Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397274.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_228.0, 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: 2969030
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 66526 characters in sequence are not A, C, G, or T
File 6 of 8
Found at i:2171013 original size:20 final size:21
Alignment explanation
Indices: 2170983--2171023 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
2170973 TATATGTCTA
2170983 ATAAATCTCAA-T-TTTTTTT
1 ATAAATCTCAACTATTTTTTT
2171002 ATAAATTCTCAACTATTTTTTT
1 ATAAA-TCTCAACTATTTTTTT
2171024 TCAATTAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.26
20 6 0.32
21 1 0.05
22 7 0.37
ACGTcount: A:0.32, C:0.12, G:0.00, T:0.56
Consensus pattern (21 bp):
ATAAATCTCAACTATTTTTTT
Found at i:2172440 original size:2 final size:2
Alignment explanation
Indices: 2172435--2172462 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2172425 TATATATGAT
2172435 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2172463 TTTGAATCCA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2176675 original size:7 final size:7
Alignment explanation
Indices: 2176659--2176708 Score: 82
Period size: 7 Copynumber: 7.1 Consensus size: 7
2176649 ATAAGGGCCC
*
2176659 AGCCAGG
1 AGCCAAG
2176666 AGCCAAG
1 AGCCAAG
2176673 AGCCAAG
1 AGCCAAG
2176680 AGCCAAG
1 AGCCAAG
2176687 AGCCAAG
1 AGCCAAG
*
2176694 AGCCGAG
1 AGCCAAG
2176701 AGCCAAG
1 AGCCAAG
2176708 A
1 A
2176709 CTCTCTCTCC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 40 1.00
ACGTcount: A:0.40, C:0.28, G:0.32, T:0.00
Consensus pattern (7 bp):
AGCCAAG
Found at i:2176851 original size:15 final size:15
Alignment explanation
Indices: 2176830--2176859 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
2176820 TCACTTGAAA
2176830 GTTTTTTT-ATTTTT
1 GTTTTTTTCATTTTT
2176844 GTTTTTTTCATTTTT
1 GTTTTTTTCATTTTT
2176859 G
1 G
2176860 CCCCCCCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.07, C:0.03, G:0.10, T:0.80
Consensus pattern (15 bp):
GTTTTTTTCATTTTT
Found at i:2187564 original size:23 final size:22
Alignment explanation
Indices: 2187532--2187574 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
2187522 TAATAATGTT
*
2187532 AATTTAATTATTACAATATTAA
1 AATTTAATTAATACAATATTAA
*
2187554 AATTTATATTAATATAATATT
1 AATTTA-ATTAATACAATATT
2187575 TTTTTGATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
AATTTAATTAATACAATATTAA
Found at i:2203187 original size:158 final size:158
Alignment explanation
Indices: 2202890--2203207 Score: 584
Period size: 158 Copynumber: 2.0 Consensus size: 158
2202880 CTCCTTTAAA
*
2202890 GCTTTTTTACATATTTTATCTATTTTTCTTACTTTCCTATTGAGTTTGTTTTTCCTCCGAAAAAG
1 GCTTTTCTACATATTTTATCTATTTTTCTTACTTTCCTATTGAGTTTGTTTTTCCTCCGAAAAAG
* *
2202955 TCTTTTTGTTATTTTTACTATCTTTTACTAGTTTGTACAAACTAATAAGGAATGGTCTGTTAAAT
66 TCTTTCTGTTATTTTTACTATATTTTACTAGTTTGTACAAACTAATAAGGAATGGTCTGTTAAAT
2203020 TCCAAAGGATAACCACTACAGTCCTTTT
131 TCCAAAGGATAACCACTACAGTCCTTTT
2203048 GCTTTTCTACATATTTTATCTATTTTTCTTACTTTCCTATTGAGTTTGTTTTTCCTCCGAAAAAG
1 GCTTTTCTACATATTTTATCTATTTTTCTTACTTTCCTATTGAGTTTGTTTTTCCTCCGAAAAAG
2203113 TCTTTCTGTTATTTTTACTATATTTTACTAGTTTGTACAAACTAATAAGGAATGGTCTGTTAAA-
66 TCTTTCTGTTATTTTTACTATATTTTACTAGTTTGTACAAACTAATAAGGAATGGTCTGTTAAAT
*
2203177 TCCTAGAGGATAACCACTACAGTCCTTTT
131 TCC-AAAGGATAACCACTACAGTCCTTTT
2203206 GC
1 GC
2203208 ACCAAGTTTC
Statistics
Matches: 155, Mismatches: 4, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
157 3 0.02
158 152 0.98
ACGTcount: A:0.25, C:0.17, G:0.11, T:0.47
Consensus pattern (158 bp):
GCTTTTCTACATATTTTATCTATTTTTCTTACTTTCCTATTGAGTTTGTTTTTCCTCCGAAAAAG
TCTTTCTGTTATTTTTACTATATTTTACTAGTTTGTACAAACTAATAAGGAATGGTCTGTTAAAT
TCCAAAGGATAACCACTACAGTCCTTTT
Found at i:2205807 original size:19 final size:19
Alignment explanation
Indices: 2205785--2205822 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
2205775 AAAGATTTAA
2205785 TATTT-TAAAAAAATTAAAT
1 TATTTATAAAAAAA-TAAAT
2205804 TATTTATAAAAAAATAAAT
1 TATTTATAAAAAAATAAAT
2205823 AAATTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TATTTATAAAAAAATAAAT
Found at i:2205825 original size:23 final size:21
Alignment explanation
Indices: 2205791--2205832 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
2205781 TTAATATTTT
*
2205791 AAAAAAATTAAATTATTTATAA
1 AAAAAAAATAAATT-TTTATAA
2205813 AAAAATAAATAAATTTTTAT
1 AAAAA-AAATAAATTTTTAT
2205833 TTTTTATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AAAAAAAATAAATTTTTATAA
Found at i:2205828 original size:20 final size:19
Alignment explanation
Indices: 2205786--2205829 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
2205776 AAGATTTAAT
*
2205786 ATTTTAAAAAAATTAAATT
1 ATTTTAAAAAAATTAAATA
2205805 ATTTATAAAAAAA-TAAATAA
1 ATTT-TAAAAAAATTAAAT-A
2205825 ATTTT
1 ATTTT
2205830 TATTTTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTTTAAAAAAATTAAATA
Found at i:2205855 original size:20 final size:20
Alignment explanation
Indices: 2205832--2205870 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2205822 TAAATTTTTA
*
2205832 TTTTTTATATTTAATTAAAC
1 TTTTATATATTTAATTAAAC
* *
2205852 TTTTATATTTTTACTTAAA
1 TTTTATATATTTAATTAAA
2205871 ATTAAATAAA
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:0.05, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTATATATTTAATTAAAC
Found at i:2206027 original size:25 final size:25
Alignment explanation
Indices: 2205999--2206047 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
2205989 AAGTAATGTT
*
2205999 TTAATTAATAATAA-TTAATTAATTA
1 TTAATT-ATAAAAATTTAATTAATTA
*
2206024 TTAATTATAAAAATTTATTTAATT
1 TTAATTATAAAAATTTAATTAATT
2206048 TAAAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
TTAATTATAAAAATTTAATTAATTA
Found at i:2211635 original size:109 final size:108
Alignment explanation
Indices: 2211399--2211607 Score: 350
Period size: 109 Copynumber: 1.9 Consensus size: 108
2211389 GTGTACTTTT
*
2211399 TCTTTAGTAGTTAAAATTACCAGTTCTTGGAAATATGGAATGACAACACAAAGGATTTTTGCTTT
1 TCTTTAGTAGTTAAAATTACCAGTTCTTGGAAATATGGAATGACAACAC-AAGGATTTTTGCATT
**
2211464 GAAATAAAAAGTTGGGACATAATATAATTAGTAGGAATACTTTT
65 GAAATAAAAAGTTGGGACATAATATAATTAGTAGGAATACTTGG
2211508 TCTTTAGTAGTTAAAATTACCAGTTCTTGGAAATATGGAATGACAACAC-AGGATTTTTGCATTG
1 TCTTTAGTAGTTAAAATTACCAGTTCTTGGAAATATGGAATGACAACACAAGGATTTTTGCATTG
**
2211572 GCATAAAAA-TTGGGACATAATATAATTAGTAGGAAT
66 AAATAAAAAGTTGGGACATAATATAATTAGTAGGAAT
2211608 GGATTGGTCT
Statistics
Matches: 97, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
106 27 0.28
107 21 0.22
109 49 0.51
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (108 bp):
TCTTTAGTAGTTAAAATTACCAGTTCTTGGAAATATGGAATGACAACACAAGGATTTTTGCATTG
AAATAAAAAGTTGGGACATAATATAATTAGTAGGAATACTTGG
Found at i:2213054 original size:2 final size:2
Alignment explanation
Indices: 2213047--2213071 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2213037 TATTCTGCTT
2213047 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2213072 TATTCAGCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2215812 original size:6 final size:6
Alignment explanation
Indices: 2215801--2215827 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2215791 GCAGTGAACG
2215801 TCTGCT TCTGCT TCTGCT TCTGCT TCT
1 TCTGCT TCTGCT TCTGCT TCTGCT TCT
2215828 ACCTCGAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.33, G:0.15, T:0.52
Consensus pattern (6 bp):
TCTGCT
Found at i:2217263 original size:3 final size:3
Alignment explanation
Indices: 2217255--2217279 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2217245 CTAACATAAC
2217255 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
2217280 AATTATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2233374 original size:3 final size:3
Alignment explanation
Indices: 2233356--2233431 Score: 68
Period size: 3 Copynumber: 25.0 Consensus size: 3
2233346 GAGCTGGAGG
*
2233356 AGA AAA AGA AGCA AGA AGA AGA AGCA A-A A-A AGA AGCA AGA AGA AGA
1 AGA AGA AGA AG-A AGA AGA AGA AG-A AGA AGA AGA AG-A AGA AGA AGA
* *
2233402 AGA AGA AG- AGA AAA AGA AGCA AAA AGA AGA
1 AGA AGA AGA AGA AGA AGA AG-A AGA AGA AGA
2233432 GGAGAAAGCT
Statistics
Matches: 61, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
2 6 0.10
3 45 0.74
4 10 0.16
ACGTcount: A:0.68, C:0.05, G:0.26, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:2233389 original size:24 final size:24
Alignment explanation
Indices: 2233358--2233403 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
2233348 GCTGGAGGAG
2233358 AAAAAGAAGCAAGAAGAAGAAGCA
1 AAAAAGAAGCAAGAAGAAGAAGCA
2233382 AAAAAGAAGCAAGAAGAAGAAG
1 AAAAAGAAGCAAGAAGAAGAAG
2233404 AAGAAGAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.67, C:0.07, G:0.26, T:0.00
Consensus pattern (24 bp):
AAAAAGAAGCAAGAAGAAGAAGCA
Found at i:2233404 original size:30 final size:30
Alignment explanation
Indices: 2233361--2233431 Score: 108
Period size: 30 Copynumber: 2.3 Consensus size: 30
2233351 GGAGGAGAAA
2233361 AAGAAGCAAGAAGAAGAAGCA-AAAAAGAAGC
1 AAGAAG-AAGAAGAAGAAG-AGAAAAAGAAGC
2233392 AAGAAGAAGAAGAAGAAGAGAAAAAGAAGC
1 AAGAAGAAGAAGAAGAAGAGAAAAAGAAGC
*
2233422 AAAAAGAAGA
1 AAGAAGAAGA
2233432 GGAGAAAGCT
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
29 1 0.03
30 31 0.82
31 6 0.16
ACGTcount: A:0.68, C:0.06, G:0.27, T:0.00
Consensus pattern (30 bp):
AAGAAGAAGAAGAAGAAGAGAAAAAGAAGC
Found at i:2233413 original size:24 final size:24
Alignment explanation
Indices: 2233362--2233437 Score: 84
Period size: 24 Copynumber: 3.2 Consensus size: 24
2233352 GAGGAGAAAA
*
2233362 AGAAGCAAGAAGAAGAAGCAA-AAA
1 AGAAGCAAGAAGAAGAAG-AAGAAG
2233386 AGAAGCAAGAAGAAGAAGAAGAAG
1 AGAAGCAAGAAGAAGAAGAAGAAG
* * *
2233410 AGAA-AAAGAAGCAAAAAGAAGAGG
1 AGAAGCAAGAAG-AAGAAGAAGAAG
2233434 AGAA
1 AGAA
2233438 AGCTAAAGAG
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
23 8 0.17
24 38 0.83
ACGTcount: A:0.66, C:0.05, G:0.29, T:0.00
Consensus pattern (24 bp):
AGAAGCAAGAAGAAGAAGAAGAAG
Found at i:2239972 original size:24 final size:22
Alignment explanation
Indices: 2239945--2239988 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
2239935 TTAATATATA
*
2239945 TTTTTAATTTTAATTTCTTATTGC
1 TTTTT-ATTTTAAATT-TTATTGC
2239969 TTTTTATTTTAAATTTTATT
1 TTTTTATTTTAAATTTTATT
2239989 TTCTATTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 9 0.47
24 5 0.26
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTTTATTTTAAATTTTATTGC
Found at i:2242994 original size:199 final size:199
Alignment explanation
Indices: 2242755--2243152 Score: 769
Period size: 199 Copynumber: 2.0 Consensus size: 199
2242745 AGGTACACAC
2242755 TCTCCAGCTATCTGATCTCATAGGACAATTGCTACTTGTGTCCTGCATTTCAGTAATTAAATAAT
1 TCTCCAGCTATCTGATCTCATAGGACAATTGCTACTTGTGTCCTGCATTTCAGTAATTAAATAAT
* * *
2242820 AGTAATATAAATGAATTCTACCTGTCTATTTGTGTACAAACCGTATAAAAGTCCATTAAGGATGT
66 AGTAATATAAATGAATTCAACCTATCTACTTGTGTACAAACCGTATAAAAGTCCATTAAGGATGT
2242885 CAAGAAAATTTCAAATTAGATTTTGTGATTACCTATCTACTTGATTAATTATTATTACTCATAAT
131 CAAGAAAATTTCAAATTAGATTTTGTGATTACCTATCTACTTGATTAATTATTATTACTCATAAT
2242950 GACA
196 GACA
2242954 TCTCCAGCTATCTGATCTCATAGGACAATTGCTACTTGTGTCCTGCATTTCAGTAATTAAATAAT
1 TCTCCAGCTATCTGATCTCATAGGACAATTGCTACTTGTGTCCTGCATTTCAGTAATTAAATAAT
2243019 AGTAATATAAATGAATTCAACCTATCTACTTGTGTACAAACCGTATAAAAGTCCATTAAGGATGT
66 AGTAATATAAATGAATTCAACCTATCTACTTGTGTACAAACCGTATAAAAGTCCATTAAGGATGT
2243084 CAAGAAAATTTCAAATTAGATTTTGTGATTACCTATCTACTTGATTAATTATTATTACTCATAAT
131 CAAGAAAATTTCAAATTAGATTTTGTGATTACCTATCTACTTGATTAATTATTATTACTCATAAT
2243149 GACA
196 GACA
2243153 CTTGTCATCT
Statistics
Matches: 196, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
199 196 1.00
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (199 bp):
TCTCCAGCTATCTGATCTCATAGGACAATTGCTACTTGTGTCCTGCATTTCAGTAATTAAATAAT
AGTAATATAAATGAATTCAACCTATCTACTTGTGTACAAACCGTATAAAAGTCCATTAAGGATGT
CAAGAAAATTTCAAATTAGATTTTGTGATTACCTATCTACTTGATTAATTATTATTACTCATAAT
GACA
Found at i:2243289 original size:15 final size:14
Alignment explanation
Indices: 2243269--2243299 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
2243259 AAATGATATT
2243269 ATAATTAAAATAATA
1 ATAATTAAAA-AATA
2243284 ATAATTAAAAAATA
1 ATAATTAAAAAATA
2243298 AT
1 AT
2243300 GAGTTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
ATAATTAAAAAATA
Found at i:2249749 original size:43 final size:44
Alignment explanation
Indices: 2249696--2249793 Score: 110
Period size: 44 Copynumber: 2.2 Consensus size: 44
2249686 GACTGGATTG
* *
2249696 TAGGGATTGTGGGATT-GATT-TTAGGTATTACAGGACTAATTTT
1 TAGGCATTGTGGGATTGGATTGTGAGG-ATTACAGGACTAATTTT
* * * *
2249739 TAGGCATTGTGTGATTGGGTTGTGAGGATTACATGACTCATTTT
1 TAGGCATTGTGGGATTGGATTGTGAGGATTACAGGACTAATTTT
*
2249783 TAGGTATTGTG
1 TAGGCATTGTG
2249794 TGACTAGTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
43 14 0.30
44 28 0.61
45 4 0.09
ACGTcount: A:0.22, C:0.06, G:0.30, T:0.42
Consensus pattern (44 bp):
TAGGCATTGTGGGATTGGATTGTGAGGATTACAGGACTAATTTT
Found at i:2249820 original size:23 final size:23
Alignment explanation
Indices: 2249794--2249837 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
2249784 AGGTATTGTG
*
2249794 TGACTAGTTTGTTAAGCATTGCT
1 TGACTAGCTTGTTAAGCATTGCT
*
2249817 TGACTAGCTTGTTAGGCATTG
1 TGACTAGCTTGTTAAGCATTG
2249838 TGTTACAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.14, G:0.25, T:0.41
Consensus pattern (23 bp):
TGACTAGCTTGTTAAGCATTGCT
Found at i:2252124 original size:29 final size:29
Alignment explanation
Indices: 2252092--2252148 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
2252082 AAATATTTAT
*
2252092 AATATCAGTCGTAGCAAAACAAGATATAC
1 AATATCAGTAGTAGCAAAACAAGATATAC
** * *
2252121 AATATTTGTAGTAGCTAAGCAAGATATA
1 AATATCAGTAGTAGCAAAACAAGATATA
2252149 TTAAATATCC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.46, C:0.12, G:0.16, T:0.26
Consensus pattern (29 bp):
AATATCAGTAGTAGCAAAACAAGATATAC
Found at i:2256333 original size:275 final size:274
Alignment explanation
Indices: 2255828--2256342 Score: 685
Period size: 275 Copynumber: 1.9 Consensus size: 274
2255818 AGATAGAGTA
* * * * *
2255828 ATCTATCTATAGATGTTCATCTAAATTGCCTTCACTTGCTTCAACAAACAAGTCATGCAATGCCT
1 ATCTATCAATAAATGTTCATCCAAATTACCTTCACATGCTTCAACAAACAAGTCATGCAATGCCT
* * ** *
2255893 ACTAACTAGTCACGCGATACCCTATCAACAGGTCATGCAATGCTTACACCCCATTCACATAATGC
66 ACCAACTAGTCACGCGATACCCTATCAACAAGTCACACAATGCTTACACCCCATTCACACAATGC
* **
2255958 CTAAGTTACACAATGACTAAAAATCAGTCATACAATACCTTAATTACACAATGAATATCAATTAG
131 CTAAGTTACACAATGACTAAAAATCAGGCATACAATACCTTAATTACACAATGAATATCAACAAG
* * * *
2256023 CCATGCAATACCCTATCTATAGATAATGCTATCTATCGATAGTTTCTGAGTCTCTTTGGTTTGCA
196 CCA-GCAATACCCTATCAATAAATAATGATATCTATCAATAGTTTCTGAGTCTCTTTGGTTTGCA
2256088 AAGCTTTTGTGTGGC
260 AAGCTTTTGTGTGGC
*
2256103 ATCTATCAATAAATTTTCATCCAAATTACCTTCACATGCTTCAACAAACAAGTCATGCAATGCCT
1 ATCTATCAATAAATGTTCATCCAAATTACCTTCACATGCTTCAACAAACAAGTCATGCAATGCCT
* *
2256168 ACCAACTAGTCACGTGATACCCTATCAACAAGTCACATAATGAC-TACACCCCATTCACACAATG
66 ACCAACTAGTCACGCGATACCCTATCAACAAGTCACACAATG-CTTACACCCCATTCACACAATG
* * * *** * *
2256232 CCTAAGTTATACAATGACTAAATA-CTAGGCATATAATGTTTTAGTTACACAATGACTATCAACC
130 CCTAAGTTACACAATGACTAAAAATC-AGGCATACAATACCTTAATTACACAATGAATATCAA-C
* * *
2256296 AAGCACA-CAGTGCCCTATCAATAAATAGTGATATCTATCAATAGTTT
193 AAGC-CAGCAATACCCTATCAATAAATAATGATATCTATCAATAGTTT
2256343 TCAAATATTT
Statistics
Matches: 205, Mismatches: 31, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
274 1 0.00
275 198 0.97
276 4 0.02
277 2 0.01
ACGTcount: A:0.35, C:0.24, G:0.11, T:0.30
Consensus pattern (274 bp):
ATCTATCAATAAATGTTCATCCAAATTACCTTCACATGCTTCAACAAACAAGTCATGCAATGCCT
ACCAACTAGTCACGCGATACCCTATCAACAAGTCACACAATGCTTACACCCCATTCACACAATGC
CTAAGTTACACAATGACTAAAAATCAGGCATACAATACCTTAATTACACAATGAATATCAACAAG
CCAGCAATACCCTATCAATAAATAATGATATCTATCAATAGTTTCTGAGTCTCTTTGGTTTGCAA
AGCTTTTGTGTGGC
Found at i:2257936 original size:27 final size:27
Alignment explanation
Indices: 2257874--2257996 Score: 122
Period size: 27 Copynumber: 4.5 Consensus size: 27
2257864 TTCCTTTTGA
* *
2257874 GGTGTGTAACAACTACATTTTTTAACAA
1 GGTGTGTAACAACTA-AATTTTTAACAT
***
2257902 GACATGTAACAACTAAATTTTTAACAT
1 GGTGTGTAACAACTAAATTTTTAACAT
* *
2257929 GGTGTGTAACAATTATATTTTTCAACAT
1 GGTGTGTAACAACTAAATTTTT-AACAT
* * *
2257957 AGTGTGTAATAACTAAATTTTCAACAT
1 GGTGTGTAACAACTAAATTTTTAACAT
*
2257984 GATGTGTAA-AACT
1 GGTGTGTAACAACT
2257997 TACATTTTCA
Statistics
Matches: 77, Mismatches: 17, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
26 4 0.05
27 39 0.51
28 34 0.44
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (27 bp):
GGTGTGTAACAACTAAATTTTTAACAT
Found at i:2257965 original size:55 final size:55
Alignment explanation
Indices: 2257874--2258009 Score: 161
Period size: 55 Copynumber: 2.5 Consensus size: 55
2257864 TTCCTTTTGA
* * *
2257874 GGTGTGTAACAACTACATTTTTTAACAAGACATGTAACAACTAAATTTTTAACAT
1 GGTGTGTAACAATTACATTTTTCAACAAGACATGTAACAACTAAATTTTCAACAT
* ** *
2257929 GGTGTGTAACAATTATATTTTTCAACATAG-TGTGTAATAACTAAATTTTCAACAT
1 GGTGTGTAACAATTACATTTTTCAACA-AGACATGTAACAACTAAATTTTCAACAT
*
2257984 GATGTGTAA-AACTTACA-TTTTCAACA
1 GGTGTGTAACAA-TTACATTTTTCAACA
2258010 CGATTTTTTG
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
54 11 0.16
55 57 0.81
56 2 0.03
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (55 bp):
GGTGTGTAACAATTACATTTTTCAACAAGACATGTAACAACTAAATTTTCAACAT
Found at i:2258003 original size:27 final size:28
Alignment explanation
Indices: 2257906--2258009 Score: 110
Period size: 27 Copynumber: 3.8 Consensus size: 28
2257896 TAACAAGACA
* *
2257906 TGTAACAAC-TAAATTTTTAACATGGTG
1 TGTAACAACTTAAATTTTCAACATGATG
*
2257933 TGTAACAA-TTATATTTTTCAACAT-AGTG
1 TGTAACAACTTA-AATTTTCAACATGA-TG
*
2257961 TGTAATAAC-TAAATTTTCAACATGATG
1 TGTAACAACTTAAATTTTCAACATGATG
*
2257988 TGTAA-AACTTACATTTTCAACA
1 TGTAACAACTTAAATTTTCAACA
2258010 CGATTTTTTG
Statistics
Matches: 65, Mismatches: 6, Indels: 12
0.78 0.07 0.14
Matches are distributed among these distances:
26 3 0.05
27 40 0.62
28 22 0.34
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.38
Consensus pattern (28 bp):
TGTAACAACTTAAATTTTCAACATGATG
Found at i:2262370 original size:45 final size:45
Alignment explanation
Indices: 2262294--2262476 Score: 222
Period size: 45 Copynumber: 4.1 Consensus size: 45
2262284 TTACACATCG
* * * * **
2262294 TGTACAGAAACATGTTACACGTCATTATTAGGTTGTTACACGCCA
1 TGTACAAAAACGTGTGACACGCCATGGTTAGGTTGTTACACGCCA
* *
2262339 TGTACAAAAACGTGTGACATGCCATGGTTAGGTTGTTACACACCA
1 TGTACAAAAACGTGTGACACGCCATGGTTAGGTTGTTACACGCCA
* * * * *
2262384 TGTACAAAAACATATTACACGCCATGATTAGGTTGTTACACGTCA
1 TGTACAAAAACGTGTGACACGCCATGGTTAGGTTGTTACACGCCA
* * *
2262429 TGTACAAAGACGTGTGACACGCCATAGTTAAGTTGTTACACGCCA
1 TGTACAAAAACGTGTGACACGCCATGGTTAGGTTGTTACACGCCA
2262474 TGT
1 TGT
2262477 TAAAAAAATA
Statistics
Matches: 115, Mismatches: 23, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 115 1.00
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (45 bp):
TGTACAAAAACGTGTGACACGCCATGGTTAGGTTGTTACACGCCA
Found at i:2262483 original size:90 final size:90
Alignment explanation
Indices: 2262282--2262476 Score: 282
Period size: 90 Copynumber: 2.2 Consensus size: 90
2262272 CATGCCAGGA
* * * * * *
2262282 TGTTACACATCGTGTACAGAAACATGTTACACGTCATTATTAGGTTGTTACACGCCATGTACAAA
1 TGTTACACACCATGTACAAAAACATATTACACGCCATGATTAGGTTGTTACACGCCATGTACAAA
* * *
2262347 AACGTGTGACATGCCATGGTTAGGT
66 AACGTGTGACACGCCATAGTTAAGT
*
2262372 TGTTACACACCATGTACAAAAACATATTACACGCCATGATTAGGTTGTTACACGTCATGTACAAA
1 TGTTACACACCATGTACAAAAACATATTACACGCCATGATTAGGTTGTTACACGCCATGTACAAA
*
2262437 GACGTGTGACACGCCATAGTTAAGT
66 AACGTGTGACACGCCATAGTTAAGT
*
2262462 TGTTACACGCCATGT
1 TGTTACACACCATGT
2262477 TAAAAAAATA
Statistics
Matches: 93, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
90 93 1.00
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (90 bp):
TGTTACACACCATGTACAAAAACATATTACACGCCATGATTAGGTTGTTACACGCCATGTACAAA
AACGTGTGACACGCCATAGTTAAGT
Found at i:2262505 original size:29 final size:29
Alignment explanation
Indices: 2262460--2262637 Score: 183
Period size: 29 Copynumber: 6.3 Consensus size: 29
2262450 CCATAGTTAA
2262460 GTTGTTACACGCCATGTTAAAAAAATACT
1 GTTGTTACACGCCATGTTAAAAAAATACT
*
2262489 GTGGTTACACGCCATGTTAAAAAAATACT
1 GTTGTTACACGCCATGTTAAAAAAATACT
* *
2262518 GTGGTTACACGCCATG-T-ACAAAA-AC-
1 GTTGTTACACGCCATGTTAAAAAAATACT
* *
2262543 -ATGTTACACTCCATGGTTAAAAAAA-A--
1 GTTGTTACACGCCAT-GTTAAAAAAATACT
2262569 GTTGTTACACGCCATGTTGAAAAAAAATACT
1 GTTGTTACACGCCATGTT--AAAAAAATACT
* * * * *
2262600 GTTATTACACTCCATCTTGAAAAAATATT
1 GTTGTTACACGCCATGTTAAAAAAATACT
2262629 GTTGTTACA
1 GTTGTTACA
2262638 TGTCATATTC
Statistics
Matches: 126, Mismatches: 14, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
24 11 0.09
25 1 0.01
26 6 0.05
27 23 0.18
28 8 0.06
29 62 0.49
31 15 0.12
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (29 bp):
GTTGTTACACGCCATGTTAAAAAAATACT
Found at i:2262608 original size:82 final size:81
Alignment explanation
Indices: 2262462--2262614 Score: 211
Period size: 82 Copynumber: 1.9 Consensus size: 81
2262452 ATAGTTAAGT
*
2262462 TGTTACACGCCATGTTAAAAAAATACTGTGGTTACACGCCATGTTAAAAAAATACTGTGGTTACA
1 TGTTACACGCCATGTTAAAAAAATAC-GTGGTTACACGCCATGTTAAAAAAATACTGTGATTACA
2262527 CGCCATGTACAAAAACA
65 CGCCATGTACAAAAACA
* * *
2262544 TGTTACACTCCATGGTTAAAAAAA-A-GTTGTTACACGCCATGTTGAAAAAAAATACTGTTATTA
1 TGTTACACGCCAT-GTTAAAAAAATACGTGGTTACACGCCATGTT--AAAAAAATACTGTGATTA
*
2262607 CACTCCAT
63 CACGCCAT
2262615 CTTGAAAAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
80 17 0.27
82 36 0.57
83 10 0.16
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (81 bp):
TGTTACACGCCATGTTAAAAAAATACGTGGTTACACGCCATGTTAAAAAAATACTGTGATTACAC
GCCATGTACAAAAACA
Found at i:2263073 original size:23 final size:23
Alignment explanation
Indices: 2263047--2263090 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
2263037 TGGTATCTTC
*
2263047 AAAGTGCTAGAAAGAGAAATCTG
1 AAAGTGCGAGAAAGAGAAATCTG
*
2263070 AAAGTGCGAGAGAGAGAAATC
1 AAAGTGCGAGAAAGAGAAATC
2263091 GAGAGCATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.48, C:0.09, G:0.30, T:0.14
Consensus pattern (23 bp):
AAAGTGCGAGAAAGAGAAATCTG
Found at i:2264648 original size:23 final size:24
Alignment explanation
Indices: 2264614--2264665 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
2264604 TTAAAAGATT
*
2264614 AAAAAATGAAAATGAAAATAAAGA
1 AAAAAATGAAAAAGAAAATAAAGA
* *
2264638 AAAAAAT-AAAAAGAAAGTAAAGT
1 AAAAAATGAAAAAGAAAATAAAGA
2264661 AAAAA
1 AAAAA
2264666 TTATAATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 18 0.72
24 7 0.28
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.12
Consensus pattern (24 bp):
AAAAAATGAAAAAGAAAATAAAGA
Found at i:2264803 original size:121 final size:121
Alignment explanation
Indices: 2264582--2264834 Score: 307
Period size: 121 Copynumber: 2.1 Consensus size: 121
2264572 TTAATGTTTC
2264582 AAAATTTTAAAGAAAATACAAATTAAAAGATTAAAAAATGAAAATGAAAATAAAGAAAAAAATAA
1 AAAATTTTAAAGAAAATACAAATTAAAAGATTAAAAAATGAAAATGAAAATAAAGAAAAAAATAA
* * *
2264647 AAAGAAAGTAAAGTAAAAATTATAATAATAATTTAATAATAAA-TAAGTAAAATT-TT
66 AAAGAAAGTAAAATAAAAATCATAATAACAATTTAATAATAAATTAA-T-AAATTATT
* * * *
2264703 AAAATTTTAAAGAAAATAGAAATT-TAATATTAAAAAATGAAAAATGAAAAT-AGGAAAAAAATA
1 AAAATTTTAAAGAAAATACAAATTAAAAGATTAAAAAATG-AAAATGAAAATAAAGAAAAAAATA
** * * * * *
2264766 AAACTAAATTAAAATAAAAAATCATATTGACATTTTAATAGTAAATTAATAAATTATT
65 AAAAGAAAGTAAAAT-AAAAATCATAATAACAATTTAATAATAAATTAATAAATTATT
*
2264824 AATATTTTAAA
1 AAAATTTTAAA
2264835 ATTTTAATGA
Statistics
Matches: 113, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
120 40 0.35
121 70 0.62
122 3 0.03
ACGTcount: A:0.63, C:0.02, G:0.07, T:0.28
Consensus pattern (121 bp):
AAAATTTTAAAGAAAATACAAATTAAAAGATTAAAAAATGAAAATGAAAATAAAGAAAAAAATAA
AAAGAAAGTAAAATAAAAATCATAATAACAATTTAATAATAAATTAATAAATTATT
Found at i:2266110 original size:23 final size:22
Alignment explanation
Indices: 2266067--2266110 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
2266057 AAATACAAAC
* **
2266067 ATATTTTTATTATAATTTAATA
1 ATATTTTTATTAAAAGATAATA
2266089 ATATTTTGTATTAAAAGATAAT
1 ATATTTT-TATTAAAAGATAAT
2266111 TAAACCATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (22 bp):
ATATTTTTATTAAAAGATAATA
Found at i:2266238 original size:45 final size:45
Alignment explanation
Indices: 2266186--2266275 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 45
2266176 TAAATAATAC
*
2266186 TAAATAATATTATTTATTACATTTATTATA-TTCAAATAATATTAT
1 TAAATAATATTATTTATAACATTTATTATAGTT-AAATAATATTAT
* * *
2266231 TAAATAATATTTTTTATAATATTTGTTATAGTTAAATAATATTAT
1 TAAATAATATTATTTATAACATTTATTATAGTTAAATAATATTAT
2266276 GATATTAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
45 38 0.95
46 2 0.05
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (45 bp):
TAAATAATATTATTTATAACATTTATTATAGTTAAATAATATTAT
Found at i:2267915 original size:19 final size:19
Alignment explanation
Indices: 2267891--2267932 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
2267881 AAATGAGAAA
2267891 TAAAAAA-TCCAACAAAAAG
1 TAAAAAATTCCAA-AAAAAG
*
2267910 TAAAAAATTCCAAAAAAAT
1 TAAAAAATTCCAAAAAAAG
2267929 TAAA
1 TAAA
2267933 CCACTAGACC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.69, C:0.12, G:0.02, T:0.17
Consensus pattern (19 bp):
TAAAAAATTCCAAAAAAAG
Found at i:2268302 original size:27 final size:27
Alignment explanation
Indices: 2268268--2268346 Score: 106
Period size: 27 Copynumber: 2.9 Consensus size: 27
2268258 TAATATAAAT
*
2268268 AATGTATTATTTTGATAAAAGTAATA-C
1 AATGTATTATTTTGATAAAA-TAAAACC
**
2268295 AATGTATTATTTTGATGTAATAAAACC
1 AATGTATTATTTTGATAAAATAAAACC
2268322 AATGTATTATTTTGATGAAAATAAA
1 AATGTATTATTTTGAT-AAAATAAA
2268347 GCTTGCAGAG
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
26 4 0.09
27 35 0.78
28 6 0.13
ACGTcount: A:0.44, C:0.04, G:0.11, T:0.41
Consensus pattern (27 bp):
AATGTATTATTTTGATAAAATAAAACC
Found at i:2269925 original size:20 final size:21
Alignment explanation
Indices: 2269878--2269919 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
2269868 TATTATCCTC
2269878 ATGTTTTTAATGAAAAAGGTT
1 ATGTTTTTAATGAAAAAGGTT
2269899 ATGTTTTTAATGAAAAAGGTT
1 ATGTTTTTAATGAAAAAGGTT
2269920 CTTTTTCATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.43
Consensus pattern (21 bp):
ATGTTTTTAATGAAAAAGGTT
Found at i:2272829 original size:2 final size:2
Alignment explanation
Indices: 2272822--2272850 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2272812 TAATGGCCCA
2272822 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 A
2272851 ATTTAACTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2273212 original size:16 final size:15
Alignment explanation
Indices: 2273187--2273217 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
2273177 AACTAAAGAG
2273187 TTAAAAATAAATAAA
1 TTAAAAATAAATAAA
2273202 TTAATAAATAAATAAA
1 TTAA-AAATAAATAAA
2273218 AAATTTTGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
TTAAAAATAAATAAA
Found at i:2275989 original size:27 final size:27
Alignment explanation
Indices: 2275923--2276005 Score: 78
Period size: 27 Copynumber: 3.1 Consensus size: 27
2275913 CAAATAATAT
* * *
2275923 AAATAATGCATTATTTAGATGAAAGTA
1 AAATCATGAATTATTTTGATGAAAGTA
* * *
2275950 ATA-CAATGTATTATTTTGATGGAAGTA
1 AAATC-ATGAATTATTTTGATGAAAGTA
* *
2275977 AAATCATGAATTATTTTGATAAAAATA
1 AAATCATGAATTATTTTGATGAAAGTA
2276004 AA
1 AA
2276006 GCTTGCAAGG
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
27 43 0.98
28 1 0.02
ACGTcount: A:0.47, C:0.04, G:0.13, T:0.36
Consensus pattern (27 bp):
AAATCATGAATTATTTTGATGAAAGTA
Found at i:2279038 original size:3 final size:3
Alignment explanation
Indices: 2279030--2279057 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2279020 TTTTAGTGTA
2279030 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2279058 TCTTGAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2280838 original size:4 final size:4
Alignment explanation
Indices: 2280829--2280853 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2280819 CTATTTTTTG
2280829 TGAT TGAT TGAT TGAT TGAT TGAT T
1 TGAT TGAT TGAT TGAT TGAT TGAT T
2280854 AGAGCCCACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TGAT
Found at i:2298440 original size:27 final size:27
Alignment explanation
Indices: 2298386--2298441 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
2298376 ATGTGGTAAA
* * * *
2298386 GACGTGGCAAAACATGACATAGAGGAT
1 GACGTGACAAAACATGACACAAAAGAT
*
2298413 GACGTGACAAAACATGATACAAAAGAT
1 GACGTGACAAAACATGACACAAAAGAT
2298440 GA
1 GA
2298442 TGTAGTGAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.46, C:0.14, G:0.25, T:0.14
Consensus pattern (27 bp):
GACGTGACAAAACATGACACAAAAGAT
Found at i:2298627 original size:27 final size:28
Alignment explanation
Indices: 2298597--2298657 Score: 81
Period size: 27 Copynumber: 2.2 Consensus size: 28
2298587 TGACACAGTG
* *
2298597 AAACACA-ACACAGAAGGTGATGTGGCA
1 AAACACAGACACAGAAGATGATGTGACA
*
2298624 AAACA-AGACACATAAGATGATGTGACA
1 AAACACAGACACAGAAGATGATGTGACA
2298651 AAACACA
1 AAACACA
2298658 TTATAGACAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 1 0.03
27 27 0.93
28 1 0.03
ACGTcount: A:0.51, C:0.18, G:0.20, T:0.11
Consensus pattern (28 bp):
AAACACAGACACAGAAGATGATGTGACA
Found at i:2302784 original size:12 final size:12
Alignment explanation
Indices: 2302767--2302791 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2302757 ATGCTAGTTA
2302767 AAGAGAAAAAAG
1 AAGAGAAAAAAG
2302779 AAGAGAAAAAAG
1 AAGAGAAAAAAG
2302791 A
1 A
2302792 CACAAAGCAC
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:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (12 bp):
AAGAGAAAAAAG
Found at i:2302983 original size:31 final size:32
Alignment explanation
Indices: 2302934--2303020 Score: 122
Period size: 31 Copynumber: 2.7 Consensus size: 32
2302924 TGAAAAGGTC
*
2302934 AAGCATAACCTCACATTGCCTTTTCATGGGATA
1 AAGCATAA-CTCACATTGCCTTTTCATAGGATA
* *
2302967 AAGCAT-ACTTACATTGCCTTTTCATAGGATC
1 AAGCATAACTCACATTGCCTTTTCATAGGATA
*
2302998 AAGCATAACTCACACTGCCTTTT
1 AAGCATAACTCACATTGCCTTTT
2303021 TAAAAAATAG
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
31 27 0.56
32 15 0.31
33 6 0.12
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (32 bp):
AAGCATAACTCACATTGCCTTTTCATAGGATA
Found at i:2309137 original size:2 final size:2
Alignment explanation
Indices: 2309120--2309154 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
2309110 ACTACACTGT
* *
2309120 TA TA CA TA TA TG TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2309155 GATCGATACA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2311397 original size:4 final size:4
Alignment explanation
Indices: 2311374--2311417 Score: 52
Period size: 4 Copynumber: 11.0 Consensus size: 4
2311364 AATTGTTAGT
* * * *
2311374 TATA TGTA TATG TATG TATA TATA TACA TATA TATA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
2311418 AGTTTCTAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (4 bp):
TATA
Found at i:2311399 original size:6 final size:6
Alignment explanation
Indices: 2311374--2311417 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
2311364 AATTGTTAGT
* * * *
2311374 TATATG TATATG TATGTA TATATA TACATA TATATA TATATA TA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TA
2311418 AGTTTCTAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (6 bp):
TATATA
Found at i:2313575 original size:5 final size:5
Alignment explanation
Indices: 2313565--2313589 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2313555 TAGGGTGGTG
2313565 TTTCA TTTCA TTTCA TTTCA TTTCA
1 TTTCA TTTCA TTTCA TTTCA TTTCA
2313590 AAGGTTATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (5 bp):
TTTCA
Found at i:2316691 original size:2 final size:2
Alignment explanation
Indices: 2316684--2316709 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2316674 ACAGTATTTG
2316684 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
2316710 TAGTAGAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2317565 original size:57 final size:56
Alignment explanation
Indices: 2317504--2317634 Score: 133
Period size: 56 Copynumber: 2.3 Consensus size: 56
2317494 ATTATATTAG
* * * * *
2317504 TTTTTAATATATTTAATTAGTTTTGATTTCGTGCCTCCACATA-AAAATTTATGAATT
1 TTTTTAATATAATTAATT-GTTTTGATCTCGCGCAT-CAAATATAAAATTTATGAATT
* * *
2317561 TTTTT-ATATAATTAATTTTTTTGATCTCGCGTATCAAATATTAAAATTTATGATTT
1 TTTTTAATATAATTAATTGTTTTGATCTCGCGCATCAAATA-TAAAATTTATGAATT
2317617 TTTTTAATATTAA-TAATT
1 TTTTTAATA-TAATTAATT
2317635 ATAATAAAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
54 5 0.08
55 12 0.19
56 29 0.47
57 13 0.21
58 3 0.05
ACGTcount: A:0.33, C:0.08, G:0.07, T:0.53
Consensus pattern (56 bp):
TTTTTAATATAATTAATTGTTTTGATCTCGCGCATCAAATATAAAATTTATGAATT
Found at i:2329171 original size:19 final size:21
Alignment explanation
Indices: 2329147--2329185 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
2329137 TTTAATTTAA
2329147 AATAAAAAT-ATAA-AAATAT
1 AATAAAAATAATAAGAAATAT
*
2329166 AATAAATATAATAAGAAATA
1 AATAAAAATAATAAGAAATA
2329186 AAAAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 4 0.24
21 5 0.29
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (21 bp):
AATAAAAATAATAAGAAATAT
Found at i:2329186 original size:19 final size:16
Alignment explanation
Indices: 2329145--2329189 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 16
2329135 TATTTAATTT
2329145 AAAATAAAAATATAAA
1 AAAATAAAAATATAAA
*
2329161 AATATAATAAATATAATA
1 AAAATAA-AAATATAA-A
2329179 AGAAATAAAAA
1 A-AAATAAAAA
2329190 ATTATTTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 6 0.25
17 8 0.33
18 5 0.21
19 5 0.21
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (16 bp):
AAAATAAAAATATAAA
Found at i:2335682 original size:2 final size:2
Alignment explanation
Indices: 2335675--2335703 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2335665 ATAAGTACAT
2335675 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2335704 GCGCTTGGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2336455 original size:26 final size:27
Alignment explanation
Indices: 2336417--2336470 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 27
2336407 CCTTGTTGCC
2336417 AGATAATATACAGATACAGAGATCGAT
1 AGATAATATACAGATACAGAGATCGAT
* *
2336444 AGATAA-ATACAGATACAGGGATTGAT
1 AGATAATATACAGATACAGAGATCGAT
2336470 A
1 A
2336471 AATACAGGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 19 0.76
27 6 0.24
ACGTcount: A:0.48, C:0.09, G:0.20, T:0.22
Consensus pattern (27 bp):
AGATAATATACAGATACAGAGATCGAT
Found at i:2336473 original size:22 final size:24
Alignment explanation
Indices: 2336417--2336477 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 24
2336407 CCTTGTTGCC
2336417 AGATAATATACAGATACAGAGATCGAT
1 AGATAA-ATACAGATACAGAGA--GAT
2336444 AGATAAATACAGATACAG-G-GAT
1 AGATAAATACAGATACAGAGAGAT
*
2336466 TGATAAATACAG
1 AGATAAATACAG
2336478 GGAGGAAGGG
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
22 14 0.42
25 1 0.03
26 12 0.36
27 6 0.18
ACGTcount: A:0.49, C:0.10, G:0.20, T:0.21
Consensus pattern (24 bp):
AGATAAATACAGATACAGAGAGAT
Found at i:2343236 original size:19 final size:20
Alignment explanation
Indices: 2343200--2343241 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
2343190 TTATATTAAA
*
2343200 AATATATAAAAAT-TAAAAT
1 AATATATAAAAATAAAAAAT
* *
2343219 AATATATACAAGTAAAAAAT
1 AATATATAAAAATAAAAAAT
2343239 AAT
1 AAT
2343242 TAATAAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (20 bp):
AATATATAAAAATAAAAAAT
Found at i:2343239 original size:17 final size:18
Alignment explanation
Indices: 2343197--2343239 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
2343187 TAATTATATT
*
2343197 AAAAATATATAAAAATTA
1 AAAAATATATAAAAAGTA
*
2343215 AAATAATATAT-ACAAGTA
1 AAA-AATATATAAAAAGTA
2343233 AAAAATA
1 AAAAATA
2343240 ATTAATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 4 0.18
18 11 0.50
19 7 0.32
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (18 bp):
AAAAATATATAAAAAGTA
Found at i:2344102 original size:30 final size:30
Alignment explanation
Indices: 2344068--2344126 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
2344058 AGAAGTTAAT
2344068 GAAGAGATTCAAAATGATCATAAAAATCAA
1 GAAGAGATTCAAAATGATCATAAAAATCAA
*
2344098 GAAGAGATTCAAAATGATCATAGAAATCA
1 GAAGAGATTCAAAATGATCATAAAAATCA
2344127 TAATGAAGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.54, C:0.10, G:0.15, T:0.20
Consensus pattern (30 bp):
GAAGAGATTCAAAATGATCATAAAAATCAA
Found at i:2345870 original size:18 final size:19
Alignment explanation
Indices: 2345847--2345885 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
2345837 CAGCATTACA
2345847 AGTTTA-ATTAATTATATG
1 AGTTTACATTAATTATATG
*
2345865 AGTTTATCTTTAATTATATG
1 AGTTTA-CATTAATTATATG
2345885 A
1 A
2345886 AATTAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
20 12 0.67
ACGTcount: A:0.36, C:0.03, G:0.10, T:0.51
Consensus pattern (19 bp):
AGTTTACATTAATTATATG
Found at i:2346525 original size:336 final size:336
Alignment explanation
Indices: 2345849--2346565 Score: 861
Period size: 343 Copynumber: 2.1 Consensus size: 336
2345839 GCATTACAAG
* *
2345849 TTTAATTAAT--TATATGAGTTTATCTTTAATTATATGAAATTAAAAAAAAATTAAGTTTCAAAA
1 TTTAATTAATAATATATGAGTTTATCCTTAATTAGATGAAATTAAAAAAAAATTAAGTTTCAAAA
* ** *
2345912 CTATTGTAATATCATAACTTCTCTTTATATATATATATTATAAGTTTATATAAATATTGGTATTT
66 CTATTCTAATATCATAACTTCTCTTTATATATATATATTATAAGTTTATATAAATAAAGGTATAT
* **
2345977 ATATTATAATTAATAATTTTATAAGTTATAATTTTTGTATTATTAACACAAAATAGAAAGGAAAT
131 ACATTATAATTAATAATTTTATAAGTTATAATTTTTGTAACATTAACACAAAATAGAAAGGAAAT
* * * * * ** *
2346042 ATGTTTATATTTAAAATATAGATACTAAAGGTATATGTATAATAGTAATTATATTCATTATCAAT
196 ATGTTTACATTTAAAATATAGAAACTAAAAGTATATATATAATAATAATTATATTCACCATAAAT
* *
2346107 TAACACAATATATAAAGTATATATATATTTATACAAAGATATTACACGTTAAGTAATAATCATAG
261 TAACACAATATATAAAG-ATATATATA-TTATACAAAGACATTACAAGTTAAGTAATAATCATAG
2346172 TTTCATGAATTAA
324 TTTCATGAATTAA
2346185 TTTAATTAATAATATAT-A-TTTATCCTTAATTAGAT--AA-TATAAAAAAAATTAAGTTTCAAA
1 TTTAATTAATAATATATGAGTTTATCCTTAATTAGATGAAATTA-AAAAAAAATTAAGTTTCAAA
* * * * *
2346245 ACTATTCTAATCTTATAACTTCTTTTTAGATATATATATATATATATATACTATTTTATATACAT
65 ACTATTCTAATATCATAACTTC--TCT---T-TATATATATATAT-TATA--AGTTTATATAAAT
* *
2346310 AAAGGTATATACATTATAATTAATAATTTTATAAGTTATAATTTTTGTAACGTTAATACAAAATA
121 AAAGGTATATACATTATAATTAATAATTTTATAAGTTATAATTTTTGTAACATTAACACAAAATA
* * * *
2346375 GAAAGTAAATGTGTTTACATTTAAAGTATATAAACTAAAAGTATATATAT-ATAATAATTATATT
186 GAAAGGAAATATGTTTACATTTAAAATATAGAAACTAAAAGTATATATATAATAATAATTATA-T
* * * * *
2346439 TC-CCATAAATTAACATATTATATAAAG-TATATCTA-T-TA-AAAGACATTATAAGTTAATTAA
250 TCACCATAAATTAACACAATATATAAAGATATATATATTATACAAAGACATTACAAGTTAAGTAA
*
2346499 TAATCATAGTTTCATGATTTAA
315 TAATCATAGTTTCATGAATTAA
** *
2346521 TTTAATTAATAATATA--AGTTTATTTTTAATTACATGAAATTAAAA
1 TTTAATTAATAATATATGAGTTTATCCTTAATTAGATGAAATTAAAA
2346566 CAAACATAAT
Statistics
Matches: 325, Mismatches: 39, Indels: 32
0.82 0.10 0.08
Matches are distributed among these distances:
333 2 0.01
334 41 0.13
335 1 0.00
336 96 0.30
337 3 0.01
338 11 0.03
339 3 0.01
340 20 0.06
341 4 0.01
342 31 0.10
343 113 0.35
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (336 bp):
TTTAATTAATAATATATGAGTTTATCCTTAATTAGATGAAATTAAAAAAAAATTAAGTTTCAAAA
CTATTCTAATATCATAACTTCTCTTTATATATATATATTATAAGTTTATATAAATAAAGGTATAT
ACATTATAATTAATAATTTTATAAGTTATAATTTTTGTAACATTAACACAAAATAGAAAGGAAAT
ATGTTTACATTTAAAATATAGAAACTAAAAGTATATATATAATAATAATTATATTCACCATAAAT
TAACACAATATATAAAGATATATATATTATACAAAGACATTACAAGTTAAGTAATAATCATAGTT
TCATGAATTAA
Found at i:2369414 original size:31 final size:31
Alignment explanation
Indices: 2369341--2369413 Score: 103
Period size: 32 Copynumber: 2.4 Consensus size: 31
2369331 CTTAGAAATG
*
2369341 GAAAAGAAAAATAATTTCAAAATTTGAGAAA
1 GAAAAGAAAAATAATTCCAAAATTTGAGAAA
* *
2369372 GAAAAGGAAAAATAATTCCAAATTTTGGGAAA
1 GAAAA-GAAAAATAATTCCAAAATTTGAGAAA
2369404 -AAAAGAAAAA
1 GAAAAGAAAAA
2369414 AAGGTAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 6 0.16
31 9 0.24
32 23 0.61
ACGTcount: A:0.62, C:0.04, G:0.15, T:0.19
Consensus pattern (31 bp):
GAAAAGAAAAATAATTCCAAAATTTGAGAAA
Found at i:2376246 original size:19 final size:19
Alignment explanation
Indices: 2376222--2376263 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
2376212 ATTGTCGGTG
*
2376222 ATTTTTTATATAAAATATT
1 ATTTTTTATATAAAATAAT
*
2376241 ATTTTTTTTATAAAATAAT
1 ATTTTTTATATAAAATAAT
2376260 ATTT
1 ATTT
2376264 AAAAAAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTTTTTATATAAAATAAT
Found at i:2377147 original size:30 final size:31
Alignment explanation
Indices: 2377107--2377170 Score: 103
Period size: 30 Copynumber: 2.1 Consensus size: 31
2377097 GTATTCAATC
* *
2377107 AAGCTCTTATATTTTTATTTTAAA-CTAAAT
1 AAGCCCTTATATTTTTATTTTAAATCAAAAT
2377137 AAGCCCTTATATTTTTATTTTAAATCAAAAT
1 AAGCCCTTATATTTTTATTTTAAATCAAAAT
2377168 AAG
1 AAG
2377171 TGTTTATAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 23 0.74
31 8 0.26
ACGTcount: A:0.39, C:0.11, G:0.05, T:0.45
Consensus pattern (31 bp):
AAGCCCTTATATTTTTATTTTAAATCAAAAT
Found at i:2377507 original size:29 final size:29
Alignment explanation
Indices: 2377461--2377516 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
2377451 TTAATCCAAA
*
2377461 ATAAAAGTATAAAGACTTGA-TTGAATACT
1 ATAAAAGAATAAAGACTT-ATTTGAATACT
2377490 ATAAAAGAAT-AAGAACTTATTTGAATA
1 ATAAAAGAATAAAG-ACTTATTTGAATA
2377517 TTTTTGAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 4 0.17
29 20 0.83
ACGTcount: A:0.52, C:0.05, G:0.12, T:0.30
Consensus pattern (29 bp):
ATAAAAGAATAAAGACTTATTTGAATACT
Found at i:2389586 original size:20 final size:21
Alignment explanation
Indices: 2389563--2389609 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
2389553 AAAACTCAAA
2389563 ATTAAAATTCAATTAAAA-AT
1 ATTAAAATTCAATTAAAATAT
* * *
2389583 ATTAAATTTGATTTAAAATAT
1 ATTAAAATTCAATTAAAATAT
2389604 ATTAAA
1 ATTAAA
2389610 TTAAATCATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (21 bp):
ATTAAAATTCAATTAAAATAT
Found at i:2390317 original size:15 final size:16
Alignment explanation
Indices: 2390281--2390320 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
2390271 TCAAAATAGA
2390281 ATTGTTGAAAAACTCT
1 ATTGTTGAAAAACTCT
*
2390297 AATGTTGAAAAACT-T
1 ATTGTTGAAAAACTCT
*
2390312 TTTGTTGAA
1 ATTGTTGAA
2390321 TTTTGCTTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.38, C:0.07, G:0.15, T:0.40
Consensus pattern (16 bp):
ATTGTTGAAAAACTCT
Found at i:2392624 original size:23 final size:24
Alignment explanation
Indices: 2392564--2392624 Score: 67
Period size: 23 Copynumber: 2.6 Consensus size: 24
2392554 ATCATTAGAC
*
2392564 TATTTTTATCTTTTAATAAAATAA
1 TATTTTTATCATTTAATAAAATAA
2392588 -ATTCTTTA--ATTTTAATAAAA-AA
1 TATT-TTTATCA-TTTAATAAAATAA
2392610 TATTTTTATCATTTA
1 TATTTTTATCATTTA
2392625 CTACTTAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 11
0.72 0.02 0.26
Matches are distributed among these distances:
22 6 0.19
23 20 0.65
24 5 0.16
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (24 bp):
TATTTTTATCATTTAATAAAATAA
Found at i:2394415 original size:9 final size:9
Alignment explanation
Indices: 2394401--2394445 Score: 81
Period size: 9 Copynumber: 5.0 Consensus size: 9
2394391 AGTTCCATCA
2394401 TCCTTCTTT
1 TCCTTCTTT
2394410 TCCTTCTTT
1 TCCTTCTTT
*
2394419 TCCCTCTTT
1 TCCTTCTTT
2394428 TCCTTCTTT
1 TCCTTCTTT
2394437 TCCTTCTTT
1 TCCTTCTTT
2394446 GTTTCTTCCC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 34 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (9 bp):
TCCTTCTTT
Found at i:2394695 original size:24 final size:24
Alignment explanation
Indices: 2394649--2394696 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
2394639 GGCGATAACG
* * *
2394649 GTCCCTATCCCTGTCTCTGTCTCT
1 GTCCCTATCCCTATCCCTATCTCT
*
2394673 GTCCCTCTCCCTATCCCTATCTCT
1 GTCCCTATCCCTATCCCTATCTCT
2394697 ATCTCGGCCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.06, C:0.46, G:0.08, T:0.40
Consensus pattern (24 bp):
GTCCCTATCCCTATCCCTATCTCT
Found at i:2401227 original size:55 final size:55
Alignment explanation
Indices: 2401161--2401379 Score: 206
Period size: 55 Copynumber: 4.0 Consensus size: 55
2401151 TTTTTCATCA
* * * *
2401161 TAACAACTACATTTTTCAACATAATGTGTAATAACTAAAATTTTAAAATAACGTG
1 TAACAACTACATTTTTCAACATAATGTGTAATAACTAAATTTTTAACATGACATG
* * * * * *
2401216 TAACAACTACATTTTTCTATATATTGTGTAACAACTAAATTTTTAACTTGGCATG
1 TAACAACTACATTTTTCAACATAATGTGTAATAACTAAATTTTTAACATGACATG
* * * * * *
2401271 TAATAACTATATTTTTCAATATAGTG-GAAAATGACTAAATTTTTAACATGACATG
1 TAACAACTACATTTTTCAACATAATGTG-TAATAACTAAATTTTTAACATGACATG
* * ** * * * *
2401326 TAACAATTATATTTTTCAACATAACATGCAACAATTAAATTTTTAGCATGACAT
1 TAACAACTACATTTTTCAACATAATGTGTAATAACTAAATTTTTAACATGACAT
2401380 ACAACAATTA
Statistics
Matches: 132, Mismatches: 30, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
54 1 0.01
55 130 0.98
56 1 0.01
ACGTcount: A:0.41, C:0.13, G:0.08, T:0.38
Consensus pattern (55 bp):
TAACAACTACATTTTTCAACATAATGTGTAATAACTAAATTTTTAACATGACATG
Found at i:2401231 original size:27 final size:28
Alignment explanation
Indices: 2401161--2401259 Score: 110
Period size: 28 Copynumber: 3.6 Consensus size: 28
2401151 TTTTTCATCA
* *
2401161 TAACAACTACATTTTTCAACATAATGTG
1 TAACAACTAAATTTTTCAAAATAATGTG
* * *
2401189 TAATAACTAAAATTTT-AAAATAACGTG
1 TAACAACTAAATTTTTCAAAATAATGTG
* * * *
2401216 TAACAACTACATTTTTCTATATATTGTG
1 TAACAACTAAATTTTTCAAAATAATGTG
2401244 TAACAACTAAATTTTT
1 TAACAACTAAATTTTT
2401260 AACTTGGCAT
Statistics
Matches: 57, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
27 22 0.39
28 35 0.61
ACGTcount: A:0.41, C:0.13, G:0.06, T:0.39
Consensus pattern (28 bp):
TAACAACTAAATTTTTCAAAATAATGTG
Found at i:2401341 original size:28 final size:27
Alignment explanation
Indices: 2401306--2401389 Score: 114
Period size: 27 Copynumber: 3.1 Consensus size: 27
2401296 GGAAAATGAC
*
2401306 TAAATTTTTAACATGACATGTAACAAT
1 TAAATTTTTAACATGACATGCAACAAT
* *
2401333 TATATTTTTCAACATAACATGCAACAAT
1 TAAATTTTT-AACATGACATGCAACAAT
* *
2401361 TAAATTTTTAGCATGACATACAACAAT
1 TAAATTTTTAACATGACATGCAACAAT
2401388 TA
1 TA
2401390 CACTTTCAAC
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
27 25 0.51
28 24 0.49
ACGTcount: A:0.44, C:0.14, G:0.06, T:0.36
Consensus pattern (27 bp):
TAAATTTTTAACATGACATGCAACAAT
Found at i:2402734 original size:31 final size:31
Alignment explanation
Indices: 2402668--2402734 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
2402658 ATTGAAATAG
*
2402668 AAAATTTTAAAGATTATACTCAAAAGATTTG
1 AAAATTTTAAAGATTATACTCAAAAGATTTA
* *
2402699 AAAATTTTAAA-AATATTA-TCTAAAAGTTTTA
1 AAAATTTTAAAGATTA-TACTC-AAAAGATTTA
2402730 AAAAT
1 AAAAT
2402735 ACATGAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
30 5 0.16
31 26 0.84
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.37
Consensus pattern (31 bp):
AAAATTTTAAAGATTATACTCAAAAGATTTA
Found at i:2403655 original size:23 final size:23
Alignment explanation
Indices: 2403628--2403702 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 23
2403618 TAGGGTTTAA
* *
2403628 CATTGCGTGATTGGTTCG-TATGT
1 CATTGCGTGAGTGGTT-GATAAGT
2403651 CATTGCGTGAGTGGTTGATAAGT
1 CATTGCGTGAGTGGTTGATAAGT
* * * *
2403674 CATTGCATGAATGATTGATAGGT
1 CATTGCGTGAGTGGTTGATAAGT
*
2403697 TATTGC
1 CATTGC
2403703 ATGAATATGG
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
22 1 0.02
23 43 0.98
ACGTcount: A:0.21, C:0.11, G:0.29, T:0.39
Consensus pattern (23 bp):
CATTGCGTGAGTGGTTGATAAGT
Found at i:2403703 original size:23 final size:23
Alignment explanation
Indices: 2403649--2403708 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
2403639 TGGTTCGTAT
* * *
2403649 GTCATTGCGTGAGTGGTTGATAA
1 GTCATTGCATGAATGATTGATAA
*
2403672 GTCATTGCATGAATGATTGATAG
1 GTCATTGCATGAATGATTGATAA
*
2403695 GTTATTGCATGAAT
1 GTCATTGCATGAAT
2403709 ATGGTTTAGG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.27, C:0.08, G:0.28, T:0.37
Consensus pattern (23 bp):
GTCATTGCATGAATGATTGATAA
Found at i:2407620 original size:26 final size:26
Alignment explanation
Indices: 2407588--2407664 Score: 109
Period size: 26 Copynumber: 2.9 Consensus size: 26
2407578 AACATTGTTA
*
2407588 TGTATCATTTCCAAATTATTTTTTGT
1 TGTATCATTTACAAATTATTTTTTGT
* *
2407614 TGTATCATTAACAAATTATTCTTTGT
1 TGTATCATTTACAAATTATTTTTTGT
*
2407640 TGTATCATTTATAAATTATTCTTTT
1 TGTATCATTTACAAATTATT-TTTT
2407665 TTATATTACT
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
26 41 0.93
27 3 0.07
ACGTcount: A:0.27, C:0.10, G:0.06, T:0.56
Consensus pattern (26 bp):
TGTATCATTTACAAATTATTTTTTGT
Found at i:2408008 original size:23 final size:23
Alignment explanation
Indices: 2407979--2408510 Score: 268
Period size: 23 Copynumber: 23.1 Consensus size: 23
2407969 AATGGTGTGC
* *
2407979 ATGGAATTGTATGACTAGTTGAT
1 ATGGAATCGCATGACTAGTTGAT
* **
2408002 ATTGAATCGCGCGACTAGTTGAT
1 ATGGAATCGCATGACTAGTTGAT
**
2408025 ATGGAATCGCGCGACTAGTTGAT
1 ATGGAATCGCATGACTAGTTGAT
*
2408048 ATGGAATCTCATGACTAGTTGAT
1 ATGGAATCGCATGACTAGTTGAT
* *
2408071 ATGGAATTGCATGACTATTTGAT
1 ATGGAATCGCATGACTAGTTGAT
* *
2408094 TTGGAATCACATGACTAGTTGAT
1 ATGGAATCGCATGACTAGTTGAT
* * * **
2408117 ATTGAATCGCGTGAGTAGTAAAT
1 ATGGAATCGCATGACTAGTTGAT
* * * * *
2408140 ATGAAATCACGTAAACCA-TTGAT
1 ATGGAATCGCAT-GACTAGTTGAT
* * *
2408163 ATGAAATCGCATGACCAGTTAAT
1 ATGGAATCGCATGACTAGTTGAT
*
2408186 ATAGAATCG-AGTGACTAGTTGAT
1 ATGGAATCGCA-TGACTAGTTGAT
* * * * **
2408209 ATTGAATCACGTGATTAGTAAAT
1 ATGGAATCGCATGACTAGTTGAT
*
2408232 ATGGAAT--CATGCGAGTAGTTGAT
1 ATGGAATCGCAT--GACTAGTTGAT
**
2408255 ATAAAATCGCATGACTAGTTGAT
1 ATGGAATCGCATGACTAGTTGAT
* * * * * **
2408278 ATTGAATCACTTGAGTGGTAAAT
1 ATGGAATCGCATGACTAGTTGAT
* *** *
2408301 ATGAAATCATGTGACTAGTCGAT
1 ATGGAATCGCATGACTAGTTGAT
* * * *
2408324 A-GTGAATCACGTGACTAG-TAACC
1 ATG-GAATCGCATGACTAGTTGA-T
* * *
2408347 ATAGAATCGCGTGACTAGTTAAT
1 ATGGAATCGCATGACTAGTTGAT
* * * *
2408370 ATGGAATTGCTTGATTATTTGAT
1 ATGGAATCGCATGACTAGTTGAT
* * *
2408393 TTGGAATCACATGACTAGTTAAT
1 ATGGAATCGCATGACTAGTTGAT
* *
2408416 ATGGAATCACATGACTATTTGAT
1 ATGGAATCGCATGACTAGTTGAT
* * * * *
2408439 TTAGAGTCTCGA-GATTAGTTGAT
1 ATGGAATCGC-ATGACTAGTTGAT
* * *
2408462 ATAGAATCGCATGACTATTTAAT
1 ATGGAATCGCATGACTAGTTGAT
* ** * *
2408485 ATAGAATTACGTGACTATTTGAT
1 ATGGAATCGCATGACTAGTTGAT
2408508 ATG
1 ATG
2408511 ATATTATAGG
Statistics
Matches: 385, Mismatches: 110, Indels: 28
0.74 0.21 0.05
Matches are distributed among these distances:
21 2 0.01
22 8 0.02
23 366 0.95
24 6 0.02
25 3 0.01
ACGTcount: A:0.33, C:0.12, G:0.22, T:0.33
Consensus pattern (23 bp):
ATGGAATCGCATGACTAGTTGAT
Found at i:2408093 original size:69 final size:69
Alignment explanation
Indices: 2407989--2408510 Score: 332
Period size: 69 Copynumber: 7.6 Consensus size: 69
2407979 ATGGAATTGT
* * * * * * *
2407989 ATGACTAGTTGATATTGAATCGCGCGACTAGTTGATATGGAATCGCGCGACTAGTTGATATGGAA
1 ATGACTAGTTAATATGGAATCACGTGACTAGTTGATATGGAATCACGTGACTAGTTGATATAGAA
*
2408054 TCTC
66 TCGC
* ** * * * * *
2408058 ATGACTAGTTGATATGGAATTGCATGACTATTTGATTTGGAATCACATGACTAGTTGATATTGAA
1 ATGACTAGTTAATATGGAATCACGTGACTAGTTGATATGGAATCACGTGACTAGTTGATATAGAA
2408123 TCGC
66 TCGC
* * * * * * * * * * *
2408127 GTGAGTAGTAAATATGAAATCACGTAAACCA-TTGATATGAAATCGCATGACCAGTTAATATAGA
1 ATGACTAGTTAATATGGAATCACGT-GACTAGTTGATATGGAATCACGTGACTAGTTGATATAGA
2408191 ATCG-
65 ATCGC
* * * ** * * * *
2408195 AGTGACTAGTTGATATTGAATCACGTGATTAGTAAATATGGAATCATGCGAGTAGTTGATATAAA
1 A-TGACTAGTTAATATGGAATCACGTGACTAGTTGATATGGAATCACGTGACTAGTTGATATAGA
2408260 ATCGC
65 ATCGC
* * * * * ** * * *
2408265 ATGACTAGTTGATATTGAATCACTTGAGTGGTAAATATGAAATCATGTGACTAGTCGATAGT-GA
1 ATGACTAGTTAATATGGAATCACGTGACTAGTTGATATGGAATCACGTGACTAGTTGATA-TAGA
*
2408329 ATCAC
65 ATCGC
* * * * * ** * * * * *
2408334 GTGACTAG-TAACCATAGAATCGCGTGACTAGTTAATATGGAATTGCTTGATTATTTGATTTGGA
1 ATGACTAGTTAA-TATGGAATCACGTGACTAGTTGATATGGAATCACGTGACTAGTTGATATAGA
*
2408398 ATCAC
65 ATCGC
* * * * * * * *
2408403 ATGACTAGTTAATATGGAATCACATGACTATTTGATTTAGAGTCTCGAGATTAGTTGATATAGAA
1 ATGACTAGTTAATATGGAATCACGTGACTAGTTGATATGGAATCACGTGACTAGTTGATATAGAA
2408468 TCGC
66 TCGC
* * * *
2408472 ATGACTATTTAATATAGAATTACGTGACTATTTGATATG
1 ATGACTAGTTAATATGGAATCACGTGACTAGTTGATATG
2408511 ATATTATAGG
Statistics
Matches: 347, Mismatches: 98, Indels: 16
0.75 0.21 0.03
Matches are distributed among these distances:
68 5 0.01
69 334 0.96
70 8 0.02
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (69 bp):
ATGACTAGTTAATATGGAATCACGTGACTAGTTGATATGGAATCACGTGACTAGTTGATATAGAA
TCGC
Found at i:2408440 original size:46 final size:46
Alignment explanation
Indices: 2407979--2408438 Score: 298
Period size: 46 Copynumber: 10.0 Consensus size: 46
2407969 AATGGTGTGC
* * * * *
2407979 ATGGAATTGTATGACTAGTTGATATTGAATCGCGCGACTAGTTGAT
1 ATGGAATCGCATGACTAGTTGATATGGAATCACGTGACTAGTTGAT
** * *
2408025 ATGGAATCGCGCGACTAGTTGATATGGAATCTCATGACTAGTTGAT
1 ATGGAATCGCATGACTAGTTGATATGGAATCACGTGACTAGTTGAT
* * * *
2408071 ATGGAATTGCATGACTATTTGATTTGGAATCACATGACTAGTTGAT
1 ATGGAATCGCATGACTAGTTGATATGGAATCACGTGACTAGTTGAT
* * * ** * * *
2408117 ATTGAATCGCGTGAGTAGTAAATATGAAATCACGTAAACCA-TTGAT
1 ATGGAATCGCATGACTAGTTGATATGGAATCACGT-GACTAGTTGAT
* * * *
2408163 ATGAAATCGCATGACCAGTTAATATAGAATCGA-GTGACTAGTTGAT
1 ATGGAATCGCATGACTAGTTGATATGGAATC-ACGTGACTAGTTGAT
* * * * ** * * *
2408209 ATTGAATCACGTGATTAGTAAATATGGAATCATGCGAGTAGTTGAT
1 ATGGAATCGCATGACTAGTTGATATGGAATCACGTGACTAGTTGAT
** * * * * **
2408255 ATAAAATCGCATGACTAGTTGATATTGAATCACTTGAGTGGTAAAT
1 ATGGAATCGCATGACTAGTTGATATGGAATCACGTGACTAGTTGAT
* *** * * *
2408301 ATGAAATCATGTGACTAGTCGATA-GTGAATCACGTGACTAG-TAACC
1 ATGGAATCGCATGACTAGTTGATATG-GAATCACGTGACTAGTTGA-T
* * * ** * * *
2408347 ATAGAATCGCGTGACTAGTTAATATGGAATTGCTTGATTATTTGAT
1 ATGGAATCGCATGACTAGTTGATATGGAATCACGTGACTAGTTGAT
* * * * *
2408393 TTGGAATCACATGACTAGTTAATATGGAATCACATGACTATTTGAT
1 ATGGAATCGCATGACTAGTTGATATGGAATCACGTGACTAGTTGAT
2408439 TTAGAGTCTC
Statistics
Matches: 314, Mismatches: 92, Indels: 16
0.74 0.22 0.04
Matches are distributed among these distances:
45 6 0.02
46 301 0.96
47 7 0.02
ACGTcount: A:0.33, C:0.12, G:0.22, T:0.32
Consensus pattern (46 bp):
ATGGAATCGCATGACTAGTTGATATGGAATCACGTGACTAGTTGAT
Found at i:2410942 original size:22 final size:21
Alignment explanation
Indices: 2410905--2410954 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 21
2410895 GGATTTTAGT
*
2410905 TGACTAACTCCGTTGATTATC
1 TGACTAACTCCATTGATTATC
2410926 TGACTAACCTCCATTGATTATC
1 TGACTAA-CTCCATTGATTATC
2410948 TGACTAA
1 TGACTAA
2410955 GATGCTTCTG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 7 0.26
22 20 0.74
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.36
Consensus pattern (21 bp):
TGACTAACTCCATTGATTATC
Found at i:2414217 original size:211 final size:210
Alignment explanation
Indices: 2413605--2414266 Score: 684
Period size: 211 Copynumber: 3.1 Consensus size: 210
2413595 TTATGCAATT
* * * * *
2413605 CATAAAAACCAATCATGTAGTGCCTAAAAAGTAGTCAATGAATGTCTCAAACTAAAATATGCATT
1 CATAAAAACCAATCACGTAATACCTAAAAAGTAGTCAA-GAATGTCTTAAAATAAAATATGCATT
* * * *
2413670 GCACAATTCACGTAACACCTACAAGCCAGTTTCGCAATACCTAATAATAAGTCACTCAATGCCTA
65 GCACAATTCACGTAGCGCCTATAAGCCAATTTCGCAATACCTAATAATAAGTCACTCAATGCCTA
* * * * *
2413735 ATATCCACTCACGTTATGCCAATATAACCAATCATGTAGTGGCCCAACGTTACGCAATACATAAC
130 ATATCCATTCACGTTATGCCAAAATAACCAATCATGTATTGACCCAACGTCACGCAATACATAAC
*
2413800 AACAAGTCACGGAATA
195 AAGAAGTCACGGAATA
* ** * * *
2413816 CATAAAAACCAATAACACAATACTTAAAAAGTAGTCAAGTAATATCTTAAAACAAAATATGCATT
1 CATAAAAACCAATCACGTAATACCTAAAAAGTAGTCAAG-AATGTCTTAAAATAAAATATGCATT
* * * * * * * *
2413881 GCACAATACATGCAGCGCTTATAAGTCAATCTCACAATACCTAATAATAAGTCATTCAATGCCTA
65 GCACAATTCACGTAGCGCCTATAAGCCAATTTCGCAATACCTAATAATAAGTCACTCAATGCCTA
* * * * *
2413946 ATATCCATTCACGTTATGCCAACATAACCAGTCATGTATT-AGTCCAACATCACACAATACATAA
130 ATATCCATTCACGTTATGCCAAAATAACCAATCATGTATTGA-CCCAACGTCACGCAATACATAA
*
2414010 CAAGAAGTCACAGAATA
194 CAAGAAGTCACGGAATA
* * * * * *
2414027 CATAAAAATCAGTCACGTAATGCCTAAAATGTAGTCAAGAATTGTCTTAAAATAAGATATGCGTT
1 CATAAAAACCAATCACGTAATACCTAAAAAGTAGTCAAGAA-TGTCTTAAAATAAAATATGCATT
* * * * * * * * * *
2414092 ACACAATTCACGTAGTGCCTATAACCCAATTTTGTAATACCTAACAATAAGTTACGCAAAGCATA
65 GCACAATTCACGTAGCGCCTATAAGCCAATTTCGCAATACCTAATAATAAGTCACTCAATGCCTA
* * *** *
2414157 ACATCCATTCACGTTATGCCAAAAT-ACCAAATAACACATTGACCCTACGTCACGCAATACATAA
130 ATATCCATTCACGTTATGCCAAAATAACC-AATCATGTATTGACCCAACGTCACGCAATACATAA
* *
2414221 -AAGCTAGTCACGGAATG
194 CAAG-AAGTCACGGAATA
* *
2414238 CATAAAAACTAGA-CATGTAATACCTAAAA
1 CATAAAAACCA-ATCACGTAATACCTAAAA
2414267 TCTATTCAAA
Statistics
Matches: 361, Mismatches: 83, Indels: 14
0.79 0.18 0.03
Matches are distributed among these distances:
210 9 0.02
211 351 0.97
212 1 0.00
ACGTcount: A:0.42, C:0.22, G:0.11, T:0.24
Consensus pattern (210 bp):
CATAAAAACCAATCACGTAATACCTAAAAAGTAGTCAAGAATGTCTTAAAATAAAATATGCATTG
CACAATTCACGTAGCGCCTATAAGCCAATTTCGCAATACCTAATAATAAGTCACTCAATGCCTAA
TATCCATTCACGTTATGCCAAAATAACCAATCATGTATTGACCCAACGTCACGCAATACATAACA
AGAAGTCACGGAATA
Found at i:2414230 original size:22 final size:22
Alignment explanation
Indices: 2414205--2414249 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2414195 TTGACCCTAC
*
2414205 GTCACGCAATACATAAAAGCTA
1 GTCACGCAATACATAAAAACTA
* *
2414227 GTCACGGAATGCATAAAAACTA
1 GTCACGCAATACATAAAAACTA
2414249 G
1 G
2414250 ACATGTAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.44, C:0.20, G:0.18, T:0.18
Consensus pattern (22 bp):
GTCACGCAATACATAAAAACTA
Found at i:2414325 original size:22 final size:22
Alignment explanation
Indices: 2414270--2414319 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
2414260 CCTAAAATCT
*
2414270 ATTCAAACAATGCATAATATCC
1 ATTCACACAATGCATAATATCC
2414292 ATTCACACAATGCATAATATCC
1 ATTCACACAATGCATAATATCC
2414314 ATTCAC
1 ATTCAC
2414320 TTAATGTCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.42, C:0.26, G:0.04, T:0.28
Consensus pattern (22 bp):
ATTCACACAATGCATAATATCC
Found at i:2415159 original size:22 final size:21
Alignment explanation
Indices: 2415133--2415181 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
2415123 TCAATTACTA
2415133 AAAACCAATCACA-CAATGCCT
1 AAAACCAATCA-AGCAATGCCT
* *
2415154 ACAAACTAATCAAGCAATTCCT
1 A-AAACCAATCAAGCAATGCCT
2415176 AAAACC
1 AAAACC
2415182 TTGTCACGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.49, C:0.31, G:0.04, T:0.16
Consensus pattern (21 bp):
AAAACCAATCAAGCAATGCCT
Found at i:2427345 original size:125 final size:125
Alignment explanation
Indices: 2427123--2427374 Score: 450
Period size: 125 Copynumber: 2.0 Consensus size: 125
2427113 AAAGGTGAAA
* *
2427123 ATTTGTATTTATTTTTGGCTTGCTACTGTGTGCTTAGTTTCTTTCTATGAGTAGATTGTTTATTA
1 ATTTGTATTTATTTTTAGCTTACTACTGTGTGCTTAGTTTCTTTCTATGAGTAGATTGTTTATTA
* *
2427188 GCTTATGTATGTTTTTTTGGTGCTGCATATTTTTGCTTACTAATGCTATTTATGTTGTTG
66 GCTTATGTATGGTTTTTTGGTGCTGCATATTTTTGCTTACTAATGCTATTTATGCTGTTG
*
2427248 ATTTGTATTTATTTTTAGCTTACTACTGTGTGCTTTGTTTCTTTCTATGAGTAGATTGTTTATTA
1 ATTTGTATTTATTTTTAGCTTACTACTGTGTGCTTAGTTTCTTTCTATGAGTAGATTGTTTATTA
*
2427313 GCTTATGTATGGTTTTTTGGTGCTGCATATTTTTGCTTACTAATGTTATTTATGCTGTTG
66 GCTTATGTATGGTTTTTTGGTGCTGCATATTTTTGCTTACTAATGCTATTTATGCTGTTG
2427373 AT
1 AT
2427375 GGTTGCAAAT
Statistics
Matches: 121, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
125 121 1.00
ACGTcount: A:0.17, C:0.10, G:0.19, T:0.55
Consensus pattern (125 bp):
ATTTGTATTTATTTTTAGCTTACTACTGTGTGCTTAGTTTCTTTCTATGAGTAGATTGTTTATTA
GCTTATGTATGGTTTTTTGGTGCTGCATATTTTTGCTTACTAATGCTATTTATGCTGTTG
Found at i:2429880 original size:21 final size:21
Alignment explanation
Indices: 2429856--2429896 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2429846 TAATATATGT
2429856 TATTT-ATGCTAAATTTTATTA
1 TATTTGATGCT-AATTTTATTA
*
2429877 TATTTGATGCTATTTTTATT
1 TATTTGATGCTAATTTTATT
2429897 TTGTTATAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.27, C:0.05, G:0.07, T:0.61
Consensus pattern (21 bp):
TATTTGATGCTAATTTTATTA
Found at i:2429972 original size:13 final size:13
Alignment explanation
Indices: 2429954--2429984 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2429944 ATTAAATATT
*
2429954 TGTAATTTAATTG
1 TGTAATTTAATTA
2429967 TGTAATTTAATTA
1 TGTAATTTAATTA
2429980 TGTAA
1 TGTAA
2429985 ATGTGTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (13 bp):
TGTAATTTAATTA
Found at i:2430980 original size:3 final size:3
Alignment explanation
Indices: 2430944--2430998 Score: 60
Period size: 3 Copynumber: 18.0 Consensus size: 3
2430934 AATAAATAGA
*
2430944 TAT T-T TAT TAAT TAT T-T TAAT TTT TAT ATAT TAT TAT TAT TAT TAT
1 TAT TAT TAT T-AT TAT TAT T-AT TAT TAT -TAT TAT TAT TAT TAT TAT
2430990 TAT TAT TAT
1 TAT TAT TAT
2430999 CAAATTACGA
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
2 4 0.09
3 33 0.73
4 8 0.18
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2432494 original size:24 final size:24
Alignment explanation
Indices: 2432467--2432517 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
2432457 TCAATATCAA
2432467 ATTAAATAA-AATTAATAAATAATT
1 ATTAAATAATAATT-ATAAATAATT
* * *
2432491 ATTAATTAATTATTATAAATATTT
1 ATTAAATAATAATTATAAATAATT
2432515 ATT
1 ATT
2432518 TAATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 20 0.87
25 3 0.13
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
ATTAAATAATAATTATAAATAATT
Found at i:2432995 original size:2 final size:2
Alignment explanation
Indices: 2432982--2433015 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
2432972 TGGGGCTCAC
* *
2432982 AT AT AG AT AT AT AT AT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2433016 TCATTTCATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2436985 original size:20 final size:21
Alignment explanation
Indices: 2436947--2436991 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
2436937 TAAAAATATG
*
2436947 ATATTTTAAAAAATCTTTAAA
1 ATATTTTAAAAAATATTTAAA
*
2436968 ATATTTTAAAAAA-ATTTAAT
1 ATATTTTAAAAAATATTTAAA
2436988 ATAT
1 ATAT
2436992 CGACAAAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
ATATTTTAAAAAATATTTAAA
Found at i:2445685 original size:13 final size:13
Alignment explanation
Indices: 2445667--2445706 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
2445657 GTCAAAAATC
*
2445667 ACTAGAGAAATGA
1 ACTAGAGAGATGA
2445680 ACTAGAGAGATGA
1 ACTAGAGAGATGA
2445693 ACTAGAGAGATGA
1 ACTAGAGAGATGA
2445706 A
1 A
2445707 ACAGAAGATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.50, C:0.07, G:0.28, T:0.15
Consensus pattern (13 bp):
ACTAGAGAGATGA
Found at i:2447539 original size:17 final size:17
Alignment explanation
Indices: 2447517--2447552 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
2447507 AATCTTATAT
2447517 AAATAATATAAAAAATA
1 AAATAATATAAAAAATA
*
2447534 AAATAATTTAAAAAATA
1 AAATAATATAAAAAATA
2447551 AA
1 AA
2447553 TTATGTCATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (17 bp):
AAATAATATAAAAAATA
Found at i:2449030 original size:17 final size:18
Alignment explanation
Indices: 2448997--2449033 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
2448987 TCCACACATG
2448997 AAGAAAGAAGAACAAAGA
1 AAGAAAGAAGAACAAAGA
2449015 AAGAAA-AAGAGA-AAAGA
1 AAGAAAGAAGA-ACAAAGA
2449032 AA
1 AA
2449034 CATCATTAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.76, C:0.03, G:0.22, T:0.00
Consensus pattern (18 bp):
AAGAAAGAAGAACAAAGA
Found at i:2464317 original size:22 final size:22
Alignment explanation
Indices: 2464292--2464430 Score: 96
Period size: 22 Copynumber: 6.4 Consensus size: 22
2464282 TTATTTTTAT
*
2464292 TTTATTATTTAAATATTAATAA
1 TTTATAATTTAAATATTAATAA
2464314 TTTATAATTTATTTAAAATATTAATAA
1 TTTAT-A---ATTT-AAATATTAATAA
* * *
2464341 TTGATAATTTAAATAATAATAT
1 TTTATAATTTAAATATTAATAA
* *
2464363 TTTAAAATATT-AATATT--TTA
1 TTTATAAT-TTAAATATTAATAA
2464383 TTTATAATTTAAATA-T--T-A
1 TTTATAATTTAAATATTAATAA
* *
2464401 TTTATGATTAAAATATTAATAA
1 TTTATAATTTAAATATTAATAA
2464423 TTT-TAATT
1 TTTATAATT
2464431 AATTTTTTAA
Statistics
Matches: 93, Mismatches: 13, Indels: 23
0.72 0.10 0.18
Matches are distributed among these distances:
18 14 0.15
19 5 0.05
20 12 0.13
21 5 0.05
22 30 0.32
23 6 0.06
26 5 0.05
27 16 0.17
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (22 bp):
TTTATAATTTAAATATTAATAA
Found at i:2464332 original size:27 final size:27
Alignment explanation
Indices: 2464296--2464435 Score: 98
Period size: 27 Copynumber: 5.2 Consensus size: 27
2464286 TTTTATTTTA
2464296 TTATTT-AAATATTAATAATTTATAAT
1 TTATTTAAAATATTAATAATTTATAAT
*
2464322 TTATTTAAAATATTAATAATTGATAAT
1 TTATTTAAAATATTAATAATTTATAAT
** *
2464349 TTAAATAATAATATTTTAA-AATATTAATATT
1 TTATTTAA-AATA--TTAATAAT-TT-ATAAT
* *
2464380 TTATTTATAAT-TT-A-AA--TATTAT
1 TTATTTAAAATATTAATAATTTATAAT
2464402 TTATGATTAAAATATTAATAATTT-TAAT
1 TTAT--TTAAAATATTAATAATTTATAAT
*
2464430 TAATTT
1 TTATTT
2464436 TTTAATTTAA
Statistics
Matches: 88, Mismatches: 13, Indels: 26
0.69 0.10 0.20
Matches are distributed among these distances:
22 7 0.08
23 1 0.01
24 6 0.07
25 2 0.02
26 12 0.14
27 29 0.33
28 10 0.11
29 4 0.05
30 8 0.09
31 9 0.10
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (27 bp):
TTATTTAAAATATTAATAATTTATAAT
Found at i:2464367 original size:38 final size:40
Alignment explanation
Indices: 2464325--2464424 Score: 114
Period size: 42 Copynumber: 2.5 Consensus size: 40
2464315 TTATAATTTA
2464325 TTTAAAATATTAATAATTGATAATTTAAATAATA-ATAT-
1 TTTAAAATATTAATAATTGATAATTTAAATAATATATATG
* * *
2464363 TTTAAAATATTAATATTTTATTTATAATTTAAATATTATTTATG
1 TTTAAAATATTAATA----ATTGATAATTTAAATAATATATATG
*
2464407 ATTAAAATATTAATAATT
1 TTTAAAATATTAATAATT
2464425 TTAATTAATT
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
38 15 0.29
40 3 0.06
42 17 0.33
43 3 0.06
44 14 0.27
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (40 bp):
TTTAAAATATTAATAATTGATAATTTAAATAATATATATG
Found at i:2464370 original size:16 final size:16
Alignment explanation
Indices: 2464351--2464382 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2464341 TTGATAATTT
2464351 AAATAATAATATTTTA
1 AAATAATAATATTTTA
*
2464367 AAATATTAATATTTTA
1 AAATAATAATATTTTA
2464383 TTTATAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AAATAATAATATTTTA
Found at i:2465452 original size:41 final size:41
Alignment explanation
Indices: 2465389--2465484 Score: 131
Period size: 41 Copynumber: 2.3 Consensus size: 41
2465379 CAAGTAAATC
* *
2465389 ATTTTCAAAG-TCCACTTTTTAAGCGTAATCAAATTTCCAAT
1 ATTTTCAAAGTTTC-CTTCTTAAGCGTAATCAAATTTCCAAT
** *
2465430 ATTTTTGAAGTTTCCTTCTTAAGCGTAATCAAATTTCTAAT
1 ATTTTCAAAGTTTCCTTCTTAAGCGTAATCAAATTTCCAAT
2465471 ATTTTCAAAGTTTC
1 ATTTTCAAAGTTTC
2465485 GGTTTCAAAG
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
41 45 0.96
42 2 0.04
ACGTcount: A:0.31, C:0.17, G:0.08, T:0.44
Consensus pattern (41 bp):
ATTTTCAAAGTTTCCTTCTTAAGCGTAATCAAATTTCCAAT
Found at i:2465725 original size:27 final size:29
Alignment explanation
Indices: 2465678--2465753 Score: 95
Period size: 27 Copynumber: 2.7 Consensus size: 29
2465668 TTATTTTCAA
* *
2465678 TTATAATTTACTTATTTTTAATTG-TT-T
1 TTATAATTTATTTATTTTTAAGTGATTAT
2465705 TTATAATTTATTTATTTTTAAGTGATTAT
1 TTATAATTTATTTATTTTTAAGTGATTAT
2465734 TT-TAATTTTATGTTATTTTT
1 TTATAA-TTTAT-TTATTTTT
2465754 TTAATTTAGT
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
27 22 0.51
28 5 0.12
29 8 0.19
30 8 0.19
ACGTcount: A:0.26, C:0.01, G:0.05, T:0.67
Consensus pattern (29 bp):
TTATAATTTATTTATTTTTAAGTGATTAT
Found at i:2465742 original size:19 final size:19
Alignment explanation
Indices: 2465715--2465760 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
2465705 TTATAATTTA
*
2465715 TTTATTTTTAAGTGATTAT
1 TTTAATTTTAAGTGATTAT
* * *
2465734 TTTAATTTTATGTTATTTT
1 TTTAATTTTAAGTGATTAT
2465753 TTTAATTT
1 TTTAATTT
2465761 AGTCATTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.70
Consensus pattern (19 bp):
TTTAATTTTAAGTGATTAT
Found at i:2469376 original size:22 final size:23
Alignment explanation
Indices: 2469348--2469394 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
2469338 ATTTTGATGC
*
2469348 ATTACTATAAGAACTAAGCT-AA
1 ATTACTATAAAAACTAAGCTCAA
*
2469370 ATTACTATAAAAATTAAGCTCAA
1 ATTACTATAAAAACTAAGCTCAA
2469393 AT
1 AT
2469395 AACTCTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.51, C:0.13, G:0.06, T:0.30
Consensus pattern (23 bp):
ATTACTATAAAAACTAAGCTCAA
Found at i:2469427 original size:20 final size:20
Alignment explanation
Indices: 2469402--2469443 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
2469392 AATAACTCTA
*
2469402 TATCATAGAATTATCAGCAC
1 TATCATAGAATTATCACCAC
*
2469422 TATCATAGAGTTATCACCAC
1 TATCATAGAATTATCACCAC
2469442 TA
1 TA
2469444 CTCTTAAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (20 bp):
TATCATAGAATTATCACCAC
Found at i:2472493 original size:17 final size:15
Alignment explanation
Indices: 2472461--2472494 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
2472451 TTGGTTTGCT
2472461 TTGAGGAAAAGGATG
1 TTGAGGAAAAGGATG
2472476 TTGAGAGAAAATGGATG
1 TTGAG-GAAAA-GGATG
2472493 TT
1 TT
2472495 TGGAAGAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 5 0.29
17 7 0.41
ACGTcount: A:0.38, C:0.00, G:0.35, T:0.26
Consensus pattern (15 bp):
TTGAGGAAAAGGATG
Found at i:2475638 original size:45 final size:45
Alignment explanation
Indices: 2475493--2475631 Score: 179
Period size: 45 Copynumber: 3.1 Consensus size: 45
2475483 GTTACACACC
* *
2475493 ATGTACAAAAATATGTTACATGTCATGGTTAGGTTGTTACATGCT
1 ATGTACAAAAATATGTTACACGCCATGGTTAGGTTGTTACATGCT
* * * * * *
2475538 ATATACAAAAATATGTGACACGCTATGGTTAGGTTATTACACGGT
1 ATGTACAAAAATATGTTACACGCCATGGTTAGGTTGTTACATGCT
* * *
2475583 ATGTATAAAAACATGTTACACGCCATGGTTAGGTTGTTACATGTT
1 ATGTACAAAAATATGTTACACGCCATGGTTAGGTTGTTACATGCT
2475628 ATGT
1 ATGT
2475632 TAAAAAAAAA
Statistics
Matches: 78, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 78 1.00
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.35
Consensus pattern (45 bp):
ATGTACAAAAATATGTTACACGCCATGGTTAGGTTGTTACATGCT
Found at i:2475703 original size:26 final size:26
Alignment explanation
Indices: 2475672--2475747 Score: 91
Period size: 26 Copynumber: 2.8 Consensus size: 26
2475662 AATAAAAACA
2475672 TATTACATGCCATGGTTAAAAAA-GGT
1 TATTACATGCCAT-GTTAAAAAATGGT
* *
2475698 TGTTACAGGCCATGTTAAAAAAAATGGT
1 TATTACATGCCATGTT--AAAAAATGGT
*
2475726 TATTACATGTCATGTTAAAAAA
1 TATTACATGCCATGTTAAAAAA
2475748 ATATTATTGT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
25 3 0.07
26 17 0.40
27 6 0.14
28 16 0.38
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.32
Consensus pattern (26 bp):
TATTACATGCCATGTTAAAAAATGGT
Found at i:2475731 original size:28 final size:27
Alignment explanation
Indices: 2475672--2475748 Score: 95
Period size: 28 Copynumber: 2.9 Consensus size: 27
2475662 AATAAAAACA
2475672 TATTACATGCCATGGTT--AAAAAAGGT
1 TATTACATGCCAT-GTTAAAAAAAAGGT
* *
2475698 TGTTACAGGCCATGTTAAAAAAAATGGT
1 TATTACATGCCATGTTAAAAAAAA-GGT
*
2475726 TATTACATGTCATGTTAAAAAAA
1 TATTACATGCCATGTTAAAAAAA
2475749 TATTATTGTT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
25 3 0.07
26 11 0.26
27 6 0.14
28 23 0.53
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.31
Consensus pattern (27 bp):
TATTACATGCCATGTTAAAAAAAAGGT
Found at i:2475760 original size:29 final size:28
Alignment explanation
Indices: 2475689--2475776 Score: 79
Period size: 28 Copynumber: 3.1 Consensus size: 28
2475679 TGCCATGGTT
*
2475689 AAAAAA-GGTTGTTACAGGCCATGTTAA
1 AAAAAATGATTGTTACAGGCCATGTTAA
* * * *
2475716 AAAAAATGGTTATTACATGTCATGTTAA
1 AAAAAATGATTGTTACAGGCCATGTTAA
* * * *
2475744 AAAAATATTATTGTTACACGCCATATTCA
1 AAAAA-ATGATTGTTACAGGCCATGTTAA
2475773 AAAA
1 AAAA
2475777 CATTTTGTTA
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
27 6 0.12
28 23 0.47
29 20 0.41
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.31
Consensus pattern (28 bp):
AAAAAATGATTGTTACAGGCCATGTTAA
Found at i:2487741 original size:6 final size:6
Alignment explanation
Indices: 2487732--2487801 Score: 58
Period size: 6 Copynumber: 11.7 Consensus size: 6
2487722 GCAAAATAAA
* *
2487732 AAAAAT AAAAGTAT AAAAGA- AAAAAT AAAATAA AAAAAT AAAAA- ATAAAT
1 AAAAAT AAAA--AT AAAA-AT AAAAAT AAAA-AT AAAAAT AAAAAT AAAAAT
2487782 AAAAAT --AAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAA
2487802 GTATACTTGA
Statistics
Matches: 52, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
4 4 0.08
5 5 0.10
6 31 0.60
7 6 0.12
8 6 0.12
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:2487749 original size:17 final size:16
Alignment explanation
Indices: 2487724--2487790 Score: 75
Period size: 17 Copynumber: 4.1 Consensus size: 16
2487714 GTTCGAGTGC
2487724 AAAATAAAAAAAATAA
1 AAAATAAAAAAAATAA
*
2487740 AAGTATAAAAGAAAA-AA
1 AA-AATAAAA-AAAATAA
2487757 TAAAAT-AAAAAAATAA
1 -AAAATAAAAAAAATAA
2487773 AAAATAAATAAAAATAA
1 AAAATAAA-AAAAATAA
2487790 A
1 A
2487791 TAAAAATAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
15 9 0.21
16 9 0.21
17 19 0.44
18 6 0.14
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (16 bp):
AAAATAAAAAAAATAA
Found at i:2487756 original size:20 final size:19
Alignment explanation
Indices: 2487724--2487801 Score: 86
Period size: 20 Copynumber: 3.9 Consensus size: 19
2487714 GTTCGAGTGC
*
2487724 AAAATAAAAAAAATAAAAGT
1 AAAAAAAAAAAAATAAAA-T
* *
2487744 ATAAAAGAAAAAATAAAAT
1 AAAAAAAAAAAAATAAAAT
2487763 AAAAAAATAAAAAAT-AAAT
1 AAAAAAA-AAAAAATAAAAT
2487782 AAAAATAAATAAAAATAAAA
1 AAAAA-AAA-AAAAATAAAA
2487802 GTATACTTGA
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
19 16 0.33
20 30 0.61
21 3 0.06
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (19 bp):
AAAAAAAAAAAAATAAAAT
Found at i:2487761 original size:12 final size:11
Alignment explanation
Indices: 2487744--2487801 Score: 55
Period size: 11 Copynumber: 5.0 Consensus size: 11
2487734 AAATAAAAGT
2487744 ATAAAAGAAAAA
1 ATAAAA-AAAAA
2487756 ATAAAATAAAAAA
1 AT-AAA-AAAAAA
*
2487769 ATAAAAAATAA
1 ATAAAAAAAAA
*
2487780 AT-AAAAATAA
1 ATAAAAAAAAA
2487790 ATAAAAATAAAA
1 ATAAAAA-AAAA
2487802 GTATACTTGA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
10 10 0.25
11 11 0.28
12 8 0.20
13 10 0.25
14 1 0.03
ACGTcount: A:0.83, C:0.00, G:0.02, T:0.16
Consensus pattern (11 bp):
ATAAAAAAAAA
Found at i:2487767 original size:34 final size:36
Alignment explanation
Indices: 2487724--2487801 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 36
2487714 GTTCGAGTGC
* *
2487724 AAAATAAAAAAAATAAAAGTATAAA-AGAAA-AAAT-
1 AAAATAAAAAAAATAAAA-AATAAATAAAAATAAATA
2487758 AAAAT-AAAAAAATAAAAAATAAATAAAAATAAATA
1 AAAATAAAAAAAATAAAAAATAAATAAAAATAAATA
2487793 AAAATAAAA
1 AAAATAAAA
2487802 GTATACTTGA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
32 5 0.13
33 16 0.42
34 9 0.24
35 5 0.13
36 3 0.08
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (36 bp):
AAAATAAAAAAAATAAAAAATAAATAAAAATAAATA
Found at i:2487772 original size:25 final size:25
Alignment explanation
Indices: 2487729--2487802 Score: 80
Period size: 25 Copynumber: 2.9 Consensus size: 25
2487719 AGTGCAAAAT
**
2487729 AAAA-AAAATAAAAGTATAAAAGAA
1 AAAATAAAATAAAAAAATAAAAGAA
2487753 AAAATAAAATAAAAAAATAAAA-AA
1 AAAATAAAATAAAAAAATAAAAGAA
*
2487777 TAAATAAAAATAAATAAAAATAAAAG
1 AAAAT-AAAAT-AA-AAAAATAAAAG
2487803 TATACTTGAT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
24 10 0.24
25 20 0.48
26 2 0.05
27 10 0.24
ACGTcount: A:0.81, C:0.00, G:0.04, T:0.15
Consensus pattern (25 bp):
AAAATAAAATAAAAAAATAAAAGAA
Done.