Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr7
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: 47983841
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869652 characters in sequence are not A, C, G, or T
File 15 of 153
Found at i:5030425 original size:17 final size:18
Alignment explanation
Indices: 5030395--5030442 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
5030385 AAAGAGAAAA
**
5030395 AAAGAAAAGGAAAAAGA-
1 AAAGAAAACAAAAAAGAG
*
5030412 AGAGAAAACAAAAAAGAG
1 AAAGAAAACAAAAAAGAG
*
5030430 AAAGAAAATAAAA
1 AAAGAAAACAAAA
5030443 GCAAAGGAGA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 14 0.56
18 11 0.44
ACGTcount: A:0.77, C:0.02, G:0.19, T:0.02
Consensus pattern (18 bp):
AAAGAAAACAAAAAAGAG
Found at i:5031971 original size:44 final size:46
Alignment explanation
Indices: 5031923--5032009 Score: 106
Period size: 46 Copynumber: 1.9 Consensus size: 46
5031913 CTAAATATAG
* *
5031923 CAGATCTCATC-CCACTG-GCTGGAGTGGAACAGATCAAATTTCGA
1 CAGATCTCATCTCCACTGAGCAGGAGCGGAACAGATCAAATTTCGA
* * * *
5031967 CAGATCTTATCTTCGCTGAGCAGGAGCGGAGCAGATCAAATTT
1 CAGATCTCATCTCCACTGAGCAGGAGCGGAACAGATCAAATTT
5032010 TGGCGAATCT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
44 10 0.29
45 4 0.11
46 21 0.60
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.24
Consensus pattern (46 bp):
CAGATCTCATCTCCACTGAGCAGGAGCGGAACAGATCAAATTTCGA
Found at i:5032012 original size:179 final size:176
Alignment explanation
Indices: 5031700--5032140 Score: 695
Period size: 179 Copynumber: 2.5 Consensus size: 176
5031690 CAGATTTTGG
* * *
5031700 CAAGCCTTATCCCACTGAGCAGGAGTGGAATAGGCTAAATATAGCAGATCTCATCCTACTGGCAC
1 CAAGCCTTATCCCACTGAGCAGGAGTGGAACAGGCTAAATATAGCAGATCTCATCCCACTGGCAG
* * * *
5031765 GAGTGGAATATATCAAATTTCGACAGATCTTATCTTCGTTGATCAGGAGCGGAGCAAATCAAATT
66 GAGTGGAACAGATCAAATTTCGACAGATCTTATCTTCGCTGAGCAGGAGCGGAGCAAATCAAATT
5031830 TTGGCGAATCTTACCTCCATGTATCGGCAATGGAGCAGATTTCAGCCA
131 TTGGCGAATCTTACCTCCATGTA--GGCAATGGAGCAGATTTCAGCCA
* * *
5031878 CCAGCCTTATCTTCACTGAGCAAGAGT-GAAGCAGGCTAAATATAGCAGATCTCATCCCACTGGC
1 CAAGCCTTATC-CCACTGAGCAGGAGTGGAA-CAGGCTAAATATAGCAGATCTCATCCCACTGGC
* *
5031942 TGGAGTGGAACAGATCAAATTTCGACAGATCTTATCTTCGCTGAGCAGGAGCGGAGCAGATCAAA
64 AGGAGTGGAACAGATCAAATTTCGACAGATCTTATCTTCGCTGAGCAGGAGCGGAGCAAATCAAA
* *
5032007 TTTTGGCGAATCTTATCTCTATGTAGGCAATGGAGCAGATTTCAGCCA
129 TTTTGGCGAATCTTACCTCCATGTAGGCAATGGAGCAGATTTCAGCCA
* *
5032055 CAAGCCTTATCCCACTGAGTAGGAGTGGAACAGGCTAAATATAGCAGATCTCATCCCACTGACAG
1 CAAGCCTTATCCCACTGAGCAGGAGTGGAACAGGCTAAATATAGCAGATCTCATCCCACTGGCAG
5032120 GAGTGGAACAGATCAAATTTC
66 GAGTGGAACAGATCAAATTTC
5032141 AGCGGATCTT
Statistics
Matches: 240, Mismatches: 20, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
176 66 0.28
177 36 0.15
178 13 0.05
179 125 0.52
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.24
Consensus pattern (176 bp):
CAAGCCTTATCCCACTGAGCAGGAGTGGAACAGGCTAAATATAGCAGATCTCATCCCACTGGCAG
GAGTGGAACAGATCAAATTTCGACAGATCTTATCTTCGCTGAGCAGGAGCGGAGCAAATCAAATT
TTGGCGAATCTTACCTCCATGTAGGCAATGGAGCAGATTTCAGCCA
Found at i:5032444 original size:132 final size:132
Alignment explanation
Indices: 5031986--5032459 Score: 568
Period size: 132 Copynumber: 3.6 Consensus size: 132
5031976 TCTTCGCTGA
* * ** *
5031986 GCAGGAGCGGAGCAGATCAAATTTTGGCGAATCTTATCTCTATGTA--GGCAATGGAGCAGATTT
1 GCAGGAGTGGAACAGATCAAATTTCAGCGAATCTTATCTCCATGTATCGGCAATGGAGCAGATTT
* * * *
5032049 CAGCCACAAGCCTTATCCCACTGAGTAGGAGTGGAACAGGCTAAATATAGCAGATCTCATCCCAC
66 CAACCACCAGCCTTATCCCACTGAGCAGGAGTGGAACAGGCTAAATATAGTAGATCTCATCCCAC
5032114 TG
131 TG
* * *
5032116 ACAGGAGTGGAACAGATCAAATTTCAGCGGATCTTGTCT-CATGTATCGGCAATGGAGCAGATTT
1 GCAGGAGTGGAACAGATCAAATTTCAGCGAATCTTATCTCCATGTATCGGCAATGGAGCAGATTT
* * * * * * * *
5032180 CAGCCACCAGCCTTATCTTCACTGAGCAGGAGTGGAGCACGCTAAA-CT-CTAGATCTTATCTTC
66 CAACCACCAGCCTTATC-CCACTGAGCAGGAGTGGAACAGGCTAAATATAGTAGATCTCATC-CC
*
5032243 GCTG
129 ACTG
* *
5032247 AGCAGGAGTGGAGCAGATCAAATTT-TGACGAATCTTATCTCCATGTATCGGCAATGGAGCAGA-
1 -GCAGGAGTGGAACAGATCAAATTTCAG-CGAATCTTATCTCCATGTATCGGCAATGGAGCAGAT
* * *
5032310 TTCAAACCACCAGCGTTATCCCACTAAGCAGGAGTAGAACAGGCTAAATATAGTAGATCTCATCC
64 TTC-AACCACCAGCCTTATCCCACTGAGCAGGAGTGGAACAGGCTAAATATAGTAGATCTCATCC
5032375 CACTG
128 CACTG
* * *
5032380 GCAGGAGTGGAATAGATCAAATTTCAGCGGATCTTATCTCCATGTATCGACAATGGAGCAGA-TT
1 GCAGGAGTGGAACAGATCAAATTTCAGCGAATCTTATCTCCATGTATCGGCAATGGAGCAGATTT
*
5032444 CAAACCACCAGTCTTA
66 C-AACCACCAGCCTTA
5032460 ACCCCCTAAA
Statistics
Matches: 290, Mismatches: 43, Indels: 20
0.82 0.12 0.06
Matches are distributed among these distances:
129 5 0.02
130 41 0.14
131 39 0.13
132 153 0.53
133 42 0.14
134 10 0.03
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.24
Consensus pattern (132 bp):
GCAGGAGTGGAACAGATCAAATTTCAGCGAATCTTATCTCCATGTATCGGCAATGGAGCAGATTT
CAACCACCAGCCTTATCCCACTGAGCAGGAGTGGAACAGGCTAAATATAGTAGATCTCATCCCAC
TG
Found at i:5032843 original size:85 final size:85
Alignment explanation
Indices: 5032627--5033188 Score: 709
Period size: 85 Copynumber: 6.6 Consensus size: 85
5032617 CAAAGATACA
*
5032627 CGCCTTAACCCCCTAAGCAGTAGGGTATCAGGCTAAAATTTACAGATCTGGGCTCGCCAAGCAGT
1 CGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGCCAAGCAGT
* *
5032692 GGCGGAGCAGATCAAAGATACA
66 GGCGGAGCAGGTCAAAG--ACT
* * *
5032714 CGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATGTACAGATCTGGGCTCGCCTAGTAGT
1 CGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGCCAAGCAGT
* *
5032779 GGCGGAGTAGGTCGAAGACT
66 GGCGGAGCAGGTCAAAGACT
** * *
5032799 CGCCTTAACCTTCTAAGCAGTAGGGTAACAGGCTAAAGTTTACAGA-CTTGGGCTCGCCGAGCAG
1 CGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATC-TGGGCTCGCCAAGCAG
*
5032863 TGGCGGAGCAGATCAAAGA-T
65 TGGCGGAGCAGGTCAAAGACT
* *
5032883 ACATGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAAATCTGGGCTCGCCGAGC
1 -C--GCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGCCAAGC
** * *
5032948 AGTGGTAGAGTAGGTCGAAGACT
63 AGTGGCGGAGCAGGTCAAAGACT
* *
5032971 CGCCTTAACCCCCTAATCAGTAGGGTAACAGGCTAAAGTTTACAGA-CTTGGGCTCGCCAAGCAG
1 CGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATC-TGGGCTCGCCAAGCAG
* *
5033035 TGGTGGAGCAAGTCAAAGACT
65 TGGCGGAGCAGGTCAAAGACT
* * * * ** * **
5033056 CACCTTAGCTCTCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCTTAGCTCTCTGAGCAGT
1 CGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGCCAAGCAGT
* *
5033121 GGTGGAGCAGGTCGAAGACT
66 GGCGGAGCAGGTCAAAGACT
* *
5033141 CGCCTTAACCCCTTAAGCAATAGGGTAACAGGCTAAAA-TTACAGATCT
1 CGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCT
5033189 TATTTTCGTT
Statistics
Matches: 414, Mismatches: 53, Indels: 19
0.85 0.11 0.04
Matches are distributed among these distances:
84 13 0.03
85 251 0.61
86 1 0.00
87 147 0.36
88 2 0.00
ACGTcount: A:0.30, C:0.23, G:0.26, T:0.21
Consensus pattern (85 bp):
CGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGCCAAGCAGT
GGCGGAGCAGGTCAAAGACT
Found at i:5032843 original size:172 final size:171
Alignment explanation
Indices: 5032627--5033185 Score: 815
Period size: 172 Copynumber: 3.3 Consensus size: 171
5032617 CAAAGATACA
* *
5032627 CGCCTTAACCCCCTAAGCAGTAGGGTATCAGGCTAAAATTTACAGA-TCTGGGCTCGCCAAGCAG
1 CGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAGTTTACAGACT-TGGGCTCGCCAAGCAG
*
5032691 TGGCGGAGCAGATCAAAGATACACGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATGTA
65 TGGCGGAGCAGATCAAAGATACA-GCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTA
* *
5032756 CAGATCTGGGCTCGCCTAGTAGTGGCGGAGTAGGTCGAAGACT
129 CAGATCTGGGCTCGCCTAGCAGTGGTGGAGTAGGTCGAAGACT
** *
5032799 CGCCTTAACCTTCTAAGCAGTAGGGTAACAGGCTAAAGTTTACAGACTTGGGCTCGCCGAGCAGT
1 CGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAGTTTACAGACTTGGGCTCGCCAAGCAGT
5032864 GGCGGAGCAGATCAAAGATACATGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTAC
66 GGCGGAGCAGATCAAAGATACA-GCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTAC
* * *
5032929 AAATCTGGGCTCGCCGAGCAGTGGTAGAGTAGGTCGAAGACT
130 AGATCTGGGCTCGCCTAGCAGTGGTGGAGTAGGTCGAAGACT
*
5032971 CGCCTTAACCCCCTAATCAGTAGGGTAACAGGCTAAAGTTTACAGACTTGGGCTCGCCAAGCAGT
1 CGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAGTTTACAGACTTGGGCTCGCCAAGCAGT
* * * *
5033036 GGTGGAGCA-AGTCAAAGACT-CA-CCTTAGCTCTCTAAGCAGTAGGGTAACAGGCTAAAATTTA
66 GGCGGAGCAGA-TCAAAGA-TACAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTA
** * *
5033098 CAGATCTTAGCTC-TCTGAGCAGTGGTGGAGCAGGTCGAAGACT
129 CAGATCTGGGCTCGCCT-AGCAGTGGTGGAGTAGGTCGAAGACT
* * *
5033141 CGCCTTAACCCCTTAAGCAATAGGGTAACAGGCTAAA-ATTACAGA
1 CGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAGTTTACAGA
5033186 TCTTATTTTC
Statistics
Matches: 352, Mismatches: 31, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
169 8 0.02
170 105 0.30
171 1 0.00
172 236 0.67
173 2 0.01
ACGTcount: A:0.30, C:0.23, G:0.26, T:0.21
Consensus pattern (171 bp):
CGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAGTTTACAGACTTGGGCTCGCCAAGCAGT
GGCGGAGCAGATCAAAGATACAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACA
GATCTGGGCTCGCCTAGCAGTGGTGGAGTAGGTCGAAGACT
Found at i:5033203 original size:85 final size:85
Alignment explanation
Indices: 5032456--5033189 Score: 666
Period size: 87 Copynumber: 8.5 Consensus size: 85
5032446 AACCACCAGT
* * * * *
5032456 CTTAACCCCCTAAACAGTAGGGTAACAGGCTAAAAACTACAGATCTT-GTCTC-CTTAAGCTGTA
1 CTTAACCCCCTAAGCAGTAGGGTAACAGGCT-AAAATTACAGATCTTGGGCTCGC-TAAGCAGTG
*
5032519 GTGGAGCAGATCAAAGATACACGC
64 GTGGAGCAGATCAAAG--ACTCGC
* * * * * * * * ** * * *
5032543 TTTAACTCCTTAAGCAATAGGGTCACAAGTTAAAGATTATAGATCTT-ATCTC-CTTAAGAAATA
1 CTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAA-ATTACAGATCTTGGGCTCGC-TAAGCAGTG
* * *
5032606 ATGGAACAGATCAAAGATACACGC
64 GTGGAGCAGATCAAAG--ACTCGC
* *
5032630 CTTAACCCCCTAAGCAGTAGGGTATCAGGCTAAAATTTACAGATC-TGGGCTCGCCAAGCAGTGG
1 CTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAA-TTACAGATCTTGGGCTCGCTAAGCAGTGG
* *
5032694 CGGAGCAGATCAAAGATACACGC
65 TGGAGCAGATCAAAG--ACTCGC
*
5032717 CTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATGTACAGATC-TGGGCTCGCCT-AGTAGTG
1 CTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAAT-TACAGATCTTGGGCTCG-CTAAGCAGTG
* * * *
5032780 GCGGAGTAGGTCGAAGACTCGC
64 GTGGAGCAGATCAAAGACTCGC
** * **
5032802 CTTAACCTTCTAAGCAGTAGGGTAACAGGCTAAAGTTTACAGA-CTTGGGCTCGCCGAGCAGTGG
1 CTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAA-ATTACAGATCTTGGGCTCGCTAAGCAGTGG
*
5032866 CGGAGCAGATCAAAGA-TACATGC
65 TGGAGCAGATCAAAGACT-C--GC
* **
5032889 CTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAAATC-TGGGCTCGCCGAGCAGTGG
1 CTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAA-TTACAGATCTTGGGCTCGCTAAGCAGTGG
* * * *
5032953 TAGAGTAGGTCGAAGACTCGC
65 TGGAGCAGATCAAAGACTCGC
* * *
5032974 CTTAACCCCCTAATCAGTAGGGTAACAGGCTAAAGTTTACAGA-CTTGGGCTCGCCAAGCAGTGG
1 CTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAA-ATTACAGATCTTGGGCTCGCTAAGCAGTGG
*
5033038 TGGAGCA-AGTCAAAGACTCAC
65 TGGAGCAGA-TCAAAGACTCGC
* * * * * *
5033059 CTTAGCTCTCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCTT-AGCTCTCTGAGCAGTGG
1 CTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAA-TTACAGATCTTGGGCTCGCTAAGCAGTGG
* *
5033123 TGGAGCAGGTCGAAGACTCGC
65 TGGAGCAGATCAAAGACTCGC
* *
5033144 CTTAACCCCTTAAGCAATAGGGTAACAGGCTAAAATTACAGATCTT
1 CTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTACAGATCTT
5033190 ATTTTCGTTG
Statistics
Matches: 542, Mismatches: 84, Indels: 45
0.81 0.13 0.07
Matches are distributed among these distances:
84 15 0.03
85 243 0.45
86 10 0.02
87 270 0.50
88 4 0.01
ACGTcount: A:0.32, C:0.23, G:0.24, T:0.22
Consensus pattern (85 bp):
CTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTACAGATCTTGGGCTCGCTAAGCAGTGGT
GGAGCAGATCAAAGACTCGC
Found at i:5033459 original size:29 final size:29
Alignment explanation
Indices: 5033426--5033489 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
5033416 CCAAATTAAA
5033426 CACCCCACTAAACCGA-CCACTAACTCCAT
1 CACCCCACTAAACC-ATCCACTAACTCCAT
* *
5033455 CACCCTACTAAACCATCCACTACCTCCAT
1 CACCCCACTAAACCATCCACTAACTCCAT
5033484 CACCCC
1 CACCCC
5033490 TACACCCTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
28 1 0.03
29 30 0.97
ACGTcount: A:0.31, C:0.52, G:0.02, T:0.16
Consensus pattern (29 bp):
CACCCCACTAAACCATCCACTAACTCCAT
Found at i:5033502 original size:37 final size:37
Alignment explanation
Indices: 5033455--5033526 Score: 144
Period size: 37 Copynumber: 1.9 Consensus size: 37
5033445 CTAACTCCAT
5033455 CACCCTACTAAACCATCCACTACCTCCATCACCCCTA
1 CACCCTACTAAACCATCCACTACCTCCATCACCCCTA
5033492 CACCCTACTAAACCATCCACTACCTCCATCACCCC
1 CACCCTACTAAACCATCCACTACCTCCATCACCCC
5033527 CACTAACTCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.29, C:0.53, G:0.00, T:0.18
Consensus pattern (37 bp):
CACCCTACTAAACCATCCACTACCTCCATCACCCCTA
Found at i:5033531 original size:18 final size:18
Alignment explanation
Indices: 5033508--5033543 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
5033498 ACTAAACCAT
*
5033508 CCACTACCTCCATCACCC
1 CCACTAACTCCATCACCC
5033526 CCACTAACTCCATCACCC
1 CCACTAACTCCATCACCC
5033544 TACTTGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.58, G:0.00, T:0.17
Consensus pattern (18 bp):
CCACTAACTCCATCACCC
Found at i:5033955 original size:19 final size:21
Alignment explanation
Indices: 5033930--5033974 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
5033920 GTTATGTTTC
*
5033930 ATATTAT-TATAT-TATATAT
1 ATATTATGTAAATATATATAT
*
5033949 TTATTATGTAAATATATATAT
1 ATATTATGTAAATATATATAT
5033970 ATATT
1 ATATT
5033975 CTTAAGCGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 6 0.29
20 4 0.19
21 11 0.52
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
ATATTATGTAAATATATATAT
Found at i:5034195 original size:21 final size:21
Alignment explanation
Indices: 5034162--5034212 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
5034152 TATTATCCCC
** *
5034162 CATATTTAATGTTATCGTCAA
1 CATATTTTTTGTTATCATCAA
* *
5034183 CATATTTTTTGTTATTATCAT
1 CATATTTTTTGTTATCATCAA
5034204 CATATTTTT
1 CATATTTTT
5034213 AATATTATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.27, C:0.12, G:0.06, T:0.55
Consensus pattern (21 bp):
CATATTTTTTGTTATCATCAA
Found at i:5034661 original size:126 final size:126
Alignment explanation
Indices: 5034426--5034669 Score: 382
Period size: 126 Copynumber: 1.9 Consensus size: 126
5034416 CATTGATCTT
* * * *
5034426 CTCTTAAAATTTTTCAAAATAAAGGCAATGTTCGATAGTTAAATAATTCGAAGAATCGTGCCGTA
1 CTCTAAAAAATTTTCAAAATAAAGGCAATGTTCGATAGTTAAAGAATTCGAAGAATCGTGCCCTA
* *
5034491 ACGTACTGGGTTTCGCTTTCTTTGTTTGTCTTGAATATTCGAATATCCTCTTACCAATTCA
66 AAGTACTGGGTTTCACTTTCTTTGTTTGTCTTGAATATTCGAATATCCTCTTACCAATTCA
*
5034552 CTCTAAAAAATTTTCAAAATAAAGGCAATGTTC-AGTATTTAAAGAATTCGAAGAATCGTGCCCT
1 CTCTAAAAAATTTTCAAAATAAAGGCAATGTTCGA-TAGTTAAAGAATTCGAAGAATCGTGCCCT
* * *
5034616 AAAGTACTGTGTTTCACTTTCTTTGTTTGTTTTGAATATTCGAATATTCTCTTA
65 AAAGTACTGGGTTTCACTTTCTTTGTTTGTCTTGAATATTCGAATATCCTCTTA
5034670 AGGCTAAAAC
Statistics
Matches: 107, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
125 1 0.01
126 106 0.99
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (126 bp):
CTCTAAAAAATTTTCAAAATAAAGGCAATGTTCGATAGTTAAAGAATTCGAAGAATCGTGCCCTA
AAGTACTGGGTTTCACTTTCTTTGTTTGTCTTGAATATTCGAATATCCTCTTACCAATTCA
Found at i:5043813 original size:135 final size:135
Alignment explanation
Indices: 5043571--5043988 Score: 522
Period size: 135 Copynumber: 3.1 Consensus size: 135
5043561 CTACTTAGTA
* * ** * *
5043571 AAGATAAAGCTGATGATTGGGATCTGCTCCATCGCCGGTACGTGGAGATAAGATTCTCCAAAATT
1 AAGATAAGGCTGATGACTGAAATCTGCTCCATCGCCGATACATGGAGATAAGATTCTCCAAAATT
* * * * *
5043636 CGATCTGCTTCACTCTTGCTCAATGAAGATAAGATCTAGTATATTTAGCCTGCTTCACTCCTGCT
66 TGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTGGTATATTTAGCCTGCTCCACTCCTGCT
5043701 CAGTG
131 CAGTG
* * * * * * * *
5043706 AAGATAAGGTTGGTGGCTGAAATCTGCTCCATTGTCGATCCATGGAGATAAGTTTCACCAAAATT
1 AAGATAAGGCTGATGACTGAAATCTGCTCCATCGCCGATACATGGAGATAAGATTCTCCAAAATT
* * *
5043771 TGATCTGC-TCTGCTCCTGCTCAGCGAAGATAAGA-CTTGGTATATTTAGCCTACTCCACTCCTG
66 TGATCTGCTTC-ACTCCTGCTCAGTGAAGATAAGATC-TGGTATATTTAGCCTGCTCCACTCCTG
5043834 CTCAGTG
129 CTCAGTG
* * * * *
5043841 AAGATAAAGCTGATGATTGGAATCTGCTCCATCGCCGGTACGTGGAGATAAGATTCTCCAAAA-T
1 AAGATAAGGCTGATGACTGAAATCTGCTCCATCGCCGATACATGGAGATAAGATTCTCCAAAATT
*
5043905 TCATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTGG--TATTTAGCCTGCTCCACTCCTGCT
66 TGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTGGTATATTTAGCCTGCTCCACTCCTGCT
*
5043968 CAGTA
131 CAGTG
5043973 AAGATAAGGCTGATGA
1 AAGATAAGGCTGATGA
5043989 TATCTGCCAT
Statistics
Matches: 238, Mismatches: 41, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
132 42 0.18
134 35 0.15
135 161 0.68
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.29
Consensus pattern (135 bp):
AAGATAAGGCTGATGACTGAAATCTGCTCCATCGCCGATACATGGAGATAAGATTCTCCAAAATT
TGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTGGTATATTTAGCCTGCTCCACTCCTGCT
CAGTG
Found at i:5051854 original size:229 final size:229
Alignment explanation
Indices: 5051453--5051910 Score: 916
Period size: 229 Copynumber: 2.0 Consensus size: 229
5051443 TTGAGATCAC
5051453 CGAATCCGATGAGAGAGTTAAAAATTTAATAAATTAATACCTATGAGTCAAATGCGAATATAAAA
1 CGAATCCGATGAGAGAGTTAAAAATTTAATAAATTAATACCTATGAGTCAAATGCGAATATAAAA
5051518 GCATTTTTAGATTAGTGAATTTGGTGATTTAAAAGAATTAATTAGGTAAATTGGGTCGAGAATGA
66 GCATTTTTAGATTAGTGAATTTGGTGATTTAAAAGAATTAATTAGGTAAATTGGGTCGAGAATGA
5051583 GGTATCGAGACCTCGACTTCATAAATCGAGCCATAAATATTTTTAGAAATATTTATGGAGTGTTG
131 GGTATCGAGACCTCGACTTCATAAATCGAGCCATAAATATTTTTAGAAATATTTATGGAGTGTTG
5051648 GTGAGGTAGTATTAAAATTTAGTCAGAAAATTTT
196 GTGAGGTAGTATTAAAATTTAGTCAGAAAATTTT
5051682 CGAATCCGATGAGAGAGTTAAAAATTTAATAAATTAATACCTATGAGTCAAATGCGAATATAAAA
1 CGAATCCGATGAGAGAGTTAAAAATTTAATAAATTAATACCTATGAGTCAAATGCGAATATAAAA
5051747 GCATTTTTAGATTAGTGAATTTGGTGATTTAAAAGAATTAATTAGGTAAATTGGGTCGAGAATGA
66 GCATTTTTAGATTAGTGAATTTGGTGATTTAAAAGAATTAATTAGGTAAATTGGGTCGAGAATGA
5051812 GGTATCGAGACCTCGACTTCATAAATCGAGCCATAAATATTTTTAGAAATATTTATGGAGTGTTG
131 GGTATCGAGACCTCGACTTCATAAATCGAGCCATAAATATTTTTAGAAATATTTATGGAGTGTTG
5051877 GTGAGGTAGTATTAAAATTTAGTCAGAAAATTTT
196 GTGAGGTAGTATTAAAATTTAGTCAGAAAATTTT
5051911 GATGTTTGGG
Statistics
Matches: 229, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
229 229 1.00
ACGTcount: A:0.38, C:0.08, G:0.20, T:0.33
Consensus pattern (229 bp):
CGAATCCGATGAGAGAGTTAAAAATTTAATAAATTAATACCTATGAGTCAAATGCGAATATAAAA
GCATTTTTAGATTAGTGAATTTGGTGATTTAAAAGAATTAATTAGGTAAATTGGGTCGAGAATGA
GGTATCGAGACCTCGACTTCATAAATCGAGCCATAAATATTTTTAGAAATATTTATGGAGTGTTG
GTGAGGTAGTATTAAAATTTAGTCAGAAAATTTT
Found at i:5057353 original size:46 final size:46
Alignment explanation
Indices: 5057265--5057355 Score: 110
Period size: 46 Copynumber: 2.0 Consensus size: 46
5057255 TGTTACCTTG
* * *
5057265 ATGATGTGCTTGAGAGGAAAAGAGGAAGGATAATATAAGAGAATTA
1 ATGATGTGCTTAAGAGGAAAAGAGAAAGGATAAAATAAGAGAATTA
* * * **
5057311 ATGATGTGCTTAAGCGGAAAAGTGAAAGGGTAAAATGTGAGAATT
1 ATGATGTGCTTAAGAGGAAAAGAGAAAGGATAAAATAAGAGAATT
5057356 GAAAAGGTAA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
46 37 1.00
ACGTcount: A:0.43, C:0.03, G:0.31, T:0.23
Consensus pattern (46 bp):
ATGATGTGCTTAAGAGGAAAAGAGAAAGGATAAAATAAGAGAATTA
Found at i:5059465 original size:23 final size:23
Alignment explanation
Indices: 5059435--5059481 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
5059425 AGTTTTGAAC
*
5059435 TTAAAAAATGGCAGATAAAATAG
1 TTAAAAAATGGCAGAGAAAATAG
5059458 TTAAAAAATGGCAGAGAAAATAG
1 TTAAAAAATGGCAGAGAAAATAG
5059481 T
1 T
5059482 ATGGTTGCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.55, C:0.04, G:0.19, T:0.21
Consensus pattern (23 bp):
TTAAAAAATGGCAGAGAAAATAG
Found at i:5063300 original size:35 final size:35
Alignment explanation
Indices: 5063261--5063329 Score: 138
Period size: 35 Copynumber: 2.0 Consensus size: 35
5063251 TTGTCCACGG
5063261 TCTTTCATGAATTCCCTTGTTAACTCAGGTTCATA
1 TCTTTCATGAATTCCCTTGTTAACTCAGGTTCATA
5063296 TCTTTCATGAATTCCCTTGTTAACTCAGGTTCAT
1 TCTTTCATGAATTCCCTTGTTAACTCAGGTTCAT
5063330 CTTTATTGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.22, C:0.23, G:0.12, T:0.43
Consensus pattern (35 bp):
TCTTTCATGAATTCCCTTGTTAACTCAGGTTCATA
Found at i:5078335 original size:26 final size:26
Alignment explanation
Indices: 5078284--5078335 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
5078274 TAATTTGTTA
* **
5078284 TAAAATTAATATATTTAACTTTAATT
1 TAAAATTAATAAATTTAACTACAATT
5078310 TAAAATTAAATAAATTTAA-TACAATT
1 TAAAATT-AATAAATTTAACTACAATT
5078336 ATACATTAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (26 bp):
TAAAATTAATAAATTTAACTACAATT
Found at i:5099080 original size:28 final size:28
Alignment explanation
Indices: 5099049--5099108 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
5099039 CATATTAATA
5099049 GGGTATAGGAAAAGTCTCATAACTTATG
1 GGGTATAGGAAAAGTCTCATAACTTATG
* * * *
5099077 GGGTATAGGAAGAGTTTTATAATTTATG
1 GGGTATAGGAAAAGTCTCATAACTTATG
5099105 GGGT
1 GGGT
5099109 TGATAATGAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.05, G:0.30, T:0.33
Consensus pattern (28 bp):
GGGTATAGGAAAAGTCTCATAACTTATG
Found at i:5099294 original size:25 final size:26
Alignment explanation
Indices: 5099266--5099342 Score: 67
Period size: 25 Copynumber: 3.1 Consensus size: 26
5099256 TTTAAAATAA
5099266 AATAGTATTTATTATATAAT-TAATT
1 AATAGTATTTATTATATAATATAATT
* *
5099291 AATA-CATATTATTA-ACAATATAATT
1 AATAGTAT-TTATTATATAATATAATT
5099316 --T-GTATTTATTATATAAAATATAATT
1 AATAGTATTTATTATAT--AATATAATT
5099341 AA
1 AA
5099343 CAATAATTGT
Statistics
Matches: 40, Mismatches: 4, Indels: 14
0.69 0.07 0.24
Matches are distributed among these distances:
22 6 0.15
23 4 0.10
24 6 0.15
25 24 0.60
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.47
Consensus pattern (26 bp):
AATAGTATTTATTATATAATATAATT
Found at i:5114304 original size:24 final size:24
Alignment explanation
Indices: 5114277--5114324 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
5114267 TCAAAATAAG
5114277 CGAAAAGTTTTCCTTCTCTTTGCC
1 CGAAAAGTTTTCCTTCTCTTTGCC
5114301 CGAAAAGTTTTCCTTCTCTTTGCC
1 CGAAAAGTTTTCCTTCTCTTTGCC
5114325 ACAAACAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.17, C:0.29, G:0.12, T:0.42
Consensus pattern (24 bp):
CGAAAAGTTTTCCTTCTCTTTGCC
Found at i:5116590 original size:76 final size:74
Alignment explanation
Indices: 5116459--5116615 Score: 287
Period size: 76 Copynumber: 2.1 Consensus size: 74
5116449 CGAAGCGAAT
5116459 CAGGTAAGAACTTCTGTTTCATGGTAGTAAATTATTATTGCATTTCTAATGGACTGAGGATAAAA
1 CAGG-AAGAACTTCTGTTTCATGGTAGTAAATTATTATTGCATTTCTAATGGACTGAGGAT--AA
5116524 CTTTTCTTTCTA
63 CTTTTCTTTCTA
5116536 CAGGAAGAACTTCTGTTTCATGGTAGTAAATTATTATTGCATTTCTAATGGACTGAGGATAACTT
1 CAGGAAGAACTTCTGTTTCATGGTAGTAAATTATTATTGCATTTCTAATGGACTGAGGATAACTT
5116601 TTCTTTCTA
66 TTCTTTCTA
5116610 CAGGAA
1 CAGGAA
5116616 ATTATCCAAG
Statistics
Matches: 80, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
74 20 0.25
76 56 0.70
77 4 0.05
ACGTcount: A:0.30, C:0.13, G:0.18, T:0.39
Consensus pattern (74 bp):
CAGGAAGAACTTCTGTTTCATGGTAGTAAATTATTATTGCATTTCTAATGGACTGAGGATAACTT
TTCTTTCTA
Found at i:5124857 original size:6 final size:6
Alignment explanation
Indices: 5124848--5124880 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
5124838 TTTTTTTTTT
*
5124848 TGTGCG TGTGCG TGTGCG TGTGCG TGTGTG TGT
1 TGTGCG TGTGCG TGTGCG TGTGCG TGTGCG TGT
5124881 TTGTGAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.12, G:0.48, T:0.39
Consensus pattern (6 bp):
TGTGCG
Found at i:5125977 original size:6 final size:6
Alignment explanation
Indices: 5125968--5125997 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
5125958 TACGTGTACG
5125968 TGTATA TGTATA TGTATA TGTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA
5125998 CATGTACTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
TGTATA
Found at i:5126240 original size:18 final size:17
Alignment explanation
Indices: 5126217--5126250 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
5126207 TTTTTTTTTT
5126217 GGGGGGGGGGGTTCAAA
1 GGGGGGGGGGGTTCAAA
5126234 GGGGGGGGGGGTTCAAA
1 GGGGGGGGGGGTTCAAA
5126251 TGGTTGTGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.06, G:0.65, T:0.12
Consensus pattern (17 bp):
GGGGGGGGGGGTTCAAA
Found at i:5126827 original size:6 final size:6
Alignment explanation
Indices: 5126816--5126863 Score: 60
Period size: 6 Copynumber: 8.0 Consensus size: 6
5126806 TGGCCCCAGC
* * * *
5126816 GATGGG GATGGG GATGGG GATGGG TATGGG CATGGG CATGGG CATGGG
1 GATGGG GATGGG GATGGG GATGGG GATGGG GATGGG GATGGG GATGGG
5126864 TGTCATGGAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.17, C:0.06, G:0.58, T:0.19
Consensus pattern (6 bp):
GATGGG
Found at i:5130210 original size:43 final size:44
Alignment explanation
Indices: 5130149--5130238 Score: 164
Period size: 45 Copynumber: 2.0 Consensus size: 44
5130139 ATTTACTACT
5130149 TTCATATGATATAAAAAAA-GGGGGGGTTAATAAGAGTTAGATA
1 TTCATATGATATAAAAAAAGGGGGGGGTTAATAAGAGTTAGATA
5130192 TTCATATGATATAAAAAAAGGGGGGGGGTTAATAAGAGTTAGATA
1 TTCATATGATATAAAAAAA-GGGGGGGGTTAATAAGAGTTAGATA
5130237 TT
1 TT
5130239 TATTATAAGC
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
43 19 0.42
45 26 0.58
ACGTcount: A:0.42, C:0.02, G:0.27, T:0.29
Consensus pattern (44 bp):
TTCATATGATATAAAAAAAGGGGGGGGTTAATAAGAGTTAGATA
Found at i:5137215 original size:45 final size:45
Alignment explanation
Indices: 5137110--5137225 Score: 151
Period size: 45 Copynumber: 2.6 Consensus size: 45
5137100 ATCATACCAG
* *
5137110 AAATGAGTAAGACCATAGCTGAAAGATGCTATGGCATCATGATTC
1 AAATGAGTAAGACCATAGCTGAAAGACGCTATGGCATCACGATTC
* * *
5137155 AGACGAGTAAGACCATAGCTGAAAGACGCTATGGCATCGCGATTC
1 AAATGAGTAAGACCATAGCTGAAAGACGCTATGGCATCACGATTC
* * * *
5137200 AAATGTGTAACACCATGGTTGAAAGA
1 AAATGAGTAAGACCATAGCTGAAAGA
5137226 TACCATGGCA
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 60 1.00
ACGTcount: A:0.37, C:0.17, G:0.24, T:0.22
Consensus pattern (45 bp):
AAATGAGTAAGACCATAGCTGAAAGACGCTATGGCATCACGATTC
Found at i:5137268 original size:46 final size:46
Alignment explanation
Indices: 5137211--5137419 Score: 364
Period size: 46 Copynumber: 4.5 Consensus size: 46
5137201 AATGTGTAAC
5137211 ACCATGGTTGAAAGATACCATGGCAACATGACAGGAAATGAATAAG
1 ACCATGGTTGAAAGATACCATGGCAACATGACAGGAAATGAATAAG
*
5137257 ACCATGATTGAAAGATACCATGGCAACATGACAGGAAATGAATAAG
1 ACCATGGTTGAAAGATACCATGGCAACATGACAGGAAATGAATAAG
5137303 ACCATGGTTGAAAGATACCATGGCAACATGACAGGAAATGAATAAG
1 ACCATGGTTGAAAGATACCATGGCAACATGACAGGAAATGAATAAG
* *
5137349 ACCATGGTTGAAAGATACCACGGCAACATGACATGAAATGAATAAG
1 ACCATGGTTGAAAGATACCATGGCAACATGACAGGAAATGAATAAG
* * *
5137395 ACCATAGTTGAAAGACACTATGGCA
1 ACCATGGTTGAAAGATACCATGGCA
5137420 TCATTTCGAA
Statistics
Matches: 155, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 155 1.00
ACGTcount: A:0.44, C:0.16, G:0.22, T:0.18
Consensus pattern (46 bp):
ACCATGGTTGAAAGATACCATGGCAACATGACAGGAAATGAATAAG
Found at i:5140576 original size:10 final size:10
Alignment explanation
Indices: 5140563--5140608 Score: 65
Period size: 10 Copynumber: 4.6 Consensus size: 10
5140553 AAAATAATTT
*
5140563 AAAAATCATA
1 AAAAATTATA
5140573 AAAAATTATA
1 AAAAATTATA
**
5140583 AAAAATGGTA
1 AAAAATTATA
5140593 AAAAATTATA
1 AAAAATTATA
5140603 AAAAAT
1 AAAAAT
5140609 GGTAAACTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 31 1.00
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.24
Consensus pattern (10 bp):
AAAAATTATA
Found at i:5140586 original size:20 final size:20
Alignment explanation
Indices: 5140563--5140608 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
5140553 AAAATAATTT
5140563 AAAAATCATAAAAAATTATA
1 AAAAATCATAAAAAATTATA
**
5140583 AAAAATGGTAAAAAATTATA
1 AAAAATCATAAAAAATTATA
5140603 AAAAAT
1 AAAAAT
5140609 GGTAAACTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.24
Consensus pattern (20 bp):
AAAAATCATAAAAAATTATA
Found at i:5140609 original size:20 final size:20
Alignment explanation
Indices: 5140571--5140614 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
5140561 TTAAAAATCA
5140571 TAAAAAATTATAAAAAATGG
1 TAAAAAATTATAAAAAATGG
5140591 TAAAAAATTATAAAAAATGG
1 TAAAAAATTATAAAAAATGG
5140611 TAAA
1 TAAA
5140615 CTATACAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.25
Consensus pattern (20 bp):
TAAAAAATTATAAAAAATGG
Found at i:5140614 original size:10 final size:10
Alignment explanation
Indices: 5140563--5140614 Score: 59
Period size: 10 Copynumber: 5.2 Consensus size: 10
5140553 AAAATAATTT
*
5140563 AAAAATCATA
1 AAAAATGATA
*
5140573 AAAAATTATA
1 AAAAATGATA
*
5140583 AAAAATGGTA
1 AAAAATGATA
*
5140593 AAAAATTATA
1 AAAAATGATA
*
5140603 AAAAATGGTA
1 AAAAATGATA
5140613 AA
1 AA
5140615 CTATACAAAG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 35 1.00
ACGTcount: A:0.67, C:0.02, G:0.08, T:0.23
Consensus pattern (10 bp):
AAAAATGATA
Found at i:5152336 original size:14 final size:14
Alignment explanation
Indices: 5152317--5152344 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5152307 CGATTTTTTG
5152317 ATTAAAAAAATATT
1 ATTAAAAAAATATT
5152331 ATTAAAAAAATATT
1 ATTAAAAAAATATT
5152345 TAAAAGTGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
ATTAAAAAAATATT
Found at i:5153640 original size:30 final size:30
Alignment explanation
Indices: 5153604--5153666 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
5153594 ACTTAACAAG
5153604 CAAATGCCTCTAAAATAATAAAAAAATTAA
1 CAAATGCCTCTAAAATAATAAAAAAATTAA
* *
5153634 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAAAAAAATTAA
5153664 CAA
1 CAA
5153667 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.59, C:0.14, G:0.03, T:0.24
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAAAAAAATTAA
Found at i:5154189 original size:21 final size:21
Alignment explanation
Indices: 5154159--5154198 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5154149 TTTAATTTTT
5154159 TTCAGAATGAAAACGTTGAAG
1 TTCAGAATGAAAACGTTGAAG
* *
5154180 TTCAGGATGAAAATGTTGA
1 TTCAGAATGAAAACGTTGA
5154199 CATTGTATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.07, G:0.25, T:0.28
Consensus pattern (21 bp):
TTCAGAATGAAAACGTTGAAG
Found at i:5179407 original size:21 final size:21
Alignment explanation
Indices: 5179381--5179421 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
5179371 CATCATCAAC
5179381 CAAAACTTAAAAAATTCTCAT
1 CAAAACTTAAAAAATTCTCAT
5179402 CAAAACTTAAAAAATTCTCA
1 CAAAACTTAAAAAATTCTCA
5179422 GAGTACCATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.54, C:0.20, G:0.00, T:0.27
Consensus pattern (21 bp):
CAAAACTTAAAAAATTCTCAT
Found at i:5180996 original size:23 final size:23
Alignment explanation
Indices: 5180969--5181014 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
5180959 CGTTCACAAA
5180969 GGTACATCTTATAACAAAATAAG
1 GGTACATCTTATAACAAAATAAG
*
5180992 GGTACATCTTATAACAGAATAAG
1 GGTACATCTTATAACAAAATAAG
5181015 CTTGAATCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.46, C:0.13, G:0.15, T:0.26
Consensus pattern (23 bp):
GGTACATCTTATAACAAAATAAG
Found at i:5193082 original size:30 final size:30
Alignment explanation
Indices: 5193048--5193107 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
5193038 TTATAAAGAT
5193048 AGCAATGGAAAGATTAAAATATATTGTTAA
1 AGCAATGGAAAGATTAAAATATATTGTTAA
*
5193078 AGCAATGGAAAGATTAAAATATGTTGTTAA
1 AGCAATGGAAAGATTAAAATATATTGTTAA
5193108 TATATGTACT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.18, T:0.30
Consensus pattern (30 bp):
AGCAATGGAAAGATTAAAATATATTGTTAA
Found at i:5195466 original size:814 final size:814
Alignment explanation
Indices: 5193898--5195525 Score: 3256
Period size: 814 Copynumber: 2.0 Consensus size: 814
5193888 AATTCTCTTA
5193898 CTTAAGAGGAATATAGCACCACATCCAGCACGATAGGGCATGATCCTTTATGCCCTCGAAAATAT
1 CTTAAGAGGAATATAGCACCACATCCAGCACGATAGGGCATGATCCTTTATGCCCTCGAAAATAT
5193963 GATTAATTCTGACTTCCAAAAATTTGTAAGTTGAAAACCGCAAAAGGATGCCCAATTATTCGATC
66 GATTAATTCTGACTTCCAAAAATTTGTAAGTTGAAAACCGCAAAAGGATGCCCAATTATTCGATC
5194028 CAACGAGAAAATCGAAACCCACCACTGTAGGGCACGACTCCCGAATTTCTAGACGTTAGACATTG
131 CAACGAGAAAATCGAAACCCACCACTGTAGGGCACGACTCCCGAATTTCTAGACGTTAGACATTG
5194093 TCTTATTTTAGAATGTTAGGATTTGAACCCGATTAAGTAACGAACAAGAAAATAGCAGAATAAAT
196 TCTTATTTTAGAATGTTAGGATTTGAACCCGATTAAGTAACGAACAAGAAAATAGCAGAATAAAT
5194158 TGAGAAATTGAACACACAAATTTAACGTGGAAAAACCCCTCCAAAGAGGATAAAAAAACCACGGG
261 TGAGAAATTGAACACACAAATTTAACGTGGAAAAACCCCTCCAAAGAGGATAAAAAAACCACGGG
5194223 CAAAGATAATTTTACTATAATAGAAAAAGAACGAAGAGTACAAAAGATGGAGATAAAAACTAAAC
326 CAAAGATAATTTTACTATAATAGAAAAAGAACGAAGAGTACAAAAGATGGAGATAAAAACTAAAC
5194288 CCCGAAAACAAAGAACCCACAAAACGTAAACACAAAATTCTCTAAATGTGTTATGAGTTCTAATC
391 CCCGAAAACAAAGAACCCACAAAACGTAAACACAAAATTCTCTAAATGTGTTATGAGTTCTAATC
5194353 TCTAATGGGTGTATTTTCTAATGTTGTAAAAGAGCCTATTTATAGGCTAAAATAATCTAAACTAA
456 TCTAATGGGTGTATTTTCTAATGTTGTAAAAGAGCCTATTTATAGGCTAAAATAATCTAAACTAA
5194418 TCAGTGTTTGATTGAAACAAGTAAACAGAGTTTAACTGAAAGATTATTTTTCAAATTTGACTGAA
521 TCAGTGTTTGATTGAAACAAGTAAACAGAGTTTAACTGAAAGATTATTTTTCAAATTTGACTGAA
5194483 AATAGGAGTCTTATTTAACATAGAATTTAGAGAGTATGAGTGAAATTCTAAAGGAATCTTCGATC
586 AATAGGAGTCTTATTTAACATAGAATTTAGAGAGTATGAGTGAAATTCTAAAGGAATCTTCGATC
5194548 CTTGAACGAACGGGAAATCGCAACCCAGCACGATAGGGCACGACTCCCGAATTGCCAAACATCGA
651 CTTGAACGAACGGGAAATCGCAACCCAGCACGATAGGGCACGACTCCCGAATTGCCAAACATCGA
5194613 GTATTACCTTCGTTTTAAAGAGTTTTTAGAAAACATGAACAAAATTCTAAAGGGATAATTGATTA
716 GTATTACCTTCGTTTTAAAGAGTTTTTAGAAAACATGAACAAAATTCTAAAGGGATAATTGATTA
5194678 TTTTGAGCAAACGAGAAATTGTAACCCAGCACGT
781 TTTTGAGCAAACGAGAAATTGTAACCCAGCACGT
5194712 CTTAAGAGGAATATAGCACCACATCCAGCACGATAGGGCATGATCCTTTATGCCCTCGAAAATAT
1 CTTAAGAGGAATATAGCACCACATCCAGCACGATAGGGCATGATCCTTTATGCCCTCGAAAATAT
5194777 GATTAATTCTGACTTCCAAAAATTTGTAAGTTGAAAACCGCAAAAGGATGCCCAATTATTCGATC
66 GATTAATTCTGACTTCCAAAAATTTGTAAGTTGAAAACCGCAAAAGGATGCCCAATTATTCGATC
5194842 CAACGAGAAAATCGAAACCCACCACTGTAGGGCACGACTCCCGAATTTCTAGACGTTAGACATTG
131 CAACGAGAAAATCGAAACCCACCACTGTAGGGCACGACTCCCGAATTTCTAGACGTTAGACATTG
5194907 TCTTATTTTAGAATGTTAGGATTTGAACCCGATTAAGTAACGAACAAGAAAATAGCAGAATAAAT
196 TCTTATTTTAGAATGTTAGGATTTGAACCCGATTAAGTAACGAACAAGAAAATAGCAGAATAAAT
5194972 TGAGAAATTGAACACACAAATTTAACGTGGAAAAACCCCTCCAAAGAGGATAAAAAAACCACGGG
261 TGAGAAATTGAACACACAAATTTAACGTGGAAAAACCCCTCCAAAGAGGATAAAAAAACCACGGG
5195037 CAAAGATAATTTTACTATAATAGAAAAAGAACGAAGAGTACAAAAGATGGAGATAAAAACTAAAC
326 CAAAGATAATTTTACTATAATAGAAAAAGAACGAAGAGTACAAAAGATGGAGATAAAAACTAAAC
5195102 CCCGAAAACAAAGAACCCACAAAACGTAAACACAAAATTCTCTAAATGTGTTATGAGTTCTAATC
391 CCCGAAAACAAAGAACCCACAAAACGTAAACACAAAATTCTCTAAATGTGTTATGAGTTCTAATC
5195167 TCTAATGGGTGTATTTTCTAATGTTGTAAAAGAGCCTATTTATAGGCTAAAATAATCTAAACTAA
456 TCTAATGGGTGTATTTTCTAATGTTGTAAAAGAGCCTATTTATAGGCTAAAATAATCTAAACTAA
5195232 TCAGTGTTTGATTGAAACAAGTAAACAGAGTTTAACTGAAAGATTATTTTTCAAATTTGACTGAA
521 TCAGTGTTTGATTGAAACAAGTAAACAGAGTTTAACTGAAAGATTATTTTTCAAATTTGACTGAA
5195297 AATAGGAGTCTTATTTAACATAGAATTTAGAGAGTATGAGTGAAATTCTAAAGGAATCTTCGATC
586 AATAGGAGTCTTATTTAACATAGAATTTAGAGAGTATGAGTGAAATTCTAAAGGAATCTTCGATC
5195362 CTTGAACGAACGGGAAATCGCAACCCAGCACGATAGGGCACGACTCCCGAATTGCCAAACATCGA
651 CTTGAACGAACGGGAAATCGCAACCCAGCACGATAGGGCACGACTCCCGAATTGCCAAACATCGA
5195427 GTATTACCTTCGTTTTAAAGAGTTTTTAGAAAACATGAACAAAATTCTAAAGGGATAATTGATTA
716 GTATTACCTTCGTTTTAAAGAGTTTTTAGAAAACATGAACAAAATTCTAAAGGGATAATTGATTA
5195492 TTTTGAGCAAACGAGAAATTGTAACCCAGCACGT
781 TTTTGAGCAAACGAGAAATTGTAACCCAGCACGT
5195526 TAGGGCACGA
Statistics
Matches: 814, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
814 814 1.00
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.25
Consensus pattern (814 bp):
CTTAAGAGGAATATAGCACCACATCCAGCACGATAGGGCATGATCCTTTATGCCCTCGAAAATAT
GATTAATTCTGACTTCCAAAAATTTGTAAGTTGAAAACCGCAAAAGGATGCCCAATTATTCGATC
CAACGAGAAAATCGAAACCCACCACTGTAGGGCACGACTCCCGAATTTCTAGACGTTAGACATTG
TCTTATTTTAGAATGTTAGGATTTGAACCCGATTAAGTAACGAACAAGAAAATAGCAGAATAAAT
TGAGAAATTGAACACACAAATTTAACGTGGAAAAACCCCTCCAAAGAGGATAAAAAAACCACGGG
CAAAGATAATTTTACTATAATAGAAAAAGAACGAAGAGTACAAAAGATGGAGATAAAAACTAAAC
CCCGAAAACAAAGAACCCACAAAACGTAAACACAAAATTCTCTAAATGTGTTATGAGTTCTAATC
TCTAATGGGTGTATTTTCTAATGTTGTAAAAGAGCCTATTTATAGGCTAAAATAATCTAAACTAA
TCAGTGTTTGATTGAAACAAGTAAACAGAGTTTAACTGAAAGATTATTTTTCAAATTTGACTGAA
AATAGGAGTCTTATTTAACATAGAATTTAGAGAGTATGAGTGAAATTCTAAAGGAATCTTCGATC
CTTGAACGAACGGGAAATCGCAACCCAGCACGATAGGGCACGACTCCCGAATTGCCAAACATCGA
GTATTACCTTCGTTTTAAAGAGTTTTTAGAAAACATGAACAAAATTCTAAAGGGATAATTGATTA
TTTTGAGCAAACGAGAAATTGTAACCCAGCACGT
Found at i:5195607 original size:135 final size:132
Alignment explanation
Indices: 5195370--5195853 Score: 605
Period size: 132 Copynumber: 3.7 Consensus size: 132
5195360 TCCTTGAACG
* * * * * * ** **
5195370 AACGGGAAATCGCAACCCAGCACGATAGGGCACGACTCC-CGAATTGCCAAACATCGAGTATTAC
1 AACGAGAAATTGCAACCCAGCACGTTAGGGCACGATTCCGCGAATTGCCAAATATCAAACATCGC
* ** * *
5195434 CTTCGTTTTAAAGAGTTTTTAGAAAACATGAACAAAATTCTAAAGGGATAATT-GATTATTTTGA
66 CTTCGTTTTAAAGAGTTTTTAGAAGACATGAATGAAATTTTGAAGGGAT-ATTCGATTATTTTGA
5195498 GCA
130 GCA
* * *
5195501 AACGAGAAATTGTAACCCAGCACGTTAGGGCACGATTCCGCGAATTGTCAAATATCGAACATCGC
1 AACGAGAAATTGCAACCCAGCACGTTAGGGCACGATTCCGCGAATTGCCAAATATCAAACATCGC
* *
5195566 CTTCGTTTTAAAGGATTGTTTTTAGAAGACATGAATGAAATTTTGAAGAGATATTCGATCATTTT
66 CTTCGTTTTAAA-GA--GTTTTTAGAAGACATGAATGAAATTTTGAAGGGATATTCGATTATTTT
*
5195631 GAGAA
128 GAGCA
* *
5195636 AACGAGAAATTGCAACCCAACACGTTAGGGCACGATTCCACGAATTGCCAAATATCAAACATCGC
1 AACGAGAAATTGCAACCCAGCACGTTAGGGCACGATTCCGCGAATTGCCAAATATCAAACATCGC
* * * ** *
5195701 ATTCGTTTTAAAGAATTTTTAAAAGACATGGGTGAAATTTTGAAGGGGTATTCGATTATTTTGAG
66 CTTCGTTTTAAAGAGTTTTTAGAAGACATGAATGAAATTTTGAAGGGATATTCGATTATTTTGAG
5195766 CA
131 CA
* *
5195768 AACGTGAAATTGCAACCCAGCACGTTAGGCCACGATTCCGCGAATTGCCAAATATCAAATC-TCG
1 AACGAGAAATTGCAACCCAGCACGTTAGGGCACGATTCCGCGAATTGCCAAATATCAAA-CATCG
* *
5195832 TCTTCGTTTTAAAGAATTTTTA
65 CCTTCGTTTTAAAGAGTTTTTA
5195854 AATGAATAAT
Statistics
Matches: 308, Mismatches: 39, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
131 34 0.11
132 154 0.50
133 3 0.01
134 5 0.02
135 112 0.36
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (132 bp):
AACGAGAAATTGCAACCCAGCACGTTAGGGCACGATTCCGCGAATTGCCAAATATCAAACATCGC
CTTCGTTTTAAAGAGTTTTTAGAAGACATGAATGAAATTTTGAAGGGATATTCGATTATTTTGAG
CA
Found at i:5195914 original size:267 final size:264
Alignment explanation
Indices: 5195370--5195855 Score: 611
Period size: 267 Copynumber: 1.8 Consensus size: 264
5195360 TCCTTGAACG
* * * * ** * *
5195370 AACGGGAAATCGCAACCCAGCACGATAGGGCACGACTCCCGAATTGCCAAACATCGAGTATTACC
1 AACGAGAAATTGCAACCCAACACGATAGGGCACGACTCCCGAATTGCCAAACATCAAACATCACA
*
5195435 TTCGTTTTAAAGAGTTTTTAGAAAACATGAACAAAATTCTAAAGGGATAATTGATTATTTTGAGC
66 TTCGTTTTAAAGAATTTTTAGAAAACATGAACAAAATTCTAAAGGGATAATTGATTATTTTGAGC
* * * *
5195500 AAACGAGAAATTGTAACCCAGCACGTTAGGGCACGATTCCGCGAATTGTCAAATATCGAACATCG
131 AAACGAGAAATTGCAACCCAGCACGTTAGGCCACGATTCCGCGAATTGCCAAATATCAAACATCG
* ** * *
5195565 CCTTCGTTTTAAAGGATTGTTTTTAGAAGACATGAATGAAATTTTGAAGAGATATTCGATCATTT
196 CCTTCGTTTTAAAGAATTGTTTAAAGAAGACATGAATAAAATTTTGAAAAGATATTCGATC--TT
5195630 TGAGAA
259 TGAGAA
* * * *
5195636 AACGAGAAATTGCAACCCAACACGTTAGGGCACGATTCCACGAATTGCCAAATATCAAACATCGC
1 AACGAGAAATTGCAACCCAACACGATAGGGCACGACTCC-CGAATTGCCAAACATCAAACATCAC
**** * * *
5195701 ATTCGTTTTAAAGAATTTTTA-AAAGACATGGGTGAAATTTTGAAGGGGT-ATTCGATTATTTTG
65 ATTCGTTTTAAAGAATTTTTAGAAA-ACATGAACAAAATTCTAAAGGGATAATT-GATTATTTTG
*
5195764 AGCAAACGTGAAATTGCAACCCAGCACGTTAGGCCACGATTCCGCGAATTGCCAAATATCAAATC
128 AGCAAACGAGAAATTGCAACCCAGCACGTTAGGCCACGATTCCGCGAATTGCCAAATATCAAA-C
*
5195829 -TCGTCTTCGTTTTAAAGAATT-TTTAAA
192 ATCGCCTTCGTTTTAAAGAATTGTTTAAA
5195856 TGAATAATTA
Statistics
Matches: 187, Mismatches: 29, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
266 44 0.24
267 142 0.76
268 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (264 bp):
AACGAGAAATTGCAACCCAACACGATAGGGCACGACTCCCGAATTGCCAAACATCAAACATCACA
TTCGTTTTAAAGAATTTTTAGAAAACATGAACAAAATTCTAAAGGGATAATTGATTATTTTGAGC
AAACGAGAAATTGCAACCCAGCACGTTAGGCCACGATTCCGCGAATTGCCAAATATCAAACATCG
CCTTCGTTTTAAAGAATTGTTTAAAGAAGACATGAATAAAATTTTGAAAAGATATTCGATCTTTG
AGAA
Found at i:5197328 original size:14 final size:15
Alignment explanation
Indices: 5197309--5197338 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5197299 GAATCATAAG
5197309 ATAAAA-AAAATAGA
1 ATAAAAGAAAATAGA
5197323 ATAAAAGAAAATAGA
1 ATAAAAGAAAATAGA
5197338 A
1 A
5197339 AAGGAGACTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (15 bp):
ATAAAAGAAAATAGA
Found at i:5202671 original size:20 final size:20
Alignment explanation
Indices: 5202643--5202691 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
5202633 ATATATCCTG
*
5202643 ATTTTATTTGATTTCAATCA
1 ATTTGATTTGATTTCAATCA
*
5202663 ATTTGATTTGATTTTAATCA
1 ATTTGATTTGATTTCAATCA
*
5202683 AATTGATTT
1 ATTTGATTT
5202692 AATCGTTCCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.31, C:0.06, G:0.08, T:0.55
Consensus pattern (20 bp):
ATTTGATTTGATTTCAATCA
Found at i:5203151 original size:28 final size:28
Alignment explanation
Indices: 5203119--5203187 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 28
5203109 CATAATTTAA
5203119 ATATAAATTATTCAATTTATTT-TATTTT
1 ATATAAATTATTCAATTTATTTATA-TTT
* *
5203147 ATATAGAAATATT-TATTTATTTATATTT
1 ATATA-AATTATTCAATTTATTTATATTT
*
5203175 ATAT-ATTTATTCA
1 ATATAAATTATTCA
5203188 CTAACATGTT
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
26 5 0.15
28 20 0.61
29 8 0.24
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (28 bp):
ATATAAATTATTCAATTTATTTATATTT
Found at i:5203172 original size:14 final size:14
Alignment explanation
Indices: 5203155--5203184 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5203145 TTATATAGAA
*
5203155 ATATTTATTTATTT
1 ATATTTATATATTT
5203169 ATATTTATATATTT
1 ATATTTATATATTT
5203183 AT
1 AT
5203185 TCACTAACAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
ATATTTATATATTT
Found at i:5203262 original size:18 final size:18
Alignment explanation
Indices: 5203221--5203262 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
5203211 ACAAGTTTCA
* *
5203221 TCCAATAAAAATAATTCT
1 TCCAAAAAAAATAATTAT
*
5203239 TACAAAAAAAATAATTAT
1 TCCAAAAAAAATAATTAT
5203257 TCCAAA
1 TCCAAA
5203263 TTTCATTTAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (18 bp):
TCCAAAAAAAATAATTAT
Found at i:5203698 original size:28 final size:28
Alignment explanation
Indices: 5203647--5203700 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
5203637 TAGAAAAAAC
*
5203647 ATTAAGACATTAAATGCAATGAAAAGTT
1 ATTAAGACATTAAATGCAAAGAAAAGTT
5203675 ATTAAGACATTAAATG-AAGAGAAAAG
1 ATTAAGACATTAAATGCAA-AGAAAAG
5203701 GCTATTGTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 2 0.08
28 22 0.92
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.24
Consensus pattern (28 bp):
ATTAAGACATTAAATGCAAAGAAAAGTT
Found at i:5206524 original size:149 final size:149
Alignment explanation
Indices: 5206254--5206550 Score: 576
Period size: 149 Copynumber: 2.0 Consensus size: 149
5206244 GTCAGAACTT
5206254 CATCTGGGTTCGAACCCTACTGAGAGGTCCACTAGAGATCAGAAATTGTTGAAGAAAGAACAAGA
1 CATCTGGGTTCGAACCCTACTGAGAGGTCCACTAGAGATCAGAAATTGTTGAAGAAAGAACAAGA
*
5206319 TGTTTCTTTTGTCCCTTCCAGGCGATTGGAAAATAAAGAAATAGTTAATATATTCAAGAAAATTA
66 TGTTTCTTTTGTCCCTTCCAGGCGATCGGAAAATAAAGAAATAGTTAATATATTCAAGAAAATTA
5206384 CGTATTTACAAAATACCGC
131 CGTATTTACAAAATACCGC
5206403 CATCTGGGTTCGAACCCTACTGAGAGGTCCACTAGAGATCAGAAATTGTTGAAGAAAGAACAAGA
1 CATCTGGGTTCGAACCCTACTGAGAGGTCCACTAGAGATCAGAAATTGTTGAAGAAAGAACAAGA
*
5206468 TGTTTCTTTTGTCCCTTCCAGGCGATCGGAAAATAAAGAAATAGTTAATATATTCAAGATAATTA
66 TGTTTCTTTTGTCCCTTCCAGGCGATCGGAAAATAAAGAAATAGTTAATATATTCAAGAAAATTA
5206533 CGTATTTACAAAATACCG
131 CGTATTTACAAAATACCG
5206551 TCTCAATTCA
Statistics
Matches: 146, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 146 1.00
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.28
Consensus pattern (149 bp):
CATCTGGGTTCGAACCCTACTGAGAGGTCCACTAGAGATCAGAAATTGTTGAAGAAAGAACAAGA
TGTTTCTTTTGTCCCTTCCAGGCGATCGGAAAATAAAGAAATAGTTAATATATTCAAGAAAATTA
CGTATTTACAAAATACCGC
Found at i:5208266 original size:107 final size:106
Alignment explanation
Indices: 5208081--5208301 Score: 401
Period size: 107 Copynumber: 2.1 Consensus size: 106
5208071 TTCTTTCTTC
*
5208081 AATGAAAATCGCCACACTTCCTTTTTTCTTCTAAACAACCAATTCAAGAACCCTGCAATGGCCAA
1 AATGAAAATCGCCACACTTCCCTTTTTCTTCTAAACAACCAATTCAAGAACCCTGCAATGGCCAA
5208146 ACATATTCATTATTTTAACATCATATAACATAATATCTAAG
66 ACATATTCATTATTTTAACATCATATAACATAATATCTAAG
*
5208187 AATGAAAATCGCCACACTTCCCTTTTTCTTCTAAAACAACCTATTCAAGAACCCTGCAATGGCCA
1 AATGAAAATCGCCACACTTCCCTTTTTCTTCT-AAACAACCAATTCAAGAACCCTGCAATGGCCA
5208252 AACATATTCATTATTTTAACATCATATAACATAATATCTAAG
65 AACATATTCATTATTTTAACATCATATAACATAATATCTAAG
5208294 --TGAAAATC
1 AATGAAAATC
5208302 ATAGTATTAA
Statistics
Matches: 112, Mismatches: 2, Indels: 3
0.96 0.02 0.03
Matches are distributed among these distances:
105 8 0.07
106 31 0.28
107 73 0.65
ACGTcount: A:0.39, C:0.24, G:0.07, T:0.31
Consensus pattern (106 bp):
AATGAAAATCGCCACACTTCCCTTTTTCTTCTAAACAACCAATTCAAGAACCCTGCAATGGCCAA
ACATATTCATTATTTTAACATCATATAACATAATATCTAAG
Found at i:5215976 original size:112 final size:113
Alignment explanation
Indices: 5215772--5216002 Score: 365
Period size: 112 Copynumber: 2.1 Consensus size: 113
5215762 TTATTTCTTT
* * * *
5215772 TCTTTTGTTTTGTTTGGCGGCGATGTTACTTTTCGAGCTGACTATCACCTGCATTTTTCTCCCTC
1 TCTTCTGTTTTGTTTGGCGGCGATGTTACTCTTCAAGCTGACTATCACCCGCATTTTTCTCCCTC
* * * *
5215837 CCATAAACTCTCTCTTTCTTCATTTCTTTATCTCATTCACTCTATGTG
66 CCATAAACCCTCTCTTTCATCATTTCTTTATCTCATTCACACTATATG
*
5215885 TCTTCTGTTTTGTTTGGCGGCGATGTTAGTCTTCAAGCTGACTATCACCCGCA-TTTTCTCCCTC
1 TCTTCTGTTTTGTTTGGCGGCGATGTTACTCTTCAAGCTGACTATCACCCGCATTTTTCTCCCTC
*
5215949 CCATAAACCCTCTCTTTCATCATTTCTTTATCTCATTCGCACTATATG
66 CCATAAACCCTCTCTTTCATCATTTCTTTATCTCATTCACACTATATG
5215997 TCTTCT
1 TCTTCT
5216003 CTCTCTTCAA
Statistics
Matches: 108, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
112 60 0.56
113 48 0.44
ACGTcount: A:0.15, C:0.28, G:0.12, T:0.45
Consensus pattern (113 bp):
TCTTCTGTTTTGTTTGGCGGCGATGTTACTCTTCAAGCTGACTATCACCCGCATTTTTCTCCCTC
CCATAAACCCTCTCTTTCATCATTTCTTTATCTCATTCACACTATATG
Found at i:5222776 original size:2 final size:2
Alignment explanation
Indices: 5222769--5222793 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5222759 GCCCTTTGGT
5222769 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
5222794 TCTGTGCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:5224184 original size:64 final size:64
Alignment explanation
Indices: 5224112--5224240 Score: 240
Period size: 64 Copynumber: 2.0 Consensus size: 64
5224102 TATATTTTAA
*
5224112 TATTTTATTTTTGAAATATTATGTTTTAATCACTTATCTTATCGTCTTGTTATGAAGTGGTCAC
1 TATTTTATTTTTGAAATATTATGTTTTAATCACTTACCTTATCGTCTTGTTATGAAGTGGTCAC
*
5224176 TATTTTATTTTTGAAATGTTATGTTTTAATCACTTACCTTATCGTCTTGTTATGAAGTGGTCAC
1 TATTTTATTTTTGAAATATTATGTTTTAATCACTTACCTTATCGTCTTGTTATGAAGTGGTCAC
5224240 T
1 T
5224241 CTACCGTTAA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 63 1.00
ACGTcount: A:0.24, C:0.12, G:0.13, T:0.51
Consensus pattern (64 bp):
TATTTTATTTTTGAAATATTATGTTTTAATCACTTACCTTATCGTCTTGTTATGAAGTGGTCAC
Found at i:5225109 original size:21 final size:21
Alignment explanation
Indices: 5225083--5225125 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
5225073 GGTTCGCTGT
*
5225083 ATTGGATTAGAGGTGTATTGG
1 ATTGGATTAGAGGTGTAATGG
5225104 ATTGGATTAGAGGTGTAATGG
1 ATTGGATTAGAGGTGTAATGG
5225125 A
1 A
5225126 ATAGAGGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.37, T:0.35
Consensus pattern (21 bp):
ATTGGATTAGAGGTGTAATGG
Found at i:5225125 original size:16 final size:16
Alignment explanation
Indices: 5225106--5225138 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
5225096 TGTATTGGAT
*
5225106 TGGATTAGAGGTGTAA
1 TGGAATAGAGGTGTAA
5225122 TGGAATAGAGGTGTAA
1 TGGAATAGAGGTGTAA
5225138 T
1 T
5225139 AGCAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.36, T:0.30
Consensus pattern (16 bp):
TGGAATAGAGGTGTAA
Found at i:5225183 original size:45 final size:44
Alignment explanation
Indices: 5225117--5225211 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
5225107 GGATTAGAGG
* *
5225117 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
5225162 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
5225206 TGTAAT
1 TGTAAT
5225212 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:5225394 original size:18 final size:17
Alignment explanation
Indices: 5225373--5225407 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
5225363 TTATTATTTA
*
5225373 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
5225391 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
5225408 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:5225401 original size:28 final size:27
Alignment explanation
Indices: 5225331--5225403 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
5225321 TTTATTATCA
*
5225331 AAAATAAATAATTTAATCATATTTAAAC
1 AAAATATATAATTTAAT-ATATTTAAAC
* * **
5225359 ATAAT-TATTATTTAATATATTTTAATT
1 AAAATATATAATTTAATATA-TTTAAAC
5225386 AAAATATATAATTTAATA
1 AAAATATATAATTTAATA
5225404 AAATTCTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 3 0.08
27 18 0.50
28 15 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATATATAATTTAATATATTTAAAC
Found at i:5225520 original size:144 final size:147
Alignment explanation
Indices: 5225292--5225563 Score: 487
Period size: 144 Copynumber: 1.9 Consensus size: 147
5225282 ATGATTATTG
5225292 TTATTGTTATTTAAATTTTAATAAGATTATTTATTATCAAAAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTA--TATTATCAAAAATAAATAATTTAATCATATTTAA
*
5225357 ACATAATTATTATTTAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
64 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
5225422 AGAAATTTGTTTTGGTAAA
129 AGAAATTTGTTTTGGTAAA
*
5225441 TTATT-TTATTTAAATTTTAATAAGATTA-A-TATCAATAATAAATAATTTAATCATATTTAAAC
1 TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
5225503 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
66 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
5225564 ATATTCTTAT
Statistics
Matches: 121, Mismatches: 2, Indels: 5
0.95 0.02 0.04
Matches are distributed among these distances:
144 92 0.76
145 1 0.01
148 23 0.19
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (147 bp):
TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGCAG
AAATTTGTTTTGGTAAA
Found at i:5225538 original size:18 final size:17
Alignment explanation
Indices: 5225517--5225551 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
5225507 TTATTATTAA
*
5225517 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
5225535 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
5225552 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:5239465 original size:21 final size:21
Alignment explanation
Indices: 5239441--5239485 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
5239431 AATTTTATGT
**
5239441 ATAAAATTATTTTAAATATAA
1 ATAAAATTATCATAAATATAA
5239462 ATAAAATTATCATAAATATAA
1 ATAAAATTATCATAAATATAA
5239483 ATA
1 ATA
5239486 TTTATCTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
ATAAAATTATCATAAATATAA
Found at i:5258108 original size:30 final size:30
Alignment explanation
Indices: 5258073--5258131 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
5258063 CTTTGAGTAC
*
5258073 TTATAAATAAATATTAA-TAAATTTATTTAA
1 TTATAAATAAA-AGTAATTAAATTTATTTAA
* *
5258103 TTATAATTAAAAGTAATTAAATTTTTTTA
1 TTATAAATAAAAGTAATTAAATTTATTTA
5258132 TTTCTTTCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 4 0.16
30 21 0.84
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (30 bp):
TTATAAATAAAAGTAATTAAATTTATTTAA
Found at i:5261865 original size:8 final size:9
Alignment explanation
Indices: 5261844--5261870 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
5261834 GTTTTTATTA
5261844 AAAAAATTT
1 AAAAAATTT
5261853 AAAAAATTT
1 AAAAAATTT
5261862 AAAAAATTT
1 AAAAAATTT
5261871 TTATTTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
AAAAAATTT
Found at i:5269186 original size:18 final size:18
Alignment explanation
Indices: 5269163--5269221 Score: 54
Period size: 18 Copynumber: 3.5 Consensus size: 18
5269153 TTGTTTATTG
5269163 TTATTCAATAACAATCAA
1 TTATTCAATAACAATCAA
* * *
5269181 TTATTCAGTATCAAAC-A
1 TTATTCAATAACAATCAA
*
5269198 --A-TCAATAAAAATCAA
1 TTATTCAATAACAATCAA
5269213 TTATTCAAT
1 TTATTCAAT
5269222 CTAGTAATAC
Statistics
Matches: 30, Mismatches: 7, Indels: 8
0.67 0.16 0.18
Matches are distributed among these distances:
14 8 0.27
15 2 0.07
17 2 0.07
18 18 0.60
ACGTcount: A:0.49, C:0.15, G:0.02, T:0.34
Consensus pattern (18 bp):
TTATTCAATAACAATCAA
Found at i:5271762 original size:427 final size:427
Alignment explanation
Indices: 5270944--5272170 Score: 2229
Period size: 427 Copynumber: 2.9 Consensus size: 427
5270934 CATATGACAT
* *
5270944 ATCAGGTCGAATTTCAGTATCCACTGTAGAAATAATAAGAAAAGGATCTGATCGATATCTTCTGA
1 ATCAGGTCGAATTTCAAT-TCCTCTGTAGAAATAATAAGAAAAGGATCTGATCGATATCTTCTGA
* *
5271009 GCATAGAAACATGAAAAACATCATGAATCTTTTGCAATTCTGGAAGCAAAGCCAGACAATATGTA
65 GCATAGAAACATGAAAAACATCATGAATCTTTTGCAATTCTGGAAGCAAAGCCAGACGATATGCA
*
5271074 ACTGGTCCAACTCTCTCAATAATCTCATATGGCCCAATAAAATGAGAACTTAGTTTTCCTTTTCG
130 ACTGGTCCAACTCTCTCAATAATCTCATATGGCCCAATAAAACGAGAACTTAGTTTTCCTTTTCG
* *
5271139 ACCGAATCTCATAATTTTCTTCCGAGGTGAAACTTTTAAAAATACCTTATCACCAACCGCGTACT
195 ACCGAATCTCATAATTTTCTTCCAAGGTGAAACTTTTAGAAATACCTTATCACCAACCGCGTACT
5271204 CAATGTCTCTACGTTTCAGATCTGCATATGACTTCTGCCTGTCAAAAGCTGCTTTCAATCTTTCT
260 CAATGTCTCTACGTTTCAGATCTGCATATGACTTCTGCCTGTCAAAAGCTGCTTTCAATCTTTCT
5271269 CGAATCTTCTTAACAGTGTCTTCTGTTTCTTGAATTAATTCTGGCCCACTATTATTGCATACAAA
325 CGAATCTTCTTAACAGTGTCTTCTGTTTCTTGAATTAATTCTGGCCCACTATTATTGCATACAAA
5271334 TTCAGCTAACGGTACATAACGTTCCCAACCGATTCAAG
390 TTCAGCTAACGGTACATAACGTTCCCAACCGATTCAAG
5271372 ATCAGGTCGAATTTCAATTCCTCTGTAGAAATAATAAGAAAAGGATCTGATCGATATCTTCTGAG
1 ATCAGGTCGAATTTCAATTCCTCTGTAGAAATAATAAGAAAAGGATCTGATCGATATCTTCTGAG
5271437 CATAGAAACATGAAAAACATCATGAATCTTTTGCAATTCTGGAAGCAAAGCCAGACGATATGCAA
66 CATAGAAACATGAAAAACATCATGAATCTTTTGCAATTCTGGAAGCAAAGCCAGACGATATGCAA
* * *
5271502 TTGGTCCAACTCTATCAATAATCTCATATGGCCCAATAAAACGAGAATTTAGTTTTCCTTTTCGA
131 CTGGTCCAACTCTCTCAATAATCTCATATGGCCCAATAAAACGAGAACTTAGTTTTCCTTTTCGA
5271567 CCGAATCTCATAATTTTCTTCCAAGGTGAAACTTTTAGAAATACCTTATCACCAACCGCGTACTC
196 CCGAATCTCATAATTTTCTTCCAAGGTGAAACTTTTAGAAATACCTTATCACCAACCGCGTACTC
5271632 AATGTCTCTACGTTTCAGATCTGCATATGACTTCTGCCTGTCAAAAGCTGCTTTCAATCTTTCTC
261 AATGTCTCTACGTTTCAGATCTGCATATGACTTCTGCCTGTCAAAAGCTGCTTTCAATCTTTCTC
* *
5271697 GAATCTTCTTAATAGTGTCTTCTATTTCTTGAATTAATTCTGGCCCACTATTATTGCATACAAAT
326 GAATCTTCTTAACAGTGTCTTCTGTTTCTTGAATTAATTCTGGCCCACTATTATTGCATACAAAT
*
5271762 TCAGCTAACGGTAGATAACGTTCCCAACCGATTCAAG
391 TCAGCTAACGGTACATAACGTTCCCAACCGATTCAAG
*
5271799 ATCAGGTCTAATTTCAATTCCTCTGTAGAAATAATAAGAAAAGGATCTGATCGATATCTTCTGAG
1 ATCAGGTCGAATTTCAATTCCTCTGTAGAAATAATAAGAAAAGGATCTGATCGATATCTTCTGAG
* *
5271864 CATAGAAACATGAAAAACATCATGAATTTTTTGCAATTCTGGAAGTAAAGCCAGACGATATGCAA
66 CATAGAAACATGAAAAACATCATGAATCTTTTGCAATTCTGGAAGCAAAGCCAGACGATATGCAA
*
5271929 CTGGTCCAACTCTCTCAATAATCTCATATGGCCCAATAAAACGAGGACTTAGTTTTCCTTTTCGA
131 CTGGTCCAACTCTCTCAATAATCTCATATGGCCCAATAAAACGAGAACTTAGTTTTCCTTTTCGA
* * *
5271994 CCGAATCTCAGAATTTTCTTCCAAGGTGAAACTTTTAGAAATACCTTATCACCAATCGCATACTC
196 CCGAATCTCATAATTTTCTTCCAAGGTGAAACTTTTAGAAATACCTTATCACCAACCGCGTACTC
* *
5272059 AATGTCTCTACGTTTCAGATCTGCATATGACTTCTACCTGTCAAAAGTTGCTTTCAATCTTTCTC
261 AATGTCTCTACGTTTCAGATCTGCATATGACTTCTGCCTGTCAAAAGCTGCTTTCAATCTTTCTC
* *
5272124 GAATCTTCTTAACAGTATCTCCTGTTTCTTGAATTAATTCTGGCCCA
326 GAATCTTCTTAACAGTGTCTTCTGTTTCTTGAATTAATTCTGGCCCA
5272171 ATCATTTTCT
Statistics
Matches: 770, Mismatches: 29, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
427 753 0.98
428 17 0.02
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.32
Consensus pattern (427 bp):
ATCAGGTCGAATTTCAATTCCTCTGTAGAAATAATAAGAAAAGGATCTGATCGATATCTTCTGAG
CATAGAAACATGAAAAACATCATGAATCTTTTGCAATTCTGGAAGCAAAGCCAGACGATATGCAA
CTGGTCCAACTCTCTCAATAATCTCATATGGCCCAATAAAACGAGAACTTAGTTTTCCTTTTCGA
CCGAATCTCATAATTTTCTTCCAAGGTGAAACTTTTAGAAATACCTTATCACCAACCGCGTACTC
AATGTCTCTACGTTTCAGATCTGCATATGACTTCTGCCTGTCAAAAGCTGCTTTCAATCTTTCTC
GAATCTTCTTAACAGTGTCTTCTGTTTCTTGAATTAATTCTGGCCCACTATTATTGCATACAAAT
TCAGCTAACGGTACATAACGTTCCCAACCGATTCAAG
Found at i:5275031 original size:75 final size:75
Alignment explanation
Indices: 5274908--5275057 Score: 255
Period size: 75 Copynumber: 2.0 Consensus size: 75
5274898 TAACATAATA
5274908 ATGTGACGATCCTAGATCTATTAAAGCATAAACGAGTTCTGAGTACAATAAAAATATACCAGTCA
1 ATGTGACGATCCTAGATCTATTAAAGCATAAACGAGTTCTGAGTACAATAAAAATATACCAGTCA
5274973 CCATATTGTG
66 CCATATTGTG
* * * * *
5274983 ATGTGATGATCTTGGATCTATTAAAGCATAAACGGGTTCTGAGTACAATAAAAATATACCCGTCA
1 ATGTGACGATCCTAGATCTATTAAAGCATAAACGAGTTCTGAGTACAATAAAAATATACCAGTCA
5275048 CCATATTGTG
66 CCATATTGTG
5275058 TACATCTCCT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 70 1.00
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (75 bp):
ATGTGACGATCCTAGATCTATTAAAGCATAAACGAGTTCTGAGTACAATAAAAATATACCAGTCA
CCATATTGTG
Found at i:5276860 original size:47 final size:47
Alignment explanation
Indices: 5276769--5276860 Score: 114
Period size: 47 Copynumber: 2.0 Consensus size: 47
5276759 CCAACACACC
* * * *
5276769 AGTACGGCACTCAGTGCCTCATCGGCTTTATCGAAGTAAGTAGTAGT
1 AGTACGGCACTCAGTACCTCATCGGATTAACCGAAGTAAGTAGTAGT
* *
5276816 AGTACGGTACTTAGTACCTCATCGGATTAAACCGAAGTAA-TAGTA
1 AGTACGGCACTCAGTACCTCATCGGATT-AACCGAAGTAAGTAGTA
5276861 ACAGTATGAC
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
47 29 0.76
48 9 0.24
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (47 bp):
AGTACGGCACTCAGTACCTCATCGGATTAACCGAAGTAAGTAGTAGT
Found at i:5276905 original size:44 final size:44
Alignment explanation
Indices: 5276857--5276948 Score: 107
Period size: 44 Copynumber: 2.1 Consensus size: 44
5276847 CCGAAGTAAT
* *
5276857 AGTAACAGTATGACACACA-AGGTGCCTCATCGACTCGAA-GTCGA
1 AGTAACAATACGACACACATA-GTGCCTCATCGACTC-AAGGTCGA
** *
5276901 AGTAACAATACGACACTTATAGTGCTTCATCGACTCAAGGTCGA
1 AGTAACAATACGACACACATAGTGCCTCATCGACTCAAGGTCGA
5276945 AGTA
1 AGTA
5276949 TCCCTGAACA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
43 2 0.05
44 38 0.93
45 1 0.02
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.22
Consensus pattern (44 bp):
AGTAACAATACGACACACATAGTGCCTCATCGACTCAAGGTCGA
Found at i:5277847 original size:3 final size:3
Alignment explanation
Indices: 5277839--5277863 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5277829 TCGTTACTTT
5277839 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
5277864 AACATAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:5279396 original size:12 final size:12
Alignment explanation
Indices: 5279379--5279403 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5279369 CACAAGTTAG
5279379 TGCATTTATGTA
1 TGCATTTATGTA
5279391 TGCATTTATGTA
1 TGCATTTATGTA
5279403 T
1 T
5279404 ATAACTCATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.16, T:0.52
Consensus pattern (12 bp):
TGCATTTATGTA
Found at i:5280387 original size:17 final size:16
Alignment explanation
Indices: 5280367--5280405 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
5280357 AAACCCAATT
5280367 CAATATTATAATTCCAA
1 CAATATT-TAATTCCAA
*
5280384 CAATAATTTATTTCCAA
1 CAAT-ATTTAATTCCAA
5280401 CAATA
1 CAATA
5280406 GAATAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 16 0.80
18 3 0.15
ACGTcount: A:0.46, C:0.18, G:0.00, T:0.36
Consensus pattern (16 bp):
CAATATTTAATTCCAA
Found at i:5286654 original size:18 final size:18
Alignment explanation
Indices: 5286633--5286667 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5286623 TCTATAGAAG
*
5286633 TTCTTCAGTTCAGATATA
1 TTCTTCAGCTCAGATATA
5286651 TTCTTCAGCTCAGATAT
1 TTCTTCAGCTCAGATAT
5286668 TACAAGTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.20, G:0.11, T:0.43
Consensus pattern (18 bp):
TTCTTCAGCTCAGATATA
Found at i:5318214 original size:3 final size:3
Alignment explanation
Indices: 5318208--5318243 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
5318198 AAAATAATAA
5318208 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
5318244 AGAATTAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TAG
Found at i:5326154 original size:26 final size:26
Alignment explanation
Indices: 5326106--5326158 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
5326096 TAAATGAAAG
* **
5326106 TGACACTTCGGAGCATTTTAGTGATT
1 TGACACTTCGGAGCACTACAGTGATT
*
5326132 TGACACTTCGGCGCACTACAGTGATT
1 TGACACTTCGGAGCACTACAGTGATT
5326158 T
1 T
5326159 TGTACTTCAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.34
Consensus pattern (26 bp):
TGACACTTCGGAGCACTACAGTGATT
Found at i:5330703 original size:21 final size:21
Alignment explanation
Indices: 5330679--5330725 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
5330669 TGCTTTGCTT
*
5330679 TGCTTCCCTCACTGTTGCCTC
1 TGCTTCCCTCACTGCTGCCTC
*
5330700 TGCTTCCCTCGCTGCTGCCTC
1 TGCTTCCCTCACTGCTGCCTC
5330721 TGCTT
1 TGCTT
5330726 TAAGTTGTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.02, C:0.43, G:0.17, T:0.38
Consensus pattern (21 bp):
TGCTTCCCTCACTGCTGCCTC
Found at i:5338339 original size:9 final size:9
Alignment explanation
Indices: 5338325--5338371 Score: 67
Period size: 9 Copynumber: 5.1 Consensus size: 9
5338315 TATGTATTAC
5338325 GTAAGTTAT
1 GTAAGTTAT
5338334 GTAAGTTAT
1 GTAAGTTAT
* *
5338343 GATATGATAT
1 G-TAAGTTAT
5338353 GTAAGTTAT
1 GTAAGTTAT
5338362 GTAAGTTAT
1 GTAAGTTAT
5338371 G
1 G
5338372 ATTATCATCT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
9 26 0.79
10 7 0.21
ACGTcount: A:0.34, C:0.00, G:0.23, T:0.43
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:5339604 original size:24 final size:24
Alignment explanation
Indices: 5339577--5339622 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
5339567 TTATAATACA
5339577 ATATTAATTTTAGATACAAATATG
1 ATATTAATTTTAGATACAAATATG
**
5339601 ATATTAATTTTTTATACAAATA
1 ATATTAATTTTAGATACAAATA
5339623 GTATTTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (24 bp):
ATATTAATTTTAGATACAAATATG
Found at i:5341273 original size:72 final size:73
Alignment explanation
Indices: 5341143--5341302 Score: 198
Period size: 72 Copynumber: 2.2 Consensus size: 73
5341133 GCTCGATCTA
* * *
5341143 TTGCGGCGTTTTTCACCTAGCACCGCTAATGCCACTAAAAACGAAGCCATTTGATTTAAAGTAAA
1 TTGCAGCGTTTTTTACCTAACACCGCTAATGCCACTAAAAACGAAGCCATTTGATTTAAAGTAAA
5341208 ATG-TTTT
66 ATGTTTTT
* * * ** **
5341215 TTGCTGCGTTTTTTACCTAACGCCGCTAATGCCACTAAAAATGGCGTCGTTTTG-TTTAAAGTAA
1 TTGCAGCGTTTTTTACCTAACACCGCTAATGCCACTAAAAACGAAG-CCATTTGATTTAAAGTAA
5341279 AATGTTTTT
65 AATGTTTTT
*
5341288 TTGCAGCATTTTTTA
1 TTGCAGCGTTTTTTA
5341303 TTAAAAAGCC
Statistics
Matches: 75, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
72 53 0.71
73 22 0.29
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.38
Consensus pattern (73 bp):
TTGCAGCGTTTTTTACCTAACACCGCTAATGCCACTAAAAACGAAGCCATTTGATTTAAAGTAAA
ATGTTTTT
Found at i:5341455 original size:35 final size:35
Alignment explanation
Indices: 5341410--5341477 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
5341400 ATTTAATTTG
* *
5341410 TAATGTTTTATAATTGTGTACGAAAATAATTTTTA
1 TAATATTTTATAATTGTGTACAAAAATAATTTTTA
5341445 TAATATTTTATAATTGTGTACAAAAATAATTTT
1 TAATATTTTATAATTGTGTACAAAAATAATTTT
5341478 AAAAAATGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.40, C:0.03, G:0.09, T:0.49
Consensus pattern (35 bp):
TAATATTTTATAATTGTGTACAAAAATAATTTTTA
Found at i:5341816 original size:7 final size:7
Alignment explanation
Indices: 5341798--5341865 Score: 73
Period size: 7 Copynumber: 9.6 Consensus size: 7
5341788 CTCAAAAAAA
*
5341798 CTAAACA
1 CTAAACC
5341805 CTAAACC
1 CTAAACC
*
5341812 ATAAAACC
1 CT-AAACC
5341820 CTAAACC
1 CTAAACC
*
5341827 CTAGACC
1 CTAAACC
*
5341834 TTAAACC
1 CTAAACC
* *
5341841 TTAAATC
1 CTAAACC
5341848 CTAAACC
1 CTAAACC
5341855 CTAAACC
1 CTAAACC
5341862 CTAA
1 CTAA
5341866 TATAAAATAT
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
7 45 0.88
8 6 0.12
ACGTcount: A:0.46, C:0.34, G:0.01, T:0.19
Consensus pattern (7 bp):
CTAAACC
Found at i:5342036 original size:41 final size:41
Alignment explanation
Indices: 5341886--5342045 Score: 180
Period size: 41 Copynumber: 3.9 Consensus size: 41
5341876 TTTTTTGTGA
* * *
5341886 CGTTTTTATCAAAAACGCCGATATTGCTT-A-CTTATTGCGG
1 CGTTTTTATCATAAACGCCGCTACTGCTTGACCTT-TTGCGG
* * * *
5341926 CGTTTTTCTCATAAACGCCGCTACTGCTAGATCTTTTGCAG
1 CGTTTTTATCATAAACGCCGCTACTGCTTGACCTTTTGCGG
* * * *
5341967 CGTTTTTTTTATAAACGCCGCTATTGCTTGACCTTTTGTGG
1 CGTTTTTATCATAAACGCCGCTACTGCTTGACCTTTTGCGG
* *
5342008 CGTTTTTAACATAAACGCCGCTACTGCTTAACCTTTTG
1 CGTTTTTATCATAAACGCCGCTACTGCTTGACCTTTTG
5342046 GTGCATTTTC
Statistics
Matches: 100, Mismatches: 18, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
40 24 0.24
41 73 0.73
42 3 0.03
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.39
Consensus pattern (41 bp):
CGTTTTTATCATAAACGCCGCTACTGCTTGACCTTTTGCGG
Found at i:5342640 original size:22 final size:22
Alignment explanation
Indices: 5342606--5342648 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
5342596 TATCAAAACA
5342606 ATAATAACAAAAT-AGTAGCAAT
1 ATAATAACAAAATGA-TAGCAAT
* *
5342628 ATAATAGCGAAATGATAGCAA
1 ATAATAACAAAATGATAGCAA
5342649 AACAATGCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.56, C:0.09, G:0.14, T:0.21
Consensus pattern (22 bp):
ATAATAACAAAATGATAGCAAT
Found at i:5344652 original size:46 final size:46
Alignment explanation
Indices: 5344597--5344688 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
5344587 AGGCAAAGTA
*
5344597 TGAATCAATTCCGTTCCAGCTCTCTACAATATTTTGAAAGATGTCT
1 TGAATCAATTCCATTCCAGCTCTCTACAATATTTTGAAAGATGTCT
5344643 TGAATCAATTCCATTCCAGCTCTCTACAATATTTTGAAAGATGTCT
1 TGAATCAATTCCATTCCAGCTCTCTACAATATTTTGAAAGATGTCT
5344689 CGTGCACTTC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (46 bp):
TGAATCAATTCCATTCCAGCTCTCTACAATATTTTGAAAGATGTCT
Found at i:5348466 original size:18 final size:18
Alignment explanation
Indices: 5348443--5348477 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5348433 ATTATTTTAA
*
5348443 AATTTTAAAATATAAATT
1 AATTTTAAAACATAAATT
*
5348461 AATTTTGAAACATAAAT
1 AATTTTAAAACATAAAT
5348478 ATTATTAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (18 bp):
AATTTTAAAACATAAATT
Found at i:5352387 original size:2 final size:2
Alignment explanation
Indices: 5352380--5352405 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5352370 TATTTTACGA
5352380 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
5352406 TTATTTGTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:5352884 original size:7 final size:7
Alignment explanation
Indices: 5352874--5352920 Score: 53
Period size: 7 Copynumber: 6.9 Consensus size: 7
5352864 ATTTTACTTT
5352874 TTTTATA
1 TTTTATA
5352881 TTTTATA
1 TTTTATA
*
5352888 TTTTTTA
1 TTTTATA
5352895 GTTTTAT-
1 -TTTTATA
*
5352902 GTTTATA
1 TTTTATA
5352909 TTTTA-A
1 TTTTATA
5352915 TTTTAT
1 TTTTAT
5352921 TAATAAAAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
6 11 0.33
7 17 0.52
8 5 0.15
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.72
Consensus pattern (7 bp):
TTTTATA
Found at i:5353275 original size:89 final size:89
Alignment explanation
Indices: 5353119--5353296 Score: 196
Period size: 89 Copynumber: 2.0 Consensus size: 89
5353109 CATTCTACCG
* * * *
5353119 TTAAAATGTATTTAGTTACCAAACATAATTTCAATGTAGCCTTCCTTTGATTGATATAAAAATAA
1 TTAAAATGTATTTAGTTACCAAACAGAATGTCAATGTAGCCTTCCTTTGATGGATATAAAAACAA
* * *
5353184 ATTTAACTGTTAATATTTTACACA
66 ATTTAACCGCTAATATTTCACACA
* * * * * * * *
5353208 TTAAAATGTATTT-GATTACCAAATAGAGTGTCAATGTGGCCTTCTTTTTATGGGTTTAATAACA
1 TTAAAATGTATTTAG-TTACCAAACAGAATGTCAATGTAGCCTTCCTTTGATGGATATAAAAACA
*
5353272 AATTTAGCCGCTAATATTTCACACA
65 AATTTAACCGCTAATATTTCACACA
5353297 CCCTATCAAG
Statistics
Matches: 72, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
88 1 0.01
89 71 0.99
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.39
Consensus pattern (89 bp):
TTAAAATGTATTTAGTTACCAAACAGAATGTCAATGTAGCCTTCCTTTGATGGATATAAAAACAA
ATTTAACCGCTAATATTTCACACA
Found at i:5353431 original size:26 final size:25
Alignment explanation
Indices: 5353380--5353434 Score: 67
Period size: 27 Copynumber: 2.2 Consensus size: 25
5353370 TTATTATTCT
* *
5353380 AAATATTTAAAAAATTATAATTATA
1 AAATATTTAAAAAACTATAATAATA
5353405 AAATATTTAAAAAAAACTATAA-AATA
1 AAATATTT--AAAAAACTATAATAATA
5353431 AAAT
1 AAAT
5353435 GATTCAACCA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 8 0.31
26 7 0.27
27 11 0.42
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (25 bp):
AAATATTTAAAAAACTATAATAATA
Found at i:5357972 original size:18 final size:17
Alignment explanation
Indices: 5357945--5357978 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
5357935 ACTGCTGTAG
*
5357945 AAAGAAAGAAGAAAAGA
1 AAAGAAAGAAAAAAAGA
5357962 AAAGAAAAGAAAAAAAG
1 AAAG-AAAGAAAAAAAG
5357979 GAGTTCGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (17 bp):
AAAGAAAGAAAAAAAGA
Found at i:5367271 original size:7 final size:7
Alignment explanation
Indices: 5367259--5367284 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
5367249 AGGGGGTTAG
5367259 TACCATA
1 TACCATA
5367266 TACCATA
1 TACCATA
5367273 TACCATA
1 TACCATA
5367280 TACCA
1 TACCA
5367285 CAAGCATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.31, G:0.00, T:0.27
Consensus pattern (7 bp):
TACCATA
Found at i:5372213 original size:19 final size:18
Alignment explanation
Indices: 5372189--5372225 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
5372179 TTTTTGTAGG
*
5372189 AAAATATTATCTTGTGGA
1 AAAATATTATCTTATGGA
5372207 NAAAATATTATCTTATGGA
1 -AAAATATTATCTTATGGA
5372226 TTCAGGATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.05, G:0.14, T:0.38
Consensus pattern (18 bp):
AAAATATTATCTTATGGA
Found at i:5373193 original size:21 final size:21
Alignment explanation
Indices: 5373151--5373193 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
5373141 AACAGCGGTG
* ** *
5373151 GCGGTGAGATTGGTTACTATA
1 GCGGTGAGATTAGAAACAATA
5373172 GCGGTGAGATTAGAAACAATA
1 GCGGTGAGATTAGAAACAATA
5373193 G
1 G
5373194 TAGAGTACCT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.09, G:0.33, T:0.26
Consensus pattern (21 bp):
GCGGTGAGATTAGAAACAATA
Found at i:5373249 original size:77 final size:77
Alignment explanation
Indices: 5373122--5373268 Score: 276
Period size: 77 Copynumber: 1.9 Consensus size: 77
5373112 TAGTAAGACA
5373122 TACCTCCGGTAAGGTTAAAAACAGCGGTGGCGGTGAGATTGGTTACTATAGCGGTGAGATTAGAA
1 TACCTCCGGTAAGGTTAAAAACAGCGGTGGCGGTGAGATTGGTTACTATAGCGGTGAGATTAGAA
5373187 ACAATAGTAGAG
66 ACAATAGTAGAG
* *
5373199 TACCTCCGGTGAGGTTAAAAATAGCGGTGGCGGTGAGATTGGTTACTATAGCGGTGAGATTAGAA
1 TACCTCCGGTAAGGTTAAAAACAGCGGTGGCGGTGAGATTGGTTACTATAGCGGTGAGATTAGAA
5373264 ACAAT
66 ACAAT
5373269 GGTGGAGTGT
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
77 68 1.00
ACGTcount: A:0.31, C:0.13, G:0.31, T:0.24
Consensus pattern (77 bp):
TACCTCCGGTAAGGTTAAAAACAGCGGTGGCGGTGAGATTGGTTACTATAGCGGTGAGATTAGAA
ACAATAGTAGAG
Found at i:5390363 original size:21 final size:20
Alignment explanation
Indices: 5390278--5390382 Score: 61
Period size: 20 Copynumber: 5.2 Consensus size: 20
5390268 CTTAGGGTTT
*
5390278 GGTTCGAGATT-AAGTTTCAG
1 GGTTCGAGGTTAAAGTTT-AG
* ** *
5390298 TGTTCG-GGTTTGAGTTTTG
1 GGTTCGAGGTTAAAGTTTAG
* * *
5390317 GATTCGAGGCTCAATGTTTAAG
1 GGTTCGAGG-TTAAAGTTT-AG
*
5390339 GGTTCGGGGTTACAAGTTTAG
1 GGTTCGAGGTTA-AAGTTTAG
* *
5390360 GGTTCGAGTTTAAAGTTTTG
1 GGTTCGAGGTTAAAGTTTAG
5390380 GGT
1 GGT
5390383 CTAAGGTTCA
Statistics
Matches: 62, Mismatches: 18, Indels: 10
0.69 0.20 0.11
Matches are distributed among these distances:
19 8 0.13
20 22 0.35
21 19 0.31
22 13 0.21
ACGTcount: A:0.19, C:0.09, G:0.33, T:0.39
Consensus pattern (20 bp):
GGTTCGAGGTTAAAGTTTAG
Found at i:5390377 original size:20 final size:21
Alignment explanation
Indices: 5390310--5390382 Score: 60
Period size: 21 Copynumber: 3.5 Consensus size: 21
5390300 TTCGGGTTTG
* * *
5390310 AGTTTTGGATTCGAGGCT-CA
1 AGTTTAGGGTTCGAGGTTACA
*
5390330 ATGTTTAAGGGTTCGGGGTTACA
1 A-GTTT-AGGGTTCGAGGTTACA
*
5390353 AGTTTAGGGTTCGAGTTTA-A
1 AGTTTAGGGTTCGAGGTTACA
*
5390373 AGTTTTGGGT
1 AGTTTAGGGT
5390383 CTAAGGTTCA
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
20 11 0.26
21 16 0.37
22 13 0.30
23 3 0.07
ACGTcount: A:0.21, C:0.08, G:0.33, T:0.38
Consensus pattern (21 bp):
AGTTTAGGGTTCGAGGTTACA
Found at i:5391056 original size:15 final size:14
Alignment explanation
Indices: 5391023--5391056 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
5391013 CTAGTTGACA
5391023 ATTTTTTAAAAACT
1 ATTTTTTAAAAACT
* *
5391037 ATTTTTTGAAAATT
1 ATTTTTTAAAAACT
5391051 ATTTTT
1 ATTTTT
5391057 AATAAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (14 bp):
ATTTTTTAAAAACT
Found at i:5391842 original size:26 final size:24
Alignment explanation
Indices: 5391805--5391856 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
5391795 TAAATATAAA
*
5391805 TATATATGTTTAATAATATTGAAAAT
1 TATATATGTTTAA-AA-ATTAAAAAT
5391831 TATAGTAT-TTTAAAAATTAAAAAT
1 TATA-TATGTTTAAAAATTAAAAAT
5391855 TA
1 TA
5391857 AAAATTTAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 10 0.42
25 2 0.08
26 9 0.38
27 3 0.12
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (24 bp):
TATATATGTTTAAAAATTAAAAAT
Found at i:5398955 original size:16 final size:17
Alignment explanation
Indices: 5398927--5398960 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
5398917 TTAAACAAGT
*
5398927 ATAAAAGACAAAATAAA
1 ATAAAAGACAAAACAAA
5398944 ATAAAA-ACAAAACAAA
1 ATAAAAGACAAAACAAA
5398960 A
1 A
5398961 CATTTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.79, C:0.09, G:0.03, T:0.09
Consensus pattern (17 bp):
ATAAAAGACAAAACAAA
Found at i:5399982 original size:22 final size:22
Alignment explanation
Indices: 5399957--5399998 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
5399947 TGATTCATAA
* *
5399957 ATGTTAGCTTGTGTGAGCAAAT
1 ATGTCAGCTTGTATGAGCAAAT
5399979 ATGTCAGCTTGTATGAGCAA
1 ATGTCAGCTTGTATGAGCAA
5399999 TTCTGATCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (22 bp):
ATGTCAGCTTGTATGAGCAAAT
Found at i:5402234 original size:581 final size:581
Alignment explanation
Indices: 5401131--5402295 Score: 2102
Period size: 581 Copynumber: 2.0 Consensus size: 581
5401121 AGACTCAGAA
5401131 AAAAAATTGAGACTCAATGTGTTTAGAATATAACTAAATGTTTGAATGGTTTAATTACGGTATAT
1 AAAAAATTGAGACTCAATGTGTTTAGAATATAACTAAATGTTTGAATGGTTTAATTACGGTATAT
* *
5401196 TTTATAGTAATTACTCCAGAAACGGATGTGGCATCTTATAGCTTAGATCTAGCGGTCGGGTCGGG
66 TTTATAGTAATTACTCCAGAAACGAATGTGGCATCTTATAGCTTAGACCTAGCGGTCGGGTCGGG
*
5401261 TAAGGGGTGTTACAAAAACTATGTCTTTCAAAGATCGGCTTATGGCTAGTGATCAAGGATAAAAT
131 TAAGGGGTGTTACAAAAACTATGTCTTTCAAAGATCAGCTTATGGCTAGTGATCAAGGATAAAAT
* *
5401326 AAATTTAATACGATGGGCGGTTACAATAAGGACATTGTTATTGTGGATGGGGATTTTGCAACGAG
196 AAATTTAATACGATGGGCGGTTACAATAAGGACATTGTTATTATGGATGGGGATTTTACAACGAG
* *
5401391 AACGATTGATGAAGTCTGTTCTATCAAGTTCTCGGAGAGATTTCATAAGTTGATAGAGATAAGTA
261 AACGATTGATGAAGTCTGTTCTATCAAGTTCTCGGAGAGAGTTCATAAGTCGATAGAGATAAGTA
*
5401456 TAGAGCGAACGATGGTTGTTAAGTTGTTAGGAACGAGGACTAAACTTAACGCTTTGTACAATCAT
326 TAGAGCGAACAATGGTTGTTAAGTTGTTAGGAACGAGGACTAAACTTAACGCTTTGTACAATCAT
*
5401521 ATTTATGCTTTGTGAAAACCACAACCATATGTTCATCTTATGGATGTTGATAATGATTATTTTTT
391 ATTTATGCATTGTGAAAACCACAACCATATGTTCATCTTATGGATGTTGATAATGATTATTTTTT
*
5401586 GGCTAAGTTCAAAAATGAGAATAATTTTTTGACAGCTTTATCGAAAAGTCCATGAATCGTGTACG
456 GGCTAAGTTCAAAAATGAGAATAATTTTTCGACAGCTTTATCGAAAAGTCCATGAATCGTGTACG
*
5401651 ACCATTATGTTACTGTCCAACCATGGACTCCTATGTTCAATACAAGTCAACCTTATCCTCT
521 ACCATTATGTTACTGTCCAACCATGGACTCCCATGTTCAATACAAGTCAACCTTATCCTCT
*
5401712 AAAAAATTGAGACTCAATGTGTTTAGAATATAATTAAATGTTTGAATGGTTTAATTGA-GGTATA
1 AAAAAATTGAGACTCAATGTGTTTAGAATATAACTAAATGTTTGAATGGTTTAATT-ACGGTATA
*
5401776 TTTTATAGTAATTACTCCAGAAACGAATGTGGTATCTTATAGCTTAGACCTAGCGGTCGGGTCGG
65 TTTTATAGTAATTACTCCAGAAACGAATGTGGCATCTTATAGCTTAGACCTAGCGGTCGGGTCGG
*
5401841 GTAAGGGGTGTTACAAAAACTATGTCTTTCAAAGATCAGCTTATGGCTAGTGGTCAAGGATAAAA
130 GTAAGGGGTGTTACAAAAACTATGTCTTTCAAAGATCAGCTTATGGCTAGTGATCAAGGATAAAA
*
5401906 -AAATTTTAATACGATGGGTGGTTACAATAAGGACATTGTTATTATGGATGGGGATTTTACAACG
195 TAAA-TTTAATACGATGGGCGGTTACAATAAGGACATTGTTATTATGGATGGGGATTTTACAACG
5401970 AGAACGATTGATGAAGTCTGTTCTATCAAGTTCTCGGAGAGAGTTCATAAGTCGATAGAGATAAG
259 AGAACGATTGATGAAGTCTGTTCTATCAAGTTCTCGGAGAGAGTTCATAAGTCGATAGAGATAAG
* * *
5402035 TATAGAGCGAACAATGGTTGTTAAGTTGTTAGGAACGAGGACTGAATTTAACGCTTTGTACAATT
324 TATAGAGCGAACAATGGTTGTTAAGTTGTTAGGAACGAGGACTAAACTTAACGCTTTGTACAATC
5402100 ATATTTATGCATTGTGAAAACCACAACCATATGTTCATCTTATGGATGTTGATAATGATTATTTT
389 ATATTTATGCATTGTGAAAACCACAACCATATGTTCATCTTATGGATGTTGATAATGATTATTTT
* *
5402165 TTGGCTAAGTTCAAAAATGAGAATAATTTTTCGACAGCTTTATCGAAAGGTCCAT-AGGTCGTGT
454 TTGGCTAAGTTCAAAAATGAGAATAATTTTTCGACAGCTTTATCGAAAAGTCCATGA-ATCGTGT
5402229 ACGACCATTATGTTACTGTCCAACCATGGACTCCCATGTTCAATACAAGTCAACCTTATCCTCT
518 ACGACCATTATGTTACTGTCCAACCATGGACTCCCATGTTCAATACAAGTCAACCTTATCCTCT
5402293 AAA
1 AAA
5402296 TGTCGTTGCA
Statistics
Matches: 561, Mismatches: 20, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
580 4 0.01
581 556 0.99
582 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.33
Consensus pattern (581 bp):
AAAAAATTGAGACTCAATGTGTTTAGAATATAACTAAATGTTTGAATGGTTTAATTACGGTATAT
TTTATAGTAATTACTCCAGAAACGAATGTGGCATCTTATAGCTTAGACCTAGCGGTCGGGTCGGG
TAAGGGGTGTTACAAAAACTATGTCTTTCAAAGATCAGCTTATGGCTAGTGATCAAGGATAAAAT
AAATTTAATACGATGGGCGGTTACAATAAGGACATTGTTATTATGGATGGGGATTTTACAACGAG
AACGATTGATGAAGTCTGTTCTATCAAGTTCTCGGAGAGAGTTCATAAGTCGATAGAGATAAGTA
TAGAGCGAACAATGGTTGTTAAGTTGTTAGGAACGAGGACTAAACTTAACGCTTTGTACAATCAT
ATTTATGCATTGTGAAAACCACAACCATATGTTCATCTTATGGATGTTGATAATGATTATTTTTT
GGCTAAGTTCAAAAATGAGAATAATTTTTCGACAGCTTTATCGAAAAGTCCATGAATCGTGTACG
ACCATTATGTTACTGTCCAACCATGGACTCCCATGTTCAATACAAGTCAACCTTATCCTCT
Found at i:5404496 original size:79 final size:82
Alignment explanation
Indices: 5404385--5404569 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 82
5404375 GCTACTCGTT
* * *
5404385 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
5404448 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
5404465 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
5404528 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
5404545 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
5404570 CATCATTCAA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.59
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:5404569 original size:40 final size:40
Alignment explanation
Indices: 5404366--5404569 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
5404356 CGGAATTTAA
** *
5404366 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
5404406 CCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
5404446 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
5404485 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
5404525 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
5404565 CCGGA
1 CCGGA
5404570 CATCATTCAA
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.24
40 92 0.66
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:5407807 original size:41 final size:41
Alignment explanation
Indices: 5407747--5407850 Score: 174
Period size: 41 Copynumber: 2.5 Consensus size: 41
5407737 TTTAACATAT
*
5407747 TCACCGGCACTTAGTCTGCTAGGCTTATAGA-CTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATA-ACCTGATTCAGA
*
5407788 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
5407829 TCACCGGCACTTAGCCTGCTAG
1 TCACCGGCACTTAGCCTGCTAG
5407851 ACATAAAGTC
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
40 1 0.02
41 59 0.98
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
Found at i:5420281 original size:18 final size:18
Alignment explanation
Indices: 5420258--5420350 Score: 150
Period size: 18 Copynumber: 5.2 Consensus size: 18
5420248 CCCAACTACT
*
5420258 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
5420276 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
*
5420294 GTATACGTGAATAGTACT
1 GTATACGTGAATAGTACC
*
5420312 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
5420330 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
5420348 GTA
1 GTA
5420351 AACGGTCGTA
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:5420310 original size:36 final size:36
Alignment explanation
Indices: 5420258--5420350 Score: 168
Period size: 36 Copynumber: 2.6 Consensus size: 36
5420248 CCCAACTACT
*
5420258 GTATACGTGAACAGTACCGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
*
5420294 GTATACGTGAATAGTACTGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
5420330 GTATACGTGAATAGTACCGTA
1 GTATACGTGAATAGTACCGTA
5420351 AACGGTCGTA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (36 bp):
GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
Found at i:5430143 original size:4 final size:4
Alignment explanation
Indices: 5430136--5430165 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
5430126 GATTATGGAT
5430136 GGAG GGAG GGAG GGAG GGAG GGAG GGAG GG
1 GGAG GGAG GGAG GGAG GGAG GGAG GGAG GG
5430166 GGGCCCACTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.77, T:0.00
Consensus pattern (4 bp):
GGAG
Found at i:5434311 original size:16 final size:16
Alignment explanation
Indices: 5434286--5434316 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5434276 TGATATACAA
*
5434286 AAAAAGGAAAAAAAAG
1 AAAAACGAAAAAAAAG
5434302 AAAAACGAAAAAAAA
1 AAAAACGAAAAAAAA
5434317 ATTTTGGGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.84, C:0.03, G:0.13, T:0.00
Consensus pattern (16 bp):
AAAAACGAAAAAAAAG
Found at i:5434563 original size:101 final size:101
Alignment explanation
Indices: 5434309--5434569 Score: 330
Period size: 101 Copynumber: 2.5 Consensus size: 101
5434299 AAGAAAAACG
*
5434309 AAAAAAAAATTTTGGGTGCTGGCCTTTCAATGGCCGGCACCCAGTACAATTTTTTTAAAAAAAAA
1 AAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCC-GCACCCAGTACAA---TTTTAAAAAAAAA
** *
5434374 TTCTTTTTTTTGTCAGAGTCAGATATCAGTATACGAAAAAAAT
62 ---TTTTTCGTGTCAGAATCAGATATCAGTATACGAAAAAAAT
* * * *
5434417 AAAAAAAAA-TTTGGGTGTTGGCCTGTCAATGACCTGGACCTAGTACAATTTT-AAAAAAAA-TT
1 AAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCC-GCACCCAGTACAATTTTAAAAAAAAATTT
*
5434479 TTCGTGTCTGAATCAGATATCAGTATACGAAAAAAAT
65 TTCGTGTCAGAATCAGATATCAGTATACGAAAAAAAT
5434516 AAAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGACACCCAGTACAATTTT
1 -AAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCG-CACCCAGTACAATTTT
5434570 TTTTTAAATT
Statistics
Matches: 136, Mismatches: 14, Indels: 13
0.83 0.09 0.08
Matches are distributed among these distances:
99 35 0.26
100 10 0.07
101 37 0.27
103 8 0.06
104 4 0.03
107 33 0.24
108 9 0.07
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (101 bp):
AAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGCACCCAGTACAATTTTAAAAAAAAATTTT
TCGTGTCAGAATCAGATATCAGTATACGAAAAAAAT
Found at i:5434835 original size:108 final size:110
Alignment explanation
Indices: 5434627--5434836 Score: 325
Period size: 108 Copynumber: 1.9 Consensus size: 110
5434617 CACAAAAAAA
* *
5434627 TTTTTAAAATTGTACTGGGTGCCGGCCATTCACAGGCCTGCAACCAAAAAATTTTTTTTATTTTT
1 TTTTTAAAATTGCACTGGGTGCCGGCCATTCACAGGCCAGCAACCAAAAAATTTTTTTTATTTTT
* *
5434692 TTCGTATACTGATATCTGATTCTAACACGAAAAAAAAGAATTTTT
66 TTCGTATACTGATATCTGACTCTAACACAAAAAAAAAGAATTTTT
* * *
5434737 TTTTTAAAATTGCACTGGGTGCCGGCCATTGACAGGCCAGC-ACC-CAAATTTTTTTTTATTTTT
1 TTTTTAAAATTGCACTGGGTGCCGGCCATTCACAGGCCAGCAACCAAAAAATTTTTTTTATTTTT
* *
5434800 TTCGTATACTGATATCTTACTCTGACACAAAAAAAAA
66 TTCGTATACTGATATCTGACTCTAACACAAAAAAAAA
5434837 TTTAAATTTG
Statistics
Matches: 91, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
108 50 0.55
109 3 0.03
110 38 0.42
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (110 bp):
TTTTTAAAATTGCACTGGGTGCCGGCCATTCACAGGCCAGCAACCAAAAAATTTTTTTTATTTTT
TTCGTATACTGATATCTGACTCTAACACAAAAAAAAAGAATTTTT
Found at i:5435494 original size:51 final size:50
Alignment explanation
Indices: 5435361--5435552 Score: 233
Period size: 51 Copynumber: 3.8 Consensus size: 50
5435351 TGACCATTGT
* * *
5435361 TATCTGATACACGTAGTAGCCTACACATAGTACTATACACGTGATCAAGC
1 TATCTGATACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAGC
* * * *
5435411 TTTCCGGTTCACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAGGC
1 TATCTGATACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAA-GC
* * * * *
5435462 CATCTGGTACACATAGTAGCCTGCACATAGTACTACACATGTGACCATTATC
1 TATCTGATACACGTAGTAGCCTGCACATAGTACTACACACGTGACCA--AGC
*
5435514 TATC-GATACACGTAGTAGCCTGCACTTAGTACTACACAC
1 TATCTGATACACGTAGTAGCCTGCACATAGTACTACACAC
5435553 ATGTTCCTAG
Statistics
Matches: 120, Mismatches: 19, Indels: 5
0.83 0.13 0.03
Matches are distributed among these distances:
50 41 0.34
51 74 0.62
52 4 0.03
53 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (50 bp):
TATCTGATACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAGC
Found at i:5438563 original size:18 final size:17
Alignment explanation
Indices: 5438530--5438568 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
5438520 TTTTATAAAT
5438530 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
5438548 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
5438565 TGTG
1 TGTG
5438569 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:5438821 original size:23 final size:23
Alignment explanation
Indices: 5438794--5438915 Score: 172
Period size: 23 Copynumber: 5.3 Consensus size: 23
5438784 AGTGTTATTG
5438794 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * *
5438817 TTCAGTGATAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
5438840 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * ** *
5438863 TTCAGTGGTAGCTACAACTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
5438886 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
5438909 ATCAGTG
1 ATCAGTG
5438916 TGGCGCTTGT
Statistics
Matches: 83, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 83 1.00
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:5438847 original size:46 final size:46
Alignment explanation
Indices: 5438794--5438915 Score: 199
Period size: 46 Copynumber: 2.7 Consensus size: 46
5438784 AGTGTTATTG
**
5438794 ATCAGTGGTAGCTTCGGCTACATTTCAGTGATAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTGATAGCTACAACTACAT
* *
5438840 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACAACTACGT
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTGATAGCTACAACTACAT
*
5438886 ATCAGTGGTAGCTTCGGCTACATATCAGTG
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTG
5438916 TGGCGCTTGT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 71 1.00
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (46 bp):
ATCAGTGGTAGCTTCGGCTACATTTCAGTGATAGCTACAACTACAT
Found at i:5439889 original size:71 final size:71
Alignment explanation
Indices: 5439787--5439926 Score: 262
Period size: 71 Copynumber: 2.0 Consensus size: 71
5439777 TTGTATATAA
5439787 ATTGGTCATATGCCCGATTATATTTGATAAACGTTGAATGAGAAATGACATAATGTCTCATTTCA
1 ATTGGTCATATGCCCGATTATATTTGATAAACGTTGAATGAGAAATGACATAATGTCTCATTTCA
5439852 ATTACT
66 ATTACT
* *
5439858 ATTGGTCATATGCCCGATTATATTTGATAAACGTTGAATTAGAAATGACATAATGTTTCATTTCA
1 ATTGGTCATATGCCCGATTATATTTGATAAACGTTGAATGAGAAATGACATAATGTCTCATTTCA
5439923 ATTA
66 ATTA
5439927 GTTATTATGA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 67 1.00
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (71 bp):
ATTGGTCATATGCCCGATTATATTTGATAAACGTTGAATGAGAAATGACATAATGTCTCATTTCA
ATTACT
Found at i:5440229 original size:49 final size:49
Alignment explanation
Indices: 5440166--5440304 Score: 242
Period size: 49 Copynumber: 2.8 Consensus size: 49
5440156 CAATAAGTGA
*
5440166 TATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTATATGT
1 TATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGGTATATGT
5440215 TATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGGTATATGT
1 TATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGGTATATGT
* * *
5440264 TATGTGATTACGTGTAAGACCATAGTTGGACTATGACATCG
1 TATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCG
5440305 AGAAAATAAG
Statistics
Matches: 86, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 86 1.00
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.32
Consensus pattern (49 bp):
TATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGGTATATGT
Found at i:5441319 original size:21 final size:21
Alignment explanation
Indices: 5441277--5441403 Score: 89
Period size: 21 Copynumber: 6.1 Consensus size: 21
5441267 GTACATCATT
5441277 AACAGAAGCTCGA-AAG--CTG
1 AACAGAAGCTC-ATAAGAACTG
*
5441296 AACAGAAGCTCGTAAGAACTG
1 AACAGAAGCTCATAAGAACTG
* * * ** *
5441317 AACAAAAACTCATATGAGTTA
1 AACAGAAGCTCATAAGAACTG
5441338 AACAGAAGCTCATAAGAACTG
1 AACAGAAGCTCATAAGAACTG
* * ** *
5441359 AACAGAAACTCACAAGAGTTT
1 AACAGAAGCTCATAAGAACTG
* * *
5441380 AACAAAAGCTCAAAAGAGCTG
1 AACAGAAGCTCATAAGAACTG
5441401 AAC
1 AAC
5441404 GAAAACTCAT
Statistics
Matches: 81, Mismatches: 24, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
19 14 0.17
21 67 0.83
ACGTcount: A:0.48, C:0.19, G:0.18, T:0.15
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAACTG
Found at i:5441355 original size:42 final size:42
Alignment explanation
Indices: 5441296--5441432 Score: 193
Period size: 42 Copynumber: 3.3 Consensus size: 42
5441286 TCGAAAGCTG
*
5441296 AACAGAAGCTCGTAAGAACTGAACAAAAACTCATATGAGTTA
1 AACAGAAGCTCATAAGAACTGAACAAAAACTCATATGAGTTA
* * * *
5441338 AACAGAAGCTCATAAGAACTGAACAGAAACTCACAAGAGTTT
1 AACAGAAGCTCATAAGAACTGAACAAAAACTCATATGAGTTA
* * * *
5441380 AACAAAAGCTCAAAAGAGCTGAACGAAAACTCATATGAGTTA
1 AACAGAAGCTCATAAGAACTGAACAAAAACTCATATGAGTTA
5441422 AACAGAAGCTC
1 AACAGAAGCTC
5441433 GTAAAGCTAA
Statistics
Matches: 81, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 81 1.00
ACGTcount: A:0.48, C:0.18, G:0.17, T:0.17
Consensus pattern (42 bp):
AACAGAAGCTCATAAGAACTGAACAAAAACTCATATGAGTTA
Found at i:5451225 original size:25 final size:25
Alignment explanation
Indices: 5451164--5451225 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
5451154 CAAGCTTCCC
* *
5451164 ATTAATAGCTCTTTGGAGCTTCCTG
1 ATTAATGGCTCTTTGGAACTTCCTG
*
5451189 A-TAACTGCCTCTTAT-GAACTTCCTG
1 ATTAA-TGGCTCTT-TGGAACTTCCTG
5451214 ATTAATGGCTCT
1 ATTAATGGCTCT
5451226 CCGGATCTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
24 3 0.10
25 23 0.77
26 4 0.13
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.39
Consensus pattern (25 bp):
ATTAATGGCTCTTTGGAACTTCCTG
Found at i:5454651 original size:21 final size:21
Alignment explanation
Indices: 5454622--5454666 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
5454612 AAGTTTTAAG
*
5454622 CAAACACCAATCGTTATCATA
1 CAAACACCAATCGGTATCATA
* * *
5454643 CAAATACCATTCGGTATCTTA
1 CAAACACCAATCGGTATCATA
5454664 CAA
1 CAA
5454667 GTATTAATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.27, G:0.07, T:0.27
Consensus pattern (21 bp):
CAAACACCAATCGGTATCATA
Done.