Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold290
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: 778129
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.29
Warning! 94969 characters in sequence are not A, C, G, or T
File 1 of 3
Found at i:2109 original size:44 final size:43
Alignment explanation
Indices: 2059--2171 Score: 124
Period size: 44 Copynumber: 2.6 Consensus size: 43
2049 CTTAGTCTAT
* *
2059 TCCACTGCAATTTCAGGGAGATAGGATTAT-CAGCT-TTAATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATT-TGC--CTATTAATCTGC
* * *
2103 TCCACTGCAACTTCAAGAAGATAAGATTTGCCTACTTAGTCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTTGCCTA-TTAATCTGC
2147 TCCA-TGCAACTTCAGGGAGATAAGA
1 TCCACTGCAACTTCAGGGAGATAAGA
2172 CTAGATGCAA
Statistics
Matches: 59, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
42 2 0.03
43 20 0.34
44 37 0.63
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.28
Consensus pattern (43 bp):
TCCACTGCAACTTCAGGGAGATAAGATTTGCCTATTAATCTGC
Found at i:2350 original size:44 final size:44
Alignment explanation
Indices: 2205--2367 Score: 127
Period size: 44 Copynumber: 3.7 Consensus size: 44
2195 ACTTTAATCC
* * * ** * *
2205 GCTCCACTGCAACTTCAAGGAGATAGGA-TTGTCGGCTTTAATCT
1 GCTCCACTGCAACTTC-AGAAGATAAGACTTGCCATCTTCAGTCT
* * * *
2249 GCTCCAGTGCAACTTCGGGAAGATAAGATTTTCCATCTTCAGTCT
1 GCTCCACTGCAACTTC-AGAAGATAAGACTTGCCATCTTCAGTCT
*
2294 GC-CTCACTGCAACTTCAGAAGGATAAGACTTG-CTTACTT-AGTCT
1 GCTC-CACTGCAACTTCAGAA-GATAAGACTTGCCAT-CTTCAGTCT
*
2338 GCTCCACTGCAACTTCAGGGAGATAAGACT
1 GCTCCACTGCAACTTCA-GAAGATAAGACT
2368 AGATGCAATC
Statistics
Matches: 96, Mismatches: 17, Indels: 12
0.77 0.14 0.10
Matches are distributed among these distances:
44 58 0.60
45 38 0.40
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (44 bp):
GCTCCACTGCAACTTCAGAAGATAAGACTTGCCATCTTCAGTCT
Found at i:2573 original size:217 final size:217
Alignment explanation
Indices: 2197--2892 Score: 1126
Period size: 217 Copynumber: 3.2 Consensus size: 217
2187 TCTCTGCAAC
** * * * *
2197 TTTAATCCGCTCCACTGCAACTTCAAGGAGATAGGATTGTCGGCTTTAATCTGCTCCAGTGCAAC
1 TTTAATCCTATCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAATCTACTCCACTGCAAC
* * * *
2262 TTC-GGGAAGATAAGATTTTCCATCTTCAGTCTGCCTCACTGCAACTTCAGAAGGATAAGACTTG
66 TTCAGGG-AGGTAAGATTTACCATCTTCAATCTGCCTCACTGCAACTTCAGGAGGATAAGACTTG
* * * *
2326 CTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCAATCTACTTTCTGCAAC
130 CTTACTTAGCCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAAC
*
2391 ATCAGAGAGATAAGATCTGTGAT
195 TTCAGAGAGATAAGATCTGTGAT
2414 TTTAATCCTATCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAATCTACTCCACTGCAAC
1 TTTAATCCTATCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAATCTACTCCACTGCAAC
2479 TTCAGGGAGGTAAGATTTACCATCTTCAATCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGC
66 TTCAGGGAGGTAAGATTTACCATCTTCAATCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGC
* * * *
2544 GTACTTAGCCTGTTCCACTGCATCTTCAGGGAGATAAGACTAGATGCGACCTGCTCTCTGCAACT
131 TTACTTAGCCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACT
2609 TCAGAGAGATAAGATCTGTGAT
196 TCAGAGAGATAAGATCTGTGAT
2631 TTTAATCCTATCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAATCTACTCCACTGCAAC
1 TTTAATCCTATCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAATCTACTCCACTGCAAC
*
2696 TTCAGGGAGGTAAGATTTACCATCTTCAATCTGCCTCACTGCAACTTCAGGAGGATAAGACTTAC
66 TTCAGGGAGGTAAGATTTACCATCTTCAATCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGC
* *
2761 TTACTTAGCCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGGTGCGATCTGCTCTCAGCAACT
131 TTACTTAGCCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACT
2826 TCAGAGAGATAAGATCTGTGAT
196 TCAGAGAGATAAGATCTGTGAT
* * * *
2848 TTTAAT-TTGTTCCACTGCAACTTCAGGGAGATAAGATTATTGGCT
1 TTTAATCCT-ATCCACTGCAACTTCAGGGAGATAGGATTATCGGCT
2893 ACGGATTTAT
Statistics
Matches: 447, Mismatches: 30, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
216 1 0.00
217 443 0.99
218 3 0.01
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (217 bp):
TTTAATCCTATCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAATCTACTCCACTGCAAC
TTCAGGGAGGTAAGATTTACCATCTTCAATCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGC
TTACTTAGCCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACT
TCAGAGAGATAAGATCTGTGAT
Found at i:2782 original size:44 final size:45
Alignment explanation
Indices: 2298--2801 Score: 207
Period size: 44 Copynumber: 11.6 Consensus size: 45
2288 CAGTCTGCCT
* * **
2298 CACTGCAACTTCAGAAG-GATAAGACTTGCTTACTTAGTCTGCTC
1 CACTGCAACTTCAGGAGAGATAAGACTTACTTACTTAACCTGCTC
** * * *
2342 CACTGCAACTTCAGG-GAGATAAGAC-TAGATGC--AATCTACT-
1 CACTGCAACTTCAGGAGAGATAAGACTTACTTACTTAACCTGCTC
** * *
2382 TTCTGCAACATCA-GAGAGATAAGATCTGTGA-TT--TTAATCCT-ATC
1 CACTGCAACTTCAGGAGAGATAAGA-CT-T-ACTTACTTAA-CCTGCTC
* ** * *
2426 CACTGCAACTTCAGG-GAGATAGGA-TTA-TCGGCTTTAATCTACTC
1 CACTGCAACTTCAGGAGAGATAAGACTTACT-TAC-TTAACCTGCTC
* * * *
2470 CACTGCAACTTCAGG-GAGGTAAGATTTAC-CATCTTCAATCTGC-C
1 CACTGCAACTTCAGGAGAGATAAGACTTACTTA-CTT-AACCTGCTC
* * * *
2514 TCACTGCAACTTCAGGAG-GATAAGACTTGCGTACTTAGCCTGTTC
1 -CACTGCAACTTCAGGAGAGATAAGACTTACTTACTTAACCTGCTC
* ** * *
2559 CACTGCATCTTCAGG-GAGATAAGAC-TAGATGC--GACCTGCT-
1 CACTGCAACTTCAGGAGAGATAAGACTTACTTACTTAACCTGCTC
* *
2599 CTCTGCAACTTCA-GAGAGATAAGATCTGTGA-TT--TTAATCCT-ATC
1 CACTGCAACTTCAGGAGAGATAAGA-CT-T-ACTTACTTAA-CCTGCTC
* ** * *
2643 CACTGCAACTTCAGG-GAGATAGGA-TTA-TCGGCTTTAATCTACTC
1 CACTGCAACTTCAGGAGAGATAAGACTTACT-TAC-TTAACCTGCTC
* * * *
2687 CACTGCAACTTCAGG-GAGGTAAGATTTAC-CATCTTCAATCTGC-C
1 CACTGCAACTTCAGGAGAGATAAGACTTACTTA-CTT-AACCTGCTC
*
2731 TCACTGCAACTTCAGGAG-GATAAGACTTACTTACTTAGCCTGCTC
1 -CACTGCAACTTCAGGAGAGATAAGACTTACTTACTTAACCTGCTC
2776 CACTGCAACTTCAGG-GAGATAAGACT
1 CACTGCAACTTCAGGAGAGATAAGACT
2802 AGGTGCGATC
Statistics
Matches: 351, Mismatches: 60, Indels: 98
0.69 0.12 0.19
Matches are distributed among these distances:
39 2 0.01
40 43 0.12
41 15 0.04
42 2 0.01
43 22 0.06
44 184 0.52
45 79 0.23
46 4 0.01
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (45 bp):
CACTGCAACTTCAGGAGAGATAAGACTTACTTACTTAACCTGCTC
Found at i:37508 original size:44 final size:44
Alignment explanation
Indices: 37459--38170 Score: 504
Period size: 44 Copynumber: 16.3 Consensus size: 44
37449 CTTAGTCTAT
* * *
37459 TCCACTGCAACTTTAGGGAGATAGGATTATCAGCTTTAATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTGTCAGCTTTAATCTGC
* * *
37503 TCCACTGCAACTTCAGGAAGATAAGATTTGCCTA-C-TTAGTCTGC
1 TCCACTGCAACTTCAGGGAGATAAGA-TTGTC-AGCTTTAATCTGC
* * * *
37547 TCCATTGCAACTTTAGAGAGATAAGATCTGT--GATTATAATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGAT-TGTCAGCTT-TAATCTGC
* * *
37591 TCCACTTCAACTTCAGGGAGATAGGATTGTCGGCTTTAATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTGTCAGCTTTAATCTGC
* * * *
37635 TCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTG-
1 TCCACTGCAACTTCAGGGAGATAAGA-TTGTCAGCTTTAATCTGC
* **
37679 TCTCACTGCAACTTCA-GGAGGATAAGACTTGCCTA-C-TTAGCCTGC
1 TC-CACTGCAACTTCAGGGA-GATAAGA-TTGTC-AGCTTTAATCTGC
* * ***
37724 TCCACTGCAACTTCAGGGAGATAAGA--CT-AGATGCGATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTGTCAGCTTTAATCTGC
* * * *
37765 T-CTCTGCAACTTCAGAGAGATAAGATCTGTGA-TTTTAATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGAT-TGTCAGCTTTAATCTGC
* * *
37808 TCCACTTCAACTTCAGGGAGATAGGATTGTCGGCTTTAATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTGTCAGCTTTAATCTGC
* * * *
37852 TCCACTGCAACTTCAGGGAGATAAGATTTGTCATCTTCAGTCCGC
1 TCCACTGCAACTTCAGGGAGATAAGA-TTGTCAGCTTTAATCTGC
* **
37897 -CTCACTGCAACTTCA-GGAGGATAAGACTTGCTTA-C-TTAGCCTGC
1 TC-CACTGCAACTTCAGGGA-GATAAGA-TTG-TCAGCTTTAATCTGC
* * * * **
37941 TCCACTGCAACTTCAGGGAGATAAGATTTTTCATCTTCAGTCCAC
1 TCCACTGCAACTTCAGGGAGATAAGA-TTGTCAGCTTTAATCTGC
* **
37986 -CTCACTGCAACTTCA-GGAGGATAAGACTTGCTTA-C-TTAGCCTGC
1 TC-CACTGCAACTTCAGGGA-GATAAGA-TTG-TCAGCTTTAATCTGC
* * ***
38030 TCCACTGCAACTTCAGGGAGATAAGA--CT-AGATGCGATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTGTCAGCTTTAATCTGC
* * * * *
38071 T-CTCTGCAACTTCAGAGAGATAAGATCTGTGA-TTTTAATCCGC
1 TCCACTGCAACTTCAGGGAGATAAGAT-TGTCAGCTTTAATCTGC
* * *
38114 TCCACTTCAACTTCAGGGAGATAGGATTGTCGGCTTTAATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTGTCAGCTTTAATCTGC
38158 TCCACTGCAACTT
1 TCCACTGCAACTT
38171 NNNNNNNNNN
Statistics
Matches: 524, Mismatches: 101, Indels: 86
0.74 0.14 0.12
Matches are distributed among these distances:
39 2 0.00
40 45 0.09
41 10 0.02
43 30 0.06
44 308 0.59
45 123 0.23
46 6 0.01
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (44 bp):
TCCACTGCAACTTCAGGGAGATAAGATTGTCAGCTTTAATCTGC
Found at i:37810 original size:217 final size:220
Alignment explanation
Indices: 37499--37966 Score: 782
Period size: 217 Copynumber: 2.1 Consensus size: 220
37489 CAGCTTTAAT
* * * * * *
37499 CTGCTCCACTGCAACTTCAGGAAGATAAGATTTGCCTACTTAGTCTGCTCCATTGCAACTTTAGA
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTAGCATACTGAGTCTGCTCCA-TGCAACTTCAGA
37564 GAGATAAGATCTGTGATTATAATCTGCTCCACTTCAACTTCAGGGAGATAGGATTGTCGGCTTTA
65 GAGATAAGATCTGTGATTATAATCTGCTCCACTTCAACTTCAGGGAGATAGGATTGTCGGCTTTA
* *
37629 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGTCTCACTGCAACTTC
130 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCCGCCTCACTGCAACTTC
37694 AGGAGGATAAGACTTGCCTACTTAGC
195 AGGAGGATAAGACTTGCCTACTTAGC
*
37720 CTGCTCCACTGCAACTTCAGGGAGATAAGACTAG-ATGC-GA-TCTGCTCTC-TGCAACTTCAGA
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTAGCATACTGAGTCTGCTC-CATGCAACTTCAGA
*
37781 GAGATAAGATCTGTGATTTTAATCTGCTCCACTTCAACTTCAGGGAGATAGGATTGTCGGCTTTA
65 GAGATAAGATCTGTGATTATAATCTGCTCCACTTCAACTTCAGGGAGATAGGATTGTCGGCTTTA
*
37846 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTCATCTTCAGTCCGCCTCACTGCAACTTC
130 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCCGCCTCACTGCAACTTC
*
37911 AGGAGGATAAGACTTGCTTACTTAGC
195 AGGAGGATAAGACTTGCCTACTTAGC
37937 CTGCTCCACTGCAACTTCAGGGAGATAAGA
1 CTGCTCCACTGCAACTTCAGGGAGATAAGA
37967 TTTTTCATCT
Statistics
Matches: 234, Mismatches: 12, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
217 192 0.82
218 7 0.03
219 2 0.01
220 2 0.01
221 31 0.13
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (220 bp):
CTGCTCCACTGCAACTTCAGGGAGATAAGACTAGCATACTGAGTCTGCTCCATGCAACTTCAGAG
AGATAAGATCTGTGATTATAATCTGCTCCACTTCAACTTCAGGGAGATAGGATTGTCGGCTTTAA
TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCCGCCTCACTGCAACTTCA
GGAGGATAAGACTTGCCTACTTAGC
Found at i:37966 original size:89 final size:88
Alignment explanation
Indices: 37459--38170 Score: 483
Period size: 89 Copynumber: 8.1 Consensus size: 88
37449 CTTAGTCTAT
* * * * * *
37459 TCCACTGCAACTTTAGGGAGATAGGA-TT-ATCAGCTTTAATCTGCTCCACTGCAACTTCAGGAA
1 TCCACTGCAACTTCAGGGAGATAAGACTTGCTTA-C-TTAGTCTGCTCCACTGCAACTTCAGGGA
* *
37522 GATAAGATTTG-CCTACTTAGTCTGC
64 GATAAGATTTGTCAT-CTTAGTCCGC
* * * * * *
37547 TCCATTGCAACTTTAGAGAGATAAGATCTGTGATTA--TAATCTGCTCCACTTCAACTTCAGGGA
1 TCCACTGCAACTTCAGGGAGATAAGA-CT-TGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGA
* ** * *
37610 GATAGGA-TTGTCGGCTTTAATCTGC
64 GATAAGATTTGTCATC-TTAGTCCGC
* *
37635 TCCACTGCAACTTCAGGGAGATAAGATTTGC-CATCTTCAGTCTG-TCTCACTGCAACTTCA-GG
1 TCCACTGCAACTTCAGGGAGATAAGACTTGCTTA-CTT-AGTCTGCTC-CACTGCAACTTCAGGG
* *
37697 AGGATAAGACTTG-CCTACTTAG-CCTGC
63 A-GATAAGATTTGTCAT-CTTAGTCC-GC
* * * * * *
37724 TCCACTGCAACTTCAGGGAGATAAGACTAG-ATGC-GA-TCTGCT-CTCTGCAACTTCAGAGAGA
1 TCCACTGCAACTTCAGGGAGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGA
* * * * *
37785 TAAGATCTGTGATTTTAATCTGC
66 TAAGATTTGTCATCTTAGTCCGC
* * ** *
37808 TCCACTTCAACTTCAGGGAGATAGGA-TTG-TCGGCTTTAATCTGCTCCACTGCAACTTCAGGGA
1 TCCACTGCAACTTCAGGGAGATAAGACTTGCT-TAC-TTAGTCTGCTCCACTGCAACTTCAGGGA
37871 GATAAGATTTGTCATCTTCAGTCCGC
64 GATAAGATTTGTCATCTT-AGTCCGC
*
37897 -CTCACTGCAACTTCA-GGAGGATAAGACTTGCTTACTTAGCCTGCTCCACTGCAACTTCAGGGA
1 TC-CACTGCAACTTCAGGGA-GATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGA
* *
37960 GATAAGATTTTTCATCTTCAGTCCAC
64 GATAAGATTTGTCATCTT-AGTCCGC
*
37986 -CTCACTGCAACTTCA-GGAGGATAAGACTTGCTTACTTAGCCTGCTCCACTGCAACTTCAGGGA
1 TC-CACTGCAACTTCAGGGA-GATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGA
* * * *
38049 GATAAGACTAG--ATGC-GA-TCTGC
64 GATAAGATTTGTCAT-CTTAGTCCGC
* * * * * *
38071 T-CTCTGCAACTTCAGAGAGATAAGATCTGTGATT--TTAATCCGCTCCACTTCAACTTCAGGGA
1 TCCACTGCAACTTCAGGGAGATAAGA-CT-TGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGA
* ** * *
38133 GATAGGA-TTGTCGGCTTTAATCTGC
64 GATAAGATTTGTCATC-TTAGTCCGC
38158 TCCACTGCAACTT
1 TCCACTGCAACTT
38171 NNNNNNNNNN
Statistics
Matches: 506, Mismatches: 77, Indels: 82
0.76 0.12 0.12
Matches are distributed among these distances:
83 4 0.01
84 102 0.20
85 16 0.03
86 11 0.02
87 19 0.04
88 139 0.27
89 201 0.40
90 9 0.02
91 2 0.00
92 3 0.01
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (88 bp):
TCCACTGCAACTTCAGGGAGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGA
TAAGATTTGTCATCTTAGTCCGC
Found at i:38127 original size:217 final size:215
Alignment explanation
Indices: 37552--38130 Score: 658
Period size: 217 Copynumber: 2.7 Consensus size: 215
37542 TCTGCTCCAT
* * * * *
37552 TGCAACTTTAGAGAGATAAGATCTGTGATTATAATCTGCTCCACTTCAACTTCAGGGAGATAGGA
1 TGCAACTTCAGAGAGATAAGATCTGTGATTTTAACCTGCTCCACTGCAACTTCAGGGAGATAAGA
* * *
37617 TTGTCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTG-TC
66 TAGTC-GC--TAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTCATCTTCAGTCCGCTC
37681 TCACTGCAACTTCAGGAGGATAAGACTTGCCTACTTAGCCTGCTCCACTGCAACTTCAGGGAGAT
128 TCACTGCAACTTCAGGAGGATAAGACTTGCCTACTTAGCCTGCTCCACTGCAACTTCAGGGAGAT
** *
37746 AAGACTAGATGCGATCTGCTCTC
193 AAGACTAGATGCGATCACCTCAC
* * *
37769 TGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCTGCTCCACTTCAACTTCAGGGAGATAGGA
1 TGCAACTTCAGAGAGATAAGATCTGTGATTTTAACCTGCTCCACTGCAACTTCAGGGAGATAAGA
*
37834 TTGTCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTCATCTTCAGTCCGC-C
66 TAGTC-GC--TAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTCATCTTCAGTCCGCTC
*
37898 TCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGCCTGCTCCACTGCAACTTCAGGGAGAT
128 TCACTGCAACTTCAGGAGGATAAGACTTGCCTACTTAGCCTGCTCCACTGCAACTTCAGGGAGAT
* ** *
37963 AAGATTTTTCAT-CTTCAGTCCACCTCAC
193 AAGA--CTAGATGC--GA-T-CACCTCAC
* *
37991 TGCAACTTCAG-GAGGATAAGA-CT-TGCTTACTTAGCCTGCTCCACTGCAACTTCAGGGAGATA
1 TGCAACTTCAGAGA-GATAAGATCTGTGATT--TTAACCTGCTCCACTGCAACTTCAGGGAGATA
* * * * * * *
38053 AGACTAGAT-GC-GATCTGCT-CTCTGCAACTTCAGAGAGATAAGATCTGTGAT-TTTAATCCGC
63 AGA-TAG-TCGCTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTCATCTTCAGTCCGC
*
38114 TC-CACTTCAACTTCAGG
126 TCTCACTGCAACTTCAGG
38131 GAGATAGGAT
Statistics
Matches: 323, Mismatches: 26, Indels: 26
0.86 0.07 0.07
Matches are distributed among these distances:
217 214 0.66
218 30 0.09
219 10 0.03
220 5 0.02
221 5 0.02
222 56 0.17
223 2 0.01
224 1 0.00
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.29
Consensus pattern (215 bp):
TGCAACTTCAGAGAGATAAGATCTGTGATTTTAACCTGCTCCACTGCAACTTCAGGGAGATAAGA
TAGTCGCTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTCATCTTCAGTCCGCTCTCA
CTGCAACTTCAGGAGGATAAGACTTGCCTACTTAGCCTGCTCCACTGCAACTTCAGGGAGATAAG
ACTAGATGCGATCACCTCAC
Found at i:38262 original size:44 final size:42
Alignment explanation
Indices: 38199--38559 Score: 175
Period size: 44 Copynumber: 8.4 Consensus size: 42
38189 NNNNNNNNNA
38199 CAACTTCA-GGAGGATAAGACTTGCTTACTTAGCCTACTCCACTG
1 CAACTTCAGGGA-GATAAGACTTGCTT--TTAGCCTACTCCACTG
* * *** * *
38243 CAACTTCAGGGAGATAAGACTAGATGCGA-CCTGCT-CTCTG
1 CAACTTCAGGGAGATAAGACTTGCTTTTAGCCTACTCCACTG
* * *
38283 CAACTTCAGAGAGA-ATAGATCTGTGATTTTAATCC-ACTCCACTG
1 CAACTTCAGGGAGATA-AGA-CT-TGCTTTT-AGCCTACTCCACTG
* * * * * **
38327 TAACTTTAAGGAGATAGGATTATCGGC-TTTAATCTACTCCACTG
1 CAACTTCAGGGAGATAAGACT-T--GCTTTTAGCCTACTCCACTG
* * *
38371 CAACTTCAGGGAGATAAGATTTGTCATTTTCAGTCTGC-CTCACTG
1 CAACTTCAGGGAGATAAGACTTG-C-TTTT-AGCCTACTC-CACTG
*
38416 GAACTTCA-GGAGGATAAGACTTGCTTACTTAGCCTACTCCACTG
1 CAACTTCAGGGA-GATAAGACTTGCTT--TTAGCCTACTCCACTG
* * *** * * *
38460 CAACTTCAGGGAGATAAGACTAGATGCGA-TCTGCT-CTCTG
1 CAACTTCAGGGAGATAAGACTTGCTTTTAGCCTACTCCACTG
* * ** *
38500 CAACTTCAGAGAGATAAGATCTGTGATTTTAATCTTCTCCACTG
1 CAACTTCAGGGAGATAAGA-CT-TGCTTTTAGCCTACTCCACTG
38544 CAACTTCAGGGAGATA
1 CAACTTCAGGGAGATA
38560 GGATTATCGG
Statistics
Matches: 241, Mismatches: 51, Indels: 50
0.70 0.15 0.15
Matches are distributed among these distances:
39 1 0.00
40 42 0.17
41 14 0.06
42 10 0.04
43 15 0.06
44 121 0.50
45 38 0.16
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.29
Consensus pattern (42 bp):
CAACTTCAGGGAGATAAGACTTGCTTTTAGCCTACTCCACTG
Found at i:47888 original size:44 final size:43
Alignment explanation
Indices: 47838--48082 Score: 237
Period size: 44 Copynumber: 5.7 Consensus size: 43
47828 CTTAGTCTAT
*
47838 TCCACTGCAACTTCAGGGAGATAGGATTATCAGCTTTAATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATT-TCAGCTTTAATCTGC
* * * * *
47882 TCCACTGCAACTTCAAGAATATAAGATTTGCCAAC-TTAGTCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTT--CAGCTTTAATCTGC
* * * **
47926 TCCATTGCAACTTCAGGGAGATAAGA-CT-AGATGCAATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTTCAGCTTTAATCTGC
* * * ** *
47967 T-CTCTGCAACTTTAGAGAGATAAGATTTGTGATTTTAATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTTCAG-CTTTAATCTGC
*
48010 TCCACTGCAACTTCAGGGAGATAAGATTGTCGGCTTTAATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATT-TCAGCTTTAATCTGC
* *
48054 TCCACTGCAACTTTAGGAAGATAAGATTT
1 TCCACTGCAACTTCAGGGAGATAAGATTT
48083 GCTAACTTCA
Statistics
Matches: 160, Mismatches: 33, Indels: 17
0.76 0.16 0.08
Matches are distributed among these distances:
40 21 0.13
41 8 0.05
42 1 0.01
43 12 0.08
44 113 0.71
45 5 0.03
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (43 bp):
TCCACTGCAACTTCAGGGAGATAAGATTTCAGCTTTAATCTGC
Found at i:94051 original size:12 final size:11
Alignment explanation
Indices: 94018--94056 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
94008 AATAAATACT
94018 AAAAAATCTAAA
1 AAAAAAT-TAAA
*
94030 AAATAATTAAA
1 AAAAAATTAAA
94041 ATAAAAATTAAA
1 A-AAAAATTAAA
94053 AAAA
1 AAAA
94057 GTATTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 8 0.33
12 16 0.67
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.21
Consensus pattern (11 bp):
AAAAAATTAAA
Found at i:94056 original size:10 final size:10
Alignment explanation
Indices: 94018--94159 Score: 50
Period size: 10 Copynumber: 14.3 Consensus size: 10
94008 AATAAATACT
94018 AAAAAATCTAA
1 AAAAAAT-TAA
94029 AAAATAATTAAA
1 AAAA-AATT-AA
94041 ATAAAAATTAA
1 A-AAAAATTAA
*
94052 AAAAAGTATTTTA
1 AAAAA--A-TTAA
*
94065 AAAATATT--
1 AAAAAATTAA
**
94073 TTAAAATTAA
1 AAAAAATTAA
94083 AAAAAATTAA
1 AAAAAATTAA
* **
94093 AAAAGTATTTT
1 AAAA-AATTAA
94104 AAAAAATT--
1 AAAAAATTAA
* *
94112 TAAAAATT-T
1 AAAAAATTAA
94121 AAAAAATT--
1 AAAAAATTAA
**
94129 TTAAAATT-A
1 AAAAAATTAA
94138 AAAAAATTAA
1 AAAAAATTAA
94148 AAAAAA-TAA
1 AAAAAATTAA
94157 AAA
1 AAA
94160 TATTTATTAT
Statistics
Matches: 102, Mismatches: 17, Indels: 26
0.70 0.12 0.18
Matches are distributed among these distances:
8 18 0.18
9 19 0.19
10 28 0.27
11 16 0.16
12 11 0.11
13 10 0.10
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.30
Consensus pattern (10 bp):
AAAAAATTAA
Found at i:94094 original size:9 final size:9
Alignment explanation
Indices: 94075--94159 Score: 66
Period size: 9 Copynumber: 9.2 Consensus size: 9
94065 AAAATATTTT
94075 AAAATTAAAA
1 AAAATT-AAA
94085 AAAATTAAA
1 AAAATTAAA
*
94094 AAAGTATTTTAA
1 AAA--A-TTAAA
*
94106 AAAATT-TA
1 AAAATTAAA
*
94114 AAAATTTAA
1 AAAATTAAA
**
94123 AAAATT-TT
1 AAAATTAAA
94131 AAAATTAAA
1 AAAATTAAA
94140 AAAATTAAA
1 AAAATTAAA
*
94149 AAAAATAAA
1 AAAATTAAA
94158 AA
1 AA
94160 TATTTATTAT
Statistics
Matches: 62, Mismatches: 8, Indels: 11
0.77 0.10 0.14
Matches are distributed among these distances:
8 13 0.21
9 34 0.55
10 7 0.11
11 1 0.02
12 7 0.11
ACGTcount: A:0.71, C:0.00, G:0.01, T:0.28
Consensus pattern (9 bp):
AAAATTAAA
Found at i:94098 original size:40 final size:40
Alignment explanation
Indices: 94034--94126 Score: 134
Period size: 40 Copynumber: 2.3 Consensus size: 40
94024 TCTAAAAAAT
*
94034 AATTAAAATAAAAATTAAAAAAAGTATTTTAAAAATATTTTAA
1 AATT-AAA-AAAAATTAAAAAAAGTATTTTAAAAA-ATTTAAA
94077 AATTAAAAAAAATT-AAAAAAGTATTTTAAAAAATTTAAA
1 AATTAAAAAAAATTAAAAAAAGTATTTTAAAAAATTTAAA
*
94116 AATTTAAAAAA
1 AATTAAAAAAA
94127 TTTTAAAATT
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
39 16 0.33
40 18 0.38
41 7 0.15
42 3 0.06
43 4 0.08
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (40 bp):
AATTAAAAAAAATTAAAAAAAGTATTTTAAAAAATTTAAA
Found at i:94124 original size:7 final size:8
Alignment explanation
Indices: 94105--94150 Score: 56
Period size: 8 Copynumber: 5.6 Consensus size: 8
94095 AAGTATTTTA
94105 AAAAATTT
1 AAAAATTT
94113 AAAAATTT
1 AAAAATTT
94121 AAAAAATTT
1 -AAAAATTT
* *
94130 TAAAATTA
1 AAAAATTT
*
94138 AAAAAATT
1 AAAAATTT
94146 AAAAA
1 AAAAA
94151 AAATAAAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
8 24 0.75
9 8 0.25
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (8 bp):
AAAAATTT
Found at i:94133 original size:40 final size:39
Alignment explanation
Indices: 94028--94134 Score: 123
Period size: 40 Copynumber: 2.8 Consensus size: 39
94018 AAAAAATCTA
* *
94028 AAAAATAATT-AAAA-T-AAAAATTAAAAAAAGTATTTT
1 AAAAATATTTAAAAATTAAAAAATTTAAAAAAGTATTTT
* *
94064 AAAAATATTTTAAAATTAAAAAAAATTAAAAAAGTATTTT
1 AAAAATATTTAAAAATT-AAAAAATTTAAAAAAGTATTTT
*
94104 AAAAA-ATTTAAAAATTTAAAAAATTTTAAAA
1 AAAAATATTTAAAAA-TTAAAAAATTTAAAAA
94135 TTAAAAAAAT
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
36 9 0.15
37 4 0.07
38 1 0.02
39 20 0.33
40 26 0.43
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (39 bp):
AAAAATATTTAAAAATTAAAAAATTTAAAAAAGTATTTT
Found at i:94579 original size:3 final size:3
Alignment explanation
Indices: 94534--94609 Score: 59
Period size: 3 Copynumber: 25.0 Consensus size: 3
94524 CCAAAATGAC
* * * *
94534 TAA TAA TCA TAA CAA AAA TAA -AA CTAA GTAA TAA GAA -AA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA -TAA -TAA TAA TAA TAA TAA TAA
94579 TAA TAA TAA TAA TAA TACA TGAA -AA TAA TAA
1 TAA TAA TAA TAA TAA TA-A T-AA TAA TAA TAA
94610 ATCAACACAA
Statistics
Matches: 60, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
2 6 0.10
3 45 0.75
4 8 0.13
5 1 0.02
ACGTcount: A:0.66, C:0.05, G:0.04, T:0.25
Consensus pattern (3 bp):
TAA
Found at i:104394 original size:27 final size:27
Alignment explanation
Indices: 104347--104643 Score: 357
Period size: 27 Copynumber: 11.1 Consensus size: 27
104337 CACTATTATA
*
104347 ACCGAAATA-CCCCATAGGGTAGAATG
1 ACCGAAATACCCCCATAGGGTAAAATG
104373 ACCGAAATACCCCCATAGGGTAAAATG
1 ACCGAAATACCCCCATAGGGTAAAATG
* *
104400 ATCGAAATACCCCCATAGGGTAGAATG
1 ACCGAAATACCCCCATAGGGTAAAATG
* * *
104427 ACTGAAATACCCTCATAGGGTAGAATG
1 ACCGAAATACCCCCATAGGGTAAAATG
* *
104454 AACG-AATAACCCCCATAAGGTAAAATG
1 ACCGAAAT-ACCCCCATAGGGTAAAATG
* *
104481 ATCAAAATACCCCCATAGGGTAAAATG
1 ACCGAAATACCCCCATAGGGTAAAATG
* *
104508 ACTGAAATACCCCCATAGGATAAAATG
1 ACCGAAATACCCCCATAGGGTAAAATG
* * *
104535 ACCGAAATAACCCTATAGGGTAGAATG
1 ACCGAAATACCCCCATAGGGTAAAATG
* * * *
104562 ACCAAAATA-CTCCATAGGGTAGAACG
1 ACCGAAATACCCCCATAGGGTAAAATG
* * *
104588 ATCGAAATACCCCAATAGAGTAAAATG
1 ACCGAAATACCCCCATAGGGTAAAATG
*
104615 ATCGAAATACCCCCATAGGGTAAAATG
1 ACCGAAATACCCCCATAGGGTAAAATG
104642 AC
1 AC
104644 TATTATACAC
Statistics
Matches: 230, Mismatches: 37, Indels: 7
0.84 0.14 0.03
Matches are distributed among these distances:
26 33 0.14
27 194 0.84
28 3 0.01
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.18
Consensus pattern (27 bp):
ACCGAAATACCCCCATAGGGTAAAATG
Found at i:105979 original size:29 final size:29
Alignment explanation
Indices: 105943--106028 Score: 111
Period size: 29 Copynumber: 3.0 Consensus size: 29
105933 TTGACAGAAA
105943 TTTGCCATAAAGGCGTTTCCTTTTAGAGT
1 TTTGCCATAAAGGCGTTTCCTTTTAGAGT
* *
105972 TTTGCCATAAAGGC-TTACCTTTCCAGAGT
1 TTTGCCATAAAGGCGTTTCCTTT-TAGAGT
* * *
106001 TTTGCCACAAAGGTGTTTCTTTTTAGAG
1 TTTGCCATAAAGGCGTTTCCTTTTAGAG
106029 GTTCACCACA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
28 7 0.15
29 35 0.73
30 6 0.12
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.40
Consensus pattern (29 bp):
TTTGCCATAAAGGCGTTTCCTTTTAGAGT
Found at i:106013 original size:58 final size:57
Alignment explanation
Indices: 105943--106144 Score: 217
Period size: 58 Copynumber: 3.5 Consensus size: 57
105933 TTGACAGAAA
* **
105943 TTTGCCATAAAGGCGTTTCCTTTTAGAGTTTTGCCATAAAGGCTTACCTTTCCAGAGT
1 TTTGCCATAAAGGCGTTTCCTTTTAGAGGTTCACCA-AAAGGCTTACCTTTCCAGAGT
* * *
106001 TTTGCCACAAAGGTGTTTCTTTTTAGAGGTTCACCACAAAGGCTTACCTTTCCAGA-T
1 TTTGCCATAAAGGCGTTTCCTTTTAGAGGTTCACCA-AAAGGCTTACCTTTCCAGAGT
* * * * * * * * *
106058 TTTGTCATGAAGGCTTTTCCATTCAAAGGTACACTAAAAGGTTTACCTTTCCAGAGT
1 TTTGCCATAAAGGCGTTTCCTTTTAGAGGTTCACCAAAAGGCTTACCTTTCCAGAGT
* * *
106115 TTTTCCATAAAGGTGTTTCATTTTAGAGGT
1 TTTGCCATAAAGGCGTTTCCTTTTAGAGGT
106145 GTTTTAGGCG
Statistics
Matches: 115, Mismatches: 28, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
56 18 0.16
57 48 0.42
58 49 0.43
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.38
Consensus pattern (57 bp):
TTTGCCATAAAGGCGTTTCCTTTTAGAGGTTCACCAAAAGGCTTACCTTTCCAGAGT
Found at i:106128 original size:29 final size:29
Alignment explanation
Indices: 105967--106128 Score: 80
Period size: 29 Copynumber: 5.7 Consensus size: 29
105957 GTTTCCTTTT
* *
105967 AGAGTTTTGCCATAAAGGCTTACCTTTCC
1 AGAGTTTTACCATAAAGGTTTACCTTTCC
* * * **
105996 AGAGTTTTGCCACAAAGGTGTT-TCTTTTT
1 AGAGTTTTACCATAAAGGT-TTACCTTTCC
* * * *
106025 AGAGGTTCACCACAAAGGCTTACCTTTCC
1 AGAGTTTTACCATAAAGGTTTACCTTTCC
** * * *
106054 AGA-TTTTGTCATGAAGGCTTTTCCATT-C
1 AGAGTTTTACCATAAAGG-TTTACCTTTCC
* * ** *
106082 AAAGGTACACTA-AAAGGTTTACCTTTCC
1 AGAGTTTTACCATAAAGGTTTACCTTTCC
*
106110 AGAGTTTTTCCATAAAGGT
1 AGAGTTTTACCATAAAGGT
106129 GTTTCATTTT
Statistics
Matches: 90, Mismatches: 37, Indels: 12
0.65 0.27 0.09
Matches are distributed among these distances:
27 7 0.08
28 24 0.27
29 57 0.63
30 2 0.02
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (29 bp):
AGAGTTTTACCATAAAGGTTTACCTTTCC
Found at i:108909 original size:21 final size:21
Alignment explanation
Indices: 108872--108918 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
108862 TCACACGACT
*
108872 GTGTGGCTATCCCACACGCCC
1 GTGTGGCTATCCCACACACCC
*
108893 GTGTGTCTA-CCCTACACACCC
1 GTGTGGCTATCCC-ACACACCC
*
108914 ATGTG
1 GTGTG
108919 CTCACCCATG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.17, C:0.38, G:0.21, T:0.23
Consensus pattern (21 bp):
GTGTGGCTATCCCACACACCC
Found at i:117708 original size:22 final size:22
Alignment explanation
Indices: 117678--117719 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
117668 CTTCTTTACT
*
117678 TTTCTTATTCGATTTTTCGCGG
1 TTTCCTATTCGATTTTTCGCGG
*
117700 TTTCCTATTGGATTTTTCGC
1 TTTCCTATTCGATTTTTCGC
117720 AGTCAATCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.10, C:0.19, G:0.17, T:0.55
Consensus pattern (22 bp):
TTTCCTATTCGATTTTTCGCGG
Found at i:134414 original size:22 final size:22
Alignment explanation
Indices: 134383--134427 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
134373 TGATTGGTGC
134383 AATATTAATACTTTAAATATTTA
1 AATATTAATACTTTAAAT-TTTA
* *
134406 AATA-TAATATTTTGAATTTTA
1 AATATTAATACTTTAAATTTTA
134427 A
1 A
134428 GGACCAACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 11 0.55
23 4 0.20
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (22 bp):
AATATTAATACTTTAAATTTTA
Found at i:141693 original size:14 final size:17
Alignment explanation
Indices: 141662--141702 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
141652 GTTCTTAAAA
141662 TTTATTATACATTCTTT
1 TTTATTATACATTCTTT
*
141679 TTTATT-TA-ATTTTTT
1 TTTATTATACATTCTTT
141694 ATTTATTAT
1 -TTTATTAT
141703 TTGTCAACTC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 6 0.29
16 8 0.38
17 7 0.33
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTATTATACATTCTTT
Found at i:142353 original size:21 final size:20
Alignment explanation
Indices: 142329--142375 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
142319 TTTATGAATA
*
142329 TTTTTAAGAATATTATGGGTTT
1 TTTTTAA-AATATTA-GGGATT
*
142351 TTTTTTAAATATTAGGGATT
1 TTTTTAAAATATTAGGGATT
142371 TTTTT
1 TTTTT
142376 TGCATTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 10 0.43
21 7 0.30
22 6 0.26
ACGTcount: A:0.26, C:0.00, G:0.15, T:0.60
Consensus pattern (20 bp):
TTTTTAAAATATTAGGGATT
Found at i:142376 original size:21 final size:21
Alignment explanation
Indices: 142337--142376 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
142327 TATTTTTAAG
142337 AATATTATGGGTTTTTTTTTA
1 AATATTATGGGTTTTTTTTTA
*
142358 AATATTA-GGGATTTTTTTT
1 AATATTATGGGTTTTTTTTT
142377 GCATTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.25, C:0.00, G:0.15, T:0.60
Consensus pattern (21 bp):
AATATTATGGGTTTTTTTTTA
Found at i:145721 original size:19 final size:19
Alignment explanation
Indices: 145697--145734 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
145687 AGATTCATCC
145697 AAGAAAGGTATTAAGCCAA
1 AAGAAAGGTATTAAGCCAA
145716 AAGAAAGGTATTAAGCCAA
1 AAGAAAGGTATTAAGCCAA
145735 CATTACGGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.11, G:0.21, T:0.16
Consensus pattern (19 bp):
AAGAAAGGTATTAAGCCAA
Found at i:146368 original size:18 final size:17
Alignment explanation
Indices: 146347--146390 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
146337 TTCAAAAAAA
146347 TATAAATTTTGGAACTTT
1 TATAAATTTTGGAA-TTT
*
146365 TATAAATATTTTGAATTT
1 TATAAAT-TTTGGAATTT
*
146383 TAAAAATT
1 TATAAATT
146391 ATTTTGAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 1 0.04
18 16 0.70
19 6 0.26
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (17 bp):
TATAAATTTTGGAATTT
Found at i:146395 original size:19 final size:18
Alignment explanation
Indices: 146352--146400 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
146342 AAAAATATAA
*
146352 ATTTTGGAACTTTTATAAAT
1 ATTTT-GAA-TTTTAAAAAT
146372 ATTTTGAATTTTAAAAATT
1 ATTTTGAATTTTAAAAA-T
146391 ATTTTGAATT
1 ATTTTGAATT
146401 GTTTTGTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 8 0.30
19 14 0.52
20 5 0.19
ACGTcount: A:0.37, C:0.02, G:0.08, T:0.53
Consensus pattern (18 bp):
ATTTTGAATTTTAAAAAT
Found at i:146651 original size:27 final size:27
Alignment explanation
Indices: 146613--146666 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
146603 AGAGATAGTC
146613 AAATTTCACTTTGAGACACGTCAATAT
1 AAATTTCACTTTGAGACACGTCAATAT
146640 AAATTTCACTTTGAGACACGTCAATAT
1 AAATTTCACTTTGAGACACGTCAATAT
146667 GTAACAGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (27 bp):
AAATTTCACTTTGAGACACGTCAATAT
Found at i:155363 original size:20 final size:19
Alignment explanation
Indices: 155338--155377 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
155328 GTTTTTCCGG
155338 TATTGAACTCCTTAGATTAC
1 TATTGAACT-CTTAGATTAC
* *
155358 TATTGAAGTGTTAGATTAC
1 TATTGAACTCTTAGATTAC
155377 T
1 T
155378 TGTACATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.42
Consensus pattern (19 bp):
TATTGAACTCTTAGATTAC
Found at i:155740 original size:6 final size:6
Alignment explanation
Indices: 155729--155763 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
155719 GTTACCGACC
155729 AAGATG AAGATG AAGATG AAGATG AAGATG AAGAT
1 AAGATG AAGATG AAGATG AAGATG AAGATG AAGAT
155764 TTTAGTACAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.51, C:0.00, G:0.31, T:0.17
Consensus pattern (6 bp):
AAGATG
Found at i:160065 original size:27 final size:27
Alignment explanation
Indices: 160025--160081 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
160015 TCAAGTTGAT
* *
160025 GATGATAGGTCTTCCAATTGCAACACG
1 GATGATACGCCTTCCAATTGCAACACG
160052 GATGATACGCCTTCCAATTGCAACACG
1 GATGATACGCCTTCCAATTGCAACACG
160079 GAT
1 GAT
160082 AGCAATTGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (27 bp):
GATGATACGCCTTCCAATTGCAACACG
Found at i:161665 original size:28 final size:28
Alignment explanation
Indices: 161634--161703 Score: 106
Period size: 28 Copynumber: 2.5 Consensus size: 28
161624 AAATAAAAAA
* *
161634 TTACCAAAATGT-TATAACTTTTTTTTAT
1 TTACCAAAATATATATAA-ATTTTTTTAT
161662 TTACCAAAATATATATAAATTTTTTTAT
1 TTACCAAAATATATATAAATTTTTTTAT
161690 TTACCAAAATATAT
1 TTACCAAAATATAT
161704 CAAAAAAACT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
28 34 0.87
29 5 0.13
ACGTcount: A:0.40, C:0.10, G:0.01, T:0.49
Consensus pattern (28 bp):
TTACCAAAATATATATAAATTTTTTTAT
Found at i:161727 original size:17 final size:17
Alignment explanation
Indices: 161705--161745 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
161695 AAAATATATC
161705 AAAAAAACTAAAGAA-CA-
1 AAAAAAA-TAAA-AACCAG
161722 AAAAAAATAAAAACCAG
1 AAAAAAATAAAAACCAG
161739 AAAAAAA
1 AAAAAAA
161746 AACCTGAACC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 2 0.09
16 6 0.27
17 14 0.64
ACGTcount: A:0.80, C:0.10, G:0.05, T:0.05
Consensus pattern (17 bp):
AAAAAAATAAAAACCAG
Found at i:161855 original size:27 final size:27
Alignment explanation
Indices: 161777--161857 Score: 117
Period size: 27 Copynumber: 3.0 Consensus size: 27
161767 TCCCTGGGTG
**
161777 GAGGGAAGCAGGTTGGCGGCACCAAAC
1 GAGGGAAGCAGGTTGGCGGCACCAGTC
* *
161804 AAGGGAAGCAGGTTGGCTGCACCAGTC
1 GAGGGAAGCAGGTTGGCGGCACCAGTC
*
161831 GAGGGAACCAGGTTGGCGGCACCAGTC
1 GAGGGAAGCAGGTTGGCGGCACCAGTC
161858 CTACCAACCA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.26, C:0.23, G:0.40, T:0.11
Consensus pattern (27 bp):
GAGGGAAGCAGGTTGGCGGCACCAGTC
Found at i:166109 original size:17 final size:17
Alignment explanation
Indices: 166087--166123 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
166077 AGTAAGATGT
166087 CATGAATATTAGAATAG
1 CATGAATATTAGAATAG
166104 CATGAATATTAGAATAG
1 CATGAATATTAGAATAG
166121 CAT
1 CAT
166124 CTTACCCCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.08, G:0.16, T:0.30
Consensus pattern (17 bp):
CATGAATATTAGAATAG
Found at i:169039 original size:2 final size:2
Alignment explanation
Indices: 169032--169067 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
169022 AACTCGTACT
*
169032 TA TA TA TA TA TA TA TA TA TA TA -A GA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
169068 GAGATATGAG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:172321 original size:11 final size:11
Alignment explanation
Indices: 172305--172347 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
172295 TAAGAAGGAA
172305 TTTGAGAGAAT
1 TTTGAGAGAAT
*
172316 TTTGAGAGATT
1 TTTGAGAGAAT
*
172327 TTTAAGAGAAT
1 TTTGAGAGAAT
* *
172338 ATTGTGAGAA
1 TTTGAGAGAA
172348 ATGAGTAAGG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.37, C:0.00, G:0.26, T:0.37
Consensus pattern (11 bp):
TTTGAGAGAAT
Found at i:173686 original size:18 final size:19
Alignment explanation
Indices: 173663--173698 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
173653 AAAAATTATA
*
173663 AATTTTT-AAATAAAATAC
1 AATTTTTGAAAAAAAATAC
173681 AATTTTTGAAAAAAAATA
1 AATTTTTGAAAAAAAATA
173699 AAAATCTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (19 bp):
AATTTTTGAAAAAAAATAC
Found at i:173711 original size:19 final size:18
Alignment explanation
Indices: 173644--173711 Score: 57
Period size: 17 Copynumber: 3.7 Consensus size: 18
173634 CTTTTAAACA
* **
173644 AAAATATTTAAAAATTAT
1 AAAATTTTTAAAAAAAAT
*
173662 -AAATTTTTAAATAAAAT
1 AAAATTTTTAAAAAAAAT
*
173679 ACAATTTTTGAAAAAAAAT
1 AAAATTTTT-AAAAAAAAT
*
173698 AAAAATCTTTAAAA
1 -AAAATTTTTAAAA
173712 TTCAAAAAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
17 13 0.33
18 7 0.18
19 12 0.31
20 7 0.18
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.35
Consensus pattern (18 bp):
AAAATTTTTAAAAAAAAT
Found at i:174702 original size:18 final size:21
Alignment explanation
Indices: 174676--174718 Score: 56
Period size: 18 Copynumber: 2.2 Consensus size: 21
174666 TAATATTGAA
174676 TTTTGAAATT-TT-TTA-TAT
1 TTTTGAAATTGTTATTATTAT
*
174694 TTTTTAAATTGTTATTATTAT
1 TTTTGAAATTGTTATTATTAT
174715 TTTT
1 TTTT
174719 CATTTTAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 9 0.43
19 2 0.10
20 3 0.14
21 7 0.33
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.70
Consensus pattern (21 bp):
TTTTGAAATTGTTATTATTAT
Found at i:175641 original size:29 final size:29
Alignment explanation
Indices: 175583--175637 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
175573 GAAGTGGTTG
* * *
175583 TTGAACCACTAAACTTTTATTATTAAATA
1 TTGAACCACTAAACCTTAAATATTAAATA
175612 TTGAACC-CTAAACCTTAAATATTAAA
1 TTGAACCACTAAACCTTAAATATTAAA
175638 ATATATATCT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 16 0.70
29 7 0.30
ACGTcount: A:0.44, C:0.16, G:0.04, T:0.36
Consensus pattern (29 bp):
TTGAACCACTAAACCTTAAATATTAAATA
Found at i:175960 original size:35 final size:35
Alignment explanation
Indices: 175895--175965 Score: 81
Period size: 35 Copynumber: 2.0 Consensus size: 35
175885 TAGAAACATG
* * *
175895 AAATCAAAACTATAAACCCTAAACCCTAAACTCAA
1 AAATCAAAACTAGAAACCATAAACCCTAAACCCAA
* *
175930 AAATCAAAACTAGAAA-CATGAATCCTTAAACCCAA
1 AAATCAAAACTAGAAACCAT-AAACCCTAAACCCAA
175965 A
1 A
175966 CCCATAAACC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
34 2 0.07
35 28 0.93
ACGTcount: A:0.55, C:0.25, G:0.03, T:0.17
Consensus pattern (35 bp):
AAATCAAAACTAGAAACCATAAACCCTAAACCCAA
Found at i:176049 original size:28 final size:28
Alignment explanation
Indices: 175971--176067 Score: 90
Period size: 28 Copynumber: 3.5 Consensus size: 28
175961 CCAAACCCAT
* * *
175971 AAACCCTAAATCCAAAATATGAAACATG
1 AAACCATAAACCCAAAATATTAAACATG
* * * **
175999 AGACCCTAAATCCAAAACCTTAAA-ATTG
1 AAACCATAAACCCAAAATATTAAACA-TG
176027 AAACCATAAACCCAAAATATTAAACCAT-
1 AAACCATAAACCCAAAATATTAAA-CATG
176055 AAACCATAAACCC
1 AAACCATAAACCC
176068 CAAACCCCAA
Statistics
Matches: 57, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
27 1 0.02
28 54 0.95
29 1 0.02
30 1 0.02
ACGTcount: A:0.53, C:0.26, G:0.04, T:0.18
Consensus pattern (28 bp):
AAACCATAAACCCAAAATATTAAACATG
Found at i:176125 original size:188 final size:188
Alignment explanation
Indices: 175909--176272 Score: 692
Period size: 188 Copynumber: 1.9 Consensus size: 188
175899 CAAAACTATA
*
175909 AACCCTAAACCCTAAACTCAAAAATCAAAACTAGAAACATGAATCCTTAAACCCAAACCCATAAA
1 AACCATAAACCCTAAACTCAAAAATCAAAACTAGAAACATGAATCCTTAAACCCAAACCCATAAA
*
175974 CCCTAAATCCAAAATATGAAACATGAGACCCTAAATCCAAAACCTTAAAATTGAAACCATAAACC
66 CCCTAAATCCAAAATATGAAACATGAGACCCTAAACCCAAAACCTTAAAATTGAAACCATAAACC
176039 CAAAATATTAAACCATAAACCATAAACCCCAAACCCCAAAACCTTACACAATTCTAAC
131 CAAAATATTAAACCATAAACCATAAACCCCAAACCCCAAAACCTTACACAATTCTAAC
176097 AACCATAAACCCTAAACTCAAAAATCAAAACTAGAAACATGAATCCTTAAACCCAAACCCATAAA
1 AACCATAAACCCTAAACTCAAAAATCAAAACTAGAAACATGAATCCTTAAACCCAAACCCATAAA
*
176162 CCCTAAATCCAAAATATGTAACATGAGACCCTAAACCCAAAACCTTAAAATTGAAACCATAAACC
66 CCCTAAATCCAAAATATGAAACATGAGACCCTAAACCCAAAACCTTAAAATTGAAACCATAAACC
*
176227 CAAAATATTAAACCATAAACCATAAACCCCAAACCCTAAAACCTTA
131 CAAAATATTAAACCATAAACCATAAACCCCAAACCCCAAAACCTTA
176273 AACTAAACCT
Statistics
Matches: 172, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
188 172 1.00
ACGTcount: A:0.51, C:0.29, G:0.03, T:0.17
Consensus pattern (188 bp):
AACCATAAACCCTAAACTCAAAAATCAAAACTAGAAACATGAATCCTTAAACCCAAACCCATAAA
CCCTAAATCCAAAATATGAAACATGAGACCCTAAACCCAAAACCTTAAAATTGAAACCATAAACC
CAAAATATTAAACCATAAACCATAAACCCCAAACCCCAAAACCTTACACAATTCTAAC
Found at i:176224 original size:28 final size:26
Alignment explanation
Indices: 176193--176267 Score: 78
Period size: 28 Copynumber: 2.7 Consensus size: 26
176183 CATGAGACCC
176193 TAAACCCAAAACCTTAAAATTGAAACCA
1 TAAACCCAAAACCTTAAAA-T-AAACCA
**
176221 TAAACCCAAAATATTAAACCATAAACCA
1 TAAACCCAAAACCTTAAA--ATAAACCA
* *
176249 TAAACCCCAAACCCTAAAA
1 TAAACCCAAAACCTTAAAA
176268 CCTTAAACTA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
26 1 0.03
28 36 0.92
29 1 0.03
30 1 0.03
ACGTcount: A:0.55, C:0.28, G:0.01, T:0.16
Consensus pattern (26 bp):
TAAACCCAAAACCTTAAAATAAACCA
Found at i:176225 original size:21 final size:21
Alignment explanation
Indices: 176201--176252 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
176191 CCTAAACCCA
176201 AAACCTTAAAAT-TGAAACCAT
1 AAACC-TAAAATATGAAACCAT
* *
176222 AAACCCAAAATATTAAACCAT
1 AAACCTAAAATATGAAACCAT
176243 AAACCATAAA
1 AAACC-TAAA
176253 CCCCAAACCC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 5 0.19
21 18 0.69
22 3 0.12
ACGTcount: A:0.58, C:0.21, G:0.02, T:0.19
Consensus pattern (21 bp):
AAACCTAAAATATGAAACCAT
Found at i:176253 original size:56 final size:56
Alignment explanation
Indices: 176159--176267 Score: 132
Period size: 56 Copynumber: 1.9 Consensus size: 56
176149 CCAAACCCAT
* * * * *
176159 AAACCCTAAATCCAAAATATGTAACATGAGACCCTAAACCCAAAACCTTAAAATTG
1 AAACCATAAACCCAAAATATGTAACATGAAACCATAAACCCAAAACCCTAAAATTG
*
176215 AAACCATAAACCCAAAATAT-TAAACCAT-AAACCATAAACCCCAAACCCTAAAA
1 AAACCATAAACCCAAAATATGT-AA-CATGAAACCATAAACCCAAAACCCTAAAA
176268 CCTTAAACTA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
55 1 0.02
56 41 0.91
57 3 0.07
ACGTcount: A:0.52, C:0.28, G:0.04, T:0.17
Consensus pattern (56 bp):
AAACCATAAACCCAAAATATGTAACATGAAACCATAAACCCAAAACCCTAAAATTG
Found at i:176399 original size:28 final size:28
Alignment explanation
Indices: 176339--176393 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
176329 CTCGAAGCCC
* * *
176339 AAAATCCTAAACCTTAAACACTAAACTA
1 AAAATCATAAACCATAAACACAAAACTA
*
176367 AAAATCATAAACCATAAACTCAAAACT
1 AAAATCATAAACCATAAACACAAAACT
176394 CGAAATTCGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.56, C:0.24, G:0.00, T:0.20
Consensus pattern (28 bp):
AAAATCATAAACCATAAACACAAAACTA
Found at i:176489 original size:7 final size:7
Alignment explanation
Indices: 176473--176553 Score: 51
Period size: 7 Copynumber: 11.1 Consensus size: 7
176463 CCCCAACCCT
176473 AACCTCAA
1 AACCT-AA
176481 AACCTAA
1 AACCTAA
*
176488 AAACTCAA
1 AACCT-AA
176496 AA-CTCAA
1 AACCT-AA
176503 AA-CTCAA
1 AACCT-AA
176510 AA-CTATA
1 AACCTA-A
176517 AACCTAA
1 AACCTAA
176524 AACTCTAA
1 AAC-CTAA
*
176532 ATCCTAA
1 AACCTAA
*
176539 ACCCTAA
1 AACCTAA
*
176546 ACCCTAA
1 AACCTAA
176553 A
1 A
176554 CTCGAAACAC
Statistics
Matches: 66, Mismatches: 3, Indels: 9
0.85 0.04 0.12
Matches are distributed among these distances:
6 1 0.02
7 47 0.71
8 18 0.27
ACGTcount: A:0.53, C:0.30, G:0.00, T:0.17
Consensus pattern (7 bp):
AACCTAA
Found at i:176490 original size:8 final size:7
Alignment explanation
Indices: 176476--176513 Score: 58
Period size: 7 Copynumber: 5.3 Consensus size: 7
176466 CAACCCTAAC
176476 CTCAAAA
1 CTCAAAA
*
176483 CCTAAAAA
1 -CTCAAAA
176491 CTCAAAA
1 CTCAAAA
176498 CTCAAAA
1 CTCAAAA
176505 CTCAAAA
1 CTCAAAA
176512 CT
1 CT
176514 ATAAACCTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
7 22 0.79
8 6 0.21
ACGTcount: A:0.55, C:0.29, G:0.00, T:0.16
Consensus pattern (7 bp):
CTCAAAA
Found at i:176506 original size:14 final size:14
Alignment explanation
Indices: 176476--176519 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
176466 CAACCCTAAC
176476 CTCAAAACCTAAAAA
1 CTCAAAA-CTAAAAA
*
176491 CTCAAAACTCAAAA
1 CTCAAAACTAAAAA
*
176505 CTCAAAACTATAAA
1 CTCAAAACTAAAAA
176519 C
1 C
176520 CTAAAACTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 19 0.73
15 7 0.27
ACGTcount: A:0.57, C:0.27, G:0.00, T:0.16
Consensus pattern (14 bp):
CTCAAAACTAAAAA
Found at i:176540 original size:14 final size:13
Alignment explanation
Indices: 176495--176561 Score: 53
Period size: 14 Copynumber: 4.8 Consensus size: 13
176485 TAAAAACTCA
* *
176495 AAACTCAAAACTCA
1 AAACTCTAAAC-CT
*
176509 AAACTATAAACCT
1 AAACTCTAAACCT
176522 AAAACTCTAAATCCT
1 -AAACTCTAAA-CCT
*
176537 AAACCCTAAACCCT
1 AAACTCTAAA-CCT
*
176551 AAACTCGAAAC
1 AAACTCTAAAC
176562 ACAAAATGCA
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
13 2 0.05
14 38 0.88
15 3 0.07
ACGTcount: A:0.51, C:0.30, G:0.01, T:0.18
Consensus pattern (13 bp):
AAACTCTAAACCT
Found at i:176601 original size:27 final size:28
Alignment explanation
Indices: 176571--176628 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 28
176561 CACAAAATGC
*
176571 AAACCCTGAACCCTAAACA-TGACACCT
1 AAACCCTGAACCCAAAACATTGACACCT
* *
176598 AAACCTTGAACTCAAAACATTGACACCT
1 AAACCCTGAACCCAAAACATTGACACCT
176626 AAA
1 AAA
176629 TTCTAAATTC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 16 0.59
28 11 0.41
ACGTcount: A:0.45, C:0.31, G:0.07, T:0.17
Consensus pattern (28 bp):
AAACCCTGAACCCAAAACATTGACACCT
Found at i:176636 original size:7 final size:7
Alignment explanation
Indices: 176624--176649 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
176614 ACATTGACAC
176624 CTAAATT
1 CTAAATT
176631 CTAAATT
1 CTAAATT
176638 CTAAATT
1 CTAAATT
176645 CTAAA
1 CTAAA
176650 CCCTAAACCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (7 bp):
CTAAATT
Found at i:176655 original size:14 final size:14
Alignment explanation
Indices: 176623--176656 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
176613 AACATTGACA
*
176623 CCTAAATTCTAAAT
1 CCTAAATTCTAAAC
*
176637 TCTAAATTCTAAAC
1 CCTAAATTCTAAAC
176651 CCTAAA
1 CCTAAA
176657 CCTTGAACCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (14 bp):
CCTAAATTCTAAAC
Found at i:176755 original size:41 final size:39
Alignment explanation
Indices: 176710--176796 Score: 93
Period size: 41 Copynumber: 2.2 Consensus size: 39
176700 CTTAAACATG
* * * *
176710 AAACCTAAATTCTAAACCCTAACTCTTGAACACTAACCCCT
1 AAACCTAAACTCCAAA-CCTAAATCATGAACACTAA-CCCT
* *
176751 AAACCATAACCTCCAAACCTAAATCATGAACCCTAACCCT
1 AAACC-TAAACTCCAAACCTAAATCATGAACACTAACCCT
176791 AAACCT
1 AAACCT
176797 TAAAACGCAA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
39 1 0.03
40 9 0.23
41 21 0.54
42 8 0.21
ACGTcount: A:0.41, C:0.36, G:0.02, T:0.21
Consensus pattern (39 bp):
AAACCTAAACTCCAAACCTAAATCATGAACACTAACCCT
Found at i:176773 original size:20 final size:20
Alignment explanation
Indices: 176748--176795 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
176738 AACACTAACC
176748 CCTAAACCAT-AACCTCCAAA
1 CCTAAACCATGAACC-CCAAA
* * *
176768 CCTAAATCATGAACCCTAAC
1 CCTAAACCATGAACCCCAAA
176788 CCTAAACC
1 CCTAAACC
176796 TTAAAACGCA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.42, C:0.40, G:0.02, T:0.17
Consensus pattern (20 bp):
CCTAAACCATGAACCCCAAA
Found at i:180498 original size:31 final size:31
Alignment explanation
Indices: 180460--180522 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
180450 ATGCGAATGA
180460 TTGAATATCTCTCCTTTACTAGATATATGTC
1 TTGAATATCTCTCCTTTACTAGATATATGTC
180491 TTGAATATCTCTCCTTTACTAGATATATGTC
1 TTGAATATCTCTCCTTTACTAGATATATGTC
180522 T
1 T
180523 ACCTCTACGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.25, C:0.19, G:0.10, T:0.46
Consensus pattern (31 bp):
TTGAATATCTCTCCTTTACTAGATATATGTC
Found at i:185942 original size:15 final size:15
Alignment explanation
Indices: 185922--185952 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
185912 ACAATAACAA
185922 TGGCCCAAACTACAG
1 TGGCCCAAACTACAG
*
185937 TGGCCCAAATTACAG
1 TGGCCCAAACTACAG
185952 T
1 T
185953 CAGAAACCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.29, G:0.19, T:0.19
Consensus pattern (15 bp):
TGGCCCAAACTACAG
Found at i:186641 original size:11 final size:12
Alignment explanation
Indices: 186612--186641 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
186602 AAGGGGAGAG
186612 TTTTTTTGAAGT
1 TTTTTTTGAAGT
186624 TTTTTTTGAA-T
1 TTTTTTTGAAGT
186635 TTTTTTT
1 TTTTTTT
186642 AAAAGAATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.44
12 10 0.56
ACGTcount: A:0.13, C:0.00, G:0.10, T:0.77
Consensus pattern (12 bp):
TTTTTTTGAAGT
Found at i:198513 original size:26 final size:26
Alignment explanation
Indices: 198470--198519 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
198460 AGATTTTTGT
198470 TTGTTCTTGTAATACTTTATTCTTCA
1 TTGTTCTTGTAATACTTTATTCTTCA
*
198496 TTGTTCTTG-AATATCTTTTTTCTT
1 TTGTTCTTGTAATA-CTTTATTCTT
198520 TTCAAGACAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 4 0.18
26 18 0.82
ACGTcount: A:0.16, C:0.14, G:0.08, T:0.62
Consensus pattern (26 bp):
TTGTTCTTGTAATACTTTATTCTTCA
Found at i:199501 original size:44 final size:45
Alignment explanation
Indices: 199453--199903 Score: 183
Period size: 44 Copynumber: 10.3 Consensus size: 45
199443 GTATTGGCGT
* * *
199453 GAAGTAGATTGAAGATAGCA-AGTTCTGTTTTCCTATATTGGTAG-
1 GAAGTAGATCGAAGATAGCAGA-TTCTATCTTCCTATATTGGTAGC
* * * * * *
199497 GAAGTGGATCGAAGGT-GCAGATTTTATCTTCCCATACTGGTGGC
1 GAAGTAGATCGAAGATAGCAGATTCTATCTTCCTATATTGGTAGC
* * * * * *
199541 GAAGTAGATCGAAGAAAGCAGA-TCTTGTCTTCATGTATTGG-CGT
1 GAAGTAGATCGAAGATAGCAGATTC-TATCTTCCTATATTGGTAGC
* * *
199585 GAAGTAGATCGAAGATAGCAGATCCTATTTTCTTATATTGGTAG-
1 GAAGTAGATCGAAGATAGCAGATTCTATCTTCCTATATTGGTAGC
* * * * *
199629 GAAGTGGATTC-AGGAT--C----T-TGTCTTCCCATATTGGTGGC
1 GAAGTAGA-TCGAAGATAGCAGATTCTATCTTCCTATATTGGTAGC
** * * * * *
199667 GAAGTAGATTAAAGAAAGCAGA-TCTTATCTTCATGTATTGG-CGT
1 GAAGTAGATCGAAGATAGCAGATTC-TATCTTCCTATATTGGTAGC
* * * *
199711 GAAGTAGATCGAAGAAAGCAAATCCTATCTTTCTATATTGGTAGC
1 GAAGTAGATCGAAGATAGCAGATTCTATCTTCCTATATTGGTAGC
* * * * *
199756 GAAGTGGATTGAAGATAGCAGA-TCTTGTCTTTCC-ATACTGAG-GGC
1 GAAGTAGATCGAAGATAGCAGATTC-TATC-TTCCTATATTG-GTAGC
* * * * * * *
199801 GAAGTAGATCAAAGAAAGCAGA-TCTTGTCTTCATGTATTGG-CGT
1 GAAGTAGATCGAAGATAGCAGATTC-TATCTTCCTATATTGGTAGC
* * * * * * *
199845 GAAGTAGATCAAAGGTAGCAGA-TCTTGTCTTCATGTATTGG-CGT
1 GAAGTAGATCGAAGATAGCAGATTC-TATCTTCCTATATTGGTAGC
199889 GAAGTAGATCGAAGA
1 GAAGTAGATCGAAGA
199904 AAACGAATCT
Statistics
Matches: 309, Mismatches: 76, Indels: 44
0.72 0.18 0.10
Matches are distributed among these distances:
37 15 0.05
38 10 0.03
40 1 0.00
42 1 0.00
43 20 0.06
44 167 0.54
45 91 0.29
46 4 0.01
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (45 bp):
GAAGTAGATCGAAGATAGCAGATTCTATCTTCCTATATTGGTAGC
Found at i:199580 original size:88 final size:88
Alignment explanation
Indices: 199428--200255 Score: 720
Period size: 88 Copynumber: 9.5 Consensus size: 88
199418 TGAAAATAGT
* * * * * *
199428 AGATCTTGTCTTCATGTATTGGCGTGAAGTAGATTGAAGATAGCAAGTTC-TGTTTTCCTATATT
1 AGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAGC-AGATCTTGTCTTCATGTATT
* * *
199492 GGTAGGAAGTGGATCGAAGGT-GC
65 GGCAGGAAGTAGATCAAAGGTAGC
* * *** * * *
199515 AGATTTTATCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATT
1 AGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATT
* *
199580 GGC-GTGAAGTAGATCGAAGATAGC
65 GGCAG-GAAGTAGATCAAAGGTAGC
* * * * * * * ***
199604 AGATCCTATTTTCTTATATTGGTAG-GAAGTGGATTC------AG--GATCTTGTCTTCCCATAT
1 AGATCTTGTCTTCATGTATTGG-CGTGAAGTAGA-TCGAAGAAAGCAGATCTTGTCTTCATGTAT
** * **
199660 TGGTGGCGAAGTAGATTAAAGAAAGC
64 TGGCAG-GAAGTAGATCAAAGGTAGC
* * * * *
199686 AGATCTTATCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAGCAAATCCTATCTTTC-TATATT
1 AGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAGCAGATCTTGTC-TTCATGTATT
* * ** *
199750 GGTAGCGAAGTGGATTGAAGATAGC
65 GGCAG-GAAGTAGATCAAAGGTAGC
* * * *
199775 AGATCTTGTCTTTCCA--TACTGAGGGCGAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTA
1 AGATCTTGTC-TT-CATGTATTG-GCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTA
199838 TTGGC-GTGAAGTAGATCAAAGGTAGC
63 TTGGCAG-GAAGTAGATCAAAGGTAGC
* *
199864 AGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAAC-GAATCTTGTCTTCATGTATC
1 AGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAGCAG-ATCTTGTCTTCATGTATT
* * *
199928 GACATGAAGTAGATCAAAGGTAGA
65 GGCAGGAAGTAGATCAAAGGTAGC
* * *
199952 AGATATTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAAG-GGATCTTGTCTTCATGTATC
1 AGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAG-AAAGCAGATCTTGTCTTCATGTATT
* *
200016 GGCATGAAGTAGATCAAAGGTAGA
65 GGCAGGAAGTAGATCAAAGGTAGC
* * * *
200040 AGATCTTGTCTTCATGTATTGGCGTGAAGTAGATAGAAGAAAACGGATCTTGTCTTCATGTATCG
1 AGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTG
* *
200105 GCATGAAGTAGATCAAAGGTAGA
66 GCAGGAAGTAGATCAAAGGTAGC
* * **
200128 AGATCTTGTCTTCATGTATTGGTGTAAAGTAGATCGAAGAAAATAGATCTTGTCTTCATGTATTG
1 AGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTG
* * **
200193 GCATGAAGTAGATCAAGGGTATA
66 GCAGGAAGTAGATCAAAGGTAGC
* * * *
200216 AGATTTTGTCTTAATGTATCGGCATGAAGTAGATCGAAGA
1 AGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGA
200256 TATAAATCTT
Statistics
Matches: 623, Mismatches: 91, Indels: 53
0.81 0.12 0.07
Matches are distributed among these distances:
81 21 0.03
82 42 0.07
83 2 0.00
87 29 0.05
88 384 0.62
89 104 0.17
90 39 0.06
91 2 0.00
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.31
Consensus pattern (88 bp):
AGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTG
GCAGGAAGTAGATCAAAGGTAGC
Found at i:199721 original size:126 final size:126
Alignment explanation
Indices: 199428--199868 Score: 557
Period size: 126 Copynumber: 3.4 Consensus size: 126
199418 TGAAAATAGT
* * *
199428 AGATCTTGTCTTCATGTATTGGCGTGAAGTAGATTGAAGATAGCA-AGTTCTGTTTTCCTATATT
1 AGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGA-TCCTATTTT-CTATATT
* * *
199492 GGTAGGAAGTGGA-TCGAAGGTGCAGATTTTATCTTCCCATACTGGTGGCGAAGTAGATCGAAGA
64 GGTAGGAAGTGGATTC--A---G-AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGA
199556 AAGC
123 AAGC
199560 AGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTATTTTCTTATATTG
1 AGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTATTTTC-TATATTG
* *
199625 GTAGGAAGTGGATTCAG-GATCTTGTCTTCCCATATTGGTGGCGAAGTAGATTAAAGAAAGC
65 GTAGGAAGTGGATTCAGAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAAAGC
* * *
199686 AGATCTTATCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAGCAAATCCTATCTTTCTATATTG
1 AGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTAT-TTTCTATATTG
* *
199751 GTAGCGAAGTGGATTGAAGATAGCAGATCTTGTCTTTCCATACTGAG-GGCGAAGTAGATCAAAG
65 GTAG-GAAGTGGATT-----CAG-AGATCTTGTCTTCCCATACTG-GTGGCGAAGTAGATCAAAG
199815 AAAGC
122 AAAGC
* *
199820 AGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGGTAGCAGATC
1 AGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATC
199869 TTGTCTTCAT
Statistics
Matches: 276, Mismatches: 20, Indels: 24
0.86 0.06 0.08
Matches are distributed among these distances:
126 100 0.36
127 14 0.05
128 1 0.00
131 2 0.01
132 72 0.26
133 3 0.01
134 83 0.30
135 1 0.00
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (126 bp):
AGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTATTTTCTATATTGG
TAGGAAGTGGATTCAGAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAAAGC
Found at i:200260 original size:44 final size:44
Alignment explanation
Indices: 199667--200265 Score: 524
Period size: 44 Copynumber: 13.6 Consensus size: 44
199657 TATTGGTGGC
* * * * *
199667 GAAGTAGATTAAAGAAAGCAGATCTTATCTTCATGTATTGGCGT
1 GAAGTAGATCAAAGATAGAAGATCTTGTCTTCATGTATTGGCAT
* * * * * * *
199711 GAAGTAGATCGAAGAAAGCAA-ATCCTATCTTTC-TATATTGGTAGC
1 GAAGTAGATCAAAGATAG-AAGATCTTGTC-TTCATGTATTGGCA-T
* ** * * *
199756 GAAGTGGATTGAAGATAGCAGATCTTGTCTTTCCATACTGA-GGGC--
1 GAAGTAGATCAAAGATAGAAGATCTTGTC-TT-CAT-GT-ATTGGCAT
* * *
199801 GAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTATTGGCGT
1 GAAGTAGATCAAAGATAGAAGATCTTGTCTTCATGTATTGGCAT
* * *
199845 GAAGTAGATCAAAGGTAGCAGATCTTGTCTTCATGTATTGGCGT
1 GAAGTAGATCAAAGATAGAAGATCTTGTCTTCATGTATTGGCAT
* * *
199889 GAAGTAGATCGAAGA-A-AACGAATCTTGTCTTCATGTATCGACAT
1 GAAGTAGATCAAAGATAGAA-G-ATCTTGTCTTCATGTATTGGCAT
* * *
199933 GAAGTAGATCAAAGGTAGAAGATATTGTCTTCATGTATTGGCGT
1 GAAGTAGATCAAAGATAGAAGATCTTGTCTTCATGTATTGGCAT
* *
199977 GAAGTAGATCGAAGA-A-AAGGGATCTTGTCTTCATGTATCGGCAT
1 GAAGTAGATCAAAGATAGAA--GATCTTGTCTTCATGTATTGGCAT
* *
200021 GAAGTAGATCAAAGGTAGAAGATCTTGTCTTCATGTATTGGCGT
1 GAAGTAGATCAAAGATAGAAGATCTTGTCTTCATGTATTGGCAT
*
200065 GAAGTAGAT-AGAAGA-A-AACGGATCTTGTCTTCATGTATCGGCAT
1 GAAGTAGATCA-AAGATAGAA--GATCTTGTCTTCATGTATTGGCAT
* **
200109 GAAGTAGATCAAAGGTAGAAGATCTTGTCTTCATGTATTGGTGT
1 GAAGTAGATCAAAGATAGAAGATCTTGTCTTCATGTATTGGCAT
* * *
200153 AAAGTAGATCGAAGA-AAATAGATCTTGTCTTCATGTATTGGCAT
1 GAAGTAGATCAAAGATAGA-AGATCTTGTCTTCATGTATTGGCAT
* * * * * *
200197 GAAGTAGATCAAGGGTATAAGATTTTGTCTTAATGTATCGGCAT
1 GAAGTAGATCAAAGATAGAAGATCTTGTCTTCATGTATTGGCAT
* *
200241 GAAGTAGATCGAAGATATAA-ATCTT
1 GAAGTAGATCAAAGATAGAAGATCTT
200266 ATCTCCCTGA
Statistics
Matches: 457, Mismatches: 71, Indels: 55
0.78 0.12 0.09
Matches are distributed among these distances:
41 1 0.00
42 9 0.02
43 14 0.03
44 361 0.79
45 60 0.13
46 7 0.02
47 1 0.00
48 3 0.01
49 1 0.00
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (44 bp):
GAAGTAGATCAAAGATAGAAGATCTTGTCTTCATGTATTGGCAT
Found at i:200320 original size:44 final size:43
Alignment explanation
Indices: 200260--200381 Score: 154
Period size: 44 Copynumber: 2.8 Consensus size: 43
200250 CGAAGATATA
* * *
200260 AATCTTATCTCCCTGAATTTGCAGTGGAGCAGATTAAAGTCTAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAT-TAC
* *
200304 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATTAC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATTAC
* * *
200347 AGATCTTATCTCTCTGAAGTTGCAGTAGAGTAGAT
1 A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
200382 CGCAACGGAT
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
43 3 0.04
44 64 0.96
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (43 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATTAC
Found at i:200785 original size:15 final size:15
Alignment explanation
Indices: 200765--200795 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
200755 ACAATAACAA
200765 TGGCCCAAACTACAG
1 TGGCCCAAACTACAG
*
200780 TGGCCCAAATTACAG
1 TGGCCCAAACTACAG
200795 T
1 T
200796 TAGAAACCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.29, G:0.19, T:0.19
Consensus pattern (15 bp):
TGGCCCAAACTACAG
Found at i:201131 original size:13 final size:13
Alignment explanation
Indices: 201110--201143 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
201100 CTATTCTATA
*
201110 TTTTATTTTATTT
1 TTTTCTTTTATTT
201123 TTTTCTTTTATTT
1 TTTTCTTTTATTT
*
201136 TTTACTTT
1 TTTTCTTT
201144 GCTAAAATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTCTTTTATTT
Found at i:201496 original size:13 final size:12
Alignment explanation
Indices: 201465--201495 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
201455 AAGGGGAGAG
201465 TTTTTTTGAAGT
1 TTTTTTTGAAGT
201477 TTTTTTTGAAGT
1 TTTTTTTGAAGT
201489 TTTTTTT
1 TTTTTTT
201496 TAAAAGAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.13, C:0.00, G:0.13, T:0.74
Consensus pattern (12 bp):
TTTTTTTGAAGT
Found at i:219172 original size:14 final size:14
Alignment explanation
Indices: 219155--219209 Score: 76
Period size: 14 Copynumber: 4.0 Consensus size: 14
219145 TGAGGTTGAA
* *
219155 GGTGTAAGGTGTAG
1 GGTGTAGGGTTTAG
219169 GGTGTAGGGTTTAG
1 GGTGTAGGGTTTAG
219183 GGTGTAGGGTTTAG
1 GGTGTAGGGTTTAG
*
219197 GGTTTA-GGTTTAG
1 GGTGTAGGGTTTAG
219210 AGCTTAAGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
13 7 0.18
14 31 0.82
ACGTcount: A:0.16, C:0.00, G:0.47, T:0.36
Consensus pattern (14 bp):
GGTGTAGGGTTTAG
Found at i:219188 original size:21 final size:21
Alignment explanation
Indices: 219162--219204 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
219152 GAAGGTGTAA
219162 GGTGTAGGGTGTAGGGTTTAG
1 GGTGTAGGGTGTAGGGTTTAG
*
219183 GGTGTAGGGTTTAGGGTTTAG
1 GGTGTAGGGTGTAGGGTTTAG
219204 G
1 G
219205 TTTAGAGCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.51, T:0.35
Consensus pattern (21 bp):
GGTGTAGGGTGTAGGGTTTAG
Found at i:219208 original size:6 final size:7
Alignment explanation
Indices: 219073--219209 Score: 66
Period size: 7 Copynumber: 20.0 Consensus size: 7
219063 AGATTAATAT
*
219073 GGTTTAA
1 GGTTTAG
219080 GGTTTAG
1 GGTTTAG
*
219087 GG-TTAA
1 GGTTTAG
* *
219093 GCTTGAG
1 GGTTTAG
*
219100 GGCTTAG
1 GGTTTAG
*
219107 GGTGTA-
1 GGTTTAG
219113 GGTTTAG
1 GGTTTAG
* *
219120 TGTTTAA
1 GGTTTAG
219127 GGTTTAG
1 GGTTTAG
* *
219134 GAGGTTCG
1 G-GTTTAG
* *
219142 AGTTGA-
1 GGTTTAG
* *
219148 GGTTGAA
1 GGTTTAG
* *
219155 GGTGTAA
1 GGTTTAG
*
219162 GGTGTAG
1 GGTTTAG
*
219169 GGTGTAG
1 GGTTTAG
219176 GGTTTAG
1 GGTTTAG
*
219183 GGTGTAG
1 GGTTTAG
219190 GGTTTAG
1 GGTTTAG
219197 GGTTTA-
1 GGTTTAG
219203 GGTTTAG
1 GGTTTAG
219210 AGCTTAAGAT
Statistics
Matches: 97, Mismatches: 28, Indels: 10
0.72 0.21 0.07
Matches are distributed among these distances:
6 20 0.21
7 73 0.75
8 4 0.04
ACGTcount: A:0.19, C:0.02, G:0.42, T:0.36
Consensus pattern (7 bp):
GGTTTAG
Found at i:219652 original size:32 final size:32
Alignment explanation
Indices: 219616--219678 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
219606 TAAACAGTTA
*
219616 AATTTTGAAAATTTTATGAAAAGAGAAATAAC
1 AATTTTGAAAATTTGATGAAAAGAGAAATAAC
* * *
219648 AATTTTTAAAATTTGATGAAATGATAAATAA
1 AATTTTGAAAATTTGATGAAAAGAGAAATAA
219679 TATTTTATCC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.52, C:0.02, G:0.11, T:0.35
Consensus pattern (32 bp):
AATTTTGAAAATTTGATGAAAAGAGAAATAAC
Found at i:219728 original size:42 final size:43
Alignment explanation
Indices: 219673--219852 Score: 127
Period size: 42 Copynumber: 4.1 Consensus size: 43
219663 ATGAAATGAT
*
219673 AAATAATATTTTATCCTTCAA-ATTAAAACAGTCAAAATATTTA
1 AAATATTATTTTATCCTT-AATATTAAAACAGTCAAAATATTTA
** * * * *
219716 AAATATTA-TTTATCCTTAATATTTTAACGGTTAAAATGGTATGA
1 AAATATTATTTTATCCTTAATATTAAAACAGTCAAAAT-AT-TTA
* *
219760 ATAGATAAATATATTTTATTCTTACA-ATTAAAACAATCAAAATATTTA
1 A-A-AT--AT-TATTTTATCCTTA-ATATTAAAACAGTCAAAATATTTA
* * * *
219808 AAATATTA-TTTATCTTTAATATTAAAATAGTTAAAGT-TTTA
1 AAATATTATTTTATCCTTAATATTAAAACAGTCAAAATATTTA
219849 AAAT
1 AAAT
219853 TTTAGTGAAG
Statistics
Matches: 105, Mismatches: 21, Indels: 24
0.70 0.14 0.16
Matches are distributed among these distances:
41 11 0.10
42 43 0.41
43 10 0.10
44 5 0.05
45 1 0.01
46 4 0.04
47 1 0.01
48 5 0.05
49 3 0.03
50 21 0.20
51 1 0.01
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.42
Consensus pattern (43 bp):
AAATATTATTTTATCCTTAATATTAAAACAGTCAAAATATTTA
Found at i:219841 original size:92 final size:93
Alignment explanation
Indices: 219670--219842 Score: 260
Period size: 92 Copynumber: 1.9 Consensus size: 93
219660 TTGATGAAAT
*
219670 GATAAATAATATTTTATCCTTCAAATTAAAACAGTCAAAATATTTAAAATATTATTTATCCTTAA
1 GATAAATAATATTTTATCCTTCAAATTAAAACAATCAAAATATTTAAAATATTATTTATCCTTAA
** *
219735 TATTTTAACGGTTAAAATGGTATGAATA
66 TATTAAAACAGTTAAAATGGTATGAATA
* *
219763 GATAAAT-ATATTTTATTCTT-ACAATTAAAACAATCAAAATATTTAAAATATTATTTATCTTTA
1 GATAAATAATATTTTATCCTTCA-AATTAAAACAATCAAAATATTTAAAATATTATTTATCCTTA
*
219826 ATATTAAAATAGTTAAA
65 ATATTAAAACAGTTAAA
219843 GTTTTAAAAT
Statistics
Matches: 72, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
91 1 0.01
92 64 0.89
93 7 0.10
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (93 bp):
GATAAATAATATTTTATCCTTCAAATTAAAACAATCAAAATATTTAAAATATTATTTATCCTTAA
TATTAAAACAGTTAAAATGGTATGAATA
Found at i:219874 original size:42 final size:42
Alignment explanation
Indices: 219823--219907 Score: 127
Period size: 42 Copynumber: 2.0 Consensus size: 42
219813 TTATTTATCT
* * *
219823 TTAATATTAAAATAGTTAAAGTTTTAAAATTTTAGTG-AAGGA
1 TTAAAATTAAAACAGTTAAAATTTTAAAATTTTA-TGAAAGGA
219865 TTAAAATTAAAACAGTTAAAATTTTAAAATTTTATGAAAGGA
1 TTAAAATTAAAACAGTTAAAATTTTAAAATTTTATGAAAGGA
219907 T
1 T
219908 AAATGATATT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
41 2 0.05
42 37 0.95
ACGTcount: A:0.48, C:0.01, G:0.12, T:0.39
Consensus pattern (42 bp):
TTAAAATTAAAACAGTTAAAATTTTAAAATTTTATGAAAGGA
Found at i:221069 original size:96 final size:96
Alignment explanation
Indices: 220898--221092 Score: 241
Period size: 96 Copynumber: 2.0 Consensus size: 96
220888 GATGCAGCTC
* * ** * * **
220898 CCATATCATATTCTACCATTAAACCATTATCCCTTGATCTCACCAATTGTGGGAGTTGGTGATTG
1 CCATATCATATTCTACCATTAAACCATGATCCCTTGATCCCACCAAGCGGGGGAGTCGGTGATCA
220963 TGCTGGTAGTGATCACCATGGAGCTTGTGTA
66 TGCTGGTAGTGATCACCATGGAGCTTGTGTA
* * * *
220994 CCATATCCTATTCTACCATTAAGCCATGATCCGTTGATCCCA-CTAGCGGGGAGAGTCGGTGATC
1 CCATATCATATTCTACCATTAAACCATGATCCCTTGATCCCACCAAGCGGGG-GAGTCGGTGATC
*
221058 ATG-TGGATAGTGATCACCATGGAGTTTGTGTA
65 ATGCTGG-TAGTGATCACCATGGAGCTTGTGTA
221090 CCA
1 CCA
221093 GAAAATATGG
Statistics
Matches: 84, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
95 8 0.10
96 76 0.90
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.31
Consensus pattern (96 bp):
CCATATCATATTCTACCATTAAACCATGATCCCTTGATCCCACCAAGCGGGGGAGTCGGTGATCA
TGCTGGTAGTGATCACCATGGAGCTTGTGTA
Found at i:223978 original size:21 final size:21
Alignment explanation
Indices: 223945--224000 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
223935 ATTGTTTTAC
*
223945 ATAA-TTA-AAATTTTAAAAC
1 ATAATTTATAAATTTTAAAAA
* *
223964 AT-ATTTTTATAATTTCAAAAA
1 ATAATTTATA-AATTTTAAAAA
223985 ATAATTTATAAATTTT
1 ATAATTTATAAATTTT
224001 CACAATGTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
18 1 0.04
19 4 0.14
20 1 0.04
21 16 0.57
22 6 0.21
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (21 bp):
ATAATTTATAAATTTTAAAAA
Found at i:224001 original size:22 final size:22
Alignment explanation
Indices: 223945--224002 Score: 54
Period size: 22 Copynumber: 2.8 Consensus size: 22
223935 ATTGTTTTAC
*
223945 ATAA-TTA-AAATTTT-AAAAC
1 ATAATTTATAAATTTTCAAAAA
*
223964 AT-ATTTTTATAA-TTTCAAAAA
1 ATAATTTATA-AATTTTCAAAAA
223985 ATAATTTATAAATTTTCA
1 ATAATTTATAAATTTTCA
224003 CAATGTTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 9
0.71 0.07 0.21
Matches are distributed among these distances:
18 1 0.03
19 4 0.13
20 4 0.13
21 10 0.33
22 11 0.37
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (22 bp):
ATAATTTATAAATTTTCAAAAA
Found at i:224959 original size:14 final size:14
Alignment explanation
Indices: 224940--224972 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
224930 TAGGATTCAA
*
224940 GTTTAAGTCTTAAG
1 GTTTAAGGCTTAAG
224954 GTTTAAGGCTTAAG
1 GTTTAAGGCTTAAG
224968 GTTTA
1 GTTTA
224973 GGGGATTCGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.27, C:0.06, G:0.24, T:0.42
Consensus pattern (14 bp):
GTTTAAGGCTTAAG
Found at i:225385 original size:25 final size:24
Alignment explanation
Indices: 225356--225405 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
225346 GTTAAAGTTA
*
225356 AAACAATCAAAATTTTAAAATATTT
1 AAACAATCAAAATTTGAAAA-ATTT
* *
225381 AAACAGTTAAAATTTGAAAAATTT
1 AAACAATCAAAATTTGAAAAATTT
225405 A
1 A
225406 TGAAAAGAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.56, C:0.06, G:0.04, T:0.34
Consensus pattern (24 bp):
AAACAATCAAAATTTGAAAAATTT
Found at i:225482 original size:116 final size:114
Alignment explanation
Indices: 225348--225611 Score: 273
Period size: 115 Copynumber: 2.3 Consensus size: 114
225338 CATAAACAGT
*
225348 TAAAGTTAAAACAATCAAAATTTTAAAATATTTAAACAG-TTAAAAT-TTGAAAAATTTATGAAA
1 TAAAATTAAAACAATCAAAATTTTAAAATATTT-AAC-GTTTAAAATGTT-AAAAATTTATGAAA
* *
225411 AGAGAAATGATAGTTTTTAAAATTTGATGAAAGGATAAATAATATTTTATCCC
63 AGAGAAATAATA-TTTTTAAAATTTGATGAAAGGATAAATAATATATTATCCC
* * * * ** * * * *
225464 TCAAATTAAAATAGTCAAAATATT-ATTTATCCTTAACGTTTTAACTGTTAAAATTTTATGAAAT
1 TAAAATTAAAACAATCAAAATTTTAAAATAT--TTAACGTTTAAAATGTTAAAAATTTATGAAAA
* ** * *
225528 GATAAATAATATTTTTTGAATTTTATGAAAGGATAAATAATATATTATCCT
64 GAGAAATAATATTTTTAAAATTTGATGAAAGGATAAATAATATATTATCCC
*
225579 TAAAATTAAAACAATCAAAATATTAAAAATATT
1 TAAAATTAAAACAATCAAAAT-TTTAAAATATT
225612 ATTTATCCTT
Statistics
Matches: 117, Mismatches: 25, Indels: 13
0.75 0.16 0.08
Matches are distributed among these distances:
115 59 0.50
116 50 0.43
117 8 0.07
ACGTcount: A:0.48, C:0.06, G:0.08, T:0.38
Consensus pattern (114 bp):
TAAAATTAAAACAATCAAAATTTTAAAATATTTAACGTTTAAAATGTTAAAAATTTATGAAAAGA
GAAATAATATTTTTAAAATTTGATGAAAGGATAAATAATATATTATCCC
Found at i:225622 original size:42 final size:43
Alignment explanation
Indices: 225562--225647 Score: 111
Period size: 42 Copynumber: 2.0 Consensus size: 43
225552 ATGAAAGGAT
225562 AAATAATATATTATCCTTAAAATTAAAACAATCAAAATATTAA
1 AAATAATATATTATCCTTAAAATTAAAACAATCAAAATATTAA
* * * * * *
225605 AAATATTAT-TTATCCTTAATATTTAAACAGTTAAAATTTTAA
1 AAATAATATATTATCCTTAAAATTAAAACAATCAAAATATTAA
225647 A
1 A
225648 TTTTATGAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
42 29 0.78
43 8 0.22
ACGTcount: A:0.52, C:0.08, G:0.01, T:0.38
Consensus pattern (43 bp):
AAATAATATATTATCCTTAAAATTAAAACAATCAAAATATTAA
Found at i:225738 original size:100 final size:99
Alignment explanation
Indices: 225541--225723 Score: 231
Period size: 100 Copynumber: 1.8 Consensus size: 99
225531 AAATAATATT
*
225541 TTTTGAATTTTATGAAAGGATAAATAATATATTATCCTTAAAATTAAAACAATCAAAATATTAAA
1 TTTTAAATTTTATGAAAGGATAAATAATATATTATCCTTAAAATTAAAACAATCAAAATATTAAA
** * * * *
225606 AATATTATTTATCCTTAATATTTAAACAGTTAAAA
66 AATAAAATTAAACCTAAAGATTT-AACAGTTAAAA
* * * * *
225641 TTTTAAATTTTATGAAAGGATAAATGATATTTTATCCTTAAAATTAAAATAGTCAAAATATTTAA
1 TTTTAAATTTTATGAAAGGATAAATAATATATTATCCTTAAAATTAAAACAATCAAAATATTAAA
**
225706 TTTAAAATTAAACCTAAA
66 AATAAAATTAAACCTAAA
225724 AGACTTTTTA
Statistics
Matches: 70, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
100 70 1.00
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.39
Consensus pattern (99 bp):
TTTTAAATTTTATGAAAGGATAAATAATATATTATCCTTAAAATTAAAACAATCAAAATATTAAA
AATAAAATTAAACCTAAAGATTTAACAGTTAAAA
Found at i:226711 original size:96 final size:97
Alignment explanation
Indices: 226531--226731 Score: 280
Period size: 96 Copynumber: 2.1 Consensus size: 97
226521 GATTCAGCTC
* * *
226531 CCATATCATATTCTACCATTAAACCATGATCCCCTGACCTTTACCAGCTGGGAGAGTTGGTGATC
1 CCATCTCATATTCTACCATTAAACCATGATCCCCTGACCTTCACCAGCTGGGAGAGTAGGTGATC
226596 ATGTTGATAGCGATCACCATGGAGTTTATGTA
66 ATGTTGATAGCGATCACCATGGAGTTTATGTA
* * *
226628 CCATCTCATATTCTACCATTAAACCATGATCCCTTGATC-TCACCAGCTTGGAGAGTCAGG-GAT
1 CCATCTCATATTCTACCATTAAACCATGATCCCCTGACCTTCACCAGCTGGGAGAGT-AGGTGAT
* * * *
226691 CATGTTGGTAGTGATGACCATGGAGTTTGTGTA
65 CATGTTGATAGCGATCACCATGGAGTTTATGTA
*
226724 CCAGCTCA
1 CCATCTCA
226732 AAATTTCTTG
Statistics
Matches: 92, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
96 54 0.59
97 38 0.41
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.30
Consensus pattern (97 bp):
CCATCTCATATTCTACCATTAAACCATGATCCCCTGACCTTCACCAGCTGGGAGAGTAGGTGATC
ATGTTGATAGCGATCACCATGGAGTTTATGTA
Found at i:227246 original size:22 final size:22
Alignment explanation
Indices: 227221--227265 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
227211 ATGTTATAAC
**
227221 TTTTTTTATTTATTAAAATATA
1 TTTTTTTATTTACCAAAATATA
227243 TTTTTTTATTTACCAAAATATA
1 TTTTTTTATTTACCAAAATATA
227265 T
1 T
227266 CAAAAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTTTTTATTTACCAAAATATA
Found at i:227360 original size:27 final size:27
Alignment explanation
Indices: 227330--227394 Score: 105
Period size: 27 Copynumber: 2.4 Consensus size: 27
227320 CGCCAATGGG
227330 ATTGGCGGCACCAAAGGTGCCAA-AGCC
1 ATTGGCGGCACCAAAGGTGCCAATA-CC
*
227357 ATTGGCGGCACCAATGGTGCCAATACC
1 ATTGGCGGCACCAAAGGTGCCAATACC
227384 ATTGGCGGCAC
1 ATTGGCGGCAC
227395 TACTCGTATT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
27 35 0.97
28 1 0.03
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.15
Consensus pattern (27 bp):
ATTGGCGGCACCAAAGGTGCCAATACC
Found at i:227493 original size:11 final size:11
Alignment explanation
Indices: 227477--227517 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
227467 GTTGTTGCGG
227477 AAAAGAAGAGA
1 AAAAGAAGAGA
227488 AAAAG-AGAGA
1 AAAAGAAGAGA
*
227498 AAAAGAGGAGA
1 AAAAGAAGAGA
227509 AAAAGAAGA
1 AAAAGAAGA
227518 TATTTTTTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
10 10 0.37
11 17 0.63
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (11 bp):
AAAAGAAGAGA
Found at i:227558 original size:12 final size:10
Alignment explanation
Indices: 227522--227554 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
227512 AGAAGATATT
227522 TTTTGTAATA
1 TTTTGTAATA
227532 TTTTGT-ATA
1 TTTTGTAATA
227541 TTTTGTAATA
1 TTTTGTAATA
227551 TTTT
1 TTTT
227555 TTGTTTTACT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 9 0.41
10 13 0.59
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.67
Consensus pattern (10 bp):
TTTTGTAATA
Found at i:227624 original size:3 final size:3
Alignment explanation
Indices: 227618--227652 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
227608 AGTATTATTA
227618 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
227653 AAGATGTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:228443 original size:18 final size:18
Alignment explanation
Indices: 228420--228457 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
228410 GGTTGGTGGT
228420 GAAGAAGAAGGTGCTGGC
1 GAAGAAGAAGGTGCTGGC
*
228438 GAAGAAGAAGGTGGTGGC
1 GAAGAAGAAGGTGCTGGC
228456 GA
1 GA
228458 TCATTGGGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.34, C:0.08, G:0.47, T:0.11
Consensus pattern (18 bp):
GAAGAAGAAGGTGCTGGC
Found at i:234431 original size:152 final size:152
Alignment explanation
Indices: 234155--234460 Score: 587
Period size: 152 Copynumber: 2.0 Consensus size: 152
234145 CAATCGGTTT
234155 TTAAAGCTTTTAAACCTTTTTAGCCCTCAACATTTGTAATTTTTTTTATCAATTTTGTCCATATC
1 TTAAAGCTTTTAAACCTTTTTAGCCCTCAACATTTGTAATTTTTTTTATCAATTTTGTCCATATC
234220 CTTTAAAAGTAGATACATTTTAAAAATTAACCTTTTTCACATTTAAAAAAAATTATATTTA-TAT
66 CTTTAAAAGTAGATACATTTTAAAAATTAACCTTTTTCACATTTAAAAAAAATTATATTTATTAT
234284 TTATTTAAATAAAATAAAAAATA
131 TT-TTTAAATAAAATAAAAAATA
234307 TTAAAGCTTTTAAACCTTTTTAGCCCTCAACATTTGTAATTTTTTTTATCAATTTTGTCCATATC
1 TTAAAGCTTTTAAACCTTTTTAGCCCTCAACATTTGTAATTTTTTTTATCAATTTTGTCCATATC
234372 CTTTAAAAGTAGATACATTTTAAAAATTAACCTTTTTCACATTTAAAAAAAATTATATTTATTAT
66 CTTTAAAAGTAGATACATTTTAAAAATTAACCTTTTTCACATTTAAAAAAAATTATATTTATTAT
*
234437 TTTTTTAATAAAATAAAAAATA
131 TTTTTAAATAAAATAAAAAATA
234459 TT
1 TT
234461 TTAAAATTAT
Statistics
Matches: 152, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
152 147 0.97
153 5 0.03
ACGTcount: A:0.39, C:0.12, G:0.04, T:0.45
Consensus pattern (152 bp):
TTAAAGCTTTTAAACCTTTTTAGCCCTCAACATTTGTAATTTTTTTTATCAATTTTGTCCATATC
CTTTAAAAGTAGATACATTTTAAAAATTAACCTTTTTCACATTTAAAAAAAATTATATTTATTAT
TTTTTAAATAAAATAAAAAATA
Found at i:234464 original size:20 final size:20
Alignment explanation
Indices: 234439--234477 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
234429 TTTATTATTT
234439 TTTTAATAA-AATAAAAAATA
1 TTTTAA-AATAATAAAAAATA
*
234459 TTTTAAAATTATAAAAAAT
1 TTTTAAAATAATAAAAAAT
234478 TCAAAATCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TTTTAAAATAATAAAAAATA
Found at i:235106 original size:14 final size:14
Alignment explanation
Indices: 235087--235126 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
235077 TTGATTGGCA
235087 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
235101 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
235115 GGAAAATGTTTT
1 GTAAAATGTTTT
235127 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:235135 original size:20 final size:20
Alignment explanation
Indices: 235110--235149 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
235100 CGTAAAATGA
*
235110 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
235130 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
235150 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:235139 original size:34 final size:35
Alignment explanation
Indices: 235095--235161 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
235085 CAGTAAAATG
*
235095 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
235129 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
235162 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:235165 original size:14 final size:15
Alignment explanation
Indices: 235089--235165 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
235079 GATTGGCAGT
* *
235089 AAAATG-TTTTCCGT
1 AAAATGATTTTCTGG
235103 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
235117 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
235137 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
235152 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
235166 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 25 0.50
15 11 0.22
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:235226 original size:32 final size:32
Alignment explanation
Indices: 235142--235227 Score: 93
Period size: 33 Copynumber: 2.6 Consensus size: 32
235132 TCTGTAAAAT
* * **
235142 GATTTACTGGAAAATATTTTCTGGTGTTTGATT
1 GATTT-CTTGAAAATATTTTCTGCTGTTTGACA
*
235175 GA-ATCTGTGTAAAATATTTTCTGCTGTTTGACA
1 GATTTCT-TG-AAAATATTTTCTGCTGTTTGACA
235208 GATTTCTTGAAAATATTTTC
1 GATTTCTTGAAAATATTTTC
235228 CGGAAAAGTT
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
31 2 0.05
32 13 0.30
33 26 0.59
34 3 0.07
ACGTcount: A:0.27, C:0.09, G:0.17, T:0.47
Consensus pattern (32 bp):
GATTTCTTGAAAATATTTTCTGCTGTTTGACA
Found at i:235381 original size:33 final size:33
Alignment explanation
Indices: 235344--235410 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
235334 ATTCCAAATG
*
235344 TTCATCTATTTGTAGATTATACCGATTTTATTT
1 TTCATATATTTGTAGATTATACCGATTTTATTT
235377 TTCATATATTTGTAGATTATACCGATTTTATTT
1 TTCATATATTTGTAGATTATACCGATTTTATTT
235410 T
1 T
235411 ACTTCTTCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.25, C:0.10, G:0.09, T:0.55
Consensus pattern (33 bp):
TTCATATATTTGTAGATTATACCGATTTTATTT
Found at i:238111 original size:7 final size:7
Alignment explanation
Indices: 238099--238124 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
238089 AACAAATATT
238099 GGGTTTA
1 GGGTTTA
238106 GGGTTTA
1 GGGTTTA
238113 GGGTTTA
1 GGGTTTA
238120 GGGTT
1 GGGTT
238125 GGGTTGGTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.46, T:0.42
Consensus pattern (7 bp):
GGGTTTA
Found at i:238441 original size:11 final size:11
Alignment explanation
Indices: 238425--238450 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
238415 AACCATCTGT
238425 ATATAACCAAA
1 ATATAACCAAA
238436 ATATAACCAAA
1 ATATAACCAAA
238447 ATAT
1 ATAT
238451 CATCCAGCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.15, G:0.00, T:0.23
Consensus pattern (11 bp):
ATATAACCAAA
Found at i:238753 original size:18 final size:19
Alignment explanation
Indices: 238730--238773 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 19
238720 GTTGCAATCC
238730 AAGGGGAAGGGAAAAGGG-
1 AAGGGGAAGGGAAAAGGGA
*
238748 AAGGGGAAGGGAAAGGGGA
1 AAGGGGAAGGGAAAAGGGA
238767 AAGGGGA
1 AAGGGGA
238774 GAAGAAGGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 17 0.71
19 7 0.29
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (19 bp):
AAGGGGAAGGGAAAAGGGA
Found at i:238754 original size:6 final size:6
Alignment explanation
Indices: 238730--238773 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
238720 GTTGCAATCC
* * *
238730 AAGGGG AAGGGA AAAGGG AAGGGG AAGGGA AAGGGG AAAGGGG A
1 AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG -AAGGGG A
238774 GAAGAAGGCA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
6 25 0.81
7 6 0.19
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (6 bp):
AAGGGG
Found at i:238780 original size:24 final size:24
Alignment explanation
Indices: 238730--238781 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
238720 GTTGCAATCC
* **
238730 AAGGGGAAGGGAAAAGGGAAGGGG
1 AAGGGAAAGGGAAAAGGGAAGAAG
* *
238754 AAGGGAAAGGGGAAAGGGGAGAAG
1 AAGGGAAAGGGAAAAGGGAAGAAG
238778 AAGG
1 AAGG
238782 CATCATTTTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (24 bp):
AAGGGAAAGGGAAAAGGGAAGAAG
Found at i:244320 original size:26 final size:27
Alignment explanation
Indices: 244289--244344 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
244279 AAAGTACATA
244289 ATTTTAAAAATTAAAATTTAT-TTTTT
1 ATTTTAAAAATTAAAATTTATATTTTT
* *
244315 ATTTTAAAATTTTAAATTTATAATTTTT
1 ATTTTAAAAATTAAAATTTAT-ATTTTT
244343 AT
1 AT
244345 ATAAAATTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 19 0.73
28 7 0.27
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (27 bp):
ATTTTAAAAATTAAAATTTATATTTTT
Found at i:244358 original size:27 final size:25
Alignment explanation
Indices: 244295--244359 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 25
244285 CATAATTTTA
*
244295 AAAATTAAAATTTATTTTTTATTTT
1 AAAATTAAAATTTATTTTTTATTAT
*
244320 AAAATTTTAAATTTATAATTTTTA-TAT
1 AAAA-TTAAAATTTAT--TTTTTATTAT
244347 AAAATTGAAAATT
1 AAAATT-AAAATT
244360 GAAAAAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
25 4 0.12
26 12 0.36
27 11 0.33
28 6 0.18
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
AAAATTAAAATTTATTTTTTATTAT
Found at i:244564 original size:15 final size:17
Alignment explanation
Indices: 244544--244579 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
244534 AGCTAAATCG
244544 ATTTTT-AT-AATTTTT
1 ATTTTTCATAAATTTTT
244559 ATTTTTCATAAATTTTT
1 ATTTTTCATAAATTTTT
244576 -TTTT
1 ATTTT
244580 GAATCAATCG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 6 0.32
16 6 0.32
17 7 0.37
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (17 bp):
ATTTTTCATAAATTTTT
Found at i:244653 original size:23 final size:24
Alignment explanation
Indices: 244627--244672 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
244617 TCGAAATTGA
244627 TTCAACTAATTTGT-TTAGTTTGG
1 TTCAACTAATTTGTATTAGTTTGG
* *
244650 TTCAACTAGTTTGTATTGGTTTG
1 TTCAACTAATTTGTATTAGTTTG
244673 CAAGTCAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.20, C:0.09, G:0.20, T:0.52
Consensus pattern (24 bp):
TTCAACTAATTTGTATTAGTTTGG
Found at i:244943 original size:25 final size:25
Alignment explanation
Indices: 244892--244943 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
244882 AGATTTTATG
* * *
244892 TACTTTTAAATGGCAAAGAATTATA
1 TACTTTTAAATGACAAAAAAATATA
244917 TACTTTTAAATTGACAAAAAAAT-TA
1 TACTTTTAAA-TGACAAAAAAATATA
244942 TA
1 TA
244944 AATGTTGAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.37
Consensus pattern (25 bp):
TACTTTTAAATGACAAAAAAATATA
Found at i:249331 original size:22 final size:21
Alignment explanation
Indices: 249280--249339 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 21
249270 CAGTAGTCAA
249280 AATGGCTAACAGCCATAAACAG
1 AATGGCTAA-AGCCATAAACAG
* * *
249302 GATAGCTATAAGCTATAAACAG
1 AATGGCTA-AAGCCATAAACAG
249324 AATGGCTACAAGCCAT
1 AATGGCTA-AAGCCAT
249340 CAGTAACGGT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
22 29 0.97
23 1 0.03
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.18
Consensus pattern (21 bp):
AATGGCTAAAGCCATAAACAG
Found at i:249370 original size:32 final size:32
Alignment explanation
Indices: 249333--249535 Score: 280
Period size: 32 Copynumber: 6.3 Consensus size: 32
249323 GAATGGCTAC
*
249333 AAGCCATCAGTAACGGTAATATGATCGGTACA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
* * *
249365 AAGCCATTAGTAATGGTAATATGATCGGTACA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
* * *
249397 AAGCCATCAATAACGATAATATGATCGGCATA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
* *
249429 AAGCCATCAGTAACAGTAATATGATCGGAACA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
* *
249461 AAGCCATCAATAACGGTAATATGATTGGCACA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
* *
249493 AAGCCATCAGTAATGGTAATATGATTGGCACA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
*
249525 AATCCATCAGT
1 AAGCCATCAGT
249536 GGCATCGCAG
Statistics
Matches: 151, Mismatches: 20, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 151 1.00
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.23
Consensus pattern (32 bp):
AAGCCATCAGTAACGGTAATATGATCGGCACA
Found at i:249561 original size:26 final size:26
Alignment explanation
Indices: 249532--249583 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
249522 ACAAATCCAT
* *
249532 CAGTGGCATCGCAGCAAAGCTGCCAG
1 CAGTAGCATCGCAACAAAGCTGCCAG
*
249558 CAGTAGTATCGCAACAAAGCTGCCAG
1 CAGTAGCATCGCAACAAAGCTGCCAG
249584 TATAGTATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.31, C:0.29, G:0.27, T:0.13
Consensus pattern (26 bp):
CAGTAGCATCGCAACAAAGCTGCCAG
Found at i:249829 original size:27 final size:27
Alignment explanation
Indices: 249798--250168 Score: 359
Period size: 27 Copynumber: 13.8 Consensus size: 27
249788 TTGACCTCGA
*
249798 GGGTATTACGGTCATTTTACCCTACAA
1 GGGTATTACGGTCATTTTACCCTACAG
* * *
249825 GGGTATTACGGTCATTTTATCCTATAA
1 GGGTATTACGGTCATTTTACCCTACAG
** * *
249852 GGGTATTACCATTATTTTATCCTACAG
1 GGGTATTACGGTCATTTTACCCTACAG
* *
249879 GGGCATTACGGTCATTTTACCTTACAG
1 GGGTATTACGGTCATTTTACCCTACAG
* **
249906 GTGTATTACAATCATTTTACCCTACAG
1 GGGTATTACGGTCATTTTACCCTACAG
* * *
249933 GGGCATTACGGTTATTTTACCCTACTG
1 GGGTATTACGGTCATTTTACCCTACAG
* *
249960 GGGTATTATGGTCATTTTACCCTATAG
1 GGGTATTACGGTCATTTTACCCTACAG
* *
249987 GGGCATTACAGTCATTTTACCCTACAG
1 GGGTATTACGGTCATTTTACCCTACAG
*
250014 GGGCATTACGGTCATTTTACCCTACAG
1 GGGTATTACGGTCATTTTACCCTACAG
* * * *
250041 GGGTATTACGATCATTTTACCATATAA
1 GGGTATTACGGTCATTTTACCCTACAG
* * * *
250068 GGGTATTTCAGT-ATTCTACCCTACGG
1 GGGTATTACGGTCATTTTACCCTACAG
* * *
250094 GGGTATTTCGGTCATTTTATCCTATAG
1 GGGTATTACGGTCATTTTACCCTACAG
* * * * *
250121 GGGCATTTCAGTTATTTTACCCATATA-
1 GGGTATTACGGTCATTTTACCC-TACAG
* **
250148 GGGTATTTCATTCATTTTACC
1 GGGTATTACGGTCATTTTACC
250169 TTTCGAAGGT
Statistics
Matches: 283, Mismatches: 59, Indels: 4
0.82 0.17 0.01
Matches are distributed among these distances:
26 20 0.07
27 259 0.92
28 4 0.01
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (27 bp):
GGGTATTACGGTCATTTTACCCTACAG
Found at i:260277 original size:3 final size:3
Alignment explanation
Indices: 260269--260306 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
260259 TACAATACAC
260269 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
260307 GGCTACGTAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:261472 original size:25 final size:25
Alignment explanation
Indices: 261410--261475 Score: 82
Period size: 25 Copynumber: 2.7 Consensus size: 25
261400 AATGAGCTTT
261410 AAATAATTAGTATA-AATTGATTTA
1 AAATAATTAGTATATAATTGATTTA
* *
261434 AAGTAAATAGTATATAA-TGATTTTA
1 AAATAATTAGTATATAATTGA-TTTA
*
261459 AAATAATTATTATATAA
1 AAATAATTAGTATATAA
261476 AACAACTTGA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
24 15 0.43
25 20 0.57
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.41
Consensus pattern (25 bp):
AAATAATTAGTATATAATTGATTTA
Found at i:262149 original size:14 final size:14
Alignment explanation
Indices: 262130--262157 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
262120 ATTCGTCCTC
262130 TTTACACTGATTTT
1 TTTACACTGATTTT
262144 TTTACACTGATTTT
1 TTTACACTGATTTT
262158 CCCCCTCCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.07, T:0.57
Consensus pattern (14 bp):
TTTACACTGATTTT
Found at i:271041 original size:30 final size:29
Alignment explanation
Indices: 271005--271126 Score: 138
Period size: 30 Copynumber: 4.1 Consensus size: 29
270995 CTTCGGCTTC
*
271005 GGCTTCGGCTATCATACTATGAAAAGGGAT
1 GGCTTCGACTATCA-ACTATGAAAAGGGAT
*
271035 GGCTTCGACTATCAATCTATGAAAAGAGAT
1 GGCTTCGACTATCAA-CTATGAAAAGGGAT
* *
271065 GGCTTCGGCTATCAAATTATGAAAAGGGAT
1 GGCTTCGACTATC-AACTATGAAAAGGGAT
* *
271095 GG-TGACGACTATCGAACAATGAAAAGGGAT
1 GGCT-TCGACTATC-AACTATGAAAAGGGAT
271125 GG
1 GG
271127 TAATGACCAT
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
29 2 0.03
30 75 0.95
31 2 0.03
ACGTcount: A:0.34, C:0.15, G:0.27, T:0.24
Consensus pattern (29 bp):
GGCTTCGACTATCAACTATGAAAAGGGAT
Done.