Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167960.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_22, 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: 19587844
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 68000 characters in sequence are not A, C, G, or T
File 5 of 105
Found at i:559961 original size:20 final size:20
Alignment explanation
Indices: 559916--559961 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
559906 TTAATCTATT
*
559916 AATTTTTATTTTTGATTTTT
1 AATTTTTATTTTTGATTTTA
*
559936 AATTTTAATTTTTGA-TTTA
1 AATTTTTATTTTTGATTTTA
559955 AATTTTT
1 AATTTTT
559962 TAATCATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (20 bp):
AATTTTTATTTTTGATTTTA
Found at i:562090 original size:130 final size:130
Alignment explanation
Indices: 561848--562118 Score: 431
Period size: 130 Copynumber: 2.1 Consensus size: 130
561838 TACCACTGAA
* * * *
561848 AAGTTTATAATCAAAATGAAGAACCTGAGAATAAGGTGCAAATACATCAGTATCTCTACTATGCA
1 AAGTTTATAATCAAAATGAAGAACCTGAGAAAAAAGTGCAAATACACCAGTATCTCTACTATACA
561913 CTGATATATGAAGGTTATTTATCACTTAATATTGATTTTATTCTTTTT-TGGAGTGGGGGGATAC
66 CTGATATATGAAGGTTATTTATCACTTAATATTGATTTTATTCTTTTTGTGG-GTGGGGGGATAC
561977 C
130 C
561978 AAGTTTATAATCAAAATGAAGAACCAT-AGAAAAAAGTGCAAATACACCAGTATCTCTACTATAC
1 AAGTTTATAATCAAAATGAAGAACC-TGAGAAAAAAGTGCAAATACACCAGTATCTCTACTATAC
562042 ACTGATATATGAAGGTTATTTATCACTT-ATATTGATTTTATTCTTTTTTGGGGTGGGTGGGGGG
65 ACTGATATATGAAGGTTATTTATCACTTAATATTGATTTTATTC-TTTTT---GTGGGTGGGGGG
562106 ATACC
126 ATACC
562111 AAGTTTAT
1 AAGTTTAT
562119 TACCTCAGCA
Statistics
Matches: 131, Mismatches: 4, Indels: 9
0.91 0.03 0.06
Matches are distributed among these distances:
129 15 0.11
130 91 0.69
131 1 0.01
133 21 0.16
134 3 0.02
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.35
Consensus pattern (130 bp):
AAGTTTATAATCAAAATGAAGAACCTGAGAAAAAAGTGCAAATACACCAGTATCTCTACTATACA
CTGATATATGAAGGTTATTTATCACTTAATATTGATTTTATTCTTTTTGTGGGTGGGGGGATACC
Found at i:564765 original size:54 final size:54
Alignment explanation
Indices: 564673--564779 Score: 121
Period size: 54 Copynumber: 2.0 Consensus size: 54
564663 TTATGCTATA
*
564673 ATATAAATATAATATAAAAACAATATAATTTAAAATTTTAAT-AATAATAATAAT
1 ATATAAATATAATATAAAAAAAATATAATTTAAAATTTTAATCAAT-ATAATAAT
* * * *
564727 ATATAAATTTAATA-AAATTAAAAATAT-ATTTTATATTTTTATCAATATAATAA
1 ATATAAATATAATATAAA--AAAAATATAATTTAAAATTTTAATCAATATAATAA
564780 ATTATTTTCG
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
53 3 0.07
54 32 0.71
55 10 0.22
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (54 bp):
ATATAAATATAATATAAAAAAAATATAATTTAAAATTTTAATCAATATAATAAT
Found at i:568854 original size:18 final size:18
Alignment explanation
Indices: 568820--568857 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
568810 ATTAAAGTAT
*
568820 ATTAATAAAATTAATATA
1 ATTAATAAAAGTAATATA
568838 ATTAA-AAAAGTATATATA
1 ATTAATAAAAGTA-ATATA
568856 AT
1 AT
568858 AATTTTTATT
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:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (18 bp):
ATTAATAAAAGTAATATA
Found at i:569111 original size:14 final size:14
Alignment explanation
Indices: 569090--569143 Score: 53
Period size: 13 Copynumber: 4.1 Consensus size: 14
569080 AATATTAAAT
569090 TAAT-AATTTTATA
1 TAATAAATTTTATA
569103 TAATAAA-TTTAT-
1 TAATAAATTTTATA
*
569115 TAA-AAATTTGAATA
1 TAATAAATTT-TATA
*
569129 TAATAATTTTTATA
1 TAATAAATTTTATA
569143 T
1 T
569144 TTAATGTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
11 3 0.09
12 5 0.15
13 11 0.33
14 9 0.27
15 5 0.15
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (14 bp):
TAATAAATTTTATA
Found at i:569117 original size:39 final size:38
Alignment explanation
Indices: 569074--569171 Score: 119
Period size: 38 Copynumber: 2.6 Consensus size: 38
569064 AAAAATTAGC
*
569074 ATTAAAAATATTAAATTAATAATTTTATATAATAAATTT
1 ATTAAAAATATTAAATTAATAATTTT-TATAATAAATGT
* * *
569113 ATTAAAAAT-TTGAATATAATAATTTTTATATTTAATGT
1 ATTAAAAATATTAAAT-TAATAATTTTTATAATAAATGT
*
569151 -TTAAACATATTAAATTAATAA
1 ATTAAAAATATTAAATTAATAA
569172 AATTTTTTAA
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
37 13 0.25
38 19 0.37
39 19 0.37
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (38 bp):
ATTAAAAATATTAAATTAATAATTTTTATAATAAATGT
Found at i:569547 original size:18 final size:17
Alignment explanation
Indices: 569517--569551 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
569507 TCTACTCCAA
*
569517 AAAAGAAAAAAAAAAAC
1 AAAACAAAAAAAAAAAC
569534 AAAACAAAACAAAAAAAC
1 AAAACAAAA-AAAAAAAC
569552 CTCTAAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.86, C:0.11, G:0.03, T:0.00
Consensus pattern (17 bp):
AAAACAAAAAAAAAAAC
Found at i:575178 original size:18 final size:20
Alignment explanation
Indices: 575144--575189 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
575134 TATTTAACTT
575144 AAAAT-TAATTTATAATA-A
1 AAAATATAATTTATAATATA
575162 AAAATATAATTTA-AATATA
1 AAAATATAATTTATAATATA
*
575181 AAATTATAA
1 AAAATATAA
575190 AAAATTATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAATATAATTTATAATATA
Found at i:575365 original size:22 final size:21
Alignment explanation
Indices: 575337--575382 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 21
575327 ATATTTAATT
575337 AAAAATTAATTAATTATAA-ATA
1 AAAAATT--TTAATTATAATATA
*
575359 AAAAATTTTAATTTTAATATA
1 AAAAATTTTAATTATAATATA
575380 AAA
1 AAA
575383 TTATAACATG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 9 0.41
21 6 0.27
22 7 0.32
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
AAAAATTTTAATTATAATATA
Found at i:575380 original size:21 final size:22
Alignment explanation
Indices: 575330--575382 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
575320 ATGTTAAATA
575330 TTTAAT-T-AAAAATTAATTAAT
1 TTTAATATAAAAAATT-ATTAAT
*
575351 TATAA-ATAAAAAATT-TTAAT
1 TTTAATATAAAAAATTATTAAT
575371 TTTAATATAAAA
1 TTTAATATAAAA
575383 TTATAACATG
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
20 9 0.33
21 11 0.41
22 7 0.26
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TTTAATATAAAAAATTATTAAT
Found at i:578305 original size:26 final size:24
Alignment explanation
Indices: 578247--578308 Score: 72
Period size: 26 Copynumber: 2.5 Consensus size: 24
578237 CTATGAAAAT
578247 ATAAATATTTTATATAAAAGTAAA
1 ATAAATATTTTATATAAAAGTAAA
*
578271 ATCATATATTTTATTATACAAA-TATAA
1 AT-AAATATTTTA-TATA-AAAGTA-AA
578298 ATAAATATTTT
1 ATAAATATTTT
578309 TAATTTACTC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 2 0.06
25 9 0.28
26 14 0.44
27 7 0.22
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (24 bp):
ATAAATATTTTATATAAAAGTAAA
Found at i:579138 original size:2 final size:2
Alignment explanation
Indices: 579133--579167 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
579123 GTGTGTGTAC
579133 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
579168 CACACACACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:580478 original size:2 final size:2
Alignment explanation
Indices: 580466--580506 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
580456 CTAGGAAGAT
*
580466 GA GA GA AA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
580507 GGGAAGGCCT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:580982 original size:21 final size:21
Alignment explanation
Indices: 580940--580978 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
580930 AGATAATAAT
*
580940 TTTTCAATTTATTTATTTTAA
1 TTTTCAATTTAATTATTTTAA
580961 TTTT-AATTTAATTATTTT
1 TTTTCAATTTAATTATTTT
580979 TAATAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTTCAATTTAATTATTTTAA
Found at i:581449 original size:17 final size:18
Alignment explanation
Indices: 581418--581454 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
581408 CGAGTGATAA
581418 AAAATTTAATTTTTTAAAT
1 AAAATTTAA-TTTTTAAAT
581437 AAAATTTAA-TTTTAAAT
1 AAAATTTAATTTTTAAAT
581454 A
1 A
581455 TTATAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.50
19 9 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AAAATTTAATTTTTAAAT
Found at i:581779 original size:18 final size:17
Alignment explanation
Indices: 581758--581806 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
581748 TATATATAAA
581758 TATATAAAATTTTATATT
1 TATA-AAAATTTTATATT
**
581776 TATAGAAAATTTTGGATT
1 TATA-AAAATTTTATATT
581794 TA-AAAAATTTTAT
1 TATAAAAATTTTAT
581807 TTATTATTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
16 8 0.31
17 1 0.04
18 17 0.65
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (17 bp):
TATAAAAATTTTATATT
Found at i:581950 original size:27 final size:27
Alignment explanation
Indices: 581927--581985 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
581917 ATATAATATT
*
581927 TATTTAAATAGATTCAAATTTAATAAA
1 TATTTAAATAAATTCAAATTTAATAAA
*
581954 TATTTAAATAAATTTAAATATT-ATAAA
1 TATTTAAATAAATTCAAAT-TTAATAAA
581981 TATTT
1 TATTT
581986 TAAAAATAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 27 0.93
28 2 0.07
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (27 bp):
TATTTAAATAAATTCAAATTTAATAAA
Found at i:582376 original size:12 final size:11
Alignment explanation
Indices: 582361--582400 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
582351 TTATTTTATA
582361 ATTTATAAAATT
1 ATTTAT-AAATT
582373 ATTTATAAATT
1 ATTTATAAATT
*
582384 AACTTATAAATT
1 -ATTTATAAATT
582396 ATTTA
1 ATTTA
582401 AATTCAGCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 9 0.36
12 16 0.64
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (11 bp):
ATTTATAAATT
Found at i:606322 original size:22 final size:22
Alignment explanation
Indices: 606290--606344 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
606280 AAATTAATAT
*
606290 TAAT-TTTTTTAATTACAATTA
1 TAATATTTTTTAATCACAATTA
*
606311 TAATATTTTTTAATCATAATTA
1 TAATATTTTTTAATCACAATTA
*
606333 TAATAATTTTTA
1 TAATATTTTTTA
606345 TTATTTTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 4 0.13
22 26 0.87
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (22 bp):
TAATATTTTTTAATCACAATTA
Found at i:606879 original size:2 final size:2
Alignment explanation
Indices: 606872--606922 Score: 66
Period size: 2 Copynumber: 24.5 Consensus size: 2
606862 CCTAGCAATT
**
606872 TC TC TC TC TGC TC TC TGC AA TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC T-C TC TC T-C TC TC TC TC TC TC TC TC TC TC TC TC TC
606916 TC TC TC T
1 TC TC TC T
606923 TTGTCCCCTT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
2 40 0.93
3 3 0.07
ACGTcount: A:0.04, C:0.45, G:0.04, T:0.47
Consensus pattern (2 bp):
TC
Found at i:612680 original size:21 final size:21
Alignment explanation
Indices: 612648--612704 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
612638 TTAATTTTTT
* *
612648 ATTA-AATTTTTTTAATTACA
1 ATTATAATATTTTTAATCACA
*
612668 ATTATAATATTTTTAATCATA
1 ATTATAATATTTTTAATCACA
612689 ATTATAATCATTTTTA
1 ATTATAAT-ATTTTTA
612705 CTATTTTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
20 4 0.12
21 21 0.66
22 7 0.22
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTATAATATTTTTAATCACA
Found at i:613257 original size:23 final size:23
Alignment explanation
Indices: 613225--613270 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
613215 AGAAACCCTA
*
613225 GCAATTTCTCTCTCT-TGCTCTCT
1 GCAATCTCTCTCTCTCT-CTCTCT
613248 GCAATCTCTCTCTCTCTCTCTCT
1 GCAATCTCTCTCTCTCTCTCTCT
613271 CTCTTTGTCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 20 0.95
24 1 0.05
ACGTcount: A:0.09, C:0.39, G:0.07, T:0.46
Consensus pattern (23 bp):
GCAATCTCTCTCTCTCTCTCTCT
Found at i:617549 original size:27 final size:28
Alignment explanation
Indices: 617492--617559 Score: 84
Period size: 27 Copynumber: 2.4 Consensus size: 28
617482 GGAGAATCTT
**
617492 TTGGAACTTCAGTTTCAACAGCAGCGGCAG
1 TTGGAACTTCAG--TCAACAGCAGCAACAG
*
617522 TTGGAACTTCAG-CAACATCAGCAACAG
1 TTGGAACTTCAGTCAACAGCAGCAACAG
617549 TTGGAACTTCA
1 TTGGAACTTCA
617560 TCGGCGGCAG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
27 23 0.66
30 12 0.34
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.24
Consensus pattern (28 bp):
TTGGAACTTCAGTCAACAGCAGCAACAG
Found at i:617586 original size:21 final size:23
Alignment explanation
Indices: 617546--617593 Score: 73
Period size: 21 Copynumber: 2.1 Consensus size: 23
617536 ACATCAGCAA
617546 CAGTTGGAACTTCATCGGCGGCAG
1 CAGTTGGAACTT-ATCGGCGGCAG
617570 CAGTTGGAAC-T-TCGGCGGCAG
1 CAGTTGGAACTTATCGGCGGCAG
617591 CAG
1 CAG
617594 CGGCAGCAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 13 0.54
23 1 0.04
24 10 0.42
ACGTcount: A:0.21, C:0.25, G:0.35, T:0.19
Consensus pattern (23 bp):
CAGTTGGAACTTATCGGCGGCAG
Found at i:617593 original size:3 final size:3
Alignment explanation
Indices: 617587--617616 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
617577 AACTTCGGCG
*
617587 GCA GCA GCG GCA GCA GCA GCA GCA GCA GCA
1 GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA
617617 ATTGGAACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.33, G:0.37, T:0.00
Consensus pattern (3 bp):
GCA
Found at i:617594 original size:24 final size:24
Alignment explanation
Indices: 617512--617641 Score: 95
Period size: 24 Copynumber: 5.4 Consensus size: 24
617502 AGTTTCAACA
* *
617512 GCAGCGGCAGTTGGAACTTCAGCAACA
1 GCAGCAGCAGTTGGAACTTCAG---CG
* * *
617539 TCAGCAACAGTTGGAACTTCATCG
1 GCAGCAGCAGTTGGAACTTCAGCG
* *
617563 GCGGCAGCAGTTGGAACTTCGGCG
1 GCAGCAGCAGTTGGAACTTCAGCG
* * ** *
617587 GCAGCAGC-G--GCAGCAGCAGCA
1 GCAGCAGCAGTTGGAACTTCAGCG
*
617608 GCAGCAGCAATTGGAACTTCAGCG
1 GCAGCAGCAGTTGGAACTTCAGCG
617632 GCAGCAGCAG
1 GCAGCAGCAG
617642 CTGCAATTGG
Statistics
Matches: 76, Mismatches: 24, Indels: 9
0.70 0.22 0.08
Matches are distributed among these distances:
21 14 0.18
23 1 0.01
24 43 0.57
27 18 0.24
ACGTcount: A:0.27, C:0.27, G:0.32, T:0.14
Consensus pattern (24 bp):
GCAGCAGCAGTTGGAACTTCAGCG
Found at i:617673 original size:30 final size:30
Alignment explanation
Indices: 617597--617673 Score: 127
Period size: 30 Copynumber: 2.6 Consensus size: 30
617587 GCAGCAGCGG
* *
617597 CAGCAGCAGCAGCAGCAGCAATTGGAACTT
1 CAGCGGCAGCAGCAGCTGCAATTGGAACTT
617627 CAGCGGCAGCAGCAGCTGCAATTGGAACTT
1 CAGCGGCAGCAGCAGCTGCAATTGGAACTT
*
617657 CAGTGGCAGCAGCAGCT
1 CAGCGGCAGCAGCAGCT
617674 TCGTCACCAC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.29, C:0.27, G:0.30, T:0.14
Consensus pattern (30 bp):
CAGCGGCAGCAGCAGCTGCAATTGGAACTT
Found at i:622390 original size:14 final size:14
Alignment explanation
Indices: 622371--622397 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
622361 CTGTGCTTAT
622371 GTCAGGGTTTTGGG
1 GTCAGGGTTTTGGG
622385 GTCAGGGTTTTGG
1 GTCAGGGTTTTGG
622398 TTTAAACATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.07, G:0.48, T:0.37
Consensus pattern (14 bp):
GTCAGGGTTTTGGG
Found at i:630599 original size:26 final size:25
Alignment explanation
Indices: 630569--630631 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 25
630559 ATTTAAAATT
*
630569 AATAAAATAATAT-TTTATAATATAA
1 AATAAAATAATATATATA-AATATAA
630594 ATATAAAATTAA-ATATATAAATATAA
1 A-ATAAAA-TAATATATATAAATATAA
630620 AATTAAAATAAT
1 AA-TAAAATAAT
630632 TAATTAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
25 5 0.16
26 21 0.66
27 6 0.19
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (25 bp):
AATAAAATAATATATATAAATATAA
Found at i:630611 original size:20 final size:20
Alignment explanation
Indices: 630588--630626 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
630578 ATATTTTATA
630588 ATATAAATATAAAATTAAAT
1 ATATAAATATAAAATTAAAT
630608 ATATAAATATAAAATTAAA
1 ATATAAATATAAAATTAAA
630627 ATAATTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
ATATAAATATAAAATTAAAT
Found at i:630620 original size:14 final size:13
Alignment explanation
Indices: 630587--630629 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
630577 AATATTTTAT
630587 AATATAAATATAA
1 AATATAAATATAA
630600 AAT-TAAATATATA
1 AATATAAATATA-A
630613 AATATAAA-ATTAA
1 AATATAAATA-TAA
630626 AATA
1 AATA
630630 ATTAATTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 8 0.30
13 13 0.48
14 6 0.22
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
AATATAAATATAA
Found at i:631745 original size:13 final size:12
Alignment explanation
Indices: 631718--631756 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
631708 AAATCATATC
631718 ATTTTGATATTTT
1 ATTTT-ATATTTT
631731 ATTTTATATTATT
1 ATTTTATATT-TT
*
631744 ATATTATATTTT
1 ATTTTATATTTT
631756 A
1 A
631757 GATTATCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
12 8 0.33
13 16 0.67
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (12 bp):
ATTTTATATTTT
Found at i:631753 original size:20 final size:20
Alignment explanation
Indices: 631724--631762 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
631714 TATCATTTTG
* *
631724 ATATTTTATTTTATATTATT
1 ATATTATATTTTAGATTATT
631744 ATATTATATTTTAGATTAT
1 ATATTATATTTTAGATTAT
631763 CAAAGTCTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (20 bp):
ATATTATATTTTAGATTATT
Found at i:633635 original size:12 final size:14
Alignment explanation
Indices: 633589--633655 Score: 52
Period size: 13 Copynumber: 4.8 Consensus size: 14
633579 ACATAAAATT
633589 TAATTTTATATTTTA
1 TAATTTTATA-TTTA
*
633604 TTAA-ATTA-ATTTA
1 -TAATTTTATATTTA
633617 TAATTTT-TATTTA
1 TAATTTTATATTTA
*
633630 -AATTTTATATTACA
1 TAATTTTATATT-TA
633644 TCAATTTTATAT
1 T-AATTTTATAT
633656 ATTTATATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
12 9 0.21
13 15 0.36
14 2 0.05
15 3 0.07
16 13 0.31
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (14 bp):
TAATTTTATATTTA
Found at i:637460 original size:39 final size:39
Alignment explanation
Indices: 637416--637494 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
637406 GTCAACAGTC
*
637416 TCCCCCAGTCCCGTGCGAGTAAGTCCTATCAACACCTCT
1 TCCCCCAATCCCGTGCGAGTAAGTCCTATCAACACCTCT
*
637455 TCCCCCAATCCCGTGCGAGTAAGTCCTATCAATACCTCT
1 TCCCCCAATCCCGTGCGAGTAAGTCCTATCAACACCTCT
637494 T
1 T
637495 TCCGGGTCAG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.22, C:0.39, G:0.14, T:0.25
Consensus pattern (39 bp):
TCCCCCAATCCCGTGCGAGTAAGTCCTATCAACACCTCT
Found at i:637630 original size:140 final size:140
Alignment explanation
Indices: 637436--637698 Score: 490
Period size: 140 Copynumber: 1.9 Consensus size: 140
637426 CCGTGCGAGT
*
637436 AAGTCCTATCAACACCTCTTCCCCCAATCCCGTGCGAGTAAGTCCTATCAATACCTCTTTCCGGG
1 AAGTCCTATCAACACCTCTTCCCCCAATCCCGTGCGAGTAAGTCCTATCAATACCTCTTTCCGGA
*
637501 TCAGGCAACCTCATATCTCTAATGTGCTTTTGGGGTGGTCACTTGGGTATTCCGTTTCGCCCACT
66 CCAGGCAACCTCATATCTCTAATGTGCTTTTGGGGTGGTCACTTGGGTATTCCGTTTCGCCCACT
637566 TGGGTGTTCC
131 TGGGTGTTCC
* *
637576 AAGTCCTATCAACACCTCTTCCCCCAGTCCCGTGCGAGTAAGTCCTATCAATACCTCTTTTCGGA
1 AAGTCCTATCAACACCTCTTCCCCCAATCCCGTGCGAGTAAGTCCTATCAATACCTCTTTCCGGA
637641 CCAGGCAACCTCATATCTCTAATGTGCTTTTGGGGTGGTCACTTGGGTATTCCGTTTC
66 CCAGGCAACCTCATATCTCTAATGTGCTTTTGGGGTGGTCACTTGGGTATTCCGTTTC
637699 TGTTTTTGCA
Statistics
Matches: 119, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 119 1.00
ACGTcount: A:0.19, C:0.30, G:0.19, T:0.32
Consensus pattern (140 bp):
AAGTCCTATCAACACCTCTTCCCCCAATCCCGTGCGAGTAAGTCCTATCAATACCTCTTTCCGGA
CCAGGCAACCTCATATCTCTAATGTGCTTTTGGGGTGGTCACTTGGGTATTCCGTTTCGCCCACT
TGGGTGTTCC
Found at i:637807 original size:147 final size:138
Alignment explanation
Indices: 637439--637820 Score: 453
Period size: 140 Copynumber: 2.7 Consensus size: 138
637429 TGCGAGTAAG
* * ** *
637439 TCCTATCAACACCTCTTCCCCCAATCCCGTGCGAGTAAGTCCTATCAATACCTCTTTCCGGGTCA
1 TCCTATCAACACATCTCCCCCCAGCCCCGTGCGAGTAAGTCCTATCAATACCTCTTTTCGGG-CA
*
637504 GGCAACCTCATATCTCTAATGTGCTTTTGGGGTGGTCACTTGGGTATTCCGTTTCGCCCACTTGG
65 GGCAACCTCATATCTCTAATGTGCTTTTGGGGTGGTCACTTGGGTATTCCGTTTCG-CCACTTGC
* *
637569 GTGTTCCAAG
129 ATGTTCCAAC
* * * *
637579 TCCTATCAACACCTCTTCCCCCAGTCCCGTGCGAGTAAGTCCTATCAATACCTCTTTTCGGACCA
1 TCCTATCAACACATCTCCCCCCAGCCCCGTGCGAGTAAGTCCTATCAATACCTCTTTTCGG-GCA
***
637644 GGCAACCTCATATCTCTAATGTGCTTTTGGGGTGGTCACTTGGGTATTCCGTTTCTG-TTTTTGC
65 GGCAACCTCATATCTCTAATGTGCTTTTGGGGTGGTCACTTGGGTATTCCGTTTC-GCCACTTGC
*
637708 ATATTATGGCCAATC
129 AT-GT-T--CCAA-C
* *
637723 TCCGATCTGCCAACA-ATCTCCCCCCAGCCCCGTGCGAGTAAGTCCTATCAACACCTCTTTTCGG
1 TCC--TAT--CAACACATCTCCCCCCAGCCCCGTGCGAGTAAGTCCTATCAATACCTCTTTTCGG
*
637787 GCAAGACAACCTCATATCTCTAATGTGCTTTTGG
62 GC-AGGCAACCTCATATCTCTAATGTGCTTTTGG
637821 AGTAGACCAC
Statistics
Matches: 213, Mismatches: 17, Indels: 17
0.86 0.07 0.07
Matches are distributed among these distances:
139 4 0.02
140 117 0.55
141 2 0.01
143 4 0.02
144 3 0.01
146 3 0.01
147 75 0.35
148 5 0.02
ACGTcount: A:0.19, C:0.31, G:0.18, T:0.31
Consensus pattern (138 bp):
TCCTATCAACACATCTCCCCCCAGCCCCGTGCGAGTAAGTCCTATCAATACCTCTTTTCGGGCAG
GCAACCTCATATCTCTAATGTGCTTTTGGGGTGGTCACTTGGGTATTCCGTTTCGCCACTTGCAT
GTTCCAAC
Found at i:647051 original size:25 final size:23
Alignment explanation
Indices: 646995--647049 Score: 78
Period size: 22 Copynumber: 2.4 Consensus size: 23
646985 ATAATTATTT
*
646995 TATATAAAAA-TTTATTTAAATA
1 TATATAAAAATTTTATTAAAATA
647017 TAT-TAAAAATTTTATTAAAATAA
1 TATATAAAAATTTTATTAAAAT-A
647040 TATATAAAAA
1 TATATAAAAA
647050 ATAAAAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 6 0.21
22 13 0.45
23 4 0.14
24 6 0.21
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
TATATAAAAATTTTATTAAAATA
Found at i:656752 original size:17 final size:18
Alignment explanation
Indices: 656713--656754 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
656703 CAATTAAAAA
656713 AATAAATATTTTATATTAT
1 AATAAA-ATTTTATATTAT
656732 --TAAAATTTTA-ATTAT
1 AATAAAATTTTATATTAT
656747 AATAAAAT
1 AATAAAAT
656755 AAAATTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
15 5 0.24
16 6 0.29
17 10 0.48
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
AATAAAATTTTATATTAT
Found at i:658888 original size:12 final size:12
Alignment explanation
Indices: 658871--658895 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
658861 TTAAATTATA
658871 AATAATTTTTTT
1 AATAATTTTTTT
658883 AATAATTTTTTT
1 AATAATTTTTTT
658895 A
1 A
658896 TATATTATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
AATAATTTTTTT
Found at i:658980 original size:24 final size:25
Alignment explanation
Indices: 658952--659004 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
658942 CTCACTTTTA
* *
658952 ATAAAAAATTA-ATGAATTTTATTT
1 ATAAAAAATTATATAAATTTTATTC
**
658976 ATAAAATTTTATATAAATTTTATTC
1 ATAAAAAATTATATAAATTTTATTC
659001 ATAA
1 ATAA
659005 GAACAAAGAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 9 0.38
25 15 0.62
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (25 bp):
ATAAAAAATTATATAAATTTTATTC
Found at i:659298 original size:18 final size:18
Alignment explanation
Indices: 659246--659299 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 18
659236 AAAGTGAATT
*
659246 ATTTTATATTTA--ATAA
1 ATTTTATATTTATTATTA
*
659262 ATATTTA-ATTTTTTA-TA
1 AT-TTTATATTTATTATTA
659279 ATTTTATATTTATTATTA
1 ATTTTATATTTATTATTA
659297 ATT
1 ATT
659300 AATTTTAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
16 10 0.33
17 14 0.47
18 6 0.20
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
ATTTTATATTTATTATTA
Found at i:660120 original size:33 final size:32
Alignment explanation
Indices: 660065--660128 Score: 74
Period size: 33 Copynumber: 2.0 Consensus size: 32
660055 TTTATATAAA
* * *
660065 ATATAATTTAAATACATAAATTATTAATATTTT
1 ATATAATATAAATACACAAATTACTAA-ATTTT
* *
660098 ATATAATATAAATATACGAATTACTAAATTT
1 ATATAATATAAATACACAAATTACTAAATTT
660129 AATCATATTC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
32 4 0.15
33 22 0.85
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.44
Consensus pattern (32 bp):
ATATAATATAAATACACAAATTACTAAATTTT
Found at i:666182 original size:17 final size:17
Alignment explanation
Indices: 666160--666193 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
666150 TCTTTTCTAA
*
666160 ATAATTTAAATTAAATT
1 ATAATTTAAATAAAATT
666177 ATAATTTAAATAAAATT
1 ATAATTTAAATAAAATT
666194 GAAAAAAATT
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATAATTTAAATAAAATT
Found at i:666693 original size:2 final size:2
Alignment explanation
Indices: 666686--666716 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
666676 TTCACTACAA
666686 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
666717 CTAGTGTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:671572 original size:20 final size:20
Alignment explanation
Indices: 671533--671596 Score: 96
Period size: 20 Copynumber: 3.2 Consensus size: 20
671523 ACTTGAATTA
671533 ATAAAATATTATTTTT-AAT
1 ATAAAATATTATTTTTAAAT
671552 ATAAAA-ATTATTTTATAAAT
1 ATAAAATATTATTTT-TAAAT
671572 ATAAAATATTATTTTTAAAT
1 ATAAAATATTATTTTTAAAT
*
671592 GTAAA
1 ATAAA
671597 TATACAATTA
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
18 8 0.20
19 7 0.17
20 18 0.44
21 8 0.20
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
ATAAAATATTATTTTTAAAT
Found at i:671636 original size:37 final size:41
Alignment explanation
Indices: 671594--671670 Score: 108
Period size: 37 Copynumber: 2.0 Consensus size: 41
671584 TTTTAAATGT
*
671594 AAATATACAATTAAACAAAT-A-T-AAAAAT-AATATATAA
1 AAATATAAAATTAAACAAATAATTAAAAAATAAATATATAA
*
671631 AAATATAAAATTAAATAAATAATTAAAAAATAAATATATA
1 AAATATAAAATTAAACAAATAATTAAAAAATAAATATATA
671671 TATACCGGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
37 18 0.53
38 1 0.03
39 1 0.03
40 6 0.18
41 8 0.24
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (41 bp):
AAATATAAAATTAAACAAATAATTAAAAAATAAATATATAA
Found at i:671674 original size:37 final size:37
Alignment explanation
Indices: 671587--671674 Score: 97
Period size: 37 Copynumber: 2.4 Consensus size: 37
671577 ATATTATTTT
* *
671587 TAAATGTAAATATACAATTAAACAAATATAAAAATAA
1 TAAATATAAATATAAAATTAAACAAATATAAAAATAA
* * * *
671624 TATATAAAAATATAAAATTAAATAAATAATTAAAA-AA
1 TAAATATAAATATAAAATTAAACAAAT-ATAAAAATAA
*
671661 TAAATATATATATA
1 TAAATATAAATATA
671675 CCGGATCGTG
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
37 35 0.85
38 6 0.15
ACGTcount: A:0.66, C:0.02, G:0.01, T:0.31
Consensus pattern (37 bp):
TAAATATAAATATAAAATTAAACAAATATAAAAATAA
Found at i:672005 original size:33 final size:33
Alignment explanation
Indices: 671968--672042 Score: 132
Period size: 33 Copynumber: 2.3 Consensus size: 33
671958 ATAATCACCT
671968 AATCAATATCTAATATTCTCTAAATCAATATCA
1 AATCAATATCTAATATTCTCTAAATCAATATCA
* *
672001 AATCAATATTTAATATTCTTTAAATCAATATCA
1 AATCAATATCTAATATTCTCTAAATCAATATCA
672034 AATCAATAT
1 AATCAATAT
672043 AGAATATTAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.39
Consensus pattern (33 bp):
AATCAATATCTAATATTCTCTAAATCAATATCA
Found at i:676842 original size:15 final size:17
Alignment explanation
Indices: 676805--676840 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
676795 ATACAAAGAT
*
676805 AAAATATTATAAAATAA
1 AAAATATTAAAAAATAA
676822 AAAATA-TAAAAAATAA
1 AAAATATTAAAAAATAA
676838 AAA
1 AAA
676841 TAATGATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (17 bp):
AAAATATTAAAAAATAA
Found at i:682131 original size:341 final size:341
Alignment explanation
Indices: 681508--682205 Score: 1263
Period size: 341 Copynumber: 2.0 Consensus size: 341
681498 TGGCCTTATG
** * *
681508 ACAAAAATTTTAAAAAACTATCTGCTTTTCAAAAATTAAAGCAGAACTTAATTTCTAGGCAATTT
1 ACAAAAATTAAAAAAAACTATATGCTTTTCAAAAATTAAAGCAGAACTTAATTCCTAGGCAATTT
* *
681573 AGTTCATTCACGACAAGGGATAGAATGTTCACTGCAGTTTAACTTCAAAAATAGAACCAAAATAA
66 AGTTCAGTCACGACAAGGGATAGAATGTACACTGCAGTTTAACTTCAAAAATAGAACCAAAATAA
681638 AAGACTTAACTATAAATGAAACCAGAAGACCATCTATAGCAGAGTTCCAAAGATCACTGAAACAA
131 AAGACTTAACTATAAATGAAACCAGAAGACCATCTATAGCAGAGTTCCAAAGATCACTGAAACAA
681703 TCTGGCAATATAATTCTATTTCTAAATGTTTCATTCTCAATGAGACATGGCAATCTAAAACAAGA
196 TCTGGCAATATAATTCTATTTCTAAATGTTTCATTCTCAATGAGACATGGCAATCTAAAACAAGA
* *
681768 CATGGTGATACAACATGATACGAAAATAAGACATGAAGGCAACTTAGCTTAAAATTTTAGCAAAA
261 CATGGTGATACAACACGATACGAAAATAAGACACGAAGGCAACTTAGCTTAAAATTTTAGCAAAA
*
681833 ACCATATATGAGTTTA
326 ACCATATATGAATTTA
*
681849 ACAAAAATTAAAAAAAACTATATGCTTTTTAAAAATTAAAGCAGAACTTAATTCCTAGGCAATTT
1 ACAAAAATTAAAAAAAACTATATGCTTTTCAAAAATTAAAGCAGAACTTAATTCCTAGGCAATTT
681914 AGTTCAGTCACGACAAGGGATAGAATGTACACTGCAGTTTAACTTCAAAAATAGAACCAAAATAA
66 AGTTCAGTCACGACAAGGGATAGAATGTACACTGCAGTTTAACTTCAAAAATAGAACCAAAATAA
681979 AAGACTTAACTATAAATGAAACCAGAAGACCATCTATAGCAGAGTTCCAAAGATCACTGAAACAA
131 AAGACTTAACTATAAATGAAACCAGAAGACCATCTATAGCAGAGTTCCAAAGATCACTGAAACAA
*
682044 TCTGGCAATATAATTCTATTTCTAAATGTTTCATTCTCAATGAGACATGGCAATCTAAAACATGA
196 TCTGGCAATATAATTCTATTTCTAAATGTTTCATTCTCAATGAGACATGGCAATCTAAAACAAGA
*
682109 CATGGTGATACAACACGATACGAAAATAAGACACGAAGGCAACTTAGCTTAAAATTTTAGCAATA
261 CATGGTGATACAACACGATACGAAAATAAGACACGAAGGCAACTTAGCTTAAAATTTTAGCAAAA
*
682174 ACTATATATGAATTTA
326 ACCATATATGAATTTA
*
682190 AC-AAAATAAAAAAAAA
1 ACAAAAATTAAAAAAAA
682206 GTATTTTACA
Statistics
Matches: 343, Mismatches: 14, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
340 13 0.04
341 330 0.96
ACGTcount: A:0.45, C:0.16, G:0.13, T:0.26
Consensus pattern (341 bp):
ACAAAAATTAAAAAAAACTATATGCTTTTCAAAAATTAAAGCAGAACTTAATTCCTAGGCAATTT
AGTTCAGTCACGACAAGGGATAGAATGTACACTGCAGTTTAACTTCAAAAATAGAACCAAAATAA
AAGACTTAACTATAAATGAAACCAGAAGACCATCTATAGCAGAGTTCCAAAGATCACTGAAACAA
TCTGGCAATATAATTCTATTTCTAAATGTTTCATTCTCAATGAGACATGGCAATCTAAAACAAGA
CATGGTGATACAACACGATACGAAAATAAGACACGAAGGCAACTTAGCTTAAAATTTTAGCAAAA
ACCATATATGAATTTA
Found at i:683185 original size:14 final size:15
Alignment explanation
Indices: 683166--683196 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
683156 TTTAATTTCA
683166 AAAATTAATT-GATC
1 AAAATTAATTCGATC
683180 AAAATTAATTCGATC
1 AAAATTAATTCGATC
683195 AA
1 AA
683197 TTTAATTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.32
Consensus pattern (15 bp):
AAAATTAATTCGATC
Found at i:685413 original size:17 final size:18
Alignment explanation
Indices: 685373--685413 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
685363 AAAATAAAAT
685373 AATTTATTTATTGATCAA
1 AATTTATTTATTGATCAA
**
685391 AA-TTATTT-TTTTTCAA
1 AATTTATTTATTGATCAA
685407 AATTTAT
1 AATTTAT
685414 ATAATTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 8 0.40
17 10 0.50
18 2 0.10
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (18 bp):
AATTTATTTATTGATCAA
Found at i:687680 original size:29 final size:29
Alignment explanation
Indices: 687646--687703 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
687636 ATTGTGTACC
* *
687646 AAATTTGGGGTTTTAGGTTTTGAATTTTA
1 AAATTTAGAGTTTTAGGTTTTGAATTTTA
*
687675 AAATTTAGAGTTTTAGGTTTTGGATTTTA
1 AAATTTAGAGTTTTAGGTTTTGAATTTTA
687704 GGGTTTTGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (29 bp):
AAATTTAGAGTTTTAGGTTTTGAATTTTA
Found at i:687708 original size:15 final size:13
Alignment explanation
Indices: 687656--687744 Score: 63
Period size: 14 Copynumber: 6.4 Consensus size: 13
687646 AAATTTGGGG
687656 TTTTAGGTTTTGAA
1 TTTTAGGTTTTG-A
** *
687670 TTTTAAAATTTAGA
1 TTTT-AGGTTTTGA
687684 GTTTTAGGTTTTGGA
1 -TTTTAGGTTTT-GA
687699 TTTTAGGGTTTTGA
1 TTTTA-GGTTTTGA
687713 TTTTAAGG-TTTGA
1 TTTT-AGGTTTTGA
* *
687726 GGTTTAGGGTTTGA
1 -TTTTAGGTTTTGA
687740 TTTTA
1 TTTTA
687745 AAGTTTTGAA
Statistics
Matches: 60, Mismatches: 8, Indels: 15
0.72 0.10 0.18
Matches are distributed among these distances:
13 12 0.20
14 30 0.50
15 18 0.30
ACGTcount: A:0.21, C:0.00, G:0.25, T:0.54
Consensus pattern (13 bp):
TTTTAGGTTTTGA
Found at i:687731 original size:28 final size:29
Alignment explanation
Indices: 687700--687760 Score: 90
Period size: 28 Copynumber: 2.1 Consensus size: 29
687690 GGTTTTGGAT
687700 TTTAGGGTTTTGATTTT-AAGGTTTG-AGG
1 TTTAGGG-TTTGATTTTAAAGGTTTGAAGG
*
687728 TTTAGGGTTTGATTTTAAAGTTTTGAAGG
1 TTTAGGGTTTGATTTTAAAGGTTTGAAGG
687757 TTTA
1 TTTA
687761 ATTTTAGGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 9 0.30
28 14 0.47
29 7 0.23
ACGTcount: A:0.21, C:0.00, G:0.28, T:0.51
Consensus pattern (29 bp):
TTTAGGGTTTGATTTTAAAGGTTTGAAGG
Found at i:687750 original size:13 final size:13
Alignment explanation
Indices: 687697--687750 Score: 54
Period size: 14 Copynumber: 4.0 Consensus size: 13
687687 TTAGGTTTTG
*
687697 GATTTTAGGGTTTT
1 GATTTTAAGG-TTT
687711 GATTTTAAGGTTT
1 GATTTTAAGGTTT
* *
687724 GAGGTTTAGGGTTT
1 GA-TTTTAAGGTTT
*
687738 GATTTTAAAGTTT
1 GATTTTAAGGTTT
687751 TGAAGGTTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
13 13 0.39
14 20 0.61
ACGTcount: A:0.20, C:0.00, G:0.28, T:0.52
Consensus pattern (13 bp):
GATTTTAAGGTTT
Found at i:688211 original size:3 final size:3
Alignment explanation
Indices: 688205--688238 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
688195 GTTGTTGTTG
688205 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
688239 GAAATAACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:688342 original size:8 final size:10
Alignment explanation
Indices: 688310--688345 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
688300 AATAAAGCTA
*
688310 AAAAAGATAT
1 AAAAATATAT
688320 AAAAATATAT
1 AAAAATATAT
688330 AAAAATA-AT
1 AAAAATATAT
688339 AAAAATA
1 AAAAATA
688346 AAAAAAACTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
9 9 0.36
10 16 0.64
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (10 bp):
AAAAATATAT
Found at i:688352 original size:9 final size:9
Alignment explanation
Indices: 688297--688351 Score: 53
Period size: 9 Copynumber: 6.2 Consensus size: 9
688287 CATAATTAAC
688297 AATAATAAA
1 AATAATAAA
**
688306 GCTAA-AAA
1 AATAATAAA
688314 AGAT-ATAAA
1 A-ATAATAAA
688323 AATATATAAA
1 AATA-ATAAA
688333 AATAATAAA
1 AATAATAAA
688342 AATAA-AAA
1 AATAATAAA
688350 AA
1 AA
688352 ACTTGAACTA
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
8 11 0.29
9 18 0.47
10 9 0.24
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.20
Consensus pattern (9 bp):
AATAATAAA
Found at i:689851 original size:33 final size:33
Alignment explanation
Indices: 689809--689925 Score: 101
Period size: 33 Copynumber: 3.4 Consensus size: 33
689799 ATTGAGTCAT
*
689809 GAGTCAAAAATAAAGACATCGAAATTGAACTGG
1 GAGTCAAAAATAAAGAGATCGAAATTGAACTGG
* * * * *
689842 GAGTTAAAAAATACAAAATGATCGAGATTGAATTGT
1 GAG-TCAAAAATA-AAGA-GATCGAAATTGAACTGG
* * *
689878 GAGTCAAAAAAAAAGAGACCGAAATTGAA-TCGT
1 GAGTCAAAAATAAAGAGATCGAAATTGAACT-GG
689911 GAGTCAAAAAATAAA
1 GAGTC-AAAAATAAA
689926 AATGACTAGG
Statistics
Matches: 67, Mismatches: 12, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
32 1 0.01
33 21 0.31
34 19 0.28
35 10 0.15
36 16 0.24
ACGTcount: A:0.51, C:0.09, G:0.20, T:0.20
Consensus pattern (33 bp):
GAGTCAAAAATAAAGAGATCGAAATTGAACTGG
Found at i:689972 original size:103 final size:102
Alignment explanation
Indices: 689865--690103 Score: 237
Period size: 103 Copynumber: 2.3 Consensus size: 102
689855 CAAAATGATC
* *
689865 GAGATTGAATTGTGAGTCAAAAAAAAAGAGACCGAAATTGAATCGTGAGTCAAAAAATAAAAATG
1 GAGATTGAATTGTGAGTCAAAAAAAAAGAGACCGAAATTAAATCGTGAGACAAAAAATAAAAA-G
* * * * *
689930 ACTAG-GATTAAATCACAAGTCAAAGAATAATGACGATT
65 A-TAGAGATTAAACCACAAGTAAAAAAATAATCACAATT
* * * * *** *
689968 GAGATTGAACTGTGAGTCAGAAAATAAAGAAACTGGGTTTAAATCGTGAGACAGAAAATAAAAAG
1 GAGATTGAATTGTGAGTCA-AAAAAAAAGAGACCGAAATTAAATCGTGAGACAAAAAATAAAAAG
* * **
690033 ATTGAGATTGAACCACTTGTAAAAAAATAATCACAATT
65 ATAGAGATTAAACCACAAGTAAAAAAATAATCACAATT
***
690071 GAGATTGAATCACGAGTCAAAAAATAAAGAGAC
1 GAGATTGAATTGTGAGTCAAAAAA-AAAGAGAC
690104 TAAGATTGAA
Statistics
Matches: 108, Mismatches: 25, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
102 6 0.06
103 67 0.62
104 35 0.32
ACGTcount: A:0.49, C:0.10, G:0.20, T:0.21
Consensus pattern (102 bp):
GAGATTGAATTGTGAGTCAAAAAAAAAGAGACCGAAATTAAATCGTGAGACAAAAAATAAAAAGA
TAGAGATTAAACCACAAGTAAAAAAATAATCACAATT
Found at i:690225 original size:34 final size:34
Alignment explanation
Indices: 689878--690336 Score: 190
Period size: 34 Copynumber: 13.4 Consensus size: 34
689868 ATTGAATTGT
* * * * **
689878 GAGTCAAA-AAAAAAGAGACCGAAATTGAATCGT
1 GAGTCAAAGAATAAAGAGACTGAGATTAAATCAC
* *
689911 GAGTCAAAAAATAAAAATGACT-AGGATTAAATCAC
1 GAGTCAAAGAATAAAGA-GACTGA-GATTAAATCAC
* * * * **
689946 AAGTCAAAGAATAATGACGATTGAGATTGAA-CTGT
1 GAGTCAAAGAATAAAGA-GACTGAGATTAAATC-AC
* * * **
689981 GAGTCAGAA-AATAAAGAAACTGGGTTTAAATCGT
1 GAGTCA-AAGAATAAAGAGACTGAGATTAAATCAC
* * * * *
690015 GAGACAGAA-AATAAAAAGATTGAGATTGAACCAC
1 GAGTCA-AAGAATAAAGAGACTGAGATTAAATCAC
** * * * * *
690049 TTGTAAAAAAATAATCACA-ATTGAGATTGAATCAC
1 GAGTCAAAGAATAA--AGAGACTGAGATTAAATCAC
* * *
690084 GAGTCAAAAAATAAAGAGACTAAGATTGAA-CAGC
1 GAGTCAAAGAATAAAGAGACTGAGATTAAATCA-C
* * * * *
690118 AAGTTAAAGAATAACA-AGATTGGGATTGAACTGCA-
1 GAGTCAAAGAATAA-AGAGACTGAGATT-AAAT-CAC
* * * *
690153 -AGTCAGAGAATAATA-AG-CTAAGATTAAACCAA
1 GAGTCAAAGAATAA-AGAGACTGAGATTAAATCAC
* * *
690185 GAGTCAAAGAATAACGAGATTG-GAATTGAATCAC
1 GAGTCAAAGAATAAAGAGACTGAG-ATTAAATCAC
*
690219 GAGTCAAAAAATAAAGAGACTGAGATTAAATCAC
1 GAGTCAAAGAATAAAGAGACTGAGATTAAATCAC
* * * *
690253 GAGTCAAAGAATAAAAAGGCTGGGATTAAACCAC
1 GAGTCAAAGAATAAAGAGACTGAGATTAAATCAC
* *
690287 GAGTCAAAAAATAAAGATGA-TCGAGATTAAATCAT
1 GAGTCAAAGAATAAAGA-GACT-GAGATTAAATCAC
*
690322 GAGTTAAAGAATAAA
1 GAGTCAAAGAATAAA
690337 TGACGGTTGG
Statistics
Matches: 317, Mismatches: 85, Indels: 46
0.71 0.19 0.10
Matches are distributed among these distances:
31 2 0.01
32 2 0.01
33 34 0.11
34 174 0.55
35 98 0.31
36 5 0.02
37 2 0.01
ACGTcount: A:0.50, C:0.11, G:0.20, T:0.20
Consensus pattern (34 bp):
GAGTCAAAGAATAAAGAGACTGAGATTAAATCAC
Found at i:690288 original size:68 final size:67
Alignment explanation
Indices: 690068--690405 Score: 268
Period size: 68 Copynumber: 4.9 Consensus size: 67
690058 AATAATCACA
* * * * * * *
690068 ATTGAGATTGAATCACGAGTCAAAAAATAAAGAGACTAAGATTGAACAGCAAGTTAAAGAATAAC
1 ATTGGGATTGAACCACGAGTCAAAAAATAAAGAGACTGAGATTAAACA-CGAGTCAAAGAATAAA
690133 AAG
65 AAG
** * * * * *
690136 ATTGGGATTGAACTGCAAGTCAGAGAATAATA-AG-CTAAGATTAAACCAAGAGTCAAAGAATAA
1 ATTGGGATTGAACCACGAGTCAAAAAATAA-AGAGACTGAGATTAAA-CACGAGTCAAAGAATAA
**
690199 CGAG
64 AAAG
* *
690203 ATTGGAATTGAATCACGAGTCAAAAAATAAAGAGACTGAGATTAAATCACGAGTCAAAGAATAAA
1 ATTGGGATTGAACCACGAGTCAAAAAATAAAGAGACTGAGATTAAA-CACGAGTCAAAGAATAAA
690268 AAG
65 AAG
** * * *
690271 GCTGGGATTAAACCACGAGTCAAAAAATAAAGATGA-TCGAGATTAAATCATGAGTTAAAGAATA
1 ATTGGGATTGAACCACGAGTCAAAAAATAAAGA-GACT-GAGATTAAA-CACGAGTCAAAGAATA
*
690335 AATGACG
63 AA--AAG
* *** * * * *
690342 GTTGGGATTGAATGTCGAGTCATAAAATAAAAATGATTGGGATTAAACTACGAGTCAAAGAATA
1 ATTGGGATTGAACCACGAGTCAAAAAATAAAGA-GACTGAGATTAAAC-ACGAGTCAAAGAATA
690406 TATTATTACC
Statistics
Matches: 218, Mismatches: 42, Indels: 17
0.79 0.15 0.06
Matches are distributed among these distances:
66 1 0.00
67 50 0.23
68 84 0.39
69 29 0.13
70 1 0.00
71 52 0.24
72 1 0.00
ACGTcount: A:0.48, C:0.10, G:0.21, T:0.21
Consensus pattern (67 bp):
ATTGGGATTGAACCACGAGTCAAAAAATAAAGAGACTGAGATTAAACACGAGTCAAAGAATAAAA
AG
Found at i:690292 original size:135 final size:138
Alignment explanation
Indices: 690074--690405 Score: 341
Period size: 135 Copynumber: 2.4 Consensus size: 138
690064 CACAATTGAG
* * * * * *
690074 ATTGAATCACGAGTCAAAAAATAAAGAGACTAAGATTGAACAGCAAGTTAAAGAATAACAAGATT
1 ATTGAATCACGAGTCAAAAAATAAAGAGACTGAGATTAAACA-CGAGTCAAAGAATAAAAAGACT
* ** * * *
690139 GGGATTGAACTGCAAGTCAGAGAATAATA-A-GCT-AAGATTAAACCAAGAGTCAAAGAAT-AAC
65 GGGATTAAACCACAAGTCAAAAAATAA-AGATGATCAAGATTAAACCAAGAGTCAAAGAATAAAC
690200 GA-GATTGGA
129 GACGATTGGA
*
690209 ATTGAATCACGAGTCAAAAAATAAAGAGACTGAGATTAAATCACGAGTCAAAGAATAAAAAGGCT
1 ATTGAATCACGAGTCAAAAAATAAAGAGACTGAGATTAAA-CACGAGTCAAAGAATAAAAAGACT
* * * * * *
690274 GGGATTAAACCACGAGTCAAAAAATAAAGATGATCGAGATTAAATCATGAGTTAAAGAATAAATG
65 GGGATTAAACCACAAGTCAAAAAATAAAGATGATCAAGATTAAACCAAGAGTCAAAGAATAAACG
* *
690339 ACGGTTGGG
130 ACGATTGGA
** * * * *
690348 ATTGAATGTCGAGTCATAAAATAAAAATGATTGGGATTAAACTACGAGTCAAAGAATA
1 ATTGAATCACGAGTCAAAAAATAAAGA-GACTGAGATTAAAC-ACGAGTCAAAGAATA
690406 TATTATTACC
Statistics
Matches: 162, Mismatches: 27, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
134 1 0.01
135 77 0.48
136 4 0.02
137 21 0.13
138 4 0.02
139 29 0.18
140 26 0.16
ACGTcount: A:0.48, C:0.11, G:0.21, T:0.21
Consensus pattern (138 bp):
ATTGAATCACGAGTCAAAAAATAAAGAGACTGAGATTAAACACGAGTCAAAGAATAAAAAGACTG
GGATTAAACCACAAGTCAAAAAATAAAGATGATCAAGATTAAACCAAGAGTCAAAGAATAAACGA
CGATTGGA
Found at i:690396 original size:35 final size:33
Alignment explanation
Indices: 690174--690405 Score: 169
Period size: 34 Copynumber: 6.7 Consensus size: 33
690164 AATAAGCTAA
* * *
690174 GATTAAACCAAGAGTCAAAGAATAACGAGATTGG
1 GATTAAATCACGAGTCAAA-AATAAAGAGATTGG
* * * *
690208 AATTGAATCACGAGTCAAAAAATAAAGAGACTGA
1 GATTAAATCACGAGTC-AAAAATAAAGAGATTGG
* **
690242 GATTAAATCACGAGTCAAAGAATAAAAAGGCTGG
1 GATTAAATCACGAGTCAAA-AATAAAGAGATTGG
* * *
690276 GATTAAACCACGAGTCAAAAAATAAAGATGATCGA
1 GATTAAATCACGAGTC-AAAAATAAAGA-GATTGG
* * *
690311 GATTAAATCATGAGTTAAAGAATAAATGACGGTTGG
1 GATTAAATCACGAGTCAAA-AATAAA-GA-GATTGG
* ** *
690347 GATTGAATGTCGAGTCATAAAATAAAAATGATTGG
1 GATTAAATCACGAGTCA-AAAATAAAGA-GATTGG
690382 GATTAAA-CTACGAGTCAAAGAATA
1 GATTAAATC-ACGAGTCAAA-AATA
690406 TATTATTACC
Statistics
Matches: 153, Mismatches: 36, Indels: 17
0.74 0.17 0.08
Matches are distributed among these distances:
33 3 0.02
34 75 0.49
35 50 0.33
36 23 0.15
37 2 0.01
ACGTcount: A:0.47, C:0.10, G:0.21, T:0.21
Consensus pattern (33 bp):
GATTAAATCACGAGTCAAAAATAAAGAGATTGG
Found at i:695297 original size:33 final size:33
Alignment explanation
Indices: 695255--695322 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
695245 CATCATTATC
695255 ATTTTCATTGTATCTGATCTTTATAAAATCTCA
1 ATTTTCATTGTATCTGATCTTTATAAAATCTCA
*
695288 ATTTTCATTGTATTTGATCTTTATAAAATCTCA
1 ATTTTCATTGTATCTGATCTTTATAAAATCTCA
695321 AT
1 AT
695323 GATTTTGAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.31, C:0.13, G:0.06, T:0.50
Consensus pattern (33 bp):
ATTTTCATTGTATCTGATCTTTATAAAATCTCA
Found at i:695336 original size:33 final size:32
Alignment explanation
Indices: 695269--695337 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 32
695259 TCATTGTATC
* *
695269 TGATCTTTATAAAATCTCAATTTTCATTGTATT
1 TGATCTTTATAAAATCTCAATATT-ATTGGATT
695302 TGATCTTTATAAAATCTCAATGATT-TTGAGATT
1 TGATCTTTATAAAATCTCAAT-ATTATTG-GATT
695335 TGA
1 TGA
695338 AAAGTATCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 3 0.09
33 27 0.84
34 2 0.06
ACGTcount: A:0.32, C:0.10, G:0.10, T:0.48
Consensus pattern (32 bp):
TGATCTTTATAAAATCTCAATATTATTGGATT
Found at i:697280 original size:28 final size:27
Alignment explanation
Indices: 697248--697303 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
697238 TCATAATCAA
* *
697248 ATTAATCA-AATTATATTATATTATTTTT
1 ATTAAT-AGAATTACATT-TATTAATTTT
697276 ATTAATAGAATTACATTTATTAATTTT
1 ATTAATAGAATTACATTTATTAATTTT
697303 A
1 A
697304 AAAATCTAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 11 0.44
28 14 0.56
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.54
Consensus pattern (27 bp):
ATTAATAGAATTACATTTATTAATTTT
Found at i:699087 original size:23 final size:23
Alignment explanation
Indices: 699061--699104 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
699051 CTTAAAAATC
*
699061 AAAATTCACCAAAAATAATTTTT
1 AAAATTAACCAAAAATAATTTTT
* *
699084 AAAATTAATCAAAATTAATTT
1 AAAATTAACCAAAAATAATTT
699105 AATAACTAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (23 bp):
AAAATTAACCAAAAATAATTTTT
Found at i:699134 original size:18 final size:18
Alignment explanation
Indices: 699111--699146 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
699101 ATTTAATAAC
699111 TAATTAATT-AACTAAATT
1 TAATTAATTCAA-TAAATT
699129 TAATTAATTCAATAAATT
1 TAATTAATTCAATAAATT
699147 AATATGACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.88
19 2 0.12
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (18 bp):
TAATTAATTCAATAAATT
Found at i:706168 original size:49 final size:49
Alignment explanation
Indices: 706096--706196 Score: 139
Period size: 49 Copynumber: 2.1 Consensus size: 49
706086 CATTCTTTAC
* * *
706096 ATCAAATTATTGAACCTACCAATTATAATTTGCAGTCAATAATAACAAA
1 ATCAAATTATTAAACCTACCAATTATAAATTGCAGCCAATAATAACAAA
* * * *
706145 ATCAAATTATTAAAGCTACCAATTGTAAATTGCAGCCAATGATAATAAA
1 ATCAAATTATTAAACCTACCAATTATAAATTGCAGCCAATAATAACAAA
706194 ATC
1 ATC
706197 TTAACTTTAT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.47, C:0.16, G:0.08, T:0.30
Consensus pattern (49 bp):
ATCAAATTATTAAACCTACCAATTATAAATTGCAGCCAATAATAACAAA
Found at i:708427 original size:14 final size:13
Alignment explanation
Indices: 708392--708455 Score: 67
Period size: 13 Copynumber: 4.8 Consensus size: 13
708382 TTTATTTTTC
**
708392 AAAAATAAAAGAGC
1 AAAAATAAAA-AAT
708406 AAAAATAAAACAA-
1 AAAAATAAAA-AAT
708419 AAAATATAAAAAAT
1 AAAA-ATAAAAAAT
*
708433 AAAATTAAAAAAT
1 AAAAATAAAAAAT
708446 AAAAATAAAA
1 AAAAATAAAA
708456 TGAAAAAAAG
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
13 23 0.52
14 21 0.48
ACGTcount: A:0.80, C:0.03, G:0.03, T:0.14
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:708462 original size:20 final size:19
Alignment explanation
Indices: 708406--708469 Score: 74
Period size: 21 Copynumber: 3.2 Consensus size: 19
708396 ATAAAAGAGC
*
708406 AAAAATAAAACAAAAAATAT
1 AAAAATAAAATAAAAAA-AT
*
708426 AAAAAATAAAATTAAAAAAT
1 -AAAAATAAAATAAAAAAAT
*
708446 AAAAATAAAATGAAAAAAAG
1 AAAAATAAAAT-AAAAAAAT
708466 AAAA
1 AAAA
708470 CCTGCAATCA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
19 11 0.29
20 12 0.32
21 15 0.39
ACGTcount: A:0.81, C:0.02, G:0.03, T:0.14
Consensus pattern (19 bp):
AAAAATAAAATAAAAAAAT
Found at i:708463 original size:14 final size:12
Alignment explanation
Indices: 708392--708469 Score: 57
Period size: 14 Copynumber: 5.8 Consensus size: 12
708382 TTTATTTTTC
*
708392 AAAAATAAAAGAGC
1 AAAAATAAAA-A-A
708406 AAAAATAAAACAA
1 AAAAATAAAA-AA
708419 AAAATATAAAAAA
1 AAAA-ATAAAAAA
*
708432 TAAAATTAAAAAA
1 -AAAAATAAAAAA
708445 TAAAAATAAAATGAA
1 -AAAAATAAAA--AA
*
708460 AAAAAGAAAA
1 AAAAATAAAA
708470 CCTGCAATCA
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
13 23 0.42
14 30 0.55
15 2 0.04
ACGTcount: A:0.79, C:0.03, G:0.05, T:0.13
Consensus pattern (12 bp):
AAAAATAAAAAA
Found at i:708469 original size:19 final size:19
Alignment explanation
Indices: 708406--708463 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
708396 ATAAAAGAGC
**
708406 AAAAATAAAACAAAAAATAT
1 AAAAATAAAATGAAAAA-AT
*
708426 AAAAAATAAAATTAAAAAAT
1 -AAAAATAAAATGAAAAAAT
708446 AAAAATAAAATGAAAAAA
1 AAAAATAAAATGAAAAAA
708464 AGAAAACCTG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 17 0.50
20 2 0.06
21 15 0.44
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.16
Consensus pattern (19 bp):
AAAAATAAAATGAAAAAAT
Found at i:709171 original size:6 final size:6
Alignment explanation
Indices: 709160--709189 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
709150 GACCATGTGG
*
709160 GATTCT GATTCT GATTTT GATTCT GATTCT
1 GATTCT GATTCT GATTCT GATTCT GATTCT
709190 ATCCTTCACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.17, C:0.13, G:0.17, T:0.53
Consensus pattern (6 bp):
GATTCT
Found at i:709741 original size:115 final size:116
Alignment explanation
Indices: 709573--710131 Score: 369
Period size: 115 Copynumber: 4.8 Consensus size: 116
709563 GAGATGAAAT
* * * ** * **
709573 CACGAATCATAAAAAAATGATCTGGATTGAGTTAAGATAAAGTGATCAAGATGAAA-CACCAAGT
1 CACGAATCATAAAAAAATAATCTAGACTGAGCCAAGATCAAGTGATCGGGATGAAATCA-CAAGT
* * *
709637 CAAAATAAAGTGACCAAGATCGAGTCGAAATTAAAAATGATCAGGACGAAAC
65 CAAAATGAAGCGACCAAGATCGAGTCGAAATTAAAAATGATCAGGACAAAAC
*
709689 CACGAATCAT-AGAAAATAATCTAGACTGAGCCAAGATCAAGTGATCGGGATGAAATCACAAGTC
1 CACGAATCATAAAAAAATAATCTAGACTGAGCCAAGATCAAGTGATCGGGATGAAATCACAAGTC
*** * *
709753 AAAATGAAGCGACCAAGATCGAGTCGTGGTTGAAAATAAATGACCAGGATAAAAC
66 AAAATGAAGCGACCAAGATCGAGTCGAAATT---AA-AAATGATCAGGACAAAAC
* * * * * *
709808 TATGAATCATAAAAAAATAATCTGGACTGGGCCAAGATCAGGTGA-CTGGAATGAAATCACAAGT
1 CACGAATCATAAAAAAATAATCTAGACTGAGCCAAGATCAAGTGATC-GGGATGAAATCACAAGT
* * * * * ** **
709872 TAAAATGAAGCAACTAAGAGCAAGTC-AAAGTCGAAAATGATTGGGACAAAAC
65 CAAAATGAAGCGACCAAGATCGAGTCGAAA-TTAAAAATGATCAGGACAAAAC
** * * * * * ** * *
709924 CACGAATCAT-AGGAAATGATCTAGACTGAGCCAAAATCAGGTGATTGAGACAAAACCATAAGTC
1 CACGAATCATAAAAAAATAATCTAGACTGAGCCAAGATCAAGTGATCGGGATGAAATCACAAGTC
* * * * * ** * *
709988 AAAACGAAACAACCAAGATCAAATCGAGGTAAAAGTAAATGATC--GAAATGAAAC
66 AAAATGAAGCGACCAAGATCGAGTCGAAAT-TAA--AAATGATCAGGACA--AAAC
*** * * * ** **
710042 CGTAAATTATAAAAAAATGATCTAGACTAAGTGAAGATCATA-TGATCGGGACAAAATCACAAGT
1 CACGAATCATAAAAAAATAATCTAGACTGAGCCAAGATCA-AGTGATCGGGATGAAATCACAAGT
* *
710106 CAAAATGAAGCGACCAAAATCAAGTC
65 CAAAATGAAGCGACCAAGATCGAGTC
710132 AAGGTTGAAA
Statistics
Matches: 341, Mismatches: 85, Indels: 31
0.75 0.19 0.07
Matches are distributed among these distances:
115 128 0.38
116 39 0.11
117 1 0.00
118 19 0.06
119 86 0.25
120 68 0.20
ACGTcount: A:0.47, C:0.15, G:0.20, T:0.18
Consensus pattern (116 bp):
CACGAATCATAAAAAAATAATCTAGACTGAGCCAAGATCAAGTGATCGGGATGAAATCACAAGTC
AAAATGAAGCGACCAAGATCGAGTCGAAATTAAAAATGATCAGGACAAAAC
Found at i:722465 original size:16 final size:16
Alignment explanation
Indices: 722437--722487 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
722427 GATTGGAGCA
722437 AAAAGGAAAAAAAAAT
1 AAAAGGAAAAAAAAAT
*
722453 AAAAGAAAGAAAAAAAT
1 AAAAGGAA-AAAAAAAT
* *
722470 GAAAA-TAAAATAAAAT
1 -AAAAGGAAAAAAAAAT
722486 AA
1 AA
722488 TAATAATAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 2 0.07
16 14 0.47
17 10 0.33
18 4 0.13
ACGTcount: A:0.80, C:0.00, G:0.10, T:0.10
Consensus pattern (16 bp):
AAAAGGAAAAAAAAAT
Found at i:723818 original size:24 final size:24
Alignment explanation
Indices: 723791--723837 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
723781 CTCGATACCA
723791 TGTG-AAAAAACTAAAAAATAAAAT
1 TGTGTAAAAAA-TAAAAAATAAAAT
* *
723815 TGTGTGAAAAATAAAGAATAAAA
1 TGTGTAAAAAATAAAAAATAAAA
723838 CTGAATGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.64, C:0.02, G:0.13, T:0.21
Consensus pattern (24 bp):
TGTGTAAAAAATAAAAAATAAAAT
Found at i:724034 original size:14 final size:15
Alignment explanation
Indices: 724015--724043 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
724005 TTAATTCTAG
724015 ATATACAAA-TATAA
1 ATATACAAATTATAA
724029 ATATACAAATTATAA
1 ATATACAAATTATAA
724044 GGTTACAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (15 bp):
ATATACAAATTATAA
Found at i:724485 original size:18 final size:18
Alignment explanation
Indices: 724462--724497 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
724452 CAAAGGTTCC
*
724462 TTTATAGTTTTCATATTA
1 TTTATAATTTTCATATTA
*
724480 TTTATAATTTTCTTATTA
1 TTTATAATTTTCATATTA
724498 AGTATACTAA
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:0.28, C:0.06, G:0.03, T:0.64
Consensus pattern (18 bp):
TTTATAATTTTCATATTA
Found at i:725253 original size:101 final size:101
Alignment explanation
Indices: 725138--725340 Score: 262
Period size: 101 Copynumber: 2.0 Consensus size: 101
725128 AATTTCATAA
* * * * ** * *
725138 AAAATTTTGATGGATTCTACAGAATTTTGAATCGTGATTGGTTAATTATACTACAATTATTATAG
1 AAAATTTTGATGGATCCCACAGAATTCTAAATCGTGATTAATTAATTATACTACAATCATTATAA
* *
725203 GTGATATGCTCCTTTTGTCTTTTTAACAAAGTAAAT
66 GTAATATGCTCCCTTTGTCTTTTTAACAAAGTAAAT
* * * * *
725239 AAAATTTTGATGGATCCCACATAATTCTAAATTGTGATTAATTCATTATATTATAATCATTATAA
1 AAAATTTTGATGGATCCCACAGAATTCTAAATCGTGATTAATTAATTATACTACAATCATTATAA
*
725304 GTAATATGCTCCCTTTGTTTTTTTAACAAAGTAAAT
66 GTAATATGCTCCCTTTGTCTTTTTAACAAAGTAAAT
725340 A
1 A
725341 GTTTGAAAAG
Statistics
Matches: 86, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
101 86 1.00
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.42
Consensus pattern (101 bp):
AAAATTTTGATGGATCCCACAGAATTCTAAATCGTGATTAATTAATTATACTACAATCATTATAA
GTAATATGCTCCCTTTGTCTTTTTAACAAAGTAAAT
Found at i:730929 original size:9 final size:9
Alignment explanation
Indices: 730917--730946 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
730907 GATATTTTAT
730917 TAATTAAAA
1 TAATTAAAA
730926 TAATTAAAA
1 TAATTAAAA
730935 TATATTAAAA
1 TA-ATTAAAA
730945 TA
1 TA
730947 TAAAAATTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (9 bp):
TAATTAAAA
Found at i:730943 original size:10 final size:10
Alignment explanation
Indices: 730919--730948 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
730909 TATTTTATTA
730919 ATTAAAATA-
1 ATTAAAATAT
730928 ATTAAAATAT
1 ATTAAAATAT
730938 ATTAAAATAT
1 ATTAAAATAT
730948 A
1 A
730949 AAAATTCAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
ATTAAAATAT
Found at i:731017 original size:29 final size:29
Alignment explanation
Indices: 730985--731042 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
730975 TAAAGTCAAC
730985 TATAAAATGCTTAAATTTAACTATTTGAA
1 TATAAAATGCTTAAATTTAACTATTTGAA
731014 TATAAAATGCTTAAATTTAACTATTTGAA
1 TATAAAATGCTTAAATTTAACTATTTGAA
731043 CAAACACTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (29 bp):
TATAAAATGCTTAAATTTAACTATTTGAA
Found at i:731539 original size:22 final size:23
Alignment explanation
Indices: 731488--731539 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
731478 GAACAATTAA
*
731488 AATTATTCATTTTGAACAAACTT
1 AATTATTCATTTTAAACAAACTT
*
731511 -ATCTATT-ATTTTAAACAGACTT
1 AAT-TATTCATTTTAAACAAACTT
731533 AATTATT
1 AATTATT
731540 TATCTTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
22 19 0.76
23 6 0.24
ACGTcount: A:0.38, C:0.12, G:0.04, T:0.46
Consensus pattern (23 bp):
AATTATTCATTTTAAACAAACTT
Found at i:736456 original size:23 final size:23
Alignment explanation
Indices: 736429--736484 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
736419 AACTATCTAT
*
736429 TTTTGAACAATTGAAATTGTTCA
1 TTTTGAACAATTGAAACTGTTCA
*
736452 TTTTGAACAGTTGAAACTGTTCA
1 TTTTGAACAATTGAAACTGTTCA
736475 TTTTGAACAA
1 TTTTGAACAA
736485 ACTTATTTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.41
Consensus pattern (23 bp):
TTTTGAACAATTGAAACTGTTCA
Found at i:739754 original size:25 final size:25
Alignment explanation
Indices: 739726--739776 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
739716 TCCAGACATC
739726 CACTCATTTGACGTCTCAGATCAGT
1 CACTCATTTGACGTCTCAGATCAGT
*
739751 CACTCATTTGATGTCTCAGATCAGT
1 CACTCATTTGACGTCTCAGATCAGT
739776 C
1 C
739777 TATCTGTTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.33
Consensus pattern (25 bp):
CACTCATTTGACGTCTCAGATCAGT
Found at i:745133 original size:113 final size:113
Alignment explanation
Indices: 744883--745222 Score: 546
Period size: 112 Copynumber: 3.1 Consensus size: 113
744873 TTTTATTTAT
* * *
744883 ATATTATAATAAATTTTTAAAATTTTTTAATATAAAAATACAATGTAACATATTTTTTTTTGTTA
1 ATATTATAATAAATTTTTAAAATTTTTCAATATGAAATTACAATGTAACATATTTTTTTTTGTTA
744948 AAACTTGATATTCTTATTAAGCTC-ATACAAAATACATAAATTTATTG
66 AAACTTGATATTCTTATTAAGCTCAATACAAAATACATAAATTTATTG
* * * * *
744995 ATATTATAATAGATTTTCAAAATTTTTCAATATGAAATTACAATATAACATATCTTTTTTTATTA
1 ATATTATAATAAATTTTTAAAATTTTTCAATATGAAATTACAATGTAACATATTTTTTTTTGTTA
* *
745060 AAACTTCATATTTTTATTAAGCTCAATACAAAATACATAAATTTATTG
66 AAACTTGATATTCTTATTAAGCTCAATACAAAATACATAAATTTATTG
745108 ATATTATAATAAATTTTTAAAATTTTTCAATATGAAATTACAATGT--CAT-TTTTTTTTTGTTA
1 ATATTATAATAAATTTTTAAAATTTTTCAATATGAAATTACAATGTAACATATTTTTTTTTGTTA
*
745170 AAACTTGATATTCTTATTAAACTCAATACAAAATACATAAATTTATTG
66 AAACTTGATATTCTTATTAAGCTCAATACAAAATACATAAATTTATTG
745218 A-ATTA
1 ATATTA
745223 CATTAAATAT
Statistics
Matches: 209, Mismatches: 18, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
109 4 0.02
110 57 0.27
111 3 0.01
112 79 0.38
113 66 0.32
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.45
Consensus pattern (113 bp):
ATATTATAATAAATTTTTAAAATTTTTCAATATGAAATTACAATGTAACATATTTTTTTTTGTTA
AAACTTGATATTCTTATTAAGCTCAATACAAAATACATAAATTTATTG
Found at i:754318 original size:23 final size:24
Alignment explanation
Indices: 754292--754337 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
754282 TATAATACTA
754292 TTAATA-ATTTACAAAAT-AAATAT
1 TTAATATATTTA-AAAATCAAATAT
*
754315 TTAATATTTTTAAAAATCAAATA
1 TTAATATATTTAAAAATCAAATA
754338 AATAAGTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.41
Consensus pattern (24 bp):
TTAATATATTTAAAAATCAAATAT
Found at i:756693 original size:29 final size:26
Alignment explanation
Indices: 756631--756686 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
756621 AAACAGTATT
756631 AAAAA-TTATTATAATTATAATTGAA
1 AAAAATTTATTATAATTATAATTGAA
*
756656 AAAAATTTATTATAATTGTAATTGAA
1 AAAAATTTATTATAATTATAATTGAA
756682 AAAAA
1 AAAAA
756687 AAATTTAATG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 5 0.17
26 24 0.83
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (26 bp):
AAAAATTTATTATAATTATAATTGAA
Found at i:760207 original size:19 final size:19
Alignment explanation
Indices: 760185--760227 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
760175 CAATTCGAAT
*
760185 TTTTATTTTATTAATA-AAA
1 TTTTATATT-TTAATATAAA
*
760204 TTTTATATTTTCATATAAA
1 TTTTATATTTTAATATAAA
760223 TTTTA
1 TTTTA
760228 AAAAATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTTATATTTTAATATAAA
Found at i:766280 original size:22 final size:22
Alignment explanation
Indices: 766237--766294 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 22
766227 ATTTTTTTTT
766237 ATTTTTATATATTATTGTAATAA
1 ATTTTTATATA-TATTGTAATAA
766260 GATTTTTA-ATATATT-TAAATAA
1 -ATTTTTATATATATTGT-AATAA
766282 ATTTTTATATATA
1 ATTTTTATATATA
766295 ATAATTATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
21 8 0.25
22 14 0.44
23 3 0.09
24 7 0.22
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.55
Consensus pattern (22 bp):
ATTTTTATATATATTGTAATAA
Found at i:766401 original size:18 final size:18
Alignment explanation
Indices: 766379--766427 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
766369 ATATTTTTAT
766379 TTAAAATTTAATTTGAATA
1 TTAAAATTTAATTT-AATA
*
766398 -TAAAATATATATTTAATA
1 TTAAAATTTA-ATTTAATA
*
766416 TTCAAATTTAAT
1 TTAAAATTTAAT
766428 CCAAATCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 14 0.56
19 11 0.44
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (18 bp):
TTAAAATTTAATTTAATA
Found at i:768796 original size:22 final size:22
Alignment explanation
Indices: 768763--768805 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
768753 AAAAGTACCT
*
768763 CAATACAAAATCAGCCAAACAA
1 CAATACAAAATCAGCAAAACAA
768785 CAATA-AATAATCAGCAAAACA
1 CAATACAA-AATCAGCAAAACA
768806 TCAAATTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.60, C:0.23, G:0.05, T:0.12
Consensus pattern (22 bp):
CAATACAAAATCAGCAAAACAA
Found at i:773629 original size:71 final size:71
Alignment explanation
Indices: 773513--773653 Score: 194
Period size: 71 Copynumber: 2.0 Consensus size: 71
773503 TTTGTAACTG
* * * *
773513 GAATTTTATCCTGTTTGATGGAATTTCAACATCCTTTTTTGGGTGATAATTGCTG-CTTGTAGGC
1 GAATTTTATCCTGTTTGATGGAATTGCAACAGCCTTTTCTGGGTGATAATTGCTGTC-TGTAGCC
773577 TTTGACA
65 TTTGACA
* * * *
773584 GAATTTTATCTTGTTTGATGGTATTGGAACAGCCTTTTCTGGGTGATAATTGGTGTCTGTAGCCT
1 GAATTTTATCCTGTTTGATGGAATTGCAACAGCCTTTTCTGGGTGATAATTGCTGTCTGTAGCCT
773649 TTGAC
66 TTGAC
773654 TGAAGAATAA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
71 60 0.98
72 1 0.02
ACGTcount: A:0.20, C:0.13, G:0.23, T:0.43
Consensus pattern (71 bp):
GAATTTTATCCTGTTTGATGGAATTGCAACAGCCTTTTCTGGGTGATAATTGCTGTCTGTAGCCT
TTGACA
Found at i:776338 original size:24 final size:23
Alignment explanation
Indices: 776297--776343 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
776287 TTTTTTTTTG
*
776297 TTTTCTCATTTTTTAATGCATAT
1 TTTTCTCATTTTTGAATGCATAT
* *
776320 TTTTTTCATTTGTTGAATGGATAT
1 TTTTCTCATTT-TTGAATGCATAT
776344 AAGAGATAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.21, C:0.09, G:0.11, T:0.60
Consensus pattern (23 bp):
TTTTCTCATTTTTGAATGCATAT
Found at i:780614 original size:12 final size:12
Alignment explanation
Indices: 780597--780631 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
780587 ATTAATTTTA
780597 AAATTTTAATAT
1 AAATTTTAATAT
780609 AAATTTTAATAT
1 AAATTTTAATAT
780621 --ATTTTAATAT
1 AAATTTTAATAT
780631 A
1 A
780632 TTTAAGTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.45
12 12 0.55
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
AAATTTTAATAT
Found at i:780627 original size:22 final size:20
Alignment explanation
Indices: 780590--780631 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 20
780580 TTGATTTATT
780590 AATTTTAAAATTTTAATATA
1 AATTTTAAAATTTTAATATA
780610 AATTTTAATATATTTTAATATA
1 AATTTTAA-A-ATTTTAATATA
780632 TTTAAGTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 8 0.40
21 1 0.05
22 11 0.55
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
AATTTTAAAATTTTAATATA
Found at i:780641 original size:10 final size:10
Alignment explanation
Indices: 780591--780634 Score: 56
Period size: 10 Copynumber: 4.4 Consensus size: 10
780581 TGATTTATTA
780591 ATTTTAA-A-
1 ATTTTAATAT
780599 ATTTTAATAT
1 ATTTTAATAT
780609 AAATTTTAATAT
1 --ATTTTAATAT
780621 ATTTTAATAT
1 ATTTTAATAT
780631 ATTT
1 ATTT
780635 AAGTATAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
8 7 0.22
9 1 0.03
10 14 0.44
12 10 0.31
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (10 bp):
ATTTTAATAT
Found at i:780689 original size:17 final size:19
Alignment explanation
Indices: 780660--780699 Score: 50
Period size: 17 Copynumber: 2.2 Consensus size: 19
780650 ATTTTTATGT
780660 TATAAAAATTTAA-A-AAA
1 TATAAAAATTTAATATAAA
780677 TATATAAAA-TTAATATAAA
1 TATA-AAAATTTAATATAAA
780696 TATA
1 TATA
780700 CAATTCGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
17 8 0.40
18 5 0.25
19 7 0.35
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TATAAAAATTTAATATAAA
Found at i:780721 original size:8 final size:8
Alignment explanation
Indices: 780708--780741 Score: 68
Period size: 8 Copynumber: 4.2 Consensus size: 8
780698 TACAATTCGA
780708 TTTAATTT
1 TTTAATTT
780716 TTTAATTT
1 TTTAATTT
780724 TTTAATTT
1 TTTAATTT
780732 TTTAATTT
1 TTTAATTT
780740 TT
1 TT
780742 GATCTAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTAATTT
Found at i:781215 original size:16 final size:16
Alignment explanation
Indices: 781196--781235 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
781186 AATTAATTCG
*
781196 ATTAAAATTTATTTGA
1 ATTAAAATTTATTTAA
*
781212 ATTAAAATTTTTTTAA
1 ATTAAAATTTATTTAA
*
781228 ATTTAAAT
1 ATTAAAAT
781236 AATTTTACAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
ATTAAAATTTATTTAA
Found at i:783094 original size:22 final size:22
Alignment explanation
Indices: 783056--783109 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
783046 ATAATTATTT
* *
783056 TATATAAAATATATA-TTTAAA
1 TATATAAAAAATTTATTTTAAA
783077 TATATCAAAAAATTTATTTTAAA
1 TATAT-AAAAAATTTATTTTAAA
*
783100 -AAATAAAAAA
1 TATATAAAAAA
783110 ATTAAAAATC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 11 0.39
22 11 0.39
23 6 0.21
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (22 bp):
TATATAAAAAATTTATTTTAAA
Found at i:783856 original size:14 final size:15
Alignment explanation
Indices: 783815--783857 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
783805 TTGATTAATT
783815 TCAAATTTAATTATA
1 TCAAATTTAATTATA
* *
783830 TAAAATTAAATTA-A
1 TCAAATTTAATTATA
*
783844 TCAAATTTTATTAT
1 TCAAATTTAATTAT
783858 TTTATTTTTA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
14 11 0.50
15 11 0.50
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (15 bp):
TCAAATTTAATTATA
Found at i:790519 original size:15 final size:15
Alignment explanation
Indices: 790499--790529 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
790489 CGCATTTATC
790499 GGATATAACGAATAA
1 GGATATAACGAATAA
*
790514 GGATATAATGAATAA
1 GGATATAACGAATAA
790529 G
1 G
790530 ATAACGGTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.03, G:0.23, T:0.23
Consensus pattern (15 bp):
GGATATAACGAATAA
Found at i:796918 original size:21 final size:21
Alignment explanation
Indices: 796893--796943 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
796883 TGAAATATGG
*
796893 ATTTTATTTTTTTAATAAATA
1 ATTTTATTTGTTTAATAAATA
* *
796914 ATTTTAGTTGTTTACTAAATA
1 ATTTTATTTGTTTAATAAATA
*
796935 ACTTTATTT
1 ATTTTATTT
796944 AAAAAATTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (21 bp):
ATTTTATTTGTTTAATAAATA
Found at i:798166 original size:21 final size:21
Alignment explanation
Indices: 798124--798162 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
798114 TGAAATATGG
*
798124 ATTTTAATTTTTTAATCAATA
1 ATTTTAATTGTTTAATCAATA
*
798145 ATTTTAGTTGTTT-ATCAA
1 ATTTTAATTGTTTAATCAA
798163 ATAACCTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.56
Consensus pattern (21 bp):
ATTTTAATTGTTTAATCAATA
Found at i:799390 original size:2 final size:2
Alignment explanation
Indices: 799383--799410 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
799373 TTATCCTTAA
799383 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
799411 TTCAAAAACC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:815138 original size:7 final size:7
Alignment explanation
Indices: 815126--815164 Score: 60
Period size: 7 Copynumber: 5.3 Consensus size: 7
815116 TAAATTAAAA
815126 TATATTT
1 TATATTT
815133 TATATTT
1 TATATTT
815140 TATATTTTT
1 TATA--TTT
815149 TATATTT
1 TATATTT
815156 TATATTT
1 TATATTT
815163 TA
1 TA
815165 AATAAATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 23 0.77
9 7 0.23
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TATATTT
Found at i:815161 original size:16 final size:16
Alignment explanation
Indices: 815125--815163 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
815115 TTAAATTAAA
*
815125 ATATATTTTATATTTT
1 ATATTTTTTATATTTT
815141 ATATTTTTTATATTTT
1 ATATTTTTTATATTTT
815157 ATATTTT
1 ATATTTT
815164 AAATAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
ATATTTTTTATATTTT
Found at i:815212 original size:28 final size:26
Alignment explanation
Indices: 815171--815222 Score: 77
Period size: 28 Copynumber: 1.9 Consensus size: 26
815161 TTTAAATAAA
815171 TTAAATAAAATTATCTAACAAAATAT
1 TTAAATAAAATTATCTAACAAAATAT
*
815197 TTAAATACCAAATTATCTAATAAAAT
1 TTAAATA--AAATTATCTAACAAAAT
815223 TATCAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 7 0.30
28 16 0.70
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.35
Consensus pattern (26 bp):
TTAAATAAAATTATCTAACAAAATAT
Found at i:815218 original size:15 final size:13
Alignment explanation
Indices: 815174--815226 Score: 54
Period size: 13 Copynumber: 3.9 Consensus size: 13
815164 AAATAAATTA
815174 AATAAAATTATCT
1 AATAAAATTATCT
* *
815187 AACAAAA-TATTT
1 AATAAAATTATCT
815199 AAATACCAAATTATCT
1 -AATA--AAATTATCT
815215 AATAAAATTATC
1 AATAAAATTATC
815227 AAATTTATGG
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
12 4 0.12
13 17 0.53
15 7 0.22
16 4 0.12
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (13 bp):
AATAAAATTATCT
Found at i:815364 original size:19 final size:19
Alignment explanation
Indices: 815336--815373 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
815326 TAAAGTTTAA
815336 ATTTTAATA-TATATATTTT
1 ATTTTAATATTAT-TATTTT
*
815355 ATTTTCATATTATTATTTT
1 ATTTTAATATTATTATTTT
815374 TTCAAAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (19 bp):
ATTTTAATATTATTATTTT
Found at i:815407 original size:3 final size:3
Alignment explanation
Indices: 815399--815431 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
815389 ATTAGATGGT
815399 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
815432 GTCATGACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:818179 original size:9 final size:10
Alignment explanation
Indices: 818159--818196 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
818149 TTTATCTAAA
*
818159 TAATAATTTT
1 TAATTATTTT
818169 TAATT-TTTT
1 TAATTATTTT
*
818178 TAATTAATTT
1 TAATTATTTT
818188 TAATTATTT
1 TAATTATTT
818197 AAACAAAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
9 9 0.38
10 15 0.62
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (10 bp):
TAATTATTTT
Found at i:818522 original size:24 final size:24
Alignment explanation
Indices: 818495--818559 Score: 60
Period size: 24 Copynumber: 2.8 Consensus size: 24
818485 ACGTTGGTAC
818495 AAAAATTATATAAATAAAAAATAT
1 AAAAATTATATAAATAAAAAATAT
* * * * * *
818519 AAAAATAACATAACTTAAAATTTT
1 AAAAATTATATAAATAAAAAATAT
*
818543 AAAAAAT-TATAAATAAA
1 AAAAATTATATAAATAAA
818560 TTTAATAAAA
Statistics
Matches: 30, Mismatches: 11, Indels: 1
0.71 0.26 0.02
Matches are distributed among these distances:
23 7 0.23
24 23 0.77
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (24 bp):
AAAAATTATATAAATAAAAAATAT
Found at i:818613 original size:25 final size:25
Alignment explanation
Indices: 818575--818633 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
818565 TAAAATCAAA
**
818575 AAATTATATTTTAT-ATTTTCGATAT
1 AAATTATAAATTATAATTTT-GATAT
*
818600 AAATTATAAATTATAATTTTTATAT
1 AAATTATAAATTATAATTTTGATAT
*
818625 AAAATATAA
1 AAATTATAA
818634 TATAAATATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 24 0.83
26 5 0.17
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (25 bp):
AAATTATAAATTATAATTTTGATAT
Found at i:818640 original size:30 final size:30
Alignment explanation
Indices: 818604--818660 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
818594 CGATATAAAT
818604 TATAAATTATAAT-TTTTATATAAAATATAA
1 TATAAA-TATAATATTTTATATAAAATATAA
*
818634 TATAAATATAATATTTTATATGAAATA
1 TATAAATATAATATTTTATATAAAATA
818661 ATAACACGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 6 0.24
30 19 0.76
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (30 bp):
TATAAATATAATATTTTATATAAAATATAA
Done.