Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 100 of 290
Found at i:34233554 original size:14 final size:14
Alignment explanation
Indices: 34233508--34233555 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
34233498 TTTTTATTCA
*
34233508 TTTATTATATGGAT
1 TTTATTATATGAAT
*
34233522 TTCATTATAAT-AGAT
1 TTTATTAT-ATGA-AT
34233537 TTTATTATATGAAT
1 TTTATTATATGAAT
34233551 TTTAT
1 TTTAT
34233556 ATTAATATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
14 16 0.57
15 12 0.43
ACGTcount: A:0.33, C:0.02, G:0.08, T:0.56
Consensus pattern (14 bp):
TTTATTATATGAAT
Found at i:34234119 original size:22 final size:23
Alignment explanation
Indices: 34234076--34234124 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
34234066 ATGTATACCT
*
34234076 TTTTAGAATTTTATAATTATATA
1 TTTTAGAATTTTATAATAATATA
34234099 TTTTA-AATTTTTATAA-AATATA
1 TTTTAGAA-TTTTATAATAATATA
34234121 TTTT
1 TTTT
34234125 TAAAAGAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (23 bp):
TTTTAGAATTTTATAATAATATA
Found at i:34238308 original size:40 final size:39
Alignment explanation
Indices: 34238277--34238486 Score: 233
Period size: 40 Copynumber: 5.3 Consensus size: 39
34238267 GGACTAAGAT
* *
34238277 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
1 CCGAAGGCATTCGTGCGAGATACAAA-TCCGGGTTAAGTC
* *
34238317 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
* *
34238357 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* ** *
34238397 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGAT-ACAAATCCGGGTTAAGTC
* * * * *
34238437 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
34238476 CCGAAGGCATT
1 CCGAAGGCATT
34238487 TGAACGAGGA
Statistics
Matches: 153, Mismatches: 13, Indels: 9
0.87 0.07 0.05
Matches are distributed among these distances:
39 33 0.22
40 117 0.76
41 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGAAGGCATTCGTGCGAGATACAAATCCGGGTTAAGTC
Found at i:34238440 original size:120 final size:120
Alignment explanation
Indices: 34238224--34238486 Score: 300
Period size: 120 Copynumber: 2.2 Consensus size: 120
34238214 TTGAATGCTG
* *
34238224 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
* *
34238288 TGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
66 CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACTAAA
* * * * **
34238344 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGAT-CCGAAGGCAT
* ** * * * *
34238407 TCGTGCGAGTTGTTAAA-TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
65 TCGTGCGAGAT-ACAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
* *
34238463 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
34238487 TGAACGAGGA
Statistics
Matches: 120, Mismatches: 20, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
119 38 0.32
120 73 0.61
121 9 0.08
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:34238506 original size:79 final size:80
Alignment explanation
Indices: 34238277--34238521 Score: 228
Period size: 80 Copynumber: 3.1 Consensus size: 80
34238267 GGACTAAGAT
* * * * * * * ** *
34238277 CCGAAGGCATTTGTGCGAGATAC-AAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGA-GATAC
1 CCGAAGGCATTCGTGCGAGTTACTAAA-ACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGA-GC
34238340 TAAATCCGGGTTAAGTC
64 TAAATCCGGGTTAAGTC
* * * ** ** *
34238357 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTA
1 CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
*
34238422 AATCCGGGTTATGTC
66 AATCCGGGTTAAGTC
* * *
34238437 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTGAACGAGGAGCTA
1 CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
* *
34238501 TATCC-GGTTAAATC
66 AATCCGGGTTAAGTC
34238515 CCGAAGG
1 CCGAAGG
34238522 TACGTGATTT
Statistics
Matches: 138, Mismatches: 25, Indels: 6
0.82 0.15 0.04
Matches are distributed among these distances:
78 14 0.10
79 46 0.33
80 75 0.54
81 3 0.02
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
AATCCGGGTTAAGTC
Found at i:34246258 original size:40 final size:39
Alignment explanation
Indices: 34246227--34246436 Score: 233
Period size: 40 Copynumber: 5.3 Consensus size: 39
34246217 GGACTAAGAT
* *
34246227 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
1 CCGAAGGCATTCGTGCGAGATACAAA-TCCGGGTTAAGTC
* *
34246267 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
* *
34246307 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* ** *
34246347 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGAT-ACAAATCCGGGTTAAGTC
* * * * *
34246387 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
34246426 CCGAAGGCATT
1 CCGAAGGCATT
34246437 TGAACGAGGA
Statistics
Matches: 153, Mismatches: 13, Indels: 9
0.87 0.07 0.05
Matches are distributed among these distances:
39 33 0.22
40 117 0.76
41 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGAAGGCATTCGTGCGAGATACAAATCCGGGTTAAGTC
Found at i:34246390 original size:120 final size:120
Alignment explanation
Indices: 34246174--34246436 Score: 300
Period size: 120 Copynumber: 2.2 Consensus size: 120
34246164 TTGAATGCTG
* *
34246174 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
* *
34246238 TGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
66 CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACTAAA
* * * * **
34246294 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGAT-CCGAAGGCAT
* ** * * * *
34246357 TCGTGCGAGTTGTTAAA-TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
65 TCGTGCGAGAT-ACAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
* *
34246413 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
34246437 TGAACGAGGA
Statistics
Matches: 120, Mismatches: 20, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
119 38 0.32
120 73 0.61
121 9 0.08
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:34246456 original size:79 final size:80
Alignment explanation
Indices: 34246227--34246471 Score: 228
Period size: 80 Copynumber: 3.1 Consensus size: 80
34246217 GGACTAAGAT
* * * * * * * ** *
34246227 CCGAAGGCATTTGTGCGAGATAC-AAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGA-GATAC
1 CCGAAGGCATTCGTGCGAGTTACTAAA-ACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGA-GC
34246290 TAAATCCGGGTTAAGTC
64 TAAATCCGGGTTAAGTC
* * * ** ** *
34246307 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTA
1 CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
*
34246372 AATCCGGGTTATGTC
66 AATCCGGGTTAAGTC
* * *
34246387 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTGAACGAGGAGCTA
1 CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
* *
34246451 TATCC-GGTTAAATC
66 AATCCGGGTTAAGTC
34246465 CCGAAGG
1 CCGAAGG
34246472 TACGTGATTT
Statistics
Matches: 138, Mismatches: 25, Indels: 6
0.82 0.15 0.04
Matches are distributed among these distances:
78 14 0.10
79 46 0.33
80 75 0.54
81 3 0.02
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
AATCCGGGTTAAGTC
Found at i:34249969 original size:78 final size:81
Alignment explanation
Indices: 34249815--34249975 Score: 283
Period size: 78 Copynumber: 2.0 Consensus size: 81
34249805 TGTTCACCAA
34249815 AAAAAAATCCAACTCTATTATTTATTTTATGATATATTTTTTATTTTTATTTATATGATAAATAA
1 AAAAAAATCCAACTCTATTATTTATTTTATGA-ATA-TTTTTATTTTTATTTATATGATAAATAA
34249880 TATAATATAAATATTATT
64 TATAATATAAATATTATT
34249898 AAAAAAATCCAACTCTATTATTTATTTTATG-ATA-TTTT-TTTTTATTTATATGATAAATAATA
1 AAAAAAATCCAACTCTATTATTTATTTTATGAATATTTTTATTTTTATTTATATGATAAATAATA
34249960 TAATATAAATATTATT
66 TAATATAAATATTATT
34249976 CCGAAACGTC
Statistics
Matches: 78, Mismatches: 0, Indels: 5
0.94 0.00 0.06
Matches are distributed among these distances:
78 40 0.51
79 4 0.05
81 3 0.04
83 31 0.40
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.50
Consensus pattern (81 bp):
AAAAAAATCCAACTCTATTATTTATTTTATGAATATTTTTATTTTTATTTATATGATAAATAATA
TAATATAAATATTATT
Found at i:34250055 original size:26 final size:23
Alignment explanation
Indices: 34249998--34250055 Score: 62
Period size: 28 Copynumber: 2.3 Consensus size: 23
34249988 TTATTTCTAT
34249998 TTAAAATTTTAATAAATATATAA
1 TTAAAATTTTAATAAATATATAA
*
34250021 TTACTAAATTTTAAATAAAATAATATAC
1 TTA--AAATTTT-AAT-AAAT-ATATAA
34250049 TTAAAAT
1 TTAAAAT
34250056 ATGAAAACAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
23 3 0.10
25 7 0.24
26 7 0.24
27 4 0.14
28 8 0.28
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (23 bp):
TTAAAATTTTAATAAATATATAA
Found at i:34259145 original size:25 final size:26
Alignment explanation
Indices: 34259116--34259164 Score: 75
Period size: 25 Copynumber: 1.9 Consensus size: 26
34259106 AAGCAGCAGC
34259116 AAGGAGAA-GAAAAGAAAA-AGAAAGA
1 AAGGAGAAGGAAAA-AAAATAGAAAGA
34259141 AAGGAGAAGGAAAAAAAATAGAAA
1 AAGGAGAAGGAAAAAAAATAGAAA
34259165 AGAGAAAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (26 bp):
AAGGAGAAGGAAAAAAAATAGAAAGA
Found at i:34259293 original size:43 final size:43
Alignment explanation
Indices: 34259246--34259388 Score: 183
Period size: 43 Copynumber: 3.5 Consensus size: 43
34259236 TGATTTTTTT
*
34259246 TTGTTAGATATTATTATTGTTAGTAAAAAAACCCTTATTATTA
1 TTGTTAGTTATTATTATTGTTAGTAAAAAAACCCTTATTATTA
** **
34259289 TTGTTAGTTATTATTATTGTTAGTAAAAAAACTATTATTAGGA
1 TTGTTAGTTATTATTATTGTTAGTAAAAAAACCCTTATTATTA
*
34259332 TTGTT-G--GTTATTATTGTTAGT-AAAAAA-CCTTA--ATTA
1 TTGTTAGTTATTATTATTGTTAGTAAAAAAACCCTTATTATTA
34259368 TTGTTAGTTATTATTATTGTT
1 TTGTTAGTTATTATTATTGTT
34259389 GATTTATATT
Statistics
Matches: 86, Mismatches: 11, Indels: 10
0.80 0.10 0.09
Matches are distributed among these distances:
36 7 0.08
37 1 0.01
38 3 0.03
39 17 0.20
40 14 0.16
42 1 0.01
43 43 0.50
ACGTcount: A:0.34, C:0.04, G:0.13, T:0.50
Consensus pattern (43 bp):
TTGTTAGTTATTATTATTGTTAGTAAAAAAACCCTTATTATTA
Found at i:34259301 original size:16 final size:16
Alignment explanation
Indices: 34259280--34259312 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
34259270 AAAAAAACCC
34259280 TTATTATTATTGTTAG
1 TTATTATTATTGTTAG
34259296 TTATTATTATTGTTAG
1 TTATTATTATTGTTAG
34259312 T
1 T
34259313 AAAAAAACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (16 bp):
TTATTATTATTGTTAG
Found at i:34259325 original size:40 final size:40
Alignment explanation
Indices: 34259246--34259388 Score: 175
Period size: 40 Copynumber: 3.5 Consensus size: 40
34259236 TGATTTTTTT
*
34259246 TTGTTAGATATTATTATTGTTAGTAAAAAAACCCTTATTATTA
1 TTGTTAGTTATTATTATTGTTAGTAAAAAAA--C-TATTATTA
34259289 TTGTTAGTTATTATTATTGTTAGTAAAAAAACTATTATTA
1 TTGTTAGTTATTATTATTGTTAGTAAAAAAACTATTATTA
* * * *
34259329 -GGATT-GTTGGTTATTATTGTTAGTAAAAAACCT-TAATTA
1 TTG-TTAGTT-ATTATTATTGTTAGTAAAAAAACTATTATTA
34259368 TTGTTAGTTATTATTATTGTT
1 TTGTTAGTTATTATTATTGTT
34259389 GATTTATATT
Statistics
Matches: 89, Mismatches: 7, Indels: 12
0.82 0.06 0.11
Matches are distributed among these distances:
39 22 0.25
40 36 0.40
41 1 0.01
43 30 0.34
ACGTcount: A:0.34, C:0.04, G:0.13, T:0.50
Consensus pattern (40 bp):
TTGTTAGTTATTATTATTGTTAGTAAAAAAACTATTATTA
Found at i:34259878 original size:16 final size:16
Alignment explanation
Indices: 34259857--34259889 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
34259847 CTTAGAGGGG
34259857 CATTAATAGAACGGGA
1 CATTAATAGAACGGGA
34259873 CATTAATAGAACGGGA
1 CATTAATAGAACGGGA
34259889 C
1 C
34259890 CATCAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.15, G:0.24, T:0.18
Consensus pattern (16 bp):
CATTAATAGAACGGGA
Found at i:34266451 original size:150 final size:151
Alignment explanation
Indices: 34265863--34266534 Score: 1082
Period size: 151 Copynumber: 4.5 Consensus size: 151
34265853 TATTTTTAAA
*
34265863 ATTTTTAAAATTTTCGGATTCTATTTTTTAAAATATACTATTTTCGTATTTTATTTTTTATATTA
1 ATTTTTAAAATTTTCGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTTTTATATTA
34265928 TTTTAGTACATAATGCTTCAAATGCATTATTCTAGTGTTTTTTATATTAATTTAGTAAATAACCC
66 TTTTAGTACATAATGCTTCAAATGCATTATTCTAGTGTTTTTTATATTAATTTAGTAAATAACCC
34265993 TGATCTTAGCCCTTTGTTTGT
131 TGATCTTAGCCCTTTGTTTGT
*
34266014 ATTTTTAAAATTTTCAGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTTTTATATTA
1 ATTTTTAAAATTTTCGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTTTTATATTA
34266079 TTTTAGTACATAATGCTTCAAATGCATTATTCTAGTGTTTTTTATATTAATTTAGTAAATAACCC
66 TTTTAGTACATAATGCTTCAAATGCATTATTCTAGTGTTTTTTATATTAATTTAGTAAATAACCC
34266144 TGATCTTAGCCCTTTGTTTGT
131 TGATCTTAGCCCTTTGTTTGT
* *
34266165 ATTTTTAAAATTTTCAGATTTTATTTTTTAAAATATACTATTTTCGTATTTCATTTTTTTATATT
1 ATTTTTAAAATTTTCGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTA-TTTTTTATATT
* * *
34266230 ATTTTAGTACATAATGGTTCAAATGTATTATTTTAGTG-TTTTTATATTAATTTAGTAAATAACC
65 ATTTTAGTACATAATGCTTCAAATGCATTATTCTAGTGTTTTTTATATTAATTTAGTAAATAACC
* * *
34266294 TTGATTTTGGCCCTTTGTTTGT
130 CTGATCTTAGCCCTTTGTTTGT
*
34266316 ATTTTTAAAATTTTTGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTTTTATATTA
1 ATTTTTAAAATTTTCGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTTTTATATTA
* * * *
34266381 TTTTAGTATATAATGTTTCAAATGTATTATTTTAGTG-TTTTTATATTAATTTAGTAAATAACCC
66 TTTTAGTACATAATGCTTCAAATGCATTATTCTAGTGTTTTTTATATTAATTTAGTAAATAACCC
* * * *
34266445 TAAT-TTTGTCTCTTT-TTTAT
131 TGATCTTAG-CCCTTTGTTTGT
* **
34266465 ATTTTTAAAATTTTTGGATTTTATTTTTTAAAATATACTATTTTCGTGCTTTATTTTTATATATT
1 ATTTTTAAAATTTTCGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTTT-TATATT
*
34266530 TTTTT
65 ATTTT
34266535 TAAAAAAACC
Statistics
Matches: 496, Mismatches: 22, Indels: 7
0.94 0.04 0.01
Matches are distributed among these distances:
149 63 0.13
150 91 0.18
151 296 0.60
152 46 0.09
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.56
Consensus pattern (151 bp):
ATTTTTAAAATTTTCGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTTTTATATTA
TTTTAGTACATAATGCTTCAAATGCATTATTCTAGTGTTTTTTATATTAATTTAGTAAATAACCC
TGATCTTAGCCCTTTGTTTGT
Found at i:34266625 original size:16 final size:16
Alignment explanation
Indices: 34266570--34266635 Score: 62
Period size: 16 Copynumber: 4.2 Consensus size: 16
34266560 GCCCCCAAAA
*
34266570 TTTATTTTTTTCATAT
1 TTTATTTTTTTAATAT
* *
34266586 TTTATTTTTTTAGTAA
1 TTTATTTTTTTAATAT
**
34266602 GATA-TTTTTTAATAT
1 TTTATTTTTTTAATAT
* *
34266617 TTTATTTTTATACTAT
1 TTTATTTTTTTAATAT
34266633 TTT
1 TTT
34266636 CGTAAAATAG
Statistics
Matches: 38, Mismatches: 11, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
15 11 0.29
16 27 0.71
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.70
Consensus pattern (16 bp):
TTTATTTTTTTAATAT
Found at i:34266832 original size:21 final size:21
Alignment explanation
Indices: 34266807--34266849 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
34266797 ATGAATGAAA
34266807 ATATAAAATAAATACAAACAT
1 ATATAAAATAAATACAAACAT
34266828 ATATAAAATAAATACAAACAT
1 ATATAAAATAAATACAAACAT
34266849 A
1 A
34266850 CCTTAATATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.67, C:0.09, G:0.00, T:0.23
Consensus pattern (21 bp):
ATATAAAATAAATACAAACAT
Found at i:34267089 original size:21 final size:20
Alignment explanation
Indices: 34267053--34267093 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
34267043 TGCCCCCTGC
34267053 TTCTCCTTCTCTTCTTTCTT
1 TTCTCCTTCTCTTCTTTCTT
*
34267073 TTCTTCTTCTCCTTCTTTCTT
1 TTCTCCTTCT-CTTCTTTCTT
34267094 CCCAAAATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (20 bp):
TTCTCCTTCTCTTCTTTCTT
Found at i:34274180 original size:15 final size:15
Alignment explanation
Indices: 34274155--34274228 Score: 67
Period size: 15 Copynumber: 4.7 Consensus size: 15
34274145 AAAATAACAA
34274155 ATTATATATTTTTTAT
1 ATTA-ATATTTTTTAT
*
34274171 ATTAATATTTTTTAA
1 ATTAATATTTTTTAT
* * *
34274186 AATATTGTTTTTTAACT
1 ATTAATATTTTTT-A-T
*
34274203 AATAATATATTTTTAT
1 ATTAATAT-TTTTTAT
34274219 ATTAATATTT
1 ATTAATATTT
34274229 ATATATATCT
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
15 22 0.47
16 13 0.28
17 7 0.15
18 5 0.11
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (15 bp):
ATTAATATTTTTTAT
Found at i:34276698 original size:13 final size:13
Alignment explanation
Indices: 34276682--34276706 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34276672 AATTTAAGTA
34276682 TATATTATATTAT
1 TATATTATATTAT
34276695 TATATTATATTA
1 TATATTATATTA
34276707 ATTAAATAAA
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TATATTATATTAT
Found at i:34276719 original size:38 final size:40
Alignment explanation
Indices: 34276641--34276719 Score: 94
Period size: 38 Copynumber: 2.0 Consensus size: 40
34276631 AATAATATAC
* *
34276641 ATATATTAATAATTATTATATATTTACTTATAATTTAAGT
1 ATATATTAATAATTATTATATATTTAATTATAATTAAAGT
34276681 ATATATT-AT-ATTATTATATTATATTAATTA-AA-TAAAGT
1 ATATATTAATAATTATTATA-TAT-TTAATTATAATTAAAGT
34276719 A
1 A
34276720 AATAAATTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
38 15 0.43
39 7 0.20
40 13 0.37
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.51
Consensus pattern (40 bp):
ATATATTAATAATTATTATATATTTAATTATAATTAAAGT
Found at i:34276927 original size:13 final size:13
Alignment explanation
Indices: 34276909--34276945 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
34276899 AAAACAGGGG
* *
34276909 AAAGAAAGGAGGA
1 AAAGAAAGAAAGA
34276922 AAAGAAAGAAAGA
1 AAAGAAAGAAAGA
34276935 AAAGAAAGAAA
1 AAAGAAAGAAA
34276946 AGGAAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (13 bp):
AAAGAAAGAAAGA
Found at i:34280910 original size:93 final size:93
Alignment explanation
Indices: 34280798--34280969 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
34280788 CGCCCATAAG
* *
34280798 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
34280863 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
34280891 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
34280956 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
34280970 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:34280966 original size:46 final size:46
Alignment explanation
Indices: 34280791--34280966 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
34280781 TGTAACCCGC
* * *
34280791 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
34280837 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
34280887 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
34280930 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
34280967 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:34285777 original size:143 final size:143
Alignment explanation
Indices: 34285519--34285807 Score: 551
Period size: 143 Copynumber: 2.0 Consensus size: 143
34285509 AAAACCAAAG
*
34285519 TTTATATATGACGGACACTACAGCAAAACAGGTTTTTAGCGGCCTTTTTTTGGGAGCAAAAAATT
1 TTTATATATGACGGACACTACAGCAAAACAGGTTTTTAGCGGCCTTTTTTTGGGAGCAAAAAATG
34285584 CCGCTAAAGACAACACCACTAACATTTTGCGGCGTTTAGGTAAGAAACACCACTAAAGAACATGA
66 CCGCTAAAGACAACACCACTAACATTTTGCGGCGTTTAGGTAAGAAACACCACTAAAGAACATGA
34285649 CCTTTAGCGGTGT
131 CCTTTAGCGGTGT
*
34285662 TTTATATATGACGGACACTACAGCAAAACAGGTTTTTAGTGGCCTTTTTTTGGGAGCAAAAAATG
1 TTTATATATGACGGACACTACAGCAAAACAGGTTTTTAGCGGCCTTTTTTTGGGAGCAAAAAATG
*
34285727 CCGCTAAAGACAACACCGCTAACATTTTGCGGCGTTTAGGTAAGAAACACCACTAAAGAACATGA
66 CCGCTAAAGACAACACCACTAACATTTTGCGGCGTTTAGGTAAGAAACACCACTAAAGAACATGA
34285792 CCTTTAGCGGTGT
131 CCTTTAGCGGTGT
34285805 TTT
1 TTT
34285808 GAGACATGAC
Statistics
Matches: 143, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
143 143 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (143 bp):
TTTATATATGACGGACACTACAGCAAAACAGGTTTTTAGCGGCCTTTTTTTGGGAGCAAAAAATG
CCGCTAAAGACAACACCACTAACATTTTGCGGCGTTTAGGTAAGAAACACCACTAAAGAACATGA
CCTTTAGCGGTGT
Found at i:34285899 original size:42 final size:42
Alignment explanation
Indices: 34285811--34285994 Score: 226
Period size: 42 Copynumber: 4.3 Consensus size: 42
34285801 GTGTTTTGAG
* *
34285811 ACATGACCTTTAGCGGCGCTTTTTTCAAAAACGCCACTAAAGA
1 ACATGACCTTTAGCGGCGCTTTTCTC-AAAACGCCGCTAAAGA
* * *
34285854 ACGTGACCTTTAGTGGCGCTTTTCTCAAAACGCCGCTAAAAA
1 ACATGACCTTTAGCGGCGCTTTTCTCAAAACGCCGCTAAAGA
* * * *
34285896 ACGTGACCTTTAGTGGCGTTTTTCTCAAAACGCTGCTAAAGA
1 ACATGACCTTTAGCGGCGCTTTTCTCAAAACGCCGCTAAAGA
* **
34285938 ACATGACCTTTAGCGGCACTTTTCATACAAAA-AACGCTAAAGA
1 ACATGACCTTTAGCGGCGCTTTTC-T-CAAAACGCCGCTAAAGA
34285981 ACATGACCTTTAGC
1 ACATGACCTTTAGC
34285995 AGCTTTTTTG
Statistics
Matches: 124, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
42 73 0.59
43 46 0.37
44 5 0.04
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (42 bp):
ACATGACCTTTAGCGGCGCTTTTCTCAAAACGCCGCTAAAGA
Found at i:34286073 original size:154 final size:152
Alignment explanation
Indices: 34285857--34286149 Score: 401
Period size: 154 Copynumber: 1.9 Consensus size: 152
34285847 CTAAAGAACG
* * * *
34285857 TGACCTTTAGTGGCGCTTTTCTCAAAACGCCGCTAAAAAACGTGACCTTTAGTGGCGTTTTTCTC
1 TGACCTTTAGCGGCGCTTTTCTCAAAACGCCGCTAAAAAACGTGACATTTAGCGGCGCTTTTCTC
* *
34285922 AAAACGCTGCTAAAGAACATGACCTTTAGCGGCACTTTTCATACAAAAAA-CGCTAAAGAACATG
66 AAAACGCCGCTAAAGAACATGACCTTTAGCAGCACTTTTC-T-CAAAAAACCGCTAAAGAACATG
34285986 ACCTTTAGCAGCTTTTTTGAGACA
129 ACCTTTAGCAGCTTTTTTGAGACA
* * *
34286010 TGACCTTTAGCGGCGCTTTTCATACAAAA-GCCGCTAAAGAATGTGACATTTAGCGGTGCTTTTC
1 TGACCTTTAGCGGCGCTTTTC-T-CAAAACGCCGCTAAAAAACGTGACATTTAGCGGCGCTTTTC
* ** *
34286074 TCAAAACGCCGCTAAAGAACATGACCTTTAGCATCGTTTTTCTCAAAAAACGCCGCTAAAGAACG
64 TCAAAACGCCGCTAAAGAACATGACCTTTAGCAGCACTTTTCTCAAAAAA--CCGCTAAAGAACA
34286139 TGACCTTTAGC
127 TGACCTTTAGC
34286150 GGCGCTTTTC
Statistics
Matches: 122, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
152 7 0.06
153 21 0.17
154 67 0.55
155 27 0.22
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (152 bp):
TGACCTTTAGCGGCGCTTTTCTCAAAACGCCGCTAAAAAACGTGACATTTAGCGGCGCTTTTCTC
AAAACGCCGCTAAAGAACATGACCTTTAGCAGCACTTTTCTCAAAAAACCGCTAAAGAACATGAC
CTTTAGCAGCTTTTTTGAGACA
Found at i:34286093 original size:111 final size:111
Alignment explanation
Indices: 34285899--34286106 Score: 278
Period size: 111 Copynumber: 1.9 Consensus size: 111
34285889 CTAAAAAACG
* * * *
34285899 TGACCTTTAGTGGCGTTTTTCTCAAAACGCTGCTAAAGAACATGACCTTTAGCGGCACTTTTCAT
1 TGACCTTTAGCGGCGCTTTTCTCAAAACGCCGCTAAAGAACATGACATTTAGCGGCACTTTTCAT
34285964 ACAAAAAACGCTAAAGAACATGACCTTTAGCAGCTTTTTTGAGACA
66 ACAAAAAACGCTAAAGAACATGACCTTTAGCAGCTTTTTTGAGACA
** **
34286010 TGACCTTTAGCGGCGCTTTTCATACAAAA-GCCGCTAAAGAATGTGACATTTAGCGGTGCTTTTC
1 TGACCTTTAGCGGCGCTTTTC-T-CAAAACGCCGCTAAAGAACATGACATTTAGCGGCACTTTTC
**
34286074 -T-CAAAACGCCGCTAAAGAACATGACCTTTAGCA
64 ATACAAAA-AACGCTAAAGAACATGACCTTTAGCA
34286107 TCGTTTTTCT
Statistics
Matches: 84, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
110 5 0.06
111 44 0.52
112 30 0.36
113 5 0.06
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (111 bp):
TGACCTTTAGCGGCGCTTTTCTCAAAACGCCGCTAAAGAACATGACATTTAGCGGCACTTTTCAT
ACAAAAAACGCTAAAGAACATGACCTTTAGCAGCTTTTTTGAGACA
Found at i:34286104 original size:42 final size:42
Alignment explanation
Indices: 34286007--34286249 Score: 344
Period size: 42 Copynumber: 5.7 Consensus size: 42
34285997 CTTTTTTGAG
34286007 ACATGACCTTTAGCGGCGCTTTTCATACAAAA-GCCGCTAAAGA
1 ACATGACCTTTAGCGGCGCTTTTC-T-CAAAACGCCGCTAAAGA
** * *
34286050 ATGTGACATTTAGCGGTGCTTTTCTCAAAACGCCGCTAAAGA
1 ACATGACCTTTAGCGGCGCTTTTCTCAAAACGCCGCTAAAGA
** *
34286092 ACATGACCTTTAGCATCGTTTTTCTCAAAAAACGCCGCTAAAGA
1 ACATGACCTTTAGCGGCGCTTTTCTC--AAAACGCCGCTAAAGA
*
34286136 ACGTGACCTTTAGCGGCGCTTTTCTCAAAACGCCGCTAAAGA
1 ACATGACCTTTAGCGGCGCTTTTCTCAAAACGCCGCTAAAGA
* *
34286178 AAATGACCTTTAGCGGCGCTTTTCTCAAAACGTCGCTAAAGA
1 ACATGACCTTTAGCGGCGCTTTTCTCAAAACGCCGCTAAAGA
*
34286220 ACATGACCTTTAGCGGCACTTTTCTCAAAA
1 ACATGACCTTTAGCGGCGCTTTTCTCAAAA
34286250 AACTGCTAAA
Statistics
Matches: 177, Mismatches: 20, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
41 5 0.03
42 114 0.64
43 20 0.11
44 38 0.21
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.26
Consensus pattern (42 bp):
ACATGACCTTTAGCGGCGCTTTTCTCAAAACGCCGCTAAAGA
Found at i:34286114 original size:196 final size:194
Alignment explanation
Indices: 34285779--34286192 Score: 573
Period size: 196 Copynumber: 2.1 Consensus size: 194
34285769 AGAAACACCA
* *
34285779 CTAAAGAACATGACCTTTAGCGGTGTTTTGAGACATGACCTTTAGCGGCGCTTTTTTCAAAAACG
1 CTAAAGAACATGACCTTTAGCGCTGTTTTGAGACATGACCTTTAGCGGCGC-TTTTTCAAAAAAG
* * *
34285844 CCACTAAAGAACGTGACCTTTAGTGGCGCTTTTCTCAAAACGCCGCTAAAAAACGTGACCTTTAG
65 CCACTAAAGAACGTGACATTTAGCGGCGCTTTTCTCAAAACGCCGCTAAAAAACATGACCTTTAG
** *
34285909 TGGCGTTTTTCTC-AAAACGCTGCTAAAGAACATGACCTTTAGCGGCACTTTTCATACAAAA-AA
130 CAGCGTTTTTCTCAAAAACGCCGCTAAAGAACATGACCTTTAGCGGCACTTTTC-T-CAAAACAA
34285972 CG
193 CG
*
34285974 CTAAAGAACATGACCTTTAGCAGCTTTTTTGAGACATGACCTTTAGCGGCGC-TTTTCATACAAA
1 CTAAAGAACATGACCTTTAGC-GCTGTTTTGAGACATGACCTTTAGCGGCGCTTTTTCA-A-AAA
* * * *
34286038 AGCCGCTAAAGAATGTGACATTTAGCGGTGCTTTTCTCAAAACGCCGCTAAAGAACATGACCTTT
63 AGCCACTAAAGAACGTGACATTTAGCGGCGCTTTTCTCAAAACGCCGCTAAAAAACATGACCTTT
* * * *
34286103 AGCATCGTTTTTCTCAAAAAACGCCGCTAAAGAACGTGACCTTTAGCGGCGCTTTTCTCAAAACG
128 AGCAGCGTTTTTCTC-AAAAACGCCGCTAAAGAACATGACCTTTAGCGGCACTTTTCTCAAAACA
*
34286168 CCG
192 ACG
*
34286171 CTAAAGAAAATGACCTTTAGCG
1 CTAAAGAACATGACCTTTAGCG
34286193 GCGCTTTTCT
Statistics
Matches: 194, Mismatches: 19, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
194 6 0.03
195 22 0.11
196 106 0.55
197 23 0.12
198 37 0.19
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.27
Consensus pattern (194 bp):
CTAAAGAACATGACCTTTAGCGCTGTTTTGAGACATGACCTTTAGCGGCGCTTTTTCAAAAAAGC
CACTAAAGAACGTGACATTTAGCGGCGCTTTTCTCAAAACGCCGCTAAAAAACATGACCTTTAGC
AGCGTTTTTCTCAAAAACGCCGCTAAAGAACATGACCTTTAGCGGCACTTTTCTCAAAACAACG
Found at i:34286243 original size:128 final size:129
Alignment explanation
Indices: 34286010--34286252 Score: 382
Period size: 128 Copynumber: 1.9 Consensus size: 129
34286000 TTTTGAGACA
** *
34286010 TGACCTTTAGCGGCGCTTTTCATACAAAAGCCGCTAAAGAATGTGACATTTAGCGGTGCTTTTCT
1 TGACCTTTAGCGGCGCTTTTCATACAAAAGCCGCTAAAGAAAATGACATTTAGCGGCGCTTTTCT
* **
34286075 CAAAACGCCGCTAAAGAACATGACCTTTAGCATCGTTTTTCTCAAAAAACGCCGCTAAAGAACG
66 CAAAACGCCGCTAAAGAACATGACCTTTAGCAGCACTTTTCTCAAAAAACGCCGCTAAAGAACG
*
34286139 TGACCTTTAGCGGCGCTTTTC-T-CAAAACGCCGCTAAAGAAAATGACCTTTAGCGGCGCTTTTC
1 TGACCTTTAGCGGCGCTTTTCATACAAAA-GCCGCTAAAGAAAATGACATTTAGCGGCGCTTTTC
* *
34286202 TCAAAACGTCGCTAAAGAACATGACCTTTAGCGGCACTTTTCTCAAAAAAC
65 TCAAAACGCCGCTAAAGAACATGACCTTTAGCAGCACTTTTCTCAAAAAAC
34286253 TGCTAAAGGT
Statistics
Matches: 104, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
127 5 0.05
128 78 0.75
129 21 0.20
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.26
Consensus pattern (129 bp):
TGACCTTTAGCGGCGCTTTTCATACAAAAGCCGCTAAAGAAAATGACATTTAGCGGCGCTTTTCT
CAAAACGCCGCTAAAGAACATGACCTTTAGCAGCACTTTTCTCAAAAAACGCCGCTAAAGAACG
Found at i:34286252 original size:86 final size:84
Alignment explanation
Indices: 34286009--34286249 Score: 349
Period size: 86 Copynumber: 2.8 Consensus size: 84
34285999 TTTTTGAGAC
* * *
34286009 ATGACCTTTAGCGGCGCTTTTCATACAAAA-GCCGCTAAAGAATGTGACATTTAGCGGTGCTTTT
1 ATGACCTTTAGCGGCGCTTTTC-T-CAAAACGCCGCTAAAGAACGTGACCTTTAGCGGCGCTTTT
*
34286073 CTCAAAACGCCGCTAAAGAAC
64 CTCAAAACGCCGCTAAAGAAA
** *
34286094 ATGACCTTTAGCATCGTTTTTCTCAAAAAACGCCGCTAAAGAACGTGACCTTTAGCGGCGCTTTT
1 ATGACCTTTAGCGGCGCTTTTCTC--AAAACGCCGCTAAAGAACGTGACCTTTAGCGGCGCTTTT
34286159 CTCAAAACGCCGCTAAAGAAA
64 CTCAAAACGCCGCTAAAGAAA
* * *
34286180 ATGACCTTTAGCGGCGCTTTTCTCAAAACGTCGCTAAAGAACATGACCTTTAGCGGCACTTTTCT
1 ATGACCTTTAGCGGCGCTTTTCTCAAAACGCCGCTAAAGAACGTGACCTTTAGCGGCGCTTTTCT
34286245 CAAAA
66 CAAAA
34286250 AACTGCTAAA
Statistics
Matches: 140, Mismatches: 13, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
83 1 0.01
84 44 0.31
85 23 0.16
86 72 0.51
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (84 bp):
ATGACCTTTAGCGGCGCTTTTCTCAAAACGCCGCTAAAGAACGTGACCTTTAGCGGCGCTTTTCT
CAAAACGCCGCTAAAGAAA
Found at i:34292258 original size:18 final size:18
Alignment explanation
Indices: 34292214--34292302 Score: 67
Period size: 18 Copynumber: 5.1 Consensus size: 18
34292204 TATGTATTAC
* *
34292214 GTAAATTATGTAAGTAAT
1 GTAAGTTATGTAAGTTAT
*
34292232 GTAAATTATGTAAGTTAT
1 GTAAGTTATGTAAGTTAT
* * *
34292250 TTAAGTTATGATATGATAT
1 GTAAGTTATG-TAAGTTAT
* * *
34292269 -TTATTTATGT-A-CTAT
1 GTAAGTTATGTAAGTTAT
34292284 GTAAGTTATGTAAGTTAT
1 GTAAGTTATGTAAGTTAT
34292302 G
1 G
34292303 ATTAGCATAT
Statistics
Matches: 55, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
15 3 0.05
16 8 0.15
17 2 0.04
18 36 0.65
19 6 0.11
ACGTcount: A:0.36, C:0.01, G:0.17, T:0.46
Consensus pattern (18 bp):
GTAAGTTATGTAAGTTAT
Found at i:34292330 original size:13 final size:13
Alignment explanation
Indices: 34292312--34292337 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
34292302 GATTAGCATA
34292312 TTTAAATTTTAAC
1 TTTAAATTTTAAC
34292325 TTTAAATTTTAAC
1 TTTAAATTTTAAC
34292338 CCTTTAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (13 bp):
TTTAAATTTTAAC
Found at i:34294922 original size:18 final size:18
Alignment explanation
Indices: 34294901--34294942 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
34294891 TGATTTGGGA
34294901 AAATTTAGGG-ATTAAGGG
1 AAATTTAGGGAATT-AGGG
*
34294919 AAATTTAGGGAATTGGGG
1 AAATTTAGGGAATTAGGG
34294937 AAATTT
1 AAATTT
34294943 TGTTAGGGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 19 0.86
19 3 0.14
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (18 bp):
AAATTTAGGGAATTAGGG
Found at i:34295934 original size:21 final size:22
Alignment explanation
Indices: 34295899--34295948 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
34295889 ATACCTTGAC
34295899 CCTTAAATCCCTAAA-CCATAAA
1 CCTTAAATCCCTAAAGCC-TAAA
*
34295921 CCTTAAA-GCCTAAAGCCTAAA
1 CCTTAAATCCCTAAAGCCTAAA
*
34295942 CTTTAAA
1 CCTTAAA
34295949 ACATAACCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 16 0.64
22 9 0.36
ACGTcount: A:0.44, C:0.28, G:0.04, T:0.24
Consensus pattern (22 bp):
CCTTAAATCCCTAAAGCCTAAA
Found at i:34296158 original size:22 final size:22
Alignment explanation
Indices: 34296130--34296172 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
34296120 TTATTAAAAT
34296130 CCCTAACC-CTTAAACCATAATA
1 CCCTAACCAC-TAAACCATAATA
*
34296152 CCCTAACCACTAAACCTTAAT
1 CCCTAACCACTAAACCATAAT
34296173 TACTAAGGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.40, C:0.37, G:0.00, T:0.23
Consensus pattern (22 bp):
CCCTAACCACTAAACCATAATA
Found at i:34296210 original size:22 final size:21
Alignment explanation
Indices: 34296185--34296252 Score: 59
Period size: 22 Copynumber: 3.1 Consensus size: 21
34296175 CTAAGGCCAT
34296185 AACTATAATACACTAAACCCTA
1 AACTATAA-ACACTAAACCCTA
*
34296207 AACTACAAAC-CTTAAACCCTA
1 AACTATAAACAC-TAAACCCTA
* *
34296228 AACCT-TAAAACATTAAACTCTA
1 AA-CTAT-AAACACTAAACCCTA
34296250 AAC
1 AAC
34296253 CCAATATACT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
20 1 0.03
21 14 0.37
22 23 0.61
ACGTcount: A:0.50, C:0.28, G:0.00, T:0.22
Consensus pattern (21 bp):
AACTATAAACACTAAACCCTA
Found at i:34296222 original size:14 final size:14
Alignment explanation
Indices: 34296194--34296236 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
34296184 TAACTATAAT
*
34296194 ACACTAAACCCTAA
1 ACACTAAACCTTAA
34296208 ACTAC-AAACCTTAA
1 AC-ACTAAACCTTAA
*
34296222 ACCCTAAACCTTAA
1 ACACTAAACCTTAA
34296236 A
1 A
34296237 ACATTAAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 1 0.04
14 22 0.88
15 2 0.08
ACGTcount: A:0.49, C:0.33, G:0.00, T:0.19
Consensus pattern (14 bp):
ACACTAAACCTTAA
Found at i:34296251 original size:50 final size:50
Alignment explanation
Indices: 34296197--34296294 Score: 128
Period size: 50 Copynumber: 2.0 Consensus size: 50
34296187 CTATAATACA
* *
34296197 CTAAACCCTAA-ACTAC-AAACCTTAAACCCTAAACCTTAAAACATTAAACT
1 CTAAACCC-AATA-TACTAAACATTAAACCATAAACCTTAAAACATTAAACT
* *
34296247 CTAAACCCAATATACTAAACATTAAAGCATAAACCTTAAAACCTTAAA
1 CTAAACCCAATATACTAAACATTAAACCATAAACCTTAAAACATTAAA
34296295 ACCATAAACC
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
49 5 0.12
50 37 0.88
ACGTcount: A:0.50, C:0.27, G:0.01, T:0.22
Consensus pattern (50 bp):
CTAAACCCAATATACTAAACATTAAACCATAAACCTTAAAACATTAAACT
Found at i:34296290 original size:8 final size:7
Alignment explanation
Indices: 34296262--34296351 Score: 65
Period size: 7 Copynumber: 12.6 Consensus size: 7
34296252 CCCAATATAC
*
34296262 TAAACAT
1 TAAACCT
* *
34296269 TAAAGCA
1 TAAACCT
34296276 TAAACCT
1 TAAACCT
34296283 TAAAACCT
1 T-AAACCT
*
34296291 TAAAACCA
1 T-AAACCT
*
34296299 TAAACCA
1 TAAACCT
*
34296306 TAGACCT
1 TAAACCT
34296313 TAAACCT
1 TAAACCT
*
34296320 TAAACAT
1 TAAACCT
*
34296327 TAAATCT
1 TAAACCT
34296334 TAAAACC-
1 T-AAACCT
*
34296341 TAAACCC
1 TAAACCT
34296348 TAAA
1 TAAA
34296352 ATAAAATTAT
Statistics
Matches: 67, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
6 5 0.07
7 44 0.66
8 18 0.27
ACGTcount: A:0.51, C:0.23, G:0.02, T:0.23
Consensus pattern (7 bp):
TAAACCT
Found at i:34296329 original size:14 final size:14
Alignment explanation
Indices: 34296213--34296337 Score: 60
Period size: 14 Copynumber: 8.7 Consensus size: 14
34296203 CCTAAACTAC
**
34296213 AAACCTTAAACCCT
1 AAACCTTAAACATT
34296227 AAACCTTAAAACATT
1 AAACCTT-AAACATT
*
34296242 AAA-CTCTAAACCCAAT
1 AAACCT-TAAA--CATT
*
34296258 ATA-C-TAAACATT
1 AAACCTTAAACATT
* * *
34296270 AAAGCATAAACCTT
1 AAACCTTAAACATT
34296284 AAAACCTTAAAACCA-T
1 -AAACCTT-AAA-CATT
* * *
34296300 AAACCATAGACCTT
1 AAACCTTAAACATT
34296314 AAACCTTAAACATT
1 AAACCTTAAACATT
*
34296328 AAATCTTAAA
1 AAACCTTAAA
34296338 ACCTAAACCC
Statistics
Matches: 84, Mismatches: 17, Indels: 20
0.69 0.14 0.17
Matches are distributed among these distances:
12 5 0.06
13 2 0.02
14 46 0.55
15 20 0.24
16 10 0.12
17 1 0.01
ACGTcount: A:0.50, C:0.24, G:0.02, T:0.24
Consensus pattern (14 bp):
AAACCTTAAACATT
Found at i:34296430 original size:41 final size:41
Alignment explanation
Indices: 34296373--34296467 Score: 129
Period size: 41 Copynumber: 2.3 Consensus size: 41
34296363 ATTTTTTATG
* *
34296373 GCTTGA-CTTTTAGCGGCGTTTTAATCACAAACGTCGCTATT
1 GCTTGACCTTTT-GCGGCGTTTTAATCACAAACGCCGCTACT
* *
34296414 GCTTGACCTTTTGCGGCGTTTTTATTACAAACGCCGCTACT
1 GCTTGACCTTTTGCGGCGTTTTAATCACAAACGCCGCTACT
*
34296455 ACTTGACCTTTTG
1 GCTTGACCTTTTG
34296468 TGTCATTTAG
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
41 43 0.90
42 5 0.10
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.38
Consensus pattern (41 bp):
GCTTGACCTTTTGCGGCGTTTTAATCACAAACGCCGCTACT
Found at i:34296492 original size:14 final size:14
Alignment explanation
Indices: 34296473--34296504 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
34296463 TTTTGTGTCA
*
34296473 TTTAGGGTTTAAGG
1 TTTAGGGATTAAGG
34296487 TTTAGGGATTAAGG
1 TTTAGGGATTAAGG
34296501 TTTA
1 TTTA
34296505 TGATTTATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.25, C:0.00, G:0.31, T:0.44
Consensus pattern (14 bp):
TTTAGGGATTAAGG
Found at i:34297148 original size:41 final size:41
Alignment explanation
Indices: 34297086--34297323 Score: 144
Period size: 41 Copynumber: 5.8 Consensus size: 41
34297076 CGTTTGGATA
** * * *
34297086 AAAAACGCCACTAGAGCTCAGCCTTTTA-CGGGGTTTTAACC
1 AAAAACGCCACTATTGATCAG-CTTTTAGCGGCGTTTGAACC
*
34297127 AAAAACGCCACTATTGATCAGCTTTTAGCGGCGTTTGGACC
1 AAAAACGCCACTATTGATCAGCTTTTAGCGGCGTTTGAACC
* * * * * *
34297168 TAAAACGCCATTATTGCTC-GATTTTTAGCAGCGTTTGGGA-C
1 AAAAACGCCACTATTGATCAG-CTTTTAGCGGCGTTT-GAACC
* * * * *
34297209 AAAAACGCCACTATTGCTCAACTTTCAACGGCGTTTGGACC
1 AAAAACGCCACTATTGATCAGCTTTTAGCGGCGTTTGAACC
* * * * * *
34297250 TAAAACGCCACAATTGCTCA-ATTCTTAGCGGTGTTTGGGA-C
1 AAAAACGCCACTATTGATCAGCTT-TTAGCGGCGTTT-GAACC
* * * * *
34297291 AAAAAAGCCATTACTGCTCAACTTTTAGCGGCG
1 AAAAACGCCACTATTGATCAGCTTTTAGCGGCG
34297324 ACCACTATTG
Statistics
Matches: 158, Mismatches: 31, Indels: 16
0.77 0.15 0.08
Matches are distributed among these distances:
40 12 0.08
41 138 0.87
42 8 0.05
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.27
Consensus pattern (41 bp):
AAAAACGCCACTATTGATCAGCTTTTAGCGGCGTTTGAACC
Found at i:34297212 original size:82 final size:82
Alignment explanation
Indices: 34297126--34297323 Score: 279
Period size: 82 Copynumber: 2.4 Consensus size: 82
34297116 GGGTTTTAAC
* * ** *
34297126 CAAAAACGCCACTATTGATCAGCTTTTAGCGGCGTTTGGACCTAAAACGCCATTATTGCTCGATT
1 CAAAAACGCCACTATTGCTCAACTTTTAGCGGCGTTTGGACCTAAAACGCCACAATTGCTCAATT
*
34297191 TTTAGCAGCGTTTGGGA
66 CTTAGCAGCGTTTGGGA
* *
34297208 CAAAAACGCCACTATTGCTCAACTTTCAACGGCGTTTGGACCTAAAACGCCACAATTGCTCAATT
1 CAAAAACGCCACTATTGCTCAACTTTTAGCGGCGTTTGGACCTAAAACGCCACAATTGCTCAATT
* *
34297273 CTTAGCGGTGTTTGGGA
66 CTTAGCAGCGTTTGGGA
* * *
34297290 CAAAAAAGCCATTACTGCTCAACTTTTAGCGGCG
1 CAAAAACGCCACTATTGCTCAACTTTTAGCGGCG
34297324 ACCACTATTG
Statistics
Matches: 101, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
82 101 1.00
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (82 bp):
CAAAAACGCCACTATTGCTCAACTTTTAGCGGCGTTTGGACCTAAAACGCCACAATTGCTCAATT
CTTAGCAGCGTTTGGGA
Found at i:34297381 original size:68 final size:68
Alignment explanation
Indices: 34297257--34297391 Score: 191
Period size: 68 Copynumber: 2.0 Consensus size: 68
34297247 ACCTAAAACG
* * **
34297257 CCACAATTGCTCAATTCTTAGCGGTGTTTGGGACAAAAAAGCCATTACTGCTCAACTTTTAGCGG
1 CCACAATTGCTCAATTCTTAGCAGTGTTTGGGACAAAAAAGCCAGTACTGAACAACTTTTAGCGG
34297322 CGA
66 CGA
* * *
34297325 CCACTATTGCTCAAATT-TTAGCAGTGTTTGGGACAAAAACGCCAGTATTGAACAACTTTTAGCG
1 CCACAATTGCTC-AATTCTTAGCAGTGTTTGGGACAAAAAAGCCAGTACTGAACAACTTTTAGCG
34297389 GCG
65 GCG
34297392 TTTGGACCTA
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
68 55 0.93
69 4 0.07
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (68 bp):
CCACAATTGCTCAATTCTTAGCAGTGTTTGGGACAAAAAAGCCAGTACTGAACAACTTTTAGCGG
CGA
Found at i:34297386 original size:41 final size:41
Alignment explanation
Indices: 34297325--34297476 Score: 180
Period size: 41 Copynumber: 3.7 Consensus size: 41
34297315 TTAGCGGCGA
* * *
34297325 CCACTATTGCTCAAATTTTAGCAGTGTTTGGGACAAAAACG
1 CCACTATTGCTCAACTTTTAGCGGCGTTTGGGACAAAAACG
* ** *
34297366 CCAGTATTGAACAACTTTTAGCGGCGTTT-GGACCTAAAACG
1 CCACTATTGCTCAACTTTTAGCGGCGTTTGGGA-CAAAAACG
* * *
34297407 CCACTATTGCTCAACTTTTAGTGGCGTTTGGTAGAAAAACG
1 CCACTATTGCTCAACTTTTAGCGGCGTTTGGGACAAAAACG
* *
34297448 CCACTATTGCTCAACTTTTTGCTGCGTTT
1 CCACTATTGCTCAACTTTTAGCGGCGTTT
34297477 TCCTTCTAGC
Statistics
Matches: 92, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
40 3 0.03
41 87 0.95
42 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (41 bp):
CCACTATTGCTCAACTTTTAGCGGCGTTTGGGACAAAAACG
Found at i:34297459 original size:150 final size:150
Alignment explanation
Indices: 34297179--34297466 Score: 416
Period size: 150 Copynumber: 1.9 Consensus size: 150
34297169 AAAACGCCAT
* * **
34297179 TATTGCTCGATTTTTAGCAGCGTTTGGGACAAAAACGCCACTATTGCTCAACTTTCAACGGCGTT
1 TATTGCTCAAATTTTAGCAGCGTTTGGGACAAAAACGCCACTATTGAACAACTTTCAACGGCGTT
* *
34297244 TGGACCTAAAACGCCACAATTGCTCAATTCTTAGCGGTGTTTGGGACAAAAAAGCCATTACTGCT
66 TGGACCTAAAACGCCACAATTGCTCAATTCTTAGCGGCGTTTGGGACAAAAAAGCCACTACTGCT
34297309 CAACTTTTAGCGGCGACCAC
131 CAACTTTTAGCGGCGACCAC
* * * *
34297329 TATTGCTCAAATTTTAGCAGTGTTTGGGACAAAAACGCCAGTATTGAACAACTTTTAGCGGCGTT
1 TATTGCTCAAATTTTAGCAGCGTTTGGGACAAAAACGCCACTATTGAACAACTTTCAACGGCGTT
* * * * * *
34297394 TGGACCTAAAACGCCACTATTGCTCAACTT-TTAGTGGCGTTTGGTAGAAAAACGCCACTATTGC
66 TGGACCTAAAACGCCACAATTGCTCAA-TTCTTAGCGGCGTTTGGGACAAAAAAGCCACTACTGC
34297458 TCAACTTTT
130 TCAACTTTT
34297467 TGCTGCGTTT
Statistics
Matches: 121, Mismatches: 16, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
150 119 0.98
151 2 0.02
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.30
Consensus pattern (150 bp):
TATTGCTCAAATTTTAGCAGCGTTTGGGACAAAAACGCCACTATTGAACAACTTTCAACGGCGTT
TGGACCTAAAACGCCACAATTGCTCAATTCTTAGCGGCGTTTGGGACAAAAAAGCCACTACTGCT
CAACTTTTAGCGGCGACCAC
Found at i:34297463 original size:82 final size:82
Alignment explanation
Indices: 34297325--34297476 Score: 205
Period size: 82 Copynumber: 1.9 Consensus size: 82
34297315 TTAGCGGCGA
* *
34297325 CCACTATTGCTCAAATTTTAGCAGTGTTTGGGACAAAAACGCCAGTATTGAACAACTTTTAGCGG
1 CCACTATTGCTCAAATTTTAGCAGCGTTTGGGACAAAAACGCCACTATTGAACAACTTTTAGCGG
34297390 CGTTTGGACCTAAAACG
66 CGTTTGGACCTAAAACG
* ** * * ** * *
34297407 CCACTATTGCTCAACTTTTAGTGGCGTTTGGTAGAAAAACGCCACTATTGCTCAACTTTTTGCTG
1 CCACTATTGCTCAAATTTTAGCAGCGTTTGGGACAAAAACGCCACTATTGAACAACTTTTAGCGG
34297472 CGTTT
66 CGTTT
34297477 TCCTTCTAGC
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
82 59 1.00
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (82 bp):
CCACTATTGCTCAAATTTTAGCAGCGTTTGGGACAAAAACGCCACTATTGAACAACTTTTAGCGG
CGTTTGGACCTAAAACG
Found at i:34298734 original size:9 final size:9
Alignment explanation
Indices: 34298716--34298748 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
34298706 TTATTTAAGT
34298716 TAACTCGAA
1 TAACTCGAA
*
34298725 TAATTCGAA
1 TAACTCGAA
34298734 TAACTCGAA
1 TAACTCGAA
34298743 TAACTC
1 TAACTC
34298749 AATTTTTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.27
Consensus pattern (9 bp):
TAACTCGAA
Found at i:34298801 original size:10 final size:10
Alignment explanation
Indices: 34298751--34298801 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
34298741 AATAACTCAA
*
34298751 TTTTTCAATT
1 TTTTTCAAAT
*
34298761 TTTTTCAAAA
1 TTTTTCAAAT
*
34298771 TTATTCAAAAT
1 TTTTTC-AAAT
*
34298782 TTTTT-TAAT
1 TTTTTCAAAT
34298791 TTTTTCAAAT
1 TTTTTCAAAT
34298801 T
1 T
34298802 AAATCGAGTT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
9 8 0.25
10 17 0.53
11 7 0.22
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.61
Consensus pattern (10 bp):
TTTTTCAAAT
Found at i:34307934 original size:20 final size:20
Alignment explanation
Indices: 34307887--34307934 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
34307877 TTTTAAGGTT
**
34307887 TTTATTTAATTTTTAATTTA
1 TTTATTTAATTAATAATTTA
*
34307907 TGTT-TTTAATTAATAATTTC
1 T-TTATTTAATTAATAATTTA
34307927 TTTATTTA
1 TTTATTTA
34307935 TACAGGCAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 2 0.09
20 19 0.83
21 2 0.09
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTATTTAATTAATAATTTA
Found at i:34308894 original size:25 final size:24
Alignment explanation
Indices: 34308862--34308909 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
34308852 TTCTTTAGAA
34308862 TTTTTAAA-ATTTTAAAATTTTAAT
1 TTTTTAAATATTTT-AAATTTTAAT
*
34308886 TTTTATAAATATTTTGAATTTTAA
1 TTTT-TAAATATTTTAAATTTTAA
34308910 AAATTATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 4 0.19
25 12 0.57
26 5 0.24
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (24 bp):
TTTTTAAATATTTTAAATTTTAAT
Found at i:34308907 original size:19 final size:19
Alignment explanation
Indices: 34308874--34308926 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 19
34308864 TTTAAAATTT
34308874 TAAA-ATTTT-AATTTTTA
1 TAAATATTTTGAATTTTTA
34308891 TAAATATTTTGAA-TTTTA
1 TAAATATTTTGAATTTTTA
*
34308909 AAAATTATTTTG-ATTTTT
1 TAAA-TATTTTGAATTTTT
34308927 TTAATTTTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
17 4 0.13
18 14 0.45
19 13 0.42
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
TAAATATTTTGAATTTTTA
Found at i:34308932 original size:18 final size:18
Alignment explanation
Indices: 34308878--34308932 Score: 56
Period size: 19 Copynumber: 3.0 Consensus size: 18
34308868 AAATTTTAAA
* *
34308878 ATTTTAATTTTTATAAAT
1 ATTTTGATTTTTATAATT
* *
34308896 ATTTTGAATTTTAAAAATT
1 ATTTTG-ATTTTTATAATT
*
34308915 ATTTTGATTTTTTTAATT
1 ATTTTGATTTTTATAATT
34308933 TTTGTTTAGA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
18 14 0.48
19 15 0.52
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (18 bp):
ATTTTGATTTTTATAATT
Found at i:34309306 original size:28 final size:27
Alignment explanation
Indices: 34309265--34309325 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 27
34309255 AAAAATAAAA
*
34309265 TAAAAACATAAAAACATGTATATTAAT
1 TAAAAACATAAAAACATATATATTAAT
* *
34309292 TAAAAACTTGAAAAACATATTTATTAAT
1 TAAAAACAT-AAAAACATATATATTAAT
34309320 TAAAAA
1 TAAAAA
34309326 TATTAATTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 8 0.27
28 22 0.73
ACGTcount: A:0.59, C:0.07, G:0.03, T:0.31
Consensus pattern (27 bp):
TAAAAACATAAAAACATATATATTAAT
Found at i:34310119 original size:16 final size:17
Alignment explanation
Indices: 34310100--34310151 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
34310090 TTTTCCCATT
34310100 TTAT-AATTTTTAAAAA
1 TTATAAATTTTTAAAAA
* *
34310116 TTATAAATTTTTATAAT
1 TTATAAATTTTTAAAAA
* *
34310133 TTTTGAATTTTTTAAAAA
1 TTAT-AAATTTTTAAAAA
34310151 T
1 T
34310152 CTAATTTTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
16 4 0.14
17 13 0.46
18 11 0.39
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
TTATAAATTTTTAAAAA
Found at i:34312593 original size:9 final size:9
Alignment explanation
Indices: 34312579--34312678 Score: 53
Period size: 9 Copynumber: 10.7 Consensus size: 9
34312569 GCAAAAGATG
34312579 ATAAAAATT
1 ATAAAAATT
**
34312588 ATAAAAAAAGA
1 AT--AAAAATT
*
34312599 ATTAAAATT
1 ATAAAAATT
34312608 ATAAAAATCGT
1 ATAAAAAT--T
*
34312619 AAAAAAATT
1 ATAAAAATT
34312628 -TATAAAATT
1 ATA-AAAATT
* *
34312637 GTAAAAA-A
1 ATAAAAATT
34312645 AT-AAAATAT
1 ATAAAAAT-T
34312654 ATAAAAATAT
1 ATAAAAAT-T
*
34312664 AAAAAAATT
1 ATAAAAATT
34312673 ATAAAA
1 ATAAAA
34312679 TTTTATAAAG
Statistics
Matches: 69, Mismatches: 13, Indels: 18
0.69 0.13 0.18
Matches are distributed among these distances:
7 4 0.06
8 2 0.03
9 32 0.46
10 16 0.23
11 15 0.22
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.27
Consensus pattern (9 bp):
ATAAAAATT
Found at i:34312630 original size:21 final size:20
Alignment explanation
Indices: 34312602--34312646 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
34312592 AAAAAGAATT
34312602 AAAA-TTATAAAAATCGTAAA
1 AAAATTTAT-AAAATCGTAAA
*
34312622 AAAATTTATAAAATTGTAAA
1 AAAATTTATAAAATCGTAAA
34312642 AAAAT
1 AAAAT
34312647 AAAATATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.29
Consensus pattern (20 bp):
AAAATTTATAAAATCGTAAA
Found at i:34312650 original size:16 final size:17
Alignment explanation
Indices: 34312629--34312667 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
34312619 AAAAAAATTT
*
34312629 ATAAAAT-TGTAAAAAA
1 ATAAAATATATAAAAAA
*
34312645 ATAAAATATATAAAAAT
1 ATAAAATATATAAAAAA
34312662 ATAAAA
1 ATAAAA
34312668 AAATTATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (17 bp):
ATAAAATATATAAAAAA
Found at i:34312656 original size:25 final size:25
Alignment explanation
Indices: 34312622--34312671 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
34312612 AAATCGTAAA
* * *
34312622 AAAATTTATAAAATTGTAAAAAAAT
1 AAAATATATAAAAATATAAAAAAAT
34312647 AAAATATATAAAAATATAAAAAAAT
1 AAAATATATAAAAATATAAAAAAAT
34312672 TATAAAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (25 bp):
AAAATATATAAAAATATAAAAAAAT
Found at i:34312912 original size:9 final size:9
Alignment explanation
Indices: 34312891--34312954 Score: 58
Period size: 9 Copynumber: 6.9 Consensus size: 9
34312881 TTTTGATGCA
34312891 TTTTATAATT
1 TTTTATAA-T
*
34312901 TTTTATTAT
1 TTTTATAAT
*
34312910 TTTTATAAAA
1 TTTTAT-AAT
34312920 TTTTAT-AT
1 TTTTATAAT
**
34312928 TTTTATGGT
1 TTTTATAAT
34312937 TTTTATAAT
1 TTTTATAAT
34312946 TTTTGATAA
1 TTTT-ATAA
34312955 ATATTAAATA
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
8 7 0.16
9 19 0.43
10 18 0.41
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.66
Consensus pattern (9 bp):
TTTTATAAT
Found at i:34312931 original size:18 final size:19
Alignment explanation
Indices: 34312891--34312933 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
34312881 TTTTGATGCA
**
34312891 TTTTATAATTTTTTATTAT
1 TTTTATAAAATTTTATTAT
34312910 TTTTATAAAATTTTA-TAT
1 TTTTATAAAATTTTATTAT
34312928 TTTTAT
1 TTTTAT
34312934 GGTTTTTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTTATAAAATTTTATTAT
Found at i:34312939 original size:27 final size:29
Alignment explanation
Indices: 34312890--34312944 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 29
34312880 TTTTTGATGC
*
34312890 ATTTTATAATTTTTTATTATTTTTATAAA
1 ATTTTATAATTTTTTATGATTTTTATAAA
*
34312919 ATTTTAT-A-TTTTTATGGTTTTTATAA
1 ATTTTATAATTTTTTATGATTTTTATAA
34312945 TTTTTGATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 16 0.67
28 1 0.04
29 7 0.29
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (29 bp):
ATTTTATAATTTTTTATGATTTTTATAAA
Found at i:34312987 original size:28 final size:30
Alignment explanation
Indices: 34312956--34313017 Score: 76
Period size: 28 Copynumber: 2.1 Consensus size: 30
34312946 TTTTGATAAA
*
34312956 TATTAAATATTAAAT-ATTTTTA-T-ATTTT
1 TATTAAA-ATTAAATAAATTTTATTGATTTT
*
34312984 TATTAAAATTCAATAAATTTTATTGATTTT
1 TATTAAAATTAAATAAATTTTATTGATTTT
34313014 TATT
1 TATT
34313018 TTTTATAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 6 0.21
28 13 0.45
29 1 0.03
30 9 0.31
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (30 bp):
TATTAAAATTAAATAAATTTTATTGATTTT
Found at i:34313703 original size:21 final size:23
Alignment explanation
Indices: 34313679--34313726 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
34313669 GACCTATAAA
34313679 ATTTAT-AATT-TAATATAAAAT
1 ATTTATGAATTATAATATAAAAT
*
34313700 ATTTATGAATTATTATATAAAAT
1 ATTTATGAATTATAATATAAAAT
34313723 -TTTA
1 ATTTA
34313727 ATTAAAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 6 0.25
22 8 0.33
23 10 0.42
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
ATTTATGAATTATAATATAAAAT
Found at i:34314462 original size:7 final size:7
Alignment explanation
Indices: 34314450--34314481 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
34314440 ATCCAGGTGG
34314450 ACCAATT
1 ACCAATT
34314457 ACCAATT
1 ACCAATT
34314464 ACCAATT
1 ACCAATT
34314471 ACCAATT
1 ACCAATT
34314478 ACCA
1 ACCA
34314482 CTTGCCCCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.25
Consensus pattern (7 bp):
ACCAATT
Found at i:34316240 original size:23 final size:22
Alignment explanation
Indices: 34316214--34316283 Score: 63
Period size: 21 Copynumber: 3.2 Consensus size: 22
34316204 TTTTTATAAT
34316214 TTTTTAAAAATATAAATTTGAAA
1 TTTTTAAAAATAT-AATTTGAAA
* **
34316237 TTTTTATAAATATTTTTTGAAA
1 TTTTTAAAAATATAATTTGAAA
* * *
34316259 -TTTTGAAAAT-TATTTTGAAT
1 TTTTTAAAAATATAATTTGAAA
34316279 TTTTT
1 TTTTT
34316284 TGTAGAGATG
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
20 8 0.21
21 12 0.31
22 7 0.18
23 12 0.31
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (22 bp):
TTTTTAAAAATATAATTTGAAA
Found at i:34316255 original size:22 final size:20
Alignment explanation
Indices: 34316230--34316282 Score: 63
Period size: 22 Copynumber: 2.6 Consensus size: 20
34316220 AAAATATAAA
*
34316230 TTTGAAATTTTTATAAATATTT
1 TTTGAAATTTTTA-AAAT-TAT
*
34316252 TTTGAAATTTTGAAAATTAT
1 TTTGAAATTTTTAAAATTAT
34316272 TTTG-AATTTTT
1 TTTGAAATTTTT
34316283 TTGTAGAGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 6 0.21
20 6 0.21
21 4 0.14
22 12 0.43
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (20 bp):
TTTGAAATTTTTAAAATTAT
Found at i:34316283 original size:21 final size:20
Alignment explanation
Indices: 34316211--34316283 Score: 58
Period size: 20 Copynumber: 3.4 Consensus size: 20
34316201 ATTTTTTTAT
*
34316211 AATTTTTTAAAAATATAAATTTG
1 AATTTTTT-AAAAT-T-ATTTTG
34316234 AAATTTTTATAAATATT-TTTTG
1 -AATTTTT-TAAA-ATTATTTTG
* *
34316256 AAATTTTGAAAATTATTTTG
1 AATTTTTTAAAATTATTTTG
34316276 AATTTTTT
1 AATTTTTT
34316284 TGTAGAGATG
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
19 3 0.07
20 14 0.34
21 6 0.15
22 4 0.10
24 11 0.27
25 3 0.07
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (20 bp):
AATTTTTTAAAATTATTTTG
Found at i:34317135 original size:35 final size:35
Alignment explanation
Indices: 34317089--34317159 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
34317079 TCTAGGATCA
*
34317089 CATATATTTGAAGATCCCCTTCCATATTTGCCAAG
1 CATATATTTGAAGATCACCTTCCATATTTGCCAAG
* *
34317124 CATATCTTTGAAGATCACTTTCCATATTTGCCAAG
1 CATATATTTGAAGATCACCTTCCATATTTGCCAAG
34317159 C
1 C
34317160 TTAGGAGATG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.28, C:0.25, G:0.11, T:0.35
Consensus pattern (35 bp):
CATATATTTGAAGATCACCTTCCATATTTGCCAAG
Found at i:34321556 original size:33 final size:32
Alignment explanation
Indices: 34321505--34321572 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 32
34321495 TTCAAGGTCA
*
34321505 TCATTATAGCCTCAATGGCATCAGT-CCTACTAG
1 TCATCATAGCCTCAATGGCATCA-TCCCTAC-AG
**
34321538 TCATCATAGCCTTGATGGCATCATCCCTACAG
1 TCATCATAGCCTCAATGGCATCATCCCTACAG
34321570 TCA
1 TCA
34321573 ACTTCTAAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
32 6 0.19
33 25 0.81
ACGTcount: A:0.26, C:0.29, G:0.15, T:0.29
Consensus pattern (32 bp):
TCATCATAGCCTCAATGGCATCATCCCTACAG
Found at i:34322292 original size:35 final size:35
Alignment explanation
Indices: 34322249--34322318 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
34322239 CTAGGATCAT
34322249 ATATCTTTGAAGATC-CTCTTCCATATTTGCCAAGC
1 ATATCTTTGAAGATCAC-CTTCCATATTTGCCAAGC
* *
34322284 ATATCTTTGAAGATCACGTTCCGTATTTGCCAAGC
1 ATATCTTTGAAGATCACCTTCCATATTTGCCAAGC
34322319 TCCGGAGATG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 31 0.97
36 1 0.03
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.36
Consensus pattern (35 bp):
ATATCTTTGAAGATCACCTTCCATATTTGCCAAGC
Found at i:34323781 original size:8 final size:8
Alignment explanation
Indices: 34323764--34323793 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
34323754 TTTTATTTTC
34323764 TTTC-AAT
1 TTTCAAAT
34323771 TTTCAAAT
1 TTTCAAAT
34323779 TTTCAAAT
1 TTTCAAAT
34323787 TTTCAAA
1 TTTCAAA
34323794 ACAATGTATG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 4 0.18
8 18 0.82
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (8 bp):
TTTCAAAT
Found at i:34324295 original size:15 final size:15
Alignment explanation
Indices: 34324275--34324304 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
34324265 GGTAAATAAA
34324275 AGTCACTATTTTTAT
1 AGTCACTATTTTTAT
*
34324290 AGTCACTCTTTTTAT
1 AGTCACTATTTTTAT
34324305 CTTTCTAACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.17, G:0.07, T:0.53
Consensus pattern (15 bp):
AGTCACTATTTTTAT
Found at i:34326051 original size:7 final size:7
Alignment explanation
Indices: 34326041--34326069 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
34326031 AGTATACAGT
34326041 AAAAATA
1 AAAAATA
34326048 AAAAATA
1 AAAAATA
34326055 AAAAATA
1 AAAAATA
34326062 AAAAATA
1 AAAAATA
34326069 A
1 A
34326070 TGATATCATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AAAAATA
Found at i:34326610 original size:7 final size:7
Alignment explanation
Indices: 34326594--34326623 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
34326584 ACAAAGATGT
*
34326594 TAAAGCA
1 TAAAGAA
34326601 TAAAGAA
1 TAAAGAA
34326608 TAAAGAA
1 TAAAGAA
34326615 TAAAGAA
1 TAAAGAA
34326622 TA
1 TA
34326624 GTGCGAGGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.67, C:0.03, G:0.13, T:0.17
Consensus pattern (7 bp):
TAAAGAA
Found at i:34332249 original size:13 final size:13
Alignment explanation
Indices: 34332231--34332271 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
34332221 TAGTATTTGC
34332231 CACATATAATTAT
1 CACATATAATTAT
**
34332244 CACATAT--TTGC
1 CACATATAATTAT
34332255 CACATATAATTAT
1 CACATATAATTAT
34332268 CACA
1 CACA
34332272 CATTCACTCA
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
11 9 0.41
13 13 0.59
ACGTcount: A:0.41, C:0.22, G:0.02, T:0.34
Consensus pattern (13 bp):
CACATATAATTAT
Found at i:34332256 original size:24 final size:24
Alignment explanation
Indices: 34332224--34332271 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
34332214 TCACATTTAG
34332224 TATTTGCCACATATAATTATCACA
1 TATTTGCCACATATAATTATCACA
34332248 TATTTGCCACATATAATTATCACA
1 TATTTGCCACATATAATTATCACA
34332272 CATTCACTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.21, G:0.04, T:0.38
Consensus pattern (24 bp):
TATTTGCCACATATAATTATCACA
Found at i:34333872 original size:42 final size:42
Alignment explanation
Indices: 34333759--34333877 Score: 114
Period size: 43 Copynumber: 2.8 Consensus size: 42
34333749 TGATGTATTG
* * * * *
34333759 TACCAATGCCATGTGCCAGACATGGTCTTACATGGAAATCTCA
1 TACCGATGCCATGTCCCAGATATGGTCTTACA-CGAAACCTCA
* * **
34333802 TATCGATGCCAATAG-CCCAGCTATGGTCTTACACGATGCCTCA
1 TACCGATGCC-AT-GTCCCAGATATGGTCTTACACGAAACCTCA
*
34333845 TGCCGATGCCATGTCCCAGATATGGTCTTACAC
1 TACCGATGCCATGTCCCAGATATGGTCTTACAC
34333878 TGGCTCACAT
Statistics
Matches: 61, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
41 1 0.02
42 20 0.33
43 22 0.36
44 17 0.28
45 1 0.02
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (42 bp):
TACCGATGCCATGTCCCAGATATGGTCTTACACGAAACCTCA
Found at i:34333920 original size:48 final size:48
Alignment explanation
Indices: 34333844--34333936 Score: 159
Period size: 48 Copynumber: 1.9 Consensus size: 48
34333834 ACGATGCCTC
* *
34333844 ATGCCGATGCCATGTCCCAGATATGGTCTTACACTGGCTCACATAACA
1 ATGCCGATGCCATGTCCCAGACAAGGTCTTACACTGGCTCACATAACA
*
34333892 ATGCCGATGCCATGTCCCAGGCAAGGTCTTACACTGGCTCACATA
1 ATGCCGATGCCATGTCCCAGACAAGGTCTTACACTGGCTCACATA
34333937 TTGCCATGGT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.26, C:0.30, G:0.20, T:0.24
Consensus pattern (48 bp):
ATGCCGATGCCATGTCCCAGACAAGGTCTTACACTGGCTCACATAACA
Found at i:34346547 original size:27 final size:27
Alignment explanation
Indices: 34346517--34346571 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
34346507 TGCTTCTAGA
34346517 ATCCAGGTTTTGCAATTTATTCAATTT
1 ATCCAGGTTTTGCAATTTATTCAATTT
34346544 ATCCAGGTTTTGCAATTTATTCAATTT
1 ATCCAGGTTTTGCAATTTATTCAATTT
34346571 A
1 A
34346572 GTCCCTAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.27, C:0.15, G:0.11, T:0.47
Consensus pattern (27 bp):
ATCCAGGTTTTGCAATTTATTCAATTT
Found at i:34348101 original size:44 final size:44
Alignment explanation
Indices: 34348033--34348124 Score: 123
Period size: 44 Copynumber: 2.1 Consensus size: 44
34348023 CCGATGTAAC
*
34348033 AGTAGCAGTACGACACACATAGTGCCTCATCGACTCGAA-GTCGA
1 AGTAACAGTACGACACACATAGTGCCTCATCGACTC-AAGGTCGA
* ** *
34348077 AGTAACAGTATGACACTTATAGTGCCTTATCGACTCAAGGTCGA
1 AGTAACAGTACGACACACATAGTGCCTCATCGACTCAAGGTCGA
34348121 AGTA
1 AGTA
34348125 TCCCTGAACA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
43 2 0.05
44 40 0.95
ACGTcount: A:0.33, C:0.23, G:0.22, T:0.23
Consensus pattern (44 bp):
AGTAACAGTACGACACACATAGTGCCTCATCGACTCAAGGTCGA
Found at i:34353647 original size:48 final size:48
Alignment explanation
Indices: 34353536--34353650 Score: 121
Period size: 47 Copynumber: 2.4 Consensus size: 48
34353526 TCGATTAAAG
* *
34353536 GGTT-TTTGTGAACTTCCTGTTAAATTGGCTCTTTGTGAGCTTCCCGATA
1 GGTTCTTTGTGAACTTCC--TTAAATTGGCTATCTGTGAGCTTCCCGATA
**
34353585 GTGTTCGCT-TGAACTTCC-TAATATTGGCTATCTG-GAGCTTCCCGATA
1 G-GTTCTTTGTGAACTTCCTTAA-ATTGGCTATCTGTGAGCTTCCCGATA
34353632 TGGTTCTTTGTGAACTTCC
1 -GGTTCTTTGTGAACTTCC
34353651 CGATTATGGC
Statistics
Matches: 55, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
47 21 0.38
48 20 0.36
49 1 0.02
50 12 0.22
51 1 0.02
ACGTcount: A:0.17, C:0.21, G:0.22, T:0.41
Consensus pattern (48 bp):
GGTTCTTTGTGAACTTCCTTAAATTGGCTATCTGTGAGCTTCCCGATA
Found at i:34353673 original size:24 final size:24
Alignment explanation
Indices: 34353619--34353744 Score: 78
Period size: 24 Copynumber: 5.2 Consensus size: 24
34353609 TGGCTATCTG
* *
34353619 GAGCTTCCCGATATGGTTCTTTGT
1 GAGCTTCCCGATATGGCTCTTTAT
*
34353643 GAACTTCCCGATTATGGCT-TTTAT
1 GAGCTTCCCGA-TATGGCTCTTTAT
* * ***
34353667 GAGCTTCCTGTTATATAGC-CCAGAT
1 GAGCTTCCCG--ATATGGCTCTTTAT
* *
34353692 AAGCTTCCCCATA-GGCTCTTTAT
1 GAGCTTCCCGATATGGCTCTTTAT
* * * *
34353715 GAGCTTCCCGAAATGGTTCTGTGT
1 GAGCTTCCCGATATGGCTCTTTAT
34353739 GAGCTT
1 GAGCTT
34353745 TTTGTTACAA
Statistics
Matches: 74, Mismatches: 22, Indels: 12
0.69 0.20 0.11
Matches are distributed among these distances:
22 2 0.03
23 16 0.22
24 35 0.47
25 20 0.27
26 1 0.01
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (24 bp):
GAGCTTCCCGATATGGCTCTTTAT
Found at i:34363131 original size:32 final size:31
Alignment explanation
Indices: 34363086--34363153 Score: 127
Period size: 31 Copynumber: 2.2 Consensus size: 31
34363076 AATATTTTCA
34363086 ACAACTTAATTTTTTAAACATTATGATGACTC
1 ACAA-TTAATTTTTTAAACATTATGATGACTC
34363118 ACAATTAATTTTTTAAACATTATGATGACTC
1 ACAATTAATTTTTTAAACATTATGATGACTC
34363149 ACAAT
1 ACAAT
34363154 GAAAACTGCT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 32 0.89
32 4 0.11
ACGTcount: A:0.40, C:0.15, G:0.06, T:0.40
Consensus pattern (31 bp):
ACAATTAATTTTTTAAACATTATGATGACTC
Found at i:34363395 original size:15 final size:15
Alignment explanation
Indices: 34363372--34363419 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
34363362 TAACATAAAC
*
34363372 TCAACACTTAAATTT
1 TCAATACTTAAATTT
*
34363387 TCAATACTT-ATTTT
1 TCAATACTTAAATTT
*
34363401 TCCAATAATTAAATTT
1 T-CAATACTTAAATTT
34363417 TCA
1 TCA
34363420 TTTTATAAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
14 5 0.19
15 17 0.63
16 5 0.19
ACGTcount: A:0.38, C:0.17, G:0.00, T:0.46
Consensus pattern (15 bp):
TCAATACTTAAATTT
Found at i:34376462 original size:25 final size:25
Alignment explanation
Indices: 34376428--34376475 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
34376418 TGGGTAATCT
*
34376428 TGATATAATATCTCTTGAGTATACC
1 TGATATAATACCTCTTGAGTATACC
34376453 TGATATAATACCTCTTGAGTATA
1 TGATATAATACCTCTTGAGTATA
34376476 TGTTACGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (25 bp):
TGATATAATACCTCTTGAGTATACC
Found at i:34378379 original size:20 final size:20
Alignment explanation
Indices: 34378329--34378382 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
34378319 TTTAAGAGCC
* *
34378329 ACACGCCCGTATGTCTTGCG
1 ACACGCCCGTGTGGCTTGCG
* *
34378349 ACATGCCCGTGTGGCTTGGG
1 ACACGCCCGTGTGGCTTGCG
34378369 ACACGCCCGTGTGG
1 ACACGCCCGTGTGG
34378383 GCAGGCCGTG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.13, C:0.31, G:0.33, T:0.22
Consensus pattern (20 bp):
ACACGCCCGTGTGGCTTGCG
Found at i:34380677 original size:39 final size:39
Alignment explanation
Indices: 34380632--34380947 Score: 578
Period size: 39 Copynumber: 8.1 Consensus size: 39
34380622 ATGCAAGACA
34380632 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
34380671 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
34380710 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
*
34380749 CTAGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
*
34380788 CTGGAAATGTATCCGGGCTAAAGTCCTGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
34380827 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
*
34380866 CTGGAAATGTATCCGGGCTAAAGTCCCGTAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
* * *
34380905 CAGGAAATGTATCCGAGCTAAAGTCCCGCAGGCTTTGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
34380944 CTGG
1 CTGG
34380948 TAATATAATT
Statistics
Matches: 267, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 267 1.00
ACGTcount: A:0.21, C:0.25, G:0.30, T:0.24
Consensus pattern (39 bp):
CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
Found at i:34383407 original size:42 final size:42
Alignment explanation
Indices: 34383296--34383459 Score: 145
Period size: 42 Copynumber: 3.9 Consensus size: 42
34383286 TACCATACCA
* * * * * *
34383296 ATGCCATATCCTAGATATGGTCTTACATG-GGATCTCGTATCG
1 ATGCCATATCCCAGACATGGTCTTACACGAAG-TCTCATATTG
* *
34383338 ATGCCAATAGCCCAG-CTATAGTCTTACACGAAGTCTCATATTG
1 ATGCC-ATATCCCAGAC-ATGGTCTTACACGAAGTCTCATATTG
** *
34383381 ATGCCATATCCCAGACATGGTCTTACATAAAGTCTCAAATTG
1 ATGCCATATCCCAGACATGGTCTTACACGAAGTCTCATATTG
* * *
34383423 ATGCCATTTCCCATATATGGTCTTACAC-ATAGTCTCA
1 ATGCCATATCCCAGACATGGTCTTACACGA-AGTCTCA
34383460 GTAACCCTAA
Statistics
Matches: 100, Mismatches: 17, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
41 1 0.01
42 66 0.66
43 32 0.32
44 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (42 bp):
ATGCCATATCCCAGACATGGTCTTACACGAAGTCTCATATTG
Found at i:34390811 original size:42 final size:38
Alignment explanation
Indices: 34390770--34390856 Score: 115
Period size: 36 Copynumber: 2.3 Consensus size: 38
34390760 TAGAAATGAA
34390770 AAAAAAATATGTAAGATTTCAATGTGTATTCGGCCTTATG
1 AAAAAAA-AT-TAAGATTTCAATGTGTATTCGGCCTTATG
*
34390810 --AATAAATTAAGATTTCAATGTGTATTCGGCCTTATG
1 AAAAAAAATTAAGATTTCAATGTGTATTCGGCCTTATG
*
34390846 AATAAATAATT
1 AA-AAAAAATT
34390857 CGAATATTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
36 29 0.71
37 2 0.05
38 4 0.10
39 6 0.15
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.37
Consensus pattern (38 bp):
AAAAAAAATTAAGATTTCAATGTGTATTCGGCCTTATG
Found at i:34390828 original size:36 final size:36
Alignment explanation
Indices: 34390781--34390852 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
34390771 AAAAAATATG
34390781 TAAGATTTCAATGTGTATTCGGCCTTATGAATAAAT
1 TAAGATTTCAATGTGTATTCGGCCTTATGAATAAAT
34390817 TAAGATTTCAATGTGTATTCGGCCTTATGAATAAAT
1 TAAGATTTCAATGTGTATTCGGCCTTATGAATAAAT
34390853 AATTCGAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (36 bp):
TAAGATTTCAATGTGTATTCGGCCTTATGAATAAAT
Found at i:34396800 original size:45 final size:46
Alignment explanation
Indices: 34396737--34396996 Score: 181
Period size: 45 Copynumber: 5.9 Consensus size: 46
34396727 ATGGATTCTG
* *
34396737 ATATGTG-TTTTCGAGTAAGACCACGTCTGGAACGTTGGCATCGAT
1 ATATGTGATTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGAT
* *
34396782 ATAAT-T-ATTTTCGTGTAAGACCACGTCTGGGACGTTGACATTGAT
1 AT-ATGTGATTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGAT
* * * * *
34396827 CTATGTGGTTAT-ATGTAAGACCACATCTGGGACGTTGGCATCGAT
1 ATATGTGATTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGAT
* * * * * * *
34396872 CTATGTGGTTAT-GTGTAAGACCATGTTTGGGACATCGGCATCG-T
1 ATATGTGATTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGAT
* *
34396916 AT-T-TGA--TTCGAGTAAGACC-CTGTCTGGAACAG-TGGCATC-A-
1 ATATGTGATTTTCGTGTAAGACCAC-GTCTGGGAC-GTTGGCATCGAT
* ** * *
34396956 ATATGAGA-TAACATGTAAGACCACGTCTGGGATGTTGGCAT
1 ATATGTGATTTTCGTGTAAGACCACGTCTGGGACGTTGGCAT
34396997 TGTATGATAT
Statistics
Matches: 169, Mismatches: 33, Indels: 28
0.73 0.14 0.12
Matches are distributed among these distances:
40 3 0.02
41 23 0.14
42 5 0.03
43 23 0.14
44 5 0.03
45 105 0.62
46 5 0.03
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (46 bp):
ATATGTGATTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGAT
Found at i:34408146 original size:22 final size:22
Alignment explanation
Indices: 34408118--34408159 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
34408108 TTCACTAAAA
34408118 ATTAATTATCTCATAATACGAG
1 ATTAATTATCTCATAATACGAG
34408140 ATTAATTATCTCATAATACG
1 ATTAATTATCTCATAATACG
34408160 GGACTTGGAT
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:0.40, C:0.14, G:0.07, T:0.38
Consensus pattern (22 bp):
ATTAATTATCTCATAATACGAG
Found at i:34409049 original size:49 final size:49
Alignment explanation
Indices: 34408916--34409081 Score: 167
Period size: 49 Copynumber: 3.4 Consensus size: 49
34408906 GGCAACGCCT
* * * *
34408916 TGTCCCAGACATGGTCTTACACTGGCTAGCA-C-ATCAAAGTCGATGGCA
1 TGTCCCAGACA-GGTCTTACACTGGCTATCATCTATCGAGGTCGATGCCA
* ** * * * * *
34408964 TGTCCCAGATAGGTCTTACACTAACTTTTATATATCGAGGCCGATGCCG
1 TGTCCCAGACAGGTCTTACACTGGCTATCATCTATCGAGGTCGATGCCA
*
34409013 TGTCCCAGACAGGTCTTACACTGGCTCTCATCTATCG-GTGTCGATGCCA
1 TGTCCCAGACAGGTCTTACACTGGCTATCATCTATCGAG-GTCGATGCCA
*
34409062 TGTCCTAGACAGGTCTTACA
1 TGTCCCAGACAGGTCTTACA
34409082 TTGACACACA
Statistics
Matches: 94, Mismatches: 21, Indels: 5
0.78 0.17 0.04
Matches are distributed among these distances:
47 14 0.15
48 11 0.12
49 69 0.73
ACGTcount: A:0.23, C:0.27, G:0.22, T:0.28
Consensus pattern (49 bp):
TGTCCCAGACAGGTCTTACACTGGCTATCATCTATCGAGGTCGATGCCA
Found at i:34409212 original size:46 final size:46
Alignment explanation
Indices: 34409110--34409311 Score: 212
Period size: 46 Copynumber: 4.4 Consensus size: 46
34409100 ACGCCATATA
* * * ** * *
34409110 CCAGACAGGTCTTACAATAGCTGTATATCTCGAGGCCGATGTATGTC
1 CCAGACATGTCTTACACTAGCTCT-CGTCTCGATGCCGATGCATGTC
* * *
34409157 CCAGACATGTCTTATACTAGCTCTCGTCTCGATACCGATGCATGTT
1 CCAGACATGTCTTACACTAGCTCTCGTCTCGATGCCGATGCATGTC
* * * * *
34409203 CCAGGCATGTCTTACATTGGCTCTCTTAAT-G-TGGCCGATGCATGTC
1 CCAGACATGTCTTACACTAGCTCTCGT-CTCGAT-GCCGATGCATGTC
*
34409249 CCAGACATGTCTTACAC-AGCTCTCGTCTCGATGCCGATGCATGTT
1 CCAGACATGTCTTACACTAGCTCTCGTCTCGATGCCGATGCATGTC
34409294 CCAGACATGTCTTACACT
1 CCAGACATGTCTTACACT
34409312 GGCACACATA
Statistics
Matches: 126, Mismatches: 24, Indels: 11
0.78 0.15 0.07
Matches are distributed among these distances:
44 1 0.01
45 38 0.30
46 66 0.52
47 21 0.17
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.30
Consensus pattern (46 bp):
CCAGACATGTCTTACACTAGCTCTCGTCTCGATGCCGATGCATGTC
Found at i:34409303 original size:91 final size:92
Alignment explanation
Indices: 34409143--34409314 Score: 292
Period size: 91 Copynumber: 1.9 Consensus size: 92
34409133 TATATCTCGA
* * *
34409143 GGCCGATGTATGTCCCAGACATGTCTTATACTAGCTCTCGTCTCGATACCGATGCATGTTCCAGG
1 GGCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTCTCGATACCGATGCATGTTCCAGA
*
34409208 CATGTCTTACATTGGCTCTCTTAATGT
66 CATGTCTTACACTGGCTCTCTTAATGT
*
34409235 GGCCGATGCATGTCCCAGACATGTCTTACAC-AGCTCTCGTCTCGATGCCGATGCATGTTCCAGA
1 GGCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTCTCGATACCGATGCATGTTCCAGA
34409299 CATGTCTTACACTGGC
66 CATGTCTTACACTGGC
34409315 ACACATATCA
Statistics
Matches: 75, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
91 46 0.61
92 29 0.39
ACGTcount: A:0.20, C:0.28, G:0.22, T:0.30
Consensus pattern (92 bp):
GGCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTCTCGATACCGATGCATGTTCCAGA
CATGTCTTACACTGGCTCTCTTAATGT
Found at i:34415665 original size:48 final size:48
Alignment explanation
Indices: 34415594--34415856 Score: 348
Period size: 48 Copynumber: 5.5 Consensus size: 48
34415584 ATGAGATCCT
*
34415594 GTGTAAGACCATGTCTGGGACATGGCATTAGCGTTGATATGTGAGCCA
1 GTGTAAGACCATGTCTGGGACATGGCATTGGCGTTGATATGTGAGCCA
* *
34415642 GTGTAAGACCATGTCTGGGACATGGCATCGGCCTTGATATGTGAGCCA
1 GTGTAAGACCATGTCTGGGACATGGCATTGGCGTTGATATGTGAGCCA
* **
34415690 GTGTAAGGCCATGTCTGGGACATGGCATTGGCGTCAATATGTGAGCCA
1 GTGTAAGACCATGTCTGGGACATGGCATTGGCGTTGATATGTGAGCCA
* * * *
34415738 GTGTAAGACCATGTCTGGGACATGGCGTTGGTGTTGGTATGCT-AGTCA
1 GTGTAAGACCATGTCTGGGACATGGCATTGGCGTTGATATG-TGAGCCA
* * * * * * *
34415786 ATATGAGACCATGTCTGGGACATGGCATTGGCTTTCATATGTGTGCTA
1 GTGTAAGACCATGTCTGGGACATGGCATTGGCGTTGATATGTGAGCCA
*
34415834 GTGTAAGACCATGTTTGGGACAT
1 GTGTAAGACCATGTCTGGGACAT
34415857 AACATCGGTT
Statistics
Matches: 183, Mismatches: 30, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
47 1 0.01
48 181 0.99
49 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.32, T:0.29
Consensus pattern (48 bp):
GTGTAAGACCATGTCTGGGACATGGCATTGGCGTTGATATGTGAGCCA
Found at i:34415891 original size:96 final size:95
Alignment explanation
Indices: 34415597--34415951 Score: 332
Period size: 96 Copynumber: 3.8 Consensus size: 95
34415587 AGATCCTGTG
* *
34415597 TAAGACCATGTCTGGGACATGGCATTAGCGTTGATATGTGAGCCAGTGTAAGACCATGTCTGGGA
1 TAAGACCATGTCTGGGACATGGCATTGGC-TTCATATGTGAGCCAGTGTAAGACCATGTCTGGGA
* * * *
34415662 CATGGCATCGG-CCTTGATATGTGAGCCAGTG
65 CATGGCATCGGTTC-TGATATGAGAGTCAGTA
* *
34415693 TAAGGCCATGTCTGGGACATGGCATTGGCGTCAATATGTGAGCCAGTGTAAGACCATGTCTGGGA
1 TAAGACCATGTCTGGGACATGGCATTGGCTTC-ATATGTGAGCCAGTGTAAGACCATGTCTGGGA
* * * ** *
34415758 CATGGCGTTGGTGT-TGGTATGCTAGTCAATA
65 CATGGCATCGGT-TCTGATATGAGAGTCAGTA
* * * *
34415789 TGAGACCATGTCTGGGACATGGCATTGGCTTTCATATGTGTGCTAGTGTAAGACCATGTTTGGGA
1 TAAGACCATGTCTGGGACATGGCATTGGC-TTCATATGTGAGCCAGTGTAAGACCATGTCTGGGA
** * *
34415854 CATAACATCGGTTCTGACATGAGATTTC-GTA
65 CATGGCATCGGTTCTGATATGAGA-GTCAGTA
* * * * * *
34415885 TAAGACCATATCCGGGATATGGCA-T--C--AATATGTGGATCCA-TGTAAGACCATGTTTGGGA
1 TAAGACCATGTCTGGGACATGGCATTGGCTTCATATGT-GAGCCAGTGTAAGACCATGTCTGGGA
34415944 CATGGCAT
65 CATGGCAT
34415952 TGGCACTCTA
Statistics
Matches: 213, Mismatches: 39, Indels: 20
0.78 0.14 0.07
Matches are distributed among these distances:
90 31 0.15
91 3 0.01
93 1 0.00
95 3 0.01
96 171 0.80
97 4 0.02
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.28
Consensus pattern (95 bp):
TAAGACCATGTCTGGGACATGGCATTGGCTTCATATGTGAGCCAGTGTAAGACCATGTCTGGGAC
ATGGCATCGGTTCTGATATGAGAGTCAGTA
Found at i:34415907 original size:144 final size:144
Alignment explanation
Indices: 34415647--34415907 Score: 310
Period size: 144 Copynumber: 1.8 Consensus size: 144
34415637 AGCCAGTGTA
* *
34415647 AGACCATGTCTGGGACATGGCATCGGCCTTGATATGTGAGCCAGTGTAAGGCCATGTCTGGGACA
1 AGACCATGTCTGGGACATGGCATCGGCCTTCATATGTGAGCCAGTGTAAGACCATGTCTGGGACA
** * * * * * *
34415712 TGGCATTGGCGTCAATATGTGAGCCAGTGTAAGACCATGTCTGGGACATGGCGTTGGTGTTGGTA
66 TAACATCGGCGTCAACATGAGAGCCAGTATAAGACCATATCCGGGACATGGCGTTGGTGTTGGTA
34415777 TGCTAGTCAATATG
131 TGCTAGTCAATATG
* * * * *
34415791 AGACCATGTCTGGGACATGGCATTGGCTTTCATATGTGTGCTAGTGTAAGACCATGTTTGGGACA
1 AGACCATGTCTGGGACATGGCATCGGCCTTCATATGTGAGCCAGTGTAAGACCATGTCTGGGACA
* * ** *
34415856 TAACATCGG-TTCTGACATGAGATTTC-GTATAAGACCATATCCGGGATATGGC
66 TAACATCGGCGTC-AACATGAGA-GCCAGTATAAGACCATATCCGGGACATGGC
34415908 ATCAATATGT
Statistics
Matches: 95, Mismatches: 20, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
143 2 0.02
144 92 0.97
145 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.28
Consensus pattern (144 bp):
AGACCATGTCTGGGACATGGCATCGGCCTTCATATGTGAGCCAGTGTAAGACCATGTCTGGGACA
TAACATCGGCGTCAACATGAGAGCCAGTATAAGACCATATCCGGGACATGGCGTTGGTGTTGGTA
TGCTAGTCAATATG
Found at i:34417761 original size:12 final size:12
Alignment explanation
Indices: 34417744--34417773 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
34417734 GTTAGTAGAG
34417744 GAGAAGGAGGCA
1 GAGAAGGAGGCA
34417756 GAGAAGGAGGCA
1 GAGAAGGAGGCA
34417768 GAGAAG
1 GAGAAG
34417774 TCTTTCTCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.43, C:0.07, G:0.50, T:0.00
Consensus pattern (12 bp):
GAGAAGGAGGCA
Found at i:34426613 original size:48 final size:48
Alignment explanation
Indices: 34426542--34426809 Score: 335
Period size: 48 Copynumber: 5.6 Consensus size: 48
34426532 ATGAGATCCT
* * * *
34426542 GTGTAAGACCGTGTTTGGGACATGGGATTGACCTTGATATGTGAGCCA
1 GTGTAAGACCATGTCTGGGACATGGCATTGGCCTTGATATGTGAGCCA
*
34426590 GTGTAAGACCAAGTCTGGGACATGGCATTGGCCTTGATATGTGAGCCA
1 GTGTAAGACCATGTCTGGGACATGGCATTGGCCTTGATATGTGAGCCA
* *
34426638 GTGTAAGACCATGTTTGGGACATGGAATCTGCGCC--GATATGTGAGCCA
1 GTGTAAGACCATGTCTGGGACATGGCAT-TG-GCCTTGATATGTGAGCCA
* * *
34426686 GTGTAAGACCATGTCTAAGG-CATGGCGTTGGCATTGATATGTGAGCCA
1 GTGTAAGACCATGTCT-GGGACATGGCATTGGCCTTGATATGTGAGCCA
* * * * * * *
34426734 GTGTAAGACCAGGTTTGGAATATGGCATTGGCGTTGATATGTGTGCTA
1 GTGTAAGACCATGTCTGGGACATGGCATTGGCCTTGATATGTGAGCCA
34426782 GTGTAAGACCATGTCTGGGACATGGCAT
1 GTGTAAGACCATGTCTGGGACATGGCAT
34426810 CGGTACTGAC
Statistics
Matches: 188, Mismatches: 26, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
46 2 0.01
47 3 0.02
48 176 0.94
49 4 0.02
50 3 0.02
ACGTcount: A:0.24, C:0.16, G:0.32, T:0.28
Consensus pattern (48 bp):
GTGTAAGACCATGTCTGGGACATGGCATTGGCCTTGATATGTGAGCCA
Found at i:34429011 original size:27 final size:27
Alignment explanation
Indices: 34428980--34429070 Score: 146
Period size: 27 Copynumber: 3.4 Consensus size: 27
34428970 GGCATAATCA
*
34428980 TCATTTTACCATACAGGGGTATTACGG
1 TCATTTTACCCTACAGGGGTATTACGG
34429007 TCATTTTACCCTACAGGGGTATTACGG
1 TCATTTTACCCTACAGGGGTATTACGG
* * *
34429034 TCATATTACCCTAAAGGGGTATTACGA
1 TCATTTTACCCTACAGGGGTATTACGG
34429061 TCATTTTACC
1 TCATTTTACC
34429071 TATTCTAGGG
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 59 1.00
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (27 bp):
TCATTTTACCCTACAGGGGTATTACGG
Found at i:34432339 original size:24 final size:24
Alignment explanation
Indices: 34432312--34432361 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
34432302 TTCTTCCCTA
*
34432312 CTAGTTATCATTTCAATAGCGCAC
1 CTAGTTATCATTTCAACAGCGCAC
*
34432336 CTAGTTATCATTTCAGCAGCGCAC
1 CTAGTTATCATTTCAACAGCGCAC
34432360 CT
1 CT
34432362 GCGCTAGACT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.26, C:0.28, G:0.14, T:0.32
Consensus pattern (24 bp):
CTAGTTATCATTTCAACAGCGCAC
Found at i:34433167 original size:51 final size:51
Alignment explanation
Indices: 34433103--34433229 Score: 157
Period size: 51 Copynumber: 2.5 Consensus size: 51
34433093 CCATGCTGCC
* * *
34433103 ATAGCTTCTTTCATCCATGTTCTTATGCTACATA-CTGCATACCAAAATGCT
1 ATAGCCTCTTTCATCTATGGTCTTATGCTACATACCT-CATACCAAAATGCT
* * * * * *
34433154 ATAGTCTCTTTCATCTATGGTCTTATGCTATATACCTTATACTAGACTGCT
1 ATAGCCTCTTTCATCTATGGTCTTATGCTACATACCTCATACCAAAATGCT
34433205 ATAGCCTCTTTCATCTATGGTCTTA
1 ATAGCCTCTTTCATCTATGGTCTTA
34433230 CACCATATAC
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
51 63 0.97
52 2 0.03
ACGTcount: A:0.24, C:0.24, G:0.11, T:0.41
Consensus pattern (51 bp):
ATAGCCTCTTTCATCTATGGTCTTATGCTACATACCTCATACCAAAATGCT
Found at i:34438580 original size:56 final size:56
Alignment explanation
Indices: 34438514--34438625 Score: 152
Period size: 56 Copynumber: 2.0 Consensus size: 56
34438504 TATAAAATAT
* * * * *
34438514 GATTTTTCATCTCCTTAGGATTTGTCAAGATATGGTTAAATTAAATAAGTAATTAG
1 GATTTGTCATCACCTTAAGATTTGTCAAGATATAGTTAAATTAAATAACTAATTAG
* * *
34438570 GATTTGTCATCACCTTAAGATTTGTCATGATATATTTAAATTAAATTACTAATTAG
1 GATTTGTCATCACCTTAAGATTTGTCAAGATATAGTTAAATTAAATAACTAATTAG
34438626 ATCTATTAAC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
56 48 1.00
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.42
Consensus pattern (56 bp):
GATTTGTCATCACCTTAAGATTTGTCAAGATATAGTTAAATTAAATAACTAATTAG
Found at i:34448164 original size:14 final size:13
Alignment explanation
Indices: 34448141--34448183 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 13
34448131 TAAGTCTTCT
34448141 AAATGTTTATACTG
1 AAATG-TTATACTG
*
34448155 AAATGATTATATTG
1 AAATG-TTATACTG
34448169 AAATGTTATTACTG
1 AAATGTTA-TACTG
34448183 A
1 A
34448184 GACTACTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 3 0.12
14 22 0.88
ACGTcount: A:0.40, C:0.05, G:0.14, T:0.42
Consensus pattern (13 bp):
AAATGTTATACTG
Found at i:34450643 original size:34 final size:34
Alignment explanation
Indices: 34450600--34450667 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 34
34450590 ACAAGAGAGC
34450600 TTTGAGAAGCTCAAG-AAGTTACTGACTGAGGCCT
1 TTTGAGAAGCTCAAGAAAG-TACTGACTGAGGCCT
*
34450634 TTTGAGAAGCTCAAGAAAGTATTGACTGAGGCCT
1 TTTGAGAAGCTCAAGAAAGTACTGACTGAGGCCT
34450668 CTGTCTTAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 29 0.91
35 3 0.09
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.26
Consensus pattern (34 bp):
TTTGAGAAGCTCAAGAAAGTACTGACTGAGGCCT
Found at i:34454085 original size:33 final size:33
Alignment explanation
Indices: 34454038--34454135 Score: 126
Period size: 34 Copynumber: 2.9 Consensus size: 33
34454028 CTGAGTGCAT
* * *
34454038 ACTGTACTGGTACTGTAATGGGCTTAGGCCC-C
1 ACTGTACTGTTACTGAAATGGGCTCAGGCCCAC
*
34454070 ACTGATACTGTTACTGAAATGGGCTCAGGCCCAG
1 ACTG-TACTGTTACTGAAATGGGCTCAGGCCCAC
*
34454104 ACTGCTACTGTTACTGAAATGGGCTGAGGCCC
1 ACTG-TACTGTTACTGAAATGGGCTCAGGCCC
34454136 TAACTAAAAC
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
32 4 0.07
33 24 0.41
34 30 0.52
ACGTcount: A:0.22, C:0.24, G:0.28, T:0.26
Consensus pattern (33 bp):
ACTGTACTGTTACTGAAATGGGCTCAGGCCCAC
Found at i:34460464 original size:40 final size:40
Alignment explanation
Indices: 34460412--34460513 Score: 143
Period size: 40 Copynumber: 2.5 Consensus size: 40
34460402 TTTAATCTTT
*
34460412 CACACTAAGTGCCATATATAGCCGAAGCTATCTCGAATCG
1 CACACTAAGTGCCATATATAGCCGAAGCTATCTAGAATCG
* *
34460452 CACACTAAGTGCC-TTTCATAACCGAAGCTATCTAGAATCG
1 CACACTAAGTGCCATAT-ATAGCCGAAGCTATCTAGAATCG
* *
34460492 CACACTTAGTGCCATACATAGC
1 CACACTAAGTGCCATATATAGC
34460514 TAAATTATCG
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
39 2 0.04
40 50 0.94
41 1 0.02
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (40 bp):
CACACTAAGTGCCATATATAGCCGAAGCTATCTAGAATCG
Found at i:34461011 original size:21 final size:20
Alignment explanation
Indices: 34460985--34461024 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
34460975 ACTTGTTTAA
34460985 CTATCAACAACAATTCAAAAT
1 CTATCAACAA-AATTCAAAAT
* *
34461006 CTATCATCAAACTTCAAAA
1 CTATCAACAAAATTCAAAA
34461025 ATCACACATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (20 bp):
CTATCAACAAAATTCAAAAT
Found at i:34468247 original size:6 final size:6
Alignment explanation
Indices: 34468238--34468288 Score: 59
Period size: 6 Copynumber: 8.3 Consensus size: 6
34468228 GATGATGATG
* *
34468238 TTTAAT TTTA-T TTTATT TTTATT TCTATTT TTTATT TTTATT TTTAGTT
1 TTTATT TTTATT TTTATT TTTATT TTTA-TT TTTATT TTTATT TTTA-TT
34468287 TT
1 TT
34468289 CCTTTAACTT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
5 5 0.12
6 26 0.65
7 9 0.22
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (6 bp):
TTTATT
Found at i:34468288 original size:19 final size:19
Alignment explanation
Indices: 34468248--34468288 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
34468238 TTTAATTTTA
*
34468248 TTTTATTTTTATTTCTATT
1 TTTTATTTTTATTTCTAGT
*
34468267 TTTTATTTTTATTTTTAGT
1 TTTTATTTTTATTTCTAGT
34468286 TTT
1 TTT
34468289 CCTTTAACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.02, G:0.02, T:0.80
Consensus pattern (19 bp):
TTTTATTTTTATTTCTAGT
Found at i:34481398 original size:61 final size:61
Alignment explanation
Indices: 34481199--34481399 Score: 233
Period size: 61 Copynumber: 3.3 Consensus size: 61
34481189 AGAGGGACAA
* *
34481199 CCTTTGTGGCAAAAATCTGGATAGGAAAGCCATTGTGGCGAGTATTGAATGTTAAAGAATG
1 CCTTTGTGGCAAAACTCTGGATAGGAAAGCCATTGTGGCGAGTAATGAATGTTAAAGAATG
* * * * * * *
34481260 CCTTTGTGGCAAAACTCTAGATAGAAAAGCCTTTTCTGGTGAGTAATAAATGTTAAAGAACG
1 CCTTTGTGGCAAAACTCTGGATAGGAAAGCC-ATTGTGGCGAGTAATGAATGTTAAAGAATG
* * * * * *
34481322 CCTTTGTGGCAAAACTTTGGACAGGAAAGCC-TCAGTGGCGAGTACTGAATATTAAGGAATG
1 CCTTTGTGGCAAAACTCTGGATAGGAAAGCCAT-TGTGGCGAGTAATGAATGTTAAAGAATG
*
34481383 GCTTTGTGGCAAAACTC
1 CCTTTGTGGCAAAACTC
34481400 AAGAAAGGTA
Statistics
Matches: 115, Mismatches: 23, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
60 1 0.01
61 63 0.55
62 51 0.44
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.27
Consensus pattern (61 bp):
CCTTTGTGGCAAAACTCTGGATAGGAAAGCCATTGTGGCGAGTAATGAATGTTAAAGAATG
Found at i:34491652 original size:154 final size:154
Alignment explanation
Indices: 34491370--34491677 Score: 519
Period size: 154 Copynumber: 2.0 Consensus size: 154
34491360 ATCCGGGGTA
34491370 AGGGGTACTTATTCTTTATGGTTACTTTATTAAGCTACCGGTAGTCGATACACAATCTCAAAAAC
1 AGGGGTACTTATTCTTTATGGTTACTTTATTAAGCTACCGGTAGTCGATACACAATCTCAAAAAC
* * *
34491435 CTGTCTTTCTTTTTCACAAACAAAACCGGAGCACCCCAAGGTGAATGACTCGGTCGGACAAAACC
66 CCGTCTTTCTTTTTCACAAACAAAACCGGAGCACCCCAAGGGGAATGACTCGGTCGAACAAAACC
* * *
34491500 CCTGTCAACAAGTTTTTGCAACTG
131 CCTATCAACAAGCTCTTGCAACTG
*
34491524 AGGGGTACTTATTCTTTATGGTTACTTTATTAAGCTGA-CGGTAGTCGATACACAATCTCAAAGA
1 AGGGGTACTTATTCTTTATGGTTACTTTATTAAGCT-ACCGGTAGTCGATACACAATCTCAAAAA
* *
34491588 CCCGTCTTTCTTTTTCACAAACAAAACTGGAGCACCCCAAGGGGAATGACTCGGTCGAATAAAAC
65 CCCGTCTTTCTTTTTCACAAACAAAACCGGAGCACCCCAAGGGGAATGACTCGGTCGAACAAAAC
34491653 CCCTATCAACAAGCTCTTGCAACTG
130 CCCTATCAACAAGCTCTTGCAACTG
34491678 TGTCTTTAAC
Statistics
Matches: 144, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
154 143 0.99
155 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (154 bp):
AGGGGTACTTATTCTTTATGGTTACTTTATTAAGCTACCGGTAGTCGATACACAATCTCAAAAAC
CCGTCTTTCTTTTTCACAAACAAAACCGGAGCACCCCAAGGGGAATGACTCGGTCGAACAAAACC
CCTATCAACAAGCTCTTGCAACTG
Found at i:34494844 original size:36 final size:36
Alignment explanation
Indices: 34494804--34494875 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
34494794 TTTTCAAAGT
34494804 CAGAACAGGGGAACCCAAATTCATTCTGACCTTGTC
1 CAGAACAGGGGAACCCAAATTCATTCTGACCTTGTC
*
34494840 CAGAACAGGGGAACCCGAATTCATTCTGACCTTGTC
1 CAGAACAGGGGAACCCAAATTCATTCTGACCTTGTC
34494876 TCACAAAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (36 bp):
CAGAACAGGGGAACCCAAATTCATTCTGACCTTGTC
Found at i:34528650 original size:21 final size:21
Alignment explanation
Indices: 34528621--34528668 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 21
34528611 GATAGATATT
34528621 AGAGTATAAAAATAAGATAGGA
1 AGAG-ATAAAAATAAGATAGGA
*
34528643 AGAGATAAAAATAAGATAGGG
1 AGAGATAAAAATAAGATAGGA
34528664 AGAGA
1 AGAGA
34528669 AGTGAAACTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.58, C:0.00, G:0.27, T:0.15
Consensus pattern (21 bp):
AGAGATAAAAATAAGATAGGA
Done.