Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold594
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: 328579
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:153630 original size:17 final size:16
Alignment explanation
Indices: 153593--153634 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
153583 AAAGATAATT
*
153593 TTTTAAA-ATTATAAA
1 TTTTAAATATTAAAAA
*
153608 TATTAAATATATAAAAA
1 TTTTAAATAT-TAAAAA
153625 TTTTAAATAT
1 TTTTAAATAT
153635 CAAATAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 6 0.27
16 2 0.09
17 14 0.64
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TTTTAAATATTAAAAA
Found at i:153631 original size:24 final size:24
Alignment explanation
Indices: 153597--153646 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
153587 ATAATTTTTT
* *
153597 AAAATTATAAATATTAAATATATA
1 AAAATTATAAATATCAAATAAATA
*
153621 AAAATTTTAAATATCAAATAAATA
1 AAAATTATAAATATCAAATAAATA
153645 AA
1 AA
153647 TATAAAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (24 bp):
AAAATTATAAATATCAAATAAATA
Found at i:156640 original size:16 final size:16
Alignment explanation
Indices: 156621--156655 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
156611 AATGTGTTTA
* *
156621 ATATTTATATATATAT
1 ATATTTAAATATAAAT
156637 ATATTTAAATATAAAT
1 ATATTTAAATATAAAT
156653 ATA
1 ATA
156656 AAGTATAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATATTTAAATATAAAT
Found at i:156777 original size:21 final size:21
Alignment explanation
Indices: 156751--156794 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
156741 TAGATTTGAG
* *
156751 GAATTGGATTTGATTTGAAAA
1 GAATTGGAATTGATTTAAAAA
156772 GAATTGGAATTGATTTAAAAA
1 GAATTGGAATTGATTTAAAAA
156793 GA
1 GA
156795 CTACAATCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.23, T:0.34
Consensus pattern (21 bp):
GAATTGGAATTGATTTAAAAA
Found at i:158103 original size:21 final size:22
Alignment explanation
Indices: 158078--158126 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
158068 TATTGTTATG
158078 TTAATAATAAGTAATA-AATTA
1 TTAATAATAAGTAATATAATTA
* *
158099 TTAAT-ATAATTAATATAATTT
1 TTAATAATAAGTAATATAATTA
158120 TTAATAA
1 TTAATAA
158127 AAAAATCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 14 0.58
22 1 0.04
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
TTAATAATAAGTAATATAATTA
Found at i:159246 original size:21 final size:22
Alignment explanation
Indices: 159222--159266 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
159212 AATATAAATA
*
159222 TAAAAAATCTTTTA-TATTGAT
1 TAAAAAATCTATTATTATTGAT
* *
159243 TAAAATATCTATTATTATTTAT
1 TAAAAAATCTATTATTATTGAT
159265 TA
1 TA
159267 TATTACTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.51
Consensus pattern (22 bp):
TAAAAAATCTATTATTATTGAT
Found at i:160984 original size:29 final size:29
Alignment explanation
Indices: 160942--160998 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
160932 AGAGGGAAGC
160942 TATGAGCATTAAGTTCATGCATAACTTCT
1 TATGAGCATTAAGTTCATGCATAACTTCT
160971 TATGAGCATTAAGTTCATGCATAACTTC
1 TATGAGCATTAAGTTCATGCATAACTTC
160999 CGTACTAAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.37
Consensus pattern (29 bp):
TATGAGCATTAAGTTCATGCATAACTTCT
Found at i:164091 original size:17 final size:17
Alignment explanation
Indices: 164069--164103 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
164059 CAAATAAATG
*
164069 AGGAAAAGAGCAAGGAT
1 AGGAAAAGAGAAAGGAT
164086 AGGAAAAGAGAAAGGAT
1 AGGAAAAGAGAAAGGAT
164103 A
1 A
164104 TGCAAAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.57, C:0.03, G:0.34, T:0.06
Consensus pattern (17 bp):
AGGAAAAGAGAAAGGAT
Found at i:164114 original size:17 final size:17
Alignment explanation
Indices: 164072--164114 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
164062 ATAAATGAGG
* *
164072 AAAAGAGCAAGGATAGG
1 AAAAGAGAAAGGATAGC
164089 AAAAGAGAAAGGATATGC
1 AAAAGAGAAAGGATA-GC
164107 AAAA-AGAA
1 AAAAGAGAA
164115 TGAACCAAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 18 0.78
18 5 0.22
ACGTcount: A:0.60, C:0.05, G:0.28, T:0.07
Consensus pattern (17 bp):
AAAAGAGAAAGGATAGC
Found at i:173083 original size:1 final size:1
Alignment explanation
Indices: 173077--173101 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
173067 TTGAAAACAT
173077 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
173102 GAAGCAAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:176609 original size:4 final size:4
Alignment explanation
Indices: 176600--176624 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
176590 AACAACGGAT
176600 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
176625 CATGTTAGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:178759 original size:31 final size:32
Alignment explanation
Indices: 178717--178776 Score: 104
Period size: 31 Copynumber: 1.9 Consensus size: 32
178707 TAATAATAGC
178717 ATGTATAATTTTTAAACTTTAAAATATATTTT
1 ATGTATAATTTTTAAACTTTAAAATATATTTT
*
178749 ATGT-TAATTTTTAAATTTTAAAATATAT
1 ATGTATAATTTTTAAACTTTAAAATATAT
178777 AAATCAAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 23 0.85
32 4 0.15
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (32 bp):
ATGTATAATTTTTAAACTTTAAAATATATTTT
Found at i:178973 original size:21 final size:21
Alignment explanation
Indices: 178944--178986 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
178934 ACGAATGTTA
178944 TTAACTTTATATCTTCATTTTT
1 TTAACTTTATATCTTC-TTTTT
*
178966 TTAA-TTTATATTTTCTTTTT
1 TTAACTTTATATCTTCTTTTT
178986 T
1 T
178987 ATAAATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
21 10 0.50
22 4 0.20
ACGTcount: A:0.21, C:0.09, G:0.00, T:0.70
Consensus pattern (21 bp):
TTAACTTTATATCTTCTTTTT
Found at i:179660 original size:14 final size:15
Alignment explanation
Indices: 179641--179670 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
179631 TATTATATTT
179641 ATAAAAAA-AGAAAA
1 ATAAAAAAGAGAAAA
179655 ATAAAAAAGAGAAAA
1 ATAAAAAAGAGAAAA
179670 A
1 A
179671 AATAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.07
Consensus pattern (15 bp):
ATAAAAAAGAGAAAA
Found at i:179783 original size:46 final size:46
Alignment explanation
Indices: 179689--179785 Score: 117
Period size: 46 Copynumber: 2.1 Consensus size: 46
179679 ATTTTAAATA
** *
179689 TTTTTATAAAATTAATGGAAATAAATTTTCTTATAAATTATTTAAT
1 TTTTTATAAAATTAATGGAAATAAATAATATTATAAATTATTTAAT
* *
179735 TTTTTATAAAATTAATTGAAATAATAATAATATTAT-AATTGTTT-AT
1 TTTTTATAAAATTAATGGAAAT-A-AATAATATTATAAATTATTTAAT
179781 TTTTT
1 TTTTT
179786 GTATTTATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
46 28 0.64
47 8 0.18
48 8 0.18
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (46 bp):
TTTTTATAAAATTAATGGAAATAAATAATATTATAAATTATTTAAT
Found at i:180805 original size:23 final size:23
Alignment explanation
Indices: 180779--180823 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
180769 ATAAAACTAC
*
180779 ATATA-TAAATAATAA-TGATAA
1 ATATATTAAAAAATAATTGATAA
180800 ATATATTAAAAAATAATTGATAA
1 ATATATTAAAAAATAATTGATAA
180823 A
1 A
180824 AAAAGTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.24
22 9 0.43
23 7 0.33
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (23 bp):
ATATATTAAAAAATAATTGATAA
Found at i:181911 original size:12 final size:13
Alignment explanation
Indices: 181868--181921 Score: 54
Period size: 13 Copynumber: 3.8 Consensus size: 13
181858 TATAAATTTT
181868 AATAAAAATATAAAA
1 AATAAAAATAT--AA
*
181883 AATTAAATATTATATA
1 AA-TAAA-AATATA-A
181899 AATAAAAATATAA
1 AATAAAAATATAA
181912 AATAAAAATA
1 AATAAAAATA
181922 AATTTTATCT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
13 11 0.32
14 5 0.15
15 7 0.21
16 7 0.21
17 4 0.12
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AATAAAAATATAA
Found at i:181916 original size:17 final size:16
Alignment explanation
Indices: 181868--181917 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
181858 TATAAATTTT
181868 AATAAAAATATAAA-A
1 AATAAAAATATAAATA
* *
181883 AAT-TAAATATTATATA
1 AATAAAAATA-TAAATA
181899 AATAAAAATATAAAATA
1 AATAAAAATAT-AAATA
181916 AA
1 AA
181918 AATAAATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
14 5 0.19
15 6 0.22
16 5 0.19
17 11 0.41
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
AATAAAAATATAAATA
Found at i:182347 original size:17 final size:16
Alignment explanation
Indices: 182319--182375 Score: 53
Period size: 19 Copynumber: 3.2 Consensus size: 16
182309 AAAAATAAAA
182319 TTTTTTAGAAAAATATT
1 TTTTTTA-AAAAATATT
182336 TTTCTTTAAAAAAGATATT
1 TTT-TTT-AAAAA-ATATT
182355 TATTTCTTAAAAAA-ATT
1 T-TTT-TTAAAAAATATT
182372 TTTT
1 TTTT
182376 AACAGGTGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
16 3 0.09
17 7 0.20
18 8 0.23
19 13 0.37
20 4 0.11
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.53
Consensus pattern (16 bp):
TTTTTTAAAAAATATT
Found at i:182355 original size:19 final size:18
Alignment explanation
Indices: 182320--182370 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 18
182310 AAAATAAAAT
*
182320 TTTTTAGAAAAATATTT-
1 TTTTTAAAAAAATATTTA
182337 TTCTTTAAAAAAGATATTTA
1 TT-TTTAAAAAA-ATATTTA
182357 TTTCTTAAAAAAAT
1 TTT-TTAAAAAAAT
182371 TTTTTAACAG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
17 2 0.07
18 8 0.28
19 9 0.31
20 10 0.34
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (18 bp):
TTTTTAAAAAAATATTTA
Found at i:183455 original size:9 final size:9
Alignment explanation
Indices: 183383--183455 Score: 52
Period size: 8 Copynumber: 8.7 Consensus size: 9
183373 ATTATATATC
183383 ATATAAAAT
1 ATATAAAAT
*
183392 AT-TAACAT
1 ATATAAAAT
183400 AT-TAAAATT
1 ATATAAAA-T
183409 ATATATAAA-
1 ATATA-AAAT
183418 ATATAAAA-
1 ATATAAAAT
183426 ATAT--AAT
1 ATATAAAAT
183433 -TATAAAAT
1 ATATAAAAT
* *
183441 AAATAACAT
1 ATATAAAAT
183450 ATATAA
1 ATATAA
183456 TATAAATATA
Statistics
Matches: 52, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
6 5 0.10
8 21 0.40
9 21 0.40
10 2 0.04
11 3 0.06
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (9 bp):
ATATAAAAT
Found at i:183455 original size:13 final size:13
Alignment explanation
Indices: 183411--183467 Score: 57
Period size: 13 Copynumber: 4.5 Consensus size: 13
183401 TTAAAATTAT
*
183411 ATATAAAATATAA
1 ATATATAATATAA
*
183424 AAATATAATTATAA
1 ATATATAA-TATAA
*
183438 A-ATA-AATA-AC
1 ATATATAATATAA
183448 ATATATAATATAA
1 ATATATAATATAA
183461 ATATATA
1 ATATATA
183468 TTATTTCATC
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
10 2 0.06
11 5 0.14
12 6 0.17
13 17 0.47
14 6 0.17
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (13 bp):
ATATATAATATAA
Found at i:183819 original size:16 final size:18
Alignment explanation
Indices: 183798--183832 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
183788 TAACACAATA
183798 ATAAAAT-A-ATAAAAAT
1 ATAAAATGATATAAAAAT
183814 ATAAAATGATATAAAAAT
1 ATAAAATGATATAAAAAT
183832 A
1 A
183833 ACATAAATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 1 0.06
18 9 0.53
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (18 bp):
ATAAAATGATATAAAAAT
Found at i:183840 original size:27 final size:27
Alignment explanation
Indices: 183800--183858 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
183790 ACACAATAAT
* *
183800 AAAATAATAAAAATATA-AAATGATATA
1 AAAATAACAAAAATACATAAATG-TATA
* *
183827 AAAATAACATAAATACATAAATGTATC
1 AAAATAACAAAAATACATAAATGTATA
183854 AAAAT
1 AAAAT
183859 TTATATAAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 22 0.81
28 5 0.19
ACGTcount: A:0.66, C:0.05, G:0.03, T:0.25
Consensus pattern (27 bp):
AAAATAACAAAAATACATAAATGTATA
Found at i:184652 original size:22 final size:23
Alignment explanation
Indices: 184591--184652 Score: 76
Period size: 22 Copynumber: 2.8 Consensus size: 23
184581 ATGTATACAA
184591 ATTTTCTCTTT-TTTCT-CTTTCT
1 ATTTT-TCTTTCTTTCTCCTTTCT
*
184613 ATTTTTCTTTCTGTCTCCTTT-T
1 ATTTTTCTTTCTTTCTCCTTTCT
*
184635 CTTTTTCTTTCTTTCTCC
1 ATTTTTCTTTCTTTCTCC
184653 CGTCCTCCCT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 5 0.14
22 26 0.74
23 4 0.11
ACGTcount: A:0.03, C:0.26, G:0.02, T:0.69
Consensus pattern (23 bp):
ATTTTTCTTTCTTTCTCCTTTCT
Found at i:187272 original size:15 final size:16
Alignment explanation
Indices: 187240--187279 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
187230 TCATCAATGA
*
187240 GAAAAAGAAGGATGAT
1 GAAAAAGAAGGATAAT
*
187256 GATAAAGAA-GATAAT
1 GAAAAAGAAGGATAAT
187271 GAAAAAGAA
1 GAAAAAGAA
187280 AAGATGATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.62, C:0.00, G:0.25, T:0.12
Consensus pattern (16 bp):
GAAAAAGAAGGATAAT
Found at i:193147 original size:24 final size:25
Alignment explanation
Indices: 193092--193147 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 25
193082 TAAAAATAAT
* *
193092 ATCAAGGCAAACATTACTTGCATTC
1 ATCAAAGCAAACATTAATTGCATTC
* *
193117 ATGAAAGCAAACA-TAATTTCATTC
1 ATCAAAGCAAACATTAATTGCATTC
193141 ATCAAAG
1 ATCAAAG
193148 AAATTCATGT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
24 15 0.58
25 11 0.42
ACGTcount: A:0.43, C:0.20, G:0.11, T:0.27
Consensus pattern (25 bp):
ATCAAAGCAAACATTAATTGCATTC
Found at i:195158 original size:114 final size:114
Alignment explanation
Indices: 195020--195242 Score: 437
Period size: 114 Copynumber: 2.0 Consensus size: 114
195010 CATCAAATTC
*
195020 ATCAACAATTAAGCACAATACATAAACATTAAAAATCACAAAATCACAAGATCATTCAAACAAAA
1 ATCAACAACTAAGCACAATACATAAACATTAAAAATCACAAAATCACAAGATCATTCAAACAAAA
195085 CATCACAAGTGCAACATAAAAATTTCATGTGACCAAAACCATGCCAAAT
66 CATCACAAGTGCAACATAAAAATTTCATGTGACCAAAACCATGCCAAAT
195134 ATCAACAACTAAGCACAATACATAAACATTAAAAATCACAAAATCACAAGATCATTCAAACAAAA
1 ATCAACAACTAAGCACAATACATAAACATTAAAAATCACAAAATCACAAGATCATTCAAACAAAA
195199 CATCACAAGTGCAACATAAAAATTTCATGTGACCAAAACCATGC
66 CATCACAAGTGCAACATAAAAATTTCATGTGACCAAAACCATGC
195243 ATATTTGGCA
Statistics
Matches: 108, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
114 108 1.00
ACGTcount: A:0.52, C:0.22, G:0.06, T:0.19
Consensus pattern (114 bp):
ATCAACAACTAAGCACAATACATAAACATTAAAAATCACAAAATCACAAGATCATTCAAACAAAA
CATCACAAGTGCAACATAAAAATTTCATGTGACCAAAACCATGCCAAAT
Found at i:195196 original size:55 final size:54
Alignment explanation
Indices: 195023--195196 Score: 140
Period size: 55 Copynumber: 3.1 Consensus size: 54
195013 CAAATTCATC
195023 AACAATTAAGCACAATACATAAACATTAAAAATCACAAAATCACAAGATCATTCA
1 AACAA-TAAGCACAATACATAAACATTAAAAATCACAAAATCACAAGATCATTCA
* * * ** ** * *
195078 AACAAAACATCACAAGTGCAACATAAAAATTTCATGTGACCAAAACCATGCCAA-AT-A-TC-
1 AACAATA-AGCACAA-T---ACATAAACATTAAAAATCA-CAAAATCA---CAAGATCATTCA
195137 AACAACTAAGCACAATACATAAACATTAAAAATCACAAAATCACAAGATCATTCA
1 AACAA-TAAGCACAATACATAAACATTAAAAATCACAAAATCACAAGATCATTCA
195192 AACAA
1 AACAA
195197 AACATCACAA
Statistics
Matches: 87, Mismatches: 18, Indels: 28
0.65 0.14 0.21
Matches are distributed among these distances:
51 3 0.03
52 2 0.02
53 1 0.01
54 10 0.11
55 29 0.33
56 1 0.01
58 1 0.01
59 24 0.28
60 10 0.11
61 1 0.01
62 2 0.02
63 3 0.03
ACGTcount: A:0.55, C:0.22, G:0.05, T:0.18
Consensus pattern (54 bp):
AACAATAAGCACAATACATAAACATTAAAAATCACAAAATCACAAGATCATTCA
Found at i:195670 original size:20 final size:19
Alignment explanation
Indices: 195645--195682 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
195635 ATTTCAACGA
195645 TTTGTATCGATACATATTTT
1 TTTGTATCGATACA-ATTTT
195665 TTTGTATCGATACAATTT
1 TTTGTATCGATACAATTT
195683 AAGCTACTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.26, C:0.11, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTGTATCGATACAATTTT
Found at i:195810 original size:52 final size:52
Alignment explanation
Indices: 195754--195882 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
195744 CACTGATCTT
*
195754 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
**
195806 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
195858 TGTATCGATACATGCAGGTAAATTT
1 TGTATCGATACATGCAGGCAAATTT
195883 TCATATTTCG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:209467 original size:1 final size:1
Alignment explanation
Indices: 209461--209505 Score: 54
Period size: 1 Copynumber: 45.0 Consensus size: 1
209451 CGTCCTCCAC
* * * *
209461 AAAAAAAAAAAAAACAAAACAAAAAAAAAACAAAAACAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
209506 GGAGTCCGGA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:209484 original size:17 final size:18
Alignment explanation
Indices: 209464--209505 Score: 70
Period size: 16 Copynumber: 2.4 Consensus size: 18
209454 CCTCCACAAA
209464 AAAAAAAAAAAC-AAAAC
1 AAAAAAAAAAACAAAAAC
209481 -AAAAAAAAAACAAAAAC
1 AAAAAAAAAAACAAAAAC
209498 AAAAAAAA
1 AAAAAAAA
209506 GGAGTCCGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 11 0.48
17 5 0.22
18 7 0.30
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAACAAAAAC
Found at i:209486 original size:16 final size:16
Alignment explanation
Indices: 209459--209505 Score: 78
Period size: 17 Copynumber: 2.9 Consensus size: 16
209449 GGCGTCCTCC
209459 ACAAAA-AAAAAAAAA
1 ACAAAACAAAAAAAAA
209474 ACAAAACAAAAAAAAA
1 ACAAAACAAAAAAAAA
209490 ACAAAAACAAAAAAAA
1 AC-AAAACAAAAAAAA
209506 GGAGTCCGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.20
16 11 0.37
17 13 0.43
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (16 bp):
ACAAAACAAAAAAAAA
Found at i:210978 original size:29 final size:30
Alignment explanation
Indices: 210935--211223 Score: 179
Period size: 30 Copynumber: 9.6 Consensus size: 30
210925 TCACCCTTCA
210935 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
1 AAAGCCCACAAGTCAGTGGCACTCTTTTTC
* * *
210964 AAAGCCCACAGGTCAGTGGCATTTTTTTTC
1 AAAGCCCACAAGTCAGTGGCACTCTTTTTC
*
210994 AAAAGCCCATAAGTCAGTGGCAAC-C---TTC
1 -AAAGCCCACAAGTCAGTGGC-ACTCTTTTTC
* * *
211022 AAAGCCCACAAATCAGTGGCACCCTTTTTT
1 AAAGCCCACAAGTCAGTGGCACTCTTTTTC
* * *
211052 GAAGCCCACAA-TCGGTGGCA-TCTTTTCC
1 AAAGCCCACAAGTCAGTGGCACTCTTTTTC
* * *
211080 AAAGTCCACAACTCCGTGGCACTCTTTTTC
1 AAAGCCCACAAGTCAGTGGCACTCTTTTTC
* * * *
211110 TTTTGTAAGCTCACAACTCTA-TAGCACTCTTTTTC
1 -----AAAGCCCACAAGTC-AGTGGCACTCTTTTTC
* * *
211145 TTTTTAAGCCCACAAGTTAGTGGCAC-CATTTTC
1 ----AAAGCCCACAAGTCAGTGGCACTCTTTTTC
*
211178 AAAAGCCCACAAGTCAGTGGCAAC-C--TTTA
1 -AAAGCCCACAAGTCAGTGGC-ACTCTTTTTC
211207 AAAGCCCACAAGTCAGT
1 AAAGCCCACAAGTCAGT
211224 AGCAACCTTC
Statistics
Matches: 210, Mismatches: 33, Indels: 35
0.76 0.12 0.13
Matches are distributed among these distances:
26 2 0.01
27 19 0.09
28 34 0.16
29 39 0.19
30 44 0.21
31 21 0.10
32 1 0.00
33 7 0.03
34 19 0.09
35 24 0.11
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (30 bp):
AAAGCCCACAAGTCAGTGGCACTCTTTTTC
Found at i:211037 original size:27 final size:27
Alignment explanation
Indices: 210995--211047 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
210985 TTTTTTTTCA
* *
210995 AAAGCCCATAAGTCAGTGGCAACCTTC
1 AAAGCCCACAAATCAGTGGCAACCTTC
*
211022 AAAGCCCACAAATCAGTGGCACCCTT
1 AAAGCCCACAAATCAGTGGCAACCTT
211048 TTTTGAAGCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (27 bp):
AAAGCCCACAAATCAGTGGCAACCTTC
Found at i:211050 original size:58 final size:59
Alignment explanation
Indices: 210931--211109 Score: 166
Period size: 58 Copynumber: 3.1 Consensus size: 59
210921 TTCCTCACCC
* * ** ***
210931 TTCAAAAGCCCACAAGTCAGTGGCATCTTTTTCAAAGCCCACAGGTCAGTGGCATTTTTT
1 TTCAAAAGCCCACAAGTCAGTGGCAAC-TCTTCAAAGCCCACAAATCAGTGGCACCCTTT
*
210991 TTCAAAAGCCCATAAGTCAGTGGCAAC-CTTCAAAGCCCACAAATCAGTGGCACCCTTT
1 TTCAAAAGCCCACAAGTCAGTGGCAACTCTTCAAAGCCCACAAATCAGTGGCACCCTTT
** * * * * * * *
211049 TT-TGAAGCCCACAA-TCGGTGGCATCTTTTCCAAAGTCCACAACTCCGTGGCACTCTTT
1 TTCAAAAGCCCACAAGTCAGTGGCAACTCTT-CAAAGCCCACAAATCAGTGGCACCCTTT
211107 TTC
1 TTC
211110 TTTTGTAAGC
Statistics
Matches: 98, Mismatches: 18, Indels: 7
0.80 0.15 0.06
Matches are distributed among these distances:
56 9 0.09
57 11 0.11
58 53 0.54
60 25 0.26
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27
Consensus pattern (59 bp):
TTCAAAAGCCCACAAGTCAGTGGCAACTCTTCAAAGCCCACAAATCAGTGGCACCCTTT
Found at i:211107 original size:30 final size:29
Alignment explanation
Indices: 210935--211107 Score: 124
Period size: 29 Copynumber: 5.9 Consensus size: 29
210925 TCACCCTTCA
*
210935 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
1 AAAGCCCACAA-TCAGTGGCACTCTTTTCC
* * * *
210964 AAAGCCCACAGGTCAGTGGCATTTTTTTTCA
1 AAAGCCCACA-ATCAGTGGCA-CTCTTTTCC
*
210995 AAAGCCCATAAGTCAGTGGCAAC-C--TT-C
1 AAAGCCCACAA-TCAGTGGC-ACTCTTTTCC
* **
211022 AAAGCCCACAAATCAGTGGCACCCTTTTTT
1 AAAGCCCAC-AATCAGTGGCACTCTTTTCC
* *
211052 GAAGCCCACAATCGGTGGCA-TCTTTTCC
1 AAAGCCCACAATCAGTGGCACTCTTTTCC
* *
211080 AAAGTCCACAACTCCGTGGCACTCTTTT
1 AAAGCCCACAA-TCAGTGGCACTCTTTT
211108 TCTTTTGTAA
Statistics
Matches: 113, Mismatches: 19, Indels: 23
0.73 0.12 0.15
Matches are distributed among these distances:
26 2 0.02
27 17 0.15
28 18 0.16
29 39 0.35
30 14 0.12
31 22 0.19
32 1 0.01
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27
Consensus pattern (29 bp):
AAAGCCCACAATCAGTGGCACTCTTTTCC
Found at i:211126 original size:35 final size:34
Alignment explanation
Indices: 211085--211159 Score: 105
Period size: 35 Copynumber: 2.2 Consensus size: 34
211075 TTTCCAAAGT
* *
211085 CCACAACTCCGTGGCACTCTTTTTCTTTTGTAAGC
1 CCACAACTCCATAGCACTCTTTTTCTTTT-TAAGC
* *
211120 TCACAACTCTATAGCACTCTTTTTCTTTTTAAGC
1 CCACAACTCCATAGCACTCTTTTTCTTTTTAAGC
211154 CCACAA
1 CCACAA
211160 GTTAGTGGCA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
34 10 0.29
35 25 0.71
ACGTcount: A:0.23, C:0.31, G:0.09, T:0.37
Consensus pattern (34 bp):
CCACAACTCCATAGCACTCTTTTTCTTTTTAAGC
Found at i:211218 original size:28 final size:29
Alignment explanation
Indices: 211150--211273 Score: 141
Period size: 28 Copynumber: 4.3 Consensus size: 29
211140 TTTTCTTTTT
*
211150 AAGCCCACAAGTTAGTGGC-ACCATTTTCAA
1 AAGCCCACAAGTCAGTGGCAACC--TTTCAA
211180 AAGCCCACAAGTCAGTGGCAACCTTT-AA
1 AAGCCCACAAGTCAGTGGCAACCTTTCAA
*
211208 AAGCCCACAAGTCAGTAGCAACC-TTCAA
1 AAGCCCACAAGTCAGTGGCAACCTTTCAA
* *
211236 AAGCACACAAGT-TGAT-GCAAACCTTTCAA
1 AAGCCCACAAGTCAG-TGGC-AACCTTTCAA
211265 AAGCCCACA
1 AAGCCCACA
211274 CAAGTTGGTG
Statistics
Matches: 84, Mismatches: 5, Indels: 11
0.84 0.05 0.11
Matches are distributed among these distances:
27 5 0.06
28 42 0.50
29 16 0.19
30 18 0.21
31 3 0.04
ACGTcount: A:0.38, C:0.29, G:0.15, T:0.18
Consensus pattern (29 bp):
AAGCCCACAAGTCAGTGGCAACCTTTCAA
Found at i:211419 original size:49 final size:48
Alignment explanation
Indices: 211293--211522 Score: 272
Period size: 48 Copynumber: 4.8 Consensus size: 48
211283 GGCGTCTCCT
* *
211293 TTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTGCC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCCC
* * *
211341 TTTAAGTCCAATATCGCTGGCCTTAAATCAGCATATTGGCACCTTCATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTC-CC
* * *
211390 TTTAAGTCCAATGTAGCTGACCTTGAATCAGCACATTGGCA-----CC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCCC
*
211433 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATACTGGCACCTTTTCCATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC--TTCC--C
* * *
211485 TTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTG
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTG
211523 ACATCCTTTT
Statistics
Matches: 153, Mismatches: 19, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
43 38 0.25
48 42 0.27
49 37 0.24
50 1 0.01
52 35 0.23
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.31
Consensus pattern (48 bp):
TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCCC
Found at i:211450 original size:43 final size:43
Alignment explanation
Indices: 211389--211478 Score: 144
Period size: 43 Copynumber: 2.1 Consensus size: 43
211379 GCACCTTCAT
* *
211389 CTTTAAGTCCAATGTAGCTGACCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATATAGCTGACCTTGAATCAGCACACTGGCAC
* *
211432 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATACTGGCAC
1 CTTTAAGTCCAATATAGCTGACCTTGAATCAGCACACTGGCAC
211475 CTTT
1 CTTT
211479 TCCATCTTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.30
Consensus pattern (43 bp):
CTTTAAGTCCAATATAGCTGACCTTGAATCAGCACACTGGCAC
Found at i:211474 original size:92 final size:95
Alignment explanation
Indices: 211293--211531 Score: 313
Period size: 92 Copynumber: 2.5 Consensus size: 95
211283 GGCGTCTCCT
* * * * * *
211293 TTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTGCCTTTAAGTCCAATATCGC
1 TTTAAGTCCAATGTAGCTGACCTTGAATCAGCACATT-G-A-CAT-CCTTTAAGTCCAATATAGC
*
211358 TGGCCTTAAATCAGCATATTGGCACC-TT-CATC
62 TGGCCTTAAATCAGCATACTGGCACCTTTCCATC
*
211390 TTTAAGTCCAATGTAGCTGACCTTGAATCAGCACATTGGCA-CCTTTAAGTCCAATATAGCTGGC
1 TTTAAGTCCAATGTAGCTGACCTTGAATCAGCACATTGACATCCTTTAAGTCCAATATAGCTGGC
*
211454 CTTGAATCAGCATACTGGCACCTTTTCCATC
66 CTTAAATCAGCATACTGGCACC-TTTCCATC
* *
211485 TTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTT
1 TTTAAGTCCAATGTAGCTGACCTTGAATCAGCACATTGACATCCTTT
211532 TTCTCATCTT
Statistics
Matches: 126, Mismatches: 12, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
92 42 0.33
94 3 0.02
95 42 0.33
96 6 0.05
97 33 0.26
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.32
Consensus pattern (95 bp):
TTTAAGTCCAATGTAGCTGACCTTGAATCAGCACATTGACATCCTTTAAGTCCAATATAGCTGGC
CTTAAATCAGCATACTGGCACCTTTCCATC
Found at i:211510 original size:52 final size:55
Alignment explanation
Indices: 211432--211569 Score: 165
Period size: 52 Copynumber: 2.6 Consensus size: 55
211422 ACATTGGCAC
* *
211432 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATACTGGCA-CC-TTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACACTGACATCCTTTTTCTCAT
* * *
211484 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACACTGACATCCTTTTTCTCAT
* * * * *
211539 CTTTAAGCCCAACATCGTTGGCCGTGAATCA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCA
211570 ACATATTGGC
Statistics
Matches: 71, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
52 37 0.52
53 2 0.03
54 5 0.07
55 27 0.38
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.33
Consensus pattern (55 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACACTGACATCCTTTTTCTCAT
Found at i:212397 original size:13 final size:13
Alignment explanation
Indices: 212379--212403 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
212369 CATAAAGTGT
212379 TGTATCGATACAA
1 TGTATCGATACAA
212392 TGTATCGATACA
1 TGTATCGATACA
212404 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:212401 original size:33 final size:33
Alignment explanation
Indices: 212359--212425 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
212349 TTCAACGATT
212359 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
212392 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
212425 T
1 T
212426 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:218743 original size:174 final size:174
Alignment explanation
Indices: 218453--218803 Score: 657
Period size: 174 Copynumber: 2.0 Consensus size: 174
218443 TTTGTAAAAC
218453 ATGGTGAATGACTCATGCAAAATTTTGTTTTTCTTAACTAATTCATTGTTTTCATTTGTTAAGAC
1 ATGGTGAATGACTCATGCAAAATTTTGTTTTTCTTAACTAATTCATTGTTTTCATTTGTTAAGAC
218518 TTTATTATTATCTTGTACCTCATTCAATTGTTTCTCTAATTCAATTAATTTCTTTTTAAGCTCAA
66 TTTATTATTATCTTGTACCTCATTCAATTGTTTCTCTAATTCAATTAATTTCTTTTTAAGCTCAA
*
218583 CATTCTCTAAACTTATTTATTTATTTTCTTCATTTAGTTTAGAG
131 CATTCTCTAAACTTATTGATTTATTTTCTTCATTTAGTTTAGAG
*
218627 ATGGTGAATGACTCATGCAAATTTTTGTTTTTCTTAACTAATTCATTGTTTTCATTTGTTAAGAC
1 ATGGTGAATGACTCATGCAAAATTTTGTTTTTCTTAACTAATTCATTGTTTTCATTTGTTAAGAC
** *
218692 TTTATTATTATCTTGTACCTCATTCAATTGTTTCTCTAATTTGATTAATTTCTTTTTAAGCTCAG
66 TTTATTATTATCTTGTACCTCATTCAATTGTTTCTCTAATTCAATTAATTTCTTTTTAAGCTCAA
218757 CATTCTCTAAACTTATTGATTTATTTTCTTCATTTAGTTTAGAG
131 CATTCTCTAAACTTATTGATTTATTTTCTTCATTTAGTTTAGAG
218801 ATG
1 ATG
218804 ATTTTCTTAT
Statistics
Matches: 172, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
174 172 1.00
ACGTcount: A:0.26, C:0.14, G:0.10, T:0.51
Consensus pattern (174 bp):
ATGGTGAATGACTCATGCAAAATTTTGTTTTTCTTAACTAATTCATTGTTTTCATTTGTTAAGAC
TTTATTATTATCTTGTACCTCATTCAATTGTTTCTCTAATTCAATTAATTTCTTTTTAAGCTCAA
CATTCTCTAAACTTATTGATTTATTTTCTTCATTTAGTTTAGAG
Found at i:219210 original size:3 final size:3
Alignment explanation
Indices: 219202--219238 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
219192 GTCAACTTTT
*
219202 TCA TCA TCA TCA TCA TCA TCA TCA TCT TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
219239 TGATGGTTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.30, C:0.32, G:0.00, T:0.38
Consensus pattern (3 bp):
TCA
Found at i:230728 original size:44 final size:45
Alignment explanation
Indices: 230679--230785 Score: 157
Period size: 44 Copynumber: 2.4 Consensus size: 45
230669 AGTTTATCCT
* *
230679 AAGCCCACCCT-CGGGTGCTCGCATTCACCCAGCAAGGATGTTGC
1 AAGCCCACCCTCCAGGTGCTCGCATTCACCCAGCAAAGATGTTGC
*
230723 AAGCCCA-CCTCCAGGTGCTCGCATTCACCTAGCAAAGATGTTGC
1 AAGCCCACCCTCCAGGTGCTCGCATTCACCCAGCAAAGATGTTGC
*
230767 AAGCCCA-CGTCCAGGTGCT
1 AAGCCCACCCTCCAGGTGCT
230786 TGAGCCACCC
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
43 3 0.05
44 55 0.95
ACGTcount: A:0.22, C:0.36, G:0.23, T:0.19
Consensus pattern (45 bp):
AAGCCCACCCTCCAGGTGCTCGCATTCACCCAGCAAAGATGTTGC
Found at i:233038 original size:20 final size:20
Alignment explanation
Indices: 233013--233066 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 20
233003 GTTAGAAGTA
233013 ATGTATCGATACAAT-T-CATC
1 ATGTATCGATACAATGTGC--C
233033 ATGTATCGATACAATGTGCC
1 ATGTATCGATACAATGTGCC
233053 ATGTATCGATACAA
1 ATGTATCGATACAA
233067 ACAGTGGTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 30 0.94
21 1 0.03
22 1 0.03
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACAATGTGCC
Found at i:233140 original size:19 final size:19
Alignment explanation
Indices: 233095--233150 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
233085 TTGCCAGTTT
**
233095 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
233115 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
*
233134 TATGTATCGATACAATG
1 CATGTATCGATACAATG
233151 TATCGATACA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:233153 original size:13 final size:13
Alignment explanation
Indices: 233135--233161 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
233125 TACAATGAAT
233135 ATGTATCGATACA
1 ATGTATCGATACA
233148 ATGTATCGATACA
1 ATGTATCGATACA
233161 A
1 A
233162 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:233157 original size:32 final size:32
Alignment explanation
Indices: 233116--233179 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
233106 ACAATTGTCC
*
233116 ATGTATCGATACAATGAAT-ATGTATCGATACA
1 ATGTATCGATACAAAGAATAATGTATCG-TACA
*
233148 ATGTATCGATACAAAGCATAATGTATCGTACA
1 ATGTATCGATACAAAGAATAATGTATCGTACA
233180 TCTGGGTGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 21 0.72
33 8 0.28
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.30
Consensus pattern (32 bp):
ATGTATCGATACAAAGAATAATGTATCGTACA
Found at i:235547 original size:22 final size:21
Alignment explanation
Indices: 235512--235561 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
235502 TTTGTTGATG
*
235512 ATTTTG-A-TGAAAAATGAAGT
1 ATTTTGAAGTGAAAAAT-AAGA
235532 ATTTTGAAGTGAAAAATAAGA
1 ATTTTGAAGTGAAAAATAAGA
*
235553 AATTTGAAG
1 ATTTTGAAG
235562 AAGATTTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 6 0.23
21 12 0.46
22 8 0.31
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAATAAGA
Found at i:235558 original size:21 final size:22
Alignment explanation
Indices: 235519--235561 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
235509 ATGATTTTGA
* *
235519 TGAAAAATGAAGTATTTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
235541 TGAAAAAT-AAGAAATTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
235562 AAGATTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.51, C:0.00, G:0.21, T:0.28
Consensus pattern (22 bp):
TGAAAAATGAAGAAATTTGAAG
Found at i:241918 original size:20 final size:19
Alignment explanation
Indices: 241893--241948 Score: 76
Period size: 20 Copynumber: 2.9 Consensus size: 19
241883 TACTGCCAGT
241893 TCCATGTATCGATACAATTG
1 TCCATGTATCGATACAA-TG
241913 TCCATGTATCGATACAATG
1 TCCATGTATCGATACAATG
** *
241932 AACATGTATCAATACAA
1 TCCATGTATCGATACAA
241949 AGCATAATGT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.30
Consensus pattern (19 bp):
TCCATGTATCGATACAATG
Found at i:241939 original size:19 final size:20
Alignment explanation
Indices: 241895--241948 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
241885 CTGCCAGTTC
**
241895 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGAA
241915 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
*
241934 CATGTATCAATACAA
1 CATGTATCGATACAA
241949 AGCATAATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.39, C:0.19, G:0.13, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:245517 original size:52 final size:52
Alignment explanation
Indices: 245367--245497 Score: 235
Period size: 52 Copynumber: 2.5 Consensus size: 52
245357 CTCGAAATAT
245367 GAAAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGG
1 GAAAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGG
* **
245419 GCAAATTTGCCTATATGTATCGATACATTTCATAGTGTATCGATACATCTGG
1 GAAAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGG
245471 GAAAATTTGCCTGCATGTATCGATACA
1 GAAAATTTGCCTGCATGTATCGATACA
245498 AAGATCAATG
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (52 bp):
GAAAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGG
Found at i:245521 original size:13 final size:13
Alignment explanation
Indices: 245503--245565 Score: 66
Period size: 13 Copynumber: 5.2 Consensus size: 13
245493 ATACAAAGAT
245503 CAATGTATCGATA
1 CAATGTATCGATA
245516 CAATGTATCGATA
1 CAATGTATCGATA
245529 C-AT-T-T-GAGT-
1 CAATGTATCGA-TA
245538 -AATGTATCGATA
1 CAATGTATCGATA
*
245550 CACTGTATCGATA
1 CAATGTATCGATA
245563 CAA
1 CAA
245566 ATCGTTGAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 14
0.72 0.04 0.25
Matches are distributed among these distances:
9 4 0.10
10 3 0.07
11 3 0.07
12 4 0.10
13 27 0.66
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:252038 original size:33 final size:33
Alignment explanation
Indices: 252001--252119 Score: 127
Period size: 33 Copynumber: 3.7 Consensus size: 33
251991 ATTAGGCTTA
* *
252001 AAAAGAGATGCCACTAACTTGTATGGGCTTTTG
1 AAAAGAGTTACCACTAACTTGTATGGGCTTTTG
* * *
252034 AAAAGGGTTACCACTGACTTGTGTGGGCTTTTG
1 AAAAGAGTTACCACTAACTTGTATGGGCTTTTG
* *
252067 AAAAGGGTTACCA-TCGACTTGTATGGGC-TTTG
1 AAAAGAGTTACCACT-AACTTGTATGGGCTTTTG
* *
252099 -AAAGAGTTGCCACCAACTTGT
1 AAAAGAGTTACCACTAACTTGT
252120 GAGTTGTGTT
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
31 16 0.22
32 5 0.07
33 53 0.72
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (33 bp):
AAAAGAGTTACCACTAACTTGTATGGGCTTTTG
Found at i:252291 original size:89 final size:88
Alignment explanation
Indices: 252136--252299 Score: 238
Period size: 89 Copynumber: 1.9 Consensus size: 88
252126 TGTTACTTAC
* * *
252136 TTGTTGGCTTTAAAAAAAGGATGTCACTAACTTGTGGGCTTTAAAAAGGGATGCCACCAACTTGT
1 TTGTGGGCTTTAAAAAAAAGATGTCACTAACTTATGGGCTTTAAAAAGGGATGCCACCAACTTGT
252201 GGGCTTTAAATAGTGTCACTGAT
66 GGGCTTTAAATAGTGTCACTGAT
* * * ***
252224 TTGTGGGCTTTTAAAAAAAAGATGTTACTGACTTATGGGCTTTGAAAAGGGATGCCATTGACTTG
1 TTGTGGGC-TTTAAAAAAAAGATGTCACTAACTTATGGGCTTTAAAAAGGGATGCCACCAACTTG
252289 TGGGCTTTAAA
65 TGGGCTTTAAA
252300 AGGGATGCTA
Statistics
Matches: 66, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
88 7 0.11
89 59 0.89
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.33
Consensus pattern (88 bp):
TTGTGGGCTTTAAAAAAAAGATGTCACTAACTTATGGGCTTTAAAAAGGGATGCCACCAACTTGT
GGGCTTTAAATAGTGTCACTGAT
Found at i:252316 original size:29 final size:30
Alignment explanation
Indices: 252134--252513 Score: 348
Period size: 30 Copynumber: 12.8 Consensus size: 30
252124 TGTGTTACTT
* * * *
252134 ACTTGTTGGCTTTAAAAAAAGGATGTCACTA
1 ACTTGTGGGCTTT-AAAAAGGGATGCCACTG
**
252165 ACTTGTGGGCTTTAAAAAGGGATGCCACCA
1 ACTTGTGGGCTTTAAAAAGGGATGCCACTG
* *
252195 ACTTGTGGGCTTTAAATA--G-TGTCACTG
1 ACTTGTGGGCTTTAAAAAGGGATGCCACTG
* ** **
252222 ATTTGTGGGCTTTTAAAAAAAAGATGTTACTG
1 ACTTGTGGGC-TTT-AAAAAGGGATGCCACTG
* * *
252254 ACTTATGGGCTTTGAAAAGGGATGCCATTG
1 ACTTGTGGGCTTTAAAAAGGGATGCCACTG
* *
252284 ACTTGTGGGCTTT-AAAAGGGATGCTACTC
1 ACTTGTGGGCTTTAAAAAGGGATGCCACTG
252313 ACTTGTGGGCTTT-AAAAGGG-TGCCACTG
1 ACTTGTGGGCTTTAAAAAGGGATGCCACTG
* *
252341 ACTTGTGGGCTTT-AAAAGGG-TTCCATTG
1 ACTTGTGGGCTTTAAAAAGGGATGCCACTG
* *
252369 GCTTGTGGGCTTTGAAAAA-GGATGCCACTA
1 ACTTGTGGGCTTT-AAAAAGGGATGCCACTG
* *
252399 ACTTGTAGGCTTTAAAAAGGG-TGCCATTG
1 ACTTGTGGGCTTTAAAAAGGGATGCCACTG
* * *
252428 ACTTGTGGGCTTTAGAAAAAGGATACCACTA
1 ACTTGTGGGCTTTA-AAAAGGGATGCCACTG
* *
252459 ACTTGTGGGCTTTAAAAAAAAGGATGCCACTA
1 ACTTGTGGGCTTT--AAAAAGGGATGCCACTG
**
252491 ACTTGTGGGCTTCGAAAAGGGAT
1 ACTTGTGGGCTTTAAAAAGGGAT
252514 TCCATGGAGT
Statistics
Matches: 292, Mismatches: 44, Indels: 27
0.80 0.12 0.07
Matches are distributed among these distances:
27 14 0.05
28 48 0.16
29 63 0.22
30 90 0.31
31 34 0.12
32 42 0.14
33 1 0.00
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.30
Consensus pattern (30 bp):
ACTTGTGGGCTTTAAAAAGGGATGCCACTG
Found at i:252322 original size:59 final size:60
Alignment explanation
Indices: 252134--252513 Score: 364
Period size: 59 Copynumber: 6.4 Consensus size: 60
252124 TGTGTTACTT
* * * * **
252134 ACTTGTTGGCTTTAAAAAAAGGATGTCACTAACTTGTGGGCTTTAAAAAGGGATGCCACCA
1 ACTTGTGGGCTTT-GAAAAAGGATGCCACTGACTTGTGGGCTTTAAAAAGGGATGCCACTG
* * * ** **
252195 ACTTGTGGGCTTT-AAATA-G-TGTCACTGATTTGTGGGCTTTTAAAAAAAAGATGTTACTG
1 ACTTGTGGGCTTTGAAAAAGGATGCCACTGACTTGTGGGC-TTT-AAAAAGGGATGCCACTG
* * * * *
252254 ACTTATGGGCTTTGAAAAGGGATGCCATTGACTTGTGGGCTTT-AAAAGGGATGCTACTC
1 ACTTGTGGGCTTTGAAAAAGGATGCCACTGACTTGTGGGCTTTAAAAAGGGATGCCACTG
* * *
252313 ACTTGTGGGCTTT--AAAAGGGTGCCACTGACTTGTGGGCTTT-AAAAGGG-TTCCATTG
1 ACTTGTGGGCTTTGAAAAAGGATGCCACTGACTTGTGGGCTTTAAAAAGGGATGCCACTG
* * * *
252369 GCTTGTGGGCTTTGAAAAAGGATGCCACTAACTTGTAGGCTTTAAAAAGGG-TGCCATTG
1 ACTTGTGGGCTTTGAAAAAGGATGCCACTGACTTGTGGGCTTTAAAAAGGGATGCCACTG
* * * *
252428 ACTTGTGGGCTTTAGAAAAAGGATACCACTAACTTGTGGGCTTTAAAAAAAAGGATGCCACTA
1 ACTTGTGGGCTTT-GAAAAAGGATGCCACTGACTTGTGGGCTTT--AAAAAGGGATGCCACTG
* *
252491 ACTTGTGGGCTTCGAAAAGGGAT
1 ACTTGTGGGCTTTGAAAAAGGAT
252514 TCCATGGAGT
Statistics
Matches: 266, Mismatches: 41, Indels: 23
0.81 0.12 0.07
Matches are distributed among these distances:
56 16 0.06
57 48 0.18
58 29 0.11
59 77 0.29
60 31 0.12
61 16 0.06
62 31 0.12
63 18 0.07
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.30
Consensus pattern (60 bp):
ACTTGTGGGCTTTGAAAAAGGATGCCACTGACTTGTGGGCTTTAAAAAGGGATGCCACTG
Found at i:252580 original size:28 final size:28
Alignment explanation
Indices: 252517--252593 Score: 77
Period size: 28 Copynumber: 2.8 Consensus size: 28
252507 AAGGGATTCC
252517 ATGGAGTTGTGGATTGTAAAAGGGTGCT
1 ATGGAGTTGTGGATTGTAAAAGGGTGCT
** * *
252545 ATAAAGTTGTTGATTTTAAAAGGGTGCCT
1 ATGGAGTTGTGGATTGTAAAAGGGTG-CT
*
252574 -TGGAGTTATGGACTT-TAAAA
1 ATGGAGTTGTGGA-TTGTAAAA
252594 AAGGTACCAC
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
28 35 0.90
29 4 0.10
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (28 bp):
ATGGAGTTGTGGATTGTAAAAGGGTGCT
Found at i:252643 original size:31 final size:30
Alignment explanation
Indices: 252582--252689 Score: 87
Period size: 31 Copynumber: 3.6 Consensus size: 30
252572 CTTGGAGTTA
* *
252582 TGGAC-TTTAAAAAA-GGTACCACAAAGTTG
1 TGGACTTTTAAAAAAGGGTGCCACGAA-TTG
*
252611 TGAACTTTTAAAAAAGGGTGCCACGGAATTG
1 TGGACTTTTAAAAAAGGGTGCCAC-GAATTG
* * *
252642 TGGAC-TTAAAAAAGAGGGTGGCACAGAGTTG
1 TGGACTTTTAAAAA-AGGGTGCCAC-GAATTG
* *
252673 TGGATTTTTTAAAAAGG
1 TGGACTTTTAAAAAAGG
252690 TGTCATGGAG
Statistics
Matches: 63, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
29 4 0.06
30 16 0.25
31 35 0.56
32 8 0.13
ACGTcount: A:0.37, C:0.10, G:0.27, T:0.26
Consensus pattern (30 bp):
TGGACTTTTAAAAAAGGGTGCCACGAATTG
Found at i:252702 original size:92 final size:92
Alignment explanation
Indices: 252576--252814 Score: 202
Period size: 92 Copynumber: 2.6 Consensus size: 92
252566 GGGTGCCTTG
* * *** *
252576 GAGTTATGGACTTT-AAAAAA-GGTACCACAAAGTTGTGAACTTTTAAAAAAGGGTGCCACGGAA
1 GAGTTGTGGACTTTAAAAAAAGGGTGCCATGGAGTTGTG-ACTTTTAAAAAAGGGTACCAC-GAA
** * * **
252639 -TTGTGGACTTAAAAAAGAGGGTGGCACA
64 GTTGTAAACTTAAAAAAAAGAGTAACACA
* ** *
252667 GAGTTGTGGATTTTTTAAAAA-GGTGTCATGGAGTTGTTGAC--TTAAAAAAGAAGGTACCACGA
1 GAGTTGTGGACTTTAAAAAAAGGGTGCCATGGAGTTG-TGACTTTTAAAAAAG--GGTACCACGA
*
252729 AGTTGTAAACTTAAAAAAAAGAGTAACATA
63 AGTTGTAAACTTAAAAAAAAGAGTAACACA
* *
252759 GAGTTGTGGACTTTAAAAAAATGGGTGCCATGGAGTTATGGACTTTAAAAAAAGGG
1 GAGTTGTGGACTTTAAAAAAA-GGGTGCCATGGAGTTGT-GACTTTTAAAAAAGGG
252815 GTGCTATAGA
Statistics
Matches: 116, Mismatches: 22, Indels: 17
0.75 0.14 0.11
Matches are distributed among these distances:
90 9 0.08
91 15 0.13
92 63 0.54
93 3 0.03
94 18 0.16
96 8 0.07
ACGTcount: A:0.39, C:0.09, G:0.26, T:0.26
Consensus pattern (92 bp):
GAGTTGTGGACTTTAAAAAAAGGGTGCCATGGAGTTGTGACTTTTAAAAAAGGGTACCACGAAGT
TGTAAACTTAAAAAAAAGAGTAACACA
Found at i:252734 original size:61 final size:60
Alignment explanation
Indices: 252558--252778 Score: 185
Period size: 61 Copynumber: 3.6 Consensus size: 60
252548 AAGTTGTTGA
* * * *
252558 TTTTAAAAGGGTGCCTTGGAGTTATGGACTT-TAAAA-AAGGTACCACAAAGTTGTGAACT
1 TTTTAAAAAGGTGCCATGGAGTTGTGGACTTAAAAAAGAAGGTACCAC-AAGTTGTGAACT
* * * * ** * *
252617 TTTAAAAAAGGGTGCCACGGAATTGTGGACTTAAAAAAGAGGGTGGCACAGAGTTGTGGATT
1 TTTTAAAAA-GGTGCCATGGAGTTGTGGACTTAAAAAAGAAGGTACCACA-AGTTGTGAACT
* * *
252679 TTTTAAAAAGGTGTCATGGAGTTGTTGACTTAAAAAAGAAGGTACCACGAAGTTGTAAACT
1 TTTTAAAAAGGTGCCATGGAGTTGTGGACTTAAAAAAGAAGGTACCAC-AAGTTGTGAACT
*** ** *
252740 TAAAAAAAAGAGTAACATAGAGTTGTGGACTTTAAAAAA
1 TTTTAAAAAG-GTGCCATGGAGTTGTGGAC-TTAAAAAA
252779 ATGGGTGCCA
Statistics
Matches: 125, Mismatches: 30, Indels: 10
0.76 0.18 0.06
Matches are distributed among these distances:
59 7 0.06
60 18 0.14
61 52 0.42
62 40 0.32
63 8 0.06
ACGTcount: A:0.38, C:0.10, G:0.25, T:0.27
Consensus pattern (60 bp):
TTTTAAAAAGGTGCCATGGAGTTGTGGACTTAAAAAAGAAGGTACCACAAGTTGTGAACT
Found at i:252775 original size:32 final size:32
Alignment explanation
Indices: 252739--252840 Score: 98
Period size: 32 Copynumber: 3.2 Consensus size: 32
252729 AGTTGTAAAC
*
252739 TTAAAAAAAAGAGTAACATAGAGTTGTGGACT
1 TTAAAAAAAAGAGTAACATAGAGTTATGGACT
* * ** *
252771 TTAAAAAAATGGGTGCCATGGAGTTATGGACT
1 TTAAAAAAAAGAGTAACATAGAGTTATGGACT
* * * *
252803 TTAAAAAAAGGGGT-GCTATAGAGATATGGACT
1 TTAAAAAAAAGAGTAAC-ATAGAGTTATGGACT
252835 TTAAAA
1 TTAAAA
252841 GGGTGCCACA
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
31 1 0.02
32 58 0.98
ACGTcount: A:0.42, C:0.07, G:0.25, T:0.26
Consensus pattern (32 bp):
TTAAAAAAAAGAGTAACATAGAGTTATGGACT
Found at i:252853 original size:28 final size:29
Alignment explanation
Indices: 252776--252865 Score: 83
Period size: 32 Copynumber: 3.0 Consensus size: 29
252766 GGACTTTAAA
* * *
252776 AAAATGGGTGCCATGGAGTTATGGACTTT
1 AAAAGGGGTGCCATAGAGATATGGACTTT
*
252805 AAAAAAAGGGGTGCTATAGAGATATGGACTTT
1 ---AAAAGGGGTGCCATAGAGATATGGACTTT
* * *
252837 AAAA-GGGTGCCACAGAGGTGTGGACTTT
1 AAAAGGGGTGCCATAGAGATATGGACTTT
252865 A
1 A
252866 GAAAAAATAC
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
28 21 0.42
29 4 0.08
32 25 0.50
ACGTcount: A:0.33, C:0.10, G:0.31, T:0.26
Consensus pattern (29 bp):
AAAAGGGGTGCCATAGAGATATGGACTTT
Found at i:259619 original size:42 final size:43
Alignment explanation
Indices: 259573--259663 Score: 125
Period size: 42 Copynumber: 2.1 Consensus size: 43
259563 TTTTTTTTGC
259573 TTTATGATTCTTTAAATAATTTT-TTTCTTTTTGT-TTTC-ATTT
1 TTTAT-ATTCTTTAAATAATTTTCTTTCTTTTT-TATTTCTATTT
*
259615 TTTATCTTCTTTAAATAATTTTCTTTCTTTTTTATTTCTATTT
1 TTTATATTCTTTAAATAATTTTCTTTCTTTTTTATTTCTATTT
259658 TCTTAT
1 T-TTAT
259664 CATCTCTATC
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
41 17 0.39
42 18 0.41
43 5 0.11
44 4 0.09
ACGTcount: A:0.19, C:0.10, G:0.02, T:0.69
Consensus pattern (43 bp):
TTTATATTCTTTAAATAATTTTCTTTCTTTTTTATTTCTATTT
Found at i:259625 original size:41 final size:44
Alignment explanation
Indices: 259580--259664 Score: 133
Period size: 41 Copynumber: 2.0 Consensus size: 44
259570 TGCTTTATGA
259580 TTCTTTAAATAATTTT-TTTCTTTTTGT-TTTC-ATTTT-TTATC
1 TTCTTTAAATAATTTTCTTTCTTTTT-TATTTCTATTTTCTTATC
259621 TTCTTTAAATAATTTTCTTTCTTTTTTATTTCTATTTTCTTATC
1 TTCTTTAAATAATTTTCTTTCTTTTTTATTTCTATTTTCTTATC
259665 ATCTCTATCA
Statistics
Matches: 40, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
41 17 0.43
42 13 0.32
43 5 0.12
44 5 0.12
ACGTcount: A:0.18, C:0.12, G:0.01, T:0.69
Consensus pattern (44 bp):
TTCTTTAAATAATTTTCTTTCTTTTTTATTTCTATTTTCTTATC
Found at i:259635 original size:21 final size:20
Alignment explanation
Indices: 259580--259648 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
259570 TGCTTTATGA
259580 TTCTTTAAATAATTTTTTTC
1 TTCTTTAAATAATTTTTTTC
*** *
259600 TT-TTTGTTTTCATTTTTTATC
1 TTCTTT-AAATAATTTTTT-TC
259621 TTCTTTAAATAATTTTCTTTC
1 TTCTTTAAATAATTTT-TTTC
*
259642 TTTTTTA
1 TTCTTTA
259649 TTTCTATTTT
Statistics
Matches: 36, Mismatches: 9, Indels: 7
0.69 0.17 0.13
Matches are distributed among these distances:
19 3 0.08
20 10 0.28
21 18 0.50
22 5 0.14
ACGTcount: A:0.19, C:0.10, G:0.01, T:0.70
Consensus pattern (20 bp):
TTCTTTAAATAATTTTTTTC
Found at i:259715 original size:14 final size:14
Alignment explanation
Indices: 259698--259725 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
259688 TTCTTTTCTC
259698 CTTTTCTTTTTTTT
1 CTTTTCTTTTTTTT
259712 CTTTTCTTTTTTTT
1 CTTTTCTTTTTTTT
259726 TGTTTTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (14 bp):
CTTTTCTTTTTTTT
Found at i:259724 original size:22 final size:22
Alignment explanation
Indices: 259688--259733 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
259678 TCTTTCTCAA
259688 TTCTTTTCTCCTTTTCTT-TTTT
1 TTCTTTTCTCCTTTT-TTGTTTT
**
259710 TTCTTTTCTTTTTTTTTGTTTT
1 TTCTTTTCTCCTTTTTTGTTTT
259732 TT
1 TT
259734 ATAATATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 2 0.10
22 19 0.90
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (22 bp):
TTCTTTTCTCCTTTTTTGTTTT
Found at i:261579 original size:6 final size:6
Alignment explanation
Indices: 261568--261640 Score: 74
Period size: 6 Copynumber: 11.3 Consensus size: 6
261558 AAAAATTTTA
**
261568 AAAAAT AAAAAT AAATTT AAAAAATT AAAAAT AAAATAT AAAAAT AAAAAAAT
1 AAAAAT AAAAAT AAAAAT -AAAAA-T AAAAAT AAAA-AT AAAAAT --AAAAAT
*
261621 AAAAAT AAGAAT AAAAAT AA
1 AAAAAT AAAAAT AAAAAT AA
261641 TAATGTGTTC
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
6 35 0.62
7 14 0.25
8 7 0.12
ACGTcount: A:0.78, C:0.00, G:0.01, T:0.21
Consensus pattern (6 bp):
AAAAAT
Found at i:261588 original size:19 final size:19
Alignment explanation
Indices: 261564--261623 Score: 75
Period size: 21 Copynumber: 3.0 Consensus size: 19
261554 TTCAAAAAAT
261564 TTTAAAAAATAAAAATAAA
1 TTTAAAAAATAAAAATAAA
261583 TTTAAAAAATTAAAAATAAAA
1 TTTAAAAAA-TAAAAAT-AAA
* *
261604 TATAAAAATAAAAAAATAAA
1 TTTAAAAA-ATAAAAATAAA
261624 AATAAGAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
19 9 0.25
20 10 0.28
21 16 0.44
22 1 0.03
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (19 bp):
TTTAAAAAATAAAAATAAA
Found at i:261616 original size:26 final size:26
Alignment explanation
Indices: 261568--261640 Score: 101
Period size: 27 Copynumber: 2.8 Consensus size: 26
261558 AAAAATTTTA
** *
261568 AAAAATAAAAATAAATTTAAAAAATT
1 AAAAATAAAAATAAAAATAAAAAAAT
261594 AAAAATAAAATATAAAAATAAAAAAAT
1 AAAAATAAAA-ATAAAAATAAAAAAAT
*
261621 AAAAATAAGAATAAAAATAA
1 AAAAATAAAAATAAAAATAA
261641 TAATGTGTTC
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
26 20 0.48
27 22 0.52
ACGTcount: A:0.78, C:0.00, G:0.01, T:0.21
Consensus pattern (26 bp):
AAAAATAAAAATAAAAATAAAAAAAT
Found at i:261628 original size:20 final size:20
Alignment explanation
Indices: 261567--261640 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
261557 AAAAAATTTT
**
261567 AAAAAATAAAAATAAATTTA
1 AAAAAATAAAAATAAAAATA
*
261587 AAAAATTAAAAATAAAATATA
1 AAAAAATAAAAATAAAA-ATA
261608 AAAATAA-AAAAATAAAAAT-
1 AAAA-AATAAAAATAAAAATA
*
261627 -AAGAATAAAAATAA
1 AAAAAATAAAAATAA
261641 TAATGTGTTC
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
17 2 0.04
18 10 0.22
20 17 0.37
21 16 0.35
22 1 0.02
ACGTcount: A:0.78, C:0.00, G:0.01, T:0.20
Consensus pattern (20 bp):
AAAAAATAAAAATAAAAATA
Found at i:261642 original size:21 final size:21
Alignment explanation
Indices: 261594--261643 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
261584 TTAAAAAATT
261594 AAAAATAAAATATAAAAATAA
1 AAAAATAAAATATAAAAATAA
*
261615 AAAAATAAAA-ATAAGAATAA
1 AAAAATAAAATATAAAAATAA
261635 AAATAATAA
1 AAA-AATAA
261644 TGTGTTCAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 12 0.44
21 15 0.56
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (21 bp):
AAAAATAAAATATAAAAATAA
Found at i:262110 original size:100 final size:106
Alignment explanation
Indices: 261922--262134 Score: 312
Period size: 100 Copynumber: 2.1 Consensus size: 106
261912 TCATTATATC
*
261922 ATTAAATTTATTAATCTTTAACTGAACTGATTAATCGAATCTAATTTTTTCTCACTTATGACAGC
1 ATTAAATTTATTAATCTTTAACTGAACTGATTAATCGAATCTAATTTTTTCTCAC-TACGACAGC
261987 TCTAGAGATGCTGATCAAACATAAATAACCTAATAAAAGTTG
65 TCTAGAGATGCTGATCAAACATAAATAACCTAATAAAAGTTG
* * * *
262029 ATTAAATTTATTAAT-TTTAATTGAATTGATTAATCGGATCTAA-TTTTT-T-A-T-CGACAGTT
1 ATTAAATTTATTAATCTTTAACTGAACTGATTAATCGAATCTAATTTTTTCTCACTACGACAGCT
* *
262088 CTAGAGATGTTGATCAAGCATAAATAACCTAATAAAAGTTG
66 CTAGAGATGCTGATCAAACATAAATAACCTAATAAAAGTTG
262129 ATTAAA
1 ATTAAA
262135 AGTAGATTTG
Statistics
Matches: 99, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
100 51 0.52
101 1 0.01
103 1 0.01
104 1 0.01
105 5 0.05
106 25 0.25
107 15 0.15
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (106 bp):
ATTAAATTTATTAATCTTTAACTGAACTGATTAATCGAATCTAATTTTTTCTCACTACGACAGCT
CTAGAGATGCTGATCAAACATAAATAACCTAATAAAAGTTG
Found at i:263179 original size:11 final size:11
Alignment explanation
Indices: 263163--263204 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
263153 AAAAAATAAT
263163 TATTTATATTA
1 TATTTATATTA
263174 TATTTATATTA
1 TATTTATATTA
*
263185 T-TTTTTATTA
1 TATTTATATTA
*
263195 TAATTATATT
1 TATTTATATT
263205 TTATATACAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
10 9 0.33
11 18 0.67
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TATTTATATTA
Found at i:263195 original size:21 final size:20
Alignment explanation
Indices: 263161--263204 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
263151 TTAAAAAATA
*
263161 ATTATTTATATTATATTTAT
1 ATTATTTATATTATAATTAT
*
263181 ATTATTTTTTATTATAATTAT
1 ATTA-TTTATATTATAATTAT
263202 ATT
1 ATT
263205 TTATATACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
ATTATTTATATTATAATTAT
Found at i:263206 original size:16 final size:16
Alignment explanation
Indices: 263162--263208 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
263152 TAAAAAATAA
*
263162 TTAT-TTATATTATAT
1 TTATATTATATTTTAT
*
263177 TTATATTATTTTTTA-
1 TTATATTATATTTTAT
263192 TTATAATTATATTTTAT
1 TTAT-ATTATATTTTAT
263209 ATACATTCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 8 0.31
16 18 0.69
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTATATTATATTTTAT
Found at i:263940 original size:18 final size:18
Alignment explanation
Indices: 263926--263959 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
263916 ATAATTTATC
263926 ATAAT-AATTTAATTTTA
1 ATAATAAATTTAATTTTA
*
263943 ATTATAAATTTAATTTT
1 ATAATAAATTTAATTTT
263960 TTATTTTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATAATAAATTTAATTTTA
Found at i:264402 original size:23 final size:22
Alignment explanation
Indices: 264363--264408 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
264353 CATAATTTAA
*
264363 AATATTTTTTAACTTTAATTTTT
1 AATATTTTATAACTTT-ATTTTT
264386 AATATTTTATATA-TTTATTTTT
1 AATATTTTATA-ACTTTATTTTT
264408 A
1 A
264409 TATAATATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 7 0.33
23 13 0.62
24 1 0.05
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (22 bp):
AATATTTTATAACTTTATTTTT
Found at i:265558 original size:9 final size:9
Alignment explanation
Indices: 265527--265568 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
265517 TTTATTTGTA
265527 AATATT-AT
1 AATATTAAT
*
265535 AATAATAAT
1 AATATTAAT
265544 AATATTAAT
1 AATATTAAT
*
265553 ATTATTAAT
1 AATATTAAT
*
265562 TATATTA
1 AATATTA
265569 TATTTAAATG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
8 5 0.18
9 23 0.82
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
AATATTAAT
Found at i:267429 original size:32 final size:32
Alignment explanation
Indices: 267380--267476 Score: 140
Period size: 32 Copynumber: 3.0 Consensus size: 32
267370 ATTTAGAATT
267380 TTTATTCAATAAATAAATACAAAATTACAAGAA
1 TTTATTCAAT-AATAAATACAAAATTACAAGAA
* *
267413 TTTATTCGATAATAAATACAAAATTACAATAA
1 TTTATTCAATAATAAATACAAAATTACAAGAA
* * *
267445 TTTATTCAATAATAGATACAGAATTGCAAGAA
1 TTTATTCAATAATAAATACAAAATTACAAGAA
267477 ATTACATGCT
Statistics
Matches: 57, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
32 48 0.84
33 9 0.16
ACGTcount: A:0.53, C:0.09, G:0.06, T:0.32
Consensus pattern (32 bp):
TTTATTCAATAATAAATACAAAATTACAAGAA
Found at i:268222 original size:23 final size:23
Alignment explanation
Indices: 268196--268246 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 23
268186 TAGATTAATT
* *
268196 AATTAGGGTTTTAGGAAACCTTA
1 AATTAAGGTTTTAAGAAACCTTA
268219 AATTTAAGGTTTTAAGAAACCTTA
1 AA-TTAAGGTTTTAAGAAACCTTA
268243 AATT
1 AATT
268247 TTACATGCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 4 0.16
24 21 0.84
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.37
Consensus pattern (23 bp):
AATTAAGGTTTTAAGAAACCTTA
Found at i:268229 original size:24 final size:24
Alignment explanation
Indices: 268202--268247 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
268192 AATTAATTAG
*
268202 GGTTTTAGGAAACCTTAAATTTAA
1 GGTTTTAAGAAACCTTAAATTTAA
268226 GGTTTTAAGAAACCTTAAATTT
1 GGTTTTAAGAAACCTTAAATTT
268248 TACATGCAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.39
Consensus pattern (24 bp):
GGTTTTAAGAAACCTTAAATTTAA
Found at i:272694 original size:20 final size:20
Alignment explanation
Indices: 272665--272704 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
272655 GTTGGGCACA
*
272665 ATGTACCGATACATTTTATC
1 ATGTACCGATACATTGTATC
*
272685 ATGTATCGATACATTGTATC
1 ATGTACCGATACATTGTATC
272705 GATACAATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTACCGATACATTGTATC
Found at i:272704 original size:13 final size:13
Alignment explanation
Indices: 272686--272710 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
272676 CATTTTATCA
272686 TGTATCGATACAT
1 TGTATCGATACAT
272699 TGTATCGATACA
1 TGTATCGATACA
272711 ATGTCCCATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:273061 original size:21 final size:20
Alignment explanation
Indices: 273037--273076 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
273027 TTTAAATGAA
273037 CAAAACTTGTTTACGATTTTT
1 CAAAACTT-TTTACGATTTTT
* *
273058 CAAATCTTTTTTCGATTTT
1 CAAAACTTTTTACGATTTT
273077 ATTCATCCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.25, C:0.15, G:0.07, T:0.53
Consensus pattern (20 bp):
CAAAACTTTTTACGATTTTT
Found at i:275389 original size:13 final size:13
Alignment explanation
Indices: 275371--275418 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
275361 GTACCCCTTT
275371 TATCGATACAATG
1 TATCGATACAATG
* *
275384 TATCGATATAGTG
1 TATCGATACAATG
* *
275397 TATCGATATAATT
1 TATCGATACAATG
275410 TATCGATAC
1 TATCGATAC
275419 TTAGAACATT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (13 bp):
TATCGATACAATG
Found at i:275479 original size:20 final size:20
Alignment explanation
Indices: 275454--275508 Score: 110
Period size: 20 Copynumber: 2.8 Consensus size: 20
275444 GGTTTTCTAG
275454 ATGTATCGATACATTATTCA
1 ATGTATCGATACATTATTCA
275474 ATGTATCGATACATTATTCA
1 ATGTATCGATACATTATTCA
275494 ATGTATCGATACATT
1 ATGTATCGATACATT
275509 TTGAAAAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTATTCA
Found at i:284187 original size:52 final size:52
Alignment explanation
Indices: 283987--284167 Score: 326
Period size: 52 Copynumber: 3.5 Consensus size: 52
283977 CGAAATATGA
* *
283987 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
284039 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
*
284091 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCAATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
*
284143 AAACTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
284168 AAGATCAGTG
Statistics
Matches: 125, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 125 1.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
Found at i:284194 original size:13 final size:13
Alignment explanation
Indices: 284176--284200 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
284166 CAAAGATCAG
284176 TGTATCGATACAA
1 TGTATCGATACAA
284189 TGTATCGATACA
1 TGTATCGATACA
284201 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:284274 original size:32 final size:33
Alignment explanation
Indices: 284238--284306 Score: 113
Period size: 32 Copynumber: 2.1 Consensus size: 33
284228 GGCAGTAGCT
284238 TACATTGTATCGATACAAAAC-TTATGTATCGA
1 TACATTGTATCGATACAAAACTTTATGTATCGA
* *
284270 TACATTGTATTGATACAACACTTTATGTATCGA
1 TACATTGTATCGATACAAAACTTTATGTATCGA
284303 TACA
1 TACA
284307 AATTATTGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 19 0.56
33 15 0.44
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (33 bp):
TACATTGTATCGATACAAAACTTTATGTATCGA
Found at i:284314 original size:33 final size:32
Alignment explanation
Indices: 284238--284315 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 32
284228 GGCAGTAGCT
* *
284238 TACATTGTATCGATACAAAACTTATGTATCGA
1 TACAATGTATTGATACAAAACTTATGTATCGA
* *
284270 TACATTGTATTGATACAACACTTTATGTATCGA
1 TACAATGTATTGATACAAAAC-TTATGTATCGA
284303 TACAAAT-TATTGA
1 TAC-AATGTATTGA
284316 AATTCAAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
32 19 0.46
33 20 0.49
34 2 0.05
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (32 bp):
TACAATGTATTGATACAAAACTTATGTATCGA
Found at i:284985 original size:55 final size:52
Alignment explanation
Indices: 284926--285315 Score: 267
Period size: 49 Copynumber: 8.1 Consensus size: 52
284916 GATATTGGGT
* *
284926 TTAAAGATGAGAAAAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAAC
1 TTAAAGATG-G-AAAAGG-TGCCAATATGCTGATTCAAGGCCAGCTACATTGAAC
* *
284981 TTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
1 TTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAAC
* *
285033 -T-----T---AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
1 TTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAAC
* * * * *
285076 TTAAAGA---AGAAGGTGCTAATATGCTGATTCAAGGCAAGCTATATTG-GC
1 TTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAAC
* * * *
285124 CT-----T---AAAGGTGCCAATGTGCTGATTCAAGGCTAGCTACATTGGAC
1 TTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAAC
* * * *
285168 TTAAAGAT-G--AAGGTGCCAATATGCTGACTCAAGGCCAACTATATTGGAC
1 TTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAAC
* * *
285217 -T-----T---AAAGGTACCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
1 TTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAAC
* * * *
285260 TTAAAGAT-G--AAGGTGCCAATATGCTAACTCAAGGCCAGCTATATTGGAC
1 TTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAAC
285309 TTAAAGA
1 TTAAAGA
285316 AGATGCCACC
Statistics
Matches: 277, Mismatches: 35, Indels: 52
0.76 0.10 0.14
Matches are distributed among these distances:
43 108 0.39
44 4 0.01
46 1 0.00
48 3 0.01
49 112 0.40
51 1 0.00
52 32 0.12
53 6 0.02
54 1 0.00
55 9 0.03
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.25
Consensus pattern (52 bp):
TTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAAC
Found at i:285053 original size:43 final size:43
Alignment explanation
Indices: 284992--285314 Score: 349
Period size: 43 Copynumber: 7.1 Consensus size: 43
284982 TAAAGATGGA
284992 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
285035 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* * *
285078 AAAGAAGAAGGTGCTAATATGCTGATTCAAGGCAAGCTATATTGGCCTT
1 -----A-AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* * *
285127 AAAGGTGCCAATGTGCTGATTCAAGGCTAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
285170 AAAGATGAAGGTGCCAATATGCTGACTCAAGGCCAACTATATTGGACTT
1 ----A--AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* * *
285219 AAAGGTACCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
285262 AAAGATGAAGGTGCCAATATGCTAACTCAAGGCCAGCTATATTGGACTT
1 ----A--AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
285311 AAAG
1 AAAG
285315 AAGATGCCAC
Statistics
Matches: 235, Mismatches: 27, Indels: 36
0.79 0.09 0.12
Matches are distributed among these distances:
43 118 0.50
44 1 0.00
45 2 0.01
47 2 0.01
48 1 0.00
49 111 0.47
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (43 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
Found at i:285128 original size:92 final size:92
Alignment explanation
Indices: 284939--285314 Score: 574
Period size: 92 Copynumber: 4.0 Consensus size: 92
284929 AAGATGAGAA
* * *
284939 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAAT
1 AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA---AGAAGGTGCCAAT
* *
285004 ATGCTGATTCAAGGCCAGCTATATTGGACTT
62 ATGCTGACTCAAGGCAAGCTATATTGGACTT
*
285035 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCTAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
* *
285100 TGATTCAAGGCAAGCTATATTGGCCTT
66 TGACTCAAGGCAAGCTATATTGGACTT
* *
285127 AAAGGTGCCAATGTGCTGATTCAAGGCTAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
285192 TGACTCAAGGCCAA-CTATATTGGACTT
66 TGACTCAAGG-CAAGCTATATTGGACTT
* *
285219 AAAGGTACCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
* *
285284 TAACTCAAGGCCAGCTATATTGGACTT
66 TGACTCAAGGCAAGCTATATTGGACTT
285311 AAAG
1 AAAG
285315 AAGATGCCAC
Statistics
Matches: 263, Mismatches: 15, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
91 2 0.01
92 212 0.81
93 3 0.01
95 41 0.16
96 5 0.02
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.26
Consensus pattern (92 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
TGACTCAAGGCAAGCTATATTGGACTT
Found at i:285447 original size:30 final size:30
Alignment explanation
Indices: 285373--286219 Score: 1065
Period size: 30 Copynumber: 28.9 Consensus size: 30
285363 TGTGCTTTTG
* *
285373 AAGGTTGCCACTGACTTGTGGGCTTTTG--
1 AAGGGTGCCACTGACTTGTGGGCTTTGGAA
* *
285401 AAGAG-GCCATTGACTTGTGGGCTTTGGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTGGAA
285430 AAGGGTGCCACTGACTTGTGGGCTTTGGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTGGAA
* *
285460 AA-GATGCCACTGACTTGCGGGCTTTGGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTGGAA
* *
285489 AAGGGTGCCACTAACTTGTGGGCTTTTGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTGGAA
* *
285519 AA-GATACCACTGACTTGTGGGCTTTGGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTGGAA
* * *
285548 AAGGGTGCCATTGACTTATGGGCTTTTGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTGGAA
* *
285578 AA-GATACCACTGACTTGT-GG--TTGGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTGGAA
*
285604 AA-GATGCCACTGACTTGTGGGCTTTGGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTGGAA
* * *
285633 AA-GATGTCACAGACTTGTGGGCTTTGGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTGGAA
* *
285662 AAGGGTGCCACTGACTTATGGGCTTTTGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTGGAA
* * *
285692 AA-GATACCATTGACTTGTGGGCTTTGGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTGGAA
285721 AAGGGTGCCACTGACTTGTGGGCTTTGGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTGGAA
* *
285751 AAGGGTACCACTAACTTGTGGGCTTTGGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTGGAA
* * *
285781 AAGGGTACCACTGACTTGTGGACTTTTGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTGGAA
285811 AAGGGTGCCACTGACTTGTGGGCTTTGGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTGGAA
*
285841 AA-GATGCCACTGACTTGTGGGCTTTGGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTGGAA
*
285870 AAAGGTGCCACTGACTTGTGGGCTTTGGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTGGAA
*
285900 AAAGGTGCCACTGACTTGT-GGCTTT-G--
1 AAGGGTGCCACTGACTTGTGGGCTTTGGAA
* *
285926 AAGGTTGCCACTGACTTGTGGGCTTTGAGAG
1 AAGGGTGCCACTGACTTGTGGGCTTTG-GAA
* * *
285957 AAGGGTGCCACTGATTTTTGGGCTTTTG--
1 AAGGGTGCCACTGACTTGTGGGCTTTGGAA
*
285985 AAGGTTGCCACTGACTTGTGGGCTTTGGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTGGAA
*
286015 AA-GATGCCACTGACTTGTGGGCTTTGGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTGGAA
*
286044 AA-GATGCCACTGACTTGTGGGCTTTGGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTGGAA
* *
286073 AAGGGTGCCACTGACTTATGGGCTTTGAGAG
1 AAGGGTGCCACTGACTTGTGGGCTTTG-GAA
*
286104 AAGGGTGCCACTGACTTGTGGGCTTTGAGAG
1 AAGGGTGCCACTGACTTGTGGGCTTTG-GAA
* *
286135 AAGGGTGCCACTGATTTGTGGGCTTTTG--
1 AAGGGTGCCACTGACTTGTGGGCTTTGGAA
* *
286163 AAGGTTGCCACTGACTTGTGGGCTTTGGGAG
1 AAGGGTGCCACTGACTTGTGGGCTTT-GGAA
*
286194 AAGGGTGCCACTGATTTGTGGGCTTT
1 AAGGGTGCCACTGACTTGTGGGCTTT
286220 AAAAAAGAGT
Statistics
Matches: 722, Mismatches: 74, Indels: 43
0.86 0.09 0.05
Matches are distributed among these distances:
26 39 0.05
27 28 0.04
28 54 0.07
29 220 0.30
30 277 0.38
31 104 0.14
ACGTcount: A:0.22, C:0.16, G:0.32, T:0.29
Consensus pattern (30 bp):
AAGGGTGCCACTGACTTGTGGGCTTTGGAA
Found at i:285491 original size:59 final size:59
Alignment explanation
Indices: 285373--286219 Score: 1110
Period size: 59 Copynumber: 14.4 Consensus size: 59
285363 TGTGCTTTTG
* * *
285373 AAGGTTGCCACTGACTTGTGGGCTTTTG--AAGAGGCCATTGACTTGTGGGCTTTGGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTTGAAAAGATGCCACTGACTTGTGGGCTTTGGAA
* *
285430 AAGGGTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACTGACTTGCGGGCTTTGGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTTGAAAAGATGCCACTGACTTGTGGGCTTTGGAA
* *
285489 AAGGGTGCCACTAACTTGTGGGCTTTTGAAAAGATACCACTGACTTGTGGGCTTTGGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTTGAAAAGATGCCACTGACTTGTGGGCTTTGGAA
* * *
285548 AAGGGTGCCATTGACTTATGGGCTTTTGAAAAGATACCACTGACTTGT-GG--TTGGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTTGAAAAGATGCCACTGACTTGTGGGCTTTGGAA
* * * *
285604 AA-GATGCCACTGACTTGTGGGCTTTGGAAAAGATGTCACAGACTTGTGGGCTTTGGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTTGAAAAGATGCCACTGACTTGTGGGCTTTGGAA
* * *
285662 AAGGGTGCCACTGACTTATGGGCTTTTGAAAAGATACCATTGACTTGTGGGCTTTGGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTTGAAAAGATGCCACTGACTTGTGGGCTTTGGAA
* * * *
285721 AAGGGTGCCACTGACTTGTGGGCTTTGGAAAAGGGTACCACTAACTTGTGGGCTTTGGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTTGAAAA-GATGCCACTGACTTGTGGGCTTTGGAA
* * *
285781 AAGGGTACCACTGACTTGTGGACTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTTGAAAA-GATGCCACTGACTTGTGGGCTTTGGAA
* * *
285841 AA-GATGCCACTGACTTGTGGGCTTTGGAAAAAGGTGCCACTGACTTGTGGGCTTTGGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTTG-AAAAGATGCCACTGACTTGTGGGCTTTGGAA
* * * *
285900 AAAGGTGCCACTGACTTGT-GGC-TTTG-AAGGTTGCCACTGACTTGTGGGCTTTGAGAG
1 AAGGGTGCCACTGACTTGTGGGCTTTTGAAAAGATGCCACTGACTTGTGGGCTTTG-GAA
* * * *
285957 AAGGGTGCCACTGATTTTTGGGCTTTTG-AAGGTTGCCACTGACTTGTGGGCTTTGGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTTGAAAAGATGCCACTGACTTGTGGGCTTTGGAA
* *
286015 AA-GATGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACTGACTTGTGGGCTTTGGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTTGAAAAGATGCCACTGACTTGTGGGCTTTGGAA
* * *
286073 AAGGGTGCCACTGACTTATGGGC-TTTGAGAGAAGGGTGCCACTGACTTGTGGGCTTTGAGAG
1 AAGGGTGCCACTGACTTGTGGGCTTTTGA-A-AA-GATGCCACTGACTTGTGGGCTTTG-GAA
* * * *
286135 AAGGGTGCCACTGATTTGTGGGCTTTTG-AAGGTTGCCACTGACTTGTGGGCTTTGGGAG
1 AAGGGTGCCACTGACTTGTGGGCTTTTGAAAAGATGCCACTGACTTGTGGGCTTT-GGAA
*
286194 AAGGGTGCCACTGATTTGTGGGCTTT
1 AAGGGTGCCACTGACTTGTGGGCTTT
286220 AAAAAAGAGT
Statistics
Matches: 706, Mismatches: 64, Indels: 38
0.87 0.08 0.05
Matches are distributed among these distances:
55 38 0.05
56 35 0.05
57 65 0.09
58 54 0.08
59 359 0.51
60 104 0.15
61 24 0.03
62 23 0.03
63 4 0.01
ACGTcount: A:0.22, C:0.16, G:0.32, T:0.29
Consensus pattern (59 bp):
AAGGGTGCCACTGACTTGTGGGCTTTTGAAAAGATGCCACTGACTTGTGGGCTTTGGAA
Found at i:287687 original size:7 final size:7
Alignment explanation
Indices: 287655--287759 Score: 94
Period size: 7 Copynumber: 14.7 Consensus size: 7
287645 ATCCGGACCC
287655 TTTTTGT
1 TTTTTGT
287662 TGTTGTTG-
1 T-TT-TTGT
287670 TTTTTG-
1 TTTTTGT
287676 TTTTTGT
1 TTTTTGT
287683 ATTTTT-T
1 -TTTTTGT
*
287690 TGCTTTGT
1 T-TTTTGT
287698 TTTTTGT
1 TTTTTGT
287705 TTTTTGTT
1 TTTTTG-T
287713 TTTTTGT
1 TTTTTGT
287720 TTTTTG-
1 TTTTTGT
287726 TTTTTGT
1 TTTTTGT
*
287733 TTTTTTT
1 TTTTTGT
287740 TGTTTTGT
1 T-TTTTGT
287748 TTTGTT-T
1 TTT-TTGT
287755 TTTTT
1 TTTTT
287760 TTGTGGAGGA
Statistics
Matches: 84, Mismatches: 4, Indels: 21
0.77 0.04 0.19
Matches are distributed among these distances:
6 18 0.21
7 38 0.45
8 25 0.30
9 3 0.04
ACGTcount: A:0.01, C:0.01, G:0.15, T:0.83
Consensus pattern (7 bp):
TTTTTGT
Found at i:287701 original size:1 final size:1
Alignment explanation
Indices: 287697--287761 Score: 58
Period size: 1 Copynumber: 65.0 Consensus size: 1
287687 TTTTGCTTTG
* * * * * * * *
287697 TTTTTTGTTTTTTGTTTTTTTGTTTTTTGTTTTTGTTTTTTTTTGTTTTGTTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
287762 GTGGAGGACG
Statistics
Matches: 48, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (1 bp):
T
Found at i:287701 original size:22 final size:21
Alignment explanation
Indices: 287655--287760 Score: 108
Period size: 21 Copynumber: 4.9 Consensus size: 21
287645 ATCCGGACCC
* *
287655 TTTTTGTTGTTGTTGTTTTTG-
1 TTTTTGTT-TTTTTTTTTTTGT
**
287676 TTTTTGTATTTTTTTGCTTTGT
1 TTTTTGT-TTTTTTTTTTTTGT
287698 TTTTTGTTTTTTGTTTTTTTGT
1 TTTTTGTTTTTT-TTTTTTTGT
287720 TTTTTGTTTTTGTTTTTTTT-T
1 TTTTTGTTTTT-TTTTTTTTGT
*
287741 GTTTTGTTTTGTTTTTTTTT
1 TTTTTGTTTT-TTTTTTTTT
287761 TGTGGAGGAC
Statistics
Matches: 73, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
21 38 0.52
22 34 0.47
23 1 0.01
ACGTcount: A:0.01, C:0.01, G:0.15, T:0.83
Consensus pattern (21 bp):
TTTTTGTTTTTTTTTTTTTGT
Found at i:287729 original size:50 final size:51
Alignment explanation
Indices: 287655--287763 Score: 154
Period size: 50 Copynumber: 2.2 Consensus size: 51
287645 ATCCGGACCC
287655 TTTTTGTTGTTGTTGTTTTTGTTTTTGTATTTTTTTGCTTTGTTTT-TTGT
1 TTTTTGTTGTTGTTGTTTTTGTTTTTGTATTTTTTTGCTTTGTTTTGTTGT
* * *
287705 TTTTTGTT-TTTTTGTTTTTTGTTTTTGTTTTTTTTTGTTTTGTTTTGTT-T
1 TTTTTGTTGTTGTTG-TTTTTGTTTTTGTATTTTTTTGCTTTGTTTTGTTGT
287755 TTTTT-TTGT
1 TTTTTGTTGT
287764 GGAGGACGCC
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
49 7 0.13
50 44 0.83
51 2 0.04
ACGTcount: A:0.01, C:0.01, G:0.16, T:0.83
Consensus pattern (51 bp):
TTTTTGTTGTTGTTGTTTTTGTTTTTGTATTTTTTTGCTTTGTTTTGTTGT
Found at i:287755 original size:15 final size:14
Alignment explanation
Indices: 287655--287759 Score: 108
Period size: 15 Copynumber: 7.4 Consensus size: 14
287645 ATCCGGACCC
*
287655 TTTTTGTTGTTGTTG
1 TTTTTGTT-TTGTTT
287670 TTTTTGTTTTTGTATT
1 TTTTTG-TTTTGT-TT
*
287686 TTTTTGCTTTGTTT
1 TTTTTGTTTTGTTT
287700 TTTGTT-TTTTG-TT
1 TTT-TTGTTTTGTTT
*
287713 TTTTTGTTTT-TTG
1 TTTTTGTTTTGTTT
*
287726 TTTTTGTTTTTTTT
1 TTTTTGTTTTGTTT
287740 TGTTTTGTTTTGTTT
1 T-TTTTGTTTTGTTT
287755 TTTTT
1 TTTTT
287760 TTGTGGAGGA
Statistics
Matches: 77, Mismatches: 6, Indels: 15
0.79 0.06 0.15
Matches are distributed among these distances:
12 2 0.03
13 20 0.26
14 16 0.21
15 30 0.39
16 9 0.12
ACGTcount: A:0.01, C:0.01, G:0.15, T:0.83
Consensus pattern (14 bp):
TTTTTGTTTTGTTT
Found at i:287761 original size:22 final size:22
Alignment explanation
Indices: 287661--287761 Score: 90
Period size: 22 Copynumber: 4.8 Consensus size: 22
287651 ACCCTTTTTG
*
287661 TTGTTGTTGTTTTTGTTTTTGTAT
1 TTGTT-TTGTTTTTTTTTTTGT-T
* *
287685 TT-TTTTGCTTTGTTTTTTG--
1 TTGTTTTGTTTTTTTTTTTGTT
*
287704 TT-TTTTG-TTTTTTTGTT-TT
1 TTGTTTTGTTTTTTTTTTTGTT
*
287723 TTGTTTT-TGTTTTTTTTTGTT
1 TTGTTTTGTTTTTTTTTTTGTT
287744 TTGTTTTGTTTTTTTTTT
1 TTGTTTTGTTTTTTTTTT
287762 GTGGAGGACG
Statistics
Matches: 63, Mismatches: 8, Indels: 14
0.74 0.09 0.16
Matches are distributed among these distances:
18 8 0.13
19 9 0.14
20 12 0.19
21 9 0.14
22 21 0.33
23 2 0.03
24 2 0.03
ACGTcount: A:0.01, C:0.01, G:0.15, T:0.83
Consensus pattern (22 bp):
TTGTTTTGTTTTTTTTTTTGTT
Found at i:301696 original size:52 final size:52
Alignment explanation
Indices: 301548--301676 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
301538 CGAAATATGA
301548 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* *
301600 CAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
301652 AAATTTGCCTGCATGTATCAATACA
1 AAATTTGCCTGCATGTATCGATACA
301677 AAGATCAGTG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:301703 original size:13 final size:13
Alignment explanation
Indices: 301685--301709 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
301675 CAAAGATCAG
301685 TGTATCGATACAA
1 TGTATCGATACAA
301698 TGTATCGATACA
1 TGTATCGATACA
301710 TTTTTTGGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:301765 original size:31 final size:31
Alignment explanation
Indices: 301727--301806 Score: 142
Period size: 31 Copynumber: 2.6 Consensus size: 31
301717 GCAGTAAGCT
301727 TACATTGTATCGATACAAAACTATATATCGA
1 TACATTGTATCGATACAAAACTATATATCGA
* *
301758 TACATTGTATCGATACAACACTATGTATCGA
1 TACATTGTATCGATACAAAACTATATATCGA
301789 TACATTGTATCGATACAA
1 TACATTGTATCGATACAA
301807 TATTTTATGA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (31 bp):
TACATTGTATCGATACAAAACTATATATCGA
Found at i:301770 original size:13 final size:13
Alignment explanation
Indices: 301752--301805 Score: 63
Period size: 13 Copynumber: 3.8 Consensus size: 13
301742 CAAAACTATA
301752 TATCGATACATTG
1 TATCGATACATTG
301765 TATCGATACAACACTATG
1 TATCGAT---ACA-T-TG
301783 TATCGATACATTG
1 TATCGATACATTG
301796 TATCGATACA
1 TATCGATACA
301806 ATATTTTATG
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
13 19 0.53
14 1 0.03
15 3 0.08
16 3 0.08
17 1 0.03
18 9 0.25
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (13 bp):
TATCGATACATTG
Found at i:301786 original size:18 final size:18
Alignment explanation
Indices: 301732--301792 Score: 69
Period size: 18 Copynumber: 3.7 Consensus size: 18
301722 AAGCTTACAT
*
301732 TGTATCGATACAAAACTA
1 TGTATCGATACAACACTA
*
301750 TATATCGAT---ACA-T-
1 TGTATCGATACAACACTA
301763 TGTATCGATACAACACTA
1 TGTATCGATACAACACTA
301781 TGTATCGATACA
1 TGTATCGATACA
301793 TTGTATCGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
13 8 0.23
14 1 0.03
15 2 0.06
16 3 0.09
17 1 0.03
18 20 0.57
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.31
Consensus pattern (18 bp):
TGTATCGATACAACACTA
Found at i:302673 original size:13 final size:13
Alignment explanation
Indices: 302657--302699 Score: 86
Period size: 13 Copynumber: 3.3 Consensus size: 13
302647 ATACATTGTT
302657 CATTGTATCGATA
1 CATTGTATCGATA
302670 CATTGTATCGATA
1 CATTGTATCGATA
302683 CATTGTATCGATA
1 CATTGTATCGATA
302696 CATT
1 CATT
302700 CTGGGTTTAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:304772 original size:51 final size:51
Alignment explanation
Indices: 304696--304813 Score: 130
Period size: 51 Copynumber: 2.3 Consensus size: 51
304686 TTCATCTCGG
* * * **
304696 GGATACTCCAATCCCGGTTCCATTTCCAAAACATCAATTTTTCTTAATCGA
1 GGATACTCCAATCCCGATTCCATTTCCAAAACACCAATTTTCCACAATCGA
* ** * *
304747 GGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTCCACAATCGA
1 GGATACTCCAATCCCGATTCCATTTCCAAAACACCAATTTTCCACAATCGA
304798 -GAGTACTCCAATCCCG
1 GGA-TACTCCAATCCCG
304814 TTATTTCATC
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
50 2 0.04
51 53 0.96
ACGTcount: A:0.31, C:0.29, G:0.10, T:0.31
Consensus pattern (51 bp):
GGATACTCCAATCCCGATTCCATTTCCAAAACACCAATTTTCCACAATCGA
Found at i:304855 original size:28 final size:28
Alignment explanation
Indices: 304801--304861 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
304791 CAATCGAGAG
*
304801 TACTCCAATCCCGTTATTTCATCGGGGA
1 TACTCCAATCCCGTTATTTCATAGGGGA
304829 TACTCCAATCCCGTTATTTC-TGAGGGGA
1 TACTCCAATCCCGTTATTTCAT-AGGGGA
*
304857 AACTC
1 TACTC
304862 TAACCTCGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 1 0.03
28 29 0.97
ACGTcount: A:0.23, C:0.28, G:0.18, T:0.31
Consensus pattern (28 bp):
TACTCCAATCCCGTTATTTCATAGGGGA
Found at i:304923 original size:51 final size:51
Alignment explanation
Indices: 304868--304971 Score: 165
Period size: 51 Copynumber: 2.0 Consensus size: 51
304858 ACTCTAACCT
* *
304868 CGATTTTA-TTTCTAAAATACCAATTTTTCACAAGCGGGGATACTCCAACTC
1 CGATTTTATTTTC-AAAACACCAATTTCTCACAAGCGGGGATACTCCAACTC
*
304919 CGATTTTATTTTCAAAACACCAATTTCTCACAATCGGGGATACTCCAACTC
1 CGATTTTATTTTCAAAACACCAATTTCTCACAAGCGGGGATACTCCAACTC
304970 CG
1 CG
304972 TTATTTTTGT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
51 45 0.92
52 4 0.08
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.32
Consensus pattern (51 bp):
CGATTTTATTTTCAAAACACCAATTTCTCACAAGCGGGGATACTCCAACTC
Found at i:305123 original size:78 final size:79
Alignment explanation
Indices: 304903--305210 Score: 379
Period size: 79 Copynumber: 3.9 Consensus size: 79
304893 TTTCACAAGC
* *
304903 GGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAA-TTTCTCACAATCGGGGATACTCCAA
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTC-CACAATCAGGGATACTCCAA
* * *
304967 CTCCGTTATTTTTGT
65 CCCCGTTATTTTCGA
*** * * *
304982 GGGGATACTCCAACCCCGGCCTTA-TTTCTAAAGCATCGATTTTCCACAATCAGGGATACTCCAA
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAACACCAATTTTCCACAATCAGGGATACTCCAA
305046 CCCCGTTATTTTCGA
65 CCCCGTTATTTTCGA
* *
305061 GGGGATACTCC-ACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCAGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCCACAATCAGGGATACTCCAAC
* *
305125 CCTGTTATTTCCGA
66 CCCGTTATTTTCGA
* *** * *
305139 GGGGATACTCCAACCCCGATTTTATTTTCAAAATATTGATTTTCCATAATCAGGGGATACTCCAG
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCCACAATCA-GGGATACTCCAA
305204 CCCCGTT
65 CCCCGTT
305211 GTCATCTCCA
Statistics
Matches: 196, Mismatches: 28, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
78 67 0.34
79 108 0.55
80 21 0.11
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (79 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCCACAATCAGGGATACTCCAAC
CCCGTTATTTTCGA
Found at i:305124 original size:157 final size:159
Alignment explanation
Indices: 304903--305210 Score: 428
Period size: 157 Copynumber: 1.9 Consensus size: 159
304893 TTTCACAAGC
* *
304903 GGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTCTCACAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTCTCACAATCAGGGATACTCCAAC
** * * *
304968 TCC-GTTATTTTTGTGGGGATACTCCAACCCCGGCCTTA-TTTCTAAAGCATCGATTTTCCACAA
66 -CCTGTTATTTCCGAGGGGATACTCCAACCCCGACCTTATTTTC-AAAACATCGATTTTCCACAA
305031 TCA-GGGATACTCCAACCCCGTTATTTTCGA
129 TCAGGGGATACTCCAACCCCGTTATTTTCGA
*
305061 GGGGATACTCC-ACCCCGATTTTATTTTCAAAACACCAATTT-TCTATAATCAGGGATACTCCAA
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTCTC-ACAATCAGGGATACTCCAA
** * * *
305124 CCCTGTTATTTCCGAGGGGATACTCCAACCCCGATTTTATTTTCAAAATATTGATTTTCCATAAT
65 CCCTGTTATTTCCGAGGGGATACTCCAACCCCGACCTTATTTTCAAAACATCGATTTTCCACAAT
*
305189 CAGGGGATACTCCAGCCCCGTT
130 CAGGGGATACTCCAACCCCGTT
305211 GTCATCTCCA
Statistics
Matches: 132, Mismatches: 14, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
156 4 0.03
157 95 0.72
158 33 0.25
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (159 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTCTCACAATCAGGGATACTCCAAC
CCTGTTATTTCCGAGGGGATACTCCAACCCCGACCTTATTTTCAAAACATCGATTTTCCACAATC
AGGGGATACTCCAACCCCGTTATTTTCGA
Done.