Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 99090824
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: 99090824
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 317 characters in sequence are not A, C, G, or T
File 278 of 318
Found at i:87974393 original size:12 final size:12
Alignment explanation
Indices: 87974343--87974401 Score: 50
Period size: 12 Copynumber: 4.8 Consensus size: 12
87974333 AATAGTATTA
87974343 TTAATTTAATA-
1 TTAATTTAATAT
**
87974354 TTAAAGTAATTAT
1 TTAATTTAA-TAT
87974367 CTTAATATTAA-AT
1 -TTAAT-TTAATAT
87974380 TTAATTTAATAT
1 TTAATTTAATAT
*
87974392 TTAGTTTAAT
1 TTAATTTAAT
87974402 CATAGTTGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
11 11 0.29
12 18 0.47
13 2 0.05
14 4 0.11
15 3 0.08
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (12 bp):
TTAATTTAATAT
Found at i:87974401 original size:17 final size:17
Alignment explanation
Indices: 87974343--87974392 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 17
87974333 AATAGTATTA
87974343 TTAATTTAATATTAAAGT
1 TTAATTTAATATTAAA-T
87974361 AATT-ATCTTAATATTAAAT
1 --TTAAT-TTAATATTAAAT
87974380 TTAATTTAATATT
1 TTAATTTAATATT
87974393 TAGTTTAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
17 10 0.36
18 2 0.07
19 3 0.11
20 13 0.46
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (17 bp):
TTAATTTAATATTAAAT
Found at i:87978107 original size:175 final size:175
Alignment explanation
Indices: 87977799--87978435 Score: 929
Period size: 175 Copynumber: 3.6 Consensus size: 175
87977789 GTAAACACGT
* * * * *
87977799 GAAAGCCAAATCTGCTGTGTCTTCGATTTGCTCCTTGTGAACACAAGGATGCCAAATCATCTTAG
1 GAAAGTCAAATCTGCTATGTCTTCGATTTGCTCCTTGTAAACACAAGAATGCCAAATCATCTTGG
* * *
87977864 ATCTGTTTTACTA-AAATCATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCCGTCGAAATGGA
66 ATCTGCTTCAGTATAAA-CATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCCGTCGAAATGGA
87977928 GATGCCAGATCTGTTATCTTGGATCTGCTTTGGTGTGAGAACATTC
130 GATGCCAGATCTGTTATCTTGGATCTGCTTTGGTGTGAGAACATTC
* *
87977974 GAAAGTCAAATTTGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGAATGCCAAATCATCTTGG
1 GAAAGTCAAATCTGCTATGTCTTCGATTTGCTCCTTGTAAACACAAGAATGCCAAATCATCTTGG
*
87978039 ATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTATCTGCTTTCCGTCGAAATGGAG
66 ATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCCGTCGAAATGGAG
*
87978104 ATGCCAGATCTGTTATCTTGGATCTGCTTTGGTGTGAGAACATCC
131 ATGCCAGATCTGTTATCTTGGATCTGCTTTGGTGTGAGAACATTC
* * * * * *
87978149 GAAAGTGAAATCTGCTATGTCTTCGATTTGCTCATCGTCGAAGATAGAGAA-GCCAAATCTTGTT
1 GAAAGTCAAATCTGCTATGTCTTCGATTTGCTCCTTGT-AAACACA-AGAATGCCAAATC-----
* * * *
87978213 ATCTTGGATCTGCTTCAGTATAATCATCTGAAGGTTAGATCTACTATGTGTCTGCTCTCCATCGA
59 ATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCCGTCGA
*
87978278 AATGGAGATGCCAGATCTGTTATCTTGGATCTGCTTTGATGTGAGAACA-TC
124 AATGGAGATGCCAGATCTGTTATCTTGGATCTGCTTTGGTGTGAGAACATTC
*
87978329 TGAAAGTCAAATCTGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGAATGCCAAATCATCTTG
1 -GAAAGTCAAATCTGCTATGTCTTCGATTTGCTCCTTGTAAACACAAGAATGCCAAATCATCTTG
* * *
87978394 GATTTGTTTCAGTATAAACATTTGAAGGTTAGATCTGCTATG
65 GATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATG
87978436 CTTTGGTCTG
Statistics
Matches: 413, Mismatches: 39, Indels: 20
0.88 0.08 0.04
Matches are distributed among these distances:
175 235 0.57
176 15 0.04
177 4 0.01
179 4 0.01
180 13 0.03
181 142 0.34
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.34
Consensus pattern (175 bp):
GAAAGTCAAATCTGCTATGTCTTCGATTTGCTCCTTGTAAACACAAGAATGCCAAATCATCTTGG
ATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCCGTCGAAATGGAG
ATGCCAGATCTGTTATCTTGGATCTGCTTTGGTGTGAGAACATTC
Found at i:87984413 original size:40 final size:40
Alignment explanation
Indices: 87984320--87984617 Score: 408
Period size: 40 Copynumber: 7.5 Consensus size: 40
87984310 AAGCCAAGTA
* * * *
87984320 CCTTCGGGATTTA-ACCAGATATAGCT-ACTCGCTC-AATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
87984358 CCTTCGGGACATAGCCCGGATATAGTAACTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
87984398 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
87984438 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
87984478 CCTTCGGGACTTAGCCCGGATGTAATAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
87984518 CCTTCGGGACTTAGCCCGGATGTAATAACTCGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
87984558 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCA-AAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACT--CGCACAAATG
87984599 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
87984618 TTATCATCCA
Statistics
Matches: 237, Mismatches: 17, Indels: 9
0.90 0.06 0.03
Matches are distributed among these distances:
38 12 0.05
39 16 0.07
40 182 0.77
41 24 0.10
42 3 0.01
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:87998406 original size:17 final size:18
Alignment explanation
Indices: 87998380--87998413 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
87998370 TTATTTTTGA
87998380 AATAAATTAATA-GCATT
1 AATAAATTAATATGCATT
*
87998397 AATAATTTAATATGCAT
1 AATAAATTAATATGCAT
87998414 ATATTTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (18 bp):
AATAAATTAATATGCATT
Found at i:87999017 original size:24 final size:24
Alignment explanation
Indices: 87998958--87999017 Score: 61
Period size: 28 Copynumber: 2.4 Consensus size: 24
87998948 TTTTTTCTCC
87998958 TAAATTTT-AATTTTATTTAATTA
1 TAAATTTTGAATTTTATTTAATTA
*
87998981 TTTAATTTATTGAATCTTTATTTAATTA
1 --TAAATT-TTGAAT-TTTATTTAATTA
87999009 -AAATTTTGA
1 TAAATTTTGA
87999018 GAAAATAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
24 4 0.13
25 9 0.30
26 2 0.07
27 3 0.10
28 12 0.40
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (24 bp):
TAAATTTTGAATTTTATTTAATTA
Found at i:88008961 original size:14 final size:15
Alignment explanation
Indices: 88008933--88008961 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
88008923 TTCACCTATC
88008933 TTTCTTATGCATTTT
1 TTTCTTATGCATTTT
88008948 TTTCTTAT-CATTTT
1 TTTCTTATGCATTTT
88008962 ATCAACTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.14, C:0.14, G:0.03, T:0.69
Consensus pattern (15 bp):
TTTCTTATGCATTTT
Found at i:88009730 original size:43 final size:43
Alignment explanation
Indices: 88009627--88009731 Score: 138
Period size: 43 Copynumber: 2.4 Consensus size: 43
88009617 TAGCTCAGCT
*
88009627 ATGGTCTTACACAAAATCAAATAACGATGCCAATGTCCCAGAC
1 ATGGTCTTACACATAATCAAATAACGATGCCAATGTCCCAGAC
* * * * * *
88009670 ATAGTCTTACACGTAATCATATAATGATGCCAATGTCTCAGGC
1 ATGGTCTTACACATAATCAAATAACGATGCCAATGTCCCAGAC
*
88009713 ATGGTCTTACATATAATCA
1 ATGGTCTTACACATAATCA
88009732 CATCTCGTTA
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 52 1.00
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (43 bp):
ATGGTCTTACACATAATCAAATAACGATGCCAATGTCCCAGAC
Found at i:88011067 original size:13 final size:13
Alignment explanation
Indices: 88011049--88011075 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
88011039 CCAAAATTTA
88011049 TTTTATTTATATT
1 TTTTATTTATATT
88011062 TTTTATTTATATT
1 TTTTATTTATATT
88011075 T
1 T
88011076 ATATTTTCTA
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:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTATTTATATT
Found at i:88011076 original size:19 final size:18
Alignment explanation
Indices: 88011045--88011088 Score: 70
Period size: 19 Copynumber: 2.4 Consensus size: 18
88011035 GCAACCAAAA
88011045 TTTATTTTATTTATATTT
1 TTTATTTTATTTATATTT
88011063 TTTATTTATATTTATATTT
1 TTTATTT-TATTTATATTT
*
88011082 TCTATTT
1 TTTATTT
88011089 CCTTTATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 7 0.29
19 17 0.71
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTATTTTATTTATATTT
Found at i:88014783 original size:40 final size:40
Alignment explanation
Indices: 88014738--88014904 Score: 158
Period size: 40 Copynumber: 4.2 Consensus size: 40
88014728 CGGAATATAA
88014738 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* *** * *
88014778 CCGGATAGAATGTCTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
* * * *
88014818 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
*** * * * *
88014858 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
88014897 CCGGATAT
1 CCGGATAT
88014905 CATTCAATTT
Statistics
Matches: 102, Mismatches: 24, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
39 14 0.14
40 88 0.86
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:88014888 original size:80 final size:79
Alignment explanation
Indices: 88014754--88014902 Score: 203
Period size: 80 Copynumber: 1.9 Consensus size: 79
88014744 ATAACCACGT
*
88014754 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTCGCACGAATGCCTTCGGGTCTTAGCC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGG-CTTAGCC
88014819 CGGATGTAGCCACTA
65 CGGATGTAGCCACTA
* * * * *
88014834 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGCTTAGC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTC-GCACGAA-TGCCTTCGGGCTTAGC
88014897 CCGGAT
64 CCGGAT
88014903 ATCATTCAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
79 15 0.25
80 46 0.75
ACGTcount: A:0.21, C:0.28, G:0.24, T:0.27
Consensus pattern (79 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGGCTTAGCCC
GGATGTAGCCACTA
Found at i:88022838 original size:40 final size:40
Alignment explanation
Indices: 88022712--88022860 Score: 153
Period size: 40 Copynumber: 3.8 Consensus size: 40
88022702 TATAACACGT
* * *
88022712 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGT-C-
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
* ** * *
88022750 GCACGAA-TGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
* *
88022790 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTCCA
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
* *
88022830 GCATAATTGTCTTCGGG-CTTAGCCCGGATAT
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATAT
88022861 CATTCAATTT
Statistics
Matches: 90, Mismatches: 17, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
38 28 0.31
39 17 0.19
40 45 0.50
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (40 bp):
GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
Found at i:88027215 original size:40 final size:40
Alignment explanation
Indices: 88027170--88027299 Score: 154
Period size: 40 Copynumber: 3.2 Consensus size: 40
88027160 CGGAATATAA
88027170 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* *** * *
88027210 CCGGATAGAATGTCTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
* * * *
88027250 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
88027290 CCGGATATAA
1 CCGGATATAA
88027300 TTTCCAGCAT
Statistics
Matches: 72, Mismatches: 17, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
39 1 0.01
40 71 0.99
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:88027314 original size:40 final size:40
Alignment explanation
Indices: 88027186--88027336 Score: 146
Period size: 40 Copynumber: 3.8 Consensus size: 40
88027176 ATAACCACGT
* * *
88027186 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTC-
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTC-CA
* ** * *
88027226 GCACGAA-TGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
* *
88027266 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTCCA
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
* * *
88027306 GCATAATTGTCTT-GGGGCTTAGCCCGGATAT
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATAT
88027337 CATTCAATTT
Statistics
Matches: 90, Mismatches: 18, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
39 18 0.20
40 70 0.78
41 2 0.02
ACGTcount: A:0.22, C:0.26, G:0.25, T:0.27
Consensus pattern (40 bp):
GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
Found at i:88032431 original size:3 final size:3
Alignment explanation
Indices: 88032423--88032487 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
88032413 AAACATACGA
88032423 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
88032471 AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AA
88032488 CAACATCCAA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:88036568 original size:3 final size:3
Alignment explanation
Indices: 88036560--88036621 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
88036550 AAACATACGA
88036560 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
88036608 AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AA
88036622 CAACATCCAA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:88041154 original size:12 final size:12
Alignment explanation
Indices: 88041139--88041178 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
88041129 TAATGAGGCA
88041139 AGAAGGAAGCAT
1 AGAAGGAAGCAT
*
88041151 AGAAAGAAGCAT
1 AGAAGGAAGCAT
88041163 AGAAGG-AGCAT
1 AGAAGGAAGCAT
*
88041174 TGAAG
1 AGAAG
88041179 TCTAAGATGC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
11 9 0.36
12 16 0.64
ACGTcount: A:0.50, C:0.07, G:0.33, T:0.10
Consensus pattern (12 bp):
AGAAGGAAGCAT
Found at i:88043219 original size:56 final size:56
Alignment explanation
Indices: 88043133--88043241 Score: 218
Period size: 56 Copynumber: 1.9 Consensus size: 56
88043123 AAGCAATGAG
88043133 GCATTAATGTAAAGGAAGAACAGAAGAGCAAATGGCCATTGCCTATATACTTTCAA
1 GCATTAATGTAAAGGAAGAACAGAAGAGCAAATGGCCATTGCCTATATACTTTCAA
88043189 GCATTAATGTAAAGGAAGAACAGAAGAGCAAATGGCCATTGCCTATATACTTT
1 GCATTAATGTAAAGGAAGAACAGAAGAGCAAATGGCCATTGCCTATATACTTT
88043242 TTCAGACCCA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (56 bp):
GCATTAATGTAAAGGAAGAACAGAAGAGCAAATGGCCATTGCCTATATACTTTCAA
Found at i:88054579 original size:5 final size:5
Alignment explanation
Indices: 88054569--88054601 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
88054559 TTTGTGTGTT
88054569 TTTTA TTTTA TTTTA -TTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
88054602 TCACACTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:88054589 original size:14 final size:14
Alignment explanation
Indices: 88054570--88054600 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
88054560 TTGTGTGTTT
88054570 TTTATTTTATTTTA
1 TTTATTTTATTTTA
88054584 TTTATTTTATTTTA
1 TTTATTTTATTTTA
88054598 TTT
1 TTT
88054601 TTCACACTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTATTTTATTTTA
Found at i:88060932 original size:22 final size:22
Alignment explanation
Indices: 88060890--88060934 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
88060880 TACTTTAGCC
*
88060890 ATTTTTATTTTTATTGCAATTT
1 ATTTTTATTTTTATTACAATTT
* *
88060912 ATTTTTGTTTTTATTATAATTT
1 ATTTTTATTTTTATTACAATTT
88060934 A
1 A
88060935 CTAACTTTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.69
Consensus pattern (22 bp):
ATTTTTATTTTTATTACAATTT
Found at i:88065868 original size:39 final size:39
Alignment explanation
Indices: 88065808--88065908 Score: 130
Period size: 39 Copynumber: 2.6 Consensus size: 39
88065798 ATCGTGATCT
* *
88065808 GAAGCCCGAAGGATAACTGAAGCACACAAGTGTTAAATG
1 GAAGCCCGAAGGATAACTGAAGCACACAAGTGCTAAACG
* * * **
88065847 GAAGCCCAAAGGCTAATTGAAGCATGCAAGTGCTAAACG
1 GAAGCCCGAAGGATAACTGAAGCACACAAGTGCTAAACG
*
88065886 GAAGCCCGAAGGTTAACTGAAGC
1 GAAGCCCGAAGGATAACTGAAGC
88065909 TCATCAGAGC
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 52 1.00
ACGTcount: A:0.39, C:0.20, G:0.27, T:0.15
Consensus pattern (39 bp):
GAAGCCCGAAGGATAACTGAAGCACACAAGTGCTAAACG
Found at i:88065921 original size:39 final size:39
Alignment explanation
Indices: 88065808--88065923 Score: 121
Period size: 39 Copynumber: 3.0 Consensus size: 39
88065798 ATCGTGATCT
* *
88065808 GAAGCCCGAAGGATAACTGAAGCACA-CAAGTGTTAAATG
1 GAAGCCCGAAGGATAACTGAAGC-CATCAAGTGCTAAACG
* * *
88065847 GAAGCCCAAAGGCTAATTGAAG-CATGCAAGTGCTAAACG
1 GAAGCCCGAAGGATAACTGAAGCCAT-CAAGTGCTAAACG
* *
88065886 GAAGCCCGAAGGTTAACTGAAGCTCATC-AGAGCTAAAC
1 GAAGCCCGAAGGATAACTGAAGC-CATCAAGTGCTAAAC
88065924 TGAAACCCCA
Statistics
Matches: 64, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
37 2 0.03
39 58 0.91
40 1 0.02
41 3 0.05
ACGTcount: A:0.39, C:0.21, G:0.25, T:0.16
Consensus pattern (39 bp):
GAAGCCCGAAGGATAACTGAAGCCATCAAGTGCTAAACG
Found at i:88069031 original size:28 final size:28
Alignment explanation
Indices: 88068999--88069068 Score: 106
Period size: 28 Copynumber: 2.5 Consensus size: 28
88068989 AATGAGATTT
88068999 GCACTAAGTGTGCGAGTTT-AATTGTATA
1 GCACTAAGTGTGCGAGTTTGAATTGTA-A
* *
88069027 GCACTAAGTGTGCGAGTTTGACTTTTAA
1 GCACTAAGTGTGCGAGTTTGAATTGTAA
88069055 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
88069069 GACTTACTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
28 34 0.87
29 5 0.13
ACGTcount: A:0.26, C:0.14, G:0.27, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGAATTGTAA
Found at i:88076167 original size:39 final size:39
Alignment explanation
Indices: 88076124--88076259 Score: 200
Period size: 39 Copynumber: 3.5 Consensus size: 39
88076114 TGGTTTGAAA
* * * *
88076124 CCCGAAGTCTAGCTGAAGCACATAAGTGCTAAATGGAAG
1 CCCGAAGGCTAACTGAAGCACACAAGTGCTAAACGGAAG
* * *
88076163 CCCGAAGGCTAATTGAAGCACACAAGTGTTAAACGGAAC
1 CCCGAAGGCTAACTGAAGCACACAAGTGCTAAACGGAAG
*
88076202 CCCAAAGGCTAACTGAAGCACACAAGTGCTAAACGGAAG
1 CCCGAAGGCTAACTGAAGCACACAAGTGCTAAACGGAAG
88076241 CCCGAAGGCTAACTGAAGC
1 CCCGAAGGCTAACTGAAGC
88076260 TCATCAGAGT
Statistics
Matches: 85, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 85 1.00
ACGTcount: A:0.38, C:0.24, G:0.24, T:0.14
Consensus pattern (39 bp):
CCCGAAGGCTAACTGAAGCACACAAGTGCTAAACGGAAG
Found at i:88083562 original size:15 final size:15
Alignment explanation
Indices: 88083542--88083570 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
88083532 ATGCCACACA
88083542 CACCGTGTTATCAAT
1 CACCGTGTTATCAAT
88083557 CACCGTGTTATCAA
1 CACCGTGTTATCAA
88083571 GCAACAATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.31
Consensus pattern (15 bp):
CACCGTGTTATCAAT
Found at i:88086506 original size:15 final size:15
Alignment explanation
Indices: 88086475--88086515 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
88086465 AACTAATTCT
*
88086475 AAAATAATAATAATAA
1 AAAATAA-AAAAATAA
*
88086491 AACATAAAAAAATAA
1 AAAATAAAAAAATAA
88086506 AAAATAAAAA
1 AAAATAAAAA
88086516 TCTACTACTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.17
Consensus pattern (15 bp):
AAAATAAAAAAATAA
Found at i:88086610 original size:5 final size:5
Alignment explanation
Indices: 88086600--88086625 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
88086590 ATTAACAACT
88086600 AATAA AATAA AATAA AATAA AATAA A
1 AATAA AATAA AATAA AATAA AATAA A
88086626 GAAAGAAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:88105322 original size:18 final size:18
Alignment explanation
Indices: 88105295--88105331 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
88105285 TTTGAAAAGT
*
88105295 TGAAATTTTTATAAGTTA
1 TGAAACTTTTATAAGTTA
*
88105313 TGAAACTTTTATATGTTA
1 TGAAACTTTTATAAGTTA
88105331 T
1 T
88105332 CAATTTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.35, C:0.03, G:0.11, T:0.51
Consensus pattern (18 bp):
TGAAACTTTTATAAGTTA
Found at i:88106175 original size:45 final size:45
Alignment explanation
Indices: 88106125--88106214 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
88106115 CAATGCTAGG
88106125 TTGGATCAGTTTTCTCAGTTCAGCTCAACTGGGCCTCTTTTCATA
1 TTGGATCAGTTTTCTCAGTTCAGCTCAACTGGGCCTCTTTTCATA
88106170 TTGGATCAGTTTTCTCAGTTCAGCTCAACTGGGCCTCTTTTCATA
1 TTGGATCAGTTTTCTCAGTTCAGCTCAACTGGGCCTCTTTTCATA
88106215 ATTAATTAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (45 bp):
TTGGATCAGTTTTCTCAGTTCAGCTCAACTGGGCCTCTTTTCATA
Found at i:88109343 original size:6 final size:6
Alignment explanation
Indices: 88109321--88109418 Score: 85
Period size: 6 Copynumber: 16.3 Consensus size: 6
88109311 AATAAAGTTC
* **
88109321 AAAATA GAAAA-A CAAAATA AAAATA AAAAT- CAAAGG AAAAT- AAAATA
1 AAAATA -AAAATA -AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
* * * *
88109368 AAAATA AAAATA AAGATAA AAAACA AAAATA AAAATA AACATA AAGATA
1 AAAATA AAAATA AAAAT-A AAAATA AAAATA AAAATA AAAATA AAAATA
88109417 AA
1 AA
88109419 TAGACTCAAT
Statistics
Matches: 76, Mismatches: 11, Indels: 9
0.79 0.11 0.09
Matches are distributed among these distances:
5 8 0.11
6 59 0.78
7 9 0.12
ACGTcount: A:0.78, C:0.04, G:0.05, T:0.13
Consensus pattern (6 bp):
AAAATA
Found at i:88109369 original size:28 final size:25
Alignment explanation
Indices: 88109321--88109406 Score: 102
Period size: 25 Copynumber: 3.3 Consensus size: 25
88109311 AATAAAGTTC
*
88109321 AAAATAGAA-AAACAAAATAAAAATA
1 AAAATA-AAGAAAAAAAATAAAAATA
88109346 AAAATCAAAGGAAAATAAAATAAAAATA
1 AAAAT-AAA-GAAAA-AAAATAAAAATA
* *
88109374 AAAATAAAGATAAAAAACAAAAATA
1 AAAATAAAGAAAAAAAATAAAAATA
88109399 AAAATAAA
1 AAAATAAA
88109407 CATAAAGATA
Statistics
Matches: 54, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
25 26 0.48
26 5 0.09
27 6 0.11
28 17 0.31
ACGTcount: A:0.79, C:0.03, G:0.05, T:0.13
Consensus pattern (25 bp):
AAAATAAAGAAAAAAAATAAAAATA
Found at i:88117194 original size:46 final size:46
Alignment explanation
Indices: 88117141--88117316 Score: 148
Period size: 46 Copynumber: 3.8 Consensus size: 46
88117131 TATTTGGGCA
* *
88117141 TCCGAACTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATG
1 TCCGAACTCGTTAAGTTGAGTCCGAGTTCACTTATGGATGTGAATG
*
88117187 TCCGAACTCGTTAAGTTGAGTCCGAGTT---TGA-GAGATGT-AACTAGG
1 TCCGAACTCGTTAAGTTGAGTCCGAGTTCACTTATG-GATGTGAA-T--G
* * * * *
88117232 CATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAA-C
1 --TCCGAACTCGTTAAGTTGAGTCCGAGTTCACTTATGGATGTGAATG
* * *
88117279 ACCTGAGCTCGTTAATTTGAGTCCGAGTTCACTTATGG
1 TCC-GAACTCGTTAAGTTGAGTCCGAGTTCACTTATGG
88117317 GCGGGTTACA
Statistics
Matches: 105, Mismatches: 13, Indels: 24
0.74 0.09 0.17
Matches are distributed among these distances:
42 3 0.03
43 8 0.08
45 3 0.03
46 57 0.54
47 25 0.24
50 6 0.06
51 3 0.03
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (46 bp):
TCCGAACTCGTTAAGTTGAGTCCGAGTTCACTTATGGATGTGAATG
Found at i:88117299 original size:93 final size:93
Alignment explanation
Indices: 88117137--88117307 Score: 254
Period size: 93 Copynumber: 1.8 Consensus size: 93
88117127 AGGATATTTG
* * **
88117137 GGCATCCGAACTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATGTCCGAACTCGTTAAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATCACCGAACTCGTTAAG
88117202 TTGAGTCCGAGTTTGAGAGATGTAACTA
66 TTGAGTCCGAGTTTGAGAGATGTAACTA
* * *
88117230 GGCATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAA-CACCTGAGCTCGTTAA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATCACC-GAACTCGTTAA
*
88117294 TTTGAGTCCGAGTT
65 GTTGAGTCCGAGTT
88117308 CACTTATGGG
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
92 2 0.03
93 67 0.97
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATCACCGAACTCGTTAAG
TTGAGTCCGAGTTTGAGAGATGTAACTA
Found at i:88120268 original size:15 final size:15
Alignment explanation
Indices: 88120250--88120285 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
88120240 ATCTTGGGTT
88120250 TCTTTATCCTGGATC
1 TCTTTATCCTGGATC
* *
88120265 TCTTTATTCTGGATT
1 TCTTTATCCTGGATC
88120280 TCTTTA
1 TCTTTA
88120286 GTTTCTCTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.14, C:0.19, G:0.11, T:0.56
Consensus pattern (15 bp):
TCTTTATCCTGGATC
Found at i:88120302 original size:39 final size:38
Alignment explanation
Indices: 88120247--88120321 Score: 105
Period size: 39 Copynumber: 1.9 Consensus size: 38
88120237 CGTATCTTGG
*
88120247 GTTTCTTTATCCTGGATCTCTTTATTCTGGATTTCTTTA
1 GTTTCTCTATCCTGGATCTCTTTATTC-GGATTTCTTTA
* * *
88120286 GTTTCTCTATCTTGGATTTCTTTATTCGGTTTTCTT
1 GTTTCTCTATCCTGGATCTCTTTATTCGGATTTCTT
88120322 GTTATCTTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
38 8 0.25
39 24 0.75
ACGTcount: A:0.11, C:0.17, G:0.13, T:0.59
Consensus pattern (38 bp):
GTTTCTCTATCCTGGATCTCTTTATTCGGATTTCTTTA
Found at i:88122387 original size:93 final size:93
Alignment explanation
Indices: 88122228--88122399 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
88122218 AGGATATTTG
* *
88122228 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGCATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGCATGCGAACGCCCGAACTCGTTGAG
88122293 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* * * *
88122321 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGCATGCGAACGCCCGAACTCGTTGAG
88122386 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
88122400 ACTTATGGGC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGCATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:88122407 original size:46 final size:46
Alignment explanation
Indices: 88122233--88122407 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
88122223 ATTTGGGCAT
* * * *
88122233 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGCATGCGAATGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAACGC
*
88122279 CCGAACTCGTTGAGTTGAGTCCGAGTT--C-GA-GAGATGT-AACTAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATG-GATGTGAAC---GC
*
88122324 ATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAACGC
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAACGC
*
88122372 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
88122408 GCGGTTACAT
Statistics
Matches: 111, Mismatches: 7, Indels: 22
0.79 0.05 0.16
Matches are distributed among these distances:
42 3 0.03
43 4 0.04
44 1 0.01
45 1 0.01
46 63 0.57
47 26 0.23
48 2 0.02
49 1 0.01
50 6 0.05
51 4 0.04
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAACGC
Found at i:88127659 original size:24 final size:24
Alignment explanation
Indices: 88127591--88127736 Score: 217
Period size: 23 Copynumber: 6.2 Consensus size: 24
88127581 GGCCTTGCCT
*
88127591 CTTTTAATAACTGGGGCAAAAGCC
1 CTTTTAATAACTGGGGCATAAGCC
*
88127615 C-TTTAATAACTGGGGCGTAAGCC
1 CTTTTAATAACTGGGGCATAAGCC
* *
88127638 CTTTTGATCACTGGGGCATAAGCC
1 CTTTTAATAACTGGGGCATAAGCC
* *
88127662 CTTTTGATAACTAGGGCATAAGCC
1 CTTTTAATAACTGGGGCATAAGCC
88127686 C-TTTAATAACTGGGGCATAAGCC
1 CTTTTAATAACTGGGGCATAAGCC
88127709 C-TTTAATAACTGGGGCATAAGCC
1 CTTTTAATAACTGGGGCATAAGCC
88127732 CTTTT
1 CTTTT
88127737 GCACTTCCTC
Statistics
Matches: 111, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
23 65 0.59
24 46 0.41
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (24 bp):
CTTTTAATAACTGGGGCATAAGCC
Found at i:88127808 original size:9 final size:9
Alignment explanation
Indices: 88127794--88127850 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
88127784 ATCTCATGTG
88127794 CATATCATA
1 CATATCATA
*
88127803 CATATCATGTG
1 CATATCA--TA
88127814 CATATCATA
1 CATATCATA
* *
88127823 CATGTCATGTG
1 CATATCA--TA
88127834 CATATCATA
1 CATATCATA
88127843 CATATCAT
1 CATATCAT
88127851 GTTTATCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:88127810 original size:20 final size:20
Alignment explanation
Indices: 88127782--88127852 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
88127772 GCATTTATGA
*
88127782 ACATCTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
88127802 ACATATCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
*
88127822 ACATGTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
88127842 ACATATCATGT
1 ACATATCATGT
88127853 TTATCAAAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.35
Consensus pattern (20 bp):
ACATATCATGTGCATATCAT
Found at i:88127817 original size:11 final size:11
Alignment explanation
Indices: 88127787--88127841 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
88127777 TATGAACATC
88127787 TCATGTGCATA
1 TCATGTGCATA
*
88127798 TCA--TACATA
1 TCATGTGCATA
88127807 TCATGTGCATA
1 TCATGTGCATA
* *
88127818 TCA--TACATG
1 TCATGTGCATA
88127827 TCATGTGCATA
1 TCATGTGCATA
88127838 TCAT
1 TCAT
88127842 ACATATCATG
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (11 bp):
TCATGTGCATA
Found at i:88129158 original size:27 final size:27
Alignment explanation
Indices: 88129096--88129160 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
88129086 GGGCATATTC
88129096 GTCATTTTACCATACAGGGGTATTACG
1 GTCATTTTACCATACAGGGGTATTACG
* *
88129123 GTCACTTTACCCTACAGGGG-ATTTACG
1 GTCATTTTACCATACAGGGGTA-TTACG
*
88129150 GTCTTTTTACC
1 GTCATTTTACC
88129161 TTTTAGGGGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 1 0.03
27 32 0.97
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (27 bp):
GTCATTTTACCATACAGGGGTATTACG
Found at i:88129414 original size:27 final size:27
Alignment explanation
Indices: 88129213--88129442 Score: 144
Period size: 27 Copynumber: 8.5 Consensus size: 27
88129203 GGTAAATCTA
* * *
88129213 CAAACCAAAGGTATTTCAGTAATTTTG
1 CAAATCAAGGGTATTTTAGTAATTTTG
* * *
88129240 TAAACCAATGGTATTTCTA-TAATTTTTAG
1 CAAATCAAGGGTATTT-TAGTAA-TTTT-G
*
88129269 -AAAGTCAAGGGTATTTT-GTAACTTTG
1 CAAA-TCAAGGGTATTTTAGTAATTTTG
* * * *
88129295 TAAATCAGGGGTATTTTGGTAATTTTA
1 CAAATCAAGGGTATTTTAGTAATTTTG
** * **
88129322 CAAATTGAGGGTATTTCAGTAATTTCA
1 CAAATCAAGGGTATTTTAGTAATTTTG
* * *
88129349 CAAACCAAGGGTATTTTGGTAATTTTA
1 CAAATCAAGGGTATTTTAGTAATTTTG
*
88129376 CAAA-CTAGGGGTATTTTAGTAATTTTG
1 CAAATC-AAGGGTATTTTAGTAATTTTG
* **** *
88129403 CAAATCGAGGGTAAAACAGTAATTCTG
1 CAAATCAAGGGTATTTTAGTAATTTTG
*
88129430 TAAATCAAGGGTA
1 CAAATCAAGGGTA
88129443 AAACAGTAAT
Statistics
Matches: 160, Mismatches: 34, Indels: 18
0.75 0.16 0.08
Matches are distributed among these distances:
26 14 0.09
27 122 0.76
28 13 0.08
29 11 0.07
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.37
Consensus pattern (27 bp):
CAAATCAAGGGTATTTTAGTAATTTTG
Found at i:88129414 original size:54 final size:53
Alignment explanation
Indices: 88129276--88129415 Score: 167
Period size: 54 Copynumber: 2.6 Consensus size: 53
88129266 TAGAAAGTCA
* * *
88129276 AGGGTATTTT-GTAACTTTGTAAATCAGGGGTATTTTGGTAATTTTACAAATTG
1 AGGGTATTTTAGTAATTTTGCAAATCA-GGGTATTTTGGTAATTTTACAAATAG
* ** *
88129329 AGGGTATTTCAGTAATTTCACAAACCAAGGGTATTTTGGTAATTTTACAAACTAG
1 AGGGTATTTTAGTAATTTTGCAAATC-AGGGTATTTTGGTAATTTTACAAA-TAG
88129384 -GGGTATTTTAGTAATTTTGCAAATCGAGGGTA
1 AGGGTATTTTAGTAATTTTGCAAATC-AGGGTA
88129416 AAACAGTAAT
Statistics
Matches: 72, Mismatches: 12, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
53 9 0.12
54 60 0.83
55 3 0.04
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.39
Consensus pattern (53 bp):
AGGGTATTTTAGTAATTTTGCAAATCAGGGTATTTTGGTAATTTTACAAATAG
Found at i:88129423 original size:81 final size:80
Alignment explanation
Indices: 88129274--88129426 Score: 202
Period size: 81 Copynumber: 1.9 Consensus size: 80
88129264 TTTAGAAAGT
* * * ***
88129274 CAAGGGTATTTTGTAACTTTGTAAATCAGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTC
1 CAAGGGTATTTTGTAACTTTGTAAAACAGGGGTATTTTAGTAATTTTACAAATCGAGGGTAAAAC
88129339 AGTAATTTCACAAAC
66 AGTAATTTCACAAAC
*
88129354 CAAGGGTATTTTGGTAA-TTT-TACAAACTAGGGGTATTTTAGTAATTTTGCAAATCGAGGGTAA
1 CAAGGGTATTTT-GTAACTTTGTA-AAAC-AGGGGTATTTTAGTAATTTTACAAATCGAGGGTAA
88129417 AACAGTAATT
63 AACAGTAATT
88129427 CTGTAAATCA
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
79 2 0.03
80 18 0.29
81 43 0.68
ACGTcount: A:0.33, C:0.09, G:0.21, T:0.37
Consensus pattern (80 bp):
CAAGGGTATTTTGTAACTTTGTAAAACAGGGGTATTTTAGTAATTTTACAAATCGAGGGTAAAAC
AGTAATTTCACAAAC
Found at i:88129603 original size:80 final size:81
Alignment explanation
Indices: 88129404--88129623 Score: 252
Period size: 80 Copynumber: 2.7 Consensus size: 81
88129394 GTAATTTTGC
* * * * * *
88129404 AAATCGAGGGTAAAACAGTAATTCTGTAAATCAAGGGTAAAACAGTAATTCTATAAATCAAGGGT
1 AAATAGAGGGTAAAACGGTAATTCTGTAAATTAGGGGTAAAACAGTAATTATGTAAATCAAGGGT
88129469 AAAACAGTAATTCAGT
66 AAAACAGTAATTCAGT
* * * *
88129485 AAATCGAGGGTAAAACGGTAATTCTGT-AAGTCGAGGGTAAAACAATAATTATGTAAATC-AGGG
1 AAATAGAGGGTAAAACGGTAATTCTGTAAATTAG-GGGTAAAACAGTAATTATGTAAATCAAGGG
88129548 TAAAAC-GATAATT-ATGT
65 TAAAACAG-TAATTCA-GT
* * *
88129565 AAATTAG-GGGTAAAACGGTAATTATGTAAATTAGGGGTAAAACGGTAATTTTGTAAATC
1 AAA-TAGAGGGTAAAACGGTAATTCTGTAAATTAGGGGTAAAACAGTAATTATGTAAATC
88129624 GGGGGTACTT
Statistics
Matches: 119, Mismatches: 15, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
79 2 0.02
80 63 0.53
81 54 0.45
ACGTcount: A:0.43, C:0.09, G:0.21, T:0.27
Consensus pattern (81 bp):
AAATAGAGGGTAAAACGGTAATTCTGTAAATTAGGGGTAAAACAGTAATTATGTAAATCAAGGGT
AAAACAGTAATTCAGT
Found at i:88129630 original size:27 final size:27
Alignment explanation
Indices: 88129393--88129623 Score: 259
Period size: 27 Copynumber: 8.6 Consensus size: 27
88129383 GGGGTATTTT
* * *
88129393 AGTAATTTTGCAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCAAGGGTAAAAC
88129420 AGTAATTCTGTAAATCAAGGGTAAAAC
1 AGTAATTCTGTAAATCAAGGGTAAAAC
*
88129447 AGTAATTCTATAAATCAAGGGTAAAAC
1 AGTAATTCTGTAAATCAAGGGTAAAAC
* *
88129474 AGTAATTCAGTAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCAAGGGTAAAAC
* * *
88129501 GGTAATTCTGTAAGTCGAGGGTAAAAC
1 AGTAATTCTGTAAATCAAGGGTAAAAC
* *
88129528 AATAATTATGTAAATC-AGGGTAAAAC
1 AGTAATTCTGTAAATCAAGGGTAAAAC
* * *
88129554 -GATAATTATGTAAATTAGGGGTAAAAC
1 AG-TAATTCTGTAAATCAAGGGTAAAAC
* * * *
88129581 GGTAATTATGTAAATTAGGGGTAAAAC
1 AGTAATTCTGTAAATCAAGGGTAAAAC
* *
88129608 GGTAATTTTGTAAATC
1 AGTAATTCTGTAAATC
88129624 GGGGGTACTT
Statistics
Matches: 182, Mismatches: 19, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
26 23 0.13
27 158 0.87
28 1 0.01
ACGTcount: A:0.42, C:0.09, G:0.21, T:0.28
Consensus pattern (27 bp):
AGTAATTCTGTAAATCAAGGGTAAAAC
Found at i:88129641 original size:107 final size:108
Alignment explanation
Indices: 88129394--88129630 Score: 302
Period size: 107 Copynumber: 2.2 Consensus size: 108
88129384 GGGTATTTTA
* * * *
88129394 GTAATTTTGCAAATCGAGGGTAAAACAGTAATTCTGTAAATCAAGGGTAAAACAGTAATTCTATA
1 GTAATTCTGTAAATCGAGGGTAAAACAGTAATTATGTAAATCAAGGGTAAAACAGTAATTATATA
*
88129459 AATCAAGGGTAAAACAGTAATTCAGTAAATCGAGGGTAAAACG
66 AATCAAGGGTAAAACAGTAATTCAGTAAATAGAGGGTAAAACG
* * *
88129502 GTAATTCTGTAAGTCGAGGGTAAAACAATAATTATGTAAATC-AGGGTAAAAC-GATAATTATGT
1 GTAATTCTGTAAATCGAGGGTAAAACAGTAATTATGTAAATCAAGGGTAAAACAG-TAATTATAT
* * *
88129565 AAATTAGGGGTAAAACGGTAATT-ATGTAAATTAG-GGGTAAAACG
65 AAATCAAGGGTAAAACAGTAATTCA-GTAAA-TAGAGGGTAAAACG
* *
88129609 GTAATTTTGTAAATCGGGGGTA
1 GTAATTCTGTAAATCGAGGGTA
88129631 CTTTGGTAAT
Statistics
Matches: 112, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
106 2 0.02
107 71 0.63
108 39 0.35
ACGTcount: A:0.41, C:0.08, G:0.23, T:0.27
Consensus pattern (108 bp):
GTAATTCTGTAAATCGAGGGTAAAACAGTAATTATGTAAATCAAGGGTAAAACAGTAATTATATA
AATCAAGGGTAAAACAGTAATTCAGTAAATAGAGGGTAAAACG
Found at i:88129650 original size:134 final size:135
Alignment explanation
Indices: 88129395--88129657 Score: 305
Period size: 134 Copynumber: 2.0 Consensus size: 135
88129385 GGTATTTTAG
* * *
88129395 TAATTTTGCAAATCGAGGGTAAAACAGTAATTCTGTAAATCAAGGGTAAAACAGTAATTCTATAA
1 TAATTATGCAAATCGAGGGTAAAACAGTAATTATGTAAATCAAGGGTAAAACAGTAATTATATAA
** *
88129460 ATCAAGGGTAAAACAGTAATTCAGTAAATCGAGGGTAAAACGGTAATTCTGTAAGTCGAGGGTAA
66 ATCAAGGGTAAAACAGTAATTCAGTAAATCGAGGGTAAAACGGTAATTCTACAAGTCGAAGGTAA
88129525 AACAA
131 AACAA
* * * * *
88129530 TAATTATGTAAATC-AGGGTAAAAC-GATAATTATGTAAATTAGGGGTAAAACGGTAATTATGTA
1 TAATTATGCAAATCGAGGGTAAAACAG-TAATTATGTAAATCAAGGGTAAAACAGTAATTATATA
* * * ** * **** *
88129593 AATTAGGGGTAAAACGGTAATTTTGTAAATCGGGGGTACTTTGGTAATTTTACAAGTCGAAGGTA
65 AATCAAGGGTAAAACAGTAATTCAGTAAATCGAGGGTAAAACGGTAATTCTACAAGTCGAAGGTA
88129658 TTTCGGTAAA
Statistics
Matches: 105, Mismatches: 22, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
133 1 0.01
134 92 0.88
135 12 0.11
ACGTcount: A:0.40, C:0.09, G:0.22, T:0.29
Consensus pattern (135 bp):
TAATTATGCAAATCGAGGGTAAAACAGTAATTATGTAAATCAAGGGTAAAACAGTAATTATATAA
ATCAAGGGTAAAACAGTAATTCAGTAAATCGAGGGTAAAACGGTAATTCTACAAGTCGAAGGTAA
AACAA
Found at i:88129657 original size:27 final size:27
Alignment explanation
Indices: 88129607--88129725 Score: 116
Period size: 27 Copynumber: 4.4 Consensus size: 27
88129597 AGGGGTAAAA
** **
88129607 CGGTAATTTTGTAAATCGGGGGTACTTT
1 CGGTAATTTTACAAATCGAAGGTA-TTT
*
88129635 -GGTAATTTTACAAGTCGAAGGTATTT
1 CGGTAATTTTACAAATCGAAGGTATTT
* *
88129661 CGGTAAATTTACAAATCGAGGGTATTT
1 CGGTAATTTTACAAATCGAAGGTATTT
* * *
88129688 CAGTATTTTTACAAA-CTAAGGGTATTT
1 CGGTAATTTTACAAATCGAA-GGTATTT
88129715 CGGTAATTTTA
1 CGGTAATTTTA
88129726 ATAAACTAAA
Statistics
Matches: 74, Mismatches: 15, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
26 5 0.07
27 69 0.93
ACGTcount: A:0.29, C:0.10, G:0.22, T:0.39
Consensus pattern (27 bp):
CGGTAATTTTACAAATCGAAGGTATTT
Found at i:88129665 original size:54 final size:54
Alignment explanation
Indices: 88129607--88129725 Score: 134
Period size: 54 Copynumber: 2.2 Consensus size: 54
88129597 AGGGGTAAAA
** * * *
88129607 CGGTAATTTTGTAAATCGGGGGTACTTT-GGTAATTTTACAAGTCGAA-GGTATTT
1 CGGTAATTTTACAAATCGAGGGTA-TTTCAGTAATTTTACAA-ACGAAGGGTATTT
* * *
88129661 CGGTAAATTTACAAATCGAGGGTATTTCAGTATTTTTACAAACTAAGGGTATTT
1 CGGTAATTTTACAAATCGAGGGTATTTCAGTAATTTTACAAACGAAGGGTATTT
88129715 CGGTAATTTTA
1 CGGTAATTTTA
88129726 ATAAACTAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
53 6 0.11
54 48 0.89
ACGTcount: A:0.29, C:0.10, G:0.22, T:0.39
Consensus pattern (54 bp):
CGGTAATTTTACAAATCGAGGGTATTTCAGTAATTTTACAAACGAAGGGTATTT
Found at i:88129739 original size:27 final size:27
Alignment explanation
Indices: 88129682--88129740 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
88129672 CAAATCGAGG
* *
88129682 GTATTTCAGTATTTTTACAAACTAAGG
1 GTATTTCAGTATTTTAACAAACTAAGA
* *
88129709 GTATTTCGGTAATTTTAATAAACTAA-A
1 GTATTTCAGT-ATTTTAACAAACTAAGA
88129736 GTATT
1 GTATT
88129741 CTAAACAGGG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 14 0.52
28 13 0.48
ACGTcount: A:0.36, C:0.08, G:0.14, T:0.42
Consensus pattern (27 bp):
GTATTTCAGTATTTTAACAAACTAAGA
Found at i:88136833 original size:13 final size:13
Alignment explanation
Indices: 88136817--88136858 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
88136807 TAATATTCTG
88136817 AAAATATTAA-AAC
1 AAAA-ATTAAGAAC
88136830 AAAAATTAAGAAC
1 AAAAATTAAGAAC
*
88136843 ACATAATTAAGAAC
1 A-AAAATTAAGAAC
88136857 AA
1 AA
88136859 GAATAAGTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
12 5 0.19
13 9 0.35
14 12 0.46
ACGTcount: A:0.67, C:0.10, G:0.05, T:0.19
Consensus pattern (13 bp):
AAAAATTAAGAAC
Found at i:88139693 original size:45 final size:45
Alignment explanation
Indices: 88139643--88139732 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
88139633 CAGTAATGAG
88139643 TTAGAAGATGAGCAAATCTGAGAATGCTGAGATGCCAAGACAGCT
1 TTAGAAGATGAGCAAATCTGAGAATGCTGAGATGCCAAGACAGCT
*
88139688 TTAGAAGATGAGCAAATCTGAGAATGTTGAGATGCCAAGACAGCT
1 TTAGAAGATGAGCAAATCTGAGAATGCTGAGATGCCAAGACAGCT
88139733 AAAAGAGTTG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.38, C:0.14, G:0.27, T:0.21
Consensus pattern (45 bp):
TTAGAAGATGAGCAAATCTGAGAATGCTGAGATGCCAAGACAGCT
Found at i:88142637 original size:40 final size:40
Alignment explanation
Indices: 88142553--88142684 Score: 110
Period size: 40 Copynumber: 3.3 Consensus size: 40
88142543 AATAGGGTTT
* * * *
88142553 TAGCGGCGTTTTATCAAAAAACGCCACAAAAATTATACAT
1 TAGCGGCGTTTGATCAAAAAACGCCACAAAAATCAGACAA
*
88142593 TAGCGGCGTTTGA-CCAAAAACGCCACTAAAAA-CAGAGCAA
1 TAGCGGCGTTTGATCAAAAAACGCCAC-AAAAATCAGA-CAA
* * * *
88142633 TAGCGGCGTTTTTGGTCAAACACCGCTA-AAAAAT-AGAGCAA
1 TAGCGGCG--TTTGATCAAAAAACGCCACAAAAATCAGA-CAA
88142674 TAGCGGCGTTT
1 TAGCGGCGTTT
88142685 TTGGTCAAAC
Statistics
Matches: 76, Mismatches: 10, Indels: 13
0.77 0.10 0.13
Matches are distributed among these distances:
39 17 0.22
40 27 0.36
41 20 0.26
42 4 0.05
43 8 0.11
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (40 bp):
TAGCGGCGTTTGATCAAAAAACGCCACAAAAATCAGACAA
Found at i:88142746 original size:41 final size:41
Alignment explanation
Indices: 88142610--88142746 Score: 181
Period size: 41 Copynumber: 3.4 Consensus size: 41
88142600 GTTTGACCAA
* *
88142610 AAACGCCACT-AAAAACAGAGCAATAGCGGCGTTTTTGGTC
1 AAACGCCGCTAAAAAACTGAGCAATAGCGGCGTTTTTGGTC
*
88142650 AAACACCGCTAAAAAA-TAGAGCAATAGCGGCGTTTTTGGTC
1 AAACGCCGCTAAAAAACT-GAGCAATAGCGGCGTTTTTGGTC
* * *
88142691 AAACGCCGCTAAAAAACTGAGTAATAACGGCGTTTTTGCTC
1 AAACGCCGCTAAAAAACTGAGCAATAGCGGCGTTTTTGGTC
88142732 AAAACGCCGC-AAAAA
1 -AAACGCCGCTAAAAA
88142747 GTCATATAAC
Statistics
Matches: 86, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
40 8 0.09
41 68 0.79
42 10 0.12
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (41 bp):
AAACGCCGCTAAAAAACTGAGCAATAGCGGCGTTTTTGGTC
Found at i:88142835 original size:47 final size:47
Alignment explanation
Indices: 88142751--88142880 Score: 153
Period size: 47 Copynumber: 2.8 Consensus size: 47
88142741 CAAAAAGTCA
*
88142751 TATAA-CCCTAAAAT-CCTAAACCCAAAAAAATCATAAACACTAATC
1 TATAACCCCTAAAATCCCTAACCCCAAAAAAATCATAAACACTAATC
88142796 TATAACCCCTAAAATCCCTAACCCCCTAAAAAAA-C-TAAACACTAATC
1 TATAACCCCTAAAATCCCTAA-CCCC-AAAAAAATCATAAACACTAATC
***
88142843 TATAACTTTTAAAA-CCCTAAACCCCAAAAAACATCATA
1 TATAACCCCTAAAATCCCT-AACCCCAAAAAA-ATCATA
88142881 TGGATGTTGA
Statistics
Matches: 73, Mismatches: 4, Indels: 13
0.81 0.04 0.14
Matches are distributed among these distances:
45 11 0.15
46 18 0.25
47 31 0.42
48 6 0.08
49 7 0.10
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (47 bp):
TATAACCCCTAAAATCCCTAACCCCAAAAAAATCATAAACACTAATC
Found at i:88143033 original size:15 final size:15
Alignment explanation
Indices: 88143004--88143047 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
88142994 ATATTTAAGA
*
88143004 TTTAAGG-TCTATGG
1 TTTAAGGTTTTATGG
*
88143018 TTTAGGGTTTTATGG
1 TTTAAGGTTTTATGG
*
88143033 TTTAAGGTTTAATGG
1 TTTAAGGTTTTATGG
88143048 CCATGGGTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
14 6 0.24
15 19 0.76
ACGTcount: A:0.20, C:0.02, G:0.30, T:0.48
Consensus pattern (15 bp):
TTTAAGGTTTTATGG
Found at i:88143192 original size:37 final size:37
Alignment explanation
Indices: 88143142--88143269 Score: 193
Period size: 37 Copynumber: 3.5 Consensus size: 37
88143132 TCGTTTGTCA
* *
88143142 CCTTCGCCCCGTGCACCGTAACCCATCCCCTCCATCG
1 CCTTCGCCCCGTGCATCGCAACCCATCCCCTCCATCG
*
88143179 CCTTCGCCCCGTGCATCGCAACCCATTCCCTCCATCG
1 CCTTCGCCCCGTGCATCGCAACCCATCCCCTCCATCG
* * *
88143216 CCTTCGCCCCATGCGTCGCAACCCATCTCCTCCATCG
1 CCTTCGCCCCGTGCATCGCAACCCATCCCCTCCATCG
*
88143253 CCTTCGCCCTGTGCATC
1 CCTTCGCCCCGTGCATC
88143270 TGCTGCATAG
Statistics
Matches: 81, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 81 1.00
ACGTcount: A:0.12, C:0.52, G:0.14, T:0.22
Consensus pattern (37 bp):
CCTTCGCCCCGTGCATCGCAACCCATCCCCTCCATCG
Found at i:88143596 original size:7 final size:7
Alignment explanation
Indices: 88143581--88143648 Score: 64
Period size: 7 Copynumber: 9.3 Consensus size: 7
88143571 AAATCTTCAA
*
88143581 AAAAATT
1 AAAATTT
88143588 AAAATTT
1 AAAATTT
*
88143595 AAAAATTA
1 -AAAATTT
*
88143603 AAAATTA
1 AAAATTT
88143610 AAAATTT
1 AAAATTT
88143617 AAAATTT
1 AAAATTT
*
88143624 AAAATTAA
1 AAAATT-T
*
88143632 AAAACTT
1 AAAATTT
88143639 AAATATTT
1 AAA-ATTT
88143647 AA
1 AA
88143649 TATTAAATAT
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
7 35 0.69
8 16 0.31
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (7 bp):
AAAATTT
Found at i:88143600 original size:14 final size:14
Alignment explanation
Indices: 88143581--88143633 Score: 81
Period size: 14 Copynumber: 3.8 Consensus size: 14
88143571 AAATCTTCAA
88143581 AAAAATTAAAATTT
1 AAAAATTAAAATTT
*
88143595 AAAAATTAAAAATT
1 AAAAATTAAAATTT
88143609 AAAAATTTAAAATTT
1 AAAAA-TTAAAATTT
88143624 -AAAATTAAAA
1 AAAAATTAAAA
88143634 AACTTAAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
13 6 0.17
14 22 0.61
15 8 0.22
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
AAAAATTAAAATTT
Found at i:88143607 original size:21 final size:20
Alignment explanation
Indices: 88143581--88143633 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 20
88143571 AAATCTTCAA
88143581 AAAAATTAAAATTTAAAAATT
1 AAAAATTAAAATTT-AAAATT
88143602 AAAAATTAAAAATTTAAAATT
1 AAAAATT-AAAATTTAAAATT
*
88143623 TAAAATTAAAA
1 AAAAATTAAAA
88143634 AACTTAAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 4 0.13
21 19 0.63
22 7 0.23
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
AAAAATTAAAATTTAAAATT
Found at i:88143634 original size:21 final size:21
Alignment explanation
Indices: 88143582--88143660 Score: 88
Period size: 22 Copynumber: 3.7 Consensus size: 21
88143572 AATCTTCAAA
*
88143582 AAAATT-AAAATTTAAAAATTA
1 AAAATTAAAAATTT-AAAATTT
88143603 AAAATTAAAAATTTAAAATTT
1 AAAATTAAAAATTTAAAATTT
*
88143624 AAAATTAAAAAACTTAAATATTT
1 AAAATT-AAAAATTTAAA-ATTT
* *
88143647 AATATTAAATATTT
1 AAAATTAAAAATTT
88143661 TAGTCCATGT
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
21 18 0.36
22 23 0.46
23 9 0.18
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (21 bp):
AAAATTAAAAATTTAAAATTT
Found at i:88144030 original size:17 final size:17
Alignment explanation
Indices: 88144005--88144037 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
88143995 AAAATTTAGC
88144005 TACTCTTTTTCTCTCGT
1 TACTCTTTTTCTCTCGT
*
88144022 TACTGTTTTTCTCTCG
1 TACTCTTTTTCTCTCG
88144038 ATCCTTCGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.27, G:0.09, T:0.58
Consensus pattern (17 bp):
TACTCTTTTTCTCTCGT
Found at i:88146910 original size:12 final size:12
Alignment explanation
Indices: 88146888--88146918 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
88146878 TACATTTTTT
88146888 TTAAA-TTAGTG
1 TTAAATTTAGTG
88146899 TTAAATTTAGTG
1 TTAAATTTAGTG
88146911 TTAAATTT
1 TTAAATTT
88146919 TTATTTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.26
12 14 0.74
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (12 bp):
TTAAATTTAGTG
Found at i:88147764 original size:40 final size:40
Alignment explanation
Indices: 88147709--88147790 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
88147699 AATTGAACCT
88147709 GATGCTGGGCAAGCTGCTGCACTTGTTCTATGTCACACTA
1 GATGCTGGGCAAGCTGCTGCACTTGTTCTATGTCACACTA
88147749 GATGCTGGGCAAGCTGCTGCACTTGTTCTATGTCACACTA
1 GATGCTGGGCAAGCTGCTGCACTTGTTCTATGTCACACTA
88147789 GA
1 GA
88147791 GAATTAGCGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.21, C:0.24, G:0.26, T:0.29
Consensus pattern (40 bp):
GATGCTGGGCAAGCTGCTGCACTTGTTCTATGTCACACTA
Found at i:88148233 original size:15 final size:15
Alignment explanation
Indices: 88148213--88148241 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
88148203 AATTCAATTT
88148213 ATAATTTGTTGCTAC
1 ATAATTTGTTGCTAC
88148228 ATAATTTGTTGCTA
1 ATAATTTGTTGCTA
88148242 ATATTCTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.10, G:0.14, T:0.48
Consensus pattern (15 bp):
ATAATTTGTTGCTAC
Found at i:88148580 original size:6 final size:7
Alignment explanation
Indices: 88148563--88148589 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
88148553 TGTTTCGTTA
88148563 AAAAAAG
1 AAAAAAG
88148570 AAAAAAG
1 AAAAAAG
88148577 AAAAAAG
1 AAAAAAG
88148584 AAAAAA
1 AAAAAA
88148590 ACCAAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:88149025 original size:31 final size:31
Alignment explanation
Indices: 88148987--88149067 Score: 98
Period size: 31 Copynumber: 2.6 Consensus size: 31
88148977 TTGTTGTATT
88148987 TTATTTATATTTATATTTAATCTA-ATTTTTA
1 TTATTTAT-TTTATATTTAATCTATATTTTTA
*
88149018 TTATTTATTTTAGT-TTTCATTCTATATTTTTA
1 TTATTTATTTTA-TATTT-AATCTATATTTTTA
88149050 TT-TTTATTTT-TATTTAAT
1 TTATTTATTTTATATTTAAT
88149068 AATGAATTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
29 3 0.07
30 10 0.23
31 22 0.50
32 9 0.20
ACGTcount: A:0.26, C:0.04, G:0.01, T:0.69
Consensus pattern (31 bp):
TTATTTATTTTATATTTAATCTATATTTTTA
Found at i:88149203 original size:15 final size:16
Alignment explanation
Indices: 88149173--88149206 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
88149163 GACTTTATAA
88149173 TATTTTTATAATATTT
1 TATTTTTATAATATTT
*
88149189 TATTTTTTTAA-ATTT
1 TATTTTTATAATATTT
88149204 TAT
1 TAT
88149207 GACCTTTAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TATTTTTATAATATTT
Found at i:88150425 original size:20 final size:20
Alignment explanation
Indices: 88150400--88150444 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
88150390 TGTTGGTCAA
88150400 GAAGACAAGGTGTACAAACT
1 GAAGACAAGGTGTACAAACT
88150420 GAAGACAAGGTGTACAAACT
1 GAAGACAAGGTGTACAAACT
88150440 GAAGA
1 GAAGA
88150445 AAGCCTTGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.47, C:0.13, G:0.27, T:0.13
Consensus pattern (20 bp):
GAAGACAAGGTGTACAAACT
Found at i:88158812 original size:21 final size:23
Alignment explanation
Indices: 88158788--88158829 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
88158778 GTCCTATGGT
88158788 CACATGGG-G-GTGTGCCTTGAC
1 CACATGGGCGTGTGTGCCTTGAC
88158809 CACATGGGCGTGTGTGCCTTG
1 CACATGGGCGTGTGTGCCTTG
88158830 TATATAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 8 0.42
22 1 0.05
23 10 0.53
ACGTcount: A:0.12, C:0.24, G:0.38, T:0.26
Consensus pattern (23 bp):
CACATGGGCGTGTGTGCCTTGAC
Found at i:88161232 original size:11 final size:12
Alignment explanation
Indices: 88161201--88161227 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
88161191 AGCAGACCCT
88161201 AAATCTTTTTTC
1 AAATCTTTTTTC
88161213 AAATCTTTTTTC
1 AAATCTTTTTTC
88161225 AAA
1 AAA
88161228 GTTTTGAATG
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:0.33, C:0.15, G:0.00, T:0.52
Consensus pattern (12 bp):
AAATCTTTTTTC
Found at i:88165381 original size:2 final size:2
Alignment explanation
Indices: 88165374--88165402 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
88165364 TGTCGTTGAG
88165374 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
88165403 CTCATGTCTG
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:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:88172823 original size:21 final size:21
Alignment explanation
Indices: 88172770--88172828 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
88172760 TTAAAATGAG
*
88172770 AATAAT-ATAATATAA-ATAA
1 AATAATAAGAATATAATATAA
88172789 AAT-ATAAGGAAATATAATATAA
1 AATAATAA-G-AATATAATATAA
88172811 AATAATAAGAATATAATA
1 AATAATAAGAATATAATA
88172829 AGTATTTTAC
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
18 2 0.06
19 4 0.12
21 16 0.47
22 8 0.24
23 4 0.12
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (21 bp):
AATAATAAGAATATAATATAA
Found at i:88172828 original size:26 final size:24
Alignment explanation
Indices: 88172773--88172828 Score: 64
Period size: 22 Copynumber: 2.4 Consensus size: 24
88172763 AAATGAGAAT
88172773 AATATAATATAAATAAAATATAAGG
1 AATATAATATAAATAAAATATAA-G
*
88172798 AA-AT-ATA-ATATAAAATAATAAG
1 AATATAATATAAATAAAAT-ATAAG
88172820 AATATAATA
1 AATATAATA
88172829 AGTATTTTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
22 11 0.41
23 9 0.33
24 5 0.19
25 2 0.07
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (24 bp):
AATATAATATAAATAAAATATAAG
Found at i:88172830 original size:11 final size:10
Alignment explanation
Indices: 88172771--88172829 Score: 57
Period size: 10 Copynumber: 5.7 Consensus size: 10
88172761 TAAAATGAGA
*
88172771 ATAATATAAT
1 ATAATAAAAT
88172781 ATAAATAAAAT
1 AT-AATAAAAT
**
88172792 ATAAGGAAAT
1 ATAATAAAAT
88172802 ATAATATAAA-
1 ATAATA-AAAT
88172812 ATAATAAGAAT
1 ATAATAA-AAT
88172823 ATAATAA
1 ATAATAA
88172830 GTATTTTACA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
9 1 0.03
10 20 0.50
11 19 0.47
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (10 bp):
ATAATAAAAT
Found at i:88173718 original size:22 final size:21
Alignment explanation
Indices: 88173692--88173733 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
88173682 ATTAGGGATA
88173692 AATTAGAAATAAATAAAAATGG
1 AATTAGAAAT-AATAAAAATGG
* *
88173714 AATTATAAATATTAAAAATG
1 AATTAGAAATAATAAAAATG
88173734 CAAGAGGACC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.29
Consensus pattern (21 bp):
AATTAGAAATAATAAAAATGG
Found at i:88175962 original size:41 final size:41
Alignment explanation
Indices: 88175917--88176073 Score: 172
Period size: 41 Copynumber: 3.8 Consensus size: 41
88175907 CGACGTTGCA
* *
88175917 AAAAACTAAACAATAGCGGCGTTTTTGGCCAAAACGCCACT
1 AAAAACTGATCAATAGCGGCGTTTTTGGCCAAAACGCCACT
* * *
88175958 AAAAACTGATCAATAGCGGTGTTTTTAGCTAAAACGCCACT
1 AAAAACTGATCAATAGCGGCGTTTTTGGCCAAAACGCCACT
* * * *
88175999 AAAAACTGATGAATAGCAGCGTTTTTATG-TAAAACGCCACT
1 AAAAACTGATCAATAGCGGCGTTTTT-GGCCAAAACGCCACT
* * * *
88176040 AAAAACTGAGCAGTAGCGGTGTTTGTGGTCCAAA
1 AAAAACTGATCAATAGCGGCGTTTTTGG-CCAAA
88176074 CACCGCAAAA
Statistics
Matches: 96, Mismatches: 17, Indels: 5
0.81 0.14 0.04
Matches are distributed among these distances:
40 1 0.01
41 91 0.95
42 4 0.04
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.24
Consensus pattern (41 bp):
AAAAACTGATCAATAGCGGCGTTTTTGGCCAAAACGCCACT
Found at i:88177742 original size:14 final size:14
Alignment explanation
Indices: 88177703--88177744 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
88177693 TTGTATTATC
*
88177703 TATTATATTATTTA
1 TATTATATTATGTA
*
88177717 TATTTTA-T-TGTA
1 TATTATATTATGTA
88177729 TATTATATTATGTA
1 TATTATATTATGTA
88177743 TA
1 TA
88177745 ATTTTAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
12 9 0.39
13 2 0.09
14 12 0.52
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (14 bp):
TATTATATTATGTA
Found at i:88181805 original size:16 final size:16
Alignment explanation
Indices: 88181784--88181818 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
88181774 TTAAAATTAC
88181784 AGAGAGAAAGAGAAAG
1 AGAGAGAAAGAGAAAG
**
88181800 AGAGAGTGAGAGAAAG
1 AGAGAGAAAGAGAAAG
88181816 AGA
1 AGA
88181819 ACCTGAAAGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.40, T:0.03
Consensus pattern (16 bp):
AGAGAGAAAGAGAAAG
Found at i:88189815 original size:45 final size:43
Alignment explanation
Indices: 88189714--88190238 Score: 173
Period size: 45 Copynumber: 11.7 Consensus size: 43
88189704 GGGACAATGT
* * * * * *
88189714 AGATAGCAGATTTGGTATCTCTGTATTGATAGGGAACAAATCGA
1 AGATAACAGATTTGGCATCTCTGTATT-AGACGGAGCAGATCGA
* * *
88189758 AGA-AGCAGATTTGGCATCTTTGTATTAGACGGGGAGTAGATCGA
1 AGATAACAGATTTGGCATCTCTGTATTAGAC--GGAGCAGATCGA
* * * **
88189802 AGATAACAGATTTGACAT-TCGTGTGTTTACATCAAAGCAGATCGA
1 AGATAACAGATTTGGCATCTC-TGT-ATTAGA-CGGAGCAGATCGA
* * *
88189847 AGATGACAGATTTGGTATCTCCGTATTAGACAGGGAGCAGATCGA
1 AGATAACAGATTTGGCATCTCTGTATTAGAC--GGAGCAGATCGA
* * * * * * * *
88189892 AAATAGCAGATCTGACAT-TCATGTGTTTACATCGAAGCAGATCAA
1 AGATAACAGATTTGGCATCTC-TGT-ATTAGA-CGGAGCAGATCGA
* *
88189937 AGATGATAGATTTGGCATCTCTGTATTAGACAAGGAGCAGATCGA
1 AGATAACAGATTTGGCATCTCTGTATTAGAC--GGAGCAGATCGA
* * * * * * * **
88189982 AGATAGCAGATCTGACAT-TCGTGTGTTTACATCGAAGCAAATAAA
1 AGATAACAGATTTGGCATCTC-TGT-ATTAGA-CGGAGCAGATCGA
* * * * ** *
88190027 AAATGATAGATTTGGCGTCTCCATATTAGACGGGGAGCAGATCAA
1 AGATAACAGATTTGGCATCTCTGTATTAGAC--GGAGCAGATCGA
* * * * * * *
88190072 AGATAGCAGATCTGACAT-TCGTGTGTTTACATCGAAACAGATCGA
1 AGATAACAGATTTGGCATCTC-TGT-ATTAGA-CGGAGCAGATCGA
* ** **
88190117 AGATGACAGATTTGGTGTCTCCT-TATTAGACGGGGAGCAGATTAA
1 AGATAACAGATTTGGCATCT-CTGTATTAGAC--GGAGCAGATCGA
* * * * * *
88190162 AGATAGCAGATCTGACAT-TCGTGTGTTTACATCGAAGCAGATCGA
1 AGATAACAGATTTGGCATCTC-TGT-ATTAGA-CGGAGCAGATCGA
* * * *
88190207 AGATAGCAGATTTGACGTCTCTGTATTTGACG
1 AGATAACAGATTTGGCATCTCTGTATTAGACG
88190239 AGGAGTAAAT
Statistics
Matches: 337, Mismatches: 111, Indels: 67
0.65 0.22 0.13
Matches are distributed among these distances:
42 2 0.01
43 28 0.08
44 43 0.13
45 228 0.68
46 30 0.09
47 6 0.02
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (43 bp):
AGATAACAGATTTGGCATCTCTGTATTAGACGGAGCAGATCGA
Found at i:88189873 original size:90 final size:90
Alignment explanation
Indices: 88189753--88190256 Score: 645
Period size: 90 Copynumber: 5.6 Consensus size: 90
88189743 TAGGGAACAA
* ** * * * *
88189753 ATCGAAGAAG-CAGATTTGGCATCTTTGTATTAGACGGGGAGTAGATCGAAGATAACAGATTTGA
1 ATCGAAGATGACAGATTTGGCATCTCCGTATTAGACGGGGAGCAGATCAAAGATAGCAGATCTGA
*
88189817 CATTCGTGTGTTTACATCAAAGCAG
66 CATTCGTGTGTTTACATCGAAGCAG
* *
88189842 ATCGAAGATGACAGATTTGGTATCTCCGTATTAGACAGGGAGCAGATCGAAA-ATAGCAGATCTG
1 ATCGAAGATGACAGATTTGGCATCTCCGTATTAGACGGGGAGCAGATC-AAAGATAGCAGATCTG
*
88189906 ACATTCATGTGTTTACATCGAAGCAG
65 ACATTCGTGTGTTTACATCGAAGCAG
* * * ** *
88189932 ATCAAAGATGATAGATTTGGCATCTCTGTATTAGACAAGGAGCAGATCGAAGATAGCAGATCTGA
1 ATCGAAGATGACAGATTTGGCATCTCCGTATTAGACGGGGAGCAGATCAAAGATAGCAGATCTGA
*
88189997 CATTCGTGTGTTTACATCGAAGCAA
66 CATTCGTGTGTTTACATCGAAGCAG
** * * * *
88190022 ATAAAAAATGATAGATTTGGCGTCTCCATATTAGACGGGGAGCAGATCAAAGATAGCAGATCTGA
1 ATCGAAGATGACAGATTTGGCATCTCCGTATTAGACGGGGAGCAGATCAAAGATAGCAGATCTGA
*
88190087 CATTCGTGTGTTTACATCGAAACAG
66 CATTCGTGTGTTTACATCGAAGCAG
** * *
88190112 ATCGAAGATGACAGATTTGGTGTCTCCTTATTAGACGGGGAGCAGATTAAAGATAGCAGATCTGA
1 ATCGAAGATGACAGATTTGGCATCTCCGTATTAGACGGGGAGCAGATCAAAGATAGCAGATCTGA
88190177 CATTCGTGTGTTTACATCGAAGCAG
66 CATTCGTGTGTTTACATCGAAGCAG
* * * * * * *
88190202 ATCGAAGAT-AGCAGATTTGACGTCTCTGTATTTGACGAGGAGTAAATCAAAGATA
1 ATCGAAGATGA-CAGATTTGGCATCTCCGTATTAGACGGGGAGCAGATCAAAGATA
88190257 TTAACATGGC
Statistics
Matches: 365, Mismatches: 46, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
89 12 0.03
90 351 0.96
91 2 0.01
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.27
Consensus pattern (90 bp):
ATCGAAGATGACAGATTTGGCATCTCCGTATTAGACGGGGAGCAGATCAAAGATAGCAGATCTGA
CATTCGTGTGTTTACATCGAAGCAG
Found at i:88191775 original size:25 final size:25
Alignment explanation
Indices: 88191746--88191794 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
88191736 ATATATATAC
88191746 ATATTTTATA-ATTTATTTATTTTAA
1 ATATTTTATATA-TTATTTATTTTAA
*
88191771 ATATTTTGTATATTATTTATTTTA
1 ATATTTTATATATTATTTATTTTA
88191795 CTTTAAACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 21 0.95
26 1 0.05
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (25 bp):
ATATTTTATATATTATTTATTTTAA
Found at i:88191866 original size:27 final size:26
Alignment explanation
Indices: 88191821--88191880 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 26
88191811 TATGTAAAAG
*
88191821 TATA-TATTTTTTTTGTATTATCTAT
1 TATATTATTTTTTTTGTATTATATAT
* *
88191846 TATATTATTTTTTATTTTATTGTATAT
1 TATATTATTTTTT-TTGTATTATATAT
88191873 TATATTAT
1 TATATTAT
88191881 GTATAATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
25 4 0.13
26 8 0.27
27 18 0.60
ACGTcount: A:0.27, C:0.02, G:0.03, T:0.68
Consensus pattern (26 bp):
TATATTATTTTTTTTGTATTATATAT
Found at i:88194394 original size:26 final size:26
Alignment explanation
Indices: 88194365--88194474 Score: 166
Period size: 26 Copynumber: 4.2 Consensus size: 26
88194355 TGATACAAAT
88194365 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
88194391 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
88194417 TGATAATAGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
88194443 TGATAATGGTTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
88194469 TGATAA
1 TGATAA
88194475 GAAATTCATG
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.35, C:0.05, G:0.23, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:88200307 original size:9 final size:9
Alignment explanation
Indices: 88200293--88200459 Score: 154
Period size: 9 Copynumber: 17.6 Consensus size: 9
88200283 ATGTATTAGT
88200293 TAAGTTATG
1 TAAGTTATG
88200302 TAAGTTGTTATG
1 TAA---GTTATG
*
88200314 TACGTTATG
1 TAAGTTATG
*
88200323 TGAGTTATG
1 TAAGTTATG
*
88200332 TAAATTATG
1 TAAGTTATG
88200341 TAAGTTATG
1 TAAGTTATG
*
88200350 TGAGTTATG
1 TAAGTTATG
88200359 TAAGTTGTTATG
1 TAA---GTTATG
*
88200371 TAAATTATG
1 TAAGTTATG
88200380 TAAGTTATG
1 TAAGTTATG
*
88200389 TGAGTTATG
1 TAAGTTATG
88200398 TAAGTTGTTATG
1 TAA---GTTATG
*
88200410 TAAATTATG
1 TAAGTTATG
*
88200419 TAAGTTATA
1 TAAGTTATG
*
88200428 TGAGTTATG
1 TAAGTTATG
88200437 TAAGTTATG
1 TAAGTTATG
* *
88200446 TAATTTATT
1 TAAGTTATG
88200455 TAAGT
1 TAAGT
88200460 AATGATCAAT
Statistics
Matches: 128, Mismatches: 21, Indels: 18
0.77 0.13 0.11
Matches are distributed among these distances:
9 102 0.80
12 26 0.20
ACGTcount: A:0.31, C:0.01, G:0.22, T:0.47
Consensus pattern (9 bp):
TAAGTTATG
Found at i:88200340 original size:39 final size:40
Alignment explanation
Indices: 88200297--88200459 Score: 168
Period size: 39 Copynumber: 4.2 Consensus size: 40
88200287 ATTAGTTAAG
88200297 TTATGTAAGTTGTTATGT-ACGTTATGT-G-AGTTATGTAAA
1 TTATGTAAG-TGTTATGTGA-GTTATGTAGTAGTTATGTAAA
*
88200336 TTATGTAA--GTTATGTGAGTTATGTAAGTTGTTATGTAAA
1 TTATGTAAGTGTTATGTGAGTTATGT-AGTAGTTATGTAAA
*
88200375 TTATGTAA--GTTATGTGAGTTATGTAAGTTGTTATGTAAA
1 TTATGTAAGTGTTATGTGAGTTATGT-AGTAGTTATGTAAA
* *
88200414 TTATGTAA--GTTATATGAGTTATGTA--AGTTATGTAAT
1 TTATGTAAGTGTTATGTGAGTTATGTAGTAGTTATGTAAA
*
88200450 TTATTTAAGT
1 TTATGTAAGT
88200460 AATGATCAAT
Statistics
Matches: 113, Mismatches: 5, Indels: 13
0.86 0.04 0.10
Matches are distributed among these distances:
36 30 0.27
37 1 0.01
38 2 0.02
39 80 0.71
ACGTcount: A:0.31, C:0.01, G:0.21, T:0.47
Consensus pattern (40 bp):
TTATGTAAGTGTTATGTGAGTTATGTAGTAGTTATGTAAA
Found at i:88200369 original size:48 final size:44
Alignment explanation
Indices: 88200308--88200447 Score: 183
Period size: 39 Copynumber: 3.4 Consensus size: 44
88200298 TATGTAAGTT
*
88200308 GTTATGTACGTTATGTGAGTTATGTAAATTATGTAAGTTATGTGA
1 GTTATGTAAGTTATGT-AGTTATGTAAATTATGTAAGTTATGTGA
88200353 GTTATGTAAG---T-T-GTTATGTAAATTATGTAAGTTATGTGA
1 GTTATGTAAGTTATGTAGTTATGTAAATTATGTAAGTTATGTGA
*
88200392 GTTATGTAAG---T-T-GTTATGTAAATTATGTAAGTTATATGA
1 GTTATGTAAGTTATGTAGTTATGTAAATTATGTAAGTTATGTGA
88200431 GTTATGTAAGTTATGTA
1 GTTATGTAAGTTATGTA
88200448 ATTTATTTAA
Statistics
Matches: 88, Mismatches: 2, Indels: 11
0.87 0.02 0.11
Matches are distributed among these distances:
39 75 0.85
41 1 0.01
42 2 0.02
43 1 0.01
45 9 0.10
ACGTcount: A:0.31, C:0.01, G:0.23, T:0.46
Consensus pattern (44 bp):
GTTATGTAAGTTATGTAGTTATGTAAATTATGTAAGTTATGTGA
Found at i:88200386 original size:57 final size:57
Alignment explanation
Indices: 88200293--88200459 Score: 196
Period size: 57 Copynumber: 2.9 Consensus size: 57
88200283 ATGTATTAGT
* *
88200293 TAAGTTATGTAAGTTGTTATGTACGTTATGTGAGTTATGTAAATTATGTAAGTTATG
1 TAAGTTATGTAAGTTGTTATGTAAGTTATGTAAGTTATGTAAATTATGTAAGTTATG
* * * *
88200350 TGAGTTATGTAAGTTGTTATGTAAATTATGTAAGTTATGTGAGTTATGTAAGTTGTTATG
1 TAAGTTATGTAAGTTGTTATGTAAGTTATGTAAGTTATGTAAATTATGTAA---GTTATG
* * * *
88200410 TAAATTATGTAAGTT-ATATG--AGTTATGTAAGTTATGTAATTTATTTAAGT
1 TAAGTTATGTAAGTTGTTATGTAAGTTATGTAAGTTATGTAAATTATGTAAGT
88200460 AATGATCAAT
Statistics
Matches: 94, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
54 2 0.02
57 69 0.73
59 4 0.04
60 19 0.20
ACGTcount: A:0.31, C:0.01, G:0.22, T:0.47
Consensus pattern (57 bp):
TAAGTTATGTAAGTTGTTATGTAAGTTATGTAAGTTATGTAAATTATGTAAGTTATG
Found at i:88200448 original size:48 final size:48
Alignment explanation
Indices: 88200293--88200448 Score: 188
Period size: 48 Copynumber: 3.2 Consensus size: 48
88200283 ATGTATTAGT
* * *
88200293 TAAGTTATGTAAGTTGTTATGTACGTTATGTGAGTTATGTAAATTATG
1 TAAGTTATGTAAGTTGTTATGTAAGTTATGTAAGTTATGTAAGTTATG
* * * * *
88200341 TAAGTTATGTGAGTTATGTAAGT-TGTTATGTAAATTATGTAAGTTATG
1 TAAGTTATGTAAGTTGT-TATGTAAGTTATGTAAGTTATGTAAGTTATG
* * * *
88200389 TGAGTTATGTAAGTTGTTATGTAAATTATGTAAGTTATATGAGTTATG
1 TAAGTTATGTAAGTTGTTATGTAAGTTATGTAAGTTATGTAAGTTATG
88200437 TAAGTTATGTAA
1 TAAGTTATGTAA
88200449 TTTATTTAAG
Statistics
Matches: 89, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
47 4 0.04
48 81 0.91
49 4 0.04
ACGTcount: A:0.31, C:0.01, G:0.22, T:0.46
Consensus pattern (48 bp):
TAAGTTATGTAAGTTGTTATGTAAGTTATGTAAGTTATGTAAGTTATG
Found at i:88201062 original size:241 final size:241
Alignment explanation
Indices: 88200639--88201366 Score: 1330
Period size: 241 Copynumber: 3.0 Consensus size: 241
88200629 TTAAGGTTAT
*
88200639 ATAAATATTCAATAGTAAATGAGATCGATAGAACTTTTTCAAAGTCTTTTTGAATTTTTTAAGAT
1 ATAAATATTCAATAGTAAATGAGATCGATAGAACTTTTTCCAAGTCTTTTTGAATTTTTTAAGAT
88200704 TCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTACAGCTCGATATAAGGCA
66 TCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTACAGCTCGATATAAGGCA
88200769 ACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGTTGGAGAGAA
131 ACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGTTGGAGAGAA
88200834 GGTCAGCTATTGTTGTAATTTTAATGAACAAGCAAGCTACATGGTA
196 GGTCAGCTATTGTTGTAATTTTAATGAACAAGCAAGCTACATGGTA
*
88200880 ATAAATATTCAATAGTAAATGAGATCGATAGAACTTTTTCCAAGTCTTTATGAATTTTTTAAGAT
1 ATAAATATTCAATAGTAAATGAGATCGATAGAACTTTTTCCAAGTCTTTTTGAATTTTTTAAGAT
*
88200945 TCATCATACGCGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTACAGCTCGATATAAGGCA
66 TCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTACAGCTCGATATAAGGCA
* * *
88201010 ACTCGTCTGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGTTAGAGAGAA
131 ACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGTTGGAGAGAA
88201075 GGTCAGCTATTGTTGTAATTTTAATGAACAAGCAAGCTACATGGTA
196 GGTCAGCTATTGTTGTAATTTTAATGAACAAGCAAGCTACATGGTA
* *
88201121 ATAAATATTCAATAGTAAATGAGCTCGATAGAACTTTTTTCAAGTCTTTTTGAATTTTTTAAGAT
1 ATAAATATTCAATAGTAAATGAGATCGATAGAACTTTTTCCAAGTCTTTTTGAATTTTTTAAGAT
* *
88201186 TCATCATACGTGGCGTTGTTACACTTAGGGAGGATCCATTATATCTTATAGCTCGATATAAGGCA
66 TCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTACAGCTCGATATAAGGCA
* *
88201251 ACCCGTCAGGTTTCCAGCTTATATACTTTGAATCTTTAAAATATTTAAAATAATGTTGGAGAGAA
131 ACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGTTGGAGAGAA
* *
88201316 GGTCAACTATTGTTGTAATTTTAATGGACAAGCAAGCTACATGGTA
196 GGTCAGCTATTGTTGTAATTTTAATGAACAAGCAAGCTACATGGTA
88201362 ATAAA
1 ATAAA
88201367 ATTAATTCAT
Statistics
Matches: 468, Mismatches: 19, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
241 468 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (241 bp):
ATAAATATTCAATAGTAAATGAGATCGATAGAACTTTTTCCAAGTCTTTTTGAATTTTTTAAGAT
TCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTACAGCTCGATATAAGGCA
ACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAATAAGGTTGGAGAGAA
GGTCAGCTATTGTTGTAATTTTAATGAACAAGCAAGCTACATGGTA
Found at i:88205489 original size:50 final size:48
Alignment explanation
Indices: 88205323--88205546 Score: 295
Period size: 49 Copynumber: 4.5 Consensus size: 48
88205313 CTGGTACGCA
* * *
88205323 TAGTAGCCTGCACATAGTACTACACATGCGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCC-GTACACG
88205372 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGTACACG
** *
88205420 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC-AATTATCCG-TACACG
* * * * *
88205470 TAGTAGCCTGCACTTAGTACTACACACGTGATCACAGTTTTCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-C-CAATTATC-CGTACACG
88205521 TAGTAGCCTGCACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
88205547 TGCGACCTCA
Statistics
Matches: 157, Mismatches: 13, Indels: 8
0.88 0.07 0.04
Matches are distributed among these distances:
48 40 0.25
49 44 0.28
50 37 0.24
51 34 0.22
52 2 0.01
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (48 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGTACACG
Found at i:88207744 original size:14 final size:14
Alignment explanation
Indices: 88207685--88207745 Score: 56
Period size: 14 Copynumber: 4.4 Consensus size: 14
88207675 GATAACAAGA
88207685 AAACC-GAATAAAG
1 AAACCAGAATAAAG
88207698 AAATCCA-AGATAGAA-
1 AAA-CCAGA-ATA-AAG
*
88207713 AACCCAGAATAAAG
1 AAACCAGAATAAAG
*
88207727 AAACCAGAGTAAAG
1 AAACCAGAATAAAG
88207741 AAACC
1 AAACC
88207746 CAAGATACGA
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
13 5 0.13
14 26 0.67
15 6 0.15
16 2 0.05
ACGTcount: A:0.59, C:0.18, G:0.15, T:0.08
Consensus pattern (14 bp):
AAACCAGAATAAAG
Found at i:88207744 original size:29 final size:28
Alignment explanation
Indices: 88207681--88207747 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 28
88207671 TAAAGATAAC
*
88207681 AAGAAAACC-GAATAAAGAAATCCAAGA
1 AAGAAACCCAGAATAAAGAAATCCAAGA
*
88207708 TAGAAAACCCAGAATAAAGAAA-CCAGAGTA
1 AAG-AAACCCAGAATAAAGAAATCCA-AG-A
88207738 AAGAAACCCA
1 AAGAAACCCA
88207748 AGATACGATA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
27 2 0.06
28 8 0.24
29 20 0.61
30 3 0.09
ACGTcount: A:0.60, C:0.18, G:0.15, T:0.07
Consensus pattern (28 bp):
AAGAAACCCAGAATAAAGAAATCCAAGA
Found at i:88209167 original size:2 final size:2
Alignment explanation
Indices: 88209160--88209186 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
88209150 GTGTTATCAC
88209160 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
88209187 TTTTATTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:88210843 original size:49 final size:49
Alignment explanation
Indices: 88210734--88210906 Score: 224
Period size: 49 Copynumber: 3.5 Consensus size: 49
88210724 CTGGTACGCA
* * *
88210734 TAGTAGCCTGCACATAGTACTACACATGTGACCAA-TATCCTGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCAGTACACG
*
88210782 TAGTAGCTTGCACTTAGTACTACACACGTGACCAATTATCCAGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCAGTACACG
* *** * *
88210831 TAGTAGCCTGCACTTAGTACTACACACGTGATCACAGTT-TTGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-C-CAATTATCCAGTACACG
88210881 TAGTAGCCTGCACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
88210907 TGCGACCTCA
Statistics
Matches: 111, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
48 32 0.29
49 42 0.38
50 33 0.30
51 4 0.04
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCAGTACACG
Found at i:88213208 original size:25 final size:25
Alignment explanation
Indices: 88213174--88213245 Score: 117
Period size: 25 Copynumber: 2.9 Consensus size: 25
88213164 GGAGGAGATG
*
88213174 GGGAAATTGGGGATTTTAGAATTTA
1 GGGAAATTGGGGATTTAAGAATTTA
*
88213199 GGGAAATTGGAGATTTAAGAATTTA
1 GGGAAATTGGGGATTTAAGAATTTA
*
88213224 GGGAAATTGGGGATTTCAGAAT
1 GGGAAATTGGGGATTTAAGAAT
88213246 CGAGGTAAAC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.35, C:0.01, G:0.32, T:0.32
Consensus pattern (25 bp):
GGGAAATTGGGGATTTAAGAATTTA
Found at i:88214973 original size:40 final size:39
Alignment explanation
Indices: 88214866--88214974 Score: 116
Period size: 39 Copynumber: 2.8 Consensus size: 39
88214856 ACATAATATT
*
88214866 TTTGCGGCGTTTT-C-AAAAACGCCGCTAATGATTAAAA
1 TTTGCGGCGTTTTACAAAAAACGCCGCTAATGATGAAAA
* * * * *
88214903 TTTGCGGCTTTTTAGAACAAACGCCGCTAATTATG-ATA
1 TTTGCGGCGTTTTACAAAAAACGCCGCTAATGATGAAAA
*
88214941 TATTGCGGCGTTTTACATAAAAACGCCACTAATG
1 T-TTGCGGCGTTTTACA-AAAAACGCCGCTAATG
88214975 CCTCTATATA
Statistics
Matches: 57, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
37 12 0.21
38 3 0.05
39 29 0.51
40 13 0.23
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Consensus pattern (39 bp):
TTTGCGGCGTTTTACAAAAAACGCCGCTAATGATGAAAA
Found at i:88216551 original size:46 final size:46
Alignment explanation
Indices: 88216484--88216709 Score: 278
Period size: 46 Copynumber: 5.0 Consensus size: 46
88216474 GCTCGCTGAA
* *
88216484 ATGAAATGTATAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* *
88216530 ATGAAATGTATAAGACCATGGTTGAAAGATACCATGGCAACGTG--
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* **
88216574 ATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAATGTGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * *
88216620 ATGAAAAGAACAAGACCATGGTTGAAAGATACCATGACAGCATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * * *
88216666 A-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 ATG-AAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATG
88216710 TCAAAGATAA
Statistics
Matches: 160, Mismatches: 17, Indels: 6
0.87 0.09 0.03
Matches are distributed among these distances:
44 41 0.26
45 1 0.01
46 118 0.74
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.20
Consensus pattern (46 bp):
ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:88216555 original size:21 final size:21
Alignment explanation
Indices: 88216485--88216556 Score: 58
Period size: 21 Copynumber: 3.2 Consensus size: 21
88216475 CTCGCTGAAA
88216485 TGAAATGTATAAGACCATGGT
1 TGAAATGTATAAGACCATGGT
* *
88216506 TGAAA-G-ATACCATGGCAACATGAT
1 TGAAATGTATA--A--G-ACCATGGT
88216530 ATGAAATGTATAAGACCATGGT
1 -TGAAATGTATAAGACCATGGT
88216552 TGAAA
1 TGAAA
88216557 GATACCATGG
Statistics
Matches: 39, Mismatches: 4, Indels: 16
0.66 0.07 0.27
Matches are distributed among these distances:
19 3 0.08
20 1 0.03
21 11 0.28
22 6 0.15
23 2 0.05
24 6 0.15
25 6 0.15
26 1 0.03
27 3 0.08
ACGTcount: A:0.42, C:0.11, G:0.22, T:0.25
Consensus pattern (21 bp):
TGAAATGTATAAGACCATGGT
Found at i:88216637 original size:90 final size:90
Alignment explanation
Indices: 88216484--88216709 Score: 281
Period size: 90 Copynumber: 2.5 Consensus size: 90
88216474 GCTCGCTGAA
* * * * * *
88216484 ATGAAATGTATAAGACCATGGTTGAAAGATACCATGGCAACATGATATGAAATGTATAAGACCAT
1 ATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAAAGAACAAGACCAT
* *
88216549 GGTTGAAAGATACCATGGCAACGTG
66 GGTTGAAAGATACCATGACAACATG
**
88216574 ATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAATGTGACATGAAAAGAACAAGACCAT
1 ATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAAAGAACAAGACCAT
*
88216639 GGTTGAAAGATACCATGACAGCATG
66 GGTTGAAAGATACCATGACAACATG
* * * * * *
88216664 ACAGAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 A-TGAAAA-GAATAAGACCATGGTTGAAAGATACCATGGCAACATG
88216710 TCAAAGATAA
Statistics
Matches: 115, Mismatches: 19, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
90 80 0.70
91 5 0.04
92 30 0.26
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.20
Consensus pattern (90 bp):
ATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAAAGAACAAGACCAT
GGTTGAAAGATACCATGACAACATG
Found at i:88217520 original size:18 final size:18
Alignment explanation
Indices: 88217497--88217532 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
88217487 TCAATGAGAT
88217497 TGTGCATAGACTACTGAC
1 TGTGCATAGACTACTGAC
88217515 TGTGCATAGACTACTGAC
1 TGTGCATAGACTACTGAC
88217533 AGCTCAACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (18 bp):
TGTGCATAGACTACTGAC
Found at i:88222886 original size:46 final size:47
Alignment explanation
Indices: 88222713--88223074 Score: 167
Period size: 46 Copynumber: 7.7 Consensus size: 47
88222703 TCATTCGTGC
* ** * *
88222713 GCCAGTGTAAGACATGCCTGGGACAT-GCATCGATCAC-ATTATG-AGA
1 GCCAGTGTAAGACATGTCTGGGACATAGCATCGGCCTCGA-GATGTA-A
* * ** * * * *
88222759 GCTAGTGTAAGACCATGTCTGGGATAGGGCATTGGCATTGAGACG-ATA
1 GCCAGTGTAAGA-CATGTCTGGGACATAGCATCGGCCTCGAGATGTA-A
* * * *
88222807 GCTAGTGTAAGACATGTTTGGAACATA-CATCGGCCTCGTGATGTAA
1 GCCAGTGTAAGACATGTCTGGGACATAGCATCGGCCTCGAGATGTAA
* *
88222853 GCCAGTGTAAGACATGTCTGGGACAT-GCGTCGG-CTACAAGATGT--
1 GCCAGTGTAAGACATGTCTGGGACATAGCATCGGCCT-CGAGATGTAA
* * *
88222897 GCCAGTATAATACCATGTCTGGGACATAGCATCGGCAC-AGAGATGTGAGA
1 GCCAGTGTAAGA-CATGTCTGGGACATAGCATCGGC-CTCGAGATGT-A-A
* * * * **
88222947 GCCAGTGTAAGAACATGTCTAGGACATGGCGTTGGCCTCGATTTCG-ATA
1 GCCAGTGTAAG-ACATGTCTGGGACATAGCATCGGCCTCGAGAT-GTA-A
* * * * *
88222996 GTCAGTGTAAGACCATGTTTGGGACATGGCATC-GACTTGATGGATG--A
1 GCCAGTGTAAGA-CATGTCTGGGACATAGCATCGGCCTCGA--GATGTAA
* *
88223043 GCAAGTGTAAGACCATGTCTGGGACATGGCAT
1 GCCAGTGTAAGA-CATGTCTGGGACATAGCAT
88223075 TGGCATTACA
Statistics
Matches: 240, Mismatches: 56, Indels: 39
0.72 0.17 0.12
Matches are distributed among these distances:
44 10 0.04
45 16 0.07
46 69 0.29
47 52 0.22
48 28 0.12
49 31 0.13
50 32 0.13
51 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.24
Consensus pattern (47 bp):
GCCAGTGTAAGACATGTCTGGGACATAGCATCGGCCTCGAGATGTAA
Found at i:88228566 original size:6 final size:6
Alignment explanation
Indices: 88228556--88228619 Score: 112
Period size: 6 Copynumber: 10.8 Consensus size: 6
88228546 TTTTATTTGT
*
88228556 TTTATT TTTATG TTTATG TTTATG TTTATG TTTATG TTTATG -TTATG
1 TTTATG TTTATG TTTATG TTTATG TTTATG TTTATG TTTATG TTTATG
88228603 TTTATG TTTATG TTTAT
1 TTTATG TTTATG TTTAT
88228620 TGTTGTTTTT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
5 5 0.09
6 51 0.91
ACGTcount: A:0.17, C:0.00, G:0.14, T:0.69
Consensus pattern (6 bp):
TTTATG
Found at i:88232124 original size:46 final size:45
Alignment explanation
Indices: 88232071--88232246 Score: 169
Period size: 46 Copynumber: 3.8 Consensus size: 45
88232061 TATTTGGGCA
88232071 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *** * *
88232117 TCCGAACTCGTTGAGTTGAGTCTGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
* * *
88232164 TCCGAGCTTGTTGAGTTGAGTCCGAGTTCAATTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
88232210 -CCCAAGCTCGTTGAGTTGAGTCCGAATTCACTTATGG
1 TCCGAA-CTCGTTGAGTTGAGTCCGAGTTCACTTATGG
88232247 GCGGGTTACA
Statistics
Matches: 103, Mismatches: 19, Indels: 16
0.75 0.14 0.12
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 4 0.04
46 60 0.58
47 30 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:88245093 original size:59 final size:58
Alignment explanation
Indices: 88244997--88245128 Score: 246
Period size: 59 Copynumber: 2.3 Consensus size: 58
88244987 AAAATTGTAC
88244997 AGCACTAAGTGTGCGAACTGAAAATATATAGCACTAAGTGTGCGAGCTGAAAATATAT
1 AGCACTAAGTGTGCGAACTGAAAATATATAGCACTAAGTGTGCGAGCTGAAAATATAT
*
88245055 AGCACTAAGTGTGCGAGCTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATATAT
1 AGCACTAAGTGTGCGAACTGAAAA-TATATAGCACTAAGTGTGCGAGCTGAAAATATAT
88245114 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
88245129 GATTCACTAT
Statistics
Matches: 72, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
58 23 0.32
59 49 0.68
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.24
Consensus pattern (58 bp):
AGCACTAAGTGTGCGAACTGAAAATATATAGCACTAAGTGTGCGAGCTGAAAATATAT
Found at i:88245117 original size:88 final size:89
Alignment explanation
Indices: 88244967--88245128 Score: 263
Period size: 88 Copynumber: 1.8 Consensus size: 89
88244957 GACAAGATTG
* * *
88244967 GCACTAAGTGTGCGGGTTTAAAAATTGTACAGCACTAAGTGTGCGAACTGAAAATATATAGCACT
1 GCACTAAGTGTGCGAGTCTAAAAATTATACAGCACTAAGTGTGCGAACTGAAAATATATAGCACT
88245032 AAGTGTGCGAGCTGAAAATATATA
66 AAGTGTGCGAGCTGAAAATATATA
* * *
88245056 GCACTAAGTGTGCGAG-CTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATATATAGCACT
1 GCACTAAGTGTGCGAGTCTAAAAATTATACAGCACTAAGTGTGCGAACTGAAAATATATAGCACT
88245120 AAGTGTGCG
66 AAGTGTGCG
88245129 GATTCACTAT
Statistics
Matches: 67, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
88 52 0.78
89 15 0.22
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.25
Consensus pattern (89 bp):
GCACTAAGTGTGCGAGTCTAAAAATTATACAGCACTAAGTGTGCGAACTGAAAATATATAGCACT
AAGTGTGCGAGCTGAAAATATATA
Found at i:88245140 original size:29 final size:29
Alignment explanation
Indices: 88244997--88245128 Score: 246
Period size: 29 Copynumber: 4.5 Consensus size: 29
88244987 AAAATTGTAC
*
88244997 AGCACTAAGTGTGCGAACTGAAAATATAT
1 AGCACTAAGTGTGCGAGCTGAAAATATAT
88245026 AGCACTAAGTGTGCGAGCTGAAAATATAT
1 AGCACTAAGTGTGCGAGCTGAAAATATAT
88245055 AGCACTAAGTGTGCGAGCTGAAAATTATAT
1 AGCACTAAGTGTGCGAGCTGAAAA-TATAT
88245085 AGCACTAAGTGTGCGAGCTGAAAATATAT
1 AGCACTAAGTGTGCGAGCTGAAAATATAT
88245114 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
88245129 GATTCACTAT
Statistics
Matches: 101, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
29 72 0.71
30 29 0.29
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.24
Consensus pattern (29 bp):
AGCACTAAGTGTGCGAGCTGAAAATATAT
Found at i:88252655 original size:59 final size:58
Alignment explanation
Indices: 88252559--88252690 Score: 246
Period size: 59 Copynumber: 2.3 Consensus size: 58
88252549 AAAATTGTAC
88252559 AGCACTAAGTGTGCGAACTGAAAATATATAGCACTAAGTGTGCGAGCTGAAAATATAT
1 AGCACTAAGTGTGCGAACTGAAAATATATAGCACTAAGTGTGCGAGCTGAAAATATAT
*
88252617 AGCACTAAGTGTGCGAGCTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATATAT
1 AGCACTAAGTGTGCGAACTGAAAA-TATATAGCACTAAGTGTGCGAGCTGAAAATATAT
88252676 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
88252691 GATTCACTAT
Statistics
Matches: 72, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
58 23 0.32
59 49 0.68
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.24
Consensus pattern (58 bp):
AGCACTAAGTGTGCGAACTGAAAATATATAGCACTAAGTGTGCGAGCTGAAAATATAT
Found at i:88252679 original size:88 final size:89
Alignment explanation
Indices: 88252529--88252690 Score: 263
Period size: 88 Copynumber: 1.8 Consensus size: 89
88252519 GACAAGATTG
* * *
88252529 GCACTAAGTGTGCGGGTTTAAAAATTGTACAGCACTAAGTGTGCGAACTGAAAATATATAGCACT
1 GCACTAAGTGTGCGAGTCTAAAAATTATACAGCACTAAGTGTGCGAACTGAAAATATATAGCACT
88252594 AAGTGTGCGAGCTGAAAATATATA
66 AAGTGTGCGAGCTGAAAATATATA
* * *
88252618 GCACTAAGTGTGCGAG-CTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATATATAGCACT
1 GCACTAAGTGTGCGAGTCTAAAAATTATACAGCACTAAGTGTGCGAACTGAAAATATATAGCACT
88252682 AAGTGTGCG
66 AAGTGTGCG
88252691 GATTCACTAT
Statistics
Matches: 67, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
88 52 0.78
89 15 0.22
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.25
Consensus pattern (89 bp):
GCACTAAGTGTGCGAGTCTAAAAATTATACAGCACTAAGTGTGCGAACTGAAAATATATAGCACT
AAGTGTGCGAGCTGAAAATATATA
Found at i:88252702 original size:29 final size:29
Alignment explanation
Indices: 88252559--88252690 Score: 246
Period size: 29 Copynumber: 4.5 Consensus size: 29
88252549 AAAATTGTAC
*
88252559 AGCACTAAGTGTGCGAACTGAAAATATAT
1 AGCACTAAGTGTGCGAGCTGAAAATATAT
88252588 AGCACTAAGTGTGCGAGCTGAAAATATAT
1 AGCACTAAGTGTGCGAGCTGAAAATATAT
88252617 AGCACTAAGTGTGCGAGCTGAAAATTATAT
1 AGCACTAAGTGTGCGAGCTGAAAA-TATAT
88252647 AGCACTAAGTGTGCGAGCTGAAAATATAT
1 AGCACTAAGTGTGCGAGCTGAAAATATAT
88252676 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
88252691 GATTCACTAT
Statistics
Matches: 101, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
29 72 0.71
30 29 0.29
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.24
Consensus pattern (29 bp):
AGCACTAAGTGTGCGAGCTGAAAATATAT
Found at i:88256392 original size:28 final size:29
Alignment explanation
Indices: 88256357--88256477 Score: 124
Period size: 28 Copynumber: 4.3 Consensus size: 29
88256347 ATAATGTGAT
*
88256357 TTGGGCCTGATGGGCCATGTGAATGAG-A
1 TTGGGCCTGATGGGCCATATGAATGAGAA
* *
88256385 TTGGGCCT-AGTGGGTCATATGAATGTGAA
1 TTGGGCCTGA-TGGGCCATATGAATGAGAA
* * *
88256414 TT-GGCCTTATAGGCCATATGAATGTGAA
1 TTGGGCCTGATGGGCCATATGAATGAGAA
* * *
88256442 TTTGGCCGGATGGGCCATATAAATGAG-A
1 TTGGGCCTGATGGGCCATATGAATGAGAA
88256470 TTGGGCCT
1 TTGGGCCT
88256478 AGTGGTCCAT
Statistics
Matches: 77, Mismatches: 12, Indels: 8
0.79 0.12 0.08
Matches are distributed among these distances:
27 1 0.01
28 53 0.69
29 23 0.30
ACGTcount: A:0.24, C:0.14, G:0.33, T:0.29
Consensus pattern (29 bp):
TTGGGCCTGATGGGCCATATGAATGAGAA
Found at i:88256488 original size:28 final size:30
Alignment explanation
Indices: 88256378--88256490 Score: 73
Period size: 28 Copynumber: 4.0 Consensus size: 30
88256368 GGGCCATGTG
* *
88256378 AATGAG-ATTGGGCCTAGTGGGT-CATATG
1 AATGAGAATTGGGCCTAGTAGGTCCATATA
* *
88256406 AATGTGAATT-GGCCTTA-TAGG-CCATATG
1 AATGAGAATTGGGCC-TAGTAGGTCCATATA
* * * *
88256434 AATGTGAATTTGGCC--GGATGGGCCATATA
1 AATGAGAATTGGGCCTAGTA-GGTCCATATA
88256463 AATGAG-ATTGGGCCTAGT-GGTCCATATA
1 AATGAGAATTGGGCCTAGTAGGTCCATATA
88256491 CGTGTGTATA
Statistics
Matches: 68, Mismatches: 8, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
27 1 0.01
28 46 0.68
29 20 0.29
30 1 0.01
ACGTcount: A:0.27, C:0.13, G:0.30, T:0.29
Consensus pattern (30 bp):
AATGAGAATTGGGCCTAGTAGGTCCATATA
Found at i:88264972 original size:16 final size:16
Alignment explanation
Indices: 88264930--88264960 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
88264920 GTAGCTCGGC
*
88264930 AAAAGCCAAAATGCTA
1 AAAAGCCGAAATGCTA
88264946 AAAAGCCGAAATGCT
1 AAAAGCCGAAATGCT
88264961 GAAATGCTGA
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:0.52, C:0.19, G:0.16, T:0.13
Consensus pattern (16 bp):
AAAAGCCGAAATGCTA
Found at i:88265121 original size:18 final size:19
Alignment explanation
Indices: 88265087--88265123 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
88265077 TAAATAGGCC
*
88265087 AAATGGGCCGGAATGGGCT
1 AAATGGGCCGCAATGGGCT
88265106 AAATGGGCC-CAATGGGCT
1 AAATGGGCCGCAATGGGCT
88265124 GTTGGGCCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.27, C:0.19, G:0.38, T:0.16
Consensus pattern (19 bp):
AAATGGGCCGCAATGGGCT
Found at i:88265255 original size:29 final size:29
Alignment explanation
Indices: 88265173--88265324 Score: 129
Period size: 29 Copynumber: 5.3 Consensus size: 29
88265163 GTGAGCATGA
*
88265173 ATAT-AATGTGATTTGGGCC-GAATGGGCC
1 ATATGAATGTGAATTGGGCCTG-ATGGGCC
* *
88265201 ATGTGAATGAG-ATTGGGCCT-AGTGGGCC
1 ATATGAATGTGAATTGGGCCTGA-TGGGCC
*
88265229 ATATGAATGTGAATTGGGTCTGATGGGCC
1 ATATGAATGTGAATTGGGCCTGATGGGCC
* * *
88265258 ATATGAACGTGAAGTGGGCCGGATGGGCC
1 ATATGAATGTGAATTGGGCCTGATGGGCC
* *
88265287 ATAT-AA-ATGATATTGGACCT-AGTGGGCC
1 ATATGAATGTGA-ATTGGGCCTGA-TGGGCC
*
88265315 ATATGCATGT
1 ATATGAATGT
88265325 ATGTAGGGGT
Statistics
Matches: 99, Mismatches: 16, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
27 5 0.05
28 43 0.43
29 49 0.49
30 2 0.02
ACGTcount: A:0.26, C:0.14, G:0.34, T:0.27
Consensus pattern (29 bp):
ATATGAATGTGAATTGGGCCTGATGGGCC
Found at i:88267074 original size:2 final size:2
Alignment explanation
Indices: 88267063--88267093 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
88267053 ATGTAAGCCC
88267063 AT AT -T 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
88267094 GCATTGGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Done.