Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold254
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: 856998
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 28123 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:280117 original size:16 final size:16
Alignment explanation
Indices: 280071--280122 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
280061 TTTGGTTCGC
**
280071 TGTATTGGATTAGAAA
1 TGTATTGGATTAGAGG
280087 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
280103 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
280119 TGTA
1 TGTA
280123 ATAGCAAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.29, C:0.00, G:0.33, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:280379 original size:18 final size:17
Alignment explanation
Indices: 280358--280392 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
280348 TTATTATTAA
*
280358 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
280376 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
280393 TCTTAATAAN
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:284545 original size:115 final size:112
Alignment explanation
Indices: 284293--284909 Score: 667
Period size: 115 Copynumber: 5.5 Consensus size: 112
284283 TTTTTTTTCT
* ** * * * *
284293 TTTTTTTTCGTGTCAGAATTAGATATTAATATACG---AAAAAAATAAAAAA-TGTTGGTACTGG
1 TTTTTTTTCGTGTCAGAATCAGATAAAAAAATACGAAAAAAAAAAAAAAAAATTTTTGGTGCTGG
* * * *
284354 CCTATCAATGGCCGACACCGAGTACA-ATTTAAAA-AAAAAAA--TTA
66 CCTGTCAATGGCCGGCACCCAGTACACA-GTAAAAGAAAAAAATTTTA
* *
284398 TTTTTTTTCGTGTAAGAATCAGATAAAAAAATACGAAAAAATAAAAATAAAAAATTTTTTGTGCT
1 TTTTTTTTCGTGTCAGAATCAGATAAAAAAATACGAAAAAA-AAAAA-AAAAAATTTTTGGTGCT
284463 GGCCTGTCAATGGCCGGCACCCAGTACACAGTAGAAAGAAAAAAATTTTA
64 GGCCTGTCAATGGCCGGCACCCAGTACACAGTA-AAAGAAAAAAATTTTA
* *
284513 ATTTTTTTCGTGTCAGAATCAGATAAAAAAATACGAAAAAAATTAAAAAAAAATTTTTGGGTGCT
1 TTTTTTTTCGTGTCAGAATCAGATAAAAAAATACGAAAAAAA-AAAAAAAAAATTTTT-GGTGCT
*
284578 GGTCTGTCAATGGCCGGCACCCAGTACACAGTACAAAGAAAATAAATTTTTTTTTA
64 GGCCTGTCAATGGCCGGCACCCAGTACACAGTA-AAAGAAAA-AAA-----TTTTA
* * *
284634 TTTTTTTTCGTGTCAGAATCAAAT-AAAAAATACG-------AAAAAAAAAATGTTGGGTGCTGG
1 TTTTTTTTCGTGTCAGAATCAGATAAAAAAATACGAAAAAAAAAAAAAAAAATTTTTGGTGCTGG
* *
284691 CCTGTTAATGGCCGGCACCCAGTACACAGTACAAAGAAAAAAAAAATTTAA
66 CCTGTCAATGGCCGGCACCCAGTACACAGTA-AAAG---AAAAAAATTTTA
* *
284742 TTTTTTTTCGTGTCAGAATCAGATAAAAAAATACGAAAAAAATAAAAAAAAATTTTGGGTGCTGG
1 TTTTTTTTCGTGTCAGAATCAGATAAAAAAATACGAAAAAAAAAAAAAAAAATTTTTGGTGCTGG
* * **
284807 CCTGTCAATGGCCGACACCCAGTACACAGT-ACAGAAAAATTTTTTTTA
66 CCTGTCAATGGCCGGCACCCAGTACACAGTAAAAGAAAAA--AATTTTA
* *
284855 TTTTTTTTCGTGTTAAAATCAGAT-AAAAAATACGAAAAAAATAAAAAAAAAATTT
1 TTTTTTTTCGTGTCAGAATCAGATAAAAAAATACGAAAAAAA-AAAAAAAAAATTT
284910 CTTTCTACTG
Statistics
Matches: 440, Mismatches: 39, Indels: 58
0.82 0.07 0.11
Matches are distributed among these distances:
105 30 0.07
108 30 0.07
109 14 0.03
110 6 0.01
111 81 0.18
112 33 0.08
113 48 0.11
114 19 0.04
115 90 0.20
116 52 0.12
120 10 0.02
121 27 0.06
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.29
Consensus pattern (112 bp):
TTTTTTTTCGTGTCAGAATCAGATAAAAAAATACGAAAAAAAAAAAAAAAAATTTTTGGTGCTGG
CCTGTCAATGGCCGGCACCCAGTACACAGTAAAAGAAAAAAATTTTA
Found at i:285006 original size:112 final size:113
Alignment explanation
Indices: 284892--285290 Score: 601
Period size: 113 Copynumber: 3.5 Consensus size: 113
284882 AAATACGAAA
* * **
284892 AAAATAAAAAAAAAATTTCTT-TCTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCA
1 AAAA-AAAAAAAAAATTTTTTGTGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACAAA
* *
284956 AAATTTTTT-TTTAT-TTTTTTCGTA-TTTTTTATCTGATTCTGACACG
65 AAATTTTTTATTTTTATTTTTTCGTATTTTTTTATCTGATTCTTACACG
285002 AAAAAAATAAAAAAAATTTTTCT-TGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACA
1 -AAAAAA-AAAAAAAATTTTT-TGTGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACA
285066 AAAAATTTTTTATTTTTATTTTTTCGTATTTTTTTATCTGATTCTTACACG
63 AAAAATTTTTTATTTTTATTTTTTCGTATTTTTTTATCTGATTCTTACACG
* ***
285117 AAAAAAAATAATTTTTTTTTGTGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACAAAA
1 AAAAAAAAAAAAAATTTTTTGTGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACAAAA
285182 AATTTTTTATTTTTATTTTTTCGTATTTTTTTATCTGATTCTTACACG
66 AATTTTTTATTTTTATTTTTTCGTATTTTTTTATCTGATTCTTACACG
* ***
285230 AAAAAAAATAATTTTTTTTTGTGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCAC
1 AAAAAAAAAAAAAATTTTTTGTGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCAC
285291 CCAAAAAAAA
Statistics
Matches: 272, Mismatches: 10, Indels: 10
0.93 0.03 0.03
Matches are distributed among these distances:
110 2 0.01
111 16 0.06
112 51 0.19
113 166 0.61
114 16 0.06
115 21 0.08
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (113 bp):
AAAAAAAAAAAAAATTTTTTGTGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACAAAA
AATTTTTTATTTTTATTTTTTCGTATTTTTTTATCTGATTCTTACACG
Found at i:303613 original size:98 final size:98
Alignment explanation
Indices: 303505--303699 Score: 318
Period size: 98 Copynumber: 2.0 Consensus size: 98
303495 TAAAATCATG
* * * *
303505 AAGGAGATATTCCTAGTTTGAGATTCTAATGGAATTGTGCCCTAACGTATTGGGTGTGATTTCTT
1 AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTT
303570 AAATATTGGATAAGTGGATGTTCTTTTAAAGTA
66 AAATATTGGATAAGTGGATGTTCTTTTAAAGTA
* *
303603 AAGGAAATATTCCGAGTTTGGGATTCTAAAGGGATCGTGCCCTAACGTATTGGGTGTGATTTCTT
1 AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTT
* *
303668 AAATCTTGGATGAGTGGATGTTCTTTTAAAGT
66 AAATATTGGATAAGTGGATGTTCTTTTAAAGT
303700 TTTATTGTAT
Statistics
Matches: 89, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
98 89 1.00
ACGTcount: A:0.27, C:0.10, G:0.25, T:0.37
Consensus pattern (98 bp):
AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTT
AAATATTGGATAAGTGGATGTTCTTTTAAAGTA
Found at i:315396 original size:93 final size:91
Alignment explanation
Indices: 315225--315440 Score: 287
Period size: 93 Copynumber: 2.4 Consensus size: 91
315215 ACAAATCACA
* * ** *
315225 ACTAGTCTTATCTCCCTGAAGTTACAATGGAGCAGACTAAGTTAGCAAGTCTTATCCTCCTGAAG
1 ACTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAAGCAAGTCGTATCCTCCTGAAG
*
315290 TTGCAGTGGGGCAGACTAAAGATCGC
66 TTGCAGTGAGGCAGACTAAAGATCGC
*
315316 ATCTAGTCTTATCTCCCTGAAGTTGCAGTGGACCAGACTAAGCAAAGCAAGTCGTATCCTCCTGA
1 A-CTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAAGCAAGTCGTATCCTCCTGA
* * *
315381 AGTTGCAGTGAGGCAGGCTGAAGATGGC
64 AGTTGCAGTGAGGCAGACTAAAGATCGC
*
315409 A--AATCTTA--TCCCTGAAGTTGCAGTGGAGCAGA
1 ACTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
315441 TAAAAGCCGA
Statistics
Matches: 111, Mismatches: 12, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
88 23 0.21
90 6 0.05
91 1 0.01
92 37 0.33
93 44 0.40
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (91 bp):
ACTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAAGCAAGTCGTATCCTCCTGAAG
TTGCAGTGAGGCAGACTAAAGATCGC
Found at i:315615 original size:216 final size:218
Alignment explanation
Indices: 315309--315828 Score: 855
Period size: 219 Copynumber: 2.4 Consensus size: 218
315299 GGCAGACTAA
*
315309 AGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGACCAGACTAAGCAAAGCAAGTCGTATC
1 AGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAAGCAAGTCGTATC
* *
315374 CTCCTGAAGTTGCAGTGAGGCAGGCTGAAGATGGCAAATCTTA-TCCCTGAAGTTGCAGT-GGAG
66 CTCCTGAAGTTGCAGTGAGGCAGGCTGAAGATGGCAAATCTTACTCCCTAAAGTTGCAGTAGGAA
* * * * *
315437 CAGATAAAAGCCGATAATCCTATCTCCCTGAAGTTGCATTAGAGTGGATTAAAACCTCAGATCTT
131 CAGATAAAAGCCGACAATCCTATCTCCCTGAAATTACAGTAGAGTGGATTAAAACATCAGATCTT
315502 ATCTCTCTGAAGTTGCAGAGAGC
196 ATCTCTCTGAAGTTGCAGAGAGC
*
315525 AGATCGCATCTAGTCTTATCTCCCTGAAGTTACAGTGGAGCAGACTAAGCAAAGCAAGTCGTATC
1 AGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAAGCAAGTCGTATC
315590 CTCCTGAAGTTGCAGTGAGGCAGGCTGAAGATGGCAAATCTTATCTCCCTAAAGTTGCAGTAGGA
66 CTCCTGAAGTTGCAGTGAGGCAGGCTGAAGATGGCAAATCTTA-CTCCCTAAAGTTGCAGTAGGA
* * * *
315655 ACAGATTAAAGCCTACAATCCTATCTCCCTGAAATTATAGTGGAGTGGATTAAAACATCAGATCT
130 ACAGATAAAAGCCGACAATCCTATCTCCCTGAAATTACAGTAGAGTGGATTAAAACATCAGATCT
* *
315720 TATCTCTTTGAAGTTGCAGAGAGT
195 TATCTCTCTGAAGTTGCAGAGAGC
* *
315744 AGATCGCATCTAGTCTTATCTCCCTGAAGATGCAGTGGAGCAGACTAAGCAAAGCAAGTCTTATC
1 AGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAAGCAAGTCGTATC
*
315809 CTCCTGAAGTTGCAATGAGG
66 CTCCTGAAGTTGCAGTGAGG
315829 ATGGCAAATC
Statistics
Matches: 282, Mismatches: 19, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
216 106 0.38
218 15 0.05
219 161 0.57
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (218 bp):
AGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAAGCAAGTCGTATC
CTCCTGAAGTTGCAGTGAGGCAGGCTGAAGATGGCAAATCTTACTCCCTAAAGTTGCAGTAGGAA
CAGATAAAAGCCGACAATCCTATCTCCCTGAAATTACAGTAGAGTGGATTAAAACATCAGATCTT
ATCTCTCTGAAGTTGCAGAGAGC
Found at i:315806 original size:45 final size:44
Alignment explanation
Indices: 315228--315822 Score: 286
Period size: 45 Copynumber: 13.5 Consensus size: 44
315218 AATCACAACT
* * **
315228 AGTCTTATCTCCCTGAAGTTACAATGGAGCAGACTAAGTTAGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAAGCA
* **
315272 AGTCTTATC-CTCCTGAAGTTGCAGTGGGGCAGACTAAAGATCGCA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGAGCAGACT-AAGAAAGCA
*
315317 TCTAGTCTTATCTCCCTGAAGTTGCAGTGGACCAGACTAAGCAAAGCA
1 ---AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAAGCA
* * **
315365 AGTCGTATC-CTCCTGAAGTTGCAGT-GAGGCAGGCTGAAGATGGCA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGAAAGCA
*
315410 AATCTTA--TCCCTGAAGTTGCAGTGGAGCAGA-T-A-AAAGCCGA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAAG-C-A
* * * * ** * * *
315451 TAATCCTATCTCCCTGAAGTTGCATTAGAGTGGA-TTA-AAACCTC
1 -AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAAGC-A
* * * * * *
315495 AGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-T-CG-CATCT
1 AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAAGCA
*
315536 AGTCTTATCTCCCTGAAGTTACAGTGGAGCAGACTAAGCAAAGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAAGCA
* * **
315581 AGTCGTATC-CTCCTGAAGTTGCAGT-GAGGCAGGCTGAAGATGGCA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGAAAGCA
* * * * **
315626 AATCTTATCTCCCTAAAGTTGCAGTAGGAACAGATTAAAGCCTA-CA
1 AGTCTTATCTCCCTGAAGTTGCAGT-GGAGCAGACT-AAG-AAAGCA
* * ** ** * *
315672 A-TCCTATCTCCCTGAAATTATAGTGGAGTGGATTAA-AACATC-
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAA-AGCA
** * * * * * *
315714 AGATCTTATCTCTTTGAAGTTGCAG-AGAGTAGA-T-CG-CATCT
1 AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAAGCA
*
315755 AGTCTTATCTCCCTGAAGATGCAGTGGAGCAGACTAAGCAAAGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAAGCA
315800 AGTCTTATC-CTCCTGAAGTTGCA
1 AGTCTTATCTC-CCTGAAGTTGCA
315823 ATGAGGATGG
Statistics
Matches: 419, Mismatches: 88, Indels: 87
0.71 0.15 0.15
Matches are distributed among these distances:
39 2 0.00
40 44 0.11
41 18 0.04
42 14 0.03
43 38 0.09
44 104 0.25
45 140 0.33
46 17 0.04
47 6 0.01
48 35 0.08
49 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (44 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAAGCA
Found at i:320010 original size:27 final size:27
Alignment explanation
Indices: 319980--320035 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
319970 TATAACTCTC
*
319980 TGAGTAGGGTCACATAGTCGTGTTACA
1 TGAGTAGGGTCACACAGTCGTGTTACA
320007 TGAGTAGGGTCACACAGTCGTGTTACA
1 TGAGTAGGGTCACACAGTCGTGTTACA
320034 TG
1 TG
320036 TCCGTATGTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.25, C:0.16, G:0.30, T:0.29
Consensus pattern (27 bp):
TGAGTAGGGTCACACAGTCGTGTTACA
Found at i:322001 original size:34 final size:34
Alignment explanation
Indices: 321963--322033 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
321953 TAATATTAAT
321963 AGATTTTCAATACTATTTCTATGGACTTGGCATC
1 AGATTTTCAATACTATTTCTATGGACTTGGCATC
321997 AGATTTTCAATACTATTTCTATGGACTTGGCATC
1 AGATTTTCAATACTATTTCTATGGACTTGGCATC
322031 AGA
1 AGA
322034 CCTTAGGACT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.39
Consensus pattern (34 bp):
AGATTTTCAATACTATTTCTATGGACTTGGCATC
Found at i:325884 original size:18 final size:18
Alignment explanation
Indices: 325861--325895 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
325851 AATAGAGTGT
325861 GTATAATAAA-ATTAAAAC
1 GTATAA-AAATATTAAAAC
325879 GTATAAAAATATTAAAA
1 GTATAAAAATATTAAAA
325896 TAATATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.63, C:0.03, G:0.06, T:0.29
Consensus pattern (18 bp):
GTATAAAAATATTAAAAC
Found at i:326483 original size:35 final size:35
Alignment explanation
Indices: 326430--326560 Score: 145
Period size: 35 Copynumber: 3.7 Consensus size: 35
326420 TTAAAGTTGA
* * *
326430 CTTTAAAAAGGTTAGGATAGACTCATCTAAGACAAC
1 CTTT-AAAAGGTTGGGATAGACACGTCTAAGACAAC
* * * * *
326466 GTTTAAAAGGTTGGGATATACCCGTATAAGGCAAC
1 CTTTAAAAGGTTGGGATAGACACGTCTAAGACAAC
*
326501 CTTTAAAAGGTTGGGATAGACACGTCTAAGCCAAC
1 CTTTAAAAGGTTGGGATAGACACGTCTAAGACAAC
* **
326536 CTTAAAAATATTGGGATAGACACGT
1 CTTTAAAAGGTTGGGATAGACACGT
326561 TTAAAGCAAT
Statistics
Matches: 80, Mismatches: 15, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
35 77 0.96
36 3 0.04
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.25
Consensus pattern (35 bp):
CTTTAAAAGGTTGGGATAGACACGTCTAAGACAAC
Found at i:327389 original size:2 final size:2
Alignment explanation
Indices: 327382--327409 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
327372 ACTCATGTTG
327382 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
327410 GCATATTAGG
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:327756 original size:22 final size:20
Alignment explanation
Indices: 327732--327768 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
327722 TGAAATAATT
*
327732 ATTATTTTCTAT-AATTAAA
1 ATTATTTTTTATAAATTAAA
327751 ATTATTTTTTATAAATTA
1 ATTATTTTTTATAAATTA
327769 TTTAAATACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (20 bp):
ATTATTTTTTATAAATTAAA
Found at i:332610 original size:163 final size:163
Alignment explanation
Indices: 332340--332665 Score: 627
Period size: 163 Copynumber: 2.0 Consensus size: 163
332330 ATATTTTTGT
332340 CTTTTTTATATAATTAATCAATAAAAATTCAATCATAATAAAGATGTGAACCCAAGACACCACAC
1 CTTTTTTATATAATTAATCAATAAAAATTCAATCATAATAAAGATGTGAACCCAAGACACCACAC
332405 ATAACAAATAATTAACTTTCCAATTAATTAATTTTTATATAATTTTTTAATAAATATATTTGTTT
66 ATAACAAATAATTAACTTTCCAATTAATTAATTTTTATATAATTTTTTAATAAATATATTTGTTT
*
332470 CTAAAAAAATTAAATTATGATAATAGAAAGTGA
131 CTAAAAAAATTAAATTATGATAAGAGAAAGTGA
332503 CTTTTTTATATAATTAATCAATAAAAATTCAATCAATAATAAAGA-GTGAACCCAAGACACCACA
1 CTTTTTTATATAATTAATCAATAAAAATTCAATC-ATAATAAAGATGTGAACCCAAGACACCACA
332567 CATAACAAATAATTAACTTTCCAATTAATTAATTTTTATATAATTTTTTAATAAATATATTTGTT
65 CATAACAAATAATTAACTTTCCAATTAATTAATTTTTATATAATTTTTTAATAAATATATTTGTT
332632 TCTAAAAAAATTAAATTATGATAAGAGAAAGTGA
130 TCTAAAAAAATTAAATTATGATAAGAGAAAGTGA
332666 GCAAACCCAT
Statistics
Matches: 161, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
163 151 0.94
164 10 0.06
ACGTcount: A:0.47, C:0.10, G:0.06, T:0.37
Consensus pattern (163 bp):
CTTTTTTATATAATTAATCAATAAAAATTCAATCATAATAAAGATGTGAACCCAAGACACCACAC
ATAACAAATAATTAACTTTCCAATTAATTAATTTTTATATAATTTTTTAATAAATATATTTGTTT
CTAAAAAAATTAAATTATGATAAGAGAAAGTGA
Found at i:333512 original size:2 final size:2
Alignment explanation
Indices: 333440--333492 Score: 88
Period size: 2 Copynumber: 26.0 Consensus size: 2
333430 TTGTTAAAAT
*
333440 TA TA TA TA TA GTG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
333483 TA TA TA TA TA
1 TA TA TA TA TA
333493 AGGTTCGAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 47 0.98
3 1 0.02
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (2 bp):
TA
Found at i:335002 original size:2 final size:2
Alignment explanation
Indices: 334987--335021 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
334977 NNNNNNNNNN
*
334987 AT AT AT AGT GT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
335022 TACATATTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 29 0.97
3 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (2 bp):
AT
Found at i:335090 original size:24 final size:24
Alignment explanation
Indices: 335052--335111 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
335042 ATCCCAGTTG
** *
335052 ATGTGGACATGTTATTTAATTGAC
1 ATGTGGACAACTTATTTAACTGAC
* *
335076 ATGTGGACAACTTATTTTACTGTC
1 ATGTGGACAACTTATTTAACTGAC
*
335100 ATGTGGATAACT
1 ATGTGGACAACT
335112 CTATATTTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.40
Consensus pattern (24 bp):
ATGTGGACAACTTATTTAACTGAC
Found at i:336879 original size:18 final size:18
Alignment explanation
Indices: 336865--336899 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
336855 AATGTGAGAG
336865 TTAAAAGCATGGTGAGTA
1 TTAAAAGCATGGTGAGTA
*
336883 TTAAAAGCATTGTGAGT
1 TTAAAAGCATGGTGAGT
336900 GAAAGAATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.06, G:0.26, T:0.31
Consensus pattern (18 bp):
TTAAAAGCATGGTGAGTA
Found at i:339520 original size:13 final size:13
Alignment explanation
Indices: 339502--339540 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
339492 ATTTGGGCCC
339502 TTTCTTTCTTTTT
1 TTTCTTTCTTTTT
*
339515 TTTCTTTTTTTTT
1 TTTCTTTCTTTTT
*
339528 TCTTTTTTCTTTT
1 T-TTCTTTCTTTT
339541 GCCTACAATG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 13 0.59
14 9 0.41
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (13 bp):
TTTCTTTCTTTTT
Found at i:339526 original size:11 final size:11
Alignment explanation
Indices: 339510--339540 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
339500 CCTTTCTTTC
339510 TTTTTTTTCTT
1 TTTTTTTTCTT
339521 TTTTTTTTCTT
1 TTTTTTTTCTT
339532 TTTTCTTTT
1 TTTT-TTTT
339541 GCCTACAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.79
12 4 0.21
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (11 bp):
TTTTTTTTCTT
Found at i:341941 original size:18 final size:18
Alignment explanation
Indices: 341909--341943 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
341899 AATGTGAGAG
341909 TTAAAAGCATGGTGAGTA
1 TTAAAAGCATGGTGAGTA
* *
341927 TTAAAAGTATTGTGAGT
1 TTAAAAGCATGGTGAGT
341944 GAAAGAATGA
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:0.37, C:0.03, G:0.26, T:0.34
Consensus pattern (18 bp):
TTAAAAGCATGGTGAGTA
Found at i:355347 original size:14 final size:14
Alignment explanation
Indices: 355308--355339 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
355298 TCTAAATCCT
*
355308 AAACCTTAAACCCC
1 AAACCTCAAACCCC
355322 AAACCTCAAACCCC
1 AAACCTCAAACCCC
355336 AAAC
1 AAAC
355340 TCCAAACCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.47, C:0.44, G:0.00, T:0.09
Consensus pattern (14 bp):
AAACCTCAAACCCC
Found at i:355386 original size:20 final size:19
Alignment explanation
Indices: 355363--355428 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 19
355353 CCAAAATCGT
355363 GAACCTTAAACATCAAACTC
1 GAACCTTAAAC-TCAAACTC
* *
355383 GAACCATAAACTCAAACCTT
1 GAACCTTAAACTCAAA-CTC
* *
355403 GAACCCTGAACCTCAAACTC
1 GAA-CCTTAAACTCAAACTC
355423 GAACCT
1 GAACCT
355429 CAGGTTCAAG
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
19 8 0.21
20 20 0.53
21 10 0.26
ACGTcount: A:0.41, C:0.33, G:0.08, T:0.18
Consensus pattern (19 bp):
GAACCTTAAACTCAAACTC
Found at i:355429 original size:13 final size:13
Alignment explanation
Indices: 355375--355430 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
355365 ACCTTAAACA
355375 TCAAACTCGAACC
1 TCAAACTCGAACC
*
355388 AT-AAACTCAAACC
1 -TCAAACTCGAACC
** *
355401 TTGAACCCTGAACC
1 TCAAACTC-GAACC
355415 TCAAACTCGAACC
1 TCAAACTCGAACC
355428 TCA
1 TCA
355431 GGTTCAAGGC
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
12 1 0.03
13 22 0.67
14 10 0.30
ACGTcount: A:0.39, C:0.36, G:0.07, T:0.18
Consensus pattern (13 bp):
TCAAACTCGAACC
Found at i:355462 original size:7 final size:7
Alignment explanation
Indices: 355430--355602 Score: 51
Period size: 7 Copynumber: 25.6 Consensus size: 7
355420 CTCGAACCTC
*
355430 AGGTTCA
1 AGGTTTA
*
355437 AGGCTTA
1 AGGTTTA
355444 AGGTTCT-
1 AGGTT-TA
355451 A-GTTTA
1 AGGTTTA
*
355457 AGGTTTC
1 AGGTTTA
* *
355464 GGGTTCA
1 AGGTTTA
* *
355471 AAGTTCA
1 AGGTTTA
*
355478 AAGTTT-
1 AGGTTTA
355484 AGGATTTA
1 AGG-TTTA
* *
355492 TGGTTTG
1 AGGTTTA
355499 A-GTTTA
1 AGGTTTA
*
355505 A-ATTTA
1 AGGTTTA
*
355511 GGGTTTA
1 AGGTTTA
355518 AGGTTTA
1 AGGTTTA
*
355525 AGGTGT-
1 AGGTTTA
*
355531 GGGTTTTA
1 AGG-TTTA
*
355539 TGGTTTA
1 AGGTTTA
355546 AGGTTTA
1 AGGTTTA
*
355553 GGGTTT-
1 AGGTTTA
*
355559 GGGTTT-
1 AGGTTTA
*
355565 AGGTTTG
1 AGGTTTA
*
355572 AGG-TTC
1 AGGTTTA
*
355578 AGAG-TAA
1 AG-GTTTA
355585 AGGTTTA
1 AGGTTTA
*
355592 AAGTTTA
1 AGGTTTA
355599 AGGT
1 AGGT
355603 AAAGGATCAA
Statistics
Matches: 123, Mismatches: 32, Indels: 22
0.69 0.18 0.12
Matches are distributed among these distances:
5 1 0.01
6 33 0.27
7 84 0.68
8 5 0.04
ACGTcount: A:0.24, C:0.04, G:0.31, T:0.41
Consensus pattern (7 bp):
AGGTTTA
Found at i:355512 original size:26 final size:27
Alignment explanation
Indices: 355472--355523 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
355462 TCGGGTTCAA
*
355472 AGTTCAAAGTTTAGGATTTATGGTTTG
1 AGTTCAAAGTTTAGGATTTAAGGTTTG
* *
355499 AGTTTAAA-TTTAGGGTTTAAGGTTT
1 AGTTCAAAGTTTAGGATTTAAGGTTT
355524 AAGGTGTGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.27, C:0.02, G:0.25, T:0.46
Consensus pattern (27 bp):
AGTTCAAAGTTTAGGATTTAAGGTTTG
Found at i:355543 original size:21 final size:22
Alignment explanation
Indices: 355509--355558 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
355499 AGTTTAAATT
355509 TAGGG-TTTAAGGTTTAAGGTG
1 TAGGGTTTTAAGGTTTAAGGTG
* *
355530 T-GGGTTTTATGGTTTAAGGTT
1 TAGGGTTTTAAGGTTTAAGGTG
355551 TAGGGTTT
1 TAGGGTTT
355559 GGGTTTAGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 3 0.12
21 16 0.64
22 6 0.24
ACGTcount: A:0.18, C:0.00, G:0.36, T:0.46
Consensus pattern (22 bp):
TAGGGTTTTAAGGTTTAAGGTG
Found at i:355543 original size:28 final size:26
Alignment explanation
Indices: 355507--355576 Score: 86
Period size: 28 Copynumber: 2.6 Consensus size: 26
355497 TGAGTTTAAA
355507 TTTAGGGTTTAAGGTTTAAGGTGTGGG
1 TTTA-GGTTTAAGGTTTAAGGTGTGGG
* *
355534 TTTTATGGTTTAAGGTTTAGGGTTTGGG
1 -TTTA-GGTTTAAGGTTTAAGGTGTGGG
*
355562 TTTAGGTTTGAGGTT
1 TTTAGGTTTAAGGTT
355577 CAGAGTAAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
26 10 0.26
27 4 0.11
28 24 0.63
ACGTcount: A:0.16, C:0.00, G:0.37, T:0.47
Consensus pattern (26 bp):
TTTAGGTTTAAGGTTTAAGGTGTGGG
Found at i:358078 original size:45 final size:44
Alignment explanation
Indices: 358018--358229 Score: 217
Period size: 44 Copynumber: 4.8 Consensus size: 44
358008 CCTATCAAAA
* * *
358018 GATGCCATAACGTCTTTCAACTATGGTCTTAGTCCTATTTACCAT
1 GATGCCATAACGTCTTTCAGCTATGGTCTTACTCCT-TTTATCAT
* * * **
358063 GATGTCATAATGTCTTTCAGCCATGGTCTTACTCACTTCCATCAT
1 GATGCCATAACGTCTTTCAGCTATGGTCTTACTC-CTTTTATCAT
* *
358108 GATGCCATAACGTCTTTCAGCTATGGTCTTACTCATTTTATCTT
1 GATGCCATAACGTCTTTCAGCTATGGTCTTACTCCTTTTATCAT
* * * * * * *
358152 GATGTCATAGCATTTTTCAGCCATGGTCTTACTCGTTTTATCCT
1 GATGCCATAACGTCTTTCAGCTATGGTCTTACTCCTTTTATCAT
* * * *
358196 GATTCCATAGCATCTTTCAACTATGGTCTTACTC
1 GATGCCATAACGTCTTTCAGCTATGGTCTTACTC
358230 ATCTGAATCA
Statistics
Matches: 139, Mismatches: 27, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
44 72 0.52
45 65 0.47
46 2 0.01
ACGTcount: A:0.22, C:0.25, G:0.14, T:0.40
Consensus pattern (44 bp):
GATGCCATAACGTCTTTCAGCTATGGTCTTACTCCTTTTATCAT
Found at i:361054 original size:23 final size:23
Alignment explanation
Indices: 360984--361070 Score: 77
Period size: 23 Copynumber: 3.8 Consensus size: 23
360974 GAAATTACGG
* * *
360984 ATAAACAGTGAAGTTTCCCTACA
1 ATAAACAGTGAAGATTCTCTATA
* * * *
361007 ATGAACAATGAAGGTT-TCCTGTA
1 ATAAACAGTGAAGATTCT-CTATA
361030 ATAAACAGTGAAGATTCTCTATA
1 ATAAACAGTGAAGATTCTCTATA
* *
361053 ATGAACAGTAAAGATTCT
1 ATAAACAGTGAAGATTCT
361071 TTGCAAAAAA
Statistics
Matches: 50, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
23 49 0.98
24 1 0.02
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.29
Consensus pattern (23 bp):
ATAAACAGTGAAGATTCTCTATA
Found at i:367937 original size:139 final size:139
Alignment explanation
Indices: 367604--368020 Score: 736
Period size: 139 Copynumber: 3.0 Consensus size: 139
367594 GATGAATTTC
* *
367604 CATGGATTACTCATCTGAAGTGGGAGTCCATTTTCATGTAACCTATTCTAAATAATTGTCTTAGT
1 CATGGATTACACATCTGAAGTGGGAGTCCATTTTCATGTTACCTATTCTAAATAATTGTCTTAGT
* *
367669 TGTTGTTGGAACTGTTAAGTTGCTGAAACGTTACAAGTTAAAAAGTGGAGCAAAATATT--G---
66 TATTGTGGGAACTGTTAAGTTGCTGAAACGTTACAAGTTAAAAAGTGGAGCAAAATATTGAGAAT
367729 AGAGGATGT
131 AGAGGATGT
367738 CATGGATTACACATCTGAAGTGGGAGTCCATTTTCATGTTACCTATTCTAAATAATTGTCTTAGT
1 CATGGATTACACATCTGAAGTGGGAGTCCATTTTCATGTTACCTATTCTAAATAATTGTCTTAGT
367803 TATTGTGGGAACTGTTAAGTTGCTGAAACGTTACAAGTTAAAAAGTGGAGCAAAATATTGAGAAT
66 TATTGTGGGAACTGTTAAGTTGCTGAAACGTTACAAGTTAAAAAGTGGAGCAAAATATTGAGAAT
367868 AGAGGATGT
131 AGAGGATGT
*
367877 CATGGATTACACATCTGAAGTGGGAGTCCGTTTTCATGTTACCTATTCTAAATAATTGTCTTAGT
1 CATGGATTACACATCTGAAGTGGGAGTCCATTTTCATGTTACCTATTCTAAATAATTGTCTTAGT
* *
367942 CATTGTGGGAACTGTTAAGTTGCTGAAACGTTACAAGTTAAAAAGTGGATCAAAATATTGAGAAT
66 TATTGTGGGAACTGTTAAGTTGCTGAAACGTTACAAGTTAAAAAGTGGAGCAAAATATTGAGAAT
368007 AGAGGATGT
131 AGAGGATGT
368016 CATGG
1 CATGG
368021 TTTGAAAATA
Statistics
Matches: 271, Mismatches: 7, Indels: 5
0.96 0.02 0.02
Matches are distributed among these distances:
134 120 0.44
136 1 0.00
139 150 0.55
ACGTcount: A:0.32, C:0.12, G:0.23, T:0.33
Consensus pattern (139 bp):
CATGGATTACACATCTGAAGTGGGAGTCCATTTTCATGTTACCTATTCTAAATAATTGTCTTAGT
TATTGTGGGAACTGTTAAGTTGCTGAAACGTTACAAGTTAAAAAGTGGAGCAAAATATTGAGAAT
AGAGGATGT
Found at i:372598 original size:18 final size:18
Alignment explanation
Indices: 372577--372612 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
372567 TAAATTAAAT
372577 TATAATATTTTT-ATACAA
1 TATAAT-TTTTTGATACAA
372595 TATAATTTTTTGATACAA
1 TATAATTTTTTGATACAA
372613 AATTCTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.50
Consensus pattern (18 bp):
TATAATTTTTTGATACAA
Found at i:379469 original size:76 final size:76
Alignment explanation
Indices: 379333--379486 Score: 254
Period size: 76 Copynumber: 2.0 Consensus size: 76
379323 TTCTCAGAAC
* * *
379333 CAGGATCTTCATTGAACCTAAATTAACATAATCCATATTAAAGGTAAATACTAAATCTGCTAGTA
1 CAGGATCTTCATTGAACCTAAATTAACATAATCCATATTAAAGGAAAATACTAAACCTGCTAATA
379398 GGTAAATTACA
66 GGTAAATTACA
* * *
379409 CAGGCTCTTCATTGAACCTTAATTAACATAATCCATATTAAAGGAAAATATTAAACCTGCTAATA
1 CAGGATCTTCATTGAACCTAAATTAACATAATCCATATTAAAGGAAAATACTAAACCTGCTAATA
379474 GGTAAATTACA
66 GGTAAATTACA
379485 CA
1 CA
379487 CCCAAAAAAC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
76 72 1.00
ACGTcount: A:0.42, C:0.17, G:0.11, T:0.30
Consensus pattern (76 bp):
CAGGATCTTCATTGAACCTAAATTAACATAATCCATATTAAAGGAAAATACTAAACCTGCTAATA
GGTAAATTACA
Found at i:381377 original size:18 final size:18
Alignment explanation
Indices: 381330--381378 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
381320 AGTTTGTCTC
*
381330 TCTCCTTTTCCCTTTCCT
1 TCTCCTTTTCTCTTTCCT
* *
381348 TCGCCTTGTCTCTTTCCT
1 TCTCCTTTTCTCTTTCCT
*
381366 TTTCCTTTTCTCT
1 TCTCCTTTTCTCT
381379 GTCCCTATCT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.00, C:0.39, G:0.04, T:0.57
Consensus pattern (18 bp):
TCTCCTTTTCTCTTTCCT
Found at i:383328 original size:18 final size:18
Alignment explanation
Indices: 383270--383328 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 18
383260 TTTTAAATTG
* *
383270 AAAAATATATAAAATCTAAA
1 AAAAAT-TAT-AAATTTATA
* *
383290 AAAAATTAT--CTTTATT
1 AAAAATTATAAATTTATA
383306 AAAAATTATAAATTTATA
1 AAAAATTATAAATTTATA
383324 AAAAA
1 AAAAA
383329 AATATTTCAC
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
16 12 0.39
18 10 0.32
19 3 0.10
20 6 0.19
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (18 bp):
AAAAATTATAAATTTATA
Found at i:391676 original size:51 final size:51
Alignment explanation
Indices: 391620--391777 Score: 316
Period size: 51 Copynumber: 3.1 Consensus size: 51
391610 GAAGAGCAGA
391620 AATAAAATTTGAGACACATATTTTAAGTTACATTAAATTTTGACAAGCGTG
1 AATAAAATTTGAGACACATATTTTAAGTTACATTAAATTTTGACAAGCGTG
391671 AATAAAATTTGAGACACATATTTTAAGTTACATTAAATTTTGACAAGCGTG
1 AATAAAATTTGAGACACATATTTTAAGTTACATTAAATTTTGACAAGCGTG
391722 AATAAAATTTGAGACACATATTTTAAGTTACATTAAATTTTGACAAGCGTG
1 AATAAAATTTGAGACACATATTTTAAGTTACATTAAATTTTGACAAGCGTG
391773 AATAA
1 AATAA
391778 TTTTAATAGC
Statistics
Matches: 107, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 107 1.00
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.35
Consensus pattern (51 bp):
AATAAAATTTGAGACACATATTTTAAGTTACATTAAATTTTGACAAGCGTG
Found at i:398661 original size:3 final size:3
Alignment explanation
Indices: 398653--398737 Score: 73
Period size: 3 Copynumber: 27.7 Consensus size: 3
398643 TAAATGGGTA
* * * **
398653 AAT AAT AAT AAT AAT AAT AA- AATT GAT TAG CTT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT
* *
398698 AAT AAT AAT AAT AAT AAT AGCTT AAT AAT AAT AAA AAT AA
1 AAT AAT AAT AAT AAT AAT A--AT AAT AAT AAT AAT AAT AA
398738 CAATGACAGG
Statistics
Matches: 66, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
2 2 0.03
3 61 0.92
4 1 0.02
5 2 0.03
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:399487 original size:22 final size:21
Alignment explanation
Indices: 399461--399514 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
399451 AAAAACAATG
*
399461 AAATAAAAGAAAACCAAATAAA
1 AAATAAAA-AAAACCAAACAAA
* *
399483 AAATAAAACAAATCAAACAAA
1 AAATAAAAAAAACCAAACAAA
*
399504 AAATGAAAAAA
1 AAATAAAAAAA
399515 TAATGGAGGA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 19 0.70
22 8 0.30
ACGTcount: A:0.78, C:0.09, G:0.04, T:0.09
Consensus pattern (21 bp):
AAATAAAAAAAACCAAACAAA
Found at i:399494 original size:16 final size:15
Alignment explanation
Indices: 399446--399506 Score: 50
Period size: 15 Copynumber: 3.9 Consensus size: 15
399436 TTTATTATTT
* **
399446 AAATAAAAAACAATG
1 AAATAAAAAAAAAAC
* *
399461 AAATAAAAGAAAACC
1 AAATAAAAAAAAAAC
399476 AAATAAAAAATAAAAC
1 AAATAAAAAA-AAAAC
399492 AAATCAAACAAAAAA
1 AAAT-AAA-AAAAAA
399507 TGAAAAAATA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
15 20 0.54
16 8 0.22
17 6 0.16
18 3 0.08
ACGTcount: A:0.77, C:0.10, G:0.03, T:0.10
Consensus pattern (15 bp):
AAATAAAAAAAAAAC
Found at i:404215 original size:44 final size:45
Alignment explanation
Indices: 404152--404246 Score: 131
Period size: 44 Copynumber: 2.1 Consensus size: 45
404142 CTATTACACC
*
404152 TCCATTCCATTCAACCAAACACA-AGA-ATACTATTACACCTCTAT
1 TCCATTACATTCAACCAAACA-ATAGATATACTATTACACCTCTAT
* * *
404196 TCCATTACATTCAACCAAACAATTGATTTACTATTACGCCTCTAT
1 TCCATTACATTCAACCAAACAATAGATATACTATTACACCTCTAT
404241 TCCATT
1 TCCATT
404247 TCGCCTCTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
43 1 0.02
44 22 0.49
45 22 0.49
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.33
Consensus pattern (45 bp):
TCCATTACATTCAACCAAACAATAGATATACTATTACACCTCTAT
Found at i:404253 original size:16 final size:16
Alignment explanation
Indices: 404228--404276 Score: 89
Period size: 16 Copynumber: 3.1 Consensus size: 16
404218 TTGATTTACT
404228 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
*
404244 ATTTCGCCTCTATTCC
1 ATTACGCCTCTATTCC
404260 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
404276 A
1 A
404277 ATACAGCGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.18, C:0.37, G:0.06, T:0.39
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:409464 original size:26 final size:26
Alignment explanation
Indices: 409384--409464 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 26
409374 GATGGTCACG
409384 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
* * *
409410 CGTGTA-T-CAGATG-GTAATGG-TCAC-A
1 TGTGTAGTAC-TATGTG-CA-GGCT-ACTA
409435 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
409461 TGTG
1 TGTG
409465 AACCGAACAT
Statistics
Matches: 40, Mismatches: 6, Indels: 18
0.62 0.09 0.28
Matches are distributed among these distances:
24 2 0.05
25 16 0.40
26 20 0.50
27 2 0.05
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.33
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCAGGCTACTA
Found at i:409775 original size:38 final size:37
Alignment explanation
Indices: 409732--409804 Score: 96
Period size: 37 Copynumber: 1.9 Consensus size: 37
409722 AGGTGTGGAA
409732 TTGAATTGAATAT-CGACTTAGAAA-TGAAAAAGTGAATT
1 TTGAATTGAAT-TGCGA-TT-GAAAGTGAAAAAGTGAATT
*
409770 TTGAATTGAATTGTGATTGAAAGTGAAAAAGTGAA
1 TTGAATTGAATTGCGATTGAAAGTGAAAAAGTGAA
409805 ATTATGAAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
36 4 0.12
37 15 0.47
38 13 0.41
ACGTcount: A:0.44, C:0.03, G:0.22, T:0.32
Consensus pattern (37 bp):
TTGAATTGAATTGCGATTGAAAGTGAAAAAGTGAATT
Found at i:411785 original size:34 final size:34
Alignment explanation
Indices: 411746--411882 Score: 265
Period size: 34 Copynumber: 4.0 Consensus size: 34
411736 TATATGACAT
411746 GTACTAGGTTTTGAGTCGATTTTGCCAAATATGA
1 GTACTAGGTTTTGAGTCGATTTTGCCAAATATGA
411780 GTACTAGGTTTTGAGTCGATTTTGCCAAATATGA
1 GTACTAGGTTTTGAGTCGATTTTGCCAAATATGA
411814 GTACTAGGTTTTGAGTCGATTTTGCCAAATATGA
1 GTACTAGGTTTTGAGTCGATTTTGCCAAATATGA
*
411848 GTACTAGGTTTTGAGTCGATTTTTCCAAATATGA
1 GTACTAGGTTTTGAGTCGATTTTGCCAAATATGA
411882 G
1 G
411883 ATCTTGTTGA
Statistics
Matches: 102, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
34 102 1.00
ACGTcount: A:0.26, C:0.12, G:0.23, T:0.39
Consensus pattern (34 bp):
GTACTAGGTTTTGAGTCGATTTTGCCAAATATGA
Found at i:429461 original size:2 final size:2
Alignment explanation
Indices: 429456--429486 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
429446 AACAGAAAAA
429456 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
429487 AAGAACTGAT
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:432974 original size:9 final size:9
Alignment explanation
Indices: 432962--432989 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
432952 TTTTATTACA
432962 ACAATTAAT
1 ACAATTAAT
432971 ACAATTAAT
1 ACAATTAAT
432980 ACAATTAAT
1 ACAATTAAT
432989 A
1 A
432990 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:433041 original size:68 final size:66
Alignment explanation
Indices: 432932--433073 Score: 257
Period size: 68 Copynumber: 2.1 Consensus size: 66
432922 NNNNNNNNNN
432932 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
432997 AAA
64 AAA
433000 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
*
433065 T
66 A
433066 TTTACTAA
1 TTTACTAA
433074 CAATTAATTT
Statistics
Matches: 73, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
66 27 0.37
67 1 0.01
68 45 0.62
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (66 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
A
Found at i:433083 original size:16 final size:16
Alignment explanation
Indices: 433062--433103 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
433052 AATAATTTGA
*
433062 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
433078 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
433094 TAGTTTTAAT
1 TAATTTTAAT
433104 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:433087 original size:22 final size:23
Alignment explanation
Indices: 433077--433138 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
433067 TTACTAACAA
* * *
433077 TTAATTTTAAT-AACAATTAGTT
1 TTAATTTTAATAAAAAAATAATT
*
433099 TTAATTTTATTAAAAAAATAATT
1 TTAATTTTAATAAAAAAATAATT
*
433122 TTAATTTTAATTAAAAA
1 TTAATTTTAATAAAAAA
433139 TGGGCCGGGC
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 10 0.30
23 23 0.70
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
TTAATTTTAATAAAAAAATAATT
Found at i:433092 original size:59 final size:66
Alignment explanation
Indices: 432932--433095 Score: 225
Period size: 68 Copynumber: 2.5 Consensus size: 66
432922 NNNNNNNNNN
432932 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAA-GTTAGATTTTA-TACAACAATTAATACAATTAATACAATTAATAATTTGAT
432997 AAA
64 AAA
433000 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
1 TTTACTAATCAAA-GTTAGATTTTA-TACAACAATTAATACAATTAATACAATTAATAATTTGAT
*
433063 AAT
64 AAA
*
433066 TTTACTAA-C-AA-TTA-ATTTTA-ATAACAATTA
1 TTTACTAATCAAAGTTAGATTTTATACAACAATTA
433096 GTTTTAATTT
Statistics
Matches: 94, Mismatches: 2, Indels: 9
0.90 0.02 0.09
Matches are distributed among these distances:
59 9 0.10
61 6 0.06
62 3 0.03
64 2 0.02
65 1 0.01
66 27 0.29
67 1 0.01
68 45 0.48
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (66 bp):
TTTACTAATCAAAGTTAGATTTTATACAACAATTAATACAATTAATACAATTAATAATTTGATAA
A
Found at i:438518 original size:14 final size:14
Alignment explanation
Indices: 438499--438526 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
438489 ACAATTTATT
438499 AATATATATTAATA
1 AATATATATTAATA
438513 AATATATATTAATA
1 AATATATATTAATA
438527 TATGTAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AATATATATTAATA
Found at i:438600 original size:32 final size:33
Alignment explanation
Indices: 438559--438643 Score: 93
Period size: 32 Copynumber: 2.6 Consensus size: 33
438549 AACTTTTCCG
* * *
438559 GAAAATATTTT-CAGGAAATCTGCCAAACAGCA
1 GAAAATATTTTACAGCAAATCTACCAAACACCA
* *
438591 GAAAATATTTTACA-CAGATTTACCAAACACCA
1 GAAAATATTTTACAGCAAATCTACCAAACACCA
* *
438623 GAAAATATTTTCCAGTAAATC
1 GAAAATATTTTACAGCAAATC
438644 ATTTTACAGA
Statistics
Matches: 42, Mismatches: 9, Indels: 3
0.78 0.17 0.06
Matches are distributed among these distances:
32 37 0.88
33 5 0.12
ACGTcount: A:0.45, C:0.19, G:0.11, T:0.26
Consensus pattern (33 bp):
GAAAATATTTTACAGCAAATCTACCAAACACCA
Found at i:438642 original size:14 final size:15
Alignment explanation
Indices: 438620--438696 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
438610 TTACCAAACA
438620 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
438634 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
438649 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
438669 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
438683 ACGGAAAA-CATTTT
1 CCAGAAAATCATTTT
438697 ACTGCCAAAC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 22 0.44
15 14 0.28
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:438661 original size:20 final size:20
Alignment explanation
Indices: 438636--438675 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
438626 AATATTTTCC
*
438636 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
438656 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
438676 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:438681 original size:34 final size:35
Alignment explanation
Indices: 438624--438690 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
438614 CAAACACCAG
*
438624 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
438659 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
438691 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:438697 original size:14 final size:14
Alignment explanation
Indices: 438659--438698 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
438649 ACAGAAAAGT
*
438659 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
438673 AAATCATTTTACGG
1 AAAACATTTTACAG
438687 AAAACATTTTAC
1 AAAACATTTTAC
438699 TGCCAAACAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:440381 original size:28 final size:28
Alignment explanation
Indices: 440321--440375 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
440311 GAAATCAAAC
*
440321 AAATTATCCAAATTTATTTTTGAAATGG
1 AAATTATCCAAATTTATTTTTAAAATGG
*
440349 AAATTATCCCAATTTATTTTTAAAATG
1 AAATTATCCAAATTTATTTTTAAAATG
440376 ATAATTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (28 bp):
AAATTATCCAAATTTATTTTTAAAATGG
Found at i:440726 original size:17 final size:17
Alignment explanation
Indices: 440704--440745 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 17
440694 AATTTAATTC
440704 TATAAAAATTATAAAAA
1 TATAAAAATTATAAAAA
440721 TAT--AAATTATAAAAA
1 TATAAAAATTATAAAAA
440736 -ATTAAAAATT
1 TA-TAAAAATT
440746 CATTCCCCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 1 0.05
15 13 0.59
17 8 0.36
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TATAAAAATTATAAAAA
Found at i:442186 original size:28 final size:30
Alignment explanation
Indices: 442123--442190 Score: 88
Period size: 28 Copynumber: 2.3 Consensus size: 30
442113 GTAATAGATT
*
442123 TATTTAATTACTTTTTATTTAATTAAATAGA
1 TATTT-ATTACTTTTTATTTAAGTAAATAGA
442154 TATTTATTA-TTTATTA-TTAAGTAAA-AGA
1 TATTTATTACTTT-TTATTTAAGTAAATAGA
442182 TATTTATTA
1 TATTTATTA
442191 ATTAAATAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
28 12 0.34
29 11 0.31
30 7 0.20
31 5 0.14
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.54
Consensus pattern (30 bp):
TATTTATTACTTTTTATTTAAGTAAATAGA
Found at i:443284 original size:5 final size:5
Alignment explanation
Indices: 443274--443301 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
443264 TATTATTATA
443274 ATAAT ATAAT ATAAT ATAAT ATAAT ATA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATA
443302 TACTTAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:443921 original size:28 final size:30
Alignment explanation
Indices: 443884--443951 Score: 88
Period size: 28 Copynumber: 2.3 Consensus size: 30
443874 ATTATTTAAT
443884 TAATAAATATCT-TTTACCT-AATAATAAA-
1 TAATAAATATCTATTTACCTAAATAA-AAAG
*
443912 TAATAAATATCTATTTACTTAAATAAAAAG
1 TAATAAATATCTATTTACCTAAATAAAAAG
443942 TAATTAAATA
1 TAA-TAAATA
443952 AATATATTAC
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
28 12 0.34
29 9 0.26
30 8 0.23
31 6 0.17
ACGTcount: A:0.53, C:0.07, G:0.01, T:0.38
Consensus pattern (30 bp):
TAATAAATATCTATTTACCTAAATAAAAAG
Found at i:449978 original size:12 final size:12
Alignment explanation
Indices: 449963--450001 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
449953 TTCTAATATT
449963 AAATAATTTTAA
1 AAATAATTTTAA
* *
449975 AAATTAACTATAA
1 AAA-TAATTTTAA
449988 AAATAATTTTAA
1 AAATAATTTTAA
450000 AA
1 AA
450002 TTTGGTTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
12 12 0.55
13 10 0.45
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (12 bp):
AAATAATTTTAA
Found at i:457799 original size:4 final size:4
Alignment explanation
Indices: 457790--457828 Score: 60
Period size: 4 Copynumber: 9.8 Consensus size: 4
457780 TATAAACCAA
* *
457790 ATAC ATAC ATAC ATAC ATGC ATAC ATAC ATGC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
457829 TATGAACATC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.46, C:0.23, G:0.05, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:457807 original size:12 final size:12
Alignment explanation
Indices: 457790--457828 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
457780 TATAAACCAA
*
457790 ATACATACATAC
1 ATACATGCATAC
457802 ATACATGCATAC
1 ATACATGCATAC
457814 ATACATGCATAC
1 ATACATGCATAC
457826 ATA
1 ATA
457829 TATGAACATC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.46, C:0.23, G:0.05, T:0.26
Consensus pattern (12 bp):
ATACATGCATAC
Found at i:459846 original size:44 final size:45
Alignment explanation
Indices: 459796--459885 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 45
459786 ACATCATTCT
*
459796 ATTCAACCAAACACA-AGAA-TACTATTACGTCTCTATTCCATTAC
1 ATTCAACCAAACA-ATAGAATTACTATTACGCCTCTATTCCATTAC
*
459840 ATTCAACCAAACAATTGAATTACTATTACGCCTCTATTCCATTAC
1 ATTCAACCAAACAATAGAATTACTATTACGCCTCTATTCCATTAC
459885 A
1 A
459886 GCGAACCAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
43 1 0.02
44 16 0.38
45 25 0.60
ACGTcount: A:0.38, C:0.27, G:0.04, T:0.31
Consensus pattern (45 bp):
ATTCAACCAAACAATAGAATTACTATTACGCCTCTATTCCATTAC
Found at i:462454 original size:41 final size:41
Alignment explanation
Indices: 462409--462494 Score: 138
Period size: 41 Copynumber: 2.1 Consensus size: 41
462399 TGACTCAGTA
462409 CACCGGCACTT-AGCCTGCTAGACATATAGTCTGAAATATTT
1 CACCGGCA-TTAAGCCTGCTAGACATATAGTCTGAAATATTT
* *
462450 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAGTGTTT
1 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATATTT
462491 CACC
1 CACC
462495 NNNNNNNNNN
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
40 2 0.05
41 40 0.95
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.28
Consensus pattern (41 bp):
CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATATTT
Found at i:482728 original size:3 final size:3
Alignment explanation
Indices: 482720--482752 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
482710 TTGGTTTTAT
482720 TTA TTA TTA TTA TTA TTA TTA TTA TTA TCTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TT
482753 TTCTGTTTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:482802 original size:96 final size:97
Alignment explanation
Indices: 482682--482876 Score: 356
Period size: 96 Copynumber: 2.0 Consensus size: 97
482672 TATAAATGGA
* * *
482682 CTATTGTAATTGGGTTTGTAATTTATTTTTGGTTTTATTTATTATTATTATTATTATTATTATTA
1 CTATTGTAATTGGGTTTGTAATTTATTTTTGGTTTTAATTAATAATATTATTATTATTATTATTA
482747 TCTATTTTCTGTTTGGGTTGATTAGTTTGGGG
66 TCTATTTTCTGTTTGGGTTGATTAGTTTGGGG
482779 CTATTGTAATT-GGTTTGTAATTTATTTTTGGTTTTAATTAATAATATTATTATTATTATTATTA
1 CTATTGTAATTGGGTTTGTAATTTATTTTTGGTTTTAATTAATAATATTATTATTATTATTATTA
482843 TCTATTTTCTGTTTGGGTTGATTAGTTTGGGG
66 TCTATTTTCTGTTTGGGTTGATTAGTTTGGGG
482875 CT
1 CT
482877 TTTATTTGTT
Statistics
Matches: 95, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
96 84 0.88
97 11 0.12
ACGTcount: A:0.21, C:0.04, G:0.17, T:0.58
Consensus pattern (97 bp):
CTATTGTAATTGGGTTTGTAATTTATTTTTGGTTTTAATTAATAATATTATTATTATTATTATTA
TCTATTTTCTGTTTGGGTTGATTAGTTTGGGG
Found at i:484853 original size:15 final size:15
Alignment explanation
Indices: 484835--484885 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
484825 TTTCGTTTCC
484835 CTTTTTTTTTTCTTT
1 CTTTTTTTTTTCTTT
* *
484850 CTTTCTTTGTTCTTT
1 CTTTTTTTTTTCTTT
**
484865 CTCTTTTACTTTC-TT
1 CT-TTTTTTTTTCTTT
484880 CTTTTT
1 CTTTTT
484886 GTGGGTGAGG
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
14 4 0.14
15 19 0.66
16 6 0.21
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (15 bp):
CTTTTTTTTTTCTTT
Found at i:486767 original size:12 final size:12
Alignment explanation
Indices: 486750--486776 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
486740 TATATGTGTT
486750 TATGAAAGACCA
1 TATGAAAGACCA
486762 TATGAAAGACCA
1 TATGAAAGACCA
486774 TAT
1 TAT
486777 TCGGCCATGT
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:0.48, C:0.15, G:0.15, T:0.22
Consensus pattern (12 bp):
TATGAAAGACCA
Found at i:496327 original size:20 final size:20
Alignment explanation
Indices: 496304--496367 Score: 80
Period size: 20 Copynumber: 3.2 Consensus size: 20
496294 AATTTTAGCT
496304 TTTTTATATAA-ATTTTGAAA
1 TTTTTATA-AATATTTTGAAA
496324 TTTTTATAAATATTTTGAAA
1 TTTTTATAAATATTTTGAAA
*
496344 TTTTGA-AAATTATTTT-AAA
1 TTTTTATAAA-TATTTTGAAA
496363 TTTTT
1 TTTTT
496368 TTTTGTAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
19 12 0.30
20 28 0.70
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.58
Consensus pattern (20 bp):
TTTTTATAAATATTTTGAAA
Found at i:496729 original size:16 final size:16
Alignment explanation
Indices: 496708--496765 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 16
496698 TTATGTAAGG
496708 ATTTATTTTTTTAATA
1 ATTTATTTTTTTAATA
* *
496724 ATTTATTTGATTAAATA
1 ATTTATTT-TTTTAATA
496741 ATAATTATTTTTTTAA-A
1 AT--TTATTTTTTTAATA
496758 ATTATATT
1 ATT-TATT
496766 ATATTAATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
15 1 0.03
16 12 0.35
17 11 0.32
18 4 0.12
19 6 0.18
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (16 bp):
ATTTATTTTTTTAATA
Found at i:499208 original size:38 final size:37
Alignment explanation
Indices: 499079--499199 Score: 224
Period size: 37 Copynumber: 3.2 Consensus size: 37
499069 ACTAAGATGA
*
499079 TTTCAAAGATAAAAGAAATCACCAGTAGACTGAATCG
1 TTTCAAACATAAAAGAAATCACCAGTAGACTGAATCG
499116 TTTCAAACATAAAAGAAATCACCAGTAGACTGAAATCG
1 TTTCAAACATAAAAGAAATCACCAGTAGACTG-AATCG
499154 TTTCAAACATAAAAGAAATCACCAGTAGACTGAATCG
1 TTTCAAACATAAAAGAAATCACCAGTAGACTGAATCG
499191 TTTCAAACA
1 TTTCAAACA
499200 CTCGAAGAAG
Statistics
Matches: 82, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
37 45 0.55
38 37 0.45
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.22
Consensus pattern (37 bp):
TTTCAAACATAAAAGAAATCACCAGTAGACTGAATCG
Found at i:501619 original size:14 final size:14
Alignment explanation
Indices: 501588--501628 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
501578 AAATGTACAG
501588 TATAATTAAA-TAA
1 TATAATTAAATTAA
501601 TATAAATTAAATTAA
1 TAT-AATTAAATTAA
*
501616 -ATAATTTAATTAA
1 TATAATTAAATTAA
501629 CTGTTTACCC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 13 0.52
14 9 0.36
15 3 0.12
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TATAATTAAATTAA
Found at i:503076 original size:22 final size:23
Alignment explanation
Indices: 503044--503087 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
503034 AAATAATTTT
503044 ATTTTTAAATAATAAGATTTAAA
1 ATTTTTAAATAATAAGATTTAAA
* *
503067 ATTTTT-AATATTAATATTTAA
1 ATTTTTAAATAATAAGATTTAA
503088 TTCAATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
ATTTTTAAATAATAAGATTTAAA
Found at i:506134 original size:162 final size:162
Alignment explanation
Indices: 505939--506261 Score: 583
Period size: 162 Copynumber: 2.0 Consensus size: 162
505929 TTATGCAGCT
*
505939 GAGTGGTGGATGATATACGGCACATGTGTTCCCGAATTACAAAAATTAGCAATTAAAGTGCTTAG
1 GAGTGGTGGATAATATACGGCACATGTGTTCCCGAATTACAAAAATTAGCAATTAAAGTGCTTAG
*
506004 TCAAACAACTTCAGCATCAAATTGCGAACGAAATTGGAGCACATTTAGTTATATTCACACCAAGG
66 TCAAACAACTTCAGCATCAAATTGCGAACGAAATTGGAGCAAATTTAGTTATATTCACACCAAGG
506069 CAAGAAATAGGTTAAAGTATAAAAAACTTGAC
131 CAAGAAATAGGTTAAAGTATAAAAAACTTGAC
* **
506101 GAGTGGTGGATAATATACTGCACATGTGTTCCCGAATTACAAAAATTAGCAATTAAAGTGCTTCT
1 GAGTGGTGGATAATATACGGCACATGTGTTCCCGAATTACAAAAATTAGCAATTAAAGTGCTTAG
*
506166 TCAAACAACTTCAGCATTAAATTGCGAACGAAATTGGAGCAAATTTAGTTATATTCACACCAAGG
66 TCAAACAACTTCAGCATCAAATTGCGAACGAAATTGGAGCAAATTTAGTTATATTCACACCAAGG
*
506231 CAAGAAATAGGTTAAAGTATAAAAAGCTTGA
131 CAAGAAATAGGTTAAAGTATAAAAAACTTGA
506262 GAAACTAGTG
Statistics
Matches: 154, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
162 154 1.00
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (162 bp):
GAGTGGTGGATAATATACGGCACATGTGTTCCCGAATTACAAAAATTAGCAATTAAAGTGCTTAG
TCAAACAACTTCAGCATCAAATTGCGAACGAAATTGGAGCAAATTTAGTTATATTCACACCAAGG
CAAGAAATAGGTTAAAGTATAAAAAACTTGAC
Found at i:507247 original size:15 final size:15
Alignment explanation
Indices: 507229--507283 Score: 58
Period size: 15 Copynumber: 3.5 Consensus size: 15
507219 AGAAAACTTT
507229 TGTTGATGTTCTTAA
1 TGTTGATGTTCTTAA
*
507244 TGTTGATGATATTCTT-T
1 TGTTGATG---TTCTTAA
507261 TGTTGATGTTCTTAA
1 TGTTGATGTTCTTAA
*
507276 TTTTGATG
1 TGTTGATG
507284 ATATTAAAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
14 5 0.15
15 15 0.45
17 8 0.24
18 5 0.15
ACGTcount: A:0.18, C:0.05, G:0.20, T:0.56
Consensus pattern (15 bp):
TGTTGATGTTCTTAA
Found at i:507258 original size:18 final size:18
Alignment explanation
Indices: 507232--507288 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
507222 AAACTTTTGT
*
507232 TGATGTTCTTAATGTTGA
1 TGATATTCTTAATGTTGA
*
507250 TGATATTCTT-TTGTTGA
1 TGATATTCTTAATGTTGA
*
507267 TG---TTCTTAATTTTGA
1 TGATATTCTTAATGTTGA
507282 TGATATT
1 TGATATT
507289 AAAACATTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
17 8 0.26
18 11 0.35
ACGTcount: A:0.21, C:0.05, G:0.18, T:0.56
Consensus pattern (18 bp):
TGATATTCTTAATGTTGA
Found at i:507261 original size:32 final size:32
Alignment explanation
Indices: 507225--507288 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
507215 TTAAAGAAAA
507225 CTTTTGTTGATGTTCTTAATGTTGATGATATT
1 CTTTTGTTGATGTTCTTAATGTTGATGATATT
*
507257 CTTTTGTTGATGTTCTTAATTTTGATGATATT
1 CTTTTGTTGATGTTCTTAATGTTGATGATATT
507289 AAAACATTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.19, C:0.06, G:0.17, T:0.58
Consensus pattern (32 bp):
CTTTTGTTGATGTTCTTAATGTTGATGATATT
Found at i:507272 original size:14 final size:14
Alignment explanation
Indices: 507225--507273 Score: 53
Period size: 14 Copynumber: 3.2 Consensus size: 14
507215 TTAAAGAAAA
507225 CTTTTGTTGATGTT
1 CTTTTGTTGATGTT
*
507239 CTTAATGTTGATGATATT
1 CTT-TTGTTGATG---TT
507257 CTTTTGTTGATGTT
1 CTTTTGTTGATGTT
507271 CTT
1 CTT
507274 AATTTTGATG
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 8 0.28
15 8 0.28
17 8 0.28
18 5 0.17
ACGTcount: A:0.14, C:0.08, G:0.18, T:0.59
Consensus pattern (14 bp):
CTTTTGTTGATGTT
Found at i:516429 original size:26 final size:26
Alignment explanation
Indices: 516400--516458 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 26
516390 AGGGAGAGCG
* * *
516400 GCGGCGCGGCGTTGGAGCCTGGGCAT
1 GCGGCGCAGCGCTGGAGCCTAGGCAT
516426 GCGGCGCAGCGCTGGAGCCTAGGCAT
1 GCGGCGCAGCGCTGGAGCCTAGGCAT
516452 GCGGCGC
1 GCGGCGC
516459 TTAGGCTTAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.10, C:0.31, G:0.47, T:0.12
Consensus pattern (26 bp):
GCGGCGCAGCGCTGGAGCCTAGGCAT
Found at i:519139 original size:10 final size:10
Alignment explanation
Indices: 519124--519152 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
519114 TGAATGGACG
519124 GTGAGATAAT
1 GTGAGATAAT
519134 GTGAGATAAT
1 GTGAGATAAT
519144 GTGAGATAA
1 GTGAGATAA
519153 AAAGTAAGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.31, T:0.28
Consensus pattern (10 bp):
GTGAGATAAT
Found at i:520315 original size:18 final size:18
Alignment explanation
Indices: 520279--520315 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
520269 AATTTTAAAG
**
520279 ATTTTTTATTTTTTCATA
1 ATTTTTTATTTTTGAATA
520297 ATTTTTTATTTTTGAATA
1 ATTTTTTATTTTTGAATA
520315 A
1 A
520316 ATATATATAT
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:0.27, C:0.03, G:0.03, T:0.68
Consensus pattern (18 bp):
ATTTTTTATTTTTGAATA
Found at i:521163 original size:24 final size:26
Alignment explanation
Indices: 521122--521185 Score: 80
Period size: 25 Copynumber: 2.5 Consensus size: 26
521112 TTTTGCAATT
*
521122 TCTCTA-AACTTTTACTAAAA-AATA
1 TCTCTAGAAATTTTACTAAAATAATA
521146 TCTCTAGAAATTTT-CTAAAATAATA
1 TCTCTAGAAATTTTACTAAAATAATA
*
521171 TCTTTAGAGAATTTT
1 TCTCTAGA-AATTTT
521186 TCTTTCTACA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 12 0.34
25 17 0.49
26 6 0.17
ACGTcount: A:0.41, C:0.12, G:0.05, T:0.42
Consensus pattern (26 bp):
TCTCTAGAAATTTTACTAAAATAATA
Found at i:521596 original size:11 final size:11
Alignment explanation
Indices: 521582--521657 Score: 61
Period size: 11 Copynumber: 6.8 Consensus size: 11
521572 AAATAATCCT
521582 TTAATATTAAA
1 TTAATATTAAA
521593 TTAATA--AAA
1 TTAATATTAAA
521602 -TAATATTAAGA
1 TTAATATTAA-A
*
521613 TCAATATTAAA
1 TTAATATTAAA
521624 TTAA-ATTTAATA
1 TTAATA-TTAA-A
521636 TTAACCTATTAAA
1 TTAA--TATTAAA
*
521649 ATAATATTA
1 TTAATATTA
521658 TTTTTTAGAA
Statistics
Matches: 53, Mismatches: 3, Indels: 18
0.72 0.04 0.24
Matches are distributed among these distances:
8 5 0.09
9 3 0.06
10 3 0.06
11 20 0.38
12 13 0.25
13 4 0.08
14 4 0.08
15 1 0.02
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:521692 original size:208 final size:208
Alignment explanation
Indices: 521334--521744 Score: 630
Period size: 208 Copynumber: 2.0 Consensus size: 208
521324 TTTATCTACA
*
521334 AGATAAATATTAAATTTAATTTAATATTAAAATAATCACTTTAATATTAAATTAATAAAATACTA
1 AGATAAATATTAAATTTAATTTAATATTAAAATAATCACTTTAATATTAAATTAATAAAATAATA
* * *
521399 TTAAGATAAGTATTTAATTAAATTTAATATTAAATCTATTAAAATAATATTATTTTTGGAACAAT
66 TTAAGATAAGTATTAAATTAAATTTAATATTAAACCTATTAAAATAATATTATTTTTAGAACAAT
* * * *
521464 TAATTTGAAATCAAATTCTTTGGTAAAATCCCAGTAAGAATGTAATTCTTCCACTATTTAACCAC
131 TAATCTGAAATCAAATTCTTTGGTAAAATCCCAGTAAGAATGTAACTCTTCCACTACTCAACCAC
521529 CGAAGACCCGCCC
196 CGAAGACCCGCCC
521542 AGATAAATATTAAATTTAATTTAATATTTAAAATAATC-CTTTAATATTAAATTAATAAAATAAT
1 AGATAAATATTAAATTTAATTTAATA-TTAAAATAATCACTTTAATATTAAATTAATAAAATAAT
*
521606 ATTAAGATCAA-TATTAAATTAAATTTAATATT-AACCTATTAAAATAATATTATTTTTTAGAAT
65 ATTAAGAT-AAGTATTAAATTAAATTTAATATTAAACCTATTAAAATAATATTA-TTTTTAGAAC
* * * * * * *
521669 AGTTAATCTGAAATCAAATTCTTTGGTAGAGTCCCAGTAGGAGTGTAACTCTTTCACTGCTCAAC
128 AATTAATCTGAAATCAAATTCTTTGGTAAAATCCCAGTAAGAATGTAACTCTTCCACTACTCAAC
521734 CACCGAAGACC
193 CACCGAAGACC
521745 AACCATCACC
Statistics
Matches: 184, Mismatches: 16, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
207 19 0.10
208 152 0.83
209 13 0.07
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.37
Consensus pattern (208 bp):
AGATAAATATTAAATTTAATTTAATATTAAAATAATCACTTTAATATTAAATTAATAAAATAATA
TTAAGATAAGTATTAAATTAAATTTAATATTAAACCTATTAAAATAATATTATTTTTAGAACAAT
TAATCTGAAATCAAATTCTTTGGTAAAATCCCAGTAAGAATGTAACTCTTCCACTACTCAACCAC
CGAAGACCCGCCC
Found at i:533090 original size:9 final size:9
Alignment explanation
Indices: 533073--533109 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
533063 TGAGTTTTCG
533073 AATTCGAAT
1 AATTCGAAT
*
533082 AACTCGAAT
1 AATTCGAAT
533091 AATTCGAAT
1 AATTCGAAT
533100 AATTCGAAT
1 AATTCGAAT
533109 A
1 A
533110 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:540011 original size:18 final size:18
Alignment explanation
Indices: 539968--540015 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
539958 AAAATATATG
* *
539968 TTATAAATATTTATAAAAT
1 TTATAAATA-TAAAAAAAT
539987 TTA-AAATATAAAAAAAT
1 TTATAAATATAAAAAAAT
540004 TTATAAAT-TAAA
1 TTATAAATATAAA
540016 GGGTAAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 14 0.54
18 9 0.35
19 3 0.12
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TTATAAATATAAAAAAAT
Found at i:541114 original size:60 final size:61
Alignment explanation
Indices: 541042--541155 Score: 149
Period size: 61 Copynumber: 1.9 Consensus size: 61
541032 TGAGAATTAC
* * * *
541042 AACTAAATTG-AAATTTTTGTAAATATTGAGGGATAAATTTATTGAATTATTTACAATTCG
1 AACTAAAATGAAAACTTTTGTAAACATTGAGAGATAAATTTATTGAATTATTTACAATTCG
* * * *
541102 AACTAAAATGAAAACTTTTGTAAACATTGAGAGCTAATTTTGTTGAATTTTTTA
1 AACTAAAATGAAAACTTTTGTAAACATTGAGAGATAAATTTATTGAATTATTTA
541156 GATTTAGAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
60 9 0.20
61 36 0.80
ACGTcount: A:0.39, C:0.06, G:0.13, T:0.41
Consensus pattern (61 bp):
AACTAAAATGAAAACTTTTGTAAACATTGAGAGATAAATTTATTGAATTATTTACAATTCG
Found at i:552939 original size:15 final size:15
Alignment explanation
Indices: 552919--552967 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
552909 CTAATTAAGC
552919 TTAAATTTTAGTTAA
1 TTAAATTTTAGTTAA
552934 TTAAATTTTAGTTAA
1 TTAAATTTTAGTTAA
*
552949 TT-TATTTTAGATTAA
1 TTAAATTTTAG-TTAA
552964 TTAA
1 TTAA
552968 GTTTAACTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
14 7 0.23
15 23 0.77
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (15 bp):
TTAAATTTTAGTTAA
Found at i:565403 original size:134 final size:132
Alignment explanation
Indices: 565091--565457 Score: 427
Period size: 133 Copynumber: 2.7 Consensus size: 132
565081 GCTTCAACAA
* * * *
565091 AAACGCCGGTAAAGATAACAAATTTGAGGAAAAAATCTGAGCAAAATAGTACCGTTTTATTGTTT
1 AAACGCCGGTAAAGATATCTAATTTGAGGAAAAAATTTGAGCAAAA-CGTACCGTTTTATTGTTT
* * *
565156 CATTTTATTTCTTTAGTGGCGCATTGTAAAAAATGCCGGAAAAGATTGAATTGGCGGCGTTTTCA
65 CATTTTATTTCTTTAGTGGCGCATTGTAAAAAACGCCGGAAAAGATTGAATTAGCGGCATTTTCA
565221 GAG
130 GAG
*
565224 AAACGCCGGTAAAGATATCTAATTTGAGGAAAAAATTTG-GACAAAACGCTACCGTTTTATTGCT
1 AAACGCCGGTAAAGATATCTAATTTGAGGAAAAAATTTGAG-CAAAACG-TACCGTTTTATTGTT
* * * * * *
565288 TCATTTTATTTCTTTAGTGGTGCCTTGTAAAAAACGCC-GCAAATATTGGGATATAGTGGCATTA
64 TCATTTTATTTCTTTAGTGGCGCATTGTAAAAAACGCCGGAAAAGATT-GAAT-TAGCGGCATT-
*
565352 TT-GGAG
126 TTCAGAG
** *
565358 AAACGCCGGTAAAGATATCTAATTTGAGGAAAATTTTTGAGCAAAACGGTACCGTTTTGTTGTTT
1 AAACGCCGGTAAAGATATCTAATTTGAGGAAAAAATTTGAGCAAAAC-GTACCGTTTTATTGTTT
* * * *
565423 CCTTTT-TATGCTTTAGTGGCGAAATGTTAAAAAAC
65 CATTTTAT-TTCTTTAGTGGCGCATTG-TAAAAAAC
565458 ACCAGAAACG
Statistics
Matches: 200, Mismatches: 25, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
132 9 0.05
133 94 0.47
134 85 0.43
135 12 0.06
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.33
Consensus pattern (132 bp):
AAACGCCGGTAAAGATATCTAATTTGAGGAAAAAATTTGAGCAAAACGTACCGTTTTATTGTTTC
ATTTTATTTCTTTAGTGGCGCATTGTAAAAAACGCCGGAAAAGATTGAATTAGCGGCATTTTCAG
AG
Found at i:565835 original size:20 final size:20
Alignment explanation
Indices: 565807--565866 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
565797 ACATTTTTGT
*
565807 GTTTTGGGCTTAGAGTTTAG
1 GTTTAGGGCTTAGAGTTTAG
* *
565827 GTTTAGGGCTTGGAGATTGAG
1 GTTTAGGGCTTAGAG-TTTAG
* * *
565848 GTTTAAGGTTTAGATTTTA
1 GTTTAGGGCTTAGAGTTTA
565867 CATTTTAACG
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
20 16 0.52
21 15 0.48
ACGTcount: A:0.20, C:0.03, G:0.33, T:0.43
Consensus pattern (20 bp):
GTTTAGGGCTTAGAGTTTAG
Found at i:567734 original size:21 final size:21
Alignment explanation
Indices: 567709--567748 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
567699 AGTAGATGCA
*
567709 GCAGCGAGGGAAGCAGAGGCT
1 GCAGCGAGAGAAGCAGAGGCT
567730 GCAGCGAGAGAAGCAGAGG
1 GCAGCGAGAGAAGCAGAGG
567749 TTCAAAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.47, T:0.03
Consensus pattern (21 bp):
GCAGCGAGAGAAGCAGAGGCT
Found at i:568238 original size:21 final size:21
Alignment explanation
Indices: 568212--568251 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
568202 CGGCGCTTAG
*
568212 AAAAAAAATGCCGCTAAAGTT
1 AAAAAAAACGCCGCTAAAGTT
568233 AAAAAAAACGCCGCTAAAG
1 AAAAAAAACGCCGCTAAAG
568252 AGCATGTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.17, G:0.15, T:0.12
Consensus pattern (21 bp):
AAAAAAAACGCCGCTAAAGTT
Found at i:576000 original size:5 final size:6
Alignment explanation
Indices: 575950--575999 Score: 55
Period size: 6 Copynumber: 7.5 Consensus size: 6
575940 CAAAAATAAC
575950 AAAATA AAAATAA AAAATA AAATTTATA CAAAATA AAAATA AAAATA AAA
1 AAAATA AAAAT-A AAAATA AAA---ATA -AAAATA AAAATA AAAATA AAA
576000 TTACAAACAT
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
6 24 0.62
7 9 0.23
9 3 0.08
10 3 0.08
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (6 bp):
AAAATA
Found at i:576013 original size:29 final size:29
Alignment explanation
Indices: 575947--576013 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
575937 TAACAAAAAT
*
575947 AACAAAATAAAAATAAAAAATAAAATTTA
1 AACAAAATAAAAATAAAAAATAAAATTCA
*
575976 TACAAAATAAAAAT-AAAAATAAAATTACA
1 AACAAAATAAAAATAAAAAATAAAATT-CA
*
576005 AACATAATA
1 AACAAAATA
576014 TACTAGTAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 12 0.36
29 21 0.64
ACGTcount: A:0.73, C:0.06, G:0.00, T:0.21
Consensus pattern (29 bp):
AACAAAATAAAAATAAAAAATAAAATTCA
Found at i:577689 original size:31 final size:31
Alignment explanation
Indices: 577618--577715 Score: 116
Period size: 31 Copynumber: 3.3 Consensus size: 31
577608 ATTTGGAACC
*
577618 GACA-TTTTTT-TAATTTGGTATTTAAATTT
1 GACATTTTTTTCTAATTTGATATTTAAATTT
** *
577647 ---ATTTTGGTCTAATTTGATATCTAAATTT
1 GACATTTTTTTCTAATTTGATATTTAAATTT
577675 GACATTTTTTTCTAATTTGATATTTAAATTT
1 GACATTTTTTTCTAATTTGATATTTAAATTT
*
577706 GACACTTTTT
1 GACATTTTTT
577716 CTTAAGTTGG
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
26 1 0.02
27 4 0.07
28 17 0.30
31 34 0.61
ACGTcount: A:0.28, C:0.07, G:0.09, T:0.56
Consensus pattern (31 bp):
GACATTTTTTTCTAATTTGATATTTAAATTT
Found at i:577733 original size:31 final size:31
Alignment explanation
Indices: 577654--577733 Score: 83
Period size: 31 Copynumber: 2.6 Consensus size: 31
577644 TTTATTTTGG
* *
577654 TCTAATTTGAT-ATCTAAATTTGACATTTTTT
1 TCTAAGTTGATAAT-TAAATTTGACATTTTTC
* *
577685 TCTAATTTGATATTTAAATTTGACACTTTTTC
1 TCTAAGTTGATAATTAAATTTGACA-TTTTTC
*
577717 T-TAAGTTGGTAATTAAA
1 TCTAAGTTGATAATTAAA
577734 CTTTTTGGGG
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
31 35 0.83
32 7 0.17
ACGTcount: A:0.31, C:0.09, G:0.09, T:0.51
Consensus pattern (31 bp):
TCTAAGTTGATAATTAAATTTGACATTTTTC
Found at i:578274 original size:58 final size:58
Alignment explanation
Indices: 578194--578342 Score: 165
Period size: 60 Copynumber: 2.5 Consensus size: 58
578184 ATTGAACCTA
*
578194 AAAAAAAGCTTAGGTACCAAATTAGGAAAAA-TGCCAAGTTCAAGTACCAAATTGGGCC
1 AAAAAAAGTTTAGGTACCAAATTAGGAAAAAGTGCCAAGTTCAAGTACCAAATTGGG-C
* * * * * * * * *
578252 CAAAAAAGTTTAGGTACCAAATTAGAAAAAAAGTGTCGATTTTAGGTATCGAATTGGGC
1 AAAAAAAGTTTAGGTACCAAATTAG-GAAAAAGTGCCAAGTTCAAGTACCAAATTGGGC
*
578311 AACAAAAAGTTTAGGTACCAAATTAAGAAAAA
1 AA-AAAAAGTTTAGGTACCAAATTAGGAAAAA
578343 ATATCAAATT
Statistics
Matches: 75, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
58 23 0.31
59 12 0.16
60 40 0.53
ACGTcount: A:0.46, C:0.13, G:0.19, T:0.22
Consensus pattern (58 bp):
AAAAAAAGTTTAGGTACCAAATTAGGAAAAAGTGCCAAGTTCAAGTACCAAATTGGGC
Found at i:578987 original size:124 final size:124
Alignment explanation
Indices: 578765--579143 Score: 650
Period size: 126 Copynumber: 3.0 Consensus size: 124
578755 TTAGGGTTTT
* * * *
578765 TAGGTCCTAGAAGAAATAATTTTGAGTTGACGTTTCTGATCAAATCGTATAAAATCGCTTCTAGC
1 TAGGTCATAGAAGAAATAATTTT--TTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGC
*
578830 AGGATGCTATTTGAGAAGAATTTGTGAAAATAGCGCCCTCGTGGACGCGCTTTTGCTACAG
64 ATGATGCTATTTGAGAAGAATTTGTGAAAATAGCGCCCTCGTGGACGCGCTTTTGCTACAG
*
578891 TAGGTCATAGAAGAAATAATTTTTTTGATGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAT
1 TAGGTCATAGAAGAAATAATTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAT
578956 GATGCTATTTGAGAAGAATTTGTGAAAATAGCGCCCTCGTGGACGCGCTTTTGCTACAG
66 GATGCTATTTGAGAAGAATTTGTGAAAATAGCGCCCTCGTGGACGCGCTTTTGCTACAG
* *
579015 TAGGTCATGGAAGAAATAAAATTTTTTTGACGTTTCTGAGTAAATAGTATAAAATCGCTTCTAGC
1 TAGGTCATAGAAGAAAT--AATTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGC
579080 ATGATGCTATTTGAGAAGAATTTGTGAAAATAGCGCCCTCGTGGACGCGCTTTTGCTACAG
64 ATGATGCTATTTGAGAAGAATTTGTGAAAATAGCGCCCTCGTGGACGCGCTTTTGCTACAG
579141 TAG
1 TAG
579144 CATGTTTGGG
Statistics
Matches: 242, Mismatches: 9, Indels: 4
0.95 0.04 0.02
Matches are distributed among these distances:
124 112 0.46
126 130 0.54
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.32
Consensus pattern (124 bp):
TAGGTCATAGAAGAAATAATTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAT
GATGCTATTTGAGAAGAATTTGTGAAAATAGCGCCCTCGTGGACGCGCTTTTGCTACAG
Found at i:585034 original size:17 final size:17
Alignment explanation
Indices: 584967--585036 Score: 61
Period size: 17 Copynumber: 3.9 Consensus size: 17
584957 TATGTGAATG
*
584967 TAAAATTATTAATT-GA
1 TAAAATTATTAATTATA
* *
584983 TAAATTGTATTAATGATTA
1 TAAAAT-TATTAATTA-TA
*
585002 GTAAAATTATCAAATTATA
1 -TAAAATTAT-TAATTATA
585021 TAAAATTATTAATTAT
1 TAAAATTATTAATTAT
585037 TAGTACCAGG
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
16 5 0.12
17 13 0.31
18 9 0.21
19 6 0.14
20 9 0.21
ACGTcount: A:0.49, C:0.01, G:0.06, T:0.44
Consensus pattern (17 bp):
TAAAATTATTAATTATA
Found at i:585188 original size:9 final size:9
Alignment explanation
Indices: 585170--585205 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
585160 ATTCTCAAAT
585170 AATA-TCAA
1 AATATTCAA
585178 AATATTCAA
1 AATATTCAA
585187 AATATTCAA
1 AATATTCAA
585196 AATATTCAA
1 AATATTCAA
585205 A
1 A
585206 GGTTAGGGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 4 0.15
9 23 0.85
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.31
Consensus pattern (9 bp):
AATATTCAA
Found at i:585232 original size:21 final size:21
Alignment explanation
Indices: 585206--585426 Score: 150
Period size: 21 Copynumber: 10.1 Consensus size: 21
585196 AATATTCAAA
585206 GGTTAGGGTTTTTAAG-TAACG
1 GGTTAGGGTTTTTAAGTTAA-G
* *
585227 GGTTAGAGTTTTTAAGTTTAG
1 GGTTAGGGTTTTTAAGTTAAG
*
585248 GGTTTAGGGTTTTTAA-TTAAATTA
1 GG-TTAGGGTTTTTAAGTT-AA--G
*
585272 AGTTAGGGTTTTTAAGTTAAG
1 GGTTAGGGTTTTTAAGTTAAG
* *
585293 GGTTA-GG-TTTTAATTTAATTA
1 GGTTAGGGTTTTTAAGTTAA--G
*
585314 GGTTAGGGTTTTTAATTTAA-
1 GGTTAGGGTTTTTAAGTTAAG
585334 --TTAGGTTGATTTTTAAGTTAAG
1 GGTTAGG--G-TTTTTAAGTTAAG
* * *
585356 GGTTAGAGTTTTTAATTTAATTA
1 GGTTAGGGTTTTTAAGTTAA--G
* *
585379 GGTTAGGGTTTTTAAATTTAATTA
1 GGTTAGGGTTTTT-AAGTTAA--G
585403 GGTTAGGGTTTTTAAGTTAAG
1 GGTTAGGGTTTTTAAGTTAAG
585424 GGT
1 GGT
585427 ATTAATGGTT
Statistics
Matches: 164, Mismatches: 17, Indels: 38
0.75 0.08 0.17
Matches are distributed among these distances:
18 5 0.03
19 10 0.06
20 3 0.02
21 54 0.33
22 18 0.11
23 44 0.27
24 30 0.18
ACGTcount: A:0.27, C:0.00, G:0.25, T:0.48
Consensus pattern (21 bp):
GGTTAGGGTTTTTAAGTTAAG
Found at i:585277 original size:23 final size:23
Alignment explanation
Indices: 585251--585422 Score: 198
Period size: 23 Copynumber: 7.8 Consensus size: 23
585241 AGTTTAGGGT
* *
585251 TTAGGGTTTTTAATTAAATTAAG
1 TTAGGGTTTTTAATTTAATTAGG
* *
585274 TTAGGGTTTTTAAGTTAA--GGG
1 TTAGGGTTTTTAATTTAATTAGG
585295 TTA-GG-TTTTAATTTAATTAGG
1 TTAGGGTTTTTAATTTAATTAGG
585316 TTAGGGTTTTTAATTTAATTAGG
1 TTAGGGTTTTTAATTTAATTAGG
* * *
585339 TT--GATTTTTAAGTTAA--GGG
1 TTAGGGTTTTTAATTTAATTAGG
*
585358 TTAGAGTTTTTAATTTAATTAGG
1 TTAGGGTTTTTAATTTAATTAGG
585381 TTAGGGTTTTTAAATTTAATTAGG
1 TTAGGGTTTTT-AATTTAATTAGG
*
585405 TTAGGGTTTTTAAGTTAA
1 TTAGGGTTTTTAATTTAA
585423 GGGTATTAAT
Statistics
Matches: 125, Mismatches: 15, Indels: 18
0.79 0.09 0.11
Matches are distributed among these distances:
19 14 0.11
20 2 0.02
21 32 0.26
22 2 0.02
23 52 0.42
24 23 0.18
ACGTcount: A:0.28, C:0.00, G:0.22, T:0.49
Consensus pattern (23 bp):
TTAGGGTTTTTAATTTAATTAGG
Found at i:585319 original size:42 final size:44
Alignment explanation
Indices: 585206--585426 Score: 199
Period size: 42 Copynumber: 5.1 Consensus size: 44
585196 AATATTCAAA
* ** * *
585206 GGTTAGGGTTTTTAA-GTAA-CGGGTTAGAGTTTTTAAGTTTAG
1 GGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAG
* *
585248 GGTTTAGGGTTTTTAATTAAATTAAGTTAGGGTTTTTAAGTTAAG
1 GG-TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAG
*
585293 GGTTA-GG-TTTTAATTTAATTAGGTTAGGGTTTTTAATTTAA-
1 GGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAG
* * * * *
585334 --TTAGGTTGATTTTTAAGTTAA--GGGTTAGAGTTTTTAATTTAATTA
1 GGTTAGG--G-TTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAA--G
585379 GGTTAGGGTTTTTAAATTTAATTAGGTTAGGGTTTTTAAGTTAAG
1 GGTTAGGGTTTTT-AATTTAATTAGGTTAGGGTTTTTAAGTTAAG
585424 GGT
1 GGT
585427 ATTAATGGTT
Statistics
Matches: 145, Mismatches: 18, Indels: 29
0.76 0.09 0.15
Matches are distributed among these distances:
39 3 0.02
40 1 0.01
42 53 0.37
43 15 0.10
44 20 0.14
45 30 0.21
47 23 0.16
ACGTcount: A:0.27, C:0.00, G:0.25, T:0.48
Consensus pattern (44 bp):
GGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAG
Found at i:585336 original size:65 final size:67
Alignment explanation
Indices: 585205--585426 Score: 316
Period size: 65 Copynumber: 3.4 Consensus size: 67
585195 AAATATTCAA
*
585205 AGGTTAGGGTTTTTAAG-TAACGGGTTAGAGTTTTTAAGTTT-A--GGGTTTAGGGTTTTTAATT
1 AGGTTAGGGTTTTTAAGTTAA-GGGTTAGAGTTTTTAA-TTTAATTAGG-TTAGGGTTTTTAATT
*
585266 AAATT
63 TAATT
*
585271 AAGTTAGGGTTTTTAAGTTAAGGGTTAG-G-TTTTAATTTAATTAGGTTAGGGTTTTTAATTTAA
1 AGGTTAGGGTTTTTAAGTTAAGGGTTAGAGTTTTTAATTTAATTAGGTTAGGGTTTTTAATTTAA
585334 TT
66 TT
*
585336 AGGTT--GATTTTTAAGTTAAGGGTTAGAGTTTTTAATTTAATTAGGTTAGGGTTTTTAAATTTA
1 AGGTTAGGGTTTTTAAGTTAAGGGTTAGAGTTTTTAATTTAATTAGGTTAGGGTTTTT-AATTTA
585399 ATT
65 ATT
585402 AGGTTAGGGTTTTTAAGTTAAGGGT
1 AGGTTAGGGTTTTTAAGTTAAGGGT
585427 ATTAATGGTT
Statistics
Matches: 141, Mismatches: 6, Indels: 16
0.87 0.04 0.10
Matches are distributed among these distances:
63 23 0.16
64 8 0.06
65 51 0.36
66 39 0.28
67 3 0.02
68 17 0.12
ACGTcount: A:0.27, C:0.00, G:0.25, T:0.47
Consensus pattern (67 bp):
AGGTTAGGGTTTTTAAGTTAAGGGTTAGAGTTTTTAATTTAATTAGGTTAGGGTTTTTAATTTAA
TT
Found at i:585422 original size:29 final size:24
Alignment explanation
Indices: 585356--585417 Score: 108
Period size: 24 Copynumber: 2.6 Consensus size: 24
585346 TTAAGTTAAG
*
585356 GGTTAGAGTTTTT-AATTTAATTA
1 GGTTAGGGTTTTTAAATTTAATTA
585379 GGTTAGGGTTTTTAAATTTAATTA
1 GGTTAGGGTTTTTAAATTTAATTA
585403 GGTTAGGGTTTTTAA
1 GGTTAGGGTTTTTAA
585418 GTTAAGGGTA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
23 12 0.32
24 25 0.68
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (24 bp):
GGTTAGGGTTTTTAAATTTAATTA
Found at i:585471 original size:9 final size:9
Alignment explanation
Indices: 585453--585498 Score: 85
Period size: 9 Copynumber: 5.2 Consensus size: 9
585443 ATTCTCAAAT
585453 AATA-TCAA
1 AATATTCAA
585461 AATATTCAA
1 AATATTCAA
585470 AATATTCAA
1 AATATTCAA
585479 AATATTCAA
1 AATATTCAA
585488 AATATTCAA
1 AATATTCAA
585497 AA
1 AA
585499 ATTTCTATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
8 4 0.11
9 33 0.89
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (9 bp):
AATATTCAA
Found at i:585530 original size:25 final size:25
Alignment explanation
Indices: 585501--585616 Score: 122
Period size: 25 Copynumber: 4.9 Consensus size: 25
585491 ATTCAAAAAT
585501 TTCTATTTTATTACATCAAATAAAC
1 TTCTATTTTATTACATCAAATAAAC
585526 TTCTATTTTATTACATCAAAT-AA-
1 TTCTATTTTATTACATCAAATAAAC
** * *
585549 TATC-A--AAATAAC-T-AAA-AAAA
1 T-TCTATTTTATTACATCAAATAAAC
585569 TTCTATTTTATTACATCAAATAAAC
1 TTCTATTTTATTACATCAAATAAAC
*
585594 TCCTATTTTATTACATCAAATAA
1 TTCTATTTTATTACATCAAATAA
585617 TATCAAAATA
Statistics
Matches: 74, Mismatches: 8, Indels: 18
0.74 0.08 0.18
Matches are distributed among these distances:
19 7 0.09
20 3 0.04
21 4 0.05
22 4 0.05
23 3 0.04
24 7 0.09
25 46 0.62
ACGTcount: A:0.45, C:0.15, G:0.00, T:0.41
Consensus pattern (25 bp):
TTCTATTTTATTACATCAAATAAAC
Found at i:585573 original size:68 final size:68
Alignment explanation
Indices: 585495--585626 Score: 246
Period size: 68 Copynumber: 1.9 Consensus size: 68
585485 CAAAATATTC
* *
585495 AAAAATTTCTATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAA
1 AAAAAATTCTATTTTATTACATCAAATAAACTCCTATTTTATTACATCAAATAATATCAAAATAA
585560 CTA
66 CTA
585563 AAAAAATTCTATTTTATTACATCAAATAAACTCCTATTTTATTACATCAAATAATATCAAAATA
1 AAAAAATTCTATTTTATTACATCAAATAAACTCCTATTTTATTACATCAAATAATATCAAAATA
585627 TTCAAAATAT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 62 1.00
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.39
Consensus pattern (68 bp):
AAAAAATTCTATTTTATTACATCAAATAAACTCCTATTTTATTACATCAAATAATATCAAAATAA
CTA
Found at i:586711 original size:7 final size:7
Alignment explanation
Indices: 586701--586725 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
586691 TTATATACAT
586701 AATACTA
1 AATACTA
586708 AATACTA
1 AATACTA
586715 AATACTA
1 AATACTA
586722 AATA
1 AATA
586726 TCAATCGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:587991 original size:14 final size:11
Alignment explanation
Indices: 587948--587987 Score: 64
Period size: 11 Copynumber: 3.6 Consensus size: 11
587938 AAGAGAATTT
587948 TTGA-AGGAAA
1 TTGAGAGGAAA
587958 TTGAGAGGAAA
1 TTGAGAGGAAA
587969 TTGAGAGGAAA
1 TTGAGAGGAAA
587980 TTTGAGAG
1 -TTGAGAG
587988 AGGATTAGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 4 0.14
11 17 0.61
12 7 0.25
ACGTcount: A:0.42, C:0.00, G:0.35, T:0.23
Consensus pattern (11 bp):
TTGAGAGGAAA
Found at i:592095 original size:28 final size:29
Alignment explanation
Indices: 592064--592118 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
592054 TATATATTTT
*
592064 AAATAGTTTTAATA-ATTTAAATTTTTAG
1 AAATACTTTTAATATATTTAAATTTTTAG
* *
592092 AAATACTTTTTATATATTTGAATTTTT
1 AAATACTTTTAATATATTTAAATTTTT
592119 TAAATTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 12 0.52
29 11 0.48
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (29 bp):
AAATACTTTTAATATATTTAAATTTTTAG
Found at i:592123 original size:28 final size:27
Alignment explanation
Indices: 592060--592123 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
592050 ATTTTATATA
*
592060 TTTTAAATAGTTTTAATAATTTAAATT
1 TTTTAAATACTTTTAATAATTTAAATT
* * *
592087 TTTAGAAATACTTTTTATATATTTGAATT
1 TTT-TAAATACTTTTAATA-ATTTAAATT
592116 TTTTAAAT
1 TTTTAAAT
592124 TTAAAAAATT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
27 3 0.10
28 16 0.53
29 11 0.37
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.56
Consensus pattern (27 bp):
TTTTAAATACTTTTAATAATTTAAATT
Found at i:593389 original size:36 final size:36
Alignment explanation
Indices: 593306--593390 Score: 86
Period size: 36 Copynumber: 2.4 Consensus size: 36
593296 CTAAAATTGT
* * *
593306 AGCAAAA-T-TAATAATAAAACAAGAGCTATATAAT
1 AGCAAAATTATAATAACAAAACAAGAGCAATATAAA
* * *
593340 ATCCAAATAATAATAACAAAAC-AGTAGCAATATAAA
1 AGCAAAATTATAATAACAAAACAAG-AGCAATATAAA
593376 AGCAAAATTATAATA
1 AGCAAAATTATAATA
593391 CAACAATGAA
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
34 5 0.13
35 2 0.05
36 32 0.82
ACGTcount: A:0.60, C:0.11, G:0.07, T:0.22
Consensus pattern (36 bp):
AGCAAAATTATAATAACAAAACAAGAGCAATATAAA
Found at i:594141 original size:11 final size:11
Alignment explanation
Indices: 594125--594149 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
594115 ATTTTTTAAC
594125 TTTAAAATACT
1 TTTAAAATACT
594136 TTTAAAATACT
1 TTTAAAATACT
594147 TTT
1 TTT
594150 TTTAATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (11 bp):
TTTAAAATACT
Found at i:597865 original size:28 final size:28
Alignment explanation
Indices: 597833--597923 Score: 119
Period size: 28 Copynumber: 3.2 Consensus size: 28
597823 AAATTAAGGC
* **
597833 AGTTCACGATAGGGGTTTGCCATAGGTG
1 AGTTCACGATAAGGGTTCACCATAGGTG
597861 AGTTCACGATAAGGGTTCACCATAGGTG
1 AGTTCACGATAAGGGTTCACCATAGGTG
** * *
597889 AGTTTGCCATAAGGGTTCACCATATGTG
1 AGTTCACGATAAGGGTTCACCATAGGTG
597917 AGTTCAC
1 AGTTCAC
597924 CAGACATAGG
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 54 1.00
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.29
Consensus pattern (28 bp):
AGTTCACGATAAGGGTTCACCATAGGTG
Found at i:597923 original size:15 final size:15
Alignment explanation
Indices: 597852--597925 Score: 66
Period size: 15 Copynumber: 5.2 Consensus size: 15
597842 TAGGGGTTTG
*
597852 CCATAGGTGAGTTCA
1 CCATAAGTGAGTTCA
*
597867 CGATAAG-G-GTTCA
1 CCATAAGTGAGTTCA
* **
597880 CCATAGGTGAGTTTG
1 CCATAAGTGAGTTCA
597895 CCATAAG-G-GTTCA
1 CCATAAGTGAGTTCA
*
597908 CCATATGTGAGTTCA
1 CCATAAGTGAGTTCA
597923 CCA
1 CCA
597926 GACATAGGAG
Statistics
Matches: 45, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
13 19 0.42
14 4 0.09
15 22 0.49
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (15 bp):
CCATAAGTGAGTTCA
Found at i:603661 original size:164 final size:164
Alignment explanation
Indices: 603372--604726 Score: 1173
Period size: 164 Copynumber: 8.4 Consensus size: 164
603362 TATACTATTT
* * * *
603372 ATAACCAAAG-AAAATAAGCATTTATAAGACACGATGGAGTATAGA-TTT-AGTCATCGTTAAAA
1 ATAACCAAAGCAAAATAAGCATTTATAAAACACAATGGAATATAAACTTTAAGT-ATCGTTAAAA
* * * *
603434 GATATATAATTTGAAAACCATCTTACTTA--ATAATAAAAACAAAATAAGCATTTATAATAAAAT
65 GATATATAATTCGAAAACCATTTTACTTATTAAAACAAAAACAAAATAAGCATTTATAATAAAAT
* * * * * *
603497 ACAAGTTTAAGTATAATAAAAGATGTATGATTCCG
130 AGAGGTTTAGGTATAGTGAAAGGTGTATGATTCCG
* * * *
603532 ATAACGAAAGCGAAATAAGAATTTATAAAACACGATGGAATATAAACTTTAAGTATCGTTAAAAG
1 ATAACCAAAGCAAAATAAGCATTTATAAAACACAATGGAATATAAACTTTAAGTATCGTTAAAAG
*
603597 ATATATAAATT-GAAAACCATTTTATTTATTAAAACAAAAACAAAATAAGCATTTATAATAAAAT
66 ATATAT-AATTCGAAAACCATTTTACTTATTAAAACAAAAACAAAATAAGCATTTATAATAAAAT
* * **
603661 ATAAGTTTAGGTATAGAAAAAGGTG--TGATTCCG
130 AGAGGTTTAGGTATAGTGAAAGGTGTATGATTCCG
* * * * *
603694 GTAACGAAAGCAAAATAAGTATTTATAGAACACAATGGAATATAAACTTTAGGTATCGTTAAAAG
1 ATAACCAAAGCAAAATAAGCATTTATAAAACACAATGGAATATAAACTTTAAGTATCGTTAAAAG
* * ** *
603759 ATATATAATTTG-AAACCATTTTGCTTATTAAAACAGGAACAAAATAATCATTTATAATAAAATA
66 ATATATAATTCGAAAACCATTTTACTTATTAAAACAAAAACAAAATAAGCATTTATAATAAAATA
* * * * ** *
603823 CAAGTTTAGGTATTGTAAAAGAAGTA--A----A
131 GAGGTTTAGGTATAGTGAAAGGTGTATGATTCCG
* * * * * * * * ** *
603851 ATAAGCATTTA-TAAAGTACG-A-TGA-AATATA-AACTTTAAGTAT---CGTTAAAAGATAT--
1 ATAACCA--AAGCAAAATAAGCATTTATAAAACACAA-TGGAA-TATAAAC-TT-TAAG-TATCG
* *** * * * * *
603906 ATAATTCAT-TATAATTCAAAAATCATTATACTTATTAAAATAAAAACAAAAGTAAGCATCTATA
59 TTAAAAGATATATAATTCGAAAACCATTTTACTTATTAAAACAAAAACAAAA-TAAGCATTTATA
*
603970 ATAAAATAGAGGTTTAGGTATAGTGAAAGGTGGATGATTCCG
123 ATAAAATAGAGGTTTAGGTATAGTGAAAGGTGTATGATTCCG
* ** *
604012 ATAACGAAAGCAAAATTAA-CATTTATAGTACACAATGAAATATAAACTTTAAGTATCGTTAAAA
1 ATAACCAAAGCAAAA-TAAGCATTTATAAAACACAATGGAATATAAACTTTAAGTATCGTTAAAA
* * * * *
604076 AATATATAATTCGAAAACCGTCTTACTTATTAAAACAGAAACAAAATAAGCATTTATAATGAAAT
65 GATATATAATTCGAAAACCATTTTACTTATTAAAACAAAAACAAAATAAGCATTTATAATAAAAT
* * *
604141 AGAGGTTTAGGTATAGCGGAAGGTGTATGATTCCT
130 AGAGGTTTAGGTATAGTGAAAGGTGTATGATTCCG
* * * ** **
604176 ATAACCAAAGCAAAATAAGTATTGATATAACACTCGTAAAATATAAACTTTAAGTATCGTTAAAA
1 ATAACCAAAGCAAAATAAGCATTTATAAAACAC-AATGGAATATAAACTTTAAGTATCGTTAAAA
* * * *
604241 GATATCTAATTTGAAAA-CAATTTACTTATTGAAACAAAAACAAAATAAGC----ATAATAAAAT
65 GATATATAATTCGAAAACCATTTTACTTATTAAAACAAAAACAAAATAAGCATTTATAATAAAAT
604301 AGAGGTTTAGGTATAGTGAAAGGTGTATGATTCCG
130 AGAGGTTTAGGTATAGTGAAAGGTGTATGATTCCG
* * *
604336 ATAACCAAAGAAAAATAAGCATTTATATAACATCCAT-G-----AAA---T-A-TATCGTTAAAA
1 ATAACCAAAGCAAAATAAGCATTTATAAAACA-CAATGGAATATAAACTTTAAGTATCGTTAAAA
* * *
604390 GATATATAATTCGAAAACCGA-TTTACTTATTAAAACAAAAACAAATTATGCATTTATAACAAAA
65 GATATATAATTCGAAAACC-ATTTTACTTATTAAAACAAAAACAAAATAAGCATTTATAATAAAA
* * *
604454 TAGAGGTATAGATATGGTGAAAGGTGTATGATTCCG
129 TAGAGGTTTAGGTATAGTGAAAGGTGTATGATTCCG
* * * * *
604490 ATAACCAAAGCAAAATAAGCATTTATAATATATAATGAAATATAAATTTTAAGTATCGTTAAAAG
1 ATAACCAAAGCAAAATAAGCATTTATAAAACACAATGGAATATAAACTTTAAGTATCGTTAAAAG
* * * * * *
604555 ATATATAATTCGAAAATCGTTCTACTTATT-AAA-AAAAATAAAGTACGCATTTATAATAAAATA
66 ATATATAATTCGAAAACCATTTTACTTATTAAAACAAAAACAAAATAAGCATTTATAATAAAATA
*
604618 GAGGTATAGGTATGGTGAAAGGTGAAAGGTGTATGATTCCG
131 GAGGT-T---TA-GGT-ATA-GTGAAAGGTGTATGATTCCG
* * * ** * * *
604659 ATAACCAAAGCAAAACAAGCATTTATATAACACTCATAAAATATAAACTTTAAGCATAGTTGAAA
1 ATAACCAAAGCAAAATAAGCATTTATAAAACAC-AATGGAATATAAACTTTAAGTATCGTTAAAA
604724 GAT
65 GAT
604727 GTAGTTTAGG
Statistics
Matches: 969, Mismatches: 161, Indels: 120
0.78 0.13 0.10
Matches are distributed among these distances:
149 26 0.03
150 29 0.03
151 2 0.00
153 10 0.01
154 107 0.11
155 45 0.05
156 8 0.01
157 6 0.01
158 6 0.01
159 5 0.01
160 84 0.09
161 110 0.11
162 149 0.15
163 24 0.02
164 199 0.21
165 78 0.08
166 2 0.00
167 2 0.00
168 1 0.00
169 48 0.05
170 28 0.03
ACGTcount: A:0.48, C:0.10, G:0.13, T:0.29
Consensus pattern (164 bp):
ATAACCAAAGCAAAATAAGCATTTATAAAACACAATGGAATATAAACTTTAAGTATCGTTAAAAG
ATATATAATTCGAAAACCATTTTACTTATTAAAACAAAAACAAAATAAGCATTTATAATAAAATA
GAGGTTTAGGTATAGTGAAAGGTGTATGATTCCG
Done.