Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168048.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_3, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 33276047
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 139000 characters in sequence are not A, C, G, or T
File 158 of 190
Found at i:25622234 original size:10 final size:10
Alignment explanation
Indices: 25622219--25622252 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
25622209 ATTTTTTCTT
25622219 TTTTCACATA
1 TTTTCACATA
25622229 TTTTCACATA
1 TTTTCACATA
**
25622239 TTTTTTCATA
1 TTTTCACATA
25622249 TTTT
1 TTTT
25622253 GCATAATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.24, C:0.15, G:0.00, T:0.62
Consensus pattern (10 bp):
TTTTCACATA
Found at i:25624313 original size:19 final size:21
Alignment explanation
Indices: 25624275--25624315 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
25624265 ATCAATTTTT
25624275 AAATTTTACAAATATAATTAA
1 AAATTTTACAAATATAATTAA
*
25624296 AAATTTT-CATATAT-ATTAA
1 AAATTTTACAAATATAATTAA
25624315 A
1 A
25624316 TATATTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 6 0.32
21 7 0.37
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (21 bp):
AAATTTTACAAATATAATTAA
Found at i:25627577 original size:197 final size:196
Alignment explanation
Indices: 25627222--25627607 Score: 501
Period size: 197 Copynumber: 2.0 Consensus size: 196
25627212 ACAATATTGC
* * *
25627222 TATATTATTGGCTTAACTTAAGTGACTTCCCTTGCACTTCAGAAAGGGTAACTCTTTATTCACTG
1 TATATTATTGGCTTAACTAAAGTGACTTCCCTTGCACTTCAGAAAGGCTAACCCTTTATTCACTG
* * * *
25627287 TTATTTGTATCCTTTTACAATGTTCTTCATACTAGGCTATACTGGGAAAAGGAGCACACAATGCA
66 TTATTTGTATCCTTTTACAATGTTCTTCATAATAGGCTATAATGGAAAAAAGAGCACACAATGCA
* * * *
25627352 TTTGGTTGACACTTATTCTGCTTTTAGGTGTTT-GATTGATTTCAAATGCATGGGGATTTGTCCG
131 GTTGGTTGACAATTATTATGCATTTAGGT-TTTGGATTGATTTCAAATGCATGGGGATTTGTCCG
25627416 CT
195 CT
* * * *
25627418 TATATTATTGGCTTGA-TAAAGTGACTTCTCC-TGCACTTCATAAAGAGACTAACCCTTTCTTCG
1 TATATTATTGGCTTAACTAAAGTGACTTC-CCTTGCACTTCAGAAAG-G-CTAACCCTTTATTCA
* * *
25627481 CTGCTT-TTTGTGTCCTTTTACAATGTTCTTCATAATAGGCTGTAATGGAAAAAAGAGCACAGAA
63 CTG-TTATTTGTATCCTTTTACAATGTTCTTCATAATAGGCTATAATGGAAAAAAGAGCACACAA
* * * *
25627545 TGCAGTTGTTTGGCAATTTTTATGCATTTAGGTTTTGGATTGATTTCAAATGTATGGGGATTT
127 TGCAGTTGGTTGACAATTATTATGCATTTAGGTTTTGGATTGATTTCAAATGCATGGGGATTT
25627608 TAGGAAGTTA
Statistics
Matches: 163, Mismatches: 22, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
195 24 0.15
196 21 0.13
197 116 0.71
198 2 0.01
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.39
Consensus pattern (196 bp):
TATATTATTGGCTTAACTAAAGTGACTTCCCTTGCACTTCAGAAAGGCTAACCCTTTATTCACTG
TTATTTGTATCCTTTTACAATGTTCTTCATAATAGGCTATAATGGAAAAAAGAGCACACAATGCA
GTTGGTTGACAATTATTATGCATTTAGGTTTTGGATTGATTTCAAATGCATGGGGATTTGTCCGC
T
Found at i:25629967 original size:3 final size:3
Alignment explanation
Indices: 25629953--25629984 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
25629943 ACTACTTCCA
*
25629953 CCT CCA CCT CCT CCT CCT CCT CCT CCT CCT CC
1 CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CC
25629985 ACCGCTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.03, C:0.69, G:0.00, T:0.28
Consensus pattern (3 bp):
CCT
Found at i:25632580 original size:22 final size:22
Alignment explanation
Indices: 25632552--25632594 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
25632542 TTTTTTTTTC
* *
25632552 CTTAATTCTAGGGATACAAATG
1 CTTAATTCTAGAGATAAAAATG
25632574 CTTAATTCTAGAGATAAAAAT
1 CTTAATTCTAGAGATAAAAAT
25632595 ATAAATATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.33
Consensus pattern (22 bp):
CTTAATTCTAGAGATAAAAATG
Found at i:25640049 original size:15 final size:15
Alignment explanation
Indices: 25640026--25640055 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
25640016 CATCCTTGTT
25640026 CAAACTGATATCGAG
1 CAAACTGATATCGAG
*
25640041 CAAATTGATATCGAG
1 CAAACTGATATCGAG
25640056 GAGGCTGATC
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:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (15 bp):
CAAACTGATATCGAG
Found at i:25640540 original size:34 final size:34
Alignment explanation
Indices: 25640501--25640565 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
25640491 AACATCTCTT
* *
25640501 TTGAAATTTAAACATTATATTGCTATTTTGTCTC
1 TTGAAATTTAAACATTAAATTACTATTTTGTCTC
* *
25640535 TTGAAATTTAAATATTAAATTATTATTTTGT
1 TTGAAATTTAAACATTAAATTACTATTTTGT
25640566 TTAAAAATTC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.34, C:0.06, G:0.08, T:0.52
Consensus pattern (34 bp):
TTGAAATTTAAACATTAAATTACTATTTTGTCTC
Found at i:25661837 original size:15 final size:15
Alignment explanation
Indices: 25661817--25661867 Score: 70
Period size: 15 Copynumber: 3.5 Consensus size: 15
25661807 AAAAGTTTTG
25661817 ATTTTAATATATTTA
1 ATTTTAATATATTTA
*
25661832 ATTTTAA-AGT-TTTG
1 ATTTTAATA-TATTTA
25661846 ATTTTAATATATTTA
1 ATTTTAATATATTTA
25661861 ATTTTAA
1 ATTTTAA
25661868 AGTTAATAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
14 12 0.39
15 19 0.61
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (15 bp):
ATTTTAATATATTTA
Found at i:25661844 original size:29 final size:29
Alignment explanation
Indices: 25661808--25661871 Score: 128
Period size: 29 Copynumber: 2.2 Consensus size: 29
25661798 AAATTAGAAA
25661808 AAAGTTTTGATTTTAATATATTTAATTTT
1 AAAGTTTTGATTTTAATATATTTAATTTT
25661837 AAAGTTTTGATTTTAATATATTTAATTTT
1 AAAGTTTTGATTTTAATATATTTAATTTT
25661866 AAAGTT
1 AAAGTT
25661872 AATAACACAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (29 bp):
AAAGTTTTGATTTTAATATATTTAATTTT
Found at i:25662858 original size:16 final size:16
Alignment explanation
Indices: 25662837--25662878 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
25662827 TGATGTGTGC
25662837 TTGATTGCTTCTATCT
1 TTGATTGCTTCTATCT
*
25662853 TTGATTACTTCTATCT
1 TTGATTGCTTCTATCT
25662869 TTGATTGCTT
1 TTGATTGCTT
25662879 GTTGTCTCTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.14, C:0.17, G:0.12, T:0.57
Consensus pattern (16 bp):
TTGATTGCTTCTATCT
Found at i:25663232 original size:14 final size:13
Alignment explanation
Indices: 25663195--25663233 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
25663185 TTTTAATGTC
25663195 AAAAAGTAAAAAA
1 AAAAAGTAAAAAA
*
25663208 AATAAATTAAAATAA
1 AA-AAAGTAAAA-AA
25663223 AAAAAGTAAAA
1 AAAAAGTAAAA
25663234 GTTTTAGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 2 0.09
14 16 0.73
15 4 0.18
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.15
Consensus pattern (13 bp):
AAAAAGTAAAAAA
Found at i:25664950 original size:17 final size:18
Alignment explanation
Indices: 25664915--25664954 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
25664905 ATGATCTATC
25664915 TTTTTCCTTTTTAATATT
1 TTTTTCCTTTTTAATATT
25664933 TTTTTCCTTTCTTAAT-TT
1 TTTTTCCTTT-TTAATATT
25664951 TTTT
1 TTTT
25664955 AATTAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTTCCTTTTTAATATT
Found at i:25680232 original size:133 final size:133
Alignment explanation
Indices: 25680026--25680273 Score: 304
Period size: 133 Copynumber: 1.9 Consensus size: 133
25680016 ATGCAAAATA
* *
25680026 TTTAAAGTTTTCAAAAATTTATCAAGCCTTTGCTTAGATGAGTAATTTCAAATTTTCAAAAATTA
1 TTTAAAGTTTTCAAAAATTTATCAAGCATTTACTTAGATGAGTAATTTCAAATTTTCAAAAATTA
* *
25680091 TCGAACCTCAACTTAGA-GAAGCCTTTTAAAATTTTTAAAAGTTATCAAGCATTTGTATAAAAGA
66 TCAAACCTCAACTTAGAGGAA-CCTTTTAAAATTTTTAAAAATTATCAAGCATTTGTATAAAAGA
25680155 GCCT
130 GCCT
* * ** * *
25680159 TTTAAAGTTTTCAAAAGTTGT-T-GAGCATTTACTTAGATGAGTTGTTTTAAGTTTTCAAAAAGT
1 TTTAAAGTTTTCAAAAATT-TATCAAGCATTTACTTAGATGAGTAATTTCAAATTTTCAAAAA-T
* *** * *
25680222 TATTAAACCTCTGTTTAGAGGAACTTTTTAAAGTTTTTAAAAATTATCAAGC
64 TATCAAACCTCAACTTAGAGGAACCTTTTAAAATTTTTAAAAATTATCAAGC
25680274 CTCTATTTAG
Statistics
Matches: 96, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
132 32 0.33
133 60 0.62
134 4 0.04
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (133 bp):
TTTAAAGTTTTCAAAAATTTATCAAGCATTTACTTAGATGAGTAATTTCAAATTTTCAAAAATTA
TCAAACCTCAACTTAGAGGAACCTTTTAAAATTTTTAAAAATTATCAAGCATTTGTATAAAAGAG
CCT
Found at i:25680240 original size:45 final size:44
Alignment explanation
Indices: 25680191--25680356 Score: 136
Period size: 45 Copynumber: 3.7 Consensus size: 44
25680181 GAGCATTTAC
* *
25680191 TTAGATGAGTTGTTTTAAGTTTTCAAAAAGTTATTAAACCTCTGT
1 TTAGATGAGTT-TTTTAAGTTTTTAAAAAGTTATTAAACCTCTAT
* * * * *
25680236 TTAGAGGAACTTTTTAAAGTTTTTAAAAA-TTATCAAGCCTCTAT
1 TTAGATG-AGTTTTTTAAGTTTTTAAAAAGTTATTAAACCTCTAT
** * ** *
25680280 TTAGATGAGCCATTTTAAGTTTTTAAAAAGTTATTGAGTCTATAT
1 TTAGATGAG-TTTTTTAAGTTTTTAAAAAGTTATTAAACCTCTAT
* ** *
25680325 TTAGAAGAGCCTTTTAAATTTTTCAAAAAGTT
1 TTAGATGAGTTTTTTAAGTTTTT-AAAAAGTT
25680357 GTTGAGTCTC
Statistics
Matches: 98, Mismatches: 19, Indels: 8
0.78 0.15 0.06
Matches are distributed among these distances:
43 1 0.01
44 46 0.47
45 48 0.49
46 3 0.03
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (44 bp):
TTAGATGAGTTTTTTAAGTTTTTAAAAAGTTATTAAACCTCTAT
Found at i:25680252 original size:89 final size:89
Alignment explanation
Indices: 25680151--25680362 Score: 217
Period size: 89 Copynumber: 2.4 Consensus size: 89
25680141 ATTTGTATAA
* * ***
25680151 AAGAGCCTTTTAAAGTTTTCAAAAGTTGTTGAGCATTTACTTAGATGAGTTGTTTTAAGTTTTCA
1 AAGAACCTTTTAAAGTTTTCAAAAGTTGTTGAGCATCTACTTAGATGAGCCATTTTAAGTTTTCA
* *
25680216 AAAAGTTATTAAACCTCTGTTTAG
66 AAAAGTTATTAAACCTATATTTAG
* * * * * ** * * *
25680240 AGGAACTTTTTAAAGTTTTTAAAAATTATCAAGCCTCTATTTAGATGAGCCATTTTAAGTTTTTA
1 AAGAACCTTTTAAAGTTTTCAAAAGTTGTTGAGCATCTACTTAGATGAGCCATTTTAAGTTTTCA
* **
25680305 AAAAGTTATTGAGTCTATATTTAG
66 AAAAGTTATTAAACCTATATTTAG
* *
25680329 AAGAGCCTTTTAAATTTTTCAAAAAGTTGTTGAG
1 AAGAACCTTTTAAAGTTTTC-AAAAGTTGTTGAG
25680363 TCTCTAGTAA
Statistics
Matches: 93, Mismatches: 29, Indels: 1
0.76 0.24 0.01
Matches are distributed among these distances:
89 84 0.90
90 9 0.10
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.42
Consensus pattern (89 bp):
AAGAACCTTTTAAAGTTTTCAAAAGTTGTTGAGCATCTACTTAGATGAGCCATTTTAAGTTTTCA
AAAAGTTATTAAACCTATATTTAG
Found at i:25680290 original size:133 final size:132
Alignment explanation
Indices: 25680026--25680317 Score: 293
Period size: 133 Copynumber: 2.2 Consensus size: 132
25680016 ATGCAAAATA
* * * *
25680026 TTTAAAGTTTTCAAAAATTTATCAAGCCTTTGCTTAGATGAGTAATTTCAAATTTTCAAAAATTA
1 TTTAAAGTTTTCAAAAGTTT-T-GAGCATTTACTTAGATGAGTAATTTCAAATTTTCAAAAATTA
* * * *
25680091 TCGAACCTCAACTTAGAGAAGCCTTTTAAAATTTTTAAAAGTTATCAAGCATTTGTATAAAAGAG
64 TCAAACCTCAACTTAGAGAAGCCTTTTAAAATTTTTAAAAATTATCAAGCATCTATATAAAAGAG
25680156 CC-T
129 CCAT
** * *
25680159 TTTAAAGTTTTCAAAAGTTGTTGAGCATTTACTTAGATGAGTTGTTTTAAGTTTTCAAAAAGTTA
1 TTTAAAGTTTTCAAAAGTT-TTGAGCATTTACTTAGATGAGTAATTTCAAATTTTCAAAAA-TTA
* *** * * * * * *
25680224 TTAAACCTCTGTTTAGAGGAA-CTTTTTAAAGTTTTTAAAAATTATCAAGCCTCTATTTAGATGA
64 TCAAACCTCAACTTAGA-GAAGCCTTTTAAAATTTTTAAAAATTATCAAGCATCTATATAAAAGA
25680288 GCCAT
128 GCCAT
*
25680293 TTT-AAGTTTTTAAAAAGTTATTGAG
1 TTTAAAG-TTTTCAAAAGTT-TTGAG
25680318 TCTATATTTA
Statistics
Matches: 130, Mismatches: 24, Indels: 9
0.80 0.15 0.06
Matches are distributed among these distances:
132 32 0.25
133 74 0.57
134 24 0.18
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (132 bp):
TTTAAAGTTTTCAAAAGTTTTGAGCATTTACTTAGATGAGTAATTTCAAATTTTCAAAAATTATC
AAACCTCAACTTAGAGAAGCCTTTTAAAATTTTTAAAAATTATCAAGCATCTATATAAAAGAGCC
AT
Found at i:25680362 original size:45 final size:45
Alignment explanation
Indices: 25680078--25680368 Score: 168
Period size: 44 Copynumber: 6.6 Consensus size: 45
25680068 TAATTTCAAA
* * * *
25680078 TTTTCAAAAA-TTATCGAACCTCAACTTAG-AGAAGCCTTTTAAAAT
1 TTTTCAAAAAGTTATTGAGCCTCTATTTAGAAG-AGCCTTTT-AAAT
** * * * * * *
25680123 TTTT--AAAAGTTATCAAGCATTTGTATAAAAGAGCCTTTTAAAG
1 TTTTCAAAAAGTTATTGAGCCTCTATTTAGAAGAGCCTTTTAAAT
* * * * * * * *
25680166 TTTTC-AAAAGTTGTTGAGCATTTACTTAGATGAG-TTGTTTTAAG
1 TTTTCAAAAAGTTATTGAGCCTCTATTTAGAAGAGCCT-TTTAAAT
* * * * * *
25680210 TTTTCAAAAAGTTATTAAACCTCTGTTTAGAGGAACTTTTTAAAGT
1 TTTTCAAAAAGTTATTGAGCCTCTATTTAGAAGAGCCTTTTAAA-T
** * *
25680256 TTTT-AAAAA-TTATCAAGCCTCTATTTAGATGAGCCATTTTAAGT
1 TTTTCAAAAAGTTATTGAGCCTCTATTTAGAAGAGCC-TTTTAAAT
* *
25680300 TTTT-AAAAAGTTATTGAGTCTATATTTAGAAGAGCCTTTTAAAT
1 TTTTCAAAAAGTTATTGAGCCTCTATTTAGAAGAGCCTTTTAAAT
* *
25680344 TTTTCAAAAAGTTGTTGAGTCTCTA
1 TTTTCAAAAAGTTATTGAGCCTCTA
25680369 GTAAAAAAAG
Statistics
Matches: 190, Mismatches: 46, Indels: 20
0.74 0.18 0.08
Matches are distributed among these distances:
43 12 0.06
44 91 0.48
45 81 0.43
46 6 0.03
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.41
Consensus pattern (45 bp):
TTTTCAAAAAGTTATTGAGCCTCTATTTAGAAGAGCCTTTTAAAT
Found at i:25680685 original size:13 final size:13
Alignment explanation
Indices: 25680663--25680701 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
25680653 AATTTTTTTA
*
25680663 ATTTTTATATATT
1 ATTTTAATATATT
**
25680676 ATTTTAATATAAA
1 ATTTTAATATATT
25680689 ATTTTAATATATT
1 ATTTTAATATATT
25680702 TAAGTTGATT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
ATTTTAATATATT
Found at i:25682505 original size:23 final size:23
Alignment explanation
Indices: 25682457--25682505 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
25682447 TGCCTTTTTT
*
25682457 AAAAAATAATAATAAATATGAGA
1 AAAAAATAATAATAAATATGAAA
25682480 AAAAAATAA-AATTAAATAAT-AAA
1 AAAAAATAATAA-TAAAT-ATGAAA
25682503 AAA
1 AAA
25682506 TTAAAGTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 2 0.09
23 19 0.83
24 2 0.09
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (23 bp):
AAAAAATAATAATAAATATGAAA
Found at i:25682567 original size:14 final size:13
Alignment explanation
Indices: 25682548--25682616 Score: 59
Period size: 14 Copynumber: 5.0 Consensus size: 13
25682538 CATTAAAAAC
*
25682548 TAAAATACATATTA
1 TAAAATA-ATAATA
25682562 TAAAATAATAATA
1 TAAAATAATAATA
*
25682575 TAATAAAAATAACTA
1 TAA-AATAATAA-TA
*
25682590 -AAGATAATAATAA
1 TAAAATAATAAT-A
25682603 TAATAATAATAATA
1 TAA-AATAATAATA
25682617 ATAATGAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
12 1 0.02
13 15 0.33
14 19 0.42
15 10 0.22
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.30
Consensus pattern (13 bp):
TAAAATAATAATA
Found at i:25682573 original size:3 final size:3
Alignment explanation
Indices: 25682561--25682621 Score: 74
Period size: 3 Copynumber: 20.7 Consensus size: 3
25682551 AATACATATT
*
25682561 ATA A-A ATA ATA AT- ATA ATA AAA ATA ACTA A-A GATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA -ATA ATA ATA ATA
25682605 ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA AT
25682622 GAAAATGATT
Statistics
Matches: 51, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
2 5 0.10
3 42 0.82
4 4 0.08
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:25684240 original size:8 final size:8
Alignment explanation
Indices: 25684229--25684272 Score: 52
Period size: 9 Copynumber: 5.1 Consensus size: 8
25684219 TAAATATGCC
*
25684229 TATTTTTA
1 TATTATTA
25684237 TATTATTA
1 TATTATTA
25684245 TTATTATTA
1 -TATTATTA
25684254 TTATTATTA
1 -TATTATTA
25684263 TTATTATTA
1 -TATTATTA
25684272 T
1 T
25684273 TATGTTTTGA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
8 8 0.24
9 26 0.76
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (8 bp):
TATTATTA
Found at i:25684245 original size:3 final size:3
Alignment explanation
Indices: 25684237--25684275 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
25684227 CCTATTTTTA
25684237 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
25684276 GTTTTGATCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:25686467 original size:98 final size:99
Alignment explanation
Indices: 25686297--25686483 Score: 299
Period size: 98 Copynumber: 1.9 Consensus size: 99
25686287 TCACATTAGG
25686297 TTAATTACCCAATTTTTGGTGAGTTTAAGCAGTTTGGTTTGGCAATGTTGTTTGACAAAAATCAC
1 TTAATTACCCAATTTTTGGTGAGTTTAAGCAGTTTGGTTTGGCAATGTTGTTTGACAAAAATCAC
*
25686362 CTTACATCTCATCAGACATACGGCAACAGTTGGC
66 CTTACATCTCATCAAACATACGGCAACAGTTGGC
* * *
25686396 TTAATTACCTAA-TTTTGGTGGGTTTAAGCAGTTTGGTTTGGCAAT-TATGTTTGACAACAATCA
1 TTAATTACCCAATTTTTGGTGAGTTTAAGCAGTTTGGTTTGGCAATGT-TGTTTGACAAAAATCA
25686459 -CTATACATCTCATCAAACATACGGC
65 CCT-TACATCTCATCAAACATACGGC
25686484 TACTCTACTT
Statistics
Matches: 82, Mismatches: 4, Indels: 5
0.90 0.04 0.05
Matches are distributed among these distances:
97 3 0.04
98 68 0.83
99 11 0.13
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (99 bp):
TTAATTACCCAATTTTTGGTGAGTTTAAGCAGTTTGGTTTGGCAATGTTGTTTGACAAAAATCAC
CTTACATCTCATCAAACATACGGCAACAGTTGGC
Found at i:25686622 original size:30 final size:31
Alignment explanation
Indices: 25686552--25686650 Score: 105
Period size: 30 Copynumber: 3.3 Consensus size: 31
25686542 TAAATAATAA
* *
25686552 AAAATCTCT-AATCTTTAATTTATATTGAAAT
1 AAAATCTTTAAAT-TTTAATTTATATTTAAAT
25686583 -AAATCTTTAAATTTTAATTTATATTTAAAT
1 AAAATCTTTAAATTTTAATTTATATTTAAAT
* * **
25686613 AAAAT-TTTAACTTTTAACTTATACATAAAT
1 AAAATCTTTAAATTTTAATTTATATTTAAAT
*
25686643 AAACTCTT
1 AAAATCTT
25686651 AATTAAAATT
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
30 49 0.84
31 9 0.16
ACGTcount: A:0.43, C:0.09, G:0.01, T:0.46
Consensus pattern (31 bp):
AAAATCTTTAAATTTTAATTTATATTTAAAT
Found at i:25686697 original size:17 final size:16
Alignment explanation
Indices: 25686663--25686721 Score: 54
Period size: 17 Copynumber: 3.8 Consensus size: 16
25686653 TTAAAATTAT
25686663 TTTTATTTAAAATAAAA
1 TTTTATTT-AAATAAAA
25686680 TTTTATTTAAATACAAA
1 TTTTATTTAAATA-AAA
**
25686697 ---TA-ACAAATAAAA
1 TTTTATTTAAATAAAA
25686709 TTTTATTTAAATA
1 TTTTATTTAAATA
25686722 CAATAAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 11
0.69 0.08 0.23
Matches are distributed among these distances:
12 3 0.09
13 5 0.15
14 2 0.06
15 2 0.06
16 10 0.30
17 11 0.33
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (16 bp):
TTTTATTTAAATAAAA
Found at i:25686705 original size:29 final size:29
Alignment explanation
Indices: 25686671--25686762 Score: 134
Period size: 29 Copynumber: 3.2 Consensus size: 29
25686661 ATTTTTATTT
25686671 AAAATAAAATTTTATTTAAATACAAATAA
1 AAAATAAAATTTTATTTAAATACAAATAA
*
25686700 CAAATAAAATTTTATTTAAATAC-AATAA
1 AAAATAAAATTTTATTTAAATACAAATAA
*
25686728 AAATATAAAAATTTATTTAAATA-AAATAA
1 AAA-ATAAAATTTTATTTAAATACAAATAA
25686757 TAAAAT
1 -AAAAT
25686763 TTATAGATTT
Statistics
Matches: 57, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
28 7 0.12
29 47 0.82
30 3 0.05
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (29 bp):
AAAATAAAATTTTATTTAAATACAAATAA
Found at i:25688616 original size:24 final size:24
Alignment explanation
Indices: 25688571--25688616 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
25688561 TTAATTTTTT
* *
25688571 TAACACAACCTAAATAATACGACA
1 TAACACAACATAAATAACACGACA
*
25688595 TAACACAACATAATTAACACGA
1 TAACACAACATAAATAACACGA
25688617 TTAAACACAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.54, C:0.24, G:0.04, T:0.17
Consensus pattern (24 bp):
TAACACAACATAAATAACACGACA
Found at i:25699139 original size:16 final size:16
Alignment explanation
Indices: 25699120--25699161 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
25699110 ATTTTATTTA
* *
25699120 TTAATAATTATAGTTT
1 TTAAAAATTATAGATT
25699136 TTAAAAAATTATAGATT
1 TT-AAAAATTATAGATT
25699153 TTAAAAATT
1 TTAAAAATT
25699162 TTTACTTGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (16 bp):
TTAAAAATTATAGATT
Found at i:25699147 original size:17 final size:17
Alignment explanation
Indices: 25699125--25699159 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
25699115 ATTTATTAAT
*
25699125 AATTATAGTTTTTAAAA
1 AATTATAGATTTTAAAA
25699142 AATTATAGATTTTAAAA
1 AATTATAGATTTTAAAA
25699159 A
1 A
25699160 TTTTTACTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (17 bp):
AATTATAGATTTTAAAA
Found at i:25700249 original size:57 final size:60
Alignment explanation
Indices: 25700120--25700274 Score: 208
Period size: 57 Copynumber: 2.6 Consensus size: 60
25700110 TTGTACAAGG
* * *
25700120 AAAATTCATACTTTCAACTTTTCCTTAAAATATTTTTCTTGATAATTTTTATTTTTAAGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAATATTTTTCTTGATAATTTTTAATTTTAAGA
* * * *
25700180 AAAATTGGTACTTTCAACTTTTTCTCAAAATGTTTTT-TT-TTAA-TTTTAATTTTAAGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAATATTTTTCTTGATAATTTTTAATTTTAAGA
*
25700237 AAAATTGATACTTTCAACCTTTCCTCAAAATACTTTTT
1 AAAATTGATACTTTCAACTTTTCCTCAAAATA-TTTTT
25700275 GAAAAATTTA
Statistics
Matches: 83, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
57 41 0.49
58 8 0.10
59 2 0.02
60 32 0.39
ACGTcount: A:0.33, C:0.13, G:0.05, T:0.50
Consensus pattern (60 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAATATTTTTCTTGATAATTTTTAATTTTAAGA
Found at i:25700502 original size:3 final size:3
Alignment explanation
Indices: 25700494--25700525 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
25700484 TAATTTAGAA
25700494 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
25700526 ATAAATGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:25701315 original size:3 final size:3
Alignment explanation
Indices: 25701309--25701379 Score: 108
Period size: 3 Copynumber: 23.7 Consensus size: 3
25701299 AAAAAATCAA
25701309 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
25701356 AAT AAT AACA AAT AAT AAA AAT AA
1 AAT AAT AA-T AAT AAT AAT AAT AA
25701380 ACGAAAAAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.03
3 58 0.94
4 2 0.03
ACGTcount: A:0.69, C:0.01, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:25701380 original size:6 final size:6
Alignment explanation
Indices: 25701300--25701430 Score: 63
Period size: 6 Copynumber: 21.7 Consensus size: 6
25701290 GAAAAGATAA
* * * * * * *
25701300 AAAAAT CAAAAT AATAAT AATAAT AATAAT AATAAT AATAAT AATAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
* * * * *
25701348 AATAAT -ATAAT AATAAC AAATAAT AAAAAT AAACGAA- AAAAATT AAAATT
1 AAAAAT AAAAAT AAAAAT AAA-AAT AAAAAT AAA--AAT AAAAA-T AAAAAT
* *
25701398 AAAATT AAAATT AAAAA- ATAAAAT AAAAA- AAAA
1 AAAAAT AAAAAT AAAAAT A-AAAAT AAAAAT AAAA
25701431 TGGGCCCATC
Statistics
Matches: 109, Mismatches: 8, Indels: 17
0.81 0.06 0.13
Matches are distributed among these distances:
5 12 0.11
6 82 0.75
7 13 0.12
8 2 0.02
ACGTcount: A:0.73, C:0.02, G:0.01, T:0.24
Consensus pattern (6 bp):
AAAAAT
Found at i:25701424 original size:12 final size:12
Alignment explanation
Indices: 25701307--25701427 Score: 61
Period size: 15 Copynumber: 9.3 Consensus size: 12
25701297 TAAAAAAATC
25701307 AAAATAATAATAA
1 AAAATAA-AATAA
25701320 TAATAATAATAATAA
1 -AA-AATAA-AATAA
25701335 TAATAATAATAATAA
1 -AA-AATAA-AATAA
*
25701350 TAATATAATAATAA
1 -AAAATAA-AATAA
*
25701364 CAAAT--AAT-A
1 AAAATAAAATAA
25701373 AAAATAAACGA-AA
1 AAAATAAA--ATAA
*
25701386 AAAATTAAAATTA
1 AAAA-TAAAATAA
*
25701399 AAATTAAAATTAA
1 AAAATAAAA-TAA
25701412 AAAATAAAATAA
1 AAAATAAAATAA
25701424 AAAA
1 AAAA
25701428 AAATGGGCCC
Statistics
Matches: 90, Mismatches: 8, Indels: 20
0.76 0.07 0.17
Matches are distributed among these distances:
9 5 0.06
10 3 0.03
11 1 0.01
12 13 0.14
13 23 0.26
14 16 0.18
15 29 0.32
ACGTcount: A:0.72, C:0.02, G:0.01, T:0.26
Consensus pattern (12 bp):
AAAATAAAATAA
Found at i:25701769 original size:87 final size:87
Alignment explanation
Indices: 25701604--25701888 Score: 349
Period size: 87 Copynumber: 3.3 Consensus size: 87
25701594 AAATCTTGAT
* * * * *
25701604 CAAAGCTCATCTAATCAGAGGCTCAACAACTTTTTAAAAAAATAAATAAGGCTCCTCTAAGCAGA
1 CAAAGCTCATCTAAACAGAGGCTCAACGAC--TTTAGAAAAATAAACAAAGCTCCTCTAAGCAGA
*
25701669 GGCTCAACGACTTTGGAAAGATAAA
64 GGCTCAACGACTTT-GAAAAATAAA
* * *
25701694 CAAAGCTCATTTAAACAGAGGCTCAACGACTTT-GAAAAATAAACAAAGCTCATCTAAACAGAGG
1 CAAAGCTCATCTAAACAGAGGCTCAACGACTTTAGAAAAATAAACAAAGCTCCTCTAAGCAGAGG
*
25701758 CTCAACAACTTTGAAAAATAAA
66 CTCAACGACTTTGAAAAATAAA
* * * * * * *
25701780 TAAAGCATC-TCTAAGCAGAAGCTTAATGACTTTGGACAAATAAACAAAGCTCCTCTAAGCAGAG
1 CAAAGC-TCATCTAAACAGAGGCTCAACGACTTTAGAAAAATAAACAAAGCTCCTCTAAGCAGAG
25701844 GCTCAACGACTTTGAAAAATAAA
65 GCTCAACGACTTTGAAAAATAAA
* *
25701867 CAAAGCTCCTCTAAATAGAGGC
1 CAAAGCTCATCTAAACAGAGGC
25701889 ACCATAACTT
Statistics
Matches: 168, Mismatches: 24, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
86 35 0.21
87 103 0.61
88 3 0.02
90 27 0.16
ACGTcount: A:0.44, C:0.20, G:0.15, T:0.21
Consensus pattern (87 bp):
CAAAGCTCATCTAAACAGAGGCTCAACGACTTTAGAAAAATAAACAAAGCTCCTCTAAGCAGAGG
CTCAACGACTTTGAAAAATAAA
Found at i:25701843 original size:130 final size:132
Alignment explanation
Indices: 25701604--25701888 Score: 416
Period size: 130 Copynumber: 2.2 Consensus size: 132
25701594 AAATCTTGAT
* *
25701604 CAAAGCTCATCTAATCAGAGGCTCAACAACTTTTTAAAAAAATAAATAAGGCTCCTCTAAGCAGA
1 CAAAGCTCATCTAAACAGAGGCTCAACAAC-TTTTAAAAAAATAAATAAAGCTCCTCTAAGCAGA
* *
25701669 GGCTCAACGACTTTGGAAAGATAAACAAAGCTCATTTAAACAGAGGCTCAACGACTTTGAAAAAT
65 AGCTCAACGACTTTGGAAAGATAAACAAAGCTCATCTAAACAGAGGCTCAACGACTTTGAAAAAT
25701734 AAA
130 AAA
*
25701737 CAAAGCTCATCTAAACAGAGGCTCAACAAC-TTT-GAAAAATAAATAAAGCAT-CTCTAAGCAGA
1 CAAAGCTCATCTAAACAGAGGCTCAACAACTTTTAAAAAAATAAATAAAGC-TCCTCTAAGCAGA
* * * *
25701799 AGCTTAATGACTTTGGACAA-ATAAACAAAGCTCCTCTAAGCAGAGGCTCAACGACTTTGAAAAA
65 AGCTCAACGACTTTGGA-AAGATAAACAAAGCTCATCTAAACAGAGGCTCAACGACTTTGAAAAA
25701863 TAAA
129 TAAA
* *
25701867 CAAAGCTCCTCTAAATAGAGGC
1 CAAAGCTCATCTAAACAGAGGC
25701889 ACCATAACTT
Statistics
Matches: 139, Mismatches: 11, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
130 104 0.75
131 6 0.04
133 29 0.21
ACGTcount: A:0.44, C:0.20, G:0.15, T:0.21
Consensus pattern (132 bp):
CAAAGCTCATCTAAACAGAGGCTCAACAACTTTTAAAAAAATAAATAAAGCTCCTCTAAGCAGAA
GCTCAACGACTTTGGAAAGATAAACAAAGCTCATCTAAACAGAGGCTCAACGACTTTGAAAAATA
AA
Found at i:25701899 original size:43 final size:43
Alignment explanation
Indices: 25701604--25701888 Score: 329
Period size: 43 Copynumber: 6.5 Consensus size: 43
25701594 AAATCTTGAT
* * * *
25701604 CAAAGCTCATCTAATCAGAGGCTCAACAACTTTTTAAAAAAATAAA
1 CAAAGCTCCTCTAAACAGAGGCTCAACGAC--TTT-GAAAAATAAA
* * * *
25701650 TAAGGCTCCTCTAAGCAGAGGCTCAACGACTTTGGAAAGATAAA
1 CAAAGCTCCTCTAAACAGAGGCTCAACGACTTT-GAAAAATAAA
* *
25701694 CAAAGCTCATTTAAACAGAGGCTCAACGACTTTGAAAAATAAA
1 CAAAGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAA
* *
25701737 CAAAGCTCATCTAAACAGAGGCTCAACAACTTTGAAAAATAAA
1 CAAAGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAA
* * * * * *
25701780 TAAAGCAT-CTCTAAGCAGAAGCTTAATGACTTTGGACAAATAAA
1 CAAAGC-TCCTCTAAACAGAGGCTCAACGACTTT-GAAAAATAAA
*
25701824 CAAAGCTCCTCTAAGCAGAGGCTCAACGACTTTGAAAAATAAA
1 CAAAGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAA
*
25701867 CAAAGCTCCTCTAAATAGAGGC
1 CAAAGCTCCTCTAAACAGAGGC
25701889 ACCATAACTT
Statistics
Matches: 205, Mismatches: 31, Indels: 9
0.84 0.13 0.04
Matches are distributed among these distances:
43 104 0.51
44 76 0.37
46 25 0.12
ACGTcount: A:0.44, C:0.20, G:0.15, T:0.21
Consensus pattern (43 bp):
CAAAGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAA
Found at i:25702921 original size:11 final size:11
Alignment explanation
Indices: 25702905--25702940 Score: 54
Period size: 11 Copynumber: 3.1 Consensus size: 11
25702895 TTACTTTGGG
25702905 TCTTTTTTTTT
1 TCTTTTTTTTT
25702916 TCTTTTTTTTT
1 TCTTTTTTTTT
25702927 TCTCTTATTTTTT
1 TCT-TT-TTTTTT
25702940 T
1 T
25702941 GTCAAGCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 14 0.61
12 2 0.09
13 7 0.30
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.86
Consensus pattern (11 bp):
TCTTTTTTTTT
Found at i:25702925 original size:13 final size:14
Alignment explanation
Indices: 25702907--25702940 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
25702897 ACTTTGGGTC
*
25702907 TTTTTTTTTTCTT-
1 TTTTTTTTCTCTTA
25702920 TTTTTTTTCTCTTA
1 TTTTTTTTCTCTTA
25702934 TTTTTTT
1 TTTTTTT
25702941 GTCAAGCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.03, C:0.09, G:0.00, T:0.88
Consensus pattern (14 bp):
TTTTTTTTCTCTTA
Found at i:25710478 original size:19 final size:18
Alignment explanation
Indices: 25710451--25710489 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
25710441 ATTTGGGTCG
*
25710451 TTAGGTTCTTAACGTACTT
1 TTAGCTTCTT-ACGTACTT
*
25710470 TTAGCTTCTTAGGTACTT
1 TTAGCTTCTTACGTACTT
25710488 TT
1 TT
25710490 TTTTACCACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.18, C:0.15, G:0.15, T:0.51
Consensus pattern (18 bp):
TTAGCTTCTTACGTACTT
Found at i:25713524 original size:58 final size:60
Alignment explanation
Indices: 25713453--25713596 Score: 220
Period size: 58 Copynumber: 2.4 Consensus size: 60
25713443 TGATAATAAA
* * * *
25713453 AAAAATTGGTACTTCCAACTTTTTCTCAAAATATTTTTTTTGA-AA-TTTTAATTTTAAG
1 AAAAATTGATACTTTCAACTTTTCCTCAAAATATTTTTCTTGATAATTTTTAATTTTAAG
* *
25713511 AAAAATTGATACTTTCAACTTTTCCTTAAAATATTTTTCTTGATAATTTTTATTTTTAAG
1 AAAAATTGATACTTTCAACTTTTCCTCAAAATATTTTTCTTGATAATTTTTAATTTTAAG
25713571 AAAAATTGATACTTTCAACTTTTCCT
1 AAAAATTGATACTTTCAACTTTTCCT
25713597 TAAAGTACTT
Statistics
Matches: 78, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
58 38 0.49
59 2 0.03
60 38 0.49
ACGTcount: A:0.34, C:0.12, G:0.06, T:0.49
Consensus pattern (60 bp):
AAAAATTGATACTTTCAACTTTTCCTCAAAATATTTTTCTTGATAATTTTTAATTTTAAG
Found at i:25713572 original size:60 final size:58
Alignment explanation
Indices: 25713453--25713628 Score: 225
Period size: 60 Copynumber: 3.1 Consensus size: 58
25713443 TGATAATAAA
* * * * *
25713453 AAAAATTGGTACTTCCAACTTTTTCTCAAAATATTTTTTTTGAAATTTTAATTTTAAG
1 AAAAATTGATACTTTCAACTTTTCCTTAAAATATTTTTCTTGAAATTTTAATTTTAAG
*
25713511 AAAAATTGATACTTTCAACTTTTCCTTAAAATATTTTTCTTGATAATTTTTATTTTTAAG
1 AAAAATTGATACTTTCAACTTTTCCTTAAAATATTTTTCTTGA-AA-TTTTAATTTTAAG
* *
25713571 AAAAATTGATACTTTCAACTTTTCCTTAAAGTA-CTTT-TTGAAAATTTT-ATTTT-AG
1 AAAAATTGATACTTTCAACTTTTCCTTAAAATATTTTTCTTG-AAATTTTAATTTTAAG
25713626 AAA
1 AAA
25713629 TTTTACTTCC
Statistics
Matches: 106, Mismatches: 9, Indels: 9
0.85 0.07 0.07
Matches are distributed among these distances:
55 5 0.05
56 4 0.04
57 4 0.04
58 43 0.41
59 6 0.06
60 44 0.42
ACGTcount: A:0.35, C:0.10, G:0.06, T:0.48
Consensus pattern (58 bp):
AAAAATTGATACTTTCAACTTTTCCTTAAAATATTTTTCTTGAAATTTTAATTTTAAG
Found at i:25713703 original size:61 final size:62
Alignment explanation
Indices: 25713629--25713806 Score: 195
Period size: 61 Copynumber: 2.9 Consensus size: 62
25713619 ATTTTAGAAA
* * *
25713629 TTTTACTTCCAAGAAAAATTGATAATTTTAACTTTTCCCTAAAAATATATTTTTT-AAA-CTT
1 TTTTATTTTCAAGAGAAATTGATAATTTTAACTTTT-CCTAAAAATATATTTTTTAAAACCTT
*
25713690 TTTTATTTTCAAGAGGAATTGAT-ATTTTCAACTTTTCCTAAAAATAT-TTTTTTAAAACCCTT
1 TTTTATTTTCAAGAGAAATTGATAATTTT-AACTTTTCCTAAAAATATATTTTTTAAAA-CCTT
* * * * *
25713752 TTTCATTTTC-AGAGAAATTGATACTTTCAAATTTTTCTTAAAAATATATATTTTT
1 TTTTATTTTCAAGAGAAATTGATAATTT-TAACTTTTCCTAAAAATATAT-TTTTT
25713807 TTGAAACTTT
Statistics
Matches: 99, Mismatches: 10, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
59 6 0.06
60 19 0.19
61 37 0.37
62 31 0.31
63 1 0.01
64 5 0.05
ACGTcount: A:0.35, C:0.12, G:0.05, T:0.48
Consensus pattern (62 bp):
TTTTATTTTCAAGAGAAATTGATAATTTTAACTTTTCCTAAAAATATATTTTTTAAAACCTT
Found at i:25713835 original size:6 final size:6
Alignment explanation
Indices: 25713826--25713879 Score: 60
Period size: 6 Copynumber: 9.2 Consensus size: 6
25713816 TAATTTTAAG
*
25713826 AAAAAT AAAAA- AATATAT AAAAAT AAAAAT AAAAAT -AAAAT -AAAAT
1 AAAAAT AAAAAT AA-AAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
25713872 AAGAAAT A
1 AA-AAAT A
25713880 CCAAATAATT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
5 12 0.29
6 23 0.55
7 7 0.17
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.19
Consensus pattern (6 bp):
AAAAAT
Found at i:25714730 original size:3 final size:3
Alignment explanation
Indices: 25714722--25714813 Score: 62
Period size: 3 Copynumber: 28.7 Consensus size: 3
25714712 ATCAATCAAA
* * *
25714722 AAT AAT AAT AAT AAT AAT -AT AAT AGCA- AAT AAT AAA AAT AAA AAA
1 AAT AAT AAT AAT AAT AAT AAT AAT A--AT AAT AAT AAT AAT AAT AAT
*
25714767 AAT AAAC AAT AAAT AAAT AAAT AAAT AAAT AAT AAT AAT AAT AAT AA
1 AAT -AAT AAT -AAT -AAT -AAT -AAT -AAT AAT AAT AAT AAT AAT AA
25714814 AAGAAAAAAA
Statistics
Matches: 77, Mismatches: 6, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
2 3 0.04
3 51 0.66
4 22 0.29
5 1 0.01
ACGTcount: A:0.72, C:0.02, G:0.01, T:0.25
Consensus pattern (3 bp):
AAT
Found at i:25714781 original size:4 final size:4
Alignment explanation
Indices: 25714774--25714798 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
25714764 AAAAATAAAC
25714774 AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA A
25714799 TAATAATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:25715054 original size:25 final size:26
Alignment explanation
Indices: 25715015--25715063 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
25715005 AGATAGTATA
*
25715015 AAAATTAAAATAAATTTAA-AAAATT
1 AAAATTAAAATAAATATAATAAAATT
25715040 AAAATTATAAA-AAATATAATAAAA
1 AAAATTA-AAATAAATATAATAAAA
25715064 AAATCTATGC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (26 bp):
AAAATTAAAATAAATATAATAAAATT
Found at i:25715497 original size:21 final size:20
Alignment explanation
Indices: 25715446--25715497 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
25715436 ATCAATAATT
25715446 TAAATAATATTATATTATAAA
1 TAAAT-ATATTATATTATAAA
* * *
25715467 TAATAAATATTAATTTTTTAAA
1 TAA-ATATATT-ATATTATAAA
25715489 TAAATATAT
1 TAAATATAT
25715498 AAAAAATTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 13 0.52
22 12 0.48
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TAAATATATTATATTATAAA
Found at i:25715509 original size:28 final size:26
Alignment explanation
Indices: 25715462--25715513 Score: 77
Period size: 28 Copynumber: 1.9 Consensus size: 26
25715452 ATATTATATT
*
25715462 ATAAATAATAAATATTAATTTTTTAA
1 ATAAATAATAAAAATTAATTTTTTAA
25715488 ATAAATATATAAAAAATTAATTTTTT
1 ATAAATA-AT-AAAAATTAATTTTTT
25715514 TTAAAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 7 0.30
27 2 0.09
28 14 0.61
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
ATAAATAATAAAAATTAATTTTTTAA
Found at i:25715574 original size:20 final size:22
Alignment explanation
Indices: 25715549--25715589 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
25715539 AATATTATTT
*
25715549 AATTTATTTA-TAA-AATATAA
1 AATTTATATATTAATAATATAA
25715569 AATTTATATATTAATAATATA
1 AATTTATATATTAATAATATA
25715590 TCAAATATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 3 0.17
22 6 0.33
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
AATTTATATATTAATAATATAA
Found at i:25715761 original size:16 final size:15
Alignment explanation
Indices: 25715728--25715765 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
25715718 AAAGAAATGA
25715728 AAATATT-AATATTT
1 AAATATTAAATATTT
*
25715742 AAATATTAAATTTATT
1 AAATATTAAATAT-TT
25715758 AAATATTA
1 AAATATTA
25715766 TTAATAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AAATATTAAATATTT
Found at i:25716593 original size:27 final size:27
Alignment explanation
Indices: 25716563--25716615 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
25716553 TTTAAATTTG
*
25716563 ATTTAATTTTATATT-ATATAAAATTAT
1 ATTTAATTTGAT-TTGATATAAAATTAT
*
25716590 ATTTAATTTGATTTGATATTAAATTA
1 ATTTAATTTGATTTGATATAAAATTA
25716616 ATAAAATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 2 0.09
27 21 0.91
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (27 bp):
ATTTAATTTGATTTGATATAAAATTAT
Found at i:25716603 original size:37 final size:37
Alignment explanation
Indices: 25716548--25716622 Score: 107
Period size: 37 Copynumber: 2.0 Consensus size: 37
25716538 TTTTATTTTT
* *
25716548 TTATATTTAAATTTGATTTAATTTTATATTATATAAAA
1 TTATATTTAAATTTGATTTAATATTAAATTA-ATAAAA
*
25716586 TTATATTT-AATTTGATTTGATATTAAATTAATAAAA
1 TTATATTTAAATTTGATTTAATATTAAATTAATAAAA
25716622 T
1 T
25716623 ATTATTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
36 7 0.21
37 19 0.56
38 8 0.24
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (37 bp):
TTATATTTAAATTTGATTTAATATTAAATTAATAAAA
Found at i:25717591 original size:14 final size:13
Alignment explanation
Indices: 25717567--25717593 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
25717557 ATATTATATA
25717567 AAAATAATTTTTT
1 AAAATAATTTTTT
25717580 AAAATAATTTTTT
1 AAAATAATTTTTT
25717593 A
1 A
25717594 TTTATATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AAAATAATTTTTT
Found at i:25717611 original size:8 final size:8
Alignment explanation
Indices: 25717592--25717634 Score: 50
Period size: 8 Copynumber: 5.1 Consensus size: 8
25717582 AATAATTTTT
25717592 TATTTATA
1 TATTTATA
25717600 TATATGTATA
1 TAT-T-TATA
*
25717610 TAATTATA
1 TATTTATA
*
25717618 TATTTAAA
1 TATTTATA
25717626 TATTTATA
1 TATTTATA
25717634 T
1 T
25717635 TTAAAAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
8 21 0.72
9 2 0.07
10 6 0.21
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (8 bp):
TATTTATA
Found at i:25719739 original size:12 final size:12
Alignment explanation
Indices: 25719722--25719748 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
25719712 GTGTTGGGCC
25719722 ATGCTGAGATGT
1 ATGCTGAGATGT
25719734 ATGCTGAGATGT
1 ATGCTGAGATGT
25719746 ATG
1 ATG
25719749 ATGACTGACG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.07, G:0.33, T:0.33
Consensus pattern (12 bp):
ATGCTGAGATGT
Found at i:25727319 original size:2 final size:2
Alignment explanation
Indices: 25727312--25727340 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
25727302 GACATGACAT
25727312 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
25727341 CGACAGAGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:25729724 original size:6 final size:6
Alignment explanation
Indices: 25729693--25729727 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
25729683 TATTCAAAAG
* *
25729693 ATTAAA AATAAA AATAAA ATTAAA ATTAAA ATTAA
1 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAA
25729728 TGATAAAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (6 bp):
ATTAAA
Found at i:25729988 original size:40 final size:40
Alignment explanation
Indices: 25729916--25729991 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
25729906 AATATTAAAA
***
25729916 ATTAATAATAATAAAATATTATTTATTTATTTATTAGTTT
1 ATTAATAATAATAAAATATTATTTAGCAATTTATTAGTTT
*
25729956 ATTATATAATAAT-AAATTTTATTTAGCAATTTATTA
1 ATTA-ATAATAATAAAATATTATTTAGCAATTTATTA
25729992 TATAATAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 23 0.74
41 8 0.26
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (40 bp):
ATTAATAATAATAAAATATTATTTAGCAATTTATTAGTTT
Found at i:25733111 original size:12 final size:13
Alignment explanation
Indices: 25733070--25733112 Score: 54
Period size: 12 Copynumber: 3.4 Consensus size: 13
25733060 TTATAATAAA
*
25733070 AATTATATTTATAT
1 AATTA-ATTAATAT
25733084 AATTAATTAA-AT
1 AATTAATTAATAT
25733096 AATTAATTAATA-
1 AATTAATTAATAT
25733108 AATTA
1 AATTA
25733113 TAATTTAACT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 17 0.63
13 5 0.19
14 5 0.19
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
AATTAATTAATAT
Found at i:25733613 original size:22 final size:22
Alignment explanation
Indices: 25733545--25733614 Score: 67
Period size: 21 Copynumber: 3.3 Consensus size: 22
25733535 GCAAGTATTA
* *
25733545 AAAAAATTTTC-TAAAGGAATTT
1 AAAATATTTTCTTAAA-AAATTT
25733567 -AAAT-TTTTCTTAAAAAATTT
1 AAAATATTTTCTTAAAAAATTT
*
25733587 GAAATATTTT-TTAAAAAATTAT
1 AAAATATTTTCTTAAAAAATT-T
25733609 AAAATA
1 AAAATA
25733615 ATAAAAAACA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
20 10 0.24
21 21 0.51
22 10 0.24
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.41
Consensus pattern (22 bp):
AAAATATTTTCTTAAAAAATTT
Found at i:25733694 original size:29 final size:29
Alignment explanation
Indices: 25733661--25733716 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
25733651 ATGAAAACTT
*
25733661 AAAAACTCAAGAAAATCAAAATTTTAAGA
1 AAAAACTCAAAAAAATCAAAATTTTAAGA
* *
25733690 AAAAATTCAAAAAAATGAAAATTTTAA
1 AAAAACTCAAAAAAATCAAAATTTTAA
25733717 AACAAATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.64, C:0.07, G:0.05, T:0.23
Consensus pattern (29 bp):
AAAAACTCAAAAAAATCAAAATTTTAAGA
Found at i:25733718 original size:17 final size:17
Alignment explanation
Indices: 25733698--25733731 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
25733688 GAAAAAATTC
25733698 AAAA-AAATGAAAATTTT
1 AAAACAAAT-AAAATTTT
25733715 AAAACAAATAAAATTTT
1 AAAACAAATAAAATTTT
25733732 CTTAAATTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (17 bp):
AAAACAAATAAAATTTT
Found at i:25733756 original size:18 final size:18
Alignment explanation
Indices: 25733741--25733776 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
25733731 TCTTAAATTC
25733741 AAAAAATTCAAAAAATAA
1 AAAAAATTCAAAAAATAA
*
25733759 AAAAAATTGAAAATAATA
1 AAAAAATTCAAAA-AATA
25733777 TAAATCTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19
Consensus pattern (18 bp):
AAAAAATTCAAAAAATAA
Found at i:25733841 original size:9 final size:9
Alignment explanation
Indices: 25733829--25733904 Score: 52
Period size: 10 Copynumber: 8.4 Consensus size: 9
25733819 ATTATGAAAA
25733829 TTTTTAA-T
1 TTTTTAATT
25733837 TTTTTATATT
1 TTTTTA-ATT
* *
25733847 TTATGAATT
1 TTTTTAATT
25733856 TTTTTATATT
1 TTTTTA-ATT
*
25733866 TTTTTAGTT
1 TTTTTAATT
25733875 TTTTT--TT
1 TTTTTAATT
*
25733882 AATTTTAA-T
1 -TTTTTAATT
25733891 TTTTTATATT
1 TTTTTA-ATT
25733901 TTTT
1 TTTT
25733905 AGCATATTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
7 2 0.04
8 15 0.28
9 17 0.32
10 19 0.36
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (9 bp):
TTTTTAATT
Found at i:25733850 original size:27 final size:27
Alignment explanation
Indices: 25733820--25733902 Score: 80
Period size: 27 Copynumber: 3.1 Consensus size: 27
25733810 TTTTTAAAAA
25733820 TTATGAAAATTTTTAATTTTTTATATT
1 TTATGAAAATTTTTAATTTTTTATATT
**
25733847 TTATGAATTTTTTTATATTTTTT-TAGTT
1 TTATGAAAATTTTTA-ATTTTTTATA-TT
* ***
25733875 TTTTTTTAA-TTTTAATTTTTTATATT
1 TTATGAAAATTTTTAATTTTTTATATT
25733901 TT
1 TT
25733903 TTAGCATATT
Statistics
Matches: 45, Mismatches: 8, Indels: 7
0.75 0.13 0.12
Matches are distributed among these distances:
26 11 0.24
27 22 0.49
28 12 0.27
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (27 bp):
TTATGAAAATTTTTAATTTTTTATATT
Found at i:25733860 original size:19 final size:17
Alignment explanation
Indices: 25733828--25733932 Score: 81
Period size: 19 Copynumber: 5.9 Consensus size: 17
25733818 AATTATGAAA
25733828 ATTTTTAA-TTTTTTAT
1 ATTTTTAATTTTTTTAT
25733844 ATTTTATGAATTTTTTTAT
1 ATTTT-T-AATTTTTTTAT
* *
25733863 ATTTTTTTAGTTTTTTTTT
1 A--TTTTTAATTTTTTTAT
*
25733882 AATTTTAA-TTTTTTAT
1 ATTTTTAATTTTTTTAT
*
25733898 ATTTTTTAGCA-TATTTTAT
1 A-TTTTTA--ATTTTTTTAT
*
25733917 ATTTTTAAATTTTTTA
1 ATTTTTAATTTTTTTA
25733933 GAATTTTAAA
Statistics
Matches: 72, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
16 14 0.19
17 17 0.24
18 8 0.11
19 28 0.39
20 1 0.01
21 4 0.06
ACGTcount: A:0.25, C:0.01, G:0.03, T:0.71
Consensus pattern (17 bp):
ATTTTTAATTTTTTTAT
Found at i:25733904 original size:10 final size:10
Alignment explanation
Indices: 25733836--25733887 Score: 54
Period size: 10 Copynumber: 5.3 Consensus size: 10
25733826 AAATTTTTAA
25733836 TTTTTTATAT
1 TTTTTTATAT
* *
25733846 TTTATGA-AT
1 TTTTTTATAT
25733855 TTTTTTATAT
1 TTTTTTATAT
*
25733865 TTTTTTAGTTT
1 TTTTTTA-TAT
25733876 TTTTTTA-AT
1 TTTTTTATAT
25733885 TTT
1 TTT
25733888 AATTTTTTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
9 11 0.32
10 14 0.41
11 9 0.26
ACGTcount: A:0.19, C:0.00, G:0.04, T:0.77
Consensus pattern (10 bp):
TTTTTTATAT
Found at i:25733905 original size:9 final size:9
Alignment explanation
Indices: 25733829--25733932 Score: 69
Period size: 9 Copynumber: 11.7 Consensus size: 9
25733819 ATTATGAAAA
25733829 TTTTTA-AT
1 TTTTTATAT
25733837 TTTTTATAT
1 TTTTTATAT
*
25733846 TTTATGA-ATT
1 TTT-TTATA-T
25733856 TTTTTATAT
1 TTTTTATAT
25733865 TTTTT-TAGT
1 TTTTTATA-T
25733874 TTTTT-T-T
1 TTTTTATAT
25733881 TAATTTTA-AT
1 T--TTTTATAT
25733891 TTTTTATAT
1 TTTTTATAT
*
25733900 TTTTTAGCAT
1 TTTTTA-TAT
*
25733910 ATTTTATA-
1 TTTTTATAT
*
25733918 TTTTTAAAT
1 TTTTTATAT
25733927 TTTTTA
1 TTTTTA
25733933 GAATTTTAAA
Statistics
Matches: 77, Mismatches: 7, Indels: 23
0.72 0.07 0.21
Matches are distributed among these distances:
7 2 0.03
8 19 0.25
9 40 0.52
10 16 0.21
ACGTcount: A:0.24, C:0.01, G:0.03, T:0.72
Consensus pattern (9 bp):
TTTTTATAT
Found at i:25733913 original size:27 final size:25
Alignment explanation
Indices: 25733830--25733941 Score: 86
Period size: 27 Copynumber: 4.2 Consensus size: 25
25733820 TTATGAAAAT
*
25733830 TTTTAATTTTTTATATTTTAT-GAA
1 TTTTAATTTTTTATATTTTTTAGAA
**
25733854 TTTTTTTATATTTTTT-TAGTTTTTTTTTAA
1 ---TTTTA-ATTTTTTATA--TTTTTTAGAA
25733884 TTTTAATTTTTTATATTTTTTAGCATA
1 TTTTAATTTTTTATATTTTTTAG-A-A
*
25733911 TTTT-ATATTTTTAAATTTTTTAGAA
1 TTTTAAT-TTTTTATATTTTTTAGAA
25733936 TTTTAA
1 TTTTAA
25733942 AAAAAATTTA
Statistics
Matches: 71, Mismatches: 5, Indels: 19
0.75 0.05 0.20
Matches are distributed among these distances:
25 11 0.15
26 12 0.17
27 34 0.48
28 7 0.10
29 5 0.07
30 2 0.03
ACGTcount: A:0.26, C:0.01, G:0.04, T:0.70
Consensus pattern (25 bp):
TTTTAATTTTTTATATTTTTTAGAA
Found at i:25733977 original size:19 final size:19
Alignment explanation
Indices: 25733917--25733991 Score: 64
Period size: 19 Copynumber: 3.9 Consensus size: 19
25733907 CATATTTTAT
*
25733917 ATTTTTAAA-TTTTTTAGA
1 ATTTTTAAATTTTTTTAAA
* ****
25733935 ATTTTAAAAAAAATTTATAA
1 ATTTTTAAATTTTTTTA-AA
25733955 A-TTTTAAGATTTTTTTAAA
1 ATTTTTAA-ATTTTTTTAAA
25733974 ATTTTTAAATTTTTTTAA
1 ATTTTTAAATTTTTTTAA
25733992 TTTGCAAATT
Statistics
Matches: 43, Mismatches: 10, Indels: 7
0.72 0.17 0.12
Matches are distributed among these distances:
18 8 0.19
19 22 0.51
20 13 0.30
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (19 bp):
ATTTTTAAATTTTTTTAAA
Found at i:25733988 original size:9 final size:9
Alignment explanation
Indices: 25733884--25733994 Score: 50
Period size: 9 Copynumber: 12.1 Consensus size: 9
25733874 TTTTTTTTAA
25733884 TTTT-AATT
1 TTTTAAATT
*
25733892 TTTTATATT
1 TTTTAAATT
* *
25733901 TTTTAGCATA
1 TTTTA-AATT
*
25733911 TTTTATA-T
1 TTTTAAATT
25733919 TTTTAAATT
1 TTTTAAATT
25733928 TTTTAGAATT
1 TTTTA-AATT
** *
25733938 TTAAAAAAAAT
1 TT--TTAAATT
*
25733949 TTATAAA--
1 TTTTAAATT
25733956 TTTTAAGATTT
1 TTTTAA-A-TT
*
25733967 TTTTAAAAT
1 TTTTAAATT
25733976 TTTTAAATT
1 TTTTAAATT
*
25733985 TTTTTAATT
1 TTTTAAATT
25733994 T
1 T
25733995 GCAAATTTTA
Statistics
Matches: 79, Mismatches: 14, Indels: 19
0.71 0.12 0.17
Matches are distributed among these distances:
7 5 0.06
8 11 0.14
9 37 0.47
10 14 0.18
11 11 0.14
12 1 0.01
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.61
Consensus pattern (9 bp):
TTTTAAATT
Found at i:25735771 original size:20 final size:20
Alignment explanation
Indices: 25735748--25735785 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
25735738 TTTAAATAGA
25735748 TTTA-GTTATAAAATAATTAT
1 TTTATGTTATAAAA-AATTAT
*
25735768 TTTATTTTATAAAAAATT
1 TTTATGTTATAAAAAATT
25735786 TAAAATATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (20 bp):
TTTATGTTATAAAAAATTAT
Found at i:25740515 original size:11 final size:11
Alignment explanation
Indices: 25740499--25740534 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
25740489 AAGGAAGAAG
25740499 AAGGAGAAAGA
1 AAGGAGAAAGA
25740510 AAGGAGGAAAGA
1 AAGGA-GAAAGA
*
25740522 AAGAAGAAAGA
1 AAGGAGAAAGA
25740533 AA
1 AA
25740535 AAAAATAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (11 bp):
AAGGAGAAAGA
Found at i:25740797 original size:117 final size:117
Alignment explanation
Indices: 25740676--25740912 Score: 332
Period size: 117 Copynumber: 2.0 Consensus size: 117
25740666 GATTTGTAAG
* * * *
25740676 ATTTATATTAATTTTATGGTAAATTTAGGTTTGATATATGTTAAGATTTATATTT-GTCTTGAAA
1 ATTTATACTAATTTTATCGTAAATTTAGGTTTGATATATATTAAGATTTATATTTGGTCTTAAAA
*
25740740 ATTTTTATATTTGATATTTTTTAAAATTTAATAATAATGATTGAAATTAAAAA
66 ATTTTTATATTTGATA-TTTTTAAAATTTAATAATAATGATTGAAATAAAAAA
* * * * * * * *
25740793 ATTTATGCTGATTTTATCTTAAATTTGGGTTTTATGTGTATTAAGATTTATATTTGGTTTTAAAA
1 ATTTATACTAATTTTATCGTAAATTTAGGTTTGATATATATTAAGATTTATATTTGGTCTTAAAA
*
25740858 ATTTTTATATTTGATATTTTTAAAATTTAATAATAATTATTGAAATAAAAAA
66 ATTTTTATATTTGATATTTTTAAAATTTAATAATAATGATTGAAATAAAAAA
25740910 ATT
1 ATT
25740913 ATTGTATTAA
Statistics
Matches: 105, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
117 82 0.78
118 23 0.22
ACGTcount: A:0.38, C:0.01, G:0.10, T:0.51
Consensus pattern (117 bp):
ATTTATACTAATTTTATCGTAAATTTAGGTTTGATATATATTAAGATTTATATTTGGTCTTAAAA
ATTTTTATATTTGATATTTTTAAAATTTAATAATAATGATTGAAATAAAAAA
Found at i:25740927 original size:17 final size:17
Alignment explanation
Indices: 25740884--25740927 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
25740874 TTTTTAAAAT
25740884 TTAATAATAATTATTGAA
1 TTAATAA-AATTATTGAA
* * *
25740902 ATAAAAAAATTATTGTA
1 TTAATAAAATTATTGAA
25740919 TTAATAAAA
1 TTAATAAAA
25740928 GGTTGGTAAA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.39
Consensus pattern (17 bp):
TTAATAAAATTATTGAA
Found at i:25746208 original size:21 final size:23
Alignment explanation
Indices: 25746166--25746218 Score: 65
Period size: 21 Copynumber: 2.4 Consensus size: 23
25746156 TCTAACGTTT
*
25746166 TATTTTTTGGATTACTTATAAGA
1 TATTTTTTAGATTACTTATAAGA
* *
25746189 TTTTTTTTAGATTA-TT-TAAGG
1 TATTTTTTAGATTACTTATAAGA
25746210 TATTTTTTA
1 TATTTTTTA
25746219 TAAAAAAAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 12 0.46
22 2 0.08
23 12 0.46
ACGTcount: A:0.26, C:0.02, G:0.11, T:0.60
Consensus pattern (23 bp):
TATTTTTTAGATTACTTATAAGA
Found at i:25746313 original size:62 final size:62
Alignment explanation
Indices: 25746197--25746340 Score: 152
Period size: 62 Copynumber: 2.3 Consensus size: 62
25746187 GATTTTTTTT
* * *
25746197 AGATTATTTAAGGTATTTTTTATAAAAAAAAGTCTTAAATAATGCTGATCAATTT-TTTAAA
1 AGATTATTTAAGGTATTTTTTATAAAAAAAAGCCTTAAATAATCCTCATCAATTTCTTTAAA
* * *
25746258 AGATTATTTAAAGTATTTTTT-TACCAAAAAATA-CCTTAAATAATCCTCTTTAATTTGCTTTAA
1 AGATTATTTAAGGTATTTTTTATA--AAAAAA-AGCCTTAAATAATCCTCATCAATTT-CTTTAA
*
25746321 G
62 A
*
25746322 A-ATTATTTAAGGTGTTTTT
1 AGATTATTTAAGGTATTTTT
25746341 CATGCTAAAC
Statistics
Matches: 69, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
60 2 0.03
61 20 0.29
62 24 0.35
63 17 0.25
64 6 0.09
ACGTcount: A:0.38, C:0.08, G:0.09, T:0.45
Consensus pattern (62 bp):
AGATTATTTAAGGTATTTTTTATAAAAAAAAGCCTTAAATAATCCTCATCAATTTCTTTAAA
Found at i:25755519 original size:22 final size:21
Alignment explanation
Indices: 25755494--25755555 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 21
25755484 AATAACTATT
*
25755494 ATATATATATAAATTTATTTAA
1 ATATATATA-AAATTTATTAAA
25755516 ATATAT-TAAAATTTTTATTAAA
1 ATATATATAAAA--TTTATTAAA
25755538 ATAATATATAAAAATTTA
1 AT-ATATAT-AAAATTTA
25755556 AAAACATATA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
20 3 0.09
21 2 0.06
22 16 0.47
23 8 0.24
24 1 0.03
25 4 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
ATATATATAAAATTTATTAAA
Found at i:25755532 original size:18 final size:20
Alignment explanation
Indices: 25755496--25755532 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
25755486 TAACTATTAT
*
25755496 ATATATATAAATTTATTTAA
1 ATATATATAAAATTATTTAA
25755516 ATATAT-TAAAATT-TTTA
1 ATATATATAAAATTATTTA
25755533 TTAAAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 4 0.25
19 6 0.38
20 6 0.38
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATATATAAAATTATTTAA
Found at i:25760549 original size:2 final size:2
Alignment explanation
Indices: 25760542--25760573 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
25760532 CTTGTTCAAC
25760542 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25760574 TATCCTCCTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25761866 original size:30 final size:29
Alignment explanation
Indices: 25761827--25761897 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 29
25761817 CGTGGCATCT
* *
25761827 AAATGAATTTTCATCTTTTAA-TTAGTATTC
1 AAATAAATTTTAAT-TTTTAATTTA-TATTC
*
25761857 AAATAAATTTTTAATTTTTAATTTATATTT
1 AAATAAA-TTTTAATTTTTAATTTATATTC
25761887 AAATAAATTTT
1 AAATAAATTTT
25761898 TAATATGACC
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
29 4 0.11
30 23 0.64
31 9 0.25
ACGTcount: A:0.39, C:0.04, G:0.03, T:0.54
Consensus pattern (29 bp):
AAATAAATTTTAATTTTTAATTTATATTC
Found at i:25761898 original size:30 final size:30
Alignment explanation
Indices: 25761842--25761901 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
25761832 AATTTTCATC
25761842 TTTTAATTAGTATTCAAATAAATTTTTAAT
1 TTTTAATTAGTATTCAAATAAATTTTTAAT
*
25761872 TTTTAATTTA-TATTTAAATAAATTTTTAAT
1 TTTTAA-TTAGTATTCAAATAAATTTTTAAT
25761902 ATGACCCTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 25 0.89
31 3 0.11
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (30 bp):
TTTTAATTAGTATTCAAATAAATTTTTAAT
Found at i:25768274 original size:68 final size:68
Alignment explanation
Indices: 25768165--25768296 Score: 212
Period size: 68 Copynumber: 1.9 Consensus size: 68
25768155 ATGATATAAT
* *
25768165 TACTATGGTGATATGATTATTAAAGTGATTTAATTACCAATAATCTTATATTAACATGTTTAATA
1 TACTATGGTGATATGATTATCAAAGTGATTTAATTACCAATAATCTTAAATTAACATGTTTAATA
25768230 CAA
66 CAA
* *
25768233 TACTATGGTGATAAT-ATTATCAAAGTGATTTGATTATCAATAATCTTAAATTAACATGTTTAAT
1 TACTATGGTGAT-ATGATTATCAAAGTGATTTAATTACCAATAATCTTAAATTAACATGTTTAAT
25768297 GTAATATTAT
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
68 57 0.97
69 2 0.03
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.42
Consensus pattern (68 bp):
TACTATGGTGATATGATTATCAAAGTGATTTAATTACCAATAATCTTAAATTAACATGTTTAATA
CAA
Found at i:25773886 original size:48 final size:48
Alignment explanation
Indices: 25773823--25773914 Score: 134
Period size: 48 Copynumber: 1.9 Consensus size: 48
25773813 CCAAAGATTT
*
25773823 ATGGATCCATACATCT-TGA-CAGGAAAGGAATCAATAAAAAAGAAGGAA
1 ATGGATCCATACATCTCT-ATCA-GAAAAGAATCAATAAAAAAGAAGGAA
*
25773871 ATGGATCCATGCATCTCTATCAGAAAAGAATCAATAAAAAAGAA
1 ATGGATCCATACATCTCTATCAGAAAAGAATCAATAAAAAAGAA
25773915 ATAATAGGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
48 37 0.93
49 3 0.08
ACGTcount: A:0.50, C:0.14, G:0.17, T:0.18
Consensus pattern (48 bp):
ATGGATCCATACATCTCTATCAGAAAAGAATCAATAAAAAAGAAGGAA
Found at i:25778396 original size:26 final size:25
Alignment explanation
Indices: 25778356--25778409 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
25778346 TATTATAAAA
*
25778356 AAAATAAAAGAAAGGCCAAGCAGTG
1 AAAATAAAAAAAAGGCCAAGCAGTG
* *
25778381 AAAATAAAAAACAAGGCCATGTAGTG
1 AAAATAAAAAA-AAGGCCAAGCAGTG
25778407 AAA
1 AAA
25778410 GAATAGTTGG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 10 0.40
26 15 0.60
ACGTcount: A:0.57, C:0.11, G:0.20, T:0.11
Consensus pattern (25 bp):
AAAATAAAAAAAAGGCCAAGCAGTG
Found at i:25778712 original size:7 final size:7
Alignment explanation
Indices: 25778702--25778738 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
25778692 TTAAGTTTCA
25778702 TTATTTT
1 TTATTTT
25778709 TTA-TTT
1 TTATTTT
25778715 TTATTTT
1 TTATTTT
*
25778722 TTATATT
1 TTATTTT
25778729 TTATTTT
1 TTATTTT
25778736 TTA
1 TTA
25778739 AAATCAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
6 6 0.22
7 21 0.78
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (7 bp):
TTATTTT
Found at i:25778720 original size:13 final size:14
Alignment explanation
Indices: 25778702--25778738 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
25778692 TTAAGTTTCA
25778702 TTATTTTTTAT-TT
1 TTATTTTTTATATT
25778715 TTATTTTTTATATT
1 TTATTTTTTATATT
25778729 TTATTTTTTA
1 TTATTTTTTA
25778739 AAATCAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (14 bp):
TTATTTTTTATATT
Found at i:25778759 original size:42 final size:42
Alignment explanation
Indices: 25778713--25778796 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 42
25778703 TATTTTTTAT
* *
25778713 TTTTATTTTTTATATTTTATTTTTTAAAATCAAAATTTATAA
1 TTTTATATTTTATATTTTATTATTTAAAATCAAAATTTATAA
* *
25778755 TTTTATATTTTATATTTTATTATTTCAAATCAAACTTTATAA
1 TTTTATATTTTATATTTTATTATTTAAAATCAAAATTTATAA
25778797 GCATTTCAGT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.60
Consensus pattern (42 bp):
TTTTATATTTTATATTTTATTATTTAAAATCAAAATTTATAA
Found at i:25778771 original size:14 final size:14
Alignment explanation
Indices: 25778702--25778779 Score: 52
Period size: 13 Copynumber: 5.6 Consensus size: 14
25778692 TTAAGTTTCA
*
25778702 TTATTTTTTAT-TT
1 TTATATTTTATATT
*
25778715 TTATTTTTTATATT
1 TTATATTTTATATT
* **
25778729 TTATTTTTTA-AAA
1 TTATATTTTATATT
* * *
25778742 TCAAAATTTATAATT
1 TTATATTTTAT-ATT
25778757 TTATATTTTATATT
1 TTATATTTTATATT
25778771 TTATTATTT
1 TTA-TATTT
25778780 CAAATCAAAC
Statistics
Matches: 50, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
13 18 0.36
14 18 0.36
15 14 0.28
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.69
Consensus pattern (14 bp):
TTATATTTTATATT
Found at i:25779427 original size:11 final size:13
Alignment explanation
Indices: 25779382--25779440 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
25779372 TGATAAATTT
25779382 AAATATAATATAA
1 AAATATAATATAA
* *
25779395 TAATATGATAT-A
1 AAATATAATATAA
25779407 AAA-ATAATATAAA
1 AAATATAATAT-AA
* *
25779420 AAATATATATTTTA
1 AAATATA-ATATAA
25779434 AAATATA
1 AAATATA
25779441 TATTTAATTT
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
11 6 0.17
12 3 0.08
13 13 0.36
14 11 0.31
15 3 0.08
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.36
Consensus pattern (13 bp):
AAATATAATATAA
Found at i:25779429 original size:24 final size:24
Alignment explanation
Indices: 25779381--25779429 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
25779371 TTGATAAATT
* *
25779381 TAAATATAATATAATAATATGATA
1 TAAAAATAATATAAAAATATGATA
25779405 TAAAAATAATATAAAAAATAT-ATA
1 TAAAAATAATAT-AAAAATATGATA
25779429 T
1 T
25779430 TTTAAAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (24 bp):
TAAAAATAATATAAAAATATGATA
Found at i:25779438 original size:14 final size:14
Alignment explanation
Indices: 25779419--25779445 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
25779409 AATAATATAA
25779419 AAAATATATATTTT
1 AAAATATATATTTT
25779433 AAAATATATATTT
1 AAAATATATATTT
25779446 AATTTATTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAAATATATATTTT
Found at i:25783041 original size:22 final size:19
Alignment explanation
Indices: 25783001--25783036 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
25782991 GTGGAAAGAT
25783001 AAAGAAAGAAGAGAATGAA
1 AAAGAAAGAAGAGAATGAA
25783020 AAAGAAAGAAGA-AATGA
1 AAAGAAAGAAGAGAATGA
25783037 TTGAATGAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.69, C:0.00, G:0.25, T:0.06
Consensus pattern (19 bp):
AAAGAAAGAAGAGAATGAA
Found at i:25783277 original size:16 final size:17
Alignment explanation
Indices: 25783256--25783297 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
25783246 TACTTTATTT
*
25783256 AATTAATATTTA-ATTA
1 AATTAATATTTAGAATA
*
25783272 AATTAAAATTTAGAATA
1 AATTAATATTTAGAATA
*
25783289 ATTTAATAT
1 AATTAATAT
25783298 AAAGTTAGTA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (17 bp):
AATTAATATTTAGAATA
Found at i:25791390 original size:18 final size:17
Alignment explanation
Indices: 25791367--25791403 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
25791357 GATAAGCAAG
*
25791367 AAAAAGAAGGAAAAAGAA
1 AAAAAGAAAGAAAAA-AA
25791385 AAAAAGAAAGAAAAAAA
1 AAAAAGAAAGAAAAAAA
25791402 AA
1 AA
25791404 GAACCAGAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAGAAAAAAA
Found at i:25791412 original size:16 final size:15
Alignment explanation
Indices: 25791364--25791418 Score: 60
Period size: 14 Copynumber: 3.5 Consensus size: 15
25791354 CCAGATAAGC
25791364 AAGAAAAAGAAGGAAA-
1 AAGAAAAA-AA-GAAAG
25791380 AAGAAAAAAAGAAAG
1 AAGAAAAAAAGAAAG
25791395 AA-AAAAAAAGAACCAG
1 AAGAAAAAAAGAA--AG
25791411 AAGAAAAA
1 AAGAAAAA
25791419 TAAATAATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
14 14 0.40
15 4 0.11
16 12 0.34
17 5 0.14
ACGTcount: A:0.78, C:0.04, G:0.18, T:0.00
Consensus pattern (15 bp):
AAGAAAAAAAGAAAG
Found at i:25791749 original size:49 final size:48
Alignment explanation
Indices: 25791614--25791919 Score: 257
Period size: 49 Copynumber: 6.3 Consensus size: 48
25791604 GGCTCATCTG
* * * * * *
25791614 AGCAGAAACTTAACAACTTTAAAAT-TC-TCTTCAAAAAGCTCCTCTC
1 AGCAGAGACTCAACAATTTTAAAATCTCATATTGAAAAAGCTTCTCTC
25791660 AGCAGAGACTCAACAACTTTTAAAATTCTCATATTGAAAAAGC-TCATCTC
1 AGCAGAGACTCAACAA-TTTTAAAA-TCTCATATTGAAAAAGCTTC-TCTC
* * * *
25791710 AGTAGAGACTCAACAATTTTAAGGATCTCATGTTAAAAAAGCTTCTCTC
1 AGCAGAGACTCAACAATTTTAA-AATCTCATATTGAAAAAGCTTCTCTC
* *
25791759 AGCAGAGACTCAACAACTTTAAAATTTCATATTGAAAAAGCTTCTCTC
1 AGCAGAGACTCAACAATTTTAAAATCTCATATTGAAAAAGCTTCTCTC
* * * * *
25791807 AACAGAGGCTCAACATTTTTAATAAAAAAATCTTATTTTGAAAAAG-TTCATCTC
1 AGCAGAGACTCAACA-ATTT--T---AAAATCTCATATTGAAAAAGCTTC-TCTC
* * * *
25791861 AGCAAAGGCTCAACAATTTTAAAATGT--T-TCTGAAAAAGCTCCTCTC
1 AGCAGAGACTCAACAATTTTAAAATCTCATAT-TGAAAAAGCTTCTCTC
*
25791907 AGCAGAGGCTCAA
1 AGCAGAGACTCAA
25791920 ATCGAATACT
Statistics
Matches: 215, Mismatches: 29, Indels: 32
0.78 0.11 0.12
Matches are distributed among these distances:
45 1 0.00
46 39 0.18
47 9 0.04
48 42 0.20
49 50 0.23
50 32 0.15
51 2 0.01
53 6 0.03
54 34 0.16
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.29
Consensus pattern (48 bp):
AGCAGAGACTCAACAATTTTAAAATCTCATATTGAAAAAGCTTCTCTC
Found at i:25791827 original size:97 final size:99
Alignment explanation
Indices: 25791646--25791828 Score: 291
Period size: 97 Copynumber: 1.9 Consensus size: 99
25791636 AATTCTCTTC
25791646 AAAAAGCTCCTCTCAGCAGAGACTCAACAACTTTTAAAATTCTCATATTGAAAAAGCTCATCTCA
1 AAAAAGCTCCTCTCAGCAGAGACTCAACAACTTTTAAAATTCTCATATTGAAAAAGCTCATCTCA
**
25791711 GTAGAGACTCAACAATTTTAAGGATCTCATGTTA
66 ACAGAGACTCAACAATTTTAAGGATCTCATGTTA
*
25791745 AAAAAGCTTCTCTCAGCAGAGACTCAACAAC-TTTAAAATT-TCATATTGAAAAAGCTTC-TCTC
1 AAAAAGCTCCTCTCAGCAGAGACTCAACAACTTTTAAAATTCTCATATTGAAAAAGC-TCATCTC
* *
25791807 AACAGAGGCTCAACATTTTTAA
65 AACAGAGACTCAACAATTTTAA
25791829 TAAAAAAATC
Statistics
Matches: 78, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
97 37 0.47
98 11 0.14
99 30 0.38
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.28
Consensus pattern (99 bp):
AAAAAGCTCCTCTCAGCAGAGACTCAACAACTTTTAAAATTCTCATATTGAAAAAGCTCATCTCA
ACAGAGACTCAACAATTTTAAGGATCTCATGTTA
Found at i:25792907 original size:18 final size:17
Alignment explanation
Indices: 25792884--25792926 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
25792874 GTGTGTGAAC
25792884 TTTTTTGTTTTTGA-TT
1 TTTTTTGTTTTTGACTT
* *
25792900 TGTTTTTTTTTTTTACTT
1 T-TTTTTGTTTTTGACTT
25792918 TTTTTTGTT
1 TTTTTTGTT
25792927 GAAAATGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 1 0.05
17 18 0.82
18 3 0.14
ACGTcount: A:0.05, C:0.02, G:0.09, T:0.84
Consensus pattern (17 bp):
TTTTTTGTTTTTGACTT
Found at i:25793738 original size:68 final size:67
Alignment explanation
Indices: 25793637--25793764 Score: 186
Period size: 68 Copynumber: 1.9 Consensus size: 67
25793627 TTTTTTTTAC
* * * *
25793637 AGAAAAAAAATTTTTGATTTTAGAAACCCTTTTTTTTATGTGGGTCTTCTTTTTTGTTTTTTACA
1 AGAAAAAAAATTTTTGATTTGAGAAACCCTTTTTTTTAGGTGGCTCTTCTTCTTT-TTTTTTACA
25793702 AAA
65 AAA
*
25793705 AGAAAAAAAATTTTTGATTCTGA-AAACCTTTTTTTTTAGGTGGCTCTTCTTCTTTTTTTT
1 AGAAAAAAAATTTTTGATT-TGAGAAACCCTTTTTTTTAGGTGGCTCTTCTTCTTTTTTTT
25793765 AATCCCTCAT
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
67 5 0.09
68 47 0.87
69 2 0.04
ACGTcount: A:0.27, C:0.10, G:0.12, T:0.51
Consensus pattern (67 bp):
AGAAAAAAAATTTTTGATTTGAGAAACCCTTTTTTTTAGGTGGCTCTTCTTCTTTTTTTTTACAA
AA
Found at i:25794007 original size:11 final size:10
Alignment explanation
Indices: 25793978--25794030 Score: 70
Period size: 10 Copynumber: 5.0 Consensus size: 10
25793968 TGAATCGGAT
*
25793978 AAGAAAGAAA
1 AAGAAAAAAA
25793988 AAGAAAAAAA
1 AAGAAAAAAA
25793998 AAGAAGAAAAA
1 AAGAA-AAAAA
25794009 AAGAAAAAAA
1 AAGAAAAAAA
25794019 ATAGAAGAAAAA
1 A-AGAA-AAAAA
25794031 TGAATAATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
10 20 0.51
11 14 0.36
12 5 0.13
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (10 bp):
AAGAAAAAAA
Found at i:25794011 original size:21 final size:22
Alignment explanation
Indices: 25793985--25794030 Score: 85
Period size: 21 Copynumber: 2.1 Consensus size: 22
25793975 GATAAGAAAG
25793985 AAAAAGAAAAAAAA-AGAAGAA
1 AAAAAGAAAAAAAATAGAAGAA
25794006 AAAAAGAAAAAAAATAGAAGAA
1 AAAAAGAAAAAAAATAGAAGAA
25794028 AAA
1 AAA
25794031 TGAATAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.02
Consensus pattern (22 bp):
AAAAAGAAAAAAAATAGAAGAA
Found at i:25794039 original size:3 final size:3
Alignment explanation
Indices: 25794033--25794062 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
25794023 AAGAAAAATG
25794033 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
25794063 TAAAAAAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:25794042 original size:21 final size:19
Alignment explanation
Indices: 25793982--25794030 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 19
25793972 TCGGATAAGA
*
25793982 AAGAAAAAGAAAAAAAAAG
1 AAGAAAAAGAAAAAAATAG
25794001 AAGAAAAAAAGAAAAAAAATAG
1 AAG--AAAAAG-AAAAAAATAG
25794023 AAGAAAAA
1 AAGAAAAA
25794031 TGAATAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 3 0.12
20 5 0.19
21 6 0.23
22 12 0.46
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (19 bp):
AAGAAAAAGAAAAAAATAG
Found at i:25795011 original size:58 final size:56
Alignment explanation
Indices: 25794937--25795330 Score: 287
Period size: 57 Copynumber: 6.8 Consensus size: 56
25794927 TGAAAACATG
* *
25794937 GTTTTTAATTGAAAAAAATTAAATATACAAAGATTACGTTTCTTAAAATTAAAAAGTA
1 GTTTTTAATTAAAAAAAATTAAACATACAAA-ATTACGTTTCTT-AAATTAAAAAGTA
* * * *
25794995 GTTTTTAATT-AAAAAAATTAAGCATATCAAAATTACATTTCTTAAACTAAAAACGTG
1 GTTTTTAATTAAAAAAAATTAAACATA-CAAAATTACGTTTCTTAAATTAAAAA-GTA
* * * **
25795052 GATCTTAATTGAAAAAAAAATTAAACATACGAAAATTACGTTTTTTAAAGTGGAAAAGTA
1 GTTTTTAATT--AAAAAAAATTAAACATAC-AAAATTACGTTTCTTAAA-TTAAAAAGTA
** * * * * *
25795112 CCTTTTAATTGAAAAAAAAAAATTAAACATACAAAGAGTA-TTTTTTTGAAGTAAAAACGTA
1 GTTTTTAATT----AAAAAAAATTAAACATACAAA-ATTACGTTTCTTAAATTAAAAA-GTA
* * * * * *
25795173 ATCTTTAATTAAAAAAAATTTAACATACAAAGACTACGTTTCTTAAATTGAGAACGTA
1 GTTTTTAATTAAAAAAAATTAAACATACAAA-ATTACGTTTCTTAAATT-AAAAAGTA
* * *
25795231 GTCTTTAATTGAAAAAAAA-T-AACATACATAAACTACATTTCTTAAATTGAAAATA-TA
1 GTTTTTAATT-AAAAAAAATTAAACATACA-AAATTACGTTTCTTAAATT-AAAA-AGTA
* *
25795288 GTATTTTAGTGAAAAAAAA-TAAACATACAAAAATTACGTTTCT
1 GT-TTTTAATTAAAAAAAATTAAACATAC-AAAATTACGTTTCT
25795331 GATTGTAGAA
Statistics
Matches: 273, Mismatches: 44, Indels: 38
0.77 0.12 0.11
Matches are distributed among these distances:
56 9 0.03
57 100 0.37
58 60 0.22
59 13 0.05
60 44 0.16
61 25 0.09
62 22 0.08
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.33
Consensus pattern (56 bp):
GTTTTTAATTAAAAAAAATTAAACATACAAAATTACGTTTCTTAAATTAAAAAGTA
Found at i:25795189 original size:62 final size:62
Alignment explanation
Indices: 25795063--25795190 Score: 147
Period size: 61 Copynumber: 2.1 Consensus size: 62
25795053 ATCTTAATTG
* * *
25795063 AAAAAAAAATTAAACATACGAAAATTACGTTTTTTAAAGTGGAAAAGTACCTTTTAATTGAA
1 AAAAAAAAATTAAACATACGAAAAGTACGTTTTTTAAAGTGAAAAAGTACCTTTTAATTAAA
* * *
25795125 AAAAAAAAATTAAACATAC-AAAGAGTA-TTTTTTTGAAGT-AAAAACGTA-ATCTTTAATTAAA
1 AAAAAAAAATTAAACATACGAAA-AGTACGTTTTTTAAAGTGAAAAA-GTACCT-TTTAATTAAA
25795186 AAAAA
1 AAAAA
25795191 TTTAACATAC
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
60 5 0.09
61 30 0.53
62 22 0.39
ACGTcount: A:0.54, C:0.07, G:0.09, T:0.30
Consensus pattern (62 bp):
AAAAAAAAATTAAACATACGAAAAGTACGTTTTTTAAAGTGAAAAAGTACCTTTTAATTAAA
Found at i:25795219 original size:119 final size:119
Alignment explanation
Indices: 25794940--25795330 Score: 314
Period size: 117 Copynumber: 3.3 Consensus size: 119
25794930 AAACATGGTT
* * * *
25794940 TTTAATTGAAAAAAATTAAATATACAAAGATTACGTTTCTTAAAATTAAAAAGTAGTTTTTAATT
1 TTTAATTAAAAAAAATTAAACATACAAAGATTACGTTTCTT-AAATTGAAAAGTA-CTTTTAATT
* * *
25795005 -----AAAAAAATTAAGCATATCAAAATTACATTTCTTAAACTAAAAACGTGGATC
64 GAAAAAAAAAAATTAAACATATCAAAAGTACATTTCTTAAACTAAAAACGTGAATC
* *
25795056 -TTAATTGAAAAAAAAATTAAACATACGAAA-ATTACGTTTTTTAAAGTGGAAAAGTACCTTTTA
1 TTTAATT--AAAAAAAATTAAACATAC-AAAGATTACGTTTCTTAAA-TTGAAAAGTA-CTTTTA
* * * *
25795119 ATTGAAAAAAAAAAATTAAACATA-CAAAGAGTA-TTTTTTTGAAGTAAAAACGT-AATC
61 ATTGAAAAAAAAAAATTAAACATATCAAA-AGTACATTTCTTAAACTAAAAACGTGAATC
* * * *
25795176 TTTAATTAAAAAAAATTTAACATACAAAGACTACGTTTCTTAAATTGAGAACGTAGTCTTTAATT
1 TTTAATTAAAAAAAATTAAACATACAAAGATTACGTTTCTTAAATTGA-AAAGTACT-TTTAATT
* * * ** *
25795241 G---AAAAAAAA-T-AACATA-CATAAACTACATTTCTTAAATTGAAAATATAGTAT-
64 GAAAAAAAAAAATTAAACATATCA-AAAGTACATTTCTTAAACTAAAAACGT-GAATC
* * *
25795292 TTTAGTGAAAAAAAA-TAAACATACAAAAATTACGTTTCT
1 TTTAATTAAAAAAAATTAAACATACAAAGATTACGTTTCT
25795331 GATTGTAGAA
Statistics
Matches: 223, Mismatches: 34, Indels: 37
0.76 0.12 0.13
Matches are distributed among these distances:
114 11 0.05
115 43 0.19
116 24 0.11
117 45 0.20
118 10 0.04
119 43 0.19
120 3 0.01
121 26 0.12
122 18 0.08
ACGTcount: A:0.50, C:0.09, G:0.09, T:0.33
Consensus pattern (119 bp):
TTTAATTAAAAAAAATTAAACATACAAAGATTACGTTTCTTAAATTGAAAAGTACTTTTAATTGA
AAAAAAAAAATTAAACATATCAAAAGTACATTTCTTAAACTAAAAACGTGAATC
Found at i:25798751 original size:29 final size:30
Alignment explanation
Indices: 25798698--25798755 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
25798688 TATTATGAAT
25798698 CAAATTTAAATATAAAAAATAAAATTTAAC
1 CAAATTTAAATATAAAAAATAAAATTTAAC
**
25798728 CAAATTTAAAT-TAAAATTTAAAATTTAA
1 CAAATTTAAATATAAAAAATAAAATTTAA
25798756 ATTTCAGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.34
Consensus pattern (30 bp):
CAAATTTAAATATAAAAAATAAAATTTAAC
Found at i:25800577 original size:25 final size:25
Alignment explanation
Indices: 25800541--25800594 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
25800531 TTATAATAAT
* *
25800541 AATTAGAATGTATAGATAATTTTTA
1 AATTAGAATGTATAAATAATTTTAA
25800566 AATTA-AAGTGTATAAATAATTTTAA
1 AATTAGAA-TGTATAAATAATTTTAA
25800591 AATT
1 AATT
25800595 GGTAAATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 2 0.08
25 24 0.92
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.43
Consensus pattern (25 bp):
AATTAGAATGTATAAATAATTTTAA
Found at i:25802531 original size:30 final size:29
Alignment explanation
Indices: 25802471--25802527 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
25802461 TAAAGCACAT
* * *
25802471 TGTTTTCCTAAGTGCACTAACTGCTTTTA
1 TGTTTTACTAAGTACACTAACTACTTTTA
25802500 TGTTTTACTAAGTACACTAACTACTTTT
1 TGTTTTACTAAGTACACTAACTACTTTT
25802528 TATGGTTTGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.25, C:0.19, G:0.11, T:0.46
Consensus pattern (29 bp):
TGTTTTACTAAGTACACTAACTACTTTTA
Found at i:25816221 original size:2 final size:2
Alignment explanation
Indices: 25816214--25816238 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
25816204 CTCGATTTAT
25816214 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
25816239 TACGGAGTAT
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:25819789 original size:2 final size:2
Alignment explanation
Indices: 25819782--25819816 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
25819772 ATGTTAAGCA
25819782 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
25819817 TCACCTCACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:25823100 original size:17 final size:17
Alignment explanation
Indices: 25823078--25823111 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
25823068 TCAATATTTA
*
25823078 TTTATTTTTTCATTTGT
1 TTTATTTCTTCATTTGT
25823095 TTTATTTCTTCATTTGT
1 TTTATTTCTTCATTTGT
25823112 GATTGATTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.12, C:0.09, G:0.06, T:0.74
Consensus pattern (17 bp):
TTTATTTCTTCATTTGT
Found at i:25832332 original size:24 final size:25
Alignment explanation
Indices: 25832236--25832342 Score: 64
Period size: 24 Copynumber: 4.3 Consensus size: 25
25832226 TATAATTATC
* * *
25832236 TAATAAATAAT-TAATATAAATAAC
1 TAATAAATAATATAATCTGAATAAA
25832260 TAA-AAATTAA-ATTAATACATGAATAAA
1 TAATAAA-TAATA-TAAT-C-TGAATAAA
25832287 TAATAAATAATATAATCT-AATAAA
1 TAATAAATAATATAATCTGAATAAA
* * *
25832311 TTATATATGAA-ATAAT-TGAATACA
1 TAATAAAT-AATATAATCTGAATAAA
*
25832335 TAAAAAAT
1 TAATAAAT
25832343 TAACAAATGA
Statistics
Matches: 65, Mismatches: 9, Indels: 18
0.71 0.10 0.20
Matches are distributed among these distances:
23 4 0.06
24 33 0.51
25 7 0.11
26 1 0.02
27 16 0.25
28 4 0.06
ACGTcount: A:0.61, C:0.04, G:0.03, T:0.33
Consensus pattern (25 bp):
TAATAAATAATATAATCTGAATAAA
Found at i:25832399 original size:16 final size:17
Alignment explanation
Indices: 25832378--25832410 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
25832368 TAATAATTTT
25832378 TTATTT-ATAAAAAATA
1 TTATTTGATAAAAAATA
*
25832394 TTATTTGATATAAAATA
1 TTATTTGATAAAAAATA
25832411 ATTTTAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (17 bp):
TTATTTGATAAAAAATA
Found at i:25832966 original size:11 final size:11
Alignment explanation
Indices: 25832952--25832994 Score: 59
Period size: 11 Copynumber: 3.7 Consensus size: 11
25832942 TAAAAAAATG
25832952 AAAAAAAGAAA
1 AAAAAAAGAAA
25832963 AAAAAAAGAAA
1 AAAAAAAGAAA
*
25832974 AACAAAAGAAA
1 AAAAAAAGAAA
25832985 TGAAAAAAAG
1 --AAAAAAAG
25832995 CTCATAAGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 21 0.75
13 7 0.25
ACGTcount: A:0.84, C:0.02, G:0.12, T:0.02
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:25833969 original size:40 final size:40
Alignment explanation
Indices: 25833917--25833994 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
25833907 AAAATTACAT
* * *
25833917 TTTTTATTTTAGAAATATCATCTTTTTAATAAAGACTGCG
1 TTTTTATCTTAGAAACATCATCTTTTTAACAAAGACTGCG
* * *
25833957 TTTTTATCTTAGAAACATCGTTTTTTTAACAAATACTG
1 TTTTTATCTTAGAAACATCATCTTTTTAACAAAGACTG
25833995 TATTTTTTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.32, C:0.12, G:0.09, T:0.47
Consensus pattern (40 bp):
TTTTTATCTTAGAAACATCATCTTTTTAACAAAGACTGCG
Found at i:25834001 original size:40 final size:40
Alignment explanation
Indices: 25833893--25834001 Score: 101
Period size: 40 Copynumber: 2.7 Consensus size: 40
25833883 AATATATTTT
* * * * * *
25833893 TCATGTTTTTAACAAAAATTACATTTTTTATTTTAGAAATA
1 TCATCTTTTTAACAAAGACTGCA-TTTTTATCTTAGAAACA
* *
25833934 TCATCTTTTTAATAAAGACTGCGTTTTTATCTTAGAAACA
1 TCATCTTTTTAACAAAGACTGCATTTTTATCTTAGAAACA
* * * *
25833974 TCGTTTTTTTAACAAATACTGTATTTTT
1 TCATCTTTTTAACAAAGACTGCATTTTT
25834002 TTTATCTTAG
Statistics
Matches: 54, Mismatches: 14, Indels: 1
0.78 0.20 0.01
Matches are distributed among these distances:
40 37 0.69
41 17 0.31
ACGTcount: A:0.33, C:0.11, G:0.07, T:0.49
Consensus pattern (40 bp):
TCATCTTTTTAACAAAGACTGCATTTTTATCTTAGAAACA
Done.