Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007863.1 Hibiscus syriacus cultivar Beakdansim tig00110234_pilon, 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: 1653362
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 8
Found at i:664418 original size:83 final size:83
Alignment explanation
Indices: 664305--664668 Score: 392
Period size: 83 Copynumber: 4.4 Consensus size: 83
664295 GCGTTTGTGA
* * * *
664305 GAAAAAAAACTACTATAGGTGAACCCTATTACGGCATTTGTATAAAAACGCCACGAAAGTACTAA
1 GAAAAAATACCACTATAGGTGAACCCTATTACGACATTTGTATAAAAACGCCACTAAAGTACTAA
* *
664370 TATGTTGCTACATTTACT
66 TATGTTGCGACATTTATT
* * *
664388 GAAAAAATACCACTATAGGTAAACCCTATTACGACATTTGAATAAAAACGCCACTAAAGTTCTAA
1 GAAAAAATACCACTATAGGTGAACCCTATTACGACATTTGTATAAAAACGCCACTAAAGTACTAA
*
664453 TCTGTTGCGACATTTATT
66 TATGTTGCGACATTTATT
* * ** *
664471 GAAAAAACACCACTATAGGTGAACCTTATTGTGACATTTGTATAAAAACACCACTAAAGTACTAA
1 GAAAAAATACCACTATAGGTGAACCCTATTACGACATTTGTATAAAAACGCCACTAAAGTACTAA
* *
664536 TATGATT-CGGCGTTTATT
66 TATG-TTGCGACATTTATT
* * * * ** *** * *
664554 GAAAAAATGCCATTATAGATGGA-CCTATTGTGGTGTTTGTATAGAAACGCCACTAAAGTACTAC
1 GAAAAAATACCACTATAGGTGAACCCTATTACGACATTTGTATAAAAACGCCACTAAAGTACTAA
* *
664618 TCTGTTGTGACATTT-TT
66 TATGTTGCGACATTTATT
* *
664635 CGATAAAAATGCCACTATAGATGAACCCTATTAC
1 -GA-AAAAATACCACTATAGGTGAACCCTATTAC
664669 ATCGTTTATA
Statistics
Matches: 235, Mismatches: 41, Indels: 9
0.82 0.14 0.03
Matches are distributed among these distances:
81 4 0.02
82 44 0.19
83 179 0.76
84 8 0.03
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.30
Consensus pattern (83 bp):
GAAAAAATACCACTATAGGTGAACCCTATTACGACATTTGTATAAAAACGCCACTAAAGTACTAA
TATGTTGCGACATTTATT
Found at i:665822 original size:21 final size:20
Alignment explanation
Indices: 665778--665973 Score: 134
Period size: 19 Copynumber: 9.8 Consensus size: 20
665768 TATATGATTT
* *
665778 AAGAGTATGGATACTTT-AC
1 AAGAGTATCGATACTTTCCC
*
665797 AAGAGTATGGATACTTTCCCC
1 AAGAGTATCGATACTTT-CCC
* *
665818 AAGAGTAACAATACTTT-CC
1 AAGAGTATCGATACTTTCCC
* *
665837 AAGCA-TATCAATACATTACCC
1 AAG-AGTATCGATAC-TTTCCC
665858 AAGAGTTATCGATACTTTACCC
1 AAGAG-TATCGATACTTT-CCC
* * * *
665880 AATAGTATGGATAC-ATGCC
1 AAGAGTATCGATACTTTCCC
*
665899 AAGAGTATCGACACTTTACCC
1 AAGAGTATCGATACTTT-CCC
* *
665920 AAGAGTATGGATACTTT-AC
1 AAGAGTATCGATACTTTCCC
*
665939 AA-ATGTATAGATACTTTCCC
1 AAGA-GTATCGATACTTTCCC
* *
665959 TAGAGTATCAATACT
1 AAGAGTATCGATACT
665974 CAGAGTAACA
Statistics
Matches: 139, Mismatches: 25, Indels: 25
0.74 0.13 0.13
Matches are distributed among these distances:
18 1 0.01
19 58 0.42
20 17 0.12
21 48 0.35
22 15 0.11
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (20 bp):
AAGAGTATCGATACTTTCCC
Found at i:665833 original size:40 final size:40
Alignment explanation
Indices: 665778--665966 Score: 147
Period size: 40 Copynumber: 4.7 Consensus size: 40
665768 TATATGATTT
*
665778 AAGAGTATGGATACTTTA-CAAGAGTATGGATACTTTCCCC
1 AAGAGTATCGATACTTTACCAAGAGTATGGATACTTT-CCC
* * ** *
665818 AAGAGTAACAATACTTT-CCAAGCA-TATCAATACATTACCC
1 AAGAGTATCGATACTTTACCAAG-AGTATGGATAC-TTTCCC
* * *
665858 AAGAGTTATCGATACTTTACCCAATAGTATGGATAC-ATGCC
1 AAGAG-TATCGATACTTTA-CCAAGAGTATGGATACTTTCCC
* *
665899 AAGAGTATCGACACTTTACCCAAGAGTATGGATACTTT-AC
1 AAGAGTATCGATACTTTA-CCAAGAGTATGGATACTTTCCC
* * *
665939 AA-ATGTATAGATACTTTCCCTAGAGTAT
1 AAGA-GTATCGATACTTTACCAAGAGTAT
665967 CAATACTCAG
Statistics
Matches: 118, Mismatches: 22, Indels: 19
0.74 0.14 0.12
Matches are distributed among these distances:
39 10 0.08
40 75 0.64
41 21 0.18
42 1 0.01
43 11 0.09
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (40 bp):
AAGAGTATCGATACTTTACCAAGAGTATGGATACTTTCCC
Found at i:667313 original size:19 final size:19
Alignment explanation
Indices: 667289--667327 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
667279 TAGTAGAGGA
667289 CTAAGGGAAACGTAAGACT
1 CTAAGGGAAACGTAAGACT
667308 CTAAGGGAAACGTAAGACT
1 CTAAGGGAAACGTAAGACT
667327 C
1 C
667328 CTACTTCAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.41, C:0.18, G:0.26, T:0.15
Consensus pattern (19 bp):
CTAAGGGAAACGTAAGACT
Found at i:672467 original size:16 final size:18
Alignment explanation
Indices: 672448--672490 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
672438 TAAAAAAGAA
672448 GAAAAATGAGA-AAAA-T
1 GAAAAATGAGATAAAAGT
*
672464 GAAAAATGAAATAAAAGT
1 GAAAAATGAGATAAAAGT
672482 G-AAAATGAG
1 GAAAAATGAG
672491 GGTTCAAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 10 0.43
17 11 0.48
18 2 0.09
ACGTcount: A:0.65, C:0.00, G:0.21, T:0.14
Consensus pattern (18 bp):
GAAAAATGAGATAAAAGT
Found at i:673433 original size:62 final size:62
Alignment explanation
Indices: 673360--673553 Score: 289
Period size: 62 Copynumber: 3.0 Consensus size: 62
673350 ACTTGTAAAA
673360 TAGGAGCATACATATTCATTCATAAACACTAAAATGACATCATACATGCATACTTACGCATT
1 TAGGAGCATACATATTCATTCATAAACACTAAAATGACATCATACATGCATACTTACGCATT
* * *
673422 TAGGAGTATACATATTCATTAATAAACACTAAAATAACATCATACATGCATACTTACGCATTTGT
1 TAGGAGCATACATATTCATTCATAAACACTAAAATGACATCATACATGCATACTTACGCA--T-T
*
673487 AAAATAGGAGCATACATATTCATTCATAAACACTAAAATGACATCATACATGCATACTTAGGCAT
1 ----TAGGAGCATACATATTCATTCATAAACACTAAAATGACATCATACATGCATACTTACGCAT
673552 T
62 T
673553 T
1 T
673554 TTAAAATAAA
Statistics
Matches: 118, Mismatches: 7, Indels: 14
0.85 0.05 0.10
Matches are distributed among these distances:
62 58 0.49
64 1 0.01
65 1 0.01
66 1 0.01
67 1 0.01
69 56 0.47
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.30
Consensus pattern (62 bp):
TAGGAGCATACATATTCATTCATAAACACTAAAATGACATCATACATGCATACTTACGCATT
Found at i:673533 original size:69 final size:69
Alignment explanation
Indices: 673422--673561 Score: 235
Period size: 69 Copynumber: 2.0 Consensus size: 69
673412 CTTACGCATT
*
673422 TAGGAGTATACATATTCATTAATAAACACTAAAATAACATCATACATGCATACTTACGCATTTGT
1 TAGGAGCATACATATTCATTAATAAACACTAAAATAACATCATACATGCATACTTACGCATTTGT
673487 AAAA
66 AAAA
* * * *
673491 TAGGAGCATACATATTCATTCATAAACACTAAAATGACATCATACATGCATACTTAGGCATTTTT
1 TAGGAGCATACATATTCATTAATAAACACTAAAATAACATCATACATGCATACTTACGCATTTGT
673556 AAAA
66 AAAA
673560 TA
1 TA
673562 AAAAATACAT
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.31
Consensus pattern (69 bp):
TAGGAGCATACATATTCATTAATAAACACTAAAATAACATCATACATGCATACTTACGCATTTGT
AAAA
Found at i:673546 original size:131 final size:131
Alignment explanation
Indices: 673312--673553 Score: 430
Period size: 131 Copynumber: 1.8 Consensus size: 131
673302 AGTGAAATTC
* * * *
673312 ATAAACACTAAAATGATATCATATATGCATACTTAGGCACTTGTAAAATAGGAGCATACATATTC
1 ATAAACACTAAAATAACATCATACATGCATACTTACGCACTTGTAAAATAGGAGCATACATATTC
673377 ATTCATAAACACTAAAATGACATCATACATGCATACTTACGCATTTAGGAGTATACATATTCATT
66 ATTCATAAACACTAAAATGACATCATACATGCATACTTACGCATTTAGGAGTATACATATTCATT
673442 A
131 A
*
673443 ATAAACACTAAAATAACATCATACATGCATACTTACGCATTTGTAAAATAGGAGCATACATATTC
1 ATAAACACTAAAATAACATCATACATGCATACTTACGCACTTGTAAAATAGGAGCATACATATTC
*
673508 ATTCATAAACACTAAAATGACATCATACATGCATACTTAGGCATTT
66 ATTCATAAACACTAAAATGACATCATACATGCATACTTACGCATTT
673554 TTAAAATAAA
Statistics
Matches: 105, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
131 105 1.00
ACGTcount: A:0.43, C:0.18, G:0.10, T:0.30
Consensus pattern (131 bp):
ATAAACACTAAAATAACATCATACATGCATACTTACGCACTTGTAAAATAGGAGCATACATATTC
ATTCATAAACACTAAAATGACATCATACATGCATACTTACGCATTTAGGAGTATACATATTCATT
A
Found at i:674956 original size:21 final size:21
Alignment explanation
Indices: 674932--674973 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
674922 TAGAGATAAA
674932 GGCTCCGCCGTCCAGAGTTGT
1 GGCTCCGCCGTCCAGAGTTGT
*
674953 GGCTTCGCCGTCCAGAGTTGT
1 GGCTCCGCCGTCCAGAGTTGT
674974 AGCGTCATCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.10, C:0.31, G:0.33, T:0.26
Consensus pattern (21 bp):
GGCTCCGCCGTCCAGAGTTGT
Found at i:678309 original size:21 final size:20
Alignment explanation
Indices: 678283--678326 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
678273 GAGATGATTA
* *
678283 AAAAGAAGGAATAATAAGAAG
1 AAAAGAAGAAACAATAA-AAG
678304 AAAAGAAGAAACAATAAAAG
1 AAAAGAAGAAACAATAAAAG
678324 AAA
1 AAA
678327 GAAAAAGGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.73, C:0.02, G:0.18, T:0.07
Consensus pattern (20 bp):
AAAAGAAGAAACAATAAAAG
Found at i:689984 original size:21 final size:21
Alignment explanation
Indices: 689912--690031 Score: 138
Period size: 21 Copynumber: 5.7 Consensus size: 21
689902 CGGTGTTTGA
*
689912 GTGCATGGATGCACTGCA-TG
1 GTGCATGGATGCACTGCAGGG
* *
689932 GTTCATCGATGCACT--AGTGCAG
1 GTGCATGGATGCACTGCAG-G--G
* *
689954 GTGGATGGATGCACTACAGGG
1 GTGCATGGATGCACTGCAGGG
*
689975 ATGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTGCAGGG
689996 GTGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTGCAGGG
690017 GTGCATGGATGCACT
1 GTGCATGGATGCACT
690032 TTGACACCCT
Statistics
Matches: 84, Mismatches: 10, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
18 1 0.01
20 13 0.15
21 54 0.64
22 13 0.15
23 1 0.01
24 2 0.02
ACGTcount: A:0.22, C:0.19, G:0.37, T:0.23
Consensus pattern (21 bp):
GTGCATGGATGCACTGCAGGG
Found at i:690025 original size:63 final size:62
Alignment explanation
Indices: 689913--690031 Score: 152
Period size: 63 Copynumber: 1.9 Consensus size: 62
689903 GGTGTTTGAG
* * *
689913 TGCATGGATGCACTGCATGGTTCATCGATGCACTAGTGCAGGTGGATGGATGCACTACAGGGA
1 TGCATGGATGCACTGCAGGGTGCATCGATGCACTAGTG-AGGTGCATGGATGCACTACAGGGA
*
689976 TGCATGGATGCACTGCAGGGGTGCATGGATGCACTGCAG-G-GGTGCATGGATGCACT
1 TGCATGGATGCACTGCA-GGGTGCATCGATGCACT--AGTGAGGTGCATGGATGCACT
690032 TTGACACCCT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
63 32 0.65
64 14 0.29
65 1 0.02
66 2 0.04
ACGTcount: A:0.22, C:0.19, G:0.36, T:0.23
Consensus pattern (62 bp):
TGCATGGATGCACTGCAGGGTGCATCGATGCACTAGTGAGGTGCATGGATGCACTACAGGGA
Found at i:690132 original size:29 final size:29
Alignment explanation
Indices: 690111--690168 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
690101 AAACTTTGAA
690111 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
690140 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
690169 TGCCTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:690158 original size:30 final size:30
Alignment explanation
Indices: 690111--690170 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
690101 AAACTTTGAA
690111 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
690140 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
690171 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:690314 original size:21 final size:21
Alignment explanation
Indices: 690281--690320 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
690271 TTGTTTAATG
*
690281 AAAAAGATGTCAATTGTTAAC
1 AAAAAGATATCAATTGTTAAC
*
690302 AAAATGATATCAATTGTTA
1 AAAAAGATATCAATTGTTA
690321 CCAATTGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.47, C:0.07, G:0.12, T:0.33
Consensus pattern (21 bp):
AAAAAGATATCAATTGTTAAC
Found at i:690670 original size:20 final size:20
Alignment explanation
Indices: 690645--690682 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
690635 ACTTTATGCA
*
690645 ATACCAATTGTTTAAATTTG
1 ATACCAATTGTTAAAATTTG
690665 ATACCAATTGTTAAAATT
1 ATACCAATTGTTAAAATT
690683 AAGTACATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.42
Consensus pattern (20 bp):
ATACCAATTGTTAAAATTTG
Found at i:693440 original size:20 final size:20
Alignment explanation
Indices: 693411--693484 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
693401 GCAGCCTTCG
*
693411 TGCATAGATGCACAGCAGGA
1 TGCATCGATGCACAGCAGGA
**
693431 TGCATCGATGCACAGCCTTGA
1 TGCATCGATGCACAG-CAGGA
* *
693452 TACATCGATGCACAGAAGGA
1 TGCATCGATGCACAGCAGGA
693472 TGCATCGATGCAC
1 TGCATCGATGCAC
693485 TAATTGCATT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 28 0.62
21 17 0.38
ACGTcount: A:0.31, C:0.24, G:0.26, T:0.19
Consensus pattern (20 bp):
TGCATCGATGCACAGCAGGA
Found at i:693552 original size:22 final size:23
Alignment explanation
Indices: 693519--693561 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
693509 ATGGATGCAC
693519 TGCATGGTGCATCG-ATGCACTAG
1 TGCATGGTGCAT-GAATGCACTAG
693542 TGCA-GGTGCATGAATGCACT
1 TGCATGGTGCATGAATGCACT
693562 GCAGGGATGC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 1 0.05
22 14 0.74
23 4 0.21
ACGTcount: A:0.23, C:0.21, G:0.30, T:0.26
Consensus pattern (23 bp):
TGCATGGTGCATGAATGCACTAG
Found at i:693574 original size:21 final size:20
Alignment explanation
Indices: 693505--693603 Score: 110
Period size: 21 Copynumber: 4.8 Consensus size: 20
693495 CGGTGTTTGA
*
693505 GTGCATGGATGCACTGCATG
1 GTGCATGGATGCACTGCAGG
*
693525 GTGCATCGATGCACTAGTGCA-G
1 GTGCATGGATGCAC---TGCAGG
*
693547 GTGCATGAATGCACTGCAGG
1 GTGCATGGATGCACTGCAGG
693567 GATGCATGGATGCACTGCAGGG
1 G-TGCATGGATGCACTGCA-GG
*
693589 GTGCGTGGATGCACT
1 GTGCATGGATGCACT
693604 TTGACACCCT
Statistics
Matches: 68, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
19 4 0.06
20 15 0.22
21 29 0.43
22 16 0.24
23 4 0.06
ACGTcount: A:0.21, C:0.20, G:0.36, T:0.22
Consensus pattern (20 bp):
GTGCATGGATGCACTGCAGG
Found at i:693741 original size:30 final size:29
Alignment explanation
Indices: 693683--693741 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
693673 AAACTTTGAA
*
693683 TAAATTCAATTAAGTCCAAAAACATTTTG
1 TAAATTCAATCAAGTCCAAAAACATTTTG
693712 TAAATTCAATCAAGTCCAAAAACCATTTTG
1 TAAATTCAATCAAGTCCAAAAA-CATTTTG
693742 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 21 0.75
30 7 0.25
ACGTcount: A:0.44, C:0.17, G:0.07, T:0.32
Consensus pattern (29 bp):
TAAATTCAATCAAGTCCAAAAACATTTTG
Found at i:705279 original size:2 final size:2
Alignment explanation
Indices: 705272--705313 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
705262 CCTTAAAGTA
705272 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
705314 CTGCAAAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:706815 original size:23 final size:22
Alignment explanation
Indices: 706780--706822 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
706770 ATAATTATTT
706780 AAAAAATTAAATAAAAAATACC
1 AAAAAATTAAATAAAAAATACC
*
706802 AAAAATATTTAATAAAAAATA
1 AAAAA-ATTAAATAAAAAATA
706823 ATTTTTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (22 bp):
AAAAAATTAAATAAAAAATACC
Found at i:711947 original size:30 final size:31
Alignment explanation
Indices: 711881--711947 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 31
711871 TTATGTTTTG
* * *
711881 ATCATTTGTGTTATTCAACTATTAAATTTTA
1 ATCATTTATATTATTCAACTATTAAACTTTA
* * *
711912 GTCATTTATATTATT-AATTATTACACTTTA
1 ATCATTTATATTATTCAACTATTAAACTTTA
711942 ATCATT
1 ATCATT
711948 GAGTTATTAA
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
30 17 0.59
31 12 0.41
ACGTcount: A:0.33, C:0.10, G:0.04, T:0.52
Consensus pattern (31 bp):
ATCATTTATATTATTCAACTATTAAACTTTA
Found at i:712060 original size:30 final size:31
Alignment explanation
Indices: 712026--712096 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
712016 CATGAAATTC
* **
712026 AGATAAAATACTATTTTTA-TCTTAATTTTT
1 AGATAAAATACTATTTTGATTCTTAAACTTT
*
712056 AGATAAAATATTATTTTGATTCTTAAACTTT
1 AGATAAAATACTATTTTGATTCTTAAACTTT
*
712087 AAATAAAATA
1 AGATAAAATA
712097 TCAATTTGAT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
30 17 0.49
31 18 0.51
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (31 bp):
AGATAAAATACTATTTTGATTCTTAAACTTT
Found at i:712093 original size:31 final size:31
Alignment explanation
Indices: 712028--712106 Score: 88
Period size: 31 Copynumber: 2.6 Consensus size: 31
712018 TGAAATTCAG
* * ** *
712028 ATAAAATACTATTTTTA-TCTTAATTTTTAG
1 ATAAAATATTATTTTGATTCTTAAACTTTAA
712058 ATAAAATATTATTTTGATTCTTAAACTTTAA
1 ATAAAATATTATTTTGATTCTTAAACTTTAA
* *
712089 ATAAAATATCAATTTGAT
1 ATAAAATATTATTTTGAT
712107 CATTGAATTC
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 15 0.37
31 26 0.63
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.48
Consensus pattern (31 bp):
ATAAAATATTATTTTGATTCTTAAACTTTAA
Found at i:715829 original size:3 final size:3
Alignment explanation
Indices: 715821--715854 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
715811 GTCGACCTCA
715821 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
715855 TCAATTATGA
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):
TAT
Found at i:723484 original size:20 final size:20
Alignment explanation
Indices: 723455--723493 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
723445 TTTCCACCAC
*
723455 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
723475 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
723494 TATGGGCTCT
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:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:733552 original size:20 final size:20
Alignment explanation
Indices: 733515--733553 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
733505 TTTCCACCAC
*
733515 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
* *
733535 ATGCATCTATATTATCCTA
1 ATGCAACTATATGATCCTA
733554 CATGAGTTAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.23, G:0.08, T:0.36
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:735139 original size:22 final size:22
Alignment explanation
Indices: 735096--735139 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
735086 GGCATGGATT
**
735096 GGTTATTTTCGCATTACGGTTA
1 GGTTATTTTCGCATTAAAGTTA
735118 GGTTGATTTTCGCA-TAAAGTTA
1 GGTT-ATTTTCGCATTAAAGTTA
735140 TTAATTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.23, C:0.11, G:0.23, T:0.43
Consensus pattern (22 bp):
GGTTATTTTCGCATTAAAGTTA
Found at i:750801 original size:34 final size:33
Alignment explanation
Indices: 750758--750829 Score: 135
Period size: 34 Copynumber: 2.2 Consensus size: 33
750748 CTGTCTTGTC
750758 TCATTTACAGCCCTAATCATGCTTAGCTAAATTT
1 TCATTTACAGCCCTAATCATGCTTAGCTAAA-TT
750792 TCATTTACAGCCCTAATCATGCTTAGCTAAATT
1 TCATTTACAGCCCTAATCATGCTTAGCTAAATT
750825 TCATT
1 TCATT
750830 AGCCAAAGGC
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 7 0.18
34 31 0.82
ACGTcount: A:0.29, C:0.24, G:0.08, T:0.39
Consensus pattern (33 bp):
TCATTTACAGCCCTAATCATGCTTAGCTAAATT
Found at i:751785 original size:18 final size:18
Alignment explanation
Indices: 751741--751800 Score: 75
Period size: 18 Copynumber: 3.2 Consensus size: 18
751731 ACCGGTCATA
* *
751741 ACCCGACCCGACCCATTG
1 ACCCGACCTGACCCGTTG
751759 ACCCGACCTGACCCGTTG
1 ACCCGACCTGACCCGTTG
751777 ACCCGACCTGTTGACCCGTTG
1 ACCCGACC---TGACCCGTTG
751798 ACC
1 ACC
751801 GTTGACCGTC
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
18 24 0.65
21 13 0.35
ACGTcount: A:0.18, C:0.45, G:0.20, T:0.17
Consensus pattern (18 bp):
ACCCGACCTGACCCGTTG
Found at i:751815 original size:17 final size:16
Alignment explanation
Indices: 751781--751827 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 16
751771 CCGTTGACCC
751781 GACCTGTTGACCCGTT
1 GACCTGTTGACCCGTT
751797 GACC-GTTGACCGTCGTT
1 GACCTGTTGACC--CGTT
751814 GACCACTGTTGACC
1 GA-C-CTGTTGACC
751828 AAAACTTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 7 0.27
16 4 0.15
17 6 0.23
18 1 0.04
19 1 0.04
20 7 0.27
ACGTcount: A:0.15, C:0.32, G:0.26, T:0.28
Consensus pattern (16 bp):
GACCTGTTGACCCGTT
Found at i:754326 original size:47 final size:46
Alignment explanation
Indices: 754265--754377 Score: 131
Period size: 47 Copynumber: 2.4 Consensus size: 46
754255 TTCGATTTGA
*
754265 ATTCTGA-TGATACTTGCCATGGATTCTGATCTGATA-TCGACATGG
1 ATTCTGATTGATACTTGACATGGATTCTGATCTGATACTCGACAT-G
* * * *
754310 ATTCTGATCTGATACTTGACTTGGATTCTGATCTGTTACTTGACCTG
1 ATTCTGAT-TGATACTTGACATGGATTCTGATCTGATACTCGACATG
754357 ATTTCTGATATGATACTTGAC
1 A-TTCTGAT-TGATACTTGAC
754378 CTGATTTATG
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
45 7 0.12
47 28 0.48
48 23 0.40
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.40
Consensus pattern (46 bp):
ATTCTGATTGATACTTGACATGGATTCTGATCTGATACTCGACATG
Found at i:754339 original size:24 final size:24
Alignment explanation
Indices: 754265--754377 Score: 135
Period size: 24 Copynumber: 4.8 Consensus size: 24
754255 TTCGATTTGA
*
754265 ATTCTGA--TGATACTTGCCATGG
1 ATTCTGATCTGATACTTGACATGG
*
754287 ATTCTGATCTGATA-TCGACATGG
1 ATTCTGATCTGATACTTGACATGG
*
754310 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
* *
754334 ATTCTGATCTGTTACTTGACCT-G
1 ATTCTGATCTGATACTTGACATGG
*
754357 ATTTCTGATATGATACTTGAC
1 A-TTCTGATCTGATACTTGAC
754378 CTGATTTATG
Statistics
Matches: 79, Mismatches: 8, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
22 7 0.09
23 23 0.29
24 49 0.62
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.40
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:756467 original size:7 final size:7
Alignment explanation
Indices: 756446--756477 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
756436 ATAACCCTAC
756446 CCGTTGA
1 CCGTTGA
756453 CTCGTTGA
1 C-CGTTGA
756461 CCGTTGA
1 CCGTTGA
756468 CCGTTGA
1 CCGTTGA
756475 CCG
1 CCG
756478 GTGTTGACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.12, C:0.31, G:0.28, T:0.28
Consensus pattern (7 bp):
CCGTTGA
Found at i:758978 original size:24 final size:24
Alignment explanation
Indices: 758951--759057 Score: 93
Period size: 24 Copynumber: 4.7 Consensus size: 24
758941 ATTTGAATTT
758951 TGATCTTATACTTGACATGGATTC
1 TGATCTTATACTTGACATGGATTC
758975 TGA---TAT-C-TGACATGGATTC
1 TGATCTTATACTTGACATGGATTC
* *
758994 TGATCTGATACTTGACTTGGATTC
1 TGATCTTATACTTGACATGGATTC
* *
759018 TGATCTGT-TGCTTGACCT-GATTTC
1 TGATCT-TATACTTGACATGGA-TTC
* *
759042 TGATATGATACTTGAC
1 TGATCTTATACTTGAC
759058 CTGATTTATG
Statistics
Matches: 67, Mismatches: 8, Indels: 16
0.74 0.09 0.18
Matches are distributed among these distances:
19 15 0.22
20 1 0.01
21 3 0.04
22 2 0.03
23 3 0.04
24 43 0.64
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TGATCTTATACTTGACATGGATTC
Found at i:759058 original size:24 final size:24
Alignment explanation
Indices: 758991--759064 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 24
758981 CTGACATGGA
*
758991 TTCTGATCTGATACTTGACTTGGA-
1 TTCTGATCTGATACTTGACCT-GAT
* *
759015 TTCTGATCTGTTGCTTGACCTGAT
1 TTCTGATCTGATACTTGACCTGAT
*
759039 TTCTGATATGATACTTGACCTGAT
1 TTCTGATCTGATACTTGACCTGAT
759063 TT
1 TT
759065 ATGTTTTGAT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
23 2 0.05
24 41 0.95
ACGTcount: A:0.19, C:0.18, G:0.19, T:0.45
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACCTGAT
Found at i:761479 original size:21 final size:21
Alignment explanation
Indices: 761455--761494 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
761445 TTAAAAAGTA
761455 AAAAATAAAAATATTTTTATT
1 AAAAATAAAAATATTTTTATT
*
761476 AAAAATAAATATATTTTTA
1 AAAAATAAAAATATTTTTA
761495 AAAACCTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
AAAAATAAAAATATTTTTATT
Found at i:761487 original size:19 final size:18
Alignment explanation
Indices: 761463--761498 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
761453 TAAAAAATAA
*
761463 AAATATTTTTATTAAAAAT
1 AAATATATTT-TTAAAAAT
761482 AAATATATTTTTAAAAA
1 AAATATATTTTTAAAAA
761499 CCTTTTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AAATATATTTTTAAAAAT
Found at i:762579 original size:34 final size:35
Alignment explanation
Indices: 762542--762736 Score: 222
Period size: 34 Copynumber: 5.8 Consensus size: 35
762532 AGTTTTTTGA
762542 ATATATATAATATAGTTTTTGAAAACA-TTTGAAAA-T
1 ATATATAT-ATATAG-TTTTG-AAACATTTTGAAAACT
762578 ATATA-ATATATAGCTTTTGAAA-A-TTTG--AA-T
1 ATATATATATATAG-TTTTGAAACATTTTGAAAACT
762608 ATATA-ATATATAGCTTTTGAAAACATTTTGAAAACT
1 ATATATATATATAG-TTTTG-AAACATTTTGAAAACT
762644 -TATATA-ATATAGTTTTTGAAACATTTTGAAAACT
1 ATATATATATATAG-TTTTGAAACATTTTGAAAACT
762678 -TATATATATATAG-TTTG-AACATTTTGAAAACT
1 ATATATATATATAGTTTTGAAACATTTTGAAAACT
762710 ATATA-ATATATAGTTTTGAAACATTTT
1 ATATATATATATAGTTTTGAAACATTTT
762737 TTGAAAACAT
Statistics
Matches: 146, Mismatches: 2, Indels: 24
0.85 0.01 0.14
Matches are distributed among these distances:
30 22 0.15
31 3 0.02
32 29 0.20
33 19 0.13
34 41 0.28
35 25 0.17
36 7 0.05
ACGTcount: A:0.43, C:0.05, G:0.09, T:0.43
Consensus pattern (35 bp):
ATATATATATATAGTTTTGAAACATTTTGAAAACT
Found at i:762755 original size:66 final size:66
Alignment explanation
Indices: 762565--762736 Score: 184
Period size: 65 Copynumber: 2.6 Consensus size: 66
762555 AGTTTTTGAA
* *
762565 AACA-TTTGAAAA--TATATAATATATAGCTTTTGAAA-A-TTTGAATA--TATA-ATATATAGC
1 AACATTTTGAAAACTTATAT-A-ATATAGTTTTTGAAACATTTTGAAAACTTATATATATATAG-
762622 TTTTG
63 -TTTG
762627 AAAACATTTTGAAAACTTATATAATATAGTTTTTGAAACATTTTGAAAACTTATATATATATAGT
1 --AACATTTTGAAAACTTATATAATATAGTTTTTGAAACATTTTGAAAACTTATATATATATAGT
762692 TTG
64 TTG
762695 AACATTTTGAAAAC-TATATAATATA-TAGTTTTGAAACATTTT
1 AACATTTTGAAAACTTATATAATATAGT--TTTTGAAACATTTT
762737 TTGAAAACAT
Statistics
Matches: 96, Mismatches: 2, Indels: 18
0.83 0.02 0.16
Matches are distributed among these distances:
64 5 0.05
65 33 0.34
66 30 0.31
67 12 0.12
68 4 0.04
69 4 0.04
70 8 0.08
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.42
Consensus pattern (66 bp):
AACATTTTGAAAACTTATATAATATAGTTTTTGAAACATTTTGAAAACTTATATATATATAGTTT
G
Found at i:762773 original size:17 final size:17
Alignment explanation
Indices: 762751--762783 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
762741 AAACATTTTA
762751 ATATATATTATATATAT
1 ATATATATTATATATAT
*
762768 ATATATATTCTATATA
1 ATATATATTATATATA
762784 ATAGTTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (17 bp):
ATATATATTATATATAT
Found at i:762892 original size:22 final size:20
Alignment explanation
Indices: 762862--762918 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
762852 TATTATATTA
762862 TTTGTTGTTTATTTTTTATTT
1 TTTGTTGTTTATTTTTT-TTT
762883 TTATGTTGTTT-TTTTTTTTT
1 TT-TGTTGTTTATTTTTTTTT
* *
762903 TTTTTTATTTATTTTT
1 TTTGTTGTTTATTTTT
762919 AGGTCCAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 6 0.19
20 10 0.31
21 8 0.25
22 8 0.25
ACGTcount: A:0.09, C:0.00, G:0.07, T:0.84
Consensus pattern (20 bp):
TTTGTTGTTTATTTTTTTTT
Found at i:765027 original size:14 final size:14
Alignment explanation
Indices: 764972--765028 Score: 55
Period size: 14 Copynumber: 4.0 Consensus size: 14
764962 ATAGTAGAAT
764972 AATTAAAT-TATGTCA
1 AATTAAATATAT-T-A
764987 AATTAGAATATA-TA
1 AATTA-AATATATTA
*
765001 AATTAAATTTATTA
1 AATTAAATATATTA
*
765015 AGTTAAATATATTA
1 AATTAAATATATTA
765029 CTAATAGTAG
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
13 5 0.14
14 20 0.56
15 6 0.17
16 3 0.08
17 2 0.06
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.42
Consensus pattern (14 bp):
AATTAAATATATTA
Found at i:776757 original size:18 final size:17
Alignment explanation
Indices: 776716--776765 Score: 91
Period size: 17 Copynumber: 2.9 Consensus size: 17
776706 TTGAATATGA
776716 ATATCAGACTTGTCAGG
1 ATATCAGACTTGTCAGG
776733 ATATCAGACTTGTCAGG
1 ATATCAGACTTGTCAGG
776750 AGTATCAGACTTGTCA
1 A-TATCAGACTTGTCA
776766 AGACCACCAG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 18 0.56
18 14 0.44
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (17 bp):
ATATCAGACTTGTCAGG
Found at i:777024 original size:29 final size:28
Alignment explanation
Indices: 776965--777039 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 28
776955 GCCCCTAATT
* *
776965 TTTTTTGTATTTATAATTAGGACCTTCAA
1 TTTTTTATATTTATAATTAGGA-CTCCAA
776994 TTTTTTATATTTATAATTAAGG-CTCCAA
1 TTTTTTATATTTATAATT-AGGACTCCAA
*
777022 ATTTTTATAATTTCATAA
1 TTTTTTAT-ATTT-ATAA
777040 AAATTTTAGT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
28 12 0.30
29 21 0.52
30 7 0.17
ACGTcount: A:0.32, C:0.09, G:0.07, T:0.52
Consensus pattern (28 bp):
TTTTTTATATTTATAATTAGGACTCCAA
Found at i:777182 original size:116 final size:117
Alignment explanation
Indices: 776993--777233 Score: 337
Period size: 116 Copynumber: 2.1 Consensus size: 117
776983 AGGACCTTCA
*
776993 ATTTTTTATATTTATAATTAAGGCTCCAAATTTTTATAATTTCATAAAAATTTTAGTTTTTAACC
1 ATTTTTTATATTTATAATTAAGGCTCCAAATTTTTATAAGTTCATAAAAATTTTAGTTTTTAACC
* *
777058 CTCTTTTTCCATTTCTCTTA-TAATTCATCCAATTTTTAATTAAATTTAACC
66 CTCTTTTTCCATTTATCTTATTAATTCATCCAATTTTGAATTAAATTTAACC
* * *
777109 ATTTTTTATATTTATAATT-AGGAC-CTCTAATTTTTATAAGTTCAT-AACATGTTTAGTTTTTT
1 ATTTTTTATATTTATAATTAAGG-CTC-CAAATTTTTATAAGTTCATAAAAAT-TTTAGTTTTTA
* * *
777171 ACCCTCTTTTTCCATTTATCTTATTTATTCATTCAATTTTGAATTAAATTTAATC
63 ACCCTCTTTTTCCATTTATCTTATTAATTCATCCAATTTTGAATTAAATTTAACC
777226 ATATTTTT
1 AT-TTTTT
777234 CTCTTTTTTT
Statistics
Matches: 111, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
115 8 0.07
116 69 0.62
117 29 0.26
118 5 0.05
ACGTcount: A:0.30, C:0.13, G:0.04, T:0.53
Consensus pattern (117 bp):
ATTTTTTATATTTATAATTAAGGCTCCAAATTTTTATAAGTTCATAAAAATTTTAGTTTTTAACC
CTCTTTTTCCATTTATCTTATTAATTCATCCAATTTTGAATTAAATTTAACC
Found at i:778960 original size:22 final size:22
Alignment explanation
Indices: 778920--778961 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
778910 ATTTTCCTTT
*
778920 TCAAAAAATATTTACAATATAA
1 TCAAAAAATATTGACAATATAA
* *
778942 TCAAAAATTATTGATAATAT
1 TCAAAAAATATTGACAATAT
778962 CATTCATGTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (22 bp):
TCAAAAAATATTGACAATATAA
Found at i:780036 original size:19 final size:19
Alignment explanation
Indices: 779995--780043 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
779985 ATTATCTATT
* *
779995 ATTTTATATTAATTTATAC
1 ATTTAATATTAATTAATAC
780014 ATTTAATATTAATATAATA-
1 ATTTAATATTAAT-TAATAC
*
780033 ATTTAGTATTA
1 ATTTAATATTA
780044 TGTTAATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 22 0.85
20 4 0.15
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (19 bp):
ATTTAATATTAATTAATAC
Found at i:780374 original size:30 final size:30
Alignment explanation
Indices: 780302--780411 Score: 123
Period size: 30 Copynumber: 3.7 Consensus size: 30
780292 TTCCTAGAAA
* * *
780302 ATGTAATTCATTTTACCTAAAATAGTTTT-
1 ATGTAATTCATTTTACATAAAACAATTTTC
* * *
780331 AGGTAATTCATTTTACGTAAAACATTTTTC
1 ATGTAATTCATTTTACATAAAACAATTTTC
*
780361 ATGTAATTTATTTTACATAAAACAATTTTC
1 ATGTAATTCATTTTACATAAAACAATTTTC
** *
780391 AAATAATTCATTTTATATAAA
1 ATGTAATTCATTTTACATAAA
780412 TTATTTTCCA
Statistics
Matches: 68, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
29 25 0.37
30 43 0.63
ACGTcount: A:0.39, C:0.10, G:0.05, T:0.45
Consensus pattern (30 bp):
ATGTAATTCATTTTACATAAAACAATTTTC
Found at i:781485 original size:30 final size:28
Alignment explanation
Indices: 781410--781486 Score: 91
Period size: 30 Copynumber: 2.6 Consensus size: 28
781400 ATAAAAAATT
*
781410 TAAGGACTAAAATGTAAAAAAATAAAGTC
1 TAAGGAC-CAAATGTAAAAAAATAAAGTC
* *
781439 TAGGGACCTAAGTGTAAAAAATATAAAGTC
1 TAAGGACC-AAATGTAAAAAA-ATAAAGTC
781469 TAAGGACCAATATGTAAA
1 TAAGGACCAA-ATGTAAA
781487 GAATTTAATC
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
29 19 0.47
30 21 0.52
ACGTcount: A:0.52, C:0.09, G:0.17, T:0.22
Consensus pattern (28 bp):
TAAGGACCAAATGTAAAAAAATAAAGTC
Found at i:783000 original size:3 final size:3
Alignment explanation
Indices: 782992--783024 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
782982 TTTGGGTTTG
782992 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
783025 AGGGATTGGG
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:783317 original size:44 final size:42
Alignment explanation
Indices: 783269--783350 Score: 110
Period size: 44 Copynumber: 1.9 Consensus size: 42
783259 AAGACGATGA
*
783269 TGATCCAACTTCTTATATGATGGAATCGAGCAAAGTGTTGGTGT
1 TGATCCAACTTCTTACATGAT-GAATCGAGCAAAG-GTTGGTGT
* * *
783313 TGATCTAACTTCTTACATGATTAATCGAGCTAAGGTTG
1 TGATCCAACTTCTTACATGATGAATCGAGCAAAGGTTG
783351 AACAAATTCT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 4 0.12
43 11 0.32
44 19 0.56
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (42 bp):
TGATCCAACTTCTTACATGATGAATCGAGCAAAGGTTGGTGT
Found at i:783526 original size:163 final size:166
Alignment explanation
Indices: 783190--783538 Score: 408
Period size: 165 Copynumber: 2.1 Consensus size: 166
783180 TCCTCGAATG
783190 AGTTCTTCTCATTATGAAC-TCTCCACTGGAAATGTTGATCCACCTTCTTCTATGATGAAATCAA
1 AGTTCTTCTCATTATGAACTTCTCCACTGGAAATGTTGATCCACCTTCTTCTATGATGAAATCAA
* * ** *
783254 GCGAAAAGACGATGATGATCCAACTTCTTATATGATGGAATCGAGCAAAGTGTTGGTGTTGATCT
66 GCGAAAAGACGATGATGATCCAACTCCTTATACGATGGAATCGAGCAAAGTGTCAGTGTTGATCC
* *
783319 AACTTCTTACATGATTAATCGAGCTAAGGTTGAACA
131 AACTCCTTACATGATGAATCGAGCTAAGGTTGAACA
* * * * * * * *
783355 AATTCTTCTCATTATGAACTTCTTCATTGGAAATGTTGATCCACC-TCTTTTTTTATGGATTCGA
1 AGTTCTTCTCATTATGAACTTCTCCACTGGAAATGTTGATCCACCTTCTTCTATGATGAAATC-A
* * * * *
783419 A-C-AAAGTGATGATGTTGATCCAACTCCTTATGCGATGG-AT-GAGCCAAG-GTCAGTGTT-AT
65 AGCGAAA-AGACGATGATGATCCAACTCCTTATACGATGGAATCGAGCAAAGTGTCAGTGTTGA-
**
783478 TCCAACTCCTTATGTGATGGAATCGAGCTAAGGTTGAACA
128 TCCAACTCCTTACATGAT-GAATCGAGCTAAGGTTGAACA
783518 AGTTCTTCTCATTATGAACTT
1 AGTTCTTCTCATTATGAACTT
783539 TTTCTCCCTC
Statistics
Matches: 156, Mismatches: 23, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
161 1 0.01
162 21 0.13
163 47 0.30
164 5 0.03
165 57 0.37
166 25 0.16
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (166 bp):
AGTTCTTCTCATTATGAACTTCTCCACTGGAAATGTTGATCCACCTTCTTCTATGATGAAATCAA
GCGAAAAGACGATGATGATCCAACTCCTTATACGATGGAATCGAGCAAAGTGTCAGTGTTGATCC
AACTCCTTACATGATGAATCGAGCTAAGGTTGAACA
Found at i:783899 original size:283 final size:283
Alignment explanation
Indices: 783347--784273 Score: 1378
Period size: 283 Copynumber: 3.3 Consensus size: 283
783337 TCGAGCTAAG
* * * *
783347 GTTGAACAAATTCTTCTCATTATGAACTTCTTCATTGGAAATGTTGATCCACCT-CTTTTTTTAT
1 GTTGAACAAATTCTTCTCATTAGGAACTTCTTCATTGGAAATGTTGATCCACCTCCTTCTGTGAT
* * *
783411 GGATTCGAACAAAGTGATGATGTTGATCCAACTCCTTATGCGATGGATGAGCCAAGGTCAGTGTT
66 GGATTCGAACAAAGTGATGATGTTGATCCAACTTCTTATGCGATGGATGAGCCAAGGTCGGTGAT
* * * *
783476 ATTCCAACTCCTTATGTGATGGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTTT
131 GTTCCAACTTCTTATGTGATGGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATAAACTTCT
* * * * * **
783541 TCTCCCTCATCGGATGAGTTCTTCTCATTATGAACCCTTTTATTGAAAATGTTGATCCACCTTAT
196 TCTCCCTCATCGGATGAGTTCTTCTCATTATAAACCCTTTCATTGGAAATATTGATCTACCTCCT
**
783606 TCTTTGATGGAATCGAGTGAAA-
261 TCAGTGATGGAATCGAGTGAAAT
* *
783628 GATGGAACAAGTTCTTCTCATTAGGAACTTCTTCATTGGAAATGTTGATCCACCTCCTTCTGTGA
1 G-TTGAACAAATTCTTCTCATTAGGAACTTCTTCATTGGAAATGTTGATCCACCTCCTTCTGTGA
* * *
783693 TGGATTTGAACAAAGTGATGATGTTGATCCAGA-TTTTTATGCGATGGATGAGCCAAGGTTGGTG
65 TGGATTCGAACAAAGTGATGATGTTGATCCA-ACTTCTTATGCGATGGATGAGCCAAGGTCGGTG
* *
783757 ATGCTT-CAACTTCTTATCTGATGGAATCGAGCTAAGGTTGAACAAGTTCTTCTTATTATAAACT
129 ATG-TTCCAACTTCTTATGTGATGGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATAAACT
*
783821 TCTTCTCCCTCATCGGATGAGTTCTTCTCATTATAAACCCTTCCATTGGAAATATTGATCTACCT
193 TCTTCTCCCTCATCGGATGAGTTCTTCTCATTATAAACCCTTTCATTGGAAATATTGATCTACCT
*
783886 CCTTCAGTGATGGAATCGGGTGAAAT
258 CCTTCAGTGATGGAATCGAGTGAAAT
* * * * *
783912 GTTGAACCAGTTCTTCTCATTAGGAACTTTTTCATTGGAAATGTTAATCCACCTCCTTCTATGAT
1 GTTGAACAAATTCTTCTCATTAGGAACTTCTTCATTGGAAATGTTGATCCACCTCCTTCTGTGAT
* * *
783977 GGATTCGAACAAAGTGATGATGTTGATACAACTTCTTATGCGATGGATGAACCAAGGTCGATGAT
66 GGATTCGAACAAAGTGATGATGTTGATCCAACTTCTTATGCGATGGATGAGCCAAGGTCGGTGAT
*
784042 GTTCCAATTTCTTATGTGATGGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATAAACTTCT
131 GTTCCAACTTCTTATGTGATGGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATAAACTTCT
* *
784107 TCTCCCTCATCGAATGAGTTCTTCTCATTACAAACCCTTTCATTGGAAATATTGATCTACCTCCT
196 TCTCCCTCATCGGATGAGTTCTTCTCATTATAAACCCTTTCATTGGAAATATTGATCTACCTCCT
784172 TCAGTGATGGAATCGAGTGAAAT
261 TCAGTGATGGAATCGAGTGAAAT
* * * *
784195 GTTGAAAAAATTCTTTTCATTATGAATTTAC-TCATTGGAAATGTTGATCCACCTCCTTCTGTGA
1 GTTGAACAAATTCTTCTCATTAGGAACTT-CTTCATTGGAAATGTTGATCCACCTCCTTCTGTGA
*
784259 TGGAATCGAACAAAG
65 TGGATTCGAACAAAG
784274 GTTGAACAAG
Statistics
Matches: 581, Mismatches: 57, Indels: 14
0.89 0.09 0.02
Matches are distributed among these distances:
281 1 0.00
282 53 0.09
283 523 0.90
284 4 0.01
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (283 bp):
GTTGAACAAATTCTTCTCATTAGGAACTTCTTCATTGGAAATGTTGATCCACCTCCTTCTGTGAT
GGATTCGAACAAAGTGATGATGTTGATCCAACTTCTTATGCGATGGATGAGCCAAGGTCGGTGAT
GTTCCAACTTCTTATGTGATGGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATAAACTTCT
TCTCCCTCATCGGATGAGTTCTTCTCATTATAAACCCTTTCATTGGAAATATTGATCTACCTCCT
TCAGTGATGGAATCGAGTGAAAT
Found at i:784934 original size:37 final size:37
Alignment explanation
Indices: 784848--784921 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 37
784838 TTCTAGGGAG
784848 ACAATCCTAAGAATAACTCAAACAACATTCCAGAAAA
1 ACAATCCTAAGAATAACTCAAACAACATTCCAGAAAA
* * **
784885 ACAATCTTAAGAATGACTCAAACAATTTTCCAGAAAA
1 ACAATCCTAAGAATAACTCAAACAACATTCCAGAAAA
784922 GTGATCCTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.51, C:0.22, G:0.07, T:0.20
Consensus pattern (37 bp):
ACAATCCTAAGAATAACTCAAACAACATTCCAGAAAA
Found at i:786640 original size:30 final size:30
Alignment explanation
Indices: 786560--786663 Score: 115
Period size: 30 Copynumber: 3.6 Consensus size: 30
786550 TTAAGGACTA
* *
786560 AAATGTAAAAAA-CTAAAGTTTA-GGTCCT
1 AAATGTAAAAAATCTAAAGTCTAGGGACCT
* * *
786588 AAGTGT-AAAAATATAAAATCTAGGGACCT
1 AAATGTAAAAAATCTAAAGTCTAGGGACCT
*
786617 AAATATAAAAAATCTAAAGTCTAGGGACCT
1 AAATGTAAAAAATCTAAAGTCTAGGGACCT
* *
786647 ATATGTAAAGAATCTAA
1 AAATGTAAAAAATCTAA
786664 TCTTATAGGG
Statistics
Matches: 61, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
27 5 0.08
28 12 0.20
29 9 0.15
30 35 0.57
ACGTcount: A:0.49, C:0.11, G:0.14, T:0.26
Consensus pattern (30 bp):
AAATGTAAAAAATCTAAAGTCTAGGGACCT
Found at i:788370 original size:3 final size:3
Alignment explanation
Indices: 788362--788486 Score: 153
Period size: 3 Copynumber: 41.7 Consensus size: 3
788352 TAAATAAGAA
* * *
788362 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT AAA CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
788410 TAAT TTT TAT TAT TAT TAT TAT TTT TGT T-T TAT TAT TAT TAT TTT
1 T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
788455 TAT TAA TAT TAG TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
788487 AATAAACAAT
Statistics
Matches: 105, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
2 2 0.02
3 100 0.95
4 3 0.03
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:789788 original size:12 final size:12
Alignment explanation
Indices: 789758--789795 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
789748 ATTACTTTTA
789758 TATTTTAATTAT
1 TATTTTAATTAT
**
789770 TGCTTTAATTAT
1 TATTTTAATTAT
789782 TATTTT-ATTAT
1 TATTTTAATTAT
789793 TAT
1 TAT
789796 CTTAGTCATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
11 8 0.36
12 14 0.64
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (12 bp):
TATTTTAATTAT
Found at i:790648 original size:20 final size:21
Alignment explanation
Indices: 790625--790676 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
790615 AGAAATTAAA
790625 AATTCATTTATTT-AATTTTT
1 AATTCATTTATTTAAATTTTT
* *
790645 AATTCTTTTCTTTCAAATTTTT
1 AATTCATTTATTT-AAATTTTT
790667 -ATT-ATTTATT
1 AATTCATTTATT
790677 ATTTTTATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 16 0.62
21 3 0.12
22 7 0.27
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (21 bp):
AATTCATTTATTTAAATTTTT
Found at i:795342 original size:11 final size:11
Alignment explanation
Indices: 795326--795362 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
795316 AAGAAAGAAG
795326 AAAAAAAAAGA
1 AAAAAAAAAGA
*
795337 AAAAAAAAGGA
1 AAAAAAAAAGA
795348 AAAAAAAAAGA
1 AAAAAAAAAGA
795359 AAAA
1 AAAA
795363 GGAAAATTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:795350 original size:6 final size:6
Alignment explanation
Indices: 795315--795368 Score: 53
Period size: 6 Copynumber: 9.3 Consensus size: 6
795305 CTCATTCAGC
*
795315 AAAGAA AGAAG-A AAA-AA AAAGAA AAA-AA AAGGAA AAA-AA AAAGAA
1 AAAGAA A-AAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
795360 AAAGGAA AA
1 AAA-GAA AA
795369 TTGAATCAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
5 15 0.38
6 17 0.43
7 8 0.20
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:795352 original size:18 final size:18
Alignment explanation
Indices: 795328--795368 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
795318 GAAAGAAGAA
*
795328 AAAAAAAGAAAAAAAAAGG
1 AAAAAAA-AAAGAAAAAGG
795347 AAAAAAAAAAGAAAAAGG
1 AAAAAAAAAAGAAAAAGG
795365 AAAA
1 AAAA
795369 TTGAATCAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAGAAAAAGG
Found at i:795368 original size:12 final size:10
Alignment explanation
Indices: 795323--795362 Score: 62
Period size: 10 Copynumber: 3.8 Consensus size: 10
795313 GCAAAGAAAG
795323 AAGAAAAAAA
1 AAGAAAAAAA
795333 AAGAAAAAAA
1 AAGAAAAAAA
795343 AAGGAAAAAAAA
1 AA-G-AAAAAAA
795355 AAGAAAAA
1 AAGAAAAA
795363 GGAAAATTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 17 0.61
11 2 0.07
12 9 0.32
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (10 bp):
AAGAAAAAAA
Found at i:797643 original size:81 final size:83
Alignment explanation
Indices: 797508--797710 Score: 347
Period size: 81 Copynumber: 2.5 Consensus size: 83
797498 TGCAATATAC
*
797508 TCATAGCATCTTCTGGAAGTGTTCATTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAA
1 TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAA
*
797573 TTT-G-AGATGAATGTGA
66 TTTGGAAGAGGAATGTGA
797589 TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAA
1 TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAA
*
797654 TTTGGAAGAGGAATGTGC
66 TTTGGAAGAGGAATGTGA
* *
797672 TAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGAT
1 TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGAT
797711 TTGATTTGAT
Statistics
Matches: 115, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
81 67 0.58
82 1 0.01
83 47 0.41
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (83 bp):
TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAA
TTTGGAAGAGGAATGTGA
Found at i:800008 original size:54 final size:54
Alignment explanation
Indices: 799917--800065 Score: 208
Period size: 54 Copynumber: 2.8 Consensus size: 54
799907 CCAGCATAAG
* * *
799917 CCACATGAGAGGATGAATATGTTGTCAAATGTTTTACGAACATCTGAGCAGAAA
1 CCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAGCAGAAA
* * *
799971 CTACAGGAAAGGATGAATGTGTTGTCAAAGGTTTTACGAACATCTGAGCAGAAG
1 CCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAGCAGAAA
* ***
800025 CCATAGGAAAGGATGAATGCACTGTCAAATGTTTTACGAAC
1 CCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
800066 CTGCTATTCT
Statistics
Matches: 83, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 83 1.00
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.25
Consensus pattern (54 bp):
CCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAGCAGAAA
Found at i:800443 original size:22 final size:22
Alignment explanation
Indices: 800414--800468 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
800404 ATCTACATTC
* *
800414 TTCAAAGATGATAGATTTTCTT
1 TTCAAAGATGACAGATTCTCTT
*
800436 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
800458 TTCAAAGATGA
1 TTCAAAGATGA
800469 AAACTTTATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCTCTT
Found at i:802035 original size:76 final size:76
Alignment explanation
Indices: 801146--802028 Score: 1640
Period size: 76 Copynumber: 11.6 Consensus size: 76
801136 CTATTTCCCA
801146 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
801211 AGCCTTAGGGT
66 AGCCTTAGGGT
801222 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
801287 AGCCTTAGGGT
66 AGCCTTAGGGT
801298 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
801363 AGCCTTAGGGT
66 AGCCTTAGGGT
801374 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
801439 AGCCTTAGGGT
66 AGCCTTAGGGT
801450 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
801515 AGCCTTAGGGT
66 AGCCTTAGGGT
* * *
801526 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAACCTTCGGGAGCTTTTTGATGTTTTTAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
*
801591 AGCCTTCGGGT
66 AGCCTTAGGGT
801602 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
*
801667 AGCCTTCGGGT
66 AGCCTTAGGGT
*
801678 CATCTGTAAGTCCTTCAGTGCATGATGTTTCAAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
* * *
801743 AGCATTCGAGT
66 AGCCTTAGGGT
801754 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
801819 AGCCTTAGGGT
66 AGCCTTAGGGT
*
801830 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
*
801895 AGCCTTCGGGT
66 AGCCTTAGGGT
*
801906 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGTCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
*
801971 AGCCTTCGGGT
66 AGCCTTAGGGT
*
801982 CATCTGTAAGTCCTTCAGTGCATGATGCTTCCAAAAAGCCTTCGGGA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGA
802029 GTTTTTTTTT
Statistics
Matches: 787, Mismatches: 20, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
76 787 1.00
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.36
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:802220 original size:3 final size:3
Alignment explanation
Indices: 802214--802280 Score: 80
Period size: 3 Copynumber: 22.0 Consensus size: 3
802204 TTAATTTTTT
* * * *
802214 TTA TTA TTA TTA TTT TTGT TTA TTA TTA TTA TTT TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
802260 GTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA
802281 AATAAACAAT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
3 52 0.95
4 3 0.05
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:802710 original size:14 final size:15
Alignment explanation
Indices: 802691--802719 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
802681 ACGAGGACAG
802691 AAAACAGA-AGAAAA
1 AAAACAGAGAGAAAA
802705 AAAACAGAGAGAAAA
1 AAAACAGAGAGAAAA
802720 GAACCGAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.76, C:0.07, G:0.17, T:0.00
Consensus pattern (15 bp):
AAAACAGAGAGAAAA
Found at i:803878 original size:18 final size:17
Alignment explanation
Indices: 803857--803890 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
803847 TTACTATATT
* *
803857 AAAATAAATTTTTGTCA
1 AAAAAAAATGTTTGTCA
803874 AAAAAAAATGTTTGTCA
1 AAAAAAAATGTTTGTCA
803891 TTTATTTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.35
Consensus pattern (17 bp):
AAAAAAAATGTTTGTCA
Found at i:804349 original size:3 final size:3
Alignment explanation
Indices: 804341--804379 Score: 62
Period size: 3 Copynumber: 13.0 Consensus size: 3
804331 GGTGACGACA
804341 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -TCT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT
804380 CGTATGTTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 1 0.03
3 32 0.94
4 1 0.03
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:805379 original size:43 final size:43
Alignment explanation
Indices: 805326--805505 Score: 234
Period size: 43 Copynumber: 4.2 Consensus size: 43
805316 TTGATCATTT
* ** * *
805326 TCCTAATTCTACATGCAATCCTCTGCGGAGGGCATCATCCCCA
1 TCCTGATTCTACATGGGATCCTCTACGGAGGGCATCATCCCCG
*
805369 TCCTGATTCTACATGGGATCCTCTACGGAGGGCATCATCCACG
1 TCCTGATTCTACATGGGATCCTCTACGGAGGGCATCATCCCCG
* * *
805412 TCCTAATTCTACATGGGATCCTCTACGGATGGCATCATCCTCG
1 TCCTGATTCTACATGGGATCCTCTACGGAGGGCATCATCCCCG
* * * *
805455 TCTTGATTCTGCATGGGATACTCTACGGAGGACATCATCCCCG
1 TCCTGATTCTACATGGGATCCTCTACGGAGGGCATCATCCCCG
*
805498 TTCTGATT
1 TCCTGATT
805506 ATGTTGGGAT
Statistics
Matches: 119, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 119 1.00
ACGTcount: A:0.21, C:0.30, G:0.20, T:0.29
Consensus pattern (43 bp):
TCCTGATTCTACATGGGATCCTCTACGGAGGGCATCATCCCCG
Found at i:808569 original size:24 final size:23
Alignment explanation
Indices: 808513--808571 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 23
808503 CAGTCGAAAC
*
808513 TGCCACATAGAATTGCACCGAAG
1 TGCCACGTAGAATTGCACCGAAG
**
808536 TGCCGTGTAGAATATGCACCGAAG
1 TGCCACGTAGAAT-TGCACCGAAG
808560 TGCCACGTAGAA
1 TGCCACGTAGAA
808572 ATTGTCTCGA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 10 0.33
24 20 0.67
ACGTcount: A:0.32, C:0.24, G:0.25, T:0.19
Consensus pattern (23 bp):
TGCCACGTAGAATTGCACCGAAG
Found at i:808607 original size:23 final size:23
Alignment explanation
Indices: 808554--808651 Score: 117
Period size: 23 Copynumber: 4.2 Consensus size: 23
808544 AGAATATGCA
808554 CCGAAGTG-CCACGTAGAAATTGTC
1 CCGAAG-GACCACGTAGAAA-TGTC
* *
808578 TCGAAGGACCACATAGAAATGTC
1 CCGAAGGACCACGTAGAAATGTC
* * *
808601 CCAAAGGACCGCGTAGATATGTC
1 CCGAAGGACCACGTAGAAATGTC
*
808624 CCGAAGGACCACGTAGAATTGTC
1 CCGAAGGACCACGTAGAAATGTC
808647 CCGAA
1 CCGAA
808652 TGACAGCATA
Statistics
Matches: 62, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
23 47 0.76
24 15 0.24
ACGTcount: A:0.33, C:0.26, G:0.24, T:0.17
Consensus pattern (23 bp):
CCGAAGGACCACGTAGAAATGTC
Found at i:808663 original size:23 final size:23
Alignment explanation
Indices: 808554--808664 Score: 93
Period size: 23 Copynumber: 4.8 Consensus size: 23
808544 AGAATATGCA
*
808554 CCGAAGTG-CCACGTAGAAATTGTC
1 CCGAAG-GACCACATAG-AATTGTC
* *
808578 TCGAAGGACCACATAGAAATGTC
1 CCGAAGGACCACATAGAATTGTC
* * *
808601 CCAAAGGACCGCGTAG-ATATGTC
1 CCGAAGGACCACATAGAAT-TGTC
*
808624 CCGAAGGACCACGTAGAATTGTC
1 CCGAAGGACCACATAGAATTGTC
*
808647 CCGAATGA-CAGCATAGAA
1 CCGAAGGACCA-CATAGAA
808665 CCATTGACTC
Statistics
Matches: 71, Mismatches: 12, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
22 3 0.04
23 54 0.76
24 14 0.20
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.17
Consensus pattern (23 bp):
CCGAAGGACCACATAGAATTGTC
Found at i:814325 original size:30 final size:30
Alignment explanation
Indices: 814150--814313 Score: 249
Period size: 30 Copynumber: 5.5 Consensus size: 30
814140 GTTAACATAA
*
814150 CAAAAATAGAAATTTAAAGGAATAAAATAG
1 CAAAAATAGAAATTTAAAGGACTAAAATAG
* * *
814180 TAAAAATAGAAAATTAAAGGACTAAACTAG
1 CAAAAATAGAAATTTAAAGGACTAAAATAG
814210 CAAAAATAGAAATTTAAAGGACTAAAATAG
1 CAAAAATAGAAATTTAAAGGACTAAAATAG
* *
814240 AAAAAATATAAATTTAAAGGACTAAAATAG
1 CAAAAATAGAAATTTAAAGGACTAAAATAG
*
814270 AAAAAATA-AAATTTTAAAGGACTAAAATAG
1 CAAAAATAGAAA-TTTAAAGGACTAAAATAG
814300 CAAAAATAGAAATT
1 CAAAAATAGAAATT
814314 GGAAAGGCTA
Statistics
Matches: 122, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
29 3 0.02
30 116 0.95
31 3 0.02
ACGTcount: A:0.62, C:0.05, G:0.12, T:0.21
Consensus pattern (30 bp):
CAAAAATAGAAATTTAAAGGACTAAAATAG
Found at i:816160 original size:40 final size:40
Alignment explanation
Indices: 816096--816228 Score: 128
Period size: 43 Copynumber: 3.3 Consensus size: 40
816086 GTGAAATGGC
**
816096 TCCTACGTGATGAGGAGATATGGTT-GGTAGATGACACGGT
1 TCCTACGTGATGAGGAG-GCTGGTTAGGTAGATGACACGGT
** * *
816136 TCCTACGTGATGAGGACGGCTGGTTATCTAAGGGTGACACGGC
1 TCCTACGTGATGAGGA-GGCTGGTTAGGT-A-GATGACACGGT
*
816179 TCCTACGTGATGAGGAGGTCTGGTTAGG--GATGACATGGT
1 TCCTACGTGATGAGGAGG-CTGGTTAGGTAGATGACACGGT
*
816218 TCCTATGTGAT
1 TCCTACGTGAT
816229 AAGAACGGTA
Statistics
Matches: 76, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
39 18 0.24
40 21 0.28
41 2 0.03
42 3 0.04
43 32 0.42
ACGTcount: A:0.22, C:0.16, G:0.35, T:0.28
Consensus pattern (40 bp):
TCCTACGTGATGAGGAGGCTGGTTAGGTAGATGACACGGT
Found at i:816185 original size:83 final size:82
Alignment explanation
Indices: 816046--816228 Score: 251
Period size: 83 Copynumber: 2.2 Consensus size: 82
816036 GAGGGTGATT
*** *
816046 ACACGGTTCCTACACAATGAGGACGGCTAGTTATCTAAGGGTGAAATGGCTCCTACGTGATGAGG
1 ACACGGTTCCTACGTGATGAGGACGGCTAGTTATCTAAGGGTGAAACGGCTCCTACGTGATGAGG
816111 AGATATGGTT-GGTAGATG
66 AGATATGGTTAGG--GATG
* *
816129 ACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAAGGGTGACACGGCTCCTACGTGATGAGG
1 ACACGGTTCCTACGTGATGAGGACGGCTAGTTATCTAAGGGTGAAACGGCTCCTACGTGATGAGG
* *
816194 AGGTCTGGTTAGGGATG
66 AGATATGGTTAGGGATG
* *
816211 ACATGGTTCCTATGTGAT
1 ACACGGTTCCTACGTGAT
816229 AAGAACGGTA
Statistics
Matches: 89, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
82 20 0.22
83 67 0.75
84 2 0.02
ACGTcount: A:0.24, C:0.17, G:0.33, T:0.26
Consensus pattern (82 bp):
ACACGGTTCCTACGTGATGAGGACGGCTAGTTATCTAAGGGTGAAACGGCTCCTACGTGATGAGG
AGATATGGTTAGGGATG
Found at i:816202 original size:43 final size:43
Alignment explanation
Indices: 816062--816204 Score: 152
Period size: 43 Copynumber: 3.4 Consensus size: 43
816052 TTCCTACACA
* * *
816062 ATGAGGACGGCTAGTTATCTAAGGGTGAAATGGCTCCTACGTG
1 ATGAGGACGGCTGGTTATCTAAGGGTGACACGGCTCCTACGTG
** ** * *
816105 ATGAGGA-GATATGGTT-GGT-A-GATGACACGGTTCCTACGTG
1 ATGAGGACG-GCTGGTTATCTAAGGGTGACACGGCTCCTACGTG
816145 ATGAGGACGGCTGGTTATCTAAGGGTGACACGGCTCCTACGTG
1 ATGAGGACGGCTGGTTATCTAAGGGTGACACGGCTCCTACGTG
816188 ATGAGGA-GGTCTGGTTA
1 ATGAGGACGG-CTGGTTA
816205 GGGATGACAT
Statistics
Matches: 79, Mismatches: 15, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
40 28 0.35
41 3 0.04
42 5 0.06
43 43 0.54
ACGTcount: A:0.24, C:0.15, G:0.35, T:0.26
Consensus pattern (43 bp):
ATGAGGACGGCTGGTTATCTAAGGGTGACACGGCTCCTACGTG
Found at i:816371 original size:66 final size:66
Alignment explanation
Indices: 816258--816414 Score: 176
Period size: 66 Copynumber: 2.4 Consensus size: 66
816248 AGGGATAATG
* * * * *
816258 GTTTCAAGAGAAACCGACTCAAATAT-GATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-T
1 GTTTCAAGGGAAACAGACTCAAAGATGGGTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAACT
816321 T
66 T
* * * * * *
816322 CGTTTCAAGTGAAA-TGATCTCAAAGATGGGTATTTCACGAGAAATTGTCTTAAGGGAGACAAAA
1 -GTTTCAAGGGAAACAGA-CTCAAAGATGGGTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
816386 CTT
64 CTT
816389 GTTTCAAGGGAAACAGACTCAAAGAT
1 GTTTCAAGGGAAACAGACTCAAAGAT
816415 TATAAATTTT
Statistics
Matches: 77, Mismatches: 11, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
64 2 0.03
65 20 0.26
66 51 0.66
67 4 0.05
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.25
Consensus pattern (66 bp):
GTTTCAAGGGAAACAGACTCAAAGATGGGTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAACT
T
Found at i:816597 original size:36 final size:37
Alignment explanation
Indices: 816543--816627 Score: 102
Period size: 36 Copynumber: 2.3 Consensus size: 37
816533 AATAACTTTG
**
816543 AAAA-TTGTATTTCGAGAGAAACAGTCTCAAATTAGAC
1 AAAATTTGT-TTTCGAGAGAAACAGTCTCAAACGAGAC
** *
816580 AAAATTTGTTTT-GAGAGAAATTGTCTCAAGCGAGAC
1 AAAATTTGTTTTCGAGAGAAACAGTCTCAAACGAGAC
816616 AAAATTTGTTTT
1 AAAATTTGTTTT
816628 TAAGAAAATA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
36 31 0.74
37 7 0.17
38 4 0.10
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.33
Consensus pattern (37 bp):
AAAATTTGTTTTCGAGAGAAACAGTCTCAAACGAGAC
Found at i:816643 original size:36 final size:36
Alignment explanation
Indices: 816576--816645 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 36
816566 GTCTCAAATT
* **
816576 AGACAAAATTTGTTTTGAGAGAAATTGTCTCAAGCG
1 AGACAAAATTTGTTTTAAGAGAAATAATCTCAAGCG
816612 AGACAAAATTTGTTTTTAAGA-AAATAATCTCAAG
1 AGACAAAATTTG-TTTTAAGAGAAATAATCTCAAG
816646 GTCGATAGAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
36 23 0.77
37 7 0.23
ACGTcount: A:0.41, C:0.10, G:0.17, T:0.31
Consensus pattern (36 bp):
AGACAAAATTTGTTTTAAGAGAAATAATCTCAAGCG
Found at i:822566 original size:60 final size:59
Alignment explanation
Indices: 822492--822684 Score: 169
Period size: 59 Copynumber: 3.2 Consensus size: 59
822482 ATTTGATGAT
* * * *
822492 TTTAAGGGATTAAAATAA-AACTAACAGAAACTTGAGAGG-CTAAAATAAAAAAAACAAAAA
1 TTTAAAGGACTAAAATAACAA-AAACAGAAA-TTGAAAGGACTAAAAT-AAAAAAACAAAAA
* * * ***
822552 TTTAAAGGACTAAAATAACAAAAATAGAAATTTAAAGGACTAAAATAGAAAAATTGAAA
1 TTTAAAGGACTAAAATAACAAAAACAGAAATTGAAAGGACTAAAATAAAAAAACAAAAA
* * * *
822611 TTTAAAGGACTAAAATAGCAAAAACA-AACATTTAAAGGACTAAAATAGTAAAAATAGAAAA
1 TTTAAAGGACTAAAATAACAAAAACAGAA-ATTGAAAGGACTAAAATA-AAAAAACA-AAAA
*
822672 -TTAAAGGGCTAAA
1 TTTAAAGGACTAAA
822685 CAGTAATTAC
Statistics
Matches: 112, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
58 2 0.02
59 57 0.51
60 48 0.43
61 5 0.04
ACGTcount: A:0.60, C:0.07, G:0.13, T:0.20
Consensus pattern (59 bp):
TTTAAAGGACTAAAATAACAAAAACAGAAATTGAAAGGACTAAAATAAAAAAACAAAAA
Found at i:822633 original size:59 final size:60
Alignment explanation
Indices: 822531--822684 Score: 204
Period size: 59 Copynumber: 2.6 Consensus size: 60
822521 ACTTGAGAGG
** * * *
822531 CTAAAATAAAAAAAACAAAAATTTAAAGGACTAAAATAACAAAAATAGAA-ATTTAAAGGA
1 CTAAAATAGTAAAAATAGAAATTTAAAGGACTAAAATAACAAAAACA-AACATTTAAAGGA
* *
822591 CTAAAATAG-AAAAATTGAAATTTAAAGGACTAAAATAGCAAAAACAAACATTTAAAGGA
1 CTAAAATAGTAAAAATAGAAATTTAAAGGACTAAAATAACAAAAACAAACATTTAAAGGA
* *
822650 CTAAAATAGTAAAAATAGAAAATTAAAGGGCTAAA
1 CTAAAATAGTAAAAATAGAAATTTAAAGGACTAAA
822685 CAGTAATTAC
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
58 2 0.02
59 51 0.61
60 30 0.36
ACGTcount: A:0.62, C:0.07, G:0.11, T:0.19
Consensus pattern (60 bp):
CTAAAATAGTAAAAATAGAAATTTAAAGGACTAAAATAACAAAAACAAACATTTAAAGGA
Found at i:822690 original size:29 final size:30
Alignment explanation
Indices: 822531--822684 Score: 186
Period size: 30 Copynumber: 5.2 Consensus size: 30
822521 ACTTGAGAGG
** * *
822531 CTAAAATAAAAAAAACAAAAATTTAAAGGA
1 CTAAAATAGTAAAAATAGAAATTTAAAGGA
**
822561 CTAAAATAACAAAAATAGAAATTTAAAGGA
1 CTAAAATAGTAAAAATAGAAATTTAAAGGA
*
822591 CTAAAATAG-AAAAATTGAAATTTAAAGGA
1 CTAAAATAGTAAAAATAGAAATTTAAAGGA
* *
822620 CTAAAATAGCAAAAACA-AACATTTAAAGGA
1 CTAAAATAGTAAAAATAGAA-ATTTAAAGGA
* *
822650 CTAAAATAGTAAAAATAGAAAATTAAAGGG
1 CTAAAATAGTAAAAATAGAAATTTAAAGGA
822680 CTAAA
1 CTAAA
822685 CAGTAATTAC
Statistics
Matches: 110, Mismatches: 11, Indels: 6
0.87 0.09 0.05
Matches are distributed among these distances:
29 30 0.27
30 78 0.71
31 2 0.02
ACGTcount: A:0.62, C:0.07, G:0.11, T:0.19
Consensus pattern (30 bp):
CTAAAATAGTAAAAATAGAAATTTAAAGGA
Found at i:824086 original size:3 final size:3
Alignment explanation
Indices: 824063--824111 Score: 66
Period size: 3 Copynumber: 16.7 Consensus size: 3
824053 ATTAAATTGT
*
824063 TAA TAA -AA TGAA TAC TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
824108 -AA TA
1 TAA TA
824112 TCAGGATAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 4 0.10
3 34 0.83
4 3 0.07
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:825056 original size:18 final size:19
Alignment explanation
Indices: 825033--825070 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
825023 CTAAAACAAT
*
825033 AACAAAATAA-AAATCTTA
1 AACAAAATAAGAAATATTA
*
825051 AACAAAGTAAGAAATATTA
1 AACAAAATAAGAAATATTA
825070 A
1 A
825071 GTTGCAAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.66, C:0.08, G:0.05, T:0.21
Consensus pattern (19 bp):
AACAAAATAAGAAATATTA
Found at i:826300 original size:12 final size:12
Alignment explanation
Indices: 826274--826328 Score: 85
Period size: 12 Copynumber: 4.7 Consensus size: 12
826264 ATATACAAAT
826274 ACCTAACTC-TC
1 ACCTAACTCTTC
826285 ACCTAACTCTTC
1 ACCTAACTCTTC
*
826297 ACCTAATTCTTC
1 ACCTAACTCTTC
*
826309 GCCTAACTCTTC
1 ACCTAACTCTTC
826321 ACCTAACT
1 ACCTAACT
826329 AAATTGATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
11 9 0.23
12 30 0.77
ACGTcount: A:0.25, C:0.40, G:0.02, T:0.33
Consensus pattern (12 bp):
ACCTAACTCTTC
Found at i:827962 original size:3 final size:3
Alignment explanation
Indices: 827947--828033 Score: 156
Period size: 3 Copynumber: 29.0 Consensus size: 3
827937 TTTTTACCCA
* *
827947 TAT TAT AAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
827995 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
828034 AAATATATAT
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 80 1.00
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:830243 original size:15 final size:13
Alignment explanation
Indices: 830223--830260 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
830213 TTTATATGTT
830223 TTATTTTATTTGCAA
1 TTATTTTATTT-C-A
830238 TTATTTTATTTCA
1 TTATTTTATTTCA
830251 TTA-TTTATTT
1 TTATTTTATTT
830261 TGCTGTCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.30
13 4 0.17
14 1 0.04
15 11 0.48
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (13 bp):
TTATTTTATTTCA
Found at i:833526 original size:15 final size:16
Alignment explanation
Indices: 833500--833532 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
833490 GTTGGGATCA
833500 ATACATTTTTGCATAC
1 ATACATTTTTGCATAC
833516 ATACA-TTTTGCATAC
1 ATACATTTTTGCATAC
833531 AT
1 AT
833533 GCATCATTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.42
Consensus pattern (16 bp):
ATACATTTTTGCATAC
Found at i:840878 original size:11 final size:11
Alignment explanation
Indices: 840862--840935 Score: 84
Period size: 11 Copynumber: 6.9 Consensus size: 11
840852 TGCTTGAAGA
840862 AAAAAAGAAAG
1 AAAAAAGAAAG
840873 AAAAAAGAAAG
1 AAAAAAGAAAG
*
840884 AAAAGAGAAAAAG
1 AAAA-A-AGAAAG
840897 AAAAAA-AAAG
1 AAAAAAGAAAG
840907 -AAAAAG-AA-
1 AAAAAAGAAAG
*
840915 AAAAAAGAGAG
1 AAAAAAGAAAG
840926 AAAAAAGAAA
1 AAAAAAGAAA
840936 AAGGGGAGTC
Statistics
Matches: 54, Mismatches: 3, Indels: 12
0.78 0.04 0.17
Matches are distributed among these distances:
9 13 0.24
10 5 0.09
11 25 0.46
12 2 0.04
13 9 0.17
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAG
Found at i:840894 original size:16 final size:16
Alignment explanation
Indices: 840859--840936 Score: 74
Period size: 16 Copynumber: 4.9 Consensus size: 16
840849 TTATGCTTGA
840859 AGAAAA-AAAG-AAAG
1 AGAAAAGAAAGAAAAG
*
840873 AAAAAAGAAAGAAAAG
1 AGAAAAGAAAGAAAAG
*
840889 AGAAAAAGAAA-AAAAA
1 AG-AAAAGAAAGAAAAG
*
840905 AGAAAAAGAAAAAAAAG
1 AG-AAAAGAAAGAAAAG
840922 AGAGAAA-AAAGAAAA
1 AGA-AAAGAAAGAAAA
840937 AGGGGAGTCA
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
14 5 0.09
15 4 0.07
16 28 0.52
17 17 0.31
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (16 bp):
AGAAAAGAAAGAAAAG
Found at i:840901 original size:24 final size:22
Alignment explanation
Indices: 840858--840938 Score: 87
Period size: 23 Copynumber: 3.7 Consensus size: 22
840848 ATTATGCTTG
840858 AAGAAAAA-AAGAAAGAAAAAAGA
1 AAGAAAAAGAA-AAAGAAAAAA-A
840881 AAGAAAAGAGAAAAAGAAAAAAA
1 AAGAAAA-AGAAAAAGAAAAAAA
* *
840904 AAGAAAAAGAAAAA-AAAGAGA
1 AAGAAAAAGAAAAAGAAAAAAA
*
840925 GA-AAAAAGAAAAAG
1 AAGAAAAAGAAAAAG
840939 GGGAGTCAAG
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
20 11 0.21
21 6 0.12
22 7 0.13
23 15 0.29
24 11 0.21
25 2 0.04
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (22 bp):
AAGAAAAAGAAAAAGAAAAAAA
Found at i:840921 original size:33 final size:33
Alignment explanation
Indices: 840861--840938 Score: 104
Period size: 33 Copynumber: 2.4 Consensus size: 33
840851 ATGCTTGAAG
* *
840861 AAAAAAAGAAAGAAAAAAGAAAGAAAAGAGAAA
1 AAAAAAAAAAAGAAAAAAGAAAAAAAAGAGAAA
*
840894 AAGAAAAAAAAAG-AAAAAGAAAAAAAAGAGAGA
1 AA-AAAAAAAAAGAAAAAAGAAAAAAAAGAGAAA
*
840927 AAAAAGAAAAAG
1 AAAAAAAAAAAG
840939 GGGAGTCAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
32 9 0.22
33 22 0.55
34 9 0.22
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (33 bp):
AAAAAAAAAAAGAAAAAAGAAAAAAAAGAGAAA
Found at i:843155 original size:114 final size:114
Alignment explanation
Indices: 842955--843620 Score: 944
Period size: 114 Copynumber: 5.8 Consensus size: 114
842945 AATCTATCAT
* * * *
842955 TTGATAGATTAGCTTTTCCAAAGAAGGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAGA
1 TTGATGGATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
*
843020 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAAA
66 AGTTCATAATGAGAAGAACTTGTTCAACCTTTTACCTGAATTCATCAAA
843069 TTGATGGATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
*
843134 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAAA
66 AGTTCATAATGAGAAGAACTTGTTCAACCTTTTACCTGAATTCATCAAA
*
843183 TTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
*
843248 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAAA
66 AGTTCATAATGAGAAGAACTTGTTCAACCTTTTACCTGAATTCATCAAA
* *
843297 TTGATGGATTATCTTTTCCAGAGAAAGTTTATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* * * *
843362 AGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATC-AT
66 AGTTCATAATGAGAAGAACTTGTTCAACCTTTTACCTGAATTCATCAAA
* * * * *
843410 TTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAG
1 TTGATGGATTATCTTTTCCAGAGAAG-GTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAG
* *** *
843474 AATAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTGAATTCATC-AT
62 AAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACCTGAATTCATCAAA
* * * * * * *
843526 TTGATGTATCAACATTGCCAG-GTAGAGTTCATAATGAAAAGAACTCGTCATCTGAAGAAGGAAG
1 TTGATGGATTATCTTTTCCAGAGAAG-GTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAG
*
843590 AAGAAGTTCATAATAAGAAGAACTTGTTCAA
62 AAGAAGTTCATAATGAGAAGAACTTGTTCAA
843621 TAATTCTATC
Statistics
Matches: 523, Mismatches: 25, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
112 2 0.00
113 34 0.07
114 329 0.63
115 1 0.00
116 157 0.30
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.30
Consensus pattern (114 bp):
TTGATGGATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
AGTTCATAATGAGAAGAACTTGTTCAACCTTTTACCTGAATTCATCAAA
Found at i:843952 original size:3 final size:3
Alignment explanation
Indices: 843937--844016 Score: 124
Period size: 3 Copynumber: 26.7 Consensus size: 3
843927 TTTTTACCCA
* * *
843937 TAT TAT AAT TAT TAT TAT TAT TAT TAT TAT TAT CAT CAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
843985 TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
844017 AATATATATT
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 71 1.00
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:844028 original size:11 final size:10
Alignment explanation
Indices: 844012--844052 Score: 55
Period size: 11 Copynumber: 3.8 Consensus size: 10
844002 TTATTATTAT
844012 TATTAAATATA
1 TATTAAATA-A
844023 TATTAAATACA
1 TATTAAATA-A
844034 TATATAAATAA
1 TAT-TAAATAA
844045 TATTAAAT
1 TATTAAAT
844053 TACAAAGCCC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 5 0.18
11 17 0.61
12 6 0.21
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (10 bp):
TATTAAATAA
Found at i:847724 original size:18 final size:18
Alignment explanation
Indices: 847697--847738 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
847687 TTTTTGTAAA
847697 AATT-AATAAAA-ATAAT
1 AATTAAATAAAACATAAT
*
847713 ATATTAAATAAAACATGAT
1 A-ATTAAATAAAACATAAT
847732 AATTAAA
1 AATTAAA
847739 AGTTTAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 1 0.05
17 3 0.14
18 13 0.59
19 5 0.23
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (18 bp):
AATTAAATAAAACATAAT
Found at i:847849 original size:25 final size:23
Alignment explanation
Indices: 847810--847858 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 23
847800 GTTAATTTAC
* *
847810 TTAATTTTTAGAATTTCATGTTA
1 TTAATTTTTAGAATTCCATCTTA
847833 TTAATTTCTATAGAATTCCATCTTA
1 TTAATTT-T-TAGAATTCCATCTTA
847858 T
1 T
847859 AAAAAATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 7 0.32
24 1 0.05
25 14 0.64
ACGTcount: A:0.31, C:0.10, G:0.06, T:0.53
Consensus pattern (23 bp):
TTAATTTTTAGAATTCCATCTTA
Found at i:850479 original size:60 final size:59
Alignment explanation
Indices: 850301--850470 Score: 175
Period size: 59 Copynumber: 2.8 Consensus size: 59
850291 ACATGTATAA
* * * * * *
850301 TTTAGGATTAAATTGAAATGTTCAAAAAGTTTGGGGGCCAATTTAGAATGAAGATCAGAG
1 TTTAGGATGAAATTGAAATGTT-TAAAAGTTTAGAGACCAATTTAGAATGAAGATCATAG
* * * *
850361 TTTGGGGATGAAAATGAAATG-TTAAAAGTTTA-AGGACTAATTTAGTATGATA-ATCATAG
1 TTT-AGGATGAAATTGAAATGTTTAAAAGTTTAGA-GACCAATTTAGAATGA-AGATCATAG
*
850420 TTTATGGATGAAATTGAAATGTTTAAAAGTTTAGAGACCAATTTAAAATGA
1 TTTA-GGATGAAATTGAAATGTTTAAAAGTTTAGAGACCAATTTAGAATGA
850471 GGGCCATAGA
Statistics
Matches: 89, Mismatches: 15, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
59 45 0.51
60 29 0.33
61 15 0.17
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.33
Consensus pattern (59 bp):
TTTAGGATGAAATTGAAATGTTTAAAAGTTTAGAGACCAATTTAGAATGAAGATCATAG
Found at i:851390 original size:2 final size:2
Alignment explanation
Indices: 851385--851432 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
851375 ATATCTTTTA
851385 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
851427 AT AT AT
1 AT AT AT
851433 CAGTTTATGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:852277 original size:30 final size:31
Alignment explanation
Indices: 852211--852280 Score: 124
Period size: 31 Copynumber: 2.3 Consensus size: 31
852201 AACGTGTCAC
*
852211 AAAAATAAACTTATTCTTATTAGAAACTAAA
1 AAAAACAAACTTATTCTTATTAGAAACTAAA
852242 AAAAACAAACTTATTCTTATTAGAAACT-AA
1 AAAAACAAACTTATTCTTATTAGAAACTAAA
852272 AAAAACAAA
1 AAAAACAAA
852281 GAAAAAAGAT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
30 11 0.29
31 27 0.71
ACGTcount: A:0.59, C:0.11, G:0.03, T:0.27
Consensus pattern (31 bp):
AAAAACAAACTTATTCTTATTAGAAACTAAA
Found at i:855202 original size:19 final size:19
Alignment explanation
Indices: 855178--855226 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 19
855168 GCATCGGTAC
855178 ACTGTTCAATGTTCACAGT
1 ACTGTTCAATGTTCACAGT
*
855197 ACTGTTCATCAATGTTCACGGT
1 ACTG-T--TCAATGTTCACAGT
855219 ACTGTTCA
1 ACTGTTCA
855227 TAAAAAAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 7 0.27
20 1 0.04
21 1 0.04
22 17 0.65
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.37
Consensus pattern (19 bp):
ACTGTTCAATGTTCACAGT
Found at i:855211 original size:22 final size:22
Alignment explanation
Indices: 855183--855227 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
855173 GGTACACTGT
855183 TCAATGTTCACAGTACTGTTCA
1 TCAATGTTCACAGTACTGTTCA
*
855205 TCAATGTTCACGGTACTGTTCA
1 TCAATGTTCACAGTACTGTTCA
855227 T
1 T
855228 AAAAAAAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (22 bp):
TCAATGTTCACAGTACTGTTCA
Found at i:861964 original size:24 final size:22
Alignment explanation
Indices: 861937--861987 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
861927 ATATATATAT
*
861937 ATATACACATATATAGTTTAAAGA
1 ATATACA-ATATA-AGTTTAAAAA
* *
861961 ATATATAATATAATTTTAAAAA
1 ATATACAATATAAGTTTAAAAA
861983 ATATA
1 ATATA
861988 TTATATAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 13 0.54
23 5 0.21
24 6 0.25
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.37
Consensus pattern (22 bp):
ATATACAATATAAGTTTAAAAA
Found at i:861979 original size:22 final size:21
Alignment explanation
Indices: 861953--862030 Score: 88
Period size: 22 Copynumber: 3.7 Consensus size: 21
861943 ACATATATAG
861953 TTTAAAGAATATATAATATAAT
1 TTTAAA-AATATATAATATAAT
*
861975 TTTAAAAAATATATTATATAATT
1 TTT-AAAAATATATAATATAA-T
* *
861998 TTTGAAAACATAT--TATAAT
1 TTTAAAAATATATAATATAAT
862017 TTTAAAAATATATA
1 TTTAAAAATATATA
862031 GTTTTTAATA
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
19 12 0.25
20 5 0.10
22 24 0.50
23 7 0.15
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.44
Consensus pattern (21 bp):
TTTAAAAATATATAATATAAT
Found at i:862035 original size:16 final size:16
Alignment explanation
Indices: 861989--862046 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
861979 AAAAATATAT
861989 TATATAATTTTTGAAAACA
1 TATATAA-TTTT-AAAA-A
862008 TATTATAATTTTAAAAA
1 TA-TATAATTTTAAAAA
* * *
862025 TATATAGTTTTTAATA
1 TATATAATTTTAAAAA
862041 TATATA
1 TATATA
862047 TTATTACTAC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
16 17 0.49
17 3 0.09
18 4 0.11
19 6 0.17
20 5 0.14
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (16 bp):
TATATAATTTTAAAAA
Found at i:870491 original size:3 final size:3
Alignment explanation
Indices: 870479--870524 Score: 56
Period size: 3 Copynumber: 15.3 Consensus size: 3
870469 ATTATTCAAT
* * * *
870479 TTA TTT TTA TTA TTA TTA TTA TTA TTA GTA TTA GTA TTA GTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
870525 ATATCTTTAA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:870510 original size:12 final size:12
Alignment explanation
Indices: 870485--870524 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
870475 CAATTTATTT
*
870485 TTATTATTATTA
1 TTATTATTAGTA
870497 TTATTATTAGTA
1 TTATTATTAGTA
*
870509 TTAGTATTAGTA
1 TTATTATTAGTA
870521 TTAT
1 TTAT
870525 ATATCTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (12 bp):
TTATTATTAGTA
Found at i:872391 original size:21 final size:19
Alignment explanation
Indices: 872361--872399 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
872351 TTGTTCGATA
872361 AAATTATAATAAAAATATTT
1 AAATTATAAT-AAAATATTT
*
872381 AAATTAGTAATTAAATATT
1 AAATTA-TAATAAAATATT
872400 ATTTGATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (19 bp):
AAATTATAATAAAATATTT
Found at i:873985 original size:2 final size:2
Alignment explanation
Indices: 873978--874040 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
873968 CAATTACATG
873978 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
874020 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
874041 CACGATACTT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:874946 original size:30 final size:30
Alignment explanation
Indices: 874905--875006 Score: 120
Period size: 30 Copynumber: 3.5 Consensus size: 30
874895 TCTATAAAAT
*
874905 ATTTATTTATATTTTGAAGCTTATTGTGTC
1 ATTTATATATATTTTGAAGCTTATTGTGTC
* ****
874935 ATTTATATATATTTT-AATC-TATAAAAT-
1 ATTTATATATATTTTGAAGCTTATTGTGTC
*
874962 ATTTATTTATATTTTGAAGCTTATTGTGTC
1 ATTTATATATATTTTGAAGCTTATTGTGTC
874992 ATTTATATATATTTT
1 ATTTATATATATTTT
875007 AAAACCAAAG
Statistics
Matches: 56, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
27 14 0.25
28 7 0.12
29 7 0.12
30 28 0.50
ACGTcount: A:0.30, C:0.05, G:0.08, T:0.57
Consensus pattern (30 bp):
ATTTATATATATTTTGAAGCTTATTGTGTC
Found at i:874962 original size:57 final size:57
Alignment explanation
Indices: 874894--875008 Score: 230
Period size: 57 Copynumber: 2.0 Consensus size: 57
874884 ACGTGTTTCC
874894 ATCTATAAAATATTTATTTATATTTTGAAGCTTATTGTGTCATTTATATATATTTTA
1 ATCTATAAAATATTTATTTATATTTTGAAGCTTATTGTGTCATTTATATATATTTTA
874951 ATCTATAAAATATTTATTTATATTTTGAAGCTTATTGTGTCATTTATATATATTTTA
1 ATCTATAAAATATTTATTTATATTTTGAAGCTTATTGTGTCATTTATATATATTTTA
875008 A
1 A
875009 AACCAAAGGT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.34, C:0.05, G:0.07, T:0.54
Consensus pattern (57 bp):
ATCTATAAAATATTTATTTATATTTTGAAGCTTATTGTGTCATTTATATATATTTTA
Found at i:875196 original size:13 final size:13
Alignment explanation
Indices: 875178--875206 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
875168 TCGATCAGAT
875178 CCAAGATTCATTA
1 CCAAGATTCATTA
875191 CCAAGATTCATTA
1 CCAAGATTCATTA
875204 CCA
1 CCA
875207 TCCTTAGTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.28, G:0.07, T:0.28
Consensus pattern (13 bp):
CCAAGATTCATTA
Found at i:877889 original size:199 final size:199
Alignment explanation
Indices: 877271--877939 Score: 824
Period size: 200 Copynumber: 3.4 Consensus size: 199
877261 TTACCTATCA
* * * * *
877271 ACCAAAGCTTTCGAGTTTGATTCCACTCAGCTCAAGAATGCATCGACCGTATGATAGCAGCGAGG
1 ACCAAAGCTTTCGAGTTCGATTTCACTCAGCTCAAGAGTGCATCGACCGCATGGTAGCAGCGAGG
* * * * *
877336 AACTACCTTTCGGTCAAACTTCGAACCGAGGTCTTTAAGCCAAGAAGAAGACCTAGGATGACTGT
66 AACTACCTTCCAGTCAAACTTCGAACCGAGGTCTTTAAGCCAAGAAGAACACCTAGGTTGACTGC
* * * *
877401 GATATGGCAACAAGGAATCACTTCCCAGTCAAGTTTCGACATAGCTTAAGGCGAGAAGAGCTATT
131 AATGTGGCAACAAGGAACCACTTCCCAGTCAAGTTTC-ACATAGCTTAAAGCGAGAAGAGCTATT
877466 TGCCG
195 TGCCG
* * * * *
877471 ACTAAAGCTTTCTAGTTCGATTTCGCTCAGCTCAAGAGTGCATTTGACCCCATGGTAGCAGCGAG
1 ACCAAAGCTTTCGAGTTCGATTTCACTCAGCTCAAGAGTGCA-TCGACCGCATGGTAGCAGCGAG
** * *** *
877536 GAACTACCTTCTTGTCAAACTGCGAACCGAGGTCTTTAAATTAAGAAGAACACCTAGATTGACTG
65 GAACTACCTTCCAGTCAAACTTCGAACCGAGGTCTTTAAGCCAAGAAGAACACCTAGGTTGACTG
* * * *
877601 CAATGTGGCAACAATGAACCACTT-CCAGTCAAGTTTTAACATAGCTTAACGTGAGAAGAGCTAT
130 CAATGTGGCAACAAGGAACCACTTCCCAGTCAAG-TTTCACATAGCTTAAAGCGAGAAGAGCTAT
*
877665 TTGTCG
194 TTGCCG
* * * * * *
877671 ACAAAAGCTTTCAAGTTCGATTTCGCTCAGCTCGAGAGTGCATCGACCGCATGGTAGTAGAGAGG
1 ACCAAAGCTTTCGAGTTCGATTTCACTCAGCTCAAGAGTGCATCGACCGCATGGTAGCAGCGAGG
* * *
877736 AACTACCTTCCAGTCAAACTTCGAACTGAGGCCTTTAAGCCAAGAAGAATACCTAGGTTGACTGC
66 AACTACCTTCCAGTCAAACTTCGAACCGAGGTCTTTAAGCCAAGAAGAACACCTAGGTTGACTGC
* *
877801 AATGTGGCAACAAGGAACCACTTCCCAGTC-TGATTTCATCATAGCTTAAAGCAAGAAGAGCTAT
131 AATGTGGCAACAAGGAACCACTTCCCAGTCAAG-TTTCA-CATAGCTTAAAGCGAGAAGAGCTAT
*
877865 CTGCCG
194 TTGCCG
* * * * * *
877871 ACCAAAG-TTTTGAGTTCGA-TTCACTCAGCTCGAGAGTGCATCGACCGCAAGATAGCAGTGATG
1 ACCAAAGCTTTCGAGTTCGATTTCACTCAGCTCAAGAGTGCATCGACCGCATGGTAGCAGCGAGG
877934 AACTAC
66 AACTAC
877940 ATACGGCCGA
Statistics
Matches: 401, Mismatches: 64, Indels: 10
0.84 0.13 0.02
Matches are distributed among these distances:
198 44 0.11
199 111 0.28
200 151 0.38
201 95 0.24
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (199 bp):
ACCAAAGCTTTCGAGTTCGATTTCACTCAGCTCAAGAGTGCATCGACCGCATGGTAGCAGCGAGG
AACTACCTTCCAGTCAAACTTCGAACCGAGGTCTTTAAGCCAAGAAGAACACCTAGGTTGACTGC
AATGTGGCAACAAGGAACCACTTCCCAGTCAAGTTTCACATAGCTTAAAGCGAGAAGAGCTATTT
GCCG
Found at i:878434 original size:27 final size:27
Alignment explanation
Indices: 878402--878456 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
878392 TTTTGAAAAC
*
878402 ATAGTTTTTGAGAATATA-ATATATAAT
1 ATAGTTTTT-AAAATATATATATATAAT
*
878429 ATAGTTTTTAAAATATATGTATATAAT
1 ATAGTTTTTAAAATATATATATATAAT
878456 A
1 A
878457 CATTATTACT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 7 0.28
27 18 0.72
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (27 bp):
ATAGTTTTTAAAATATATATATATAAT
Found at i:881410 original size:33 final size:32
Alignment explanation
Indices: 881349--881410 Score: 74
Period size: 33 Copynumber: 1.9 Consensus size: 32
881339 ATATATTTAT
*
881349 TTTAAAATTTTTATTATAAACTTTATTATGGA
1 TTTAAAATTTTTATTATAAACTTAATTATGGA
881381 TTTAAATATTTTT-TTAAATAAA-TTAATTAT
1 TTTAAA-ATTTTTATT--ATAAACTTAATTAT
881411 TTTAATAAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
32 8 0.31
33 13 0.50
34 5 0.19
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (32 bp):
TTTAAAATTTTTATTATAAACTTAATTATGGA
Found at i:881952 original size:108 final size:108
Alignment explanation
Indices: 881759--881957 Score: 240
Period size: 108 Copynumber: 1.8 Consensus size: 108
881749 CGCATTTTTA
* * * * **** *
881759 AAGCTGATGGGGCCTTAGAAATCTGACGATAACAAAATAGGTTAATTACTTGATTTGTTATCAAT
1 AAGCTGACGGAGCCTTAGAAATCCGACGATAAAAAAATAGGTTAATTACTTGAAACATTATCAAC
* * **
881824 ATTATCTACATATTAGGTAGCGCTTAAAATGTTACCAAAGTTT
66 ATAATCAACATAACAGGTAGCGCTTAAAATGTTACCAAAGTTT
881867 AAGCTGACGGAGCCTTAGAAATCCGACGATAAAAAAATAGGTTAATTAC-TGAAAACATTATCAA
1 AAGCTGACGGAGCCTTAGAAATCCGACGATAAAAAAATAGGTTAATTACTTG-AAACATTATCAA
*
881931 CCATAAT-AACATAACATGTAGCGCTTA
65 -CATAATCAACATAACAGGTAGCGCTTA
881958 TTTAATATAA
Statistics
Matches: 75, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
107 2 0.03
108 69 0.92
109 4 0.05
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (108 bp):
AAGCTGACGGAGCCTTAGAAATCCGACGATAAAAAAATAGGTTAATTACTTGAAACATTATCAAC
ATAATCAACATAACAGGTAGCGCTTAAAATGTTACCAAAGTTT
Done.