Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold220
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: 3999181
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 12171 characters in sequence are not A, C, G, or T
File 3 of 19
Found at i:489862 original size:5 final size:5
Alignment explanation
Indices: 489852--489878 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
489842 ATACAGCAGA
489852 TGAGC TGAGC TGAGC TGAGC TGAGC TG
1 TGAGC TGAGC TGAGC TGAGC TGAGC TG
489879 GCTAGTATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.19, G:0.41, T:0.22
Consensus pattern (5 bp):
TGAGC
Found at i:497037 original size:23 final size:26
Alignment explanation
Indices: 496987--497040 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 26
496977 ATAAATTAAA
496987 TAAT-ATTATTTTATTACAAATTTAT
1 TAATAATTATTTTATTACAAATTTAT
*
497012 TAATAATTA-TTT-TTA-AAATTTTT
1 TAATAATTATTTTATTACAAATTTAT
497035 TAATAA
1 TAATAA
497041 AATAACACTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 13 0.48
24 3 0.11
25 7 0.26
26 4 0.15
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (26 bp):
TAATAATTATTTTATTACAAATTTAT
Found at i:499858 original size:20 final size:21
Alignment explanation
Indices: 499833--499871 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
499823 ACATAAATTC
499833 TTAAAATT-TTTTAATTAAAA
1 TTAAAATTATTTTAATTAAAA
499853 TTAAAATTATTTTAATTAA
1 TTAAAATTATTTTAATTAA
499872 TCAAATTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTAAAATTATTTTAATTAAAA
Found at i:500720 original size:4 final size:4
Alignment explanation
Indices: 500703--500740 Score: 58
Period size: 4 Copynumber: 9.5 Consensus size: 4
500693 GGTATAAGCA
* *
500703 TAAT TAAT TGAT TAAT TAAT TAAT TAAC TAAT TAAT TA
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TA
500741 TGTGCCCCTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (4 bp):
TAAT
Found at i:502457 original size:27 final size:26
Alignment explanation
Indices: 502397--502462 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 26
502387 TTAAAATAAA
* *
502397 ATATATATTAATA-ATTTTATATTAT
1 ATATATTTTTATATATTTTATATTAT
*
502422 ATATGTTTTTATATATTTATATATTCAT
1 ATATATTTTTATATATTT-TATATT-AT
502450 AT-TATTTTTATAT
1 ATATATTTTTATAT
502463 TATACTTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
25 10 0.29
26 4 0.12
27 16 0.47
28 4 0.12
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (26 bp):
ATATATTTTTATATATTTTATATTAT
Found at i:505412 original size:3 final size:3
Alignment explanation
Indices: 505404--505430 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
505394 ATAGCCTTGC
505404 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
505431 AGGATAAGTG
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:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:508506 original size:14 final size:15
Alignment explanation
Indices: 508472--508500 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
508462 AATTTTAATA
508472 ATTTATCAAACATTT
1 ATTTATCAAACATTT
508487 ATTTATCAAA-ATTT
1 ATTTATCAAACATTT
508501 TGTTATACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTTATCAAACATTT
Found at i:509945 original size:16 final size:17
Alignment explanation
Indices: 509920--509963 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
509910 TTTTACATAA
*
509920 ATTATAAAATTTTAATT
1 ATTATTAAATTTTAATT
*
509937 -TTATTAAATTTTTATT
1 ATTATTAAATTTTAATT
*
509953 ATTAATAAATT
1 ATTATTAAATT
509964 AAATTATTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTATTAAATTTTAATT
Found at i:510031 original size:15 final size:15
Alignment explanation
Indices: 510011--510078 Score: 50
Period size: 15 Copynumber: 4.5 Consensus size: 15
510001 AAAAAATTTA
510011 ATATTTATATATAAT
1 ATATTTATATATAAT
*
510026 ATATTTTTATA-AAT
1 ATATTTATATATAAT
*
510040 ATTATTT-TAATAAAAT
1 A-TATTTAT-ATATAAT
* * * *
510056 ATAATAATAAATTAT
1 ATATTTATATATAAT
510071 ATATTTAT
1 ATATTTAT
510079 TAAGTCAATT
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
14 5 0.12
15 31 0.76
16 5 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
ATATTTATATATAAT
Found at i:510167 original size:24 final size:22
Alignment explanation
Indices: 510140--510185 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
510130 ATTTTTTAAC
510140 AATAAAATTTAAATAAAATATAAT
1 AATAAAA-TTAAAT-AAATATAAT
*
510164 AATAAAATTAAATACATATAAT
1 AATAAAATTAAATAAATATAAT
510186 TTATACAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 8 0.38
23 6 0.29
24 7 0.33
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (22 bp):
AATAAAATTAAATAAATATAAT
Found at i:511476 original size:22 final size:21
Alignment explanation
Indices: 511446--511489 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
511436 CAAATAAAAT
511446 AATTAAAAAATAAAATTTTTAA
1 AATTAAAAAA-AAAATTTTTAA
* *
511468 AATTTAAAAACAAATTTTTAA
1 AATTAAAAAAAAAATTTTTAA
511489 A
1 A
511490 TAAATTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (21 bp):
AATTAAAAAAAAAATTTTTAA
Found at i:511527 original size:11 final size:11
Alignment explanation
Indices: 511513--511537 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
511503 TATTCTCATA
511513 TTTTTAAATAT
1 TTTTTAAATAT
511524 TTTTTAAATAT
1 TTTTTAAATAT
511535 TTT
1 TTT
511538 AATTTTTAAT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTTTAAATAT
Found at i:511582 original size:14 final size:14
Alignment explanation
Indices: 511565--511631 Score: 59
Period size: 14 Copynumber: 4.8 Consensus size: 14
511555 AACATTTAAA
511565 ATTTTTTAAATTAT
1 ATTTTTTAAATTAT
*
511579 ATTTTTT--TTTAT
1 ATTTTTTAAATTAT
*
511591 ATCTTTTAAACTT-T
1 ATTTTTTAAA-TTAT
*
511605 ATATTTTAAATATAT
1 ATTTTTTAAAT-TAT
511620 ATTTTTTCAAAT
1 ATTTTTT-AAAT
511632 AATAATATTC
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
12 10 0.24
13 1 0.02
14 18 0.43
15 9 0.21
16 4 0.10
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (14 bp):
ATTTTTTAAATTAT
Found at i:512347 original size:16 final size:15
Alignment explanation
Indices: 512326--512365 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
512316 GCCTTCTCAA
512326 AAAAAAAAAAGAAAGC
1 AAAAAAAAAAGAAA-C
*
512342 AAAAAAAAGAGAAAC
1 AAAAAAAAAAGAAAC
512357 AAAAGAAAA
1 AAAA-AAAA
512366 TCCTCTCTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 5 0.23
16 17 0.77
ACGTcount: A:0.82, C:0.05, G:0.12, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAGAAAC
Found at i:517282 original size:2 final size:2
Alignment explanation
Indices: 517277--517318 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
517267 AAACTTAAGG
517277 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
517319 CCTTAAGAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:517387 original size:19 final size:19
Alignment explanation
Indices: 517348--517414 Score: 61
Period size: 18 Copynumber: 3.6 Consensus size: 19
517338 TTTTCAATGG
*
517348 GATAGTTTTTTAAGAGAGT
1 GATAGTTTTTTTAGAGAGT
517367 GAGGTAGTTTTTTTAG-G-GT
1 GA--TAGTTTTTTTAGAGAGT
517386 GATAGTTATTTTTA-A-AGT
1 GATAGTT-TTTTTAGAGAGT
*
517404 GGTAGTTTTTT
1 GATAGTTTTTT
517415 AAGTAGTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
17 9 0.22
18 14 0.34
19 6 0.15
20 1 0.02
21 11 0.27
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.49
Consensus pattern (19 bp):
GATAGTTTTTTTAGAGAGT
Found at i:531430 original size:59 final size:60
Alignment explanation
Indices: 531316--531430 Score: 187
Period size: 59 Copynumber: 1.9 Consensus size: 60
531306 AATTATTGAG
* *
531316 TTTGAAATATCAAAAGCAAATCAACCAAAAAGGAAAGCTTATTTACACGTTATTACAGAT
1 TTTGAAATATCAAAAGCAAATCAACCAAAAAGGAAAGCCTATTTACACGTAATTACAGAT
* *
531376 TTTGAAATATCAAAAGCAAGTCAA-CAAAATGGAAAGCCTATTTACACGTAATTAC
1 TTTGAAATATCAAAAGCAAATCAACCAAAAAGGAAAGCCTATTTACACGTAATTAC
531431 TAGGTTTCAC
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
59 28 0.55
60 23 0.45
ACGTcount: A:0.46, C:0.16, G:0.12, T:0.26
Consensus pattern (60 bp):
TTTGAAATATCAAAAGCAAATCAACCAAAAAGGAAAGCCTATTTACACGTAATTACAGAT
Found at i:536635 original size:6 final size:6
Alignment explanation
Indices: 536624--536681 Score: 61
Period size: 6 Copynumber: 10.3 Consensus size: 6
536614 TCTTTAGCTC
* *
536624 TCTTTT TC-TTT TCTTTT TC-CTT TCCTTT TCTTTT TCTTTT TC--TT
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT
*
536668 TCTTTT TTTTTT TC
1 TCTTTT TCTTTT TC
536682 CCCTCTGAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
4 4 0.09
5 9 0.21
6 30 0.70
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (6 bp):
TCTTTT
Found at i:536640 original size:11 final size:11
Alignment explanation
Indices: 536624--536678 Score: 69
Period size: 11 Copynumber: 5.1 Consensus size: 11
536614 TCTTTAGCTC
536624 TCTTTTTCTTT
1 TCTTTTTCTTT
*
536635 TCTTTTTCCTT
1 TCTTTTTCTTT
*
536646 TCCTTTTCTTTT
1 TCTTTTTC-TTT
536658 TCTTTTTC-TT
1 TCTTTTTCTTT
536668 TCTTTTT-TTT
1 TCTTTTTCTTT
536678 T
1 T
536679 TTCCCCTCTG
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
10 12 0.32
11 17 0.45
12 9 0.24
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (11 bp):
TCTTTTTCTTT
Found at i:536675 original size:17 final size:17
Alignment explanation
Indices: 536624--536681 Score: 82
Period size: 17 Copynumber: 3.5 Consensus size: 17
536614 TCTTTAGCTC
536624 TCTTTTTCTTTTCTTTT
1 TCTTTTTCTTTTCTTTT
* *
536641 TCCTTTCCTTTTCTTTT
1 TCTTTTTCTTTTCTTTT
536658 TCTTTTTC-TTTCTTTT
1 TCTTTTTCTTTTCTTTT
*
536674 TTTTTTTC
1 TCTTTTTC
536682 CCCTCTGAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
16 15 0.42
17 21 0.58
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (17 bp):
TCTTTTTCTTTTCTTTT
Found at i:536680 original size:22 final size:23
Alignment explanation
Indices: 536625--536681 Score: 80
Period size: 22 Copynumber: 2.5 Consensus size: 23
536615 CTTTAGCTCT
*
536625 CTTTTTCTTTTCTTTTTCCTTTC
1 CTTTTTTTTTTCTTTTTCCTTTC
*
536648 CTTTTCTTTTTCTTTTT-CTTTC
1 CTTTTTTTTTTCTTTTTCCTTTC
*
536670 TTTTTTTTTTTC
1 CTTTTTTTTTTC
536682 CCCTCTGAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 15 0.50
23 15 0.50
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (23 bp):
CTTTTTTTTTTCTTTTTCCTTTC
Found at i:541607 original size:2 final size:2
Alignment explanation
Indices: 541600--541632 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
541590 TTTTCGTTTT
541600 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 T
541633 GTGAAAATGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:542434 original size:14 final size:16
Alignment explanation
Indices: 542408--542441 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
542398 ATTGCATGTT
542408 TAAATTAAAATTTAG-
1 TAAATTAAAATTTAGA
542423 TAAATT-AAATTTAGA
1 TAAATTAAAATTTAGA
542438 TAAA
1 TAAA
542442 ATTTAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (16 bp):
TAAATTAAAATTTAGA
Found at i:546798 original size:2 final size:2
Alignment explanation
Indices: 546791--546818 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
546781 CTCCATTGAA
546791 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
546819 CTTAAAATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:550258 original size:2 final size:2
Alignment explanation
Indices: 550251--550304 Score: 90
Period size: 2 Copynumber: 27.0 Consensus size: 2
550241 CCTTTTTGAA
* *
550251 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
550293 AT AT AT AT AT AT
1 AT AT AT AT AT AT
550305 CACAAAAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:567056 original size:9 final size:9
Alignment explanation
Indices: 567042--567088 Score: 51
Period size: 9 Copynumber: 5.0 Consensus size: 9
567032 GATTCTTTGA
567042 ATATTTTTT
1 ATATTTTTT
567051 ATATTTTTT
1 ATATTTTTT
567060 AT-TTTTAAATT
1 ATATTTT---TT
*
567071 ATAATTTTT
1 ATATTTTTT
567080 ATATTTTTT
1 ATATTTTTT
567089 TAAAAAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
8 4 0.12
9 21 0.66
11 4 0.12
12 3 0.09
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (9 bp):
ATATTTTTT
Found at i:568539 original size:14 final size:14
Alignment explanation
Indices: 568520--568551 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
568510 ATATTTAATT
568520 TAAATTTGGAGGCA
1 TAAATTTGGAGGCA
568534 TAAATTTGGAGGCA
1 TAAATTTGGAGGCA
568548 TAAA
1 TAAA
568552 CAGATAACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.41, C:0.06, G:0.25, T:0.28
Consensus pattern (14 bp):
TAAATTTGGAGGCA
Found at i:574745 original size:26 final size:23
Alignment explanation
Indices: 574689--574766 Score: 79
Period size: 22 Copynumber: 3.3 Consensus size: 23
574679 AAACAGGAAA
* *
574689 AATAAATAAATAATTATAAATGT
1 AATAAATAAAAAATTATAAATAT
*
574712 AA-ATATAAAAAATATATTAATATAT
1 AATAAATAAAAAAT-TA-TAA-ATAT
*
574737 AATAAAT-AATAATTATAAATAT
1 AATAAATAAAAAATTATAAATAT
574759 AATAAATA
1 AATAAATA
574767 TCTATAAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
22 20 0.44
23 7 0.16
24 5 0.11
25 10 0.22
26 3 0.07
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (23 bp):
AATAAATAAAAAATTATAAATAT
Found at i:574772 original size:19 final size:19
Alignment explanation
Indices: 574711--574774 Score: 67
Period size: 19 Copynumber: 3.2 Consensus size: 19
574701 ATTATAAATG
*
574711 TAAATATAAAAAATATAT-
1 TAAATATAATAAATATATA
574729 TAATATATAATAAATAATAATTA
1 TAA-ATATAATAAAT-AT-A-TA
*
574752 TAAATATAATAAATATCTA
1 TAAATATAATAAATATATA
574771 TAAA
1 TAAA
574775 AATAGACTGA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
18 3 0.08
19 16 0.41
20 2 0.05
21 3 0.08
22 12 0.31
23 3 0.08
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (19 bp):
TAAATATAATAAATATATA
Found at i:580353 original size:2 final size:2
Alignment explanation
Indices: 580348--580373 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
580338 ACACACACAC
580348 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
580374 TGCTGCATTA
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:585076 original size:20 final size:24
Alignment explanation
Indices: 585050--585102 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 24
585040 ACATTCGAGA
585050 ATAAATATTATTTAA-AAT-TAA-
1 ATAAATATTATTTAATAATATAAT
585071 AT-AATATT-TTTAATAATATAAT
1 ATAAATATTATTTAATAATATAAT
585093 ATAAATATTA
1 ATAAATATTA
585103 AATTAAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
19 5 0.19
20 9 0.33
21 5 0.19
22 2 0.07
23 6 0.22
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
ATAAATATTATTTAATAATATAAT
Found at i:585151 original size:21 final size:21
Alignment explanation
Indices: 585127--585192 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
585117 TTTATAAATA
*
585127 TAAAAAATATAATTATATTAT
1 TAAAATATATAATTATATTAT
*
585148 T-AAATTTAATAATT-TATTTAT
1 TAAAATAT-ATAATTATA-TTAT
585169 TAAAATAT-TAATTATA-TA-
1 TAAAATATATAATTATATTAT
585187 TAAAAT
1 TAAAAT
585193 TAAAAAAATC
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
18 6 0.16
19 2 0.05
20 11 0.29
21 14 0.37
22 5 0.13
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TAAAATATATAATTATATTAT
Found at i:585690 original size:3 final size:3
Alignment explanation
Indices: 585684--585720 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
585674 TTATTAAATC
585684 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
585721 CTTTTCCTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:588962 original size:2 final size:2
Alignment explanation
Indices: 588955--588984 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
588945 TGGTTTTTCA
588955 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
588985 GTATGCTTTT
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:590381 original size:3 final size:3
Alignment explanation
Indices: 590373--590404 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
590363 AATTTTCCTT
590373 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
590405 TTCCAAAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:593664 original size:34 final size:34
Alignment explanation
Indices: 593597--593812 Score: 283
Period size: 34 Copynumber: 6.4 Consensus size: 34
593587 CTCAATGGTG
* * *
593597 TGTTGATTAAAT-GGTGATTTAGTAGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * * *
593630 TGTTGATTAAATGGGTGATTTGGTGGTTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* *
593664 TGTTGACTAAAT-GAAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
*
593697 TGTTGATTAAATGGGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* *
593731 TGTTGATTAAATGGGTGATTTGGTGGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
593765 TGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
593799 TGTTGATTAAATGG
1 TGTTGATTAAATGG
593813 TGGTTTTTAC
Statistics
Matches: 160, Mismatches: 21, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
33 39 0.24
34 121 0.76
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:593778 original size:68 final size:67
Alignment explanation
Indices: 593597--593814 Score: 310
Period size: 67 Copynumber: 3.2 Consensus size: 67
593587 CTCAATGGTG
* * * * *
593597 TGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 TGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
593662 AT
66 AT
* ** * *
593664 TGTTGACTAAATGAAGATTTGGTAGCTTACCATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 TGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
593729 AT
66 AT
* * *
593731 TGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTTGC
1 TGTTGATTAAAT-GGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGC
593796 CAT
65 CAT
593799 TGTTGATTAAATGGTG
1 TGTTGATTAAATGGTG
593815 GTTTTTACCA
Statistics
Matches: 132, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
67 72 0.55
68 60 0.45
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (67 bp):
TGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
AT
Found at i:598295 original size:34 final size:34
Alignment explanation
Indices: 598226--598443 Score: 287
Period size: 34 Copynumber: 6.5 Consensus size: 34
598216 AAGTGGGAGA
* * *
598226 ATTGTTGATTAAAT-GGTGATTTAGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
598259 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
598293 ATTGTTGACTAAAT-GAAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
598326 ATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
598360 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
598394 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
598428 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
598444 TGGTTTTTAC
Statistics
Matches: 162, Mismatches: 21, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
33 41 0.25
34 121 0.75
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:598409 original size:68 final size:67
Alignment explanation
Indices: 598226--598445 Score: 314
Period size: 67 Copynumber: 3.3 Consensus size: 67
598216 AAGTGGGAGA
* * * * *
598226 ATTGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
598291 CC
66 CC
* ** * *
598293 ATTGTTGACTAAATGAAGATTTGGTAGCTTACCATTGTTGATTAAATGGGAAATTTGGTAGCTTA
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
598358 CC
66 CC
* * *
598360 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTT
1 ATTGTTGATTAAAT-GGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTT
598425 GCC
65 GCC
598428 ATTGTTGATTAAATGGTG
1 ATTGTTGATTAAATGGTG
598446 GTTTTTACCA
Statistics
Matches: 134, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
67 74 0.55
68 60 0.45
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (67 bp):
ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
CC
Found at i:601448 original size:2 final size:2
Alignment explanation
Indices: 601441--601471 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
601431 TATAAAAGTA
601441 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 A
601472 CACCTTTCGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:604325 original size:25 final size:26
Alignment explanation
Indices: 604291--604348 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 26
604281 AAAATTAAAA
*
604291 AATATATTAACATATA-AAATTTATTT
1 AATATATTAA-ATATATAAATTTAATT
*
604317 AATAT-TTAAATTTATAAATTTAATT
1 AATATATTAAATATATAAATTTAATT
*
604342 AAAATAT
1 AATATAT
604349 AATTTTGAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 4 0.15
25 17 0.63
26 6 0.22
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (26 bp):
AATATATTAAATATATAAATTTAATT
Found at i:613359 original size:68 final size:69
Alignment explanation
Indices: 613266--613403 Score: 208
Period size: 68 Copynumber: 2.0 Consensus size: 69
613256 TTTCCTGCTG
613266 GTCTTCGTATTTGATTGACCTAATTAACTTCAAAACCTATAATGTTAATATTAAACAG-AGTTAA
1 GTCTTCGTATTTGATTGACCTAATTAACTTCAAAACCTATAATGTTAATATTAAACAGAAGTTAA
613330 TTTT
66 TTTT
* ** *
613334 GTCTTCGTACTTT-ATTGGCCTAATTAACTTCAAAATTTATAATGTTAATATTAAATAGACAGTT
1 GTCTTCGTA-TTTGATTGACCTAATTAACTTCAAAACCTATAATGTTAATATTAAACAGA-AGTT
613398 AATTTT
64 AATTTT
613404 CCTTATTAAT
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
68 50 0.79
69 3 0.05
70 10 0.16
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (69 bp):
GTCTTCGTATTTGATTGACCTAATTAACTTCAAAACCTATAATGTTAATATTAAACAGAAGTTAA
TTTT
Found at i:625106 original size:3 final size:3
Alignment explanation
Indices: 625100--625145 Score: 65
Period size: 3 Copynumber: 15.0 Consensus size: 3
625090 ATCAACTTTC
* *
625100 TCT TCT TCT TGT TCT TCT TCG TCT TCT TCT TCT TCT TCT TCAT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC-T TCT
625146 CAGCTTCCCA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.02, C:0.30, G:0.04, T:0.63
Consensus pattern (3 bp):
TCT
Found at i:628228 original size:15 final size:15
Alignment explanation
Indices: 628202--628231 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
628192 TAATAAGCTA
628202 AATAATAATAATATT
1 AATAATAATAATATT
628217 AATAATAATAATATT
1 AATAATAATAATATT
628232 TCTTAAACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AATAATAATAATATT
Found at i:629608 original size:3 final size:3
Alignment explanation
Indices: 629600--629670 Score: 79
Period size: 3 Copynumber: 23.7 Consensus size: 3
629590 TGGAGGTTAC
* * * *
629600 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGC GGT GGG GGA GGA
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT
* * *
629648 GGT GCT GCT AGT GGT GGT GGT GG
1 GGT GGT GGT GGT GGT GGT GGT GG
629671 GAATGGATCG
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.04, C:0.04, G:0.65, T:0.27
Consensus pattern (3 bp):
GGT
Found at i:631147 original size:46 final size:46
Alignment explanation
Indices: 631095--631233 Score: 278
Period size: 46 Copynumber: 3.0 Consensus size: 46
631085 TGCTGTAGAC
631095 TTTGCCCTTGTTATCAAATATGAATCATTAGATGACCCTTTTTTAA
1 TTTGCCCTTGTTATCAAATATGAATCATTAGATGACCCTTTTTTAA
631141 TTTGCCCTTGTTATCAAATATGAATCATTAGATGACCCTTTTTTAA
1 TTTGCCCTTGTTATCAAATATGAATCATTAGATGACCCTTTTTTAA
631187 TTTGCCCTTGTTATCAAATATGAATCATTAGATGACCCTTTTTTAA
1 TTTGCCCTTGTTATCAAATATGAATCATTAGATGACCCTTTTTTAA
631233 T
1 T
631234 CTGAAAAAGA
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 93 1.00
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.44
Consensus pattern (46 bp):
TTTGCCCTTGTTATCAAATATGAATCATTAGATGACCCTTTTTTAA
Found at i:632875 original size:4 final size:4
Alignment explanation
Indices: 632866--632890 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
632856 ATAAGCAGAA
632866 TCAT TCAT TCAT TCAT TCAT TCAT T
1 TCAT TCAT TCAT TCAT TCAT TCAT T
632891 TAAACTCAGG
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:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (4 bp):
TCAT
Found at i:633315 original size:72 final size:72
Alignment explanation
Indices: 633196--633339 Score: 209
Period size: 72 Copynumber: 2.0 Consensus size: 72
633186 GACAAACTGT
* * *
633196 ACACTTTTGACTCGTGAACTCTGCTACCAGCTCTGCTGATGGTAAAAGGAAATGATTGAATTTAA
1 ACACTTTTGACTCATGAACTCTGCTACAAGCTCTGCTGAAGGTAAAAGGAAATGATTGAATTTAA
633261 AGGGGAA
66 AGGGGAA
* * * *
633268 ACACTTTTGACTCATGAACTTTGCTGCAAGTTCTGCTGACAGG-AAAAGGTAATGATTGAATTTA
1 ACACTTTTGACTCATGAACTCTGCTACAAGCTCTGCTGA-AGGTAAAAGGAAATGATTGAATTTA
633332 AAGGGGAA
65 AAGGGGAA
633340 TCAAGAGAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
72 62 0.97
73 2 0.03
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (72 bp):
ACACTTTTGACTCATGAACTCTGCTACAAGCTCTGCTGAAGGTAAAAGGAAATGATTGAATTTAA
AGGGGAA
Found at i:639736 original size:2 final size:2
Alignment explanation
Indices: 639729--639761 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
639719 TTTTAATCTT
*
639729 TC TC TC TC TC TC TC TC TC TC -C TC TC TC GC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
639762 AAATTTTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.00, C:0.52, G:0.03, T:0.45
Consensus pattern (2 bp):
TC
Found at i:644575 original size:63 final size:64
Alignment explanation
Indices: 644464--644692 Score: 316
Period size: 64 Copynumber: 3.6 Consensus size: 64
644454 CATCTTCAAC
* * * *
644464 GCCCCACTATGTATCTATGAACAAGGGCTTTTATTTTTCAGAAGTATTTTGGGTATTGAGCTAA
1 GCCCAACTCTGTATCTATGAACAAGGGCTTTTATTTTTTACAAGTATTTTGGGTATTGAGCTAA
* * *
644528 GCCCAACTCTGTATC-ATGAACAAGCGCTTTTATTTTTTACAAATATTTTGGGTTTTGAGCTAA
1 GCCCAACTCTGTATCTATGAACAAGGGCTTTTATTTTTTACAAGTATTTTGGGTATTGAGCTAA
*
644591 GCCCAACTCTGAATCTATGAACAAGGGCTTTTATTTTTTACAAGTATTTTGGGTATTGAGCTAA
1 GCCCAACTCTGTATCTATGAACAAGGGCTTTTATTTTTTACAAGTATTTTGGGTATTGAGCTAA
* * * * * * *
644655 ACCTAACTTTGCATATATGAACATGAGCTTTTATTTTT
1 GCCCAACTCTGTATCTATGAACAAGGGCTTTTATTTTT
644693 CGCAAGCATT
Statistics
Matches: 146, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
63 57 0.39
64 89 0.61
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (64 bp):
GCCCAACTCTGTATCTATGAACAAGGGCTTTTATTTTTTACAAGTATTTTGGGTATTGAGCTAA
Found at i:644855 original size:62 final size:61
Alignment explanation
Indices: 644766--644881 Score: 155
Period size: 59 Copynumber: 1.9 Consensus size: 61
644756 AGCTAGCCCA
* ** *
644766 GCTGTGCATCTATGAACATGGGCTTTTATTATTCACAAGTATTGTGGG-ATTGAGCTTTCTCT
1 GCTGTGCATATATGAACATGCAC-TTT-TTATTCACAAGCATTGTGGGCATTGAGCTTTCTCT
*
644828 GCTGTGCATATAT-AACATGCACTTTTTATTCACAAGCATTTTGGGCATTGAGCT
1 GCTGTGCATATATGAACATGCACTTTTTATTCACAAGCATTGTGGGCATTGAGCT
644882 AACCTAGCTG
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
59 18 0.38
60 11 0.23
61 7 0.15
62 12 0.25
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.39
Consensus pattern (61 bp):
GCTGTGCATATATGAACATGCACTTTTTATTCACAAGCATTGTGGGCATTGAGCTTTCTCT
Found at i:645054 original size:63 final size:64
Alignment explanation
Indices: 644734--645148 Score: 218
Period size: 63 Copynumber: 6.7 Consensus size: 64
644724 CATGCAAGAA
* * * *
644734 TTTCACAAGCATTTT-GGTATTTAGCTAGCCCAGCTGTGCATCTA-TGAACATGGGCTTTTATT
1 TTTCACAAGCATTTTAGGTATTGAGCTAGCCCATCTATGCATCTACTGAACATGAGCTTTTATT
* * * * ** * * *
644796 ATTCACAAGTATTGT-GGGATTGAGCTTTCTC-TGCTGTGCATATA-T-AACATGCA-C-TTT-T
1 TTTCACAAGCATTTTAGGTATTGAGCTAGCCCAT-CTATGCATCTACTGAACATG-AGCTTTTAT
644854 T
64 T
* * * * * * * * * * * * *
644855 ATTCACAAGCATTTTGGGCATTGAGCTAACCTAGC--TGTATCTTC-GAAAACGGGTTTTTGTT
1 TTTCACAAGCATTTTAGGTATTGAGCTAGCCCATCTATGCATCTACTGAACATGAGCTTTTATT
* * * * * * * * *
644916 TTTCAGATGCA-TTTCGGCTGTTGA-CGTA-CCCAACTATGCATCT-CTAAACATGGGTTTTTCT
1 TTTCACAAGCATTTTAGG-TATTGAGC-TAGCCCATCTATGCATCTACTGAACATGAGCTTTTAT
644977 T
64 T
* ** * *
644978 ATTCGTAAGCATTTAAGGTATTGAGCTAGCCCATCTCTGCATCTAC-GAACATGAGCTTTTATT
1 TTTCACAAGCATTTTAGGTATTGAGCTAGCCCATCTATGCATCTACTGAACATGAGCTTTTATT
* * * ** * *
645041 TTTCACAATCATTTTGGGTTTTGAGGAAGCCCATTTGTGCATCT-CTGAACATGAGCTTTTATT
1 TTTCACAAGCATTTTAGGTATTGAGCTAGCCCATCTATGCATCTACTGAACATGAGCTTTTATT
* * *
645104 TTTCACAAGCATTTTAGGTACTGAGCTAGCTCAACTATGCATCTA
1 TTTCACAAGCATTTTAGGTATTGAGCTAGCCCATCTATGCATCTA
645149 TGGACTTGGT
Statistics
Matches: 260, Mismatches: 73, Indels: 38
0.70 0.20 0.10
Matches are distributed among these distances:
58 5 0.02
59 19 0.07
60 28 0.11
61 24 0.09
62 68 0.26
63 115 0.44
64 1 0.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.38
Consensus pattern (64 bp):
TTTCACAAGCATTTTAGGTATTGAGCTAGCCCATCTATGCATCTACTGAACATGAGCTTTTATT
Found at i:646309 original size:62 final size:62
Alignment explanation
Indices: 646157--646559 Score: 304
Period size: 62 Copynumber: 6.5 Consensus size: 62
646147 TTCATTATCG
* * * * * * ** **
646157 ACATGGGCTTCTATTATTCAAAAGCA--TTGGTTATTGGGTTAGCCCAGCTATGTTTCTAACA
1 ACATGGGCTTTTATTTTTCACAAGCATTTTGGATATTGAGCTAGCCCAGC-ATGCATCTATGA
* * * * * *
646218 ACATGGGCTTTTATTTATCACAAGTATTTTGGTTATTGTGCAAGCCCATCATGCATCTATGA
1 ACATGGGCTTTTATTTTTCACAAGCATTTTGGATATTGAGCTAGCCCAGCATGCATCTATGA
* * * * * *
646280 ACAAGCGCTGTTATTTTTCACAAGCATTTTGGATATTTGAGCTAGTCCACCATGCATTTATGA
1 ACATGGGCTTTTATTTTTCACAAGCATTTTGGATA-TTGAGCTAGCCCAGCATGCATCTATGA
* * * * * *
646343 ACATGGGATTTTATTATTCAGAAGCA-TTTGGGTTTTCG-GCTAGCCCATGTATGCATC-ATTG-
1 ACATGGGCTTTTATTTTTCACAAGCATTTTGGATATT-GAGCTAGCCCA-GCATGCATCTA-TGA
* * * ** *
646404 ACATGGGCTCATT-TCTTTCACAAGCAGTTTGGATATTGAGCTAGATCAGCTATGCATCTTTGA
1 ACATGGGCT-TTTATTTTTCACAAGCATTTTGGATATTGAGCTAGCCCAGC-ATGCATCTATGA
* *
646467 ACAT-GGCTTTTATTTTTCATAAGCATTTT-GAGTATTGAGCTAGCCCAGCTTTGCATCTATGA
1 ACATGGGCTTTTATTTTTCACAAGCATTTTGGA-TATTGAGCTAGCCCAGC-ATGCATCTATGA
* * *
646529 GCACGAGCTTTTATTTTT-ACAAGCATTTTGG
1 ACATGGGCTTTTATTTTTCACAAGCATTTTGG
646560 GCATGCCTAA
Statistics
Matches: 267, Mismatches: 59, Indels: 30
0.75 0.17 0.08
Matches are distributed among these distances:
61 56 0.21
62 134 0.50
63 77 0.29
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38
Consensus pattern (62 bp):
ACATGGGCTTTTATTTTTCACAAGCATTTTGGATATTGAGCTAGCCCAGCATGCATCTATGA
Found at i:648858 original size:17 final size:16
Alignment explanation
Indices: 648828--648859 Score: 55
Period size: 16 Copynumber: 1.9 Consensus size: 16
648818 TACTAATGGG
648828 TTTTTCTTTTTTCTTC
1 TTTTTCTTTTTTCTTC
648844 TTTTTCTTTTCTTCTT
1 TTTTTCTTTT-TTCTT
648860 TAGCTATCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTTCTTTTTTCTTC
Found at i:652345 original size:322 final size:322
Alignment explanation
Indices: 651760--652393 Score: 1268
Period size: 322 Copynumber: 2.0 Consensus size: 322
651750 CTGGGTTGCT
651760 TATTCCTGCATAATTAAGCATTAAGTGGCCTTCAGGTACGCCGTACTGCAGCAATGAATTCATGA
1 TATTCCTGCATAATTAAGCATTAAGTGGCCTTCAGGTACGCCGTACTGCAGCAATGAATTCATGA
651825 TCACTTGTAATCTAAGGGTCAGTACTGGAGATAATTAAAATTGAGTCTAAAAACAAAATTAGAGA
66 TCACTTGTAATCTAAGGGTCAGTACTGGAGATAATTAAAATTGAGTCTAAAAACAAAATTAGAGA
651890 ATTCAATGATGACATGAAGACATCATCTCTCTTAAAACTGATCACTTTGAAGCTTTAAAATGGAT
131 ATTCAATGATGACATGAAGACATCATCTCTCTTAAAACTGATCACTTTGAAGCTTTAAAATGGAT
651955 TAACAAAAGTAGCCAGCTCATTACAGCTTATGTTATTCGCTTCTTCTATGGCATATAATCAACAG
196 TAACAAAAGTAGCCAGCTCATTACAGCTTATGTTATTCGCTTCTTCTATGGCATATAATCAACAG
652020 CACCTGACTATAACATCTAAGTTCTCATTTCTCCGATTCATTCCACAAAACATTAAGTGGCC
261 CACCTGACTATAACATCTAAGTTCTCATTTCTCCGATTCATTCCACAAAACATTAAGTGGCC
652082 TATTCCTGCATAATTAAGCATTAAGTGGCCTTCAGGTACGCCGTACTGCAGCAATGAATTCATGA
1 TATTCCTGCATAATTAAGCATTAAGTGGCCTTCAGGTACGCCGTACTGCAGCAATGAATTCATGA
652147 TCACTTGTAATCTAAGGGTCAGTACTGGAGATAATTAAAATTGAGTCTAAAAACAAAATTAGAGA
66 TCACTTGTAATCTAAGGGTCAGTACTGGAGATAATTAAAATTGAGTCTAAAAACAAAATTAGAGA
652212 ATTCAATGATGACATGAAGACATCATCTCTCTTAAAACTGATCACTTTGAAGCTTTAAAATGGAT
131 ATTCAATGATGACATGAAGACATCATCTCTCTTAAAACTGATCACTTTGAAGCTTTAAAATGGAT
652277 TAACAAAAGTAGCCAGCTCATTACAGCTTATGTTATTCGCTTCTTCTATGGCATATAATCAACAG
196 TAACAAAAGTAGCCAGCTCATTACAGCTTATGTTATTCGCTTCTTCTATGGCATATAATCAACAG
652342 CACCTGACTATAACATCTAAGTTCTCATTTCTCCGATTCATTCCACAAAACA
261 CACCTGACTATAACATCTAAGTTCTCATTTCTCCGATTCATTCCACAAAACA
652394 CCAATGGCGG
Statistics
Matches: 312, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
322 312 1.00
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (322 bp):
TATTCCTGCATAATTAAGCATTAAGTGGCCTTCAGGTACGCCGTACTGCAGCAATGAATTCATGA
TCACTTGTAATCTAAGGGTCAGTACTGGAGATAATTAAAATTGAGTCTAAAAACAAAATTAGAGA
ATTCAATGATGACATGAAGACATCATCTCTCTTAAAACTGATCACTTTGAAGCTTTAAAATGGAT
TAACAAAAGTAGCCAGCTCATTACAGCTTATGTTATTCGCTTCTTCTATGGCATATAATCAACAG
CACCTGACTATAACATCTAAGTTCTCATTTCTCCGATTCATTCCACAAAACATTAAGTGGCC
Found at i:656260 original size:24 final size:23
Alignment explanation
Indices: 656229--656277 Score: 89
Period size: 24 Copynumber: 2.1 Consensus size: 23
656219 TCACTTTGAC
656229 TTATTGTTCTTCTTGCCACAAGT
1 TTATTGTTCTTCTTGCCACAAGT
656252 TTATATGTTCTTCTTGCCACAAGT
1 TTAT-TGTTCTTCTTGCCACAAGT
656276 TT
1 TT
656278 TAGTTAATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 4 0.16
24 21 0.84
ACGTcount: A:0.18, C:0.20, G:0.12, T:0.49
Consensus pattern (23 bp):
TTATTGTTCTTCTTGCCACAAGT
Found at i:658722 original size:6 final size:6
Alignment explanation
Indices: 658713--658746 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
658703 CAAGGCTAAG
*
658713 GCTCAT GCTCAT GCTCAT GCTCAT GCTTAT GCTC
1 GCTCAT GCTCAT GCTCAT GCTCAT GCTCAT GCTC
658747 GAATCCAGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.15, C:0.32, G:0.18, T:0.35
Consensus pattern (6 bp):
GCTCAT
Found at i:658881 original size:14 final size:14
Alignment explanation
Indices: 658862--658888 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
658852 TACTCATTTT
658862 AAATATAAATATAA
1 AAATATAAATATAA
658876 AAATATAAATATA
1 AAATATAAATATA
658889 TTTAATTTTA
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:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AAATATAAATATAA
Found at i:658967 original size:15 final size:14
Alignment explanation
Indices: 658947--658985 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
658937 TATTTATATT
658947 TAAAAATATCTTAAA
1 TAAAAATAT-TTAAA
658962 TAAAAATA-TTAAA
1 TAAAAATATTTAAA
*
658975 TATAAATATTT
1 TAAAAATATTT
658986 TAAAAAATCG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 12 0.55
14 2 0.09
15 8 0.36
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (14 bp):
TAAAAATATTTAAA
Found at i:659539 original size:22 final size:21
Alignment explanation
Indices: 659503--659545 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
659493 TATAAATACA
*
659503 TTTAATTTTTTAAAAAATTAT
1 TTTAATTATTTAAAAAATTAT
*
659524 TTTAATGTATTTAAAATATTAT
1 TTTAAT-TATTTAAAAAATTAT
659546 ATCTATACAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
TTTAATTATTTAAAAAATTAT
Found at i:660663 original size:2 final size:2
Alignment explanation
Indices: 660646--660684 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
660636 ATAGCCACTA
*
660646 AT AT AT -T AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
660685 GTTATTTGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:662939 original size:22 final size:22
Alignment explanation
Indices: 662883--662930 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
662873 AATATTTTTC
*
662883 TAAATATTAATATTTATAATAAT
1 TAAATATT-ATATTTATAATAAA
662906 TAAATATTATATTTATATATAAA
1 TAAATATTATATTTATA-ATAAA
662929 TA
1 TA
662931 TAAATATATG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TAAATATTATATTTATAATAAA
Found at i:663513 original size:18 final size:19
Alignment explanation
Indices: 663487--663523 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
663477 TTTTTCATAA
*
663487 AATTTTTAG-ATTTTATTT
1 AATTGTTAGTATTTTATTT
663505 AATTGTTAGTATTTTATTT
1 AATTGTTAGTATTTTATTT
663524 TTATTTTAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (19 bp):
AATTGTTAGTATTTTATTT
Found at i:663532 original size:19 final size:17
Alignment explanation
Indices: 663490--663533 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 17
663480 TTCATAAAAT
663490 TTTTAGATTTTATTTAA
1 TTTTAGATTTTATTTAA
*
663507 TTGTTAGTATTTTATTTTTA
1 TT-TTAG-ATTTTA-TTTAA
663527 TTTTAGA
1 TTTTAGA
663534 AAAAAATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
17 2 0.09
18 5 0.22
19 10 0.43
20 6 0.26
ACGTcount: A:0.25, C:0.00, G:0.09, T:0.66
Consensus pattern (17 bp):
TTTTAGATTTTATTTAA
Found at i:670025 original size:15 final size:15
Alignment explanation
Indices: 669993--670026 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
669983 CTTAAATATT
* *
669993 ATTTTTTTAATAATA
1 ATTTTTTTAAAAAAA
670008 ATTTTTTTAAAAAAA
1 ATTTTTTTAAAAAAA
670023 ATTT
1 ATTT
670027 ACTGTTTATA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTTTTTTAAAAAAA
Found at i:671051 original size:20 final size:20
Alignment explanation
Indices: 671026--671068 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
671016 CATTAATTAA
671026 AAAAAAATATTGATCGATAT
1 AAAAAAATATTGATCGATAT
671046 AAAAAAATATTGATCGATAT
1 AAAAAAATATTGATCGATAT
671066 AAA
1 AAA
671069 TTTTATCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.58, C:0.05, G:0.09, T:0.28
Consensus pattern (20 bp):
AAAAAAATATTGATCGATAT
Found at i:674279 original size:2 final size:2
Alignment explanation
Indices: 674272--674306 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
674262 TTTATGTAGT
674272 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 T
674307 TAATTCTTTT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:674590 original size:2 final size:2
Alignment explanation
Indices: 674585--674615 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
674575 TAATTGTGTG
*
674585 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
674616 ATAAAACGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:675264 original size:2 final size:2
Alignment explanation
Indices: 675257--675302 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
675247 ATTTTGGAAG
675257 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
675299 CT CT
1 CT CT
675303 ATGTGTATGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:676456 original size:2 final size:2
Alignment explanation
Indices: 676449--676475 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
676439 CTCATATCCC
676449 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
676476 CTAAAGGCCA
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:677513 original size:188 final size:188
Alignment explanation
Indices: 677196--677535 Score: 680
Period size: 188 Copynumber: 1.8 Consensus size: 188
677186 GAATCTGAGA
677196 TTAAAAAGAAGCAATAAGAAGCAAAGCGACAAGGCAGAAACAGACACAAGAAATAATAACAAGAT
1 TTAAAAAGAAGCAATAAGAAGCAAAGCGACAAGGCAGAAACAGACACAAGAAATAATAACAAGAT
677261 TGACCACTTCAAGGGGGTACTCATAAAAGTTAAAAGATAATCACACAAAACTCCCATCCGTCAAA
66 TGACCACTTCAAGGGGGTACTCATAAAAGTTAAAAGATAATCACACAAAACTCCCATCCGTCAAA
677326 TTCTCACACCTTGCATTATATGCATTATCTGGAAATGGGCAATATGGGAGCCCTTTCT
131 TTCTCACACCTTGCATTATATGCATTATCTGGAAATGGGCAATATGGGAGCCCTTTCT
677384 TTAAAAAGAAGCAATAAGAAGCAAAGCGACAAGGCAGAAACAGACACAAGAAATAATAACAAGAT
1 TTAAAAAGAAGCAATAAGAAGCAAAGCGACAAGGCAGAAACAGACACAAGAAATAATAACAAGAT
677449 TGACCACTTCAAGGGGGTACTCATAAAAGTTAAAAGATAATCACACAAAACTCCCATCCGTCAAA
66 TGACCACTTCAAGGGGGTACTCATAAAAGTTAAAAGATAATCACACAAAACTCCCATCCGTCAAA
677514 TTCTCACACCTTGCATTATATG
131 TTCTCACACCTTGCATTATATG
677536 GAAATGGGCA
Statistics
Matches: 152, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
188 152 1.00
ACGTcount: A:0.44, C:0.20, G:0.16, T:0.20
Consensus pattern (188 bp):
TTAAAAAGAAGCAATAAGAAGCAAAGCGACAAGGCAGAAACAGACACAAGAAATAATAACAAGAT
TGACCACTTCAAGGGGGTACTCATAAAAGTTAAAAGATAATCACACAAAACTCCCATCCGTCAAA
TTCTCACACCTTGCATTATATGCATTATCTGGAAATGGGCAATATGGGAGCCCTTTCT
Found at i:683023 original size:2 final size:2
Alignment explanation
Indices: 683016--683043 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
683006 GGTAGATAAT
683016 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
683044 TATATATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:683048 original size:2 final size:2
Alignment explanation
Indices: 683043--683069 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
683033 ACACACACAC
683043 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
683070 GTTGGTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:684875 original size:20 final size:21
Alignment explanation
Indices: 684842--684881 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
684832 TAAGGATTAT
*
684842 ATTTTTTTTAATTTTTTAATG
1 ATTTTATTTAATTTTTTAATG
684863 ATTTTATTT-ATTTTTTAAT
1 ATTTTATTTAATTTTTTAAT
684882 TAATACTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (21 bp):
ATTTTATTTAATTTTTTAATG
Found at i:685280 original size:21 final size:20
Alignment explanation
Indices: 685243--685304 Score: 71
Period size: 19 Copynumber: 3.3 Consensus size: 20
685233 AATTTTATTT
685243 ATTTATTTTTA--ATTTAAAA
1 ATTTATTTTTATTATTT-AAA
685262 ATTTATTTTTATTATTTAAA
1 ATTTATTTTTATTATTTAAA
*
685282 A-TTA-TTTTATTA-TTAAT
1 ATTTATTTTTATTATTTAAA
685299 ATTTAT
1 ATTTAT
685305 ATATTTTAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
17 5 0.13
18 11 0.29
19 14 0.37
20 4 0.11
21 4 0.11
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
ATTTATTTTTATTATTTAAA
Found at i:685284 original size:28 final size:28
Alignment explanation
Indices: 685230--685284 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
685220 TTAAATAATA
**
685230 AAAAATTTTATTTATTTATTTTTAATTT
1 AAAAATTTTATTTATTTATTTAAAATTT
*
685258 AAAAA-TTTATTTTTATTATTTAAAATT
1 AAAAATTTTATTTAT-TTATTTAAAATT
685285 ATTTTATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (28 bp):
AAAAATTTTATTTATTTATTTAAAATTT
Found at i:685289 original size:18 final size:20
Alignment explanation
Indices: 685243--685295 Score: 67
Period size: 18 Copynumber: 2.8 Consensus size: 20
685233 AATTTTATTT
*
685243 ATTTATTTT-TAATTTAAAA
1 ATTTATTTTATTATTTAAAA
685262 ATTTATTTTTATTATTT-AAA
1 ATTTA-TTTTATTATTTAAAA
685282 A-TTATTTTATTATT
1 ATTTATTTTATTATT
685296 AATATTTATA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
18 10 0.32
19 8 0.26
20 8 0.26
21 5 0.16
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
ATTTATTTTATTATTTAAAA
Found at i:685304 original size:18 final size:18
Alignment explanation
Indices: 685260--685304 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
685250 TTTAATTTAA
685260 AAATTTATTTTTATTATTT
1 AAATTTA-TTTTATTATTT
*
685279 AAAATTATTTTATTA-TT
1 AAATTTATTTTATTATTT
685296 AATATTTAT
1 AA-ATTTAT
685305 ATATTTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 4 0.17
18 13 0.57
19 6 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
AAATTTATTTTATTATTT
Found at i:687220 original size:6 final size:6
Alignment explanation
Indices: 687209--687236 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
687199 TCAAATTTTA
687209 TTTAAT TTTAAT TTTAAT TTTAAT TTTA
1 TTTAAT TTTAAT TTTAAT TTTAAT TTTA
687237 TTAAATAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTAAT
Found at i:687403 original size:23 final size:24
Alignment explanation
Indices: 687363--687413 Score: 86
Period size: 23 Copynumber: 2.2 Consensus size: 24
687353 ATTTGTAATT
687363 TTTTATATAAAAAATCTAAATTTA
1 TTTTATATAAAAAATCTAAATTTA
*
687387 TTTTATAT-CAAAATCTAAATTTA
1 TTTTATATAAAAAATCTAAATTTA
687410 TTTT
1 TTTT
687414 GATTTAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 18 0.69
24 8 0.31
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (24 bp):
TTTTATATAAAAAATCTAAATTTA
Found at i:687815 original size:3 final size:3
Alignment explanation
Indices: 687809--687843 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
687799 TAAAAAAAAA
687809 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
687844 GGATAATGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:688312 original size:40 final size:46
Alignment explanation
Indices: 688261--688344 Score: 108
Period size: 45 Copynumber: 2.0 Consensus size: 46
688251 AATATTTTAT
688261 ATTTATAAAAAT-TTGATA-AGTTA-ATA-AT-TTATATTATATAA
1 ATTTATAAAAATATTGATATAGTTATATATATATTATATTATATAA
* *
688302 ATTT-TAAAAATATTTATATATTTATATATATATTATATTATAT
1 ATTTATAAAAATATTGATATAGTTATATATATATTATATTATAT
688345 TGTATATTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
40 7 0.19
41 9 0.25
42 4 0.11
43 3 0.08
44 2 0.06
45 11 0.31
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (46 bp):
ATTTATAAAAATATTGATATAGTTATATATATATTATATTATATAA
Found at i:688340 original size:5 final size:5
Alignment explanation
Indices: 688315--688391 Score: 68
Period size: 5 Copynumber: 14.8 Consensus size: 5
688305 TTAAAAATAT
688315 TTATA -TAT- TTATA TATATA TTATA TTATA TTGTATA TTATA TTATA
1 TTATA TTATA TTATA T-TATA TTATA TTATA -T-TATA TTATA TTATA
* * *
688361 TTTTAA TTATT TTTTA TTATA TTTATA TTAT
1 TTAT-A TTATA TTATA TTATA -TTATA TTAT
688392 CAAGTATTCA
Statistics
Matches: 59, Mismatches: 6, Indels: 14
0.75 0.08 0.18
Matches are distributed among these distances:
4 6 0.10
5 33 0.56
6 16 0.27
7 4 0.07
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (5 bp):
TTATA
Found at i:688362 original size:10 final size:10
Alignment explanation
Indices: 688315--688391 Score: 68
Period size: 11 Copynumber: 7.4 Consensus size: 10
688305 TTAAAAATAT
688315 TTATA-TAT-
1 TTATATTATA
688323 TTATATATATA
1 TTATAT-TATA
688334 TTATATTATA
1 TTATATTATA
688344 TTGTATATTATA
1 -T-TATATTATA
*
688356 TTATATTTTAA
1 TTATATTAT-A
* *
688367 TTATTTTTTA
1 TTATATTATA
688377 TTATATTTATA
1 TTATA-TTATA
688388 TTAT
1 TTAT
688392 CAAGTATTCA
Statistics
Matches: 58, Mismatches: 4, Indels: 11
0.79 0.05 0.15
Matches are distributed among these distances:
8 5 0.09
10 19 0.33
11 25 0.43
12 9 0.16
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (10 bp):
TTATATTATA
Found at i:689520 original size:24 final size:24
Alignment explanation
Indices: 689493--689542 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
689483 AAGATATATT
689493 TAATATATA-AATTATTTATATTTA
1 TAATATATATAATTA-TTATATTTA
* *
689517 TAATTTATATTATTATTATATTTA
1 TAATATATATAATTATTATATTTA
689541 TA
1 TA
689543 TAATTAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
TAATATATATAATTATTATATTTA
Found at i:689522 original size:13 final size:13
Alignment explanation
Indices: 689506--689542 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
689496 TATATAAATT
689506 ATTTATATTTATA
1 ATTTATATTTATA
*
689519 ATTTATA-TTATT
1 ATTTATATTTATA
689531 A-TTATATTTATA
1 ATTTATATTTATA
689543 TAATTAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
11 5 0.24
12 9 0.43
13 7 0.33
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
ATTTATATTTATA
Found at i:689542 original size:17 final size:18
Alignment explanation
Indices: 689514--689548 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
689504 TTATTTATAT
*
689514 TTATAATTTATATTATTA
1 TTATAATTTATATAATTA
689532 TTAT-ATTTATATAATTA
1 TTATAATTTATATAATTA
689549 ATAATAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTATAATTTATATAATTA
Found at i:690495 original size:15 final size:14
Alignment explanation
Indices: 690463--690529 Score: 59
Period size: 15 Copynumber: 4.6 Consensus size: 14
690453 TATTAATTAA
690463 ATTACTTTATCAATAT
1 ATTA-TTTAT-AATAT
690479 ATTATTTATAATAAT
1 ATTATTTATAAT-AT
690494 ATTATATT-TAATAT
1 ATTAT-TTATAATAT
*
690508 ATTAATTAATAAT-T
1 ATT-ATTTATAATAT
690522 -TTATTTAT
1 ATTATTTAT
690530 TTTTTTTAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
12 5 0.11
13 2 0.04
14 10 0.22
15 22 0.49
16 6 0.13
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (14 bp):
ATTATTTATAATAT
Found at i:690507 original size:27 final size:25
Alignment explanation
Indices: 690451--690528 Score: 68
Period size: 25 Copynumber: 3.0 Consensus size: 25
690441 AAAATATTTT
* * *
690451 TATATTAATTAAATTACTTTA-TCAA
1 TATATTAATT-AATAATTTTATTTAA
*
690476 TATATTATTTATAATAATATTATATTTAA
1 TATATTA-AT-TAATAAT-TT-TATTTAA
690505 TATATTAATTAATAATTTTATTTA
1 TATATTAATTAATAATTTTATTTA
690529 TTTTTTTTAA
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
25 13 0.30
26 7 0.16
27 10 0.23
28 3 0.07
29 10 0.23
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (25 bp):
TATATTAATTAATAATTTTATTTAA
Found at i:691274 original size:7 final size:7
Alignment explanation
Indices: 691264--691331 Score: 56
Period size: 7 Copynumber: 10.1 Consensus size: 7
691254 ATGATATAAT
691264 TATAAAA
1 TATAAAA
691271 TAT-AAA
1 TATAAAA
*
691277 TATAATA
1 TATAAAA
691284 TA-AAAA
1 TATAAAA
*
691290 T-TAAGA
1 TATAAAA
*
691296 T-T-TAA
1 TATAAAA
691301 TATAAAA
1 TATAAAA
691308 TATAAAA
1 TATAAAA
691315 TATAAATA
1 TATAAA-A
691323 TATTAAAA
1 TA-TAAAA
691331 T
1 T
691332 TGTTATAATA
Statistics
Matches: 49, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
5 2 0.04
6 16 0.33
7 22 0.45
8 5 0.10
9 4 0.08
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.35
Consensus pattern (7 bp):
TATAAAA
Found at i:691281 original size:19 final size:18
Alignment explanation
Indices: 691242--691324 Score: 80
Period size: 19 Copynumber: 4.4 Consensus size: 18
691232 GTTAAATATG
* *
691242 ATAATATTAAATAT-GAT
1 ATAATATAAAATATAAAT
691259 ATAATTATAAAATATAAAT
1 ATAA-TATAAAATATAAAT
691278 ATAATATAAAA-ATTAAGAT
1 ATAATATAAAATA-TAA-AT
*
691297 TTAATATAAAATATAAAAT
1 ATAATATAAAATAT-AAAT
691316 ATAAATATA
1 AT-AATATA
691325 TTAAAATTGT
Statistics
Matches: 55, Mismatches: 4, Indels: 11
0.79 0.06 0.16
Matches are distributed among these distances:
17 5 0.09
18 19 0.35
19 22 0.40
20 9 0.16
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (18 bp):
ATAATATAAAATATAAAT
Found at i:691389 original size:9 final size:9
Alignment explanation
Indices: 691351--691392 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
691341 ATTAATTATT
*
691351 AATATATTA
1 AATATTTTA
691360 AA-ATTTATA
1 AATATTT-TA
*
691369 AAAATTTTA
1 AATATTTTA
691378 AATATTTTA
1 AATATTTTA
691387 AATATT
1 AATATT
691393 ATTATAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
8 3 0.10
9 22 0.76
10 4 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
AATATTTTA
Found at i:699507 original size:56 final size:56
Alignment explanation
Indices: 699416--699531 Score: 205
Period size: 56 Copynumber: 2.1 Consensus size: 56
699406 AAGCTAACTA
* *
699416 CTATTGCATATTAATTGCCCTGCATTTTCCTTTTCTAAATATATATTTTGGAGAAT
1 CTATTGCATATTAATTGCCCTGCATTTTCCGTTTCTAAACATATATTTTGGAGAAT
*
699472 CTATTGCATATTAATTGCCCTGCATTTTCCGTTTCTAAACATATATTTTGGAGCAT
1 CTATTGCATATTAATTGCCCTGCATTTTCCGTTTCTAAACATATATTTTGGAGAAT
699528 CTAT
1 CTAT
699532 ACGATAATGA
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.26, C:0.18, G:0.11, T:0.45
Consensus pattern (56 bp):
CTATTGCATATTAATTGCCCTGCATTTTCCGTTTCTAAACATATATTTTGGAGAAT
Found at i:701217 original size:2 final size:2
Alignment explanation
Indices: 701210--701236 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
701200 CACCAAAAGA
701210 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
701237 ACAATTGACG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:707093 original size:2 final size:2
Alignment explanation
Indices: 707086--707123 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
707076 AACAAAAACA
*
707086 AT AT AT AT AT AT AT AT AT AT -T AT AT AT GT 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
707124 CATACATACA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:707111 original size:17 final size:17
Alignment explanation
Indices: 707089--707122 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
707079 AAAAACAATA
707089 TATATATATATATATAT
1 TATATATATATATATAT
*
707106 TATATATGTATATATAT
1 TATATATATATATATAT
707123 ACATACATAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
TATATATATATATATAT
Found at i:707111 original size:19 final size:19
Alignment explanation
Indices: 707087--707123 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
707077 ACAAAAACAA
707087 TATATATATATATATATAT
1 TATATATATATATATATAT
*
707106 TATATATGTATATATATA
1 TATATATATATATATATA
707124 CATACATACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (19 bp):
TATATATATATATATATAT
Found at i:708099 original size:3 final size:3
Alignment explanation
Indices: 708091--708117 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
708081 TGAAAGAACT
708091 TGC TGC TGC TGC TGC TGC TGC TGC TGC
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC
708118 AAGGGCTTCC
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:0.00, C:0.33, G:0.33, T:0.33
Consensus pattern (3 bp):
TGC
Found at i:714289 original size:14 final size:14
Alignment explanation
Indices: 714270--714296 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
714260 TAAAACGAAC
714270 ATCCCAAACCAAAT
1 ATCCCAAACCAAAT
714284 ATCCCAAACCAAA
1 ATCCCAAACCAAA
714297 AAAAATCCTC
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:0.52, C:0.37, G:0.00, T:0.11
Consensus pattern (14 bp):
ATCCCAAACCAAAT
Found at i:714503 original size:19 final size:18
Alignment explanation
Indices: 714474--714513 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
714464 CCCATATCCC
714474 AAACAAAAATTAAGGAAAAA
1 AAACAAAAATTAA--AAAAA
714494 AAAC-AAAATTAAAAAAA
1 AAACAAAAATTAAAAAAA
714511 AAA
1 AAA
714514 TAGAAAACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 8 0.40
19 8 0.40
20 4 0.20
ACGTcount: A:0.80, C:0.05, G:0.05, T:0.10
Consensus pattern (18 bp):
AAACAAAAATTAAAAAAA
Found at i:714520 original size:19 final size:19
Alignment explanation
Indices: 714474--714513 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
714464 CCCATATCCC
*
714474 AAACAAAAATTAAGGAAAAA
1 AAAC-AAAATTAAGAAAAAA
714494 AAACAAAATTAA-AAAAAA
1 AAACAAAATTAAGAAAAAA
714512 AA
1 AA
714514 TAGAAAACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 8 0.42
20 4 0.21
ACGTcount: A:0.80, C:0.05, G:0.05, T:0.10
Consensus pattern (19 bp):
AAACAAAATTAAGAAAAAA
Found at i:716065 original size:12 final size:13
Alignment explanation
Indices: 716043--716076 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
716033 ATTTTTATAC
*
716043 ATTATAATAATAT
1 ATTAAAATAATAT
716056 -TTAAAATAATAT
1 ATTAAAATAATAT
716068 ATTAAAATA
1 ATTAAAATA
716077 TTTTAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
ATTAAAATAATAT
Found at i:717465 original size:2 final size:2
Alignment explanation
Indices: 717458--717487 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
717448 TGATATGTAC
717458 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
717488 GTAGACAGAG
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:717905 original size:22 final size:22
Alignment explanation
Indices: 717846--717912 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 22
717836 TAGTATTTAA
*
717846 TATAAATTTAA-TTAT-T-ATT
1 TATAAATATAATTTATATAATT
* *
717865 TATAAATATGATTTTTATAATT
1 TATAAATATAATTTATATAATT
*
717887 TATAAATA-AA-TTATAT-ATA
1 TATAAATATAATTTATATAATT
717906 TATAAAT
1 TATAAAT
717913 GATGATAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
19 18 0.46
20 8 0.21
21 2 0.05
22 11 0.28
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (22 bp):
TATAAATATAATTTATATAATT
Found at i:721156 original size:6 final size:6
Alignment explanation
Indices: 721145--721182 Score: 58
Period size: 6 Copynumber: 6.2 Consensus size: 6
721135 AGATTATGCA
*
721145 TAGCCT TAGCCT TAGCCT TAGCCT AAGGCCT TAGCCT T
1 TAGCCT TAGCCT TAGCCT TAGCCT TA-GCCT TAGCCT T
721183 GAGTGTTGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 24 0.83
7 5 0.17
ACGTcount: A:0.18, C:0.32, G:0.18, T:0.32
Consensus pattern (6 bp):
TAGCCT
Found at i:721524 original size:3 final size:3
Alignment explanation
Indices: 721518--721551 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
721508 TATTCTCTTA
721518 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATGT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT
721552 CTTTCTTGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:721728 original size:2 final size:2
Alignment explanation
Indices: 721721--721747 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
721711 AATATTCGTC
721721 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
721748 CATTGATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:725570 original size:2 final size:2
Alignment explanation
Indices: 725563--725604 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
725553 TTTCCGAATC
725563 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
725605 CAAAGAAAGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:727113 original size:5 final size:5
Alignment explanation
Indices: 727103--727130 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
727093 TACAGGCACC
727103 GCTGA GCTGA GCTGA GCTGA GCTGA GCT
1 GCTGA GCTGA GCTGA GCTGA GCTGA GCT
727131 AGCCCCAGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.21, G:0.39, T:0.21
Consensus pattern (5 bp):
GCTGA
Found at i:727599 original size:20 final size:21
Alignment explanation
Indices: 727574--727622 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
727564 TACAGAAGAA
727574 TCTAGAATACTT-TGGAATGT
1 TCTAGAATACTTCTGGAATGT
* *
727594 TTTAGAA-AGTTCTGGAATGT
1 TCTAGAATACTTCTGGAATGT
727614 TCTAGAATA
1 TCTAGAATA
727623 TCGTGAAAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 3 0.12
20 20 0.83
21 1 0.04
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (21 bp):
TCTAGAATACTTCTGGAATGT
Found at i:727652 original size:40 final size:40
Alignment explanation
Indices: 727603--727716 Score: 174
Period size: 40 Copynumber: 2.9 Consensus size: 40
727593 TTTTAGAAAG
* * *
727603 TTCTGGAATGTTCTAGAATATCGTGAAAGGCTCTGGAAGA
1 TTCTAGAATGTTCTAGAATATTGTGGAAGGCTCTGGAAGA
* *
727643 TTCTAGAATGTTCTAAAATATTATGGAAGGCTCTGGAAGA
1 TTCTAGAATGTTCTAGAATATTGTGGAAGGCTCTGGAAGA
*
727683 TTCTAGAATGTTTTAGAATATTGTGGAAGGCTCT
1 TTCTAGAATGTTCTAGAATATTGTGGAAGGCTCT
727717 AGAACTTTAT
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 66 1.00
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.34
Consensus pattern (40 bp):
TTCTAGAATGTTCTAGAATATTGTGGAAGGCTCTGGAAGA
Found at i:727993 original size:12 final size:12
Alignment explanation
Indices: 727950--727982 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
727940 ATATAGAGGA
727950 ATAGAGAGAAAG
1 ATAGAGAGAAAG
727962 ATAGAGAGAAAG
1 ATAGAGAGAAAG
*
727974 ATATAGAGA
1 ATAGAGAGA
727983 GGAATAGAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.58, C:0.00, G:0.30, T:0.12
Consensus pattern (12 bp):
ATAGAGAGAAAG
Found at i:731361 original size:20 final size:20
Alignment explanation
Indices: 731336--731382 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
731326 TACAGAAGAA
731336 TCTAGAACACTT-TGGAATGT
1 TCTAGAA-ACTTCTGGAATGT
* *
731356 TTTAGAAAGTTCTGGAATGT
1 TCTAGAAACTTCTGGAATGT
731376 TCTAGAA
1 TCTAGAA
731383 TATCGTGGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.36
Consensus pattern (20 bp):
TCTAGAAACTTCTGGAATGT
Found at i:731392 original size:40 final size:40
Alignment explanation
Indices: 731365--731474 Score: 166
Period size: 40 Copynumber: 2.8 Consensus size: 40
731355 TTTTAGAAAG
* * *
731365 TTCTGGAATGTTCTAGAATATCGTGGAAGGCTCTGGAAGA
1 TTCTAGAATGTTCTAGAATATTGTGGAAGGTTCTGGAAGA
* *
731405 TTTTAGAATATTCTAGAATATTGTGGAAGGTTCTGGAAGA
1 TTCTAGAATGTTCTAGAATATTGTGGAAGGTTCTGGAAGA
*
731445 TTCTAGAATGTTTTAGAATATTGTGGAAGG
1 TTCTAGAATGTTCTAGAATATTGTGGAAGG
731475 CTCTAGAACT
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 62 1.00
ACGTcount: A:0.30, C:0.07, G:0.27, T:0.35
Consensus pattern (40 bp):
TTCTAGAATGTTCTAGAATATTGTGGAAGGTTCTGGAAGA
Found at i:731755 original size:12 final size:12
Alignment explanation
Indices: 731712--731744 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
731702 ATATAGAGGA
731712 ATAGAGAGAAAG
1 ATAGAGAGAAAG
731724 ATAGAGAGAAAG
1 ATAGAGAGAAAG
*
731736 ATATAGAGA
1 ATAGAGAGA
731745 GGAATAGAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.58, C:0.00, G:0.30, T:0.12
Consensus pattern (12 bp):
ATAGAGAGAAAG
Found at i:733435 original size:18 final size:17
Alignment explanation
Indices: 733407--733461 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
733397 GTATTATAAA
733407 AAATTTTATATTTATAT
1 AAATTTTATATTTATAT
733424 AAATTTTAATATATTA-AT
1 AAATTTT-ATAT-TTATAT
733442 -AA-TTTATA-TTATAT
1 AAATTTTATATTTATAT
733456 AAATTT
1 AAATTT
733462 AAATAAAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
13 3 0.09
14 2 0.06
15 5 0.15
16 5 0.15
17 9 0.27
18 6 0.18
19 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
AAATTTTATATTTATAT
Found at i:733457 original size:32 final size:32
Alignment explanation
Indices: 733411--733483 Score: 94
Period size: 32 Copynumber: 2.2 Consensus size: 32
733401 TATAAAAAAT
* *
733411 TTTATATTTATATAAATTTTAAT-ATATTAATAA
1 TTTATA-TTATATAAATTTAAATAAAATTAAT-A
*
733444 TTTATATTATATAAATTTAAATAAAATTGATA
1 TTTATATTATATAAATTTAAATAAAATTAATA
733476 TTTATATT
1 TTTATATT
733484 TGAGAGTGTG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
32 24 0.67
33 12 0.33
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.53
Consensus pattern (32 bp):
TTTATATTATATAAATTTAAATAAAATTAATA
Found at i:733460 original size:15 final size:15
Alignment explanation
Indices: 733411--733462 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
733401 TATAAAAAAT
733411 TTTATATTTATATAAA
1 TTTATA-TTATATAAA
*
733427 TTT-TAATATATTAATAA
1 TTTATATTATA-T-A-AA
733444 TTTATATTATATAAA
1 TTTATATTATATAAA
733459 TTTA
1 TTTA
733463 AATAAAATTG
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 4 0.13
15 9 0.30
16 5 0.17
17 6 0.20
18 6 0.20
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TTTATATTATATAAA
Found at i:736814 original size:3 final size:3
Alignment explanation
Indices: 736806--736841 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
736796 TAATTTTTAA
736806 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
736842 TTTTACTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:740121 original size:13 final size:14
Alignment explanation
Indices: 740096--740137 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
740086 TAATAAAATA
740096 TTAAAATTTTAATT
1 TTAAAATTTTAATT
740110 TTAAAA-TTTAA-T
1 TTAAAATTTTAATT
**
740122 AAAAAATTTTAATT
1 TTAAAATTTTAATT
740136 TT
1 TT
740138 TTTAATAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
12 5 0.23
13 10 0.45
14 7 0.32
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TTAAAATTTTAATT
Done.