Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 184 of 226
Found at i:58764427 original size:151 final size:151
Alignment explanation
Indices: 58764209--58764631 Score: 587
Period size: 151 Copynumber: 2.8 Consensus size: 151
58764199 AAAATTTTGA
* * *
58764209 TTTTTTTTAATAAGAGAAAGTTTAGATTTT-AACAAAT-AAAAA-TAGTTTTTTTAGTTATTTTA
1 TTTTTTTTAAAAAGAGAAAGTTTAGATTTTGAA-AAATAAAAAATTTG-TTTTTTAGTAATTTTA
* ** *
58764271 AAGGAAAGTTCAATTTTTTAAAACAAAATTTTTATTTTTTTTCAACTATTTCAAAGTAAAAGCTT
64 AAGGAAAGTTTAAAATTTTAAAACAAAATTTTTATTTTTTTTCAACTATTTCAAAATAAAAGCTT
58764336 TAATCTTTAAGAAAAATAGT-TT
129 TAATCTTTAAGAAAAATAGTGTT
* *
58764358 TTTTTTTTAAAAAGGAGAAAGTTTAGTTTTTGAAAAATAAAAAATTTGTTTTTTAGTCATTTTAA
1 TTTTTTTTAAAAA-GAGAAAGTTTAGATTTTGAAAAATAAAAAATTTGTTTTTTAGTAATTTTAA
58764423 AGGAAAGTTTAAAATTTTAAAAC-AAATTTTTGATTTTTTTTCAACTATTTCAAAATAAAAGCTT
65 AGGAAAGTTTAAAATTTTAAAACAAAATTTTT-ATTTTTTTTCAACTATTTCAAAATAAAAGCTT
58764487 TAATCTTTAAGAAAAATAGTGTT
129 TAATCTTTAAGAAAAATAGTGTT
* * *
58764510 TTTTTTTT--AAAGAGAAAGTTTAGATTTTGGAAAATAAAAATATATATTTTTTAAGTAATTTTA
1 TTTTTTTTAAAAAGAGAAAGTTTAGATTTTGAAAAATAAAAA-ATTTGTTTTTT-AGTAATTTT-
* *
58764573 AAAGGAAAGTTTAAAATTTTAAAACAAAATTTTGA--TTTTTT-AACTATTTCGAAATAAAA
63 AAAGGAAAGTTTAAAATTTTAAAACAAAATTTTTATTTTTTTTCAACTATTTCAAAATAAAA
58764632 TTTTGATTTT
Statistics
Matches: 249, Mismatches: 15, Indels: 20
0.88 0.05 0.07
Matches are distributed among these distances:
149 56 0.22
150 46 0.18
151 102 0.41
152 38 0.15
153 7 0.03
ACGTcount: A:0.42, C:0.04, G:0.10, T:0.44
Consensus pattern (151 bp):
TTTTTTTTAAAAAGAGAAAGTTTAGATTTTGAAAAATAAAAAATTTGTTTTTTAGTAATTTTAAA
GGAAAGTTTAAAATTTTAAAACAAAATTTTTATTTTTTTTCAACTATTTCAAAATAAAAGCTTTA
ATCTTTAAGAAAAATAGTGTT
Found at i:58764632 original size:30 final size:32
Alignment explanation
Indices: 58764588--58764663 Score: 102
Period size: 30 Copynumber: 2.4 Consensus size: 32
58764578 AAAGTTTAAA
* *
58764588 ATTTTAAAACAAAATTTTGA-TTTTTT-AACT
1 ATTTCAAAATAAAATTTTGATTTTTTTCAACT
* *
58764618 ATTTCGAAATAAAATTTTGATTTTTTTCAAGT
1 ATTTCAAAATAAAATTTTGATTTTTTTCAACT
58764650 ATTTCAAAATAAAA
1 ATTTCAAAATAAAA
58764664 GCTTTAATCT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
30 17 0.44
31 6 0.15
32 16 0.41
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.46
Consensus pattern (32 bp):
ATTTCAAAATAAAATTTTGATTTTTTTCAACT
Found at i:58765813 original size:41 final size:40
Alignment explanation
Indices: 58765763--58765864 Score: 114
Period size: 41 Copynumber: 2.5 Consensus size: 40
58765753 GGCAAAAATC
* *** *
58765763 GAGCATTAGCAGCGTTTTTTTTAAAAACGCCGCTAAAAAAG
1 GAGCATTAGCAGCGATTTTAAAAAAAAAGCCGCT-AAAAAG
* *
58765804 GAGCATTAGCCGCGATTTTAAAAAAAAAGTCGCTAAAAAG
1 GAGCATTAGCAGCGATTTTAAAAAAAAAGCCGCTAAAAAG
* *
58765844 GAGCATTAGCAGTGCTTTTAA
1 GAGCATTAGCAGCGATTTTAA
58765865 GCAAAACACC
Statistics
Matches: 51, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
40 24 0.47
41 27 0.53
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (40 bp):
GAGCATTAGCAGCGATTTTAAAAAAAAAGCCGCTAAAAAG
Found at i:58765882 original size:40 final size:39
Alignment explanation
Indices: 58765754--58765882 Score: 105
Period size: 40 Copynumber: 3.2 Consensus size: 39
58765744 CACTACACTG
** * ** *
58765754 GCAAAAATCGAGCATTAGCAGCGTTTTTTTTAAAAACGCC
1 GCAAAAAAGGAGCATTAGCAGCG-ATTTTAAAAAAACACC
* * *
58765794 GCTAAAAAAGGAGCATTAGCCGCGATTTTAAAAAAAAAGTC
1 GC-AAAAAAGGAGCATTAGCAGCGATTTTAAAAAAACA-CC
* * * *
58765835 GCTAAAAAGGAGCATTAGCAGTGCTTTTAAGCAAAACACC
1 GCAAAAAAGGAGCATTAGCAGCGATTTTAA-AAAAACACC
58765875 GCAAAAAA
1 GCAAAAAA
58765883 CCAAAGCCCA
Statistics
Matches: 69, Mismatches: 17, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
40 43 0.62
41 26 0.38
ACGTcount: A:0.43, C:0.18, G:0.19, T:0.21
Consensus pattern (39 bp):
GCAAAAAAGGAGCATTAGCAGCGATTTTAAAAAAACACC
Found at i:58766033 original size:41 final size:40
Alignment explanation
Indices: 58765939--58766237 Score: 261
Period size: 41 Copynumber: 7.3 Consensus size: 40
58765929 CGATTTCAAA
* * * *
58765939 AAAGCGCCGCTAATGCTCGGGGCTATAGCGGCGTTTTGATG
1 AAAGCGCCGCTAATG-TTGGGGCTTTAGCGGCGTTTTTAGG
* *
58765980 -AAGCGCCGCTAATGGTTGGGGCTTTAACGACGTTTTTAGG
1 AAAGCGCCGCTAAT-GTTGGGGCTTTAGCGGCGTTTTTAGG
* * * *
58766020 GAAGCGCCGCTAATGCTGGAGGCTTTAGCGGCGTTTTTTGA
1 AAAGCGCCGCTAATGTTGG-GGCTTTAGCGGCGTTTTTAGG
*
58766061 AAAGCGCCGCTAATGCTGTGGGCTTTAGCGGCGTTTTT-GG
1 AAAGCGCCGCTAATGTTG-GGGCTTTAGCGGCGTTTTTAGG
* *
58766101 TAAAGCGCCGCTAATGTTGTGGCCTTTAGCGACGTTTTT-GG
1 -AAAGCGCCGCTAATGTTG-GGGCTTTAGCGGCGTTTTTAGG
** * *
58766142 AGAA-CTGTTGCTAATGCTTTGGCCTTTAGCGGCGTTTTT-GG
1 A-AAGC-GCCGCTAATG-TTGGGGCTTTAGCGGCGTTTTTAGG
* *
58766183 AAAAGCGCCGCTAATGCTGGGGTCTTTAGTGGCGCTTTTTTA--
1 -AAAGCGCCGCTAATGTTGGGG-CTTTAGCGGCG--TTTTTAGG
58766225 AAAGCGCCGCTAA
1 AAAGCGCCGCTAA
58766238 AAACATTTTA
Statistics
Matches: 218, Mismatches: 26, Indels: 28
0.80 0.10 0.10
Matches are distributed among these distances:
40 42 0.19
41 166 0.76
42 5 0.02
43 5 0.02
ACGTcount: A:0.18, C:0.20, G:0.31, T:0.30
Consensus pattern (40 bp):
AAAGCGCCGCTAATGTTGGGGCTTTAGCGGCGTTTTTAGG
Found at i:58766097 original size:82 final size:80
Alignment explanation
Indices: 58765938--58766237 Score: 322
Period size: 82 Copynumber: 3.7 Consensus size: 80
58765928 GCGATTTCAA
* * *
58765938 AAAAGCGCCGCTAATGCTCGGGGCTATAGCGGCG--TTTTGATGAAGCGCCGCTAATGGTTGGGG
1 AAAAGCGCCGCTAATGCT-GGGGCTTTAGCGGCGTTTTTTGA-AAAGCGCCGCTAATGCTT-GGG
* *
58766001 CTTTAACGACGTTTTTAGG
63 CTTTAGCGGCGTTTTT-GG
*
58766020 -GAAGCGCCGCTAATGCTGGAGGCTTTAGCGGCGTTTTTTGAAAAGCGCCGCTAATGCTGTGGGC
1 AAAAGCGCCGCTAATGCTGG-GGCTTTAGCGGCGTTTTTTGAAAAGCGCCGCTAATGCT-TGGGC
58766084 TTTAGCGGCGTTTTTGG
64 TTTAGCGGCGTTTTTGG
* * * * * * ** *
58766101 TAAAGCGCCGCTAATGTTGTGGCCTTTAGCGACGTTTTTGGAGAA-CTGTTGCTAATGCTTTGGC
1 AAAAGCGCCGCTAATGCTG-GGGCTTTAGCGGCGTTTTTTGAAAAGC-GCCGCTAATGC-TTGGG
58766165 CTTTAGCGGCGTTTTTGG
63 CTTTAGCGGCGTTTTTGG
*
58766183 AAAAGCGCCGCTAATGCTGGGGTCTTTAGTGGCGCTTTTTT-AAAAGCGCCGCTAA
1 AAAAGCGCCGCTAATGCTGGGG-CTTTAGCGGCG-TTTTTTGAAAAGCGCCGCTAA
58766238 AAACATTTTA
Statistics
Matches: 183, Mismatches: 24, Indels: 22
0.80 0.10 0.10
Matches are distributed among these distances:
80 2 0.01
81 33 0.18
82 133 0.73
83 15 0.08
ACGTcount: A:0.19, C:0.20, G:0.31, T:0.30
Consensus pattern (80 bp):
AAAAGCGCCGCTAATGCTGGGGCTTTAGCGGCGTTTTTTGAAAAGCGCCGCTAATGCTTGGGCTT
TAGCGGCGTTTTTGG
Found at i:58766157 original size:123 final size:121
Alignment explanation
Indices: 58765938--58766237 Score: 369
Period size: 123 Copynumber: 2.4 Consensus size: 121
58765928 GCGATTTCAA
* * *
58765938 AAAAGCGCCGCTAATGCTCGGGGCTATAGCGGCG-TTTTGATGAAGCGCCGCTAATGGTTGGGGC
1 AAAAGCGCCGCTAATGCT-GGGGCTTTAGCGGCGTTTTTG-TAAAGCGCCGCTAATGGTTGGGCC
* *
58766002 TTTAACGACGTTTTTAGGGAAGCGCCGCTAATGC-TGGAGGCTTTAGCGGCGTTTTTTG
64 TTTAACGACGTTTTTAGGGAAGCGCCGCTAATGCTTGG-GCCTTTAGCGGCGTTTTTGG
58766060 AAAAGCGCCGCTAATGCTGTGGGCTTTAGCGGCGTTTTTGGTAAAGCGCCGCTAAT-GTTGTGGC
1 AAAAGCGCCGCTAATGCTG-GGGCTTTAGCGGCGTTTTT-GTAAAGCGCCGCTAATGGTTG-GGC
* ** *
58766124 CTTTAGCGACGTTTTT-GGAGAA-CTGTTGCTAATGCTTTGGCCTTTAGCGGCGTTTTTGG
63 CTTTAACGACGTTTTTAGG-GAAGC-GCCGCTAATGCTTGGGCCTTTAGCGGCGTTTTTGG
*
58766183 AAAAGCGCCGCTAATGCTGGGGTCTTTAGTGGCGCTTTTT-TAAAAGCGCCGCTAA
1 AAAAGCGCCGCTAATGCTGGGG-CTTTAGCGGCG-TTTTTGT-AAAGCGCCGCTAA
58766238 AAACATTTTA
Statistics
Matches: 158, Mismatches: 10, Indels: 19
0.84 0.05 0.10
Matches are distributed among these distances:
121 1 0.01
122 42 0.27
123 107 0.68
124 8 0.05
ACGTcount: A:0.19, C:0.20, G:0.31, T:0.30
Consensus pattern (121 bp):
AAAAGCGCCGCTAATGCTGGGGCTTTAGCGGCGTTTTTGTAAAGCGCCGCTAATGGTTGGGCCTT
TAACGACGTTTTTAGGGAAGCGCCGCTAATGCTTGGGCCTTTAGCGGCGTTTTTGG
Found at i:58767120 original size:21 final size:22
Alignment explanation
Indices: 58767099--58767151 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
58767089 GTATGAATTT
*
58767099 AGGGATTAGGGA-TTATGGTTTA
1 AGGG-TTAGGGATTTAAGGTTTA
58767121 AGGGTT-GGGATTTAAGGTTTA
1 AGGGTTAGGGATTTAAGGTTTA
58767142 AGGGTTAGGG
1 AGGGTTAGGG
58767152 GTTAGACGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 4 0.14
21 17 0.61
22 7 0.25
ACGTcount: A:0.25, C:0.00, G:0.42, T:0.34
Consensus pattern (22 bp):
AGGGTTAGGGATTTAAGGTTTA
Found at i:58767240 original size:272 final size:265
Alignment explanation
Indices: 58766757--58767247 Score: 691
Period size: 272 Copynumber: 1.8 Consensus size: 265
58766747 AGGGTTTTTG
** *
58766757 GTTTAGGGTATATGATTAATTTAAGATTTAAGACCGGTTTAGGAGTTACTATTTTAAAGTTTATG
1 GTTTAGGGTATATGATTAATTTAAGATTTAAGACCAATTTAGGAGTTACTATATTAAAGTTTATG
* * * * * *
58766822 GGGTATGGATTTAAGGATTATGGTTTAAGGGTTGCGATTTAAAGGTTTGGGGTTTGGGGTTTGAT
66 GAGTATGAATTTAAGGATTATGGTTTAAGGGTTGCGATTTAAAGGTTTAGGGTTAGGGGTTAGAC
* * ** *
58766887 GTTAGGGGTTAAGAATATGATTTAAGTTTTAGGGATTCAGGGGTTGAGTTAGGGTTTTAGGTTTA
131 GTTAGGGGTTAAGAATATGATTTAAGGTTTAAGGATTCAGGGGTCAAGTTAGAGTTTTAGGTTTA
58766952 GATTAATTAGTTTTTAATTTATATTTTAAATATTTTCTTATATAATTATAAAAGAGATAGTAATA
196 GATTAATTAGTTTTTAATTTATATTTTAAATATTTTCTTATATAATTATAAAAGAGATAGTAATA
58767017 AATTT
261 AATTT
* * *
58767022 GTTTAGGGTATATGATTAATTTAATATTTAAGGCCAATTTAGGAGTTACTATATTAAGGTTTATG
1 GTTTAGGGTATATGATTAATTTAAGATTTAAGACCAATTTAGGAGTTACTATATTAAAGTTTATG
*
58767087 GAGTATGAATTTAGGGATTAGGGATTATGGTTTAAGGGTTGGGATTT-AAGGTTTAAGGGTTAGG
66 GAGTATGAATTT----A--A-GGATTATGGTTTAAGGGTTGCGATTTAAAGGTTT-AGGGTTAGG
* *
58767151 GGTTAGACGTTAGGGGTTAAGAATATGATTTAGGGTTTAAGGATTCA-GTGTCAAGTT-GAGTTT
123 GGTTAGACGTTAGGGGTTAAGAATATGATTTAAGGTTTAAGGATTCAGGGGTCAAGTTAGAGTTT
58767214 TAGGTTTAGATTAATTAGTTTTTTTAATTTATAT
188 TAGGTTTAGATTAATTAG--TTTTTAATTTATAT
58767248 GTATTGAATG
Statistics
Matches: 196, Mismatches: 20, Indels: 13
0.86 0.09 0.06
Matches are distributed among these distances:
265 69 0.35
269 1 0.01
270 23 0.12
271 15 0.08
272 88 0.45
ACGTcount: A:0.29, C:0.02, G:0.26, T:0.43
Consensus pattern (265 bp):
GTTTAGGGTATATGATTAATTTAAGATTTAAGACCAATTTAGGAGTTACTATATTAAAGTTTATG
GAGTATGAATTTAAGGATTATGGTTTAAGGGTTGCGATTTAAAGGTTTAGGGTTAGGGGTTAGAC
GTTAGGGGTTAAGAATATGATTTAAGGTTTAAGGATTCAGGGGTCAAGTTAGAGTTTTAGGTTTA
GATTAATTAGTTTTTAATTTATATTTTAAATATTTTCTTATATAATTATAAAAGAGATAGTAATA
AATTT
Found at i:58767291 original size:18 final size:18
Alignment explanation
Indices: 58767257--58767291 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
58767247 TGTATTGAAT
*
58767257 GGTTAATTTAGGATTTAA
1 GGTTAATTAAGGATTTAA
*
58767275 GGTTAATTAAGGGTTTA
1 GGTTAATTAAGGATTTA
58767292 GTACTTGGGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.26, T:0.43
Consensus pattern (18 bp):
GGTTAATTAAGGATTTAA
Found at i:58767849 original size:83 final size:83
Alignment explanation
Indices: 58767661--58767856 Score: 200
Period size: 83 Copynumber: 2.4 Consensus size: 83
58767651 GTGTAATCTA
* * * * *
58767661 TTAGTGGCGTTTATGCTAAAAACGCCGCAATGATGTATTAATGTTTTTCAAAACGTCACTGTTTC
1 TTAGTGGCGTTTTTGCTAAAAACGCCGCAATGATGGATTAAAGTTTTTCAAAACGGCACCGTTTC
* **
58767726 ACTTCAGGACTTTAAATT
66 ACTTCAAGAAGTTAAATT
* ** * *
58767744 TTAGTGGCGTTTTTACGGAAAACGCCGGAACT-ATGGATTAAAGTTTCTT-AAAACGGCGCCGTT
1 TTAGTGGCGTTTTTGCTAAAAACGCCGCAA-TGATGGATTAAAGTTT-TTCAAAACGGCACCGTT
* *
58767807 TCTA-TTCAATAAGTTAATTT
64 TC-ACTTCAAGAAGTTAAATT
*
58767827 TTAGTGGCGTTTTTGCTAAAAACGCTGCAA
1 TTAGTGGCGTTTTTGCTAAAAACGCCGCAA
58767857 ATATATATTG
Statistics
Matches: 90, Mismatches: 20, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
83 86 0.96
84 4 0.04
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (83 bp):
TTAGTGGCGTTTTTGCTAAAAACGCCGCAATGATGGATTAAAGTTTTTCAAAACGGCACCGTTTC
ACTTCAAGAAGTTAAATT
Found at i:58767875 original size:83 final size:83
Alignment explanation
Indices: 58767737--58767891 Score: 193
Period size: 83 Copynumber: 1.9 Consensus size: 83
58767727 CTTCAGGACT
* * * * *
58767737 TTAAATTTTAGTGGCGTTTTTACGGAAAACGCCGGAACTATGGATTAAAGTTTCTTAAAACGGCG
1 TTAAATTTTAGTGGCGTTTTTACGAAAAACGCCGCAAATATAGATTAAAGGTTCTTAAAACGGCG
58767802 CCGTTTCTATTCAATAAG
66 CCGTTTCTATTCAATAAG
* * * * * * *
58767820 TTAATTTTTAGTGGCGTTTTTGCTAAAAACGCTGCAAATATATATTGAAGGTTCTTAAAACGGTG
1 TTAAATTTTAGTGGCGTTTTTACGAAAAACGCCGCAAATATAGATTAAAGGTTCTTAAAACGGCG
*
58767885 CTGTTTC
66 CCGTTTC
58767892 AGAATTTAAT
Statistics
Matches: 59, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
83 59 1.00
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (83 bp):
TTAAATTTTAGTGGCGTTTTTACGAAAAACGCCGCAAATATAGATTAAAGGTTCTTAAAACGGCG
CCGTTTCTATTCAATAAG
Found at i:58768106 original size:14 final size:14
Alignment explanation
Indices: 58768087--58768124 Score: 69
Period size: 13 Copynumber: 2.8 Consensus size: 14
58768077 ATCGAAAGGA
58768087 AAAGAAAAAAATAC
1 AAAGAAAAAAATAC
58768101 AAAG-AAAAAATAC
1 AAAGAAAAAAATAC
58768114 AAAGAAAAAAA
1 AAAGAAAAAAA
58768125 ATCAGAGGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 13 0.57
14 10 0.43
ACGTcount: A:0.82, C:0.05, G:0.08, T:0.05
Consensus pattern (14 bp):
AAAGAAAAAAATAC
Found at i:58769144 original size:12 final size:12
Alignment explanation
Indices: 58769129--58769190 Score: 60
Period size: 12 Copynumber: 5.4 Consensus size: 12
58769119 ATCATATCAT
58769129 AACTTATATATA
1 AACTTATATATA
*
58769141 AACTTACATA-A
1 AACTTATATATA
*
58769152 TAAC-T-TACAT-
1 -AACTTATATATA
*
58769162 AACTTATATAAA
1 AACTTATATATA
58769174 AACTTATATATA
1 AACTTATATATA
58769186 AACTT
1 AACTT
58769191 GCATAACTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
9 3 0.08
10 3 0.08
11 5 0.13
12 28 0.72
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (12 bp):
AACTTATATATA
Found at i:58769150 original size:21 final size:21
Alignment explanation
Indices: 58769126--58769200 Score: 55
Period size: 21 Copynumber: 3.4 Consensus size: 21
58769116 TCAATCATAT
58769126 CATAACTTATATATAAACTTA
1 CATAACTTATATATAAACTTA
* *
58769147 CATAA-TAACT-TACATAACTTA
1 CATAACTTA-TATATA-AACTTA
* *
58769168 TATAAAAACTTATATATAAACTTG
1 CAT---AACTTATATATAAACTTA
58769192 CATAACTTA
1 CATAACTTA
58769201 CATAATATCA
Statistics
Matches: 40, Mismatches: 7, Indels: 14
0.66 0.11 0.23
Matches are distributed among these distances:
20 5 0.12
21 20 0.50
24 10 0.25
25 5 0.12
ACGTcount: A:0.48, C:0.15, G:0.01, T:0.36
Consensus pattern (21 bp):
CATAACTTATATATAAACTTA
Found at i:58769165 original size:9 final size:9
Alignment explanation
Indices: 58769151--58769376 Score: 82
Period size: 9 Copynumber: 24.9 Consensus size: 9
58769141 AACTTACATA
58769151 ATAACTTAC
1 ATAACTTAC
*
58769160 ATAACTTAT
1 ATAACTTAC
*
58769169 ATAAAAACTTATAT
1 AT---AAC-T-TAC
*
58769183 ATAAACTTGC
1 ATAA-CTTAC
58769193 ATAACTTAC
1 ATAACTTAC
*
58769202 ATAA-TATCAT
1 ATAACT-T-AC
58769212 AATAACTTAC
1 A-TAACTTAC
*
58769222 ATAA--TAT
1 ATAACTTAC
* *
58769229 ATAGCCTAC
1 ATAACTTAC
* *
58769238 ATAAATTGC
1 ATAACTTAC
*
58769247 ATAACTCAC
1 ATAACTTAC
58769256 ATAA--TAC
1 ATAACTTAC
*
58769263 ACAACTTAC
1 ATAACTTAC
* *
58769272 GTAACTTAA
1 ATAACTTAC
*
58769281 ACAACTTAC
1 ATAACTTAC
58769290 ATAA--TAC
1 ATAACTTAC
58769297 ATAACTTAC
1 ATAACTTAC
*
58769306 ATTAATATTATAC
1 A-T-A-ACT-TAC
58769319 ATAACTTAC
1 ATAACTTAC
58769328 ATAACTTA-
1 ATAACTTAC
58769336 ATTAA-TTA-
1 A-TAACTTAC
*
58769344 AT-ATTATAC
1 ATAACT-TAC
58769353 ATAACTTAC
1 ATAACTTAC
58769362 --AACTTAC
1 ATAACTTAC
58769369 ATAACTTA
1 ATAACTTA
58769377 ATACATTATA
Statistics
Matches: 162, Mismatches: 28, Indels: 54
0.66 0.11 0.22
Matches are distributed among these distances:
6 1 0.01
7 26 0.16
8 8 0.05
9 86 0.53
10 14 0.09
11 9 0.06
12 8 0.05
13 5 0.03
14 5 0.03
ACGTcount: A:0.47, C:0.17, G:0.02, T:0.34
Consensus pattern (9 bp):
ATAACTTAC
Found at i:58769168 original size:33 final size:32
Alignment explanation
Indices: 58769126--58769225 Score: 109
Period size: 33 Copynumber: 3.2 Consensus size: 32
58769116 TCAATCATAT
58769126 CATAACTTATATATAAACTTACATAATAACTTA
1 CATAACTTATATA-AAACTTACATAATAACTTA
* *
58769159 CATAACTTATATAAAAACTTATAT-ATAAACTTG
1 CATAACTTATAT-AAAACTTACATAAT-AACTTA
* *
58769192 CATAACTTACATAATA--T-CATAATAACTTA
1 CATAACTTATATAAAACTTACATAATAACTTA
58769221 CATAA
1 CATAA
58769226 TATATAGCCT
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
29 12 0.21
30 3 0.05
32 5 0.09
33 37 0.64
34 1 0.02
ACGTcount: A:0.49, C:0.15, G:0.01, T:0.35
Consensus pattern (32 bp):
CATAACTTATATAAAACTTACATAATAACTTA
Found at i:58769226 original size:12 final size:12
Alignment explanation
Indices: 58769127--58769227 Score: 55
Period size: 12 Copynumber: 9.2 Consensus size: 12
58769117 CAATCATATC
*
58769127 ATAACTTATAT-
1 ATAACTTACATA
58769138 ATAAACTTACATA
1 AT-AACTTACATA
58769151 ATAACTTAC---
1 ATAACTTACATA
*
58769160 ATAACTTATATA
1 ATAACTTACATA
* *
58769172 AAAACTTATAT-
1 ATAACTTACATA
*
58769183 ATAAACTTGC---
1 AT-AACTTACATA
58769193 ATAACTTACATA
1 ATAACTTACATA
58769205 AT-A--T-CATA
1 ATAACTTACATA
58769213 ATAACTTACATA
1 ATAACTTACATA
58769225 ATA
1 ATA
58769228 TATAGCCTAC
Statistics
Matches: 70, Mismatches: 7, Indels: 25
0.69 0.07 0.25
Matches are distributed among these distances:
8 6 0.09
9 16 0.23
10 2 0.03
11 5 0.07
12 39 0.56
13 2 0.03
ACGTcount: A:0.50, C:0.14, G:0.01, T:0.36
Consensus pattern (12 bp):
ATAACTTACATA
Found at i:58769773 original size:19 final size:18
Alignment explanation
Indices: 58769749--58769802 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 18
58769739 TAATGTTTAC
*
58769749 TATATTATTATTTTAATAT
1 TATATTATTA-TTTAATAA
58769768 TATATTA-TATTTAATAA
1 TATATTATTATTTAATAA
*
58769785 TACTTTTATTATTTAATA
1 TA-TATTATTATTTAATA
58769803 CATTAGCAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 9 0.29
18 6 0.19
19 16 0.52
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (18 bp):
TATATTATTATTTAATAA
Found at i:58771569 original size:16 final size:16
Alignment explanation
Indices: 58771545--58771578 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
58771535 TAATACTAAT
*
58771545 TAATTTTTTATATTAA
1 TAATGTTTTATATTAA
*
58771561 TAATGTTTTATTTTAA
1 TAATGTTTTATATTAA
58771577 TA
1 TA
58771579 TTTAATATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (16 bp):
TAATGTTTTATATTAA
Found at i:58771699 original size:43 final size:42
Alignment explanation
Indices: 58771650--58771917 Score: 259
Period size: 43 Copynumber: 6.3 Consensus size: 42
58771640 ACGATACTTT
* ** *
58771650 TAGCGGCGTTTGTAATCAAAGCGTTGCTAAAGGTCTTGAGCTA
1 TAGCGGCGTTTGTAA-AAAAGCGCCGCTAAAGGTCCTGAGCTA
** *
58771693 TAGCGGCGTCTGTGGGAAAAA-CGCCGCTAAAGGTCTTGAGCTA
1 TAGCGGCGT-T-TGTAAAAAAGCGCCGCTAAAGGTCCTGAGCTA
* * ** * *
58771736 TAGCGACGTTTTTGGGAAAAGCGTCGCTAAAGGTCCTGATCTA
1 TAGCGGCGTTTGT-AAAAAAGCGCCGCTAAAGGTCCTGAGCTA
* *
58771779 TAGCGGCATTTGTGGAAAAAGCGCCGCTAAAGGTCCTGAGCTA
1 TAGCGGCGTTTGT-AAAAAAGCGCCGCTAAAGGTCCTGAGCTA
* * * * *
58771822 TATCGGTGTTTGTGGAAAAAGCGCCGCTAAAGGTCCTAACCTA
1 TAGCGGCGTTTGT-AAAAAAGCGCCGCTAAAGGTCCTGAGCTA
** *
58771865 TAGCGGCGTTTGTGTAAAAGCGCCGCTAAAGGTCCTGACCTA
1 TAGCGGCGTTTGTAAAAAAGCGCCGCTAAAGGTCCTGAGCTA
*
58771907 TAGCAGCGTTT
1 TAGCGGCGTTT
58771918 ATTTCAAAAA
Statistics
Matches: 193, Mismatches: 28, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
41 1 0.01
42 43 0.22
43 142 0.74
44 4 0.02
45 3 0.02
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (42 bp):
TAGCGGCGTTTGTAAAAAAGCGCCGCTAAAGGTCCTGAGCTA
Found at i:58771770 original size:86 final size:85
Alignment explanation
Indices: 58771667--58771910 Score: 317
Period size: 86 Copynumber: 2.8 Consensus size: 85
58771657 GTTTGTAATC
* * * * *
58771667 AAAGCGTTGCTAAAGGTCTTGAGCTATAGCGGCGTCTGTGGGAAAAACGCCGCTAAAGGTCTTGA
1 AAAGCGTCGCTAAAGGTCCTGACCTATAGCGGCGTTTGT-GGAAAAACGCCGCTAAAGGTCCTGA
* *
58771732 GCTATAGCGACGTTTTTGGGA
65 GCTATAGCGACGTTTGTGGAA
* *
58771753 AAAGCGTCGCTAAAGGTCCTGATCTATAGCGGCATTTGTGGAAAAAGCGCCGCTAAAGGTCCTGA
1 AAAGCGTCGCTAAAGGTCCTGACCTATAGCGGCGTTTGTGGAAAAA-CGCCGCTAAAGGTCCTGA
* **
58771818 GCTATATCGGTGTTTGTGGAA
65 GCTATAGCGACGTTTGTGGAA
* * * * *
58771839 AAAGCGCCGCTAAAGGTCCTAACCTATAGCGGCGTTTGTGTAAAAGCGCCGCTAAAGGTCCTGAC
1 AAAGCGTCGCTAAAGGTCCTGACCTATAGCGGCGTTTGTGGAAAAACGCCGCTAAAGGTCCTGAG
58771904 CTATAGC
66 CTATAGC
58771911 AGCGTTTATT
Statistics
Matches: 138, Mismatches: 19, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
85 31 0.22
86 107 0.78
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (85 bp):
AAAGCGTCGCTAAAGGTCCTGACCTATAGCGGCGTTTGTGGAAAAACGCCGCTAAAGGTCCTGAG
CTATAGCGACGTTTGTGGAA
Found at i:58771927 original size:129 final size:129
Alignment explanation
Indices: 58771675--58771939 Score: 327
Period size: 129 Copynumber: 2.1 Consensus size: 129
58771665 TCAAAGCGTT
* * * *
58771675 GCTAAAGGTCTTGAGCTATAGCGGCGTCTGTGGGAAAAACGCCGCTAAAGGTCTTGAGCTATAGC
1 GCTAAAGGTCCTGAGCTATAGCGGCGTCTGTGGGAAAAACGCCGCTAAAGGTCCTAACCTATAGC
* * * * * *
58771740 GACGTTTTTGGGAAAAGCGTCGCTAAAGGTCCTGATCTATAGCGGCATTTGTGGAAAAAGCGCC
66 GACGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGACCTATAGCAGCATTTGTGCAAAAAACGCC
* * *
58771804 GCTAAAGGTCCTGAGCTATATCGGTGTTTGT-GGAAAAAGCGCCGCTAAAGGTCCTAACCTATAG
1 GCTAAAGGTCCTGAGCTATAGCGGCGTCTGTGGGAAAAA-CGCCGCTAAAGGTCCTAACCTATAG
* * * * *
58771868 CGGCGTTTGT-GTAAAAGCGCCGCTAAAGGTCCTGACCTATAGCAGCGTTTATTTCAAAAAACGC
65 CGACGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGACCTATAGCAGCATTT-GTGCAAAAAACGC
*
58771932 T
129 C
58771933 GCTAAAG
1 GCTAAAG
58771940 TTAGCGACGC
Statistics
Matches: 115, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
128 42 0.37
129 73 0.63
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.25
Consensus pattern (129 bp):
GCTAAAGGTCCTGAGCTATAGCGGCGTCTGTGGGAAAAACGCCGCTAAAGGTCCTAACCTATAGC
GACGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGACCTATAGCAGCATTTGTGCAAAAAACGCC
Found at i:58771937 original size:86 final size:85
Alignment explanation
Indices: 58771667--58771939 Score: 311
Period size: 86 Copynumber: 3.2 Consensus size: 85
58771657 GTTTGTAATC
* * * * *
58771667 AAAGCGTTGCTAAAGGTCTTGAGCTATAGCGGCGTCTGTGGGAAAAA-CGCCGCTAAAGGTCTTG
1 AAAGCGCTGCTAAAGGTCCTGACCTATAGCGGCGTTTGT-GGAAAAAGCGCCGCTAAAGGTCCTG
*
58771731 AGCTATAGCGACGTTTTTGGGA
65 AGCTATAGCG-CGTTTTTGGAA
* *
58771753 AAAGCG-TCGCTAAAGGTCCTGATCTATAGCGGCATTTGTGGAAAAAGCGCCGCTAAAGGTCCTG
1 AAAGCGCT-GCTAAAGGTCCTGACCTATAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCCTG
*
58771817 AGCTATATCG-GTGTTTGTGGAA
65 AGCTATAGCGCGT-TTT-TGGAA
* * *
58771839 AAAGCGCCGCTAAAGGTCCTAACCTATAGCGGCGTTTGT-GTAAAAGCGCCGCTAAAGGTCCTGA
1 AAAGCGCTGCTAAAGGTCCTGACCTATAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCCTGA
* **
58771903 CCTATAGCAGCGTTTATTTCAA
66 GCTATAGC-GCGTTT-TTGGAA
*
58771925 AAAACGCTGCTAAAG
1 AAAGCGCTGCTAAAG
58771940 TTAGCGACGC
Statistics
Matches: 161, Mismatches: 18, Indels: 16
0.83 0.09 0.08
Matches are distributed among these distances:
84 2 0.01
85 41 0.25
86 115 0.71
87 3 0.02
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (85 bp):
AAAGCGCTGCTAAAGGTCCTGACCTATAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCCTGA
GCTATAGCGCGTTTTTGGAA
Found at i:58773484 original size:23 final size:23
Alignment explanation
Indices: 58773458--58773521 Score: 96
Period size: 23 Copynumber: 2.9 Consensus size: 23
58773448 TAGAACTATC
*
58773458 ACCCTCCAAGCACAACCAAATAT
1 ACCCTCCAAACACAACCAAATAT
*
58773481 ACCCTTCAAACACAACC-AATAT
1 ACCCTCCAAACACAACCAAATAT
58773503 ACCC-CCAAACACAACCAAA
1 ACCCTCCAAACACAACCAAA
58773522 AAGTGGTGAG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
21 11 0.30
22 11 0.30
23 15 0.41
ACGTcount: A:0.47, C:0.41, G:0.02, T:0.11
Consensus pattern (23 bp):
ACCCTCCAAACACAACCAAATAT
Found at i:58775618 original size:16 final size:16
Alignment explanation
Indices: 58775597--58775630 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
58775587 ACCGAAATAA
58775597 ATAATATATATTATAT
1 ATAATATATATTATAT
*
58775613 ATAATATATATTTTAT
1 ATAATATATATTATAT
58775629 AT
1 AT
58775631 TTTATATTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATAATATATATTATAT
Found at i:58776246 original size:16 final size:17
Alignment explanation
Indices: 58776213--58776246 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
58776203 TTTTTAAAAA
*
58776213 AGTATTTATATTATTTT
1 AGTATTTATATAATTTT
58776230 AGTATTTA-ATAATTTT
1 AGTATTTATATAATTTT
58776246 A
1 A
58776247 ATTTTTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (17 bp):
AGTATTTATATAATTTT
Found at i:58784239 original size:24 final size:24
Alignment explanation
Indices: 58784211--58784263 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
58784201 TTTCTAGAAG
*
58784211 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGCATTTATTAGTATAATAT
* *
58784235 ATTTAGCATTTATTAGTATAGTTT
1 ATTTAGCATTTATTAGTATAATAT
58784259 ATTTA
1 ATTTA
58784264 ACTTACTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.34, C:0.02, G:0.09, T:0.55
Consensus pattern (24 bp):
ATTTAGCATTTATTAGTATAATAT
Found at i:58786998 original size:25 final size:25
Alignment explanation
Indices: 58786961--58787092 Score: 74
Period size: 25 Copynumber: 5.5 Consensus size: 25
58786951 GATTTTTCGA
58786961 AAAATTT-TAAAAAATTAGAATTTTT
1 AAAATTTAT-AAAAATTAGAATTTTT
*
58786986 AAAATTTATAAAAA-T-GAA---AT
1 AAAATTTATAAAAATTAGAATTTTT
*
58787006 AAAA---ATAAAATAATAGAAATTATTT
1 AAAATTTATAAAA-ATTAG-AATT-TTT
58787031 AAAA---ATAAAAATTAG-ATTTTT
1 AAAATTTATAAAAATTAGAATTTTT
*
58787052 TAAATGTTATAAAAAATTAGAATTTTT
1 AAAAT-TTAT-AAAAATTAGAATTTTT
*
58787079 AAAAAATTATAAAA
1 -AAAATTTATAAAA
58787093 TTTATTAAAA
Statistics
Matches: 85, Mismatches: 6, Indels: 31
0.70 0.05 0.25
Matches are distributed among these distances:
17 6 0.07
18 1 0.01
19 1 0.01
20 6 0.07
21 8 0.09
22 3 0.04
23 3 0.04
24 5 0.06
25 25 0.29
26 14 0.16
27 10 0.12
28 3 0.04
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (25 bp):
AAAATTTATAAAAATTAGAATTTTT
Found at i:58787076 original size:27 final size:26
Alignment explanation
Indices: 58787037--58787092 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 26
58787027 ATTTAAAAAT
* **
58787037 AAAAATTAGATTTTTTAAATGTTATA
1 AAAAATTAGATTTTTAAAAAATTATA
58787063 AAAAATTAGAATTTTTAAAAAATTATA
1 AAAAATTAG-ATTTTTAAAAAATTATA
58787090 AAA
1 AAA
58787093 TTTATTAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 9 0.35
27 17 0.65
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.39
Consensus pattern (26 bp):
AAAAATTAGATTTTTAAAAAATTATA
Found at i:58787092 original size:26 final size:25
Alignment explanation
Indices: 58787035--58787092 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 25
58787025 TTATTTAAAA
* **
58787035 ATAAAAATTAGATTTTTTAAATGTT
1 ATAAAAATTAGATTTTTAAAAAATT
58787060 ATAAAAAATTAGAATTTTTAAAAAATT
1 AT-AAAAATTAG-ATTTTTAAAAAATT
58787087 ATAAAA
1 ATAAAA
58787093 TTTATTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 2 0.07
26 13 0.46
27 13 0.46
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (25 bp):
ATAAAAATTAGATTTTTAAAAAATT
Found at i:58787110 original size:21 final size:19
Alignment explanation
Indices: 58787062--58787115 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 19
58787052 TAAATGTTAT
*
58787062 AAAAAAT-TAGAATTTTTA
1 AAAAAATATAAAATTTTTA
*
58787080 AAAAATTATAAAATTTATTA
1 AAAAAATATAAAATTT-TTA
58787100 AAAATAATATAAAATT
1 AAAA-AATATAAAATT
58787116 ACAAAAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
18 6 0.20
19 7 0.23
20 7 0.23
21 10 0.33
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (19 bp):
AAAAAATATAAAATTTTTA
Found at i:58787113 original size:29 final size:29
Alignment explanation
Indices: 58787081--58787146 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
58787071 GAATTTTTAA
*
58787081 AAAATTATAAAATTTATT-AAAAATAATAT
1 AAAATTATAAAA-ATATTAAAAAATAATAT
* *
58787110 AAAATTACAAAAATATTAAAAAATTATAT
1 AAAATTATAAAAATATTAAAAAATAATAT
58787139 AAAATTAT
1 AAAATTAT
58787147 GGAAAGGAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 4 0.12
29 28 0.88
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (29 bp):
AAAATTATAAAAATATTAAAAAATAATAT
Found at i:58787121 original size:19 final size:19
Alignment explanation
Indices: 58787099--58787135 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
58787089 AAAATTTATT
*
58787099 AAAAATAATATAAAATTAC
1 AAAAATAATAAAAAATTAC
*
58787118 AAAAATATTAAAAAATTA
1 AAAAATAATAAAAAATTA
58787136 TATAAAATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (19 bp):
AAAAATAATAAAAAATTAC
Found at i:58787144 original size:10 final size:10
Alignment explanation
Indices: 58787081--58787146 Score: 50
Period size: 10 Copynumber: 6.8 Consensus size: 10
58787071 GAATTTTTAA
58787081 AAAATTATA-
1 AAAATTATAT
*
58787090 AAATTTAT-T
1 AAAATTATAT
*
58787099 AAAAATAATAT
1 -AAAATTATAT
*
58787110 AAAATTACA-
1 AAAATTATAT
*
58787119 AAAA-TATTAA
1 AAAATTA-TAT
58787129 AAAATTATAT
1 AAAATTATAT
58787139 AAAATTAT
1 AAAATTAT
58787147 GGAAAGGAGT
Statistics
Matches: 44, Mismatches: 7, Indels: 11
0.71 0.11 0.18
Matches are distributed among these distances:
8 2 0.05
9 12 0.27
10 27 0.61
11 3 0.07
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (10 bp):
AAAATTATAT
Found at i:58793162 original size:18 final size:18
Alignment explanation
Indices: 58793119--58793162 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
58793109 ACTCAATCCA
* *
58793119 AACCCAAGTATCCAACCC
1 AACCCAATTACCCAACCC
58793137 AACCCAATTACCCAACCC
1 AACCCAATTACCCAACCC
58793155 AACCCAAT
1 AACCCAAT
58793163 CATAAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.41, C:0.45, G:0.02, T:0.11
Consensus pattern (18 bp):
AACCCAATTACCCAACCC
Found at i:58793212 original size:6 final size:6
Alignment explanation
Indices: 58793203--58793231 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
58793193 AAATAAAATT
58793203 CTAAAA CTAAAA CTAAAA CTAAAA CTAAA
1 CTAAAA CTAAAA CTAAAA CTAAAA CTAAA
58793232 GTCTAAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.66, C:0.17, G:0.00, T:0.17
Consensus pattern (6 bp):
CTAAAA
Found at i:58793322 original size:9 final size:9
Alignment explanation
Indices: 58793305--58793380 Score: 107
Period size: 9 Copynumber: 8.4 Consensus size: 9
58793295 GTAGTGATTC
58793305 AATTCGGTT
1 AATTCGGTT
*
58793314 AACTCGGTT
1 AATTCGGTT
*
58793323 AATTCGGGT
1 AATTCGGTT
*
58793332 AATTCAGTT
1 AATTCGGTT
*
58793341 AATTCGGGT
1 AATTCGGTT
*
58793350 AATTCGGGT
1 AATTCGGTT
58793359 AATTCGGTT
1 AATTCGGTT
58793368 AATTCGGTT
1 AATTCGGTT
58793377 AATT
1 AATT
58793381 TTTAAACAAA
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 59 1.00
ACGTcount: A:0.25, C:0.12, G:0.24, T:0.39
Consensus pattern (9 bp):
AATTCGGTT
Found at i:58793335 original size:27 final size:27
Alignment explanation
Indices: 58793305--58793380 Score: 125
Period size: 27 Copynumber: 2.8 Consensus size: 27
58793295 GTAGTGATTC
*
58793305 AATTCGGTTAACTCGGTTAATTCGGGT
1 AATTCGGTTAATTCGGTTAATTCGGGT
* *
58793332 AATTCAGTTAATTCGGGTAATTCGGGT
1 AATTCGGTTAATTCGGTTAATTCGGGT
58793359 AATTCGGTTAATTCGGTTAATT
1 AATTCGGTTAATTCGGTTAATT
58793381 TTTAAACAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.25, C:0.12, G:0.24, T:0.39
Consensus pattern (27 bp):
AATTCGGTTAATTCGGTTAATTCGGGT
Found at i:58796286 original size:23 final size:23
Alignment explanation
Indices: 58796255--58796305 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
58796245 ACCTACTTTC
*
58796255 TTACTGTAGTAATTTTCAAGATA
1 TTACAGTAGTAATTTTCAAGATA
**
58796278 TTACAGTAGTAATTTTCGTGATA
1 TTACAGTAGTAATTTTCAAGATA
58796301 TTACA
1 TTACA
58796306 CATCTTTTGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCAAGATA
Found at i:58817452 original size:25 final size:25
Alignment explanation
Indices: 58817398--58817459 Score: 97
Period size: 25 Copynumber: 2.4 Consensus size: 25
58817388 CTTATAACTC
* *
58817398 ACCTAAATTTGCTATTTATGCTTTT
1 ACCTGAATTTCCTATTTATGCTTTT
58817423 ACCTGAATTTCCTATTTATGCTTTT
1 ACCTGAATTTCCTATTTATGCTTTT
58817448 ACCTGAACTTTC
1 ACCTGAA-TTTC
58817460 ATGGAAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
25 30 0.88
26 4 0.12
ACGTcount: A:0.23, C:0.21, G:0.08, T:0.48
Consensus pattern (25 bp):
ACCTGAATTTCCTATTTATGCTTTT
Found at i:58817664 original size:50 final size:50
Alignment explanation
Indices: 58817540--58817829 Score: 282
Period size: 50 Copynumber: 5.7 Consensus size: 50
58817530 AATAATTACA
* * * **
58817540 TGCCAAAGCCATGTCCCAGACATGGTCTTACATAGGATGTTACTTGTA-C--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CTT-CTCATATCGG
* * *
58817589 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACTTCTCATATCGG
* * ** * *
58817639 TGCCCATGCCATGTCCCAAACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACTTCTCATATCGG
* *
58817689 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTT-TCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CTTCTCATATCGG
* * *
58817739 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACTTCTCAT-A--TC---GG
* *
58817795 TGCCAATGCCATCTCCCAAACATGGTCTTACATGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGG
58817830 AATCTCTTTA
Statistics
Matches: 203, Mismatches: 27, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
47 4 0.02
48 4 0.02
49 35 0.17
50 123 0.61
51 2 0.01
53 2 0.01
56 33 0.16
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACTTCTCATATCGG
Found at i:58819228 original size:29 final size:30
Alignment explanation
Indices: 58819163--58819228 Score: 71
Period size: 31 Copynumber: 2.2 Consensus size: 30
58819153 AGCCAATCCC
* *
58819163 TCCAACACACCAATACTCATAAGAGTTACCA
1 TCCAACACACCAATACTCACAAGAGCTA-CA
* * *
58819194 ACCAACACATCAATGCTCACAAGAGCTA-A
1 TCCAACACACCAATACTCACAAGAGCTACA
58819223 TCCAAC
1 TCCAAC
58819229 CAACACACCA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
29 6 0.21
31 23 0.79
ACGTcount: A:0.42, C:0.33, G:0.08, T:0.17
Consensus pattern (30 bp):
TCCAACACACCAATACTCACAAGAGCTACA
Found at i:58819233 original size:33 final size:33
Alignment explanation
Indices: 58819122--58819239 Score: 132
Period size: 33 Copynumber: 3.6 Consensus size: 33
58819112 GTACATCGTC
* *
58819122 AATCCAACCAAACACACCATATGCTCACATGAGCC
1 AATCCAACC-AACACACCA-ATGCTCACAAGAGCT
** * *
58819157 AATCCCTCCAACACACCAATACTCATAAGAG-T
1 AATCCAACCAACACACCAATGCTCACAAGAGCT
* *
58819189 TA-CCAACCAACACATCAATGCTCACAAGAGCT
1 AATCCAACCAACACACCAATGCTCACAAGAGCT
58819221 AATCCAACCAACACACCAA
1 AATCCAACCAACACACCAA
58819240 ACAGAGAGTA
Statistics
Matches: 67, Mismatches: 14, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
31 23 0.34
32 3 0.04
33 25 0.37
34 9 0.13
35 7 0.10
ACGTcount: A:0.42, C:0.36, G:0.07, T:0.14
Consensus pattern (33 bp):
AATCCAACCAACACACCAATGCTCACAAGAGCT
Found at i:58823236 original size:43 final size:44
Alignment explanation
Indices: 58823171--58823285 Score: 146
Period size: 44 Copynumber: 2.6 Consensus size: 44
58823161 AACTTGTACA
* *
58823171 ATGCCTACGTCCCAAACGAGGTCTTACATGT-AATC-AAATATCG
1 ATGCCGACGTCCCAGACGAGGTCTTACATGTAAATCTAAAT-TCG
* *
58823214 ATGCC-ACTGTCCCAGACAAGGTCTTACATGTAAATCTCAATTCG
1 ATGCCGAC-GTCCCAGACGAGGTCTTACATGTAAATCTAAATTCG
*
58823258 ATGCCGACGTCCCAGACGTGGTCTTACA
1 ATGCCGACGTCCCAGACGAGGTCTTACA
58823286 CGAAATCACA
Statistics
Matches: 63, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
42 2 0.03
43 26 0.41
44 30 0.48
45 5 0.08
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (44 bp):
ATGCCGACGTCCCAGACGAGGTCTTACATGTAAATCTAAATTCG
Found at i:58824649 original size:33 final size:33
Alignment explanation
Indices: 58824588--58824650 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
58824578 TACTCTAAAG
**
58824588 AAGATGGCTGAAGAGCATTAGGCCACTATGAGC
1 AAGATGGCTGAAGAGCAAAAGGCCACTATGAGC
* *
58824621 AAGATGGGTGAAGAGCAAAAGGCTACTATG
1 AAGATGGCTGAAGAGCAAAAGGCCACTATG
58824651 GTGAGCTCGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.37, C:0.14, G:0.32, T:0.17
Consensus pattern (33 bp):
AAGATGGCTGAAGAGCAAAAGGCCACTATGAGC
Found at i:58825104 original size:16 final size:16
Alignment explanation
Indices: 58825083--58825113 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
58825073 GTATGGAATG
*
58825083 AAAATTTTGAGTTGAA
1 AAAATTTTAAGTTGAA
58825099 AAAATTTTAAGTTGA
1 AAAATTTTAAGTTGA
58825114 TTTACTAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.16, T:0.39
Consensus pattern (16 bp):
AAAATTTTAAGTTGAA
Found at i:58825697 original size:104 final size:104
Alignment explanation
Indices: 58825512--58825702 Score: 292
Period size: 104 Copynumber: 1.8 Consensus size: 104
58825502 GCTATTCCGG
* **
58825512 AGTAGCGAGCTTAACTCAACTTACTCAAATAAATAAAGGTTGTGAGTATAACTCATCTAACCTTA
1 AGTAGCGAGCTTAACTCAACTTACTCAAATAAATAAAGGGTAAGAGTATAACTCATCTAACCTTA
* * *
58825577 AAACATCAGTTGAGAGCGTAGGTCCACGAACTGTTTCAA
66 AAACATCAGCTAAGAGCATAGGTCCACGAACTGTTTCAA
* * * *
58825616 AGTAGCGAGCTTCACTCAACTTACTCACATAAATGAAGGGTAAGAGTATAACTCATCTAACCTTT
1 AGTAGCGAGCTTAACTCAACTTACTCAAATAAATAAAGGGTAAGAGTATAACTCATCTAACCTTA
58825681 AAACATCAGCTAAGAGCATAGG
66 AAACATCAGCTAAGAGCATAGG
58825703 ATTGCGAGCT
Statistics
Matches: 77, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
104 77 1.00
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (104 bp):
AGTAGCGAGCTTAACTCAACTTACTCAAATAAATAAAGGGTAAGAGTATAACTCATCTAACCTTA
AAACATCAGCTAAGAGCATAGGTCCACGAACTGTTTCAA
Found at i:58828417 original size:18 final size:17
Alignment explanation
Indices: 58828384--58828422 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
58828374 TTTTATAAAT
58828384 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
58828402 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
58828419 TGTG
1 TGTG
58828423 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:58828540 original size:8 final size:8
Alignment explanation
Indices: 58828527--58828555 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
58828517 CACTAGAGAC
58828527 CAGTGTTA
1 CAGTGTTA
58828535 CAGTGTTA
1 CAGTGTTA
58828543 CAGTGTTA
1 CAGTGTTA
58828551 CAGTG
1 CAGTG
58828556 AGTCCCGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (8 bp):
CAGTGTTA
Found at i:58828669 original size:23 final size:23
Alignment explanation
Indices: 58828642--58828717 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
58828632 AGTGTTATTG
58828642 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
58828665 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
58828688 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
58828711 ATCAGTG
1 ATCAGTG
58828718 TGGCACTTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:58830584 original size:17 final size:17
Alignment explanation
Indices: 58830562--58830604 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
58830552 AGGTCTCCGA
58830562 CGAGCTTCCAACCAAAT
1 CGAGCTTCCAACCAAAT
58830579 CGAGCTTCCAACCAAAT
1 CGAGCTTCCAACCAAAT
*
58830596 CAAGCTTCC
1 CGAGCTTCC
58830605 GATGATCTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.33, C:0.37, G:0.12, T:0.19
Consensus pattern (17 bp):
CGAGCTTCCAACCAAAT
Found at i:58835303 original size:30 final size:30
Alignment explanation
Indices: 58835267--58835327 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
58835257 TTATACATGC
58835267 CTAAACACCATTACCACATTCACCAAAATA
1 CTAAACACCATTACCACATTCACCAAAATA
58835297 CTAAACACCATTACCACATTCACCAAAATA
1 CTAAACACCATTACCACATTCACCAAAATA
58835327 C
1 C
58835328 CATTACATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.46, C:0.34, G:0.00, T:0.20
Consensus pattern (30 bp):
CTAAACACCATTACCACATTCACCAAAATA
Found at i:58851160 original size:364 final size:364
Alignment explanation
Indices: 58850486--58851173 Score: 1225
Period size: 364 Copynumber: 1.9 Consensus size: 364
58850476 CAACCCAAAT
* * *
58850486 GACCTAATAGGATCCGGATCTTCGACCCAGATCTGACACGGAAAAAGAATGCTCACCTACAATCA
1 GACCGAATAGGATCCGGATCTTCGACCCAGATCTGACACAGAAAAAGAATGCTCACCTACAAGCA
*
58850551 TAGTTCGTTGGGGACCCCGCTGAAATGCCAAATGTCCGCAAAGATAGCTCGCACAGAAAGCTTGT
66 TAGTTCGTTGGGGACCCCGCTGAAATGCCAAATGTCCGCAAAGATAGCTCGCACAAAAAGCTTGT
* *
58850616 AAGGAGAGCTCGTGTAAGCCTCGTAGGAATGAGGTTGCAAGTTATGTTCGCAGAAGGGATCACGA
131 AAGGAAAGCTCGTGTAAGCCTCGTAGGAATGAGGTTGCAAGTTATGTCCGCAGAAGGGATCACGA
*
58850681 GCACTACAAGGGATCCCCACTCGTGACTAGCAGGCATGAAGCTCGCTGGAGGAGTCAATCCCTGG
196 GCACTACAAGGGATCCCCACTCGTGACTAGCAAGCATGAAGCTCGCTGGAGGAGTCAATCCCTGG
* *
58850746 ATCAGAAAGGGCCGCGTGCTCCGTAGACACGCATCCAATAAGCCAAGGGATGCTTAGGTAATGTC
261 ATCAGAAAGGACCGCGTGCTCCGTAGACACGCATCCAATAAGCCAAGGGATGCTTAGGGAATGTC
58850811 AGCACCAGGGACAAGGAATGTCAGTACCATCAGCCCCAA
326 AGCACCAGGGACAAGGAATGTCAGTACCATCAGCCCCAA
* * * *
58850850 GACCGAATAGGATCCGGATCTTCGACCCGGATCTGACTCAGAAAAAGAATGCTCACCTGCAGGCA
1 GACCGAATAGGATCCGGATCTTCGACCCAGATCTGACACAGAAAAAGAATGCTCACCTACAAGCA
58850915 TAGTTCGTTGGGGACCCCGCT-AGAATGCCAAATGTCCGCAAAGATAGCTCGCACAAAAAGCTTG
66 TAGTTCGTTGGGGACCCCGCTGA-AATGCCAAATGTCCGCAAAGATAGCTCGCACAAAAAGCTTG
58850979 TAAGGAAAGCTCGTGTAAGCCTCGTAGGAATGAGGTTGCAAGTTATGTCCGCAGAAGGGATCACG
130 TAAGGAAAGCTCGTGTAAGCCTCGTAGGAATGAGGTTGCAAGTTATGTCCGCAGAAGGGATCACG
*
58851044 AGCACTACAAGGGATCCCTACTCGTGACTAGCAAGCATGAAGCTCGCTGGAGGAGTCAATCCCTG
195 AGCACTACAAGGGATCCCCACTCGTGACTAGCAAGCATGAAGCTCGCTGGAGGAGTCAATCCCTG
*
58851109 GATCAGAAAGGACCGCGTGCTCCGTAGACACGCATCTAATAAGCCAAGGGATGCTTAGGGAATGT
260 GATCAGAAAGGACCGCGTGCTCCGTAGACACGCATCCAATAAGCCAAGGGATGCTTAGGGAATGT
58851174 TAGTACCATC
Statistics
Matches: 308, Mismatches: 15, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
363 1 0.00
364 307 1.00
ACGTcount: A:0.30, C:0.24, G:0.27, T:0.19
Consensus pattern (364 bp):
GACCGAATAGGATCCGGATCTTCGACCCAGATCTGACACAGAAAAAGAATGCTCACCTACAAGCA
TAGTTCGTTGGGGACCCCGCTGAAATGCCAAATGTCCGCAAAGATAGCTCGCACAAAAAGCTTGT
AAGGAAAGCTCGTGTAAGCCTCGTAGGAATGAGGTTGCAAGTTATGTCCGCAGAAGGGATCACGA
GCACTACAAGGGATCCCCACTCGTGACTAGCAAGCATGAAGCTCGCTGGAGGAGTCAATCCCTGG
ATCAGAAAGGACCGCGTGCTCCGTAGACACGCATCCAATAAGCCAAGGGATGCTTAGGGAATGTC
AGCACCAGGGACAAGGAATGTCAGTACCATCAGCCCCAA
Found at i:58857115 original size:69 final size:69
Alignment explanation
Indices: 58857038--58857430 Score: 365
Period size: 69 Copynumber: 5.7 Consensus size: 69
58857028 GCAAAGTTGG
* * * * *
58857038 GACCTCCAAAACAGTTAGTGAGACCAAAGCTCCCAGCTATAAAATTAAGGTTCGCAAGCGAAGAG
1 GACCTCCAAAACAGTTAGCGAGAGCAAAGCTCCCAGCTATAAAATCAAGGCTCGCAGGCGAAGAG
*
58857103 CCGT
66 CCGC
* * * *
58857107 GACCTCCAAAACAGTTAGCGAGAGCAAAGCTCCCAGCTGTAAAATCAGGGCTCGCGGGCAAAGAG
1 GACCTCCAAAACAGTTAGCGAGAGCAAAGCTCCCAGCTATAAAATCAAGGCTCGCAGGCGAAGAG
* *
58857172 TCAC
66 CCGC
* * * * *
58857176 GACCTCCAAAATAGTTAGCGAAAGCAAAGCTCCTAGCTGTAAAATCAAGGCTCGCAGGTGAAGAG
1 GACCTCCAAAACAGTTAGCGAGAGCAAAGCTCCCAGCTATAAAATCAAGGCTCGCAGGCGAAGAG
*
58857241 CTGC
66 CCGC
* * * * *
58857245 AACCTCTAAAACAGTTAGCGAGAGCAAAGCTCCCAGCTATAAAATCAAGGTTCACAGGTGAAGAG
1 GACCTCCAAAACAGTTAGCGAGAGCAAAGCTCCCAGCTATAAAATCAAGGCTCGCAGGCGAAGAG
* *
58857310 TCGT
66 CCGC
* * * * * * * * * ** *
58857314 GAACTCCAAAGCAATTAGCAAGAGCAAAACTCTCAACT-TCAAAATCAGGGCTCACAAACGAAGG
1 GACCTCCAAAACAGTTAGCGAGAGCAAAGCTCCCAGCTAT-AAAATCAAGGCTCGCAGGCGAAGA
*
58857378 GTCGC
65 GCCGC
* * * * * * *
58857383 GACTTCCAAAACAATTATCGAGAGCAAAACTTCTAGCTGTAAAATCAA
1 GACCTCCAAAACAGTTAGCGAGAGCAAAGCTCCCAGCTATAAAATCAA
58857431 AGCTAGTAGG
Statistics
Matches: 263, Mismatches: 59, Indels: 4
0.81 0.18 0.01
Matches are distributed among these distances:
68 1 0.00
69 261 0.99
70 1 0.00
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.17
Consensus pattern (69 bp):
GACCTCCAAAACAGTTAGCGAGAGCAAAGCTCCCAGCTATAAAATCAAGGCTCGCAGGCGAAGAG
CCGC
Found at i:58857421 original size:207 final size:207
Alignment explanation
Indices: 58857039--58857430 Score: 507
Period size: 207 Copynumber: 1.9 Consensus size: 207
58857029 CAAAGTTGGG
* * *
58857039 ACCTCCAAAACAGTTAGTGAGACCAAAGCTCCCAGCTATAAAATTAAGGTTCGCAAGCGAAGAGC
1 ACCTCCAAAACAGTTAGCGAGACCAAAGCTCCCAGCTATAAAATCAAGGTTCACAAGCGAAGAGC
* * * * * * ***
58857104 CGTGACCTCCAAAACAGTTAGCGAGAGCAAAGCTCCCAGCTGTAAAATCAGGGCTCGCGGGCAAA
66 CGTGAACTCCAAAACAATTAGCAAGAGCAAAACTCCCAACTGTAAAATCAGGGCTCACAAACAAA
* * *
58857169 GAGTCACGACCTCCAAAATAGTTAGCGAAAGCAAAGCTCCTAGCTGTAAAATCAAGGCTCGCAGG
131 GAGTCACGACCTCCAAAACAATTAGCGAAAGCAAAACTCCTAGCTGTAAAATCAAGGCTCGCAGG
58857234 TGAAGAGCTGCA
196 TGAAGAGCTGCA
* * * * *
58857246 ACCTCTAAAACAGTTAGCGAGAGCAAAGCTCCCAGCTATAAAATCAAGGTTCACAGGTGAAGAGT
1 ACCTCCAAAACAGTTAGCGAGACCAAAGCTCCCAGCTATAAAATCAAGGTTCACAAGCGAAGAGC
* * *
58857311 CGTGAACTCCAAAGCAATTAGCAAGAGCAAAACTCTCAACT-TCAAAATCAGGGCTCACAAACGA
66 CGTGAACTCCAAAACAATTAGCAAGAGCAAAACTCCCAACTGT-AAAATCAGGGCTCACAAACAA
* * * * * *
58857375 AGGGTCGCGACTTCCAAAACAATTATCGAGAGCAAAACTTCTAGCTGTAAAATCAA
130 AGAGTCACGACCTCCAAAACAATTAGCGAAAGCAAAACTCCTAGCTGTAAAATCAA
58857431 AGCTAGTAGG
Statistics
Matches: 155, Mismatches: 29, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
206 1 0.01
207 154 0.99
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.17
Consensus pattern (207 bp):
ACCTCCAAAACAGTTAGCGAGACCAAAGCTCCCAGCTATAAAATCAAGGTTCACAAGCGAAGAGC
CGTGAACTCCAAAACAATTAGCAAGAGCAAAACTCCCAACTGTAAAATCAGGGCTCACAAACAAA
GAGTCACGACCTCCAAAACAATTAGCGAAAGCAAAACTCCTAGCTGTAAAATCAAGGCTCGCAGG
TGAAGAGCTGCA
Found at i:58857478 original size:53 final size:53
Alignment explanation
Indices: 58857420--58857525 Score: 151
Period size: 53 Copynumber: 2.0 Consensus size: 53
58857410 AACTTCTAGC
*
58857420 TGTAAAATCAAAGCTAGTAGG-CAAAAAGTCGTAACCTCCAAAATAGTTAGTGA
1 TGTAAAATCAAAGCTAGTAGGTC-AAAAGTCGCAACCTCCAAAATAGTTAGTGA
* * * *
58857473 TGTAAAATCAAGGCTCGTAGGTCAAGAGTCGCGACCTCCAAAATAGTTAGTGA
1 TGTAAAATCAAAGCTAGTAGGTCAAAAGTCGCAACCTCCAAAATAGTTAGTGA
58857526 GACCAAAGCT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
53 46 0.98
54 1 0.02
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.23
Consensus pattern (53 bp):
TGTAAAATCAAAGCTAGTAGGTCAAAAGTCGCAACCTCCAAAATAGTTAGTGA
Found at i:58859985 original size:582 final size:582
Alignment explanation
Indices: 58858876--58860027 Score: 1856
Period size: 582 Copynumber: 2.0 Consensus size: 582
58858866 CAATTGCCCC
*
58858876 CTACACCATCAACAACCCTAAGATTAGTAGAAATAATTAACAAGTCAGTACCTCCACTAACCCTC
1 CTACACCATCAACAACCCTAAGATTAGTAGAAATAATTAACAAGTCAATACCTCCACTAACCCTC
* * * ** * * * *
58858941 TCCTATTACTCGAACTCAATAAGGGCAAATGGACAAAACGACATCTTAGAATAATGGTTGAAGAA
66 TCCTATTACTCGAACTAAAGAAGGGCAAATGGACAAAACAACATCCCACAATAATAGTAGAAAAA
* *
58859006 ATTCGCAAGCTCCTCCAAACACCCCGTCAATATTATGCCCAGCTGATCGAGGGAATCGTGAGGCC
131 ATTCGCAAGCTCCTCCAAACACCCAGTCAATATCATGCCCAGCTGATCGAGGGAATCGTGAGGCC
* * * *
58859071 AAGTACTCATCGCTGGTTGCCCAGCAACTGATCGTGCGACCTCTTAGTTGTCGCCAGCCCTCCAA
196 AAGTACTCATCGCTAGTTGCCCACCAACGGATCATGCGACCTCTTAGTTGTCGCCAGCCCTCCAA
* * *
58859136 CCATTTAGGCTAAGATCCTCCAAATAGAATCTGAAGACATTCCTCACAGTCAGAATTGCCTCCAG
261 CCATTTAGGCTAAGATCCTCCAAACAGAATCTAAAGACATTCCTCACAGTCAGAATCGCCTCCAG
* **
58859201 AGCCTCTAAAGTTGCTCGATAGCCTCATTAGTGGCAAGACTCCTCTGGAAGGCGTGCATGTCTTC
326 AGCCTCTAAAGTTGCTCGATAGCCTCATCAGTGGCAAGACTCCTCTAAAAGGCGTGCATGTCTTC
58859266 ACTAGGGGAGGACCACCTAGTTGGGAACACAAAGTCTTCACCAAGTATGCTGCGAGTTTGGATAT
391 ACTAGGGGAGGACCACCTAGTTGGGAACACAAAGTCTTCACCAAGTATGCTGCGAGTTTGGATAT
*
58859331 ACGTCCCCCATTCCAAGTGAAGTTTATTGCATTGATTTCGTATAATCGTCTGCACCTTCCAACAA
456 ACGTCCCCCATTCCAAGTGAAGATTATTGCATTGATTTCGTATAATCGTCTGCACCTTCCAACAA
* *
58859396 GGGGAAAAGTAGTAGAACCCTGCTGGTTCCCCCACATTAGTCCCTTTCAATTAGTACCTCAT
521 AGGGAAAAGTAGTAGAACCCTGCTGATTCCCCCACATTAGTCCCTTTCAATTAGTACCTCAT
* * *
58859458 CTACACCATCAATAACCCTAAGATTAGTAGAAGTAATTAACAAGTCAATACCTCCTCTAACCCTC
1 CTACACCATCAACAACCCTAAGATTAGTAGAAATAATTAACAAGTCAATACCTCCACTAACCCTC
* **
58859523 TCCTATTGCTCGAACTAAAGAAGGGCAAATGGACGGAACAACATCCCACAATAATAGTAGAAAAA
66 TCCTATTACTCGAACTAAAGAAGGGCAAATGGACAAAACAACATCCCACAATAATAGTAGAAAAA
* *
58859588 ATTCGCAGGCTCCTCCAAACACCCAGTCAATATCATGCCCAGCTGATCGAGGGAATCGTGATGCC
131 ATTCGCAAGCTCCTCCAAACACCCAGTCAATATCATGCCCAGCTGATCGAGGGAATCGTGAGGCC
*
58859653 AAGTACTCATCGTTAGTTGCCCACCAACGGATCATGCGACCTCTTAGTTGTCGCCAGCCCTCCAA
196 AAGTACTCATCGCTAGTTGCCCACCAACGGATCATGCGACCTCTTAGTTGTCGCCAGCCCTCCAA
* * * * *
58859718 CCATTTAGGCTGAGATCCTCCAAGCAGAATCTAAAGACATTCCTCACAGTTAGAATCGTCTCTAG
261 CCATTTAGGCTAAGATCCTCCAAACAGAATCTAAAGACATTCCTCACAGTCAGAATCGCCTCCAG
* *
58859783 AGCCTTTGAAGTTGCTCGATAGCCTCATCAGTGGCAAGACTCCTCTAAAAGGCGTGCATGTCTTC
326 AGCCTCTAAAGTTGCTCGATAGCCTCATCAGTGGCAAGACTCCTCTAAAAGGCGTGCATGTCTTC
* *
58859848 ACTAGGGGAGGACCACCTAGTTGGGAACCCAAAGTCTTCGCCAAGTATGCTGC-AGGTTTGGATA
391 ACTAGGGGAGGACCACCTAGTTGGGAACACAAAGTCTTCACCAAGTATGCTGCGA-GTTTGGATA
* * * *
58859912 TACGTCCCCCGTTTCAAGTGAAGATTATTGCATTGATTTTGTATAATCGTCTGCGCCTTCCAACA
455 TACGTCCCCCATTCCAAGTGAAGATTATTGCATTGATTTCGTATAATCGTCTGCACCTTCCAACA
*
58859977 AAGGGAAAAGTAGTAGAACCCTGCTGATTCCCCCATATTAGTCCCTTTCAA
520 AAGGGAAAAGTAGTAGAACCCTGCTGATTCCCCCACATTAGTCCCTTTCAA
58860028 CTTGTATAAG
Statistics
Matches: 521, Mismatches: 48, Indels: 2
0.91 0.08 0.00
Matches are distributed among these distances:
581 1 0.00
582 520 1.00
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (582 bp):
CTACACCATCAACAACCCTAAGATTAGTAGAAATAATTAACAAGTCAATACCTCCACTAACCCTC
TCCTATTACTCGAACTAAAGAAGGGCAAATGGACAAAACAACATCCCACAATAATAGTAGAAAAA
ATTCGCAAGCTCCTCCAAACACCCAGTCAATATCATGCCCAGCTGATCGAGGGAATCGTGAGGCC
AAGTACTCATCGCTAGTTGCCCACCAACGGATCATGCGACCTCTTAGTTGTCGCCAGCCCTCCAA
CCATTTAGGCTAAGATCCTCCAAACAGAATCTAAAGACATTCCTCACAGTCAGAATCGCCTCCAG
AGCCTCTAAAGTTGCTCGATAGCCTCATCAGTGGCAAGACTCCTCTAAAAGGCGTGCATGTCTTC
ACTAGGGGAGGACCACCTAGTTGGGAACACAAAGTCTTCACCAAGTATGCTGCGAGTTTGGATAT
ACGTCCCCCATTCCAAGTGAAGATTATTGCATTGATTTCGTATAATCGTCTGCACCTTCCAACAA
AGGGAAAAGTAGTAGAACCCTGCTGATTCCCCCACATTAGTCCCTTTCAATTAGTACCTCAT
Found at i:58865018 original size:7 final size:7
Alignment explanation
Indices: 58865006--58865033 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
58864996 CCTCAATCTC
58865006 TAAAATA
1 TAAAATA
58865013 TAAAATA
1 TAAAATA
58865020 TAAAATA
1 TAAAATA
58865027 TAAAATA
1 TAAAATA
58865034 CTGTATGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
TAAAATA
Found at i:58866787 original size:14 final size:14
Alignment explanation
Indices: 58866764--58866807 Score: 70
Period size: 14 Copynumber: 3.1 Consensus size: 14
58866754 GATTTATGGT
*
58866764 TTAAGGGTTAGGGG
1 TTAAGAGTTAGGGG
58866778 TTAAGAGTTAGGGG
1 TTAAGAGTTAGGGG
*
58866792 TTAAGTGTTAGGGG
1 TTAAGAGTTAGGGG
58866806 TT
1 TT
58866808 TAGGGTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.23, C:0.00, G:0.43, T:0.34
Consensus pattern (14 bp):
TTAAGAGTTAGGGG
Found at i:58870039 original size:19 final size:19
Alignment explanation
Indices: 58869981--58870067 Score: 79
Period size: 19 Copynumber: 4.5 Consensus size: 19
58869971 TCACATGGTA
58869981 TATTTTTATAATTTTTTATT
1 TATTTTTATAA-TTTTTATT
* * *
58870001 ACATTTTTATTA-TTTAATT
1 -TATTTTTATAATTTTTATT
58870020 TATTTTTATAATTTTTATT
1 TATTTTTATAATTTTTATT
* *
58870039 TATTTTTTAGAATGTATT-TT
1 TA-TTTTTATAAT-TTTTATT
58870059 TATTTTTAT
1 TATTTTTAT
58870068 TACATATGGA
Statistics
Matches: 54, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
18 9 0.17
19 20 0.37
20 13 0.24
21 12 0.22
ACGTcount: A:0.26, C:0.01, G:0.02, T:0.70
Consensus pattern (19 bp):
TATTTTTATAATTTTTATT
Found at i:58870045 original size:20 final size:19
Alignment explanation
Indices: 58869983--58870065 Score: 69
Period size: 20 Copynumber: 4.2 Consensus size: 19
58869973 ACATGGTATA
*
58869983 TTTTTATAATTTTTTATTACA
1 TTTTTATAATTTTTT-TTA-T
* **
58870004 TTTTTATTATTTAATTTA-
1 TTTTTATAATTTTTTTTAT
58870022 TTTTTATAATTTTTATTTAT
1 TTTTTATAATTTTT-TTTAT
* *
58870042 TTTTTAGAATGTATTTTTAT
1 TTTTTATAAT-TTTTTTTAT
58870062 TTTT
1 TTTT
58870066 ATTACATATG
Statistics
Matches: 51, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
18 11 0.22
19 4 0.08
20 21 0.41
21 15 0.29
ACGTcount: A:0.25, C:0.01, G:0.02, T:0.71
Consensus pattern (19 bp):
TTTTTATAATTTTTTTTAT
Found at i:58870905 original size:26 final size:25
Alignment explanation
Indices: 58870876--58870930 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 25
58870866 TAGAAATGTT
58870876 TTTAAAATTTTTAAT-TTTTTATATA
1 TTTAAAATTTTTAATATTTTTA-ATA
*
58870901 CTTTAGAATTTTTAATATTTTTAATA
1 -TTTAAAATTTTTAATATTTTTAATA
58870927 TTTA
1 TTTA
58870931 TACTTTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 4 0.15
26 17 0.63
27 6 0.22
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (25 bp):
TTTAAAATTTTTAATATTTTTAATA
Found at i:58870978 original size:19 final size:18
Alignment explanation
Indices: 58870945--58870999 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
58870935 TTTTTAAAAA
*
58870945 TATAAA-TTTTAGAATTT
1 TATAAATTTTTTGAATTT
58870962 GTATAAATTTTTTGAATTT
1 -TATAAATTTTTTGAATTT
*
58870981 TAAAAATTATTTT-AATTT
1 TATAAATT-TTTTGAATTT
58870999 T
1 T
58871000 TATTGAGAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 19 0.58
19 14 0.42
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (18 bp):
TATAAATTTTTTGAATTT
Found at i:58870987 original size:18 final size:18
Alignment explanation
Indices: 58870951--58870999 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
58870941 AAAATATAAA
* *
58870951 TTTTAGAATTTGTATAAAT
1 TTTTTGAATTT-TAAAAAT
58870970 TTTTTGAATTTTAAAAAT
1 TTTTTGAATTTTAAAAAT
58870988 TATTTT-AATTTT
1 T-TTTTGAATTTT
58871000 TATTGAGAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 13 0.48
19 14 0.52
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (18 bp):
TTTTTGAATTTTAAAAAT
Found at i:58880705 original size:17 final size:17
Alignment explanation
Indices: 58880660--58880706 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
58880650 CTCTTTTTTC
58880660 TTTTCTTCCCTAATTAT
1 TTTTCTTCCCTAATTAT
* *
58880677 TTTTCCTACCCT-TTTAT
1 TTTT-CTTCCCTAATTAT
58880694 TATTTCTTCCCTA
1 T-TTTCTTCCCTA
58880707 GTTTCACTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
17 15 0.62
18 9 0.38
ACGTcount: A:0.15, C:0.28, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTTCTTCCCTAATTAT
Found at i:58882815 original size:29 final size:29
Alignment explanation
Indices: 58882768--58882843 Score: 100
Period size: 30 Copynumber: 2.6 Consensus size: 29
58882758 AATAAAAATA
*
58882768 AATAAAAGTTATAAAAATA-TTAAATTTT
1 AATAAAAATTATAAAAATATTTAAATTTT
* *
58882796 AATAAAAAATATAAGAAATATTTAATTTTT
1 AATAAAAATTATAA-AAATATTTAAATTTT
*
58882826 ATTAAAAATTATAAAAAT
1 AATAAAAATTATAAAAAT
58882844 TATAAAAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
28 12 0.29
29 9 0.22
30 20 0.49
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (29 bp):
AATAAAAATTATAAAAATATTTAAATTTT
Found at i:58882842 original size:9 final size:9
Alignment explanation
Indices: 58882828--58882860 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
58882818 TAATTTTTAT
58882828 TAAAAATTA
1 TAAAAATTA
58882837 TAAAAATTA
1 TAAAAATTA
*
58882846 TAAAAATTG
1 TAAAAATTA
58882855 TAAAAA
1 TAAAAA
58882861 AGTATAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (9 bp):
TAAAAATTA
Found at i:58882851 original size:19 final size:18
Alignment explanation
Indices: 58882828--58882869 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
58882818 TAATTTTTAT
*
58882828 TAAAAATTATAAAAATTA
1 TAAAAATTATAAAAAGTA
*
58882846 TAAAAATTGTAAAAAAGTA
1 TAAAAATTAT-AAAAAGTA
58882865 TAAAA
1 TAAAA
58882870 TATATAGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.29
Consensus pattern (18 bp):
TAAAAATTATAAAAAGTA
Found at i:58883202 original size:27 final size:25
Alignment explanation
Indices: 58883172--58883267 Score: 79
Period size: 27 Copynumber: 3.6 Consensus size: 25
58883162 AATCTTACAA
**
58883172 ATTTTTATATTTTTACGATTTATATAT
1 ATTTTTATATTTTTAAAATTTA-A-AT
58883199 ATTTTT-TAATTTTTAAAATTTAAAT
1 ATTTTTAT-ATTTTTAAAATTTAAAT
*
58883224 TTTTTTATATTTTTATTAAAGTTT-AAT
1 ATTTTTATATTTTTA--AAA-TTTAAAT
58883251 AATTTTTATAATTTTTA
1 -ATTTTTAT-ATTTTTA
58883268 TTGATTTTTA
Statistics
Matches: 58, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
25 14 0.24
26 3 0.05
27 24 0.41
28 10 0.17
29 7 0.12
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.64
Consensus pattern (25 bp):
ATTTTTATATTTTTAAAATTTAAAT
Found at i:58883268 original size:9 final size:9
Alignment explanation
Indices: 58883171--58883291 Score: 69
Period size: 9 Copynumber: 13.8 Consensus size: 9
58883161 AAATCTTACA
58883171 AATTTTTAT
1 AATTTTTAT
*
58883180 -ATTTTTAC
1 AATTTTTAT
* *
58883188 GATTTATAT
1 AATTTTTAT
58883197 ATATTTTT-T
1 A-ATTTTTAT
58883206 AATTTTTA-
1 AATTTTTAT
*
58883214 AA-ATTTA-
1 AATTTTTAT
*
58883221 AATTTTTTT
1 AATTTTTAT
58883230 ATATTTTTATT
1 A-ATTTTTA-T
* *
58883241 AAAGTTTAAT
1 -AATTTTTAT
58883251 AATTTTTAT
1 AATTTTTAT
58883260 AATTTTTATT
1 AATTTTTA-T
*
58883270 GATTTTTAT
1 AATTTTTAT
58883279 --TTTTTAT
1 AATTTTTAT
58883286 -ATTTTT
1 AATTTTT
58883292 TGTCACATGT
Statistics
Matches: 88, Mismatches: 14, Indels: 21
0.72 0.11 0.17
Matches are distributed among these distances:
7 13 0.15
8 23 0.26
9 25 0.28
10 20 0.23
11 6 0.07
12 1 0.01
ACGTcount: A:0.31, C:0.01, G:0.02, T:0.66
Consensus pattern (9 bp):
AATTTTTAT
Found at i:58883278 original size:10 final size:10
Alignment explanation
Indices: 58883221--58883279 Score: 59
Period size: 10 Copynumber: 6.0 Consensus size: 10
58883211 TTAAAATTTA
58883221 AATTTTT-TT
1 AATTTTTATT
58883230 ATATTTTTATT
1 A-ATTTTTATT
** *
58883241 AAAGTTTAAT
1 AATTTTTATT
58883251 AATTTTTA-T
1 AATTTTTATT
58883260 AATTTTTATT
1 AATTTTTATT
*
58883270 GATTTTTATT
1 AATTTTTATT
58883280 TTTTATATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
9 10 0.24
10 28 0.68
11 3 0.07
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (10 bp):
AATTTTTATT
Found at i:58883284 original size:7 final size:8
Alignment explanation
Indices: 58883172--58883291 Score: 55
Period size: 8 Copynumber: 13.8 Consensus size: 8
58883162 AATCTTACAA
58883172 ATTTTTAT
1 ATTTTTAT
*
58883180 ATTTTTACG
1 ATTTTTA-T
58883189 ATTTATATAT
1 ATTT-T-TAT
58883199 ATTTTT-T
1 ATTTTTAT
*
58883206 AATTTTTAAA
1 -ATTTTT-AT
**
58883216 ATTTAAAT
1 ATTTTTAT
*
58883224 TTTTTTAT
1 ATTTTTAT
58883232 ATTTTTATT
1 ATTTTTA-T
* *
58883241 AAAGTTTAAT
1 --ATTTTTAT
58883251 AATTTTTAT
1 -ATTTTTAT
58883260 AATTTTTATT
1 -ATTTTTA-T
58883270 GATTTTTAT
1 -ATTTTTAT
58883279 -TTTTTAT
1 ATTTTTAT
58883286 ATTTTT
1 ATTTTT
58883292 TGTCACATGT
Statistics
Matches: 86, Mismatches: 15, Indels: 22
0.70 0.12 0.18
Matches are distributed among these distances:
7 8 0.09
8 31 0.36
9 26 0.30
10 14 0.16
11 7 0.08
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.67
Consensus pattern (8 bp):
ATTTTTAT
Found at i:58883518 original size:92 final size:90
Alignment explanation
Indices: 58883414--58883632 Score: 255
Period size: 89 Copynumber: 2.4 Consensus size: 90
58883404 TGCATTTTGG
* * *
58883414 CAATTGAGTGCAAAAAAAAAGTAGGGGCTTAATTGCATTTTTTGAAAAAATTT-AGGGTCTTTTT
1 CAATTGAATGCAAAAAAAAAGTAGGGGTTTAATTGCATTTTTTGAAAAAATTTGAGGG-C--CTT
* *
58883478 TTTTATGTATTTTGACAGTTCAAGTACC
63 TTTGATGTATTTTGAAAGTTCAAGTACC
* * * * *
58883506 CAATTGAATGCAAAAAAAAA-CAGGGATTTAATTACTTTTTTTGAAAAAGTTTGAGGGCCTTTTT
1 CAATTGAATGCAAAAAAAAAGTAGGGGTTTAATTGCATTTTTTGAAAAAATTTGAGGGCCTTTTT
*
58883570 GATGTATTTTGAAAGTTCAAGTATC
66 GATGTATTTTGAAAGTTCAAGTACC
*
58883595 CAATT-AAGTGCAAAAGTAAAAAGTAAGGGTTTAATTGC
1 CAATTGAA-TGCAAAA--AAAAAGTAGGGGTTTAATTGC
58883633 TTCTTTTTTT
Statistics
Matches: 107, Mismatches: 15, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
88 2 0.02
89 39 0.36
91 32 0.30
92 34 0.32
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (90 bp):
CAATTGAATGCAAAAAAAAAGTAGGGGTTTAATTGCATTTTTTGAAAAAATTTGAGGGCCTTTTT
GATGTATTTTGAAAGTTCAAGTACC
Found at i:58885413 original size:286 final size:289
Alignment explanation
Indices: 58884911--58885436 Score: 658
Period size: 286 Copynumber: 1.8 Consensus size: 289
58884901 ATGCCAATTG
* * *
58884911 GATTAGTAAAATCTTAAATTTACCACTCAACTAATATTTTATTTTGAGAATATTTTATACTTTTT
1 GATTAGTAAAACCTTAAATTTACCACTCAACTAAAACTTTATTTTGAGAATATTTTATACTTTTT
** * *
58884976 TAATACGCACAATTTATTATCTTCACCAGTTGTATATCTATATACTTACTATCAATAATACCCCA
66 TAATACGCACAATTTATTATCCCCACCAGTTGTATATC-ATATACTTACTATCAATAAAACACCA
* * * * *
58885041 AACTGAGTTGGTGTCATGGGTTAACCAAGTACCAACTCGATTAGGAAATTATGGAAATGTCCTTC
130 AACTAAGTTGGTGTCATAGGTTAACCAAGCACCAACTAGATTAGGAAATTATGAAAATGTCCTTC
* * * * * * * *
58885106 TATAATTAAAATGAGTTATATTATTTAAAGGTATTTTAGTTTTTTTTTCCATTTTAACAGAAACC
195 GATAATAAAAATAAATTATATTATTCAAAGGCACTTTAGTCTTTTTTTCCATTTTAACAGAAACC
58885171 AAATGATGAGATTTGAACCCACACTGATTT
260 AAATGATGAGATTTGAACCCACACTGATTT
*
58885201 GATTAGTAAAACCTTAAATTTACCACTCGAGC-AAAACTTTATTTT-A-ATATATTTTATACATT
1 GATTAGTAAAACCTTAAATTTACCACTC-AACTAAAACTTTATTTTGAGA-ATATTTTATAC--T
* *
58885263 CTTTTTAATATGTACAATTTATTATCCCCACCAGTTGTATATC-TATAC-TA-T-T-AATAAAAC
62 -TTTTTAATACGCACAATTTATTATCCCCACCAGTTGTATATCATATACTTACTATCAATAAAAC
* ** **
58885323 ATCTGACTAAGTTGGTGTCATAGGTTAACCGGGCACCAACTTAG-TTAGGAAATTATGAAAATGT
126 ACCAAACTAAGTTGGTGTCATAGGTTAACCAAGCACCAAC-TAGATTAGGAAATTATGAAAATGT
58885387 CCTTCCGA-AATAAAAATAAATTATATTATTCAAAGGCACTTTAGTCTTTT
190 CCTT-CGATAATAAAAATAAATTATATTATTCAAAGGCACTTTAGTCTTTT
58885437 CATTTAGGAA
Statistics
Matches: 201, Mismatches: 28, Indels: 18
0.81 0.11 0.07
Matches are distributed among these distances:
286 96 0.48
287 5 0.02
288 2 0.01
289 14 0.07
290 43 0.21
291 3 0.01
292 38 0.19
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.38
Consensus pattern (289 bp):
GATTAGTAAAACCTTAAATTTACCACTCAACTAAAACTTTATTTTGAGAATATTTTATACTTTTT
TAATACGCACAATTTATTATCCCCACCAGTTGTATATCATATACTTACTATCAATAAAACACCAA
ACTAAGTTGGTGTCATAGGTTAACCAAGCACCAACTAGATTAGGAAATTATGAAAATGTCCTTCG
ATAATAAAAATAAATTATATTATTCAAAGGCACTTTAGTCTTTTTTTCCATTTTAACAGAAACCA
AATGATGAGATTTGAACCCACACTGATTT
Found at i:58894252 original size:11 final size:11
Alignment explanation
Indices: 58894232--58894275 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
58894222 AGATAAATGT
*
58894232 TATTTAATTAA
1 TATTTTATTAA
58894243 TATTTTATTAA
1 TATTTTATTAA
* *
58894254 GATTTTTATTAT
1 TA-TTTTATTAA
58894266 TATTTTATTA
1 TATTTTATTA
58894276 TTAAATGATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 19 0.68
12 9 0.32
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:58896105 original size:57 final size:57
Alignment explanation
Indices: 58895974--58896119 Score: 188
Period size: 57 Copynumber: 2.5 Consensus size: 57
58895964 ATTGACGGTA
*
58895974 AAAAGGATCTAGCCCGGACGGGTGATCCTATCCTGATATAGCCTCCCGAAGAATATGTGTG
1 AAAAGGATCTAGCCCGGACGGGTGAT-C--T-CTGATATAGCCTCCCGAAGAACATGTGTG
*
58896035 AAAAAGATCTAGCCCGGACGGGTGATCT-TGATATAGCCCTCCCGAAGAACATGTG-G
1 AAAAGGATCTAGCCCGGACGGGTGATCTCTGATATAG-CCTCCCGAAGAACATGTGTG
* *
58896091 AAAATGGATTTAGCCCGGACGGGTAATCT
1 AAAA-GGATCTAGCCCGGACGGGTGATCT
58896120 GAATTAGGGT
Statistics
Matches: 78, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
56 13 0.17
57 38 0.49
58 1 0.01
60 1 0.01
61 25 0.32
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (57 bp):
AAAAGGATCTAGCCCGGACGGGTGATCTCTGATATAGCCTCCCGAAGAACATGTGTG
Found at i:58896292 original size:67 final size:67
Alignment explanation
Indices: 58896184--58896318 Score: 225
Period size: 67 Copynumber: 2.0 Consensus size: 67
58896174 GTAATTGTCG
*
58896184 TTGCAGGGGATTTAACCTGAACTGGTAATCCCGCTATAAGAAATGAGGTTCGCGGGAGTGTGGTC
1 TTGCAGGGGATTTAACCTGAACTGGTAATCCCGCTATAAGAAATGAGGTTCGCGGGAGTGTGCTC
58896249 TC
66 TC
* * * *
58896251 TTGCAGGGGATTTAGCCTGGACTGGTAATCTCGCTGTAAGAAATGAGGTTCGCGGGAGTGTGCTC
1 TTGCAGGGGATTTAACCTGAACTGGTAATCCCGCTATAAGAAATGAGGTTCGCGGGAGTGTGCTC
58896316 TC
66 TC
58896318 T
1 T
58896319 GAATTGGAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
67 63 1.00
ACGTcount: A:0.21, C:0.18, G:0.33, T:0.28
Consensus pattern (67 bp):
TTGCAGGGGATTTAACCTGAACTGGTAATCCCGCTATAAGAAATGAGGTTCGCGGGAGTGTGCTC
TC
Found at i:58905561 original size:36 final size:36
Alignment explanation
Indices: 58905514--58905587 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
58905504 TACGAGTCAT
58905514 TATCGAAGGGGATTCATTAACAACAGTCAAGAAATG
1 TATCGAAGGGGATTCATTAACAACAGTCAAGAAATG
58905550 TATCGAAGGGGATTCATTAACAACAGTCAAGAAATG
1 TATCGAAGGGGATTCATTAACAACAGTCAAGAAATG
58905586 TA
1 TA
58905588 AGTCTTTGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.42, C:0.14, G:0.22, T:0.23
Consensus pattern (36 bp):
TATCGAAGGGGATTCATTAACAACAGTCAAGAAATG
Found at i:58908776 original size:29 final size:29
Alignment explanation
Indices: 58908727--58908801 Score: 118
Period size: 29 Copynumber: 2.6 Consensus size: 29
58908717 GTATGTTTGT
*
58908727 ATTTA-TTTTATATTTT-CATTCATTCATA
1 ATTTATTTTTA-ATTTTGAATTCATTCATA
58908755 ATTTATTTTTAATTTTGAATTCATTCATA
1 ATTTATTTTTAATTTTGAATTCATTCATA
58908784 ATTTATTTTTAATTTTGA
1 ATTTATTTTTAATTTTGA
58908802 TTGAAGTAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
28 10 0.23
29 34 0.77
ACGTcount: A:0.29, C:0.07, G:0.03, T:0.61
Consensus pattern (29 bp):
ATTTATTTTTAATTTTGAATTCATTCATA
Found at i:58908871 original size:16 final size:16
Alignment explanation
Indices: 58908843--58908914 Score: 53
Period size: 16 Copynumber: 4.5 Consensus size: 16
58908833 TAAAGAATGT
58908843 TTTATTT-TTATGTAA
1 TTTATTTGTTATGTAA
*
58908858 TTTATTTGTTATGT-G
1 TTTATTTGTTATGTAA
*
58908873 TGTT-TTAGGTTGAT-TAGA
1 T-TTATT-TGTT-ATGTA-A
*
58908891 TTTATTTTTTATGTAA
1 TTTATTTGTTATGTAA
58908907 TTTATTTG
1 TTTATTTG
58908915 ACATATTGTT
Statistics
Matches: 43, Mismatches: 6, Indels: 15
0.67 0.09 0.23
Matches are distributed among these distances:
15 10 0.23
16 22 0.51
17 8 0.19
18 3 0.07
ACGTcount: A:0.21, C:0.00, G:0.15, T:0.64
Consensus pattern (16 bp):
TTTATTTGTTATGTAA
Found at i:58911214 original size:6 final size:6
Alignment explanation
Indices: 58911205--58911245 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
58911195 GCTAGAGGCA
* * *
58911205 GAGCCC GAGCCC GAGCCC GAGCCT AAGACC GAGCCC GAGCC
1 GAGCCC GAGCCC GAGCCC GAGCCC GAGCCC GAGCCC GAGCC
58911246 TAAGCCACAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.22, C:0.44, G:0.32, T:0.02
Consensus pattern (6 bp):
GAGCCC
Found at i:58911246 original size:18 final size:18
Alignment explanation
Indices: 58911215--58911249 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
58911205 GAGCCCGAGC
58911215 CCGAGCCCGAGCCTAAGA
1 CCGAGCCCGAGCCTAAGA
58911233 CCGAGCCCGAGCCTAAG
1 CCGAGCCCGAGCCTAAG
58911250 CCACAACCGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.26, C:0.40, G:0.29, T:0.06
Consensus pattern (18 bp):
CCGAGCCCGAGCCTAAGA
Found at i:58911912 original size:48 final size:48
Alignment explanation
Indices: 58911804--58911904 Score: 159
Period size: 48 Copynumber: 2.1 Consensus size: 48
58911794 ATTAATTGCA
* *
58911804 AAATTACA-ACATTAAAACACTAAAACTTGGAACAAACTTTGTAATAT
1 AAATTAAATACATTAAAACACTAAAAATTGGAACAAACTTTGTAATAT
* *
58911851 AAATTAAATACATTACAACATTAAAAATTGGAACAAACTTTGTAATAT
1 AAATTAAATACATTAAAACACTAAAAATTGGAACAAACTTTGTAATAT
58911899 AAATTA
1 AAATTA
58911905 GGTACATTGG
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
47 7 0.14
48 42 0.86
ACGTcount: A:0.52, C:0.12, G:0.06, T:0.30
Consensus pattern (48 bp):
AAATTAAATACATTAAAACACTAAAAATTGGAACAAACTTTGTAATAT
Found at i:58916632 original size:27 final size:26
Alignment explanation
Indices: 58916593--58916672 Score: 133
Period size: 27 Copynumber: 3.0 Consensus size: 26
58916583 CACCAATGAT
58916593 TCGGGGAATCAGCACTTAGCAACCCC
1 TCGGGGAATCAGCACTTAGCAACCCC
*
58916619 TCGGGAGAATCAGCACTTAGCAACCCT
1 TCGGG-GAATCAGCACTTAGCAACCCC
58916646 TCGGGGGAATCAGCACTTAGCAACCCC
1 TC-GGGGAATCAGCACTTAGCAACCCC
58916673 CTTCACATTT
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
26 5 0.10
27 42 0.84
28 3 0.06
ACGTcount: A:0.28, C:0.33, G:0.24, T:0.16
Consensus pattern (26 bp):
TCGGGGAATCAGCACTTAGCAACCCC
Found at i:58916710 original size:42 final size:42
Alignment explanation
Indices: 58916651--58916787 Score: 166
Period size: 42 Copynumber: 3.5 Consensus size: 42
58916641 ACCCTTCGGG
58916651 GGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATATGGT
1 GGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATATGGT
* *
58916693 GGAATCAGCACTTAGCAA-CCAC--CA-A--TGAG-T-TGG-
1 GGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATATGGT
* * *
58916726 GGAATCAACACTTAGCAACCCCTTTCACATTTAAGATACGGT
1 GGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATATGGT
58916768 GGAATCAGCACTTAGCAACC
1 GGAATCAGCACTTAGCAACC
58916788 ACCAATGAAT
Statistics
Matches: 78, Mismatches: 8, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
33 17 0.22
34 5 0.06
35 1 0.01
36 5 0.06
37 1 0.01
38 1 0.01
39 5 0.06
40 1 0.01
41 5 0.06
42 37 0.47
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (42 bp):
GGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATATGGT
Found at i:58916823 original size:75 final size:75
Alignment explanation
Indices: 58916649--58916824 Score: 298
Period size: 75 Copynumber: 2.3 Consensus size: 75
58916639 CAACCCTTCG
* *
58916649 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATATGGTGGAATCAGCACTTAGCAACCA
1 GGGGAATCAGCACTTAGCAACCCCTTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACCA
* *
58916714 CCAATGAGTT
66 CCAATGAATC
*
58916724 GGGGAATCAACACTTAGCAACCCCTTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACCA
1 GGGGAATCAGCACTTAGCAACCCCTTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACCA
58916789 CCAATGAATC
66 CCAATGAATC
*
58916799 GGGGAATTAGCACTTAGCAACCCCTT
1 GGGGAATCAGCACTTAGCAACCCCTT
58916825 GGGGGAATCA
Statistics
Matches: 94, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 94 1.00
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.22
Consensus pattern (75 bp):
GGGGAATCAGCACTTAGCAACCCCTTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACCA
CCAATGAATC
Found at i:58934360 original size:41 final size:41
Alignment explanation
Indices: 58934315--58934417 Score: 154
Period size: 41 Copynumber: 2.5 Consensus size: 41
58934305 TGATTCAGAA
** *
58934315 CACCGG-GATTAAGCCTGCTAGACATATAGTTTGAAATTTTT
1 CACCGGCG-TTAAGCCTGCTAGACATATAGTCCGAAATATTT
*
58934356 CACCGGCGTTAAGCCTGCTAGACGTATAGTCCGAAATATTT
1 CACCGGCGTTAAGCCTGCTAGACATATAGTCCGAAATATTT
58934397 CACCGGCGTTAAGCCTGCTAG
1 CACCGGCGTTAAGCCTGCTAG
58934418 GCACAAAGCC
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
41 56 0.98
42 1 0.02
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.28
Consensus pattern (41 bp):
CACCGGCGTTAAGCCTGCTAGACATATAGTCCGAAATATTT
Found at i:58934758 original size:37 final size:37
Alignment explanation
Indices: 58934639--58934758 Score: 111
Period size: 37 Copynumber: 3.2 Consensus size: 37
58934629 ACATAAGAAA
*
58934639 CATACTTTAATTTCCAACTCAATAACTTGATTAAATG
1 CATACATTAATTTCCAACTCAATAACTTGATTAAATG
* * * *
58934676 CATACA-TATATGTTCGAATCTCCCTATAA-TT-ATAAAATT
1 CATACATTA-AT-TTCCAA-CT--CAATAACTTGATTAAATG
* *
58934715 CATACATTAATTCCCAACTCAATAACTTGATTATATG
1 CATACATTAATTTCCAACTCAATAACTTGATTAAATG
58934752 CATACAT
1 CATACAT
58934759 ATTTATATTC
Statistics
Matches: 64, Mismatches: 11, Indels: 16
0.70 0.12 0.18
Matches are distributed among these distances:
35 5 0.08
36 4 0.06
37 21 0.33
38 9 0.14
39 16 0.25
40 4 0.06
41 5 0.08
ACGTcount: A:0.38, C:0.20, G:0.05, T:0.37
Consensus pattern (37 bp):
CATACATTAATTTCCAACTCAATAACTTGATTAAATG
Found at i:58936077 original size:13 final size:12
Alignment explanation
Indices: 58936058--58936087 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
58936048 CTCAAACGAT
58936058 CAAATTTTCACA
1 CAAATTTTCACA
58936070 CGAAATTTTCACA
1 C-AAATTTTCACA
58936083 CAAAT
1 CAAAT
58936088 AACTTAACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.23, G:0.03, T:0.30
Consensus pattern (12 bp):
CAAATTTTCACA
Found at i:58938639 original size:42 final size:43
Alignment explanation
Indices: 58938590--58938695 Score: 142
Period size: 42 Copynumber: 2.5 Consensus size: 43
58938580 ATTTATGTGG
* * *
58938590 ACAAATGCCGCTATAGAACATGATCTTTAGCAACGCTTTTCCG
1 ACAAATGCCGCTAAAGAACATGATCTTTAGCAACACTTTTCCC
* **
58938633 A-AAATGCCGCTAAAGAGCATGATCTTTAGCGGCACTTTTCCC
1 ACAAATGCCGCTAAAGAACATGATCTTTAGCAACACTTTTCCC
*
58938675 ACAAACGCCGCTAAAGAACAT
1 ACAAATGCCGCTAAAGAACAT
58938696 AACTTTTAGT
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
42 36 0.67
43 18 0.33
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (43 bp):
ACAAATGCCGCTAAAGAACATGATCTTTAGCAACACTTTTCCC
Found at i:58938704 original size:43 final size:43
Alignment explanation
Indices: 58938625--58938818 Score: 164
Period size: 43 Copynumber: 4.6 Consensus size: 43
58938615 TTTAGCAACG
* * * *
58938625 CTTTT-CCGAAAATGCCGCTAAAGAGCATGA-TCTTTAGCGGCA
1 CTTTTCCCTAAAACGCCGCTAAAGAACATAACT-TTTAGCGGCA
* *
58938667 CTTTTCCC-ACAAACGCCGCTAAAGAACATAACTTTTAGTGGCG
1 CTTTTCCCTA-AAACGCCGCTAAAGAACATAACTTTTAGCGGCA
* * * *
58938710 C--TTCCCTAAAGATGCTGCTAAATAACATAACCTTTAGCGGCA
1 CTTTTCCCTAAA-ACGCCGCTAAAGAACATAACTTTTAGCGGCA
* ** * * **
58938752 CTTTCCCCTAAAACGCCATTAAAAAACATGACTTTTAGCAACA
1 CTTTTCCCTAAAACGCCGCTAAAGAACATAACTTTTAGCGGCA
*
58938795 CTTTTCCCAAAAACGCCGCTAAAG
1 CTTTTCCCTAAAACGCCGCTAAAG
58938819 GTCATGAAAA
Statistics
Matches: 119, Mismatches: 26, Indels: 13
0.75 0.16 0.08
Matches are distributed among these distances:
41 7 0.06
42 33 0.28
43 70 0.59
44 9 0.08
ACGTcount: A:0.33, C:0.27, G:0.14, T:0.25
Consensus pattern (43 bp):
CTTTTCCCTAAAACGCCGCTAAAGAACATAACTTTTAGCGGCA
Found at i:58944291 original size:24 final size:26
Alignment explanation
Indices: 58944267--58944316 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
58944257 ACAACGCATT
58944267 AATTAAAAATATT-TTTAAATAATTAA
1 AATTAAAAATATTATTTAAATAATT-A
*
58944293 AATTAAAAATATTATTTTAATAAT
1 AATTAAAAATATTATTTAAATAAT
58944317 ATTACATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 13 0.59
27 9 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
AATTAAAAATATTATTTAAATAATTA
Found at i:58944460 original size:16 final size:16
Alignment explanation
Indices: 58944439--58944469 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
58944429 GTTATTATGA
58944439 TTGATTAAAAAACAAC
1 TTGATTAAAAAACAAC
58944455 TTGATTAAAAAACAA
1 TTGATTAAAAAACAA
58944470 GTATTTGGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.10, G:0.06, T:0.26
Consensus pattern (16 bp):
TTGATTAAAAAACAAC
Found at i:58944728 original size:120 final size:120
Alignment explanation
Indices: 58944598--58945013 Score: 685
Period size: 119 Copynumber: 3.5 Consensus size: 120
58944588 AATTATTTTA
* *
58944598 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATATTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT-AAATTATATTT
* *
58944662 TATAGTATCATATATTATGATTTTAGTAAATTCATATAACAATATTGATTATTAAG
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
* *
58944718 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATCATCTTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
* *
58944783 ATA-TATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTTAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
* *
58944837 AATTTTATTTAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
*
58944902 ATAGTATCATATATTATGCTTTGAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
*
58944957 AATTTTATTAAATTATATATTTT-ATTATAATATATTTAATAATAATTATGATTAAAT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATG-TTAAAT
58945014 ATGATTAAAT
Statistics
Matches: 277, Mismatches: 16, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
119 138 0.50
120 137 0.49
121 2 0.01
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
Found at i:58944747 original size:18 final size:17
Alignment explanation
Indices: 58944719--58944753 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
58944709 ATTATTAAGA
*
58944719 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
58944736 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
58944754 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:58944862 original size:13 final size:15
Alignment explanation
Indices: 58944842--58944897 Score: 64
Period size: 15 Copynumber: 3.8 Consensus size: 15
58944832 TTTAGAATTT
58944842 TATTTAATTAT-ATA
1 TATTTAATTATAATA
58944856 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
58944870 TATTTAATAATAAT-
1 TATTTAATTATAATA
58944884 TATGTTAAATTATA
1 TAT-TT-AATTATA
58944898 TTTTATAGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
13 9 0.25
14 8 0.22
15 13 0.36
16 6 0.17
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:58944872 original size:16 final size:16
Alignment explanation
Indices: 58944851--58944897 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
58944841 TTATTTAATT
58944851 ATATATTTTAATTATA
1 ATATATTTTAATTATA
*
58944867 ATATA-TTTAATAATA
1 ATATATTTTAATTATA
*
58944882 AT-TATGTTAAATTATA
1 ATATAT-TTTAATTATA
58944898 TTTTATAGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 2 0.08
15 11 0.42
16 13 0.50
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
ATATATTTTAATTATA
Found at i:58945205 original size:44 final size:44
Alignment explanation
Indices: 58945156--58945244 Score: 119
Period size: 44 Copynumber: 2.0 Consensus size: 44
58945146 ACCTCTATTC
58945156 CATTCAACCAAACACA-AGA-ATACTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACA-ATAGATATACTATTACGCCT-TATTCCATTA
* * *
58945200 CATTCAACCAAACAATTGATTTGCTATTACGCCTTATTCCATTA
1 CATTCAACCAAACAATAGATATACTATTACGCCTTATTCCATTA
58945244 C
1 C
58945245 GCTTCTATTC
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
43 1 0.03
44 27 0.68
45 12 0.30
ACGTcount: A:0.35, C:0.28, G:0.06, T:0.31
Consensus pattern (44 bp):
CATTCAACCAAACAATAGATATACTATTACGCCTTATTCCATTA
Found at i:58945255 original size:16 final size:16
Alignment explanation
Indices: 58945225--58945270 Score: 76
Period size: 16 Copynumber: 2.9 Consensus size: 16
58945215 TTGATTTGCT
58945225 ATTACGCCT-TATTCC
1 ATTACGCCTCTATTCC
*
58945240 ATTACGCTTCTATTCC
1 ATTACGCCTCTATTCC
58945256 ATTACGCCTCTATTC
1 ATTACGCCTCTATTC
58945271 AAATACAGCG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
15 8 0.29
16 20 0.71
ACGTcount: A:0.20, C:0.33, G:0.07, T:0.41
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:58948026 original size:27 final size:28
Alignment explanation
Indices: 58947976--58948033 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 28
58947966 ATTATGGTCA
*
58947976 AAGTTGTTACTAAAGTCAGTTAGCAGTT
1 AAGTGGTTACTAAAGTCAGTTAGCAGTT
**
58948004 AAGTGGTTACT-AAGTTGGTTAGCAGTT
1 AAGTGGTTACTAAAGTCAGTTAGCAGTT
58948031 AAG
1 AAG
58948034 AAGTTAGCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 17 0.63
28 10 0.37
ACGTcount: A:0.31, C:0.09, G:0.26, T:0.34
Consensus pattern (28 bp):
AAGTGGTTACTAAAGTCAGTTAGCAGTT
Found at i:58952599 original size:27 final size:28
Alignment explanation
Indices: 58952557--58952614 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 28
58952547 ATTATGGTCA
* *
58952557 AAGTTGTTACTAAAGTTTGTTAGCAGTT
1 AAGTGGTTACTAAAGTTGGTTAGCAGTT
*
58952585 AAGTGGTTACT-AAGTTGGTTAGTAGTT
1 AAGTGGTTACTAAAGTTGGTTAGCAGTT
58952612 AAG
1 AAG
58952615 AAGTTAGCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 17 0.63
28 10 0.37
ACGTcount: A:0.29, C:0.05, G:0.26, T:0.40
Consensus pattern (28 bp):
AAGTGGTTACTAAAGTTGGTTAGCAGTT
Found at i:58952620 original size:27 final size:28
Alignment explanation
Indices: 58952562--58952620 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
58952552 GGTCAAAGTT
* **
58952562 GTTACTAAAGTTTGTTAGCAGTTAAGTG
1 GTTACTAAAGTTGGTTAGCAGTTAAGAA
*
58952590 GTTACT-AAGTTGGTTAGTAGTTAAGAA
1 GTTACTAAAGTTGGTTAGCAGTTAAGAA
58952617 GTTA
1 GTTA
58952621 GCTACTGCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 21 0.78
28 6 0.22
ACGTcount: A:0.31, C:0.05, G:0.25, T:0.39
Consensus pattern (28 bp):
GTTACTAAAGTTGGTTAGCAGTTAAGAA
Found at i:58954112 original size:21 final size:22
Alignment explanation
Indices: 58954081--58954121 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
58954071 AACATAAATC
*
58954081 CTAAGCCCCTAATCCTTAAACT
1 CTAAGCCCCTAAACCTTAAACT
58954103 CTAA-CCCCTAAACCTTAAA
1 CTAAGCCCCTAAACCTTAAA
58954122 TACCAACCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.37, C:0.37, G:0.02, T:0.24
Consensus pattern (22 bp):
CTAAGCCCCTAAACCTTAAACT
Found at i:58954129 original size:21 final size:21
Alignment explanation
Indices: 58954086--58954143 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
58954076 AAATCCTAAG
* *
58954086 CCCCTAATCCTTAAACTCTAA
1 CCCCTAAACCTTAAACTCCAA
58954107 CCCCTAAACCTTAAA-TACCAA
1 CCCCTAAACCTTAAACT-CCAA
* *
58954128 CCCTTAAACCATAAAC
1 CCCCTAAACCTTAAAC
58954144 CATAATCTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
20 1 0.03
21 30 0.97
ACGTcount: A:0.40, C:0.38, G:0.00, T:0.22
Consensus pattern (21 bp):
CCCCTAAACCTTAAACTCCAA
Found at i:58954161 original size:15 final size:15
Alignment explanation
Indices: 58954137--58954173 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
58954127 ACCCTTAAAC
58954137 CATAAA-CCATAATCT
1 CATAAACCCATAAT-T
58954152 C-TAAACCCATAATT
1 CATAAACCCATAATT
58954166 CATAAACC
1 CATAAACC
58954174 TTAAAATAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.46, C:0.30, G:0.00, T:0.24
Consensus pattern (15 bp):
CATAAACCCATAATT
Found at i:58954224 original size:14 final size:14
Alignment explanation
Indices: 58954190--58954248 Score: 55
Period size: 14 Copynumber: 4.2 Consensus size: 14
58954180 TAGTAACACT
* * *
58954190 TAAACCTTATACCT
1 TAAACCCTAAACCA
58954204 TAAACCCTAAACCA
1 TAAACCCTAAACCA
* * *
58954218 TATACCCTCAATCA
1 TAAACCCTAAACCA
*
58954232 TAAACCCTAAACTA
1 TAAACCCTAAACCA
58954246 TAA
1 TAA
58954249 TGATAATTAA
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
14 35 1.00
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.25
Consensus pattern (14 bp):
TAAACCCTAAACCA
Found at i:58954620 original size:74 final size:76
Alignment explanation
Indices: 58954534--58954709 Score: 232
Period size: 74 Copynumber: 2.3 Consensus size: 76
58954524 AGATAAAATG
*
58954534 CTTTTTT-CGGCGTTTTTCAAAAAGAGCCGCTAATGCCACTAAAGCTCAACATAGAA-CACAGCG
1 CTTTTTTGCGGCGTTTTTCAAAAAGAGCCGCTAATGCCACTAAAGCTCAACATAAAATCACAGCG
*
58954597 TTGTGTTTAAT
66 TTGTGCTTAAT
* * * * *
58954608 -TTTTTTGCGGCGTTTTTCAAAAAGCGCTGCTAATGCCACTGAAGCTCAACATAAAATGACGGCG
1 CTTTTTTGCGGCGTTTTTCAAAAAGAGCCGCTAATGCCACTAAAGCTCAACATAAAATCACAGCG
58954672 TTGTGCTTAAT
66 TTGTGCTTAAT
* *
58954683 CTTTTTACGGCGACGTTTTTCAAAAAG
1 CTTTTT--TGCGGCGTTTTTCAAAAAG
58954710 TCGCTAATGC
Statistics
Matches: 88, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
73 6 0.07
74 45 0.51
75 15 0.17
76 5 0.06
78 17 0.19
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.32
Consensus pattern (76 bp):
CTTTTTTGCGGCGTTTTTCAAAAAGAGCCGCTAATGCCACTAAAGCTCAACATAAAATCACAGCG
TTGTGCTTAAT
Found at i:58955451 original size:22 final size:21
Alignment explanation
Indices: 58955426--58955469 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
58955416 TGATAAACTT
58955426 TAATATATA-ATTATATTATTTA
1 TAATATATATATTA-ATT-TTTA
*
58955448 TAATTTATATATTAATTTTTA
1 TAATATATATATTAATTTTTA
58955469 T
1 T
58955470 CAACTTAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 11 0.55
23 4 0.20
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TAATATATATATTAATTTTTA
Found at i:58967605 original size:17 final size:16
Alignment explanation
Indices: 58967572--58967610 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
58967562 CCCCAAATTA
* *
58967572 TTTTTTTTCTTTTTTT
1 TTTTTTTTCTCTCTTT
58967588 TATTTTTTTCTCTCTTT
1 T-TTTTTTTCTCTCTTT
58967605 TTTTTT
1 TTTTTT
58967611 ATGCTTTAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.03, C:0.10, G:0.00, T:0.87
Consensus pattern (16 bp):
TTTTTTTTCTCTCTTT
Found at i:58968654 original size:18 final size:16
Alignment explanation
Indices: 58968629--58968684 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 16
58968619 CCAAATAAGT
58968629 AAAATAAAATAAAATA
1 AAAATAAAATAAAATA
*
58968645 AAGTAAT-AAATAAAGTA
1 AA--AATAAAATAAAATA
58968662 AAAATAATAATAAAAATA
1 AAAATAA-AAT-AAAATA
58968680 AAAAT
1 AAAAT
58968685 TGGGTTGCCT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
15 3 0.09
16 3 0.09
17 14 0.42
18 13 0.39
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (16 bp):
AAAATAAAATAAAATA
Found at i:58968657 original size:12 final size:11
Alignment explanation
Indices: 58968621--58968681 Score: 65
Period size: 12 Copynumber: 5.6 Consensus size: 11
58968611 ATTAATATCC
58968621 AAAT-AAGT-A
1 AAATAAAGTAA
*
58968630 AAATAAAAT-A
1 AAATAAAGTAA
58968640 AAATAAAGTAA
1 AAATAAAGTAA
58968651 TAAATAAAGTAA
1 -AAATAAAGTAA
*
58968663 AAATAATAATAA
1 AAATAA-AGTAA
58968675 AAATAAA
1 AAATAAA
58968682 AATTGGGTTG
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
9 4 0.09
10 12 0.27
11 8 0.18
12 21 0.47
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (11 bp):
AAATAAAGTAA
Found at i:58983799 original size:43 final size:43
Alignment explanation
Indices: 58983693--58983934 Score: 227
Period size: 43 Copynumber: 5.8 Consensus size: 43
58983683 CCGCTAAAAG
* * * *
58983693 TCATGAACTTTACCGGCGCTTATCCCACAAACGCCGCTA-AGA
1 TCATGAATTTTAGCGGCGCTTTTTCCACAAACGCCGCTATAGA
*
58983735 TCAT-AACTTTTAGCGGCGCTTTTTCCACAAACGCCGCTATAGG
1 TCATGAA-TTTTAGCGGCGCTTTTTCCACAAACGCCGCTATAGA
*
58983778 TCATGAATTTTAGCGGCGC--TTTCC-C---CGCCGCTATAGG
1 TCATGAATTTTAGCGGCGCTTTTTCCACAAACGCCGCTATAGA
* * * *
58983815 TCATCATTTTTAGCGGTGCTTTTCCCACAAACGCCGCTATAGA
1 TCATGAATTTTAGCGGCGCTTTTTCCACAAACGCCGCTATAGA
* *
58983858 ACA--AATCTTTAGCGGCGCTTTTTCATACAAACGCCGCTATAGA
1 TCATGAAT-TTTAGCGGCGCTTTTTC-CACAAACGCCGCTATAGA
* ** * *
58983901 AC-TGACCTTTAGCGACGCTTTTTACACAAACGCC
1 TCATGAATTTTAGCGGCGCTTTTTCCACAAACGCC
58983935 ACTAAAAACA
Statistics
Matches: 167, Mismatches: 20, Indels: 26
0.78 0.09 0.12
Matches are distributed among these distances:
37 28 0.17
39 4 0.02
40 2 0.01
41 9 0.05
42 56 0.34
43 65 0.39
44 3 0.02
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (43 bp):
TCATGAATTTTAGCGGCGCTTTTTCCACAAACGCCGCTATAGA
Found at i:58983810 original size:37 final size:37
Alignment explanation
Indices: 58983766--58983836 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
58983756 TTTCCACAAA
*
58983766 CGCCGCTATAGGTCATGAATTTTAGCGGCGCTTTCCC
1 CGCCGCTATAGGTCATCAATTTTAGCGGCGCTTTCCC
* *
58983803 CGCCGCTATAGGTCATCATTTTTAGCGGTGCTTT
1 CGCCGCTATAGGTCATCAATTTTAGCGGCGCTTT
58983837 TCCCACAAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.15, C:0.27, G:0.24, T:0.34
Consensus pattern (37 bp):
CGCCGCTATAGGTCATCAATTTTAGCGGCGCTTTCCC
Found at i:58983878 original size:79 final size:78
Alignment explanation
Indices: 58983724--58983878 Score: 213
Period size: 80 Copynumber: 2.0 Consensus size: 78
58983714 ATCCCACAAA
* **
58983724 CGCCGCTAAGATCATAACTTTTAGCGGCGCTTTTTCCACAAACGCCGCTATAGGTCATGAATTTT
1 CGCCGCTAAGATCATAACTTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGAACA-GAATTTT
58983789 AGCGGCGCTTTCCC
65 AGCGGCGCTTTCCC
* * * *
58983803 CGCCGCTATAGGTCATCATTTTTAGCGGTGCTTTTCCCACAAACGCCGCTATAGAACA-AATCTT
1 CGCCGCTA-AGATCATAACTTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGAACAGAAT-TT
58983867 TAGCGGCGCTTT
64 TAGCGGCGCTTT
58983879 TTCATACAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
78 3 0.04
79 22 0.33
80 42 0.63
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.30
Consensus pattern (78 bp):
CGCCGCTAAGATCATAACTTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGAACAGAATTTTA
GCGGCGCTTTCCC
Found at i:58983912 original size:122 final size:122
Alignment explanation
Indices: 58983701--58983921 Score: 304
Period size: 122 Copynumber: 1.8 Consensus size: 122
58983691 AGTCATGAAC
*
58983701 TTTACCGGCGCTTATCCCACAAACGCCGCTAAGATCATAACTTTTAGCGGCGCTTTTTCCACAAA
1 TTTACCGGCGCTTATCCCACAAACGCCGCTAAGAACATAACTTTTAGCGGCGCTTTTTCCACAAA
** * *
58983766 CGCCGCTATAGGTCATGAATTTTAGCGGCGCTTTCCCCGCCGCTATAGGTCATCATT
66 CGCCGCTATAGAACATGAACTTTAGCGACGCTTTCCCCGCCGCTATAGGTCATCATT
* * * *
58983823 TTTAGCGGTGCTTTTCCCACAAACGCCGCTATAGAACA-AA-TCTTTAGCGGCGCTTTTTCATAC
1 TTTACCGGCGCTTATCCCACAAACGCCGCTA-AGAACATAACT-TTTAGCGGCGCTTTTTC-CAC
*
58983886 AAACGCCGCTATAGAAC-TGACCTTTAGCGACGCTTT
63 AAACGCCGCTATAGAACATGAACTTTAGCGACGCTTT
58983922 TTACACAAAC
Statistics
Matches: 86, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
121 1 0.01
122 63 0.73
123 22 0.26
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.29
Consensus pattern (122 bp):
TTTACCGGCGCTTATCCCACAAACGCCGCTAAGAACATAACTTTTAGCGGCGCTTTTTCCACAAA
CGCCGCTATAGAACATGAACTTTAGCGACGCTTTCCCCGCCGCTATAGGTCATCATT
Found at i:58984290 original size:43 final size:43
Alignment explanation
Indices: 58984207--58984293 Score: 102
Period size: 43 Copynumber: 2.0 Consensus size: 43
58984197 ACATATGCAA
* * * * * *
58984207 GGTAATAAAACATACAATGCATTTTCTTTATTAAGTAAATCTT
1 GGTAATAAAACATACAATACATGTACTTAATCAAGGAAATCTT
* *
58984250 GGTAATAAAAGATATAATACATGTACTTAATCAAGGAAATCTT
1 GGTAATAAAACATACAATACATGTACTTAATCAAGGAAATCTT
58984293 G
1 G
58984294 TGATGAACTC
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (43 bp):
GGTAATAAAACATACAATACATGTACTTAATCAAGGAAATCTT
Found at i:58987974 original size:21 final size:21
Alignment explanation
Indices: 58987950--58987989 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
58987940 CCTAGCCCTT
* *
58987950 AACCCTTAAACCTTAAACCCC
1 AACCATTAAACCATAAACCCC
58987971 AACCATTAAACCATAAACC
1 AACCATTAAACCATAAACC
58987990 ATAAATCATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.38, G:0.00, T:0.17
Consensus pattern (21 bp):
AACCATTAAACCATAAACCCC
Found at i:58987987 original size:7 final size:7
Alignment explanation
Indices: 58987971--58988119 Score: 79
Period size: 7 Copynumber: 21.1 Consensus size: 7
58987961 CTTAAACCCC
58987971 AACCATTA
1 AACCA-TA
58987979 AACCATA
1 AACCATA
58987986 AACCATA
1 AACCATA
*
58987993 AATCATA
1 AACCATA
*
58988000 ATCCATA
1 AACCATA
*
58988007 ATCCATA
1 AACCATA
*
58988014 ATCCATA
1 AACCATA
*
58988021 ATCCATA
1 AACCATA
*
58988028 ATCCATA
1 AACCATA
*
58988035 ATCCATA
1 AACCATA
* *
58988042 AA-CTTT
1 AACCATA
*
58988048 AA-GATA
1 AACCATA
*
58988054 GTAACTCCTA
1 --AAC-CATA
* *
58988064 AAACTTA
1 AACCATA
*
58988071 AACCCTA
1 AACCATA
58988078 AACCATA
1 AACCATA
* *
58988085 TACCCTA
1 AACCATA
58988092 AACCATA
1 AACCATA
* *
58988099 TACCCTA
1 AACCATA
58988106 AACCATA
1 AACCATA
58988113 AA-CATA
1 AACCATA
58988119 A
1 A
58988120 TTAATTCAAT
Statistics
Matches: 113, Mismatches: 24, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
6 10 0.09
7 92 0.81
8 9 0.08
10 2 0.02
ACGTcount: A:0.48, C:0.27, G:0.01, T:0.24
Consensus pattern (7 bp):
AACCATA
Found at i:58988005 original size:21 final size:22
Alignment explanation
Indices: 58987981--58988042 Score: 94
Period size: 21 Copynumber: 3.0 Consensus size: 22
58987971 AACCATTAAA
*
58987981 CCATAAACCATAAAT-CATAAT
1 CCATAATCCATAAATCCATAAT
58988002 CCATAATCCAT-AATCCATAAT
1 CCATAATCCATAAATCCATAAT
58988023 CCATAATCCAT-AATCCATAA
1 CCATAATCCATAAATCCATAA
58988043 ACTTTAAGAT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
20 3 0.08
21 36 0.92
ACGTcount: A:0.47, C:0.27, G:0.00, T:0.26
Consensus pattern (22 bp):
CCATAATCCATAAATCCATAAT
Done.