Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009288.1 Hibiscus syriacus cultivar Beakdansim tig00112981_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 633898
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
File 2 of 3
Found at i:231809 original size:59 final size:59
Alignment explanation
Indices: 231732--231908 Score: 236
Period size: 59 Copynumber: 3.0 Consensus size: 59
231722 TGTTAACCCG
* * * *
231732 GACACATAAGGT-TGTGCCCACTATCTGCGCTAGTTATACTTTAGTGCAGT-CTCGAATAT
1 GACACATAAGGTCT-TGCCCACCATATGCACTAGTTATACTTTAGTGCAATCCT-GAATAT
231791 GACACATAAGGTCTTGCCC-CCATATGCACTAGTTATACTTTAGTGCAATCCTGAATAT
1 GACACATAAGGTCTTGCCCACCATATGCACTAGTTATACTTTAGTGCAATCCTGAATAT
* * *
231849 GACACATAAGGTCATGGCCACCATATGCACTAGTTATACTTTAGTGTAATCCCT-AATAT
1 GACACATAAGGTCTTGCCCACCATATGCACTAGTTATACTTTAGTGCAAT-CCTGAATAT
231908 G
1 G
231909 TAGCTTGCTA
Statistics
Matches: 107, Mismatches: 7, Indels: 8
0.88 0.06 0.07
Matches are distributed among these distances:
58 49 0.46
59 54 0.50
60 4 0.04
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.31
Consensus pattern (59 bp):
GACACATAAGGTCTTGCCCACCATATGCACTAGTTATACTTTAGTGCAATCCTGAATAT
Found at i:232082 original size:22 final size:22
Alignment explanation
Indices: 232057--232116 Score: 120
Period size: 22 Copynumber: 2.7 Consensus size: 22
232047 AACATTCGCA
232057 ATAAACATCATATATATTCATG
1 ATAAACATCATATATATTCATG
232079 ATAAACATCATATATATTCATG
1 ATAAACATCATATATATTCATG
232101 ATAAACATCATATATA
1 ATAAACATCATATATA
232117 ATAACTAGTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.48, C:0.13, G:0.03, T:0.35
Consensus pattern (22 bp):
ATAAACATCATATATATTCATG
Found at i:235428 original size:29 final size:29
Alignment explanation
Indices: 235384--235442 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
235374 TCATCATTCC
*
235384 TTAAGGAATTCTATCCATTTCCTTTATTT
1 TTAAGGAATTCAATCCATTTCCTTTATTT
235413 TTAAGGAATTCAATCCATTTCCTTTATTT
1 TTAAGGAATTCAATCCATTTCCTTTATTT
235442 T
1 T
235443 CACTCCTTGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.25, C:0.17, G:0.07, T:0.51
Consensus pattern (29 bp):
TTAAGGAATTCAATCCATTTCCTTTATTT
Found at i:244762 original size:58 final size:58
Alignment explanation
Indices: 244671--244924 Score: 269
Period size: 59 Copynumber: 4.3 Consensus size: 58
244661 ATATGCACCA
* * **
244671 TAGTGCTAA-CCCGAGTATGTCACATAAGGTTGTGCCAACCATCTACACTAGTTATAATT
1 TAGTGC-AATCCCGAATATGACACATAAGGTCATGCCAACCA-CTACACTAGTTATAATT
* * ** *
244730 TAGTGCAGT-CCGAATATGTCACATAAGGTTGTGCCAACTATCTACACTAGTTATAATT
1 TAGTGCAATCCCGAATATGACACATAAGGTCATGCCAACCA-CTACACTAGTTATAATT
* * * * *
244788 TAGTGCAGTCCCGAATATGACACATAAGGTCATTCCCACCACAAGCACTAGTTATACTT
1 TAGTGCAATCCCGAATATGACACATAAGGTCATGCCAACCACTA-CACTAGTTATAATT
* * ** * *
244847 TAGTGCAATCTCGAATATGACACGTAAGGTCATGCCCGCCACATGCACTAGTTATACTT
1 TAGTGCAATCCCGAATATGACACATAAGGTCATGCCAACCAC-TACACTAGTTATAATT
244906 TAGTGCAATCCCGAATATG
1 TAGTGCAATCCCGAATATG
244925 CAACCTGCTG
Statistics
Matches: 172, Mismatches: 19, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
58 59 0.34
59 113 0.66
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (58 bp):
TAGTGCAATCCCGAATATGACACATAAGGTCATGCCAACCACTACACTAGTTATAATT
Found at i:249315 original size:19 final size:19
Alignment explanation
Indices: 249270--249315 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
249260 AATCTCTTTA
*
249270 ATTTGTTTATTTAATTATT
1 ATTTTTTTATTTAATTATT
*
249289 -TTTCTTTTATTTAATTCTT
1 ATTT-TTTTATTTAATTATT
249308 ATTTTTTT
1 ATTTTTTT
249316 TTATTTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 3 0.13
19 17 0.74
20 3 0.13
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.74
Consensus pattern (19 bp):
ATTTTTTTATTTAATTATT
Found at i:252432 original size:15 final size:14
Alignment explanation
Indices: 252386--252428 Score: 59
Period size: 15 Copynumber: 3.0 Consensus size: 14
252376 TGTAGTAGAC
* *
252386 TTTATTTCATTCTA
1 TTTATTTTATTTTA
252400 TTTATTTTATTTTGA
1 TTTATTTTATTTT-A
252415 TTTATTTTATTTTA
1 TTTATTTTATTTTA
252429 ATTTTTTCTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 12 0.46
15 14 0.54
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTATTTTATTTTA
Found at i:255848 original size:9 final size:9
Alignment explanation
Indices: 255834--255859 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
255824 AATAATAAAT
255834 TTATTTTAA
1 TTATTTTAA
255843 TTATTTTAA
1 TTATTTTAA
255852 TTATTTTA
1 TTATTTTA
255860 CTAACTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (9 bp):
TTATTTTAA
Found at i:260980 original size:24 final size:24
Alignment explanation
Indices: 260942--261011 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 24
260932 CAAATTAGAG
* * *
260942 TCCATGTCAAGTATCGTATAAAAA
1 TCCAGGTCAAATATCATATAAAAA
* * *
260966 TTCAGGTCAAATATCATATCAGAA
1 TCCAGGTCAAATATCATATAAAAA
* *
260990 TCCAGGTCAAAAATCAGATAAA
1 TCCAGGTCAAATATCATATAAA
261012 CTATTTATAT
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.44, C:0.17, G:0.13, T:0.26
Consensus pattern (24 bp):
TCCAGGTCAAATATCATATAAAAA
Found at i:261744 original size:29 final size:29
Alignment explanation
Indices: 261708--261774 Score: 93
Period size: 28 Copynumber: 2.3 Consensus size: 29
261698 CATTTTACAT
261708 AAATAGCACCCTTTTTAAAAT-AATTACCA
1 AAATAGCACCC-TTTTAAAATAAATTACCA
* *
261737 AAATAGCA-CCTTTTAAATTAAATTCCCA
1 AAATAGCACCCTTTTAAAATAAATTACCA
261765 AAATAGCACC
1 AAATAGCACC
261775 AAAATTGAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 8 0.24
28 17 0.50
29 9 0.26
ACGTcount: A:0.45, C:0.22, G:0.04, T:0.28
Consensus pattern (29 bp):
AAATAGCACCCTTTTAAAATAAATTACCA
Found at i:261803 original size:29 final size:29
Alignment explanation
Indices: 261752--261832 Score: 126
Period size: 29 Copynumber: 2.8 Consensus size: 29
261742 GCACCTTTTA
* *
261752 AATTAAATTCCCAAAATAGCACCAAAATTG
1 AATT-AATTCCCAGAATATCACCAAAATTG
261782 AATTAATTCCCAGAATATCACCAAAATTG
1 AATTAATTCCCAGAATATCACCAAAATTG
*
261811 AATTAATTCTCAGAATATCACC
1 AATTAATTCCCAGAATATCACC
261833 GGTCAACGGT
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 44 0.92
30 4 0.08
ACGTcount: A:0.46, C:0.21, G:0.06, T:0.27
Consensus pattern (29 bp):
AATTAATTCCCAGAATATCACCAAAATTG
Found at i:261860 original size:5 final size:5
Alignment explanation
Indices: 261847--261904 Score: 53
Period size: 5 Copynumber: 10.8 Consensus size: 5
261837 AACGGTCAAC
* * *
261847 GGTCA GGTCG GGTCG GGTCAAT GGTCG GGTCG GGTCAAC GGTCG GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTC--G GGTCG GGTCG
261896 GGTCG GGTC
1 GGTCG GGTC
261905 AAAATCGGTC
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
5 36 0.82
7 8 0.18
ACGTcount: A:0.09, C:0.21, G:0.50, T:0.21
Consensus pattern (5 bp):
GGTCG
Found at i:261865 original size:22 final size:21
Alignment explanation
Indices: 261840--261906 Score: 88
Period size: 22 Copynumber: 3.3 Consensus size: 21
261830 ACCGGTCAAC
261840 GGTCAACGGTCAGGTCGGGTCG
1 GGTCAACGGTC-GGTCGGGTCG
261862 GGTCAA---T-GGTCGGGTCG
1 GGTCAACGGTCGGTCGGGTCG
261879 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTC-GGTCGGGTCG
261901 GGTCAA
1 GGTCAA
261907 AATCGGTCAA
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
17 16 0.40
19 1 0.03
20 1 0.03
22 22 0.55
ACGTcount: A:0.13, C:0.21, G:0.46, T:0.19
Consensus pattern (21 bp):
GGTCAACGGTCGGTCGGGTCG
Found at i:261872 original size:17 final size:17
Alignment explanation
Indices: 261852--261899 Score: 87
Period size: 17 Copynumber: 2.8 Consensus size: 17
261842 TCAACGGTCA
*
261852 GGTCGGGTCGGGTCAAT
1 GGTCGGGTCGGGTCAAC
261869 GGTCGGGTCGGGTCAAC
1 GGTCGGGTCGGGTCAAC
261886 GGTCGGGTCGGGTC
1 GGTCGGGTCGGGTC
261900 GGGTCAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.08, C:0.21, G:0.50, T:0.21
Consensus pattern (17 bp):
GGTCGGGTCGGGTCAAC
Found at i:262653 original size:3 final size:3
Alignment explanation
Indices: 262647--262679 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
262637 AATTCAATTA
262647 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
262680 TTCAAATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:264239 original size:18 final size:19
Alignment explanation
Indices: 264211--264246 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
264201 ATACTTCCCT
*
264211 AGCTGTGGTATCGATACCA
1 AGCTGTGGTATCAATACCA
264230 AGCT-TGGTATCAATACC
1 AGCTGTGGTATCAATACC
264247 CTTTTTGCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (19 bp):
AGCTGTGGTATCAATACCA
Found at i:270986 original size:21 final size:21
Alignment explanation
Indices: 270960--271004 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
270950 GGTTTTTTTG
270960 TAATAAAATGATATTATTAAT
1 TAATAAAATGATATTATTAAT
* ** *
270981 TAATAATATTTTATTATTTAT
1 TAATAAAATGATATTATTAAT
271002 TAA
1 TAA
271005 AATAATAGAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
TAATAAAATGATATTATTAAT
Found at i:271062 original size:35 final size:36
Alignment explanation
Indices: 270978--271075 Score: 103
Period size: 35 Copynumber: 2.8 Consensus size: 36
270968 TGATATTATT
*
270978 AATTAATAA-TATT-TTATTATTTATTAAAATAATA
1 AATTAATAATTATTATTTTTATTTATTAAAATAATA
* * *
271012 GATTAGTTAATTTATTATTTTTATTTATT-AATTAATA
1 AATTA-ATAA-TTATTATTTTTATTTATTAAAATAATA
**
271049 AATTAATAATTATTATTTAGATTTATT
1 AATTAATAATTATTATTTTTATTTATT
271076 TTTTGAATAA
Statistics
Matches: 52, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
34 4 0.08
35 19 0.37
36 3 0.06
37 15 0.29
38 11 0.21
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (36 bp):
AATTAATAATTATTATTTTTATTTATTAAAATAATA
Found at i:294448 original size:23 final size:22
Alignment explanation
Indices: 294409--294453 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
294399 TTATTATATT
*
294409 TTTAATATTTTGTATTTAATTTA
1 TTTAATATTTTGAATTT-ATTTA
294432 TTTAAGTATTTT-AATTTATTTA
1 TTTAA-TATTTTGAATTTATTTA
294454 ATATTTTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 5 0.25
23 9 0.45
24 6 0.30
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.64
Consensus pattern (22 bp):
TTTAATATTTTGAATTTATTTA
Found at i:294460 original size:17 final size:18
Alignment explanation
Indices: 294423--294461 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
294413 ATATTTTGTA
294423 TTTAATTTATTTAAGTAT
1 TTTAATTTATTTAAGTAT
294441 TTTAATTTATTTAA-TAT
1 TTTAATTTATTTAAGTAT
294458 TTTA
1 TTTA
294462 CTTATATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (18 bp):
TTTAATTTATTTAAGTAT
Found at i:300265 original size:16 final size:16
Alignment explanation
Indices: 300244--300274 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
300234 TATTTTTTCA
300244 AATAATCATAATAAAC
1 AATAATCATAATAAAC
*
300260 AATAATTATAATAAA
1 AATAATCATAATAAA
300275 AAAAGTTATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (16 bp):
AATAATCATAATAAAC
Found at i:301252 original size:50 final size:50
Alignment explanation
Indices: 301184--301301 Score: 123
Period size: 50 Copynumber: 2.3 Consensus size: 50
301174 AGGCGCGCTC
* * ** *
301184 CAAGGGACGCG-CTATACCCACGTGTATTCCATGTCAGCATATAGCGCGGTT
1 CAAGGGGCGCGCCT-TACCCACGTG-ATGCCAAATCAGCATATAGCGCGGTG
* *
301235 C-AGGGGCGCGCCTTACCCCACGTGGTGCCAAATCAGCATATAGTGCGGTG
1 CAAGGGGCGCGCCTTA-CCCACGTGATGCCAAATCAGCATATAGCGCGGTG
*
301285 CAAGGGGCGCGCTTTAC
1 CAAGGGGCGCGCCTTAC
301302 TGCAAAGGGT
Statistics
Matches: 56, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
50 32 0.57
51 24 0.43
ACGTcount: A:0.21, C:0.29, G:0.30, T:0.20
Consensus pattern (50 bp):
CAAGGGGCGCGCCTTACCCACGTGATGCCAAATCAGCATATAGCGCGGTG
Found at i:303546 original size:19 final size:19
Alignment explanation
Indices: 303522--303565 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
303512 TTAAGAGATG
303522 AAAAATTATATAATTAATA
1 AAAAATTATATAATTAATA
303541 AAAAATTATATAATTAATA
1 AAAAATTATATAATTAATA
303560 AAAAAT
1 AAAAAT
303566 ATAAAAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAAATTATATAATTAATA
Found at i:304946 original size:27 final size:28
Alignment explanation
Indices: 304916--304973 Score: 73
Period size: 29 Copynumber: 2.1 Consensus size: 28
304906 ATAAGACAAT
*
304916 AAAATATCA-TCATTGAATTTTTTTAAC
1 AAAATATCACTCAATGAATTTTTTTAAC
* *
304943 AAAATGTCACGTCAATGATTTTTTTTAAC
1 AAAATATCAC-TCAATGAATTTTTTTAAC
304972 AA
1 AA
304974 GTGACCAAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 8 0.31
29 18 0.69
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.41
Consensus pattern (28 bp):
AAAATATCACTCAATGAATTTTTTTAAC
Found at i:305300 original size:24 final size:24
Alignment explanation
Indices: 305273--305344 Score: 126
Period size: 24 Copynumber: 3.0 Consensus size: 24
305263 TAATGATGTG
305273 ATATTATCTTATGGTGATATGTCA
1 ATATTATCTTATGGTGATATGTCA
* *
305297 ATATTACCTTATGGTGATATGTTA
1 ATATTATCTTATGGTGATATGTCA
305321 ATATTATCTTATGGTGATATGTCA
1 ATATTATCTTATGGTGATATGTCA
305345 GCATCACCAT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.29, C:0.08, G:0.17, T:0.46
Consensus pattern (24 bp):
ATATTATCTTATGGTGATATGTCA
Found at i:306561 original size:27 final size:26
Alignment explanation
Indices: 306520--306583 Score: 76
Period size: 25 Copynumber: 2.4 Consensus size: 26
306510 ACGATACAAT
*
306520 ATTTTATGGTAGGAGAGTTAATTTATAAA
1 ATTTT-TGGAAGGAGAG--AATTTATAAA
*
306549 A-TTTTGGAAGGAGCGAATTTATAAA
1 ATTTTTGGAAGGAGAGAATTTATAAA
306574 ATTTTTGGAA
1 ATTTTTGGAA
306584 AACAAAAACA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
25 11 0.34
26 8 0.25
27 9 0.28
28 3 0.09
29 1 0.03
ACGTcount: A:0.38, C:0.02, G:0.22, T:0.39
Consensus pattern (26 bp):
ATTTTTGGAAGGAGAGAATTTATAAA
Found at i:311055 original size:18 final size:18
Alignment explanation
Indices: 311032--311067 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
311022 GATACACTTT
311032 TAGTTTAAAATCGTCGAA
1 TAGTTTAAAATCGTCGAA
311050 TAGTTTAAAATCGTCGAA
1 TAGTTTAAAATCGTCGAA
311068 AACGGCTCTG
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:0.11, G:0.17, T:0.33
Consensus pattern (18 bp):
TAGTTTAAAATCGTCGAA
Found at i:312976 original size:55 final size:53
Alignment explanation
Indices: 312890--313465 Score: 332
Period size: 55 Copynumber: 10.7 Consensus size: 53
312880 CTACTCTCTT
*
312890 TTCTTTCAGGGAGTATAGGACTTGGAA-AATCTTTGAAAAGTGCGTCTGCTCACTC
1 TTCTTTCAGGGAGTATAGGAC-TCGAACAATCTTTGAAAAGTG-GTCTGCTC-CTC
*
312945 TTCTTTCAGGGAGTATAGGACTCGAACAATCTTCAT-AAAA-TGGGTCTGATCCTTC
1 TTCTTTCAGGGAGTATAGGACTCGAACAATCTT--TGAAAAGT-GGTCTGCTCC-TC
* * *
313000 TTCTTTC-------A-AGGACTCGAACAATTTTTTGCAAACGTGTAGT-T-CT-CTA
1 TTCTTTCAGGGAGTATAGGACTCGAACAA-TCTTTG-AAAAGTG--GTCTGCTCCTC
* * *
313046 TTTTTTCAAGGAGTATAGGACTCGAACAATCTTCGATAAA-TAGGTCTGCTCCTTC
1 TTCTTTCAGGGAGTATAGGACTCGAACAATCTTTGA-AAAGT-GGTCTGCTCC-TC
* * * * * *
313101 TTCTTTCCA-TGAGTATAAGACTCGAACAATCTTCAGCAAACGT-GTTTGTTCCCTC
1 TTCTTT-CAGGGAGTATAGGACTCGAACAATCTT-TG-AAAAGTGGTCTGCT-CCTC
* * * *
313156 TTCTTTCAGGGAGTATAGGACTCGAACAATCTTTAGCAAACG-GGCCCGCTCTTTC
1 TTCTTTCAGGGAGTATAGGACTCGAACAATCTTT-G-AAAAGTGGTCTGCTC-CTC
* * **
313211 TTCTTTCAAGGAGTATAGGACTCGAACAATCTTTGGCAAACG-GGTCCACTCCTTC
1 TTCTTTCAGGGAGTATAGGACTCGAACAATCTTT-G-AAAAGTGGTCTGCTCC-TC
* * * * *
313266 TTCTTTCCGGGAGTATATGACTCAAACAATCTTCGGAAAA-TAGGTTTGCTCCTTC
1 TTCTTTCAGGGAGTATAGGACTCGAACAATCTT-TGAAAAGT-GGTCTGCTCC-TC
* * * * * *
313321 TTCTTTCAAGGAGTATAGGACTTGAA-AACTCTTAGAAAAATAGGTCCGCTCTTTC
1 TTCTTTCAGGGAGTATAGGACTCGAACAA-TCTTTGAAAAGT-GGTCTGCTC-CTC
* * * * *
313376 TTCTGTCAAGGAGTATAGGACTCGAACAATCTTCAGAAAACG-GGTATGCTCCATT
1 TTCTTTCAGGGAGTATAGGACTCGAACAATCTT-TGAAAA-GTGGTCTGCTCC-TC
* * *
313431 TTCTTTAAGGGAGTATAGGACTTGAAAAATCTTTG
1 TTCTTTCAGGGAGTATAGGACTCGAACAATCTTTG
313466 GCAAACATGT
Statistics
Matches: 414, Mismatches: 62, Indels: 91
0.73 0.11 0.16
Matches are distributed among these distances:
46 8 0.02
47 14 0.03
48 9 0.02
49 2 0.00
50 2 0.00
51 2 0.00
52 3 0.01
53 10 0.02
54 33 0.08
55 308 0.74
56 20 0.05
57 3 0.01
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (53 bp):
TTCTTTCAGGGAGTATAGGACTCGAACAATCTTTGAAAAGTGGTCTGCTCCTC
Found at i:313445 original size:165 final size:164
Alignment explanation
Indices: 313051--313452 Score: 472
Period size: 165 Copynumber: 2.4 Consensus size: 164
313041 CTCTATTTTT
** *
313051 TCAAGGAGTATAGGACTCGAACAATCTTCGATAAATAGGTCTGCTCCTTCTTCTTTCCA-TGAGT
1 TCAAGGAGTATAGGACTCGAACAATCTTCGA-AAACGGGTCTGCTCCTTCTTCTTT-CAGGGAGT
* * * * *
313115 ATAAGACTCGAACAATCTTCAGCAAACGTGTTTGTTCCCTCTTCTTTCAGGGAGTATAGGACTCG
64 ATAAGACTCAAACAATCTTCAGAAAAAGTGTTTGCTCCCTCTTCTTTCAAGGAGTATAGGACTCG
* * *
313180 AACAATCTTTAGCAAACGGGCCCGCTCTTTCTTCTT
129 AACAATCTTTAGAAAACAGGCCCGCTCTTTCTTCTG
* * ** *
313216 TCAAGGAGTATAGGACTCGAACAATCTTTGGCAAACGGGTCCACTCCTTCTTCTTTCCGGGAGTA
1 TCAAGGAGTATAGGACTCGAACAATC-TTCGAAAACGGGTCTGCTCCTTCTTCTTTCAGGGAGTA
* * * *
313281 TATGACTCAAACAATCTTCGGAAAATAG-GTTTGCTCCTTCTTCTTTCAAGGAGTATAGGACTTG
65 TAAGACTCAAACAATCTTCAGAAAA-AGTGTTTGCTCCCTCTTCTTTCAAGGAGTATAGGACTCG
* *
313345 AA-AA-CTCTTAGAAAAATAGGTCCGCTCTTTCTTCTG
129 AACAATCT-TTAG-AAAACAGGCCCGCTCTTTCTTCTG
* *
313381 TCAAGGAGTATAGGACTCGAACAATCTTCAGAAAACGGGTATGCTCCATT-TTCTTTAAGGGAGT
1 TCAAGGAGTATAGGACTCGAACAATCTTC-GAAAACGGGTCTGCTCC-TTCTTCTTTCAGGGAGT
*
313445 ATAGGACT
64 ATAAGACT
313453 TGAAAAATCT
Statistics
Matches: 200, Mismatches: 30, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
163 2 0.01
164 9 0.05
165 183 0.92
166 6 0.03
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (164 bp):
TCAAGGAGTATAGGACTCGAACAATCTTCGAAAACGGGTCTGCTCCTTCTTCTTTCAGGGAGTAT
AAGACTCAAACAATCTTCAGAAAAAGTGTTTGCTCCCTCTTCTTTCAAGGAGTATAGGACTCGAA
CAATCTTTAGAAAACAGGCCCGCTCTTTCTTCTG
Found at i:319836 original size:18 final size:18
Alignment explanation
Indices: 319813--319848 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
319803 GATACACTTT
319813 TAGTTTAAAATCGTCGAA
1 TAGTTTAAAATCGTCGAA
319831 TAGTTTAAAATCGTCGAA
1 TAGTTTAAAATCGTCGAA
319849 AACGGCTCTG
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:0.11, G:0.17, T:0.33
Consensus pattern (18 bp):
TAGTTTAAAATCGTCGAA
Found at i:321761 original size:55 final size:53
Alignment explanation
Indices: 321672--322247 Score: 345
Period size: 55 Copynumber: 10.7 Consensus size: 53
321662 TCTACTCTCT
* *
321672 CTCTTCTTTCAGGTAGTATAGGACTTGGAA-AATCTTTGAAAAGTGCGTCTGCTC
1 CTCTTCTTTCAGGGAGTATAGGAC-TCGAACAATCTTTGAAAAGTG-GTCTGCTC
*
321726 ACTCTTCTTTCAGGGAGTATAGGACTCGAACAATCTTCAT-AAAA-TGGGTCTGATC
1 -CTCTTCTTTCAGGGAGTATAGGACTCGAACAATCTT--TGAAAAGT-GGTCTGCTC
* *
321781 CTTCTTCTTTC-------A-AGGACTCGAACAATTTTTTGCAAACGTGTAGT-T-CT-
1 C-TCTTCTTTCAGGGAGTATAGGACTCGAACAA-TCTTTG-AAAAGTG--GTCTGCTC
* * * *
321828 CTATTTTTTCAAGGAGTATAGGACTCGAACAATCTTCGATAAA-TAGGTCTGCTC
1 CTCTTCTTTCAGGGAGTATAGGACTCGAACAATCTTTGA-AAAGT-GGTCTGCTC
* * * * *
321882 CTTCTTCTTTCCA-TGAGTATAAGACTCGAACAATCTTCAGCAAACGT-GTTTGCTCC
1 C-TCTTCTTT-CAGGGAGTATAGGACTCGAACAATCTT-TG-AAAAGTGGTCTGCT-C
* * *
321938 CCCTTCTTTCAGGGAGTATAGGACTCGAACAATCTTTAGCAAACG-GGTCCGCTC
1 CTCTTCTTTCAGGGAGTATAGGACTCGAACAATCTTT-G-AAAAGTGGTCTGCTC
* * * * *
321992 CTTCTTCTTTCAAGGAGTATAGGACTCGAACAATCTTCGGCAGACG-GGTCCGCTC
1 C-TCTTCTTTCAGGGAGTATAGGACTCGAACAATCTT-TG-AAAAGTGGTCTGCTC
* * * *
322047 CTTCTTCTTTCCGGGAGTATATGACTCAAACAATCTTCGGAAAA-TAGGTCTGCT-
1 C-TCTTCTTTCAGGGAGTATAGGACTCGAACAATCTT-TGAAAAGT-GGTCTGCTC
* * * * *
322101 C-CTTCTTTCAAGGAGTATAGGACTTGAA-AACTCTTAGAAAAATAGGTCCGCTC
1 CTCTTCTTTCAGGGAGTATAGGACTCGAACAA-TCTTTGAAAAGT-GGTCTGCTC
* * * *
322154 TTTCTTCTGTCAAGGAGTATAGGACTCGAACAATCTTCAGAAAACG-GGTCTGCTC
1 -CTCTTCTTTCAGGGAGTATAGGACTCGAACAATCTT-TGAAAA-GTGGTCTGCTC
* * * *
322209 CATTTTCTTTAAGGGAGTATAGGACTTGAAAAATCTTTG
1 C-TCTTCTTTCAGGGAGTATAGGACTCGAACAATCTTTG
322248 GCAAACATGT
Statistics
Matches: 420, Mismatches: 55, Indels: 93
0.74 0.10 0.16
Matches are distributed among these distances:
46 8 0.02
47 14 0.03
48 9 0.02
49 2 0.00
50 2 0.00
51 9 0.02
52 38 0.09
53 10 0.02
54 27 0.06
55 278 0.66
56 20 0.05
57 3 0.01
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.32
Consensus pattern (53 bp):
CTCTTCTTTCAGGGAGTATAGGACTCGAACAATCTTTGAAAAGTGGTCTGCTC
Found at i:322188 original size:162 final size:163
Alignment explanation
Indices: 321836--322234 Score: 477
Period size: 162 Copynumber: 2.4 Consensus size: 163
321826 CTCTATTTTT
** **
321836 TCAAGGAGTATAGGACTCGAACAATCTTC-GATAAATAGGTCTGCTCCTTCTTCTTTCCATGAGT
1 TCAAGGAGTATAGGACTCGAACAATCTTCGGA-AAACGGGTCTGCTCCTTCTTCTTTCCGGGAGT
* * * * *
321900 ATAAGACTCGAACAATCTTCAGCAAACGTGTTTGCTCCCCCTTCTTTCAGGGAGTATAGGACTCG
65 ATAAGACTCAAACAATCTTCAGAAAAAGTGTCTGCT--CCCTTCTTTCAAGGAGTATAGGACTCG
* * *
321965 AACAATCTTTAGCAAACGGGTCCGCTCCTTCTTCTT
128 AACAATCTTTAGAAAACAGGTCCGCTCCTTCTTCTG
* * *
322001 TCAAGGAGTATAGGACTCGAACAATCTTCGGCAGACGGGTCCGCTCCTTCTTCTTTCCGGGAGTA
1 TCAAGGAGTATAGGACTCGAACAATCTTCGGAAAACGGGTCTGCTCCTTCTTCTTTCCGGGAGTA
* * *
322066 TATGACTCAAACAATCTTCGGAAAATAG-GTCTGCT-CCTTCTTTCAAGGAGTATAGGACTTGAA
66 TAAGACTCAAACAATCTTCAGAAAA-AGTGTCTGCTCCCTTCTTTCAAGGAGTATAGGACTCGAA
* *
322129 -AA-CTCTTAGAAAAATAGGTCCGCTCTTTCTTCTG
130 CAATCT-TTAG-AAAACAGGTCCGCTCCTTCTTCTG
* **
322163 TCAAGGAGTATAGGACTCGAACAATCTTCAGAAAACGGGTCTGCTCCATT-TTCTTTAAGGGAGT
1 TCAAGGAGTATAGGACTCGAACAATCTTCGGAAAACGGGTCTGCTCC-TTCTTCTTTCCGGGAGT
*
322227 ATAGGACT
65 ATAAGACT
322235 TGAAAAATCT
Statistics
Matches: 202, Mismatches: 27, Indels: 13
0.83 0.11 0.05
Matches are distributed among these distances:
160 2 0.01
161 6 0.03
162 107 0.53
163 2 0.01
165 83 0.41
166 2 0.01
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (163 bp):
TCAAGGAGTATAGGACTCGAACAATCTTCGGAAAACGGGTCTGCTCCTTCTTCTTTCCGGGAGTA
TAAGACTCAAACAATCTTCAGAAAAAGTGTCTGCTCCCTTCTTTCAAGGAGTATAGGACTCGAAC
AATCTTTAGAAAACAGGTCCGCTCCTTCTTCTG
Found at i:322277 original size:110 final size:110
Alignment explanation
Indices: 321825--322280 Score: 460
Period size: 110 Copynumber: 4.2 Consensus size: 110
321815 AACGTGTAGT
* * *
321825 TCTCTATTTTTTCAAGGAGTATAGGACTCGAACAATCTTC-GATAAATAGGTCTGCTCCTTCTTC
1 TCTCTCTTCTTTCAAGGAGTATAGGACTCGAACAATCTTCAGA-AAACAGGTCTGCTCCTTCTTC
* * * * * **
321889 TTTCCATGAGTATAAGACTCGAACAATCTTCAGCAAAC-GTGTTTGC
65 TTTCAAGGAGTATAGGACTCGAAAAATCTTCGGCAAACAG-GTCCGC
* * * * * * *
321935 TCCCCCTTCTTTCAGGGAGTATAGGACTCGAACAATCTTTAGCAAACGGGTCCGCTCCTTCTTCT
1 TCTCTCTTCTTTCAAGGAGTATAGGACTCGAACAATCTTCAGAAAACAGGTCTGCTCCTTCTTCT
* * *
322000 TTCAAGGAGTATAGGACTCGAACAATCTTCGGCAGACGGGTCCGC
66 TTCAAGGAGTATAGGACTCGAAAAATCTTCGGCAAACAGGTCCGC
** * * * *
322045 TC-CTTCTTCTTTCCGGGAGTATATGACTCAAACAATCTTCGGAAAATAGGTCTGCT-C--CTTC
1 TCTC-TCTTCTTTCAAGGAGTATAGGACTCGAACAATCTTCAGAAAACAGGTCTGCTCCTTCTTC
* * * ** *
322106 TTTCAAGGAGTATAGGACTTGAAAACTCTTAGAAAAATAGGTCCGC
65 TTTCAAGGAGTATAGGACTCGAAAAATCTTCGGCAAACAGGTCCGC
* * *
322152 TCTTTCTTCTGTCAAGGAGTATAGGACTCGAACAATCTTCAGAAAACGGGTCTGCTCCATT-TTC
1 TCTCTCTTCTTTCAAGGAGTATAGGACTCGAACAATCTTCAGAAAACAGGTCTGCTCC-TTCTTC
* * *
322216 TTT-AAGGGAGTATAGGACTTGAAAAATCTTTGGCAAACATGTCCGC
65 TTTCAA-GGAGTATAGGACTCGAAAAATCTTCGGCAAACAGGTCCGC
*
322262 TCTCTCTTTTTTCAAGGAG
1 TCTCTCTTCTTTCAAGGAG
322281 AAAACGGGTT
Statistics
Matches: 283, Mismatches: 54, Indels: 18
0.80 0.15 0.05
Matches are distributed among these distances:
107 87 0.31
108 1 0.00
109 4 0.01
110 189 0.67
111 2 0.01
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (110 bp):
TCTCTCTTCTTTCAAGGAGTATAGGACTCGAACAATCTTCAGAAAACAGGTCTGCTCCTTCTTCT
TTCAAGGAGTATAGGACTCGAAAAATCTTCGGCAAACAGGTCCGC
Found at i:328062 original size:17 final size:18
Alignment explanation
Indices: 328040--328075 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
328030 ACGTTTTGTT
328040 ATTTTAAATAAAA-AATA
1 ATTTTAAATAAAACAATA
*
328057 ATTTTAATTAAAACAATA
1 ATTTTAAATAAAACAATA
328075 A
1 A
328076 ATTGATGTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (18 bp):
ATTTTAAATAAAACAATA
Found at i:330812 original size:765 final size:767
Alignment explanation
Indices: 329302--330834 Score: 3025
Period size: 765 Copynumber: 2.0 Consensus size: 767
329292 TTTAAAACCC
329302 AAAAGAGCTCCAGACCACATGATATTAAGGGTGTATTCTGTAACCTTATCGCCGGGAAGGAAGAT
1 AAAAGAGCTCCAGACCACATGATATTAAGGGTGTATTC-GTAACCTTATCGCCGGGAAGGAAGAT
329367 TGTCGTCCACCGCCGCACTCAGGTGACCGTTTGACGTCGAATTTCAAGGGAAGCTTCGCCTTGAC
65 TGTCGTCCACCGCCGCACTCAGGTGACCGTTTGACGTCGAATTTCAAGGGAAGCTTCGCCTTGAC
329432 GCCAGGAACTCGAATATGGCATTGGTTTTGCGAGAAAACGTTTTCAACTCCACGAAATAGCCATG
130 GCCAGGAACTCGAATATGGCATTGGTTTTGCGAGAAAACGTTTTCAACTCCACGAAATAGCCATG
329497 GAACCTCTCTGCTTTGCTGTCGACCACCGTTGGATCGGCTTGATTTTAAAGTATGTTGTTCGTCG
195 GAACCTCTCTGCTTTGCTGTCGACCACCGTTGGATCGGCTTGATTTTAAAGTATGTTGTTCGTCG
329562 ACGTCTTGGGAGTCTTTCCACCGTTTGGATCGTCGAATGGATCCTCCAATCAATGGAAATGAATG
260 ACGTCTTGGGAGTCTTTCCACCGTTTGGATCGTCGAATGGATCCTCCAATCAATGGAAATGAATG
329627 TCGGCTGAAAATATGAGTCTCCTTTCTCTCTTCTTTTATTTACTTTCGCTTTTCACTTTATTTTC
325 TCGGCTGAAAATATGAGTCTCCTTTCTCTCTTCTTTTATTTACTTTCGCTTTTCACTTTATTTTC
329692 ATCCCAAGCCCCCCTTTTGTATTGGTTTTCAACTGATTTTATAGCCTTCTAAGAAAATCTCCTTC
390 ATCCCAAGCCCCCCTTTTGTATTGGTTTTCAACTGATTTTATAGCCTTCTAAGAAAATCTCCTTC
329757 CTTTGAATGATGGGATACGATAATCCCCTTCCAACGAGAGATGGATTTCCTTTCCATTTGAGTTT
455 CTTTGAATGATGGGATACGATAATCCCCTTCCAACGAGAGATGGATTTCCTTTCCATTTGAGTTT
329822 ATTTTCATTAAATCATGGGATTTGAATATGATTTGTTTGAAATAAATAATCCTTTTTTGAAAGAG
520 ATTTTCATTAAATCATGGGATTTGAATATGATTTGTTTGAAATAAATAATCCTTTTTTGAAAGAG
329887 GGATTCTTTCTATTGATGGCTGATGAAAATAAGGGACATCGATGCATTGGCGCGTGACGAGTGCT
585 GGATTCTTTCTATTGATGGCTGATGAAAATAAGGGACATCGATGCATTGGCGCGTGACGAGTGCT
329952 CCACGATTGGCTTGTAAAGGAGTTGTTCGGACTTGCTTGTAAATGAGCTCAATCGTATAGGGAGT
650 CCACGATTGGCTTGTAAAGGAGTTGTTCGGACTTGCTTGTAAATGAGCTCAATCGTATAGGGAGT
330017 TGATTCCAACTATAAATTAATCTGGCCCTGGAATCAT-AAAAATAAAATTTAG
715 TGATTCCAACTATAAATTAATCTGGCCCTGGAATCATAAAAAATAAAATTTAG
*
330069 AAAAGAGCTCCAGACCACATGATATTAAGGGTGTATTC-TAACCTTATCGCCGGGAAGGGAGATT
1 AAAAGAGCTCCAGACCACATGATATTAAGGGTGTATTCGTAACCTTATCGCCGGGAAGGAAGATT
330133 GTCGTCCACCGCCGCACTCAGGTGACCGTTTGACGTCGAATTTCAAGGGAAGCTTCGCCTTGACG
66 GTCGTCCACCGCCGCACTCAGGTGACCGTTTGACGTCGAATTTCAAGGGAAGCTTCGCCTTGACG
330198 CCAGGAACTCGAATATGGCATTGGTTTTGCGAGAAAACGTTTTCAACTCCACGAAATAGCCATGG
131 CCAGGAACTCGAATATGGCATTGGTTTTGCGAGAAAACGTTTTCAACTCCACGAAATAGCCATGG
*
330263 AACCTCTCTGCTTTGCTGTCGACCACCGTTGGATCGGCTTGATTTTAAAGTATGTTGTTCGTCGG
196 AACCTCTCTGCTTTGCTGTCGACCACCGTTGGATCGGCTTGATTTTAAAGTATGTTGTTCGTCGA
330328 CGTCTTGGGAGTCTTTCCACCGTTTGGATCGTCGAATGGATCCTCCAATCAATGGAAATGAATGT
261 CGTCTTGGGAGTCTTTCCACCGTTTGGATCGTCGAATGGATCCTCCAATCAATGGAAATGAATGT
330393 CGGCTGAAAATATGAGTCTCCTTTCTCTCTTCTTTTATTTACTTTCGCTTTTCACTTTATTTTCA
326 CGGCTGAAAATATGAGTCTCCTTTCTCTCTTCTTTTATTTACTTTCGCTTTTCACTTTATTTTCA
330458 TCCCAAGCCCCCCTTTTGTATTGGTTTTCAACTGATTTTATAGCCTTCTAAGAAAATCTCCTTCC
391 TCCCAAGCCCCCCTTTTGTATTGGTTTTCAACTGATTTTATAGCCTTCTAAGAAAATCTCCTTCC
330523 TTTGAATGATGGGATACGATAATCCCCTTCCAACGAGAGATGGATTTCCTTTCCATTTGAGTTTA
456 TTTGAATGATGGGATACGATAATCCCCTTCCAACGAGAGATGGATTTCCTTTCCATTTGAGTTTA
330588 TTTTCATTAAATCATGGGATTTGAATATGATTTGTTTGAAATAAATAATCCTTTTTTGAAAGAGG
521 TTTTCATTAAATCATGGGATTTGAATATGATTTGTTTGAAATAAATAATCCTTTTTTGAAAGAGG
330653 GATTCTTTCTATTGATGGCTGATGAAAATAAGGGACATCGATGCATTGGCGCGTGACGAGTGCTC
586 GATTCTTTCTATTGATGGCTGATGAAAATAAGGGACATCGATGCATTGGCGCGTGACGAGTGCTC
330718 CACGATTGGCTTGTAAAGGAGTTGTTCGGACTTGCTTGTAAATGAGCTCAATCGTATAGGGAGTT
651 CACGATTGGCTTGTAAAGGAGTTGTTCGGACTTGCTTGTAAATGAGCTCAATCGTATAGGGAGTT
330783 GATTCCAACTATAAATTAATCTGGCCCTGGAATCATAAAAAATAAAATTTAG
716 GATTCCAACTATAAATTAATCTGGCCCTGGAATCATAAAAAATAAAATTTAG
330835 TAATATATTA
Statistics
Matches: 763, Mismatches: 2, Indels: 3
0.99 0.00 0.00
Matches are distributed among these distances:
765 710 0.93
766 15 0.02
767 38 0.05
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (767 bp):
AAAAGAGCTCCAGACCACATGATATTAAGGGTGTATTCGTAACCTTATCGCCGGGAAGGAAGATT
GTCGTCCACCGCCGCACTCAGGTGACCGTTTGACGTCGAATTTCAAGGGAAGCTTCGCCTTGACG
CCAGGAACTCGAATATGGCATTGGTTTTGCGAGAAAACGTTTTCAACTCCACGAAATAGCCATGG
AACCTCTCTGCTTTGCTGTCGACCACCGTTGGATCGGCTTGATTTTAAAGTATGTTGTTCGTCGA
CGTCTTGGGAGTCTTTCCACCGTTTGGATCGTCGAATGGATCCTCCAATCAATGGAAATGAATGT
CGGCTGAAAATATGAGTCTCCTTTCTCTCTTCTTTTATTTACTTTCGCTTTTCACTTTATTTTCA
TCCCAAGCCCCCCTTTTGTATTGGTTTTCAACTGATTTTATAGCCTTCTAAGAAAATCTCCTTCC
TTTGAATGATGGGATACGATAATCCCCTTCCAACGAGAGATGGATTTCCTTTCCATTTGAGTTTA
TTTTCATTAAATCATGGGATTTGAATATGATTTGTTTGAAATAAATAATCCTTTTTTGAAAGAGG
GATTCTTTCTATTGATGGCTGATGAAAATAAGGGACATCGATGCATTGGCGCGTGACGAGTGCTC
CACGATTGGCTTGTAAAGGAGTTGTTCGGACTTGCTTGTAAATGAGCTCAATCGTATAGGGAGTT
GATTCCAACTATAAATTAATCTGGCCCTGGAATCATAAAAAATAAAATTTAG
Found at i:337488 original size:55 final size:55
Alignment explanation
Indices: 337429--338054 Score: 425
Period size: 55 Copynumber: 11.6 Consensus size: 55
337419 TGGAAGACGT
* *
337429 GTCTGCTCCCTCTTCTTTCAGGGAGTATAGGACTCGAACAACCTTCATAAAATGA
1 GTCTGCTCCCTCTTCTTTCAGGGAGTATAGGACTCGAACAATCTTCAGAAAATGA
* * * * * * *
337484 GTCTGATCCTTCTTCTTTC-------A-AGGACTCGAACAATTTTCGGCAAACGT
1 GTCTGCTCCCTCTTCTTTCAGGGAGTATAGGACTCGAACAATCTTCAGAAAATGA
* * * * * * *
337531 GT-AGTTCTCTTTTTTTTCTA-TGAGTATAGGACTCGAGCAATCTTC-GACAAAT-A
1 GTCTGCTCCCTCTTCTTTC-AGGGAGTATAGGACTCGAACAATCTTCAGA-AAATGA
*** * * *
337584 GGTCTGCTTGTTCTTCTTT-ATGGGAGTATAAGACTCAAACAATCTTCAGAAAATGT
1 -GTCTGCTCCCTCTTCTTTCA-GGGAGTATAGGACTCGAACAATCTTCAGAAAATGA
* * * * *
337640 GTCCGCTCCCTCTTCTTTCAGGGAGTATAGGACTCGAACAATCTTCGGCAAACGG
1 GTCTGCTCCCTCTTCTTTCAGGGAGTATAGGACTCGAACAATCTTCAGAAAATGA
* * * *
337695 GTCTGCTCCTTCTTCTTTCAAGGAGTATAGGACTCGAACAATCTT-TGACAAATGG
1 GTCTGCTCCCTCTTCTTTCAGGGAGTATAGGACTCGAACAATCTTCAGA-AAATGA
* * * * * *
337750 GTCCGCTCCTTCTTCTTTCCGGGAGTATATGACTCAAATAATCTTC-GAAAAT-A
1 GTCTGCTCCCTCTTCTTTCAGGGAGTATAGGACTCGAACAATCTTCAGAAAATGA
** * * * * *
337803 GGTCCACTCCTTTTTCTTTCAAGGAGTATAGGACTTGAAAAATCTTC-GAAAAAT-A
1 -GTCTGCTCCCTCTTCTTTCAGGGAGTATAGGACTCGAACAATCTTCAG-AAAATGA
*
337858 GGTCTGCT--C-CTTCTTTCAAGGAGTATAGGACTCGAACAATCTTCAGAAAACTG-
1 -GTCTGCTCCCTCTTCTTTCAGGGAGTATAGGACTCGAACAATCTTCAGAAAA-TGA
* * * * * * *
337911 GTATGCTCCCTTTTCTTTAAGGGAGTATAGGACTTGAA-AAGTCTTCAGGAAACGT
1 GTCTGCTCCCTCTTCTTTCAGGGAGTATAGGACTCGAACAA-TCTTCAGAAAATGA
* * * * * * *
337966 TTCCGCTCCCTCTTTTTTCAGGGAGTATAGGACTTGAACAATCTTTAGAAAACGG
1 GTCTGCTCCCTCTTCTTTCAGGGAGTATAGGACTCGAACAATCTTCAGAAAATGA
** ** *
338021 GTCCACTCTTTCTTCTTTCAAGGAGTATAGGACT
1 GTCTGCTCCCTCTTCTTTCAGGGAGTATAGGACT
338055 TGAATAGTTT
Statistics
Matches: 451, Mismatches: 91, Indels: 58
0.75 0.15 0.10
Matches are distributed among these distances:
46 10 0.02
47 22 0.05
48 1 0.00
52 42 0.09
53 5 0.01
54 69 0.15
55 297 0.66
56 5 0.01
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (55 bp):
GTCTGCTCCCTCTTCTTTCAGGGAGTATAGGACTCGAACAATCTTCAGAAAATGA
Found at i:337938 original size:216 final size:217
Alignment explanation
Indices: 337651--338058 Score: 540
Period size: 216 Copynumber: 1.9 Consensus size: 217
337641 TCCGCTCCCT
* * * *
337651 CTTCTTTCAGGGAGTATAGGACTCGAACAATCTTCGGCAAACGGGTCTGCTCCTTCTTCTTTCAA
1 CTTCTTTCAAGGAGTATAGGACTCGAACAATCTTCAGAAAACGGGTATGCTCCTTCTTCTTTCAA
* * * *
337716 GGAGTATAGGACTCGAACAA-TCTT-TGACAAATGGGTCCGCTCCTTCTTCTTTCCGGGAGTATA
66 GGAGTATAGGACTCGAA-AAGTCTTCAG-CAAACGGGTCCGCTCCCTCTTCTTTCAGGGAGTATA
* * * *
337779 TGACTCAAATAATC-TTCGAAAATAGGTCCACTCCTTT-TTCTTTCAAGGAGTATAGGACTTGAA
129 GGACTCAAACAATCTTTAGAAAACAGGTCCACT-CTTTCTTCTTTCAAGGAGTATAGGACTTGAA
337842 AAATCTTCGAAAAATAGGTCTGCTC
193 AAATCTTCGAAAAATAGGTCTGCTC
*
337867 CTTCTTTCAAGGAGTATAGGACTCGAACAATCTTCAGAAAACTGGTATGCTCCCTT-TTCTTT-A
1 CTTCTTTCAAGGAGTATAGGACTCGAACAATCTTCAGAAAACGGGTATGCT-CCTTCTTCTTTCA
* * ** *
337930 AGGGAGTATAGGACTTGAAAAGTCTTCAGGAAACGTTTCCGCTCCCTCTTTTTTCAGGGAGTATA
65 A-GGAGTATAGGACTCGAAAAGTCTTCAGCAAACGGGTCCGCTCCCTCTTCTTTCAGGGAGTATA
** *
337995 GGACTTGAACAATCTTTAGAAAACGGGTCCACTCTTTCTTCTTTCAAGGAGTATAGGACTTGAA
129 GGACTCAAACAATCTTTAGAAAACAGGTCCACTCTTTCTTCTTTCAAGGAGTATAGGACTTGAA
338059 TAGTTTGCCT
Statistics
Matches: 165, Mismatches: 21, Indels: 11
0.84 0.11 0.06
Matches are distributed among these distances:
215 4 0.02
216 115 0.70
217 46 0.28
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (217 bp):
CTTCTTTCAAGGAGTATAGGACTCGAACAATCTTCAGAAAACGGGTATGCTCCTTCTTCTTTCAA
GGAGTATAGGACTCGAAAAGTCTTCAGCAAACGGGTCCGCTCCCTCTTCTTTCAGGGAGTATAGG
ACTCAAACAATCTTTAGAAAACAGGTCCACTCTTTCTTCTTTCAAGGAGTATAGGACTTGAAAAA
TCTTCGAAAAATAGGTCTGCTC
Found at i:337943 original size:271 final size:271
Alignment explanation
Indices: 337539--338054 Score: 666
Period size: 271 Copynumber: 1.9 Consensus size: 271
337529 GTGTAGTTCT
* * ** * *
337539 CTTTTTTTTCTATGAGTATAGGACTCGAGCAATCTTCGACAAATAGGTCTGCTTGTTCTTCTTTA
1 CTTTTTTTTCAAGGAGTATAGGACTCGAAAAATCTTCGAAAAATAGGTCTGC-T-TCCTTCTTTA
* * *
337604 TGGGAGTATAAGACTCAAACAATCTTCAGAAAATGTGTCCGCTCCCTCTTCTTTCAGGGAGTATA
64 TAGGAGTATAAGACTCAAACAATCTTCAGAAAATGTGTACGCTCCCTCTTCTTTAAGGGAGTATA
* *
337669 GGACTCGAACAA-TCTTC-GGCAAACGGGTCTGCTCCTTCTTCTTTCAAGGAGTATAGGACTCGA
129 GGACTCGAA-AAGTCTTCAGG-AAACGGGTCCGCTCCCTCTTCTTTCAAGGAGTATAGGACTCGA
* * ** *
337732 ACAATCTTT-GACAAATGGGTCCGCTCCTTCTTCTTTCCGGGAGTATATGACTCAAATAATCTTC
192 ACAATCTTTAGA-AAACGGGTCCACTCCTTCTTCTTTCAAGGAGTATAGGACTCAAATAATCTTC
337796 GAAAATAGGTCCACTC
256 GAAAATAGGTCCACTC
*
337812 CTTTTTCTTTCAAGGAGTATAGGACTTGAAAAATCTTCGAAAAATAGGTCTGC-TCCTTCTTTCA
1 CTTTTT-TTTCAAGGAGTATAGGACTCGAAAAATCTTCGAAAAATAGGTCTGCTTCCTTCTTT-A
* * * *
337876 -AGGAGTATAGGACTCGAACAATCTTCAGAAAACTG-GTATGCTCCCTTTTCTTTAAGGGAGTAT
64 TAGGAGTATAAGACTCAAACAATCTTCAGAAAA-TGTGTACGCTCCCTCTTCTTTAAGGGAGTAT
* ** * * *
337939 AGGACTTGAAAAGTCTTCAGGAAACGTTTCCGCTCCCTCTTTTTTCAGGGAGTATAGGACTTGAA
128 AGGACTCGAAAAGTCTTCAGGAAACGGGTCCGCTCCCTCTTCTTTCAAGGAGTATAGGACTCGAA
*
338004 CAATCTTTAGAAAACGGGTCCACTCTTTCTTCTTTCAAGGAGTATAGGACT
193 CAATCTTTAGAAAACGGGTCCACTCCTTCTTCTTTCAAGGAGTATAGGACT
338055 TGAATAGTTT
Statistics
Matches: 209, Mismatches: 28, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
270 2 0.01
271 154 0.74
272 7 0.03
273 6 0.03
274 40 0.19
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (271 bp):
CTTTTTTTTCAAGGAGTATAGGACTCGAAAAATCTTCGAAAAATAGGTCTGCTTCCTTCTTTATA
GGAGTATAAGACTCAAACAATCTTCAGAAAATGTGTACGCTCCCTCTTCTTTAAGGGAGTATAGG
ACTCGAAAAGTCTTCAGGAAACGGGTCCGCTCCCTCTTCTTTCAAGGAGTATAGGACTCGAACAA
TCTTTAGAAAACGGGTCCACTCCTTCTTCTTTCAAGGAGTATAGGACTCAAATAATCTTCGAAAA
TAGGTCCACTC
Found at i:338058 original size:55 final size:55
Alignment explanation
Indices: 337552--338054 Score: 452
Period size: 55 Copynumber: 9.2 Consensus size: 55
337542 TTTTTTCTAT
* ** * ** *
337552 GAGTATAGGACTCGAGCAATCTTC-GACAAATAGGTCTGCTTGTTCTTCTTT-ATGG
1 GAGTATAGGACTCGAACAATCTTCAGA-AAACGGGTCCGCTCCTTCTTCTTTCA-AG
* * * * * *
337607 GAGTATAAGACTCAAACAATCTTCAGAAAATGTGTCCGCTCCCTCTTCTTTCAGG
1 GAGTATAGGACTCGAACAATCTTCAGAAAACGGGTCCGCTCCTTCTTCTTTCAAG
* * *
337662 GAGTATAGGACTCGAACAATCTTCGGCAAACGGGTCTGCTCCTTCTTCTTTCAAG
1 GAGTATAGGACTCGAACAATCTTCAGAAAACGGGTCCGCTCCTTCTTCTTTCAAG
* * **
337717 GAGTATAGGACTCGAACAATCTT-TGACAAATGGGTCCGCTCCTTCTTCTTTCCGG
1 GAGTATAGGACTCGAACAATCTTCAGA-AAACGGGTCCGCTCCTTCTTCTTTCAAG
* * * ** * *
337772 GAGTATATGACTCAAATAATCTTC-GAAAATAGGTCCACTCCTTTTTCTTTCAAG
1 GAGTATAGGACTCGAACAATCTTCAGAAAACGGGTCCGCTCCTTCTTCTTTCAAG
* * ** *
337826 GAGTATAGGACTTGAAAAATCTTC-GAAAAATAGGTCTGCT-C--CTTCTTTCAAG
1 GAGTATAGGACTCGAACAATCTTCAG-AAAACGGGTCCGCTCCTTCTTCTTTCAAG
* **
337878 GAGTATAGGACTCGAACAATCTTCAGAAAACTGGTATGCTCCCTT-TTCTTT-AAGG
1 GAGTATAGGACTCGAACAATCTTCAGAAAACGGGTCCGCT-CCTTCTTCTTTCAA-G
* * ** * * *
337933 GAGTATAGGACTTGAA-AAGTCTTCAGGAAACGTTTCCGCTCCCTCTTTTTTCAGG
1 GAGTATAGGACTCGAACAA-TCTTCAGAAAACGGGTCCGCTCCTTCTTCTTTCAAG
* * * *
337988 GAGTATAGGACTTGAACAATCTTTAGAAAACGGGTCCACTCTTTCTTCTTTCAAG
1 GAGTATAGGACTCGAACAATCTTCAGAAAACGGGTCCGCTCCTTCTTCTTTCAAG
338043 GAGTATAGGACT
1 GAGTATAGGACT
338055 TGAATAGTTT
Statistics
Matches: 370, Mismatches: 63, Indels: 30
0.80 0.14 0.06
Matches are distributed among these distances:
52 43 0.12
53 1 0.00
54 54 0.15
55 266 0.72
56 6 0.02
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (55 bp):
GAGTATAGGACTCGAACAATCTTCAGAAAACGGGTCCGCTCCTTCTTCTTTCAAG
Found at i:338718 original size:31 final size:31
Alignment explanation
Indices: 338682--338740 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
338672 AACTTAAAAG
* * *
338682 AGTTTTGCAATATTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
338713 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
338741 CAATATAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:338791 original size:22 final size:22
Alignment explanation
Indices: 338765--338807 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
338755 TAATAAATTA
338765 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
338787 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
338808 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:338816 original size:22 final size:22
Alignment explanation
Indices: 338767--338815 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
338757 ATAAATTATT
**
338767 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
338789 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
338812 TAAA
1 TAAA
338816 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:338819 original size:54 final size:54
Alignment explanation
Indices: 338755--339001 Score: 485
Period size: 54 Copynumber: 4.6 Consensus size: 54
338745 ATAACTACAA
338755 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
338809 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
338863 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
338917 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
338971 TAATAAATTATTTAAAATAAATCAATCCATA
1 TAATAAATTATTTAAAATAAATCAATCCATA
339002 CAACTACAAT
Statistics
Matches: 191, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
54 191 1.00
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
Found at i:338825 original size:32 final size:31
Alignment explanation
Indices: 338787--339228 Score: 215
Period size: 32 Copynumber: 16.4 Consensus size: 31
338777 CAATCCATAT
338787 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
338819 TTTAAAATAAATCAAT-C---C--AT--AT-
1 TTTAAAATAAATCAATCCATACTAATAAATA
338841 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
338873 TTTAAAATAAATCAAT-C---C--AT--AT-
1 TTTAAAATAAATCAATCCATACTAATAAATA
*
338895 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
338927 TTTAAAATAAATCAAT-C---C--AT--AT-
1 TTTAAAATAAATCAATCCATACTAATAAATA
338949 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
*
338981 TTTAAAATAAATCAATCCATAC-AACTACA-A
1 TTTAAAATAAATCAATCCATACTAA-TAAATA
339011 --T--AATAAATCAATCC--A-T-AT-----
1 TTTAAAATAAATCAATCCATACTAATAAATA
*
339029 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
339061 TTTAAAATAAATC-A---ATAC--AT--AT-
1 TTTAAAATAAATCAATCCATACTAATAAATA
*
339083 TTTAAAATAAATCAATCCATAC-AACTACA-A
1 TTTAAAATAAATCAATCCATACTAA-TAAATA
339113 --T--AATAAATCAATCC--A-T-AT-----
1 TTTAAAATAAATCAATCCATACTAATAAATA
*
339131 TTTAAAATAAATCAAACCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
339163 TTTAAAATAAATCAAT-C---C--AT--AT-
1 TTTAAAATAAATCAATCCATACTAATAAATA
* *
339185 TTTAAAATAATTCAATACATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
339217 TTTAAAATAAAT
1 TTTAAAATAAAT
339229 TATTTTAAAA
Statistics
Matches: 324, Mismatches: 6, Indels: 160
0.66 0.01 0.33
Matches are distributed among these distances:
20 2 0.01
22 102 0.31
23 12 0.04
24 9 0.03
25 2 0.01
26 48 0.15
27 1 0.00
28 19 0.06
30 6 0.02
31 11 0.03
32 112 0.35
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (31 bp):
TTTAAAATAAATCAATCCATACTAATAAATA
Found at i:338845 original size:22 final size:22
Alignment explanation
Indices: 338819--338861 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
338809 TAATAAATTA
338819 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
338841 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
338862 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:338870 original size:22 final size:22
Alignment explanation
Indices: 338821--338869 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
338811 ATAAATTATT
**
338821 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
338843 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
338866 TAAA
1 TAAA
338870 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:338899 original size:22 final size:22
Alignment explanation
Indices: 338873--338915 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
338863 TAATAAATTA
338873 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
338895 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATCCATA
338916 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:338924 original size:22 final size:22
Alignment explanation
Indices: 338875--338923 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
338865 ATAAATTATT
**
338875 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
338897 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATCCATA-TAA
338920 TAAA
1 TAAA
338924 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:338953 original size:22 final size:22
Alignment explanation
Indices: 338927--338969 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
338917 TAATAAATTA
338927 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
338949 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
338970 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:338978 original size:22 final size:22
Alignment explanation
Indices: 338929--338977 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
338919 ATAAATTATT
**
338929 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
338951 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
338974 TAAA
1 TAAA
338978 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:339077 original size:22 final size:22
Alignment explanation
Indices: 339052--339098 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
339042 AATTCATACT
339052 AATAAAT-TATTTAAAATAAATC
1 AATAAATAT-TTTAAAATAAATC
*
339074 AATACATATTTTAAAATAAATC
1 AATAAATATTTTAAAATAAATC
339096 AAT
1 AAT
339099 CCATACAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 22 0.96
23 1 0.04
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.36
Consensus pattern (22 bp):
AATAAATATTTTAAAATAAATC
Found at i:339082 original size:54 final size:54
Alignment explanation
Indices: 339012--339228 Score: 322
Period size: 54 Copynumber: 4.1 Consensus size: 54
339002 CAACTACAAT
*
339012 AATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* *
339066 AATAAATCAATACATATTTTAAAATAAATCAATCCATAC-AACTACA--A--T--
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAA-TAAATTATTTAA
*
339114 AATAAATCAATCCATATTTTAAAATAAATCAAACCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* *
339168 AATAAATCAATCCATATTTTAAAATAATTCAATACATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
339222 AATAAAT
1 AATAAAT
339229 TATTTTAAAA
Statistics
Matches: 146, Mismatches: 9, Indels: 16
0.85 0.05 0.09
Matches are distributed among these distances:
48 40 0.27
49 2 0.01
50 2 0.01
52 2 0.01
53 2 0.01
54 98 0.67
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.34
Consensus pattern (54 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
Found at i:339103 original size:22 final size:22
Alignment explanation
Indices: 339061--339151 Score: 101
Period size: 22 Copynumber: 4.0 Consensus size: 22
339051 TAATAAATTA
*
339061 TTTAAAATAAATCAATACATAT
1 TTTAAAATAAATCAATCCATAT
*
339083 TTTAAAATAAATCAATCCATACAAC
1 TTTAAAATAAATCAATCCAT---AT
**
339108 TACAATAATAAATCAATCCATAT
1 TTTAA-AATAAATCAATCCATAT
*
339131 TTTAAAATAAATCAAACCATA
1 TTTAAAATAAATCAATCCATA
339152 CTAATAAATT
Statistics
Matches: 57, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
22 34 0.60
23 4 0.07
25 4 0.07
26 15 0.26
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:339106 original size:102 final size:102
Alignment explanation
Indices: 338981--339206 Score: 407
Period size: 102 Copynumber: 2.2 Consensus size: 102
338971 TAATAAATTA
**
338981 TTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATT
1 TTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAAAC
339046 CATACTAATAAATTATTTAAAATAAATCAATACATAT
66 CATACTAATAAATTATTTAAAATAAATCAATACATAT
339083 TTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAAAC
1 TTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAAAC
*
339148 CATACTAATAAATTATTTAAAATAAATCAATCCATAT
66 CATACTAATAAATTATTTAAAATAAATCAATACATAT
* *
339185 TTTAAAATAATTCAATACATAC
1 TTTAAAATAAATCAATCCATAC
339207 TAATAAATTA
Statistics
Matches: 119, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
102 119 1.00
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.33
Consensus pattern (102 bp):
TTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAAAC
CATACTAATAAATTATTTAAAATAAATCAATACATAT
Found at i:339189 original size:22 final size:22
Alignment explanation
Indices: 339163--339205 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
339153 TAATAAATTA
*
339163 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATACATAT
*
339185 TTTAAAATAATTCAATACATA
1 TTTAAAATAAATCAATACATA
339206 CTAATAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATACATAT
Found at i:339237 original size:15 final size:15
Alignment explanation
Indices: 339208--339357 Score: 197
Period size: 15 Copynumber: 10.5 Consensus size: 15
339198 AATACATACT
339208 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
339222 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
339237 AATAAA-TA---T-C
1 AATAAATTATTTTAA
** *
339247 AATCCA-TATTTTAT
1 AATAAATTATTTTAA
339261 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
339276 AATAAATTATTTTAC
1 AATAAATTATTTTAA
*
339291 AATAACTTATTTTAA
1 AATAAATTATTTTAA
339306 AATAAATTATTTTAA
1 AATAAATTATTTTAA
339321 AATAAATTATTTTAA
1 AATAAATTATTTTAA
339336 AATAAATTATTTTAA
1 AATAAATTATTTTAA
339351 AATAAAT
1 AATAAAT
339358 AACCTTATTA
Statistics
Matches: 119, Mismatches: 11, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
10 6 0.05
11 1 0.01
13 1 0.01
14 15 0.13
15 96 0.81
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:339385 original size:45 final size:44
Alignment explanation
Indices: 339275--339378 Score: 138
Period size: 45 Copynumber: 2.4 Consensus size: 44
339265 AATTATTTTA
* * * **
339275 AAATAAATTATTTTACAATAACTTATTTTAAAATAAATTATTTT
1 AAATAAATTATTTTAAAATAAATTATTTTAAAATAAATAACCTT
339319 AAAATAAATTATTTTAAAATAAATTATTTTAAAATAAATAACCTT
1 -AAATAAATTATTTTAAAATAAATTATTTTAAAATAAATAACCTT
*
339364 -ATTAAATTATTTTAA
1 AAATAAATTATTTTAA
339379 TAAATAACCA
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
43 14 0.26
45 39 0.74
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (44 bp):
AAATAAATTATTTTAAAATAAATTATTTTAAAATAAATAACCTT
Found at i:339387 original size:26 final size:27
Alignment explanation
Indices: 339338--339392 Score: 85
Period size: 26 Copynumber: 2.0 Consensus size: 27
339328 TATTTTAAAA
*
339338 TAAATTATTTTAAAATAAATAACCTTAT
1 TAAATTATTTT-AAATAAATAACCATAT
339366 TAAATTATTTT-AATAAATAACCATAT
1 TAAATTATTTTAAATAAATAACCATAT
339392 T
1 T
339393 TTATAATTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 15 0.58
28 11 0.42
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (27 bp):
TAAATTATTTTAAATAAATAACCATAT
Found at i:340268 original size:2 final size:2
Alignment explanation
Indices: 340261--340304 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
340251 TCAGCTTTAT
340261 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
340303 TA
1 TA
340305 GCCTTTATCG
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:340496 original size:2 final size:2
Alignment explanation
Indices: 340489--340524 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
340479 AGCTCAGCTT
340489 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
340525 ATTACATTCT
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:344745 original size:8 final size:8
Alignment explanation
Indices: 344732--344756 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
344722 TTTAATCCCT
344732 TTTTTTTA
1 TTTTTTTA
344740 TTTTTTTA
1 TTTTTTTA
344748 TTTTTTTA
1 TTTTTTTA
344756 T
1 T
344757 GATTAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTTTTA
Found at i:344789 original size:23 final size:23
Alignment explanation
Indices: 344741--344798 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
344731 TTTTTTTTAT
*
344741 TTTTTTATTTTTTTATGATTAAA
1 TTTTTTATTTTTTTATGATCAAA
*
344764 TTTTTTATTTATTTT-TTATC--A
1 TTTTTTATTT-TTTTATGATCAAA
*
344785 TATTTTATTTTTTT
1 TTTTTTATTTTTTT
344799 CCTCGACTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 4 0.13
21 10 0.32
23 13 0.42
24 4 0.13
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.76
Consensus pattern (23 bp):
TTTTTTATTTTTTTATGATCAAA
Found at i:344849 original size:18 final size:17
Alignment explanation
Indices: 344812--344852 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
344802 CGACTTATTA
**
344812 TTATTTTCTTTTTTTCC
1 TTATTTTCTTTTTTAAC
344829 TTATTTTCATTTTTTAAC
1 TTATTTTC-TTTTTTAAC
344847 TTATTT
1 TTATTT
344853 AATATTTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.73
Consensus pattern (17 bp):
TTATTTTCTTTTTTAAC
Found at i:344908 original size:3 final size:3
Alignment explanation
Indices: 344902--344961 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
344892 TTCCCTTTGA
344902 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
344950 ATT ATT ATT ATT
1 ATT ATT ATT ATT
344962 TTTCTCTCTT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:349462 original size:95 final size:94
Alignment explanation
Indices: 349294--349644 Score: 539
Period size: 95 Copynumber: 3.7 Consensus size: 94
349284 CATTATAATT
*
349294 TTATAAATATACAATAAAACTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGCTTTAT
1 TTAT-AATATACAAT-AAACTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTAT
349359 GGATAAGATTCAGCTAGCCTGATAAAGGTGA
64 GGATAAGATTCAGCTAGCCTGATAAAGGTGA
* *
349390 TTATAATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAATGCCCCGGCTTTATA
1 TTATAATATACAATAAA-CTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATG
349455 GATAAGATTCAGCTAGCCTGATAAAGGTGA
65 GATAAGATTCAGCTAGCCTGATAAAGGTGA
* *
349485 TTATAATATACAATAAATCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGTCCTC-TCTTTAT
1 TTATAATATACAATAAA-CTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACG-CCCCGGCTTTAT
*
349549 GGATAATATTCAGCTAGCCTGATAAAGGTGA
64 GGATAAGATTCAGCTAGCCTGATAAAGGTGA
* * *
349580 TTAT-A-ATACAATGATA-TTAAGATGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATG
1 TTATAATATACAAT-AAACTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATG
349642 GAT
65 GAT
349645 TCAACTAGCC
Statistics
Matches: 237, Mismatches: 14, Indels: 12
0.90 0.05 0.05
Matches are distributed among these distances:
91 3 0.01
92 41 0.17
93 7 0.03
94 6 0.03
95 173 0.73
96 7 0.03
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (94 bp):
TTATAATATACAATAAACTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGG
ATAAGATTCAGCTAGCCTGATAAAGGTGA
Found at i:350962 original size:36 final size:34
Alignment explanation
Indices: 350916--351002 Score: 95
Period size: 36 Copynumber: 2.5 Consensus size: 34
350906 ATAAGGGGTC
*
350916 GTCTCGCTTGAGACTAATTTACTC-AAAACAAAGTTT
1 GTCTCTCTTGAGAC-AATTT-CTCTAAAACAAAG-TT
* *
350952 GTCTCTCTTGAGACAGTTTCTCTTGAAACAAAGTT
1 GTCTCTCTTGAGACAATTTCTC-TAAAACAAAGTT
*
350987 GTCTCTCTTGAAACAA
1 GTCTCTCTTGAGACAA
351003 ATTTTGTGTC
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
34 3 0.07
35 20 0.45
36 21 0.48
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (34 bp):
GTCTCTCTTGAGACAATTTCTCTAAAACAAAGTT
Found at i:351014 original size:21 final size:20
Alignment explanation
Indices: 350941--351018 Score: 76
Period size: 21 Copynumber: 4.0 Consensus size: 20
350931 AATTTACTCA
350941 AAACAAAGTTTGTCTCTCTTG
1 AAACAAAG-TTGTCTCTCTTG
*
350962 AGAC--AG-T-T-TCTCTTG
1 AAACAAAGTTGTCTCTCTTG
350977 AAACAAAGTTGTCTCTCTTG
1 AAACAAAGTTGTCTCTCTTG
* *
350997 AAACAAATTTTGTGTCTCTTG
1 AAACAAA-GTTGTCTCTCTTG
351018 A
1 A
351019 GACAGTTTCC
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
15 10 0.21
16 1 0.02
17 3 0.06
18 1 0.02
19 3 0.06
20 14 0.30
21 15 0.32
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.38
Consensus pattern (20 bp):
AAACAAAGTTGTCTCTCTTG
Found at i:351055 original size:29 final size:29
Alignment explanation
Indices: 351023--351097 Score: 132
Period size: 29 Copynumber: 2.6 Consensus size: 29
351013 TCTTGAGACA
*
351023 GTTTCCCTTGAAACAAAATCTTTGAATAT
1 GTTTTCCTTGAAACAAAATCTTTGAATAT
*
351052 GTTTTCCTTGAAACAAGATCTTTGAATAT
1 GTTTTCCTTGAAACAAAATCTTTGAATAT
351081 GTTTTCCTTGAAACAAA
1 GTTTTCCTTGAAACAAA
351098 TTTCATCTCC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (29 bp):
GTTTTCCTTGAAACAAAATCTTTGAATAT
Found at i:351172 original size:73 final size:73
Alignment explanation
Indices: 351083--351241 Score: 221
Period size: 73 Copynumber: 2.2 Consensus size: 73
351073 TTGAATATGT
** * * *
351083 TTTC-CTTGAAACAAATTTCATCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCT
1 TTTCTCTTGAAACAAATTTCATCTCCCTTGAGACAGTTTCCCTTGAAACAAAGTTCTGTCTCTCT
* *
351147 TGAGACAG
66 AGAGACAA
** *
351155 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAGTTCTGTCTCTCT
1 TTTCTCTTGAAACAAATTTCATCTCCCTTGAGACAGTTTCCCTTGAAACAAAGTTCTGTCTCTCT
351220 AGAGACAA
66 AGAGACAA
351228 TTTCTCTTGAAACA
1 TTTCTCTTGAAACA
351242 TCAACCTTTG
Statistics
Matches: 76, Mismatches: 10, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
72 4 0.05
73 72 0.95
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (73 bp):
TTTCTCTTGAAACAAATTTCATCTCCCTTGAGACAGTTTCCCTTGAAACAAAGTTCTGTCTCTCT
AGAGACAA
Found at i:351182 original size:36 final size:36
Alignment explanation
Indices: 351083--351241 Score: 203
Period size: 37 Copynumber: 4.4 Consensus size: 36
351073 TTGAATATGT
** *
351083 TTTC-CTTGAAACAAATTTCATCTCCCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* * *
351118 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACAG
351155 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* * * *
351191 TTTCCCTTGAAACAAAGTTCTGTCTCTCTAGAGACAA
1 TTTCTCTTGAAACAAA-TTTTGTCTCTCTTGAGACAG
351228 TTTCTCTTGAAACA
1 TTTCTCTTGAAACA
351242 TCAACCTTTG
Statistics
Matches: 107, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
35 4 0.04
36 43 0.40
37 60 0.56
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:351453 original size:42 final size:42
Alignment explanation
Indices: 351384--351503 Score: 163
Period size: 42 Copynumber: 2.9 Consensus size: 42
351374 GCGTTTCTCA
* *
351384 ACAAACGCCGCTAAA-ACTCA-TACTTTAGTGGTGTTTATTTG
1 ACAAACACCGCTAAATA-TCAGTACTTTAGTGGCGTTTATTTG
* *
351425 ATAAACACCGCTAAATATCAGTACTTTAGTGACGTTTATTTG
1 ACAAACACCGCTAAATATCAGTACTTTAGTGGCGTTTATTTG
* *
351467 ACAAATACCACTAAATATCAGTACTTTAGTGGCGTTT
1 ACAAACACCGCTAAATATCAGTACTTTAGTGGCGTTT
351504 GTAAACAAAC
Statistics
Matches: 69, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
41 16 0.23
42 53 0.77
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (42 bp):
ACAAACACCGCTAAATATCAGTACTTTAGTGGCGTTTATTTG
Found at i:351728 original size:41 final size:40
Alignment explanation
Indices: 351372--351748 Score: 175
Period size: 41 Copynumber: 9.2 Consensus size: 40
351362 GTAACATTAA
* *
351372 TGGCGTTTCTCAACAAACGCCGCTAAA-ACTCATACTTTAG
1 TGGCGTTT-TCAACAAACACCGCTAAATACTCGTACTTTAG
* ** *
351412 TGGTGTTTATTTGATAAACACCGCTAAATA-TCAGTACTTTAG
1 TGGCG-TT-TTCAACAAACACCGCTAAATACTC-GTACTTTAG
* ** * *
351454 TGACGTTTATTTGACAAATACCACTAAATA-TCAGTACTTTAG
1 TGGCG-TT-TTCAACAAACACCGCTAAATACTC-GTACTTTAG
* * * * * *
351496 TGGCGTTTGTAAACAAACGCCGCCATATAATCGTTCTTTAG
1 TGGCGTTT-TCAACAAACACCGCTAAATACTCGTACTTTAG
* * ** *
351537 TGGCATTTTTAAACAAACACCGC--AATA-GGGTACATATATCG
1 TGGC-GTTTTCAACAAACACCGCTAAATACTCGTAC-T-T-TAG
* ** *
351578 TGGCGTTTTTAGACAAACGTCGCTAAA-ACCTTGTACTTTAG
1 TGGCGTTTTCA-ACAAACACCGCTAAATA-CTCGTACTTTAG
* * ** *
351619 TGGCATTTT-TA-AAACACCGCTAAA-ACATAATACTTTAA
1 TGGCGTTTTCAACAAACACCGCTAAATAC-TCGTACTTTAG
*
351657 TGGCGTTTT-AAGCAAAAAATGCCGCTAAATACTCGTACTTTAG
1 TGGCGTTTTCAA-C-AAACA--CCGCTAAATACTCGTACTTTAG
* * *
351700 TGGCATTTTCCAACAAACACCGCTAAATACTCATACTATAG
1 TGGCGTTTT-CAACAAACACCGCTAAATACTCGTACTTTAG
351741 T-GCGTTTT
1 TGGCGTTTT
351749 TGAATAAACG
Statistics
Matches: 261, Mismatches: 52, Indels: 48
0.72 0.14 0.13
Matches are distributed among these distances:
37 1 0.00
38 32 0.12
39 5 0.02
40 17 0.07
41 108 0.41
42 58 0.22
43 31 0.12
44 7 0.03
45 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.32
Consensus pattern (40 bp):
TGGCGTTTTCAACAAACACCGCTAAATACTCGTACTTTAG
Found at i:354795 original size:43 final size:42
Alignment explanation
Indices: 354722--354848 Score: 218
Period size: 43 Copynumber: 3.0 Consensus size: 42
354712 AGGTAATTAG
354722 CGGCGTTTGTTCCAAAAACGCCGCTATAGATATGACCTTTTA
1 CGGCGTTTGTTCCAAAAACGCCGCTATAGATATGACCTTTTA
354764 CGGCGTTTGTTCCAAAAAACGCCGCTATAGATATGACCTTTTA
1 CGGCGTTTGTTCC-AAAAACGCCGCTATAGATATGACCTTTTA
* *
354807 CGGCGTTTGTTCCAAAAACGACTCTATAGATATCGACCTTTT
1 CGGCGTTTGTTCCAAAAACGCCGCTATAGATAT-GACCTTTT
354849 GTGACATTTT
Statistics
Matches: 81, Mismatches: 2, Indels: 3
0.94 0.02 0.03
Matches are distributed among these distances:
42 31 0.38
43 50 0.62
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (42 bp):
CGGCGTTTGTTCCAAAAACGCCGCTATAGATATGACCTTTTA
Found at i:355113 original size:33 final size:34
Alignment explanation
Indices: 355052--355173 Score: 176
Period size: 33 Copynumber: 3.5 Consensus size: 34
355042 TTGGAGATAA
355052 TTTCTCTTGAAACACAAAAAAAAAACCTTTGAAATCG
1 TTTCTCTTGAAACAC---AAAAAAACCTTTGAAATCG
*
355089 TTTCTCTTGAAACAC-AAAAAACCTTTGAAACCG
1 TTTCTCTTGAAACACAAAAAAACCTTTGAAATCG
355122 TTTCTCTTGAAACACAAAAAAACCTTTGAAAAT-G
1 TTTCTCTTGAAACACAAAAAAACCTTTG-AAATCG
*
355156 TTTTTCTTGAAACACAAA
1 TTTCTCTTGAAACACAAA
355174 GACCTTCGAG
Statistics
Matches: 80, Mismatches: 3, Indels: 7
0.89 0.03 0.08
Matches are distributed among these distances:
33 32 0.40
34 30 0.38
35 3 0.04
37 15 0.19
ACGTcount: A:0.43, C:0.20, G:0.08, T:0.30
Consensus pattern (34 bp):
TTTCTCTTGAAACACAAAAAAACCTTTGAAATCG
Found at i:355142 original size:34 final size:34
Alignment explanation
Indices: 355052--355173 Score: 174
Period size: 34 Copynumber: 3.5 Consensus size: 34
355042 TTGGAGATAA
*
355052 TTTCTCTTGAAACACAAAAAAAAAACCTTTGAAATCG
1 TTTCTCTTGAAACAC---AAAAAAACCTTTGAAAACG
*
355089 TTTCTCTTGAAACAC-AAAAAACCTTTGAAACCG
1 TTTCTCTTGAAACACAAAAAAACCTTTGAAAACG
*
355122 TTTCTCTTGAAACACAAAAAAACCTTTGAAAATG
1 TTTCTCTTGAAACACAAAAAAACCTTTGAAAACG
*
355156 TTTTTCTTGAAACACAAA
1 TTTCTCTTGAAACACAAA
355174 GACCTTCGAG
Statistics
Matches: 80, Mismatches: 4, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
33 32 0.40
34 33 0.41
37 15 0.19
ACGTcount: A:0.43, C:0.20, G:0.08, T:0.30
Consensus pattern (34 bp):
TTTCTCTTGAAACACAAAAAAACCTTTGAAAACG
Found at i:355546 original size:167 final size:167
Alignment explanation
Indices: 355172--355697 Score: 674
Period size: 167 Copynumber: 3.2 Consensus size: 167
355162 TTGAAACACA
* * ** *
355172 AAGACCTTCGAGTTCGACTACACTCAGCTTCGAGGGCACATCATTTGTAGCATAACTCAAGACTA
1 AAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTA
* * * ** * *
355237 GAAGGGTTATCTG--CC-AAAGACCTTAGAGTTTGATTCCATTCAACTCAAAGGCGCATCATTTG
66 GAAGGGTTATCTGTACCAAAAGACCTTCGAGTTTGACTACGCTCAACTCCAAGGCACATCATTTG
*
355299 CAGCATAACTTAAGGT-AAGAAGGGCTATCTGCC-A--
131 CAGCATAACTTAA-GTCGAGAAGGGCTATCTGCCAACC
355333 AAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTA
1 AAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTA
* * *
355398 GAAGGGTT-TTTGTCACCAAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCATATCA-TT
66 GAAGGGTTATCTGT-ACCAAAAGACCTTCGAGTTTGACTACGCTCAACTCCAAGGCACATCATTT
* *
355461 GCAGTATAACTTAAGTCGAGAAGGGTTATCTGCCAACC
130 GCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAACC
* * *
355499 ACAGACCCTCGAGTTTGATTACACTCAGCTTCGAGGGCACGTCATTTACTGCATAACTCAAGGCT
1 A-AGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCT
** * *
355564 AGAAGGGTTATCTGTTAATAAAAGACCATCGAGTTCGACTACGCTCAACTCCAAGGCACATCATT
65 AGAAGGGTTATCTG-TACCAAAAGACCTTCGAGTTTGACTACGCTCAACTCCAAGGCACATCATT
* * *
355629 TGTAGCATAGCTTAAGTCGAGAATGGCTATCTGCCAACC
129 TGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAACC
* *
355668 AAAGACCTTCGAGTTCGATTACACTAAGCT
1 -AAGACCCTCGAGTTCGATTACACTCAGCT
355698 CAGAGGCAAA
Statistics
Matches: 316, Mismatches: 36, Indels: 18
0.85 0.10 0.05
Matches are distributed among these distances:
160 3 0.01
161 68 0.22
162 2 0.01
163 32 0.10
164 35 0.11
166 1 0.00
167 69 0.22
168 44 0.14
169 61 0.19
170 1 0.00
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.25
Consensus pattern (167 bp):
AAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTA
GAAGGGTTATCTGTACCAAAAGACCTTCGAGTTTGACTACGCTCAACTCCAAGGCACATCATTTG
CAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAACC
Found at i:355672 original size:84 final size:83
Alignment explanation
Indices: 355170--355697 Score: 446
Period size: 84 Copynumber: 6.4 Consensus size: 83
355160 TCTTGAAACA
* * *
355170 CAAAGACCTTCGAGTTCGACTACACTCAGCTTCGAGGGCACATCATTTGTAGCATAACTCAAGAC
1 CAAAGACCTTCGAGTTCGACTACACTCAGCTTCGAAGGCACATCATTTGCAGCATAACTCAAGTC
355235 TAGAAGGGTTATCTG--C
66 TAGAAGGGTTATCTGCAC
* * * * * * * * *
355251 CAAAGACCTTAGAGTTTGATTCCATTCAAC-TCAAAGGCGCATCATTTGCAGCATAACTTAAGGT
1 CAAAGACCTTCGAGTTCGACTACACTCAGCTTCGAAGGCACATCATTTGCAGCATAACTCAA-GT
* *
355315 -AAGAAGGGCTATCTG--C
65 CTAGAAGGGTTATCTGCAC
* * * * *
355331 CAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGC
1 CAAAGACCTTCGAGTTCGACTACACTCAGCTTCGAAGGCACATCATTTGCAGCATAACTCAAGTC
*
355396 TAGAAGGGTT-TTTGTCAC
66 TAGAAGGGTTATCTG-CAC
* * * * * *
355414 CAAAAGACCTTCGAGTTTGACTACGCTCAGC-TCCAAGGCATATCA-TTGCAGTATAACTTAAGT
1 C-AAAGACCTTCGAGTTCGACTACACTCAGCTTCGAAGGCACATCATTTGCAGCATAACTCAAGT
*
355477 CGAGAAGGGTTATCTGCCAAC
65 CTAGAAGGGTTATCTG-C-AC
* * * * * * * * *
355498 CACAGACCCTCGAGTTTGATTACACTCAGCTTCGAGGGCACGTCATTTACTGCATAACTCAAGGC
1 CAAAGACCTTCGAGTTCGACTACACTCAGCTTCGAAGGCACATCATTTGCAGCATAACTCAAGTC
* *
355563 TAGAAGGGTTATCTGTTAAT
66 TAGAAGGGTTATCTG--CAC
* * * * * * * *
355583 AAAAGACCATCGAGTTCGACTACGCTCAAC-TCCAAGGCACATCATTTGTAGCATAGCTTAAGTC
1 CAAAGACCTTCGAGTTCGACTACACTCAGCTTCGAAGGCACATCATTTGCAGCATAACTCAAGTC
* * *
355647 GAGAATGGCTATCTGCCAAC
66 TAGAAGGGTTATCTG-C-AC
* *
355667 CAAAGACCTTCGAGTTCGATTACACTAAGCT
1 CAAAGACCTTCGAGTTCGACTACACTCAGCT
355698 CAGAGGCAAA
Statistics
Matches: 345, Mismatches: 88, Indels: 24
0.75 0.19 0.05
Matches are distributed among these distances:
80 68 0.20
81 59 0.17
82 24 0.07
83 42 0.12
84 100 0.29
85 52 0.15
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.25
Consensus pattern (83 bp):
CAAAGACCTTCGAGTTCGACTACACTCAGCTTCGAAGGCACATCATTTGCAGCATAACTCAAGTC
TAGAAGGGTTATCTGCAC
Found at i:356273 original size:2 final size:2
Alignment explanation
Indices: 356262--356315 Score: 69
Period size: 2 Copynumber: 28.5 Consensus size: 2
356252 CTGATGTGAC
* *
356262 AT AT AT -T AT AT AT TT AT CT -T AT A- AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
356301 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
356316 AATTATATGT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
1 3 0.07
2 43 0.93
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:357561 original size:27 final size:26
Alignment explanation
Indices: 357525--357580 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 26
357515 TTCTAATCCC
*
357525 TTTTATTTT-ATTTTATTTATTTATTT
1 TTTTATTTTAAATTT-TTTATTTATTT
357551 TTTTATGTTTAAATTTTTTATTTATTT
1 TTTTAT-TTTAAATTTTTTATTTATTT
357578 TTT
1 TTT
357581 ATCCTATTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 6 0.22
27 17 0.63
28 4 0.15
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.79
Consensus pattern (26 bp):
TTTTATTTTAAATTTTTTATTTATTT
Found at i:357702 original size:3 final size:3
Alignment explanation
Indices: 357696--357728 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
357686 TTCCCTTTGA
357696 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
357729 TTCTCTCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:361802 original size:35 final size:35
Alignment explanation
Indices: 361756--361823 Score: 127
Period size: 35 Copynumber: 1.9 Consensus size: 35
361746 AATTAACTGG
*
361756 TTCTTTTAGTCTTGTAATTTTTCTAACTAGAACGC
1 TTCTTTTAGTCTTGTAATTTTGCTAACTAGAACGC
361791 TTCTTTTAGTCTTGTAATTTTGCTAACTAGAAC
1 TTCTTTTAGTCTTGTAATTTTGCTAACTAGAAC
361824 TACTACTCCT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.24, C:0.16, G:0.12, T:0.49
Consensus pattern (35 bp):
TTCTTTTAGTCTTGTAATTTTGCTAACTAGAACGC
Found at i:371020 original size:42 final size:43
Alignment explanation
Indices: 370969--371050 Score: 130
Period size: 42 Copynumber: 1.9 Consensus size: 43
370959 ATATTTTCCG
**
370969 GAAAATATTTTTTGGTATTTGATAGTTGTAATTG-TTTTTACA
1 GAAAATATTTTTCAGTATTTGATAGTTGTAATTGATTTTTACA
*
371011 GAAAATATTTTTCAGTGTTTGATAGTTGTAATTGATTTTT
1 GAAAATATTTTTCAGTATTTGATAGTTGTAATTGATTTTT
371051 CCAATGTAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
42 31 0.86
43 5 0.14
ACGTcount: A:0.28, C:0.02, G:0.17, T:0.52
Consensus pattern (43 bp):
GAAAATATTTTTCAGTATTTGATAGTTGTAATTGATTTTTACA
Found at i:371246 original size:39 final size:36
Alignment explanation
Indices: 371174--371246 Score: 85
Period size: 39 Copynumber: 1.9 Consensus size: 36
371164 TTATACGTTT
* *
371174 AATATTAAATTAATATTTTAATATCATTTTAATAAA
1 AATATTAAATTAAAATTTTAATATCATTATAATAAA
371210 AATATTAATTATTAAAATATTTAATATACA-TATAATA
1 AATATTAA--ATTAAAAT-TTTAATAT-CATTATAATA
371247 TAATTTTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
36 8 0.26
38 7 0.23
39 14 0.45
40 2 0.06
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (36 bp):
AATATTAAATTAAAATTTTAATATCATTATAATAAA
Found at i:371841 original size:26 final size:26
Alignment explanation
Indices: 371812--371871 Score: 111
Period size: 26 Copynumber: 2.3 Consensus size: 26
371802 AGTTAGGCCG
371812 GGTTGCTCCATTTGATACTGCATCTT
1 GGTTGCTCCATTTGATACTGCATCTT
371838 GGTTGCTCCATTTGATACTGCATCTT
1 GGTTGCTCCATTTGATACTGCATCTT
*
371864 GCTTGCTC
1 GGTTGCTC
371872 GCGATCGGCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.13, C:0.25, G:0.20, T:0.42
Consensus pattern (26 bp):
GGTTGCTCCATTTGATACTGCATCTT
Found at i:373267 original size:31 final size:31
Alignment explanation
Indices: 373229--373355 Score: 130
Period size: 31 Copynumber: 4.1 Consensus size: 31
373219 GAACCTCGGC
* *
373229 AATTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AATTGTCCATATGTCCCGAAGAACATAGGTA
* ***
373260 AATTGTCCATATGTTCTTTAGAACATAGGTA
1 AATTGTCCATATGTCCCGAAGAACATAGGTA
* *
373291 TATTGTCTATATGTCCCGAA-AGACATAGGTA
1 AATTGTCCATATGTCCCGAAGA-ACATAGGTA
* * *
373322 ATTCTGTCCATATGTTCCGTAGAACATAGGTA
1 AAT-TGTCCATATGTCCCGAAGAACATAGGTA
373354 AA
1 AA
373356 CCCTCGACTC
Statistics
Matches: 75, Mismatches: 18, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
30 1 0.01
31 49 0.65
32 24 0.32
33 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.31
Consensus pattern (31 bp):
AATTGTCCATATGTCCCGAAGAACATAGGTA
Found at i:373348 original size:63 final size:62
Alignment explanation
Indices: 373230--373353 Score: 169
Period size: 62 Copynumber: 2.0 Consensus size: 62
373220 AACCTCGGCA
* **
373230 ATTGTCCATAGGTCCCGAAGAACCTAGGTAAATTGTCCATATGTTCTTTAGAACATAGGTAT
1 ATTGTCCATAGGTCCCGAAGAACATAGGTAAATTGTCCATATGTTCCGTAGAACATAGGTAT
* * *
373292 ATTGTCTATATGTCCCGAA-AGACATAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTA
1 ATTGTCCATAGGTCCCGAAGA-ACATAGGTAAAT-TGTCCATATGTTCCGTAGAACATAGGTA
373354 AACCCTCGAC
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
61 1 0.02
62 27 0.50
63 26 0.48
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (62 bp):
ATTGTCCATAGGTCCCGAAGAACATAGGTAAATTGTCCATATGTTCCGTAGAACATAGGTAT
Found at i:373872 original size:10 final size:10
Alignment explanation
Indices: 373848--373880 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
373838 CTCCACGGTG
373848 GAGAAGA-GA
1 GAGAAGATGA
373857 -AGAAGATGA
1 GAGAAGATGA
373866 GAGAAGATGA
1 GAGAAGATGA
373876 GAGAA
1 GAGAA
373881 TTGTGTGGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 6 0.27
9 2 0.09
10 14 0.64
ACGTcount: A:0.55, C:0.00, G:0.39, T:0.06
Consensus pattern (10 bp):
GAGAAGATGA
Found at i:379625 original size:2 final size:2
Alignment explanation
Indices: 379618--379645 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
379608 TTTTATTTGA
379618 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
379646 GAATGGTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:380740 original size:60 final size:60
Alignment explanation
Indices: 380617--380740 Score: 151
Period size: 60 Copynumber: 2.1 Consensus size: 60
380607 GACCTTCCCC
* * * *
380617 CTATATGATATTGTTTTGTTGAGTCCCTCAATTATTAAAATTTACAAAATAGTCCCTTAA
1 CTATAAGATATTGTTTTGTTGAGTCCCTCAACTATTAAAAGTTACAAAATAGTCACTTAA
* ** * *
380677 CTATAAGATGTTGTTTTGTTGAGTCTTTCAACTATTAAAAGTTATAAAAT-GATCACTTGA
1 CTATAAGATATTGTTTTGTTGAGTCCCTCAACTATTAAAAGTTACAAAATAG-TCACTTAA
380737 CTAT
1 CTAT
380741 TCATATATTC
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
59 1 0.02
60 53 0.98
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (60 bp):
CTATAAGATATTGTTTTGTTGAGTCCCTCAACTATTAAAAGTTACAAAATAGTCACTTAA
Found at i:382114 original size:67 final size:67
Alignment explanation
Indices: 382042--382176 Score: 270
Period size: 67 Copynumber: 2.0 Consensus size: 67
382032 TCAAATTTTT
382042 ATTATAAACTAAAATAAATTTTTTGTTATAAAATTTCTTATCAATTTTGTTGTTTTATATTTACA
1 ATTATAAACTAAAATAAATTTTTTGTTATAAAATTTCTTATCAATTTTGTTGTTTTATATTTACA
382107 TA
66 TA
382109 ATTATAAACTAAAATAAATTTTTTGTTATAAAATTTCTTATCAATTTTGTTGTTTTATATTTACA
1 ATTATAAACTAAAATAAATTTTTTGTTATAAAATTTCTTATCAATTTTGTTGTTTTATATTTACA
382174 TA
66 TA
382176 A
1 A
382177 CTCACATGTT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 68 1.00
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.52
Consensus pattern (67 bp):
ATTATAAACTAAAATAAATTTTTTGTTATAAAATTTCTTATCAATTTTGTTGTTTTATATTTACA
TA
Found at i:383074 original size:19 final size:22
Alignment explanation
Indices: 383052--383097 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 22
383042 TTATTTTACT
383052 TTAA-CTTA-AATA-TTTAAAA
1 TTAATCTTATAATATTTTAAAA
*
383071 TTAATTTTTATAATATTTTAAAA
1 TTAA-TCTTATAATATTTTAAAA
383094 TTAA
1 TTAA
383098 GATAAAAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 4 0.18
21 3 0.14
22 4 0.18
23 11 0.50
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (22 bp):
TTAATCTTATAATATTTTAAAA
Found at i:383170 original size:30 final size:29
Alignment explanation
Indices: 383083--383484 Score: 165
Period size: 30 Copynumber: 13.3 Consensus size: 29
383073 AATTTTTATA
* *
383083 ATATTTTAAAATTAAGATAAAAATGAGATAT
1 ATATTTTTAAATTAAGATAAAAAT-A-AAAT
* * *
383114 ATATTTTTCAGTTAAGATACAAATAAAAT
1 ATATTTTTAAATTAAGATAAAAATAAAAT
*
383143 ATATTTCTTAAATTAAAATAAAAATAAAAT
1 ATATTT-TTAAATTAAGATAAAAATAAAAT
* * *
383173 -T-TTAAATTAAGATTAAGATTAAGATTAAAATAAAATAT
1 ATATT--TTTAA-ATTAAGA-TAA-A-AATA----AA-AT
** *
383211 ATATTTTTAGGTTAAGATAAGAAT-AAAT
1 ATATTTTTAAATTAAGATAAAAATAAAAT
* * * *
383239 CATATTTAATAATTTAATG-TAAGAATAGAAT
1 -ATATTT-TTAAATTAA-GATAAAAATAAAAT
** * * **
383270 ATATCTAATAATTTAAG-TCAATAATTTAAT
1 ATAT-TTTTAAATTAAGAT-AAAAATAAAAT
383300 ATA--TTTAATATTTAAGATAAAAATAAAAT
1 ATATTTTTAA-A-TTAAGATAAAAATAAAAT
* * * *
383329 ATATTTTCAAAAGTTAATATAATAA-AAAGT
1 ATATTTT-TAAA-TTAAGATAAAAATAAAAT
* * *
383359 ATATTTTTTAAGTTAAGGTAAGAATAAAAT
1 ATA-TTTTTAAATTAAGATAAAAATAAAAT
* * *
383389 ATATTTTATAAGTTAAGATAAGATTAAAAT
1 ATATTTT-TAAATTAAGATAAAAATAAAAT
**
383419 ATATTTTT-AATTAAGATAAGGATAAAAT
1 ATATTTTTAAATTAAGATAAAAATAAAAT
* * * *
383447 ATGTTTAATAAGTTAAGATAAAAATAAATT
1 ATATTT-TTAAATTAAGATAAAAATAAAAT
383477 ATATTTTT
1 ATATTTTT
383485 TAATGTTAAG
Statistics
Matches: 283, Mismatches: 57, Indels: 64
0.70 0.14 0.16
Matches are distributed among these distances:
27 3 0.01
28 26 0.09
29 56 0.20
30 128 0.45
31 45 0.16
32 3 0.01
33 2 0.01
34 1 0.00
36 3 0.01
37 8 0.03
38 5 0.02
39 1 0.00
40 2 0.01
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.39
Consensus pattern (29 bp):
ATATTTTTAAATTAAGATAAAAATAAAAT
Found at i:383232 original size:42 final size:41
Alignment explanation
Indices: 383150--383238 Score: 108
Period size: 42 Copynumber: 2.1 Consensus size: 41
383140 AATATATTTC
383150 TTAAATTAAAATAAAAATAAAATTTTAAATTAAGATTAAGA
1 TTAAATTAAAATAAAAATAAAATTTTAAATTAAGATTAAGA
* * **
383191 TTAAGATTAAAATAAAATATATATTTTTAGGTTAAGA-TAAGA
1 TTAA-ATTAAAATAAAA-ATAAAATTTTAAATTAAGATTAAGA
*
383233 ATAAAT
1 TTAAAT
383239 CATATTTAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
41 6 0.15
42 20 0.49
43 15 0.37
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (41 bp):
TTAAATTAAAATAAAAATAAAATTTTAAATTAAGATTAAGA
Found at i:383353 original size:60 final size:58
Alignment explanation
Indices: 383190--383484 Score: 205
Period size: 60 Copynumber: 5.0 Consensus size: 58
383180 TAAGATTAAG
** * * *
383190 ATTAAGATTAA-AATAAAATATATATTTTTAGGTTAAGATAAGAA-TAAATCATATTTAATA
1 ATTAAGA-TAAGAATAAAATATAT-TTTAAAAGTTAAGATAATAATTAAAT-ATATTT-TTA
* * * * *
383250 ATTTAATG-TAAGAATAGAATATA-TCTAATAATTTAAG-TCAATAATTTAATATATTTAATA
1 A-TTAA-GATAAGAATAAAATATATTTTAA-AAGTTAAGAT-AATAATTAAATATATTT-TTA
* * *
383310 TTTAAGATAAAAATAAAATATATTTTCAAAAGTTAATATAATAA--AAAGTATATTTTTTA
1 ATTAAGATAAGAATAAAATATATTTT-AAAAGTTAAGATAATAATTAAA-TATA-TTTTTA
* * *
383369 AGTTAAGGTAAGAATAAAATATATTTTATAAGTTAAGATAA-GATTAAAATATATTTTTA
1 A-TTAAGATAAGAATAAAATATATTTTAAAAGTTAAGATAATAATT-AAATATATTTTTA
* * *
383428 ATTAAGATAAGGATAAAATAT-GTTTAATAAGTTAAGATAA-AAATAAATTATATTTTT
1 ATTAAGATAAGAATAAAATATATTTTAA-AAGTTAAGATAATAATTAAA-TATATTTTT
383485 TAATGTTAAG
Statistics
Matches: 189, Mismatches: 28, Indels: 38
0.74 0.11 0.15
Matches are distributed among these distances:
57 7 0.04
58 45 0.24
59 45 0.24
60 67 0.35
61 24 0.13
62 1 0.01
ACGTcount: A:0.51, C:0.01, G:0.08, T:0.40
Consensus pattern (58 bp):
ATTAAGATAAGAATAAAATATATTTTAAAAGTTAAGATAATAATTAAATATATTTTTA
Found at i:383391 original size:119 final size:117
Alignment explanation
Indices: 383083--383494 Score: 296
Period size: 119 Copynumber: 3.4 Consensus size: 117
383073 AATTTTTATA
* * *
383083 ATATTTTAAAA-TTAAGATAAAAATGAGATATATATTTTTCAGTTAAGATACA-AATAAAATATA
1 ATATTTTAAAAGTTAAGATAAAAAT-AAATATAT-TTTTTAAGTTAAGGTA-AGAATAAAATATA
* ** * * * * * *
383146 TTTCTTAAATTAAAATAAAAATAAAATTTTAAATTAAGATTAAGATTAAGATTAAAATAAAAT
63 TCTAATAAGTTAAGATAAAATTAAAA---TATATT--TA-T-A-ATTAAGATAAAAATAAAAT
** * * ** * * *
383209 ATATATTTTTAGGTTAAGATAAGAATAAATCATATTTAATAATTTAATGTAAGAATAGAATATAT
1 ATAT-TTTAAAAGTTAAGATAAAAATAAAT-ATATTTTTTAAGTTAAGGTAAGAATAAAATATAT
* * *
383274 CTAATAATTTAAG-TCAATAATT-TAATATATTTAATATTTAAGATAAAAATAAAAT
64 CTAATAAGTTAAGAT-AA-AATTAAAATATATTT-ATAATTAAGATAAAAATAAAAT
* *
383329 ATATTTTCAAAAGTTAATATAATAAA-AAGTATATTTTTTAAGTTAAGGTAAGAATAAAATATAT
1 ATATTTT-AAAAGTTAAGATAA-AAATAAATATATTTTTTAAGTTAAGGTAAGAATAAAATATAT
* * * * **
383393 TTTATAAGTTAAGATAAGATTAAAATATATTTTTAATTAAGATAAGGATAAAAT
64 CTAATAAGTTAAGATAAAATTAAAATATATTTATAATTAAGATAAAAATAAAAT
*
383447 AT-GTTTAATAAGTTAAGATAAAAATAAATTATATTTTTTAATGTTAAG
1 ATATTTTAA-AAGTTAAGATAAAAATAAA-TATATTTTTTAA-GTTAAG
383495 ATGTGAATTT
Statistics
Matches: 225, Mismatches: 46, Indels: 37
0.73 0.15 0.12
Matches are distributed among these distances:
116 5 0.02
117 16 0.07
118 35 0.16
119 59 0.26
120 35 0.16
121 3 0.01
122 1 0.00
123 1 0.00
124 5 0.02
126 6 0.03
127 40 0.18
128 19 0.08
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.39
Consensus pattern (117 bp):
ATATTTTAAAAGTTAAGATAAAAATAAATATATTTTTTAAGTTAAGGTAAGAATAAAATATATCT
AATAAGTTAAGATAAAATTAAAATATATTTATAATTAAGATAAAAATAAAAT
Found at i:386096 original size:28 final size:29
Alignment explanation
Indices: 386064--386121 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
386054 TATAACCTAG
386064 TTGAATGG-TTTTTTTCTAGAGTAAATGA
1 TTGAATGGTTTTTTTTCTAGAGTAAATGA
*
386092 TTGAATGGTTTTTTTTCTTGAGTAAATGA
1 TTGAATGGTTTTTTTTCTAGAGTAAATGA
386121 T
1 T
386122 GATCGAAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 8 0.29
29 20 0.71
ACGTcount: A:0.26, C:0.03, G:0.21, T:0.50
Consensus pattern (29 bp):
TTGAATGGTTTTTTTTCTAGAGTAAATGA
Found at i:387508 original size:24 final size:24
Alignment explanation
Indices: 387479--387567 Score: 126
Period size: 24 Copynumber: 3.8 Consensus size: 24
387469 TAACAAACAA
* *
387479 GTTCGTGGACATATAAATGAGCAC
1 GTTCGTGAACATATAAACGAGCAC
387503 GTTCGTGAACATATAAACGAGCAC
1 GTTCGTGAACATATAAACGAGCAC
*
387527 GTTCGTGAACATATAAACGAACAC
1 GTTCGTGAACATATAAACGAGCAC
**
387551 GTTCACGAACAT-TAAAC
1 GTTCGTGAACATATAAAC
387568 AAACATGTTC
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
23 5 0.08
24 55 0.92
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.22
Consensus pattern (24 bp):
GTTCGTGAACATATAAACGAGCAC
Found at i:387572 original size:23 final size:24
Alignment explanation
Indices: 387500--387594 Score: 95
Period size: 24 Copynumber: 4.0 Consensus size: 24
387490 TATAAATGAG
** * *
387500 CACGTTCGTGAACATATAAACGAG
1 CACGTTCACGAACATATAAACAAA
** *
387524 CACGTTCGTGAACATATAAACGAA
1 CACGTTCACGAACATATAAACAAA
387548 CACGTTCACGAACAT-TAAACAAA
1 CACGTTCACGAACATATAAACAAA
* *
387571 CATGTTCACGAACA-ATAAATAAA
1 CACGTTCACGAACATATAAACAAA
387594 C
1 C
387595 GAGCACAGAT
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
23 28 0.44
24 36 0.56
ACGTcount: A:0.44, C:0.22, G:0.14, T:0.20
Consensus pattern (24 bp):
CACGTTCACGAACATATAAACAAA
Found at i:392981 original size:65 final size:65
Alignment explanation
Indices: 392819--392962 Score: 195
Period size: 65 Copynumber: 2.2 Consensus size: 65
392809 AATGCATTTT
* * *
392819 GTGTACCGATGCACAACCATGCATCGATGCACTCTTGATTTTATTGAAACATCGAATGTATTTTA
1 GTGTACCGATGCACAACCATGCATCGATGCACTCTGGATCTTATTGAAACATCGAATGTATATTA
* * *
392884 -CGTACCGATGCACATACCATGCATCAATGCACTCCTGGCTCTT-TTGAAACATCGAATGTA-AT
1 GTGTACCGATGCACA-ACCATGCATCGATGCACT-CTGGATCTTATTGAAACATCGAATGTATAT
392946 TA
64 TA
392948 GTGTACCGATGCACA
1 GTGTACCGATGCACA
392963 CCAAGTGTAC
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
64 16 0.23
65 47 0.68
66 6 0.09
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (65 bp):
GTGTACCGATGCACAACCATGCATCGATGCACTCTGGATCTTATTGAAACATCGAATGTATATTA
Found at i:401175 original size:23 final size:22
Alignment explanation
Indices: 401104--401183 Score: 90
Period size: 21 Copynumber: 3.5 Consensus size: 22
401094 CATGGCAGTG
401104 TGCATCGATGCATCCCTTTGAATA
1 TGCATCGATGCAT-CC-TTGAATA
* *
401128 TGCATCGATACAT-CATGAATA
1 TGCATCGATGCATCCTTGAATA
*
401149 TGCATCGATGCACTCCTTGAATG
1 TGCATCGATGCA-TCCTTGAATA
*
401172 TGCATCAATGCA
1 TGCATCGATGCA
401184 CACTGCCATG
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
21 17 0.35
22 2 0.04
23 17 0.35
24 12 0.25
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (22 bp):
TGCATCGATGCATCCTTGAATA
Found at i:405214 original size:20 final size:20
Alignment explanation
Indices: 405189--405236 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
405179 ACCGTTGGGC
* *
405189 TTGATATTACTGTAGTAGTA
1 TTGATATTACTATAGCAGTA
*
405209 TTGATACTACTATAGCAGTA
1 TTGATATTACTATAGCAGTA
*
405229 TCGATATT
1 TTGATATT
405237 CATTTTACAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.42
Consensus pattern (20 bp):
TTGATATTACTATAGCAGTA
Found at i:405310 original size:20 final size:20
Alignment explanation
Indices: 405277--405346 Score: 88
Period size: 20 Copynumber: 3.5 Consensus size: 20
405267 TACTATTCAT
* *
405277 TACTGTTCACACAGTATCGG
1 TACTATTCATACAGTATCGG
*
405297 TACTATTTATACAGTATCGG
1 TACTATTCATACAGTATCGG
**
405317 TACTATTCATACAGTA-CAA
1 TACTATTCATACAGTATCGG
405336 TACTATTCATA
1 TACTATTCATA
405347 AAAAATTTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 12 0.27
20 32 0.73
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.36
Consensus pattern (20 bp):
TACTATTCATACAGTATCGG
Found at i:408114 original size:19 final size:20
Alignment explanation
Indices: 408070--408121 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
408060 TACTGTTCAA
* *
408070 TACTGTTCACACAGTATCAG
1 TACTATTCATACAGTATCAG
*
408090 TACTATTTATACAGTATCA-
1 TACTATTCATACAGTATCAG
408109 TACTATTCATACA
1 TACTATTCATACA
408122 ACAATACTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.35, C:0.21, G:0.08, T:0.37
Consensus pattern (20 bp):
TACTATTCATACAGTATCAG
Found at i:410232 original size:17 final size:17
Alignment explanation
Indices: 410210--410242 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
410200 GGCCAAGAGC
410210 ATGTATTTTCATTAAAT
1 ATGTATTTTCATTAAAT
410227 ATGTATTTTCATTAAA
1 ATGTATTTTCATTAAA
410243 AAAATCATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.52
Consensus pattern (17 bp):
ATGTATTTTCATTAAAT
Found at i:412260 original size:26 final size:24
Alignment explanation
Indices: 412212--412260 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 24
412202 TTATACTTGT
*
412212 TAAATTTGATGATTTCAAATAAAC
1 TAAATTTGATGATTTAAAATAAAC
*
412236 TAAATTTTATTGATTTTAAAATAAA
1 TAAATTTGA-TGA-TTTAAAATAAA
412261 GAATGTTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 8 0.38
25 3 0.14
26 10 0.48
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (24 bp):
TAAATTTGATGATTTAAAATAAAC
Found at i:413658 original size:141 final size:141
Alignment explanation
Indices: 413354--413677 Score: 329
Period size: 141 Copynumber: 2.3 Consensus size: 141
413344 GACCTTCGTG
* * * * * *
413354 ATAA-AAAAAAGAATATTGTTTTTCATAGATGTCTCATGTTTAAACAATTATGTATACAGGGTGT
1 ATAATAAAAAAGAATATTGTTTTTCATAGATGTCTCAGGTTCAAGCAACTACGTATACAGGGTAT
* * * * * *
413418 GTGTGCGTCGATTATCAATTAGTAAAAGAAAGTTTTGTTTTTTATGATAAAATATAAATCTCATT
66 GTATGCGTCGATTATCAATGAGTAAAAAAAAGTGTTGTTTTTCATGATAAAATACAAATCTCATT
413483 AAACGATCTCA
131 AAACGATCTCA
* ** * * * * * *
413494 GTGGTAAAAGCAAG-A-GTTATTTTTCATAGATGCCTCAGGTTCAAGTAACTACGTTTTCAGGGT
1 ATAATAAAA--AAGAATATTGTTTTTCATAGATGTCTCAGGTTCAAGCAACTACGTATACAGGGT
*
413557 ATGTATGCGTCGATTATCAATCGA-TAAAAAAAAGTGTTG-TTTTCATGGTAAAATACAGAA-CT
64 ATGTATGCGTCGATTATCAAT-GAGTAAAAAAAAGTGTTGTTTTTCATGATAAAATACA-AATCT
* *
413619 CGTTAAATGATCTCA
127 CATTAAACGATCTCA
* *
413634 ATAATAAAAAAGAATATTGTTTTT-TTAGATGTCTCGGGTTCAAG
1 ATAATAAAAAAGAATATTGTTTTTCATAGATGTCTCAGGTTCAAG
413678 AAGTTACATC
Statistics
Matches: 145, Mismatches: 32, Indels: 15
0.76 0.17 0.08
Matches are distributed among these distances:
138 3 0.02
139 18 0.12
140 44 0.30
141 75 0.52
142 2 0.01
143 3 0.02
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.36
Consensus pattern (141 bp):
ATAATAAAAAAGAATATTGTTTTTCATAGATGTCTCAGGTTCAAGCAACTACGTATACAGGGTAT
GTATGCGTCGATTATCAATGAGTAAAAAAAAGTGTTGTTTTTCATGATAAAATACAAATCTCATT
AAACGATCTCA
Found at i:419358 original size:21 final size:21
Alignment explanation
Indices: 419328--419375 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
419318 AATATGTAAG
*
419328 TTATCCTTATATAAATAACTA
1 TTATCTTTATATAAATAACTA
419349 TTATCTTTATATAAATAACTA
1 TTATCTTTATATAAATAACTA
419370 TTATCT
1 TTATCT
419376 AAAATCTGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (21 bp):
TTATCTTTATATAAATAACTA
Found at i:420297 original size:10 final size:10
Alignment explanation
Indices: 420282--420350 Score: 66
Period size: 10 Copynumber: 6.1 Consensus size: 10
420272 GATAACACAA
420282 ATGAACGAAC
1 ATGAACGAAC
420292 ATGAACGAAC
1 ATGAACGAAC
420302 GGATGTAAACGAAC
1 --ATG--AACGAAC
420316 ATGAACGAAC
1 ATGAACGAAC
420326 GGATGTAAACGAAC
1 --ATG--AACGAAC
420340 ATGAACGAAC
1 ATGAACGAAC
420350 A
1 A
420351 GATGTAAATG
Statistics
Matches: 51, Mismatches: 0, Indels: 16
0.76 0.00 0.24
Matches are distributed among these distances:
10 25 0.49
12 12 0.24
14 14 0.27
ACGTcount: A:0.48, C:0.17, G:0.23, T:0.12
Consensus pattern (10 bp):
ATGAACGAAC
Found at i:420312 original size:24 final size:24
Alignment explanation
Indices: 420285--420374 Score: 153
Period size: 24 Copynumber: 3.8 Consensus size: 24
420275 AACACAAATG
420285 AACGAACATGAACGAACGGATGTA
1 AACGAACATGAACGAACGGATGTA
420309 AACGAACATGAACGAACGGATGTA
1 AACGAACATGAACGAACGGATGTA
*
420333 AACGAACATGAACGAACAGATGTA
1 AACGAACATGAACGAACGGATGTA
* *
420357 AATGAACATAAACGAACG
1 AACGAACATGAACGAACG
420375 TAAACGAACA
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 62 1.00
ACGTcount: A:0.49, C:0.17, G:0.22, T:0.12
Consensus pattern (24 bp):
AACGAACATGAACGAACGGATGTA
Found at i:420336 original size:14 final size:13
Alignment explanation
Indices: 420295--420374 Score: 61
Period size: 10 Copynumber: 6.6 Consensus size: 13
420285 AACGAACATG
420295 AACGAACGGATGTA
1 AACGAAC-GATGTA
420309 AACGAAC-ATG--
1 AACGAACGATGTA
420319 AACGAACGGATGTA
1 AACGAAC-GATGTA
420333 AACGAAC-ATG--
1 AACGAACGATGTA
420343 AACGAACAGATGTA
1 AACGAAC-GATGTA
*
420357 AATGAAC-A--TA
1 AACGAACGATGTA
420367 AACGAACG
1 AACGAACG
420375 TAAACGAACA
Statistics
Matches: 55, Mismatches: 2, Indels: 21
0.71 0.03 0.27
Matches are distributed among these distances:
10 22 0.40
12 13 0.24
14 20 0.36
ACGTcount: A:0.49, C:0.16, G:0.23, T:0.12
Consensus pattern (13 bp):
AACGAACGATGTA
Found at i:420368 original size:10 final size:10
Alignment explanation
Indices: 420355--420415 Score: 50
Period size: 10 Copynumber: 5.8 Consensus size: 10
420345 CGAACAGATG
420355 TAAATGAACA
1 TAAATGAACA
* *
420365 TAAACGAACG
1 TAAATGAACA
*
420375 TAAACGAACACAA
1 TAAATG-A-AC-A
* *
420388 TAAATTAACG
1 TAAATGAACA
420398 TAAATGAACA
1 TAAATGAACA
420408 TAAATGAA
1 TAAATGAA
420416 AATAGATTTC
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
10 30 0.75
11 3 0.08
12 3 0.08
13 4 0.10
ACGTcount: A:0.57, C:0.13, G:0.11, T:0.18
Consensus pattern (10 bp):
TAAATGAACA
Found at i:421698 original size:21 final size:20
Alignment explanation
Indices: 421612--421769 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
421602 AAATGACCAA
**
421612 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
421631 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
421651 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
421671 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
421692 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
421713 CAAATTCGCATTGCGATTTTT
1 CAAAATCGCAACGCGA-TTTT
* *
421734 CAAAATCGCAACGCGAATAT
1 CAAAATCGCAACGCGATTTT
*
421754 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
421770 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 42 0.40
21 45 0.43
22 1 0.01
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:421798 original size:20 final size:20
Alignment explanation
Indices: 421736--421929 Score: 212
Period size: 20 Copynumber: 9.7 Consensus size: 20
421726 CGATTTTTCA
* ** *
421736 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
421756 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
421776 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
421796 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
421816 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
421836 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
421856 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
421876 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
421896 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
*
421917 AAATTGCAACGCG
1 AAATCGCAACGCG
421930 ATATTTAAAG
Statistics
Matches: 145, Mismatches: 24, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 125 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:421820 original size:60 final size:60
Alignment explanation
Indices: 421736--421929 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 60
421726 CGATTTTTCA
* ** * *
421736 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
421796 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
421856 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
*
421917 AAATTGCAACGCG
1 AAATCGCAACGCG
421930 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 22, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 81 0.73
61 30 0.27
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:422351 original size:33 final size:33
Alignment explanation
Indices: 422312--422382 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
422302 TTCACTTAGA
*
422312 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
422345 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
422378 TTTCA
1 TTTCA
422383 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:422505 original size:20 final size:20
Alignment explanation
Indices: 422461--422570 Score: 108
Period size: 21 Copynumber: 5.8 Consensus size: 20
422451 TGCAGAAGAG
*
422461 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
***
422482 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
422502 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
422523 TCGCAAC--GAG-A-G--AA
1 TCGCAACGAGAGAATGAAAA
*
422537 TCGCAACGCGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
422556 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
422571 CGCAACGCGA
Statistics
Matches: 73, Mismatches: 8, Indels: 17
0.74 0.08 0.17
Matches are distributed among these distances:
14 9 0.12
16 4 0.05
17 2 0.03
19 15 0.21
20 20 0.27
21 23 0.32
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:422518 original size:41 final size:38
Alignment explanation
Indices: 422454--422570 Score: 145
Period size: 41 Copynumber: 3.1 Consensus size: 38
422444 TTCAATTTGC
* *
422454 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
422492 AGAATGACTGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
422533 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
422566 AGAAT
1 AGAAT
422571 CGCAACGCGA
Statistics
Matches: 71, Mismatches: 3, Indels: 13
0.82 0.03 0.15
Matches are distributed among these distances:
33 23 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 33 0.46
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:422540 original size:14 final size:14
Alignment explanation
Indices: 422521--422577 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
422511 GAGAAATGAA
422521 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
422535 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
422554 AATCGCAACGAGAG
1 AATCGCAACGAGAG
422568 AATCGCAACG
1 AATCGCAACG
422578 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:422553 original size:33 final size:33
Alignment explanation
Indices: 422513--422593 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
422503 CGCAACGAGA
422513 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
422546 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
422579 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
422594 TTGCGATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:422611 original size:19 final size:19
Alignment explanation
Indices: 422589--422686 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
422579 GAAACCAAAA
*
422589 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
422608 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
422622 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
422641 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
422655 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
422674 TCGCGTTGCGATT
1 TCGCGTTGCGATT
422687 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.23, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:422630 original size:14 final size:14
Alignment explanation
Indices: 422611--422700 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
422601 TTTCATTTCG
422611 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
422625 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
422644 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
422658 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
422677 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
422691 CGTTGCGATT
1 CGTTGCGATT
422701 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 1 0.02
16 5 0.08
17 5 0.08
18 1 0.02
19 20 0.32
ACGTcount: A:0.09, C:0.24, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Done.