Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr6
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 47432654
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2298022 characters in sequence are not A, C, G, or T
File 32 of 136
Found at i:10335306 original size:16 final size:16
Alignment explanation
Indices: 10335281--10335314 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
10335271 TGTGTTTTGC
* *
10335281 TTTGATTGCATGGCAT
1 TTTGACTGCATAGCAT
10335297 TTTGACTGCATAGCAT
1 TTTGACTGCATAGCAT
10335313 TT
1 TT
10335315 CATCATAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.15, G:0.21, T:0.44
Consensus pattern (16 bp):
TTTGACTGCATAGCAT
Found at i:10338992 original size:5 final size:5
Alignment explanation
Indices: 10338984--10339027 Score: 52
Period size: 5 Copynumber: 8.6 Consensus size: 5
10338974 AAATAAAAAG
* * *
10338984 AGAAA AGAAA AGAAA AGAAAA ACAAA AAAAA AGAAA AAAAA AGA
1 AGAAA AGAAA AGAAA AG-AAA AGAAA AGAAA AGAAA AGAAA AGA
10339028 GGACAAGGTG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
5 29 0.88
6 4 0.12
ACGTcount: A:0.84, C:0.02, G:0.14, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:10338997 original size:10 final size:10
Alignment explanation
Indices: 10338963--10339027 Score: 67
Period size: 10 Copynumber: 6.1 Consensus size: 10
10338953 TACTTCACCT
* *
10338963 AAAATAAAAT
1 AAAAAAAAAG
10338973 AAAATAAAAAG
1 AAAA-AAAAAG
10338984 AGAAAAGAAAAG
1 A-AAAA-AAAAG
*
10338996 AAAAGAAAAAC
1 AAAA-AAAAAG
10339007 AAAAAAAAAG
1 AAAAAAAAAG
10339017 AAAAAAAAAG
1 AAAAAAAAAG
10339027 A
1 A
10339028 GGACAAGGTG
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
10 20 0.43
11 17 0.36
12 10 0.21
ACGTcount: A:0.83, C:0.02, G:0.11, T:0.05
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:10340063 original size:92 final size:88
Alignment explanation
Indices: 10339906--10340301 Score: 283
Period size: 92 Copynumber: 4.4 Consensus size: 88
10339896 ATCATAGCAA
* * *
10339906 ATCTTATCTCCCTGAAGTTGCAGT-GAAGCAGACTAAAGATAGCAAATCTTATTTCCCTAAAGTT
1 ATCTTATCTCTCTGAAGTTGCAGTAG-AGCAGA-T---CATAGCAAA-CTTATCTCCCTAAAGTT
10339970 GCAGTGGAACGAATTGAAGCTATAAATTGTAG
60 GCAGTGGAAC-AATTGAAGCTATAAA-TG-AG
* * *
10340002 ATCTTGTCTCTCTGAAGTTGTAGTAGAGCAGATCATAGCAAACATTATCTCCCTGAAGTTGCAGT
1 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCATAGCAAAC-TTATCTCCCTAAAGTTGCAGT
* ** *
10340067 GGAGCAGGTGAAG-T-TACA--AG
65 GGAACAATTGAAGCTATAAATGAG
* * * * * *
10340087 -TCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAAGATAGCGAATCTTATTTCCCTAAAGTTG
1 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGA-T---CATAGC-AAACTTATCTCCCTAAAGTTG
* * *
10340151 CAATGGAACAGATTAAAACTATAAATCGCAG
61 CAGTGGAACA-ATTGAAGCTATAAAT-G-AG
* * *
10340182 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCATATCAAACCTTATCTCCCTGAAGTTACAGT
1 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCATAGCAAA-CTTATCTCCCTAAAGTTGCAGT
* **
10340247 GGAACAGGTT-AA-AAATAAACT-A-
65 GGAACA-ATTGAAGCTATAAA-TGAG
*
10340269 ATCTTATCTC-CTTGAAGTTGCAGTGGAGCAGAT
1 ATCTTATCTCTC-TGAAGTTGCAGTAGAGCAGAT
10340302 TGAAGACGGG
Statistics
Matches: 242, Mismatches: 40, Indels: 45
0.74 0.12 0.14
Matches are distributed among these distances:
84 26 0.11
85 3 0.01
86 1 0.00
87 30 0.12
88 29 0.12
89 9 0.04
90 7 0.03
91 15 0.06
92 62 0.26
95 4 0.02
96 55 0.23
97 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (88 bp):
ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCATAGCAAACTTATCTCCCTAAAGTTGCAGTG
GAACAATTGAAGCTATAAATGAG
Found at i:10340072 original size:41 final size:41
Alignment explanation
Indices: 10340008--10340117 Score: 107
Period size: 43 Copynumber: 2.6 Consensus size: 41
10339998 GTAGATCTTG
* * *
10340008 TCTCTCTGAAGTTGTAGTAGAGCAGATCATAG-CAA-ACATTA
1 TCTCCCTGAAGTTGCAGTGGAGCAGATCA-AGTCAAGAC-TTA
* * *
10340049 TCTCCCTGAAGTTGCAGTGGAGCAGGTGAAGTTACAAGTCTTA
1 TCTCCCTGAAGTTGCAGTGGAGCAGATCAAG-T-CAAGACTTA
*
10340092 TCTCCCTAAAGTTGCAGTGGAGCAGA
1 TCTCCCTGAAGTTGCAGTGGAGCAGA
10340118 CTGAAGATAG
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
40 2 0.04
41 24 0.42
43 30 0.53
44 1 0.02
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (41 bp):
TCTCCCTGAAGTTGCAGTGGAGCAGATCAAGTCAAGACTTA
Found at i:10340104 original size:43 final size:45
Alignment explanation
Indices: 10340046--10340435 Score: 197
Period size: 44 Copynumber: 8.6 Consensus size: 45
10340036 ATAGCAAACA
* * *
10340046 TTATCTCCCTGAAGTTGCAGTGGAGCAG-GTGAAGTTA-C-AAGTC
1 TTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAAGATAGCGAA-TC
10340089 TTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAAGATAGCGAATC
1 TTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAAGATAGCGAATC
* * * * * * *
10340134 TTATTTCCCTAAAGTTGCAATGGAACAGATTAAAACTATAAATCGCAGATC
1 TTATCTCCCTAAAGTTGCAGTGGAGCAGACT-GAA-GAT--AGCG-A-ATC
* * * * * * *
10340185 TTATCTCTCTGAAGTTGCAGTAGAGCAGA-T---CATATCAAACC
1 TTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAAGATAGCGAATC
* * * ** * * * *
10340226 TTATCTCCCTGAAGTTACAGTGGAACAGGTTAAAAATAAACTAATC
1 TTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAAGAT-AGCGAATC
* * * *
10340272 TTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGACGGGCTA-CAAATC
1 TTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAAGA-----TAGCGAATC
* * * * * ** * *
10340321 TTATCTCCCTGAAGTTACAGTGGAGTAGATTAAAGCCA-CAAACC
1 TTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAAGATAGCGAATC
* * * * *
10340365 TTATCTCCCTGAAGTTGTAGTGGACCAGATTGAAGATA-CCAATC
1 TTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAAGATAGCGAATC
10340409 TTATCTCCCTAAAGTTGCAGTGGAGCA
1 TTATCTCCCTAAAGTTGCAGTGGAGCA
10340436 AATTAAAGCT
Statistics
Matches: 274, Mismatches: 54, Indels: 37
0.75 0.15 0.10
Matches are distributed among these distances:
41 26 0.09
42 2 0.01
43 30 0.11
44 72 0.26
45 34 0.12
46 39 0.14
47 2 0.01
49 39 0.14
50 3 0.01
51 27 0.10
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.28
Consensus pattern (45 bp):
TTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAAGATAGCGAATC
Found at i:10340209 original size:180 final size:183
Alignment explanation
Indices: 10339905--10340307 Score: 573
Period size: 180 Copynumber: 2.2 Consensus size: 183
10339895 GATCATAGCA
* *
10339905 AATCTTATCTCCCTGAAGTTGCAGTGAAGCAGACTAAAGATAGCAAATCTTATTTCCCTAAAGTT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTAAAGTT
* * * * * * *
10339970 GCAGTGGAACGAATTGAAGCTATAAATTGTAGATCTTGTCTCTCTGAAGTTGTAGTAGAGCAGAT
66 GCAATGGAACGAATTAAAACTATAAATCGCAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGAT
* * * * *
10340035 CATAGCAAACATTATCTCCCTGAAGTTGCAGTGGAGCAGG-T-GAAGT-TAC-
131 CATAGCAAACATTATCTCCCTGAAGTTACAGTGGAACAGGTTAAAAATAAACT
* *
10340084 AAGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAAGATAGCGAATCTTATTTCCCTAAAGT
1 AA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTAAAGT
10340149 TGCAATGGAAC-AGATTAAAACTATAAATCGCAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAG
65 TGCAATGGAACGA-ATTAAAACTATAAATCGCAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAG
* *
10340213 ATCATATCAAACCTTATCTCCCTGAAGTTACAGTGGAACAGGTTAAAAATAAACT
129 ATCATAGCAAACATTATCTCCCTGAAGTTACAGTGGAACAGGTTAAAAATAAACT
* *
10340268 AATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGA
10340308 CGGGCTACAA
Statistics
Matches: 197, Mismatches: 21, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
179 3 0.02
180 151 0.77
181 1 0.01
182 3 0.02
183 37 0.19
184 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (183 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTAAAGTT
GCAATGGAACGAATTAAAACTATAAATCGCAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGAT
CATAGCAAACATTATCTCCCTGAAGTTACAGTGGAACAGGTTAAAAATAAACT
Found at i:10340334 original size:49 final size:44
Alignment explanation
Indices: 10340182--10340486 Score: 274
Period size: 44 Copynumber: 6.8 Consensus size: 44
10340172 TAAATCGCAG
* * * *
10340182 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCATA--T-CAA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAA
* * * * ** *
10340223 ACCTTATCTCCCTGAAGTTACAGTGGAACAGGTTAAAAATAAACTA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCT--ACAA
*
10340269 ATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGACGGGCTACAA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AA-A---GCTACAA
* * *
10340318 ATCTTATCTCCCTGAAGTTACAGTGGAGTAGATTAAAGCCACAA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAA
* * * * * *
10340362 ACCTTATCTCCCTGAAGTTGTAGTGGACCAGATTGAAGATACCA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAA
* * *
10340406 ATCTTATCTCCCTAAAGTTGCAGTGGAGCAAATTAAAGCTACTA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAA
* * * *
10340450 ATCCTATCTCCCTGAAGTTGTAGTGAAGCGGATTAAA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA
10340487 ACAATAAATC
Statistics
Matches: 210, Mismatches: 44, Indels: 17
0.77 0.16 0.06
Matches are distributed among these distances:
41 29 0.14
43 1 0.00
44 108 0.51
46 31 0.15
47 3 0.01
48 3 0.01
49 34 0.16
51 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.28
Consensus pattern (44 bp):
ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAA
Found at i:10340370 original size:180 final size:175
Alignment explanation
Indices: 10339907--10340381 Score: 420
Period size: 180 Copynumber: 2.6 Consensus size: 175
10339897 TCATAGCAAA
* * * * *
10339907 TCTTATCTCCCTGAAGTTGCAGTGAAGCAGACTAAAGATAGCAAATCTTATTTCCCTAAAGTTGC
1 TCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATCTCCCTAAAGTTAC
* * * * * ** * *
10339972 AGTGGAAC-GAATTGAAGCTATAAATTGTAGATCTTGTCTCTCTGAAGTTGTAGTAGAGCAGATC
66 AATGGAACAG-ATTAAAACCACAAA----CCA-CTTATCTCTCTGAAGTTGCAGTAGAGCAGATC
* * * * *
10340036 ATAGCAAACATTATCTCCCTGAAGTTGCAGTGGAGCAGGTGAAGTTACAAG
125 ATAGCAAACATTATCTCCCTGAAGTTACAGTGGAACAGGTAAAATAACAAG
* * *
10340087 TCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAAGATAGCGAATCTTATTTCCCTAAAGTTGC
1 TCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATCTCCCTAAAGTTAC
* *
10340152 AATGGAACAGATTAAAACTATAAATCGCAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCA
66 AATGGAACAGATTAAAACCACAAA-C-C--A-CTTATCTCTCTGAAGTTGCAGTAGAGCAGATCA
* *
10340217 TATCAAACCTTATCTCCCTGAAGTTACAGTGGAACAGGTTAAAAATAAACTAA-
126 TAGCAAACATTATCTCCCTGAAGTTACAGTGGAACAGG-T-AAAAT-AAC-AAG
* * * *
10340270 TCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGACGGGCTA-CAAATCTTATCTCCCTGAA
1 TCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAAGA-----TAGCAAATCTTATCTCCCTAAA
* ** * *
10340334 GTTACAGTGGAGTAGATTAAAGCCACAAA-C-CTTATCTCCCTGAAGTTG
61 GTTACAATGGAACAGATTAAAACCACAAACCACTTATCTCTCTGAAGTTG
10340382 TAGTGGACCA
Statistics
Matches: 250, Mismatches: 32, Indels: 26
0.81 0.10 0.08
Matches are distributed among these distances:
177 1 0.00
180 164 0.66
181 2 0.01
182 3 0.01
183 37 0.15
184 3 0.01
187 38 0.15
188 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.28
Consensus pattern (175 bp):
TCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATCTCCCTAAAGTTAC
AATGGAACAGATTAAAACCACAAACCACTTATCTCTCTGAAGTTGCAGTAGAGCAGATCATAGCA
AACATTATCTCCCTGAAGTTACAGTGGAACAGGTAAAATAACAAG
Found at i:10340435 original size:137 final size:131
Alignment explanation
Indices: 10339903--10340490 Score: 395
Period size: 137 Copynumber: 4.3 Consensus size: 131
10339893 AAGATCATAG
* * * * *
10339903 CAAATCTTATCTCCCTGAAGTTGCAGTGAAGCAGACTAAAGATAGCAAATCTTATTTCCCTAAAG
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG--A-CAAACCTTATCTCCCTGAAG
** * * * * *
10339968 TTGCAGTGGAAC-GAATTGAAGCTATAAATTGTAGATCTTGTCTCTCTGAAGTTGTAGTAGAGCA
63 TTGCAGTGGAACAG-ATTGAAG--AT--A--CCA-ATCTTATCTCCCTAAAGTTGCAGTGGAGCA
* *
10340032 GATCATA-G---
120 GATTAAACGCTA
* * ** *
10340040 CAAA-CATTATCTCCCTGAAGTTGCAGTGGAGCAG-GTGAAGTTACAAGTCTTATCTCCCTAAAG
1 CAAATC-TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG--ACAAACCTTATCTCCCTGAAG
* * * * * *
10340103 TTGCAGTGGAGCAGACTGAAGATAGCGAATCTTATTTCCCTAAAGTTGCAATGGAACAGATTAAA
63 TTGCAGTGGAACAGATTGAAGATA-CCAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATT-AA
**
10340168 ACTATAAA
126 ACGCT--A
* * * * * *
10340176 TCGCAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCATA-TCAAACCTTATCTCCCTGAAG
1 ---CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGACAAACCTTATCTCCCTGAAG
* * * * * * *
10340240 TTACAGTGGAACAGGTTAAAAATAAACTAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGA
63 TTGCAGTGGAACAGATTGAAGAT--ACCAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATT-A
10340305 AGACGGGCTA
125 A-AC--GCTA
* *
10340315 CAAATCTTATCTCCCTGAAGTTACAGTGGAGTAGATTAAAGCCACAAACCTTATCTCCCTGAAGT
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG--ACAAACCTTATCTCCCTGAAGT
* * *
10340380 TGTAGTGGACCAGATTGAAGATACCAATCTTATCTCCCTAAAGTTGCAGTGGAGCAAATTAAA-G
64 TGCAGTGGAACAGATTGAAGATACCAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAACG
10340444 CTA
129 CTA
* * * * *
10340447 CTAATCCTATCTCCCTGAAGTTGTAGTGAAGCGGATTAAA-ACAA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGACAA
10340491 TAAATCCTAT
Statistics
Matches: 356, Mismatches: 73, Indels: 52
0.74 0.15 0.11
Matches are distributed among these distances:
129 29 0.08
130 3 0.01
131 1 0.00
132 37 0.10
133 2 0.01
135 36 0.10
136 43 0.12
137 99 0.28
138 33 0.09
139 70 0.20
140 2 0.01
141 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (131 bp):
CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGACAAACCTTATCTCCCTGAAGTTG
CAGTGGAACAGATTGAAGATACCAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAACGCT
A
Found at i:10353348 original size:80 final size:80
Alignment explanation
Indices: 10353264--10353417 Score: 227
Period size: 80 Copynumber: 1.9 Consensus size: 80
10353254 TATCTGTCCC
* * * * * *
10353264 AACTCAATTGTGAAATTACCAAAAATTTATTCTTTTTACAGAGTAACAAATATTATTTTAATGGT
1 AACTCAATTGTAAAATTACCAAAAACTTATTCCTTTTACAAAGTAACAAAGATTATTTTAAGGGT
10353329 ATTTATGTCCAACTT
66 ATTTATGTCCAACTT
* *
10353344 AACTCAATTGTAAAATTACCAAAAACTTATTCCTTTTACAAAGTAATAAAGATTATTTTGAGGGT
1 AACTCAATTGTAAAATTACCAAAAACTTATTCCTTTTACAAAGTAACAAAGATTATTTTAAGGGT
*
10353409 GTTTATGTC
66 ATTTATGTC
10353418 ATTTTATATT
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
80 65 1.00
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (80 bp):
AACTCAATTGTAAAATTACCAAAAACTTATTCCTTTTACAAAGTAACAAAGATTATTTTAAGGGT
ATTTATGTCCAACTT
Found at i:10357173 original size:16 final size:17
Alignment explanation
Indices: 10357149--10357180 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
10357139 TATGATAAGC
10357149 AAATAATAAGGTAAGTG
1 AAATAATAAGGTAAGTG
10357166 AAAT-ATAAGGTAAGT
1 AAATAATAAGGTAAGT
10357181 ACTATTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.53, C:0.00, G:0.22, T:0.25
Consensus pattern (17 bp):
AAATAATAAGGTAAGTG
Found at i:10357719 original size:21 final size:21
Alignment explanation
Indices: 10357646--10357755 Score: 141
Period size: 23 Copynumber: 5.1 Consensus size: 21
10357636 GGCTTTCCCG
10357646 ATCAGGCACTTTATGTGTCGT
1 ATCAGGCACTTTATGTGTCGT
10357667 ACATCAGGCACTTTATGTGTCGT
1 --ATCAGGCACTTTATGTGTCGT
10357690 ATCTCAGGCACTTTATGTGTCGT
1 A--TCAGGCACTTTATGTGTCGT
* *
10357713 ATCAGGCACCTCATGTGTCGT
1 ATCAGGCACTTTATGTGTCGT
* *
10357734 TTCAGGCAC-TTATGTGTTGT
1 ATCAGGCACTTTATGTGTCGT
10357754 AT
1 AT
10357756 ACTAATCAGG
Statistics
Matches: 79, Mismatches: 6, Indels: 7
0.86 0.07 0.08
Matches are distributed among these distances:
20 10 0.13
21 27 0.34
23 42 0.53
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.37
Consensus pattern (21 bp):
ATCAGGCACTTTATGTGTCGT
Found at i:10360513 original size:67 final size:67
Alignment explanation
Indices: 10360404--10360532 Score: 197
Period size: 67 Copynumber: 1.9 Consensus size: 67
10360394 TTTTCAATTC
* * * *
10360404 AGAGAGCACACTCCTGCGAACCTCATTTCTTACAGTGTGATTATCAGTCCAGGCTAAATCCCCTG
1 AGAGAGCACACTCCTGCGAACCTCATTTCTTACAGCGGGATTACCAGTCCAAGCTAAATCCCCTG
10360469 CA
66 CA
*
10360471 AGAGAGCACACT-CTCGCGAACCTCATTTCTTATAGCGGGATTACCAGTCCAAGCTAAATCCC
1 AGAGAGCACACTCCT-GCGAACCTCATTTCTTACAGCGGGATTACCAGTCCAAGCTAAATCCC
10360533 TGTAATATAA
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
66 2 0.04
67 54 0.96
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.24
Consensus pattern (67 bp):
AGAGAGCACACTCCTGCGAACCTCATTTCTTACAGCGGGATTACCAGTCCAAGCTAAATCCCCTG
CA
Found at i:10360754 original size:57 final size:58
Alignment explanation
Indices: 10360681--10360796 Score: 173
Period size: 57 Copynumber: 2.0 Consensus size: 58
10360671 GCTAAATCCA
10360681 TTTTCCACATATTCTTCGGGAGGGCTATATC-AA-GATCACCCATCCGGGCTAGATAT
1 TTTTCCACATATTCTTCGGGAGGGCTATATCAAAGGATCACCCATCCGGGCTAGATAT
*
10360737 TTTTCACACATATTCTTCGGGAGGGCTATATCAGGAAAGGATCACCCGTCCGGGCTAGAT
1 TTTTC-CACATATTCTTCGGGAGGGCTATATC---AAAGGATCACCCATCCGGGCTAGAT
10360797 CCTTTTTACC
Statistics
Matches: 53, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
56 5 0.09
57 26 0.49
61 2 0.04
62 20 0.38
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.28
Consensus pattern (58 bp):
TTTTCCACATATTCTTCGGGAGGGCTATATCAAAGGATCACCCATCCGGGCTAGATAT
Found at i:10362996 original size:26 final size:26
Alignment explanation
Indices: 10362944--10362998 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
10362934 CATTCTAGGA
*
10362944 AAGAAAGACTTTGTAGCATAATTTGG
1 AAGAAAGACTTTGTAGCATAATATGG
* *
10362970 AAGAAAGCCTTTGTGGCGA-AATATGG
1 AAGAAAGACTTTGTAGC-ATAATATGG
10362996 AAG
1 AAG
10362999 GAATTCCCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 24 0.96
27 1 0.04
ACGTcount: A:0.38, C:0.09, G:0.27, T:0.25
Consensus pattern (26 bp):
AAGAAAGACTTTGTAGCATAATATGG
Found at i:10364296 original size:58 final size:57
Alignment explanation
Indices: 10364226--10364346 Score: 152
Period size: 57 Copynumber: 2.1 Consensus size: 57
10364216 ATAGAAGTGG
* *
10364226 TGAAAATTGAGAAACAGGAAACATTTGAAAATGATTATGATTTTCTCCAAAATGAAAA
1 TGAAAATGGAG-AACAGGAAACATTTGAAAATGAATATGATTTTCTCCAAAATGAAAA
* ** ** * *
10364284 TTAAAATGGAGAATTGGAGTCATTTGAAAATGAATGTGGTTTTCTCCAAAATGAAAA
1 TGAAAATGGAGAACAGGAAACATTTGAAAATGAATATGATTTTCTCCAAAATGAAAA
10364341 TGAAAA
1 TGAAAA
10364347 ATGAACAAGA
Statistics
Matches: 53, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
57 44 0.83
58 9 0.17
ACGTcount: A:0.45, C:0.07, G:0.18, T:0.29
Consensus pattern (57 bp):
TGAAAATGGAGAACAGGAAACATTTGAAAATGAATATGATTTTCTCCAAAATGAAAA
Found at i:10368824 original size:19 final size:18
Alignment explanation
Indices: 10368784--10368824 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
10368774 AATATTAGAC
*
10368784 ATTTCAATTTCACATTAA
1 ATTTCAATTTCACACTAA
*
10368802 ATTTCAATTTTCACACTAT
1 ATTTCAA-TTTCACACTAA
10368821 ATTT
1 ATTT
10368825 TGTTTATTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.34, C:0.17, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTTCAATTTCACACTAA
Found at i:10373407 original size:21 final size:21
Alignment explanation
Indices: 10373381--10373422 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
10373371 AGGGGGAAAA
*
10373381 CATTCCTGATGGCTTTTCTTT
1 CATTCCTGATGGCTTTCCTTT
10373402 CATTCCTGATGGCTTTCCTTT
1 CATTCCTGATGGCTTTCCTTT
10373423 TTGCCCTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.10, C:0.26, G:0.14, T:0.50
Consensus pattern (21 bp):
CATTCCTGATGGCTTTCCTTT
Found at i:10374339 original size:25 final size:25
Alignment explanation
Indices: 10374310--10374377 Score: 93
Period size: 25 Copynumber: 2.7 Consensus size: 25
10374300 AAGCCAAACC
10374310 AAGCCTTTGTGGTGAATTCTCT-GTA
1 AAGCCTTTGTGGTGAATTCTCTAG-A
** *
10374335 AAGCCTTTGTGACGAAATCTCTAGA
1 AAGCCTTTGTGGTGAATTCTCTAGA
10374360 AAGCCTTTGTGGTGAATT
1 AAGCCTTTGTGGTGAATT
10374378 ACCTGATGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
25 35 0.97
26 1 0.03
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (25 bp):
AAGCCTTTGTGGTGAATTCTCTAGA
Found at i:10378524 original size:21 final size:21
Alignment explanation
Indices: 10378500--10378552 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
10378490 CCCTGCCCAT
10378500 GTGGCCCATACGACCTGGCCC
1 GTGGCCCATACGACCTGGCCC
10378521 GTGGCCCATACGACCTGGCCC
1 GTGGCCCATACGACCTGGCCC
* *
10378542 ATAGCCCATAC
1 GTGGCCCATAC
10378553 ACCCAAAGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.19, C:0.42, G:0.25, T:0.15
Consensus pattern (21 bp):
GTGGCCCATACGACCTGGCCC
Found at i:10380714 original size:43 final size:43
Alignment explanation
Indices: 10380653--10380742 Score: 171
Period size: 43 Copynumber: 2.1 Consensus size: 43
10380643 TCGTAGACTA
10380653 TGTGAGATTCAAAATAAGGTTACATGGTCATGTCCCCAGACCG
1 TGTGAGATTCAAAATAAGGTTACATGGTCATGTCCCCAGACCG
*
10380696 TGTGAGATTCAAAATAAGGTTACATGGTCGTGTCCCCAGACCG
1 TGTGAGATTCAAAATAAGGTTACATGGTCATGTCCCCAGACCG
10380739 TGTG
1 TGTG
10380743 TGGCACATGA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.27
Consensus pattern (43 bp):
TGTGAGATTCAAAATAAGGTTACATGGTCATGTCCCCAGACCG
Found at i:10385983 original size:18 final size:18
Alignment explanation
Indices: 10385960--10385994 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
10385950 AATGTTTCTC
10385960 ATTTC-TCATTTTCTATTT
1 ATTTCTTCA-TTTCTATTT
10385978 ATTTCTTCATTTCTATT
1 ATTTCTTCATTTCTATT
10385995 CATACACGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.66
Consensus pattern (18 bp):
ATTTCTTCATTTCTATTT
Found at i:10387418 original size:14 final size:14
Alignment explanation
Indices: 10387401--10387454 Score: 65
Period size: 14 Copynumber: 3.9 Consensus size: 14
10387391 TAGCCATTTT
10387401 TATTTTTATTTTAA
1 TATTTTTATTTTAA
*
10387415 TATTTTTGTTTTTAA
1 TATTTTT-ATTTTAA
*
10387430 T-TTTTTAATTTAA
1 TATTTTTATTTTAA
*
10387443 TTTTTTTATTTT
1 TATTTTTATTTT
10387455 GTTTGATTCT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
13 6 0.18
14 21 0.62
15 7 0.21
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (14 bp):
TATTTTTATTTTAA
Found at i:10387453 original size:13 final size:13
Alignment explanation
Indices: 10387403--10387453 Score: 57
Period size: 13 Copynumber: 3.7 Consensus size: 13
10387393 GCCATTTTTA
10387403 TTTTTATTTTAATAT
1 TTTTTA-TTTAAT-T
*
10387418 TTTTGTTTTTAATT
1 TTTT-TATTTAATT
*
10387432 TTTTAATTTAATT
1 TTTTTATTTAATT
10387445 TTTTTATTT
1 TTTTTATTT
10387454 TGTTTGATTC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
13 15 0.48
14 5 0.16
15 10 0.32
16 1 0.03
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (13 bp):
TTTTTATTTAATT
Found at i:10390802 original size:16 final size:15
Alignment explanation
Indices: 10390781--10390810 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
10390771 CTATCTTTTA
10390781 TTTTTATTGTTATTTG
1 TTTTTATT-TTATTTG
10390797 TTTTTATTTTATTT
1 TTTTTATTTTATTT
10390811 ATTAAACTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.13, C:0.00, G:0.07, T:0.80
Consensus pattern (15 bp):
TTTTTATTTTATTTG
Found at i:10391730 original size:40 final size:40
Alignment explanation
Indices: 10391686--10391765 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
10391676 GGTTTGGTTA
10391686 GTGGCCTGACTATGTTTCATCATTTGCATTTTTGAATTCT
1 GTGGCCTGACTATGTTTCATCATTTGCATTTTTGAATTCT
10391726 GTGGCCTGACTATGTTTCATCATTTGCATTTTTGAATTCT
1 GTGGCCTGACTATGTTTCATCATTTGCATTTTTGAATTCT
10391766 CTCTTTACTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.47
Consensus pattern (40 bp):
GTGGCCTGACTATGTTTCATCATTTGCATTTTTGAATTCT
Found at i:10393772 original size:76 final size:76
Alignment explanation
Indices: 10393685--10393834 Score: 266
Period size: 77 Copynumber: 2.0 Consensus size: 76
10393675 TGCATTTCAT
10393685 ATTCCTATTTTGCAAGTATTTTTAAATCTGTTTTGG-TTTTTTTTGTTGGTTTTCAATCCACGAA
1 ATTCCTATTTTGCAAGTATTTTTAAATCTGTTTTGGTTTTTTTTTGTTGGTTTTCAATCCACGAA
10393749 GGTAAGGTTGC
66 GGTAAGGTTGC
* *
10393760 ATTCCATATTTTGCAAGTATTTTTCAATCTGTTTTGGTTTTTTTTTGTTTGTTTTCAATCCACGA
1 ATTCC-TATTTTGCAAGTATTTTTAAATCTGTTTTGGTTTTTTTTTGTTGGTTTTCAATCCACGA
10393825 AGGTAAGGTT
65 AGGTAAGGTT
10393835 TATCGCTTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
75 5 0.07
76 30 0.42
77 36 0.51
ACGTcount: A:0.20, C:0.12, G:0.17, T:0.51
Consensus pattern (76 bp):
ATTCCTATTTTGCAAGTATTTTTAAATCTGTTTTGGTTTTTTTTTGTTGGTTTTCAATCCACGAA
GGTAAGGTTGC
Found at i:10394429 original size:16 final size:16
Alignment explanation
Indices: 10394408--10394438 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
10394398 GCATGTTTGA
*
10394408 TATATGTTATATTAAT
1 TATATGCTATATTAAT
10394424 TATATGCTATATTAA
1 TATATGCTATATTAA
10394439 GTATTTTGTA
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:0.39, C:0.03, G:0.06, T:0.52
Consensus pattern (16 bp):
TATATGCTATATTAAT
Found at i:10400373 original size:19 final size:19
Alignment explanation
Indices: 10400349--10400390 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
10400339 ATTTTAACTT
*
10400349 TTAATTAATC-TTAATTAA
1 TTAATTAACCTTTAATTAA
10400367 CTTAATTAACCTTTAATTAA
1 -TTAATTAACCTTTAATTAA
10400387 TTAA
1 TTAA
10400391 CACTAAACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.48
Consensus pattern (19 bp):
TTAATTAACCTTTAATTAA
Found at i:10400384 original size:11 final size:10
Alignment explanation
Indices: 10400349--10400386 Score: 51
Period size: 9 Copynumber: 3.8 Consensus size: 10
10400339 ATTTTAACTT
*
10400349 TTAATTAATC
1 TTAATTAACC
10400359 TTAATTAA-C
1 TTAATTAACC
10400368 TTAATTAACC
1 TTAATTAACC
10400378 TTTAATTAA
1 -TTAATTAA
10400387 TTAACACTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.35
10 9 0.35
11 8 0.31
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (10 bp):
TTAATTAACC
Found at i:10403382 original size:19 final size:19
Alignment explanation
Indices: 10403345--10403382 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
10403335 AAAAATCACA
*
10403345 TTTTTTATATTTAATATAT
1 TTTTTTATATTTAAAATAT
10403364 TTTTTTA-ATTTCAAAATAT
1 TTTTTTATATTT-AAAATAT
10403383 ATAGTGACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTTTTATATTTAAAATAT
Found at i:10403771 original size:19 final size:19
Alignment explanation
Indices: 10403734--10403771 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
10403724 AAAAATCACA
*
10403734 TTTTTTATATTTAATATAT
1 TTTTTTATATTTAAAATAT
10403753 TTTTTTA-ATTTCAAAATAT
1 TTTTTTATATTT-AAAATAT
10403772 ATAGTGACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTTTTATATTTAAAATAT
Found at i:10403804 original size:389 final size:389
Alignment explanation
Indices: 10403087--10403864 Score: 1540
Period size: 389 Copynumber: 2.0 Consensus size: 389
10403077 CCCTTTACCC
10403087 CCAAATAAAAGATCATCCAACAAAAATTTCTAAACATAAATAGTAATAATTTTATTTACATCTAC
1 CCAAATAAAAGATCATCCAACAAAAATTTCTAAACATAAATAGTAATAATTTTATTTACATCTAC
10403152 TATTTATATTATTAAATTAAATTTTACACTTTTTACTATTTATGTTATTGAATCGTTTAATCATA
66 TATTTATATTATTAAATTAAATTTTACACTTTTTACTATTTATGTTATTGAATCGTTTAATCATA
10403217 TTAAATCTTTATAAATTTATGTTAAAATTGAATTATTGAATGATGCCATAAATATTTGTGTTAAA
131 TTAAATCTTTATAAATTTATGTTAAAATTGAATTATTGAATGATGCCATAAATATTTGTGTTAAA
10403282 ATTTTATGTTGGTGTCAATTTCACATTTTATCTTTAAGATAAATTTTATTTAAAAAAATCACATT
196 ATTTTATGTTGGTGTCAATTTCACATTTTATCTTTAAGATAAATTTTATTTAAAAAAATCACATT
10403347 TTTTATATTTAATATATTTTTTTAATTTCAAAATATATAGTGACAAGAATTAGAAGATAATTGAA
261 TTTTATATTTAATATATTTTTTTAATTTCAAAATATATAGTGACAAGAATTAGAAGATAATTGAA
10403412 ACAACTAAGCAAGCAAAGAAGCTAACCCGTATATAAAATATTAATAAATAAATTATGAGGGGAT
326 ACAACTAAGCAAGCAAAGAAGCTAACCCGTATATAAAATATTAATAAATAAATTATGAGGGGAT
10403476 CCAAATAAAAGATCATCCAACAAAAATTTCTAAACATAAATAGTAATAATTTTATTTACATCTAC
1 CCAAATAAAAGATCATCCAACAAAAATTTCTAAACATAAATAGTAATAATTTTATTTACATCTAC
10403541 TATTTATATTATTAAATTAAATTTTACACTTTTTACTATTTATGTTATTGAATCGTTTAATCATA
66 TATTTATATTATTAAATTAAATTTTACACTTTTTACTATTTATGTTATTGAATCGTTTAATCATA
10403606 TTAAATCTTTATAAATTTATGTTAAAATTGAATTATTG-ATGATGCCATAAAATATTTGTGTTAA
131 TTAAATCTTTATAAATTTATGTTAAAATTGAATTATTGAATGATGCCAT-AAATATTTGTGTTAA
10403670 AATTTTATGTTGGTGTCAATTTCACATTTTATCTTTAAGATAAATTTTATTTAAAAAAATCACAT
195 AATTTTATGTTGGTGTCAATTTCACATTTTATCTTTAAGATAAATTTTATTTAAAAAAATCACAT
10403735 TTTTTATATTTAATATATTTTTTTAATTTCAAAATATATAGTGACAAGAATTAGAAGATAATTGA
260 TTTTTATATTTAATATATTTTTTTAATTTCAAAATATATAGTGACAAGAATTAGAAGATAATTGA
10403800 AACAACTAAGCAAGCAAAGAAGCTAACCCGTATATAAAATATTAATAAATAAATTATGAGGGGAT
325 AACAACTAAGCAAGCAAAGAAGCTAACCCGTATATAAAATATTAATAAATAAATTATGAGGGGAT
10403865 GAAAATTAAT
Statistics
Matches: 388, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
388 10 0.03
389 378 0.97
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.41
Consensus pattern (389 bp):
CCAAATAAAAGATCATCCAACAAAAATTTCTAAACATAAATAGTAATAATTTTATTTACATCTAC
TATTTATATTATTAAATTAAATTTTACACTTTTTACTATTTATGTTATTGAATCGTTTAATCATA
TTAAATCTTTATAAATTTATGTTAAAATTGAATTATTGAATGATGCCATAAATATTTGTGTTAAA
ATTTTATGTTGGTGTCAATTTCACATTTTATCTTTAAGATAAATTTTATTTAAAAAAATCACATT
TTTTATATTTAATATATTTTTTTAATTTCAAAATATATAGTGACAAGAATTAGAAGATAATTGAA
ACAACTAAGCAAGCAAAGAAGCTAACCCGTATATAAAATATTAATAAATAAATTATGAGGGGAT
Found at i:10404654 original size:15 final size:15
Alignment explanation
Indices: 10404635--10404677 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
10404625 CTACTCATTT
10404635 TATTTTTAATTTA-A
1 TATTTTTAATTTAGA
*
10404649 TAATTTATAATTTAGA
1 T-ATTTTTAATTTAGA
*
10404665 TATTTTTATTTTA
1 TATTTTTAATTTA
10404678 TTAAAATTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 1 0.04
15 21 0.88
16 2 0.08
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (15 bp):
TATTTTTAATTTAGA
Found at i:10407143 original size:21 final size:21
Alignment explanation
Indices: 10407108--10407158 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
10407098 GAATTTTTTG
* *
10407108 AAAATTATATCAAAATTCTTTT
1 AAAATT-TTTCAAAATTCCTTT
*
10407130 ATAATTTTTCAAAATTCCTTT
1 AAAATTTTTCAAAATTCCTTT
10407151 AAAATTTT
1 AAAATTTT
10407159 AAAAAAATCT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 20 0.80
22 5 0.20
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (21 bp):
AAAATTTTTCAAAATTCCTTT
Found at i:10407164 original size:21 final size:21
Alignment explanation
Indices: 10407119--10407164 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
10407109 AAATTATATC
* * **
10407119 AAAATTCTTTTATAATTTTTC
1 AAAATTCCTTTAAAATTTTAA
10407140 AAAATTCCTTTAAAATTTTAA
1 AAAATTCCTTTAAAATTTTAA
10407161 AAAA
1 AAAA
10407165 ATCTAAAAAG
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:0.46, C:0.09, G:0.00, T:0.46
Consensus pattern (21 bp):
AAAATTCCTTTAAAATTTTAA
Found at i:10415400 original size:16 final size:16
Alignment explanation
Indices: 10415379--10415411 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
10415369 TCATACATTA
10415379 CCTTGACACCTCACTG
1 CCTTGACACCTCACTG
10415395 CCTTGACACCTCACTG
1 CCTTGACACCTCACTG
10415411 C
1 C
10415412 AACATTACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.45, G:0.12, T:0.24
Consensus pattern (16 bp):
CCTTGACACCTCACTG
Found at i:10417386 original size:42 final size:43
Alignment explanation
Indices: 10417327--10417413 Score: 158
Period size: 43 Copynumber: 2.0 Consensus size: 43
10417317 AGATAAATCA
10417327 ATAAATTAAATCCTTTAGAT-AAAAAAACCAAATTCTGTAAGG
1 ATAAATTAAATCCTTTAGATAAAAAAAACCAAATTCTGTAAGG
*
10417369 ATAAATTAAATCCTTTAGATAAAAAAAACCAAATTTTGTAAGG
1 ATAAATTAAATCCTTTAGATAAAAAAAACCAAATTCTGTAAGG
10417412 AT
1 AT
10417414 TTTTTATCTG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
42 20 0.47
43 23 0.53
ACGTcount: A:0.51, C:0.10, G:0.09, T:0.30
Consensus pattern (43 bp):
ATAAATTAAATCCTTTAGATAAAAAAAACCAAATTCTGTAAGG
Found at i:10424598 original size:48 final size:48
Alignment explanation
Indices: 10424520--10424724 Score: 239
Period size: 48 Copynumber: 4.2 Consensus size: 48
10424510 TCGGAATAAA
* * * * * * *
10424520 AACAGATTTCTCGGTAGCCTGCACACAGTCCGTACCACCTTTGTGTGAT
1 AACAGA-TTATCGGTGGCCTACACACAGTCCGTGCCACCCTTGTATCAT
* * * *
10424569 AACAGATTCTCGGTGGCCTACACATAGTCCGTGCCACCCTTATATCTT
1 AACAGATTATCGGTGGCCTACACACAGTCCGTGCCACCCTTGTATCAT
* *
10424617 AACAGGTTATTGGTGGCCTACACACAGTCCGTGCCACCCTTGTATCAT
1 AACAGATTATCGGTGGCCTACACACAGTCCGTGCCACCCTTGTATCAT
* * * *
10424665 AACAGAATATCGGTGGCCTGCACACAGTCCGTGCCACTCTTGTGTCAT
1 AACAGATTATCGGTGGCCTACACACAGTCCGTGCCACCCTTGTATCAT
*
10424713 AACAGAATATCG
1 AACAGATTATCG
10424725 ATGTGCATAG
Statistics
Matches: 135, Mismatches: 21, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
48 129 0.96
49 6 0.04
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (48 bp):
AACAGATTATCGGTGGCCTACACACAGTCCGTGCCACCCTTGTATCAT
Found at i:10430373 original size:48 final size:48
Alignment explanation
Indices: 10430285--10430494 Score: 240
Period size: 48 Copynumber: 4.4 Consensus size: 48
10430275 CATTGTTCAA
* * * * * *
10430285 ATAACAGATTTCTCGGTGGCCTGCACACAGTCCATACCACCTTTGTGTG
1 ATAACAGA-TTATCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTATC
* * * *
10430334 ATAATAGATTCTCGGTGGCCTGCACATAGTCCGTGCCACCCTTATATC
1 ATAACAGATTATCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTATC
* * * *
10430382 TTAACAGGTTATTGGTGGCCTGCACACAGTCTGTGCCACCCTTGTATC
1 ATAACAGATTATCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTATC
* * * *
10430430 ATTACAGAATATCGGTGGCCCGCACACAGTCCGTGCCACCCTTGTGTC
1 ATAACAGATTATCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTATC
*
10430478 ATAACAGAATATCGGTG
1 ATAACAGATTATCGGTG
10430495 CGCATAGTAG
Statistics
Matches: 136, Mismatches: 25, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
48 129 0.95
49 7 0.05
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (48 bp):
ATAACAGATTATCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTATC
Found at i:10432304 original size:49 final size:49
Alignment explanation
Indices: 10432220--10432342 Score: 156
Period size: 49 Copynumber: 2.5 Consensus size: 49
10432210 ACCCTAAAGG
* **
10432220 CCCACATGGTCTGCATGATTTCACACAGCCATGTGCCCCACATGGCCTA
1 CCCACATGGCCTGCATGATTTCACACAGCCATGTGCCCCACACAGCCTA
* * * * *
10432269 CCCATATGGCCTGCATGATTTCATACGGTCGTGTGCCCCACACAGCCTA
1 CCCACATGGCCTGCATGATTTCACACAGCCATGTGCCCCACACAGCCTA
* *
10432318 CCCACACGACCTGCATGATTTCACA
1 CCCACATGGCCTGCATGATTTCACA
10432343 TGGCCGTGGG
Statistics
Matches: 62, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
49 62 1.00
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (49 bp):
CCCACATGGCCTGCATGATTTCACACAGCCATGTGCCCCACACAGCCTA
Found at i:10433402 original size:22 final size:24
Alignment explanation
Indices: 10433362--10433407 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 24
10433352 ATTACATAAC
10433362 TTTTAATTATGTTAAAATTGATTT
1 TTTTAATTATGTTAAAATTGATTT
*
10433386 TTTTAA-TAT-TTATAATTGATTT
1 TTTTAATTATGTTAAAATTGATTT
10433408 AATTAGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 12 0.57
23 3 0.14
24 6 0.29
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.61
Consensus pattern (24 bp):
TTTTAATTATGTTAAAATTGATTT
Found at i:10436018 original size:14 final size:14
Alignment explanation
Indices: 10436001--10436034 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
10435991 ATTGTTAAAC
* *
10436001 TTAAAATATATATT
1 TTAAAATATACATA
10436015 TTAAAATATACATA
1 TTAAAATATACATA
10436029 TTAAAA
1 TTAAAA
10436035 ACATTTATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (14 bp):
TTAAAATATACATA
Found at i:10436223 original size:14 final size:15
Alignment explanation
Indices: 10436204--10436232 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
10436194 AATAATATTT
10436204 TATTA-TTGGTTTTA
1 TATTATTTGGTTTTA
10436218 TATTATTTGGTTTTA
1 TATTATTTGGTTTTA
10436233 ATTTTTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.21, C:0.00, G:0.14, T:0.66
Consensus pattern (15 bp):
TATTATTTGGTTTTA
Found at i:10441619 original size:353 final size:353
Alignment explanation
Indices: 10440969--10441678 Score: 1404
Period size: 353 Copynumber: 2.0 Consensus size: 353
10440959 GGGCATTCAA
10440969 AATA-AGGACACACTGGCATGTCTCAGTCTGTGTCCATGCCCTTGTAACTCACTGACTTGGGTCA
1 AATATAGGACACACTGGCATGTCTCAGTCTGTGTCCATGCCCTTGTAACTCACTGACTTGGGTCA
10441033 CACGGCCAAGCCGCACGCCCGTGTGCTAGGCCGTGTGAGTATACTGACTTGTATTCTTTAGAAGA
66 CACGGCCAAGCCGCACGCCCGTGTGCTAGGCCGTGTGAGTATACTGACTTGTATTCTTTAGAAGA
10441098 TACAGGGGACACACGACCGTGTCACTTGGCCATGTGTCACACACGGCTGAGACACACCCGTGTCT
131 TACAGGGGACACACGACCGTGTCACTTGGCCATGTGTCACACACGGCTGAGACACACCCGTGTCT
10441163 CTACTCATATGAACAAAAATAGGTCATTTTCCAAGCCGCATTTCTCACCCAATTTGGAACCAACC
196 CTACTCATATGAACAAAAATAGGTCATTTTCCAAGCCGCATTTCTCACCCAATTTGGAACCAACC
10441228 TAAACTCAACAATTTGCATATAACCAAGTCATAAATAGGCATCCAAAACAAGCCAGAATCAAGTC
261 TAAACTCAACAATTTGCATATAACCAAGTCATAAATAGGCATCCAAAACAAGCCAGAATCAAGTC
10441293 TTAAACATGTAATATTTCACATACAACC
326 TTAAACATGTAATATTTCACATACAACC
10441321 AATATAGGACACACTGGCATGTCTCAGTCTGTGTCCATGCCCTTGTAACTCACTGACTTGGGTCA
1 AATATAGGACACACTGGCATGTCTCAGTCTGTGTCCATGCCCTTGTAACTCACTGACTTGGGTCA
10441386 CACGGCCAAGCCGCACGCCCGTGTGCTAGGCCGTGTGAGTATACTGACTTGTATTCTTTAGAAGA
66 CACGGCCAAGCCGCACGCCCGTGTGCTAGGCCGTGTGAGTATACTGACTTGTATTCTTTAGAAGA
10441451 TACAGGGGACACACGACCGTGTCACTTGGCCATGTGTCACACACGGCTGAGACACACCCGTGTCT
131 TACAGGGGACACACGACCGTGTCACTTGGCCATGTGTCACACACGGCTGAGACACACCCGTGTCT
*
10441516 CTACTCATATGAACAAAAATAGGTCCTTTTCCAAGCCGCATTTCTCACCCAATTTGGAACCAACC
196 CTACTCATATGAACAAAAATAGGTCATTTTCCAAGCCGCATTTCTCACCCAATTTGGAACCAACC
10441581 TAAACTCAACAATTTGCATATAACCAAGTCATAAATAGGCATCCAAAACAAGCCAGAATCAAGTC
261 TAAACTCAACAATTTGCATATAACCAAGTCATAAATAGGCATCCAAAACAAGCCAGAATCAAGTC
10441646 TTAAACATGTAATATTTCACATACAACC
326 TTAAACATGTAATATTTCACATACAACC
10441674 AATAT
1 AATAT
10441679 GCCTTTAGGC
Statistics
Matches: 356, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
352 4 0.01
353 352 0.99
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (353 bp):
AATATAGGACACACTGGCATGTCTCAGTCTGTGTCCATGCCCTTGTAACTCACTGACTTGGGTCA
CACGGCCAAGCCGCACGCCCGTGTGCTAGGCCGTGTGAGTATACTGACTTGTATTCTTTAGAAGA
TACAGGGGACACACGACCGTGTCACTTGGCCATGTGTCACACACGGCTGAGACACACCCGTGTCT
CTACTCATATGAACAAAAATAGGTCATTTTCCAAGCCGCATTTCTCACCCAATTTGGAACCAACC
TAAACTCAACAATTTGCATATAACCAAGTCATAAATAGGCATCCAAAACAAGCCAGAATCAAGTC
TTAAACATGTAATATTTCACATACAACC
Found at i:10442704 original size:25 final size:25
Alignment explanation
Indices: 10442673--10442734 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 25
10442663 ACAAGTTGTA
10442673 AACGGTAAGCTCCTTCGAGCTAAAT
1 AACGGTAAGCTCCTTCGAGCTAAAT
* * * * *
10442698 AATGGTAAGTTTCTTCTAGCTGAAT
1 AACGGTAAGCTCCTTCGAGCTAAAT
*
10442723 AACGATAAGCTC
1 AACGGTAAGCTC
10442735 ATGCGATCTG
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.29
Consensus pattern (25 bp):
AACGGTAAGCTCCTTCGAGCTAAAT
Found at i:10445297 original size:26 final size:29
Alignment explanation
Indices: 10445259--10445313 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 29
10445249 ATGGACAAGT
10445259 GACACAGGTGTGTGT-C-AG-CCGTGTGG
1 GACACAGGTGTGTGTGCTAGACCGTGTGG
10445285 GACACACGG-GTGTGTGCTAGACCGTGTGG
1 GACACA-GGTGTGTGTGCTAGACCGTGTGG
10445314 AGCCACACAG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
26 12 0.48
27 3 0.12
28 2 0.08
29 8 0.32
ACGTcount: A:0.16, C:0.20, G:0.42, T:0.22
Consensus pattern (29 bp):
GACACAGGTGTGTGTGCTAGACCGTGTGG
Found at i:10445321 original size:30 final size:28
Alignment explanation
Indices: 10445260--10445324 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 28
10445250 TGGACAAGTG
10445260 ACACAGGTGTGTGTCAGCCGTGTGGGAC
1 ACACAGGTGTGTGTCAGCCGTGTGGGAC
* *
10445288 ACACGGGTGTGTG-CTAGACCGTGTGGAGCC
1 ACACAGGTGTGTGTC-AG-CCGTGTGG-GAC
10445318 ACACAGG
1 ACACAGG
10445325 CCAGTTCTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
27 1 0.03
28 14 0.45
29 8 0.26
30 8 0.26
ACGTcount: A:0.20, C:0.23, G:0.38, T:0.18
Consensus pattern (28 bp):
ACACAGGTGTGTGTCAGCCGTGTGGGAC
Found at i:10446258 original size:35 final size:35
Alignment explanation
Indices: 10446209--10446280 Score: 85
Period size: 35 Copynumber: 2.1 Consensus size: 35
10446199 TAAACATACA
*
10446209 TGCTCTGTTTTGTTCTATT-ATGT-TCTGCTCTACTC
1 TGCTCTGTTCTGTTCTATTCA-GTAT-TGCTCTACTC
* *
10446244 TGCTTTGTTCTGTTCTGTTCAGTATTGCTCTACTC
1 TGCTCTGTTCTGTTCTATTCAGTATTGCTCTACTC
10446279 TG
1 TG
10446281 TTCCATCCTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
35 30 0.94
36 2 0.06
ACGTcount: A:0.08, C:0.22, G:0.17, T:0.53
Consensus pattern (35 bp):
TGCTCTGTTCTGTTCTATTCAGTATTGCTCTACTC
Found at i:10448940 original size:29 final size:29
Alignment explanation
Indices: 10448876--10448932 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
10448866 GGCAAGTGAG
* * *
10448876 ACAGGTGTGTGTCAGGCTATGTGGGACAC
1 ACAGGCGTGTGTCAGGCCACGTGGGACAC
*
10448905 ACAGGCGTGTGTCAGGCCGCGTGGGACA
1 ACAGGCGTGTGTCAGGCCACGTGGGACA
10448933 TACGGGCGAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.19, C:0.21, G:0.40, T:0.19
Consensus pattern (29 bp):
ACAGGCGTGTGTCAGGCCACGTGGGACAC
Found at i:10449901 original size:25 final size:25
Alignment explanation
Indices: 10449863--10449922 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
10449853 TAAGCATACA
* *
10449863 TGCTCTGTTCTGTTCTATTA-TGTTC
1 TGCTCTGTTCTGTTC-AGTATTGCTC
*
10449888 TGCTCTGTTGTGTTCAGTATTGCTC
1 TGCTCTGTTCTGTTCAGTATTGCTC
10449913 TGCTCTGTTC
1 TGCTCTGTTC
10449923 CATCCTATTC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 3 0.10
25 27 0.90
ACGTcount: A:0.07, C:0.22, G:0.20, T:0.52
Consensus pattern (25 bp):
TGCTCTGTTCTGTTCAGTATTGCTC
Found at i:10461442 original size:18 final size:18
Alignment explanation
Indices: 10461419--10461770 Score: 238
Period size: 18 Copynumber: 19.4 Consensus size: 18
10461409 GCTATTACAA
* *
10461419 TATATGTATGTGAGCCCT
1 TATATGTATGCGAACCCT
*
10461437 TATATGTATACGAACCCT
1 TATATGTATGCGAACCCT
10461455 TATATGTAT--G----C-
1 TATATGTATGCGAACCCT
10461466 -A-ATGTATGCGAATCCCT
1 TATATGTATGCGAA-CCCT
*
10461483 ATATATGTGTG-GAAACCCT
1 -TATATGTATGCG-AACCCT
* *
10461502 TATATGTATGTGAACCCC
1 TATATGTATGCGAACCCT
*
10461520 TATATGTATAAGTGAACCCT
1 TATATGTAT--GCGAACCCT
**
10461540 TATATGTATAAGAACCCCT
1 TATATGTATGCGAA-CCCT
** *
10461559 ATATATGTATGTAAACTCT
1 -TATATGTATGCGAACCCT
*
10461578 TATATGTATGCGAAGCCT
1 TATATGTATGCGAACCCT
*
10461596 TAGATATGTATGCAAACCCT
1 T--ATATGTATGCGAACCCT
** *
10461616 TATATGTATGTAAACTCT
1 TATATGTATGCGAACCCT
* *
10461634 TATAAGTATGCGAAGCCT
1 TATATGTATGCGAACCCT
*
10461652 TAGATATGTATGCAAACCCT
1 T--ATATGTATGCGAACCCT
** *
10461672 TATATGTATGTAAACTCT
1 TATATGTATGCGAACCCT
* *
10461690 TATAAGTATGCGAAGCCT
1 TATATGTATGCGAACCCT
*
10461708 TAGATATGTATGCAAACCCT
1 T--ATATGTATGCGAACCCT
** *
10461728 TATATGTATATGGACCCT
1 TATATGTATGCGAACCCT
**
10461746 TATGCGTATGCGAACCCT
1 TATATGTATGCGAACCCT
10461764 TATATGT
1 TATATGT
10461771 TTGGGAAACA
Statistics
Matches: 261, Mismatches: 50, Indels: 46
0.73 0.14 0.13
Matches are distributed among these distances:
9 6 0.02
10 1 0.00
11 1 0.00
12 1 0.00
16 2 0.01
18 154 0.59
19 14 0.05
20 82 0.31
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (18 bp):
TATATGTATGCGAACCCT
Found at i:10461544 original size:56 final size:55
Alignment explanation
Indices: 10461467--10461770 Score: 328
Period size: 56 Copynumber: 5.4 Consensus size: 55
10461457 TATGTATGCA
* * * * *
10461467 ATGTATGCGAATCCC-TATATATGTGTGGAAACCCTTATATGTATGTGAACCCCTAT
1 ATGTATGCGAA-CCCTTA-ATATGTATGCAAACCCTTATATGTATGTAAACTCTTAT
* *
10461523 ATGTATAAGTGAACCCTT-ATATGTATAAG-AACCCCTATATATGTATGTAAACTCTTAT
1 ATGTAT--GCGAACCCTTAATATGTAT--GCAAACCCT-TATATGTATGTAAACTCTTAT
*
10461581 ATGTATGCGAAGCCTTAGATATGTATGCAAACCCTTATATGTATGTAAACTCTTAT
1 ATGTATGCGAACCCTTA-ATATGTATGCAAACCCTTATATGTATGTAAACTCTTAT
* *
10461637 AAGTATGCGAAGCCTTAGATATGTATGCAAACCCTTATATGTATGTAAACTCTTAT
1 ATGTATGCGAACCCTTA-ATATGTATGCAAACCCTTATATGTATGTAAACTCTTAT
* * * ** *
10461693 AAGTATGCGAAGCCTTAGATATGTATGCAAACCCTTATATGTATATGGACCCTTAT
1 ATGTATGCGAACCCTTA-ATATGTATGCAAACCCTTATATGTATGTAAACTCTTAT
**
10461749 GCGTATGCGAACCCTT-ATATGT
1 ATGTATGCGAACCCTTAATATGT
10461771 TTGGGAAACA
Statistics
Matches: 222, Mismatches: 17, Indels: 20
0.86 0.07 0.08
Matches are distributed among these distances:
54 6 0.03
56 163 0.73
57 15 0.07
58 38 0.17
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.34
Consensus pattern (55 bp):
ATGTATGCGAACCCTTAATATGTATGCAAACCCTTATATGTATGTAAACTCTTAT
Found at i:10461747 original size:38 final size:36
Alignment explanation
Indices: 10461467--10461770 Score: 248
Period size: 38 Copynumber: 8.1 Consensus size: 36
10461457 TATGTATGCA
* *
10461467 ATGTATGCGAATCCCTATATATGTGTGGAAACCCTTAT
1 ATGTATGCGAA-CCCT-TATATGTATGCAAACCCTTAT
* * **
10461505 ATGTATGTGAACCCCTATATGTATAAGTGAACCCTTAT
1 ATGTATGCGAACCCTTATATGTAT--GCAAACCCTTAT
** * *
10461543 ATGTATAAGAACCCCTATATATGTATGTAAACTCTTAT
1 ATGTATGCGAA-CCCT-TATATGTATGCAAACCCTTAT
*
10461581 ATGTATGCGAAGCCTTAGATATGTATGCAAACCCTTAT
1 ATGTATGCGAACCCTT--ATATGTATGCAAACCCTTAT
** * * * *
10461619 ATGTATGTAAACTCTTATAAGTATGCGAAGCCTTAGAT
1 ATGTATGCGAACCCTTATATGTATGCAAACCCTT--AT
* * *
10461657 ATGTATGCAAACCCTTATATGTATGTAAACTCTTAT
1 ATGTATGCGAACCCTTATATGTATGCAAACCCTTAT
* *
10461693 AAGTATGCGAAGCCTTAGATATGTATGCAAACCCTTAT
1 ATGTATGCGAACCCTT--ATATGTATGCAAACCCTTAT
** * ** *
10461731 ATGTATATGGACCCTTATGCGTATGCGAACCCTTAT
1 ATGTATGCGAACCCTTATATGTATGCAAACCCTTAT
10461767 ATGT
1 ATGT
10461771 TTGGGAAACA
Statistics
Matches: 214, Mismatches: 42, Indels: 22
0.77 0.15 0.08
Matches are distributed among these distances:
36 60 0.28
37 6 0.03
38 136 0.64
39 3 0.01
40 9 0.04
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.34
Consensus pattern (36 bp):
ATGTATGCGAACCCTTATATGTATGCAAACCCTTAT
Found at i:10465805 original size:20 final size:20
Alignment explanation
Indices: 10465780--10465818 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
10465770 TTTTATTTTA
*
10465780 TAGAACTATGGTATAATATT
1 TAGAACCATGGTATAATATT
*
10465800 TAGAACCATGGTCTAATAT
1 TAGAACCATGGTATAATAT
10465819 GTAGTATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.36
Consensus pattern (20 bp):
TAGAACCATGGTATAATATT
Found at i:10468235 original size:12 final size:12
Alignment explanation
Indices: 10468218--10468242 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
10468208 TCCTTCACCC
10468218 TTAAAAAATATA
1 TTAAAAAATATA
10468230 TTAAAAAATATA
1 TTAAAAAATATA
10468242 T
1 T
10468243 CATTTTGTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
TTAAAAAATATA
Found at i:10468520 original size:42 final size:42
Alignment explanation
Indices: 10468461--10468586 Score: 252
Period size: 42 Copynumber: 3.0 Consensus size: 42
10468451 GATAAAAACA
10468461 ATTTAAGTATCGTTGTTTTAATTAGTGGGTAAGCATGACTAT
1 ATTTAAGTATCGTTGTTTTAATTAGTGGGTAAGCATGACTAT
10468503 ATTTAAGTATCGTTGTTTTAATTAGTGGGTAAGCATGACTAT
1 ATTTAAGTATCGTTGTTTTAATTAGTGGGTAAGCATGACTAT
10468545 ATTTAAGTATCGTTGTTTTAATTAGTGGGTAAGCATGACTAT
1 ATTTAAGTATCGTTGTTTTAATTAGTGGGTAAGCATGACTAT
10468587 CTCCATTAAC
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 84 1.00
ACGTcount: A:0.29, C:0.07, G:0.21, T:0.43
Consensus pattern (42 bp):
ATTTAAGTATCGTTGTTTTAATTAGTGGGTAAGCATGACTAT
Found at i:10471486 original size:23 final size:22
Alignment explanation
Indices: 10471460--10471502 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
10471450 TTAATTTTTG
*
10471460 TTAATTATTTATGTTTTGAATAT
1 TTAATTATTTAT-TCTTGAATAT
*
10471483 TTAATTTTTTATTCTTGAAT
1 TTAATTATTTATTCTTGAAT
10471503 TTATTCTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.28, C:0.02, G:0.07, T:0.63
Consensus pattern (22 bp):
TTAATTATTTATTCTTGAATAT
Found at i:10477752 original size:14 final size:15
Alignment explanation
Indices: 10477733--10477763 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
10477723 TAACAAAGGC
10477733 TACAAAAGGAGA-AT
1 TACAAAAGGAGATAT
10477747 TACAAAAGGAGATAT
1 TACAAAAGGAGATAT
10477762 TA
1 TA
10477764 GTACATAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.55, C:0.06, G:0.19, T:0.19
Consensus pattern (15 bp):
TACAAAAGGAGATAT
Found at i:10478882 original size:6 final size:6
Alignment explanation
Indices: 10478871--10478914 Score: 52
Period size: 6 Copynumber: 6.7 Consensus size: 6
10478861 TTACAAAATG
10478871 AAATTT AAATTT AAAATGTTAT AAATTT AAATTT AAATTT AAAT
1 AAATTT AAATTT -AAA--TT-T AAATTT AAATTT AAATTT AAAT
10478915 ATCTTTTCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
6 23 0.68
7 5 0.15
9 5 0.15
10 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (6 bp):
AAATTT
Found at i:10484201 original size:39 final size:43
Alignment explanation
Indices: 10484158--10484267 Score: 129
Period size: 45 Copynumber: 2.6 Consensus size: 43
10484148 TTTTCCATTA
*
10484158 TGCTATTACACCTCTATTCCATT-CAACCAA-ATACA-AGA-T
1 TGCTATTACACCTCTATTCCATTACAACCAACAAACAGAGATT
* ** *
10484197 TGCTATTACGCCTCTATTCCATTACATTCAATCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCATTACAACCAA-CAAACAG-AGATT
10484242 TGCTATTACACCTCTATTCCATTACA
1 TGCTATTACACCTCTATTCCATTACA
10484268 CCTCTATTCC
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
39 22 0.37
40 5 0.08
42 4 0.07
44 2 0.03
45 26 0.44
ACGTcount: A:0.31, C:0.27, G:0.06, T:0.35
Consensus pattern (43 bp):
TGCTATTACACCTCTATTCCATTACAACCAACAAACAGAGATT
Found at i:10484267 original size:16 final size:16
Alignment explanation
Indices: 10484246--10484299 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
10484236 TTGATTTGCT
10484246 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
10484262 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
* *
10484278 ATTACGCCTCTAATCC
1 ATTACACCTCTATTCC
*
10484294 AATACA
1 ATTACA
10484300 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.30, C:0.35, G:0.02, T:0.33
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:10497238 original size:20 final size:22
Alignment explanation
Indices: 10497213--10497253 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
10497203 TAATCTTGAA
10497213 AATTAAA-TC-ATTTATTTAAT
1 AATTAAAGTCAATTTATTTAAT
*
10497233 AATTAAAGTCAATTTTTTTAA
1 AATTAAAGTCAATTTATTTAA
10497254 ATAAAAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 2 0.11
22 9 0.50
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (22 bp):
AATTAAAGTCAATTTATTTAAT
Found at i:10498143 original size:24 final size:24
Alignment explanation
Indices: 10498116--10498165 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
10498106 TTAAAAGTCT
10498116 AAACCCATTAAAATTTAAAACCCA
1 AAACCCATTAAAATTTAAAACCCA
* * *
10498140 AAACCCGTTAATATTTAAAACTCA
1 AAACCCATTAAAATTTAAAACCCA
10498164 AA
1 AA
10498166 TTGATAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.52, C:0.22, G:0.02, T:0.24
Consensus pattern (24 bp):
AAACCCATTAAAATTTAAAACCCA
Found at i:10500020 original size:101 final size:101
Alignment explanation
Indices: 10499879--10500103 Score: 333
Period size: 101 Copynumber: 2.2 Consensus size: 101
10499869 TAAATTGACG
* * * *
10499879 GATAAGACCATAACTGGGTTATGGCACTATGAATATAAGACCATGGTTGGACCATGGCATTGTTT
1 GATAAGACCATAACTGGGTTATGACACTATGAACATAAGACCATGATTGGACCATGGCAGTGTTT
*
10499944 ATATGTAAAACCATAGCTGGGTTATGGCATTCTGAT
66 ATATGTAAAACCATAGCTGGGCTATGGCATTCTGAT
* * * *
10499980 GATAAGACCATAACTGAGTTATGACATTATGAACGTAAGACCGTGATTGGACCATGGCAGTGTTT
1 GATAAGACCATAACTGGGTTATGACACTATGAACATAAGACCATGATTGGACCATGGCAGTGTTT
*
10500045 ATATGTAAGACCATAGCTGGGCTATGGCATTCTGAT
66 ATATGTAAAACCATAGCTGGGCTATGGCATTCTGAT
* * *
10500081 TATAAGACAATAATTGGGTTATG
1 GATAAGACCATAACTGGGTTATG
10500104 GCAATACGAA
Statistics
Matches: 110, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
101 110 1.00
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (101 bp):
GATAAGACCATAACTGGGTTATGACACTATGAACATAAGACCATGATTGGACCATGGCAGTGTTT
ATATGTAAAACCATAGCTGGGCTATGGCATTCTGAT
Found at i:10500161 original size:24 final size:24
Alignment explanation
Indices: 10500112--10500162 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
10500102 TGGCAATACG
* *
10500112 AATGTAAAGGATGAATTGATGGAA
1 AATGTAAAGGATGAATTGACGAAA
10500136 AATGTAAAGGATGAATTGACGAAA
1 AATGTAAAGGATGAATTGACGAAA
10500160 AAT
1 AAT
10500163 TACCTAAGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.49, C:0.02, G:0.25, T:0.24
Consensus pattern (24 bp):
AATGTAAAGGATGAATTGACGAAA
Found at i:10504704 original size:2 final size:2
Alignment explanation
Indices: 10504697--10504743 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
10504687 GGATATTATA
10504697 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
10504739 TG TG T
1 TG TG T
10504744 TCTATTGTTG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:10505074 original size:101 final size:100
Alignment explanation
Indices: 10504855--10505093 Score: 318
Period size: 101 Copynumber: 2.4 Consensus size: 100
10504845 TGAATTGACG
* * *
10504855 GATAAGACCATAACTGGGTTATGG-CACTATGAACGTAAGATCATGGTTGACCATGGTAATGTTT
1 GATAAGACCATAACTGGGTTA-GGACACTATGAATGTAAGACCATGGTTGACCATGGCAATGTTT
* * *
10504919 ATATGTAAGACCATAGTTGGACTATGACATTCTGAT
65 ATATGAAAGACCAAAGCTGGACTATGACATTCTGAT
*
10504955 GATAAGACCATAACTGGGTTAGGACACTATGAATGTAAGACCATGGTTGGACCATGGCAGTGTTT
1 GATAAGACCATAACTGGGTTAGGACACTATGAATGTAAGACCATGGTT-GACCATGGCAATGTTT
* * * *
10505020 ATATGAAAGACCAAAGCTGGGCTATGGCATTTTGTT
65 ATATGAAAGACCAAAGCTGGACTATGACATTCTGAT
* * * *
10505056 GATAAGAACATAATTGGGTTATGACAATATGAATGTAA
1 GATAAGACCATAACTGGGTTAGGACACTATGAATGTAA
10505094 AGGATGAATT
Statistics
Matches: 122, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
99 2 0.02
100 43 0.35
101 77 0.63
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.29
Consensus pattern (100 bp):
GATAAGACCATAACTGGGTTAGGACACTATGAATGTAAGACCATGGTTGACCATGGCAATGTTTA
TATGAAAGACCAAAGCTGGACTATGACATTCTGAT
Found at i:10505136 original size:24 final size:24
Alignment explanation
Indices: 10505087--10505137 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
10505077 TGACAATATG
* *
10505087 AATGTAAAGGATGAATTGATGGAA
1 AATGTAAAGGATGAATTGACGAAA
10505111 AATGTAAAGGATGAATTGACGAAA
1 AATGTAAAGGATGAATTGACGAAA
10505135 AAT
1 AAT
10505138 TACCCAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.49, C:0.02, G:0.25, T:0.24
Consensus pattern (24 bp):
AATGTAAAGGATGAATTGACGAAA
Found at i:10507920 original size:10 final size:10
Alignment explanation
Indices: 10507898--10507971 Score: 77
Period size: 10 Copynumber: 7.9 Consensus size: 10
10507888 CACAAATAAA
*
10507898 CAAAAGTTGT
1 CAAAAGTTAT
*
10507908 CAAAGGTTAT
1 CAAAAGTTAT
10507918 CAAAAG-T-T
1 CAAAAGTTAT
*
10507926 ---AAGGTAT
1 CAAAAGTTAT
*
10507933 CAAAAGTTGT
1 CAAAAGTTAT
10507943 CAAAAGTTAT
1 CAAAAGTTAT
10507953 CAAAAGTTAT
1 CAAAAGTTAT
10507963 CAAAAGTTA
1 CAAAAGTTA
10507972 AGAGATTGTA
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
5 3 0.06
6 1 0.02
7 1 0.02
8 1 0.02
9 1 0.02
10 46 0.87
ACGTcount: A:0.46, C:0.09, G:0.16, T:0.28
Consensus pattern (10 bp):
CAAAAGTTAT
Found at i:10507923 original size:20 final size:20
Alignment explanation
Indices: 10507898--10507971 Score: 86
Period size: 20 Copynumber: 4.0 Consensus size: 20
10507888 CACAAATAAA
*
10507898 CAAAAGTTGTCAAAGGTTAT
1 CAAAAGTTGTCAAAAGTTAT
*
10507918 CAAAAG-T-T---AAGGTAT
1 CAAAAGTTGTCAAAAGTTAT
10507933 CAAAAGTTGTCAAAAGTTAT
1 CAAAAGTTGTCAAAAGTTAT
*
10507953 CAAAAGTTATCAAAAGTTA
1 CAAAAGTTGTCAAAAGTTA
10507972 AGAGATTGTA
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
15 11 0.24
16 1 0.02
17 1 0.02
18 1 0.02
19 1 0.02
20 30 0.67
ACGTcount: A:0.46, C:0.09, G:0.16, T:0.28
Consensus pattern (20 bp):
CAAAAGTTGTCAAAAGTTAT
Found at i:10507935 original size:15 final size:16
Alignment explanation
Indices: 10507910--10507940 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
10507900 AAAGTTGTCA
10507910 AAGGTTATCAAAAGTT
1 AAGGTTATCAAAAGTT
10507926 AAGG-TATCAAAAGTT
1 AAGGTTATCAAAAGTT
10507941 GTCAAAAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.45, C:0.06, G:0.19, T:0.29
Consensus pattern (16 bp):
AAGGTTATCAAAAGTT
Found at i:10509748 original size:3 final size:3
Alignment explanation
Indices: 10509688--10509739 Score: 88
Period size: 3 Copynumber: 17.7 Consensus size: 3
10509678 TATTATTATT
*
10509688 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A-C AAC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
10509735 ATC AT
1 ATC AT
10509740 TTTCATCATT
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
2 2 0.04
3 45 0.96
ACGTcount: A:0.37, C:0.33, G:0.00, T:0.31
Consensus pattern (3 bp):
ATC
Found at i:10519284 original size:3 final size:3
Alignment explanation
Indices: 10519244--10519275 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
10519234 TTACAATATT
10519244 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
10519276 TTTCATCATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:10522167 original size:13 final size:13
Alignment explanation
Indices: 10522135--10522175 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
10522125 AAAACAAGCA
* *
10522135 AAAAAAAAAAAAA
1 AAAAAAGAAAAAG
10522148 AAAAAAGAAAAAG
1 AAAAAAGAAAAAG
*
10522161 AAAAAAGAAGAAG
1 AAAAAAGAAAAAG
10522174 AA
1 AA
10522176 GAAGACTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAAG
Found at i:10522171 original size:16 final size:16
Alignment explanation
Indices: 10522134--10522178 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
10522124 CAAAACAAGC
10522134 AAAAAA-AAAAA-AAA
1 AAAAAAGAAAAAGAAA
10522148 AAAAAAGAAAAAGAAA
1 AAAAAAGAAAAAGAAA
* *
10522164 AAAGAAGAAGAAGAA
1 AAAAAAGAAAAAGAA
10522179 GACTATTTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
14 6 0.22
15 5 0.19
16 16 0.59
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (16 bp):
AAAAAAGAAAAAGAAA
Found at i:10533873 original size:27 final size:27
Alignment explanation
Indices: 10533843--10533897 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
10533833 TTACTATCAA
*
10533843 ATGGTAATCAAGTCTTTTACCATAAAG
1 ATGGTAATCAAGTCATTTACCATAAAG
* *
10533870 ATGGTAATTAAGTCATTTACGATAAAG
1 ATGGTAATCAAGTCATTTACCATAAAG
10533897 A
1 A
10533898 CAAATGACCC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.33
Consensus pattern (27 bp):
ATGGTAATCAAGTCATTTACCATAAAG
Found at i:10541440 original size:78 final size:77
Alignment explanation
Indices: 10541214--10541454 Score: 299
Period size: 78 Copynumber: 3.1 Consensus size: 77
10541204 AATTAAAGGT
* *
10541214 AAATAAAATCCGTTTCAGGATTGATTCCCGTCGTTTAACGATTTTATTCCAAATTTTGTTTTATT
1 AAATAAAATCCGTTTCAGGATTGATTCCC-ACGTTCAACGATTTTATT-CAAATTTTGTTTTATT
* *
10541279 TCGAAAAACAAGTA
64 TCCAAAAACGAGTA
* *
10541293 AAATAAAATCCGTTTCGGGATTGATTCCCATGTTCAACGATTTTATTTCAAATTTTGTTTTATTT
1 AAATAAAATCCGTTTCAGGATTGATTCCCACGTTCAACGATTTTA-TTCAAATTTTGTTTTATTT
10541358 CCAAAAACGAGTA
65 CCAAAAACGAGTA
* * * *
10541371 AAATAAAATCCATTTCAGGATTTATTCCCACCGTTCAACAGA-TTTATT-ACATTTTGATTTTGT
1 AAATAAAATCCGTTTCAGGATTGATTCCCA-CGTTCAAC-GATTTTATTCAAATTTTG-TTTTAT
*
10541434 TGCCAAAAACGAG-A
63 TTCCAAAAACGAGTA
*
10541448 AATTAAA
1 AAATAAA
10541455 TAAAATAAAA
Statistics
Matches: 144, Mismatches: 14, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
77 14 0.10
78 87 0.60
79 41 0.28
80 2 0.01
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (77 bp):
AAATAAAATCCGTTTCAGGATTGATTCCCACGTTCAACGATTTTATTCAAATTTTGTTTTATTTC
CAAAAACGAGTA
Found at i:10541551 original size:74 final size:74
Alignment explanation
Indices: 10541457--10541664 Score: 281
Period size: 84 Copynumber: 2.7 Consensus size: 74
10541447 AAATTAAATA
* *
10541457 AAATAAAATCTATTTCGGGATTTATTCTCGCCGTTTAACAAGATTTTATTTTGTTTCCAAATTAG
1 AAATAAAATCTGTTTCGGGATTTATTCTCGCCATTTAACAAGATTTTATTTTGTTTCCAAATTAG
10541522 AATAGAATT
66 AATAGAATT
*
10541531 AAATAAAATCTGTTTTGGGATTTATTCTCGCCATTTAACAAGATTTTATTTGATTTTATTTTGTT
1 AAATAAAATCTGTTTCGGGATTTATTCTCGCCATTTAAC---A----A---GATTTTATTTTGTT
*
10541596 TCCAAATTAGGATAGAATT
56 TCCAAATTAGAATAGAATT
*
10541615 AAATAAAATCTGTTTCGGGATTTATTCTCGCCATTTAAAAAGATTTTATT
1 AAATAAAATCTGTTTCGGGATTTATTCTCGCCATTTAACAAGATTTTATT
10541665 CGATATTGTT
Statistics
Matches: 118, Mismatches: 6, Indels: 20
0.82 0.04 0.14
Matches are distributed among these distances:
74 45 0.38
77 2 0.02
81 2 0.02
84 69 0.58
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.44
Consensus pattern (74 bp):
AAATAAAATCTGTTTCGGGATTTATTCTCGCCATTTAACAAGATTTTATTTTGTTTCCAAATTAG
AATAGAATT
Found at i:10541599 original size:84 final size:84
Alignment explanation
Indices: 10541498--10541685 Score: 322
Period size: 84 Copynumber: 2.2 Consensus size: 84
10541488 CGTTTAACAA
*
10541498 GATTTTATTTTGTTTCCAAATTAGAATAGAATTAAATAAAATCTGTTTTGGGATTTATTCTCGCC
1 GATTTTATTTTGTTTCCAAATTAGAATAGAATTAAATAAAATCTGTTTCGGGATTTATTCTCGCC
* *
10541563 ATTTAACAAGATTTTATTT
66 ATTTAAAAAGATTTTATTC
*
10541582 GATTTTATTTTGTTTCCAAATTAGGATAGAATTAAATAAAATCTGTTTCGGGATTTATTCTCGCC
1 GATTTTATTTTGTTTCCAAATTAGAATAGAATTAAATAAAATCTGTTTCGGGATTTATTCTCGCC
10541647 ATTTAAAAAGATTTTATTC
66 ATTTAAAAAGATTTTATTC
* *
10541666 GATATTGTTTTGTTTCCAAA
1 GATTTTATTTTGTTTCCAAA
10541686 AAAAGACGTA
Statistics
Matches: 98, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
84 98 1.00
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.46
Consensus pattern (84 bp):
GATTTTATTTTGTTTCCAAATTAGAATAGAATTAAATAAAATCTGTTTCGGGATTTATTCTCGCC
ATTTAAAAAGATTTTATTC
Found at i:10558236 original size:22 final size:23
Alignment explanation
Indices: 10558187--10558237 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
10558177 AAAGACAAGT
*
10558187 GAACAGGAAATATTCTCTAGCAA
1 GAACAGGAAATATTCTCCAGCAA
* *
10558210 AAACAGTAAATATTC-CCAGCAA
1 GAACAGGAAATATTCTCCAGCAA
10558232 GAACAG
1 GAACAG
10558238 ACGCATGAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.47, C:0.20, G:0.16, T:0.18
Consensus pattern (23 bp):
GAACAGGAAATATTCTCCAGCAA
Found at i:10558247 original size:57 final size:58
Alignment explanation
Indices: 10558114--10558248 Score: 179
Period size: 57 Copynumber: 2.4 Consensus size: 58
10558104 AAAAATTGAT
* * *
10558114 GCAAGAAAAGACGAGTGAACATGAAATATTCTCTGACGAAAATAGTAAATATTCCCTA
1 GCAAGAAAAGACGAGTGAACAGGAAATATTCTCTGACAAAAACAGTAAATATTCCCTA
*
10558172 -CAAGAAAAGACAAGTGAACAGGAAATATTCTCT-AGCAAAAACAGTAAATATTCCC-A
1 GCAAGAAAAGACGAGTGAACAGGAAATATTCTCTGA-CAAAAACAGTAAATATTCCCTA
*
10558228 GCAAGAACAGACGCA-TGAACA
1 GCAAGAAAAGACG-AGTGAACA
10558249 TTATATTAAT
Statistics
Matches: 68, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
56 2 0.03
57 65 0.96
58 1 0.01
ACGTcount: A:0.47, C:0.18, G:0.17, T:0.18
Consensus pattern (58 bp):
GCAAGAAAAGACGAGTGAACAGGAAATATTCTCTGACAAAAACAGTAAATATTCCCTA
Found at i:10559194 original size:15 final size:15
Alignment explanation
Indices: 10559174--10559203 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
10559164 CTATGCATGC
*
10559174 AAAATACTAAAGACA
1 AAAATACAAAAGACA
10559189 AAAATACAAAAGACA
1 AAAATACAAAAGACA
10559204 TAATAGTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.13, G:0.07, T:0.10
Consensus pattern (15 bp):
AAAATACAAAAGACA
Found at i:10560252 original size:23 final size:23
Alignment explanation
Indices: 10560192--10560253 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 23
10560182 TTTAAGGAGG
*
10560192 TATAATGCTCTCCTTTTTAATTGATA
1 TATAATGCTC-CC--TTTAAATGATA
10560218 TA-ACA-GCT-CCTTTAAATGATA
1 TATA-ATGCTCCCTTTAAATGATA
10560239 TATAATGCTCCCTTT
1 TATAATGCTCCCTTT
10560254 GTATGTAACT
Statistics
Matches: 31, Mismatches: 1, Indels: 11
0.72 0.02 0.26
Matches are distributed among these distances:
21 13 0.42
22 4 0.13
23 7 0.23
25 4 0.13
26 3 0.10
ACGTcount: A:0.29, C:0.19, G:0.08, T:0.44
Consensus pattern (23 bp):
TATAATGCTCCCTTTAAATGATA
Found at i:10563345 original size:15 final size:14
Alignment explanation
Indices: 10563310--10563348 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
10563300 TGTTTATTAA
*
10563310 TTTCTTAGATTTTT
1 TTTCTTAGTTTTTT
10563324 TTT-TTAGTTTTATT
1 TTTCTTAGTTTT-TT
10563338 TTTCTTAGTTT
1 TTTCTTAGTTT
10563349 CTAATTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 7 0.32
14 8 0.36
15 7 0.32
ACGTcount: A:0.13, C:0.05, G:0.08, T:0.74
Consensus pattern (14 bp):
TTTCTTAGTTTTTT
Found at i:10567697 original size:22 final size:22
Alignment explanation
Indices: 10567672--10567721 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
10567662 GGTGCTAGGG
*
10567672 TGCAGGGATAAGGGT-GGTTGGC
1 TGCAGGAAT-AGGGTAGGTTGGC
*
10567694 TGCAGGAATAGGGTAGTTTGGC
1 TGCAGGAATAGGGTAGGTTGGC
10567716 TGCAGG
1 TGCAGG
10567722 CATTCTGGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 5 0.20
22 20 0.80
ACGTcount: A:0.20, C:0.10, G:0.46, T:0.24
Consensus pattern (22 bp):
TGCAGGAATAGGGTAGGTTGGC
Found at i:10567920 original size:18 final size:17
Alignment explanation
Indices: 10567867--10567931 Score: 62
Period size: 17 Copynumber: 3.6 Consensus size: 17
10567857 ATTAATATCC
10567867 AAATAAGTAATAAATAAT
1 AAATAAGTAA-AAATAAT
10567885 AAAATAA--AATAAAGTAAT
1 -AAATAAGTAA-AAA-TAAT
10567903 AAATAAGGTAAAAATAAT
1 AAATAA-GTAAAAATAAT
*
10567921 AAATAAATAAA
1 AAATAAGTAAA
10567932 TAAATAAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
17 16 0.39
18 14 0.34
19 9 0.22
20 2 0.05
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (17 bp):
AAATAAGTAAAAATAAT
Found at i:10567925 original size:4 final size:4
Alignment explanation
Indices: 10567875--10567939 Score: 53
Period size: 4 Copynumber: 15.5 Consensus size: 4
10567865 CCAAATAAGT
* *
10567875 AATA AAT- AATAA AATAA AATA AAGT- AATA AATA AGGTA AAAA TAATA
1 AATA AATA AAT-A AAT-A AATA AA-TA AATA AATA A-ATA AATA -AATA
10567922 AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AA
10567940 AATTGGATTG
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
3 4 0.08
4 32 0.63
5 15 0.29
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:10567929 original size:26 final size:25
Alignment explanation
Indices: 10567871--10567942 Score: 85
Period size: 25 Copynumber: 2.8 Consensus size: 25
10567861 ATATCCAAAT
*
10567871 AAGTAATAAAT-AATAAAATAAAATA
1 AAGTAATAAATAAATAAAA-ATAATA
*
10567896 AAGTAATAAATAAGGTAAAAATAATA
1 AAGTAATAAATAA-ATAAAAATAATA
10567922 AA-TAAATAAATAAATAAAAAT
1 AAGT-AATAAATAAATAAAAAT
10567943 TGGATTGCCT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
25 19 0.46
26 17 0.41
27 5 0.12
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.24
Consensus pattern (25 bp):
AAGTAATAAATAAATAAAAATAATA
Found at i:10570433 original size:55 final size:55
Alignment explanation
Indices: 10570349--10570460 Score: 215
Period size: 55 Copynumber: 2.0 Consensus size: 55
10570339 TTCAGATGCT
10570349 TGTGGGGATTTTCATTTTGCAACCCACGAAAAGTTGGCAGTAACTGGATTAAACC
1 TGTGGGGATTTTCATTTTGCAACCCACGAAAAGTTGGCAGTAACTGGATTAAACC
*
10570404 TGTGGGGATTTTCTTTTTGCAACCCACGAAAAGTTGGCAGTAACTGGATTAAACC
1 TGTGGGGATTTTCATTTTGCAACCCACGAAAAGTTGGCAGTAACTGGATTAAACC
10570459 TG
1 TG
10570461 ACTTTAACTC
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (55 bp):
TGTGGGGATTTTCATTTTGCAACCCACGAAAAGTTGGCAGTAACTGGATTAAACC
Found at i:10571928 original size:15 final size:14
Alignment explanation
Indices: 10571907--10571942 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
10571897 ATAATCCTTA
*
10571907 ATAATTATCTTAAT
1 ATAATTATCCTAAT
10571921 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
10571936 ATAATTA
1 ATAATTA
10571943 AAATAAAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:10578396 original size:13 final size:13
Alignment explanation
Indices: 10578370--10578421 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 13
10578360 CAACTAGGGT
10578370 AGGAAAAAGAAAA
1 AGGAAAAAGAAAA
10578383 AGGAGAAAAGAAAAA
1 AGGA-AAAAG-AAAA
*
10578398 GAGGAAAAATGTAAA
1 -AGGAAAAA-GAAAA
*
10578413 AGAAAAAAG
1 AGGAAAAAG
10578422 CTGCAAATAG
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
13 5 0.15
14 12 0.36
15 11 0.33
16 5 0.15
ACGTcount: A:0.71, C:0.00, G:0.25, T:0.04
Consensus pattern (13 bp):
AGGAAAAAGAAAA
Found at i:10580578 original size:97 final size:96
Alignment explanation
Indices: 10580413--10580610 Score: 369
Period size: 97 Copynumber: 2.1 Consensus size: 96
10580403 TTAATATGTG
10580413 AATCTAACCGTAAGACTCTACACATATTAACATCTTTTTACTTTAGCCATTATTTTAACTTAAAT
1 AATCTAACCGTAAGACTCTACACATATTAACATCTTTTTACTTTAGCCATTATTTTAACTTAAAT
*
10580478 ATAACTTTGTGGGGAGTTGTTTAATTAAAAT
66 ATAACTTTGTGGGGAGTTATTTAATTAAAAT
*
10580509 AATCTAACCGTAGGACTCTACACATATTAACAATCTTTTTACTTTAGCCATTATTTTAACTTAAA
1 AATCTAACCGTAAGACTCTACACATATTAAC-ATCTTTTTACTTTAGCCATTATTTTAACTTAAA
10580574 TATAACTTTGTGGGGAGTTATTTAATTAAAAT
65 TATAACTTTGTGGGGAGTTATTTAATTAAAAT
10580606 AATCT
1 AATCT
10580611 TGATTGTACA
Statistics
Matches: 99, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
96 30 0.30
97 69 0.70
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (96 bp):
AATCTAACCGTAAGACTCTACACATATTAACATCTTTTTACTTTAGCCATTATTTTAACTTAAAT
ATAACTTTGTGGGGAGTTATTTAATTAAAAT
Found at i:10581822 original size:26 final size:28
Alignment explanation
Indices: 10581764--10581827 Score: 78
Period size: 31 Copynumber: 2.2 Consensus size: 28
10581754 AAATACAACT
*
10581764 ATTAATTATATTTCTCTGTTTTTTTTGCCAC
1 ATTAATTATATTTCTC-GTTTATTTT--CAC
10581795 ATTAATTATATTTCTC-TTTATTTT-AC
1 ATTAATTATATTTCTCGTTTATTTTCAC
10581821 ATTAATT
1 ATTAATT
10581828 TAAAATAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
26 9 0.28
29 7 0.22
31 16 0.50
ACGTcount: A:0.25, C:0.12, G:0.03, T:0.59
Consensus pattern (28 bp):
ATTAATTATATTTCTCGTTTATTTTCAC
Found at i:10582514 original size:9 final size:9
Alignment explanation
Indices: 10582500--10582551 Score: 59
Period size: 9 Copynumber: 5.8 Consensus size: 9
10582490 ATTCAATTTG
*
10582500 GTTAATTCG
1 GTTAATTCA
*
10582509 GGTAATTCA
1 GTTAATTCA
*
10582518 GTTAATTCT
1 GTTAATTCA
*
10582527 GGTAATTCA
1 GTTAATTCA
*
10582536 GTTAATTCG
1 GTTAATTCA
10582545 GTTAATT
1 GTTAATT
10582552 TTTAACCAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 35 1.00
ACGTcount: A:0.27, C:0.10, G:0.19, T:0.44
Consensus pattern (9 bp):
GTTAATTCA
Found at i:10582521 original size:18 final size:18
Alignment explanation
Indices: 10582500--10582551 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
10582490 ATTCAATTTG
10582500 GTTAATTCGGGTAATTCA
1 GTTAATTCGGGTAATTCA
*
10582518 GTTAATTCTGGTAATTCA
1 GTTAATTCGGGTAATTCA
*
10582536 GTTAATTCGGTTAATT
1 GTTAATTCGGGTAATT
10582552 TTTAACCAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.27, C:0.10, G:0.19, T:0.44
Consensus pattern (18 bp):
GTTAATTCGGGTAATTCA
Found at i:10582532 original size:27 final size:27
Alignment explanation
Indices: 10582494--10582552 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
10582484 GTAGTGATTC
*
10582494 AATTTGGTTAATTCGGGTAATTCAGTT
1 AATTTGGTTAATTCAGGTAATTCAGTT
* *
10582521 AATTCTGG-TAATTCAGTTAATTCGGTT
1 AATT-TGGTTAATTCAGGTAATTCAGTT
10582548 AATTT
1 AATTT
10582553 TTAACCAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 1 0.04
27 24 0.86
28 3 0.11
ACGTcount: A:0.27, C:0.08, G:0.19, T:0.46
Consensus pattern (27 bp):
AATTTGGTTAATTCAGGTAATTCAGTT
Found at i:10583617 original size:22 final size:22
Alignment explanation
Indices: 10583586--10583629 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
10583576 TTGCAGAGGT
*
10583586 AATTTTTGCTTCTTCTTCCATC
1 AATTTCTGCTTCTTCTTCCATC
10583608 AATTTCTGCTTCTTCTTCCATC
1 AATTTCTGCTTCTTCTTCCATC
10583630 GTTTTCTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.14, C:0.30, G:0.05, T:0.52
Consensus pattern (22 bp):
AATTTCTGCTTCTTCTTCCATC
Found at i:10583635 original size:22 final size:22
Alignment explanation
Indices: 10583587--10583636 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
10583577 TGCAGAGGTA
10583587 ATTTT-TGCTTCTTCTTCCATC
1 ATTTTCTGCTTCTTCTTCCATC
*
10583608 AATTTCTGCTTCTTCTTCCATC
1 ATTTTCTGCTTCTTCTTCCATC
*
10583630 GTTTTCT
1 ATTTTCT
10583637 TATTTGGTGG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 4 0.16
22 21 0.84
ACGTcount: A:0.10, C:0.28, G:0.06, T:0.56
Consensus pattern (22 bp):
ATTTTCTGCTTCTTCTTCCATC
Found at i:10587353 original size:49 final size:49
Alignment explanation
Indices: 10587296--10587398 Score: 163
Period size: 49 Copynumber: 2.1 Consensus size: 49
10587286 TCATGTGTTA
* *
10587296 TAATTTTATAAAGTCTTGAGCTTTTGATTCATGATATTGA-ACTTAATTT
1 TAATTTTATAAAGTCTTCACCTTTTGATTCATGATATT-ATACTTAATTT
*
10587345 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTATACTTAATTT
1 TAATTTTATAAAGTCTTCACCTTTTGATTCATGATATTATACTTAATTT
10587394 TAATT
1 TAATT
10587399 AGTTTTTTTT
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
48 1 0.02
49 49 0.98
ACGTcount: A:0.31, C:0.09, G:0.10, T:0.50
Consensus pattern (49 bp):
TAATTTTATAAAGTCTTCACCTTTTGATTCATGATATTATACTTAATTT
Found at i:10590159 original size:45 final size:44
Alignment explanation
Indices: 10590076--10590171 Score: 140
Period size: 45 Copynumber: 2.2 Consensus size: 44
10590066 ATTACAACAT
*
10590076 CATTCCATTCAACCAAACACAAGAATACTATTACGCCTCTAGTC
1 CATTACATTCAACCAAACACAAGAATACTATTACGCCTCTAGTC
* *
10590120 CATTACATTCAACCAAACA-ATTGAATTACTATTACGCCTCTATTC
1 CATTACATTCAACCAAACACA-AGAA-TACTATTACGCCTCTAGTC
10590165 CATTACA
1 CATTACA
10590172 GTTCTATTCC
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
43 1 0.02
44 21 0.45
45 25 0.53
ACGTcount: A:0.36, C:0.29, G:0.05, T:0.29
Consensus pattern (44 bp):
CATTACATTCAACCAAACACAAGAATACTATTACGCCTCTAGTC
Found at i:10592332 original size:27 final size:27
Alignment explanation
Indices: 10592293--10592362 Score: 77
Period size: 27 Copynumber: 2.6 Consensus size: 27
10592283 ATTTAATCAG
* * *
10592293 AGTACGCCACAAAGGTGATCCGTACAA
1 AGTATGCCACAAAGGCGATCCATACAA
* * * *
10592320 AGTATGCCCCAAAGGCGATTCATTCAG
1 AGTATGCCACAAAGGCGATCCATACAA
10592347 AGTATGCCACAAAGGC
1 AGTATGCCACAAAGGC
10592363 TGACAAGATG
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.34, C:0.26, G:0.23, T:0.17
Consensus pattern (27 bp):
AGTATGCCACAAAGGCGATCCATACAA
Found at i:10595085 original size:30 final size:31
Alignment explanation
Indices: 10595051--10595116 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 31
10595041 TTTTTTTAAA
* *
10595051 TTTTATTCTAAATTTGCCCCA-TTTTTTCGT
1 TTTTATACTAAATTTGACCCATTTTTTTCGT
* * *
10595081 TTTTA-ACTCAATTTGATCCATTTTTTTTGT
1 TTTTATACTAAATTTGACCCATTTTTTTCGT
10595111 TTTTAT
1 TTTTAT
10595117 CATGACTATG
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
29 11 0.38
30 18 0.62
ACGTcount: A:0.18, C:0.15, G:0.06, T:0.61
Consensus pattern (31 bp):
TTTTATACTAAATTTGACCCATTTTTTTCGT
Found at i:10595174 original size:12 final size:12
Alignment explanation
Indices: 10595157--10595188 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
10595147 TTATTTATTG
10595157 TTATTATTAATA
1 TTATTATTAATA
*
10595169 TTATTATTACTA
1 TTATTATTAATA
10595181 TTATTATT
1 TTATTATT
10595189 TCATTCATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (12 bp):
TTATTATTAATA
Found at i:10600171 original size:16 final size:16
Alignment explanation
Indices: 10600150--10600183 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
10600140 TTTCAGGGAT
10600150 GAATACATACAGAATG
1 GAATACATACAGAATG
10600166 GAATACATACAGAATG
1 GAATACATACAGAATG
10600182 GA
1 GA
10600184 GATTTCGAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.21, T:0.18
Consensus pattern (16 bp):
GAATACATACAGAATG
Found at i:10609695 original size:3 final size:3
Alignment explanation
Indices: 10609687--10609723 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
10609677 AATCAGATCC
10609687 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
10609724 GAGTACCGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:10611966 original size:23 final size:23
Alignment explanation
Indices: 10611922--10611974 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
10611912 ATTACTACTC
*
10611922 TATATACATGCGCATAGATTTTT
1 TATATACATGCACATAGATTTTT
10611945 TATATA-ATGCACATATG-TTTTT
1 TATATACATGCACATA-GATTTTT
10611967 TAGTATAC
1 TA-TATAC
10611975 GTTTATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 15 0.58
23 11 0.42
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.45
Consensus pattern (23 bp):
TATATACATGCACATAGATTTTT
Found at i:10620884 original size:13 final size:13
Alignment explanation
Indices: 10620866--10620894 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
10620856 AAGTGAGAAA
10620866 TGTATGACAACAT
1 TGTATGACAACAT
10620879 TGTATGACAACAT
1 TGTATGACAACAT
10620892 TGT
1 TGT
10620895 GCAAACAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (13 bp):
TGTATGACAACAT
Found at i:10631127 original size:142 final size:134
Alignment explanation
Indices: 10630946--10631206 Score: 344
Period size: 134 Copynumber: 1.9 Consensus size: 134
10630936 TTTTGAGTGC
* *
10630946 TATAAAAATTGGAGTTGAATCAATAAGTCTTAACATTTTCAACCTTATCTATAATTATAAAAAAT
1 TATAAAAATTGGAGTTCAATCAATAAATCTTAACATTTTCAACCTTATCTAT--TTAT-AAAAA-
* * * *
10631011 ATATAAATCAAACATTTTTTTAGTTTTTTCATACAAATCCACTATCATTATTTATTTATTTCTAT
62 AGAT--ATCAAACA-TTTTCTAG-TTTTTCATACAAATCCACAATCACTATTTATTTATTTCTAT
10631076 TATTTTACATGA
123 TATTTTACATGA
* *
10631088 TATAAAAATATTGAGTTCAATCTATAAATC-TAACATTTTCAACCTTATCTATTTATAAAAAAGA
1 TATAAAAAT-TGGAGTTCAATCAATAAATCTTAACATTTTCAACCTTATCTATTTATAAAAAAGA
* *
10631152 TGTCAAACATTTTCTAGTTTTTCATGCAAATCCACAATCACTATTTATTTATTTC
65 TATCAAACATTTTCTAGTTTTTCATACAAATCCACAATCACTATTTATTTATTTC
10631207 CTAATCCAAG
Statistics
Matches: 108, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
134 35 0.32
135 7 0.06
136 7 0.06
138 3 0.03
139 5 0.05
140 4 0.04
142 31 0.29
143 16 0.15
ACGTcount: A:0.38, C:0.14, G:0.05, T:0.43
Consensus pattern (134 bp):
TATAAAAATTGGAGTTCAATCAATAAATCTTAACATTTTCAACCTTATCTATTTATAAAAAAGAT
ATCAAACATTTTCTAGTTTTTCATACAAATCCACAATCACTATTTATTTATTTCTATTATTTTAC
ATGA
Found at i:10632010 original size:23 final size:23
Alignment explanation
Indices: 10631977--10632021 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
10631967 AACTCGAAGT
* * *
10631977 ATAATAGTACTTGATTAAGTTTA
1 ATAATAATACTCGATCAAGTTTA
10632000 ATAATAATACTCGATCAAGTTT
1 ATAATAATACTCGATCAAGTTT
10632022 GAACCCAACT
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:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (23 bp):
ATAATAATACTCGATCAAGTTTA
Found at i:10641325 original size:29 final size:29
Alignment explanation
Indices: 10641283--10641346 Score: 110
Period size: 29 Copynumber: 2.2 Consensus size: 29
10641273 GGGTAAATTG
*
10641283 AAAGATTGAATATTTGAAATTGGCTGGAT
1 AAAGATTAAATATTTGAAATTGGCTGGAT
*
10641312 AAAGATTAAATATTTGAAATTGGTTGGAT
1 AAAGATTAAATATTTGAAATTGGCTGGAT
10641341 AAAGAT
1 AAAGAT
10641347 CAACTTATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.42, C:0.02, G:0.22, T:0.34
Consensus pattern (29 bp):
AAAGATTAAATATTTGAAATTGGCTGGAT
Found at i:10641404 original size:18 final size:18
Alignment explanation
Indices: 10641381--10641419 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
10641371 GATTCTGTAA
10641381 TTAGTTTAAATTTGATCT
1 TTAGTTTAAATTTGATCT
*
10641399 TTAGTTTAAATTTGATTT
1 TTAGTTTAAATTTGATCT
10641417 TTA
1 TTA
10641420 AATTTTGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.28, C:0.03, G:0.10, T:0.59
Consensus pattern (18 bp):
TTAGTTTAAATTTGATCT
Found at i:10644567 original size:5 final size:5
Alignment explanation
Indices: 10644557--10644582 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
10644547 ATAATATTAA
10644557 AAATT AAATT AAATT AAATT AAATT A
1 AAATT AAATT AAATT AAATT AAATT A
10644583 TTATTTAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
AAATT
Found at i:10650297 original size:17 final size:18
Alignment explanation
Indices: 10650271--10650304 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
10650261 CTTATTCGAT
10650271 TTTTTCTTT-CCCTTAGC
1 TTTTTCTTTCCCCTTAGC
*
10650288 TTTTTGTTTCCCCTTAG
1 TTTTTCTTTCCCCTTAG
10650305 AGGACGAAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.06, C:0.26, G:0.09, T:0.59
Consensus pattern (18 bp):
TTTTTCTTTCCCCTTAGC
Found at i:10653056 original size:32 final size:31
Alignment explanation
Indices: 10652947--10653078 Score: 111
Period size: 32 Copynumber: 4.3 Consensus size: 31
10652937 TTAATTACTT
*
10652947 TAATATTAAATT-AATATAATACTGATAAAGA
1 TAATATTAAATTAAATATAATACT-ATTAAGA
* *
10652978 TAAATATTAGATTAAAT-T--TAATATTAAGA
1 T-AATATTAAATTAAATATAATACTATTAAGA
10653007 TAATCACTTTAATATTAAATATAATACTATTAAGA
1 TAAT-A--TTAA-ATTAAATATAATACTATTAAGA
10653042 TAAGTATTAAATTAAAT-TAA-A-TATTAA-A
1 TAA-TATTAAATTAAATATAATACTATTAAGA
10653070 T-ATATTAAA
1 TAATATTAAA
10653079 ATAATATTAT
Statistics
Matches: 86, Mismatches: 5, Indels: 25
0.74 0.04 0.22
Matches are distributed among these distances:
26 7 0.08
27 1 0.01
28 5 0.06
29 14 0.16
30 4 0.05
31 7 0.08
32 25 0.29
33 8 0.09
35 14 0.16
36 1 0.01
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (31 bp):
TAATATTAAATTAAATATAATACTATTAAGA
Found at i:10653084 original size:64 final size:65
Alignment explanation
Indices: 10652959--10653087 Score: 163
Period size: 64 Copynumber: 2.0 Consensus size: 65
10652949 ATATTAAATT
* * ***
10652959 AATATAATACTGATAAAGATAAATATTAGATTAAATTTAATATTAAGATAATCACTTTAATATTA
1 AATATAATACTGATAAAGATAAATATTAAATTAAATTAAATATTAAGATAATCAAAATAATATTA
* * *
10653024 AATATAATACT-ATTAAGATAAGTATTAAATTAAATTAAATATTAA-ATATATTAAAATAATATT
1 AATATAATACTGATAAAGATAAATATTAAATTAAATTAAATATTAAGATA-ATCAAAATAATATT
10653087 A
65 A
10653088 TTTTGGAATA
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
63 3 0.05
64 41 0.75
65 11 0.20
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (65 bp):
AATATAATACTGATAAAGATAAATATTAAATTAAATTAAATATTAAGATAATCAAAATAATATTA
Found at i:10655043 original size:15 final size:15
Alignment explanation
Indices: 10655023--10655060 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
10655013 CTACATCTTT
10655023 TATAATAAT-TTATA
1 TATAATAATATTATA
10655037 GTATAATAATACTTATA
1 -TATAATAATA-TTATA
10655054 TATAATA
1 TATAATA
10655061 GTAATACATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 7 0.33
17 5 0.24
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (15 bp):
TATAATAATATTATA
Found at i:10655087 original size:14 final size:15
Alignment explanation
Indices: 10655068--10655096 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
10655058 ATAGTAATAC
10655068 ATTATATATT-TATT
1 ATTATATATTATATT
10655082 ATTATATATTATATT
1 ATTATATATTATATT
10655097 GCTTGAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
ATTATATATTATATT
Found at i:10655292 original size:30 final size:30
Alignment explanation
Indices: 10655258--10655331 Score: 89
Period size: 30 Copynumber: 2.4 Consensus size: 30
10655248 TATATTATAA
10655258 TAATAGTTATATATGTATTAATA-ATTTTA-G
1 TAATAGTTATATAT-TA-TAATATATTTTATG
10655288 TAATAGTTATATATTATAATATTATTTTATG
1 TAATAGTTATATATTATAATA-TATTTTATG
* *
10655319 TATTAGTAATATA
1 TAATAGTTATATA
10655332 CTAATTTAGT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
28 5 0.13
29 2 0.05
30 20 0.51
31 12 0.31
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (30 bp):
TAATAGTTATATATTATAATATATTTTATG
Done.