Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001121.1 Hibiscus syriacus cultivar Beakdansim tig00002218_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: 83124
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:11648 original size:83 final size:83
Alignment explanation
Indices: 11509--11675 Score: 325
Period size: 83 Copynumber: 2.0 Consensus size: 83
11499 AGGTAAAAGG
*
11509 TCTGCAGTCTGCGGTCCACATCTGCAGGCATCTGCAGCAGAAGAGGTGGACCAAAAGTCTGCAGT
1 TCTGCAGTCTGCGGACCACATCTGCAGGCATCTGCAGCAGAAGAGGTGGACCAAAAGTCTGCAGT
11574 CTGCAAGAAGAAGACTGT
66 CTGCAAGAAGAAGACTGT
11592 TCTGCAGTCTGCGGACCACATCTGCAGGCATCTGCAGCAGAAGAGGTGGACCAAAAGTCTGCAGT
1 TCTGCAGTCTGCGGACCACATCTGCAGGCATCTGCAGCAGAAGAGGTGGACCAAAAGTCTGCAGT
11657 CTGCAAGAAGAAGACTGT
66 CTGCAAGAAGAAGACTGT
11675 T
1 T
11676 TGTTTTTTAA
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 83 1.00
ACGTcount: A:0.28, C:0.24, G:0.29, T:0.19
Consensus pattern (83 bp):
TCTGCAGTCTGCGGACCACATCTGCAGGCATCTGCAGCAGAAGAGGTGGACCAAAAGTCTGCAGT
CTGCAAGAAGAAGACTGT
Found at i:11844 original size:22 final size:22
Alignment explanation
Indices: 11814--11862 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
11804 TCCATACAAC
*
11814 TAAAATAATAAAT-TATTTAAAA
1 TAAATTAATAAATAT-TTTAAAA
**
11836 TAAATTAATCCATATTTTAAAA
1 TAAATTAATAAATATTTTAAAA
11858 TAAAT
1 TAAAT
11863 CAATCCATAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 22 0.96
23 1 0.04
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (22 bp):
TAAATTAATAAATATTTTAAAA
Found at i:11867 original size:22 final size:22
Alignment explanation
Indices: 11829--11871 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
11819 TAATAAATTA
*
11829 TTTAAAATAAATTAATCCATAT
1 TTTAAAATAAATCAATCCATAT
11851 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
11872 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:11880 original size:22 final size:22
Alignment explanation
Indices: 11831--11879 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
11821 ATAAATTATT
* **
11831 TAAAATAAATTAATCCATATTT
1 TAAAATAAATCAATCCATATAA
11853 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
11876 TAAA
1 TAAA
11880 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:11883 original size:54 final size:54
Alignment explanation
Indices: 11819--12231 Score: 380
Period size: 54 Copynumber: 7.5 Consensus size: 54
11809 ACAACTAAAA
*
11819 TAATAAATTATTTAAAATAAATTAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* *** * * *
11873 TAATAAATTATTTAAAATAAATCAATCTATACAACTACAAT-AATAAATCAAT-C
1 TAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAAATCAATCCATAC
*
11926 T-AT--A-T-TTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCTATAC
1 TAATAAATTATTTAAAATAAATCAAT-C---C--AT--A-T-TTTAAAATAAATCAATCCATAC
11985 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
12039 TAATAAATTATTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* * ** *
12093 TAATAAATTATTTAAAATAAATCAATACATACAACTACAATAATAAATCAATCCATATTT
1 TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATA--C
* * * * * *
12153 TAAAATAAATCAATTCATACAAATAAAT---TA-TTTAAAATAAATCAATCCATAC
1 T--AATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
12205 AAATAAATTATTTAAAATAAATCAATC
1 TAATAAATTATTTAAAATAAATCAATC
12232 GATACTAATA
Statistics
Matches: 294, Mismatches: 39, Indels: 55
0.76 0.10 0.14
Matches are distributed among these distances:
48 16 0.05
49 2 0.01
50 20 0.07
52 2 0.01
53 2 0.01
54 159 0.54
55 9 0.03
56 3 0.01
57 9 0.03
58 27 0.09
59 3 0.01
60 4 0.01
62 20 0.07
63 2 0.01
64 16 0.05
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
Found at i:11889 original size:32 final size:32
Alignment explanation
Indices: 11851--12376 Score: 381
Period size: 32 Copynumber: 18.7 Consensus size: 32
11841 TAATCCATAT
11851 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
11883 TTTAAAATAAATCAATCTATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
* **
11913 --T--AATAAATCAATCTATA-TTTTAAA--A
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
11938 -------TAAATCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
11963 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
11995 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
12017 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
12049 TTTAAAATAAATCAAT---T-C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
12071 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
12103 TTTAAAATAAATCAATACATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
12133 --T--AATAAATCAATCC--A-T-AT------
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
12151 TTTAAAATAAATCAATTCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
12183 TTTAAAATAAATCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
12215 TTTAAAATAAATCAATCGATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
12247 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
12269 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
12301 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
12323 TTTAAATTAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
12355 TTTAAAATAAATCAATCCATAC
1 TTTAAAATAAATCAATCCATAC
12377 AACTACAACA
Statistics
Matches: 401, Mismatches: 25, Indels: 136
0.71 0.04 0.24
Matches are distributed among these distances:
20 1 0.00
22 89 0.22
23 11 0.03
24 6 0.01
25 6 0.01
26 42 0.10
28 14 0.03
29 1 0.00
30 6 0.01
31 9 0.02
32 216 0.54
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:11970 original size:14 final size:14
Alignment explanation
Indices: 11953--12006 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
11943 CAATCCATAC
11953 AAATAAATTATTTA
1 AAATAAATTATTTA
*
11967 AAATAAATCAATCTATA
1 AAATAAAT-TAT-T-TA
*
11984 CTAATAAATTATTTA
1 -AAATAAATTATTTA
11999 AAATAAAT
1 AAATAAAT
12007 CAATCCATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 15 0.47
15 4 0.12
16 2 0.06
17 4 0.12
18 7 0.22
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATAAATTATTTA
Found at i:12021 original size:22 final size:22
Alignment explanation
Indices: 11995--12037 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
11985 TAATAAATTA
11995 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
12017 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
12038 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:12046 original size:22 final size:22
Alignment explanation
Indices: 11997--12045 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
11987 ATAAATTATT
**
11997 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
12019 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
12042 TAAA
1 TAAA
12046 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:12075 original size:22 final size:22
Alignment explanation
Indices: 12049--12091 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
12039 TAATAAATTA
*
12049 TTTAAAATAAATCAATTCATAT
1 TTTAAAATAAATCAATCCATAT
12071 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
12092 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:12100 original size:22 final size:22
Alignment explanation
Indices: 12051--12099 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
12041 ATAAATTATT
* **
12051 TAAAATAAATCAATTCATATTT
1 TAAAATAAATCAATCCATATAA
12073 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
12096 TAAA
1 TAAA
12100 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:12190 original size:14 final size:14
Alignment explanation
Indices: 12173--12258 Score: 55
Period size: 14 Copynumber: 5.6 Consensus size: 14
12163 CAATTCATAC
12173 AAATAAATTATTTA
1 AAATAAATTATTTA
* *
12187 AAATAAATCAATCCATA
1 AAATAAAT-TAT--TTA
12204 CAAATAAATTATTTA
1 -AAATAAATTATTTA
* *
12219 AAATAAATCAATCGATA
1 AAATAAAT-TAT--TTA
*
12236 CTAATAAATTATTTA
1 -AAATAAATTATTTA
12251 AAATAAAT
1 AAATAAAT
12259 CAATCCATAT
Statistics
Matches: 54, Mismatches: 10, Indels: 16
0.68 0.12 0.20
Matches are distributed among these distances:
14 23 0.43
15 8 0.15
17 8 0.15
18 15 0.28
ACGTcount: A:0.57, C:0.08, G:0.01, T:0.34
Consensus pattern (14 bp):
AAATAAATTATTTA
Found at i:12212 original size:220 final size:220
Alignment explanation
Indices: 11819--12231 Score: 756
Period size: 220 Copynumber: 1.9 Consensus size: 220
11809 ACAACTAAAA
*
11819 TAATAAATTATTTAAAATAAATTAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
*
11884 TTAAAATAAATCAATCTATACAACTACAATAATAAATCAATCTATATTTTAAAATAAATCAATCC
66 TTAAAATAAATCAATCTATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCC
* *
11949 ATACAAATAAATTATTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCA
131 ATACAAATAAATTATTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCCA
12014 TATTTTAAAATAAATCAATCCATAC
196 TATTTTAAAATAAATCAATCCATAC
*
12039 TAATAAATTATTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
*
12104 TTAAAATAAATCAATAC-ATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATT
66 TTAAAATAAATCAAT-CTATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATC
12168 CATACAAATAAATTATTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATC
130 CATACAAATAAATTATTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATC
12232 GATACTAATA
Statistics
Matches: 186, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
220 185 0.99
221 1 0.01
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (220 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
TTAAAATAAATCAATCTATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCC
ATACAAATAAATTATTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCCA
TATTTTAAAATAAATCAATCCATAC
Found at i:12264 original size:252 final size:252
Alignment explanation
Indices: 11931--12446 Score: 969
Period size: 252 Copynumber: 2.0 Consensus size: 252
11921 CAATCTATAT
*
11931 TTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCTATACTAATAAATTAT
1 TTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCGATACTAATAAATTAT
11996 TTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT
66 TTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT
*
12061 CAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATACATACA
131 CAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATACATACA
*
12126 ACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATTCATACAAATAAATTA
196 ACTACAACAATAAATCAATCCATATTTTAAAATAAATCAATTCATACAAATAAATTA
12183 TTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCGATACTAATAAATTAT
1 TTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCGATACTAATAAATTAT
12248 TTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT
66 TTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT
* * *
12313 CAATCCATATTTTAAATTAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATACA
131 CAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATACATACA
*
12378 ACTACAACAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTA
196 ACTACAACAATAAATCAATCCATATTTTAAAATAAATCAATTCATACAAATAAATTA
12435 TTTAAAATAAAT
1 TTTAAAATAAAT
12447 TATTTTAAAA
Statistics
Matches: 257, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
252 257 1.00
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.34
Consensus pattern (252 bp):
TTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCGATACTAATAAATTAT
TTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT
CAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATACATACA
ACTACAACAATAAATCAATCCATATTTTAAAATAAATCAATTCATACAAATAAATTA
Found at i:12273 original size:22 final size:22
Alignment explanation
Indices: 12247--12289 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
12237 TAATAAATTA
12247 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
12269 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
12290 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:12275 original size:54 final size:53
Alignment explanation
Indices: 12134--12375 Score: 340
Period size: 54 Copynumber: 4.3 Consensus size: 53
12124 CAACTACAAT
*
12134 AATAAATCAATCCATATTTTAAAATAAATCAATTCATACAAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAA-TCATACTAATAAATTATTTAA
12188 AATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCGATACTAATAAATTATTTAA
1 AATAAATCAAT-C---C--AT--A-T-TTTAAAATAAATCAATC-ATACTAATAAATTATTTAA
12252 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAAT-CATACTAATAAATTATTTAA
*
12306 AATAAATCAATCCATATTTTAAATTAAATCAATCTATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATC-ATACTAATAAATTATTTAA
12360 AATAAATCAATCCATA
1 AATAAATCAATCCATA
12376 CAACTACAAC
Statistics
Matches: 173, Mismatches: 2, Indels: 26
0.86 0.01 0.13
Matches are distributed among these distances:
53 1 0.01
54 113 0.65
55 3 0.02
56 1 0.01
58 3 0.02
60 3 0.02
62 1 0.01
63 4 0.02
64 44 0.25
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (53 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCATACTAATAAATTATTTAA
Found at i:12298 original size:22 final size:22
Alignment explanation
Indices: 12249--12297 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
12239 ATAAATTATT
**
12249 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
12271 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
12294 TAAA
1 TAAA
12298 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:12411 original size:22 final size:22
Alignment explanation
Indices: 12386--12481 Score: 75
Period size: 22 Copynumber: 4.2 Consensus size: 22
12376 CAACTACAAC
12386 AATAAATCAATCCATATTTTAA
1 AATAAATCAATCCATATTTTAA
* **
12408 AATAAATCAATTCATACTAATAA
1 AATAAATCAATCCATA-TTTTAA
* ** * **
12431 ATTATTTAAAATAAATTATTTTAA
1 AATAAAT-CAATCCA-TATTTTAA
*
12455 AATAAATCAATCCATATTTTAT
1 AATAAATCAATCCATATTTTAA
12477 AATAA
1 AATAA
12482 TTTATTTTAA
Statistics
Matches: 53, Mismatches: 18, Indels: 6
0.69 0.23 0.08
Matches are distributed among these distances:
22 27 0.51
23 12 0.23
24 12 0.23
25 2 0.04
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (22 bp):
AATAAATCAATCCATATTTTAA
Found at i:12485 original size:47 final size:50
Alignment explanation
Indices: 12292--12513 Score: 142
Period size: 47 Copynumber: 4.4 Consensus size: 50
12282 AATCCATACT
* * * *
12292 AATAAATTA-TTTAAAATAAATCAATCCATATTTTAAATTAAATCAAT-CTATACT
1 AATAAATTATTTTAAAATAAATCAATCCATA--CT-AA-TAAAT-AATATTTTA-A
* ** *
12346 AATAAATTA-TTTAAAATAAATCAATCCATAC-AACTACAACAATA-AAT-C
1 AATAAATTATTTTAAAATAAATCAATCCATACTAA-TA-AATAATATTTTAA
** *
12394 AATCCA-TATTTTAAAATAAATCAATTCATACTAATAAAT--TA-TTTAA
1 AATAAATTATTTTAAAATAAATCAATCCATACTAATAAATAATATTTTAA
**
12440 AATAAATTATTTTAAAATAAATCAATCCATA-TTTTATAATAATTTATTTTAA
1 AATAAATTATTTTAAAATAAATCAATCCATACTAATA-AATAA--TATTTTAA
*
12492 AATAAATTATTTTATAATAAAT
1 AATAAATTATTTTAAAATAAAT
12514 TATTTTAAAA
Statistics
Matches: 138, Mismatches: 18, Indels: 26
0.76 0.10 0.14
Matches are distributed among these distances:
45 3 0.02
46 7 0.05
47 30 0.22
48 27 0.20
49 2 0.01
50 9 0.07
51 4 0.03
52 26 0.19
54 30 0.22
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (50 bp):
AATAAATTATTTTAAAATAAATCAATCCATACTAATAAATAATATTTTAA
Found at i:12555 original size:16 final size:15
Alignment explanation
Indices: 12426--12543 Score: 139
Period size: 15 Copynumber: 7.5 Consensus size: 15
12416 AATTCATACT
12426 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
12440 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
12455 AATAAATCAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
*
12477 AATAATTTATTTTAA
1 AATAAATTATTTTAA
*
12492 AATAAATTATTTTAT
1 AATAAATTATTTTAA
12507 AATAAATTATTTTAA
1 AATAAATTATTTTAA
12522 AATAAATTATTTTAA
1 AATAAATTATTTTAA
12537 AATAAAT
1 AATAAAT
12544 AACTTTTTAA
Statistics
Matches: 90, Mismatches: 6, Indels: 15
0.81 0.05 0.14
Matches are distributed among these distances:
14 9 0.10
15 64 0.71
17 1 0.01
18 2 0.02
19 3 0.03
20 1 0.01
22 10 0.11
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.46
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:18268 original size:3 final size:3
Alignment explanation
Indices: 18260--18403 Score: 54
Period size: 3 Copynumber: 46.7 Consensus size: 3
18250 AATATTAATG
* *
18260 TAA TAA TAA TAA TAA -ATA TAA T-A TAA TATA TAC T-A TAA TATG TACA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TA-A TAA TAA TAA TA-A TA-A
* * *
18306 TAAA TAA T-A TAC T-A TGA TAA T-A TAA TATA TAA TAT TAA T-A TAA
1 T-AA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA
*
18349 TAA TAA TAA TATA TAC TATA TATA TACA CTAA TTAA T-A TAA T-A TAA
1 TAA TAA TAA TA-A TAA TA-A TA-A TA-A -TAA -TAA TAA TAA TAA TAA
18395 TATA TAA TA
1 TA-A TAA TA
18404 TATATATCAT
Statistics
Matches: 109, Mismatches: 14, Indels: 36
0.69 0.09 0.23
Matches are distributed among these distances:
2 15 0.14
3 62 0.57
4 29 0.27
5 3 0.03
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:18270 original size:17 final size:16
Alignment explanation
Indices: 18235--18561 Score: 93
Period size: 17 Copynumber: 19.4 Consensus size: 16
18225 GCTAATCATA
*
18235 AATATAATTA-AATAT
1 AATATAAATATAATAT
* *
18250 AATATTAATGTAATAAT
1 AATATAAATATAAT-AT
18267 AATAATAAATATAATAT
1 AAT-ATAAATATAATAT
*
18284 AATATATACTATAATAT
1 AATATA-AATATAATAT
* *
18301 -GTACATAA-ATAATAT
1 AATATA-AATATAATAT
*
18316 ACTATGATAATATAATATAT
1 AATAT-A-AATAT-A-ATAT
*
18336 AATATTAATATAATAAT
1 AATATAAATATAAT-AT
* *
18353 AATA-ATATATACTAT
1 AATATAAATATAATAT
*
18368 ATATATACACTAATTAATAT
1 A-ATATA-AAT-A-TAATAT
18388 AATATAATATATAATAT
1 AATATAA-ATATAATAT
* *
18405 -ATATATCATATTAT-T
1 AATATA-AATATAATAT
*
18420 AATATATATACT-ATAT
1 AATATAAATA-TAATAT
* *
18436 AACAT-ACTAT-ATAT
1 AATATAAATATAATAT
*
18450 AATA-ATAATATACTAT
1 AATATA-AATATAATAT
*
18466 AACATATATAATACGTGATAT
1 -A-ATATA-AATA--TAATAT
18487 AATACT-AATAT-ATAGT
1 AATA-TAAATATAATA-T
* *
18503 ACATATTATAACATACTAT
1 A-ATA-TA-AATATAATAT
*
18522 AATATATAATATTATAT
1 AATATA-AATATAATAT
* *
18539 AATAATATATATCATAT
1 AAT-ATAAATATAATAT
*
18556 ATTATA
1 AATATA
18562 TAAACATTGT
Statistics
Matches: 237, Mismatches: 40, Indels: 69
0.68 0.12 0.20
Matches are distributed among these distances:
14 8 0.03
15 32 0.14
16 55 0.23
17 65 0.27
18 32 0.14
19 23 0.10
20 18 0.08
21 4 0.02
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.40
Consensus pattern (16 bp):
AATATAAATATAATAT
Found at i:18282 original size:5 final size:5
Alignment explanation
Indices: 18235--18561 Score: 120
Period size: 5 Copynumber: 61.2 Consensus size: 5
18225 GCTAATCATA
*
18235 AATAT AAT-T AAATAT AATATT AATGT AATAAT AATAAT AAATAT AATAT
1 AATAT AATAT -AATAT AATA-T AATAT AAT-AT AAT-AT -AATAT AATAT
* *
18284 AATAT ATACTAT AATAT GTACAT AA-AT AATAT ACTATGAT AATAT AATATAT
1 AATAT A-A-TAT AATAT -AATAT AATAT AATAT A--AT-AT AATAT -A-ATAT
* *
18336 AATATT AATAT AATAAT AATA- ATATAT ACTAT ATATAT ACA-CT AAT-T
1 AATA-T AATAT AAT-AT AATAT A-ATAT AATAT A-ATAT A-ATAT AATAT
* *
18383 AATAT AATAT AATATAT AATAT ATATAT CATAT TAT-T AATAT -ATAT
1 AATAT AATAT -A-ATAT AATAT A-ATAT AATAT AATAT AATAT AATAT
* * * *
18429 ACTATAT AACAT ACTAT -ATAT AATAAT AATAT ACTAT AACAT -ATAT
1 A--ATAT AATAT AATAT AATAT AAT-AT AATAT AATAT AATAT AATAT
* * *
18475 AATACGT GATAT AATACT AATAT -ATAGT ACATAT --TAT AACAT ACTAT
1 AATA--T AATAT AATA-T AATAT AATA-T A-ATAT AATAT AATAT AATAT
* * *
18522 AATATAT AATAT TATAT AATAAT ATATAT CATAT ATTAT A
1 -A-ATAT AATAT AATAT AAT-AT A-ATAT AATAT AATAT A
18562 TAAACATTGT
Statistics
Matches: 248, Mismatches: 31, Indels: 86
0.68 0.08 0.24
Matches are distributed among these distances:
3 3 0.01
4 27 0.11
5 118 0.48
6 63 0.25
7 34 0.14
8 3 0.01
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.40
Consensus pattern (5 bp):
AATAT
Found at i:18327 original size:13 final size:12
Alignment explanation
Indices: 18235--18564 Score: 162
Period size: 12 Copynumber: 27.6 Consensus size: 12
18225 GCTAATCATA
18235 AATATAAT-TA-
1 AATATAATATAT
18245 AATATAATAT-T
1 AATATAATATAT
*
18256 AATGTAATA-AT
1 AATATAATATAT
18267 AATAATAA-ATAT
1 AAT-ATAATATAT
18279 AATATAATATAT
1 AATATAATATAT
* *
18291 ACTATAATATGT
1 AATATAATATAT
*
18303 -ACAT-A-A-AT
1 AATATAATATAT
*
18311 AATATACTATGAT
1 AATATAATAT-AT
18324 AATATAATATAT
1 AATATAATATAT
18336 AATATTAATATAAT
1 AATA-TAATAT-AT
18350 AATAATAATATAT
1 AAT-ATAATATAT
*
18363 ACTAT-ATATAT
1 AATATAATATAT
*
18374 ACACTA-ATTAATAT
1 A-A-TATAAT-ATAT
18388 AATATAATATAT
1 AATATAATATAT
18400 AATAT-ATATAT
1 AATATAATATAT
* *
18411 CATATTAT-TAAT
1 AATATAATAT-AT
*
18423 ATATATACTATAT
1 A-ATATAATATAT
*
18436 AACATACTATATAT
1 AATATA--ATATAT
18450 AATAATAATATACT
1 AAT-ATAATATA-T
18464 -ATA-ACATATAT
1 AATATA-ATATAT
**
18475 AATA-CGTGATAT
1 AATATAAT-ATAT
18487 AATACTAATATAT
1 AATA-TAATATAT
* *
18500 AGTA-CATATTAT
1 AATATAATA-TAT
* *
18512 AACATACTATA-
1 AATATAATATAT
18523 ATATATAATAT-T
1 A-ATATAATATAT
18535 -ATATAATA-AT
1 AATATAATATAT
*
18545 ATATATCATATAT
1 A-ATATAATATAT
*
18558 TATATAA
1 AATATAA
18565 ACATTGTAAT
Statistics
Matches: 244, Mismatches: 36, Indels: 78
0.68 0.10 0.22
Matches are distributed among these distances:
8 1 0.00
9 4 0.02
10 18 0.07
11 46 0.19
12 92 0.38
13 53 0.22
14 26 0.11
15 4 0.02
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (12 bp):
AATATAATATAT
Found at i:18337 original size:40 final size:38
Alignment explanation
Indices: 18260--18564 Score: 176
Period size: 39 Copynumber: 7.9 Consensus size: 38
18250 AATATTAATG
18260 TAATAATAATAATAA-ATATAATATAATATATACTATAATAT
1 TAAT-ATAATAATAATA-AT-ATATAATATATA-TATAATAT
*
18301 GTACATA-AATAAT-ATACTATGATAATATAATATATAATAT
1 -TA-ATATAATAATAATAATAT-ATAATAT-ATATATAATAT
*
18341 TAATATAATAATAATAATATATACTATATATATACACTAAT
1 TAATATAATAATAATAATATATAATATATATATA-A-T-AT
*
18382 T-A-AT-ATAAT-ATAATATATAATATATATATCATAT
1 TAATATAATAATAATAATATATAATATATATATAATAT
* *
18416 T-AT-TAAT-ATATATACTATATAACATACTATATATAATAA
1 TAATATAATAATA-ATAATATAT-A-ATA-TATATATAATAT
* * ** *
18455 TAATATACT-ATAA-CATATATAATACGTGATATAATAC
1 TAATATAATAATAATAATATATAATATAT-ATATAATAT
* * *
18492 TAATAT-ATAGTACAT-AT-TATAACATA-CTATAATAT
1 TAATATAATAATA-ATAATATATAATATATATATAATAT
*
18527 ATAATATTATATAATAAT-ATATATCATATATTATATAA
1 -TAATA-TA-ATAATAATAATATATAATATA-TATATAA
18565 ACATTGTAAT
Statistics
Matches: 209, Mismatches: 25, Indels: 59
0.71 0.09 0.20
Matches are distributed among these distances:
34 7 0.03
35 10 0.05
36 16 0.08
37 46 0.22
38 26 0.12
39 47 0.22
40 28 0.13
41 24 0.11
42 3 0.01
43 2 0.01
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (38 bp):
TAATATAATAATAATAATATATAATATATATATAATAT
Found at i:18423 original size:64 final size:62
Alignment explanation
Indices: 18260--18563 Score: 205
Period size: 64 Copynumber: 4.7 Consensus size: 62
18250 AATATTAATG
* * *
18260 TAATA-ATAATA-ATAAATATAAT-ATAATATATACTATAATATGTACATAAATAATATACTATG
1 TAATATATAATATATATATATAATAATAATATATACTAT-ATATATACATAATTAATATA--AT-
18322 A
62 A
18323 TAATATAATATATAATATTAATATAATAATAATAATATATACTATATATATACACTAATTAATAT
1 TAATAT-ATA-AT-ATA-T-ATAT-ATAATAATAATATATACTATATATATACA-TAATTAATAT
18388 AATA
59 AATA
* * *
18392 TAATATATAATATATATATCATATTATTAATATATA-TACTATATA-ACAT-ACTATATATAATA
1 TAATATATAATATATATAT-ATAATAATAATATATACTA-TATATATACATAATTA-ATATAAT-
18454 A
62 A
* * * * *
18455 TAATATACT-ATA-ACATATATAATACGTGATATAATACTAATATATAGTACATATTATAACATA
1 TAATATA-TAATATATATATATAATA-ATAATAT-ATACT-ATATATA-TACATAAT-TAATATA
*
18518 CTA
60 ATA
*
18521 TAATATATAATAT-TATATAATAAT-ATATATCATATATTATATA
1 TAATATATAATATATATAT-ATAATAATA-AT-ATATACTATATA
18564 AACATTGTAA
Statistics
Matches: 195, Mismatches: 19, Indels: 52
0.73 0.07 0.20
Matches are distributed among these distances:
61 8 0.04
62 18 0.09
63 24 0.12
64 32 0.16
65 12 0.06
66 30 0.15
67 15 0.08
68 6 0.03
69 8 0.04
70 5 0.03
71 13 0.07
72 24 0.12
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (62 bp):
TAATATATAATATATATATATAATAATAATATATACTATATATATACATAATTAATATAATA
Found at i:19128 original size:21 final size:20
Alignment explanation
Indices: 19090--19128 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
19080 TGCTAATATC
* *
19090 AAATTTTAAATAATTTAACA
1 AAATTTTAAAAAAATTAACA
19110 AAATATTTAAAAAAATTAA
1 AAAT-TTTAAAAAAATTAA
19129 ATTATAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (20 bp):
AAATTTTAAAAAAATTAACA
Found at i:28668 original size:40 final size:41
Alignment explanation
Indices: 28591--28668 Score: 131
Period size: 42 Copynumber: 1.9 Consensus size: 41
28581 AAGCCACTTT
*
28591 GGGGTCGACCTTTTGGGTTGAAGCTTTAGTATTTGAGTTTTG
1 GGGGTCGACCTTTTGGGGTG-AGCTTTAGTATTTGAGTTTTG
28633 GGGGTCGACCTTTTGGGGTG-GCTTTAGTATTTGAGT
1 GGGGTCGACCTTTTGGGGTGAGCTTTAGTATTTGAGT
28669 GAGGGAAAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
40 16 0.46
42 19 0.54
ACGTcount: A:0.13, C:0.10, G:0.36, T:0.41
Consensus pattern (41 bp):
GGGGTCGACCTTTTGGGGTGAGCTTTAGTATTTGAGTTTTG
Found at i:30196 original size:19 final size:19
Alignment explanation
Indices: 30172--30213 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
30162 ATACACAAAA
30172 GAAATGCCAAATCAAGAAC
1 GAAATGCCAAATCAAGAAC
*
30191 GAAATGGCAAATCAAGAAC
1 GAAATGCCAAATCAAGAAC
30210 GAAA
1 GAAA
30214 GGGCGTGGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.55, C:0.17, G:0.19, T:0.10
Consensus pattern (19 bp):
GAAATGCCAAATCAAGAAC
Found at i:30225 original size:23 final size:19
Alignment explanation
Indices: 30179--30217 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
30169 AAAGAAATGC
*
30179 CAAATCAAGAACGAAATGG
1 CAAATCAAGAACGAAAGGG
30198 CAAATCAAGAACGAAAGGG
1 CAAATCAAGAACGAAAGGG
30217 C
1 C
30218 GTGGAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.51, C:0.18, G:0.23, T:0.08
Consensus pattern (19 bp):
CAAATCAAGAACGAAAGGG
Found at i:34105 original size:56 final size:56
Alignment explanation
Indices: 34043--34149 Score: 187
Period size: 56 Copynumber: 1.9 Consensus size: 56
34033 TATCATTGAG
*
34043 ACTGTATAATAAGTGTTAAAATACGATAATTTAATATATATTTTTATAACACTGCA
1 ACTGTATAATAAGTGTTAAAATACGATAATTTAATATATAATTTTATAACACTGCA
* *
34099 ACTGTATAATAAGTGTTAAAATATGGTAATTTAATATATAATTTTATAACA
1 ACTGTATAATAAGTGTTAAAATACGATAATTTAATATATAATTTTATAACA
34150 GTTGGATAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
56 48 1.00
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (56 bp):
ACTGTATAATAAGTGTTAAAATACGATAATTTAATATATAATTTTATAACACTGCA
Found at i:37208 original size:3 final size:3
Alignment explanation
Indices: 37200--37275 Score: 50
Period size: 3 Copynumber: 24.7 Consensus size: 3
37190 CCCACTTCAA
* *
37200 TTC TTC TTC TAT- TTC TTC TTTC TTC TTC TGT- ATC TTT TTC TTC TTC
1 TTC TTC TTC T-TC TTC TTC -TTC TTC TTC T-TC TTC TTC TTC TTC TTC
* *
37246 TAAT- TTC TTC TTC TTC ATC TTT TTC TTC TT
1 T--TC TTC TTC TTC TTC TTC TTC TTC TTC TT
37276 ACATTCTCTT
Statistics
Matches: 57, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
2 3 0.05
3 47 0.82
4 6 0.11
5 1 0.02
ACGTcount: A:0.07, C:0.25, G:0.01, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:38703 original size:21 final size:22
Alignment explanation
Indices: 38673--38718 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
38663 ATAAAAATAA
* * *
38673 AAAATTAAAGATATGATACAAG
1 AAAATTAAAGAAATAAAACAAG
38695 AAAA-TAAAGAAATAAAACAAG
1 AAAATTAAAGAAATAAAACAAG
38716 AAA
1 AAA
38719 TATTGATATC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.70, C:0.04, G:0.11, T:0.15
Consensus pattern (22 bp):
AAAATTAAAGAAATAAAACAAG
Found at i:39156 original size:17 final size:18
Alignment explanation
Indices: 39118--39163 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
39108 GTTTATGACA
39118 GAATTGGAATCTGTGAAG
1 GAATTGGAATCTGTGAAG
*
39136 GAATTGGAATCTGT-CAG
1 GAATTGGAATCTGTGAAG
39153 GAATTGGAATC
1 GAATTGGAATC
39164 CAATTACATA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 13 0.48
18 14 0.52
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.28
Consensus pattern (18 bp):
GAATTGGAATCTGTGAAG
Found at i:39719 original size:33 final size:33
Alignment explanation
Indices: 39681--39743 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
39671 CTAAACCCGA
39681 ACCCGACCCGAATATCACACTTAAAAAAACCCT
1 ACCCGACCCGAATATCACACTTAAAAAAACCCT
*
39714 ACCCGAGCCGAATATCACACTTAAAAAAAC
1 ACCCGACCCGAATATCACACTTAAAAAAAC
39744 TGACCCGAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.44, C:0.33, G:0.08, T:0.14
Consensus pattern (33 bp):
ACCCGACCCGAATATCACACTTAAAAAAACCCT
Found at i:40005 original size:254 final size:255
Alignment explanation
Indices: 39531--40069 Score: 643
Period size: 254 Copynumber: 2.1 Consensus size: 255
39521 CACGACACAA
* *
39531 AATAAAAAAAATATTTTTATTCAATAAAAACATTGACTTAATTGAAAAAAATTATATATAGAGGG
1 AATAAAAAAAATATTTTTATTCAATAAAAACAATGACTTAATTGAAAAAAATAATATATAGAGGG
*
39596 GTATTATTGTAATTATTCCTAAATATATAAGATAAAATTATATATTTTTTTCGGGTCGGTCCGGT
66 GTATTATTGTAATTATTCCTAAATATATAAGATAAAATTATATATTATTTTCGGGTCGG--CGGT
* * *
39661 TTTTTTCACTCTAAACCCGAACCCGACCCGAATATCACACTTAAAAAAACCCTACCCGAGCCGAA
129 ATTTTTCACCCTAAACCCGAACCCGACCCGAATATCACACTTAAAAAAACCCGACCCGAGCCGAA
* * * * ***
39726 TATCACACTTAAAAAAACTGACCCGAATCGAACA-A-AA-TA-AAGTTTCACCCGACCCGAAAT
194 AATCAAACTT--AAAAACCGACCCGAACCGAACATAGAATTAGAAACCTCACCCGACCCGAAAT
*
39786 AATAAAAAAAATATTTTTATTCAATAAAAACAATGACTTAATTGAAAAAAA-AATATATTGAGGG
1 AATAAAAAAAATATTTTTATTCAATAAAAACAATGACTTAATTGAAAAAAATAATATATAGAGGG
* *
39850 GTATTATTGTAATTGTTCCTAAATATATAAGGTAAAATTATATATATATTTTCGGGTC-G-GGTA
66 GTATTATTGTAATTATTCCTAAATATATAAGATAAAATTATATAT-TATTTTCGGGTCGGCGGTA
*
39913 TTTTTCACCCTAAACCCGAACTCGACCCGACCTGAATATCACACTTAAAAAAAACGACCCGACCC
130 TTTTTCACCCTAAACCCG-A----ACCCGACCCGAATATCACACTT--AAAAAA--ACCCGACCC
* ** * * * *
39978 GA-CC-AAAAT-AAAGTT-TCACCCGACCCGACCCGAATATATGAATTAGAAACCTGACCCGACC
186 GAGCCGAAAATCAAACTTAAAAACCGACCCGAACCGAACATA-GAATTAGAAACCTCACCCGACC
40039 CGAAAT
250 CGAAAT
40045 AAT-AAAAAAATATTTTTATTCAATA
1 AATAAAAAAAATATTTTTATTCAATA
40070 TATGAATAAA
Statistics
Matches: 245, Mismatches: 24, Indels: 27
0.83 0.08 0.09
Matches are distributed among these distances:
251 20 0.08
252 1 0.00
254 69 0.28
255 62 0.25
256 21 0.09
257 6 0.02
258 34 0.14
259 22 0.09
260 10 0.04
ACGTcount: A:0.42, C:0.19, G:0.11, T:0.28
Consensus pattern (255 bp):
AATAAAAAAAATATTTTTATTCAATAAAAACAATGACTTAATTGAAAAAAATAATATATAGAGGG
GTATTATTGTAATTATTCCTAAATATATAAGATAAAATTATATATTATTTTCGGGTCGGCGGTAT
TTTTCACCCTAAACCCGAACCCGACCCGAATATCACACTTAAAAAAACCCGACCCGAGCCGAAAA
TCAAACTTAAAAACCGACCCGAACCGAACATAGAATTAGAAACCTCACCCGACCCGAAAT
Found at i:40151 original size:27 final size:27
Alignment explanation
Indices: 40121--40179 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
40111 AAATTTCAAT
40121 TCCATCCAAGAAGGGAATTGAATTCCA
1 TCCATCCAAGAAGGGAATTGAATTCCA
* ** * *
40148 TCCATTCTTGGATGGAATTGAATTCCA
1 TCCATCCAAGAAGGGAATTGAATTCCA
40175 TCCAT
1 TCCAT
40180 TTTTTGATGG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.31
Consensus pattern (27 bp):
TCCATCCAAGAAGGGAATTGAATTCCA
Found at i:40180 original size:27 final size:27
Alignment explanation
Indices: 40134--40193 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
40124 ATCCAAGAAG
40134 GGAATTGAATTCCATCCATTCTTGGAT
1 GGAATTGAATTCCATCCATTCTTGGAT
* *
40161 GGAATTGAATTCCATCCATTTTTTGAT
1 GGAATTGAATTCCATCCATTCTTGGAT
40188 GGAATT
1 GGAATT
40194 CACTTTCCCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (27 bp):
GGAATTGAATTCCATCCATTCTTGGAT
Found at i:41463 original size:23 final size:23
Alignment explanation
Indices: 41432--41484 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
41422 TAGGCTACCA
* *
41432 AAAGACAGAGATAAAAATGCCTT
1 AAAGGCAGAGATAAAAATGCCAT
**
41455 AAAGGCAGAGATAAACGTGCCAT
1 AAAGGCAGAGATAAAAATGCCAT
41478 AAAGGCA
1 AAAGGCA
41485 CAGAACATGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.49, C:0.15, G:0.23, T:0.13
Consensus pattern (23 bp):
AAAGGCAGAGATAAAAATGCCAT
Found at i:46165 original size:17 final size:17
Alignment explanation
Indices: 46143--46190 Score: 78
Period size: 17 Copynumber: 2.8 Consensus size: 17
46133 TTGATTGAAG
46143 TTTAAACTCAAATTCAA
1 TTTAAACTCAAATTCAA
*
46160 TTTAAACTTAAATTCAA
1 TTTAAACTCAAATTCAA
*
46177 TTTAAGCTCAAATT
1 TTTAAACTCAAATT
46191 AAAATTTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.44, C:0.15, G:0.02, T:0.40
Consensus pattern (17 bp):
TTTAAACTCAAATTCAA
Found at i:53066 original size:58 final size:55
Alignment explanation
Indices: 52992--53190 Score: 204
Period size: 56 Copynumber: 3.5 Consensus size: 55
52982 TTAACTTATT
* * *
52992 AAATATATTTTATTATTAACTTAATTTGAGATTGTTTTATTATTTTTTTAATTTAA
1 AAATATATTTTATTATTATCTTAATTTGAAATTATTTTATT-TTTTTTTAATTTAA
** * *
53048 AAATATATATATTATTATTATCTTAGCTTAAATATATATTTTATTCTTATTTTAATTTAA
1 AAATATAT-T-TTATTATTATCTTAATTTGAA-AT-TATTTTATT-TTTTTTTAATTTAA
* * * *
53108 ACAA-ATATTTTATTCTTATTTTAATTTGAAAATATTTTATTTTTATTTTAAATTTTA
1 A-AATATATTTTATTATTATCTTAATTTGAAATTATTTTATTTTT-TTTT-AATTTAA
53165 AAATATATTTTATT-TTATCTTAATTT
1 AAATATATTTTATTATTATCTTAATTT
53191 ACAAATATTT
Statistics
Matches: 118, Mismatches: 17, Indels: 16
0.78 0.11 0.11
Matches are distributed among these distances:
55 2 0.02
56 34 0.29
57 19 0.16
58 32 0.27
59 3 0.03
60 26 0.22
61 2 0.02
ACGTcount: A:0.36, C:0.04, G:0.03, T:0.58
Consensus pattern (55 bp):
AAATATATTTTATTATTATCTTAATTTGAAATTATTTTATTTTTTTTTAATTTAA
Found at i:53091 original size:29 final size:28
Alignment explanation
Indices: 52957--53202 Score: 187
Period size: 29 Copynumber: 8.6 Consensus size: 28
52947 TTTATATATC
*
52957 TTTAAAAGTATATTTTATT-TTCATCTTAA
1 TTTAAAA-TATATTTTATTCTT-ATTTTAA
* * **
52986 CTTATTAAATATATTTTATTATTAACTTAA
1 -TT-TAAAATATATTTTATTCTTATTTTAA
* * * * *
53016 TTTGAGAT-TGTTTTATTATTTTTTTAA
1 TTTAAAATATATTTTATTCTTATTTTAA
* * *
53043 TTTAAAAATATATATATTATTATTATCTTAG
1 TTT-AAAATATAT-T-TTATTCTTATTTTAA
*
53074 CTTAAATATATATTTTATTCTTATTTTAA
1 TTTAAA-ATATATTTTATTCTTATTTTAA
*
53103 TTTAAACAAATATTTTATTCTTATTTTAA
1 TTTAAA-ATATATTTTATTCTTATTTTAA
* *
53132 TTTGAAA-ATATTTTATTTTTATTTTAAA
1 TTTAAAATATATTTTATTCTTATTTT-AA
*
53160 TTTTAAAATATATTTTATT-TTATCTTAA
1 -TTTAAAATATATTTTATTCTTATTTTAA
*
53188 TTTACAA-ATATTTTA
1 TTTAAAATATATTTTA
53203 AAATTTTTAA
Statistics
Matches: 180, Mismatches: 26, Indels: 24
0.78 0.11 0.10
Matches are distributed among these distances:
26 8 0.04
27 41 0.23
28 12 0.07
29 59 0.33
30 34 0.19
31 26 0.14
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.57
Consensus pattern (28 bp):
TTTAAAATATATTTTATTCTTATTTTAA
Found at i:53212 original size:9 final size:9
Alignment explanation
Indices: 53188--53235 Score: 55
Period size: 10 Copynumber: 5.2 Consensus size: 9
53178 TTTATCTTAA
53188 TTTACAAATAT
1 TTTA-AAAT-T
53199 TTTAAAATT
1 TTTAAAATT
53208 TTT--AATT
1 TTTAAAATT
53215 TTTAAAATAT
1 TTTAAAAT-T
53225 TTTAAAATT
1 TTTAAAATT
53234 TT
1 TT
53236 ACCCATAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
7 7 0.21
9 10 0.29
10 13 0.38
11 4 0.12
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (9 bp):
TTTAAAATT
Found at i:53216 original size:116 final size:116
Alignment explanation
Indices: 52996--53203 Score: 257
Period size: 116 Copynumber: 1.8 Consensus size: 116
52986 CTTATTAAAT
* * *
52996 ATATTTTATTATTAACTTAATTTGAGATTGTTTTATTATTTTTTTAATTTAAAAATATATATATT
1 ATATTTTATTATTAACTTAATTTGAAAATATTTTATTATTTTTTTAATTTAAAAATATATATATT
* *
53061 ATTATTATCTTAGCTTAAATATATATTTTATTCTTATTTTAATTTAAACAA
66 ATTATTATCTTAACTTAAATATATATTTAATTCTTATTTTAATTTAAACAA
* ** *
53112 ATATTTTATTCTTATTTTAATTTGAAAATATTTTATT-TTTATTTTAAATTTTAAAATATAT-T-
1 ATATTTTATTATTAACTTAATTTGAAAATATTTTATTATTT-TTTT-AATTTAAAAATATATATA
*
53174 TTATT-TTATCTTAATTTACAA-ATAT-TTTAA
64 TTATTATTATCTTAACTTA-AATATATATTTAA
53204 AATTTTTAAT
Statistics
Matches: 79, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
113 4 0.05
114 15 0.19
115 10 0.13
116 36 0.46
117 14 0.18
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (116 bp):
ATATTTTATTATTAACTTAATTTGAAAATATTTTATTATTTTTTTAATTTAAAAATATATATATT
ATTATTATCTTAACTTAAATATATATTTAATTCTTATTTTAATTTAAACAA
Found at i:53217 original size:16 final size:17
Alignment explanation
Indices: 53198--53229 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
53188 TTTACAAATA
53198 TTTTAAAAT-TTTTAAT
1 TTTTAAAATATTTTAAT
53214 TTTTAAAATATTTTAA
1 TTTTAAAATATTTTAA
53230 AATTTTACCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTTAAAATATTTTAAT
Found at i:54102 original size:2 final size:2
Alignment explanation
Indices: 54097--54125 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
54087 TTTTCGAGAC
54097 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
54126 ACTTTTTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:54236 original size:12 final size:12
Alignment explanation
Indices: 54219--54247 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
54209 TCAAAGAAAA
54219 GCTTTCTATTAT
1 GCTTTCTATTAT
54231 GCTTTCTATTAT
1 GCTTTCTATTAT
54243 GCTTT
1 GCTTT
54248 AGAAGAAACA
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:0.14, C:0.17, G:0.10, T:0.59
Consensus pattern (12 bp):
GCTTTCTATTAT
Found at i:58659 original size:21 final size:21
Alignment explanation
Indices: 58630--58672 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
58620 ATATAAATTG
*
58630 TGTATCGATGCACTGCTACAA
1 TGTACCGATGCACTGCTACAA
58651 TGTACCGATGCACTGCTACAA
1 TGTACCGATGCACTGCTACAA
58672 T
1 T
58673 AACTTCAGCT
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:0.28, C:0.26, G:0.19, T:0.28
Consensus pattern (21 bp):
TGTACCGATGCACTGCTACAA
Found at i:64156 original size:24 final size:24
Alignment explanation
Indices: 64124--64202 Score: 116
Period size: 24 Copynumber: 3.5 Consensus size: 24
64114 CAGAGCACGT
64124 TATTATTATGGATATGCTTAGGTG
1 TATTATTATGGATATGCTTAGGTG
64148 ---TATTAT---TATGCTTAGGTG
1 TATTATTATGGATATGCTTAGGTG
64166 TATTATTATGGATATGCTTAGGTG
1 TATTATTATGGATATGCTTAGGTG
64190 TATTATTATGGAT
1 TATTATTATGGAT
64203 CTTGAGGGTA
Statistics
Matches: 49, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
18 12 0.24
21 12 0.24
24 25 0.51
ACGTcount: A:0.25, C:0.04, G:0.23, T:0.48
Consensus pattern (24 bp):
TATTATTATGGATATGCTTAGGTG
Found at i:64159 original size:18 final size:18
Alignment explanation
Indices: 64136--64175 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
64126 TTATTATGGA
64136 TATGCTTAGGTGTATTAT
1 TATGCTTAGGTGTATTAT
64154 TATGCTTAGGTGTATTAT
1 TATGCTTAGGTGTATTAT
64172 TATG
1 TATG
64176 GATATGCTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.23, C:0.05, G:0.23, T:0.50
Consensus pattern (18 bp):
TATGCTTAGGTGTATTAT
Found at i:71703 original size:7 final size:7
Alignment explanation
Indices: 71691--71717 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
71681 TGAGATTGAG
71691 ATTGAAT
1 ATTGAAT
71698 ATTGAAT
1 ATTGAAT
71705 ATTGAAT
1 ATTGAAT
71712 ATTGAA
1 ATTGAA
71718 GTCGTGATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (7 bp):
ATTGAAT
Found at i:82450 original size:32 final size:32
Alignment explanation
Indices: 82391--82475 Score: 109
Period size: 32 Copynumber: 2.7 Consensus size: 32
82381 ACCTTCACCC
* * *
82391 AATCCCTAAATCTCT-AAATCTCTAATATCCA
1 AATCCCTAAATCTTTAAAATCTCCAATATACA
* *
82422 AATCCCTATATCTTTAAAATCTCCAATATATA
1 AATCCCTAAATCTTTAAAATCTCCAATATACA
*
82454 AATCCCTAAACCTTTAAAATCT
1 AATCCCTAAATCTTTAAAATCT
82476 TAATCTCCAC
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
31 13 0.28
32 33 0.72
ACGTcount: A:0.40, C:0.26, G:0.00, T:0.34
Consensus pattern (32 bp):
AATCCCTAAATCTTTAAAATCTCCAATATACA
Done.