Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 85040211
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: 85040211
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 160 characters in sequence are not A, C, G, or T
File 148 of 292
Found at i:44027702 original size:40 final size:39
Alignment explanation
Indices: 44027657--44027864 Score: 218
Period size: 40 Copynumber: 5.2 Consensus size: 39
44027647 CGGAATACAA
*
44027657 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* *
44027697 CCGGATATAACGACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
44027737 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* ** * *
44027777 CCGGATGTAGTCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
* ** * * *
44027817 CCAGATATAATTACTAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
44027857 CCGGATAT
1 CCGGATAT
44027865 CATTCAATTG
Statistics
Matches: 142, Mismatches: 25, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
39 1 0.01
40 141 0.99
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (39 bp):
CCGGATATAACCACTGCACAAATGCCTTCGGGTCTTAGC
Found at i:44027797 original size:80 final size:80
Alignment explanation
Indices: 44027657--44027864 Score: 247
Period size: 80 Copynumber: 2.6 Consensus size: 80
44027647 CGGAATACAA
* * *
44027657 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGCCCGGATATAACGACTTGCACAAATG
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATATAACGACTAGCACAAATG
*
44027722 CCTTCGGGTATTAGC
66 CCTTCGGGTATTAAC
* * * *
44027737 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGTC-ACTAGCACAATT
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATATA-ACGACTAGCACAAAT
*
44027801 GCCTTCGGGTCTTAAC
65 GCCTTCGGGTATTAAC
* ** * ** * *
44027817 CCAGATATAATTACTAGCATAAATGTCTTCGGGACTTAGCCCGGATAT
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATAT
44027865 CATTCAATTG
Statistics
Matches: 108, Mismatches: 19, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
80 107 0.99
81 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (80 bp):
CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATATAACGACTAGCACAAATG
CCTTCGGGTATTAAC
Found at i:44037309 original size:25 final size:25
Alignment explanation
Indices: 44037281--44037328 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
44037271 TTATACCATG
* * *
44037281 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
44037306 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
44037329 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:44037431 original size:20 final size:20
Alignment explanation
Indices: 44037371--44037431 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
44037361 ATAAATATGG
*
44037371 TATGTATGAGATGCACATGA
1 TATGTATGATATGCACATGA
*
44037391 CATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
44037411 TATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
44037431 T
1 T
44037432 GTAATCATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.33
Consensus pattern (20 bp):
TATGTATGATATGCACATGA
Found at i:44037508 original size:24 final size:24
Alignment explanation
Indices: 44037481--44037623 Score: 209
Period size: 24 Copynumber: 6.0 Consensus size: 24
44037471 GAGGAAGTGA
44037481 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
44037505 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
44037529 AAAAGGGCTTATGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
*
44037552 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
* * *
44037576 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
*
44037600 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
44037624 ATGATAAAGC
Statistics
Matches: 111, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
23 23 0.21
24 77 0.69
25 11 0.10
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:44037574 original size:47 final size:47
Alignment explanation
Indices: 44037481--44037623 Score: 207
Period size: 47 Copynumber: 3.0 Consensus size: 47
44037471 GAGGAAGTGA
44037481 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTATC
*
44037529 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
* * *
44037576 GAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTA-TAAAAG-GGCTTATGCC-CCAGTTAT
44037624 ATGATAAAGC
Statistics
Matches: 88, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
47 43 0.49
48 34 0.39
49 11 0.12
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (47 bp):
AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
Found at i:44037597 original size:71 final size:72
Alignment explanation
Indices: 44037481--44037624 Score: 220
Period size: 71 Copynumber: 2.0 Consensus size: 72
44037471 GAGGAAGTGA
*
44037481 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAG-GGCTTATGCC-
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGC-TAGGCCT
44037544 CCAGTTAT
65 CCAGTTAT
** * *
44037552 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGCTAGGCCTC
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGCTAGGCCTC
44037617 CAGTTAT
66 CAGTTAT
44037624 A
1 A
44037625 TGATAAAGCA
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
71 54 0.82
72 12 0.18
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (72 bp):
AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGCTAGGCCTC
CAGTTAT
Found at i:44037875 original size:30 final size:31
Alignment explanation
Indices: 44037815--44037877 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
44037805 CGTTTACAGT
44037815 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
44037846 AAAGGCTTCGGCCCAGTGTTATG-AATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
44037876 AA
1 AA
44037878 CATGAAAAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 9 0.30
31 21 0.70
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.24
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:44048565 original size:40 final size:39
Alignment explanation
Indices: 44048470--44048652 Score: 145
Period size: 40 Copynumber: 4.6 Consensus size: 39
44048460 TGCTGGAAAT
* * * * **
44048470 TATAACCGGGTTAAGACCCGAAGGCAATGTGCTAGTGGC
1 TATATCCGGGCTAAGACCCGAAGGCATTGTGCGAGTCAC
*
44048509 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCAT
1 TATATCCGGGCTAAGACCCGAAGGCATT-GTGCGAGTCAC
* * *
44048549 TCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-AATC-G
1 TATATCCGGGCTAAGACCCGAAGGCA-TTGTGCGAGTCAC
* * * * * *
44048587 TGATATCCGGGTTAAGTCCCGTAGGCCTTGGTGCGGGTTAC
1 T-ATATCCGGGCTAAGACCCGAAGGCATT-GTGCGAGTCAC
* * *
44048628 CATATCCGGGCTATGTCCCGAAGGC
1 TATATCCGGGCTAAGACCCGAAGGC
44048653 GTTTGAACGA
Statistics
Matches: 115, Mismatches: 23, Indels: 11
0.77 0.15 0.07
Matches are distributed among these distances:
38 3 0.03
39 52 0.45
40 58 0.50
41 2 0.02
ACGTcount: A:0.22, C:0.25, G:0.30, T:0.23
Consensus pattern (39 bp):
TATATCCGGGCTAAGACCCGAAGGCATTGTGCGAGTCAC
Found at i:44048593 original size:79 final size:80
Alignment explanation
Indices: 44048475--44048657 Score: 185
Period size: 79 Copynumber: 2.3 Consensus size: 80
44048465 GAAATTATAA
* * * *
44048475 CCGGGTTAAGACCCGAAGGCA-ATGTGCTAGTGGCTATATCCGGGCTAAGACCCGAAGGCATTCG
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAATCGCTATATCCGGGCTAAGACCCGAAGGCATTCG
*
44048539 TGCGAGTCATTC-TAT
66 TGCGAGTCA-CCATAT
* * * * *
44048554 CCGGGCTAAGACCCGAAGGCATTTGTGC-AATCG-TGATATCCGGGTTAAGTCCCGTAGGCCTTG
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAATCGCT-ATATCCGGGCTAAGACCCGAAGGCATTC
* *
44048617 GTGCGGGTTACCATAT
65 GTGCGAGTCACCATAT
* * *
44048633 CCGGGCTATGTCCCGAAGGCGTTTG
1 CCGGGCTAAGACCCGAAGGCATTTG
44048658 AACGAGTAGC
Statistics
Matches: 86, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
78 2 0.02
79 79 0.92
80 5 0.06
ACGTcount: A:0.21, C:0.25, G:0.31, T:0.24
Consensus pattern (80 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCTAATCGCTATATCCGGGCTAAGACCCGAAGGCATTCG
TGCGAGTCACCATAT
Found at i:44053274 original size:40 final size:40
Alignment explanation
Indices: 44053188--44053371 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 40
44053178 TGCTGGAAAT
* * * * * **
44053188 TATAACCGGGTTAAGACCCGAAGGCAATGGTGCTAGTGGC
1 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCAC
*
44053228 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCAT
1 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCAC
* * * * *
44053268 TCTATCCGGGCTAAGACCCAAAGGCATTTGTGC-AATC-G
1 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCAC
* * * * * * *
44053306 TGATATCCGGGTTAAGTCCCGTAGGCCTTGGTGCGGGTTAC
1 T-ATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCAC
* * *
44053347 CATATCCGGGCTATGTCCCGAAGGC
1 TATATCCGGGCTAAGACCCGAAGGC
44053372 GTTTGAACGA
Statistics
Matches: 113, Mismatches: 28, Indels: 6
0.77 0.19 0.04
Matches are distributed among these distances:
38 1 0.01
39 28 0.25
40 84 0.74
ACGTcount: A:0.23, C:0.24, G:0.29, T:0.23
Consensus pattern (40 bp):
TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCAC
Found at i:44056178 original size:17 final size:17
Alignment explanation
Indices: 44056122--44056178 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
44056112 ATAACAGATT
*
44056122 TAAAATATAATAAATA-A
1 TAAAA-ATAATAATTATA
44056139 T-AAAA-AATATATT-TA
1 TAAAAATAATA-ATTATA
*
44056154 TAAGAATAATAATTATA
1 TAAAAATAATAATTATA
44056171 TAAAAATA
1 TAAAAATA
44056179 TAAAATATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
14 4 0.12
15 5 0.16
16 9 0.28
17 14 0.44
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (17 bp):
TAAAAATAATAATTATA
Found at i:44063567 original size:7 final size:7
Alignment explanation
Indices: 44063557--44063590 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
44063547 ATTATTTTTA
44063557 TTTGTTC
1 TTTGTTC
44063564 TTTGTTC
1 TTTGTTC
44063571 TTTGTTC
1 TTTGTTC
44063578 TTTGTTC
1 TTTGTTC
44063585 TTTGTT
1 TTTGTT
44063591 TACAAATTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.00, C:0.12, G:0.15, T:0.74
Consensus pattern (7 bp):
TTTGTTC
Found at i:44066176 original size:25 final size:25
Alignment explanation
Indices: 44066147--44066194 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
44066137 TTATAATATG
* * *
44066147 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
44066172 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
44066195 GTTTATACAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:44066265 original size:9 final size:9
Alignment explanation
Indices: 44066233--44066309 Score: 55
Period size: 9 Copynumber: 7.9 Consensus size: 9
44066223 TTTGATAAAC
44066233 ATGATATGT
1 ATGATATGT
* *
44066242 ATGGTATGCAC
1 ATGATATG--T
44066253 ATGATATGT
1 ATGATATGT
*
44066262 ATGATATGCAC
1 ATGATATG--T
*
44066273 ATGACATGT
1 ATGATATGT
*
44066282 ATGATATGCAC
1 ATGATATG--T
44066293 ATGATATGT
1 ATGATATGT
44066302 ATGATATG
1 ATGATATG
44066310 CACACGAGAT
Statistics
Matches: 52, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
9 30 0.58
11 22 0.42
ACGTcount: A:0.34, C:0.09, G:0.22, T:0.35
Consensus pattern (9 bp):
ATGATATGT
Found at i:44066321 original size:20 final size:20
Alignment explanation
Indices: 44066231--44066313 Score: 148
Period size: 20 Copynumber: 4.2 Consensus size: 20
44066221 ATTTTGATAA
*
44066231 ACATGATATGTATGGTATGC
1 ACATGATATGTATGATATGC
44066251 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
44066271 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
44066291 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
44066311 ACA
1 ACA
44066314 CGAGATGTTC
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 60 1.00
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:44066410 original size:23 final size:22
Alignment explanation
Indices: 44066368--44066482 Score: 162
Period size: 23 Copynumber: 5.1 Consensus size: 22
44066358 AGGAAGTGCA
44066368 AAAGGGCTTATGCCCAGTTATT
1 AAAGGGCTTATGCCCAGTTATT
44066390 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATG-CCCAGTTATT
44066413 AAAGGGCTTATG-CCAGTTATAT
1 AAAGGGCTTATGCCCAGTTAT-T
*
44066435 AAAGGGCTTATGCCCAGTTGTT
1 AAAGGGCTTATGCCCAGTTATT
*
44066457 AAAAGGGCTT-TACCCCAGTTATT
1 -AAAGGGCTTAT-GCCCAGTTATT
44066480 AAA
1 AAA
44066483 AGAGGCTAGG
Statistics
Matches: 85, Mismatches: 3, Indels: 10
0.87 0.03 0.10
Matches are distributed among these distances:
21 8 0.09
22 30 0.35
23 47 0.55
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (22 bp):
AAAGGGCTTATGCCCAGTTATT
Found at i:44066438 original size:45 final size:45
Alignment explanation
Indices: 44066367--44066482 Score: 166
Period size: 45 Copynumber: 2.6 Consensus size: 45
44066357 GAGGAAGTGC
44066367 AAAAGGGCTTATGCCCAGTTATTAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCAGTTATTAAAGGGCTTATG-CCCAGTTATT
*
44066413 -AAAGGGCTTATG-CCAGTTATATAAAGGGCTTATGCCCAGTTGTT
1 AAAAGGGCTTATGCCCAGTTAT-TAAAGGGCTTATGCCCAGTTATT
*
44066457 AAAAGGGCTT-TACCCCAGTTATTAAA
1 AAAAGGGCTTAT-GCCCAGTTATTAAA
44066483 AGAGGCTAGG
Statistics
Matches: 64, Mismatches: 2, Indels: 9
0.85 0.03 0.12
Matches are distributed among these distances:
44 18 0.28
45 38 0.59
46 8 0.12
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (45 bp):
AAAAGGGCTTATGCCCAGTTATTAAAGGGCTTATGCCCAGTTATT
Found at i:44066731 original size:31 final size:31
Alignment explanation
Indices: 44066696--44066776 Score: 119
Period size: 31 Copynumber: 2.6 Consensus size: 31
44066686 CGTTTACAGT
44066696 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
44066727 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
44066758 AAAGGGCTAT-GGCCCAGTA
1 AAA-GGCT-TCGGCCCAGTA
44066777 CATGTTGAGA
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
31 32 0.71
32 12 0.27
33 1 0.02
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.22
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:44074296 original size:24 final size:24
Alignment explanation
Indices: 44074264--44074310 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
44074254 TTATAATATG
* * *
44074264 AAAATGACCGTTTTGCCCCTAGGT
1 AAAATGACCATTATACCCCTAGGT
44074288 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
44074311 GTTTATACAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.26
Consensus pattern (24 bp):
AAAATGACCATTATACCCCTAGGT
Found at i:44074381 original size:9 final size:9
Alignment explanation
Indices: 44074349--44074425 Score: 55
Period size: 9 Copynumber: 7.9 Consensus size: 9
44074339 TTTGATAAAC
44074349 ATGATATGT
1 ATGATATGT
* *
44074358 ATGGTATGCAC
1 ATGATATG--T
44074369 ATGATATGT
1 ATGATATGT
*
44074378 ATGATATGCAC
1 ATGATATG--T
*
44074389 ATGACATGT
1 ATGATATGT
*
44074398 ATGATATGCAC
1 ATGATATG--T
44074409 ATGATATGT
1 ATGATATGT
44074418 ATGATATG
1 ATGATATG
44074426 CACACGAGAT
Statistics
Matches: 52, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
9 30 0.58
11 22 0.42
ACGTcount: A:0.34, C:0.09, G:0.22, T:0.35
Consensus pattern (9 bp):
ATGATATGT
Found at i:44074437 original size:20 final size:20
Alignment explanation
Indices: 44074347--44074429 Score: 148
Period size: 20 Copynumber: 4.2 Consensus size: 20
44074337 ATTTTGATAA
*
44074347 ACATGATATGTATGGTATGC
1 ACATGATATGTATGATATGC
44074367 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
44074387 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
44074407 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
44074427 ACA
1 ACA
44074430 CGAGATGTTT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 60 1.00
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:44074567 original size:47 final size:48
Alignment explanation
Indices: 44074483--44074602 Score: 187
Period size: 47 Copynumber: 2.6 Consensus size: 48
44074473 GAGGAAGTGC
44074483 AAAAGGGCTTATGCCCCAGTTAT-TAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATATAAAGGGCTTATGCCCCAGTTATT
*
44074530 -AAAGGGCTTATG-CCCAGTTATGATAAAGGGCTTATGCCCCAGTTGTT
1 AAAAGGGCTTATGCCCCAGTTAT-ATAAAGGGCTTATGCCCCAGTTATT
44074577 AAAAGGGCTT-TGCCCCAGTTAT-TAAA
1 AAAAGGGCTTATGCCCCAGTTATATAAA
44074603 AGAGGCTAGG
Statistics
Matches: 68, Mismatches: 1, Indels: 9
0.87 0.01 0.12
Matches are distributed among these distances:
45 9 0.13
46 16 0.24
47 25 0.37
48 18 0.26
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (48 bp):
AAAAGGGCTTATGCCCCAGTTATATAAAGGGCTTATGCCCCAGTTATT
Found at i:44074603 original size:23 final size:24
Alignment explanation
Indices: 44074483--44074623 Score: 193
Period size: 23 Copynumber: 6.0 Consensus size: 24
44074473 GAGGAAGTGC
44074483 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
44074507 -AAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
44074530 -AAAGGGCTTATG-CCCAGTTATG
1 AAAAGGGCTTATGCCCCAGTTATT
*
44074552 ATAAAGGGCTTATGCCCCAGTTGTT
1 A-AAAGGGCTTATGCCCCAGTTATT
44074577 AAAAGGGCTT-TGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
44074600 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
44074624 ATGATAAAGC
Statistics
Matches: 106, Mismatches: 5, Indels: 11
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.08
23 53 0.50
24 27 0.25
25 17 0.16
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:44074853 original size:31 final size:32
Alignment explanation
Indices: 44074818--44074899 Score: 114
Period size: 31 Copynumber: 2.6 Consensus size: 32
44074808 CGTTTACAGT
44074818 AAAGGCTTCGGCCCAGTAATATGAAATATG-A
1 AAAGGCTTCGGCCCAGTAATATGAAATATGAA
**
44074849 AAAGGCTTCGGCCCAGTGTTATGAAATATGAA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGAA
44074881 AAAGGGCTAT-GGCCCAGTA
1 AAA-GGCT-TCGGCCCAGTA
44074900 CATGTTGAGA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
31 28 0.62
32 4 0.09
33 12 0.27
34 1 0.02
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.22
Consensus pattern (32 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGAA
Found at i:44079236 original size:46 final size:45
Alignment explanation
Indices: 44079093--44079350 Score: 175
Period size: 46 Copynumber: 5.6 Consensus size: 45
44079083 GTCTCGATGC
* *
44079093 CATGTCCTAGACATGGTCTTACACTGGCTATCATCTACGAGTCTGATG
1 CATGTCCCAGACATGGTCTTACACTGGCTA-CATC-ACGAG-CTAATG
* * * *
44079141 CCATGTACCAGACATGGTCTTACACTGAC-ACATCTCGTAGCCAATG
1 -CATGTCCCAGACATGGTCTTACACTGGCTACATCACG-AGCTAATG
* *
44079187 CATGTCCCAGACAT-GTCTTATACTGGCTTACATCCCGAGACTAATG
1 CATGTCCCAGACATGGTCTTACACTGGC-TACATCACGAG-CTAATG
* * * * **
44079233 CATGTCCCAGACAT-GTCTTACACTAGAACT-TATCTCAATGCCGATG
1 CATGTCCCAGACATGGTCTTACACT-G-GCTACATCACGA-GCTAATG
* * * * * * *
44079279 CCATGTCCTAGACATGGTCTTACACTGGCTCTCATAATGTGGTCGATG
1 -CATGTCCCAGACATGGTCTTACACTGGCT-ACATCACGAGCT-AATG
44079327 CATGTCCCAGACAT-GTCTTACACT
1 CATGTCCCAGACATGGTCTTACACT
44079351 AGCTCACACA
Statistics
Matches: 168, Mismatches: 29, Indels: 27
0.75 0.13 0.12
Matches are distributed among these distances:
44 11 0.07
45 15 0.09
46 62 0.37
47 37 0.22
48 18 0.11
49 25 0.15
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.29
Consensus pattern (45 bp):
CATGTCCCAGACATGGTCTTACACTGGCTACATCACGAGCTAATG
Found at i:44079328 original size:94 final size:92
Alignment explanation
Indices: 44079087--44079352 Score: 292
Period size: 94 Copynumber: 2.8 Consensus size: 92
44079077 GGTAAAGTCT
* *
44079087 CGATGCCATGTCCTAGACATGGTCTTACACTGGCTATCATCTACGAGTCTGATGCCATGTACCAG
1 CGATGCCATGTCCTAGACATGGTCTTACACTGGCT-TCAT-AACGAGTCTGATG-CATGTCCCAG
*
44079152 ACATGGTCTTACACT-GACACATCTCGTAGC
63 ACAT-GTCTTACACTAGACACATCTCATAGC
* * * ** * *
44079182 CAATG-CATGTCCCAGACAT-GTCTTATACTGGCTTACATCCCGAGACTAATGCATGTCCCAGAC
1 CGATGCCATGTCCTAGACATGGTCTTACACTGGCTT-CATAACGAGTCTGATGCATGTCCCAGAC
44079245 ATGTCTTACACTAGA-ACTTATCTCA-ATGC
65 ATGTCTTACACTAGACAC--ATCTCATA-GC
* *
44079274 CGATGCCATGTCCTAGACATGGTCTTACACTGGCTCTCATAATGTGGTC-GATGCATGTCCCAGA
1 CGATGCCATGTCCTAGACATGGTCTTACACTGGCT-TCATAACG-AGTCTGATGCATGTCCCAGA
44079338 CATGTCTTACACTAG
64 CATGTCTTACACTAG
44079353 CTCACACAAA
Statistics
Matches: 144, Mismatches: 18, Indels: 19
0.80 0.10 0.10
Matches are distributed among these distances:
90 12 0.08
91 16 0.11
92 21 0.15
93 29 0.20
94 59 0.41
95 7 0.05
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (92 bp):
CGATGCCATGTCCTAGACATGGTCTTACACTGGCTTCATAACGAGTCTGATGCATGTCCCAGACA
TGTCTTACACTAGACACATCTCATAGC
Found at i:44083114 original size:46 final size:46
Alignment explanation
Indices: 44083047--44083221 Score: 201
Period size: 46 Copynumber: 3.8 Consensus size: 46
44083037 TGTAACCCGC
44083047 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGTCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGTCGTTCGCAT
* * * * *
44083093 CCATAAGTGAACTCGGACTCAACTCAATGAGCTCGGAT-GCCTAG-TT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG-TCG-TTCGCAT
* *** * * *
44083139 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGTTCGGTCGTTCGCAT
44083186 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
44083222 ATGCCCAAAC
Statistics
Matches: 102, Mismatches: 22, Indels: 10
0.76 0.16 0.07
Matches are distributed among these distances:
46 69 0.68
47 33 0.32
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.23
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGTCGTTCGCAT
Found at i:44083162 original size:93 final size:93
Alignment explanation
Indices: 44083055--44083226 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
44083045 GCCCATAAGT
* * *
44083055 GAACTCGGACTCAACTCAACGAGTTCGGTCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
44083120 TGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
44083148 GAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
44083213 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
44083227 CAAACATCCT
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:44083241 original size:46 final size:46
Alignment explanation
Indices: 44083052--44083241 Score: 142
Period size: 46 Copynumber: 4.1 Consensus size: 46
44083042 CCCGCCCATA
* * *
44083052 AGTGAACTCGGACTCAACTCAACGAGTTCGG-TCGTTCGCATCCAT--A
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGAT-G--CCCATACATCCT
* * *
44083098 AGTGAACTCGGACTCAACTCAATGAGCTCGGATGCCTAGTTACATCTCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCA--TACATC-CT
* * * * * *
44083147 --CGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCAT--A
1 AGTGAACTCGGACTCAACTCAACGAGTTC-G-GATGCCCATACATCCT
*
44083191 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAACATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCATACATCCT
44083237 AGTGA
1 AGTGA
44083242 CATGTCACTT
Statistics
Matches: 110, Mismatches: 22, Indels: 24
0.71 0.14 0.15
Matches are distributed among these distances:
44 10 0.09
45 1 0.01
46 65 0.59
47 29 0.26
48 1 0.01
49 4 0.04
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (46 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCATACATCCT
Found at i:44087674 original size:31 final size:31
Alignment explanation
Indices: 44087636--44087695 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
44087626 TTCATATTTC
*
44087636 ATATTTCATAACACTGGGCCGAAGCCTTTTT
1 ATATTTCATAACACTAGGCCGAAGCCTTTTT
**
44087667 ATATTTCATATTACTAGGCCGAAGCCTTT
1 ATATTTCATAACACTAGGCCGAAGCCTTT
44087696 ACTGTAAACG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.37
Consensus pattern (31 bp):
ATATTTCATAACACTAGGCCGAAGCCTTTTT
Found at i:44087935 original size:24 final size:24
Alignment explanation
Indices: 44087884--44088025 Score: 218
Period size: 24 Copynumber: 6.0 Consensus size: 24
44087874 CTGCTTTCGT
*
44087884 ATAACTGGAGGC-TTAGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
*
44087909 ATAACTGGGGCAAAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
44087933 ATAACTGGGGAATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
44087956 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
44087980 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
44088003 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
44088026 GCCCTTTTAA
Statistics
Matches: 109, Mismatches: 5, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
23 45 0.41
24 52 0.48
25 12 0.11
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:44087959 original size:23 final size:23
Alignment explanation
Indices: 44087905--44088024 Score: 204
Period size: 23 Copynumber: 5.1 Consensus size: 23
44087895 CTTAGCCTCT
*
44087905 TTTAATAACTGGGGCAAAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
*
44087928 TTTTAATAACTGGGGAATAAGCCC
1 -TTTAATAACTGGGGCATAAGCCC
44087952 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
44087975 TTTTAATAACTGGGGCATAAGCCC
1 -TTTAATAACTGGGGCATAAGCCC
44087999 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
44088022 TTT
1 TTT
44088025 TGCCCTTTTA
Statistics
Matches: 92, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
23 48 0.52
24 44 0.48
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (23 bp):
TTTAATAACTGGGGCATAAGCCC
Found at i:44087959 original size:47 final size:47
Alignment explanation
Indices: 44087905--44088025 Score: 224
Period size: 47 Copynumber: 2.6 Consensus size: 47
44087895 CTTAGCCTCT
*
44087905 TTTAATAACTGGGGCAAAAGCCCTTTTAATAACTGGGGAATAAGCCC
1 TTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGAATAAGCCC
*
44087952 TTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGAATAAGCCC
44087999 TTTAATAACTGGGGCATAAGCCCTTTT
1 TTTAATAACTGGGGCATAAGCCCTTTT
44088026 GCCCTTTTAA
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 72 1.00
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.29
Consensus pattern (47 bp):
TTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGAATAAGCCC
Found at i:44095999 original size:47 final size:46
Alignment explanation
Indices: 44095947--44096136 Score: 299
Period size: 47 Copynumber: 4.1 Consensus size: 46
44095937 CCTAGCCTCT
* *
44095947 TTTAATAACTGGGGCAAAAGCCCTTTTAATAACTAGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC-TTTAATAACTGGGGCATAAGCCC
44095994 TTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC-TTTAATAACTGGGGCATAAGCCC
*
44096041 TTTAATAACTGGGGCATAAGCCCTTTAATAATTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCCC
* * *
44096087 TTTTAATAACTGGGGCATAAGCCCTTTAATCACTGAGGCATAATCCC
1 -TTTAATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCCC
44096134 TTT
1 TTT
44096137 TGCACTTCCT
Statistics
Matches: 135, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
46 25 0.19
47 110 0.81
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (46 bp):
TTTAATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCCC
Found at i:44096001 original size:23 final size:23
Alignment explanation
Indices: 44095947--44096136 Score: 299
Period size: 23 Copynumber: 8.1 Consensus size: 23
44095937 CCTAGCCTCT
*
44095947 TTTAATAACTGGGGCAAAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
*
44095970 TTTTAATAACTAGGGCATAAGCCC
1 -TTTAATAACTGGGGCATAAGCCC
44095994 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
44096017 TTTTAATAACTGGGGCATAAGCCC
1 -TTTAATAACTGGGGCATAAGCCC
44096041 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
*
44096064 TTTAATAATTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
44096087 TTTTAATAACTGGGGCATAAGCCC
1 -TTTAATAACTGGGGCATAAGCCC
* * *
44096111 TTTAATCACTGAGGCATAATCCC
1 TTTAATAACTGGGGCATAAGCCC
44096134 TTT
1 TTT
44096137 TGCACTTCCT
Statistics
Matches: 156, Mismatches: 8, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
23 90 0.58
24 66 0.42
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (23 bp):
TTTAATAACTGGGGCATAAGCCC
Found at i:44096068 original size:70 final size:70
Alignment explanation
Indices: 44095926--44096136 Score: 325
Period size: 70 Copynumber: 3.0 Consensus size: 70
44095916 TTGCTTTCGT
* * *
44095926 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTTAATAACTAGGGCATAA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCATAAGCCC-TTTAATAACTGGGGCATAA
44095990 GCCCTTTA
63 GCCCTTTA
44095998 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCC
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCC
44096063 CTTTA
66 CTTTA
* * * *
44096068 ATAATTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTAATCACTGAGGCATAATCC
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCC
44096133 CTTT
66 CTTT
44096137 TGCACTTCCT
Statistics
Matches: 131, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
70 91 0.69
71 28 0.21
72 12 0.09
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (70 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCC
CTTTA
Found at i:44096137 original size:47 final size:48
Alignment explanation
Indices: 44095926--44096137 Score: 292
Period size: 47 Copynumber: 4.5 Consensus size: 48
44095916 TTGCTTTCGT
* *
44095926 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTTA
1 ATAACT-GAGGCATAAGCC-CTTTTAATAACTGGGGCATAAGCCCTTTTA
44095975 ATAACT-AGGGCATAAGCCC-TTTAATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGA-GGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTTA
*
44096022 ATAACTGGGGCATAAGCCC-TTTAATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGAGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTTA
* *
44096068 ATAATTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGAGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTTA
* *
44096115 ATCACTGAGGCATAATCCCTTTT
1 ATAACTGAGGCATAAGCCCTTTT
44096138 GCACTTCCTC
Statistics
Matches: 151, Mismatches: 8, Indels: 10
0.89 0.05 0.06
Matches are distributed among these distances:
46 22 0.15
47 114 0.75
48 5 0.03
49 10 0.07
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.29
Consensus pattern (48 bp):
ATAACTGAGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTTA
Found at i:44096212 original size:20 final size:20
Alignment explanation
Indices: 44096187--44096253 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
44096177 TTATGAATAC
44096187 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
44096207 ATCATGTGCATAGCATACAT
1 ATCATGTGCATATCATACAT
*
44096227 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
44096247 ACCATGT
1 ATCATGT
44096254 TTACTAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:44102763 original size:22 final size:21
Alignment explanation
Indices: 44102723--44102763 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
44102713 AAACATTTTC
*
44102723 AGATTAAATCAAATAAAAGAA
1 AGATTAAACCAAATAAAAGAA
*
44102744 AGATTAAACCCAAATCAAAG
1 AGATTAAA-CCAAATAAAAG
44102764 TGGCTGTCGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.61, C:0.12, G:0.10, T:0.17
Consensus pattern (21 bp):
AGATTAAACCAAATAAAAGAA
Found at i:44104938 original size:13 final size:13
Alignment explanation
Indices: 44104920--44104945 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
44104910 GTTGTAAAGA
44104920 AAGAGAGGTGAGT
1 AAGAGAGGTGAGT
44104933 AAGAGAGGTGAGT
1 AAGAGAGGTGAGT
44104946 CATTAAGACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.46, T:0.15
Consensus pattern (13 bp):
AAGAGAGGTGAGT
Found at i:44118685 original size:15 final size:15
Alignment explanation
Indices: 44118659--44118739 Score: 76
Period size: 15 Copynumber: 5.5 Consensus size: 15
44118649 ACAAAGATAA
*
44118659 CAAGAAAAAGAAATC
1 CAAGATAAAGAAATC
* *
44118674 CAAGATAGAGAAACC
1 CAAGATAAAGAAATC
*
44118689 CGA-ATAAAGAAATC
1 CAAGATAAAGAAATC
*
44118703 C-AGAATAAAGAGATC
1 CAAG-ATAAAGAAATC
* *
44118718 CAGGATAAAGAAACC
1 CAAGATAAAGAAATC
44118733 CAAGATA
1 CAAGATA
44118740 CGATACTATG
Statistics
Matches: 52, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
13 1 0.02
14 10 0.19
15 40 0.77
16 1 0.02
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (15 bp):
CAAGATAAAGAAATC
Found at i:44124506 original size:99 final size:100
Alignment explanation
Indices: 44124319--44124561 Score: 319
Period size: 99 Copynumber: 2.4 Consensus size: 100
44124309 TCTATTGTGA
* * * *
44124319 GGTCGCATGTGTAGCACTAAGTGCAGGCTACTATGCGTACCTGAAAACTGTGATCACGTGTGTAG
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGAAAACTGTGATCACGTGTGTAG
* * **
44124384 TACTAAGTGCAGGCTAGTACGTGTATCAGATGGTT
66 TACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * * *
44124419 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-T-TGGTCACGTGTGTA
1 -GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGAAAACTGTGATCACGTGTGTA
44124482 GTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
65 GTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * * *
44124518 GGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTAGCAGA
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGA
44124562 TAGCTTTGGC
Statistics
Matches: 124, Mismatches: 18, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
98 38 0.31
99 45 0.36
100 1 0.01
101 40 0.32
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (100 bp):
GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGAAAACTGTGATCACGTGTGTAG
TACTAAGTGCAGGCTACTACGTGTACCAGATAATT
Found at i:44124563 original size:49 final size:49
Alignment explanation
Indices: 44124326--44124550 Score: 306
Period size: 49 Copynumber: 4.5 Consensus size: 49
44124316 TGAGGTCGCA
* * * * * *
44124326 TGTGTAGCACTAAGTGCAGGCTACTATGCGTACCTGAAAACTGTGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-T-TGGTCACG
* * **
44124377 TGTGTAGTACTAAGTGCAGGCTAGTACGTGTATCAGATGGTTAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT-GGTCACG
44124427 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACG
* *
44124476 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACG
*
44124525 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
44124551 TGCGTAGCAG
Statistics
Matches: 156, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
49 80 0.51
50 45 0.29
51 31 0.20
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.29
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACG
Found at i:44132416 original size:14 final size:14
Alignment explanation
Indices: 44132397--44132425 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
44132387 TTTTGGAAAA
44132397 ATGATTGAATTAAG
1 ATGATTGAATTAAG
44132411 ATGATTGAATTAAG
1 ATGATTGAATTAAG
44132425 A
1 A
44132426 CAATACCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (14 bp):
ATGATTGAATTAAG
Found at i:44142643 original size:25 final size:25
Alignment explanation
Indices: 44142615--44142662 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
44142605 TTATACCATG
* * *
44142615 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
44142640 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
44142663 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:44142765 original size:20 final size:20
Alignment explanation
Indices: 44142705--44142765 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
44142695 ATAAATATGG
*
44142705 TATGTATGAGATGCACATGA
1 TATGTATGATATGCACATGA
*
44142725 CATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
44142745 TATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
44142765 T
1 T
44142766 GTAATCATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.33
Consensus pattern (20 bp):
TATGTATGATATGCACATGA
Found at i:44142842 original size:24 final size:24
Alignment explanation
Indices: 44142815--44142958 Score: 209
Period size: 24 Copynumber: 6.0 Consensus size: 24
44142805 GAGGAAGTGA
*
44142815 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
*
44142839 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
44142863 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
44142887 GAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* *
44142911 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
44142935 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
44142959 ATGATAAAGC
Statistics
Matches: 112, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
24 101 0.90
25 11 0.10
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:44143186 original size:30 final size:31
Alignment explanation
Indices: 44143126--44143188 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
44143116 CGTTTACAGT
44143126 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
44143157 AAAGGCTTCGGCCCAGTGTTATG-AATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
44143187 AA
1 AA
44143189 CATGAAAAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 9 0.30
31 21 0.70
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.24
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:44144463 original size:42 final size:42
Alignment explanation
Indices: 44144402--44144518 Score: 150
Period size: 42 Copynumber: 2.8 Consensus size: 42
44144392 TTAGGGTTAT
*
44144402 TGAGA-TTACGTGTACGACCATATCTGGGATATGGCATCGATA
1 TGAGACTTA-GTGTAAGACCATATCTGGGATATGGCATCGATA
* *
44144444 TGAGACTTAGTGTAAGACCATAGCTGGGCTATTGGCATCGATA
1 TGAGACTTAGTGTAAGACCATATCTGGGATA-TGGCATCGATA
* *
44144487 AGAGAC-CA-TGTAAGACCATATCTGGGATATGG
1 TGAGACTTAGTGTAAGACCATATCTGGGATATGG
44144519 AATTGGTATG
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
40 3 0.05
41 19 0.29
42 25 0.38
43 19 0.29
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.26
Consensus pattern (42 bp):
TGAGACTTAGTGTAAGACCATATCTGGGATATGGCATCGATA
Found at i:44148135 original size:28 final size:29
Alignment explanation
Indices: 44148103--44148217 Score: 137
Period size: 29 Copynumber: 4.0 Consensus size: 29
44148093 TACCTGTATC
* *
44148103 TGGCCCATTAAGCCC-AATCATATTCATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
*
44148131 TGGCCCATTAGGCCCAAATCACCTGT-ATA
1 TGGCCCATTAGGCCCAAATCACAT-TCATA
*
44148160 TGGCCCATTAGGCCCAAATCACATTTATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
* * *
44148189 TGGCCCGTTAGGCAC-AGTCACATTCATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
44148217 T
1 T
44148218 TCATGCTCAC
Statistics
Matches: 76, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
28 27 0.36
29 48 0.63
30 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.27
Consensus pattern (29 bp):
TGGCCCATTAGGCCCAAATCACATTCATA
Found at i:44148486 original size:24 final size:24
Alignment explanation
Indices: 44148436--44148486 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
44148426 GTAGCTAAAC
* * * *
44148436 TTTCGGCTTTTCGGCATTTTAGCT
1 TTTCGGCATTTCGACATTTCAGAT
44148460 TTTCGGCATTTCGACATTTCAGAT
1 TTTCGGCATTTCGACATTTCAGAT
44148484 TTT
1 TTT
44148487 GCCGATCCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.49
Consensus pattern (24 bp):
TTTCGGCATTTCGACATTTCAGAT
Found at i:44152660 original size:28 final size:29
Alignment explanation
Indices: 44152628--44152746 Score: 163
Period size: 29 Copynumber: 4.2 Consensus size: 29
44152618 CACATGCCTG
*
44152628 CATATGGCCCATTAAGCCC-AATCACATT
1 CATATGGCCCATTAGGCCCAAATCACATT
*
44152656 CATATGGCCCATTAGGCCCAAATCACCTGT
1 CATATGGCCCATTAGGCCCAAATCACAT-T
44152686 -ATATGGCCCATTAGGCCCAAATCACATT
1 CATATGGCCCATTAGGCCCAAATCACATT
* * *
44152714 TATATGGCCCGTTAGGCCC-AGTCACATT
1 CATATGGCCCATTAGGCCCAAATCACATT
44152742 CATAT
1 CATAT
44152747 TCATTCTCAC
Statistics
Matches: 82, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
28 31 0.38
29 50 0.61
30 1 0.01
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.26
Consensus pattern (29 bp):
CATATGGCCCATTAGGCCCAAATCACATT
Found at i:44159685 original size:89 final size:89
Alignment explanation
Indices: 44159534--44159706 Score: 321
Period size: 89 Copynumber: 1.9 Consensus size: 89
44159524 TTATAAATCA
44159534 ATATCATTAAACCAAATTTAACAAATCTCAATCACATGTACATTCATTATACTTATAAATTCATA
1 ATATCATTAAACCAAATTTAACAAATCTCAATCACATGTACATTCATTATACTTATAAATTCATA
44159599 GAACCACATTAAATAACTCGATTT
66 GAACCACATTAAATAACTCGATTT
*
44159623 ATATCATTAAACCAAATTTAACAAATCTCAGTCACATGTACATTCATTATACTTA-AACATTCAT
1 ATATCATTAAACCAAATTTAACAAATCTCAATCACATGTACATTCATTATACTTATAA-ATTCAT
44159687 AGAACCACATTAAATAACTC
65 AGAACCACATTAAATAACTC
44159707 CACTTATCTT
Statistics
Matches: 82, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
88 2 0.02
89 80 0.98
ACGTcount: A:0.44, C:0.20, G:0.03, T:0.32
Consensus pattern (89 bp):
ATATCATTAAACCAAATTTAACAAATCTCAATCACATGTACATTCATTATACTTATAAATTCATA
GAACCACATTAAATAACTCGATTT
Found at i:44160384 original size:43 final size:43
Alignment explanation
Indices: 44160336--44160478 Score: 205
Period size: 43 Copynumber: 3.3 Consensus size: 43
44160326 TTCAACGAAC
* * *
44160336 TCGCACATTTAGTGCTAATTAATTAACCAAAGCTATAATTGTA
1 TCGCACACTTAGTGCTAATTAATTAGCCGAAGCTATAATTGTA
** *
44160379 TCGCACACTTAGTGCCGATTAATTAGCTGAAGCTATAATTGTA
1 TCGCACACTTAGTGCTAATTAATTAGCCGAAGCTATAATTGTA
* **
44160422 TTGCACTGTTAGTGCTAATTAATTAGCCGAAGCTATAATTGTA
1 TCGCACACTTAGTGCTAATTAATTAGCCGAAGCTATAATTGTA
44160465 TCGCACACTTAGTG
1 TCGCACACTTAGTG
44160479 TCATTATATT
Statistics
Matches: 85, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 85 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (43 bp):
TCGCACACTTAGTGCTAATTAATTAGCCGAAGCTATAATTGTA
Found at i:44166914 original size:43 final size:43
Alignment explanation
Indices: 44166853--44166992 Score: 199
Period size: 43 Copynumber: 3.3 Consensus size: 43
44166843 AACGAACTCA
* * * *
44166853 CACACATAGTGCTAATTAATTAACCAAAGCTATAATTGTATCG
1 CACACTTAGTGCCAATTAATTAGCCGAAGCTATAATTGTATCG
* *
44166896 CACACTTAGTGCCAATTAATTAGCTGAAGCTATAATTGTATTG
1 CACACTTAGTGCCAATTAATTAGCCGAAGCTATAATTGTATCG
**
44166939 CACTGTTAGTGCCAATTAATTAGCCGAAGCTATAATTGTATCG
1 CACACTTAGTGCCAATTAATTAGCCGAAGCTATAATTGTATCG
*
44166982 TACACTTAGTG
1 CACACTTAGTG
44166993 TCATTATATT
Statistics
Matches: 84, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 84 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Consensus pattern (43 bp):
CACACTTAGTGCCAATTAATTAGCCGAAGCTATAATTGTATCG
Found at i:44168421 original size:13 final size:13
Alignment explanation
Indices: 44168403--44168428 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
44168393 GTTTGAGTTG
44168403 GTTCGTATGTGAT
1 GTTCGTATGTGAT
44168416 GTTCGTATGTGAT
1 GTTCGTATGTGAT
44168429 AGATGGTAGC
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:0.15, C:0.08, G:0.31, T:0.46
Consensus pattern (13 bp):
GTTCGTATGTGAT
Found at i:44175402 original size:33 final size:31
Alignment explanation
Indices: 44175355--44175415 Score: 95
Period size: 33 Copynumber: 1.9 Consensus size: 31
44175345 AGACTTGTCC
*
44175355 AAAATAAATCAATAAATTAAAAGACCAAATAAT
1 AAAATAAATAAAT-AATTAAAA-ACCAAATAAT
44175388 AAAATAAATAAATAATTAAAAACCAAAT
1 AAAATAAATAAATAATTAAAAACCAAAT
44175416 TATCAAAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 7 0.26
32 8 0.30
33 12 0.44
ACGTcount: A:0.69, C:0.08, G:0.02, T:0.21
Consensus pattern (31 bp):
AAAATAAATAAATAATTAAAAACCAAATAAT
Found at i:44175428 original size:31 final size:33
Alignment explanation
Indices: 44175355--44175428 Score: 89
Period size: 31 Copynumber: 2.3 Consensus size: 33
44175345 AGACTTGTCC
* *
44175355 AAAATAAATCAATAAATTAAAAGACCAAATAAT
1 AAAAGAAATAAATAAATTAAAAGACCAAATAAT
* *
44175388 AAAATAAATAAAT-AATTAAAA-ACCAAATTAT
1 AAAAGAAATAAATAAATTAAAAGACCAAATAAT
*
44175419 CAAAGAAATA
1 AAAAGAAATA
44175429 TTTTAAAATG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
31 17 0.46
32 8 0.22
33 12 0.32
ACGTcount: A:0.68, C:0.08, G:0.03, T:0.22
Consensus pattern (33 bp):
AAAAGAAATAAATAAATTAAAAGACCAAATAAT
Found at i:44176076 original size:36 final size:36
Alignment explanation
Indices: 44176036--44176108 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
44176026 TTTTCTGGGC
44176036 TACCTAGTACTTTTCCGAATAGGAGTGCTATGGCTT
1 TACCTAGTACTTTTCCGAATAGGAGTGCTATGGCTT
44176072 TACCTAGTACTTTTCCGAATAGGAGTGCTATGGCTT
1 TACCTAGTACTTTTCCGAATAGGAGTGCTATGGCTT
44176108 T
1 T
44176109 CACGTGCTCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (36 bp):
TACCTAGTACTTTTCCGAATAGGAGTGCTATGGCTT
Found at i:44181866 original size:25 final size:25
Alignment explanation
Indices: 44181820--44181870 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
44181810 CCCTTATAAT
* *
44181820 GTGAAAATGACCTTTTTGCCCCTAG
1 GTGAAAATGACCTTTATACCCCTAG
44181845 GTGAAAATGA-CTATTATACCCCTAG
1 GTGAAAATGACCT-TTATACCCCTAG
44181870 G
1 G
44181871 GTTATGTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 2 0.09
25 21 0.91
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (25 bp):
GTGAAAATGACCTTTATACCCCTAG
Found at i:44181925 original size:10 final size:10
Alignment explanation
Indices: 44181914--44181958 Score: 63
Period size: 10 Copynumber: 4.4 Consensus size: 10
44181904 TTTCTACATA
*
44181914 ATATGCCATA
1 ATATGCCATG
44181924 ATATGCCATG
1 ATATGCCATG
*
44181934 ATATACACATG
1 ATATGC-CATG
44181945 ATATGCCATG
1 ATATGCCATG
44181955 ATAT
1 ATAT
44181959 ATATATATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
10 22 0.71
11 9 0.29
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (10 bp):
ATATGCCATG
Found at i:44181962 original size:2 final size:2
Alignment explanation
Indices: 44181955--44181982 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
44181945 ATATGCCATG
44181955 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
44181983 GCATGGGTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44182089 original size:24 final size:25
Alignment explanation
Indices: 44182019--44182087 Score: 102
Period size: 25 Copynumber: 2.8 Consensus size: 25
44182009 AGGAAGTGCT
* * *
44182019 AAAGGGCTATGCCCCAGTTTACCGA
1 AAAGGGCTTTGCCCCAGTTTATCAA
44182044 AAAGGGCTTTGCCCCAGTTTATCAA
1 AAAGGGCTTTGCCCCAGTTTATCAA
*
44182069 AAAGGGCTTTACCCCAGTT
1 AAAGGGCTTTGCCCCAGTT
44182088 ATTAAAAGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.25
Consensus pattern (25 bp):
AAAGGGCTTTGCCCCAGTTTATCAA
Found at i:44182100 original size:24 final size:25
Alignment explanation
Indices: 44182030--44182100 Score: 76
Period size: 25 Copynumber: 2.9 Consensus size: 25
44182020 AAGGGCTATG
* *
44182030 CCCCAGTTTACCGAAAAG-GGCTTTG
1 CCCCAGTTTATC-AAAAGAGGCTTTA
44182055 CCCCAGTTTATCAAAA-AGGGCTTTA
1 CCCCAGTTTATCAAAAGA-GGCTTTA
*
44182080 CCCCAG-TTATTAAAAGAGGCT
1 CCCCAGTTTATCAAAAGAGGCT
44182101 AGGCCTCCAG
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
24 16 0.40
25 24 0.60
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (25 bp):
CCCCAGTTTATCAAAAGAGGCTTTA
Found at i:44182345 original size:31 final size:32
Alignment explanation
Indices: 44182307--44182381 Score: 118
Period size: 31 Copynumber: 2.4 Consensus size: 32
44182297 CATTTACAGT
*
44182307 AAAGGCTTCGGCCCAGTTGTATGAATAATG-A
1 AAAGGCTTCGGCCCAGTGGTATGAATAATGTA
44182338 AAAGGCTTCGGCCCAGTGGTATGAATAATGTA
1 AAAGGCTTCGGCCCAGTGGTATGAATAATGTA
*
44182370 AAA-GCATCGGCC
1 AAAGGCTTCGGCC
44182382 TAGTATATGC
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
31 37 0.90
32 4 0.10
ACGTcount: A:0.32, C:0.19, G:0.27, T:0.23
Consensus pattern (32 bp):
AAAGGCTTCGGCCCAGTGGTATGAATAATGTA
Found at i:44183746 original size:30 final size:30
Alignment explanation
Indices: 44183706--44183766 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
44183696 TTCCCGAGCC
*
44183706 TAGGGACAAAAGTGTAATTATGCAAAAGTT
1 TAGGGACAAAAATGTAATTATGCAAAAGTT
* * *
44183736 TAGGGGCAAAAATGTAATTTTGCCAAAGTT
1 TAGGGACAAAAATGTAATTATGCAAAAGTT
44183766 T
1 T
44183767 GTATTAAATG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.39, C:0.08, G:0.23, T:0.30
Consensus pattern (30 bp):
TAGGGACAAAAATGTAATTATGCAAAAGTT
Found at i:44187818 original size:29 final size:28
Alignment explanation
Indices: 44187730--44187831 Score: 89
Period size: 29 Copynumber: 3.5 Consensus size: 28
44187720 TACTCAATCA
* *
44187730 CGCACACTTAGTGCCACGT-GATTCAAGCC
1 CGCACACTTAGTG-C-CGTACATTCAAGCT
* * * * *
44187759 CGCACACATAGTGCCATATAGTCCAAACT
1 CGCACACTTAGTGCCGTACA-TTCAAGCT
44187788 CGCACACTTAGTGCCGTACATTACAAGCT
1 CGCACACTTAGTGCCGTACATT-CAAGCT
*
44187817 CGCACACTCAGTGCC
1 CGCACACTTAGTGCC
44187832 AATCTCGTCA
Statistics
Matches: 58, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
27 2 0.03
28 3 0.05
29 53 0.91
ACGTcount: A:0.27, C:0.34, G:0.18, T:0.21
Consensus pattern (28 bp):
CGCACACTTAGTGCCGTACATTCAAGCT
Found at i:44195772 original size:29 final size:28
Alignment explanation
Indices: 44195684--44195785 Score: 89
Period size: 29 Copynumber: 3.5 Consensus size: 28
44195674 TACTCAATCA
* *
44195684 CGCACACTTAGTGCCACGT-GATTCAAGCC
1 CGCACACTTAGTG-C-CGTACATTCAAGCT
* * * * *
44195713 CGCACACATAGTGCCATATAGTCCAAACT
1 CGCACACTTAGTGCCGTACA-TTCAAGCT
44195742 CGCACACTTAGTGCCGTACATTACAAGCT
1 CGCACACTTAGTGCCGTACATT-CAAGCT
*
44195771 CGCACACTCAGTGCC
1 CGCACACTTAGTGCC
44195786 AATCTCGTCA
Statistics
Matches: 58, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
27 2 0.03
28 3 0.05
29 53 0.91
ACGTcount: A:0.27, C:0.34, G:0.18, T:0.21
Consensus pattern (28 bp):
CGCACACTTAGTGCCGTACATTCAAGCT
Found at i:44203770 original size:11 final size:10
Alignment explanation
Indices: 44203738--44203782 Score: 65
Period size: 10 Copynumber: 4.4 Consensus size: 10
44203728 TTTGTACATA
44203738 ATATGCCAT-
1 ATATGCCATG
44203747 ATTATGCCATG
1 A-TATGCCATG
44203758 ATATGCACATG
1 ATATGC-CATG
44203769 ATATGCCATG
1 ATATGCCATG
44203779 ATAT
1 ATAT
44203783 ATATATATGC
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
9 1 0.03
10 21 0.64
11 11 0.33
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (10 bp):
ATATGCCATG
Found at i:44203902 original size:24 final size:25
Alignment explanation
Indices: 44203827--44203895 Score: 95
Period size: 25 Copynumber: 2.8 Consensus size: 25
44203817 AGGAAGTGCT
* *
44203827 AAAGGGCTATGCCCCAGTTTACCG-A
1 AAAGGGCTTTGCCCCAGTTTA-TGAA
44203852 AAAGGGCTTTGCCCCAGTTTATGAA
1 AAAGGGCTTTGCCCCAGTTTATGAA
*
44203877 AAAGGGCTTTGCCCTAGTT
1 AAAGGGCTTTGCCCCAGTT
44203896 ATTAAAAGAG
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
24 1 0.03
25 39 0.98
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.26
Consensus pattern (25 bp):
AAAGGGCTTTGCCCCAGTTTATGAA
Found at i:44203908 original size:24 final size:25
Alignment explanation
Indices: 44203827--44203908 Score: 82
Period size: 25 Copynumber: 3.4 Consensus size: 25
44203817 AGGAAGTGCT
* *
44203827 AAAG-GGCTATGCCCCAGTTTACCGA
1 AAAGAGGCTTTGCCCCAGTTTA-TGA
44203852 AAAG-GGCTTTGCCCCAGTTTATGA
1 AAAGAGGCTTTGCCCCAGTTTATGA
* *
44203876 AAA-AGGGCTTTGCCCTAG-TTATTA
1 AAAGA-GGCTTTGCCCCAGTTTATGA
44203900 AAAGAGGCT
1 AAAGAGGCT
44203909 AGGCCTCCAG
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
24 17 0.34
25 33 0.66
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (25 bp):
AAAGAGGCTTTGCCCCAGTTTATGA
Found at i:44204155 original size:31 final size:31
Alignment explanation
Indices: 44204117--44204195 Score: 140
Period size: 31 Copynumber: 2.5 Consensus size: 31
44204107 CGTTTATAGT
44204117 AAAGGCTTTGGCCCAGTGGTATGAATAATGA
1 AAAGGCTTTGGCCCAGTGGTATGAATAATGA
*
44204148 AAAGGCTTTGGCCCAGTGGTATGAATAATGT
1 AAAGGCTTTGGCCCAGTGGTATGAATAATGA
*
44204179 AAAGGCTTCGGCCCAGT
1 AAAGGCTTTGGCCCAGT
44204196 ATATGCTGAG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (31 bp):
AAAGGCTTTGGCCCAGTGGTATGAATAATGA
Found at i:44206015 original size:25 final size:25
Alignment explanation
Indices: 44205952--44206040 Score: 79
Period size: 25 Copynumber: 3.6 Consensus size: 25
44205942 CATGTACATG
* ** * *
44205952 TATGCTCATACGAGCTGCAAATTGG
1 TATGCTCACACGAGCTATAAATCGA
* * * *
44205977 TATACTCACTCGAGCTGTAGATCGA
1 TATGCTCACACGAGCTATAAATCGA
* *
44206002 TATGCTCTCACGAGCTATAAATCGG
1 TATGCTCACACGAGCTATAAATCGA
44206027 TATGCTCACACGAG
1 TATGCTCACACGAG
44206041 TAATGTGTAA
Statistics
Matches: 50, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
25 50 1.00
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.27
Consensus pattern (25 bp):
TATGCTCACACGAGCTATAAATCGA
Found at i:44207358 original size:43 final size:42
Alignment explanation
Indices: 44207263--44207385 Score: 131
Period size: 43 Copynumber: 2.9 Consensus size: 42
44207253 ACTGAGATGT
* * * *
44207263 GATTACATGCAAGACCATGTTTGGGACATTGGCATTGTATTGA
1 GATTACGTGTAAGACCATGTATGGGACATTGGCATCGTATT-A
*
44207306 GATTACGTGTAAGACCATGTCTGGGACATTGGCATCGTTAATT-
1 GATTACGTGTAAGACCATGTATGGGACATTGGCATCG-T-ATTA
* * * *
44207349 GATTTCGTGTAAGACCTTGTATGGGATAGTGGCATCG
1 GATTACGTGTAAGACCATGTATGGGACATTGGCATCG
44207386 ATATGTGTTA
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
43 65 0.94
44 1 0.01
45 3 0.04
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.33
Consensus pattern (42 bp):
GATTACGTGTAAGACCATGTATGGGACATTGGCATCGTATTA
Found at i:44212051 original size:27 final size:27
Alignment explanation
Indices: 44212021--44212086 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
44212011 TAGTTTACCA
* * * *
44212021 AATTACTGAAATATCCCTATAAGGTAG
1 AATTACCGAAATACCCCCAGAAGGTAG
*
44212048 AATTACCGAAATACCCCCAGAAGGTTG
1 AATTACCGAAATACCCCCAGAAGGTAG
44212075 AATTACCGAAAT
1 AATTACCGAAAT
44212087 TGTAACACCC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (27 bp):
AATTACCGAAATACCCCCAGAAGGTAG
Found at i:44213532 original size:40 final size:40
Alignment explanation
Indices: 44213486--44213596 Score: 147
Period size: 40 Copynumber: 2.8 Consensus size: 40
44213476 ATAACCACGT
*
44213486 GCACGAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCACGAATGCCTTCGGGTCTTAGCCCGGATAGAA-GCACTA
*
44213526 GCACGAATGCCTTCGGGTCTTAGCCCGGAT-GTAGCCACTA
1 GCACGAATGCCTTCGGGTCTTAGCCCGGATAGAAG-CACTA
*
44213566 GCAC-AATTGCCTTCGGGTCTTAACCCGGATA
1 GCACGAA-TGCCTTCGGGTCTTAGCCCGGATA
44213597 TAATTTCCAG
Statistics
Matches: 64, Mismatches: 3, Indels: 7
0.86 0.04 0.09
Matches are distributed among these distances:
38 1 0.02
39 4 0.06
40 59 0.92
ACGTcount: A:0.22, C:0.29, G:0.26, T:0.23
Consensus pattern (40 bp):
GCACGAATGCCTTCGGGTCTTAGCCCGGATAGAAGCACTA
Found at i:44220982 original size:40 final size:40
Alignment explanation
Indices: 44220937--44221047 Score: 147
Period size: 40 Copynumber: 2.8 Consensus size: 40
44220927 ATAACCACGT
*
44220937 GCACGAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCACGAATGCCTTCGGGTCTTAGCCCGGATAGAA-GCACTA
*
44220977 GCACGAATGCCTTCGGGTCTTAGCCCGGAT-GTAGCCACTA
1 GCACGAATGCCTTCGGGTCTTAGCCCGGATAGAAG-CACTA
*
44221017 GCAC-AATTGCCTTCGGGTCTTAACCCGGATA
1 GCACGAA-TGCCTTCGGGTCTTAGCCCGGATA
44221048 TAATTTCCAG
Statistics
Matches: 64, Mismatches: 3, Indels: 7
0.86 0.04 0.09
Matches are distributed among these distances:
38 1 0.02
39 4 0.06
40 59 0.92
ACGTcount: A:0.22, C:0.29, G:0.26, T:0.23
Consensus pattern (40 bp):
GCACGAATGCCTTCGGGTCTTAGCCCGGATAGAAGCACTA
Found at i:44222532 original size:27 final size:27
Alignment explanation
Indices: 44222493--44223172 Score: 791
Period size: 27 Copynumber: 25.3 Consensus size: 27
44222483 GGCTGTCACA
44222493 GAAATACCCCTGTAAGGTAGAATTACT
1 GAAATACCCCTGTAAGGTAGAATTACT
* *
44222520 TAAATACCCCTGTAAGGTAGAATTACC
1 GAAATACCCCTGTAAGGTAGAATTACT
* * *
44222547 AAAATACCCCTATAAGGTAGAATTACC
1 GAAATACCCCTGTAAGGTAGAATTACT
* * *
44222574 GGAATACCCCTATAGGGTAGAATTACT
1 GAAATACCCCTGTAAGGTAGAATTACT
* * *
44222601 AAAATAACCCTGTAAGGTAGAATTACC
1 GAAATACCCCTGTAAGGTAGAATTACT
*
44222628 GAAATACCCCTGTATGGTAGAATTACT
1 GAAATACCCCTGTAAGGTAGAATTACT
*
44222655 GAAATACCCCTGTAAGGTAGAATTACC
1 GAAATACCCCTGTAAGGTAGAATTACT
* * * * *
44222682 AAAATACCCTTATAGGGTAAAATTACT
1 GAAATACCCCTGTAAGGTAGAATTACT
* * *
44222709 AAAATACCCTTGTAAAGTAGAATTACT
1 GAAATACCCCTGTAAGGTAGAATTACT
44222736 GAAATACCCCTGT-AGTGTAGAATTACT
1 GAAATACCCCTGTAAG-GTAGAATTACT
* * *
44222763 AAAATACCCTTGTAAGGTAGAATTACC
1 GAAATACCCCTGTAAGGTAGAATTACT
* * *
44222790 GAAATACCCGTGTAGGGTAAAATTACT
1 GAAATACCCCTGTAAGGTAGAATTACT
*
44222817 GAAATA-CCCTGTAAGGTAGAATTACC
1 GAAATACCCCTGTAAGGTAGAATTACT
* * *
44222843 GAAATACCTCTGTAGGGTAAAATTACT
1 GAAATACCCCTGTAAGGTAGAATTACT
* *
44222870 AAAATA-CCCTGTAAGGTAGAATTACC
1 GAAATACCCCTGTAAGGTAGAATTACT
* * * ** *
44222896 AAAATATCCCTATAATATAGAATTACC
1 GAAATACCCCTGTAAGGTAGAATTACT
*
44222923 GAAATACCCCTATAAGGTAGAATTACT
1 GAAATACCCCTGTAAGGTAGAATTACT
* *
44222950 GAAATACCCCTGTAGGGTAGAATTATT
1 GAAATACCCCTGTAAGGTAGAATTACT
*
44222977 GAAATACCCCTGTAAAGTAGAATTA-T
1 GAAATACCCCTGTAAGGTAGAATTACT
*
44223003 CGAAATACCCCTGTAGGGTAGAATTACT
1 -GAAATACCCCTGTAAGGTAGAATTACT
* *
44223031 GAAATACCCCCGTAAGGTAGAATTACC
1 GAAATACCCCTGTAAGGTAGAATTACT
*
44223058 GAAATACCCCTGTAGGGTAGAATTACT
1 GAAATACCCCTGTAAGGTAGAATTACT
*
44223085 GAAATACCCC-GTAGGGTAGAATTA-T
1 GAAATACCCCTGTAAGGTAGAATTACT
* *
44223110 CGAAATACCCTTGT-AGTGTAGAAATACT
1 -GAAATACCCCTGTAAG-GTAGAATTACT
* *
44223138 G-AATACCCCTGTAGGGTAGAATTACC
1 GAAATACCCCTGTAAGGTAGAATTACT
*
44223164 GAGATACCC
1 GAAATACCC
44223173 TCGTGGGGCA
Statistics
Matches: 558, Mismatches: 83, Indels: 24
0.84 0.12 0.04
Matches are distributed among these distances:
25 1 0.00
26 90 0.16
27 463 0.83
28 4 0.01
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (27 bp):
GAAATACCCCTGTAAGGTAGAATTACT
Found at i:44222580 original size:54 final size:54
Alignment explanation
Indices: 44222493--44223172 Score: 909
Period size: 54 Copynumber: 12.7 Consensus size: 54
44222483 GGCTGTCACA
** * *
44222493 GAAATACCCCTGTAAGGTAGAATTACTTAAATACCCCTGTAAGGTAGAATTACC
1 GAAATACCCCTGTAAGGTAGAATTACCGAAATACCCCTGTAGGGTAGAATTACT
* * * *
44222547 AAAATACCCCTATAAGGTAGAATTACCGGAATACCCCTATAGGGTAGAATTACT
1 GAAATACCCCTGTAAGGTAGAATTACCGAAATACCCCTGTAGGGTAGAATTACT
* * *
44222601 AAAATAACCCTGTAAGGTAGAATTACCGAAATACCCCTGTATGGTAGAATTACT
1 GAAATACCCCTGTAAGGTAGAATTACCGAAATACCCCTGTAGGGTAGAATTACT
* * * *
44222655 GAAATACCCCTGTAAGGTAGAATTACCAAAATACCCTTATAGGGTAAAATTACT
1 GAAATACCCCTGTAAGGTAGAATTACCGAAATACCCCTGTAGGGTAGAATTACT
* * * * *
44222709 AAAATACCCTTGTAAAGTAGAATTACTGAAATACCCCTGTAGTGTAGAATTACT
1 GAAATACCCCTGTAAGGTAGAATTACCGAAATACCCCTGTAGGGTAGAATTACT
* * * *
44222763 AAAATACCCTTGTAAGGTAGAATTACCGAAATACCCGTGTAGGGTAAAATTACT
1 GAAATACCCCTGTAAGGTAGAATTACCGAAATACCCCTGTAGGGTAGAATTACT
* *
44222817 GAAATA-CCCTGTAAGGTAGAATTACCGAAATACCTCTGTAGGGTAAAATTACT
1 GAAATACCCCTGTAAGGTAGAATTACCGAAATACCCCTGTAGGGTAGAATTACT
* * * * *** *
44222870 AAAATA-CCCTGTAAGGTAGAATTACCAAAATATCCCTATAATATAGAATTACC
1 GAAATACCCCTGTAAGGTAGAATTACCGAAATACCCCTGTAGGGTAGAATTACT
* * *
44222923 GAAATACCCCTATAAGGTAGAATTACTGAAATACCCCTGTAGGGTAGAATTATT
1 GAAATACCCCTGTAAGGTAGAATTACCGAAATACCCCTGTAGGGTAGAATTACT
* *
44222977 GAAATACCCCTGTAAAGTAGAATTATCGAAATACCCCTGTAGGGTAGAATTACT
1 GAAATACCCCTGTAAGGTAGAATTACCGAAATACCCCTGTAGGGTAGAATTACT
*
44223031 GAAATACCCCCGTAAGGTAGAATTACCGAAATACCCCTGTAGGGTAGAATTACT
1 GAAATACCCCTGTAAGGTAGAATTACCGAAATACCCCTGTAGGGTAGAATTACT
* * * * *
44223085 GAAATACCCC-GTAGGGTAGAATTATCGAAATACCCTTGTAGTGTAGAAATACT
1 GAAATACCCCTGTAAGGTAGAATTACCGAAATACCCCTGTAGGGTAGAATTACT
* *
44223138 G-AATACCCCTGTAGGGTAGAATTACCGAGATACCC
1 GAAATACCCCTGTAAGGTAGAATTACCGAAATACCC
44223173 TCGTGGGGCA
Statistics
Matches: 550, Mismatches: 74, Indels: 5
0.87 0.12 0.01
Matches are distributed among these distances:
52 8 0.01
53 154 0.28
54 388 0.71
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (54 bp):
GAAATACCCCTGTAAGGTAGAATTACCGAAATACCCCTGTAGGGTAGAATTACT
Found at i:44223782 original size:25 final size:24
Alignment explanation
Indices: 44223754--44223821 Score: 73
Period size: 27 Copynumber: 2.7 Consensus size: 24
44223744 ATTCTGTTAA
*
44223754 GTGGCTTTACCACAATCTGATTCTG
1 GTGGCTATACCACAATCTG-TTCTG
*
44223779 GTGGCTATGCCACAAATATCTGTTCTG
1 GTGGCTATACCAC--A-ATCTGTTCTG
*
44223806 GTGGCTCTACCACAAT
1 GTGGCTATACCACAAT
44223822 ATCCGTATCT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
24 2 0.06
25 12 0.33
27 17 0.47
28 5 0.14
ACGTcount: A:0.22, C:0.25, G:0.21, T:0.32
Consensus pattern (24 bp):
GTGGCTATACCACAATCTGTTCTG
Found at i:44223809 original size:27 final size:26
Alignment explanation
Indices: 44223768--44223859 Score: 103
Period size: 27 Copynumber: 3.4 Consensus size: 26
44223758 CTTTACCACA
*
44223768 ATCTGATTCTGGTGGCTATGCCACAAAT
1 ATCTG-TTCTGGTGGCTCTGCCAC-AAT
*
44223796 ATCTGTTCTGGTGGCTCTACCACAAT
1 ATCTGTTCTGGTGGCTCTGCCACAAT
* * * *
44223822 ATCCGTATCTGGTGACTCTGTCATAAT
1 ATCTGT-TCTGGTGGCTCTGCCACAAT
44223849 ATCTGTTCTGG
1 ATCTGTTCTGG
44223860 CAGCCATGCT
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
26 13 0.24
27 37 0.67
28 5 0.09
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.36
Consensus pattern (26 bp):
ATCTGTTCTGGTGGCTCTGCCACAAT
Found at i:44224006 original size:6 final size:6
Alignment explanation
Indices: 44223977--44224061 Score: 57
Period size: 6 Copynumber: 13.8 Consensus size: 6
44223967 TTGCATTCAC
* * *
44223977 ATTCTG ATTTTG ATTCTA ATTCTG ATTCTG -TCACCTG ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG
* * * *
44224026 -TCACCTG AATCTG ATTCTG ATTCTC ATTTTG ATTCT
1 AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCT
44224062 AGTTATGATA
Statistics
Matches: 59, Mismatches: 14, Indels: 12
0.69 0.16 0.14
Matches are distributed among these distances:
5 2 0.03
6 50 0.85
7 6 0.10
8 1 0.02
ACGTcount: A:0.19, C:0.20, G:0.13, T:0.48
Consensus pattern (6 bp):
ATTCTG
Found at i:44224019 original size:19 final size:19
Alignment explanation
Indices: 44223995--44224044 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
44223985 TTTGATTCTA
44223995 ATTCTGATTCTGTCACCTG
1 ATTCTGATTCTGTCACCTG
44224014 ATTCTGATTCTGTCACCTG
1 ATTCTGATTCTGTCACCTG
*
44224033 AATCTGATTCTG
1 ATTCTGATTCTG
44224045 ATTCTCATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.18, C:0.24, G:0.16, T:0.42
Consensus pattern (19 bp):
ATTCTGATTCTGTCACCTG
Found at i:44228042 original size:43 final size:44
Alignment explanation
Indices: 44227945--44228066 Score: 131
Period size: 43 Copynumber: 2.8 Consensus size: 44
44227935 ACCGAGATGT
* * * *
44227945 GATTACATGCAAGACCATGTATGGGACATTGGCA-CTGTATTGA
1 GATTACCTGTAAGACCATGTATGGGACATTGGCATCTGTAATCA
* *
44227988 GATTACCTGTAAGACCATGTTTGGGACATTGGCATCTTTAATCA
1 GATTACCTGTAAGACCATGTATGGGACATTGGCATCTGTAATCA
* * * * *
44228032 -ATTTCTTGTAAGACCCTGTCTAGGACATTGGCATC
1 GATTACCTGTAAGACCATGTATGGGACATTGGCATC
44228067 GATATGTGTT
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
43 61 0.91
44 6 0.09
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (44 bp):
GATTACCTGTAAGACCATGTATGGGACATTGGCATCTGTAATCA
Found at i:44237579 original size:2 final size:2
Alignment explanation
Indices: 44237572--44237599 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
44237562 GAATTCATTC
44237572 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
44237600 TTCGTGCCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44237874 original size:39 final size:39
Alignment explanation
Indices: 44237815--44237977 Score: 218
Period size: 39 Copynumber: 4.2 Consensus size: 39
44237805 TTTAACCCGA
* ** *
44237815 ATATTTTTCCAGCACGTAGCCTGCGGACCTCAAGTCCGG
1 ATATTTTTCTAGCATATAGCCTGCGGACCTCATGTCCGG
* * *
44237854 ATATATTTCTAGCATATAGCCTGCAGACCTCATGTCCAG
1 ATATTTTTCTAGCATATAGCCTGCGGACCTCATGTCCGG
* * * * *
44237893 ATATTTTTCCAGCATATAGCCTGTGGACCTTATGTTCGA
1 ATATTTTTCTAGCATATAGCCTGCGGACCTCATGTCCGG
44237932 ATATTTTTCTAGCATATAGCCTGCGGACCTCATGTCCGG
1 ATATTTTTCTAGCATATAGCCTGCGGACCTCATGTCCGG
44237971 ATATTTT
1 ATATTTT
44237978 CAATCTCATA
Statistics
Matches: 104, Mismatches: 20, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 104 1.00
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.34
Consensus pattern (39 bp):
ATATTTTTCTAGCATATAGCCTGCGGACCTCATGTCCGG
Found at i:44248212 original size:38 final size:38
Alignment explanation
Indices: 44248161--44248237 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
44248151 TCCAAAATCA
44248161 AGCAATTCATGCTATGTTAGTTTCAAGTACAATTCAGT
1 AGCAATTCATGCTATGTTAGTTTCAAGTACAATTCAGT
44248199 AGCAATTCATGCTATGTTAGTTTCAAGTACAATTCAGT
1 AGCAATTCATGCTATGTTAGTTTCAAGTACAATTCAGT
44248237 A
1 A
44248238 CATACATTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (38 bp):
AGCAATTCATGCTATGTTAGTTTCAAGTACAATTCAGT
Found at i:44249810 original size:21 final size:21
Alignment explanation
Indices: 44249771--44249811 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
44249761 AATAATTTGA
** *
44249771 ATAAATTTTATGTATTTTAAT
1 ATAAATTTTATAAAATTTAAT
44249792 ATAAATTTTATAAAATTTAA
1 ATAAATTTTATAAAATTTAA
44249812 AAATTTTCTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
ATAAATTTTATAAAATTTAAT
Found at i:44249877 original size:18 final size:18
Alignment explanation
Indices: 44249850--44249884 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
44249840 AATATTTTTA
44249850 TAATTCTTTATAAATTTC
1 TAATTCTTTATAAATTTC
* *
44249868 TAATTTTTTATGAATTT
1 TAATTCTTTATAAATTT
44249885 TATAATTTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.60
Consensus pattern (18 bp):
TAATTCTTTATAAATTTC
Found at i:44249982 original size:32 final size:30
Alignment explanation
Indices: 44249937--44250019 Score: 76
Period size: 32 Copynumber: 2.7 Consensus size: 30
44249927 TTCTTTTACT
* *
44249937 TAAATAATAAATTAAGTCCTCATAAAATAA
1 TAAAAAATCAATTAAGTCCTCATAAAATAA
* * **
44249967 CTAAAAAAATCAATTAAATCATTGTAAAATAA
1 -T-AAAAAATCAATTAAGTCCTCATAAAATAA
* *
44249999 TGAAAAATCAATTAAGCCCTC
1 TAAAAAATCAATTAAGTCCTC
44250020 CACGCCAATC
Statistics
Matches: 40, Mismatches: 11, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
30 15 0.38
31 2 0.05
32 23 0.57
ACGTcount: A:0.54, C:0.13, G:0.05, T:0.28
Consensus pattern (30 bp):
TAAAAAATCAATTAAGTCCTCATAAAATAA
Found at i:44253132 original size:30 final size:30
Alignment explanation
Indices: 44253098--44253156 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
44253088 CATCTGATAG
44253098 TTAACTTGCAATAAAGTGAGATCTTTTTTT
1 TTAACTTGCAATAAAGTGAGATCTTTTTTT
*
44253128 TTAACTTGTAATAAAGTGAGATCTTTTTT
1 TTAACTTGCAATAAAGTGAGATCTTTTTT
44253157 GAACTTTTGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.31, C:0.08, G:0.14, T:0.47
Consensus pattern (30 bp):
TTAACTTGCAATAAAGTGAGATCTTTTTTT
Found at i:44253544 original size:98 final size:98
Alignment explanation
Indices: 44253375--44253567 Score: 341
Period size: 98 Copynumber: 2.0 Consensus size: 98
44253365 TAACTTTATT
* * * *
44253375 TAAGGATTCACTCATTTTTTTGCGTTGTGGTGGAGCAATTGGAACATATACACATATGCAAAAAT
1 TAAGGATTCACTCATCTTTGTGCGTTGTGATAGAGCAATTGGAACATATACACATATGCAAAAAT
*
44253440 TTACTGTCGATGTTACACGGTCTAGGCTATTTA
66 TTACTGTCGATGTTACACAGTCTAGGCTATTTA
44253473 TAAGGATTCACTCATCTTTGTGCGTTGTGATAGAGCAATTGGAACATATACACATATGCAAAAAT
1 TAAGGATTCACTCATCTTTGTGCGTTGTGATAGAGCAATTGGAACATATACACATATGCAAAAAT
44253538 TTACTGTCGATGTTACACAGTCTAGGCTAT
66 TTACTGTCGATGTTACACAGTCTAGGCTAT
44253568 GTAGGCTGTG
Statistics
Matches: 90, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 90 1.00
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (98 bp):
TAAGGATTCACTCATCTTTGTGCGTTGTGATAGAGCAATTGGAACATATACACATATGCAAAAAT
TTACTGTCGATGTTACACAGTCTAGGCTATTTA
Found at i:44255963 original size:22 final size:24
Alignment explanation
Indices: 44255937--44255984 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
44255927 AACATGTTAT
*
44255937 AAAATAAA-AATA-CAGAGAGTAA
1 AAAATAAAGAAGATCAGAGAGTAA
*
44255959 AAAATAAAGAAGATGAGAGAGTAA
1 AAAATAAAGAAGATCAGAGAGTAA
44255983 AA
1 AA
44255985 GCGAGAGCGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 8 0.36
23 3 0.14
24 11 0.50
ACGTcount: A:0.67, C:0.02, G:0.19, T:0.12
Consensus pattern (24 bp):
AAAATAAAGAAGATCAGAGAGTAA
Found at i:44256235 original size:2 final size:2
Alignment explanation
Indices: 44256223--44256253 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
44256213 AACCTCAAGT
*
44256223 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
44256254 TAAAACTGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:44256924 original size:14 final size:14
Alignment explanation
Indices: 44256905--44256934 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
44256895 CAATGAACGT
44256905 ATGGTTTGAAATAA
1 ATGGTTTGAAATAA
44256919 ATGGTTTGAAATAA
1 ATGGTTTGAAATAA
44256933 AT
1 AT
44256935 TAATAATAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.20, T:0.37
Consensus pattern (14 bp):
ATGGTTTGAAATAA
Found at i:44260540 original size:15 final size:16
Alignment explanation
Indices: 44260520--44260550 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
44260510 TAGACTTTTC
44260520 TTTATTTAA-TAATTA
1 TTTATTTAATTAATTA
44260535 TTTATTTAATTAATTA
1 TTTATTTAATTAATTA
44260551 AATCAATGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTATTTAATTAATTA
Found at i:44264560 original size:14 final size:14
Alignment explanation
Indices: 44264541--44264569 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
44264531 ACTATAACAA
44264541 TAGTCACTAACCTT
1 TAGTCACTAACCTT
44264555 TAGTCACTAACCTT
1 TAGTCACTAACCTT
44264569 T
1 T
44264570 GGTAAACTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.28, G:0.07, T:0.38
Consensus pattern (14 bp):
TAGTCACTAACCTT
Found at i:44267213 original size:18 final size:18
Alignment explanation
Indices: 44267192--44267236 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
44267182 TGTTTTCCTG
44267192 GTCAAAATTATAATGGTA
1 GTCAAAATTATAATGGTA
*
44267210 GTCAAAATTATAATGGTG
1 GTCAAAATTATAATGGTA
44267228 GTCAAAATT
1 GTCAAAATT
44267237 GCTCTCTGCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.42, C:0.07, G:0.18, T:0.33
Consensus pattern (18 bp):
GTCAAAATTATAATGGTA
Found at i:44275803 original size:17 final size:17
Alignment explanation
Indices: 44275781--44275815 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
44275771 ATTGAGAGTT
44275781 CTTATGAAGCAATTTAA
1 CTTATGAAGCAATTTAA
44275798 CTTATGAAGCAATTTAA
1 CTTATGAAGCAATTTAA
44275815 C
1 C
44275816 CAGATTTTAA
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:0.40, C:0.14, G:0.11, T:0.34
Consensus pattern (17 bp):
CTTATGAAGCAATTTAA
Found at i:44283844 original size:20 final size:19
Alignment explanation
Indices: 44283821--44283868 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 19
44283811 AAAAAAAAGA
* *
44283821 TTTTCAATATTCTTAAGATT
1 TTTTTAATATTCTTAA-AAT
* *
44283841 TTTTTTATATTTTTAAAAT
1 TTTTTAATATTCTTAAAAT
44283860 TTTTTAATA
1 TTTTTAATA
44283869 ATTTTACAGA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.62
Consensus pattern (19 bp):
TTTTTAATATTCTTAAAAT
Found at i:44284853 original size:17 final size:17
Alignment explanation
Indices: 44284827--44284866 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
44284817 TTTTAAACAA
*
44284827 TATATTTTATTATTT-AT
1 TATATATTATT-TTTAAT
44284844 TATATATTATTTTTAAT
1 TATATATTATTTTTAAT
44284861 TATATA
1 TATATA
44284867 CCTATGTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 3 0.14
17 18 0.86
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TATATATTATTTTTAAT
Found at i:44290301 original size:20 final size:20
Alignment explanation
Indices: 44290247--44290294 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
44290237 GTAATTTGTC
44290247 AAATAAAGAAATTTTTATGA
1 AAATAAAGAAATTTTTATGA
44290267 AAATAAAGAAATTTTTATGA
1 AAATAAAGAAATTTTTATGA
44290287 AAATAAAG
1 AAATAAAG
44290295 TTATTTTGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.58, C:0.00, G:0.10, T:0.31
Consensus pattern (20 bp):
AAATAAAGAAATTTTTATGA
Found at i:44291871 original size:29 final size:30
Alignment explanation
Indices: 44291839--44291900 Score: 101
Period size: 29 Copynumber: 2.1 Consensus size: 30
44291829 ACTTAACAAG
44291839 CAAATG-CTTCTAAAATAATAA-AAAATTAA
1 CAAATGCCTT-TAAAATAATAAGAAAATTAA
44291868 CAAATGCCTTTAAAATAATAAGAAAATTAA
1 CAAATGCCTTTAAAATAATAAGAAAATTAA
44291898 CAA
1 CAA
44291901 TAAAATAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
29 17 0.55
30 14 0.45
ACGTcount: A:0.58, C:0.11, G:0.05, T:0.26
Consensus pattern (30 bp):
CAAATGCCTTTAAAATAATAAGAAAATTAA
Found at i:44292488 original size:9 final size:9
Alignment explanation
Indices: 44292474--44292520 Score: 76
Period size: 9 Copynumber: 5.2 Consensus size: 9
44292464 TTGGTTTTTA
44292474 AACTCGAAT
1 AACTCGAAT
44292483 AACTCGAAT
1 AACTCGAAT
*
44292492 AATTCGAAT
1 AACTCGAAT
44292501 AACTCGAAT
1 AACTCGAAT
*
44292510 AATTCGAAT
1 AACTCGAAT
44292519 AA
1 AA
44292521 ATTACTCCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 35 1.00
ACGTcount: A:0.47, C:0.17, G:0.11, T:0.26
Consensus pattern (9 bp):
AACTCGAAT
Found at i:44292500 original size:18 final size:18
Alignment explanation
Indices: 44292477--44292520 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
44292467 GTTTTTAAAC
44292477 TCGAATAACTCGAATAAT
1 TCGAATAACTCGAATAAT
44292495 TCGAATAACTCGAATAAT
1 TCGAATAACTCGAATAAT
44292513 TCGAATAA
1 TCGAATAA
44292521 ATTACTCCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.45, C:0.16, G:0.11, T:0.27
Consensus pattern (18 bp):
TCGAATAACTCGAATAAT
Found at i:44292734 original size:9 final size:9
Alignment explanation
Indices: 44292720--44292746 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
44292710 CAAAGCCATT
44292720 CCCCTCCCC
1 CCCCTCCCC
44292729 CCCCTCCCC
1 CCCCTCCCC
44292738 CCCCTCCCC
1 CCCCTCCCC
44292747 TCAATTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.00, C:0.89, G:0.00, T:0.11
Consensus pattern (9 bp):
CCCCTCCCC
Found at i:44293305 original size:19 final size:19
Alignment explanation
Indices: 44293278--44293315 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
44293268 AAAGTTAATA
* *
44293278 ACAACTTTGATTACGGTGG
1 ACAAATTTGATTACAGTGG
44293297 ACAAATTTGATTACAGTGG
1 ACAAATTTGATTACAGTGG
44293316 GTGACAGTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.32
Consensus pattern (19 bp):
ACAAATTTGATTACAGTGG
Found at i:44294324 original size:86 final size:84
Alignment explanation
Indices: 44294172--44294343 Score: 247
Period size: 86 Copynumber: 2.0 Consensus size: 84
44294162 AATCTTTATC
*
44294172 TTCCATATATGTTATTCTCTTTCCTTTACCATATTTGATTCTCTATTTTTCATAAAATATTAAAT
1 TTCCATATATGTTATTATCTTTCCTTTACCATATTTGATTCTCTATTTTTCATAAAATATTAAAT
*
44294237 TCCATTTTATAT-ATCTATT
66 TCCATTTCATATCA-CTATT
* * * *
44294256 TTCCATATCTGTTATTATCTTTCCTTTCCCATATATTTGATTTTCTATTTTTCATAAAATATTCA
1 TTCCATATATGTTATTATCTTTCCTTTACC--ATATTTGATTCTCTATTTTTCATAAAATATTAA
*
44294321 ATTCCCTTTCATATCACTATT
64 ATTCCATTTCATATCACTATT
44294342 TT
1 TT
44294344 ACACCGTTGT
Statistics
Matches: 78, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
84 27 0.35
86 50 0.64
87 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.02, T:0.53
Consensus pattern (84 bp):
TTCCATATATGTTATTATCTTTCCTTTACCATATTTGATTCTCTATTTTTCATAAAATATTAAAT
TCCATTTCATATCACTATT
Found at i:44294355 original size:86 final size:86
Alignment explanation
Indices: 44294181--44294375 Score: 236
Period size: 86 Copynumber: 2.3 Consensus size: 86
44294171 CTTCCATATA
*
44294181 TGTTATTCTCTTTCCTTTACC--ATATTTGATTCTCTATTTTTCATAAAATATTAAATTCCATTT
1 TGTTATTCTCTTTCCTTTCCCATATATTTGATTCTCTATTTTTCATAAAATATTAAATTCCATTT
* * *
44294244 TATATATCTATTTTCCATATC
66 CATATATCTATTTTACACATC
* * * *
44294265 TGTTATTATCTTTCCTTTCCCATATATTTGATTTTCTATTTTTCATAAAATATTCAATTCCCTTT
1 TGTTATTCTCTTTCCTTTCCCATATATTTGATTCTCTATTTTTCATAAAATATTAAATTCCATTT
*
44294330 CATATCA-CTATTTTACACCGT-
66 CATAT-ATCTATTTTACA-CATC
* * *
44294351 TGTTATTCTTTTTCTTTTCCTATAT
1 TGTTATTCTCTTTCCTTTCCCATAT
44294376 TTCACTTTTC
Statistics
Matches: 94, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
84 19 0.20
86 73 0.78
87 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.03, T:0.54
Consensus pattern (86 bp):
TGTTATTCTCTTTCCTTTCCCATATATTTGATTCTCTATTTTTCATAAAATATTAAATTCCATTT
CATATATCTATTTTACACATC
Found at i:44295511 original size:16 final size:15
Alignment explanation
Indices: 44295492--44295544 Score: 67
Period size: 16 Copynumber: 3.6 Consensus size: 15
44295482 AAAATAAAAT
44295492 AATAATACAATATCTA
1 AATAATA-AATATCTA
44295508 AATAATGAAATATC-A
1 AATAAT-AAATATCTA
44295523 AATAAT--ATATCTA
1 AATAATAAATATCTA
44295536 AATAATAAA
1 AATAATAAA
44295545 CAAAAGTGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
12 5 0.15
13 7 0.21
15 8 0.24
16 12 0.36
17 1 0.03
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.30
Consensus pattern (15 bp):
AATAATAAATATCTA
Found at i:44297474 original size:42 final size:43
Alignment explanation
Indices: 44297333--44297603 Score: 191
Period size: 42 Copynumber: 6.4 Consensus size: 43
44297323 TTATGTAAAA
* * * * * *
44297333 AAACGCTGCTAAAGAACATGACTTTTAGCGGCAC--TTTCAAGA
1 AAACGCCGCTAAAGAACGTGACCTTTAGCGGCGCTTTTTCTA-C
* * * * *
44297375 AAACGCCGCTAAATAACATGACTTTTAGCGGCACTTTCTT-GA-
1 AAACGCCGCTAAAGAACGTGACCTTTAGCGGCGCTTT-TTCTAC
*
44297417 AAACGCCGCTAAAAAACGTGACCTTTAGCGGCGCTTTTTCTAC
1 AAACGCCGCTAAAGAACGTGACCTTTAGCGGCGCTTTTTCTAC
* * * * *
44297460 AAATGCCGCTAAA-AATGTGACCTTTAGCAGCTCTTTTTGTAC
1 AAACGCCGCTAAAGAACGTGACCTTTAGCGGCGCTTTTTCTAC
* * * *
44297502 AAACGCCACTAAAGAACCTGACCTTTAGAGGCGC-TTTTCTTC
1 AAACGCCGCTAAAGAACGTGACCTTTAGCGGCGCTTTTTCTAC
* * * * *
44297544 AAAATGCAGCTAAAGGTCACGT--TCTTTAGCGGCGCTTTTATC-GC
1 -AAACGCCGCTAAA-G-AACGTGACCTTTAGCGGCGCTTTT-TCTAC
44297588 AAACGCCGCTAAAGAA
1 AAACGCCGCTAAAGAA
44297604 TTAGCAGCGC
Statistics
Matches: 185, Mismatches: 33, Indels: 23
0.77 0.14 0.10
Matches are distributed among these distances:
41 3 0.02
42 109 0.59
43 59 0.32
44 7 0.04
45 7 0.04
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACGTGACCTTTAGCGGCGCTTTTTCTAC
Found at i:44298454 original size:13 final size:14
Alignment explanation
Indices: 44298428--44298456 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
44298418 ACTAACGACG
44298428 AATTAAACCATTAT
1 AATTAAACCATTAT
44298442 AATTAAA-CATTAT
1 AATTAAACCATTAT
44298455 AA
1 AA
44298457 ATATTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAACCATTAT
Found at i:44303566 original size:9 final size:9
Alignment explanation
Indices: 44303552--44303662 Score: 120
Period size: 9 Copynumber: 12.6 Consensus size: 9
44303542 TATTTATGTA
44303552 TTATGTAAG
1 TTATGTAAG
44303561 TTATGTAAG
1 TTATGTAAG
*
44303570 TTATGTGAG
1 TTATGTAAG
* *
44303579 GTATGTGAG
1 TTATGTAAG
44303588 TTATGTAAG
1 TTATGTAAG
44303597 TTATGTAAG
1 TTATGTAAG
*
44303606 TTATGATATG
1 TTATG-TAAG
* * *
44303616 ATATAT-AT
1 TTATGTAAG
44303624 TTATGT-A-
1 TTATGTAAG
44303631 TTATGTAAG
1 TTATGTAAG
*
44303640 TTATGTAAA
1 TTATGTAAG
44303649 TTATGTAAG
1 TTATGTAAG
44303658 TTATG
1 TTATG
44303663 AAATTTAAAC
Statistics
Matches: 86, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.07
8 6 0.07
9 68 0.79
10 6 0.07
ACGTcount: A:0.32, C:0.00, G:0.22, T:0.46
Consensus pattern (9 bp):
TTATGTAAG
Found at i:44304230 original size:2 final size:2
Alignment explanation
Indices: 44304225--44304255 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
44304215 AAAATTGCAA
44304225 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
44304256 ATTTCTATAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:44304759 original size:24 final size:24
Alignment explanation
Indices: 44304732--44304784 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
44304722 AATGTTTTAT
44304732 AATATAATATAAATTTTAGATACA
1 AATATAATATAAATTTTAGATACA
* *
44304756 AATATAATATTAATTTTAGTTACA
1 AATATAATATAAATTTTAGATACA
44304780 AATAT
1 AATAT
44304785 TATAACATAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.42
Consensus pattern (24 bp):
AATATAATATAAATTTTAGATACA
Found at i:44306169 original size:47 final size:47
Alignment explanation
Indices: 44306100--44306195 Score: 165
Period size: 47 Copynumber: 2.0 Consensus size: 47
44306090 CGTTTTATCA
* *
44306100 AAAGTAGAAGTATTTAATCATTAATATTGCCTTGTTACAATATAACC
1 AAAGTAGAAGTATTTAATCATTAATACTGCCTTGTTACAACATAACC
*
44306147 AAAGTAGAAGTATTTAATCATTAATACTGCCTTGTTACAACATTACC
1 AAAGTAGAAGTATTTAATCATTAATACTGCCTTGTTACAACATAACC
44306194 AA
1 AA
44306196 TCACGTAGCA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.34
Consensus pattern (47 bp):
AAAGTAGAAGTATTTAATCATTAATACTGCCTTGTTACAACATAACC
Found at i:44307320 original size:29 final size:29
Alignment explanation
Indices: 44307265--44307427 Score: 102
Period size: 29 Copynumber: 5.6 Consensus size: 29
44307255 CCTAAACTCA
*
44307265 TAAACCATAAAACCCTAAACTCC--AACCTT
1 TAAACCAT-AAACCATAAAC-CCTAAACCTT
* *
44307294 TAAACCATAAACCATAATCCCTAAACCTA
1 TAAACCATAAACCATAAACCCTAAACCTT
* * * *
44307323 TAATCCATAATCCATAAACCTTAAA-ATAT
1 TAAACCATAAACCATAAACCCTAAACCT-T
*
44307352 T-AACTCATAAACCATAAACCCCTGAACC-T
1 TAAAC-CATAAACCATAAA-CCCTAAACCTT
** * * **
44307381 TAAACCCCAACCCTTAAACCCTAAACCCA
1 TAAACCATAAACCATAAACCCTAAACCTT
* *
44307410 TAATCCATAAACCTTAAA
1 TAAACCATAAACCATAAA
44307428 ATATTAACTC
Statistics
Matches: 102, Mismatches: 24, Indels: 16
0.72 0.17 0.11
Matches are distributed among these distances:
27 2 0.02
28 20 0.20
29 72 0.71
30 8 0.08
ACGTcount: A:0.45, C:0.32, G:0.01, T:0.22
Consensus pattern (29 bp):
TAAACCATAAACCATAAACCCTAAACCTT
Found at i:44307325 original size:15 final size:14
Alignment explanation
Indices: 44307301--44307339 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
44307291 CTTTAAACCA
44307301 TAAACCATAATCCC
1 TAAACCATAATCCC
*
44307315 TAAACCTATAATCCA
1 TAAACC-ATAATCCC
*
44307330 TAATCCATAA
1 TAAACCATAA
44307340 ACCTTAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.46, C:0.28, G:0.00, T:0.26
Consensus pattern (14 bp):
TAAACCATAATCCC
Found at i:44307330 original size:22 final size:22
Alignment explanation
Indices: 44307294--44307347 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
44307284 CTCCAACCTT
*
44307294 TAAACC-ATAAACCATAATCCC
1 TAAACCTATAAACCATAATCCA
*
44307315 TAAACCTATAATCCATAATCCA
1 TAAACCTATAAACCATAATCCA
44307337 TAAACCT-TAAA
1 TAAACCTATAAA
44307348 ATATTAACTC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 9 0.31
22 20 0.69
ACGTcount: A:0.48, C:0.28, G:0.00, T:0.24
Consensus pattern (22 bp):
TAAACCTATAAACCATAATCCA
Done.