17 bp):
TTCTATTTAAATATTTT
Found at i:363402 original size:31 final size:29
Alignment explanation
Indices: 363367--363532 Score: 127
Period size: 31 Copynumber: 5.4 Consensus size: 29
363357 CTTAATTGAG
363367 ATTTTTAAAAAAATTAAGAGGTTTAATAAGA
1 ATTTTTAAAAAAATTAA-AGGTTTAATAA-A
* * *
363398 ATTTTTTAAAAAGATT-AGGGTCTAATTAAA
1 A-TTTTTAAAAAAATTAAAGGTTTAA-TAAA
* * *
363428 ATTTTTTTAAAAAATTAAAAGATTTAATGATA
1 A-TTTTTAAAAAAATT-AAAGGTTTAAT-AAA
* *
363460 ATTTTTAAAAAAAAATAAAGATTTAATTAAA
1 ATTTTT-AAAAAAATTAAAGGTTTAA-TAAA
*
363491 ATTTTTAAAAAATTTGAAAGGTTTAATGAAA
1 ATTTTTAAAAAAATT-AAAGGTTTAAT-AAA
* *
363522 AGTTGTAAAAA
1 ATTTTTAAAAA
363533 TGTTGGTAAA
Statistics
Matches: 109, Mismatches: 17, Indels: 18
0.76 0.12 0.12
Matches are distributed among these distances:
30 29 0.27
31 50 0.46
32 30 0.28
ACGTcount: A:0.51, C:0.01, G:0.10, T:0.38
Consensus pattern (29 bp):
ATTTTTAAAAAAATTAAAGGTTTAATAAA
Found at i:363496 original size:62 final size:61
Alignment explanation
Indices: 363358--363519 Score: 164
Period size: 62 Copynumber: 2.6 Consensus size: 61
363348 TTTTGGATGC
* * * * * * * * * *
363358 TTAATTGAGATTTTTAAAAAAATTAAGAGGTTTAATAAGAATTTTTTAAAAAGATTAGGGT
1 TTAATTAAAATTTTTTAAAAAATTAAAAGGTTTAATGAGAATTTTTAAAAAAAATAAAGAT
* * *
363419 CTAATTAAAATTTTTTTAAAAAATTAAAAGATTTAATGATAATTTTTAAAAAAAAATAAAGAT
1 TTAATTAAAA-TTTTTTAAAAAATTAAAAGGTTTAATGAGAATTTTT-AAAAAAAATAAAGAT
*
363482 TTAATTAAAA-TTTTTAAAAAATTTGAAAGGTTTAATGA
1 TTAATTAAAATTTTTTAAAAAA-TTAAAAGGTTTAATGA
363520 AAAGTTGTAA
Statistics
Matches: 82, Mismatches: 16, Indels: 5
0.80 0.16 0.05
Matches are distributed among these distances:
61 18 0.22
62 45 0.55
63 19 0.23
ACGTcount: A:0.49, C:0.01, G:0.10, T:0.40
Consensus pattern (61 bp):
TTAATTAAAATTTTTTAAAAAATTAAAAGGTTTAATGAGAATTTTTAAAAAAAATAAAGAT
Found at i:371004 original size:13 final size:13
Alignment explanation
Indices: 370986--371010 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
370976 CCATGTGAAA
370986 TTTTTAAAAAATG
1 TTTTTAAAAAATG
370999 TTTTTAAAAAAT
1 TTTTTAAAAAAT
371011 TAAAGATATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (13 bp):
TTTTTAAAAAATG
Found at i:371718 original size:2 final size:2
Alignment explanation
Indices: 371713--371742 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
371703 AAAAAAAAAA
371713 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
371743 TCAAAGTTTA
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:380047 original size:22 final size:20
Alignment explanation
Indices: 380019--380058 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
380009 TGTATGGAAA
380019 AGTGAAAGGTTGAAAAGAAAAG
1 AGTGAAA-G-TGAAAAGAAAAG
380041 AGTGAAAGTGAAAAGAAA
1 AGTGAAAGTGAAAAGAAA
380059 TAAATTTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.56
21 1 0.06
22 7 0.39
ACGTcount: A:0.57, C:0.00, G:0.30, T:0.12
Consensus pattern (20 bp):
AGTGAAAGTGAAAAGAAAAG
Found at i:380833 original size:59 final size:59
Alignment explanation
Indices: 380741--380855 Score: 151
Period size: 59 Copynumber: 1.9 Consensus size: 59
380731 GAAACATTAG
* * *
380741 GGACTAACTTGGACAAAAAAGAGTTCAAGCCCTAATGTAAGAATAATTGACAAGTTTAA
1 GGACTAAATTGGACAAAAAAAAGTTCAAGCCCTAATGTAAGAACAATTGACAAGTTTAA
* ** *
380800 GGACTAAATTGGACAAAAAAAAGTTTC-GGCCCTAATGTGGGAACAATTGCCAAGTT
1 GGACTAAATTGGACAAAAAAAAG-TTCAAGCCCTAATGTAAGAACAATTGACAAGTT
380856 CAGGTACTAC
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
59 45 0.94
60 3 0.06
ACGTcount: A:0.41, C:0.15, G:0.21, T:0.23
Consensus pattern (59 bp):
GGACTAAATTGGACAAAAAAAAGTTCAAGCCCTAATGTAAGAACAATTGACAAGTTTAA
Found at i:392731 original size:20 final size:21
Alignment explanation
Indices: 392703--392743 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
392693 ATTTCTTGGC
* *
392703 AGGCCATGTGATG-TTGTGCA
1 AGGCAATGTAATGTTTGTGCA
392723 AGGCAATGTAATGTTTGTGCA
1 AGGCAATGTAATGTTTGTGCA
392744 GATTGCATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.24, C:0.12, G:0.32, T:0.32
Consensus pattern (21 bp):
AGGCAATGTAATGTTTGTGCA
Found at i:393319 original size:2 final size:2
Alignment explanation
Indices: 393312--393348 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
393302 CTGATCAGGT
393312 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
393349 TTATATATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:396382 original size:31 final size:30
Alignment explanation
Indices: 396347--396411 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
396337 CAATTTTTTG
* *
396347 AAATTTGGATCAAATCAAAATTTCATATATA
1 AAATTTGCATAAAATCAAAATTT-ATATATA
* *
396378 AAA-TTGCATAAAATCAAAGTTTATGTATA
1 AAATTTGCATAAAATCAAAATTTATATATA
396407 AAATT
1 AAATT
396412 ACACATCGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 9 0.31
30 17 0.59
31 3 0.10
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.35
Consensus pattern (30 bp):
AAATTTGCATAAAATCAAAATTTATATATA
Found at i:398269 original size:17 final size:18
Alignment explanation
Indices: 398247--398280 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
398237 TACTTCATAG
*
398247 TAAAAA-TAAAATAATTT
1 TAAAAATTAAAAAAATTT
398264 TAAAAATTAAAAAAATT
1 TAAAAATTAAAAAAATT
398281 AACATTAAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
TAAAAATTAAAAAAATTT
Found at i:409870 original size:24 final size:23
Alignment explanation
Indices: 409841--409891 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
409831 TTATTTTATT
*
409841 TTTATAATTTTA-TATTTTTAATA
1 TTTATAATTATACT-TTTTTAATA
409864 GTTTATAATTATACTTTTTTAATA
1 -TTTATAATTATACTTTTTTAATA
409888 TTTA
1 TTTA
409892 GAATAATGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 4 0.16
24 20 0.80
25 1 0.04
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (23 bp):
TTTATAATTATACTTTTTTAATA
Found at i:412248 original size:23 final size:22
Alignment explanation
Indices: 412214--412257 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
412204 GTAAAAAATA
*
412214 AAAATTGATTTTGCTTTTATTC
1 AAAATTGATTTTGATTTTATTC
* *
412236 AAAATTGTTTTTTTATTTTATT
1 AAAATTG-ATTTTGATTTTATT
412258 AATTTATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.27, C:0.05, G:0.07, T:0.61
Consensus pattern (22 bp):
AAAATTGATTTTGATTTTATTC
Found at i:420335 original size:22 final size:21
Alignment explanation
Indices: 420310--420362 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
420300 GCTGATTTTC
*
420310 TATTGTTATGCTATAATTTTAT
1 TATT-TTATACTATAATTTTAT
* *
420332 TATTATATTACTATTATTTTAT
1 TATTTTA-TACTATAATTTTAT
420354 TATTATTAT
1 TATT-TTAT
420363 TATTATTTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 2 0.08
22 21 0.84
23 2 0.08
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (21 bp):
TATTTTATACTATAATTTTAT
Found at i:420336 original size:3 final size:3
Alignment explanation
Indices: 420328--420369 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
420318 TGCTATAATT
*
420328 TTA TTA TTA -TA TTA CTA TTA TT- TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
420370 TTGATATTGT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 4 0.11
3 31 0.89
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:420346 original size:14 final size:14
Alignment explanation
Indices: 420329--420365 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
420319 GCTATAATTT
420329 TATTATTATATTAC
1 TATTATTATATTAC
* *
420343 TATTATTTTATTAT
1 TATTATTATATTAC
420357 TATTATTAT
1 TATTATTAT
420366 TATTTTGATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (14 bp):
TATTATTATATTAC
Found at i:420377 original size:20 final size:20
Alignment explanation
Indices: 420320--420371 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
420310 TATTGTTATG
*
420320 CTATAATTTTATTATTATATTA
1 CTATTATTTTATTA-T-TATTA
420342 CTATTATTTTATTATTATTA
1 CTATTATTTTATTATTATTA
*
420362 TTATTATTTT
1 CTATTATTTT
420372 GATATTGTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 14 0.50
21 1 0.04
22 13 0.46
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (20 bp):
CTATTATTTTATTATTATTA
Found at i:423546 original size:12 final size:11
Alignment explanation
Indices: 423531--423608 Score: 58
Period size: 11 Copynumber: 7.4 Consensus size: 11
423521 TAAAAATTAA
423531 AAAAAGTATTTT
1 AAAAA-TATTTT
423543 AAAAATATTTT
1 AAAAATATTTT
423554 --AAA-A--TT
1 AAAAATATTTT
* *
423560 AAAAAAAATTT
1 AAAAATATTTT
423571 AAAAAGTATTTT
1 AAAAA-TATTTT
* *
423583 AAAAAAATTTA
1 AAAAATATTTT
*
423594 AAAAAAATTTT
1 AAAAATATTTT
423605 AAAA
1 AAAA
423609 TTAAAAAAAT
Statistics
Matches: 55, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
6 2 0.04
8 4 0.07
9 4 0.07
11 31 0.56
12 14 0.25
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.35
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:423557 original size:22 final size:22
Alignment explanation
Indices: 423522--423608 Score: 83
Period size: 22 Copynumber: 4.1 Consensus size: 22
423512 AAATTAAAAT
*
423522 AAAAATTAAAAAAAGTATTTTAA
1 AAAAATT-TAAAAAGTATTTTAA
* * *
423545 AAATATTT-TAAA--A-TTAAA
1 AAAAATTTAAAAAGTATTTTAA
423563 AAAAATTTAAAAAGTATTTTAA
1 AAAAATTTAAAAAGTATTTTAA
**
423585 AAAAATTTAAAAAAAATTTTAA
1 AAAAATTTAAAAAGTATTTTAA
423607 AA
1 AA
423609 TTAAAAAAAT
Statistics
Matches: 51, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
18 11 0.22
19 4 0.08
21 4 0.08
22 26 0.51
23 6 0.12
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAAATTTAAAAAGTATTTTAA
Found at i:423563 original size:17 final size:17
Alignment explanation
Indices: 423541--423574 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
423531 AAAAAGTATT
* *
423541 TTAAAAATATTTTAAAA
1 TTAAAAAAAATTTAAAA
423558 TTAAAAAAAATTTAAAA
1 TTAAAAAAAATTTAAAA
423575 AGTATTTTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TTAAAAAAAATTTAAAA
Found at i:423567 original size:10 final size:10
Alignment explanation
Indices: 423554--423626 Score: 53
Period size: 10 Copynumber: 7.3 Consensus size: 10
423544 AAAATATTTT
423554 AAAATTAAAA
1 AAAATTAAAA
423564 AAAATTTAAAA
1 AAAA-TTAAAA
**
423575 AGTATTTTAAAA
1 A--AAATTAAAA
*
423587 AAATTTAAAA
1 AAAATTAAAA
**
423597 AAAATT--TT
1 AAAATTAAAA
423605 AAAATT-AAA
1 AAAATTAAAA
423614 AAAATTAAAA
1 AAAATTAAAA
423624 AAA
1 AAA
423627 GTATTTTAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
8 6 0.12
9 6 0.12
10 23 0.46
11 7 0.14
12 7 0.14
13 1 0.02
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.29
Consensus pattern (10 bp):
AAAATTAAAA
Found at i:423572 original size:11 final size:11
Alignment explanation
Indices: 423554--423608 Score: 67
Period size: 11 Copynumber: 5.0 Consensus size: 11
423544 AAAATATTTT
423554 AAAA-TTAAAA
1 AAAATTTAAAA
423564 AAAATTTAAAA
1 AAAATTTAAAA
** *
423575 AGTATTTTAAA
1 AAAATTTAAAA
423586 AAAATTTAAAA
1 AAAATTTAAAA
423597 AAAATTTTAAAA
1 AAAA-TTTAAAA
423609 TTAAAAAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
10 4 0.11
11 26 0.70
12 7 0.19
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (11 bp):
AAAATTTAAAA
Found at i:423604 original size:51 final size:51
Alignment explanation
Indices: 423538--423637 Score: 157
Period size: 51 Copynumber: 2.0 Consensus size: 51
423528 TAAAAAAAGT
* * *
423538 ATTTTAAAAATATTTTAAAATTAAAAAAAATT-TAAAAAGTATTTTAAAAAA
1 ATTTAAAAAAAATTTTAAAATT-AAAAAAATTAAAAAAAGTATTTTAAAAAA
423589 ATTTAAAAAAAATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAA
1 ATTTAAAAAAAATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAA
423638 GTATTTTAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
50 9 0.20
51 36 0.80
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (51 bp):
ATTTAAAAAAAATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAAAA
Found at i:423615 original size:40 final size:40
Alignment explanation
Indices: 423511--423600 Score: 112
Period size: 40 Copynumber: 2.2 Consensus size: 40
423501 ATTTATTTTA
* *
423511 AAAATTAAAATAAAAATTAAAAAAAGTATTTTAAAAATATTTT
1 AAAA-TAAAA-AAAAATT-TAAAAAGTATTTTAAAAATAATTT
*
423554 AAAATTAAAAAAAATTTAAAAAGTATTTTAAAAA-AATTT
1 AAAATAAAAAAAAATTTAAAAAGTATTTTAAAAATAATTT
423593 AAAA-AAAA
1 AAAATAAAA
423601 TTTTAAAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
38 3 0.07
39 8 0.19
40 17 0.40
41 7 0.16
42 4 0.09
43 4 0.09
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (40 bp):
AAAATAAAAAAAAATTTAAAAAGTATTTTAAAAATAATTT
Found at i:423637 original size:11 final size:11
Alignment explanation
Indices: 423623--423647 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
423613 AAAAATTAAA
423623 AAAAGTATTTT
1 AAAAGTATTTT
423634 AAAAGTATTTT
1 AAAAGTATTTT
423645 AAA
1 AAA
423648 GTTAAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:429781 original size:27 final size:25
Alignment explanation
Indices: 429719--429782 Score: 74
Period size: 27 Copynumber: 2.5 Consensus size: 25
429709 CGAATATAAT
* *
429719 AAATATATTTTTTATTTTTATTTTA
1 AAATAAATTTTTAATTTTTATTTTA
**
429744 AAATACTTTTTTAATTTTTTATTTTTA
1 AAATAAATTTTTAA-TTTTTA-TTTTA
429771 AAATAAATTTTT
1 AAATAAATTTTT
429783 GGTGTTTATT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
25 11 0.34
26 6 0.19
27 15 0.47
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (25 bp):
AAATAAATTTTTAATTTTTATTTTA
Found at i:434229 original size:32 final size:32
Alignment explanation
Indices: 434188--434256 Score: 129
Period size: 32 Copynumber: 2.2 Consensus size: 32
434178 ATATAGAAAA
*
434188 ATATGCTTTTAGTATGTTTCGGCTACGTGATT
1 ATATGCTTTTAGTATGTTTAGGCTACGTGATT
434220 ATATGCTTTTAGTATGTTTAGGCTACGTGATT
1 ATATGCTTTTAGTATGTTTAGGCTACGTGATT
434252 ATATG
1 ATATG
434257 TAAGATTTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.22, C:0.10, G:0.22, T:0.46
Consensus pattern (32 bp):
ATATGCTTTTAGTATGTTTAGGCTACGTGATT
Found at i:438746 original size:31 final size:31
Alignment explanation
Indices: 438710--438776 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
438700 CAAAATGGTC
* * *
438710 ATTGAATTATTCGAAAGTTTTCATTTAAGAT
1 ATTGAACTATTCAAAAATTTTCATTTAAGAT
* * *
438741 ATTGAACTATTCAAAAATTTTTATTTAGGTT
1 ATTGAACTATTCAAAAATTTTCATTTAAGAT
438772 ATTGA
1 ATTGA
438777 GTTTTTAAGT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.46
Consensus pattern (31 bp):
ATTGAACTATTCAAAAATTTTCATTTAAGAT
Found at i:439530 original size:23 final size:22
Alignment explanation
Indices: 439485--439530 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
439475 TAGAACAAAG
* *
439485 AAAAAATCAAGTACCAGATTGA
1 AAAAAATCAAGTACCAAACTGA
*
439507 AAAAAACTCAGGTACCAAACTGA
1 AAAAAA-TCAAGTACCAAACTGA
439530 A
1 A
439531 CATTGAAGCC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.54, C:0.17, G:0.13, T:0.15
Consensus pattern (22 bp):
AAAAAATCAAGTACCAAACTGA
Found at i:440448 original size:31 final size:31
Alignment explanation
Indices: 440410--440471 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
440400 ACAACCTAGA
*
440410 AACTTAAATAAATACTTTTGAAGAATTCAAT
1 AACTTAAATAAAGACTTTTGAAGAATTCAAT
* *
440441 AACTTAAATGAAGACTTTTGAATAATTCAAT
1 AACTTAAATAAAGACTTTTGAAGAATTCAAT
440472 CACTATTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.47, C:0.10, G:0.08, T:0.35
Consensus pattern (31 bp):
AACTTAAATAAAGACTTTTGAAGAATTCAAT
Found at i:444735 original size:34 final size:34
Alignment explanation
Indices: 444694--444770 Score: 154
Period size: 34 Copynumber: 2.3 Consensus size: 34
444684 TGGCTACTTA
444694 TTTTATCCCGAATCATAATCTTTCTAACCCTAAT
1 TTTTATCCCGAATCATAATCTTTCTAACCCTAAT
444728 TTTTATCCCGAATCATAATCTTTCTAACCCTAAT
1 TTTTATCCCGAATCATAATCTTTCTAACCCTAAT
444762 TTTTATCCC
1 TTTTATCCC
444771 AAGAATGTGC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.27, C:0.27, G:0.03, T:0.43
Consensus pattern (34 bp):
TTTTATCCCGAATCATAATCTTTCTAACCCTAAT
Found at i:445975 original size:29 final size:31
Alignment explanation
Indices: 445931--445997 Score: 97
Period size: 29 Copynumber: 2.3 Consensus size: 31
445921 ACTTCTTCTT
*
445931 CTTTTTA-ATTTTTTTGAATTTTTAT-AA-A
1 CTTTTTATATTTGTTTGAATTTTTATGAATA
445959 CTTTTTATATTTGTTTGAATTTTTATGAATA
1 CTTTTTATATTTGTTTGAATTTTTATGAATA
445990 -TTTTTATA
1 CTTTTTATA
445998 ACTTTTAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
28 7 0.20
29 17 0.49
30 10 0.29
31 1 0.03
ACGTcount: A:0.27, C:0.03, G:0.06, T:0.64
Consensus pattern (31 bp):
CTTTTTATATTTGTTTGAATTTTTATGAATA
Found at i:448049 original size:30 final size:30
Alignment explanation
Indices: 448010--448079 Score: 72
Period size: 30 Copynumber: 2.3 Consensus size: 30
448000 AAAAGAAAGA
* *
448010 TTTGGAAATTCCT-ATTAAGCCCCT-AAATC
1 TTTGAAAATT-CTAATTAACCCCCTAAAATC
* *
448039 TTTTGAAAATTTTAATTATCCCCCTAAAATC
1 -TTTGAAAATTCTAATTAACCCCCTAAAATC
448070 TTTGAAAATT
1 TTTGAAAATT
448080 TTAAGTACCC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
29 1 0.03
30 28 0.82
31 5 0.15
ACGTcount: A:0.34, C:0.19, G:0.07, T:0.40
Consensus pattern (30 bp):
TTTGAAAATTCTAATTAACCCCCTAAAATC
Found at i:456031 original size:31 final size:31
Alignment explanation
Indices: 455989--456047 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
455979 GGTTAGACTA
455989 AAATTTCAAAAGTACAAGGACTAAAATTAAC
1 AAATTTCAAAAGTACAAGGACTAAAATTAAC
* **
456020 AAATTTGAAAAGTACTGGGACTAAAATT
1 AAATTTCAAAAGTACAAGGACTAAAATT
456048 GATCAAATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.51, C:0.10, G:0.14, T:0.25
Consensus pattern (31 bp):
AAATTTCAAAAGTACAAGGACTAAAATTAAC
Found at i:466411 original size:2 final size:2
Alignment explanation
Indices: 466404--466432 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
466394 CCTGATTGGA
466404 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 A
466433 CCCTTAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:472190 original size:37 final size:37
Alignment explanation
Indices: 472149--472227 Score: 133
Period size: 37 Copynumber: 2.1 Consensus size: 37
472139 TTGAATAAGA
472149 TTGAATCGAATACTTAGATTGATT-TCAGAGAAGGGTT
1 TTGAATCGAATACTTAGATTGATTCT-AGAGAAGGGTT
*
472186 TTGAATCGAATATTTAGATTGATTCTAGAGAAGGGTT
1 TTGAATCGAATACTTAGATTGATTCTAGAGAAGGGTT
472223 TTGAA
1 TTGAA
472228 CCGGTTGATT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
37 39 0.98
38 1 0.03
ACGTcount: A:0.33, C:0.06, G:0.24, T:0.37
Consensus pattern (37 bp):
TTGAATCGAATACTTAGATTGATTCTAGAGAAGGGTT
Found at i:472833 original size:19 final size:18
Alignment explanation
Indices: 472809--472845 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
472799 CGGCCCTTTT
472809 TTTTAAAATAAAAAAAATA
1 TTTTAAAA-AAAAAAAATA
*
472828 TTTTAAAAAATAAAAATA
1 TTTTAAAAAAAAAAAATA
472846 AAAACATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
TTTTAAAAAAAAAAAATA
Found at i:482998 original size:137 final size:137
Alignment explanation
Indices: 482826--484208 Score: 979
Period size: 137 Copynumber: 10.0 Consensus size: 137
482816 ATTAATAAGT
* *
482826 TTCTTTATGAATATATGTATATATTTTGTTGTTTGGTTACGTAGAAAGTAAATTGA-AGTGGATT
1 TTCTTTATGAATATAAGTATATATTTTGTTGTTTGGTTACTTAGAAAGTAAATT-ATAGTGGATT
* * * * *
482890 AAGTTTAATTTAACCATTTTAATTGTCTCAATTTCGTAATTTAGGTGAAAAAATTTAGTGTTCTT
65 AAGCTTAATTTAGCTACTTTAATTGTCTCAATTTCGTCATTTAGGTGAAAAAATTTAGTGTTCTT
482955 TTTGGTGG
130 TTTGGTGG
* *
482963 TTCTTTATGAATGTAAGTATATATTTTGTTCTTTGGTTACTTAGAAAGTAAATTATAGTGGATTA
1 TTCTTTATGAATATAAGTATATATTTTGTTGTTTGGTTACTTAGAAAGTAAATTATAGTGGATTA
* * * ** * ** ** *
483028 AGCTTAATATAGCTACTTTAGTTGTCGTGAA-----AAATTTTGGTG-TTATTTTTGGTGGTTC-
66 AGCTTAATTTAGCTACTTTAATTGTC-TCAATTTCGTCATTTAGGTGAAAAAATTTAGT-GTTCT
*
483086 -TTT--A--
129 TTTTGGTGG
* *
483090 -------TGAATATAAGTATATATTTTGTTGTTTGGTTATTTAGAAAGTAAATTTTAGTGGATTA
1 TTCTTTATGAATATAAGTATATATTTTGTTGTTTGGTTACTTAGAAAGTAAATTATAGTGGATTA
* *
483148 AGCTTAATTTAGCTACTTTAATTGTCTCAATTTCGTCATTTAGGTGAAAAATTTTAGTGTTCATT
66 AGCTTAATTTAGCTACTTTAATTGTCTCAATTTCGTCATTTAGGTGAAAAAATTTAGTGTTCTTT
483213 TTGGTGG
131 TTGGTGG
* *
483220 TTCTTTATGAATATAAGTATATATTTTGTTGTTGGGTTACTTAGAAAGTAAATTATAGTGGAATA
1 TTCTTTATGAATATAAGTATATATTTTGTTGTTTGGTTACTTAGAAAGTAAATTATAGTGGATTA
* *
483285 AGCTTAAGTTAGCTACTTTAATT-TCT-AAGTTTGGTCATTTAGGTGAAAAACA-TTAGTGTTCT
66 AGCTTAATTTAGCTACTTTAATTGTCTCAA-TTTCGTCATTTAGGTGAAAAA-ATTTAGTG----
*
483347 TTTGCTATTTTTTTGATGG
125 -TT-C----TTTTTGGTGG
* * * *
483366 TTCTTTATGAATATATGTATATAATTTGTTGTTTGTTTACTTAGAAAGTAAATTATAGCGGGA-T
1 TTCTTTATGAATATAAGTATATATTTTGTTGTTTGGTTACTTAGAAAGTAAATTATAG-TGGATT
* *
483430 AAGCTTAATTTACACTACTTTAATTGTCTAAATTTCGTCATTTAGGTGAAAAAA-TT-GT-TAT-
65 AAGCTTAATTTA-GCTACTTTAATTGTCTCAATTTCGTCATTTAGGTGAAAAAATTTAGTGT-TC
** **
483491 TAGTAAGT--
128 TTTTTGGTGG
*** * ** **
483499 TTCTTTATGAATATGTCTATATGTTTTGTTGTTTGGTTACTTAGAAAGTAAATGGTAGTGGGGTA
1 TTCTTTATGAATATAAGTATATATTTTGTTGTTTGGTTACTTAGAAAGTAAATTATAGTGGATTA
* * * * *
483564 AGCTTAA-GTATGCTACTTTAGTTTTCTAAATTTCGTCACTTAGGTGAAAAAATTTAGTGTTCTT
66 AGCTTAATTTA-GCTACTTTAATTGTCTCAATTTCGTCATTTAGGTGAAAAAATTTAGTG-----
**
483628 TTGCTATTTTTTATGG
125 TT-C--TTTTTGGTGG
* * * * * * *
483644 TTCATTATGAATATATGTATATAATTTATTGTTTGGTTACCTACAAAGTAAATTACAGTGGGA-T
1 TTCTTTATGAATATAAGTATATATTTTGTTGTTTGGTTACTTAGAAAGTAAATTATAGT-GGATT
* * * * ** * **
483708 AACCTTAATTTAGCTACTTTACTTGTCTAAATGTATTCGTTTAGGTGAAAAGCTTTAGTGTCTTT
65 AAGCTTAATTTAGCTACTTTAATTGTCTCAATTTCGTCATTTAGGTGAAAAAATTTA--G-----
* ** *
483773 TGTTATTTTTTTTTATAG
123 TG---TTCTTTTTGGTGG
*** * *
483791 TTCTTTATGAATATCTTTATATATTTTGTTGTTTGGTCACTTAGAAAGCAAATTATCA-TGGATT
1 TTCTTTATGAATATAAGTATATATTTTGTTGTTTGGTTACTTAGAAAGTAAATTAT-AGTGGATT
* * * * ** *
483855 GAGCTTAATTTAGCTACTTTCATTGTCTAAAATTCGTCATTTAGGTGAAAATTTTTTGTGTTCTT
65 AAGCTTAATTTAGCTACTTTAATTGTCTCAATTTCGTCATTTAGGTGAAAAAATTTAGTGTTC-T
**
483920 TTGTTATTAGCAAG
129 TT-TTGGT-G---G
** * *
483934 TTTCTTTATGAATATGTGTATATATTTTGTTGTTTGGTTTCTTAGAAAGTAAATTGTAGTGGGA-
1 -TTCTTTATGAATATAAGTATATATTTTGTTGTTTGGTTACTTAGAAAGTAAATTATAGT-GGAT
* * * * *
483998 TAAGCTTAATTTAGCTACTTTAATTGTCTAAAATTAGTCATTTAGGTGAAAAACTTTCGTGTTTC
64 TAAGCTTAATTTAGCTACTTTAATTGTCTCAATTTCGTCATTTAGGTGAAAAAATTTAGTG-TTC
** *
484063 TTTTGTTATTAG
128 -TTT-TTGGTGG
** * * * * *
484075 TAAGTTTATGCACAAGCATATGTATATA--TTGCTT-TTTGGTTGCTTAGAAAGTATATTATGGT
1 T-TCTTTATG---AA-TATAAGTATATATTTTG-TTGTTTGGTTACTTAGAAAGTAAATTATAGT
* * * *
484137 GGAATAAGCTTAATTTAGCTACTTTAGTTGTC-CAAATTTCGTCATTTAGGTGAAAAATTTTAAT
60 GGATTAAGCTTAATTTAGCTACTTTAATTGTCTC-AATTTCGTCATTTAGGTGAAAAAATTTAGT
484201 GTTCTTTT
124 GTTCTTTT
484209 GGTTTTTTGG
Statistics
Matches: 1006, Mismatches: 157, Indels: 163
0.76 0.12 0.12
Matches are distributed among these distances:
119 3 0.00
120 78 0.08
124 12 0.01
125 7 0.01
126 3 0.00
131 3 0.00
132 47 0.05
133 75 0.07
134 2 0.00
135 5 0.00
136 30 0.03
137 157 0.16
138 6 0.01
139 4 0.00
140 6 0.01
141 13 0.01
142 7 0.01
143 85 0.08
144 110 0.11
145 119 0.12
146 83 0.08
147 120 0.12
148 24 0.02
149 2 0.00
150 3 0.00
152 2 0.00
ACGTcount: A:0.28, C:0.08, G:0.17, T:0.47
Consensus pattern (137 bp):
TTCTTTATGAATATAAGTATATATTTTGTTGTTTGGTTACTTAGAAAGTAAATTATAGTGGATTA
AGCTTAATTTAGCTACTTTAATTGTCTCAATTTCGTCATTTAGGTGAAAAAATTTAGTGTTCTTT
TTGGTGG
Found at i:483179 original size:257 final size:257
Alignment explanation
Indices: 482826--483304 Score: 798
Period size: 257 Copynumber: 1.9 Consensus size: 257
482816 ATTAATAAGT
*
482826 TTCTTTATGAATATATGTATATATTTTGTTGTTTGGTTACGTAGAAAGTAAATTGAAGTGGATTA
1 TTCTTTATGAATATAAGTATATATTTTGTTGTTTGGTTACGTAGAAAGTAAATTGAAGTGGATTA
* * *
482891 AGTTTAATTTAACCATTTTAATTGTCTCAATTTCGTAATTTAGGTGAAAAAATTTAGTGTTCTTT
66 AGCTTAATTTAACCACTTTAATTGTCTCAATTTCGTAATTTAGGTGAAAAAATTTAGTGTTCATT
* *
482956 TTGGTGGTTCTTTATGAATGTAAGTATATATTTTGTTCTTTGGTTACTTAGAAAGTAAATTATAG
131 TTGGTGGTTCTTTATGAATATAAGTATATATTTTGTTCTTGGGTTACTTAGAAAGTAAATTATAG
*
483021 TGGATTAAGCTTAA-TATAGCTACTTTAGTTGTCGTGAAAAATTTTGGTGTTATTTTTGGTGG
196 TGGAATAAGCTTAAGT-TAGCTACTTTAGTTGTCGTGAAAAATTTTGGTGTTATTTTTGGTGG
** **
483083 TTCTTTATGAATATAAGTATATATTTTGTTGTTTGGTTATTTAGAAAGTAAATTTTAGTGGATTA
1 TTCTTTATGAATATAAGTATATATTTTGTTGTTTGGTTACGTAGAAAGTAAATTGAAGTGGATTA
* * * *
483148 AGCTTAATTTAGCTACTTTAATTGTCTCAATTTCGTCATTTAGGTGAAAAATTTTAGTGTTCATT
66 AGCTTAATTTAACCACTTTAATTGTCTCAATTTCGTAATTTAGGTGAAAAAATTTAGTGTTCATT
*
483213 TTGGTGGTTCTTTATGAATATAAGTATATATTTTGTTGTTGGGTTACTTAGAAAGTAAATTATAG
131 TTGGTGGTTCTTTATGAATATAAGTATATATTTTGTTCTTGGGTTACTTAGAAAGTAAATTATAG
483278 TGGAATAAGCTTAAGTTAGCTACTTTA
196 TGGAATAAGCTTAAGTTAGCTACTTTA
483305 ATTTCTAAGT
Statistics
Matches: 205, Mismatches: 16, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
257 204 1.00
258 1 0.00
ACGTcount: A:0.29, C:0.06, G:0.18, T:0.47
Consensus pattern (257 bp):
TTCTTTATGAATATAAGTATATATTTTGTTGTTTGGTTACGTAGAAAGTAAATTGAAGTGGATTA
AGCTTAATTTAACCACTTTAATTGTCTCAATTTCGTAATTTAGGTGAAAAAATTTAGTGTTCATT
TTGGTGGTTCTTTATGAATATAAGTATATATTTTGTTCTTGGGTTACTTAGAAAGTAAATTATAG
TGGAATAAGCTTAAGTTAGCTACTTTAGTTGTCGTGAAAAATTTTGGTGTTATTTTTGGTGG
Found at i:483388 original size:146 final size:148
Alignment explanation
Indices: 483211--483482 Score: 431
Period size: 146 Copynumber: 1.9 Consensus size: 148
483201 TTAGTGTTCA
* *
483211 TTTTGGTGGTTCTTTATGAATATAAGTATATATTTTGTTGTTGGGTTACTTAGAAAGTAAATTAT
1 TTTTGATGGTTCTTTATGAATATAAGTATATAATTTGTTGTTGGGTTACTTAGAAAGTAAATTAT
* * * *
483276 AGTGGAATAAGCTTAAGTTA-GCTACTTTAATT-TCTAAGTTTGGTCATTTAGGTGAAAAACATT
66 AGCGGAATAAGCTTAAGTTACACTACTTTAATTGTCTAAATTTCGTCATTTAGGTGAAAAACATT
483339 AGTGTTCTTTTGCTATTT
131 AGTGTTCTTTTGCTATTT
* * *
483357 TTTTGATGGTTCTTTATGAATATATGTATATAATTTGTTGTTTGTTTACTTAGAAAGTAAATTAT
1 TTTTGATGGTTCTTTATGAATATAAGTATATAATTTGTTGTTGGGTTACTTAGAAAGTAAATTAT
* *
483422 AGCGGGATAAGCTTAATTTACACTACTTTAATTGTCTAAATTTCGTCATTTAGGTGAAAAA
66 AGCGGAATAAGCTTAAGTTACACTACTTTAATTGTCTAAATTTCGTCATTTAGGTGAAAAA
483483 ATTGTTATTA
Statistics
Matches: 113, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
146 77 0.68
147 11 0.10
148 25 0.22
ACGTcount: A:0.30, C:0.07, G:0.18, T:0.45
Consensus pattern (148 bp):
TTTTGATGGTTCTTTATGAATATAAGTATATAATTTGTTGTTGGGTTACTTAGAAAGTAAATTAT
AGCGGAATAAGCTTAAGTTACACTACTTTAATTGTCTAAATTTCGTCATTTAGGTGAAAAACATT
AGTGTTCTTTTGCTATTT
Found at i:483615 original size:133 final size:133
Alignment explanation
Indices: 483366--483617 Score: 362
Period size: 133 Copynumber: 1.9 Consensus size: 133
483356 TTTTTGATGG
* * *
483366 TTCTTTATGAATATATGTATATAATTTGTTGTTTGTTTACTTAGAAAGTAAATTATAGCGGGATA
1 TTCTTTATGAATATATCTATATAATTTGTTGTTTGGTTACTTAGAAAGTAAATGATAGCGGGATA
* *
483431 AGCTTAATTTACACTACTTTAATTGTCTAAATTTCGTCATTTAGGTGAAAAAATTGTTATTAGTA
66 AGCTTAATGTACACTACTTTAATTGTCTAAATTTCGTCACTTAGGTGAAAAAATTGTTATTAGTA
483496 AGT
131 AGT
* ** * * *
483499 TTCTTTATGAATATGTCTATATGTTTTGTTGTTTGGTTACTTAGAAAGTAAATGGTAGTGGGGTA
1 TTCTTTATGAATATATCTATATAATTTGTTGTTTGGTTACTTAGAAAGTAAATGATAGCGGGATA
** * *
483564 AGCTTAA-GTATGCTACTTTAGTTTTCTAAATTTCGTCACTTAGGTGAAAAAATT
66 AGCTTAATGTACACTACTTTAATTGTCTAAATTTCGTCACTTAGGTGAAAAAATT
483618 TAGTGTTCTT
Statistics
Matches: 104, Mismatches: 15, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
132 41 0.39
133 63 0.61
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (133 bp):
TTCTTTATGAATATATCTATATAATTTGTTGTTTGGTTACTTAGAAAGTAAATGATAGCGGGATA
AGCTTAATGTACACTACTTTAATTGTCTAAATTTCGTCACTTAGGTGAAAAAATTGTTATTAGTA
AGT
Found at i:483905 original size:424 final size:424
Alignment explanation
Indices: 483083--484072 Score: 1189
Period size: 424 Copynumber: 2.3 Consensus size: 424
483073 TTTTTGGTGG
** * *
483083 TTCTTTATGAATATAAGTATATATTTTGTTGTTTGGTTATTTAGAAAGTAAATTTTAGT-GGATT
1 TTCTTTATGAATATGTGTATATATTTTGTTGTTTGGTTACTTAGAAAGTAAATTGTAGTGGGA-T
* *
483147 AAGCTTAATTTAGCTACTTTAATTGTCTCAATTTCGTCATTTAGGTGAAAAATTTTAGTG-----
65 AAGCTTAATTTAGCTACTTTAATTGTCTAAATTTCGTCATTTAGGTGAAAAAATTTAGTGTTCTT
* * * * * *
483207 TT-C-A-TTTTGGTGGTTCTTTATGAATATAAGTATATATTTTGTTGTTGGGTTACTTAGAAAGT
130 TTGCTATTTTTGATGGTTCATTATGAATATAAGTATATAATTTATTGTTGGGTTACCTACAAAGT
* * * * *
483269 AAATTATAGTGGAATAAGCTTAAGTTAGCTACTTTAATTTCTAAGTTTGGTCATTTAGGTGAAAA
195 AAATTACAGTGGAATAACCTTAAGTTAGCTACTTTAATTTCTAAATGTAGTCATTTAGGTGAAAA
*
483334 ACATTAGTGTTCTTTTGCTATTTTTTTGATGGTTCTTTATGAATATATGTATATAATTTGTTGTT
260 ACATTAGTGTTCTTTTGCTATTTTTTTGATAGTTCTTTATGAATATATGTATATAATTTGTTGTT
* * * *
483399 TGTTTACTTAGAAAGTAAATTATAGCGGGATAAGCTTAATTTACACTACTTTAATTGTCTAAATT
325 TGGTCACTTAGAAAGCAAATTATA-CGGGATAAGCTTAATTTACACTACTTTAATTGTCTAAAAT
*
483464 TCGTCATTTAGGTGAAAA-AATTGTTATTAGTAAGT
389 TCGTCATTTAGGTGAAAATAATTGTTATTAGCAAGT
* * * *
483499 TTCTTTATGAATATGTCTATATGTTTTGTTGTTTGGTTACTTAGAAAGTAAATGGTAGTGGGGTA
1 TTCTTTATGAATATGTGTATATATTTTGTTGTTTGGTTACTTAGAAAGTAAATTGTAGTGGGATA
* * * *
483564 AGCTTAA-GTATGCTACTTTAGTTTTCTAAATTTCGTCACTTAGGTGAAAAAATTTAGTGTTCTT
66 AGCTTAATTTA-GCTACTTTAATTGTCTAAATTTCGTCATTTAGGTGAAAAAATTTAGTGTTCTT
* * *
483628 TTGCTATTTTTTATGGTTCATTATGAATATATGTATATAATTTATTGTTTGGTTACCTACAAAGT
130 TTGCTATTTTTGATGGTTCATTATGAATATAAGTATATAATTTATTGTTGGGTTACCTACAAAGT
* * * * *
483693 AAATTACAGTGGGATAACCTTAATTTAGCTACTTTACTTGTCTAAATGTATTCGTTTAGGTGAAA
195 AAATTACAGTGGAATAACCTTAAGTTAGCTACTTTAATT-TCTAAATGTAGTCATTTAGGTGAAA
* * * * * * *
483758 AGCTTTAGTG-TCTTTTGTTATTTTTTTTTATAGTTCTTTATGAATATCTTTATATATTTTGTTG
259 AACATTAGTGTTCTTTTGCTA-TTTTTTTGATAGTTCTTTATGAATATATGTATATAATTTGTTG
* * * *
483822 TTTGGTCACTTAGAAAGCAAATTAT-CATGGATTGAGCTTAATTTA-GCTACTTTCATTGTCTAA
323 TTTGGTCACTTAGAAAGCAAATTATAC-GGGA-TAAGCTTAATTTACACTACTTTAATTGTCTAA
**
483885 AATTCGTCATTTAGGTGAAAATTTTTTGTGTTCTTTTGTTATTAGCAAGT
386 AATTCGTCATTTAGGTGAAAA----------T-AATTGTTATTAGCAAGT
*
483935 TTCTTTATGAATATGTGTATATATTTTGTTGTTTGGTTTCTTAGAAAGTAAATTGTAGTGGGATA
1 TTCTTTATGAATATGTGTATATATTTTGTTGTTTGGTTACTTAGAAAGTAAATTGTAGTGGGATA
* * * *
484000 AGCTTAATTTAGCTACTTTAATTGTCTAAAATTAGTCATTTAGGTGAAAAACTTTCGTGTTTCTT
66 AGCTTAATTTAGCTACTTTAATTGTCTAAATTTCGTCATTTAGGTGAAAAAATTTAGTG-TTCTT
*
484065 TTGTTATT
130 TTGCTATT
484073 AGTAAGTTTA
Statistics
Matches: 480, Mismatches: 66, Indels: 35
0.83 0.11 0.06
Matches are distributed among these distances:
415 2 0.00
416 104 0.22
417 2 0.00
421 2 0.00
422 1 0.00
423 2 0.00
424 131 0.27
425 100 0.21
436 122 0.25
437 14 0.03
ACGTcount: A:0.28, C:0.08, G:0.17, T:0.47
Consensus pattern (424 bp):
TTCTTTATGAATATGTGTATATATTTTGTTGTTTGGTTACTTAGAAAGTAAATTGTAGTGGGATA
AGCTTAATTTAGCTACTTTAATTGTCTAAATTTCGTCATTTAGGTGAAAAAATTTAGTGTTCTTT
TGCTATTTTTGATGGTTCATTATGAATATAAGTATATAATTTATTGTTGGGTTACCTACAAAGTA
AATTACAGTGGAATAACCTTAAGTTAGCTACTTTAATTTCTAAATGTAGTCATTTAGGTGAAAAA
CATTAGTGTTCTTTTGCTATTTTTTTGATAGTTCTTTATGAATATATGTATATAATTTGTTGTTT
GGTCACTTAGAAAGCAAATTATACGGGATAAGCTTAATTTACACTACTTTAATTGTCTAAAATTC
GTCATTTAGGTGAAAATAATTGTTATTAGCAAGT
Found at i:483982 original size:144 final size:143
Alignment explanation
Indices: 483484--484209 Score: 707
Period size: 145 Copynumber: 5.0 Consensus size: 143
483474 GGTGAAAAAA
* * *
483484 TTGTTATTAGTAAGTTTCTTTATGAATATGTCTATATGTTTTGTTGTTTGGTTACTTAGAAAGTA
1 TTGTTATTAGTAAGTTTCTTTATGAATATATGTATATATTTTGTTGTTTGGTTACTTAGAAAGTA
** * * * * *
483549 AATGGTAGTGGGGTAAGCTTAA-GTATGCTACTTTAGTTTTCTAAATTTCGTCACTTAGGTGAAA
66 AATTATAGT-GGATAAGCTTAATTTA-GCTACTTTAGTTGTCTAAAATTCGTCATTTAGGTGAAA
*
483613 AAATTTAGTGTTCTT
129 AACTTTAGTGTTCTT
* ** * * * * * * *
483628 TTGCTATTTTTTATGGTTCATTATGAATATATGTATATAATTTATTGTTTGGTTACCTACAAAGT
1 TTGTTA-TTAGTAAGTTTCTTTATGAATATATGTATATATTTTGTTGTTTGGTTACTTAGAAAGT
* * * ** *
483693 AAATTACAGTGGGATAACCTTAATTTAGCTACTTTACTTGTCT-AAATGTATTCGTTTAGGTGAA
65 AAATTATAGT-GGATAAGCTTAATTTAGCTACTTTAGTTGTCTAAAAT-TCGTCATTTAGGTGAA
*
483757 AAGCTTTAGTG-TCTT
128 AAACTTTAGTGTTCTT
** * * *
483772 TTGTTATTTTTTTTTATAG-TTCTTTATGAATATCTTTATATATTTTGTTGTTTGGTCACTTAGA
1 TTGTTA----TTAGTA-AGTTTCTTTATGAATATATGTATATATTTTGTTGTTTGGTTACTTAGA
* *
483836 AAGCAAATTATCA-TGGATTGAGCTTAATTTAGCTACTTTCA-TTGTCTAAAATTCGTCATTTAG
61 AAGTAAATTAT-AGTGGA-TAAGCTTAATTTAGCTACTTT-AGTTGTCTAAAATTCGTCATTTAG
** *
483899 GTGAAAATTTTTTGTGTTCTT
123 GTGAAAAACTTTAGTGTTCTT
* * *
483920 TTGTTATTAGCAAGTTTCTTTATGAATATGTGTATATATTTTGTTGTTTGGTTTCTTAGAAAGTA
1 TTGTTATTAGTAAGTTTCTTTATGAATATATGTATATATTTTGTTGTTTGGTTACTTAGAAAGTA
* * *
483985 AATTGTAGTGGGATAAGCTTAATTTAGCTACTTTAATTGTCTAAAATTAGTCATTTAGGTGAAAA
66 AATTATAGT-GGATAAGCTTAATTTAGCTACTTTAGTTGTCTAAAATTCGTCATTTAGGTGAAAA
*
484050 ACTTTCGTGTTTCTT
130 ACTTTAGTG-TTCTT
* ** * * *
484065 TTGTTATTAGTAAGTTTATGCA-CAAGCATATGTATATA--TTGCTT-TTTGGTTGCTTAGAAAG
1 TTGTTATTAGTAAGTTTCTTTATGAA-TATATGTATATATTTTG-TTGTTTGGTTACTTAGAAAG
* * * *
484126 TATATTATGGTGGAATAAGCTTAATTTAGCTACTTTAGTTGTCCAAATTTCGTCATTTAGGTGAA
64 TAAATTATAGTGG-ATAAGCTTAATTTAGCTACTTTAGTTGTCTAAAATTCGTCATTTAGGTGAA
* *
484191 AAATTTTAATGTTCTT
128 AAACTTTAGTGTTCTT
484207 TTG
1 TTG
484210 GTTTTTTGGG
Statistics
Matches: 482, Mismatches: 80, Indels: 42
0.80 0.13 0.07
Matches are distributed among these distances:
142 10 0.02
143 86 0.18
144 129 0.27
145 135 0.28
146 5 0.01
147 100 0.21
148 17 0.04
ACGTcount: A:0.27, C:0.09, G:0.17, T:0.47
Consensus pattern (143 bp):
TTGTTATTAGTAAGTTTCTTTATGAATATATGTATATATTTTGTTGTTTGGTTACTTAGAAAGTA
AATTATAGTGGATAAGCTTAATTTAGCTACTTTAGTTGTCTAAAATTCGTCATTTAGGTGAAAAA
CTTTAGTGTTCTT
Found at i:484162 original size:143 final size:143
Alignment explanation
Indices: 483523--484209 Score: 521
Period size: 144 Copynumber: 4.8 Consensus size: 143
483513 GTCTATATGT
* ** ** * *
483523 TTTGTTGTTTGGTTACTTAGAAAGTAAATGGTAGTGGGGTAAGCTTAA-GTATGCTACTTTAGTT
1 TTTGTTGTTTGGTTGCTTAGAAAGTAAATTATAGTGGAATAAGCTTAATTTA-GCTACTTTAATT
* * * * * * *** * * *
483587 TTCTAAATTTCGTCACTTAGGTGAAAAAATTTAGTGTTCTTTTGCTATTTTTTATGGTTCAT-TA
65 GTCTAAAATTCGTCATTTAGGTGAAAAACTTTCGTGTTCTTTTGTTA-TTAGCA-AGTTTATGCA
* *
483651 TGAATATATGTATATAA
128 TCAACATATGTATAT-A
* * * * * * * *
483668 TTTATTGTTTGGTTACCTACAAAGTAAATTACAGTGGGATAACCTTAATTTAGCTACTTTACTTG
1 TTTGTTGTTTGGTTGCTTAGAAAGTAAATTATAGTGGAATAAGCTTAATTTAGCTACTTTAATTG
** * * * ***
483733 TCT-AAATGTATTCGTTTAGGTGAAAAGCTTTAGTG-TCTTTTGTTATTTTTTTTTATAGTTCT-
66 TCTAAAAT-TCGTCATTTAGGTGAAAAACTTTCGTGTTCTTTTGTTA----TTAGCA-AGTT-TA
* * * * *
483795 T-TATGAATATCTTTATATA
124 TGCATCAACATATGTATATA
** * * * *
483814 TTTTGTTGTTTGGTCACTTAGAAAGCAAATTATCA-TGGATTGAGCTTAATTTAGCTACTTTCAT
1 -TTTGTTGTTTGGTTGCTTAGAAAGTAAATTAT-AGTGGAATAAGCTTAATTTAGCTACTTTAAT
** * * **
483878 TGTCTAAAATTCGTCATTTAGGTGAAAATTTTTTGTGTTCTTTTGTTATTAGCAAGTTTCTTTAT
64 TGTCTAAAATTCGTCATTTAGGTGAAAAACTTTCGTGTTCTTTTGTTATTAGCAAGTTTATGCAT
* * *
483943 GAATATGTGTATATA
129 CAACATATGTATATA
* * *
483958 TTTTGTTGTTTGGTTTCTTAGAAAGTAAATTGTAGTGGGATAAGCTTAATTTAGCTACTTTAATT
1 -TTTGTTGTTTGGTTGCTTAGAAAGTAAATTATAGTGGAATAAGCTTAATTTAGCTACTTTAATT
* *
484023 GTCTAAAATTAGTCATTTAGGTGAAAAACTTTCGTGTTTCTTTTGTTATTAGTAAGTTTATGCA-
65 GTCTAAAATTCGTCATTTAGGTGAAAAACTTTCGTG-TTCTTTTGTTATTAGCAAGTTTATGCAT
484087 CAAGCATATGTATATA
129 CAA-CATATGTATATA
* * *
484103 -TTGCTT-TTTGGTTGCTTAGAAAGTATATTATGGTGGAATAAGCTTAATTTAGCTACTTTAGTT
1 TTTG-TTGTTTGGTTGCTTAGAAAGTAAATTATAGTGGAATAAGCTTAATTTAGCTACTTTAATT
* * * **
484166 GTCCAAATTTCGTCATTTAGGTGAAAAATTTTAATGTTCTTTTG
65 GTCTAAAATTCGTCATTTAGGTGAAAAACTTTCGTGTTCTTTTG
484210 GTTTTTTGGG
Statistics
Matches: 449, Mismatches: 77, Indels: 35
0.80 0.14 0.06
Matches are distributed among these distances:
142 9 0.02
143 90 0.20
144 122 0.27
145 108 0.24
146 3 0.01
147 102 0.23
148 15 0.03
ACGTcount: A:0.27, C:0.09, G:0.17, T:0.46
Consensus pattern (143 bp):
TTTGTTGTTTGGTTGCTTAGAAAGTAAATTATAGTGGAATAAGCTTAATTTAGCTACTTTAATTG
TCTAAAATTCGTCATTTAGGTGAAAAACTTTCGTGTTCTTTTGTTATTAGCAAGTTTATGCATCA
ACATATGTATATA
Found at i:490240 original size:15 final size:15
Alignment explanation
Indices: 490220--490260 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
490210 TCTTTTTTCT
*
490220 TATATACATTCATCA
1 TATATACATACATCA
490235 TATATACATACATCA
1 TATATACATACATCA
*
490250 CATAATACATA
1 TAT-ATACATA
490261 AGCATCATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 16 0.70
16 7 0.30
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.34
Consensus pattern (15 bp):
TATATACATACATCA
Found at i:490537 original size:4 final size:4
Alignment explanation
Indices: 490528--490552 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
490518 CCTCTTTTAC
490528 ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT A
490553 AGCATCATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:490654 original size:2 final size:2
Alignment explanation
Indices: 490649--490673 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
490639 ACACACATAC
490649 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
490674 GCAGGTTAGT
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:490877 original size:29 final size:29
Alignment explanation
Indices: 490830--490888 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
490820 TCTCAGCAAC
*
490830 AGTACGGAGGGTACTCGAGCTCGGGTGTA
1 AGTACGGAAGGTACTCGAGCTCGGGTGTA
*
490859 AGTACGGAAAGGTAC-CGAGCTCGTGTGTA
1 AGTACGG-AAGGTACTCGAGCTCGGGTGTA
490888 A
1 A
490889 ATTTCGGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 21 0.78
30 6 0.22
ACGTcount: A:0.25, C:0.17, G:0.37, T:0.20
Consensus pattern (29 bp):
AGTACGGAAGGTACTCGAGCTCGGGTGTA
Found at i:494716 original size:31 final size:31
Alignment explanation
Indices: 494681--494743 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
494671 ATACATTGGT
494681 TGGAAAACCAGCAAAGTAGAATAGACTAGAC
1 TGGAAAACCAGCAAAGTAGAATAGACTAGAC
494712 TGGAAAACCAGCAAAGTAGAATAGACTAGAC
1 TGGAAAACCAGCAAAGTAGAATAGACTAGAC
494743 T
1 T
494744 TTCTCATACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.48, C:0.16, G:0.22, T:0.14
Consensus pattern (31 bp):
TGGAAAACCAGCAAAGTAGAATAGACTAGAC
Found at i:500332 original size:2 final size:2
Alignment explanation
Indices: 500327--500352 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
500317 GTTGTGATAA
500327 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
500353 TTTTTTTTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:500664 original size:29 final size:30
Alignment explanation
Indices: 500630--500708 Score: 90
Period size: 29 Copynumber: 2.7 Consensus size: 30
500620 GGCCCATTTA
*
500630 ATTTTTGAAAATTCTCATTA-TTCTTTTTT
1 ATTTTTGAAAATTCTCATTAGCTCTTTTTT
** * *
500659 ATTTTTTTAAATTTTAATTAAGCTCTTTTTT
1 ATTTTTGAAAATTCTCATT-AGCTCTTTTTT
500690 -TTTTTGAAAATTCTCATTA
1 ATTTTTGAAAATTCTCATTA
500709 ATCTCAGGAA
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
29 16 0.41
30 15 0.38
31 8 0.21
ACGTcount: A:0.27, C:0.09, G:0.04, T:0.61
Consensus pattern (30 bp):
ATTTTTGAAAATTCTCATTAGCTCTTTTTT
Found at i:500709 original size:30 final size:30
Alignment explanation
Indices: 500630--500709 Score: 92
Period size: 30 Copynumber: 2.7 Consensus size: 30
500620 GGCCCATTTA
*
500630 ATTTTTGAAAATTCTCATT-ATTCTTTTTT
1 ATTTTTGAAAATTCTCATTAACTCTTTTTT
** * *
500659 ATTTTTTTAAATTTTAATTAAGCTCTTTTTT
1 ATTTTTGAAAATTCTCATTAA-CTCTTTTTT
500690 -TTTTTGAAAATTCTCATTAA
1 ATTTTTGAAAATTCTCATTAA
500710 TCTCAGGAAA
Statistics
Matches: 40, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
29 15 0.38
30 17 0.43
31 8 0.20
ACGTcount: A:0.28, C:0.09, G:0.04, T:0.60
Consensus pattern (30 bp):
ATTTTTGAAAATTCTCATTAACTCTTTTTT
Found at i:501046 original size:23 final size:23
Alignment explanation
Indices: 501020--501064 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
501010 CAAAAACTAT
501020 ATTA-TCCCTAAAAAATAGGTTTC
1 ATTATTCCCTAAAAAA-AGGTTTC
* *
501043 ATTATTCTCTATAAAAAGGTTT
1 ATTATTCCCTAAAAAAAGGTTT
501065 AATTTTGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (23 bp):
ATTATTCCCTAAAAAAAGGTTTC
Found at i:502666 original size:13 final size:11
Alignment explanation
Indices: 502636--502665 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
502626 AAATTTTTTT
502636 TATTTTTAAAA
1 TATTTTTAAAA
502647 TATTTTTAAAA
1 TATTTTTAAAA
502658 TATATTTT
1 TAT-TTTT
502666 TTAATTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.78
12 4 0.22
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TATTTTTAAAA
Found at i:509907 original size:5 final size:5
Alignment explanation
Indices: 509897--509927 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
509887 GTCTTTAGAG
509897 TTATA TTATA TTATA TTATA TTAT- TTATA TT
1 TTATA TTATA TTATA TTATA TTATA TTATA TT
509928 TAAAAAATAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (5 bp):
TTATA
Found at i:511637 original size:2 final size:2
Alignment explanation
Indices: 511630--511668 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
511620 TTTGGGTAGA
511630 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 A
511669 AAATTTGAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:512614 original size:18 final size:19
Alignment explanation
Indices: 512581--512617 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
512571 AATTATATAA
*
512581 ATATACTATTTTAAAAAAT
1 ATATACTATATTAAAAAAT
512600 ATATA-TATATTAAAAAAT
1 ATATACTATATTAAAAAAT
512618 TAATAGACTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (19 bp):
ATATACTATATTAAAAAAT
Found at i:512903 original size:5 final size:5
Alignment explanation
Indices: 512893--512918 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
512883 TGAGCATTCG
512893 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
512919 AATTTTTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:513385 original size:24 final size:25
Alignment explanation
Indices: 513346--513392 Score: 87
Period size: 24 Copynumber: 1.9 Consensus size: 25
513336 TTTATGGCAT
513346 AATATTAAAAAAAAATTGGAGGGAA
1 AATATTAAAAAAAAATTGGAGGGAA
513371 AATATT-AAAAAAAATTGGAGGG
1 AATATTAAAAAAAAATTGGAGGG
513393 GGGAGGGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 16 0.73
25 6 0.27
ACGTcount: A:0.57, C:0.00, G:0.21, T:0.21
Consensus pattern (25 bp):
AATATTAAAAAAAAATTGGAGGGAA
Found at i:513465 original size:31 final size:30
Alignment explanation
Indices: 513430--513489 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
513420 GGAGGTGGGA
*
513430 TGGGAAAGGAATAAAAGTTTTAGGGGAAAAG
1 TGGG-AAGGAATAAAAATTTTAGGGGAAAAG
* * *
513461 TGGGAGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGAATAAAAATTTTAGGGGAAAA
513490 TAAAAGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (30 bp):
TGGGAAGGAATAAAAATTTTAGGGGAAAAG
Found at i:513630 original size:29 final size:30
Alignment explanation
Indices: 513571--513630 Score: 68
Period size: 30 Copynumber: 2.0 Consensus size: 30
513561 AAAGGGAGGG
* * **
513571 GAGTAAAAGTTTTGGGGGGAAAGTGGGAAA
1 GAGTAAAAGTTTTGAGGGAAAAGTGAAAAA
*
513601 GAGTAAGAGTTTTGAGGGAAAAGT-AAAAA
1 GAGTAAAAGTTTTGAGGGAAAAGTGAAAAA
513630 G
1 G
513631 GTTTGGGAGT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
29 4 0.16
30 21 0.84
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (30 bp):
GAGTAAAAGTTTTGAGGGAAAAGTGAAAAA
Found at i:525751 original size:2 final size:2
Alignment explanation
Indices: 525744--525782 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
525734 GAATACTGTT
525744 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
525783 TAACATTGAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:533336 original size:15 final size:16
Alignment explanation
Indices: 533313--533345 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
533303 TAAATAAAAT
533313 ATTATTAATTAATAAA
1 ATTATTAATTAATAAA
*
533329 ATTA-TAATTTATAAA
1 ATTATTAATTAATAAA
533344 AT
1 AT
533346 CATTTAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTATTAATTAATAAA
Found at i:535971 original size:19 final size:19
Alignment explanation
Indices: 535947--536033 Score: 77
Period size: 20 Copynumber: 4.4 Consensus size: 19
535937 AAAGTATTTT
535947 AAAAATATTTTAAAATTAA
1 AAAAATATTTTAAAATTAA
****
535966 AAAAATAAAAAAAAATTATTTTA
1 AAAAATATTTTAAAATTA----A
*
535989 AAAAA-ATTTTTAAATTAA
1 AAAAATATTTTAAAATTAA
536007 AAAAAGTATTTTAAAATTAA
1 AAAAA-TATTTTAAAATTAA
536027 AAAAATA
1 AAAAATA
536034 AATAAAAAAT
Statistics
Matches: 52, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
18 6 0.12
19 16 0.31
20 17 0.33
22 7 0.13
23 6 0.12
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (19 bp):
AAAAATATTTTAAAATTAA
Found at i:535989 original size:41 final size:41
Alignment explanation
Indices: 535908--536011 Score: 138
Period size: 41 Copynumber: 2.5 Consensus size: 41
535898 ACCAAAAATT
535908 TATTTTAAAAATTAAAATAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATTAAAA-AAAAA-TAAAAAAAGTATTTTAAAAA
*
535952 TATTTTAAAATTAAAAAAATAA-AAAAAAATTATTTTAAAAA
1 TATTTTAAAATTAAAAAAA-AATAAAAAAAGTATTTTAAAAA
* *
535993 AATTTTTAAATTAAAAAAA
1 TATTTTAAAATTAAAAAAA
536012 GTATTTTAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
41 35 0.62
42 3 0.05
43 12 0.21
44 6 0.11
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (41 bp):
TATTTTAAAATTAAAAAAAAATAAAAAAAGTATTTTAAAAA
Found at i:535999 original size:12 final size:14
Alignment explanation
Indices: 535974--536022 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 14
535964 AAAAAAATAA
535974 AAAAAAATTATTTT
1 AAAAAAATTATTTT
*
535988 AAAAAAATTTTTAAATT
1 AAAAAAATTATT---TT
*
536005 AAAAAAAGTATTTT
1 AAAAAAATTATTTT
536019 AAAA
1 AAAA
536023 TTAAAAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
14 17 0.59
17 12 0.41
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (14 bp):
AAAAAAATTATTTT
Found at i:536041 original size:19 final size:19
Alignment explanation
Indices: 536000--536051 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
535990 AAAAATTTTT
** *
536000 AAATTAAAAAAAGTATTTTA
1 AAATTAAAAAAA-TAAATAA
536020 AAATTAAAAAAATAAATAA
1 AAATTAAAAAAATAAATAA
*
536039 AAAATAAAAAAAT
1 AAATTAAAAAAAT
536052 TTATTATTCG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (19 bp):
AAATTAAAAAAATAAATAA
Found at i:537569 original size:238 final size:239
Alignment explanation
Indices: 537147--537700 Score: 776
Period size: 239 Copynumber: 2.3 Consensus size: 239
537137 TTTTACACCA
* * * *
537147 ATATTCAATAGTTCGATGGGGGAATATCAGGTTCATTTATACCAAACATGTCCAAAAGAAAAGCA
1 ATATTCAACAGTTTGAAGGGGGAATATCAGGTTCATTTATACCAAACATATCCAAAAGAAAAGCA
* * * *
537212 CATTAGAAGTATGTGTTAAATCTCATAACGGTCAAGCCACGTCAACGAGCCTAGATGCTTGGAAC
66 CATTAGAAGTATGCGTTAAATCTCATAACAGTAAAGCCACGTCAACGAGCCTAGATGCTCGGAAC
* * *
537277 ATGTTTTCGTTGAAGCATCACATTGAGTTTATTGTCCATAGATTATAGCTTCTAAGAGTAA-TCA
131 ATGTTTTCGTTGAAGCATCACATCGAGTTTATTGTCCATAGATCATACCTTCTAAGAGTAATTCA
*
537341 CAGCAAATATCACATTTAACTAGAACCCACGTCGGATTA-TGAAC
196 CAGCAAATATCACATTTAACTAGAACCCACGTCGGACTAGT-AAC
* * * * *
537385 ATATTCAACAGTTTGAAGGGGGAATATCAGGTTCATTTATTCCGAACATATCCGAAAGAGAAGTA
1 ATATTCAACAGTTTGAAGGGGGAATATCAGGTTCATTTATACCAAACATATCCAAAAGAAAAGCA
* * *
537450 CATTAGAAGTATGCGTTAGAATCTTATAACAGTAAAGCCATGTCAATGAGCCTAGATGCTCGGAA
66 CATTAGAAGTATGCGTTA-AATCTCATAACAGTAAAGCCACGTCAACGAGCCTAGATGCTCGG-A
*
537515 ACATGTTGTT-GTTGAAGCA-C-CATCGAGTTTATTGTCCATGGATCATACCTTCTAAGAGTAAT
129 ACATGTT-TTCGTTGAAGCATCACATCGAGTTTATTGTCCATAGATCATACCTTCTAAGAGTAAT
* * * *
537577 TCACAGGAAATATCGCATTTAACTAGAACCCACTTTGGACTAGTAAC
193 TCACAGCAAATATCACATTTAACTAGAACCCACGTCGGACTAGTAAC
* * * *
537624 ATATTCAACGGTTTGAAGGGGGAATATCGGGTTCATTTATACCTAACATATCCAAAAGATAAGCA
1 ATATTCAACAGTTTGAAGGGGGAATATCAGGTTCATTTATACCAAACATATCCAAAAGAAAAGCA
537689 CATTAGAAGTAT
66 CATTAGAAGTAT
537701 AATGGTAAAG
Statistics
Matches: 279, Mismatches: 32, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
238 110 0.39
239 149 0.53
240 18 0.06
241 2 0.01
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.29
Consensus pattern (239 bp):
ATATTCAACAGTTTGAAGGGGGAATATCAGGTTCATTTATACCAAACATATCCAAAAGAAAAGCA
CATTAGAAGTATGCGTTAAATCTCATAACAGTAAAGCCACGTCAACGAGCCTAGATGCTCGGAAC
ATGTTTTCGTTGAAGCATCACATCGAGTTTATTGTCCATAGATCATACCTTCTAAGAGTAATTCA
CAGCAAATATCACATTTAACTAGAACCCACGTCGGACTAGTAAC
Found at i:538540 original size:30 final size:29
Alignment explanation
Indices: 538499--538570 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 29
538489 GAAGACATAT
*
538499 ATATATTATATAGACAATGTCTAGGATAAAC
1 ATATA-TATATAGA-AATCTCTAGGATAAAC
* *
538530 ATGTATATATAAGAAATCTCTAGGATTAAC
1 ATATATATAT-AGAAATCTCTAGGATAAAC
*
538560 CTATATATATA
1 ATATATATATA
538571 TATATGCATG
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
29 1 0.03
30 27 0.77
31 7 0.20
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.35
Consensus pattern (29 bp):
ATATATATATAGAAATCTCTAGGATAAAC
Found at i:549267 original size:12 final size:12
Alignment explanation
Indices: 549250--549279 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
549240 AAAGATATTA
549250 TATATATATATG
1 TATATATATATG
549262 TATATATATATG
1 TATATATATATG
*
549274 AATATA
1 TATATA
549280 CTAACGGTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (12 bp):
TATATATATATG
Found at i:552428 original size:96 final size:96
Alignment explanation
Indices: 552264--552471 Score: 267
Period size: 96 Copynumber: 2.2 Consensus size: 96
552254 GGTTTCACCT
* * *
552264 CCTTCAAAAGCGGTGGTCTCGATGTTCGAAGCAACCGTGGAACTTAGAACATTGATTTGATCATA
1 CCTTCAAAAGCGGTGGACTCGATGTTCGAAGCAACCGTAGAACTTAGAACACTGATTTGATCATA
*
552329 AATATTTTCCTCCTGCGTGAAGAACTGACCA
66 AATATCTTCCTCCTGCGTGAAGAACTGACCA
* * * * * *
552360 CCTTCAAAAGCTGT-GACGTCGATGTTCGAAGCAACTGTAGAATTTAGAACGCT-ATTTAGGTTA
1 CCTTCAAAAGCGGTGGAC-TCGATGTTCGAAGCAACCGTAGAACTTAGAACACTGATTT-GATCA
*
552423 TAAATATCTTCCTCCTGCGTGAAGAATTGACCA
64 TAAATATCTTCCTCCTGCGTGAAGAACTGACCA
* *
552456 ACTTCATAAGCGGTGG
1 CCTTCAAAAGCGGTGG
552472 CGCCGCCATC
Statistics
Matches: 95, Mismatches: 14, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
95 6 0.06
96 88 0.93
97 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (96 bp):
CCTTCAAAAGCGGTGGACTCGATGTTCGAAGCAACCGTAGAACTTAGAACACTGATTTGATCATA
AATATCTTCCTCCTGCGTGAAGAACTGACCA
Found at i:553267 original size:22 final size:21
Alignment explanation
Indices: 553218--553287 Score: 72
Period size: 20 Copynumber: 3.4 Consensus size: 21
553208 TCATATATTA
*
553218 ATATAAATATTTATTATTTAT
1 ATATAAATATTAATTATTTAT
* *
553239 ATA-AAATATTAATTTTTTGT
1 ATATAAATATTAATTATTTAT
*
553259 ATAATAAATATTAATTCTTTA-
1 AT-ATAAATATTAATTATTTAT
*
553280 ATAAAAAT
1 ATATAAAT
553288 TTATAAAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
20 21 0.51
21 6 0.15
22 14 0.34
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (21 bp):
ATATAAATATTAATTATTTAT
Found at i:556091 original size:3 final size:3
Alignment explanation
Indices: 556077--556133 Score: 105
Period size: 3 Copynumber: 19.0 Consensus size: 3
556067 GCGGTGGTTT
*
556077 TGG TGT TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG
556125 TGG TGG TGG
1 TGG TGG TGG
556134 AGATGCTGGA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.00, C:0.00, G:0.65, T:0.35
Consensus pattern (3 bp):
TGG
Found at i:556891 original size:19 final size:19
Alignment explanation
Indices: 556847--556893 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 19
556837 TTAAATATTT
556847 TTTATAAAAGTACAAAAGA
1 TTTATAAAAGTACAAAAGA
556866 TTGTATAAAA-TACATACAA-A
1 TT-TATAAAAGTACA-A-AAGA
556886 TTTATAAA
1 TTTATAAA
556894 TGAACGAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 12 0.48
20 11 0.44
21 2 0.08
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.32
Consensus pattern (19 bp):
TTTATAAAAGTACAAAAGA
Found at i:561542 original size:21 final size:22
Alignment explanation
Indices: 561505--561547 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
561495 CCAATTAACC
561505 TAGCCCAAACACTAAACCCAAT
1 TAGCCCAAACACTAAACCCAAT
*
561527 TAGCCTAAAC-CTAAACCCAAT
1 TAGCCCAAACACTAAACCCAAT
561548 ACCCCAGCCC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.44, C:0.35, G:0.05, T:0.16
Consensus pattern (22 bp):
TAGCCCAAACACTAAACCCAAT
Found at i:564776 original size:102 final size:102
Alignment explanation
Indices: 564660--565034 Score: 328
Period size: 102 Copynumber: 3.7 Consensus size: 102
564650 TTTGATATTT
* * ** * * * **
564660 TAGAGCGACAAATCAGTGGTTATTACTCGTTAATTTGCCAGTAATCAAAGTGATAAGCAGATAAT
1 TAGAGTGAAAAATCAGTGACTATTACTTGTTAATTAGCTACCAATCAAAGTGATAAGCAGATAAT
564725 TTGTTTATTCCACGATTGAATTTAGTCTTTTGATCTC
66 TTGTTTATTCCACGATTGAATTTAGTCTTTTGATCTC
* * * * *
564762 TAGAGTGAAGAATCAGTGACTGTAACTTGTTAATTAGCTACCAATCAGAGTGCTAAGCAGATAAT
1 TAGAGTGAAAAATCAGTGACTATTACTTGTTAATTAGCTACCAATCAAAGTGATAAGCAGATAAT
*** * * * ** *
564827 TT-TGTTATT-TGGGAGCTAAATTT-GTGATTTAATTGTAAATT
66 TTGT-TTATTCCACGA-TTGAATTTAGT--CTT--TTG-ATCTC
* * * * ** *
564868 TAGATTGAAAAATCAGTGATTATTAATTTTTAATTAGCTAATAATCAGAGTGATAAGCAGAT--T
1 TAGAGTGAAAAATCAGTGACTATTACTTGTTAATTAGCTACCAATCAAAGTGATAAGCAGATAAT
* *
564931 TTGTTTATTCCACAATTGAATGTAGTCTTTTGATCTC
66 TTGTTTATTCCACGATTGAATTTAGTCTTTTGATCTC
* * * *
564968 TAGAGCGAAAAATCAGTGACTATCATTTGTTAATTAGCTACCAATCAAAGTGTTAAGCAGATAAT
1 TAGAGTGAAAAATCAGTGACTATTACTTGTTAATTAGCTACCAATCAAAGTGATAAGCAGATAAT
565033 TT
66 TT
565035 TGTTATTTGG
Statistics
Matches: 207, Mismatches: 54, Indels: 24
0.73 0.19 0.08
Matches are distributed among these distances:
100 54 0.26
101 8 0.04
102 67 0.32
103 4 0.02
104 13 0.06
105 7 0.03
106 54 0.26
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.37
Consensus pattern (102 bp):
TAGAGTGAAAAATCAGTGACTATTACTTGTTAATTAGCTACCAATCAAAGTGATAAGCAGATAAT
TTGTTTATTCCACGATTGAATTTAGTCTTTTGATCTC
Found at i:564959 original size:206 final size:207
Alignment explanation
Indices: 564669--565056 Score: 607
Period size: 206 Copynumber: 1.9 Consensus size: 207
564659 TTAGAGCGAC
* * * *
564669 AAATCAGTGGTTATTACTCGTTAATTTGCCAGTAATCAAAGTGATAAGCAGATAATTTGTTTATT
1 AAATCAGTGATTATTAATCGTTAATTAGCCAATAATCAAAGTGATAAGCAGAT-ATTTGTTTATT
* * * * *
564734 CCACGATTGAATTTAGTCTTTTGATCTCTAGAGTGAAGAATCAGTGACTGTAACTTGTTAATTAG
65 CCACAATTGAATGTAGTCTTTTGATCTCTAGAGCGAAAAATCAGTGACTATAACTTGTTAATTAG
*
564799 CTACCAATCAGAGTGCTAAGCAGATAATTTTGTTATTTGGGAGCTAAATTTGTGATTTAATTGTA
130 CTACCAATCAAAGTGCTAAGCAGATAATTTTGTTATTTGGGAGCTAAATTTGTGATTTAATTGTA
564864 AATTTAGATTGAA
195 AATTTAGATTGAA
** * *
564877 AAATCAGTGATTATTAATTTTTAATTAGCTAATAATCAGAGTGATAAGCAGAT-TTTGTTTATTC
1 AAATCAGTGATTATTAATCGTTAATTAGCCAATAATCAAAGTGATAAGCAGATATTTGTTTATTC
* *
564941 CACAATTGAATGTAGTCTTTTGATCTCTAGAGCGAAAAATCAGTGACTATCATTTGTTAATTAGC
66 CACAATTGAATGTAGTCTTTTGATCTCTAGAGCGAAAAATCAGTGACTATAACTTGTTAATTAGC
*
565006 TACCAATCAAAGTGTTAAGCAGATAATTTTGTTATTTGGGAGCTAAATTTG
131 TACCAATCAAAGTGCTAAGCAGATAATTTTGTTATTTGGGAGCTAAATTTG
565057 GAATTTGATT
Statistics
Matches: 163, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
206 118 0.72
208 45 0.28
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (207 bp):
AAATCAGTGATTATTAATCGTTAATTAGCCAATAATCAAAGTGATAAGCAGATATTTGTTTATTC
CACAATTGAATGTAGTCTTTTGATCTCTAGAGCGAAAAATCAGTGACTATAACTTGTTAATTAGC
TACCAATCAAAGTGCTAAGCAGATAATTTTGTTATTTGGGAGCTAAATTTGTGATTTAATTGTAA
ATTTAGATTGAA
Found at i:573274 original size:2 final size:2
Alignment explanation
Indices: 573267--573301 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
573257 NNNNNNNAGC
573267 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
573302 CGAATGCATG
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:574164 original size:69 final size:69
Alignment explanation
Indices: 574052--574188 Score: 202
Period size: 69 Copynumber: 2.0 Consensus size: 69
574042 GAAGGTAAAA
** * * *
574052 AAATCGAAAACTGAAATTGAATTGTCACTTTTTGCATGCACTAGGGTAAGATATGTTTTGATGAA
1 AAATCGAAAACCAAAATCGAATTGTCACTTTTTGCATGCACTAGGATAAGATATGTTTCGATGAA
574117 TAAC
66 TAAC
* * *
574121 AAATCGAAAACCAAAATCGAATTGTCATTTTTTGCATGTACTAGGATGAGATATGTTTCGATGAA
1 AAATCGAAAACCAAAATCGAATTGTCACTTTTTGCATGCACTAGGATAAGATATGTTTCGATGAA
574186 TAA
66 TAA
574189 TCTCTAGCGG
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
69 60 1.00
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (69 bp):
AAATCGAAAACCAAAATCGAATTGTCACTTTTTGCATGCACTAGGATAAGATATGTTTCGATGAA
TAAC
Found at i:575229 original size:21 final size:21
Alignment explanation
Indices: 575196--575275 Score: 106
Period size: 21 Copynumber: 3.8 Consensus size: 21
575186 TTCATCTGCA
*
575196 TACCCTCCTCCACCTTCGGCT
1 TACCCTCCACCACCTTCGGCT
* *
575217 TATCCTCCACCACATTCGGCT
1 TACCCTCCACCACCTTCGGCT
* *
575238 TACCCTCCACCACCTTCCGCA
1 TACCCTCCACCACCTTCGGCT
*
575259 TACCCTCCGCCACCTTC
1 TACCCTCCACCACCTTC
575276 ATCGTATCCC
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.15, C:0.53, G:0.07, T:0.25
Consensus pattern (21 bp):
TACCCTCCACCACCTTCGGCT
Found at i:587680 original size:17 final size:17
Alignment explanation
Indices: 587642--587694 Score: 54
Period size: 17 Copynumber: 3.0 Consensus size: 17
587632 AAAATTTATA
*
587642 AATAAAATATTCAAAA-
1 AATAAAACATTCAAAAT
587658 ATATAAAACATTCAAAAT
1 A-ATAAAACATTCAAAAT
*
587676 AATAATAATCAATCAAAAT
1 AATAA-AA-CATTCAAAAT
587695 CAAAATAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
16 1 0.03
17 18 0.58
18 3 0.10
19 9 0.29
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.26
Consensus pattern (17 bp):
AATAAAACATTCAAAAT
Found at i:590307 original size:21 final size:20
Alignment explanation
Indices: 590266--590325 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 20
590256 AATTATTGTT
590266 TTAAAATATTTAT-AA-AAAA
1 TTAAAA-ATTTATAAATAAAA
590285 TTAAAAATTTATCAAATAAAA
1 TTAAAAATTTAT-AAATAAAA
* * *
590306 TTTAAAAGTCATAAATAAAA
1 TTAAAAATTTATAAATAAAA
590326 AATTATTTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
18 6 0.17
19 6 0.17
20 10 0.29
21 13 0.37
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (20 bp):
TTAAAAATTTATAAATAAAA
Found at i:590310 original size:22 final size:20
Alignment explanation
Indices: 590265--590312 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 20
590255 AAATTATTGT
590265 TTTAAAATATTTATAAAAAA
1 TTTAAAATATTTATAAAAAA
590285 -TTAAAA-ATTTATCAAATAAAA
1 TTTAAAATATTTAT--AA-AAAA
590306 TTTAAAA
1 TTTAAAA
590313 GTCATAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
18 6 0.25
19 6 0.25
20 2 0.08
21 4 0.17
22 6 0.25
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (20 bp):
TTTAAAATATTTATAAAAAA
Found at i:591518 original size:19 final size:17
Alignment explanation
Indices: 591494--591537 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
591484 AATAAATTAT
591494 AAATATTAAAAAGTCAAAA
1 AAATATTAAAAA-T-AAAA
*
591513 AAATATTCAAAATAAAA
1 AAATATTAAAAATAAAA
591530 AAA-ATTAA
1 AAATATTAA
591538 CATAAAGTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 4 0.17
17 7 0.30
18 1 0.04
19 11 0.48
ACGTcount: A:0.70, C:0.05, G:0.02, T:0.23
Consensus pattern (17 bp):
AAATATTAAAAATAAAA
Found at i:592868 original size:12 final size:11
Alignment explanation
Indices: 592853--592916 Score: 54
Period size: 9 Copynumber: 6.4 Consensus size: 11
592843 ATAAAAATTA
592853 AAAAATTATTTT
1 AAAAA-TATTTT
592865 AAAAATATTTT
1 AAAAATATTTT
592876 --AAA-A-TTT
1 AAAAATATTTT
592883 AAAAA-A-TTT
1 AAAAATATTTT
592892 AAAAAGTATTTT
1 AAAAA-TATTTT
592904 AAAAA-A-TTT
1 AAAAATATTTT
592913 AAAA
1 AAAA
592917 TTTAAAAAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
7 3 0.06
8 1 0.02
9 22 0.47
10 1 0.02
11 7 0.15
12 13 0.28
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:592890 original size:9 final size:9
Alignment explanation
Indices: 592862--592935 Score: 73
Period size: 9 Copynumber: 8.0 Consensus size: 9
592852 AAAAAATTAT
592862 TTTAAAAATA
1 TTTAAAAA-A
*
592872 TTT-TAAAA
1 TTTAAAAAA
592880 TTTAAAAAA
1 TTTAAAAAA
592889 TTTAAAAAGTA
1 TTTAAAAA--A
592900 TTTTAAAAAA
1 -TTTAAAAAA
592910 TTT--AAAA
1 TTTAAAAAA
592917 TTTAAAAAA
1 TTTAAAAAA
592926 TTTAATAAAA
1 TTTAA-AAAA
592936 GTATTTTAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
7 7 0.13
8 4 0.07
9 27 0.49
10 8 0.15
11 1 0.02
12 8 0.15
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (9 bp):
TTTAAAAAA
Found at i:592901 original size:28 final size:26
Alignment explanation
Indices: 592862--592956 Score: 86
Period size: 30 Copynumber: 3.4 Consensus size: 26
592852 AAAAAATTAT
592862 TTTAAAAATATTTT-AAAATTTAAAAAA
1 TTTAAAAATATTTTAAAAATTT--AAAA
592889 TTTAAAAAGTATTTTAAAAAATTTAAAA
1 TTTAAAAA-TATTTT-AAAAATTTAAAA
592917 TTTAAAAA-ATTTAATAAAAGTATTTTAAAA
1 TTTAAAAATATTT--TAAAA--A-TTTAAAA
*
592947 TTAAAAAATA
1 TTTAAAAATA
592957 ATAAATAATA
Statistics
Matches: 58, Mismatches: 1, Indels: 14
0.79 0.01 0.19
Matches are distributed among these distances:
26 4 0.07
27 12 0.21
28 19 0.33
29 1 0.02
30 21 0.36
31 1 0.02
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (26 bp):
TTTAAAAATATTTTAAAAATTTAAAA
Found at i:592923 original size:37 final size:39
Alignment explanation
Indices: 592845--592946 Score: 154
Period size: 39 Copynumber: 2.6 Consensus size: 39
592835 AAATTAAAAT
* *
592845 AAAAATTAAAAAATTATTTTAAAAATATTTTAAAATTTA
1 AAAAATTTAAAAAGTATTTTAAAAATATTTTAAAATTTA
592884 AAAAATTTAAAAAGTATTTTAAAAA-A-TTTAAAATTTA
1 AAAAATTTAAAAAGTATTTTAAAAATATTTTAAAATTTA
592921 AAAAATTTAATAAAAGTATTTTAAAA
1 AAAAATTT-A-AAAAGTATTTTAAAA
592947 TTAAAAAATA
Statistics
Matches: 59, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
37 19 0.32
38 2 0.03
39 38 0.64
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (39 bp):
AAAAATTTAAAAAGTATTTTAAAAATATTTTAAAATTTA
Found at i:592941 original size:29 final size:27
Alignment explanation
Indices: 592862--592955 Score: 79
Period size: 28 Copynumber: 3.4 Consensus size: 27
592852 AAAAAATTAT
*
592862 TTTAAAAATATTTT--AAAATTTAAAAAA
1 TTTAAAAA-ATTTTAAAAAATTT-TAAAA
592889 TTTAAAAAGTATTTTAAAAAA-TTTAAAA
1 TTTAAAAA--ATTTTAAAAAATTTTAAAA
*
592917 TTTAAAAAATTTAATAAAAGTATTTTAAAA
1 TTTAAAAAATTT--TAAAA-AATTTTAAAA
592947 -TTAAAAAAT
1 TTTAAAAAAT
592956 AATAAATAAT
Statistics
Matches: 58, Mismatches: 2, Indels: 12
0.81 0.03 0.17
Matches are distributed among these distances:
26 4 0.07
27 8 0.14
28 23 0.40
29 12 0.21
30 11 0.19
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (27 bp):
TTTAAAAAATTTTAAAAAATTTTAAAA
Found at i:592948 original size:37 final size:36
Alignment explanation
Indices: 592831--592946 Score: 132
Period size: 39 Copynumber: 3.2 Consensus size: 36
592821 AAATAAATAC
* *
592831 TTAAAAA-TTAAAA--T-AAAAATTAAAAAATTATT
1 TTAAAAATTTAAAATTTAAAAAATTTAAAAAGTATT
592863 TTAAAAATATTTTAAAATTTAAAAAATTTAAAAAGTATT
1 TT-AAAA-A-TTTAAAATTTAAAAAATTTAAAAAGTATT
592902 TTAAAAAATTTAAAATTTAAAAAATTTAATAAAAGTATT
1 TT-AAAAATTTAAAATTTAAAAAATTT-A-AAAAGTATT
592941 TTAAAA
1 TTAAAA
592947 TTAAAAAATA
Statistics
Matches: 73, Mismatches: 2, Indels: 12
0.84 0.02 0.14
Matches are distributed among these distances:
32 2 0.03
33 4 0.05
34 1 0.01
36 6 0.08
37 19 0.26
38 7 0.10
39 34 0.47
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (36 bp):
TTAAAAATTTAAAATTTAAAAAATTTAAAAAGTATT
Found at i:594826 original size:31 final size:31
Alignment explanation
Indices: 594791--594858 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
594781 ACAAAATGGC
594791 CATTGAACTATTTAAAAATTTTCATATAAGT
1 CATTGAACTATTTAAAAATTTTCATATAAGT
* * *
594822 CATTGAACTATTTAAAAGTTTTTATTTAAGT
1 CATTGAACTATTTAAAAATTTTCATATAAGT
594853 CATTGA
1 CATTGA
594859 GTTGTTAAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (31 bp):
CATTGAACTATTTAAAAATTTTCATATAAGT
Found at i:603549 original size:46 final size:46
Alignment explanation
Indices: 603489--603582 Score: 161
Period size: 46 Copynumber: 2.0 Consensus size: 46
603479 CCATAGCAAA
**
603489 TTGTGAAACTTAGGTATGGTATTTCAATAAAGAAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTATTTCAATAAAGAAAACCATACTGAG
*
603535 TTGTGAAAAGTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTATTTCAATAAAGAAAACCATACTGAG
603581 TT
1 TT
603583 ACAGTATTGT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (46 bp):
TTGTGAAAAGTAGGTATGGTATTTCAATAAAGAAAACCATACTGAG
Found at i:607210 original size:30 final size:30
Alignment explanation
Indices: 607176--607243 Score: 136
Period size: 30 Copynumber: 2.3 Consensus size: 30
607166 TCGGCGACGG
607176 TGGCGGCGGCAATGCTTCCACCGGAAATAT
1 TGGCGGCGGCAATGCTTCCACCGGAAATAT
607206 TGGCGGCGGCAATGCTTCCACCGGAAATAT
1 TGGCGGCGGCAATGCTTCCACCGGAAATAT
607236 TGGCGGCG
1 TGGCGGCG
607244 ATAAAGGAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.21, C:0.26, G:0.34, T:0.19
Consensus pattern (30 bp):
TGGCGGCGGCAATGCTTCCACCGGAAATAT
Found at i:614611 original size:29 final size:30
Alignment explanation
Indices: 614574--614644 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 30
614564 CTTTTTATTT
* *
614574 GTCACCCAACTAT-AAGAAGTTAGAAAATG-
1 GTCATCCAACTATGAA-AAGTTACAAAATGA
*
614603 GTCATCCAACCATGAAAAGTTACAAAATGA
1 GTCATCCAACTATGAAAAGTTACAAAATGA
*
614633 GT-ATTCAACTAT
1 GTCATCCAACTAT
614645 TCAACTTTGT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
29 31 0.89
30 4 0.11
ACGTcount: A:0.44, C:0.18, G:0.14, T:0.24
Consensus pattern (30 bp):
GTCATCCAACTATGAAAAGTTACAAAATGA
Found at i:615394 original size:24 final size:24
Alignment explanation
Indices: 615350--615396 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
615340 GATGCGGTAT
* **
615350 TCAATTTGATATTTATTTTTAATC
1 TCAATTTGATACTTAAATTTAATC
615374 TCAATTTGATACTTAAATTTAAT
1 TCAATTTGATACTTAAATTTAAT
615397 TTTAGTGTCC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.09, G:0.04, T:0.53
Consensus pattern (24 bp):
TCAATTTGATACTTAAATTTAATC
Found at i:617477 original size:13 final size:12
Alignment explanation
Indices: 617459--617492 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
617449 ACATAAATTC
617459 AAACAAATAAGGA
1 AAACAAAT-AGGA
617472 AAACAAATAGGA
1 AAACAAATAGGA
617484 ACAACAAAT
1 A-AACAAAT
617493 TAAAAAAGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 5 0.25
13 15 0.75
ACGTcount: A:0.68, C:0.12, G:0.12, T:0.09
Consensus pattern (12 bp):
AAACAAATAGGA
Found at i:618360 original size:121 final size:117
Alignment explanation
Indices: 618216--618436 Score: 293
Period size: 118 Copynumber: 1.9 Consensus size: 117
618206 TTTATTTTTA
*
618216 AGCTCAAGCTCGGCTCGAGATATAATC-AAGCTATTCGAGCAAGCTCGATTAAGC-TCATTTATC
1 AGCTCAAGCTCAGCTCGAGATATAATCGAA-C---T-GAGCAAGCTCGATTAAGCTTCATTTATC
618279 AATTTTTGTACTCAAGCTTGAACTTTAGCTCAATTAAGCTCATATGTATTAAATCTTG
61 AATTTTTGTACTCAAGCTTGAACTTTAGCTC-ATTAAGCTCATATGTATTAAATCTTG
* ** * **
618337 AGCTCAAGCTCAGCTTGAGATATAATCGAACTGCTCAAGCTCGATTCAGCTTTTTTTATCAATTT
1 AGCTCAAGCTCAGCTCGAGATATAATCGAACTGAGCAAGCTCGATTAAGCTTCATTTATCAATTT
* *
618402 TTGTACTCTAGCTTGAGCTTTAGCTCATTAAGCTC
66 TTGTACTCAAGCTTGAACTTTAGCTCATTAAGCTC
618437 GTACTTGTTA
Statistics
Matches: 89, Mismatches: 9, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
117 24 0.27
118 37 0.42
121 26 0.29
122 2 0.02
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (117 bp):
AGCTCAAGCTCAGCTCGAGATATAATCGAACTGAGCAAGCTCGATTAAGCTTCATTTATCAATTT
TTGTACTCAAGCTTGAACTTTAGCTCATTAAGCTCATATGTATTAAATCTTG
Found at i:622729 original size:22 final size:22
Alignment explanation
Indices: 622703--622747 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
622693 TTACTATGAT
*
622703 TTTTAATTATTTTAATTTATTA
1 TTTTAATTATTTTAAATTATTA
* *
622725 TTTTATTTCTTTTAAATTATTA
1 TTTTAATTATTTTAAATTATTA
622747 T
1 T
622748 AGGAGCTTGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTTAATTATTTTAAATTATTA
Found at i:627074 original size:16 final size:16
Alignment explanation
Indices: 627053--627083 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
627043 AATGTTAGAG
627053 CACATAAATTTGAAAT
1 CACATAAATTTGAAAT
*
627069 CACATATATTTGAAA
1 CACATAAATTTGAAA
627084 ACTTTTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.13, G:0.06, T:0.32
Consensus pattern (16 bp):
CACATAAATTTGAAAT
Found at i:627239 original size:17 final size:16
Alignment explanation
Indices: 627219--627265 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
627209 TTCTTTAGAT
* *
627219 TTTTTTTAATTTTATAA
1 TTTTTTAAATATT-TAA
627236 TTTTTATAAATATTTAA
1 TTTTT-TAAATATTTAA
627253 TTTTTTAAA-ATTT
1 TTTTTTAAATATTT
627266 TTTTGTAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 4 0.15
16 4 0.15
17 13 0.48
18 6 0.22
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTTTTAAATATTTAA
Found at i:627240 original size:18 final size:17
Alignment explanation
Indices: 627212--627263 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
627202 TTATATATTC
* *
627212 TTTAGATTTTTTTTAATT
1 TTTA-ATTTTTTTAAATA
*
627230 TTATAATTTTTATAAATA
1 TT-TAATTTTTTTAAATA
*
627248 TTTAATTTTTTAAAAT
1 TTTAATTTTTTTAAAT
627264 TTTTTTGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
17 12 0.43
18 14 0.50
19 2 0.07
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
TTTAATTTTTTTAAATA
Found at i:629951 original size:31 final size:31
Alignment explanation
Indices: 629906--629971 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
629896 ACAAAAAATG
* *
629906 GTTATTGAATTATTAGAAAATTTTCATTTAA
1 GTTATTAAACTATTAGAAAATTTTCATTTAA
* *
629937 GTTATTAAACTATTAGAAAGTTTTTATTTAA
1 GTTATTAAACTATTAGAAAATTTTCATTTAA
629968 GTTA
1 GTTA
629972 CTGAGATGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.03, G:0.11, T:0.48
Consensus pattern (31 bp):
GTTATTAAACTATTAGAAAATTTTCATTTAA
Found at i:632025 original size:2 final size:2
Alignment explanation
Indices: 632018--632042 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
632008 TATATGTATA
632018 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
632043 ATCTTTAAAA
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:636926 original size:127 final size:127
Alignment explanation
Indices: 636700--636954 Score: 465
Period size: 127 Copynumber: 2.0 Consensus size: 127
636690 GTCCTTGTTG
* * *
636700 CGTGTTTAAAACTGTGCCAAAACATTCGATTGAAACTATGTCTTCTGATGTTCATATTTCTTTCT
1 CGTGTTTAAAAATGTGCCAAAACATTCGATTGAAACTATGTCTTCTGACGTTCATAGTTCTTTCT
*
636765 GAAGGTGTATGCTATTGGGACACTACCTTAAAGGTCTCGAGTATCGGATGGAGCTAATCGAA
66 GAACGTGTATGCTATTGGGACACTACCTTAAAGGTCTCGAGTATCGGATGGAGCTAATCGAA
*
636827 CGTGTTTAAAAATGTGCCAAAACATTTGATTGAAACTATGTCTTCTGACGTTCATAGTTCTTTCT
1 CGTGTTTAAAAATGTGCCAAAACATTCGATTGAAACTATGTCTTCTGACGTTCATAGTTCTTTCT
636892 GAACGTGTATGCTATTGGGACACTACCTTAAAGGTCTCGAGTATCGGATGGAGCTAATCGAA
66 GAACGTGTATGCTATTGGGACACTACCTTAAAGGTCTCGAGTATCGGATGGAGCTAATCGAA
636954 C
1 C
636955 TTTTATCCTC
Statistics
Matches: 123, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
127 123 1.00
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (127 bp):
CGTGTTTAAAAATGTGCCAAAACATTCGATTGAAACTATGTCTTCTGACGTTCATAGTTCTTTCT
GAACGTGTATGCTATTGGGACACTACCTTAAAGGTCTCGAGTATCGGATGGAGCTAATCGAA
Found at i:638004 original size:2 final size:2
Alignment explanation
Indices: 637997--638026 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
637987 AGCTGTGTAC
637997 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
638027 TATCTATTAT
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:645689 original size:18 final size:16
Alignment explanation
Indices: 645648--645696 Score: 66
Period size: 14 Copynumber: 3.1 Consensus size: 16
645638 TTCAAAAGGT
645648 TGTAAATTATCCTTTA
1 TGTAAATTATCCTTTA
645664 T-T-AATTATCCTTTA
1 TGTAAATTATCCTTTA
645678 GGTGTAAATTATCCTTTA
1 --TGTAAATTATCCTTTA
645696 T
1 T
645697 TAATTTTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
14 12 0.41
15 1 0.03
16 3 0.10
17 1 0.03
18 12 0.41
ACGTcount: A:0.29, C:0.12, G:0.08, T:0.51
Consensus pattern (16 bp):
TGTAAATTATCCTTTA
Found at i:648997 original size:29 final size:29
Alignment explanation
Indices: 648964--649021 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
648954 TTTAAAAATT
* * *
648964 GAATTATATGAAAATTGAAAATTTTTAAA
1 GAATTAGATAAAAATTAAAAATTTTTAAA
648993 GAATTAGATAAAAATTAAAAATTTTTAAA
1 GAATTAGATAAAAATTAAAAATTTTTAAA
649022 AATAAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (29 bp):
GAATTAGATAAAAATTAAAAATTTTTAAA
Found at i:649037 original size:16 final size:17
Alignment explanation
Indices: 649000--649037 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
648990 AAAGAATTAG
*
649000 ATAAAAATTAAAAATTT
1 ATAAAAATTAAAAATAT
*
649017 TTAAAAA-TAAAAATAT
1 ATAAAAATTAAAAATAT
649033 ATAAA
1 ATAAA
649038 TATGAATTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
ATAAAAATTAAAAATAT
Found at i:649574 original size:47 final size:46
Alignment explanation
Indices: 649518--649640 Score: 135
Period size: 47 Copynumber: 2.7 Consensus size: 46
649508 AAAAATTATG
* **
649518 AAAACTTTTCAATTTTTATATAATATTTTTTTTAAATTTATAT-ATTTT
1 AAAAATTTTCAATTTTTATATAATATTTTAGTT---TTTATATAATTTT
*
649566 -AAAATTTTCAGTTTTTATATAATATTTTAGTTTTTATATAATTTT
1 AAAAATTTTCAATTTTTATATAATATTTTAGTTTTTATATAATTTT
**
649611 AAAAAAATTCAATTTTTAT-TAAATATTTTA
1 AAAAATTTTCAATTTTTATAT-AATATTTTA
649641 TATAACTTTA
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
44 7 0.11
45 6 0.09
46 24 0.37
47 28 0.43
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (46 bp):
AAAAATTTTCAATTTTTATATAATATTTTAGTTTTTATATAATTTT
Found at i:649599 original size:19 final size:20
Alignment explanation
Indices: 649569--649607 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
649559 ATATTTTAAA
649569 ATTTTCAGTTTTTATATAAT
1 ATTTTCAGTTTTTATATAAT
649589 ATTTT-AGTTTTTATATAAT
1 ATTTTCAGTTTTTATATAAT
649608 TTTAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.62
Consensus pattern (20 bp):
ATTTTCAGTTTTTATATAAT
Found at i:649609 original size:17 final size:18
Alignment explanation
Indices: 649567--649611 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 18
649557 ATATATTTTA
649567 AAATTTTCAGTTTTTATAT
1 AAATTTT-AGTTTTTATAT
649586 AATATTTTAGTTTTTATAT
1 AA-ATTTTAGTTTTTATAT
649605 -AATTTTA
1 AAATTTTA
649612 AAAAAATTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.24
18 1 0.04
19 13 0.52
20 5 0.20
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.60
Consensus pattern (18 bp):
AAATTTTAGTTTTTATAT
Found at i:649640 original size:46 final size:44
Alignment explanation
Indices: 649525--649640 Score: 126
Period size: 46 Copynumber: 2.5 Consensus size: 44
649515 ATGAAAACTT
** **
649525 TTCAATTTTTATATAATATTTTTTTTAAATTTATATATTTTAAAATT
1 TTCAATTTTTATATAATATTTTAGTT---TTTATATATTTTAAAAAA
*
649572 TTCAGTTTTTATATAATATTTTAGTTTTTATATAATTTTAAAAAAA
1 TTCAATTTTTATATAATATTTTAGTTTTTATAT-ATTTT-AAAAAA
649618 TTCAATTTTTAT-TAAATATTTTA
1 TTCAATTTTTATAT-AATATTTTA
649641 TATAACTTTA
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
44 7 0.12
45 6 0.10
46 24 0.40
47 23 0.38
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.59
Consensus pattern (44 bp):
TTCAATTTTTATATAATATTTTAGTTTTTATATATTTTAAAAAA
Found at i:654078 original size:18 final size:19
Alignment explanation
Indices: 654057--654098 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
654047 TATATACTTC
*
654057 TTTATATATTATT-TATTT
1 TTTAGATATTATTATATTT
*
654075 TTTAGATTTTATTAATATTT
1 TTTAGATATTATT-ATATTT
654095 TTTA
1 TTTA
654099 ATTTTTAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 11 0.55
20 9 0.45
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (19 bp):
TTTAGATATTATTATATTT
Found at i:654345 original size:2 final size:2
Alignment explanation
Indices: 654338--654364 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
654328 GAATTAACCT
654338 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 T
654365 TAATTTGATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:658969 original size:132 final size:133
Alignment explanation
Indices: 658730--659250 Score: 678
Period size: 132 Copynumber: 4.0 Consensus size: 133
658720 ATTGCTTTCC
* *
658730 CTGTATGTCACGAATTTGGGTTTTATGTG-TTCTTTTACCTGACTGCTAACTCATATCATTTTCC
1 CTGTATGTCACGAATCTGGGTTTTATGTGTTTCTTTTACCTGACTGCTAACTCATATCATTTTGC
* *
658794 TCATCCTATCTCATATCAAGAATCATAGACTTA-GGATGTCTTTGTACTGCTTATATCGGTTAAT
66 TCATCCCATCTCATATCAAGAATCATAGAC-TACGGATGCCTTTGTACTGCTTATATCGGTTAAT
*
658858 ATGT
130 ATAT
** *
658862 CTGTATGTCACGAATCTGGGTTTTATCCG-TTCTTTTACCTGACTGCTAACTC-TAATAATTTTG
1 CTGTATGTCACGAATCTGGGTTTTATGTGTTTCTTTTACCTGACTGCTAACTCAT-ATCATTTTG
* * * *
658925 CTCGTCCCGTCTCGTATCAAGAATCATAGACCACGGATGCCTTTGTACTGCTTATATCGGTTAAT
65 CTCATCCCATCTCATATCAAGAATCATAGACTACGGATGCCTTTGTACTGCTTATATCGGTTAAT
*
658990 ATAC
130 ATAT
* *
658994 CTGTATGTCAC-AATCTGGGTTTGATGTGTTTCTTTTACCTGACTGCTAACTCGTATCATTTTGC
1 CTGTATGTCACGAATCTGGGTTTTATGTGTTTCTTTTACCTGACTGCTAACTCATATCATTTTGC
* ** * * *
659058 TCATGCCATCTCATATCAAGAATCATAGACTGTGGATGTCTTTGTACTGCTCATATCAGTTAATA
66 TCATCCCATCTCATATCAAGAATCATAGACTACGGATGCCTTTGTACTGCTTATATCGGTTAATA
659123 TAT
131 TAT
* *
659126 CTGTATGTCACGAATCTTGGTTTTA--TGTTTCTTTGACCTGACTGCTAACTCATATCATTTTGC
1 CTGTATGTCACGAATCTGGGTTTTATGTGTTTCTTTTACCTGACTGCTAACTCATATCATTTTGC
* * * * ** * * * *
659189 TCGTCCCGTTTCGTATTGAGAATCATAGACTGCAGATGCCTTTGTACTGCATATATCTGTTA
66 TCATCCCATCTCATATCAAGAATCATAGACTACGGATGCCTTTGTACTGCTTATATCGGTTA
659251 TTCAAAAAAT
Statistics
Matches: 339, Mismatches: 45, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
131 101 0.30
132 226 0.67
133 12 0.04
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.40
Consensus pattern (133 bp):
CTGTATGTCACGAATCTGGGTTTTATGTGTTTCTTTTACCTGACTGCTAACTCATATCATTTTGC
TCATCCCATCTCATATCAAGAATCATAGACTACGGATGCCTTTGTACTGCTTATATCGGTTAATA
TAT
Found at i:682985 original size:37 final size:37
Alignment explanation
Indices: 682920--683028 Score: 177
Period size: 37 Copynumber: 3.0 Consensus size: 37
682910 TACGTATGAT
* *
682920 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
682955 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
682992 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
683029 TAAAGCTATC
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
35 10 0.14
36 3 0.04
37 56 0.81
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:683071 original size:52 final size:52
Alignment explanation
Indices: 682992--683358 Score: 515
Period size: 52 Copynumber: 7.2 Consensus size: 52
682982 TAAGTGTAGC
* * **
682992 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTAT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
683045 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
* *
683097 CAC---T---TTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
*
683143 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
* *
683195 CAC---T---TTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
*
683241 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
* * *
683293 CACTTTCCACTTGTCACTTGATTAGATAAGTGTAGCCGAAGCTATCACCTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
683345 CACTTTGTCACTTG
1 CACTTT-TCACTTG
683359 ATCAGAAGTA
Statistics
Matches: 283, Mismatches: 18, Indels: 26
0.87 0.06 0.08
Matches are distributed among these distances:
46 86 0.30
49 1 0.00
52 181 0.64
53 15 0.05
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (52 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
Found at i:683102 original size:98 final size:98
Alignment explanation
Indices: 682992--683350 Score: 592
Period size: 98 Copynumber: 3.6 Consensus size: 98
682982 TAAGTGTAGC
* ** *
682992 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTTCACTT
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTT
683057 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
66 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
683090 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTT
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTT
683155 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
66 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
683188 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTT
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTT
683253 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
66 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* * * *
683286 CACTTATCACTTTCCACTTGTCACTTGATTAGATAAGTGTAGCCGAAGCTATCACCTATCACTTT
1 CACTTATCAC--T----TTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTT
683351 GTCACTTGAT
Statistics
Matches: 247, Mismatches: 8, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
98 202 0.82
100 1 0.00
104 44 0.18
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (98 bp):
CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTT
GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:683265 original size:150 final size:144
Alignment explanation
Indices: 683003--683364 Score: 535
Period size: 150 Copynumber: 2.4 Consensus size: 144
682993 ACTTATCACT
* **
683003 TTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTTCACTTGTCACTTGATC
1 TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCAC---T---TTGTCACTTGATC
* *
683068 AGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGC
60 AGATAAGTATAGCCGAAGCTATCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGC
683133 TATCACTTATCACTTTCCAC
125 TATCACTTATCACTTTCCAC
*
683153 TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCTCTTGATCAGATAA
1 TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTTGATCAGATAA
*
683218 GTATAGCCGAAGCTATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGC
66 GTATAGCCGAAGCTATCACTTATCAC--T----TTGTCACTTGATCAGATAAGTATAGCCGAAGC
683283 TATCACTTATCACTTTCCAC
125 TATCACTTATCACTTTCCAC
* *
683303 TTGTCACTTGATTAGATAAGTGTAGCCGAAGCTATCACCTATCACTTTGTCACTTGATCAGA
1 TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTTGATCAGA
683365 AGTACTCAAA
Statistics
Matches: 196, Mismatches: 10, Indels: 12
0.90 0.05 0.06
Matches are distributed among these distances:
144 43 0.22
146 1 0.01
147 1 0.01
150 151 0.77
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.34
Consensus pattern (144 bp):
TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTTGATCAGATAA
GTATAGCCGAAGCTATCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCAC
TTATCACTTTCCAC
Found at i:687074 original size:29 final size:30
Alignment explanation
Indices: 687018--687074 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
687008 TTGGGTTTTC
* *
687018 CCACACGGGCTGGACACATGGCCCTGTGAG
1 CCACACGGGCTGGACACACGGCCATGTGAG
*
687048 CCACATGGGCTGG-CACACGGCCATGTG
1 CCACACGGGCTGGACACACGGCCATGTG
687075 CCAGACCATG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 12 0.50
30 12 0.50
ACGTcount: A:0.19, C:0.33, G:0.33, T:0.14
Consensus pattern (30 bp):
CCACACGGGCTGGACACACGGCCATGTGAG
Done.