Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009592.1 Hibiscus syriacus cultivar Beakdansim tig00116971_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: 7920512
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 39
Found at i:188655 original size:16 final size:17
Alignment explanation
Indices: 188611--188663 Score: 74
Period size: 17 Copynumber: 3.2 Consensus size: 17
188601 CTTGTAACTA
*
188611 ATAATAATAAT-ATAAT
1 ATAATAATAGTAATAAT
188627 AATAATAATAGTAATAAT
1 -ATAATAATAGTAATAAT
188645 ATAAT-ATAGTAATAAT
1 ATAATAATAGTAATAAT
188661 ATA
1 ATA
188664 TGCAAACTCG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
16 14 0.41
17 15 0.44
18 5 0.15
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (17 bp):
ATAATAATAGTAATAAT
Found at i:189147 original size:12 final size:12
Alignment explanation
Indices: 189130--189155 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
189120 AATGACTAAA
189130 AATAATTAAATT
1 AATAATTAAATT
189142 AATAATTAAATT
1 AATAATTAAATT
189154 AA
1 AA
189156 ATATATAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
AATAATTAAATT
Found at i:189496 original size:10 final size:11
Alignment explanation
Indices: 189466--189497 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
189456 TGTATATTAT
189466 TATATATAT-A
1 TATATATATAA
189476 TATATATATAA
1 TATATATATAA
189487 TAT-TATATAA
1 TATATATATAA
189497 T
1 T
189498 GTGTAAATAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 17 0.81
11 4 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
TATATATATAA
Found at i:190711 original size:22 final size:22
Alignment explanation
Indices: 190683--190727 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
190673 TTATCTTCTG
190683 GCATAAGATAGAACACTAATTT
1 GCATAAGATAGAACACTAATTT
190705 GCATAAGATAGAACACTAATTT
1 GCATAAGATAGAACACTAATTT
190727 G
1 G
190728 TAGAGTCGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (22 bp):
GCATAAGATAGAACACTAATTT
Found at i:192313 original size:13 final size:13
Alignment explanation
Indices: 192289--192327 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
192279 GGCTTTGTAA
*
192289 ATAATAATAATATT
1 ATAAT-ATAATAAT
192303 ATAATATAATAAT
1 ATAATATAATAAT
*
192316 ATATTATAATAA
1 ATAATATAATAA
192328 AAAATGTCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 18 0.78
14 5 0.22
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
ATAATATAATAAT
Found at i:192731 original size:36 final size:36
Alignment explanation
Indices: 192691--192811 Score: 197
Period size: 36 Copynumber: 3.4 Consensus size: 36
192681 ATCACCCTTT
192691 CGTGAAGGTTGAAAATGACTGACTTCACTACTCTTC
1 CGTGAAGGTTGAAAATGACTGACTTCACTACTCTTC
*
192727 CGTGAAGGTTGAAAATGACTGACTTCACTAATCTTC
1 CGTGAAGGTTGAAAATGACTGACTTCACTACTCTTC
* * *
192763 AGTGAAGGCTGAAAATGACTTACTTCACTACTCTTC
1 CGTGAAGGTTGAAAATGACTGACTTCACTACTCTTC
*
192799 CATGAAGGTTGAA
1 CGTGAAGGTTGAA
192812 TTATACTGAG
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 77 1.00
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.30
Consensus pattern (36 bp):
CGTGAAGGTTGAAAATGACTGACTTCACTACTCTTC
Found at i:192976 original size:20 final size:20
Alignment explanation
Indices: 192951--193086 Score: 98
Period size: 20 Copynumber: 6.8 Consensus size: 20
192941 ACAGATGACT
* *
192951 CGAAGGATTTAAAAATTACC
1 CGAAGGTTTTAAAAATAACC
* *
192971 CGAAGGTTTTACAAATGACC
1 CGAAGGTTTTAAAAATAACC
* *
192991 TGGAGGTTTTAAAAATAACC
1 CGAAGGTTTTAAAAATAACC
* *
193011 C-AGAGGTTTTATAAATGACC
1 CGA-AGGTTTTAAAAATAACC
* * *
193031 CGGAGGTTTTACAAATAACT
1 CGAAGGTTTTAAAAATAACC
* *
193051 C-AGAGGTTTTACAAATGACC
1 CGA-AGGTTTTAAAAATAACC
*
193071 C-AGAGGTTTTACAAAT
1 CGA-AGGTTTTAAAAAT
193087 GACTGGGAAA
Statistics
Matches: 95, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
20 95 1.00
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (20 bp):
CGAAGGTTTTAAAAATAACC
Found at i:192989 original size:40 final size:39
Alignment explanation
Indices: 192958--193086 Score: 161
Period size: 40 Copynumber: 3.2 Consensus size: 39
192948 ACTCGAAGGA
*
192958 TTTAAAAATTACCC-GAAGGTTTTACAAATGACCTGGAGGT
1 TTTAAAAATAACCCAG-AGGTTTTACAAATGACC-GGAGGT
*
192998 TTTAAAAATAACCCAGAGGTTTTATAAATGACCCGGAGGT
1 TTTAAAAATAACCCAGAGGTTTTACAAATGA-CCGGAGGT
* * *
193038 TTTACAAATAACTCAGAGGTTTTACAAATGACCCAGAGGT
1 TTTAAAAATAACCCAGAGGTTTTACAAATGA-CCGGAGGT
*
193078 TTTACAAAT
1 TTTAAAAAT
193087 GACTGGGAAA
Statistics
Matches: 81, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
40 78 0.96
41 3 0.04
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (39 bp):
TTTAAAAATAACCCAGAGGTTTTACAAATGACCGGAGGT
Found at i:193061 original size:60 final size:60
Alignment explanation
Indices: 192958--193089 Score: 176
Period size: 60 Copynumber: 2.2 Consensus size: 60
192948 ACTCGAAGGA
* * *
192958 TTTAAAAATTACCCGAAGGTTTTACAAATGACCTGGAGGTTTTAAAAATAACCCAGAGGT
1 TTTAAAAATGACCCGAAGGTTTTACAAATAACCTAGAGGTTTTAAAAATAACCCAGAGGT
* * * *
193018 TTTATAAATGACCCGGAGGTTTTACAAATAA-CTCAGAGGTTTTACAAATGACCCAGAGGT
1 TTTAAAAATGACCCGAAGGTTTTACAAATAACCT-AGAGGTTTTAAAAATAACCCAGAGGT
*
193078 TTTACAAATGAC
1 TTTAAAAATGAC
193090 TGGGAAATGA
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
59 2 0.03
60 61 0.97
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (60 bp):
TTTAAAAATGACCCGAAGGTTTTACAAATAACCTAGAGGTTTTAAAAATAACCCAGAGGT
Found at i:193087 original size:20 final size:20
Alignment explanation
Indices: 192974--193089 Score: 160
Period size: 20 Copynumber: 5.8 Consensus size: 20
192964 AATTACCCGA
**
192974 AGGTTTTACAAATGACCTGG
1 AGGTTTTACAAATGACCCAG
* *
192994 AGGTTTTAAAAATAACCCAG
1 AGGTTTTACAAATGACCCAG
* *
193014 AGGTTTTATAAATGACCCGG
1 AGGTTTTACAAATGACCCAG
* *
193034 AGGTTTTACAAATAACTCAG
1 AGGTTTTACAAATGACCCAG
193054 AGGTTTTACAAATGACCCAG
1 AGGTTTTACAAATGACCCAG
193074 AGGTTTTACAAATGAC
1 AGGTTTTACAAATGAC
193090 TGGGAAATGA
Statistics
Matches: 83, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 83 1.00
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (20 bp):
AGGTTTTACAAATGACCCAG
Found at i:202957 original size:3 final size:3
Alignment explanation
Indices: 202943--203010 Score: 86
Period size: 3 Copynumber: 23.0 Consensus size: 3
202933 CAGTTTGTTT
* * *
202943 TTA TTT TTA TTA TTA TTA TTA TAA TT- TT- TTA TTA TTA TTA TACA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
202987 TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
203011 AATAAATATT
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
2 4 0.07
3 51 0.89
4 2 0.04
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:202973 original size:22 final size:22
Alignment explanation
Indices: 202946--203010 Score: 85
Period size: 22 Copynumber: 2.8 Consensus size: 22
202936 TTTGTTTTTA
202946 TTTTTATTATTATTATTATAAT
1 TTTTTATTATTATTATTATAAT
* *
202968 TTTTTATTATTATTATACATTAT
1 TTTTTATTATTATTAT-TATAAT
202991 TATTATTATTATTATTATTA
1 T-TT-TTATTATTATTATTA
203011 AATAAATATT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
22 16 0.43
23 5 0.14
24 3 0.08
25 13 0.35
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (22 bp):
TTTTTATTATTATTATTATAAT
Found at i:202976 original size:19 final size:21
Alignment explanation
Indices: 202947--203005 Score: 95
Period size: 19 Copynumber: 2.9 Consensus size: 21
202937 TTGTTTTTAT
202947 TTTTATTATTATTATTATA-A
1 TTTTATTATTATTATTATACA
202967 TTTT-TTATTATTATTATACA
1 TTTTATTATTATTATTATACA
202987 TTATTATTATTATTATTAT
1 TT-TTATTATTATTATTAT
203006 TATTAAATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
19 14 0.39
20 7 0.19
21 2 0.06
22 13 0.36
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTTATTATTATTATTATACA
Found at i:204807 original size:137 final size:139
Alignment explanation
Indices: 204536--204801 Score: 375
Period size: 137 Copynumber: 1.9 Consensus size: 139
204526 ACTTTAAGAA
* *
204536 AAATAATATTTTAATATTTATTTAATATTAAGAAATGACAGTCTTAAAGCAACTGGAAGTCCATT
1 AAATAATATTTTAATATTTATTTAATATTAAGAAAAGACAGTCTTAAAGCAACTAGAAGTCCATT
* * * *
204601 TTCTGATATTTTTAAATAAATAAATATTTTAATTTTATAAATTATATATATTAATCTATTTTTTA
66 TTCTGATATTTATAAATAAATAAATATCTTAATTTTATAAATTATATAAATTAATATATTTTTTA
204666 ATTATTTTT
131 ATTATTTTT
* *
204675 AAATAAATATTTT-AT-TTT-TTTAATATTAAGAAAAGAGCTGTCTTAAAGCACCTAGAAGTCC-
1 AAAT-AATATTTTAATATTTATTTAATATTAAGAAAAGA-CAGTCTTAAAGCAACTAGAAGTCCA
*
204736 TTTTCTGATATTTATAAATAAATAAATATCTT-A-TTTATATA-TATATAAATTAATATATTTTC
64 TTTTCTGATATTTATAAATAAATAAATATCTTAATTTTATAAATTATATAAATTAATATATTTT-
204798 TTAA
128 TTAA
204802 AATTATAAAT
Statistics
Matches: 115, Mismatches: 9, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
134 18 0.16
135 11 0.10
136 1 0.01
137 47 0.41
138 24 0.21
139 6 0.05
140 8 0.07
ACGTcount: A:0.41, C:0.07, G:0.06, T:0.46
Consensus pattern (139 bp):
AAATAATATTTTAATATTTATTTAATATTAAGAAAAGACAGTCTTAAAGCAACTAGAAGTCCATT
TTCTGATATTTATAAATAAATAAATATCTTAATTTTATAAATTATATAAATTAATATATTTTTTA
ATTATTTTT
Found at i:207647 original size:8 final size:7
Alignment explanation
Indices: 207627--207665 Score: 51
Period size: 7 Copynumber: 5.3 Consensus size: 7
207617 CATACATACA
207627 TTTGCAT
1 TTTGCAT
207634 TTTGCAT
1 TTTGCAT
207641 CTTTGCAT
1 -TTTGCAT
*
207649 TTTTCATT
1 TTTGCA-T
207657 TTTGCAT
1 TTTGCAT
207664 TT
1 TT
207666 ATACTTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
7 15 0.54
8 13 0.46
ACGTcount: A:0.13, C:0.15, G:0.10, T:0.62
Consensus pattern (7 bp):
TTTGCAT
Found at i:207647 original size:15 final size:15
Alignment explanation
Indices: 207627--207665 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
207617 CATACATACA
207627 TTTGCATTTTGCATC
1 TTTGCATTTTGCATC
* *
207642 TTTGCATTTTTCATT
1 TTTGCATTTTGCATC
207657 TTTGCATTT
1 TTTGCATTT
207666 ATACTTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.13, C:0.15, G:0.10, T:0.62
Consensus pattern (15 bp):
TTTGCATTTTGCATC
Found at i:207782 original size:20 final size:20
Alignment explanation
Indices: 207744--207788 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
207734 GCATTTTACA
* *
207744 TATTTGCATTTTTACGTTTG
1 TATTTACATTTTCACGTTTG
*
207764 TATTTACATTTTCATGTTTG
1 TATTTACATTTTCACGTTTG
*
207784 CATTT
1 TATTT
207789 GCATCTTTGC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.18, C:0.11, G:0.11, T:0.60
Consensus pattern (20 bp):
TATTTACATTTTCACGTTTG
Found at i:210183 original size:1 final size:1
Alignment explanation
Indices: 210172--210263 Score: 58
Period size: 1 Copynumber: 92.0 Consensus size: 1
210162 AAGAAGAAGG
* * * * * * * * * *
210172 AAAAAAGAAAAATAAAGAAAAATAAAAATAAAAAAAAACAAAAACAAAAACAAAAACAAAAACAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * **
210237 AAACAAAAACAAAAAAAGGAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
210264 GGAAAATTGA
Statistics
Matches: 65, Mismatches: 26, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 65 1.00
ACGTcount: A:0.85, C:0.08, G:0.04, T:0.03
Consensus pattern (1 bp):
A
Found at i:210193 original size:18 final size:17
Alignment explanation
Indices: 210179--210253 Score: 89
Period size: 18 Copynumber: 4.4 Consensus size: 17
210169 AGGAAAAAAG
* * *
210179 AAAAATAAAGAAAAATA
1 AAAAAAAAACAAAAACA
*
210196 AAAATAAAA-AAAAACA
1 AAAAAAAAACAAAAACA
210212 AAAACAAAAACAAAAACA
1 AAAA-AAAAACAAAAACA
210230 AAAACAAAAACAAAAACA
1 AAAA-AAAAACAAAAACA
210248 AAAAAA
1 AAAAAA
210254 GGAAAAAAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
16 10 0.19
17 13 0.25
18 29 0.56
ACGTcount: A:0.85, C:0.09, G:0.01, T:0.04
Consensus pattern (17 bp):
AAAAAAAAACAAAAACA
Found at i:210198 original size:6 final size:6
Alignment explanation
Indices: 210189--210251 Score: 94
Period size: 6 Copynumber: 10.8 Consensus size: 6
210179 AAAAATAAAG
* *
210189 AAAAAT AAAAAT AAAAA- -AAAAC AAAAAC AAAAAC AAAAAC AAAAAC
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC
210235 AAAAAC AAAAAC AAAAA
1 AAAAAC AAAAAC AAAAA
210252 AAGGAAAAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.07
6 51 0.93
ACGTcount: A:0.86, C:0.11, G:0.00, T:0.03
Consensus pattern (6 bp):
AAAAAC
Found at i:210204 original size:22 final size:22
Alignment explanation
Indices: 210173--210253 Score: 99
Period size: 22 Copynumber: 3.6 Consensus size: 22
210163 AGAAGAAGGA
* * * *
210173 AAAAAGAAAAATAAAGAAAAAT
1 AAAAACAAAAAAAAACAAAAAC
*
210195 AAAAATAAAAAAAAACAAAAAC
1 AAAAACAAAAAAAAACAAAAAC
210217 AAAAACAAAAACAAAAACAAAAAC
1 AAAAAC-AAAA-AAAAACAAAAAC
210241 AAAAACAAAAAAA
1 AAAAACAAAAAAA
210254 GGAAAAAAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
22 26 0.50
23 8 0.15
24 18 0.35
ACGTcount: A:0.85, C:0.09, G:0.02, T:0.04
Consensus pattern (22 bp):
AAAAACAAAAAAAAACAAAAAC
Found at i:214606 original size:50 final size:50
Alignment explanation
Indices: 214526--214675 Score: 237
Period size: 50 Copynumber: 3.0 Consensus size: 50
214516 TTGACCAGAA
*
214526 ATCTGGGCAGAAGCCACAGGAAAGGATGAATGTGTTTTCAAATGTTTTAC
1 ATCTGGGCAGAAGCCACAGGAAATGATGAATGTGTTTTCAAATGTTTTAC
* * *
214576 ATCTAGGCAGAAGCCACAGGAAATGATGAATATGTTTACAAATGTTTTAC
1 ATCTGGGCAGAAGCCACAGGAAATGATGAATGTGTTTTCAAATGTTTTAC
* * *
214626 ATCTGGGCAGAAACCACAGGAAATGATGAATGTATTGTCAAATGTTTTAC
1 ATCTGGGCAGAAGCCACAGGAAATGATGAATGTGTTTTCAAATGTTTTAC
214676 GAACCAGTTA
Statistics
Matches: 90, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 90 1.00
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (50 bp):
ATCTGGGCAGAAGCCACAGGAAATGATGAATGTGTTTTCAAATGTTTTAC
Found at i:215075 original size:22 final size:22
Alignment explanation
Indices: 215047--215101 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
215037 ATCTACATTC
215047 TTCAAAGATGATAAATTCTCTT
1 TTCAAAGATGATAAATTCTCTT
* *
215069 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAAATTCTCTT
215091 TTCAAAGATGA
1 TTCAAAGATGA
215102 AAGCTTTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAAATTCTCTT
Found at i:215871 original size:76 final size:76
Alignment explanation
Indices: 215772--216195 Score: 735
Period size: 76 Copynumber: 5.6 Consensus size: 76
215762 CTATTTACCA
215772 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
215837 AGCCTTAGGGT
66 AGCCTTAGGGT
215848 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
215913 AGCCTTAGGGT
66 AGCCTTAGGGT
*
215924 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
215989 AGCCTTAGGGT
66 AGCCTTAGGGT
* * *
216000 TATCTGTAAGTCGTGCAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
216065 AGCCTTAGGGT
66 AGCCTTAGGGT
*
216076 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
216141 AACCTTAGGTT
66 AGCCTTAGGGT
* * * *
216152 AATCTGTAAGTCCTTCAGTGCTTGATGTTTTC-AAAA-CCTTCGGG
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGG
216196 TCATCTGTAA
Statistics
Matches: 333, Mismatches: 15, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
74 8 0.02
75 4 0.01
76 321 0.96
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:216275 original size:94 final size:91
Alignment explanation
Indices: 216129--216371 Score: 407
Period size: 94 Copynumber: 2.6 Consensus size: 91
216119 GGGAGCTTTT
* * * *
216129 TGATGTTTTC-AAAACCTTAGGTTAATCTGTAAGTCCTTCAGTGCTTGATGTTTTCAAAACCTTC
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTC
216193 GGGTCATCTGTAAGTCCTTCAGTGCA
66 GGGTCATCTGTAAGTCCTTCAGTGCA
216219 TGATGTTTTCAAAAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACC
1 TGATGTTTTC---AAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACC
216284 TTCGGGTCATCTGTAAGTCCTTCAGTGCA
63 TTCGGGTCATCTGTAAGTCCTTCAGTGCA
*
216313 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAA
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAA
216372 CATTTCCATC
Statistics
Matches: 144, Mismatches: 5, Indels: 7
0.92 0.03 0.04
Matches are distributed among these distances:
90 10 0.07
91 48 0.33
94 86 0.60
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (91 bp):
TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTC
GGGTCATCTGTAAGTCCTTCAGTGCA
Found at i:216345 original size:46 final size:45
Alignment explanation
Indices: 216129--216371 Score: 396
Period size: 45 Copynumber: 5.3 Consensus size: 45
216119 GGGAGCTTTT
* * * *
216129 TGATGTTTTCAAAACCTTAGGTTAATCTGTAAGTCCTTCAGTGCT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
216174 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
216219 TGATGTTTTCAAAAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTC----AAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
216268 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
*
216313 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
1 TGATGTTTTC-AAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
216359 TGATGTTTTCAAA
1 TGATGTTTTCAAA
216372 CATTTCCATC
Statistics
Matches: 188, Mismatches: 5, Indels: 10
0.93 0.02 0.05
Matches are distributed among these distances:
45 99 0.53
46 44 0.23
49 45 0.24
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
Found at i:216500 original size:3 final size:3
Alignment explanation
Indices: 216480--216562 Score: 103
Period size: 3 Copynumber: 27.0 Consensus size: 3
216470 ATTTTTCAAT
* * * * *
216480 TTA TTT TTA TTT TTA TTA TTA TTA TAA TTT TTA TTA TTA TTA TTA TACA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
216529 TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
216563 AATAAATATT
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
3 63 0.93
4 5 0.07
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:217103 original size:65 final size:65
Alignment explanation
Indices: 217020--217157 Score: 249
Period size: 65 Copynumber: 2.1 Consensus size: 65
217010 GACAGCCACA
*
217020 GAAAGCAAGAACAGACAGAGAGCTACGACAGCGAGCAAGAACGGAGAAAACCACGAAAACAACCT
1 GAAAGCAAGAACAGACAGAGAGCTACGACAGCGAGCAAGAACGGAGAAAACCACGAAAACAACCC
* *
217085 GAAAGCAAGAACAGACAGAGAGCTACGATAGCGAGCAAGAACGGAGAAAACCACGACAACAACCC
1 GAAAGCAAGAACAGACAGAGAGCTACGACAGCGAGCAAGAACGGAGAAAACCACGAAAACAACCC
217150 GAAAGCAA
1 GAAAGCAA
217158 ACCAAAACAC
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
65 70 1.00
ACGTcount: A:0.49, C:0.23, G:0.25, T:0.03
Consensus pattern (65 bp):
GAAAGCAAGAACAGACAGAGAGCTACGACAGCGAGCAAGAACGGAGAAAACCACGAAAACAACCC
Found at i:218272 original size:137 final size:134
Alignment explanation
Indices: 218139--218389 Score: 332
Period size: 136 Copynumber: 1.9 Consensus size: 134
218129 TTAATATTTA
* * *
218139 TTTA-TTTTTT-ATATTAAGAAATGA-C-AGTCTTAAAGCAACTGGATGTCCATTTTCTGATATT
1 TTTATTTTTTTAATATTAAGAAAAGAGCTA-TCTTAAAGCAACTAGAAGTCC-TTTTCTGATATT
* * * *
218200 TTTAAATAAATAAATATTTTACTTTTATAAATTATATATATTAATCTATTTT-TTAATTATTTTA
64 TATAAATAAATAAATATCTTA--TTTATAAA-TATATAAATTAATATATTTTCTTAATTATTTTA
218264 GATAAATAT
126 GATAAATAT
* *
218273 TTTATTTTTTTAATATTAAGAAAAGAGCTATCTTAAAGCACCTAGAAGTCCTTTTTTGATATTTA
1 TTTATTTTTTTAATATTAAGAAAAGAGCTATCTTAAAGCAACTAGAAGTCCTTTTCTGATATTTA
*
218338 TAAATAAATAAATATCTTATTTATATATATATAAATTAATATATTTTCTTAA
66 TAAATAAATAAATATCTTATTTATAAATATATAAATTAATATATTTTCTTAA
218390 AATTATAAAT
Statistics
Matches: 102, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
133 18 0.18
134 15 0.15
135 6 0.06
136 43 0.42
137 19 0.19
138 1 0.01
ACGTcount: A:0.39, C:0.07, G:0.06, T:0.48
Consensus pattern (134 bp):
TTTATTTTTTTAATATTAAGAAAAGAGCTATCTTAAAGCAACTAGAAGTCCTTTTCTGATATTTA
TAAATAAATAAATATCTTATTTATAAATATATAAATTAATATATTTTCTTAATTATTTTAGATAA
ATAT
Found at i:220065 original size:16 final size:16
Alignment explanation
Indices: 220044--220075 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
220034 ATAAATAAAC
220044 GAACATAAACGAACAA
1 GAACATAAACGAACAA
220060 GAACATAAACGAACAA
1 GAACATAAACGAACAA
220076 AATTTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.19, G:0.12, T:0.06
Consensus pattern (16 bp):
GAACATAAACGAACAA
Found at i:220155 original size:10 final size:10
Alignment explanation
Indices: 220140--220198 Score: 57
Period size: 10 Copynumber: 5.7 Consensus size: 10
220130 CATTTAATAA
220140 ATAAACGAAC
1 ATAAACGAAC
220150 ATAAACGAAC
1 ATAAACGAAC
** *
220160 ACGAAC-ATAA
1 ATAAACGA-AC
220170 ATGAACACGAAC
1 AT-AA-ACGAAC
220182 ATAAACGAAC
1 ATAAACGAAC
220192 ATAAACG
1 ATAAACG
220199 TTGGAGACCC
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
9 1 0.03
10 29 0.74
11 3 0.08
12 5 0.13
13 1 0.03
ACGTcount: A:0.58, C:0.20, G:0.12, T:0.10
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:220165 original size:16 final size:16
Alignment explanation
Indices: 220144--220192 Score: 89
Period size: 16 Copynumber: 3.1 Consensus size: 16
220134 TAATAAATAA
220144 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
220160 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
220176 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
220192 A
1 A
220193 TAAACGTTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.57, C:0.22, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:221240 original size:24 final size:24
Alignment explanation
Indices: 221213--221263 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
221203 TATTGGGTAA
* *
221213 AACATAAATGAATGAACATAAACG
1 AACATAAACGAACGAACATAAACG
* *
221237 AACATAACCGAACGAACATAATCG
1 AACATAAACGAACGAACATAAACG
221261 AAC
1 AAC
221264 GAACATAACC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.55, C:0.20, G:0.12, T:0.14
Consensus pattern (24 bp):
AACATAAACGAACGAACATAAACG
Found at i:221250 original size:14 final size:14
Alignment explanation
Indices: 221233--221278 Score: 83
Period size: 14 Copynumber: 3.3 Consensus size: 14
221223 AATGAACATA
221233 AACGAACATAACCG
1 AACGAACATAACCG
*
221247 AACGAACATAATCG
1 AACGAACATAACCG
221261 AACGAACATAACCG
1 AACGAACATAACCG
221275 AACG
1 AACG
221279 TTCACGAACG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.50, C:0.26, G:0.15, T:0.09
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:228690 original size:2 final size:2
Alignment explanation
Indices: 228683--228722 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
228673 AGCTAAAGTC
228683 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
228723 TAAATCTAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:228829 original size:19 final size:20
Alignment explanation
Indices: 228790--228833 Score: 56
Period size: 22 Copynumber: 2.2 Consensus size: 20
228780 ACAATTGAAT
228790 TTGCCACGACATTTCATTCAA
1 TTGCCACGACA-TTCATTCAA
228811 CTTGCCACGACA-T-ATTCAA
1 -TTGCCACGACATTCATTCAA
228830 TTGC
1 TTGC
228834 AACCACACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.18
19 6 0.27
20 1 0.05
22 11 0.50
ACGTcount: A:0.27, C:0.30, G:0.11, T:0.32
Consensus pattern (20 bp):
TTGCCACGACATTCATTCAA
Found at i:231703 original size:15 final size:15
Alignment explanation
Indices: 231683--231720 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
231673 GAGGAACAGC
231683 AAGCTAGCTTCCTTA
1 AAGCTAGCTTCCTTA
231698 AAGCTAGCTTCCTTA
1 AAGCTAGCTTCCTTA
231713 AAGCTAGC
1 AAGCTAGC
231721 CCAGCTACGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (15 bp):
AAGCTAGCTTCCTTA
Found at i:247615 original size:15 final size:15
Alignment explanation
Indices: 247595--247632 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
247585 GAGGAACAGC
247595 AAGCTAGCTTCCTTA
1 AAGCTAGCTTCCTTA
247610 AAGCTAGCTTCCTTA
1 AAGCTAGCTTCCTTA
247625 AAGCTAGC
1 AAGCTAGC
247633 CCAGCTACGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (15 bp):
AAGCTAGCTTCCTTA
Found at i:262357 original size:169 final size:170
Alignment explanation
Indices: 262028--262367 Score: 673
Period size: 169 Copynumber: 2.0 Consensus size: 170
262018 CTTGTCAATT
262028 TATCTAAAGTGCTGAAGCAATGTGAGGAGTCCAACCTTGTGCTAAACTAGGATAAATGTCACCTT
1 TATCTAAAGTGCTGAAGCAATGTGAGGAGTCCAACCTTGTGCTAAACTAGGATAAATGTCACCTT
262093 ATGGTGACAGAAAATTTGTGTTGGGACACAAAATTTCTCATCGTGACATCAAGCTTGATAAATCC
66 ATGGTGACAGAAAATTTGTGTTGGGACACAAAATTTCTCATCGTGACATCAAGCTTGATAAATCC
262158 AAGGTGTAAGTGATTGAGAATCTGCCTTCACCTACCACTG
131 AAGGTGTAAGTGATTGAGAATCTGCCTTCACCTACCACTG
262198 TATCTAAAGTGCTGAAGCAATGTGAGGAGTCCAACCTTGTGCTAAACTAGGATAAATGTCACCTT
1 TATCTAAAGTGCTGAAGCAATGTGAGGAGTCCAACCTTGTGCTAAACTAGGATAAATGTCACCTT
262263 ATGGTGACAGAAAA-TTGTGTTGGGACACAAAATTTCTCATCGTGACATCAAGCTTGATAAATCC
66 ATGGTGACAGAAAATTTGTGTTGGGACACAAAATTTCTCATCGTGACATCAAGCTTGATAAATCC
262327 AAGGTGTAAGTGATTGAGAATCTGCCTTCACCTACCACTG
131 AAGGTGTAAGTGATTGAGAATCTGCCTTCACCTACCACTG
262367 T
1 T
262368 GAAGGGCATA
Statistics
Matches: 170, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
169 91 0.54
170 79 0.46
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (170 bp):
TATCTAAAGTGCTGAAGCAATGTGAGGAGTCCAACCTTGTGCTAAACTAGGATAAATGTCACCTT
ATGGTGACAGAAAATTTGTGTTGGGACACAAAATTTCTCATCGTGACATCAAGCTTGATAAATCC
AAGGTGTAAGTGATTGAGAATCTGCCTTCACCTACCACTG
Found at i:264726 original size:20 final size:21
Alignment explanation
Indices: 264684--264728 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
264674 AGAGTATCGG
*
264684 TACCATAGTATAGAAGTATCGA
1 TACCATAG-ATAGAAGTACCGA
*
264706 TACCATAG-TAGAGGTACCGA
1 TACCATAGATAGAAGTACCGA
264726 TAC
1 TAC
264729 TATTAAGCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 13 0.62
22 8 0.38
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (21 bp):
TACCATAGATAGAAGTACCGA
Found at i:265119 original size:49 final size:49
Alignment explanation
Indices: 265058--265254 Score: 315
Period size: 49 Copynumber: 4.0 Consensus size: 49
265048 TGTGTATAGA
**
265058 AATGAAAGTTAAATGCATAACGGTGCATTTCAACATAAAAGTGTGCCACT
1 AATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAG-GTGCCACT
*
265108 -ATAAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACT
1 AATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACT
* * *
265156 AATGGAAGTTAAATGCATAACGGTGCATTTCGGCATACAAGGTTCCACT
1 AATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACT
265205 AATGAAAGTTAAATGCATAACGGTGCATTTTCGGCATAAAAGGTGCCACT
1 AATGAAAGTTAAATGCATAACGGTGCA-TTTCGGCATAAAAGGTGCCACT
265255 CATGCTATTA
Statistics
Matches: 135, Mismatches: 10, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
48 8 0.06
49 107 0.79
50 20 0.15
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.26
Consensus pattern (49 bp):
AATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACT
Found at i:272779 original size:2 final size:2
Alignment explanation
Indices: 272772--272804 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
272762 GGTGTCACAT
272772 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
272805 TAAACCATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:273346 original size:46 final size:46
Alignment explanation
Indices: 273291--273548 Score: 312
Period size: 46 Copynumber: 5.6 Consensus size: 46
273281 ACATTTAAAT
* * *
273291 TATGGCATCCTTTCATGCCTTAATGCATCATTCCATGCATTTTAGT
1 TATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGA
* * *
273337 TATGACATCCTTTCATACCTTAATTCATCCTTTCATGCATTTTAGA
1 TATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGA
* * * *
273383 TATTGCATCCTTTCATGCATTTTAGATATGGGATCCTTTCATG--TGTT--A
1 TATGGCATCCTTTCATGC--CTT--A-AT-GCATCCTTTCATGCATTTTAGA
*
273431 -AT-GCATCCTTTCATGCCTTTATGCATCCTTTCATGCATTTTAGA
1 TATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGA
*
273475 TATGGCATCCTTTTATGCCTTAATGCATCCTTTCATGCATTTTAGA
1 TATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGA
273521 TATGGCATCCTTTCATGCCTTAATGCAT
1 TATGGCATCCTTTCATGCCTTAATGCAT
273549 AAAACTTTTT
Statistics
Matches: 180, Mismatches: 20, Indels: 24
0.80 0.09 0.11
Matches are distributed among these distances:
40 12 0.07
41 2 0.01
42 3 0.02
44 3 0.02
45 2 0.01
46 136 0.76
47 2 0.01
48 3 0.02
50 4 0.02
51 2 0.01
52 11 0.06
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.43
Consensus pattern (46 bp):
TATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGA
Found at i:273398 original size:26 final size:26
Alignment explanation
Indices: 273362--273538 Score: 156
Period size: 26 Copynumber: 7.5 Consensus size: 26
273352 TACCTTAATT
273362 CATCCTTTCATGCATTTTAGATATTG
1 CATCCTTTCATGCATTTTAGATATTG
*
273388 CATCCTTTCATGCATTTTAGATATGG
1 CATCCTTTCATGCATTTTAGATATTG
* *
273414 GATCCTTTCATG--TGTT--A-A-TG
1 CATCCTTTCATGCATTTTAGATATTG
*
273434 CATCCTTTCATGC--CTT---TA-TG
1 CATCCTTTCATGCATTTTAGATATTG
*
273454 CATCCTTTCATGCATTTTAGATATGG
1 CATCCTTTCATGCATTTTAGATATTG
* *
273480 CATCCTTTTATGC--CTT--A-A-TG
1 CATCCTTTCATGCATTTTAGATATTG
*
273500 CATCCTTTCATGCATTTTAGATATGG
1 CATCCTTTCATGCATTTTAGATATTG
273526 CATCCTTTCATGC
1 CATCCTTTCATGC
273539 CTTAATGCAT
Statistics
Matches: 123, Mismatches: 14, Indels: 28
0.75 0.08 0.17
Matches are distributed among these distances:
20 43 0.35
21 2 0.02
22 6 0.05
24 6 0.05
25 3 0.02
26 63 0.51
ACGTcount: A:0.21, C:0.22, G:0.14, T:0.44
Consensus pattern (26 bp):
CATCCTTTCATGCATTTTAGATATTG
Found at i:273440 original size:20 final size:20
Alignment explanation
Indices: 273415--273548 Score: 106
Period size: 20 Copynumber: 6.1 Consensus size: 20
273405 TAGATATGGG
**
273415 ATCCTTTCATGTGTTAATGC
1 ATCCTTTCATGCCTTAATGC
*
273435 ATCCTTTCATGCCTTTATGC
1 ATCCTTTCATGCCTTAATGC
*
273455 ATCCTTTCATGCATTTTAGATATGGC
1 ATCCTTTCATGC--CTT--A-AT-GC
*
273481 ATCCTTTTATGCCTTAATGC
1 ATCCTTTCATGCCTTAATGC
*
273501 ATCCTTTCATGCATTTTAGATATGGC
1 ATCCTTTCATGC--CTT--A-AT-GC
273527 ATCCTTTCATGCCTTAATGC
1 ATCCTTTCATGCCTTAATGC
273547 AT
1 AT
273549 AAAACTTTTT
Statistics
Matches: 92, Mismatches: 10, Indels: 24
0.73 0.08 0.19
Matches are distributed among these distances:
20 46 0.50
21 4 0.04
22 6 0.07
24 5 0.05
25 4 0.04
26 27 0.29
ACGTcount: A:0.21, C:0.23, G:0.13, T:0.43
Consensus pattern (20 bp):
ATCCTTTCATGCCTTAATGC
Found at i:276320 original size:2 final size:2
Alignment explanation
Indices: 276313--276340 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
276303 GGTGTCACAT
276313 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
276341 CACACACAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:276889 original size:46 final size:46
Alignment explanation
Indices: 276840--277258 Score: 676
Period size: 46 Copynumber: 9.1 Consensus size: 46
276830 ACATTTAAAT
* **
276840 TATGGCATCCTTTCATGCCTTAATGCATCCTTCCATGCATTTTATT
1 TATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGA
* * *
276886 TATGGCATCCTTTCATACCTTAATGCATCCTTTCATGAATTTTACA
1 TATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGA
* *
276932 TATGGCATCTTTTCATGCCTTAATGCATCATTTCATGCATTTTAGA
1 TATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGA
276978 TATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGA
1 TATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGA
* *
277024 TATGGCATCATTTCATGCCTTAATGCATCCTTTCATGCATTTTAGT
1 TATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGA
* *
277070 TATGGAATCCTTTCATACCTTAATGCATCCTTTCATGCATTTTAGA
1 TATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGA
*
277116 TAAGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGA
1 TATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGA
* **
277162 TATGGCATCCTTTCATGCCTTAAAGCATTATTTCATGCATTTTAGA
1 TATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGA
* *
277208 TATGGCATCCTTTCATGCCTTAATGCACCCTTTCATGCATTTTAGT
1 TATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGA
277254 TATGG
1 TATGG
277259 TCTAAAACTT
Statistics
Matches: 343, Mismatches: 30, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 343 1.00
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.42
Consensus pattern (46 bp):
TATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGA
Found at i:300825 original size:16 final size:16
Alignment explanation
Indices: 300804--300835 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
300794 TGTGATGAAC
*
300804 TTTTCTTGCGTTAGGG
1 TTTTCTTGCGATAGGG
300820 TTTTCTTGCGATAGGG
1 TTTTCTTGCGATAGGG
300836 CTGTTTGCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.09, C:0.12, G:0.31, T:0.47
Consensus pattern (16 bp):
TTTTCTTGCGATAGGG
Found at i:302306 original size:12 final size:12
Alignment explanation
Indices: 302289--302334 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
302279 CTTCAAAGAG
302289 ATTTTATATTTA
1 ATTTTATATTTA
302301 ATTTTATA-TTA
1 ATTTTATATTTA
*
302312 TATTTGAT-TTTA
1 -ATTTTATATTTA
302324 ATTTTAATATT
1 ATTTT-ATATT
302335 AATATTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
11 7 0.25
12 19 0.68
13 2 0.07
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (12 bp):
ATTTTATATTTA
Found at i:302343 original size:14 final size:14
Alignment explanation
Indices: 302324--302441 Score: 80
Period size: 14 Copynumber: 9.2 Consensus size: 14
302314 TTTGATTTTA
302324 ATTTTAATATTAAT
1 ATTTTAATATTAAT
302338 ATTTTAA-A-TAA-
1 ATTTTAATATTAAT
*
302349 A-TTAAATATTAAT
1 ATTTTAATATTAAT
*
302362 TTTTTAATATT-AT
1 ATTTTAATATTAAT
*
302375 ATTATAGATATT-A-
1 ATTTTA-ATATTAAT
*
302388 ATTTTAATATTGAT
1 ATTTTAATATTAAT
*
302402 TTTTTAA-A-TAA-
1 ATTTTAATATTAAT
*
302413 A-TTAAATATTAAT
1 ATTTTAATATTAAT
*
302426 TTTTTAATATT-AT
1 ATTTTAATATTAAT
302439 ATT
1 ATT
302442 ATAGATATTT
Statistics
Matches: 80, Mismatches: 13, Indels: 23
0.69 0.11 0.20
Matches are distributed among these distances:
10 8 0.10
11 3 0.04
12 16 0.20
13 18 0.22
14 35 0.44
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (14 bp):
ATTTTAATATTAAT
Found at i:302386 original size:28 final size:24
Alignment explanation
Indices: 302329--302392 Score: 74
Period size: 24 Copynumber: 2.5 Consensus size: 24
302319 TTTTAATTTT
*
302329 AATATTAATATTTTAAATAAATTA
1 AATATTAATTTTTTAAATAAATTA
*
302353 AATATTAATTTTTTAATATTATATTA
1 AATATTAATTTTTTAA-A-TAAATTA
302379 TAGATATTAATTTT
1 -A-ATATTAATTTT
302393 AATATTGATT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 15 0.44
25 1 0.03
26 6 0.18
27 1 0.03
28 11 0.32
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (24 bp):
AATATTAATTTTTTAAATAAATTA
Found at i:302404 original size:40 final size:36
Alignment explanation
Indices: 302353--302437 Score: 98
Period size: 38 Copynumber: 2.2 Consensus size: 36
302343 AAATAAATTA
*
302353 AATATTAATTTTTTAATATTATATTATAGATATTAATTTT
1 AATATTAATTTTTTAA-A-TAAATTA-A-ATATTAATTTT
*
302393 AATATTGATTTTTTAAATAAATTAAATATTAATTTTTT
1 AATATTAATTTTTTAAATAAATTAAATATTAA--TTTT
302431 AATATTA
1 AATATTA
302438 TATTATAGAT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
36 7 0.17
37 1 0.03
38 16 0.40
39 1 0.03
40 15 0.38
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.55
Consensus pattern (36 bp):
AATATTAATTTTTTAAATAAATTAAATATTAATTTT
Found at i:302407 original size:64 final size:64
Alignment explanation
Indices: 302302--302458 Score: 257
Period size: 64 Copynumber: 2.5 Consensus size: 64
302292 TTATATTTAA
*
302302 TTTT-ATATTATATT-T-GATTTTAATTTTAATATTAATATTTTAAATAAATTAAATATTAATT
1 TTTTAATATTATATTATAGATATTAATTTTAATATTAATATTTTAAATAAATTAAATATTAATT
* *
302363 TTTTAATATTATATTATAGATATTAATTTTAATATTGATTTTTTAAATAAATTAAATATTAATT
1 TTTTAATATTATATTATAGATATTAATTTTAATATTAATATTTTAAATAAATTAAATATTAATT
302427 TTTTAATATTATATTATAGATATTTAATTTTA
1 TTTTAATATTATATTATAGATA-TTAATTTTA
302459 TATCATATAA
Statistics
Matches: 89, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
61 4 0.04
62 10 0.11
63 1 0.01
64 65 0.73
65 9 0.10
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (64 bp):
TTTTAATATTATATTATAGATATTAATTTTAATATTAATATTTTAAATAAATTAAATATTAATT
Found at i:302513 original size:20 final size:19
Alignment explanation
Indices: 302453--302514 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
302443 TAGATATTTA
*
302453 ATTTTATATCA-TATAAATT
1 ATTTTATAT-ATTATTAATT
*
302472 ATTTTATATATTATTAA-A
1 ATTTTATATATTATTAATT
302490 ATTTTATAT-TTATTTTAATT
1 ATTTTATATATTA--TTAATT
302510 ATTTT
1 ATTTT
302515 GATTTAAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 3 0.08
18 10 0.28
19 18 0.50
20 5 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTATATATTATTAATT
Found at i:303014 original size:31 final size:31
Alignment explanation
Indices: 302977--303036 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
302967 TAGTTGTATG
* * *
302977 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATCTCAATATTGCAAAACTAA
303008 AATTATTTAAATCTCAATATTGCAAAACT
1 AATTATTTAAATCTCAATATTGCAAAACT
303037 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (31 bp):
AATTATTTAAATCTCAATATTGCAAAACTAA
Found at i:305219 original size:31 final size:32
Alignment explanation
Indices: 305181--305269 Score: 103
Period size: 31 Copynumber: 2.8 Consensus size: 32
305171 AAAGTTTAAT
305181 TTAAATTTTTAAAAATTTTAAAGGAATC-AAA
1 TTAAATTTTTAAAAATTTTAAAGGAATCTAAA
* *
305212 TTAAATTTGTTAAAATTTTTAAA--AGTCTAAA
1 TTAAATTT-TTAAAAATTTTAAAGGAATCTAAA
*
305243 TTATAATTTTTTAAAATTTTGAAAGGA
1 TTA-AATTTTTAAAAATTTT-AAAGGA
305270 CCATGGCTTC
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
30 3 0.06
31 23 0.48
32 21 0.44
34 1 0.02
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (32 bp):
TTAAATTTTTAAAAATTTTAAAGGAATCTAAA
Found at i:305232 original size:32 final size:32
Alignment explanation
Indices: 305181--305269 Score: 103
Period size: 32 Copynumber: 2.8 Consensus size: 32
305171 AAAGTTTAAT
*
305181 TTAAATTTTTAAAAATTTTAAAGGAATC-AAA
1 TTAAATTTTTAAAATTTTTAAAGGAATCTAAA
*
305212 TTAAATTTGTTAAAATTTTTAAA--AGTCTAAA
1 TTAAATTT-TTAAAATTTTTAAAGGAATCTAAA
*
305243 TTATAATTTTTTAAAATTTTGAAAGGA
1 TTA-AA-TTTTTAAAATTTTTAAAGGA
305270 CCATGGCTTC
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
30 3 0.06
31 14 0.29
32 28 0.57
33 3 0.06
34 1 0.02
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (32 bp):
TTAAATTTTTAAAATTTTTAAAGGAATCTAAA
Found at i:312656 original size:4 final size:4
Alignment explanation
Indices: 312647--312675 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
312637 TATTAACCTA
312647 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
312676 GAAATAAACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:317842 original size:23 final size:23
Alignment explanation
Indices: 317811--317947 Score: 121
Period size: 23 Copynumber: 5.9 Consensus size: 23
317801 AAACATGCCA
*
317811 ACCGAAGTGCCACATATAATTGC
1 ACCGGAGTGCCACATATAATTGC
* * *
317834 ACCGGAGTGCCGCGTAGAATTGC
1 ACCGGAGTGCCACATATAATTGC
* * * *
317857 ACCTGAGTGCCGCGTAAAATTGC
1 ACCGGAGTGCCACATATAATTGC
* *
317880 ACCGTAGTGCCATATAATAATTGC
1 ACCGGAGTGCCACAT-ATAATTGC
* * *
317904 ACCGGAGTGCCGCGTAGAATTGC
1 ACCGGAGTGCCACATATAATTGC
* *
317927 ACCGTAGTGCCATATAATAAT
1 ACCGGAGTGCCACAT-ATAAT
317948 ATCCATAAGG
Statistics
Matches: 90, Mismatches: 22, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
23 68 0.76
24 22 0.24
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.23
Consensus pattern (23 bp):
ACCGGAGTGCCACATATAATTGC
Found at i:317905 original size:24 final size:24
Alignment explanation
Indices: 317874--317947 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 24
317864 TGCCGCGTAA
317874 AATTGCACCGTAGTGCCATATAAT
1 AATTGCACCGTAGTGCCATATAAT
* *** *
317898 AATTGCACCGGAGTGCCGCGT-AG
1 AATTGCACCGTAGTGCCATATAAT
317921 AATTGCACCGTAGTGCCATATAAT
1 AATTGCACCGTAGTGCCATATAAT
317945 AAT
1 AAT
317948 ATCCATAAGG
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
23 18 0.46
24 21 0.54
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.26
Consensus pattern (24 bp):
AATTGCACCGTAGTGCCATATAAT
Found at i:317914 original size:47 final size:47
Alignment explanation
Indices: 317851--317947 Score: 176
Period size: 47 Copynumber: 2.1 Consensus size: 47
317841 TGCCGCGTAG
*
317851 AATTGCACCTGAGTGCCGCGTAAAATTGCACCGTAGTGCCATATAAT
1 AATTGCACCGGAGTGCCGCGTAAAATTGCACCGTAGTGCCATATAAT
*
317898 AATTGCACCGGAGTGCCGCGTAGAATTGCACCGTAGTGCCATATAAT
1 AATTGCACCGGAGTGCCGCGTAAAATTGCACCGTAGTGCCATATAAT
317945 AAT
1 AAT
317948 ATCCATAAGG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (47 bp):
AATTGCACCGGAGTGCCGCGTAAAATTGCACCGTAGTGCCATATAAT
Found at i:318203 original size:103 final size:103
Alignment explanation
Indices: 317954--318270 Score: 570
Period size: 103 Copynumber: 3.1 Consensus size: 103
317944 TAATATCCAT
* * *
317954 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
318019 GACTTCACACATGTTCCAAAGAATAC--ATA--TCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
318053 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
318118 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
318156 AAGAACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
318221 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
318259 AAGGACCACATA
1 AAGGACCACATA
318271 GACCCTCGAC
Statistics
Matches: 209, Mismatches: 5, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
99 88 0.42
101 3 0.01
103 118 0.56
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:323743 original size:23 final size:23
Alignment explanation
Indices: 323717--323841 Score: 117
Period size: 23 Copynumber: 5.3 Consensus size: 23
323707 CACCACAGCT
323717 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
323740 CATATAATTGCACCGGAA-TGCCG
1 CATATAATTGCACC-GAAGTGCCA
* * *
323763 CGTAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* *
323786 TATAATAATTGCACCGGAGTGCCA
1 CAT-ATAATTGCACCGAAGTGCCA
* * * *
323810 CGTAGAATTCCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
323833 TATAATAAT
1 CAT-ATAAT
323842 GTCCATAAGG
Statistics
Matches: 81, Mismatches: 17, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
22 2 0.02
23 53 0.65
24 26 0.32
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:323814 original size:47 final size:47
Alignment explanation
Indices: 323722--323841 Score: 188
Period size: 47 Copynumber: 2.6 Consensus size: 47
323712 CAGCTCATAT
* * *
323722 AATTGCACCGAAGTGCCACAT-ATAATTGCACCGGAATGCCGCGTAG
1 AATTGCACCGTAGTGCCATATAATAATTGCACCGGAATGCCACGTAG
*
323768 AATTGCACCGTAGTGCCATATAATAATTGCACCGGAGTGCCACGTAG
1 AATTGCACCGTAGTGCCATATAATAATTGCACCGGAATGCCACGTAG
*
323815 AATTCCACCGTAGTGCCATATAATAAT
1 AATTGCACCGTAGTGCCATATAATAAT
323842 GTCCATAAGG
Statistics
Matches: 68, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
46 19 0.28
47 49 0.72
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.23
Consensus pattern (47 bp):
AATTGCACCGTAGTGCCATATAATAATTGCACCGGAATGCCACGTAG
Found at i:324027 original size:103 final size:103
Alignment explanation
Indices: 323848--324168 Score: 554
Period size: 103 Copynumber: 3.1 Consensus size: 103
323838 TAATGTCCAT
* * * *
323848 AAGGACCACATATCATTCCTTAAGAATCATATATATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
* *
323913 GACTTCACACATATTCCAAAGAATACATATAAGTCTCG
66 GACTTCACACATGTTCCAAAGAATACATATAAGTCCCG
*
323951 AAGGACCATATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
324016 GACTTCACACATGTTCCAAAGAATACATATATA-TCCCG
66 GACTTCACACATGTTCCAAAGAATACATATA-AGTCCCG
324054 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
324119 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATAAGTCCCG
324157 AAGGACCACATA
1 AAGGACCACATA
324169 GACCCTCGAC
Statistics
Matches: 207, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
103 206 1.00
104 1 0.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATAAGTCCCG
Found at i:325001 original size:2 final size:2
Alignment explanation
Indices: 324994--325026 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
324984 ATTAAGTAAA
324994 AT AT 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 AT AT A
325027 ATTTTTCTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:332993 original size:40 final size:41
Alignment explanation
Indices: 332918--332998 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
332908 CGTTATAGAG
*
332918 TGTTTTTCTTGTAACTTCCTCATATTTAGGAAAAGAAACTT
1 TGTTTTCCTTGTAACTTCCTCATATTTAGGAAAAGAAACTT
332959 TGTTTTCCTTGTAACTTCCTCATATTTAGG-AAAGAAACTT
1 TGTTTTCCTTGTAACTTCCTCATATTTAGGAAAAGAAACTT
332999 ACTTTGGAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
40 10 0.26
41 29 0.74
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.43
Consensus pattern (41 bp):
TGTTTTCCTTGTAACTTCCTCATATTTAGGAAAAGAAACTT
Found at i:343406 original size:2 final size:2
Alignment explanation
Indices: 343399--343439 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
343389 ATGCAAAATT
343399 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
343440 CAAAACCTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:347813 original size:17 final size:17
Alignment explanation
Indices: 347787--347828 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
347777 ATATAAAATT
347787 GGTA-CGATACTCAAGG
1 GGTACCGATACTCAAGG
347803 GGTACCGATACTCAAGG
1 GGTACCGATACTCAAGG
347820 GGTACCGAT
1 GGTACCGAT
347829 GCTACTTTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 4 0.16
17 21 0.84
ACGTcount: A:0.29, C:0.21, G:0.31, T:0.19
Consensus pattern (17 bp):
GGTACCGATACTCAAGG
Found at i:349393 original size:19 final size:19
Alignment explanation
Indices: 349371--349407 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
349361 TTTTCATTCA
349371 ATATCAATTTATTCAATTT
1 ATATCAATTTATTCAATTT
* *
349390 ATATCCATTTATTTAATT
1 ATATCAATTTATTCAATT
349408 AGCCCAACGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.11, G:0.00, T:0.54
Consensus pattern (19 bp):
ATATCAATTTATTCAATTT
Found at i:349524 original size:23 final size:24
Alignment explanation
Indices: 349483--349598 Score: 134
Period size: 23 Copynumber: 5.0 Consensus size: 24
349473 CATCACTGAT
*
349483 CATATAATTT-TCACCGAAGTG-CCA
1 CATAGAATTTGTC-CCGAAG-GACCA
* *
349507 CATA-AATTTGTCCTGAAGGACCG
1 CATAGAATTTGTCCCGAAGGACCA
*
349530 CATAGAATTTTTCCCGAAGGACCA
1 CATAGAATTTGTCCCGAAGGACCA
349554 CATAGAA-TTGTCCCGAAGGACCA
1 CATAGAATTTGTCCCGAAGGACCA
*
349577 CGTAGAA-TTGTCCCGAAGGACC
1 CATAGAATTTGTCCCGAAGGACC
349599 GCGTAGAACT
Statistics
Matches: 82, Mismatches: 7, Indels: 7
0.85 0.07 0.07
Matches are distributed among these distances:
22 1 0.01
23 52 0.63
24 29 0.35
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (24 bp):
CATAGAATTTGTCCCGAAGGACCA
Found at i:349557 original size:47 final size:46
Alignment explanation
Indices: 349483--349598 Score: 137
Period size: 47 Copynumber: 2.5 Consensus size: 46
349473 CATCACTGAT
* * *
349483 CATATAATTTTCACCGAAGTG-CCACATA-AATTTGTCCTGAAGGACCG
1 CATAGAATTTTC-CCGAAG-GACCACATAGAA-TTGTCCCGAAGGACCA
349530 CATAGAATTTTTCCCGAAGGACCACATAGAATTGTCCCGAAGGACCA
1 CATAGAA-TTTTCCCGAAGGACCACATAGAATTGTCCCGAAGGACCA
* *
349577 CGTAGAATTGTCCCGAAGGACC
1 CATAGAATTTTCCCGAAGGACC
349599 GCGTAGAACT
Statistics
Matches: 61, Mismatches: 5, Indels: 7
0.84 0.07 0.10
Matches are distributed among these distances:
46 15 0.25
47 39 0.64
48 7 0.11
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (46 bp):
CATAGAATTTTCCCGAAGGACCACATAGAATTGTCCCGAAGGACCA
Found at i:349742 original size:15 final size:15
Alignment explanation
Indices: 349724--349762 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
349714 AAAGAGTACA
*
349724 TTCACATAGGATATT
1 TTCACATAGGACATT
* *
349739 TTCACGTAGGACGTT
1 TTCACATAGGACATT
349754 TTCACATAG
1 TTCACATAG
349763 AATAAATGTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (15 bp):
TTCACATAGGACATT
Found at i:355777 original size:23 final size:23
Alignment explanation
Indices: 355751--355795 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
355741 CTTATATAAT
* *
355751 TTGCACCGAAGTACCACGTAGAA
1 TTGCACCAAAGTACCACATAGAA
*
355774 TTGCACCAAAGTTCCACATAGA
1 TTGCACCAAAGTACCACATAGA
355796 TTTTTCCCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.27, G:0.18, T:0.20
Consensus pattern (23 bp):
TTGCACCAAAGTACCACATAGAA
Found at i:355818 original size:23 final size:23
Alignment explanation
Indices: 355763--355935 Score: 152
Period size: 23 Copynumber: 7.5 Consensus size: 23
355753 GCACCGAAGT
* *
355763 ACCACGTAGAA-TTGCACCAAAGT
1 ACCACGTAGAATTTTC-CCAAAGG
* * * *
355786 TCCACATAGATTTTTCCCAAAAG
1 ACCACGTAGAATTTTCCCAAAGG
* *
355809 ATCGCGTAGAATTTGTCCCAAAGG
1 ACCACGTAGAATTT-TCCCAAAGG
*
355833 ACCACGTAGAATTTTCCCGAAGG
1 ACCACGTAGAATTTTCCCAAAGG
* *
355856 AGCACGTAGAATTTTCCCGAAGG
1 ACCACGTAGAATTTTCCCAAAGG
* *
355879 ACCACGTAGAATTGTCCCGAAGG
1 ACCACGTAGAATTTTCCCAAAGG
** *
355902 ACCATATAG-ATTTGTCCCGAAGG
1 ACCACGTAGAATTT-TCCCAAAGG
*
355925 ACCGCGTAGAA
1 ACCACGTAGAA
355936 CCCTCGACTC
Statistics
Matches: 122, Mismatches: 24, Indels: 7
0.80 0.16 0.05
Matches are distributed among these distances:
22 3 0.02
23 95 0.78
24 24 0.20
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.22
Consensus pattern (23 bp):
ACCACGTAGAATTTTCCCAAAGG
Found at i:355891 original size:46 final size:47
Alignment explanation
Indices: 355813--355935 Score: 178
Period size: 46 Copynumber: 2.7 Consensus size: 47
355803 CAAAAGATCG
* * *
355813 CGTAGAATTTGTCCCAAAGGACCACGTAGAATTTTCCCGAAGGAGCA
1 CGTAGAATTTGTCCCGAAGGACCACGTAGAATTGTCCCGAAGGACCA
355860 CGTAGAATTT-TCCCGAAGGACCACGTAGAATTGTCCCGAAGGACCA
1 CGTAGAATTTGTCCCGAAGGACCACGTAGAATTGTCCCGAAGGACCA
** *
355906 TATAG-ATTTGTCCCGAAGGACCGCGTAGAA
1 CGTAGAATTTGTCCCGAAGGACCACGTAGAA
355936 CCCTCGACTC
Statistics
Matches: 69, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
45 4 0.06
46 55 0.80
47 10 0.14
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.21
Consensus pattern (47 bp):
CGTAGAATTTGTCCCGAAGGACCACGTAGAATTGTCCCGAAGGACCA
Found at i:356455 original size:27 final size:28
Alignment explanation
Indices: 356414--356472 Score: 70
Period size: 27 Copynumber: 2.1 Consensus size: 28
356404 GTTCTTATAG
356414 AATATATTCACAT-AAATCATATACTT-AT
1 AATATATTCACATAAAAT-ATATA-TTCAT
*
356442 AATAT-TTCATATAAAATATATATTCAT
1 AATATATTCACATAAAATATATATTCAT
356469 AATA
1 AATA
356473 ATGAAATCGA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 2 0.07
27 17 0.61
28 9 0.32
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (28 bp):
AATATATTCACATAAAATATATATTCAT
Found at i:359205 original size:16 final size:16
Alignment explanation
Indices: 359184--359216 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
359174 CACGTGATGA
359184 TTATTTTC-TTTTCATT
1 TTATTTTCATTTT-ATT
359200 TTATTTTCATTTTATT
1 TTATTTTCATTTTATT
359216 T
1 T
359217 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCATTTTATT
Found at i:359206 original size:11 final size:11
Alignment explanation
Indices: 359186--359216 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
359176 CGTGATGATT
*
359186 ATTTTCTTTTC
1 ATTTTATTTTC
359197 ATTTTATTTTC
1 ATTTTATTTTC
359208 ATTTTATTT
1 ATTTTATTT
359217 ACTGTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.16, C:0.10, G:0.00, T:0.74
Consensus pattern (11 bp):
ATTTTATTTTC
Found at i:363506 original size:26 final size:25
Alignment explanation
Indices: 363475--363545 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 25
363465 CCTCTTAAAT
363475 TTTTAACTTTTTCTTTTCTCTTTC-
1 TTTTAACTTTTTCTTTTCTCTTTCA
*
363499 -TTT-A-TTAATT-TTTTCTCTTTCA
1 TTTTAACTT-TTTCTTTTCTCTTTCA
*
363521 TTTTAACTTTTACTTTTTCTCTTTC
1 TTTTAACTTTTTC-TTTTCTCTTTC
363546 CTTCATTCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
21 13 0.35
22 3 0.08
23 6 0.16
24 2 0.05
25 2 0.05
26 11 0.30
ACGTcount: A:0.13, C:0.18, G:0.00, T:0.69
Consensus pattern (25 bp):
TTTTAACTTTTTCTTTTCTCTTTCA
Found at i:363565 original size:47 final size:46
Alignment explanation
Indices: 363475--363565 Score: 112
Period size: 47 Copynumber: 2.0 Consensus size: 46
363465 CCTCTTAAAT
* * * *
363475 TTTTAACTTTTTCTTTTCTCTTTCTTTATTAATTTTTTCTCTTTCA
1 TTTTAACTTTTACTTTTCTCTTTCTTCATTAATCTTCTCTCTTTCA
*
363521 TTTTAACTTTTACTTTTTCTCTTTCCTTCATTCATCTTCT-TCTTT
1 TTTTAACTTTTAC-TTTTCTCTTT-CTTCATTAATCTTCTCTCTTT
363566 TGTTATTCTC
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
46 12 0.32
47 15 0.39
48 11 0.29
ACGTcount: A:0.12, C:0.21, G:0.00, T:0.67
Consensus pattern (46 bp):
TTTTAACTTTTACTTTTCTCTTTCTTCATTAATCTTCTCTCTTTCA
Found at i:371563 original size:65 final size:64
Alignment explanation
Indices: 371364--371573 Score: 173
Period size: 65 Copynumber: 3.2 Consensus size: 64
371354 TGCACTAAGA
* * * * * * *
371364 GTGCATCAATACATCAAGTGCATTCGATGTTTCA-AAATAGC-CAGAGTGCATTGATGCATGG-C
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAA-ATCTC--AGTGCATCGATGCAGGGAT
371426 TG
63 TG
* *
371428 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAAT-CTCAGTGCATCGATGCA-GGGAT
371493 T-
63 TG
* **
371494 -TGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAAT-TCATGGTGCATCGATGCAGGGAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCTCA--GTGCATCGATGCAGGGAT
371556 TG
63 TG
*
371558 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
371574 CTCTGAAAAA
Statistics
Matches: 119, Mismatches: 16, Indels: 21
0.76 0.10 0.13
Matches are distributed among these distances:
62 3 0.03
63 8 0.07
64 43 0.36
65 58 0.49
66 5 0.04
67 2 0.02
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATCTCAGTGCATCGATGCAGGGATTG
Found at i:374197 original size:23 final size:23
Alignment explanation
Indices: 374167--374246 Score: 85
Period size: 23 Copynumber: 3.5 Consensus size: 23
374157 GCATGACCCT
374167 GTGCATCGATGCACATTCAAGGC
1 GTGCATCGATGCACATTCAAGGC
**
374190 GTGCATCGATG--CA-TCAACAC
1 GTGCATCGATGCACATTCAAGGC
* *
374210 GATGAATCGATGCACATTCAAAGGG
1 G-TGCATCGATGCACATTC-AAGGC
374235 GTGCATCGATGC
1 GTGCATCGATGC
374247 TTTGTTAAGT
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
20 6 0.13
21 11 0.24
23 13 0.29
24 12 0.27
25 3 0.07
ACGTcount: A:0.29, C:0.24, G:0.26, T:0.21
Consensus pattern (23 bp):
GTGCATCGATGCACATTCAAGGC
Found at i:378202 original size:22 final size:21
Alignment explanation
Indices: 378160--378199 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
378150 AAGACTATTT
378160 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
**
378181 TCATTTTTGTATTTTGAAA
1 TCATTTTTCAATTTTGAAA
378200 ATAGAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:380266 original size:66 final size:65
Alignment explanation
Indices: 380144--380304 Score: 177
Period size: 66 Copynumber: 2.5 Consensus size: 65
380134 TGCACTAAGA
* * * *
380144 GTGCATCGATGCATCAAGTGCATTTGATG-TTTCAAAATAGCCAGATTGCATTGATGCATGGCT-
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCAGAGTGCATCGATGCATGG-TA
380207 G
65 G
* * *
380208 GTGTATCGATGCATCAAAATGCATTCGATGTTTTCATAAA-ATCCTA-AGTGCATCGATGCATTG
1 GTGCATCGATGCATC-AAATGCATTCGATGTTTTCA-AAATAGCC-AGAGTGCATCGATGCATGG
*
380271 TAT
63 TAG
*
380274 GTGCATCGATGCATGAAATGCATTCGATGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTT
380305 CAATTTAATT
Statistics
Matches: 82, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
64 14 0.17
65 29 0.35
66 35 0.43
67 4 0.05
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCAGAGTGCATCGATGCATGGTAG
Found at i:381819 original size:15 final size:15
Alignment explanation
Indices: 381801--381839 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
381791 ATAGAGTACA
**
381801 TTCACATAGGATGTT
1 TTCACATAGGACATT
*
381816 TTCACGTAGGACATT
1 TTCACATAGGACATT
381831 TTCACATAG
1 TTCACATAG
381840 AATAAATGTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (15 bp):
TTCACATAGGACATT
Found at i:384437 original size:94 final size:94
Alignment explanation
Indices: 384276--384466 Score: 382
Period size: 94 Copynumber: 2.0 Consensus size: 94
384266 CCAATGACAC
384276 ACAACTTTTCTTTAACGACAATCACTTATTTCCAAACTCTCAAAATTGTAATGTTTTCAACTTTG
1 ACAACTTTTCTTTAACGACAATCACTTATTTCCAAACTCTCAAAATTGTAATGTTTTCAACTTTG
384341 TCGCAACATTCACAACAACCTTTCATGTT
66 TCGCAACATTCACAACAACCTTTCATGTT
384370 ACAACTTTTCTTTAACGACAATCACTTATTTCCAAACTCTCAAAATTGTAATGTTTTCAACTTTG
1 ACAACTTTTCTTTAACGACAATCACTTATTTCCAAACTCTCAAAATTGTAATGTTTTCAACTTTG
384435 TCGCAACATTCACAACAACCTTTCATGTT
66 TCGCAACATTCACAACAACCTTTCATGTT
384464 ACA
1 ACA
384467 GTTAATAATC
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
94 97 1.00
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.37
Consensus pattern (94 bp):
ACAACTTTTCTTTAACGACAATCACTTATTTCCAAACTCTCAAAATTGTAATGTTTTCAACTTTG
TCGCAACATTCACAACAACCTTTCATGTT
Found at i:387851 original size:23 final size:24
Alignment explanation
Indices: 387791--387854 Score: 85
Period size: 24 Copynumber: 2.7 Consensus size: 24
387781 CGCCACATAT
387791 ATTTGTCCCAAAGGACCGCGTAAA
1 ATTTGTCCCAAAGGACCGCGTAAA
* * * *
387815 ATTTGTCCCGAAGGATCTCGTAGA
1 ATTTGTCCCAAAGGACCGCGTAAA
387839 A-TTGTCCCAAAGGACC
1 ATTTGTCCCAAAGGACC
387855 ACATAGATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 13 0.38
24 21 0.62
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.23
Consensus pattern (24 bp):
ATTTGTCCCAAAGGACCGCGTAAA
Found at i:387861 original size:23 final size:23
Alignment explanation
Indices: 387793--387885 Score: 96
Period size: 23 Copynumber: 4.0 Consensus size: 23
387783 CCACATATAT
* *
387793 TTGTCCCAAAGGACCGCGTAAAA
1 TTGTCCCAAAGGACCACGTAGAA
* * *
387816 TTTGTCCCGAAGGATCTCGTAGAA
1 -TTGTCCCAAAGGACCACGTAGAA
* *
387840 TTGTCCCAAAGGACCACATAGAT
1 TTGTCCCAAAGGACCACGTAGAA
* *
387863 TTGTTCCGAAGGACCACGTAGAA
1 TTGTCCCAAAGGACCACGTAGAA
387886 CCCTCGACTA
Statistics
Matches: 56, Mismatches: 13, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
23 37 0.66
24 19 0.34
ACGTcount: A:0.31, C:0.24, G:0.23, T:0.23
Consensus pattern (23 bp):
TTGTCCCAAAGGACCACGTAGAA
Found at i:387883 original size:46 final size:47
Alignment explanation
Indices: 387793--387885 Score: 125
Period size: 46 Copynumber: 2.0 Consensus size: 47
387783 CCACATATAT
* * * *
387793 TTGTCCCAAAGGACCGCGTAAAATTTGTCCCGAAGGATCTCGTAGAA
1 TTGTCCCAAAGGACCACATAAAATTTGTCCCGAAGGACCACGTAGAA
* *
387840 TTGTCCCAAAGGACCACAT-AGATTTGTTCCGAAGGACCACGTAGAA
1 TTGTCCCAAAGGACCACATAAAATTTGTCCCGAAGGACCACGTAGAA
387886 CCCTCGACTA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
46 23 0.57
47 17 0.43
ACGTcount: A:0.31, C:0.24, G:0.23, T:0.23
Consensus pattern (47 bp):
TTGTCCCAAAGGACCACATAAAATTTGTCCCGAAGGACCACGTAGAA
Found at i:388021 original size:15 final size:15
Alignment explanation
Indices: 387988--388036 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
387978 GTGTGTCTTA
*
387988 TTCATATAGTG-TATA
1 TTCATATAG-GATATT
388003 TTCATATAGGATATT
1 TTCATATAGGATATT
* *
388018 TTCACATAGGACATT
1 TTCATATAGGATATT
388033 TTCA
1 TTCA
388037 CATATGGACT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
14 1 0.03
15 29 0.97
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (15 bp):
TTCATATAGGATATT
Found at i:388037 original size:15 final size:15
Alignment explanation
Indices: 388003--388071 Score: 68
Period size: 15 Copynumber: 4.5 Consensus size: 15
387993 ATAGTGTATA
* *
388003 TTCATATAGGATATT
1 TTCACATAGGACATT
388018 TTCACATAGGACATT
1 TTCACATAGGACATT
*
388033 TTCACATATGGACTTT
1 TTCACATA-GGACATT
* *
388049 ATTCTCATAGTAC-TT
1 -TTCACATAGGACATT
388064 TTCACATA
1 TTCACATA
388072 ACATATATTC
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
14 7 0.15
15 23 0.50
16 9 0.20
17 7 0.15
ACGTcount: A:0.30, C:0.17, G:0.10, T:0.42
Consensus pattern (15 bp):
TTCACATAGGACATT
Found at i:391090 original size:25 final size:25
Alignment explanation
Indices: 391062--391139 Score: 81
Period size: 25 Copynumber: 3.2 Consensus size: 25
391052 CTTCTAGGAA
391062 TAAAATATTTTAAAATTAGACAATG
1 TAAAATATTTTAAAATTAGACAATG
* * * *
391087 T-AAATACTTTTCATATAAAGA-AA-A
1 TAAAATA-TTTTAAAAT-TAGACAATG
391111 TAAAATATTTTAAAATTAGACAATG
1 TAAAATATTTTAAAATTAGACAATG
391136 TAAA
1 TAAA
391140 TACTTTTCAT
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
23 3 0.08
24 15 0.38
25 19 0.47
26 3 0.08
ACGTcount: A:0.54, C:0.05, G:0.06, T:0.35
Consensus pattern (25 bp):
TAAAATATTTTAAAATTAGACAATG
Found at i:391091 original size:24 final size:25
Alignment explanation
Indices: 391064--391146 Score: 91
Period size: 24 Copynumber: 3.4 Consensus size: 25
391054 TCTAGGAATA
391064 AAATA-TTTTAAAATTAGACAATGT
1 AAATACTTTTAAAATTAGACAATGT
* * * * *
391088 AAATACTTTTCATATAAAGAAAAT-A
1 AAATACTTTTAAAAT-TAGACAATGT
391113 AAATA-TTTTAAAATTAGACAATGT
1 AAATACTTTTAAAATTAGACAATGT
391137 AAATACTTTT
1 AAATACTTTT
391147 CATATAAAGA
Statistics
Matches: 45, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
23 6 0.13
24 17 0.38
25 16 0.36
26 6 0.13
ACGTcount: A:0.51, C:0.06, G:0.06, T:0.37
Consensus pattern (25 bp):
AAATACTTTTAAAATTAGACAATGT
Found at i:391130 original size:49 final size:49
Alignment explanation
Indices: 391060--391175 Score: 214
Period size: 49 Copynumber: 2.4 Consensus size: 49
391050 ACCTTCTAGG
391060 AATAAAATATTTTAAAATTAGACAATGTAAATACTTTTCATATAAAGAA
1 AATAAAATATTTTAAAATTAGACAATGTAAATACTTTTCATATAAAGAA
391109 AATAAAATATTTTAAAATTAGACAATGTAAATACTTTTCATATAAAGAA
1 AATAAAATATTTTAAAATTAGACAATGTAAATACTTTTCATATAAAGAA
* *
391158 AATCAAACATTTTAAAAT
1 AATAAAATATTTTAAAAT
391176 ATTTTAAAAG
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
49 65 1.00
ACGTcount: A:0.53, C:0.07, G:0.05, T:0.34
Consensus pattern (49 bp):
AATAAAATATTTTAAAATTAGACAATGTAAATACTTTTCATATAAAGAA
Found at i:391170 original size:24 final size:24
Alignment explanation
Indices: 391088--391170 Score: 69
Period size: 24 Copynumber: 3.4 Consensus size: 24
391078 TAGACAATGT
391088 AAATACTTTTCATATAAAGAAAATA
1 AAATA-TTTTCATATAAAGAAAATA
* * * * *
391113 AAATATTTTAAAAT-TAGACAATGT
1 AAATATTTTCATATAAAGAAAAT-A
*
391137 AAATACTTTTCATATAAAGAAAATC
1 AAATA-TTTTCATATAAAGAAAATA
*
391162 AAACATTTT
1 AAATATTTT
391171 AAAATATTTT
Statistics
Matches: 44, Mismatches: 11, Indels: 7
0.71 0.18 0.11
Matches are distributed among these distances:
23 6 0.14
24 16 0.36
25 16 0.36
26 6 0.14
ACGTcount: A:0.52, C:0.08, G:0.05, T:0.35
Consensus pattern (24 bp):
AAATATTTTCATATAAAGAAAATA
Found at i:392699 original size:48 final size:48
Alignment explanation
Indices: 392625--392716 Score: 157
Period size: 48 Copynumber: 1.9 Consensus size: 48
392615 ACACTTTAAG
* *
392625 AATGTTACAATAACTATCCAAGCAATAGCGATCAAGAGAAAAGCTCTT
1 AATGTTACAACAACTATCCAAACAATAGCGATCAAGAGAAAAGCTCTT
*
392673 AATGTTACAACACCTATCCAAACAATAGCGATCAAGAGAAAAGC
1 AATGTTACAACAACTATCCAAACAATAGCGATCAAGAGAAAAGC
392717 CCTTTCACTC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.46, C:0.21, G:0.14, T:0.20
Consensus pattern (48 bp):
AATGTTACAACAACTATCCAAACAATAGCGATCAAGAGAAAAGCTCTT
Found at i:393675 original size:16 final size:16
Alignment explanation
Indices: 393645--393674 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
393635 CTTTTATGGG
393645 TTATGACCTCTTTTTC
1 TTATGACCTCTTTTTC
393661 TTATG-CCTCTTTTT
1 TTATGACCTCTTTTT
393675 TTAAACTCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.10, C:0.23, G:0.07, T:0.60
Consensus pattern (16 bp):
TTATGACCTCTTTTTC
Found at i:394740 original size:29 final size:29
Alignment explanation
Indices: 394671--394744 Score: 112
Period size: 29 Copynumber: 2.6 Consensus size: 29
394661 TTACATCTCT
* * * *
394671 TTGTAGTAGTCATCGACATAATTTCTACC
1 TTGTTGTAGTCTTTGACATAAATTCTACC
394700 TTGTTGTAGTCTTTGACATAAATTCTACC
1 TTGTTGTAGTCTTTGACATAAATTCTACC
394729 TTGTTGTAGTCTTTGA
1 TTGTTGTAGTCTTTGA
394745 AGTCGTTGCT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.23, C:0.16, G:0.16, T:0.45
Consensus pattern (29 bp):
TTGTTGTAGTCTTTGACATAAATTCTACC
Found at i:395982 original size:13 final size:12
Alignment explanation
Indices: 395960--395998 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
395950 AATTCCTTCG
395960 TTTTCTTTTTTT
1 TTTTCTTTTTTT
395972 TTTTACTTTTTTT
1 TTTT-CTTTTTTT
*
395985 TTTCCTTTTGTTT
1 TTTTCTTTT-TTT
395998 T
1 T
395999 GTTTTGTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
12 9 0.38
13 15 0.62
ACGTcount: A:0.03, C:0.10, G:0.03, T:0.85
Consensus pattern (12 bp):
TTTTCTTTTTTT
Found at i:396392 original size:3 final size:3
Alignment explanation
Indices: 396380--396411 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
396370 TAAAGATAAG
396380 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
396412 TGATAGAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:397142 original size:24 final size:23
Alignment explanation
Indices: 397104--397159 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 23
397094 TCGAAACGGT
*
397104 CACGTAGAATTTGCATCGAAGTGC
1 CACGTAG-ATTTGCACCGAAGTGC
397128 CACGTAGATTATGCACCGAAGTGC
1 CACGTAGATT-TGCACCGAAGTGC
*
397152 CACATAGA
1 CACGTAGA
397160 ATTGTCTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 3 0.10
24 26 0.90
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.21
Consensus pattern (23 bp):
CACGTAGATTTGCACCGAAGTGC
Found at i:397178 original size:23 final size:23
Alignment explanation
Indices: 397151--397207 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
397141 CACCGAAGTG
* *
397151 CCACATAGAATTGTCTCAAAGAA
1 CCACATAGAATTATCCCAAAGAA
*
397174 CCACATAGAATTATCCCAAAGGA
1 CCACATAGAATTATCCCAAAGAA
*
397197 CCGCATAGAAT
1 CCACATAGAAT
397208 CCCTCAACTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.42, C:0.25, G:0.14, T:0.19
Consensus pattern (23 bp):
CCACATAGAATTATCCCAAAGAA
Found at i:399846 original size:203 final size:205
Alignment explanation
Indices: 399497--399904 Score: 802
Period size: 203 Copynumber: 2.0 Consensus size: 205
399487 TCACCTTTTT
399497 CTCTGTATCCTTCCTTCCATTCTCTACTGGTGTTCCTCCATTAAGGGTCTCTAAGGAGAGGTGAG
1 CTCTGTATCCTTCCTTCCATTCTCTACTGGTGTTCCTCCATTAAGGGTCTCTAAGGAGAGGTGAG
399562 CTAGGCATCCGAGAGGAGCTAGCAAGCTAAGGCGAGTCGTGGTGGTTGAGGAGAGCTCCGGCTTC
66 CTAGGCATCCGAGAGGAGCTAGCAAGCTAAGGCGAGTCGTGGTGGTTGAGGAGAGCTCCGGCTTC
399627 GTGCGTACAAGACTTCTTCTCCCTTCCTCTTTGCTGTTA-TTTCCA-TTGATTTTGAGTTTATGG
131 GTGCGTACAAGACTTCTTCTCCCTTCCTCTTTGCTGTTATTTTCCATTTGATTTTGAGTTTATGG
399690 AACAGATGAA
196 AACAGATGAA
399700 CTCTGTATCCTTCCTTCCATTCTCTACTGGTGTTCCTCCATTAAGGGTCTCTAAGGAGAGGTGAG
1 CTCTGTATCCTTCCTTCCATTCTCTACTGGTGTTCCTCCATTAAGGGTCTCTAAGGAGAGGTGAG
399765 CTAGGCATCCGAGAGGAGCTAGCAAGCTAAGGCGAGTCGTGGTGGTTGAGGAGAGCTCCGGCTTC
66 CTAGGCATCCGAGAGGAGCTAGCAAGCTAAGGCGAGTCGTGGTGGTTGAGGAGAGCTCCGGCTTC
399830 GTGCGTACAAGACTTCTTCTCCCTTCCTCTTTGCTGTTATTTTCCATTTGATTTTGAGTTTATGG
131 GTGCGTACAAGACTTCTTCTCCCTTCCTCTTTGCTGTTATTTTCCATTTGATTTTGAGTTTATGG
399895 AACAGATGAA
196 AACAGATGAA
399905 TTTCATGTTT
Statistics
Matches: 203, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
203 169 0.83
204 6 0.03
205 28 0.14
ACGTcount: A:0.20, C:0.23, G:0.25, T:0.32
Consensus pattern (205 bp):
CTCTGTATCCTTCCTTCCATTCTCTACTGGTGTTCCTCCATTAAGGGTCTCTAAGGAGAGGTGAG
CTAGGCATCCGAGAGGAGCTAGCAAGCTAAGGCGAGTCGTGGTGGTTGAGGAGAGCTCCGGCTTC
GTGCGTACAAGACTTCTTCTCCCTTCCTCTTTGCTGTTATTTTCCATTTGATTTTGAGTTTATGG
AACAGATGAA
Found at i:416566 original size:41 final size:41
Alignment explanation
Indices: 416492--416789 Score: 271
Period size: 40 Copynumber: 7.3 Consensus size: 41
416482 TAAACATCGG
* * *
416492 TAAATACTCATACTTTAGT-TCATTTTTATATAAACCCCGC
1 TAAATACTCGTACTTTAGTGGCATTTTTATATAAACGCCGC
* *
416532 TAAAGACTCGTACTTTAGTGACATTTTTATATAAACGCCGC
1 TAAATACTCGTACTTTAGTGGCATTTTTATATAAACGCCGC
* * * * *
416573 TAAATACT-GAATTTTAGTGGCATTTTAAGAACAAACGCCGC
1 TAAATACTCGTACTTTAGTGGCATTTTTA-TATAAACGCCGC
*
416614 TAAATACTTGTACTTTAGTGGCATTTTTATATAAACGCCGC
1 TAAATACTCGTACTTTAGTGGCATTTTTATATAAACGCCGC
* ** * * * *
416655 TAAATA-TTGTACTTTAGTTCCGTTTGTATACAAATGCCGC
1 TAAATACTCGTACTTTAGTGGCATTTTTATATAAACGCCGC
* * * * ** * * *
416695 CAAAGACTCATATTTTAGCAGCACTTTTATATAAATGCTGC
1 TAAATACTCGTACTTTAGTGGCATTTTTATATAAACGCCGC
* * * * *
416736 TAAATAAT-GTACTTTAGTGGTACTTTTATACAAATGCCGC
1 TAAATACTCGTACTTTAGTGGCATTTTTATATAAACGCCGC
416776 TAAATACTCGTACT
1 TAAATACTCGTACT
416790 GTAATGACGT
Statistics
Matches: 207, Mismatches: 46, Indels: 9
0.79 0.18 0.03
Matches are distributed among these distances:
40 97 0.47
41 93 0.45
42 17 0.08
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.36
Consensus pattern (41 bp):
TAAATACTCGTACTTTAGTGGCATTTTTATATAAACGCCGC
Found at i:416671 original size:82 final size:80
Alignment explanation
Indices: 416502--416789 Score: 290
Period size: 81 Copynumber: 3.5 Consensus size: 80
416492 TAAATACTCA
* * * *
416502 TACTTTAGT-TCATTTTTATATAAACCCCGCTAAAGACTCGTACTTTAGTGACATTTTTATATAA
1 TACTTTAGTGGCA-TTTTATACAAACGCCGCTAAAGACTCGTACTTTAGTGGCATTTTTATATAA
*
416566 ACGCCGCTAAATACTG
65 ACGCCGCTAAATAATG
* * * * *
416582 AATTTTAGTGGCATTTTAAGAACAAACGCCGCTAAATACTTGTACTTTAGTGGCATTTTTATATA
1 TACTTTAGTGGCATTTT-A-TACAAACGCCGCTAAAGACTCGTACTTTAGTGGCATTTTTATATA
*
416647 AACGCCGCTAAATATTG
64 AACGCCGCTAAATAATG
** * * * * * ** *
416664 TACTTTAGTTCCGTTTGTATACAAATGCCGCCAAAGACTCATATTTTAGCAGCACTTTTATATAA
1 TACTTTAGTGGCATTT-TATACAAACGCCGCTAAAGACTCGTACTTTAGTGGCATTTTTATATAA
* *
416729 ATGCTGCTAAATAATG
65 ACGCCGCTAAATAATG
* * *
416745 TACTTTAGTGGTACTTTTATACAAATGCCGCTAAATACTCGTACT
1 TACTTTAGTGGCA-TTTTATACAAACGCCGCTAAAGACTCGTACT
416790 GTAATGACGT
Statistics
Matches: 167, Mismatches: 36, Indels: 9
0.79 0.17 0.04
Matches are distributed among these distances:
80 11 0.07
81 85 0.51
82 70 0.42
83 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (80 bp):
TACTTTAGTGGCATTTTATACAAACGCCGCTAAAGACTCGTACTTTAGTGGCATTTTTATATAAA
CGCCGCTAAATAATG
Found at i:416804 original size:41 final size:41
Alignment explanation
Indices: 416492--416804 Score: 249
Period size: 41 Copynumber: 7.7 Consensus size: 41
416482 TAAACATCGG
* * *
416492 TAAATACTCATACTTTAGT-TCATTTTTATATAAACCCCGC
1 TAAATACTCGTACTTTAGTGACATTTTTATATAAACGCCGC
*
416532 TAAAGACTCGTACTTTAGTGACATTTTTATATAAACGCCGC
1 TAAATACTCGTACTTTAGTGACATTTTTATATAAACGCCGC
* * * * * *
416573 TAAATACT-GAATTTTAGTGGCATTTTAAGAACAAACGCCGC
1 TAAATACTCGTACTTTAGTGACATTTTTA-TATAAACGCCGC
* *
416614 TAAATACTTGTACTTTAGTGGCATTTTTATATAAACGCCGC
1 TAAATACTCGTACTTTAGTGACATTTTTATATAAACGCCGC
* ** * * * *
416655 TAAATA-TTGTACTTTAGTTCCGTTTGTATACAAATGCCGC
1 TAAATACTCGTACTTTAGTGACATTTTTATATAAACGCCGC
* * * * * * * *
416695 CAAAGACTCATATTTTAG-CAGCACTTTTATATAAATGCTGC
1 TAAATACTCGTACTTTAGTGA-CATTTTTATATAAACGCCGC
* ** * * *
416736 TAAATAAT-GTACTTTAGTGGTACTTTTATACAAATGCCGC
1 TAAATACTCGTACTTTAGTGACATTTTTATATAAACGCCGC
* * *
416776 TAAATACTCGTACTGTAATGACGTTTTTA
1 TAAATACTCGTACTTTAGTGACATTTTTA
416805 GAATAAATGC
Statistics
Matches: 215, Mismatches: 51, Indels: 13
0.77 0.18 0.05
Matches are distributed among these distances:
40 96 0.45
41 102 0.47
42 17 0.08
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (41 bp):
TAAATACTCGTACTTTAGTGACATTTTTATATAAACGCCGC
Found at i:420274 original size:16 final size:16
Alignment explanation
Indices: 420236--420277 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
420226 TTTCTCTTTC
420236 TCTTTTTATTATTATT
1 TCTTTTTATTATTATT
420252 TCATTTTT-TTATTATT
1 TC-TTTTTATTATTATT
*
420268 TTTTTTTATT
1 TCTTTTTATT
420278 TTAGATGAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 5 0.22
16 13 0.57
17 5 0.22
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.79
Consensus pattern (16 bp):
TCTTTTTATTATTATT
Found at i:420401 original size:41 final size:42
Alignment explanation
Indices: 420356--420452 Score: 106
Period size: 42 Copynumber: 2.3 Consensus size: 42
420346 AAGGTCTTTT
* * *
420356 AGATGTCCCGAAGGACTT-ATCATCTTGCTCGACAGACTGAC
1 AGATGACCCGAAGGACTTAATCATCATGCTCGAAAGACTGAC
* * * *
420397 AGATGACCCGAAAGATTTAATCATCATGCTCGAAAGGCTTAC
1 AGATGACCCGAAGGACTTAATCATCATGCTCGAAAGACTGAC
* *
420439 TGATGGCCCGAAGG
1 AGATGACCCGAAGG
420453 TTTACTAAGT
Statistics
Matches: 45, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
41 15 0.33
42 30 0.67
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.23
Consensus pattern (42 bp):
AGATGACCCGAAGGACTTAATCATCATGCTCGAAAGACTGAC
Found at i:420650 original size:42 final size:41
Alignment explanation
Indices: 420568--420674 Score: 135
Period size: 42 Copynumber: 2.6 Consensus size: 41
420558 GTCCGAGGGT
* *
420568 CTTATAGATGGCCCGAAGAACTTATCATCTTGCTCGAAAGA
1 CTTACAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGA
* * *
420609 CTTACAGATGACCCGAAGGATTTAATCATCATT-CTTGAAAGA
1 CTTACAGATGGCCCGAAGGACTT-ATCATC-TTGCTCGAAAGA
*
420651 CTTACTGATGGCCCGAAGGACTTA
1 CTTACAGATGGCCCGAAGGACTTA
420675 CTAAGTAAGA
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
41 20 0.36
42 34 0.61
43 2 0.04
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (41 bp):
CTTACAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGA
Found at i:420888 original size:42 final size:41
Alignment explanation
Indices: 420806--420916 Score: 150
Period size: 42 Copynumber: 2.7 Consensus size: 41
420796 GCCCAAAGGT
* *
420806 CTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGA
1 CTTACAGATGGCCCGAAGGACTTATCATCATGCTCGAAAGA
* * *
420847 CTTACAGATGACCCGAAGGATTTAATCATCATGCTTGAAAGA
1 CTTACAGATGGCCCGAAGGACTT-ATCATCATGCTCGAAAGA
* *
420889 CTTACTGATGGCCTGAAGGACTTATCAT
1 CTTACAGATGGCCCGAAGGACTTATCAT
420917 ATTTAAAAAT
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
41 25 0.42
42 35 0.58
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.28
Consensus pattern (41 bp):
CTTACAGATGGCCCGAAGGACTTATCATCATGCTCGAAAGA
Found at i:421116 original size:42 final size:41
Alignment explanation
Indices: 421045--421146 Score: 123
Period size: 42 Copynumber: 2.5 Consensus size: 41
421035 AAGGTCATAT
* * *
421045 AGATGGCCTGAAGGACTTATCATCTTGCTCAAAAGAGTTAC
1 AGATGGCCCGAAGGACTTATCATCATGCTCAAAAGACTTAC
* * *
421086 AGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTAC
1 AGATGGCCCGAAGGACTT-ATCATCATGCTCAAAAGACTTAC
* *
421128 AGATGGCTCGAAGGGCTTA
1 AGATGGCCCGAAGGACTTA
421147 CTAAGTAAGA
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
41 16 0.32
42 34 0.68
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.25
Consensus pattern (41 bp):
AGATGGCCCGAAGGACTTATCATCATGCTCAAAAGACTTAC
Found at i:423882 original size:205 final size:204
Alignment explanation
Indices: 423530--423960 Score: 693
Period size: 205 Copynumber: 2.1 Consensus size: 204
423520 CTGAATTCAG
*
423530 CTTTATTGTATATATATTATAATCTCCTTTATCGGGCTAGCTGAAGGATGCATCTCATCACAAAG
1 CTTTATTGTATATATATTATAATCACCTTTATCGGGCTAGCTGAAGGATGCATCTCATCACAAAG
* * *
423595 TCTTATACCTGACAGTTACAGTGGAGCAAACACCGAACTACCAAGTATCCAAGCAATGTCATGGT
66 TCTTAGACCTGACAATTACAGTGGAACAAACACCGAACTACCAAGTATCCAAGCAATGTCATGGT
*
423660 TTGAATACATTCTATTCATAAAGCCAGGGCTTTTGAGTTTCCTCTATAACCAATTGCTTTAGTGG
131 TTGAATACAATCTATTCATAAAGCCAGGGCTTTTGAGTTTCCTCTATAACCAATTG-TTTAGTGG
423725 AATAGCTCAA
195 AATAGCTCAA
* *
423735 CTTTATTGTATATATATTATAATCACCTTTATTGGGCTAGCTGAAGGATTCATCTCATCACAAAG
1 CTTTATTGTATATATATTATAATCACCTTTATCGGGCTAGCTGAAGGATGCATCTCATCACAAAG
* ** * ** *
423800 TCTTCGACCTGACAATTGTAGTGGAACAAACACCGAACTGCCAAGTATCTGAGCACTGTCATGGT
66 TCTTAGACCTGACAATTACAGTGGAACAAACACCGAACTACCAAGTATCCAAGCAATGTCATGGT
*
423865 TTGAATACAATCTATTCATAAAGCCAGGGTTTTTGAGTTTCCTCTATAACCAATTGTTTAGTGGA
131 TTGAATACAATCTATTCATAAAGCCAGGGCTTTTGAGTTTCCTCTATAACCAATTGTTTAGTGGA
*
423930 ATAGCTCAG
196 ATAGCTCAA
*
423939 CTTTATTGTATACATA-TATAAT
1 CTTTATTGTATATATATTATAAT
423961 TACATTCTAG
Statistics
Matches: 209, Mismatches: 17, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
203 6 0.03
204 32 0.15
205 171 0.82
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (204 bp):
CTTTATTGTATATATATTATAATCACCTTTATCGGGCTAGCTGAAGGATGCATCTCATCACAAAG
TCTTAGACCTGACAATTACAGTGGAACAAACACCGAACTACCAAGTATCCAAGCAATGTCATGGT
TTGAATACAATCTATTCATAAAGCCAGGGCTTTTGAGTTTCCTCTATAACCAATTGTTTAGTGGA
ATAGCTCAA
Found at i:430273 original size:21 final size:21
Alignment explanation
Indices: 430222--430274 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
430212 GTTATGACTA
*
430222 TCGCAATTCGATTTTACAATT
1 TCGCAATGCGATTTTACAATT
** *
430243 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-ACAATT
430264 TCGCAATGCGA
1 TCGCAATGCGA
430275 ATAAGTAAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 22 0.88
22 3 0.12
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.36
Consensus pattern (21 bp):
TCGCAATGCGATTTTACAATT
Found at i:430289 original size:20 final size:21
Alignment explanation
Indices: 430264--430315 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
430254 TTTTCCCAAT
*
430264 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
430284 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
430305 TCGCAATGCGA
1 TCGCAATGCGA
430316 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:430377 original size:41 final size:42
Alignment explanation
Indices: 430301--430411 Score: 138
Period size: 41 Copynumber: 2.7 Consensus size: 42
430291 GCGAATTTGG
* * *
430301 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAAT-AC
1 AAAATCGCAACGCGATACTGACTTTCGCAAAGCGATAATGAC
*
430342 AAAATCGCAACGCGATACTGACTTTCGCAAAGCGATACTGAC
1 AAAATCGCAACGCGATACTGACTTTCGCAAAGCGATAATGAC
** *
430384 --TTTCGCAACGCGATTCTGACTTTCGCAA
1 AAAATCGCAACGCGATACTGACTTTCGCAA
430412 CGAGATTCTG
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
40 25 0.40
41 35 0.56
42 2 0.03
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (42 bp):
AAAATCGCAACGCGATACTGACTTTCGCAAAGCGATAATGAC
Found at i:430422 original size:20 final size:20
Alignment explanation
Indices: 430305--430413 Score: 130
Period size: 20 Copynumber: 5.4 Consensus size: 20
430295 ATTTGGAAAA
* *
430305 TCGCAATGCGATACTGACTA
1 TCGCAACGCGATACTGACTT
* **
430325 TCGCAACGCGATAAT-ACAAAA
1 TCGCAACGCGATACTGAC--TT
430346 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
*
430366 TCGCAAAGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
*
430386 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATACTGACTT
430406 TCGCAACG
1 TCGCAACG
430414 AGATTCTGAA
Statistics
Matches: 77, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
19 2 0.03
20 58 0.75
21 15 0.19
22 2 0.03
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:430429 original size:20 final size:20
Alignment explanation
Indices: 430386--430431 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
430376 ATACTGACTT
* ***
430386 TCGCAACGCGATTCTGACTT
1 TCGCAACGAGATTCTGAAAA
430406 TCGCAACGAGATTCTGAAAA
1 TCGCAACGAGATTCTGAAAA
430426 TCGCAA
1 TCGCAA
430432 TCATCTTCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (20 bp):
TCGCAACGAGATTCTGAAAA
Found at i:430430 original size:40 final size:40
Alignment explanation
Indices: 430300--430431 Score: 156
Period size: 40 Copynumber: 3.3 Consensus size: 40
430290 TGCGAATTTG
* * *
430300 GAAAATCGCAATGCGATACTGACTATCGCAACGCGATAAT
1 GAAAATCGCAACGCGATACTGACTTTCGCAACGCGATACT
* *
430340 ACAAAATCGCAACGCGATACTGACTTTCGCAAAGCGATACT
1 -GAAAATCGCAACGCGATACTGACTTTCGCAACGCGATACT
*** * * *
430381 GACTTTCGCAACGCGATTCTGACTTTCGCAACGAGATTCT
1 GAAAATCGCAACGCGATACTGACTTTCGCAACGCGATACT
430421 GAAAATCGCAA
1 GAAAATCGCAA
430432 TCATCTTCAA
Statistics
Matches: 75, Mismatches: 16, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
40 40 0.53
41 35 0.47
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (40 bp):
GAAAATCGCAACGCGATACTGACTTTCGCAACGCGATACT
Found at i:430740 original size:20 final size:20
Alignment explanation
Indices: 430648--430731 Score: 150
Period size: 20 Copynumber: 4.2 Consensus size: 20
430638 CGGGGAAATT
* *
430648 GCAACGCAAAAATGACTATC
1 GCAACGCGAAAATGGCTATC
430668 GCAACGCGAAAATGGCTATC
1 GCAACGCGAAAATGGCTATC
430688 GCAACGCGAAAATGGCTATC
1 GCAACGCGAAAATGGCTATC
430708 GCAACGCGAAAATGGCTATC
1 GCAACGCGAAAATGGCTATC
430728 GCAA
1 GCAA
430732 TGAGAAAATC
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 62 1.00
ACGTcount: A:0.38, C:0.25, G:0.23, T:0.14
Consensus pattern (20 bp):
GCAACGCGAAAATGGCTATC
Done.