Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr3
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: 36364294
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2168405 characters in sequence are not A, C, G, or T
File 79 of 91
Found at i:29219230 original size:40 final size:40
Alignment explanation
Indices: 29219186--29219271 Score: 136
Period size: 40 Copynumber: 2.1 Consensus size: 40
29219176 AATTAGTACT
* * *
29219186 CCTACTAGAGGTAAATTAAGCGGTCTGATGTTGATCCAAA
1 CCTACTAGAGGGAAATTAAGAGGTCTGATGTTGACCCAAA
*
29219226 CCTACTAGAGGGATATTAAGAGGTCTGATGTTGACCCAAA
1 CCTACTAGAGGGAAATTAAGAGGTCTGATGTTGACCCAAA
29219266 CCTACT
1 CCTACT
29219272 GGTTGATCCA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (40 bp):
CCTACTAGAGGGAAATTAAGAGGTCTGATGTTGACCCAAA
Found at i:29230139 original size:22 final size:22
Alignment explanation
Indices: 29230114--29230155 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
29230104 GGTTATTAGG
29230114 TTTATCATGTATACGCATTGTA
1 TTTATCATGTATACGCATTGTA
29230136 TTTATCATGTATACGCATTG
1 TTTATCATGTATACGCATTG
29230156 AAGTTTTAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.45
Consensus pattern (22 bp):
TTTATCATGTATACGCATTGTA
Found at i:29230835 original size:1 final size:1
Alignment explanation
Indices: 29230829--29230854 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
29230819 AATAAGAATG
29230829 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
29230855 CTTCTAGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:29247987 original size:14 final size:15
Alignment explanation
Indices: 29247968--29247997 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
29247958 GTTGATGAAT
29247968 AATGAAAAG-ATAAA
1 AATGAAAAGAATAAA
29247982 AATGAAAAGAATAAA
1 AATGAAAAGAATAAA
29247997 A
1 A
29247998 GAAATATAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.73, C:0.00, G:0.13, T:0.13
Consensus pattern (15 bp):
AATGAAAAGAATAAA
Found at i:29250874 original size:54 final size:53
Alignment explanation
Indices: 29250792--29250899 Score: 207
Period size: 54 Copynumber: 2.0 Consensus size: 53
29250782 ATATAACTGC
29250792 TGTTTATGTGGATGATTTGAACATTATTGAAAATCTTGAAGAGTTATCAAAAA
1 TGTTTATGTGGATGATTTGAACATTATTGAAAATCTTGAAGAGTTATCAAAAA
29250845 NTGTTTATGTGGATGATTTGAACATTATTGAAAATCTTGAAGAGTTATCAAAAA
1 -TGTTTATGTGGATGATTTGAACATTATTGAAAATCTTGAAGAGTTATCAAAAA
29250899 T
1 T
29250900 CATGAATTAC
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
53 1 0.02
54 53 0.98
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (53 bp):
TGTTTATGTGGATGATTTGAACATTATTGAAAATCTTGAAGAGTTATCAAAAA
Found at i:29252768 original size:15 final size:15
Alignment explanation
Indices: 29252748--29252802 Score: 74
Period size: 15 Copynumber: 3.7 Consensus size: 15
29252738 TTTACAATGC
* *
29252748 AATGTGATTACAGGT
1 AATGTGATTGCAAGT
29252763 AATGTGATTGCAAGT
1 AATGTGATTGCAAGT
* *
29252778 AATGTAATTGCAAGC
1 AATGTGATTGCAAGT
29252793 AATGTGATTG
1 AATGTGATTG
29252803 TAGGGAAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.35, C:0.07, G:0.25, T:0.33
Consensus pattern (15 bp):
AATGTGATTGCAAGT
Found at i:29253067 original size:44 final size:45
Alignment explanation
Indices: 29253019--29253124 Score: 108
Period size: 50 Copynumber: 2.3 Consensus size: 45
29253009 TTTAATGTCA
*
29253019 TATATTTTATTTTATT-T-TTTAATATAATTTTTTATATTATATAT
1 TATATTTTATTTTATTCTATTTAATATAAATTTTTAT-TTATATAT
* * *
29253063 TATATTTTAATTTCTTTTACCTATTTTATATAAATTTTTATTTTTATAT
1 TATATTTT-ATTT-TATT--CTATTTAATATAAATTTTTATTTATATAT
*
29253112 TTTATTTTATTTT
1 TATATTTTATTTT
29253125 TTGATTTTTA
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
44 8 0.16
45 4 0.08
46 3 0.06
47 1 0.02
48 4 0.08
49 15 0.29
50 16 0.31
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (45 bp):
TATATTTTATTTTATTCTATTTAATATAAATTTTTATTTATATAT
Found at i:29253119 original size:12 final size:12
Alignment explanation
Indices: 29253019--29253132 Score: 54
Period size: 13 Copynumber: 9.1 Consensus size: 12
29253009 TTTAATGTCA
29253019 TATATTTTATTT
1 TATATTTTATTT
* *
29253031 TATTTTTTAATAT
1 TATATTTT-ATTT
* *
29253044 AATTTTTTATATT
1 TATATTTTAT-TT
*
29253057 ATATATTATATTT
1 -TATATTTTATTT
*
29253070 TA-A-TTTCTTT
1 TATATTTTATTT
*
29253080 TACCTATTTTA-TA
1 TA--TATTTTATTT
*
29253093 TAAATTTTTATTTT
1 TATA-TTTTA-TTT
29253107 TATATTTTATTT
1 TATATTTTATTT
*
29253119 TATTTTTTGATTT
1 TATATTTT-ATTT
29253132 T
1 T
29253133 TAGATTATAT
Statistics
Matches: 76, Mismatches: 15, Indels: 21
0.68 0.13 0.19
Matches are distributed among these distances:
10 7 0.09
11 2 0.03
12 26 0.34
13 27 0.36
14 14 0.18
ACGTcount: A:0.27, C:0.03, G:0.01, T:0.69
Consensus pattern (12 bp):
TATATTTTATTT
Found at i:29253327 original size:13 final size:14
Alignment explanation
Indices: 29253270--29253347 Score: 71
Period size: 13 Copynumber: 6.0 Consensus size: 14
29253260 CTGTAATCAC
*
29253270 ATTATATT-TATTA
1 ATTATATTATAATA
29253283 ATTATA--AT-ATA
1 ATTATATTATAATA
29253294 ATTATATTATAAT-
1 ATTATATTATAATA
*
29253307 CTTATATTATAATA
1 ATTATATTATAATA
29253321 ATT-TATTATAA-A
1 ATTATATTATAATA
*
29253333 ATAAATATTATAATA
1 AT-TATATTATAATA
29253348 TATTTTAACT
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
11 8 0.15
12 4 0.08
13 28 0.53
14 12 0.23
15 1 0.02
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (14 bp):
ATTATATTATAATA
Found at i:29277377 original size:371 final size:369
Alignment explanation
Indices: 29276217--29278076 Score: 2685
Period size: 370 Copynumber: 5.0 Consensus size: 369
29276207 AATTTAAACA
* * *
29276217 TTTAAGTATAAAAGAGATATCTATATACTATAAATTCAGGTTCACGTAGAATAAGAGAATATAGA
1 TTTAAGTATAAAAGAGATATCTATATACTATAGATT-AGGTTCATGCAGAATAAGAGAATATAGA
*
29276282 CAAAAAATAATATTAAATTGTAATTGATAAATATTAAATGAATCTATATTCTAAGCATTAAAAGT
65 TAAAAAATAATATTAAATTGTAATTGATAAATATTAAATGAATCTATATTCTAAGCATTAAAAGT
29276347 TAGAAATTATTATTTTTAAGTATTTTTTATTAAAATAAATAAAAGTAAAAAAATAAATAAAAAAA
130 TAGAAATTATTATTTTTAAGTATTTTTTATTAAAATAAATAAAAGTAAAAAAA-AAA-AAAAAAA
29276412 ACCCTTCAAATGTCAAAAACAACTTATTTTTAACATAAGGTGTAAAAAAAATTAATTCAATAGAA
193 ACCCTTCAAATGTCAAAAACAACTTATTTTTAACATAAGGTGTAAAAAAAATTAATTCAATAGAA
29276477 AACGAAAGGT--AAAAAAAAAAAGAGTTCTAATTTG-ATGACACTTGTCATTCAATTGAAGACTC
258 AACGAAAGGTAAAAAAAAAAAAAGAGTTCTAA-TTGAATGACACTTGTCATTCAATTGAAGACTC
29276539 AATTGAAAAAAATT-AAAAGAAATTGAAACATCCTACTTTTATATATAT
322 AATTGAAAAAAATTGAAAA-AAATTGAAACATCCTACTTTTATATATAT
* * * *
29276587 TTTAAGTATAAACGAGATATTTATATACTATAGATTAGGGTTTATGTAGAATAAGAGAATATAGA
1 TTTAAGTATAAAAGAGATATCTATATACTATAGATTA-GGTTCATGCAGAATAAGAGAATATAGA
*
29276652 CAAAAAATAATATTAAATTGTAATTGATAAATATTAAATGAATCTATATTCTAAGCATTAAAAGT
65 TAAAAAATAATATTAAATTGTAATTGATAAATATTAAATGAATCTATATTCTAAGCATTAAAAGT
29276717 TAGAAATTATTATTTTTAAGTATTTTTTATTAAAATAAATAAAAGTAAAAAAATAAATAAAAAAA
130 TAGAAATTATTATTTTTAAGTATTTTTTATTAAAATAAATAAAAGTAAAAAAA-AAA-AAAAAAA
29276782 ACCCTTCAAATGTCAAAAACAACTTATTTTTAACATAAGGTGTAAAAAAAATTAATTCAATAGAA
193 ACCCTTCAAATGTCAAAAACAACTTATTTTTAACATAAGGTGTAAAAAAAATTAATTCAATAGAA
29276847 AACGAAAGGT--AAAAAAAAAAAGAGTTCTAATTTG-ATGACACTTGTCATTCAATTGAAGACTC
258 AACGAAAGGTAAAAAAAAAAAAAGAGTTCTAA-TTGAATGACACTTGTCATTCAATTGAAGACTC
29276909 AATTGAAAAAAATT-AAAAGAAATTGAAACATCCTACTTTTATATATAT
322 AATTGAAAAAAATTGAAAA-AAATTGAAACATCCTACTTTTATATATAT
* * *
29276957 TTTAAGTATAAACGAGATATTTATATACTATAGATTAGGGTTTATGCAGAATAAGAGAATATAGA
1 TTTAAGTATAAAAGAGATATCTATATACTATAGATTA-GGTTCATGCAGAATAAGAGAATATAGA
* *
29277022 TAAAAAATAATATTAAATTGTAATTGATAAATATTAAATGAATATATATTCTAAGCATTAAAAAT
65 TAAAAAATAATATTAAATTGTAATTGATAAATATTAAATGAATCTATATTCTAAGCATTAAAAGT
* *
29277087 TAGAAATTATTGTTTTTAAGTA-TTTTTATTAAAATAAATAAAAGTAAAAAAACAAAAAAAAAAC
130 TAGAAATTATTATTTTTAAGTATTTTTTATTAAAATAAATAAAAGTAAAAAAAAAAAAAAAAAAC
* * *
29277151 CCTTCAAATGTTAAAAACAACTTATTTTTGACCTAAGGTGTAAAAAAAATTAATTCAATAGAAAA
195 CCTTCAAATGTCAAAAACAACTTATTTTTAACATAAGGTGTAAAAAAAATTAATTCAATAGAAAA
* * * *
29277216 CGAAATGTCAAAAAAATAAAAAAGAGTTATAATTGAACGACACTTGTCATTCAATTAAAGACTCA
260 CGAAAGGT-AAAAAAA-AAAAAAGAGTTCTAATTGAATGACACTTGTCATTCAATTGAAGACTCA
*
29277281 ATTGAAATAAATTGAAAAAAATTGAAACATCCTACTTTTATATATAT
323 ATTGAAAAAAATTGAAAAAAATTGAAACATCCTACTTTTATATATAT
* ** * * *
29277328 TTTAAGTATAAAAGAGATATCTATATGCTATAGATTCAAATTCATGCAGAAAAAGAAAATATAAA
1 TTTAAGTATAAAAGAGATATCTATATACTATAGATT-AGGTTCATGCAGAATAAGAGAATATAGA
* * *
29277393 TAAAAAATAATATTAAAATATAATTGATAAATATTAAATGAATCTATTTTCTAAGCATTAAAAGT
65 TAAAAAATAATATTAAATTGTAATTGATAAATATTAAATGAATCTATATTCTAAGCATTAAAAGT
* * *
29277458 TAAAAATTATT-GTTTTAAGTATTTTTTATTAAAATAAATAAAAGT--AAAAAATAAAAAAAAAC
130 TAGAAATTATTATTTTTAAGTATTTTTTATTAAAATAAATAAAAGTAAAAAAAAAAAAAAAAAAC
* *
29277520 CCTTAAAATGTCAAAAACAACTTATTTTTTACATAAGGTGTAAAAAAAAATTAATTCAATAGAAA
195 CCTTCAAATGTCAAAAACAACTTATTTTTAACATAAGGTGT-AAAAAAAATTAATTC-------A
29277585 ATGAAAGGTTAAAACGAAAGGTCAAAAAAATAAAAAAGAGTTCTAATTGAATGACACTTGTCATT
252 AT---A-G--AAAACGAAAGGT-AAAAAAA-AAAAAAGAGTTCTAATTGAATGACACTTGTCATT
* *
29277650 CAATTGAAGACTCAATTAAAAAAAATTGAAAAAAATTAAAACATCCTACTTTTATATATAT
309 CAATTGAAGACTCAATTGAAAAAAATTGAAAAAAATTGAAACATCCTACTTTTATATATAT
* * ** *
29277711 TTTAAGTATAAAGGAGATATCTATATATTATAGATTTAAATAT-ATGCAAAATAAGAGAATATAG
1 TTTAAGTATAAAAGAGATATCTATATACTATAGA-TTAGGT-TCATGCAGAATAAGAGAATATAG
* * * * *
29277775 ATAAAAAATAATATTAAATTATAATTAATAAATATTAAACGAATCTATTTTTTAAGCATTAAAAG
64 ATAAAAAATAATATTAAATTGTAATTGATAAATATTAAATGAATCTATATTCTAAGCATTAAAAG
* *
29277840 TTAAAAATTATTA-TTTTAAGTA-TTTTTATTAAAATAAATAAAAGT-AAAAAACAAAAAAAAAA
129 TTAGAAATTATTATTTTTAAGTATTTTTTATTAAAATAAATAAAAGTAAAAAAAAAAAAAAAAAA
* * * * *
29277902 CTCTTCCAATGT-AAACAACAACTCATTTTTGACATAAGGTGTAAAAAAAATTAATTCAATAAAA
194 CCCTTCAAATGTCAAA-AACAACTTATTTTTAACATAAGGTGTAAAAAAAATTAATTCAATAGAA
** * * *
29277966 AATAAAAGGTTAAAAAAAGAAAAAAGAGTTATAATTAAATGACATTTGTCATTCAATTGAAGACT
258 AACGAAAGG-TAAAAAAA-AAAAAAGAGTTCTAATTGAATGACACTTGTCATTCAATTGAAGACT
* * * *
29278031 CTATT-AAAAAAATTGAAAAAAATTAAAACATTCTACTGTTATATAT
321 CAATTGAAAAAAATTGAAAAAAATTGAAACATCCTACTTTTATATAT
29278077 GTTATAGATA
Statistics
Matches: 1385, Mismatches: 76, Indels: 60
0.91 0.05 0.04
Matches are distributed among these distances:
367 78 0.06
368 41 0.03
369 146 0.11
370 543 0.39
371 229 0.17
372 6 0.00
375 3 0.00
377 3 0.00
380 1 0.00
381 1 0.00
382 41 0.03
383 290 0.21
384 3 0.00
ACGTcount: A:0.51, C:0.07, G:0.09, T:0.32
Consensus pattern (369 bp):
TTTAAGTATAAAAGAGATATCTATATACTATAGATTAGGTTCATGCAGAATAAGAGAATATAGAT
AAAAAATAATATTAAATTGTAATTGATAAATATTAAATGAATCTATATTCTAAGCATTAAAAGTT
AGAAATTATTATTTTTAAGTATTTTTTATTAAAATAAATAAAAGTAAAAAAAAAAAAAAAAAACC
CTTCAAATGTCAAAAACAACTTATTTTTAACATAAGGTGTAAAAAAAATTAATTCAATAGAAAAC
GAAAGGTAAAAAAAAAAAAAGAGTTCTAATTGAATGACACTTGTCATTCAATTGAAGACTCAATT
GAAAAAAATTGAAAAAAATTGAAACATCCTACTTTTATATATAT
Found at i:29278244 original size:754 final size:737
Alignment explanation
Indices: 29276217--29278082 Score: 2289
Period size: 754 Copynumber: 2.5 Consensus size: 737
29276207 AATTTAAACA
* * * * * *
29276217 TTTAAGTATAAAAGAGATATCTATATACTATAAATTCAG-GT-TCACGTAGAATAAGAGAATATA
1 TTTAAGTATAAACGAGATATCTATATACTATAGATT-AGAATAT-ATGCAAAATAAGAGAATATA
* * * * *
29276280 GACAAAAAATAATATTAAATTGTAATTGATAAATATTAAATGAATCTATATTCTAAGCATTAAAA
64 GATAAAAAATAATATTAAATTATAATTAATAAATATTAAACGAATATATATTCTAAGCATTAAAA
* * *
29276345 GTTAGAAATTATT-ATTTTTAAGTATTTTTTATTAAAATAAATAAAAGTAAAAAAATAAATAAAA
129 ATTAAAAATTATTGA-TTTTAAGTA-TTTTTATTAAAATAAATAAAAGTAAAAAAA-CAA-AAAA
* * *
29276409 AAAACCCTTCAAATGTCAAAAACAACTTATTTTTAACATAAGGTGTAAAAAAAATTAATTCAATA
190 AAAACCCTTCAAATGTTAAAAACAACTCATTTTTGACATAAGGTGTAAAAAAAATTAATTCAATA
* * * ** * *
29276474 GAAAACGAAAGGT---AAAAA-AAAAAAGAGTTCTAATTTGATGACACTTGTCATTCAATTGAAG
255 AAAAACAAAAGGTCAAAAAAAGAAAAAAGAGTTATAATTAAACGACACTTGTCATTCAATTAAAG
* * *
29276535 ACTCAATTGAAAAAAATT-AAAAGAAATTGAAACATCCTACTTTTATATATATTTTAAGTATAAA
320 ACTCAATTGAAAAAAATTGAAAA-AAATTAAAACATCCTACTGTTATATATATTATAAGTATAAA
* * * * * *** * * * * * *
29276599 CGAGATATTTATAT-ACTATAGATTAGGGTTTATGTAGAATAAGAGAATATAGACAAAAAATAAT
384 AGAGATATCTATATGA-TACAAATAAAAATTCATGCAGAAAAAGAAAATATAAATAAAAAATAAT
* * * * *
29276663 ATTAAATTGTAATTGATAAATATTAAATGAATCTA-T-ATTCTAAGCATTAAAAGTTAGAAATTA
448 ATTAAAATATAATT-ATAAATATTAAATGAACCTACTCA--CTAAGCATTAAAAGATAAAAATTA
* * *** *
29276726 TTATTTTTAAGTATTTTTTATTAAAATAAATAAAAGTAAAAAAATAAATAAAAAAAACCCTTCAA
510 TT-GTTATAAG-AAAATTTATTAAAATAAATAAAAGTAAAAAAAT-AATAAAAAAAACCCTTAAA
29276791 ATGTCAAAAACAACTTATTTTTAACATAAGGTGTAAAAAAAATTAATTCAATAGAAAACGAAAGG
572 ATGTCAAAAACAACTTATTTTTAACATAAGGTGTAAAAAAAATTAATTCAATAGAAAACGAAAGG
*
29276856 TAAAAAAAAAAAGAGTTCTAATTTGATGACACTTGTCATTCAATTGAAGACTCAATTGAAAAAAA
637 TAAAAAAAAAAAGAGTTCTAATTTGATGACACTTGTCATTCAATTGAAGACTCAATTAAAAAAAA
*
29276921 TTAAAAGAAATTGAAACATCCTACTTTTATATATAT
702 TTAAAAGAAATTAAAACATCCTACTTTTATATATAT
* ** * *
29276957 TTTAAGTATAAACGAGATATTTATATACTATAGATTAGGGTTTATGCAGAATAAGAGAATATAGA
1 TTTAAGTATAAACGAGATATCTATATACTATAGATTAGAATATATGCAAAATAAGAGAATATAGA
* * *
29277022 TAAAAAATAATATTAAATTGTAATTGATAAATATTAAATGAATATATATTCTAAGCATTAAAAAT
66 TAAAAAATAATATTAAATTATAATTAATAAATATTAAACGAATATATATTCTAAGCATTAAAAAT
* *
29277087 TAGAAATTATTGTTTTTAAGTATTTTTATTAAAATAAATAAAAGTAAAAAAACAAAAAAAAAACC
131 TAAAAATTATTGATTTTAAGTATTTTTATTAAAATAAATAAAAGTAAAAAAACAAAAAAAAAACC
* * *
29277152 CTTCAAATGTTAAAAACAACTTATTTTTGACCTAAGGTGTAAAAAAAATTAATTCAATAGAAAAC
196 CTTCAAATGTTAAAAACAACTCATTTTTGACATAAGGTGTAAAAAAAATTAATTCAATAAAAAAC
* * * *
29277217 GAAATGTCAAAAAAATAAAAAAGAGTTATAATTGAACGACACTTGTCATTCAATTAAAGACTCAA
261 AAAAGGTCAAAAAAAGAAAAAAGAGTTATAATTAAACGACACTTGTCATTCAATTAAAGACTCAA
* * * *
29277282 TTGAAATAAATTGAAAAAAATTGAAACATCCTACTTTTATATATATTTTAAGTATAAAAGAGATA
326 TTGAAAAAAATTGAAAAAAATTAAAACATCCTACTGTTATATATATTATAAGTATAAAAGAGATA
* * * **
29277347 TCTATATGCTATAGATTCAAATTCATGCAGAAAAAGAAAATATAAATAAAAAATAATATTAAAAT
391 TCTATATGATACAAATAAAAATTCATGCAGAAAAAGAAAATATAAATAAAAAATAATATTAAAAT
* * ** * *
29277412 ATAATTGATAAATATTAAATGAATCTATTTTCTAAGCATTAAAAGTTAAAAATTATTGTTTTAAG
456 ATAATT-ATAAATATTAAATGAACCTACTCACTAAGCATTAAAAGATAAAAATTATTGTTATAAG
***
29277477 TATTTTTTATTAAAATAAATAAAAGT-AAAAAAT-A-AAAAAAAACCCTTAAAATGTCAAAAACA
520 -AAAATTTATTAAAATAAATAAAAGTAAAAAAATAATAAAAAAAACCCTTAAAATGTCAAAAACA
*
29277539 ACTTATTTTTTACATAAGGTGTAAAAAAAAATTAATTCAATAGAAAATGAAAGGTTAAAACGAAA
584 ACTTATTTTTAACATAAGGTGT-AAAAAAAATTAATTC-------AAT---A-G--AAAACGAAA
29277604 GGTCAAAAAAATAAAAAAGAGTTCTAA-TTGAATGACACTTGTCATTCAATTGAAGACTCAATTA
635 GGT---AAAAA-AAAAAAGAGTTCTAATTTG-ATGACACTTGTCATTCAATTGAAGACTCAATTA
29277668 AAAAAAATTGAAAA-AAATTAAAACATCCTACTTTTATATATAT
695 AAAAAAATT-AAAAGAAATTAAAACATCCTACTTTTATATATAT
* *
29277711 TTTAAGTATAAAGGAGATATCTATATATTATAGATTTA-AATATATGCAAAATAAGAGAATATAG
1 TTTAAGTATAAACGAGATATCTATATACTATAGA-TTAGAATATATGCAAAATAAGAGAATATAG
* * * *
29277775 ATAAAAAATAATATTAAATTATAATTAATAAATATTAAACGAATCTATTTTTTAAGCATTAAAAG
65 ATAAAAAATAATATTAAATTATAATTAATAAATATTAAACGAATATATATTCTAAGCATTAAAAA
29277840 TTAAAAATTATT-ATTTTAAGTATTTTTATTAAAATAAATAAAAGT-AAAAAACAAAAAAAAAAC
130 TTAAAAATTATTGATTTTAAGTATTTTTATTAAAATAAATAAAAGTAAAAAAACAAAAAAAAAAC
* *
29277903 TCTTCCAATG-TAAACAACAACTCATTTTTGACATAAGGTGTAAAAAAAATTAATTCAATAAAAA
195 CCTTCAAATGTTAAA-AACAACTCATTTTTGACATAAGGTGTAAAAAAAATTAATTCAATAAAAA
* * * * *
29277967 ATAAAAGGTTAAAAAAAGAAAAAAGAGTTATAATTAAATGACATTTGTCATTCAATTGAAGACTC
259 ACAAAAGGTCAAAAAAAGAAAAAAGAGTTATAATTAAACGACACTTGTCATTCAATTAAAGACTC
* * *
29278032 TATT-AAAAAAATTGAAAAAAATTAAAACATTCTACTGTTATATATGTTATA
324 AATTGAAAAAAATTGAAAAAAATTAAAACATCCTACTGTTATATATATTATA
29278083 GATATATAAT
Statistics
Matches: 1014, Mismatches: 79, Indels: 55
0.88 0.07 0.05
Matches are distributed among these distances:
736 48 0.05
737 94 0.09
738 2 0.00
739 39 0.04
740 175 0.17
741 205 0.20
742 5 0.00
744 3 0.00
747 1 0.00
748 1 0.00
750 12 0.01
751 45 0.04
752 131 0.13
753 40 0.04
754 206 0.20
755 7 0.01
ACGTcount: A:0.51, C:0.07, G:0.09, T:0.32
Consensus pattern (737 bp):
TTTAAGTATAAACGAGATATCTATATACTATAGATTAGAATATATGCAAAATAAGAGAATATAGA
TAAAAAATAATATTAAATTATAATTAATAAATATTAAACGAATATATATTCTAAGCATTAAAAAT
TAAAAATTATTGATTTTAAGTATTTTTATTAAAATAAATAAAAGTAAAAAAACAAAAAAAAAACC
CTTCAAATGTTAAAAACAACTCATTTTTGACATAAGGTGTAAAAAAAATTAATTCAATAAAAAAC
AAAAGGTCAAAAAAAGAAAAAAGAGTTATAATTAAACGACACTTGTCATTCAATTAAAGACTCAA
TTGAAAAAAATTGAAAAAAATTAAAACATCCTACTGTTATATATATTATAAGTATAAAAGAGATA
TCTATATGATACAAATAAAAATTCATGCAGAAAAAGAAAATATAAATAAAAAATAATATTAAAAT
ATAATTATAAATATTAAATGAACCTACTCACTAAGCATTAAAAGATAAAAATTATTGTTATAAGA
AAATTTATTAAAATAAATAAAAGTAAAAAAATAATAAAAAAAACCCTTAAAATGTCAAAAACAAC
TTATTTTTAACATAAGGTGTAAAAAAAATTAATTCAATAGAAAACGAAAGGTAAAAAAAAAAAGA
GTTCTAATTTGATGACACTTGTCATTCAATTGAAGACTCAATTAAAAAAAATTAAAAGAAATTAA
AACATCCTACTTTTATATATAT
Found at i:29280283 original size:18 final size:18
Alignment explanation
Indices: 29280260--29280296 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
29280250 TCAAGTCTAA
29280260 TTTTGCATCAGCTTGACT
1 TTTTGCATCAGCTTGACT
29280278 TTTTGCATCAGCTTGACT
1 TTTTGCATCAGCTTGACT
29280296 T
1 T
29280297 CATTTATAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.22, G:0.16, T:0.46
Consensus pattern (18 bp):
TTTTGCATCAGCTTGACT
Found at i:29289975 original size:22 final size:22
Alignment explanation
Indices: 29289931--29290002 Score: 81
Period size: 22 Copynumber: 3.3 Consensus size: 22
29289921 GCGTGACTAG
* *
29289931 TTTTTAGGTATTACGTGACTGA
1 TTTTTAGGCATTACATGACTGA
* *
29289953 TTTTTAGGCATTTCATGATTGA
1 TTTTTAGGCATTACATGACTGA
** *
29289975 TTTTTAAACATTGCATGACTGA
1 TTTTTAGGCATTACATGACTGA
29289997 TTTTTA
1 TTTTTA
29290003 AGTAATGACT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.25, C:0.10, G:0.17, T:0.49
Consensus pattern (22 bp):
TTTTTAGGCATTACATGACTGA
Found at i:29290041 original size:23 final size:23
Alignment explanation
Indices: 29290014--29290115 Score: 93
Period size: 22 Copynumber: 4.5 Consensus size: 23
29290004 GTAATGACTA
29290014 AGTCACGCAATGCCTTA-CTAACC
1 AGTCACGCAATGCCTTATC-AACC
* *
29290037 AGTCATGCAATG-CTTATCAACT
1 AGTCACGCAATGCCTTATCAACC
* * * *
29290059 AGTAACACAATGTCATATCAACC
1 AGTCACGCAATGCCTTATCAACC
* **
29290082 AGTCACGCAATACC-TAAAAACC
1 AGTCACGCAATGCCTTATCAACC
29290104 AGTCACGCAATG
1 AGTCACGCAATG
29290116 TTAAAAACTC
Statistics
Matches: 63, Mismatches: 14, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
22 33 0.52
23 30 0.48
ACGTcount: A:0.37, C:0.28, G:0.13, T:0.22
Consensus pattern (23 bp):
AGTCACGCAATGCCTTATCAACC
Found at i:29290103 original size:22 final size:22
Alignment explanation
Indices: 29290078--29290213 Score: 87
Period size: 22 Copynumber: 6.2 Consensus size: 22
29290068 ATGTCATATC
29290078 AACCAGTCACGCAATACCTAAA
1 AACCAGTCACGCAATACCTAAA
**
29290100 AACCAGTCACGCAAT-GTTAAA
1 AACCAGTCACGCAATACCTAAA
* * *
29290121 AACTC-GTCACGTAATGCTTAAA
1 AAC-CAGTCACGCAATACCTAAA
** **
29290143 AATTAGTCACGCAATATTTAAA
1 AACCAGTCACGCAATACCTAAA
* * * * *
29290165 AACTAATCACACAATGCCCAAA
1 AACCAGTCACGCAATACCTAAA
* * * *
29290187 AATCAATTATGCAATACCTAAA
1 AACCAGTCACGCAATACCTAAA
29290209 AACCA
1 AACCA
29290214 CCAAAACTAC
Statistics
Matches: 87, Mismatches: 24, Indels: 6
0.74 0.21 0.05
Matches are distributed among these distances:
21 16 0.18
22 71 0.82
ACGTcount: A:0.46, C:0.24, G:0.09, T:0.21
Consensus pattern (22 bp):
AACCAGTCACGCAATACCTAAA
Found at i:29290188 original size:44 final size:43
Alignment explanation
Indices: 29290104--29290189 Score: 100
Period size: 44 Copynumber: 2.0 Consensus size: 43
29290094 CCTAAAAACC
** ** **
29290104 AGTCACGCAATGTTAAAAACTCGTCACGTAATGCTTAAAAATT
1 AGTCACGCAATGTTAAAAACTAATCACACAATGCCCAAAAATT
*
29290147 AGTCACGCAATATTTAAAAACTAATCACACAATGCCCAAAAAT
1 AGTCACGCAAT-GTTAAAAACTAATCACACAATGCCCAAAAAT
29290190 CAATTATGCA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
43 11 0.31
44 24 0.69
ACGTcount: A:0.44, C:0.21, G:0.10, T:0.24
Consensus pattern (43 bp):
AGTCACGCAATGTTAAAAACTAATCACACAATGCCCAAAAATT
Found at i:29292689 original size:55 final size:55
Alignment explanation
Indices: 29292622--29292731 Score: 211
Period size: 55 Copynumber: 2.0 Consensus size: 55
29292612 TATTTTGAAA
29292622 GTTGGTTCTATCATATTCTTTACAGTTATTTAAAATCTTTTATTGTACTTCTTTT
1 GTTGGTTCTATCATATTCTTTACAGTTATTTAAAATCTTTTATTGTACTTCTTTT
*
29292677 GTTGGTTGTATCATATTCTTTACAGTTATTTAAAATCTTTTATTGTACTTCTTTT
1 GTTGGTTCTATCATATTCTTTACAGTTATTTAAAATCTTTTATTGTACTTCTTTT
29292732 ATCATTTAAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.22, C:0.12, G:0.10, T:0.56
Consensus pattern (55 bp):
GTTGGTTCTATCATATTCTTTACAGTTATTTAAAATCTTTTATTGTACTTCTTTT
Found at i:29294994 original size:21 final size:21
Alignment explanation
Indices: 29294969--29295030 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
29294959 TTCTAATAAA
29294969 ATTAATTTTTAAAATATTAAT
1 ATTAATTTTTAAAATATTAAT
* * *
29294990 ATTAAATTATAAAATA-AAAT
1 ATTAATTTTTAAAATATTAAT
* *
29295010 ATTACTAGTTTAAAATATTAA
1 ATTAAT-TTTTAAAATATTAA
29295031 AAATTAAATT
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
20 7 0.23
21 22 0.71
22 2 0.06
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (21 bp):
ATTAATTTTTAAAATATTAAT
Found at i:29295025 original size:42 final size:42
Alignment explanation
Indices: 29294976--29295055 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
29294966 AAAATTAATT
*
29294976 TTTAAAATATT-AATATTAAATTATAAAATAAAATATTACTAG
1 TTTAAAATATTAAAAATTAAATTAT-AAATAAAATATTACTAG
29295018 TTTAAAATATTAAAAATTAAATTATAAATAAAATATTA
1 TTTAAAATATTAAAAATTAAATTATAAATAAAATATTA
29295056 ACATTTAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
42 24 0.67
43 12 0.33
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (42 bp):
TTTAAAATATTAAAAATTAAATTATAAATAAAATATTACTAG
Found at i:29295046 original size:12 final size:12
Alignment explanation
Indices: 29295026--29295097 Score: 51
Period size: 12 Copynumber: 5.9 Consensus size: 12
29295016 AGTTTAAAAT
*
29295026 ATTAAAAATTAA
1 ATTATAAATTAA
29295038 ATTATAAA-TAA
1 ATTATAAATTAA
*
29295049 AATATTAACATTTAA
1 ATTA-TAA-A-TTAA
*
29295064 ATTAT-AATT-T
1 ATTATAAATTAA
*
29295074 ATTAATAAAATAA
1 ATT-ATAAATTAA
29295087 ATTATAAATTA
1 ATTATAAATTA
29295098 TTAATATCTA
Statistics
Matches: 46, Mismatches: 7, Indels: 14
0.69 0.10 0.21
Matches are distributed among these distances:
10 3 0.07
11 10 0.22
12 21 0.46
13 5 0.11
14 1 0.02
15 6 0.13
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (12 bp):
ATTATAAATTAA
Found at i:29295046 original size:21 final size:22
Alignment explanation
Indices: 29294966--29295101 Score: 82
Period size: 23 Copynumber: 6.0 Consensus size: 22
29294956 AACTTCTAAT
* *
29294966 AAAATTAATTTTTAAAATATT-
1 AAAATTAAATTATAAAATATTA
*
29294987 AATATTAAATTATAAAATA--A
1 AAAATTAAATTATAAAATATTA
* *
29295007 AATATTACTAGTT-TAAAATATTA
1 AAAATTA--AATTATAAAATATTA
29295030 AAAATTAAATTATAAATAAAATATTA
1 AAAATTAAA-T-T--ATAAAATATTA
* * **
29295056 ACATTTAAATTATAATTTATTA
1 AAAATTAAATTATAAAATATTA
* *
29295078 ATAAAATAAATTATAAATTATTA
1 A-AAATTAAATTATAAAATATTA
29295101 A
1 A
29295102 TATCTAAAAA
Statistics
Matches: 90, Mismatches: 14, Indels: 20
0.73 0.11 0.16
Matches are distributed among these distances:
20 7 0.08
21 24 0.27
22 14 0.16
23 26 0.29
24 1 0.01
25 1 0.01
26 17 0.19
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (22 bp):
AAAATTAAATTATAAAATATTA
Found at i:29295054 original size:26 final size:26
Alignment explanation
Indices: 29295020--29295070 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
29295010 ATTACTAGTT
29295020 TAAAATATTAAAAATTAAATTATAAA
1 TAAAATATTAAAAATTAAATTATAAA
* *
29295046 TAAAATATTAACATTTAAATTATAA
1 TAAAATATTAAAAATTAAATTATAA
29295071 TTTATTAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (26 bp):
TAAAATATTAAAAATTAAATTATAAA
Found at i:29295395 original size:24 final size:22
Alignment explanation
Indices: 29295363--29295467 Score: 72
Period size: 24 Copynumber: 4.5 Consensus size: 22
29295353 AATAATTGAT
*
29295363 AATAATAATATTTTGAATTAATAA
1 AATATTAATATTTT-AA-TAATAA
*
29295387 AATATTAATATTTTAA-AATAT
1 AATATTAATATTTTAATAATAA
* * *
29295408 TA-ATGAATAATTT-ATCAATAA
1 AATATTAATATTTTAAT-AATAA
29295429 AATATTAATATTTTAAATAAATAAA
1 AATATTAATATTTT-AAT-AAT-AA
29295454 TAATTATTAATATT
1 -AA-TATTAATATT
29295468 GAAAAATAAA
Statistics
Matches: 63, Mismatches: 10, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
19 1 0.02
20 9 0.14
21 10 0.16
22 9 0.14
23 2 0.03
24 18 0.29
25 2 0.03
26 2 0.03
27 10 0.16
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (22 bp):
AATATTAATATTTTAATAATAA
Found at i:29295445 original size:134 final size:136
Alignment explanation
Indices: 29295298--29295584 Score: 431
Period size: 139 Copynumber: 2.1 Consensus size: 136
29295288 ATTATCAATG
*
29295298 ATTAATTTTTTAAATAAATAAATAATTATTAATATTCAAAAAT-A-AAATGAAATAAAATAA-TT
1 ATTAATATTTTAAATAAATAAATAATTATTAATATTCAAAAATAAGAAATGAAATAAAATAAGTT
* * *
29295360 GATAATAATAATATTTTGAATT-AATAAAATATTAATATTTTAAAATATTAATGAATAATTTATC
66 -ATAATAATAATA-TTTAAATTAAATAAAATATTAATATTTTAAAATATTAATGAATAACTTATA
29295424 AATAAAAT
129 AATAAAAT
*
29295432 ATTAATATTTTAAATAAATAAATAATTATTAATATTGAAAAATAAAATGAAATGAAATAAAATAA
1 ATTAATATTTTAAATAAATAAATAATTATTAATATTCAAAAAT--AA-GAAATGAAATAAAATAA
* *
29295497 GTTATAATAATAATATTTAAATTAAATTAAATATTAATATTTTAAAATATTAATGATTAACTTAT
63 GTTATAATAATAATATTTAAATTAAATAAAATATTAATATTTTAAAATATTAATGAATAACTTAT
29295562 AAATAAAAT
128 AAATAAAAT
29295571 ATTAATA-TTTAAAT
1 ATTAATATTTTAAAT
29295585 TATTAATTAT
Statistics
Matches: 139, Mismatches: 7, Indels: 10
0.89 0.04 0.06
Matches are distributed among these distances:
134 41 0.29
137 1 0.01
138 14 0.10
139 81 0.58
140 2 0.01
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (136 bp):
ATTAATATTTTAAATAAATAAATAATTATTAATATTCAAAAATAAGAAATGAAATAAAATAAGTT
ATAATAATAATATTTAAATTAAATAAAATATTAATATTTTAAAATATTAATGAATAACTTATAAA
TAAAAT
Found at i:29295453 original size:66 final size:65
Alignment explanation
Indices: 29295300--29295584 Score: 211
Period size: 66 Copynumber: 4.2 Consensus size: 65
29295290 TATCAATGAT
* ** * * * *
29295300 TAATTTTTTAAATAAATAAATAATTATTAATATTCAAAAATA-AAATGAAATAA-AATAATTGAT
1 TAATATTTTAAATAAAT-AA-AA-TATTAATATTTTAAAATATTAATG-AATAATTATAAAT-AA
29295363 AATAA
61 AATAA
* * *
29295368 TAATATTTTGAATTAATAAAATATTAATATTTTAAAATATTAATGAATAATTTATCAATAAAATA
1 TAATATTTTAAATAAATAAAATATTAATATTTTAAAATATTAATGAATAA-TTATAAATAAAATA
*
29295433 T
65 A
** * *
29295434 TAATATTTTAAATAAATAAATAATTATTAATATTGAAAAATA-AAATGAAATGAAATA-AAATAA
1 TAATATTTTAAATAAAT-AA-AA-TATTAATATTTTAAAATATTAATG-AAT-AATTATAAATAA
*
29295497 GTTATAA
61 --AATAA
* *
29295504 TAATAATATTTAAATTAAATTAAATATTAATATTTTAAAATATTAATGATTAACTTATAAATAAA
1 TAAT-AT-TTTAAA-TAAATAAAATATTAATATTTTAAAATATTAATGAATAA-TTATAAATAAA
*
29295569 ATAT
62 ATAA
29295573 TAATA-TTTAAAT
1 TAATATTTTAAAT
29295585 TATTAATTAT
Statistics
Matches: 173, Mismatches: 28, Indels: 35
0.73 0.12 0.15
Matches are distributed among these distances:
65 22 0.13
66 32 0.18
67 8 0.05
68 26 0.15
69 30 0.17
70 29 0.17
71 14 0.08
72 7 0.04
73 5 0.03
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (65 bp):
TAATATTTTAAATAAATAAAATATTAATATTTTAAAATATTAATGAATAATTATAAATAAAATAA
Found at i:29295517 original size:25 final size:25
Alignment explanation
Indices: 29295489--29295545 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
29295479 TGAAATGAAA
*
29295489 TAAAATAAGTTATAATAATAATA-TT
1 TAAAATAAATTA-AATAATAATATTT
* *
29295514 TAAATTAAATTAAATATTAATATTT
1 TAAAATAAATTAAATAATAATATTT
29295539 TAAAATA
1 TAAAATA
29295546 TTAATGATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 9 0.33
25 18 0.67
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (25 bp):
TAAAATAAATTAAATAATAATATTT
Found at i:29295582 original size:26 final size:25
Alignment explanation
Indices: 29295539--29295618 Score: 81
Period size: 26 Copynumber: 3.0 Consensus size: 25
29295529 ATTAATATTT
*
29295539 TAAAATATTAATGATTAACTTATAAA
1 TAAAATATTAAT-ATTAAATTATAAA
*
29295565 TAAAATATTAATATTTAAATTATTAAT
1 TAAAATATTAATA-TTAAATTA-TAAA
*
29295592 TATAAATATT-TTAATTAAATTATAAA
1 TA-AAATATTAAT-ATTAAATTATAAA
29295618 T
1 T
29295619 TATTAATATT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
25 1 0.02
26 23 0.50
27 14 0.30
28 8 0.17
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (25 bp):
TAAAATATTAATATTAAATTATAAA
Found at i:29295585 original size:66 final size:66
Alignment explanation
Indices: 29295363--29295605 Score: 208
Period size: 69 Copynumber: 3.6 Consensus size: 66
29295353 AATAATTGAT
* * * * *
29295363 AATAATAATATTTTGAATTAATAAAATATTAATATTTTAAAATATTAATGAATAATTTATCAATA
1 AATAATAATATTTTAAATTAATTAAATATTAATATTTTAAAATATTAATGATTAAATTATAAATA
29295428 A
66 A
* * * ** * *
29295429 AATATTAATATTTTAAATAAATAAATAATTATTAATATTGAAAAATA-AAATGAAATGAAA-TA-
1 AATAATAATATTTTAAAT---TAATTAAATATTAATATTTTAAAATATTAATG--ATTAAATTAT
29295491 AAATAA
61 AAATAA
* *
29295497 GTTATAATAATAATATTTAAATTAAATTAAATATTAATATTTTAAAATATTAATGATTAACTTAT
1 --AATAATAAT-AT-TTTAAATT-AATTAAATATTAATATTTTAAAATATTAATGATTAAATTAT
29295562 AAATAA
61 AAATAA
* * *
29295568 AATATTAATA-TTTAAATT-ATTAATTATAAATATTTTAA
1 AATAATAATATTTTAAATTAATTAAATATTAATATTTTAA
29295606 TTAAATTATA
Statistics
Matches: 139, Mismatches: 25, Indels: 28
0.72 0.13 0.15
Matches are distributed among these distances:
64 18 0.13
66 24 0.17
68 10 0.07
69 35 0.25
70 33 0.24
71 12 0.09
72 7 0.05
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.42
Consensus pattern (66 bp):
AATAATAATATTTTAAATTAATTAAATATTAATATTTTAAAATATTAATGATTAAATTATAAATA
A
Found at i:29295588 original size:15 final size:15
Alignment explanation
Indices: 29295523--29295632 Score: 63
Period size: 15 Copynumber: 7.3 Consensus size: 15
29295513 TTAAATTAAA
29295523 TTAAA-TATTAATATT
1 TTAAATTATTAATA-T
*
29295538 TTAAAATATTAATGA-
1 TTAAATTATTAAT-AT
*
29295553 TTAACTTA-TAA-A-
1 TTAAATTATTAATAT
*
29295565 -TAAAATATTAATAT
1 TTAAATTATTAATAT
29295579 TTAAATTATTAAT-T
1 TTAAATTATTAATAT
* *
29295593 ATAAATATTTTAATTAAAT
1 TTAAAT-TATTAA-T--AT
29295612 TATAAATTATTAATAT
1 T-TAAATTATTAATAT
29295628 TTAAA
1 TTAAA
29295633 AATCTAATAA
Statistics
Matches: 74, Mismatches: 9, Indels: 24
0.69 0.08 0.22
Matches are distributed among these distances:
11 5 0.07
12 4 0.05
13 1 0.01
14 9 0.12
15 31 0.42
16 11 0.15
17 1 0.01
18 1 0.01
19 6 0.08
20 5 0.07
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (15 bp):
TTAAATTATTAATAT
Found at i:29295602 original size:22 final size:20
Alignment explanation
Indices: 29295561--29295618 Score: 64
Period size: 22 Copynumber: 2.9 Consensus size: 20
29295551 GATTAACTTA
* *
29295561 TAAA-TAAAATATTAATATT
1 TAAATTAAATTATAAATATT
29295580 TAAATTATTAATTATAAATATT
1 TAAATTA--AATTATAAATATT
*
29295602 TTAATTAAATTATAAAT
1 TAAATTAAATTATAAAT
29295619 TATTAATATT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
19 4 0.12
20 12 0.36
22 17 0.52
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TAAATTAAATTATAAATATT
Found at i:29295609 original size:34 final size:34
Alignment explanation
Indices: 29295507--29295625 Score: 106
Period size: 34 Copynumber: 3.6 Consensus size: 34
29295497 GTTATAATAA
* *
29295507 TAATATTTAAATTAAATTAAATATTAATATTTTAA-
1 TAATATTTAAATT--ATTAATTATAAATATTTTAAT
* ***
29295542 -AATA-TT-AATGATTAACTTATAAATAAAAT-AT
1 TAATATTTAAATTATTAA-TTATAAATATTTTAAT
29295573 TAATATTTAAATTATTAATTATAAATATTTTAAT
1 TAATATTTAAATTATTAATTATAAATATTTTAAT
29295607 TAA-ATTATAAATTATTAAT
1 TAATATT-TAAATTATTAAT
29295626 ATTTAAAAAT
Statistics
Matches: 67, Mismatches: 10, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
30 6 0.09
31 8 0.12
32 7 0.10
33 17 0.25
34 29 0.43
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (34 bp):
TAATATTTAAATTATTAATTATAAATATTTTAAT
Found at i:29295614 original size:20 final size:21
Alignment explanation
Indices: 29295574--29295618 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
29295564 ATAAAATATT
29295574 AATATTTAAATTATTAATTATA
1 AATATTTAAATTA-TAATTATA
*
29295596 AATATTTTAATTA-AATTATA
1 AATATTTAAATTATAATTATA
29295616 AAT
1 AAT
29295619 TATTAATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.45
22 12 0.55
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AATATTTAAATTATAATTATA
Found at i:29295691 original size:15 final size:15
Alignment explanation
Indices: 29295671--29295702 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
29295661 ATAAAAAATA
29295671 TTTTATCTTTTTATT
1 TTTTATCTTTTTATT
*
29295686 TTTTATTTTTTTATT
1 TTTTATCTTTTTATT
29295701 TT
1 TT
29295703 AAAATTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTTATCTTTTTATT
Found at i:29301177 original size:29 final size:30
Alignment explanation
Indices: 29301138--29301278 Score: 153
Period size: 29 Copynumber: 4.7 Consensus size: 30
29301128 TAACAAAGTA
* * *
29301138 TTTTTGAATATGACGTGTAATAATAATA-T
1 TTTTTCAATATGACGTGTAACAACAATATT
29301167 TTTTTCAATATGACGTGTAACAACAATATTTT
1 TTTTTCAATATGACGTGTAACAACAATA--TT
29301199 TTTTTCAATAT-ATCGTGTAACAACAATA-T
1 TTTTTCAATATGA-CGTGTAACAACAATATT
* * * * *
29301228 TTTTTGAATATGGCTTGTAATAATAATATT
1 TTTTTCAATATGACGTGTAACAACAATATT
*
29301258 TTTTTTAATATGACGTGTAAC
1 TTTTTCAATATGACGTGTAAC
29301279 CTAACCATGA
Statistics
Matches: 94, Mismatches: 12, Indels: 11
0.80 0.10 0.09
Matches are distributed among these distances:
29 48 0.51
30 18 0.19
31 1 0.01
32 27 0.29
ACGTcount: A:0.35, C:0.09, G:0.11, T:0.45
Consensus pattern (30 bp):
TTTTTCAATATGACGTGTAACAACAATATT
Found at i:29301203 original size:61 final size:59
Alignment explanation
Indices: 29301138--29301278 Score: 176
Period size: 61 Copynumber: 2.4 Consensus size: 59
29301128 TAACAAAGTA
* * *
29301138 TTTTTGAATATGACGTGTAATAATAATATTTTTTCAATATGACGTGTAACAACAATATTT
1 TTTTTTAATATGACGTGTAACAACAATATTTTTTCAATATGACGTGTAACAACAATA-TT
* * * * *
29301198 TTTTTTCAATAT-ATCGTGTAACAACAATATTTTTTGAATATGGCTTGTAATAATAATATT
1 TTTTTT-AATATGA-CGTGTAACAACAATATTTTTTCAATATGACGTGTAACAACAATATT
29301258 TTTTTTAATATGACGTGTAAC
1 TTTTTTAATATGACGTGTAAC
29301279 CTAACCATGA
Statistics
Matches: 70, Mismatches: 8, Indels: 7
0.82 0.09 0.08
Matches are distributed among these distances:
59 13 0.19
60 15 0.21
61 42 0.60
ACGTcount: A:0.35, C:0.09, G:0.11, T:0.45
Consensus pattern (59 bp):
TTTTTTAATATGACGTGTAACAACAATATTTTTTCAATATGACGTGTAACAACAATATT
Found at i:29301394 original size:45 final size:45
Alignment explanation
Indices: 29301334--29301429 Score: 156
Period size: 45 Copynumber: 2.1 Consensus size: 45
29301324 TTAATCATAG
* *
29301334 CATGTAACAATCTAACCATGACGTGTCACATGTTTTTGTATATGA
1 CATGTAACAACCTAACCATGACGTGTCACATGTTTTTATATATGA
* *
29301379 CGTGTAACAACCTAACCATGTCGTGTCACATGTTTTTATATATGA
1 CATGTAACAACCTAACCATGACGTGTCACATGTTTTTATATATGA
29301424 CATGTA
1 CATGTA
29301430 TATTTTTATA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (45 bp):
CATGTAACAACCTAACCATGACGTGTCACATGTTTTTATATATGA
Found at i:29317917 original size:31 final size:31
Alignment explanation
Indices: 29317860--29317925 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
29317850 AATGAATATT
**
29317860 AAGTACAAGAAGAAAATGCATTTAAAAAAAA
1 AAGTACAAGAAGAAAATGCAAATAAAAAAAA
* *
29317891 AAGTACAAGAAGAAAATGGAAATAAAAAAAG
1 AAGTACAAGAAGAAAATGCAAATAAAAAAAA
29317922 AAGT
1 AAGT
29317926 TACATGTGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.65, C:0.05, G:0.17, T:0.14
Consensus pattern (31 bp):
AAGTACAAGAAGAAAATGCAAATAAAAAAAA
Found at i:29325414 original size:34 final size:33
Alignment explanation
Indices: 29325349--29325418 Score: 79
Period size: 34 Copynumber: 2.1 Consensus size: 33
29325339 TGTTACACAC
* *
29325349 TTTAGCATAAGATGCTACATGCCAAAGTCAAAAG
1 TTTAACATAAGATGCTACAAGCCAAAGTC-AAAG
* *
29325383 TTTAACATCAGATGTTACAAGCC-AAGATCAAAG
1 TTTAACATAAGATGCTACAAGCCAAAG-TCAAAG
29325416 TTT
1 TTT
29325419 CAAGGCCAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
33 10 0.32
34 21 0.68
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.27
Consensus pattern (33 bp):
TTTAACATAAGATGCTACAAGCCAAAGTCAAAG
Found at i:29325512 original size:23 final size:23
Alignment explanation
Indices: 29325486--29325529 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
29325476 AAGGTTAAAG
* *
29325486 TTTCAGTATCAGATGTTACACGC
1 TTTCAATATCAAATGTTACACGC
29325509 TTTCAATATCAAATGTTACAC
1 TTTCAATATCAAATGTTACAC
29325530 ACCAAGGCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.36
Consensus pattern (23 bp):
TTTCAATATCAAATGTTACACGC
Found at i:29338280 original size:45 final size:45
Alignment explanation
Indices: 29338216--29338304 Score: 178
Period size: 45 Copynumber: 2.0 Consensus size: 45
29338206 GGCGTGCCAC
29338216 CACCTTGACTCTGTCACTGCATATATGTATACATTGCATACACAA
1 CACCTTGACTCTGTCACTGCATATATGTATACATTGCATACACAA
29338261 CACCTTGACTCTGTCACTGCATATATGTATACATTGCATACACA
1 CACCTTGACTCTGTCACTGCATATATGTATACATTGCATACACA
29338305 GACATGGGCT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.31
Consensus pattern (45 bp):
CACCTTGACTCTGTCACTGCATATATGTATACATTGCATACACAA
Found at i:29342876 original size:3 final size:3
Alignment explanation
Indices: 29342868--29342909 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
29342858 CATTATAGTA
**
29342868 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AGA ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
29342910 GGTGTTTGAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:29343558 original size:18 final size:18
Alignment explanation
Indices: 29343537--29343573 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
29343527 GGTATCTCAA
* *
29343537 ATTTCAGTAACTTAGATT
1 ATTTCAATAACTTAAATT
29343555 ATTTCAATAACTTAAATT
1 ATTTCAATAACTTAAATT
29343573 A
1 A
29343574 CGTATAACAA
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:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (18 bp):
ATTTCAATAACTTAAATT
Found at i:29349120 original size:28 final size:28
Alignment explanation
Indices: 29349044--29349120 Score: 81
Period size: 25 Copynumber: 2.9 Consensus size: 28
29349034 TCTTTTCCTA
*
29349044 TAGTAACAGGAAGATATGGCGAAACTAC
1 TAGTAACAGGAAGATATGGCAAAACTAC
* * *
29349072 TAGT-A-AGTAA-AT-TGTCCAAAATTAC
1 TAGTAACAGGAAGATATG-GCAAAACTAC
29349097 TAGTAACAGGAAGATATGGCAAAA
1 TAGTAACAGGAAGATATGGCAAAA
29349121 ATCGACAATA
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
24 2 0.05
25 13 0.34
26 5 0.13
27 5 0.13
28 11 0.29
29 2 0.05
ACGTcount: A:0.45, C:0.12, G:0.21, T:0.22
Consensus pattern (28 bp):
TAGTAACAGGAAGATATGGCAAAACTAC
Found at i:29356609 original size:24 final size:24
Alignment explanation
Indices: 29356582--29356662 Score: 78
Period size: 24 Copynumber: 3.4 Consensus size: 24
29356572 ATCTAACTTG
*
29356582 AGTTATAATATAGTACTATTAGTT
1 AGTTATAATATAATACTATTAGTT
29356606 AGTTA-AATTATAATATCTAATTAG--
1 AGTTATAA-TATAATA-CT-ATTAGTT
* *
29356630 AGTTATATTATAATATTATTAGTT
1 AGTTATAATATAATACTATTAGTT
*
29356654 AATTATAAT
1 AGTTATAAT
29356663 TAGATTATGA
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
22 5 0.11
23 3 0.07
24 30 0.65
25 3 0.07
26 5 0.11
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (24 bp):
AGTTATAATATAATACTATTAGTT
Found at i:29356633 original size:48 final size:49
Alignment explanation
Indices: 29356571--29356664 Score: 129
Period size: 48 Copynumber: 1.9 Consensus size: 49
29356561 CTATATGAAT
* *
29356571 TATCTAACTTGAGTTATAATATAGTACTATTAGTTAGTTA-AATTATAA
1 TATCTAACTTGAGTTATAATATAATACTATTAGTTAATTATAATTATAA
* *
29356619 TATCTAA-TTAGAGTTATATTATAATATTATTAGTTAATTATAATTA
1 TATCTAACTT-GAGTTATAATATAATACTATTAGTTAATTATAATTA
29356665 GATTATGAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
47 2 0.05
48 33 0.82
49 5 0.12
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47
Consensus pattern (49 bp):
TATCTAACTTGAGTTATAATATAATACTATTAGTTAATTATAATTATAA
Found at i:29375937 original size:73 final size:73
Alignment explanation
Indices: 29375816--29375956 Score: 230
Period size: 73 Copynumber: 1.9 Consensus size: 73
29375806 TTACTTTACG
* *
29375816 AAGTTCCTCCTTATACAAACCTAAATGACTTATTCCTATGTTCTAGTCAGAATCGTTGATTTCAC
1 AAGTTCCTCCTTATACAAACCTAAATGACCTATTCCTATGTTCAAGTCAGAATCGTTGATTTCAC
29375881 TTTCCTCA
66 TTTCCTCA
* *
29375889 AAGTTCCTCCTTCA-ACAAACCTAAATGACCTATTCCTTTGTTCAAGTCAGAATTGTTGATTTCA
1 AAGTTCCTCCTT-ATACAAACCTAAATGACCTATTCCTATGTTCAAGTCAGAATCGTTGATTTCA
29375953 CTTT
65 CTTT
29375957 GCTACCTCTT
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
73 62 0.98
74 1 0.02
ACGTcount: A:0.28, C:0.24, G:0.10, T:0.38
Consensus pattern (73 bp):
AAGTTCCTCCTTATACAAACCTAAATGACCTATTCCTATGTTCAAGTCAGAATCGTTGATTTCAC
TTTCCTCA
Found at i:29388164 original size:47 final size:47
Alignment explanation
Indices: 29388110--29388209 Score: 173
Period size: 47 Copynumber: 2.1 Consensus size: 47
29388100 GGAGTTTGTA
29388110 TCTTGCAGTACTTAACCTGTCTTCCGTGCTTGGTGAACTACAACCAT
1 TCTTGCAGTACTTAACCTGTCTTCCGTGCTTGGTGAACTACAACCAT
* * *
29388157 TCTTGCAGTACTTAACCTGTCTTCCGTGCTTGTTGACCTACCACCAT
1 TCTTGCAGTACTTAACCTGTCTTCCGTGCTTGGTGAACTACAACCAT
29388204 TCTTGC
1 TCTTGC
29388210 CTAGGCATAT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.18, C:0.30, G:0.16, T:0.36
Consensus pattern (47 bp):
TCTTGCAGTACTTAACCTGTCTTCCGTGCTTGGTGAACTACAACCAT
Found at i:29392908 original size:2 final size:2
Alignment explanation
Indices: 29392901--29392939 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
29392891 AGAGTTTACG
29392901 CT CT CT CT CT CT CT CT CT CT 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 CT CT C
29392940 ACACACACAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:29398114 original size:98 final size:98
Alignment explanation
Indices: 29397955--29398151 Score: 394
Period size: 98 Copynumber: 2.0 Consensus size: 98
29397945 CAAGCTTATT
29397955 TCTATCATGTTCTACTAAACAAGCAGGAGAAATAAGTTGTTATATTTGGACAAGGAGATCAACAA
1 TCTATCATGTTCTACTAAACAAGCAGGAGAAATAAGTTGTTATATTTGGACAAGGAGATCAACAA
29398020 ATCTGAATCTAAACATTAGTAGACAAGCCATGA
66 ATCTGAATCTAAACATTAGTAGACAAGCCATGA
29398053 TCTATCATGTTCTACTAAACAAGCAGGAGAAATAAGTTGTTATATTTGGACAAGGAGATCAACAA
1 TCTATCATGTTCTACTAAACAAGCAGGAGAAATAAGTTGTTATATTTGGACAAGGAGATCAACAA
29398118 ATCTGAATCTAAACATTAGTAGACAAGCCATGA
66 ATCTGAATCTAAACATTAGTAGACAAGCCATGA
29398151 T
1 T
29398152 GACCAGACTG
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
98 99 1.00
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (98 bp):
TCTATCATGTTCTACTAAACAAGCAGGAGAAATAAGTTGTTATATTTGGACAAGGAGATCAACAA
ATCTGAATCTAAACATTAGTAGACAAGCCATGA
Found at i:29401188 original size:23 final size:19
Alignment explanation
Indices: 29401147--29401187 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
29401137 TAGAGAGACC
29401147 ACTGGATAAAAACAAACTT
1 ACTGGATAAAAACAAACTT
29401166 ACTGGATAAAAACAAACTT
1 ACTGGATAAAAACAAACTT
29401185 ACT
1 ACT
29401188 TCTCATAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.51, C:0.17, G:0.10, T:0.22
Consensus pattern (19 bp):
ACTGGATAAAAACAAACTT
Found at i:29423005 original size:9 final size:10
Alignment explanation
Indices: 29422983--29423015 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
29422973 TTAAAAAAGT
29422983 TTTTAAATAA
1 TTTTAAATAA
29422993 TTTTAAA-AA
1 TTTTAAATAA
29423002 TTTTAAATAA
1 TTTTAAATAA
29423012 TTTT
1 TTTT
29423016 TTATTTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 9 0.41
10 13 0.59
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (10 bp):
TTTTAAATAA
Found at i:29423025 original size:19 final size:19
Alignment explanation
Indices: 29422977--29423015 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
29422967 CAATATTTAA
29422977 AAAAGTTTTTAAATAATTTT
1 AAAA-TTTTTAAATAATTTT
*
29422997 AAAAATTTTAAATAATTTT
1 AAAATTTTTAAATAATTTT
29423016 TTATTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (19 bp):
AAAATTTTTAAATAATTTT
Found at i:29431743 original size:2 final size:2
Alignment explanation
Indices: 29431736--29431767 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
29431726 ATTGACATCC
29431736 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29431768 CTTAAATACG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29439096 original size:13 final size:13
Alignment explanation
Indices: 29439078--29439102 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29439068 TAAGAATATT
29439078 TAAAAAATAAAAA
1 TAAAAAATAAAAA
29439091 TAAAAAATAAAA
1 TAAAAAATAAAA
29439103 CATGCCTGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (13 bp):
TAAAAAATAAAAA
Found at i:29465838 original size:18 final size:18
Alignment explanation
Indices: 29465792--29465840 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
29465782 TTAAAAAAAT
* **
29465792 AAAAATAAAAAATAATTA
1 AAAAATAAAAAAAAACCA
* *
29465810 AATAATTAAAAAAAACCA
1 AAAAATAAAAAAAAACCA
29465828 AAAAATAAAAAAA
1 AAAAATAAAAAAA
29465841 TAAAATAAAA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.80, C:0.04, G:0.00, T:0.16
Consensus pattern (18 bp):
AAAAATAAAAAAAAACCA
Found at i:29466300 original size:16 final size:15
Alignment explanation
Indices: 29466263--29466302 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 15
29466253 ACAATCAACA
29466263 ATAAAAAATATAAAT
1 ATAAAAAATATAAAT
*
29466278 ACAAAAATATATAAAAT
1 ATAAAAA-ATAT-AAAT
29466295 ATAAAAAA
1 ATAAAAAA
29466303 ATGGGGCTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 6 0.29
16 5 0.24
17 10 0.48
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.23
Consensus pattern (15 bp):
ATAAAAAATATAAAT
Found at i:29467138 original size:2 final size:2
Alignment explanation
Indices: 29467131--29467166 Score: 54
Period size: 2 Copynumber: 17.5 Consensus size: 2
29467121 GTTTAGAAGA
*
29467131 AT AT AT AT AT AA AT AT AT AT ACT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT A
29467167 AAATAAGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:29468466 original size:2 final size:2
Alignment explanation
Indices: 29468459--29468515 Score: 64
Period size: 2 Copynumber: 28.5 Consensus size: 2
29468449 CCAACAACAT
29468459 TA TA TA TA TA TA TA CT- TA TA TA TA TA GTA 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
* *
29468502 -A TA TG TA TG TA TA T
1 TA TA TA TA TA TA TA T
29468516 GAATATTTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
1 2 0.04
2 42 0.89
3 3 0.06
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (2 bp):
TA
Found at i:29468509 original size:21 final size:24
Alignment explanation
Indices: 29468461--29468515 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 24
29468451 AACAACATTA
29468461 TATATATATATACTTATATATATAG
1 TATATATATATAC-TATATATATAG
29468486 TATATATATATA-TATA-ATAT-G
1 TATATATATATACTATATATATAG
*
29468507 TATGTATAT
1 TATATATAT
29468516 GAATATTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 9 0.31
22 4 0.14
23 4 0.14
25 12 0.41
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (24 bp):
TATATATATATACTATATATATAG
Found at i:29469570 original size:25 final size:26
Alignment explanation
Indices: 29469544--29469632 Score: 71
Period size: 24 Copynumber: 3.5 Consensus size: 26
29469534 TATGCTTATT
29469544 TTATTTTTATTTTTTTATATATTTT-
1 TTATTTTTATTTTTTTATATATTTTC
*
29469569 TTATTATTATGTTTTTT-TAT-TTTTC
1 TTATTTTTAT-TTTTTTATATATTTTC
** * * *
29469594 CCA-TTTTATCTATTTAT-TATTTTG
1 TTATTTTTATTTTTTTATATATTTTC
29469618 TTATTTATTATTTTT
1 TTATTT-TTATTTTT
29469633 AATTATTGTC
Statistics
Matches: 47, Mismatches: 11, Indels: 11
0.68 0.16 0.16
Matches are distributed among these distances:
23 5 0.11
24 15 0.32
25 15 0.32
26 12 0.26
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.74
Consensus pattern (26 bp):
TTATTTTTATTTTTTTATATATTTTC
Found at i:29484047 original size:38 final size:38
Alignment explanation
Indices: 29483989--29484114 Score: 218
Period size: 38 Copynumber: 3.3 Consensus size: 38
29483979 AAACAACCAA
* *
29483989 TAATTTA-TTTCATTACTAATGAATGATGTAACACTTT
1 TAATTTAGTTTAATCACTAATGAATGATGTAACACTTT
29484026 TAATTTAGTTTAATCACTAATGAATGATGTAACACTTT
1 TAATTTAGTTTAATCACTAATGAATGATGTAACACTTT
29484064 TAATTTAGTTTAATCACTAATGAATGATGTAACACTTT
1 TAATTTAGTTTAATCACTAATGAATGATGTAACACTTT
*
29484102 TAATTTAATTTAA
1 TAATTTAGTTTAA
29484115 GAATTTAGAT
Statistics
Matches: 85, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
37 7 0.08
38 78 0.92
ACGTcount: A:0.37, C:0.10, G:0.09, T:0.44
Consensus pattern (38 bp):
TAATTTAGTTTAATCACTAATGAATGATGTAACACTTT
Found at i:29484067 original size:21 final size:21
Alignment explanation
Indices: 29484005--29484105 Score: 60
Period size: 19 Copynumber: 5.2 Consensus size: 21
29483995 ATTTCATTAC
29484005 TAATGAATGATGTAACACTTT
1 TAATGAATGATGTAACACTTT
** *
29484026 TAATTTA-G-TTTAATCAC---
1 TAATGAATGATGTAA-CACTTT
29484043 TAATGAATGATGTAACACTTT
1 TAATGAATGATGTAACACTTT
** *
29484064 TAATTTA-G-TTTAATCAC---
1 TAATGAATGATGTAA-CACTTT
29484081 TAATGAATGATGTAACACTTT
1 TAATGAATGATGTAACACTTT
29484102 TAAT
1 TAAT
29484106 TTAATTTAAG
Statistics
Matches: 56, Mismatches: 12, Indels: 24
0.61 0.13 0.26
Matches are distributed among these distances:
17 10 0.18
18 8 0.14
19 16 0.29
20 8 0.14
21 14 0.25
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.42
Consensus pattern (21 bp):
TAATGAATGATGTAACACTTT
Found at i:29488644 original size:11 final size:10
Alignment explanation
Indices: 29488620--29488667 Score: 51
Period size: 11 Copynumber: 4.5 Consensus size: 10
29488610 AAGAGAGAGT
*
29488620 AAAGTAAAATA
1 AAAG-AAAAAA
29488631 AAAGAACAAAA
1 AAAGAA-AAAA
29488642 AAAGAAGAAAA
1 AAAGAA-AAAA
*
29488653 AGAGAAAAAA
1 AAAGAAAAAA
29488663 AAAGA
1 AAAGA
29488668 GAGAGAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
10 10 0.31
11 22 0.69
ACGTcount: A:0.79, C:0.02, G:0.15, T:0.04
Consensus pattern (10 bp):
AAAGAAAAAA
Found at i:29488645 original size:22 final size:21
Alignment explanation
Indices: 29488633--29488676 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
29488623 GTAAAATAAA
29488633 AGAACAAAAAAAGAAGAAAAAG
1 AGAA-AAAAAAAGAAGAAAAAG
29488655 AGAAAAAAAAAGAGAGAGAAAA
1 AGAAAAAAAAAGA-AGA-AAAA
29488677 AAGTGTGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 9 0.45
22 7 0.35
23 4 0.20
ACGTcount: A:0.77, C:0.02, G:0.20, T:0.00
Consensus pattern (21 bp):
AGAAAAAAAAAGAAGAAAAAG
Found at i:29507135 original size:39 final size:40
Alignment explanation
Indices: 29507063--29507145 Score: 107
Period size: 39 Copynumber: 2.1 Consensus size: 40
29507053 AGTTTTAATA
* **
29507063 AAAACTTTCCACGAATTTATTAATTTTTTAAATAAAACT-
1 AAAACTTTCCACAAATTTATTAATTTTCAAAATAAAACTC
*
29507102 AAAACTTCTCCA-AAATTTATTAATTTTCAAAATAAGACTC
1 AAAACTT-TCCACAAATTTATTAATTTTCAAAATAAAACTC
29507142 AAAA
1 AAAA
29507146 TTAATAAACT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
39 30 0.79
40 8 0.21
ACGTcount: A:0.47, C:0.14, G:0.02, T:0.36
Consensus pattern (40 bp):
AAAACTTTCCACAAATTTATTAATTTTCAAAATAAAACTC
Found at i:29515924 original size:24 final size:24
Alignment explanation
Indices: 29515875--29515921 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
29515865 TAAACATGAA
*
29515875 AAACTAAATATCACCAAATAAAAG
1 AAACTAAATAACACCAAATAAAAG
*
29515899 AAACTAAATAACAATCAAATAAA
1 AAACTAAATAAC-ACCAAATAAA
29515922 GAACATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.66, C:0.15, G:0.02, T:0.17
Consensus pattern (24 bp):
AAACTAAATAACACCAAATAAAAG
Found at i:29518021 original size:2 final size:2
Alignment explanation
Indices: 29518014--29518044 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
29518004 CTGTGAACCT
29518014 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29518045 TCTAATCAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29524591 original size:14 final size:15
Alignment explanation
Indices: 29524572--29524600 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
29524562 TCATAAATTC
29524572 TCTTC-TCATTTCTT
1 TCTTCTTCATTTCTT
29524586 TCTTCTTCATTTCTT
1 TCTTCTTCATTTCTT
29524601 CGATCTAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.07, C:0.28, G:0.00, T:0.66
Consensus pattern (15 bp):
TCTTCTTCATTTCTT
Found at i:29524789 original size:24 final size:25
Alignment explanation
Indices: 29524747--29524798 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 25
29524737 CTCCCTTTTA
*
29524747 TTTTGTTTGTTTATCTTGTTTTATT
1 TTTTGTTTGTTTATCTTGTGTTATT
*
29524772 TTTTGTATT-TTTAT-TTGTGTTGTT
1 TTTTGT-TTGTTTATCTTGTGTTATT
29524796 TTT
1 TTT
29524799 ATTTTGATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 11 0.46
25 11 0.46
26 2 0.08
ACGTcount: A:0.08, C:0.02, G:0.13, T:0.77
Consensus pattern (25 bp):
TTTTGTTTGTTTATCTTGTGTTATT
Found at i:29529130 original size:2 final size:2
Alignment explanation
Indices: 29529123--29529148 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
29529113 TCTTATAATA
29529123 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
29529149 CATACTTCAC
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:29534225 original size:2 final size:2
Alignment explanation
Indices: 29534214--29534296 Score: 122
Period size: 2 Copynumber: 43.5 Consensus size: 2
29534204 NNNNNNNAAC
29534214 AT AT -T AT AT AT A- AT AT AT AT A- 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
29534253 -T ACT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29534294 AT A
1 AT A
29534297 GTCGCTTGAG
Statistics
Matches: 75, Mismatches: 0, Indels: 12
0.86 0.00 0.14
Matches are distributed among these distances:
1 5 0.07
2 68 0.91
3 2 0.03
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29534280 original size:39 final size:38
Alignment explanation
Indices: 29534218--29534291 Score: 139
Period size: 39 Copynumber: 1.9 Consensus size: 38
29534208 NNNAACATAT
29534218 TATATATAATATATATAATATATATATATATATATTAC
1 TATATATAATATATATAATATATATATATATATATTAC
29534256 TATATATATATATATATAATATATATATATATATAT
1 TATATATA-ATATATATAATATATATATATATATAT
29534292 ATATAGTCGC
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
38 8 0.23
39 27 0.77
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (38 bp):
TATATATAATATATATAATATATATATATATATATTAC
Found at i:29544745 original size:6 final size:6
Alignment explanation
Indices: 29544734--29544771 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
29544724 CATATATAGC
29544734 GCATTA GCATTA GCATTA GCATTA GCATTA GCATTA GC
1 GCATTA GCATTA GCATTA GCATTA GCATTA GCATTA GC
29544772 TTATGCAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (6 bp):
GCATTA
Found at i:29548889 original size:29 final size:29
Alignment explanation
Indices: 29548856--29548912 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
29548846 AAGATTTACA
29548856 AGAATAGGTACAAGAGAAGAAGTTGTACG
1 AGAATAGGTACAAGAGAAGAAGTTGTACG
* *
29548885 AGAATAGGTGCAAGAGAATAAGTTGTAC
1 AGAATAGGTACAAGAGAAGAAGTTGTAC
29548913 ATAAATAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.44, C:0.07, G:0.30, T:0.19
Consensus pattern (29 bp):
AGAATAGGTACAAGAGAAGAAGTTGTACG
Found at i:29560198 original size:33 final size:33
Alignment explanation
Indices: 29560139--29560213 Score: 87
Period size: 33 Copynumber: 2.3 Consensus size: 33
29560129 TATTGACGTG
* * * *
29560139 ACATACTAATATATTATAATTAATGATAATATA
1 ACATATTAACATATTATAATGAATGATAACATA
* * *
29560172 ACATGTTAACATATTATAATGGATGATGACATA
1 ACATATTAACATATTATAATGAATGATAACATA
29560205 ACATATTAA
1 ACATATTAA
29560214 TTTGATATAA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (33 bp):
ACATATTAACATATTATAATGAATGATAACATA
Found at i:29561795 original size:20 final size:20
Alignment explanation
Indices: 29561767--29561804 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
29561757 AGGATGTAAT
29561767 TCTTGTG-TTATCTGTTCTAA
1 TCTTGTGTTTAT-TGTTCTAA
*
29561787 TCTTTTGTTTATTGTTCT
1 TCTTGTGTTTATTGTTCT
29561805 TCGCTGTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.11, C:0.13, G:0.13, T:0.63
Consensus pattern (20 bp):
TCTTGTGTTTATTGTTCTAA
Found at i:29568043 original size:37 final size:37
Alignment explanation
Indices: 29567993--29568065 Score: 146
Period size: 37 Copynumber: 2.0 Consensus size: 37
29567983 CCTCCCTCCT
29567993 CCTCTACTTGAATTTATAAATAAAGAACATTCTTTCG
1 CCTCTACTTGAATTTATAAATAAAGAACATTCTTTCG
29568030 CCTCTACTTGAATTTATAAATAAAGAACATTCTTTC
1 CCTCTACTTGAATTTATAAATAAAGAACATTCTTTC
29568066 ACATTTTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.36, C:0.19, G:0.07, T:0.38
Consensus pattern (37 bp):
CCTCTACTTGAATTTATAAATAAAGAACATTCTTTCG
Found at i:29578957 original size:37 final size:36
Alignment explanation
Indices: 29578905--29578978 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 36
29578895 GTTTGAACAT
29578905 TTTAATAATTTTTAAAAATTT-GGAATAAATGATCA
1 TTTAATAATTTTTAAAAATTTAGGAATAAATGATCA
29578940 NTTTAATTAATTTTTAAAAATTTAGGAATAAATGATCA
1 -TTTAA-TAATTTTTAAAAATTTAGGAATAAATGATCA
29578978 T
1 T
29578979 ATATATATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
36 5 0.14
37 17 0.47
38 14 0.39
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.43
Consensus pattern (36 bp):
TTTAATAATTTTTAAAAATTTAGGAATAAATGATCA
Found at i:29578984 original size:2 final size:2
Alignment explanation
Indices: 29578977--29579001 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
29578967 ATAAATGATC
29578977 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
29579002 CTCAATCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29579862 original size:7 final size:7
Alignment explanation
Indices: 29579850--29579880 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
29579840 GAATCTCAGT
29579850 AGAGTAG
1 AGAGTAG
29579857 AGAGTAG
1 AGAGTAG
29579864 AGAGTAG
1 AGAGTAG
29579871 AGAGTAG
1 AGAGTAG
29579878 AGA
1 AGA
29579881 CCATTTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.45, C:0.00, G:0.42, T:0.13
Consensus pattern (7 bp):
AGAGTAG
Found at i:29599559 original size:29 final size:29
Alignment explanation
Indices: 29599500--29599600 Score: 87
Period size: 29 Copynumber: 3.5 Consensus size: 29
29599490 ATAAGAGGTA
* * * * * *
29599500 TATATGAAAAAGTATAAAAGAATAAATTG
1 TATATGAATAGGTACAAAAAAAGAAACTG
*
29599529 TATATGAATAGGTACAATAAAAGAAACTG
1 TATATGAATAGGTACAAAAAAAGAAACTG
* * * *
29599558 TACATGAATAGATACAAAAAAAGAAAGTA
1 TATATGAATAGGTACAAAAAAAGAAACTG
29599587 TATAT-AAGTAGGTA
1 TATATGAA-TAGGTA
29599601 TACGAGAATA
Statistics
Matches: 57, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
28 2 0.04
29 55 0.96
ACGTcount: A:0.55, C:0.04, G:0.16, T:0.25
Consensus pattern (29 bp):
TATATGAATAGGTACAAAAAAAGAAACTG
Found at i:29603942 original size:10 final size:10
Alignment explanation
Indices: 29603904--29603976 Score: 51
Period size: 10 Copynumber: 6.9 Consensus size: 10
29603894 CGGCCAAAAG
29603904 GAGAGGAAGA
1 GAGAGGAAGA
*
29603914 GAAAAGAGAAG-
1 G-AGAG-GAAGA
29603925 GA-AGGAAGA
1 GAGAGGAAGA
29603934 GAGAGGAAGGA
1 GAGAGGAA-GA
29603945 GAGAGAAGAAGA
1 GAGAG--GAAGA
* *
29603957 AAGAGAAAGA
1 GAGAGGAAGA
29603967 GAGAGAGAAG
1 GAGAG-GAAG
29603977 GAAGAACAGA
Statistics
Matches: 50, Mismatches: 5, Indels: 15
0.71 0.07 0.21
Matches are distributed among these distances:
8 4 0.08
9 4 0.08
10 15 0.30
11 14 0.28
12 10 0.20
13 3 0.06
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (10 bp):
GAGAGGAAGA
Found at i:29603995 original size:33 final size:32
Alignment explanation
Indices: 29603900--29603996 Score: 98
Period size: 33 Copynumber: 3.1 Consensus size: 32
29603890 ACGCCGGCCA
29603900 AAAG-GAGAGGAA-GAGA-AAAGAGAAG-GAAG
1 AAAGAGAGAGGAAGGAGAGAAAGAGAAGAG-AG
*
29603929 GAAGAGAGAGGAAGGAGAGAGAAGAAGAA-AGAG
1 AAAGAGAGAGGAAGGAGAGA-AAG-AGAAGAGAG
29603962 AAAGAGAGAGAGAAGGA-AGAACAGAGAAGAGAG
1 AAAGAGAGAG-GAAGGAGAGAA-AGAGAAGAGAG
29603995 AA
1 AA
29603997 GCCGAAAGAG
Statistics
Matches: 57, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
29 3 0.05
30 8 0.14
31 4 0.07
32 6 0.11
33 25 0.44
34 11 0.19
ACGTcount: A:0.58, C:0.01, G:0.41, T:0.00
Consensus pattern (32 bp):
AAAGAGAGAGGAAGGAGAGAAAGAGAAGAGAG
Found at i:29603997 original size:7 final size:7
Alignment explanation
Indices: 29603911--29603997 Score: 62
Period size: 7 Copynumber: 13.0 Consensus size: 7
29603901 AAGGAGAGGA
*
29603911 AGAGAAA
1 AGAGAAG
29603918 AGAGAAG
1 AGAGAAG
29603925 -GAAGGAAG
1 AG-A-GAAG
*
29603933 AGAGAGG
1 AGAGAAG
*
29603940 A-AGGAG
1 AGAGAAG
29603946 AGAGAAG
1 AGAGAAG
29603953 A-AGAA-
1 AGAGAAG
29603958 AGAGAA-
1 AGAGAAG
29603964 AGAG-AG
1 AGAGAAG
29603970 AGAGAAG
1 AGAGAAG
*
29603977 -GAAGAAC
1 AG-AGAAG
29603984 AGAGAAG
1 AGAGAAG
29603991 AGAGAAG
1 AGAGAAG
29603998 CCGAAAGAGA
Statistics
Matches: 64, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
5 2 0.03
6 22 0.34
7 33 0.52
8 6 0.09
9 1 0.02
ACGTcount: A:0.57, C:0.01, G:0.41, T:0.00
Consensus pattern (7 bp):
AGAGAAG
Found at i:29604004 original size:45 final size:48
Alignment explanation
Indices: 29603910--29604018 Score: 122
Period size: 45 Copynumber: 2.4 Consensus size: 48
29603900 AAAGGAGAGG
* *
29603910 AAGAGAAA-AGAGA-AGGAAGGAAGAGAGAGGAAGGAGAGAGAAGAAGA
1 AAGAGAAAGAGAGAGA-GAAGGAAGAGACAGGAAGAAGAGAGAAGAAGA
**
29603957 AAGAGAAAGAGAGAGAGAAGGAAGA-ACA-G-AGAAGAGAGAAGCCGA
1 AAGAGAAAGAGAGAGAGAAGGAAGAGACAGGAAGAAGAGAGAAGAAGA
29604002 AAGAGAAAG-GAAGAGAG
1 AAGAGAAAGAG-AGAGAG
29604019 GGGGAAAAAG
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
44 1 0.02
45 28 0.51
46 1 0.02
47 10 0.18
48 14 0.25
49 1 0.02
ACGTcount: A:0.57, C:0.03, G:0.40, T:0.00
Consensus pattern (48 bp):
AAGAGAAAGAGAGAGAGAAGGAAGAGACAGGAAGAAGAGAGAAGAAGA
Found at i:29604034 original size:45 final size:45
Alignment explanation
Indices: 29603944--29604049 Score: 108
Period size: 45 Copynumber: 2.4 Consensus size: 45
29603934 GAGAGGAAGG
*
29603944 AGAGAGAAGAAGAAAGAGAAAGAGAGAGAGAAGGAAGAACAGAGA
1 AGAGAGAAGAAGAAAGAGAAAGAGAGAGAGAAGGAAAAACAGAGA
** ** **
29603989 AGAGAGAAGCCGAAAGAGAAAG-GAAGAGAGGGGGAAAAAGGGAGA
1 AGAGAGAAGAAGAAAGAGAAAGAG-AGAGAGAAGGAAAAACAGAGA
**
29604034 AG-CCGAAGAAGAAAGA
1 AGAGAGAAGAAGAAAGA
29604050 AAGGGAGAGG
Statistics
Matches: 49, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
44 11 0.22
45 38 0.78
ACGTcount: A:0.56, C:0.05, G:0.40, T:0.00
Consensus pattern (45 bp):
AGAGAGAAGAAGAAAGAGAAAGAGAGAGAGAAGGAAAAACAGAGA
Found at i:29605378 original size:2 final size:2
Alignment explanation
Indices: 29605371--29605411 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
29605361 TAATTATGAA
29605371 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29605412 ACTTAGTCTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:29608398 original size:2 final size:2
Alignment explanation
Indices: 29608393--29608429 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
29608383 ACCATAAGAC
29608393 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29608430 GTAGAGAGGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:29608499 original size:2 final size:2
Alignment explanation
Indices: 29608492--29608528 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
29608482 AGAGNACAAC
29608492 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29608529 GTAGCAGAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:29608538 original size:102 final size:101
Alignment explanation
Indices: 29608393--29608588 Score: 365
Period size: 102 Copynumber: 1.9 Consensus size: 101
29608383 ACCATAAGAC
*
29608393 ATATATATATATATATATATATATATATATATATATAGTAGAGAGGCATTTTGATCGTAATGATA
1 ATATATATATATATATATATATATATATATATATATAGCAGAGAGGCATTTTGATCGTAATGATA
29608458 CGATGAGAATAAATAAGATCAGCTAGAGNACAACTAT
66 CGATGAGAATAAATAAGATCAGCTAGAG-ACAACTAT
*
29608495 ATATATATATATATATATATATATATATATATATGTAGCAGAGAGGCATTTTGATCGTAATGATA
1 ATATATATATATATATATATATATATATATATATATAGCAGAGAGGCATTTTGATCGTAATGATA
29608560 CGATGAGAATAAATAAGATCAGCTAGAGA
66 CGATGAGAATAAATAAGATCAGCTAGAGA
29608589 AAGTGGAAAC
Statistics
Matches: 92, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
101 1 0.01
102 91 0.99
ACGTcount: A:0.44, C:0.07, G:0.16, T:0.33
Consensus pattern (101 bp):
ATATATATATATATATATATATATATATATATATATAGCAGAGAGGCATTTTGATCGTAATGATA
CGATGAGAATAAATAAGATCAGCTAGAGACAACTAT
Found at i:29617904 original size:18 final size:19
Alignment explanation
Indices: 29617877--29617922 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
29617867 GTCAGAAACG
29617877 AAAG-ACGCCGCCT-GGCT
1 AAAGTACGCCGCCTCGGCT
29617894 AAAGTACGCCGCCTCGGCT
1 AAAGTACGCCGCCTCGGCT
29617913 AAAGTACGCC
1 AAAGTACGCC
29617923 CATCTCCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 4 0.15
18 9 0.33
19 14 0.52
ACGTcount: A:0.26, C:0.35, G:0.26, T:0.13
Consensus pattern (19 bp):
AAAGTACGCCGCCTCGGCT
Found at i:29624625 original size:39 final size:39
Alignment explanation
Indices: 29624578--29624653 Score: 143
Period size: 39 Copynumber: 1.9 Consensus size: 39
29624568 ACCTTGGTAA
*
29624578 TTATATGTTTTCAACTTTTTTACTTTACAGAATTGGTGG
1 TTATATGTTTTCAACTTTTTCACTTTACAGAATTGGTGG
29624617 TTATATGTTTTCAACTTTTTCACTTTACAGAATTGGT
1 TTATATGTTTTCAACTTTTTCACTTTACAGAATTGGT
29624654 TTTTGATTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.24, C:0.12, G:0.13, T:0.51
Consensus pattern (39 bp):
TTATATGTTTTCAACTTTTTCACTTTACAGAATTGGTGG
Found at i:29624893 original size:107 final size:106
Alignment explanation
Indices: 29624774--29625191 Score: 545
Period size: 107 Copynumber: 3.9 Consensus size: 106
29624764 CACCCTACGG
* * * * *
29624774 AATTGGTATTTGATTTTGGCAATTAAGAGATTTTAAATATATTTTGTCGTTGTCTTCTTTTTAAA
1 AATTGGTCTTTGATTTTGGCAATTAAGAGATTTTAAATATATTCTATCATTATCTTCTTTTTAAA
*
29624839 TCTAATTTTTTAAATTG-TTATAAAATCAAATTCACCTTATGA
66 TCTAA-TTTTTAAA-TGATTACAAAATCAAATTCACCTTATGA
* * * *
29624881 AATTGGTCTTTGATTTTGACAGTTAAGATATTTTAAATATATTTTATCATTAT-TTCTTTTTAAA
1 AATTGGTCTTTGATTTTGGCAATTAAGAGATTTTAAATATATTCTATCATTATCTTCTTTTTAAA
* * * *
29624945 TCTAATTTTTAAACGATTACAAAATCAAATTTTAAACGTTACGA
66 TCTAATTTTTAAATGATTACAAAATCAAA--TT-CACCTTATGA
* * *
29624989 AATTGTTCTTTGATTTTGGCAATTAAGAGATTTTTAAATATATTCTACCCTTATCTTCTTTTTAA
1 AATTGGTCTTTGATTTTGGCAATTAAGAGA-TTTTAAATATATTCTATCATTATCTTCTTTTTAA
* * *
29625054 ATTTAATTTTTAAATTATTACAGAATCAAATTCACCTTATGA
65 ATCTAATTTTTAAATGATTACAAAATCAAATTCACCTTATGA
* *
29625096 AATTGGTCTTTGATTTTGGCAGTTGAA-ATATTTTAAATATATTCTATCATTATCTTCTTTTTAA
1 AATTGGTCTTTGATTTTGGCAATT-AAGAGATTTTAAATATATTCTATCATTATCTTCTTTTTAA
*
29625160 ATCTAATGTTTAAATGATTACAAAATCAAATT
65 ATCTAATTTTTAAATGATTACAAAATCAAATT
29625192 TTACACGTTT
Statistics
Matches: 269, Mismatches: 35, Indels: 15
0.84 0.11 0.05
Matches are distributed among these distances:
104 1 0.00
105 20 0.07
106 76 0.28
107 79 0.29
108 37 0.14
109 20 0.07
110 36 0.13
ACGTcount: A:0.34, C:0.10, G:0.09, T:0.47
Consensus pattern (106 bp):
AATTGGTCTTTGATTTTGGCAATTAAGAGATTTTAAATATATTCTATCATTATCTTCTTTTTAAA
TCTAATTTTTAAATGATTACAAAATCAAATTCACCTTATGA
Found at i:29624991 original size:22 final size:24
Alignment explanation
Indices: 29624942--29624991 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
29624932 ATTTCTTTTT
*
29624942 AAATCTAATTTTTAAACGATTACA
1 AAATCTAAATTTTAAACGATTACA
*
29624966 AAATC-AAATTTTAAACG-TTACG
1 AAATCTAAATTTTAAACGATTACA
29624988 AAAT
1 AAAT
29624992 TGTTCTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 8 0.33
23 11 0.46
24 5 0.21
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.34
Consensus pattern (24 bp):
AAATCTAAATTTTAAACGATTACA
Found at i:29625083 original size:215 final size:216
Alignment explanation
Indices: 29624782--29625200 Score: 673
Period size: 215 Copynumber: 1.9 Consensus size: 216
29624772 GGAATTGGTA
* ** * *
29624782 TTTGATTTTGGCAATTAAGAGATTTTAAATATATTTTGTCGTTGTCTTCTTTTTAAATCTAATTT
1 TTTGATTTTGGCAATTAAGAGATTTTAAATATATTCTACCCTTATCTTCTTTTTAAATCTAATTT
* *
29624847 TTTAAATTGTTATAAAATCAAATTCACCTTATGAAATTGGTCTTTGATTTTGACAGTT-AAGATA
66 TTTAAATTATTACAAAATCAAATTCACCTTATGAAATTGGTCTTTGATTTTGACAGTTGAA-ATA
* *
29624911 TTTTAAATATATTTTATCATTAT-TTCTTTTTAAATCTAATTTTTAAACGATTACAAAATCAAAT
130 TTTTAAATATATTCTATCATTATCTTCTTTTTAAATCTAATGTTTAAACGATTACAAAATCAAAT
29624975 TTTAAACGTTACGAAATTGTTC
195 TTTAAACGTTACGAAATTGTTC
*
29624997 TTTGATTTTGGCAATTAAGAGATTTTTAAATATATTCTACCCTTATCTTCTTTTTAAATTTAA-T
1 TTTGATTTTGGCAATTAAGAGA-TTTTAAATATATTCTACCCTTATCTTCTTTTTAAATCTAATT
* *
29625061 TTTTAAATTATTACAGAATCAAATTCACCTTATGAAATTGGTCTTTGATTTTGGCAGTTGAAATA
65 TTTTAAATTATTACAAAATCAAATTCACCTTATGAAATTGGTCTTTGATTTTGACAGTTGAAATA
*
29625126 TTTTAAATATATTCTATCATTATCTTCTTTTTAAATCTAATGTTTAAATGATTACAAAATCAAAT
130 TTTTAAATATATTCTATCATTATCTTCTTTTTAAATCTAATGTTTAAACGATTACAAAATCAAAT
*
29625191 TTTACACGTT
195 TTTAAACGTT
29625201 TATTTCTGAT
Statistics
Matches: 187, Mismatches: 14, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
215 103 0.55
216 84 0.45
ACGTcount: A:0.33, C:0.10, G:0.09, T:0.47
Consensus pattern (216 bp):
TTTGATTTTGGCAATTAAGAGATTTTAAATATATTCTACCCTTATCTTCTTTTTAAATCTAATTT
TTTAAATTATTACAAAATCAAATTCACCTTATGAAATTGGTCTTTGATTTTGACAGTTGAAATAT
TTTAAATATATTCTATCATTATCTTCTTTTTAAATCTAATGTTTAAACGATTACAAAATCAAATT
TTAAACGTTACGAAATTGTTC
Found at i:29629498 original size:138 final size:139
Alignment explanation
Indices: 29629238--29629513 Score: 401
Period size: 138 Copynumber: 2.0 Consensus size: 139
29629228 TAAGGTATAA
* *
29629238 GTGATATTTTTTGTACCTTGGTAGTTATATATTTTCAGCTTTTTCATCTTAAAGAATTGGTTTTT
1 GTGATATTTTTTGTACCTTGGTAGTTATATATTTTCAACTTTTTCATCTTAAAGAATTGGTTTTA
* * * *
29629303 GACACTTAAAATATATATACTGCTATTATATTTCTTTTTGAGTTGTTAGGTTCTTTCTTCCTTCA
66 GACACTTAAAATATATATACTACGATTATATTCCTCTTTGAGTTGTTAGGTTCTTTCTTCCTTCA
29629368 ATTTTCTGC
131 ATTTTCTGC
* *
29629377 GTGATA-TTTTTGTAGCTTGGTGGTTATATATTTTCAACTTTTTCATCTTAAAGAATTGGTTTTA
1 GTGATATTTTTTGTACCTTGGTAGTTATATATTTTCAACTTTTTCATCTTAAAGAATTGGTTTTA
* * ** * * * *
29629441 GACATTTAAGATATATATTTTACGATTATCTTCCTCTTTGAGTTGTTAGGTTGTTTCTTTCTTTA
66 GACACTTAAAATATATATACTACGATTATATTCCTCTTTGAGTTGTTAGGTTCTTTCTTCCTTCA
29629506 ATTTTCTG
131 ATTTTCTG
29629514 TTCCCCATGT
Statistics
Matches: 121, Mismatches: 16, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
138 115 0.95
139 6 0.05
ACGTcount: A:0.22, C:0.12, G:0.14, T:0.52
Consensus pattern (139 bp):
GTGATATTTTTTGTACCTTGGTAGTTATATATTTTCAACTTTTTCATCTTAAAGAATTGGTTTTA
GACACTTAAAATATATATACTACGATTATATTCCTCTTTGAGTTGTTAGGTTCTTTCTTCCTTCA
ATTTTCTGC
Found at i:29636409 original size:17 final size:17
Alignment explanation
Indices: 29636365--29636409 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
29636355 TTTAGAATCC
*
29636365 TATTTTATTTAGTATTT
1 TATTTTATTTAGGATTT
* **
29636382 TAATTGGTTTAGGATTT
1 TATTTTATTTAGGATTT
29636399 TATTTTATTTA
1 TATTTTATTTA
29636410 TTTTATTTAG
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.11, T:0.64
Consensus pattern (17 bp):
TATTTTATTTAGGATTT
Found at i:29644820 original size:18 final size:18
Alignment explanation
Indices: 29644799--29644851 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
29644789 TATTATCGTG
29644799 TTTAAATATGTATACATA
1 TTTAAATATGTATACATA
*
29644817 TTTAAATATGTATATATA
1 TTTAAATATGTATACATA
* * *
29644835 TATAAACATATATACAT
1 TTTAAATATGTATACAT
29644852 GATACATTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (18 bp):
TTTAAATATGTATACATA
Found at i:29644993 original size:16 final size:15
Alignment explanation
Indices: 29644968--29645011 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
29644958 ATAAATTTTA
29644968 TATATGTTATTTATAT
1 TATATGTTA-TTATAT
*
29644984 TATATTTTATTATAT
1 TATATGTTATTATAT
29644999 T-TGATGTTATTAT
1 TAT-ATGTTATTAT
29645012 TATTTTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 1 0.04
15 16 0.64
16 8 0.32
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.64
Consensus pattern (15 bp):
TATATGTTATTATAT
Found at i:29669367 original size:49 final size:49
Alignment explanation
Indices: 29669263--29669368 Score: 194
Period size: 49 Copynumber: 2.2 Consensus size: 49
29669253 AAACATTAAG
*
29669263 AAATAGAAATTTCATTAATCCAACTTTCATGACCTACCACCTCGAAAAC
1 AAATAGTAATTTCATTAATCCAACTTTCATGACCTACCACCTCGAAAAC
*
29669312 AAATAGTAATTTCATTAATCCAACTTTCATGACCTACCACTTCGAAAAC
1 AAATAGTAATTTCATTAATCCAACTTTCATGACCTACCACCTCGAAAAC
29669361 AAATAGTA
1 AAATAGTA
29669369 TATACAGTAT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 55 1.00
ACGTcount: A:0.42, C:0.24, G:0.07, T:0.28
Consensus pattern (49 bp):
AAATAGTAATTTCATTAATCCAACTTTCATGACCTACCACCTCGAAAAC
Found at i:29674037 original size:17 final size:18
Alignment explanation
Indices: 29674006--29674053 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
29673996 ATTTAATTAA
*
29674006 TTTGTATTAAAATTTTGT
1 TTTGTATTAAAATTTTAT
*
29674024 TTTG-ATTAATATTTTAT
1 TTTGTATTAAAATTTTAT
* *
29674041 TTTTTATAAAAAT
1 TTTGTATTAAAAT
29674054 ATATTAAACA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
17 14 0.58
18 10 0.42
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.60
Consensus pattern (18 bp):
TTTGTATTAAAATTTTAT
Found at i:29686068 original size:2 final size:2
Alignment explanation
Indices: 29686061--29686096 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
29686051 ATGATATTTG
* *
29686061 AT AT AT AT AT AT AT AT AC AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29686097 GACGAAAGGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:29686082 original size:12 final size:12
Alignment explanation
Indices: 29686061--29686096 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
29686051 ATGATATTTG
*
29686061 ATATATATATAT
1 ATATACATATAT
29686073 ATATACATATAT
1 ATATACATATAT
29686085 ATATACATATAT
1 ATATACATATAT
29686097 GACGAAAGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (12 bp):
ATATACATATAT
Found at i:29697561 original size:19 final size:20
Alignment explanation
Indices: 29697534--29697580 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
29697524 AACAAAGAGC
*
29697534 AAAAGAAAGCAGAGCAAA-A-
1 AAAAAAAAGCAGAG-AAACAG
29697553 AAAAAAAAGCAGAGAAACAG
1 AAAAAAAAGCAGAGAAACAG
29697573 AAAAAAAA
1 AAAAAAAA
29697581 ATAGTATGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 3 0.12
19 14 0.56
20 8 0.32
ACGTcount: A:0.74, C:0.09, G:0.17, T:0.00
Consensus pattern (20 bp):
AAAAAAAAGCAGAGAAACAG
Found at i:29698176 original size:2 final size:2
Alignment explanation
Indices: 29698169--29698246 Score: 104
Period size: 2 Copynumber: 39.0 Consensus size: 2
29698159 AATTTATAGC
* *
29698169 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT TT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
**
29698210 ACT NC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29698247 TATTTTATTT
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.02
2 64 0.97
3 1 0.02
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:29700127 original size:30 final size:30
Alignment explanation
Indices: 29700024--29700127 Score: 90
Period size: 30 Copynumber: 3.5 Consensus size: 30
29700014 ATACAAATTT
*
29700024 AAATAAGTCTTTATATTTTAATTATGTTTAATC
1 AAATAAGTCTTTATA-TTT--TTATTTTTAATC
* * *
29700057 AAAT-A---TTAATATTTTTATTTTTAGTT
1 AAATAAGTCTTTATATTTTTATTTTTAATC
* *
29700083 AAATAAATTTTTATATTTTTATTTTTAATC
1 AAATAAGTCTTTATATTTTTATTTTTAATC
*
29700113 AAATAAGTCATTATA
1 AAATAAGTCTTTATA
29700128 GTTAAGAATT
Statistics
Matches: 57, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
26 13 0.23
27 1 0.02
28 3 0.05
29 5 0.09
30 30 0.53
32 1 0.02
33 4 0.07
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (30 bp):
AAATAAGTCTTTATATTTTTATTTTTAATC
Found at i:29700221 original size:33 final size:33
Alignment explanation
Indices: 29700177--29700271 Score: 93
Period size: 33 Copynumber: 2.9 Consensus size: 33
29700167 ATATCACGTA
* * * * *
29700177 ACGTAACATGTTAATCTATTATAACTGATGATG
1 ACGTAATATGTTAATATATCATAACTAATAATG
* *
29700210 ATGTAATATGTTAATATATCATAATTAATAATG
1 ACGTAATATGTTAATATATCATAACTAATAATG
* * *
29700243 ACGTGATATGTTAATTTAACATAA-TAATA
1 ACGTAATATGTTAATATATCATAACTAATA
29700272 TGATAATATG
Statistics
Matches: 51, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
32 5 0.10
33 46 0.90
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.39
Consensus pattern (33 bp):
ACGTAATATGTTAATATATCATAACTAATAATG
Found at i:29701102 original size:18 final size:17
Alignment explanation
Indices: 29701075--29701137 Score: 67
Period size: 16 Copynumber: 3.7 Consensus size: 17
29701065 ATATAAATTT
29701075 ATAAAA-AAAATTTAAA
1 ATAAAATAAAATTTAAA
29701091 ATAAAGATAAAATTTTAAA
1 ATAAA-ATAAAA-TTTAAA
* *
29701110 ATTATA-AAAATTTAAA
1 ATAAAATAAAATTTAAA
*
29701126 ACAAAATAAAAT
1 ATAAAATAAAAT
29701138 AATATATATA
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
16 14 0.37
17 10 0.26
18 5 0.13
19 9 0.24
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (17 bp):
ATAAAATAAAATTTAAA
Found at i:29701879 original size:15 final size:14
Alignment explanation
Indices: 29701855--29701900 Score: 60
Period size: 14 Copynumber: 3.3 Consensus size: 14
29701845 ATCAAAATCA
29701855 TAAA-TAAAAATTAT
1 TAAATTAAAAA-TAT
29701869 TAAATTAAAAAT-T
1 TAAATTAAAAATAT
29701882 TAAAGTTAAAAATAT
1 TAAA-TTAAAAATAT
29701897 TAAA
1 TAAA
29701901 AATAAAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
13 5 0.17
14 13 0.45
15 11 0.38
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (14 bp):
TAAATTAAAAATAT
Found at i:29701906 original size:15 final size:15
Alignment explanation
Indices: 29701856--29701907 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
29701846 TCAAAATCAT
29701856 AAATAAAAATTATT-A
1 AAATAAAAA-TATTAA
*
29701871 AATTAAAAAT-TTAA
1 AAATAAAAATATTAA
**
29701885 AGTTAAAAATATTAA
1 AAATAAAAATATTAA
29701900 AAATAAAA
1 AAATAAAA
29701908 TAAGTAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
13 2 0.06
14 11 0.35
15 18 0.58
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (15 bp):
AAATAAAAATATTAA
Found at i:29706043 original size:16 final size:18
Alignment explanation
Indices: 29706024--29706056 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
29706014 TACAATGAAC
29706024 ATTAATT-TTT-TAAATT
1 ATTAATTATTTATAAATT
29706040 ATTAATTATTTATAAAT
1 ATTAATTATTTATAAAT
29706057 AGTTGAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTAATTATTTATAAATT
Found at i:29710035 original size:16 final size:16
Alignment explanation
Indices: 29710011--29710041 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29710001 ATTATGTGAT
*
29710011 AATAGAATAAAATAAA
1 AATAAAATAAAATAAA
29710027 AATAAAATAAAATAA
1 AATAAAATAAAATAA
29710042 TTATTACTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.19
Consensus pattern (16 bp):
AATAAAATAAAATAAA
Found at i:29710206 original size:16 final size:19
Alignment explanation
Indices: 29710168--29710207 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
29710158 ATAAAAACAT
*
29710168 ATTTTATTATTTATGTGAT
1 ATTTTATTATTTATGTGAG
29710187 ATTTTATT-TTTAT-T-AG
1 ATTTTATTATTTATGTGAG
29710203 ATTTT
1 ATTTT
29710208 TTAAATATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 6 0.30
17 1 0.05
18 5 0.25
19 8 0.40
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68
Consensus pattern (19 bp):
ATTTTATTATTTATGTGAG
Found at i:29710271 original size:89 final size:90
Alignment explanation
Indices: 29710172--29710339 Score: 225
Period size: 89 Copynumber: 1.9 Consensus size: 90
29710162 AAACATATTT
* *
29710172 TATTATTTATG-TG-ATATTTTATTTTTATTAGATTTTTTAAATATTAATAATTTAGAATTTAAT
1 TATTATTTATGATGAAT-TTTTA-TTTTATTAGATTTTTAAAATATTAATAATTGAGAATTTAAT
*
29710235 TAAAATATTCATAATTAATCATTTAAA
64 TAAAATATTAATAATTAATCATTTAAA
* ** * *
29710262 TATTA-TTATGATTAATTTTTATTTTATTTTATTTTTAAAATATTAATAATTGATAATTTATTTA
1 TATTATTTATGATGAATTTTTATTTTATTAGATTTTTAAAATATTAATAATTGAGAATTTAATTA
29710326 AAATATTAATAATT
66 AAATATTAATAATT
29710340 GATAATTTCA
Statistics
Matches: 68, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
89 55 0.81
90 11 0.16
91 2 0.03
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (90 bp):
TATTATTTATGATGAATTTTTATTTTATTAGATTTTTAAAATATTAATAATTGAGAATTTAATTA
AAATATTAATAATTAATCATTTAAA
Found at i:29710328 original size:27 final size:27
Alignment explanation
Indices: 29710295--29710347 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
29710285 TTATTTTATT
29710295 TTTAAAATATTAATAATTGATAATTTA
1 TTTAAAATATTAATAATTGATAATTTA
29710322 TTTAAAATATTAATAATTGATAATTT
1 TTTAAAATATTAATAATTGATAATTT
29710348 CAATANNNNN
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (27 bp):
TTTAAAATATTAATAATTGATAATTTA
Found at i:29723932 original size:2 final size:2
Alignment explanation
Indices: 29723925--29723978 Score: 81
Period size: 2 Copynumber: 26.5 Consensus size: 2
29723915 ACAGCCATGA
29723925 AT AT AT AT AT AT AT AT AT AT AT AT AT AT NAT 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
* *
29723968 GT AT GT AT AT A
1 AT AT AT AT AT A
29723979 CATGATTTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
2 45 0.96
3 2 0.04
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29724503 original size:3 final size:3
Alignment explanation
Indices: 29724497--29724526 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
29724487 AAAATAAACA
*
29724497 TAT TAT TAT TAT TAT GAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
29724527 AGATATAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:29734248 original size:17 final size:17
Alignment explanation
Indices: 29734219--29734251 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
29734209 ATTTATTATT
29734219 ATTATTATAAATATAAA
1 ATTATTATAAATATAAA
29734236 ATTA-TATATAATATAA
1 ATTATTATA-AATATAA
29734252 TTATTTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATTATTATAAATATAAA
Found at i:29738838 original size:2 final size:2
Alignment explanation
Indices: 29738831--29738867 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
29738821 AACCCAAAGA
29738831 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29738868 GATGCAAGCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:29740652 original size:33 final size:33
Alignment explanation
Indices: 29740610--29740675 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
29740600 CCCAGAATCA
29740610 AAATCCAAGACATAATAACTCCTGTGAACAAAG
1 AAATCCAAGACATAATAACTCCTGTGAACAAAG
29740643 AAATCCAAGACATAATAACTCCTGTGAACAAAG
1 AAATCCAAGACATAATAACTCCTGTGAACAAAG
29740676 GAGTCTAGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.48, C:0.21, G:0.12, T:0.18
Consensus pattern (33 bp):
AAATCCAAGACATAATAACTCCTGTGAACAAAG
Done.