Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold337
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1638316
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.28
Warning! 264207 characters in sequence are not A, C, G, or T
File 3 of 5
Found at i:381952 original size:35 final size:35
Alignment explanation
Indices: 381898--381965 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
381888 TTGCTGTTTT
*
381898 AGTATTTAAGAGAAGATTTTTCTCCGAATTTTTGA
1 AGTATTTAAGAGAAGATTTTCCTCCGAATTTTTGA
* *
381933 AGTATTTAATAGAATATTTTCCTCCGAATTTTT
1 AGTATTTAAGAGAAGATTTTCCTCCGAATTTTT
381966 AACAAATCCC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.46
Consensus pattern (35 bp):
AGTATTTAAGAGAAGATTTTCCTCCGAATTTTTGA
Found at i:395987 original size:30 final size:30
Alignment explanation
Indices: 395951--396014 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
395941 AAGAAGCAGC
395951 ATTTACTAGGCATATATAACAAGAGTTATT
1 ATTTACTAGGCATATATAACAAGAGTTATT
395981 ATTTACTAGGCATATATAACAAGAGTTATT
1 ATTTACTAGGCATATATAACAAGAGTTATT
396011 ATTT
1 ATTT
396015 TCCACTGACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.39
Consensus pattern (30 bp):
ATTTACTAGGCATATATAACAAGAGTTATT
Found at i:398119 original size:14 final size:15
Alignment explanation
Indices: 398038--398118 Score: 112
Period size: 15 Copynumber: 5.5 Consensus size: 15
398028 AGTGAGACAA
398038 GGTCAGGGGAATCAG
1 GGTCAGGGGAATCAG
* *
398053 GGTCAGGGGGA-CAA
1 GGTCAGGGGAATCAG
398067 GGTCAGGGGAATCAG
1 GGTCAGGGGAATCAG
* *
398082 GGTCAGGGGGA-CAA
1 GGTCAGGGGAATCAG
398096 GGTCAGGGGAATCAG
1 GGTCAGGGGAATCAG
398111 GGTCAGGG
1 GGTCAGGG
398119 AGAGAAGACC
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
14 24 0.43
15 32 0.57
ACGTcount: A:0.26, C:0.14, G:0.49, T:0.11
Consensus pattern (15 bp):
GGTCAGGGGAATCAG
Found at i:398131 original size:29 final size:29
Alignment explanation
Indices: 398033--398118 Score: 172
Period size: 29 Copynumber: 3.0 Consensus size: 29
398023 GGGTTAGTGA
398033 GACAAGGTCAGGGGAATCAGGGTCAGGGG
1 GACAAGGTCAGGGGAATCAGGGTCAGGGG
398062 GACAAGGTCAGGGGAATCAGGGTCAGGGG
1 GACAAGGTCAGGGGAATCAGGGTCAGGGG
398091 GACAAGGTCAGGGGAATCAGGGTCAGGG
1 GACAAGGTCAGGGGAATCAGGGTCAGGG
398119 AGAGAAGACC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 57 1.00
ACGTcount: A:0.28, C:0.14, G:0.48, T:0.10
Consensus pattern (29 bp):
GACAAGGTCAGGGGAATCAGGGTCAGGGG
Found at i:399292 original size:25 final size:24
Alignment explanation
Indices: 399205--399294 Score: 83
Period size: 25 Copynumber: 3.5 Consensus size: 24
399195 AAGAAGGGGG
* *
399205 AATCTAGGTTAAACAATAACAAAGA
1 AATCTAGG-TCAACAATAATAAAGA
*
399230 AATGTAGGTCAA-AATAATAACAGAAAA
1 AATCTAGGTCAACAATAATAA-AG---A
399257 TAATCTAGGTCAATCAATAATAAAGA
1 -AATCTAGGTCAA-CAATAATAAAGA
399283 AATCTAGGTCAA
1 AATCTAGGTCAA
399295 ATAGGTGCTG
Statistics
Matches: 54, Mismatches: 4, Indels: 14
0.75 0.06 0.19
Matches are distributed among these distances:
23 7 0.13
24 5 0.09
25 19 0.35
26 1 0.02
27 1 0.02
28 11 0.20
29 2 0.04
30 8 0.15
ACGTcount: A:0.53, C:0.11, G:0.13, T:0.22
Consensus pattern (24 bp):
AATCTAGGTCAACAATAATAAAGA
Found at i:400429 original size:2 final size:2
Alignment explanation
Indices: 400422--400459 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
400412 TTAAATTCTT
*
400422 GA GA GA GA GA GA GG GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
400460 TATTTGCTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
GA
Found at i:402092 original size:22 final size:22
Alignment explanation
Indices: 402064--402108 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
402054 TTTTCACTGT
402064 TACAACAAGCACCTGTTTACAC
1 TACAACAAGCACCTGTTTACAC
402086 TACAACAAGCACCTGTTTACAC
1 TACAACAAGCACCTGTTTACAC
402108 T
1 T
402109 TACCTCTCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.31, G:0.09, T:0.24
Consensus pattern (22 bp):
TACAACAAGCACCTGTTTACAC
Found at i:403790 original size:2 final size:2
Alignment explanation
Indices: 403783--403828 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
403773 TTTACAATGA
403783 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
403825 TC TC
1 TC TC
403829 GGGAGAGAGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:404307 original size:24 final size:24
Alignment explanation
Indices: 404274--404321 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
404264 TTTTATAAAT
*
404274 GCTTCATTTAATTACAATGTCGAG
1 GCTTCATTTAATTACAATGCCGAG
* * *
404298 GCTTCGTTTATTTTCAATGCCGAG
1 GCTTCATTTAATTACAATGCCGAG
404322 ATATACAACA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.40
Consensus pattern (24 bp):
GCTTCATTTAATTACAATGCCGAG
Found at i:408802 original size:30 final size:30
Alignment explanation
Indices: 408766--408833 Score: 127
Period size: 30 Copynumber: 2.3 Consensus size: 30
408756 CACTAACATT
*
408766 TTATACATCAGCCGAGGGAACTAACAACCA
1 TTATACATCAGACGAGGGAACTAACAACCA
408796 TTATACATCAGACGAGGGAACTAACAACCA
1 TTATACATCAGACGAGGGAACTAACAACCA
408826 TTATACAT
1 TTATACAT
408834 GTAATCATCC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.41, C:0.24, G:0.15, T:0.21
Consensus pattern (30 bp):
TTATACATCAGACGAGGGAACTAACAACCA
Found at i:409813 original size:19 final size:19
Alignment explanation
Indices: 409789--409828 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
409779 ATTTGNGCAA
* *
409789 CAAAAACTTTAACCTGCTC
1 CAAAAACCTTAACCTCCTC
409808 CAAAAACCTTAACCTCCTC
1 CAAAAACCTTAACCTCCTC
409827 CA
1 CA
409829 GCATCCAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.38, G:0.03, T:0.23
Consensus pattern (19 bp):
CAAAAACCTTAACCTCCTC
Found at i:410211 original size:29 final size:29
Alignment explanation
Indices: 410169--410275 Score: 214
Period size: 29 Copynumber: 3.7 Consensus size: 29
410159 NNNNNNNNNN
410169 TAGATTTCTTATTTTATACACAAAAACTG
1 TAGATTTCTTATTTTATACACAAAAACTG
410198 TAGATTTCTTATTTTATACACAAAAACTG
1 TAGATTTCTTATTTTATACACAAAAACTG
410227 TAGATTTCTTATTTTATACACAAAAACTG
1 TAGATTTCTTATTTTATACACAAAAACTG
410256 TAGATTTCTTATTTTATACA
1 TAGATTTCTTATTTTATACA
410276 AGTACTTATT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 78 1.00
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.44
Consensus pattern (29 bp):
TAGATTTCTTATTTTATACACAAAAACTG
Found at i:415280 original size:2 final size:2
Alignment explanation
Indices: 415273--415367 Score: 174
Period size: 2 Copynumber: 48.0 Consensus size: 2
415263 GAATACCTTG
*
415273 GA GA GA GA GA AA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
415315 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
415357 GA GA GA G- GA GA
1 GA GA GA GA GA GA
415368 TTGNNNNNNN
Statistics
Matches: 90, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
1 1 0.01
2 89 0.99
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:415388 original size:2 final size:2
Alignment explanation
Indices: 415381--415414 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
415371 NNNNNNNNNN
415381 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
415415 GTGTCATTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:419640 original size:67 final size:67
Alignment explanation
Indices: 419541--419720 Score: 294
Period size: 66 Copynumber: 2.7 Consensus size: 67
419531 TCAGACTTCT
*
419541 GTGGCCAGCAAGATATGCACCAGTGTTGTCTGACCTGTGAGATATATT-AGAATCCAGTCAGACA
1 GTGGCCAGCGAGATATGCACCAGTGTTGTCTGACCTGTGAGATAT-TTGAGAATCCAGTCAGACA
419605 GCC
65 GCC
* *
419608 GTGGCCAGCGAGATATGCACCAAG-GTTTTCTGACCTGTGA-ATATTTGAGAGTCCAGTCAGACA
1 GTGGCCAGCGAGATATGCACC-AGTGTTGTCTGACCTGTGAGATATTTGAGAATCCAGTCAGACA
419671 GCC
65 GCC
419674 GTGGCCAGCGAGATATGCACCAGTGTTGTCTGACCTGTGAGATATTT
1 GTGGCCAGCGAGATATGCACCAGTGTTGTCTGACCTGTGAGATATTT
419721 CAGTATTGTC
Statistics
Matches: 105, Mismatches: 4, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
65 4 0.04
66 58 0.55
67 41 0.39
68 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (67 bp):
GTGGCCAGCGAGATATGCACCAGTGTTGTCTGACCTGTGAGATATTTGAGAATCCAGTCAGACAG
CC
Found at i:421139 original size:35 final size:35
Alignment explanation
Indices: 421093--421346 Score: 490
Period size: 35 Copynumber: 7.3 Consensus size: 35
421083 GGCCAAGAAN
421093 AGTGTTCCACGGTCACCACAGACACTAGATACCAC
1 AGTGTTCCACGGTCACCACAGACACTAGATACCAC
421128 AGTGTTCCACGGTCACCACAGACACTAGATACCAC
1 AGTGTTCCACGGTCACCACAGACACTAGATACCAC
421163 AGTGTTCCACGGTCACCACAGACACTAGATACCAC
1 AGTGTTCCACGGTCACCACAGACACTAGATACCAC
421198 AGTGTTCCACGGTCACCACAGACACTAGATACCAC
1 AGTGTTCCACGGTCACCACAGACACTAGATACCAC
421233 AGTGTTCCACGGTCACCACAGACACTAGATACCAC
1 AGTGTTCCACGGTCACCACAGACACTAGATACCAC
*
421268 AGTGTTCCACGGTCCCCACAGACACTAGATACCAC
1 AGTGTTCCACGGTCACCACAGACACTAGATACCAC
*
421303 AGTGTTCCACGGTCACCACAGACAATAGATACCAC
1 AGTGTTCCACGGTCACCACAGACACTAGATACCAC
421338 AGTGTTCCA
1 AGTGTTCCA
421347 GCTACAGAGA
Statistics
Matches: 216, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
35 216 1.00
ACGTcount: A:0.31, C:0.34, G:0.17, T:0.18
Consensus pattern (35 bp):
AGTGTTCCACGGTCACCACAGACACTAGATACCAC
Found at i:422512 original size:30 final size:30
Alignment explanation
Indices: 422477--422537 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
422467 ATTTCGAACT
422477 GCCGGTCAATAGACTGCGATCTATTAGACC
1 GCCGGTCAATAGACTGCGATCTATTAGACC
* *
422507 GCCGGTCAATAGACTTCGATCTATTGGACC
1 GCCGGTCAATAGACTGCGATCTATTAGACC
422537 G
1 G
422538 NNNNNNNNNN
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.25, C:0.26, G:0.25, T:0.25
Consensus pattern (30 bp):
GCCGGTCAATAGACTGCGATCTATTAGACC
Found at i:423394 original size:2 final size:2
Alignment explanation
Indices: 423316--423378 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
423306 CAATATGATC
423316 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
423358 CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT C
423379 CTACTTTCCC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:425034 original size:45 final size:45
Alignment explanation
Indices: 424964--425145 Score: 328
Period size: 45 Copynumber: 4.0 Consensus size: 45
424954 TCATAGTTTG
*
424964 GGGACCGTCGGAACCCTTGTAAATGTACCTTAGCAGTAGGCATTAA
1 GGGACCGTCGG-ACCCTTGTTAATGTACCTTAGCAGTAGGCATTAA
*
425010 GGGACCATCGGACCCTTGTTAATGTACCTTAGCAGTAGGCATTAA
1 GGGACCGTCGGACCCTTGTTAATGTACCTTAGCAGTAGGCATTAA
*
425055 GGGACCGCCGGACCCTTGTTAATGTACCTTAGCAGTAGGCATTAA
1 GGGACCGTCGGACCCTTGTTAATGTACCTTAGCAGTAGGCATTAA
425100 GGGACCGTCGGACCCTTGTTAATGTACCTTAGCAGTAGGCATTAA
1 GGGACCGTCGGACCCTTGTTAATGTACCTTAGCAGTAGGCATTAA
425145 G
1 G
425146 AAGTATTAGC
Statistics
Matches: 131, Mismatches: 5, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
45 121 0.92
46 10 0.08
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (45 bp):
GGGACCGTCGGACCCTTGTTAATGTACCTTAGCAGTAGGCATTAA
Found at i:431091 original size:2 final size:2
Alignment explanation
Indices: 431084--431117 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
431074 GCCTGGCATA
*
431084 CT CT CT CT CA CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
431118 GCCCTAAGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.03, C:0.50, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:431195 original size:2 final size:2
Alignment explanation
Indices: 431188--431221 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
431178 GGTTGGTGTA
431188 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
431222 GCCCTAAGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:431243 original size:104 final size:104
Alignment explanation
Indices: 431082--431515 Score: 726
Period size: 104 Copynumber: 4.3 Consensus size: 104
431072 CTGCCTGGCA
*
431082 TACTCTCTCTCACTCTCTCTCTCTCTCTCTCTCTCTGCCCTAAGGGGCTCATCACTACATCCAAG
1 TACTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGCCCTAAGGGGCTCATCACTACATCCAAG
*
431147 TTCTTCACTGTCCCTCCCAAAATACCGATCAGGTTGGTG
66 TTCTTCACTGTCCCTCCCAAAATACCCATCAGGTTGGTG
431186 TACTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGCCCTAAGGGGCTCATCACTACATCCAAG
1 TACTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGCCCTAAGGGGCTCATCACTACATCCAAG
*
431251 TTCTTCACTGTCCCTCCCAAAATACCGATCAGGTTGGTG
66 TTCTTCACTGTCCCTCCCAAAATACCCATCAGGTTGGTG
431290 TA--CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGCCCTAAGGGGCTCATCACTACATCCAAG
1 TACTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGCCCTAAGGGGCTCATCACTACATCCAAG
431353 TTCTTCACTGTCCCTCCCAAAATACCCATCAGGTTGGTG
66 TTCTTCACTGTCCCTCCCAAAATACCCATCAGGTTGGTG
* * * *
431392 TA--------CACACACACTCTCTCTCTCTCTCTCTGCCCTAAGGGGCTCATCACTACATCCAAG
1 TACTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGCCCTAAGGGGCTCATCACTACATCCAAG
*
431449 TTTTTCACTGTCCCTCCCAAAATACCCATCAGGTTGGTG
66 TTCTTCACTGTCCCTCCCAAAATACCCATCAGGTTGGTG
431488 TACTCTCTCTCTCTCTCTCTCTCTCTCT
1 TACTCTCTCTCTCTCTCTCTCTCTCTCT
431516 GCCCTAACTC
Statistics
Matches: 311, Mismatches: 11, Indels: 16
0.92 0.03 0.05
Matches are distributed among these distances:
96 91 0.29
102 101 0.32
104 119 0.38
ACGTcount: A:0.17, C:0.38, G:0.12, T:0.33
Consensus pattern (104 bp):
TACTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGCCCTAAGGGGCTCATCACTACATCCAAG
TTCTTCACTGTCCCTCCCAAAATACCCATCAGGTTGGTG
Found at i:431299 original size:2 final size:2
Alignment explanation
Indices: 431292--431323 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
431282 GGTTGGTGTA
431292 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
431324 GCCCTAAGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:431304 original size:96 final size:96
Alignment explanation
Indices: 431196--431522 Score: 546
Period size: 96 Copynumber: 3.3 Consensus size: 96
431186 TACTCTCTCT
431196 CTCTCTCTCTCTCTCTCTCTCTCTCTGCCCTAAGGGGCTCATCACTACATCCAAGTTCTTCACTG
1 CTCTCTCTCTCTCTCTCTCTCTCTCTGCCCTAAGGGGCTCATCACTACATCCAAGTTCTTCACTG
*
431261 TCCCTCCCAAAATACCGATCAGGTTGGTGTA
66 TCCCTCCCAAAATACCCATCAGGTTGGTGTA
431292 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGCCCTAAGGGGCTCATCACTACATCCAAGTTCT
1 ------CTCTCTCTCTCTCTCTCTCTCTCTCTGCCCTAAGGGGCTCATCACTACATCCAAGTTCT
431357 TCACTGTCCCTCCCAAAATACCCATCAGGTTGGTGTA
60 TCACTGTCCCTCCCAAAATACCCATCAGGTTGGTGTA
* * * * *
431394 CACACACACTCTCTCTCTCTCTCTCTGCCCTAAGGGGCTCATCACTACATCCAAGTTTTTCACTG
1 CTCTCTCTCTCTCTCTCTCTCTCTCTGCCCTAAGGGGCTCATCACTACATCCAAGTTCTTCACTG
431459 TCCCTCCCAAAATACCCATCAGGTTGGTGTA
66 TCCCTCCCAAAATACCCATCAGGTTGGTGTA
431490 CTCTCTCTCTCTCTCTCTCTCTCTCTGCCCTAA
1 CTCTCTCTCTCTCTCTCTCTCTCTCTGCCCTAA
431523 CTCCCTGGAA
Statistics
Matches: 215, Mismatches: 10, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
96 120 0.56
102 95 0.44
ACGTcount: A:0.17, C:0.38, G:0.12, T:0.33
Consensus pattern (96 bp):
CTCTCTCTCTCTCTCTCTCTCTCTCTGCCCTAAGGGGCTCATCACTACATCCAAGTTCTTCACTG
TCCCTCCCAAAATACCCATCAGGTTGGTGTA
Found at i:431307 original size:102 final size:102
Alignment explanation
Indices: 431086--431515 Score: 728
Period size: 102 Copynumber: 4.3 Consensus size: 102
431076 CTGGCATACT
*
431086 CTCTCTCACTCTCTCTCTCTCTCTCTCTCTCTGCCCTAAGGGGCTCATCACTACATCCAAGTTCT
1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGCCCTAAGGGGCTCATCACTACATCCAAGTTCT
*
431151 TCACTGTCCCTCCCAAAATACCGATCAGGTTGGTGTA
66 TCACTGTCCCTCCCAAAATACCCATCAGGTTGGTGTA
431188 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGCCCTAAGGGGCTCATCACTACATCCAAGTT
1 --CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGCCCTAAGGGGCTCATCACTACATCCAAGTT
*
431253 CTTCACTGTCCCTCCCAAAATACCGATCAGGTTGGTGTA
64 CTTCACTGTCCCTCCCAAAATACCCATCAGGTTGGTGTA
431292 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGCCCTAAGGGGCTCATCACTACATCCAAGTTCT
1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGCCCTAAGGGGCTCATCACTACATCCAAGTTCT
431357 TCACTGTCCCTCCCAAAATACCCATCAGGTTGGTGTA
66 TCACTGTCCCTCCCAAAATACCCATCAGGTTGGTGTA
* * * * *
431394 ------CACACACACTCTCTCTCTCTCTCTCTGCCCTAAGGGGCTCATCACTACATCCAAGTTTT
1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGCCCTAAGGGGCTCATCACTACATCCAAGTTCT
431453 TCACTGTCCCTCCCAAAATACCCATCAGGTTGGTGTA
66 TCACTGTCCCTCCCAAAATACCCATCAGGTTGGTGTA
431490 CTCTCTCTCTCTCTCTCTCTCTCTCT
1 CTCTCTCTCTCTCTCTCTCTCTCTCT
431516 GCCCTAACTC
Statistics
Matches: 309, Mismatches: 11, Indels: 14
0.93 0.03 0.04
Matches are distributed among these distances:
96 91 0.29
102 117 0.38
104 101 0.33
ACGTcount: A:0.17, C:0.38, G:0.12, T:0.33
Consensus pattern (102 bp):
CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGCCCTAAGGGGCTCATCACTACATCCAAGTTCT
TCACTGTCCCTCCCAAAATACCCATCAGGTTGGTGTA
Found at i:431497 original size:2 final size:2
Alignment explanation
Indices: 431490--431515 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
431480 GGTTGGTGTA
431490 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
431516 GCCCTAACTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:433361 original size:18 final size:18
Alignment explanation
Indices: 433338--433373 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
433328 CTCTCTGTGT
433338 TTAGATATTGGGGAGAAA
1 TTAGATATTGGGGAGAAA
433356 TTAGATATTGGGGAGAAA
1 TTAGATATTGGGGAGAAA
433374 AACATGATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.33, T:0.28
Consensus pattern (18 bp):
TTAGATATTGGGGAGAAA
Found at i:434372 original size:335 final size:332
Alignment explanation
Indices: 433707--434607 Score: 955
Period size: 335 Copynumber: 2.7 Consensus size: 332
433697 CCAAATTTTC
* ** **** * *
433707 AAAAATCTTCTTCTCTACTCCCACGCATGTGAGG-AAAAAACCGGTTGCATGGTTATAATGTCGA
1 AAAAATCTTCTTCTCTACTCCCACACAAATG-GGCAAAAAACTAAATGCATGGTTATGATGTCCA
* * * * * *
433771 TGAAGCCCTCTACCAAAATTGTGAAATTTATGGCCCCAGGGTCAGGGGTTCTGGCCTAGGGTGGG
65 TGAAGCCCTCTACCTAAATTGTGAAATTCATGACCCCTGGGTCAGGGGTTCAGGTCTAGGGTGGG
* * * * *
433836 GCCAATATGGTCATATAGTAAAAATGTATTAAATCTTAGAAAATCTTCTTCTTTACTACCATATA
130 GCCAATATGGCCATATAGTAAAAATGTATTAAATCTTA-AAAAACTTCTTCTTTACTCCCACACA
* *** * * * * * * *
433901 TATTTTTTAAAAACTAAATGCCTGATTATGATGTCGATGAAGCCCTCTACCAAAATTGTGAAATT
194 T-GTGAGTAAAAACTGAATACATGGTTATGATGTCCATGAAGCCCTCTAACAAAATTATGAAATT
* * * * * * *
433966 TATGGCCCCAGGGTCAGGGGCTCTGGCCTAGGGTGGGGCCAATATGGCCATGTAGTAAAAATGTA
258 CATGACCCCAGGGTAAGGGACTCAGGCCTAGGGCGGGGCCAATATGGCCATATAGTAAAAATGTA
434031 TTAAATCTTA
323 TTAAATCTTA
* * * ** ** *
434041 GAAAATCTTCTTCTCTACTCCCATATAAATTTGTTAAAAACTAAATGCATGATTATGATGTCCAT
1 AAAAATCTTCTTCTCTACTCCCACACAAATGGGCAAAAAACTAAATGCATGGTTATGATGTCCAT
* * * *
434106 GAGGCCCTCAACCTAAATTGTGAAATGCATGACCCCTGGGTCAGGGGTTCAGGATCTAGGGTGAG
66 GAAGCCCTCTACCTAAATTGTGAAATTCATGACCCCTGGGTCAGGGGTTCAGG-TCTAGGGTGGG
* *
434171 GCCAATATGGCCAAATAGTAAAAATGTATCAAATCTTAAAAAACTTCTTCTTTACTCCCACACAT
130 GCCAATATGGCCATATAGTAAAAATGTATTAAATCTTAAAAAACTTCTTCTTTACTCCCACACAT
* * *
434236 GTGAGTAAAAATCTGAATACATGGTTATGATGTCCATGAGGGCCTCTAATAAAATTATG-AATGT
195 GTGAGTAAAAA-CTGAATACATGGTTATGATGTCCATGAAGCCCTCTAACAAAATTATGAAAT-T
*** * * * *
434300 CATGACCCCTTTGTAAGGTATTCAGGATCTAGGGCGGGGCCAATATGGCCATATAGTAAAACTGT
258 CATGACCCCAGGGTAAGGGACTCAGG-CCTAGGGCGGGGCCAATATGGCCATATAGTAAAAATGT
*
434365 TTTAAATCTTA
322 ATTAAATCTTA
** * *
434376 AAAAATCTTCTTCTCTACTCCCACACATGTGGGCAAAAAACTGAATACATGGTTATGATGTCCAT
1 AAAAATCTTCTTCTCTACTCCCACACAAATGGGCAAAAAACTAAATGCATGGTTATGATGTCCAT
* ** * *
434441 GATA-ACCTCTA-CTAAAATTGTGAAATTCATGACCCCTTTGTTAGGTGTTCAGGCTCTAGGGTG
66 GA-AGCCCTCTACCT-AAATTGTGAAATTCATGACCCCTGGGTCAGGGGTTCAGG-TCTAGGGTG
* * * *
434504 GGGCCAATATGGCTATATAGTAAAACTGTTTTAAATCTTAAAAAATCTTCTTCTCTACTCCCACA
128 GGGCCAATATGGCCATATAGTAAAAATGTATTAAATCTTAAAAAA-CTTCTTCTTTACTCCCACA
* * *
434569 CATGTGGGCAAAAAACTGAATACATGGTTATGATATCCA
192 CATGTGAG-TAAAAACTGAATACATGGTTATGATGTCCA
434608 CAATCTCCTT
Statistics
Matches: 465, Mismatches: 93, Indels: 16
0.81 0.16 0.03
Matches are distributed among these distances:
333 11 0.02
334 171 0.37
335 230 0.49
336 48 0.10
337 5 0.01
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (332 bp):
AAAAATCTTCTTCTCTACTCCCACACAAATGGGCAAAAAACTAAATGCATGGTTATGATGTCCAT
GAAGCCCTCTACCTAAATTGTGAAATTCATGACCCCTGGGTCAGGGGTTCAGGTCTAGGGTGGGG
CCAATATGGCCATATAGTAAAAATGTATTAAATCTTAAAAAACTTCTTCTTTACTCCCACACATG
TGAGTAAAAACTGAATACATGGTTATGATGTCCATGAAGCCCTCTAACAAAATTATGAAATTCAT
GACCCCAGGGTAAGGGACTCAGGCCTAGGGCGGGGCCAATATGGCCATATAGTAAAAATGTATTA
AATCTTA
Found at i:434473 original size:168 final size:166
Alignment explanation
Indices: 433707--434661 Score: 986
Period size: 167 Copynumber: 5.7 Consensus size: 166
433697 CCAAATTTTC
* * ** * * *
433707 AAAAATCTTCTTCTCTACTCCCACGCATGTGAGG-AAAAAACCGGTTGCATGGTTATAATGTCGA
1 AAAAATCTTCTTCTCTACTCCCACACATGTG-GGTAAAAAACTGAATACATGGTTATGATGTCCA
* * * * * *
433771 TGAAGCCCTCTACCAAAATTGTGAAATTTATGGCCCCAGGGTCAGGGGTTCTGGCCTAGGGTGGG
65 TGAA-CCCTCTACTAAAATTGTGAAATTCATGACCCCTGGGTCAGGGGTTCAGGTCTAGGGTGGG
*
433836 GCCAATATGGTCATATAGTAAAAATGTATTAAATCTTA
129 GCCAATATGGCCATATAGTAAAAATGTATTAAATCTTA
* * * * * * *** * * * * * *
433874 GAAAATCTTCTTCTTTACTACCATATATATTTTTTAAAAACTAAATGCCTGATTATGATGTCGAT
1 AAAAATCTTCTTCTCTACTCCCACACATGTGGGTAAAAAACTGAATACATGGTTATGATGTCCAT
* * * * * * *
433939 GAAGCCCTCTACCAAAATTGTGAAATTTATGGCCCCAGGGTCAGGGGCTCTGGCCTAGGGTGGGG
66 GAA-CCCTCTACTAAAATTGTGAAATTCATGACCCCTGGGTCAGGGGTTCAGGTCTAGGGTGGGG
*
434004 CCAATATGGCCATGTAGTAAAAATGTATTAAATCTTA
130 CCAATATGGCCATATAGTAAAAATGTATTAAATCTTA
* * * ** ** * * * *
434041 GAAAATCTTCTTCTCTACTCCCATATAAATTTGTTAAAAACTAAATGCATGATTATGATGTCCAT
1 AAAAATCTTCTTCTCTACTCCCACACATGTGGGTAAAAAACTGAATACATGGTTATGATGTCCAT
* * * *
434106 GAGGCCCTCAACCT-AAATTGTGAAATGCATGACCCCTGGGTCAGGGGTTCAGGATCTAGGGTGA
66 GA-ACCCTCTA-CTAAAATTGTGAAATTCATGACCCCTGGGTCAGGGGTTCAGG-TCTAGGGTGG
* *
434170 GGCCAATATGGCCAAATAGTAAAAATGTATCAAATCTTA
128 GGCCAATATGGCCATATAGTAAAAATGTATTAAATCTTA
* * *
434209 AAAAA-CTTCTTCTTTACTCCCACACATGTGAGTAAAAATCTGAATACATGGTTATGATGTCCAT
1 AAAAATCTTCTTCTCTACTCCCACACATGTGGGTAAAAAACTGAATACATGGTTATGATGTCCAT
** * * ** * ** *
434273 GAGGGCCTCTAATAAAATTATG-AATGTCATGACCCCTTTGTAAGGTATTCAGGATCTAGGGCGG
66 GA-ACCCTCTACTAAAATTGTGAAAT-TCATGACCCCTGGGTCAGGGGTTCAGG-TCTAGGGTGG
* *
434337 GGCCAATATGGCCATATAGTAAAACTGTTTTAAATCTTA
128 GGCCAATATGGCCATATAGTAAAAATGTATTAAATCTTA
*
434376 AAAAATCTTCTTCTCTACTCCCACACATGTGGGCAAAAAACTGAATACATGGTTATGATGTCCAT
1 AAAAATCTTCTTCTCTACTCCCACACATGTGGGTAAAAAACTGAATACATGGTTATGATGTCCAT
* ** * *
434441 GATAACCTCTACTAAAATTGTGAAATTCATGACCCCTTTGTTAGGTGTTCAGGCTCTAGGGTGGG
66 GA-ACCCTCTACTAAAATTGTGAAATTCATGACCCCTGGGTCAGGGGTTCAGG-TCTAGGGTGGG
* * *
434506 GCCAATATGGCTATATAGTAAAACTGTTTTAAATCTTA
129 GCCAATATGGCCATATAGTAAAAATGTATTAAATCTTA
* *
434544 AAAAATCTTCTTCTCTACTCCCACACATGTGGGCAAAAAACTGAATACATGGTTATGATATCCA-
1 AAAAATCTTCTTCTCTACTCCCACACATGTGGGTAAAAAACTGAATACATGGTTATGATGTCCAT
* * * *
434608 CAATCTCCTTTACCT-AAATTGTGAAATTCATGGCCCCTTGGTCAGGGGTTCAGG
66 GAA-C-CCTCTA-CTAAAATTGTGAAATTCATGACCCCTGGGTCAGGGGTTCAGG
434662 ACATGAAGCA
Statistics
Matches: 685, Mismatches: 92, Indels: 21
0.86 0.12 0.03
Matches are distributed among these distances:
166 5 0.01
167 379 0.55
168 296 0.43
169 5 0.01
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.30
Consensus pattern (166 bp):
AAAAATCTTCTTCTCTACTCCCACACATGTGGGTAAAAAACTGAATACATGGTTATGATGTCCAT
GAACCCTCTACTAAAATTGTGAAATTCATGACCCCTGGGTCAGGGGTTCAGGTCTAGGGTGGGGC
CAATATGGCCATATAGTAAAAATGTATTAAATCTTA
Found at i:444014 original size:11 final size:11
Alignment explanation
Indices: 443998--444022 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
443988 TCCATTATGG
443998 TATATTTAGTC
1 TATATTTAGTC
444009 TATATTTAGTC
1 TATATTTAGTC
444020 TAT
1 TAT
444023 CCGAAAAGTA
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:0.28, C:0.08, G:0.08, T:0.56
Consensus pattern (11 bp):
TATATTTAGTC
Found at i:445855 original size:4 final size:4
Alignment explanation
Indices: 445848--445919 Score: 144
Period size: 4 Copynumber: 18.0 Consensus size: 4
445838 AATTTTTTTT
445848 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
445896 TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC
445920 CTTTATATTT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 68 1.00
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (4 bp):
TATC
Found at i:449594 original size:61 final size:62
Alignment explanation
Indices: 449499--449851 Score: 502
Period size: 61 Copynumber: 5.8 Consensus size: 62
449489 ATGCTTAAGC
*
449499 AGATCATATCTTTATATCTGGCTAACC-GTTGTTCTATATTGATTTATCATGATATCCAAGT
1 AGATCATATCTTTATATCTGGCTGACCTGTTGTTCTATATTGATTTATCATGATATCCAAGT
* *
449560 AGATCATATCTTTATATCTGGCT-ACCTGTTGTTCTAGATTGTTTTATCATGATATCCAAGT
1 AGATCATATCTTTATATCTGGCTGACCTGTTGTTCTATATTGATTTATCATGATATCCAAGT
* * * * *
449621 ACATAATATCTTTATATCTGG-TGACCAGTTGTTCTACATTGATTTATCATGATATCCAAGA
1 AGATCATATCTTTATATCTGGCTGACCTGTTGTTCTATATTGATTTATCATGATATCCAAGT
* * *
449682 AGATCAAATCTTTATATCTGGCT-ACCTGTTATTCTATATTGATTTATCGTGATATCCAAGT
1 AGATCATATCTTTATATCTGGCTGACCTGTTGTTCTATATTGATTTATCATGATATCCAAGT
* * * * *
449743 ACATAATATCTTTATATCTGG-TGACCAGTTGTTCTACATTGATTTATCATGATATCCAAGA
1 AGATCATATCTTTATATCTGGCTGACCTGTTGTTCTATATTGATTTATCATGATATCCAAGT
* *
449804 AGATCAAATCTTTATATCTGGCT-ACCTGTTATTCTATATTGATTTATC
1 AGATCATATCTTTATATCTGGCTGACCTGTTGTTCTATATTGATTTATC
449852 NNNNNNNNNN
Statistics
Matches: 257, Mismatches: 30, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
60 5 0.02
61 250 0.97
62 2 0.01
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.42
Consensus pattern (62 bp):
AGATCATATCTTTATATCTGGCTGACCTGTTGTTCTATATTGATTTATCATGATATCCAAGT
Found at i:449728 original size:122 final size:122
Alignment explanation
Indices: 449504--449851 Score: 608
Period size: 122 Copynumber: 2.9 Consensus size: 122
449494 TAAGCAGATC
* * * *
449504 ATATCTTTATATCTGGCTAACC-GTTGTTCTATATTGATTTATCATGATATCCAAGTAGATCATA
1 ATATCTTTATATCTGG-TGACCAGTTGTTCTACATTGATTTATCATGATATCCAAGAAGATCAAA
* * *
449568 TCTTTATATCTGGCTACCTGTTGTTCTAGATTGTTTTATCATGATATCCAAGTACATA
65 TCTTTATATCTGGCTACCTGTTATTCTATATTGATTTATCATGATATCCAAGTACATA
449626 ATATCTTTATATCTGGTGACCAGTTGTTCTACATTGATTTATCATGATATCCAAGAAGATCAAAT
1 ATATCTTTATATCTGGTGACCAGTTGTTCTACATTGATTTATCATGATATCCAAGAAGATCAAAT
*
449691 CTTTATATCTGGCTACCTGTTATTCTATATTGATTTATCGTGATATCCAAGTACATA
66 CTTTATATCTGGCTACCTGTTATTCTATATTGATTTATCATGATATCCAAGTACATA
449748 ATATCTTTATATCTGGTGACCAGTTGTTCTACATTGATTTATCATGATATCCAAGAAGATCAAAT
1 ATATCTTTATATCTGGTGACCAGTTGTTCTACATTGATTTATCATGATATCCAAGAAGATCAAAT
449813 CTTTATATCTGGCTACCTGTTATTCTATATTGATTTATC
66 CTTTATATCTGGCTACCTGTTATTCTATATTGATTTATC
449852 NNNNNNNNNN
Statistics
Matches: 217, Mismatches: 8, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
121 4 0.02
122 213 0.98
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (122 bp):
ATATCTTTATATCTGGTGACCAGTTGTTCTACATTGATTTATCATGATATCCAAGAAGATCAAAT
CTTTATATCTGGCTACCTGTTATTCTATATTGATTTATCATGATATCCAAGTACATA
Found at i:450939 original size:4 final size:4
Alignment explanation
Indices: 450932--450987 Score: 112
Period size: 4 Copynumber: 14.0 Consensus size: 4
450922 GTATATATAT
450932 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
450980 ATAG ATAG
1 ATAG ATAG
450988 NTATATATAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (4 bp):
ATAG
Found at i:451942 original size:21 final size:21
Alignment explanation
Indices: 451916--451965 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
451906 GGATTTGTTT
*
451916 GGACGAATTAGCTATATGCTC
1 GGACGAATTAGCTATATGCTA
* * *
451937 GGACGAATTAGTTATTTGTTA
1 GGACGAATTAGCTATATGCTA
451958 GGACGAAT
1 GGACGAAT
451966 AAGGATTTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.30, C:0.12, G:0.26, T:0.32
Consensus pattern (21 bp):
GGACGAATTAGCTATATGCTA
Found at i:452097 original size:62 final size:61
Alignment explanation
Indices: 451904--452100 Score: 186
Period size: 62 Copynumber: 3.2 Consensus size: 61
451894 TTTAACAAAA
* * * *
451904 TAGGATTTGTTTGGACGAATTAGCTATATGCTCGGACGAATTAGTTATTTGTTAGGACGAAT
1 TAGGATTTGTTTGGACAAATTAGCTATTTGTTCGGACGAATTAG-TATTTGTTCGGACGAAT
* * * * *
451966 AAGGATTTGTTT-GATAAAATTAGCTATTTGTTCGGACGGATAAGTAATTTGTACGGAC-AACTT
1 TAGGATTTGTTTGGA-CAAATTAGCTATTTGTTCGGACGAATTAGT-ATTTGTTCGGACGAA--T
* * * *
452029 TA-GATTTGTTTGGACAAATTAG-GATTTTTTCGGTCGAATTAGCTATTTTTTTCGGACGAAT
1 TAGGATTTGTTTGGACAAATTAGCTATTTGTTCGGACGAATTAG-TA-TTTGTTCGGACGAAT
452090 TAGGATTTGTT
1 TAGGATTTGTT
452101 AAAATGTTTT
Statistics
Matches: 108, Mismatches: 18, Indels: 18
0.75 0.12 0.12
Matches are distributed among these distances:
61 24 0.22
62 78 0.72
63 6 0.06
ACGTcount: A:0.27, C:0.09, G:0.23, T:0.40
Consensus pattern (61 bp):
TAGGATTTGTTTGGACAAATTAGCTATTTGTTCGGACGAATTAGTATTTGTTCGGACGAAT
Found at i:452188 original size:20 final size:21
Alignment explanation
Indices: 452147--452191 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
452137 TTTTTCAGAT
*
452147 GAATTAGGTATTTCTTCTGAC
1 GAATTAGGTATTTCTTCGGAC
452168 GAATTAGG-ATTTGCTT-GGAC
1 GAATTAGGTATTT-CTTCGGAC
452188 GAAT
1 GAAT
452192 AATTTAATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.27, C:0.11, G:0.24, T:0.38
Consensus pattern (21 bp):
GAATTAGGTATTTCTTCGGAC
Found at i:464031 original size:21 final size:20
Alignment explanation
Indices: 464005--464054 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
463995 TGCTTCTTAT
464005 TTATGTCGACATGCAACTGAG
1 TTATGTC-ACATGCAACTGAG
* * *
464026 TTATGTTCACATGCTACTTAT
1 TTATG-TCACATGCAACTGAG
464047 TTATGTCA
1 TTATGTCA
464055 TTTTGAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 3 0.12
21 20 0.80
22 2 0.08
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.40
Consensus pattern (20 bp):
TTATGTCACATGCAACTGAG
Found at i:465218 original size:4 final size:4
Alignment explanation
Indices: 465209--465280 Score: 144
Period size: 4 Copynumber: 18.0 Consensus size: 4
465199 AAGGACCGGA
465209 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
465257 TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC
465281 AACGTTTCTC
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 68 1.00
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (4 bp):
TATC
Found at i:465997 original size:179 final size:179
Alignment explanation
Indices: 465809--466166 Score: 684
Period size: 179 Copynumber: 2.0 Consensus size: 179
465799 AATCTCTCTC
465809 TCTCTCTCTCAATTTTGATATTTATCTTCAATTCAGAGTTACTTGGCTAGAAAATTCAAATTAAA
1 TCTCTCTCTCAATTTTGATATTTATCTTCAATTCAGAGTTACTTGGCTAGAAAATTCAAATTAAA
465874 CAAGAAATTTGTTTTGGAAGAATAAAAAA-ATATGGTCTATCAATGTCACGACGATTTATTAATA
66 CAAGAAATTTGTTTTGGAAGAATAAAAAAGATATGGTCTATCAATGTCACGACGATTTATTAATA
465938 AACGAT-TTTCCAATATTCCTTATATGAATTGTATAATCTACTTTTACTT
131 AACG-TCTTTCCAATATTCCTTATATGAATTGTATAATCTACTTTTACTT
465987 NTCTCTCTCTCAATTTTGATATTTATCTTCAATTCAGAGTTACTTGGCTAGAAAATTCAAATTAA
1 -TCTCTCTCTCAATTTTGATATTTATCTTCAATTCAGAGTTACTTGGCTAGAAAATTCAAATTAA
466052 ACAAGAAATTTGTTTTGGAAGAATAAAAAAGATATGGTCTATCAATGTCACGACGATTTATTAAT
65 ACAAGAAATTTGTTTTGGAAGAATAAAAAAGATATGGTCTATCAATGTCACGACGATTTATTAAT
466117 AAACGTCTTTCCAATATTCCTTATATGAATTGTATAATCTACTTTTACTT
130 AAACGTCTTTCCAATATTCCTTATATGAATTGTATAATCTACTTTTACTT
466167 GATACATCAT
Statistics
Matches: 177, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
179 95 0.54
180 82 0.46
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40
Consensus pattern (179 bp):
TCTCTCTCTCAATTTTGATATTTATCTTCAATTCAGAGTTACTTGGCTAGAAAATTCAAATTAAA
CAAGAAATTTGTTTTGGAAGAATAAAAAAGATATGGTCTATCAATGTCACGACGATTTATTAATA
AACGTCTTTCCAATATTCCTTATATGAATTGTATAATCTACTTTTACTT
Found at i:469047 original size:21 final size:21
Alignment explanation
Indices: 469021--469066 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
469011 TTTCCCGTGG
469021 GCTCACCGTGCGATCA-TGTGC
1 GCTCACCGTGCGATCACT-TGC
*
469042 GCTCACCGTGCGTTCACTTGC
1 GCTCACCGTGCGATCACTTGC
469063 GCTC
1 GCTC
469067 TCCGCTCCGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 22 0.96
22 1 0.04
ACGTcount: A:0.11, C:0.37, G:0.26, T:0.26
Consensus pattern (21 bp):
GCTCACCGTGCGATCACTTGC
Found at i:469921 original size:2 final size:2
Alignment explanation
Indices: 469914--469948 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
469904 ATCATATTTC
*
469914 AG AG AG AG AG AG AG AG AG AG AG AA AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
469949 ATGTGGGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:474794 original size:11 final size:11
Alignment explanation
Indices: 474778--474816 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
474768 CGCTATGCCG
474778 TTCAGTCACCT
1 TTCAGTCACCT
*
474789 TTCAGTTACCT
1 TTCAGTCACCT
474800 TTCAG-CTACCT
1 TTCAGTC-ACCT
474811 TTCAGT
1 TTCAGT
474817 TATTGTAGCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.18, C:0.31, G:0.10, T:0.41
Consensus pattern (11 bp):
TTCAGTCACCT
Found at i:479163 original size:2 final size:2
Alignment explanation
Indices: 479156--479206 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
479146 ACCTCTGCAG
479156 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
479198 GA GA GA GA G
1 GA GA GA GA G
479207 CACTTCATAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:487060 original size:53 final size:53
Alignment explanation
Indices: 486971--487077 Score: 155
Period size: 53 Copynumber: 2.0 Consensus size: 53
486961 GTCACAGCTT
* *
486971 ATTAATATACGTATGATCTAGACTCATCGGAAATAGCCGAAAAGTGGTGCCAG
1 ATTAATATACGTATGATCTACACTCATCAGAAATAGCCGAAAAGTGGTGCCAG
*
487024 ATTAATATACGTATGATCTACACT-AGT-AGAATATAGCCGAAGAGTGGTGCCAG
1 ATTAATATACGTATGATCTACACTCA-TCAGAA-ATAGCCGAAAAGTGGTGCCAG
487077 A
1 A
487078 GCTGGTTGTT
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
52 4 0.08
53 45 0.92
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.25
Consensus pattern (53 bp):
ATTAATATACGTATGATCTACACTCATCAGAAATAGCCGAAAAGTGGTGCCAG
Found at i:490903 original size:16 final size:16
Alignment explanation
Indices: 490877--490914 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
490867 TGCGTAAATG
490877 ACTAGTGCTACTATT-CT
1 ACTA-TGCTACT-TTGCT
490894 ACTATGCTACTTTGCT
1 ACTATGCTACTTTGCT
490910 ACTAT
1 ACTAT
490915 ATGCAGTGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 2 0.10
16 14 0.70
17 4 0.20
ACGTcount: A:0.24, C:0.24, G:0.11, T:0.42
Consensus pattern (16 bp):
ACTATGCTACTTTGCT
Found at i:498069 original size:2 final size:2
Alignment explanation
Indices: 498062--498097 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
498052 AAAAGCATGC
498062 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
498098 TATTCAGTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:505358 original size:2 final size:2
Alignment explanation
Indices: 505351--505382 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
505341 TCAGTGCCTT
505351 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
505383 NNNNNNNNNN
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:510322 original size:2 final size:2
Alignment explanation
Indices: 510315--510357 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
510305 CACATTTAAC
510315 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
510357 G
1 G
510358 TTTGTTATGC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:512848 original size:2 final size:2
Alignment explanation
Indices: 512841--512894 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
512831 TCTGTATAAT
512841 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
512883 TC TC TC TC TC TC
1 TC TC TC TC TC TC
512895 AAATTTTATT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:513466 original size:2 final size:2
Alignment explanation
Indices: 513459--513515 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
513449 GTACATGTTT
513459 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
513501 TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC T
513516 TGCTTACGCA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:518667 original size:2 final size:2
Alignment explanation
Indices: 518662--518705 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
518652 TGTGTGTGTG
518662 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
518704 GA
1 GA
518706 ATAAACATAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:522919 original size:2 final size:2
Alignment explanation
Indices: 522912--522958 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
522902 AAACCCACAT
522912 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
522954 TC TC T
1 TC TC T
522959 GAAATATGAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:524023 original size:2 final size:2
Alignment explanation
Indices: 524016--524055 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
524006 TGTAAGTTTC
524016 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
524056 CAAACATACA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:524984 original size:166 final size:166
Alignment explanation
Indices: 524708--525169 Score: 678
Period size: 166 Copynumber: 2.8 Consensus size: 166
524698 GTCACATTTA
* * *
524708 TCTCAGCAACAATTTATCACAGATGCTTGAAATTTTTACACAGTGTTTGTTAAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTGTTTGTTTAGGCATGCCATAT
* * *
524773 CAAGGGATATATTTTTGTACCAATC-GAACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTT
66 TATGGGATATATTTTTGTACCAATCAG-ACGTCAACTT-TTGTTAAATGACGACTTTGCTTATTT
*
524837 TTTAACCAAAATTTTCAAAC-AATTTTCGTCAAAGATT
129 TTTAACCAAAATTTTCAAACAAATTTTCCTCAAAGATT
*
524874 TCTCAGCAACTATTTATCGCAGATACTTGAAATTTTTACACAGTGTTTGTTTAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTGTTTGTTTAGGCATGCCATAT
*
524939 TATGGGATATATTTTTGTACCAATCAGACGTCAACTTATTGTTAAATGACGACTTTGTTTA-TTT
66 TATGGGATATATTTTTGTACCAATCAGACGTCAACTT-TTGTTAAATGACGACTTTGCTTATTTT
*
525003 TTAGCCAAAATTTTCAAACAAATTTTCCTCAAAGATT
130 TTAACCAAAATTTTCAAACAAATTTTCCTCAAAGATT
* * * * *
525040 TCTCAGCAGCTATTAATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTGTTTGTTTAGGCATGCCATAT
* * * * * *
525105 TATGGGAAATATTTCTGTACCAATCAGATGCCAGCTTTCTGTTAAATGTCGACTTTGCTTATTTT
66 TATGGGATATATTTTTGTACCAATCAGACGTCAACTTT-TGTTAAATGACGACTTTGCTTATTTT
525170 GCATATTTAC
Statistics
Matches: 268, Mismatches: 24, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
165 22 0.08
166 242 0.90
167 4 0.01
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (166 bp):
TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTGTTTGTTTAGGCATGCCATAT
TATGGGATATATTTTTGTACCAATCAGACGTCAACTTTTGTTAAATGACGACTTTGCTTATTTTT
TAACCAAAATTTTCAAACAAATTTTCCTCAAAGATT
Found at i:526985 original size:2 final size:2
Alignment explanation
Indices: 526941--526969 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
526931 NNNNNNNNNN
526941 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 A
526970 CTACATGTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:527036 original size:2 final size:2
Alignment explanation
Indices: 527029--527064 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
527019 GTAAGTATCT
527029 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
527065 AAGACTACAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:527106 original size:99 final size:99
Alignment explanation
Indices: 526941--527143 Score: 388
Period size: 99 Copynumber: 2.1 Consensus size: 99
526931 NNNNNNNNNN
*
526941 AGAGAGAGAGAGAGAGAGAGAGAGAGAGACTACATGTCTGAGAGAATAAGTAAGATGCACATGTT
1 AGAGAGAGAGAGAGAGAGAGAGAGAAAGACTACATGTCTGAGAGAATAAGTAAGATGCACATGTT
527006 TACATGCATAAGAGTAAGTATCTGAGAGAGAGAG
66 TACATGCATAAGAGTAAGTATCTGAGAGAGAGAG
527040 AGAGAGAGAGAGAGAGAGAGAGAGAAAGACTACATGTCTGAGAGAATAAGTAAGATGCACATGTT
1 AGAGAGAGAGAGAGAGAGAGAGAGAAAGACTACATGTCTGAGAGAATAAGTAAGATGCACATGTT
*
527105 TACATGTATAAGAGTAAGTATCTGAGAGAGAGAG
66 TACATGCATAAGAGTAAGTATCTGAGAGAGAGAG
527139 AGAGA
1 AGAGA
527144 CTACATGTCT
Statistics
Matches: 102, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
99 102 1.00
ACGTcount: A:0.43, C:0.07, G:0.32, T:0.17
Consensus pattern (99 bp):
AGAGAGAGAGAGAGAGAGAGAGAGAAAGACTACATGTCTGAGAGAATAAGTAAGATGCACATGTT
TACATGCATAAGAGTAAGTATCTGAGAGAGAGAG
Found at i:527331 original size:2 final size:2
Alignment explanation
Indices: 527326--527350 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
527316 AATGTGTGAA
527326 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 A
527351 TTACATGTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:527650 original size:2 final size:2
Alignment explanation
Indices: 527643--527682 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
527633 AGGAGGAATA
*
527643 AG AG AG AG AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
527683 CATGTTTAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:527933 original size:2 final size:2
Alignment explanation
Indices: 527926--527956 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
527916 ATGTAGGGAT
527926 AG AG AG AG AG AG AG -G AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
527957 CACCTCTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
AG
Found at i:527946 original size:15 final size:15
Alignment explanation
Indices: 527926--527954 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
527916 ATGTAGGGAT
527926 AGAGAGAGAGAGAGG
1 AGAGAGAGAGAGAGG
527941 AGAGAGAGAGAGAG
1 AGAGAGAGAGAGAG
527955 AGCACCTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (15 bp):
AGAGAGAGAGAGAGG
Found at i:532354 original size:46 final size:46
Alignment explanation
Indices: 532287--532382 Score: 129
Period size: 46 Copynumber: 2.1 Consensus size: 46
532277 GACACTGTTG
* * * * *
532287 CTGTGTAGGTGAACTCTGCACAAAAACAAAGCGTCATCAATGGTCT
1 CTGTGTACGTGAAATCTGCACAAAAACAAAGCGTCAACAATAGACT
* *
532333 CTGTGTACGTGAAATCTGCACAAAAATAATGCGTCAACAATAGACT
1 CTGTGTACGTGAAATCTGCACAAAAACAAAGCGTCAACAATAGACT
532379 CTGT
1 CTGT
532383 ATCTGTGTGT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (46 bp):
CTGTGTACGTGAAATCTGCACAAAAACAAAGCGTCAACAATAGACT
Found at i:532397 original size:52 final size:51
Alignment explanation
Indices: 532341--532481 Score: 130
Period size: 50 Copynumber: 2.8 Consensus size: 51
532331 CTCTGTGTAC
532341 GTGAAATCTGCACAAAAATAATGCGTCAACAATAGACTCTGTATCTGTGTGT
1 GTGAAATCTGCACAAAAATAAT-CGTCAACAATAGACTCTGTATCTGTGTGT
** * * * *
532393 GTGAAATCTGCATGTATAA-CAT-GTCATCAATAGACTTTGTATCTGTGTGT
1 GTGAAATCTGCA-CAAAAATAATCGTCAACAATAGACTCTGTATCTGTGTGT
* * * *
532443 GTGAACTCT--ACATATATAACACGT-AACAATAGACTCTGT
1 GTGAAATCTGCACAAAAATAA-TCGTCAACAATAGACTCTGT
532482 GCTTTGTGTA
Statistics
Matches: 69, Mismatches: 16, Indels: 11
0.72 0.17 0.11
Matches are distributed among these distances:
47 1 0.01
48 2 0.03
49 13 0.19
50 36 0.52
52 14 0.20
53 3 0.04
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (51 bp):
GTGAAATCTGCACAAAAATAATCGTCAACAATAGACTCTGTATCTGTGTGT
Found at i:532490 original size:50 final size:50
Alignment explanation
Indices: 532364--532481 Score: 175
Period size: 50 Copynumber: 2.4 Consensus size: 50
532354 AAAAATAATG
* *
532364 CGTCAACAATAGACTCTGTATCTGTGTGTGTGAAATCTGCATGTATAACA
1 CGTCAACAATAGACTCTGTATCTGTGTGTGTGAAATCTACATATATAACA
* * * *
532414 TGTCATCAATAGACTTTGTATCTGTGTGTGTGAACTCTACATATATAACA
1 CGTCAACAATAGACTCTGTATCTGTGTGTGTGAAATCTACATATATAACA
532464 CGT-AACAATAGACTCTGT
1 CGTCAACAATAGACTCTGT
532482 GCTTTGTGTA
Statistics
Matches: 59, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
49 13 0.22
50 46 0.78
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Consensus pattern (50 bp):
CGTCAACAATAGACTCTGTATCTGTGTGTGTGAAATCTACATATATAACA
Found at i:535455 original size:10 final size:10
Alignment explanation
Indices: 535440--535485 Score: 65
Period size: 10 Copynumber: 4.6 Consensus size: 10
535430 GGTAAGTCTA
535440 AGCAACATAC
1 AGCAACATAC
*
535450 AGCAACATAA
1 AGCAACATAC
* *
535460 AGTAACACAC
1 AGCAACATAC
535470 AGCAACATAC
1 AGCAACATAC
535480 AGCAAC
1 AGCAAC
535486 TCATAGCACA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 30 1.00
ACGTcount: A:0.52, C:0.28, G:0.11, T:0.09
Consensus pattern (10 bp):
AGCAACATAC
Found at i:537275 original size:39 final size:39
Alignment explanation
Indices: 537221--537697 Score: 746
Period size: 39 Copynumber: 12.3 Consensus size: 39
537211 CTGTACAACT
* *
537221 CAACCTGCTATACATACAGGTAACATAGAATTATACATA
1 CAACCTGCTATACGTACAGGTAACCTAGAATTATACATA
*
537260 CAACCTGCTATACATACAGGTAACCTAGAATTATACATA
1 CAACCTGCTATACGTACAGGTAACCTAGAATTATACATA
* *
537299 CAACCTGCTATATGTACAGGTAACATAGAATTATACATA
1 CAACCTGCTATACGTACAGGTAACCTAGAATTATACATA
* *
537338 CAACCTGCTATACATACAGGTAACCTAGATTTATACATA
1 CAACCTGCTATACGTACAGGTAACCTAGAATTATACATA
* * *
537377 CAATCTGATATACATACAGGTAACCTAGAATTATACATA
1 CAACCTGCTATACGTACAGGTAACCTAGAATTATACATA
* * *
537416 CAACCTGTTATACATACAGGTAACATAGAATTATACATA
1 CAACCTGCTATACGTACAGGTAACCTAGAATTATACATA
* *
537455 CAATCTGCTATACGTACAGGTAACATAGAATTATACATA
1 CAACCTGCTATACGTACAGGTAACCTAGAATTATACATA
* * *
537494 CAATCTGATATATGTACAGGTAACCTAGAATTATACATA
1 CAACCTGCTATACGTACAGGTAACCTAGAATTATACATA
537533 CAACCTGCTATACGTACAGGTAACCTAGAATTATACATA
1 CAACCTGCTATACGTACAGGTAACCTAGAATTATACATA
537572 CAACCTGCTATACGTACAGGTAACCTAGAATTATACATA
1 CAACCTGCTATACGTACAGGTAACCTAGAATTATACATA
*
537611 CAACCTGCTATACGTACAGGTAA-C---ATTTATACATA
1 CAACCTGCTATACGTACAGGTAACCTAGAATTATACATA
537646 CAACCTGCTATACGTACAGGTAACCTAGAATTATACATA
1 CAACCTGCTATACGTACAGGTAACCTAGAATTATACATA
*
537685 CAACCTGTTATAC
1 CAACCTGCTATAC
537698 NATGTGTAAA
Statistics
Matches: 408, Mismatches: 26, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
35 33 0.08
36 1 0.00
38 1 0.00
39 373 0.91
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.27
Consensus pattern (39 bp):
CAACCTGCTATACGTACAGGTAACCTAGAATTATACATA
Found at i:537428 original size:16 final size:16
Alignment explanation
Indices: 537329--537433 Score: 57
Period size: 16 Copynumber: 5.7 Consensus size: 16
537319 TAACATAGAA
537329 TTATACATACAACCTG
1 TTATACATACAACCTG
*
537345 CTATACATACAGGTAACCTAG
1 TTATACATAC----AACCT-G
*
537366 ATTTATACATACAATCTG
1 --TTATACATACAACCTG
*
537384 ATATACATACAGGTAACCTAG
1 TTATACATAC----AACCT-G
537405 AATTATACATACAACCTG
1 --TTATACATACAACCTG
537423 TTATACATACA
1 TTATACATACA
537434 GGTAACATAG
Statistics
Matches: 69, Mismatches: 6, Indels: 28
0.67 0.06 0.27
Matches are distributed among these distances:
16 29 0.42
18 2 0.03
19 9 0.13
20 9 0.13
21 2 0.03
23 18 0.26
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.30
Consensus pattern (16 bp):
TTATACATACAACCTG
Found at i:538065 original size:172 final size:172
Alignment explanation
Indices: 537779--538120 Score: 675
Period size: 172 Copynumber: 2.0 Consensus size: 172
537769 ACATTGACTT
537779 TATGTCGCTTACATCGTTATTGTTTTTACTGTCTAAATTTGTCTTGCTGATTCTCGTGAGAGTGT
1 TATGTCGCTTACATCGTTATTGTTTTTACTGTCTAAATTTGTCTTGCTGATTCTCGTGAGAGTGT
537844 GAAGTGATAAAAATTGCCATGATTACAGGGAACTACTGGGACGATTAAAACGATGCATTACTGGT
66 GAAGTGATAAAAATTGCCATGATTACAGGGAACTACTGGGACGATTAAAACGATGCATTACTGGT
537909 CCGATTTACTGACGCCAAAAAAATCCGTTGAATGAATGTGTG
131 CCGATTTACTGACGCCAAAAAAATCCGTTGAATGAATGTGTG
*
537951 TATGTCGCTTACATTGTTATTGTTTTTACTGTCTAAATTTGTCTTGCTGATTCTCGTGAGAGTGT
1 TATGTCGCTTACATCGTTATTGTTTTTACTGTCTAAATTTGTCTTGCTGATTCTCGTGAGAGTGT
538016 GAAGTGATAAAAATTGCCATGATTACAGGGAACTACTGGGACGATTAAAACGATGCATTACTGGT
66 GAAGTGATAAAAATTGCCATGATTACAGGGAACTACTGGGACGATTAAAACGATGCATTACTGGT
538081 CCGATTTACTGACGCCAAAAAAATCCGTTGAATGAATGTG
131 CCGATTTACTGACGCCAAAAAAATCCGTTGAATGAATGTG
538121 NCATACAACC
Statistics
Matches: 169, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
172 169 1.00
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (172 bp):
TATGTCGCTTACATCGTTATTGTTTTTACTGTCTAAATTTGTCTTGCTGATTCTCGTGAGAGTGT
GAAGTGATAAAAATTGCCATGATTACAGGGAACTACTGGGACGATTAAAACGATGCATTACTGGT
CCGATTTACTGACGCCAAAAAAATCCGTTGAATGAATGTGTG
Found at i:538250 original size:23 final size:23
Alignment explanation
Indices: 538224--538285 Score: 57
Period size: 16 Copynumber: 3.0 Consensus size: 23
538214 CTGCTATATG
538224 TACAGGTAACGTAGAATTATACA
1 TACAGGTAACGTAGAATTATACA
* *
538247 TAC----AACCT-G-CT-ATACA
1 TACAGGTAACGTAGAATTATACA
538263 TACAGGTAACGTAGAATTATACA
1 TACAGGTAACGTAGAATTATACA
538286 AACAACCTGC
Statistics
Matches: 28, Mismatches: 4, Indels: 14
0.61 0.09 0.30
Matches are distributed among these distances:
16 8 0.29
17 1 0.04
18 1 0.04
19 4 0.14
20 4 0.14
21 1 0.04
22 1 0.04
23 8 0.29
ACGTcount: A:0.42, C:0.18, G:0.15, T:0.26
Consensus pattern (23 bp):
TACAGGTAACGTAGAATTATACA
Found at i:538335 original size:117 final size:122
Alignment explanation
Indices: 538122--538350 Score: 351
Period size: 117 Copynumber: 1.9 Consensus size: 122
538112 ATGAATGTGN
* *
538122 CATACAACCTGCTATACATACATGTAACGTAGAATTATATACTAGTATACAATCTGCTATACATA
1 CATACAACCTGCTATACATACAGGTAACGTAGAATTATATACTAG-ATACAACCTGCTATACATA
*
538187 CAGGTAACATAGAATTATACATACAACCTGCTATATGTACAGGTAACGTAGAATTATA
65 CAGGTAACATAGAATTATACATACAACCTGCTATACGTACAGGTAACGTAGAATTATA
*
538245 CATACAACCTGCTATACATACAGGTAACGTAGAA-T-TATAC-A-A-ACAACCTGCTATACGTAC
1 CATACAACCTGCTATACATACAGGTAACGTAGAATTATATACTAGATACAACCTGCTATACATAC
* * *
538305 TGGTAACCTAGAATTATACATACAACCTGCTATACGTACATGTAAC
66 AGGTAACATAGAATTATACATACAACCTGCTATACGTACAGGTAAC
538351 CATTGTAAAG
Statistics
Matches: 99, Mismatches: 7, Indels: 6
0.88 0.06 0.05
Matches are distributed among these distances:
117 58 0.59
118 1 0.01
120 1 0.01
121 5 0.05
122 1 0.01
123 33 0.33
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.28
Consensus pattern (122 bp):
CATACAACCTGCTATACATACAGGTAACGTAGAATTATATACTAGATACAACCTGCTATACATAC
AGGTAACATAGAATTATACATACAACCTGCTATACGTACAGGTAACGTAGAATTATA
Found at i:538351 original size:39 final size:39
Alignment explanation
Indices: 538122--538350 Score: 305
Period size: 39 Copynumber: 5.7 Consensus size: 39
538112 ATGAATGTGN
*
538122 CATACAACCTGCTATACATACATGTAACGTAGAATTATATA
1 CATACAACCTGCTATACATACAGGTAACGTAGAA-T-TATA
* *
538163 CTAGTATACAATCTGCTATACATACAGGTAACATAGAATTATA
1 C----ATACAACCTGCTATACATACAGGTAACGTAGAATTATA
**
538206 CATACAACCTGCTATATGTACAGGTAACGTAGAATTATA
1 CATACAACCTGCTATACATACAGGTAACGTAGAATTATA
538245 CATACAACCTGCTATACATACAGGTAACGTAGAATTATA
1 CATACAACCTGCTATACATACAGGTAACGTAGAATTATA
* * * *
538284 CAAACAACCTGCTATACGTACTGGTAACCTAGAATTATA
1 CATACAACCTGCTATACATACAGGTAACGTAGAATTATA
* *
538323 CATACAACCTGCTATACGTACATGTAAC
1 CATACAACCTGCTATACATACAGGTAAC
538351 CATTGTAAAG
Statistics
Matches: 168, Mismatches: 16, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
39 131 0.78
41 1 0.01
43 5 0.03
44 1 0.01
45 30 0.18
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.28
Consensus pattern (39 bp):
CATACAACCTGCTATACATACAGGTAACGTAGAATTATA
Found at i:539202 original size:154 final size:154
Alignment explanation
Indices: 538922--539232 Score: 604
Period size: 154 Copynumber: 2.0 Consensus size: 154
538912 TACTAGCTCT
538922 GGCTAGCAGGTTAACCCTTTAGCTCGATCGGTAGAGTGCTAGACTGGTGAGCCAGAGGACCTGGG
1 GGCTAGCAGGTTAACCCTTTAGCTCGATCGGTAGAGTGCTAGACTGGTGAGCCAGAGGACCTGGG
*
538987 TTGAAACTCCAGCAGAGGCAATAAGTGTCTCTGTTACATTTGGCGCCAACATTGGGGCATTATGT
66 TTCAAACTCCAGCAGAGGCAATAAGTGTCTCTGTTACATTTGGCGCCAACATTGGGGCATTATGT
539052 GACGGTCAGACCGGTTCCAATACC
131 GACGGTCAGACCGGTTCCAATACC
*
539076 GGCTAGCGGGTTAACCCTTTAGCTCGATCGGTAGAGTGCTAGACTGGTGAGCCAGAGGACCTGGG
1 GGCTAGCAGGTTAACCCTTTAGCTCGATCGGTAGAGTGCTAGACTGGTGAGCCAGAGGACCTGGG
539141 TTCAAACTCCAGCAGAGGCAATAAGTGTCTCTGTTACATTTGGCGCCAACATTGGGGCATTATGT
66 TTCAAACTCCAGCAGAGGCAATAAGTGTCTCTGTTACATTTGGCGCCAACATTGGGGCATTATGT
539206 GACGGTCAGACCGGTTCCAATACC
131 GACGGTCAGACCGGTTCCAATACC
539230 GGC
1 GGC
539233 GCCAGATAGC
Statistics
Matches: 155, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
154 155 1.00
ACGTcount: A:0.23, C:0.23, G:0.30, T:0.24
Consensus pattern (154 bp):
GGCTAGCAGGTTAACCCTTTAGCTCGATCGGTAGAGTGCTAGACTGGTGAGCCAGAGGACCTGGG
TTCAAACTCCAGCAGAGGCAATAAGTGTCTCTGTTACATTTGGCGCCAACATTGGGGCATTATGT
GACGGTCAGACCGGTTCCAATACC
Found at i:539984 original size:8 final size:8
Alignment explanation
Indices: 539971--540056 Score: 109
Period size: 8 Copynumber: 10.8 Consensus size: 8
539961 CCGGGCGTCC
539971 GTCCGTGT
1 GTCCGTGT
539979 GTCCGTGT
1 GTCCGTGT
*
539987 GTCCGTGG
1 GTCCGTGT
539995 GTCCGTGT
1 GTCCGTGT
*
540003 GTCCGTGG
1 GTCCGTGT
* *
540011 GTCCATGG
1 GTCCGTGT
*
540019 GTCTGTGT
1 GTCCGTGT
*
540027 GTCCGTGG
1 GTCCGTGT
*
540035 GTCCGTGC
1 GTCCGTGT
540043 GTCCGTGT
1 GTCCGTGT
540051 GTCCGT
1 GTCCGT
540057 CCGTCACACT
Statistics
Matches: 67, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 67 1.00
ACGTcount: A:0.01, C:0.26, G:0.41, T:0.33
Consensus pattern (8 bp):
GTCCGTGT
Found at i:540003 original size:24 final size:24
Alignment explanation
Indices: 539971--540056 Score: 136
Period size: 24 Copynumber: 3.6 Consensus size: 24
539961 CCGGGCGTCC
*
539971 GTCCGTGTGTCCGTGTGTCCGTGG
1 GTCCGTGTGTCCGTGGGTCCGTGG
*
539995 GTCCGTGTGTCCGTGGGTCCATGG
1 GTCCGTGTGTCCGTGGGTCCGTGG
* *
540019 GTCTGTGTGTCCGTGGGTCCGTGC
1 GTCCGTGTGTCCGTGGGTCCGTGG
540043 GTCCGTGTGTCCGT
1 GTCCGTGTGTCCGT
540057 CCGTCACACT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 56 1.00
ACGTcount: A:0.01, C:0.26, G:0.41, T:0.33
Consensus pattern (24 bp):
GTCCGTGTGTCCGTGGGTCCGTGG
Found at i:540356 original size:172 final size:172
Alignment explanation
Indices: 540070--541038 Score: 1697
Period size: 172 Copynumber: 5.6 Consensus size: 172
540060 TCACACTTTT
* *
540070 TTGTAAGCGCTCTCATGCCTACAAATTTTGCCGGATTTTCATCAAATTTATACCAAATGTTTATA
1 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATA
* * *
540135 TCACTATTATCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGGA
66 CCACTAATACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGGA
540200 CTTTGACCACAATAATGACTCCGTTTTATCAAAAAATTGACC
131 CTTTGACCACAATAATGACTCCGTTTTATCAAAAAATTGACC
*
540242 TTGTAAGCGCTCTCATGCCTACAAATTTTGAAGGATTTTCATTAAATTTATACCAAATGTTTATA
1 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATA
* *
540307 CCACTAATACCTTGGTCGAGTTCAAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGGA
66 CCACTAATACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGGA
* *
540372 CTATGACCACAATAATGACTCTGTTTTATCAAAAAATTGACC
131 CTTTGACCACAATAATGACTCCGTTTTATCAAAAAATTGACC
*
540414 TTGTAAGCGCTCTCATGCCTACAAATTTTGATGGATTTTCATTAAATTTATACCAAATGTTTATA
1 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATA
*
540479 TCACTAATACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGGA
66 CCACTAATACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGGA
*
540544 CTTTGACCACAATAATGACTTCGTTTTATCAAAAAATTGACC
131 CTTTGACCACAATAATGACTCCGTTTTATCAAAAAATTGACC
* *
540586 TTGTAAGCGCTCTCATGCCTACAAACTTTGACGGATTTTC-TTCAAATTTATACCAAATATTTAT
1 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATT-AAATTTATACCAAATGTTTAT
540650 ACCACTAATACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGG
65 ACCACTAATACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGG
* * * *
540715 ACTTTAACCACAATCATGACCCCGTTTTATCCAAAAATTGACC
130 ACTTTGACCACAATAATGACTCCGTTTTATCAAAAAATTGACC
*
540758 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATCAAATTTATACCAAATGTTTATA
1 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATA
*
540823 CCACTAATACCTTGGTCAAGTTTGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGGA
66 CCACTAATACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGGA
* *
540888 CTATGACCACAATAATGACTCCGTTTTATCCAAAAATTGACC
131 CTTTGACCACAATAATGACTCCGTTTTATCAAAAAATTGACC
*
540930 TTGTAAGCGCTCTCATGCCTACAAATTTTGATGGATTTTCATTAAATTTATACCAAATGTTTATA
1 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATA
*
540995 CCACTAATACCTTGGTCAAGTTCGAAAATCAGCCTTGGTCGATA
66 CCACTAATACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATA
541039 GACTCGATAC
Statistics
Matches: 757, Mismatches: 38, Indels: 4
0.95 0.05 0.01
Matches are distributed among these distances:
171 2 0.00
172 754 1.00
173 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (172 bp):
TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATA
CCACTAATACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGGA
CTTTGACCACAATAATGACTCCGTTTTATCAAAAAATTGACC
Found at i:541148 original size:37 final size:37
Alignment explanation
Indices: 541097--541244 Score: 233
Period size: 37 Copynumber: 4.0 Consensus size: 37
541087 CTTGTTTCAT
* * *
541097 TTGAATTCTTTATGATAGATACTTATTGGTTCGACTA
1 TTGAATTCTCTATGATTGATACTTATTGGTTGGACTA
* * *
541134 CTGAATTCTTTATGATTGATATTTATTGGTTGGACTA
1 TTGAATTCTCTATGATTGATACTTATTGGTTGGACTA
541171 TTGAATTCTCTATGATTGATACTTATTGGTTGGACTA
1 TTGAATTCTCTATGATTGATACTTATTGGTTGGACTA
*
541208 TTGAATTCTCTATGATTGATACTTATTAGTTGGACTA
1 TTGAATTCTCTATGATTGATACTTATTGGTTGGACTA
541245 ACCTATTTGT
Statistics
Matches: 103, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 103 1.00
ACGTcount: A:0.26, C:0.10, G:0.18, T:0.47
Consensus pattern (37 bp):
TTGAATTCTCTATGATTGATACTTATTGGTTGGACTA
Found at i:541421 original size:19 final size:19
Alignment explanation
Indices: 541397--541455 Score: 91
Period size: 19 Copynumber: 3.1 Consensus size: 19
541387 GGGATAGATT
*
541397 CTATAGGCTGAGAATGATC
1 CTATAGGCTGAGATTGATC
*
541416 CTATAGGCTGAGATTGGTC
1 CTATAGGCTGAGATTGATC
*
541435 CTTTAGGCTGAGATTGATC
1 CTATAGGCTGAGATTGATC
541454 CT
1 CT
541456 GGGTAGGATT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (19 bp):
CTATAGGCTGAGATTGATC
Found at i:541619 original size:36 final size:36
Alignment explanation
Indices: 541572--541725 Score: 272
Period size: 36 Copynumber: 4.3 Consensus size: 36
541562 GTGGTGGCTA
541572 CTATTGGTTGAATTAATCCATTTGTTACAATAAGTC
1 CTATTGGTTGAATTAATCCATTTGTTACAATAAGTC
541608 CTATTGGTTGAATTAATCCATTTGTTACAATAAGTC
1 CTATTGGTTGAATTAATCCATTTGTTACAATAAGTC
** *
541644 CTGCTGGTTGAATTAATCCATTTGTTACAAGAAGTC
1 CTATTGGTTGAATTAATCCATTTGTTACAATAAGTC
*
541680 CTATTGGCTGAATTAATCCATTTGTTACAATAAGTC
1 CTATTGGTTGAATTAATCCATTTGTTACAATAAGTC
541716 CTATTGGTTG
1 CTATTGGTTG
541726 GAATGATAAC
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 110 1.00
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.40
Consensus pattern (36 bp):
CTATTGGTTGAATTAATCCATTTGTTACAATAAGTC
Found at i:557481 original size:46 final size:46
Alignment explanation
Indices: 557425--557514 Score: 126
Period size: 46 Copynumber: 2.0 Consensus size: 46
557415 AAACTCAAAA
* *
557425 TGACTCGTATTGCGAGACAGAATCTGCAATAATGTGAAAAATTCAG
1 TGACTCGTATTGCAAGACAGAATCTCCAATAATGTGAAAAATTCAG
* * * *
557471 TGACTTGTATTGCAAGACGGAATTTCCATTAATGTGAAAAATTC
1 TGACTCGTATTGCAAGACAGAATCTCCAATAATGTGAAAAATTC
557515 TAATATTTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (46 bp):
TGACTCGTATTGCAAGACAGAATCTCCAATAATGTGAAAAATTCAG
Found at i:559893 original size:2 final size:2
Alignment explanation
Indices: 559841--559874 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
559831 TATCTCCTCT
559841 GA GA GA GA GA GA GA GA GA GA G- GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
559875 TATTTTTGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
GA
Found at i:561991 original size:29 final size:26
Alignment explanation
Indices: 561912--561978 Score: 134
Period size: 26 Copynumber: 2.6 Consensus size: 26
561902 TGCAGATCTA
561912 TAATATTATTGCACAAATACATTTCT
1 TAATATTATTGCACAAATACATTTCT
561938 TAATATTATTGCACAAATACATTTCT
1 TAATATTATTGCACAAATACATTTCT
561964 TAATATTATTGCACA
1 TAATATTATTGCACA
561979 GGTGTTAGAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.39, C:0.15, G:0.04, T:0.42
Consensus pattern (26 bp):
TAATATTATTGCACAAATACATTTCT
Found at i:564672 original size:146 final size:144
Alignment explanation
Indices: 564408--564917 Score: 745
Period size: 146 Copynumber: 3.5 Consensus size: 144
564398 TANAACTGTT
* * *
564408 GGTCATAAGCAATATTTGTGTGTAGTAAGAACATT-CAATGCTTCTCCATAAGAAAGATAAT-GA
1 GGTCATAAGCAATCTTTGTGTGAAGTAAGAAC-TTCCAATGTTTCTCCATAAGAAAGAT-ATGGA
* *
564471 CCAGACATGAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAA
64 CCAGACACGAATTTTGTA-TTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAA
* *
564536 GGTCATGACACATCCATC
128 GGTCATGACACA-CCTTA
* *
564554 GGTCATAAGCAATCTTTGTGTGAAGTAAGAACTTCTAATGTTTCTCCATAAAAAAGATATGGACC
1 GGTCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACC
* *
564619 GGACACAAATTTTGTATTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGG
66 AGACACGAATTTTGTA-TTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGG
*
564684 TTATGACACACCCTTA
130 TCATGACACA-CCTTA
*** * *
564700 GGTCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATAACTCTTCATAAGAAAGTTATGGACC
1 GGTCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACC
* * *
564765 ACACACGAATTTTGTATTTCTCTGTCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGGT
66 AGACACGAATTTTGTATTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGGT
564830 CATGACACACCTTTA
131 CATGACACACC-TTA
*
564845 GGTCATAAGCAATCTTTGTCTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACC
1 GGTCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACC
*
564910 GGACACGA
66 AGACACGA
564918 TTGTACAGAC
Statistics
Matches: 326, Mismatches: 35, Indels: 7
0.89 0.10 0.02
Matches are distributed among these distances:
144 2 0.01
145 127 0.39
146 197 0.60
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (144 bp):
GGTCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACC
AGACACGAATTTTGTATTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGGT
CATGACACACCTTA
Found at i:564938 original size:8 final size:8
Alignment explanation
Indices: 564925--564968 Score: 61
Period size: 8 Copynumber: 5.5 Consensus size: 8
564915 CGATTGTACA
564925 GACAGACG
1 GACAGACG
564933 GACAGACG
1 GACAGACG
* *
564941 GACGGACA
1 GACAGACG
*
564949 GACGGACG
1 GACAGACG
564957 GACAGACG
1 GACAGACG
564965 GACA
1 GACA
564969 AGGTGATTCC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 32 1.00
ACGTcount: A:0.36, C:0.25, G:0.39, T:0.00
Consensus pattern (8 bp):
GACAGACG
Found at i:564939 original size:12 final size:12
Alignment explanation
Indices: 564922--564967 Score: 83
Period size: 12 Copynumber: 3.8 Consensus size: 12
564912 ACACGATTGT
*
564922 ACAGACAGACGG
1 ACAGACGGACGG
564934 ACAGACGGACGG
1 ACAGACGGACGG
564946 ACAGACGGACGG
1 ACAGACGGACGG
564958 ACAGACGGAC
1 ACAGACGGAC
564968 AAGGTGATTC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.37, C:0.26, G:0.37, T:0.00
Consensus pattern (12 bp):
ACAGACGGACGG
Found at i:567188 original size:2 final size:2
Alignment explanation
Indices: 567181--567228 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
567171 TTAAAAGCAT
567181 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
567223 GA GA GA
1 GA GA GA
567229 TGATACAACG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:567321 original size:2 final size:2
Alignment explanation
Indices: 567314--567373 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
567304 ACTTGATATG
567314 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
567356 GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA
567374 TTTTCAGTCT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:567748 original size:13 final size:13
Alignment explanation
Indices: 567730--567754 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
567720 TTCTACGGGC
567730 TTAGTGGCTGCTG
1 TTAGTGGCTGCTG
567743 TTAGTGGCTGCT
1 TTAGTGGCTGCT
567755 AGCTTCAGCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.16, G:0.36, T:0.40
Consensus pattern (13 bp):
TTAGTGGCTGCTG
Found at i:572423 original size:162 final size:157
Alignment explanation
Indices: 572095--572512 Score: 465
Period size: 162 Copynumber: 2.6 Consensus size: 157
572085 TGATTGGATA
* * **
572095 AACTTGAAATCT-CACTACCTGATGATGCTTCCAAACAAGTTTCAGCTTTCCTG-CCCAATCGG-
1 AACTTTAAATCTACACTACCTGAGGATGCTTCCAAACAAGTTTCAGCTTTCCTGACATAAT-GGT
* * * *
572157 TTCT-TGAGAAGATTTTTAAAGATTTACTCTATTTATTCCTATGTAAAAAGTCGACCCCCCATTG
65 TTCTGAGAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAAAGCCCACCCCCCATTG
572221 TGGCCCCACCGAACCCCCAAGGGTCATTCAC
130 TGGCCCCACCGAACCCCCAAGGG---TTCAC
* *
572252 AACTTTAAATCTACACTACCTGAGGATGCTT-CAATACAAGTTTCCGCTTTACTGACATAATGGT
1 AACTTTAAATCTACACTACCTGAGGATGCTTCCAA-ACAAGTTTCAGCTTTCCTGACATAATGGT
*
572316 TTCTGAGAAGAAGATTTTTTAAAGATTTACTCTATATATTCCTATGTAAAAATTGCCCCCCCCCC
65 TTCTGAG-AGAAGA-TTTTTAAAGATTTACTCTATATATTCCTATGTAAAAA--G--CCCACCCC
* * * *
572381 CCATTGTGGCCCCAACC-TATCCCCGATGG-TCAC
124 CCATTGTGGCCCC-ACCGAACCCCCAAGGGTTCAC
* * * * *
572414 GATTTTAAATCTACACTACCTGAGGATGCTTCCAACCAAGTTTCAGCTTTCCTGA-ATGATTGCT
1 AACTTTAAATCTACACTACCTGAGGATGCTTCCAAACAAGTTTCAGCTTTCCTGACAT-AATGGT
*
572478 TTCTGGGTAGAAGATTTTTAAAGATTTACTCTATA
65 TTCTGAG-AGAAGATTTTTAAAGATTTACTCTATA
572513 AAGTCGACCC
Statistics
Matches: 223, Mismatches: 24, Indels: 24
0.82 0.09 0.09
Matches are distributed among these distances:
157 14 0.06
158 36 0.16
159 8 0.04
160 1 0.00
161 29 0.13
162 102 0.46
163 3 0.01
164 1 0.00
166 26 0.12
167 3 0.01
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (157 bp):
AACTTTAAATCTACACTACCTGAGGATGCTTCCAAACAAGTTTCAGCTTTCCTGACATAATGGTT
TCTGAGAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAAAGCCCACCCCCCATTGT
GGCCCCACCGAACCCCCAAGGGTTCAC
Found at i:574473 original size:20 final size:20
Alignment explanation
Indices: 574445--574483 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
574435 GGATCTGAAT
*
574445 GAACTCATCCATTAGCATAG
1 GAACACATCCATTAGCATAG
574465 GAACACATCCATTAGCATA
1 GAACACATCCATTAGCATA
574484 CTGATAGATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.26, G:0.13, T:0.23
Consensus pattern (20 bp):
GAACACATCCATTAGCATAG
Found at i:576453 original size:1 final size:1
Alignment explanation
Indices: 576447--576474 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
576437 TGATAATTAT
576447 GGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGG
576475 NNNNNNNNNN
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:576978 original size:2 final size:2
Alignment explanation
Indices: 576971--577025 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
576961 AATTAACAAC
576971 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
577013 AG AG AG AG AG AG A
1 AG AG AG AG AG AG A
577026 ATTTCGACGA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:578941 original size:18 final size:18
Alignment explanation
Indices: 578918--578963 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
578908 GCGAACAAAT
*
578918 AAACAAACAAGCAAAAAA
1 AAACAAACAAACAAAAAA
* * *
578936 AAACAAAAAAACCAAACA
1 AAACAAACAAACAAAAAA
578954 AAACAAACAA
1 AAACAAACAA
578964 CAACGAATAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.78, C:0.20, G:0.02, T:0.00
Consensus pattern (18 bp):
AAACAAACAAACAAAAAA
Found at i:580855 original size:21 final size:21
Alignment explanation
Indices: 580831--581656 Score: 1296
Period size: 21 Copynumber: 39.3 Consensus size: 21
580821 TACCAAACAA
580831 GATACCA-ATCAGTGAACACAC
1 GATACCATA-CAGTGAACACAC
*
580852 GATACCATACAGTGAACACCC
1 GATACCATACAGTGAACACAC
* *
580873 TATACCATACAGTGAACACTC
1 GATACCATACAGTGAACACAC
* * *
580894 TATACAATACAGTGAACACAT
1 GATACCATACAGTGAACACAC
580915 GATACCATACAGTGAACACAC
1 GATACCATACAGTGAACACAC
* *
580936 AATACCATACAGTGAACACAT
1 GATACCATACAGTGAACACAC
* *
580957 AATACCATACAGTGAACACAT
1 GATACCATACAGTGAACACAC
* *
580978 AATACCATACAGTGAACACAT
1 GATACCATACAGTGAACACAC
580999 GATACCATACAGTGAACACAC
1 GATACCATACAGTGAACACAC
*
581020 GGTACCATACAGTGAACACAC
1 GATACCATACAGTGAACACAC
581041 GATACCATACAGTGAACACAC
1 GATACCATACAGTGAACACAC
581062 GATACCATACAGTGAACACAC
1 GATACCATACAGTGAACACAC
581083 GATACCATACAGTGAACACAC
1 GATACCATACAGTGAACACAC
581104 GATACCATACAGTGAACACAC
1 GATACCATACAGTGAACACAC
581125 GATACCATACAGTGAACACAC
1 GATACCATACAGTGAACACAC
581146 GATACCATACAGTGAACACAC
1 GATACCATACAGTGAACACAC
581167 GATACCATACAGTGAACACAC
1 GATACCATACAGTGAACACAC
581188 GATACCATACAGTGAACACAC
1 GATACCATACAGTGAACACAC
581209 GATACCATACAGTGAACACAC
1 GATACCATACAGTGAACACAC
581230 GATACCATACAGTGAACACAC
1 GATACCATACAGTGAACACAC
* **
581251 GATACAATACAGTGAACACTT
1 GATACCATACAGTGAACACAC
581272 GATACCATACAGTGAACACAC
1 GATACCATACAGTGAACACAC
* * *
581293 GATACCATATAGTTAACACAT
1 GATACCATACAGTGAACACAC
581314 GATACCATACAGTGAACACAC
1 GATACCATACAGTGAACACAC
*
581335 GATACCATACAGTGAAAACAC
1 GATACCATACAGTGAACACAC
581356 GATACCATACAGTGAACACAC
1 GATACCATACAGTGAACACAC
* *
581377 GATACCATACAGTGAAAACAT
1 GATACCATACAGTGAACACAC
* * ** *
581398 GATATCATAAAAAGAACACTC
1 GATACCATACAGTGAACACAC
581419 GATACCATACAGTGAACACAC
1 GATACCATACAGTGAACACAC
581440 GATACCATACAGTGAACACAC
1 GATACCATACAGTGAACACAC
581461 GATACCATACAGTGAACACAC
1 GATACCATACAGTGAACACAC
*
581482 GATACCATACAGTGAACACAG
1 GATACCATACAGTGAACACAC
581503 GATACCATACAGTGAACACAC
1 GATACCATACAGTGAACACAC
581524 GATACCATACAGTGAACACAC
1 GATACCATACAGTGAACACAC
581545 GATACCATACAGTGAACACAC
1 GATACCATACAGTGAACACAC
* *
581566 GATACCATAAAATGAACACAC
1 GATACCATACAGTGAACACAC
* *
581587 GATACCATACAGTGAAAACAT
1 GATACCATACAGTGAACACAC
* *
581608 GATACCATAAAAG-GAACACTC
1 GATACCAT-ACAGTGAACACAC
**
581629 GATACCATACAGTGAACACTT
1 GATACCATACAGTGAACACAC
581650 GATACCA
1 GATACCA
581657 GAGAGAGAGA
Statistics
Matches: 745, Mismatches: 57, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
20 3 0.00
21 738 0.99
22 4 0.01
ACGTcount: A:0.44, C:0.26, G:0.14, T:0.16
Consensus pattern (21 bp):
GATACCATACAGTGAACACAC
Found at i:581663 original size:2 final size:2
Alignment explanation
Indices: 581656--581720 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
581646 ACTTGATACC
581656 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
581698 AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG A
581721 TTAAAACATC
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:582586 original size:4 final size:4
Alignment explanation
Indices: 582573--582603 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
582563 TCTCTCTCTC
582573 GTCT GT-T GTCT GTCT GTCT GTCT GTCT GTCT
1 GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT
582604 CTCTCTCTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.00, C:0.23, G:0.26, T:0.52
Consensus pattern (4 bp):
GTCT
Found at i:582608 original size:2 final size:2
Alignment explanation
Indices: 582601--582662 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
582591 TGTCTGTCTG
582601 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
582643 TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC
582663 AGCTTTCTTG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:586133 original size:2 final size:2
Alignment explanation
Indices: 586126--586160 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
586116 ATGGTTCTAN
586126 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
586161 CACTACCTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:596357 original size:11 final size:11
Alignment explanation
Indices: 596341--596376 Score: 63
Period size: 11 Copynumber: 3.3 Consensus size: 11
596331 GAGTTGCACT
596341 GCATATCATTA
1 GCATATCATTA
*
596352 GCATATCATTT
1 GCATATCATTA
596363 GCATATCATTA
1 GCATATCATTA
596374 GCA
1 GCA
596377 CTTAGGGTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.36
Consensus pattern (11 bp):
GCATATCATTA
Found at i:598828 original size:54 final size:54
Alignment explanation
Indices: 598525--598807 Score: 449
Period size: 54 Copynumber: 5.2 Consensus size: 54
598515 GTGGTGGATC
* *
598525 TACACTAGTGGTGTGGGCTCTACCTGTACTGTGGCTGATACTCTCCAGAGATTG
1 TACACTAGTGGTGTGGGCCCTACCTGTACTGTGGCCGATACTCTCCAGAGATTG
* * *
598579 TACACTAGTGGTGTGGGCTCTACCTGTACTGTGTCTGATACTCTCCAGAGATTG
1 TACACTAGTGGTGTGGGCCCTACCTGTACTGTGGCCGATACTCTCCAGAGATTG
* * * *
598633 TACACTAGTGGTGTGGGTCCTACCTGTACTGTGACCGATACTCTACAGAGATTC
1 TACACTAGTGGTGTGGGCCCTACCTGTACTGTGGCCGATACTCTCCAGAGATTG
* *
598687 TACACTAGTGGTGTGGGCCCTACCTGTACTGTGGCCAATACTCTTCAGAGATTG
1 TACACTAGTGGTGTGGGCCCTACCTGTACTGTGGCCGATACTCTCCAGAGATTG
* *
598741 TACACTAGTGGTGTGGGCCCTACCTGTACTGTGGCCGATACTCTTCAGAGATTC
1 TACACTAGTGGTGTGGGCCCTACCTGTACTGTGGCCGATACTCTCCAGAGATTG
598795 TACACTAGTGGTG
1 TACACTAGTGGTG
598808 AATTCTACAC
Statistics
Matches: 215, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 215 1.00
ACGTcount: A:0.20, C:0.23, G:0.26, T:0.31
Consensus pattern (54 bp):
TACACTAGTGGTGTGGGCCCTACCTGTACTGTGGCCGATACTCTCCAGAGATTG
Found at i:598828 original size:72 final size:71
Alignment explanation
Indices: 598741--598873 Score: 212
Period size: 72 Copynumber: 1.9 Consensus size: 71
598731 TCAGAGATTG
* * *
598741 TACACTAGTGGTGTGGGCCCTACCTGTACTGTGGCCGATACTCTTCAGAGATTCTACACTAGTGG
1 TACACTAGTAGTGTGGGCCATACCTGTACTGTGGCCGA-AATCTTCAGAGATTCTACACTAGTGG
598806 TGAATTC
65 TGAATTC
* *
598813 TACACTAGTAGTGTGGGTCATACCTGTACTGTGGCTGAAATCTTCAGAGATTCTACACTAG
1 TACACTAGTAGTGTGGGCCATACCTGTACTGTGGCCGAAATCTTCAGAGATTCTACACTAG
598874 AAGGGCGGGC
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
71 22 0.39
72 34 0.61
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.31
Consensus pattern (71 bp):
TACACTAGTAGTGTGGGCCATACCTGTACTGTGGCCGAAATCTTCAGAGATTCTACACTAGTGGT
GAATTC
Found at i:598863 original size:179 final size:179
Alignment explanation
Indices: 598633--598997 Score: 486
Period size: 179 Copynumber: 2.0 Consensus size: 179
598623 CCAGAGATTG
* * * *
598633 TACACTAGTGGTGTGGGTCCTACCTGTACTGTGACCGATACTCTACAGAGATTCTACACTAG-TG
1 TACACTAGTAGTGTGGGTCATACCTGTACTGTGACCGATAATCTACAGAGATTCTACACTAGAAG
* * * *
598697 GTGTGGGCCCTACCTGTACTGTGGCCAATACTCTTC-AGAGATTGTACACTAGTGGTGTGGGCCC
66 G-GCGGGCACTACCTGTACTGTGGACAATACTC-TCAAGAGATTCTACACTAGTGGTGTGGGCCC
*
598761 TACCTGTACTGTGGCCGATACTCTTCAGAGAT-TCTACACTAGTGGTGAATTC
129 TACCTGTACTGTGGCCGATACTCTCCAGAGATCT-TACACTAGTGGTGAA-TC
* * *
598813 TACACTAGTAGTGTGGGTCATACCTGTACTGTGGCTGA-AATCTTCAGAGATTCTACACTAGAAG
1 TACACTAGTAGTGTGGGTCATACCTGTACTGTGACCGATAATCTACAGAGATTCTACACTAGAAG
* * ** * *
598877 GGCGGGCACTACCTGTGCTGTGTATGATACTCTCAAGAGATTCTACACTAGTGGTGTGGTCTCTA
66 GGCGGGCACTACCTGTACTGTGGACAATACTCTCAAGAGATTCTACACTAGTGGTGTGGGCCCTA
* *
598942 CCTGTACTGTGGCCGATGCTCTCCAGAGATCTTACACTAGTGGTGGATC
131 CCTGTACTGTGGCCGATACTCTCCAGAGATCTTACACTAGTGGTGAATC
598991 TACACTA
1 TACACTA
598998 ATGGTGGATT
Statistics
Matches: 162, Mismatches: 20, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
178 11 0.07
179 114 0.70
180 37 0.23
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.30
Consensus pattern (179 bp):
TACACTAGTAGTGTGGGTCATACCTGTACTGTGACCGATAATCTACAGAGATTCTACACTAGAAG
GGCGGGCACTACCTGTACTGTGGACAATACTCTCAAGAGATTCTACACTAGTGGTGTGGGCCCTA
CCTGTACTGTGGCCGATACTCTCCAGAGATCTTACACTAGTGGTGAATC
Found at i:598906 original size:125 final size:126
Alignment explanation
Indices: 598683--598932 Score: 337
Period size: 125 Copynumber: 2.0 Consensus size: 126
598673 CTCTACAGAG
* * *
598683 ATTCTACACTAGTGGTGTGGGCCCTACCTGTACTGTGGCCAATACTCTTCAGAGATTGTACACTA
1 ATTCTACACTAGTAGTGTGGGCCATACCTGTACTGTGGCCAATACTCTTCAGAGATTCTACACTA
* * * *
598748 GTGGTGTGGGCCCTACCTGTACTGTGGCCGATACTCTTC-AGAGATTCTACACTAGTGGTGA
66 GAGGTGCGGGCACTACCTGTACTGTGGACGATACTC-TCAAGAGATTCTACACTAGTGGTGA
* *
598809 ATTCTACACTAGTAGTGTGGGTCATACCTGTACTGTGGCTGAA-A-TCTTCAGAGATTCTACACT
1 ATTCTACACTAGTAGTGTGGGCCATACCTGTACTGTGGC-CAATACTCTTCAGAGATTCTACACT
* * *
598872 AGAAGG-GCGGGCACTACCTGTGCTGTGTATGATACTCTCAAGAGATTCTACACTAGTGGTG
65 AG-AGGTGCGGGCACTACCTGTACTGTGGACGATACTCTCAAGAGATTCTACACTAGTGGTG
598933 TGGTCTCTAC
Statistics
Matches: 109, Mismatches: 12, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
124 2 0.02
125 66 0.61
126 39 0.36
127 2 0.02
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30
Consensus pattern (126 bp):
ATTCTACACTAGTAGTGTGGGCCATACCTGTACTGTGGCCAATACTCTTCAGAGATTCTACACTA
GAGGTGCGGGCACTACCTGTACTGTGGACGATACTCTCAAGAGATTCTACACTAGTGGTGA
Found at i:598943 original size:54 final size:52
Alignment explanation
Indices: 598809--598986 Score: 164
Period size: 54 Copynumber: 3.3 Consensus size: 52
598799 CTAGTGGTGA
* * *
598809 ATTCTACACTAGTAGTGTGGGTCATACCTGTACTGTGGCTGA-AATCTTCAGAG
1 ATTCTACACTAGTGGTGT-GGTCCTACCTGTACTGTGGCTGATACTC-TCAGAG
* * * * **
598862 ATTCTACACTAGAAGG-GCGGGCACTACCTGTGCTGTGTATGATACTCTCAAGAG
1 ATTCTACACTAG-TGGTGTGGTC-CTACCTGTACTGTGGCTGATACTCTC-AGAG
* *
598916 ATTCTACACTAGTGGTGTGGTCTCTACCTGTACTGTGGCCGATGCTCTCCAGAG
1 ATTCTACACTAGTGGTGTGGTC-CTACCTGTACTGTGGCTGATACTCT-CAGAG
598970 A-TCTTACACTAGTGGTG
1 ATTC-TACACTAGTGGTG
598987 GATCTACACT
Statistics
Matches: 100, Mismatches: 18, Indels: 13
0.76 0.14 0.10
Matches are distributed among these distances:
52 3 0.03
53 34 0.34
54 62 0.62
55 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.30
Consensus pattern (52 bp):
ATTCTACACTAGTGGTGTGGTCCTACCTGTACTGTGGCTGATACTCTCAGAG
Found at i:599010 original size:18 final size:17
Alignment explanation
Indices: 598969--599021 Score: 79
Period size: 18 Copynumber: 3.0 Consensus size: 17
598959 GCTCTCCAGA
598969 GATCTTACACTAGTGGTG
1 GATC-TACACTAGTGGTG
*
598987 GATCTACACTAATGGTG
1 GATCTACACTAGTGGTG
599004 GATTCTACACTAGTGGTG
1 GA-TCTACACTAGTGGTG
599022 TGGGCCCTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
17 14 0.44
18 18 0.56
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (17 bp):
GATCTACACTAGTGGTG
Found at i:599977 original size:22 final size:22
Alignment explanation
Indices: 599970--600222 Score: 183
Period size: 22 Copynumber: 11.9 Consensus size: 22
599960 TCAACAGAGG
599970 TTTACAGCACAGTAAACAGGGA
1 TTTACAGCACAGTAAACAGGGA
* *
599992 TTTACAGCACAGTAATCA-GAA
1 TTTACAGCACAGTAAACAGGGA
*
600013 GTTTACATCACAGTAAACA-GG-
1 -TTTACAGCACAGTAAACAGGGA
* *
600034 TTTACAGCACAGTAATCA-GAA
1 TTTACAGCACAGTAAACAGGGA
*
600055 GTTTACATCACAGTAAACA-GG-
1 -TTTACAGCACAGTAAACAGGGA
* *
600076 TTTACAGCACAGTAATCA-GAA
1 TTTACAGCACAGTAAACAGGGA
*
600097 GTTTACATCACAGTAAACA-GG-
1 -TTTACAGCACAGTAAACAGGGA
* *
600118 TTTACAGCACAGTAATCA-GAA
1 TTTACAGCACAGTAAACAGGGA
*
600139 GTTTACATCACAGTAAACA-GG-
1 -TTTACAGCACAGTAAACAGGGA
* * *
600160 TTTACAGCACTGCAAAC-GGAGG
1 TTTACAGCACAGTAAACAGG-GA
* ** *
600182 TTTACGGCAGGGTAAACA-TGA
1 TTTACAGCACAGTAAACAGGGA
600203 GTTTACAGCACAGTAAACAG
1 -TTTACAGCACAGTAAACAG
600223 AGACATGATA
Statistics
Matches: 183, Mismatches: 35, Indels: 25
0.75 0.14 0.10
Matches are distributed among these distances:
20 66 0.36
21 4 0.02
22 113 0.62
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (22 bp):
TTTACAGCACAGTAAACAGGGA
Found at i:600051 original size:42 final size:42
Alignment explanation
Indices: 599964--600223 Score: 376
Period size: 42 Copynumber: 6.1 Consensus size: 42
599954 GCGCTGTCAA
* *
599964 CAGAGGTTTACAGCACAGTAAACAGGGATTTACAGCACAGTAAT
1 CAGAAGTTTACATCACAGTAAACA-GG-TTTACAGCACAGTAAT
600008 CAGAAGTTTACATCACAGTAAACAGGTTTACAGCACAGTAAT
1 CAGAAGTTTACATCACAGTAAACAGGTTTACAGCACAGTAAT
600050 CAGAAGTTTACATCACAGTAAACAGGTTTACAGCACAGTAAT
1 CAGAAGTTTACATCACAGTAAACAGGTTTACAGCACAGTAAT
600092 CAGAAGTTTACATCACAGTAAACAGGTTTACAGCACAGTAAT
1 CAGAAGTTTACATCACAGTAAACAGGTTTACAGCACAGTAAT
* * *
600134 CAGAAGTTTACATCACAGTAAACAGGTTTACAGCACTGCAAA
1 CAGAAGTTTACATCACAGTAAACAGGTTTACAGCACAGTAAT
* * ** ** *
600176 CGGAGGTTTACGGCAGGGTAAACATGAGTTTACAGCACAGTAAA
1 CAGAAGTTTACATCACAGTAAACA-G-GTTTACAGCACAGTAAT
600220 CAGA
1 CAGA
600224 GACATGATAG
Statistics
Matches: 200, Mismatches: 14, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
42 157 0.79
43 3 0.01
44 40 0.20
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.22
Consensus pattern (42 bp):
CAGAAGTTTACATCACAGTAAACAGGTTTACAGCACAGTAAT
Found at i:601429 original size:21 final size:21
Alignment explanation
Indices: 601405--601467 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
601395 ATTTGAAAAA
601405 AATTAATTGAAAACAAAGTGC
1 AATTAATTGAAAACAAAGTGC
601426 AATTAA---AAAACTAAA----
1 AATTAATTGAAAAC-AAAGTGC
601441 AATTAATTGAAAACAAAGTGC
1 AATTAATTGAAAACAAAGTGC
601462 AATTAA
1 AATTAA
601468 AATGGTAAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 16
0.68 0.00 0.32
Matches are distributed among these distances:
15 6 0.18
17 3 0.09
18 10 0.29
19 3 0.09
21 12 0.35
ACGTcount: A:0.59, C:0.08, G:0.10, T:0.24
Consensus pattern (21 bp):
AATTAATTGAAAACAAAGTGC
Found at i:601434 original size:17 final size:17
Alignment explanation
Indices: 601409--601469 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
601399 GAAAAAAATT
*
601409 AATTGAAAACAAAGTGC
1 AATTAAAAACAAAGTGC
* *
601426 AATTAAAAAACTAAAAAT-T
1 AATT-AAAAAC--AAAGTGC
*
601445 AATTGAAAACAAAGTGC
1 AATTAAAAACAAAGTGC
601462 AATTAAAA
1 AATTAAAA
601470 TGGTAAACAT
Statistics
Matches: 33, Mismatches: 7, Indels: 8
0.69 0.15 0.17
Matches are distributed among these distances:
16 4 0.12
17 11 0.33
18 10 0.30
19 4 0.12
20 4 0.12
ACGTcount: A:0.61, C:0.08, G:0.10, T:0.21
Consensus pattern (17 bp):
AATTAAAAACAAAGTGC
Found at i:602691 original size:23 final size:23
Alignment explanation
Indices: 602661--602785 Score: 223
Period size: 23 Copynumber: 5.4 Consensus size: 23
602651 ACACACAGCG
*
602661 TAAAACCACTTATACAACCACTA
1 TAAAACCACTTATACAGCCACTA
602684 TAAAACCACTTATACAGCCACTA
1 TAAAACCACTTATACAGCCACTA
* *
602707 TAAAACGACTTATACAACCACTA
1 TAAAACCACTTATACAGCCACTA
602730 TAAAACCACTTATACAGCCACTA
1 TAAAACCACTTATACAGCCACTA
602753 TAAAACCACTTATACAGCCACTA
1 TAAAACCACTTATACAGCCACTA
602776 TAAAACCACT
1 TAAAACCACT
602786 AAACCACTAA
Statistics
Matches: 97, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 97 1.00
ACGTcount: A:0.46, C:0.30, G:0.03, T:0.22
Consensus pattern (23 bp):
TAAAACCACTTATACAGCCACTA
Found at i:616254 original size:4 final size:4
Alignment explanation
Indices: 616245--616320 Score: 73
Period size: 4 Copynumber: 19.0 Consensus size: 4
616235 CATTTGTACC
* * * *
616245 CATT CATT CATT TATT CATT CGTT CACT CATT CATT CATT CATT CATC
1 CATT CATT CATT CATT CATT CATT CATT CATT CATT CATT CATT CATT
* * *
616293 CATT CACT -ATTT CATT TAAT CATT CATT
1 CATT CATT CA-TT CATT CATT CATT CATT
616321 TGGATCTCAT
Statistics
Matches: 56, Mismatches: 14, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
3 1 0.02
4 54 0.96
5 1 0.02
ACGTcount: A:0.25, C:0.25, G:0.01, T:0.49
Consensus pattern (4 bp):
CATT
Found at i:618064 original size:4 final size:4
Alignment explanation
Indices: 618055--618098 Score: 54
Period size: 4 Copynumber: 11.0 Consensus size: 4
618045 TTGTGTAACG
* *
618055 GACA GACA GACA GACA GA-A GAACG GACG GACA GACA GACA GACA
1 GACA GACA GACA GACA GACA G-ACA GACA GACA GACA GACA GACA
618099 CACAAGGGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
3 2 0.06
4 33 0.92
5 1 0.03
ACGTcount: A:0.48, C:0.23, G:0.30, T:0.00
Consensus pattern (4 bp):
GACA
Found at i:618086 original size:24 final size:24
Alignment explanation
Indices: 618051--618096 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
618041 AAATTTGTGT
618051 AACGGACAGACAGACAGACAGAAG
1 AACGGACAGACAGACAGACAGAAG
*
618075 AACGGACGGACAGACAGACAGA
1 AACGGACAGACAGACAGACAGA
618097 CACACAAGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.48, C:0.22, G:0.30, T:0.00
Consensus pattern (24 bp):
AACGGACAGACAGACAGACAGAAG
Found at i:619108 original size:15 final size:15
Alignment explanation
Indices: 619088--619143 Score: 94
Period size: 15 Copynumber: 3.7 Consensus size: 15
619078 TGGAAACACT
*
619088 GGGGGAAATGGGGGC
1 GGGGGAAATGGCGGC
*
619103 GGGGGAAATGGCGGT
1 GGGGGAAATGGCGGC
619118 GGGGGAAATGGCGGC
1 GGGGGAAATGGCGGC
619133 GGGGGAAATGG
1 GGGGGAAATGG
619144 GGGAACTGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 38 1.00
ACGTcount: A:0.21, C:0.07, G:0.62, T:0.09
Consensus pattern (15 bp):
GGGGGAAATGGCGGC
Found at i:619121 original size:30 final size:30
Alignment explanation
Indices: 619087--619143 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
619077 GTGGAAACAC
*
619087 TGGGGGAAATGGGGGCGGGGGAAATGGCGG
1 TGGGGGAAATGGCGGCGGGGGAAATGGCGG
619117 TGGGGGAAATGGCGGCGGGGGAAATGG
1 TGGGGGAAATGGCGGCGGGGGAAATGG
619144 GGGAACTGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.21, C:0.07, G:0.61, T:0.11
Consensus pattern (30 bp):
TGGGGGAAATGGCGGCGGGGGAAATGGCGG
Found at i:621683 original size:26 final size:27
Alignment explanation
Indices: 621619--621683 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 27
621609 GCATATCAGT
*
621619 GTTTTCTGGTTGTGAGGAACCTACTACT
1 GTTTTCTGGTTGTGAGGAACCTAC-ACA
* *
621647 GTTTACTGGTTGTGA-GACATCTAC-CA
1 GTTTTCTGGTTGTGAGGA-ACCTACACA
621673 GTTTTCTGGTT
1 GTTTTCTGGTT
621684 TAAGATACAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
26 11 0.34
27 2 0.06
28 19 0.59
ACGTcount: A:0.17, C:0.17, G:0.25, T:0.42
Consensus pattern (27 bp):
GTTTTCTGGTTGTGAGGAACCTACACA
Found at i:621840 original size:28 final size:27
Alignment explanation
Indices: 621796--621910 Score: 86
Period size: 28 Copynumber: 3.9 Consensus size: 27
621786 AGACATTTAT
* *
621796 CACTGTTTCTGGCTGTGAGATACCTAC
1 CACTCTTTCTGGTTGTGAGATACCTAC
*
621823 CACTCTTTCCTGGTTGTGAAATATCTACAATGTAC
1 CACTCTTT-CTGGTTGTGAGATA-C--C----TAC
*
621858 CACTGCTTTCTGGTTGTGAGATATCTAC
1 CACT-CTTTCTGGTTGTGAGATACCTAC
* *
621886 CACTGTTTTCTGGTTTTGAGATACC
1 CACT-CTTTCTGGTTGTGAGATACC
621911 GGTACCTTCA
Statistics
Matches: 71, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
27 7 0.10
28 37 0.52
29 1 0.01
31 1 0.01
32 1 0.01
35 20 0.28
36 4 0.06
ACGTcount: A:0.20, C:0.23, G:0.19, T:0.38
Consensus pattern (27 bp):
CACTCTTTCTGGTTGTGAGATACCTAC
Found at i:622000 original size:28 final size:28
Alignment explanation
Indices: 621923--622272 Score: 510
Period size: 28 Copynumber: 12.6 Consensus size: 28
621913 TACCTTCATG
* *
621923 TACCACTGTTATCTGGTTGTGAGACACC
1 TACCACTGTTTTCTGGTTGTGAGATACC
* * * * *
621951 TTCTAGTG-TTT-T-GTCTGTGAGACATC
1 TACCACTGTTTTCTGGT-TGTGAGATACC
*
621977 TACAACTGTTTTCTGGTTGTGAGATACC
1 TACCACTGTTTTCTGGTTGTGAGATACC
*
622005 TACCACTGCTTTCTGGTTGTGAGATACC
1 TACCACTGTTTTCTGGTTGTGAGATACC
*
622033 TACCACTGTTTTCTGGTTGTGAGATATC
1 TACCACTGTTTTCTGGTTGTGAGATACC
622061 TACCACTGTTTTCTGGTTGTGAGATACC
1 TACCACTGTTTTCTGGTTGTGAGATACC
*
622089 TACCACTGTTTTCTAGTTGTGAGATACC
1 TACCACTGTTTTCTGGTTGTGAGATACC
*
622117 TACCAGTGTTTTCTGGTTGTGAGATACC
1 TACCACTGTTTTCTGGTTGTGAGATACC
* *
622145 TACCACTGTTTTCTGGTTGTGAGACATC
1 TACCACTGTTTTCTGGTTGTGAGATACC
*
622173 TACCACTGTTTTCTGGTAGTGAGATACC
1 TACCACTGTTTTCTGGTTGTGAGATACC
*
622201 TACCAGTGTTTTCTGGTTGT-AGATACC
1 TACCACTGTTTTCTGGTTGTGAGATACC
*
622228 TACCAGTGTTTTCTGGTTGTGAGATACC
1 TACCACTGTTTTCTGGTTGTGAGATACC
622256 TACCACTGTTTTCTGGT
1 TACCACTGTTTTCTGGT
622273 CCACCTGTAC
Statistics
Matches: 290, Mismatches: 27, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
25 2 0.01
26 16 0.06
27 32 0.11
28 238 0.82
29 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.39
Consensus pattern (28 bp):
TACCACTGTTTTCTGGTTGTGAGATACC
Found at i:624180 original size:2 final size:2
Alignment explanation
Indices: 624173--624326 Score: 74
Period size: 2 Copynumber: 80.5 Consensus size: 2
624163 GATACGTCTC
* * * *
624173 AG AG AG AG AG AG AG AG AC AG AG AG AC AG AC AG AG AG AG AG AC
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* * * * * *
624215 AG -G CAG AG AG AG AG AT AT AG AA AC AG AG A- AA AG AG AG AC AG
1 AG AG -AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* * * * *
624256 -G AA AA AG AG AG AA AG -G A- AG AG A- AA AG TAG AG AG AG AT AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -AG AG AG AG AG AG
* *
624295 A- AG AG AG AG AG -G AG AG AG A- AA AC AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
624327 TATATAGATT
Statistics
Matches: 116, Mismatches: 25, Indels: 22
0.71 0.15 0.13
Matches are distributed among these distances:
1 9 0.08
2 104 0.90
3 3 0.03
ACGTcount: A:0.55, C:0.05, G:0.38, T:0.03
Consensus pattern (2 bp):
AG
Found at i:624261 original size:15 final size:15
Alignment explanation
Indices: 624243--624273 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
624233 AGAAACAGAG
*
624243 AAAAGAGAGACAGGA
1 AAAAGAGAGAAAGGA
624258 AAAAGAGAGAAAGGA
1 AAAAGAGAGAAAGGA
624273 A
1 A
624274 GAGAAAAGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.65, C:0.03, G:0.32, T:0.00
Consensus pattern (15 bp):
AAAAGAGAGAAAGGA
Done.