Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397255.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_44.0, whole genome shotgun sequence
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: 14367614
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 51264 characters in sequence are not A, C, G, or T
File 3 of 31
Found at i:1309664 original size:25 final size:26
Alignment explanation
Indices: 1309617--1309670 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
1309607 TCGAAATAGA
* *
1309617 AAAAAAATTATAACGGTTAGAAATTT
1 AAAAAAATTATAACAGTTAGAAAATT
**
1309643 AAAAAAATTATGTCAGTT-GAAAATT
1 AAAAAAATTATAACAGTTAGAAAATT
1309668 AAA
1 AAA
1309671 TTAATAAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 9 0.38
26 15 0.62
ACGTcount: A:0.56, C:0.04, G:0.11, T:0.30
Consensus pattern (26 bp):
AAAAAAATTATAACAGTTAGAAAATT
Found at i:1313687 original size:173 final size:174
Alignment explanation
Indices: 1313392--1313737 Score: 568
Period size: 173 Copynumber: 2.0 Consensus size: 174
1313382 ATGGGTGGCC
* *
1313392 TCATCCAAAGAAAGAGAGAAGTTTAAAAACTATGATATGATGGTGAGGAAGATAAGGTTGTCAAG
1 TCATCCAAAGAAAGAGAGAAGTTTAAAAACTATGAGATGATGGTGAGGAAGATAAGGCTGTCAAG
*
1313457 GTATTTCATGTATCAATTTCTAACAACAAAATTTGACTGCTAAGTCGAATTTTTCTTTTCCAAAA
66 GTATTTCATGTATCAATTTCTAACAACAAAATTTGACTGCTAAATCGAATTTTTCTTTTCCAAAA
* *
1313522 AATTTATGGACTAAATGCAGTGAATATTAATTTCCAGGTCTCCG
131 AATTTATGGACTAAATGCAGTGAACATTAATTTCCACGTCTCCG
*
1313566 TCATCCAAAGAAAGAGAGAAGTTTAAAAACTTTGAGATGATGGTGAGGAAGATAAGGCTGTCAAG
1 TCATCCAAAGAAAGAGAGAAGTTTAAAAACTATGAGATGATGGTGAGGAAGATAAGGCTGTCAAG
* * * ** *
1313631 GTA-TTCATGTATCAATTTCTAACTACAAAGTTTGACTGGTAAATTTAATTTTTCTTTTTCAAAA
66 GTATTTCATGTATCAATTTCTAACAACAAAATTTGACTGCTAAATCGAATTTTTCTTTTCCAAAA
*
1313695 AATTTATGGACTAAATGCAGTGAACATTAATTTCTACGTCTCC
131 AATTTATGGACTAAATGCAGTGAACATTAATTTCCACGTCTCC
1313738 TAGTTTAATT
Statistics
Matches: 159, Mismatches: 13, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
173 94 0.59
174 65 0.41
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (174 bp):
TCATCCAAAGAAAGAGAGAAGTTTAAAAACTATGAGATGATGGTGAGGAAGATAAGGCTGTCAAG
GTATTTCATGTATCAATTTCTAACAACAAAATTTGACTGCTAAATCGAATTTTTCTTTTCCAAAA
AATTTATGGACTAAATGCAGTGAACATTAATTTCCACGTCTCCG
Found at i:1313782 original size:67 final size:67
Alignment explanation
Indices: 1313674--1313804 Score: 226
Period size: 67 Copynumber: 2.0 Consensus size: 67
1313664 GACTGGTAAA
* * *
1313674 TTTAATTTTTCTTTTTCAAAAAATTTATGGACTAAATGCAGTGAACATTAATTTCTACGTCTCCT
1 TTTAATTTTTCTTTTCCAAAAAATTTATGGACTAAAAGCAGTGAACATTAATTTCCACGTCTCCT
1313739 AG
66 AG
*
1313741 TTTAATTTTTCTTTTCCAAAAAATTTATGGACTAAAAGCAGTGAACATTAATTTCCAGGTCTCC
1 TTTAATTTTTCTTTTCCAAAAAATTTATGGACTAAAAGCAGTGAACATTAATTTCCACGTCTCC
1313805 AGTAAAGGTC
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 60 1.00
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (67 bp):
TTTAATTTTTCTTTTCCAAAAAATTTATGGACTAAAAGCAGTGAACATTAATTTCCACGTCTCCT
AG
Found at i:1315131 original size:64 final size:63
Alignment explanation
Indices: 1315058--1315209 Score: 175
Period size: 64 Copynumber: 2.4 Consensus size: 63
1315048 TTACTATAAC
*
1315058 ATTATAAAAAAATTAATATTTATTAATTACATATAG-CATCTAAAAT-TCATATTTATATGTAT-
1 ATTATAAAAAAATCAATATTTATTAATTACATA-AGACATCTAAAATCT-ATA-TT-TATGTATA
1315120 TT
62 TT
* ** *
1315122 ATTATAAAAACATCAATATTTATTAATTATGTAAGACATTTAAAATCTATATTTATGTATATT
1 ATTATAAAAAAATCAATATTTATTAATTACATAAGACATCTAAAATCTATATTTATGTATATT
* *
1315185 CTCTCTAAAAAAATCAATATTTATT
1 AT-TATAAAAAAATCAATATTTATT
1315210 GTATTCATCA
Statistics
Matches: 76, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
62 7 0.09
63 7 0.09
64 61 0.80
65 1 0.01
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (63 bp):
ATTATAAAAAAATCAATATTTATTAATTACATAAGACATCTAAAATCTATATTTATGTATATT
Found at i:1315343 original size:9 final size:9
Alignment explanation
Indices: 1315317--1315346 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
1315307 AAAAAAATTT
1315317 TAATTTAAA
1 TAATTTAAA
1315326 TAATATTAAA
1 TAAT-TTAAA
1315336 TAATTTAAA
1 TAATTTAAA
1315345 TA
1 TA
1315347 GTAATATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (9 bp):
TAATTTAAA
Found at i:1315437 original size:37 final size:36
Alignment explanation
Indices: 1315367--1315456 Score: 92
Period size: 37 Copynumber: 2.4 Consensus size: 36
1315357 AACTGAAAAA
* * *
1315367 ATTTATAATTTAAATATTAATATATTTTTAATTTTTAAT
1 ATTTA-AA-TTAAATATTAATATATATTAAATTTAT-AT
1315406 ATTTAAATTAAATATTAATAT-TCATTAAATTTATAT
1 ATTTAAATTAAATATTAATATAT-ATTAAATTTATAT
* *
1315442 TTTTAAATTTAATAT
1 ATTTAAATTAAATAT
1315457 AACAATTTGT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
36 16 0.36
37 22 0.49
38 2 0.04
39 5 0.11
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (36 bp):
ATTTAAATTAAATATTAATATATATTAAATTTATAT
Found at i:1329394 original size:26 final size:27
Alignment explanation
Indices: 1329355--1329407 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
1329345 TATTGAAATA
1329355 ATATATTTAATATTATTATAAAAAATTG
1 ATATATTT-ATATTATTATAAAAAATTG
* *
1329383 ATATATTT-TATTGTTATATAAAATT
1 ATATATTTATATTATTATAAAAAATT
1329408 ATTAAAATAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 15 0.65
28 8 0.35
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (27 bp):
ATATATTTATATTATTATAAAAAATTG
Found at i:1329467 original size:108 final size:107
Alignment explanation
Indices: 1329288--1329482 Score: 327
Period size: 108 Copynumber: 1.8 Consensus size: 107
1329278 TATTTTGCTT
*
1329288 TTATATAAAATTATTAAAATAGAGTATTTAACAATATAAAACATAGAAATAACTAGATATTGAAA
1 TTATATAAAATTATTAAAATAGAGCATTTAACAATATAAAACATAGAAATAACTAGATATTGAAA
*
1329353 TAATATATTTAATATTATTATAAAAAATTGATATATTTTATTG
66 TAATATA-TTAAAATTATTATAAAAAATTGATATATTTTATTG
* * * *
1329396 TTATATAAAATTATTAAAATAGAGCATTTAATAATATAAAAGATAGATATACCTAGATATTGAAA
1 TTATATAAAATTATTAAAATAGAGCATTTAACAATATAAAACATAGAAATAACTAGATATTGAAA
1329461 TAATATATTAAAATTATTATAA
66 TAATATATTAAAATTATTATAA
1329483 TTAAGTTAAT
Statistics
Matches: 81, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
107 14 0.17
108 67 0.83
ACGTcount: A:0.52, C:0.03, G:0.07, T:0.38
Consensus pattern (107 bp):
TTATATAAAATTATTAAAATAGAGCATTTAACAATATAAAACATAGAAATAACTAGATATTGAAA
TAATATATTAAAATTATTATAAAAAATTGATATATTTTATTG
Found at i:1329519 original size:108 final size:107
Alignment explanation
Indices: 1329292--1329515 Score: 258
Period size: 108 Copynumber: 2.1 Consensus size: 107
1329282 TTGCTTTTAT
*
1329292 ATAAAATTATTAAAATAGAGTATTTAACAATATAAAACATAGAAATAACTAGATATTGAAATAAT
1 ATAAAATTATTAAAATAGAGCATTTAACAATATAAAACATAGAAATAACTAGATATTGAAATAAT
* **** * *
1329357 ATATTTAATATTATTATAAAAAATTGATATATTTTATTGTTAT
66 ATATTTAAAATTATTATAAAAAATTGATATAAAAAATAG-TAC
* * * *
1329400 ATAAAATTATTAAAATAGAGCATTTAATAATATAAAAGATAGATATACCTAGATATTGAAATAAT
1 ATAAAATTATTAAAATAGAGCATTTAACAATATAAAACATAGAAATAACTAGATATTGAAATAAT
* *
1329465 ATA-TTAAAATTATTATAATTAAGTT-A-ATAAAAAATAG-AC
66 ATATTTAAAATTATTATAA-AAAATTGATATAAAAAATAGTAC
1329504 ATCAATAATTAT
1 AT-AA-AATTAT
1329516 ATTATATAAT
Statistics
Matches: 99, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
104 3 0.03
105 2 0.02
106 12 0.12
107 15 0.15
108 67 0.68
ACGTcount: A:0.53, C:0.04, G:0.07, T:0.37
Consensus pattern (107 bp):
ATAAAATTATTAAAATAGAGCATTTAACAATATAAAACATAGAAATAACTAGATATTGAAATAAT
ATATTTAAAATTATTATAAAAAATTGATATAAAAAATAGTAC
Found at i:1329611 original size:197 final size:198
Alignment explanation
Indices: 1329365--1329731 Score: 524
Period size: 197 Copynumber: 1.9 Consensus size: 198
1329355 ATATATTTAA
* * *
1329365 TATTATTATAAAAAATTGATATATTTTATTGTTATATAAAATTATTAAAATAGAGCATTTAATAA
1 TATTATTATAAAAAATTGATATATTTTACTATTATATAAAATTATTAAAATAGAACATTTAATAA
* * * *
1329430 TATAAAAGATAGATATACCTAGATATTGAAATAATATATTAAAATTATTATAATTAAGTTAATA-
66 TATAAAACATAGACATAACTAGATATTGAAATAATATATTAAAATCATTATAATTAAGTTAATAT
* *
1329494 AAAAATA-GA-CATCAATAATTATATTATATAATAAAAATAATAATTAAATATTACTGTTGTTAT
131 AAAAATATCATCATCAATAATTATATTAGATAATAAAAATAATAATTAAATATTACTGTTGTTAT
1329557 TAT
196 TAT
** * *
1329560 TATTATTATTAAAATGTTGATATTATTTTGCTATTATATAAAATTATTAAAATAGAATATTTAAT
1 TATTATTA-TAAAAAATTGATA-TATTTTACTATTATATAAAATTATTAAAATAGAACATTTAAT
* * * *
1329625 AATATAAAACATAGACATAACTAGATTTTGAAATAATATATTGATATCATTATAATTAAGTTATT
64 AATATAAAACATAGACATAACTAGATATTGAAATAATATATTAAAATCATTATAATTAAGTTAAT
* *
1329690 ATACAAATATCATCATTAATAATTATATTAGATAATAAAAAT
129 ATAAAAATATCATCATCAATAATTATATTAGATAATAAAAAT
1329732 TAAATAATAC
Statistics
Matches: 148, Mismatches: 19, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
195 8 0.05
196 11 0.07
197 95 0.64
198 6 0.04
199 1 0.01
200 27 0.18
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.41
Consensus pattern (198 bp):
TATTATTATAAAAAATTGATATATTTTACTATTATATAAAATTATTAAAATAGAACATTTAATAA
TATAAAACATAGACATAACTAGATATTGAAATAATATATTAAAATCATTATAATTAAGTTAATAT
AAAAATATCATCATCAATAATTATATTAGATAATAAAAATAATAATTAAATATTACTGTTGTTAT
TAT
Found at i:1330096 original size:11 final size:11
Alignment explanation
Indices: 1330073--1330101 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1330063 ATATCAATTT
1330073 AATAATT-AAA
1 AATAATTAAAA
1330083 AATAATTAAAA
1 AATAATTAAAA
1330094 AATAATTA
1 AATAATTA
1330102 TAACATCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.39
11 11 0.61
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
AATAATTAAAA
Found at i:1330492 original size:25 final size:26
Alignment explanation
Indices: 1330446--1330497 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 26
1330436 AATAGTAATT
*
1330446 ATAAAATCAATTTTATATAATAAATA
1 ATAAAATCAATTATATATAATAAATA
1330472 ATAAAAT-AATTATAT-TAAATAAATA
1 ATAAAATCAATTATATAT-AATAAATA
1330497 A
1 A
1330498 ATAGTCAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 1 0.04
25 16 0.67
26 7 0.29
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (26 bp):
ATAAAATCAATTATATATAATAAATA
Found at i:1334248 original size:2 final size:2
Alignment explanation
Indices: 1334241--1334288 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1334231 TCGCCTCTAA
1334241 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1334283 AT AT AT
1 AT AT AT
1334289 GCAATGCCCT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1341618 original size:26 final size:26
Alignment explanation
Indices: 1341582--1341634 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
1341572 GAATAGGATT
*
1341582 AATTTTATAATTTTAAAAATTAGATA
1 AATTTTATAATTTTAAAAATTAAATA
* *
1341608 AATTTTGTAATTTTGAAAATTAAATA
1 AATTTTATAATTTTAAAAATTAAATA
1341634 A
1 A
1341635 GATAAATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (26 bp):
AATTTTATAATTTTAAAAATTAAATA
Found at i:1341751 original size:55 final size:56
Alignment explanation
Indices: 1341630--1341822 Score: 189
Period size: 55 Copynumber: 3.5 Consensus size: 56
1341620 TTGAAAATTA
* * * * *
1341630 AATAAGATAAATTT-TATAATTATAAAGAGACGAATAAGAAAAAAAACATTTATATTG
1 AATAGGATAAATTTCTATAATTTTGAA-AGACGAAGAAGAAAAAAAACATTTTTA-TG
* * *
1341687 AATATGATAAATTTCT-TAATTTTGAAAGACGAAGAAGAAAAATAACTTTTTTATG
1 AATAGGATAAATTTCTATAATTTTGAAAGACGAAGAAGAAAAAAAACATTTTTATG
* * *** * *
1341742 AATAGGATAAA-TTCTATAATTTTGAAGGATG-AGTAAGAAAGGCAGCATTTTCATG
1 AATAGGATAAATTTCTATAATTTTGAAAGACGAAG-AAGAAAAAAAACATTTTTATG
1341797 AATAGGATAAATTTC-ATAATTTTGAA
1 AATAGGATAAATTTCTATAATTTTGAA
1341823 CAGGCGAAAA
Statistics
Matches: 116, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
54 6 0.05
55 62 0.53
56 26 0.22
57 21 0.18
58 1 0.01
ACGTcount: A:0.47, C:0.05, G:0.15, T:0.33
Consensus pattern (56 bp):
AATAGGATAAATTTCTATAATTTTGAAAGACGAAGAAGAAAAAAAACATTTTTATG
Found at i:1341909 original size:94 final size:94
Alignment explanation
Indices: 1341740--1341933 Score: 266
Period size: 94 Copynumber: 2.1 Consensus size: 94
1341730 AACTTTTTTA
* * * * * * *
1341740 TGAATAGGATAAATTCTATAATTTTGAAGGATGAGTAAGAAAGGCAGCATTTTCATGAATAGGAT
1 TGAATAGGAAAAATTCCATAATTTCGAAAGATGAGCAAGAAAAGCAGCATTCTCATGAATAGGAT
*
1341805 AAATTTCATAATTTTGAACAGGCGAAAAT
66 AAATTTCATAATTTTGAACAGACGAAAAT
1341834 TGAATAGGAAAAATTCCATAATTTCGAAAGATGAGCAAGAAAAAG-AGCATTCTCATGAATAGGA
1 TGAATAGGAAAAATTCCATAATTTCGAAAGATGAGCAAG-AAAAGCAGCATTCTCATGAATAGGA
* *
1341898 T-AATTTCCATAATTTTGAAGAGACGAACAT
65 TAAATTT-CATAATTTTGAACAGACGAAAAT
1341928 TGAATA
1 TGAATA
1341934 AAAATAGCAT
Statistics
Matches: 88, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
93 5 0.06
94 79 0.90
95 4 0.05
ACGTcount: A:0.43, C:0.09, G:0.19, T:0.28
Consensus pattern (94 bp):
TGAATAGGAAAAATTCCATAATTTCGAAAGATGAGCAAGAAAAGCAGCATTCTCATGAATAGGAT
AAATTTCATAATTTTGAACAGACGAAAAT
Found at i:1342084 original size:79 final size:81
Alignment explanation
Indices: 1341950--1342109 Score: 261
Period size: 79 Copynumber: 2.0 Consensus size: 81
1341940 GCATTCTCAT
* * *
1341950 AAGATAAATTCTATAATTTTAATAGCATAATTAGTTATAAAAATTCTATAAGTTTGAAGAGGTGA
1 AAGATAAATTCCATAATTTT-ATAGCATAATTAATTACAAAAATTCTATAAGTTTGAAGAGGTGA
1342015 ACAAGAGGATAAAGCAC
65 ACAAGAGGATAAAGCAC
*
1342032 AAGATAAATTCCATAA-TTT-TAGCATAATTAATTACATAAATTCTATAAGTTTGAAGAGGTGAA
1 AAGATAAATTCCATAATTTTATAGCATAATTAATTACAAAAATTCTATAAGTTTGAAGAGGTGAA
1342095 CAAGAGGATAAAGCA
66 CAAGAGGATAAAGCA
1342110 TAATTAGTTA
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
79 56 0.76
81 3 0.04
82 15 0.20
ACGTcount: A:0.46, C:0.08, G:0.16, T:0.30
Consensus pattern (81 bp):
AAGATAAATTCCATAATTTTATAGCATAATTAATTACAAAAATTCTATAAGTTTGAAGAGGTGAA
CAAGAGGATAAAGCAC
Found at i:1351784 original size:17 final size:17
Alignment explanation
Indices: 1351762--1351794 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1351752 TAATTATTTT
1351762 ATTA-TTAATTATAAAAA
1 ATTATTTAATT-TAAAAA
1351779 ATTATTTAATTTAAAA
1 ATTATTTAATTTAAAA
1351795 TAAAAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
ATTATTTAATTTAAAAA
Found at i:1355258 original size:26 final size:27
Alignment explanation
Indices: 1355224--1355275 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
1355214 AATCAAATTC
1355224 TTATA-TTTTATTTTTAA-TTAAATAAG
1 TTATATTTTTA-TTTTAAGTTAAATAAG
1355250 TTATATTTTTATTTTAAGTTAAATAA
1 TTATATTTTTATTTTAAGTTAAATAA
1355276 ACTCTTATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 11 0.46
27 13 0.54
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (27 bp):
TTATATTTTTATTTTAAGTTAAATAAG
Found at i:1355271 original size:27 final size:26
Alignment explanation
Indices: 1355224--1355275 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
1355214 AATCAAATTC
1355224 TTATATTTTATTTTTAATTAAATAAG
1 TTATATTTTATTTTTAATTAAATAAG
1355250 TTATATTTT-TATTTTAAGTTAAATAA
1 TTATATTTTAT-TTTTAA-TTAAATAA
1355276 ACTCTTATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 1 0.04
26 15 0.62
27 8 0.33
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (26 bp):
TTATATTTTATTTTTAATTAAATAAG
Found at i:1355407 original size:48 final size:48
Alignment explanation
Indices: 1355322--1355421 Score: 137
Period size: 48 Copynumber: 2.1 Consensus size: 48
1355312 ATTTGTCATT
* *
1355322 ATAAGTAATGTAGCATTAACATAGCACACTAATATATTATAATTAACA
1 ATAAATAATGTAGCATTAACATAGCACACTAACATATTATAATTAACA
* * * * *
1355370 ATAAATAATGTGGCATTAACGTAGCATATTAACATATTATAATTAATA
1 ATAAATAATGTAGCATTAACATAGCACACTAACATATTATAATTAACA
1355418 ATAA
1 ATAA
1355422 TGTAACATGT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.48, C:0.10, G:0.09, T:0.33
Consensus pattern (48 bp):
ATAAATAATGTAGCATTAACATAGCACACTAACATATTATAATTAACA
Found at i:1355592 original size:26 final size:23
Alignment explanation
Indices: 1355562--1355610 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
1355552 ATAATAGTTT
1355562 ATTTGATTCAAAACAAAAATAAAAAA
1 ATTTGATT--AAAC-AAAATAAAAAA
*
1355588 ATTTGATTAAACATAATAAAAAA
1 ATTTGATTAAACAAAATAAAAAA
1355611 TAAACTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 10 0.45
24 4 0.18
26 8 0.36
ACGTcount: A:0.63, C:0.06, G:0.04, T:0.27
Consensus pattern (23 bp):
ATTTGATTAAACAAAATAAAAAA
Found at i:1365974 original size:2 final size:2
Alignment explanation
Indices: 1365967--1365999 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1365957 AATCCCTCCC
*
1365967 AG AG AG AG AG AG AG AG AG AG AG AG AG AG GG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1366000 TTTAGAGTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1368810 original size:6 final size:6
Alignment explanation
Indices: 1368775--1368831 Score: 51
Period size: 6 Copynumber: 9.5 Consensus size: 6
1368765 AGACCAAGGA
* * * * * *
1368775 GCTGTT GCTGCT GATGGT GGTGTT GCTGTT GTTGTT GCTCTT GCTGTT
1 GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT
*
1368823 GCTTTT GCT
1 GCTGTT GCT
1368832 TTATAACTTG
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.02, C:0.16, G:0.33, T:0.49
Consensus pattern (6 bp):
GCTGTT
Found at i:1389124 original size:19 final size:20
Alignment explanation
Indices: 1389092--1389129 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
1389082 TTCCTCGGGA
1389092 TTTTCTTTTCCCTC-CTTCG
1 TTTTCTTTTCCCTCTCTTCG
1389111 TTTTCTTTAT-CCTCTCTTC
1 TTTTCTTT-TCCCTCTCTTC
1389130 CATTTTCCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.03, C:0.34, G:0.03, T:0.61
Consensus pattern (20 bp):
TTTTCTTTTCCCTCTCTTCG
Found at i:1394406 original size:27 final size:27
Alignment explanation
Indices: 1394378--1394431 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
1394368 AATTAATAAT
*
1394378 AACTGAAAATATTTTTATTATATTTATA
1 AACT-AAAATATTTTTATAATATTTATA
*
1394406 AACTCAAATATTTTTATAATATTTAT
1 AACTAAAATATTTTTATAATATTTAT
1394432 CACCATTGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 20 0.83
28 4 0.17
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.50
Consensus pattern (27 bp):
AACTAAAATATTTTTATAATATTTATA
Found at i:1398024 original size:11 final size:12
Alignment explanation
Indices: 1398006--1398033 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1397996 GATTCTAAAT
1398006 GAAAAAAAAAAA
1 GAAAAAAAAAAA
1398018 GAAAAAAAAAAA
1 GAAAAAAAAAAA
1398030 GAAA
1 GAAA
1398034 GTGCTCATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (12 bp):
GAAAAAAAAAAA
Found at i:1410710 original size:2 final size:2
Alignment explanation
Indices: 1410703--1410740 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1410693 TTCAAGCTTT
1410703 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1410741 TATAAATATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:1422684 original size:24 final size:24
Alignment explanation
Indices: 1422657--1422715 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
1422647 CCGCTCATGG
*
1422657 TCACGACCACGAT-CCCGAGCTCGA
1 TCACGACCACG-TGCCCGAGCGCGA
* * *
1422681 TCACGATCACGTGCTCGATCGCGA
1 TCACGACCACGTGCCCGAGCGCGA
1422705 TCACGACCACG
1 TCACGACCACG
1422716 GTCTCTCTCT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
23 1 0.03
24 28 0.97
ACGTcount: A:0.24, C:0.39, G:0.22, T:0.15
Consensus pattern (24 bp):
TCACGACCACGTGCCCGAGCGCGA
Found at i:1422687 original size:18 final size:18
Alignment explanation
Indices: 1422664--1422710 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
1422654 TGGTCACGAC
*
1422664 CACGATCCCGAGCTCGAT
1 CACGATCACGAGCTCGAT
*
1422682 CACGATCACGTGCTCGAT
1 CACGATCACGAGCTCGAT
*
1422700 CGCGATCACGA
1 CACGATCACGA
1422711 CCACGGTCTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.23, C:0.36, G:0.23, T:0.17
Consensus pattern (18 bp):
CACGATCACGAGCTCGAT
Found at i:1425117 original size:278 final size:273
Alignment explanation
Indices: 1424586--1425132 Score: 925
Period size: 278 Copynumber: 2.0 Consensus size: 273
1424576 ACATCTTTGG
* *
1424586 AATTGGATTGTAAAAGTATTGGGGATTGCGAAATAATCAGCCCCTTACCAGGTATACCTTTATAG
1 AATTGGATTGTAAAAGTATTGGGGATTGAGAAATAATCAGCCCCTTACCAGGGATACCTTTATAG
* *
1424651 GATGATTCTTAATGGTACAACAATACCTAAAGAGTGGAAAATCACCTATATCTGGAGATGGTTTC
66 GATGATTCTTAATGGTACAACAATACCTAAAGAGTGGAAAATCACCTACATCTGGAGATGATTTC
*
1424716 TACATCCTACCATATTAAAGCAACTTATCAAGGGGTCAATTGAAACAAACCCGTTCACCCTTACC
131 TACATCCTACCATATTAAAGCAACTTATCAAGGGGTCAATTGAAACAAACCCATTCACCCTTACC
* *
1424781 AGTAAATAGCTGTGATACCTGTTATCCTTTTTTCAACTTGATCAGACTCCAAGTACAAATTATCA
196 AGTAAATAGCTGTGATACCTGTTATCCTTTTTTCAACTTGAACAGACTCCAAGTACAAAATATCA
1424846 CAGAACAGGCAGA
261 CAGAACAGGCAGA
1424859 AATTGGATTGTAAAAGTATTGGGGATTGAGAAATATAGTAATCAGCCCCTTACCAGGGATACCTT
1 AATTGGATTGTAAAAGTATTGGGGATTGAG--A-A-A-TAATCAGCCCCTTACCAGGGATACCTT
* *
1424924 TATAGGATGATTCTTAATGGTACAACAATACCTAAAGAGTGGAAGATCACCTACGTCTGGAGATG
61 TATAGGATGATTCTTAATGGTACAACAATACCTAAAGAGTGGAAAATCACCTACATCTGGAGATG
1424989 ATTTCTACATCCTACCATATTAAAGCAACTTATCAAGGGGTCAATTGAAACAAACCCATTCACCC
126 ATTTCTACATCCTACCATATTAAAGCAACTTATCAAGGGGTCAATTGAAACAAACCCATTCACCC
* *
1425054 TTACCAGTAAATAGGCTGTGATACCTGTT-TTCTTTTTTCAACTTGAACAGACTCCACGTACAAA
191 TTACCAGTAAATA-GCTGTGATACCTGTTATCCTTTTTTCAACTTGAACAGACTCCAAGTACAAA
*
1425118 ATATTACAGAACAGG
255 ATATCACAGAACAGG
1425133 AAGACACTCA
Statistics
Matches: 256, Mismatches: 12, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
273 29 0.11
275 1 0.00
276 1 0.00
277 1 0.00
278 209 0.82
279 15 0.06
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.29
Consensus pattern (273 bp):
AATTGGATTGTAAAAGTATTGGGGATTGAGAAATAATCAGCCCCTTACCAGGGATACCTTTATAG
GATGATTCTTAATGGTACAACAATACCTAAAGAGTGGAAAATCACCTACATCTGGAGATGATTTC
TACATCCTACCATATTAAAGCAACTTATCAAGGGGTCAATTGAAACAAACCCATTCACCCTTACC
AGTAAATAGCTGTGATACCTGTTATCCTTTTTTCAACTTGAACAGACTCCAAGTACAAAATATCA
CAGAACAGGCAGA
Found at i:1432021 original size:3 final size:3
Alignment explanation
Indices: 1432013--1432094 Score: 58
Period size: 3 Copynumber: 26.3 Consensus size: 3
1432003 ATGACTATTC
* * *
1432013 GGT GGT GGT GGT GGT GGT GGT GGT GCG- GAT GGT GAT GGT GGC GGT
1 GGT GGT GGT GGT GGT GGT GGT GGT G-GT GGT GGT GGT GGT GGT GGT
* * * *
1432058 GGT GAGCT TGC GGAC GAT GGT GGT GGT GGT GGT GGT G
1 GGT G-G-T GGT GG-T GGT GGT GGT GGT GGT GGT GGT G
1432095 ATGAGTTATT
Statistics
Matches: 62, Mismatches: 12, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
3 56 0.90
4 5 0.08
5 1 0.02
ACGTcount: A:0.06, C:0.06, G:0.60, T:0.28
Consensus pattern (3 bp):
GGT
Found at i:1435107 original size:24 final size:24
Alignment explanation
Indices: 1435080--1435154 Score: 141
Period size: 24 Copynumber: 3.1 Consensus size: 24
1435070 CACTCTCCAA
1435080 ATCTGCCATGACCCAAGAATCACT
1 ATCTGCCATGACCCAAGAATCACT
1435104 ATCTGCCATGACCCAAGAATCACT
1 ATCTGCCATGACCCAAGAATCACT
*
1435128 ATCTGCCATAACCCAAGAATCACT
1 ATCTGCCATGACCCAAGAATCACT
1435152 ATC
1 ATC
1435155 CGAATCAGCC
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.35, C:0.33, G:0.11, T:0.21
Consensus pattern (24 bp):
ATCTGCCATGACCCAAGAATCACT
Found at i:1439038 original size:13 final size:14
Alignment explanation
Indices: 1439022--1439054 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1439012 AGACTTTGGA
*
1439022 GAGAAGTTTTGAT-
1 GAGAAGTTTCGATC
1439035 GAGAAGTTTCGATC
1 GAGAAGTTTCGATC
1439049 GAGAAG
1 GAGAAG
1439055 AAAGTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.33, C:0.06, G:0.33, T:0.27
Consensus pattern (14 bp):
GAGAAGTTTCGATC
Found at i:1439231 original size:17 final size:17
Alignment explanation
Indices: 1439209--1439246 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1439199 TTTATAAGTT
1439209 TTTAGTGTTCGCGTTTG
1 TTTAGTGTTCGCGTTTG
* *
1439226 TTTAGTGTTTGTGTTTG
1 TTTAGTGTTCGCGTTTG
1439243 TTTA
1 TTTA
1439247 AATTTTTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.08, C:0.05, G:0.26, T:0.61
Consensus pattern (17 bp):
TTTAGTGTTCGCGTTTG
Found at i:1440040 original size:23 final size:23
Alignment explanation
Indices: 1440007--1440051 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1439997 AAATATTAAT
* * *
1440007 ATTTAATTTAAAATATTAAAATA
1 ATTTAAATTAAAAAAATAAAATA
1440030 ATTTAAATTAAAAAAATAAAAT
1 ATTTAAATTAAAAAAATAAAAT
1440052 TTAAAATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
ATTTAAATTAAAAAAATAAAATA
Found at i:1440045 original size:18 final size:18
Alignment explanation
Indices: 1440010--1440058 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
1440000 TATTAATATT
**
1440010 TAATTTAAAATATTAAAA
1 TAATTTAAAATAAAAAAA
*
1440028 TAATTTAAATTAAAAAAA
1 TAATTTAAAATAAAAAAA
1440046 TAAAATTTAAAAT
1 T--AATTTAAAAT
1440059 TTTCAATACT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 16 0.64
20 9 0.36
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TAATTTAAAATAAAAAAA
Found at i:1454632 original size:14 final size:14
Alignment explanation
Indices: 1454621--1454647 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1454611 AAATGATATT
1454621 AATGAAACGATACA
1 AATGAAACGATACA
1454635 AATGAAACGATAC
1 AATGAAACGATAC
1454648 GATTGTTGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.15, G:0.15, T:0.15
Consensus pattern (14 bp):
AATGAAACGATACA
Found at i:1459517 original size:25 final size:25
Alignment explanation
Indices: 1459467--1459517 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
1459457 AATAAAAGTT
* *
1459467 ATTCACAAGATGTTAAATAAATAAA
1 ATTCACAAAATGTTAAATAAAGAAA
* *
1459492 ATTCACAAAATGTTAATTGAAGAAA
1 ATTCACAAAATGTTAAATAAAGAAA
1459517 A
1 A
1459518 AAGAGAAATC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.55, C:0.08, G:0.10, T:0.27
Consensus pattern (25 bp):
ATTCACAAAATGTTAAATAAAGAAA
Found at i:1462265 original size:18 final size:18
Alignment explanation
Indices: 1462242--1462277 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1462232 AACTAATACC
1462242 CTTATTCTCTATATTATA
1 CTTATTCTCTATATTATA
1462260 CTTATTCTCTATATTATA
1 CTTATTCTCTATATTATA
1462278 ATTTTTTTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.17, G:0.00, T:0.56
Consensus pattern (18 bp):
CTTATTCTCTATATTATA
Found at i:1466451 original size:20 final size:20
Alignment explanation
Indices: 1466426--1466467 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1466416 TTATAATGCT
* * *
1466426 AAAAAATGCCTGATTTAGGA
1 AAAAAATACCTAATTTAAGA
1466446 AAAAAATACCTAATTTAAGA
1 AAAAAATACCTAATTTAAGA
1466466 AA
1 AA
1466468 CAGGCCAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.55, C:0.10, G:0.12, T:0.24
Consensus pattern (20 bp):
AAAAAATACCTAATTTAAGA
Found at i:1467100 original size:17 final size:16
Alignment explanation
Indices: 1467072--1467111 Score: 53
Period size: 19 Copynumber: 2.3 Consensus size: 16
1467062 TTTTCATGTT
1467072 TTAAATATATAAGATATTA
1 TTAAATATA-AA-ATA-TA
1467091 TTAAATATAAAATATA
1 TTAAATATAAAATATA
1467107 TTAAA
1 TTAAA
1467112 ATTAAACACA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.33
17 3 0.14
18 2 0.10
19 9 0.43
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (16 bp):
TTAAATATAAAATATA
Found at i:1467113 original size:17 final size:18
Alignment explanation
Indices: 1467072--1467117 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
1467062 TTTTCATGTT
*
1467072 TTAAATATATAAGATATTA
1 TTAAA-ATATAAAATATTA
1467091 TT-AAATATAAAATA-TA
1 TTAAAATATAAAATATTA
1467107 TTAAAAT-TAAA
1 TTAAAATATAAA
1467118 CACAAATACA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 8 0.32
17 13 0.52
18 2 0.08
19 2 0.08
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (18 bp):
TTAAAATATAAAATATTA
Found at i:1467313 original size:21 final size:21
Alignment explanation
Indices: 1467253--1467313 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
1467243 ATTAATAACG
*
1467253 TAATT-AATAT-A-TTTAATA
1 TAATTAAATATAATTTTATTA
* *
1467271 TAATTAAATAAAAATATT-TTA
1 TAATTAAAT-ATAATTTTATTA
1467292 TAATTAAATATAATTTTATTA
1 TAATTAAATATAATTTTATTA
1467313 T
1 T
1467314 TTAAATTTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
18 5 0.15
19 3 0.09
20 7 0.21
21 16 0.48
22 2 0.06
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TAATTAAATATAATTTTATTA
Found at i:1467463 original size:12 final size:14
Alignment explanation
Indices: 1467437--1467476 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
1467427 TTTTTATAAA
1467437 ATTTAAAA-AATTT
1 ATTTAAAATAATTT
1467450 A-TTAAAATAA-TT
1 ATTTAAAATAATTT
*
1467462 ATTTAAAATTATTT
1 ATTTAAAATAATTT
1467476 A
1 A
1467477 AGTAAGATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
12 9 0.39
13 11 0.48
14 3 0.13
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
ATTTAAAATAATTT
Found at i:1468008 original size:23 final size:23
Alignment explanation
Indices: 1467962--1468008 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
1467952 ATGTATAAAA
* *
1467962 ATAAAATTTTAAAATATTTTAAT
1 ATAAAATTTTAAAATATATGAAT
1467985 ATAAATATTTTAAAAT-TATGAAT
1 ATAAA-ATTTTAAAATATATGAAT
1468008 A
1 A
1468009 CTATTTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
ATAAAATTTTAAAATATATGAAT
Found at i:1472616 original size:25 final size:25
Alignment explanation
Indices: 1472588--1472639 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
1472578 AAAAATGATC
1472588 TTAGAACAACAATATGTGTCAAGGA
1 TTAGAACAACAATATGTGTCAAGGA
1472613 TTAGAACAACAATATGTGTCAAGGA
1 TTAGAACAACAATATGTGTCAAGGA
1472638 TT
1 TT
1472640 TCAAAAACTA
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:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (25 bp):
TTAGAACAACAATATGTGTCAAGGA
Found at i:1480538 original size:2 final size:2
Alignment explanation
Indices: 1480522--1480562 Score: 55
Period size: 2 Copynumber: 20.0 Consensus size: 2
1480512 TATTTAAAAG
* *
1480522 TA TA TA CA TA CA TA TA TA TA TA TA TA TA TA TA TA TA CTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
1480563 AAAGGCAACA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:1496001 original size:3 final size:3
Alignment explanation
Indices: 1495995--1496202 Score: 85
Period size: 3 Copynumber: 67.3 Consensus size: 3
1495985 TGTCTTCGGG
*
1495995 CTT CTT CTT GC-T CTT -TC CTT GCTT CTT CTT C-T CTT C-T CTT CTT
1 CTT CTT CTT -CTT CTT CTT CTT -CTT CTT CTT CTT CTT CTT CTT CTT
* * * *
1496038 GGCTT CTT TTT CTT CTT CTT CTT CTT -TT CTT CTGG CTT CCT CTT CCT
1 --CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT-T CTT CTT CTT CTT
* * * *
1496085 CTCT CTT CTT GGCTT CTT CTT CTT C-T CTT TTT CTGG CTT CCT CTT CCT
1 CT-T CTT CTT --CTT CTT CTT CTT CTT CTT CTT CT-T CTT CTT CTT CTT
* * *
1496133 C-C CTT -TT CTT GGCTT CTT CTT CCT C-C CTT -TT CTT GGCTT CTT CTT
1 CTT CTT CTT CTT --CTT CTT CTT CTT CTT CTT CTT CTT --CTT CTT CTT
*
1496178 CTT CTCT CTTT CTAG CTT CTT CTT C
1 CTT CT-T C-TT CT-T CTT CTT CTT C
1496203 CTCCTCTTTC
Statistics
Matches: 155, Mismatches: 24, Indels: 52
0.67 0.10 0.23
Matches are distributed among these distances:
2 16 0.10
3 109 0.70
4 17 0.11
5 13 0.08
ACGTcount: A:0.00, C:0.35, G:0.07, T:0.58
Consensus pattern (3 bp):
CTT
Found at i:1496025 original size:27 final size:25
Alignment explanation
Indices: 1495995--1496239 Score: 143
Period size: 24 Copynumber: 9.6 Consensus size: 25
1495985 TGTCTTCGGG
1495995 CTTCTTCTTGCTCTTTCCTT-GCTTCTT
1 CTTCTTCTT-CTC-TT-CTTGGCTTCTT
1496022 CTTC-TCTTCTCTTCTTGGCTTCTTTTT
1 CTTCTTCTTCTCTTCTTGGCTTC---TT
*
1496049 CTTCTTCTTCTTCTTTTCTTCTGGCTTCCT
1 CTTCTTCTTC-TC--TTC-T-TGGCTTCTT
*
1496079 CTTCCTC-TCTCTTCTTGGCTTCTT
1 CTTCTTCTTCTCTTCTTGGCTTCTT
* *
1496103 CTTCTTC-TCT-TTTTCTGGCTTCCT
1 CTTCTTCTTCTCTTCT-TGGCTTCTT
* * *
1496127 CTTCCTC-CCTTTTCTTGGCTTCTT
1 CTTCTTCTTCTCTTCTTGGCTTCTT
* * *
1496151 CTTCCTC-CCTTTTCTTGGCTTCTT
1 CTTCTTCTTCTCTTCTTGGCTTCTT
*
1496175 CTTCTTC-TCTCTT-TCTAGCTTCTT
1 CTTCTTCTTCTCTTCT-TGGCTTCTT
*
1496199 CTTCCTCCTCTT-TCTTCCTGGCTTCTT
1 CTT-CT--TCTTCTCTTCTTGGCTTCTT
*
1496226 CCTCTTGCTT-TCTT
1 CTTCTT-CTTCTCTT
1496240 TCCCTTTCAA
Statistics
Matches: 182, Mismatches: 17, Indels: 40
0.76 0.07 0.17
Matches are distributed among these distances:
23 7 0.04
24 94 0.52
25 16 0.09
26 9 0.05
27 26 0.14
28 8 0.04
29 4 0.02
30 7 0.04
31 3 0.02
32 1 0.01
33 7 0.04
ACGTcount: A:0.00, C:0.35, G:0.07, T:0.57
Consensus pattern (25 bp):
CTTCTTCTTCTCTTCTTGGCTTCTT
Found at i:1496053 original size:17 final size:19
Alignment explanation
Indices: 1496019--1496110 Score: 68
Period size: 17 Copynumber: 4.7 Consensus size: 19
1496009 TTCCTTGCTT
1496019 CTTCTTCTCTTCTCTTCTTGG
1 CTTCTTCT-TT-TCTTCTTGG
1496040 CTTC-T-TTTTCTTCTT--
1 CTTCTTCTTTTCTTCTTGG
1496055 CTTCTTCTTTTCTTC-TGG
1 CTTCTTCTTTTCTTCTTGG
*
1496073 CTTCCTCTTCCTCTCTCTTCTTGG
1 C-T--TCTT-CT-TTTCTTCTTGG
1496097 CTTCTTCTTCTTCT
1 CTTCTTCTT-TTCT
1496111 CTTTTTCTGG
Statistics
Matches: 58, Mismatches: 2, Indels: 23
0.70 0.02 0.28
Matches are distributed among these distances:
15 4 0.07
16 2 0.03
17 15 0.26
18 3 0.05
19 3 0.05
20 6 0.10
21 12 0.21
22 2 0.03
23 7 0.12
24 4 0.07
ACGTcount: A:0.00, C:0.34, G:0.07, T:0.60
Consensus pattern (19 bp):
CTTCTTCTTTTCTTCTTGG
Found at i:1496053 original size:54 final size:56
Alignment explanation
Indices: 1495995--1496154 Score: 169
Period size: 57 Copynumber: 3.0 Consensus size: 56
1495985 TGTCTTCGGG
* * *
1495995 CTTCTTCTTGCTCTTTC-CTTGCTTCTTCTT-CTCTTCTCTTCTTGGCTTCTTTTTCTT
1 CTTCTTCTT-CT-TTTCTCTGGCTTCCTCTTCCTC-TCTCTTCTTGGCTTCTTCTTCTT
1496052 CTTCTTCTTCTTTTCTTCTGGCTTCCTCTTCCTCTCTCTTCTTGG------CTTCTT
1 CTTCTTCTTCTTTTC-TCTGGCTTCCTCTTCCTCTCTCTTCTTGGCTTCTTCTTCTT
* *
1496103 CTTCTTC-TCTTTT-TCTGGCTTCCTCTTCCTCCCTTTTCTTGGCTTCTTCTTC
1 CTTCTTCTTCTTTTCTCTGGCTTCCTCTTCCTCTCTCTTCTTGGCTTCTTCTTC
1496155 CTCCCTTTTC
Statistics
Matches: 89, Mismatches: 5, Indels: 21
0.77 0.04 0.18
Matches are distributed among these distances:
48 27 0.30
50 6 0.07
51 12 0.13
54 4 0.04
55 4 0.04
56 2 0.02
57 31 0.35
58 3 0.03
ACGTcount: A:0.00, C:0.34, G:0.07, T:0.58
Consensus pattern (56 bp):
CTTCTTCTTCTTTTCTCTGGCTTCCTCTTCCTCTCTCTTCTTGGCTTCTTCTTCTT
Found at i:1496109 original size:48 final size:50
Alignment explanation
Indices: 1496047--1496223 Score: 204
Period size: 48 Copynumber: 3.6 Consensus size: 50
1496037 TGGCTTCTTT
* *
1496047 TTCTTCTTCTTCTTCTTTTCTTCTGGCTTCCTCTTCCTCTCTCTTCTTGGC
1 TTCTTCTTCCTCCTC-TTTCTTCTGGCTTCCTCTTCCTCTCTCTTCTTGGC
* * *
1496098 TTCTTCTT-CTTCTCTTT-TTCTGGCTTCCTCTTCCTCCCTTTTCTTGGC
1 TTCTTCTTCCTCCTCTTTCTTCTGGCTTCCTCTTCCTCTCTCTTCTTGGC
* * *
1496146 TTCTTCTTCCTCC-C-TT-TTCTTGGCTTCTTCTTCTTCTCTCTT-TCTAGC
1 TTCTTCTTCCTCCTCTTTCTTC-TGGCTTCCTCTTCCTCTCTCTTCT-TGGC
1496194 TTCTTCTTCCTCCTCTTTCTTCCTGGCTTC
1 TTCTTCTTCCTCCTCTTTCTT-CTGGCTTC
1496224 TTCCTCTTGC
Statistics
Matches: 108, Mismatches: 11, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
47 6 0.06
48 72 0.67
49 7 0.06
50 5 0.05
51 17 0.16
52 1 0.01
ACGTcount: A:0.01, C:0.36, G:0.07, T:0.56
Consensus pattern (50 bp):
TTCTTCTTCCTCCTCTTTCTTCTGGCTTCCTCTTCCTCTCTCTTCTTGGC
Found at i:1496154 original size:72 final size:73
Alignment explanation
Indices: 1496051--1496226 Score: 228
Period size: 72 Copynumber: 2.4 Consensus size: 73
1496041 TTCTTTTTCT
* * * * *
1496051 TCTTCTTCTTCTTTTCTTCTGGCTTCCTCTTCCTCTCTCTTCTTGGCTTCTTCTTCTTCTCTTTT
1 TCTTCCTCCTCTTTTC-T-TGGCTTCTTCTTCCTCCCTCTTCTTGGCTTCTTCTTCTTCTCTCTT
*
1496116 TCTGGCTTCC
64 TCTAGCTTCC
*
1496126 TCTTCCTCC-CTTTTCTTGGCTTCTTCTTCCTCCCTTTTCTTGGCTTCTTCTTCTTCTCTCTTTC
1 TCTTCCTCCTCTTTTCTTGGCTTCTTCTTCCTCCCTCTTCTTGGCTTCTTCTTCTTCTCTCTTTC
*
1496190 TAGCTTCT
66 TAGCTTCC
*
1496198 TCTTCCTCCTCTTTCTTCCTGGCTTCTTC
1 TCTTCCTCCTC-TT-TTCTTGGCTTCTTC
1496227 CTCTTGCTTT
Statistics
Matches: 89, Mismatches: 9, Indels: 6
0.86 0.09 0.06
Matches are distributed among these distances:
72 59 0.66
73 2 0.02
74 8 0.09
75 20 0.22
ACGTcount: A:0.01, C:0.36, G:0.07, T:0.56
Consensus pattern (73 bp):
TCTTCCTCCTCTTTTCTTGGCTTCTTCTTCCTCCCTCTTCTTGGCTTCTTCTTCTTCTCTCTTTC
TAGCTTCC
Found at i:1497283 original size:51 final size:51
Alignment explanation
Indices: 1497220--1497320 Score: 175
Period size: 51 Copynumber: 2.0 Consensus size: 51
1497210 GAAAGCCTCT
* * *
1497220 AACCTACTTTTAAAGTTAAAATCTTACCTTAAATGCTGCTTGGAGGACTCA
1 AACCAACTTTTAAAGCTAAAATCTTACCTTAAAAGCTGCTTGGAGGACTCA
1497271 AACCAACTTTTAAAGCTAAAATCTTACCTTAAAAGCTGCTTGGAGGACTC
1 AACCAACTTTTAAAGCTAAAATCTTACCTTAAAAGCTGCTTGGAGGACTC
1497321 TCGAATCAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.31
Consensus pattern (51 bp):
AACCAACTTTTAAAGCTAAAATCTTACCTTAAAAGCTGCTTGGAGGACTCA
Found at i:1506564 original size:21 final size:21
Alignment explanation
Indices: 1506540--1506583 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1506530 TAACATTATG
1506540 ATTTGAAATAAAAAT-ATAAAA
1 ATTT-AAATAAAAATAATAAAA
* *
1506561 ATTTAATTAAATATAATAAAA
1 ATTTAAATAAAAATAATAAAA
1506582 AT
1 AT
1506584 AAAAACCTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (21 bp):
ATTTAAATAAAAATAATAAAA
Found at i:1506655 original size:2 final size:2
Alignment explanation
Indices: 1506648--1506695 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
1506638 TTTCATCAAC
* * *
1506648 AT AT AT AT AT AT AT AC AT AC AT AT AT AT AT AT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1506690 AT AT AT
1 AT AT AT
1506696 GTATGTATGT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1528887 original size:22 final size:22
Alignment explanation
Indices: 1528859--1528904 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
1528849 ATTCTCTCAA
*
1528859 ATCTCACTTTAGCTAACATTTG
1 ATCTCACTTTAGCTAACATGTG
1528881 ATCTCACTTTAGCTAACATGTG
1 ATCTCACTTTAGCTAACATGTG
1528903 AT
1 AT
1528905 TTCCCATTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (22 bp):
ATCTCACTTTAGCTAACATGTG
Found at i:1533164 original size:2 final size:2
Alignment explanation
Indices: 1533157--1533182 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1533147 CCTCAATTCA
1533157 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1533183 GTAGATATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1542941 original size:39 final size:39
Alignment explanation
Indices: 1542897--1543019 Score: 246
Period size: 39 Copynumber: 3.2 Consensus size: 39
1542887 ATGCATTTAC
1542897 GCAAGTCTTTACTGAAAAAGTTTCGATTTATACTCTATT
1 GCAAGTCTTTACTGAAAAAGTTTCGATTTATACTCTATT
1542936 GCAAGTCTTTACTGAAAAAGTTTCGATTTATACTCTATT
1 GCAAGTCTTTACTGAAAAAGTTTCGATTTATACTCTATT
1542975 GCAAGTCTTTACTGAAAAAGTTTCGATTTATACTCTATT
1 GCAAGTCTTTACTGAAAAAGTTTCGATTTATACTCTATT
1543014 GCAAGT
1 GCAAGT
1543020 ATTTTTGAAA
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 84 1.00
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (39 bp):
GCAAGTCTTTACTGAAAAAGTTTCGATTTATACTCTATT
Found at i:1550037 original size:39 final size:38
Alignment explanation
Indices: 1549994--1550102 Score: 121
Period size: 41 Copynumber: 2.8 Consensus size: 38
1549984 TGTCGGAGTA
** *
1549994 AAAAATTTTTTAAAAATAAAAACATAAACATGTGACATT
1 AAAAATTTTAAAAAAATAAAAA-ATAAACATGTGACACT
* *
1550033 AAAAATTTTGAAAAAAATAAAAAAAATAAACTTGTGGCACT
1 AAAAATTTT-AAAAAAAT--AAAAAATAAACATGTGACACT
*
1550074 AAAAA-TTAAAAAAAATAAAAAATAAACAT
1 AAAAATTTTAAAAAAATAAAAAATAAACAT
1550103 ATAAAGTACA
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
37 12 0.20
39 17 0.28
40 8 0.13
41 18 0.30
42 5 0.08
ACGTcount: A:0.63, C:0.06, G:0.06, T:0.25
Consensus pattern (38 bp):
AAAAATTTTAAAAAAATAAAAAATAAACATGTGACACT
Found at i:1550730 original size:18 final size:18
Alignment explanation
Indices: 1550707--1550743 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1550697 TTAACTCTTA
*
1550707 ATATATATATGTATTTAT
1 ATATATATATGTATGTAT
*
1550725 ATATATGTATGTATGTAT
1 ATATATATATGTATGTAT
1550743 A
1 A
1550744 GATTTTAACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (18 bp):
ATATATATATGTATGTAT
Found at i:1550743 original size:14 final size:14
Alignment explanation
Indices: 1550708--1550743 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1550698 TAACTCTTAA
*
1550708 TATATATATGTATT
1 TATATATATGTATG
1550722 TATATATATGTATG
1 TATATATATGTATG
*
1550736 TATGTATA
1 TATATATA
1550744 GATTTTAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (14 bp):
TATATATATGTATG
Found at i:1551194 original size:23 final size:22
Alignment explanation
Indices: 1551151--1551193 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1551141 ACTCTTCATT
1551151 TTTTTAAAAAATTATAATTTTA
1 TTTTTAAAAAATTATAATTTTA
*
1551173 TTTTTATAAATATTA-AATTTT
1 TTTTTA-AAAAATTATAATTTT
1551194 TTGTTGTCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTTTAAAAAATTATAATTTTA
Found at i:1559014 original size:22 final size:23
Alignment explanation
Indices: 1558965--1559027 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 23
1558955 TTTTATGTGT
*
1558965 ATAAATAATAATAAATTATAAACA
1 ATAACTAATAA-AAATTATAAACA
* * *
1558989 ATAAGTTATAAAAATTA-AGACA
1 ATAACTAATAAAAATTATAAACA
1559011 ATAACTAAT-AAAATTAT
1 ATAACTAATAAAAATTAT
1559028 TAAGTGTAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
21 7 0.21
22 11 0.33
23 6 0.18
24 9 0.27
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (23 bp):
ATAACTAATAAAAATTATAAACA
Found at i:1559233 original size:216 final size:211
Alignment explanation
Indices: 1558863--1559322 Score: 608
Period size: 216 Copynumber: 2.2 Consensus size: 211
1558853 AATATACAAA
*
1558863 TTATGTATAAATTAAATATATGTATATATATAATATTATTTTATTATATATATAAAATTAATGAC
1 TTATGTATAAATTAAATATATGTATATATATAATATTACTTTATTATATATATAAAATTAATGAC
****
1558928 ACAACTTATATATTATAATATTTTAATTTTTATGTGTATAAATAATAATAAATTATAAACAATAA
66 ACAACTTATATATTATAATATTTTAATCAAAATGTGTATAAATAATAATAAATTATAAACAATAA
*
1558993 GTTATAAAAATTAAGACAATAACTAATAAAATTATTAAGTGTAATCATATAAATAAAATCTATTA
131 GTTATAAAAACTAAGACAATAACTAATAAAATTATTAAGTGTAATCATATAAATAAAATCTATTA
*
1559058 TAAGTTATAGTAATGC
196 TAAGTTATAGTAATAC
* *
1559074 TTATGTATAAATTAAATATATGTATATATCTAATATATTACTTTATTATGTATATATGAAATTAA
1 TTATGTATAAATTAAATATATGTATATATAT-A-ATATTACTTTATTA--TATATATAAAATTAA
* * * * * *
1559139 TGACATAATTTATATGTTATATTGTTTTATATCAAAATTTGTATAAATAATAACT-AATTATAAA
62 TGACACAACTTATATATTATAATATTTTA-ATCAAAATGTGTATAAATAATAA-TAAATTATAAA
* *** * * *
1559203 TAATATA-TTATAAAAACTAAGGTGATAACTAATAAAGTTATTAAGTGTAATGATATAAATAAAG
125 CAATA-AGTTATAAAAACTAAGACAATAACTAATAAAATTATTAAGTGTAATCATATAAATAAAA
*
1559267 TTTATTATAAGTTATAGTAATAC
189 TCTATTATAAGTTATAGTAATAC
1559290 TTATGTATAAATT--ATATA--TATATATATAATATT
1 TTATGTATAAATTAAATATATGTATATATATAATATT
1559323 TATACAATTA
Statistics
Matches: 218, Mismatches: 24, Indels: 15
0.85 0.09 0.06
Matches are distributed among these distances:
210 5 0.02
211 31 0.14
212 9 0.04
213 13 0.06
214 5 0.02
215 38 0.17
216 115 0.53
217 2 0.01
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.43
Consensus pattern (211 bp):
TTATGTATAAATTAAATATATGTATATATATAATATTACTTTATTATATATATAAAATTAATGAC
ACAACTTATATATTATAATATTTTAATCAAAATGTGTATAAATAATAATAAATTATAAACAATAA
GTTATAAAAACTAAGACAATAACTAATAAAATTATTAAGTGTAATCATATAAATAAAATCTATTA
TAAGTTATAGTAATAC
Found at i:1559309 original size:2 final size:2
Alignment explanation
Indices: 1559302--1559347 Score: 53
Period size: 2 Copynumber: 24.5 Consensus size: 2
1559292 ATGTATAAAT
* *
1559302 TA TA TA TA TA TA TA TA -A TA TT TA TA CA -A T- TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1559341 TA TA TA T
1 TA TA TA T
1559348 TCATAACATT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
1 3 0.08
2 35 0.92
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1563967 original size:24 final size:24
Alignment explanation
Indices: 1563949--1563995 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1563939 GTAATGTTAT
1563949 AATTAAAATAA-AAAATAATATAAA
1 AATTAAAA-AATAAAATAATATAAA
*
1563973 AATTAAAAAATAAAATAAAATAA
1 AATTAAAAAATAAAATAATATAA
1563996 GTAAAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 2 0.10
24 19 0.90
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (24 bp):
AATTAAAAAATAAAATAATATAAA
Found at i:1563981 original size:19 final size:18
Alignment explanation
Indices: 1563953--1564090 Score: 71
Period size: 19 Copynumber: 7.0 Consensus size: 18
1563943 TGTTATAATT
*
1563953 AAAATAAAAAATAATATA
1 AAAATAAAAAATAAAATA
1563971 AAAATTAAAAAATAAAATAA
1 AAAA-TAAAAAATAAAAT-A
1563991 AATAAGTAAAAAAAATTAAAATA
1 AA-AA-T--AAAAAA-TAAAATA
** * *
1564014 AAATATATACTATTAAAAATG
1 AAA-ATA-AAAAAT-AAAATA
* * *
1564035 ATATTAAAGAAATAAAAACA
1 AAAATAAA-AAAT-AAAATA
*
1564055 AAATATAAAAAATATAATA
1 AAA-ATAAAAAATAAAATA
1564074 AAAAT-AAAAATAAAATA
1 AAAATAAAAAATAAAATA
1564091 GATAATATTA
Statistics
Matches: 91, Mismatches: 18, Indels: 23
0.69 0.14 0.17
Matches are distributed among these distances:
17 11 0.12
18 6 0.07
19 20 0.22
20 20 0.22
21 16 0.18
22 2 0.02
23 10 0.11
24 6 0.07
ACGTcount: A:0.73, C:0.01, G:0.02, T:0.23
Consensus pattern (18 bp):
AAAATAAAAAATAAAATA
Found at i:1563987 original size:31 final size:30
Alignment explanation
Indices: 1563952--1564097 Score: 86
Period size: 31 Copynumber: 4.6 Consensus size: 30
1563942 ATGTTATAAT
1563952 TAAAATAAAAAATAATATAAAAATTAAAAAA
1 TAAAATAAAAAATAATA-AAAAATTAAAAAA
1563983 TAAAATAAAATAAGTAA-AAAAAATT--AAAA
1 TAAAATAAAA-AA-TAATAAAAAATTAAAAAA
* * * *
1564012 TAAAATATATACTATTAAAAATGATATTAAAGAAA
1 TAAAATAAAAAATAAT-AAAA--A-ATTAAA-AAA
*
1564047 TAAAA-ACAAAAT-ATAAAAAATATAATAAAAA
1 TAAAATAAAAAATAATAAAAAAT-T-A-AAAAA
1564078 TAAAAATAAAATAGATAATA
1 T-AAAATAAAA-A-ATAATA
1564098 TTAAAAATAT
Statistics
Matches: 88, Mismatches: 9, Indels: 31
0.69 0.07 0.24
Matches are distributed among these distances:
27 2 0.02
28 1 0.01
29 18 0.20
30 2 0.02
31 23 0.26
32 16 0.18
33 7 0.08
34 6 0.07
35 10 0.11
36 3 0.03
ACGTcount: A:0.72, C:0.01, G:0.03, T:0.24
Consensus pattern (30 bp):
TAAAATAAAAAATAATAAAAAATTAAAAAA
Found at i:1577849 original size:21 final size:20
Alignment explanation
Indices: 1577811--1577870 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
1577801 AAAATATGTT
* *
1577811 TTTAAAATTA-ATAAATTAA
1 TTTAAAAATATATATATTAA
1577830 TATTAAAAATATATATATT-A
1 T-TTAAAAATATATATATTAA
*
1577850 TTTAAAAATCTATATTATTAA
1 TTTAAAAATATATA-TATTAA
1577871 GTAATACGCT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
19 13 0.38
20 14 0.41
21 7 0.21
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
TTTAAAAATATATATATTAA
Found at i:1577856 original size:19 final size:20
Alignment explanation
Indices: 1577832--1577869 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1577822 TAAATTAATA
1577832 TTAAAAATATATA-TATTAT
1 TTAAAAATATATATTATTAT
*
1577851 TTAAAAATCTATATTATTA
1 TTAAAAATATATATTATTA
1577870 AGTAATACGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (20 bp):
TTAAAAATATATATTATTAT
Found at i:1602340 original size:51 final size:51
Alignment explanation
Indices: 1602264--1602366 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
1602254 AAAAGAGAAA
1602264 GGCTAAGCCTTGTCCGAATGACTGATGGACACGTTCTAATCCTATGGTTTT
1 GGCTAAGCCTTGTCCGAATGACTGATGGACACGTTCTAATCCTATGGTTTT
1602315 GGCTAAGCCTTGTCCGAATGACTGATGGACACGTTCTAATCCTATGGTTTT
1 GGCTAAGCCTTGTCCGAATGACTGATGGACACGTTCTAATCCTATGGTTTT
1602366 G
1 G
1602367 CTTTCATCAC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.33
Consensus pattern (51 bp):
GGCTAAGCCTTGTCCGAATGACTGATGGACACGTTCTAATCCTATGGTTTT
Found at i:1605652 original size:24 final size:23
Alignment explanation
Indices: 1605594--1605653 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 23
1605584 AATTTTTTAT
1605594 ATATT-ATAT-ATTTTTTAATAA
1 ATATTAATATAATTTTTTAATAA
* * *
1605615 ATTTTTATATTAATTTTTTATTAA
1 ATATTAATA-TAATTTTTTAATAA
1605639 ATAATTAATATAATT
1 AT-ATTAATATAATT
1605654 AAAAAAATAC
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
21 4 0.13
22 3 0.10
23 1 0.03
24 18 0.58
25 5 0.16
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
ATATTAATATAATTTTTTAATAA
Found at i:1605829 original size:18 final size:19
Alignment explanation
Indices: 1605789--1605830 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
1605779 AAAAAAATAA
* *
1605789 AATTTTTATTTATATTATT
1 AATTATTATATATATTATT
1605808 -ATTATTATATATATT-TT
1 AATTATTATATATATTATT
1605825 AATTAT
1 AATTAT
1605831 ATTCTATTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
AATTATTATATATATTATT
Found at i:1605978 original size:15 final size:16
Alignment explanation
Indices: 1605960--1605994 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1605950 TTATTATGTG
*
1605960 AATTTT-ATTTTTAAT
1 AATTTTAATTTTTAAA
1605975 AATTTTAATTTTTAAA
1 AATTTTAATTTTTAAA
1605991 AATT
1 AATT
1605995 AAAAAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
AATTTTAATTTTTAAA
Found at i:1627090 original size:22 final size:22
Alignment explanation
Indices: 1627065--1627115 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
1627055 TGTGTGATTG
*
1627065 GTTTTTAGGTATTATGTGACTA
1 GTTTTTAGGTATTATGTAACTA
*
1627087 GTTTTTAGGTATTGTGTAACTA
1 GTTTTTAGGTATTATGTAACTA
*
1627109 ATTTTTA
1 GTTTTTA
1627116 AATAATGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.24, C:0.04, G:0.20, T:0.53
Consensus pattern (22 bp):
GTTTTTAGGTATTATGTAACTA
Found at i:1627279 original size:21 final size:22
Alignment explanation
Indices: 1627255--1627326 Score: 92
Period size: 22 Copynumber: 3.2 Consensus size: 22
1627245 AATAATTTTC
1627255 AAAATCAGTC-ACACAATACCTA
1 AAAATCAG-CAACACAATACCTA
*
1627277 AAAATTAGCAACACAATACCTAA
1 AAAATCAGCAACACAATACCT-A
* *
1627300 AAAATTAGCAACATAATACCTA
1 AAAATCAGCAACACAATACCTA
1627322 AAAAT
1 AAAAT
1627327 TGATTATGCA
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
21 1 0.02
22 24 0.52
23 21 0.46
ACGTcount: A:0.56, C:0.21, G:0.04, T:0.19
Consensus pattern (22 bp):
AAAATCAGCAACACAATACCTA
Found at i:1627280 original size:22 final size:22
Alignment explanation
Indices: 1627265--1627327 Score: 108
Period size: 23 Copynumber: 2.8 Consensus size: 22
1627255 AAAATCAGTC
1627265 ACACAATACCTAAAAATTAGCA
1 ACACAATACCTAAAAATTAGCA
1627287 ACACAATACCTAAAAAATTAGCA
1 ACACAATACCT-AAAAATTAGCA
*
1627310 ACATAATACCTAAAAATT
1 ACACAATACCTAAAAATT
1627328 GATTATGCAA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
22 18 0.46
23 21 0.54
ACGTcount: A:0.56, C:0.21, G:0.03, T:0.21
Consensus pattern (22 bp):
ACACAATACCTAAAAATTAGCA
Found at i:1627559 original size:60 final size:60
Alignment explanation
Indices: 1627444--1627571 Score: 141
Period size: 60 Copynumber: 2.1 Consensus size: 60
1627434 GCCTACTCGA
* * * * * *
1627444 TAAAGAATGTTCAAAATGCTCAAAGGTTTTTCTTCATATATCAAAAATAATTCCAAAATGC
1 TAAA-AATGCTCAAAATGCTCAAAAGTTTGTCTTCATATATAAAAAATAACTCCAAAAAGC
* * * *
1627505 TTAAAAATGCTCAAAATGTTCAAAAG-TTGTCTTCGTGTATAAAAAATTACTCCAAAAAGC
1 -TAAAAATGCTCAAAATGCTCAAAAGTTTGTCTTCATATATAAAAAATAACTCCAAAAAGC
1627565 TAAAAAT
1 TAAAAAT
1627572 ACTTAAACGT
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
59 7 0.12
60 27 0.48
61 18 0.32
62 4 0.07
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.31
Consensus pattern (60 bp):
TAAAAATGCTCAAAATGCTCAAAAGTTTGTCTTCATATATAAAAAATAACTCCAAAAAGC
Found at i:1628024 original size:21 final size:21
Alignment explanation
Indices: 1627998--1628039 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1627988 ATAATTTCGA
1627998 TCAAAATTTAAAAAGATCAAG
1 TCAAAATTTAAAAAGATCAAG
1628019 TCAAAATTTAAAAAGATCAAG
1 TCAAAATTTAAAAAGATCAAG
1628040 GTGTTTTACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.57, C:0.10, G:0.10, T:0.24
Consensus pattern (21 bp):
TCAAAATTTAAAAAGATCAAG
Found at i:1628685 original size:81 final size:81
Alignment explanation
Indices: 1628550--1628712 Score: 281
Period size: 81 Copynumber: 2.0 Consensus size: 81
1628540 TGTGTAACGA
*
1628550 TCCAAGTCTAACTACTGGTCCAACAACTCTTTGAGTCTAAACCACGTGCACGTGGCCCTTAAAAG
1 TCCAAGTCTAACTACTAGTCCAACAACTCTTTGAGTCTAAACCACGTGCACGTGGCCCTTAAAAG
1628615 CTTAAGCTCAAGTTAT
66 CTTAAGCTCAAGTTAT
* * *
1628631 TCCAAGTCTAACTACTAGTCCAGCAACTCTTTGAGTCTCAACCATGTGCACGTGGCCCTTAAAAG
1 TCCAAGTCTAACTACTAGTCCAACAACTCTTTGAGTCTAAACCACGTGCACGTGGCCCTTAAAAG
*
1628696 TTTAAGCTCAAGTTAT
66 CTTAAGCTCAAGTTAT
1628712 T
1 T
1628713 ATTGAGTTAC
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
81 77 1.00
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (81 bp):
TCCAAGTCTAACTACTAGTCCAACAACTCTTTGAGTCTAAACCACGTGCACGTGGCCCTTAAAAG
CTTAAGCTCAAGTTAT
Found at i:1628878 original size:26 final size:26
Alignment explanation
Indices: 1628848--1628899 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
1628838 CAGACATCAC
1628848 ATCCACAAGT-TCAAGATCTCATCAGA
1 ATCCACAAGTCT-AAGATCTCATCAGA
*
1628874 ATCCACAAGTCTGAGATCTCATCAGA
1 ATCCACAAGTCTAAGATCTCATCAGA
1628900 GCAATGTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 23 0.96
27 1 0.04
ACGTcount: A:0.37, C:0.27, G:0.13, T:0.23
Consensus pattern (26 bp):
ATCCACAAGTCTAAGATCTCATCAGA
Found at i:1628978 original size:59 final size:59
Alignment explanation
Indices: 1628901--1629013 Score: 217
Period size: 59 Copynumber: 1.9 Consensus size: 59
1628891 CTCATCAGAG
1628901 CAATGTTCACATCCATAGGTCCAAGATCTCATCAAAGCAATGTGAAGCTCACATGAGAT
1 CAATGTTCACATCCATAGGTCCAAGATCTCATCAAAGCAATGTGAAGCTCACATGAGAT
*
1628960 CAATGTTCACATCCATAGGTCCAAGATCTCATCAGAGCAATGTGAAGCTCACAT
1 CAATGTTCACATCCATAGGTCCAAGATCTCATCAAAGCAATGTGAAGCTCACAT
1629014 CGGACTGGTG
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.24
Consensus pattern (59 bp):
CAATGTTCACATCCATAGGTCCAAGATCTCATCAAAGCAATGTGAAGCTCACATGAGAT
Found at i:1629729 original size:2 final size:2
Alignment explanation
Indices: 1629722--1629759 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1629712 TTCACTATCT
1629722 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1629760 ATTAGGGAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1630370 original size:2 final size:2
Alignment explanation
Indices: 1630363--1630388 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1630353 TGATAATTAC
1630363 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1630389 ATTAATCATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1633406 original size:17 final size:17
Alignment explanation
Indices: 1633386--1633434 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
1633376 ATATTATAAT
1633386 ATAATTCTAATTAAATA
1 ATAATTCTAATTAAATA
*
1633403 ATAA---T-ATTATATA
1 ATAATTCTAATTAAATA
1633416 ATAATTCTAATTAAATA
1 ATAATTCTAATTAAATA
1633433 AT
1 AT
1633435 TTATATAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
13 11 0.42
14 1 0.04
16 1 0.04
17 13 0.50
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (17 bp):
ATAATTCTAATTAAATA
Found at i:1633411 original size:30 final size:30
Alignment explanation
Indices: 1633375--1633434 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
1633365 TAACTAACAG
1633375 AATATTATA-ATATAATTCTAATTAAATAAT
1 AATATTATATA-ATAATTCTAATTAAATAAT
1633405 AATATTATATAATAATTCTAATTAAATAAT
1 AATATTATATAATAATTCTAATTAAATAAT
1633435 TTATATAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (30 bp):
AATATTATATAATAATTCTAATTAAATAAT
Found at i:1638996 original size:24 final size:24
Alignment explanation
Indices: 1638968--1639242 Score: 79
Period size: 24 Copynumber: 10.9 Consensus size: 24
1638958 TTTATAATAT
1638968 TATAATAAAATAAATAT-AAATAAGA
1 TATAA-AAAATAAATATAAAATAA-A
1638993 -ATAAAAAATTAAA-ATAAAATAAA
1 TATAAAAAA-TAAATATAAAATAAA
* * *
1639016 TATAAAAAATTAATATTTATATAAA
1 TATAAAAAATAAATA-TAAAATAAA
* * *
1639041 TAGATAAAACAAAT-TAAAATAAAA
1 TATAAAAAATAAATATAAAAT-AAA
* *
1639065 TATATAATATAAAAAATATATTAAAGAAA
1 TATA-AA-A-AATAAATATA--AAATAAA
*
1639094 TA-AAAAAA-ATATATAAAAT---
1 TATAAAAAATAAATATAAAATAAA
* * *
1639113 TATAATAATAATAAAAATAAATTATGAC
1 TATAA-AA-AATAAATATAAA--ATAAA
* *
1639141 T-TTAAAAATTAATATAAAAATATGATA
1 TATAAAAAATAAATAT-AAAATA--A-A
1639168 TTATATAAAAATAATAATATAAATATAAA
1 -TATA-AAAAAT-A-AATATAAA-ATAAA
* *
1639197 TATATTAAAATAAA-ATAAAATTTAA
1 TATA-AAAAATAAATATAAAA-TAAA
* *
1639222 -ATAATAAATAAAAATAAAATA
1 TATAAAAAATAAATATAAAATA
1639243 TATGACATTA
Statistics
Matches: 188, Mismatches: 29, Indels: 68
0.66 0.10 0.24
Matches are distributed among these distances:
19 2 0.01
20 2 0.01
21 2 0.01
22 5 0.03
23 29 0.15
24 47 0.25
25 37 0.20
26 10 0.05
27 11 0.06
28 15 0.08
29 7 0.04
30 10 0.05
31 3 0.02
32 8 0.04
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.31
Consensus pattern (24 bp):
TATAAAAAATAAATATAAAATAAA
Found at i:1639085 original size:48 final size:47
Alignment explanation
Indices: 1638963--1639213 Score: 126
Period size: 47 Copynumber: 5.1 Consensus size: 47
1638953 AATATTTTAT
*
1638963 AATATTATAATA-AAATAA-ATATAAATAAGA-ATAAAAAATTAAAATAA
1 AATA-TATAATATAAAAAATATATAAATAA-ATA-AAAAAATTAAAATAA
*
1639010 AATAAATATAA-A-AAATTAATATTTATATAAATAGATAAAACAAATTAAAATAA
1 AAT--ATATAATATAAA--AA-A--TATATAAATAAATAAAA-AAATTAAAATAA
* * *
1639063 AATATATAATATAAAAAATATATTAAAGAAATAAAAAAAAT-ATATAA
1 AATATATAATATAAAAAATATA-TAAATAAATAAAAAAATTAAAATAA
* * ** *
1639110 AAT-TATAATAATAATAAAA-ATA-AATTATGACTTTAAAAATTAATATAAA
1 AATATATAAT-ATAA-AAAATATATAA--ATAAATAAAAAAATTAAAAT-AA
* *
1639159 AATATGATATTATATAAAAATA-ATAATATAAATATAAATATATTAAAATAA
1 AATAT-ATAATATA-AAAAATATATAA-ATAAATA-AAA-AAATTAAAATAA
1639210 AATA
1 AATA
1639214 AAATTTAAAT
Statistics
Matches: 159, Mismatches: 19, Indels: 48
0.70 0.08 0.21
Matches are distributed among these distances:
45 2 0.01
46 6 0.04
47 31 0.19
48 21 0.13
49 18 0.11
50 16 0.10
51 24 0.15
52 13 0.08
53 28 0.18
ACGTcount: A:0.66, C:0.01, G:0.02, T:0.31
Consensus pattern (47 bp):
AATATATAATATAAAAAATATATAAATAAATAAAAAAATTAAAATAA
Found at i:1639174 original size:106 final size:104
Alignment explanation
Indices: 1639086--1639415 Score: 380
Period size: 110 Copynumber: 3.1 Consensus size: 104
1639076 AAAAATATAT
* *
1639086 TAAAGAAATAAAAAAAATATATAAAATTATAATAATAATAAAAATAAAT-TATGACTTTAAAA-A
1 TAAATAAATAAAAAAAA-ATATAAAATTATAATAATAATAAAAATAAATATATGACATTAAAATA
1639149 TTAATATAAAAATATGATATTATATAAAAATAATAATATAAATA
65 -T-AT-TAAAAA-ATGATATTATATAAAAATAATAATATAAATA
* * *
1639193 TAAATATATTAAAATAAA-ATAAAATT-TAAATAATAAATAAAAATAAAATATATGACATTAAAA
1 TAAATAAATAAAAAAAAATATAAAATTAT-AATAAT-AATAAAAAT-AAATATATGACATTAAAA
*
1639256 TATATTAAGAAATGATATTATATAAAAATTAATAATATAAATA
63 TATATTAAAAAATGATATTATATAAAAA-TAATAATATAAATA
* * * *
1639299 TAAATAATTAAAAATAAAATATAAAATATTATAATAATAATAAAAATAAAAGATATGATATAAAA
1 TAAATAAATAAAAA-AAAATAT-AAA-ATTATAATAATAATAAAAAT-AAATATATGACATTAAA
* *
1639364 ATATATTTAAGAAATGATATTATATAAAAATTAATAATAAAAAATA
62 ATATA-TTAAAAAATGATATTATATAAAAA-TAATAAT-ATAAATA
1639410 TAAATA
1 TAAATA
1639416 TATTAAACTT
Statistics
Matches: 196, Mismatches: 14, Indels: 22
0.84 0.06 0.09
Matches are distributed among these distances:
104 1 0.01
105 31 0.16
106 40 0.20
107 22 0.11
108 15 0.08
109 33 0.17
110 41 0.21
111 13 0.07
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (104 bp):
TAAATAAATAAAAAAAAATATAAAATTATAATAATAATAAAAATAAATATATGACATTAAAATAT
ATTAAAAAATGATATTATATAAAAATAATAATATAAATA
Found at i:1639193 original size:110 final size:106
Alignment explanation
Indices: 1639086--1639415 Score: 395
Period size: 106 Copynumber: 3.1 Consensus size: 106
1639076 AAAAATATAT
*
1639086 TAAAGAAATAAAAAAAATATATAAAATTATAATAATAATAAAAAT-AAATTATGACTTTAAAAAT
1 TAAATAAATAAAAAAAA-ATATAAAATTATAATAATAATAAAAATAAAATTATGACTTTAAAAA-
*
1639150 TAATATAAAAATATGATATTATATAAAAA-TAATAATATAAATA
64 TAATATAAGAA-ATGATATTATATAAAAATTAATAATATAAATA
* * * *
1639193 TAAATATATTAAAATAAA-ATAAAATT-TAAATAATAAATAAAAATAAAATATATGACATT-AAA
1 TAAATAAATAAAAAAAAATATAAAATTAT-AATAAT-AATAAAAATAAAAT-TATGACTTTAAAA
1639255 AT-ATATTAAGAAATGATATTATATAAAAATTAATAATATAAATA
63 ATAATA-TAAGAAATGATATTATATAAAAATTAATAATATAAATA
* * *
1639299 TAAATAATTAAAAATAAAATATAAAATATTATAATAATAATAAAAATAAAAGATATGA-TATAAA
1 TAAATAAATAAAAA-AAAATAT-AAA-ATTATAATAATAATAAAAATAAAA-TTATGACTTTAAA
* *
1639363 AATATATTTAAGAAATGATATTATATAAAAATTAATAATAAAAAATA
62 AATA-ATATAAGAAATGATATTATATAAAAATTAATAAT-ATAAATA
1639410 TAAATA
1 TAAATA
1639416 TATTAAACTT
Statistics
Matches: 192, Mismatches: 15, Indels: 28
0.82 0.06 0.12
Matches are distributed among these distances:
104 1 0.01
105 34 0.18
106 41 0.21
107 24 0.12
108 11 0.06
109 26 0.14
110 40 0.21
111 15 0.08
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (106 bp):
TAAATAAATAAAAAAAAATATAAAATTATAATAATAATAAAAATAAAATTATGACTTTAAAAATA
ATATAAGAAATGATATTATATAAAAATTAATAATATAAATA
Found at i:1639205 original size:29 final size:29
Alignment explanation
Indices: 1638969--1639422 Score: 101
Period size: 29 Copynumber: 15.0 Consensus size: 29
1638959 TTATAATATT
* * *
1638969 ATAATAAAATAAATATAAATAAGAATAAAA
1 ATAATAATATAAATATAAAT-ATATTAAAA
* *
1638999 A-ATTAAAATAAA-ATAAATATA--AAAA
1 ATAATAATATAAATATAAATATATTAAAA
** *
1639024 AT--TAATATTTATATAAATAGA-TAAAA
1 ATAATAATATAAATATAAATATATTAAAA
*
1639050 CA-AATTAAAATAAAATATATAATATA--AAAA
1 -ATAA-TAATAT-AAATATA-AATATATTAAAA
* * *
1639080 ATATATTAA-AGAAATAAAAAAAATATATAAAA
1 ATA-A-TAATATAAAT-ATAAATATAT-TAAAA
*
1639112 TTATAATAATAATAAAAATAAATTATGACTTTAAAA
1 --ATAATAAT-ATAAATATAAA-TAT-A--TTAAAA
* *
1639148 AT--TAATATAAAAATATGATATTATATAAAA
1 ATAATAATATAAATATA-AATA-TAT-TAAAA
1639178 ATAATAATATAAATATAAATATATT-AAA
1 ATAATAATATAAATATAAATATATTAAAA
* *
1639206 ATAA-AATA-AAATTTAAATAATAAATAAAA
1 ATAATAATATAAATATAAAT-AT-ATTAAAA
1639235 ATAA-AATATATGACAT-TAAAATATATTAAGAA
1 ATAATAATATA--A-ATAT-AAATATATTAA-AA
* *
1639267 ATGATATTATATAAAAATTAATAATATAAATATAAATA
1 AT-A-A-TA-ATATAAA-T-ATAA-ATATAT-TAAA-A
* *
1639305 ATTAAAAATA-AAATATAAA-ATATT-ATA
1 A-TAATAATATAAATATAAATATATTAAAA
* *
1639332 ATAATAATAAAAATAAAAGATATGATATAAAA
1 ATAATAATATAAATATAA-ATAT-AT-TAAAA
* * *
1639364 AT-AT-ATTTAAGAAAT-GATATTATATAAAA
1 ATAATAATATAA-ATATAAATA-TAT-TAAAA
*
1639393 ATTAATAATAAAAAATATAAATATATTAAA
1 A-TAATAAT-ATAAATATAAATATATTAAA
1639423 CTTATATTTT
Statistics
Matches: 322, Mismatches: 40, Indels: 123
0.66 0.08 0.25
Matches are distributed among these distances:
24 6 0.02
25 13 0.04
26 20 0.06
27 18 0.06
28 17 0.05
29 53 0.16
30 36 0.11
31 41 0.13
32 49 0.15
33 18 0.06
34 16 0.05
35 6 0.02
36 9 0.03
37 13 0.04
38 6 0.02
39 1 0.00
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (29 bp):
ATAATAATATAAATATAAATATATTAAAA
Found at i:1654485 original size:12 final size:12
Alignment explanation
Indices: 1654468--1654501 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1654458 TTAATGCATT
*
1654468 AAAAAAGAAAGA
1 AAAAAAGAAAAA
*
1654480 AAAAAACAAAAA
1 AAAAAAGAAAAA
1654492 AAAAAAGAAA
1 AAAAAAGAAA
1654502 TCTAATAACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.88, C:0.03, G:0.09, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAAAA
Found at i:1673995 original size:2 final size:2
Alignment explanation
Indices: 1673988--1674030 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1673978 NNNNNNNNNN
1673988 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1674030 T
1 T
1674031 CAAACTATCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1674549 original size:31 final size:30
Alignment explanation
Indices: 1674498--1674557 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
1674488 AATATCTAAG
*
1674498 TCTAGGGCAAATGTATATATATAGTAATAA
1 TCTAGGGCAAATATATATATATAGTAATAA
* *
1674528 TCTAGGGCTATATATATATATATATTAATA
1 TCTAGGGC-AAATATATATATATAGTAATA
1674558 TATTAATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 8 0.31
31 18 0.69
ACGTcount: A:0.42, C:0.07, G:0.13, T:0.38
Consensus pattern (30 bp):
TCTAGGGCAAATATATATATATAGTAATAA
Found at i:1678042 original size:2 final size:2
Alignment explanation
Indices: 1678035--1678063 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1678025 TATGCAACAT
1678035 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1678064 CTATGGTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1680335 original size:108 final size:108
Alignment explanation
Indices: 1680210--1680415 Score: 322
Period size: 108 Copynumber: 1.9 Consensus size: 108
1680200 TAAAATGACT
* * *
1680210 AAATATATTGATTTAGTTATAACTTTTACAATTTACAAATACATATTCTTTTGAAATTATTCAAC
1 AAATATATTGATTTAGTTACAACTTTTAAAATTTACAAATACACATTCTTTTGAAATTATTCAAC
*
1680275 TCTTATCCAATTTACTTTTTATATAAAATTACTTAAATTAGCA
66 TCTTATCCAATTTACATTTTATATAAAATTACTTAAATTAGCA
* * *
1680318 AAATATGTTGATTTAGTTACAATTTTTAAAATTTATAAATACACATTCTTTTGAAATTATTCAAC
1 AAATATATTGATTTAGTTACAACTTTTAAAATTTACAAATACACATTCTTTTGAAATTATTCAAC
* * *
1680383 TTTTATCCAATTTACATTTTATTTAAATTTACT
66 TCTTATCCAATTTACATTTTATATAAAATTACT
1680416 CAAAATTTCT
Statistics
Matches: 88, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
108 88 1.00
ACGTcount: A:0.38, C:0.11, G:0.04, T:0.47
Consensus pattern (108 bp):
AAATATATTGATTTAGTTACAACTTTTAAAATTTACAAATACACATTCTTTTGAAATTATTCAAC
TCTTATCCAATTTACATTTTATATAAAATTACTTAAATTAGCA
Found at i:1681458 original size:24 final size:24
Alignment explanation
Indices: 1681409--1681458 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
1681399 ATATTGACGT
* * *
1681409 CAACGATGATGTTAGTGTTAATGC
1 CAACGATGATGTCAGTGTCAACGC
1681433 CAACGATGATGTCA-TCGTCAACGC
1 CAACGATGATGTCAGT-GTCAACGC
1681457 CA
1 CA
1681459 TCTTTTAACG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 1 0.05
24 21 0.95
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (24 bp):
CAACGATGATGTCAGTGTCAACGC
Found at i:1682863 original size:5 final size:5
Alignment explanation
Indices: 1682853--1682877 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1682843 GTGGTCACCC
1682853 CCCCT CCCCT CCCCT CCCCT CCCCT
1 CCCCT CCCCT CCCCT CCCCT CCCCT
1682878 TTCCTTTGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.80, G:0.00, T:0.20
Consensus pattern (5 bp):
CCCCT
Found at i:1683669 original size:2 final size:2
Alignment explanation
Indices: 1683662--1683691 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1683652 CAGTTACTTT
1683662 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1683692 AAATATCAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1690701 original size:2 final size:2
Alignment explanation
Indices: 1690690--1690723 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1690680 TTATCTCCAC
*
1690690 CT CT -T CT CT CT CT TT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1690724 CATATCCCTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:1690809 original size:48 final size:48
Alignment explanation
Indices: 1690735--1690833 Score: 162
Period size: 48 Copynumber: 2.1 Consensus size: 48
1690725 ATATCCCTCC
* *
1690735 AAAATAATATGAATGCCCGCACATGTGAAACAAGAAAAATGGTAAATT
1 AAAATAATATAAATGCCCACACATGTGAAACAAGAAAAATGGTAAATT
* *
1690783 AAAATACTATAAATGGCCACACATGTGAAACAAGAAAAATGGTAAATT
1 AAAATAATATAAATGCCCACACATGTGAAACAAGAAAAATGGTAAATT
1690831 AAA
1 AAA
1690834 GTTACTTGGT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.53, C:0.12, G:0.15, T:0.20
Consensus pattern (48 bp):
AAAATAATATAAATGCCCACACATGTGAAACAAGAAAAATGGTAAATT
Found at i:1691954 original size:16 final size:17
Alignment explanation
Indices: 1691933--1691966 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1691923 ACAGAATTAT
1691933 AAATATTT-ATTTTTAA
1 AAATATTTAATTTTTAA
1691949 AAATATTTAATTTTTAA
1 AAATATTTAATTTTTAA
1691966 A
1 A
1691967 TATGATTTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AAATATTTAATTTTTAA
Found at i:1692943 original size:13 final size:14
Alignment explanation
Indices: 1692916--1692948 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1692906 TTACAAAAAA
1692916 AAAAAAAAAGAAAG
1 AAAAAAAAAGAAAG
*
1692930 AAAAGAAAAG-AAG
1 AAAAAAAAAGAAAG
1692943 AAAAAA
1 AAAAAA
1692949 CAGTCACTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAGAAAG
Found at i:1693003 original size:10 final size:10
Alignment explanation
Indices: 1692962--1693008 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
1692952 TCACTGCTGC
* *
1692962 AAAGAGCAAC
1 AAAGAGAAAG
1692972 AAAGAGAAAG
1 AAAGAGAAAG
*
1692982 AAA-AGGAGAG
1 AAAGA-GAAAG
1692992 AAAGAGAAAG
1 AAAGAGAAAG
1693002 AAAGAGA
1 AAAGAGA
1693009 CGACAGACAG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
9 1 0.03
10 29 0.94
11 1 0.03
ACGTcount: A:0.66, C:0.04, G:0.30, T:0.00
Consensus pattern (10 bp):
AAAGAGAAAG
Found at i:1693054 original size:12 final size:11
Alignment explanation
Indices: 1693037--1693072 Score: 56
Period size: 10 Copynumber: 3.3 Consensus size: 11
1693027 ACACATATAC
1693037 AGAGAGAAAGAG
1 AGAGAGAAA-AG
1693049 AGAGAGAAAAG
1 AGAGAGAAAAG
1693060 AGA-AGAAAAG
1 AGAGAGAAAAG
1693070 AGA
1 AGA
1693073 AGGGGAGGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.42
11 5 0.21
12 9 0.38
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (11 bp):
AGAGAGAAAAG
Found at i:1695872 original size:3 final size:3
Alignment explanation
Indices: 1695864--1695895 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1695854 ATTGATCAGC
1695864 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1695896 ATTCTCCTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1697196 original size:2 final size:2
Alignment explanation
Indices: 1697189--1697224 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1697179 CAGGTAGGTC
*
1697189 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT TT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1697225 TTCACTACAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:1697773 original size:24 final size:24
Alignment explanation
Indices: 1697725--1697776 Score: 68
Period size: 26 Copynumber: 2.1 Consensus size: 24
1697715 AAGTTTGCAG
*
1697725 CTTTGATTTTCTCTCTTTCTCTCT
1 CTTTGATTTTCTCTCCTTCTCTCT
*
1697749 CTTTGTATTTGTCTCTCCTTTTCTCT
1 CTTTG-ATTT-TCTCTCCTTCTCTCT
1697775 CT
1 CT
1697777 CATATCAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 5 0.21
25 4 0.17
26 15 0.62
ACGTcount: A:0.04, C:0.29, G:0.06, T:0.62
Consensus pattern (24 bp):
CTTTGATTTTCTCTCCTTCTCTCT
Found at i:1697773 original size:26 final size:24
Alignment explanation
Indices: 1697725--1697777 Score: 70
Period size: 28 Copynumber: 2.0 Consensus size: 24
1697715 AAGTTTGCAG
1697725 CTTTGATTTTCTCTCTTTCTCTCT
1 CTTTGATTTTCTCTCTTTCTCTCT
1697749 CTTTGTATTTGTCTCTCCTTTTCTCTCT
1 CTTTG-ATTT-TCTCT-C-TTTCTCTCT
1697777 C
1 C
1697778 ATATCAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 5 0.20
25 4 0.16
26 5 0.20
27 1 0.04
28 10 0.40
ACGTcount: A:0.04, C:0.30, G:0.06, T:0.60
Consensus pattern (24 bp):
CTTTGATTTTCTCTCTTTCTCTCT
Found at i:1698950 original size:21 final size:21
Alignment explanation
Indices: 1698924--1698963 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1698914 GCATCAACAC
1698924 CAACAACAACAACAACAGCTA
1 CAACAACAACAACAACAGCTA
* *
1698945 CAACAACAACCACACCAGC
1 CAACAACAACAACAACAGC
1698964 AGGCAAAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.53, C:0.40, G:0.05, T:0.03
Consensus pattern (21 bp):
CAACAACAACAACAACAGCTA
Found at i:1704597 original size:4 final size:4
Alignment explanation
Indices: 1704582--1704637 Score: 55
Period size: 4 Copynumber: 13.8 Consensus size: 4
1704572 AAGTAAAATT
1704582 TTTA TTTAA TTTA TTTA TTTA TTTA TATTA -TTA -TTA -TTA CTTTTA
1 TTTA TTT-A TTTA TTTA TTTA TTTA T-TTA TTTA TTTA TTTA --TTTA
1704627 TTTA TTTA TTT
1 TTTA TTTA TTT
1704638 TTGTCAATTC
Statistics
Matches: 47, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
3 9 0.19
4 28 0.60
5 7 0.15
6 3 0.06
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:1705004 original size:15 final size:15
Alignment explanation
Indices: 1704984--1705014 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1704974 GAGTTATCAC
1704984 TAAGGGGCATATATA
1 TAAGGGGCATATATA
1704999 TAAGGGGCATATATA
1 TAAGGGGCATATATA
1705014 T
1 T
1705015 TCAGCAGTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.26, T:0.29
Consensus pattern (15 bp):
TAAGGGGCATATATA
Found at i:1705069 original size:19 final size:19
Alignment explanation
Indices: 1705045--1705125 Score: 108
Period size: 19 Copynumber: 4.1 Consensus size: 19
1705035 ACTCTCTAGT
1705045 AGCAGCAATCATTGTAACG
1 AGCAGCAATCATTGTAACG
**
1705064 AGCAGCAATCATTGTTCTCTAG
1 AGCAGCAATCATTG-TAAC--G
1705086 TAGCAGCAATCATTGTAACG
1 -AGCAGCAATCATTGTAACG
1705106 AGCAGCAATCATTGTAACG
1 AGCAGCAATCATTGTAACG
1705125 A
1 A
1705126 TCCAAGTCTA
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
19 34 0.63
20 3 0.06
22 3 0.06
23 14 0.26
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.25
Consensus pattern (19 bp):
AGCAGCAATCATTGTAACG
Found at i:1705090 original size:23 final size:23
Alignment explanation
Indices: 1705037--1705101 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
1705027 ACACATCAAC
1705037 TCTCTAGTAGCAGCAATCATTG-
1 TCTCTAGTAGCAGCAATCATTGT
**
1705059 TAAC--G-AGCAGCAATCATTGT
1 TCTCTAGTAGCAGCAATCATTGT
1705079 TCTCTAGTAGCAGCAATCATTGT
1 TCTCTAGTAGCAGCAATCATTGT
1705102 AACGAGCAGC
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
19 14 0.40
20 3 0.09
22 3 0.09
23 15 0.43
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (23 bp):
TCTCTAGTAGCAGCAATCATTGT
Found at i:1705096 original size:42 final size:42
Alignment explanation
Indices: 1705037--1705120 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
1705027 ACACATCAAC
1705037 TCTCTAGTAGCAGCAATCATTGTAACGAGCAGCAATCATTGT
1 TCTCTAGTAGCAGCAATCATTGTAACGAGCAGCAATCATTGT
1705079 TCTCTAGTAGCAGCAATCATTGTAACGAGCAGCAATCATTGT
1 TCTCTAGTAGCAGCAATCATTGTAACGAGCAGCAATCATTGT
1705121 AACGATCCAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (42 bp):
TCTCTAGTAGCAGCAATCATTGTAACGAGCAGCAATCATTGT
Found at i:1705908 original size:90 final size:87
Alignment explanation
Indices: 1705797--1706063 Score: 271
Period size: 90 Copynumber: 3.0 Consensus size: 87
1705787 GTGTGGCCTT
*
1705797 GATGAGATCTTGGTCCTGTGGATCCTGTGGATGTGATGTGTGGCCTTGATGAGGACATCAAGAAA
1 GATGAGAT-TTGGT-CT-TGG-TCCTGTGGATGTGATGTGTGACCTTGATGAGGACATCAAGAAA
* * *
1705862 TTTGAGTTGGTAAGATGAGTG-CTCTG
62 TTTGAGTGGGTGAGAT-AGTGAATCTG
* * *
1705888 G-TGAGA-----TCTTGGTCCTGTGGATGTGATGTGTGACCTTAACGAGGACATTAAGAAATTTG
1 GATGAGATTTGGTCTTGGTCCTGTGGATGTGATGTGTGACCTTGATGAGGACATCAAGAAATTTG
* *
1705947 AGTGGGTGAGATTGTGATATGTG
66 AGTGGGTGAGATAGTGA-ATCTG
* *
1705970 GATGTGATGTATGG-CTTTGGTCCTGTGGATGTGATGTGTGATCTTGATGAGGACATCAAGAAAT
1 GATGAGAT-T-TGGTC-TTGGTCCTGTGGATGTGATGTGTGACCTTGATGAGGACATCAAGAAAT
* *
1706034 TTGAGTGGGTGAGATTGTGATATGTG
63 TTGAGTGGGTGAGATAGTGA-ATCTG
1706060 GATG
1 GATG
1706064 TGATGTGTGG
Statistics
Matches: 151, Mismatches: 14, Indels: 23
0.80 0.07 0.12
Matches are distributed among these distances:
80 3 0.02
81 53 0.35
82 7 0.05
83 6 0.04
84 1 0.01
89 1 0.01
90 79 0.52
91 1 0.01
ACGTcount: A:0.23, C:0.09, G:0.35, T:0.33
Consensus pattern (87 bp):
GATGAGATTTGGTCTTGGTCCTGTGGATGTGATGTGTGACCTTGATGAGGACATCAAGAAATTTG
AGTGGGTGAGATAGTGAATCTG
Found at i:1706064 original size:90 final size:90
Alignment explanation
Indices: 1705896--1706074 Score: 313
Period size: 90 Copynumber: 2.0 Consensus size: 90
1705886 TGGTGAGATC
*
1705896 TTGGTCCTGTGGATGTGATGTGTGACCTTAACGAGGACATTAAGAAATTTGAGTGGGTGAGATTG
1 TTGGTCCTGTGGATGTGATGTGTGACCTTAACGAGGACATCAAGAAATTTGAGTGGGTGAGATTG
1705961 TGATATGTGGATGTGATGTATGGCT
66 TGATATGTGGATGTGATGTATGGCT
* * *
1705986 TTGGTCCTGTGGATGTGATGTGTGATCTTGATGAGGACATCAAGAAATTTGAGTGGGTGAGATTG
1 TTGGTCCTGTGGATGTGATGTGTGACCTTAACGAGGACATCAAGAAATTTGAGTGGGTGAGATTG
*
1706051 TGATATGTGGATGTGATGTGTGGC
66 TGATATGTGGATGTGATGTATGGC
1706075 CTTGATGAGG
Statistics
Matches: 84, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
90 84 1.00
ACGTcount: A:0.22, C:0.07, G:0.36, T:0.35
Consensus pattern (90 bp):
TTGGTCCTGTGGATGTGATGTGTGACCTTAACGAGGACATCAAGAAATTTGAGTGGGTGAGATTG
TGATATGTGGATGTGATGTATGGCT
Found at i:1706094 original size:63 final size:63
Alignment explanation
Indices: 1705993--1706118 Score: 216
Period size: 63 Copynumber: 2.0 Consensus size: 63
1705983 GCTTTGGTCC
* *
1705993 TGTGGATGTGATGTGTGATCTTGATGAGGACATCAAGAAATTTGAGTGGGTGAGATTGTGATA
1 TGTGGATGTGATGTGTGACCTTGATGAGGACATCAAGAAATTTAAGTGGGTGAGATTGTGATA
* *
1706056 TGTGGATGTGATGTGTGGCCTTGATGAGGACATTAAGAAATTTAAGTGGGTGAGATTGTGATA
1 TGTGGATGTGATGTGTGACCTTGATGAGGACATCAAGAAATTTAAGTGGGTGAGATTGTGATA
1706119 CTTTCATGTT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 59 1.00
ACGTcount: A:0.27, C:0.05, G:0.35, T:0.33
Consensus pattern (63 bp):
TGTGGATGTGATGTGTGACCTTGATGAGGACATCAAGAAATTTAAGTGGGTGAGATTGTGATA
Done.