Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015120.1 Kokia drynarioides strain JFW-HI SEQ_130164, whole genome shotgun sequence
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: 618428
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 267 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:396987 original size:30 final size:30
Alignment explanation
Indices: 396951--397012 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
396941 TCAAATTAAC
396951 TATTTAAAAAATGATATTATTTTAATAATT
1 TATTTAAAAAATGATATTATTTTAATAATT
396981 TATTTAAAAAATGATATTATTTTAATAATT
1 TATTTAAAAAATGATATTATTTTAATAATT
397011 TA
1 TA
397013 ATATTAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (30 bp):
TATTTAAAAAATGATATTATTTTAATAATT
Found at i:397002 original size:17 final size:17
Alignment explanation
Indices: 396951--397002 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
396941 TCAAATTAAC
396951 TATTTAAAAAATGATAT
1 TATTTAAAAAATGATAT
* *
396968 TATTT---TAATAAT-T
1 TATTTAAAAAATGATAT
396981 TATTTAAAAAATGATAT
1 TATTTAAAAAATGATAT
396998 TATTT
1 TATTT
397003 TAATAATTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 8
0.69 0.10 0.21
Matches are distributed among these distances:
13 6 0.22
14 5 0.19
16 5 0.19
17 11 0.41
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (17 bp):
TATTTAAAAAATGATAT
Found at i:399465 original size:10 final size:9
Alignment explanation
Indices: 399412--399569 Score: 66
Period size: 10 Copynumber: 16.4 Consensus size: 9
399402 AGTATTTGAA
399412 ATAAAATATT
1 ATAAAA-ATT
*
399422 A-AAAATTT
1 ATAAAAATT
*
399430 ATATAAACTT
1 ATA-AAAATT
* * *
399440 ACAAGAACT
1 ATAAAAATT
399449 ATAAAAAATT
1 AT-AAAAATT
399459 CATAAAAACTT
1 -ATAAAAA-TT
*
399470 ATAAATATT
1 ATAAAAATT
* *
399479 ATATAAGTT
1 ATAAAAATT
*
399488 CTAATAAATT
1 ATAA-AAATT
*
399498 ATAAAAATA
1 ATAAAAATT
*
399507 AAAAAATATT
1 ATAAAA-ATT
* *
399517 AAAAAAAAAT
1 -ATAAAAATT
*
399527 ATAAAAAATC
1 AT-AAAAATT
*
399537 ATAATAAGTT
1 ATAA-AAATT
*
399547 CTAATAAATT
1 ATAA-AAATT
399557 ATAAAAATT
1 ATAAAAATT
399566 ATAA
1 ATAA
399570 TCTTTTAATA
Statistics
Matches: 109, Mismatches: 29, Indels: 21
0.69 0.18 0.13
Matches are distributed among these distances:
8 3 0.03
9 40 0.37
10 56 0.51
11 10 0.09
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (9 bp):
ATAAAAATT
Found at i:399560 original size:30 final size:29
Alignment explanation
Indices: 399481--399563 Score: 78
Period size: 30 Copynumber: 2.8 Consensus size: 29
399471 TAAATATTAT
399481 ATAAGTTCTAATAAATTAT-AAAAATAAA
1 ATAAGTTCTAATAAATTATAAAAAATAAA
* * ** * * *
399509 AAAATATTAAAAAAAAATATAAAAAATCATA
1 ATAA-GTTCTAATAAATTATAAAAAAT-AAA
399540 ATAAGTTCTAATAAATTATAAAAA
1 ATAAGTTCTAATAAATTATAAAAA
399564 TTATAATCTT
Statistics
Matches: 39, Mismatches: 13, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
28 3 0.08
29 10 0.26
30 21 0.54
31 5 0.13
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (29 bp):
ATAAGTTCTAATAAATTATAAAAAATAAA
Found at i:399569 original size:29 final size:29
Alignment explanation
Indices: 399468--399570 Score: 93
Period size: 29 Copynumber: 3.6 Consensus size: 29
399458 TCATAAAAAC
*
399468 TTATAAATATTAT-ATAAGTTCTAATAAA
1 TTATAAAAATTATAATAAGTTCTAATAAA
* * * ** *
399496 TTATAAAAA-TAAAAAAATATTAAAAAAAA
1 TTATAAAAATTATAATAA-GTTCTAATAAA
* *
399525 ATATAAAAAATCATAATAAGTTCTAATAAA
1 TTAT-AAAAATTATAATAAGTTCTAATAAA
399555 TTATAAAAATTATAAT
1 TTATAAAAATTATAAT
399571 CTTTTAATAA
Statistics
Matches: 54, Mismatches: 17, Indels: 7
0.69 0.22 0.09
Matches are distributed among these distances:
27 2 0.04
28 11 0.20
29 21 0.39
30 15 0.28
31 5 0.09
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (29 bp):
TTATAAAAATTATAATAAGTTCTAATAAA
Found at i:400281 original size:3 final size:3
Alignment explanation
Indices: 400273--400297 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
400263 GATGAAAATT
400273 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
400298 TTATCGATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:400508 original size:10 final size:9
Alignment explanation
Indices: 400466--400713 Score: 92
Period size: 10 Copynumber: 25.6 Consensus size: 9
400456 TTAAATGATT
400466 TTTTTATAA
1 TTTTTATAA
400475 TTTATTA-AA
1 TTT-TTATAA
*
400484 TTTATTATATT
1 TTT-TTATA-A
400495 TTTTTATAA
1 TTTTTATAA
400504 GTTTTTATGAA
1 -TTTTTAT-AA
400515 TTTTTATAA
1 TTTTTATAA
400524 GTTTTTATAAA
1 -TTTTTAT-AA
* * *
400535 ATTCTAAATA
1 TTTTTATA-A
400545 TATTTTATTAA
1 T-TTTTA-TAA
*
400556 ATTTTATAA
1 TTTTTATAA
*
400565 CTTTTTAGAA
1 -TTTTTATAA
** *
400575 TGTAGTAGAA
1 T-TTTTATAA
400585 -TTTTATAA
1 TTTTTATAA
400593 TTTTTATAA
1 TTTTTATAA
* * **
400602 ATTATAGTGTT
1 TTTTTA-T-AA
400613 TGTTTTATAA
1 T-TTTTATAA
*
400623 TTTTTGT-A
1 TTTTTATAA
400631 TTTTTATAA
1 TTTTTATAA
*
400640 GTTTATATCAA
1 -TTTTTAT-AA
*
400651 TTTTT-TTA
1 TTTTTATAA
400659 TTTTTAATAA
1 TTTTT-ATAA
*
400669 GTTTTTATGAT
1 -TTTTTAT-AA
400680 TCTTTTATAA
1 T-TTTTATAA
*
400690 TTTTTTATGA
1 -TTTTTATAA
400700 -TTTTATAA
1 TTTTTATAA
400708 TATTTT
1 T-TTTT
400714 TATGAGAAAA
Statistics
Matches: 178, Mismatches: 34, Indels: 53
0.67 0.13 0.20
Matches are distributed among these distances:
8 25 0.14
9 38 0.21
10 82 0.46
11 28 0.16
12 5 0.03
ACGTcount: A:0.32, C:0.02, G:0.06, T:0.60
Consensus pattern (9 bp):
TTTTTATAA
Found at i:400660 original size:28 final size:27
Alignment explanation
Indices: 400614--400673 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 27
400604 TATAGTGTTT
400614 GTTTTATAATTTTTGTATTTTT-ATAA
1 GTTTTATAATTTTTGTATTTTTAATAA
*
400640 GTTTATATCAATTTTTTTATTTTTAATAA
1 GTTT-TAT-AATTTTTGTATTTTTAATAA
400669 GTTTT
1 GTTTT
400674 TATGATTCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 4 0.13
27 3 0.10
28 15 0.50
29 8 0.27
ACGTcount: A:0.27, C:0.02, G:0.07, T:0.65
Consensus pattern (27 bp):
GTTTTATAATTTTTGTATTTTTAATAA
Found at i:400685 original size:29 final size:27
Alignment explanation
Indices: 400615--400716 Score: 98
Period size: 29 Copynumber: 3.6 Consensus size: 27
400605 ATAGTGTTTG
*
400615 TTTTATAATTTTTGTATTTTTATAAGT
1 TTTTATAATTTTTTTATTTTTATAAGT
*
400642 TTATATCAATTTTTTTATTTTTAATAAGT
1 TTTTAT-AATTTTTTTATTTTT-ATAAGT
* * *
400671 TTTTATGATTCTTTTATAATTTTT-TATGA
1 TTTTATAATT-TTTT-T-ATTTTTATAAGT
*
400700 TTTTATAATATTTTTAT
1 TTTTATAATTTTTTTAT
400717 GAGAAAAAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 11
0.77 0.10 0.14
Matches are distributed among these distances:
26 2 0.03
27 6 0.10
28 21 0.34
29 26 0.42
30 1 0.02
31 6 0.10
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (27 bp):
TTTTATAATTTTTTTATTTTTATAAGT
Found at i:400715 original size:19 final size:18
Alignment explanation
Indices: 400652--400718 Score: 66
Period size: 21 Copynumber: 3.6 Consensus size: 18
400642 TTATATCAAT
400652 TTTTTTAT--TTTTAATAA
1 TTTTTTATGATTTT-ATAA
*
400669 GTTTTTATGATTCTTTTATAA
1 TTTTTTATGA---TTTTATAA
400690 TTTTTTATGATTTTATAA
1 TTTTTTATGATTTTATAA
400708 TATTTTTATGA
1 T-TTTTTATGA
400719 GAAAAAATAA
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
17 7 0.17
18 9 0.21
19 9 0.21
21 13 0.31
22 4 0.10
ACGTcount: A:0.27, C:0.01, G:0.06, T:0.66
Consensus pattern (18 bp):
TTTTTTATGATTTTATAA
Found at i:407572 original size:19 final size:19
Alignment explanation
Indices: 407548--407584 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
407538 AATATTATTT
407548 TTAAAAC-ACATCATAAATC
1 TTAAAACTACAT-ATAAATC
407567 TTAAAACTACATATAAAT
1 TTAAAACTACATATAAAT
407585 TTTGATTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.54, C:0.16, G:0.00, T:0.30
Consensus pattern (19 bp):
TTAAAACTACATATAAATC
Found at i:415938 original size:18 final size:18
Alignment explanation
Indices: 415915--415949 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
415905 TACGCCCGCT
415915 ACTCCCAAGGCGGAGACC
1 ACTCCCAAGGCGGAGACC
*
415933 ACTCCCACGGCGGAGAC
1 ACTCCCAAGGCGGAGAC
415950 GGTAAGCGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.40, G:0.29, T:0.06
Consensus pattern (18 bp):
ACTCCCAAGGCGGAGACC
Found at i:422847 original size:6 final size:6
Alignment explanation
Indices: 422836--422931 Score: 67
Period size: 6 Copynumber: 16.7 Consensus size: 6
422826 GGCCCAACAG
* * * *
422836 AATTTA AATTT- ATTTTA AAATTA AATTT- ATTTTA AGTTTA AATTT-
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
* * * * *
422881 ACTTAA AATTTA AATTT- -ATTATA ACTTTA AGTTTA AATTTA AAATTA
1 AATTTA AATTTA AATTTA AATT-TA AATTTA AATTTA AATTTA AATTTA
422928 AATT
1 AATT
422932 AATGTCTAAA
Statistics
Matches: 68, Mismatches: 16, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
4 3 0.04
5 12 0.18
6 51 0.75
7 2 0.03
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (6 bp):
AATTTA
Found at i:422861 original size:17 final size:17
Alignment explanation
Indices: 422839--422931 Score: 89
Period size: 17 Copynumber: 5.4 Consensus size: 17
422829 CCAACAGAAT
422839 TTAAATTTATTTTAAAA
1 TTAAATTTATTTTAAAA
**
422856 TTAAATTTATTTTAAGT
1 TTAAATTTATTTTAAAA
*
422873 TTAAATTTA-CTTAAAA
1 TTAAATTTATTTTAAAA
* **
422889 TTTAAATTTATTATAACT
1 -TTAAATTTATTTTAAAA
* *
422907 TTAAGTTTAAATTTAAAA
1 TTAAATTT-ATTTTAAAA
422925 TTAAATT
1 TTAAATT
422932 AATGTCTAAA
Statistics
Matches: 58, Mismatches: 15, Indels: 5
0.74 0.19 0.06
Matches are distributed among these distances:
16 4 0.07
17 40 0.69
18 14 0.24
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (17 bp):
TTAAATTTATTTTAAAA
Found at i:422881 original size:34 final size:33
Alignment explanation
Indices: 422838--422931 Score: 116
Period size: 34 Copynumber: 2.7 Consensus size: 33
422828 CCCAACAGAA
* *
422838 TTTAAATTTATTTTAAAATTAAATTTATTTTAAG
1 TTTAAATTTA-TTTAAAATTAAATTTATTATAAC
*
422872 TTTAAATTTACTTAAAATTTAAATTTATTATAAC
1 TTTAAATTTATTTAAAA-TTAAATTTATTATAAC
*
422906 TTTAAGTTTAAATTTAAAATTAAATT
1 TTTAAATTT--ATTTAAAATTAAATT
422932 AATGTCTAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
33 6 0.12
34 32 0.62
35 7 0.13
36 7 0.13
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (33 bp):
TTTAAATTTATTTAAAATTAAATTTATTATAAC
Found at i:422933 original size:23 final size:23
Alignment explanation
Indices: 422849--422942 Score: 57
Period size: 23 Copynumber: 4.0 Consensus size: 23
422839 TTAAATTTAT
* * *
422849 TTTAAAATTAAATTTATTTTAAG
1 TTTAAAATTAAATTAAGTTTAAA
* * *
422872 TTT-AAATTTACTTAAAATTTAAA
1 TTTAAAATTAAATT-AAGTTTAAA
** *
422895 TTTATTA-TAACTTTAAGTTTAAA
1 TTTAAAATTAA-ATTAAGTTTAAA
*
422918 TTTAAAATTAAATTAATGTCTAAA
1 TTTAAAATTAAATTAA-GTTTAAA
422942 T
1 T
422943 GAAAAAACAA
Statistics
Matches: 52, Mismatches: 14, Indels: 9
0.69 0.19 0.12
Matches are distributed among these distances:
22 8 0.15
23 31 0.60
24 13 0.25
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (23 bp):
TTTAAAATTAAATTAAGTTTAAA
Found at i:423571 original size:3 final size:3
Alignment explanation
Indices: 423563--423647 Score: 62
Period size: 3 Copynumber: 27.0 Consensus size: 3
423553 CCCATAGCCT
* * ** * *
423563 TAA TAA TAA TAA TAT TAA TAA TAGGA TAA TAT TAA TGG CAT TAA TTAA
1 TAA TAA TAA TAA TAA TAA TAA TA--A TAA TAA TAA TAA TAA TAA -TAA
* *
423611 TAA TAG TAA TTA TAA TAA TTAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA
423648 CTTTTTTAAA
Statistics
Matches: 63, Mismatches: 15, Indels: 8
0.73 0.17 0.09
Matches are distributed among these distances:
3 54 0.86
4 6 0.10
5 3 0.05
ACGTcount: A:0.55, C:0.01, G:0.06, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:423629 original size:22 final size:22
Alignment explanation
Indices: 423564--423647 Score: 71
Period size: 22 Copynumber: 3.6 Consensus size: 22
423554 CCATAGCCTT
*
423564 AATAATAATAATATTAA-TAAT
1 AATAATAATAATAATAATTAAT
* *
423585 AGGATAATATTAATGGCATTAATTAAT
1 A--ATAATAATAAT---AATAATTAAT
* *
423612 AATAGTAATTATAATAATTAAT
1 AATAATAATAATAATAATTAAT
423634 AATAATAATAATAA
1 AATAATAATAATAA
423648 CTTTTTTAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
21 1 0.02
22 21 0.42
23 10 0.20
25 8 0.16
26 5 0.10
27 5 0.10
ACGTcount: A:0.56, C:0.01, G:0.06, T:0.37
Consensus pattern (22 bp):
AATAATAATAATAATAATTAAT
Found at i:424741 original size:57 final size:58
Alignment explanation
Indices: 424659--425037 Score: 354
Period size: 58 Copynumber: 6.6 Consensus size: 58
424649 TGACCTTGAA
*
424659 ATTTTA-CCTCAAACTTCCAAAAATTCCATTTTTGACCCTAAAACTTCCAAAAATTAC
1 ATTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCTAAAACTTCCAAAAATTAC
* *
424716 ATTTTAGCCTCGAACTTCC-AAAATTCCATTTTT-AACCTCAAAACTTCCAAAAATTAC
1 ATTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCT-AAAACTTCCAAAAATTAC
** * *
424773 ATTTTCACCCT-GAACTTTTAAAAATTCCATTTTTGACACC-AAAACATCCAAAAAATAC
1 ATTTT-ACCCTCGAACTTCCAAAAATTCCATTTTTGAC-CCTAAAACTTCCAAAAATTAC
* * *
424831 ATTTTTACCC-CTACACTTCCAAAAATTCCATTTTTGA-TCTCGAAACTT---AAAATTAC
1 A-TTTTACCCTCGA-ACTTCCAAAAATTCCATTTTTGACCCT-AAAACTTCCAAAAATTAC
* * * * *
424887 ATTTTTACCCCCAAACCTCCAAAAATTTCATTTTTGACCCTAAAACTTTC-AAAATTACC
1 A-TTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCTAAAACTTCCAAAAATTA-C
* ** * * *
424946 ATTTTACCCCCGAAAGT-CTAAAACTCCATTTTTAACCCTAAAA-TTCTCAAAAATTACC
1 ATTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCTAAAACTTC-CAAAAATTA-C
* *
425004 ATCTTACCCTCGAA-TGTCCAAAAATTCTATTTTT
1 ATTTTACCCTCGAACT-TCCAAAAATTCCATTTTT
425038 TATCCCGATT
Statistics
Matches: 268, Mismatches: 34, Indels: 38
0.79 0.10 0.11
Matches are distributed among these distances:
56 50 0.19
57 77 0.29
58 93 0.35
59 46 0.17
60 2 0.01
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.34
Consensus pattern (58 bp):
ATTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCTAAAACTTCCAAAAATTAC
Found at i:424748 original size:28 final size:29
Alignment explanation
Indices: 424660--425037 Score: 241
Period size: 30 Copynumber: 13.1 Consensus size: 29
424650 GACCTTGAAA
424660 TTTTA-CCTCAAACTTCCAAAAATTCCAT
1 TTTTACCCTCAAACTTCCAAAAATTCCAT
* *
424688 TTTTGACCCTAAAACTTCCAAAAATTACA-
1 TTTT-ACCCTCAAACTTCCAAAAATTCCAT
* *
424717 TTTTAGCCTCGAACTTCC-AAAATTCCAT
1 TTTTACCCTCAAACTTCCAAAAATTCCAT
* *
424745 TTTTAACCTCAAAACTTCCAAAAATTACAT
1 TTTTACCCTC-AAACTTCCAAAAATTCCAT
* * **
424775 TTTCACCCT-GAACTTTTAAAAATTCCAT
1 TTTTACCCTCAAACTTCCAAAAATTCCAT
* * * *
424803 TTTTGACACC-AAAACATCCAAAAAATACAT
1 TTTT-AC-CCTCAAACTTCCAAAAATTCCAT
*
424833 TTTTACCC-CTACACTTCCAAAAATTCCAT
1 TTTTACCCTC-AAACTTCCAAAAATTCCAT
* *
424862 TTTTGA-TCTCGAAACTT---AAAATTACAT
1 TTTT-ACCCTC-AAACTTCCAAAAATTCCAT
* * *
424889 TTTTACCCCCAAACCTCCAAAAATTTCAT
1 TTTTACCCTCAAACTTCCAAAAATTCCAT
* *
424918 TTTTGACCCTAAAACTTTC-AAAATTACCA-
1 TTTT-ACCCTCAAACTTCCAAAAATT-CCAT
* * * *
424947 TTTTACCCCCGAAA-GT-CTAAAACTCCAT
1 TTTTACCCTC-AAACTTCCAAAAATTCCAT
*
424975 TTTTAACCCT-AAAATTCTCAAAAATTACCA-
1 TTTT-ACCCTCAAACTTC-CAAAAATT-CCAT
* * *
425005 TCTTACCCTCGAA-TGTCCAAAAATTCTAT
1 TTTTACCCTCAAACT-TCCAAAAATTCCAT
425034 TTTT
1 TTTT
425038 TATCCCGATT
Statistics
Matches: 270, Mismatches: 52, Indels: 55
0.72 0.14 0.15
Matches are distributed among these distances:
26 6 0.02
27 30 0.11
28 61 0.23
29 83 0.31
30 87 0.32
31 3 0.01
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.34
Consensus pattern (29 bp):
TTTTACCCTCAAACTTCCAAAAATTCCAT
Found at i:424911 original size:115 final size:113
Alignment explanation
Indices: 424660--424982 Score: 339
Period size: 115 Copynumber: 2.8 Consensus size: 113
424650 GACCTTGAAA
* * *
424660 TTTTACCTCAAACTTCCAAAAATTCCATTTTTGACCCTAAAACTTCCAAAAATTACATTTTAGCC
1 TTTTACCCCAAACTTCCAAAAATTCCATTTTTGACCCTAAAACATCCAAAAAATACATTTTAGCC
*
424725 TCGAACTTCCAAAATTCCATTTTTAACCTCAAAACTTCCAAAAATTACAT
66 CCGAACTTCCAAAATTCCATTTTTAACCTCAAAACTT-C-AAAATTACAT
* ** **
424775 TTTCACCCTGAACTTTTAAAAATTCCATTTTTGACACC-AAAACATCCAAAAAATACATTTTTA-
1 TTTTACCCCAAACTTCCAAAAATTCCATTTTTGAC-CCTAAAACATCCAAAAAATACA-TTTTAG
* * * *
424838 CCCCTACACTTCCAAAAATTCCATTTTTGATCTCGAAACTT-AAAATTACAT
64 CCCCGA-ACTTCC-AAAATTCCATTTTTAACCTCAAAACTTCAAAATTACAT
* * * * * *
424889 TTTTACCCCCAAACCTCCAAAAATTTCATTTTTGACCCTAAAACTTTC-AAAATTACCATTTTAC
1 TTTTA-CCCCAAACTTCCAAAAATTCCATTTTTGACCCTAAAACATCCAAAAAATA-CATTTTAG
** * *
424953 CCCCGAAAGTCTAAAACTCCATTTTTAACC
64 CCCCGAACTTCCAAAATTCCATTTTTAACC
424983 CTAAAATTCT
Statistics
Matches: 170, Mismatches: 30, Indels: 18
0.78 0.14 0.08
Matches are distributed among these distances:
113 15 0.09
114 30 0.18
115 88 0.52
116 13 0.08
117 24 0.14
ACGTcount: A:0.37, C:0.27, G:0.03, T:0.34
Consensus pattern (113 bp):
TTTTACCCCAAACTTCCAAAAATTCCATTTTTGACCCTAAAACATCCAAAAAATACATTTTAGCC
CCGAACTTCCAAAATTCCATTTTTAACCTCAAAACTTCAAAATTACAT
Found at i:425107 original size:58 final size:57
Alignment explanation
Indices: 424908--425117 Score: 190
Period size: 58 Copynumber: 3.6 Consensus size: 57
424898 CAAACCTCCA
* * * * *
424908 AAAATTTCATTTTTGACCCTAAAACTTTCAAAATTACCATTTTACCCCCGAAAGTCT
1 AAAATTTCATTTTTAACCCCAAAATTTTCAAAATTACCATTTTACCCTCGAATGTCT
* * * * * *
424965 AAAACTCCATTTTTAACCCTAAAATTCTCAAAAATTACCATCTTACCCTCGAATGTCC
1 AAAATTTCATTTTTAACCCCAAAATTTTC-AAAATTACCATTTTACCCTCGAATGTCT
* * * * * * *
425023 AAAAATTCTATTTTTTATCCC-GATTTTTCTAAAATTACCGTTTTACCCTCGGATGTCT
1 AAAATTTC-ATTTTTAACCCCAAAATTTTC-AAAATTACCATTTTACCCTCGAATGTCT
*
425081 AAAATTTCATTTTAAACCCC-AAATTTTCCCAAAATTA
1 AAAATTTCATTTTTAACCCCAAAATTTT--CAAAATTA
425118 TCGTTTTGCC
Statistics
Matches: 121, Mismatches: 28, Indels: 7
0.78 0.18 0.04
Matches are distributed among these distances:
57 38 0.31
58 73 0.60
59 10 0.08
ACGTcount: A:0.34, C:0.24, G:0.05, T:0.37
Consensus pattern (57 bp):
AAAATTTCATTTTTAACCCCAAAATTTTCAAAATTACCATTTTACCCTCGAATGTCT
Found at i:425172 original size:29 final size:28
Alignment explanation
Indices: 425109--425181 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
425099 CCAAATTTTC
* *
425109 CCAAAATTATCGTTTTGCCCCCAAGAAT
1 CCAAAATTATCATTTTACCCCCAAGAAT
*
425137 CCAAAATTATCATTTTACCCCC-GGATAT
1 CCAAAATTATCATTTTACCCCCAAGA-AT
*
425165 CCAAAAATTCTCATTTT
1 CC-AAAATTATCATTTT
425182 CAACTTCGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
27 2 0.05
28 24 0.62
29 13 0.33
ACGTcount: A:0.33, C:0.27, G:0.07, T:0.33
Consensus pattern (28 bp):
CCAAAATTATCATTTTACCCCCAAGAAT
Found at i:428726 original size:20 final size:20
Alignment explanation
Indices: 428701--428745 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
428691 AGACAAAGAT
428701 GACATTGCCAAAAATAATTG
1 GACATTGCCAAAAATAATTG
428721 GACATTGCCAAAAATAATTG
1 GACATTGCCAAAAATAATTG
428741 GACAT
1 GACAT
428746 AAACAAATGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (20 bp):
GACATTGCCAAAAATAATTG
Found at i:428752 original size:20 final size:20
Alignment explanation
Indices: 428709--428752 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
428699 ATGACATTGC
***
428709 CAAAAATAATTGGACATTGC
1 CAAAAATAATTGGACATAAA
428729 CAAAAATAATTGGACATAAA
1 CAAAAATAATTGGACATAAA
428749 CAAA
1 CAAA
428753 TGGCTTTAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.55, C:0.14, G:0.11, T:0.20
Consensus pattern (20 bp):
CAAAAATAATTGGACATAAA
Found at i:431986 original size:100 final size:100
Alignment explanation
Indices: 431847--432086 Score: 338
Period size: 100 Copynumber: 2.4 Consensus size: 100
431837 GCACCATGAA
* * * *
431847 ACATGACGGGAAAGGTCCAAGACCACAACGGCGGATCCAGTACCACAAAGATACAAAAGGGAAGG
1 ACATGACGAGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCACAAAGATACAAAAGGGAAGG
* *
431912 GTTTAAGTCGTAATGGTAAACCTTATACCTCAGAG
66 GTTTAAGTCGCAACGGTAAACCTTATACCTCAGAG
* * * **
431947 ACATGACGAGAAAGATTTAAGACCGCAATGGCGGATCCAGTACCGCAAAGATATGAAAGGGAAGG
1 ACATGACGAGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCACAAAGATACAAAAGGGAAGG
* *
432012 GTTTAAGTCGCAACGGTGAACCTTGTACCTCAGAG
66 GTTTAAGTCGCAACGGTAAACCTTATACCTCAGAG
* *
432047 ACATGACGAGAAAAATCTAAG-CCGCAACGGTGGATCCAGT
1 ACATGACGAGAAAGATCTAAGACCGCAACGGCGGATCCAGT
432087 GCCGCGAAGA
Statistics
Matches: 123, Mismatches: 17, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
99 17 0.14
100 106 0.86
ACGTcount: A:0.37, C:0.20, G:0.26, T:0.17
Consensus pattern (100 bp):
ACATGACGAGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCACAAAGATACAAAAGGGAAGG
GTTTAAGTCGCAACGGTAAACCTTATACCTCAGAG
Found at i:432024 original size:50 final size:50
Alignment explanation
Indices: 431872--432374 Score: 251
Period size: 50 Copynumber: 10.2 Consensus size: 50
431862 TCCAAGACCA
* ** * *
431872 CAACGGCGGATCCAGTACCACAAAGATACAAAAGGGAAGGGTTTAAGTCG
1 CAACGGCGGATCCAGTACCACAAAGACATGAAAGGGAAAGATTTAAGTCG
* * ** * * * * * *
431922 TAATGG-TAAACCTTA-TACCTCAGAGACATG-ACGAGAAAGATTTAAGACCG
1 CAACGGCGGATCC--AGTACCACAAAGACATGAAAGGGAAAGATTTAAG-TCG
* * * * *
431972 CAATGGCGGATCCAGTACCGCAAAGATATGAAAGGGAAGGGTTTAAGTCG
1 CAACGGCGGATCCAGTACCACAAAGACATGAAAGGGAAAGATTTAAGTCG
* * * * * * * * * *
432022 CAACGG-TGAACCTTGTACCTCAGAGACATG-ACGAGAAAAATCTAAGCCG
1 CAACGGCGGATCC-AGTACCACAAAGACATGAAAGGGAAAGATTTAAGTCG
* * * * *
432071 CAACGGTGGATCCAGTGCCGCGAAGACATG-AAGGGAAAGATCTAAGTCG
1 CAACGGCGGATCCAGTACCACAAAGACATGAAAGGGAAAGATTTAAGTCG
* * * * * * *
432120 CAACGACGGATCTAGTACCACGAAGACA--CAAGGGAAAGGTTTAATTCA
1 CAACGGCGGATCCAGTACCACAAAGACATGAAAGGGAAAGATTTAAGTCG
* * * * * *
432168 AAATGGCGGA-CCTAGTACCTCAAAGACAT-AAAGAGAAAGATCT-AGACCG
1 CAACGGCGGATCC-AGTACCACAAAGACATGAAAGGGAAAGATTTAAG-TCG
* * ** *
432217 CAACGGCGGATCCGGTACCACAAAGATACAAAAGGGAAAGGTTTAAGTCG
1 CAACGGCGGATCCAGTACCACAAAGACATGAAAGGGAAAGATTTAAGTCG
* * * *
432267 CAACGGCGGA-CCATGAACCTCAAAAGACAAGAAA-GGAAAGATTTAAGCCG
1 CAACGGCGGATCCA-GTACCAC-AAAGACATGAAAGGGAAAGATTTAAGTCG
* ** ** *
432317 CAACGGCGAATCCAGTACCATGAAGATTTG-AAGGAGAAAGGTTTAAGTCG
1 CAACGGCGGATCCAGTACCACAAAGACATGAAAGG-GAAAGATTTAAGTCG
*
432367 CAATGGCG
1 CAACGGCG
432375 AACTCGATAC
Statistics
Matches: 330, Mismatches: 103, Indels: 40
0.70 0.22 0.08
Matches are distributed among these distances:
47 1 0.00
48 38 0.12
49 127 0.38
50 134 0.41
51 30 0.09
ACGTcount: A:0.38, C:0.20, G:0.26, T:0.16
Consensus pattern (50 bp):
CAACGGCGGATCCAGTACCACAAAGACATGAAAGGGAAAGATTTAAGTCG
Found at i:432098 original size:49 final size:49
Alignment explanation
Indices: 432045--432147 Score: 125
Period size: 49 Copynumber: 2.1 Consensus size: 49
432035 TGTACCTCAG
* ** * *
432045 AGACATGACGAGAAAAATCTAAGCCGCAACGGTGGATCCAGTGCCGCGA
1 AGACATGAAGAGAAAAATCTAAGCCGCAACGACGGATCCAGTACCACGA
* * * *
432094 AGACATGAAGGGAAAGATCTAAGTCGCAACGACGGATCTAGTACCACGA
1 AGACATGAAGAGAAAAATCTAAGCCGCAACGACGGATCCAGTACCACGA
432143 AGACA
1 AGACA
432148 CAAGGGAAAG
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.38, C:0.22, G:0.27, T:0.13
Consensus pattern (49 bp):
AGACATGAAGAGAAAAATCTAAGCCGCAACGACGGATCCAGTACCACGA
Found at i:432336 original size:100 final size:99
Alignment explanation
Indices: 432093--432374 Score: 297
Period size: 100 Copynumber: 2.9 Consensus size: 99
432083 CAGTGCCGCG
* * * * * *
432093 AAGACATGAAGGGAAAGATCTAAGTCGCAACGACGGATCTAGTACCACGAAG--ACACAAGGGAA
1 AAGACAAGAAAGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCACGAAGATACAAAAGGGAA
* ** *
432156 AGGTTTAATTCAAAATGGCGGACCTAGTACCTCA
66 AGGTTTAAGTCGCAATGGCGGACCTAGAACCTCA
* * *
432190 AAGAC-ATAAAGAGAAAGATCT-AGACCGCAACGGCGGATCCGGTACCACAAAGATACAAAAGGG
1 AAGACAAGAAAG-GAAAGATCTAAG-CCGCAACGGCGGATCCAGTACCACGAAGATACAAAAGGG
*
432253 AAAGGTTTAAGTCGCAACGGCGGACC-ATGAACCTCAA
64 AAAGGTTTAAGTCGCAATGGCGGACCTA-GAACCTC-A
* * * ***
432290 AAGACAAGAAAGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCATGAAGAT-TTGAAGGAGA
1 AAGACAAGAAAGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCACGAAGATACAAAAGG-GA
432354 AAGGTTTAAGTCGCAATGGCG
65 AAGGTTTAAGTCGCAATGGCG
432375 AACTCGATAC
Statistics
Matches: 152, Mismatches: 24, Indels: 15
0.80 0.13 0.08
Matches are distributed among these distances:
96 5 0.03
97 37 0.24
98 1 0.01
99 40 0.26
100 62 0.41
101 7 0.05
ACGTcount: A:0.40, C:0.19, G:0.26, T:0.15
Consensus pattern (99 bp):
AAGACAAGAAAGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCACGAAGATACAAAAGGGAA
AGGTTTAAGTCGCAATGGCGGACCTAGAACCTCA
Found at i:432959 original size:22 final size:22
Alignment explanation
Indices: 432916--432959 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
432906 TTAATGGCAT
*
432916 TAATTAATAATACTAATTATAA
1 TAATTAATAATACTAATAATAA
432938 TAATTAATAATAAC-AATAATAA
1 TAATTAATAAT-ACTAATAATAA
432960 CTTTTTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (22 bp):
TAATTAATAATACTAATAATAA
Found at i:433630 original size:29 final size:30
Alignment explanation
Indices: 433578--433866 Score: 293
Period size: 30 Copynumber: 9.7 Consensus size: 30
433568 GGAGGTCCCC
* * *
433578 AAACTTCTCTAAAATTATATTTTTAACCTTG
1 AAACTTC-CAAAAATTACATTTTTAACCTCG
* *
433609 AAACTTCCAAAAATTACATTTTT-ACCCCT
1 AAACTTCCAAAAATTACATTTTTAACCTCG
* *
433638 AAACTTCCAAAAATTCCATTTTTAACC-CTA
1 AAACTTCCAAAAATTACATTTTTAACCTC-G
* * *
433668 AAACTTCTAAAAATTACATTTTTAGCCCCG
1 AAACTTCCAAAAATTACATTTTTAACCTCG
* **
433698 -AACTTCC-AAAATTACATTTTTGACCTTA
1 AAACTTCCAAAAATTACATTTTTAACCTCG
* *
433726 AAACTTCCAAAAATTACATTTTCACCCTCG
1 AAACTTCCAAAAATTACATTTTTAACCTCG
* *
433756 -AACTTCCAAAAATTACATTTTTGACCCCG
1 AAACTTCCAAAAATTACATTTTTAACCTCG
* *
433785 AAACTTCCAAAAATTACATTTCTACCCTCG
1 AAACTTCCAAAAATTACATTTTTAACCTCG
* * * *
433815 -AACCTCCAAAAATTCCATTTTTGATCTCG
1 AAACTTCCAAAAATTACATTTTTAACCTCG
*
433844 AAACTTTCAAAAATTACCATTTT
1 AAACTTCCAAAAATTA-CATTTT
433867 ACCCCCGCAT
Statistics
Matches: 211, Mismatches: 39, Indels: 16
0.79 0.15 0.06
Matches are distributed among these distances:
28 16 0.08
29 87 0.41
30 94 0.45
31 14 0.07
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (30 bp):
AAACTTCCAAAAATTACATTTTTAACCTCG
Found at i:433894 original size:118 final size:117
Alignment explanation
Indices: 433588--433946 Score: 370
Period size: 117 Copynumber: 3.1 Consensus size: 117
433578 AAACTTCTCT
* * ** * ** *
433588 AAAATTATATTTTTAACCTTGAAACTTCCAAAAATTACATTTTTACCCCTAAACTTCCAAAAATT
1 AAAATTACATTTTTGACCTCAAAACTTCCAAAAATTACATTTTCACCCCCGAACTTACAAAAATT
* * ** * *
433653 CCATTTTTAACCCTAAAACTTCTAAAAATTACATTTTTAGCCC-CGAACTTCC-
66 ACATTTTTGACCCCGAAACTTCCAAAAATTACA-TTTTA-CCCTCGAACCTCCA
* * *
433705 AAAATTACATTTTTGACCTTAAAACTTCCAAAAATTACATTTTCACCCTCGAACTTCCAAAAATT
1 AAAATTACATTTTTGACCTCAAAACTTCCAAAAATTACATTTTCACCCCCGAACTTACAAAAATT
433770 ACATTTTTGACCCCGAAACTTCCAAAAATTACATTTCTACCCTCGAACCTCCA
66 ACATTTTTGACCCCGAAACTTCCAAAAATTACATTT-TACCCTCGAACCTCCA
* * * * *
433823 AAAATTCCATTTTTGATCTCGAAACTTTCAAAAATTACCATTTT-ACCCCCGCA-TATACAAAAA
1 AAAATTACATTTTTGACCTCAAAACTTCCAAAAATTA-CATTTTCACCCCCGAACT-TACAAAAA
* * **
433886 CTT-TATTTTTGACCTCGAAAC-TCTCAAAAATTACCATTTTACCCTCGAATGTCCA
64 -TTACATTTTTGACCCCGAAACTTC-CAAAAATTA-CATTTTACCCTCGAACCTCCA
433941 AAAATT
1 AAAATT
433947 TCGTTTTTTG
Statistics
Matches: 209, Mismatches: 25, Indels: 15
0.84 0.10 0.06
Matches are distributed among these distances:
116 6 0.03
117 99 0.47
118 91 0.44
119 13 0.06
ACGTcount: A:0.37, C:0.25, G:0.04, T:0.34
Consensus pattern (117 bp):
AAAATTACATTTTTGACCTCAAAACTTCCAAAAATTACATTTTCACCCCCGAACTTACAAAAATT
ACATTTTTGACCCCGAAACTTCCAAAAATTACATTTTACCCTCGAACCTCCA
Found at i:433932 original size:30 final size:30
Alignment explanation
Indices: 433588--433934 Score: 257
Period size: 30 Copynumber: 11.8 Consensus size: 30
433578 AAACTTCTCT
* * *
433588 AAAATTATATTTTT-AACCTTGAAACTTCCA
1 AAAATTACATTTTTGACCCTCGAAACTT-CA
*
433618 AAAATTACATTTTT-ACCC-CTAAACTTCCA
1 AAAATTACATTTTTGACCCTCGAAACTT-CA
* * *
433647 AAAATTCCATTTTTAACCCT-AAAACTTCTA
1 AAAATTACATTTTTGACCCTCGAAACTTC-A
*
433677 AAAATTACATTTTT-AGCCC-CG-AACTTCC
1 AAAATTACATTTTTGA-CCCTCGAAACTTCA
**
433705 AAAATTACATTTTTGA-CCTTAAAACTTCCA
1 AAAATTACATTTTTGACCCTCGAAACTT-CA
*
433735 AAAATTACA-TTTTCACCCTCG-AACTTCCA
1 AAAATTACATTTTTGACCCTCGAAACTT-CA
433764 AAAATTACATTTTTGACCC-CGAAACTTCCA
1 AAAATTACATTTTTGACCCTCGAAACTT-CA
* * *
433794 AAAATTACATTTCT-ACCCTCGAACCTCCA
1 AAAATTACATTTTTGACCCTCGAAACTTCA
* *
433823 AAAATTCCATTTTTGA-TCTCGAAACTTTCA
1 AAAATTACATTTTTGACCCTCGAAAC-TTCA
* * *
433853 AAAATTACCA-TTTT-ACCCCCGCATA-TACA
1 AAAATTA-CATTTTTGACCCTCG-AAACTTCA
*
433882 AAAACTT-TATTTTTGA-CCTCGAAACTCTCA
1 AAAA-TTACATTTTTGACCCTCGAAACT-TCA
433912 AAAATTACCA-TTTT-ACCCTCGAA
1 AAAATTA-CATTTTTGACCCTCGAA
433935 TGTCCAAAAA
Statistics
Matches: 257, Mismatches: 34, Indels: 52
0.75 0.10 0.15
Matches are distributed among these distances:
27 2 0.01
28 17 0.07
29 105 0.41
30 128 0.50
31 5 0.02
ACGTcount: A:0.37, C:0.26, G:0.04, T:0.34
Consensus pattern (30 bp):
AAAATTACATTTTTGACCCTCGAAACTTCA
Found at i:433945 original size:29 final size:28
Alignment explanation
Indices: 433613--433946 Score: 184
Period size: 29 Copynumber: 11.4 Consensus size: 28
433603 ACCTTGAAAC
* *
433613 TTCCAAAAATTACATTTTTACCC-CTAAA
1 TTCCAAAAATTACATTTTGACCCTC-GAA
* * **
433641 CTTCCAAAAATTCCATTTTTAACCCTAAAA
1 -TTCCAAAAATTACA-TTTTGACCCTCGAA
* *
433671 CTTCTAAAAATTACATTTTTAGCCC-CGAA
1 -TTCCAAAAATTACATTTTGA-CCCTCGAA
* **
433700 CTTCC-AAAATTACATTTTTGACCTTAAAA
1 -TTCCAAAAATTACA-TTTTGACCCTCGAA
*
433729 CTTCCAAAAATTACATTTTCACCCTCGAA
1 -TTCCAAAAATTACATTTTGACCCTCGAA
433758 CTTCCAAAAATTACATTTTTGACCC-CGAAA
1 -TTCCAAAAATTACA-TTTTGACCCTCG-AA
433788 CTTCCAAAAATTACATTTCT-ACCCTCGAA
1 -TTCCAAAAATTACATTT-TGACCCTCGAA
* * *
433817 CCTCCAAAAATTCCATTTTTGA-TCTCGAAA
1 -TTCCAAAAATTACA-TTTTGACCCTCG-AA
* * *
433847 CTTTCAAAAATTACCATTTT-ACCCCCGCA
1 -TTCCAAAAATTA-CATTTTGACCCTCGAA
* *
433876 TATACAAAAACTTTA-TTTTTGA-CCTCGAAA
1 T-TCCAAAAA--TTACATTTTGACCCTCG-AA
*
433906 CTCTCAAAAATTACCATTTT-ACCCTCGAA
1 TTC-CAAAAATTA-CATTTTGACCCTCGAA
433935 TGTCCAAAAATT
1 T-TCCAAAAATT
433947 TCGTTTTTTG
Statistics
Matches: 245, Mismatches: 35, Indels: 50
0.74 0.11 0.15
Matches are distributed among these distances:
28 15 0.06
29 119 0.49
30 106 0.43
31 5 0.02
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.33
Consensus pattern (28 bp):
TTCCAAAAATTACATTTTGACCCTCGAA
Found at i:433954 original size:59 final size:56
Alignment explanation
Indices: 433588--433946 Score: 332
Period size: 59 Copynumber: 6.1 Consensus size: 56
433578 AAACTTCTCT
* * * *
433588 AAAATTATATTTTTAACCTTGAAACTTCCAAAAATTACATTTTTACCC-CTAAACTTCCA
1 AAAATTACATTTTTGACCTCGAAACTT-CAAAAATTACA-TTTTACCCTC-GAA-TTCCA
* * *
433647 AAAATTCCATTTTTAACC-CTAAAACTTCTAAAAATTACATTTTTAGCCC-CGAACTTCC-
1 AAAATTACATTTTTGACCTC-GAAACTTC-AAAAATTACA-TTTTA-CCCTCGAA-TTCCA
**
433705 AAAATTACATTTTTGACCTTAAAACTTCCAAAAATTACATTTTCACCCTCGAACTTCCA
1 AAAATTACATTTTTGACCTCGAAACTT-CAAAAATTACATTTT-ACCCTCGAA-TTCCA
* *
433764 AAAATTACATTTTTGACCCCGAAACTTCCAAAAATTACATTTCTACCCTCGAACCTCCA
1 AAAATTACATTTTTGACCTCGAAACTT-CAAAAATTACATTT-TACCCTCGAA-TTCCA
* * * * *
433823 AAAATTCCATTTTTGATCTCGAAACTTTCAAAAATTACCATTTTACCCCCGCATATACA
1 AAAATTACATTTTTGACCTCGAAAC-TTCAAAAATTA-CATTTTACCCTCGAAT-TCCA
*
433882 AAAACTT-TATTTTTGACCTCGAAACTCTCAAAAATTACCATTTTACCCTCGAATGTCCA
1 AAAA-TTACATTTTTGACCTCGAAACT-TCAAAAATTA-CATTTTACCCTCGAAT-TCCA
433941 AAAATT
1 AAAATT
433947 TCGTTTTTTG
Statistics
Matches: 261, Mismatches: 25, Indels: 29
0.83 0.08 0.09
Matches are distributed among these distances:
57 7 0.03
58 47 0.18
59 193 0.74
60 14 0.05
ACGTcount: A:0.37, C:0.25, G:0.04, T:0.34
Consensus pattern (56 bp):
AAAATTACATTTTTGACCTCGAAACTTCAAAAATTACATTTTACCCTCGAATTCCA
Found at i:437434 original size:9 final size:9
Alignment explanation
Indices: 437402--437440 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
437392 GATAAAATTT
437402 TTAATTT-A
1 TTAATTTAA
437410 TTAATTTAA
1 TTAATTTAA
**
437419 TCGATTTAA
1 TTAATTTAA
437428 TTAATTTAA
1 TTAATTTAA
437437 TTAA
1 TTAA
437441 AAATTATTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
8 7 0.27
9 19 0.73
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (9 bp):
TTAATTTAA
Found at i:441721 original size:24 final size:25
Alignment explanation
Indices: 441670--441735 Score: 64
Period size: 25 Copynumber: 2.6 Consensus size: 25
441660 TGACGGATTC
*
441670 AAATAATTTTAAATTTTATAAGTTAT
1 AAATAATTTT-AATTTTATAAGTAAT
441696 AAAT-ATTTTAATTTTA-AATGTAAT
1 AAATAATTTTAATTTTATAA-GTAAT
* * *
441720 AATTCATTTTATTTTT
1 AAATAATTTTAATTTT
441736 TATACGATGA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
23 2 0.06
24 14 0.40
25 15 0.43
26 4 0.11
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.55
Consensus pattern (25 bp):
AAATAATTTTAATTTTATAAGTAAT
Found at i:451778 original size:18 final size:18
Alignment explanation
Indices: 451755--451821 Score: 71
Period size: 18 Copynumber: 3.7 Consensus size: 18
451745 ATATGAACAG
451755 AAGTTCATCAAGACCTAA
1 AAGTTCATCAAGACCTAA
***
451773 AAGTTCATCAAGTTGTAA
1 AAGTTCATCAAGACCTAA
* * *
451791 CAAATTGAACAAGACCTAA
1 -AAGTTCATCAAGACCTAA
451810 AAGTTCATCAAG
1 AAGTTCATCAAG
451822 TTGTACCAAA
Statistics
Matches: 36, Mismatches: 12, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
18 24 0.67
19 12 0.33
ACGTcount: A:0.45, C:0.18, G:0.13, T:0.24
Consensus pattern (18 bp):
AAGTTCATCAAGACCTAA
Found at i:451813 original size:37 final size:37
Alignment explanation
Indices: 451763--451838 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
451753 AGAAGTTCAT
451763 CAAGACCTAAAAGTTCATCAAGTTGTAACAAATTGAA
1 CAAGACCTAAAAGTTCATCAAGTTGTAACAAATTGAA
*
451800 CAAGACCTAAAAGTTCATCAAGTTGTACCAAATTGAA
1 CAAGACCTAAAAGTTCATCAAGTTGTAACAAATTGAA
451837 CA
1 CA
451839 GAAGAAAGGC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.45, C:0.18, G:0.13, T:0.24
Consensus pattern (37 bp):
CAAGACCTAAAAGTTCATCAAGTTGTAACAAATTGAA
Found at i:458144 original size:20 final size:20
Alignment explanation
Indices: 458121--458183 Score: 76
Period size: 19 Copynumber: 3.2 Consensus size: 20
458111 AAAAAAAAAA
458121 CAAAATAATTTTTAAAAATT
1 CAAAATAATTTTTAAAAATT
**
458141 CAAAATAAAATTT-AAAATT
1 CAAAATAATTTTTAAAAATT
*
458160 CAAAAT-ATTTATAAAAATT
1 CAAAATAATTTTTAAAAATT
458179 ACAAA
1 -CAAA
458184 TTTCATGTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
18 3 0.08
19 18 0.50
20 15 0.42
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.33
Consensus pattern (20 bp):
CAAAATAATTTTTAAAAATT
Found at i:464411 original size:17 final size:17
Alignment explanation
Indices: 464389--464436 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
464379 AAAAAGTGAT
464389 AAAAATAGATAAAAAAG
1 AAAAATAGATAAAAAAG
*
464406 AAAAATATGA-GAAAAAG
1 AAAAATA-GATAAAAAAG
464423 AAAAA-A-ATAAAAAA
1 AAAAATAGATAAAAAA
464437 AATATTTCGT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
14 1 0.04
15 5 0.19
16 1 0.04
17 18 0.67
18 2 0.07
ACGTcount: A:0.79, C:0.00, G:0.10, T:0.10
Consensus pattern (17 bp):
AAAAATAGATAAAAAAG
Found at i:468886 original size:16 final size:18
Alignment explanation
Indices: 468862--468914 Score: 56
Period size: 17 Copynumber: 2.9 Consensus size: 18
468852 TTGATTTTTT
468862 TTTATAAA-TATTTTGAA
1 TTTATAAATTATTTTGAA
*
468879 TTTA-AAATTATTTTGAC
1 TTTATAAATTATTTTGAA
*
468896 TTTTTGAAAATTATTTTGA
1 TTTAT--AAATTATTTTGA
468915 TTTTTTTGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
16 3 0.10
17 15 0.50
20 12 0.40
ACGTcount: A:0.36, C:0.02, G:0.08, T:0.55
Consensus pattern (18 bp):
TTTATAAATTATTTTGAA
Found at i:468907 original size:20 final size:19
Alignment explanation
Indices: 468870--468919 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 19
468860 TTTTTATAAA
*
468870 TATTTTGA-ATTT-AAAAT
1 TATTTTGATTTTTGAAAAT
468887 TATTTTGACTTTTTGAAAAT
1 TATTTTGA-TTTTTGAAAAT
468907 TATTTTGATTTTT
1 TATTTTGATTTTT
468920 TTGTAATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 8 0.28
19 8 0.28
20 13 0.45
ACGTcount: A:0.30, C:0.02, G:0.08, T:0.60
Consensus pattern (19 bp):
TATTTTGATTTTTGAAAAT
Found at i:468927 original size:20 final size:20
Alignment explanation
Indices: 468882--468919 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
468872 TTTTGAATTT
468882 AAAATTATTTTGACTTTTTG
1 AAAATTATTTTGACTTTTTG
468902 AAAATTATTTTGA-TTTTT
1 AAAATTATTTTGACTTTTT
468920 TTGTAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.32, C:0.03, G:0.08, T:0.58
Consensus pattern (20 bp):
AAAATTATTTTGACTTTTTG
Found at i:469351 original size:28 final size:28
Alignment explanation
Indices: 469320--469375 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
469310 ATTAACCCTT
* * *
469320 TTTTTAATTAATTACGTAAATAACTTAA
1 TTTTTAATTAAATAAGAAAATAACTTAA
*
469348 TTTTTTATTAAATAAGAAAATAACTTAA
1 TTTTTAATTAAATAAGAAAATAACTTAA
469376 AATCTACAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (28 bp):
TTTTTAATTAAATAAGAAAATAACTTAA
Found at i:469717 original size:64 final size:65
Alignment explanation
Indices: 469599--469724 Score: 161
Period size: 64 Copynumber: 2.0 Consensus size: 65
469589 AAATGATTTA
** *
469599 CTATTTATATTTTTAAAATAAATTTAAAAATTTTTTGGTGGTGTCACCACTTTCCATAAATATTC
1 CTATTTATATTTTTAAAATAAATTTAAAAAAATTTTGGTGGTGTCACCAATTTCCATAAATATTC
*
469664 CTATTTAT-TTTTT-AAA-AAATTTAAAAAAATTTT-GTGGTGTCATCATCAATTTCCTTAAATA
1 CTATTTATATTTTTAAAATAAATTTAAAAAAATTTTGGTGGTGTCA-C--CAATTTCCATAAATA
469725 AGTTTTTTTA
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
61 9 0.17
62 16 0.30
63 3 0.06
64 18 0.33
65 8 0.15
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.46
Consensus pattern (65 bp):
CTATTTATATTTTTAAAATAAATTTAAAAAAATTTTGGTGGTGTCACCAATTTCCATAAATATTC
Found at i:470104 original size:18 final size:18
Alignment explanation
Indices: 470083--470118 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
470073 ATTATATAAT
470083 ATTTAAATATATAGTTTA
1 ATTTAAATATATAGTTTA
*
470101 ATTTAAATATATATTTTA
1 ATTTAAATATATAGTTTA
470119 TTTTTGGTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
ATTTAAATATATAGTTTA
Found at i:470140 original size:96 final size:100
Alignment explanation
Indices: 470025--470222 Score: 269
Period size: 104 Copynumber: 2.0 Consensus size: 100
470015 AATTTATTTA
*
470025 TTTGGTGGAGTAATTTTAAATGGCATCA-C-TTAA-TTGATTTTT-TTATTTATTATATAATATT
1 TTTGGTGGAGTAATATTAAATGGCATCACCATTAATTTGATTTTTATTATTTATTATATAATATT
470086 TAAATATATAGTTTAATTTAAATATATATTTTATT
66 TAAATATATAGTTTAATTTAAATATATATTTTATT
* ** * *
470121 TTTGGTGGAGTCATATTAAATGGTGTCACCCGATTAATTTTTGTTTTTTATTATTTATTATTTAA
1 TTTGGTGGAGTAATATTAAATGGCATCA-CC-ATTAA--TTTGATTTTTATTATTTATTATATAA
*
470186 TATTTAAATATATAGTTTAATTTAAATGTATATTTTA
62 TATTTAAATATATAGTTTAATTTAAATATATATTTTA
470223 CGCCATCAAT
Statistics
Matches: 87, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
96 24 0.28
98 1 0.01
100 4 0.05
103 8 0.09
104 50 0.57
ACGTcount: A:0.32, C:0.04, G:0.11, T:0.53
Consensus pattern (100 bp):
TTTGGTGGAGTAATATTAAATGGCATCACCATTAATTTGATTTTTATTATTTATTATATAATATT
TAAATATATAGTTTAATTTAAATATATATTTTATT
Found at i:470210 original size:18 final size:18
Alignment explanation
Indices: 470187--470222 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
470177 ATTATTTAAT
470187 ATTTAAATATATAGTTTA
1 ATTTAAATATATAGTTTA
* *
470205 ATTTAAATGTATATTTTA
1 ATTTAAATATATAGTTTA
470223 CGCCATCAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (18 bp):
ATTTAAATATATAGTTTA
Found at i:470310 original size:25 final size:26
Alignment explanation
Indices: 470266--470319 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
470256 ATTATTTATT
**
470266 TTTAAAATTTTAAATTTATT-TTTAA
1 TTTAAAATTTTAAAAATATTGTTTAA
*
470291 TTTAAAATTTTAAAAATATTGTTTTA
1 TTTAAAATTTTAAAAATATTGTTTAA
470317 TTT
1 TTT
470320 TGGTGGAGCC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 18 0.72
26 7 0.28
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (26 bp):
TTTAAAATTTTAAAAATATTGTTTAA
Found at i:472634 original size:24 final size:25
Alignment explanation
Indices: 472588--472636 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
472578 TAATATTTTA
*
472588 ATATTTTTATTTATTTTAAAAATAT
1 ATATTTATATTTATTTTAAAAATAT
472613 ATATTTATATTTA-TTTAAAAATAT
1 ATATTTATATTTATTTTAAAAATAT
472637 GATAAAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 11 0.48
25 12 0.52
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
ATATTTATATTTATTTTAAAAATAT
Found at i:472648 original size:25 final size:24
Alignment explanation
Indices: 472594--472650 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
472584 TTTAATATTT
**
472594 TTATTTATTTTAAAAATATATATT
1 TTATTTATTTTAAAAATATATAAA
472618 TATATTTA-TTTAAAAATATGATAAAA
1 T-TATTTATTTTAAAAATAT-AT-AAA
472644 TTATTTA
1 TTATTTA
472651 AAGTTTTATC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
24 12 0.43
25 14 0.50
26 2 0.07
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (24 bp):
TTATTTATTTTAAAAATATATAAA
Found at i:473233 original size:16 final size:16
Alignment explanation
Indices: 473208--473239 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
473198 ACAAAAATCC
473208 AGCATATATTTTTCTG
1 AGCATATATTTTTCTG
*
473224 AGCATTTATTTTTCTG
1 AGCATATATTTTTCTG
473240 GTTAATTAAA
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:0.22, C:0.12, G:0.12, T:0.53
Consensus pattern (16 bp):
AGCATATATTTTTCTG
Found at i:478466 original size:24 final size:24
Alignment explanation
Indices: 478438--478485 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
478428 TTAAGAAATG
478438 AAAAGTCTTTTCTATCCCAATGAT
1 AAAAGTCTTTTCTATCCCAATGAT
478462 AAAAGTCTTTTCTATCCCAATGAT
1 AAAAGTCTTTTCTATCCCAATGAT
478486 GCAAAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.21, G:0.08, T:0.38
Consensus pattern (24 bp):
AAAAGTCTTTTCTATCCCAATGAT
Found at i:478613 original size:12 final size:14
Alignment explanation
Indices: 478585--478617 Score: 52
Period size: 12 Copynumber: 2.5 Consensus size: 14
478575 TGTATTTAAA
478585 AAATAATATATAAT
1 AAATAATATATAAT
478599 AAATAATA-A-AAT
1 AAATAATATATAAT
478611 AAATAAT
1 AAATAAT
478618 TTGAAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 10 0.53
13 1 0.05
14 8 0.42
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AAATAATATATAAT
Found at i:479923 original size:20 final size:20
Alignment explanation
Indices: 479858--479923 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 20
479848 TTTTATAATT
479858 TTTTAAAAATATAAATTTTGAAA
1 TTTTAAAAAT-T--ATTTTGAAA
* * *
479881 TTTTTATATATAATTTT--AA
1 -TTTTAAAAATTATTTTGAAA
479900 TTTTAAAAATTATTTTGAAA
1 TTTTAAAAATTATTTTGAAA
479920 TTTT
1 TTTT
479924 TTTGTAATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
18 13 0.38
19 2 0.06
20 6 0.18
21 5 0.15
24 8 0.24
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
TTTTAAAAATTATTTTGAAA
Found at i:481670 original size:19 final size:19
Alignment explanation
Indices: 481632--481670 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
481622 TTTATTTATA
*
481632 TTAATATAATAATAATTAT
1 TTAATATAATAATAAATAT
481651 TTAATATTAAT-ATAAATAT
1 TTAATA-TAATAATAAATAT
481670 T
1 T
481671 AATGTAAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TTAATATAATAATAAATAT
Found at i:486849 original size:22 final size:21
Alignment explanation
Indices: 486806--486849 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
486796 ATAATACGGG
* * *
486806 TTTAAAAGTTTGTTTTATTTT
1 TTTAAAAGTTAGTTTAAGTTT
486827 TTTAAAGAGTTAGTTTAAGTTT
1 TTTAAA-AGTTAGTTTAAGTTT
486849 T
1 T
486850 GTGAAAAAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.27, C:0.00, G:0.14, T:0.59
Consensus pattern (21 bp):
TTTAAAAGTTAGTTTAAGTTT
Found at i:488428 original size:162 final size:161
Alignment explanation
Indices: 488037--488486 Score: 433
Period size: 162 Copynumber: 2.8 Consensus size: 161
488027 GACAGATCAA
* *
488037 TCCGCTGATTTATGATCATGA-CTTTCTACTTACGGGATTTTACGAA--TCTCGTAATCTACTAA
1 TCCGCTGATTTATGATCATGACCTTT-TACTTACGAGATTTTACGAATTTCTGGT--TC-ACTAA
* * * * ** * *
488099 TTTACGATAACAACCTTC-GACTTTTGGGATTTTATGAATCTCGCAGTCTACTGATTTACGATGA
62 TTTACGATAACGACCTTCTG-CTTATGGGATTTTACGAATCTCACAGTCCGCTGATTTACAATCA
* ** *
488163 CGACTTTCTACTTATGAGATTTTACTAATCTCACGG
126 CGACCTTCTACTTACAAGATTTTACGAATCTCACGG
* * * * * *
488199 TCCGCTGATTTATGATTACGACCTTCTACTTACGAGATTTCATGAATCTTGC-GGTCCACTAATT
1 TCCGCTGATTTATGATCATGACCTTTTACTTACGAGATTTTACGAAT-TT-CTGGTTCACTAATT
* * * * *
488263 TACGCTGACGACCTTCTGCTTACGGGATTTTACGAATCTCACAGTCCGTTGATTTTCAATCACGA
64 TACGATAACGACCTTCTGCTTATGGGATTTTACGAATCTCACAGTCCGCTGATTTACAATCACGA
* **
488328 CCTTCTGCTTACAAGATTTTACGAATCTCGTGG
129 CCTTCTACTTACAAGATTTTACGAATCTCACGG
* * * *
488361 TCTGTTGATTTATGATCATGACCTTTTACTTACGAGATTTTACGAATTTCATGGTTCGCTGATTT
1 TCCGCTGATTTATGATCATGACCTTTTACTTACGAGATTTTACGAATTTC-TGGTTCACTAATTT
* ** * * * * *
488426 ACGATCACGATTTTTTACTTATGGGATTTTACAAATCTCATAGTCCGCTGATTTACGATCA
65 ACGATAACGACCTTCTGCTTATGGGATTTTACGAATCTCACAGTCCGCTGATTTACAATCA
488487 TGACTTTTTG
Statistics
Matches: 230, Mismatches: 50, Indels: 16
0.78 0.17 0.05
Matches are distributed among these distances:
160 1 0.00
161 2 0.01
162 218 0.95
163 5 0.02
165 3 0.01
166 1 0.00
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.38
Consensus pattern (161 bp):
TCCGCTGATTTATGATCATGACCTTTTACTTACGAGATTTTACGAATTTCTGGTTCACTAATTTA
CGATAACGACCTTCTGCTTATGGGATTTTACGAATCTCACAGTCCGCTGATTTACAATCACGACC
TTCTACTTACAAGATTTTACGAATCTCACGG
Found at i:488495 original size:54 final size:54
Alignment explanation
Indices: 488037--488486 Score: 342
Period size: 54 Copynumber: 8.3 Consensus size: 54
488027 GACAGATCAA
* * * * ** *
488037 TCCGCTGATTTATGATCATGACTTTCTACTTACGGGATTTTACGAATCTCGTAA
1 TCCGCTGATTTACGATCACGACCTTCTACTTACGAGATTTTACGAATCTCACAG
** * * * * ** * * *
488091 TCTACTAATTTACGATAACAACCTTCGACTTTTGGGATTTTATGAATCTCGCAG
1 TCCGCTGATTTACGATCACGACCTTCTACTTACGAGATTTTACGAATCTCACAG
** * * * * *
488145 TCTACTGATTTACGATGACGACTTTCTACTTATGAGATTTTACTAATCTCACGG
1 TCCGCTGATTTACGATCACGACCTTCTACTTACGAGATTTTACGAATCTCACAG
* * * * ** *
488199 TCCGCTGATTTATGATTACGACCTTCTACTTACGAGATTTCATGAATCTTGCGG
1 TCCGCTGATTTACGATCACGACCTTCTACTTACGAGATTTTACGAATCTCACAG
* * * * * *
488253 TCCACTAATTTACGCTGACGACCTTCTGCTTACGGGATTTTACGAATCTCACAG
1 TCCGCTGATTTACGATCACGACCTTCTACTTACGAGATTTTACGAATCTCACAG
* * * * * ***
488307 TCCGTTGATTTTCAATCACGACCTTCTGCTTACAAGATTTTACGAATCTCGTGG
1 TCCGCTGATTTACGATCACGACCTTCTACTTACGAGATTTTACGAATCTCACAG
* * * * * * **
488361 TCTGTTGATTTATGATCATGACCTTTTACTTACGAGATTTTACGAATTTCATGG
1 TCCGCTGATTTACGATCACGACCTTCTACTTACGAGATTTTACGAATCTCACAG
* ** * * * * *
488415 TTCGCTGATTTACGATCACGATTTTTTACTTATGGGATTTTACAAATCTCATAG
1 TCCGCTGATTTACGATCACGACCTTCTACTTACGAGATTTTACGAATCTCACAG
488469 TCCGCTGATTTACGATCA
1 TCCGCTGATTTACGATCA
488487 TGACTTTTTG
Statistics
Matches: 313, Mismatches: 83, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
54 313 1.00
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.38
Consensus pattern (54 bp):
TCCGCTGATTTACGATCACGACCTTCTACTTACGAGATTTTACGAATCTCACAG
Found at i:489143 original size:13 final size:13
Alignment explanation
Indices: 489098--489169 Score: 56
Period size: 16 Copynumber: 5.2 Consensus size: 13
489088 TATTATTTCA
489098 AAAAAATAATTTT
1 AAAAAATAATTTT
**
489111 AATAATTTTATATTTT
1 AA-AA-AATA-ATTTT
489127 AAAAAATAA-TTT
1 AAAAAATAATTTT
*
489139 AAAAATTTTATATTTT
1 AAAAA--ATA-ATTTT
489155 AAAAAATAATTTT
1 AAAAAATAATTTT
489168 AA
1 AA
489170 TAATTTTAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
12 8 0.17
13 10 0.22
14 8 0.17
15 5 0.11
16 15 0.33
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AAAAAATAATTTT
Found at i:489159 original size:29 final size:29
Alignment explanation
Indices: 489077--489177 Score: 159
Period size: 28 Copynumber: 3.4 Consensus size: 29
489067 ATTAAAATTA
*
489077 TTTAATAATTTTATTATTTCAAAAAAATAAT
1 TTTAATAATTTTA-TATTT-TAAAAAATAAT
489108 TTTAATAATTTTATATTTTAAAAAATAA-
1 TTTAATAATTTTATATTTTAAAAAATAAT
*
489136 TTTAAAAATTTTATATTTTAAAAAATAAT
1 TTTAATAATTTTATATTTTAAAAAATAAT
489165 TTTAATAATTTTA
1 TTTAATAATTTTA
489178 AAATCATTTG
Statistics
Matches: 66, Mismatches: 3, Indels: 4
0.90 0.04 0.05
Matches are distributed among these distances:
28 27 0.41
29 21 0.32
30 5 0.08
31 13 0.20
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (29 bp):
TTTAATAATTTTATATTTTAAAAAATAAT
Found at i:489605 original size:21 final size:21
Alignment explanation
Indices: 489576--489615 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
489566 GTTACATGCG
* *
489576 TGTAAAATTGTGATAAAATTT
1 TGTAAAATTATAATAAAATTT
*
489597 TGTAGAATTATAATAAAAT
1 TGTAAAATTATAATAAAAT
489616 ATATCATAAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.40
Consensus pattern (21 bp):
TGTAAAATTATAATAAAATTT
Found at i:491330 original size:9 final size:9
Alignment explanation
Indices: 491316--491344 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
491306 TATAGGTTTG
491316 TTTGTTTTT
1 TTTGTTTTT
491325 TTTG-TTTT
1 TTTGTTTTT
491333 TTTGTTTTT
1 TTTGTTTTT
491342 TTT
1 TTT
491345 TTATGATTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (9 bp):
TTTGTTTTT
Found at i:491336 original size:17 final size:17
Alignment explanation
Indices: 491311--491344 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
491301 GTCTGTATAG
491311 GTTTGTTTGTTTTTTTT
1 GTTTGTTTGTTTTTTTT
*
491328 GTTTTTTTGTTTTTTTT
1 GTTTGTTTGTTTTTTTT
491345 TTATGATTGG
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:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (17 bp):
GTTTGTTTGTTTTTTTT
Found at i:498405 original size:15 final size:14
Alignment explanation
Indices: 498365--498406 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 14
498355 AAATTGGAAT
498365 TTATTTTTAAA-TA
1 TTATTTTTAAATTA
*
498378 -TATTTTTATATTA
1 TTATTTTTAAATTA
498391 TTATTTTTGAAATTA
1 TTATTTTT-AAATTA
498406 T
1 T
498407 AAAAAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 9 0.38
13 2 0.08
14 7 0.29
15 6 0.25
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (14 bp):
TTATTTTTAAATTA
Found at i:499430 original size:13 final size:13
Alignment explanation
Indices: 499412--499453 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
499402 ATTAAATTAA
499412 AAAAAAATTATTT
1 AAAAAAATTATTT
*
499425 AAAAAAGCTTATTT
1 AAAAAA-ATTATTT
*
499439 AATAAAATT-TTT
1 AAAAAAATTATTT
499451 AAA
1 AAA
499454 TATTAATATA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
12 5 0.21
13 8 0.33
14 11 0.46
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (13 bp):
AAAAAAATTATTT
Found at i:502412 original size:5 final size:5
Alignment explanation
Indices: 502402--502431 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
502392 GTGATGATGC
502402 AGAGG AGAGG AGAGG AGAGG AGAGG AGAGG
1 AGAGG AGAGG AGAGG AGAGG AGAGG AGAGG
502432 GGACAAAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (5 bp):
AGAGG
Found at i:506668 original size:6 final size:6
Alignment explanation
Indices: 506657--506681 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
506647 TTAGAAGCTT
506657 TCAGAC TCAGAC TCAGAC TCAGAC T
1 TCAGAC TCAGAC TCAGAC TCAGAC T
506682 ACAGTCTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.32, G:0.16, T:0.20
Consensus pattern (6 bp):
TCAGAC
Found at i:506827 original size:6 final size:6
Alignment explanation
Indices: 506808--506854 Score: 85
Period size: 6 Copynumber: 7.8 Consensus size: 6
506798 CCTTAAATCT
*
506808 CTCTTC CTCCTC CTCTTC CTCTTC CTCTTC CTCTTC CTCTTC CTCTT
1 CTCTTC CTCTTC CTCTTC CTCTTC CTCTTC CTCTTC CTCTTC CTCTT
506855 GTCTAACAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (6 bp):
CTCTTC
Found at i:507630 original size:18 final size:18
Alignment explanation
Indices: 507594--507631 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
507584 TGATTTTCAG
*
507594 GAAGATAAACAAAGGGTT
1 GAAGATAAACAAAGAGTT
507612 GAAGA-AAACAATAGAGTT
1 GAAGATAAACAA-AGAGTT
507630 GA
1 GA
507632 GATCTTATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.53, C:0.05, G:0.26, T:0.16
Consensus pattern (18 bp):
GAAGATAAACAAAGAGTT
Found at i:512601 original size:16 final size:16
Alignment explanation
Indices: 512577--512611 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
512567 TCCAAACCTG
512577 AAGCAACTTAAATCCA
1 AAGCAACTTAAATCCA
* *
512593 AAGCGACTTAAATTCA
1 AAGCAACTTAAATCCA
512609 AAG
1 AAG
512612 TTGACCCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.49, C:0.20, G:0.11, T:0.20
Consensus pattern (16 bp):
AAGCAACTTAAATCCA
Found at i:514747 original size:17 final size:17
Alignment explanation
Indices: 514725--514803 Score: 76
Period size: 17 Copynumber: 4.8 Consensus size: 17
514715 TAAACTCATT
*
514725 TTAAATTCATTTTAAGA
1 TTAAATTTATTTTAAGA
* *
514742 TTAAATTTATCTTAAAA
1 TTAAATTTATTTTAAGA
514759 TT-AA-TTATTTTAA-A
1 TTAAATTTATTTTAAGA
*
514773 TTTAAATTTGA-TTTAAGT
1 -TTAAATTT-ATTTTAAGA
514791 TTAAATTTATTTT
1 TTAAATTTATTTT
514804 TAAATTTAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
14 1 0.02
15 10 0.20
16 5 0.10
17 34 0.67
18 1 0.02
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (17 bp):
TTAAATTTATTTTAAGA
Found at i:514830 original size:6 final size:6
Alignment explanation
Indices: 514767--514813 Score: 51
Period size: 6 Copynumber: 8.0 Consensus size: 6
514757 AATTAATTAT
* * **
514767 TTTAAA TTTAAA TTT-GA TTTAAG TTTAAA TTTATT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
514814 ATCATTATAA
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
5 4 0.12
6 28 0.88
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:515566 original size:21 final size:22
Alignment explanation
Indices: 515536--515585 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 22
515526 TAATAACTAT
515536 TAATAATAACAACAGTAAT-AA
1 TAATAATAACAACAGTAATAAA
* *
515557 TAATAGTAACAGCAGTAATAAA
1 TAATAATAACAACAGTAATAAA
515579 TAATAAT
1 TAATAAT
515586 TAATATTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 17 0.68
22 8 0.32
ACGTcount: A:0.58, C:0.08, G:0.08, T:0.26
Consensus pattern (22 bp):
TAATAATAACAACAGTAATAAA
Found at i:516847 original size:29 final size:29
Alignment explanation
Indices: 516748--517214 Score: 230
Period size: 30 Copynumber: 15.9 Consensus size: 29
516738 GCCTTGAAGG
* *
516748 CCCCTAAACTTCTCCAAAATTATATTTTTGA
1 CCCCTAAACTT-TCAAAAATTACATTTTT-A
* * *
516779 -CCCTGAACTTCCAAAAATCCTA-TTTTTTAA
1 CCCCTAAACTTTCAAAAAT--TACATTTTT-A
* * *
516809 TCTCGAAACTTTCAAAAA-TACATTTTATA
1 CCCCTAAACTTTCAAAAATTACATTTT-TA
516838 CCCCTAAAC-TTCTAAAAATTACATTTTATA
1 CCCCTAAACTTTC-AAAAATTACATTTT-TA
* * * *
516868 CCCTTAAACTTCCAAAAATTCCATTTTAA
1 CCCCTAAACTTTCAAAAATTACATTTTTA
* * * *
516897 TCCCGAAACTTTTAAAAAATACA--TTTA
1 CCCCTAAACTTTCAAAAATTACATTTTTA
* *
516924 CTCCC-AAACTTCCAAAAATTCCATTTTTGA
1 C-CCCTAAACTTTCAAAAATTACATTTTT-A
516954 -CCCTAAAAC-TTCTAAAAATTACATTTTTA
1 CCCCT-AAACTTTC-AAAAATTACATTTTTA
* * *
516983 -CCCTCGAAC-TTCTAAAAATTCCATTTTGA
1 CCCCT-AAACTTTC-AAAAATTACATTTTTA
* * * *
517012 TCTCAAAACTTT-AGAAAATTATA-TTTTA
1 CCCCTAAACTTTCA-AAAATTACATTTTTA
* * *
517040 ACCCTCGAACTTTCAAAAATTTCATTTTTAA
1 CCCCT-AAACTTTCAAAAATTACATTTTT-A
* *
517071 CCCCAAAACTTCCAAAAATTACATTTTTA
1 CCCCTAAACTTTCAAAAATTACATTTTTA
* * * * *
517100 -CACTCGAAC-TTCCAAAACTCCATTTTTAA
1 CCCCT-AAACTTTCAAAAATTACATTTTT-A
* *
517129 CCTCGAAACTTTCAAAAATTAC-TATTTTA
1 CCCCTAAACTTTCAAAAATTACAT-TTTTA
* * *
517158 CCCTTAAAC-TTCCAAAATTCCATTTTTGA
1 CCCCTAAACTTTCAAAAATTACATTTTT-A
* * *
517187 CCTCGAAACTTTCAAAAATCAACATTTT
1 CCCCTAAACTTTCAAAAAT-TACATTTT
517215 ACCTTTGGAT
Statistics
Matches: 328, Mismatches: 77, Indels: 62
0.70 0.16 0.13
Matches are distributed among these distances:
27 17 0.05
28 48 0.15
29 117 0.36
30 119 0.36
31 27 0.08
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.36
Consensus pattern (29 bp):
CCCCTAAACTTTCAAAAATTACATTTTTA
Found at i:516993 original size:86 final size:86
Alignment explanation
Indices: 516753--517174 Score: 238
Period size: 88 Copynumber: 4.8 Consensus size: 86
516743 GAAGGCCCCT
* * * ** * *
516753 AAACTTCTCCAAAATTATATTTT-TGACCCT-GAACTTCCAAAAATCCTATTTTTTAATCTCGAA
1 AAACTTC-CAAAAATTACATTTTAT-ACCCTAAAACTTCCAAAAAT--TACATTTTAACCCCGAA
*
516816 ACTT-TCAAAAATACATTTTA-TACCCC
62 ACTTCTAAAAAATACA-TTTACT--CCC
* * * *
516842 TAAACTTCTAAAAATTACATTTTATACCCTTAAACTTCCAAAAATTCCATTTTAATCCCGAAACT
1 -AAACTTCCAAAAATTACATTTTATACCCTAAAACTTCCAAAAATTACATTTTAACCCCGAAACT
*
516907 TTTAAAAAATACATTTACTCCC
65 TCTAAAAAATACATTTACTCCC
* * *
516929 AAACTTCCAAAAATTCCATTTT-TGACCCTAAAACTTCTAAAAATTACATTTTTACCCTCG-AAC
1 AAACTTCCAAAAATTACATTTTAT-ACCCTAAAACTTCCAAAAATTACATTTTAACCC-CGAAAC
* * *
516992 TTCTAAAAATTCCATTTTGA-TCTCA
64 TTCTAAAAAATACA-TTT-ACTC-CC
* * ** * * *
517017 AAACTT-TAGAAAATTATATTTTA-ACCCTCGAACTTTCAAAAATTTCATTTTTAACCCCAAAAC
1 AAACTTCCA-AAAATTACATTTTATACCCTAAAACTTCCAAAAATTACA-TTTTAACCCCGAAAC
* * * *
517080 TTCCAAAAATTACATTTTTACACTC
64 TTCTAAAAAATACA--TTTACTCCC
* * * * * * **
517105 GAACTTCC-AAAACTCCATTTT-TAACCTCGAAACTTTCAAAAATTACTATTTT-ACCCTTAAAC
1 AAACTTCCAAAAATTACATTTTATACCCT-AAAACTTCCAAAAATTAC-ATTTTAACCCCGAAAC
*
517167 TTCCAAAA
64 TTCTAAAA
517175 TTCCATTTTT
Statistics
Matches: 267, Mismatches: 46, Indels: 41
0.75 0.13 0.12
Matches are distributed among these distances:
85 1 0.00
86 62 0.23
87 61 0.23
88 88 0.33
89 34 0.13
90 21 0.08
ACGTcount: A:0.38, C:0.23, G:0.03, T:0.36
Consensus pattern (86 bp):
AAACTTCCAAAAATTACATTTTATACCCTAAAACTTCCAAAAATTACATTTTAACCCCGAAACTT
CTAAAAAATACATTTACTCCC
Found at i:517212 original size:117 final size:113
Alignment explanation
Indices: 516843--517214 Score: 371
Period size: 117 Copynumber: 3.2 Consensus size: 113
516833 TTATACCCCT
* **
516843 AAAC-TTCTAAAAATTACATTTTATACCCTTAAACTTCCAAAAATTCCATTTTAATCC-CGAAAC
1 AAACTTTC-AAAAATTACATTTT-TACACTCGAACTTCC-AAAATTCCATTTTAA-CCTCGAAAC
*
516906 TTTTAAAAAATAC-A-TTTACTCC-CAAACTTCCAAAAATTCCATTTTTGACCCTA
62 -TTTAAAAATTACTATTTTAC-CCTCAAACTTCC-AAAATTCCATTTTTGACCC-A
* * * * *
516959 AAAC-TTCTAAAAATTACATTTTTACCCTCGAACTTCTAAAAATTCCATTTTGATCTCAAAACTT
1 AAACTTTC-AAAAATTACATTTTTACACTCGAACTTC-CAAAATTCCATTTTAACCTCGAAACTT
* * * *
517023 TAGAAAATTA-TATTTTAACCCTCGAACTTTCAAAAATTTCATTTTTAACCCCA
64 TA-AAAATTACTATTTT-ACCCTCAAAC-TTCCAAAATTCCATTTTTGA-CCCA
* *
517076 AAACTTCCAAAAATTACATTTTTACACTCGAACTTCCAAAACTCCATTTTTAACCTCGAAACTTT
1 AAACTTTCAAAAATTACATTTTTACACTCGAACTTCCAAAATTCCA-TTTTAACCTCGAAACTTT
* *
517141 CAAAAATTACTATTTTACCCTTAAACTTCCAAAATTCCATTTTTGACCTCG
65 -AAAAATTACTATTTTACCCTCAAACTTCCAAAATTCCATTTTTGACC-CA
*
517192 AAACTTTCAAAAATCAACATTTT
1 AAACTTTCAAAAAT-TACATTTT
517215 ACCTTTGGAT
Statistics
Matches: 215, Mismatches: 26, Indels: 29
0.80 0.10 0.11
Matches are distributed among these distances:
114 5 0.02
115 40 0.19
116 66 0.31
117 89 0.41
118 15 0.07
ACGTcount: A:0.38, C:0.23, G:0.03, T:0.36
Consensus pattern (113 bp):
AAACTTTCAAAAATTACATTTTTACACTCGAACTTCCAAAATTCCATTTTAACCTCGAAACTTTA
AAAATTACTATTTTACCCTCAAACTTCCAAAATTCCATTTTTGACCCA
Found at i:517218 original size:29 final size:30
Alignment explanation
Indices: 516753--517214 Score: 261
Period size: 29 Copynumber: 15.7 Consensus size: 30
516743 GAAGGCCCCT
* * *
516753 AAACTTCTCCAAAATTATATTTTTGACC-CTG
1 AAACTTC-CAAAAATTACATTTTTAACCTC-G
* *
516784 -AACTTCCAAAAATCCTA-TTTTTTAATCTCG
1 AAACTTCCAAAAAT--TACATTTTTAACCTCG
* * *
516814 AAACTTTCAAAAA-TACA-TTTTATACCCCT
1 AAACTTCCAAAAATTACATTTTTA-ACCTCG
* * *
516843 AAACTTCTAAAAATTACATTTTATACCCT-T
1 AAACTTCCAAAAATTACATTTT-TAACCTCG
*
516873 AAACTTCCAAAAATTCCA-TTTTAATCC-CG
1 AAACTTCCAAAAATTACATTTTTAA-CCTCG
** * *
516902 AAACTTTTAAAAAATACA--TTT-A-CTCCC
1 AAACTTCCAAAAATTACATTTTTAACCT-CG
* * *
516929 AAACTTCCAAAAATTCCATTTTTGACC-CTA
1 AAACTTCCAAAAATTACATTTTTAACCTC-G
* *
516959 AAACTTCTAAAAATTACATTTTTACCCTCG
1 AAACTTCCAAAAATTACATTTTTAACCTCG
* * * * *
516989 -AACTTCTAAAAATTCCA-TTTTGATCTCA
1 AAACTTCCAAAAATTACATTTTTAACCTCG
* *
517017 AAACTT-TAGAAAATTATA-TTTTAACCCTCG
1 AAACTTCCA-AAAATTACATTTTTAA-CCTCG
* * * *
517047 -AACTTTCAAAAATTTCATTTTTAACCCCA
1 AAACTTCCAAAAATTACATTTTTAACCTCG
517076 AAACTTCCAAAAATTACATTTTT-ACACTCG
1 AAACTTCCAAAAATTACATTTTTAAC-CTCG
* *
517106 -AACTTCC-AAAACTCCATTTTTAACCTCG
1 AAACTTCCAAAAATTACATTTTTAACCTCG
* * *
517134 AAACTTTCAAAAATTAC-TATTTTACCCT-T
1 AAACTTCCAAAAATTACAT-TTTTAACCTCG
* *
517163 AAACTTCC-AAAATTCCATTTTTGACCTCG
1 AAACTTCCAAAAATTACATTTTTAACCTCG
* *
517192 AAACTTTCAAAAATCAACATTTT
1 AAACTTCCAAAAAT-TACATTTT
517215 ACCTTTGGAT
Statistics
Matches: 331, Mismatches: 66, Indels: 68
0.71 0.14 0.15
Matches are distributed among these distances:
25 1 0.00
27 16 0.05
28 51 0.15
29 124 0.37
30 110 0.33
31 27 0.08
32 2 0.01
ACGTcount: A:0.38, C:0.23, G:0.03, T:0.36
Consensus pattern (30 bp):
AAACTTCCAAAAATTACATTTTTAACCTCG
Found at i:517302 original size:59 final size:58
Alignment explanation
Indices: 516843--517302 Score: 390
Period size: 58 Copynumber: 7.9 Consensus size: 58
516833 TTATACCCCT
** *
516843 AAAC-TTCTAAAAATTACATTTTATACCCTTAAACTTCCAAAAATTCCA-TTTTAATCC-CG
1 AAACTTTC-AAAAATTACA-TTT-TACCCTCGAACTTCCAAAAATTCCATTTTTGA-CCTCG
* * * *
516902 AAACTTTTAAAAAATACA-TTTACTCC-CAAACTTCCAAAAATTCCATTTTTGACC-CTA
1 AAACTTTCAAAAATTACATTTTAC-CCTCGAACTTCCAAAAATTCCATTTTTGACCTC-G
* * *
516959 AAAC-TTCTAAAAATTACATTTTTACCCTCGAACTTCTAAAAATTCCA-TTTTGATCTCA
1 AAACTTTC-AAAAATTACA-TTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCTCG
* * * * * *
517017 AAACTTT-AGAAAATTATATTTTAACCCTCGAACTTTCAAAAATTTCATTTTTAACCCCA
1 AAACTTTCA-AAAATTACATTTT-ACCCTCGAACTTCCAAAAATTCCATTTTTGACCTCG
* * * *
517076 AAACTTCCAAAAATTACATTTTTACACTCGAACTTCC-AAAACTCCATTTTTAACCTCG
1 AAACTTTCAAAAATTACA-TTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCTCG
**
517134 AAACTTTCAAAAATTACTATTTTACCCTTAAACTTCC-AAAATTCCATTTTTGACCTCG
1 AAACTTTCAAAAATTAC-ATTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCTCG
* * * * ** *
517192 AAACTTTCAAAAATCAACATTTTACCTTTGGA-TGTCCAAAAACTT-TGTTTTTGACGTCG
1 AAACTTTCAAAAAT-TACATTTTACCCTCGAACT-TCCAAAAA-TTCCATTTTTGACCTCG
* *
517251 AAACTTTCAAAAAATACCATTTTACCCTCGAA-TGTCCAAAAATTTCATTTTT
1 AAACTTTCAAAAATTA-CATTTTACCCTCGAACT-TCCAAAAATTCCATTTTT
517303 TATCCCAATT
Statistics
Matches: 334, Mismatches: 45, Indels: 44
0.79 0.11 0.10
Matches are distributed among these distances:
56 26 0.08
57 28 0.08
58 141 0.42
59 130 0.39
60 9 0.03
ACGTcount: A:0.37, C:0.23, G:0.04, T:0.36
Consensus pattern (58 bp):
AAACTTTCAAAAATTACATTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCTCG
Found at i:518855 original size:19 final size:19
Alignment explanation
Indices: 518820--518884 Score: 73
Period size: 18 Copynumber: 3.5 Consensus size: 19
518810 AATTTGTATA
*
518820 TATATATT-TAAA-AATTT
1 TATATATTATAAATTATTT
518837 TATATATTATAAATTATTT
1 TATATATTATAAATTATTT
*
518856 T-TATTTTATATAATTATATT
1 TATATATTATA-AATTAT-TT
518876 TATATATTA
1 TATATATTA
518885 AAAAATAGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
17 8 0.20
18 12 0.30
19 11 0.28
20 3 0.08
21 6 0.15
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TATATATTATAAATTATTT
Found at i:519564 original size:61 final size:61
Alignment explanation
Indices: 519442--519564 Score: 183
Period size: 61 Copynumber: 2.0 Consensus size: 61
519432 AATTAATAGA
* *****
519442 GAAGTGTAGTAGCAATTTTGAGTAAAATGATTCAATTACACAGTATTTGAAATTTTTTTTT
1 GAAGTGTAGTAGCAATTTTGAGTAAAACGATTCAATTACACAGTATTTGAAAGAAAATTTT
*
519503 GAAGTGTAGTAGCAATTTTGAGTAAAACGATTCAATTCCACAGTATTTGAAAGAAAATTTT
1 GAAGTGTAGTAGCAATTTTGAGTAAAACGATTCAATTACACAGTATTTGAAAGAAAATTTT
519564 G
1 G
519565 TTATTCACTA
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
61 55 1.00
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37
Consensus pattern (61 bp):
GAAGTGTAGTAGCAATTTTGAGTAAAACGATTCAATTACACAGTATTTGAAAGAAAATTTT
Found at i:524761 original size:17 final size:17
Alignment explanation
Indices: 524731--524770 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
524721 TAGCAGAATA
*
524731 TAAATATATCTTAAAAT
1 TAAATTTATCTTAAAAT
* *
524748 TAAATTTATTTTAAATT
1 TAAATTTATCTTAAAAT
524765 TAAATT
1 TAAATT
524771 GGAAATTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
TAAATTTATCTTAAAAT
Found at i:524766 original size:6 final size:6
Alignment explanation
Indices: 524741--524804 Score: 53
Period size: 6 Copynumber: 10.8 Consensus size: 6
524731 TAAATATATC
* * *
524741 TTAAAA TTAAAT TT-ATT TTAAAT TTAAAT TGGAAAT TTAAAT TT--AT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT T-TAAAT TTAAAT TTAAAT
*
524787 TATAAAT TTGAAT TTAAA
1 T-TAAAT TTAAAT TTAAA
524805 ATACATTTAA
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
4 3 0.07
5 5 0.11
6 30 0.65
7 8 0.17
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.48
Consensus pattern (6 bp):
TTAAAT
Found at i:524795 original size:17 final size:17
Alignment explanation
Indices: 524757--524816 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
524747 TTAAATTTAT
*
524757 TTTAAATTTAAATTGGAAA
1 TTTAAATTTAAAAT--AAA
**
524776 TTTAAATTTATTATAAA
1 TTTAAATTTAAAATAAA
* *
524793 TTTGAATTTAAAATACA
1 TTTAAATTTAAAATAAA
524810 TTTAAAT
1 TTTAAAT
524817 AATATCCAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
17 22 0.67
19 11 0.33
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:524815 original size:23 final size:23
Alignment explanation
Indices: 524762--524816 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
524752 TTTATTTTAA
**
524762 ATTTAAATTGGAAATTTAAATTT
1 ATTTAAATTGGAAATTTAAATAC
*
524785 ATTATAAATTTG-AATTTAAAATAC
1 ATT-TAAATTGGAAATTT-AAATAC
524809 ATTTAAAT
1 ATTTAAAT
524817 AATATCCAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 13 0.48
24 14 0.52
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.45
Consensus pattern (23 bp):
ATTTAAATTGGAAATTTAAATAC
Found at i:526664 original size:30 final size:29
Alignment explanation
Indices: 526578--526857 Score: 234
Period size: 29 Copynumber: 9.6 Consensus size: 29
526568 CTCTAAATTG
*
526578 TCCAAAAATTA-TTTTTTACCCCTAAACT
1 TCCAAAAATTACATTTTTACCCCTAAACT
*
526606 TCCAAAAATTCCATTTTTACCCCTAAACT
1 TCCAAAAATTACATTTTTACCCCTAAACT
* * **
526635 TTCAAAAATTCCATTTTTAACGTCTAAACT
1 TCCAAAAATTACATTTTT-ACCCCTAAACT
* * *
526665 TTCGAAAAGTACA-TTTTACCCCTAAACT
1 TCCAAAAATTACATTTTTACCCCTAAACT
* *
526693 TCCAAAAA-TATCATTTTTTACTCCAAAACT
1 TCCAAAAATTA-CA-TTTTTACCCCTAAACT
* * *
526723 TCAAAAAATTACATTTTGACCCCAAAACT
1 TCCAAAAATTACATTTTTACCCCTAAACT
** *
526752 TCCAAAAATTACATTTTTA-TGCTCGAACT
1 TCCAAAAATTACATTTTTACCCCT-AAACT
*
526781 TCC-AAAATT-CTATTTTTGACCCCGAAACT
1 TCCAAAAATTAC-ATTTTT-ACCCCTAAACT
**
526810 TTTAAAAATTAGCA-TTTTACCCCTAAA-T
1 TCCAAAAATTA-CATTTTTACCCCTAAACT
*
526838 GTCCAAAAATTTTCATTTTT
1 -TCCAAAAA-TTACATTTTT
526858 GATCTCGATT
Statistics
Matches: 203, Mismatches: 33, Indels: 30
0.76 0.12 0.11
Matches are distributed among these distances:
27 3 0.01
28 41 0.20
29 97 0.48
30 58 0.29
31 3 0.01
32 1 0.00
ACGTcount: A:0.36, C:0.23, G:0.04, T:0.37
Consensus pattern (29 bp):
TCCAAAAATTACATTTTTACCCCTAAACT
Found at i:530495 original size:145 final size:145
Alignment explanation
Indices: 530232--530521 Score: 535
Period size: 145 Copynumber: 2.0 Consensus size: 145
530222 ACTTACCAAA
*
530232 GTGTTTCTTTGTAACAAACTATATTACAACTTGACCCTTATATTTGCAAAAGCCCTAAAATACAC
1 GTGTTTCTTTGTAACAAACTATATTACAACTTGACCCGTATATTTGCAAAAGCCCTAAAATACAC
* *
530297 ACCGAACGGGAGTACGTTCGGAGGCGGTCACAAAGCATTTCAAACCAAGGTGTTTTAAGCTTGTA
66 ACCGAACGGAAGTACGTTCGGAGGCGGTCACAAAGCATTCCAAACCAAGGTGTTTTAAGCTTGTA
530362 AAAGGTCTAAGAAAC
131 AAAGGTCTAAGAAAC
530377 GTGTTTCTTTGTAACAAACTATATTACAACTTGACCCGTATATTTGCAAAAGCCCTAAAATACAC
1 GTGTTTCTTTGTAACAAACTATATTACAACTTGACCCGTATATTTGCAAAAGCCCTAAAATACAC
*
530442 ACCGAACGGAAGTACGTTTGGAGGCGGTCACAAAGCATTCCAAACCAAGGTGTTTTAAGCTTGTA
66 ACCGAACGGAAGTACGTTCGGAGGCGGTCACAAAGCATTCCAAACCAAGGTGTTTTAAGCTTGTA
*
530507 AAGGGTCTAAGAAAC
131 AAAGGTCTAAGAAAC
530522 TAACACCAAG
Statistics
Matches: 140, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
145 140 1.00
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (145 bp):
GTGTTTCTTTGTAACAAACTATATTACAACTTGACCCGTATATTTGCAAAAGCCCTAAAATACAC
ACCGAACGGAAGTACGTTCGGAGGCGGTCACAAAGCATTCCAAACCAAGGTGTTTTAAGCTTGTA
AAAGGTCTAAGAAAC
Found at i:537914 original size:3 final size:3
Alignment explanation
Indices: 537906--537936 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
537896 ACCATACATA
537906 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
537937 GATAATACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:543049 original size:2 final size:2
Alignment explanation
Indices: 542982--543033 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
542972 CAATTCAGCA
542982 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
543024 AT AT AT AT AT
1 AT AT AT AT AT
543034 GTTGACTCTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:545344 original size:31 final size:31
Alignment explanation
Indices: 545325--545386 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
545315 TATATTAATT
*
545325 GTCCAGTGACTTAAATAAAAACTTTTGAATA
1 GTCCAGTAACTTAAATAAAAACTTTTGAATA
* *
545356 GTTCAGTAACTTAAATAAAAACTTTCGAATA
1 GTCCAGTAACTTAAATAAAAACTTTTGAATA
545387 ATAATGACCA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.44, C:0.13, G:0.11, T:0.32
Consensus pattern (31 bp):
GTCCAGTAACTTAAATAAAAACTTTTGAATA
Found at i:556047 original size:6 final size:6
Alignment explanation
Indices: 556036--556062 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
556026 AGAATTTCCA
556036 AAAAAG AAAAAG AAAAAG AAAAAG AAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAA
556063 TTGAATTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:556279 original size:7 final size:7
Alignment explanation
Indices: 556267--556305 Score: 78
Period size: 7 Copynumber: 5.6 Consensus size: 7
556257 TGGTTCGTTT
556267 GGCAAAA
1 GGCAAAA
556274 GGCAAAA
1 GGCAAAA
556281 GGCAAAA
1 GGCAAAA
556288 GGCAAAA
1 GGCAAAA
556295 GGCAAAA
1 GGCAAAA
556302 GGCA
1 GGCA
556306 GATCACGGAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.54, C:0.15, G:0.31, T:0.00
Consensus pattern (7 bp):
GGCAAAA
Found at i:558831 original size:29 final size:29
Alignment explanation
Indices: 558795--559012 Score: 192
Period size: 30 Copynumber: 7.4 Consensus size: 29
558785 CTTTATTTTG
* *
558795 TTTA-AAAATTATATTTTGATCCCTAAAC
1 TTTATAAAATTATATTTTAACCCCTAAAC
* *
558823 TTTATAAAATTTTATTTTTAACCCCTAAGC
1 TTTATAAAATTATA-TTTTAACCCCTAAAC
* *
558853 TTTCTAAAATTTTATTTTTAACCCCTAAAC
1 TTTATAAAATTATA-TTTTAACCCCTAAAC
* * **
558883 TTTTTAAAAATCATATTTTAACCATTAAAC
1 TTTAT-AAAATTATATTTTAACCCCTAAAC
*
558913 TTTCCA-AAAAATATATTTTAACCCCTAAAC
1 TTT--ATAAAATTATATTTTAACCCCTAAAC
558943 TTT-TCAAAAATTATA-TTTAACCCCTAAAC
1 TTTAT--AAAATTATATTTTAACCCCTAAAC
* *** *
558972 TCTATTAAAATCCCATTTTTACCCCTAAAC
1 TTTA-TAAAATTATATTTTAACCCCTAAAC
559002 TTTATAAAATT
1 TTTATAAAATT
559013 TCATTTTGAC
Statistics
Matches: 155, Mismatches: 24, Indels: 21
0.77 0.12 0.10
Matches are distributed among these distances:
28 4 0.03
29 36 0.23
30 107 0.69
31 8 0.05
ACGTcount: A:0.39, C:0.19, G:0.01, T:0.42
Consensus pattern (29 bp):
TTTATAAAATTATATTTTAACCCCTAAAC
Found at i:559196 original size:22 final size:21
Alignment explanation
Indices: 559178--559216 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
559168 AAATTTAAGC
559178 CTTT-GATCTT-TTTTATTTA
1 CTTTAGATCTTGTTTTATTTA
559197 CTTTAGATCTTGTTTTATTT
1 CTTTAGATCTTGTTTTATTT
559217 TAAACTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.22
20 6 0.33
21 8 0.44
ACGTcount: A:0.15, C:0.10, G:0.08, T:0.67
Consensus pattern (21 bp):
CTTTAGATCTTGTTTTATTTA
Found at i:561287 original size:17 final size:17
Alignment explanation
Indices: 561262--561326 Score: 103
Period size: 17 Copynumber: 3.8 Consensus size: 17
561252 TTGGGCCCAA
561262 TAAATTTAAATTTATTT
1 TAAATTTAAATTTATTT
* *
561279 TAAAATTAAGTTTATTT
1 TAAATTTAAATTTATTT
561296 TAAATTTAAATTTATTT
1 TAAATTTAAATTTATTT
*
561313 GAAATTTAAATTTA
1 TAAATTTAAATTTA
561327 AAATCTATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 43 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
TAAATTTAAATTTATTT
Found at i:561303 original size:23 final size:23
Alignment explanation
Indices: 561264--561340 Score: 72
Period size: 23 Copynumber: 3.4 Consensus size: 23
561254 GGGCCCAATA
*
561264 AATTTAAATTT-ATTTTAAAATT
1 AATTTAAATTTAAATTTAAAATT
*
561286 AAGTTT-ATTTTAAATTT-AAATT
1 AA-TTTAAATTTAAATTTAAAATT
*
561308 TATTTGAAATTTAAATTTAAAATCT
1 AATTT-AAATTTAAATTTAAAAT-T
561333 -ATTTAAAT
1 AATTTAAAT
561341 AATGTCCAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
21 3 0.07
22 12 0.27
23 21 0.47
24 8 0.18
25 1 0.02
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (23 bp):
AATTTAAATTTAAATTTAAAATT
Found at i:561330 original size:7 final size:6
Alignment explanation
Indices: 561262--561328 Score: 61
Period size: 6 Copynumber: 11.7 Consensus size: 6
561252 TTGGGCCCAA
* * * *
561262 TAAATT TAAATT T-ATTT TAAAAT TAAGTT T-ATTT TAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
561308 T--ATT TGAAATT TAAATT TAAA
1 TAAATT T-AAATT TAAATT TAAA
561329 ATCTATTTAA
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
4 4 0.08
5 8 0.16
6 33 0.67
7 4 0.08
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (6 bp):
TAAATT
Found at i:563159 original size:29 final size:30
Alignment explanation
Indices: 563113--563407 Score: 258
Period size: 30 Copynumber: 9.9 Consensus size: 30
563103 CCTCGAAGGT
* *
563113 CCCT-AAACTATCCGAAAAGTCCATTTTT-A
1 CCCTCAAACT-TCCAAAAATTCCATTTTTGA
*
563142 CCCTCGAACTTCCAAAAA-TCTCATTTTTGA
1 CCCTCAAACTTCCAAAAATTC-CATTTTTGA
*
563172 CCCTAAAACTTCCAAAAATTTCCA-TTTTGA
1 CCCTCAAACTTCCAAAAA-TTCCATTTTTGA
* *
563202 CCC-CAAAACTTTCAAAAATTCC-TTTTTTA
1 CCCTC-AAACTTCCAAAAATTCCATTTTTGA
* *
563231 CCCTCAAACTTTCAAAAATTCCTTTTTTGA
1 CCCTCAAACTTCCAAAAATTCCATTTTTGA
* *
563261 CACC-AAAACTTCCAAAAATT-CATTTTTTTAA
1 C-CCTCAAACTTCCAAAAATTCCA--TTTTTGA
* *
563292 CCCTAAAACTTCCAAAAATTCCTTTTTTGA
1 CCCTCAAACTTCCAAAAATTCCATTTTTGA
563322 CCC-CAAAACTTCCAAAAATAT-CATTTTTGA
1 CCCTC-AAACTTCCAAAAAT-TCCATTTTTGA
* *
563352 -CCTCGAAAC-TCCTAAAATTTCATTTTT-A
1 CCCTC-AAACTTCCAAAAATTCCATTTTTGA
*
563380 ACCTCGAAAC-TCCAAAAATTCCATTTTT
1 CCCTC-AAACTTCCAAAAATTCCATTTTT
563408 ACCTCGAATG
Statistics
Matches: 227, Mismatches: 20, Indels: 38
0.80 0.07 0.13
Matches are distributed among these distances:
28 4 0.02
29 90 0.40
30 102 0.45
31 28 0.12
32 3 0.01
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (30 bp):
CCCTCAAACTTCCAAAAATTCCATTTTTGA
Found at i:563259 original size:59 final size:59
Alignment explanation
Indices: 563148--563407 Score: 294
Period size: 59 Copynumber: 4.4 Consensus size: 59
563138 TTTACCCTCG
* *
563148 AACTTCCAAAAATCTCATTTTTGACCCTAAAACTTCCAAAAATTTCC-ATTTTGACCCCAA
1 AACTTCCAAAAAT-TCATTTTTTACCCTAAAACTTCCAAAAA-TTCCTTTTTTGACCCCAA
* * * * *
563208 AACTTTCAAAAATTCCTTTTTTACCCTCAAACTTTCAAAAATTCCTTTTTTGACACCAA
1 AACTTCCAAAAATTCATTTTTTACCCTAAAACTTCCAAAAATTCCTTTTTTGACCCCAA
563267 AACTTCCAAAAATTCATTTTTTTAACCCTAAAACTTCCAAAAATTCCTTTTTTGACCCCAA
1 AACTTCCAAAAATTCA-TTTTTT-ACCCTAAAACTTCCAAAAATTCCTTTTTTGACCCCAA
* * * * * * * *
563328 AACTTCCAAAAATATCATTTTTGA-CCTCGAAAC-TCCTAAAATTTCATTTTTAACCTCGA
1 AACTTCCAAAAAT-TCATTTTTTACCCT-AAAACTTCCAAAAATTCCTTTTTTGACCCCAA
563387 AAC-TCCAAAAATTCCATTTTT
1 AACTTCCAAAAATT-CATTTTT
563408 ACCTCGAATG
Statistics
Matches: 174, Mismatches: 20, Indels: 14
0.84 0.10 0.07
Matches are distributed among these distances:
57 1 0.01
58 20 0.11
59 75 0.43
60 23 0.13
61 52 0.30
62 3 0.02
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.36
Consensus pattern (59 bp):
AACTTCCAAAAATTCATTTTTTACCCTAAAACTTCCAAAAATTCCTTTTTTGACCCCAA
Found at i:563408 original size:29 final size:30
Alignment explanation
Indices: 563117--563441 Score: 244
Period size: 30 Copynumber: 10.9 Consensus size: 30
563107 GAAGGTCCCT
* * *
563117 AAACTATCCGAAAAGTCCATTTTTACCCTC-
1 AAACT-TCCAAAAATTCCATTTTTAACCTCA
* *
563147 GAACTTCCAAAAA-TCTCATTTTTGACC-CTA
1 AAACTTCCAAAAATTC-CATTTTTAACCTC-A
* *
563177 AAACTTCCAAAAATTTCCA-TTTTGACCCCA
1 AAACTTCCAAAAA-TTCCATTTTTAACCTCA
* * *
563207 AAACTTTCAAAAATTCCTTTTTTACCCTC-
1 AAACTTCCAAAAATTCCATTTTTAACCTCA
* * *
563236 AAACTTTCAAAAATTCCTTTTTTGACAC-CA
1 AAACTTCCAAAAATTCCATTTTTAAC-CTCA
563266 AAACTTCCAAAAATT-CATTTTTTTAACC-CTA
1 AAACTTCCAAAAATTCCA--TTTTTAACCTC-A
* * *
563297 AAACTTCCAAAAATTCCTTTTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTTTAACCTCA
* *
563327 AAACTTCCAAAAATAT-CATTTTTGACCTCG
1 AAACTTCCAAAAAT-TCCATTTTTAACCTCA
* * *
563357 AAAC-TCCTAAAATTTCATTTTTAACCTCG
1 AAACTTCCAAAAATTCCATTTTTAACCTCA
*
563386 AAAC-TCCAAAAATTCCATTTTT-ACCTCG
1 AAACTTCCAAAAATTCCATTTTTAACCTCA
** *
563414 AATGTT-TAAAAATTCCATCTTTTAACCT
1 AAACTTCCAAAAATTCCAT-TTTTAACCT
563442 TGAGCTTCCC
Statistics
Matches: 249, Mismatches: 27, Indels: 38
0.79 0.09 0.12
Matches are distributed among these distances:
28 23 0.09
29 92 0.37
30 103 0.41
31 28 0.11
32 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.35
Consensus pattern (30 bp):
AAACTTCCAAAAATTCCATTTTTAACCTCA
Found at i:563431 original size:28 final size:28
Alignment explanation
Indices: 563127--563415 Score: 171
Period size: 29 Copynumber: 9.8 Consensus size: 28
563117 AAACTATCCG
*
563127 AAAAGTCCATTTTTACCCTCG-AACTTCCA
1 AAAATTCCATTTTTA-CCTCGAAAC-TCCA
*
563156 AAAA-TCTCATTTTTGACC-CTAAAACTTCCA
1 AAAATTC-CATTTTT-ACCTC-GAAAC-TCCA
* * * *
563186 AAAATTTCCATTTTGACCCCAAAACTTTCA
1 AAAA-TTCCATTTTTACCTCGAAAC-TCCA
* *
563216 AAAATTCCTTTTTTACCCTC-AAACTTTCA
1 AAAATTCCATTTTTA-CCTCGAAAC-TCCA
* *
563245 AAAATTCCTTTTTTGACAC-CAAAACTTCCA
1 AAAATTCCATTTTT-AC-CTCGAAAC-TCCA
*
563275 AAAATT-CATTTTTTTAACC-CTAAAACTTCCA
1 AAAATTCCA--TTTTT-ACCTC-GAAAC-TCCA
* * *
563306 AAAATTCCTTTTTTGACCCCAAAACTTCCA
1 AAAATTCCATTTTT-ACCTCGAAAC-TCCA
*
563336 AAAATAT-CATTTTTGACCTCGAAACTCCT
1 AAAAT-TCCATTTTT-ACCTCGAAACTCCA
*
563365 AAAATTTCATTTTTAACCTCGAAACTCCA
1 AAAATTCCATTTTT-ACCTCGAAACTCCA
563394 AAAATTCCATTTTTACCTCGAA
1 AAAATTCCATTTTTACCTCGAA
563416 TGTTTAAAAA
Statistics
Matches: 224, Mismatches: 18, Indels: 37
0.80 0.06 0.13
Matches are distributed among these distances:
28 12 0.05
29 89 0.40
30 88 0.39
31 32 0.14
32 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.35
Consensus pattern (28 bp):
AAAATTCCATTTTTACCTCGAAACTCCA
Found at i:571418 original size:9 final size:9
Alignment explanation
Indices: 571404--571433 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
571394 ATTGCAAAAC
571404 TTCAAGAAA
1 TTCAAGAAA
571413 TTCAAGAAA
1 TTCAAGAAA
571422 TTCAAGAAA
1 TTCAAGAAA
571431 TTC
1 TTC
571434 CAGCAATAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.50, C:0.13, G:0.10, T:0.27
Consensus pattern (9 bp):
TTCAAGAAA
Found at i:572725 original size:27 final size:28
Alignment explanation
Indices: 572673--572725 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
572663 TTTGTCTTTG
*
572673 ATTTCTTACGTTGCTACTTGAAATTATT
1 ATTTCATACGTTGCTACTTGAAATTATT
572701 ATTTCATACGTTG-TAC-TGATAATTA
1 ATTTCATACGTTGCTACTTGA-AATTA
572726 ATTTAATAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 3 0.13
27 8 0.35
28 12 0.52
ACGTcount: A:0.28, C:0.13, G:0.11, T:0.47
Consensus pattern (28 bp):
ATTTCATACGTTGCTACTTGAAATTATT
Found at i:576766 original size:29 final size:30
Alignment explanation
Indices: 576725--576781 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
576715 TTTGAATCAC
* *
576725 AATTAGAGTTTCACGTATATAATTACACCA
1 AATTAAAGTTTCACGTATACAATTACACCA
*
576755 AATTAAAG-TTCATGTATACAATTACAC
1 AATTAAAGTTTCACGTATACAATTACAC
576782 ATTAAATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 17 0.71
30 7 0.29
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.33
Consensus pattern (30 bp):
AATTAAAGTTTCACGTATACAATTACACCA
Found at i:579355 original size:25 final size:27
Alignment explanation
Indices: 579318--579369 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
579308 ATTGTTTTAT
* *
579318 TTTTTGTTA-TTTTAA-ATTTTTTTCA
1 TTTTTCTTATTTTTAATATTTATTTCA
*
579343 TTTTTCTTGTTTTTAATATTTATTTCA
1 TTTTTCTTATTTTTAATATTTATTTCA
579370 AGAAAATAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 7 0.32
26 6 0.27
27 9 0.41
ACGTcount: A:0.19, C:0.06, G:0.04, T:0.71
Consensus pattern (27 bp):
TTTTTCTTATTTTTAATATTTATTTCA
Found at i:582572 original size:19 final size:20
Alignment explanation
Indices: 582544--582597 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
582534 TTTTTCTATT
*
582544 ATTTTAATAATTTTTATAATA
1 ATTTT-ATAATTTTTATAACA
* *
582565 A-TTTATAA-ATTTCTAACA
1 ATTTTATAATTTTTATAACA
582583 ATTTTATAATTTTTA
1 ATTTTATAATTTTTA
582598 AAATTTTAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 5
0.72 0.14 0.14
Matches are distributed among these distances:
18 8 0.31
19 11 0.42
20 6 0.23
21 1 0.04
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.56
Consensus pattern (20 bp):
ATTTTATAATTTTTATAACA
Found at i:582609 original size:18 final size:17
Alignment explanation
Indices: 582544--582605 Score: 61
Period size: 20 Copynumber: 3.4 Consensus size: 17
582534 TTTTTCTATT
582544 ATTTTAATAATTTTTATAA
1 ATTTT-ATAATTTTTA-AA
* *
582563 TAATTTATAAATTTCTAACA
1 -ATTTTAT-AATTTTTAA-A
582583 ATTTTATAATTTTTAAA
1 ATTTTATAATTTTTAAA
582600 ATTTTA
1 ATTTTA
582606 ATAAAAGTTC
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
17 7 0.19
18 8 0.22
19 9 0.25
20 12 0.33
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTTTATAATTTTTAAA
Found at i:584687 original size:58 final size:58
Alignment explanation
Indices: 584587--584741 Score: 172
Period size: 58 Copynumber: 2.7 Consensus size: 58
584577 GTTTGGAGAA
* * * ** *
584587 TTTGGGGTCAAAACATAATTTTAGAAAAG-TTTAGGGGAAAAAT-TGCAATTTTAGGAAAG
1 TTTGGGGTC-AAATATGATTTTAGAAAAGATTAAGGGTCAAAATAT--AATTTTAAGAAAG
* *
584646 TTT-GGGTCAAATGTGATTTTGGAAAAGATTAAGGGTCAAAATATAATTTTAAGAAAG
1 TTTGGGGTCAAATATGATTTTAGAAAAGATTAAGGGTCAAAATATAATTTTAAGAAAG
* *
584703 TTTGGGGTCAAATATGATTTTAGCAAAGTTTAAGGGTCA
1 TTTGGGGTCAAATATGATTTTAGAAAAGATTAAGGGTCA
584742 TAATGTGATT
Statistics
Matches: 81, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
57 30 0.37
58 47 0.58
59 4 0.05
ACGTcount: A:0.38, C:0.05, G:0.24, T:0.33
Consensus pattern (58 bp):
TTTGGGGTCAAATATGATTTTAGAAAAGATTAAGGGTCAAAATATAATTTTAAGAAAG
Found at i:584710 original size:29 final size:29
Alignment explanation
Indices: 584587--584733 Score: 117
Period size: 30 Copynumber: 5.1 Consensus size: 29
584577 GTTTGGAGAA
*
584587 TTTGGGGTCAAAACATAATTTTAGAAAAG
1 TTTGGGGTCAAAATATAATTTTAGAAAAG
* *
584616 TTTAGGGG-AAAAAT-TGCAATTTTAGGAAAG
1 TTT-GGGGTCAAAATAT--AATTTTAGAAAAG
* * *
584646 TTT-GGGTC-AAATGTGATTTTGGAAAAG
1 TTTGGGGTCAAAATATAATTTTAGAAAAG
**
584673 ATTAAGGGTCAAAATATAATTTTA-AGAAAG
1 -TTTGGGGTCAAAATATAATTTTAGA-AAAG
* *
584703 TTTGGGGTC-AAATATGATTTTAGCAAAG
1 TTTGGGGTCAAAATATAATTTTAGAAAAG
584731 TTT
1 TTT
584734 AAGGGTCATA
Statistics
Matches: 93, Mismatches: 15, Indels: 21
0.72 0.12 0.16
Matches are distributed among these distances:
27 10 0.11
28 29 0.31
29 21 0.23
30 33 0.35
ACGTcount: A:0.38, C:0.05, G:0.23, T:0.34
Consensus pattern (29 bp):
TTTGGGGTCAAAATATAATTTTAGAAAAG
Found at i:584722 original size:28 final size:28
Alignment explanation
Indices: 584604--584753 Score: 117
Period size: 30 Copynumber: 5.2 Consensus size: 28
584594 TCAAAACATA
* *
584604 ATTTTAGAAAAGTTTAGGG-GAAAAATTG
1 ATTTTAGAAAAGTTTAGGGTCAAATA-TG
* *
584632 CAATTTTAGGAAAGTTT-GGGTCAAATGTG
1 --ATTTTAGAAAAGTTTAGGGTCAAATATG
* * *
584661 ATTTTGGAAAAGATTAAGGGTCAAAATATA
1 ATTTTAGAAAAG-TTTAGGGTC-AAATATG
*
584691 ATTTTA-AGAAAGTTTGGGGTCAAATATG
1 ATTTTAGA-AAAGTTTAGGGTCAAATATG
* *
584719 ATTTTAGCAAAGTTTAAGGGTCATAATGTG
1 ATTTTAGAAAAGTTT-AGGGTCA-AATATG
584749 ATTTT
1 ATTTT
584754 GGGAAAGATT
Statistics
Matches: 96, Mismatches: 16, Indels: 16
0.75 0.12 0.12
Matches are distributed among these distances:
27 10 0.10
28 21 0.22
29 24 0.25
30 41 0.43
ACGTcount: A:0.37, C:0.04, G:0.23, T:0.35
Consensus pattern (28 bp):
ATTTTAGAAAAGTTTAGGGTCAAATATG
Found at i:584760 original size:58 final size:57
Alignment explanation
Indices: 584633--584760 Score: 166
Period size: 58 Copynumber: 2.2 Consensus size: 57
584623 GAAAAATTGC
* *
584633 AATTTTAGGAAAGTTTGGGTCAAATGTGATTTTGGAAAAGATTAAGGGTCAAAATAT
1 AATTTTAGGAAAGTTTGGGTCAAATATGATTTTAGAAAAGATTAAGGGTCAAAATAT
* * * * *
584690 AATTTTAAGAAAGTTTGGGGTCAAATATGATTTTAGCAAAGTTTAAGGGTCATAATGT
1 AATTTTAGGAAAGTTT-GGGTCAAATATGATTTTAGAAAAGATTAAGGGTCAAAATAT
* *
584748 GATTTTGGGAAAG
1 AATTTTAGGAAAG
584761 ATTGTGGCTT
Statistics
Matches: 60, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
57 15 0.25
58 45 0.75
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.34
Consensus pattern (57 bp):
AATTTTAGGAAAGTTTGGGTCAAATATGATTTTAGAAAAGATTAAGGGTCAAAATAT
Found at i:587139 original size:85 final size:85
Alignment explanation
Indices: 586975--587139 Score: 204
Period size: 85 Copynumber: 1.9 Consensus size: 85
586965 CTTCATTGAC
* * ** *
586975 TTGGTCTACTTCTCTATATCTCATTAGGAAGATGACCGTCTTATTGATTTAATTCACTTCTTTGT
1 TTGGTCCACTTCTCTATATCTCATCAGGAAGATGACCGTCTTATTGATTTAACCCACTTCTCTGT
*
587040 ATTTAATCAAGAAGACGAAT
66 ATCTAATCAAGAAGACGAAT
* * ** * *
587060 TTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGTTTTATTTTTTTGACCCGCTTCTCTGT
1 TTGGTCCACTTCTCTATATCTCATCAGGAAGATGACCGTCTTATTGATTTAACCCACTTCTCTGT
* *
587125 ATCTCATCAGGAAGA
66 ATCTAATCAAGAAGA
587140 TAGGGATTTG
Statistics
Matches: 66, Mismatches: 14, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
85 66 1.00
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (85 bp):
TTGGTCCACTTCTCTATATCTCATCAGGAAGATGACCGTCTTATTGATTTAACCCACTTCTCTGT
ATCTAATCAAGAAGACGAAT
Found at i:587218 original size:209 final size:208
Alignment explanation
Indices: 586850--587471 Score: 738
Period size: 209 Copynumber: 3.0 Consensus size: 208
586840 GGCTTCATCT
* * * *
586850 TTTGGTCTACTTCTTTGTATCTCATTAGGAAGATGACCGCTTTATTGCTTCGACCCACTTCTTTG
1 TTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGCTTTGACCCACTTCTCTG
* * * * *
586915 TATCTCATCAGGAAGATA-AGAGTTTGAGGTTTCACTCG-CATTAAAAGC-T-GCTTCATTGACT
66 TATCTCATCAGGAAGATAGGGA-TTTGAAGTCTCATTCGTC-TT--AAGCTTCGCTTCATTGATT
* * * * * * *
586976 TGGTCTACTTCTCTATATCTCATTAGGAAGATGACCGTCTTATTGATTTAATTCACTTCTTTGTA
127 TGGTCTACTTCTCTGTATCTCATCAGAAAGATGACCGCCTCATTGATTTAATCCACTTCTCTGTA
587041 TTTAATCAAGAAGACGAA
192 TTT-ATCAAGAAGACGAA
* * ** *
587059 TTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGTTTTATTTTTTTGACCCGCTTCTCTG
1 TTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGCTTTGACCCACTTCTCTG
* * * *
587124 TATCTCATCAGGAAGATAGGGATTTGAAGTCTCATTTGTCTTTAGCTTCGCCTCATTGATTTGAT
66 TATCTCATCAGGAAGATAGGGATTTGAAGTCTCATTCGTCTTAAGCTTCGCTTCATTGATTTGGT
* *
587189 CTACTTCTTTGTATCTCATCAGAAAGATGATCGCCTCATTGATTTAATCCACTTCTCTGTATCTT
131 CTACTTCTCTGTATCTCATCAGAAAGATGACCGCCTCATTGATTTAATCCACTTCTCTGTAT-TT
**
587254 ATC-AGAAAGGTGAA
195 ATCAAG-AAGACGAA
* * *
587268 TTTGGTCTACTTCTCTGTATCTCATCAGAAAGTTGACTGCTTTATTGCTTTGACCCACTTCTCTG
1 TTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGCTTTGACCCACTTCTCTG
*
587333 TATCTCATCAGGAAGAT-GGTG-TTTGAAGTCTCATTCGTATTAAGCTTCGCTTCATTGATTTGG
66 TATCTCATCAGGAAGATAGG-GATTTGAAGTCTCATTCGTCTTAAGCTTCGCTTCATTGATTTGG
* * * * * *
587396 TTTACTTATCTGTATCTCATCA-AGAAGATGTCTGCCTCATTTATTTAATCCACTTCTCTGTAGC
130 TCTACTTCTCTGTATCTCATCAGA-AAGATGACCGCCTCATTGATTTAATCCACTTCTCTGTA-T
*
587460 TCATCAAGAAGA
193 TTATCAAGAAGA
587472 TGACCACTTT
Statistics
Matches: 351, Mismatches: 52, Indels: 21
0.83 0.12 0.05
Matches are distributed among these distances:
207 4 0.01
208 102 0.29
209 240 0.68
210 5 0.01
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40
Consensus pattern (208 bp):
TTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGCTTTGACCCACTTCTCTG
TATCTCATCAGGAAGATAGGGATTTGAAGTCTCATTCGTCTTAAGCTTCGCTTCATTGATTTGGT
CTACTTCTCTGTATCTCATCAGAAAGATGACCGCCTCATTGATTTAATCCACTTCTCTGTATTTA
TCAAGAAGACGAA
Found at i:587223 original size:48 final size:48
Alignment explanation
Indices: 587171--587262 Score: 148
Period size: 48 Copynumber: 1.9 Consensus size: 48
587161 GTCTTTAGCT
* * *
587171 TCGCCTCATTGATTTGATCTACTTCTTTGTATCTCATCAGAAAGATGA
1 TCGCCTCATTGATTTAATCCACTTCTCTGTATCTCATCAGAAAGATGA
*
587219 TCGCCTCATTGATTTAATCCACTTCTCTGTATCTTATCAGAAAG
1 TCGCCTCATTGATTTAATCCACTTCTCTGTATCTCATCAGAAAG
587263 GTGAATTTGG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.25, C:0.23, G:0.13, T:0.39
Consensus pattern (48 bp):
TCGCCTCATTGATTTAATCCACTTCTCTGTATCTCATCAGAAAGATGA
Found at i:587294 original size:85 final size:85
Alignment explanation
Indices: 587182--587343 Score: 227
Period size: 85 Copynumber: 1.9 Consensus size: 85
587172 CGCCTCATTG
* *
587182 ATTTGATCTACTTCTTTGTATCTCATCAGAAAGATGA-TCGCCTCATTGATTTAATCCACTTCTC
1 ATTTGATCTACTTCTCTGTATCTCATCAGAAAGATGACT-GCCTCATTGATTTAACCCACTTCTC
*
587246 TGTATCTTATCAGAAAGGTGA
65 TGTATCTCATCAGAAAGGTGA
* * * * * *
587267 ATTTGGTCTACTTCTCTGTATCTCATCAGAAAGTTGACTGCTTTATTGCTTTGACCCACTTCTCT
1 ATTTGATCTACTTCTCTGTATCTCATCAGAAAGATGACTGCCTCATTGATTTAACCCACTTCTCT
587332 GTATCTCATCAG
66 GTATCTCATCAG
587344 GAAGATGGTG
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
85 66 0.99
86 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.14, T:0.40
Consensus pattern (85 bp):
ATTTGATCTACTTCTCTGTATCTCATCAGAAAGATGACTGCCTCATTGATTTAACCCACTTCTCT
GTATCTCATCAGAAAGGTGA
Found at i:587561 original size:171 final size:171
Alignment explanation
Indices: 587276--587803 Score: 632
Period size: 171 Copynumber: 3.2 Consensus size: 171
587266 AATTTGGTCT
* ** * *
587276 ACTTCTCTGTATCTCATC-AGAAAGTTGACTGCTTTATTGCTTTGACCCACTTCTCTGTATCTCA
1 ACTTCTCTGTATCTCATCAAG-AAGATGACCACTTTATTGCTTTGACCCAATTCTTTGTATCTCA
* *
587340 TCAGGAAGATGGTGTTTGAAGTCTCATTCGTATTAAGCTTCGCTTCATTGATTTGGTTTACTTAT
65 TCAGGAAGATGGAGTTTGAAGTCTCATTCGTATTAAGCTTCGCTTCATTGATTTGGTTTACTTCT
*
587405 CTGTATCTCATCAAGAAGATGTCTGCCTCATTTATTTAATCC
130 CTGTATCTCATCAAGAAGATGACTGCCTCATTTATTTAATCC
* *
587447 ACTTCTCTGTAGCTCATCAAGAAGATGACCACTTTATTGCTTTGACCCATTTCTTTGTATCTCAT
1 ACTTCTCTGTATCTCATCAAGAAGATGACCACTTTATTGCTTTGACCCAATTCTTTGTATCTCAT
* * * *
587512 TAGGAAGATGGGGCTTAAAGTCTCATTCGTATTAAGCTTCGCTTCATTGATTTGGTTTACTTCTC
66 CAGGAAGATGGAGTTTGAAGTCTCATTCGTATTAAGCTTCGCTTCATTGATTTGGTTTACTTCTC
** * *
587577 TGTATCTCATCAAGAAGATGACAACCTCATTGATTTAATTC
131 TGTATCTCATCAAGAAGATGACTGCCTCATTTATTTAATCC
* * * *
587618 ACTTCTCTATATCTCATCAAGAAGACG--GA---T-TTG-GTT----CAATTCTTTGTATCTCAT
1 ACTTCTCTGTATCTCATCAAGAAGATGACCACTTTATTGCTTTGACCCAATTCTTTGTATCTCAT
* * * * * *
587672 CAGGAAGATGGAGTTTGAAGTCTCATTCGTATTGAGCTTCACTACATTAACTTGGTCTACTTCTC
66 CAGGAAGATGGAGTTTGAAGTCTCATTCGTATTAAGCTTCGCTTCATTGATTTGGTTTACTTCTC
* * * * * *
587737 TGTATTTAATTAGGAAGATGACTGCCTTATTGT-TTTAATCA
131 TGTATCTCATCAAGAAGATGACTGCCTCATT-TATTTAATCC
*
587778 ATTTCTCTGTATCTCATCAAGAAGAT
1 ACTTCTCTGTATCTCATCAAGAAGAT
587804 AGATTTGGCT
Statistics
Matches: 310, Mismatches: 45, Indels: 15
0.84 0.12 0.04
Matches are distributed among these distances:
160 125 0.40
164 2 0.01
165 3 0.01
166 1 0.00
169 1 0.00
171 176 0.57
172 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.40
Consensus pattern (171 bp):
ACTTCTCTGTATCTCATCAAGAAGATGACCACTTTATTGCTTTGACCCAATTCTTTGTATCTCAT
CAGGAAGATGGAGTTTGAAGTCTCATTCGTATTAAGCTTCGCTTCATTGATTTGGTTTACTTCTC
TGTATCTCATCAAGAAGATGACTGCCTCATTTATTTAATCC
Found at i:587793 original size:160 final size:160
Alignment explanation
Indices: 587497--587820 Score: 416
Period size: 160 Copynumber: 2.0 Consensus size: 160
587487 TTTGACCCAT
* * * * *
587497 TTCTTTGTATCTCATTAGGAAGATGGGGCTTAAAGTCTCATTCGTATTAAGCTTCGCTTCATTGA
1 TTCTTTGTATCTCATCAGGAAGATGGAGCTTAAAGTCTCATTCGTATTAAGCTTCACTACATTAA
* * *
587562 TTTGGTTTACTTCTCTGTATCTCATCAAGAAGATGACAACCTCATTGATTTAATTCACTTCTCTA
66 CTTGGTCTACTTCTCTGTATCTAATCAAGAAGATGACAACCTCATTGATTTAATTCACTTCTCTA
* *
587627 TATCTCATCAAGAAGACGGATTTGGTTCAA
131 TATCTCATCAAGAAGACAGATTTGGCTCAA
* * *
587657 TTCTTTGTATCTCATCAGGAAGATGGAGTTTGAAGTCTCATTCGTATTGAGCTTCACTACATTAA
1 TTCTTTGTATCTCATCAGGAAGATGGAGCTTAAAGTCTCATTCGTATTAAGCTTCACTACATTAA
* * * ** * * *
587722 CTTGGTCTACTTCTCTGTATTTAATTAGGAAGATGACTGCCTTATTGTTTTAA-TCAATTTCTCT
66 CTTGGTCTACTTCTCTGTATCTAATCAAGAAGATGACAACCTCATTGATTTAATTC-ACTTCTCT
* * *
587786 GTATCTCATCAAGAAGATAGATTTGGCTCAC
130 ATATCTCATCAAGAAGACAGATTTGGCTCAA
587817 TTCT
1 TTCT
587821 CTACATCTTG
Statistics
Matches: 139, Mismatches: 24, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
159 2 0.01
160 137 0.99
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.40
Consensus pattern (160 bp):
TTCTTTGTATCTCATCAGGAAGATGGAGCTTAAAGTCTCATTCGTATTAAGCTTCACTACATTAA
CTTGGTCTACTTCTCTGTATCTAATCAAGAAGATGACAACCTCATTGATTTAATTCACTTCTCTA
TATCTCATCAAGAAGACAGATTTGGCTCAA
Found at i:588303 original size:49 final size:49
Alignment explanation
Indices: 588132--589002 Score: 496
Period size: 49 Copynumber: 17.6 Consensus size: 49
588122 TAAAGGTACT
** * * * *
588132 GGGTTCGCCGTCACGACCTCAACATTTCCCTTCATATCTTCATGGTACC
1 GGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCAAATCTTCATGGTATC
** * * * * * ** * *
588181 GAATTCGTCGTCGCGGCCTCGATCC-TTCACATCACGTCTTCTAAGGTATT
1 GGGTTCGCCGTTGCGGCCTC-AACCTTTCCCTTCAAATCTTC-ATGGTATC
* *
588231 GGGTTTGCCTGTTGCGACCTCAACCTTTCCCTTCAAATCTTCATGGTATC
1 GGGTTCGCC-GTTGCGGCCTCAACCTTTCCCTTCAAATCTTCATGGTATC
** ** * * ** * *
588281 GGGTTCATCGTTGCAACTTCAACCTTTCCCATCACGTCTTTTAAGGTATC
1 GGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCAAATC-TTCATGGTATC
* ** * * * * * *
588331 AGGTTTACCGTTACGACCTCAACCCTTT-CCTTTATATCATCATAGTA-C
1 GGGTTCGCCGTTGCGGCCTCAA-CCTTTCCCTTCAAATCTTCATGGTATC
* * * * ** * *
588379 TTGGTTCACCGTTACGGCCTCAACCTTTCCCATCACGTCTTCTAAGGTACC
1 -GGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCAAATCTTC-ATGGTATC
* * * *
588430 GAGTTCGCCTATTGCGGCCTCAACCTTTCCCTTCAAATTTTCATGGTACC
1 GGGTTCGCC-GTTGCGGCCTCAACCTTTCCCTTCAAATCTTCATGGTATC
* * * * * ** * *
588480 GAGTTTGTCGTTGCGGCCTCAACCTCTCCCATCACGTCTTTTAAGGTATC
1 GGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCAAATC-TTCATGGTATC
* * *
588530 GGGTTCACCGTTGCGACCTCAACCTTTCCCTTCAAATCTTCATGGTATG
1 GGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCAAATCTTCATGGTATC
** * ** * *
588579 GGGTTCGCTATTGCGGCCTCAACCTTTCCCATCATGTATTCTAAGGTATC
1 GGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCAAATCTTC-ATGGTATC
** * ** * * * * *
588629 -TATTTGCCGTTGTAGTCTTAACATTTCCCTTTAAATCTTCATGGTAAC
1 GGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCAAATCTTCATGGTATC
* * *
588677 GGGTTCGCCGTTGCGGCCTCAACCCTTT-CCTTCATATCTTCATGATACC
1 GGGTTCGCCGTTGCGGCCTCAA-CCTTTCCCTTCAAATCTTCATGGTATC
* *** ** * * * *
588726 AGGTTCGTTATTATGACCTCAACCTTTCCCATCACATCTTCTAAGGTATC
1 GGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCAAATCTTC-ATGGTATC
* * ** * *
588776 GGATTTGTTGTTGTGGCCTCAACATTTCCCTTCAAATCTTCATGGTATC
1 GGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCAAATCTTCATGGTATC
* * * * * *
588825 GAGTTCGCCGTTGCGGCCTCAACCTTTCCCATGATATCTACTAAGGTATC
1 GGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCAAATCTTC-ATGGTATC
** * ** * *
588875 GGGTTCGCTATTACAACCTCAACCTTTCTCTTTAAATCTTCATGGTAAT-
1 GGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCAAATCTTCATGGT-ATC
* * * * *
588924 GGGTTCGCTGTTGCGACCTCAACCCTTT-CCGTCATATCTTCATGGTACC
1 GGGTTCGCCGTTGCGGCCTCAA-CCTTTCCCTTCAAATCTTCATGGTATC
* *
588973 GAGTTCGCCGTTGCAGCCTCAACCTTTCCC
1 GGGTTCGCCGTTGCGGCCTCAACCTTTCCC
589003 ATTACATCTT
Statistics
Matches: 609, Mismatches: 191, Indels: 44
0.72 0.23 0.05
Matches are distributed among these distances:
48 23 0.04
49 323 0.53
50 210 0.34
51 53 0.09
ACGTcount: A:0.19, C:0.30, G:0.17, T:0.34
Consensus pattern (49 bp):
GGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCAAATCTTCATGGTATC
Found at i:588314 original size:100 final size:99
Alignment explanation
Indices: 588119--589004 Score: 574
Period size: 99 Copynumber: 8.9 Consensus size: 99
588109 TCTTTAATCT
** * * *
588119 TTCTAAAGGTA-CTGGGTTCGCCGTCACGACCTCAACATTTCCCTTCATATCTTCATGGTACCGA
1 TTCT-AAGGTATC-GGGTTCGCCGTTGCGACCTCAACCTTTCCCTTCAAATCTTCATGGTACCGG
* * * * *
588183 ATTCGTCGTCGCGGCCTCGATCC-TTCACATCACGTC
64 GTTCATCGTTGCGGCCTC-AACCTTTCCCATCACGTC
* * *
588219 TTCTAAGGTATTGGGTTTGCCTGTTGCGACCTCAACCTTTCCCTTCAAATCTTCATGGTATCGGG
1 TTCTAAGGTATCGGGTTCGCC-GTTGCGACCTCAACCTTTCCCTTCAAATCTTCATGGTACCGGG
** *
588284 TTCATCGTTGCAACTTCAACCTTTCCCATCACGTC
65 TTCATCGTTGCGGCCTCAACCTTTCCCATCACGTC
* * ** * * * * * **
588319 TTTTAAGGTATCAGGTTTACCGTTACGACCTCAACCCTTT-CCTTTATATCATCATAGTACTTGG
1 TTCTAAGGTATCGGGTTCGCCGTTGCGACCTCAA-CCTTTCCCTTCAAATCTTCATGGTACCGGG
* *
588383 TTCACCGTTACGGCCTCAACCTTTCCCATCACGTC
65 TTCATCGTTGCGGCCTCAACCTTTCCCATCACGTC
* * * * * *
588418 TTCTAAGGTACCGAGTTCGCCTATTGCGGCCTCAACCTTTCCCTTCAAATTTTCATGGTACCGAG
1 TTCTAAGGTATCGGGTTCGCC-GTTGCGACCTCAACCTTTCCCTTCAAATCTTCATGGTACCGGG
** *
588483 TTTGTCGTTGCGGCCTCAACCTCTCCCATCACGTC
65 TTCATCGTTGCGGCCTCAACCTTTCCCATCACGTC
* * **
588518 TTTTAAGGTATCGGGTTCACCGTTGCGACCTCAACCTTTCCCTTCAAATCTTCATGGTATGGGGT
1 TTCTAAGGTATCGGGTTCGCCGTTGCGACCTCAACCTTTCCCTTCAAATCTTCATGGTACCGGGT
* * * *
588583 TC-GCTATTGCGGCCTCAACCTTTCCCATCATGTA
66 TCATC-GTTGCGGCCTCAACCTTTCCCATCACGTC
** * * * * * * *
588617 TTCTAAGGTATC-TATTTGCCGTTG-TAGTCTTAACATTTCCCTTTAAATCTTCATGGTAACGGG
1 TTCTAAGGTATCGGGTTCGCCGTTGCGA-CCTCAACCTTTCCCTTCAAATCTTCATGGTACCGGG
** * **
588680 TTCGCCGTTGCGGCCTCAACCCTTT-CCTTCATATC
65 TTCATCGTTGCGGCCTCAA-CCTTTCCCATCACGTC
* * * * *** ** * * * * *
588715 TTC-ATGATACCAGGTTCGTTATTATGACCTCAACCTTTCCCATCACATCTTCTAAGGTATCGGA
1 TTCTAAGGTATCGGGTTCGCCGTTGCGACCTCAACCTTTCCCTTCAAATCTTC-ATGGTACCGGG
** * * * * **
588779 TTTGTTGTTGTGGCCTCAACATTTCCCTTCAAATC
65 TTCATCGTTGCGGCCTCAACCTTTCCCATCACGTC
* * * * * * * * *
588814 TTC-ATGGTATCGAGTTCGCCGTTGCGGCCTCAACCTTTCCCATGATATCTACTAAGGTATCGGG
1 TTCTAAGGTATCGGGTTCGCCGTTGCGACCTCAACCTTTCCCTTCAAATCTTC-ATGGTACCGGG
* * * ** * * * **
588878 TTC-GCTATTACAACCTCAACCTTTCTCTTTAAATC
65 TTCATC-GTTGCGGCCTCAACCTTTCCCATCACGTC
* * * * *
588913 TTC-ATGGTAAT-GGGTTCGCTGTTGCGACCTCAACCCTTT-CCGTCATATCTTCATGGTACCGA
1 TTCTAAGGT-ATCGGGTTCGCCGTTGCGACCTCAA-CCTTTCCCTTCAAATCTTCATGGTACCGG
** *
588975 GTTCGCCGTTGCAGCCTCAACCTTTCCCAT
64 GTTCATCGTTGCGGCCTCAACCTTTCCCAT
589005 TACATCTTTT
Statistics
Matches: 614, Mismatches: 154, Indels: 38
0.76 0.19 0.05
Matches are distributed among these distances:
97 6 0.01
98 121 0.20
99 321 0.52
100 166 0.27
ACGTcount: A:0.19, C:0.30, G:0.17, T:0.35
Consensus pattern (99 bp):
TTCTAAGGTATCGGGTTCGCCGTTGCGACCTCAACCTTTCCCTTCAAATCTTCATGGTACCGGGT
TCATCGTTGCGGCCTCAACCTTTCCCATCACGTC
Done.