Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr13
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: 91551117
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2824764 characters in sequence are not A, C, G, or T
File 170 of 276
Found at i:55657490 original size:44 final size:41
Alignment explanation
Indices: 55657437--55657527 Score: 101
Period size: 44 Copynumber: 2.1 Consensus size: 41
55657427 TTATTATTGG
* *
55657437 TTTTATAAAATTTGAAATGTATATTTAAAATGTTTTATAATATTA
1 TTTT-TAAAATTTGAAATATATATTTAAAA--TTTTA-AATATAA
* * *
55657482 TTTTTAAAATTTTAAATATATTTTTTAAATTTTAAATATAA
1 TTTTTAAAATTTGAAATATATATTTAAAATTTTAAATATAA
55657523 TTTTT
1 TTTTT
55657528 TTAATATTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
41 11 0.27
42 5 0.12
44 21 0.51
45 4 0.10
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (41 bp):
TTTTTAAAATTTGAAATATATATTTAAAATTTTAAATATAA
Found at i:55657505 original size:20 final size:20
Alignment explanation
Indices: 55657437--55657527 Score: 92
Period size: 20 Copynumber: 4.2 Consensus size: 20
55657427 TTATTATTGG
* *
55657437 TTTTATAAAATTTGAAATGTA
1 TTTT-TAAAATTTTAAATATA
*
55657458 TATTTAAAATGTTTTATAATATTA
1 TTTTTAAAA--TTTTA-AATA-TA
55657482 TTTTTAAAATTTTAAATATA
1 TTTTTAAAATTTTAAATATA
*
55657502 TTTTTTAAATTTTAAATATAA
1 TTTTTAAAATTTTAAATAT-A
55657523 TTTTT
1 TTTTT
55657528 TTAATATTAT
Statistics
Matches: 60, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
20 25 0.42
21 13 0.22
22 9 0.15
23 3 0.05
24 10 0.17
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (20 bp):
TTTTTAAAATTTTAAATATA
Found at i:55659176 original size:30 final size:30
Alignment explanation
Indices: 55659141--55659219 Score: 104
Period size: 30 Copynumber: 2.6 Consensus size: 30
55659131 TGGTTACTCT
* *
55659141 GGGTGAAATGAACTCAAACAGCCTATGTCC
1 GGGTGATATGAACTCAAACAGCCCATGTCC
** *
55659171 GGGTGATATGAACTTGAACCGCCCATGTCC
1 GGGTGATATGAACTCAAACAGCCCATGTCC
*
55659201 GGGTGATATTAACTCAAAC
1 GGGTGATATGAACTCAAAC
55659220 TGCTCATATC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.30, C:0.23, G:0.24, T:0.23
Consensus pattern (30 bp):
GGGTGATATGAACTCAAACAGCCCATGTCC
Found at i:55661131 original size:26 final size:26
Alignment explanation
Indices: 55661102--55661155 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
55661092 AAAAAAGACT
55661102 TATTTTTATTGAATCGATATCTATAA
1 TATTTTTATTGAATCGATATCTATAA
55661128 TATTTTTATTGAATCGATATCTATAA
1 TATTTTTATTGAATCGATATCTATAA
55661154 TA
1 TA
55661156 ATATATAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.50
Consensus pattern (26 bp):
TATTTTTATTGAATCGATATCTATAA
Found at i:55661905 original size:21 final size:23
Alignment explanation
Indices: 55661879--55661926 Score: 73
Period size: 21 Copynumber: 2.2 Consensus size: 23
55661869 TGACCAGTTG
*
55661879 TAATATATATTTTTA-AT-TTTT
1 TAATATAAATTTTTATATATTTT
55661900 TAATATAAATTTTTATATATTTT
1 TAATATAAATTTTTATATATTTT
55661923 TAAT
1 TAAT
55661927 TTTTTAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 14 0.58
22 2 0.08
23 8 0.33
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
TAATATAAATTTTTATATATTTT
Found at i:55661912 original size:14 final size:14
Alignment explanation
Indices: 55661893--55661944 Score: 59
Period size: 14 Copynumber: 3.5 Consensus size: 14
55661883 ATATATTTTT
55661893 AATTTTTTAATATA
1 AATTTTTTAATATA
* *
55661907 AATTTTTATATATTTTT
1 AATTTTT-TA-A-TATA
55661924 AATTTTTTAATATA
1 AATTTTTTAATATA
55661938 AATTTTT
1 AATTTTT
55661945 ACTTTTTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
14 16 0.52
15 3 0.10
16 3 0.10
17 9 0.29
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
AATTTTTTAATATA
Found at i:55661920 original size:31 final size:31
Alignment explanation
Indices: 55661882--55661945 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
55661872 CCAGTTGTAA
55661882 TATATATTTTTAATTTTTTAATATAAATTTT
1 TATATATTTTTAATTTTTTAATATAAATTTT
55661913 TATATATTTTTAATTTTTTAATATAAATTTT
1 TATATATTTTTAATTTTTTAATATAAATTTT
55661944 TA
1 TA
55661946 CTTTTTAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (31 bp):
TATATATTTTTAATTTTTTAATATAAATTTT
Found at i:55661942 original size:21 final size:21
Alignment explanation
Indices: 55661913--55661967 Score: 76
Period size: 20 Copynumber: 2.6 Consensus size: 21
55661903 TATAAATTTT
*
55661913 TATATATTTTTAATTTTTTAA
1 TATATATTTTTAACTTTTTAA
*
55661934 TATAAATTTTT-ACTTTTTAA
1 TATATATTTTTAACTTTTTAA
55661954 TATATATATTTTAA
1 TATATAT-TTTTAA
55661968 AGAAAGTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 14 0.48
21 14 0.48
22 1 0.03
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
TATATATTTTTAACTTTTTAA
Found at i:55662131 original size:15 final size:15
Alignment explanation
Indices: 55662107--55662142 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
55662097 ATCTTTAAAA
55662107 ATAA-TTAAAAAATT
1 ATAATTTAAAAAATT
55662121 ATAATTTAAAAAATT
1 ATAATTTAAAAAATT
55662136 AT-ATTTA
1 ATAATTTA
55662143 GATTTAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATAATTTAAAAAATT
Found at i:55662149 original size:20 final size:22
Alignment explanation
Indices: 55662124--55662164 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
55662114 AAAAATTATA
55662124 ATTTAAA-AAAT-TATATTTAG
1 ATTTAAATAAATGTATATTTAG
55662144 ATTTAAATAAATGTATATTTA
1 ATTTAAATAAATGTATATTTA
55662165 AAATTTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.37
21 4 0.21
22 8 0.42
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (22 bp):
ATTTAAATAAATGTATATTTAG
Found at i:55662248 original size:16 final size:16
Alignment explanation
Indices: 55662222--55662308 Score: 62
Period size: 16 Copynumber: 5.7 Consensus size: 16
55662212 TTGACAGGTC
55662222 ATATCTTTAAAAATAAT
1 ATAT-TTTAAAAATAAT
* **
55662239 ATATTTTAAATATTTT
1 ATATTTTAAAAATAAT
55662255 ATATTATT--AAA-AA-
1 ATATT-TTAAAAATAAT
*
55662268 ATA-TTTAAAAGTAAT
1 ATATTTTAAAAATAAT
55662283 A-ATTTTAAAAA-ATAT
1 ATATTTTAAAAATA-AT
55662298 ATATTTTAAAA
1 ATATTTTAAAA
55662309 TTTTAAAAAT
Statistics
Matches: 54, Mismatches: 8, Indels: 17
0.68 0.10 0.22
Matches are distributed among these distances:
11 2 0.04
12 1 0.02
13 5 0.09
14 4 0.07
15 13 0.24
16 23 0.43
17 6 0.11
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (16 bp):
ATATTTTAAAAATAAT
Found at i:55662301 original size:43 final size:43
Alignment explanation
Indices: 55662227--55662323 Score: 112
Period size: 43 Copynumber: 2.3 Consensus size: 43
55662217 AGGTCATATC
* * *
55662227 TTTAAAAATAATATATTTTAAATATTTTATATTATTAAAAAATA
1 TTTAAAAATAATATATTTTAAAAAATATATATT-TTAAAAAATA
*
55662271 TTTAAAAGTAATA-ATTTTAAAAAATATATATTTT--AAAAT-
1 TTTAAAAATAATATATTTTAAAAAATATATATTTTAAAAAATA
*
55662310 TTTAAAAATGATAT
1 TTTAAAAATAATAT
55662324 TATAAAACAT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
39 11 0.24
40 5 0.11
42 2 0.04
43 16 0.35
44 12 0.26
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (43 bp):
TTTAAAAATAATATATTTTAAAAAATATATATTTTAAAAAATA
Found at i:55662323 original size:22 final size:24
Alignment explanation
Indices: 55662283--55662330 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 24
55662273 TAAAAGTAAT
* *
55662283 AATTTTAAAAAATATATATTTTAA
1 AATTTTAAAAAATAGATATTATAA
55662307 AATTTT-AAAAAT-GATATTATAA
1 AATTTTAAAAAATAGATATTATAA
55662329 AA
1 AA
55662331 CATTTCAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 10 0.45
23 6 0.27
24 6 0.27
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (24 bp):
AATTTTAAAAAATAGATATTATAA
Found at i:55662432 original size:24 final size:21
Alignment explanation
Indices: 55662405--55662464 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 21
55662395 TGACAAATAA
55662405 AAAAAACTTAAAAAGTAAATAAAT
1 AAAAAACTTAAAAAG--AA-AAAT
55662429 AAAAAACTTAAAAAGAAAAAT
1 AAAAAACTTAAAAAGAAAAAT
* *
55662450 AAAAAAATGAAAAAG
1 AAAAAACTTAAAAAG
55662465 GACAAAGAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 17 0.50
22 2 0.06
24 15 0.44
ACGTcount: A:0.75, C:0.03, G:0.07, T:0.15
Consensus pattern (21 bp):
AAAAAACTTAAAAAGAAAAAT
Found at i:55662449 original size:25 final size:23
Alignment explanation
Indices: 55662399--55662456 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 23
55662389 AATAAATGAC
*
55662399 AAAT-AAAAAAAACTTAAAAAGT
1 AAATAAAAAAAAACTTAAAAAGA
55662421 AAATAAATAAAAAACTTAAAAAGAA
1 AAATAAA-AAAAAACTTAAAAAG-A
55662446 AAATAAAAAAA
1 AAATAAAAAAA
55662457 TGAAAAAGGA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 4 0.12
23 2 0.06
24 19 0.59
25 7 0.22
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.16
Consensus pattern (23 bp):
AAATAAAAAAAAACTTAAAAAGA
Found at i:55666305 original size:8 final size:9
Alignment explanation
Indices: 55666287--55666316 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
55666277 AAAAGTCTCC
55666287 AATTAAAAA
1 AATTAAAAA
55666296 AATTAAAAA
1 AATTAAAAA
55666305 AATTAAAAA
1 AATTAAAAA
55666314 AAT
1 AAT
55666317 CAATTAAACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (9 bp):
AATTAAAAA
Found at i:55668098 original size:22 final size:22
Alignment explanation
Indices: 55668070--55668129 Score: 104
Period size: 22 Copynumber: 2.8 Consensus size: 22
55668060 AATAGTTGGG
*
55668070 CAGCTTGGGGAAGAGAAATCAA
1 CAGCTTGGGAAAGAGAAATCAA
55668092 CAGCTTGGGAAAGAGAAATCAA
1 CAGCTTGGGAAAGAGAAATCAA
55668114 CAGCTTGGGAAA-AGAA
1 CAGCTTGGGAAAGAGAA
55668130 GCATCAGCTC
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
21 4 0.11
22 33 0.89
ACGTcount: A:0.43, C:0.13, G:0.30, T:0.13
Consensus pattern (22 bp):
CAGCTTGGGAAAGAGAAATCAA
Found at i:55669016 original size:20 final size:19
Alignment explanation
Indices: 55668993--55669048 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 19
55668983 TTTTGTACAA
55668993 TTTATATATTTTAAAATATT
1 TTTATATATTTTAAAAT-TT
* *
55669013 TTTATGA-CTTTTAATATTT
1 TTTAT-ATATTTTAAAATTT
*
55669032 TTTTTATCATTTTAAAA
1 TTTATAT-ATTTTAAAA
55669049 AGAAAAAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
18 1 0.04
19 6 0.21
20 20 0.71
21 1 0.04
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.61
Consensus pattern (19 bp):
TTTATATATTTTAAAATTT
Found at i:55676065 original size:46 final size:46
Alignment explanation
Indices: 55676007--55676181 Score: 298
Period size: 46 Copynumber: 3.8 Consensus size: 46
55675997 TGTAACCCGC
* * * *
55676007 CCATAAGCGAACTCGGACTCAACTCAATGA-TCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGT-TCGGACATTCGCAT
55676053 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
55676099 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
55676145 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
55676182 TGCTCAACCA
Statistics
Matches: 124, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
46 123 0.99
47 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:55690289 original size:50 final size:45
Alignment explanation
Indices: 55690230--55690337 Score: 128
Period size: 44 Copynumber: 2.3 Consensus size: 45
55690220 CTGTATCAAC
55690230 CTCACACACTAAGTTCCAATATACAGATATATAGCTGAAGCTATCTCGAT
1 CTCACACACTAAGTTCCAA-AT----ATATATAGCTGAAGCTATCTCGAT
* * *
55690280 CTCGCACACTAAG-TGCAAATATATATAGCTGAAGCTATCTTGAT
1 CTCACACACTAAGTTCCAAATATATATAGCTGAAGCTATCTCGAT
*
55690324 TTCACACACTAAGT
1 CTCACACACTAAGT
55690338 GCACATAATT
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
44 34 0.65
48 2 0.04
49 4 0.08
50 12 0.23
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.29
Consensus pattern (45 bp):
CTCACACACTAAGTTCCAAATATATATAGCTGAAGCTATCTCGAT
Found at i:55690317 original size:44 final size:44
Alignment explanation
Indices: 55690256--55690354 Score: 148
Period size: 44 Copynumber: 2.3 Consensus size: 44
55690246 CAATATACAG
*
55690256 ATATATAGCTGAAGCTATCTCGATCTCGCACACTAAGTGCAAAT
1 ATATATAGCTGAAGCTATCTCGATCTCACACACTAAGTGCAAAT
* * *
55690300 ATATATAGCTGAAGCTATCTTGATTTCACACACTAAGTGCACAT
1 ATATATAGCTGAAGCTATCTCGATCTCACACACTAAGTGCAAAT
55690344 A-AT-TAGCTGAA
1 ATATATAGCTGAA
55690355 TCATCGTTGA
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
42 8 0.16
43 2 0.04
44 41 0.80
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.29
Consensus pattern (44 bp):
ATATATAGCTGAAGCTATCTCGATCTCACACACTAAGTGCAAAT
Found at i:55690865 original size:21 final size:20
Alignment explanation
Indices: 55690841--55690881 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
55690831 ACTTGTATAA
55690841 CTATCATCAAACATTCAAAAT
1 CTATCATCAAACA-TCAAAAT
*
55690862 CTATCATTAAACATCAAAAT
1 CTATCATCAAACATCAAAAT
55690882 ACTCATGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.29
Consensus pattern (20 bp):
CTATCATCAAACATCAAAAT
Found at i:55695158 original size:17 final size:18
Alignment explanation
Indices: 55695129--55695171 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
55695119 CAGAATAGCC
55695129 AAAGGGAAGAAAG-AAAG
1 AAAGGGAAGAAAGAAAAG
55695146 AAAGGAGAA-AAAGAAAAG
1 AAAGG-GAAGAAAGAAAAG
*
55695164 AAAAGGAA
1 AAAGGGAA
55695172 AAATTAGGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 12 0.52
18 11 0.48
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (18 bp):
AAAGGGAAGAAAGAAAAG
Found at i:55695548 original size:11 final size:11
Alignment explanation
Indices: 55695522--55695555 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
55695512 GATTAAAATT
*
55695522 GAAATTAAAGTA
1 GAAATTGAA-TA
55695534 GAAATTGAATA
1 GAAATTGAATA
55695545 GAAATTGAATA
1 GAAATTGAATA
55695556 ATAAATTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 13 0.62
12 8 0.38
ACGTcount: A:0.56, C:0.00, G:0.18, T:0.26
Consensus pattern (11 bp):
GAAATTGAATA
Found at i:55696359 original size:47 final size:47
Alignment explanation
Indices: 55696306--55696406 Score: 114
Period size: 47 Copynumber: 2.1 Consensus size: 47
55696296 GCCAGTGTGT
** * *
55696306 CGTACTGCTACT-GTTACTTCGGTTTAATCCGATGAGGTACTGAGTAC
1 CGTACTGCTACTAGTTACTTCGG-CAAAGCCGATGAGGCACTGAGTAC
* * *
55696353 CGTACTGTTACTATTTACTTCGGCAAAGCCGATGAGGCACTGAGTGC
1 CGTACTGCTACTAGTTACTTCGGCAAAGCCGATGAGGCACTGAGTAC
*
55696400 CATACTG
1 CGTACTG
55696407 GTGTGTTGGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
47 36 0.80
48 9 0.20
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.31
Consensus pattern (47 bp):
CGTACTGCTACTAGTTACTTCGGCAAAGCCGATGAGGCACTGAGTAC
Found at i:55696510 original size:36 final size:36
Alignment explanation
Indices: 55696470--55696551 Score: 101
Period size: 36 Copynumber: 2.3 Consensus size: 36
55696460 TGAATAAAGG
* * * *
55696470 TACTGAATGACTGACTGTTACTGAATAATTGATTGT
1 TACTGAATGAATGACTGCTACTAAAAAATTGATTGT
* *
55696506 TACTGAATAAATGATTGCTACTAAAAAATTGATTGT
1 TACTGAATGAATGACTGCTACTAAAAAATTGATTGT
*
55696542 TTCTGAATGA
1 TACTGAATGA
55696552 TATTGATTAA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (36 bp):
TACTGAATGAATGACTGCTACTAAAAAATTGATTGT
Found at i:55696520 original size:18 final size:18
Alignment explanation
Indices: 55696470--55696549 Score: 81
Period size: 18 Copynumber: 4.4 Consensus size: 18
55696460 TGAATAAAGG
* * *
55696470 TACTGAATGACTGACTGT
1 TACTGAATAAATGATTGT
*
55696488 TACTGAATAATTGATTGT
1 TACTGAATAAATGATTGT
*
55696506 TACTGAATAAATGATTGC
1 TACTGAATAAATGATTGT
*
55696524 TACT-AAAAAATTGATTGT
1 TACTGAATAAA-TGATTGT
*
55696542 TTCTGAAT
1 TACTGAAT
55696550 GATATTGATT
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
17 5 0.10
18 44 0.86
19 2 0.04
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.39
Consensus pattern (18 bp):
TACTGAATAAATGATTGT
Found at i:55696576 original size:28 final size:28
Alignment explanation
Indices: 55696532--55696585 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
55696522 GCTACTAAAA
* **
55696532 AATTGATTGTTTCTGAATGATATTGATT
1 AATTGATTGTATCTGAAAAATATTGATT
55696560 AATTGATTGGTAT-TGAAAAATATTGA
1 AATTGATT-GTATCTGAAAAATATTGA
55696586 CTGATATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
28 19 0.86
29 3 0.14
ACGTcount: A:0.35, C:0.02, G:0.19, T:0.44
Consensus pattern (28 bp):
AATTGATTGTATCTGAAAAATATTGATT
Found at i:55697447 original size:21 final size:21
Alignment explanation
Indices: 55697416--55697471 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
55697406 CAGGCTCTCA
*
55697416 ACATAGCCGTGTGACCTAGCG
1 ACATCGCCGTGTGACCTAGCG
* * *
55697437 ATATCGCCGTGTGATCTAGTG
1 ACATCGCCGTGTGACCTAGCG
*
55697458 ACATGGCCGTGTGA
1 ACATCGCCGTGTGA
55697472 GTCACACACC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.21, C:0.23, G:0.30, T:0.25
Consensus pattern (21 bp):
ACATCGCCGTGTGACCTAGCG
Found at i:55701347 original size:50 final size:47
Alignment explanation
Indices: 55701281--55701394 Score: 140
Period size: 46 Copynumber: 2.4 Consensus size: 47
55701271 AGTTGTATCA
*
55701281 ATCTTGCACACTAAGTGCCAATATAAATATATATAGCTAAAGCTATCTCG
1 ATCTCGCACACTAAGTGCCAA-AT--ATATATATAGCTAAAGCTATCTCG
* * *
55701331 ATCTCGCACACCAAGTG-CAAATATATATATAGCTGAAGCTATCTTG
1 ATCTCGCACACTAAGTGCCAAATATATATATAGCTAAAGCTATCTCG
* *
55701377 ATTTCGTACACTAAGTGC
1 ATCTCGCACACTAAGTGC
55701395 ACATAATTAG
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
46 36 0.64
48 2 0.04
49 3 0.05
50 15 0.27
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (47 bp):
ATCTCGCACACTAAGTGCCAAATATATATATAGCTAAAGCTATCTCG
Found at i:55701920 original size:21 final size:20
Alignment explanation
Indices: 55701896--55701936 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
55701886 ACTTGTATAA
55701896 CTATCATCAAACATTCAAAAT
1 CTATCATCAAACA-TCAAAAT
*
55701917 CTATCATTAAACATCAAAAT
1 CTATCATCAAACATCAAAAT
55701937 ACTCATGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.29
Consensus pattern (20 bp):
CTATCATCAAACATCAAAAT
Found at i:55709078 original size:53 final size:53
Alignment explanation
Indices: 55708998--55709101 Score: 190
Period size: 53 Copynumber: 2.0 Consensus size: 53
55708988 ATACTCAGAT
* *
55708998 TTTGACTTGGAATAGATCAATATATCATTGATAAACACAACCAAAAATCTAAA
1 TTTGACTTGGAATAGATCAATATATCATCGATAAACAAAACCAAAAATCTAAA
55709051 TTTGACTTGGAATAGATCAATATATCATCGATAAACAAAACCAAAAATCTA
1 TTTGACTTGGAATAGATCAATATATCATCGATAAACAAAACCAAAAATCTA
55709102 TCCAAATAAG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.47, C:0.15, G:0.10, T:0.28
Consensus pattern (53 bp):
TTTGACTTGGAATAGATCAATATATCATCGATAAACAAAACCAAAAATCTAAA
Found at i:55715676 original size:25 final size:26
Alignment explanation
Indices: 55715648--55715698 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
55715638 CATTTATGCT
* *
55715648 CTTTCGAGC-CATGATCAGTAAGCTC
1 CTTTCAAGCTCATGAACAGTAAGCTC
*
55715673 CTTTCAAGCTGATGAACAGTAAGCTC
1 CTTTCAAGCTCATGAACAGTAAGCTC
55715699 ATACGAGCTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.27
Consensus pattern (26 bp):
CTTTCAAGCTCATGAACAGTAAGCTC
Found at i:55715721 original size:23 final size:22
Alignment explanation
Indices: 55715691--55715780 Score: 65
Period size: 23 Copynumber: 3.8 Consensus size: 22
55715681 CTGATGAACA
55715691 GTAAGCTCATACGAGCTGAAACG
1 GTAAGCTCATACGAGCTGAAA-G
* *
55715714 GTAAGCTCCA-ATGAGATGAAAG
1 GTAAGCT-CATACGAGCTGAAAG
* *
55715736 AGTAAGCTCTTACGAGCTAATATATTG
1 -GTAAGCTCATACGAGCTGA-A-A--G
*
55715763 TTAAGCTCATACGAGCTG
1 GTAAGCTCATACGAGCTG
55715781 TGGTGAGTCC
Statistics
Matches: 51, Mismatches: 9, Indels: 11
0.72 0.13 0.15
Matches are distributed among these distances:
22 2 0.04
23 29 0.57
24 3 0.06
25 1 0.02
26 15 0.29
27 1 0.02
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.24
Consensus pattern (22 bp):
GTAAGCTCATACGAGCTGAAAG
Found at i:55717105 original size:19 final size:21
Alignment explanation
Indices: 55717067--55717107 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
55717057 TGTTTTTGTA
*
55717067 TAGCTTCCTCATGTTCCCATG
1 TAGCTTCCTCATGATCCCATG
55717088 TAGCTTCCTC-T-ATCCCATG
1 TAGCTTCCTCATGATCCCATG
55717107 T
1 T
55717108 TTATGCCAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 1 0.05
21 10 0.53
ACGTcount: A:0.15, C:0.34, G:0.12, T:0.39
Consensus pattern (21 bp):
TAGCTTCCTCATGATCCCATG
Found at i:55742987 original size:34 final size:34
Alignment explanation
Indices: 55742948--55743017 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
55742938 GTACCAGTGA
*
55742948 TGACGTCAAGAGCATCTCTGTCTTCTCGGCGACG
1 TGACGTCAAGAGCATCTCTGTCCTCTCGGCGACG
*
55742982 TGACGTCAAGAGCATCTCTGTCCTCTCTGCGACG
1 TGACGTCAAGAGCATCTCTGTCCTCTCGGCGACG
55743016 TG
1 TG
55743018 TAGCATGAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.17, C:0.30, G:0.26, T:0.27
Consensus pattern (34 bp):
TGACGTCAAGAGCATCTCTGTCCTCTCGGCGACG
Found at i:55764924 original size:33 final size:33
Alignment explanation
Indices: 55764882--55764948 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
55764872 ATATTAAAAT
55764882 TCAATAGAGATTGAACTTTTATAATTTAGTCTA
1 TCAATAGAGATTGAACTTTTATAATTTAGTCTA
55764915 TCAATAGAGATTGAACTTTTATAATTTAGTCTA
1 TCAATAGAGATTGAACTTTTATAATTTAGTCTA
55764948 T
1 T
55764949 GAACTATAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.36, C:0.09, G:0.12, T:0.43
Consensus pattern (33 bp):
TCAATAGAGATTGAACTTTTATAATTTAGTCTA
Found at i:55770484 original size:40 final size:40
Alignment explanation
Indices: 55770440--55770703 Score: 360
Period size: 40 Copynumber: 6.7 Consensus size: 40
55770430 GCTCCTCGTT
* *
55770440 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
55770480 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
55770520 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
55770560 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
55770600 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
55770639 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAT-TTAGTAAC-TCGCA
55770680 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
55770704 CATCATTCAA
Statistics
Matches: 206, Mismatches: 12, Indels: 13
0.89 0.05 0.06
Matches are distributed among these distances:
38 2 0.01
39 49 0.24
40 146 0.71
41 9 0.04
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:55778610 original size:42 final size:42
Alignment explanation
Indices: 55778490--55778722 Score: 393
Period size: 42 Copynumber: 5.6 Consensus size: 42
55778480 CAAACACATT
* * * * *
55778490 TGCCTTCGGGTCTTAACCCGG--ACATATCAACTTGCATAAT
1 TGCCTTCGGGTCTTAGCCCGGATATATATCAACTCGCACAAA
55778530 TGCCTTCGGGTCTTAGCCCGG--ATATATCAACTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATATCAACTCGCACAAA
55778570 TGCCTTCGGGTCTTAGCCCGGATATATATCAACTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATATCAACTCGCACAAA
55778612 TGCCTTCGGGTCTTAGCCCGGATATATATCAACTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATATCAACTCGCACAAA
55778654 TGCCTTCGGGTCTTAGCCCGGATATATATCAACTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATATCAACTCGCACAAA
55778696 TGCCTTCGGGTCTTAGCCCGGATATAT
1 TGCCTTCGGGTCTTAGCCCGGATATAT
55778723 TCCAATGCTC
Statistics
Matches: 186, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
40 56 0.30
42 130 0.70
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.27
Consensus pattern (42 bp):
TGCCTTCGGGTCTTAGCCCGGATATATATCAACTCGCACAAA
Found at i:55785188 original size:30 final size:31
Alignment explanation
Indices: 55785140--55785220 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 31
55785130 GCCCGTGTAG
* *
55785140 GTGCCTGTGTGGGTCCACACGCCC-ATATGGC
1 GTGCCCGTGT-GGCCCACACGCCCAATATGGC
* *
55785171 GTGCCGGTGTGGCCCACACGCCCAATTTGGC
1 GTGCCCGTGTGGCCCACACGCCCAATATGGC
*
55785202 ATAGCCCGTGTGGCCCACA
1 GT-GCCCGTGTGGCCCACA
55785221 AGGCCACACC
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
30 12 0.28
31 16 0.37
32 15 0.35
ACGTcount: A:0.15, C:0.35, G:0.31, T:0.20
Consensus pattern (31 bp):
GTGCCCGTGTGGCCCACACGCCCAATATGGC
Found at i:55785218 original size:32 final size:30
Alignment explanation
Indices: 55785154--55785220 Score: 89
Period size: 32 Copynumber: 2.2 Consensus size: 30
55785144 CTGTGTGGGT
* *
55785154 CCACACGCCCATATGGCGTGCCGGTGTGGC
1 CCACACGCCCATATGGCATGCCCGTGTGGC
*
55785184 CCACACGCCCAATTTGGCATAGCCCGTGTGGC
1 CCACACGCCC-ATATGGCAT-GCCCGTGTGGC
55785216 CCACA
1 CCACA
55785221 AGGCCACACC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
30 10 0.31
31 7 0.22
32 15 0.47
ACGTcount: A:0.18, C:0.39, G:0.27, T:0.16
Consensus pattern (30 bp):
CCACACGCCCATATGGCATGCCCGTGTGGC
Found at i:55794575 original size:3 final size:3
Alignment explanation
Indices: 55794561--55794610 Score: 55
Period size: 3 Copynumber: 16.3 Consensus size: 3
55794551 GAGAGAAAGG
* * * *
55794561 AGA AGG AGA AGA AGA AGA AAA AGA AGA AGA CCGA AGA TGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA -AGA AGA AGA AGA AGA
55794607 AGA A
1 AGA A
55794611 AAAAAGGTAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
3 36 0.95
4 2 0.05
ACGTcount: A:0.62, C:0.04, G:0.32, T:0.02
Consensus pattern (3 bp):
AGA
Found at i:55794786 original size:16 final size:18
Alignment explanation
Indices: 55794750--55794786 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
55794740 TAGTGTTTTG
*
55794750 TATTTTGTTATAGTTATT
1 TATTTTGTTATAGTAATT
55794768 TATTTTGTTA-A-TAATT
1 TATTTTGTTATAGTAATT
55794784 TAT
1 TAT
55794787 GGGATTAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 1 0.06
18 10 0.56
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (18 bp):
TATTTTGTTATAGTAATT
Found at i:55795100 original size:95 final size:95
Alignment explanation
Indices: 55794988--55795293 Score: 317
Period size: 95 Copynumber: 3.0 Consensus size: 95
55794978 ATTTTATAGC
* * **
55794988 TATTTTATTAGTAATTTATGATTAGGCTACATAAATTGCAAGTGTTTAGTGGTTTAGTGTATTAT
1 TATTTTGTTAGTAATTTATGATTAGGTTACATAAATTGTTAGTGTTTAGTGGTTTAGTGTATTAT
55795053 GATTTTTTAGTAATGTATTTTAAAAAAAAT
66 GATTTTTTAGTAATGTATTTTAAAAAAAAT
55795083 TATTTTGTTAGTAATTTATGATTAGGTTACATAAATTGTTAGTGTTTAGTGGTTTAGTGTATTAG
1 TATTTTGTTAGTAATTTATGATTAGGTTACATAAATTGTTAGTGTTTAGTGGTTTAGTGTA-T--
*
55795148 AGTATTGTGATTTTTTTAGTAATAATATGTTTTAAAAAATAAT
63 --TA---TGA-TTTTTTAGTAAT-GTA--TTTTAAAAAA-AAT
* *
55795191 AATTTTATAGCTATTTTATTTGTAATTTATGATTAGGTTATATAAATTGTTAGTGTTTAGTGGTT
1 TA-TTT-T-G-----TTA---GTAATTTATGATTAGGTTACATAAATTGTTAGTGTTTAGTGGTT
*
55795256 TAGTGTATTATAATTTTTTAGTAATGTA-TTTAAAAAAA
55 TAGTGTATTATGATTTTTTAGTAATGTATTTTAAAAAAA
55795294 TAAATTTTTA
Statistics
Matches: 178, Mismatches: 9, Indels: 38
0.79 0.04 0.17
Matches are distributed among these distances:
95 57 0.32
96 1 0.01
100 2 0.01
103 3 0.02
104 12 0.07
105 3 0.02
106 9 0.05
107 10 0.06
108 4 0.02
109 5 0.03
110 13 0.07
111 3 0.02
114 2 0.01
116 3 0.02
118 1 0.01
119 50 0.28
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.50
Consensus pattern (95 bp):
TATTTTGTTAGTAATTTATGATTAGGTTACATAAATTGTTAGTGTTTAGTGGTTTAGTGTATTAT
GATTTTTTAGTAATGTATTTTAAAAAAAAT
Found at i:55795259 original size:214 final size:209
Alignment explanation
Indices: 55794768--55795295 Score: 677
Period size: 214 Copynumber: 2.4 Consensus size: 209
55794758 TATAGTTATT
* * * * * *
55794768 TATTTTGTTAATAATTTATGGGATTAGGT-TACAAATTGTTAGTGTTTAGTTGTTTAGGGTATTG
1 TATTTTATTAGTAATTTAT--GATTAGGTATATAAATTGTTAGTGTTTAGTGGTTTAGTGTATTA
*
55794832 TGATTTTTTAGTAATTTAATTTTTTAAAAAATAATTTTATAGTTATTTTGTTAGTAATTTATGAT
64 TGATTTTTTAGTAATGT-A--TTTT--AAAA-AA----ATAGTTATTTTGTTAGTAATTTATGAT
* *
55794897 AAGGTTATAAAAATTGCTAGTGTTTAGTGGTTTAGTGTATTAGTGTATTGTGGTTTTTTTAATAA
119 AAGGTTACAAAAATTGCTAGTGTTTAGTGGTTTAGTGTATTAGAGTATTGTGGTTTTTTTAATAA
55794962 TATATTTTAAAAAATAATTTTATAGC
184 TATATTTTAAAAAATAATTTTATAGC
* **
55794988 TATTTTATTAGTAATTTATGATTAGGCTACATAAATTGCAAGTGTTTAGTGGTTTAGTGTATTAT
1 TATTTTATTAGTAATTTATGATTAGG-TATATAAATTGTTAGTGTTTAGTGGTTTAGTGTATTAT
* *
55795053 GATTTTTTAGTAATGTATTTTAAAAAAA-A-TTATTTTGTTAGTAATTTATGATTAGGTTACATA
65 GATTTTTTAGTAATGTATTTTAAAAAAATAGTTATTTTGTTAGTAATTTATGATAAGGTTACAAA
* * *
55795116 AATTGTTAGTGTTTAGTGGTTTAGTGTATTAGAGTATTGTGATTTTTTTAGTAATAATATGTTTT
130 AATTGCTAGTGTTTAGTGGTTTAGTGTATTAGAGTATTGTG-GTTTTTT--TAATAATATATTTT
55795181 AAAAAATAATAATTTTATAGC
192 --AAAA-AATAATTTTATAGC
*
55795202 TATTTTATTTGTAATTTATGATTAGGTTATATAAATTGTTAGTGTTTAGTGGTTTAGTGTATTAT
1 TATTTTATTAGTAATTTATGATTAGG-TATATAAATTGTTAGTGTTTAGTGGTTTAGTGTATTAT
*
55795267 AATTTTTTAGTAATGTA-TTTAAAAAAATA
65 GATTTTTTAGTAATGTATTTTAAAAAAATA
55795296 AATTTTTAGT
Statistics
Matches: 276, Mismatches: 23, Indels: 24
0.85 0.07 0.07
Matches are distributed among these distances:
208 70 0.25
209 7 0.03
210 1 0.00
211 13 0.05
213 14 0.05
214 93 0.34
215 4 0.01
217 4 0.01
218 7 0.03
219 2 0.01
220 61 0.22
ACGTcount: A:0.32, C:0.02, G:0.16, T:0.50
Consensus pattern (209 bp):
TATTTTATTAGTAATTTATGATTAGGTATATAAATTGTTAGTGTTTAGTGGTTTAGTGTATTATG
ATTTTTTAGTAATGTATTTTAAAAAAATAGTTATTTTGTTAGTAATTTATGATAAGGTTACAAAA
ATTGCTAGTGTTTAGTGGTTTAGTGTATTAGAGTATTGTGGTTTTTTTAATAATATATTTTAAAA
AATAATTTTATAGC
Found at i:55795324 original size:106 final size:115
Alignment explanation
Indices: 55795088--55795331 Score: 303
Period size: 119 Copynumber: 2.2 Consensus size: 115
55795078 AAAATTATTT
55795088 TGTTAGTAATTTATGATTAGGTTACATAAATTGTTAGTGTTTAGTGGTTTAGTGTATTAGAGTAT
1 TGTTAGTAATTTATGATTAGGTTACATAAATTGTTAGTGTTTAGTGGTTTAGTGTATTA-AGTA-
*
55795153 TGTGATTTTTTTAGTAATAATATGTTTTAAAAAATAATAATTTTATAGCTATTTTA
64 --T-ATTTTTTTAGTAATAATA-GTTTAAAAAAATAATAATTTTATAGCTATTTTA
*
55795209 T-TT-GTAATTTATGATTAGGTTATATAAATTGTTAGTGTTTAGTGGTTTAGTGTATT-A-TA-A
1 TGTTAGTAATTTATGATTAGGTTACATAAATTGTTAGTGTTTAGTGGTTTAGTGTATTAAGTATA
* * *
55795269 -TTTTTTAGTAAT-GTA-TTTAAAAAAAT-A-AATTTT-TAGTTATTTTG
66 TTTTTTTAGTAATAATAGTTTAAAAAAATAATAATTTTATAGCTATTTTA
*
55795313 TGTTAATAATTTATGATTA
1 TGTTAGTAATTTATGATTA
55795332 TAAATTGTTA
Statistics
Matches: 115, Mismatches: 6, Indels: 19
0.82 0.04 0.14
Matches are distributed among these distances:
104 10 0.09
105 8 0.07
106 14 0.12
107 10 0.09
109 2 0.02
110 12 0.10
111 1 0.01
116 2 0.02
117 1 0.01
119 52 0.45
120 2 0.02
121 1 0.01
ACGTcount: A:0.32, C:0.01, G:0.16, T:0.51
Consensus pattern (115 bp):
TGTTAGTAATTTATGATTAGGTTACATAAATTGTTAGTGTTTAGTGGTTTAGTGTATTAAGTATA
TTTTTTTAGTAATAATAGTTTAAAAAAATAATAATTTTATAGCTATTTTA
Found at i:55795401 original size:15 final size:16
Alignment explanation
Indices: 55795372--55795403 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
55795362 TGTGATTTTT
55795372 TAATGTAACTTTTATA
1 TAATGTAACTTTTATA
55795388 TAATGTAA-TTTTATA
1 TAATGTAACTTTTATA
55795403 T
1 T
55795404 TATTATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (16 bp):
TAATGTAACTTTTATA
Found at i:55797525 original size:33 final size:33
Alignment explanation
Indices: 55797470--55797535 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
55797460 TCCTCTAAAG
* *
55797470 CCGTATCCACCACCGTACTCTACTCCTCCTGGC
1 CCGTATCCACCACCATACTCTACTCCCCCTGGC
** *
55797503 CCGTATCCACCGTCATATTCTACTCCCCCTGGC
1 CCGTATCCACCACCATACTCTACTCCCCCTGGC
55797536 TCAAGTTCAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.15, C:0.47, G:0.12, T:0.26
Consensus pattern (33 bp):
CCGTATCCACCACCATACTCTACTCCCCCTGGC
Found at i:55801237 original size:27 final size:26
Alignment explanation
Indices: 55801155--55801241 Score: 93
Period size: 27 Copynumber: 3.2 Consensus size: 26
55801145 TGTGGGCCCC
*
55801155 ACTAGTCGCGGCTACCAAGAAGGCTCA
1 ACTAGTCGCGCCTACC-AGAAGGCTCA
* * *
55801182 ACAAGTCGCACCTACCATGAAGGCACA
1 ACTAGTCGCGCCTACCA-GAAGGCTCA
* *
55801209 ACTAGTCGCGCCTGCCAGATAGACTCA
1 ACTAGTCGCGCCTACCAGA-AGGCTCA
55801236 ACTAGT
1 ACTAGT
55801242 TGAGCTTGTC
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
26 3 0.06
27 46 0.94
ACGTcount: A:0.31, C:0.31, G:0.22, T:0.16
Consensus pattern (26 bp):
ACTAGTCGCGCCTACCAGAAGGCTCA
Found at i:55807114 original size:18 final size:18
Alignment explanation
Indices: 55807087--55807131 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
55807077 GCCCATACCT
* *
55807087 GACACAAGTCACGGCCAC
1 GACACTAGTCACGCCCAC
*
55807105 GACACTAGTCGCGCCCAC
1 GACACTAGTCACGCCCAC
*
55807123 GACTCTAGT
1 GACACTAGT
55807132 TAAGATAGAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.38, G:0.22, T:0.13
Consensus pattern (18 bp):
GACACTAGTCACGCCCAC
Found at i:55811557 original size:31 final size:31
Alignment explanation
Indices: 55811519--55811599 Score: 144
Period size: 31 Copynumber: 2.6 Consensus size: 31
55811509 CTCAGCATAT
55811519 ACTGGGCCGAAGCCTTTACATTATTCATACC
1 ACTGGGCCGAAGCCTTTACATTATTCATACC
* *
55811550 ACTGGGCCGAAGCCTTTTCATTATTCATATC
1 ACTGGGCCGAAGCCTTTACATTATTCATACC
55811581 ACTGGGCCGAAGCCTTTAC
1 ACTGGGCCGAAGCCTTTAC
55811600 TGTAAACGGT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.30
Consensus pattern (31 bp):
ACTGGGCCGAAGCCTTTACATTATTCATACC
Found at i:55811846 original size:25 final size:25
Alignment explanation
Indices: 55811818--55811887 Score: 113
Period size: 25 Copynumber: 2.8 Consensus size: 25
55811808 CTCTTTTAAT
*
55811818 AACTGGGGCAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
55811843 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
55811868 AACTGGGGCATAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
55811888 GCACTTCCTC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.27
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:55811957 original size:11 final size:11
Alignment explanation
Indices: 55811920--55811983 Score: 80
Period size: 11 Copynumber: 6.1 Consensus size: 11
55811910 ACCCAACCCA
55811920 TGCATAT-ATG
1 TGCATATCATG
**
55811930 TATATATCATG
1 TGCATATCATG
55811941 -GCATATCATG
1 TGCATATCATG
55811951 TGCATATCATG
1 TGCATATCATG
55811962 TGCATATCATG
1 TGCATATCATG
*
55811973 -GCATATTATG
1 TGCATATCATG
55811983 T
1 T
55811984 ACAAATCAGT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
10 22 0.48
11 24 0.52
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (11 bp):
TGCATATCATG
Found at i:55811957 original size:21 final size:21
Alignment explanation
Indices: 55811933--55811983 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 21
55811923 ATATATGTAT
55811933 ATATCATG-GCATATCATGTGC
1 ATATCATGTGCATATCATG-GC
55811954 ATATCATGTGCATATCATGGC
1 ATATCATGTGCATATCATGGC
*
55811975 ATATTATGT
1 ATATCATGT
55811984 ACAAATCAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
21 18 0.64
22 10 0.36
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (21 bp):
ATATCATGTGCATATCATGGC
Found at i:55811972 original size:32 final size:31
Alignment explanation
Indices: 55811920--55811983 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 31
55811910 ACCCAACCCA
*
55811920 TGCATATATGTATATATCATGGCATATCATG
1 TGCATATATGTACATATCATGGCATATCATG
* *
55811951 TGCATATCATGTGCATATCATGGCATATTATG
1 TGCATAT-ATGTACATATCATGGCATATCATG
55811983 T
1 T
55811984 ACAAATCAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 7 0.24
32 22 0.76
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (31 bp):
TGCATATATGTACATATCATGGCATATCATG
Found at i:55811991 original size:21 final size:22
Alignment explanation
Indices: 55811945--55811991 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
55811935 ATCATGGCAT
* *
55811945 ATCATGTGCATATCATGTGCAT
1 ATCATGTGCATATCATGTACAA
*
55811967 ATCATG-GCATATTATGTACAA
1 ATCATGTGCATATCATGTACAA
55811988 ATCA
1 ATCA
55811992 GTATCACATG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (22 bp):
ATCATGTGCATATCATGTACAA
Found at i:55814479 original size:19 final size:20
Alignment explanation
Indices: 55814443--55814481 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
55814433 CCTACCTACC
55814443 CAAATAAACCAAATTACCCA
1 CAAATAAACCAAATTACCCA
*
55814463 CAAATAAACC-CATTACCCA
1 CAAATAAACCAAATTACCCA
55814482 ATAAGCCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.51, C:0.33, G:0.00, T:0.15
Consensus pattern (20 bp):
CAAATAAACCAAATTACCCA
Found at i:55816263 original size:230 final size:230
Alignment explanation
Indices: 55815860--55816319 Score: 857
Period size: 230 Copynumber: 2.0 Consensus size: 230
55815850 TCACCAACGT
* *
55815860 CCACACATCAATGCTAGGGAGCAAGAGAAGCAACCTCTTTCTGTGGAGGCATGTTTAAGTCGGAT
1 CCACACATCAATGCTAGGGAGCAAGAGAAGCAACCTCTGTCTGTGGAGGCACGTTTAAGTCGGAT
55815925 CGAAGCTCGACTTGAAACAATGGAAAACCAAGTCTCCACAATCCTTGACATCCTACAAAGCCATT
66 CGAAGCTCGACTTGAAACAATGGAAAACCAAGTCTCCACAATCCTTGACATCCTACAAAGCCATT
55815990 ACCCCCAACTCCAACAAAATCATTAAAAGACACATAGGGAGTATTCTGAACTTTTCTTTTACATG
131 ACCCCCAACTCCAACAAAATCATTAAAAGACACATAGGGAGTATTCTGAACTTTTCTTTTACATG
*
55816055 TTATTAAGAGCTGCTATTTTTATTTCATTTAACAC
196 TTATTAAGAGCTGCTATTTTTATTTCAGTTAACAC
55816090 CCACACATCAATGCTAGGGAGCAAGAGAAGCAACCTCTGTCTGTGGAGGCACGTTTAAGTCGGAT
1 CCACACATCAATGCTAGGGAGCAAGAGAAGCAACCTCTGTCTGTGGAGGCACGTTTAAGTCGGAT
* *
55816155 CGAAGCTCGACTTGGAACAATGGAAAACCAAGTCTCCACAATCCTTGACATCCTACAACGCCATT
66 CGAAGCTCGACTTGAAACAATGGAAAACCAAGTCTCCACAATCCTTGACATCCTACAAAGCCATT
* *
55816220 ACCCCCAACTCCAACAAAGTCATTAAAAGACACATAGGGAGTATTTTGAACTTTTCTTTTACATG
131 ACCCCCAACTCCAACAAAATCATTAAAAGACACATAGGGAGTATTCTGAACTTTTCTTTTACATG
55816285 TTATTAAGAGCTGCTATTTTTATTTCAGTTAACAC
196 TTATTAAGAGCTGCTATTTTTATTTCAGTTAACAC
55816320 TTGCTGGAGG
Statistics
Matches: 223, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
230 223 1.00
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.27
Consensus pattern (230 bp):
CCACACATCAATGCTAGGGAGCAAGAGAAGCAACCTCTGTCTGTGGAGGCACGTTTAAGTCGGAT
CGAAGCTCGACTTGAAACAATGGAAAACCAAGTCTCCACAATCCTTGACATCCTACAAAGCCATT
ACCCCCAACTCCAACAAAATCATTAAAAGACACATAGGGAGTATTCTGAACTTTTCTTTTACATG
TTATTAAGAGCTGCTATTTTTATTTCAGTTAACAC
Found at i:55823847 original size:34 final size:34
Alignment explanation
Indices: 55823804--55823872 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
55823794 ATTGACTAAG
55823804 AAATTAGTCTAAGAGCTAATGTGGTGTTCTTTAA
1 AAATTAGTCTAAGAGCTAATGTGGTGTTCTTTAA
55823838 AAATTAGTCTAAGAGCTAATGTGGTGTTCTTTAA
1 AAATTAGTCTAAGAGCTAATGTGGTGTTCTTTAA
55823872 A
1 A
55823873 TTTGGTGTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.38
Consensus pattern (34 bp):
AAATTAGTCTAAGAGCTAATGTGGTGTTCTTTAA
Found at i:55827786 original size:42 final size:42
Alignment explanation
Indices: 55827735--55827852 Score: 146
Period size: 42 Copynumber: 2.8 Consensus size: 42
55827725 CTAAGATTAC
* * *
55827735 GTGTGAGACCATATCTGGGAAATGGCATTGGTATAAGACTTT
1 GTGTAAGACCATATCTGGGAAATGGCATCGATATAAGACTTT
* * *
55827777 GTGTAAGACCATATCTGGGATATGGCATCGATATGAGATTTT
1 GTGTAAGACCATATCTGGGAAATGGCATCGATATAAGACTTT
* * *
55827819 GTGTAAGACCATAGCTGGGCTATTGGCATCGATA
1 GTGTAAGACCATATCTGGG-AAATGGCATCGATA
55827853 CAAGGTTTAC
Statistics
Matches: 65, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
42 54 0.83
43 11 0.17
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.31
Consensus pattern (42 bp):
GTGTAAGACCATATCTGGGAAATGGCATCGATATAAGACTTT
Found at i:55831184 original size:59 final size:59
Alignment explanation
Indices: 55831092--55831210 Score: 229
Period size: 59 Copynumber: 2.0 Consensus size: 59
55831082 AAATACTTAG
*
55831092 AATGACTACATTGGTATAATATAAGTGTGATGTTTTTGTTTCCTCAAGCTTTCAGTTTT
1 AATGACTACATTAGTATAATATAAGTGTGATGTTTTTGTTTCCTCAAGCTTTCAGTTTT
55831151 AATGACTACATTAGTATAATATAAGTGTGATGTTTTTGTTTCCTCAAGCTTTCAGTTTT
1 AATGACTACATTAGTATAATATAAGTGTGATGTTTTTGTTTCCTCAAGCTTTCAGTTTT
55831210 A
1 A
55831211 CTCTTCAATA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.27, C:0.12, G:0.16, T:0.45
Consensus pattern (59 bp):
AATGACTACATTAGTATAATATAAGTGTGATGTTTTTGTTTCCTCAAGCTTTCAGTTTT
Found at i:55832282 original size:27 final size:22
Alignment explanation
Indices: 55832231--55832279 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
55832221 CCACTTGCAG
55832231 TATGTGATGTGACTTGACTCAT
1 TATGTGATGTGACTTGACTCAT
55832253 TATGTGATGTGACTTGACTCAT
1 TATGTGATGTGACTTGACTCAT
55832275 TATGT
1 TATGT
55832280 TATATTGTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.22, C:0.12, G:0.22, T:0.43
Consensus pattern (22 bp):
TATGTGATGTGACTTGACTCAT
Found at i:55835874 original size:27 final size:27
Alignment explanation
Indices: 55835836--55835888 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
55835826 AATCTGGACA
* *
55835836 TCGCCCTTTCACAAAGGATAGCTATTT
1 TCGCACTTTCACAAAGAATAGCTATTT
*
55835863 TCGCACTTTCACAACGAATAGCTATT
1 TCGCACTTTCACAAAGAATAGCTATT
55835889 CTAAATGGCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.32
Consensus pattern (27 bp):
TCGCACTTTCACAAAGAATAGCTATTT
Found at i:55835998 original size:21 final size:22
Alignment explanation
Indices: 55835972--55836038 Score: 84
Period size: 22 Copynumber: 3.1 Consensus size: 22
55835962 CTTTAAAATT
55835972 AAATTTTAAAAAT-TTTATTTA
1 AAATTTTAAAAATATTTATTTA
*
55835993 AAATTTTAAAAAATAATT-TTTA
1 AAATTTT-AAAAATATTTATTTA
* *
55836015 AAATTTTTAAAATATGTATTTA
1 AAATTTTAAAAATATTTATTTA
55836037 AA
1 AA
55836039 TGTTATAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
21 14 0.36
22 23 0.59
23 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (22 bp):
AAATTTTAAAAATATTTATTTA
Found at i:55836039 original size:21 final size:21
Alignment explanation
Indices: 55835970--55836048 Score: 61
Period size: 22 Copynumber: 3.7 Consensus size: 21
55835960 ATCTTTAAAA
* *
55835970 TTAAATTTTAAAAAT-TTTAT
1 TTAAATTTTTAAAATATATAT
* * *
55835990 TTAAAATTTTAAAAAATAATTT
1 TTAAATTTTTAAAATAT-ATAT
*
55836012 TTAAAATTTTTAAAATATGTAT
1 TT-AAATTTTTAAAATATATAT
*
55836034 TTAAATGTTATAAAA
1 TTAAAT-TTTTAAAA
55836049 CAAATAATAA
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
20 12 0.27
21 5 0.11
22 15 0.33
23 13 0.29
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (21 bp):
TTAAATTTTTAAAATATATAT
Found at i:55836129 original size:14 final size:13
Alignment explanation
Indices: 55836104--55836147 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 13
55836094 TAAATATTTT
55836104 ATAATATTAAAAA
1 ATAATATTAAAAA
*
55836117 ATAATATT-TAAA
1 ATAATATTAAAAA
55836129 AT--T-TTAAAAA
1 ATAATATTAAAAA
55836139 ATAATATTA
1 ATAATATTA
55836148 TAAAGCATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 8
0.71 0.06 0.23
Matches are distributed among these distances:
9 2 0.08
10 6 0.24
12 6 0.24
13 11 0.44
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
ATAATATTAAAAA
Found at i:55836135 original size:22 final size:22
Alignment explanation
Indices: 55836096--55836151 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
55836086 ATATATTTTA
*
55836096 AATATTTTATAATATTAAAAAAT
1 AATA-TTTAAAATATTAAAAAAT
*
55836119 AATATTTAAAATTTTAAAAAAT
1 AATATTTAAAATATTAAAAAAT
55836141 AATATTATAAA
1 AATATT-TAAA
55836152 GCATTTAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 22 0.73
23 8 0.27
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
AATATTTAAAATATTAAAAAAT
Found at i:55836157 original size:25 final size:21
Alignment explanation
Indices: 55836096--55836161 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 21
55836086 ATATATTTTA
*
55836096 AATATTTTATAATATTAAAAAAT
1 AATA-TTTAAAAT-TTAAAAAAT
55836119 AATATTTAAAATTTTAAAAAAT
1 AATATTTAAAA-TTTAAAAAAT
55836141 AATATTATAAAGCATTTAAAA
1 AATATT-TAAA--ATTTAAAA
55836162 TATTGTAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
22 21 0.55
23 9 0.24
24 7 0.18
25 1 0.03
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (21 bp):
AATATTTAAAATTTAAAAAAT
Found at i:55844166 original size:17 final size:16
Alignment explanation
Indices: 55844144--55844186 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 16
55844134 TAACATCATA
55844144 TTGTTTAATATTATATG
1 TTGTTTAATA-TATATG
55844161 TTGTTTAA-A-ATATG
1 TTGTTTAATATATATG
55844175 TTGTTTTAATAT
1 TTG-TTTAATAT
55844187 CAACATTTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 8 0.35
15 5 0.22
16 2 0.09
17 8 0.35
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (16 bp):
TTGTTTAATATATATG
Found at i:55844365 original size:26 final size:24
Alignment explanation
Indices: 55844334--55844382 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 24
55844324 AATAACTTTT
*
55844334 TTTAAAAATATAATAAATTAAATATA
1 TTTAAAAACATAA-AAA-TAAATATA
55844360 TTTAAAAACATAAAAATAAATAT
1 TTTAAAAACATAAAAATAAATAT
55844383 TAAAACAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.32
25 3 0.14
26 12 0.55
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (24 bp):
TTTAAAAACATAAAAATAAATATA
Found at i:55856049 original size:16 final size:17
Alignment explanation
Indices: 55856026--55856063 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
55856016 AATAAACAAT
55856026 TAAA-TAAATT-GGAAA
1 TAAATTAAATTGGGAAA
55856041 TAAATTAAATTGGGAAA
1 TAAATTAAATTGGGAAA
55856058 TAAATT
1 TAAATT
55856064 CAGATTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 4 0.19
16 6 0.29
17 11 0.52
ACGTcount: A:0.55, C:0.00, G:0.13, T:0.32
Consensus pattern (17 bp):
TAAATTAAATTGGGAAA
Found at i:55857703 original size:4 final size:4
Alignment explanation
Indices: 55857694--55857731 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
55857684 TTGAGCCTTA
*
55857694 ATTT ATTT ATTT ATTT -TTC ATTTT ATTT ATTT ATTT AT
1 ATTT ATTT ATTT ATTT ATTT A-TTT ATTT ATTT ATTT AT
55857732 GTACAATTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
3 2 0.07
4 25 0.83
5 3 0.10
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
ATTT
Found at i:55857988 original size:22 final size:22
Alignment explanation
Indices: 55857963--55858011 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
55857953 ACAAAAATCG
*
55857963 ATCAATCATGTATACTTACCAT
1 ATCAATCATGCATACTTACCAT
55857985 ATCAATCATGCATACTTACCAT
1 ATCAATCATGCATACTTACCAT
*
55858007 TTCAA
1 ATCAA
55858012 CCCTCCACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.35
Consensus pattern (22 bp):
ATCAATCATGCATACTTACCAT
Found at i:55863893 original size:95 final size:99
Alignment explanation
Indices: 55863725--55863938 Score: 285
Period size: 95 Copynumber: 2.2 Consensus size: 99
55863715 TATGAGAGCT
*
55863725 AGTGTAAGAGCATGTCTGGGACATGGCATCGGCACCGATAGATGAAAGCCAGTGGAAGACCATGT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCACCGATAGATGAAAGCCAGTGGAAGACCATGT
*
55863790 CTGAGACATGGCATC-GCCTT-A-AT-ATG-TGTC
66 CTGAGACATGGCATCGGCCTTGATATAAAGAT-TC
* * * * * * *
55863820 AGTGTAAGACCATGTCTGGGACATGGGATTGGTACCGATAGATGAGAGCTAGTGTAAGAGCATGT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCACCGATAGATGAAAGCCAGTGGAAGACCATGT
*
55863885 CTGGGACATGGCATCGGCCTTGATATACAAGATTC
66 CTGAGACATGGCATCGGCCTTGATATA-AAGATTC
55863920 AGTGTAAGACCATGTCTGG
1 AGTGTAAGACCATGTCTGG
55863939 TTTGTGGCAT
Statistics
Matches: 103, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
95 71 0.69
96 5 0.05
97 1 0.01
98 2 0.02
100 23 0.22
101 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.24
Consensus pattern (99 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCACCGATAGATGAAAGCCAGTGGAAGACCATGT
CTGAGACATGGCATCGGCCTTGATATAAAGATTC
Found at i:55863924 original size:50 final size:49
Alignment explanation
Indices: 55863725--55864000 Score: 201
Period size: 50 Copynumber: 5.7 Consensus size: 49
55863715 TATGAGAGCT
* * * *
55863725 AGTGTAAGAGCATGTCTGGGACATGGCATCGGCAC-CGATAGATGAA-AGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC-CTTGATATAT-AAGA-TC
* * **
55863775 AGTGGAAGACCATGTCTGAGACATGGCATC-GCCTT-A-ATATGTG-TC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTTGATATATAAGATC
* * * * *
55863820 AGTGTAAGACCATGTCTGGGACATGGGATTGGTACC--GATAGATGAGAGC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGG--CCTTGATATATAAGATC
* *
55863869 TAGTGTAAGAGCATGTCTGGGACATGGCATCGGCCTTGATATACAAGATTC
1 -AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTTGATATATAAGA-TC
**** * * * * *
55863920 AGTGTAAGACCATGTCTGGTTTGTGGCATCGACTTTGATGTGTAAG-TG
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTTGATATATAAGATC
*
55863968 AGTGTAAGACCATGTCCGGGACATGGCATCGGC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC
55864001 ACTTTAACCT
Statistics
Matches: 175, Mismatches: 39, Indels: 26
0.73 0.16 0.11
Matches are distributed among these distances:
45 27 0.15
46 1 0.01
47 4 0.02
48 39 0.22
49 3 0.02
50 100 0.57
51 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.25
Consensus pattern (49 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTTGATATATAAGATC
Found at i:55873397 original size:50 final size:49
Alignment explanation
Indices: 55873329--55873517 Score: 202
Period size: 50 Copynumber: 3.8 Consensus size: 49
55873319 TGATGCTAGG
*
55873329 GATATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACC
1 GATAGATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC-CC
* **
55873379 GATAGATGAGAGCCAGTGTAAGTGCATGTCTGGGACATGGCATCGGCCTC
1 GATAGATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCC-C
* * * * * * **
55873429 GACATACGAGAGTTAGTGTAAGACCATGTCTGGGATATGGCATCGACTTT
1 GATAGATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC-CC
** *
55873479 GAT-G-TGTCAGCTAGTGTAAGACCATGTCAGGGACATGGC
1 GATAGATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGC
55873518 GTTGGCGCCT
Statistics
Matches: 114, Mismatches: 23, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
48 29 0.25
49 1 0.01
50 84 0.74
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (49 bp):
GATAGATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCC
Found at i:55882366 original size:20 final size:20
Alignment explanation
Indices: 55882317--55882366 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
55882307 GCACACGCCT
*
55882317 GTGTGGCCTCAGACATGCCC
1 GTGTGGCCTGAGACATGCCC
*
55882337 GTGTGGCCTGGGACATGCCC
1 GTGTGGCCTGAGACATGCCC
55882357 GTGTGGCCTG
1 GTGTGGCCTG
55882367 CCCGTGGGGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.10, C:0.30, G:0.38, T:0.22
Consensus pattern (20 bp):
GTGTGGCCTGAGACATGCCC
Found at i:55883352 original size:52 final size:52
Alignment explanation
Indices: 55883220--55883386 Score: 185
Period size: 52 Copynumber: 3.2 Consensus size: 52
55883210 TCTTACACGG
* * *
55883220 ATCACATCACACACTGATGCCATATCTCAGATATGGTCTTATAC-AGAACCACATT
1 ATCACATCACAC-C-GATGCCATAGCCCAGATATGGTCTTATACGGGAA-CACA-T
**
55883275 ATCATGTCACACCGATGCCATAGCCCAGATATGGTCTTATACGGGAACACAT
1 ATCACATCACACCGATGCCATAGCCCAGATATGGTCTTATACGGGAACACAT
** * * *
55883327 ATCACATTGCACCGATGCCATAGCCCA-ACTATGGTCATAAACGGGCACACAT
1 ATCACATCACACCGATGCCATAGCCCAGA-TATGGTCTTATACGGGAACACAT
55883379 ATCACATC
1 ATCACATC
55883387 TTTTCCGTCG
Statistics
Matches: 97, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
51 1 0.01
52 51 0.53
53 31 0.32
54 4 0.04
55 10 0.10
ACGTcount: A:0.33, C:0.29, G:0.15, T:0.23
Consensus pattern (52 bp):
ATCACATCACACCGATGCCATAGCCCAGATATGGTCTTATACGGGAACACAT
Found at i:55887401 original size:39 final size:38
Alignment explanation
Indices: 55887358--55887493 Score: 112
Period size: 39 Copynumber: 3.3 Consensus size: 38
55887348 CTATAGAGGC
*
55887358 ATTAGTGGCGTTTTACTAAAAACGCCGCAATATATAAGA
1 ATTAGCGGCGTTTTA-TAAAAACGCCGCAATATATAAGA
* * *
55887397 ATTAGCGGCACTTTTATAAAAACGCCGCAAAGTGGCTATAGAGGT
1 ATTAGCGGC-GTTTTATAAAAACGCCGC-AA-T--ATATA-A-GA
* * *
55887442 ATTAGTGGCGTTTTA-AGTAAAACTCCGCAATATATTAGA
1 ATTAGCGGCGTTTTATA--AAAACGCCGCAATATATAAGA
55887481 ATTAGCGGCGTTT
1 ATTAGCGGCGTTT
55887494 GTTTCAAAGT
Statistics
Matches: 77, Mismatches: 11, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
39 33 0.43
40 8 0.10
41 4 0.05
43 6 0.08
44 8 0.10
45 18 0.23
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.29
Consensus pattern (38 bp):
ATTAGCGGCGTTTTATAAAAACGCCGCAATATATAAGA
Found at i:55887830 original size:21 final size:21
Alignment explanation
Indices: 55887794--55887844 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
55887784 TTGAGTTTTG
* *
55887794 GGGTTTATAATTTTAAGGTTTA
1 GGGTTT-TAATATTAAGGTTCA
*
55887816 GGGTTTTAATATTAATGTTCA
1 GGGTTTTAATATTAAGGTTCA
*
55887837 TGGTTTTA
1 GGGTTTTA
55887845 GGGGTTAGGC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 19 0.76
22 6 0.24
ACGTcount: A:0.25, C:0.02, G:0.22, T:0.51
Consensus pattern (21 bp):
GGGTTTTAATATTAAGGTTCA
Found at i:55888300 original size:14 final size:14
Alignment explanation
Indices: 55888281--55888314 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
55888271 TATGATTTTA
55888281 GGGTTTAAAGTTTG
1 GGGTTTAAAGTTTG
**
55888295 GGGTTTAGGGTTTG
1 GGGTTTAAAGTTTG
55888309 GGGTTT
1 GGGTTT
55888315 GGTGTTCATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.44, T:0.44
Consensus pattern (14 bp):
GGGTTTAAAGTTTG
Found at i:55888409 original size:15 final size:15
Alignment explanation
Indices: 55888391--55888422 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
55888381 TTTAATTTAG
55888391 AAGATAAATATAAAT
1 AAGATAAATATAAAT
*
55888406 AAGATAAATATATAT
1 AAGATAAATATAAAT
55888421 AA
1 AA
55888423 ATTATTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (15 bp):
AAGATAAATATAAAT
Found at i:55889281 original size:37 final size:37
Alignment explanation
Indices: 55889240--55889327 Score: 131
Period size: 37 Copynumber: 2.4 Consensus size: 37
55889230 TTCCCTTAAA
* **
55889240 TCTCCCCGTGCATTGCAACCCATCTCCTCCGTCACCT
1 TCTCCCCGTGCATCGCAACCCATCTCCTCAATCACCT
*
55889277 TCTCCCCGTGCATCGCAACCCATCTCCTCAATCTCCT
1 TCTCCCCGTGCATCGCAACCCATCTCCTCAATCACCT
*
55889314 TCGCCCCGTGCATC
1 TCTCCCCGTGCATC
55889328 TGCTGCATAG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.14, C:0.49, G:0.11, T:0.26
Consensus pattern (37 bp):
TCTCCCCGTGCATCGCAACCCATCTCCTCAATCACCT
Found at i:55901286 original size:14 final size:15
Alignment explanation
Indices: 55901264--55901300 Score: 67
Period size: 14 Copynumber: 2.5 Consensus size: 15
55901254 TTAGTTTAAT
55901264 AATTATATGAAGTAA
1 AATTATATGAAGTAA
55901279 AA-TATATGAAGTAA
1 AATTATATGAAGTAA
55901293 AATTATAT
1 AATTATAT
55901301 TATATACTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 14 0.67
15 7 0.33
ACGTcount: A:0.54, C:0.00, G:0.11, T:0.35
Consensus pattern (15 bp):
AATTATATGAAGTAA
Found at i:55902776 original size:15 final size:17
Alignment explanation
Indices: 55902742--55902775 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
55902732 GATGTTTCTA
55902742 ATTCAAAAGTAATATAT
1 ATTCAAAAGTAATATAT
55902759 ATTCAAAAGTAATATAT
1 ATTCAAAAGTAATATAT
55902776 TTTTTTCAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.35
Consensus pattern (17 bp):
ATTCAAAAGTAATATAT
Found at i:55902853 original size:30 final size:30
Alignment explanation
Indices: 55902817--55902988 Score: 138
Period size: 30 Copynumber: 5.5 Consensus size: 30
55902807 TTACATAATA
55902817 CATAACTTACATAATTTAAAGTTCAAATTT
1 CATAACTTACATAATTTAAAGTTCAAATTT
** *
55902847 CATAACTTACATAATACATAACTTACATAATTT
1 CATAACTTACATAATTTA-AAGTT-CA-AATTT
* *
55902880 -A-AA--GACCA-AATTTCATAAATTACATAATTT
1 CATAACTTA-CATAATTT-A-AAGTT-CA-AATTT
55902910 ACATAACTTACATAATAATTTAAAGTTCAAATTT
1 -CATAACTTAC---ATAATTTAAAGTTCAAATTT
* *
55902944 CATAACTTACATAATATAAAGATCAAATTT
1 CATAACTTACATAATTTAAAGTTCAAATTT
55902974 CATAACTTACATAAT
1 CATAACTTACATAAT
55902989 ACATAACTTA
Statistics
Matches: 117, Mismatches: 11, Indels: 28
0.75 0.07 0.18
Matches are distributed among these distances:
29 4 0.03
30 66 0.56
31 6 0.05
32 4 0.03
33 17 0.15
34 6 0.05
35 3 0.03
36 4 0.03
37 2 0.02
38 5 0.04
ACGTcount: A:0.47, C:0.15, G:0.02, T:0.36
Consensus pattern (30 bp):
CATAACTTACATAATTTAAAGTTCAAATTT
Found at i:55902874 original size:46 final size:46
Alignment explanation
Indices: 55902807--55902959 Score: 234
Period size: 46 Copynumber: 3.2 Consensus size: 46
55902797 CTCACCTAAT
55902807 TTACATAATACATAACTTACATAATTTAAAGTTCAAATTTCATAAC
1 TTACATAATACATAACTTACATAATTTAAAGTTCAAATTTCATAAC
** *
55902853 TTACATAATACATAACTTACATAATTTAAAGACCAAATTTCATAAA
1 TTACATAATACATAACTTACATAATTTAAAGTTCAAATTTCATAAC
55902899 TTACATAATTTACATAACTTACATAATAATTTAAAGTTCAAATTTCATAAC
1 TTACATAA--TACATAACTTAC---ATAATTTAAAGTTCAAATTTCATAAC
55902950 TTACATAATA
1 TTACATAATA
55902960 TAAAGATCAA
Statistics
Matches: 96, Mismatches: 6, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
46 51 0.53
48 12 0.12
49 2 0.02
51 31 0.32
ACGTcount: A:0.47, C:0.14, G:0.02, T:0.37
Consensus pattern (46 bp):
TTACATAATACATAACTTACATAATTTAAAGTTCAAATTTCATAAC
Found at i:55902995 original size:127 final size:125
Alignment explanation
Indices: 55902817--55903051 Score: 407
Period size: 127 Copynumber: 1.9 Consensus size: 125
55902807 TTACATAATA
* *
55902817 CATAACTTACATAATTTAAAGTTCAAATTTCATAACTTACATAATACATAACTTACATAATTTAA
1 CATAACTTACATAATATAAAGATCAAATTTCATAACTTACATAATACATAACTTACATAATTTAA
*
55902882 AGACCAAATTTCATAAATTACATAATTTACATAACTTACATAATAATTTAAAGTTCAAATTT
66 AGACCAAAATTCATAAATTACATAA--TACATAACTTACATAATAATTTAAAGTTCAAATTT
55902944 CATAACTTACATAATATAAAGATCAAATTTCATAACTTACATAATACATAACTTACATAATTTAA
1 CATAACTTACATAATATAAAGATCAAATTTCATAACTTACATAATACATAACTTACATAATTTAA
* *
55903009 AGATCAAAATTCATAACTTACATAATACATAACTTACATAATA
66 AGACCAAAATTCATAAATTACATAATACATAACTTACATAATA
55903052 CATGACTTAC
Statistics
Matches: 103, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
125 18 0.17
127 85 0.83
ACGTcount: A:0.48, C:0.15, G:0.02, T:0.35
Consensus pattern (125 bp):
CATAACTTACATAATATAAAGATCAAATTTCATAACTTACATAATACATAACTTACATAATTTAA
AGACCAAAATTCATAAATTACATAATACATAACTTACATAATAATTTAAAGTTCAAATTT
Found at i:55902997 original size:46 final size:46
Alignment explanation
Indices: 55902944--55903051 Score: 198
Period size: 46 Copynumber: 2.3 Consensus size: 46
55902934 GTTCAAATTT
*
55902944 CATAACTTACATAATATAAAGATCAAATTTCATAACTTACATAATA
1 CATAACTTACATAATATAAAGATCAAAATTCATAACTTACATAATA
*
55902990 CATAACTTACATAATTTAAAGATCAAAATTCATAACTTACATAATA
1 CATAACTTACATAATATAAAGATCAAAATTCATAACTTACATAATA
55903036 CATAACTTACATAATA
1 CATAACTTACATAATA
55903052 CATGACTTAC
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 59 1.00
ACGTcount: A:0.50, C:0.16, G:0.02, T:0.32
Consensus pattern (46 bp):
CATAACTTACATAATATAAAGATCAAAATTCATAACTTACATAATA
Found at i:55908589 original size:21 final size:21
Alignment explanation
Indices: 55908564--55908606 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
55908554 AGGCAGCAAT
* *
55908564 AGGGAGGCAGCGGCAGTAGCG
1 AGGGAGGCAGAGGCAGCAGCG
*
55908585 AGGGAGGTAGAGGCAGCAGCG
1 AGGGAGGCAGAGGCAGCAGCG
55908606 A
1 A
55908607 TGGCAGCAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.16, G:0.51, T:0.05
Consensus pattern (21 bp):
AGGGAGGCAGAGGCAGCAGCG
Found at i:55908891 original size:31 final size:31
Alignment explanation
Indices: 55908829--55908914 Score: 109
Period size: 31 Copynumber: 2.7 Consensus size: 31
55908819 TTAGATTTAA
* * *
55908829 TGTTTTTGATTGTATTTATTATGCTACATTTGT
1 TGTTTTTGGTTGGATTTA--ATGCTACATTTGC
* *
55908862 TGTTTTTGGTTGGATTTCATGCTATATTTGC
1 TGTTTTTGGTTGGATTTAATGCTACATTTGC
55908893 TGTTTTTGGTTGGATTTAATGC
1 TGTTTTTGGTTGGATTTAATGC
55908915 AAGAAGGGTT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
31 32 0.68
33 15 0.32
ACGTcount: A:0.15, C:0.07, G:0.21, T:0.57
Consensus pattern (31 bp):
TGTTTTTGGTTGGATTTAATGCTACATTTGC
Found at i:55912793 original size:26 final size:26
Alignment explanation
Indices: 55912754--55912809 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
55912744 TGATACAAAT
55912754 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
55912780 TGATAAT-GGTTTAGGTAAATGTTCCA
1 TGATAATAGG-TTAGGTAAATGTTCCA
55912806 TGAT
1 TGAT
55912810 GGGAATTTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
25 2 0.07
26 27 0.93
ACGTcount: A:0.32, C:0.07, G:0.23, T:0.38
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:55919830 original size:26 final size:26
Alignment explanation
Indices: 55919801--55919908 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
55919791 TGGTACAAAT
55919801 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
55919827 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
55919853 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
55919879 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
55919905 TGAT
1 TGAT
55919909 GGGCATTTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:55921627 original size:27 final size:27
Alignment explanation
Indices: 55921530--55921634 Score: 135
Period size: 27 Copynumber: 3.9 Consensus size: 27
55921520 AGGAAGCGTC
*
55921530 CTGGTGGCTATGCCACAATTATCTG-AT
1 CTGGTGGCTCTGCCACAA-TATCTGTAT
55921557 CTGGTGGCTCTGCCACATATATCTGT-T
1 CTGGTGGCTCTGCCACA-ATATCTGTAT
55921584 CTGGTGGCTCTGCCACAATATCTGTAT
1 CTGGTGGCTCTGCCACAATATCTGTAT
* *
55921611 CTGGTGACT-TCGTCACAATATCTG
1 CTGGTGGCTCT-GCCACAATATCTG
55921635 GCAGCCTCGC
Statistics
Matches: 71, Mismatches: 3, Indels: 8
0.87 0.04 0.10
Matches are distributed among these distances:
26 9 0.13
27 61 0.86
28 1 0.01
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATATCTGTAT
Found at i:55924510 original size:26 final size:27
Alignment explanation
Indices: 55924461--55924512 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
55924451 AGTAAAGACT
*
55924461 AATGAAATAAAAAAAATCTATTTAAAC
1 AATGAAATAAAAAAAAACTATTTAAAC
55924488 AATGAAATAAAAAAAAACT-TTTAAA
1 AATGAAATAAAAAAAAACTATTTAAA
55924513 TGATAATGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 6 0.25
27 18 0.75
ACGTcount: A:0.65, C:0.06, G:0.04, T:0.25
Consensus pattern (27 bp):
AATGAAATAAAAAAAAACTATTTAAAC
Found at i:55931576 original size:40 final size:40
Alignment explanation
Indices: 55931517--55931773 Score: 448
Period size: 40 Copynumber: 6.5 Consensus size: 40
55931507 GGATTGATAA
55931517 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
55931556 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
55931596 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
55931636 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
55931676 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
55931716 CCGGGCTAAGTCCCGAAGGCATTTGAGCAAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
*
55931756 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
55931774 TACTTGGTTT
Statistics
Matches: 211, Mismatches: 5, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
39 27 0.13
40 184 0.87
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:55933643 original size:43 final size:43
Alignment explanation
Indices: 55933605--55933714 Score: 123
Period size: 43 Copynumber: 2.6 Consensus size: 43
55933595 TCCTAGCTAT
* *
55933605 AGTCTTACATGTTATCACATATCGATGCCTCTGTCCTAGACAG
1 AGTCTTACACGTAATCACATATCGATGCCTCTGTCCTAGACAG
* * ** *
55933648 GGTCTTACACGTAATCTCATATCGATGCCGATGTCCCAGACATG
1 AGTCTTACACGTAATCACATATCGATGCCTCTGTCCTAGACA-G
* *
55933692 -GTCTTACACGAAATCACACATCG
1 AGTCTTACACGTAATCACATATCG
55933715 GAAGTCCTAA
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
43 55 0.98
44 1 0.02
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.28
Consensus pattern (43 bp):
AGTCTTACACGTAATCACATATCGATGCCTCTGTCCTAGACAG
Found at i:55935406 original size:40 final size:42
Alignment explanation
Indices: 55935320--55935416 Score: 121
Period size: 40 Copynumber: 2.4 Consensus size: 42
55935310 CGAATATGTT
* * *
55935320 TGGCACTTAGTGTACG-TTTTGAGATAGCTTCGGCTATATAG
1 TGGCACTTAGTGTGCGAATTGGAGATAGCTTCGGCTATATAG
*
55935361 -AGCACTTAGTGTGCGAATTGGA-ATAGCTTCGGCTATAT-G
1 TGGCACTTAGTGTGCGAATTGGAGATAGCTTCGGCTATATAG
*
55935400 TGGCACTAAGTGTGCGA
1 TGGCACTTAGTGTGCGA
55935417 TACCAAGATA
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
39 1 0.02
40 43 0.90
41 4 0.08
ACGTcount: A:0.24, C:0.15, G:0.29, T:0.32
Consensus pattern (42 bp):
TGGCACTTAGTGTGCGAATTGGAGATAGCTTCGGCTATATAG
Found at i:55941223 original size:25 final size:25
Alignment explanation
Indices: 55941187--55941249 Score: 110
Period size: 25 Copynumber: 2.6 Consensus size: 25
55941177 TTTTGGGGGG
55941187 GGGTTAGG-TTTTTCTTTTTTTTTT
1 GGGTTAGGTTTTTTCTTTTTTTTTT
55941211 GGGTTAGGTTTTTTCTTTTTTTTTT
1 GGGTTAGGTTTTTTCTTTTTTTTTT
*
55941236 TGGTTAGGTTTTTT
1 GGGTTAGGTTTTTT
55941250 TTTGGGGAGG
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
24 8 0.22
25 29 0.78
ACGTcount: A:0.05, C:0.03, G:0.22, T:0.70
Consensus pattern (25 bp):
GGGTTAGGTTTTTTCTTTTTTTTTT
Found at i:55943911 original size:20 final size:20
Alignment explanation
Indices: 55943888--55943945 Score: 89
Period size: 21 Copynumber: 2.9 Consensus size: 20
55943878 TTTTTTGGGG
*
55943888 GGGTTAAGTTTTTTTTTTTT
1 GGGTTAGGTTTTTTTTTTTT
55943908 GGGTTAGGTTTTTTCTTTTTT
1 GGGTTAGGTTTTTT-TTTTTT
*
55943929 TGGTTAGGTTTTTTTTT
1 GGGTTAGGTTTTTTTTT
55943946 GGGGAGGGCT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 16 0.46
21 19 0.54
ACGTcount: A:0.07, C:0.02, G:0.22, T:0.69
Consensus pattern (20 bp):
GGGTTAGGTTTTTTTTTTTT
Found at i:55949409 original size:70 final size:70
Alignment explanation
Indices: 55949302--55949554 Score: 298
Period size: 70 Copynumber: 3.6 Consensus size: 70
55949292 TTGCTAAGTA
* **
55949302 TGTTGGAA-GCTACGG-TTTTTATCCTACGAGCCTTAGTATGGTAGCTTA-GAGCTTTGCTCTCG
1 TGTT-GAAGGCTACGGTTTTTTATCCTGCGAGCCTTAGTATGACAGC-TAGGAGCTTTGCTCTCG
55949364 CTAACTG
64 CTAACTG
*
55949371 TGTTGAAGGCTACGGTTTTTTATCCTGCGAGCCTTAGTATGACAGCTAGGAGCTTTGCTCTTGCT
1 TGTTGAAGGCTACGGTTTTTTATCCTGCGAGCCTTAGTATGACAGCTAGGAGCTTTGCTCTCGCT
55949436 AACTG
66 AACTG
* * * * *
55949441 TGTT-AGAGGCTACGATTTTTTATCTTGCGAGTCTTAGTATGACAGCTAGGAGCTTTGTTATCGC
1 TGTTGA-AGGCTACGGTTTTTTATCCTGCGAGCCTTAGTATGACAGCTAGGAGCTTTGCTCTCGC
** *
55949505 TAGTTA
65 TAACTG
* * * * *
55949511 TGTTGGAGGCTGCAGTTTTTTATCTTGCGAACCTTAGTATGACA
1 TGTTGAAGGCTACGGTTTTTTATCCTGCGAGCCTTAGTATGACA
55949555 CAAATGTTGT
Statistics
Matches: 160, Mismatches: 19, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
68 3 0.02
69 14 0.09
70 143 0.89
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.38
Consensus pattern (70 bp):
TGTTGAAGGCTACGGTTTTTTATCCTGCGAGCCTTAGTATGACAGCTAGGAGCTTTGCTCTCGCT
AACTG
Found at i:55951592 original size:43 final size:43
Alignment explanation
Indices: 55951538--55951685 Score: 158
Period size: 43 Copynumber: 3.4 Consensus size: 43
55951528 AATGCCATAT
*
55951538 CCCAGATATGGTCTTACACGTTATCACATATTGATGCCAATGG
1 CCCAGACATGGTCTTACACGTTATCACATATTGATGCCAATGG
** * **
55951581 CCCAGACATGGTCTTACACGAAATCATATAACGATGCCAATGTG
1 CCCAGACATGGTCTTACACGTTATCACATATTGATGCCAATG-G
* * *
55951625 -CTAGACATGGTCTTACAC-TTAATCGCA-ATATGATGCCAATGC
1 CCCAGACATGGTCTTACACGTT-ATCACATAT-TGATGCCAATGG
*
55951667 CCCAAACATGGTCTTACAC
1 CCCAGACATGGTCTTACAC
55951686 ATAATCACGT
Statistics
Matches: 85, Mismatches: 16, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
42 1 0.01
43 83 0.98
44 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (43 bp):
CCCAGACATGGTCTTACACGTTATCACATATTGATGCCAATGG
Found at i:55955262 original size:40 final size:40
Alignment explanation
Indices: 55955117--55955300 Score: 209
Period size: 40 Copynumber: 4.7 Consensus size: 40
55955107 TTGAATGATG
* *
55955117 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAA-A
** * *
55955156 TCCGAACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
55955196 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
55955235 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
55955276 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
55955301 AACGAGGAGC
Statistics
Matches: 124, Mismatches: 14, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
39 52 0.42
40 62 0.50
41 10 0.08
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:55955322 original size:79 final size:79
Alignment explanation
Indices: 55955169--55955333 Score: 194
Period size: 79 Copynumber: 2.1 Consensus size: 79
55955159 GAACTAAGAT
* ** *
55955169 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
*
55955234 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
*
55955248 CCGAAGGCATTTGTGCGA-ATTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAG
1 CCGAAGGCATTTGTGCGAGA-TACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-
* *
55955310 CTATATCC-GGTTAAATT
62 CTAAATCCGGGTTAAATC
55955327 CCGAAGG
1 CCGAAGG
55955334 TACGTGATTT
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
78 3 0.04
79 46 0.62
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
ATCCGGGTTAAATC
Found at i:55961160 original size:29 final size:30
Alignment explanation
Indices: 55961121--55961199 Score: 101
Period size: 29 Copynumber: 2.7 Consensus size: 30
55961111 CTTAATAATC
55961121 AACCGCGCACACTTAGTGCCATGTAC-TGTA
1 AACC-CGCACACTTAGTGCCATGTACATGTA
* *
55961151 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATGTA
55961180 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
55961200 ATCTCATGAT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 32 0.76
30 4 0.10
ACGTcount: A:0.29, C:0.30, G:0.16, T:0.24
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATGTA
Found at i:55968493 original size:29 final size:29
Alignment explanation
Indices: 55968452--55968509 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
55968442 TAGAAGGTAG
55968452 AAAACTATTTCTAGAAGGTAAAAAAACTA
1 AAAACTATTTCTAGAAGGTAAAAAAACTA
* *
55968481 AAAATTATTTCTAGAAGGTAGAAAAACTA
1 AAAACTATTTCTAGAAGGTAAAAAAACTA
55968510 TCTAATTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.53, C:0.09, G:0.12, T:0.26
Consensus pattern (29 bp):
AAAACTATTTCTAGAAGGTAAAAAAACTA
Found at i:55978847 original size:28 final size:28
Alignment explanation
Indices: 55978815--55978877 Score: 126
Period size: 28 Copynumber: 2.2 Consensus size: 28
55978805 AAAAAAAGAT
55978815 AAATTTTGAAATTTTTATAAATTTTTTG
1 AAATTTTGAAATTTTTATAAATTTTTTG
55978843 AAATTTTGAAATTTTTATAAATTTTTTG
1 AAATTTTGAAATTTTTATAAATTTTTTG
55978871 AAATTTT
1 AAATTTT
55978878 TTGTAATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (28 bp):
AAATTTTGAAATTTTTATAAATTTTTTG
Found at i:55978880 original size:10 final size:10
Alignment explanation
Indices: 55978818--55978888 Score: 87
Period size: 10 Copynumber: 7.3 Consensus size: 10
55978808 AAAAGATAAA
55978818 TTTTGAAATT
1 TTTTGAAATT
55978828 TTTAT-AAATT
1 TTT-TGAAATT
55978838 TTTTGAAA--
1 TTTTGAAATT
55978846 TTTTGAAATT
1 TTTTGAAATT
55978856 TTTAT-AAATT
1 TTT-TGAAATT
55978866 TTTTGAAATT
1 TTTTGAAATT
*
55978876 TTTTGTAATT
1 TTTTGAAATT
55978886 TTT
1 TTT
55978889 GTTGAGAAAG
Statistics
Matches: 54, Mismatches: 1, Indels: 12
0.81 0.01 0.18
Matches are distributed among these distances:
8 8 0.15
9 2 0.04
10 42 0.78
11 2 0.04
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (10 bp):
TTTTGAAATT
Found at i:55980157 original size:14 final size:15
Alignment explanation
Indices: 55980124--55980159 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
55980114 CCACTTGTTT
*
55980124 TTTTAATTTTATATA
1 TTTTAGTTTTATATA
55980139 TTTTAGTTTTATA-A
1 TTTTAGTTTTATATA
55980153 TTTTAGT
1 TTTTAGT
55980160 CATTTGTAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.67
Consensus pattern (15 bp):
TTTTAGTTTTATATA
Found at i:55984355 original size:19 final size:19
Alignment explanation
Indices: 55984328--55984385 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
55984318 TAAAAATAAA
55984328 AGTTGAATTCAAACAAATG
1 AGTTGAATTCAAACAAATG
* * *
55984347 AGTTTAATTTATGA-AAA-G
1 AGTTGAATTCA-AACAAATG
*
55984365 AATTGAATTCAAACAAATG
1 AGTTGAATTCAAACAAATG
55984384 AG
1 AG
55984386 CTTAATTTAT
Statistics
Matches: 28, Mismatches: 8, Indels: 6
0.67 0.19 0.14
Matches are distributed among these distances:
17 1 0.04
18 12 0.43
19 14 0.50
20 1 0.04
ACGTcount: A:0.48, C:0.07, G:0.16, T:0.29
Consensus pattern (19 bp):
AGTTGAATTCAAACAAATG
Found at i:55984373 original size:37 final size:37
Alignment explanation
Indices: 55984330--55984403 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
55984320 AAAATAAAAG
*
55984330 TTGAATTCAAACAAATGAGTTTAATTTATGAAAAGAA
1 TTGAATTCAAACAAATGAGCTTAATTTATGAAAAGAA
55984367 TTGAATTCAAACAAATGAGCTTAATTTATGAAAAGAA
1 TTGAATTCAAACAAATGAGCTTAATTTATGAAAAGAA
55984404 GAAAGTCAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.49, C:0.07, G:0.14, T:0.31
Consensus pattern (37 bp):
TTGAATTCAAACAAATGAGCTTAATTTATGAAAAGAA
Found at i:55992720 original size:46 final size:46
Alignment explanation
Indices: 55992653--55992825 Score: 192
Period size: 46 Copynumber: 3.7 Consensus size: 46
55992643 TGTAACCCGC
* *
55992653 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCAGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCAGACGTTCGCAT
* * *
55992699 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTC--A-GAC--GTTCGCAT
* * *
55992749 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCTGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCAGACGTTCGCAT
*
55992792 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTC
55992826 GGATGCTCAA
Statistics
Matches: 106, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 3 0.03
45 2 0.02
46 58 0.55
47 26 0.25
48 3 0.03
49 3 0.03
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.30, G:0.19, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCAGACGTTCGCAT
Found at i:55992772 original size:93 final size:93
Alignment explanation
Indices: 55992660--55992831 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
55992650 CGCCCATAAG
* *
55992660 CGAACTCGGACTCAACTCAACGAGCTCAGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
55992725 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
* *
55992753 CGAACTCGGACTCAACTCAACGAGTTCTGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
55992818 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
55992832 TCAATCATCC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:56003590 original size:33 final size:33
Alignment explanation
Indices: 56003548--56003612 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
56003538 TCGTATTCAC
*
56003548 GATGTGTTCCACGTCTCGATGTTGAGGCGTTAT
1 GATGTGTTCCACATCTCGATGTTGAGGCGTTAT
*
56003581 GATGTGTTCCACATCTCTATGTTGAGGCGTTA
1 GATGTGTTCCACATCTCGATGTTGAGGCGTTA
56003613 CTGCTCTGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.17, C:0.18, G:0.28, T:0.37
Consensus pattern (33 bp):
GATGTGTTCCACATCTCGATGTTGAGGCGTTAT
Found at i:56007586 original size:18 final size:18
Alignment explanation
Indices: 56007563--56007640 Score: 58
Period size: 18 Copynumber: 4.6 Consensus size: 18
56007553 AAATAATTGT
*
56007563 AAAAATGATAATTATTTA
1 AAAAATAATAATTATTTA
* *
56007581 AAAAATAATAACTAATT-
1 AAAAATAATAATTATTTA
* * *
56007598 GAACA-AATAA-T-TGT-
1 AAAAATAATAATTATTTA
*
56007612 AAAAATGATAATTATTTA
1 AAAAATAATAATTATTTA
56007630 AAAAATAATAA
1 AAAAATAATAA
56007641 ATAATTGTAA
Statistics
Matches: 44, Mismatches: 12, Indels: 8
0.69 0.19 0.12
Matches are distributed among these distances:
14 4 0.09
15 5 0.11
16 6 0.14
17 5 0.11
18 24 0.55
ACGTcount: A:0.60, C:0.03, G:0.05, T:0.32
Consensus pattern (18 bp):
AAAAATAATAATTATTTA
Found at i:56007603 original size:49 final size:49
Alignment explanation
Indices: 56007550--56007647 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
56007540 ACAACCTTGA
*
56007550 AACAAATAATTGTAAAAATGATAATTATTTAAAAAATAATAACTAATTG
1 AACAAATAATTGTAAAAATGATAATTATTTAAAAAATAATAAATAATTG
56007599 AACAAATAATTGTAAAAATGATAATTATTTAAAAAATAATAAATAATTG
1 AACAAATAATTGTAAAAATGATAATTATTTAAAAAATAATAAATAATTG
56007648 TAATTTAAAT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.33
Consensus pattern (49 bp):
AACAAATAATTGTAAAAATGATAATTATTTAAAAAATAATAAATAATTG
Found at i:56007782 original size:24 final size:24
Alignment explanation
Indices: 56007755--56007828 Score: 67
Period size: 24 Copynumber: 3.1 Consensus size: 24
56007745 TAATTGTAAA
56007755 AATTATAATTATTTTTAAATGTAT
1 AATTATAATTATTTTTAAATGTAT
* ** * ** *
56007779 AATTATTACAAATTTTAAATAAAA
1 AATTATAATTATTTTTAAATGTAT
* *
56007803 AATTCTAATTATTTTTAATTGTAT
1 AATTATAATTATTTTTAAATGTAT
56007827 AA
1 AA
56007829 GTATTACAAG
Statistics
Matches: 34, Mismatches: 16, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (24 bp):
AATTATAATTATTTTTAAATGTAT
Found at i:56016467 original size:2 final size:2
Alignment explanation
Indices: 56016460--56017279 Score: 1590
Period size: 2 Copynumber: 411.0 Consensus size: 2
56016450 TCATCGATTA
*
56016460 AG AG AG AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* **
56016502 AG AG AG AG AG AG AG AG AG AG AG -G AT CC A- AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
56016542 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
56016584 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
56016626 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
56016668 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
56016710 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
56016752 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
56016794 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
56016836 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
56016878 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
56016920 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
56016962 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
56017004 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
56017046 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
56017088 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
56017130 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
56017172 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
56017214 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
56017256 AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG
56017280 GATCCAAAAC
Statistics
Matches: 810, Mismatches: 6, Indels: 4
0.99 0.01 0.00
Matches are distributed among these distances:
1 2 0.00
2 808 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:56019056 original size:12 final size:12
Alignment explanation
Indices: 56019016--56019058 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
56019006 TTAAACATAA
56019016 AAAAATT-AAAT
1 AAAAATTAAAAT
* *
56019027 TAAAATTGAAAGT
1 AAAAATT-AAAAT
56019040 AAAAATTAAAAT
1 AAAAATTAAAAT
56019052 AAAAATT
1 AAAAATT
56019059 CTTTTCGGGC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
11 6 0.23
12 11 0.42
13 9 0.35
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (12 bp):
AAAAATTAAAAT
Found at i:56021857 original size:42 final size:43
Alignment explanation
Indices: 56021767--56021879 Score: 142
Period size: 42 Copynumber: 2.7 Consensus size: 43
56021757 ATATCGTACA
* * * *
56021767 ATGCCAACGTCTCGGACGTGGTCTTACATGTAATCAGACATCG
1 ATGCCAACGTCCCAGATGTGGTCTTACATGTAATCACACATCG
*
56021810 ATGCC-ACTGTCCTAGATAG-GGTCTTACATG-AATCACACATCG
1 ATGCCAAC-GTCCCAGAT-GTGGTCTTACATGTAATCACACATCG
56021852 ATGCCAACGTCCCAGATGTGGTCTTACA
1 ATGCCAACGTCCCAGATGTGGTCTTACA
56021880 GGAGAACACA
Statistics
Matches: 60, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
41 1 0.02
42 35 0.58
43 23 0.38
44 1 0.02
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.26
Consensus pattern (43 bp):
ATGCCAACGTCCCAGATGTGGTCTTACATGTAATCACACATCG
Done.