Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 259 of 290
Found at i:89258075 original size:44 final size:44
Alignment explanation
Indices: 89257922--89258462 Score: 180
Period size: 44 Copynumber: 12.5 Consensus size: 44
89257912 GATCGAGTCT
* * * *
89257922 TATCTCCCTGAAGTTACAGTGGAGCAGACT-AAG-TAGGCAAGTCT
1 TATCTCCCTGAAGTTGCAGT-GAGCAGATTAAAGCT-GGCAAATCC
* * * *
89257966 TATC-CACCTGAAGTTGCAGTGAGGCAGACTGAAGGTGGCAAATCT
1 TATCTC-CCTGAAGTTGCAGTGA-GCAGATTAAAGCTGGCAAATCC
* *
89258011 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCTGG-TAATCC
1 TATCTCCCTGAAGTTGCAGT-GAGCAGATTAAAGCTGGCAAATCC
* * * * * * *
89258055 TATTTCGCTGAAGTTGCAGTGAGCGGATTAAAACCT--TAGATCT
1 TATCTCCCTGAAGTTGCAGTGAGCAGATT-AAAGCTGGCAAATCC
* ** * * * * * *
89258098 TATCTCTCTGAAGTTGCAAAGAACAGATCACA--T--CTAGTCT
1 TATCTCCCTGAAGTTGCAGTGAGCAGATTAAAGCTGGCAAATCC
* * * *
89258138 TATC-CTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCT
1 TATCTC-CCTGAAGTTGCAGTGA-GCAGATTAAAGCTGGCAAATCC
* * * *
89258183 TATCTCCTTGAAGTTGTAGTGGAGCAGATTAAAGCCGG-TAATCC
1 TATCTCCCTGAAGTTGCAGT-GAGCAGATTAAAGCTGGCAAATCC
* * * * * *
89258227 TATC-CCGCTGAAGTTGTAGT-AGGCGGATTAAAACCT--TATATCT
1 TATCTCC-CTGAAGTTGCAGTGA-GCAGATT-AAAGCTGGCAAATCC
** * * * * *
89258270 TATCTCTTTGAAGTTGCAGAGAGCAGA-T--CGCAT--CTAGTCT
1 TATCTCCCTGAAGTTGCAGTGAGCAGATTAAAGC-TGGCAAATCC
* * * * *
89258310 TATCTCCCTGAAGTTGCAGTGGAACGGACT-AAG-TAAGCAAATCT
1 TATCTCCCTGAAGTTGCAGT-GAGCAGATTAAAGCT-GGCAAATCC
* * * * * *
89258354 TATCTTCCTGAATTTGCAGTGAGGCAGACTGAAGATGGCAAATCT
1 TATCTCCCTGAAGTTGCAGTGA-GCAGATTAAAGCTGGCAAATCC
* * *
89258399 TATCTCCCTGAAGTGGTAGTGGAGCAGATTAAAG-TCGG-TAATCC
1 TATCTCCCTGAAGTTGCAGT-GAGCAGATTAAAGCT-GGCAAATCC
89258443 TATC-CCGCTGAAGTTGCAGT
1 TATCTCC-CTGAAGTTGCAGT
89258463 AGGCGGATTA
Statistics
Matches: 375, Mismatches: 87, Indels: 70
0.70 0.16 0.13
Matches are distributed among these distances:
39 2 0.01
40 42 0.11
41 11 0.03
42 5 0.01
43 71 0.19
44 124 0.33
45 110 0.29
46 10 0.03
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (44 bp):
TATCTCCCTGAAGTTGCAGTGAGCAGATTAAAGCTGGCAAATCC
Found at i:89258209 original size:172 final size:172
Alignment explanation
Indices: 89257961--89258330 Score: 582
Period size: 172 Copynumber: 2.2 Consensus size: 172
89257951 TAAGTAGGCA
* *
89257961 AGTCTTATCCACCTGAAGTTGCAGTGAGGCAGACTGAAGGTGGCAAATCTTATCTCCCTGAAGTT
1 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTT
* **
89258026 ACAGTGGAGCAGATTAAAGCTGGTAATCCTATTTCGCTGAAGTTGCAGT-GAGCGGATTAAAACC
66 ACAGTGGAGCAGATTAAAGCCGGTAATCCTATCCCGCTGAAGTTGCAGTAG-GCGGATTAAAACC
89258090 TTAGATCTTATCTCTCTGAAGTTGCAAAGAACAGATCACATCT
130 TTAGATCTTATCTCTCTGAAGTTGCAAAGAACAGATCACATCT
*
89258133 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCTTGAAGTT
1 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTT
** *
89258198 GTAGTGGAGCAGATTAAAGCCGGTAATCCTATCCCGCTGAAGTTGTAGTAGGCGGATTAAAACCT
66 ACAGTGGAGCAGATTAAAGCCGGTAATCCTATCCCGCTGAAGTTGCAGTAGGCGGATTAAAACCT
* * * * *
89258263 TATATCTTATCTCTTTGAAGTTGCAGAGAGCAGATCGCATCT
131 TAGATCTTATCTCTCTGAAGTTGCAAAGAACAGATCACATCT
89258305 AGTCTTAT-CTCCCTGAAGTTGCAGTG
1 AGTCTTATCCT-CCTGAAGTTGCAGTG
89258331 GAACGGACTA
Statistics
Matches: 182, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
171 2 0.01
172 179 0.98
173 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (172 bp):
AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTT
ACAGTGGAGCAGATTAAAGCCGGTAATCCTATCCCGCTGAAGTTGCAGTAGGCGGATTAAAACCT
TAGATCTTATCTCTCTGAAGTTGCAAAGAACAGATCACATCT
Found at i:89258357 original size:216 final size:216
Alignment explanation
Indices: 89258135--89258543 Score: 728
Period size: 216 Copynumber: 1.9 Consensus size: 216
89258125 TCACATCTAG
* *
89258135 TCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCTTGAAGTTGT
1 TCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTGGT
*
89258200 AGTGGAGCAGATTAAAGCCGGTAATCCTATCCCGCTGAAGTTGTAGTAGGCGGATTAAAACCTTA
66 AGTGGAGCAGATTAAAGCCGGTAATCCTATCCCGCTGAAGTTGCAGTAGGCGGATTAAAACCTTA
* *
89258265 TATCTTATCTCTTTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGT
131 GATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGT
89258330 GGAACGGACTAAGTAAGCAAA
196 GGAACGGACTAAGTAAGCAAA
* *
89258351 TCTTATCTTCCTGAATTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTGGT
1 TCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTGGT
*
89258416 AGTGGAGCAGATTAAAGTCGGTAATCCTATCCCGCTGAAGTTGCAGTAGGCGGATTAAAACCTTA
66 AGTGGAGCAGATTAAAGCCGGTAATCCTATCCCGCTGAAGTTGCAGTAGGCGGATTAAAACCTTA
* *
89258481 GATCTTATCTCTCTGAAGTTGCAGAGAGCGGATCGCATTTAGTCTTATCTCCCTGAAGTTGCA
131 GATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCA
89258544 CCAGGAGCAA
Statistics
Matches: 183, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
216 183 1.00
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (216 bp):
TCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTGGT
AGTGGAGCAGATTAAAGCCGGTAATCCTATCCCGCTGAAGTTGCAGTAGGCGGATTAAAACCTTA
GATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGT
GGAACGGACTAAGTAAGCAAA
Found at i:89258412 original size:172 final size:172
Alignment explanation
Indices: 89257961--89258431 Score: 573
Period size: 172 Copynumber: 2.7 Consensus size: 172
89257951 TAAGTAGGCA
*
89257961 AGTCTTATCCACCTGAAGTTGCAGTGAGGCAGACTGAAGGT-GGCAAATCTTATCTCCCTGAAGT
1 AGTCTTATCCACCTGAAGTTGCAGTGAGGCAGACTGAA-GTAGGCAAATCTTATCTTCCTGAAGT
* * * *
89258025 TACAGTGGAGCAGATTAAAGCTGGTAATCCTATTTCGCTGAAGTTGCAGTGAGCGGATTAAAACC
65 TGCAGTGGAGCAGATTAAAGCTGGTAATCCTATCTCCCTGAAGTTGTAGTGAGCGGATTAAAACC
89258090 TTAGATCTTATCTCTCTGAAGTTGCAAAGAACAGATCACATCT
130 TTAGATCTTATCTCTCTGAAGTTGCAAAGAACAGATCACATCT
*
89258133 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAG-ATGGCAAATCTTATC-TCCTTGAAG
1 AGTCTTATCCACCTGAAGTTGCAGTGAGGCAGACTGAAGTA-GGCAAATCTTATCTTCC-TGAAG
* *
89258196 TTGTAGTGGAGCAGATTAAAGCCGGTAATCCTATC-CCGCTGAAGTTGTAGT-AGGCGGATTAAA
64 TTGCAGTGGAGCAGATTAAAGCTGGTAATCCTATCTCC-CTGAAGTTGTAGTGA-GCGGATTAAA
* * * * *
89258259 ACCTTATATCTTATCTCTTTGAAGTTGCAGAGAGCAGATCGCATCT
127 ACCTTAGATCTTATCTCTCTGAAGTTGCAAAGAACAGATCACATCT
* * * *
89258305 AGTCTTATCTC-CCTGAAGTTGCAGTG-GAACGGACT-AAGTAAGCAAATCTTATCTTCCTGAAT
1 AGTCTTATC-CACCTGAAGTTGCAGTGAG-GCAGACTGAAGTAGGCAAATCTTATCTTCCTGAAG
* * * * * * *
89258367 TTGCAGT-GAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTGGTAGTGGAGCAGATTAA
64 TTGCAGTGGA-GCAGATTAAAGCTGG-TAATCCTATCTCCCTGAAGTTGTAGT-GAGCGGATTAA
89258431 A
126 A
89258432 GTCGGTAATC
Statistics
Matches: 259, Mismatches: 26, Indels: 27
0.83 0.08 0.09
Matches are distributed among these distances:
170 2 0.01
171 42 0.16
172 202 0.78
173 12 0.05
174 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (172 bp):
AGTCTTATCCACCTGAAGTTGCAGTGAGGCAGACTGAAGTAGGCAAATCTTATCTTCCTGAAGTT
GCAGTGGAGCAGATTAAAGCTGGTAATCCTATCTCCCTGAAGTTGTAGTGAGCGGATTAAAACCT
TAGATCTTATCTCTCTGAAGTTGCAAAGAACAGATCACATCT
Found at i:89259936 original size:19 final size:20
Alignment explanation
Indices: 89259895--89259936 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
89259885 GTTTCTATGT
* *
89259895 CATTGTGATATTTATTATTG
1 CATTGTGATATTTAATATAG
*
89259915 CATTGT-ATATTTAATGTAG
1 CATTGTGATATTTAATATAG
89259934 CAT
1 CAT
89259937 CACATCATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.50
Consensus pattern (20 bp):
CATTGTGATATTTAATATAG
Found at i:89263991 original size:19 final size:19
Alignment explanation
Indices: 89263967--89264004 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
89263957 GATTGTACTA
89263967 GTCAAAATGCATCAGACAT
1 GTCAAAATGCATCAGACAT
*
89263986 GTCAAAATGTATCAGACAT
1 GTCAAAATGCATCAGACAT
89264005 AAGTGGATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.18, G:0.16, T:0.24
Consensus pattern (19 bp):
GTCAAAATGCATCAGACAT
Found at i:89266087 original size:13 final size:13
Alignment explanation
Indices: 89266071--89266136 Score: 89
Period size: 13 Copynumber: 5.1 Consensus size: 13
89266061 TTTAAACCAA
89266071 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
* *
89266084 ACTTCTCAAAAGT
1 ACTTTTCAAAAGC
*
89266097 ACTTTTCCACAA-C
1 ACTTTT-CAAAAGC
89266110 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
89266123 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
89266136 A
1 A
89266137 TTACCAAACT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
12 4 0.09
13 37 0.82
14 4 0.09
ACGTcount: A:0.38, C:0.26, G:0.06, T:0.30
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:89266595 original size:17 final size:18
Alignment explanation
Indices: 89266569--89266602 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
89266559 AAATTAGAGA
89266569 ATAAAAAAATAA-AAATC
1 ATAAAAAAATAAGAAATC
*
89266586 ATAAATAAATAAGAAAT
1 ATAAAAAAATAAGAAAT
89266603 AAAAAGTGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (18 bp):
ATAAAAAAATAAGAAATC
Found at i:89267040 original size:19 final size:20
Alignment explanation
Indices: 89267005--89267043 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
89266995 TAAATAACTT
89267005 AAAATACGTAATAAATATAA
1 AAAATACGTAATAAATATAA
*
89267025 AAAATTCGTAAT-AATATAA
1 AAAATACGTAATAAATATAA
89267044 TAATAAGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (20 bp):
AAAATACGTAATAAATATAA
Found at i:89268616 original size:13 final size:13
Alignment explanation
Indices: 89268598--89268622 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
89268588 CAATAACTCC
89268598 AAAAATATTTAAT
1 AAAAATATTTAAT
89268611 AAAAATATTTAA
1 AAAAATATTTAA
89268623 AGGTTCGGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AAAAATATTTAAT
Found at i:89272130 original size:194 final size:194
Alignment explanation
Indices: 89271801--89272190 Score: 780
Period size: 194 Copynumber: 2.0 Consensus size: 194
89271791 TATTTTAAAT
89271801 AATTTAACTAGAGTAAGAGAACAAGTTGGATATGGATAAGTGTATAATAATTTCATGTCTTTAAA
1 AATTTAACTAGAGTAAGAGAACAAGTTGGATATGGATAAGTGTATAATAATTTCATGTCTTTAAA
89271866 AATTGTTAACAAGCCAAAATTTTATTGATGCTTAAAATCTTTCAGCTTCATTTAATTTTTGAAAA
66 AATTGTTAACAAGCCAAAATTTTATTGATGCTTAAAATCTTTCAGCTTCATTTAATTTTTGAAAA
89271931 TATTTTCTATTTTTTAAAAATTAAAAAACATATTTGATAAAGAGGAATAAAATTTTGTTAATGA
131 TATTTTCTATTTTTTAAAAATTAAAAAACATATTTGATAAAGAGGAATAAAATTTTGTTAATGA
89271995 AATTTAACTAGAGTAAGAGAACAAGTTGGATATGGATAAGTGTATAATAATTTCATGTCTTTAAA
1 AATTTAACTAGAGTAAGAGAACAAGTTGGATATGGATAAGTGTATAATAATTTCATGTCTTTAAA
89272060 AATTGTTAACAAGCCAAAATTTTATTGATGCTTAAAATCTTTCAGCTTCATTTAATTTTTGAAAA
66 AATTGTTAACAAGCCAAAATTTTATTGATGCTTAAAATCTTTCAGCTTCATTTAATTTTTGAAAA
89272125 TATTTTCTATTTTTTAAAAATTAAAAAACATATTTGATAAAGAGGAATAAAATTTTGTTAATGA
131 TATTTTCTATTTTTTAAAAATTAAAAAACATATTTGATAAAGAGGAATAAAATTTTGTTAATGA
89272189 AA
1 AA
89272191 ACAGGATTGG
Statistics
Matches: 196, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
194 196 1.00
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.39
Consensus pattern (194 bp):
AATTTAACTAGAGTAAGAGAACAAGTTGGATATGGATAAGTGTATAATAATTTCATGTCTTTAAA
AATTGTTAACAAGCCAAAATTTTATTGATGCTTAAAATCTTTCAGCTTCATTTAATTTTTGAAAA
TATTTTCTATTTTTTAAAAATTAAAAAACATATTTGATAAAGAGGAATAAAATTTTGTTAATGA
Found at i:89298916 original size:75 final size:75
Alignment explanation
Indices: 89298788--89299161 Score: 712
Period size: 75 Copynumber: 5.0 Consensus size: 75
89298778 TCAGTAACAT
89298788 GATTCATTCGACTTGCTACAAAATTAAAAGCCAAGTAAGTCTACCTTCTCCGTCAATCCCCATTC
1 GATTCATTCGACTTGCTACAAAATT-AAAGCCAAGTAAGTCTACCTTCTCCGTCAATCCCCATTC
89298853 CACAAGTTGGG
65 CACAAGTTGGG
89298864 GATTCATTCGACTTGCTACAAAATTAAAGCCAAGTAAGTCTACCTTCTCCGTCAATCCCCATTCC
1 GATTCATTCGACTTGCTACAAAATTAAAGCCAAGTAAGTCTACCTTCTCCGTCAATCCCCATTCC
89298929 ACAAGTTGGG
66 ACAAGTTGGG
89298939 GATTCATTCGACTTGCTACAAAATTAAAGCCAAGTAAGTCTACCTTCTCCGTCAATCCCCATTCC
1 GATTCATTCGACTTGCTACAAAATTAAAGCCAAGTAAGTCTACCTTCTCCGTCAATCCCCATTCC
89299004 ACAAGTTGGG
66 ACAAGTTGGG
89299014 GATTCATTCGACTTGCTACAAAATTAAAGCCAAGTAAGTCTACCTTCTCCGTCAATCCCCATTCC
1 GATTCATTCGACTTGCTACAAAATTAAAGCCAAGTAAGTCTACCTTCTCCGTCAATCCCCATTCC
89299079 ACAAGTTGGG
66 ACAAGTTGGG
* *
89299089 GATTCATTCGAGTTGCTACAAAATTAAAAGCCAAGTAAGTCTACCTTCTCCATCAATCCCCATTC
1 GATTCATTCGACTTGCTACAAAATT-AAAGCCAAGTAAGTCTACCTTCTCCGTCAATCCCCATTC
89299154 CACAAGTT
65 CACAAGTT
89299162 CGGGTCATCC
Statistics
Matches: 295, Mismatches: 2, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
75 224 0.76
76 71 0.24
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.28
Consensus pattern (75 bp):
GATTCATTCGACTTGCTACAAAATTAAAGCCAAGTAAGTCTACCTTCTCCGTCAATCCCCATTCC
ACAAGTTGGG
Found at i:89299969 original size:22 final size:22
Alignment explanation
Indices: 89299915--89299971 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 22
89299905 ATAAAACAAA
* * *
89299915 AACAGCAAAATAGTAGCAATAT
1 AACAACAAAATAGTAGCAAAAC
* * *
89299937 AATAACGAAATGGTAGCAAAAC
1 AACAACAAAATAGTAGCAAAAC
89299959 AACAACAAAATAG
1 AACAACAAAATAG
89299972 CAGTGAAATG
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.58, C:0.14, G:0.14, T:0.14
Consensus pattern (22 bp):
AACAACAAAATAGTAGCAAAAC
Found at i:89306829 original size:6 final size:6
Alignment explanation
Indices: 89306808--89306852 Score: 51
Period size: 6 Copynumber: 8.0 Consensus size: 6
89306798 TCGAAATGGT
* *
89306808 TCAAAA T-AAAA -AAAAA TCAAAA TCAAAA TCAAAA TTAAAA T-AAAA
1 TCAAAA TCAAAA TCAAAA TCAAAA TCAAAA TCAAAA TCAAAA TCAAAA
89306853 AAAAAGAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
5 12 0.34
6 23 0.66
ACGTcount: A:0.73, C:0.09, G:0.00, T:0.18
Consensus pattern (6 bp):
TCAAAA
Found at i:89306829 original size:16 final size:16
Alignment explanation
Indices: 89306808--89306870 Score: 72
Period size: 16 Copynumber: 3.8 Consensus size: 16
89306798 TCGAAATGGT
89306808 TCAAAATAAAAAAAAA
1 TCAAAATAAAAAAAAA
*
89306824 TCAAAATCAAAATCAAAA
1 TCAAAAT-AAAA-AAAAA
*
89306842 TTAAAATAAAAAAAAA
1 TCAAAATAAAAAAAAA
**
89306858 GAAAAATAAAAAA
1 TCAAAATAAAAAA
89306871 TAAAAGTCAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
16 22 0.55
17 8 0.20
18 10 0.25
ACGTcount: A:0.78, C:0.06, G:0.02, T:0.14
Consensus pattern (16 bp):
TCAAAATAAAAAAAAA
Found at i:89306837 original size:12 final size:11
Alignment explanation
Indices: 89306810--89306868 Score: 50
Period size: 11 Copynumber: 5.4 Consensus size: 11
89306800 GAAATGGTTC
*
89306810 AAAAT-AAAAA
1 AAAATCAAAAT
89306820 AAAATCAAAAT
1 AAAATCAAAAT
89306831 CAAAATCAAAATT
1 -AAAATCAAAA-T
*
89306844 AAAAT-AAAAA
1 AAAATCAAAAT
**
89306854 AAAAGAAAAAT
1 AAAATCAAAAT
89306865 AAAA
1 AAAA
89306869 AATAAAAGTC
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
10 9 0.22
11 16 0.39
12 15 0.37
13 1 0.02
ACGTcount: A:0.80, C:0.05, G:0.02, T:0.14
Consensus pattern (11 bp):
AAAATCAAAAT
Found at i:89306853 original size:6 final size:6
Alignment explanation
Indices: 89306810--89306875 Score: 50
Period size: 6 Copynumber: 11.5 Consensus size: 6
89306800 GAAATGGTTC
* * * *
89306810 AAAAT- AAAA-A AAAATC AAAATC AAAATC AAAATT AAAAT- AAAA-A
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
*
89306854 AAAAGA AAAATAA AAAATA AAA
1 AAAATA AAAAT-A AAAATA AAA
89306876 GTCAAAAGCA
Statistics
Matches: 53, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
5 16 0.30
6 31 0.58
7 6 0.11
ACGTcount: A:0.80, C:0.05, G:0.02, T:0.14
Consensus pattern (6 bp):
AAAATA
Found at i:89306857 original size:28 final size:27
Alignment explanation
Indices: 89306808--89306875 Score: 66
Period size: 28 Copynumber: 2.4 Consensus size: 27
89306798 TCGAAATGGT
**
89306808 TCAAAATAAAAAAAAATCAAAATCAAAA
1 TCAAAATAAAAAAAAA-CAAAAGAAAAA
89306836 TCAAAATTAAAATAAAAA-AAAAGAAAAA
1 TCAAAA-TAAAA-AAAAACAAAAGAAAAA
*
89306864 TAAAAAATAAAA
1 T-CAAAATAAAA
89306876 GTCAAAAGCA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
28 20 0.59
29 9 0.26
30 5 0.15
ACGTcount: A:0.78, C:0.06, G:0.01, T:0.15
Consensus pattern (27 bp):
TCAAAATAAAAAAAAACAAAAGAAAAA
Found at i:89306882 original size:28 final size:28
Alignment explanation
Indices: 89306850--89306915 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 28
89306840 AATTAAAATA
* *
89306850 AAAAAAAAGAAAAATAAAAAATAAAAGTC
1 AAAAGAAA-AAAAAGAAAAAATAAAAGTC
* * *
89306879 AAAAGCAAAAAGAGAAAAAATCAAAGTC
1 AAAAGAAAAAAAAGAAAAAATAAAAGTC
*
89306907 AAAACAAAA
1 AAAAGAAAA
89306916 TATGAAAAGA
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
28 24 0.80
29 6 0.20
ACGTcount: A:0.76, C:0.08, G:0.09, T:0.08
Consensus pattern (28 bp):
AAAAGAAAAAAAAGAAAAAATAAAAGTC
Found at i:89307319 original size:12 final size:12
Alignment explanation
Indices: 89307290--89307330 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 12
89307280 ATGAAGTTCA
89307290 AAAAAAAAAGATG
1 AAAAAAAAA-ATG
*
89307303 AAAAATGAAAATG
1 AAAAA-AAAAATG
89307316 AAAAAAAAAATG
1 AAAAAAAAAATG
89307328 AAA
1 AAA
89307331 GAGTAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 9 0.36
13 13 0.52
14 3 0.12
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.10
Consensus pattern (12 bp):
AAAAAAAAAATG
Found at i:89307554 original size:87 final size:87
Alignment explanation
Indices: 89307404--89307952 Score: 737
Period size: 87 Copynumber: 6.3 Consensus size: 87
89307394 AGTTGAAAAC
* *
89307404 CCTGCATTAACAGCGAAGTAGATCAAAAACGAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGT
1 CCTGCATTAACAGCGAAGCAGATCAAAAATGAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGT
*
89307469 TAAAGATAGCATATTTTGCCTT
66 TAAAGATAGCAGATTTTGCCTT
* * *
89307491 CCTACATTAACAGCGAAGCAGATCAAAAATGAAGTCTTGCCTCCATCGGTTGCACTGGAGCTGGT
1 CCTGCATTAACAGCGAAGCAGATCAAAAATGAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGT
* *
89307556 TAAAAATAGTAGATTTTGCCTT
66 TAAAGATAGCAGATTTTGCCTT
* ** *
89307578 CCTGTATTAACAGTAAAGCAGAT-AGACAATGAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGG
1 CCTGCATTAACAGCGAAGCAGATCA-AAAATGAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGG
*
89307642 TTAAAGATAGCATATTTTGCCTT
65 TTAAAGATAGCAGATTTTGCCTT
* * *
89307665 CCTACATTAACAGCGAAGCAGATCAAAAATGAAGTCTTGCCTCCATCGGTTGCAATGGAGCTGGT
1 CCTGCATTAACAGCGAAGCAGATCAAAAATGAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGT
* *
89307730 TAAAAATAGTAGATTTTGCCTT
66 TAAAGATAGCAGATTTTGCCTT
* **
89307752 CCTGTATTAACAGTAAAGCAGAT-AGAAAATGAAGCCTTGCCTCCATCGGTTGCAGTGGAGCT-G
1 CCTGCATTAACAGCGAAGCAGATCA-AAAATGAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGG
* *
89307815 TTAAAG-GAGTAGATTTTGCCTT
65 TTAAAGATAGCAGATTTTGCCTT
* * ** ** *
89307837 CCTGCGTTAACAGCGAAGCAGTTTGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGT
1 CCTGCATTAACAGCGAAGCAGATCAAAAATGAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGT
*
89307902 TAAAGATAGCAGATATTGCCTT
66 TAAAGATAGCAGATTTTGCCTT
* * * *
89307924 CCTGCATTGACAGTGGAGCAGATCGAAAA
1 CCTGCATTAACAGCGAAGCAGATCAAAAA
89307953 CGGTGAATCT
Statistics
Matches: 402, Mismatches: 54, Indels: 12
0.86 0.12 0.03
Matches are distributed among these distances:
85 67 0.17
86 15 0.04
87 319 0.79
88 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (87 bp):
CCTGCATTAACAGCGAAGCAGATCAAAAATGAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGT
TAAAGATAGCAGATTTTGCCTT
Found at i:89307699 original size:174 final size:174
Alignment explanation
Indices: 89307429--89307952 Score: 818
Period size: 174 Copynumber: 3.0 Consensus size: 174
89307419 AAGTAGATCA
*
89307429 AAAACGAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCATATTTTGCCTTCCT
1 AAAATGAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCATATTTTGCCTTCCT
*
89307494 ACATTAACAGCGAAGCAGATCAAAAATGAAGTCTTGCCTCCATCGGTTGCACTGGAGCTGGTTAA
66 ACATTAACAGCGAAGCAGATCAAAAATGAAGTCTTGCCTCCATCGGTTGCAATGGAGCTGGTTAA
89307559 AAATAGTAGATTTTGCCTTCCTGTATTAACAGTAAAGCAGATAG
131 AAATAGTAGATTTTGCCTTCCTGTATTAACAGTAAAGCAGATAG
*
89307603 ACAATGAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCATATTTTGCCTTCCT
1 AAAATGAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCATATTTTGCCTTCCT
89307668 ACATTAACAGCGAAGCAGATCAAAAATGAAGTCTTGCCTCCATCGGTTGCAATGGAGCTGGTTAA
66 ACATTAACAGCGAAGCAGATCAAAAATGAAGTCTTGCCTCCATCGGTTGCAATGGAGCTGGTTAA
89307733 AAATAGTAGATTTTGCCTTCCTGTATTAACAGTAAAGCAGATAG
131 AAATAGTAGATTTTGCCTTCCTGTATTAACAGTAAAGCAGATAG
* * *
89307777 AAAATGAAGCCTTGCCTCCATCGGTTGCAGTGGAGCT-GTTAAAG-GAGTAGATTTTGCCTTCCT
1 AAAATGAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCATATTTTGCCTTCCT
* * * ** ** * * *
89307840 GCGTTAACAGCGAAGCAGTTTGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAA
66 ACATTAACAGCGAAGCAGATCAAAAATGAAGTCTTGCCTCCATCGGTTGCAATGGAGCTGGTTAA
* * * * * ** *
89307905 AGATAGCAGATATTGCCTTCCTGCATTGACAGTGGAGCAGATCG
131 AAATAGTAGATTTTGCCTTCCTGTATTAACAGTAAAGCAGATAG
89307949 AAAA
1 AAAA
89307953 CGGTGAATCT
Statistics
Matches: 325, Mismatches: 25, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
172 111 0.34
173 7 0.02
174 207 0.64
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (174 bp):
AAAATGAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCATATTTTGCCTTCCT
ACATTAACAGCGAAGCAGATCAAAAATGAAGTCTTGCCTCCATCGGTTGCAATGGAGCTGGTTAA
AAATAGTAGATTTTGCCTTCCTGTATTAACAGTAAAGCAGATAG
Found at i:89308006 original size:43 final size:43
Alignment explanation
Indices: 89307957--89308168 Score: 264
Period size: 43 Copynumber: 4.9 Consensus size: 43
89307947 CGAAAACGGT
* *
89307957 GAATCTTATCTTCCCCAGGAGTAGGGAAATAGATCTAAGTGGC
1 GAATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGCGGC
* * *
89308000 GGATCTTATCTTCCCTAGGAGTAGGGAAACAGATCT-AGACGAC
1 GAATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAG-CGGC
* * *
89308043 AAATCTAATCTTCTCCAGGAGTAGGGAAACAGATCTAAGCGGC
1 GAATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGCGGC
* * * *
89308086 GGATCTTATCTGCCCCAAGAGTAGGGAAACAGATCTAAGCGGT
1 GAATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGCGGC
* * * *
89308129 GAATCTTATTTTCCCCATGAGTAGGGAAACAAATTTAAGC
1 GAATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGC
89308169 CACTAGTCCT
Statistics
Matches: 143, Mismatches: 24, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
42 2 0.01
43 139 0.97
44 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (43 bp):
GAATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGCGGC
Found at i:89314138 original size:3 final size:3
Alignment explanation
Indices: 89314130--89314163 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
89314120 TGTTATGACA
89314130 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
89314164 TCTTAAGTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:89320830 original size:28 final size:28
Alignment explanation
Indices: 89320798--89320869 Score: 108
Period size: 28 Copynumber: 2.6 Consensus size: 28
89320788 TTTAATAAGT
*
89320798 TCGCACACTTAGTGCTTAATAATCAAAC
1 TCGCACACTTAGTGCTTAACAATCAAAC
* *
89320826 TCGCACACTTAGTGCTTCACAATTAAAC
1 TCGCACACTTAGTGCTTAACAATCAAAC
*
89320854 TCGCACATTTAGTGCT
1 TCGCACACTTAGTGCT
89320870 AATCTCTTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.31
Consensus pattern (28 bp):
TCGCACACTTAGTGCTTAACAATCAAAC
Found at i:89326166 original size:5 final size:5
Alignment explanation
Indices: 89326156--89326223 Score: 68
Period size: 5 Copynumber: 13.4 Consensus size: 5
89326146 GCAACCCAAT
* *
89326156 TTTTA TTTTA TTATT- TATTA TTTTA TTTTA TTTTA -TTTA CTTTA TTTATTA
1 TTTTA TTTTA TT-TTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA -TT-TTA
*
89326207 CTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TT
89326224 ATTTATTACT
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
4 6 0.11
5 40 0.75
6 4 0.08
7 3 0.06
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:89326189 original size:31 final size:30
Alignment explanation
Indices: 89326156--89326237 Score: 103
Period size: 31 Copynumber: 2.6 Consensus size: 30
89326146 GCAACCCAAT
*
89326156 TTTTATTTTATTATTTATTATTTTATTTTA
1 TTTTATTTTATTATTTATTACTTTATTTTA
89326186 TTTTA-TTTACTTTATTTATTACTTTATTTTA
1 TTTTATTTTA--TTATTTATTACTTTATTTTA
*
89326217 TTTTATTATTTATTACTTATT
1 TTTTA-T-TTTATTATTTATT
89326238 TGGATATTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
29 4 0.09
30 5 0.11
31 24 0.53
32 8 0.18
34 4 0.09
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (30 bp):
TTTTATTTTATTATTTATTACTTTATTTTA
Found at i:89327701 original size:101 final size:101
Alignment explanation
Indices: 89327464--89327826 Score: 618
Period size: 101 Copynumber: 3.6 Consensus size: 101
89327454 TTTAACATGT
* *
89327464 TGGGCTGAGTAACCGGGGTAGGGTGCTTGGCTATTATCTCTCTTCGTGTCAAAACGTTCGATGTG
1 TGGGCTGAGTAACCGGGGTGGGGTGCTTGGCTGTTATCTCTCTTCGTGTCAAAACGTTCGATGTG
89327529 TTCTTAAGAAAAAATTATAAAAAAATTAAGAGTCTGC
66 TTCTTAAGAAAAAATTAT-AAAAAATTAAGAGTCTGC
* * *
89327566 TGGGCTGAGTAACTGGGGTGGGGTGTTTGGTTGTTATCTCTCTTCGTGTCAAAACGTTCGATGTG
1 TGGGCTGAGTAACCGGGGTGGGGTGCTTGGCTGTTATCTCTCTTCGTGTCAAAACGTTCGATGTG
89327631 TTCTTAAGAAAAAATTATAAAAAATTAAGAGTCTGC
66 TTCTTAAGAAAAAATTATAAAAAATTAAGAGTCTGC
* * * * *
89327667 TGGGCTGAGTAACTGCGGTGGGGGGTTTGGTTGTTATCTCTCTTCGTGTCAAAACGTTCGATGTG
1 TGGGCTGAGTAACCGGGGTGGGGTGCTTGGCTGTTATCTCTCTTCGTGTCAAAACGTTCGATGTG
89327732 TTCTTAAGAAAAAATTATAAAAAATTAAGAGTCTGC
66 TTCTTAAGAAAAAATTATAAAAAATTAAGAGTCTGC
*
89327768 TGGGCTGAGTAACCGGGGTGGGGTGCTTGGCTGTTATCTCTCTTCGTGTCAAAAGGTTC
1 TGGGCTGAGTAACCGGGGTGGGGTGCTTGGCTGTTATCTCTCTTCGTGTCAAAACGTTC
89327827 AGTATATTCC
Statistics
Matches: 248, Mismatches: 13, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
101 170 0.69
102 78 0.31
ACGTcount: A:0.25, C:0.14, G:0.28, T:0.33
Consensus pattern (101 bp):
TGGGCTGAGTAACCGGGGTGGGGTGCTTGGCTGTTATCTCTCTTCGTGTCAAAACGTTCGATGTG
TTCTTAAGAAAAAATTATAAAAAATTAAGAGTCTGC
Found at i:89327901 original size:12 final size:13
Alignment explanation
Indices: 89327877--89327911 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
89327867 AAATCAAAAT
*
89327877 AAATAAAACAGAA
1 AAATAAAAAAGAA
89327890 AAA-AAAAAAGAA
1 AAATAAAAAAGAA
89327902 AAATAAAAAA
1 AAATAAAAAA
89327912 ATATAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.86, C:0.03, G:0.06, T:0.06
Consensus pattern (13 bp):
AAATAAAAAAGAA
Found at i:89328492 original size:15 final size:15
Alignment explanation
Indices: 89328467--89328501 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
89328457 GACTCTATTT
*
89328467 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
89328481 TAATTAATATTAAGA
1 TAATTAATATTAAGA
89328496 TAATTA
1 TAATTA
89328502 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:89330152 original size:14 final size:14
Alignment explanation
Indices: 89330130--89330164 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
89330120 GTACCTCGTT
*
89330130 AAAATCTTATTAAG
1 AAAAACTTATTAAG
89330144 AAAAACTTATTAAG
1 AAAAACTTATTAAG
89330158 AAAAACT
1 AAAAACT
89330165 CTATGAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.57, C:0.09, G:0.06, T:0.29
Consensus pattern (14 bp):
AAAAACTTATTAAG
Found at i:89338918 original size:21 final size:21
Alignment explanation
Indices: 89338876--89338918 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
89338866 CTGGGGTAAA
*
89338876 TAATTAATATATAACAATGTT
1 TAATTAATATATAACAAGGTT
* *
89338897 TAATTAATTTATAATAAGGTT
1 TAATTAATATATAACAAGGTT
89338918 T
1 T
89338919 TGTTTGTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (21 bp):
TAATTAATATATAACAAGGTT
Found at i:89340730 original size:17 final size:18
Alignment explanation
Indices: 89340704--89340737 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
89340694 AAATTTGAGA
89340704 ATAAAAAAATAA-AAATC
1 ATAAAAAAATAAGAAATC
*
89340721 ATAAATAAATAAGAAAT
1 ATAAAAAAATAAGAAAT
89340738 AGAAATTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (18 bp):
ATAAAAAAATAAGAAATC
Found at i:89341914 original size:14 final size:15
Alignment explanation
Indices: 89341895--89341928 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
89341885 CCAAATACAA
*
89341895 CCCAAAAC-CCGAAG
1 CCCAAAACACCCAAG
89341909 CCCAAAACACCCAAG
1 CCCAAAACACCCAAG
89341924 CCCAA
1 CCCAA
89341929 TTTCATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.44, C:0.47, G:0.09, T:0.00
Consensus pattern (15 bp):
CCCAAAACACCCAAG
Found at i:89343047 original size:3 final size:3
Alignment explanation
Indices: 89343041--89343101 Score: 68
Period size: 3 Copynumber: 20.0 Consensus size: 3
89343031 TTTTAGTGTC
* * * **
89343041 ATT ATT ATT ATT ATT AAT ATT ATT ATT ATT ATT ATC ATT ACT GCT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
89343089 ATT AATT ATT ATT
1 ATT -ATT ATT ATT
89343102 GGCTTTATTT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
3 46 0.94
4 3 0.06
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:89343362 original size:109 final size:109
Alignment explanation
Indices: 89343172--89343477 Score: 551
Period size: 109 Copynumber: 2.8 Consensus size: 109
89343162 TTAGTTTCNC
*
89343172 TTTT-AAAAACTTTTCAAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAA
1 TTTTCAAAAA-TTTTC-AAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAA
89343236 GGTACTGGGTTTCGATTTCTCGTTCCACTAAATGACTTAATATCCT
64 GGTACTGGGTTTCGATTTCTCGTTCCACTAAATGACTTAATATCCT
89343282 TTTTCAAAAATTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGG
1 TTTTCAAAAATTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGG
89343347 TACTGGGTTTCGATTTCTCGTTCCACTAAATGACTTAATATCCT
66 TACTGGGTTTCGATTTCTCGTTCCACTAAATGACTTAATATCCT
*
89343391 TTTTCAAAAATTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTACCCTAAGG
1 TTTTCAAAAATTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGG
* *
89343456 TGCTGGGTTTTGATTTCTCGTT
66 TACTGGGTTTCGATTTCTCGTT
89343478 TAACCAAACT
Statistics
Matches: 191, Mismatches: 4, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
109 177 0.93
110 9 0.05
111 5 0.03
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (109 bp):
TTTTCAAAAATTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGG
TACTGGGTTTCGATTTCTCGTTCCACTAAATGACTTAATATCCT
Found at i:89348885 original size:88 final size:88
Alignment explanation
Indices: 89348733--89348909 Score: 327
Period size: 88 Copynumber: 2.0 Consensus size: 88
89348723 AAACCAATGA
* *
89348733 GCAGAGAATCTGGAATACAAATAGCACCAAAGGTCATAATCCAGAAACCTGTATCCTTTTCCTAC
1 GCAGAGAATCTGGAATACAAATAGCACCAAAGGTCATAATCCAAAAACCTGTATCCTTTCCCTAC
89348798 AAGGATAGCAAAAAGGTTCCTTG
66 AAGGATAGCAAAAAGGTTCCTTG
*
89348821 GCAGAGAATCTGGAATACAAATAGCACCAAAGGTCATAATCTAAAAACCTGTATCCTTTCCCTAC
1 GCAGAGAATCTGGAATACAAATAGCACCAAAGGTCATAATCCAAAAACCTGTATCCTTTCCCTAC
89348886 AAGGATAGCAAAAAGGTTCCTTG
66 AAGGATAGCAAAAAGGTTCCTTG
89348909 G
1 G
89348910 AATTACGACT
Statistics
Matches: 86, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
88 86 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.23
Consensus pattern (88 bp):
GCAGAGAATCTGGAATACAAATAGCACCAAAGGTCATAATCCAAAAACCTGTATCCTTTCCCTAC
AAGGATAGCAAAAAGGTTCCTTG
Found at i:89353726 original size:88 final size:88
Alignment explanation
Indices: 89353574--89353750 Score: 257
Period size: 88 Copynumber: 2.0 Consensus size: 88
89353564 TCAGCTCAAG
*
89353574 ATCAGACACCATAATTCATCACCATACCTCCCAAAAATGAATGGGGCCGTGGAAGCAGCAAACAA
1 ATCAGACACCACAATTCATCACCATACCTCCCAAAAATGAATGGGGCCGTGGAAGCAGCAAACAA
* *
89353639 AAATATCAAGAAGATTGTAGGGA
66 AAACATCAAGAAAATTGTAGGGA
* * * * * *
89353662 ATCAGACACCACAATTCGTCACCGTATCGT-CCAAAAATGAATGGTGTCGTGGAAGCAGCTAACA
1 ATCAGACACCACAATTCATCACCATA-CCTCCCAAAAATGAATGGGGCCGTGGAAGCAGCAAACA
89353726 AAAACATCAAGAAAATTGTAGGGA
65 AAAACATCAAGAAAATTGTAGGGA
89353750 A
1 A
89353751 AATGACTGAA
Statistics
Matches: 79, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
88 77 0.97
89 2 0.03
ACGTcount: A:0.41, C:0.21, G:0.20, T:0.18
Consensus pattern (88 bp):
ATCAGACACCACAATTCATCACCATACCTCCCAAAAATGAATGGGGCCGTGGAAGCAGCAAACAA
AAACATCAAGAAAATTGTAGGGA
Found at i:89355723 original size:96 final size:96
Alignment explanation
Indices: 89355559--89356920 Score: 1642
Period size: 96 Copynumber: 14.0 Consensus size: 96
89355549 GTAACCATAG
* * * *
89355559 ATTGCAATTAAAAAGATCGAAGCCACAACGGCGAATCTTACTTTCAGGCGATGTATCGAAACAGA
1 ATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTTCAGGCGATGCAGCGGAACAGA
89355624 TTGAAGCTACAACGGCGAGTCTCACTTCCCC
66 TTGAAGCTACAACGGCGAGTCTCACTTCCCC
* * *
89355655 ATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTTCAGGCGATGTATCGAAACAGA
1 ATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTTCAGGCGATGCAGCGGAACAGA
89355720 TTGAAGCTACAACGGCGAGTCTCACTTCCCC
66 TTGAAGCTACAACGGCGAGTCTCACTTCCCC
* * * *
89355751 ATTGCAATTTAAAAGATCGAAGCCACAACGGTGAATCTTACTTCCAGGCGATGCAACGGAACAAA
1 ATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTTCAGGCGATGCAGCGGAACAGA
*
89355816 TTGAAGCTACAACGACGAGTCTCACTTCCCC
66 TTGAAGCTACAACGGCGAGTCTCACTTCCCC
* * * *
89355847 ATTGCAATTTAAAAGATCGAAGCCACAACGGTGAATCTTACTTCCAGGCGATGCAACGGAACAAA
1 ATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTTCAGGCGATGCAGCGGAACAGA
89355912 TTGAAGCTACAACGGCGAGTCTCACTTCCCTAAC
66 TTGAAGCTACAACGGCGAGTCTCACTTCCC---C
* * *
89355946 ATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCCAGGCGATGCAACGGAACAAA
1 ATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTTCAGGCGATGCAGCGGAACAGA
*
89356011 TTGAAGCTACAACGACGAGTCTCACTTCCCC
66 TTGAAGCTACAACGGCGAGTCTCACTTCCCC
* * *
89356042 ATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCCAGGCGATGCAACGGAACATA
1 ATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTTCAGGCGATGCAGCGGAACAGA
*
89356107 TTGAAGCTACAACAGCGAGTCTCACTTCCCCAAC
66 TTGAAGCTACAACGGCGAGTCTCACTT-CCC--C
* * * * ** * * * *
89356141 ATTGC-AGTCAAATAGATTGAAGCTACAATAGCGAGTCTCAC-ATCATTGGCGATGCAACGGAAC
1 ATTGCAATTTAAA-AGATCGAAGCCACAACGGCGAATCTTACTTTCA--GGCGATGCAGCGGAAC
** *
89356204 AGATTGAAGCTACAATAGCG-GATCTTACTTCCCTAAC
63 AGATTGAAGCTACAACGGCGAG-TCTCACTTCCC---C
* * *
89356241 ATTGCAATTAAAAAGATCGAAGCCACAATGGCGAGTCTTACTTTCAGGCGATGCAGCGGAACAGA
1 ATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTTCAGGCGATGCAGCGGAACAGA
89356306 TTGAAGCTACAACGGCGAGTCTCACTTCCCC
66 TTGAAGCTACAACGGCGAGTCTCACTTCCCC
* * * * *
89356337 ATTACAATTAAAAAGATCGAAGCCACAATGGCAAATCTTACTTTCAGGCGATGCAGCGAAACAGA
1 ATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTTCAGGCGATGCAGCGGAACAGA
89356402 TTGAAGCTACAACGGCGAGTCTCACTTCCCC
66 TTGAAGCTACAACGGCGAGTCTCACTTCCCC
* * * * *
89356433 ATTACAATTAAAAAGATCGAAGCCACAATGGCAAATCTTACTTTCAGGCGATGCAGCGAAACAGA
1 ATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTTCAGGCGATGCAGCGGAACAGA
89356498 TTGAAGCTACAACGGCGAGTCTCACTTCCCC
66 TTGAAGCTACAACGGCGAGTCTCACTTCCCC
* * * * *
89356529 ATTACAATTAAAAAGATCGAAGCCACAATGGCAAATCTTACTTTCAGGCGATGCAGCGAAACAGA
1 ATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTTCAGGCGATGCAGCGGAACAGA
*
89356594 TTGAAGCTACAACGGCGAATCTCACTTCCCCGAC
66 TTGAAGCTACAACGGCGAGTCTCACTT-CCC--C
* * * * * * *
89356628 ATTGCAATTTAAAAGATTGAGGCCACGACGGCGGATCTTACTTCCAAGCGAT-CTAGAGGAACAG
1 ATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTTCAGGCGATGC-AGCGGAACAG
* *
89356692 ATTGAAGCTACAATGGCG-GATCTCACTCCCTCGAC
65 ATTGAAGCTACAACGGCGAG-TCTCACTTCC-C--C
* * * * * * **
89356727 ATTGTAATTTAAAAGATTGAGGCCACGACGGC-AGATCTTACTTCCAAGTAATGCAGCGGAACAG
1 ATTGCAATTTAAAAGATCGAAGCCACAACGGCGA-ATCTTACTTTCAGGCGATGCAGCGGAACAG
* * *
89356791 ATTGAAGCTACAATGGCGAATCTCACTCCCCTGAC
65 ATTGAAGCTACAACGGCGAGTCTCACTTCCC---C
* * * * * * *
89356826 ATTGCAA-TTAAAAGATTGAGGCCACAACGGCAAATCTTA-TTTCTAAGCAGGTACAGTGGAACA
1 ATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTTC-AGGC-GATGCAGCGGAACA
* * * *
89356889 GATTGAAGCTACAATGACGAATCTCGCTTCCC
64 GATTGAAGCTACAACGGCGAGTCTCACTTCCC
89356921 TGACATTTTA
Statistics
Matches: 1164, Mismatches: 75, Indels: 51
0.90 0.06 0.04
Matches are distributed among these distances:
96 648 0.56
97 9 0.01
98 43 0.04
99 381 0.33
100 75 0.06
101 8 0.01
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.22
Consensus pattern (96 bp):
ATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTTCAGGCGATGCAGCGGAACAGA
TTGAAGCTACAACGGCGAGTCTCACTTCCCC
Found at i:89357341 original size:14 final size:15
Alignment explanation
Indices: 89357322--89357357 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
89357312 ACCCAAATAC
*
89357322 AGCCCAAAAC-CCGA
1 AGCCCAAAACACCCA
89357336 AGCCCAAAACACCCA
1 AGCCCAAAACACCCA
89357351 AGCCCAA
1 AGCCCAA
89357358 TTTCATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.44, C:0.44, G:0.11, T:0.00
Consensus pattern (15 bp):
AGCCCAAAACACCCA
Found at i:89357690 original size:106 final size:106
Alignment explanation
Indices: 89357505--89357715 Score: 395
Period size: 106 Copynumber: 2.0 Consensus size: 106
89357495 AGAAAGAAGC
*
89357505 AAGGAAAAAATATATATCAAAAACAGTAACAAAAATGGGCTATAAAAGTCGGTTGTAACTCAATT
1 AAGGAAAAAATATATATCAAAAACAGTAACAAAAATGGGCTATAAAAGCCGGTTGTAACTCAATT
89357570 TCAGGGGGTTTTTTTTCTTCTTTTTCCGACCTTTGTAACGT
66 TCAGGGGGTTTTTTTTCTTCTTTTTCCGACCTTTGTAACGT
89357611 AAGGAAAAAATATATATCAAAAACAGTAACAAAAATGGGCTATAAAAGCCGGTTGTAACTCAATT
1 AAGGAAAAAATATATATCAAAAACAGTAACAAAAATGGGCTATAAAAGCCGGTTGTAACTCAATT
* *
89357676 TCAGGGGTTTTTTTTTCTTCTTTTTCTGACCTTTGTAACG
66 TCAGGGGGTTTTTTTTCTTCTTTTTCCGACCTTTGTAACG
89357716 CATATTAGCA
Statistics
Matches: 102, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
106 102 1.00
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (106 bp):
AAGGAAAAAATATATATCAAAAACAGTAACAAAAATGGGCTATAAAAGCCGGTTGTAACTCAATT
TCAGGGGGTTTTTTTTCTTCTTTTTCCGACCTTTGTAACGT
Found at i:89358583 original size:3 final size:3
Alignment explanation
Indices: 89358577--89358637 Score: 68
Period size: 3 Copynumber: 20.0 Consensus size: 3
89358567 TTTTAGTGTC
* * * **
89358577 ATT ATT ATT ATT ATT AAT ATT ATT ATT ATT ATT ATC ATT ACT GCT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
89358625 ATT AATT ATT ATT
1 ATT -ATT ATT ATT
89358638 GGCTTTATTT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
3 46 0.94
4 3 0.06
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:89373042 original size:28 final size:28
Alignment explanation
Indices: 89372944--89373042 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
89372934 CATGAGATTT
* * **
89372944 GCACTAAGTGTGCGGGTTTAAATTGCATA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
*
89372973 GCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
89373001 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
89373029 ACACTAAGTGTGCG
1 GCACTAAGTGTGCG
89373043 GACTTACTAT
Statistics
Matches: 63, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
28 46 0.73
29 17 0.27
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:89375855 original size:23 final size:22
Alignment explanation
Indices: 89375812--89375855 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
89375802 TATAACCCAT
* *
89375812 ACCAAATCATGCCAAATCATAA
1 ACCAAATCATACCAAAACATAA
*
89375834 ACCAAAGTCATACTAAAACATA
1 ACCAAA-TCATACCAAAACATA
89375856 TGTTTCATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.52, C:0.25, G:0.05, T:0.18
Consensus pattern (22 bp):
ACCAAATCATACCAAAACATAA
Found at i:89376692 original size:44 final size:42
Alignment explanation
Indices: 89376551--89376715 Score: 127
Period size: 43 Copynumber: 3.9 Consensus size: 42
89376541 AGCTCGTACA
* ** * * *
89376551 ATGCCAACGTCCCAGATGTGGTCTTACATGTAATCAATTATCG
1 ATGCCAACGTCCCAAACATGGTCTTACACGAAATCAAATA-CG
* * * * *
89376594 ATACC-ACTGTCACAGACAGGGTCTTACACGAAATCAAATATG
1 ATGCCAAC-GTCCCAAACATGGTCTTACACGAAATCAAATACG
*
89376636 ATGCCAATGTCCCAAACATGGTCTTACACGTAAGTATCAAAT-CG
1 ATGCCAACGTCCCAAACATGGTCTTACACG-AA--ATCAAATACG
* ** *
89376680 ATGCCAACGTCCCAGATGTGGTCTTACATGAAATCA
1 ATGCCAACGTCCCAAACATGGTCTTACACGAAATCA
89376716 CATATCGGAA
Statistics
Matches: 97, Mismatches: 20, Indels: 12
0.75 0.16 0.09
Matches are distributed among these distances:
41 4 0.04
42 26 0.27
43 34 0.35
44 26 0.27
45 7 0.07
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (42 bp):
ATGCCAACGTCCCAAACATGGTCTTACACGAAATCAAATACG
Found at i:89377885 original size:26 final size:26
Alignment explanation
Indices: 89377849--89377898 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
89377839 CATATCCAGG
89377849 TATTGTTGTCTCAGAGCATCTTCAAA
1 TATTGTTGTCTCAGAGCATCTTCAAA
89377875 TATTGTTGTCTCAGAGCATCTTCA
1 TATTGTTGTCTCAGAGCATCTTCA
89377899 GGCTCCCACG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (26 bp):
TATTGTTGTCTCAGAGCATCTTCAAA
Found at i:89386676 original size:22 final size:22
Alignment explanation
Indices: 89386648--89386705 Score: 107
Period size: 22 Copynumber: 2.6 Consensus size: 22
89386638 TAATCTGATT
89386648 ATGGCTCTGTGCCAACCTAAAA
1 ATGGCTCTGTGCCAACCTAAAA
89386670 ATGGCTCTGTGCCAACCTAAAA
1 ATGGCTCTGTGCCAACCTAAAA
*
89386692 ATGGCTCTATGCCA
1 ATGGCTCTGTGCCA
89386706 TCTTGACTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (22 bp):
ATGGCTCTGTGCCAACCTAAAA
Found at i:89386897 original size:32 final size:31
Alignment explanation
Indices: 89386802--89386884 Score: 85
Period size: 32 Copynumber: 2.6 Consensus size: 31
89386792 CCCAAGGTTG
* ** *
89386802 TGTGCCAATTATATTACCGTCATTGATGGCTA
1 TGTGCCAATTATAATACCGT-ACCGATGGCTT
** *
89386834 TGTGCCAAACATAATACAGTTACCGATGGCTT
1 TGTGCCAATTATAATACCG-TACCGATGGCTT
89386866 TGTGCCAATTATAATACCG
1 TGTGCCAATTATAATACCG
89386885 CTACGGAAGG
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
32 39 0.98
33 1 0.03
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (31 bp):
TGTGCCAATTATAATACCGTACCGATGGCTT
Found at i:89387129 original size:32 final size:32
Alignment explanation
Indices: 89387093--89387155 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
89387083 TGTCACCGTA
* *
89387093 TTGGGCTTTGGCCCACTT-ATTCTGTTATTGGT
1 TTGGGC-TAGGCCCAATTGATTCTGTTATTGGT
89387125 TTGGGCTAGGCCCAATTGATTCTGTTATTGG
1 TTGGGCTAGGCCCAATTGATTCTGTTATTGG
89387156 CTGTGACCGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 9 0.32
32 19 0.68
ACGTcount: A:0.13, C:0.17, G:0.27, T:0.43
Consensus pattern (32 bp):
TTGGGCTAGGCCCAATTGATTCTGTTATTGGT
Found at i:89392983 original size:30 final size:30
Alignment explanation
Indices: 89392949--89393013 Score: 123
Period size: 30 Copynumber: 2.2 Consensus size: 30
89392939 GAAATGACCA
89392949 CACACGCCCATATGCCAAGGCTGTGTGCCT
1 CACACGCCCATATGCCAAGGCTGTGTGCCT
89392979 CACACGCCCATATGCCAAGGCTGTGTGCCT
1 CACACGCCCATATGCCAAGGCTGTGTGCCT
89393009 -ACACG
1 CACACG
89393014 GTCATCAGAC
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 5 0.14
30 30 0.86
ACGTcount: A:0.22, C:0.37, G:0.23, T:0.18
Consensus pattern (30 bp):
CACACGCCCATATGCCAAGGCTGTGTGCCT
Found at i:89395604 original size:40 final size:40
Alignment explanation
Indices: 89395544--89395684 Score: 169
Period size: 40 Copynumber: 3.5 Consensus size: 40
89395534 CGGATGTAAC
89395544 AACCAGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
1 AACCAGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
* *
89395584 AACCCGCACGGATGCCTTCGGGACTTAACCCGGTTATAAT
1 AACCAGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
* ** * *
89395624 AACTAGCAC-AATTGCCTTC-GGATCTTAGTCCGGATATAGT
1 AACCAGCACGAA-TGCCTTCGGGA-CTTAACCCGGTTATAAT
* *
89395664 AACTAGCACAAATGCCTTCGG
1 AACCAGCACGAATGCCTTCGG
89395685 ATCTTCGTCC
Statistics
Matches: 88, Mismatches: 9, Indels: 7
0.85 0.09 0.07
Matches are distributed among these distances:
39 4 0.05
40 81 0.92
41 3 0.03
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AACCAGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
Found at i:89395685 original size:40 final size:40
Alignment explanation
Indices: 89395534--89395700 Score: 149
Period size: 40 Copynumber: 4.2 Consensus size: 40
89395524 GAATTTGGCT
* * * * **
89395534 CGGATGTAACAACCAGCACGAATGCCTTCGGGA-CTTAACC
1 CGGATATAATAACTAGCACAAATGCCTTC-GGATCTTAGTC
* ** ** **
89395574 CGGTTATAATAACCCGCACGGATGCCTTCGGGA-CTTAACC
1 CGGATATAATAACTAGCACAAATGCCTTC-GGATCTTAGTC
* *
89395614 CGGTTATAATAACTAGCACAATTGCCTTCGGATCTTAGTC
1 CGGATATAATAACTAGCACAAATGCCTTCGGATCTTAGTC
* *
89395654 CGGATATAGTAACTAGCACAAATGCCTTCGGATCTTCGTC
1 CGGATATAATAACTAGCACAAATGCCTTCGGATCTTAGTC
89395694 CGGATAT
1 CGGATAT
89395701 CATCCGAATA
Statistics
Matches: 110, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
39 3 0.03
40 107 0.97
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (40 bp):
CGGATATAATAACTAGCACAAATGCCTTCGGATCTTAGTC
Found at i:89397481 original size:40 final size:40
Alignment explanation
Indices: 89397415--89397490 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
89397405 TAGTGCCTCA
*
89397415 TATAGCCGAAGCTATTCCAATTCGCACACTAAGTGCTATT
1 TATAGCCGAAGCTATTCCAATACGCACACTAAGTGCTATT
**
89397455 TATAGCCGAAGCTATTTTGAA-ACGCACACTAAGTGC
1 TATAGCCGAAGCTA-TTCCAATACGCACACTAAGTGC
89397491 CAAACATAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
40 28 0.88
41 4 0.12
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.28
Consensus pattern (40 bp):
TATAGCCGAAGCTATTCCAATACGCACACTAAGTGCTATT
Found at i:89399714 original size:27 final size:27
Alignment explanation
Indices: 89399684--89399861 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
89399674 ATATTGAGTC
* * * *
89399684 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
89399711 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
89399738 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
89399766 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
89399793 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
89399820 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
89399847 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
89399862 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:89399823 original size:82 final size:81
Alignment explanation
Indices: 89399705--89399860 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
89399695 TGCTATATAA
* *
89399705 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
89399770 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
89399787 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
89399851 CACTTAGTGC
65 CACTTAGTGC
89399861 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:89428857 original size:33 final size:33
Alignment explanation
Indices: 89428812--89428875 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
89428802 AGAAACAGAC
*
89428812 TAGGCCTGAGCCC-ATCACAGAAACAATATCAGG
1 TAGGCCTAAGCCCAAT-ACAGAAACAATATCAGG
* *
89428845 TAGGCCTAAGCCCAATACAGAATCAGTATCA
1 TAGGCCTAAGCCCAATACAGAAACAATATCA
89428876 TATGCAGATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 25 0.93
34 2 0.07
ACGTcount: A:0.38, C:0.27, G:0.19, T:0.17
Consensus pattern (33 bp):
TAGGCCTAAGCCCAATACAGAAACAATATCAGG
Found at i:89436895 original size:13 final size:13
Alignment explanation
Indices: 89436877--89436901 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
89436867 TGAAGGGGGT
89436877 GGCAACCCTAGTA
1 GGCAACCCTAGTA
89436890 GGCAACCCTAGT
1 GGCAACCCTAGT
89436902 TAGAATACTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.32, G:0.24, T:0.16
Consensus pattern (13 bp):
GGCAACCCTAGTA
Found at i:89445348 original size:20 final size:20
Alignment explanation
Indices: 89445323--89445363 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
89445313 CAAGTCATTA
89445323 GGGTTACCAATTTGGTTGCG
1 GGGTTACCAATTTGGTTGCG
89445343 GGGTTACCAATTTGGTTGCG
1 GGGTTACCAATTTGGTTGCG
89445363 G
1 G
89445364 TCCTACATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.15, C:0.15, G:0.37, T:0.34
Consensus pattern (20 bp):
GGGTTACCAATTTGGTTGCG
Found at i:89448277 original size:12 final size:13
Alignment explanation
Indices: 89448254--89448278 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
89448244 TACACCTGCA
89448254 TTTTAAATTTTTT
1 TTTTAAATTTTTT
89448267 TTTTAAATTTTT
1 TTTTAAATTTTT
89448279 AATAAAGCAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTAAATTTTTT
Found at i:89451820 original size:8 final size:8
Alignment explanation
Indices: 89451797--89451838 Score: 66
Period size: 8 Copynumber: 5.0 Consensus size: 8
89451787 TTGGTGTTGG
89451797 TTTTATTTT
1 TTTTA-TTT
89451806 ATTTTATTT
1 -TTTTATTT
89451815 TTTTATTT
1 TTTTATTT
89451823 TTTTATTT
1 TTTTATTT
89451831 TTTTATTT
1 TTTTATTT
89451839 GCTTCAGCGT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
8 24 0.75
9 3 0.09
10 5 0.16
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (8 bp):
TTTTATTT
Found at i:89451977 original size:18 final size:19
Alignment explanation
Indices: 89451956--89451991 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
89451946 TTTTTAAAAA
89451956 ATTTAATT-TTAGTCTTTC
1 ATTTAATTGTTAGTCTTTC
*
89451974 ATTTAATTGTTCGTCTTT
1 ATTTAATTGTTAGTCTTT
89451992 TTAATTTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.19, C:0.11, G:0.08, T:0.61
Consensus pattern (19 bp):
ATTTAATTGTTAGTCTTTC
Found at i:89453642 original size:27 final size:27
Alignment explanation
Indices: 89453611--89453685 Score: 123
Period size: 27 Copynumber: 2.7 Consensus size: 27
89453601 GTACCTTCAT
89453611 AAAATGTCTATGTGGTACTTATATTTG
1 AAAATGTCTATGTGGTACTTATATTTG
89453638 AAAATGTCTATGTGGTACTTATATTTG
1 AAAATGTCTATGTGGTACTTATATTTG
* *
89453665 AAAATGTTCAATGTAGTACTT
1 AAAATG-TCTATGTGGTACTT
89453686 GAACTATTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
27 33 0.73
28 12 0.27
ACGTcount: A:0.32, C:0.08, G:0.17, T:0.43
Consensus pattern (27 bp):
AAAATGTCTATGTGGTACTTATATTTG
Found at i:89453848 original size:23 final size:22
Alignment explanation
Indices: 89453807--89453861 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
89453797 ATATAAAAAC
*
89453807 CTAAA-TAAAAAAATTAAATTAAA
1 CTAAACTAAAAAAATCAAA-T-AA
89453830 CTAAACTAAAAAAA-CAAATAA
1 CTAAACTAAAAAAATCAAATAA
89453851 CTAAATCTAAA
1 CTAAA-CTAAA
89453862 CAACATAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 7 0.24
22 6 0.21
23 8 0.28
24 8 0.28
ACGTcount: A:0.67, C:0.11, G:0.00, T:0.22
Consensus pattern (22 bp):
CTAAACTAAAAAAATCAAATAA
Found at i:89454257 original size:26 final size:26
Alignment explanation
Indices: 89454221--89454272 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
89454211 TGTTGGAACC
89454221 TTGATTTCAAATGAGAAAG-TTTTCGG
1 TTGATTTCAAATGAG-AAGCTTTTCGG
89454247 TTGATTTCAAATGAGAAGCTTTTCGG
1 TTGATTTCAAATGAGAAGCTTTTCGG
89454273 AGAAGATGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 3 0.12
26 22 0.88
ACGTcount: A:0.29, C:0.10, G:0.23, T:0.38
Consensus pattern (26 bp):
TTGATTTCAAATGAGAAGCTTTTCGG
Found at i:89465154 original size:47 final size:47
Alignment explanation
Indices: 89465071--89466791 Score: 3343
Period size: 47 Copynumber: 36.6 Consensus size: 47
89465061 TATTTGAATA
89465071 AATGTGAAAGTGTATATATGTGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATA--TGTGATAAGGCCTAATGGCCGATGTGATG
89465120 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
89465167 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
89465214 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
89465261 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
89465308 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
89465355 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
89465402 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
89465449 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
89465496 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
89465543 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
89465590 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
89465637 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
89465684 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
89465731 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
89465778 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
89465825 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
89465872 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
89465919 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
89465966 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
89466013 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
89466060 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
89466107 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
89466154 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
89466201 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
89466248 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
89466295 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
89466342 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
89466389 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
89466436 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
89466483 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
89466530 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
89466577 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
89466624 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
89466671 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * * *
89466718 AATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
89466765 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
89466792 TCCCGAAGGG
Statistics
Matches: 1660, Mismatches: 12, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
47 1642 0.99
49 18 0.01
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.30
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:89466966 original size:37 final size:37
Alignment explanation
Indices: 89466910--89466988 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
89466900 CCGAGCTCTA
* * *
89466910 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
89466947 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
89466984 AAGAC
1 AAGAC
89466989 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:89468902 original size:43 final size:43
Alignment explanation
Indices: 89468854--89468956 Score: 206
Period size: 43 Copynumber: 2.4 Consensus size: 43
89468844 TTGGTTTTCA
89468854 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
89468897 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
89468940 GCACTAAGTGTGCGGGC
1 GCACTAAGTGTGCGGGC
89468957 TTGAAATGCA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.22, C:0.16, G:0.36, T:0.26
Consensus pattern (43 bp):
GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
Found at i:89468973 original size:29 final size:29
Alignment explanation
Indices: 89468938--89469011 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
89468928 GTTGTGAGAT
* *
89468938 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
89468967 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
89468996 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
89469012 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:89469447 original size:40 final size:40
Alignment explanation
Indices: 89469324--89469599 Score: 290
Period size: 40 Copynumber: 6.9 Consensus size: 40
89469314 TCGAATGATG
** *
89469324 TCCGGGCTAAGTCCCGAAG-GC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCT-AGTGA-TATA
* ** * * *
89469364 TCCGGACTAAGAT-CCGAAG-GCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGAGCATTCATGCTAGTGA-TATA
*
89469404 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
*
89469444 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
* *
89469484 TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
* ** * * *
89469524 TCCGTGCTAAACCCCGAAGAGCATTCGTGCTGGTGTTATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
* * *
89469564 TCCGGGCTAGGTCCCGAAGAGCAATCATGCTGGTGA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA
89469600 CGTGTATTCG
Statistics
Matches: 203, Mismatches: 29, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
39 1 0.00
40 183 0.90
41 19 0.09
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
Found at i:89469540 original size:120 final size:121
Alignment explanation
Indices: 89469324--89469600 Score: 328
Period size: 120 Copynumber: 2.3 Consensus size: 121
89469314 TCGAATGATG
**
89469324 TCCGGGCTAAGTCCCGAAG-GC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCT-AGTGACCATATCCGGACTAAGATCCGAAGGCAT
* * ** *
89469387 TGGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTA
65 TCGTGCGAGTGACTAAATCCGGGCTAAACCCCGAAGAGCATTCATGCTAGTGATATA
** * *
89469444 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA-TGTATCCGGGCTAAGTTCCGAAGAGCAT
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGACCATATCCGGACTAAGATCCGAAG-GCAT
* * * * * *
89469508 TCGTGCTAGTGA-TATATCCGTGCTAAACCCCGAAGAGCATTCGTGCTGGTGTTATA
65 TCGTGCGAGTGACTAAATCCGGGCTAAACCCCGAAGAGCATTCATGCTAGTGATATA
* * *
89469564 TCCGGGCTAGGTCCCGAAGAGCAATCATGCTGGTGAC
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGAC
89469601 GTGTATTCGG
Statistics
Matches: 133, Mismatches: 20, Indels: 7
0.83 0.12 0.04
Matches are distributed among these distances:
120 107 0.80
121 20 0.15
122 6 0.05
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (121 bp):
TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGACCATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTGACTAAATCCGGGCTAAACCCCGAAGAGCATTCATGCTAGTGATATA
Found at i:89473159 original size:47 final size:47
Alignment explanation
Indices: 89473096--89473895 Score: 1528
Period size: 47 Copynumber: 17.0 Consensus size: 47
89473086 ATGATAGTAT
89473096 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
89473143 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
89473190 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
89473237 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
89473284 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
89473331 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
89473378 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
89473425 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
89473472 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
89473519 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
89473566 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
89473613 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
89473660 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
89473707 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
89473754 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
* *
89473801 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAG
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
* * * * * *
89473848 GGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
89473895 G
1 G
89473896 TCCCGAAGGG
Statistics
Matches: 743, Mismatches: 10, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
47 743 1.00
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
Found at i:89474070 original size:37 final size:37
Alignment explanation
Indices: 89474014--89474092 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
89474004 CCGAGCTCTA
* * *
89474014 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
89474051 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
89474088 AAGAC
1 AAGAC
89474093 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:89483518 original size:13 final size:13
Alignment explanation
Indices: 89483500--89483525 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
89483490 GAGAGTTACT
89483500 TGGGTTAGGGACA
1 TGGGTTAGGGACA
89483513 TGGGTTAGGGACA
1 TGGGTTAGGGACA
89483526 CGGGCATGTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.46, T:0.23
Consensus pattern (13 bp):
TGGGTTAGGGACA
Found at i:89492707 original size:28 final size:27
Alignment explanation
Indices: 89492673--89492725 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
89492663 TAGTATCAGG
*
89492673 TGGGCCTTAGCCCATTAACAGAATCAAA
1 TGGGCCTAAGCCCATT-ACAGAATCAAA
* *
89492701 TGGGCCTAATCCCATTATAGAATCA
1 TGGGCCTAAGCCCATTACAGAATCA
89492726 GTATTAGATG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 8 0.36
28 14 0.64
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.25
Consensus pattern (27 bp):
TGGGCCTAAGCCCATTACAGAATCAAA
Found at i:89492901 original size:22 final size:22
Alignment explanation
Indices: 89492876--89492921 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
89492866 ACCAGATCAA
*
89492876 CTCAACACCGTAGACAGAACGG
1 CTCAACACCATAGACAGAACGG
*
89492898 CTCAACACCATAGATAGAACGG
1 CTCAACACCATAGACAGAACGG
89492920 CT
1 CT
89492922 AAAGGCCGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.37, C:0.30, G:0.20, T:0.13
Consensus pattern (22 bp):
CTCAACACCATAGACAGAACGG
Found at i:89495452 original size:28 final size:28
Alignment explanation
Indices: 89495409--89495474 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
89495399 CCATCACAAA
* * *
89495409 AACAGTATCAGGTGGGCCTTAGCCCATT
1 AACAGAATCAGATGGGCCTAAGCCCATT
89495437 AACAGAATCAGATGGGCCTAAGCCCATT
1 AACAGAATCAGATGGGCCTAAGCCCATT
89495465 -ACAGAATCAG
1 AACAGAATCAG
89495475 TATCAGATGC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
27 10 0.29
28 25 0.71
ACGTcount: A:0.33, C:0.24, G:0.23, T:0.20
Consensus pattern (28 bp):
AACAGAATCAGATGGGCCTAAGCCCATT
Found at i:89495643 original size:22 final size:22
Alignment explanation
Indices: 89495615--89495665 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
89495605 CACTAAGTCA
89495615 ACAGAACGACTCAACACCGTAG
1 ACAGAACGACTCAACACCGTAG
*
89495637 ACAGAACGGCTCAACACCGTAG
1 ACAGAACGACTCAACACCGTAG
*
89495659 ATAGAAC
1 ACAGAAC
89495666 TGCTAAAGGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.41, C:0.29, G:0.20, T:0.10
Consensus pattern (22 bp):
ACAGAACGACTCAACACCGTAG
Found at i:89495764 original size:22 final size:25
Alignment explanation
Indices: 89495705--89495765 Score: 65
Period size: 27 Copynumber: 2.5 Consensus size: 25
89495695 CTGCCAGTTA
*
89495705 ACAGAACGGCTATAAGCCATAAGTATC
1 ACAGAACGGCTAAAAGCCAT-A-TATC
*
89495732 ACAGAAAGGCTAAAAGCC-T-TAT-
1 ACAGAACGGCTAAAAGCCATATATC
89495754 ACAGAACGGCTA
1 ACAGAACGGCTA
89495766 CAGGCCGTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
22 11 0.35
23 3 0.10
26 1 0.03
27 16 0.52
ACGTcount: A:0.43, C:0.21, G:0.20, T:0.16
Consensus pattern (25 bp):
ACAGAACGGCTAAAAGCCATATATC
Found at i:89511140 original size:18 final size:19
Alignment explanation
Indices: 89511105--89511140 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
89511095 ATTCTAACTC
89511105 TATCTCACAATAATTAAAA
1 TATCTCACAATAATTAAAA
*
89511124 TATCTCATAAT-ATTAAA
1 TATCTCACAATAATTAAA
89511141 TTCTTTTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (19 bp):
TATCTCACAATAATTAAAA
Found at i:89522648 original size:46 final size:46
Alignment explanation
Indices: 89522598--89522773 Score: 180
Period size: 46 Copynumber: 3.8 Consensus size: 46
89522588 TGGTTGAGCA
*
89522598 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
89522644 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* * *
89522691 TCCAAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * *
89522737 CCCGAGA-TTGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGA-ACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
89522774 GCGGGTTACA
Statistics
Matches: 106, Mismatches: 16, Indels: 16
0.77 0.12 0.12
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 60 0.57
47 29 0.27
48 3 0.03
50 5 0.05
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:89522754 original size:93 final size:93
Alignment explanation
Indices: 89522595--89522766 Score: 274
Period size: 93 Copynumber: 1.8 Consensus size: 93
89522585 GGATGGTTGA
* * * *
89522595 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCGAACTCGTTGAGT
89522660 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
89522688 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACGCCCGAGA-TTGTTGAG
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCGA-ACTCGTTGAG
89522752 TTGAGTCCGAGTTCG
65 TTGAGTCCGAGTTCG
89522767 CTTATGGGCG
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
93 71 0.99
94 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (93 bp):
GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:89525737 original size:15 final size:15
Alignment explanation
Indices: 89525698--89525777 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
89525688 GTATCTTGGG
*
89525698 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
89525713 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
* *
89525728 TTTCTTTATTCCGGG
1 TTTCTTTATTCTGGA
*
89525743 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
89525758 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
89525772 TTTCTT
1 TTTCTT
89525778 GTTATCTTTG
Statistics
Matches: 53, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
14 10 0.19
15 41 0.77
16 2 0.04
ACGTcount: A:0.10, C:0.19, G:0.14, T:0.57
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:89525767 original size:30 final size:30
Alignment explanation
Indices: 89525689--89525776 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 30
89525679 CATAGTATCG
* * *
89525689 TATCTTGGGTTTCTTTA-TCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCC-GGATTTCTC
*
89525719 TAT-TCTGGATTTCTTTATTCCGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCCGGATTTCTC
*
89525749 TATCTTGGATTTCTTTATT-CGGTTTTCT
1 TATCTTGGATTTCTTTATTCCGGATTTCT
89525777 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
29 9 0.18
30 37 0.74
31 4 0.08
ACGTcount: A:0.10, C:0.18, G:0.16, T:0.56
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCCGGATTTCTC
Found at i:89528216 original size:46 final size:46
Alignment explanation
Indices: 89528163--89528338 Score: 228
Period size: 46 Copynumber: 3.8 Consensus size: 46
89528153 TATTTGGGCA
89528163 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
*** * * * * *
89528209 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTA-ACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATGCGA-ACG
*
89528256 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* *
89528302 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
89528339 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 18, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
46 73 0.67
47 36 0.33
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:89528318 original size:93 final size:93
Alignment explanation
Indices: 89528159--89528330 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
89528149 AGGATATTTG
*
89528159 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
89528224 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* *
89528252 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
89528317 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
89528331 ACTTATGGGC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:89530048 original size:34 final size:34
Alignment explanation
Indices: 89530005--89530086 Score: 105
Period size: 34 Copynumber: 2.4 Consensus size: 34
89529995 GTATGTTACC
89530005 ATTAACATGCTTATAATA-AGT-ATATACAGTAGCA
1 ATTAACATGCTTATAATAGA-TCATA-ACAGTAGCA
*
89530039 ATTATCATGCTTATAATAGATCATAACAGTAGCA
1 ATTAACATGCTTATAATAGATCATAACAGTAGCA
* *
89530073 ATAAACTTGCTTAT
1 ATTAACATGCTTAT
89530087 TATGTATTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
34 38 0.90
35 4 0.10
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.34
Consensus pattern (34 bp):
ATTAACATGCTTATAATAGATCATAACAGTAGCA
Found at i:89534014 original size:14 final size:15
Alignment explanation
Indices: 89533991--89534023 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
89533981 CACTTTGTGG
*
89533991 TAATTTTATTT-TTT
1 TAATTATATTTATTT
89534005 TAATTATATTTATTT
1 TAATTATATTTATTT
89534020 TAAT
1 TAAT
89534024 AAACGTTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TAATTATATTTATTT
Found at i:89535060 original size:26 final size:26
Alignment explanation
Indices: 89535030--89535082 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
89535020 TAGTGATTTG
*
89535030 TTTTATATTCTAATGTTAATTTCTTA
1 TTTTATATTCCAATGTTAATTTCTTA
* *
89535056 TTTTATATTCCGATGTTAATTTTTTA
1 TTTTATATTCCAATGTTAATTTCTTA
89535082 T
1 T
89535083 GTCCCATGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.25, C:0.08, G:0.06, T:0.62
Consensus pattern (26 bp):
TTTTATATTCCAATGTTAATTTCTTA
Found at i:89538921 original size:68 final size:67
Alignment explanation
Indices: 89538849--89538998 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
89538839 CATCATGTGT
* * * *
89538849 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
89538911 ATGTAG
62 ATGTAG
** * *
89538917 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
89538982 AG
66 AG
89538984 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
89538999 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:89538954 original size:64 final size:64
Alignment explanation
Indices: 89538873--89539056 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
89538863 AGACATTATG
* *
89538873 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
89538937 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
89539002 AA
63 AA
* * * *
89539004 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
89539057 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:89556851 original size:23 final size:23
Alignment explanation
Indices: 89556821--89556865 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
89556811 CGTAAAGTCT
89556821 GCAACATAGTCCTCAAATGCTTC
1 GCAACATAGTCCTCAAATGCTTC
89556844 GCAACATAGTCCTCAAATGCTT
1 GCAACATAGTCCTCAAATGCTT
89556866 TGCATGCTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (23 bp):
GCAACATAGTCCTCAAATGCTTC
Found at i:89581182 original size:42 final size:42
Alignment explanation
Indices: 89581066--89581218 Score: 182
Period size: 42 Copynumber: 3.6 Consensus size: 42
89581056 ACTACACCAA
* ** *
89581066 GCCATATCCCAGATATGGTCTTACATGGGATCT-AGTATCCAT
1 GCCATATCCCAGATATGGTCTTACACGAAATCTCA-TATCGAT
* * *
89581108 GCCAATAGCCCAGTTATGGTTTTACACGAAATCTCATATCGAT
1 GCC-ATATCCCAGATATGGTCTTACACGAAATCTCATATCGAT
* * *
89581151 GCCATATCCCAGATATGGTCTTAGACAAAATCTCATATTGAT
1 GCCATATCCCAGATATGGTCTTACACGAAATCTCATATCGAT
*
89581193 TCCATATCCCAGATATGGTCTTACAC
1 GCCATATCCCAGATATGGTCTTACAC
89581219 ATAGTCTCGG
Statistics
Matches: 94, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
42 60 0.64
43 33 0.35
44 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (42 bp):
GCCATATCCCAGATATGGTCTTACACGAAATCTCATATCGAT
Found at i:89588794 original size:42 final size:42
Alignment explanation
Indices: 89588683--89588837 Score: 204
Period size: 42 Copynumber: 3.7 Consensus size: 42
89588673 TACTACACCA
* ** *
89588683 ATGCCATATCCCAGTTATGGTCTTACATGGGATCT-AGTATCC
1 ATGCCATATCCCAGTTATGGTCTTACACGAAATCTCA-TATCG
* *
89588725 ATGCCAATAGCCCAGCTATGGTCTTACACGAAATCTCATATCG
1 ATGCC-ATATCCCAGTTATGGTCTTACACGAAATCTCATATCG
* *
89588768 ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATTG
1 ATGCCATATCCCAGTTATGGTCTTACACGAAATCTCATATCG
*
89588810 ATGCCATATCCCAGTTATGGCCTTACAC
1 ATGCCATATCCCAGTTATGGTCTTACAC
89588838 ATAGTCTCGA
Statistics
Matches: 100, Mismatches: 11, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
42 65 0.65
43 34 0.34
44 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (42 bp):
ATGCCATATCCCAGTTATGGTCTTACACGAAATCTCATATCG
Found at i:89590291 original size:20 final size:20
Alignment explanation
Indices: 89590262--89590306 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
89590252 AGCACATGTA
* *
89590262 TTCATAAAATTTTAGAATTT
1 TTCATAAAATTTTACAACTT
*
89590282 TTCATCAAATTTTACAACTT
1 TTCATAAAATTTTACAACTT
89590302 TTCAT
1 TTCAT
89590307 TTTAGTCCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.13, G:0.02, T:0.49
Consensus pattern (20 bp):
TTCATAAAATTTTACAACTT
Found at i:89597884 original size:20 final size:20
Alignment explanation
Indices: 89597855--89597899 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
89597845 AGTACATGTA
*
89597855 TTCATAAAATTTTAGAATTT
1 TTCATAAAATTTTACAATTT
*
89597875 TTCATCAAATTTTACAATTT
1 TTCATAAAATTTTACAATTT
89597895 TTCAT
1 TTCAT
89597900 TTTAGTCCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.36, C:0.11, G:0.02, T:0.51
Consensus pattern (20 bp):
TTCATAAAATTTTACAATTT
Found at i:89599653 original size:29 final size:29
Alignment explanation
Indices: 89599590--89599657 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
89599580 TAATCAACCG
*
89599590 CGCACACTTAGTGCCATGTACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
89599619 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
89599648 CGCACACTTA
1 CGCACACTTA
89599658 CCTTTTCCGC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
28 3 0.09
29 30 0.91
ACGTcount: A:0.28, C:0.29, G:0.13, T:0.29
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:89599769 original size:174 final size:174
Alignment explanation
Indices: 89599479--89599806 Score: 611
Period size: 174 Copynumber: 1.9 Consensus size: 174
89599469 AACTCAAGGT
* *
89599479 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
89599544 GAAAATATATATTGAGTTCGCACACATAGTGCGTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGAGTTCGCACACATAGTGCGTAATAATCAACCGCGCACACTTAGTGCCATGT
89599609 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
89599653 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
* *
89599718 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGAGTTCGCACACATAGTGCGTAATAATCAACCGCGCACACTTAGTGCCATGT
*
89599783 ACTTTAAACTCGCACACTTAGTGC
131 ACTTTAAACTCACACACTTAGTGC
89599807 TGTACAATTT
Statistics
Matches: 149, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
174 149 1.00
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGAGTTCGCACACATAGTGCGTAATAATCAACCGCGCACACTTAGTGCCATGT
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:89599798 original size:29 final size:30
Alignment explanation
Indices: 89599759--89599837 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
89599749 CTTAATAATC
89599759 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
89599789 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
89599818 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
89599838 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:89602340 original size:40 final size:39
Alignment explanation
Indices: 89602242--89602464 Score: 241
Period size: 40 Copynumber: 5.6 Consensus size: 39
89602232 TCCTCGTTCA
* * * * *
89602242 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
* *
89602281 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
89602320 GAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
* *
89602360 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
* * * * * *
89602400 AAAGGCCTTC-GGATCTTAATCCGGATGTATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCAC
* *
89602441 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
89602465 CAGCATTCAA
Statistics
Matches: 160, Mismatches: 20, Indels: 7
0.86 0.11 0.04
Matches are distributed among these distances:
39 37 0.23
40 115 0.72
41 8 0.05
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
Found at i:89602464 original size:120 final size:119
Alignment explanation
Indices: 89602242--89602464 Score: 272
Period size: 120 Copynumber: 1.9 Consensus size: 119
89602232 TCCTCGTTCA
* * * *
89602242 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGATT
1 AATGCCTTCGGGACATAACCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATG
* *
89602307 TAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
66 TAACAACTAGCACGAAAGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * *
89602361 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTC-GGATCTTAATCCGGA
1 AATGCCTTCGGGACATAACCCGGATTTAGTAACTCACAC-AAGGCCTTCGGGA-CATAACCCGGA
* *
89602425 TGTATTC-ACTTAGCAC-AAAGCCTTCGGGACTTAGCCCGGA
64 TGTA-ACAAC-TAGCACGAAAGCCTTCGGGACTTAACCCGGA
89602465 CAGCATTCAA
Statistics
Matches: 87, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
119 37 0.43
120 44 0.51
121 6 0.07
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (119 bp):
AATGCCTTCGGGACATAACCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATG
TAACAACTAGCACGAAAGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:89610251 original size:40 final size:40
Alignment explanation
Indices: 89610151--89610322 Score: 222
Period size: 40 Copynumber: 4.3 Consensus size: 40
89610141 GCTCCTCGTT
* * *
89610151 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
*
89610191 C-AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
89610230 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
89610270 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGG-ATTTAGTAACTCGCA
89610310 CAAATGCCTTCGG
1 CAAATGCCTTCGG
89610323 ATCTTAGTCC
Statistics
Matches: 119, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.29
40 80 0.67
41 4 0.03
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:89620189 original size:45 final size:43
Alignment explanation
Indices: 89620150--89620309 Score: 202
Period size: 45 Copynumber: 3.7 Consensus size: 43
89620140 ATATGTGTTC
*
89620150 TCGTGTAAGACCACGTCTGGGACATTGGCATCGATATATGTGGT
1 TCGTGTAAGACCACGTCTGGGACATTGGCATCGATATAT-TGAT
*
89620194 TACGTGTAAGACCATGTCTGGGACATTGGCATCG-TAT-TTGAT
1 T-CGTGTAAGACCACGTCTGGGACATTGGCATCGATATATTGAT
* *
89620236 TCGTGTAAGACC-CTGTCTGGGACAGTGGCATCGATATA-AGAT
1 TCGTGTAAGACCAC-GTCTGGGACATTGGCATCGATATATTGAT
* *
89620278 AGCATGTAAGACCACGTCTGGGACATTGGCAT
1 -TCGTGTAAGACCACGTCTGGGACATTGGCAT
89620310 TGTATGATAT
Statistics
Matches: 102, Mismatches: 8, Indels: 13
0.83 0.07 0.11
Matches are distributed among these distances:
41 29 0.28
42 10 0.10
43 27 0.26
44 5 0.05
45 31 0.30
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (43 bp):
TCGTGTAAGACCACGTCTGGGACATTGGCATCGATATATTGAT
Found at i:89630898 original size:39 final size:39
Alignment explanation
Indices: 89630838--89630960 Score: 167
Period size: 39 Copynumber: 3.2 Consensus size: 39
89630828 ACTTAGTGAT
* *
89630838 GAATTATATCCGGACTAAAGGTTCGCAGGCTATATGCTG
1 GAATTATGTCCGGACTTAAGGTTCGCAGGCTATATGCTG
* * *
89630877 GAATTATGTCCGGGCTTAAGG-TCTGTAGGCTATATGTTG
1 GAATTATGTCCGGACTTAAGGTTC-GCAGGCTATATGCTG
* *
89630916 GAATTATGTTCGGACTTAAGGTCCGCAGGCTATATGCTG
1 GAATTATGTCCGGACTTAAGGTTCGCAGGCTATATGCTG
89630955 GAATTA
1 GAATTA
89630961 CGTCTGGGCT
Statistics
Matches: 72, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
38 2 0.03
39 69 0.96
40 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.32
Consensus pattern (39 bp):
GAATTATGTCCGGACTTAAGGTTCGCAGGCTATATGCTG
Found at i:89630981 original size:39 final size:39
Alignment explanation
Indices: 89630855--89630985 Score: 158
Period size: 39 Copynumber: 3.4 Consensus size: 39
89630845 ATCCGGACTA
* *
89630855 AAGGTTCGCAGGCTATATGCTGGAATTATGTCCGGGCTT
1 AAGGTCCGCAGGCTATATGCTGGAATTATGTCTGGGCTT
* * * *
89630894 AAGGTCTGTAGGCTATATGTTGGAATTATGT-TCGGACTT
1 AAGGTCCGCAGGCTATATGCTGGAATTATGTCT-GGGCTT
*
89630933 AAGGTCCGCAGGCTATATGCTGGAATTACGTCTGGGC-T
1 AAGGTCCGCAGGCTATATGCTGGAATTATGTCTGGGCTT
*
89630971 AAAGTCCCGCAGGCT
1 AAGGT-CCGCAGGCT
89630986 TCGAGCTGGT
Statistics
Matches: 77, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
38 5 0.06
39 71 0.92
40 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.30, T:0.30
Consensus pattern (39 bp):
AAGGTCCGCAGGCTATATGCTGGAATTATGTCTGGGCTT
Found at i:89630985 original size:78 final size:78
Alignment explanation
Indices: 89630838--89630985 Score: 199
Period size: 78 Copynumber: 1.9 Consensus size: 78
89630828 ACTTAGTGAT
* * * * *
89630838 GAATTATATCCGGACTAAAGGTTCGCAGGCTATATGCTGGAATTATGTCCGGGCTTAAGGTCTGT
1 GAATTATATCCGGACTAAAGGTCCGCAGGCTATATGCTGGAATTACGTCCGGGCTTAAAGTCCGC
89630903 AGGCTATATGTTG
66 AGGCTATATGTTG
* * * *
89630916 GAATTATGTTCGGACTTAAGGTCCGCAGGCTATATGCTGGAATTACGTCTGGGC-TAAAGTCCCG
1 GAATTATATCCGGACTAAAGGTCCGCAGGCTATATGCTGGAATTACGTCCGGGCTTAAAGT-CCG
89630980 CAGGCT
65 CAGGCT
89630986 TCGAGCTGGT
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
77 5 0.08
78 55 0.92
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (78 bp):
GAATTATATCCGGACTAAAGGTCCGCAGGCTATATGCTGGAATTACGTCCGGGCTTAAAGTCCGC
AGGCTATATGTTG
Found at i:89639681 original size:27 final size:28
Alignment explanation
Indices: 89639597--89639694 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 28
89639587 CATGAGATTG
* * * *
89639597 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
89639626 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
89639654 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
89639681 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
89639695 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 24 0.38
28 22 0.34
29 18 0.28
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:89639705 original size:27 final size:27
Alignment explanation
Indices: 89639625--89639707 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
89639615 TAAATTGTAC
* *
89639625 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
89639653 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
89639680 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
89639707 A
1 A
89639708 TTTTTGAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.60
28 20 0.40
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:89639708 original size:29 final size:27
Alignment explanation
Indices: 89639597--89639708 Score: 98
Period size: 28 Copynumber: 4.0 Consensus size: 27
89639587 CATGAGATTG
** * *
89639597 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGC-GACTT-AATTATATA
* *
89639626 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGA-CTTAATTATATA
* *
89639654 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGACTTAATTATATA
*
89639681 GCACTGAGTGTGCGGACTTAATATATAT
1 GCACTAAGTGTGC-GACTTAAT-TATAT
89639709 TTTTGAATCA
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
27 23 0.32
28 28 0.39
29 21 0.29
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
GCACTAAGTGTGCGACTTAATTATATA
Found at i:89645350 original size:39 final size:39
Alignment explanation
Indices: 89645294--89645441 Score: 190
Period size: 39 Copynumber: 3.8 Consensus size: 39
89645284 ACTCAGTGAT
* *
89645294 GAATTATATCCAGACTTAAGGTCCGCAGGCTATATGCTG
1 GAATTATGTCCGGACTTAAGGTCCGCAGGCTATATGCTG
* *
89645333 GGATTATGTCCGGACTTAAGGTCCGCAGGCTATATGTTG
1 GAATTATGTCCGGACTTAAGGTCCGCAGGCTATATGCTG
* * *
89645372 GAATTATGTTCGGACTTAAGGCCCGTAGGCTATATGCTG
1 GAATTATGTCCGGACTTAAGGTCCGCAGGCTATATGCTG
* * *
89645411 GAATTACGTCCGGGC-TAAAGTCTCGCAGGCT
1 GAATTATGTCCGGACTTAAGGTC-CGCAGGCT
89645442 TCGAGCTGGT
Statistics
Matches: 93, Mismatches: 15, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
38 5 0.05
39 88 0.95
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (39 bp):
GAATTATGTCCGGACTTAAGGTCCGCAGGCTATATGCTG
Found at i:89661680 original size:11 final size:11
Alignment explanation
Indices: 89661664--89661689 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
89661654 TATGAATTGA
89661664 GTTACACTTAT
1 GTTACACTTAT
89661675 GTTACACTTAT
1 GTTACACTTAT
89661686 GTTA
1 GTTA
89661690 TGCTTGATGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.46
Consensus pattern (11 bp):
GTTACACTTAT
Found at i:89666923 original size:27 final size:27
Alignment explanation
Indices: 89666846--89666968 Score: 122
Period size: 27 Copynumber: 4.6 Consensus size: 27
89666836 TTAGTTTACC
* * *
89666846 AAATTACTGAAATACCCTCGACTTGTA
1 AAATTACTGAAATATCCTCAATTTGTA
* * * * * *
89666873 AAACTAC-CAAAGTACCCCCGATTTATA
1 AAATTACTGAAA-TATCCTCAATTTGTA
89666900 AAATTACTGAAATATCCTCAATTTGTA
1 AAATTACTGAAATATCCTCAATTTGTA
* * *
89666927 AAATTACCGAAATACCCTCAATTTGCA
1 AAATTACTGAAATATCCTCAATTTGTA
89666954 AAATTACTGAAATAT
1 AAATTACTGAAATAT
89666969 TTTTGTAAGA
Statistics
Matches: 78, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
26 3 0.04
27 72 0.92
28 3 0.04
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.29
Consensus pattern (27 bp):
AAATTACTGAAATATCCTCAATTTGTA
Found at i:89666928 original size:54 final size:54
Alignment explanation
Indices: 89666840--89666968 Score: 161
Period size: 54 Copynumber: 2.4 Consensus size: 54
89666830 AATACTTTAG
* * * *
89666840 TTTACCAAATTACTGAAATACCCTCGACTTGTAAAACTACC-AAAGTACCCCCGA
1 TTTACAAAATTACTGAAATATCCTCAACTTGTAAAACTACCGAAA-TACCCCCAA
* * * *
89666894 TTTATAAAATTACTGAAATATCCTCAATTTGTAAAATTACCGAAATACCCTCAA
1 TTTACAAAATTACTGAAATATCCTCAACTTGTAAAACTACCGAAATACCCCCAA
*
89666948 TTTGCAAAATTACTGAAATAT
1 TTTACAAAATTACTGAAATAT
89666969 TTTTGTAAGA
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
54 61 0.95
55 3 0.05
ACGTcount: A:0.40, C:0.22, G:0.08, T:0.30
Consensus pattern (54 bp):
TTTACAAAATTACTGAAATATCCTCAACTTGTAAAACTACCGAAATACCCCCAA
Found at i:89667008 original size:27 final size:27
Alignment explanation
Indices: 89666978--89667041 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 27
89666968 TTTTTGTAAG
89666978 ATAGAATTACCATTTTACCCTCGATTT
1 ATAGAATTACCATTTTACCCTCGATTT
*
89667005 ATAGAATTACCATTTTACCCTTGATTT
1 ATAGAATTACCATTTTACCCTCGATTT
* *
89667032 ACAAAATTAC
1 ATAGAATTAC
89667042 TAAAATACCC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.39
Consensus pattern (27 bp):
ATAGAATTACCATTTTACCCTCGATTT
Found at i:89667050 original size:27 final size:27
Alignment explanation
Indices: 89666993--89667107 Score: 122
Period size: 27 Copynumber: 4.3 Consensus size: 27
89666983 ATTACCATTT
* * * ***
89666993 TACCCTCGATTTATAGAATTACCATTT
1 TACCCTTGATTTACAAAATTACCAAAA
*
89667020 TACCCTTGATTTACAAAATTACTAAAA
1 TACCCTTGATTTACAAAATTACCAAAA
*
89667047 TACCCTTGGTTTACAAAATTACCAAAA
1 TACCCTTGATTTACAAAATTACCAAAA
* ***
89667074 TACCCCTGATTTGTGAAATTACCAAAA
1 TACCCTTGATTTACAAAATTACCAAAA
89667101 TACCCTT
1 TACCCTT
89667108 ATAGGATAGA
Statistics
Matches: 73, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 73 1.00
ACGTcount: A:0.37, C:0.23, G:0.07, T:0.34
Consensus pattern (27 bp):
TACCCTTGATTTACAAAATTACCAAAA
Found at i:89667120 original size:27 final size:27
Alignment explanation
Indices: 89667090--89667474 Score: 414
Period size: 27 Copynumber: 14.3 Consensus size: 27
89667080 TGATTTGTGA
* * *
89667090 AATTACCAAAATACCCTTATAGGATAG
1 AATTACCGAAATACCCTTGTAGGGTAG
*
89667117 AATTATCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCTTGTAGGGTAG
* *
89667144 AATTACTGAAATACACTTGTAGGGTAG
1 AATTACCGAAATACCCTTGTAGGGTAG
* *
89667171 AAATACC-AGAATACCCATGTAGGGTAG
1 AATTACCGA-AATACCCTTGTAGGGTAG
* *
89667198 AATTACCGAAATACCCCTGTAGGGTAA
1 AATTACCGAAATACCCTTGTAGGGTAG
*
89667225 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCTTGTAGGGTAG
** * *
89667252 AATTACTAAAATACCCCTGTAAGGTAG
1 AATTACCGAAATACCCTTGTAGGGTAG
* * *
89667279 AATTATCGAAATACCCCTGTAGGGTAC
1 AATTACCGAAATACCCTTGTAGGGTAG
* * * *
89667306 AATTACTGAAATACCCCTATAAGGTAG
1 AATTACCGAAATACCCTTGTAGGGTAG
*
89667333 AATTACCGAAATACCCGTGTAGGGTAG
1 AATTACCGAAATACCCTTGTAGGGTAG
* * *
89667360 AATTACTGAAATACCCCTGTAAGGTAG
1 AATTACCGAAATACCCTTGTAGGGTAG
* *
89667387 AATTATCGAAATA-CCTCTGAAGGGTAG
1 AATTACCGAAATACCCT-TGTAGGGTAG
** * *
89667414 AATTATTGAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCTTGTAGGGTAG
* ** *
89667441 AATTACCGAGATACCCTTGGGGGGTAA
1 AATTACCGAAATACCCTTGTAGGGTAG
89667468 AATTACC
1 AATTACC
89667475 ATTTTTCCCC
Statistics
Matches: 302, Mismatches: 52, Indels: 8
0.83 0.14 0.02
Matches are distributed among these distances:
26 3 0.01
27 296 0.98
28 3 0.01
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (27 bp):
AATTACCGAAATACCCTTGTAGGGTAG
Found at i:89667485 original size:108 final size:107
Alignment explanation
Indices: 89667098--89667475 Score: 461
Period size: 108 Copynumber: 3.5 Consensus size: 107
89667088 GAAATTACCA
* * * * * * *
89667098 AAATACCCTTATAGGATAGAATTATCGAAATACCCTTGTAGGGTAGAATTACTGAAATACACTTG
1 AAATACCCCTATAGGGTAGAATTACCGAAATACCCCTGTAGGGTAGAATTAC-CAAATACCCCTG
* * * * * *
89667163 TAGGGTAGAAATA-CCAGAATACCCATGTAGGGTAGAATTACCG
65 TAAGGTAGAATTATCGA-AATACCCCTGAAGGGTAGAATTACTG
* * *
89667206 AAATACCCCTGTAGGGTAAAATTACCGAAATACCCCTGTAGGGTAGAATTACTAAAATACCCCTG
1 AAATACCCCTATAGGGTAGAATTACCGAAATACCCCTGTAGGGTAGAATTAC-CAAATACCCCTG
* *
89667271 TAAGGTAGAATTATCGAAATACCCCTGTAGGGTACAATTACTG
65 TAAGGTAGAATTATCGAAATACCCCTGAAGGGTAGAATTACTG
* * *
89667314 AAATACCCCTATAAGGTAGAATTACCGAAATACCCGTGTAGGGTAGAATTACTGAAATACCCCTG
1 AAATACCCCTATAGGGTAGAATTACCGAAATACCCCTGTAGGGTAGAATTAC-CAAATACCCCTG
* *
89667379 TAAGGTAGAATTATCGAAATACCTCTGAAGGGTAGAATTATTG
65 TAAGGTAGAATTATCGAAATACCCCTGAAGGGTAGAATTACTG
* * ** *
89667422 AAATACCCCTATAGGGTAGAATTACCGAGATACCCTTGGGGGGTAAAATTACCA
1 AAATACCCCTATAGGGTAGAATTACCGAAATACCCCTGTAGGGTAGAATTACCA
89667476 TTTTTCCCCT
Statistics
Matches: 238, Mismatches: 31, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
107 1 0.00
108 235 0.99
109 2 0.01
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (107 bp):
AAATACCCCTATAGGGTAGAATTACCGAAATACCCCTGTAGGGTAGAATTACCAAATACCCCTGT
AAGGTAGAATTATCGAAATACCCCTGAAGGGTAGAATTACTG
Found at i:89667933 original size:31 final size:31
Alignment explanation
Indices: 89667895--89667961 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
89667885 CTGATTTTTT
89667895 ATTCTGTTACCTGATACTAATTCCGATTCTG
1 ATTCTGTTACCTGATACTAATTCCGATTCTG
* * *
89667926 ATTCTGTTACCTGATACTGATTCTGATTTTG
1 ATTCTGTTACCTGATACTAATTCCGATTCTG
89667957 ATTCT
1 ATTCT
89667962 AGTTCTGACA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.21, C:0.19, G:0.13, T:0.46
Consensus pattern (31 bp):
ATTCTGTTACCTGATACTAATTCCGATTCTG
Found at i:89669956 original size:27 final size:27
Alignment explanation
Indices: 89669925--89670266 Score: 216
Period size: 27 Copynumber: 12.7 Consensus size: 27
89669915 TTAGTTTACC
*
89669925 AAATTACTGAAATACCCTCGACTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
* * *
89669952 AAATTAC-CAAAGTACCCCCGATTTATA
1 AAATTACTGAAA-TACCCTCGATTTGTA
* *
89669979 AAATTACTGAAATATCCTTGATTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
*
89670006 AAATTA-TCGAAATACCCTC-AGTTTGCA
1 AAATTACT-GAAATACCCTCGA-TTTGTA
89670033 AAATTACTGAAATACCCTCGATTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
* **
89670060 AAATTACTGAAATA-CTTCTG-TAAGATA
1 AAATTACTGAAATACCCTC-GATTTG-TA
* * ** **
89670087 GAATTAC-CATTTTACCCTCGATTTACA
1 AAATTACTGA-AATACCCTCGATTTGTA
* ** * **
89670114 AAATTAC-CATTTTACCATCGATTTACA
1 AAATTACTGA-AATACCCTCGATTTGTA
* * *
89670141 AAATTACTGAAATACCCTTGGTTTATA
1 AAATTACTGAAATACCCTCGATTTGTA
** ***
89670168 AAATTACCAAAATACCCTCGATCAATA
1 AAATTACTGAAATACCCTCGATTTGTA
** *
89670195 AAATTACCAAAATACCC-CTGGTTTGTA
1 AAATTACTGAAATACCCTC-GATTTGTA
** *
89670222 AAATTACCAAAATACCC-CTGATTTGTG
1 AAATTACTGAAATACCCTC-GATTTGTA
89670249 AAATTACTGAAATACCCT
1 AAATTACTGAAATACCCT
89670267 TGTAGGGTAG
Statistics
Matches: 253, Mismatches: 48, Indels: 27
0.77 0.15 0.08
Matches are distributed among these distances:
26 12 0.05
27 231 0.91
28 10 0.04
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (27 bp):
AAATTACTGAAATACCCTCGATTTGTA
Found at i:89670007 original size:54 final size:53
Alignment explanation
Indices: 89669925--89670268 Score: 244
Period size: 54 Copynumber: 6.4 Consensus size: 53
89669915 TTAGTTTACC
* *
89669925 AAATTACTGAAATACCCTCGACTTGTAAAATTACCAAAGTACCCCCGATTTATA
1 AAATTACTGAAATACCCTTGATTTGTAAAATTACCAAA-TACCCCCGATTTATA
* * * **
89669979 AAATTACTGAAATATCCTTGATTTGTAAAATTATCGAAATACCCTC-AGTTTGCA
1 AAATTACTGAAATACCCTTGATTTGTAAAATTA-CCAAATACCCCCGA-TTTATA
* * ** * **
89670033 AAATTACTGAAATACCCTCGATTTGTAAAATTACTGAAATACTTCTG-TAAGATA
1 AAATTACTGAAATACCCTTGATTTGTAAAATTAC-CAAATACCCCCGAT-TTATA
* * ** * ** ** ** *
89670087 GAATTAC-CATTTTACCCTCGATTTACAAAATTACCATTTTACCATCGATTTACA
1 AAATTACTGA-AATACCCTTGATTTGTAAAATTACCA-AATACCCCCGATTTATA
* * * **
89670141 AAATTACTGAAATACCCTTGGTTTATAAAATTACCAAAATACCCTCGATCAATA
1 AAATTACTGAAATACCCTTGATTTGTAAAATTACC-AAATACCCCCGATTTATA
** * * * * *
89670195 AAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCCTGATTTGTG
1 AAATTACTGAAATACCCTTGATTTGTAAAATTACC-AAATACCCCCGATTTATA
89670249 AAATTACTGAAATACCCTTG
1 AAATTACTGAAATACCCTTG
89670269 TAGGGTAGAA
Statistics
Matches: 221, Mismatches: 59, Indels: 20
0.74 0.20 0.07
Matches are distributed among these distances:
53 5 0.02
54 209 0.95
55 7 0.03
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.32
Consensus pattern (53 bp):
AAATTACTGAAATACCCTTGATTTGTAAAATTACCAAATACCCCCGATTTATA
Found at i:89670062 original size:81 final size:81
Alignment explanation
Indices: 89669925--89670266 Score: 241
Period size: 81 Copynumber: 4.2 Consensus size: 81
89669915 TTAGTTTACC
*
89669925 AAATTACTGAAATACCCTCGACTTGTAAAATTACCAAAGTACCCCCGATTTATAAAATTACTGAA
1 AAATTACTGAAATACCCTCGACTTGCAAAATTACCAAAGTACCCCCGATTTATAAAATTACTGAA
89669990 ATATCCTTGATTTGTA
66 ATATCCTTGATTTGTA
* * * *
89670006 AAATTA-TCGAAATACCCTC-AGTTTGCAAAATTACTGAAA-TACCCTCGATTTGTAAAATTACT
1 AAATTACT-GAAATACCCTCGA-CTTGCAAAATTAC-CAAAGTACCCCCGATTTATAAAATTACT
* **
89670068 GAAATA-CTTCTG-TAAGATA
63 GAAATATCCT-TGATTTG-TA
* * ** * * *** ** *
89670087 GAATTAC-CATTTTACCCTCGATTTACAAAATTACCATTTTACCATCGATTTACAAAATTACTGA
1 AAATTACTGA-AATACCCTCGACTTGCAAAATTACCAAAGTACCCCCGATTTATAAAATTACTGA
* * *
89670151 AATACCCTTGGTTTATA
65 AATATCCTTGATTTGTA
** * * * * * **
89670168 AAATTACCAAAATACCCTCGATCAAT--AAAATTACCAAAATACCCCTGGTTTGTAAAATTACCA
1 AAATTACTGAAATACCCTCGA-C-TTGCAAAATTACCAAAGTACCCCCGATTTATAAAATTACTG
* * *
89670231 AAATACCCCTGATTTGTG
64 AAATATCCTTGATTTGTA
89670249 AAATTACTGAAATACCCT
1 AAATTACTGAAATACCCT
89670267 TGTAGGGTAG
Statistics
Matches: 201, Mismatches: 46, Indels: 28
0.73 0.17 0.10
Matches are distributed among these distances:
80 8 0.04
81 184 0.92
82 8 0.04
83 1 0.00
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (81 bp):
AAATTACTGAAATACCCTCGACTTGCAAAATTACCAAAGTACCCCCGATTTATAAAATTACTGAA
ATATCCTTGATTTGTA
Done.