Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold211
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1275876
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.29
Warning! 151255 characters in sequence are not A, C, G, or T
File 3 of 4
Found at i:461867 original size:60 final size:60
Alignment explanation
Indices: 461773--463396 Score: 2442
Period size: 60 Copynumber: 27.1 Consensus size: 60
461763 GGAAAAACTA
* *
461773 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATATAAGTGTTGCTATCCTACTCCCTG
1 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATATAAGTGTTGCCATCCTACTGCCTG
*
461833 TACTGGTGACTTTTAGGTTTAGAATTATGTTACATA-AACGTGTTGCCATCCTACTGCCTG
1 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATATAA-GTGTTGCCATCCTACTGCCTG
461893 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATA-AACGTGTTGCCATCCTACTGCCTG
1 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATATAA-GTGTTGCCATCCTACTGCCTG
* * * *
461953 AACTGGTGACTTTAAGGTTT-GAATTATGTTATATATATAAGTGTTGCAATCATACTGCCTG
1 AACTGGTGACTTTTAGGTTTAGAATTATG-T-TACATATAAGTGTTGCCATCCTACTGCCTG
* *
462014 AACTGGTGACTTATACGTACATGTAGGTTTAGAATTATGTTACATATAAGTGTTGCAATCCTACC
1 AACTGGTGAC---T---T---T-TAGGTTTAGAATTATGTTACATATAAGTGTTGCCATCCTACT
462079 GCCTG
56 GCCTG
* *
462084 -ACTGGTGACTTTTAGGTTT-GAATTATGTTACATAAAAGTGTTGCCATCCTTCTGCCTG
1 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATATAAGTGTTGCCATCCTACTGCCTG
* * * *
462142 -ACCGGTGACTTTTAGGTTTAGAA-TATGTAACATATAATTG-TGCTATCCTACTGCCTG
1 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATATAAGTGTTGCCATCCTACTGCCTG
*
462199 -ACTGGTAACTTTTAGGTTTAGAATTATGTTACATATAAGTGTTGCCATCCTACTGCCTG
1 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATATAAGTGTTGCCATCCTACTGCCTG
* * *
462258 AACTGGTGAATTTAAGGTTTAGAATTATGTTACATA-AACGTATTGCCATCCTACTGCCTG
1 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATATAA-GTGTTGCCATCCTACTGCCTG
* * * *
462318 AACTGGTGACTTTTAGGCTTAGAATTATGTTATATAAAATTG-TGCCATCCTACTGCCTG
1 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATATAAGTGTTGCCATCCTACTGCCTG
* * * *
462377 AACTGGTGATTTTTAGGTTTAGAATCATGTTACATATAAGTGTTGCTATTCTACTGCCTG
1 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATATAAGTGTTGCCATCCTACTGCCTG
* * * *
462437 -ATTGTTGACTTTTAGGTTTAGAATTATGTTACATAAAAGTGTTGCAATCCTACTGCCTG
1 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATATAAGTGTTGCCATCCTACTGCCTG
*
462496 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATAAAAGTGTTGCCATCCTACTGCCTG
1 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATATAAGTGTTGCCATCCTACTGCCTG
* * *
462556 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATA-AGAGTGTTGTCATCTTTCTGCCT-
1 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATATA-AGTGTTGCCATCCTACTGCCTG
462615 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATATAAGTGTTGCCATCCTACTGCCTG
1 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATATAAGTGTTGCCATCCTACTGCCTG
* * *
462675 AACTGGTGACTTTTAGGTTTAGAATTATGTTATATATAAGTGTTGCTATCCAACTGCCTG
1 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATATAAGTGTTGCCATCCTACTGCCTG
*
462735 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATAAAAGTGTTGCCATCCTACTGCCTG
1 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATATAAGTGTTGCCATCCTACTGCCTG
* * *
462795 AACTGGTGACTTTTAGGTTTAGAATTATGTTATATATAATTG-TGCCACCCTACTGCCTG
1 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATATAAGTGTTGCCATCCTACTGCCTG
* * *
462854 AACTGGTGACTTTTGGGTTTAGAATTATGTTACATAAAAGTGTTGCAATCCTACTGCCTG
1 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATATAAGTGTTGCCATCCTACTGCCTG
462914 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATATAAGTGTTGCCATCCTACTGCCTG
1 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATATAAGTGTTGCCATCCTACTGCCTG
* * *
462974 AACTGGTGACTTTTAGGTTTAGAATTATGTTATATATAAGTGTTGCTATCCAACTGCCTG
1 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATATAAGTGTTGCCATCCTACTGCCTG
* * *
463034 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATA-AGAGTGTTGTCATCTTTCTGCCT-
1 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATATA-AGTGTTGCCATCCTACTGCCTG
* *
463093 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATAAAAGTGTTGCAATCCTACTGCCTG
1 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATATAAGTGTTGCCATCCTACTGCCTG
*
463153 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATAAAAGTGTTGCCATCCTACTGCCTG
1 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATATAAGTGTTGCCATCCTACTGCCTG
463213 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATA-AACGTGTTGCCATCCTACTGCCTG
1 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATATAA-GTGTTGCCATCCTACTGCCTG
463273 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATA-AACGTGTTGCCATCCTACTGCCTG
1 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATATAA-GTGTTGCCATCCTACTGCCTG
463333 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATA-AACGTGTTGCCATCCTACTGCCTG
1 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATATAA-GTGTTGCCATCCTACTGCCTG
463393 AACT
1 AACT
463397 AGGAATGTAG
Statistics
Matches: 1438, Mismatches: 95, Indels: 62
0.90 0.06 0.04
Matches are distributed among these distances:
57 36 0.03
58 82 0.06
59 308 0.21
60 918 0.64
61 36 0.03
62 2 0.00
63 1 0.00
64 1 0.00
66 1 0.00
67 1 0.00
69 9 0.01
70 28 0.02
71 7 0.00
72 8 0.01
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.38
Consensus pattern (60 bp):
AACTGGTGACTTTTAGGTTTAGAATTATGTTACATATAAGTGTTGCCATCCTACTGCCTG
Found at i:462422 original size:179 final size:179
Alignment explanation
Indices: 461773--463396 Score: 2450
Period size: 179 Copynumber: 9.0 Consensus size: 179
461763 GGAAAAACTA
* * * *
461773 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATATAAGTGTTGCTATCCTACTCCCTGTACTG
1 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATAAAAGTGTTGCCATCCTACTGCCTGAACTG
461838 GTGACTTTTAGGTTTAGAATTATGTTACATA-AACGTGTTGCCATCCTACTGCCTGAACTGGTGA
66 GTGACTTTTAGGTTTAGAATTATGTTACATATAA-GTGTTGCCATCCTACTGCCTGAACTGGTGA
461902 CTTTTAGGTTTAGAATTATGTTACATAAACGTGTTGCCATCCTACTGCCTG
130 CTTTTAGGTTTAGAATTATGTTACATAAA-GTGTTGCCATCCTACTGCCTG
* * * *
461953 AACTGGTGACTTTAAGGTTT-GAATTATGTTATATATATAAGTGTTGCAATCATACTGCCTGAAC
1 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATA-A-AAGTGTTGCCATCCTACTGCCTGAAC
* *
462017 TGGTGACTTATACGTACATGTAGGTTTAGAATTATGTTACATATAAGTGTTGCAATCCTACCGCC
64 TGGTGAC---T---T---T-TAGGTTTAGAATTATGTTACATATAAGTGTTGCCATCCTACTGCC
*
462082 TG-ACTGGTGACTTTTAGGTTT-GAATTATGTTACATAAAAGTGTTGCCATCCTTCTGCCTG
119 TGAACTGGTGACTTTTAGGTTTAGAATTATGTTACAT-AAAGTGTTGCCATCCTACTGCCTG
* * * * *
462142 -ACCGGTGACTTTTAGGTTTAGAA-TATGTAACATATAATTG-TGCTATCCTACTGCCTG-ACTG
1 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATAAAAGTGTTGCCATCCTACTGCCTGAACTG
* *
462203 GTAACTTTTAGGTTTAGAATTATGTTACATATAAGTGTTGCCATCCTACTGCCTGAACTGGTGAA
66 GTGACTTTTAGGTTTAGAATTATGTTACATATAAGTGTTGCCATCCTACTGCCTGAACTGGTGAC
* *
462268 TTTAAGGTTTAGAATTATGTTACATAAACGTATTGCCATCCTACTGCCTG
131 TTTTAGGTTTAGAATTATGTTACATAAA-GTGTTGCCATCCTACTGCCTG
* * *
462318 AACTGGTGACTTTTAGGCTTAGAATTATGTTATATAAAATTG-TGCCATCCTACTGCCTGAACTG
1 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATAAAAGTGTTGCCATCCTACTGCCTGAACTG
* * * * * *
462382 GTGATTTTTAGGTTTAGAATCATGTTACATATAAGTGTTGCTATTCTACTGCCTG-ATTGTTGAC
66 GTGACTTTTAGGTTTAGAATTATGTTACATATAAGTGTTGCCATCCTACTGCCTGAACTGGTGAC
*
462446 TTTTAGGTTTAGAATTATGTTACATAAAAGTGTTGCAATCCTACTGCCTG
131 TTTTAGGTTTAGAATTATGTTACAT-AAAGTGTTGCCATCCTACTGCCTG
462496 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATAAAAGTGTTGCCATCCTACTGCCTGAACTG
1 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATAAAAGTGTTGCCATCCTACTGCCTGAACTG
* * *
462561 GTGACTTTTAGGTTTAGAATTATGTTACATA-AGAGTGTTGTCATCTTTCTGCCT-AACTGGTGA
66 GTGACTTTTAGGTTTAGAATTATGTTACATATA-AGTGTTGCCATCCTACTGCCTGAACTGGTGA
462624 CTTTTAGGTTTAGAATTATGTTACATATAAGTGTTGCCATCCTACTGCCTG
130 CTTTTAGGTTTAGAATTATGTTACATA-AAGTGTTGCCATCCTACTGCCTG
* * * *
462675 AACTGGTGACTTTTAGGTTTAGAATTATGTTATATATAAGTGTTGCTATCCAACTGCCTGAACTG
1 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATAAAAGTGTTGCCATCCTACTGCCTGAACTG
*
462740 GTGACTTTTAGGTTTAGAATTATGTTACATAAAAGTGTTGCCATCCTACTGCCTGAACTGGTGAC
66 GTGACTTTTAGGTTTAGAATTATGTTACATATAAGTGTTGCCATCCTACTGCCTGAACTGGTGAC
* * *
462805 TTTTAGGTTTAGAATTATGTTATATATAATTG-TGCCACCCTACTGCCTG
131 TTTTAGGTTTAGAATTATGTTACATA-AAGTGTTGCCATCCTACTGCCTG
* *
462854 AACTGGTGACTTTTGGGTTTAGAATTATGTTACATAAAAGTGTTGCAATCCTACTGCCTGAACTG
1 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATAAAAGTGTTGCCATCCTACTGCCTGAACTG
462919 GTGACTTTTAGGTTTAGAATTATGTTACATATAAGTGTTGCCATCCTACTGCCTGAACTGGTGAC
66 GTGACTTTTAGGTTTAGAATTATGTTACATATAAGTGTTGCCATCCTACTGCCTGAACTGGTGAC
* * *
462984 TTTTAGGTTTAGAATTATGTTATATATAAGTGTTGCTATCCAACTGCCTG
131 TTTTAGGTTTAGAATTATGTTACATA-AAGTGTTGCCATCCTACTGCCTG
* * * *
463034 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATAAGAGTGTTGTCATCTTTCTGCCT-AACTG
1 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATAAAAGTGTTGCCATCCTACTGCCTGAACTG
* *
463098 GTGACTTTTAGGTTTAGAATTATGTTACATAAAAGTGTTGCAATCCTACTGCCTGAACTGGTGAC
66 GTGACTTTTAGGTTTAGAATTATGTTACATATAAGTGTTGCCATCCTACTGCCTGAACTGGTGAC
463163 TTTTAGGTTTAGAATTATGTTACATAAAAGTGTTGCCATCCTACTGCCTG
131 TTTTAGGTTTAGAATTATGTTACAT-AAAGTGTTGCCATCCTACTGCCTG
*
463213 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATAAACGTGTTGCCATCCTACTGCCTGAACTG
1 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATAAAAGTGTTGCCATCCTACTGCCTGAACTG
463278 GTGACTTTTAGGTTTAGAATTATGTTACATA-AACGTGTTGCCATCCTACTGCCTGAACTGGTGA
66 GTGACTTTTAGGTTTAGAATTATGTTACATATAA-GTGTTGCCATCCTACTGCCTGAACTGGTGA
463342 CTTTTAGGTTTAGAATTATGTTACATAAACGTGTTGCCATCCTACTGCCTG
130 CTTTTAGGTTTAGAATTATGTTACATAAA-GTGTTGCCATCCTACTGCCTG
463393 AACT
1 AACT
463397 AGGAATGTAG
Statistics
Matches: 1319, Mismatches: 92, Indels: 66
0.89 0.06 0.04
Matches are distributed among these distances:
174 45 0.03
175 21 0.02
176 33 0.03
177 21 0.02
178 121 0.09
179 645 0.49
180 244 0.18
181 30 0.02
184 9 0.01
185 15 0.01
186 4 0.00
187 1 0.00
188 26 0.02
189 37 0.03
190 23 0.02
191 42 0.03
192 2 0.00
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.38
Consensus pattern (179 bp):
AACTGGTGACTTTTAGGTTTAGAATTATGTTACATAAAAGTGTTGCCATCCTACTGCCTGAACTG
GTGACTTTTAGGTTTAGAATTATGTTACATATAAGTGTTGCCATCCTACTGCCTGAACTGGTGAC
TTTTAGGTTTAGAATTATGTTACATAAAGTGTTGCCATCCTACTGCCTG
Found at i:462795 original size:239 final size:239
Alignment explanation
Indices: 461773--463396 Score: 2466
Period size: 239 Copynumber: 6.8 Consensus size: 239
461763 GGAAAAACTA
* * * *
461773 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATATAAGTGTTGCTATCCTACTCCCTGTACTG
1 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATAAAAGTGTTGCCATCCTACTGCCTGAACTG
461838 GTGACTTTTAGGTTTAGAATTATGTTACATAAACGTGTTGCCATCCTACTGCCTGAACTGGTGAC
66 GTGACTTTTAGGTTTAGAATTATGTTACATAAA-GTGTTGCCATCCTACTGCCTGAACTGGTGAC
*
461903 TTTTAGGTTTAGAATTATGTTACATA-AACGTGTTGCCATCCTACTGCCTGAACTGGTGACTTTA
130 TTTTAGGTTTAGAATTATGTTACATATAA-GTGTTGCCATCCTACTGCCTGAACTGGTGACTTTT
* * *
461967 AGGTTT-GAATTATGTTATATATATAAGTGTTGCAATCATACTGCCTG
194 AGGTTTAGAATTATG-T-TACATATAAGTGTTGCCATCCTACTGCCTG
* * *
462014 AACTGGTGACTTATACGTACATGTAGGTTTAGAATTATGTTACATATAAGTGTTGCAATCCTACC
1 AACTGGTGAC---T---T---T-TAGGTTTAGAATTATGTTACATAAAAGTGTTGCCATCCTACT
*
462079 GCCTG-ACTGGTGACTTTTAGGTTT-GAATTATGTTACATAAAAGTGTTGCCATCCTTCTGCCTG
56 GCCTGAACTGGTGACTTTTAGGTTTAGAATTATGTTACAT-AAAGTGTTGCCATCCTACTGCCTG
* * * *
462142 -ACCGGTGACTTTTAGGTTTAGAA-TATGTAACATATAATTG-TGCTATCCTACTGCCTG-ACTG
120 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATATAAGTGTTGCCATCCTACTGCCTGAACTG
*
462203 GTAACTTTTAGGTTTAGAATTATGTTACATATAAGTGTTGCCATCCTACTGCCTG
185 GTGACTTTTAGGTTTAGAATTATGTTACATATAAGTGTTGCCATCCTACTGCCTG
* * * *
462258 AACTGGTGAATTTAAGGTTTAGAATTATGTTACATAAACGTATTGCCATCCTACTGCCTGAACTG
1 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATAAAAGTGTTGCCATCCTACTGCCTGAACTG
* * * *
462323 GTGACTTTTAGGCTTAGAATTATGTTATATAAAAT-TGTGCCATCCTACTGCCTGAACTGGTGAT
66 GTGACTTTTAGGTTTAGAATTATGTTACATAAAGTGT-TGCCATCCTACTGCCTGAACTGGTGAC
* * * * *
462387 TTTTAGGTTTAGAATCATGTTACATATAAGTGTTGCTATTCTACTGCCTG-ATTGTTGACTTTTA
130 TTTTAGGTTTAGAATTATGTTACATATAAGTGTTGCCATCCTACTGCCTGAACTGGTGACTTTTA
* *
462451 GGTTTAGAATTATGTTACATAAAAGTGTTGCAATCCTACTGCCTG
195 GGTTTAGAATTATGTTACATATAAGTGTTGCCATCCTACTGCCTG
462496 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATAAAAGTGTTGCCATCCTACTGCCTGAACTG
1 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATAAAAGTGTTGCCATCCTACTGCCTGAACTG
* * *
462561 GTGACTTTTAGGTTTAGAATTATGTTACATAAGAGTGTTGTCATCTTTCTGCCT-AACTGGTGAC
66 GTGACTTTTAGGTTTAGAATTATGTTACATAA-AGTGTTGCCATCCTACTGCCTGAACTGGTGAC
462625 TTTTAGGTTTAGAATTATGTTACATATAAGTGTTGCCATCCTACTGCCTGAACTGGTGACTTTTA
130 TTTTAGGTTTAGAATTATGTTACATATAAGTGTTGCCATCCTACTGCCTGAACTGGTGACTTTTA
* * *
462690 GGTTTAGAATTATGTTATATATAAGTGTTGCTATCCAACTGCCTG
195 GGTTTAGAATTATGTTACATATAAGTGTTGCCATCCTACTGCCTG
462735 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATAAAAGTGTTGCCATCCTACTGCCTGAACTG
1 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATAAAAGTGTTGCCATCCTACTGCCTGAACTG
* * *
462800 GTGACTTTTAGGTTTAGAATTATGTTATATATAATTG-TGCCACCCTACTGCCTGAACTGGTGAC
66 GTGACTTTTAGGTTTAGAATTATGTTACATA-AAGTGTTGCCATCCTACTGCCTGAACTGGTGAC
* * *
462864 TTTTGGGTTTAGAATTATGTTACATAAAAGTGTTGCAATCCTACTGCCTGAACTGGTGACTTTTA
130 TTTTAGGTTTAGAATTATGTTACATATAAGTGTTGCCATCCTACTGCCTGAACTGGTGACTTTTA
462929 GGTTTAGAATTATGTTACATATAAGTGTTGCCATCCTACTGCCTG
195 GGTTTAGAATTATGTTACATATAAGTGTTGCCATCCTACTGCCTG
* * * *
462974 AACTGGTGACTTTTAGGTTTAGAATTATGTTATATATAAGTGTTGCTATCCAACTGCCTGAACTG
1 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATAAAAGTGTTGCCATCCTACTGCCTGAACTG
* * *
463039 GTGACTTTTAGGTTTAGAATTATGTTACATAAGAGTGTTGTCATCTTTCTGCCT-AACTGGTGAC
66 GTGACTTTTAGGTTTAGAATTATGTTACATAA-AGTGTTGCCATCCTACTGCCTGAACTGGTGAC
* *
463103 TTTTAGGTTTAGAATTATGTTACATAAAAGTGTTGCAATCCTACTGCCTGAACTGGTGACTTTTA
130 TTTTAGGTTTAGAATTATGTTACATATAAGTGTTGCCATCCTACTGCCTGAACTGGTGACTTTTA
*
463168 GGTTTAGAATTATGTTACATAAAAGTGTTGCCATCCTACTGCCTG
195 GGTTTAGAATTATGTTACATATAAGTGTTGCCATCCTACTGCCTG
*
463213 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATAAACGTGTTGCCATCCTACTGCCTGAACTG
1 AACTGGTGACTTTTAGGTTTAGAATTATGTTACATAAAAGTGTTGCCATCCTACTGCCTGAACTG
463278 GTGACTTTTAGGTTTAGAATTATGTTACATAAACGTGTTGCCATCCTACTGCCTGAACTGGTGAC
66 GTGACTTTTAGGTTTAGAATTATGTTACATAAA-GTGTTGCCATCCTACTGCCTGAACTGGTGAC
463343 TTTTAGGTTTAGAATTATGTTACATA-AACGTGTTGCCATCCTACTGCCTGAACT
130 TTTTAGGTTTAGAATTATGTTACATATAA-GTGTTGCCATCCTACTGCCTGAACT
463397 AGGAATGTAG
Statistics
Matches: 1266, Mismatches: 88, Indels: 59
0.90 0.06 0.04
Matches are distributed among these distances:
234 42 0.03
235 39 0.03
236 34 0.03
237 14 0.01
238 232 0.18
239 603 0.48
240 74 0.06
241 11 0.01
244 37 0.03
245 18 0.01
246 24 0.02
247 13 0.01
248 24 0.02
249 34 0.03
250 23 0.02
251 44 0.03
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.38
Consensus pattern (239 bp):
AACTGGTGACTTTTAGGTTTAGAATTATGTTACATAAAAGTGTTGCCATCCTACTGCCTGAACTG
GTGACTTTTAGGTTTAGAATTATGTTACATAAAGTGTTGCCATCCTACTGCCTGAACTGGTGACT
TTTAGGTTTAGAATTATGTTACATATAAGTGTTGCCATCCTACTGCCTGAACTGGTGACTTTTAG
GTTTAGAATTATGTTACATATAAGTGTTGCCATCCTACTGCCTG
Found at i:471899 original size:49 final size:49
Alignment explanation
Indices: 471841--471941 Score: 184
Period size: 49 Copynumber: 2.1 Consensus size: 49
471831 CGAAAGCCAA
* *
471841 GAAAGTTCGTTCGAGATTCTCGTGTATTATGGTTAACGTAAGAACTGTT
1 GAAAGTTCGTTCGAGATTCTCGTGTATTATCGTTAACGCAAGAACTGTT
471890 GAAAGTTCGTTCGAGATTCTCGTGTATTATCGTTAACGCAAGAACTGTT
1 GAAAGTTCGTTCGAGATTCTCGTGTATTATCGTTAACGCAAGAACTGTT
471939 GAA
1 GAA
471942 CACTGCACTC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.35
Consensus pattern (49 bp):
GAAAGTTCGTTCGAGATTCTCGTGTATTATCGTTAACGCAAGAACTGTT
Found at i:474248 original size:21 final size:21
Alignment explanation
Indices: 474222--474399 Score: 166
Period size: 21 Copynumber: 8.5 Consensus size: 21
474212 NNNNNNNNNN
474222 TAACGAGATATTTACTCGTAA
1 TAACGAGATATTTACTCGTAA
* * *
474243 TAACGAGATCTTTTCTCGTTA
1 TAACGAGATATTTACTCGTAA
* *
474264 TAACGAGATAATTAACTCGTTA
1 TAACGAGAT-ATTTACTCGTAA
* *
474286 TAACGAGATCTTTTCTCGTAA
1 TAACGAGATATTTACTCGTAA
* *
474307 TTACGAAATAATTTACTCGTAA
1 TAACGAGAT-ATTTACTCGTAA
* * * *
474329 TAACGAGATCTTTTCTCATTA
1 TAACGAGATATTTACTCGTAA
474350 TAACGAGACTA---ACTCGTAA
1 TAACGAGA-TATTTACTCGTAA
474369 TAACGAGATCATTT-CTCGTAA
1 TAACGAGAT-ATTTACTCGTAA
*
474390 TTACGAGATA
1 TAACGAGATA
474400 AAAATATTTT
Statistics
Matches: 125, Mismatches: 25, Indels: 15
0.76 0.15 0.09
Matches are distributed among these distances:
18 1 0.01
19 14 0.11
20 1 0.01
21 73 0.58
22 36 0.29
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (21 bp):
TAACGAGATATTTACTCGTAA
Found at i:474289 original size:43 final size:43
Alignment explanation
Indices: 474222--474400 Score: 231
Period size: 43 Copynumber: 4.3 Consensus size: 43
474212 NNNNNNNNNN
* *
474222 TAACGAGAT-ATTTACTCGTAATAACGAGATCTTTTCTCGTTA
1 TAACGAGATAATTAACTCGTAATAACGAGATCTTTTCTCGTAA
*
474264 TAACGAGATAATTAACTCGTTATAACGAGATCTTTTCTCGTAA
1 TAACGAGATAATTAACTCGTAATAACGAGATCTTTTCTCGTAA
* * * * *
474307 TTACGAAATAATTTACTCGTAATAACGAGATCTTTTCTCATTA
1 TAACGAGATAATTAACTCGTAATAACGAGATCTTTTCTCGTAA
* *
474350 TAACGAG---ACTAACTCGTAATAACGAGATCATTTCTCGTAA
1 TAACGAGATAATTAACTCGTAATAACGAGATCTTTTCTCGTAA
*
474390 TTACGAGATAA
1 TAACGAGATAA
474401 AAATATTTTT
Statistics
Matches: 116, Mismatches: 17, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
40 34 0.29
42 9 0.08
43 73 0.63
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (43 bp):
TAACGAGATAATTAACTCGTAATAACGAGATCTTTTCTCGTAA
Found at i:477493 original size:46 final size:46
Alignment explanation
Indices: 477435--477525 Score: 173
Period size: 46 Copynumber: 2.0 Consensus size: 46
477425 TTCCTACTTA
477435 TATCAGTTCTACAACTGACATTTTACCCAATCCTTCAGTCGATCTG
1 TATCAGTTCTACAACTGACATTTTACCCAATCCTTCAGTCGATCTG
*
477481 TATCTGTTCTACAACTGACATTTTACCCAATCCTTCAGTCGATCT
1 TATCAGTTCTACAACTGACATTTTACCCAATCCTTCAGTCGATCT
477526 TTAAATTAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.25, C:0.29, G:0.10, T:0.36
Consensus pattern (46 bp):
TATCAGTTCTACAACTGACATTTTACCCAATCCTTCAGTCGATCTG
Found at i:478781 original size:2 final size:2
Alignment explanation
Indices: 478774--478818 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
478764 AAGGAATGGA
478774 CT CT CT CT CT CT 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 CT CT CT CT CT CT
478816 CT C
1 CT C
478819 AGTTACATTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:507308 original size:179 final size:176
Alignment explanation
Indices: 507006--507538 Score: 786
Period size: 166 Copynumber: 3.0 Consensus size: 176
506996 GTGAAATGGA
* * *
507006 GTACCCTATATGCAATATTTTGCCAAAAAATGACTAGGTTCAAATGCTGGTATATTTTTTCATAA
1 GTACCCTATATGCAATATTTTGCCAAAAAATGTCTAAGTTCAAAAGCTGG--TATTTTTTCATAA
*
507071 ATTATCAGCAATCAAAATCCTAGCAATATGCACACCTCTAATATATGTACAATTGATCTTCAAAA
64 ATTAT-AGGAATCAAAATCCTAGCAATATGCACACCTCTAATATATGTACAATTGATCTTCAAAA
507136 GAACAACTTCTTATCTTGAAAACTGTAGGAGGAGTTATCCGTAAAATGAGG
128 GAACAACTTCTTATCTTGAAAACTGTAGGAGGAGTTATCC-T-AAATGAGG
*
507187 GTACCCTATATGCAATATTTTGCCAAAAAATGTTTAAGTTCAAAAGCTGGTATTTTTTCATAAAT
1 GTACCCTATATGCAATATTTTGCCAAAAAATGTCTAAGTTCAAAAGCTGGTATTTTTTCATAAAT
*
507252 TATTGGAAGTCAAAATCCTAGCAATATGCACACCTCTAATATATGTACAATTGATCTTCAAAAGA
66 TATAGGAA-TCAAAATCCTAGCAATATGCACACCTCTAATATATGTACAATTGATCTTCAAAAGA
507317 ACAACTTCTTATCTTGAAAACTGTAGGAGGAGTTATCC---------
130 ACAACTTCTTATCTTGAAAACTGTAGGAGGAGTTATCCTAAATGAGG
*
507355 GTA--CTATATGCAATATTTTGCCAAAAAAT-TACTAAGTTCAAAAGCTGGTACTTTTTCATAAA
1 GTACCCTATATGCAATATTTTGCCAAAAAATGT-CTAAGTTCAAAAGCTGGTATTTTTTCATAAA
* *
507417 TTATCGGAAATCAAAATCCTAGCAATATGCACACCTCTTATATATGTACAATTGATCTTCAAAAG
65 TTATAGG-AATCAAAATCCTAGCAATATGCACACCTCTAATATATGTACAATTGATCTTCAAAAG
*
507482 AACAACTTCCTT-TCATGAAAACTGTAGGAGGAGTTATCCATACAATGAGG
129 AACAACTT-CTTATCTTGAAAACTGTAGGAGGAGTTATCC-TA-AATGAGG
507532 GTACCCT
1 GTACCCT
507539 TTTGGCAACC
Statistics
Matches: 324, Mismatches: 11, Indels: 36
0.87 0.03 0.10
Matches are distributed among these distances:
165 1 0.00
166 149 0.46
167 5 0.02
168 3 0.01
177 3 0.01
178 3 0.01
179 114 0.35
181 46 0.14
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (176 bp):
GTACCCTATATGCAATATTTTGCCAAAAAATGTCTAAGTTCAAAAGCTGGTATTTTTTCATAAAT
TATAGGAATCAAAATCCTAGCAATATGCACACCTCTAATATATGTACAATTGATCTTCAAAAGAA
CAACTTCTTATCTTGAAAACTGTAGGAGGAGTTATCCTAAATGAGG
Found at i:509514 original size:17 final size:18
Alignment explanation
Indices: 509475--509514 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
509465 CAAAAAACAT
509475 TTAAA-ATGAATAATTAA
1 TTAAATATGAATAATTAA
509492 TT-AATATGAATAATT-A
1 TTAAATATGAATAATTAA
509508 TTAAATA
1 TTAAATA
509515 AAACTTCTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (18 bp):
TTAAATATGAATAATTAA
Found at i:512555 original size:10 final size:10
Alignment explanation
Indices: 512540--512624 Score: 134
Period size: 10 Copynumber: 8.2 Consensus size: 10
512530 GCATCTTTTT
*
512540 ACCCCAGTGA
1 ACCCCAATGA
512550 ACCCCAATGA
1 ACCCCAATGA
512560 TACCCCAATGA
1 -ACCCCAATGA
512571 ACCCCAATGA
1 ACCCCAATGA
512581 TACCCCAATGA
1 -ACCCCAATGA
512592 ACCCCAATGA
1 ACCCCAATGA
512602 ACCCCAATGA
1 ACCCCAATGA
512612 TACCCCAATGA
1 -ACCCCAATGA
512623 AC
1 AC
512625 TTTGAAATAC
Statistics
Matches: 71, Mismatches: 1, Indels: 6
0.91 0.01 0.08
Matches are distributed among these distances:
10 41 0.58
11 30 0.42
ACGTcount: A:0.38, C:0.39, G:0.11, T:0.13
Consensus pattern (10 bp):
ACCCCAATGA
Found at i:512624 original size:21 final size:21
Alignment explanation
Indices: 512539--512622 Score: 143
Period size: 21 Copynumber: 4.0 Consensus size: 21
512529 TGCATCTTTT
*
512539 TACCCCAGTGAACCCCAATGA
1 TACCCCAATGAACCCCAATGA
512560 TACCCCAATGAACCCCAATGA
1 TACCCCAATGAACCCCAATGA
512581 TACCCCAATGAACCCCAATGA
1 TACCCCAATGAACCCCAATGA
512602 -ACCCCAATGATACCCCAATGA
1 TACCCCAATGA-ACCCCAATGA
512623 ACTTTGAAAT
Statistics
Matches: 61, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
20 10 0.16
21 51 0.84
ACGTcount: A:0.37, C:0.38, G:0.11, T:0.14
Consensus pattern (21 bp):
TACCCCAATGAACCCCAATGA
Found at i:512624 original size:31 final size:31
Alignment explanation
Indices: 512540--512622 Score: 132
Period size: 31 Copynumber: 2.6 Consensus size: 31
512530 GCATCTTTTT
*
512540 ACCCCAGTGAACCCCAATGATACCCCAATGA
1 ACCCCAATGAACCCCAATGATACCCCAATGA
512571 ACCCCAATGATACCCCAATGA-ACCCCAATGA
1 ACCCCAATGA-ACCCCAATGATACCCCAATGA
512602 ACCCCAATGATACCCCAATGA
1 ACCCCAATGA-ACCCCAATGA
512623 ACTTTGAAAT
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
31 40 0.80
32 10 0.20
ACGTcount: A:0.37, C:0.39, G:0.11, T:0.13
Consensus pattern (31 bp):
ACCCCAATGAACCCCAATGATACCCCAATGA
Found at i:513148 original size:11 final size:11
Alignment explanation
Indices: 513128--513253 Score: 131
Period size: 11 Copynumber: 12.0 Consensus size: 11
513118 ATTTCAAAGT
*
513128 TCATTAGGGTA
1 TCATTGGGGTA
513139 TCATTGGGGT-
1 TCATTGGGGTA
*
513149 TCATTGGGATA
1 TCATTGGGGTA
*
513160 TCATT-TGGTA
1 TCATTGGGGTA
*
513170 TCATAGGGGTA
1 TCATTGGGGTA
*
513181 TCATTAGGTGTA
1 TCATT-GGGGTA
513193 T--TT-GGGTA
1 TCATTGGGGTA
513201 TCATTGGGGTA
1 TCATTGGGGTA
*
513212 ACATTGGGGT-
1 TCATTGGGGTA
*
513222 TCACTGGGGTA
1 TCATTGGGGTA
513233 TCATTGGGGT-
1 TCATTGGGGTA
513243 TCATTGGGGTA
1 TCATTGGGGTA
513254 AAAAGACGCA
Statistics
Matches: 94, Mismatches: 13, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
8 5 0.05
10 38 0.40
11 45 0.48
12 6 0.06
ACGTcount: A:0.20, C:0.10, G:0.33, T:0.37
Consensus pattern (11 bp):
TCATTGGGGTA
Found at i:513150 original size:21 final size:22
Alignment explanation
Indices: 513128--513253 Score: 108
Period size: 21 Copynumber: 6.0 Consensus size: 22
513118 ATTTCAAAGT
513128 TCATTAGGGTATCATTGGGGT-
1 TCATTAGGGTATCATTGGGGTA
*
513149 TCATT-GGGATATCATT-TGGTA
1 TCATTAGGG-TATCATTGGGGTA
*
513170 TCA-TAGGGGTATCATTAGGTGTA
1 TCATTA-GGGTATCATT-GGGGTA
513193 T--TT-GGGTATCATTGGGGTA
1 TCATTAGGGTATCATTGGGGTA
* * *
513212 ACATTGGGGT-TCACTGGGGTA
1 TCATTAGGGTATCATTGGGGTA
*
513233 TCATTGGGGT-TCATTGGGGTA
1 TCATTAGGGTATCATTGGGGTA
513254 AAAAGACGCA
Statistics
Matches: 87, Mismatches: 8, Indels: 20
0.76 0.07 0.17
Matches are distributed among these distances:
19 5 0.06
20 17 0.20
21 53 0.61
22 8 0.09
23 4 0.05
ACGTcount: A:0.20, C:0.10, G:0.33, T:0.37
Consensus pattern (22 bp):
TCATTAGGGTATCATTGGGGTA
Found at i:513251 original size:31 final size:32
Alignment explanation
Indices: 513128--513253 Score: 136
Period size: 31 Copynumber: 4.0 Consensus size: 32
513118 ATTTCAAAGT
*
513128 TCATTAGGGTATCATTGGGGT-TCATTGGGATA
1 TCATT-GGGTATCATTGGGGTATCATTGGGGTA
* * *
513160 TCATTTGGTATCATAGGGGTATCATTAGGTGTA
1 TCATTGGGTATCATTGGGGTATCATT-GGGGTA
*
513193 T--TTGGGTATCATTGGGGTAACATTGGGGT-
1 TCATTGGGTATCATTGGGGTATCATTGGGGTA
*
513222 TCACTGGGGTATCATTGGGGT-TCATTGGGGTA
1 TCA-TTGGGTATCATTGGGGTATCATTGGGGTA
513254 AAAAGACGCA
Statistics
Matches: 78, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
29 1 0.01
30 4 0.05
31 42 0.54
32 26 0.33
33 5 0.06
ACGTcount: A:0.20, C:0.10, G:0.33, T:0.37
Consensus pattern (32 bp):
TCATTGGGTATCATTGGGGTATCATTGGGGTA
Found at i:517669 original size:2 final size:2
Alignment explanation
Indices: 517662--517695 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
517652 AATATAACAA
* *
517662 AT AT AT AT AT AT TT AT AT AT AT AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
517696 CTATGTAGGT
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:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:518264 original size:28 final size:28
Alignment explanation
Indices: 518221--518665 Score: 572
Period size: 28 Copynumber: 16.1 Consensus size: 28
518211 CGTACAGATT
*
518221 AACAAAATACA-GAGGAGTCATAGAAACA
1 AACAAAATACACG-GGAGTCATAGTAACA
*
518249 AACAAAATACACAGGAGTCATAGTAACA
1 AACAAAATACACGGGAGTCATAGTAACA
*
518277 AGCAAAATACACGGGAGTCATAGTAACA
1 AACAAAATACACGGGAGTCATAGTAACA
*
518305 AAC--AA-A-A----AGTCATAGTAAAA
1 AACAAAATACACGGGAGTCATAGTAACA
518325 AACAAAATACA-GTGGAGTCATAGTAACA
1 AACAAAATACACG-GGAGTCATAGTAACA
518353 AACAAAATACACGGGAGTCA-AGGTAACA
1 AACAAAATACACGGGAGTCATA-GTAACA
518381 AACAAAATACACGGGAGTCATAGTAACA
1 AACAAAATACACGGGAGTCATAGTAACA
*
518409 AACAAAATACGCGGGAGTCATAGTAACA
1 AACAAAATACACGGGAGTCATAGTAACA
518437 AACAAAATACACGGGAGTCATAGTAACA
1 AACAAAATACACGGGAGTCATAGTAACA
* * *
518465 AGCGAAATACACGGGAGTCATAGTAACG
1 AACAAAATACACGGGAGTCATAGTAACA
518493 AACAAAATACACGGGAGTCATAGTAACA
1 AACAAAATACACGGGAGTCATAGTAACA
* * *
518521 AGCAAAATACAGGGGAGTTATAGTAACA
1 AACAAAATACACGGGAGTCATAGTAACA
* *
518549 AACAAAATATACGGGAGTCATATAGTTACA
1 AACAAAATACACGGGAGTC--ATAGTAACA
* *
518579 AACAAAAAACAGGGGAGTCATAGTAACA
1 AACAAAATACACGGGAGTCATAGTAACA
* *
518607 AGCGAAATACACGGGAGTCATAGTAACA
1 AACAAAATACACGGGAGTCATAGTAACA
** * *
518635 ATTAAAA-AAACAGGAGTCATAGTAACA
1 AACAAAATACACGGGAGTCATAGTAACA
518662 AACA
1 AACA
518666 GGTTACATCG
Statistics
Matches: 365, Mismatches: 38, Indels: 29
0.84 0.09 0.07
Matches are distributed among these distances:
20 15 0.04
22 2 0.01
23 1 0.00
24 2 0.01
25 1 0.00
26 2 0.01
27 21 0.06
28 295 0.81
29 2 0.01
30 24 0.07
ACGTcount: A:0.50, C:0.16, G:0.19, T:0.15
Consensus pattern (28 bp):
AACAAAATACACGGGAGTCATAGTAACA
Found at i:518317 original size:20 final size:20
Alignment explanation
Indices: 518292--518331 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
518282 AATACACGGG
*
518292 AGTCATAGTAACAAACAAAA
1 AGTCATAGTAAAAAACAAAA
518312 AGTCATAGTAAAAAACAAAA
1 AGTCATAGTAAAAAACAAAA
518332 TACAGTGGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (20 bp):
AGTCATAGTAAAAAACAAAA
Found at i:524271 original size:2 final size:2
Alignment explanation
Indices: 524264--524316 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
524254 AGGGGTAAGT
524264 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
524306 TC TC TC TC TC T
1 TC TC TC TC TC T
524317 NNNNNNNNNN
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:529312 original size:13 final size:13
Alignment explanation
Indices: 529294--529320 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
529284 TGAGTTTGAT
529294 CCAAATGATGTGA
1 CCAAATGATGTGA
529307 CCAAATGATGTGA
1 CCAAATGATGTGA
529320 C
1 C
529321 AAACACTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (13 bp):
CCAAATGATGTGA
Found at i:530119 original size:13 final size:14
Alignment explanation
Indices: 530091--530128 Score: 60
Period size: 13 Copynumber: 2.7 Consensus size: 14
530081 TCACAGGTAC
530091 TGAACATGTATGTAA
1 TGAACATG-ATGTAA
530106 TGAACATG-TGTAA
1 TGAACATGATGTAA
530119 TGAACATGAT
1 TGAACATGAT
530129 TACAATGTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 13 0.59
14 1 0.05
15 8 0.36
ACGTcount: A:0.39, C:0.08, G:0.21, T:0.32
Consensus pattern (14 bp):
TGAACATGATGTAA
Found at i:534413 original size:14 final size:14
Alignment explanation
Indices: 534394--534421 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
534384 CAACGAAATA
534394 GATCACTATTTAGT
1 GATCACTATTTAGT
534408 GATCACTATTTAGT
1 GATCACTATTTAGT
534422 ACACAATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (14 bp):
GATCACTATTTAGT
Found at i:535327 original size:26 final size:26
Alignment explanation
Indices: 535297--535376 Score: 142
Period size: 26 Copynumber: 3.1 Consensus size: 26
535287 ATCAGATTGT
*
535297 AGGCCCTAACAATCACACACTGACGC
1 AGGCCCTAACAATCACACACTGATGC
535323 AGGCCCTAACAATCACACACTGATGC
1 AGGCCCTAACAATCACACACTGATGC
*
535349 AGGCCCTGACAATCACACACTGATGC
1 AGGCCCTAACAATCACACACTGATGC
535375 AG
1 AG
535377 AACTTGTTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 52 1.00
ACGTcount: A:0.34, C:0.35, G:0.17, T:0.14
Consensus pattern (26 bp):
AGGCCCTAACAATCACACACTGATGC
Found at i:539806 original size:41 final size:41
Alignment explanation
Indices: 539753--539838 Score: 154
Period size: 41 Copynumber: 2.1 Consensus size: 41
539743 CCCATTGTCG
539753 GATACCCACGGGTGATCGCGTTTATTACTTATCACCCAGGT
1 GATACCCACGGGTGATCGCGTTTATTACTTATCACCCAGGT
* *
539794 GATACCCACGGGTGATCGCGTTTTTTACTTATCACCCTGGT
1 GATACCCACGGGTGATCGCGTTTATTACTTATCACCCAGGT
539835 GATA
1 GATA
539839 AGTAAAAGAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.21, C:0.26, G:0.22, T:0.31
Consensus pattern (41 bp):
GATACCCACGGGTGATCGCGTTTATTACTTATCACCCAGGT
Found at i:542937 original size:1 final size:1
Alignment explanation
Indices: 542931--542974 Score: 70
Period size: 1 Copynumber: 44.0 Consensus size: 1
542921 AATATTGTCA
* *
542931 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCTCCCCTCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
542975 ACAACTACTA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.00, C:0.95, G:0.00, T:0.05
Consensus pattern (1 bp):
C
Found at i:543434 original size:86 final size:86
Alignment explanation
Indices: 543285--543449 Score: 276
Period size: 86 Copynumber: 1.9 Consensus size: 86
543275 TGTCGCCACC
*
543285 TTCATATCCCGCATGAATCACCAAAGAAAGCATTTTAGATAAACCTACACAAATATGGCTGCTGA
1 TTCATATCCCGCATGAATCACCAAAGAAAGCATTTTAGATAAACCTACACAAAAATGGCTGCTGA
543350 AGTAAATGAAAAGTAGAAAGA
66 AGTAAATGAAAAGTAGAAAGA
* * * * *
543371 TTCATATCCTGCATGAATCACGAAAGAAAGCATTTTAGGTAAACCTACACAAAAATTGTTGCTGA
1 TTCATATCCCGCATGAATCACCAAAGAAAGCATTTTAGATAAACCTACACAAAAATGGCTGCTGA
543436 AGTAAATGAAAAGT
66 AGTAAATGAAAAGT
543450 GTGACAACTT
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
86 73 1.00
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.24
Consensus pattern (86 bp):
TTCATATCCCGCATGAATCACCAAAGAAAGCATTTTAGATAAACCTACACAAAAATGGCTGCTGA
AGTAAATGAAAAGTAGAAAGA
Found at i:544355 original size:9 final size:11
Alignment explanation
Indices: 544326--544350 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
544316 ACTGACAATG
544326 AATATTACATA
1 AATATTACATA
544337 AATATTACATA
1 AATATTACATA
544348 AAT
1 AAT
544351 TACATTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (11 bp):
AATATTACATA
Found at i:564798 original size:10 final size:9
Alignment explanation
Indices: 564783--564856 Score: 61
Period size: 10 Copynumber: 8.6 Consensus size: 9
564773 ATATGTCAGA
564783 GTACTACAAT
1 GTACTAC-AT
564793 GTACTACAT
1 GTACTACAT
*
564802 GT-C-AGA-
1 GTACTACAT
564808 GTACTACAAT
1 GTACTAC-AT
564818 GTACTACAT
1 GTACTACAT
*
564827 GT-C-AGA-
1 GTACTACAT
564833 GTACTACAAT
1 GTACTAC-AT
564843 GTACTACAT
1 GTACTACAT
564852 GTACT
1 GTACT
564857 GCTACAAGTA
Statistics
Matches: 52, Mismatches: 4, Indels: 17
0.71 0.05 0.23
Matches are distributed among these distances:
6 4 0.08
7 6 0.12
8 4 0.08
9 17 0.33
10 21 0.40
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (9 bp):
GTACTACAT
Found at i:564809 original size:25 final size:25
Alignment explanation
Indices: 564775--564853 Score: 158
Period size: 25 Copynumber: 3.2 Consensus size: 25
564765 TGTTGTGAAT
564775 ATGTCAGAGTACTACAATGTACTAC
1 ATGTCAGAGTACTACAATGTACTAC
564800 ATGTCAGAGTACTACAATGTACTAC
1 ATGTCAGAGTACTACAATGTACTAC
564825 ATGTCAGAGTACTACAATGTACTAC
1 ATGTCAGAGTACTACAATGTACTAC
564850 ATGT
1 ATGT
564854 ACTGCTACAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 54 1.00
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.29
Consensus pattern (25 bp):
ATGTCAGAGTACTACAATGTACTAC
Found at i:564813 original size:15 final size:15
Alignment explanation
Indices: 564793--564840 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
564783 GTACTACAAT
564793 GTACTACATGTCAGA
1 GTACTACATGTCAGA
*
564808 GTACTACA----A-T
1 GTACTACATGTCAGA
564818 GTACTACATGTCAGA
1 GTACTACATGTCAGA
564833 GTACTACA
1 GTACTACA
564841 ATGTACTACA
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
10 8 0.31
11 1 0.04
14 1 0.04
15 16 0.62
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (15 bp):
GTACTACATGTCAGA
Found at i:569624 original size:21 final size:21
Alignment explanation
Indices: 569598--569837 Score: 239
Period size: 21 Copynumber: 11.2 Consensus size: 21
569588 AAATATTTTT
*
569598 ATCTCGTAATTACGAGAAAAG
1 ATCTCGTTATTACGAGAAAAG
* * **
569619 ATCTCGTTAGTACGAGTTAATT
1 ATCTCGTTATTACGAG-AAAAG
569641 ATCTCGTTATTACGAGAAAAG
1 ATCTCGTTATTACGAGAAAAG
**
569662 ATCTCGTTATTACGAG-TTAG
1 ATCTCGTTATTACGAGAAAAG
569682 TTATCTCGTTATTACGAGAAAAG
1 --ATCTCGTTATTACGAGAAAAG
*
569705 ATCTCGTAATTACGAGAAAAG
1 ATCTCGTTATTACGAGAAAAG
**
569726 ATCTCGTTATTACGAGATAATT
1 ATCTCGTTATTACGAGA-AAAG
* * ***
569748 TTCTCGTTATTACGAGTTATTT
1 ATCTCGTTATTACGAG-AAAAG
* * **
569770 TTCTCGTTATTACGAGTTAATT
1 ATCTCGTTATTACGAG-AAAAG
*
569792 TTCTCGTTATTACGAGAAAAG
1 ATCTCGTTATTACGAGAAAAG
569813 ATCTCGTTATTACGAGAAAAG
1 ATCTCGTTATTACGAGAAAAG
569834 ATCT
1 ATCT
569838 ATATAAAATG
Statistics
Matches: 188, Mismatches: 25, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
20 2 0.01
21 94 0.50
22 90 0.48
23 2 0.01
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (21 bp):
ATCTCGTTATTACGAGAAAAG
Found at i:569645 original size:43 final size:43
Alignment explanation
Indices: 569596--569837 Score: 281
Period size: 43 Copynumber: 5.6 Consensus size: 43
569586 AAAAATATTT
* *
569596 TTATCTCGTAATTACGAGAAAAGATCTCGTTAGTACGAGTTAA
1 TTATCTCGTTATTACGAGAAAAGATCTCGTTATTACGAGTTAA
*
569639 TTATCTCGTTATTACGAGAAAAGATCTCGTTATTACGAGTTAG
1 TTATCTCGTTATTACGAGAAAAGATCTCGTTATTACGAGTTAA
* *
569682 TTATCTCGTTATTACGAGAAAAGATCTCGTAATTACGAG-AAA
1 TTATCTCGTTATTACGAGAAAAGATCTCGTTATTACGAGTTAA
** *** *
569724 AGATCTCGTTATTACGAGATAATTTTCTCGTTATTACGAGTTAT
1 TTATCTCGTTATTACGAGA-AAAGATCTCGTTATTACGAGTTAA
* * *** *
569768 TTTTCTCGTTATTACGAGTTAATTTTCTCGTTATTACGAG-AAA
1 TTATCTCGTTATTACGAG-AAAAGATCTCGTTATTACGAGTTAA
**
569811 AGATCTCGTTATTACGAGAAAAGATCT
1 TTATCTCGTTATTACGAGAAAAGATCT
569838 ATATAAAATG
Statistics
Matches: 169, Mismatches: 27, Indels: 7
0.83 0.13 0.03
Matches are distributed among these distances:
42 23 0.14
43 110 0.65
44 36 0.21
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (43 bp):
TTATCTCGTTATTACGAGAAAAGATCTCGTTATTACGAGTTAA
Found at i:569646 original size:22 final size:22
Alignment explanation
Indices: 569596--569828 Score: 215
Period size: 22 Copynumber: 10.8 Consensus size: 22
569586 AAAAATATTT
* *
569596 TTATCTCGTAATTACGAG-AAA
1 TTATCTCGTTATTACGAGTTAA
** *
569617 AGATCTCGTTAGTACGAGTTAA
1 TTATCTCGTTATTACGAGTTAA
*
569639 TTATCTCGTTATTACGAG-AAA
1 TTATCTCGTTATTACGAGTTAA
** *
569660 AGATCTCGTTATTACGAGTTAG
1 TTATCTCGTTATTACGAGTTAA
*
569682 TTATCTCGTTATTACGAG-AAA
1 TTATCTCGTTATTACGAGTTAA
** * *
569703 AGATCTCGTAATTACGAG-AAA
1 TTATCTCGTTATTACGAGTTAA
** *
569724 AGATCTCGTTATTACGAGATAA
1 TTATCTCGTTATTACGAGTTAA
* *
569746 TTTTCTCGTTATTACGAGTTAT
1 TTATCTCGTTATTACGAGTTAA
*
569768 TTTTCTCGTTATTACGAGTTAA
1 TTATCTCGTTATTACGAGTTAA
* *
569790 TTTTCTCGTTATTACGAG-AAA
1 TTATCTCGTTATTACGAGTTAA
**
569811 AGATCTCGTTATTACGAG
1 TTATCTCGTTATTACGAG
569829 AAAAGATCTA
Statistics
Matches: 177, Mismatches: 32, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
21 85 0.48
22 92 0.52
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.38
Consensus pattern (22 bp):
TTATCTCGTTATTACGAGTTAA
Found at i:570555 original size:21 final size:21
Alignment explanation
Indices: 570498--570758 Score: 261
Period size: 21 Copynumber: 12.2 Consensus size: 21
570488 TTTCAAAAAT
570498 AGATCTTTTCTCGTAATTACG
1 AGATCTTTTCTCGTAATTACG
* ** *
570519 AGATAATTAACTCGTAATAACG
1 AGAT-CTTTTCTCGTAATTACG
*
570541 AGATCTTTTCTCGTAATAACG
1 AGATCTTTTCTCGTAATTACG
* *
570562 AGATCCTTTCTCATAATTACG
1 AGATCTTTTCTCGTAATTACG
570583 AGATCTTTTCTCGTAATTACG
1 AGATCTTTTCTCGTAATTACG
* ** *
570604 AGATAATTAACTCGTAATGACG
1 AGAT-CTTTTCTCGTAATTACG
* ** * *
570626 AGATAATTAACTCGTAATAACA
1 AGAT-CTTTTCTCGTAATTACG
570648 AGATCTTTTCTCGTAATTACG
1 AGATCTTTTCTCGTAATTACG
570669 AGATCTTTTCTCGTAATTACG
1 AGATCTTTTCTCGTAATTACG
* ** *
570690 AGATAATTAACTCGTAATAACG
1 AGAT-CTTTTCTCGTAATTACG
* ** *
570712 AGATAATTAACTCGTAATAACG
1 AGAT-CTTTTCTCGTAATTACG
570734 AGATCTTTTCTCGTAATTACG
1 AGATCTTTTCTCGTAATTACG
570755 AGAT
1 AGAT
570759 ATAAATATTT
Statistics
Matches: 206, Mismatches: 31, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
21 113 0.55
22 93 0.45
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (21 bp):
AGATCTTTTCTCGTAATTACG
Found at i:570662 original size:65 final size:64
Alignment explanation
Indices: 570529--570759 Score: 284
Period size: 65 Copynumber: 3.6 Consensus size: 64
570519 AGATAATTAA
* * ** * * * *
570529 CTCGTAATAACGAGATCTTTTCTCGTAATAACGAGATCCTT-TCTCATAATTACGAGATCTTTT
1 CTCGTAATTACGAGATCTTTTCTCGTAATTACGAGATAATTAACTCGTAATAACAAGATCTTTT
* ** *
570592 CTCGTAATTACGAGATAATTAACTCGTAATGACGAGATAATTAACTCGTAATAACAAGATCTTTT
1 CTCGTAATTACGAGAT-CTTTTCTCGTAATTACGAGATAATTAACTCGTAATAACAAGATCTTTT
* * **
570657 CTCGTAATTACGAGATCTTTTCTCGTAATTACGAGATAATTAACTCGTAATAACGAGATAATTAA
1 CTCGTAATTACGAGATCTTTTCTCGTAATTACGAGATAATTAACTCGTAATAACAAGAT-CTTTT
*
570722 CTCGTAATAACGAGATCTTTTCTCGTAATTACGAGATA
1 CTCGTAATTACGAGATCTTTTCTCGTAATTACGAGATA
570760 TAAATATTTT
Statistics
Matches: 145, Mismatches: 20, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
63 15 0.10
64 57 0.39
65 73 0.50
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (64 bp):
CTCGTAATTACGAGATCTTTTCTCGTAATTACGAGATAATTAACTCGTAATAACAAGATCTTTT
Found at i:570684 original size:86 final size:86
Alignment explanation
Indices: 570498--570758 Score: 452
Period size: 86 Copynumber: 3.0 Consensus size: 86
570488 TTTCAAAAAT
* **
570498 AGATCTTTTCTCGTAATTACGAGATAATTAACTCGTAATAACGAGAT-CTTTTCTCGTAATAACG
1 AGATCTTTTCTCGTAATTACGAGATAATTAACTCGTAATAACGAGATAATTAACTCGTAATAACG
* *
570562 AGATCCTTTCTCATAATTACG
66 AGATCTTTTCTCGTAATTACG
* *
570583 AGATCTTTTCTCGTAATTACGAGATAATTAACTCGTAATGACGAGATAATTAACTCGTAATAACA
1 AGATCTTTTCTCGTAATTACGAGATAATTAACTCGTAATAACGAGATAATTAACTCGTAATAACG
570648 AGATCTTTTCTCGTAATTACG
66 AGATCTTTTCTCGTAATTACG
570669 AGATCTTTTCTCGTAATTACGAGATAATTAACTCGTAATAACGAGATAATTAACTCGTAATAACG
1 AGATCTTTTCTCGTAATTACGAGATAATTAACTCGTAATAACGAGATAATTAACTCGTAATAACG
570734 AGATCTTTTCTCGTAATTACG
66 AGATCTTTTCTCGTAATTACG
570755 AGAT
1 AGAT
570759 ATAAATATTT
Statistics
Matches: 166, Mismatches: 9, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
85 46 0.28
86 120 0.72
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (86 bp):
AGATCTTTTCTCGTAATTACGAGATAATTAACTCGTAATAACGAGATAATTAACTCGTAATAACG
AGATCTTTTCTCGTAATTACG
Found at i:605439 original size:65 final size:65
Alignment explanation
Indices: 605317--605550 Score: 314
Period size: 65 Copynumber: 3.6 Consensus size: 65
605307 GAAAATTCGA
* *
605317 AGGGGTTTCAAAATATCGCGGCCATAATATTTTGAACCCTACCTCTCCAAAAGGAATTGGAAACA
1 AGGGGGTTCAATATATCGCGGCCATAATATTTTGAACCC--CCTCTCCAAAAGGAATTGGAAACA
605382 GT
64 GT
* * *
605384 TGGGGGTTCAATATATCGTGGCCTTAATATTTTGAACCCCCTCTCCAAAAGGAATTGGAAACAGT
1 AGGGGGTTCAATATATCGCGGCCATAATATTTTGAACCCCCTCTCCAAAAGGAATTGGAAACAGT
* * *
605449 AGGGGGTTCAATATATCGCGGCCATAATATTTTGAACCCCCTCTCCAAGAGCAA-T-GAAA-ATT
1 AGGGGGTTCAATATATCGCGGCCATAATATTTTGAACCCCCTCTCCAAAAGGAATTGGAAACAGT
605511 CGAGGGGGTTTCAA-ATTATCGCGGCCATAATATTTTGAAC
1 --AGGGGG-TTCAATA-TATCGCGGCCATAATATTTTGAAC
605551 ATATGTATGT
Statistics
Matches: 152, Mismatches: 11, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
62 2 0.01
63 4 0.03
64 8 0.05
65 104 0.68
67 34 0.22
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (65 bp):
AGGGGGTTCAATATATCGCGGCCATAATATTTTGAACCCCCTCTCCAAAAGGAATTGGAAACAGT
Found at i:605597 original size:33 final size:32
Alignment explanation
Indices: 605560--605621 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
605550 CATATGTATG
*
605560 TATCGCAGCAATATTTTAAACCCGGGTTCATAA
1 TATCGCA-CAATATATTAAACCCGGGTTCATAA
* * *
605593 TATCGCATAATATATTGAACCTGGGTTCA
1 TATCGCACAATATATTAAACCCGGGTTCA
605622 ATATTTCGCG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
32 18 0.72
33 7 0.28
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32
Consensus pattern (32 bp):
TATCGCACAATATATTAAACCCGGGTTCATAA
Found at i:608022 original size:13 final size:13
Alignment explanation
Indices: 608004--608033 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
607994 ATAAGATATC
*
608004 ATTTCTTTTTGTG
1 ATTTCTTTTTGAG
608017 ATTTCTTTTTGAG
1 ATTTCTTTTTGAG
608030 ATTT
1 ATTT
608034 AATGATAGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.13, C:0.07, G:0.13, T:0.67
Consensus pattern (13 bp):
ATTTCTTTTTGAG
Found at i:612996 original size:41 final size:42
Alignment explanation
Indices: 612934--613034 Score: 116
Period size: 42 Copynumber: 2.4 Consensus size: 42
612924 GTTTATCAGC
* *
612934 TGTTAACTATAGTTAACGGATCC-TAAACTATAGTTAACGAT
1 TGTTAACTATAGTTTACGGATCCGTAAACTATAGTTAACGAA
* * * *
612975 TCGTTAACTATAGTTTA-GGATCCGTTAACTGTATTTCACGAA
1 T-GTTAACTATAGTTTACGGATCCGTAAACTATAGTTAACGAA
*
613017 TGTAAACTATAGTTTACG
1 TGTTAACTATAGTTTACG
613035 AATGATAATC
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
41 21 0.42
42 29 0.58
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.37
Consensus pattern (42 bp):
TGTTAACTATAGTTTACGGATCCGTAAACTATAGTTAACGAA
Found at i:613000 original size:21 final size:21
Alignment explanation
Indices: 612935--613004 Score: 88
Period size: 21 Copynumber: 3.3 Consensus size: 21
612925 TTTATCAGCT
612935 GTTAACTATAGTTAACGGATCC
1 GTTAACTATAGTTAA-GGATCC
* * *
612957 -TAAACTATAGTTAACGATTC
1 GTTAACTATAGTTAAGGATCC
*
612977 GTTAACTATAGTTTAGGATCC
1 GTTAACTATAGTTAAGGATCC
612998 GTTAACT
1 GTTAACT
613005 GTATTTCACG
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
20 4 0.10
21 36 0.90
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (21 bp):
GTTAACTATAGTTAAGGATCC
Found at i:613038 original size:20 final size:21
Alignment explanation
Indices: 612938--613037 Score: 80
Period size: 21 Copynumber: 4.8 Consensus size: 21
612928 ATCAGCTGTT
* * *
612938 AACTATAGTTAACGGATCCTA
1 AACTATAGTTTACGAATCGTA
* * *
612959 AACTATAGTTAACGATTCGTT
1 AACTATAGTTTACGAATCGTA
* *
612980 AACTATAGTTTA-GGATCCGTT
1 AACTATAGTTTACGAAT-CGTA
*
613001 AACTGTA-TTTCACGAAT-GTA
1 AACTATAGTTT-ACGAATCGTA
613021 AACTATAGTTTACGAAT
1 AACTATAGTTTACGAAT
613038 GATAATCATA
Statistics
Matches: 64, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
20 19 0.30
21 42 0.66
22 3 0.05
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (21 bp):
AACTATAGTTTACGAATCGTA
Found at i:613048 original size:20 final size:20
Alignment explanation
Indices: 612938--613052 Score: 65
Period size: 21 Copynumber: 5.6 Consensus size: 20
612928 ATCAGCTGTT
* * *
612938 AACTATAGTTAACGGATCCTA
1 AACTATAGTTTACGAAT-GTA
* * *
612959 AACTATAGTTAACGATTCGTT
1 AACTATAGTTTACGAAT-GTA
* *
612980 AACTATAGTTTA-GGATCCGTT
1 AACTATAGTTTACGAAT--GTA
*
613001 AACTGTA-TTTCACGAATGTA
1 AACTATAGTTT-ACGAATGTA
613021 AACTATAGTTTACGAATGATA
1 AACTATAGTTTACGAATG-TA
*
613042 ATC-ATAGTTTA
1 AACTATAGTTTA
613053 TCTATCTGTA
Statistics
Matches: 77, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
20 28 0.36
21 46 0.60
22 3 0.04
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.36
Consensus pattern (20 bp):
AACTATAGTTTACGAATGTA
Found at i:613319 original size:20 final size:20
Alignment explanation
Indices: 613296--613359 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
613286 CGACGTTAAT
613296 CTATATTTCACGTCTGTAAA
1 CTATATTTCACGTCTGTAAA
* * *
613316 CTATAGTTAACG-C-GATAAT
1 CTATATTTCACGTCTG-TAAA
* *
613335 CTATGTTTCACATCTGTAAA
1 CTATATTTCACGTCTGTAAA
613355 CTATA
1 CTATA
613360 GTTAACACTG
Statistics
Matches: 32, Mismatches: 9, Indels: 6
0.68 0.19 0.13
Matches are distributed among these distances:
18 1 0.03
19 12 0.38
20 18 0.56
21 1 0.03
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.38
Consensus pattern (20 bp):
CTATATTTCACGTCTGTAAA
Found at i:613351 original size:39 final size:40
Alignment explanation
Indices: 613273--613365 Score: 152
Period size: 39 Copynumber: 2.4 Consensus size: 40
613263 TACGGATCAA
* *
613273 AAACTATAGTTAACGACGTTAATCTATATTTCACGTCTGT
1 AAACTATAGTTAACGACGATAATCTATATTTCACATCTGT
*
613313 AAACTATAGTTAACG-CGATAATCTATGTTTCACATCTGT
1 AAACTATAGTTAACGACGATAATCTATATTTCACATCTGT
613352 AAACTATAGTTAAC
1 AAACTATAGTTAAC
613366 ACTGAAAATA
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
39 35 0.70
40 15 0.30
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.35
Consensus pattern (40 bp):
AAACTATAGTTAACGACGATAATCTATATTTCACATCTGT
Found at i:618011 original size:8 final size:8
Alignment explanation
Indices: 617972--618013 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
617962 GATCACATTT
617972 TGTCCGTC
1 TGTCCGTC
617980 -GTCCGTC
1 TGTCCGTC
*
617987 TGTCCGCC
1 TGTCCGTC
* *
617995 CGTCTGTC
1 TGTCCGTC
618003 TGTCCGTC
1 TGTCCGTC
618011 TGT
1 TGT
618014 AAAGTTTTTA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.00, C:0.38, G:0.26, T:0.36
Consensus pattern (8 bp):
TGTCCGTC
Found at i:620373 original size:166 final size:165
Alignment explanation
Indices: 620111--620794 Score: 831
Period size: 166 Copynumber: 4.2 Consensus size: 165
620101 TATTCCTATA
* *
620111 CTGGCCTAATAG-TTTTGAGAAGAAGACTTTTAAAGATTTTCTC----TA-TA-TATG-AAAA-T
1 CTGGCCTAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATATTACTATGTAAAACA
* * * * * *
620167 TTATCCCCCATTGTGGCCCCGCCCTACCCCCAGGGACCATGATTTGAACCAACTTAAATCTACAC
66 TGATCCCCAATTGTGGCCCCACCCTACCCACAGGGACCATGATTTGAACAAACTTGAATCTACAC
620232 TACCTGAGGATGCTTCCATTTTAATTTGAGCTTTT
131 TACCTGAGGATGCTTCCATTTTAATTTGAGCTTTT
* * * *
620267 CTGGCCTAATAGTTTTTGAGAAGAAGATTTTTAAAGATTGTCTCGATACATTCCT-TCGTAAAAC
1 CTGGCCTAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATATTACTAT-GTAAAAC
620331 ATGATCCCTCAATTGTGGCCCCACCCTACCCACAGGGACCATGATTTGAACAAACTTGAATCTAC
65 ATGATCCC-CAATTGTGGCCCCACCCTACCCACAGGGACCATGATTTGAACAAACTTGAATCTAC
* *
620396 ACTACCTGAGGATGCTTCCATTTTAATTTTAGCTTTC
129 ACTACCTGAGGATGCTTCCATTTTAATTTGAGCTTTT
* * *
620433 CTGGGCTAATAGTTTTTGGGAAGAAGATTTGTAAAGATTTTCTCTATATATTACTATGTAAAA-A
1 CTGGCCTAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATATTACTATGTAAAACA
* * * *
620497 TCCATTCCCCAATTGTGGCCCCATCATA-CCACCAGGGACTATGATTTGAACAAACTTGAATCTA
66 T-GA-TCCCCAATTGTGGCCCCACCCTACCCA-CAGGGACCATGATTTGAACAAACTTGAATCTA
*
620561 CACTACCTGAGGATGCTCCCATTTTAATTTGAGCTTTT
128 CACTACCTGAGGATGCTTCCATTTTAATTTGAGCTTTT
* * * * *
620599 CTGGCCTGATAGTTTTTGAGAAG-A-TTTTTTAAAGATTTTCTCTATATAATACTATGTTAAACT
1 CTGGCCTAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATATTACTATGTAAAACA
** * * * *
620662 TGATCCCCCTCTTGTGGCCCCTCCCTACCCCCGGGGACCATAATTTGAACAAACTTGAATCTACA
66 TGAT-CCCCAATTGTGGCCCCACCCTACCCACAGGGACCATGATTTGAACAAACTTGAATCTACA
* *** **
620727 CTACCTGAGGATGCCTCCA-CACAAGTTAAAGCTTTT
130 CTACCTGAGGATGCTTCCATTTTAA-TTTGAGCTTTT
* *
620763 CAGGCCGAATAGTTTTTGAGAAGAAGATTTTT
1 CTGGCCTAATAGTTTTTGAGAAGAAGATTTTT
620795 GAAAAATACC
Statistics
Matches: 451, Mismatches: 56, Indels: 32
0.84 0.10 0.06
Matches are distributed among these distances:
156 12 0.03
157 29 0.06
161 1 0.00
162 2 0.00
163 5 0.01
164 132 0.29
165 16 0.04
166 249 0.55
167 5 0.01
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.33
Consensus pattern (165 bp):
CTGGCCTAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATATTACTATGTAAAACA
TGATCCCCAATTGTGGCCCCACCCTACCCACAGGGACCATGATTTGAACAAACTTGAATCTACAC
TACCTGAGGATGCTTCCATTTTAATTTGAGCTTTT
Found at i:620788 original size:330 final size:322
Alignment explanation
Indices: 620113--620793 Score: 868
Period size: 330 Copynumber: 2.1 Consensus size: 322
620103 TTCCTATACT
** *
620113 GGCCTAATAG-TTTTGAGAAGAAGACTTTTAAAGATTTTCTCTATATATGAAAATTTATCCCCCA
1 GGCCTAATAGTTTTTGAGAAGAAGA-TTTTAAAGATTTTCTCTATATATGAAAATCCATCCCCAA
* * * *
620177 TTGTGGCCCCGCCCTACCCCCAGGGACCATGATTTGAACCAACTTAAATCTACACTACCTGAGGA
65 TTGTGGCCCCACCATACCACCAGGGACCATGATTTGAACAAACTTAAATCTACACTACCTGAGGA
*
620242 TGCTTCCATTTTAATTTGAGCTTTTCTGGCCTAATAGTTTTTGAGAAGAAGATTTTTAAAGATTG
130 TGCTCCCATTTTAATTTGAGCTTTTCTGGCCTAATAGTTTTTGAGAAGAAGATTTTTAAAGATTG
* * *
620307 TCTCGATACATTCCTTCGTAAAACATGATCCCTCAATTGTGGCCCCACCCTACCCACAGGGACCA
195 TCTCGATACAATACTTCGTAAAACATGATCCCCCAATTGTGGCCCCACCCTACCCACAGGGACCA
* * *** ** *
620372 TGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCTTCCATTTTAATTTTAGCTTTCCT
260 TAATTTGAACAAACTTGAATCTACACTACCTGAGGATGCCTCCATCACAATTAAAGCTTTCCA
* *
620435 GGGCTAATAGTTTTTGGGAAGAAGATTTGTAAAGATTTTCTCTATATATTACTATGTAAAAATCC
1 GGCCTAATAGTTTTTGAGAAGAAGATTT-TAAAGATTTTCTC----TA-TA-TATG--AAAATCC
* * *
620500 ATTCCCCAATTGTGGCCCCATCATACCACCAGGGACTATGATTTGAACAAACTTGAATCTACACT
57 A-TCCCCAATTGTGGCCCCACCATACCACCAGGGACCATGATTTGAACAAACTTAAATCTACACT
* *
620565 ACCTGAGGATGCTCCCATTTTAATTTGAGCTTTTCTGGCCTGATAGTTTTTGAGAAG-A-TTTTT
121 ACCTGAGGATGCTCCCATTTTAATTTGAGCTTTTCTGGCCTAATAGTTTTTGAGAAGAAGATTTT
* * * * * ** *
620628 TAAAGATTTTCTCTATATAATACTAT-GTTAAACTTGATCCCCCTCTTGTGGCCCCTCCCTACCC
186 TAAAGATTGTCTCGATACAATACT-TCGTAAAACATGATCCCCCAATTGTGGCCCCACCCTACCC
* *
620692 CCGGGGACCATAATTTGAACAAACTTGAATCTACACTACCTGAGGATGCCTCCA-CACAAGTTAA
250 ACAGGGACCATAATTTGAACAAACTTGAATCTACACTACCTGAGGATGCCTCCATCACAA-TTAA
*
620756 AGCTTTTCA
314 AGCTTTCCA
*
620765 GGCCGAATAGTTTTTGAGAAGAAGATTTT
1 GGCCTAATAGTTTTTGAGAAGAAGATTTT
620794 TGAAAAATAC
Statistics
Matches: 306, Mismatches: 40, Indels: 19
0.84 0.11 0.05
Matches are distributed among these distances:
322 12 0.04
323 26 0.08
327 2 0.01
328 2 0.01
329 7 0.02
330 139 0.45
331 8 0.03
332 110 0.36
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.33
Consensus pattern (322 bp):
GGCCTAATAGTTTTTGAGAAGAAGATTTTAAAGATTTTCTCTATATATGAAAATCCATCCCCAAT
TGTGGCCCCACCATACCACCAGGGACCATGATTTGAACAAACTTAAATCTACACTACCTGAGGAT
GCTCCCATTTTAATTTGAGCTTTTCTGGCCTAATAGTTTTTGAGAAGAAGATTTTTAAAGATTGT
CTCGATACAATACTTCGTAAAACATGATCCCCCAATTGTGGCCCCACCCTACCCACAGGGACCAT
AATTTGAACAAACTTGAATCTACACTACCTGAGGATGCCTCCATCACAATTAAAGCTTTCCA
Found at i:624563 original size:21 final size:21
Alignment explanation
Indices: 624527--624583 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
624517 AAACTTTTAA
* *
624527 AAACTTTAAAGATGGAAAAAT
1 AAACTTGAAAGTTGGAAAAAT
* *
624548 CAATTTGAAAGTTGGAAAAAT
1 AAACTTGAAAGTTGGAAAAAT
624569 AAACTTGAAAGTTGG
1 AAACTTGAAAGTTGG
624584 GAATTCCAAG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.49, C:0.05, G:0.19, T:0.26
Consensus pattern (21 bp):
AAACTTGAAAGTTGGAAAAAT
Found at i:626018 original size:2 final size:2
Alignment explanation
Indices: 626013--626052 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
626003 AAAAAAAGAG
*
626013 TC TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
626053 ACCATTGTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:626764 original size:21 final size:21
Alignment explanation
Indices: 626719--626764 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
626709 TTACGCCGAC
* *
626719 TTGTCAGATCTTTTTAACGAC
1 TTGTCAGATCTTTATAACGAA
**
626740 TTGTCAGATCTTTATGTCGAA
1 TTGTCAGATCTTTATAACGAA
626761 TTGT
1 TTGT
626765 TACTTATTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.22, C:0.15, G:0.17, T:0.46
Consensus pattern (21 bp):
TTGTCAGATCTTTATAACGAA
Found at i:628643 original size:2 final size:2
Alignment explanation
Indices: 628636--628685 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
628626 GGTTTAAGCG
* *
628636 GT GT GT GT GT GT GT GC GT GT GT GT TT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
628678 GT GT GT GT
1 GT GT GT GT
628686 TCCCTTAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.02, G:0.48, T:0.50
Consensus pattern (2 bp):
GT
Found at i:630451 original size:32 final size:32
Alignment explanation
Indices: 630415--630493 Score: 77
Period size: 32 Copynumber: 2.5 Consensus size: 32
630405 GATCCAACAA
* *
630415 GTGCCGAGTTTACTAGATGTCGAATTAACCAG
1 GTGCCGAATTTACTAGATGCCGAATTAACCAG
* * * *
630447 GTGCCAAATTTACTTGATGCCGAGTTTACCAG
1 GTGCCGAATTTACTAGATGCCGAATTAACCAG
* * *
630479 ATGCCGGATTCACTA
1 GTGCCGAATTTACTA
630494 TTTTCGATGC
Statistics
Matches: 36, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.29
Consensus pattern (32 bp):
GTGCCGAATTTACTAGATGCCGAATTAACCAG
Found at i:630481 original size:16 final size:16
Alignment explanation
Indices: 630416--630484 Score: 57
Period size: 16 Copynumber: 4.3 Consensus size: 16
630406 ATCCAACAAG
* *
630416 TGCCGAGTTTACTAGA
1 TGCCGAATTTACCAGA
* * *
630432 TGTCGAATTAACCAGG
1 TGCCGAATTTACCAGA
* **
630448 TGCCAAATTTACTTGA
1 TGCCGAATTTACCAGA
*
630464 TGCCGAGTTTACCAGA
1 TGCCGAATTTACCAGA
630480 TGCCG
1 TGCCG
630485 GATTCACTAT
Statistics
Matches: 38, Mismatches: 15, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (16 bp):
TGCCGAATTTACCAGA
Found at i:639752 original size:13 final size:13
Alignment explanation
Indices: 639734--639767 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
639724 ATTTATATAG
639734 TATGTATTGTTAA
1 TATGTATTGTTAA
639747 TATGTATTGTTAA
1 TATGTATTGTTAA
639760 TATGTATT
1 TATGTATT
639768 AACTGAACAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.15, T:0.56
Consensus pattern (13 bp):
TATGTATTGTTAA
Found at i:649768 original size:42 final size:42
Alignment explanation
Indices: 649700--649779 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 42
649690 TTCTATTGAT
* * *
649700 TATGTCGACATGCAAGATAAAGATGTTGACATGCAAGATAAA
1 TATGTCAACATGCAACATAAAGATGTTAACATGCAAGATAAA
**
649742 TATGTCAACATGCAACATAACTATGTTAACATGCAAGA
1 TATGTCAACATGCAACATAAAGATGTTAACATGCAAGA
649780 AAACTGCGAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.25
Consensus pattern (42 bp):
TATGTCAACATGCAACATAAAGATGTTAACATGCAAGATAAA
Found at i:649784 original size:21 final size:21
Alignment explanation
Indices: 649707--649779 Score: 101
Period size: 21 Copynumber: 3.5 Consensus size: 21
649697 GATTATGTCG
* *
649707 ACATGCAAGATAAAGATGTTG
1 ACATGCAAGATAAATATGTTA
*
649728 ACATGCAAGATAAATATGTCA
1 ACATGCAAGATAAATATGTTA
* *
649749 ACATGCAACATAACTATGTTA
1 ACATGCAAGATAAATATGTTA
649770 ACATGCAAGA
1 ACATGCAAGA
649780 AAACTGCGAT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.45, C:0.15, G:0.16, T:0.23
Consensus pattern (21 bp):
ACATGCAAGATAAATATGTTA
Found at i:652496 original size:21 final size:21
Alignment explanation
Indices: 652472--652602 Score: 129
Period size: 21 Copynumber: 6.2 Consensus size: 21
652462 ATTTGTTGGN
* *
652472 ATAAGTAAGTTTCATGTTGAC
1 ATAAATAAGTTGCATGTTGAC
**
652493 ATAAATAAGTTGCATGTCAAC
1 ATAAATAAGTTGCATGTTGAC
* *
652514 TTAAATAAGTTACATGTTGAC
1 ATAAATAAGTTGCATGTTGAC
*
652535 ATAAATAAGTTGCATG-TCAGC
1 ATAAATAAGTTGCATGTTGA-C
** ** *
652556 ATATTTATCTTGCATGTTAAC
1 ATAAATAAGTTGCATGTTGAC
*
652577 ATAAATAAGTTGCATGTCGAC
1 ATAAATAAGTTGCATGTTGAC
652598 ATAAA
1 ATAAA
652603 AAGGTAGCAT
Statistics
Matches: 86, Mismatches: 22, Indels: 4
0.77 0.20 0.04
Matches are distributed among these distances:
20 2 0.02
21 82 0.95
22 2 0.02
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.34
Consensus pattern (21 bp):
ATAAATAAGTTGCATGTTGAC
Found at i:652535 original size:42 final size:42
Alignment explanation
Indices: 652472--652602 Score: 163
Period size: 42 Copynumber: 3.1 Consensus size: 42
652462 ATTTGTTGGN
* *
652472 ATAAGTAAGTTTCATGTTGACATAAATAAGTTGCATGTCAAC
1 ATAAATAAGTTACATGTTGACATAAATAAGTTGCATGTCAAC
* *
652514 TTAAATAAGTTACATGTTGACATAAATAAGTTGCATGTCAGC
1 ATAAATAAGTTACATGTTGACATAAATAAGTTGCATGTCAAC
** ** * * *
652556 ATATTTATCTTGCATGTTAACATAAATAAGTTGCATGTCGAC
1 ATAAATAAGTTACATGTTGACATAAATAAGTTGCATGTCAAC
652598 ATAAA
1 ATAAA
652603 AAGGTAGCAT
Statistics
Matches: 74, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 74 1.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.34
Consensus pattern (42 bp):
ATAAATAAGTTACATGTTGACATAAATAAGTTGCATGTCAAC
Found at i:652760 original size:42 final size:42
Alignment explanation
Indices: 652691--652770 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
652681 ATTGCAGTTT
*
652691 TCTTGCATGTCAACATAGTTATGTTGCATGTTGACATAACTA
1 TCTTGCATGTCAACATAGTTATGTTGCATGTCGACATAACTA
* *
652733 TCTTGCATGTCAACATATTTATTTTGCATGTCGACATA
1 TCTTGCATGTCAACATAGTTATGTTGCATGTCGACATA
652771 TTTGATAGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (42 bp):
TCTTGCATGTCAACATAGTTATGTTGCATGTCGACATAACTA
Found at i:652771 original size:21 final size:21
Alignment explanation
Indices: 652691--652773 Score: 94
Period size: 21 Copynumber: 4.0 Consensus size: 21
652681 ATTGCAGTTT
*
652691 TCTTGCATGTCAACATAGTTA
1 TCTTGCATGTCAACATATTTA
* ** **
652712 TGTTGCATGTTGACATAACTA
1 TCTTGCATGTCAACATATTTA
652733 TCTTGCATGTCAACATATTTA
1 TCTTGCATGTCAACATATTTA
* *
652754 TTTTGCATGTCGACATATTT
1 TCTTGCATGTCAACATATTT
652774 GATAGAAAAA
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (21 bp):
TCTTGCATGTCAACATATTTA
Found at i:661155 original size:8 final size:8
Alignment explanation
Indices: 661142--661168 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
661132 ATTGACATTC
661142 GGAACTCG
1 GGAACTCG
661150 GGAACTCG
1 GGAACTCG
661158 GGAACTCG
1 GGAACTCG
661166 GGA
1 GGA
661169 TTTTTCATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.26, C:0.22, G:0.41, T:0.11
Consensus pattern (8 bp):
GGAACTCG
Found at i:667608 original size:14 final size:14
Alignment explanation
Indices: 667589--667615 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
667579 AAACCACTTA
667589 AATTAGGGCACCAT
1 AATTAGGGCACCAT
667603 AATTAGGGCACCA
1 AATTAGGGCACCA
667616 ATTATAAAAC
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:0.37, C:0.22, G:0.22, T:0.19
Consensus pattern (14 bp):
AATTAGGGCACCAT
Found at i:674145 original size:438 final size:436
Alignment explanation
Indices: 673324--674376 Score: 1438
Period size: 438 Copynumber: 2.4 Consensus size: 436
673314 CCCATCCCTG
* * *
673324 CTAATTACGTATTAAATGGGCGT-ACAATTGATCTTTTCTGATGGATATTGTTACGATCAACAAC
1 CTAATTACGTAATAAATGGGCGTGACAA-TGATTTTTTCTGATAGATATTGTTACGATCAACAAC
* * * * * *
673388 TTTGCTTCAATAATGCTTTACAAAATCTTTATCGTTTTTTAAATCATTTGTAATAGATTTTAAGA
65 TTTGCTTCTATAATGCATTACAAAATCTTTATC-TTTTTTAAGTTATTTGTAATAGACTTTACGA
* * *
673453 GTGCCTTGGCCATAATATTTTTATGGGGCCAGCCCCTTTTTCTTAATTTCTTTGAAAAGGACTTA
129 GTGCCTTGGCCCT-A-A--TTTAAGGGGCCAGCCCCTTTTTCTTGATTTCTTTGAAAAGGACTTA
*
673518 AGAATACTAACATTTTTTGTTCTTACACCCATCTAAAATTGTAGATCATTTTTGAGATACAAATG
190 AAAATACTAACATTTTTTGTTCTTACACCCATCTAAAATTGTAGATCATTTTTGAGATACAAATG
* *
673583 ATTTAATATTTTAGGGGCCAGCCCTCTAGATCCTTAATGGGGACAGAAATTCGCGTTTTGATAGG
255 ATTGAATATTTTAGGGGCAAGCCCTCTAGATCCTTAATGGGGACAGAAATTCGCGTTTTGATAGG
* * * * * *
673648 TGGAATCGATTTGAATTATAAATTCATACATTTTCTTTACTATAATGTCTAACAAAATATTTCTG
320 TGGAATCGATTTAAATCATAAATTCAAACATTTTCTTTACCATAATGTCTAACAAAATATGTCTA
* * * * *
673713 CTTCTCTAGATATATTGTGTCAAAGA-TTAAGTACTTTGG-CCCCTAGAAGTGC
385 CTTCTCCAGATATATTGCGTCAAA-ATTTAAGTACGTTGGTCCCCTA-AACTCC
* * *
673765 CTTATTACGTAATAAATGGGCGTGACAATGATTTTTTCTAATAGATATTGGTACGATCAACAACT
1 CTAATTACGTAATAAATGGGCGTGACAATGATTTTTTCTGATAGATATTGTTACGATCAACAACT
* * * *
673830 TCGCTTTTATAATGCATTACAAAATCTTTATCTTTTTTAAGTTATTTGCAATAGAGTTTACGAGT
66 TTGCTTCTATAATGCATTACAAAATCTTTATCTTTTTTAAGTTATTTGTAATAGACTTTACGAGT
* *
673895 GCCTTGGCCCCTAATTTAAGGGGCAAGCCCCCTTTTTCTTGATTTCTTTGAAAAGGTCTTAAAAA
131 GCCTTGG-CCCTAATTTAAGGGGCCAG-CCCCTTTTTCTTGATTTCTTTGAAAAGGACTTAAAAA
* *
673960 TACTAACATTTTTTGTTCTTACACCCATCTAAAATTGTTGATCATTTTTTAGATACAAATGATTG
194 TACTAACATTTTTTGTTCTTACACCCATCTAAAATTGTAGATCATTTTTGAGATACAAATGATTG
674025 AATATTTTAGGGGCAAGCCCTCTAGATCCTTAATGGGGACAGAAATTC-CTGTTTTGAT-GCG-G
259 AATATTTTAGGGGCAAGCCCTCTAGATCCTTAATGGGGACAGAAATTCGC-GTTTTGATAG-GTG
* ** *
674087 AGAATCGATTTAAATCATTAATTCAAACATTTTCTCTT-CCATGTTGTCTATCAAAATATGTCTA
322 -GAATCGATTTAAATCATAAATTCAAACATTTTCT-TTACCATAATGTCTAACAAAATATGTCTA
* *
674151 CTTCTCCAGTTATATTGCGTCAAAATTTAAGTACGTTGGTCCCTTAAACTCC
385 CTTCTCCAGATATATTGCGTCAAAATTTAAGTACGTTGGTCCCCTAAACTCC
* ***
674203 CTAATTACGTAATAAATGGGCGTGGCAATGATTTAACCTGATAGATATTGTTACGATCAACAACT
1 CTAATTACGTAATAAATGGGCGTGACAATGATTTTTTCTGATAGATATTGTTACGATCAACAACT
* * * *
674268 TTGCTTCTATAATACATTACAAAATCTTTATCGTTTTCAAGTTATTCGTAATAGACTTTACGAGT
66 TTGCTTCTATAATGCATTACAAAATCTTTATCTTTTTTAAGTTATTTGTAATAGACTTTACGAGT
*
674333 -CTCTTGGTCCCTAATTAAAGGGGCCAGCCCCTTTTTCTTGATTT
131 GC-CTTGG-CCCTAATTTAAGGGGCCAGCCCCTTTTTCTTGATTT
674377 TGTTGGAAAG
Statistics
Matches: 542, Mismatches: 60, Indels: 24
0.87 0.10 0.04
Matches are distributed among these distances:
437 33 0.06
438 376 0.69
439 8 0.01
440 36 0.07
441 85 0.16
442 4 0.01
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.38
Consensus pattern (436 bp):
CTAATTACGTAATAAATGGGCGTGACAATGATTTTTTCTGATAGATATTGTTACGATCAACAACT
TTGCTTCTATAATGCATTACAAAATCTTTATCTTTTTTAAGTTATTTGTAATAGACTTTACGAGT
GCCTTGGCCCTAATTTAAGGGGCCAGCCCCTTTTTCTTGATTTCTTTGAAAAGGACTTAAAAATA
CTAACATTTTTTGTTCTTACACCCATCTAAAATTGTAGATCATTTTTGAGATACAAATGATTGAA
TATTTTAGGGGCAAGCCCTCTAGATCCTTAATGGGGACAGAAATTCGCGTTTTGATAGGTGGAAT
CGATTTAAATCATAAATTCAAACATTTTCTTTACCATAATGTCTAACAAAATATGTCTACTTCTC
CAGATATATTGCGTCAAAATTTAAGTACGTTGGTCCCCTAAACTCC
Found at i:675246 original size:435 final size:433
Alignment explanation
Indices: 674556--675380 Score: 1156
Period size: 435 Copynumber: 1.9 Consensus size: 433
674546 CTGTATAGTA
* * *
674556 TACACCTATCTAGAATTGTTGTTAATTTTTTAGATACAAATGATTGAATATTTTAGGGGCAGCCC
1 TACACCTATCTAGAATTGTTGTCAATTTTTGAGATACAAATGATTGAATATTATAGGGGCAGCCC
* * * * *
674621 TCTAGATCCTAAATGGGGACAGACATTGGTGTTTTGATCAGTGGAATCGATTAGCATTATCAATA
66 TCTAGATCCTAAATAGGGACAGACATTGGTCTTTTGATCAGTAGAATCGATTAGAATCATCAATA
* * *
674686 TAGACATTTGCTCGTCTACATTGCCTAACAAAATATGTCTCCTTCTCTAGATATTTTGCGTCAAA
131 CAGACATTTGCTCGTCTACAATGCCTAACAAAATATGTCTCCTTCTCTAGATA-TTTGCATCAAA
* *
674751 GTTTAAGTACTTTGGCCCCTAAAATCCCTAATTACGTAATAAACGGGTGTGGCAATGATTTTTTC
195 GTTTAAGTACTTCGGCCCCTAAAATCCCTAATTACGTAATAAACGGGCGTGGCAATGATTTTTTC
* * *
674816 TTATAGAGATTGTTACGATCAACAACTTTGCTTCTATAAAGCATTACAAAATCTTTATCGTTTTT
260 TGATAGAGATTGTTACGATCAACAACTTTCCTTCTATAAAGCATTACAAAATCTTTATCATTTTT
*
674881 AAGTTATAT-GTAATAGAGTTTACGAGAGTCTT-GGCCCATTAAAAAAAGGGACCAGCCCCTTTT
325 AAGTTAT-TCGTAATAGAGTTAACGAGAGT-TTCGGCCCATT-AAAAAAGGGACCAGCCCCTTTT
674944 TCTTGAGTTCATTTGAAAGGTCTCACCAATACTGATATTTTTGTTCT
387 TCTTGAGTTCATTTGAAAGGTCTCACCAATACTGATATTTTTGTTCT
*
674991 TACACTTATCTAGAATTGTTGATCAA-TTTTGAGATACAAATGATTGAATATTATAGGGGCCAGC
1 TACACCTATCTAGAATTGTTG-TCAATTTTTGAGATACAAATGATTGAATATTATAGGGG-CAGC
* * * *
675055 CCTCTAGGTCCTTATTAGGGACAGACGA-TGGTCTTTTGATTAGTAGAATCGATTAGAATCATCA
64 CCTCTAGATCCTAAATAGGGACAGAC-ATTGGTCTTTTGATCAGTAGAATCGATTAGAATCATCA
* * * * * *
675119 ATGCAGACATTTTCTCTTCTACAATGCTTAACAAATTATGTCTCTTTCTCTAGATA-TTGCATCA
128 ATACAGACATTTGCTCGTCTACAATGCCTAACAAAATATGTCTCCTTCTCTAGATATTTGCATCA
* * *
675183 AAGTTTAAGTACTTCGGCCCCTAAAAATCCCTAATTACGTCATAAATGGGCGTGGCGATGATTTT
193 AAGTTTAAGTACTTCGGCCCCT-AAAATCCCTAATTACGTAATAAACGGGCGTGGCAATGATTTT
* * * * *
675248 TTCTGATAGATATTGTTAGGATCAACAACTTTCCTTCTATAACGCATTACAAACTTTTTATCATT
257 TTCTGATAGAGATTGTTACGATCAACAACTTTCCTTCTATAAAGCATTACAAAATCTTTATCATT
** * * * * *
675313 TTTCTGTTATTCGTTATAGAGTTAACGAGTGTTTCGGCCCCTTAAAAAAGGGCCCAGTCCCTTTT
322 TTTAAGTTATTCGTAATAGAGTTAACGAGAGTTTCGGCCCATTAAAAAAGGGACCAGCCCCTTTT
675378 TCT
387 TCT
675381 ATATTTTGTT
Statistics
Matches: 341, Mismatches: 43, Indels: 13
0.86 0.11 0.03
Matches are distributed among these distances:
434 54 0.16
435 178 0.52
436 108 0.32
437 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (433 bp):
TACACCTATCTAGAATTGTTGTCAATTTTTGAGATACAAATGATTGAATATTATAGGGGCAGCCC
TCTAGATCCTAAATAGGGACAGACATTGGTCTTTTGATCAGTAGAATCGATTAGAATCATCAATA
CAGACATTTGCTCGTCTACAATGCCTAACAAAATATGTCTCCTTCTCTAGATATTTGCATCAAAG
TTTAAGTACTTCGGCCCCTAAAATCCCTAATTACGTAATAAACGGGCGTGGCAATGATTTTTTCT
GATAGAGATTGTTACGATCAACAACTTTCCTTCTATAAAGCATTACAAAATCTTTATCATTTTTA
AGTTATTCGTAATAGAGTTAACGAGAGTTTCGGCCCATTAAAAAAGGGACCAGCCCCTTTTTCTT
GAGTTCATTTGAAAGGTCTCACCAATACTGATATTTTTGTTCT
Found at i:691735 original size:10 final size:9
Alignment explanation
Indices: 691720--691762 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 9
691710 ATCCTAACTG
691720 TTTGTTTTGT
1 TTTGTTTT-T
691730 TTTGTTTTT
1 TTTGTTTTT
691739 TTTCGTTTTT
1 TTT-GTTTTT
691749 TGTTGGTTTTT
1 T-TT-GTTTTT
691760 TTT
1 TTT
691763 TGCCAGAAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 4 0.13
10 17 0.57
11 9 0.30
ACGTcount: A:0.00, C:0.02, G:0.16, T:0.81
Consensus pattern (9 bp):
TTTGTTTTT
Found at i:693790 original size:20 final size:20
Alignment explanation
Indices: 693767--693824 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
693757 GTTATGTCTT
*
693767 CTTAACAGAAATTATGCCAA
1 CTTATCAGAAATTATGCCAA
* *
693787 CTTATCAGAATATTTTGTCAA
1 CTTATCAGAA-ATTATGCCAA
*
693808 CTTGTCAGATAATTATG
1 CTTATCAGA-AATTATG
693825 ACGACTTACT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 9 0.29
21 21 0.68
22 1 0.03
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (20 bp):
CTTATCAGAAATTATGCCAA
Found at i:694056 original size:27 final size:27
Alignment explanation
Indices: 694026--694188 Score: 120
Period size: 27 Copynumber: 6.5 Consensus size: 27
694016 ATGAAGATCA
* *
694026 GACAAGTCGACATTACTTATCTGAAAT
1 GACAAGTCGACATTAATAATCTGAAAT
*
694053 GACAAGTCGACATTAATAATCTGACAT
1 GACAAGTCGACATTAATAATCTGAAAT
*
694080 GACAAGTCGACATGAA-AATC-----T
1 GACAAGTCGACATTAATAATCTGAAAT
*
694101 GACAAGTCGACATTAATTATCT-AACAT
1 GACAAGTCGACATTAATAATCTGAA-AT
* * *
694128 GATAAGTCGACATGAA-GATC-----T
1 GACAAGTCGACATTAATAATCTGAAAT
*
694149 GACAAGTCGACATTAACT-ATCTGACAT
1 GACAAGTCGACATTAA-TAATCTGAAAT
*
694176 GAAAAGTCGACAT
1 GACAAGTCGACAT
694189 GAAGTCTGAC
Statistics
Matches: 111, Mismatches: 12, Indels: 26
0.74 0.08 0.17
Matches are distributed among these distances:
21 31 0.28
22 6 0.05
26 7 0.06
27 67 0.60
ACGTcount: A:0.40, C:0.18, G:0.17, T:0.25
Consensus pattern (27 bp):
GACAAGTCGACATTAATAATCTGAAAT
Found at i:694076 original size:75 final size:75
Alignment explanation
Indices: 693986--694140 Score: 249
Period size: 75 Copynumber: 2.1 Consensus size: 75
693976 CATATAGGTT
* * *
693986 GACATTAATTATCTGACATGACAAGTCGACATGAAGATCAGACAAGTCGACATTACTTATCTGAA
1 GACATTAATAATCTGACATGACAAGTCGACATGAAAATCAGACAAGTCGACATTAATTATCT-AA
694051 -ATGACAAGTC
65 CATGACAAGTC
*
694061 GACATTAATAATCTGACATGACAAGTCGACATGAAAATCTGACAAGTCGACATTAATTATCTAAC
1 GACATTAATAATCTGACATGACAAGTCGACATGAAAATCAGACAAGTCGACATTAATTATCTAAC
*
694126 ATGATAAGTC
66 ATGACAAGTC
694136 GACAT
1 GACAT
694141 GAAGATCTGA
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
74 2 0.03
75 72 0.97
ACGTcount: A:0.40, C:0.18, G:0.16, T:0.26
Consensus pattern (75 bp):
GACATTAATAATCTGACATGACAAGTCGACATGAAAATCAGACAAGTCGACATTAATTATCTAAC
ATGACAAGTC
Found at i:694105 original size:21 final size:21
Alignment explanation
Indices: 694079--694302 Score: 76
Period size: 21 Copynumber: 9.7 Consensus size: 21
694069 TAATCTGACA
694079 TGACAAGTCGACATGAAAATC
1 TGACAAGTCGACATGAAAATC
* *
694100 TGACAAGTCGACATTAATTATCTAAC
1 TGACAAGTCGACATGAA--A---ATC
* *
694126 ATGATAAGTCGACATGAAGATC
1 -TGACAAGTCGACATGAAAATC
* *
694148 TGACAAGTCGACATTAACTATC
1 TGACAAGTCGACATGAA-AATC
*
694170 TGACATGAAAAGTCGACATG-AAGTC
1 TGAC-----AAGTCGACATGAAAATC
* *
694195 TGACAAGTTGACAT-AATTATCTAAC
1 TGACAAGTCGACATGAA--A---ATC
*
694220 ATGACAAGTCGACATGAAGATC
1 -TGACAAGTCGACATGAAAATC
* **
694242 TGACAAG-CTGACATTATTATCTGAC
1 TGACAAGTC-GACATGA--AAAT--C
*
694267 ATGACAAGTCGACATGAAGATC
1 -TGACAAGTCGACATGAAAATC
*
694289 TGAAAAGTCGACAT
1 TGACAAGTCGACAT
694303 TAATTACCTG
Statistics
Matches: 151, Mismatches: 25, Indels: 54
0.66 0.11 0.23
Matches are distributed among these distances:
20 11 0.07
21 57 0.38
22 13 0.09
23 3 0.02
24 2 0.01
25 8 0.05
26 29 0.19
27 28 0.19
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (21 bp):
TGACAAGTCGACATGAAAATC
Found at i:694244 original size:47 final size:48
Alignment explanation
Indices: 694052--694316 Score: 403
Period size: 48 Copynumber: 5.6 Consensus size: 48
694042 TTATCTGAAA
* *
694052 TGACAAGTCGACATTAATAATCTGACATGACAAGTCGACATGAAAATC
1 TGACAAGTCGACATTAATTATCTGACATGACAAGTCGACATGAAGATC
* *
694100 TGACAAGTCGACATTAATTATCTAACATGATAAGTCGACATGAAGATC
1 TGACAAGTCGACATTAATTATCTGACATGACAAGTCGACATGAAGATC
* *
694148 TGACAAGTCGACATTAACTATCTGACATGAAAAGTCGACATGAAG-TC
1 TGACAAGTCGACATTAATTATCTGACATGACAAGTCGACATGAAGATC
* *
694195 TGACAAGTTGACA-TAATTATCTAACATGACAAGTCGACATGAAGATC
1 TGACAAGTCGACATTAATTATCTGACATGACAAGTCGACATGAAGATC
694242 TGACAAG-CTGACATT-ATTATCTGACATGACAAGTCGACATGAAGATC
1 TGACAAGTC-GACATTAATTATCTGACATGACAAGTCGACATGAAGATC
* *
694289 TGAAAAGTCGACATTAATTACCTGACAT
1 TGACAAGTCGACATTAATTATCTGACAT
694317 CAGTGCAAGT
Statistics
Matches: 197, Mismatches: 15, Indels: 10
0.89 0.07 0.05
Matches are distributed among these distances:
46 28 0.14
47 70 0.36
48 99 0.50
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.25
Consensus pattern (48 bp):
TGACAAGTCGACATTAATTATCTGACATGACAAGTCGACATGAAGATC
Found at i:694255 original size:94 final size:94
Alignment explanation
Indices: 694052--694308 Score: 401
Period size: 94 Copynumber: 2.7 Consensus size: 94
694042 TTATCTGAAA
*
694052 TGACAAGTCGACATTAATAATCTGACATGACAAGTCGACATGAAAATCTGACAAGTCGACATTAA
1 TGACAAGTCGACATTAAT-ATCTGACATGACAAGTCGACATG-AAGTCTGACAAGTCGACATTAA
*
694117 TTATCTAACATGATAAGTCGACATGAAGATC
64 TTATCTAACATGACAAGTCGACATGAAGATC
* *
694148 TGACAAGTCGACATTAACTATCTGACATGAAAAGTCGACATGAAGTCTGACAAGTTGACA-TAAT
1 TGACAAGTCGACATTAA-TATCTGACATGACAAGTCGACATGAAGTCTGACAAGTCGACATTAAT
694212 TATCTAACATGACAAGTCGACATGAAGATC
65 TATCTAACATGACAAGTCGACATGAAGATC
* *
694242 TGACAAG-CTGACATTATTATCTGACATGACAAGTCGACATGAAGATCTGAAAAGTCGACATTAA
1 TGACAAGTC-GACATTAATATCTGACATGACAAGTCGACATGAAG-TCTGACAAGTCGACATTAA
694306 TTA
64 TTA
694309 CCTGACATCA
Statistics
Matches: 149, Mismatches: 8, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
93 27 0.18
94 60 0.40
95 22 0.15
96 39 0.26
97 1 0.01
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.25
Consensus pattern (94 bp):
TGACAAGTCGACATTAATATCTGACATGACAAGTCGACATGAAGTCTGACAAGTCGACATTAATT
ATCTAACATGACAAGTCGACATGAAGATC
Found at i:697327 original size:42 final size:42
Alignment explanation
Indices: 697268--697351 Score: 127
Period size: 42 Copynumber: 2.0 Consensus size: 42
697258 TATGAAGTAT
*
697268 AATTGCGTTGAATCGCAATAAGTT-TTGCGTTTAAACGCAAAA
1 AATTGCGTTGAAACGCAAT-AGTTATTGCGTTTAAACGCAAAA
697310 AATTGCGATT-AAACGCAATAGTTATTGCGTTTAAACGCAAAA
1 AATTGCG-TTGAAACGCAATAGTTATTGCGTTTAAACGCAAAA
697352 GAAATTATTT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
41 4 0.10
42 33 0.85
43 2 0.05
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (42 bp):
AATTGCGTTGAAACGCAATAGTTATTGCGTTTAAACGCAAAA
Found at i:697343 original size:22 final size:22
Alignment explanation
Indices: 697269--697349 Score: 87
Period size: 22 Copynumber: 3.8 Consensus size: 22
697259 ATGAAGTATA
* *
697269 ATTGCGTTGAATCGCAATAAGTT
1 ATTGCGTTTAAACGCAAT-AGTT
**
697292 -TTGCGTTTAAACGCAA-A-AA
1 ATTGCGTTTAAACGCAATAGTT
*
697311 ATTGCGATTAAACGCAATAGTT
1 ATTGCGTTTAAACGCAATAGTT
697333 ATTGCGTTTAAACGCAA
1 ATTGCGTTTAAACGCAA
697350 AAGAAATTAT
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
20 16 0.34
21 1 0.02
22 30 0.64
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.31
Consensus pattern (22 bp):
ATTGCGTTTAAACGCAATAGTT
Found at i:697400 original size:20 final size:20
Alignment explanation
Indices: 697375--697415 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
697365 CTGCTAAGCT
*
697375 GGCCTCAATGAGCTTCCGTA
1 GGCCTCAATAAGCTTCCGTA
697395 GGCCTCAATAAGCTTCCGTA
1 GGCCTCAATAAGCTTCCGTA
697415 G
1 G
697416 ATATGTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.24
Consensus pattern (20 bp):
GGCCTCAATAAGCTTCCGTA
Found at i:698098 original size:42 final size:42
Alignment explanation
Indices: 698048--698374 Score: 228
Period size: 42 Copynumber: 7.5 Consensus size: 42
698038 CGGCACTGAT
*
698048 GAAGCTCTGTGTGACCCTGAGGTCGGCATTGAGGGTAATGAG
1 GAAGCTCTGAGTGACCCTGAGGTCGGCATTGAGGGTAATGAG
* * *
698090 GAAGCTCTGATTGACCCTTAGGTCGGCATTGAGGGTACTGAG
1 GAAGCTCTGAGTGACCCTGAGGTCGGCATTGAGGGTAATGAG
* * *
698132 GAAGCTCTGAG-GAATCTCTGAAAGACACTGATCGGCACTGAGGG-AGCTCTGAG
1 GAAGCTCTGAGTG-A-CCCTG--AG-----G-TCGGCATTGAGGGTA---ATGAG
* *
698185 GAAGCTTTGAGCGACCCTGAGGTCGGCATTGAGGGTAATGAG
1 GAAGCTCTGAGTGACCCTGAGGTCGGCATTGAGGGTAATGAG
** * * *
698227 GAAGCTCTGAGTGACCCTGAGGTCTTCATTGAGGATAACGGG
1 GAAGCTCTGAGTGACCCTGAGGTCGGCATTGAGGGTAATGAG
* * * * *
698269 GAAGCCCTAAATGACCTTGAGGTCGGCATTGAGAGTACTGATGAG
1 GAAGCTCTGAGTGACCCTGAGGTCGGCATTGAGGGTA---ATGAG
* * * * * * *
698314 GAAGCTGTGAGAGACTCTGAAGTTGACATTGAGGGT-ACGTAG
1 GAAGCTCTGAGTGACCCTGAGGTCGGCATTGAGGGTAATG-AG
* *
698356 GAAGCCCTGAGAGACCCTG
1 GAAGCTCTGAGTGACCCTG
698375 CTCTGTTCAA
Statistics
Matches: 222, Mismatches: 44, Indels: 38
0.73 0.14 0.12
Matches are distributed among these distances:
41 3 0.01
42 135 0.61
43 3 0.01
44 12 0.05
45 32 0.14
50 4 0.02
51 12 0.05
52 4 0.02
53 16 0.07
54 1 0.00
ACGTcount: A:0.25, C:0.18, G:0.34, T:0.22
Consensus pattern (42 bp):
GAAGCTCTGAGTGACCCTGAGGTCGGCATTGAGGGTAATGAG
Found at i:698143 original size:53 final size:53
Alignment explanation
Indices: 698086--698237 Score: 128
Period size: 53 Copynumber: 3.1 Consensus size: 53
698076 TTGAGGGTAA
**
698086 TGAGGAAGCTCTGATTGACCCTTAGGTCGGCATTGAGGGTACTGAGGAAGCTC
1 TGAGGAAGCTCTGAAAGACCCTTAGGTCGGCATTGAGGGTACTGAGGAAGCTC
* * * *
698139 TGAGGAATCTCTGAAAGACAC-T-GATCGGC---------ACTGAGGGAGCTC
1 TGAGGAAGCTCTGAAAGACCCTTAGGTCGGCATTGAGGGTACTGAGGAAGCTC
* ** * *
698181 TGAGGAAGCTTTGAGCGACCCTGAGGTCGGCATTGAGGGTAATGAGGAAGCTC
1 TGAGGAAGCTCTGAAAGACCCTTAGGTCGGCATTGAGGGTACTGAGGAAGCTC
698234 TGAG
1 TGAG
698238 TGACCCTGAG
Statistics
Matches: 73, Mismatches: 15, Indels: 22
0.66 0.14 0.20
Matches are distributed among these distances:
42 28 0.38
44 6 0.08
51 6 0.08
52 1 0.01
53 32 0.44
ACGTcount: A:0.25, C:0.18, G:0.35, T:0.22
Consensus pattern (53 bp):
TGAGGAAGCTCTGAAAGACCCTTAGGTCGGCATTGAGGGTACTGAGGAAGCTC
Found at i:698359 original size:87 final size:84
Alignment explanation
Indices: 698197--698363 Score: 194
Period size: 87 Copynumber: 2.0 Consensus size: 84
698187 AGCTTTGAGC
* * * *
698197 GACCCTGAGGTCGGCATTGAGGGTAATGAGGAAGCTCTGAGTGACCCTGAGGTCTTCATTGAGGA
1 GACCCTGAGGTCGGCATTGAGAGTAATGAGGAAGCTCTGAGAGACCCTGAAGTCTACATTGAGGA
*
698262 TAACGGGGAAGCCCTAAAT
66 TAACGAGGAAGCCCTAAAT
* * *
698281 GACCTTGAGGTCGGCATTGAGAGTACTGATGAGGAAGCTGTGAGAGACTCTGAAGT-TGACATTG
1 GACCCTGAGGTCGGCATTGAGAGTA---ATGAGGAAGCTCTGAGAGACCCTGAAGTCT-ACATTG
*
698345 AGGGT-ACGTAGGAAGCCCT
62 AGGATAACG-AGGAAGCCCT
698364 GAGAGACCCT
Statistics
Matches: 69, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
84 23 0.33
86 4 0.06
87 42 0.61
ACGTcount: A:0.26, C:0.17, G:0.34, T:0.22
Consensus pattern (84 bp):
GACCCTGAGGTCGGCATTGAGAGTAATGAGGAAGCTCTGAGAGACCCTGAAGTCTACATTGAGGA
TAACGAGGAAGCCCTAAAT
Found at i:699919 original size:12 final size:12
Alignment explanation
Indices: 699895--699927 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
699885 ATCACCTGTT
699895 GTCCGTC-GTCC
1 GTCCGTCTGTCC
*
699906 GTCTGTCTGTCC
1 GTCCGTCTGTCC
699918 GTCCGTCTGT
1 GTCCGTCTGT
699928 AAACTTTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 6 0.32
12 13 0.68
ACGTcount: A:0.00, C:0.36, G:0.27, T:0.36
Consensus pattern (12 bp):
GTCCGTCTGTCC
Found at i:705318 original size:1 final size:1
Alignment explanation
Indices: 705312--705336 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
705302 GTGTGGAAAC
705312 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
705337 GTATAGGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:706861 original size:39 final size:39
Alignment explanation
Indices: 706807--706884 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
706797 AATGAATTTA
706807 ATCACAATTGAATTGAATACATGTATGACCCGATCTTTC
1 ATCACAATTGAATTGAATACATGTATGACCCGATCTTTC
706846 ATCACAATTGAATTGAATACATGTATGACCCGATCTTTC
1 ATCACAATTGAATTGAATACATGTATGACCCGATCTTTC
706885 TTAACGTGTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (39 bp):
ATCACAATTGAATTGAATACATGTATGACCCGATCTTTC
Found at i:709493 original size:43 final size:43
Alignment explanation
Indices: 709433--709799 Score: 373
Period size: 43 Copynumber: 8.6 Consensus size: 43
709423 AAAAATATTT
* *
709433 TTATCTCGTAATTACGAGAAAAGATCTCGTTATTACGAGTTAA
1 TTATCTCGTTATAACGAGAAAAGATCTCGTTATTACGAGTTAA
*
709476 TTTTCTCGTTATAACGAGAAAAGATCTCGTTATTACGAGTTAA
1 TTATCTCGTTATAACGAGAAAAGATCTCGTTATTACGAGTTAA
* * * * *
709519 TTATCTCGTAATTACAAGAAAAAATCTCGTTATTACGAG-AAA
1 TTATCTCGTTATAACGAGAAAAGATCTCGTTATTACGAGTTAA
** * ** * *
709561 AGATCTCGTTATAACGAGTTAATTATCTCGTTATAACGAG-AAA
1 TTATCTCGTTATAACGAG-AAAAGATCTCGTTATTACGAGTTAA
** * * ** * *
709604 AGATCTCGTTATTACGAGTTAATTATCTCGTAATTACGAG-AAA
1 TTATCTCGTTATAACGAG-AAAAGATCTCGTTATTACGAGTTAA
** * * **
709647 AGATCTCGTTATTACGAGAAAATATCTAATTATTACGAGTTAA
1 TTATCTCGTTATAACGAGAAAAGATCTCGTTATTACGAGTTAA
709690 TTATCTCGTTATAACGAGAAAAGATCTCGTTATTACGAGTTAA
1 TTATCTCGTTATAACGAGAAAAGATCTCGTTATTACGAGTTAA
* *
709733 TTATCTCGTTATAACGAGAAAAGATCTCGTAATTACGAG-AAA
1 TTATCTCGTTATAACGAGAAAAGATCTCGTTATTACGAGTTAA
** * *
709775 AGATCTCGTTATTACGAAAAAAGAT
1 TTATCTCGTTATAACGAGAAAAGAT
709800 TTATATAAAT
Statistics
Matches: 283, Mismatches: 39, Indels: 5
0.87 0.12 0.02
Matches are distributed among these distances:
42 54 0.19
43 229 0.81
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.33
Consensus pattern (43 bp):
TTATCTCGTTATAACGAGAAAAGATCTCGTTATTACGAGTTAA
Found at i:709547 original size:64 final size:63
Alignment explanation
Indices: 709435--709796 Score: 382
Period size: 64 Copynumber: 5.7 Consensus size: 63
709425 AAATATTTTT
* * * * *
709435 ATCTCGTAATTACGAGAAAAGATCTCGTTATTACGAGTTAATTTTCTCGTTATAACGAGAAAAG
1 ATCTCGTTATTACGAGAAAAGATCTCGTTATTACGAG-AAAATATCTCGTTATTACGAGAAAAG
* ** * * *
709499 ATCTCGTTATTACGAGTTAATTATCTCGTAATTACAAGAAAAAATCTCGTTATTACGAGAAAAG
1 ATCTCGTTATTACGAG-AAAAGATCTCGTTATTACGAGAAAATATCTCGTTATTACGAGAAAAG
* * ** * * * **
709563 ATCTCGTTATAACGAGTTAATTATCTCGTTATAACGAGAAAAGATCTCGTTATTACGAGTTAATT
1 ATCTCGTTATTACGAG-AAAAGATCTCGTTATTACGAGAAAATATCTCGTTATTACGAG-AAAAG
* ** * **
709628 ATCTCGTAATTACGAGAAAAGATCTCGTTATTACGAGAAAATATCTAATTATTACGAGTTAATT
1 ATCTCGTTATTACGAGAAAAGATCTCGTTATTACGAGAAAATATCTCGTTATTACGAG-AAAAG
* * * *
709692 ATCTCGTTATAACGAGAAAAGATCTCGTTATTACGAGTTAATTATCTCGTTATAACGAGAAAAG
1 ATCTCGTTATTACGAGAAAAGATCTCGTTATTACGAG-AAAATATCTCGTTATTACGAGAAAAG
* *
709756 ATCTCGTAATTACGAGAAAAGATCTCGTTATTACGAAAAAA
1 ATCTCGTTATTACGAGAAAAGATCTCGTTATTACGAGAAAA
709797 GATTTATATA
Statistics
Matches: 252, Mismatches: 43, Indels: 7
0.83 0.14 0.02
Matches are distributed among these distances:
63 2 0.01
64 202 0.80
65 48 0.19
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Consensus pattern (63 bp):
ATCTCGTTATTACGAGAAAAGATCTCGTTATTACGAGAAAATATCTCGTTATTACGAGAAAAG
Found at i:709559 original size:107 final size:107
Alignment explanation
Indices: 709435--709791 Score: 615
Period size: 107 Copynumber: 3.3 Consensus size: 107
709425 AAATATTTTT
*
709435 ATCTCGTAATTACGAGAAAAGATCTCGTTATTACGAGTTAATTTTCTCGTTATAACGAGAAAAGA
1 ATCTCGTAATTACGAGAAAAGATCTCGTTATTACGAGTTAATTATCTCGTTATAACGAGAAAAGA
* *
709500 TCTCGTTATTACGAGTTAATTATCTCGTAATTACAAGAAAAA
66 TCTCGTTATTACGAGTTAATTATCTCGTAATTACGAGAAAAG
* *
709542 ATCTCGTTATTACGAGAAAAGATCTCGTTATAACGAGTTAATTATCTCGTTATAACGAGAAAAGA
1 ATCTCGTAATTACGAGAAAAGATCTCGTTATTACGAGTTAATTATCTCGTTATAACGAGAAAAGA
709607 TCTCGTTATTACGAGTTAATTATCTCGTAATTACGAGAAAAG
66 TCTCGTTATTACGAGTTAATTATCTCGTAATTACGAGAAAAG
* * **
709649 ATCTCGTTATTACGAGAAAATATCTAATTATTACGAGTTAATTATCTCGTTATAACGAGAAAAGA
1 ATCTCGTAATTACGAGAAAAGATCTCGTTATTACGAGTTAATTATCTCGTTATAACGAGAAAAGA
* *
709714 TCTCGTTATTACGAGTTAATTATCTCGTTATAACGAGAAAAG
66 TCTCGTTATTACGAGTTAATTATCTCGTAATTACGAGAAAAG
709756 ATCTCGTAATTACGAGAAAAGATCTCGTTATTACGA
1 ATCTCGTAATTACGAGAAAAGATCTCGTTATTACGA
709792 AAAAAGATTT
Statistics
Matches: 235, Mismatches: 15, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
107 235 1.00
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (107 bp):
ATCTCGTAATTACGAGAAAAGATCTCGTTATTACGAGTTAATTATCTCGTTATAACGAGAAAAGA
TCTCGTTATTACGAGTTAATTATCTCGTAATTACGAGAAAAG
Found at i:710457 original size:21 final size:21
Alignment explanation
Indices: 710427--710514 Score: 70
Period size: 21 Copynumber: 4.1 Consensus size: 21
710417 CATTTTGAAA
*
710427 AGATCTTTTCTCATAA-TATCG
1 AGATCGTTTCTCATAATTA-CG
*
710448 AGATCGTTTCTCGTAATTACG
1 AGATCGTTTCTCATAATTACG
** * *
710469 AGATAATTAACTCGTAATTACG
1 AGATCGTT-TCTCATAATTACG
* **
710491 AGATCTTTTCTTGTAATTACG
1 AGATCGTTTCTCATAATTACG
710512 AGA
1 AGA
710515 AAATAAACTC
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
21 36 0.64
22 20 0.36
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.39
Consensus pattern (21 bp):
AGATCGTTTCTCATAATTACG
Found at i:710507 original size:43 final size:43
Alignment explanation
Indices: 710440--710732 Score: 442
Period size: 43 Copynumber: 6.8 Consensus size: 43
710430 TCTTTTCTCA
* *
710440 TAATATCGAGATCGTTTCTCGTAATTACGAGATAATTAACTCG
1 TAATAACGAGATCTTTTCTCGTAATTACGAGATAATTAACTCG
* * * *
710483 TAATTACGAGATCTTTTCTTGTAATTACGAGAAAATAAACTCG
1 TAATAACGAGATCTTTTCTCGTAATTACGAGATAATTAACTCG
* * *
710526 TAATAACGAGATCTTTTCTCGTTATAACGAGATAATTAAGTCG
1 TAATAACGAGATCTTTTCTCGTAATTACGAGATAATTAACTCG
* *
710569 TAATAACGAGAGCTTTTCTCGTAATTACGAGAAAATTAACTCG
1 TAATAACGAGATCTTTTCTCGTAATTACGAGATAATTAACTCG
* * *
710612 TAATAACGAGATCTTTTCTCGTTATAACGAGATTATTAACTCG
1 TAATAACGAGATCTTTTCTCGTAATTACGAGATAATTAACTCG
* *
710655 TAATAACGAGTTCTTTTCTCGTAATTACGAGAAAATTAACTCG
1 TAATAACGAGATCTTTTCTCGTAATTACGAGATAATTAACTCG
710698 TAATAACGAGATCTTTTCTCGTAATTACGAGATAA
1 TAATAACGAGATCTTTTCTCGTAATTACGAGATAA
710733 AAATATTTTT
Statistics
Matches: 220, Mismatches: 30, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 220 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Consensus pattern (43 bp):
TAATAACGAGATCTTTTCTCGTAATTACGAGATAATTAACTCG
Found at i:713154 original size:2 final size:2
Alignment explanation
Indices: 713149--713200 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
713139 TTGCTGCGCG
713149 CT CT CT CT CT CT 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 CT CT CT CT CT CT
713191 CT CT CT CT CT
1 CT CT CT CT CT
713201 TACAATGTAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:714566 original size:66 final size:65
Alignment explanation
Indices: 714485--714740 Score: 364
Period size: 66 Copynumber: 4.0 Consensus size: 65
714475 TTAGATACCT
*
714485 TATGTTCGCATTGAAACACAATGTAGGGCCAATAACACTTCCTTGCACTATACCAAAAAACTTAT
1 TATGTTCGCATTGAAACACAATGCAGGGCCAATAACACTTCCTTGCACTATACC-AAAAACTTAT
714550 A
65 A
* *
714551 TATGTTCGCAATGAAACACAATGC-GTGGCCAATAACACTTCCTTGCACTACACCAAAAAC-T-T
1 TATGTTCGCATTGAAACACAATGCAG-GGCCAATAACACTTCCTTGCACTATACCAAAAACTTAT
714613 A
65 A
* *
714614 TA--TTCGCATTGAAACACATTGCAGGGCCAATAAC-CATTCCTTGCACTATACCAAGAACTTAT
1 TATGTTCGCATTGAAACACAATGCAGGGCCAATAACAC-TTCCTTGCACTATACCAAAAACTTAT
714676 A
65 A
*
714677 TATGCTT-GCATTGAAACACATTGCAGGGCCAATAACACTTCCTTGCACTATACCAAAAAACTTA
1 TATG-TTCGCATTGAAACACAATGCAGGGCCAATAACACTTCCTTGCACTATACC-AAAAACTTA
714741 GGCCTAACAA
Statistics
Matches: 172, Mismatches: 8, Indels: 20
0.86 0.04 0.10
Matches are distributed among these distances:
60 1 0.01
61 48 0.28
62 2 0.01
63 8 0.05
64 1 0.01
65 52 0.30
66 60 0.35
ACGTcount: A:0.36, C:0.25, G:0.12, T:0.26
Consensus pattern (65 bp):
TATGTTCGCATTGAAACACAATGCAGGGCCAATAACACTTCCTTGCACTATACCAAAAACTTATA
Found at i:714709 original size:65 final size:65
Alignment explanation
Indices: 714492--714740 Score: 350
Period size: 65 Copynumber: 3.9 Consensus size: 65
714482 CCTTATGTTC
*
714492 GCATTGAAACACAATGTAGGGCCAATAACACTTCCTTGCACTATACCAAAAAACTTATATATG-T
1 GCATTGAAACACAATGCAGGGCCAATAACACTTCCTTGCACTATACC-AAAAACTTATATATGCT
714556 T
65 T
* *
714557 CGCAATGAAACACAATGC-GTGGCCAATAACACTTCCTTGCACTACACCAAAAACTTATAT-T-C
1 -GCATTGAAACACAATGCAG-GGCCAATAACACTTCCTTGCACTATACCAAAAACTTATATATGC
714619 --
64 TT
* *
714619 GCATTGAAACACATTGCAGGGCCAATAAC-CATTCCTTGCACTATACCAAGAACTTATATATGCT
1 GCATTGAAACACAATGCAGGGCCAATAACAC-TTCCTTGCACTATACCAAAAACTTATATATGCT
714683 T
65 T
*
714684 GCATTGAAACACATTGCAGGGCCAATAACACTTCCTTGCACTATACCAAAAAACTTA
1 GCATTGAAACACAATGCAGGGCCAATAACACTTCCTTGCACTATACC-AAAAACTTA
714741 GGCCTAACAA
Statistics
Matches: 165, Mismatches: 8, Indels: 20
0.85 0.04 0.10
Matches are distributed among these distances:
60 1 0.01
61 51 0.31
62 2 0.01
63 1 0.01
64 1 0.01
65 58 0.35
66 51 0.31
ACGTcount: A:0.37, C:0.25, G:0.12, T:0.25
Consensus pattern (65 bp):
GCATTGAAACACAATGCAGGGCCAATAACACTTCCTTGCACTATACCAAAAACTTATATATGCTT
Found at i:714736 original size:127 final size:127
Alignment explanation
Indices: 714483--714740 Score: 389
Period size: 127 Copynumber: 2.0 Consensus size: 127
714473 ATTTAGATAC
* *
714483 CTTATGTTCGCATTGAAACACAATGTAGGGCCAATAACACTTCCTTGCACTATACCAAAAAACTT
1 CTTATATTCGCATTGAAACACAATGCAGGGCCAATAACACTTCCTTGCACTATACCAAAAAACTT
714548 ATATATGTTCGCAATGAAACACAATGCGTGGCCAATAACACTTCCTTGCACTACACCAAAAA
66 ATATATGTTCGCAATGAAACACAATGCGTGGCCAATAACACTTCCTTGCACTACACCAAAAA
* *
714610 CTTATATTCGCATTGAAACACATTGCAGGGCCAATAAC-CATTCCTTGCACTATACC-AAGAACT
1 CTTATATTCGCATTGAAACACAATGCAGGGCCAATAACAC-TTCCTTGCACTATACCAAAAAACT
* * *
714673 TATATATGCTT-GCATTGAAACACATTGCAG-GGCCAATAACACTTCCTTGCACTATACCAAAAA
65 TATATATG-TTCGCAATGAAACACAATGC-GTGGCCAATAACACTTCCTTGCACTACACC-AAAA
714736 A
127 A
714737 CTTA
1 CTTA
714741 GGCCTAACAA
Statistics
Matches: 120, Mismatches: 7, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
126 57 0.47
127 63 0.52
ACGTcount: A:0.36, C:0.25, G:0.12, T:0.26
Consensus pattern (127 bp):
CTTATATTCGCATTGAAACACAATGCAGGGCCAATAACACTTCCTTGCACTATACCAAAAAACTT
ATATATGTTCGCAATGAAACACAATGCGTGGCCAATAACACTTCCTTGCACTACACCAAAAA
Found at i:715041 original size:17 final size:17
Alignment explanation
Indices: 715019--715052 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
715009 ACCATAACAC
715019 TGATGACATATAAATAA
1 TGATGACATATAAATAA
*
715036 TGATGATATATAAATAA
1 TGATGACATATAAATAA
715053 AATTTAGAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.12, T:0.32
Consensus pattern (17 bp):
TGATGACATATAAATAA
Found at i:715130 original size:29 final size:28
Alignment explanation
Indices: 715082--715139 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 28
715072 ATGTTTTAAT
715082 CGGATAAAAACGAAATTTTAACAAAAAAA
1 CGGATAAAAACGAAATTTT-ACAAAAAAA
* *
715111 CGGATAAAAGCGGAAA-TTTACGAAAAAA
1 CGGATAAAAAC-GAAATTTTACAAAAAAA
715139 C
1 C
715140 TCGGAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 9 0.35
29 13 0.50
30 4 0.15
ACGTcount: A:0.57, C:0.12, G:0.16, T:0.16
Consensus pattern (28 bp):
CGGATAAAAACGAAATTTTACAAAAAAA
Found at i:733906 original size:188 final size:187
Alignment explanation
Indices: 733588--733963 Score: 743
Period size: 188 Copynumber: 2.0 Consensus size: 187
733578 CAAACACTTT
733588 TTTGACTAAGATCATTTACAAGCATAAAAAAGATTTTCATGTTTGCCGCACGACAAAACAAGAAT
1 TTTGACTAAGATCATTTACAAGCATAAAAAAGATTTTCATGTTTGCCGCACGACAAAACAAGAAT
733653 TTTCTCGAAAAGAAAGATGTCAGGTGATAATGGTCCGAAGTATACGTTCCAGTTTTTGGATGGAA
66 TTTCTCGAAAAGAAAGATGTCAGGTGATAATGGTCCGAAGTATACGTTCCAGTTTTTGGATGGAA
733718 GAAAATTTCCCTCTTTCGATACGAAAGAGAACAAAGAATTCTTCTTGAAATGGTTTG
131 GAAAATTTCCCTCTTTCGATACGAAAGAGAACAAAGAATTCTTCTTGAAATGGTTTG
733775 TNTTGACTAAGATCATTTACAAGCATAAAAAAGATTTTCATGTTTGCCGCACGACAAAACAAGAA
1 T-TTGACTAAGATCATTTACAAGCATAAAAAAGATTTTCATGTTTGCCGCACGACAAAACAAGAA
733840 TTTTCTCGAAAAGAAAGATGTCAGGTGATAATGGTCCGAAGTATACGTTCCAGTTTTTGGATGGA
65 TTTTCTCGAAAAGAAAGATGTCAGGTGATAATGGTCCGAAGTATACGTTCCAGTTTTTGGATGGA
733905 AGAAAATTTCCCTCTTTCGATACGAAAGAGAACAAAGAATTCTTCTTGAAATGGTTTG
130 AGAAAATTTCCCTCTTTCGATACGAAAGAGAACAAAGAATTCTTCTTGAAATGGTTTG
733963 T
1 T
733964 ACAGCATTGT
Statistics
Matches: 188, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
187 1 0.01
188 187 0.99
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (187 bp):
TTTGACTAAGATCATTTACAAGCATAAAAAAGATTTTCATGTTTGCCGCACGACAAAACAAGAAT
TTTCTCGAAAAGAAAGATGTCAGGTGATAATGGTCCGAAGTATACGTTCCAGTTTTTGGATGGAA
GAAAATTTCCCTCTTTCGATACGAAAGAGAACAAAGAATTCTTCTTGAAATGGTTTG
Found at i:737333 original size:164 final size:164
Alignment explanation
Indices: 737062--737388 Score: 629
Period size: 164 Copynumber: 2.0 Consensus size: 164
737052 GAACCTTGTC
737062 AATCAATACACCTCTAAACTATTATTAATGAGAACAGGGCGTTGTTTTACAAAAGAACTTTCGAC
1 AATCAATACACCTCTAAACTATTATTAATGAGAACAGGGCGTTGTTTTACAAAAGAACTTTCGAC
737127 CATGCAAAATTCATAAATGCTCATTATTTAAAAGTGACTATGTACATGTTTTAACTTCATTCC-A
66 CATGCAAAATTCATAAATGCTCATTATTTAAAAGTGACTATGTACATGTTTTAACTTCATTCCAA
*
737191 AATAATATACTTATATGAATTGAAAATTGAAAGG
131 AACAATATACTTATATGAATTGAAAATTGAAAGG
737225 NAATCAATACACCTCTAAACTATTATTAATGAGAACAGGGCGTTGTTTTACAAAAGAACTTTCGA
1 -AATCAATACACCTCTAAACTATTATTAATGAGAACAGGGCGTTGTTTTACAAAAGAACTTTCGA
737290 CCATGCAAAATTCATAAATGCTCATTATTTAAAAGTGACTATGTACATGTTTTAACTTCATTCCA
65 CCATGCAAAATTCATAAATGCTCATTATTTAAAAGTGACTATGTACATGTTTTAACTTCATTCCA
737355 AAACAATATACTTATATGAATTGAAAATTGAAAG
130 AAACAATATACTTATATGAATTGAAAATTGAAAG
737389 AGGGGGGGCT
Statistics
Matches: 161, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
164 128 0.80
165 33 0.20
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (164 bp):
AATCAATACACCTCTAAACTATTATTAATGAGAACAGGGCGTTGTTTTACAAAAGAACTTTCGAC
CATGCAAAATTCATAAATGCTCATTATTTAAAAGTGACTATGTACATGTTTTAACTTCATTCCAA
AACAATATACTTATATGAATTGAAAATTGAAAGG
Found at i:746156 original size:54 final size:55
Alignment explanation
Indices: 745943--746369 Score: 637
Period size: 54 Copynumber: 7.8 Consensus size: 55
745933 ATGTGTCTGC
* * *
745943 CAAAGTCACTCATCTCATAGCAGACTGCACAGACGGTCCCAAATACAGGGTAGGT
1 CAAAGTCACTCACCGCATAGCGGACTGCACAGACGGTCCCAAATACAGGGTAGGT
*
745998 CAAAGTCACTCACCGCATAGCGGACTGCACAGATGGTCCCAAATACAGGGTAGGT
1 CAAAGTCACTCACCGCATAGCGGACTGCACAGACGGTCCCAAATACAGGGTAGGT
* * * *
746053 CAAAGTCACTCACCACAAAGCGGACTGCACAGATGGTCCCAAATACAGGGTAGGC
1 CAAAGTCACTCACCGCATAGCGGACTGCACAGACGGTCCCAAATACAGGGTAGGT
* *
746108 CAAAGTCACTAACTGCATAG-GGACTGCACAGACGGTCCCAAATACAGGGTAGGT
1 CAAAGTCACTCACCGCATAGCGGACTGCACAGACGGTCCCAAATACAGGGTAGGT
* * * * * * * *
746162 TAAAGTCACACATCTCAAAGCAGACTGCACGGAGGGTCCCAAATACAGGGTAGGT
1 CAAAGTCACTCACCGCATAGCGGACTGCACAGACGGTCCCAAATACAGGGTAGGT
* *
746217 CAAAGTCACTCACCGCATAG-GGACTGCACAGACAGTCACAAATACAGGGTAGGT
1 CAAAGTCACTCACCGCATAGCGGACTGCACAGACGGTCCCAAATACAGGGTAGGT
746271 CAAAGTCACTCACCGCATAG-GGACTGCACAGACGGTCCCAAATACAGGGTAGGT
1 CAAAGTCACTCACCGCATAGCGGACTGCACAGACGGTCCCAAATACAGGGTAGGT
*
746325 CAAAGTCACTCACCGCATAG-GGACTGCACAGACGGTCACAAATAC
1 CAAAGTCACTCACCGCATAGCGGACTGCACAGACGGTCCCAAATAC
746370 TAGTGCTGAA
Statistics
Matches: 335, Mismatches: 36, Indels: 3
0.90 0.10 0.01
Matches are distributed among these distances:
54 170 0.51
55 165 0.49
ACGTcount: A:0.33, C:0.27, G:0.24, T:0.15
Consensus pattern (55 bp):
CAAAGTCACTCACCGCATAGCGGACTGCACAGACGGTCCCAAATACAGGGTAGGT
Found at i:746182 original size:109 final size:109
Alignment explanation
Indices: 745943--746369 Score: 658
Period size: 109 Copynumber: 3.9 Consensus size: 109
745933 ATGTGTCTGC
* *
745943 CAAAGTCACTCATCTCATAGCAGACTGCACAGACGGTCCCAAATACAGGGTAGGTCAAAGTCACT
1 CAAAGTCACTCACCTCAAAGCAGACTGCACAGACGGTCCCAAATACAGGGTAGGTCAAAGTCACT
* *
746008 CACCGCATAGCGGACTGCACAGATGGTCCCAAATACAGGGTAGGT
66 CACCGCATAG-GGACTGCACAGACGGTCACAAATACAGGGTAGGT
* * * *
746053 CAAAGTCACTCACCACAAAGCGGACTGCACAGATGGTCCCAAATACAGGGTAGGCCAAAGTCACT
1 CAAAGTCACTCACCTCAAAGCAGACTGCACAGACGGTCCCAAATACAGGGTAGGTCAAAGTCACT
* * *
746118 AACTGCATAGGGACTGCACAGACGGTCCCAAATACAGGGTAGGT
66 CACCGCATAGGGACTGCACAGACGGTCACAAATACAGGGTAGGT
* * * * *
746162 TAAAGTCACACATCTCAAAGCAGACTGCACGGAGGGTCCCAAATACAGGGTAGGTCAAAGTCACT
1 CAAAGTCACTCACCTCAAAGCAGACTGCACAGACGGTCCCAAATACAGGGTAGGTCAAAGTCACT
*
746227 CACCGCATAGGGACTGCACAGACAGTCACAAATACAGGGTAGGT
66 CACCGCATAGGGACTGCACAGACGGTCACAAATACAGGGTAGGT
* * *
746271 CAAAGTCACTCACCGCATAG-GGACTGCACAGACGGTCCCAAATACAGGGTAGGTCAAAGTCACT
1 CAAAGTCACTCACCTCAAAGCAGACTGCACAGACGGTCCCAAATACAGGGTAGGTCAAAGTCACT
746335 CACCGCATAGGGACTGCACAGACGGTCACAAATAC
66 CACCGCATAGGGACTGCACAGACGGTCACAAATAC
746370 TAGTGCTGAA
Statistics
Matches: 287, Mismatches: 30, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
108 75 0.26
109 145 0.51
110 67 0.23
ACGTcount: A:0.33, C:0.27, G:0.24, T:0.15
Consensus pattern (109 bp):
CAAAGTCACTCACCTCAAAGCAGACTGCACAGACGGTCCCAAATACAGGGTAGGTCAAAGTCACT
CACCGCATAGGGACTGCACAGACGGTCACAAATACAGGGTAGGT
Found at i:747312 original size:54 final size:54
Alignment explanation
Indices: 747229--747365 Score: 229
Period size: 54 Copynumber: 2.5 Consensus size: 54
747219 TTCAGCACTA
747229 ACAAATACAGGGTAGGTCAAAGTCACTCACCGAATAGGGACTGCACAGACGGTC
1 ACAAATACAGGGTAGGTCAAAGTCACTCACCGAATAGGGACTGCACAGACGGTC
* * *
747283 CCAAATGCAGGGTAGGTCAAAGTCACTCACCGCATAGGGACTGCACAGACGGTC
1 ACAAATACAGGGTAGGTCAAAGTCACTCACCGAATAGGGACTGCACAGACGGTC
* *
747337 ACAAATACAGGTTAAGTCAAAGTCACTCA
1 ACAAATACAGGGTAGGTCAAAGTCACTCA
747366 ACTTGACCAC
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 76 1.00
ACGTcount: A:0.35, C:0.25, G:0.24, T:0.16
Consensus pattern (54 bp):
ACAAATACAGGGTAGGTCAAAGTCACTCACCGAATAGGGACTGCACAGACGGTC
Found at i:747405 original size:49 final size:52
Alignment explanation
Indices: 747230--747407 Score: 166
Period size: 54 Copynumber: 3.4 Consensus size: 52
747220 TCAGCACTAA
* **
747230 CAAATACAGGGTAGGTCAAAGTCACTCAC-CGAATAGGGACTGCACAGACGGTCC
1 CAAATGCAGGGTAGGTCAAAGTCACTCACAC--ATA-GGACCACACAGACGGTCC
* ** *
747284 CAAATGCAGGGTAGGTCAAAGTCACTCACCGCATAGGGACTGCACAGACGGTCA
1 CAAATGCAGGGTAGGTCAAAGTCACTCA-CACATA-GGACCACACAGACGGTCC
* * * * *
747338 CAAATACAGGTTAAGTCAAAGTCACTCA-AC-T-TGACCACACAGATGGTCC
1 CAAATGCAGGGTAGGTCAAAGTCACTCACACATAGGACCACACAGACGGTCC
*
747387 CAAATGTAGGGTAGGTCAAAG
1 CAAATGCAGGGTAGGTCAAAG
747408 CAGACTGCAT
Statistics
Matches: 107, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
49 30 0.28
51 1 0.01
52 1 0.01
54 73 0.68
55 1 0.01
56 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.25, T:0.17
Consensus pattern (52 bp):
CAAATGCAGGGTAGGTCAAAGTCACTCACACATAGGACCACACAGACGGTCC
Found at i:747557 original size:13 final size:13
Alignment explanation
Indices: 747539--747568 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
747529 ATATGAAAAG
*
747539 CATTTACCATAAT
1 CATTTACAATAAT
747552 CATTTACAATAAT
1 CATTTACAATAAT
747565 CATT
1 CATT
747569 CATCATTACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (13 bp):
CATTTACAATAAT
Found at i:747849 original size:54 final size:54
Alignment explanation
Indices: 747767--747902 Score: 254
Period size: 54 Copynumber: 2.5 Consensus size: 54
747757 NNNNNNNNNN
747767 CAAATACAGGGTAGGTCAAAGTCACTCACCGCATAGGGACTGCACAGACGGTCA
1 CAAATACAGGGTAGGTCAAAGTCACTCACCGCATAGGGACTGCACAGACGGTCA
747821 CAAATACAGGGTAGGTCAAAGTCACTCACCGCATAGGGACTGCACAGACGGTCA
1 CAAATACAGGGTAGGTCAAAGTCACTCACCGCATAGGGACTGCACAGACGGTCA
* *
747875 CAAATACAGGTTAAGTCAAAGTCACTCA
1 CAAATACAGGGTAGGTCAAAGTCACTCA
747903 ACTTGACCAC
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 80 1.00
ACGTcount: A:0.35, C:0.25, G:0.24, T:0.16
Consensus pattern (54 bp):
CAAATACAGGGTAGGTCAAAGTCACTCACCGCATAGGGACTGCACAGACGGTCA
Found at i:758171 original size:40 final size:40
Alignment explanation
Indices: 758127--758366 Score: 480
Period size: 40 Copynumber: 6.0 Consensus size: 40
758117 ATTGAAATGC
758127 ATAACCTGTAGATACAATAGACGAGCATTGTCTGAAATCT
1 ATAACCTGTAGATACAATAGACGAGCATTGTCTGAAATCT
758167 ATAACCTGTAGATACAATAGACGAGCATTGTCTGAAATCT
1 ATAACCTGTAGATACAATAGACGAGCATTGTCTGAAATCT
758207 ATAACCTGTAGATACAATAGACGAGCATTGTCTGAAATCT
1 ATAACCTGTAGATACAATAGACGAGCATTGTCTGAAATCT
758247 ATAACCTGTAGATACAATAGACGAGCATTGTCTGAAATCT
1 ATAACCTGTAGATACAATAGACGAGCATTGTCTGAAATCT
758287 ATAACCTGTAGATACAATAGACGAGCATTGTCTGAAATCT
1 ATAACCTGTAGATACAATAGACGAGCATTGTCTGAAATCT
758327 ATAACCTGTAGATACAATAGACGAGCATTGTCTGAAATCT
1 ATAACCTGTAGATACAATAGACGAGCATTGTCTGAAATCT
758367 GTTGACGATC
Statistics
Matches: 200, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 200 1.00
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (40 bp):
ATAACCTGTAGATACAATAGACGAGCATTGTCTGAAATCT
Found at i:759729 original size:65 final size:66
Alignment explanation
Indices: 759625--759759 Score: 245
Period size: 65 Copynumber: 2.1 Consensus size: 66
759615 TGAACTGCGT
* *
759625 TCTAGAACGCAGTTCGCAATTCAAAATTTATAATTCATAATTGAGG-TATGACATTTCCAGGGTC
1 TCTAGAACGCAGTTCGCAATTCAAAATTTATAATTCATAATTAAGGTTATGAAATTTCCAGGGTC
759689 A
66 A
759690 TCTAGAACGCAGTTCGCAATTCAAAATTTATAATTCATAATTAAGGTTATGAAATTTCCAGGGTC
1 TCTAGAACGCAGTTCGCAATTCAAAATTTATAATTCATAATTAAGGTTATGAAATTTCCAGGGTC
759755 A
66 A
759756 TCTA
1 TCTA
759760 CTGGTGGCAT
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
65 45 0.67
66 22 0.33
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (66 bp):
TCTAGAACGCAGTTCGCAATTCAAAATTTATAATTCATAATTAAGGTTATGAAATTTCCAGGGTC
A
Found at i:759862 original size:231 final size:224
Alignment explanation
Indices: 759466--759881 Score: 573
Period size: 231 Copynumber: 1.8 Consensus size: 224
759456 TGAACTGCAT
* * * *
759466 TCTAGAACACAGTTCGCAATTCAAAATTTATGATTCATATATGGGGCCTGAAATTTTCAGGGTCA
1 TCTAGAACACAGTTCGCAATTCAAAATTTATAATTCATATATAGGGCATGAAATTTCCAGGGTCA
* * * * *
759531 TCTACTAGTGGTATACCACTGTGAATATATGGTAAAGTGGTCATCTCTTGTTTTTGAGATTCCAG
66 TCTACTAGTGGCATACCACTCTGAAAATATGGTAAAGTGGTCATCTATAGTTTTTGAGATTCCAG
* *
759596 TTTTTCTGCAATTGAAAAGTGAACTGCGTTCTAGAACGCAGTTCGCAATTCAAAATTTATAATTC
131 CTTATCTGCAATTGAAAAGTGAACTGCGTTCTAGAACGCAGTTCGCAATTCAAAATTTATAATTC
759661 ATAATTGAGGTATGACATTTCCAGGGTCA
196 ATAATTGAGGTATGACATTTCCAGGGTCA
* **
759690 TCTAGAACGCAGTTCGCAATTCAAAATTTATAATTCATA-ATTAAGGTTATGAAATTTCCAGGGT
1 TCTAGAACACAGTTCGCAATTCAAAATTTATAATTCATATA-T-AGGGCATGAAATTTCCAGGGT
* * *
759754 CATCTACTGGTGGCATACCATTAGCGCTCTTAAAATATGGTGAAGTGGTCATCTATAGTTTTTGA
64 CATCTACTAGTGGCATACC---A---CTCTGAAAATATGGTAAAGTGGTCATCTATAGTTTTTGA
** *
759819 GATTCGGGCTTATCTGCAATTGAAAAGTGAACTGCGTTCTAGAACGCAGTTTGCAATTCAAAA
123 GATTCCAGCTTATCTGCAATTGAAAAGTGAACTGCGTTCTAGAACGCAGTTCGCAATTCAAAA
759882 ATCAAAGTGA
Statistics
Matches: 164, Mismatches: 20, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
223 1 0.01
224 38 0.23
225 33 0.20
228 1 0.01
231 91 0.55
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (224 bp):
TCTAGAACACAGTTCGCAATTCAAAATTTATAATTCATATATAGGGCATGAAATTTCCAGGGTCA
TCTACTAGTGGCATACCACTCTGAAAATATGGTAAAGTGGTCATCTATAGTTTTTGAGATTCCAG
CTTATCTGCAATTGAAAAGTGAACTGCGTTCTAGAACGCAGTTCGCAATTCAAAATTTATAATTC
ATAATTGAGGTATGACATTTCCAGGGTCA
Found at i:761476 original size:2 final size:2
Alignment explanation
Indices: 761469--761495 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
761459 TTTTTAAAAT
761469 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 T
761496 GGTAAAATTA
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:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:773173 original size:2 final size:2
Alignment explanation
Indices: 773166--773216 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
773156 CATAAAGAAA
773166 AG AG AG AG AG AG AG 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 AG AG AG AG AG AG AG
773208 AG AG AG AG A
1 AG AG AG AG A
773217 TGAACAGTTA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:781249 original size:33 final size:32
Alignment explanation
Indices: 781158--781236 Score: 131
Period size: 32 Copynumber: 2.4 Consensus size: 32
781148 CCTAGCCATC
781158 TTTCCCCCGGGAAAAATGGCTATATAGCAGTT
1 TTTCCCCCGGGAAAAATGGCTATATAGCAGTT
* *
781190 CTTCCCCCCGGAAAAATGGCTATATAGCAGTT
1 TTTCCCCCGGGAAAAATGGCTATATAGCAGTT
781222 TTTCCCCCAGGGAAA
1 TTTCCCCC-GGGAAA
781237 GCTGACTATA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
32 37 0.88
33 5 0.12
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25
Consensus pattern (32 bp):
TTTCCCCCGGGAAAAATGGCTATATAGCAGTT
Found at i:807544 original size:50 final size:50
Alignment explanation
Indices: 807469--807601 Score: 185
Period size: 50 Copynumber: 2.7 Consensus size: 50
807459 TGTACCTTCA
**** *
807469 TAACGCACTTTGAAAATTTTTTTCAAAGTGGGTTAACTTGGTCCAAAATT
1 TAACGCACTTTGAAAAAAAATTTCAAAGTGCGTTAACTTGGTCCAAAATT
* * *
807519 TAACGCACTTTGAAAAAAAATTTCAAAGTGCGTTGATTTTGTCCAAAATT
1 TAACGCACTTTGAAAAAAAATTTCAAAGTGCGTTAACTTGGTCCAAAATT
*
807569 TAACGCAATTTGAAAAAAAATTTCAAAGTGCGT
1 TAACGCACTTTGAAAAAAAATTTCAAAGTGCGT
807602 AATTTTTTCA
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 74 1.00
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.34
Consensus pattern (50 bp):
TAACGCACTTTGAAAAAAAATTTCAAAGTGCGTTAACTTGGTCCAAAATT
Found at i:818616 original size:14 final size:14
Alignment explanation
Indices: 818597--818624 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
818587 TTGTTTAAGG
818597 GGTCATCTCAAAGT
1 GGTCATCTCAAAGT
818611 GGTCATCTCAAAGT
1 GGTCATCTCAAAGT
818625 TTGTTAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (14 bp):
GGTCATCTCAAAGT
Found at i:818708 original size:20 final size:19
Alignment explanation
Indices: 818663--818708 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
818653 GGATTTTGTC
**
818663 TTTTTTTTGCATTTTTTTT
1 TTTTTTTTGCATTTTTTCA
818682 TTCTTTTTTGCATTTTTTACA
1 TT-TTTTTTGCATTTTTT-CA
818703 TTTTTT
1 TTTTTT
818709 AAAAACTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 2 0.09
20 19 0.83
21 2 0.09
ACGTcount: A:0.09, C:0.09, G:0.04, T:0.78
Consensus pattern (19 bp):
TTTTTTTTGCATTTTTTCA
Found at i:830131 original size:15 final size:15
Alignment explanation
Indices: 830112--830149 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
830102 ATTTTCTTTT
*
830112 TTATATATTTCTCTTA
1 TTATATATTTAT-TTA
830128 -TATATATTTATTTA
1 TTATATATTTATTTA
830142 TTATATAT
1 TTATATAT
830150 ATTTTGCCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 3 0.15
15 17 0.85
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (15 bp):
TTATATATTTATTTA
Found at i:839177 original size:2 final size:2
Alignment explanation
Indices: 839170--839279 Score: 157
Period size: 2 Copynumber: 55.0 Consensus size: 2
839160 TTGAGACCCC
* * *
839170 CT CT CT CT CT CT CT GT CT CT GT CT CT CT CT GT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
* * *
839212 CT TT CT CT CT GT CT CC 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 CT CT CT CT CT CT
*
839254 CT CT CT CT CT CT CT CT AT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
839280 AAAATCAAAA
Statistics
Matches: 94, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 94 1.00
ACGTcount: A:0.01, C:0.45, G:0.04, T:0.50
Consensus pattern (2 bp):
CT
Found at i:839440 original size:12 final size:12
Alignment explanation
Indices: 839423--839450 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
839413 ATATCGTATG
839423 TTCATATAATGA
1 TTCATATAATGA
839435 TTCATATAATGA
1 TTCATATAATGA
839447 TTCA
1 TTCA
839451 AAATTACATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (12 bp):
TTCATATAATGA
Found at i:845374 original size:2 final size:2
Alignment explanation
Indices: 845299--845365 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
845289 TTTGAATTTT
845299 AG AG AG AG AG AG AG 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 AG AG AG AG AG AG AG
845341 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
845366 ACGGAGAGAA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:845374 original size:11 final size:10
Alignment explanation
Indices: 845299--845382 Score: 58
Period size: 10 Copynumber: 8.6 Consensus size: 10
845289 TTTGAATTTT
845299 AGAGAGAGA-G
1 AGAGAGA-ACG
845309 AGAGAGAGA-G
1 AGAGAGA-ACG
845319 AGAGAGAGA-G
1 AGAGAGA-ACG
845329 AGAGAGAGA-G
1 AGAGAGA-ACG
845339 AGAGAGAGA-G
1 AGAGAGA-ACG
845349 AGAGAGAGA-G
1 AGAGAGA-ACG
845359 AGAGAGAACG
1 AGAGAGAACG
845369 -GAGAGAACG
1 AGAGAGAACG
845378 -GAGAG
1 AGAGAG
845383 TGAGAGGATC
Statistics
Matches: 73, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
9 15 0.21
10 58 0.79
ACGTcount: A:0.49, C:0.02, G:0.49, T:0.00
Consensus pattern (10 bp):
AGAGAGAACG
Found at i:855526 original size:23 final size:23
Alignment explanation
Indices: 855500--855544 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
855490 AGCAAAGTGC
* * *
855500 TAAAGAAATGTAAAAAACAAAAT
1 TAAAAAAATATAAAAAAAAAAAT
855523 TAAAAAAATATAAAAAAAAAAA
1 TAAAAAAATATAAAAAAAAAAA
855545 CAAAAACAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.78, C:0.02, G:0.04, T:0.16
Consensus pattern (23 bp):
TAAAAAAATATAAAAAAAAAAAT
Found at i:855550 original size:23 final size:24
Alignment explanation
Indices: 855505--855568 Score: 60
Period size: 23 Copynumber: 2.7 Consensus size: 24
855495 AGTGCTAAAG
* * **
855505 AAATGTAAAAAACAAAATTAAAA-
1 AAATATAAAAAAAAAAACAAAAAC
855528 AAATATAAAAAAAAAAACAAAAAC
1 AAATATAAAAAAAAAAACAAAAAC
*
855552 AAA-ACAAAACAAAAAAA
1 AAATATAAAA-AAAAAAA
855569 ACCCCAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
23 24 0.71
24 10 0.29
ACGTcount: A:0.81, C:0.08, G:0.02, T:0.09
Consensus pattern (24 bp):
AAATATAAAAAAAAAAACAAAAAC
Found at i:855555 original size:16 final size:16
Alignment explanation
Indices: 855536--855566 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
855526 AAAAATATAA
855536 AAAAAAAAACAAAAAC
1 AAAAAAAAACAAAAAC
*
855552 AAAACAAAACAAAAA
1 AAAAAAAAACAAAAA
855567 AAACCCCAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (16 bp):
AAAAAAAAACAAAAAC
Found at i:855555 original size:28 final size:28
Alignment explanation
Indices: 855511--855569 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
855501 AAAGAAATGT
** *
855511 AAAAAACAAAATTAAAA-AAATATAAAAA
1 AAAAAACAAAAACAAAACAAA-ACAAAAA
855539 AAAAAACAAAAACAAAACAAAACAAAAA
1 AAAAAACAAAAACAAAACAAAACAAAAA
855567 AAA
1 AAA
855570 CCCCAAAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 24 0.89
29 3 0.11
ACGTcount: A:0.85, C:0.08, G:0.00, T:0.07
Consensus pattern (28 bp):
AAAAAACAAAAACAAAACAAAACAAAAA
Found at i:887577 original size:15 final size:15
Alignment explanation
Indices: 887560--887605 Score: 76
Period size: 15 Copynumber: 3.1 Consensus size: 15
887550 CTTTTTGGGG
887560 TTTTTTT-TTTTTTT
1 TTTTTTTGTTTTTTT
*
887574 GTTTTTTGTTTTTTT
1 TTTTTTTGTTTTTTT
887589 TTTTTTTGTTTTTTT
1 TTTTTTTGTTTTTTT
887604 TT
1 TT
887606 GGCTTTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
14 6 0.21
15 23 0.79
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (15 bp):
TTTTTTTGTTTTTTT
Done.