Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A03
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: 108673976
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.31
Warning! 5040000 characters in sequence are not A, C, G, or T
File 320 of 333
Found at i:104336181 original size:10 final size:10
Alignment explanation
Indices: 104336166--104336223 Score: 62
Period size: 10 Copynumber: 5.6 Consensus size: 10
104336156 TTTTATTTCA
*
104336166 AAAAAAAGGG
1 AAAAAAAGAG
*
104336176 AAAAAAAGAA
1 AAAAAAAGAG
104336186 AAAAAAAGAG
1 AAAAAAAGAG
* *
104336196 AAAAAAATAAA
1 AAAAAAA-GAG
104336207 AAAAAAATGAG
1 AAAAAAA-GAG
104336218 AAAAAA
1 AAAAAA
104336224 GAAAAAAGAA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
10 24 0.60
11 16 0.40
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (10 bp):
AAAAAAAGAG
Found at i:104336187 original size:7 final size:7
Alignment explanation
Indices: 104336177--104336237 Score: 58
Period size: 7 Copynumber: 8.9 Consensus size: 7
104336167 AAAAAAGGGA
104336177 AAAAAAG
1 AAAAAAG
104336184 -AAAAA-
1 AAAAAAG
*
104336189 AAAAGAG
1 AAAAAAG
104336196 AAAAAA-
1 AAAAAAG
104336202 ATAAAAA-
1 A-AAAAAG
104336209 AAAAATGAG
1 AAAAA--AG
104336218 AAAAAAG
1 AAAAAAG
104336225 AAAAAAG
1 AAAAAAG
104336232 AAAAAA
1 AAAAAA
104336238 TGGAGAGGCC
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
6 14 0.30
7 26 0.57
8 1 0.02
9 5 0.11
ACGTcount: A:0.85, C:0.00, G:0.11, T:0.03
Consensus pattern (7 bp):
AAAAAAG
Found at i:104336190 original size:20 final size:20
Alignment explanation
Indices: 104336165--104336230 Score: 89
Period size: 20 Copynumber: 3.2 Consensus size: 20
104336155 CTTTTATTTC
*
104336165 AAAAAAAAGGGAAAAAAAGA
1 AAAAAAAAGAGAAAAAAAGA
*
104336185 AAAAAAAAGAGAAAAAAATA
1 AAAAAAAAGAGAAAAAAAGA
104336205 AAAAAAAA-ATGAGAAAAAAGA
1 AAAAAAAAGA-GA-AAAAAAGA
104336226 AAAAA
1 AAAAA
104336231 GAAAAAATGG
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
19 1 0.02
20 28 0.68
21 12 0.29
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (20 bp):
AAAAAAAAGAGAAAAAAAGA
Found at i:104337328 original size:79 final size:80
Alignment explanation
Indices: 104337185--104337413 Score: 307
Period size: 79 Copynumber: 2.8 Consensus size: 80
104337175 CAAAATTCAG
* *
104337185 CGCCTTAATCCCCTAAGCGGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGG----ATTCGCAGATCTTATCTCCCTAAGCAGTA
*
104337250 GTGGAGTAGATCGAAGACT
62 GTGGAGCAGATCGAAGACT
* * * *
104337269 TGCCTTAATCCCTTAAGTAGTAGGGTAATAGG-TTCGCAGATCTTATCTCCCTAAGCAGTAGTGG
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGATTCGCAGATCTTATCTCCCTAAGCAGTAGTGG
104337333 AGCAGATCGAAGACT
66 AGCAGATCGAAGACT
*
104337348 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGG----ATTCGCAGATCTTATCTCCCTAAGCAGTA
104337413 G
62 G
104337414 GGTAACAGGT
Statistics
Matches: 128, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
79 73 0.57
84 55 0.43
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (80 bp):
CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGATTCGCAGATCTTATCTCCCTAAGCAGTAGTGG
AGCAGATCGAAGACT
Found at i:104337457 original size:127 final size:127
Alignment explanation
Indices: 104337304--104337540 Score: 438
Period size: 127 Copynumber: 1.9 Consensus size: 127
104337294 TAATAGGTTC
*
104337304 GCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACTCGCCTTAATCCCCTAAGCAGT
1 GCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACTCACCTTAATCCCCTAAGCAGT
*
104337369 AGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAGGGTAACAGGTTAAATTT
66 AGGGTAACAGGTTAAATTTGCAAATCTTATCTCCCTAAGCAGTAGGGTAACAGGTTAAATTT
*
104337431 GCAGATCTTATCTCCCTAAGTAGTAGTGGAGCAGATCGAAGACTCACCTTAATCCCCTAAGCAGT
1 GCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACTCACCTTAATCCCCTAAGCAGT
*
104337496 AGGGTAACAGGTTAAATTTGCAAATCTTATCTCCTTAAGCAGTAG
66 AGGGTAACAGGTTAAATTTGCAAATCTTATCTCCCTAAGCAGTAG
104337541 TGAAGCAGAT
Statistics
Matches: 106, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
127 106 1.00
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (127 bp):
GCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACTCACCTTAATCCCCTAAGCAGT
AGGGTAACAGGTTAAATTTGCAAATCTTATCTCCCTAAGCAGTAGGGTAACAGGTTAAATTT
Found at i:104337489 original size:84 final size:84
Alignment explanation
Indices: 104337401--104337919 Score: 755
Period size: 84 Copynumber: 6.2 Consensus size: 84
104337391 GATCTTATCT
*
104337401 CCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGTAGTAGTGGAGCAGA
1 CCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGA
*
104337466 TCGAAGACTCACCTTAATC
66 TCGAAGACTCGCCTTAATC
* * *
104337485 CCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAAATCTTATCTCCTTAAGCAGTAGTGAAGCAGA
1 CCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGA
104337550 TCGAAGACTCGCCTTAATC
66 TCGAAGACTCGCCTTAATC
*
104337569 CCCTAAGCGGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGA
1 CCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGA
104337634 TCGAAGACTCGCCTTAATC
66 TCGAAGACTCGCCTTAATC
* * * *
104337653 CTCTAAGCAGTAGGGTAACAGG-----TTCGCAGATCTTATCTCCCTAAGCAGTAGCGGAGCAAA
1 CCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGA
104337713 TCGACGACGACTCGCCTTAATC
66 TCGA--A-GACTCGCCTTAATC
*
104337735 CCCTAAGTAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGA
1 CCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGA
* *
104337800 TCGAAGACCCGCTTTAATC
66 TCGAAGACTCGCCTTAATC
* * * *
104337819 CCCTAAGCAGTAAGGTAACAAGTTAAATTTGCAGATCTTA--TCCCTAAGCAATAGCGGAGCAGA
1 CCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGA
* * *
104337882 TTGAAGACAATGCACCTTAACC
66 TCGAAGAC--T-CGCCTTAATC
104337904 CCCTAAGCAGTAGGGT
1 CCCTAAGCAGTAGGGT
104337920 CCAAGATGAT
Statistics
Matches: 392, Mismatches: 32, Indels: 21
0.88 0.07 0.05
Matches are distributed among these distances:
79 39 0.10
81 1 0.00
82 62 0.16
84 228 0.58
85 23 0.06
87 39 0.10
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (84 bp):
CCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGA
TCGAAGACTCGCCTTAATC
Found at i:104337612 original size:211 final size:206
Alignment explanation
Indices: 104337195--104337624 Score: 698
Period size: 211 Copynumber: 2.1 Consensus size: 206
104337185 CGCCTTAATC
* *
104337195 CCCTAAGCGGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGTAGA
1 CCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGA
** * * * *
104337260 TCGAAGACTTGCCTTAATCCCTTAAGTAGTAGGGTAATAGGTTCGCAGATCTTATCTCCCTAAGC
66 TCGAAGACTCACCTTAATCCCCTAAGCAGTAGGGTAACAGGTTCGCAAATCTTATCTCCCTAAGC
*
104337325 AGTAGTGGAGCAGATCGAAGACTCGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGC
131 AGTAGTGAAGCAGATCGAAGACTCGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGC
104337390 AGATCTTATCT
196 AGATCTTATCT
*
104337401 CCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGTAGTAGTGGAGCAGA
1 CCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGA
* *
104337466 TCGAAGACTCACCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAAATCTTATCTCCT
66 TCGAAGACTCACCTTAATCCCCTAAGCAGTAGGGTAACAGG-----TTCGCAAATCTTATCTCCC
*
104337531 TAAGCAGTAGTGAAGCAGATCGAAGACTCGCCTTAATCCCCTAAGCGGTAGGGTAACAGGTTAAA
126 TAAGCAGTAGTGAAGCAGATCGAAGACTCGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAA
104337596 TTTGCAGATCTTATCT
191 TTTGCAGATCTTATCT
104337612 CCCTAAGCAGTAG
1 CCCTAAGCAGTAG
104337625 TGGAGCAGAT
Statistics
Matches: 206, Mismatches: 13, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
206 98 0.48
211 108 0.52
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (206 bp):
CCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGA
TCGAAGACTCACCTTAATCCCCTAAGCAGTAGGGTAACAGGTTCGCAAATCTTATCTCCCTAAGC
AGTAGTGAAGCAGATCGAAGACTCGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGC
AGATCTTATCT
Found at i:104337757 original size:250 final size:248
Alignment explanation
Indices: 104337401--104337919 Score: 747
Period size: 250 Copynumber: 2.1 Consensus size: 248
104337391 GATCTTATCT
* * * *
104337401 CCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGTAGTAGTGGAGCAGA
1 CCCTAAGCAGTAGGGTAACAGG----ATTCGCAGATCTTATCTCCCTAAGCAGTAGCGGAGCAAA
*
104337466 TCGAAGACTCACCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAAATCTTATCTCCT
62 TCGAAGACTCACCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAAATCTTATCTCCC
* * * *
104337531 TAAGCAGTAGTGAAGCAGATCGAAGACTCGCCTTAATCCCCTAAGCGGTAGGGTAACAGGTTAAA
127 TAAGCAGTAGTGAAGCAGATCGAAGACCCGCCTTAATCCCCTAAGCAGTAAGGTAACAAGTTAAA
* * * *
104337596 TTTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAC-T-CGCCTTAATC
192 TTTGCAGATCTTA--TCCCTAAGCAATAGCGGAGCAGATCGAAGACATGCACCTTAACC
*
104337653 CTCTAAGCAGTAGGGTAACAGG-TTCGCAGATCTTATCTCCCTAAGCAGTAGCGGAGCAAATCGA
1 CCCTAAGCAGTAGGGTAACAGGATTCGCAGATCTTATCTCCCTAAGCAGTAGCGGAGCAAATCGA
* * *
104337717 CGACGACTCGCCTTAATCCCCTAAGTAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCT
66 --A-GACTCACCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAAATCTTATCTCCCT
* *
104337782 AAGCAGTAGTGGAGCAGATCGAAGACCCGCTTTAATCCCCTAAGCAGTAAGGTAACAAGTTAAAT
128 AAGCAGTAGTGAAGCAGATCGAAGACCCGCCTTAATCCCCTAAGCAGTAAGGTAACAAGTTAAAT
*
104337847 TTGCAGATCTTATCCCTAAGCAATAGCGGAGCAGATTGAAGACAATGCACCTTAACC
193 TTGCAGATCTTATCCCTAAGCAATAGCGGAGCAGATCGAAGAC-ATGCACCTTAACC
104337904 CCCTAAGCAGTAGGGT
1 CCCTAAGCAGTAGGGT
104337920 CCAAGATGAT
Statistics
Matches: 240, Mismatches: 21, Indels: 13
0.88 0.08 0.05
Matches are distributed among these distances:
247 38 0.16
248 28 0.12
249 1 0.00
250 129 0.54
251 23 0.10
252 21 0.09
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (248 bp):
CCCTAAGCAGTAGGGTAACAGGATTCGCAGATCTTATCTCCCTAAGCAGTAGCGGAGCAAATCGA
AGACTCACCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAAATCTTATCTCCCTAAG
CAGTAGTGAAGCAGATCGAAGACCCGCCTTAATCCCCTAAGCAGTAAGGTAACAAGTTAAATTTG
CAGATCTTATCCCTAAGCAATAGCGGAGCAGATCGAAGACATGCACCTTAACC
Found at i:104337786 original size:166 final size:164
Alignment explanation
Indices: 104337401--104337919 Score: 684
Period size: 166 Copynumber: 3.1 Consensus size: 164
104337391 GATCTTATCT
*
104337401 CCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGTAGTAGTGGAGCAGA
1 CCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGA
* * *
104337466 TCGAAGACTCACCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAAATCTTATCTCCT
66 TCGAAGACTCGCCTTAATCCCCTAAGCAGTAGGGTAACAGG----ATTCGCAAATCTTATCTCCC
* *
104337531 TAAGCAGTAGTGAAGCAGATCGAAGACTCGCCTTAATC
127 TAAGCAGTAGCGAAGCAAATCGAAGACTCGCCTTAATC
*
104337569 CCCTAAGCGGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGA
1 CCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGA
* *
104337634 TCGAAGACTCGCCTTAATCCTCTAAGCAGTAGGGTAACAGG-TTCGCAGATCTTATCTCCCTAAG
66 TCGAAGACTCGCCTTAATCCCCTAAGCAGTAGGGTAACAGGATTCGCAAATCTTATCTCCCTAAG
*
104337698 CAGTAGCGGAGCAAATCGACGACGACTCGCCTTAATC
131 CAGTAGCGAAGCAAATCGA--A-GACTCGCCTTAATC
*
104337735 CCCTAAGTAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGA
1 CCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGA
* * * * * *
104337800 TCGAAGACCCGCTTTAATCCCCTAAGCAGTAAGGTAACAAGTTAAATTTGCAGATCTTA--TCCC
66 TCGAAGACTCGCCTTAATCCCCTAAGCAGTAGGGTAAC-AG---GATTCGCAAATCTTATCTCCC
* * * * * *
104337863 TAAGCAATAGCGGAGCAGATTGAAGACAATGCACCTTAACC
127 TAAGCAGTAGCGAAGCAAATCGAAGAC--T-CGCCTTAATC
104337904 CCCTAAGCAGTAGGGT
1 CCCTAAGCAGTAGGGT
104337920 CCAAGATGAT
Statistics
Matches: 316, Mismatches: 24, Indels: 21
0.88 0.07 0.06
Matches are distributed among these distances:
163 36 0.11
165 1 0.00
166 114 0.36
167 3 0.01
168 103 0.33
169 47 0.15
171 12 0.04
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (164 bp):
CCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGA
TCGAAGACTCGCCTTAATCCCCTAAGCAGTAGGGTAACAGGATTCGCAAATCTTATCTCCCTAAG
CAGTAGCGAAGCAAATCGAAGACTCGCCTTAATC
Found at i:104338679 original size:19 final size:19
Alignment explanation
Indices: 104338655--104338722 Score: 113
Period size: 19 Copynumber: 3.7 Consensus size: 19
104338645 AATCTTTAAG
104338655 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
104338674 GATATGCAATATTAGATAT
1 GATATGCAATCTTAGATAT
104338693 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
104338710 GATATGCAATCTT
1 GATATGCAATCTT
104338723 GAAGATATAA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.36
19 29 0.64
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:104338744 original size:22 final size:21
Alignment explanation
Indices: 104338717--104338760 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
104338707 TATGATATGC
104338717 AATCTT-GAAGATATAATCTTGT
1 AATCTTAG-AGATATAAT-TTGT
*
104338739 AATCTTAGAGATTTAATTTGT
1 AATCTTAGAGATATAATTTGT
104338760 A
1 A
104338761 GATATCCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 14 0.70
23 1 0.05
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (21 bp):
AATCTTAGAGATATAATTTGT
Found at i:104338747 original size:41 final size:36
Alignment explanation
Indices: 104338661--104338733 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
104338651 TAAGGATATG
*
104338661 CAATCTTAGATATGATATGCAATATTAGATATGATA
1 CAATCTTAGATATGATATGCAATATTAGATATAATA
*
104338697 CAATCTTAGATATGATATGCAATCTTGAAGATATAAT
1 CAATCTTAGATATGATATGCAATATT--AGATATAAT
104338734 CTTGTAATCT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
36 25 0.76
38 8 0.24
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.36
Consensus pattern (36 bp):
CAATCTTAGATATGATATGCAATATTAGATATAATA
Found at i:104340182 original size:19 final size:19
Alignment explanation
Indices: 104340132--104340188 Score: 93
Period size: 18 Copynumber: 3.2 Consensus size: 19
104340122 TGGTTTCGAC
104340132 AGATATGATA--CAATCTT
1 AGATATGATATGCAATCTT
104340149 AGATATGAT-TGCAATCTT
1 AGATATGATATGCAATCTT
104340167 AGATATGATATGCAATCTT
1 AGATATGATATGCAATCTT
104340186 AGA
1 AGA
104340189 AGATATGATT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.24
18 16 0.43
19 12 0.32
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.35
Consensus pattern (19 bp):
AGATATGATATGCAATCTT
Found at i:104340214 original size:22 final size:22
Alignment explanation
Indices: 104340149--104340211 Score: 71
Period size: 23 Copynumber: 3.0 Consensus size: 22
104340139 ATACAATCTT
104340149 AGATATGAT-TGCAATCTT---
1 AGATATGATATGCAATCTTAGA
104340167 AGATATGATATGCAATCTTAGA
1 AGATATGATATGCAATCTTAGA
* *
104340189 AGATATGATTTTGTAATCTTAGA
1 AGATATGA-TATGCAATCTTAGA
104340212 GATTTAATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
18 9 0.24
19 9 0.24
22 8 0.21
23 12 0.32
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.38
Consensus pattern (22 bp):
AGATATGATATGCAATCTTAGA
Found at i:104341835 original size:39 final size:39
Alignment explanation
Indices: 104341792--104342067 Score: 435
Period size: 39 Copynumber: 7.1 Consensus size: 39
104341782 CATAAACAAA
* * *
104341792 ATATAACACCAGCATGAATGCTTTCGGGACTTAGCCCAG
1 ATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCGG
* *
104341831 ATATAGCACCAGCACGAATGCCTTCGGGACTTAGCCCAG
1 ATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCGG
* *
104341870 ATATAATACCAGCACGAATGCCTTCAGGACTTAGCCCGG
1 ATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCGG
*
104341909 ATATAGCACCAGCACGAATGCCTTCGGGACTTAGCCCGG
1 ATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCGG
* *
104341948 ATATAATACCAGCACGAATGCCTTCAGGACTTAGCCCGG
1 ATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCGG
* * *
104341987 ATATAATACCAGCATGAATGCCTTCAGGACTTAGCCCGG
1 ATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCGG
104342026 ATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCGG
1 ATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCGG
104342065 ATA
1 ATA
104342068 ATTTTCCAGC
Statistics
Matches: 220, Mismatches: 17, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 220 1.00
ACGTcount: A:0.30, C:0.28, G:0.22, T:0.20
Consensus pattern (39 bp):
ATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCGG
Found at i:104342104 original size:39 final size:39
Alignment explanation
Indices: 104342061--104342151 Score: 114
Period size: 39 Copynumber: 2.3 Consensus size: 39
104342051 GGGACTTAGC
* *
104342061 CCGGATAATTTTCCAGCACT-TAGCCTGCGGACTTTAAGT
1 CCGGATAATTTTCCAGCA-TAAAGCCTGCGGACTTCAAGT
*
104342100 CCGGAT-ATATTTCTAGCATAAAGCCTGCGGACTTCAAGT
1 CCGGATAAT-TTTCCAGCATAAAGCCTGCGGACTTCAAGT
104342139 CCGGATATATTTT
1 CCGGATA-ATTTT
104342152 TCCAATACCA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
38 3 0.07
39 37 0.82
40 3 0.07
41 2 0.04
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (39 bp):
CCGGATAATTTTCCAGCATAAAGCCTGCGGACTTCAAGT
Found at i:104343049 original size:3 final size:3
Alignment explanation
Indices: 104343043--104343083 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
104343033 ATTATTATTA
104343043 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
104343084 ATTATGTAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:104343394 original size:42 final size:42
Alignment explanation
Indices: 104343345--104343440 Score: 140
Period size: 42 Copynumber: 2.3 Consensus size: 42
104343335 AAGGGAGCAA
* *
104343345 CACAGGGTCCTTAGAGATGCTT-TCAGGTGAATAAGGGAATAG
1 CACAGGGTCCTTAGAGATACTTGT-AGGTGAAGAAGGGAATAG
*
104343387 CACAGGGTCCTTAGAGATACTTGTAGGTGAAGAAGGGAGTAG
1 CACAGGGTCCTTAGAGATACTTGTAGGTGAAGAAGGGAATAG
*
104343429 CGCAGGGTCCTT
1 CACAGGGTCCTT
104343441 TTCAAGTAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
42 48 0.98
43 1 0.02
ACGTcount: A:0.28, C:0.16, G:0.33, T:0.23
Consensus pattern (42 bp):
CACAGGGTCCTTAGAGATACTTGTAGGTGAAGAAGGGAATAG
Found at i:104344088 original size:21 final size:21
Alignment explanation
Indices: 104344059--104344108 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
104344049 CTGGTATATG
104344059 GTTAGTCAAGTGGTTAGCATTT
1 GTTA-TCAAGTGGTTAGCATTT
**
104344081 GTTATCAAGTGGTTAGTGTTT
1 GTTATCAAGTGGTTAGCATTT
104344102 GTTATCA
1 GTTATCA
104344109 CTCACCAGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.22, C:0.08, G:0.26, T:0.44
Consensus pattern (21 bp):
GTTATCAAGTGGTTAGCATTT
Found at i:104344318 original size:43 final size:42
Alignment explanation
Indices: 104344240--104344392 Score: 182
Period size: 43 Copynumber: 3.6 Consensus size: 42
104344230 TTTTAGGACC
* *
104344240 TTTAGCGGCGCTCTTAT-AAAAACACCACTAAAGACCTGTACT
1 TTTAGCGGCGCTTTTTTAAAAAACACCACT-AAGACCTGTACT
*
104344282 TTTAGCGGCGCTTTTTTAAAAAACGCCACTATAGACCTGTACT
1 TTTAGCGGCGCTTTTTTAAAAAACACCACTA-AGACCTGTACT
* * * * * *
104344325 TTTAGCTGCGCTTTTATAAAAAAACACCGCTAATGACCAGGACC
1 TTTAGCGGCGCTTTT-TTAAAAAACACCACTAA-GACCTGTACT
104344369 TTTAGCGGCGCTTTTTTAAAAAAC
1 TTTAGCGGCGCTTTTTTAAAAAAC
104344393 GCCGCTAATT
Statistics
Matches: 95, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
42 16 0.17
43 45 0.47
44 34 0.36
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (42 bp):
TTTAGCGGCGCTTTTTTAAAAAACACCACTAAGACCTGTACT
Found at i:104345312 original size:18 final size:18
Alignment explanation
Indices: 104345280--104345317 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
104345270 TACAATATAG
104345280 TAGTAAAAATATTATTTAA
1 TAGTAAAAATATTA-TTAA
*
104345299 TAGTAAAAA-GTTATTAA
1 TAGTAAAAATATTATTAA
104345316 TA
1 TA
104345318 CTTGATAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 3 0.17
19 9 0.50
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (18 bp):
TAGTAAAAATATTATTAA
Found at i:104350288 original size:41 final size:41
Alignment explanation
Indices: 104350242--104350543 Score: 376
Period size: 41 Copynumber: 7.4 Consensus size: 41
104350232 GGTTACGGGA
** *
104350242 TTTTTAGCGGCGTTTTAGAAAAAGCGCCGTTAATGCTCTGG
1 TTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGG
*
104350283 TTTTTAGCGGCGTTTTAGCAAAAGCGCCGCTAATGCTCTGG
1 TTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGG
* *
104350324 TTTTTAGCGGCGTTTTACCAAAACCGCCGCTAATGCTTTGG
1 TTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGG
* *
104350365 TTTTTAGCGGCATTTTACCTAAAGCGCCGCTAATGCTCTGG
1 TTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGG
* * *
104350406 TTTTTGGCGGCGTTTTACCGAAAGTGCCGCTAATGCTCTGG
1 TTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGG
* * * *
104350447 TTTTTAGCGGCGTTTTACCGAAAGTGCCACTAATGCTTTGG
1 TTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGG
* * **
104350488 -TTTTAGCGGCATTTTTGACTAAAA-CGCCGCTGTTGCTCT-G
1 TTTTTAGCGGC-GTTTT-ACCAAAAGCGCCGCTAATGCTCTGG
* *
104350528 TTTTTACCGGTGTTTT
1 TTTTTAGCGGCGTTTT
104350544 TTTTAGAACG
Statistics
Matches: 231, Mismatches: 27, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
40 15 0.06
41 211 0.91
42 5 0.02
ACGTcount: A:0.18, C:0.21, G:0.25, T:0.36
Consensus pattern (41 bp):
TTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGG
Found at i:104350867 original size:42 final size:42
Alignment explanation
Indices: 104350762--104350847 Score: 136
Period size: 42 Copynumber: 2.0 Consensus size: 42
104350752 AAAAAGAAAA
* * * *
104350762 AAGGGAGCAACACATGGTCCTTAGAGATACTTGCCGGTGAAG
1 AAGGGAGCAACAAAGGGTCCTTAGAGATACTTACAGGTGAAG
104350804 AAGGGAGCAACAAAGGGTCCTTAGAGATACTTACAGGTGAAG
1 AAGGGAGCAACAAAGGGTCCTTAGAGATACTTACAGGTGAAG
104350846 AA
1 AA
104350848 CGGGGCAGCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.36, C:0.16, G:0.30, T:0.17
Consensus pattern (42 bp):
AAGGGAGCAACAAAGGGTCCTTAGAGATACTTACAGGTGAAG
Found at i:104352057 original size:26 final size:26
Alignment explanation
Indices: 104352028--104352135 Score: 207
Period size: 26 Copynumber: 4.2 Consensus size: 26
104352018 TGATATAAAT
104352028 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
104352054 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
104352080 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
104352106 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
104352132 TGAT
1 TGAT
104352136 GGGAATTTCA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 80 1.00
ACGTcount: A:0.31, C:0.06, G:0.27, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:104353425 original size:14 final size:14
Alignment explanation
Indices: 104353406--104353440 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
104353396 TTTTGGTAAG
104353406 CTGCAAAATTTGGA
1 CTGCAAAATTTGGA
104353420 CTGCAAAATTTGGA
1 CTGCAAAATTTGGA
104353434 CTGCAAA
1 CTGCAAA
104353441 GTGCATGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (14 bp):
CTGCAAAATTTGGA
Found at i:104355738 original size:30 final size:29
Alignment explanation
Indices: 104355699--104355773 Score: 75
Period size: 30 Copynumber: 2.6 Consensus size: 29
104355689 GACATTTAAT
*
104355699 AATAAATTTAAAATATAATATATAATAAAA
1 AATATATTTAAAATATAATA-ATAATAAAA
* *
104355729 AATATATTTATAAGA-ATAATAATTATATAA
1 AATATATTTA-AA-ATATAATAATAATAAAA
104355759 AATATA--TAAAATATA
1 AATATATTTAAAATATA
104355774 TTGGTTTAGA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
26 1 0.03
27 5 0.13
28 2 0.05
30 22 0.56
31 8 0.21
32 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (29 bp):
AATATATTTAAAATATAATAATAATAAAA
Found at i:104356275 original size:19 final size:19
Alignment explanation
Indices: 104356251--104356359 Score: 154
Period size: 19 Copynumber: 5.9 Consensus size: 19
104356241 AATCATATCT
*
104356251 TCTAAGATTGTATATCATA
1 TCTAAGATTGCATATCATA
104356270 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
*
104356288 TCTAAGATCGCA-ATCATA
1 TCTAAGATTGCATATCATA
104356306 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
*
104356323 TCTAAGATTGCATATCACA
1 TCTAAGATTGCATATCATA
*
104356342 TCTAAGATTGAATATCAT
1 TCTAAGATTGCATATCAT
104356360 TGAAGATTAT
Statistics
Matches: 81, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
17 16 0.20
18 32 0.40
19 33 0.41
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.36
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:104356287 original size:18 final size:18
Alignment explanation
Indices: 104356251--104356351 Score: 141
Period size: 18 Copynumber: 5.6 Consensus size: 18
104356241 AATCATATCT
*
104356251 TCTAAGATTGTATATCATA
1 TCTAAGATTGCA-ATCATA
104356270 TCTAAGATTGCAATCATA
1 TCTAAGATTGCAATCATA
*
104356288 TCTAAGATCGCAATCATA
1 TCTAAGATTGCAATCATA
*
104356306 TCTAAGATTG-TATCATA
1 TCTAAGATTGCAATCATA
*
104356323 TCTAAGATTGCATATCACA
1 TCTAAGATTGCA-ATCATA
104356342 TCTAAGATTG
1 TCTAAGATTG
104356352 AATATCATTG
Statistics
Matches: 74, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
17 16 0.22
18 32 0.43
19 26 0.35
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.36
Consensus pattern (18 bp):
TCTAAGATTGCAATCATA
Found at i:104356366 original size:36 final size:36
Alignment explanation
Indices: 104356253--104356367 Score: 114
Period size: 36 Copynumber: 3.2 Consensus size: 36
104356243 TCATATCTTC
* *
104356253 TAAGATTGTATATCATATCTAAGATTGCAATCAT-ATC
1 TAAGATTGCATATCATATCTAAGATTG-AAT-ATCATA
*
104356290 TAAGATCGCA-ATCATATCTAAGATTG--TATCATA
1 TAAGATTGCATATCATATCTAAGATTGAATATCATA
*
104356323 TCTAAGATTGCATATCACATCTAAGATTGAATATCAT-
1 --TAAGATTGCATATCATATCTAAGATTGAATATCATA
104356360 TGAAGATT
1 T-AAGATT
104356368 ATATTTCCAT
Statistics
Matches: 66, Mismatches: 5, Indels: 15
0.77 0.06 0.17
Matches are distributed among these distances:
32 2 0.03
33 3 0.05
35 10 0.15
36 37 0.56
37 8 0.12
38 6 0.09
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (36 bp):
TAAGATTGCATATCATATCTAAGATTGAATATCATA
Found at i:104357076 original size:205 final size:205
Alignment explanation
Indices: 104356722--104357426 Score: 1187
Period size: 205 Copynumber: 3.4 Consensus size: 205
104356712 AAATTAACTT
* * * * *
104356722 CTTCGATTTGTTC-CTTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTTAACGTAAGCA
1 CTTCGATTTGTTCTC-TGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAACA
* * * *
104356786 CGTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTATGCACAAGGATGCCAAACTATCT
65 CGTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATACCAAACCATCT
* * *
104356851 TGGATCTGCTTCAGCATAAACATCTGAAGGTGAGATCTGCCATGTATCTACTCTCCATTGAAGTG
130 TGGATCTGCTTCAGCATAAACATCTGAAGGTGAGATCTGCTATGTATCTACTCTCTATTGAAGTA
104356916 GAGATGCCAGA
195 GAGATGCCAGA
* * *
104356927 CTTCGATTTGTTCTCTGACACTACAGAGACGACAAATCATCTTAGATTTGCTTCATCATAAATAC
1 CTTCGATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAACAC
*
104356992 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAATGATACCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATACCAAACCATCTT
* *
104357057 GGATCTGCTTCAACATAAACATCTGAAGGTGAGATCTGCTATGTATCTACTCTCTATTGAATTAG
131 GGATCTGCTTCAGCATAAACATCTGAAGGTGAGATCTGCTATGTATCTACTCTCTATTGAAGTAG
104357122 AGATGCCAGA
196 AGATGCCAGA
* *
104357132 CTTCGATTTGTTCTCTGACACTACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAATAC
1 CTTCGATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAACAC
*
104357197 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATATCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATACCAAACCATCTT
*
104357262 GGATCTGCTTCAGCATAAACATCTGAAGGTGAGATCTGCTATGTATCTGCTCTCTATTGAAGTAG
131 GGATCTGCTTCAGCATAAACATCTGAAGGTGAGATCTGCTATGTATCTACTCTCTATTGAAGTAG
104357327 AGATGCCAGA
196 AGATGCCAGA
*
104357337 CTTCGATTTGTTCTCTGACAATACAGAGATGACAAATCATCTTAGATTTGCTTCATCGTAAACAC
1 CTTCGATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAACAC
104357402 GTGAAAGCCAAATCAGCTATGTCTT
66 GTGAAAGCCAAATCAGCTATGTCTT
104357427 TGATCTGCTC
Statistics
Matches: 472, Mismatches: 27, Indels: 2
0.94 0.05 0.00
Matches are distributed among these distances:
205 471 1.00
206 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (205 bp):
CTTCGATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAACAC
GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATACCAAACCATCTT
GGATCTGCTTCAGCATAAACATCTGAAGGTGAGATCTGCTATGTATCTACTCTCTATTGAAGTAG
AGATGCCAGA
Found at i:104357479 original size:44 final size:44
Alignment explanation
Indices: 104357423--104357507 Score: 125
Period size: 44 Copynumber: 1.9 Consensus size: 44
104357413 ATCAGCTATG
* *
104357423 TCTTTGATCTGCTCTCCGCCAATACAGAGATGCCAAATCTGGTA
1 TCTTCGATCTGCTCTCCGACAATACAGAGATGCCAAATCTGGTA
* * *
104357467 TCTTCGATCTGCTCTCTGACAATACAGAGATGTCGAATCTG
1 TCTTCGATCTGCTCTCCGACAATACAGAGATGCCAAATCTG
104357508 CTGTTTTCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.31
Consensus pattern (44 bp):
TCTTCGATCTGCTCTCCGACAATACAGAGATGCCAAATCTGGTA
Found at i:104358549 original size:7 final size:7
Alignment explanation
Indices: 104358534--104358601 Score: 70
Period size: 7 Copynumber: 9.7 Consensus size: 7
104358524 GGCCTCTCCA
*
104358534 TTTTGCT
1 TTTTTCT
104358541 TTTTTCT
1 TTTTTCT
104358548 TTTTTCT
1 TTTTTCT
*
104358555 CTTTTTAT
1 -TTTTTCT
104358563 TTTTAT-T
1 TTTT-TCT
104358570 TTTTTC-
1 TTTTTCT
104358576 TTTTTC-
1 TTTTTCT
104358582 TTTTTCTT
1 TTTTTC-T
104358590 TTTTTCT
1 TTTTTCT
104358597 TTTTT
1 TTTTT
104358602 TCCTTTTTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
6 13 0.24
7 28 0.52
8 13 0.24
ACGTcount: A:0.03, C:0.12, G:0.01, T:0.84
Consensus pattern (7 bp):
TTTTTCT
Found at i:104358611 original size:9 final size:8
Alignment explanation
Indices: 104358540--104358611 Score: 69
Period size: 8 Copynumber: 8.8 Consensus size: 8
104358530 TCCATTTTGC
104358540 TTTTTTCT
1 TTTTTTCT
104358548 TTTTTCTCT
1 TTTTT-TCT
104358557 TTTTATT-T
1 TTTT-TTCT
104358565 TTATTTT-T
1 TT-TTTTCT
104358573 TTCTTTT-T
1 TT-TTTTCT
*
104358581 CTTTTTCT
1 TTTTTTCT
104358589 TTTTTTCT
1 TTTTTTCT
104358597 TTTTTTCCT
1 TTTTTT-CT
104358606 TTTTTT
1 TTTTTT
104358612 TGAAATAGAA
Statistics
Matches: 56, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
7 4 0.07
8 33 0.59
9 18 0.32
10 1 0.02
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (8 bp):
TTTTTTCT
Found at i:104358612 original size:20 final size:20
Alignment explanation
Indices: 104358541--104358600 Score: 93
Period size: 20 Copynumber: 3.0 Consensus size: 20
104358531 CCATTTTGCT
104358541 TTTTTCTTTTTTCTCTTTTTA
1 TTTTTCTTTTTT-TCTTTTTA
* *
104358562 TTTTTATTTTTTTCTTTTTC
1 TTTTTCTTTTTTTCTTTTTA
104358582 TTTTTCTTTTTTTCTTTTT
1 TTTTTCTTTTTTTCTTTTT
104358601 TTCCTTTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
20 25 0.69
21 11 0.31
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (20 bp):
TTTTTCTTTTTTTCTTTTTA
Found at i:104365659 original size:7 final size:7
Alignment explanation
Indices: 104365615--104365749 Score: 54
Period size: 7 Copynumber: 19.4 Consensus size: 7
104365605 TGAATTTTAA
*
104365615 AATAGAT
1 AATATAT
104365622 AATATAT
1 AATATAT
104365629 GATAGTATAT
1 -A-A-TATAT
*
104365639 AA-AAAT
1 AATATAT
*
104365645 AATTTAT
1 AATATAT
104365652 AATATAT
1 AATATAT
104365659 AATATA-
1 AATATAT
* *
104365665 AAAATGT
1 AATATAT
* *
104365672 AAGTTTTT
1 AA-TATAT
104365680 AA-A-AT
1 AATATAT
*
104365685 AATGTAT
1 AATATAT
104365692 AATATA-
1 AATATAT
*
104365698 AATAAAT
1 AATATAT
104365705 AATTATAT
1 AA-TATAT
104365713 AAGATATAT
1 -A-ATATAT
104365722 AAGT-TA-
1 AA-TATAT
104365728 AA-ATAT
1 AATATAT
104365734 AATATAT
1 AATATAT
104365741 AATA-AT
1 AATATAT
104365747 AAT
1 AAT
104365750 TTACAAATTT
Statistics
Matches: 96, Mismatches: 16, Indels: 33
0.66 0.11 0.23
Matches are distributed among these distances:
5 5 0.05
6 23 0.24
7 42 0.44
8 12 0.12
9 8 0.08
10 6 0.06
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (7 bp):
AATATAT
Found at i:104365713 original size:21 final size:20
Alignment explanation
Indices: 104365681--104365792 Score: 61
Period size: 21 Copynumber: 5.6 Consensus size: 20
104365671 TAAGTTTTTA
*
104365681 AAATAATGTATAATATAAAT
1 AAATAATATATAATATAAAT
* *
104365701 AAATAATTATATAAGATATAT
1 AAATAA-TATATAATATAAAT
* *
104365722 AAGTTAAAATATAATATATAAT
1 AA-ATAATATATAATATA-AAT
* * * **
104365744 -AATAATTTACAAATTTTGA-
1 AAATAATATA-TAATATAAAT
*
104365763 AAAT-ATAAATAATAT-AAT
1 AAATAATATATAATATAAAT
104365781 AAATAATATATA
1 AAATAATATATA
104365793 TAATAAGTTA
Statistics
Matches: 65, Mismatches: 20, Indels: 15
0.65 0.20 0.15
Matches are distributed among these distances:
17 1 0.02
18 8 0.12
19 9 0.14
20 15 0.23
21 27 0.42
22 5 0.08
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.37
Consensus pattern (20 bp):
AAATAATATATAATATAAAT
Found at i:104365784 original size:12 final size:13
Alignment explanation
Indices: 104365765--104365795 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
104365755 AATTTTGAAA
104365765 ATATAAATAATAT
1 ATATAAATAATAT
104365778 A-ATAAATAATAT
1 ATATAAATAATAT
104365790 ATATAA
1 ATATAA
104365796 TAAGTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
ATATAAATAATAT
Found at i:104365812 original size:17 final size:16
Alignment explanation
Indices: 104365768--104365833 Score: 60
Period size: 17 Copynumber: 4.0 Consensus size: 16
104365758 TTTGAAAATA
* *
104365768 TAAATAATATAATAAA
1 TAAAAAATATAATAAT
* *
104365784 TAATATATATAATAAGT
1 TAAAAAATATAATAA-T
104365801 TAAAAAATATAATATAT
1 TAAAAAATATAATA-AT
**
104365818 GCAAAAATATAATAAT
1 TAAAAAATATAATAAT
104365834 ATATAAAAGA
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
16 14 0.35
17 25 0.62
18 1 0.03
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (16 bp):
TAAAAAATATAATAAT
Found at i:104365926 original size:18 final size:19
Alignment explanation
Indices: 104365884--104365926 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
104365874 CATAATAAGT
*
104365884 AATAATAATATATAATGAA
1 AATAATAATATATAATCAA
* *
104365903 AGTAATACT-TATAATCAA
1 AATAATAATATATAATCAA
104365921 AATAAT
1 AATAAT
104365927 TTTATAATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.33
Consensus pattern (19 bp):
AATAATAATATATAATCAA
Found at i:104367518 original size:83 final size:83
Alignment explanation
Indices: 104367299--104367568 Score: 351
Period size: 83 Copynumber: 3.2 Consensus size: 83
104367289 TTCGATTTGT
* * * * *
104367299 AAGGATGTCAAATCATCTTGAGTCTGTCTGAAAACATTTGAGAGTCATATCTGCAAGGTCCTCGA
1 AAGGATGCCAAACCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGA
*
104367364 CTTGTTCCTTGTAAGCAC
66 TTTGTTCCTTGTAAGCAC
* * * * *
104367382 AAGGGTGCTTAAACCATCTTCAGTCTGTTTGAGAACATTTGAGAGTTATATCTGCAATGTCCTTG
1 AAGGATGC-CAAACCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCG
104367447 ATTTGTTCCTTGTAAGCAC
65 ATTTGTTCCTTGTAAGCAC
* * * *
104367466 AAGGATGCCAAACCATCTTGAGTCTGTTTGAGAACATCTAAGAGTCAAATCTGCTATGTCCTCGA
1 AAGGATGCCAAACCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGA
**
104367531 TTTGTTCCTTGTAAATAC
66 TTTGTTCCTTGTAAGCAC
* * *
104367549 AAGAATACCAAATCATCTTG
1 AAGGATGCCAAACCATCTTG
104367569 GATCTGCTTC
Statistics
Matches: 161, Mismatches: 25, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
83 88 0.55
84 73 0.45
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.33
Consensus pattern (83 bp):
AAGGATGCCAAACCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGA
TTTGTTCCTTGTAAGCAC
Found at i:104367704 original size:119 final size:119
Alignment explanation
Indices: 104367492--104367845 Score: 586
Period size: 119 Copynumber: 3.0 Consensus size: 119
104367482 CTTGAGTCTG
* * * *
104367492 TTTGAGAACATCTAAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAATACAAGAATAC
1 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCTTTGTAAACACAAGAATAC
104367557 CAAATCATCTTGGATCTGCTTCAATATAAACATCTGAAGGTTAGATCTGCTATA
66 CAAATCATCTTGGATCTGCTTCAATATAAACATCTGAAGGTTAGATCTGCTATA
104367611 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCTTTGTAAACACAAGAATAC
1 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCTTTGTAAACACAAGAATAC
* * *
104367676 CAAATCATCTTGGATCTGCTTCAGTATAATCATCTGAAGGTTAGATCTGCTATC
66 CAAATCATCTTGGATCTGCTTCAATATAAACATCTGAAGGTTAGATCTGCTATA
104367730 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTT-TCTTGTAAACACAAGAATA
1 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCT-TTGTAAACACAAGAATA
* **
104367794 CCAAATCATCTTGGATCTGCTTCAACATAAATGTCTGAA-GTCTAGATCTGCT
65 CCAAATCATCTTGGATCTGCTTCAATATAAACATCTGAAGGT-TAGATCTGCT
104367846 GTTTTCAATT
Statistics
Matches: 221, Mismatches: 12, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
118 3 0.01
119 218 0.99
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (119 bp):
TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCTTTGTAAACACAAGAATAC
CAAATCATCTTGGATCTGCTTCAATATAAACATCTGAAGGTTAGATCTGCTATA
Found at i:104373710 original size:19 final size:19
Alignment explanation
Indices: 104373686--104373725 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
104373676 TATAACCTTG
*
104373686 AATGCATATGATATG-ATGT
1 AATGCAAATG-TATGAATGT
104373705 AATGCAAATGTATGAATGT
1 AATGCAAATGTATGAATGT
104373724 AA
1 AA
104373726 CAAAGGCATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.42, C:0.05, G:0.20, T:0.33
Consensus pattern (19 bp):
AATGCAAATGTATGAATGT
Found at i:104377704 original size:7 final size:7
Alignment explanation
Indices: 104377660--104377789 Score: 58
Period size: 7 Copynumber: 18.6 Consensus size: 7
104377650 TGAATTTTAA
*
104377660 AATAGAT
1 AATATAT
104377667 AATATAT
1 AATATAT
104377674 GATAGTATAT
1 -A-A-TATAT
*
104377684 AA-AAAT
1 AATATAT
*
104377690 AATTTAT
1 AATATAT
104377697 AATATAT
1 AATATAT
104377704 AATATA-
1 AATATAT
* *
104377710 AAAATGT
1 AATATAT
* *
104377717 AAGTTTTT
1 AA-TATAT
104377725 AA-A-AT
1 AATATAT
*
104377730 AATGTAT
1 AATATAT
104377737 AATATA-
1 AATATAT
*
104377743 AATAAAT
1 AATATAT
104377750 AATTATAT
1 AA-TATAT
104377758 AAGATATAT
1 -A-ATATAT
104377767 AA-AT-T
1 AATATAT
*
104377772 AAAATAT
1 AATATAT
104377779 AATATAT
1 AATATAT
104377786 AATA
1 AATA
104377790 ATTTACAAAT
Statistics
Matches: 92, Mismatches: 17, Indels: 28
0.67 0.12 0.20
Matches are distributed among these distances:
5 6 0.07
6 18 0.20
7 43 0.47
8 11 0.12
9 8 0.09
10 6 0.07
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (7 bp):
AATATAT
Found at i:104377748 original size:21 final size:21
Alignment explanation
Indices: 104377724--104377790 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
104377714 TGTAAGTTTT
*
104377724 TAAAATAATGTATAATATAAA
1 TAAAATAATATATAATATAAA
* *
104377745 T-AAATAATTATATAAGATATA
1 TAAAATAA-TATATAATATAAA
* *
104377766 TAAATTAAAATATAATATATAA
1 TAAAATAATATATAATATA-AA
104377788 TAA
1 TAA
104377791 TTTACAAATT
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
20 6 0.17
21 21 0.58
22 9 0.25
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (21 bp):
TAAAATAATATATAATATAAA
Found at i:104377792 original size:21 final size:21
Alignment explanation
Indices: 104377734--104377859 Score: 60
Period size: 21 Copynumber: 5.5 Consensus size: 21
104377724 TAAAATAATG
* *
104377734 TATAATATA-AATAAATAATTA
1 TATAATATATAATAATTAA-AA
*
104377755 TATAAGATAT-ATAAATTAAAA
1 TATAATATATAAT-AATTAAAA
104377776 TATAATATATAATAATTTACAAA
1 TATAATATATAATAA-TTA-AAA
* *
104377799 TTTTGAAAATATAAATAATATAATAA
1 -TAT-AATATAT-AATAAT-TAA-AA
104377825 -ATAATATATATAATAAGTTAAAAAA
1 TAT-A-ATATATAATAA-TT--AAAA
104377850 TATAATATAT
1 TATAATATAT
104377860 GCAAAAAATA
Statistics
Matches: 81, Mismatches: 9, Indels: 27
0.69 0.08 0.23
Matches are distributed among these distances:
21 22 0.27
22 10 0.12
23 3 0.04
24 16 0.20
25 17 0.21
26 13 0.16
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.37
Consensus pattern (21 bp):
TATAATATATAATAATTAAAA
Found at i:104377826 original size:12 final size:13
Alignment explanation
Indices: 104377807--104377837 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
104377797 AATTTTGAAA
104377807 ATATAAATAATAT
1 ATATAAATAATAT
104377820 A-ATAAATAATAT
1 ATATAAATAATAT
104377832 ATATAA
1 ATATAA
104377838 TAAGTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
ATATAAATAATAT
Found at i:104377884 original size:19 final size:19
Alignment explanation
Indices: 104377804--104377884 Score: 76
Period size: 21 Copynumber: 4.1 Consensus size: 19
104377794 ACAAATTTTG
104377804 AAAATATAAATAATATAATAA
1 AAAATAT-AATAATAT-ATAA
*
104377825 ATAATATATATAATA-AGTTAA
1 AAAATATA-ATAATATA--TAA
**
104377846 AAAATATAAT-ATATGCAA
1 AAAATATAATAATATATAA
104377864 AAAATATAATAATATATAA
1 AAAATATAATAATATATAA
104377883 AA
1 AA
104377885 GAGATGTAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
18 12 0.24
19 12 0.24
20 3 0.06
21 22 0.45
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.31
Consensus pattern (19 bp):
AAAATATAATAATATATAA
Found at i:104377969 original size:18 final size:19
Alignment explanation
Indices: 104377927--104377969 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
104377917 CATAATAAGT
*
104377927 AATAATAATATATAATTAA
1 AATAATAATATATAATCAA
* *
104377946 AGTAATACT-TATAATCAA
1 AATAATAATATATAATCAA
104377964 AATAAT
1 AATAAT
104377970 TTTATAATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (19 bp):
AATAATAATATATAATCAA
Found at i:104385568 original size:18 final size:18
Alignment explanation
Indices: 104385532--104385694 Score: 170
Period size: 18 Copynumber: 8.9 Consensus size: 18
104385522 AATCATATCT
*
104385532 TCTAAGATTGTATATCATA
1 TCTAAGATTGCA-ATCATA
104385551 TCTAAGATTGCAATCATA
1 TCTAAGATTGCAATCATA
*
104385569 TCTAAGATTG-TATCATA
1 TCTAAGATTGCAATCATA
*
104385586 TCTAAGATTGTAATCATA
1 TCTAAGATTGCAATCATA
*
104385604 TCTAAGATTG-TATCATA
1 TCTAAGATTGCAATCATA
* *
104385621 TCTACGATTGCAATAATA
1 TCTAAGATTGCAATCATA
* * *
104385639 TCAAACATAG-ATATTCATA
1 TCTAAGATTGCA-A-TCATA
*
104385658 TCTAAGATTGCATATCACA
1 TCTAAGATTGCA-ATCATA
104385677 TCTAAGATTGCATATCAT
1 TCTAAGATTGCA-ATCAT
104385695 TGAAGATTAT
Statistics
Matches: 122, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
17 32 0.26
18 44 0.36
19 43 0.35
20 3 0.02
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (18 bp):
TCTAAGATTGCAATCATA
Found at i:104385590 original size:35 final size:36
Alignment explanation
Indices: 104385532--104385694 Score: 213
Period size: 35 Copynumber: 4.5 Consensus size: 36
104385522 AATCATATCT
104385532 TCTAAGATTGTATATCATATCTAAGATTGCAATCATA
1 TCTAAGATTG-ATATCATATCTAAGATTGCAATCATA
*
104385569 TCTAAGATTG-TATCATATCTAAGATTGTAATCATA
1 TCTAAGATTGATATCATATCTAAGATTGCAATCATA
* *
104385604 TCTAAGATTG-TATCATATCTACGATTGCAATAATA
1 TCTAAGATTGATATCATATCTAAGATTGCAATCATA
* * * *
104385639 TCAAACATAGATATTCATATCTAAGATTGCATATCACA
1 TCTAAGATTGATA-TCATATCTAAGATTGCA-ATCATA
104385677 TCTAAGATTGCATATCAT
1 TCTAAGATTG-ATATCAT
104385695 TGAAGATTAT
Statistics
Matches: 109, Mismatches: 13, Indels: 7
0.84 0.10 0.05
Matches are distributed among these distances:
35 63 0.58
36 2 0.02
37 26 0.24
38 15 0.14
39 3 0.03
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (36 bp):
TCTAAGATTGATATCATATCTAAGATTGCAATCATA
Found at i:104386200 original size:42 final size:42
Alignment explanation
Indices: 104386095--104386203 Score: 137
Period size: 42 Copynumber: 2.6 Consensus size: 42
104386085 ACGAAAATGA
* * *
104386095 AAGAAGGGAGCAGCAAAAGGTCCTTAGAGGTACTTGCAGGTG
1 AAGAAGGGAGCAGCACAGGGTCCTTAGAGATACTTGCAGGTG
* * * *
104386137 AAGAAGGGAACAACACAGGGTCTTTAGAGATCCTTGCAGGTG
1 AAGAAGGGAGCAGCACAGGGTCCTTAGAGATACTTGCAGGTG
* *
104386179 AAGAAGGGAGCAGTACGGGGTCCTT
1 AAGAAGGGAGCAGCACAGGGTCCTT
104386204 TTCAAGTAAA
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.32, C:0.16, G:0.35, T:0.17
Consensus pattern (42 bp):
AAGAAGGGAGCAGCACAGGGTCCTTAGAGATACTTGCAGGTG
Found at i:104386865 original size:21 final size:21
Alignment explanation
Indices: 104386841--104386881 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
104386831 ATGGTTAGTC
104386841 AAGTGGTTAGTATTTGTTATT
1 AAGTGGTTAGTATTTGTTATT
*
104386862 AAGTGGTTAGTGTTTGTTAT
1 AAGTGGTTAGTATTTGTTAT
104386882 CACTCACTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.22, C:0.00, G:0.27, T:0.51
Consensus pattern (21 bp):
AAGTGGTTAGTATTTGTTATT
Found at i:104387084 original size:42 final size:42
Alignment explanation
Indices: 104387020--104387119 Score: 137
Period size: 42 Copynumber: 2.4 Consensus size: 42
104387010 ACAAAAAGGA
* * * *
104387020 AAGAAGGGAGCAGCATAGGGTCCTTAGAGATACTTGTAGGTG
1 AAGAAGGGAACAGCACAAGGTCCTTAGAGATACTTGCAGGTG
*
104387062 AAGAAGGGAATAGCACAAGGTCCTTAGAGATACTTGCAGGTG
1 AAGAAGGGAACAGCACAAGGTCCTTAGAGATACTTGCAGGTG
* *
104387104 AAAAAGGGAGCAGCAC
1 AAGAAGGGAACAGCAC
104387120 GGGGTTCTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.36, C:0.14, G:0.33, T:0.17
Consensus pattern (42 bp):
AAGAAGGGAACAGCACAAGGTCCTTAGAGATACTTGCAGGTG
Found at i:104389512 original size:19 final size:19
Alignment explanation
Indices: 104389488--104389527 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
104389478 TATACCCTCT
104389488 TTACTAATAGTTTTTTTAA
1 TTACTAATAGTTTTTTTAA
104389507 TTACTAATAGTTTTTTTAA
1 TTACTAATAGTTTTTTTAA
104389526 TT
1 TT
104389528 TTAAAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.60
Consensus pattern (19 bp):
TTACTAATAGTTTTTTTAA
Found at i:104393056 original size:21 final size:21
Alignment explanation
Indices: 104393032--104393078 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
104393022 CATTTGTAAA
*
104393032 ATTTTATTACTTTATTTATTT
1 ATTTTAGTACTTTATTTATTT
104393053 ATTTTAGTACTTTATTTATTT
1 ATTTTAGTACTTTATTTATTT
*
104393074 TTTTT
1 ATTTT
104393079 CATTTTTAGT
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:0.21, C:0.04, G:0.02, T:0.72
Consensus pattern (21 bp):
ATTTTAGTACTTTATTTATTT
Found at i:104393248 original size:9 final size:9
Alignment explanation
Indices: 104393236--104393302 Score: 50
Period size: 9 Copynumber: 7.1 Consensus size: 9
104393226 ATAATTAAAA
104393236 AATATTTTT
1 AATATTTTT
104393245 AATATTTTAT
1 AATATTTT-T
104393255 AAT-TTTTT
1 AATATTTTT
104393263 AAATAATTTTT
1 -AAT-ATTTTT
*
104393274 AA-ATTTTAAA
1 AATATTTT--T
104393284 AATATTTTT
1 AATATTTTT
104393293 -ATAATTTTT
1 AAT-ATTTTT
104393302 A
1 A
104393303 TGAAGTTTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 17
0.71 0.03 0.26
Matches are distributed among these distances:
8 8 0.17
9 21 0.45
10 8 0.17
11 10 0.21
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
AATATTTTT
Found at i:104393278 original size:20 final size:21
Alignment explanation
Indices: 104393244--104393302 Score: 77
Period size: 20 Copynumber: 2.9 Consensus size: 21
104393234 AAAATATTTT
*
104393244 TAATATTTTATAATTTTTTAAA
1 TAAT-TTTTATAATTTTTAAAA
*
104393266 TAATTTTTA-AATTTTAAAAA
1 TAATTTTTATAATTTTTAAAA
104393286 T-ATTTTTATAATTTTTA
1 TAATTTTTATAATTTTTA
104393303 TGAAGTTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 7 0.21
20 17 0.52
21 5 0.15
22 4 0.12
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TAATTTTTATAATTTTTAAAA
Found at i:104393296 original size:28 final size:28
Alignment explanation
Indices: 104393239--104393302 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 28
104393229 ATTAAAAAAT
*
104393239 ATTTTTAATATTTTATAATTTTTTAAATA
1 ATTTTTAATATTTTAAAATTTTTT-AATA
104393268 ATTTTTAA-ATTTTAAAAATATTTTT-ATA
1 ATTTTTAATATTTT-AAAAT-TTTTTAATA
104393296 ATTTTTA
1 ATTTTTA
104393303 TGAAGTTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
28 15 0.47
29 12 0.38
30 5 0.16
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (28 bp):
ATTTTTAATATTTTAAAATTTTTTAATA
Found at i:104393324 original size:39 final size:38
Alignment explanation
Indices: 104393245--104393323 Score: 108
Period size: 38 Copynumber: 2.1 Consensus size: 38
104393235 AAATATTTTT
*
104393245 AATATTTTATAATTTTTTAAATAATTTTTAAATTTTAAA
1 AATATTTTATAATTTTTT-AATAAGTTTTAAATTTTAAA
104393284 AATATTTTTATAA-TTTTT-ATGAAGTTTTAAATTTTAAA
1 AATA-TTTTATAATTTTTTAAT-AAGTTTTAAATTTTAAA
104393322 AA
1 AA
104393324 AAATTAATTA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
37 2 0.05
38 18 0.49
39 9 0.24
40 8 0.22
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (38 bp):
AATATTTTATAATTTTTTAATAAGTTTTAAATTTTAAA
Found at i:104394722 original size:26 final size:26
Alignment explanation
Indices: 104394693--104394744 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
104394683 GATCTTTTTC
104394693 CCCTTATTTATTTATTTATTTTCTTT
1 CCCTTATTTATTTATTTATTTTCTTT
104394719 CCCTTATTTATTTATTTATTTTCTTT
1 CCCTTATTTATTTATTTATTTTCTTT
104394745 TGATTATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.69
Consensus pattern (26 bp):
CCCTTATTTATTTATTTATTTTCTTT
Found at i:104394751 original size:26 final size:26
Alignment explanation
Indices: 104394696--104394753 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
104394686 CTTTTTCCCC
*
104394696 TTATTTATTTATTTATTTTCTTTCCC
1 TTATTTATTTATTTATTTTCTTTCCA
**
104394722 TTATTTATTTATTTATTTTCTTTTGA
1 TTATTTATTTATTTATTTTCTTTCCA
104394748 TTATTT
1 TTATTT
104394754 TTATCAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.17, C:0.09, G:0.02, T:0.72
Consensus pattern (26 bp):
TTATTTATTTATTTATTTTCTTTCCA
Found at i:104395868 original size:17 final size:17
Alignment explanation
Indices: 104395848--104395880 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
104395838 ATTAATAATT
*
104395848 ATATTTTAACTAATAAA
1 ATATTTTAAATAATAAA
104395865 ATATTTTAAATAATAA
1 ATATTTTAAATAATAA
104395881 TCACATTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
ATATTTTAAATAATAAA
Found at i:104398205 original size:14 final size:15
Alignment explanation
Indices: 104398186--104398242 Score: 53
Period size: 17 Copynumber: 3.5 Consensus size: 15
104398176 AATCTTTAAG
104398186 GATATG-CAATCTTA
1 GATATGACAATCTTA
104398200 GATATGATACAATCTTA
1 GATATG--ACAATCTTA
104398217 GATATGATATGCAATCTTA
1 GATATG--A--CAATCTTA
104398236 GATATGA
1 GATATGA
104398243 TATGCAATCT
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
14 6 0.16
17 18 0.47
19 14 0.37
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.35
Consensus pattern (15 bp):
GATATGACAATCTTA
Found at i:104398227 original size:36 final size:38
Alignment explanation
Indices: 104398186--104398264 Score: 126
Period size: 36 Copynumber: 2.1 Consensus size: 38
104398176 AATCTTTAAG
104398186 GATATGCAATCTTAGATATGATA-CAATCTT-AGATAT
1 GATATGCAATCTTAGATATGATAGCAATCTTAAGATAT
104398222 GATATGCAATCTTAGATATGATATGCAATCTTGAAGATAT
1 GATATGCAATCTTAGATATGATA-GCAATCTT-AAGATAT
104398262 GAT
1 GAT
104398265 CTTATAATCT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
36 23 0.59
38 7 0.18
40 9 0.23
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.35
Consensus pattern (38 bp):
GATATGCAATCTTAGATATGATAGCAATCTTAAGATAT
Found at i:104398233 original size:19 final size:19
Alignment explanation
Indices: 104398186--104398264 Score: 126
Period size: 19 Copynumber: 4.2 Consensus size: 19
104398176 AATCTTTAAG
104398186 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
104398205 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
104398222 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
104398241 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
104398262 GAT
1 GAT
104398265 CTTATAATCT
Statistics
Matches: 56, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
17 17 0.30
19 30 0.54
21 9 0.16
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:104398677 original size:16 final size:15
Alignment explanation
Indices: 104398649--104398700 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 15
104398639 TCTATGCATG
104398649 TATATAT-ATTATAT
1 TATATATCATTATAT
104398663 TATATATCATGTATAT
1 TATATATCAT-TATAT
104398679 CGTATATCATCTATTATAT
1 --TATAT-ATC-ATTATAT
104398698 TAT
1 TAT
104398701 TTATGTTTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
14 7 0.22
15 2 0.06
16 5 0.16
17 3 0.09
18 5 0.16
19 8 0.25
20 2 0.06
ACGTcount: A:0.37, C:0.08, G:0.04, T:0.52
Consensus pattern (15 bp):
TATATATCATTATAT
Found at i:104399879 original size:23 final size:20
Alignment explanation
Indices: 104399863--104399910 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 20
104399853 TATATATAAA
104399863 TTTTATTATATGTTATATAT
1 TTTTATTATATGTTATATAT
*
104399883 TTTTATTATA--TTATTTA-
1 TTTTATTATATGTTATATAT
104399900 TTTTATTATAT
1 TTTTATTATAT
104399911 TTTTATATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 10 0.38
18 6 0.23
20 10 0.38
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (20 bp):
TTTTATTATATGTTATATAT
Found at i:104399888 original size:20 final size:18
Alignment explanation
Indices: 104399851--104399918 Score: 75
Period size: 18 Copynumber: 3.7 Consensus size: 18
104399841 TTTGTAACAC
* *
104399851 TATATATATAAATTTTAT
1 TATATTTATATATTTTAT
104399869 TATATGTTATATATTTTTAT
1 TATAT-TTATATA-TTTTAT
*
104399889 TATA-TTATTTATTTTAT
1 TATATTTATATATTTTAT
*
104399906 TATATTTTTATAT
1 TATATTTATATAT
104399919 GTAAAATATT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
17 10 0.24
18 17 0.40
19 5 0.12
20 10 0.24
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (18 bp):
TATATTTATATATTTTAT
Found at i:104399917 original size:25 final size:28
Alignment explanation
Indices: 104399865--104399918 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
104399855 TATATAAATT
*
104399865 TTATTATATGTTATATATTTTTATTATA
1 TTATTATATGTTATATATATTTATTATA
*
104399893 TTATT-TATTTTAT-TATATTT-TTATA
1 TTATTATATGTTATATATATTTATTATA
104399918 T
1 T
104399919 GTAAAATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 6 0.25
26 6 0.25
27 7 0.29
28 5 0.21
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.69
Consensus pattern (28 bp):
TTATTATATGTTATATATATTTATTATA
Found at i:104407930 original size:26 final size:26
Alignment explanation
Indices: 104407901--104407956 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
104407891 TGATAAAAAT
104407901 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
104407927 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
104407953 TGAT
1 TGAT
104407957 GGGCATTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.30, C:0.07, G:0.27, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:104417289 original size:17 final size:17
Alignment explanation
Indices: 104417267--104417300 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
104417257 ATATCATATC
104417267 ATATCATATCTAAGATT
1 ATATCATATCTAAGATT
104417284 ATATCATATCTAAGATT
1 ATATCATATCTAAGATT
104417301 GCATATCCTT
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:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (17 bp):
ATATCATATCTAAGATT
Found at i:104419537 original size:46 final size:46
Alignment explanation
Indices: 104419485--104419849 Score: 473
Period size: 46 Copynumber: 8.0 Consensus size: 46
104419475 GCTTTTTGAA
* *
104419485 ATGAAATGTGTAAGACCATGATTGAAAGATACCAGGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
*
104419531 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACAGGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
*
104419577 ATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* *
104419623 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAACAGGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* *
104419669 ATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAATATGA-
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
** * ** ** * *
104419714 CGGGAATGAATAAGACCATGGTTGAAAGATACCATGGCAATGTAAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* * * *
104419760 ATGAAATGAGCAAGACCATGGTTGAAAGATACCATGGCAACCTGAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* * * * *
104419806 A-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 ATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATG
104419850 TCAAAGATAA
Statistics
Matches: 283, Mismatches: 34, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
45 38 0.13
46 245 0.87
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.21
Consensus pattern (46 bp):
ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
Found at i:104419797 original size:183 final size:184
Alignment explanation
Indices: 104419488--104419834 Score: 493
Period size: 183 Copynumber: 1.9 Consensus size: 184
104419478 TTTTGAAATG
* **
104419488 AAATGTGTAAGACCATGATTGAAAGATACCAGGGCAACATGATATGAAATGTGTAAGACCATGGT
1 AAATGTGTAAGACCATGATTGAAAGATACCAGGGCAACATGATAGGAAATGAATAAGACCATGGT
* * * *
104419553 TGAAAGATACCATGGCAACAGGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
66 TGAAAGATACCATGGCAACAGAACATAAAATGAGCAAGACCATGGTTGAAAGATACCATGGCAAC
* * *
104419618 ATGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGACAACAGGATATA
131 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGATACCATGACAACAGGATATA
* * * * *
104419672 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAATATGA-CGGGAATGAATAAGACCATGGT
1 AAATGTGTAAGACCATGATTGAAAGATACCAGGGCAACATGATAGGAAATGAATAAGACCATGGT
* *
104419736 TGAAAGATACCATGGCAA-TGTAACATGAAATGAGCAAGACCATGGTTGAAAGATACCATGGCAA
66 TGAAAGATACCATGGCAACAG-AACATAAAATGAGCAAGACCATGGTTGAAAGATACCATGGCAA
*
104419800 CCTGACAGAAAATGAGTAAGACCATAGTTGAAAGA
130 CATGACAGAAAATGAGTAAGACCATAGTTGAAAGA
104419835 CACTATGGCA
Statistics
Matches: 143, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
182 2 0.01
183 102 0.71
184 39 0.27
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.21
Consensus pattern (184 bp):
AAATGTGTAAGACCATGATTGAAAGATACCAGGGCAACATGATAGGAAATGAATAAGACCATGGT
TGAAAGATACCATGGCAACAGAACATAAAATGAGCAAGACCATGGTTGAAAGATACCATGGCAAC
ATGACAGAAAATGAGTAAGACCATAGTTGAAAGATACCATGACAACAGGATATA
Found at i:104419863 original size:137 final size:137
Alignment explanation
Indices: 104419485--104419866 Score: 457
Period size: 137 Copynumber: 2.8 Consensus size: 137
104419475 GCTTTTTGAA
* *
104419485 ATGAAATGTGTAAGACCATGATTGAAAGATACCAGGGCAACATGATATG-AAATGTGTAAGACCA
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATA-GAAAATGTGTAAGACCA
* * * **
104419549 TGGTTGAAAGATACCATGGCAACAGGAT-ATAAAATGTGTAAGACCATGGTTGAAAGATACCATG
65 TGGTTGAAAGATACCATGGCATCATG-TCA-AAGATGAATAAGACCATGGTTGAAAGATACCATG
* *
104419613 GCAACATGAT
128 GCAACATAAC
* * *
104419623 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAACAGGATATAAAATGTGTAAGACCAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATAGAAAATGTGTAAGACCAT
* **
104419688 GGTTGAAAGATACCATGGCAAT-ATGAC-GGGAATGAATAAGACCATGGTTGAAAGATACCATGG
66 GGTTGAAAGATACCATGGC-ATCATGTCAAAG-ATGAATAAGACCATGGTTGAAAGATACCATGG
**
104419751 CAATGTAAC
129 CAACATAAC
* * * * *
104419760 ATGAAATGAGCAAGACCATGGTTGAAAGATACCATGGCAACCTGACAGAAAATGAGTAAGACCAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATAGAAAATGTGTAAGACCAT
* * * *
104419825 AGTTGAAAGACACTATGGCATCATGTCAAAGATAAATAAGAC
66 GGTTGAAAGATACCATGGCATCATGTCAAAGATGAATAAGAC
104419867 TGTGGATGGG
Statistics
Matches: 206, Mismatches: 32, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
136 2 0.01
137 122 0.59
138 81 0.39
139 1 0.00
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.21
Consensus pattern (137 bp):
ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATAGAAAATGTGTAAGACCAT
GGTTGAAAGATACCATGGCATCATGTCAAAGATGAATAAGACCATGGTTGAAAGATACCATGGCA
ACATAAC
Found at i:104425175 original size:26 final size:26
Alignment explanation
Indices: 104425146--104425253 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
104425136 TGGTACAAAT
104425146 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
104425172 TGATAACGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
104425198 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
104425224 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
104425250 TGAT
1 TGAT
104425254 TGGAATTTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.31, C:0.06, G:0.27, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:104428174 original size:16 final size:17
Alignment explanation
Indices: 104428153--104428185 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
104428143 ATGATGGAGC
104428153 ATGAAAT-ATTGATATA
1 ATGAAATGATTGATATA
104428169 ATGAAATGATTGATATA
1 ATGAAATGATTGATATA
104428186 TACTTATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
ATGAAATGATTGATATA
Found at i:104430214 original size:20 final size:19
Alignment explanation
Indices: 104430163--104430214 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 19
104430153 AAAGCGCACA
* *
104430163 AAATTATAAAAATTAGTAT
1 AAATTATAAAAAATAATAT
*
104430182 AAATGATACAAAAATAATAT
1 AAATTATA-AAAAATAATAT
*
104430202 AAATTATTAAAAA
1 AAATTATAAAAAA
104430215 CTTGCAAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (19 bp):
AAATTATAAAAAATAATAT
Found at i:104432549 original size:27 final size:27
Alignment explanation
Indices: 104432394--104432550 Score: 85
Period size: 28 Copynumber: 5.9 Consensus size: 27
104432384 AGGAGGTTAC
104432394 AAATTAAGATAATTAAGAA-TTTAAATTT
1 AAATTAAGATAATTAA-AATTTTAAA-TT
* * * * * *
104432422 AAATTAGGGTATTTAGAGTTTTAATTT
1 AAATTAAGATAATTAAAATTTTAAATT
* *
104432449 AGA-TAAGATAATTAGGAA-TTT-AATT
1 AAATTAAGATAATTA-AAATTTTAAATT
* * *
104432474 -AA-TAGGTTAAATAAAATTTTAGAATT
1 AAATTAAGATAATTAAAATTTTA-AATT
* * * *
104432500 TAGTTAAGATAATTAAGAGTTTAAATT
1 AAATTAAGATAATTAAAATTTTAAATT
104432527 AAATT-AGTATAATTAAAATTTTAA
1 AAATTAAG-ATAATTAAAATTTTAA
104432551 TTTATTTAAA
Statistics
Matches: 94, Mismatches: 27, Indels: 17
0.68 0.20 0.12
Matches are distributed among these distances:
23 2 0.02
24 12 0.13
25 3 0.03
26 17 0.18
27 29 0.31
28 31 0.33
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (27 bp):
AAATTAAGATAATTAAAATTTTAAATT
Found at i:104434417 original size:53 final size:52
Alignment explanation
Indices: 104434277--104434435 Score: 194
Period size: 52 Copynumber: 3.0 Consensus size: 52
104434267 GACGGAAAAT
* * * **
104434277 ATGTGATATGTGCTTCTGTATAAGACCATAGCAGGGTTATGGCATCGGTAAA
1 ATGTGATATGTGCTTCCGTATAAGACCATAGCTGGGATATGGCATCGGTATG
* * *
104434329 ATGTGAT-TCATGCTCCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATG
1 ATGTGATAT-GTGCTTCCGTATAAGACCATAGCTGGGATATGGCATCGGTATG
* * *
104434381 ATGTGATAATGTGATTCCGTATAAGACCATATCTGGGATATGACATCGGTATG
1 ATGTGAT-ATGTGCTTCCGTATAAGACCATAGCTGGGATATGGCATCGGTATG
104434434 AT
1 AT
104434436 ATGTGATCCG
Statistics
Matches: 91, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
51 1 0.01
52 50 0.55
53 39 0.43
54 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.31
Consensus pattern (52 bp):
ATGTGATATGTGCTTCCGTATAAGACCATAGCTGGGATATGGCATCGGTATG
Found at i:104440538 original size:23 final size:23
Alignment explanation
Indices: 104440512--104440555 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
104440502 ATGCACATCA
104440512 GTTTACAGTTTCGATAATTATCT
1 GTTTACAGTTTCGATAATTATCT
104440535 GTTTACAGTTTCGATAATTAT
1 GTTTACAGTTTCGATAATTAT
104440556 TAGCAGATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.27, C:0.11, G:0.14, T:0.48
Consensus pattern (23 bp):
GTTTACAGTTTCGATAATTATCT
Found at i:104441008 original size:17 final size:17
Alignment explanation
Indices: 104440969--104441032 Score: 53
Period size: 17 Copynumber: 3.8 Consensus size: 17
104440959 ATAGCTTTGG
*
104440969 TCTTTCTCCTTT-TCTT
1 TCTTTTTCCTTTCTCTT
*
104440985 T-TCTTTCCTTTCTCTT
1 TCTTTTTCCTTTCTCTT
* *
104441001 TCTTTTTCCCTTCTGTT
1 TCTTTTTCCTTTCTCTT
104441018 TCGTTTGTT-CTTTCT
1 TC-TTT-TTCCTTTCT
104441033 TTCTTTTCTA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
15 8 0.21
16 6 0.16
17 14 0.37
18 8 0.21
19 2 0.05
ACGTcount: A:0.00, C:0.28, G:0.05, T:0.67
Consensus pattern (17 bp):
TCTTTTTCCTTTCTCTT
Found at i:104443371 original size:27 final size:26
Alignment explanation
Indices: 104443329--104443434 Score: 88
Period size: 27 Copynumber: 4.0 Consensus size: 26
104443319 AGGAGGTTAC
104443329 AAATTAAGATAATTAAGAATTTAAATT
1 AAATTAAGATAATTAA-AATTTAAATT
* * * *
104443356 AAATTAGGATATTTAAAGTTTTAATT
1 AAATTAAGATAATTAAAATTTAAATT
* * *
104443382 -TATATAAGATAATTAGGAGTTTAAATT
1 AAAT-TAAGATAATTA-AAATTTAAATT
* * *
104443409 AAATTAATATATTTAAAATTTTAATT
1 AAATTAAGATAATTAAAATTTAAATT
104443435 TATTTAAAAA
Statistics
Matches: 61, Mismatches: 15, Indels: 7
0.73 0.18 0.08
Matches are distributed among these distances:
25 2 0.03
26 25 0.41
27 32 0.52
28 2 0.03
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.43
Consensus pattern (26 bp):
AAATTAAGATAATTAAAATTTAAATT
Found at i:104443413 original size:53 final size:53
Alignment explanation
Indices: 104443333--104443437 Score: 165
Period size: 53 Copynumber: 2.0 Consensus size: 53
104443323 GGTTACAAAT
* *
104443333 TAAGATAATTAAGAATTTAAATTAAATTAGGATATTTAAAGTTTTAATTTATA
1 TAAGATAATTAAGAATTTAAATTAAATTAAGATATTTAAAATTTTAATTTATA
* * *
104443386 TAAGATAATTAGGAGTTTAAATTAAATTAATATATTTAAAATTTTAATTTAT
1 TAAGATAATTAAGAATTTAAATTAAATTAAGATATTTAAAATTTTAATTTAT
104443438 TTAAAAAGAG
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 47 1.00
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.45
Consensus pattern (53 bp):
TAAGATAATTAAGAATTTAAATTAAATTAAGATATTTAAAATTTTAATTTATA
Found at i:104444539 original size:168 final size:167
Alignment explanation
Indices: 104444256--104444763 Score: 693
Period size: 168 Copynumber: 3.0 Consensus size: 167
104444246 CTTTGGGAAC
* * * *
104444256 TCATGTTTATGTTCCTTATCCTCATCTTGTTTTTCCTTGCACTCGGGTATTTTTGGATATTCGGC
1 TCATCTTTATGTTCCTTATCCTCATCTTG-TTTTCCTTGTACTCGGGTATTTTCGGATATTCGAC
*
104444321 ATT-ATGTTTCTCATGCTCTTTAGGCTTTTCCCATTTGGGGAAATCGGGTTTTTCTTTCTAGTAC
65 -TTCGTGTTTCTCATGCTCTTTAGGCTTTTCCCATTTGGGGAAATCGGGTTTTTCTTTCTAGTAC
*
104444385 TCTTCGTGCTCTTTCGATTCGTGTGACTCGTGGCACTCT
129 TCTTCGTGCTCTTTCGATTCGTGTGACTCGTGGAACTCT
* * *
104444424 TCATCTTTATGTTCCTTA-CTCTTATCTTGCTTTTCCTTGTACT-GGGTTATTTCCGGATATTCA
1 TCATCTTTATGTTCCTTATC-CTCATCTTG-TTTTCCTTGTACTCGGG-TATTTTCGGATATTCG
* * ** *
104444487 ACTTCGTGTTTCTCGTGCTCTTTAGGCTTTTGCTGTTTGGGGAACTCGGGTTTTTCTTTCTCA-T
63 ACTTCGTGTTTCTCATGCTCTTTAGGCTTTTCCCATTTGGGGAAATCGGGTTTTTCTTTCT-AGT
* * *
104444551 ACTCTTCGTGCTCCTTCGATTCGCGTGATTCGTGGAACTCT
127 ACTCTTCGTGCTCTTTCGATTCGTGTGACTCGTGGAACTCT
* *
104444592 TCATTTTTATGTTCCTTATCCTCATCTTGTTTGTCCTTGTACTCGGGTATTTTCAGATATTCGAC
1 TCATCTTTATGTTCCTTATCCTCATCTTGTTT-TCCTTGTACTCGGGTATTTTCGGATATTCGAC
* * *
104444657 TTCGTGTTTCTCATGCTCTTTAGGCTTTTCCCATTTGGGGAAATCGGGTTTGTCTTTATTGTACT
65 TTCGTGTTTCTCATGCTCTTTAGGCTTTTCCCATTTGGGGAAATCGGGTTTTTCTTTCTAGTACT
* *
104444722 CTTCGTGCT-TCTTCGATTTGTGTGACTCGTGGTACTCT
130 CTTCGTGCTCT-TTCGATTCGTGTGACTCGTGGAACTCT
104444760 TCAT
1 TCAT
104444764 GTTGTTTGTA
Statistics
Matches: 295, Mismatches: 36, Indels: 18
0.85 0.10 0.05
Matches are distributed among these distances:
167 9 0.03
168 281 0.95
169 5 0.02
ACGTcount: A:0.12, C:0.22, G:0.19, T:0.47
Consensus pattern (167 bp):
TCATCTTTATGTTCCTTATCCTCATCTTGTTTTCCTTGTACTCGGGTATTTTCGGATATTCGACT
TCGTGTTTCTCATGCTCTTTAGGCTTTTCCCATTTGGGGAAATCGGGTTTTTCTTTCTAGTACTC
TTCGTGCTCTTTCGATTCGTGTGACTCGTGGAACTCT
Found at i:104446475 original size:7 final size:7
Alignment explanation
Indices: 104446465--104446500 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
104446455 TTTTTTATAC
104446465 TAATAAA
1 TAATAAA
104446472 TAATAAA
1 TAATAAA
104446479 TAATGAAA
1 TAAT-AAA
*
104446487 TAATATA
1 TAATAAA
104446494 TAATAAA
1 TAATAAA
104446501 AGGAAGATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
7 19 0.73
8 7 0.27
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (7 bp):
TAATAAA
Found at i:104446489 original size:15 final size:14
Alignment explanation
Indices: 104446465--104446500 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
104446455 TTTTTTATAC
104446465 TAATAAATAATAAA
1 TAATAAATAATAAA
*
104446479 TAATGAAATAATATA
1 TAAT-AAATAATAAA
104446494 TAATAAA
1 TAATAAA
104446501 AGGAAGATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (14 bp):
TAATAAATAATAAA
Found at i:104446533 original size:10 final size:10
Alignment explanation
Indices: 104446518--104446590 Score: 62
Period size: 10 Copynumber: 7.2 Consensus size: 10
104446508 TAATATAGGG
104446518 AATAATATAT
1 AATAATATAT
104446528 AATAATATAT
1 AATAATATAT
* *
104446538 GAT-ATGTAAT
1 AATAATAT-AT
104446548 AA-AATATAT
1 AATAATATAT
*
104446557 AAATAAAATAT
1 -AATAATATAT
104446568 AATGAA-ATAT
1 AAT-AATATAT
104446578 AATAATATGAT
1 AATAATAT-AT
104446589 AA
1 AA
104446591 CTATCATATA
Statistics
Matches: 51, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
9 7 0.14
10 32 0.63
11 12 0.24
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.34
Consensus pattern (10 bp):
AATAATATAT
Found at i:104448556 original size:44 final size:44
Alignment explanation
Indices: 104448493--104449393 Score: 1138
Period size: 44 Copynumber: 20.5 Consensus size: 44
104448483 TGCTTTCTGT
* * *
104448493 AGAGACGCCACATCTGCTATCCTT-GATCTGCTCTTTGTCAATAC
1 AGAGACGCCAAATCTGCTAT-CTTCGATCTGCTCTCTGACAATAC
* * *
104448537 AGAGATGCCAAACCTGCTATC-TCTGATCTGCTCT-TTATCAATAC
1 AGAGACGCCAAATCTGCTATCTTC-GATCTGCTCTCTGA-CAATAC
* * * * *
104448581 AGAGACGCCAAATCTGTTACCTTTGATCTGCTCTCTGTCAATAT
1 AGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATAC
* * *
104448625 AGAGATGACAAATCTGCTATCTTCG-TCCTGCTCTCTGTCAATAC
1 AGAGACGCCAAATCTGCTATCTTCGAT-CTGCTCTCTGACAATAC
* * *
104448669 AGAGACACCAAATCTACTATCTTCGATCTGCTCTCTAACAATAC
1 AGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATAC
* * * * *
104448713 AGAAACGCAAAATCT-ATCATCTTCAATCTACTCTCTGACAATAC
1 AGAGACGCCAAATCTGCT-ATCTTCGATCTGCTCTCTGACAATAC
* **
104448757 AGAGATGCCAAATCTG-TCATCTTCGATCTGCTCTCTGTTAATAC
1 AGAGACGCCAAATCTGCT-ATCTTCGATCTGCTCTCTGACAATAC
* * *
104448801 AAAGACGCCAAATCTGCTATCTTTGATTTGCTCTCTGACAATAC
1 AGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATAC
* * *
104448845 AGAGACACCAAATTTGCTATCTTCGATCTGCTTTCTGACAATAC
1 AGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATAC
104448889 AGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATAC
1 AGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATAC
*
104448933 AGAGACGCCAAATATG-TCATCTTCGATCTGCTCTCTGACAATAC
1 AGAGACGCCAAATCTGCT-ATCTTCGATCTGCTCTCTGACAATAC
*
104448977 AGAGACGCCAAATATG-TCATCTTCGATCTGCTCTCTGACAATAC
1 AGAGACGCCAAATCTGCT-ATCTTCGATCTGCTCTCTGACAATAC
* * *
104449021 AGAGACGCCAAATATG-TCATCTTCGATATGCTCTCTGTCAATAC
1 AGAGACGCCAAATCTGCT-ATCTTCGATCTGCTCTCTGACAATAC
* * ** *
104449065 AGAGACGCCAAATCTACTATCTTTGATCTATTCTCTGACAATAT
1 AGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATAC
*
104449109 AGAGACACCAAATCTGCTATCTTCGATCTGCTCTCTGACAATAC
1 AGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATAC
*
104449153 AGAGACGCCAAATCTGCTATCTTTGATCTGCTCTCTGACAATAC
1 AGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATAC
* *
104449197 AGAGAAGCCAAATCTG-TCATCTTCGATCTGCTCTCTGTCAATAC
1 AGAGACGCCAAATCTGCT-ATCTTCGATCTGCTCTCTGACAATAC
* * *
104449241 AGAGACGCCAAATCTGCTATCTTTGATATGTTCTCTGACAATAC
1 AGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATAC
* *
104449285 AGAGACGCCAAATCTACTATCTTTGATCTGCTCTCTGACAATAC
1 AGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATAC
* * * * *
104449329 AAAGACGCCAAATCTACTATCTTCAATTTGCTCTCTGATAATAC
1 AGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATAC
*
104449373 AGAGACGCCAAATCAGCTATC
1 AGAGACGCCAAATCTGCTATC
104449394 GGTGATCTAC
Statistics
Matches: 751, Mismatches: 92, Indels: 28
0.86 0.11 0.03
Matches are distributed among these distances:
42 1 0.00
43 6 0.01
44 738 0.98
45 6 0.01
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (44 bp):
AGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATAC
Found at i:104454558 original size:22 final size:23
Alignment explanation
Indices: 104454532--104454575 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 23
104454522 CCTGATCAGA
104454532 ATACGACACAT-AAGTGCCTGAC
1 ATACGACACATAAAGTGCCTGAC
104454554 ATACGACACATAAAGTGCCTGA
1 ATACGACACATAAAGTGCCTGA
104454576 TCAGTAAAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.18
Consensus pattern (23 bp):
ATACGACACATAAAGTGCCTGAC
Found at i:104454805 original size:23 final size:24
Alignment explanation
Indices: 104454766--104454860 Score: 75
Period size: 28 Copynumber: 3.6 Consensus size: 24
104454756 AAATGTCCAA
* *
104454766 CCAAAACACA-CTGGTATAATCCT
1 CCAAAACACACCAGATATAATCCT
104454789 CCAAAACACACCAGTATCATATAATCCT
1 CCAAAACACACCAG----ATATAATCCT
*
104454817 CCCAAACACACCAGAATAATATAATCCAT
1 CCAAAACACACCAG----ATATAATCC-T
104454846 CCAAAACACACCAGA
1 CCAAAACACACCAGA
104454861 ATAGCACAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
23 10 0.17
24 2 0.03
25 1 0.02
28 33 0.55
29 14 0.23
ACGTcount: A:0.45, C:0.33, G:0.05, T:0.17
Consensus pattern (24 bp):
CCAAAACACACCAGATATAATCCT
Found at i:104454862 original size:29 final size:28
Alignment explanation
Indices: 104454780--104454863 Score: 132
Period size: 28 Copynumber: 3.0 Consensus size: 28
104454770 AACACACTGG
* *
104454780 TATAATCCTCCAAAACACACCAGTATCA
1 TATAATCCTCCAAAACACACCAGAATAA
*
104454808 TATAATCCTCCCAAACACACCAGAATAA
1 TATAATCCTCCAAAACACACCAGAATAA
104454836 TATAATCCATCCAAAACACACCAGAATA
1 TATAATCC-TCCAAAACACACCAGAATA
104454864 GCACAAAGTG
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 33 0.65
29 18 0.35
ACGTcount: A:0.46, C:0.31, G:0.04, T:0.19
Consensus pattern (28 bp):
TATAATCCTCCAAAACACACCAGAATAA
Found at i:104460441 original size:30 final size:30
Alignment explanation
Indices: 104460405--104460464 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
104460395 TATAAAGGTG
104460405 GTTTTATCCATGTCCCCAGGATGCATCTTT
1 GTTTTATCCATGTCCCCAGGATGCATCTTT
*
104460435 GTTTTATCCATGTCCTCAGGATGCATCTTT
1 GTTTTATCCATGTCCCCAGGATGCATCTTT
104460465 ATTTGATTGT
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:0.17, C:0.25, G:0.17, T:0.42
Consensus pattern (30 bp):
GTTTTATCCATGTCCCCAGGATGCATCTTT
Found at i:104464673 original size:12 final size:12
Alignment explanation
Indices: 104464656--104464680 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
104464646 GATTTTTGCT
104464656 AATTGCTCCTGC
1 AATTGCTCCTGC
104464668 AATTGCTCCTGC
1 AATTGCTCCTGC
104464680 A
1 A
104464681 TTTTTTCTGA
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:0.20, C:0.32, G:0.16, T:0.32
Consensus pattern (12 bp):
AATTGCTCCTGC
Found at i:104468476 original size:19 final size:19
Alignment explanation
Indices: 104468452--104468574 Score: 200
Period size: 19 Copynumber: 6.7 Consensus size: 19
104468442 AATCTTTAAG
104468452 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
104468471 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
104468490 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
104468507 GATATACAATCTTAGATAT
1 GATATGCAATCTTAGATAT
104468526 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
104468543 GATATACAATCTTAGATAT
1 GATATGCAATCTTAGATAT
104468562 GATATGCAATCTT
1 GATATGCAATCTT
104468575 GAAGATAAGA
Statistics
Matches: 99, Mismatches: 1, Indels: 8
0.92 0.01 0.07
Matches are distributed among these distances:
17 34 0.34
19 65 0.66
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:104468517 original size:55 final size:54
Alignment explanation
Indices: 104468452--104468574 Score: 203
Period size: 55 Copynumber: 2.2 Consensus size: 54
104468442 AATCTTTAAG
104468452 GATATGCAATCTTAGATATGATATGCAATCTTAGATATG-ATACAATCTTAGATAT
1 GATATGCAATCTTAGATATGATA--CAATCTTAGATATGAATACAATCTTAGATAT
*
104468507 GATATACAATCTTAGATATGATACAATCTTAGATATGATATACAATCTTAGATAT
1 GATATGCAATCTTAGATATGATACAATCTTAGATATGA-ATACAATCTTAGATAT
104468562 GATATGCAATCTT
1 GATATGCAATCTT
104468575 GAAGATAAGA
Statistics
Matches: 64, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
53 14 0.22
55 50 0.78
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (54 bp):
GATATGCAATCTTAGATATGATACAATCTTAGATATGAATACAATCTTAGATAT
Found at i:104468564 original size:36 final size:36
Alignment explanation
Indices: 104468458--104468574 Score: 207
Period size: 36 Copynumber: 3.2 Consensus size: 36
104468448 TAAGGATATG
*
104468458 CAATCTTAGATATGATATGCAATCTTAGATATGATA
1 CAATCTTAGATATGATATACAATCTTAGATATGATA
104468494 CAATCTTAGATATGATATACAATCTTAGATATGATA
1 CAATCTTAGATATGATATACAATCTTAGATATGATA
104468530 CAATCTTAGATATGATATACAATCTTAGATATGATA
1 CAATCTTAGATATGATATACAATCTTAGATATGATA
104468566 TGCAATCTT
1 --CAATCTT
104468575 GAAGATAAGA
Statistics
Matches: 78, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
36 71 0.91
38 7 0.09
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (36 bp):
CAATCTTAGATATGATATACAATCTTAGATATGATA
Found at i:104471701 original size:13 final size:13
Alignment explanation
Indices: 104471683--104471712 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
104471673 ATATATGGTT
104471683 AATAGAAATAAAA
1 AATAGAAATAAAA
104471696 AATAGAAATAAAA
1 AATAGAAATAAAA
104471709 AATA
1 AATA
104471713 TACACGATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.17
Consensus pattern (13 bp):
AATAGAAATAAAA
Found at i:104472374 original size:25 final size:24
Alignment explanation
Indices: 104472338--104472400 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 24
104472328 TATATACGCA
*
104472338 AATATATT-AAAAA-TATATACAT
1 AATATATTAAAAAAGAATATACAT
104472360 ATATCATATTAAAAAAAGAATATACAT
1 A-AT-ATATT-AAAAAAGAATATACAT
*
104472387 AATATATAAAAAAA
1 AATATATTAAAAAA
104472401 CATGATATGG
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
22 1 0.03
23 2 0.06
24 11 0.32
25 4 0.12
26 7 0.21
27 9 0.26
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (24 bp):
AATATATTAAAAAAGAATATACAT
Found at i:104472384 original size:27 final size:24
Alignment explanation
Indices: 104472352--104472400 Score: 71
Period size: 27 Copynumber: 1.9 Consensus size: 24
104472342 TATTAAAAAT
104472352 ATATACATATATCATATTAAAAAAAGA
1 ATATACATA-AT-ATA-TAAAAAAAGA
104472379 ATATACATAATATATAAAAAAA
1 ATATACATAATATATAAAAAAA
104472401 CATGATATGG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 8 0.36
25 3 0.14
26 2 0.09
27 9 0.41
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.29
Consensus pattern (24 bp):
ATATACATAATATATAAAAAAAGA
Found at i:104472700 original size:26 final size:28
Alignment explanation
Indices: 104472648--104472700 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 28
104472638 TATACGTATA
***
104472648 ATATAGTTATATAAAAAATACGTACAAC
1 ATATAGTTATATAAAAAATAAACACAAC
104472676 ATATAG-TAT-TAAAAAATAAACACAA
1 ATATAGTTATATAAAAAATAAACACAA
104472701 TATAGATGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 13 0.59
27 3 0.14
28 6 0.27
ACGTcount: A:0.58, C:0.09, G:0.06, T:0.26
Consensus pattern (28 bp):
ATATAGTTATATAAAAAATAAACACAAC
Found at i:104472839 original size:36 final size:35
Alignment explanation
Indices: 104472758--104472839 Score: 94
Period size: 38 Copynumber: 2.3 Consensus size: 35
104472748 GCATGAGATA
*
104472758 ATATA-AAAAATATAATATTCAAAATATATACATG
1 ATATATAAAAATACAATATTCAAAATATATACATG
* * *
104472792 ATATATGTAAAAGTACAATATTACAAGATATATACGTG
1 ATATA--TAAAAATACAATATT-CAAAATATATACATG
104472830 ATATATAAAA
1 ATATATAAAA
104472840 TGTATACATG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
34 5 0.12
36 5 0.12
37 12 0.30
38 18 0.45
ACGTcount: A:0.55, C:0.06, G:0.07, T:0.32
Consensus pattern (35 bp):
ATATATAAAAATACAATATTCAAAATATATACATG
Found at i:104472865 original size:20 final size:20
Alignment explanation
Indices: 104472778--104472865 Score: 62
Period size: 20 Copynumber: 4.5 Consensus size: 20
104472768 TATAATATTC
104472778 AAAATATATACATGATATAT
1 AAAATATATACATGATATAT
* *
104472798 GTAAA-A-GTACA--ATAT-T
1 -AAAATATATACATGATATAT
*
104472814 ACAAGATATATACGTGATATAT
1 A-AA-ATATATACATGATATAT
*
104472836 AAAATGTATACATGATATAT
1 AAAATATATACATGATATAT
104472856 AGAAA-ATATA
1 A-AAATATATA
104472866 ATATTTAAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 17
0.67 0.11 0.22
Matches are distributed among these distances:
16 3 0.06
17 5 0.10
18 1 0.02
19 7 0.14
20 21 0.41
21 12 0.24
22 2 0.04
ACGTcount: A:0.52, C:0.06, G:0.10, T:0.32
Consensus pattern (20 bp):
AAAATATATACATGATATAT
Found at i:104472894 original size:58 final size:56
Alignment explanation
Indices: 104472769--104472895 Score: 132
Period size: 58 Copynumber: 2.2 Consensus size: 56
104472759 TATAAAAAAT
*
104472769 ATAATATTCAAAATATATACATGATATATGTAAAAGTACAATATTACAAGATATATAC
1 ATAATA-T-AAAATATATACATGATATATGTAAAAGTACAATATTAAAAGATATATAC
* * *
104472827 GTGATATATAAAATGTATACATGATATATAG-AAAA-TATAATATTTAAAAGAATAATATAC
1 AT-A-ATATAAAATATATACATGATATAT-GTAAAAGTACAATA-TTAAAAG-AT-ATATAC
104472887 ATAATATAA
1 ATAATATAA
104472896 GAGTATTTAA
Statistics
Matches: 58, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
57 6 0.10
58 36 0.62
59 6 0.10
60 10 0.17
ACGTcount: A:0.54, C:0.06, G:0.08, T:0.33
Consensus pattern (56 bp):
ATAATATAAAATATATACATGATATATGTAAAAGTACAATATTAAAAGATATATAC
Found at i:104472897 original size:20 final size:19
Alignment explanation
Indices: 104472842--104472897 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 19
104472832 ATATAAAATG
*
104472842 TATACATGATATATAGAAAA
1 TATACATAATATA-AGAAAA
* *
104472862 TATA-ATATTTAAAAGAATAA
1 TATACATA-ATATAAGAA-AA
104472882 TATACATAATATAAGA
1 TATACATAATATAAGA
104472898 GTATTTAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
19 6 0.21
20 19 0.68
21 3 0.11
ACGTcount: A:0.57, C:0.04, G:0.07, T:0.32
Consensus pattern (19 bp):
TATACATAATATAAGAAAA
Found at i:104473262 original size:22 final size:22
Alignment explanation
Indices: 104473234--104473280 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 22
104473224 ATAATATTAG
104473234 AATAATAATGAA-AATATTTAAT
1 AATAATAAT-AACAATATTTAAT
104473256 AATAATAATAACAATATTTAAT
1 AATAATAATAACAATATTTAAT
104473278 AAT
1 AAT
104473281 GAAACAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 2 0.08
22 22 0.92
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (22 bp):
AATAATAATAACAATATTTAAT
Found at i:104475193 original size:26 final size:26
Alignment explanation
Indices: 104475156--104475239 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
104475146 TGATACAAAT
* *
104475156 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
104475182 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
104475208 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
104475234 TGATAA
1 TGATAA
104475240 GAATTTCATG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:104484633 original size:19 final size:17
Alignment explanation
Indices: 104484602--104484680 Score: 54
Period size: 19 Copynumber: 4.4 Consensus size: 17
104484592 CTTCTATTTC
104484602 AAAAAAAAAGGAAAAAG
1 AAAAAAAAAGGAAAAAG
104484619 AAAAGAAAAAGGGAAAAA-
1 AAAA-AAAAA-GGAAAAAG
* *
104484637 AATAAAAATAA-AAATAAAA
1 AA-AAAAA-AAGGAA-AAAG
*
104484656 AAGAGAAAAAATGAAAAAG
1 AA-A-AAAAAAGGAAAAAG
104484675 AAAAAA
1 AAAAAA
104484681 TGGAGAGGCC
Statistics
Matches: 50, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
17 9 0.18
18 14 0.28
19 21 0.42
20 6 0.12
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (17 bp):
AAAAAAAAAGGAAAAAG
Found at i:104484656 original size:29 final size:29
Alignment explanation
Indices: 104484605--104484679 Score: 84
Period size: 28 Copynumber: 2.7 Consensus size: 29
104484595 CTATTTCAAA
* * *
104484605 AAAAAAGGAAAAAG-AAAA-GAAAAAGGG
1 AAAAAATGAAAAAGAAAAATAAAAAAGAG
*
104484632 AAAAAAAT-AAAAATAAAAATAAAAAAGAG
1 -AAAAAATGAAAAAGAAAAATAAAAAAGAG
104484661 AAAAAATGAAAAAGAAAAA
1 AAAAAATGAAAAAGAAAAA
104484680 ATGGAGAGGC
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
27 5 0.13
28 17 0.44
29 17 0.44
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (29 bp):
AAAAAATGAAAAAGAAAAATAAAAAAGAG
Found at i:104484681 original size:14 final size:14
Alignment explanation
Indices: 104484633--104484682 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
104484623 GAAAAAGGGA
104484633 AAAAAAT-AAAAA-
1 AAAAAATGAAAAAG
* *
104484645 TAAAAATAAAAAAGAG
1 AAAAAAT-GAAAA-AG
104484661 AAAAAATGAAAAAG
1 AAAAAATGAAAAAG
104484675 AAAAAATG
1 AAAAAATG
104484683 GAGAGGCCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
12 6 0.19
14 14 0.45
15 5 0.16
16 6 0.19
ACGTcount: A:0.80, C:0.00, G:0.10, T:0.10
Consensus pattern (14 bp):
AAAAAATGAAAAAG
Found at i:104485863 original size:84 final size:84
Alignment explanation
Indices: 104485628--104486323 Score: 1066
Period size: 84 Copynumber: 8.3 Consensus size: 84
104485618 CAAAATTCAG
*
104485628 CGCCTTAATCCCCTAAGCAATAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
104485693 GTGGAGCAGATCGAAGACT
66 GTGGAGCAGATCGAAGACT
*
104485712 CGCCTTAAT-CCCTAAGCAATAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
*
104485776 GTGGAGTAGATCGAAGACT
66 GTGGAGCAGATCGAAGACT
* * *
104485795 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCTCTAAGTAGCA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
*
104485860 GTGGAGTAGATCGAAGACT
66 GTGGAGCAGATCGAAGACT
* *
104485879 CGCCTTAATCCCTTAAGCAGTAGGGTAATAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
* * *
104485944 GCGAAGCAGATCGACGACT
66 GTGGAGCAGATCGAAGACT
*
104485963 CGCCTTAATCCCCTAAGCGGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
104486028 GTGGAGCAGATCGAAGACT
66 GTGGAGCAGATCGAAGACT
* *
104486047 CGCCTTAATCCCCTAAGAAGTAGGGTAACAGG-----TTCGCAGATCTTATCTCCCTAAGCAGTA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
104486107 GTGGAGCAGATCGACGACGACT
66 GTGGAGCAGATCGA--A-GACT
* *
104486129 CACCTTAATCCCCTAAACAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
*
104486194 GTGGAGCAGATCGAAGACC
66 GTGGAGCAGATCGAAGACT
* * *
104486213 CGTCTTAATCCCTTAAGCAGTAGGGTAACAGGTTTAATTTGCAGATCTTA--TCCCTAAGCAGTA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
*
104486276 GCGGAGCAGATCGAAGACGAT
66 GTGGAGCAGATCGAAGAC--T
* *
104486297 GCACCTTAACCCCCTAAGCAGTAGGGT
1 -CGCCTTAATCCCCTAAGCAGTAGGGT
104486324 CCAAGATGAT
Statistics
Matches: 561, Mismatches: 39, Indels: 23
0.90 0.06 0.04
Matches are distributed among these distances:
79 41 0.07
81 1 0.00
82 63 0.11
83 82 0.15
84 310 0.55
85 23 0.04
87 41 0.07
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.25
Consensus pattern (84 bp):
CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
GTGGAGCAGATCGAAGACT
Found at i:104486240 original size:334 final size:331
Alignment explanation
Indices: 104485627--104486323 Score: 1096
Period size: 334 Copynumber: 2.1 Consensus size: 331
104485617 ACAAAATTCA
*
104485627 GCGCCTTAATCCCCTAAGCAATAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGT
1 GCGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGT
*
104485692 AGTGGAGCAGATCGAAGACTCGCCTTAATCCCTAAGCAATAGGGTAACAGGTTAAATTTGCAGAT
66 AGTGGAGCAGATCGAAGACTCGCCTTAATCCCTAAGCAATAGGGTAACAGG----ATTCGCAGAT
* * *
104485757 CTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGACTCGCCTTAATCCCCTAAGCAGTAGGGTA
127 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACTCACCTTAATCCCCTAAACAGTAGGGTA
* * * *
104485822 ACAGGTTAAATTTGCAGATCTTATCTCTCTAAGTAGCAGTGGAGTAGATCGAAGACTCGCCTTAA
192 ACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGCAGTGGAGCAGATCGAAGACCCGCCTTAA
*
104485887 TCCCTTAAGCAGTAGGGTAATAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAGCGAAGCA
257 TCCCTTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTA--TCCCTAAGCAGTAGCGAAGCA
*
104485952 GATCGACGAC-T
320 GATCGAAGACAT
*
104485963 -CGCCTTAATCCCCTAAGCGGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGT
1 GCGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGT
104486027 AGTGGAGCAGATCGAAGACTCGCCTTAATCCCCTAAG-AAGTAGGGTAACAGG-TTCGCAGATCT
66 AGTGGAGCAGATCGAAGACTCGCCTTAAT-CCCTAAGCAA-TAGGGTAACAGGATTCGCAGATCT
104486090 TATCTCCCTAAGCAGTAGTGGAGCAGATCGACGACGACTCACCTTAATCCCCTAAACAGTAGGGT
129 TATCTCCCTAAGCAGTAGTGGAGCAGATCGA--A-GACTCACCTTAATCCCCTAAACAGTAGGGT
* *
104486155 AACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACCCGTCTTA
191 AACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGCAGTGGAGCAGATCGAAGACCCGCCTTA
* *
104486220 ATCCCTTAAGCAGTAGGGTAACAGGTTTAATTTGCAGATCTTATCCCTAAGCAGTAGCGGAGCAG
256 ATCCCTTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCCCTAAGCAGTAGCGAAGCAG
104486285 ATCGAAGACGAT
321 ATCGAAGAC-AT
* *
104486297 GCACCTTAACCCCCTAAGCAGTAGGGT
1 GCGCCTTAATCCCCTAAGCAGTAGGGT
104486324 CCAAGATGAT
Statistics
Matches: 334, Mismatches: 19, Indels: 17
0.90 0.05 0.05
Matches are distributed among these distances:
331 40 0.12
332 29 0.09
333 1 0.00
334 129 0.39
335 116 0.35
336 19 0.06
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (331 bp):
GCGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGT
AGTGGAGCAGATCGAAGACTCGCCTTAATCCCTAAGCAATAGGGTAACAGGATTCGCAGATCTTA
TCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACTCACCTTAATCCCCTAAACAGTAGGGTAACAG
GTTAAATTTGCAGATCTTATCTCCCTAAGCAGCAGTGGAGCAGATCGAAGACCCGCCTTAATCCC
TTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCCCTAAGCAGTAGCGAAGCAGATCGA
AGACAT
Found at i:104486271 original size:41 final size:41
Alignment explanation
Indices: 104486139--104486276 Score: 120
Period size: 41 Copynumber: 3.3 Consensus size: 41
104486129 CACCTTAATC
*
104486139 CCCTAAACAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCT
1 CCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTA--T
* * ** *** *
104486182 CCCTAAGCAGTAGTGG-AGCAGATCGAA-GACCCG-TCTTAAT
1 CCCTAAGCAGTAG-GGTAACAGGTTAAATTTGCAGATCTT-AT
*
104486222 CCCTTAAGCAGTAGGGTAACAGGTTTAATTTGCAGATCTTAT
1 CCC-TAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTAT
104486264 CCCTAAGCAGTAG
1 CCCTAAGCAGTAG
104486277 CGGAGCAGAT
Statistics
Matches: 72, Mismatches: 17, Indels: 14
0.70 0.17 0.14
Matches are distributed among these distances:
40 6 0.08
41 31 0.43
42 10 0.14
43 23 0.32
44 2 0.03
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (41 bp):
CCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTAT
Found at i:104486727 original size:8 final size:8
Alignment explanation
Indices: 104486713--104486769 Score: 55
Period size: 8 Copynumber: 6.9 Consensus size: 8
104486703 ACAAGTTCAA
104486713 AAAAAAAG
1 AAAAAAAG
*
104486721 GAAAAAAG
1 AAAAAAAG
104486729 AAAAGAAA-
1 AAAA-AAAG
104486737 AAGATAAAA-
1 AA-A-AAAAG
104486746 AAGAAAAAG
1 AA-AAAAAG
104486755 AAAAAAAG
1 AAAAAAAG
104486763 AAAAAAA
1 AAAAAAA
104486770 ATAGAGAGGC
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
8 29 0.67
9 13 0.30
10 1 0.02
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (8 bp):
AAAAAAAG
Found at i:104486746 original size:21 final size:21
Alignment explanation
Indices: 104486713--104486768 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
104486703 ACAAGTTCAA
104486713 AAAAAAAGGAAAAAAG-AAAAG
1 AAAAAAA-GAAAAAAGAAAAAG
* *
104486734 AAAAAGATAAAAAAGAAAAAG
1 AAAAAAAGAAAAAAGAAAAAG
104486755 AAAAAAAGAAAAAA
1 AAAAAAAGAAAAAA
104486769 AATAGAGAGG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 7 0.23
21 23 0.77
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (21 bp):
AAAAAAAGAAAAAAGAAAAAG
Found at i:104486747 original size:15 final size:14
Alignment explanation
Indices: 104486713--104486767 Score: 76
Period size: 14 Copynumber: 3.9 Consensus size: 14
104486703 ACAAGTTCAA
*
104486713 AAAAAAAGGAAAA-
1 AAAAAAAGAAAAAG
*
104486726 AAGAAAAGAAAAAG
1 AAAAAAAGAAAAAG
104486740 ATAAAAAAGAAAAAG
1 A-AAAAAAGAAAAAG
104486755 AAAAAAAGAAAAA
1 AAAAAAAGAAAAA
104486768 AAATAGAGAG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
13 11 0.30
14 13 0.35
15 13 0.35
ACGTcount: A:0.84, C:0.00, G:0.15, T:0.02
Consensus pattern (14 bp):
AAAAAAAGAAAAAG
Found at i:104487963 original size:27 final size:27
Alignment explanation
Indices: 104487928--104488044 Score: 139
Period size: 27 Copynumber: 4.3 Consensus size: 27
104487918 TACTGAAATG
*
104487928 CCCTCGATTTATAGAATTACCATTTTA
1 CCCTCGATTTACAGAATTACCATTTTA
* * **
104487955 CCTTTGATTTACAGAATTACTGTTTTA
1 CCCTCGATTTACAGAATTACCATTTTA
104487982 CCCTCGATTTACA-ACATTACCATTTTA
1 CCCTCGATTTACAGA-ATTACCATTTTA
* *
104488009 CCCTC-AGTTTACAAAATTACCGTTTTA
1 CCCTCGA-TTTACAGAATTACCATTTTA
104488036 CCCTCGATT
1 CCCTCGATT
104488045 GTGAAATTAC
Statistics
Matches: 76, Mismatches: 10, Indels: 8
0.81 0.11 0.09
Matches are distributed among these distances:
26 2 0.03
27 72 0.95
28 2 0.03
ACGTcount: A:0.27, C:0.25, G:0.08, T:0.40
Consensus pattern (27 bp):
CCCTCGATTTACAGAATTACCATTTTA
Found at i:104487990 original size:54 final size:54
Alignment explanation
Indices: 104487928--104488044 Score: 157
Period size: 54 Copynumber: 2.2 Consensus size: 54
104487918 TACTGAAATG
* ** * *
104487928 CCCTCGATTTATAGA-ATTACCATTTTA-CCTTTGATTTACAGAATTACTGTTTTA
1 CCCTCGATTTACA-ACATTACCATTTTACCCTCAG-TTTACAAAATTACCGTTTTA
104487982 CCCTCGATTTACAACATTACCATTTTACCCTCAGTTTACAAAATTACCGTTTTA
1 CCCTCGATTTACAACATTACCATTTTACCCTCAGTTTACAAAATTACCGTTTTA
104488036 CCCTCGATT
1 CCCTCGATT
104488045 GTGAAATTAC
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
53 1 0.02
54 51 0.91
55 4 0.07
ACGTcount: A:0.27, C:0.25, G:0.08, T:0.40
Consensus pattern (54 bp):
CCCTCGATTTACAACATTACCATTTTACCCTCAGTTTACAAAATTACCGTTTTA
Found at i:104488066 original size:27 final size:26
Alignment explanation
Indices: 104488043--104488200 Score: 147
Period size: 27 Copynumber: 5.8 Consensus size: 26
104488033 TTACCCTCGA
* **
104488043 TTGTGAAATTACTGAAATACCCCT-G
1 TTGTAAAATTACCAAAATACCCCTAG
*
104488068 TTAGATAGAATTACCAAAATACCCCTAG
1 TT-G-TAAAATTACCAAAATACCCCTAG
104488096 TTTGTAAAATTACCAAAATACCCCTAG
1 -TTGTAAAATTACCAAAATACCCCTAG
* * *
104488123 TTAGTAAAAATTACCGAAATACCACTGG
1 TT-GT-AAAATTACCAAAATACCCCTAG
* * * *
104488151 TTTGTGAAATTACCGAAATACCCTCAAT
1 -TTGTAAAATTACCAAAATACCC-CTAG
104488179 TTGTAAAATTACCAAAATACCC
1 TTGTAAAATTACCAAAATACCC
104488201 ATGATTTACA
Statistics
Matches: 110, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
25 2 0.02
26 3 0.03
27 77 0.70
28 24 0.22
29 4 0.04
ACGTcount: A:0.40, C:0.21, G:0.11, T:0.28
Consensus pattern (26 bp):
TTGTAAAATTACCAAAATACCCCTAG
Found at i:104488143 original size:55 final size:55
Alignment explanation
Indices: 104488043--104488200 Score: 189
Period size: 55 Copynumber: 2.9 Consensus size: 55
104488033 TTACCCTCGA
* *
104488043 TTGTGAAATTACTGAAATACCCCT-GTTAG-ATAGAATTACCAAAATACCCCTAGT
1 TTGTGAAATTACCGAAATACCCCTAGTTAGTA-AAAATTACCAAAATACCCCTAGT
* * * * *
104488097 TTGTAAAATTACCAAAATACCCCTAGTTAGTAAAAATTACCGAAATACCACTGGT
1 TTGTGAAATTACCGAAATACCCCTAGTTAGTAAAAATTACCAAAATACCCCTAGT
* *
104488152 TTGTGAAATTACCGAAATA-CCCTCAATTTGT-AAAATTACCAAAATACCC
1 TTGTGAAATTACCGAAATACCCCT-AGTTAGTAAAAATTACCAAAATACCC
104488201 ATGATTTACA
Statistics
Matches: 88, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
54 41 0.47
55 46 0.52
56 1 0.01
ACGTcount: A:0.40, C:0.21, G:0.11, T:0.28
Consensus pattern (55 bp):
TTGTGAAATTACCGAAATACCCCTAGTTAGTAAAAATTACCAAAATACCCCTAGT
Found at i:104488207 original size:27 final size:26
Alignment explanation
Indices: 104488076--104488216 Score: 115
Period size: 27 Copynumber: 5.2 Consensus size: 26
104488066 TGTTAGATAG
*
104488076 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCATA-TTTGTAA
* *
104488103 AATTACCAAAATACCCCTAGTTAGTAAA
1 AATTACCAAAATACCCATA-TTTGT-AA
* * *
104488131 AATTACCGAAATA-CCACTGGTTTGTGA
1 AATTACCAAAATACCCA-T-ATTTGTAA
*
104488158 AATTACCGAAATACCC-TCAATTTGTAA
1 AATTACCAAAATACCCAT--ATTTGTAA
**
104488185 AATTACCAAAATACCCATGATTTACAA
1 AATTACCAAAATACCCAT-ATTTGTAA
104488212 AATTA
1 AATTA
104488217 TAGAAATACC
Statistics
Matches: 95, Mismatches: 13, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
26 1 0.01
27 72 0.76
28 22 0.23
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.28
Consensus pattern (26 bp):
AATTACCAAAATACCCATATTTGTAA
Done.