Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D01
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: 64473564
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1880000 characters in sequence are not A, C, G, or T
File 134 of 213
Found at i:39466889 original size:115 final size:113
Alignment explanation
Indices: 39466688--39467179 Score: 574
Period size: 114 Copynumber: 4.3 Consensus size: 113
39466678 CTTTTGGGGA
* * *
39466688 TTTAGCGGTGTTTTTGAGAAAGCGCCGCAAAAAAACATAAGCCTAACGACGCCGTTTTTTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACATAAGCCCAACGACGCCGTTTTCTGAGCT
* * **
39466753 TTCGGGGATTTAGCAGAATTTTTGAAAAAGCGCCGCTAATGCTGGGGGC
66 TTCGGGGATTTAGCGGCATTTTT-AAAAAGCGCCGCTAATGCTCAGGGC
* * * *
39466802 TTTAGCGGCGTTTTTG-GAAAACCACCGCAAAAAAATCATAAGCCCAACGACGTCGTTTTCTCAG
1 TTTAGCGGCGTTTTTGAG-AAAGCGCCGCAAAAAAA-CATAAGCCCAACGACGCCGTTTTCTGAG
* *
39466866 CTTTCGGGGATTTAGCGGCATTTTTTAGAAAGCGCCGCTAATGCTCAAGGC
64 CTTTCGGGGATTTAGCGGCA-TTTTTAAAAAGCGCCGCTAATGCTCAGGGC
** * * * * *
39466917 TTTAGCGATGTTTTTGATAAAGTGCCGCAAAAAAACCTAAGCCCAACGACGCTGTTTACTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACATAAGCCCAACGACGCCGTTTTCTGAGCT
* *
39466982 TTCGGGGATTTAGCGGCGTTTTTAAGAATGCGCCGCTAATGCTCAGGGC
66 TTCGGGGATTTAGCGGCATTTTTAA-AAAGCGCCGCTAATGCTCAGGGC
* * * * *
39467031 TTTAGCGGCTTTTTTGAGAAAGCGCTGCAAAGAAACCTAAGCCCAACGACGCCGTTTTTTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACATAAGCCCAACGACGCCGTTTTCTGAGCT
** * * * * *
39467096 TTCGCAGATTTAGCGGCGTTTTTAGGAAAGCCCCGC-AATGGTTAGGGC
66 TTCGGGGATTTAGCGGCATTTTTA-AAAAGCGCCGCTAATGCTCAGGGC
** * *
39467144 TTTAGTTGCGTTTTTTAGAAAGCGCCACAAAAAAAC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAAC
39467180 CTAATCCCGC
Statistics
Matches: 320, Mismatches: 52, Indels: 13
0.83 0.14 0.03
Matches are distributed among these distances:
113 46 0.14
114 178 0.56
115 91 0.28
116 5 0.02
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.28
Consensus pattern (113 bp):
TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACATAAGCCCAACGACGCCGTTTTCTGAGCT
TTCGGGGATTTAGCGGCATTTTTAAAAAGCGCCGCTAATGCTCAGGGC
Found at i:39466982 original size:229 final size:227
Alignment explanation
Indices: 39466688--39467179 Score: 596
Period size: 229 Copynumber: 2.2 Consensus size: 227
39466678 CTTTTGGGGA
* * **
39466688 TTTAGCGGTGTTTTTGAGAAAGCGCCGCAAAAAAACATAAGCCTAACGACGCCGTTTTTTGAGCT
1 TTTAGCGATGTTTTTGAGAAAGCGCCGCAAAAAAACATAAGCCCAACGACGCCGTTTACTGAGCT
**
39466753 TTCGGGGATTTAGCAGAATTTTTGAA-AAAGCGCCGCTAATGCTGGGGGCTTTAGCGGCGTTTTT
66 TTCGGGGATTTAGCAGAATTTTT-AAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGC-TTTTT
* **
39466817 GGA-AAACCACCGCAAAAAAATCATAAGCCCAACGACGTCGTTTTCTCAGCTTTCGGGGATTTAG
129 GGAGAAACCACCGCAAAAAAA-CATAAGCCCAACGACGCCGTTTTCTCAGCTTTCGCAGATTTAG
* *
39466881 CGGCATTTTTTA-GAAAGCGCCGCTAATGCTCAAGGC
193 CGGC-GTTTTTAGGAAAGCCCCGC-AATGCTCAAGGC
* * * *
39466917 TTTAGCGATGTTTTTGATAAAGTGCCGCAAAAAAACCTAAGCCCAACGACGCTGTTTACTGAGCT
1 TTTAGCGATGTTTTTGAGAAAGCGCCGCAAAAAAACATAAGCCCAACGACGCCGTTTACTGAGCT
* ** * *
39466982 TTCGGGGATTTAGCGGCGTTTTTAAGAATGCGCCGCTAATGCTCAGGGCTTTAGCGGCTTTTTTG
66 TTCGGGGATTTAGCAGAATTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCTTTTTGG
* * * * * * *
39467047 AGAAAGCGCTGCAAAGAAACCTAAGCCCAACGACGCCGTTTTTTGAGCTTTCGCAGATTTAGCGG
131 AGAAACCACCGCAAAAAAACATAAGCCCAACGACGCCGTTTTCTCAGCTTTCGCAGATTTAGCGG
* * *
39467112 CGTTTTTAGGAAAGCCCCGCAATGGTTAGGGC
196 CGTTTTTAGGAAAGCCCCGCAATGCTCAAGGC
* * * *
39467144 TTTAGTTG-CGTTTTTTAGAAAGCGCCACAAAAAAAC
1 TTTAG-CGATGTTTTTGAGAAAGCGCCGCAAAAAAAC
39467180 CTAATCCCGC
Statistics
Matches: 223, Mismatches: 36, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
227 43 0.19
228 61 0.27
229 119 0.53
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.28
Consensus pattern (227 bp):
TTTAGCGATGTTTTTGAGAAAGCGCCGCAAAAAAACATAAGCCCAACGACGCCGTTTACTGAGCT
TTCGGGGATTTAGCAGAATTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCTTTTTGG
AGAAACCACCGCAAAAAAACATAAGCCCAACGACGCCGTTTTCTCAGCTTTCGCAGATTTAGCGG
CGTTTTTAGGAAAGCCCCGCAATGCTCAAGGC
Found at i:39467458 original size:15 final size:15
Alignment explanation
Indices: 39467438--39467481 Score: 63
Period size: 14 Copynumber: 3.0 Consensus size: 15
39467428 CATATTTTAA
*
39467438 GGTTTAGGGAGTATG
1 GGTTTAGGGATTATG
39467453 GGTTTAGGGATTAT-
1 GGTTTAGGGATTATG
*
39467467 GGATTAGGGATTATG
1 GGTTTAGGGATTATG
39467482 ATTTAAGTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 13 0.50
15 13 0.50
ACGTcount: A:0.23, C:0.00, G:0.41, T:0.36
Consensus pattern (15 bp):
GGTTTAGGGATTATG
Found at i:39467815 original size:7 final size:7
Alignment explanation
Indices: 39467803--39467851 Score: 53
Period size: 7 Copynumber: 6.9 Consensus size: 7
39467793 AAATTAAGGT
39467803 TTAGGGG
1 TTAGGGG
39467810 TTAGGGG
1 TTAGGGG
39467817 TTTAGGGG
1 -TTAGGGG
**
39467825 TTAGATG
1 TTAGGGG
39467832 TTAGGGG
1 TTAGGGG
* *
39467839 TTAAGAG
1 TTAGGGG
39467846 TTAGGG
1 TTAGGG
39467852 ATTTAAGGTT
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
7 26 0.79
8 7 0.21
ACGTcount: A:0.20, C:0.00, G:0.47, T:0.33
Consensus pattern (7 bp):
TTAGGGG
Found at i:39467820 original size:15 final size:15
Alignment explanation
Indices: 39467799--39467866 Score: 63
Period size: 15 Copynumber: 4.7 Consensus size: 15
39467789 GTTGAAATTA
39467799 AGGTTTAGGGGTTAG
1 AGGTTTAGGGGTTAG
*
39467814 GGGTTTAGGGGTTAG
1 AGGTTTAGGGGTTAG
*
39467829 ATG-TTAGGGGTTA-
1 AGGTTTAGGGGTTAG
*
39467842 AGAG-TTAGGGATTTA-
1 AG-GTTTAGGG-GTTAG
39467857 AGGTTTAGGG
1 AGGTTTAGGG
39467867 ATTCAGGGGT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
13 1 0.02
14 18 0.40
15 26 0.58
ACGTcount: A:0.22, C:0.00, G:0.44, T:0.34
Consensus pattern (15 bp):
AGGTTTAGGGGTTAG
Found at i:39468007 original size:303 final size:297
Alignment explanation
Indices: 39467338--39468008 Score: 754
Period size: 299 Copynumber: 2.2 Consensus size: 297
39467328 ATTATTTAAA
* * ** * * *
39467338 ATAATTGTAAAAGAGATAATAATAAATTTGTTTAGGGTTTTTG-GT-TTAGTGTATATGATTTAT
1 ATAATTGTAAAAGAGATAATAATAAATTTATTGA-GAATTATGAGTATAAG-GTATAT-AATTAT
* * * * *
39467401 TTAAGATTTAAGGCCGGTTTAGGAGTTCATATTTTAAGGTTTAGGGAGTATGGGTTTAGGGATTA
63 TTAAGATTTAAAGCCAGTTTAGGAGTTCAGATTTTAAGGTTTAGAGAGTATGGATTTAGGGATTA
* * * * *
39467466 TGGATTAGGGATTATGATTTAAGTGTTGGGATTTAAGATTTAGGGGTTAGAAGGTTAGGGATTTA
128 TGAATTAGGGAGTATGATTTAAGGGTTGGAAATTAAGATTTAGGGGTTAGAAGGTTAGGGATTTA
*
39467531 GGGGTTAGACGTGCTAAGGGTTAAAAGCTAGGGATTCAGGGGTCGAGTTAGGGTTTTAGGTTTAG
193 GGGGTTAGACGT-CTAAGGGTTAAAAGCTAGGGATTCAGGGGTCGAGTTAAGGTTTTAGGTTTAG
39467596 ATTAATAATTTTTTTAATTTATATTTTAAATATGTTCTTAT
257 ATTAATAATTTTTTTAATTTATATTTTAAATATGTTCTTAT
* * ** * * * *
39467637 ATAATTGTAAAAGAGATAATAATAAATTTGTTTAGGGTTTTTAGTTTAAGGTATATGATTAATTT
1 ATAATTGTAAAAGAGATAATAATAAATTTATTGAGAATTATGAGTATAAGGTATATAATT-ATTT
39467702 AAGATTTAAAGCCAGTTTAGGAGTTCAGATTTTAAGGTTTAGAGAGTATGGATTTAGGGATTATG
65 AAGATTTAAAGCCAGTTTAGGAGTTCAGATTTTAAGGTTTAGAGAGTATGGATTTAGGGATTATG
* * *
39467767 AATTAGGGAGTATGGTTTAAGGGTT-GAAATTAAGGTTTAGGGGTTAG-GGGTTTAGGGGTTAGA
130 AATTAGGGAGTATGATTTAAGGGTTGGAAATTAAGATTTAGGGGTTAGAAGG-TTA--GG---GA
* * *
39467830 TGTTAGGGGTTAAGA-GT-T-AGGGATTTAAGGTTTAGGGATTCAGGGGTCGAGTTAAGGTTTT-
189 T-TTAGGGGTT-AGACGTCTAAGGG-TTAAAAG-CTAGGGATTCAGGGGTCGAGTTAAGGTTTTA
*
39467891 GAGTTTAGATTAATTATTTTTTTAATTTATATTTTAAATATGTTCTTAT
250 G-GTTTAGATTAATAATTTTTTTAATTTATATTTTAAATATGTTCTTAT
* *
39467940 ATAATTGTAAAAGGGATAATAATAAATCAAATATATTGA-AATTATGAGTAT-A-GTTTA-AATT
1 ATAATTGTAAAAGAGATAATAATAAAT----T-TATTGAGAATTATGAGTATAAGGTATATAATT
39468001 ATTTAAGA
61 ATTTAAGA
39468009 GATATATAAT
Statistics
Matches: 320, Mismatches: 33, Indels: 34
0.83 0.09 0.09
Matches are distributed among these distances:
297 2 0.01
298 30 0.09
299 127 0.40
300 5 0.02
301 4 0.01
302 7 0.02
303 111 0.35
304 14 0.04
305 7 0.02
306 1 0.00
307 8 0.03
308 4 0.01
ACGTcount: A:0.32, C:0.02, G:0.25, T:0.41
Consensus pattern (297 bp):
ATAATTGTAAAAGAGATAATAATAAATTTATTGAGAATTATGAGTATAAGGTATATAATTATTTA
AGATTTAAAGCCAGTTTAGGAGTTCAGATTTTAAGGTTTAGAGAGTATGGATTTAGGGATTATGA
ATTAGGGAGTATGATTTAAGGGTTGGAAATTAAGATTTAGGGGTTAGAAGGTTAGGGATTTAGGG
GTTAGACGTCTAAGGGTTAAAAGCTAGGGATTCAGGGGTCGAGTTAAGGTTTTAGGTTTAGATTA
ATAATTTTTTTAATTTATATTTTAAATATGTTCTTAT
Found at i:39468553 original size:106 final size:106
Alignment explanation
Indices: 39468432--39469285 Score: 585
Period size: 106 Copynumber: 7.7 Consensus size: 106
39468422 ATTTTATAAA
* * *
39468432 AAATCAATCTATAAAAAACAAAATAAAAAATTTTTAGCATAGCAAAACGTCGTCATTTTGTTCAA
1 AAATCAATTTATAAAAAATAAAATAAAAAATTTTTAGCATAGCAAAACGGCGTCATTTTGTTCAA
*
39468497 AATGAAATAGCGGTGTTTTGTATATAAACGCTGCAAAAAAT
66 AATGAAATAGCGGTGTTTTGTATATAAACGCCGCAAAAAAT
39468538 AAATCAATTTATAAAAAAATAAAAT-AAAAATTTTTAGCATAGCAAAACGGCGTCATTTTGTTCA
1 AAATCAATTTAT-AAAAAATAAAATAAAAAATTTTTAGCATAGCAAAACGGCGTCATTTTGTTCA
* * * *
39468602 AAATGAAATAGCGGCGTTTTGTATAAAAACTCTGCAAAAAAT
65 AAATGAAATAGCGGTGTTTTGTATATAAACGCCGCAAAAAAT
* *
39468644 AAATCAATTTATAAAAAAATAAAATAAAAAATTTTTAGCATAGCAAAACGACGTCATTTTGTATA
1 AAATCAATTTAT-AAAAAATAAAATAAAAAATTTTTAGCATAGCAAAACGGCGTCATTTTGT-TC
**** * * *
39468709 AAAATGCCGCAAA-AAAATTAATCAATT-TATAATAAA------ATAAAAT
64 AAAAT---G-AAATAGCGGT-GT--TTTGTAT-ATAAACGCCGCAAAAAAT
* * * * ** ****** * *
39468752 AAA-AAATTTTTAGCATAGCAAAACGGCGTCATTTTT-GTTCAAAATGAAATAATATTTTGCGGC
1 AAATCAATTTATA-AAAAATAAAA-TAAAAAATTTTTAG--C-ATA-G-CA-AA-A-----CGGC
* * * * *
39468815 GT-TTTTATGAT-AAACGCTGAAAAAGATAAGCAATAGCGACG-TTTGTTATAAAAACGCCGCAA
52 GTCATTT-TGTTCAAA--ATG---AA-AT-AGC----G-G-TGTTTTG-TATATAAACGCCGCAA
39468877 AAAAT
102 AAAAT
* * * *
39468882 AAATCAATTTATAAAAAA-ATAA-AAAAAA--TTTAACATAGTAAAACGGTGTCATTTTGTTCAA
1 AAATCAATTTATAAAAAATAAAATAAAAAATTTTTAGCATAGCAAAACGGCGTCATTTTGTTCAA
* * *
39468943 AATGAAATAATATTTTGCGGCGTTTTTATGAAAAATATAAAAACGCCACAAAAAAT
66 AATG--A-AATA----GC-G-GTGTTT-TG-----TATATAAACGCCGCAAAAAAT
*
39468999 AAATCAATTTATAAAAAATAAAATAAAAAATTTTTAGAATAGCAAAACGGCGTCATTTTGTTCAA
1 AAATCAATTTATAAAAAATAAAATAAAAAATTTTTAGCATAGCAAAACGGCGTCATTTTGTTCAA
** *
39469064 AATGAAATAGCGGCATTTTGTATATAAATGCCGCAAAAAAT
66 AATGAAATAGCGGTGTTTTGTATATAAACGCCGCAAAAAAT
39469105 AAATCAATTTATAAAAAAATAAAATAAAAAATTTTTAGCATAGCAAAACGGCGTCATTTTGTTCA
1 AAATCAATTTAT-AAAAAATAAAATAAAAAATTTTTAGCATAGCAAAACGGCGTCATTTTGTTCA
* * * *
39469170 AAATGAAATAACGGTGTTTT-TTTATAAAAAGCCGCAAAAATT
65 AAATGAAATAGCGGTGTTTTGTATAT-AAACGCCGCAAAAAAT
* *
39469212 AAATCAATTTATAAAAAACAAAATAAAAAATTTTTAGCATAACAAAACGGCGTCATTTTGTTCAA
1 AAATCAATTTATAAAAAATAAAATAAAAAATTTTTAGCATAGCAAAACGGCGTCATTTTGTTCAA
39469277 AATGAAATA
66 AATGAAATA
39469286 ATATTTTGAG
Statistics
Matches: 593, Mismatches: 87, Indels: 136
0.73 0.11 0.17
Matches are distributed among these distances:
106 208 0.35
107 153 0.26
108 21 0.04
109 1 0.00
110 2 0.00
111 6 0.01
112 19 0.03
113 11 0.02
114 17 0.03
115 8 0.01
116 1 0.00
117 41 0.07
118 13 0.02
119 17 0.03
120 2 0.00
121 35 0.06
122 1 0.00
123 4 0.01
124 5 0.01
125 6 0.01
127 1 0.00
129 3 0.01
130 11 0.02
131 7 0.01
ACGTcount: A:0.48, C:0.11, G:0.11, T:0.29
Consensus pattern (106 bp):
AAATCAATTTATAAAAAATAAAATAAAAAATTTTTAGCATAGCAAAACGGCGTCATTTTGTTCAA
AATGAAATAGCGGTGTTTTGTATATAAACGCCGCAAAAAAT
Found at i:39468797 original size:83 final size:83
Alignment explanation
Indices: 39468618--39468786 Score: 279
Period size: 83 Copynumber: 2.0 Consensus size: 83
39468608 AATAGCGGCG
*
39468618 TTTTGTATAAAAACT-CTGC-AAAAAATAAATCAATTTATAAAAAAATAAAATAAAAAATTTTTA
1 TTTTGTATAAAAA-TGCCGCAAAAAAATAAATCAATTTATAAAAAAATAAAATAAAAAATTTTTA
39468681 GCATAGCAAAACGACGTCA
65 GCATAGCAAAACGACGTCA
* *
39468700 TTTTGTATAAAAATGCCGCAAAAAAATTAATCAATTTATAATAAAATAAAATAAAAAATTTTTAG
1 TTTTGTATAAAAATGCCGCAAAAAAATAAATCAATTTATAAAAAAATAAAATAAAAAATTTTTAG
*
39468765 CATAGCAAAACGGCGTCA
66 CATAGCAAAACGACGTCA
39468783 TTTT
1 TTTT
39468787 TGTTCAAAAT
Statistics
Matches: 81, Mismatches: 4, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
81 1 0.01
82 16 0.20
83 64 0.79
ACGTcount: A:0.51, C:0.11, G:0.08, T:0.30
Consensus pattern (83 bp):
TTTTGTATAAAAATGCCGCAAAAAAATAAATCAATTTATAAAAAAATAAAATAAAAAATTTTTAG
CATAGCAAAACGACGTCA
Found at i:39469056 original size:461 final size:462
Alignment explanation
Indices: 39468432--39469428 Score: 1242
Period size: 461 Copynumber: 2.1 Consensus size: 462
39468422 ATTTTATAAA
* * * * *
39468432 AAATCAATCTATAAAAAACAAAATAAAAAATTTTTAGCATAGCAAAACGTCGTCATTTTGTTCAA
1 AAATCAATTTATAAAAAA-ATAATAAAAAAATTTTAGAATAGCAAAACGGCGTCATTTTGTTCAA
* * **
39468497 AATG--A-AATA----GC-G-GTGTTT-TG-----TATATAAACGCTGCAAAAAATAAATCAATT
65 AATGAAATAATATTTTGCGGCGTTTTTATGAAAAATATAAAAACGCCACAAAAAATAAATCAATT
*
39468547 TATAAAAAAATAAAATAAAAATTTTTAGCATAGCAAAACGGCGTCATTTTGTTCAAAATGAAATA
130 TATAAAAAAATAAAATAAAAATTTTTAGAATAGCAAAACGGCGTCATTTTGTTCAAAATGAAATA
* *
39468612 GCGGCGTTTTGTATAAAAACT-CTGCAAAAAATAAATCAATTTATAAAAAAATAAAATAAAAAAT
195 GCGGCATTTTGTATAAAAA-TGCCGCAAAAAATAAATCAATTTATAAAAAAATAAAATAAAAAAT
39468676 TTTTAGCATAGCAAAACGACGTCATTTTG-T-AT-AA-AA-AT-GCCGCAAAAAAATT-AATCAA
259 TTTTAGCATAGCAAAACGACGTCATTTTGTTAATAAATAATATAGCCGC--AAAAATTAAATCAA
* *
39468734 TTTATAATAAAATAAAATAAAAAATTTTTAGCATAGCAAAACGGCGTCATTTTTGTTCAAAATGA
322 TTTATAA-AAAACAAAATAAAAAATTTTTAGCATAACAAAACGGCGTCA-TTTTGTTCAAAATGA
* * * *
39468799 AATAATATTTTGCGGCGTTTTTATGATAAACGCTGAAAAAGATAAGCAATAGCGACGTTTGT-TA
385 AATAATATTTTGAGGC--ATTT-T--TAAACGCCGAAAAAGATAAGCAATAACGACGTTT-TCTA
39468863 TAAAAACGCCGCAAAAAAT
444 TAAAAACGCCGCAAAAAAT
* *
39468882 AAATCAATTTATAAAAAAAT-A-AAAAAAA-TTTA-ACATAGTAAAACGGTGTCATTTTGTTCAA
1 AAATCAATTTATAAAAAAATAATAAAAAAATTTTAGA-ATAGCAAAACGGCGTCATTTTGTTCAA
39468943 AATGAAATAATATTTTGCGGCGTTTTTATGAAAAATATAAAAACGCCACAAAAAATAAATCAATT
65 AATGAAATAATATTTTGCGGCGTTTTTATGAAAAATATAAAAACGCCACAAAAAATAAATCAATT
39469008 TAT-AAAAAATAAAATAAAAAATTTTTAGAATAGCAAAACGGCGTCATTTTGTTCAAAATGAAAT
130 TATAAAAAAATAAAAT-AAAAATTTTTAGAATAGCAAAACGGCGTCATTTTGTTCAAAATGAAAT
*
39469072 AGCGGCATTTTGTATATAAATGCCGCAAAAAATAAATCAATTTATAAAAAAATAAAATAAAAAAT
194 AGCGGCATTTTGTATAAAAATGCCGCAAAAAATAAATCAATTTATAAAAAAATAAAATAAAAAAT
*
39469137 TTTTAGCATAGCAAAACGGCGTCATTTTGTTCAAAATGAAATAACGGTGTTTTTTTATAAAAAGC
259 TTTTAGCATAGCAAAACGACGTCATTTTGTT---AAT-AAATAA-----------TAT----AGC
39469202 CGCAAAAATTAAATCAATTTATAAAAAACAAAATAAAAAATTTTTAGCATAACAAAACGGCGTCA
305 CGCAAAAATTAAATCAATTTATAAAAAACAAAATAAAAAATTTTTAGCATAACAAAACGGCGTCA
* * *
39469267 TTTTGTTCAAAATGAAATAATATTTTGAGGCATTTTTAAACGCCGCAAAGGATAAGCAATAACGG
370 TTTTGTTCAAAATGAAATAATATTTTGAGGCATTTTTAAACGCCGAAAAAGATAAGCAATAACGA
*
39469332 CGTTTTCTGTAAAAACGCCGCAAAAAAT
435 CGTTTTCTATAAAAACGCCGCAAAAAAT
39469360 AAATCAATTTATAAAAAAATAAAATAAAAAAATTTTAGAATAGCAAAACGGCGTCATTTTGTTCA
1 AAATCAATTTATAAAAAAAT--AATAAAAAAATTTTAGAATAGCAAAACGGCGTCATTTTGTTCA
39469425 AAAT
64 AAAT
39469429 AAAGTATAAA
Statistics
Matches: 468, Mismatches: 28, Indels: 69
0.83 0.05 0.12
Matches are distributed among these distances:
446 32 0.07
447 6 0.01
448 2 0.00
449 5 0.01
450 17 0.04
453 2 0.00
454 1 0.00
455 5 0.01
456 2 0.00
460 13 0.03
461 165 0.35
462 1 0.00
466 2 0.00
468 2 0.00
469 2 0.00
477 1 0.00
478 69 0.15
480 1 0.00
481 6 0.01
482 7 0.01
483 62 0.13
484 47 0.10
485 13 0.03
486 5 0.01
ACGTcount: A:0.48, C:0.11, G:0.12, T:0.29
Consensus pattern (462 bp):
AAATCAATTTATAAAAAAATAATAAAAAAATTTTAGAATAGCAAAACGGCGTCATTTTGTTCAAA
ATGAAATAATATTTTGCGGCGTTTTTATGAAAAATATAAAAACGCCACAAAAAATAAATCAATTT
ATAAAAAAATAAAATAAAAATTTTTAGAATAGCAAAACGGCGTCATTTTGTTCAAAATGAAATAG
CGGCATTTTGTATAAAAATGCCGCAAAAAATAAATCAATTTATAAAAAAATAAAATAAAAAATTT
TTAGCATAGCAAAACGACGTCATTTTGTTAATAAATAATATAGCCGCAAAAATTAAATCAATTTA
TAAAAAACAAAATAAAAAATTTTTAGCATAACAAAACGGCGTCATTTTGTTCAAAATGAAATAAT
ATTTTGAGGCATTTTTAAACGCCGAAAAAGATAAGCAATAACGACGTTTTCTATAAAAACGCCGC
AAAAAAT
Found at i:39469122 original size:107 final size:106
Alignment explanation
Indices: 39468861--39469286 Score: 520
Period size: 107 Copynumber: 3.9 Consensus size: 106
39468851 CGACGTTTGT
* * *
39468861 TATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAA-ATAA-AAAAAA--TTTAACATAGTA
1 TATAAAAA-GCCGCAAAAAATAAATCAATTTATAAAAAATAAAATAAAAAATTTTTAGCATAGCA
* *
39468922 AAACGGTGTCATTTTGTTCAAAATGAAATAATATTTTGCGGCGTTTTTATGAAAAA
65 AAACGGCGTCATTTTGTTCAAAATGAAAT-A-A-----CGGC-ATTTT-T-----A
* *
39468978 TATAAAAACGCCACAAAAAATAAATCAATTTATAAAAAATAAAATAAAAAATTTTTAGAATAGCA
1 TATAAAAA-GCCGCAAAAAATAAATCAATTTATAAAAAATAAAATAAAAAATTTTTAGCATAGCA
*
39469043 AAACGGCGTCATTTTGTTCAAAATGAAATAGCGGCATTTTGTA
65 AAACGGCGTCATTTTGTTCAAAATGAAATAACGGCATTTT-TA
*
39469086 TAT-AAATGCCGCAAAAAATAAATCAATTTATAAAAAAATAAAATAAAAAATTTTTAGCATAGCA
1 TATAAAAAGCCGCAAAAAATAAATCAATTTAT-AAAAAATAAAATAAAAAATTTTTAGCATAGCA
** *
39469150 AAACGGCGTCATTTTGTTCAAAATGAAATAACGGTGTTTTTT
65 AAACGGCGTCATTTTGTTCAAAATGAAATAACGGCATTTTTA
* * *
39469192 TATAAAAAGCCGCAAAAATTAAATCAATTTATAAAAAACAAAATAAAAAATTTTTAGCATAACAA
1 TATAAAAAGCCGCAAAAAATAAATCAATTTATAAAAAATAAAATAAAAAATTTTTAGCATAGCAA
39469257 AACGGCGTCATTTTGTTCAAAATGAAATAA
66 AACGGCGTCATTTTGTTCAAAATGAAATAA
39469287 TATTTTGAGG
Statistics
Matches: 283, Mismatches: 20, Indels: 23
0.87 0.06 0.07
Matches are distributed among these distances:
106 88 0.31
107 97 0.34
108 4 0.01
113 5 0.02
114 4 0.01
117 38 0.13
118 3 0.01
119 6 0.02
120 1 0.00
121 37 0.13
ACGTcount: A:0.50, C:0.11, G:0.11, T:0.29
Consensus pattern (106 bp):
TATAAAAAGCCGCAAAAAATAAATCAATTTATAAAAAATAAAATAAAAAATTTTTAGCATAGCAA
AACGGCGTCATTTTGTTCAAAATGAAATAACGGCATTTTTA
Found at i:39472244 original size:43 final size:43
Alignment explanation
Indices: 39472145--39472409 Score: 275
Period size: 43 Copynumber: 6.2 Consensus size: 43
39472135 AGATATGTTT
* *
39472145 TAGCGGCGTTTGCGTG-AAAAGCGCCGCTAAAGGTC-TGTTCTA
1 TAGCGGCGTTTGTG-GAAAAAGCGCCGCTAAAGGTCTTGATCTA
* * * * *
39472187 TAGTGGCATCTGTGGGAAAAGCGCCACTAAAGGTCTTGATCTA
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGATCTA
*
39472230 TAGCGACGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGATCTA
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGATCTA
*** ** *
39472273 TAGCGGCGTTTGCAAAAAAAATGTCGCTAAAGGTCTTGATCTA
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGATCTA
* * ** * * * * *
39472316 TAGCAGCGTTTATTAAAAAATCACTGTTAAAGGTCCTGATCTA
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGATCTA
* *
39472359 TAGCGGCGTTTGTGG-GAAAGCGCCGCTAAAGGTCCTGATCTA
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGATCTA
39472401 TAGCGGCGT
1 TAGCGGCGT
39472410 ATATTTCTAT
Statistics
Matches: 182, Mismatches: 39, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
41 1 0.01
42 59 0.32
43 122 0.67
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (43 bp):
TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGATCTA
Found at i:39472749 original size:20 final size:22
Alignment explanation
Indices: 39472716--39472756 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
39472706 AGACCAATTT
39472716 TTCTCCTAAATTTT-AATTTAA
1 TTCTCCTAAATTTTCAATTTAA
*
39472737 TTCT-CTAATTTTTCAATTTA
1 TTCTCCTAAATTTTCAATTTA
39472757 TTGATTTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.29, C:0.15, G:0.00, T:0.56
Consensus pattern (22 bp):
TTCTCCTAAATTTTCAATTTAA
Found at i:39497006 original size:79 final size:81
Alignment explanation
Indices: 39496870--39497054 Score: 218
Period size: 79 Copynumber: 2.3 Consensus size: 81
39496860 TTGAATGATG
* *
39496870 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
39496934 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
39496949 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
39497011 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* * *
39497029 ACGGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
39497055 AACGAGTAGC
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
78 1 0.01
79 56 0.62
80 33 0.37
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:39497061 original size:40 final size:40
Alignment explanation
Indices: 39496870--39497054 Score: 216
Period size: 40 Copynumber: 4.7 Consensus size: 40
39496860 TTGAATGATG
* * * *
39496870 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
39496910 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
39496950 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
39496989 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
39497030 -CGGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
39497055 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
39 35 0.28
40 79 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:39497076 original size:79 final size:79
Alignment explanation
Indices: 39496923--39497077 Score: 190
Period size: 79 Copynumber: 2.0 Consensus size: 79
39496913 GGACTAAGAT
* * **
39496923 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
39496988 ATCCGGGTTAAGTC
66 ATCCGGGTTAAGTC
* * *
39497002 CCGAAGGCAATTGTGCGAGTTACT-ATAACGGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
*
39497065 TATATCC-GGTTAA
63 TAAATCCGGGTTAA
39497078 ATTCTGAAGG
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
78 2 0.03
79 38 0.58
80 25 0.38
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAGTC
Found at i:39504748 original size:40 final size:39
Alignment explanation
Indices: 39504664--39504847 Score: 194
Period size: 40 Copynumber: 4.6 Consensus size: 39
39504654 TTGAATGATG
* * * *
39504664 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
39504704 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
*
39504744 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
* *
39504783 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AA
*
39504824 --CGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
39504848 AACGGGTAGC
Statistics
Matches: 123, Mismatches: 17, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
39 56 0.46
40 57 0.46
41 10 0.08
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:39504765 original size:39 final size:40
Alignment explanation
Indices: 39504664--39504847 Score: 191
Period size: 39 Copynumber: 4.7 Consensus size: 40
39504654 TTGAATGATG
* *
39504664 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
39504703 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
* *
39504744 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* * *
39504783 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
** *
39504822 AACGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
39504848 AACGGGTAGC
Statistics
Matches: 124, Mismatches: 14, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
39 57 0.46
40 54 0.44
41 12 0.10
42 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:39504800 original size:79 final size:80
Alignment explanation
Indices: 39504664--39504847 Score: 223
Period size: 79 Copynumber: 2.3 Consensus size: 80
39504654 TTGAATGATG
* *
39504664 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
39504728 TGTGCGAGATACTAAT
66 TGTGCGAGATACT-AT
* * * **
39504744 TCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAA
*
39504806 TTGTGCGAGTTACTAT
65 TTGTGCGAGATACTAT
** *
39504822 AACGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
39504848 AACGGGTAGC
Statistics
Matches: 90, Mismatches: 11, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
78 11 0.12
79 61 0.68
80 18 0.20
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTAT
Found at i:39504865 original size:79 final size:78
Alignment explanation
Indices: 39504717--39504880 Score: 188
Period size: 79 Copynumber: 2.1 Consensus size: 78
39504707 GGACTAAGAT
* ** ** *
39504717 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATAACGGGCTAAGCCCGAAGGCATTTGAACGAGGTACTAA
*
39504782 ATCCGGGTTAAGTC
66 ATCC-GGTTAAATC
* *
39504796 CCGAAGGCAATTGTGCGAGTTACT-ATAACGGGCTATGTCCCGAAGGCATTTGAACG-GGTAGCT
1 CCGAAGGCAATTGTGCGAGATACTAATAACGGGCTAAG-CCCGAAGGCATTTGAACGAGGTA-CT
* *
39504859 ATATCCGGTTAAATT
64 AAATCCGGTTAAATC
39504874 CCGAAGG
1 CCGAAGG
39504881 TACGTGATTT
Statistics
Matches: 72, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
78 27 0.38
79 45 0.62
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (78 bp):
CCGAAGGCAATTGTGCGAGATACTAATAACGGGCTAAGCCCGAAGGCATTTGAACGAGGTACTAA
ATCCGGTTAAATC
Found at i:39508844 original size:50 final size:49
Alignment explanation
Indices: 39508759--39508880 Score: 163
Period size: 50 Copynumber: 2.5 Consensus size: 49
39508749 TTACATTTCT
* * * *
39508759 GGTAAGGCATGTTAGTTGCTAACCAGCTTGGCGTTATGGGTGATGCCAAC
1 GGTAGGGCATGTTAGTTGATAACCAGCCTGACGTTATGGGTGATG-CAAC
* *
39508809 GGTAGGGCATGTTAGTTGTTAACCAGCCTGACGTTATGGGTGATGCATC
1 GGTAGGGCATGTTAGTTGATAACCAGCCTGACGTTATGGGTGATGCAAC
* *
39508858 GATAGGGTATGTTAGTTGATAAC
1 GGTAGGGCATGTTAGTTGATAAC
39508881 AATGGCAAAG
Statistics
Matches: 64, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
49 23 0.36
50 41 0.64
ACGTcount: A:0.23, C:0.15, G:0.32, T:0.30
Consensus pattern (49 bp):
GGTAGGGCATGTTAGTTGATAACCAGCCTGACGTTATGGGTGATGCAAC
Found at i:39509058 original size:66 final size:66
Alignment explanation
Indices: 39508975--39509106 Score: 221
Period size: 66 Copynumber: 2.0 Consensus size: 66
39508965 ATGGGATCCG
* * *
39508975 AGGTTAGTACAAGGAAGGGCTTGGGAAATAGT-AAGAAAATGTGAAAAATGGATTTCTTGTATAT
1 AGGTTAGCACAAGGAAGGGCATGGGAAAGAGTGAA-AAAATGTGAAAAATGGATTTCTTGTATAT
39509039 AA
65 AA
39509041 AGGTTAGCACAAGGAAGGGCATGGGAAAGAGTGAAAAAATGTGAAAAATGGATTTCTTGTATATA
1 AGGTTAGCACAAGGAAGGGCATGGGAAAGAGTGAAAAAATGTGAAAAATGGATTTCTTGTATATA
39509106 A
66 A
39509107 TGCATGTTAT
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
66 60 0.97
67 2 0.03
ACGTcount: A:0.42, C:0.05, G:0.28, T:0.25
Consensus pattern (66 bp):
AGGTTAGCACAAGGAAGGGCATGGGAAAGAGTGAAAAAATGTGAAAAATGGATTTCTTGTATATA
A
Found at i:39511087 original size:35 final size:35
Alignment explanation
Indices: 39511047--39511115 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 35
39511037 GTGGTAGAAG
* *
39511047 TTAAAATAAGGAGGTAAAATGGTAAAGTGGTTAAA
1 TTAAAATAAGAAGGTAAAATGGTAAAGTGATTAAA
* *
39511082 TTAAAATAAGAAGGTGAAGTGGTAAAGTGATTAA
1 TTAAAATAAGAAGGTAAAATGGTAAAGTGATTAA
39511116 GTGTTTCTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.48, C:0.00, G:0.26, T:0.26
Consensus pattern (35 bp):
TTAAAATAAGAAGGTAAAATGGTAAAGTGATTAAA
Found at i:39511480 original size:16 final size:17
Alignment explanation
Indices: 39511432--39511482 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 17
39511422 TCATTTGCTA
*
39511432 TCATTTTCTCATTTTTTT
1 TCATTTTCTC-TATTTTT
*
39511450 TCA-TTTCTTTATTTTT
1 TCATTTTCTCTATTTTT
*
39511466 T-ATTTTCTCTCTTTTT
1 TCATTTTCTCTATTTTT
39511482 T
1 T
39511483 GACAAACAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 1 0.04
16 19 0.68
17 5 0.18
18 3 0.11
ACGTcount: A:0.10, C:0.16, G:0.00, T:0.75
Consensus pattern (17 bp):
TCATTTTCTCTATTTTT
Found at i:39514277 original size:17 final size:17
Alignment explanation
Indices: 39514222--39514278 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 17
39514212 ACTTAGGTAG
39514222 TATGCGAACCTC-TGATAT
1 TATGCGAA-CTCATG-TAT
* * *
39514240 TTTGCAAACTCATTTTAT
1 TATGCGAACTCA-TGTAT
39514258 TATGCGAACTCATGTAT
1 TATGCGAACTCATGTAT
39514275 TATG
1 TATG
39514279 TTGCTATGCG
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
17 11 0.35
18 19 0.61
19 1 0.03
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (17 bp):
TATGCGAACTCATGTAT
Found at i:39526639 original size:30 final size:30
Alignment explanation
Indices: 39526604--39526666 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
39526594 AAACTATTTC
39526604 CATTTACTGAAAGTATGTGATTAGTGAGGA
1 CATTTACTGAAAGTATGTGATTAGTGAGGA
*
39526634 CATTTACTGAAAGTATGTGATTTGTGAGGA
1 CATTTACTGAAAGTATGTGATTAGTGAGGA
39526664 CAT
1 CAT
39526667 GCTGAGCATG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.32, C:0.08, G:0.25, T:0.35
Consensus pattern (30 bp):
CATTTACTGAAAGTATGTGATTAGTGAGGA
Found at i:39532239 original size:33 final size:33
Alignment explanation
Indices: 39532196--39532261 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
39532186 TTTCTGGATA
39532196 TTGTAATTTGCAAGAGTTGTTGCGGGCTAGACG
1 TTGTAATTTGCAAGAGTTGTTGCGGGCTAGACG
* *
39532229 TTGTAGTTTGCAAGAGTTGTTGTGGGCTAGACG
1 TTGTAATTTGCAAGAGTTGTTGCGGGCTAGACG
39532262 AGAAGAAGGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.20, C:0.11, G:0.35, T:0.35
Consensus pattern (33 bp):
TTGTAATTTGCAAGAGTTGTTGCGGGCTAGACG
Found at i:39538253 original size:16 final size:16
Alignment explanation
Indices: 39538232--39538264 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
39538222 TTCTAGAAAC
*
39538232 TCTAAAAATAGTTATA
1 TCTAAAAATAGATATA
39538248 TCTAAAAATAGATATA
1 TCTAAAAATAGATATA
39538264 T
1 T
39538265 TTACTTGGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.36
Consensus pattern (16 bp):
TCTAAAAATAGATATA
Found at i:39540450 original size:96 final size:96
Alignment explanation
Indices: 39540334--39540509 Score: 316
Period size: 96 Copynumber: 1.8 Consensus size: 96
39540324 TACTTTCTTA
*
39540334 TCTAGTTGGATATTTAATTGGACATTGGAAACCCTTATGATCTTTTGAACTAGACCAATAACATT
1 TCTAGTTGGATATTTAATTGGACATTGGAAACCCTTATGATCTTTTGAACTACACCAATAACATT
39540399 GCACAAAAGGTGATATCTCAAACATCTTCTC
66 GCACAAAAGGTGATATCTCAAACATCTTCTC
* * *
39540430 TCTATTTGGATATTTAATTGGACATTGGAAACCCTTATGATCTTTTGAACTACACTAATAATATT
1 TCTAGTTGGATATTTAATTGGACATTGGAAACCCTTATGATCTTTTGAACTACACCAATAACATT
39540495 GCACAAAAGGTGATA
66 GCACAAAAGGTGATA
39540510 GTTGAATCGT
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
96 76 1.00
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (96 bp):
TCTAGTTGGATATTTAATTGGACATTGGAAACCCTTATGATCTTTTGAACTACACCAATAACATT
GCACAAAAGGTGATATCTCAAACATCTTCTC
Found at i:39547443 original size:6 final size:6
Alignment explanation
Indices: 39547432--39547482 Score: 59
Period size: 6 Copynumber: 8.5 Consensus size: 6
39547422 AGTTTATTTG
** *
39547432 TTTTAT TTTTAT TTTTAT TTTTAT TATTT-T TCGTAT TTTTAT TGTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT T-TTTAT TTTTAT TTTTAT TTTTAT
39547480 TTT
1 TTT
39547483 CTTCAATTTG
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
5 1 0.03
6 33 0.89
7 3 0.08
ACGTcount: A:0.16, C:0.02, G:0.04, T:0.78
Consensus pattern (6 bp):
TTTTAT
Found at i:39557553 original size:20 final size:20
Alignment explanation
Indices: 39557528--39557567 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
39557518 CTCCTTCATT
39557528 GGTACATGAGTTTTATGCTA
1 GGTACATGAGTTTTATGCTA
39557548 GGTACATGAGTTTTATGCTA
1 GGTACATGAGTTTTATGCTA
39557568 ACCTTTATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.10, G:0.25, T:0.40
Consensus pattern (20 bp):
GGTACATGAGTTTTATGCTA
Found at i:39562875 original size:24 final size:24
Alignment explanation
Indices: 39562843--39562911 Score: 84
Period size: 24 Copynumber: 2.9 Consensus size: 24
39562833 TTTACTGCAA
* *
39562843 TATTGAGTGGCTTGTCCAGAACAC
1 TATTGAGTGGCTTGGCCACAACAC
**
39562867 TATTGAGTGGCTTGGCCACAACGT
1 TATTGAGTGGCTTGGCCACAACAC
* *
39562891 TATTGAGTGGTTTGACCACAA
1 TATTGAGTGGCTTGGCCACAA
39562912 TGATGCAGCT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (24 bp):
TATTGAGTGGCTTGGCCACAACAC
Found at i:39562973 original size:64 final size:64
Alignment explanation
Indices: 39562867--39563018 Score: 214
Period size: 64 Copynumber: 2.4 Consensus size: 64
39562857 TCCAGAACAC
* * * ** *
39562867 TATTGAGTGGCTTGGCCACAACGTTATTGAGTGGTTTGACCACAATGATGCAGCTTGACTGCGA
1 TATTGAGTGGCTTGGCCACAATGTTATTGAGTGGCTTCACCACAACAATACAGCTTGACTGCGA
* *
39562931 TATTGAGTGGCTTTGCCACAATGTTATTGAGTGGCTTCACCACAACAATACAGCTTGACTGTGA
1 TATTGAGTGGCTTGGCCACAATGTTATTGAGTGGCTTCACCACAACAATACAGCTTGACTGCGA
* *
39562995 TATTGAATGGCTTGGCCATAATGT
1 TATTGAGTGGCTTGGCCACAATGT
39563019 GGTGTGTTAT
Statistics
Matches: 77, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
64 77 1.00
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (64 bp):
TATTGAGTGGCTTGGCCACAATGTTATTGAGTGGCTTCACCACAACAATACAGCTTGACTGCGA
Found at i:39571573 original size:69 final size:70
Alignment explanation
Indices: 39571441--39571573 Score: 214
Period size: 69 Copynumber: 1.9 Consensus size: 70
39571431 TAGTTTATTA
* * * * *
39571441 CTAATTAATTTGCTGCTGTAATGCTGTAAATTATTGGCTGTCCAAATTAGGACAAATTTATGGTA
1 CTAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGTA
39571506 CTTAG
66 CTTAG
39571511 CTAATTAATATGCTGCTGTAATACT-TAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGT
1 CTAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGT
39571574 GTTATGTACT
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
69 35 0.60
70 23 0.40
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (70 bp):
CTAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGTA
CTTAG
Found at i:39573038 original size:47 final size:47
Alignment explanation
Indices: 39572961--39573173 Score: 313
Period size: 47 Copynumber: 4.6 Consensus size: 47
39572951 TATTTGAATA
*
39572961 AATGTGAAAGTG--TATATGTGATAAGACCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
39573006 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGCGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
39573053 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * * *
39573100 AATGCGAAAGTGTATATATGTGATAGGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
39573147 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
39573174 TCCCGAAGGG
Statistics
Matches: 151, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
45 12 0.08
47 139 0.92
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.28
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:39575409 original size:25 final size:25
Alignment explanation
Indices: 39575381--39575508 Score: 100
Period size: 25 Copynumber: 5.2 Consensus size: 25
39575371 CAGGTCATGA
*
39575381 GAGCTTACTGATTCTCAGCTCGTAT
1 GAGCTTACCGATTCTCAGCTCGTAT
* * *
39575406 GAGCTTACCGATAT-TCAACTTGCAT
1 GAGCTTACCGAT-TCTCAGCTCGTAT
**
39575431 GAGCTTGTCG-TTACTCAGCTCGTAT
1 GAGCTTACCGATT-CTCAGCTCGTAT
* * * *
39575456 GAGCTTACCGATT-ACAACTCATAA
1 GAGCTTACCGATTCTCAGCTCGTAT
* * *
39575480 GAGCATACCGATTCTTAGCTCATAT
1 GAGCTTACCGATTCTCAGCTCGTAT
39575505 GAGC
1 GAGC
39575509 ATACATGTAC
Statistics
Matches: 78, Mismatches: 20, Indels: 10
0.72 0.19 0.09
Matches are distributed among these distances:
23 1 0.01
24 20 0.26
25 54 0.69
26 3 0.04
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (25 bp):
GAGCTTACCGATTCTCAGCTCGTAT
Found at i:39575509 original size:25 final size:24
Alignment explanation
Indices: 39575446--39575512 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
39575436 TGTCGTTACT
* *
39575446 CAGCTCGTATGAGCTTACCGATTA
1 CAGCTCATATGAGCATACCGATTA
* *
39575470 CAACTCATAAGAGCATACCGATT-
1 CAGCTCATATGAGCATACCGATTA
39575493 CTTAGCTCATATGAGCATAC
1 C--AGCTCATATGAGCATAC
39575513 ATGTACAAGA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
23 1 0.03
24 19 0.54
25 15 0.43
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.27
Consensus pattern (24 bp):
CAGCTCATATGAGCATACCGATTA
Found at i:39577788 original size:50 final size:50
Alignment explanation
Indices: 39577664--39577886 Score: 198
Period size: 50 Copynumber: 4.5 Consensus size: 50
39577654 GATAATAACA
* * ** * * *
39577664 TGCCAAAGCCATGTCCCAGACATGGTCTTACACGGGATGTTTCAT-GCAT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
* * * * ** * *
39577713 TGCCAATGCCATATTCTAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
* ** *
39577763 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCTTCTCAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
* * * ** *
39577813 TGCCAACT-CCATGTCCAAGGCATGGTCTTACATGGAACCTCTGGTCTCGG
1 TGCCAA-TGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
39577863 TGCCAATGCCATGTCCCAGACATG
1 TGCCAATGCCATGTCCCAGACATG
39577887 CTCGTCTCGG
Statistics
Matches: 136, Mismatches: 35, Indels: 5
0.77 0.20 0.03
Matches are distributed among these distances:
49 37 0.27
50 98 0.72
51 1 0.01
ACGTcount: A:0.22, C:0.28, G:0.23, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
Found at i:39577958 original size:84 final size:84
Alignment explanation
Indices: 39577807--39577970 Score: 229
Period size: 84 Copynumber: 2.0 Consensus size: 84
39577797 GGACCTCTCT
* * ** * *
39577807 TCTCAGTGCCAACTCCATGTCCAAGGCATGGTCTTACATGGAACCTCTGGTCTCGGTGCCAATGC
1 TCTCAGTGCCAACGCCATGTCCAAGACATGGTCTTACATGGAACCTCTCATCTCGATGCCAACGC
39577872 CATGTCCCAGACATGCTCG
66 CATGTCCCAGACATGCTCG
* * * *
39577891 TCTCGGTGCCAACGCCATGTCCCAGACATTGTCTTACATGGGACCTCTCATCTCGATGCCAACGC
1 TCTCAGTGCCAACGCCATGTCCAAGACATGGTCTTACATGGAACCTCTCATCTCGATGCCAACGC
*
39577956 CATGTGCCAGACATG
66 CATGTCCCAGACATG
39577971 GTCTTACATG
Statistics
Matches: 69, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
84 69 1.00
ACGTcount: A:0.21, C:0.33, G:0.22, T:0.24
Consensus pattern (84 bp):
TCTCAGTGCCAACGCCATGTCCAAGACATGGTCTTACATGGAACCTCTCATCTCGATGCCAACGC
CATGTCCCAGACATGCTCG
Found at i:39577966 original size:50 final size:50
Alignment explanation
Indices: 39577891--39577988 Score: 160
Period size: 50 Copynumber: 2.0 Consensus size: 50
39577881 GACATGCTCG
* *
39577891 TCTCGGTGCCAACGCCATGTCCCAGACATTGTCTTACATGGGACCTCTCA
1 TCTCGATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCA
* *
39577941 TCTCGATGCCAACGCCATGTGCCAGACATGGTCTTACATGGGATCTCT
1 TCTCGATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
39577989 TTACCCAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.20, C:0.32, G:0.21, T:0.27
Consensus pattern (50 bp):
TCTCGATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCA
Found at i:39583004 original size:17 final size:18
Alignment explanation
Indices: 39582976--39583009 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
39582966 TCTCCCAAAA
*
39582976 TTCAATTTTATTTAATTT
1 TTCAATTTTATTAAATTT
39582994 TTCAA-TTTATTAAATT
1 TTCAATTTTATTAAATT
39583010 CTTAGTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (18 bp):
TTCAATTTTATTAAATTT
Found at i:39594827 original size:25 final size:25
Alignment explanation
Indices: 39594799--39594850 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
39594789 CTTGACTTAG
39594799 AGCTAGTTTAGTATTACTTCTCAAA
1 AGCTAGTTTAGTATTACTTCTCAAA
39594824 AGCTAGTTTAGTATTACTTCTCAAA
1 AGCTAGTTTAGTATTACTTCTCAAA
39594849 AG
1 AG
39594851 TTTTTAGACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38
Consensus pattern (25 bp):
AGCTAGTTTAGTATTACTTCTCAAA
Found at i:39595122 original size:31 final size:30
Alignment explanation
Indices: 39595087--39595175 Score: 92
Period size: 30 Copynumber: 2.9 Consensus size: 30
39595077 ATTTTAGAAG
*
39595087 GTTAAAGTGATAAATTTTGTAAATATTAAGA
1 GTTAAATTGATAAATTTT-TAAATATTAAGA
* *
39595118 GTTAAATTTATTAAATTTTT-TATATTTAAGA
1 GTTAAATTGA-TAAATTTTTAAATA-TTAAGA
*
39595149 -TTAAATTGATAGAATGTTTAAATATTA
1 GTTAAATTGATA-AATTTTTAAATATTA
39595176 GAGGATTAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
29 2 0.04
30 20 0.42
31 18 0.38
32 8 0.17
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (30 bp):
GTTAAATTGATAAATTTTTAAATATTAAGA
Found at i:39595134 original size:32 final size:31
Alignment explanation
Indices: 39595097--39595192 Score: 92
Period size: 30 Copynumber: 3.1 Consensus size: 31
39595087 GTTAAAGTGA
39595097 TAAATTTTGTAAATATTAAGAGTTAAATTTAT
1 TAAATTTT-TAAATATTAAGAGTTAAATTTAT
* *
39595129 TAAATTTTT-TATATTTAAGA-TTAAATTGA-
1 TAAATTTTTAAATA-TTAAGAGTTAAATTTAT
*
39595158 TAGAATGTTTAAATATT-AGAGGATTAAATTTAT
1 TA-AATTTTTAAATATTAAGA-G-TTAAATTTAT
39595191 TA
1 TA
39595193 TTAGATCACT
Statistics
Matches: 52, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
29 5 0.10
30 19 0.37
31 10 0.19
32 16 0.31
33 2 0.04
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (31 bp):
TAAATTTTTAAATATTAAGAGTTAAATTTAT
Found at i:39595153 original size:30 final size:32
Alignment explanation
Indices: 39595097--39595192 Score: 94
Period size: 32 Copynumber: 3.1 Consensus size: 32
39595087 GTTAAAGTGA
39595097 TAAATTTTGTAAATATTAAGAGTTAAATTTAT
1 TAAATTTTGTAAATATTAAGAGTTAAATTTAT
* * *
39595129 TAAATTTTTTATAT-TTAAGA-TTAAATTGA-
1 TAAATTTTGTAAATATTAAGAGTTAAATTTAT
*
39595158 TAGAATGTT-TAAATATT-AGAGGATTAAATTTAT
1 TA-AATTTTGTAAATATTAAGA-G-TTAAATTTAT
39595191 TA
1 TA
39595193 TTAGATCACT
Statistics
Matches: 52, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
29 9 0.17
30 15 0.29
31 6 0.12
32 20 0.38
33 2 0.04
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (32 bp):
TAAATTTTGTAAATATTAAGAGTTAAATTTAT
Found at i:39595766 original size:9 final size:9
Alignment explanation
Indices: 39595752--39595776 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
39595742 AAAATATTTA
39595752 TTTTAATAT
1 TTTTAATAT
39595761 TTTTAATAT
1 TTTTAATAT
39595770 TTTTAAT
1 TTTTAAT
39595777 GTATCATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
TTTTAATAT
Found at i:39595807 original size:11 final size:11
Alignment explanation
Indices: 39595791--39595821 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
39595781 CATATATATT
39595791 TAAAAATTATA
1 TAAAAATTATA
*
39595802 TAAAAATAATA
1 TAAAAATTATA
39595813 TAAAAATTA
1 TAAAAATTA
39595822 ATACGGGTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
TAAAAATTATA
Found at i:39600705 original size:24 final size:24
Alignment explanation
Indices: 39600678--39600784 Score: 85
Period size: 24 Copynumber: 4.3 Consensus size: 24
39600668 ATATAAATTT
39600678 TAAATACTTTTTA-AATAAATAATA
1 TAAATA-TTTTTATAATAAATAATA
* * * *
39600702 TAAATATATATACAAAAAATAA-A
1 TAAATATTTTTATAATAAATAATA
*
39600725 TAAATATTTAAATTATTTATAAAATAATA
1 TAAATATTT---TTA-TAAT-AAATAATA
39600754 TAAATACTTTTTA-AATAAATAATA
1 TAAATA-TTTTTATAATAAATAATA
39600778 TAAATAT
1 TAAATAT
39600785 ATATACAAAA
Statistics
Matches: 66, Mismatches: 9, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
23 14 0.21
24 28 0.42
25 2 0.03
26 2 0.03
27 4 0.06
28 6 0.09
29 7 0.11
30 3 0.05
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (24 bp):
TAAATATTTTTATAATAAATAATA
Found at i:39600763 original size:76 final size:73
Alignment explanation
Indices: 39600678--39600822 Score: 254
Period size: 76 Copynumber: 1.9 Consensus size: 73
39600668 ATATAAATTT
39600678 TAAATACTTTTTAAATAAATAATATAAATATATATACAAAAAATAAATAAATATTTAAATTATTT
1 TAAATACTTTTTAAATAAATAATATAAATATATATACAAAAAATAAAT-AATA--TAAATTATTT
39600743 ATAAAATAATA
63 ATAAAATAATA
*
39600754 TAAATACTTTTTAAATAAATAATATAAATATATATACAAAAAATAAATGATATAAATTATTTATA
1 TAAATACTTTTTAAATAAATAATATAAATATATATACAAAAAATAAATAATATAAATTATTTATA
39600819 AAAT
66 AAAT
39600823 TTAATTTAAA
Statistics
Matches: 68, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
73 17 0.25
75 3 0.04
76 48 0.71
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.38
Consensus pattern (73 bp):
TAAATACTTTTTAAATAAATAATATAAATATATATACAAAAAATAAATAATATAAATTATTTATA
AAATAATA
Found at i:39600797 original size:24 final size:24
Alignment explanation
Indices: 39600745--39600799 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
39600735 AATTATTTAT
* *
39600745 AAAATAATATAAATACTTTTTAAA
1 AAAATAATATAAATACTATATAAA
*
39600769 TAAATAATATAAATA-TATATACAA
1 AAAATAATATAAATACTATATA-AA
39600793 AAAATAA
1 AAAATAA
39600800 ATGATATAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 4 0.15
24 22 0.85
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.33
Consensus pattern (24 bp):
AAAATAATATAAATACTATATAAA
Found at i:39603398 original size:61 final size:57
Alignment explanation
Indices: 39603275--39603405 Score: 145
Period size: 61 Copynumber: 2.2 Consensus size: 57
39603265 ATCACTTTAA
* * ** *
39603275 TATTAAATTAATATAATACTTATCAAGATAAGTATTGGATAAATTTAATATTAGATC
1 TATTAAATTAATAGAATACTTATCAAGATAAATATTAAATAAATTTAATATTAAATC
* * *
39603332 TATTAAATTAATAGAATATTTATCTACAAGATAAATATTAAATTTAATTTAATATTAAATT
1 TATTAAATTAATAGAATACTTA--T-CAAGATAAATATTAAA-TAAATTTAATATTAAATC
*
39603393 TATTAAAATAATA
1 TATTAAATTAATA
39603406 TTATTTTTGG
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
57 20 0.33
59 1 0.02
60 13 0.21
61 27 0.44
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (57 bp):
TATTAAATTAATAGAATACTTATCAAGATAAATATTAAATAAATTTAATATTAAATC
Found at i:39603402 original size:17 final size:17
Alignment explanation
Indices: 39603363--39603399 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
39603353 ATCTACAAGA
39603363 TAAATATTAAATTTAAT
1 TAAATATTAAATTTAAT
*
39603380 TTAATATTAAATTT-AT
1 TAAATATTAAATTTAAT
39603396 TAAA
1 TAAA
39603400 ATAATATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TAAATATTAAATTTAAT
Found at i:39607580 original size:27 final size:27
Alignment explanation
Indices: 39607549--39607726 Score: 187
Period size: 27 Copynumber: 6.6 Consensus size: 27
39607539 TAAATTGTAC
*
39607549 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
39607576 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
39607602 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGAATTGACTATGT
* *
39607630 GGCACTAAGTGTGCGAGATGGACTATGT
1 AGCACTAAGTGTGCGA-ATTGACTATGT
* * * *
39607658 GGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
39607685 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
39607712 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
39607727 GGCTCAATAA
Statistics
Matches: 127, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 103 0.81
28 24 0.19
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAATTGACTATGT
Found at i:39607665 original size:82 final size:81
Alignment explanation
Indices: 39607550--39607705 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
39607540 AAATTGTACA
* * * *
39607550 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGAATGGACTATGTGGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
39607614 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
39607631 GCACTAAGTGTGCGAGATGGACTATGTGGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-ATGGACTATGTGGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
39607696 TGCGAGTTGA
65 TGCGAATTGA
39607706 TTATATAGCA
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 15 0.23
82 49 0.75
83 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.28
Consensus pattern (81 bp):
GCACTAAGTGTGCGAATGGACTATGTGGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:39607717 original size:82 final size:81
Alignment explanation
Indices: 39607546--39607726 Score: 211
Period size: 82 Copynumber: 2.2 Consensus size: 81
39607536 GATTAAATTG
* * * *
39607546 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGAATGGACTATGTGGCACTAAGTGTGCGAAATGAATACGATGCACTAA
39607611 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
39607627 TGCGGCACTAAGTGTGCGAGATGGACTATGTGGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-ATGGACTATGTGGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
39607691 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
39607709 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
39607727 GGCTCAATAA
Statistics
Matches: 82, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
81 18 0.22
82 64 0.78
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGAATGGACTATGTGGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:39610453 original size:20 final size:19
Alignment explanation
Indices: 39610411--39610457 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
39610401 ACATAAGTTC
39610411 TAATTAAAGTAAGTTAAGT
1 TAATTAAAGTAAGTTAAGT
*
39610430 TAATTAAA-TAAAGATTATGT
1 TAATTAAAGT-AAG-TTAAGT
39610450 TAATTAAA
1 TAATTAAA
39610458 CCAAATTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 1 0.04
19 11 0.44
20 13 0.52
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (19 bp):
TAATTAAAGTAAGTTAAGT
Found at i:39618096 original size:3 final size:3
Alignment explanation
Indices: 39618088--39618112 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
39618078 AACATATCCG
39618088 CCA CCA CCA CCA CCA CCA CCA CCA C
1 CCA CCA CCA CCA CCA CCA CCA CCA C
39618113 TTAATCTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.68, G:0.00, T:0.00
Consensus pattern (3 bp):
CCA
Found at i:39620089 original size:72 final size:73
Alignment explanation
Indices: 39619972--39620119 Score: 230
Period size: 72 Copynumber: 2.0 Consensus size: 73
39619962 ATATCGAATA
*
39619972 AAATCTTGTTAAACAGCGGGAATAAATTCTGAAACAGATTTTATTTAATTCAATTC-AATTTGGA
1 AAATCTTGTTAAACAGCGGGAATAAATTCTGAAACAAATTTTATTTAATTCAATTCTAATTTGGA
39620036 AACAAAAT
66 AACAAAAT
* *
39620044 AAATCTTGTTAAACAGCGGGAATCAA-TCTCGAAA-AAATTTTTATTTAATTCTATTCTAATTTG
1 AAATCTTGTTAAACAGCGGGAATAAATTCT-GAAACAAA-TTTTATTTAATTCAATTCTAATTTG
39620107 GAAACAAAAT
64 GAAACAAAAT
39620117 AAA
1 AAA
39620120 ATGAAATAAA
Statistics
Matches: 70, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
71 5 0.07
72 46 0.66
73 19 0.27
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.34
Consensus pattern (73 bp):
AAATCTTGTTAAACAGCGGGAATAAATTCTGAAACAAATTTTATTTAATTCAATTCTAATTTGGA
AACAAAAT
Found at i:39620270 original size:87 final size:88
Alignment explanation
Indices: 39620103--39620295 Score: 228
Period size: 87 Copynumber: 2.2 Consensus size: 88
39620093 TCTATTCTAA
* * * * *
39620103 TTTGGAAACAAAATAAAATGAAATAAAATATTGTTAAATGACGAGAAAAAAATCCCAAAATAGAT
1 TTTGAAAACAAAATCAAATCAAATAAAATATTATTAAATGACGAGAAAAAAATCACAAAATAGAT
*
39620168 TTTATTTAATTTAATTTCTCGTT
66 TTTATTTAATTTAATTTCTCATT
* * * * ** *
39620191 TTT-AACAACAAAATCAAATCAAATAAATTTTTATTAAATGATGAG-AACAAATCATGAAATATA
1 TTTGAA-AACAAAATCAAATCAAATAAAATATTATTAAATGACGAGAAAAAAATCACAAAATAGA
*
39620254 TTTTATTTAATTTAATTTTTCATT
65 TTTTATTTAATTTAATTTCTCATT
*
39620278 TTTGGAAACAAAATCAAA
1 TTTGAAAACAAAATCAAA
39620296 ATGTAATAAA
Statistics
Matches: 88, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
87 51 0.58
88 37 0.42
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (88 bp):
TTTGAAAACAAAATCAAATCAAATAAAATATTATTAAATGACGAGAAAAAAATCACAAAATAGAT
TTTATTTAATTTAATTTCTCATT
Found at i:39622595 original size:16 final size:16
Alignment explanation
Indices: 39622569--39622608 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
39622559 ATTTATACTT
39622569 ATTTGTAATTTTTTAAA
1 ATTT-TAATTTTTTAAA
* *
39622586 ATTTTAATTTTTTTAT
1 ATTTTAATTTTTTAAA
39622602 ATTTTAA
1 ATTTTAA
39622609 AAATATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (16 bp):
ATTTTAATTTTTTAAA
Found at i:39629009 original size:207 final size:207
Alignment explanation
Indices: 39628654--39629072 Score: 829
Period size: 207 Copynumber: 2.0 Consensus size: 207
39628644 CTATGTAAAA
39628654 TATTTTCTTAAAAATATTTCATAAAAGTTATTTTTAATGAAACACATATACATTTTAGATTTTCT
1 TATTTTCTTAAAAATATTTCATAAAAGTTATTTTTAATGAAACACATATACATTTTAGATTTTCT
39628719 TATCTTTTCATTGTCTAATTGAGTTTATTTCATATATAAAAACTTATATTTTAAATTGTTTTTGC
66 TATCTTTTCATTGTCTAATTGAGTTTATTTCATATATAAAAACTTATATTTTAAATTGTTTTTGC
39628784 ATATATTAAAAATATTTTGTTAATTTCATGTTCTTTACAATGTCATTTTTTAGTTACATGACTAA
131 ATATATTAAAAATATTTTGTTAATTTCATGTTCTTTACAATGTCATTTTTTAGTTACATGACTAA
39628849 GTGAGTATTTTT
196 GTGAGTATTTTT
39628861 TATTTTCTTAAAAATATTTCATAAAAGTTATTTTTAATGAAACACATATACATTTTAGATTTTCT
1 TATTTTCTTAAAAATATTTCATAAAAGTTATTTTTAATGAAACACATATACATTTTAGATTTTCT
*
39628926 TATCTTTTCATTGTCTAATTGAGTTTATTTCATATATAAAAATTTATATTTTAAATTGTTTTTGC
66 TATCTTTTCATTGTCTAATTGAGTTTATTTCATATATAAAAACTTATATTTTAAATTGTTTTTGC
39628991 ATATATTAAAAATATTTTGTTAATTTCATGTTCTTTACAATGTCATTTTTTAGTTACATGACTAA
131 ATATATTAAAAATATTTTGTTAATTTCATGTTCTTTACAATGTCATTTTTTAGTTACATGACTAA
39629056 GTGAGTATTTTT
196 GTGAGTATTTTT
39629068 TATTT
1 TATTT
39629073 AAAAATGTGA
Statistics
Matches: 211, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
207 211 1.00
ACGTcount: A:0.33, C:0.08, G:0.08, T:0.51
Consensus pattern (207 bp):
TATTTTCTTAAAAATATTTCATAAAAGTTATTTTTAATGAAACACATATACATTTTAGATTTTCT
TATCTTTTCATTGTCTAATTGAGTTTATTTCATATATAAAAACTTATATTTTAAATTGTTTTTGC
ATATATTAAAAATATTTTGTTAATTTCATGTTCTTTACAATGTCATTTTTTAGTTACATGACTAA
GTGAGTATTTTT
Found at i:39629277 original size:15 final size:15
Alignment explanation
Indices: 39629257--39629308 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
39629247 AGTACAAAAA
39629257 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
39629272 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
39629291 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
39629306 ATT
1 ATT
39629309 AATATTAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:39632072 original size:10 final size:10
Alignment explanation
Indices: 39632067--39632091 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
39632057 TTCAAAATGT
39632067 GCCAAAATAA
1 GCCAAAATAA
39632077 GCCAAAATAA
1 GCCAAAATAA
39632087 GCCAA
1 GCCAA
39632092 TTCACAATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.56, C:0.24, G:0.12, T:0.08
Consensus pattern (10 bp):
GCCAAAATAA
Found at i:39636445 original size:17 final size:18
Alignment explanation
Indices: 39636411--39636450 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
39636401 GGGAAAAGAG
*
39636411 AAAGAAAAAGAATGTGAA
1 AAAGAAAAAAAATGTGAA
*
39636429 CAAGAAAAAAAAT-TGAA
1 AAAGAAAAAAAATGTGAA
39636446 AAAGA
1 AAAGA
39636451 GTTTGATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.70, C:0.03, G:0.17, T:0.10
Consensus pattern (18 bp):
AAAGAAAAAAAATGTGAA
Found at i:39642935 original size:27 final size:27
Alignment explanation
Indices: 39642904--39643081 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
39642894 TAAATTGTAC
39642904 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
39642931 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
39642957 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
39642985 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
39643013 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
39643040 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
39643067 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
39643082 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:39643018 original size:82 final size:81
Alignment explanation
Indices: 39642905--39643060 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
39642895 AAATTGTACA
* *
39642905 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
39642969 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
39642986 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
39643051 TGCGAGTTGA
65 TGCGAATTGA
39643061 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:39643072 original size:82 final size:81
Alignment explanation
Indices: 39642901--39643081 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
39642891 GATTAAATTG
* *
39642901 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
39642966 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
39642982 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
39643046 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
39643064 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
39643082 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:39650847 original size:27 final size:27
Alignment explanation
Indices: 39650816--39650993 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
39650806 TAAATTGTAC
39650816 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
39650843 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
39650869 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
39650897 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
39650925 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
39650952 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
39650979 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
39650994 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:39650930 original size:82 final size:81
Alignment explanation
Indices: 39650817--39650972 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
39650807 AAATTGTACA
* *
39650817 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
39650881 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
39650898 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
39650963 TGCGAGTTGA
65 TGCGAATTGA
39650973 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:39650984 original size:82 final size:81
Alignment explanation
Indices: 39650813--39650993 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
39650803 GATTAAATTG
* *
39650813 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
39650878 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
39650894 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
39650958 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
39650976 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
39650994 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:39658044 original size:42 final size:41
Alignment explanation
Indices: 39657974--39658052 Score: 95
Period size: 42 Copynumber: 1.9 Consensus size: 41
39657964 GTGATTTCCA
* *
39657974 TATAAGACCATATATGAGATATGACATCGGCATGCGATCTCG
1 TATAAGACCATATATGAGACATGACATCGACAT-CGATCTCG
* * * *
39658016 TATAAGACCATGTCTGGGACATGGCATCGACATCGAT
1 TATAAGACCATATATGAGACATGACATCGACATCGAT
39658053 ATGTGAGCCA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
41 4 0.13
42 27 0.87
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (41 bp):
TATAAGACCATATATGAGACATGACATCGACATCGATCTCG
Found at i:39658133 original size:50 final size:50
Alignment explanation
Indices: 39658018--39658344 Score: 288
Period size: 50 Copynumber: 6.6 Consensus size: 50
39658008 CGATCTCGTA
* * * * *
39658018 TAAGACCATGTCTGGGACATGGCATCGACATCGATATGTGA-G--CCAGTG
1 TAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCA-TG
* *
39658066 TAATACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATG
1 TAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATG
* *
39658116 TAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGTGAGGTCCCATG
1 TAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATG
* * * * **
39658166 GAAAACCATGTCTGGGACATGGCGTTGGCACCGGGATGAGAGGTCCCCCG
1 TAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATG
* * * * ** *
39658216 TAAGACCATGTCTAGGACATTGCATGGGCACTG-GTATGAGAACTCCTATG
1 TAAGACCATGTCTGGGACATGGCATTGGCACCGAG-ATGAGAGGTCCCATG
* * * * * * ** *
39658266 TAAGACCATATCTGGGATATGACATTGGCA--GTATAGGAAACATCTCATG
1 TAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATGAGAGGTCCCATG
* *
39658315 TAGGACCATGTCTGGGACATGGCTTTGGCA
1 TAAGACCATGTCTGGGACATGGCATTGGCA
39658345 TGTTATTATT
Statistics
Matches: 228, Mismatches: 45, Indels: 11
0.80 0.16 0.04
Matches are distributed among these distances:
48 35 0.15
49 36 0.16
50 154 0.68
51 3 0.01
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.23
Consensus pattern (50 bp):
TAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATG
Found at i:39659871 original size:23 final size:23
Alignment explanation
Indices: 39659834--39659884 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
39659824 GGGAGAGAAA
* *
39659834 TGTAATATCCTGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
39659857 TGTAATACCCCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
*
39659880 AGTAA
1 TGTAA
39659885 GAAAGTAGGT
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:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (23 bp):
TGTAATACCCCGAAAATTACTAC
Found at i:39660266 original size:137 final size:137
Alignment explanation
Indices: 39660089--39660362 Score: 521
Period size: 137 Copynumber: 2.0 Consensus size: 137
39660079 TGAAGGACCA
* *
39660089 ATGCTGTAAATATTTTAATGGTGGAATAATCTAGAAACTAAGGAAAATGGATGAATTAGGACCAA
1 ATGCTGTAAATATTTTAAGGGTGGAATAATCTAGAAACTAAGGAAAATGGACGAATTAGGACCAA
39660154 ATTGAAAAGGTGAAGAATTTTGAGGGACTAAATCACAATTTTACCAAATTAAGTGACGACTCAAT
66 ATTGAAAAGGTGAAGAATTTTGAGGGACTAAATCACAATTTTACCAAATTAAGTGACGACTCAAT
39660219 GATGGAT
131 GATGGAT
39660226 ATGCTGTAAATATTTTAAGGGTGGAATAATCTAGAAACTAAGGAAAATGGACGAATTAGGACCAA
1 ATGCTGTAAATATTTTAAGGGTGGAATAATCTAGAAACTAAGGAAAATGGACGAATTAGGACCAA
*
39660291 ATTGAAAAGGTGAAGAATTTTGAGGGACTAAATCACAATTTTACCAAATTAAGTGATGACTCAAT
66 ATTGAAAAGGTGAAGAATTTTGAGGGACTAAATCACAATTTTACCAAATTAAGTGACGACTCAAT
39660356 GATGGAT
131 GATGGAT
39660363 TTTTTAAAGA
Statistics
Matches: 134, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
137 134 1.00
ACGTcount: A:0.42, C:0.09, G:0.22, T:0.27
Consensus pattern (137 bp):
ATGCTGTAAATATTTTAAGGGTGGAATAATCTAGAAACTAAGGAAAATGGACGAATTAGGACCAA
ATTGAAAAGGTGAAGAATTTTGAGGGACTAAATCACAATTTTACCAAATTAAGTGACGACTCAAT
GATGGAT
Found at i:39670478 original size:27 final size:27
Alignment explanation
Indices: 39670447--39670597 Score: 187
Period size: 27 Copynumber: 5.6 Consensus size: 27
39670437 TAAATTGTAC
39670447 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
39670474 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
39670500 ATGCACTAAGTGTGCGAGTTTGACTATGT
1 A-GCACTAAGTGTGCGA-TTTGACTATGT
* *
39670529 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
39670556 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
39670583 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
39670598 GACTCAATAT
Statistics
Matches: 107, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
27 84 0.79
28 22 0.21
29 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:39670534 original size:55 final size:55
Alignment explanation
Indices: 39670447--39670597 Score: 200
Period size: 55 Copynumber: 2.8 Consensus size: 55
39670437 TAAATTGTAC
* *
39670447 AGCACTAAGTGTGCGA-TTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGT
** *
39670500 ATGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGT
1 A-GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGT
* * *
39670556 AGCACTAAGTGTGCGAG-TTGATTATATAGCACTGAGTGTGCG
1 AGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCG
39670598 GACTCAATAT
Statistics
Matches: 87, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
53 1 0.01
54 37 0.43
55 48 0.55
56 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.31
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGT
Found at i:39670545 original size:82 final size:82
Alignment explanation
Indices: 39670447--39670597 Score: 223
Period size: 82 Copynumber: 1.8 Consensus size: 82
39670437 TAAATTGTAC
* *
39670447 AGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGT
1 AGCACTAAGTGTGCGATTTGACTACGTAGCACTAAGTGTGCGAAATGAATAT-ATAGCACTAAGT
39670511 GTGCGAGTTTGACTATGT
65 GTGCGAGTTTGACTATGT
* ** * *
39670529 AGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTG
1 AGCACTAAGTGTGCGATTTGACTACGTAGCACTAAGTGTGCGAAATGAATATATAGCACTAAGTG
39670594 TGCG
66 TGCG
39670598 GACTCAATAT
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
81 2 0.03
82 59 0.97
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.31
Consensus pattern (82 bp):
AGCACTAAGTGTGCGATTTGACTACGTAGCACTAAGTGTGCGAAATGAATATATAGCACTAAGTG
TGCGAGTTTGACTATGT
Found at i:39674081 original size:41 final size:41
Alignment explanation
Indices: 39674035--39674159 Score: 250
Period size: 41 Copynumber: 3.0 Consensus size: 41
39674025 TATTATATAA
39674035 CCATATTTTTCATGTAAAATCATATGTGATCTTGTAATAGC
1 CCATATTTTTCATGTAAAATCATATGTGATCTTGTAATAGC
39674076 CCATATTTTTCATGTAAAATCATATGTGATCTTGTAATAGC
1 CCATATTTTTCATGTAAAATCATATGTGATCTTGTAATAGC
39674117 CCATATTTTTCATGTAAAATCATATGTGATCTTGTAATAGC
1 CCATATTTTTCATGTAAAATCATATGTGATCTTGTAATAGC
39674158 CC
1 CC
39674160 GTATCGAACT
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 84 1.00
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (41 bp):
CCATATTTTTCATGTAAAATCATATGTGATCTTGTAATAGC
Found at i:39674092 original size:21 final size:21
Alignment explanation
Indices: 39674067--39674133 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
39674057 TATGTGATCT
39674067 TGTAATAGCCCATATTTTTCA
1 TGTAATAGCCCATATTTTTCA
** ** *
39674088 TGTAA-A-ATCATATGTGATCT
1 TGTAATAGCCCATAT-TTTTCA
39674108 TGTAATAGCCCATATTTTTCA
1 TGTAATAGCCCATATTTTTCA
39674129 TGTAA
1 TGTAA
39674134 AATCATATGT
Statistics
Matches: 33, Mismatches: 10, Indels: 6
0.67 0.20 0.12
Matches are distributed among these distances:
19 5 0.15
20 9 0.27
21 14 0.42
22 5 0.15
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (21 bp):
TGTAATAGCCCATATTTTTCA
Found at i:39686190 original size:27 final size:27
Alignment explanation
Indices: 39686160--39686337 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
39686150 ATATTGAGTC
* * * *
39686160 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
39686187 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
39686214 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
39686242 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
39686269 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
39686296 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
39686323 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
39686338 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:39686299 original size:82 final size:81
Alignment explanation
Indices: 39686181--39686336 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
39686171 TGCTATATAA
* *
39686181 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
39686246 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
39686263 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
39686327 CACTTAGTGC
65 CACTTAGTGC
39686337 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:39688188 original size:17 final size:17
Alignment explanation
Indices: 39688166--39688200 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
39688156 CATTGCAAAG
39688166 AACCATTGATGGCTCGA
1 AACCATTGATGGCTCGA
39688183 AACCATTGATGGCTCGA
1 AACCATTGATGGCTCGA
39688200 A
1 A
39688201 TCCCCTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (17 bp):
AACCATTGATGGCTCGA
Found at i:39693506 original size:25 final size:25
Alignment explanation
Indices: 39693444--39693508 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
39693434 GTCATTAGGG
*
39693444 TTACCGAT-TTTAGCTCTTATGAGC
1 TTACCGATATTTAGCTCATATGAGC
* *
39693468 TTACCAATACTTAGCTCATATGAGC
1 TTACCGATATTTAGCTCATATGAGC
*
39693493 TTACCGTTATTTAGCT
1 TTACCGATATTTAGCT
39693509 TGGAGAAGCT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
24 7 0.21
25 27 0.79
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.40
Consensus pattern (25 bp):
TTACCGATATTTAGCTCATATGAGC
Found at i:39693518 original size:25 final size:25
Alignment explanation
Indices: 39693489--39693600 Score: 143
Period size: 25 Copynumber: 4.5 Consensus size: 25
39693479 TAGCTCATAT
* *
39693489 GAGCTTACCGTTATTTAGCTTGGAG
1 GAGCTTACCGTTATTCAGCTCGGAG
* * *
39693514 AAGCTTCCCGTTATTCAGCTCAGAG
1 GAGCTTACCGTTATTCAGCTCGGAG
* **
39693539 GAGTTTACAATTATTCAGCTCGGAG
1 GAGCTTACCGTTATTCAGCTCGGAG
*
39693564 GAGCTTGCCGTTATTCAGCTCGGAG
1 GAGCTTACCGTTATTCAGCTCGGAG
39693589 GAGCTTACCGTT
1 GAGCTTACCGTT
39693601 TACAGCTTGT
Statistics
Matches: 71, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 71 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.31
Consensus pattern (25 bp):
GAGCTTACCGTTATTCAGCTCGGAG
Found at i:39705715 original size:23 final size:24
Alignment explanation
Indices: 39705688--39705733 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
39705678 AAGAATAATT
*
39705688 TTCATTGAATATATAT-AATGATA
1 TTCATTGAATATACATGAATGATA
39705711 TTCATTGAATATACATGAATGAT
1 TTCATTGAATATACATGAATGAT
39705734 CTTGATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.41
Consensus pattern (24 bp):
TTCATTGAATATACATGAATGATA
Found at i:39709438 original size:16 final size:17
Alignment explanation
Indices: 39709407--39709439 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
39709397 TGAAAGTTAA
*
39709407 GAATTTAAAATTAAAAG
1 GAATTTAAAATAAAAAG
39709424 GAATTT-AAATAAAAAG
1 GAATTTAAAATAAAAAG
39709440 TCCCTTTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.61, C:0.00, G:0.12, T:0.27
Consensus pattern (17 bp):
GAATTTAAAATAAAAAG
Found at i:39714820 original size:52 final size:51
Alignment explanation
Indices: 39714717--39714864 Score: 169
Period size: 50 Copynumber: 2.9 Consensus size: 51
39714707 ACATGCATGG
* * * * *
39714717 TTTAA-GATGTAAAC-TAAATAAAATATGAGTTACTTAATACATGACTAAA
1 TTTAATGATGTAAACTTAACTAACATAAGAGTTACATAATGCATGACTAAA
*
39714766 TTTAATGATGTAAACTTTAACTAACATAAGAGTTACATAATGCATGTC-ATAA
1 TTTAATGATGTAAAC-TTAACTAACATAAGAGTTACATAATGCATGACTA-AA
* * *
39714818 TTT-ATGATGCAAACTTAACTAACGTGAGAGTTACATAATGCATGACT
1 TTTAATGATGTAAACTTAACTAACATAAGAGTTACATAATGCATGACT
39714865 TTATTAAATG
Statistics
Matches: 84, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
49 5 0.06
50 38 0.45
51 11 0.13
52 30 0.36
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (51 bp):
TTTAATGATGTAAACTTAACTAACATAAGAGTTACATAATGCATGACTAAA
Found at i:39719389 original size:14 final size:14
Alignment explanation
Indices: 39719370--39719399 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
39719360 AGTGAGAGAG
*
39719370 GAGAGAAGAGTTGT
1 GAGAGAAGAGATGT
39719384 GAGAGAAGAGATGT
1 GAGAGAAGAGATGT
39719398 GA
1 GA
39719400 ATGAGGGATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.43, T:0.17
Consensus pattern (14 bp):
GAGAGAAGAGATGT
Found at i:39720060 original size:19 final size:18
Alignment explanation
Indices: 39720011--39720061 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 18
39720001 ATGTTCAAAT
*
39720011 TTTTAATACAATTTAATTA
1 TTTT-ATACAAATTAATTA
*
39720030 TTTTATAAAAATTAATTA
1 TTTTATACAAATTAATTA
39720048 TTTTATGACAAATT
1 TTTTAT-ACAAATT
39720062 CTATCGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 18 0.64
19 10 0.36
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (18 bp):
TTTTATACAAATTAATTA
Found at i:39720195 original size:24 final size:25
Alignment explanation
Indices: 39720155--39720201 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
39720145 AAATTTCAGA
*
39720155 AAGAATTTCTCAGAAAC-ACTTTTG
1 AAGAATTCCTCAGAAACAACTTTTG
39720179 AAGAATTCCTTCA-AAACAACTTT
1 AAGAATTCC-TCAGAAACAACTTT
39720202 CTTCTCAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.32
Consensus pattern (25 bp):
AAGAATTCCTCAGAAACAACTTTTG
Found at i:39730346 original size:22 final size:21
Alignment explanation
Indices: 39730321--39730364 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
39730311 TCATAAACTT
39730321 TAATATATA-ATTATATTATTTA
1 TAATATATATATTA-ATT-TTTA
*
39730343 TAATTTATATATTAATTTTTA
1 TAATATATATATTAATTTTTA
39730364 T
1 T
39730365 CAACTCAGCT
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:39731184 original size:34 final size:34
Alignment explanation
Indices: 39731146--39731210 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
39731136 AAGTTTGGGG
39731146 GAGTTGCAAAGAAGTATAAAATGCTCTAAAATTT
1 GAGTTGCAAAGAAGTATAAAATGCTCTAAAATTT
*
39731180 GAGTTGCAAAGAAGTATGAAATGCTCTAAAA
1 GAGTTGCAAAGAAGTATAAAATGCTCTAAAA
39731211 ATTGTAGTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.45, C:0.09, G:0.20, T:0.26
Consensus pattern (34 bp):
GAGTTGCAAAGAAGTATAAAATGCTCTAAAATTT
Found at i:39733919 original size:102 final size:102
Alignment explanation
Indices: 39733743--39733973 Score: 336
Period size: 102 Copynumber: 2.3 Consensus size: 102
39733733 ATTGAATATA
* * * *
39733743 AAGGGGATTGCTAAGTGCTGATTCCAACAAGGGGTTGCTAAGTGTTGATTCCCCGATTCATTGGT
1 AAGGGGGTTGCTAAGTGCTGATTCCCACAAAGGGTTGCTAAGTGTTGATTCCCCGAATCATTGGT
* * * *
39733808 AGTTGCTAAGTGCTGATTCCACTGTATTTTAAATGTG
66 AGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGAG
* * *
39733845 AAGGGGGTTGCTAAGTGTTGATTCCCCCAAAGGGTTGCTAAGTGTTGATTCCTCGAATCATTGGT
1 AAGGGGGTTGCTAAGTGCTGATTCCCACAAAGGGTTGCTAAGTGTTGATTCCCCGAATCATTGGT
*
39733910 GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGAG
66 AGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGAG
* *
39733947 AAAGGGGTTGCTAAGTACTGATTCCCA
1 AAGGGGGTTGCTAAGTGCTGATTCCCA
39733974 GATTCATTGG
Statistics
Matches: 113, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
102 113 1.00
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (102 bp):
AAGGGGGTTGCTAAGTGCTGATTCCCACAAAGGGTTGCTAAGTGTTGATTCCCCGAATCATTGGT
AGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGAG
Found at i:39733999 original size:75 final size:76
Alignment explanation
Indices: 39733876--39734074 Score: 285
Period size: 75 Copynumber: 2.6 Consensus size: 76
39733866 TTCCCCCAAA
*
39733876 GGGTTGCTAAGTGTTGATTCCTCGAATCATTGGTGGTTGCTAAGTGCTGATCCCACCGTA-TCTT
1 GGGTTGCTAAGTGCTGATTCC-CGAATCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATTCTT
39733940 AAATGAG-AAAG
65 AAATGAGAAAAG
* * * *
39733951 GGGTTGCTAAGTACTGATTCCCAGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATTTTT
1 GGGTTGCTAAGTGCTGATTCCC-GAATCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATTCTT
* *
39734016 GAATGTGAAAAG
65 AAATGAGAAAAG
*
39734028 GGTTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGC
1 GGGTTGCTAAGTGCTGATT-CCCGAATCATTGGTGGTTGCTAAGTGC
39734075 AGAATCCACC
Statistics
Matches: 110, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
74 1 0.01
75 54 0.49
76 8 0.07
77 44 0.40
78 3 0.03
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.34
Consensus pattern (76 bp):
GGGTTGCTAAGTGCTGATTCCCGAATCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATTCTTA
AATGAGAAAAG
Found at i:39742218 original size:50 final size:49
Alignment explanation
Indices: 39742147--39742334 Score: 218
Period size: 50 Copynumber: 3.8 Consensus size: 49
39742137 TTATCATTCG
*
39742147 ATACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACA
1 ATACACATAGTAGCCTTCACATAGTACTACACACGTGA-CAAGTTTTACA
* *
39742197 ATCCACATAGTAGCCTCCACATAGTACTACACACGTGACCAAAGATTTT-CA
1 ATACACATAGTAGCCTTCACATAGTACTACACACGTGA-C-AAG-TTTTACA
* * * * * *
39742248 ATACACAT-GTAGCCTTCACTTTGTACTACACATGTGACCATTATTTATCG
1 ATACACATAGTAGCCTTCACATAGTACTACACACGTGACAAGT-TTTA-CA
*
39742298 ATACACGTAGTAGCCTTCACATAGTACTACACACGTG
1 ATACACATAGTAGCCTTCACATAGTACTACACACGTG
39742335 TTCATCGATA
Statistics
Matches: 116, Mismatches: 16, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
47 1 0.01
48 4 0.03
49 1 0.01
50 69 0.59
51 37 0.32
52 4 0.03
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.28
Consensus pattern (49 bp):
ATACACATAGTAGCCTTCACATAGTACTACACACGTGACAAGTTTTACA
Found at i:39742309 original size:101 final size:101
Alignment explanation
Indices: 39742147--39742334 Score: 254
Period size: 101 Copynumber: 1.9 Consensus size: 101
39742137 TTATCATTCG
* *
39742147 ATACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACAATCCACATAGTAGCC
1 ATACACATAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACAATACACATAGTAGCC
39742212 TCCACATAGTACTACACACGTGACCAAAGATTTTCA
66 TCCACATAGTACTACACACGTGACCAAAGATTTTCA
* * * * * * *
39742248 ATACACAT-GTAGCCTTCACTTTGTACTACACATGTGA-CCATTATTTATCGATACACGTAGTAG
1 ATACACATAGTAGCCTTCACATAGTACTACACACGTGATCAAGT-TTTA-CAATACACATAGTAG
*
39742311 CCTTCACATAGTACTACACACGTG
64 CCTCCACATAGTACTACACACGTG
39742335 TTCATCGATA
Statistics
Matches: 75, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
99 3 0.04
100 30 0.40
101 42 0.56
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.28
Consensus pattern (101 bp):
ATACACATAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACAATACACATAGTAGCC
TCCACATAGTACTACACACGTGACCAAAGATTTTCA
Found at i:39743692 original size:20 final size:22
Alignment explanation
Indices: 39743669--39743716 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
39743659 GAGCTGTTAC
39743669 AAAAATAA-T-CAAAATTCACT
1 AAAAATAATTGCAAAATTCACT
* *
39743689 AAAAATAATTGTAAAATTGACT
1 AAAAATAATTGCAAAATTCACT
39743711 AAAAAT
1 AAAAAT
39743717 TAACATGTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 8 0.33
21 1 0.04
22 15 0.62
ACGTcount: A:0.60, C:0.08, G:0.04, T:0.27
Consensus pattern (22 bp):
AAAAATAATTGCAAAATTCACT
Found at i:39752516 original size:12 final size:12
Alignment explanation
Indices: 39752499--39752531 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
39752489 AGCCACACGC
*
39752499 CCGTGTGCCAGG
1 CCGTGTACCAGG
39752511 CCGTGTACCAGG
1 CCGTGTACCAGG
39752523 CCGTGTACC
1 CCGTGTACC
39752532 CTTTCGAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.12, C:0.36, G:0.33, T:0.18
Consensus pattern (12 bp):
CCGTGTACCAGG
Found at i:39754538 original size:28 final size:27
Alignment explanation
Indices: 39754475--39754626 Score: 223
Period size: 27 Copynumber: 5.6 Consensus size: 27
39754465 ATATTAAGTC
* * *
39754475 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
*
39754502 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
*
39754530 CGCACACTTAGTGCTACATAGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
39754557 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
* *
39754585 CGCACACTTAGTGCTACTTAGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
39754612 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
39754627 GCACAATTTA
Statistics
Matches: 116, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
27 65 0.56
28 51 0.44
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:39754560 original size:55 final size:55
Alignment explanation
Indices: 39754475--39754626 Score: 250
Period size: 55 Copynumber: 2.8 Consensus size: 55
39754465 ATATTAAGTC
* * * *
39754475 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAATTCGCACACTTAGTGCTACATAATCAAACT
*
39754530 CGCACACTTAGTGCTACATAGTCAATTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAATTCGCACACTTAGTGCTACATAATCAAACT
*
39754585 CGCACACTTAGTGCTACTTAGTCAATTCGCACACTTAGTGCT
1 CGCACACTTAGTGCTACATAGTCAATTCGCACACTTAGTGCT
39754627 GCACAATTTA
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 91 1.00
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.28
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAGTCAATTCGCACACTTAGTGCTACATAATCAAACT
Found at i:39756090 original size:27 final size:27
Alignment explanation
Indices: 39756060--39756237 Score: 187
Period size: 27 Copynumber: 6.6 Consensus size: 27
39756050 ATATCGAGCC
* * *
39756060 CGCACACTCAGTGCTATAAAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
39756087 CGCACACTTAGTGCCACATAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
39756114 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
39756142 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
39756169 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * *
39756196 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
39756223 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
39756238 GTACAATTTA
Statistics
Matches: 128, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
27 105 0.82
28 23 0.18
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:39756173 original size:82 final size:81
Alignment explanation
Indices: 39756081--39756236 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
39756071 TGCTATAAAA
*
39756081 TCAACTCGCACACTTAGTGCCA-CATAATCAAATCGCACACTTAGTGCTACATAATCAAACTCGC
1 TCAACTCGCACACTTAGTG-CATCATAATCAAATCGCACACTTAGTGCAACATAATCAAA-TCGC
39756145 ACACTTAGTGCCGCATGG
64 ACACTTAGTGCCGCATGG
* * ** *
39756163 TCAATTCGCACACTTAGTGCATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCAC
1 TCAACTCGCACACTTAGTGCATCATAATCAAATCGCACACTTAGTGCAACATAATCAAATCGCAC
39756228 ACTTAGTGC
66 ACTTAGTGC
39756237 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 17 0.25
82 50 0.75
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCATCATAATCAAATCGCACACTTAGTGCAACATAATCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:39764091 original size:27 final size:27
Alignment explanation
Indices: 39764060--39764132 Score: 101
Period size: 27 Copynumber: 2.7 Consensus size: 27
39764050 GTATATTGAG
* * *
39764060 CCCGCACACTCAGTGCTATGTAATCAA
1 CCCGCACACTTAGTGCCACGTAATCAA
39764087 CCCGCACACTTAGTGCCACGTAATCAA
1 CCCGCACACTTAGTGCCACGTAATCAA
**
39764114 ATCGCACACTTAGTGCCAC
1 CCCGCACACTTAGTGCCAC
39764133 ATAGTCCATT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.29, C:0.36, G:0.15, T:0.21
Consensus pattern (27 bp):
CCCGCACACTTAGTGCCACGTAATCAA
Found at i:39764180 original size:27 final size:27
Alignment explanation
Indices: 39764089--39764238 Score: 178
Period size: 27 Copynumber: 5.5 Consensus size: 27
39764079 GTAATCAACC
* * *
39764089 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCCACATAGTCAATT
*
39764116 CGCACACTTAGTGCCACATAGTCCATTT
1 CGCACACTTAGTGCCACATAGT-CAATT
* *
39764144 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCCACATAGTCAATT
* *
39764171 CGCACACTTAGTG-CATCATATTCATTT
1 CGCACACTTAGTGCCA-CATAGTCAATT
*
39764198 CGCACACTTAGTGCAACATAGTCGAA-T
1 CGCACACTTAGTGCCACATAGTC-AATT
39764225 CGCACACTTAGTGC
1 CGCACACTTAGTGC
39764239 TGTACAATTT
Statistics
Matches: 105, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
26 1 0.01
27 79 0.75
28 25 0.24
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCCACATAGTCAATT
Found at i:39764201 original size:82 final size:81
Alignment explanation
Indices: 39764089--39764238 Score: 212
Period size: 82 Copynumber: 1.8 Consensus size: 81
39764079 GTAATCAACC
* * *
39764089 CGCACACTTAGTGCCACGTAATCAAATCGCACACTTAGTGCCACATAGTCCATTTCGCACACTTA
1 CGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTCCA-ATCGCACACTTA
39764154 GTGCCGCATGGTCAATT
65 GTGCCGCATGGTCAATT
* ** *
39764171 CGCACACTTAGTG-CATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAATCGCACACTTA
1 CGCACACTTAGTGCCA-CATAATCAAATCGCACACTTAGTGCAACATAGTCCAATCGCACACTTA
39764235 GTGC
65 GTGC
39764239 TGTACAATTT
Statistics
Matches: 60, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
81 17 0.28
82 43 0.72
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27
Consensus pattern (81 bp):
CGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTCCAATCGCACACTTAG
TGCCGCATGGTCAATT
Found at i:39770053 original size:56 final size:57
Alignment explanation
Indices: 39769967--39770102 Score: 195
Period size: 56 Copynumber: 2.4 Consensus size: 57
39769957 ACCATGGCAT
* * *
39769967 TGATATATGTGTGCGAGTAAGACCATGTTTAACACGTTGGCATCGATATGTGATT-A
1 TGATATATGTGTGCGAGTAAGACCACGTTTAACACGTTGACATCAATATGTGATTCA
* *
39770023 TGATATATGTGTGCGAGTAAGACCACGTTTAATACGTTGACATCAATATGTGATTCC
1 TGATATATGTGTGCGAGTAAGACCACGTTTAACACGTTGACATCAATATGTGATTCA
* *
39770080 T-ATATACGTTTGCGAGTAAGACC
1 TGATATATGTGTGCGAGTAAGACC
39770103 CTATCTGGGA
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
56 71 0.99
57 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (57 bp):
TGATATATGTGTGCGAGTAAGACCACGTTTAACACGTTGACATCAATATGTGATTCA
Found at i:39787270 original size:22 final size:22
Alignment explanation
Indices: 39787245--39787291 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
39787235 ACAAGATATA
39787245 TGGCAGTTTATATGCAATTATG
1 TGGCAGTTTATATGCAATTATG
*
39787267 TGGCAGTTTATCTGCAATTATG
1 TGGCAGTTTATATGCAATTATG
39787289 TGG
1 TGG
39787292 TAGCTTGTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.23, C:0.11, G:0.26, T:0.40
Consensus pattern (22 bp):
TGGCAGTTTATATGCAATTATG
Found at i:39794776 original size:50 final size:49
Alignment explanation
Indices: 39794720--39794991 Score: 348
Period size: 50 Copynumber: 5.4 Consensus size: 49
39794710 TATTCCAGAT
* ** * * * *
39794720 ATGGTCTTACATGAGATTTCTCATATCGGTGCCCATGCCATGTCCAATAC
1 ATGGTCTTACATGGGACCTCTTATCTCGGTGCCAACGCCATGTCCAA-AC
** * *
39794770 ATGGTCTTACGGGGGACCTCTCATCTTGGTGCCAACGCCATGTCCCAAAC
1 ATGGTCTTACATGGGACCTCTTATCTCGGTGCCAACGCCATGT-CCAAAC
*
39794820 ATGGTCTTACATGAGACCTCTTATCTCGGTGCCAACGCCATGTCCCAAAC
1 ATGGTCTTACATGGGACCTCTTATCTCGGTGCCAACGCCATGT-CCAAAC
* *
39794870 ATGGTCTTACATGGGACCCCTTATCTCGGTTCCAACAG-CATGTCCAAGAC
1 ATGGTCTTACATGGGACCTCTTATCTCGGTGCCAAC-GCCATGTCCAA-AC
*
39794920 ATGGTCTTACATGGGACCTCTTATCTCGGTGCCAACGCCATGTCCCAGAC
1 ATGGTCTTACATGGGACCTCTTATCTCGGTGCCAACGCCATGT-CCAAAC
39794970 ATGGTCTTACATGGGACCTCTT
1 ATGGTCTTACATGGGACCTCTT
39794992 TACCCAAATG
Statistics
Matches: 197, Mismatches: 20, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
49 5 0.03
50 184 0.93
51 8 0.04
ACGTcount: A:0.22, C:0.30, G:0.21, T:0.28
Consensus pattern (49 bp):
ATGGTCTTACATGGGACCTCTTATCTCGGTGCCAACGCCATGTCCAAAC
Found at i:39800279 original size:29 final size:28
Alignment explanation
Indices: 39800243--39800320 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 28
39800233 TCATGAGATT
39800243 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
**
39800273 -GCACTAAGTGTGCGAATTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
*
39800300 TGGCACTAAGTGAGCGTGGTT
1 -GGCACTAAGTGTGCG-GGTT
39800321 GATTATTAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
27 5 0.12
29 33 0.82
30 2 0.05
ACGTcount: A:0.28, C:0.14, G:0.29, T:0.28
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:39800538 original size:174 final size:174
Alignment explanation
Indices: 39800273--39800600 Score: 575
Period size: 174 Copynumber: 1.9 Consensus size: 174
39800263 AAATTGTACA
*
39800273 GCACTAAGTGTGCGAATTTAAAGTACATGGCACTAAGTGAGCGTGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAATTTAAAGTACATGGCACTAAGTGAGCGCGGTTGATTATTAAGCACTATG
* *
39800338 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACCTTACCGAGTCGA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACCTTACCGAGTCAA
39800403 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
* * * *
39800447 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAATTTAAAGTACATGGCACTAAGTGAGCGCGGTTGATTATTAAGCACTATG
* *
39800512 TGTGCGAACGCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACCTTACCGAGTCAA
39800577 TTTTGGACAGCGGAAAAGGTAAGT
131 TTTTGGACAGCGGAAAAGGTAAGT
39800601 ACCTTGAGTT
Statistics
Matches: 145, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
174 145 1.00
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.30
Consensus pattern (174 bp):
GCACTAAGTGTGCGAATTTAAAGTACATGGCACTAAGTGAGCGCGGTTGATTATTAAGCACTATG
TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACCTTACCGAGTCAA
TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Found at i:39816908 original size:39 final size:39
Alignment explanation
Indices: 39816790--39817052 Score: 313
Period size: 39 Copynumber: 6.6 Consensus size: 39
39816780 GCTCCTCGTT
*
39816790 CAAATGCCTTCGGGACATTAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGG-C-TTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
39816831 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
39816871 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
*
39816910 CAAATGCCTTCGGGCTTAGCCCGAAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
*
39816949 CAAATGCCTTTGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
* * *
39816988 CAAATGCCTTCGGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGG-GCTTAGCCCGGA-ATTAGT-ATC-TCGCA
39817029 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGG-CTTAGCCCGGA
39817053 CATCATTCAA
Statistics
Matches: 201, Mismatches: 14, Indels: 16
0.87 0.06 0.07
Matches are distributed among these distances:
39 128 0.64
40 46 0.23
41 27 0.13
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
Found at i:39824816 original size:40 final size:40
Alignment explanation
Indices: 39824772--39825033 Score: 328
Period size: 39 Copynumber: 6.7 Consensus size: 40
39824762 GCTCCTCGTT
* *
39824772 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
39824812 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
*
39824852 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCACA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
39824891 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
39824930 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
39824969 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
39825010 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
39825034 CATCATTCAA
Statistics
Matches: 203, Mismatches: 11, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
38 2 0.01
39 126 0.62
40 64 0.32
41 11 0.05
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:39838649 original size:17 final size:18
Alignment explanation
Indices: 39838627--39838661 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
39838617 TTACATTAAA
39838627 GTGTTTT-AGTGAAAACC
1 GTGTTTTCAGTGAAAACC
*
39838644 GTGTTTTCATTGAAAACC
1 GTGTTTTCAGTGAAAACC
39838662 TTCTTAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (18 bp):
GTGTTTTCAGTGAAAACC
Found at i:39839753 original size:29 final size:29
Alignment explanation
Indices: 39839696--39839797 Score: 127
Period size: 29 Copynumber: 3.6 Consensus size: 29
39839686 TACGTGTATC
* *
39839696 TGGCCCATTAAGCCC-AATCATATTTATA
1 TGGCCCATTAGGCCCAAATCACATTTATA
**
39839724 TGGCCCATTAGGCCTTAATCAC-TTATATA
1 TGGCCCATTAGGCCCAAATCACATT-TATA
* *
39839753 TGACCCATTAGTCCCAAATCACATTTATA
1 TGGCCCATTAGGCCCAAATCACATTTATA
39839782 TGGCCCATTAGGCCCA
1 TGGCCCATTAGGCCCA
39839798 GTTACATTCA
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
28 15 0.24
29 45 0.73
30 2 0.03
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.30
Consensus pattern (29 bp):
TGGCCCATTAGGCCCAAATCACATTTATA
Found at i:39841242 original size:21 final size:22
Alignment explanation
Indices: 39841200--39841242 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
39841190 AGAGCATAAA
*
39841200 TTACACAATATACATTATTATT
1 TTACACAATATACATTAATATT
39841222 TTACAC-ATATATCA-TAATATT
1 TTACACAATATA-CATTAATATT
39841243 CACGCATCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.42, C:0.14, G:0.00, T:0.44
Consensus pattern (22 bp):
TTACACAATATACATTAATATT
Found at i:39841905 original size:15 final size:15
Alignment explanation
Indices: 39841885--39841944 Score: 68
Period size: 15 Copynumber: 3.9 Consensus size: 15
39841875 TAATATAATT
39841885 AATGATATATATAAA
1 AATGATATATATAAA
39841900 AATGATATATACT-AA
1 AATGATATATA-TAAA
* *
39841915 AATCATATAATATACA
1 AATGATAT-ATATAAA
*
39841931 AATAATATATATAA
1 AATGATATATATAA
39841945 CGAATATATG
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
15 26 0.68
16 12 0.32
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.33
Consensus pattern (15 bp):
AATGATATATATAAA
Found at i:39842042 original size:17 final size:17
Alignment explanation
Indices: 39841977--39842044 Score: 52
Period size: 17 Copynumber: 3.9 Consensus size: 17
39841967 AATGTATAGT
39841977 AAAATAAATAATAT-A-
1 AAAATAAATAATATAAC
*
39841992 AAAATACATATAACATATAGC
1 AAAATA-A-AT-A-ATATAAC
*
39842013 AAAAATACA-AATATAAC
1 -AAAATAAATAATATAAC
39842030 AAAATAAATAATATA
1 AAAATAAATAATATA
39842045 TATAATGCAA
Statistics
Matches: 41, Mismatches: 4, Indels: 14
0.69 0.07 0.24
Matches are distributed among these distances:
15 6 0.15
16 8 0.20
17 14 0.34
18 2 0.05
19 4 0.10
20 1 0.02
22 6 0.15
ACGTcount: A:0.68, C:0.07, G:0.01, T:0.24
Consensus pattern (17 bp):
AAAATAAATAATATAAC
Found at i:39845361 original size:40 final size:40
Alignment explanation
Indices: 39845309--39845581 Score: 377
Period size: 40 Copynumber: 6.8 Consensus size: 40
39845299 ATTACCACAA
* * ** *
39845309 GCACAATTGCCTTCGGGTCTTAACCCGGGCATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
39845349 GCACGAATGCCTTCGGGTCTTAGCCCGGATATATCAACTT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
39845389 GCACAATTGCCTTCGGGTCTTAGCCCGGATATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGG--ATATATCAACTC
*
39845431 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
39845471 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* * *
39845511 GCACGAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATATCAACTC
* *
39845551 GCACAATTGCCTTCGGGACTTAGCCCGGATA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATA
39845582 AAATTCAAAT
Statistics
Matches: 211, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
39 1 0.00
40 169 0.80
41 4 0.02
42 37 0.18
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.24
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
Found at i:39848632 original size:60 final size:60
Alignment explanation
Indices: 39848562--39848682 Score: 242
Period size: 60 Copynumber: 2.0 Consensus size: 60
39848552 TCACTTACGA
39848562 AGAAGAACTGATAGATATTTTAGCTCATGAAGAGAAGGTTTTATGAAACAATAGAGTTTC
1 AGAAGAACTGATAGATATTTTAGCTCATGAAGAGAAGGTTTTATGAAACAATAGAGTTTC
39848622 AGAAGAACTGATAGATATTTTAGCTCATGAAGAGAAGGTTTTATGAAACAATAGAGTTTC
1 AGAAGAACTGATAGATATTTTAGCTCATGAAGAGAAGGTTTTATGAAACAATAGAGTTTC
39848682 A
1 A
39848683 TTGGTTATGA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.40, C:0.08, G:0.21, T:0.30
Consensus pattern (60 bp):
AGAAGAACTGATAGATATTTTAGCTCATGAAGAGAAGGTTTTATGAAACAATAGAGTTTC
Found at i:39850401 original size:88 final size:88
Alignment explanation
Indices: 39850247--39850422 Score: 262
Period size: 88 Copynumber: 2.0 Consensus size: 88
39850237 GATATTTTAG
* * *
39850247 CCTTGTGATCTTATGAGACTATTGGATATAGTTGGCATACAATAGGATTGTGAGTACTTACCTTT
1 CCTTATGATCTTATGAGACCATTGGATATAGTTAGCATACAATAGGATTGTGAGTACTTACCTTT
* *
39850312 GTGATGTGATTTTTAGGTGTTGA
66 GTAATGTGATTTTTAGGCGTTGA
* * * *
39850335 CCTTATGATCTTATGAGACCGTTGGATATAGTTAGTATACCATAGGATTGTGATTACTTACCTTT
1 CCTTATGATCTTATGAGACCATTGGATATAGTTAGCATACAATAGGATTGTGAGTACTTACCTTT
*
39850400 GTAATGTGATTTTTGGGCGTTGA
66 GTAATGTGATTTTTAGGCGTTGA
39850423 GGCCAAAGGA
Statistics
Matches: 78, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
88 78 1.00
ACGTcount: A:0.24, C:0.11, G:0.24, T:0.41
Consensus pattern (88 bp):
CCTTATGATCTTATGAGACCATTGGATATAGTTAGCATACAATAGGATTGTGAGTACTTACCTTT
GTAATGTGATTTTTAGGCGTTGA
Found at i:39890429 original size:20 final size:19
Alignment explanation
Indices: 39890399--39890435 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
39890389 TAGACATAAT
39890399 TTTCTTTAAAAACTTGGCA
1 TTTCTTTAAAAACTTGGCA
39890418 TTTCTTTAAAAACTTGGC
1 TTTCTTTAAAAACTTGGC
39890436 TTACTTAGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.43
Consensus pattern (19 bp):
TTTCTTTAAAAACTTGGCA
Done.