Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D07
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: 58101237
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1550000 characters in sequence are not A, C, G, or T
File 2 of 199
Found at i:312549 original size:9 final size:9
Alignment explanation
Indices: 312531--312566 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
312521 TAGTTTCTCA
312531 TTTC-TTTC
1 TTTCTTTTC
312539 TTTCTTTTC
1 TTTCTTTTC
*
312548 TTTCTTTCC
1 TTTCTTTTC
312557 TTTCTTTTC
1 TTTCTTTTC
312566 T
1 T
312567 CCCTGCTTCG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
8 4 0.16
9 21 0.84
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTCTTTTC
Found at i:312549 original size:13 final size:13
Alignment explanation
Indices: 312531--312563 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
312521 TAGTTTCTCA
*
312531 TTTCTTTCTTTCT
1 TTTCTTTCTTTCC
312544 TTTCTTTCTTTCC
1 TTTCTTTCTTTCC
312557 TTTCTTT
1 TTTCTTT
312564 TCTCCCTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTCTTTCTTTCC
Found at i:312638 original size:22 final size:21
Alignment explanation
Indices: 312601--312658 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 21
312591 CTTTCTATTC
312601 TTTA-TTTATT-TCATTTACTT
1 TTTATTTTATTAT-ATTTACTT
312621 ATTTATTTTATTATATTTACTT
1 -TTTATTTTATTATATTTACTT
*
312643 TATTATTATATTATAT
1 T-TTATTTTATTATAT
312659 ATTTTATTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
21 5 0.15
22 27 0.82
23 1 0.03
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTATTTTATTATATTTACTT
Found at i:312639 original size:14 final size:14
Alignment explanation
Indices: 312600--312648 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 14
312590 TCTTTCTATT
312600 CTTTATT-TATTT-
1 CTTTATTATATTTA
*
312612 CATTTACT-TATTTA
1 C-TTTATTATATTTA
*
312626 TTTTATTATATTTA
1 CTTTATTATATTTA
312640 CTTTATTAT
1 CTTTATTAT
312649 TATATTATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
12 1 0.03
13 15 0.50
14 14 0.47
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.67
Consensus pattern (14 bp):
CTTTATTATATTTA
Found at i:312665 original size:17 final size:17
Alignment explanation
Indices: 312619--312667 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
312609 TTTCATTTAC
*
312619 TTATTTATTTTATTATA
1 TTATATATTTTATTATA
312636 TT-TACT-TTATTATTATA
1 TTATA-TATT-TTATTATA
312653 TTATATATTTTATTA
1 TTATATATTTTATTA
312668 ATAAATATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
16 3 0.11
17 20 0.74
18 4 0.15
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (17 bp):
TTATATATTTTATTATA
Found at i:314796 original size:18 final size:18
Alignment explanation
Indices: 314758--314793 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
314748 TTATTATTTT
*
314758 TAAAATTTACTATTAAAA
1 TAAAATTTAATATTAAAA
314776 TAAAATTTAAATATTAAA
1 TAAAATTT-AATATTAAA
314794 TAATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAATTTAATATTAAAA
Found at i:317772 original size:32 final size:32
Alignment explanation
Indices: 317731--317803 Score: 128
Period size: 32 Copynumber: 2.3 Consensus size: 32
317721 CAGAACACTG
*
317731 AAATCGAGCAGTACCACCGGCCCACATGAAAA
1 AAATGGAGCAGTACCACCGGCCCACATGAAAA
*
317763 AAATGGAGCAGTACCATCGGCCCACATGAAAA
1 AAATGGAGCAGTACCACCGGCCCACATGAAAA
317795 AAATGGAGC
1 AAATGGAGC
317804 GTAAATTAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.41, C:0.26, G:0.22, T:0.11
Consensus pattern (32 bp):
AAATGGAGCAGTACCACCGGCCCACATGAAAA
Found at i:348067 original size:5 final size:5
Alignment explanation
Indices: 348047--348085 Score: 60
Period size: 5 Copynumber: 7.6 Consensus size: 5
348037 TCAATGTCAC
*
348047 AAACA AAAGTA AAACA AAACA AAACA AAACA AAACA AAA
1 AAACA AAA-CA AAACA AAACA AAACA AAACA AAACA AAA
348086 AAATTACACA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
5 27 0.87
6 4 0.13
ACGTcount: A:0.79, C:0.15, G:0.03, T:0.03
Consensus pattern (5 bp):
AAACA
Found at i:358285 original size:22 final size:22
Alignment explanation
Indices: 358258--358300 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
358248 AAAATTATAA
*
358258 AAATTAAAAAAAATCAAAATTT
1 AAATTAAAAAAAATAAAAATTT
*
358280 AAATTAAAAATAATAAAAATT
1 AAATTAAAAAAAATAAAAATT
358301 CAAAAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (22 bp):
AAATTAAAAAAAATAAAAATTT
Found at i:375140 original size:18 final size:18
Alignment explanation
Indices: 375081--375140 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
375071 TATATTAATC
*
375081 ATATTTTATTATATGAA-A
1 ATATTTTATT-TATAAATA
*
375099 ATATTTTTTTTATAAATA
1 ATATTTTATTTATAAATA
* * *
375117 AAATTTTATTTGTAAATT
1 ATATTTTATTTATAAATA
375135 ATATTT
1 ATATTT
375141 AAGATATTAT
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
17 5 0.15
18 29 0.85
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
ATATTTTATTTATAAATA
Found at i:382445 original size:5 final size:5
Alignment explanation
Indices: 382435--382459 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
382425 GTTAATACAG
382435 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
382460 CAGGTTAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:389612 original size:18 final size:17
Alignment explanation
Indices: 389589--389637 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
389579 ATATAATAAA
389589 TTATTTAATATTACAATT
1 TTATTTAATATTA-AATT
*
389607 TTATTTCAATAATAAATT
1 TTATTT-AATATTAAATT
**
389625 TTAAATAATATTA
1 TTATTTAATATTA
389638 TTCATATATT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 6 0.23
18 14 0.54
19 6 0.23
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (17 bp):
TTATTTAATATTAAATT
Found at i:401573 original size:13 final size:15
Alignment explanation
Indices: 401555--401586 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
401545 TCTTTCCCTA
401555 TTTTTCAT-G-TTCT
1 TTTTTCATCGTTTCT
401568 TTTTTCATCGTTTCT
1 TTTTTCATCGTTTCT
401583 TTTT
1 TTTT
401587 CTTTTCGACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 1 0.06
15 8 0.47
ACGTcount: A:0.06, C:0.16, G:0.06, T:0.72
Consensus pattern (15 bp):
TTTTTCATCGTTTCT
Found at i:403135 original size:31 final size:31
Alignment explanation
Indices: 403069--403139 Score: 80
Period size: 29 Copynumber: 2.4 Consensus size: 31
403059 TTTTAAAATT
403069 TGAAAAGTA-AAGAGACTAAATTCCTAGAAA
1 TGAAAAGTATAAGAGACTAAATTCCTAGAAA
403099 T-AAAAGTATAA-AGACTAAA-TCCTA-AATTTA
1 TGAAAAGTATAAGAGACTAAATTCCTAGAA---A
403129 TGAAAAGTATA
1 TGAAAAGTATA
403140 GGGACTTATG
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
27 2 0.06
28 5 0.14
29 15 0.42
30 5 0.14
31 9 0.25
ACGTcount: A:0.54, C:0.08, G:0.13, T:0.25
Consensus pattern (31 bp):
TGAAAAGTATAAGAGACTAAATTCCTAGAAA
Found at i:408129 original size:70 final size:70
Alignment explanation
Indices: 408008--408143 Score: 213
Period size: 70 Copynumber: 1.9 Consensus size: 70
407998 TACAATGAGC
*
408008 AATTTTTAACAATAGAAATGGATGAAATTTTTAACAGAATGGCTTATTTGCTCTTTTATCTAACA
1 AATTTTTAACAATAGAAATGGATGAAATTTTTAACAGAATGGCTTACTTGCTCTTTTATCTAACA
408073 TGCCT
66 TGCCT
* *
408078 AATTTTTAACAATATAAATGGATGAATTTTTTAACAGAAAT-G-TTAACTTGCTCTTTTATCTAA
1 AATTTTTAACAATAGAAATGGATGAAATTTTTAACAG-AATGGCTT-ACTTGCTCTTTTATCTAA
408141 CAT
64 CAT
408144 ATTTAGTTTC
Statistics
Matches: 61, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
69 2 0.03
70 56 0.92
71 3 0.05
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.41
Consensus pattern (70 bp):
AATTTTTAACAATAGAAATGGATGAAATTTTTAACAGAATGGCTTACTTGCTCTTTTATCTAACA
TGCCT
Found at i:412269 original size:29 final size:28
Alignment explanation
Indices: 412236--412320 Score: 120
Period size: 29 Copynumber: 3.0 Consensus size: 28
412226 TTTAAAATAT
412236 TTTTAAAATACTTTGTTATTATTTTTTAA
1 TTTTAAAATACTTT-TTATTATTTTTTAA
412265 TTTTAAAATACTTTTTAAATT-TTTTTTAA
1 TTTTAAAATACTTTTT--ATTATTTTTTAA
*
412294 TTTTAAAATACTTTTT-TTAATTTTTAA
1 TTTTAAAATACTTTTTATTATTTTTTAA
412321 AATAAATTTT
Statistics
Matches: 52, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
26 2 0.04
27 7 0.13
28 2 0.04
29 38 0.73
30 3 0.06
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.62
Consensus pattern (28 bp):
TTTTAAAATACTTTTTATTATTTTTTAA
Found at i:412285 original size:19 final size:18
Alignment explanation
Indices: 412217--412287 Score: 61
Period size: 19 Copynumber: 3.7 Consensus size: 18
412207 ATTTTTAATT
412217 TTTTTAAATTTTAAAATA
1 TTTTTAAATTTTAAAATA
** *
412235 TTTTTAAAATACTTTGTTATTA
1 TTTTT-AAAT--TTT-AAAATA
*
412257 TTTTTTAATTTTAAAATA
1 TTTTTAAATTTTAAAATA
412275 CTTTTTAAATTTT
1 -TTTTTAAATTTT
412288 TTTTAATTTT
Statistics
Matches: 40, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
18 8 0.20
19 18 0.45
21 6 0.15
22 8 0.20
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.61
Consensus pattern (18 bp):
TTTTTAAATTTTAAAATA
Found at i:412310 original size:20 final size:21
Alignment explanation
Indices: 412285--412324 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
412275 CTTTTTAAAT
412285 TTTTTTTAA-TTTTAAAATAC
1 TTTTTTTAATTTTTAAAATAC
412305 TTTTTTTAATTTTTAAAATA
1 TTTTTTTAATTTTTAAAATA
412325 AATTTTTGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTTTTTAATTTTTAAAATAC
Found at i:412330 original size:20 final size:20
Alignment explanation
Indices: 412287--412331 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
412277 TTTTAAATTT
**
412287 TTTTTAATTTTAAAATACTT
1 TTTTTAATTTTAAAATACAA
412307 TTTTTAATTTTTAAAATA-AA
1 TTTTTAA-TTTTAAAATACAA
412327 TTTTT
1 TTTTT
412332 GGTATTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTTAATTTTAAAATACAA
Found at i:412375 original size:20 final size:20
Alignment explanation
Indices: 412285--412376 Score: 71
Period size: 21 Copynumber: 4.4 Consensus size: 20
412275 CTTTTTAAAT
*
412285 TTTTTTTAATTTTAAA-ATA
1 TTTTTTTATTTTTAAATATA
*
412304 CTTTTTTTAATTTTTAAAATAAA
1 -TTTTTTT-ATTTTT-AAATATA
* *
412327 TTTTTGGTATTTATT-AATTTA
1 TTTTT-TTATTT-TTAAATATA
*
412348 TTAATTTTATTTTTAAATATA
1 TT-TTTTTATTTTTAAATATA
412369 TTTTTTTA
1 TTTTTTTA
412377 AAATATGCAT
Statistics
Matches: 56, Mismatches: 9, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
20 14 0.25
21 23 0.41
22 14 0.25
23 5 0.09
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.64
Consensus pattern (20 bp):
TTTTTTTATTTTTAAATATA
Found at i:420426 original size:22 final size:23
Alignment explanation
Indices: 420396--420441 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
420386 TCCATTTCTA
* *
420396 TTTCCTTTTAAC-TTTTTTTTTG
1 TTTCATTTTAACATTTTCTTTTG
420418 TTTCATTTTAACATTTTCTTTTG
1 TTTCATTTTAACATTTTCTTTTG
420441 T
1 T
420442 ATGAAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.13, C:0.13, G:0.04, T:0.70
Consensus pattern (23 bp):
TTTCATTTTAACATTTTCTTTTG
Found at i:423113 original size:5 final size:5
Alignment explanation
Indices: 423103--423128 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
423093 TGAGCATTTG
423103 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
423129 AATTTTCGAG
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:424089 original size:30 final size:31
Alignment explanation
Indices: 424047--424107 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
424037 GGATTGGGAG
* *
424047 GGGAAGGGAGTAAAAGTTTTGGGGAGAAAGT
1 GGGAAGGGAGTAAAAGTTTTGAGGAAAAAGT
424078 GGGAA-GGAGTAAAAGTTTTGAGGAAAAAGT
1 GGGAAGGGAGTAAAAGTTTTGAGGAAAAAGT
424108 AAAAAGGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 23 0.82
31 5 0.18
ACGTcount: A:0.39, C:0.00, G:0.41, T:0.20
Consensus pattern (31 bp):
GGGAAGGGAGTAAAAGTTTTGAGGAAAAAGT
Found at i:424170 original size:9 final size:9
Alignment explanation
Indices: 424156--424183 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
424146 TATAGTTTGA
424156 TATTCGAAT
1 TATTCGAAT
424165 TATTCGAAT
1 TATTCGAAT
424174 TATTCGAAT
1 TATTCGAAT
424183 T
1 T
424184 CGAAAACTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:433317 original size:3 final size:3
Alignment explanation
Indices: 433309--433352 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
433299 GTGGAATGGA
433309 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GA
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GA
433353 AAATATATAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:445630 original size:33 final size:34
Alignment explanation
Indices: 445588--445655 Score: 111
Period size: 33 Copynumber: 2.0 Consensus size: 34
445578 CACAGTAACT
*
445588 TAAACAAAAAATTTTGAATAGTTCAATGACTAAA
1 TAAACAAAAAATTTTGAATAGTTCAATGACAAAA
*
445622 TAAA-AAAAACTTTTGAATAGTTCAATGACAAAA
1 TAAACAAAAAATTTTGAATAGTTCAATGACAAAA
445655 T
1 T
445656 TGTGACTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 28 0.88
34 4 0.12
ACGTcount: A:0.53, C:0.09, G:0.09, T:0.29
Consensus pattern (34 bp):
TAAACAAAAAATTTTGAATAGTTCAATGACAAAA
Found at i:449705 original size:22 final size:22
Alignment explanation
Indices: 449667--449720 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
449657 CCGGCCCATT
*
449667 TTTTAATAAA-TACAAAAAATTTA
1 TTTTAA-AAATTACAAAAAA-GTA
449690 TTTTAAAAATTA-AAAAAAGTA
1 TTTTAAAAATTACAAAAAAGTA
449711 TTTTAAAAAT
1 TTTTAAAAAT
449721 ATTTTAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 12 0.41
22 9 0.31
23 8 0.28
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (22 bp):
TTTTAAAAATTACAAAAAAGTA
Found at i:449735 original size:17 final size:16
Alignment explanation
Indices: 449713--449778 Score: 52
Period size: 16 Copynumber: 4.3 Consensus size: 16
449703 AAAAAGTATT
449713 TTAAAAATATTTTAAAA
1 TTAAAAA-ATTTTAAAA
449730 TTAAAAAA---TAATAA
1 TTAAAAAATTTTAA-AA
*
449744 --AAAACATTTTAAAA
1 TTAAAAAATTTTAAAA
*
449758 TTAAAAAATTTAAAAA
1 TTAAAAAATTTTAAAA
*
449774 ATAAA
1 TTAAA
449779 TATATTTATT
Statistics
Matches: 39, Mismatches: 4, Indels: 13
0.70 0.07 0.23
Matches are distributed among these distances:
12 5 0.13
13 3 0.08
14 4 0.10
15 3 0.08
16 17 0.44
17 7 0.18
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (16 bp):
TTAAAAAATTTTAAAA
Found at i:449771 original size:27 final size:27
Alignment explanation
Indices: 449710--449774 Score: 94
Period size: 28 Copynumber: 2.4 Consensus size: 27
449700 TAAAAAAAGT
* *
449710 ATTTTAAAAATATTTTAAAATTAAAAA
1 ATTTAAAAAACATTTTAAAATTAAAAA
*
449737 ATAATAAAAAACATTTTAAAATTAAAAA
1 AT-TTAAAAAACATTTTAAAATTAAAAA
449765 ATTTAAAAAA
1 ATTTAAAAAA
449775 TAAATATATT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 9 0.27
28 24 0.73
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.34
Consensus pattern (27 bp):
ATTTAAAAAACATTTTAAAATTAAAAA
Found at i:450562 original size:30 final size:30
Alignment explanation
Indices: 450528--450592 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
450518 CAACGTAACA
*
450528 AACAAATGCCTCTAAAATAATAACAAAATT
1 AACAAATGCATCTAAAATAATAACAAAATT
*
450558 AACAAATGCATTTAAAATAATAACAAAATT
1 AACAAATGCATCTAAAATAATAACAAAATT
450588 AACAA
1 AACAA
450593 TAAAATAAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.60, C:0.14, G:0.03, T:0.23
Consensus pattern (30 bp):
AACAAATGCATCTAAAATAATAACAAAATT
Found at i:467407 original size:26 final size:26
Alignment explanation
Indices: 467378--467430 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
467368 TAAGTATTAT
*
467378 AATTTAATATTTTTATATAAT-TTTTA
1 AATTTAATA-GTTTATATAATATTTTA
**
467404 AATTTTGTAGTTTATATAATATTTTA
1 AATTTAATAGTTTATATAATATTTTA
467430 A
1 A
467431 TATTATTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (26 bp):
AATTTAATAGTTTATATAATATTTTA
Found at i:480466 original size:3 final size:3
Alignment explanation
Indices: 480458--480485 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
480448 CTATCTCAGG
480458 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
480486 AGAGATATAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:485079 original size:21 final size:21
Alignment explanation
Indices: 485051--485096 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
485041 CTATGGTGCC
485051 GAAG-AATGGATGAATCTATA
1 GAAGCAATGGATGAATCTATA
*
485071 GAAGCAATGGATGAATCTGTA
1 GAAGCAATGGATGAATCTATA
485092 GAAGC
1 GAAGC
485097 CATTGTAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 4 0.17
21 20 0.83
ACGTcount: A:0.41, C:0.09, G:0.28, T:0.22
Consensus pattern (21 bp):
GAAGCAATGGATGAATCTATA
Found at i:492010 original size:17 final size:18
Alignment explanation
Indices: 491988--492021 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
491978 CTCTTTTATT
491988 TTTTTAGT-TTTACTTTA
1 TTTTTAGTATTTACTTTA
492005 TTTTTAGTATTTACTTT
1 TTTTTAGTATTTACTTT
492022 TAAAAGTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.18, C:0.06, G:0.06, T:0.71
Consensus pattern (18 bp):
TTTTTAGTATTTACTTTA
Found at i:498886 original size:19 final size:21
Alignment explanation
Indices: 498862--498904 Score: 63
Period size: 19 Copynumber: 2.1 Consensus size: 21
498852 GAATTTAGGT
*
498862 TTAAAATTTAGAAT-TTAA-A
1 TTAAAATTTAAAATATTAATA
498881 TTAAAATTTAAAATATTAATA
1 TTAAAATTTAAAATATTAATA
498902 TTA
1 TTA
498905 CAACAACGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 13 0.62
20 4 0.19
21 4 0.19
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
TTAAAATTTAAAATATTAATA
Found at i:500269 original size:45 final size:45
Alignment explanation
Indices: 500220--500337 Score: 114
Period size: 45 Copynumber: 2.6 Consensus size: 45
500210 TACGGGAGCC
*
500220 GGTGGAGGTGATGGTGGTGGAGGTGAATGATAATGGATT-GGTGGG
1 GGTGGAGGTGATGGTGGTGGAGGTGAATG-TAATGAATTGGGTGGG
* * * **
500265 GGTGGGGGTGAAGGTGATGGAGGTGGTTTGTAATGAATTGGGGGTGGG
1 GGTGGAGGTGATGGTGGTGGAGGT-GAATGTAATGAATT--GGGTGGG
*
500313 GGT-GATGGTGATGGTGGTGGGGGTG
1 GGTGGA-GGTGATGGTGGTGGAGGTG
500338 GGGGTGATGG
Statistics
Matches: 58, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
45 29 0.50
46 3 0.05
47 2 0.03
48 24 0.41
ACGTcount: A:0.16, C:0.00, G:0.57, T:0.27
Consensus pattern (45 bp):
GGTGGAGGTGATGGTGGTGGAGGTGAATGTAATGAATTGGGTGGG
Found at i:500289 original size:21 final size:21
Alignment explanation
Indices: 500265--500347 Score: 55
Period size: 21 Copynumber: 4.0 Consensus size: 21
500255 GATTGGTGGG
500265 GGTGGGGGTGAAGGTGATGGA
1 GGTGGGGGTGAAGGTGATGGA
** *
500286 GGT-GGTTTGTAA--TGAATTGGG
1 GGTGGGGGTG-AAGGTG-A-TGGA
* *
500307 GGTGGGGGTGATGGTGATGGT
1 GGTGGGGGTGAAGGTGATGGA
**
500328 GGTGGGGGTGGGGGTGATGG
1 GGTGGGGGTGAAGGTGATGG
500348 CGTGTACTCT
Statistics
Matches: 47, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
19 2 0.04
20 5 0.11
21 33 0.70
22 5 0.11
23 2 0.04
ACGTcount: A:0.13, C:0.00, G:0.60, T:0.27
Consensus pattern (21 bp):
GGTGGGGGTGAAGGTGATGGA
Found at i:500761 original size:39 final size:38
Alignment explanation
Indices: 500691--500835 Score: 98
Period size: 39 Copynumber: 3.7 Consensus size: 38
500681 TGGTGGAGGA
* *
500691 GATGGTGGAGGTGGTGATGGA--TAAGTAGGTGGCGGGGGT
1 GATGGTGGAGGTGGGGATGGAGGT-GGT-GGTGG-GGGGGT
*
500730 GATGGTGGAGGTGGGGATGGAGGTGGTGGTGGTGGAGAGT
1 GATGGTGGAGGTGGGGATGGAGGTGGTGGTGG-GG-GGGT
* * * * *
500770 AAACTGGTGGAGGTGGTGAAGGCGGTGGAGGTGAGGGGGGT
1 -GA-TGGTGGAGGTGGGGATGGAGGTGGTGGTG-GGGGGGT
* *
500811 GGTGGTGGTGGTGGTGG-TGGAGGTG
1 GATGGTGGAGGTGG-GGATGGAGGTG
500836 AATAAACAGG
Statistics
Matches: 83, Mismatches: 16, Indels: 14
0.73 0.14 0.12
Matches are distributed among these distances:
39 44 0.53
40 6 0.07
41 5 0.06
42 27 0.33
43 1 0.01
ACGTcount: A:0.15, C:0.02, G:0.61, T:0.22
Consensus pattern (38 bp):
GATGGTGGAGGTGGGGATGGAGGTGGTGGTGGGGGGGT
Found at i:500835 original size:24 final size:24
Alignment explanation
Indices: 500679--500835 Score: 54
Period size: 24 Copynumber: 6.4 Consensus size: 24
500669 TACTGGTGAA
* *
500679 GGTGGTGGAGGAGATGGTGGAGGT
1 GGTGGTGGTGGAGGTGGTGGAGGT
* * * *
500703 GGTGATGGAT--AAGTAGGTGGCGGG
1 GGTGGTGG-TGGAGGT-GGTGGAGGT
*
500727 GGTGATGGTGGAGGTGGGGATGGAGGT
1 GGTGGTGGTGGAGGT--GG-TGGAGGT
* **
500754 GGTGGTGGTGGA-G-AGTAAACTGGT
1 GGTGGTGGTGGAGGTGGTGGA--GGT
* * *
500778 GGAGGTGGTGAAGGCGGTGGAGGT
1 GGTGGTGGTGGAGGTGGTGGAGGT
* * *
500802 GAG-GGGGGTGGTGGTGGTGGTGGT
1 G-GTGGTGGTGGAGGTGGTGGAGGT
*
500826 GGTGGAGGTG
1 GGTGGTGGTG
500836 AATAAACAGG
Statistics
Matches: 96, Mismatches: 25, Indels: 24
0.66 0.17 0.17
Matches are distributed among these distances:
22 2 0.02
23 5 0.05
24 62 0.65
25 5 0.05
26 6 0.06
27 16 0.17
ACGTcount: A:0.15, C:0.02, G:0.61, T:0.22
Consensus pattern (24 bp):
GGTGGTGGTGGAGGTGGTGGAGGT
Found at i:500910 original size:48 final size:45
Alignment explanation
Indices: 500858--500956 Score: 117
Period size: 48 Copynumber: 2.1 Consensus size: 45
500848 GCGGGGGCGA
* *
500858 TGGTGGAGGCGGAGGAGGAGAGTACACAGGTGGCGGCGGAGGTGGAGG
1 TGGTGAAGGCGGAGGAGGAGAGTACAC---TGGCGGCGGAGGCGGAGG
* * * *
500906 TGGTGAAGGGGGAGGGGGAGAGTATACTGGCGGCGGCGGCGGAGG
1 TGGTGAAGGCGGAGGAGGAGAGTACACTGGCGGCGGAGGCGGAGG
500951 TGGTGA
1 TGGTGA
500957 TTGTGGAATA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
45 22 0.49
48 23 0.51
ACGTcount: A:0.19, C:0.10, G:0.59, T:0.12
Consensus pattern (45 bp):
TGGTGAAGGCGGAGGAGGAGAGTACACTGGCGGCGGAGGCGGAGG
Found at i:510697 original size:12 final size:12
Alignment explanation
Indices: 510680--510705 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
510670 TGAATTTTAT
510680 TTTAGAAAACCA
1 TTTAGAAAACCA
510692 TTTAGAAAACCA
1 TTTAGAAAACCA
510704 TT
1 TT
510706 ACATGTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (12 bp):
TTTAGAAAACCA
Found at i:511726 original size:7 final size:7
Alignment explanation
Indices: 511714--511744 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
511704 TTTTAACTCT
511714 AAAAAAG
1 AAAAAAG
511721 AAAAAAG
1 AAAAAAG
511728 AAAAAAG
1 AAAAAAG
511735 AAAAAA-
1 AAAAAAG
511741 AAAA
1 AAAA
511745 GGAAGGTAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.17
7 20 0.83
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:512210 original size:20 final size:20
Alignment explanation
Indices: 512187--512226 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
512177 TTTTTAAACA
512187 TTTTAAAATATTTTA-ATTTT
1 TTTTAAAAT-TTTTACATTTT
*
512207 TTTTATAATTTTTACATTTT
1 TTTTAAAATTTTTACATTTT
512227 AAAACAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTAAAATTTTTACATTTT
Found at i:515828 original size:27 final size:27
Alignment explanation
Indices: 515787--515889 Score: 156
Period size: 27 Copynumber: 3.8 Consensus size: 27
515777 TAGTATTGGC
515787 GCCTATCT-GGAAGGCGCCAATGGTGGT
1 GCCTATCTAGG-AGGCGCCAATGGTGGT
* *
515814 GCCTATTTGGGAGGCGCCAATGGTGGT
1 GCCTATCTAGGAGGCGCCAATGGTGGT
515841 GCCTATCTAGGAGGCGCCAATGGTGGT
1 GCCTATCTAGGAGGCGCCAATGGTGGT
515868 GCCATAT-TAGGAGGCGCCAATG
1 GCC-TATCTAGGAGGCGCCAATG
515890 CTGTGATTTT
Statistics
Matches: 71, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
27 66 0.93
28 5 0.07
ACGTcount: A:0.19, C:0.21, G:0.37, T:0.22
Consensus pattern (27 bp):
GCCTATCTAGGAGGCGCCAATGGTGGT
Found at i:519557 original size:18 final size:15
Alignment explanation
Indices: 519519--519560 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
519509 ACAAAATCAA
519519 ATAAAATTTAATTAT
1 ATAAAATTTAATTAT
519534 AT-AAATGTTACATTAT
1 ATAAAAT-TTA-ATTAT
*
519550 ATAAAAATTAA
1 ATAAAATTTAA
519561 ATAAGTTAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
14 4 0.17
15 6 0.26
16 10 0.43
17 3 0.13
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (15 bp):
ATAAAATTTAATTAT
Found at i:519726 original size:37 final size:37
Alignment explanation
Indices: 519673--519744 Score: 135
Period size: 37 Copynumber: 1.9 Consensus size: 37
519663 TAAAAAACCC
519673 AAACTTTTAATAAAATGATTTTTAATTTTTTATAATT
1 AAACTTTTAATAAAATGATTTTTAATTTTTTATAATT
*
519710 AAACTTTTAATGAAATGATTTTTAATTTTTTATAA
1 AAACTTTTAATAAAATGATTTTTAATTTTTTATAA
519745 ACTTTATATG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.53
Consensus pattern (37 bp):
AAACTTTTAATAAAATGATTTTTAATTTTTTATAATT
Found at i:519976 original size:27 final size:25
Alignment explanation
Indices: 519940--520152 Score: 179
Period size: 27 Copynumber: 8.8 Consensus size: 25
519930 ATATCCTCAC
519940 ATTACAATATTCATACAAAATTACAAA
1 ATTACAATATTCATACAAAA-TA-AAA
519967 ATTACAATATTCATAC---A-AAAA
1 ATTACAATATTCATACAAAATAAAA
* *
519988 ATTGCAATATTCATACAAAATTATAAT
1 ATTACAATATTCATACAAAA-TA-AAA
*
520015 ATTACAACATTCATAC---A-AAAA
1 ATTACAATATTCATACAAAATAAAA
*
520036 A-TATAATATTCATACAAAATTACAAA
1 ATTACAATATTCATACAAAA-TA-AAA
520062 ATTACAATATTCATAC---A-AAAA
1 ATTACAATATTCATACAAAATAAAA
*
520083 ATTACAATATTCATACAAAACTATAAT
1 ATTACAATATTCATACAAAA-TA-AAA
520110 ATTACAATATTCATAC--AA-AAAA
1 ATTACAATATTCATACAAAATAAAA
* *
520132 TTTATAATATTCATACAAAAT
1 ATTACAATATTCATACAAAAT
520153 TACAATATTC
Statistics
Matches: 152, Mismatches: 12, Indels: 46
0.72 0.06 0.22
Matches are distributed among these distances:
20 12 0.08
21 40 0.26
22 19 0.12
23 2 0.01
24 7 0.05
25 3 0.02
26 6 0.04
27 63 0.41
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.31
Consensus pattern (25 bp):
ATTACAATATTCATACAAAATAAAA
Found at i:519998 original size:95 final size:90
Alignment explanation
Indices: 519887--520176 Score: 343
Period size: 95 Copynumber: 3.1 Consensus size: 90
519877 AATTAATTAT
* * *
519887 AAAATAATCACAATATTCATACAAAAAATTACAATATTACAATATATCCTCACATTACAATATTC
1 AAAA-AATTACAATATTCATAC--AAAATTATAATATTACAATAT-TCATCACA-TA-AATATTC
519952 ATACAAAATTACAAAATTACAATATTCATAC
60 ATACAAAATTACAAAATTACAATATTCATAC
* * *
519983 AAAAAATTGCAATATTCATACAAAATTATAATATTACAACATTCATACAAAAAATATAATATTCA
1 AAAAAATTACAATATTCATACAAAATTATAATATTACAATATTCAT-C---ACATA-AATATTCA
520048 TACAAAATTACAAAATTACAATATTCATAC
61 TACAAAATTACAAAATTACAATATTCATAC
* * * *
520078 AAAAAATTACAATATTCATACAAAACTATAATATTACAATATTCAT-ACA-AAAAATTTATA-AT
1 AAAAAATTACAATATTCATACAAAATTATAATATTACAATATTCATCACATAAATATTCATACAA
*
520140 ATTCATACAAAATTACAATATTCATAC
66 AAT--TACAAAATTACAATATTCATAC
520167 AAAAAATTAC
1 AAAAAATTAC
520177 TAATCCAAAA
Statistics
Matches: 173, Mismatches: 15, Indels: 19
0.84 0.07 0.09
Matches are distributed among these distances:
87 3 0.02
88 8 0.05
89 33 0.19
90 2 0.01
92 3 0.02
93 20 0.12
95 98 0.57
96 6 0.03
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (90 bp):
AAAAAATTACAATATTCATACAAAATTATAATATTACAATATTCATCACATAAATATTCATACAA
AATTACAAAATTACAATATTCATAC
Found at i:520010 original size:48 final size:48
Alignment explanation
Indices: 519887--520161 Score: 362
Period size: 48 Copynumber: 5.7 Consensus size: 48
519877 AATTAATTAT
* *
519887 AAAATAATCACAATATTCATACAAAAAATTACAATATTACAATATATCCT-C
1 AAAA-AATTACAATATTCATAC--AAAATTACAATATTACAATAT-TCATAC
* *
519938 ---ACATTACAATATTCATACAAAATTACAAAATTACAATATTCATAC
1 AAAAAATTACAATATTCATACAAAATTACAATATTACAATATTCATAC
* * *
519983 AAAAAATTGCAATATTCATACAAAATTATAATATTACAACATTCATAC
1 AAAAAATTACAATATTCATACAAAATTACAATATTACAATATTCATAC
* *
520031 AAAAAA-TATAATATTCATACAAAATTACAAAATTACAATATTCATAC
1 AAAAAATTACAATATTCATACAAAATTACAATATTACAATATTCATAC
* *
520078 AAAAAATTACAATATTCATACAAAACTATAATATTACAATATTCATAC
1 AAAAAATTACAATATTCATACAAAATTACAATATTACAATATTCATAC
*
520126 AAAAAATTTATAATATTCATACAAAATTACAATATT
1 AAAAAA-TTACAATATTCATACAAAATTACAATATT
520162 CATACAAAAA
Statistics
Matches: 197, Mismatches: 21, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
44 3 0.02
45 21 0.11
47 57 0.29
48 90 0.46
49 26 0.13
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (48 bp):
AAAAAATTACAATATTCATACAAAATTACAATATTACAATATTCATAC
Found at i:520155 original size:41 final size:41
Alignment explanation
Indices: 520110--520295 Score: 170
Period size: 41 Copynumber: 4.5 Consensus size: 41
520100 AAACTATAAT
520110 ATTACAATATTCATACAAAAAATTTATAATATTCATAC-AAA
1 ATTACAATATTCATACAAAAAA-TTATAATATTCATACAAAA
* * *
520151 ATTACAATATTCATACAAAAAATTACT-A-ATCCAAAACTATAA
1 ATTACAATATTCATACAAAAAATTA-TAATATTC-ATAC-AAAA
* * * *
520193 A-TACAA-ATTTAATTATAAAATAATTACAATATTCATAC-AAC
1 ATTACAATA-TTCA-TACAAAA-AATTATAATATTCATACAAAA
520234 ATTACAATATTCATA-AAAAAATTATAATATTCATACAAAAA
1 ATTACAATATTCATACAAAAAATTATAATATTCATAC-AAAA
*
520275 ATTTAAAATATTCATACAAAA
1 A-TTACAATATTCATACAAAA
520296 TTCTAATCTA
Statistics
Matches: 116, Mismatches: 14, Indels: 28
0.73 0.09 0.18
Matches are distributed among these distances:
39 19 0.16
40 12 0.10
41 38 0.33
42 30 0.26
43 14 0.12
44 3 0.03
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.32
Consensus pattern (41 bp):
ATTACAATATTCATACAAAAAATTATAATATTCATACAAAA
Found at i:520201 original size:68 final size:68
Alignment explanation
Indices: 520015--520232 Score: 190
Period size: 68 Copynumber: 3.3 Consensus size: 68
520005 AAATTATAAT
* * *
520015 ATTACAACATTCATACAAAAAATATAAT-ATTC-ATAC-A-AAATTACAAAATTACAATATTCAT
1 ATTACAATATTCATACAAAAAATATAATAATACAATACTATAAA-TAC-AAATTATAATATTCAT
520076 ACAAAAA
64 AC--AAA
* * *
520083 ATTACAATATTCATAC-AAAACTATAATATTACAATATTCATACAA-A-AAATTTATAATATTCA
1 ATTACAATATTCATACAAAAAATATAATAATACAATACT-ATA-AATACAAA-TTATAATATTCA
520145 TACAAA
63 TACAAA
* * * *
520151 ATTACAATATTCATACAAAAAAT-TACTAATCCAAAACTATAAATACAAATT-T-A-ATT-ATAA
1 ATTACAATATTCATACAAAAAATATAATAATACAATACTATAAATACAAATTATAATATTCATAC
520211 AATA
66 AA-A
520215 ATTACAATATTCATACAA
1 ATTACAATATTCATACAA
520233 CATTACAATA
Statistics
Matches: 126, Mismatches: 13, Indels: 26
0.76 0.08 0.16
Matches are distributed among these distances:
63 5 0.04
64 22 0.17
65 1 0.01
66 3 0.02
67 16 0.13
68 49 0.39
69 11 0.09
70 14 0.11
71 2 0.02
72 1 0.01
73 2 0.02
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (68 bp):
ATTACAATATTCATACAAAAAATATAATAATACAATACTATAAATACAAATTATAATATTCATAC
AAA
Found at i:520296 original size:83 final size:85
Alignment explanation
Indices: 520056--520296 Score: 255
Period size: 83 Copynumber: 2.8 Consensus size: 85
520046 CATACAAAAT
* *
520056 TACAAAATTACAATATTCATACAAAAAATTACAATATTCATACAAAACTATAATATTACAATATT
1 TACAAAATTACAATATTCATACAAAAAATTATAATATTCATAC-AAA--A-AAT-TTAAAATATT
*
520121 CATACAAAA-AATTTATAATATTCA
61 CATACAAAATAATTTACAATATTCA
* * * * *
520145 TACAAAATTACAATATTCATACAAAAAATTACT-A-ATCCAAAACTATAAA--TACAAAT-TTAA
1 TACAAAATTACAATATTCATACAAAAAATTA-TAATATTC-ATACAAAAAATTTA-AAATATTCA
*
520205 TTATAAAATAA-TTACAATATTCA
63 -TACAAAATAATTTACAATATTCA
*
520228 TACAACATTACAATATTCATA-AAAAAATTATAATATTCATACAAAAAATTTAAAATATTCATAC
1 TACAAAATTACAATATTCATACAAAAAATTATAATATTCATACAAAAAATTTAAAATATTCATAC
520292 AAAAT
66 AAAAT
520297 TCTAATCTAA
Statistics
Matches: 126, Mismatches: 16, Indels: 26
0.75 0.10 0.15
Matches are distributed among these distances:
81 1 0.01
82 22 0.17
83 54 0.43
84 7 0.06
85 2 0.02
86 1 0.01
88 4 0.03
89 35 0.28
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (85 bp):
TACAAAATTACAATATTCATACAAAAAATTATAATATTCATACAAAAAATTTAAAATATTCATAC
AAAATAATTTACAATATTCA
Found at i:527670 original size:33 final size:33
Alignment explanation
Indices: 527630--527698 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
527620 AATTGTTGCT
527630 TTAGTCCTTCAAAA-TTTAAAAAACATGAAGTTA
1 TTAGTCCTTCAAAATTTTAAAAAAC-TGAAGTTA
*
527663 TTAGTCCTTCAAAATTTTAAAAATCTGAAGTTA
1 TTAGTCCTTCAAAATTTTAAAAAACTGAAGTTA
527696 TTA
1 TTA
527699 TATGGTAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
33 25 0.74
34 9 0.26
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.38
Consensus pattern (33 bp):
TTAGTCCTTCAAAATTTTAAAAAACTGAAGTTA
Found at i:530122 original size:132 final size:131
Alignment explanation
Indices: 529885--530280 Score: 472
Period size: 132 Copynumber: 3.0 Consensus size: 131
529875 TCTTACCCAA
* * ** *** *
529885 TAAATTTGTCACTTCTTCAGGCAATCTCATGTACTCATACTTTCGACTAAGTTGGGAGATAAAAC
1 TAAATCTGTCACTTCTTCAGGTAGCCTCATGTACTCGGGCTCTCGACTAAGTTGGGAGATAAAAC
** * *
529950 CTCGGCCCAATCGGGGATAATGCTGAACATGTTGAGGGGCTTGTCGACTTTGGGTAGATGACACT
66 CTCGGCCTGATCGGGGATAATACTGGACATGTTGAGGGGCTTGTCG-CTTTGGGTAGATGACACT
530015 TC
130 TC
** * *
530017 TAAATCTGTCACTTCTTC-GCGTAGCCTTGTGTACTCTGGCTCTCGACTAAGTCGGGAGATAAAA
1 TAAATCTGTCACTTCTTCAG-GTAGCCTCATGTACTCGGGCTCTCGACTAAGTTGGGAGATAAAA
* * * * * *
530081 CCTCGGCCTGATCGAGGACAATACTGGACATGTTGAGGGGCTCGTTGGTTCTGGGTAGATAACAC
65 CCTCGGCCTGATCGGGGATAATACTGGACATGTTGAGGGGCTTGTCGCTT-TGGGTAGATGACAC
530146 TTC
129 TTC
* *
530149 TAAATTTGTCACTTCTTCAGGTAGCCTCATGTACTCGGGCTCTCGATTAAGTTGGGAGATAAAAC
1 TAAATCTGTCACTTCTTCAGGTAGCCTCATGTACTCGGGCTCTCGACTAAGTTGGGAGATAAAAC
* * * * *
530214 CTCGGCTTGATTGGGGATAATATTGGACATGTTGAGGGGTTTGTCGGCTTTGGGCA-ATTGACAC
66 CTCGGCCTGATCGGGGATAATACTGGACATGTTGAGGGGCTTGTC-GCTTTGGGTAGA-TGACAC
530278 TTC
129 TTC
530281 AAAAACTTTT
Statistics
Matches: 221, Mismatches: 38, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
131 4 0.02
132 213 0.96
133 4 0.02
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (131 bp):
TAAATCTGTCACTTCTTCAGGTAGCCTCATGTACTCGGGCTCTCGACTAAGTTGGGAGATAAAAC
CTCGGCCTGATCGGGGATAATACTGGACATGTTGAGGGGCTTGTCGCTTTGGGTAGATGACACTT
C
Found at i:531253 original size:4 final size:4
Alignment explanation
Indices: 531244--531271 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
531234 CTCATCAAAT
531244 TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA
531272 CAAACCTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:533152 original size:2 final size:2
Alignment explanation
Indices: 533136--533174 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
533126 ATGCATATGA
*
533136 AT AT -T AT AT AA AT AT AT AT AT AT AT AT AT AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
533175 AAAATGTGCA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:533446 original size:15 final size:13
Alignment explanation
Indices: 533382--533456 Score: 57
Period size: 15 Copynumber: 5.6 Consensus size: 13
533372 CTAAACTATC
533382 ATATAATAATAAT
1 ATATAATAATAAT
*
533395 ATGATGAATAAAAAT
1 AT-AT-AATAATAAT
533410 GATATAAATAATAAT
1 -ATAT-AATAATAAT
*
533425 AGA-AATAATAAT
1 ATATAATAATAAT
*
533437 -CATAATAATAA-
1 ATATAATAATAAT
533448 ATGATAATA
1 AT-ATAATA
533457 CATTAAAATA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
11 1 0.02
12 17 0.34
13 8 0.16
14 4 0.08
15 18 0.36
16 2 0.04
ACGTcount: A:0.61, C:0.01, G:0.07, T:0.31
Consensus pattern (13 bp):
ATATAATAATAAT
Found at i:534902 original size:41 final size:41
Alignment explanation
Indices: 534839--535171 Score: 134
Period size: 43 Copynumber: 7.8 Consensus size: 41
534829 TTTTAGTCTG
*
534839 CTCCACTGTAACCTCA-AGGAGATAAGACCTGATGCGATCTA
1 CTCCACTGTAACCTCAGA-GAGATAAGACCTGATTCGATCTA
* * * ** **
534880 CTCTACTGTAACTTCAGAGAGATAAGATCTGTGATTTTAATCCG
1 CTCCACTGTAACCTCAGAGAGATAAGA-C-CTGA-TTCGATCTA
* * * * *
534924 CTCCACTGTAA-CTTAGGGAGATAGGA--TTATATCTTTGATCTG
1 CTCCACTGTAACCTCAGAGAGATAAGACCTGAT-TC---GATCTA
* * * *
534966 CTCCGCTGTAACCTCAGGGAGATAAGATCTGCAATTCTTCGGTCTA
1 CTCCACTGTAACCTCAGAGAGATAAGACCTG--A---TTCGATCTA
* * * *
535012 CTCCGCTGTAACCTCAGGGGGATAAGACCTGATGCGATCTA
1 CTCCACTGTAACCTCAGAGAGATAAGACCTGATTCGATCTA
* * * ** **
535053 CTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCG
1 CTCCACTGTAACCTCAGAGAGATAAGA-CC-TGA-TTCGATCTA
* * * ** * *
535097 CTCCACTGTAACTTCAGGGAGATAGGATTATGTCTTCGATCTG
1 CTCCACTGTAACCTCAGAGAGATAAGA-CCTG-ATTCGATCTA
* * *
535140 CTCCGCTGTAACCTCAGGGAGATAAGATCTGA
1 CTCCACTGTAACCTCAGAGAGATAAGACCTGA
535172 AATTTCCAAC
Statistics
Matches: 219, Mismatches: 53, Indels: 40
0.70 0.17 0.13
Matches are distributed among these distances:
38 1 0.00
39 3 0.01
41 52 0.24
42 21 0.10
43 60 0.27
44 44 0.20
45 1 0.00
46 33 0.15
47 1 0.00
49 2 0.01
50 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (41 bp):
CTCCACTGTAACCTCAGAGAGATAAGACCTGATTCGATCTA
Found at i:535137 original size:87 final size:87
Alignment explanation
Indices: 534873--535176 Score: 301
Period size: 87 Copynumber: 3.5 Consensus size: 87
534863 AGACCTGATG
* * *
534873 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCTGTGATTTTAATCCGCTCCACTGTAACTT
1 CGATCTACTCCACTGTAACCTCAGAGAGATAAGATCTGTAATTTTAATCCGCTCCACTGTAACTT
*
534938 -AGGGAGATAGGATTATATCTT
66 CAGGGAGATAGGATTATGTCTT
* * * * * ** ** *
534959 TGATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGCAATTCTTCGGTCTACTCCGCTGTAAC
1 CGATCTACTCCACTGTAACCTCAGAGAGATAAGATCTGTAATT-TT-AATCCGCTCCACTGTAAC
* * * ** * *
535024 CTCAGGGGGATAAGA-CCTG-ATG
64 TTCAGGGAGATAGGATTATGTCTT
* * *
535046 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCT-TTATTTTAATCCGCTCCACTGTAACT
1 CGATCTACTCCACTGTAACCTCAGAGAGATAAGAT-CTGTAATTTTAATCCGCTCCACTGTAACT
535110 TCAGGGAGATAGGATTATGTCTT
65 TCAGGGAGATAGGATTATGTCTT
* * * *
535133 CGATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGAAATTT
1 CGATCTACTCCACTGTAACCTCAGAGAGATAAGATCTGTAATTT
535177 CCAACCTATT
Statistics
Matches: 163, Mismatches: 48, Indels: 13
0.73 0.21 0.06
Matches are distributed among these distances:
85 25 0.15
86 41 0.25
87 70 0.43
88 17 0.10
89 10 0.06
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.31
Consensus pattern (87 bp):
CGATCTACTCCACTGTAACCTCAGAGAGATAAGATCTGTAATTTTAATCCGCTCCACTGTAACTT
CAGGGAGATAGGATTATGTCTT
Found at i:535417 original size:85 final size:85
Alignment explanation
Indices: 535335--535817 Score: 767
Period size: 85 Copynumber: 5.7 Consensus size: 85
535325 GTAAGAAGAT
535335 AAGATCTGCTTCTTTAACCAGCTCCACTGCAACCAATGAAGGCAAGGCTTGTTTTCGATCTGCTT
1 AAGATCTGCTTCTTTAACCAGCTCCACTGCAACCAATGAAGGCAAGGCTTGTTTTCGATCTGCTT
* * ** **
535400 CGTGGTTAATGTAAGAAGAT
66 CGTTGTTAACGTTGGAAGGC
535420 AAGATCTGCTTCTTTAACCAGCTCCACTGCAACCAATGAAGGCAAGGCTTGTTTTCGATCTGCTT
1 AAGATCTGCTTCTTTAACCAGCTCCACTGCAACCAATGAAGGCAAGGCTTGTTTTCGATCTGCTT
535485 CGTTGTTAACGTTGGAAGGC
66 CGTTGTTAACGTTGGAAGGC
* * * * *
535505 AAGATCTGCTTCTTTAACCAACTCCATTGTAACCAATGAAGGCAAGGTTTTGTTTTCGA--TGTT
1 AAGATCTGCTTCTTTAACCAGCTCCACTGCAACCAATGAAGGCAAGG-CTTGTTTTCGATCTGCT
535568 TCGTTGTTAACGTTGGAAGGC
65 TCGTTGTTAACGTTGGAAGGC
* * *
535589 AAGATCTGCTTCTTTAACCAGCTCCACTGTAACCAATGAAGGCAAGGTTTTGTTTTCGA--TGTT
1 AAGATCTGCTTCTTTAACCAGCTCCACTGCAACCAATGAAGGCAAGG-CTTGTTTTCGATCTGCT
535652 TCGTTGTTAACGTTGGAAGGC
65 TCGTTGTTAACGTTGGAAGGC
535673 AAGATCTGCTTCTTTAACCAGCTCCACTGCAACCAATGAAGGCAAGGCTTGTTTTCGATCTGCTT
1 AAGATCTGCTTCTTTAACCAGCTCCACTGCAACCAATGAAGGCAAGGCTTGTTTTCGATCTGCTT
*
535738 CGTTGTTAACGCTGGAAGGC
66 CGTTGTTAACGTTGGAAGGC
*
535758 AAGATCTGCTTCTTTAACCAGCTCCACTGTAACCAATGAAGGCAAGGCTTTGTTTTCGAT
1 AAGATCTGCTTCTTTAACCAGCTCCACTGCAACCAATGAAGGCAAGGC-TTGTTTTCGAT
535818 GTTCACTGAT
Statistics
Matches: 376, Mismatches: 18, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
83 10 0.03
84 152 0.40
85 193 0.51
86 21 0.06
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.32
Consensus pattern (85 bp):
AAGATCTGCTTCTTTAACCAGCTCCACTGCAACCAATGAAGGCAAGGCTTGTTTTCGATCTGCTT
CGTTGTTAACGTTGGAAGGC
Found at i:535591 original size:41 final size:41
Alignment explanation
Indices: 535542--535675 Score: 112
Period size: 41 Copynumber: 3.2 Consensus size: 41
535532 TGTAACCAAT
535542 GAAGGCAAGGTTTTGTTTTCGATGTTTCGTTGTTAACGTTG
1 GAAGGCAAGGTTTTGTTTTCGATGTTTCGTTGTTAACGTTG
* * * * * * ** **
535583 GAAGGCAAGATCTGCTTCTTTAACCA-GCTCCACTG-TAACCAAT-
1 GAAGGCAAGGT-T--TTGTTT-TCGATGTTTCGTTGTTAA-CGTTG
535626 GAAGGCAAGGTTTTGTTTTCGATGTTTCGTTGTTAACGTTG
1 GAAGGCAAGGTTTTGTTTTCGATGTTTCGTTGTTAACGTTG
535667 GAAGGCAAG
1 GAAGGCAAG
535676 ATCTGCTTCT
Statistics
Matches: 65, Mismatches: 20, Indels: 16
0.64 0.20 0.16
Matches are distributed among these distances:
39 2 0.03
40 12 0.18
41 22 0.34
42 2 0.03
43 13 0.20
44 12 0.18
45 2 0.03
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.35
Consensus pattern (41 bp):
GAAGGCAAGGTTTTGTTTTCGATGTTTCGTTGTTAACGTTG
Found at i:535791 original size:253 final size:253
Alignment explanation
Indices: 535335--535820 Score: 830
Period size: 253 Copynumber: 1.9 Consensus size: 253
535325 GTAAGAAGAT
535335 AAGATCTGCTTCTTTAACCAGCTCCACTGCAACCAATGAAGGCAAGGCTTGTTTTCGATCTGCTT
1 AAGATCTGCTTCTTTAACCAGCTCCACTGCAACCAATGAAGGCAAGGCTTGTTTTCGA-CTGCTT
* *
535400 CGTGGTTAATGTAAGAAGATAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCAATGAAGGCAA
65 CGTGGTTAACGTAAGAAGACAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCAATGAAGGCAA
*
535465 GGCTTGTTTTCGATCTGCTTCGTTGTTAACGTTGGAAGGCAAGATCTGCTTCTTTAACCAACTCC
130 GGCTTGTTTTCGATCTGCTTCGTTGTTAACGCTGGAAGGCAAGATCTGCTTCTTTAACCAACTCC
* *
535530 ATTGTAACCAATGAAGGCAAGGTTTTGTTTTCGATGTTTCGTTGTTAACGTTGGAAGGC
195 ACTGTAACCAATGAAGGCAAGGCTTTGTTTTCGATGTTTCGTTGTTAACGTTGGAAGGC
* * *
535589 AAGATCTGCTTCTTTAACCAGCTCCACTGTAACCAATGAAGGCAAGGTTTTGTTTTCGA-TGTTT
1 AAGATCTGCTTCTTTAACCAGCTCCACTGCAACCAATGAAGGCAAGG-CTTGTTTTCGACTGCTT
* ** *
535653 CGTTGTTAACGTTGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCAATGAAGGCAA
65 CGTGGTTAACGTAAGAAGACAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCAATGAAGGCAA
*
535718 GGCTTGTTTTCGATCTGCTTCGTTGTTAACGCTGGAAGGCAAGATCTGCTTCTTTAACCAGCTCC
130 GGCTTGTTTTCGATCTGCTTCGTTGTTAACGCTGGAAGGCAAGATCTGCTTCTTTAACCAACTCC
535783 ACTGTAACCAATGAAGGCAAGGCTTTGTTTTCGATGTT
195 ACTGTAACCAATGAAGGCAAGGCTTTGTTTTCGATGTT
535821 CACTGATTTG
Statistics
Matches: 218, Mismatches: 13, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
253 162 0.74
254 46 0.21
255 10 0.05
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (253 bp):
AAGATCTGCTTCTTTAACCAGCTCCACTGCAACCAATGAAGGCAAGGCTTGTTTTCGACTGCTTC
GTGGTTAACGTAAGAAGACAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCAATGAAGGCAAG
GCTTGTTTTCGATCTGCTTCGTTGTTAACGCTGGAAGGCAAGATCTGCTTCTTTAACCAACTCCA
CTGTAACCAATGAAGGCAAGGCTTTGTTTTCGATGTTTCGTTGTTAACGTTGGAAGGC
Found at i:537975 original size:10 final size:9
Alignment explanation
Indices: 537946--537974 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
537936 ATATTTTGAC
537946 TTTGA-TTT
1 TTTGATTTT
537954 TTTGATTTT
1 TTTGATTTT
537963 TTTGATTTT
1 TTTGATTTT
537972 TTT
1 TTT
537975 TTGAATTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 5 0.25
9 15 0.75
ACGTcount: A:0.10, C:0.00, G:0.10, T:0.79
Consensus pattern (9 bp):
TTTGATTTT
Found at i:540537 original size:19 final size:20
Alignment explanation
Indices: 540508--540556 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
540498 CACTTCGTGA
* *
540508 AAATCTAATGCATATG-ATG
1 AAATGTAATGCAAATGCATG
*
540527 CAATGTAATGCAAATGCATG
1 AAATGTAATGCAAATGCATG
540547 AAATG-AATGC
1 AAATGTAATGC
540557 CTAAAGAGAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (20 bp):
AAATGTAATGCAAATGCATG
Found at i:542452 original size:11 final size:10
Alignment explanation
Indices: 542433--542471 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
542423 GCGCAAATGC
*
542433 ATATGAATATT
1 ATATAAATA-T
542444 ATATAAATAT
1 ATATAAATAT
542454 ATATATAATAT
1 ATATA-AATAT
542465 ATATAAA
1 ATATAAA
542472 AATGTGCATG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 8 0.31
11 18 0.69
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (10 bp):
ATATAAATAT
Found at i:542739 original size:15 final size:13
Alignment explanation
Indices: 542675--542749 Score: 57
Period size: 15 Copynumber: 5.6 Consensus size: 13
542665 CTAAACTATC
542675 ATATAATAATAAT
1 ATATAATAATAAT
*
542688 ATGATGAATAAAAAT
1 AT-AT-AATAATAAT
542703 GATATAAATAATAAT
1 -ATAT-AATAATAAT
*
542718 AGA-AATAATAAT
1 ATATAATAATAAT
*
542730 -CATAATAATAA-
1 ATATAATAATAAT
542741 ATGATAATA
1 AT-ATAATA
542750 CATTAAAATA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
11 1 0.02
12 17 0.34
13 8 0.16
14 4 0.08
15 18 0.36
16 2 0.04
ACGTcount: A:0.61, C:0.01, G:0.07, T:0.31
Consensus pattern (13 bp):
ATATAATAATAAT
Found at i:546193 original size:13 final size:14
Alignment explanation
Indices: 546169--546234 Score: 50
Period size: 13 Copynumber: 4.6 Consensus size: 14
546159 AAAAACAATT
546169 ATTTTTTCTATTTC
1 ATTTTTTCTATTTC
546183 ATTTTTT-TATTTC
1 ATTTTTTCTATTTC
*
546196 -TTTATTTACCTTTTTC
1 ATTT-TTT--CTATTTC
546212 --TTTTTCTATTTGC
1 ATTTTTTCTATTT-C
546225 ATTTCTTTCT
1 ATTT-TTTCT
546235 TCTTTTGCCA
Statistics
Matches: 42, Mismatches: 2, Indels: 14
0.72 0.03 0.24
Matches are distributed among these distances:
12 8 0.19
13 10 0.24
14 10 0.24
15 4 0.10
16 10 0.24
ACGTcount: A:0.12, C:0.15, G:0.02, T:0.71
Consensus pattern (14 bp):
ATTTTTTCTATTTC
Found at i:546231 original size:18 final size:18
Alignment explanation
Indices: 546208--546242 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
546198 TATTTACCTT
546208 TTTCTTT-TTCTATTTGCA
1 TTTCTTTCTTCT-TTTGCA
546226 TTTCTTTCTTCTTTTGC
1 TTTCTTTCTTCTTTTGC
546243 CATAAACAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.06, C:0.20, G:0.06, T:0.69
Consensus pattern (18 bp):
TTTCTTTCTTCTTTTGCA
Found at i:546472 original size:18 final size:17
Alignment explanation
Indices: 546421--546475 Score: 60
Period size: 16 Copynumber: 3.2 Consensus size: 17
546411 GGTTGTTTAT
*
546421 GAGATAAGAGGAAAGAAA
1 GAGAGAAGA-GAAAGAAA
*
546439 G-GAGAATAGAAA-AAA
1 GAGAGAAGAGAAAGAAA
546454 GAGAGAAGAGAGAAGAAA
1 GAGAGAAGAGA-AAGAAA
546472 GAGA
1 GAGA
546476 ATTAGAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 4 0.13
16 12 0.39
17 7 0.23
18 8 0.26
ACGTcount: A:0.62, C:0.00, G:0.35, T:0.04
Consensus pattern (17 bp):
GAGAGAAGAGAAAGAAA
Found at i:546491 original size:22 final size:22
Alignment explanation
Indices: 546466--546515 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
546456 GAGAAGAGAG
546466 AAGAAAGAG-AATTAGAAAAAAA
1 AAGAAAGAGCAATTA-AAAAAAA
*
546488 AAGAAAG-GCAATTAAAAAGAA
1 AAGAAAGAGCAATTAAAAAAAA
546509 AA-AAAGA
1 AAGAAAGA
546516 ATTTAGAGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 4 0.16
21 9 0.36
22 12 0.48
ACGTcount: A:0.72, C:0.02, G:0.18, T:0.08
Consensus pattern (22 bp):
AAGAAAGAGCAATTAAAAAAAA
Found at i:552179 original size:146 final size:148
Alignment explanation
Indices: 551921--552234 Score: 433
Period size: 146 Copynumber: 2.1 Consensus size: 148
551911 GGAAAATTTA
*
551921 TGATTTTTTTTAAAGAAAAGAGAATTTAGATTTTTAAAAATAAAAATATGTTTTTTAGTCATTTT
1 TGATTTTTTTTAAAGAAAAGAGAATTTAGATTTTT-AAAATAAAAATATGCTTTTTAGTCATTTT
* *
551986 AAAGGAAAAGATTAAAATTTTAAAACAAAGTTTTAATCTTTTTCAACTATTTCGAAATAAAGCTT
65 AAAGGAAAAGATTAAAATTTTAAAACAAAATTTTAATCTTTTTCAACTATTTCGAAATAAAACTT
552051 TGATTTTAAAGAAAAATAG
130 TGATTTTAAAGAAAAATAG
*
552070 TGATTTTCTTTTAAA-AAAAGAGAAAGTTTAGATTTTT-AAA-AACAA-AT-CTTTTTAGTCATT
1 TGATTTT-TTTTAAAGAAAAGAG-AA-TTTAGATTTTTAAAATAAAAATATGCTTTTTAGTCATT
* * * *
552130 TTAAAGGAAAA-ATTTAAATTTTTAAAATAAAATTTTGATCTTTTTCAACTATTTTGAAATAAAA
63 TTAAAGGAAAAGA-TTAAAATTTTAAAACAAAATTTTAATCTTTTTCAACTATTTCGAAATAAAA
* *
552194 CTTTGATTTTTAAGAAAAGTAG
127 CTTTGATTTTAAAGAAAAATAG
* *
552216 TAATTGTTTTTAAAGAAAA
1 TGATTTTTTTTAAAGAAAA
552235 CTTTAATTTT
Statistics
Matches: 148, Mismatches: 12, Indels: 13
0.86 0.07 0.08
Matches are distributed among these distances:
145 8 0.05
146 97 0.66
147 2 0.01
148 4 0.03
149 17 0.11
150 9 0.06
151 11 0.07
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (148 bp):
TGATTTTTTTTAAAGAAAAGAGAATTTAGATTTTTAAAATAAAAATATGCTTTTTAGTCATTTTA
AAGGAAAAGATTAAAATTTTAAAACAAAATTTTAATCTTTTTCAACTATTTCGAAATAAAACTTT
GATTTTAAAGAAAAATAG
Found at i:571718 original size:14 final size:14
Alignment explanation
Indices: 571699--571739 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
571689 AAGTTATTAC
571699 AAAAATAGAATTTA
1 AAAAATAGAATTTA
* **
571713 AAAAATATAAAATA
1 AAAAATAGAATTTA
571727 AAAAATAGAATTT
1 AAAAATAGAATTT
571740 TTTTATAAAA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (14 bp):
AAAAATAGAATTTA
Found at i:571787 original size:18 final size:19
Alignment explanation
Indices: 571756--571795 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
571746 AAAATTTATT
* *
571756 AAAATAATACAAAATTACA
1 AAAAAAATACAAAATCACA
571775 AAAAAAATA-AAAATCACA
1 AAAAAAATACAAAATCACA
571793 AAA
1 AAA
571796 GCATAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.75, C:0.10, G:0.00, T:0.15
Consensus pattern (19 bp):
AAAAAAATACAAAATCACA
Found at i:572209 original size:29 final size:31
Alignment explanation
Indices: 572174--572264 Score: 100
Period size: 29 Copynumber: 3.0 Consensus size: 31
572164 TTCAAAAATC
572174 TATATTTTTTATTTTCAATTTTAAAT-ATTT
1 TATATTTTTTATTTTCAATTTTAAATAATTT
*
572204 TA-ATTTTTT-TTTTGCAATTTT-TATAATTT
1 TATATTTTTTATTTT-CAATTTTAAATAATTT
* * *
572233 TATATTTTTGAATTTCAATTTTATAAAAATTT
1 TATATTTTTTATTTTCAATTTTA-AATAATTT
572265 CCAAATTTTA
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
28 6 0.12
29 20 0.40
30 15 0.30
31 3 0.06
32 6 0.12
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (31 bp):
TATATTTTTTATTTTCAATTTTAAATAATTT
Found at i:574454 original size:63 final size:61
Alignment explanation
Indices: 574340--574464 Score: 171
Period size: 63 Copynumber: 2.0 Consensus size: 61
574330 GGTTCAATAC
* * *
574340 CATTGTAAGGTGATTGTAGTAACCTTTTTCTATAATTGTAGTTTAAAGCTTTTATCCAAAT
1 CATTGTAAGGTCATTGTAGTAACCTTTTTCTATAATTGCAATTTAAAGCTTTTATCCAAAT
* *
574401 CATTGTGAGGTCATTGTAGTAACCCCATTTTT-TATAATTGCAATTTAAGGCTTTTATCCAAAT
1 CATTGTAAGGTCATTGTAGTAA--CC-TTTTTCTATAATTGCAATTTAAAGCTTTTATCCAAAT
574464 C
1 C
574465 TTATCAATTT
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
61 20 0.36
63 31 0.55
64 5 0.09
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.42
Consensus pattern (61 bp):
CATTGTAAGGTCATTGTAGTAACCTTTTTCTATAATTGCAATTTAAAGCTTTTATCCAAAT
Found at i:579556 original size:21 final size:22
Alignment explanation
Indices: 579532--579581 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
579522 GTACCTCATA
* *
579532 TTAATATACATAAAT-TGATTT
1 TTAATATAAATAAATGTAATTT
579553 TTAATAATAAATAAATGTAATTT
1 TTAAT-ATAAATAAATGTAATTT
579576 TTAATA
1 TTAATA
579582 GATATAACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 5 0.20
22 10 0.40
23 10 0.40
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (22 bp):
TTAATATAAATAAATGTAATTT
Found at i:579568 original size:22 final size:23
Alignment explanation
Indices: 579532--579581 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
579522 GTACCTCATA
* *
579532 TTAAT-ATACATAAAT-TGATTT
1 TTAATAATAAATAAATGTAATTT
579553 TTAATAATAAATAAATGTAATTT
1 TTAATAATAAATAAATGTAATTT
579576 TTAATA
1 TTAATA
579582 GATATAACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 5 0.20
22 9 0.36
23 11 0.44
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (23 bp):
TTAATAATAAATAAATGTAATTT
Found at i:579588 original size:22 final size:20
Alignment explanation
Indices: 579541--579588 Score: 51
Period size: 23 Copynumber: 2.2 Consensus size: 20
579531 ATTAATATAC
*
579541 ATAAATTGATTTTTAATAAT
1 ATAAATTAATTTTTAATAAT
579561 AAATAAATGTAATTTTTAATAGAT
1 --ATAAAT-TAATTTTTAATA-AT
579585 ATAA
1 ATAA
579589 CAATTCACTC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 10 0.43
23 11 0.48
24 2 0.09
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (20 bp):
ATAAATTAATTTTTAATAAT
Found at i:582128 original size:13 final size:14
Alignment explanation
Indices: 582110--582151 Score: 61
Period size: 13 Copynumber: 3.1 Consensus size: 14
582100 TAAAATGTAC
582110 AATATAATTAAA-T
1 AATATAATTAAATT
582123 AATATAATTAAATT
1 AATATAATTAAATT
*
582137 AA-ATAATTTAATT
1 AATATAATTAAATT
582150 AA
1 AA
582152 CTGTTTACCC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 24 0.89
14 3 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AATATAATTAAATT
Found at i:582136 original size:18 final size:18
Alignment explanation
Indices: 582115--582151 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
582105 TGTACAATAT
582115 AATTAAATAATATAATTA
1 AATTAAATAATATAATTA
*
582133 AATTAAATAATTTAATTA
1 AATTAAATAATATAATTA
582151 A
1 A
582152 CTGTTTACCC
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:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AATTAAATAATATAATTA
Found at i:584638 original size:3 final size:3
Alignment explanation
Indices: 584632--584681 Score: 73
Period size: 3 Copynumber: 16.3 Consensus size: 3
584622 TAAAAAAATT
**
584632 TAA TAA TAA TAA TAA TAA TGG TAA TAAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
584678 TAA T
1 TAA T
584682 CATGATGATG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
3 39 0.93
4 3 0.07
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:584689 original size:3 final size:3
Alignment explanation
Indices: 584683--584709 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
584673 AATAATAATC
584683 ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG
584710 GTATTAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:604197 original size:3 final size:3
Alignment explanation
Indices: 604184--604219 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
604174 AAGACACAGC
604184 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
604220 AGCATTTAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:604450 original size:19 final size:19
Alignment explanation
Indices: 604428--604478 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
604418 ATATAAATTC
604428 TAAAAGTAATTAATTTAAA
1 TAAAAGTAATTAATTTAAA
**
604447 TAAAAGTAATTTTTTTAAA
1 TAAAAGTAATTAATTTAAA
604466 -AAAA-TAA-TAATTT
1 TAAAAGTAATTAATTT
604479 CAAGTGATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
16 4 0.14
17 3 0.11
18 4 0.14
19 17 0.61
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (19 bp):
TAAAAGTAATTAATTTAAA
Found at i:613802 original size:17 final size:16
Alignment explanation
Indices: 613764--613803 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
613754 AACTCCAGAT
613764 TTTTTTATTTTTAATA
1 TTTTTTATTTTTAATA
* *
613780 TATTTTATTTTTTATAA
1 TTTTTTATTTTTAAT-A
613797 TTTTTTA
1 TTTTTTA
613804 ATAATTTACT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTTTATTTTTAATA
Found at i:615802 original size:26 final size:27
Alignment explanation
Indices: 615752--615802 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
615742 GCAGATAATA
*
615752 AAAATTTTTGAATTTTAAAGTAAATCT
1 AAAATTTTTGAATTTTAAAGAAAATCT
* *
615779 AAAA-TTTTGATTTTTATAGAAAAT
1 AAAATTTTTGAATTTTAAAGAAAAT
615803 TCAAATATCC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 17 0.81
27 4 0.19
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (27 bp):
AAAATTTTTGAATTTTAAAGAAAATCT
Found at i:618347 original size:149 final size:149
Alignment explanation
Indices: 618075--618671 Score: 941
Period size: 149 Copynumber: 4.0 Consensus size: 149
618065 GATCAGCACT
* *
618075 TTTTCCATCGTTTGATTTATTATCATCACCATTGACATGGAAAGACCCGTATTTTTTAGGTCGGT
1 TTTTCCATCATTTGATTTATTATCATCACCATTGACATGGAAAGACCCGTATTTTTTAAGTCGGT
* * **
618140 CCTAGAGAACACTTACAGAGATTAGAAGAGTTCCAGTGTGAAGAGATAATC-AGACAAGTAAAG-
66 CCTAGAGAACAATTACAGAGATCAGAAGAGTTCCAGTGTGAAGAGGCAATCAAG-CAAGTAAAGA
618203 TGCAAACACGAGGGATACCTG
130 T-CAAACACGAGGGATACCTG
618224 TTTTCCATCATTTGATTTATTATCATCACCATTGACATGGAAAGACCCGTATTTTTTAAGTCGGT
1 TTTTCCATCATTTGATTTATTATCATCACCATTGACATGGAAAGACCCGTATTTTTTAAGTCGGT
* *
618289 CCTAGAGAACAATTACAGAGATCAGAAGAGTTTCAGTATGAAGAGGCAATCAAGCAAGTAAAGAT
66 CCTAGAGAACAATTACAGAGATCAGAAGAGTTCCAGTGTGAAGAGGCAATCAAGCAAGTAAAGAT
*
618354 CAAACACGAGTGATACCTG
131 CAAACACGAGGGATACCTG
618373 TTTTCCATCATTTGATTTATTATCATCACCATTGACATGGAAAGACCCGTATTTTTTAAGTCGGT
1 TTTTCCATCATTTGATTTATTATCATCACCATTGACATGGAAAGACCCGTATTTTTTAAGTCGGT
* * * *
618438 CCTAGAGAACAATTACAGAGATCAGAAGAGTTTCAGTGTGAAGATGCGATCAGGCAAGTAAAGAT
66 CCTAGAGAACAATTACAGAGATCAGAAGAGTTCCAGTGTGAAGAGGCAATCAAGCAAGTAAAGAT
618503 CAAACACGAGGGATACCTG
131 CAAACACGAGGGATACCTG
* *
618522 TTTTCCATAATTTGATTTATTATCTTCACCATTGACATGGAAAGACCCGTATTTTTT-AGTTCGG
1 TTTTCCATCATTTGATTTATTATCATCACCATTGACATGGAAAGACCCGTATTTTTTAAG-TCGG
* * * * *
618586 TCCTGGAGAA-AAGTTACAGAGATCAGAAGAGTTCCAATGCGAAGAGGCAATTAGGCAAGTAAAG
65 TCCTAGAGAACAA-TTACAGAGATCAGAAGAGTTCCAGTGTGAAGAGGCAATCAAGCAAGTAAAG
*
618650 ATCAAACACAAGGGATACCTG
129 ATCAAACACGAGGGATACCTG
618671 T
1 T
618672 GGCTGTGGGA
Statistics
Matches: 420, Mismatches: 24, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
148 4 0.01
149 413 0.98
150 3 0.01
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.28
Consensus pattern (149 bp):
TTTTCCATCATTTGATTTATTATCATCACCATTGACATGGAAAGACCCGTATTTTTTAAGTCGGT
CCTAGAGAACAATTACAGAGATCAGAAGAGTTCCAGTGTGAAGAGGCAATCAAGCAAGTAAAGAT
CAAACACGAGGGATACCTG
Found at i:624342 original size:18 final size:18
Alignment explanation
Indices: 624297--624353 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
624287 AATATTTTTC
624297 TAAATTTTATATGAAAAGA
1 TAAA-TTTATATGAAAAGA
* *
624316 TAAAATTATCTGAAAA-A
1 TAAATTTATATGAAAAGA
624333 TAATATTTAT-T-AAAAG-
1 TAA-ATTTATATGAAAAGA
624349 TAAAT
1 TAAAT
624354 GACTTTTTGT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
15 2 0.06
16 7 0.21
17 5 0.15
18 15 0.45
19 4 0.12
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.37
Consensus pattern (18 bp):
TAAATTTATATGAAAAGA
Found at i:625540 original size:22 final size:20
Alignment explanation
Indices: 625489--625545 Score: 53
Period size: 20 Copynumber: 2.7 Consensus size: 20
625479 GTTGATCTAG
* *
625489 TTTAATCATTTTTTATTATTT
1 TTTAAT-ATTTTTTATGAATT
625510 TTTAA-ATTTGTTTATGAATT
1 TTTAATATTT-TTTATGAATT
625530 TTTAATTATTTATTTA
1 TTTAA-TATTT-TTTA
625546 ATTATTGTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 4 0.13
20 13 0.43
21 5 0.17
22 8 0.27
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.67
Consensus pattern (20 bp):
TTTAATATTTTTTATGAATT
Found at i:626791 original size:18 final size:17
Alignment explanation
Indices: 626765--626798 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
626755 ATATAAAGTT
626765 TTGGTAATTTCATTTTG
1 TTGGTAATTTCATTTTG
*
626782 TTGGTGAATTTTATTTT
1 TTGGT-AATTTCATTTT
626799 ATTTTTTGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.18, C:0.03, G:0.18, T:0.62
Consensus pattern (17 bp):
TTGGTAATTTCATTTTG
Found at i:626814 original size:22 final size:23
Alignment explanation
Indices: 626771--626817 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
626761 AGTTTTGGTA
626771 ATTTCATTTTGTTGGTGAATTTT
1 ATTTCATTTTGTTGGTGAATTTT
*
626794 ATTTTATTTT-TTGGT-ATATTTT
1 ATTTCATTTTGTTGGTGA-ATTTT
626816 AT
1 AT
626818 GCCCGTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 1 0.05
22 12 0.55
23 9 0.41
ACGTcount: A:0.19, C:0.02, G:0.13, T:0.66
Consensus pattern (23 bp):
ATTTCATTTTGTTGGTGAATTTT
Found at i:630522 original size:14 final size:14
Alignment explanation
Indices: 630503--630536 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
630493 GTGAATTTTT
630503 TAATTTG-TGAAATA
1 TAATTTGAT-AAATA
630517 TAATTTGATAAATA
1 TAATTTGATAAATA
630531 TAATTT
1 TAATTT
630537 AATTCGAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 18 0.95
15 1 0.05
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (14 bp):
TAATTTGATAAATA
Found at i:645031 original size:7 final size:7
Alignment explanation
Indices: 645019--645047 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
645009 TAAACCCTTT
645019 TACATTG
1 TACATTG
645026 TACATTG
1 TACATTG
645033 TACATTG
1 TACATTG
645040 TACATTG
1 TACATTG
645047 T
1 T
645048 TGTCTGCAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.45
Consensus pattern (7 bp):
TACATTG
Found at i:646288 original size:18 final size:18
Alignment explanation
Indices: 646242--646277 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
646232 TATCATGTAT
646242 TATATTAG-ATTTTATAAA
1 TATATTAGTA-TTTATAAA
646260 TATATTAGTATTTATAAA
1 TATATTAGTATTTATAAA
646278 ATTTTATGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 16 0.94
19 1 0.06
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (18 bp):
TATATTAGTATTTATAAA
Found at i:649599 original size:185 final size:191
Alignment explanation
Indices: 649275--649687 Score: 631
Period size: 185 Copynumber: 2.2 Consensus size: 191
649265 AATTGTTGAA
* *
649275 AGTAACATTGAAATAAACTAAAACCAGATAACCGAGGACTCCGATTATATAAACTCAAAAGCTAT
1 AGTAACATTGAAATAAACTAAAACCAGATAACCAAGGACTCCGATTATATAAACACAAAAGCTAT
* *
649340 ATGTATAAATTCAAACGGATGAATCGTATTACGTTCCTAGTAGACTATCCCCTGTCGAATAAGGT
66 ATGTATAAATTCAAACGGATGAATCGCATTACATTCCTAGTAGACTATCCCCTGTCGAATAAGGT
* **
649405 GT-TAT-A-TAA-G-TTGTGTTCCGATTTTTGCTCCTCGTACCGAACCGATCAGCATTCCT
131 GTCAATAAGTAACGATTGTGTTCCGATTTCCGCTCCTCGTACCGAACCGATCAGCATTCCT
*
649461 AGTAACATTGAAATAAACTAAAACCAAATAACCAAGGACT-CGATTATATAAACACAAAAGCTAT
1 AGTAACATTGAAATAAACTAAAACCAGATAACCAAGGACTCCGATTATATAAACACAAAAGCTAT
* * * *
649525 ATGTATAAATTCAAACTGATGAATCGCATTTCATTCCTATTAGACTATCCCCTGTCGAATAATGT
66 ATGTATAAATTCAAACGGATGAATCGCATTACATTCCTAGTAGACTATCCCCTGTCGAATAAGGT
* *
649590 GTCATATAAGTAACGATTTGTGTTCCGATTTCCGTTCCTCGTACCGAACCGATCCGCATTCCT
131 GTCA-ATAAGTAACGA-TTGTGTTCCGATTTCCGCTCCTCGTACCGAACCGATCAGCATTCCT
*
649653 AGTAAAATTGAAATAAACTAAAACCAGATAACCAA
1 AGTAACATTGAAATAAACTAAAACCAGATAACCAA
649688 ATGACAACCC
Statistics
Matches: 204, Mismatches: 16, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
185 84 0.41
186 38 0.19
187 2 0.01
188 1 0.00
189 3 0.01
190 1 0.00
192 75 0.37
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.29
Consensus pattern (191 bp):
AGTAACATTGAAATAAACTAAAACCAGATAACCAAGGACTCCGATTATATAAACACAAAAGCTAT
ATGTATAAATTCAAACGGATGAATCGCATTACATTCCTAGTAGACTATCCCCTGTCGAATAAGGT
GTCAATAAGTAACGATTGTGTTCCGATTTCCGCTCCTCGTACCGAACCGATCAGCATTCCT
Found at i:651455 original size:21 final size:21
Alignment explanation
Indices: 651408--651455 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
651398 TTAGTATTTT
651408 TTTTATAACTCAATTATGAAA
1 TTTTATAACTCAATTATGAAA
** * **
651429 AATTATCACTCAATTATTCAA
1 TTTTATAACTCAATTATGAAA
651450 TTTTAT
1 TTTTAT
651456 TTTTTGATCA
Statistics
Matches: 20, Mismatches: 7, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.12, G:0.02, T:0.46
Consensus pattern (21 bp):
TTTTATAACTCAATTATGAAA
Found at i:654013 original size:10 final size:10
Alignment explanation
Indices: 654000--654033 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
653990 ATATATATAT
*
654000 CATATCATAC
1 CATACCATAC
654010 CATACCATAC
1 CATACCATAC
*
654020 CATACCATAT
1 CATACCATAC
654030 CATA
1 CATA
654034 ATCATTGTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.41, C:0.32, G:0.00, T:0.26
Consensus pattern (10 bp):
CATACCATAC
Found at i:654023 original size:15 final size:15
Alignment explanation
Indices: 654000--654033 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
653990 ATATATATAT
*
654000 CATATCATACCATAC
1 CATACCATACCATAC
*
654015 CATACCATACCATAT
1 CATACCATACCATAC
654030 CATA
1 CATA
654034 ATCATTGTCT
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:0.41, C:0.32, G:0.00, T:0.26
Consensus pattern (15 bp):
CATACCATACCATAC
Found at i:657950 original size:14 final size:14
Alignment explanation
Indices: 657931--657957 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
657921 CTAAGTAGCG
657931 TTGTTATTTTATTA
1 TTGTTATTTTATTA
657945 TTGTTATTTTATT
1 TTGTTATTTTATT
657958 GAGCTCGATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.19, C:0.00, G:0.07, T:0.74
Consensus pattern (14 bp):
TTGTTATTTTATTA
Found at i:665652 original size:45 final size:45
Alignment explanation
Indices: 665605--665716 Score: 170
Period size: 45 Copynumber: 2.4 Consensus size: 45
665595 GCCATCCACC
*
665605 GCAACTCCGCCGCCAACTACCACTCCTGCCACACCACCACCAACCGCA
1 GCAACTCCGCCGCCAACTAACACTCCT---ACACCACCACCAACCGCA
*
665653 GCAACTCCGCCGCCAACTAACACTCCTACACCACCACCAAGCGCA
1 GCAACTCCGCCGCCAACTAACACTCCTACACCACCACCAACCGCA
*
665698 GCAGCTCCGCCGCCAACTA
1 GCAACTCCGCCGCCAACTA
665717 GTCCTCCCTC
Statistics
Matches: 61, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
45 35 0.57
48 26 0.43
ACGTcount: A:0.28, C:0.51, G:0.12, T:0.09
Consensus pattern (45 bp):
GCAACTCCGCCGCCAACTAACACTCCTACACCACCACCAACCGCA
Found at i:671984 original size:14 final size:14
Alignment explanation
Indices: 671965--671991 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
671955 ATTTATCCCT
671965 AAAATTTATGTATC
1 AAAATTTATGTATC
671979 AAAATTTATGTAT
1 AAAATTTATGTAT
671992 AATTTTAAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.44
Consensus pattern (14 bp):
AAAATTTATGTATC
Found at i:680233 original size:16 final size:16
Alignment explanation
Indices: 680212--680243 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
680202 TCAAAAAAGA
*
680212 AAAATCTGAATAGTTG
1 AAAATCCGAATAGTTG
680228 AAAATCCGAATAGTTG
1 AAAATCCGAATAGTTG
680244 GGTGACCATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.09, G:0.19, T:0.28
Consensus pattern (16 bp):
AAAATCCGAATAGTTG
Found at i:683735 original size:41 final size:41
Alignment explanation
Indices: 683678--683760 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
683668 AAAAAAAAGT
683678 ATTTTCAGTACTTAATTGAACAAGAACCAATAATGGCCACA
1 ATTTTCAGTACTTAATTGAACAAGAACCAATAATGGCCACA
683719 ATTTTCAGTACTTAATTGAACAAGAACCAATAATGGCCACA
1 ATTTTCAGTACTTAATTGAACAAGAACCAATAATGGCCACA
683760 A
1 A
683761 AATTACCCAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.27
Consensus pattern (41 bp):
ATTTTCAGTACTTAATTGAACAAGAACCAATAATGGCCACA
Found at i:688217 original size:30 final size:31
Alignment explanation
Indices: 688183--688242 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
688173 AAACCTTTTA
*
688183 TTTTCTCCC-AAAAGTTTTACTCCC-TCCCAC
1 TTTTC-CCCTAAAAATTTTACTCCCTTCCCAC
*
688213 TTTTCCCCTAAAAATTTTATTCCCTTCCCA
1 TTTTCCCCTAAAAATTTTACTCCCTTCCCA
688243 TCCCACCTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 3 0.12
30 18 0.69
31 5 0.19
ACGTcount: A:0.22, C:0.37, G:0.02, T:0.40
Consensus pattern (31 bp):
TTTTCCCCTAAAAATTTTACTCCCTTCCCAC
Found at i:691597 original size:12 final size:12
Alignment explanation
Indices: 691580--691604 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
691570 AAAAACAGAC
691580 TGTTTTGTTTTT
1 TGTTTTGTTTTT
691592 TGTTTTGTTTTT
1 TGTTTTGTTTTT
691604 T
1 T
691605 ATAATTGTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (12 bp):
TGTTTTGTTTTT
Found at i:692306 original size:199 final size:197
Alignment explanation
Indices: 691924--692480 Score: 663
Period size: 199 Copynumber: 2.8 Consensus size: 197
691914 AACAGGTGCG
* * *
691924 AGAATTTTCTTTCCTACCAAACACGCTCAAACATCCATATTCTTTTTCAGTTTTTCACCACCCCT
1 AGAATTTTCTTTCCTACCAAACACGCTCAAACATTCATATTCTTTTTCAGTTTTTCACCATCCTT
* * * * * *
691989 AATTCCATTTCTTCCAG-ATTTTTCACTCTGCTAAGCAAACCACTAATCTTGTTTCCGTATTTTT
66 TATT-CA-TTCTT-CTGTTTTTTTCACTCTGCCAAGCAAACCACTAATCTCGTTTTCGTATTTTT
* ** *
692053 GCTTTACAATCTATGAACAAGAAAGCTAACGAAGATGATGCTAATCTTTTGTAATGCAGCTAAGT
128 GCTTTACAATCTATGAACAAGAAAGCTAATGAAGACAAAGCTAATCTTTTGTAATGCAGCTAAGT
692118 GAACA
193 GAACA
* *
692123 AGAATTCTT-TTTCCTACCAAACACGCTCAAACATTCATATTCTTTTTCAGTTTTTCACCTTCTT
1 AGAATT-TTCTTTCCTACCAAACACGCTCAAACATTCATATTCTTTTTCAGTTTTTCACCATCCT
*
692187 TTATTCATTCTTCTGTTTTTTTTTTCACTCTGCCAAGCAAACCACTAAACTCGTTTTCGTATTTT
65 TTATTCATTCTTCTG---TTTTTTTCACTCTGCCAAGCAAACCACTAATCTCGTTTTCGTATTTT
* * *
692252 TGCTTTACTATCCATGAACAAGAAAGCTAATGAAGACAAAGCTAATC-TTTGTAATGCAGTTAAG
127 TGCTTTACAATCTATGAACAAGAAAGCTAATGAAGACAAAGCTAATCTTTTGTAATGCAGCTAAG
* *
692316 TGAGCC
192 TGAACA
* * * * * * * ** *
692322 GGAATTTTCTTCCCTACCTAAGACACTCAAACATTAATGTTCTTTTTTGGTTTTTCACCATCCTA
1 AGAATTTTCTTTCCTACCAAACACGCTCAAACATTCATATTCTTTTTCAGTTTTTCACCATCCTT
* ** * * *
692387 TATCCATTTCTTC-CCTTTTTTCTACTCTGCCAAGCTAACCACTAATCTCATTTTCCTAATTTTT
66 TATTCA-TTCTTCTGTTTTTTTC-ACTCTGCCAAGCAAACCACTAATCTCGTTTTCGT-ATTTTT
692451 GCTTTACAATCTATGAACAAGAAAGCTAAT
128 GCTTTACAATCTATGAACAAGAAAGCTAAT
692481 TATTTCCTTC
Statistics
Matches: 307, Mismatches: 42, Indels: 19
0.83 0.11 0.05
Matches are distributed among these distances:
196 9 0.03
197 35 0.11
198 38 0.12
199 135 0.44
200 90 0.29
ACGTcount: A:0.28, C:0.24, G:0.10, T:0.39
Consensus pattern (197 bp):
AGAATTTTCTTTCCTACCAAACACGCTCAAACATTCATATTCTTTTTCAGTTTTTCACCATCCTT
TATTCATTCTTCTGTTTTTTTCACTCTGCCAAGCAAACCACTAATCTCGTTTTCGTATTTTTGCT
TTACAATCTATGAACAAGAAAGCTAATGAAGACAAAGCTAATCTTTTGTAATGCAGCTAAGTGAA
CA
Found at i:711169 original size:19 final size:20
Alignment explanation
Indices: 711125--711179 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
711115 ATCAATAAAT
711125 ATTTAAATTATATTTTTATA
1 ATTTAAATTATATTTTTATA
* * *
711145 ATTTAATTTATTTTTTTATT
1 ATTTAAATTATATTTTTATA
* *
711165 ATTAAAATTAAATTT
1 ATTTAAATTATATTT
711180 AAGTTAGGCC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTTAAATTATATTTTTATA
Found at i:713524 original size:27 final size:26
Alignment explanation
Indices: 713494--713578 Score: 102
Period size: 27 Copynumber: 3.2 Consensus size: 26
713484 TTATGTTTTA
713494 TATATATTATTTTATTTTATTATATAT
1 TATATATTATTTTATTTTA-TATATAT
*
713521 TATAT-TATATTATATTTTAT-TATAT
1 TATATAT-TATTTTATTTTATATATAT
* *
713546 TATATATTATATTATATTATATTATAT
1 TATATATTATTTTATTTTATA-TATAT
713573 TATATA
1 TATATA
713579 AGTAAAAAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
25 20 0.40
26 3 0.06
27 27 0.54
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (26 bp):
TATATATTATTTTATTTTATATATAT
Found at i:713576 original size:5 final size:5
Alignment explanation
Indices: 713491--713577 Score: 106
Period size: 5 Copynumber: 17.2 Consensus size: 5
713481 TTTTTATGTT
* * *
713491 TTATA -TATA TTATT TTATT TTAT- TATATA TTATA TTATA TTATA TTTTA
1 TTATA TTATA TTATA TTATA TTATA T-TATA TTATA TTATA TTATA TTATA
713540 TTATA TTATATA TTATA TTATA TTATA TTATA TTATA T
1 TTATA -T-TATA TTATA TTATA TTATA TTATA TTATA T
713578 AAGTAAAAAA
Statistics
Matches: 74, Mismatches: 3, Indels: 10
0.85 0.03 0.11
Matches are distributed among these distances:
4 5 0.07
5 62 0.84
6 3 0.04
7 4 0.05
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (5 bp):
TTATA
Found at i:721089 original size:128 final size:128
Alignment explanation
Indices: 720945--721315 Score: 460
Period size: 130 Copynumber: 2.9 Consensus size: 128
720935 AACGAAATCG
* * **
720945 CTTTGCTTTTTTAAAAATTAGAATATTGTATCCGTAAATTTATTCAAAATCGATCTAAACTAAAA
1 CTTTGCTTTTTTAAAAACTAGAATATTGTATCCGTAAATTTATTCAAAATCGATCCAAACCGAAA
*
721010 TGTTATCCGCCTAACTTATTGATGTTTGTTTTCACTGTTGTTTATGGTTCAT-TTGATGTGGCT
66 TGTTATCCGCCTAACTTATTGATGTTTGTTTTTACTGTTGTTTATGGTTCATCTT-ATGTGGCT
* * * *
721073 CTTTGCTTTTTTAAAAACTAGAATACTGTAACCGTAAATTTGTTCAAAATCGATCCAAGCCGAAA
1 CTTTGCTTTTTTAAAAACTAGAATATTGTATCCGTAAATTTATTCAAAATCGATCCAAACCGAAA
* *
721138 TGTTATTCGCCTAACTTATTGATGTGTT-TACTTTTACTGTTGTTTATGGTTCATCTTATGTGGT
66 TGTTATCCGCCTAACTTATTGATGT-TTGT--TTTTACTGTTGTTTATGGTTCATCTTATGTGGC
721202 T
128 T
* * * * * *
721203 CATTGCTTTTTTAAAAGCTAAAACATTGTAAT-TGTAAATTTATTCAAAACCGATCCAAACCGAA
1 CTTTGCTTTTTTAAAAACTAGAATATTGT-ATCCGTAAATTTATTCAAAATCGATCCAAACCGAA
** * * *
721267 ATGTTATCTACCTAACTTATTGGTGTGTTTGTTTTTACTATTATTTATG
65 ATGTTATCCGCCTAACTTATT-G-ATGTTTGTTTTTACTGTTGTTTATG
721316 CGGTTCTTTG
Statistics
Matches: 208, Mismatches: 27, Indels: 14
0.84 0.11 0.06
Matches are distributed among these distances:
128 82 0.39
129 2 0.01
130 114 0.55
131 6 0.03
132 4 0.02
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (128 bp):
CTTTGCTTTTTTAAAAACTAGAATATTGTATCCGTAAATTTATTCAAAATCGATCCAAACCGAAA
TGTTATCCGCCTAACTTATTGATGTTTGTTTTTACTGTTGTTTATGGTTCATCTTATGTGGCT
Found at i:724154 original size:14 final size:13
Alignment explanation
Indices: 724128--724161 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
724118 TATAAAATTT
724128 TAATAAATAAAAA
1 TAATAAATAAAAA
*
724141 TATTAAATTAAAAA
1 TAATAAA-TAAAAA
724155 TAATAAA
1 TAATAAA
724162 AATATATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
TAATAAATAAAAA
Found at i:728985 original size:16 final size:16
Alignment explanation
Indices: 728964--729012 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 16
728954 TAATTTGAAG
728964 TGACCAAAACTCAAAA
1 TGACCAAAACTCAAAA
*
728980 TGACCAAAATTCAAAA
1 TGACCAAAACTCAAAA
* * *
728996 TAACCTAAACTCGAAA
1 TGACCAAAACTCAAAA
729012 T
1 T
729013 TAACCCGAAC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.53, C:0.22, G:0.06, T:0.18
Consensus pattern (16 bp):
TGACCAAAACTCAAAA
Found at i:731425 original size:16 final size:15
Alignment explanation
Indices: 731390--731434 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
731380 TTTTAAAAAA
731390 ATTTATGAAATTTTT
1 ATTTATGAAATTTTT
731405 ATTTATGAATATTTCTT
1 ATTTATGAA-ATTT-TT
731422 -TTTAT--AATTTTT
1 ATTTATGAAATTTTT
731434 A
1 A
731435 AATTATTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
12 2 0.07
13 4 0.15
14 1 0.04
15 9 0.33
16 9 0.33
17 2 0.07
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.62
Consensus pattern (15 bp):
ATTTATGAAATTTTT
Found at i:739880 original size:24 final size:24
Alignment explanation
Indices: 739853--739904 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
739843 TTCGTAGGTC
* *
739853 AAATAAATTATACTAATAAATGTT
1 AAATAAATCATACTAATAAATATT
*
739877 AAATATATCATACTAATAAATATT
1 AAATAAATCATACTAATAAATATT
739901 AAAT
1 AAAT
739905 CATCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.37
Consensus pattern (24 bp):
AAATAAATCATACTAATAAATATT
Found at i:755167 original size:21 final size:20
Alignment explanation
Indices: 755139--755177 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
755129 TTTGGGATTA
755139 AAATATGAAAATGATAATCC
1 AAATATGAAAATGATAATCC
755159 AAATGATGAAAATGATAAT
1 AAAT-ATGAAAATGATAAT
755178 TATTTTTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.56, C:0.05, G:0.13, T:0.26
Consensus pattern (20 bp):
AAATATGAAAATGATAATCC
Found at i:760584 original size:62 final size:63
Alignment explanation
Indices: 760487--760610 Score: 153
Period size: 62 Copynumber: 2.0 Consensus size: 63
760477 CTCTTTTAAA
* * *
760487 TTTTTTTCAAAAATCTCATTAATCTCACAAAATTTTTAAAAATTTTAATTAGATCC-CCAAAT
1 TTTTTTTCAAAAATCTCATCAAACTCACAAAATTTTTAAAAATTTTAATTAGACCCTCCAAAT
** * * *
760549 TTTTTTTCAAAAAAT-TCATCAAACTCGTAAAATTTTTGAAATTTTTATTTAGACCCTCCAAA
1 TTTTTTTC-AAAAATCTCATCAAACTCACAAAATTTTTAAAAATTTTAATTAGACCCTCCAAA
760611 ACTTAGTCTC
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
62 41 0.79
63 11 0.21
ACGTcount: A:0.39, C:0.16, G:0.03, T:0.42
Consensus pattern (63 bp):
TTTTTTTCAAAAATCTCATCAAACTCACAAAATTTTTAAAAATTTTAATTAGACCCTCCAAAT
Found at i:764837 original size:3 final size:3
Alignment explanation
Indices: 764829--764861 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
764819 TTCATGGCCT
764829 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
764862 TTAGTAACTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:765402 original size:16 final size:16
Alignment explanation
Indices: 765381--765411 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
765371 CTATACATAT
765381 TATAATTACAAAATTA
1 TATAATTACAAAATTA
*
765397 TATAATTAGAAAATT
1 TATAATTACAAAATT
765412 TTGGGAGTCG
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:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (16 bp):
TATAATTACAAAATTA
Found at i:769089 original size:29 final size:29
Alignment explanation
Indices: 769044--769099 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
769034 ATATTTTAAG
* *
769044 TTATTTTCACTATTAAAATA-TAAAATAT
1 TTATTTTCACTAGTAAAAAATTAAAATAT
*
769072 TTATTTTTACATAGTAAAAAATTAAAAT
1 TTATTTTCAC-TAGTAAAAAATTAAAAT
769100 TAATTATGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 9 0.39
29 8 0.35
30 6 0.26
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (29 bp):
TTATTTTCACTAGTAAAAAATTAAAATAT
Found at i:769544 original size:25 final size:26
Alignment explanation
Indices: 769506--769578 Score: 76
Period size: 25 Copynumber: 2.7 Consensus size: 26
769496 TATCAAATTT
*
769506 AAAATTAATAAATTATGTTTATTAA-
1 AAAATTATTAAATTATGTTTATTAAG
* * *
769531 AAAGTTATTAAATTGTGTTTTTTAAGG
1 AAAATTATTAAATTATGTTTATTAA-G
769558 AAAATTTTATTAAATTATGTT
1 AAAA--TTATTAAATTATGTT
769579 GAATACTTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
25 21 0.55
27 3 0.08
29 14 0.37
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (26 bp):
AAAATTATTAAATTATGTTTATTAAG
Done.