Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397259.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_147.0, 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: 10737078
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 75620 characters in sequence are not A, C, G, or T
File 21 of 22
Found at i:9492291 original size:7 final size:7
Alignment explanation
Indices: 9492279--9492330 Score: 52
Period size: 7 Copynumber: 7.4 Consensus size: 7
9492269 TACATCAATA
9492279 AAATAAT
1 AAATAAT
9492286 AAATAAT
1 AAATAAT
*
9492293 AATTTAAT
1 AA-ATAAT
*
9492301 TAATAAT
1 AAATAAT
*
9492308 AATTAAT
1 AAATAAT
9492315 -AATAAT
1 AAATAAT
*
9492321 TAATAAT
1 AAATAAT
9492328 AAA
1 AAA
9492331 ATTTATTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
6 5 0.14
7 26 0.72
8 5 0.14
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (7 bp):
AAATAAT
Found at i:9492293 original size:3 final size:3
Alignment explanation
Indices: 9492275--9492329 Score: 51
Period size: 3 Copynumber: 17.7 Consensus size: 3
9492265 ATATTACATC
*
9492275 AAT AA- AAT AAT AAAT AAT AAT -TT AATT AAT AAT AATT AAT AAT AATT
1 AAT AAT AAT AAT -AAT AAT AAT AAT AA-T AAT AAT AA-T AAT AAT AA-T
9492322 AAT AAT AA
1 AAT AAT AA
9492330 AATTTATTTA
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
2 3 0.07
3 29 0.66
4 12 0.27
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:9492295 original size:10 final size:10
Alignment explanation
Indices: 9492280--9492329 Score: 73
Period size: 10 Copynumber: 4.8 Consensus size: 10
9492270 ACATCAATAA
*
9492280 AATAATAAAT
1 AATAATAATT
9492290 AATAATTTAATT
1 AATAA--TAATT
9492302 AATAATAATT
1 AATAATAATT
9492312 AATAATAATT
1 AATAATAATT
9492322 AATAATAA
1 AATAATAA
9492330 AATTTATTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
10 28 0.76
12 9 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
AATAATAATT
Found at i:9492890 original size:25 final size:25
Alignment explanation
Indices: 9492842--9492890 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
9492832 TATAAAAAAA
* *
9492842 TTAAAATATTATTTTTTTTATTAAT
1 TTAAAATATTATTTTATATATTAAT
9492867 TTAAAATATTATTATTATAT-TTAA
1 TTAAAATATTATT-TTATATATTAA
9492891 AAAAATAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
TTAAAATATTATTTTATATATTAAT
Found at i:9494949 original size:23 final size:24
Alignment explanation
Indices: 9494910--9494969 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
9494900 TTTAAAAAAA
*
9494910 AACTTAAAAAAAGCTCTAATTAGG
1 AACTTAAAAAAAGCTCTAATTAGC
9494934 AACTTAAAAAAA-CTCTAATTAGC
1 AACTTAAAAAAAGCTCTAATTAGC
*
9494957 AGCTTTAAAAAAA
1 AAC-TTAAAAAAA
9494970 AGTTACTGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
23 12 0.36
24 21 0.64
ACGTcount: A:0.53, C:0.13, G:0.08, T:0.25
Consensus pattern (24 bp):
AACTTAAAAAAAGCTCTAATTAGC
Found at i:9495303 original size:25 final size:24
Alignment explanation
Indices: 9495262--9495308 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
9495252 TTTTTTTGAA
*
9495262 TAACATGAAATTGTATCTCTTACG
1 TAACATGAAATTGTATCACTTACG
* *
9495286 TAACATTATAATTTTATCACTTA
1 TAACATGA-AATTGTATCACTTA
9495309 TGAAGATTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 7 0.37
25 12 0.63
ACGTcount: A:0.36, C:0.15, G:0.06, T:0.43
Consensus pattern (24 bp):
TAACATGAAATTGTATCACTTACG
Found at i:9495693 original size:20 final size:19
Alignment explanation
Indices: 9495670--9495723 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
9495660 AGGAATTAGG
9495670 TAGTAATAAAATAATATACA
1 TAGTAATAAAATAATATA-A
*
9495690 TAGTAAT-AATTAA-ATAA
1 TAGTAATAAAATAATATAA
*
9495707 TAATAATAATAATAATA
1 TAGTAATAA-AATAATA
9495724 ACAACAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
17 7 0.25
18 4 0.14
19 9 0.32
20 8 0.29
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (19 bp):
TAGTAATAAAATAATATAA
Found at i:9495699 original size:3 final size:3
Alignment explanation
Indices: 9495673--9495724 Score: 56
Period size: 3 Copynumber: 18.0 Consensus size: 3
9495663 AATTAGGTAG
* *
9495673 TAA TAA -AA TAA T-A TACA TAG TAA TAA TTA -AA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
9495716 TAA TAA TAA
1 TAA TAA TAA
9495725 CAACAAATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
2 5 0.12
3 33 0.80
4 3 0.07
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:9495704 original size:23 final size:23
Alignment explanation
Indices: 9495673--9495724 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
9495663 AATTAGGTAG
*
9495673 TAATAAAATAAT-ATACATAGTAA
1 TAATAAAATAATAATA-ATAATAA
*
9495696 TAATTAAATAATAATAATAATAA
1 TAATAAAATAATAATAATAATAA
9495719 TAATAA
1 TAATAA
9495725 CAACAAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 22 0.88
24 3 0.12
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (23 bp):
TAATAAAATAATAATAATAATAA
Found at i:9496783 original size:242 final size:242
Alignment explanation
Indices: 9496195--9497356 Score: 999
Period size: 247 Copynumber: 4.8 Consensus size: 242
9496185 TTTAACTATA
* * ** * * *
9496195 ATTA-TTTTTATTTAATAATTAAAAATTATATATTGTTAAATAATTTTAATATGAAAATATAAAT
1 ATTATTTTTTATTTAAAAATTAAAATTTATATATCATTAAACACTTTTAATCTGAAAATATAAAT
* * *** * * *
9496259 TTAAATGTTTATTTTTTACTAAAATTAGATTTTTTTACTTAACTGACAACTTATTTTATCTCTCA
66 TTAAATATTTATTTTTTACTAAAATTAGATTTTTTTACTTAATTGACTTGTTATGTTAACTTTCA
* * * * * *
9496324 CGCATTTACG-TTAAGATTTAAAATTTAGTTATTACACCTTACATCAA----TTAT-T--ATAGT
131 CACATTTA-GATTAAGATTTAAAATTTAATTATTTCATCTT-TAT-AAGTTTTTATATCAATTGT
* * * * * *
9496381 TTTATG-CTAATGCCTATTTATATCAATTTTAAACTATAATTATTTTT-TT
193 TTTACGTC-AAGGCTTATCTATATTAATTTTGAACTATAATTATTTTTATT
* * * * *
9496430 ATTATTCTTTATTTAAAATTTAAAATTTATATA-CATTAAATATTTTTAA-CTTGAAAATATATA
1 ATTATTTTTTATTTAAAAATTAAAATTTATATATCATTAAACACTTTTAATC-TGAAAATATAAA
* * *
9496493 TTTAAAAATATATTTTTTACTAAAATTAGATTTTTTTTACTAAATTGACTTGTTATGTTAA-TTA
65 TTTAAATATTTATTTTTTACTAAAATTAGA-TTTTTTTACTTAATTGACTTGTTATGTTAACTT-
* * *
9496557 TTATACATTTAGATTAAGATTTAAAATTTAATTATTTCATCTTTATAAGTTTTTATGTCAATTGT
128 TCACACATTTAGATTAAGATTTAAAATTTAATTATTTCATCTTTATAAGTTTTTATATCAATTGT
*
9496622 TTTACGTCAAGGCTTATCTATATTAAATTTGAACTATAATTATTTTTATT
193 TTTACGTCAAGGCTTATCTATATTAATTTTGAACTATAATTATTTTTATT
* *
9496672 TTTATTTTTTATTTAAAAATTAAAATTTATATATCGTTAAACACTTTTAATCT-AATAATATAAA
1 ATTATTTTTTATTTAAAAATTAAAATTTATATATCATTAAACACTTTTAATCTGAA-AATATAAA
* * ** * * *
9496736 TTGAAATATTTGTTTTCAACTAAATTTAGATTTTTTAACTTAATTGACTTGTTATGTTAACTTTT
65 TTTAAATATTTATTTTTTACTAAAATTAGATTTTTTTACTTAATTGACTTGTTATGTTAACTTTC
* * * *
9496801 ATACGTTT-GCATTAAGATTTAAAATTTAGTTA-TTCAATATTTATAAGTTTTTATATCAATTCT
130 ACACATTTAG-ATTAAGATTTAAAATTTAATTATTTC-ATCTTTATAAGTTTTTATATCAA----
* * * * *
9496864 TATAGTTTTACATCAACGCTTTTCAATGTTAATTTTGAACTATAATTATTTTTATTTTT
189 T-T-GTTTTACGTCAAGGCTTATCTATATTAATTTTGAACTATAATTATTTTTA---TT
* * * *
9496923 ATTATTTTTTATTTAAAAATTAAAATTTATATATTATTAAACATTTTTAATAT-ATTAATATAAA
1 ATTATTTTTTATTTAAAAATTAAAATTTATATATCATTAAACACTTTTAATCTGA-AAATATAAA
** * * * * *
9496987 TTTAAATGGTTGTTTTTTACTAAAATTA-TTTTTTTTACTTAATTGACTTGTAACGTTAACTCTC
65 TTTAAATATTTATTTTTTACTAAAATTAGATTTTTTTACTTAATTGACTTGTTATGTTAACTTTC
* * * * * *
9497051 ACAAATTTACG-TT---ATGTAAAATTTAATTATTTCTTTTTTATAAATTTTTATATTAATTGTT
130 ACACATTTA-GATTAAGATTTAAAATTTAATTATTTCATCTTTATAAGTTTTTATATCAATTG-T
* * * * * *
9497112 ACCGTTGTATGTCAAGACTAATTTATATCAATTTTGAATTATAATTATTTATATTATT
193 ----TT-TACGTCAAGGCTTATCTATATTAATTTTGAACTATAATTA-TT-T-TTATT
* * * **
9497170 ATTAATTTTTATTTAAAAGTTAAAATTTATGTATCCCTAAACACTTTTAATCTGAAAATATAAAT
1 ATTATTTTTTATTTAAAAATTAAAATTTATATATCATTAAACACTTTTAATCTGAAAATATAAAT
* * * * *
9497235 TTAAATATTTATTATTTATTAAAATTAGATTTTTTT-CCTAATTAACTTGTTAAGTTAACTTTCA
66 TTAAATATTTATTTTTTACTAAAATTAGATTTTTTTACTTAATTGACTTGTTATGTTAACTTTCA
* * * * *
9497299 CATATTTACATTAAAATTTTAAAA-TTAATTATTTTA-CTTTTATGAGTTTTTATATCAA
131 CACATTTAGATTAAGA-TTTAAAATTTAATTATTTCATC-TTTATAAGTTTTTATATCAA
9497357 ATTTTATTAT
Statistics
Matches: 749, Mismatches: 128, Indels: 85
0.78 0.13 0.09
Matches are distributed among these distances:
234 2 0.00
235 59 0.08
236 82 0.11
238 4 0.01
239 1 0.00
241 47 0.06
242 116 0.15
243 47 0.06
244 1 0.00
246 3 0.00
247 173 0.23
248 57 0.08
249 1 0.00
250 68 0.09
251 87 0.12
252 1 0.00
ACGTcount: A:0.36, C:0.07, G:0.06, T:0.51
Consensus pattern (242 bp):
ATTATTTTTTATTTAAAAATTAAAATTTATATATCATTAAACACTTTTAATCTGAAAATATAAAT
TTAAATATTTATTTTTTACTAAAATTAGATTTTTTTACTTAATTGACTTGTTATGTTAACTTTCA
CACATTTAGATTAAGATTTAAAATTTAATTATTTCATCTTTATAAGTTTTTATATCAATTGTTTT
ACGTCAAGGCTTATCTATATTAATTTTGAACTATAATTATTTTTATT
Found at i:9496859 original size:22 final size:20
Alignment explanation
Indices: 9496830--9496872 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 20
9496820 TAAAATTTAG
9496830 TTATTCAATAT-TTATAAGTTT
1 TTATTCAAT-TCTTAT-AGTTT
9496851 TTATATCAATTCTTATAGTTT
1 TTAT-TCAATTCTTATAGTTT
9496872 T
1 T
9496873 ACATCAACGC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.30, C:0.07, G:0.05, T:0.58
Consensus pattern (20 bp):
TTATTCAATTCTTATAGTTT
Found at i:9503333 original size:2 final size:2
Alignment explanation
Indices: 9503328--9503361 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
9503318 ATCCCCCCTC
9503328 CT CT CT CT CT CT CT CT CT CT CT CT CT -T CT C- CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
9503362 TAACTCCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:9516278 original size:27 final size:29
Alignment explanation
Indices: 9516248--9516301 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
9516238 TTTGAAAAAA
*
9516248 ATTAAAT-AAATTTTTAT-TTTTTATTAC
1 ATTAAATCAAATTTTTATAATTTTATTAC
*
9516275 ATTAAATCAAGTTTTTATAATTTTATT
1 ATTAAATCAAATTTTTATAATTTTATT
9516302 TTAAATCAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 7 0.30
28 9 0.39
29 7 0.30
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (29 bp):
ATTAAATCAAATTTTTATAATTTTATTAC
Found at i:9520289 original size:2 final size:2
Alignment explanation
Indices: 9520282--9520310 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
9520272 CTTATAGGTT
9520282 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
9520311 TGCATACACA
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:9531324 original size:2 final size:2
Alignment explanation
Indices: 9531317--9531345 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
9531307 TGATAAACTC
9531317 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
9531346 GTGAAAATCT
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:9537821 original size:17 final size:18
Alignment explanation
Indices: 9537790--9537823 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
9537780 GAAACTCATT
*
9537790 AAAAGAAACCGCAAAAAA
1 AAAAAAAACCGCAAAAAA
9537808 AAAAAAAACC-CAAAAA
1 AAAAAAAACCGCAAAAA
9537824 TCCACCAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.76, C:0.18, G:0.06, T:0.00
Consensus pattern (18 bp):
AAAAAAAACCGCAAAAAA
Found at i:9564206 original size:30 final size:30
Alignment explanation
Indices: 9564148--9564207 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
9564138 AACTTATCTC
* *
9564148 TGATTATAAGTGACAGTTCCATCTAATACT
1 TGATTATAAGTGACAGTTCCAACAAATACT
* **
9564178 TGATTATGAGTGACAGTTTGAACAAATACT
1 TGATTATAAGTGACAGTTCCAACAAATACT
9564208 CCTTTATTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (30 bp):
TGATTATAAGTGACAGTTCCAACAAATACT
Found at i:9566413 original size:2 final size:2
Alignment explanation
Indices: 9566406--9566442 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
9566396 GACTGCAACC
9566406 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
9566443 TCTGCTCGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:9572756 original size:7 final size:7
Alignment explanation
Indices: 9572744--9572768 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
9572734 CGTGTTACCC
9572744 GTTTCGT
1 GTTTCGT
9572751 GTTTCGT
1 GTTTCGT
9572758 GTTTCGT
1 GTTTCGT
9572765 GTTT
1 GTTT
9572769 TAACTTAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.28, T:0.60
Consensus pattern (7 bp):
GTTTCGT
Found at i:9581600 original size:2 final size:2
Alignment explanation
Indices: 9581593--9581622 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
9581583 ATGCAAACCA
9581593 AG AG AG AG AG AG AG AG AG AG AG AG TAG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG -AG AG A
9581623 TAATAGAGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.47, T:0.03
Consensus pattern (2 bp):
AG
Found at i:9590431 original size:18 final size:16
Alignment explanation
Indices: 9590408--9590441 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
9590398 CAGGGGGACA
9590408 ATTTTTATATTTATATAT
1 ATTTTT-TATTT-TATAT
9590426 ATTTTTTATTTTATAT
1 ATTTTTTATTTTATAT
9590442 GTTAAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 5 0.31
18 6 0.38
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
ATTTTTTATTTTATAT
Found at i:9591362 original size:5 final size:5
Alignment explanation
Indices: 9591352--9591377 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
9591342 GAGAGAGACT
9591352 GGAAA GGAAA GGAAA GGAAA GGAAA G
1 GGAAA GGAAA GGAAA GGAAA GGAAA G
9591378 AAGAAATAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (5 bp):
GGAAA
Found at i:9605608 original size:49 final size:48
Alignment explanation
Indices: 9605550--9605705 Score: 159
Period size: 50 Copynumber: 3.2 Consensus size: 48
9605540 AAAACAGTGG
* * * *
9605550 GCTAGATAAGGCGCACTCTGTTTTAATAGCCTCAACAGCAAAACAACAC
1 GCTATATAAGGCGCACTCTGTTTTAGTAGCCTAAATAG-AAAACAACAC
* * * *
9605599 GCTATATAAGGCACACACTGTTTTAGTAGCCTAAATAGGAAACAACGC
1 GCTATATAAGGCGCACTCTGTTTTAGTAGCCTAAATAGAAAACAACAC
* * * * * *
9605647 ACTATATTAGGTGCACATTCTGTTTTTGTAGCCTAAATAGAAAACAGCAT
1 GCTATATAAGGCGCAC--TCTGTTTTAGTAGCCTAAATAGAAAACAACAC
9605697 GCTATATAA
1 GCTATATAA
9605706 CCTAAACCCC
Statistics
Matches: 85, Mismatches: 20, Indels: 3
0.79 0.19 0.03
Matches are distributed among these distances:
48 20 0.24
49 32 0.38
50 33 0.39
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.26
Consensus pattern (48 bp):
GCTATATAAGGCGCACTCTGTTTTAGTAGCCTAAATAGAAAACAACAC
Found at i:9607163 original size:140 final size:139
Alignment explanation
Indices: 9606891--9607145 Score: 384
Period size: 140 Copynumber: 1.8 Consensus size: 139
9606881 GATGTAGTAA
* * *
9606891 TCTGAAAAGGGCATGTTGATATGTTCAAACCAGGTTTTTGTAATTAAGCCATTTAATTTTGTGGT
1 TCTGAAAAGGGCATGTCGATATGTTCAAACCAGGTTCTTGTAATTAAGCCATTTAATTTTGTGAT
***
9606956 GAATCCATCCAAAGGTTTCAGTAACTCTACATGAAAAAACAATTCCCAAATACAGCAAAATTCCA
66 GAATCCATCCAAAGGTTTCAGTAACTCTACATGAAAAAACAATAAACAAATACA-CAAAATTCCA
9607021 AATCCTAGAG
130 AATCCTAGAG
* * *
9607031 TCTGAAAAGTGCATGTCGATATGTTCGAAGCAGGTTCTTGTAATTAAGCCATTTAATTTTGTGAT
1 TCTGAAAAGGGCATGTCGATATGTTCAAACCAGGTTCTTGTAATTAAGCCATTTAATTTTGTGAT
* * *
9607096 GAATTCATCCAAAGGTTTCAGTAACTCTACATTGAAACACCAATAAACAA
66 GAATCCATCCAAAGGTTTCAGTAACTCTACA-TGAAAAAACAATAAACAA
9607146 GTCCCAAATG
Statistics
Matches: 102, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
140 89 0.87
141 13 0.13
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (139 bp):
TCTGAAAAGGGCATGTCGATATGTTCAAACCAGGTTCTTGTAATTAAGCCATTTAATTTTGTGAT
GAATCCATCCAAAGGTTTCAGTAACTCTACATGAAAAAACAATAAACAAATACACAAAATTCCAA
ATCCTAGAG
Found at i:9625031 original size:147 final size:147
Alignment explanation
Indices: 9624754--9625053 Score: 503
Period size: 147 Copynumber: 2.0 Consensus size: 147
9624744 GGTCAGCTTC
9624754 TCATATTCTATCTCTACTGATCAAATGCAATATTGCAGAATGTATAATGTAAGGCGTTTGCATGT
1 TCATATTCTATCTCTACTGATCAAATGCAATATTGCAGAATGTATAATGTAAGGCGTTTGCATGT
** *
9624819 ATCAGTCAATGGAACCGTGATTTTTTGCTTTTCTTTCTTTTTCTGAAACTTTTTGTGTGGGGTTG
66 ATCAGTCAATGGAACCGTGATCCTTTGCTTCTCTTTCTTTTTCTGAAACTTTTTGTGTGGGGTTG
9624884 GACCCAAAGATATTTTT
131 GACCCAAAGATATTTTT
* * * *
9624901 TCATGTTCTGTCTCTACTGATCAAATGCAATATTGCAGAATGTATAATGTAATGTGTTTGCATGT
1 TCATATTCTATCTCTACTGATCAAATGCAATATTGCAGAATGTATAATGTAAGGCGTTTGCATGT
*
9624966 ATCAGTCAATGGAACTGTGATCCTTTG-TCTCTCTTTCTTTTTCTGAAACTTTTTGTGTGGGGTT
66 ATCAGTCAATGGAACCGTGATCCTTTGCT-TCTCTTTCTTTTTCTGAAACTTTTTGTGTGGGGTT
9625030 GGACCCAAAGATATTTTT
130 GGACCCAAAGATATTTTT
9625048 TGCATA
1 T-CATA
9625054 ATAGTTTGTT
Statistics
Matches: 142, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
146 1 0.01
147 138 0.97
148 3 0.02
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.42
Consensus pattern (147 bp):
TCATATTCTATCTCTACTGATCAAATGCAATATTGCAGAATGTATAATGTAAGGCGTTTGCATGT
ATCAGTCAATGGAACCGTGATCCTTTGCTTCTCTTTCTTTTTCTGAAACTTTTTGTGTGGGGTTG
GACCCAAAGATATTTTT
Found at i:9630306 original size:22 final size:23
Alignment explanation
Indices: 9630280--9630322 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
9630270 TGAAGTTGTT
9630280 TGTGTTCCTGTT-GGTGTTGATG
1 TGTGTTCCTGTTCGGTGTTGATG
* *
9630302 TGTGTTTCTGTTCGGTTTTGA
1 TGTGTTCCTGTTCGGTGTTGA
9630323 CCTCTGATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.05, C:0.09, G:0.33, T:0.53
Consensus pattern (23 bp):
TGTGTTCCTGTTCGGTGTTGATG
Found at i:9643818 original size:12 final size:12
Alignment explanation
Indices: 9643801--9643866 Score: 84
Period size: 12 Copynumber: 5.8 Consensus size: 12
9643791 TTCCTCCTCA
9643801 TCATCATCAAAC
1 TCATCATCAAAC
*
9643813 TCATCATCAAAT
1 TCATCATCAAAC
*
9643825 TCATCATCGAAC
1 TCATCATCAAAC
*
9643837 TCATCACCAAAC
1 TCATCATCAAAC
9643849 TCATCAT--AA-
1 TCATCATCAAAC
9643858 TCATCATCA
1 TCATCATCA
9643867 GAATAATCTA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
9 7 0.15
10 2 0.04
12 37 0.80
ACGTcount: A:0.39, C:0.32, G:0.02, T:0.27
Consensus pattern (12 bp):
TCATCATCAAAC
Found at i:9647438 original size:2 final size:2
Alignment explanation
Indices: 9647431--9647456 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9647421 GAATAAATAA
9647431 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
9647457 CTCTCTCTCT
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:9654323 original size:2 final size:2
Alignment explanation
Indices: 9654316--9654351 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
9654306 ATCAAAATCC
*
9654316 AT AT AT AT AT AT AT AT AT AT AT -T AA AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9654352 GATAAAACAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:9655710 original size:30 final size:30
Alignment explanation
Indices: 9655674--9655733 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
9655664 GAATCTTCAC
*
9655674 AGATGTGAGTAAACTCGAATCTTTACTAAT
1 AGATGTGAATAAACTCGAATCTTTACTAAT
* *
9655704 AGATGTGAATAGACTCGGATCTTTACTAAT
1 AGATGTGAATAAACTCGAATCTTTACTAAT
9655734 GTGGTCCTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.33
Consensus pattern (30 bp):
AGATGTGAATAAACTCGAATCTTTACTAAT
Found at i:9656504 original size:373 final size:375
Alignment explanation
Indices: 9655801--9656505 Score: 1189
Period size: 373 Copynumber: 1.9 Consensus size: 375
9655791 ACAAAATTAG
*
9655801 TTGCCTTGTAACATTTGATATCAAAGTAAGTCAAAATTTTCATAGATGTGACCAGACTTGGATCA
1 TTGCCTTGTAACATTTAATATCAAAGTAAGTCAAAATTTTCATAGATGTGACCAGACTTGG---A
*
9655866 AGTCTTCATTGATGTGGATACTTATCAAAGACACAAAGATCAAGGTAAACCTAAATTAATGTAAA
63 AGTCTTCACTGATGTGGATACTTATCAAAGACACAAAGATCAAGGTAAACCTAAATTAATGTAAA
* * *
9655931 AATCTCTATTTTTTATGATTAAAGAGCCACTACAATGAAAGATACAAAGTTGAAGTGGATTTAGA
128 AATCCCTATCTTCTATGATTAAAGAGCCACTACAATGAAAGATACAAAGTTGAAGTGGATTTAGA
*
9655996 CTAATGTAAGAGTCTCTCTATACGAGATTGGATTTAAATTTTGGTTTCTGACATTTGGTATCAAA
193 CTAATGTAAGAGTCTCTCTACACGAGATTGGATTTAAATTTTGGTTTCTGACATTTGGTATCAAA
* * * * *
9656061 ATAAACTTGAATCTTTTAAGGATGTGAGTAGACTCCAATCGTCATTGATGTGGATCCCCATGAGA
258 ATAAACCTGAATCCTTTAAAGATGTGAGTAGACTCCAATCGTCATTGATATGGATCCCCATGAAA
9656126 GATATAATTCTAACCAGCATAATAGCCCCTCTATACAAAATTAGGTTTAAGTT
323 GATATAATTCTAACCAGCATAATAGCCCCTCTATACAAAATTAGGTTTAAGTT
9656179 TTGCCTTGTAACATTTAATATCAAAGTAAGTCAAAATTTTCATAGATGTGACCAGACTTGG-A-T
1 TTGCCTTGTAACATTTAATATCAAAGTAAGTCAAAATTTTCATAGATGTGACCAGACTTGGAAGT
* * *
9656242 CTTCACTGGTGTGGATCCTTATCAAAGATACAAAGATCAAGGTAAACCTAAATTAATGTAAAAAT
66 CTTCACTGATGTGGATACTTATCAAAGACACAAAGATCAAGGTAAACCTAAATTAATGTAAAAAT
*
9656307 CCCTATCTTCTATGATTAAAGAGCCACTACAATGAAAGATACAAGGTTGAAGTGGATTTAGACTA
131 CCCTATCTTCTATGATTAAAGAGCCACTACAATGAAAGATACAAAGTTGAAGTGGATTTAGACTA
* * *
9656372 ATGTAAGAGTCTCTCTACATGAGATTGGATTTAAATTTTGGTTTTTGACGTTTGGTATCAAAATA
196 ATGTAAGAGTCTCTCTACACGAGATTGGATTTAAATTTTGGTTTCTGACATTTGGTATCAAAATA
**
9656437 AACCTGAATCCTTTAAAGATGTGAGTAGACTCCAATCGTCATTGATATGGATCTTCATGAAAGAT
261 AACCTGAATCCTTTAAAGATGTGAGTAGACTCCAATCGTCATTGATATGGATCCCCATGAAAGAT
9656502 ATAA
326 ATAA
9656506 AGATTGAGAT
Statistics
Matches: 307, Mismatches: 20, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
373 246 0.80
374 1 0.00
378 60 0.20
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (375 bp):
TTGCCTTGTAACATTTAATATCAAAGTAAGTCAAAATTTTCATAGATGTGACCAGACTTGGAAGT
CTTCACTGATGTGGATACTTATCAAAGACACAAAGATCAAGGTAAACCTAAATTAATGTAAAAAT
CCCTATCTTCTATGATTAAAGAGCCACTACAATGAAAGATACAAAGTTGAAGTGGATTTAGACTA
ATGTAAGAGTCTCTCTACACGAGATTGGATTTAAATTTTGGTTTCTGACATTTGGTATCAAAATA
AACCTGAATCCTTTAAAGATGTGAGTAGACTCCAATCGTCATTGATATGGATCCCCATGAAAGAT
ATAATTCTAACCAGCATAATAGCCCCTCTATACAAAATTAGGTTTAAGTT
Found at i:9683414 original size:49 final size:49
Alignment explanation
Indices: 9683361--9683458 Score: 162
Period size: 49 Copynumber: 2.0 Consensus size: 49
9683351 GTTGTCTGCG
9683361 ATTGAAGTATTGATAGATCGATTATT-ATTCTCTTTTAGTATATAAAATA
1 ATTGAAGTATTGATAGATCGATT-TTAATTCTCTTTTAGTATATAAAATA
9683410 ATTGAAGTATTGATAGATCGATTTTAAAATTCTCTTTTAGTATATAAAA
1 ATTGAAGTATTGATAGATCGATTTT--AATTCTCTTTTAGTATATAAAA
9683459 AATAATCTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
48 2 0.04
49 23 0.50
51 21 0.46
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (49 bp):
ATTGAAGTATTGATAGATCGATTTTAATTCTCTTTTAGTATATAAAATA
Found at i:9695380 original size:2 final size:2
Alignment explanation
Indices: 9695375--9695405 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
9695365 AAAAAAAGAC
9695375 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9695406 GTAGAATGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9718702 original size:28 final size:28
Alignment explanation
Indices: 9718671--9718725 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
9718661 TATTACAAAC
9718671 AAATAAATTACATCAAAAATAAATAAAT
1 AAATAAATTACATCAAAAATAAATAAAT
* *
9718699 AAATACATTACATCAAATATAAATAAA
1 AAATAAATTACATCAAAAATAAATAAA
9718726 ATTTCAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.65, C:0.09, G:0.00, T:0.25
Consensus pattern (28 bp):
AAATAAATTACATCAAAAATAAATAAAT
Found at i:9730141 original size:15 final size:16
Alignment explanation
Indices: 9730121--9730150 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
9730111 CTGTTACGTG
9730121 GATTTT-ATTTTTAAT
1 GATTTTAATTTTTAAT
9730136 GATTTTAATTTTTAA
1 GATTTTAATTTTTAA
9730151 AAATTAAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (16 bp):
GATTTTAATTTTTAAT
Found at i:9732478 original size:14 final size:14
Alignment explanation
Indices: 9732459--9732485 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
9732449 CTTTGCTCTG
9732459 CAATCAAATCTCAT
1 CAATCAAATCTCAT
9732473 CAATCAAATCTCA
1 CAATCAAATCTCA
9732486 AACTTTGCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.30, G:0.00, T:0.26
Consensus pattern (14 bp):
CAATCAAATCTCAT
Found at i:9734005 original size:20 final size:19
Alignment explanation
Indices: 9733982--9734035 Score: 58
Period size: 20 Copynumber: 2.9 Consensus size: 19
9733972 TATTTTTAAA
9733982 ATGATTAAATTAATTAATGT
1 ATGATTAAATTAATTAA-GT
* *
9734002 ATGATCAACTTAATTAAGT
1 ATGATTAAATTAATTAAGT
*
9734021 A--ATTTAATTAATTAA
1 ATGATTAAATTAATTAA
9734036 ATAGAATAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
17 11 0.38
19 3 0.10
20 15 0.52
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (19 bp):
ATGATTAAATTAATTAAGT
Found at i:9736249 original size:2 final size:2
Alignment explanation
Indices: 9736242--9736267 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9736232 ATTCTCAAGA
9736242 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
9736268 GGGTAGTTAC
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:9740972 original size:15 final size:16
Alignment explanation
Indices: 9740941--9740982 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
9740931 AAATTATAAA
*
9740941 TAAAAAATTAATATTT
1 TAAAATATTAATATTT
9740957 TAAAATATTAAT-TTT
1 TAAAATATTAATATTT
*
9740972 TAAATTATTAA
1 TAAAATATTAA
9740983 GTGAAATTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 13 0.54
16 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TAAAATATTAATATTT
Found at i:9741141 original size:17 final size:17
Alignment explanation
Indices: 9741108--9741141 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
9741098 TTAAAATTGT
*
9741108 TAATATTTTAATCATAA
1 TAATATTTAAATCATAA
*
9741125 TAATATTTAAATTATAA
1 TAATATTTAAATCATAA
9741142 ATTAAATTAC
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:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATATTTAAATCATAA
Found at i:9741295 original size:19 final size:21
Alignment explanation
Indices: 9741273--9741317 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
9741263 GATTAAATTA
9741273 TAAATAA-AA-TATTAATACT
1 TAAATAACAATTATTAATACT
*
9741292 TAAATAATCAATTATTAATATT
1 TAAATAA-CAATTATTAATACT
9741314 TAAA
1 TAAA
9741318 AGATAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 7 0.32
21 2 0.09
22 13 0.59
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATAACAATTATTAATACT
Found at i:9765448 original size:20 final size:20
Alignment explanation
Indices: 9765411--9765449 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
9765401 AGTAGTTAAA
*
9765411 TTGACATGATCATGTGATAG
1 TTGACATGATCATATGATAG
* *
9765431 TTGACATTATTATATGATA
1 TTGACATGATCATATGATA
9765450 ATTAATATTG
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:0.08, G:0.18, T:0.41
Consensus pattern (20 bp):
TTGACATGATCATATGATAG
Found at i:9767191 original size:23 final size:21
Alignment explanation
Indices: 9767157--9767204 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 21
9767147 ATCAAAGGAT
*
9767157 TTAATATTAATAATTTAT-TTA
1 TTAATATTAAT-ATTAATCTTA
9767178 TTAATATATAAATATTAATCTTA
1 TTAATAT-T-AATATTAATCTTA
9767201 TTAA
1 TTAA
9767205 CAAAATGATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 7 0.30
22 6 0.26
23 10 0.43
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
TTAATATTAATATTAATCTTA
Found at i:9773642 original size:20 final size:20
Alignment explanation
Indices: 9773619--9773656 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
9773609 ACATCCCCTT
*
9773619 CTGATTGATAACATTTCTTC
1 CTGATTGATAACACTTCTTC
*
9773639 CTGATTTATAACACTTCT
1 CTGATTGATAACACTTCT
9773657 CATCTCTATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.21, G:0.08, T:0.45
Consensus pattern (20 bp):
CTGATTGATAACACTTCTTC
Found at i:9776418 original size:20 final size:22
Alignment explanation
Indices: 9776390--9776429 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
9776380 AAAGAACAAA
9776390 TTTTCAGAG-GAGAG-GAGAAC
1 TTTTCAGAGAGAGAGAGAGAAC
*
9776410 TTTTGAGAGAGAGAGAGAGA
1 TTTTCAGAGAGAGAGAGAGA
9776430 GAGGGTGGCG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 5 0.29
22 4 0.24
ACGTcount: A:0.38, C:0.05, G:0.38, T:0.20
Consensus pattern (22 bp):
TTTTCAGAGAGAGAGAGAGAAC
Found at i:9778369 original size:2 final size:2
Alignment explanation
Indices: 9778362--9778386 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9778352 TCGCTTCTTG
9778362 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 A
9778387 AATTTCATCG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9784286 original size:171 final size:172
Alignment explanation
Indices: 9784010--9784337 Score: 444
Period size: 171 Copynumber: 1.9 Consensus size: 172
9784000 AAAACCTATA
*
9784010 TTCTAAAGAGAAATTTCTTCACCCTTTCCCGATGTTTCAGGAACTACCCAGGAAAGACATTGTTA
1 TTCTAAAGAAAAATTTCTTCACCCTTTCCCGATGTTTCAGGAACTACCCAGGAAAGACATTGTTA
* * * *
9784075 GTTCAAATGTTTACCAAAGGCGTGACATATGC-CCTTTTTTTTCTTTCCATATTGTTAGTTCAAA
66 GTTAAAATGTTTACCAAAGGCGTGACACATGCTCCTTTTTTTTCTTTCCATATTGGTAGTTAAAA
* *
9784139 TGTTACCAGTATTTCCATAATGTTCTTAAAGGAAGCATATTT
131 TCTTACCAGCATTTCCATAATGTTCTTAAAGGAAGCATATTT
* * *
9784181 TTCTATAGAAAAATTTCTTCACCCTTTTCTC-ATGTTTCAGGAACTACCCTGGAAAGACATTGTT
1 TTCTAAAGAAAAATTTCTTCACCC-TTTCCCGATGTTTCAGGAACTACCCAGGAAAGACATTGTT
** * * * ** *
9784245 AGTTAAAATGTTTATGAAAGGCTTGATACATGGTTTTTTTTTTTTTTTTTCCATATTGGTAGTTA
65 AGTTAAAATGTTTACCAAAGGCGTGACACAT-G-CTCCTTTTTTTTCTTTCCATATTGGTAGTTA
*
9784310 AAATCTTACCAGCATTTCCATATTGTTC
128 AAATCTTACCAGCATTTCCATAATGTTC
9784338 AAATGTTTGA
Statistics
Matches: 134, Mismatches: 19, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
171 79 0.59
172 6 0.04
174 49 0.37
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.41
Consensus pattern (172 bp):
TTCTAAAGAAAAATTTCTTCACCCTTTCCCGATGTTTCAGGAACTACCCAGGAAAGACATTGTTA
GTTAAAATGTTTACCAAAGGCGTGACACATGCTCCTTTTTTTTCTTTCCATATTGGTAGTTAAAA
TCTTACCAGCATTTCCATAATGTTCTTAAAGGAAGCATATTT
Found at i:9787270 original size:6 final size:7
Alignment explanation
Indices: 9787246--9787277 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
9787236 ATATTTCTTT
9787246 CTTTTCC
1 CTTTTCC
9787253 CTTTTCC
1 CTTTTCC
9787260 CTTTTCC
1 CTTTTCC
*
9787267 TTTTTCC
1 CTTTTCC
9787274 CTTT
1 CTTT
9787278 GCTTTCCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (7 bp):
CTTTTCC
Found at i:9787876 original size:164 final size:160
Alignment explanation
Indices: 9787569--9787895 Score: 492
Period size: 160 Copynumber: 2.0 Consensus size: 160
9787559 AATGGTACTT
* ** * * *
9787569 AATTGATTCGGAAACCCTAAACCTGAGTTCTAAACTGCTGTACATGATTTATAGAACTCACTGGC
1 AATTAATTCGGAAACCCTAAACCCAAGTTCGAAACTGCTGCACATGATTCATAGAACTCACTGGC
9787634 ATATACTAGTACTGCTACTGGTAATTAGACAATTCTCATAACATTTTCCAAAACAAATCATTTGA
66 ATATACTAGTACTGCTACTGGTAATTAGACAATTCTCATAACATTTTCCAAAACAAATCATTTGA
9787699 TGCACCAGTCAAAACAACAGAAGAAGCAGG
131 TGCACCAGTCAAAACAACAGAAGAAGCAGG
* * *
9787729 AATTAATTTGGAAACCCTAAACCCAAGTTCGAAGCTGCTGCACATGATTCATAGATCTCACTGGC
1 AATTAATTCGGAAACCCTAAACCCAAGTTCGAAACTGCTGCACATGATTCATAGAACTCACTGGC
* * * *
9787794 ATTTACTAGTACTGCTGCTGGTAATTAATTAGACAGTTCTCATAACATTTTCCGAAACAAATCAT
66 ATATACTAGTACTGCTACTGG----TAATTAGACAATTCTCATAACATTTTCCAAAACAAATCAT
*
9787859 TTGATGCACCAGTCAAAACAACAGAAGAAGTAGG
127 TTGATGCACCAGTCAAAACAACAGAAGAAGCAGG
9787893 AAT
1 AAT
9787896 ATCAACATAT
Statistics
Matches: 149, Mismatches: 14, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
160 75 0.50
164 74 0.50
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (160 bp):
AATTAATTCGGAAACCCTAAACCCAAGTTCGAAACTGCTGCACATGATTCATAGAACTCACTGGC
ATATACTAGTACTGCTACTGGTAATTAGACAATTCTCATAACATTTTCCAAAACAAATCATTTGA
TGCACCAGTCAAAACAACAGAAGAAGCAGG
Found at i:9791490 original size:73 final size:72
Alignment explanation
Indices: 9791370--9791649 Score: 210
Period size: 73 Copynumber: 3.8 Consensus size: 72
9791360 TACAAGAAGA
** * * * *
9791370 GAAATCTT-TAAGATATCTTGTTCAACCTTTCTCACTTTTCTGCTGCAAGAAGAGAATATTAGGA
1 GAAAT-TTCTAAGATATCTT-ACCAACCTTTCTCACTTTTATACTGCAAGAAGAGAACATTACGA
9791434 TTCC-AATTT
64 -TCCAAATTT
* * *
9791443 GAAATTTCTAAGATATCTTACCAACCTTTTTCCACTTTTATATTGCAAGAATAGAACATTACGAT
1 GAAATTTCTAAGATATCTTACCAACCTTTCT-CACTTTTATACTGCAAGAAGAGAACATTACGAT
9791508 CCAAATTT
65 CCAAATTT
* * * **
9791516 GAAATTTCTAACATATCTTACATACTAACTCTTTC-CTACTTTTATGCTACAAGAAGAGAACACA
1 GAAATTTCTAAGATATCTTAC---C-AAC-CTTTCTC-ACTTTTATACTGCAAGAAGAGAACATT
*
9791580 ACGA-CTCGAATTT
60 ACGATC-CAAATTT
* * * * * * * *
9791593 GAAATCTCT-AGACACCTTGCCAATCCTTTCCCACTTTTATGCTACAAGAAAAGAACA
1 GAAATTTCTAAGATATCTTACCAA-CCTTTCTCACTTTTATACTGCAAGAAGAGAACA
9791650 CCATGACTCA
Statistics
Matches: 171, Mismatches: 24, Indels: 25
0.78 0.11 0.11
Matches are distributed among these distances:
72 45 0.26
73 70 0.41
76 10 0.06
77 42 0.25
78 4 0.02
ACGTcount: A:0.34, C:0.21, G:0.10, T:0.34
Consensus pattern (72 bp):
GAAATTTCTAAGATATCTTACCAACCTTTCTCACTTTTATACTGCAAGAAGAGAACATTACGATC
CAAATTT
Found at i:9791592 original size:77 final size:73
Alignment explanation
Indices: 9791438--9791650 Score: 184
Period size: 77 Copynumber: 2.9 Consensus size: 73
9791428 TTAGGATTCC
* * * * * **
9791438 AATTTGAAATTTCTAAGATATCTTACCAACCTTTTTCCACTTTTATATTGCAAGAATAGAACATT
1 AATTTGAAATTTCTAACATATCTTACCAACCTCTTTCCACTTTTATACTACAAGAAGAGAACACA
9791503 ACGATCCA
66 ACGATCCA
*
9791511 AATTTGAAATTTCTAACATATCTTA-CATACTAACTCTTTCCTACTTTTATGCTACAAGAAGAGA
1 AATTTGAAATTTCTAACATATCTTACCA-AC---CTCTTTCC-ACTTTTATACTACAAGAAGAGA
*
9791575 ACACAACGA-CTCG
61 ACACAACGATC-CA
* * * * * *
9791588 AATTTGAAATCTCTAGAC--ACCTTGCCAATCCT-TTCCCACTTTTATGCTACAAGAAAAGAACA
1 AATTTGAAATTTCTA-ACATATCTTACCAA-CCTCTTTCCACTTTTATACTACAAGAAGAGAACA
9791650 C
64 C
9791651 CATGACTCAA
Statistics
Matches: 117, Mismatches: 14, Indels: 19
0.78 0.09 0.13
Matches are distributed among these distances:
72 27 0.23
73 30 0.26
74 2 0.02
76 13 0.11
77 43 0.37
78 2 0.02
ACGTcount: A:0.36, C:0.23, G:0.09, T:0.33
Consensus pattern (73 bp):
AATTTGAAATTTCTAACATATCTTACCAACCTCTTTCCACTTTTATACTACAAGAAGAGAACACA
ACGATCCA
Found at i:9797119 original size:2 final size:2
Alignment explanation
Indices: 9797103--9797139 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
9797093 ACGACACTTT
* *
9797103 TC TC TC CC TC CC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
9797140 ACACCAACAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (2 bp):
TC
Found at i:9805840 original size:3 final size:3
Alignment explanation
Indices: 9805832--9805862 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
9805822 TGGTTAAAGA
9805832 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
9805863 GAATTTTAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:9808674 original size:2 final size:2
Alignment explanation
Indices: 9808667--9808694 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
9808657 ATTGAGCTTA
9808667 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
9808695 TAGTACTGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9811716 original size:2 final size:2
Alignment explanation
Indices: 9811709--9811734 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9811699 ATATGCCTGC
9811709 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
9811735 TGGATCAAAA
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:9812088 original size:19 final size:19
Alignment explanation
Indices: 9812064--9812101 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
9812054 TCTCTCCCTC
9812064 TTTCTTTCGTTT-TTTCTCT
1 TTTCTTTC-TTTCTTTCTCT
9812083 TTTCTTTCTTTCTTTCTCT
1 TTTCTTTCTTTCTTTCTCT
9812102 CGCCCTTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.00, C:0.24, G:0.03, T:0.74
Consensus pattern (19 bp):
TTTCTTTCTTTCTTTCTCT
Found at i:9823380 original size:85 final size:86
Alignment explanation
Indices: 9823199--9823393 Score: 290
Period size: 84 Copynumber: 2.3 Consensus size: 86
9823189 CCCAAACCAT
* *
9823199 AAAA-AATAGTAAAACAATGAAACAAAGAAGCAATCGTGTGAATTATCAAAGAAAACCCATAGTC
1 AAAACAAT-GTAAAACAA-AAAACAAAGAAGCAATCATGTGAATTATCAAAGAAAACCCATAGTC
*
9823263 CTAAACCCCAGAAGTAACTTCAA
64 CTAAACCCCAGAAGTAACTTAAA
* * *
9823286 AAGAC-ATGTAAAACAAAAAACAAAGAAGCAATCATGTGAATTATCAAAG-AAACCCATATTCTT
1 AAAACAATGTAAAACAAAAAACAAAGAAGCAATCATGTGAATTATCAAAGAAAACCCATAGTCCT
9823349 AAACCCCAGAAGTAACTTAAA
66 AAACCCCAGAAGTAACTTAAA
9823370 AAAACAATGTAAAAC-AAAAACAAA
1 AAAACAATGTAAAACAAAAAACAAA
9823394 CCCCCGCCCC
Statistics
Matches: 99, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
84 45 0.45
85 40 0.40
86 9 0.09
87 5 0.05
ACGTcount: A:0.55, C:0.17, G:0.11, T:0.17
Consensus pattern (86 bp):
AAAACAATGTAAAACAAAAAACAAAGAAGCAATCATGTGAATTATCAAAGAAAACCCATAGTCCT
AAACCCCAGAAGTAACTTAAA
Found at i:9824898 original size:72 final size:70
Alignment explanation
Indices: 9824752--9824902 Score: 187
Period size: 72 Copynumber: 2.1 Consensus size: 70
9824742 CTTAAATTTT
* * *
9824752 TAAATACATCTTACCGTTAGTTAATTATAAATAAAAATATATATGAGAAAAAGTAGCTACTAGAG
1 TAAATACATCTTACCGTTAGTTAATTATAAATAAAAAAATATATAAGAAAAAATAGCTACTAGAG
*
9824817 ATCAT
66 ATCAC
* * * *
9824822 TAAATATATTTTACCGTTAGTTGATTATAAATGAAAAAAAATATATAAGAAAAAATAG-TAGTTA
1 TAAATACATCTTACCGTTAGTTAATTATAAAT--AAAAAAATATATAAGAAAAAATAGCTA-CTA
*
9824886 GAGATCGC
63 GAGATCAC
9824894 TAAATACAT
1 TAAATACAT
9824903 AGTACTATTA
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
70 29 0.43
71 2 0.03
72 37 0.54
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.32
Consensus pattern (70 bp):
TAAATACATCTTACCGTTAGTTAATTATAAATAAAAAAATATATAAGAAAAAATAGCTACTAGAG
ATCAC
Found at i:9825509 original size:30 final size:30
Alignment explanation
Indices: 9825439--9825515 Score: 77
Period size: 32 Copynumber: 2.5 Consensus size: 30
9825429 ATTGTTAATT
* *
9825439 ATAAAAA-TTTATTTAATATAAAATAAAAA
1 ATAAAAACTTAATTGAATATAAAATAAAAA
*
9825468 ATACATGAACTTAATTGAATATAATAA-AAAAA
1 ATA-A-AAACTTAATTGAATATAA-AATAAAAA
*
9825500 ATAAAAACTTATTTGA
1 ATAAAAACTTAATTGA
9825516 TTTTCTTGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
29 3 0.08
30 11 0.28
31 3 0.08
32 20 0.51
33 2 0.05
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (30 bp):
ATAAAAACTTAATTGAATATAAAATAAAAA
Found at i:9836582 original size:20 final size:21
Alignment explanation
Indices: 9836553--9836596 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
9836543 TCACTTAATT
*
9836553 AATCTCC-TTTAATTTCGAAG
1 AATCTCCTTTTAATTTCAAAG
*
9836573 AATCTTCTTTTAATTTCAAAG
1 AATCTCCTTTTAATTTCAAAG
9836594 AAT
1 AAT
9836597 GGATATATGA
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:0.34, C:0.16, G:0.07, T:0.43
Consensus pattern (21 bp):
AATCTCCTTTTAATTTCAAAG
Found at i:9840795 original size:22 final size:22
Alignment explanation
Indices: 9840768--9840817 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
9840758 TTTATAATAT
*
9840768 AATTTAGACA-TAATATTTAAAA
1 AATTTAGAAATTAAT-TTTAAAA
* *
9840790 ATTTTATAAATTAATTTTAAAA
1 AATTTAGAAATTAATTTTAAAA
9840812 AATTTA
1 AATTTA
9840818 ATAAACTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (22 bp):
AATTTAGAAATTAATTTTAAAA
Found at i:9840812 original size:23 final size:24
Alignment explanation
Indices: 9840778--9840832 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
9840768 AATTTAGACA
*
9840778 TAATATTT-AAAAATTTTATAAA-T
1 TAAT-TTTAAAAAATTTAATAAACT
9840801 TAATTTTAAAAAATTTAATAAACT
1 TAATTTTAAAAAATTTAATAAACT
*
9840825 TATTTTTA
1 TAATTTTA
9840833 TTATTTTAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 3 0.11
23 17 0.61
24 8 0.29
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (24 bp):
TAATTTTAAAAAATTTAATAAACT
Found at i:9842316 original size:137 final size:133
Alignment explanation
Indices: 9842055--9842327 Score: 438
Period size: 139 Copynumber: 2.0 Consensus size: 133
9842045 TTACAAATTG
* *
9842055 ATAATAAGGCAATGGTTANGGATCGGTTGTCACCGTACTCATCCTGTCCTAACCTAGATGTAATT
1 ATAATAAGGCAATGGTTAGGGATCGGTTGTCACCGTACTCATCCTGCCCTAACCTAGATGTAATT
9842120 AGAGCAATTAAAGACTTGTTAGTAGGCATTGGAAGGTTAGTATAAGTCATATACATATATATATA
66 AGAGCAATTAAAGACTTGTTAGTAGGCATTGGAAGGTTAGTATAAGTCATATA-ATATATATATA
9842185 TATA
130 TATA
*
9842189 ATAATAAGGCAGTGGTTCAGGGAATCGGTTGTCACCGTACTCATCCTTGCCCTAACCTAGATGTA
1 ATAATAAGGCAATGGTT-AGGG-ATCGGTTGTCACCGTACTCATCC-TGCCCTAACCTAGATGTA
* *
9842254 ATTAGAGCAATTAAAGACTTGTTAAAGTAGGCATTGGGAGGTTAGTATAAGTCATATGTATATAT
63 ATTAGAGCAATTAAAGACTTGTT--AGTAGGCATTGGAAGGTTAGTATAAGTCATAT-AATATAT
9842319 ATATATATA
125 ATATATATA
9842328 TATATATATA
Statistics
Matches: 128, Mismatches: 5, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
134 16 0.12
135 3 0.02
136 23 0.18
137 40 0.31
139 46 0.36
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.32
Consensus pattern (133 bp):
ATAATAAGGCAATGGTTAGGGATCGGTTGTCACCGTACTCATCCTGCCCTAACCTAGATGTAATT
AGAGCAATTAAAGACTTGTTAGTAGGCATTGGAAGGTTAGTATAAGTCATATAATATATATATAT
ATA
Found at i:9842319 original size:2 final size:2
Alignment explanation
Indices: 9842307--9842351 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
9842297 AGTATAAGTC
*
9842307 AT AT GT 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
9842349 AT A
1 AT A
9842352 GGAAAAGAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9846571 original size:19 final size:19
Alignment explanation
Indices: 9846547--9846586 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
9846537 TAAAATACTC
9846547 ATTTAAACAAATTAATTAT
1 ATTTAAACAAATTAATTAT
* *
9846566 ATTTAAATAAATTTATTAT
1 ATTTAAACAAATTAATTAT
9846585 AT
1 AT
9846587 CATATACCTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTTAAACAAATTAATTAT
Found at i:9852684 original size:28 final size:30
Alignment explanation
Indices: 9852644--9852699 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
9852634 ATTTAAATAA
9852644 ATTCAAATAAATT-CTTATATTTTTATTAT
1 ATTCAAATAAATTACTTATATTTTTATTAT
* *
9852673 ATTC-AATCAATTATTTATATTTTTATT
1 ATTCAAATAAATTACTTATATTTTTATT
9852700 TTAAATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (30 bp):
ATTCAAATAAATTACTTATATTTTTATTAT
Found at i:9852988 original size:29 final size:28
Alignment explanation
Indices: 9852943--9852997 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 28
9852933 TTTGATCTAA
9852943 AATAAAAATAAATAAATTGAATTAAATAT
1 AATAAAAATAAATAAATT-AATTAAATAT
*
9852972 AATAAAATATAAA-AAATTATTTAAAT
1 AATAAAA-ATAAATAAATTAATTAAAT
9852998 TATCTAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 7 0.29
29 12 0.50
30 5 0.21
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (28 bp):
AATAAAAATAAATAAATTAATTAAATAT
Found at i:9870038 original size:2 final size:2
Alignment explanation
Indices: 9870031--9870071 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
9870021 AAAAGAAGAC
*
9870031 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
9870072 AATGGTCCAG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:9881146 original size:2 final size:2
Alignment explanation
Indices: 9881134--9881169 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
9881124 CCTCACAGTT
9881134 TC TC TC T- TC TC TC TC TC TC TC TC TC TC -C TC -C TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
9881170 TTTCTCAGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 3 0.10
2 28 0.90
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:9881154 original size:8 final size:8
Alignment explanation
Indices: 9881134--9881169 Score: 51
Period size: 7 Copynumber: 4.9 Consensus size: 8
9881124 CCTCACAGTT
9881134 TCTCTCT-
1 TCTCTCTC
9881141 TCTCTCTC
1 TCTCTCTC
9881149 TCTCTCTC
1 TCTCTCTC
9881157 TCTC-CTC
1 TCTCTCTC
9881164 -CTCTCT
1 TCTCTCT
9881170 TTTCTCAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 3 0.11
7 12 0.44
8 12 0.44
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (8 bp):
TCTCTCTC
Found at i:9887911 original size:237 final size:237
Alignment explanation
Indices: 9887478--9887923 Score: 513
Period size: 237 Copynumber: 1.9 Consensus size: 237
9887468 CCGGTGATAT
* *
9887478 TTGTCTCTTCCAGGTCTATAAACACAAGTTTTGTCACTATCATATCCACTTTTTGCCATGAGAAT
1 TTGTCTCTTCCAGGTCTATAAACACAAGTTTTGTCACTACCATATCCACTTTTAGCCATGAGAAT
* * * * * *
9887543 GTGATTGGAAACATTCTTCAAACCAATATTTTCTCTAAATGAATTTGCCAATTAAATGGATAACA
66 GTGATCGAAAACATTCTTAAAACCAATATTTCCTCTAAATAAACTTGCCAATTAAATGGATAACA
* * ********** * *
9887608 ATAGACACTTATAACATATCTCAAATATNNNNNNNNNNAACATCACAAGGTAACCGCAGCCATAT
131 ATAGACACTCAAAACATATCTCAAATATTTAGAGTGTAAACATCACAAGGAAACCACAGCCATAT
9887673 CATTAACAAAGCAAGTTGCATGATTACACCTCAACTAATAAA
196 CATTAACAAAGCAAGTTGCATGATTACACCTCAACTAATAAA
* * * ** *
9887715 TTGTCTCTTCTAGGTCTTTAAGCATGAGTTTTGTCACTACCATATCGAGC-TTTAGCCATGA-AA
1 TTGTCTCTTCCAGGTCTATAAACACAAGTTTTGTCACTACCATATCCA-CTTTTAGCCATGAGAA
* * *
9887778 TTGTGATCGAAAAGATTCTTAAAACCCATGTTTCCTCTAAATAAACTT-CCACATTAAATGGATA
65 -TGTGATCGAAAACATTCTTAAAACCAATATTTCCTCTAAATAAACTTGCCA-ATTAAATGGATA
* * * *
9887842 ACAATAGACACTCAAAACATATCTCATATATTTAGAGTGTAAACATGACAAGGAAAGCACTTG-C
128 ACAATAGACACTCAAAACATATCTCAAATATTTAGAGTGTAAACATCACAAGGAAACCAC-AGCC
9887906 ATATCATTAACAAAGCAA
192 ATATCATTAACAAAGCAA
9887924 CATGCAGGAC
Statistics
Matches: 170, Mismatches: 35, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
236 5 0.03
237 163 0.96
238 2 0.01
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.30
Consensus pattern (237 bp):
TTGTCTCTTCCAGGTCTATAAACACAAGTTTTGTCACTACCATATCCACTTTTAGCCATGAGAAT
GTGATCGAAAACATTCTTAAAACCAATATTTCCTCTAAATAAACTTGCCAATTAAATGGATAACA
ATAGACACTCAAAACATATCTCAAATATTTAGAGTGTAAACATCACAAGGAAACCACAGCCATAT
CATTAACAAAGCAAGTTGCATGATTACACCTCAACTAATAAA
Found at i:9889021 original size:15 final size:16
Alignment explanation
Indices: 9888991--9889023 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
9888981 TTTAAAAAAT
9888991 AAATATTTATAATTTAA
1 AAATATTTAT-ATTTAA
9889008 AAATATTTAT-TTTAA
1 AAATATTTATATTTAA
9889023 A
1 A
9889024 TTTTTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
17 10 0.62
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AAATATTTATATTTAA
Found at i:9889437 original size:19 final size:20
Alignment explanation
Indices: 9889390--9889430 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
9889380 AACTTCAAAA
9889390 TATTGTTAAATTAAAATAACT
1 TATT-TTAAATTAAAATAACT
9889411 TAATTTTAAATTAATAATAA
1 T-ATTTTAAATTAA-AATAA
9889431 TTTTTTATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (20 bp):
TATTTTAAATTAAAATAACT
Found at i:9908645 original size:31 final size:31
Alignment explanation
Indices: 9908581--9908645 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
9908571 AATTATGTTT
* **
9908581 ATTAAAACTACAAAAATATCCTTAAGCGTGG
1 ATTAAAACTACAAAAATATCCTTAAACAAGG
* *
9908612 ATTAAAATTACAAAAATATCTTTAAACAAGG
1 ATTAAAACTACAAAAATATCCTTAAACAAGG
9908643 ATT
1 ATT
9908646 TGTCGCCCAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.49, C:0.12, G:0.09, T:0.29
Consensus pattern (31 bp):
ATTAAAACTACAAAAATATCCTTAAACAAGG
Found at i:9912943 original size:14 final size:14
Alignment explanation
Indices: 9912924--9912950 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
9912914 CAAAATTATC
9912924 ACTTATAAAAAAAA
1 ACTTATAAAAAAAA
9912938 ACTTATAAAAAAA
1 ACTTATAAAAAAA
9912951 TTTATCAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.22
Consensus pattern (14 bp):
ACTTATAAAAAAAA
Found at i:9921633 original size:2 final size:2
Alignment explanation
Indices: 9921626--9921650 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9921616 GATCCGATCC
9921626 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
9921651 CGCAGTCGCG
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:9923064 original size:126 final size:125
Alignment explanation
Indices: 9922843--9923163 Score: 457
Period size: 126 Copynumber: 2.6 Consensus size: 125
9922833 GCTGGATGGT
* * *
9922843 GGATCGAGGTTAGGTCATTGGTCAAAAT-CTATTTGGACT-CGTGAGTTTATGACATTGTTAATC
1 GGATGGAGGTTAGGTCATTGGTCAAAATCCCATTTGGA-TGCATGAGTTTATGACATTGTTAATC
* * * * *
9922906 ATATCCATTCATGTCTCTGCAATCTTTATTCACTCGAACATTATATCTGCCTTGCATGAGCA
65 ATAT-GATTCATGTCCCTGCAATCTTTATTCACTCAAACAATATATCTGCCTGGCATGAGCA
9922968 GGATGGAGGTTTAGGTCATTGGTCAAAATCCCATTTGGATGCATGAGTTTATGACATTGTTAATC
1 GGATGGAGG-TTAGGTCATTGGTCAAAATCCCATTTGGATGCATGAGTTTATGACATTGTTAATC
* * * *
9923033 ATATGATTCTTGTCCCTGCAATCTTTCTTCACTCAAACAATCTATCTTCCTGGCATGAGCA
65 ATATGATTCATGTCCCTGCAATCTTTATTCACTCAAACAATATATCTGCCTGGCATGAGCA
* * *
9923094 GGATGGAAGGTTAGGTCATTGGTTAAAATCCCATTTGGATGAATGAGTTTACGACATTGTTAATC
1 GGATGG-AGGTTAGGTCATTGGTCAAAATCCCATTTGGATGCATGAGTTTATGACATTGTTAATC
9923159 ATATG
65 ATATG
9923164 CTATAGTTGC
Statistics
Matches: 177, Mismatches: 15, Indels: 7
0.89 0.08 0.04
Matches are distributed among these distances:
125 8 0.05
126 131 0.74
127 38 0.21
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.36
Consensus pattern (125 bp):
GGATGGAGGTTAGGTCATTGGTCAAAATCCCATTTGGATGCATGAGTTTATGACATTGTTAATCA
TATGATTCATGTCCCTGCAATCTTTATTCACTCAAACAATATATCTGCCTGGCATGAGCA
Found at i:9947157 original size:25 final size:25
Alignment explanation
Indices: 9947106--9947158 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
9947096 TTAAGGGTTC
*
9947106 ATATAACAAACAGAATGGGACACGA
1 ATATAACAAACAGAATGGGAAACGA
* *
9947131 ATATAACAAACAGACTGGGAAATGA
1 ATATAACAAACAGAATGGGAAACGA
9947156 ATA
1 ATA
9947159 AGTACAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.53, C:0.13, G:0.19, T:0.15
Consensus pattern (25 bp):
ATATAACAAACAGAATGGGAAACGA
Found at i:9948281 original size:6 final size:6
Alignment explanation
Indices: 9948266--9948303 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
9948256 TGAAACTCAC
*
9948266 CTCCTG CTCCTA CTCCTG CTCCTG CTCCTG CTCCTG CT
1 CTCCTG CTCCTG CTCCTG CTCCTG CTCCTG CTCCTG CT
9948304 ACTATAGCTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.03, C:0.50, G:0.13, T:0.34
Consensus pattern (6 bp):
CTCCTG
Found at i:9959184 original size:2 final size:2
Alignment explanation
Indices: 9959171--9959215 Score: 81
Period size: 2 Copynumber: 22.0 Consensus size: 2
9959161 TGACTTGTGC
9959171 CT CT CAT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT C-T CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
9959214 CT
1 CT
9959216 GTGACCCTGT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 40 0.95
3 2 0.05
ACGTcount: A:0.02, C:0.49, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:9961545 original size:108 final size:108
Alignment explanation
Indices: 9961265--9961547 Score: 361
Period size: 108 Copynumber: 2.6 Consensus size: 108
9961255 GCTAAGAAGT
* ** * *
9961265 TCACTGGGCCAAACTTCTTGGATTGGAATAGAAATTTGAGAATCGTTCTGGAAGCAAAGACAAAG
1 TCACTGGGCCAAACTTCTTGGATTGGCATAGAAATTTGAGAATCGTTCTCAAATCAAAGAAAAAG
* * *
9961330 TCGTGTGCCTTTAAGAAAGCTTTGACAGAAGTTCCTGCTGAGT
66 TCGTATGACTTTAAGAAAGCTTTGACAGAAGTTCCTGCTGAGA
* ** * * *
9961373 TCACTGGGCCAAACTTCTTCGATTAACATAGAAATTTGAGAATTGTTCTCAAATCCAAGGAAAAG
1 TCACTGGGCCAAACTTCTTGGATTGGCATAGAAATTTGAGAATCGTTCTCAAATCAAAGAAAAAG
* * *
9961438 TTGTATGACTTTAAGAAAGCTTTGCCGGAA-TTCCTTGCTGAGA
66 TCGTATGACTTTAAGAAAGCTTTGACAGAAGTTCC-TGCTGAGA
* * * *
9961481 TCACTGAGCGAAACTTCTTGGATTGGCATAGAAATTTTAGAATCGTTCTCAAATCTAAGAAAAAG
1 TCACTGGGCCAAACTTCTTGGATTGGCATAGAAATTTGAGAATCGTTCTCAAATCAAAGAAAAAG
9961546 TC
66 TC
9961548 TTCGTCAGAA
Statistics
Matches: 147, Mismatches: 27, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
107 4 0.03
108 143 0.97
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (108 bp):
TCACTGGGCCAAACTTCTTGGATTGGCATAGAAATTTGAGAATCGTTCTCAAATCAAAGAAAAAG
TCGTATGACTTTAAGAAAGCTTTGACAGAAGTTCCTGCTGAGA
Found at i:9962991 original size:64 final size:64
Alignment explanation
Indices: 9962890--9963016 Score: 184
Period size: 64 Copynumber: 2.0 Consensus size: 64
9962880 GTATTTTATC
* * * * *
9962890 TAAGTATGATATTAATAGTTATATGAGTGAAAATAGATACGACATCTTAAAGGGATCAAGATTT
1 TAAGTACGATATTAATAGTTATATGAGTGAAAATAGATACGACACCCTAAAAGAATCAAGATTT
*
9962954 TAAGTACGATATTAATAGTTATATGAGT-AAATATAGATATGACACCCTAAAAGAATCAAGATT
1 TAAGTACGATATTAATAGTTATATGAGTGAAA-ATAGATACGACACCCTAAAAGAATCAAGATT
9963017 CTAAATAGGC
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
63 3 0.05
64 53 0.95
ACGTcount: A:0.44, C:0.08, G:0.17, T:0.31
Consensus pattern (64 bp):
TAAGTACGATATTAATAGTTATATGAGTGAAAATAGATACGACACCCTAAAAGAATCAAGATTT
Found at i:9966623 original size:16 final size:16
Alignment explanation
Indices: 9966602--9966636 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
9966592 TTGCACGATA
* *
9966602 ATCGAGTATTTACGTT
1 ATCGAGAATTTACATT
9966618 ATCGAGAATTTACATT
1 ATCGAGAATTTACATT
9966634 ATC
1 ATC
9966637 TGATTTAGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.40
Consensus pattern (16 bp):
ATCGAGAATTTACATT
Found at i:9979081 original size:20 final size:20
Alignment explanation
Indices: 9979056--9979093 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
9979046 TTTTGTTTTC
9979056 AAAATTATGTTTTCAAAAAA
1 AAAATTATGTTTTCAAAAAA
9979076 AAAATTATGTTTTCAAAA
1 AAAATTATGTTTTCAAAA
9979094 CTTCATATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (20 bp):
AAAATTATGTTTTCAAAAAA
Found at i:9979593 original size:115 final size:113
Alignment explanation
Indices: 9979448--9979661 Score: 365
Period size: 115 Copynumber: 1.9 Consensus size: 113
9979438 TAGCATAAAT
*
9979448 TATATATATATACAAATGTTTCCCAGCTAATCCATTTCTTAAGATAAGAGCCTTCCATCATATAA
1 TATATATATATACAAATGTTTCCCAGCTAATCCATTTCTTAAGATAAGAACCTTCCATCATATAA
*
9979513 GGGTTTCCCACATGAGAATTATTGGAACCATTAAGCATAAATCATATA
66 GGGTTTCCCACATGAGAATTAATGGAACCATTAAGCATAAATCATATA
* *
9979561 TATATATATATAGTCAAATGTTTCCCAGCTAATCCTTTTCTTAAGCTAAGAACCTTCCATCATAT
1 TATATATATATA--CAAATGTTTCCCAGCTAATCCATTTCTTAAGATAAGAACCTTCCATCATAT
*
9979626 AAGGGTTTCCCACATGAGCATTAATGGAACCATTAA
64 AAGGGTTTCCCACATGAGAATTAATGGAACCATTAA
9979662 TTAGCAACAG
Statistics
Matches: 94, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
113 12 0.13
115 82 0.87
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.33
Consensus pattern (113 bp):
TATATATATATACAAATGTTTCCCAGCTAATCCATTTCTTAAGATAAGAACCTTCCATCATATAA
GGGTTTCCCACATGAGAATTAATGGAACCATTAAGCATAAATCATATA
Found at i:9984896 original size:18 final size:18
Alignment explanation
Indices: 9984873--9984908 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
9984863 TTAAATGTCA
*
9984873 TATATCGATATGATTTTT
1 TATATCGATATAATTTTT
9984891 TATATCGATATAATTTTT
1 TATATCGATATAATTTTT
9984909 ATTAGTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.06, G:0.08, T:0.56
Consensus pattern (18 bp):
TATATCGATATAATTTTT
Found at i:9990330 original size:2 final size:2
Alignment explanation
Indices: 9990325--9990359 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
9990315 AGAGAGCCCA
9990325 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
9990360 TTCTGTCCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:9990374 original size:26 final size:26
Alignment explanation
Indices: 9990343--9990399 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 26
9990333 TCTCTCTCTC
9990343 TCTCTCTCTCTCTCTCTTTCTGTCCTTT
1 TCTCTCTCTCTCTC-CTTTCT-TCCTTT
* * *
9990371 TCTCTTTCTCTTTCCTTTCTTTCTTT
1 TCTCTCTCTCTCTCCTTTCTTCCTTT
9990397 TCT
1 TCT
9990400 TTCTTACTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 8 0.31
27 6 0.23
28 12 0.46
ACGTcount: A:0.00, C:0.35, G:0.02, T:0.63
Consensus pattern (26 bp):
TCTCTCTCTCTCTCCTTTCTTCCTTT
Found at i:9990400 original size:18 final size:17
Alignment explanation
Indices: 9990353--9990402 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
9990343 TCTCTCTCTC
*
9990353 TCTCTCTTTCTGTCCTTT
1 TCTCT-TTTCTTTCCTTT
9990371 TCTCTTTCTCTTTCCTTT
1 TCTCTTT-TCTTTCCTTT
*
9990389 CTTTCTTTTCTTTC
1 -TCTCTTTTCTTTC
9990403 TTACTTCCTG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 2 0.07
18 20 0.71
19 6 0.21
ACGTcount: A:0.00, C:0.32, G:0.02, T:0.66
Consensus pattern (17 bp):
TCTCTTTTCTTTCCTTT
Found at i:9992050 original size:2 final size:2
Alignment explanation
Indices: 9992043--9992083 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
9992033 AGTTATTGTT
9992043 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9992084 TCATTTTGAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:9995269 original size:40 final size:41
Alignment explanation
Indices: 9995193--9995269 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 41
9995183 TTGGCTATTC
* *
9995193 TTCACCTTAATGGGGTTTTCTAACATTGCCAAGATTGTTGG
1 TTCACCTTAATGGGGTTTCCTAACATCGCCAAGATTGTTGG
* * *
9995234 TTCACCTTAGTGGGG-TTCCTAACCTCGCCATGATTG
1 TTCACCTTAATGGGGTTTCCTAACATCGCCAAGATTG
9995270 GTGTCTTTCA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
40 17 0.55
41 14 0.45
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.36
Consensus pattern (41 bp):
TTCACCTTAATGGGGTTTCCTAACATCGCCAAGATTGTTGG
Found at i:10015260 original size:26 final size:26
Alignment explanation
Indices: 10015231--10015292 Score: 79
Period size: 26 Copynumber: 2.4 Consensus size: 26
10015221 ACCCTTTTCC
* * *
10015231 CCCAGAAAACTCTGCACTTTCGAAAA
1 CCCAGAAAACCCTGCACTTCCAAAAA
* *
10015257 CCCAGAAAACCCTTCAGTTCCAAAAA
1 CCCAGAAAACCCTGCACTTCCAAAAA
10015283 CCCAGAAAAC
1 CCCAGAAAAC
10015293 GTCTTTTCAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.42, C:0.34, G:0.10, T:0.15
Consensus pattern (26 bp):
CCCAGAAAACCCTGCACTTCCAAAAA
Found at i:10028912 original size:22 final size:23
Alignment explanation
Indices: 10028869--10028912 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
10028859 TTATTTTTTG
* *
10028869 TATTAAAAAGTATGTAACATTTA
1 TATTAAAAAGAATGTAAAATTTA
*
10028892 TATTAAAAA-AATTTAAAATTT
1 TATTAAAAAGAATGTAAAATTT
10028913 TAATATAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.41
Consensus pattern (23 bp):
TATTAAAAAGAATGTAAAATTTA
Found at i:10045545 original size:45 final size:45
Alignment explanation
Indices: 10045487--10045577 Score: 164
Period size: 45 Copynumber: 2.0 Consensus size: 45
10045477 AAAGCACATT
*
10045487 AGCAACTTGATTTGAGTTCTTATTTGTTGGCTTCTTGATGCACAG
1 AGCAACTTGATTTGAGTTCCTATTTGTTGGCTTCTTGATGCACAG
*
10045532 AGCAACTTGATTTGGGTTCCTATTTGTTGGCTTCTTGATGCACAG
1 AGCAACTTGATTTGAGTTCCTATTTGTTGGCTTCTTGATGCACAG
10045577 A
1 A
10045578 ATTGAAGAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.20, C:0.16, G:0.23, T:0.41
Consensus pattern (45 bp):
AGCAACTTGATTTGAGTTCCTATTTGTTGGCTTCTTGATGCACAG
Found at i:10053713 original size:93 final size:94
Alignment explanation
Indices: 10053553--10053729 Score: 302
Period size: 93 Copynumber: 1.9 Consensus size: 94
10053543 ATAAAATAGT
** * *
10053553 TAAGAACAAAACATTGGGTGGCACAGCAATTTGCAAGTAATCAATCCAAGGAAAAGGTTTGATCC
1 TAAGAACAAAACAAGGGGTGGCACAGCAATTTGCAAGTAATCAATCCAAGGAAAAAGTTTAATCC
10053618 ACTTACAATTCTACCAAATTTTCTGTTAG
66 ACTTACAATTCTACCAAATTTTCTGTTAG
10053647 TAAGAACAAAACAAGGGGTGGCACA-CAATTTGCAAGTAATCAATCCAAGGAAAAAGTTTAATCC
1 TAAGAACAAAACAAGGGGTGGCACAGCAATTTGCAAGTAATCAATCCAAGGAAAAAGTTTAATCC
*
10053711 ACTTATAATTCTACCAAAT
66 ACTTACAATTCTACCAAAT
10053730 CTTTTGGTAA
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
93 55 0.71
94 23 0.29
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.25
Consensus pattern (94 bp):
TAAGAACAAAACAAGGGGTGGCACAGCAATTTGCAAGTAATCAATCCAAGGAAAAAGTTTAATCC
ACTTACAATTCTACCAAATTTTCTGTTAG
Found at i:10056602 original size:50 final size:50
Alignment explanation
Indices: 10056476--10056613 Score: 170
Period size: 52 Copynumber: 2.7 Consensus size: 50
10056466 GTCCAAGCAA
* **
10056476 CCTTTTTGCATGAAAATTAGCCCAAGATCCTTAACTCCCAGACTCTGAGGTC
1 CCTTTTTGCATGAAAA-TAGCCCAAGATCCTTAAC-CCCAAACTCCAAGGTC
* * *
10056528 CCTTTTTGCATGAAAGAAAACCCAAGATCCTTAACCCCAAAGTCCAAGGTC
1 CCTTTTTGCATGAAA-ATAGCCCAAGATCCTTAACCCCAAACTCCAAGGTC
*
10056579 CC-TTTTGCATGAAAACTAGCCCAAGATTCTTAACC
1 CCTTTTTGCATGAAAA-TAGCCCAAGATCCTTAACC
10056614 AATTTTTTGG
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
49 1 0.01
50 28 0.37
51 14 0.19
52 31 0.41
53 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (50 bp):
CCTTTTTGCATGAAAATAGCCCAAGATCCTTAACCCCAAACTCCAAGGTC
Found at i:10069155 original size:36 final size:36
Alignment explanation
Indices: 10069108--10069253 Score: 249
Period size: 36 Copynumber: 4.1 Consensus size: 36
10069098 TGGACTTGAA
*
10069108 ATCCCTCCCTGTCTCAAAA-TCCATCTGATGTGAAGG
1 ATCCCTCCCTGTCTCAAAATTCC-TCTGATATGAAGG
*
10069144 ATCCCTCCCTGTCTCAGAATTCCTCTGATATGAAGG
1 ATCCCTCCCTGTCTCAAAATTCCTCTGATATGAAGG
10069180 ATCCCTCCCTGTCTCAAAATTCCTCTGATATGAAGG
1 ATCCCTCCCTGTCTCAAAATTCCTCTGATATGAAGG
*
10069216 ATCCCTTCCTGTCTCAAAATTCCTCTGATATGAAGG
1 ATCCCTCCCTGTCTCAAAATTCCTCTGATATGAAGG
10069252 AT
1 AT
10069254 GCCTAAAACT
Statistics
Matches: 105, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
36 102 0.97
37 3 0.03
ACGTcount: A:0.25, C:0.29, G:0.15, T:0.31
Consensus pattern (36 bp):
ATCCCTCCCTGTCTCAAAATTCCTCTGATATGAAGG
Found at i:10075082 original size:6 final size:7
Alignment explanation
Indices: 10075067--10075091 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
10075057 TCCAACCAAG
10075067 AAAAGAA
1 AAAAGAA
10075074 AAAAGAA
1 AAAAGAA
10075081 AAAAGAA
1 AAAAGAA
10075088 AAAA
1 AAAA
10075092 ACCACACCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:10075307 original size:9 final size:9
Alignment explanation
Indices: 10075293--10075317 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
10075283 AAGGAAGTAC
10075293 TTTTCTTTG
1 TTTTCTTTG
10075302 TTTTCTTTG
1 TTTTCTTTG
10075311 TTTTCTT
1 TTTTCTT
10075318 CTGGTTCTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.12, G:0.08, T:0.80
Consensus pattern (9 bp):
TTTTCTTTG
Found at i:10077829 original size:15 final size:15
Alignment explanation
Indices: 10077789--10077830 Score: 63
Period size: 13 Copynumber: 3.0 Consensus size: 15
10077779 AAATTTATTA
10077789 TTTATTATAT-AATT
1 TTTATTATATAAATT
10077803 TTT-TTA-ATAAATT
1 TTTATTATATAAATT
10077816 TTTATTATATAAATT
1 TTTATTATATAAATT
10077831 CCTATAAACC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 2 0.08
13 10 0.40
14 6 0.24
15 7 0.28
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTATTATATAAATT
Found at i:10088397 original size:28 final size:28
Alignment explanation
Indices: 10088373--10088428 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
10088363 TTAAATTTTC
10088373 AAATGAAGCATTTTTTATTGAAATTAAA
1 AAATGAAGCATTTTTTATTGAAATTAAA
** *
10088401 AAATGAAGTTTTTTTTATTGAAGTTAAA
1 AAATGAAGCATTTTTTATTGAAATTAAA
10088429 GAATAAAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.43, C:0.02, G:0.12, T:0.43
Consensus pattern (28 bp):
AAATGAAGCATTTTTTATTGAAATTAAA
Found at i:10119167 original size:3 final size:3
Alignment explanation
Indices: 10119159--10119183 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
10119149 GACTTAATAC
10119159 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
10119184 GCCTAATAAA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:10130358 original size:30 final size:30
Alignment explanation
Indices: 10130322--10130382 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
10130312 TTGACTGTAA
*
10130322 CCTGCTGCTCCACTCTTTCTTCTTCTTTGT
1 CCTGCTGCTCCACTCTCTCTTCTTCTTTGT
10130352 CCTGCTGCTCCACTCTCTCTTCTTCTTTGT
1 CCTGCTGCTCCACTCTCTCTTCTTCTTTGT
10130382 C
1 C
10130383 TTCATCTTCC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.03, C:0.39, G:0.10, T:0.48
Consensus pattern (30 bp):
CCTGCTGCTCCACTCTCTCTTCTTCTTTGT
Found at i:10142755 original size:42 final size:42
Alignment explanation
Indices: 10142652--10142763 Score: 124
Period size: 42 Copynumber: 2.6 Consensus size: 42
10142642 CTCTGGTCCA
* *
10142652 GCTCCACCTTC-AGAATCTGATCGCTGGACTGGTGGCAGCAGG
1 GCTCCACC-TCAAGATTCTGATCGCTGGACTAGTGGCAGCAGG
*
10142694 G--CC-CCTCAACCGCTATCTGATCGCTGGACTAGTGGCAGCAGG
1 GCTCCACCTCAA--GAT-TCTGATCGCTGGACTAGTGGCAGCAGG
10142736 GCTCCACCTCAAGATTCTGATCGACTGG
1 GCTCCACCTCAAGATTCTGATCG-CTGG
10142764 GTGGCACTGG
Statistics
Matches: 58, Mismatches: 4, Indels: 15
0.75 0.05 0.19
Matches are distributed among these distances:
38 2 0.03
39 3 0.05
40 2 0.03
41 1 0.02
42 36 0.62
43 6 0.10
44 2 0.03
45 6 0.10
ACGTcount: A:0.20, C:0.31, G:0.28, T:0.21
Consensus pattern (42 bp):
GCTCCACCTCAAGATTCTGATCGCTGGACTAGTGGCAGCAGG
Found at i:10143238 original size:15 final size:16
Alignment explanation
Indices: 10143214--10143246 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
10143204 TACGTGTAAA
10143214 ATTTTGAAATTT-TTT
1 ATTTTGAAATTTATTT
*
10143229 ATTTTTAAATTTATTT
1 ATTTTGAAATTTATTT
10143245 AT
1 AT
10143247 CAACGAGATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (16 bp):
ATTTTGAAATTTATTT
Found at i:10151708 original size:2 final size:2
Alignment explanation
Indices: 10151701--10151727 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
10151691 CTTCATGTTT
10151701 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
10151728 GAAGGGGTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:10181449 original size:53 final size:52
Alignment explanation
Indices: 10181394--10181501 Score: 119
Period size: 52 Copynumber: 2.0 Consensus size: 52
10181384 TCTCAAGCTT
* * *
10181394 TTATATTATTCTTAATTTTTTTATCCTTTATTTTTTCCAA-TAATTTACTTTTTTTA
1 TTATA-TAATCTT-ATTTCTTTAT-CTATATTTTTT--AATTAATTTACTTTTTTTA
* *
10181450 TTATATAATCTTCTTTCTTTATCTATATTTTTTAATTAATTTATTTTTTTTA
1 TTATATAATCTTATTTCTTTATCTATATTTTTTAATTAATTTACTTTTTTTA
10181502 CTAAAAATTG
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
51 2 0.04
52 15 0.33
53 10 0.22
54 8 0.17
55 6 0.13
56 5 0.11
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.67
Consensus pattern (52 bp):
TTATATAATCTTATTTCTTTATCTATATTTTTTAATTAATTTACTTTTTTTA
Found at i:10181457 original size:21 final size:22
Alignment explanation
Indices: 10181433--10181477 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
10181423 ATTTTTTCCA
*
10181433 ATAAT-TTACTTTTTTTAT-TAT
1 ATAATCTT-CTTTCTTTATCTAT
10181454 ATAATCTTCTTTCTTTATCTAT
1 ATAATCTTCTTTCTTTATCTAT
10181476 AT
1 AT
10181478 TTTTTAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.27, C:0.11, G:0.00, T:0.62
Consensus pattern (22 bp):
ATAATCTTCTTTCTTTATCTAT
Found at i:10181804 original size:59 final size:59
Alignment explanation
Indices: 10181737--10181854 Score: 166
Period size: 59 Copynumber: 2.0 Consensus size: 59
10181727 GTTGATTGAA
* * *
10181737 GGGATAATGTTGAAATAATTTCT-ATGATTTGTATCATTTTGTAAATATGTATATATTAT
1 GGGATAATGATGAAATAATTTCTAAT-ATTTATATCATTGTGTAAATATGTATATATTAT
* * *
10181796 GGGATAATGATGAAATAATTTTTAATATTTATATTATTGTGTAAGTATGTATATATTAT
1 GGGATAATGATGAAATAATTTCTAATATTTATATCATTGTGTAAATATGTATATATTAT
10181855 ATAATATATA
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
59 50 0.96
60 2 0.04
ACGTcount: A:0.36, C:0.02, G:0.15, T:0.47
Consensus pattern (59 bp):
GGGATAATGATGAAATAATTTCTAATATTTATATCATTGTGTAAATATGTATATATTAT
Found at i:10181923 original size:18 final size:20
Alignment explanation
Indices: 10181900--10181941 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
10181890 TACATCTTTT
10181900 TTAATTAA-AAATCAAATA-
1 TTAATTAATAAATCAAATAC
*
10181918 TTAATTAATAAATTAAATAC
1 TTAATTAATAAATCAAATAC
10181938 TTAA
1 TTAA
10181942 ATGTATATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (20 bp):
TTAATTAATAAATCAAATAC
Found at i:10189767 original size:21 final size:21
Alignment explanation
Indices: 10189724--10189768 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
10189714 ATAAAATGGC
** *
10189724 ATATTATTTTATAAAACATTA
1 ATATTATTCAATAAAACAATA
*
10189745 ATATTATTCAATAAAATAATA
1 ATATTATTCAATAAAACAATA
10189766 ATA
1 ATA
10189769 ATAATAATCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.42
Consensus pattern (21 bp):
ATATTATTCAATAAAACAATA
Found at i:10191418 original size:52 final size:52
Alignment explanation
Indices: 10191340--10191446 Score: 169
Period size: 52 Copynumber: 2.1 Consensus size: 52
10191330 TCGAGTGAGA
* *
10191340 GAGTGTCACAAATGGTACCTCTATCCCACATCGGAGAAGAACGGAAAGTACT
1 GAGTGTCACAAATAGCACCTCTATCCCACATCGGAGAAGAACGGAAAGTACT
* * *
10191392 GAGTGTCACAAATAGCACTTTTATCCCACATCGGAGAAGAACGGAAAGTCCT
1 GAGTGTCACAAATAGCACCTCTATCCCACATCGGAGAAGAACGGAAAGTACT
10191444 GAG
1 GAG
10191447 CTCTTTATAA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.20
Consensus pattern (52 bp):
GAGTGTCACAAATAGCACCTCTATCCCACATCGGAGAAGAACGGAAAGTACT
Found at i:10194394 original size:2 final size:2
Alignment explanation
Indices: 10194387--10194416 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
10194377 AAAAGCTGAG
10194387 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
10194417 ATATATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:10208048 original size:14 final size:14
Alignment explanation
Indices: 10208011--10208061 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
10208001 GGGTAAAATG
10208011 ATTTAGTTT-AATTA
1 ATTTA-TTTAAATTA
10208025 ATTTA-TTAAATTA
1 ATTTATTTAAATTA
*
10208038 ATTTATTTAAAAT-
1 ATTTATTTAAATTA
10208051 ATTTGATTTAA
1 ATTT-ATTTAA
10208062 TTATTTTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
12 2 0.06
13 14 0.42
14 17 0.52
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (14 bp):
ATTTATTTAAATTA
Found at i:10208054 original size:13 final size:14
Alignment explanation
Indices: 10208004--10208061 Score: 50
Period size: 14 Copynumber: 4.2 Consensus size: 14
10207994 ACGATTTGGG
*
10208004 TAAAATGATTTAGTT
1 TAAAATAATTTA-TT
*
10208019 T-AATTAATTTA-T
1 TAAAATAATTTATT
*
10208031 TAAATTAATTTATT
1 TAAAATAATTTATT
10208045 TAAAAT-ATTTGATT
1 TAAAATAATTT-ATT
10208059 TAA
1 TAA
10208062 TTATTTTTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
12 2 0.05
13 14 0.38
14 20 0.54
15 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (14 bp):
TAAAATAATTTATT
Found at i:10208067 original size:13 final size:13
Alignment explanation
Indices: 10208011--10208047 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
10208001 GGGTAAAATG
10208011 ATTTAGTTTAATTA
1 ATTTA-TTTAATTA
*
10208025 ATTTATTAAATTA
1 ATTTATTTAATTA
10208038 ATTTATTTAA
1 ATTTATTTAA
10208048 AATATTTGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 16 0.76
14 5 0.24
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (13 bp):
ATTTATTTAATTA
Found at i:10208190 original size:16 final size:16
Alignment explanation
Indices: 10208169--10208202 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
10208159 TATTAAGAAG
*
10208169 AATTAATAGTAAATTT
1 AATTAATAATAAATTT
*
10208185 AATTAATAATATATTT
1 AATTAATAATAAATTT
10208201 AA
1 AA
10208203 AATATATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (16 bp):
AATTAATAATAAATTT
Found at i:10216874 original size:2 final size:2
Alignment explanation
Indices: 10216867--10216893 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
10216857 CATGGAGGGC
10216867 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
10216894 AGTGTCTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:10217503 original size:2 final size:2
Alignment explanation
Indices: 10217498--10217522 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10217488 ATATATATAT
10217498 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
10217523 ATCGTTAAGC
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:10219200 original size:4 final size:4
Alignment explanation
Indices: 10219191--10219220 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
10219181 AGTTAATGGC
10219191 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TA
10219221 TATATATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
TAAA
Done.