Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008493.1 Hibiscus syriacus cultivar Beakdansim tig00111336_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: 691020
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:184397 original size:17 final size:17
Alignment explanation
Indices: 184368--184422 Score: 83
Period size: 17 Copynumber: 3.2 Consensus size: 17
184358 ACCGGTCACA
184368 ACCCGACCCGACCCGTTG
1 ACCCGA-CCGACCCGTTG
184386 ACCCGACCGACCCGTTG
1 ACCCGACCGACCCGTTG
* *
184403 ACCCGACCAACCCGTAG
1 ACCCGACCGACCCGTTG
184420 ACC
1 ACC
184423 TGTTGACCGT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
17 29 0.83
18 6 0.17
ACGTcount: A:0.22, C:0.49, G:0.20, T:0.09
Consensus pattern (17 bp):
ACCCGACCGACCCGTTG
Found at i:184436 original size:7 final size:7
Alignment explanation
Indices: 184414--184453 Score: 53
Period size: 7 Copynumber: 5.4 Consensus size: 7
184404 CCCGACCAAC
*
184414 CCGTAGA
1 CCGTTGA
184421 CCTGTTGA
1 CC-GTTGA
184429 CCGTTGA
1 CCGTTGA
184436 CCCGTTGA
1 -CCGTTGA
184444 CCGTTGA
1 CCGTTGA
184451 CCG
1 CCG
184454 GCGTTGACCA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
7 17 0.57
8 13 0.43
ACGTcount: A:0.15, C:0.33, G:0.28, T:0.25
Consensus pattern (7 bp):
CCGTTGA
Found at i:184437 original size:15 final size:15
Alignment explanation
Indices: 184414--184462 Score: 62
Period size: 15 Copynumber: 3.1 Consensus size: 15
184404 CCCGACCAAC
* *
184414 CCGTAGACCTGTTGA
1 CCGTTGACCCGTTGA
184429 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
184444 CCGTTGACCGGCGTTGA
1 CCGTTGACC--CGTTGA
184461 CC
1 CC
184463 ACTGTTGACC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 22 0.73
17 8 0.27
ACGTcount: A:0.14, C:0.33, G:0.29, T:0.24
Consensus pattern (15 bp):
CCGTTGACCCGTTGA
Found at i:186948 original size:23 final size:23
Alignment explanation
Indices: 186922--187004 Score: 87
Period size: 23 Copynumber: 3.6 Consensus size: 23
186912 TCCGACTTGA
* *
186922 ATTCTGTTATGATCCTGACCTGG
1 ATTCTGATATGATCATGACCTGG
* *
186945 ATTCTGATCTGAT-ATTGACATGG
1 ATTCTGATATGATCA-TGACCTGG
* *
186968 ATTCTGATCTGATACATGACCTGT
1 ATTCTGATATGAT-CATGACCTGG
186992 ATTCTGATATGAT
1 ATTCTGATATGAT
187005 ACTTGACTTG
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
23 31 0.62
24 18 0.36
25 1 0.02
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.40
Consensus pattern (23 bp):
ATTCTGATATGATCATGACCTGG
Found at i:186995 original size:24 final size:24
Alignment explanation
Indices: 186937--187011 Score: 107
Period size: 24 Copynumber: 3.2 Consensus size: 24
186927 GTTATGATCC
186937 TGACCTGGATTCTGATCTGATA-T
1 TGACCTGGATTCTGATCTGATACT
* *
186960 TGACATGGATTCTGATCTGATACA
1 TGACCTGGATTCTGATCTGATACT
* *
186984 TGACCTGTATTCTGATATGATACT
1 TGACCTGGATTCTGATCTGATACT
187008 TGAC
1 TGAC
187012 TTGAATTATG
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
23 21 0.47
24 24 0.53
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.37
Consensus pattern (24 bp):
TGACCTGGATTCTGATCTGATACT
Found at i:188882 original size:22 final size:22
Alignment explanation
Indices: 188856--188898 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
188846 TAATAAATTA
188856 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
188878 TTTAAAATAAATGAATCCATA
1 TTTAAAATAAATCAATCCATA
188899 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:0.02, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:188907 original size:22 final size:22
Alignment explanation
Indices: 188858--188906 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
188848 ATAAATTATT
**
188858 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
188880 TAAAATAAATGAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
188903 TAAA
1 TAAA
188907 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:0.02, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:188987 original size:22 final size:22
Alignment explanation
Indices: 188914--188987 Score: 62
Period size: 22 Copynumber: 3.2 Consensus size: 22
188904 AAATTATTTA
188914 AAATAAATCAATCCATAC-AACT
1 AAATAAATCAATCCATACTAA-T
**
188936 ACAATAATATATCAATCCATA-TTTT
1 A-AAT-A-A-ATCAATCCATACTAAT
188961 AAAATAAATCAATCCATACTAAT
1 -AAATAAATCAATCCATACTAAT
188984 AAAT
1 AAAT
188988 TATTTAAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 14
0.69 0.07 0.24
Matches are distributed among these distances:
22 16 0.39
23 6 0.15
24 2 0.05
25 5 0.12
26 12 0.29
ACGTcount: A:0.53, C:0.18, G:0.00, T:0.30
Consensus pattern (22 bp):
AAATAAATCAATCCATACTAAT
Found at i:188997 original size:32 final size:32
Alignment explanation
Indices: 188958--189500 Score: 387
Period size: 32 Copynumber: 19.6 Consensus size: 32
188948 CAATCCATAT
188958 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
188990 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
189012 TTTAAAATAAATCAATCAATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
189044 TTTAAAATAAATCAATCCATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
189074 --T--AATAAATCAATCC--A-T-AT------
1 TTTAAAATAAATCAATCCATACTAATAAATTA
189092 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
189124 TTTAAAATAAACCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
189146 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
189178 TTTAAAATAAATCAAT-C---C--AT--A--A
1 TTTAAAATAAATCAATCCATACTAATAAATTA
189200 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
189232 TTTAAAATAAATCAATCCATACTAAAAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
189264 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
189286 TTTAAAATAAATAAATCCATACTAATAATTTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
189318 TTTAAAATAAATCAAT-C---C--AT--ATT-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
189341 TTT-AAACAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
189372 TCTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
189394 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
189426 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
189448 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
189480 TTTTAAAATAAATCAATCCAT
1 -TTTAAAATAAATCAATCCAT
189501 TGGTGTTTAT
Statistics
Matches: 409, Mismatches: 15, Indels: 173
0.69 0.03 0.29
Matches are distributed among these distances:
20 1 0.00
22 119 0.29
23 15 0.04
24 10 0.02
25 1 0.00
26 35 0.09
28 22 0.05
30 9 0.02
31 16 0.04
32 161 0.39
33 20 0.05
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:189001 original size:134 final size:134
Alignment explanation
Indices: 188846--189338 Score: 792
Period size: 134 Copynumber: 3.6 Consensus size: 134
188836 ACAACTACAA
*
188846 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATGAATCCATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
188911 TTAAAATAAATCAATCCATACAACTACAATAATATATCAATCCATATTTTAAAATAAATCAATCC
66 TTAAAATAAATCAATCCATACAACTACAATAATATATCAATCCATATTTTAAAATAAATCAATCC
188976 ATAC
131 ATAC
*
188980 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCAATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
*
189045 TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCC
66 TTAAAATAAATCAATCCATACAACTACAATAATATATCAATCCATATTTTAAAATAAATCAATCC
189110 ATAC
131 ATAC
*
189114 TAATAAATTATTTAAAATAAACCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
** * * *
189179 TTAAAATAAATCAATCCATA-ATTTAAAATAA-ATCAATCCATACTAATAAATTATTTAAAATAA
66 TTAAAATAAATCAATCCATACAACTACAATAATAT--ATCAAT-C-CAT--A-T-TTTAAAATAA
189242 ATCAATCCATAC
123 ATCAATCCATAC
* * *
189254 TAAAAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATAAATCCATACTAATAATTTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
189319 TTAAAATAAATCAATCCATA
66 TTAAAATAAATCAATCCATA
189339 TTTTTAAACA
Statistics
Matches: 336, Mismatches: 15, Indels: 10
0.93 0.04 0.03
Matches are distributed among these distances:
132 1 0.00
133 8 0.02
134 219 0.65
135 1 0.00
136 2 0.01
138 1 0.00
139 1 0.00
140 103 0.31
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (134 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
TTAAAATAAATCAATCCATACAACTACAATAATATATCAATCCATATTTTAAAATAAATCAATCC
ATAC
Found at i:189041 original size:22 final size:22
Alignment explanation
Indices: 188992--189040 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
188982 ATAAATTATT
* **
188992 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCAATATAA
189014 TAAAATAAATCAATCAATACTAA
1 TAAAATAAATCAATCAATA-TAA
189037 TAAA
1 TAAA
189041 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:0.57, C:0.12, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCAATATAA
Found at i:189121 original size:22 final size:23
Alignment explanation
Indices: 189046--189120 Score: 82
Period size: 22 Copynumber: 3.2 Consensus size: 23
189036 ATAAATTATT
189046 TAAAATAAATCAATCCATAC-AA
1 TAAAATAAATCAATCCATACTAA
**
189068 CTACAATAATAAATCAATCCATA-TTT
1 -T--AA-AATAAATCAATCCATACTAA
189094 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATACTAA
189117 TAAA
1 TAAA
189121 TTATTTAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
22 16 0.37
23 8 0.19
25 3 0.07
26 16 0.37
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (23 bp):
TAAAATAAATCAATCCATACTAA
Found at i:189150 original size:22 final size:22
Alignment explanation
Indices: 189124--189166 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
189114 TAATAAATTA
189124 TTTAAAATAAACCAATCCATAT
1 TTTAAAATAAACCAATCCATAT
*
189146 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAACCAATCCATA
189167 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:0.16, G:0.00, T:0.33
Consensus pattern (22 bp):
TTTAAAATAAACCAATCCATAT
Found at i:189175 original size:22 final size:22
Alignment explanation
Indices: 189126--189174 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
189116 ATAAATTATT
**
189126 TAAAATAAACCAATCCATATTT
1 TAAAATAAACCAATCCATATAA
*
189148 TAAAATAAATCAATCCATACTAA
1 TAAAATAAACCAATCCATA-TAA
189171 TAAA
1 TAAA
189175 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:0.16, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAAATAAACCAATCCATATAA
Found at i:189204 original size:22 final size:22
Alignment explanation
Indices: 189177--189220 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
189167 CTAATAAATT
189177 ATTTAAAATAAATCAATCCATA
1 ATTTAAAATAAATCAATCCATA
189199 ATTTAAAATAAATCAATCCATA
1 ATTTAAAATAAATCAATCCATA
189221 CTAATAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.32
Consensus pattern (22 bp):
ATTTAAAATAAATCAATCCATA
Found at i:189236 original size:86 final size:87
Alignment explanation
Indices: 189143--189500 Score: 458
Period size: 86 Copynumber: 4.3 Consensus size: 87
189133 AACCAATCCA
*
189143 TATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAATTTAAAAT
1 TATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAAT
*
189208 AAATCAATCCATACTAATAAAT
66 AAATAAATCCATACTAATAAAT
*
189230 TA-TTTAAAATAAATCAATCCATACTAAAAAATTATTTAAAATAAATCAATCCATATTTTAAAAT
1 TATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAAT
*
189294 AAATAAATCCATACTAATAATT
66 AAATAAATCCATACTAATAAAT
* ** *
189316 TA-TTTAAAATAAATCAAT-C---C--AT--ATT-TTT-AAACAAATCAATCCATACTAATAAAT
1 TATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAA
** ** **
189370 TATCTAAAATAAAT-C-AATCCA-
65 TAAAT-AAATCCATACTAATAAAT
189391 TATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAAT
1 TATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAAT
*
189456 AAATCAATCCATACTAATAAAT
66 AAATAAATCCATACTAATAAAT
189478 TATTTTAAAATAAATCAATCCAT
1 TATTTTAAAATAAATCAATCCAT
189501 TGGTGTTTAT
Statistics
Matches: 228, Mismatches: 27, Indels: 32
0.79 0.09 0.11
Matches are distributed among these distances:
75 2 0.01
76 35 0.15
77 13 0.06
78 9 0.04
80 2 0.01
82 3 0.01
84 8 0.04
85 13 0.06
86 118 0.52
87 25 0.11
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (87 bp):
TATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAAT
AAATAAATCCATACTAATAAAT
Found at i:189261 original size:54 final size:54
Alignment explanation
Indices: 188846--189252 Score: 381
Period size: 54 Copynumber: 7.6 Consensus size: 54
188836 ACAACTACAA
*
188846 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATGAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* ** *
188900 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATATATCAATCCATA-
1 TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATAC
** * ** * ** **
188957 TTTTAAAATAAAT-CAATCCATACTAATAAAT-TATTTAAAATAAATCAATCCATA-
1 TAATAAATTATTTAAAATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCCATAC
** * ** * * **
189011 TTTTAAAATAAAT-CAATCAATACTAATAAAT-TATTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCCATAC
*
189066 -AACTACA--A--T--AATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAA-TAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
189114 TAATAAATTATTTAAAATAAACCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
189168 TAATAAATTATTTAAAATAAATCAATCCATAATTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
189222 TAATAAATTATTTAAAATAAATCAATCCATA
1 TAATAAATTATTTAAAATAAATCAATCCATA
189253 CTAAAAAATT
Statistics
Matches: 306, Mismatches: 30, Indels: 34
0.83 0.08 0.09
Matches are distributed among these distances:
48 30 0.10
49 4 0.01
50 7 0.02
51 1 0.00
52 1 0.00
53 1 0.00
54 219 0.72
55 6 0.02
56 5 0.02
57 13 0.04
58 19 0.06
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
Found at i:189290 original size:22 final size:22
Alignment explanation
Indices: 189264--189306 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
189254 TAAAAAATTA
*
189264 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATAAATCCATAT
189286 TTTAAAATAAATAAATCCATA
1 TTTAAAATAAATAAATCCATA
189307 CTAATAATTT
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:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATAAATCCATAT
Found at i:189290 original size:54 final size:54
Alignment explanation
Indices: 189232--189500 Score: 475
Period size: 54 Copynumber: 5.0 Consensus size: 54
189222 TAATAAATTA
*
189232 TTTAAAATAAATCAATCCATACTAAAAAATTATTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
* *
189286 TTTAAAATAAATAAATCCATACTAATAATTTATTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
* * *
189340 TTTTAAACAAATCAATCCATACTAATAAATTATCTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
189394 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
189448 TTTAAAATAAATCAATCCATACTAATAAATTATTTTAAAATAAATCAATCCAT
1 TTTAAAATAAATCAATCCATACTAATAAATTA-TTTAAAATAAATCAATCCAT
189501 TGGTGTTTAT
Statistics
Matches: 203, Mismatches: 11, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
54 183 0.90
55 20 0.10
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (54 bp):
TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
Found at i:189290 original size:108 final size:107
Alignment explanation
Indices: 188856--189500 Score: 500
Period size: 108 Copynumber: 6.0 Consensus size: 107
188846 TAATAAATTA
* * *
188856 TTTAAAATAAATCAATCCAT-ATTTTAAAATAAATGAATCCATACTAATAAATTATTTAAAATAA
1 TTTAAAATAAATCAATCCATAATATTAAAATAAATAAATCAAT-C-AATAAATTATTTAAAATAA
* *
188920 ATCAATCCATAC-AACTACA--A--T--AATATATCAATCCATAT
64 ATCAATCCATACTAA-TAAATTATTTAAAATAAATCAATCCATAT
* * * ** * **
188958 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCA-TATTTTAAAATAA
1 TTTAAAATAAATCAATCCATAATATTAAAATAAAT-AAATCAATCAATAAATTA-TTTAAAATAA
* *
189022 ATCAATCAATACTAATAAATTATTTAAAATAAATCAATCCATACAAC
64 ATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCAT---AT
** * * *
189069 TACAATAATAAATCAATCCAT-ATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATA
1 TTTAA-AATAAATCAATCCATAATATTAAAATAAATAAATCAAT-C-AATAAATTATTTAAAATA
* ** * ** * ** **
189133 AACCAATCCATA-TTTTAAAATAAAT-CAATCCATACTAATAAAT-T
63 AATCAATCCATACTAATAAATTATTTAAAATAAAT-C-AATCCATAT
* *
189177 ATTTAAAATAAATCAATCCATAAT-TTAAAATAAATCAATCCATACTAATAAATTATTTAAAATA
1 -TTTAAAATAAATCAATCCATAATATTAAAATAAATAAATCAAT-C-AATAAATTATTTAAAATA
*
189241 AATCAATCCATACTAAAAAATTATTTAAAATAAATCAATCCATAT
63 AATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
* * ** *
189286 TTTAAAATAAATAAATCCATACTAATAATTTATTTAAAATAAATCAATCCAT--ATT-TTT-AAA
1 TTTAAAATAAATCAATCC--A-TAAT-ATTAAAAT-AAATAAATCAATCAATAAATTATTTAAAA
* *
189347 CAAATCAATCCATACTAATAAATTATCTAAAATAAATCAATCCATAT
61 TAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
* * * ** * **
189394 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCA-TATTTTAAAATAA
1 TTTAAAATAAATCAATCCATAATATTAAAATAAAT-AAATCAATCAATAAATTA-TTTAAAATAA
189458 ATCAATCCATACTAATAAATTATTTTAAAATAAATCAATCCAT
64 ATCAATCCATACTAATAAATTA-TTTAAAATAAATCAATCCAT
189501 TGGTGTTTAT
Statistics
Matches: 430, Mismatches: 76, Indels: 67
0.75 0.13 0.12
Matches are distributed among these distances:
101 2 0.00
102 48 0.11
103 13 0.03
104 21 0.05
105 4 0.01
106 3 0.01
107 3 0.01
108 193 0.45
109 36 0.08
110 19 0.04
111 26 0.06
112 45 0.10
113 7 0.02
114 10 0.02
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (107 bp):
TTTAAAATAAATCAATCCATAATATTAAAATAAATAAATCAATCAATAAATTATTTAAAATAAAT
CAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
Found at i:189368 original size:22 final size:22
Alignment explanation
Indices: 189326--189368 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
189316 TATTTAAAAT
* **
189326 AAATCAATCCATATTTTTAAAC
1 AAATCAATCCATACTAATAAAC
189348 AAATCAATCCATACTAATAAA
1 AAATCAATCCATACTAATAAA
189369 TTATCTAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.51, C:0.19, G:0.00, T:0.30
Consensus pattern (22 bp):
AAATCAATCCATACTAATAAAC
Found at i:189423 original size:22 final size:22
Alignment explanation
Indices: 189374--189422 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
189364 ATAAATTATC
**
189374 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
189396 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
189419 TAAA
1 TAAA
189423 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:189452 original size:22 final size:22
Alignment explanation
Indices: 189426--189468 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
189416 TAATAAATTA
189426 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
189448 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
189469 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:189477 original size:22 final size:22
Alignment explanation
Indices: 189428--189476 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
189418 ATAAATTATT
**
189428 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
189450 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
189473 TAAA
1 TAAA
189477 TTATTTTAAA
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:192634 original size:13 final size:13
Alignment explanation
Indices: 192616--192643 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
192606 TGGTCAAGGC
192616 AAAAAAATATGCA
1 AAAAAAATATGCA
192629 AAAAAAATATGCA
1 AAAAAAATATGCA
192642 AA
1 AA
192644 GGTGAACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.71, C:0.07, G:0.07, T:0.14
Consensus pattern (13 bp):
AAAAAAATATGCA
Found at i:193460 original size:21 final size:24
Alignment explanation
Indices: 193427--193470 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 24
193417 TGATTTGGTC
193427 TTATCTCAATTAAA-T-GAATATT
1 TTATCTCAATTAAAGTGGAATATT
*
193449 TTAT-TCATTTAAAGTGGAATAT
1 TTATCTCAATTAAAGTGGAATAT
193471 AATGTAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 8 0.42
22 5 0.26
23 6 0.32
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.45
Consensus pattern (24 bp):
TTATCTCAATTAAAGTGGAATATT
Found at i:195127 original size:45 final size:45
Alignment explanation
Indices: 195062--195235 Score: 287
Period size: 45 Copynumber: 3.9 Consensus size: 45
195052 AATGATAAGC
* *
195062 TGGT-AAATAAGCGTACGAGCTTATGGAATAAATGGTAATTATAT
1 TGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATAT
*
195106 TGGTAAAATAAGCTTATGAGCTTATGGAATAAATGGTAAGTATAT
1 TGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATAT
* *
195151 TGGTAAAATAAGCTTACGATCTTATAGAATAAATGGTAAGTATAT
1 TGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATAT
*
195196 TGGTAAAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 TGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
195236 AAATTTTATA
Statistics
Matches: 120, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
44 4 0.03
45 116 0.97
ACGTcount: A:0.40, C:0.06, G:0.22, T:0.32
Consensus pattern (45 bp):
TGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATAT
Found at i:195160 original size:24 final size:24
Alignment explanation
Indices: 195133--195206 Score: 66
Period size: 22 Copynumber: 3.2 Consensus size: 24
195123 GAGCTTATGG
195133 AATAAATGGTAAGTATATTGGTAA
1 AATAAATGGTAAGTATATTGGTAA
* * * * *
195157 AAT-AA-GCTTACG-ATCTT-ATAG
1 AATAAATG-GTAAGTATATTGGTAA
195178 AATAAATGGTAAGTATATTGGTAA
1 AATAAATGGTAAGTATATTGGTAA
195202 AATAA
1 AATAA
195207 GCTTACGAGC
Statistics
Matches: 35, Mismatches: 10, Indels: 10
0.64 0.18 0.18
Matches are distributed among these distances:
21 5 0.14
22 10 0.29
23 10 0.29
24 10 0.29
ACGTcount: A:0.46, C:0.04, G:0.18, T:0.32
Consensus pattern (24 bp):
AATAAATGGTAAGTATATTGGTAA
Found at i:207844 original size:18 final size:18
Alignment explanation
Indices: 207817--207856 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
207807 ATCAGGTGAT
207817 AATT-GAAACTATGAATC
1 AATTAGAAACTATGAATC
207834 AATTAGAAACTATGAATC
1 AATTAGAAACTATGAATC
207852 AATTA
1 AATTA
207857 AGCGGTGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (18 bp):
AATTAGAAACTATGAATC
Found at i:216446 original size:62 final size:61
Alignment explanation
Indices: 216345--216573 Score: 201
Period size: 62 Copynumber: 3.7 Consensus size: 61
216335 AAGAGATTTC
* *
216345 TCAACCCTTGACTTCCTCAAGAAGAGAAGTCAATCTTTGTTATTTTCG-ATACCCCAGTAGAG
1 TCAACCCTTGACTTCCTCGAGAAGAGAAGTCAA-CTTTGTTATTTTCGAAT-CCCCAATAGAG
* * * *
216407 TCAACCATTGAATTCCTCGTGAAGAGAAGTCAACGTTTGTTATTTTTGAATCCCCAATAGAG
1 TCAACCCTTGACTTCCTCGAGAAGAGAAGTCAAC-TTTGTTATTTTCGAATCCCCAATAGAG
* * * * ** * ** *
216469 TCGACCCTCGACTTTCTCGGGAAGAGAAGTCAACCTTTGTTA-TCCCTGACTCTTCAGTAGAG
1 TCAACCCTTGACTTCCTCGAGAAGAGAAGTCAA-CTTTGTTATTTTC-GAATCCCCAATAGAG
** ** *
216531 TCAATACTTGACTTTATCGTGAAGAGAAGTCAACCTTTGTTAT
1 TCAACCCTTGACTTCCTCGAGAAGAGAAGTCAA-CTTTGTTAT
216574 CACTAATTTC
Statistics
Matches: 137, Mismatches: 25, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
61 2 0.01
62 132 0.96
63 3 0.02
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (61 bp):
TCAACCCTTGACTTCCTCGAGAAGAGAAGTCAACTTTGTTATTTTCGAATCCCCAATAGAG
Found at i:216856 original size:82 final size:82
Alignment explanation
Indices: 216620--216857 Score: 289
Period size: 83 Copynumber: 2.9 Consensus size: 82
216610 TCTCTTGAAA
* * *
216620 GAATAGTGGAGCAAACATGTCTTCCAAAATTGATCTGACTACACAAAAAAGAGGCACAGATCAAG
1 GAATAGTGGAGCAGACACGTCTTCCAAAATTGATCTGACTACCCAAAAAAGAGGCACAGATCAAG
* * * * *
216685 TTTGATTTCCCCTGAAT
66 TATGATCTACACTAAAT
* * * **
216702 GAATAGTGGAGCAGACACATCTTTCAAAAATTGATCTGACTACCCGAACGAGAGGCACAGATCAA
1 GAATAGTGGAGCAGACACGTC-TTCCAAAATTGATCTGACTACCCAAAAAAGAGGCACAGATCAA
* *
216767 GTCTGATCTATACTAAAT
65 GTATGATCTACACTAAAT
* * *
216785 GAATTA-TGGAGTAGACACGTCTTCCAAAATTGATATGACTACCCAAAAAAGAGGCACAAATCAA
1 GAA-TAGTGGAGCAGACACGTCTTCCAAAATTGATCTGACTACCCAAAAAAGAGGCACAGATCAA
216849 GTATGATCT
65 GTATGATCT
216858 CCCCTGAAAT
Statistics
Matches: 131, Mismatches: 23, Indels: 4
0.83 0.15 0.03
Matches are distributed among these distances:
82 63 0.48
83 66 0.50
84 2 0.02
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.24
Consensus pattern (82 bp):
GAATAGTGGAGCAGACACGTCTTCCAAAATTGATCTGACTACCCAAAAAAGAGGCACAGATCAAG
TATGATCTACACTAAAT
Found at i:216881 original size:82 final size:83
Alignment explanation
Indices: 216605--216877 Score: 313
Period size: 82 Copynumber: 3.3 Consensus size: 83
216595 ATCTTGATTC
* * * * *
216605 TGATCTCTCTTGAAA-GAATAGTGGAGCAAACATGTCTTCCAAAATTGATCTGACTACACAAAAA
1 TGATCTCCCCTGAAATGAATAGTGGAGCAGACACGTCTTCCAAAATTGATCTGACTACCCAAAAA
*
216669 AGAGGCACAGATCAAGTT
66 AGAGGCACAGATCAAGTA
* * * * *
216687 TGATTTCCCCTG-AATGAATAGTGGAGCAGACACATCTTTCAAAAATTGATCTGACTACCCGAAC
1 TGATCTCCCCTGAAATGAATAGTGGAGCAGACACGTC-TTCCAAAATTGATCTGACTACCCAAAA
* *
216751 GAGAGGCACAGATCAAGTC
65 AAGAGGCACAGATCAAGTA
*** * *
216770 TGATCTATACT-AAATGAATTA-TGGAGTAGACACGTCTTCCAAAATTGATATGACTACCCAAAA
1 TGATCTCCCCTGAAATGAA-TAGTGGAGCAGACACGTCTTCCAAAATTGATCTGACTACCCAAAA
*
216833 AAGAGGCACAAATCAAGTA
65 AAGAGGCACAGATCAAGTA
*
216852 TGATCTCCCCTGAAAT-AAGAGTGGAG
1 TGATCTCCCCTGAAATGAATAGTGGAG
216878 TAGATTTCTC
Statistics
Matches: 156, Mismatches: 29, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
81 3 0.02
82 81 0.52
83 70 0.45
84 2 0.01
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (83 bp):
TGATCTCCCCTGAAATGAATAGTGGAGCAGACACGTCTTCCAAAATTGATCTGACTACCCAAAAA
AGAGGCACAGATCAAGTA
Found at i:217014 original size:3 final size:3
Alignment explanation
Indices: 217006--217031 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
216996 TCAATTGTTA
217006 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
217032 AATAATAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:221521 original size:23 final size:23
Alignment explanation
Indices: 221493--221538 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
221483 CCAAATCAGG
*
221493 CAAAATCAGGCCCAACTAAGACC
1 CAAAATCAGACCCAACTAAGACC
*
221516 CAAAATCAGACCCGACTAAGACC
1 CAAAATCAGACCCAACTAAGACC
221539 TAACCAAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.43, C:0.35, G:0.13, T:0.09
Consensus pattern (23 bp):
CAAAATCAGACCCAACTAAGACC
Found at i:222543 original size:509 final size:496
Alignment explanation
Indices: 221582--222577 Score: 1654
Period size: 509 Copynumber: 2.0 Consensus size: 496
221572 TATAACCCAA
* *
221582 GTCTAACCCTAACCCTAGGGTATCACTTTATTCCCCAAATCAATGGCCACCATCCTCTGCCCCAA
1 GTCTAACCCTAACCCTAGGGTATCACTTCATTCCCCAAACCAATGGCCACCATCCTCTGCCCCAA
*
221647 TCCCTGCAAAACCATCCATGCACGCCGGTAGAGCCACACTCCACGCAACCCTGCAAAAACAACAG
66 TCCCTGCAAAACCATCCATGCACACCGGTAGAGCCACACTCCACGCAACCCTGCAAAAACAACAG
221712 AGAAAAAAAAACAATGATTTATAAATGCTTTGTAAACGAGTATAAAAAAACCCATGCAAAACGAG
131 AGAAAAAAAAACAATGATTTATAAATGCTTTGTAAACGAGTATAAAAAAACCCATGCAAAACGAG
221777 AAAAATCTCTAAAAAAACATTGTAAACTGTTTTTTCGAAGCAATAACAAAATTTTTTGAAGATTA
196 AAAAATCTCTAAAAAAACATTGTAAACTGTTTTTTCGAAGCAATAACAAAATTTTTTGAAGATTA
*
221842 TTTATCTTTCTGTTTCTTTAATATTTGAATAGCTTGTTGTTTTTTTCCTTTTTTTATTGTTATTG
261 TTTATCTTTCTGTTTCTTTAATATTTGAATAGCTTGTTGTTTTTTTCCTTTTTTTACTGTTATTG
221907 GGTTTAAATCTCAGGAAAAGGAAAGATTCTTCTTTTATATTTCGAAATAAAATCATACCCTTTTA
326 GGTTTAAATCTCAGGAAAAGGAAAGATTCTTCTTTTATATTTCGAAATAAAATCATACCCTTTTA
* *
221972 GTTTCATTTAAAAAACCATCAGTATGTCTCAATTAATAAACAACAACAGAGGTTTTTTAACAATA
391 GTTTCATTTAAAAAAACATCAGTATGTCTAAATTAATAAACAACAACAGAGGTTTTTTAACAATA
*
222037 TCAACCAACCATTTTGCAATAAAAACAAAAAACAATGATAG
456 TCAACCAACCATTTTACAATAAAAACAAAAAACAATGATAG
* *
222078 GTCTAACCCTAGCCCTAGGGTATCACTTCATTCCCCAAACCAATGGCCACCATGCTCTGCCCCAA
1 GTCTAACCCTAACCCTAGGGTATCACTTCATTCCCCAAACCAATGGCCACCATCCTCTGCCCCAA
*
222143 TCCCTGCAAAACCATCCATGCACATCGGTAGAGCCACACTCCACGCAACCCTGCAAAAACAACAG
66 TCCCTGCAAAACCATCCATGCACACCGGTAGAGCCACACTCCACGCAACCCTGCAAAAACAACAG
* *
222208 AGAAAAACAAAATAACAATGATTTGTAAATGCTTTGTATACGAGTAT-AAAAAACCCATGCAAAA
131 AG--AAA-AAAA-AACAATGATTTATAAATGCTTTGTAAACGAGTATAAAAAAACCCATGCAAAA
* * *
222272 CGAGAAAAATATCTATGGACTCTAAAAAAACATTGTAACCTGTTTTTTCGCAGCAATAACAAATT
192 CGAG--AAA-A---AT---CTCTAAAAAAACATTGTAAACTGTTTTTTCGAAGCAATAACAAAAT
222337 TTTTTGAAGATTATTTATCTTTCTGTTTCTTTAATATTTGAATAGCTTGTTGTTTTTTTCCTTTT
248 TTTTTGAAGATTATTTATCTTTCTGTTTCTTTAATATTTGAATAGCTTGTTGTTTTTTTCC-TTT
* *
222402 TTTTACTGCTT-TTGGGTTTAAATCTCAGGAAAATGAAAGATTCTTCTTTTATATTTTGAAATAA
312 TTTTACTG-TTATTGGGTTTAAATCTCAGGAAAAGGAAAGATTCTTCTTTTATATTTCGAAATAA
* *
222466 AATCATACCCTTTTAGTTTCATTTAAAAAAACATCAGTATGTCTAAATTAATAAATAACGACAGA
376 AATCATACCCTTTTAGTTTCATTTAAAAAAACATCAGTATGTCTAAATTAATAAACAACAACAGA
* *
222531 GTTTTTTTAACAATATCAACCAACCATTTTACAGTAAAAACAAAAAA
441 GGTTTTTTAACAATATCAACCAACCATTTTACAATAAAAACAAAAAA
222578 AAAGAAAATG
Statistics
Matches: 464, Mismatches: 21, Indels: 17
0.92 0.04 0.03
Matches are distributed among these distances:
496 126 0.27
498 3 0.01
499 25 0.05
500 32 0.07
501 3 0.01
502 1 0.00
505 2 0.00
508 104 0.22
509 166 0.36
510 2 0.00
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.32
Consensus pattern (496 bp):
GTCTAACCCTAACCCTAGGGTATCACTTCATTCCCCAAACCAATGGCCACCATCCTCTGCCCCAA
TCCCTGCAAAACCATCCATGCACACCGGTAGAGCCACACTCCACGCAACCCTGCAAAAACAACAG
AGAAAAAAAAACAATGATTTATAAATGCTTTGTAAACGAGTATAAAAAAACCCATGCAAAACGAG
AAAAATCTCTAAAAAAACATTGTAAACTGTTTTTTCGAAGCAATAACAAAATTTTTTGAAGATTA
TTTATCTTTCTGTTTCTTTAATATTTGAATAGCTTGTTGTTTTTTTCCTTTTTTTACTGTTATTG
GGTTTAAATCTCAGGAAAAGGAAAGATTCTTCTTTTATATTTCGAAATAAAATCATACCCTTTTA
GTTTCATTTAAAAAAACATCAGTATGTCTAAATTAATAAACAACAACAGAGGTTTTTTAACAATA
TCAACCAACCATTTTACAATAAAAACAAAAAACAATGATAG
Found at i:223248 original size:22 final size:21
Alignment explanation
Indices: 223216--223257 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
223206 TGTGCATGTT
*
223216 TGTTGTATTTTTATTTTTTTTA
1 TGTTGTATTTTT-TCTTTTTTA
*
223238 TGTTGTGTTTTTTCTTTTTT
1 TGTTGTATTTTTTCTTTTTT
223258 CTATTTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.07, C:0.02, G:0.12, T:0.79
Consensus pattern (21 bp):
TGTTGTATTTTTTCTTTTTTA
Found at i:228328 original size:23 final size:23
Alignment explanation
Indices: 228290--228351 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
228280 TACCAAAAAA
* *
228290 TAAAATAAAATAAAAATCCATTCT
1 TAAAAT-ATATAAAAATCAATTCT
* *
228314 TAAAATATATAAAAATTAATTTT
1 TAAAATATATAAAAATCAATTCT
*
228337 TAAAAT-TACAAAAAT
1 TAAAATATATAAAAAT
228352 ATTTTTTAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
22 8 0.24
23 19 0.58
24 6 0.18
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (23 bp):
TAAAATATATAAAAATCAATTCT
Found at i:228357 original size:21 final size:23
Alignment explanation
Indices: 228313--228361 Score: 66
Period size: 21 Copynumber: 2.2 Consensus size: 23
228303 AAATCCATTC
*
228313 TTAAAATATATAAAAATTAATTT
1 TTAAAATATACAAAAATTAATTT
*
228336 TTAAAAT-TACAAAAA-TATTTT
1 TTAAAATATACAAAAATTAATTT
228357 TTAAA
1 TTAAA
228362 TTTATAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 10 0.42
22 7 0.29
23 7 0.29
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
TTAAAATATACAAAAATTAATTT
Found at i:232113 original size:18 final size:18
Alignment explanation
Indices: 232090--232126 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
232080 AGCAGTCGAA
232090 AGAAATTATTATCCTAAT
1 AGAAATTATTATCCTAAT
232108 AGAAATTATTATCCTAAT
1 AGAAATTATTATCCTAAT
232126 A
1 A
232127 TCTTCGAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.11, G:0.05, T:0.38
Consensus pattern (18 bp):
AGAAATTATTATCCTAAT
Found at i:232518 original size:31 final size:32
Alignment explanation
Indices: 232466--232543 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 32
232456 TCTATTGTCA
* *
232466 ATTTTTGTAAGT-AATTGAACATGCTTATG-T
1 ATTTTTTTAAGTAAATTAAACATGCTTATGTT
* * *
232496 CTTTTTTTAAGTAAATTAAACATGTTTCTGTT
1 ATTTTTTTAAGTAAATTAAACATGCTTATGTT
232528 ATTTTTTGTAAGTAAA
1 ATTTTTT-TAAGTAAA
232544 ATTAGATATA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
30 10 0.26
31 14 0.36
32 7 0.18
33 8 0.21
ACGTcount: A:0.31, C:0.06, G:0.13, T:0.50
Consensus pattern (32 bp):
ATTTTTTTAAGTAAATTAAACATGCTTATGTT
Found at i:233042 original size:52 final size:52
Alignment explanation
Indices: 232956--233054 Score: 180
Period size: 52 Copynumber: 1.9 Consensus size: 52
232946 TCGAGCCAAA
232956 CTCAACAATACTCAAGCTCGACTCAGCTCATTTACACCCCTGGTCAATCAAG
1 CTCAACAATACTCAAGCTCGACTCAGCTCATTTACACCCCTGGTCAATCAAG
* *
233008 CTCAGCAATACTCAAGCTCGACTCAGCTCGTTTACACCCCTGGTCAA
1 CTCAACAATACTCAAGCTCGACTCAGCTCATTTACACCCCTGGTCAA
233055 CAGGTTAATG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.28, C:0.35, G:0.13, T:0.23
Consensus pattern (52 bp):
CTCAACAATACTCAAGCTCGACTCAGCTCATTTACACCCCTGGTCAATCAAG
Found at i:238663 original size:55 final size:55
Alignment explanation
Indices: 238569--239015 Score: 745
Period size: 55 Copynumber: 8.1 Consensus size: 55
238559 ATATCTTCGT
* ** *
238569 CAATCGTGTCTGCTCCCTATTT-TTCAGAGAGTATAAGACTCGAATGAT-TCTCGA
1 CAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCT-TCAA
* * *
238623 TAATTGTGCCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAA
1 CAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAA
* *
238678 CAATCGTGTCTGTTCCCTATTTGTTCAGAGAGTATGAGACTCGAACAATCTTCAA
1 CAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAA
238733 CAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAA
1 CAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAA
*
238788 CAATCGTGCCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAA
1 CAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAA
* *
238843 CAATTGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAAACAATCTTTAA
1 CAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCG-AACAATCTTCAA
*
238899 CAATCGTGTCTGCTCCCTATTTCTTCAAAGAGTATGAGACTCGAACAATCTTCAA
1 CAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAA
238954 CAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAA
1 CAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAA
239009 CAATCGT
1 CAATCGT
239016 TGGGAAACCT
Statistics
Matches: 368, Mismatches: 22, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
54 19 0.05
55 296 0.80
56 53 0.14
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.32
Consensus pattern (55 bp):
CAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAA
Found at i:238973 original size:221 final size:219
Alignment explanation
Indices: 238569--239015 Score: 761
Period size: 221 Copynumber: 2.0 Consensus size: 219
238559 ATATCTTCGT
* ** * *
238569 CAATCGTGTCTGCTCCCTATTTTTCAGAGAGTATAAGACTCGAATGATTCTCGATAATTGTGCCT
1 CAATCGTGCCTGCTCCCTATTTTTCAGAGAGTATAAGACTCGAACAATTCTCAACAATTGTGCCT
*
238634 GCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGTTCCCTATT
66 GCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATT
* *
238699 TGTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGA
131 TCTTCAAAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGA
238764 GTATGAGACTCGAACAATCTTCAA
196 GTATGAGACTCGAACAATCTTCAA
* *
238788 CAATCGTGCCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAA-TCTTCAACAATTGTGT
1 CAATCGTGCCTGCTCCCTATTT-TTCAGAGAGTATAAGACTCGAACAATTC-TCAACAATTGTGC
*
238852 CTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAAACAATCTTTAACAATCGTGTCTGCTCCCT
64 CTGCTCCCTATTTCTTCAGAGAGTATGAGACTCG-AACAATCTTCAACAATCGTGTCTGCTCCCT
238917 ATTTCTTCAAAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAG
128 ATTTCTTCAAAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAG
238982 AGAGTATGAGACTCGAACAATCTTCAA
193 AGAGTATGAGACTCGAACAATCTTCAA
239009 CAATCGT
1 CAATCGT
239016 TGGGAAACCT
Statistics
Matches: 214, Mismatches: 11, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
219 23 0.11
220 66 0.31
221 125 0.58
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.32
Consensus pattern (219 bp):
CAATCGTGCCTGCTCCCTATTTTTCAGAGAGTATAAGACTCGAACAATTCTCAACAATTGTGCCT
GCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATT
TCTTCAAAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGA
GTATGAGACTCGAACAATCTTCAA
Found at i:238981 original size:166 final size:165
Alignment explanation
Indices: 238569--239015 Score: 754
Period size: 166 Copynumber: 2.7 Consensus size: 165
238559 ATATCTTCGT
* ** * * *
238569 CAATCGTGTCTGCTCCCTATTT-TTCAGAGAGTATAAGACTCGAATGAT-TCTCGATAATTGTGC
1 CAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCT-TCAACAATCGTGC
*
238632 CTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGTTCCCTA
65 CTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTA
*
238697 TTTGTTCAGAGAGTATGAGACTCGAACAATCTTCAA
130 TTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAA
238733 CAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGCC
1 CAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGCC
*
238798 TGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATTGTGTCTGCTCCCTAT
66 TGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTAT
*
238863 TTCTTCAGAGAGTATGAGACTCGAAACAATCTTTAA
131 TTCTTCAGAGAGTATGAGACTCG-AACAATCTTCAA
* *
238899 CAATCGTGTCTGCTCCCTATTTCTTCAAAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTC
1 CAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGCC
238964 TGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGT
66 TGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGT
239016 TGGGAAACCT
Statistics
Matches: 267, Mismatches: 13, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
164 22 0.08
165 119 0.45
166 126 0.47
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.32
Consensus pattern (165 bp):
CAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGCC
TGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTAT
TTCTTCAGAGAGTATGAGACTCGAACAATCTTCAA
Found at i:239956 original size:8 final size:8
Alignment explanation
Indices: 239938--239989 Score: 70
Period size: 8 Copynumber: 6.5 Consensus size: 8
239928 GAACCCTTCT
239938 TTTTTTCCA
1 TTTTTT-CA
239947 TTTTTTCA
1 TTTTTTCA
239955 TTTTTT-A
1 TTTTTTCA
*
239962 TTTTTTTA
1 TTTTTTCA
*
239970 TTTTTTTA
1 TTTTTTCA
239978 TTTTTTCA
1 TTTTTTCA
239986 TTTT
1 TTTT
239990 CACTCATTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
7 7 0.17
8 28 0.68
9 6 0.15
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTTTCA
Found at i:249787 original size:17 final size:17
Alignment explanation
Indices: 249765--249832 Score: 81
Period size: 17 Copynumber: 4.2 Consensus size: 17
249755 GACCGGTCAC
*
249765 GACCCGACCCGATAGTT
1 GACCCGACCCGACAGTT
*
249782 GACCCGACCCGACCGTT
1 GACCCGACCCGACAGTT
249799 GACCCGA-CC--C-GTT
1 GACCCGACCCGACAGTT
*
249812 GACCCGACCCGACCGTT
1 GACCCGACCCGACAGTT
249829 GACC
1 GACC
249833 GTTGACCGTT
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
13 10 0.22
14 3 0.07
16 3 0.07
17 29 0.64
ACGTcount: A:0.19, C:0.44, G:0.24, T:0.13
Consensus pattern (17 bp):
GACCCGACCCGACAGTT
Found at i:249812 original size:13 final size:13
Alignment explanation
Indices: 249787--249822 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
249777 TAGTTGACCC
249787 GACCCGA-CCGTT
1 GACCCGACCCGTT
249799 GACCCGACCCGTT
1 GACCCGACCCGTT
249812 GACCCGACCCG
1 GACCCGACCCG
249823 ACCGTTGACC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 7 0.30
13 16 0.70
ACGTcount: A:0.17, C:0.47, G:0.25, T:0.11
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:249834 original size:7 final size:7
Alignment explanation
Indices: 249822--249854 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
249812 GACCCGACCC
249822 GACCGTT
1 GACCGTT
249829 GACCGTT
1 GACCGTT
249836 GACCGTT
1 GACCGTT
249843 GACCGTT
1 GACCGTT
249850 GACCG
1 GACCG
249855 GTGCTATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.24
Consensus pattern (7 bp):
GACCGTT
Found at i:249896 original size:29 final size:29
Alignment explanation
Indices: 249854--249935 Score: 146
Period size: 29 Copynumber: 2.8 Consensus size: 29
249844 ACCGTTGACC
*
249854 GGTGCTATTTTGGTAAATAATTCGGTTTT
1 GGTGCTATTCTGGTAAATAATTCGGTTTT
*
249883 GGTGCTATTCTGGTAAATAATTCAGTTTT
1 GGTGCTATTCTGGTAAATAATTCGGTTTT
249912 GGTGCTATTCTGGTAAATAATTCG
1 GGTGCTATTCTGGTAAATAATTCG
249936 AAAAAGGGTG
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.23, C:0.10, G:0.23, T:0.44
Consensus pattern (29 bp):
GGTGCTATTCTGGTAAATAATTCGGTTTT
Found at i:249948 original size:30 final size:29
Alignment explanation
Indices: 249883--249958 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
249873 ATTCGGTTTT
*****
249883 GGTGCTATTCTGGTAAATAATTCAGTTTT
1 GGTGCTATTCTGGTAAATAATTCAAAAAG
249912 GGTGCTATTCTGGTAAATAATTCGAAAAAG
1 GGTGCTATTCTGGTAAATAATTC-AAAAAG
249942 GGTGCTATT-TGTGTAAA
1 GGTGCTATTCTG-GTAAA
249959 ATGTTCAACA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
29 25 0.62
30 15 0.38
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (29 bp):
GGTGCTATTCTGGTAAATAATTCAAAAAG
Found at i:256770 original size:17 final size:17
Alignment explanation
Indices: 256748--256792 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
256738 GACCGGTCAC
*
256748 GACCCGACCCGATAGTT
1 GACCCGACCCGACAGTT
*
256765 GACCCGACCCGACCGTT
1 GACCCGACCCGACAGTT
256782 GACCCGACCCG
1 GACCCGACCCG
256793 TTGACCCGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.20, C:0.44, G:0.24, T:0.11
Consensus pattern (17 bp):
GACCCGACCCGACAGTT
Found at i:256795 original size:13 final size:13
Alignment explanation
Indices: 256770--256812 Score: 79
Period size: 13 Copynumber: 3.4 Consensus size: 13
256760 TAGTTGACCC
256770 GACCCGA-CCGTT
1 GACCCGACCCGTT
256782 GACCCGACCCGTT
1 GACCCGACCCGTT
256795 GACCCGACCCGTT
1 GACCCGACCCGTT
256808 GACCC
1 GACCC
256813 CCCGACCGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
12 7 0.23
13 23 0.77
ACGTcount: A:0.16, C:0.47, G:0.23, T:0.14
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:256823 original size:15 final size:15
Alignment explanation
Indices: 256762--256841 Score: 55
Period size: 15 Copynumber: 5.5 Consensus size: 15
256752 CGACCCGATA
256762 GTTGACCCGACCCGACC
1 GTTGACCC--CCCGACC
256779 GTTGA---CCCGACCC
1 GTTGACCCCCCGA-CC
256792 GTTGA---CCCGACCC
1 GTTGACCCCCCGA-CC
256805 GTTGACCCCCCGACC
1 GTTGACCCCCCGACC
***
256820 GTTGACCCGTTGACC
1 GTTGACCCCCCGACC
256835 GTTGACC
1 GTTGACC
256842 GGTGCTATTT
Statistics
Matches: 56, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
12 5 0.09
13 20 0.36
15 21 0.38
16 5 0.09
17 5 0.09
ACGTcount: A:0.15, C:0.44, G:0.24, T:0.17
Consensus pattern (15 bp):
GTTGACCCCCCGACC
Found at i:256884 original size:29 final size:29
Alignment explanation
Indices: 256842--256922 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
256832 ACCGTTGACC
*
256842 GGTGCTATTTTGGTAAATAATTCGGTTTT
1 GGTGCTATTCTGGTAAATAATTCGGTTTT
*
256871 GGTGCTATTCTGGTAAATAATTCAGTTTT
1 GGTGCTATTCTGGTAAATAATTCGGTTTT
256900 GGTGCTATTCT-GTAAATAATTCG
1 GGTGCTATTCTGGTAAATAATTCG
256923 AAAGGGTGCT
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
28 11 0.22
29 38 0.78
ACGTcount: A:0.23, C:0.10, G:0.22, T:0.44
Consensus pattern (29 bp):
GGTGCTATTCTGGTAAATAATTCGGTTTT
Found at i:259341 original size:15 final size:16
Alignment explanation
Indices: 259311--259344 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
259301 TAGTAGATCC
259311 TACCCAACATGATTTT
1 TACCCAACATGATTTT
*
259327 TACCC-ACATGTTTTT
1 TACCCAACATGATTTT
259342 TAC
1 TAC
259345 TCATAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.26, C:0.26, G:0.06, T:0.41
Consensus pattern (16 bp):
TACCCAACATGATTTT
Found at i:265860 original size:16 final size:17
Alignment explanation
Indices: 265835--265867 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
265825 TATTTATTAC
265835 TTTTATTATAATCTTGT
1 TTTTATTATAATCTTGT
*
265852 TTTTA-TATAATGTTGT
1 TTTTATTATAATCTTGT
265868 ATACATTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.24, C:0.03, G:0.09, T:0.64
Consensus pattern (17 bp):
TTTTATTATAATCTTGT
Found at i:266040 original size:20 final size:20
Alignment explanation
Indices: 266002--266052 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
265992 TAACTTAATG
* *
266002 AATTTT-ATTATGGACTTGT
1 AATTTTAATTATAGAATTGT
266021 AATTTTAATTATAGAATTGT
1 AATTTTAATTATAGAATTGT
*
266041 AACTTTAATTAT
1 AATTTTAATTAT
266053 CTTGTATTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 6 0.21
20 22 0.79
ACGTcount: A:0.35, C:0.04, G:0.10, T:0.51
Consensus pattern (20 bp):
AATTTTAATTATAGAATTGT
Found at i:266107 original size:6 final size:7
Alignment explanation
Indices: 266090--266115 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
266080 TAGATTCATG
266090 TTTTTAA
1 TTTTTAA
266097 TTTTTAA
1 TTTTTAA
266104 TTTTTAA
1 TTTTTAA
266111 TTTTT
1 TTTTT
266116 TCAAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTTAA
Found at i:271854 original size:22 final size:20
Alignment explanation
Indices: 271822--271888 Score: 64
Period size: 22 Copynumber: 3.1 Consensus size: 20
271812 AAATTCAAAG
*
271822 AAAATTAAAAAAAATAAATCAA
1 AAAATTGAAAAAAA-AAAT-AA
*
271844 AAAATTGAAAATAAAAAT-A
1 AAAATTGAAAAAAAAAATAA
271863 AAAATTGAACAAACAAAAAATAA
1 AAAATTG-A-AAA-AAAAAATAA
271886 AAA
1 AAA
271889 TAAAAATGGG
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
19 8 0.21
20 1 0.03
21 7 0.18
22 18 0.47
23 4 0.11
ACGTcount: A:0.76, C:0.04, G:0.03, T:0.16
Consensus pattern (20 bp):
AAAATTGAAAAAAAAAATAA
Found at i:272042 original size:18 final size:18
Alignment explanation
Indices: 272019--272055 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
272009 AGAAAGAAAA
272019 TGAATCAGTAACTCGCCG
1 TGAATCAGTAACTCGCCG
272037 TGAATCAGTAACTCGCCG
1 TGAATCAGTAACTCGCCG
272055 T
1 T
272056 TAGTCCCCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (18 bp):
TGAATCAGTAACTCGCCG
Found at i:272335 original size:12 final size:12
Alignment explanation
Indices: 272318--272363 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
272308 AAAATATTTC
272318 AAAGAAAATTAA
1 AAAGAAAATTAA
*
272330 AAAGAAATTTAA
1 AAAGAAAATTAA
* *
272342 AAAGAAAGTTGA
1 AAAGAAAATTAA
272354 AAAGAAAATT
1 AAAGAAAATT
272364 CAATATGGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.13, T:0.20
Consensus pattern (12 bp):
AAAGAAAATTAA
Found at i:280633 original size:13 final size:14
Alignment explanation
Indices: 280603--280643 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
280593 GCAAGCACTC
280603 AAAAGAAGAAAACA
1 AAAAGAAGAAAACA
*
280617 AAAAGAAGAAAAGA
1 AAAAGAAGAAAACA
*
280631 AAAGAAAAGAAAA
1 AAA-AGAAGAAAA
280644 TTACAAAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 16 0.67
15 8 0.33
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.00
Consensus pattern (14 bp):
AAAAGAAGAAAACA
Found at i:282084 original size:9 final size:9
Alignment explanation
Indices: 282070--282094 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
282060 AAGACATCAG
282070 GTGTTTTAA
1 GTGTTTTAA
282079 GTGTTTTAA
1 GTGTTTTAA
282088 GTGTTTT
1 GTGTTTT
282095 GGAAAATGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.16, C:0.00, G:0.24, T:0.60
Consensus pattern (9 bp):
GTGTTTTAA
Found at i:291866 original size:23 final size:21
Alignment explanation
Indices: 291812--291873 Score: 72
Period size: 23 Copynumber: 2.9 Consensus size: 21
291802 TTTTGGTGCA
*
291812 GAGGGAATTGA-TCCCCCCTT
1 GAGGGAATCGATTCCCCCCTT
* *
291832 GAGGGAACCGATTCCCCCTTT
1 GAGGGAATCGATTCCCCCCTT
291853 GAAGGGGAATCGATTCCCCCC
1 G-A-GGGAATCGATTCCCCCC
291874 ACAGGGGAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
20 9 0.26
21 9 0.26
22 1 0.03
23 15 0.44
ACGTcount: A:0.21, C:0.32, G:0.26, T:0.21
Consensus pattern (21 bp):
GAGGGAATCGATTCCCCCCTT
Found at i:291894 original size:19 final size:21
Alignment explanation
Indices: 291855--291899 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
291845 CCCCCTTTGA
*
291855 AGGGGAATCGATTCCCCCCAC
1 AGGGGAATCGATTCACCCCAC
291876 AGGGGAATCGA-T-ACCCCAC
1 AGGGGAATCGATTCACCCCAC
*
291895 TGGGG
1 AGGGG
291900 TTCTGTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 10 0.45
20 1 0.05
21 11 0.50
ACGTcount: A:0.24, C:0.31, G:0.31, T:0.13
Consensus pattern (21 bp):
AGGGGAATCGATTCACCCCAC
Found at i:294158 original size:15 final size:15
Alignment explanation
Indices: 294128--294169 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
294118 AAAGGGGGAG
*
294128 AAGTGTGTTTT--TT
1 AAGTGTGTTTTAAAT
294141 AAGTGTGTTTTAAAT
1 AAGTGTGTTTTAAAT
294156 AAGTGTGTTTTAAA
1 AAGTGTGTTTTAAA
294170 ATGATAAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 11 0.42
15 15 0.58
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (15 bp):
AAGTGTGTTTTAAAT
Found at i:294302 original size:11 final size:12
Alignment explanation
Indices: 294276--294300 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
294266 GGGGAGATTG
294276 TTGAAAACATTT
1 TTGAAAACATTT
294288 TTGAAAACATTT
1 TTGAAAACATTT
294300 T
1 T
294301 GATATTTCGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
TTGAAAACATTT
Found at i:295838 original size:21 final size:21
Alignment explanation
Indices: 295814--295856 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
295804 CGAATCAAGG
295814 TGTAATGGTAGATATAGGTCA
1 TGTAATGGTAGATATAGGTCA
*
295835 TGTAATGTTAGATATAGGTCA
1 TGTAATGGTAGATATAGGTCA
295856 T
1 T
295857 CTCAGGTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.37
Consensus pattern (21 bp):
TGTAATGGTAGATATAGGTCA
Found at i:296477 original size:15 final size:16
Alignment explanation
Indices: 296453--296496 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
296443 TAAAAACGTC
296453 TTTTAA-AAAAA-CAA
1 TTTTAAGAAAAATCAA
*
296467 TTTTAAGAAAAATCAT
1 TTTTAAGAAAAATCAA
296483 TTTTAAGACAAAAT
1 TTTTAAGA-AAAAT
296497 TGATATGCGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 6 0.23
15 5 0.19
16 10 0.38
17 5 0.19
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.34
Consensus pattern (16 bp):
TTTTAAGAAAAATCAA
Found at i:296792 original size:29 final size:29
Alignment explanation
Indices: 296745--296826 Score: 103
Period size: 29 Copynumber: 2.8 Consensus size: 29
296735 AAAAACATGA
*
296745 ATTTAAAGGATTAAAATAGAACAAACAAAG
1 ATTTAAAGGATTAAAATAGAA-AAACAAAC
* *
296775 ATTTAAGGGATT-AAATAGAAAAACATAC
1 ATTTAAAGGATTAAAATAGAAAAACAAAC
* *
296803 ATTTAAATGACTAAAATAGAAAAA
1 ATTTAAAGGATTAAAATAGAAAAA
296827 AATAGAAATT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
28 15 0.33
29 19 0.42
30 11 0.24
ACGTcount: A:0.59, C:0.06, G:0.12, T:0.23
Consensus pattern (29 bp):
ATTTAAAGGATTAAAATAGAAAAACAAAC
Found at i:298139 original size:16 final size:16
Alignment explanation
Indices: 298120--298171 Score: 81
Period size: 16 Copynumber: 3.3 Consensus size: 16
298110 TGAATTCCTC
298120 CTGTTCGAATTTCCCA
1 CTGTTCGAATTTCCCA
298136 CTGTTCGAA-TTCCTC-
1 CTGTTCGAATTTCC-CA
298151 CTGTTCGAATTTCCCA
1 CTGTTCGAATTTCCCA
298167 CTGTT
1 CTGTT
298172 TTTCTTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
15 14 0.42
16 19 0.58
ACGTcount: A:0.15, C:0.31, G:0.13, T:0.40
Consensus pattern (16 bp):
CTGTTCGAATTTCCCA
Found at i:298148 original size:15 final size:16
Alignment explanation
Indices: 298114--298164 Score: 79
Period size: 16 Copynumber: 3.2 Consensus size: 16
298104 CCTTTTTGAA
298114 TTCCTCCTGTTCGAAT
1 TTCCTCCTGTTCGAAT
298130 TTCC-CACTGTTCGAA-
1 TTCCTC-CTGTTCGAAT
298145 TTCCTCCTGTTCGAAT
1 TTCCTCCTGTTCGAAT
298161 TTCC
1 TTCC
298165 CACTGTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
15 14 0.44
16 18 0.56
ACGTcount: A:0.14, C:0.33, G:0.12, T:0.41
Consensus pattern (16 bp):
TTCCTCCTGTTCGAAT
Found at i:298149 original size:31 final size:31
Alignment explanation
Indices: 298111--298171 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
298101 TTACCTTTTT
298111 GAATTCCTCCTGTTCGAATTTCCCACTGTTC
1 GAATTCCTCCTGTTCGAATTTCCCACTGTTC
298142 GAATTCCTCCTGTTCGAATTTCCCACTGTT
1 GAATTCCTCCTGTTCGAATTTCCCACTGTT
298172 TTTCTTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.16, C:0.31, G:0.13, T:0.39
Consensus pattern (31 bp):
GAATTCCTCCTGTTCGAATTTCCCACTGTTC
Found at i:299463 original size:206 final size:206
Alignment explanation
Indices: 299109--299487 Score: 641
Period size: 206 Copynumber: 1.8 Consensus size: 206
299099 CTTTAGGACG
**
299109 AGTTCTTCTCATTATGAACTCTTTTGGAAATGTCAATCCCTCAAGTGAGGCGTCACTGATCCGAA
1 AGTTCTTCTCATTATGAACTCTTTTGGAAATGTCAATCCCTCAAGCAAGGCGTCACTGATCCGAA
* * * *
299174 ATGTCGTTAATCGAGTGATAGGTCGAACAAGCTCTTCTCACTATGAACTTTTTCTCCCTCTGTCG
66 ATGTCATGAATCAAGTGATAGGTCGAACAAGCTCTTCTCACTATGAACTTCTTCTCCCTCTGTCG
* *
299239 GATGAGTTCTTTTCATTATGAACTCTCCATTGAAAATGTTGATCCACCTCTTTCTGTGATGGAAT
131 GATGAGTTCTTCTCATTATGAACTCTCCATCGAAAATGTTGATCCACCTCTTTCTGTGATGGAAT
299304 CGAAAGGAACA
196 CGAAAGGAACA
* *
299315 AGTTCTTCTCATTATGAACTCTTTTGTAAATGTCAATCCCTCAAGCAAGGCGTCACTGATTCGAA
1 AGTTCTTCTCATTATGAACTCTTTTGGAAATGTCAATCCCTCAAGCAAGGCGTCACTGATCCGAA
* *
299380 ATGTCATGAATCAAGTGATAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTTTCG
66 ATGTCATGAATCAAGTGATAGGTCGAACAAGCTCTTCTCACTATGAACTTCTTCTCCCTCTGTCG
*
299445 GATGAGTTCTTCTCATTATGAACTCTCCATCGGAAATGTTGAT
131 GATGAGTTCTTCTCATTATGAACTCTCCATCGAAAATGTTGAT
299488 TTGTTTATCT
Statistics
Matches: 160, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
206 160 1.00
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (206 bp):
AGTTCTTCTCATTATGAACTCTTTTGGAAATGTCAATCCCTCAAGCAAGGCGTCACTGATCCGAA
ATGTCATGAATCAAGTGATAGGTCGAACAAGCTCTTCTCACTATGAACTTCTTCTCCCTCTGTCG
GATGAGTTCTTCTCATTATGAACTCTCCATCGAAAATGTTGATCCACCTCTTTCTGTGATGGAAT
CGAAAGGAACA
Found at i:299857 original size:36 final size:36
Alignment explanation
Indices: 299833--299979 Score: 222
Period size: 36 Copynumber: 4.1 Consensus size: 36
299823 AGTGAGAATC
*
299833 AATTTGTTTCAAGGGAAACTATCTCAAGAAAGACAA
1 AATTTGTTTCAAGGGAAACTATCTCAAGAGAGACAA
* * *
299869 AATTTGTTTCAAGGGAAACTGTCTCAAGTGAGAAAA
1 AATTTGTTTCAAGGGAAACTATCTCAAGAGAGACAA
* *
299905 AATTTGTTTCAAGGGAAATTGTCTCAAGAGAGACAA
1 AATTTGTTTCAAGGGAAACTATCTCAAGAGAGACAA
* *
299941 AATTTGTTTCAAGGGAAACTATCTCAAGCGAGATAA
1 AATTTGTTTCAAGGGAAACTATCTCAAGAGAGACAA
299977 AAT
1 AAT
299980 CTTTTGTTTC
Statistics
Matches: 100, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 100 1.00
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27
Consensus pattern (36 bp):
AATTTGTTTCAAGGGAAACTATCTCAAGAGAGACAA
Found at i:299897 original size:72 final size:72
Alignment explanation
Indices: 299813--299979 Score: 255
Period size: 72 Copynumber: 2.3 Consensus size: 72
299803 TTTTAAGAAA
**
299813 AAAC-ATCTCAAGTGAGAATCAATTTGTTTCAAGGGAAACTATCTCAAGAAAGACAAAATTTGTT
1 AAACTATCTCAAGTGAGAAAAAATTTGTTTCAAGGGAAACTATCTCAAGAAAGACAAAATTTGTT
299877 TCAAGGG
66 TCAAGGG
* * * *
299884 AAACTGTCTCAAGTGAGAAAAAATTTGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAATTTGTT
1 AAACTATCTCAAGTGAGAAAAAATTTGTTTCAAGGGAAACTATCTCAAGAAAGACAAAATTTGTT
299949 TCAAGGG
66 TCAAGGG
* *
299956 AAACTATCTCAAGCGAGATAAAAT
1 AAACTATCTCAAGTGAGAAAAAAT
299980 CTTTTGTTTC
Statistics
Matches: 86, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
71 4 0.05
72 82 0.95
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.26
Consensus pattern (72 bp):
AAACTATCTCAAGTGAGAAAAAATTTGTTTCAAGGGAAACTATCTCAAGAAAGACAAAATTTGTT
TCAAGGG
Found at i:299952 original size:21 final size:19
Alignment explanation
Indices: 299867--299958 Score: 58
Period size: 15 Copynumber: 5.1 Consensus size: 19
299857 CAAGAAAGAC
299867 AAAATTTGTTTCAAGG-G-
1 AAAATTTGTTTCAAGGAGA
* *
299884 -AAA-CTGTCTCAAGTGAGAA
1 AAAATTTGTTTCAAG-GAG-A
299903 AAAATTTGTTTCAAGG-G-
1 AAAATTTGTTTCAAGGAGA
*
299920 -AAA-TTGTCTCAAGAGAGA
1 AAAATTTGTTTCAAG-GAGA
299938 CAAAATTTGTTTCAAGG-GA
1 -AAAATTTGTTTCAAGGAGA
299957 AA
1 AA
299959 CTATCTCAAG
Statistics
Matches: 57, Mismatches: 6, Indels: 23
0.66 0.07 0.27
Matches are distributed among these distances:
15 17 0.30
16 8 0.14
17 2 0.04
18 2 0.04
19 3 0.05
20 8 0.14
21 17 0.30
ACGTcount: A:0.40, C:0.10, G:0.22, T:0.28
Consensus pattern (19 bp):
AAAATTTGTTTCAAGGAGA
Found at i:300020 original size:40 final size:40
Alignment explanation
Indices: 299970--300375 Score: 627
Period size: 40 Copynumber: 10.2 Consensus size: 40
299960 TATCTCAAGC
* * *
299970 GAGATAAAATCTTTTGTTTCAAGTAAAAACAATCTTGATT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
* *
300010 GAGATAAAATCTTCTGTTTTAAGGAAAAACGATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
300050 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
300090 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
* *
300130 GATATATAATCTTCTGTTTCAAGG-AAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
* **
300169 GAGAT-AAATATTCTGTTTCAAGGAAAAACAATCTTGAAC
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
**
300208 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAAC
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
* * *
300248 GAGATAAAATTTTATGTTTCAAGGAAAAACAATTTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
* * *
300288 GAGATAAAATCTTCCGTTTCAAGGAAAAAAAATCTTGAAT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
*
300328 GAGATAAAATCTTATGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
300368 GAGATAAA
1 GAGATAAA
300376 TTCTCTATAT
Statistics
Matches: 334, Mismatches: 30, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
38 16 0.05
39 37 0.11
40 281 0.84
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.31
Consensus pattern (40 bp):
GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
Found at i:300083 original size:23 final size:23
Alignment explanation
Indices: 300057--300125 Score: 60
Period size: 23 Copynumber: 3.3 Consensus size: 23
300047 AGTGAGATAA
300057 AATCTTCTGTTTCAAGGAAAAAC
1 AATCTTCTGTTTCAAGGAAAAAC
** * *
300080 AATC-T-TGAGT-GA-G-ATAA-
1 AATCTTCTGTTTCAAGGAAAAAC
300097 AATCTTCTGTTTCAAGGAAAAAC
1 AATCTTCTGTTTCAAGGAAAAAC
300120 AATCTT
1 AATCTT
300126 GAGTGATATA
Statistics
Matches: 32, Mismatches: 8, Indels: 12
0.62 0.15 0.23
Matches are distributed among these distances:
17 4 0.12
18 4 0.12
19 4 0.12
20 2 0.06
21 4 0.12
22 4 0.12
23 10 0.31
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.32
Consensus pattern (23 bp):
AATCTTCTGTTTCAAGGAAAAAC
Found at i:300204 original size:198 final size:198
Alignment explanation
Indices: 299945--300376 Score: 639
Period size: 198 Copynumber: 2.2 Consensus size: 198
299935 AGACAAAATT
* * ** * * * * **
299945 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTTTGTTTCAAGTAAAAACAATCTTGATT
1 TGTTTCAAGGAAAACAATCTTGAGTGAGAT-AAATATTCTGTTTCAAGGAAAAACAATCTTGAAC
* * ** *
300010 GAGATAAAATCTTCTGTTTTAAGGAAAAACGATCTTGAGTGAGATAAAATCTTCTGTTTCAAGGA
65 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAACGAGATAAAATCTTATGTTTCAAGGA
* * * * *
300075 AAAACAATCTTGAGTGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGTGATATATAAT
130 AAAACAATCTTGAGTGAGATAAAATCTTCCGTTTCAAGGAAAAAAAATCTTGAATGAGATAAAAT
*
300140 CTTC
195 CTTA
300144 TGTTTCAAGGAAAACAATCTTGAGTGAGATAAATATTCTGTTTCAAGGAAAAACAATCTTGAACG
1 TGTTTCAAGGAAAACAATCTTGAGTGAGATAAATATTCTGTTTCAAGGAAAAACAATCTTGAACG
*
300209 AGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAACGAGATAAAATTTTATGTTTCAAGGAA
66 AGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAACGAGATAAAATCTTATGTTTCAAGGAA
*
300274 AAACAATTTTGAGTGAGATAAAATCTTCCGTTTCAAGGAAAAAAAATCTTGAATGAGATAAAATC
131 AAACAATCTTGAGTGAGATAAAATCTTCCGTTTCAAGGAAAAAAAATCTTGAATGAGATAAAATC
300339 TTA
196 TTA
300342 TGTTTCAAGGAAAAACAATCTTGAGTGAGATAAAT
1 TGTTTCAAGG-AAAACAATCTTGAGTGAGATAAAT
300377 TCTCTATATT
Statistics
Matches: 209, Mismatches: 23, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
198 160 0.77
199 49 0.23
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.31
Consensus pattern (198 bp):
TGTTTCAAGGAAAACAATCTTGAGTGAGATAAATATTCTGTTTCAAGGAAAAACAATCTTGAACG
AGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAACGAGATAAAATCTTATGTTTCAAGGAA
AAACAATCTTGAGTGAGATAAAATCTTCCGTTTCAAGGAAAAAAAATCTTGAATGAGATAAAATC
TTA
Found at i:305308 original size:20 final size:20
Alignment explanation
Indices: 305283--305325 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
305273 CTATGCAAAT
* *
305283 ATGTAAATGCAAAAATGAAA
1 ATGTAAATACAAAAATAAAA
*
305303 ATGTAAATACAAACATAAAA
1 ATGTAAATACAAAAATAAAA
305323 ATG
1 ATG
305326 CAAAGATACG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.60, C:0.07, G:0.12, T:0.21
Consensus pattern (20 bp):
ATGTAAATACAAAAATAAAA
Found at i:306361 original size:14 final size:12
Alignment explanation
Indices: 306342--306394 Score: 70
Period size: 14 Copynumber: 4.1 Consensus size: 12
306332 CATGATGATT
306342 ATGCAAATGCGAA
1 ATGCAAATGC-AA
306355 GATGCAAATGCAA
1 -ATGCAAATGCAA
306368 ATGCGAAGATGCAA
1 ATGC-AA-ATGCAA
306382 ATGCAAATGCAA
1 ATGCAAATGCAA
306394 A
1 A
306395 AAATGATACA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
12 11 0.30
13 6 0.16
14 20 0.54
ACGTcount: A:0.47, C:0.15, G:0.23, T:0.15
Consensus pattern (12 bp):
ATGCAAATGCAA
Found at i:306365 original size:6 final size:6
Alignment explanation
Indices: 306342--306394 Score: 70
Period size: 6 Copynumber: 8.2 Consensus size: 6
306332 CATGATGATT
306342 ATGCAA ATGCGAA GATGCAA ATGCAA ATGCGAA GATGCAA ATGCAA ATGCAA
1 ATGCAA ATGC-AA -ATGCAA ATGCAA ATGC-AA -ATGCAA ATGCAA ATGCAA
306394 A
1 A
306395 AAATGATACA
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
6 27 0.63
7 8 0.19
8 8 0.19
ACGTcount: A:0.47, C:0.15, G:0.23, T:0.15
Consensus pattern (6 bp):
ATGCAA
Found at i:306365 original size:20 final size:20
Alignment explanation
Indices: 306342--306391 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
306332 CATGATGATT
306342 ATGCAAATGCGAAGATGCAA
1 ATGCAAATGCGAAGATGCAA
306362 ATGCAAATGCGAAGATGCAA
1 ATGCAAATGCGAAGATGCAA
306382 ATGCAAATGC
1 ATGCAAATGC
306392 AAAAAATGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.44, C:0.16, G:0.24, T:0.16
Consensus pattern (20 bp):
ATGCAAATGCGAAGATGCAA
Found at i:317993 original size:21 final size:21
Alignment explanation
Indices: 317934--317995 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
317924 ATTATCTAAT
*
317934 AAACTTGACAA-CCATAACAAC
1 AAACTTGA-AATCCATAATAAC
*
317955 AAACTTGAAATCCATAATAAG
1 AAACTTGAAATCCATAATAAC
317976 AAACTTGAAATCCATAATAA
1 AAACTTGAAATCCATAATAA
317996 TAAATCAAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 2 0.05
21 36 0.95
ACGTcount: A:0.53, C:0.19, G:0.06, T:0.21
Consensus pattern (21 bp):
AAACTTGAAATCCATAATAAC
Found at i:321214 original size:14 final size:14
Alignment explanation
Indices: 321191--321228 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
321181 CATGTCTATA
*
321191 TGCAGAGATTT-TT
1 TGCAGGGATTTATT
321204 TCGCAGGGATTTATT
1 T-GCAGGGATTTATT
321219 TGCAGGGATT
1 TGCAGGGATT
321229 ACTGAAGAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 1 0.05
14 18 0.82
15 3 0.14
ACGTcount: A:0.21, C:0.11, G:0.29, T:0.39
Consensus pattern (14 bp):
TGCAGGGATTTATT
Found at i:324866 original size:30 final size:32
Alignment explanation
Indices: 324822--324905 Score: 102
Period size: 30 Copynumber: 2.7 Consensus size: 32
324812 TGTTTTTCTT
* *
324822 ATTATTTTTGTTATATATATATTA-CGTTT-C
1 ATTAATTTTATTATATATATATTATCGTTTGC
* *
324852 ATTAATTTTATTATATATATTTTATCGTTTGT
1 ATTAATTTTATTATATATATATTATCGTTTGC
324884 ATT-ATTATTATTATATATATAT
1 ATTAATT-TTATTATATATATAT
324906 AATTATATCT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
30 21 0.46
31 8 0.17
32 17 0.37
ACGTcount: A:0.31, C:0.04, G:0.05, T:0.61
Consensus pattern (32 bp):
ATTAATTTTATTATATATATATTATCGTTTGC
Found at i:324989 original size:22 final size:24
Alignment explanation
Indices: 324963--325008 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 24
324953 TTGGTTTTGT
324963 ATTTTACATT-TTTAT-TAT-TATA
1 ATTTTAC-TTATTTATATATATATA
324985 ATTTTACTTATTTATATATATATA
1 ATTTTACTTATTTATATATATATA
325009 TATATCTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 2 0.10
22 12 0.57
23 3 0.14
24 4 0.19
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (24 bp):
ATTTTACTTATTTATATATATATA
Found at i:325053 original size:17 final size:17
Alignment explanation
Indices: 325033--325067 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
325023 TCTTTTTATG
*
325033 TTTTATTTATTATTTTC
1 TTTTATTTATTATATTC
*
325050 TTTTATTTTTTATATTC
1 TTTTATTTATTATATTC
325067 T
1 T
325068 CTACTTTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTATTTATTATATTC
Found at i:325065 original size:22 final size:22
Alignment explanation
Indices: 325020--325084 Score: 58
Period size: 22 Copynumber: 2.8 Consensus size: 22
325010 ATATCTTTTT
*
325020 TTTTCTTTTTATGTTTTATTTATTA
1 TTTTC-TTTTAT-TTTT-TATATTA
*
325045 TTTTCTTTTATTTTTTATATTC
1 TTTTCTTTTATTTTTTATATTA
* * *
325067 TCTACTTTTATCTTTTAT
1 TTTTCTTTTATTTTTTAT
325085 CTCCCTTTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
22 20 0.57
23 4 0.11
24 6 0.17
25 5 0.14
ACGTcount: A:0.15, C:0.09, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTCTTTTATTTTTTATATTA
Found at i:335505 original size:15 final size:15
Alignment explanation
Indices: 335485--335518 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
335475 TCCTAAGTCG
*
335485 AAAATAAAAAATAAA
1 AAAATAAAAAAGAAA
335500 AAAATAAAAAAGAAA
1 AAAATAAAAAAGAAA
335515 AAAA
1 AAAA
335519 CGTTTAGGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.03, T:0.09
Consensus pattern (15 bp):
AAAATAAAAAAGAAA
Found at i:335598 original size:13 final size:14
Alignment explanation
Indices: 335568--335604 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
335558 AAAAATTGAA
335568 AAAAGAAAAAGAAC
1 AAAAGAAAAAGAAC
*
335582 AAAAGAAAAAG-AG
1 AAAAGAAAAAGAAC
335595 AAAAGAAAAA
1 AAAAGAAAAA
335605 TAAGGTGGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.81, C:0.03, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAAGAAC
Found at i:338878 original size:24 final size:24
Alignment explanation
Indices: 338847--338940 Score: 66
Period size: 24 Copynumber: 3.7 Consensus size: 24
338837 TTTGGTTTTC
338847 TATTTTACATTTTTTTATTATTAT
1 TATTTTACATTTTTTTATTATTAT
338871 TATTTTAC-TTATTTATATATATATATAT
1 TATTTTACATT-TTT-T-TAT-TAT-TAT
* *
338899 TATTATTTATATATTTTTA-TATTATT
1 TA-T-TTTACATTTTTTTATTATTA-T
* *
338925 TATATTATATTTTTTT
1 TATTTTACATTTTTTT
338941 TTTCTTTTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 18
0.72 0.05 0.23
Matches are distributed among these distances:
23 2 0.04
24 22 0.39
25 4 0.07
26 9 0.16
27 3 0.05
28 7 0.12
29 2 0.04
30 7 0.12
31 1 0.02
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (24 bp):
TATTTTACATTTTTTTATTATTAT
Found at i:338900 original size:31 final size:32
Alignment explanation
Indices: 338865--338937 Score: 91
Period size: 31 Copynumber: 2.4 Consensus size: 32
338855 ATTTTTTTAT
338865 TATTATTATTTTACT-TATTTATATA-TATATA
1 TATTATTATTTTA-TATATTTATATATTATATA
* *
338896 TATTATTA-TTTATATATTTTTATATTATTTA
1 TATTATTATTTTATATATTTATATATTATATA
338927 TATTA-TATTTT
1 TATTATTATTTT
338938 TTTTTTCTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
29 1 0.03
30 15 0.41
31 21 0.57
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (32 bp):
TATTATTATTTTATATATTTATATATTATATA
Found at i:338904 original size:22 final size:23
Alignment explanation
Indices: 338879--338934 Score: 78
Period size: 22 Copynumber: 2.4 Consensus size: 23
338869 ATTATTTTAC
338879 TTATTTATATATATATATATTA-
1 TTATTTATATATATATATATTAT
* *
338901 TTATTTATATATTTTTATATTAT
1 TTATTTATATATATATATATTAT
338924 TTATATTATAT
1 TTAT-TTATAT
338935 TTTTTTTTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 20 0.67
23 4 0.13
24 6 0.20
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
TTATTTATATATATATATATTAT
Found at i:338935 original size:22 final size:22
Alignment explanation
Indices: 338849--338938 Score: 66
Period size: 22 Copynumber: 4.2 Consensus size: 22
338839 TGGTTTTCTA
* *
338849 TTTTACATT-TTTTTATTATTAT
1 TTTTATATTATTTATATTA-TAT
338871 TATTT-TACTTATTTATA-TATA-
1 T-TTTATA-TTATTTATATTATAT
* *
338892 -TATATATTA-TTATTTATATAT
1 TTTTATATTATTTATAT-TATAT
338913 TTTTATATTATTTATATTATAT
1 TTTTATATTATTTATATTATAT
338935 TTTT
1 TTTT
338939 TTTTTCTTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 18
0.69 0.08 0.23
Matches are distributed among these distances:
18 4 0.08
19 5 0.09
20 6 0.11
22 21 0.40
23 12 0.23
24 5 0.09
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (22 bp):
TTTTATATTATTTATATTATAT
Found at i:338958 original size:31 final size:33
Alignment explanation
Indices: 338912--338991 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 33
338902 TATTTATATA
* *
338912 TTTTTATATTATTTATATTATATTT-TTTTTTTC
1 TTTTTATCTT-TTTATATTATATTTATTATTTTC
* *
338945 TTTTT-TCTTTTTATGTTTTATTTATTATTTTC
1 TTTTTATCTTTTTATATTATATTTATTATTTTC
*
338977 TTTTTATTTTTTTAT
1 TTTTTATCTTTTTAT
338992 TCTCTACTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
31 12 0.30
32 15 0.38
33 13 0.32
ACGTcount: A:0.16, C:0.04, G:0.01, T:0.79
Consensus pattern (33 bp):
TTTTTATCTTTTTATATTATATTTATTATTTTC
Found at i:338963 original size:25 final size:24
Alignment explanation
Indices: 338932--338994 Score: 74
Period size: 25 Copynumber: 2.6 Consensus size: 24
338922 ATTTATATTA
*
338932 TATTTTTTTTTTCTTTTTTCTTTT
1 TATTTTTTTTTTCTATTTTCTTTT
*
338956 TATGTTTTATTTAT-TATTTTCTTTT
1 TAT-TTTT-TTTTTCTATTTTCTTTT
*
338981 TATTTTTTTATTCT
1 TATTTTTTTTTTCT
338995 CTACTTTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
23 3 0.09
24 8 0.25
25 17 0.53
26 4 0.12
ACGTcount: A:0.11, C:0.06, G:0.02, T:0.81
Consensus pattern (24 bp):
TATTTTTTTTTTCTATTTTCTTTT
Found at i:339004 original size:21 final size:20
Alignment explanation
Indices: 338978--339032 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
338968 ATTATTTTCT
338978 TTTTATTTTTTTATTCTCTAC
1 TTTTATTTTTTTATTCTC-AC
* *
338999 TTTTA-TCTTTTA-TCTCCC
1 TTTTATTTTTTTATTCTCAC
339017 TTTTATTTGTTTTATT
1 TTTTATTT-TTTTATT
339033 TTTTTACATT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 6 0.21
19 5 0.18
20 11 0.39
21 6 0.21
ACGTcount: A:0.13, C:0.15, G:0.02, T:0.71
Consensus pattern (20 bp):
TTTTATTTTTTTATTCTCAC
Found at i:339106 original size:9 final size:9
Alignment explanation
Indices: 339094--339141 Score: 62
Period size: 9 Copynumber: 5.3 Consensus size: 9
339084 GTATTATTAT
*
339094 TTTTCTTCA
1 TTTTATTCA
*
339103 TTTTATTTA
1 TTTTATTCA
339112 TTTTATTCA
1 TTTTATTCA
339121 TTTTATTCA
1 TTTTATTCA
339130 TTTGTATT-A
1 TTT-TATTCA
339139 TTT
1 TTT
339142 ACTTTATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
9 31 0.89
10 4 0.11
ACGTcount: A:0.19, C:0.08, G:0.02, T:0.71
Consensus pattern (9 bp):
TTTTATTCA
Found at i:339150 original size:18 final size:18
Alignment explanation
Indices: 339094--339151 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
339084 GTATTATTAT
*
339094 TTTTCTTCATTTTATTTA
1 TTTTATTCATTTTATTTA
*
339112 TTTTATTCATTTTATTCA
1 TTTTATTCATTTTATTTA
339130 TTTGTATT-A-TTTACTTTA
1 TTT-TATTCATTTTA-TTTA
339148 TTTT
1 TTTT
339152 TATCTTATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
17 5 0.14
18 26 0.74
19 4 0.11
ACGTcount: A:0.19, C:0.09, G:0.02, T:0.71
Consensus pattern (18 bp):
TTTTATTCATTTTATTTA
Found at i:340179 original size:20 final size:20
Alignment explanation
Indices: 340154--340195 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
340144 TCTACATACA
*
340154 TTATTTATATGTATTGAGTT
1 TTATTTATATGTAATGAGTT
340174 TTATTTATATGTAATGAGTT
1 TTATTTATATGTAATGAGTT
340194 TT
1 TT
340196 GAACCATCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.26, C:0.00, G:0.14, T:0.60
Consensus pattern (20 bp):
TTATTTATATGTAATGAGTT
Found at i:342838 original size:44 final size:44
Alignment explanation
Indices: 342786--342911 Score: 171
Period size: 44 Copynumber: 2.9 Consensus size: 44
342776 TAACACATTA
* * **
342786 TCAAGCTTCCCACACATGGGTGAATCAAATAAACAATATTTATC
1 TCAAGCTTCCCACGCATGAGTGAATCAAATAAACAATAGGTATC
* *
342830 TCAAGCTTCCCACGTATGAGTGAATCAAACAAACAATAGGTATC
1 TCAAGCTTCCCACGCATGAGTGAATCAAATAAACAATAGGTATC
* * *
342874 TCAAGCTTACCGCGCATGAGTGAATCAAATAACCAATA
1 TCAAGCTTCCCACGCATGAGTGAATCAAATAAACAATA
342912 CATATTAGGC
Statistics
Matches: 71, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 71 1.00
ACGTcount: A:0.39, C:0.23, G:0.14, T:0.24
Consensus pattern (44 bp):
TCAAGCTTCCCACGCATGAGTGAATCAAATAAACAATAGGTATC
Found at i:345165 original size:22 final size:22
Alignment explanation
Indices: 345140--345181 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
345130 TAATATATGT
345140 GTGCCCACCTTAAAATTTTATC
1 GTGCCCACCTTAAAATTTTATC
*
345162 GTGCCCACCTTGAAATTTTA
1 GTGCCCACCTTAAAATTTTA
345182 CCGATCCACG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.12, T:0.36
Consensus pattern (22 bp):
GTGCCCACCTTAAAATTTTATC
Found at i:353416 original size:55 final size:59
Alignment explanation
Indices: 353329--353443 Score: 202
Period size: 55 Copynumber: 2.0 Consensus size: 59
353319 GAATGCTTTC
353329 CTAGGAAGCTCTGAGTTCTCATAGAACATGTAGGGGGAAGTTGTTA-TTTAGCTAATTA
1 CTAGGAAGCTCTGAGTTCTCATAGAACATGTAGGGGGAAGTTGTTATTTTAGCTAATTA
353387 CTAGGAAGCTCTG-G-T-TCATAGAACATGTAGGGGGAAGTTGTTATTTTAGCTAATTA
1 CTAGGAAGCTCTGAGTTCTCATAGAACATGTAGGGGGAAGTTGTTATTTTAGCTAATTA
353443 C
1 C
353444 CTCTTAAATG
Statistics
Matches: 56, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
55 28 0.50
56 14 0.25
57 1 0.02
58 13 0.23
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (59 bp):
CTAGGAAGCTCTGAGTTCTCATAGAACATGTAGGGGGAAGTTGTTATTTTAGCTAATTA
Found at i:376679 original size:15 final size:15
Alignment explanation
Indices: 376655--376691 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
376645 TATAACATAT
376655 ATTATATTTTCAAAA
1 ATTATATTTTCAAAA
*
376670 ATTATGTTTTCAAAA
1 ATTATATTTTCAAAA
376685 ATTATAT
1 ATTATAT
376692 ATATTATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (15 bp):
ATTATATTTTCAAAA
Found at i:385027 original size:12 final size:12
Alignment explanation
Indices: 385010--385038 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
385000 TTGTTGTGCT
385010 TGCTCCTCGGGC
1 TGCTCCTCGGGC
385022 TGCTCCTCGGGC
1 TGCTCCTCGGGC
385034 TGCTC
1 TGCTC
385039 AGGCTCATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.41, G:0.31, T:0.28
Consensus pattern (12 bp):
TGCTCCTCGGGC
Found at i:386714 original size:21 final size:23
Alignment explanation
Indices: 386666--386716 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
386656 ATTCCCCTGT
*
386666 GGGGGAAATCGGTTCCCCTTCAA
1 GGGGGGAATCGGTTCCCCTTCAA
*
386689 AGGGGGAATCGGTT-CCC-TCAA
1 GGGGGGAATCGGTTCCCCTTCAA
386710 GGGGGGA
1 GGGGGGA
386717 GCGATTCCCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 10 0.40
22 3 0.12
23 12 0.48
ACGTcount: A:0.22, C:0.22, G:0.39, T:0.18
Consensus pattern (23 bp):
GGGGGGAATCGGTTCCCCTTCAA
Found at i:399491 original size:55 final size:56
Alignment explanation
Indices: 399407--399519 Score: 201
Period size: 55 Copynumber: 2.0 Consensus size: 56
399397 TTTCATAAAT
*
399407 ATGGACTTTGTTATCAAGTTCACATTTGATCCCAAATCAACAAGAGCT-TCCTATG
1 ATGGACTTTGGTATCAAGTTCACATTTGATCCCAAATCAACAAGAGCTCTCCTATG
399462 ATGGACTTTGGTATCAAGTTCACATTTGATCCCAAATCAACAAGAGCTCCTCCTATG
1 ATGGACTTTGGTATCAAGTTCACATTTGATCCCAAATCAACAAGAGCT-CTCCTATG
399519 A
1 A
399520 AGTTACTACC
Statistics
Matches: 55, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
55 47 0.85
57 8 0.15
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (56 bp):
ATGGACTTTGGTATCAAGTTCACATTTGATCCCAAATCAACAAGAGCTCTCCTATG
Found at i:409254 original size:19 final size:19
Alignment explanation
Indices: 409216--409255 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
409206 CGAATGATTG
* * *
409216 AATCGAATATAATATTTTA
1 AATCAAATATAAAATCTTA
409235 AATCAAATATAAAATCTTA
1 AATCAAATATAAAATCTTA
409254 AA
1 AA
409256 ATTAATTAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.07, G:0.03, T:0.35
Consensus pattern (19 bp):
AATCAAATATAAAATCTTA
Found at i:413776 original size:24 final size:25
Alignment explanation
Indices: 413737--413793 Score: 73
Period size: 24 Copynumber: 2.3 Consensus size: 25
413727 TGAATTTTAG
*
413737 AAAACTTTAGATTTTTT-TTCAAAT
1 AAAATTTTAGATTTTTTATTCAAAT
*
413761 AATAATTTTA-ATTTTTTATTTAAAT
1 AA-AATTTTAGATTTTTTATTCAAAT
413786 AAAATTTT
1 AAAATTTT
413794 TAAAAAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 15 0.52
25 14 0.48
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (25 bp):
AAAATTTTAGATTTTTTATTCAAAT
Found at i:414128 original size:33 final size:33
Alignment explanation
Indices: 414086--414153 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
414076 TAATTTGGAT
*
414086 AAAGGCCGCATGATTTAGCTTAGACTCAATTGA
1 AAAGGCCGCATGATTTAGCTTAAACTCAATTGA
414119 AAAGGCCGCATGATTTAGCTTAAACTCAATTGA
1 AAAGGCCGCATGATTTAGCTTAAACTCAATTGA
414152 AA
1 AA
414154 TAAAAATACA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.26
Consensus pattern (33 bp):
AAAGGCCGCATGATTTAGCTTAAACTCAATTGA
Found at i:416010 original size:11 final size:11
Alignment explanation
Indices: 415977--416010 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
415967 ACTGAAGAAT
415977 AAAAAAAATAA
1 AAAAAAAATAA
* *
415988 AAAATAAGTAA
1 AAAAAAAATAA
415999 AAAAAAAATAA
1 AAAAAAAATAA
416010 A
1 A
416011 TACCGATAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.12
Consensus pattern (11 bp):
AAAAAAAATAA
Found at i:416194 original size:24 final size:23
Alignment explanation
Indices: 416149--416197 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
416139 GCTTTCAAAG
*
416149 ATATTTATTTTAGAAAACTATAT
1 ATATTTATTTTAGAAAAATATAT
416172 ATATTATATGTTTA-AAAAATATAT
1 ATATT-TAT-TTTAGAAAAATATAT
416196 AT
1 AT
416198 TTTCAAAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 5 0.22
24 14 0.61
25 4 0.17
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (23 bp):
ATATTTATTTTAGAAAAATATAT
Found at i:416205 original size:17 final size:17
Alignment explanation
Indices: 416176--416214 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
416166 CTATATATAT
416176 TATATGTTTAAAAAATA
1 TATATGTTTAAAAAATA
*
416193 TATAT-TTTCAAAAACTA
1 TATATGTTT-AAAAAATA
416210 TATAT
1 TATAT
416215 ATTATATGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.44
Consensus pattern (17 bp):
TATATGTTTAAAAAATA
Found at i:416208 original size:41 final size:40
Alignment explanation
Indices: 416123--416261 Score: 169
Period size: 41 Copynumber: 3.5 Consensus size: 40
416113 ACCATTTTAT
* * *
416123 AAACTATATA-ATATATGCTTTCAAAGATATTTATTTT-AGA
1 AAACTATATATATATATG-TTTAAAAAATATATATTTTCA-A
416163 AAACTATATATATTATATGTTTAAAAAATATATATTTTCAA
1 AAACTATATATA-TATATGTTTAAAAAATATATATTTTCAA
**
416204 AAACTATATATATTATATGTTTTGAAAA-ATATATTTTCAA
1 AAACTATATATA-TATATGTTTAAAAAATATATATTTTCAA
416244 AAACTATAT-TATATATGT
1 AAACTATATATATATATGT
416262 GTTTTCTAAA
Statistics
Matches: 91, Mismatches: 5, Indels: 8
0.88 0.05 0.08
Matches are distributed among these distances:
38 7 0.08
39 2 0.02
40 31 0.34
41 44 0.48
42 7 0.08
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44
Consensus pattern (40 bp):
AAACTATATATATATATGTTTAAAAAATATATATTTTCAA
Found at i:416265 original size:40 final size:40
Alignment explanation
Indices: 416123--416347 Score: 165
Period size: 41 Copynumber: 5.8 Consensus size: 40
416113 ACCATTTTAT
* * *
416123 AAACTATATA-A-TATATGCTTTCAAAGATATTTATTTT-AGA
1 AAACTATATATATTATATG-TTTTAAA-AAATATATTTTCA-A
*
416163 AAACTATATATATTATATGTTTAAAAAATATATATTTTCAA
1 AAACTATATATATTATATGTTTTAAAAA-ATATATTTTCAA
*
416204 AAACTATATATATTATATGTTTTGAAAAATATATTTTCAA
1 AAACTATATATATTATATGTTTTAAAAAATATATTTTCAA
***
416244 AAACTATAT-TA-TATATGTGTTTTCTAAA-ATATTTT-AA
1 AAACTATATATATTATATGT-TTTAAAAAATATATTTTCAA
* * *
416281 AAA--ATAT-T-TTATATGTTTT-CAACA-ATGTTTTC-A
1 AAACTATATATATTATATGTTTTAAAAAATATATTTTCAA
* * *
416314 AAACTATATAT-TATACATGTTTTCAAAACTATAT
1 AAACTATATATAT-TATATGTTTTAAAAAATATAT
416348 ATTATATACA
Statistics
Matches: 156, Mismatches: 16, Indels: 27
0.78 0.08 0.14
Matches are distributed among these distances:
33 13 0.08
34 3 0.02
35 16 0.10
36 2 0.01
37 14 0.09
38 16 0.10
39 11 0.07
40 32 0.21
41 42 0.27
42 7 0.04
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (40 bp):
AAACTATATATATTATATGTTTTAAAAAATATATTTTCAA
Found at i:416328 original size:35 final size:34
Alignment explanation
Indices: 416194--416424 Score: 124
Period size: 38 Copynumber: 6.5 Consensus size: 34
416184 TAAAAAATAT
*
416194 ATATTTTCAAAAACTATATATATTATATGTTTTGAAAAA
1 ATATTTTC-AAAAC--TATATATTATATGTTTT--CAAA
*
416233 TATATTTTCAAAAACTATATTATATATGTGTTTTCTAAA
1 -ATATTTTC-AAAACTATA-TAT-TATATGTTTTC-AAA
* *
416272 ATATTTT-AAAA-AATATTTTATATGTTTTCAACA
1 ATATTTTCAAAACTATATATTATATGTTTTCAA-A
*
416305 ATGTTTTCAAAACTATATATTATA------C---
1 ATATTTTCAAAACTATATATTATATGTTTTCAAA
* *
416330 ATGTTTTCAAAACTATATATTATATACATTTTCAAAAAA
1 ATATTTTCAAAACTATATATTATAT--GTTTTC---AAA
* *
416369 ATGTTTTCAAAACTATATATTATATATATTTTCAAAAA
1 ATATTTTCAAAACTATATA-T-TATATGTTTTC--AAA
416407 ATATTTTCAAAACTATAT
1 ATATTTTCAAAACTATAT
416425 TATATTATCA
Statistics
Matches: 160, Mismatches: 9, Indels: 46
0.74 0.04 0.21
Matches are distributed among these distances:
25 24 0.15
29 1 0.01
32 2 0.01
33 18 0.11
34 6 0.04
35 12 0.08
36 4 0.03
38 33 0.21
39 31 0.19
40 24 0.15
41 5 0.03
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.45
Consensus pattern (34 bp):
ATATTTTCAAAACTATATATTATATGTTTTCAAA
Found at i:416358 original size:27 final size:25
Alignment explanation
Indices: 416305--416353 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
416295 GTTTTCAACA
416305 ATGTTTTCAAAACTATATATTATAC
1 ATGTTTTCAAAACTATATATTATAC
416330 ATGTTTTCAAAACTATATATTATA
1 ATGTTTTCAAAACTATATATTATA
416354 TACATTTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.41, C:0.10, G:0.04, T:0.45
Consensus pattern (25 bp):
ATGTTTTCAAAACTATATATTATAC
Found at i:416368 original size:27 final size:25
Alignment explanation
Indices: 416308--416366 Score: 91
Period size: 25 Copynumber: 2.4 Consensus size: 25
416298 TTCAACAATG
**
416308 TTTTCAAAACTATATATTATACATG
1 TTTTCAAAACTATATATTATACACA
*
416333 TTTTCAAAACTATATATTATATACA
1 TTTTCAAAACTATATATTATACACA
416358 TTTTCAAAA
1 TTTTCAAAA
416367 AAATGTTTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.42, C:0.12, G:0.02, T:0.44
Consensus pattern (25 bp):
TTTTCAAAACTATATATTATACACA
Done.