Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A11
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: 114316535
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4920000 characters in sequence are not A, C, G, or T
File 12 of 356
Found at i:4119287 original size:33 final size:33
Alignment explanation
Indices: 4119240--4119302 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
4119230 ATAAAATAAT
*
4119240 AAAATAAATGTTATATAATATCTAAATAATTAC
1 AAAATAAATGTTATACAATATCTAAATAATTAC
4119273 AAAATAAGAT-TTATACAATATCTAAATAAT
1 AAAATAA-ATGTTATACAATATCTAAATAAT
4119303 AATAACACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
33 26 0.93
34 2 0.07
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.35
Consensus pattern (33 bp):
AAAATAAATGTTATACAATATCTAAATAATTAC
Found at i:4122185 original size:22 final size:22
Alignment explanation
Indices: 4122160--4122202 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
4122150 TTTCCCTATT
4122160 TTACTACCATTTTGTTATTATG
1 TTACTACCATTTTGTTATTATG
* *
4122182 TTACTACTATTTTGTTGTTAT
1 TTACTACCATTTTGTTATTAT
4122203 TGCATGGATG
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:0.21, C:0.12, G:0.09, T:0.58
Consensus pattern (22 bp):
TTACTACCATTTTGTTATTATG
Found at i:4135870 original size:31 final size:32
Alignment explanation
Indices: 4135821--4135884 Score: 80
Period size: 31 Copynumber: 2.0 Consensus size: 32
4135811 ATATTAAATA
4135821 AGATATTTATTAATTAAATA-ATT-ATATTATG
1 AGATATTTATTAATTAAATATATTGA-ATTATG
*
4135852 AGATTTTTATGTAA-TAAATATATTGAATTATG
1 AGATATTTAT-TAATTAAATATATTGAATTATG
4135884 A
1 A
4135885 CAAATGTATG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
31 15 0.52
32 13 0.45
33 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (32 bp):
AGATATTTATTAATTAAATATATTGAATTATG
Found at i:4136019 original size:19 final size:19
Alignment explanation
Indices: 4135973--4136019 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
4135963 AGATTTTTAA
* * *
4135973 ATATAGATATTTTATTTTT
1 ATATATATATTTTATATAT
4135992 AT-TATTATATTTTATATAT
1 ATATA-TATATTTTATATAT
4136011 ATATATATA
1 ATATATATA
4136020 GTAAATAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 2 0.09
19 19 0.83
20 2 0.09
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
ATATATATATTTTATATAT
Found at i:4167297 original size:12 final size:12
Alignment explanation
Indices: 4167259--4167299 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
4167249 GAATGTACGC
*
4167259 GTATGAACTTAT
1 GTATGTACTTAT
*
4167271 GTATGTACATAT
1 GTATGTACTTAT
*
4167283 GTATGTACTTGT
1 GTATGTACTTAT
4167295 GTATG
1 GTATG
4167300 CATACATGCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.27, C:0.07, G:0.22, T:0.44
Consensus pattern (12 bp):
GTATGTACTTAT
Found at i:4175079 original size:20 final size:20
Alignment explanation
Indices: 4175054--4175148 Score: 55
Period size: 20 Copynumber: 4.3 Consensus size: 20
4175044 AAATATATAG
*
4175054 TTTTTATAATTTTTAATATT
1 TTTTTATAATTTTTAATAAT
*
4175074 TTTTTAAAAATAATCATTATTTATAAT
1 TTTTT----ATAAT--TT-TTAATAAT
* *
4175101 TTCTTATAATTCTTAATAAT
1 TTTTTATAATTTTTAATAAT
* * *
4175121 TCTTAATAATTTTTAAATATT
1 TTTTTATAATTTTT-AATAAT
4175142 TTTTTAT
1 TTTTTAT
4175149 TTTTAAATTT
Statistics
Matches: 55, Mismatches: 12, Indels: 15
0.67 0.15 0.18
Matches are distributed among these distances:
20 22 0.40
21 11 0.20
23 5 0.09
24 5 0.09
26 2 0.04
27 10 0.18
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTTTATAATTTTTAATAAT
Found at i:4175109 original size:10 final size:10
Alignment explanation
Indices: 4175096--4175136 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
4175086 ATCATTATTT
4175096 ATAATTTCTT-
1 ATAA-TTCTTA
4175106 ATAATTCTTA
1 ATAATTCTTA
4175116 ATAATTCTTA
1 ATAATTCTTA
*
4175126 ATAATTTTTA
1 ATAATTCTTA
4175136 A
1 A
4175137 ATATTTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
9 5 0.17
10 24 0.83
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (10 bp):
ATAATTCTTA
Found at i:4186747 original size:9 final size:9
Alignment explanation
Indices: 4186733--4186798 Score: 53
Period size: 9 Copynumber: 6.8 Consensus size: 9
4186723 TATTATTCTA
4186733 TAATTTTTT
1 TAATTTTTT
4186742 TAATTTTTT
1 TAATTTTTT
4186751 T-ATCTTTCTT
1 TAAT-TTT-TT
4186761 TATATATTTTT
1 TA-AT-TTTTT
4186772 TAGATTTTTT
1 TA-ATTTTTT
* *
4186782 GAAATTTTTA
1 -TAATTTTTT
4186792 TAATTTT
1 TAATTTT
4186799 CTAGAAAACA
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
8 2 0.04
9 19 0.40
10 14 0.30
11 7 0.15
12 5 0.11
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.70
Consensus pattern (9 bp):
TAATTTTTT
Found at i:4189347 original size:29 final size:29
Alignment explanation
Indices: 4189314--4189371 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
4189304 TGCCACTACA
4189314 CCCTCAAGAAGATTAAAAAATAATACTAG
1 CCCTCAAGAAGATTAAAAAATAATACTAG
*
4189343 CCCTCAAGAAGATTAAAATATAATACTAG
1 CCCTCAAGAAGATTAAAAAATAATACTAG
4189372 TTTAATAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.50, C:0.17, G:0.10, T:0.22
Consensus pattern (29 bp):
CCCTCAAGAAGATTAAAAAATAATACTAG
Found at i:4197830 original size:14 final size:14
Alignment explanation
Indices: 4197811--4197837 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4197801 GTTCTTTATT
4197811 TTATTTTTATTTTA
1 TTATTTTTATTTTA
4197825 TTATTTTTATTTT
1 TTATTTTTATTTT
4197838 CACAAATTGG
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:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (14 bp):
TTATTTTTATTTTA
Found at i:4202216 original size:14 final size:14
Alignment explanation
Indices: 4202197--4202223 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4202187 GTTCTTTATT
4202197 TTATTTTTATTTTA
1 TTATTTTTATTTTA
4202211 TTATTTTTATTTT
1 TTATTTTTATTTT
4202224 CATAAATGGT
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:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (14 bp):
TTATTTTTATTTTA
Found at i:4213177 original size:21 final size:18
Alignment explanation
Indices: 4213147--4213202 Score: 60
Period size: 21 Copynumber: 2.9 Consensus size: 18
4213137 TATTGAAATC
*
4213147 ATAAATAAATTAACGTGATA
1 ATAAAAAAATTAAC-T-ATA
4213167 ATTAAAAAAATTAA-TATA
1 A-TAAAAAAATTAACTATA
4213185 ATAAAAAAATATAACTAT
1 ATAAAAAAAT-TAACTAT
4213203 TAACTTTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
17 9 0.28
18 7 0.22
19 4 0.12
20 1 0.03
21 11 0.34
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (18 bp):
ATAAAAAAATTAACTATA
Found at i:4217918 original size:6 final size:6
Alignment explanation
Indices: 4217907--4217942 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
4217897 AGATAAGAGG
4217907 GGGAGA GGGAGA GGGAGA GGGAGA GGGAGA GGGAGA
1 GGGAGA GGGAGA GGGAGA GGGAGA GGGAGA GGGAGA
4217943 TATACTTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (6 bp):
GGGAGA
Found at i:4220364 original size:19 final size:20
Alignment explanation
Indices: 4220323--4220364 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
4220313 ATCAAATTAT
*
4220323 ATTTAAAATTGTATTTCATC
1 ATTTAAAATTGTATTCCATC
4220343 ATTT-AAATTGTATCTCCA-C
1 ATTTAAAATTGTAT-TCCATC
4220362 ATT
1 ATT
4220365 AATATCGTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.33, C:0.14, G:0.05, T:0.48
Consensus pattern (20 bp):
ATTTAAAATTGTATTCCATC
Found at i:4221251 original size:15 final size:15
Alignment explanation
Indices: 4221231--4221280 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
4221221 TTGACTTAAA
4221231 TTATATTTTAATTAT
1 TTATATTTTAATTAT
**
4221246 TTATA-TTTAAAAAT
1 TTATATTTTAATTAT
*
4221260 TTATGTTTTAATTAT
1 TTATATTTTAATTAT
4221275 TTATAT
1 TTATAT
4221281 AATCGTTTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
14 11 0.39
15 17 0.61
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (15 bp):
TTATATTTTAATTAT
Found at i:4221410 original size:14 final size:14
Alignment explanation
Indices: 4221391--4221421 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
4221381 TAATTGATGT
4221391 TTTAATTAAATGAA
1 TTTAATTAAATGAA
*
4221405 TTTAATTAATTGAA
1 TTTAATTAAATGAA
4221419 TTT
1 TTT
4221422 TTAAATTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (14 bp):
TTTAATTAAATGAA
Found at i:4222242 original size:10 final size:10
Alignment explanation
Indices: 4222229--4222253 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
4222219 TGTAAAATGC
4222229 AAAAAAAAGA
1 AAAAAAAAGA
4222239 AAAAAAAAGA
1 AAAAAAAAGA
4222249 AAAAA
1 AAAAA
4222254 GAGAAAGACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:4246878 original size:8 final size:8
Alignment explanation
Indices: 4246834--4246869 Score: 56
Period size: 8 Copynumber: 4.5 Consensus size: 8
4246824 AATACAACTT
4246834 AAAAT-AA
1 AAAATAAA
4246841 AAAATAAA
1 AAAATAAA
4246849 AAAATAAA
1 AAAATAAA
4246857 AAAATAAA
1 AAAATAAA
4246865 GAAAA
1 -AAAA
4246870 AGAAAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 5 0.19
8 18 0.67
9 4 0.15
ACGTcount: A:0.86, C:0.00, G:0.03, T:0.11
Consensus pattern (8 bp):
AAAATAAA
Found at i:4248069 original size:19 final size:19
Alignment explanation
Indices: 4248045--4248082 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
4248035 TTGAGATTGC
*
4248045 CAACCTATTTGCTTGAAAT
1 CAACCTATTTGCCTGAAAT
4248064 CAACCTATTTGCCTGAAAT
1 CAACCTATTTGCCTGAAAT
4248083 TATTCATTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.34
Consensus pattern (19 bp):
CAACCTATTTGCCTGAAAT
Found at i:4258808 original size:24 final size:24
Alignment explanation
Indices: 4258788--4258899 Score: 188
Period size: 24 Copynumber: 4.7 Consensus size: 24
4258778 CAGATTTGAG
4258788 TGGCACTATGTGTGCGTATTTGTA
1 TGGCACTATGTGTGCGTATTTGTA
4258812 TGGCACTATGTGTGCGTATTTGTA
1 TGGCACTATGTGTGCGTATTTGTA
*
4258836 TGGCACTATGTGTGCGTATATGTA
1 TGGCACTATGTGTGCGTATTTGTA
* * *
4258860 TGGCACTATGTGTGCGTAATTATT
1 TGGCACTATGTGTGCGTATTTGTA
4258884 TGGCACTATGTGTGCG
1 TGGCACTATGTGTGCG
4258900 GAGTTGAATC
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 83 1.00
ACGTcount: A:0.18, C:0.13, G:0.29, T:0.39
Consensus pattern (24 bp):
TGGCACTATGTGTGCGTATTTGTA
Found at i:4266442 original size:24 final size:24
Alignment explanation
Indices: 4266427--4266538 Score: 170
Period size: 24 Copynumber: 4.7 Consensus size: 24
4266417 CGGATTTGAG
4266427 TGGCACTATGTGTGCGTATTTGTA
1 TGGCACTATGTGTGCGTATTTGTA
*
4266451 TGGCACTATGTGTGCATATTTGTA
1 TGGCACTATGTGTGCGTATTTGTA
* *
4266475 TGGCACTATGTGTACGTATATGTA
1 TGGCACTATGTGTGCGTATTTGTA
* * *
4266499 TGGCACTATGTGTGCGTAATTATT
1 TGGCACTATGTGTGCGTATTTGTA
4266523 TGGCACTATGTGTGCG
1 TGGCACTATGTGTGCG
4266539 GAGTTGAATC
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 79 1.00
ACGTcount: A:0.20, C:0.13, G:0.28, T:0.39
Consensus pattern (24 bp):
TGGCACTATGTGTGCGTATTTGTA
Found at i:4271197 original size:47 final size:47
Alignment explanation
Indices: 4271146--4271279 Score: 124
Period size: 41 Copynumber: 3.0 Consensus size: 47
4271136 GGCAGGGAGC
4271146 AGATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGT
1 AGATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGT
* * * * * *
4271193 AGATC-----CA-AGATGATTTGGC-ATCTC-TGTATCAGGCG-GGGAGT
1 AGATCGAAGACATAGCTGATTTGGCTTTCACGTGT-TTA--CGTTGAAGT
4271234 AGATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAG
1 AGATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAG
4271280 CAAATCCAAG
Statistics
Matches: 63, Mismatches: 12, Indels: 24
0.64 0.12 0.24
Matches are distributed among these distances:
39 3 0.05
40 5 0.08
41 20 0.32
42 4 0.06
46 4 0.06
47 19 0.30
48 5 0.08
49 3 0.05
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (47 bp):
AGATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGT
Found at i:4271259 original size:88 final size:88
Alignment explanation
Indices: 4271110--4271330 Score: 354
Period size: 88 Copynumber: 2.5 Consensus size: 88
4271100 TGAAGATTTT
* *
4271110 CAAGATGATTTGGCATTTCTGTATCAGGCAGGGAGCAGATCGAAGACATAGCTGATTTGGCTTTC
1 CAAGATGATTTGGCATCTCTGTATCAGGCGGGGAGCAGATCGAAGACATAGCTGATTTGGCTTTC
* *
4271175 ACGTGTTTACGTTGAAGTAGATC
66 ACGTGTTTACGTTGAAGCAAATC
*
4271198 CAAGATGATTTGGCATCTCTGTATCAGGCGGGGAGTAGATCGAAGACATAGCTGATTTGGCTTTC
1 CAAGATGATTTGGCATCTCTGTATCAGGCGGGGAGCAGATCGAAGACATAGCTGATTTGGCTTTC
4271263 ACGTGTTTACGTTGAAGCAAATC
66 ACGTGTTTACGTTGAAGCAAATC
* * * *
4271286 CAAGATGATTTGGCGTCTCTGTAGC-GGCGGAGAGCAGATCAAAGA
1 CAAGATGATTTGGCATCTCTGTATCAGGCGGGGAGCAGATCGAAGA
4271331 TAACAGATTT
Statistics
Matches: 123, Mismatches: 10, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
87 17 0.14
88 106 0.86
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.28
Consensus pattern (88 bp):
CAAGATGATTTGGCATCTCTGTATCAGGCGGGGAGCAGATCGAAGACATAGCTGATTTGGCTTTC
ACGTGTTTACGTTGAAGCAAATC
Found at i:4271346 original size:44 final size:44
Alignment explanation
Indices: 4271292--4271784 Score: 768
Period size: 44 Copynumber: 11.4 Consensus size: 44
4271282 AATCCAAGAT
*
4271292 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCAAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
*
4271336 GATTTGGCGTCTCTGTAGCGGCGAAGAGCAGATCGAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
4271380 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGAT----
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
* * *
4271420 GATTTGGCATCTCTGTAGGGGCGGAGAGCAGATCGAAGATAATA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
4271464 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
* *
4271508 GATTTGGCGTCTCTGTAGCAGCGGAGAGCAGATCAAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
* *
4271552 GATTTGGCATCTCTGTAGCGGCGAAGAGCAGATCGAAGAT----
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
* *
4271592 GATTTGGCATCTCTGTAGCGGCAGAGAGCAGATCGAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
4271636 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
* * * * *
4271680 GATTTGGCGTCTCCGTGGCGACTGAGAGCAGATTGAAGATAACA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
* *
4271724 GATTTGGCGTCTCTGTAGCGGCGGAGAGTAGATCGAAGATAACG
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
4271768 GATTTGGCGTCTCTGTA
1 GATTTGGCGTCTCTGTA
4271785 TTAGACGGGA
Statistics
Matches: 411, Mismatches: 30, Indels: 16
0.90 0.07 0.04
Matches are distributed among these distances:
40 76 0.18
44 335 0.82
ACGTcount: A:0.28, C:0.17, G:0.33, T:0.22
Consensus pattern (44 bp):
GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACA
Found at i:4271421 original size:128 final size:129
Alignment explanation
Indices: 4271278--4271784 Score: 722
Period size: 128 Copynumber: 3.9 Consensus size: 129
4271268 TTTACGTTGA
* * * *
4271278 AGCAAATCCAAGAT-GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCAAAGATAACAGATTTG
1 AGCAGATCGAAGATAGATTTGGCATCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACAGATTTG
4271342 GCGTCTCTGTAGCGGCGAAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAG
66 GCGTCTCTGTAGCGGCGAAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAG
* *
4271406 AGCAGATCGAAGAT-GATTTGGCATCTCTGTAGGGGCGGAGAGCAGATCGAAGATAATAGATTTG
1 AGCAGATCGAAGATAGATTTGGCATCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACAGATTTG
* *
4271470 GCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAGCAGCGGAG
66 GCGTCTCTGTAGCGGCGAAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAG
* *
4271534 AGCAGATCAAAGATAACAGATTTGGCATCTCTGTAGCGGCGAAGAGCAGATCGAAGAT----GAT
1 AGCAGATCGAAGAT---AGATTTGGCATCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACAGAT
*
4271595 TTGGCATCTCTGTAGCGGC-AGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCG
63 TTGGCGTCTCTGTAGCGGCGA-AGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCG
4271659 GAG
127 GAG
* * * * * *
4271662 AGCAGATCGAAGATAACAGATTTGGCGTCTCCGTGGCGACTGAGAGCAGATTGAAGATAACAGAT
1 AGCAGATCGAAGAT---AGATTTGGCATCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACAGAT
* * *
4271727 TTGGCGTCTCTGTAGCGGCGGAGAGTAGATCGAAGATAACGGATTTGGCGTCTCTGTA
63 TTGGCGTCTCTGTAGCGGCGAAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTA
4271785 TTAGACGGGA
Statistics
Matches: 343, Mismatches: 26, Indels: 16
0.89 0.07 0.04
Matches are distributed among these distances:
128 249 0.73
132 94 0.27
ACGTcount: A:0.28, C:0.18, G:0.32, T:0.22
Consensus pattern (129 bp):
AGCAGATCGAAGATAGATTTGGCATCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACAGATTTG
GCGTCTCTGTAGCGGCGAAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAG
Found at i:4271482 original size:172 final size:171
Alignment explanation
Indices: 4271292--4271763 Score: 800
Period size: 172 Copynumber: 2.7 Consensus size: 171
4271282 AATCCAAGAT
*
4271292 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCAAAGATAACAGATTTGGCGTCTCTGTAGCGG
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAGCGG
4271357 CGAAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATGA
66 CG-AGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATGA
* * *
4271422 TTTGGCATCTCTGTAGGGGCGGAGAGCAGATCGAAGATAATA
130 TTTGGCATCTCTGTAGCGGCAGAGAGCAGATCGAAGATAACA
*
4271464 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAGCAG
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAGCGG
* * *
4271529 CGGAGAGCAGATCAAAGATAACAGATTTGGCATCTCTGTAGCGGCGAAGAGCAGATCGAAGATGA
66 C-GAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATGA
4271594 TTTGGCATCTCTGTAGCGGCAGAGAGCAGATCGAAGATAACA
130 TTTGGCATCTCTGTAGCGGCAGAGAGCAGATCGAAGATAACA
* * *
4271636 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCCGTGGCGA
1 GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAGCGG
* *
4271701 CTGAGAGCAGATTGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGTAGATCGAAGAT
66 C-GAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGAT
4271764 AACGGATTTG
Statistics
Matches: 281, Mismatches: 18, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
172 280 1.00
173 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.33, T:0.22
Consensus pattern (171 bp):
GATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAGCGG
CGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGATGAT
TTGGCATCTCTGTAGCGGCAGAGAGCAGATCGAAGATAACA
Found at i:4272087 original size:7 final size:7
Alignment explanation
Indices: 4272075--4272099 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
4272065 AATACAACCC
4272075 AAAATAA
1 AAAATAA
4272082 AAAATAA
1 AAAATAA
4272089 AAAATAA
1 AAAATAA
4272096 AAAA
1 AAAA
4272100 ATGAAGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAATAA
Found at i:4272099 original size:9 final size:9
Alignment explanation
Indices: 4272087--4272128 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
4272077 AATAAAAAAT
*
4272087 AAAAAATAA
1 AAAAAAGAA
*
4272096 AAAAATGAA
1 AAAAAAGAA
*
4272105 GAAAAAGAA
1 AAAAAAGAA
4272114 AAAAAAGAA
1 AAAAAAGAA
4272123 AAAAAA
1 AAAAAA
4272129 CCTAACCTCT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.86, C:0.00, G:0.10, T:0.05
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:4273316 original size:19 final size:19
Alignment explanation
Indices: 4273292--4273329 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
4273282 TTGAGATTGC
*
4273292 CAACCTATTTGCTTGAAAT
1 CAACCTATTTGCCTGAAAT
4273311 CAACCTATTTGCCTGAAAT
1 CAACCTATTTGCCTGAAAT
4273330 TATTCATTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.34
Consensus pattern (19 bp):
CAACCTATTTGCCTGAAAT
Found at i:4289156 original size:15 final size:15
Alignment explanation
Indices: 4289138--4289167 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4289128 ACATAACATC
4289138 AACCCACATATTCAT
1 AACCCACATATTCAT
*
4289153 AACCCACATTTTCAT
1 AACCCACATATTCAT
4289168 TCATGTATAT
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:0.37, C:0.33, G:0.00, T:0.30
Consensus pattern (15 bp):
AACCCACATATTCAT
Found at i:4290063 original size:29 final size:30
Alignment explanation
Indices: 4289992--4290128 Score: 108
Period size: 29 Copynumber: 4.7 Consensus size: 30
4289982 GTGCCCACTG
**
4289992 ACCGATCTCGCACACATAGTG-CTCGGTTGA
1 ACCGATCTCGCACACATAGTGCCTCAATT-A
* *
4290022 A--GAACTCGCACACACAGTGCCTCAATT-
1 ACCGATCTCGCACACATAGTGCCTCAATTA
**
4290049 ACCGATCTCGCACACATAGTG-CTCGGTTA
1 ACCGATCTCGCACACATAGTGCCTCAATTA
** * *
4290078 AAGGAAT-TTGCACACACAGTGCCTCAATT-
1 ACCG-ATCTCGCACACATAGTGCCTCAATTA
*
4290107 ACTGATCTCGCACACATAGTGC
1 ACCGATCTCGCACACATAGTGC
4290129 TCGGTTAAAA
Statistics
Matches: 82, Mismatches: 18, Indels: 15
0.71 0.16 0.13
Matches are distributed among these distances:
27 1 0.01
28 23 0.28
29 50 0.61
30 8 0.10
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (30 bp):
ACCGATCTCGCACACATAGTGCCTCAATTA
Found at i:4290115 original size:58 final size:57
Alignment explanation
Indices: 4289992--4290160 Score: 275
Period size: 58 Copynumber: 2.9 Consensus size: 57
4289982 GTGCCCACTG
* * *
4289992 ACCGATCTCGCACACATAGTGCTCGGTTGAAGAACTCGCACACACAGTGCCTCAATT
1 ACCGATCTCGCACACATAGTGCTCGGTTAAAGAATTTGCACACACAGTGCCTCAATT
4290049 ACCGATCTCGCACACATAGTGCTCGGTTAAAGGAATTTGCACACACAGTGCCTCAATT
1 ACCGATCTCGCACACATAGTGCTCGGTTAAA-GAATTTGCACACACAGTGCCTCAATT
* *
4290107 ACTGATCTCGCACACATAGTGCTCGGTTAAAAGAATTTGTACACACAGTGCCTC
1 ACCGATCTCGCACACATAGTGCTCGGTT-AAAGAATTTGCACACACAGTGCCTC
4290161 TAATCATTCG
Statistics
Matches: 105, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
57 30 0.29
58 72 0.69
59 3 0.03
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (57 bp):
ACCGATCTCGCACACATAGTGCTCGGTTAAAGAATTTGCACACACAGTGCCTCAATT
Found at i:4290150 original size:29 final size:29
Alignment explanation
Indices: 4290058--4290157 Score: 87
Period size: 29 Copynumber: 3.4 Consensus size: 29
4290048 TACCGATCTC
* *
4290058 GCACACATAGTGCTCGGTTAAAGGAATTT
1 GCACACACAGTGCTCGGTTAAAAGAATTT
** ** *
4290087 GCACACACAGTGCCTCAATT-ACTG-ATCTC
1 GCACACACAGTG-CTCGGTTAAAAGAAT-TT
*
4290116 GCACACATAGTGCTCGGTTAAAAGAATTT
1 GCACACACAGTGCTCGGTTAAAAGAATTT
*
4290145 GTACACACAGTGC
1 GCACACACAGTGC
4290158 CTCTAATCAT
Statistics
Matches: 53, Mismatches: 14, Indels: 8
0.71 0.19 0.11
Matches are distributed among these distances:
28 7 0.13
29 39 0.74
30 7 0.13
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (29 bp):
GCACACACAGTGCTCGGTTAAAAGAATTT
Found at i:4290366 original size:27 final size:28
Alignment explanation
Indices: 4290336--4290398 Score: 94
Period size: 27 Copynumber: 2.3 Consensus size: 28
4290326 AAGCCTGCTA
4290336 GGCACGAAGA-CCCGAATACACATCACC
1 GGCACGAAGAGCCCGAATACACATCACC
*
4290363 GGCACGAA-AGCCTGAATACACATCACC
1 GGCACGAAGAGCCCGAATACACATCACC
*
4290390 GACACGAAG
1 GGCACGAAG
4290399 CCTGCTAGGC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
26 1 0.03
27 31 0.97
ACGTcount: A:0.38, C:0.33, G:0.21, T:0.08
Consensus pattern (28 bp):
GGCACGAAGAGCCCGAATACACATCACC
Found at i:4290412 original size:43 final size:43
Alignment explanation
Indices: 4290363--4290604 Score: 378
Period size: 43 Copynumber: 5.7 Consensus size: 43
4290353 ACACATCACC
* * *
4290363 GGCACGAAAGCCTGAATACACATCACCGACACGAAGCCTGCTA
1 GGCACGAAGGCCCGAATACACATCACCGGCACGAAGCCTGCTA
*
4290406 GGCACGAAGGCCCGAATACATATCACCGGCACGAAGCCTGCTA
1 GGCACGAAGGCCCGAATACACATCACCGGCACGAAGCCTGCTA
* *
4290449 GGCACGAAGGCCCAAATACACATCATCGGCACGAAGCCTGCTA
1 GGCACGAAGGCCCGAATACACATCACCGGCACGAAGCCTGCTA
* *
4290492 GGCACGAAGGCCCAAATACACATCATCGGCACGAAGCCTGCTA
1 GGCACGAAGGCCCGAATACACATCACCGGCACGAAGCCTGCTA
* *
4290535 GGCACGAAGACCCGAATACACATCA-CTGCACGAAGCCTGCTA
1 GGCACGAAGGCCCGAATACACATCACCGGCACGAAGCCTGCTA
*
4290577 GGCACGAAGGCCTGAATACACATCACCG
1 GGCACGAAGGCCCGAATACACATCACCG
4290605 AGTTTCATGC
Statistics
Matches: 185, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
42 39 0.21
43 146 0.79
ACGTcount: A:0.33, C:0.33, G:0.23, T:0.12
Consensus pattern (43 bp):
GGCACGAAGGCCCGAATACACATCACCGGCACGAAGCCTGCTA
Found at i:4292040 original size:37 final size:36
Alignment explanation
Indices: 4291999--4292112 Score: 201
Period size: 37 Copynumber: 3.1 Consensus size: 36
4291989 ACACATTCTT
4291999 TATTCTCGTCAGATCAATCTCACATAATTAATATATA
1 TATTCTCGTCAGATCAATCTCACATAA-TAATATATA
4292036 TATTCTCGTCAGATCAATCTCACATTAATAATATATA
1 TATTCTCGTCAGATCAATCTCACA-TAATAATATATA
4292073 TATTCTCGTCAGATCAATCTCACATAAATAATATATA
1 TATTCTCGTCAGATCAATCTCACAT-AATAATATATA
4292110 TAT
1 TAT
4292113 CACATACCTG
Statistics
Matches: 75, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
36 1 0.01
37 71 0.95
38 3 0.04
ACGTcount: A:0.39, C:0.18, G:0.05, T:0.38
Consensus pattern (36 bp):
TATTCTCGTCAGATCAATCTCACATAATAATATATA
Found at i:4295942 original size:35 final size:35
Alignment explanation
Indices: 4295887--4295993 Score: 178
Period size: 35 Copynumber: 3.1 Consensus size: 35
4295877 CTCTTGATAA
*
4295887 TTGTCTTTCATTTGCCTATATAGCCAACGCCTCAT
1 TTGTTTTTCATTTGCCTATATAGCCAACGCCTCAT
* *
4295922 TTGTTTTTCATTTGCATATATAGCTAACGCCTCAT
1 TTGTTTTTCATTTGCCTATATAGCCAACGCCTCAT
*
4295957 TTGTTTTTCATTTGCCTATATAGCCAATGCCTCAT
1 TTGTTTTTCATTTGCCTATATAGCCAACGCCTCAT
4295992 TT
1 TT
4295994 ATTTAGAACT
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 66 1.00
ACGTcount: A:0.21, C:0.23, G:0.11, T:0.45
Consensus pattern (35 bp):
TTGTTTTTCATTTGCCTATATAGCCAACGCCTCAT
Found at i:4296190 original size:26 final size:26
Alignment explanation
Indices: 4296154--4296205 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
4296144 CCTTTAGATG
4296154 GCTATTTTCTTTGTAGTAATTGGTCA
1 GCTATTTTCTTTGTAGTAATTGGTCA
4296180 GCTATTTTCTTTGTAGTAATTGGTCA
1 GCTATTTTCTTTGTAGTAATTGGTCA
4296206 TTCACATCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.19, C:0.12, G:0.19, T:0.50
Consensus pattern (26 bp):
GCTATTTTCTTTGTAGTAATTGGTCA
Found at i:4300261 original size:31 final size:29
Alignment explanation
Indices: 4300191--4300305 Score: 110
Period size: 31 Copynumber: 3.9 Consensus size: 29
4300181 AAATGCTTAG
*
4300191 GTACCAAATTAGGAAAAAAGTCAAGTTCAG
1 GTACCAAATTA-GAAAAAAGTCAAGTTCAA
*
4300221 GTACCAAATTAGAAAAAAGTGTGAAGTTCAA
1 GTACCAAATTAGAAAAAA--GTCAAGTTCAA
* * *
4300252 GTACTAAATTAGACAAAAA--AAACTT-AA
1 GTACCAAATTAGA-AAAAAGTCAAGTTCAA
*
4300279 GTACCAAATTAGAAAAAATGACAAGTT
1 GTACCAAATTAGAAAAAA-GTCAAGTT
4300306 AAAATATCTA
Statistics
Matches: 71, Mismatches: 8, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
26 5 0.07
27 14 0.20
28 4 0.06
29 11 0.15
30 11 0.15
31 21 0.30
32 5 0.07
ACGTcount: A:0.51, C:0.11, G:0.16, T:0.22
Consensus pattern (29 bp):
GTACCAAATTAGAAAAAAGTCAAGTTCAA
Found at i:4302088 original size:17 final size:17
Alignment explanation
Indices: 4302066--4302121 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
4302056 ATTAATTATA
4302066 AAAATAATATTTTAATT
1 AAAATAATATTTTAATT
* *
4302083 AAAATAAATAAATATAA--
1 AAAAT-AAT-ATTTTAATT
4302100 AAAATAATATTTTAATGT
1 AAAATAATATTTTAAT-T
4302118 AAAA
1 AAAA
4302122 AAGAGTGGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 9
0.70 0.09 0.21
Matches are distributed among these distances:
15 5 0.17
16 3 0.10
17 10 0.33
18 7 0.23
19 5 0.17
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (17 bp):
AAAATAATATTTTAATT
Found at i:4302120 original size:20 final size:19
Alignment explanation
Indices: 4302057--4302123 Score: 63
Period size: 20 Copynumber: 3.6 Consensus size: 19
4302047 TCAGGCGATA
4302057 TTAATTATAAAAATAATATT
1 TTAATTA-AAAAATAATATT
4302077 TTAATT--AAAATAA-A--
1 TTAATTAAAAAATAATATT
*
4302091 TAAATATAAAAAATAATATT
1 TTAAT-TAAAAAATAATATT
4302111 TTAATGTAAAAAA
1 TTAAT-TAAAAAA
4302124 GAGTGGTTGT
Statistics
Matches: 38, Mismatches: 3, Indels: 12
0.72 0.06 0.23
Matches are distributed among these distances:
14 4 0.11
15 1 0.03
16 1 0.03
17 14 0.37
18 1 0.03
20 17 0.45
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (19 bp):
TTAATTAAAAAATAATATT
Found at i:4303327 original size:13 final size:13
Alignment explanation
Indices: 4303309--4303334 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4303299 TATTAATAAC
4303309 AAATTTAATATTT
1 AAATTTAATATTT
4303322 AAATTTAATATTT
1 AAATTTAATATTT
4303335 TCATACTCAA
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AAATTTAATATTT
Found at i:4319295 original size:21 final size:24
Alignment explanation
Indices: 4319269--4319311 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
4319259 TTGTTTCATT
4319269 AAAAA-TAA-TTT-TTAAAAATTC
1 AAAAATTAATTTTATTAAAAATTC
4319290 AAAAATTAATTTTATTAAAAAT
1 AAAAATTAATTTTATTAAAAAT
4319312 ATTTAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 3 0.16
23 3 0.16
24 8 0.42
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (24 bp):
AAAAATTAATTTTATTAAAAATTC
Found at i:4319311 original size:16 final size:17
Alignment explanation
Indices: 4319290--4319340 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 17
4319280 TTAAAAATTC
4319290 AAAAA-TTAATTTTATTA
1 AAAAACTTAATTTT-TTA
*
4319307 AAAATATTTAATTTTTT-
1 AAAA-ACTTAATTTTTTA
4319324 AAAAACTTAATCTTTTT
1 AAAAACTTAAT-TTTTT
4319341 TGATAAGTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
16 6 0.20
17 13 0.43
18 3 0.10
19 8 0.27
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (17 bp):
AAAAACTTAATTTTTTA
Found at i:4336785 original size:11 final size:11
Alignment explanation
Indices: 4336769--4336846 Score: 77
Period size: 11 Copynumber: 6.9 Consensus size: 11
4336759 GAATAAGTTG
*
4336769 TTTTGTTGTTA
1 TTTTGTTATTA
*
4336780 TTTTGTTATTG
1 TTTTGTTATTA
*
4336791 TTTTGTTATTG
1 TTTTGTTATTA
4336802 TTTTGTTATTA
1 TTTTGTTATTA
4336813 TTTT-TTATTA
1 TTTTGTTATTA
* *
4336823 TATTATTATACTA
1 TTTTGTTAT--TA
4336836 TTGTTGTTATT
1 TT-TTGTTATT
4336847 TGGATATAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
10 9 0.16
11 38 0.67
12 1 0.02
13 3 0.05
14 6 0.11
ACGTcount: A:0.17, C:0.01, G:0.12, T:0.71
Consensus pattern (11 bp):
TTTTGTTATTA
Found at i:4337575 original size:11 final size:11
Alignment explanation
Indices: 4337559--4337583 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
4337549 TATGATATGA
4337559 GATGTAGATAT
1 GATGTAGATAT
4337570 GATGTAGATAT
1 GATGTAGATAT
4337581 GAT
1 GAT
4337584 AACTAAGCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.28, T:0.36
Consensus pattern (11 bp):
GATGTAGATAT
Found at i:4355010 original size:26 final size:26
Alignment explanation
Indices: 4354950--4355022 Score: 67
Period size: 26 Copynumber: 2.8 Consensus size: 26
4354940 ATTTTTTTTG
* * *
4354950 TAAAATTAATAATTTATTTTTAGTTA
1 TAAAATAAAAAATATATTTTTAGTTA
*
4354976 AAAATATAAAAAATATATTTTTA-TTA
1 TAAA-ATAAAAAATATATTTTTAGTTA
* *
4355002 TTAAAATAATATATATATTTT
1 -TAAAATAAAAAATATATTTT
4355023 AACATTAATC
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
26 20 0.53
27 18 0.47
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (26 bp):
TAAAATAAAAAATATATTTTTAGTTA
Found at i:4358138 original size:13 final size:13
Alignment explanation
Indices: 4358117--4358161 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 13
4358107 TAAAAAATTC
*
4358117 TATTTTTTTTGTT
1 TATTATTTTTGTT
4358130 TATTATTTTTG-T
1 TATTATTTTTGTT
*
4358142 TATT-TTTAT-TT
1 TATTATTTTTGTT
4358153 TATTATTTT
1 TATTATTTT
4358162 ACTATATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
11 9 0.33
12 8 0.30
13 10 0.37
ACGTcount: A:0.16, C:0.00, G:0.04, T:0.80
Consensus pattern (13 bp):
TATTATTTTTGTT
Found at i:4360769 original size:53 final size:52
Alignment explanation
Indices: 4360646--4360790 Score: 175
Period size: 52 Copynumber: 2.8 Consensus size: 52
4360636 AACATGTGAC
* * * *
4360646 ATGTGCTCCCGTATAAGACTATAGCT-AGACTATGGCATCGGTGTGATGAGAT
1 ATGTGCTTCCGTATAAGACAATAGCTGGGA-TATGGCATCGGTGAGATGAGAT
* * **
4360698 ATGTGCTTCCGTATAAGACCATAGCTGGGTTATGGCATCGGTGAGATTTGATT
1 ATGTGCTTCCGTATAAGACAATAGCTGGGATATGGCATCGGTGAGATGAGA-T
* *
4360751 ATGTGCTTCTGTATAAGACAATATCTGGGATATGGCATCG
1 ATGTGCTTCCGTATAAGACAATAGCTGGGATATGGCATCG
4360791 ATGATATATG
Statistics
Matches: 80, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
52 42 0.52
53 38 0.47
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.32
Consensus pattern (52 bp):
ATGTGCTTCCGTATAAGACAATAGCTGGGATATGGCATCGGTGAGATGAGAT
Found at i:4360822 original size:47 final size:47
Alignment explanation
Indices: 4360746--4360879 Score: 139
Period size: 47 Copynumber: 2.9 Consensus size: 47
4360736 CGGTGAGATT
* * * *
4360746 TGAT-TATGTGCTTCTGTATAAGACAATATCTGGGATATGGCATCGA
1 TGATATATGTGCTTTTGTGTAAGACCATATCTGGGATATGGCATCAA
*
4360792 TGATATATGTGCTTTTGTGTAAGACCATATCTGAGATATGGCATCAA
1 TGATATATGTGCTTTTGTGTAAGACCATATCTGGGATATGGCATCAA
* * * ** *
4360839 TG-TGATTTGTG-ATTCGTGTAAGACCATGGCTGGGCTATGGC
1 TGAT-ATATGTGCTTTTGTGTAAGACCATATCTGGGATATGGC
4360880 TTCGGTGTGT
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
46 29 0.39
47 45 0.61
ACGTcount: A:0.25, C:0.13, G:0.26, T:0.35
Consensus pattern (47 bp):
TGATATATGTGCTTTTGTGTAAGACCATATCTGGGATATGGCATCAA
Found at i:4364148 original size:18 final size:18
Alignment explanation
Indices: 4364127--4364169 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
4364117 CATTCTTCTC
4364127 CCCTTTCCCCTTCTCCTT
1 CCCTTTCCCCTTCTCCTT
4364145 CCCTTTCCCCTTCTCCTT
1 CCCTTTCCCCTTCTCCTT
4364163 CCCTTTC
1 CCCTTTC
4364170 TCGTTTCGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (18 bp):
CCCTTTCCCCTTCTCCTT
Found at i:4365304 original size:35 final size:34
Alignment explanation
Indices: 4365265--4365330 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
4365255 CAAACACCAG
*
4365265 AAAACATTTTCCAGTAAGTCATTTTACAGAAATGT
1 AAAACATTTTCCAG-AAATCATTTTACAGAAATGT
*
4365300 AAAACATTTTCCAGAAATCATTTTACGGAAA
1 AAAACATTTTCCAGAAATCATTTTACAGAAA
4365331 ACATTTTACT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 15 0.52
35 14 0.48
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.32
Consensus pattern (34 bp):
AAAACATTTTCCAGAAATCATTTTACAGAAATGT
Found at i:4365323 original size:14 final size:14
Alignment explanation
Indices: 4365300--4365339 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
4365290 ACAGAAATGT
*
4365300 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
4365314 AAATCATTTTACGG
1 AAAACATTTTACAG
4365328 AAAACATTTTAC
1 AAAACATTTTAC
4365340 TGCCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:4369719 original size:16 final size:16
Alignment explanation
Indices: 4369698--4369729 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4369688 CCCTTAGTCA
*
4369698 TGATTATTTAATTAAT
1 TGATTAGTTAATTAAT
4369714 TGATTAGTTAATTAAT
1 TGATTAGTTAATTAAT
4369730 CACCTCTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (16 bp):
TGATTAGTTAATTAAT
Found at i:4378192 original size:18 final size:19
Alignment explanation
Indices: 4378171--4378207 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
4378161 TATAAAAAAT
4378171 GAAAAA-TAATAAATTTTA
1 GAAAAATTAATAAATTTTA
*
4378189 GAAAAATTATTAAATTTTA
1 GAAAAATTAATAAATTTTA
4378208 ATAAGAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (19 bp):
GAAAAATTAATAAATTTTA
Found at i:4378394 original size:10 final size:10
Alignment explanation
Indices: 4378375--4378407 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
4378365 ACATGTGATG
4378375 AAAAAT-AAT
1 AAAAATAAAT
4378384 AAAAATAAAT
1 AAAAATAAAT
*
4378394 AAAAATAAAC
1 AAAAATAAAT
4378404 AAAA
1 AAAA
4378408 GTTAAAGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 6 0.27
10 16 0.73
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (10 bp):
AAAAATAAAT
Found at i:4378557 original size:27 final size:26
Alignment explanation
Indices: 4378518--4378587 Score: 63
Period size: 27 Copynumber: 2.7 Consensus size: 26
4378508 ACTTTATAAA
*
4378518 ATTTTACAA-TTTTTATATTTCTATAT
1 ATTTTAAAATTTTTTATATTTCTA-AT
* * *
4378544 ATTTTATAATTTTTAATAAATTTTTAAT
1 ATTTTAAAATTTTT--TATATTTCTAAT
4378572 A-TTTAAAATTTTTTAT
1 ATTTTAAAATTTTTTAT
4378588 TAAAATTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
25 2 0.06
26 8 0.22
27 15 0.42
28 3 0.08
29 8 0.22
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (26 bp):
ATTTTAAAATTTTTTATATTTCTAAT
Found at i:4378571 original size:18 final size:18
Alignment explanation
Indices: 4378525--4378586 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 18
4378515 AAAATTTTAC
*
4378525 AATTTTTATATTTCT-ATA
1 AATTTTTA-ATTTTTAATA
*
4378543 TATTTTATAATTTTTAATA
1 AATTTT-TAATTTTTAATA
*
4378562 AATTTTTAATATTTAA-A
1 AATTTTTAATTTTTAATA
*
4378579 ATTTTTTA
1 AATTTTTA
4378587 TTAAAATTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
17 8 0.22
18 19 0.51
19 10 0.27
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (18 bp):
AATTTTTAATTTTTAATA
Found at i:4378606 original size:20 final size:20
Alignment explanation
Indices: 4378555--4378607 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
4378545 TTTTATAATT
*
4378555 TTTAATAA-ATTT-TTAATA
1 TTTAATAATATTTATTAAAA
*
4378573 TTTAA-AATTTTTTATTAAAA
1 TTTAATAA-TATTTATTAAAA
4378593 TTTAATAATATTTAT
1 TTTAATAATATTTAT
4378608 AGCTTTATTG
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
17 2 0.07
18 5 0.18
19 3 0.11
20 16 0.57
21 2 0.07
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTAATAATATTTATTAAAA
Found at i:4381306 original size:6 final size:6
Alignment explanation
Indices: 4381268--4381319 Score: 50
Period size: 6 Copynumber: 8.7 Consensus size: 6
4381258 TATCCAAAAG
* * * * * *
4381268 GATAAA GACAAA GACAAA GAAAAA AACAAA GATAAA GATAAA AATAAA
1 GATAAA GATAAA GATAAA GATAAA GATAAA GATAAA GATAAA GATAAA
4381316 GATA
1 GATA
4381320 GAGAGATTGA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.71, C:0.06, G:0.13, T:0.10
Consensus pattern (6 bp):
GATAAA
Found at i:4381318 original size:18 final size:18
Alignment explanation
Indices: 4381275--4381319 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
4381265 AAGGATAAAG
*
4381275 ACAAAGACAAAGAAAAAA
1 ACAAAGATAAAGAAAAAA
*
4381293 ACAAAGATAAAGATAAAA
1 ACAAAGATAAAGAAAAAA
*
4381311 ATAAAGATA
1 ACAAAGATA
4381320 GAGAGATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.73, C:0.07, G:0.11, T:0.09
Consensus pattern (18 bp):
ACAAAGATAAAGAAAAAA
Found at i:4386634 original size:7 final size:8
Alignment explanation
Indices: 4386606--4386633 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
4386596 TTTATTGATA
4386606 TTTTTATT
1 TTTTTATT
4386614 TTTTTATT
1 TTTTTATT
4386622 TTTTTATT
1 TTTTTATT
4386630 TTTT
1 TTTT
4386634 AATAAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTTATT
Found at i:4391583 original size:13 final size:12
Alignment explanation
Indices: 4391565--4391594 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
4391555 CATAAACATT
4391565 TAAAAATAATATA
1 TAAAAATAATA-A
4391578 TAAAAATAATAA
1 TAAAAATAATAA
4391590 TAAAA
1 TAAAA
4391595 TGTAAGATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (12 bp):
TAAAAATAATAA
Found at i:4398631 original size:22 final size:22
Alignment explanation
Indices: 4398606--4398662 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 22
4398596 ATATTGTTCG
4398606 ATACAGAGTTATATCAACAAAA
1 ATACAGAGTTATATCAACAAAA
* *
4398628 ATACTAGGGTTAGTATCGACAAAA
1 ATAC-AGAGTTA-TATCAACAAAA
*
4398652 AGA-AGAGTTAT
1 ATACAGAGTTAT
4398663 GATTTACTCG
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
21 1 0.03
22 10 0.34
23 6 0.21
24 12 0.41
ACGTcount: A:0.47, C:0.11, G:0.18, T:0.25
Consensus pattern (22 bp):
ATACAGAGTTATATCAACAAAA
Found at i:4403311 original size:18 final size:18
Alignment explanation
Indices: 4403288--4403380 Score: 132
Period size: 18 Copynumber: 5.2 Consensus size: 18
4403278 CCCAACTACT
*
4403288 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
4403306 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
* * *
4403324 GTATACATGGATAGTACT
1 GTATACGTGAATAGTACC
**
4403342 GTATACGTGAATAGTGTC
1 GTATACGTGAATAGTACC
4403360 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
4403378 GTA
1 GTA
4403381 AACGGTCGTA
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 64 1.00
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:4404316 original size:27 final size:27
Alignment explanation
Indices: 4404278--4404337 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
4404268 ATTTTATACG
4404278 TATAATAACATAATATAAAAACTTTTC
1 TATAATAACATAATATAAAAACTTTTC
4404305 TATAATAACATAATATAAAAACTTTTC
1 TATAATAACATAATATAAAAACTTTTC
*
4404332 TTTAAT
1 TATAAT
4404338 TGATCAAAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (27 bp):
TATAATAACATAATATAAAAACTTTTC
Found at i:4410145 original size:114 final size:114
Alignment explanation
Indices: 4410008--4410236 Score: 458
Period size: 114 Copynumber: 2.0 Consensus size: 114
4409998 AGTTGAATTG
4410008 GTTTTAAATTGGTTGTAAATAAATAAAGATGTAGCTTGAATAAAAATAATTAAATTTATATATTC
1 GTTTTAAATTGGTTGTAAATAAATAAAGATGTAGCTTGAATAAAAATAATTAAATTTATATATTC
4410073 TATAATTAAATTTAAATAAAATTATTTATTATATTATATTTCAAACCAA
66 TATAATTAAATTTAAATAAAATTATTTATTATATTATATTTCAAACCAA
4410122 GTTTTAAATTGGTTGTAAATAAATAAAGATGTAGCTTGAATAAAAATAATTAAATTTATATATTC
1 GTTTTAAATTGGTTGTAAATAAATAAAGATGTAGCTTGAATAAAAATAATTAAATTTATATATTC
4410187 TATAATTAAATTTAAATAAAATTATTTATTATATTATATTTCAAACCAA
66 TATAATTAAATTTAAATAAAATTATTTATTATATTATATTTCAAACCAA
4410236 G
1 G
4410237 CGGATCGACC
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
114 115 1.00
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.42
Consensus pattern (114 bp):
GTTTTAAATTGGTTGTAAATAAATAAAGATGTAGCTTGAATAAAAATAATTAAATTTATATATTC
TATAATTAAATTTAAATAAAATTATTTATTATATTATATTTCAAACCAA
Found at i:4424311 original size:19 final size:19
Alignment explanation
Indices: 4424287--4424323 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
4424277 TAAAAATGAG
4424287 ATAAACAAACTAATGTAAC
1 ATAAACAAACTAATGTAAC
4424306 ATAAACAAACTAATGTAA
1 ATAAACAAACTAATGTAA
4424324 ATATATATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.59, C:0.14, G:0.05, T:0.22
Consensus pattern (19 bp):
ATAAACAAACTAATGTAAC
Found at i:4429372 original size:20 final size:22
Alignment explanation
Indices: 4429344--4429385 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
4429334 AAAAATTAAG
4429344 ATGTATTAAAAT-TT-TAAAAA
1 ATGTATTAAAATATTATAAAAA
*
4429364 ATGTTTTAAAATATTATAAAAA
1 ATGTATTAAAATATTATAAAAA
4429386 CATAAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 11 0.58
21 2 0.11
22 6 0.32
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (22 bp):
ATGTATTAAAATATTATAAAAA
Found at i:4429566 original size:19 final size:19
Alignment explanation
Indices: 4429514--4429569 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 19
4429504 AATTTTTTGA
*
4429514 AATTTTATTATAATTTTTAT
1 AATTTTA-TATAATTTTAAT
* *
4429534 AATTTT-TGTCATTTATAAT
1 AATTTTATATAATTT-TAAT
*
4429553 AATTTTATATATTTTTA
1 AATTTTATATAATTTTA
4429570 TACTTTAATA
Statistics
Matches: 28, Mismatches: 6, Indels: 5
0.72 0.15 0.13
Matches are distributed among these distances:
18 6 0.21
19 11 0.39
20 11 0.39
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (19 bp):
AATTTTATATAATTTTAAT
Found at i:4429568 original size:10 final size:9
Alignment explanation
Indices: 4429521--4429571 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
4429511 TGAAATTTTA
4429521 TTATAATTT
1 TTATAATTT
4429530 TTATAATTT
1 TTATAATTT
* *
4429539 TTGTCATTT
1 TTATAATTT
*
4429548 ATAATAA-TT
1 -TTATAATTT
4429557 TTATATATTT
1 TTATA-ATTT
4429567 TTATA
1 TTATA
4429572 CTTTAATATT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
8 4 0.12
9 19 0.58
10 10 0.30
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (9 bp):
TTATAATTT
Found at i:4429576 original size:28 final size:28
Alignment explanation
Indices: 4429492--4429576 Score: 70
Period size: 28 Copynumber: 3.0 Consensus size: 28
4429482 TTTTATTATG
* *
4429492 ATAATAAGTTTTA-AT-TTTTTGAAATTTT
1 ATAATAA-TTTTATATATTTTT-ATACTTT
* *
4429520 ATTATAATTTT-TATAATTTTTGT-CATTT
1 ATAATAATTTTATAT-ATTTTTATAC-TTT
4429548 ATAATAATTTTATATATTTTTATACTTT
1 ATAATAATTTTATATATTTTTATACTTT
4429576 A
1 A
4429577 ATATTCTATA
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
27 6 0.13
28 30 0.67
29 9 0.20
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (28 bp):
ATAATAATTTTATATATTTTTATACTTT
Found at i:4431081 original size:30 final size:29
Alignment explanation
Indices: 4431025--4431081 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
4431015 AGTTTAAATA
* *
4431025 AAAAAAATTATATAATAATATTAAAATGT
1 AAAAAAATTATATAATAAAATAAAAATGT
*
4431054 AAAAAAATATATATATTAAAATAAAAAT
1 AAAAAAAT-TATATAATAAAATAAAAAT
4431082 TTAATTAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (29 bp):
AAAAAAATTATATAATAAAATAAAAATGT
Found at i:4431248 original size:11 final size:11
Alignment explanation
Indices: 4431232--4431276 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
4431222 TCATAAAACA
4431232 ATACTTAAATT
1 ATACTTAAATT
4431243 ATACTT-AATT
1 ATACTTAAATT
*
4431253 AT-C-TAAAGTG
1 ATACTTAAA-TT
4431263 ATACTTAAATT
1 ATACTTAAATT
4431274 ATA
1 ATA
4431277 TGATTTTTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
8 1 0.04
9 3 0.11
10 9 0.32
11 11 0.39
12 4 0.14
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.42
Consensus pattern (11 bp):
ATACTTAAATT
Found at i:4432250 original size:17 final size:18
Alignment explanation
Indices: 4432219--4432253 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
4432209 ATATATTATT
*
4432219 AAAATATTAATTATAAAA
1 AAAATATTAAATATAAAA
4432237 AAAATA-TAAATATAAAA
1 AAAATATTAAATATAAAA
4432254 TTACTTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAATATTAAATATAAAA
Found at i:4434055 original size:20 final size:20
Alignment explanation
Indices: 4434032--4434070 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4434022 AATTTTATTT
* *
4434032 TATTTAACTTAATTTAAAAA
1 TATTTAAATTAAATTAAAAA
4434052 TATTTAAATTAAATTAAAA
1 TATTTAAATTAAATTAAAA
4434071 TAATAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (20 bp):
TATTTAAATTAAATTAAAAA
Found at i:4435309 original size:3 final size:3
Alignment explanation
Indices: 4435301--4435340 Score: 71
Period size: 3 Copynumber: 13.0 Consensus size: 3
4435291 CAACTTTGTT
4435301 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA
4435341 CTACTACTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:4438785 original size:20 final size:19
Alignment explanation
Indices: 4438757--4438822 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 19
4438747 ACAAAACAAA
*
4438757 TCAAGATAATTTTCATAAAT
1 TCAAAATAATTTTCA-AAAT
*
4438777 TCAAAATAATTTTTAAAAT
1 TCAAAATAATTTTCAAAAT
*
4438796 TCAAAAT-ATTTATAAAAAT
1 TCAAAATAATTT-TCAAAAT
4438815 TCCAAAAT
1 T-CAAAAT
4438823 TTATAATATT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
18 4 0.10
19 18 0.44
20 19 0.46
ACGTcount: A:0.52, C:0.09, G:0.02, T:0.38
Consensus pattern (19 bp):
TCAAAATAATTTTCAAAAT
Found at i:4438795 original size:19 final size:19
Alignment explanation
Indices: 4438757--4438822 Score: 71
Period size: 19 Copynumber: 3.4 Consensus size: 19
4438747 ACAAAACAAA
* *
4438757 TCAAGATAATTTTCATAAAT
1 TCAAAATAATTTT-AAAAAT
*
4438777 TCAAAATAATTTTTAAAAT
1 TCAAAATAATTTTAAAAAT
4438796 TCAAAAT-ATTTATAAAAAT
1 TCAAAATAATTT-TAAAAAT
4438815 TCCAAAAT
1 T-CAAAAT
4438823 TTATAATATT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
18 4 0.10
19 18 0.45
20 18 0.45
ACGTcount: A:0.52, C:0.09, G:0.02, T:0.38
Consensus pattern (19 bp):
TCAAAATAATTTTAAAAAT
Found at i:4438821 original size:27 final size:27
Alignment explanation
Indices: 4438791--4438848 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
4438781 AATAATTTTT
*
4438791 AAAATTCAAAATA-TTTATAAAAATTCC
1 AAAATTCAAAATATTTTA-AAAAATTAC
* *
4438818 AAAATTTATAATATTTTAAAAAATTAC
1 AAAATTCAAAATATTTTAAAAAATTAC
4438845 AAAA
1 AAAA
4438849 ATTTCAAACA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 23 0.85
28 4 0.15
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (27 bp):
AAAATTCAAAATATTTTAAAAAATTAC
Found at i:4438824 original size:18 final size:19
Alignment explanation
Indices: 4438773--4438828 Score: 71
Period size: 19 Copynumber: 3.0 Consensus size: 19
4438763 TAATTTTCAT
*
4438773 AAATTCAAAATAATTT-TTA
1 AAATTCAAAAT-ATTTATAA
4438792 AAATTCAAAATATTTATAA
1 AAATTCAAAATATTTATAA
*
4438811 AAATTCCAAA-ATTTATAA
1 AAATTCAAAATATTTATAA
4438829 TATTTTAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
18 12 0.35
19 22 0.65
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (19 bp):
AAATTCAAAATATTTATAA
Found at i:4443709 original size:46 final size:46
Alignment explanation
Indices: 4443657--4443747 Score: 182
Period size: 46 Copynumber: 2.0 Consensus size: 46
4443647 TCTCATCCAT
4443657 AAGCCCAGTTATTTAGATAGTTGTAATTCCATTTTTATGATTCTAA
1 AAGCCCAGTTATTTAGATAGTTGTAATTCCATTTTTATGATTCTAA
4443703 AAGCCCAGTTATTTAGATAGTTGTAATTCCATTTTTATGATTCTA
1 AAGCCCAGTTATTTAGATAGTTGTAATTCCATTTTTATGATTCTA
4443748 TGTATGGTTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.44
Consensus pattern (46 bp):
AAGCCCAGTTATTTAGATAGTTGTAATTCCATTTTTATGATTCTAA
Found at i:4444536 original size:17 final size:17
Alignment explanation
Indices: 4444514--4444548 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
4444504 GTGGGCCTGG
4444514 TTGGGCTCAATTTAGGC
1 TTGGGCTCAATTTAGGC
4444531 TTGGGCTCAATTTAGGC
1 TTGGGCTCAATTTAGGC
4444548 T
1 T
4444549 CTGTATGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.17, G:0.29, T:0.37
Consensus pattern (17 bp):
TTGGGCTCAATTTAGGC
Found at i:4450710 original size:22 final size:22
Alignment explanation
Indices: 4450685--4450727 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
4450675 ATAACACTGA
4450685 TATG-ATATTTTACTTGATAATT
1 TATGCATATTTTA-TTGATAATT
* *
4450707 TATGCGTATTTTATTGTTAAT
1 TATGCATATTTTATTGATAAT
4450728 GTAGATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.28, C:0.05, G:0.12, T:0.56
Consensus pattern (22 bp):
TATGCATATTTTATTGATAATT
Found at i:4452715 original size:3 final size:3
Alignment explanation
Indices: 4452707--4452773 Score: 50
Period size: 3 Copynumber: 22.3 Consensus size: 3
4452697 TTAATTTATT
* * *
4452707 TAA TAA TAA TGA T-T TAA T-A TAA -AA TCA TAA TAA TAA TTAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA
*
4452750 TAA TAA TTA TATA TAA TATA TAA T
1 TAA TAA TAA TA-A TAA TA-A TAA T
4452774 CTAAGAAAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
2 5 0.10
3 37 0.73
4 9 0.18
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:4452749 original size:13 final size:13
Alignment explanation
Indices: 4452706--4452767 Score: 60
Period size: 13 Copynumber: 4.9 Consensus size: 13
4452696 TTTAATTTAT
*
4452706 TTAATAATAATGAT
1 TTAATAATAAT-AA
4452720 TTAAT-ATAA-AA
1 TTAATAATAATAA
*
4452731 -TCATAATAATAA
1 TTAATAATAATAA
4452743 TTAATAATAATAA
1 TTAATAATAATAA
4452756 TT-ATATATAATA
1 TTAATA-ATAATA
4452768 TATAATCTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
10 3 0.07
11 5 0.12
12 5 0.12
13 23 0.56
14 5 0.12
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (13 bp):
TTAATAATAATAA
Found at i:4455085 original size:16 final size:18
Alignment explanation
Indices: 4455066--4455103 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
4455056 TATTTTAAGA
4455066 ATAAGATATT-TAAT-AT
1 ATAAGATATTATAATAAT
*
4455082 ATAATATATTATAATAAT
1 ATAAGATATTATAATAAT
4455100 ATAA
1 ATAA
4455104 TAGAATAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 9 0.47
17 4 0.21
18 6 0.32
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (18 bp):
ATAAGATATTATAATAAT
Found at i:4461735 original size:16 final size:16
Alignment explanation
Indices: 4461714--4461744 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4461704 GATATTTTAA
4461714 TATATTATATTAATAT
1 TATATTATATTAATAT
*
4461730 TATATTATGTTAATA
1 TATATTATATTAATA
4461745 AAATAATAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
TATATTATATTAATAT
Found at i:4468134 original size:30 final size:32
Alignment explanation
Indices: 4468094--4468171 Score: 85
Period size: 30 Copynumber: 2.6 Consensus size: 32
4468084 GAGAATGTAA
*
4468094 TGCTTACACAAGCTGACAACATTTTAA-GG-T
1 TGCTCACACAAGCTGACAACATTTTAATGGAT
*
4468124 TGCTCACACAAGTTG---ACATTTTAATGGAAT
1 TGCTCACACAAGCTGACAACATTTTAATGG-AT
*
4468154 TACTCACACAAGCTGACA
1 TGCTCACACAAGCTGACA
4468172 TCGTATAGAG
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
27 9 0.24
28 2 0.05
30 27 0.71
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (32 bp):
TGCTCACACAAGCTGACAACATTTTAATGGAT
Found at i:4472640 original size:14 final size:14
Alignment explanation
Indices: 4472621--4472652 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
4472611 TCCAATCACC
4472621 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
4472635 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
4472649 GGGC
1 GGGC
4472653 TAAATGACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.16, G:0.47, T:0.31
Consensus pattern (14 bp):
GGGCCAGTTTGGTT
Found at i:4477018 original size:50 final size:50
Alignment explanation
Indices: 4476894--4477142 Score: 284
Period size: 50 Copynumber: 4.8 Consensus size: 50
4476884 GATAATAACA
* * ** * *
4476894 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
4476945 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
4476995 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
4477045 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
4477100 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
4477143 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 21, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.54
51 33 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:4477072 original size:100 final size:104
Alignment explanation
Indices: 4476893--4477142 Score: 357
Period size: 100 Copynumber: 2.4 Consensus size: 104
4476883 TGATAATAAC
**
4476893 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
4476958 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
4476995 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
4477058 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
4477100 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
4477143 TTACCCAAAT
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:4477258 original size:13 final size:13
Alignment explanation
Indices: 4477237--4477268 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
4477227 GCTTGGATCA
*
4477237 TCATCAAATAAAT
1 TCATAAAATAAAT
4477250 TCATAAAATAAAT
1 TCATAAAATAAAT
4477263 TCATAA
1 TCATAA
4477269 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:4477514 original size:30 final size:30
Alignment explanation
Indices: 4477480--4477537 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
4477470 CCTCGACTCT
*
4477480 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
4477510 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
4477538 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:4480077 original size:29 final size:30
Alignment explanation
Indices: 4480018--4480075 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
4480008 TCCGAGCCTT
*
4480018 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
4480048 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
4480076 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:4480305 original size:13 final size:13
Alignment explanation
Indices: 4480287--4480318 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
4480277 TTTCCAGCAA
4480287 TTATGAATTTATT
1 TTATGAATTTATT
4480300 TTATGAATTTATT
1 TTATGAATTTATT
*
4480313 TGATGA
1 TTATGA
4480319 TGATCCGAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:4480526 original size:50 final size:50
Alignment explanation
Indices: 4480413--4480654 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
4480403 ATTTGGGTAA
* *
4480413 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
* *
4480469 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * * *
4480519 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
4480569 AGAGATCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
*
4480619 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGC
4480655 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 90 0.54
51 30 0.18
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.27, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:4480603 original size:100 final size:103
Alignment explanation
Indices: 4480413--4480662 Score: 355
Period size: 100 Copynumber: 2.4 Consensus size: 103
4480403 ATTTGGGTAA
*
4480413 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGATCCC
* *
4480478 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
4480519 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGATCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGATCCCCTA
4480581 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
4480619 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
4480663 GTTATTATCA
Statistics
Matches: 132, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 39 0.30
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGATCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:4485246 original size:29 final size:30
Alignment explanation
Indices: 4485187--4485244 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
4485177 TCTGAGCCTT
*
4485187 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
4485217 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
4485245 AGAGTTGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:4485474 original size:13 final size:13
Alignment explanation
Indices: 4485456--4485487 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
4485446 TTTCCAGCAA
4485456 TTATGAATTTATT
1 TTATGAATTTATT
4485469 TTATGAATTTATT
1 TTATGAATTTATT
*
4485482 TGATGA
1 TTATGA
4485488 TGATCCCAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:4485701 original size:50 final size:50
Alignment explanation
Indices: 4485586--4485822 Score: 271
Period size: 50 Copynumber: 4.6 Consensus size: 50
4485576 GGTAAAGAGA
* * *
4485586 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--GAAAGG
*
4485642 TCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACGAAAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACGAAAGG
* * *
4485692 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGA-TAAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACGAA-AGG
* * * **
4485742 TCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACGAGAACA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACGA-AAGG
4485793 TCCCATGTAAGACCATGTCTGGGACATGGC
1 TCCCATGTAAGACCATGTCTGGGACATGGC
4485823 TTTGGCATGT
Statistics
Matches: 159, Mismatches: 18, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
49 3 0.02
50 84 0.53
51 30 0.19
52 2 0.01
53 3 0.02
55 2 0.01
56 35 0.22
ACGTcount: A:0.27, C:0.25, G:0.28, T:0.20
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACGAAAGG
Found at i:4485773 original size:100 final size:105
Alignment explanation
Indices: 4485585--4485830 Score: 360
Period size: 100 Copynumber: 2.4 Consensus size: 105
4485575 GGGTAAAGAG
*
4485585 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCCCTGT
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC-TAAGATCA-GAGAGGTCCCCTAT
* *
4485650 AAGACCATGTCTGGGACATGGCATGGGCACCGA-GACGA-AAG
64 AAGACCATGTCTGGGACATGGCATGGGCACC-ATCACGAGAAC
* * *
4485691 GTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GAGAT-A-AGAGGTCCCCTATAA
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTAAGATCAGAGAGGTCCCCTATAA
4485752 GACCATGTCTGGGACATGGCATGGGCACCATCACGAGAAC
66 GACCATGTCTGGGACATGGCATGGGCACCATCACGAGAAC
*
4485792 ATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
4485831 GTTATTATCA
Statistics
Matches: 129, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 47 0.36
101 38 0.29
102 1 0.01
103 4 0.03
105 2 0.02
106 36 0.28
ACGTcount: A:0.26, C:0.24, G:0.28, T:0.21
Consensus pattern (105 bp):
ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTAAGATCAGAGAGGTCCCCTATAA
GACCATGTCTGGGACATGGCATGGGCACCATCACGAGAAC
Found at i:4490815 original size:14 final size:14
Alignment explanation
Indices: 4490796--4490827 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
4490786 TCCAATCACC
4490796 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
4490810 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
4490824 GGGC
1 GGGC
4490828 TAAATGACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.16, G:0.47, T:0.31
Consensus pattern (14 bp):
GGGCCAGTTTGGTT
Found at i:4493427 original size:17 final size:17
Alignment explanation
Indices: 4493401--4493441 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
4493391 CAAGTAGATA
4493401 TCTATTGAATAATTAT-
1 TCTATTGAATAATTATG
4493417 TCTACTTGAATAATTATG
1 TCTA-TTGAATAATTATG
4493435 TCTATTG
1 TCTATTG
4493442 CTAAAAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.17
17 15 0.65
18 4 0.17
ACGTcount: A:0.32, C:0.10, G:0.10, T:0.49
Consensus pattern (17 bp):
TCTATTGAATAATTATG
Found at i:4495424 original size:24 final size:24
Alignment explanation
Indices: 4495397--4495471 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 24
4495387 CATTTTCTGT
4495397 CATGTTGCCATGGTATCTTTCAAC
1 CATGTTGCCATGGTATCTTTCAAC
* *
4495421 CATGTT-CTTAT--TCAT-TTTC-CC
1 CATGTTGC-CATGGT-ATCTTTCAAC
4495442 GTCATGTTGCCATGGTATCTTTCAAC
1 --CATGTTGCCATGGTATCTTTCAAC
4495468 CATG
1 CATG
4495472 GTCTTATTCA
Statistics
Matches: 38, Mismatches: 4, Indels: 18
0.63 0.07 0.30
Matches are distributed among these distances:
21 1 0.03
22 5 0.13
23 11 0.29
24 15 0.39
25 5 0.13
26 1 0.03
ACGTcount: A:0.19, C:0.25, G:0.15, T:0.41
Consensus pattern (24 bp):
CATGTTGCCATGGTATCTTTCAAC
Found at i:4495630 original size:46 final size:47
Alignment explanation
Indices: 4495366--4495629 Score: 349
Period size: 46 Copynumber: 5.7 Consensus size: 47
4495356 TGTCATAGTG
* *
4495366 TCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACTCATTTTCATATCATGTTGCCATGGTA
* * ***
4495412 TCTTTCAACCATGTTCTTATTCATTTTCCCGTCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACTCATTTTCATATCATGTTGCCATGGTA
* * * *
4495459 TCTTTCAACCATGGTCTTATTCA-TTTCATGTCACGCTGCCATGGTA
1 TCTTTCAACCATGGTCTTACTCATTTTCATATCATGTTGCCATGGTA
*
4495505 TCTTTCAACCATGGTCTTATTCATTTTC-TATCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACTCATTTTCATATCATGTTGCCATGGTA
* *
4495551 TCTTTCAACCATGGTCTTACACA-TTTCATATCAGGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACTCATTTTCATATCATGTTGCCATGGTA
* *
4495597 TCTTTCAACCATGGTCGTACACA-TTTCATATCA
1 TCTTTCAACCATGGTCTTACTCATTTTCATATCA
4495630 GAGAGCGCAC
Statistics
Matches: 199, Mismatches: 16, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
45 4 0.02
46 152 0.76
47 43 0.22
ACGTcount: A:0.20, C:0.24, G:0.14, T:0.42
Consensus pattern (47 bp):
TCTTTCAACCATGGTCTTACTCATTTTCATATCATGTTGCCATGGTA
Found at i:4497797 original size:28 final size:29
Alignment explanation
Indices: 4497761--4497828 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 29
4497751 ACATTTGTCA
*
4497761 TTATTTAATATATTT-ATCATATAAA-ATC
1 TTATATAATATATTTAATCA-ATAAATATC
*
4497789 TTATATAAT-TATTTAATTAATAAATATC
1 TTATATAATATATTTAATCAATAAATATC
*
4497817 TTTTATAATATA
1 TTATATAATATA
4497829 ATAAATATCT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 10 0.29
28 22 0.65
29 2 0.06
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.51
Consensus pattern (29 bp):
TTATATAATATATTTAATCAATAAATATC
Found at i:4497830 original size:21 final size:20
Alignment explanation
Indices: 4497798--4497847 Score: 75
Period size: 21 Copynumber: 2.5 Consensus size: 20
4497788 CTTATATAAT
4497798 TATTTAAT-TAATAAATATC
1 TATTTAATATAATAAATATC
*
4497817 TTTTATAATATAATAAATATC
1 TATT-TAATATAATAAATATC
4497838 TATTTAATAT
1 TATTTAATAT
4497848 CTAATACTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 3 0.11
20 10 0.37
21 14 0.52
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (20 bp):
TATTTAATATAATAAATATC
Found at i:4498915 original size:31 final size:31
Alignment explanation
Indices: 4498879--4498939 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
4498869 TTAAGTCGAA
*
4498879 TGACTTAAATAAAAACATTTAAATAGTTCAG
1 TGACTTAAATAAAAACATTTAAATAATTCAG
*
4498910 TGACTTAAATAAAAACTTTTAAATAATTCA
1 TGACTTAAATAAAAACATTTAAATAATTCA
4498940 ATAATCAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.49, C:0.10, G:0.07, T:0.34
Consensus pattern (31 bp):
TGACTTAAATAAAAACATTTAAATAATTCAG
Found at i:4504922 original size:5 final size:5
Alignment explanation
Indices: 4504912--4504943 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
4504902 TTGTGTGTTC
4504912 TTTAT TTTA- TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
4504944 TCACAAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:4504926 original size:9 final size:9
Alignment explanation
Indices: 4504912--4504942 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
4504902 TTGTGTGTTC
4504912 TTTATTTTA
1 TTTATTTTA
4504921 TTTATTTTA
1 TTTATTTTA
4504930 TTTTATTTTA
1 -TTTATTTTA
4504940 TTT
1 TTT
4504943 TTCACAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTATTTTA
Found at i:4507866 original size:2 final size:2
Alignment explanation
Indices: 4507859--4507883 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4507849 GTCTTTCAAG
4507859 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
4507884 TATATATATA
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:4510647 original size:33 final size:32
Alignment explanation
Indices: 4510594--4510656 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 32
4510584 GTCATTAGAA
*
4510594 ATTAATTATTTAAAAAATATAGAAATTAAAATCG
1 ATTAATTATGTAAAAAATATAG--ATTAAAATCG
*
4510628 ATTAATT-TGTAAAATATATAGATTAAAAT
1 ATTAATTATGTAAAAAATATAGATTAAAAT
4510657 TGATCAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 8 0.30
33 12 0.44
34 7 0.26
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (32 bp):
ATTAATTATGTAAAAAATATAGATTAAAATCG
Found at i:4512531 original size:15 final size:17
Alignment explanation
Indices: 4512502--4512539 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
4512492 ATTTAATTTT
4512502 TTAAAAATATAAAAATA
1 TTAAAAATATAAAAATA
4512519 -TAAAAATAT-AAAATA
1 TTAAAAATATAAAAATA
4512534 TTAAAA
1 TTAAAA
4512540 CGATAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
TTAAAAATATAAAAATA
Found at i:4512539 original size:8 final size:8
Alignment explanation
Indices: 4512503--4512531 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
4512493 TTTAATTTTT
4512503 TAAAAATA
1 TAAAAATA
4512511 TAAAAATA
1 TAAAAATA
4512519 TAAAAATA
1 TAAAAATA
4512527 TAAAA
1 TAAAA
4512532 TATTAAAACG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
TAAAAATA
Found at i:4513197 original size:20 final size:20
Alignment explanation
Indices: 4513174--4513213 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
4513164 TAGAAAGTTC
4513174 TACATA-AAAATTTCTAAAAA
1 TACATAGAAAATTT-TAAAAA
4513194 TACATAGAAAATTTTAAAAA
1 TACATAGAAAATTTTAAAAA
4513214 AAATAGATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.60, C:0.07, G:0.03, T:0.30
Consensus pattern (20 bp):
TACATAGAAAATTTTAAAAA
Found at i:4513225 original size:21 final size:21
Alignment explanation
Indices: 4513180--4513220 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
4513170 GTTCTACATA
*
4513180 AAAATTTCTAAAAATACATAG
1 AAAATTTCTAAAAATAAATAG
4513201 AAAATTT-TAAAAA-AAATAG
1 AAAATTTCTAAAAATAAATAG
4513220 A
1 A
4513221 TAAAAATAAA
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:0.63, C:0.05, G:0.05, T:0.27
Consensus pattern (21 bp):
AAAATTTCTAAAAATAAATAG
Found at i:4514646 original size:13 final size:13
Alignment explanation
Indices: 4514625--4514659 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
4514615 AAATTTTTCT
4514625 AAAGCACTTCTCA
1 AAAGCACTTCTCA
*
4514638 AAAGTACTTCTCA
1 AAAGCACTTCTCA
4514651 AAAGCACTT
1 AAAGCACTT
4514660 TTCCACGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.40, C:0.26, G:0.09, T:0.26
Consensus pattern (13 bp):
AAAGCACTTCTCA
Found at i:4515335 original size:19 final size:19
Alignment explanation
Indices: 4515305--4515350 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
4515295 TAGTAAATAC
* *
4515305 ATGTATAAAAATAATATACAT
1 ATGTAT-AAATTAATA-AAAT
4515326 ATGTATAAATTAATAAAAT
1 ATGTATAAATTAATAAAAT
4515345 ATGTAT
1 ATGTAT
4515351 TACTTAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 9 0.39
20 8 0.35
21 6 0.26
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.37
Consensus pattern (19 bp):
ATGTATAAATTAATAAAAT
Found at i:4515424 original size:16 final size:17
Alignment explanation
Indices: 4515398--4515431 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
4515388 TTATATTATT
4515398 ATAATAATATTAAGTAA
1 ATAATAATATTAAGTAA
*
4515415 ATAA-AATATTAATTAA
1 ATAATAATATTAAGTAA
4515431 A
1 A
4515432 AACAAAACGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (17 bp):
ATAATAATATTAAGTAA
Done.