Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold300
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: 363256
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 2 of 3
Found at i:174457 original size:12 final size:12
Alignment explanation
Indices: 174440--174464 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
174430 AATAATCATC
174440 ATAATGACAAGT
1 ATAATGACAAGT
174452 ATAATGACAAGT
1 ATAATGACAAGT
174464 A
1 A
174465 AAAGAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.16, T:0.24
Consensus pattern (12 bp):
ATAATGACAAGT
Found at i:175998 original size:12 final size:12
Alignment explanation
Indices: 175981--176009 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
175971 TTTTTAAAAT
175981 ATATATATATAC
1 ATATATATATAC
175993 ATATATATATAC
1 ATATATATATAC
176005 ATATA
1 ATATA
176010 AATAAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATATATATAC
Found at i:177784 original size:33 final size:33
Alignment explanation
Indices: 177747--177816 Score: 90
Period size: 33 Copynumber: 2.1 Consensus size: 33
177737 TAATTTTATG
*
177747 ATATAAATATTATAAAAATTAAA-ATAAA-ATATA
1 ATATAAA-AATATAAAAA-TAAATATAAATATATA
*
177780 ATATAAAAATATAAATATAAATATAAATATATA
1 ATATAAAAATATAAAAATAAATATAAATATATA
177813 ATAT
1 ATAT
177817 TTATATAACT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 4 0.12
32 13 0.39
33 16 0.48
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (33 bp):
ATATAAAAATATAAAAATAAATATAAATATATA
Found at i:177786 original size:24 final size:26
Alignment explanation
Indices: 177757--177810 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
177747 ATATAAATAT
177757 TATAAAAAT-TAAA-ATAAA-ATATAA
1 TATAAAAATATAAATATAAATATA-AA
177781 TATAAAAATATAAATATAAATATAAA
1 TATAAAAATATAAATATAAATATAAA
177807 TATA
1 TATA
177811 TAATATTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
24 9 0.33
25 4 0.15
26 11 0.41
27 3 0.11
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (26 bp):
TATAAAAATATAAATATAAATATAAA
Found at i:177797 original size:6 final size:6
Alignment explanation
Indices: 177747--177899 Score: 66
Period size: 6 Copynumber: 24.7 Consensus size: 6
177737 TAATTTTATG
* * *
177747 ATATAA ATAT-T ATAAAA AT-TAA A-ATAAA ATATAA TATAAAA ATATAA
1 ATATAA ATATAA ATATAA ATATAA ATAT-AA ATATAA -ATATAA ATATAA
** *
177794 ATATAA ATATAA ATATATA ATATTT ATATAA CT-TAA ATTATTAA TATATCAA
1 ATATAA ATATAA ATATA-A ATATAA ATATAA ATATAA A-TA-TAA -ATAT-AA
** * * *
177846 A-ATTT ATATAA ATATATA ATATTTTAA ATAT-A ATACAA ATATAT ATATAT
1 ATATAA ATATAA ATATA-A ATA---TAA ATATAA ATATAA ATATAA ATATAA
177896 ATAT
1 ATAT
177900 TTTTTTTGAC
Statistics
Matches: 111, Mismatches: 19, Indels: 34
0.68 0.12 0.21
Matches are distributed among these distances:
5 15 0.14
6 64 0.58
7 18 0.16
8 7 0.06
9 5 0.05
10 2 0.02
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (6 bp):
ATATAA
Found at i:177802 original size:20 final size:20
Alignment explanation
Indices: 177757--177813 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
177747 ATATAAATAT
* *
177757 TATAAAAATTAAAATA-AAA
1 TATAAATATAAAAATATAAA
177776 TAT-AATATAAAAATATAAA
1 TATAAATATAAAAATATAAA
*
177795 TATAAATATAAATATATAA
1 TATAAATATAAAAATATAA
177814 TATTTATATA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 10 0.30
19 9 0.27
20 14 0.42
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
TATAAATATAAAAATATAAA
Found at i:186467 original size:29 final size:27
Alignment explanation
Indices: 186435--186496 Score: 63
Period size: 29 Copynumber: 2.2 Consensus size: 27
186425 CATTATCTAA
186435 TAAATTTAAATTAATTTT-TGATAAAAAT
1 TAAATTTAAATTAATTTTAT-A-AAAAAT
** *
186463 GTAAAAATCAATTAATTTTATAAAAAAT
1 -TAAATTTAAATTAATTTTATAAAAAAT
186491 TAAATT
1 TAAATT
186497 AGTTAATGAG
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
27 4 0.15
28 6 0.22
29 16 0.59
30 1 0.04
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (27 bp):
TAAATTTAAATTAATTTTATAAAAAAT
Found at i:186681 original size:14 final size:14
Alignment explanation
Indices: 186664--186697 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
186654 ACTACGCGAA
186664 TATAAATATTTTAC
1 TATAAATATTTTAC
*
186678 TAT-AATATTTTAT
1 TATAAATATTTTAC
186691 TATAAAT
1 TATAAAT
186698 TATAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (14 bp):
TATAAATATTTTAC
Found at i:187827 original size:11 final size:11
Alignment explanation
Indices: 187767--187829 Score: 65
Period size: 11 Copynumber: 5.6 Consensus size: 11
187757 TTGATAATTT
187767 TAAATATAATA
1 TAAATATAATA
* *
187778 TAAACATGATA
1 TAAATATAATA
*
187789 TAAAAAATAAT-
1 T-AAATATAATA
187800 TAAAATATAATA
1 T-AAATATAATA
*
187812 AAAATATAATA
1 TAAATATAATA
187823 TAAATAT
1 TAAATAT
187830 TTAAATATAT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
11 36 0.84
12 7 0.16
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (11 bp):
TAAATATAATA
Found at i:187839 original size:16 final size:17
Alignment explanation
Indices: 187819--187860 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
187809 ATAAAAATAT
187819 AATATAAATATTTA-AA
1 AATATAAATATTTATAA
*
187835 TATATCAAA-ATTTATAA
1 AATAT-AAATATTTATAA
187852 AATATAAAT
1 AATATAAAT
187861 TAAAAAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (17 bp):
AATATAAATATTTATAA
Found at i:190774 original size:47 final size:45
Alignment explanation
Indices: 190705--190797 Score: 143
Period size: 47 Copynumber: 2.0 Consensus size: 45
190695 ATATATATAC
*
190705 ATATATATTAATATATATAATTGGATTAATTAGAAGTCTT-GATTA
1 ATATATATTAATATATAAAATTGGATTAATTAGAAGT-TTCGATTA
190750 ATATATATATATATATATAAAATTGGATTAATTAGAAGTTTCGATTA
1 ATATATAT-TA-ATATATAAAATTGGATTAATTAGAAGTTTCGATTA
190797 A
1 A
190798 GAATAGTTGC
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
45 8 0.18
46 4 0.09
47 32 0.73
ACGTcount: A:0.44, C:0.02, G:0.11, T:0.43
Consensus pattern (45 bp):
ATATATATTAATATATAAAATTGGATTAATTAGAAGTTTCGATTA
Found at i:194083 original size:15 final size:15
Alignment explanation
Indices: 194059--194089 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
194049 ATTTATTAAA
*
194059 ATATTTTATATATTT
1 ATATTATATATATTT
194074 ATATTATATATATTT
1 ATATTATATATATTT
194089 A
1 A
194090 AATTTAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
ATATTATATATATTT
Found at i:195719 original size:2 final size:2
Alignment explanation
Indices: 195712--195750 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
195702 TAAAGTGGTG
195712 AT AT AT 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 AT AT AT A
195751 AATTCTTTGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:195856 original size:2 final size:2
Alignment explanation
Indices: 195849--195884 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
195839 CATGCCATGG
* *
195849 AT AT AT AT AT AT AT AT AT AT AT GT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
195885 GTGCCTTTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
AT
Found at i:196195 original size:31 final size:31
Alignment explanation
Indices: 196160--196240 Score: 90
Period size: 33 Copynumber: 2.5 Consensus size: 31
196150 ACGACTGTAC
* *
196160 TAATAAGATTTTTAAAAAAATTAAAAATAAT
1 TAATAAAATTTTTAAAAAAATAAAAAATAAT
* *
196191 TAATAATTATTTTTTAAAAAAATAAAAAATTAT
1 TAATAA--AATTTTTAAAAAAATAAAAAATAAT
**
196224 TTTTAAAATTTTTAAAA
1 TAATAAAATTTTTAAAA
196241 GTAAATATTT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
31 16 0.39
33 25 0.61
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (31 bp):
TAATAAAATTTTTAAAAAAATAAAAAATAAT
Found at i:196229 original size:22 final size:24
Alignment explanation
Indices: 196180--196231 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
196170 TTTAAAAAAA
* *
196180 TTAAAAATAATTAATAATTATTTT
1 TTAAAAATAATAAAAAATTATTTT
196204 TTAAAAA-AATAAAAAATTA-TTT
1 TTAAAAATAATAAAAAATTATTTT
196226 TTAAAA
1 TTAAAA
196232 TTTTTAAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 9 0.35
23 10 0.38
24 7 0.27
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
TTAAAAATAATAAAAAATTATTTT
Found at i:196325 original size:19 final size:19
Alignment explanation
Indices: 196301--196338 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
196291 AAGATGATAT
196301 TTATTTGTAATATTATTAA
1 TTATTTGTAATATTATTAA
*
196320 TTATTTTTAATATTATTAA
1 TTATTTGTAATATTATTAA
196339 ATTAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (19 bp):
TTATTTGTAATATTATTAA
Found at i:197412 original size:2 final size:2
Alignment explanation
Indices: 197405--197442 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
197395 TTAACTAACC
197405 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
197443 TATCATTATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:197857 original size:2 final size:2
Alignment explanation
Indices: 197850--197886 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
197840 ATCATACATG
* *
197850 TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
197887 GTAAGAGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:198185 original size:3 final size:3
Alignment explanation
Indices: 198177--198219 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
198167 AAACAAACAA
198177 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
198220 TAATTAAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:198422 original size:2 final size:2
Alignment explanation
Indices: 198417--198442 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
198407 ATATACACAC
198417 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
198443 TGGTCCAACG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:204697 original size:5 final size:5
Alignment explanation
Indices: 204674--204707 Score: 50
Period size: 5 Copynumber: 6.4 Consensus size: 5
204664 TCTCCCCAGA
204674 TTCTC TCTCTC TCTCTC TTCTC TTCTC TTCTC TT
1 TTCTC T-TCTC T-TCTC TTCTC TTCTC TTCTC TT
204708 TCCTCTCCCC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 17 0.61
6 11 0.39
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (5 bp):
TTCTC
Found at i:205192 original size:20 final size:19
Alignment explanation
Indices: 205154--205193 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
205144 AATTCAGATT
* *
205154 TTATTTTTTATAAATTAAA
1 TTATTTTTTAAAAAATAAA
205173 TTATTTTTTACAAAAATAAA
1 TTATTTTTTA-AAAAATAAA
205193 T
1 T
205194 ATAAAAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (19 bp):
TTATTTTTTAAAAAATAAA
Found at i:205454 original size:17 final size:16
Alignment explanation
Indices: 205427--205468 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
205417 TATTTGTATA
*
205427 AAAATATTATTTTAATT
1 AAAATA-TATTATAATT
205444 AATAATATATTATAATT
1 AA-AATATATTATAATT
205461 AAAATATA
1 AAAATATA
205469 ACGTAAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 6 0.26
17 13 0.57
18 4 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AAAATATATTATAATT
Found at i:206424 original size:16 final size:16
Alignment explanation
Indices: 206399--206433 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
206389 TAAAATTTAA
206399 ATTTTATTTA-AAATT
1 ATTTTATTTATAAATT
206414 ATTTATATTTATAAATT
1 ATTT-TATTTATAAATT
206431 ATT
1 ATT
206434 AACCTAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 6 0.33
17 8 0.44
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
ATTTTATTTATAAATT
Found at i:209156 original size:22 final size:22
Alignment explanation
Indices: 209131--209173 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
209121 TAATTTTATT
*
209131 AAATTAATT-TTTATAATTAATA
1 AAATAAATTATTTAT-ATTAATA
209153 AAATAAATTATTTATATTAAT
1 AAATAAATTATTTATATTAAT
209174 TTTATTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
AAATAAATTATTTATATTAATA
Found at i:209362 original size:23 final size:24
Alignment explanation
Indices: 209306--209376 Score: 58
Period size: 23 Copynumber: 2.9 Consensus size: 24
209296 AAATAATTTA
*
209306 ATTTATTAA-TAATACAAATTTAATG
1 ATTTA-TAATTAATA-AAATTAAATG
*
209331 ATGTA-AATTAATAAAATTAAAT-
1 ATTTATAATTAATAAAATTAAATG
209353 ATTTATAATTTATATAAAAATTAA
1 ATTTATAA-TTA-AT-AAAATTAA
209377 TGCTAAATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
22 4 0.11
23 12 0.32
24 8 0.21
25 6 0.16
26 8 0.21
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (24 bp):
ATTTATAATTAATAAAATTAAATG
Found at i:210596 original size:23 final size:23
Alignment explanation
Indices: 210553--210603 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
210543 AGTATAATTT
* *
210553 TAAAATTATAAACATTTAATATA
1 TAAAATTATAAACATTCAATAAA
*
210576 TAAAATTTGTAAACA-TCAATAAA
1 TAAAA-TTATAAACATTCAATAAA
210599 TAAAA
1 TAAAA
210604 CATTAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 16 0.67
24 8 0.33
ACGTcount: A:0.59, C:0.06, G:0.02, T:0.33
Consensus pattern (23 bp):
TAAAATTATAAACATTCAATAAA
Found at i:210893 original size:21 final size:21
Alignment explanation
Indices: 210867--210917 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
210857 AATAATACGG
*
210867 TATTAATATTATTTTGATTT-A
1 TATTAATATTATTAT-ATTTAA
* *
210888 TTTTAAAATTATTATATTTAA
1 TATTAATATTATTATATTTAA
210909 TATTAATAT
1 TATTAATAT
210918 ATAAATTTAT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
20 4 0.17
21 20 0.83
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
TATTAATATTATTATATTTAA
Found at i:210989 original size:11 final size:11
Alignment explanation
Indices: 210973--211002 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
210963 ATTTTATATT
210973 TTAAATTTAAA
1 TTAAATTTAAA
*
210984 TTAAATTAAAA
1 TTAAATTTAAA
210995 TTAAATTT
1 TTAAATTT
211003 TATAATCACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:211637 original size:30 final size:31
Alignment explanation
Indices: 211589--211655 Score: 127
Period size: 30 Copynumber: 2.2 Consensus size: 31
211579 TTAAAATATT
211589 ATATATTTATATAAATTTTAATATATTAATA
1 ATATATTTATATAAATTTTAATATATTAATA
211620 ATATATTTATA-AAATTTTAATATATTAATA
1 ATATATTTATATAAATTTTAATATATTAATA
211650 ATATAT
1 ATATAT
211656 ATTTATATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 25 0.69
31 11 0.31
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (31 bp):
ATATATTTATATAAATTTTAATATATTAATA
Found at i:211660 original size:22 final size:21
Alignment explanation
Indices: 211565--211660 Score: 66
Period size: 19 Copynumber: 4.9 Consensus size: 21
211555 GTAGGTTTTT
*
211565 TATTATAAT-TATATTTAAAA
1 TATTATAATATATATTTAATA
* *
211585 TATTAT-ATATTTATATAA-A
1 TATTATAATATATATTTAATA
*
211604 T-TT-TAATATAT-TAATAATA
1 TATTATAATATATAT-TTAATA
211623 TATTTATAA-A-AT-TTTAATA
1 TA-TTATAATATATATTTAATA
211642 TATTAATAATATATATTTA
1 TATT-ATAATATATATTTA
211661 TATTATATAT
Statistics
Matches: 61, Mismatches: 4, Indels: 20
0.72 0.05 0.24
Matches are distributed among these distances:
17 2 0.03
18 13 0.21
19 17 0.28
20 17 0.28
21 5 0.08
22 7 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TATTATAATATATATTTAATA
Found at i:211667 original size:11 final size:11
Alignment explanation
Indices: 211589--211674 Score: 74
Period size: 11 Copynumber: 8.0 Consensus size: 11
211579 TTAAAATATT
211589 ATATATTTAT-
1 ATATATTTATA
*
211599 ATAAATTT-TA
1 ATATATTTATA
*
211609 ATATATTAATA
1 ATATATTTATA
211620 ATATATTTATA
1 ATATATTTATA
211631 A-A-ATTT-TA
1 ATATATTTATA
*
211639 ATATATTAATAA
1 ATATATTTAT-A
211651 TATATATTTATA
1 -ATATATTTATA
*
211663 TTATATATTATA
1 ATATAT-TTATA
211675 CTTATATAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
8 3 0.05
9 6 0.10
10 17 0.28
11 19 0.31
12 7 0.11
13 9 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
ATATATTTATA
Found at i:211679 original size:13 final size:13
Alignment explanation
Indices: 211639--211682 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
211629 TAAAATTTTA
* *
211639 ATATATTAATAAT
1 ATATATTTATATT
211652 ATATATTTATATT
1 ATATATTTATATT
211665 ATATA-TTATACTT
1 ATATATTTATA-TT
211678 ATATA
1 ATATA
211683 AAAATATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 5 0.18
13 23 0.82
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (13 bp):
ATATATTTATATT
Found at i:211694 original size:21 final size:21
Alignment explanation
Indices: 211665--211705 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
211655 TATTTATATT
**
211665 ATATATTATACTTATATAAAA
1 ATATATTATAAATATATAAAA
*
211686 ATATTTTATAAATATATAAA
1 ATATATTATAAATATATAAA
211706 TTTTAAAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
ATATATTATAAATATATAAAA
Found at i:212222 original size:2 final size:2
Alignment explanation
Indices: 212215--212242 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
212205 CTACCATCCA
212215 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
212243 TTGTTTTTCT
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):
AT
Found at i:212466 original size:18 final size:18
Alignment explanation
Indices: 212445--212496 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
212435 GTAGTCTTTA
212445 ATATGTATATATTTATTT
1 ATATGTATATATTTATTT
*
212463 ATATGTATGTATTT-TTT
1 ATATGTATATATTTATTT
*
212480 -TATTTATAT-TTTATTT
1 ATATGTATATATTTATTT
212496 A
1 A
212497 GAAAAGTGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 3 0.10
16 10 0.34
17 3 0.10
18 13 0.45
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATGTATATATTTATTT
Found at i:212472 original size:22 final size:22
Alignment explanation
Indices: 212446--212488 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
212436 TAGTCTTTAA
212446 TATGTATATATTTATTTATATG
1 TATGTATATATTTATTTATATG
* *
212468 TATGTATTTTTTTATTTATAT
1 TATGTATATATTTATTTATAT
212489 TTTATTTAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (22 bp):
TATGTATATATTTATTTATATG
Found at i:213731 original size:22 final size:20
Alignment explanation
Indices: 213706--213746 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
213696 TACTGAAATA
*
213706 ATTTTATTAATATATTATTTTT
1 ATTTTATAAAT-TATT-TTTTT
213728 ATTTTATAAATTATTTTTT
1 ATTTTATAAATTATTTTTT
213747 AATTATTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 4 0.22
22 10 0.56
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
ATTTTATAAATTATTTTTTT
Found at i:214122 original size:21 final size:21
Alignment explanation
Indices: 214054--214133 Score: 81
Period size: 21 Copynumber: 3.7 Consensus size: 21
214044 ATATCGTATT
*
214054 TATATATTTTTATATGTAATAA
1 TATATATTTTAATAT-TAATAA
* *
214076 T-TATATTTAATATATTAAAAA
1 TATATATTTTA-ATATTAATAA
*
214097 TTATATATTTTAATATTAATTA
1 -TATATATTTTAATATTAATAA
*
214119 TATAAATTTTAATAT
1 TATATATTTTAATAT
214134 ATTTATTTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
21 26 0.54
22 14 0.29
23 8 0.17
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (21 bp):
TATATATTTTAATATTAATAA
Found at i:214298 original size:36 final size:36
Alignment explanation
Indices: 214258--214328 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
214248 ATAAAATTTA
214258 ATAAAAATATTACAATAATTATACTTAATTATTTTT
1 ATAAAAATATTACAATAATTATACTTAATTATTTTT
* *
214294 ATAAAAATATTATAATAATTATATTTAATTATTTT
1 ATAAAAATATTACAATAATTATACTTAATTATTTT
214329 ATTATATAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (36 bp):
ATAAAAATATTACAATAATTATACTTAATTATTTTT
Found at i:223739 original size:26 final size:27
Alignment explanation
Indices: 223697--223747 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
223687 TAGGAGTGAA
*
223697 ATTATATTTTTATTTTTAA-TATAATT
1 ATTATATTTTTAATTTTAATTATAATT
223723 ATTAT-TTTTTAAATTTTAATTATAA
1 ATTATATTTTT-AATTTTAATTATAA
223748 AAAACTCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 5 0.23
26 12 0.55
27 5 0.23
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (27 bp):
ATTATATTTTTAATTTTAATTATAATT
Found at i:224358 original size:20 final size:20
Alignment explanation
Indices: 224335--224372 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
224325 TTAATTCTAA
*
224335 TTTTTTAATTTCTATTTATC
1 TTTTTAAATTTCTATTTATC
*
224355 TTTTTAAATTTTTATTTA
1 TTTTTAAATTTCTATTTA
224373 AAAAACGCTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTTTAAATTTCTATTTATC
Found at i:224465 original size:14 final size:15
Alignment explanation
Indices: 224448--224482 Score: 63
Period size: 14 Copynumber: 2.4 Consensus size: 15
224438 TTGATAATTT
224448 TAAATATAATTA-TA
1 TAAATATAATTAGTA
224462 TAAATATAATTAGTA
1 TAAATATAATTAGTA
224477 TAAATA
1 TAAATA
224483 ATTAAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (15 bp):
TAAATATAATTAGTA
Found at i:224933 original size:2 final size:2
Alignment explanation
Indices: 224926--224952 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
224916 TTATTTCAAG
224926 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 A
224953 CATCGTCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:227846 original size:20 final size:20
Alignment explanation
Indices: 227821--227876 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
227811 TTTACTCAGA
227821 TGTATCGATACATTGTTCAT
1 TGTATCGATACATTGTTCAT
* *
227841 TGTATCGACACATGGTTCAT
1 TGTATCGATACATTGTTCAT
227861 TGTATCGATACATTGT
1 TGTATCGATACATTGT
227877 ATGGATACAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATTGTTCAT
Found at i:227876 original size:13 final size:13
Alignment explanation
Indices: 227858--227887 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
227848 ACACATGGTT
227858 CATTGTATCGATA
1 CATTGTATCGATA
*
227871 CATTGTATGGATA
1 CATTGTATCGATA
227884 CATT
1 CATT
227888 CTGGGTTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:230254 original size:28 final size:28
Alignment explanation
Indices: 230212--230291 Score: 88
Period size: 28 Copynumber: 2.8 Consensus size: 28
230202 ATTCTAAATT
*
230212 TTTCATCTCGGGGATACTCCAACCCCGTTA
1 TTTCAT-T-GGGGATACTCCAACCCCATTA
*
230242 TTTCATTGGGGATACTCCAACCCTATTA
1 TTTCATTGGGGATACTCCAACCCCATTA
*** *
230270 TTTCGGAGGGGATACTCTAACC
1 TTTCATTGGGGATACTCCAACC
230292 TTGATTTTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
28 37 0.84
29 1 0.02
30 6 0.14
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.31
Consensus pattern (28 bp):
TTTCATTGGGGATACTCCAACCCCATTA
Found at i:230343 original size:79 final size:79
Alignment explanation
Indices: 230252--230450 Score: 263
Period size: 79 Copynumber: 2.5 Consensus size: 79
230242 TTTCATTGGG
* * * *** *
230252 GATACTCCAACCCTATTATTTCGGAGGGGATACTCTAACCTTGATTTTATTTCCAAAACACTAAT
1 GATACTCCAACCCTGTTATTTCAGAGGGGATACTCCAACCCCAATTTTATTTCCAAAACACAAAT
230317 TTTTCACAATCGAA
66 TTTTCACAATCGAA
** *
230331 GATACTCCAACCCTGTTATTTTTGAGGGGATACTCCAACCCCAATTTTATTTCTAAAACACAAAT
1 GATACTCCAACCCTGTTATTTCAGAGGGGATACTCCAACCCCAATTTTATTTCCAAAACACAAAT
**
230396 TTTTCACAATCGGG
66 TTTTCACAATCGAA
* **
230410 GATACTCCAACCCCGTTATTTCATCGGGGATACTCCAACCC
1 GATACTCCAACCCTGTTATTTCAGAGGGGATACTCCAACCC
230451 TGTTATTTCC
Statistics
Matches: 104, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
79 104 1.00
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.32
Consensus pattern (79 bp):
GATACTCCAACCCTGTTATTTCAGAGGGGATACTCCAACCCCAATTTTATTTCCAAAACACAAAT
TTTTCACAATCGAA
Found at i:230440 original size:28 final size:28
Alignment explanation
Indices: 230404--230480 Score: 113
Period size: 28 Copynumber: 2.8 Consensus size: 28
230394 ATTTTTCACA
230404 ATCGGGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
*
230432 ATCGGGGATACTCCAACCCTGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
230460 --CGAGAGGATACTCCAACCCCG
1 ATCG-G-GGATACTCCAACCCCG
230481 ATTTTATTTC
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
26 2 0.04
27 1 0.02
28 42 0.93
ACGTcount: A:0.23, C:0.32, G:0.19, T:0.25
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATTTC
Found at i:230442 original size:107 final size:108
Alignment explanation
Indices: 230331--230557 Score: 359
Period size: 107 Copynumber: 2.1 Consensus size: 108
230321 CACAATCGAA
** * *
230331 GATACTCCAACCCTGTTATTTTTGAGGGGATACTCCAACCCCAATTTTATTTCTAAAACA-CAAA
1 GATACTCCAACCCTGTTATTTCCGAGAGGATACTCCAACCCCAATTTTATTTCCAAAACACCAAA
*
230395 TTTTTCACAATCGGGGATACTCCAACCCCGTTA-TTTCATCGGG
66 TTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCA-AGGG
* *
230438 GATACTCCAACCCTGTTATTTCCGAGAGGATACTCCAACCCCGATTTTATTTCCAAAACACCAAT
1 GATACTCCAACCCTGTTATTTCCGAGAGGATACTCCAACCCCAATTTTATTTCCAAAACACCAAA
*
230503 TTTTTCACAATCGGGGATACTCCAACTCCGTTATTTTCAAGGG
66 TTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCAAGGG
230546 GATACTCCAACC
1 GATACTCCAACC
230558 TCGATTTTAT
Statistics
Matches: 110, Mismatches: 8, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
107 55 0.50
108 50 0.45
109 5 0.05
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (108 bp):
GATACTCCAACCCTGTTATTTCCGAGAGGATACTCCAACCCCAATTTTATTTCCAAAACACCAAA
TTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCAAGGG
Found at i:230527 original size:80 final size:80
Alignment explanation
Indices: 230432--230585 Score: 229
Period size: 80 Copynumber: 1.9 Consensus size: 80
230422 CCGTTATTTC
*
230432 ATCGGGGATACTCCAAC-CCTGTTATTTCCGAGAGGATACTCCAACCCCGATTTTATTTCCAAAA
1 ATCGGGGATACTCCAACTCC-GTTATTTCCAAGAGGATACTCCAACCCCGATTTTATTTCCAAAA
230496 CACCAATTTTTTCACA
65 CACCAATTTTTTCACA
* * * * *
230512 ATCGGGGATACTCCAACTCCGTTATTTTCAAGGGGATACTCCAACCTCGATTTTATTTTCAGAAC
1 ATCGGGGATACTCCAACTCCGTTATTTCCAAGAGGATACTCCAACCCCGATTTTATTTCCAAAAC
*
230577 ACCGATTTT
66 ACCAATTTT
230586 CCATAGTCAG
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
80 64 0.97
81 2 0.03
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (80 bp):
ATCGGGGATACTCCAACTCCGTTATTTCCAAGAGGATACTCCAACCCCGATTTTATTTCCAAAAC
ACCAATTTTTTCACA
Found at i:230614 original size:80 final size:80
Alignment explanation
Indices: 230432--230614 Score: 215
Period size: 80 Copynumber: 2.3 Consensus size: 80
230422 CCGTTATTTC
* * *
230432 ATCGGGGATACTCCAACCCTGTTATTTCCGAGAGGATACTCCAACCCCGATTTTATTTCCAAAAC
1 ATCGAGGATACTCCAACCCCGTTATTTCCAAGAGGATACTCCAACCCCGATTTTATTTCCAAAAC
*
230497 ACCAATTTTTTCACA
66 ACCAATTTTTCCACA
* * * * * * *
230512 ATCGGGGATACTCCAACTCCGTTATTTTCAAGGGGATACTCCAACCTCGATTTTATTTTCAGAAC
1 ATCGAGGATACTCCAACCCCGTTATTTCCAAGAGGATACTCCAACCCCGATTTTATTTCCAAAAC
* *
230577 ACCGA-TTTTCCATA
66 ACCAATTTTTCCACA
* *
230591 GTCAGAGGATACTCCAGCCCCGTT
1 ATC-GAGGATACTCCAACCCCGTT
230615 GTCATCTCCA
Statistics
Matches: 87, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
79 9 0.10
80 78 0.90
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.30
Consensus pattern (80 bp):
ATCGAGGATACTCCAACCCCGTTATTTCCAAGAGGATACTCCAACCCCGATTTTATTTCCAAAAC
ACCAATTTTTCCACA
Found at i:234314 original size:19 final size:19
Alignment explanation
Indices: 234290--234340 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
234280 TTTCAACGAT
234290 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
*
234309 TTGTATCGATACATAAGTT
1 TTGTATCGATACATAAGTG
234328 TTGTATCGATACA
1 TTGTATCGATACA
234341 ATGTATCGCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.39
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:234411 original size:13 final size:13
Alignment explanation
Indices: 234393--234417 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
234383 ATTACTCAAA
234393 TGTATCGATACAT
1 TGTATCGATACAT
234406 TGTATCGATACA
1 TGTATCGATACA
234418 CATATCTTTG
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:246456 original size:7 final size:7
Alignment explanation
Indices: 246444--246477 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
246434 TTTCTTTTAA
246444 AAAAAAT
1 AAAAAAT
246451 AAAAAAT
1 AAAAAAT
246458 AAAAAAT
1 AAAAAAT
246465 AAATAAA-
1 AAA-AAAT
246472 AAAAAA
1 AAAAAA
246478 GAGAGAAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 3 0.12
7 20 0.77
8 3 0.12
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:247620 original size:94 final size:94
Alignment explanation
Indices: 247495--247739 Score: 402
Period size: 94 Copynumber: 2.6 Consensus size: 94
247485 GACGCATTCT
* *
247495 CCTTTTAAAACCCACACAAGTTGGTGGCATTTTCCAATCCTCAAAGAGCAGGACGCTCTCTCCTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCTCTCTCCTT
*
247560 TCACCCTTTAGTCCTCAAAGAGCAGGATG
66 TCACCCTTTAGTCCTCAAAGAGCAGGACG
* *
247589 CCTTTTAAAGCCCACACAAGTTGATGGCA-TTTCCTAGTCCTCAAAGAGCAGGACGCTCTCTCTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCC-AGTCCTCAAAGAGCAGGACGCTCTCTCCT
247653 TTCACCCTTTAGTCCTCAAAGAGCAGGACG
65 TTCACCCTTTAGTCCTCAAAGAGCAGGACG
* * *
247683 CCTTTCAAAGCCCATACAAGTTGGTGGCATTTTCCAGTCCTCGAAGAGCAGGACGCT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCT
247740 TTTCAAAGCC
Statistics
Matches: 140, Mismatches: 9, Indels: 4
0.92 0.06 0.03
Matches are distributed among these distances:
93 5 0.04
94 130 0.93
95 5 0.04
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (94 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCTCTCTCCTT
TCACCCTTTAGTCCTCAAAGAGCAGGACG
Found at i:247854 original size:62 final size:60
Alignment explanation
Indices: 247658--248159 Score: 569
Period size: 61 Copynumber: 8.4 Consensus size: 60
247648 CTCTTTTCAC
* *
247658 CCTT-TAGTCCTCAAAGAGCAGGACG-----CCTTTCAAAGCCCATACAAGTTGGTGGCA
1 CCTTCTAGTCCTCAAAGAGCAGGACGCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
** * * *
247712 TTTTCCAGTCCTCGAAGAGCAGGACGCTTTT-C----AAAGCCCACACAAGCTGGTGGCA
1 CCTTCTAGTCCTCAAAGAGCAGGACGCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * *
247767 CCTTC-AGTCCTCAAAGAGCAAGACGCATTTTTCTTTTAAAGCCCACACAAGTTGGTGCCA
1 CCTTCTAGTCCTCAAAGAGCAGGACGC-TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * *
247827 CTTTTATAGTCCTCAAAGAGCAGGACGCCTTTTTCCTTTTAAAGCCCACAGAAGTTGGTGGCA
1 C-CTTCTAGTCCTCAAAGAGCAGGACG-C-TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
*
247890 CCTTCTAGTCCTCAAAGAGCAGGACGTCTTTTCCTTTTAAAGCCCACAGAAGTTGGTGGCA
1 CCTTCTAGTCCTCAAAGAGCAGGACG-CTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * *
247951 CCTTCTAGTCCTCAAAAAGCATGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGTA
1 CCTTCTAGTCCTCAAAGAGCAGGACG-CTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* *
248012 CTTTTCTAGTCCTCAAAGAGTAGGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 C-CTTCTAGTCCTCAAAGAGCAGGACGC-TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * ** * *
248074 CCTTCCAGTCCTCAAAAAGCAGGATGCTTTCTCCTTGCAAAGCCCATACAAGTTGATGGCA
1 CCTTCTAGTCCTCAAAGAGCAGGACGCTTT-TCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * *
248135 CCTGCTAGTCCCCAAGGAGCAGGAC
1 CCTTCTAGTCCTCAAAGAGCAGGAC
248160 TCATTTCATT
Statistics
Matches: 381, Mismatches: 49, Indels: 29
0.83 0.11 0.06
Matches are distributed among these distances:
54 21 0.06
55 47 0.12
56 1 0.00
59 1 0.00
60 25 0.07
61 158 0.41
62 96 0.25
63 32 0.08
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.26
Consensus pattern (60 bp):
CCTTCTAGTCCTCAAAGAGCAGGACGCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:247922 original size:123 final size:121
Alignment explanation
Indices: 247658--248159 Score: 566
Period size: 123 Copynumber: 4.2 Consensus size: 121
247648 CTCTTTTCAC
* * **
247658 CCTT-TAGTCCTCAAAGAGCAGGACG------CCTTTCAAAGCCCATACAAGTTGGTGGCATTTT
1 CCTTCTAGTCCTCAAAGAGCAGGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTT
* * *
247716 CCAGTCCTCGAAGAGCAGGACGCTTTT-C----AAAGCCCACACAAGCTGGTGGCA
66 CCAGTCCTCAAAAAGCAGGACGCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * *
247767 CCTTC-AGTCCTCAAAGAGCAAGACGCATTTTT-CTTTTAAAGCCCACACAAGTTGGTGCCACTT
1 CCTTCTAGTCCTCAAAGAGCAGGACGC-TTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCAC-C
** * *
247830 TTATAGTCCTCAAAGAGCAGGACGCCTTTTTCCTTTTAAAGCCCACAGAAGTTGGTGGCA
64 TTCCAGTCCTCAAAAAGCAGGACG-C-TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
*
247890 CCTTCTAGTCCTCAAAGAGCAGGACG-TCTTTTCCTTTTAAAGCCCACAGAAGTTGGTGGCACCT
1 CCTTCTAGTCCTCAAAGAGCAGGACGCT-TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCT
* * * *
247954 TCTAGTCCTCAAAAAGCATGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGTA
65 TCCAGTCCTCAAAAAGCAGGACG-CTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* *
248012 CTTTTCTAGTCCTCAAAGAGTAGGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCT
1 C-CTTCTAGTCCTCAAAGAGCAGGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCT
* ** * *
248077 TCCAGTCCTCAAAAAGCAGGATGCTTTCTCCTTGCAAAGCCCATACAAGTTGATGGCA
65 TCCAGTCCTCAAAAAGCAGGACGCTTT-TCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * *
248135 CCTGCTAGTCCCCAAGGAGCAGGAC
1 CCTTCTAGTCCTCAAAGAGCAGGAC
248160 TCATTTCATT
Statistics
Matches: 336, Mismatches: 35, Indels: 31
0.84 0.09 0.08
Matches are distributed among these distances:
109 23 0.07
115 25 0.07
116 22 0.07
117 1 0.00
118 4 0.01
119 1 0.00
122 56 0.17
123 157 0.47
124 47 0.14
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.26
Consensus pattern (121 bp):
CCTTCTAGTCCTCAAAGAGCAGGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTT
CCAGTCCTCAAAAAGCAGGACGCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:248068 original size:184 final size:182
Alignment explanation
Indices: 247662--248145 Score: 632
Period size: 184 Copynumber: 2.7 Consensus size: 182
247652 TTTCACCCTT
* **
247662 TAGTCCTCAAAGAGCAGGACGCC--TTT-C----AAAGCCCATACAAGTTGGTGGCATTTTCCAG
1 TAGTCCTCAAAGAGCAGGACGCCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAG
* *
247720 TCCTCGAAGAGCAGGACGCTTTT-C--AAAGCCCACACAAGCTGGTGGCACCTTC-AGTCCTCAA
66 TCCTCAAAGAGCAGGACGCTTTTCCTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAA
* *
247781 AGAGCAAGACGCATTTTTCTTTTAAAGCCCACACAAGTTGGTGCCACTTTTA
131 AAAGCAAGACGCATTTTCCTTTTAAAGCCCACACAAGTTGGTGCCACTTTTA
* *
247833 TAGTCCTCAAAGAGCAGGACGCCTTTTTCCTTTTAAAGCCCACAGAAGTTGGTGGCACCTTCTAG
1 TAGTCCTCAAAGAGCAGGACGCCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAG
*
247898 TCCTCAAAGAGCAGGACGTCTTTTCCTTTTAAAGCCCACAGAAGTTGGTGGCACCTTCTAGTCCT
66 TCCTCAAAGAGCAGGACG-CTTTTCC--TTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCT
* * * ** *
247963 CAAAAAGCATGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGTACTTTTC
128 CAAAAAGCAAGACGCATTTTCCTTTTAAAGCCCACACAAGTTGGTGCCACTTTTA
*
248018 TAGTCCTCAAAGAGTAGGACG-CTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAG
1 TAGTCCTCAAAGAGCAGGACGCCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAG
* * * * *
248082 TCCTCAAAAAGCAGGATGCTTTCTCCTTGCAAAGCCCATACAAGTTGATGGCACCTGCTAGTCC
66 TCCTCAAAGAGCAGGACGCTTT-TCCTT--AAAGCCCACACAAGTTGGTGGCACCTTCTAGTCC
248146 CCAAGGAGCA
Statistics
Matches: 271, Mismatches: 25, Indels: 21
0.85 0.08 0.07
Matches are distributed among these distances:
171 23 0.08
173 3 0.01
174 1 0.00
178 43 0.16
179 5 0.02
180 1 0.00
182 2 0.01
183 4 0.01
184 116 0.43
185 73 0.27
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.27
Consensus pattern (182 bp):
TAGTCCTCAAAGAGCAGGACGCCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAG
TCCTCAAAGAGCAGGACGCTTTTCCTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAA
AAAGCAAGACGCATTTTCCTTTTAAAGCCCACACAAGTTGGTGCCACTTTTA
Found at i:248779 original size:13 final size:13
Alignment explanation
Indices: 248761--248790 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
248751 ATACATGGTT
*
248761 CATTGTATCGATA
1 CATTGTATCGACA
248774 CATTGTATCGACA
1 CATTGTATCGACA
248787 CATT
1 CATT
248791 CTGGGTTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (13 bp):
CATTGTATCGACA
Found at i:251192 original size:28 final size:28
Alignment explanation
Indices: 251130--251195 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
251120 TTTTTATCTC
*
251130 GGGGATACTCCAATCCCGTTATTTCGTC
1 GGGGATACTCCAATCCCGTTATTTCGTA
* *
251158 GGAGATACTCCAA-CTCTGTTATTTTCG-A
1 GGGGATACTCCAATC-CCGTTA-TTTCGTA
251186 GGGGATACTC
1 GGGGATACTC
251196 AAACCCCGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
27 1 0.03
28 26 0.81
29 5 0.16
ACGTcount: A:0.21, C:0.24, G:0.23, T:0.32
Consensus pattern (28 bp):
GGGGATACTCCAATCCCGTTATTTCGTA
Found at i:251350 original size:79 final size:79
Alignment explanation
Indices: 251156--251359 Score: 275
Period size: 79 Copynumber: 2.6 Consensus size: 79
251146 CGTTATTTCG
* * * *
251156 TCGGAGATACTCCAACTCTGTTATTTTCGAGGGGATACTCAAACCCCGATTTTATTTTCAAAACA
1 TCGGGGATACTCCAACCCTGTTATTTTCGAGGGAATACTCAAACCCCAATTTTATTTTCAAAACA
251221 TCAATTTTTCACAA
66 TCAATTTTTCACAA
* * * *
251235 TCGGGGATACTCCAACCCCGTTATTTTCGAGAGAATACTCCAACCCCAATTTTA-TTTCTAAAAT
1 TCGGGGATACTCCAACCCTGTTATTTTCGAGGGAATACTCAAACCCCAATTTTATTTTC-AAAAC
251299 ATCAATTTTTCACAA
65 ATCAATTTTTCACAA
* *** *
251314 TCGGGGATACTCCAACCCTATTATTTTATTGGGAATACTCTAACCC
1 TCGGGGATACTCCAACCCTGTTATTTTCGAGGGAATACTCAAACCC
251360 TGTTATTTCC
Statistics
Matches: 109, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
78 4 0.04
79 105 0.96
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (79 bp):
TCGGGGATACTCCAACCCTGTTATTTTCGAGGGAATACTCAAACCCCAATTTTATTTTCAAAACA
TCAATTTTTCACAA
Found at i:251380 original size:186 final size:187
Alignment explanation
Indices: 251128--251479 Score: 505
Period size: 187 Copynumber: 1.9 Consensus size: 187
251118 ATTTTTTATC
* * * * *
251128 TCGGGGATACTCCAATCCCGTTATTTCGTCGGAGATACTCCAACTCTGTTATTTTCGAGGGGATA
1 TCGGGGATACTCCAATCCCATTATTTAGTCGGAGATACTCCAACCCTGTTATTTCCGAGAGGATA
* * *
251193 CTCAAACCCCGATTTTATTT-TCAAAACATCAA-TTTTTCACAATCGGGGATACTCCAACCCCGT
66 CTCAAACCCCGATTTAATTTCT-AAAACACCAATTTTTTCACAATCAGGGATACTCCAACCCCGT
*
251256 TATTTTCGAGAGAATACTCCAACCCCAATTTTATTTCTAAAATATCAATTTTTCACAA
130 TATTTTCAAGAGAATACTCCAACCCCAATTTTATTTCTAAAATATCAATTTTTCACAA
* * *
251314 TCGGGGATACTCCAA-CCCTATTATTTTATTGGGA-ATACTCTAACCCTGTTATTTCCGAGAGGA
1 TCGGGGATACTCCAATCCC-ATTA-TTTAGTCGGAGATACTCCAACCCTGTTATTTCCGAGAGGA
* *
251377 TACTCCAACTCCGATTTAATTTCTAAAACACCAATTTTTTCACAATCAGGGATACTCCAACCCCG
64 TACTCAAACCCCGATTTAATTTCTAAAACACCAATTTTTTCACAATCAGGGATACTCCAACCCCG
* *
251442 TTATTTTCAAGGGGATACTCCAACCCCAATTTTATTTC
129 TTATTTTCAAGAGAATACTCCAACCCCAATTTTATTTC
251480 CAGAACACCG
Statistics
Matches: 146, Mismatches: 16, Indels: 7
0.86 0.09 0.04
Matches are distributed among these distances:
185 3 0.02
186 71 0.49
187 72 0.49
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (187 bp):
TCGGGGATACTCCAATCCCATTATTTAGTCGGAGATACTCCAACCCTGTTATTTCCGAGAGGATA
CTCAAACCCCGATTTAATTTCTAAAACACCAATTTTTTCACAATCAGGGATACTCCAACCCCGTT
ATTTTCAAGAGAATACTCCAACCCCAATTTTATTTCTAAAATATCAATTTTTCACAA
Found at i:251463 original size:80 final size:80
Alignment explanation
Indices: 251348--251523 Score: 201
Period size: 80 Copynumber: 2.2 Consensus size: 80
251338 TTTATTGGGA
* * * * * *
251348 ATACTCTAACCCTGTTATTTCCGAGAGGATACTCCAACTCCGATTTAATTTCTAAAACACCAATT
1 ATACTCCAACCCCGTTATTTCCAAGAGGATACTCCAACCCCAATTTAATTTCCAAAACACCAA-T
*
251413 TTTTCACAATC-AGGG
65 TTTCCACAATCAAGGG
* * * * *
251428 ATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCCCAATTTTATTTCCAGAACACCGATT
1 ATACTCCAACCCCGTTATTTCCAAGAGGATACTCCAACCCCAATTTAATTTCCAAAACACCAATT
* *
251493 TTCCATAGTCAAGGG
66 TTCCACAATCAAGGG
*
251508 ATACTCCAGCCCCGTT
1 ATACTCCAACCCCGTT
251524 GTCATCTCCA
Statistics
Matches: 80, Mismatches: 15, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
79 9 0.11
80 71 0.89
ACGTcount: A:0.29, C:0.28, G:0.12, T:0.30
Consensus pattern (80 bp):
ATACTCCAACCCCGTTATTTCCAAGAGGATACTCCAACCCCAATTTAATTTCCAAAACACCAATT
TTCCACAATCAAGGG
Found at i:251467 original size:108 final size:107
Alignment explanation
Indices: 251237--251468 Score: 313
Period size: 107 Copynumber: 2.2 Consensus size: 107
251227 TTTCACAATC
* * * *
251237 GGGGATACTCCAACCCCGTTATTTTCGAGAGAATACTCCAACCCCAATTTTATTTCTAAAATATC
1 GGGGATACTCCAACCCCGTTATTTCCGAGAGAATACTCCAACCCCAATTTAATTTCTAAAACACC
* * *
251302 AATTTTTCACAATCGGGGATACTCCAACCCTATTATTTTATT
66 AATTTTTCACAATCAGGGATACTCCAACCCCATTATTTTATA
* * * * * *
251344 GGGAATACTCTAACCCTGTTATTTCCGAGAGGATACTCCAACTCCGATTTAATTTCTAAAACACC
1 GGGGATACTCCAACCCCGTTATTTCCGAGAGAATACTCCAACCCCAATTTAATTTCTAAAACACC
*
251409 AATTTTTTCACAATCAGGGATACTCCAACCCCGTTATTTTCA-A
66 AA-TTTTTCACAATCAGGGATACTCCAACCCCATTATTTT-ATA
251452 GGGGATACTCCAACCCC
1 GGGGATACTCCAACCCC
251469 AATTTTATTT
Statistics
Matches: 106, Mismatches: 17, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
107 57 0.54
108 48 0.45
109 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.31
Consensus pattern (107 bp):
GGGGATACTCCAACCCCGTTATTTCCGAGAGAATACTCCAACCCCAATTTAATTTCTAAAACACC
AATTTTTCACAATCAGGGATACTCCAACCCCATTATTTTATA
Found at i:253247 original size:9 final size:9
Alignment explanation
Indices: 253233--253277 Score: 51
Period size: 9 Copynumber: 5.2 Consensus size: 9
253223 TTATTCATTC
253233 AATTAATTT
1 AATTAATTT
253242 AATTAATTT
1 AATTAATTT
253251 AA-TAATTT
1 AATTAATTT
*
253259 AAATTAA-AT
1 -AATTAATTT
253268 AA-TAATTT
1 AATTAATTT
253276 AA
1 AA
253278 ATATTAATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
7 3 0.10
8 11 0.35
9 14 0.45
10 3 0.10
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
AATTAATTT
Found at i:253256 original size:12 final size:12
Alignment explanation
Indices: 253241--253293 Score: 56
Period size: 12 Copynumber: 4.3 Consensus size: 12
253231 TCAATTAATT
*
253241 TAATTAATTTAA
1 TAATTAATTAAA
253253 TAATTTAAATTAAA
1 TAA-TT-AATTAAA
253267 TAA-TAATTTAAA
1 TAATTAA-TTAAA
253279 T-ATTAATTAAA
1 TAATTAATTAAA
253290 TAAT
1 TAAT
253294 AAATATAGTA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
11 9 0.26
12 15 0.43
13 2 0.06
14 9 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TAATTAATTAAA
Found at i:253278 original size:17 final size:18
Alignment explanation
Indices: 253236--253279 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
253226 TTCATTCAAT
*
253236 TAATTT-AATTAATTTAA
1 TAATTTAAATTAATATAA
253253 TAATTTAAATTAA-ATAA
1 TAATTTAAATTAATATAA
253270 TAATTTAAAT
1 TAATTTAAAT
253280 ATTAATTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 19 0.76
18 6 0.24
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TAATTTAAATTAATATAA
Found at i:253288 original size:11 final size:11
Alignment explanation
Indices: 253260--253295 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
253250 TAATAATTTA
253260 AATTAAATAAT
1 AATTAAATAAT
*
253271 AATTTAAATATT
1 AA-TTAAATAAT
253283 AATTAAATAAT
1 AATTAAATAAT
253294 AA
1 AA
253296 ATATAGTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
AATTAAATAAT
Found at i:253453 original size:15 final size:16
Alignment explanation
Indices: 253433--253467 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
253423 TCATTAAAAA
*
253433 TTTATT-TTTAATATT
1 TTTATTATTAAATATT
253448 TTTATTATTAAATATT
1 TTTATTATTAAATATT
253464 TTTA
1 TTTA
253468 AATAATAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTATTATTAAATATT
Found at i:253514 original size:25 final size:24
Alignment explanation
Indices: 253463--253514 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
253453 TATTAAATAT
* **
253463 TTTTAAATAATAATAATTAATTTA
1 TTTTAAATAAAAATAATTAATAAA
*
253487 TTTTAAATAAAAATACCTTAATAAA
1 TTTTAAATAAAAATA-ATTAATAAA
253512 TTT
1 TTT
253515 ATTTCGAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (24 bp):
TTTTAAATAAAAATAATTAATAAA
Found at i:253837 original size:20 final size:22
Alignment explanation
Indices: 253793--253837 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
253783 ATCGTATTTA
*
253793 TAATTTTTTATCATATTTTAAT
1 TAATTTTTTATCATATTATAAT
*
253815 TAATTTTTT-T-ATATTATATT
1 TAATTTTTTATCATATTATAAT
253835 TAA
1 TAA
253838 AATTGTATAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 11 0.52
21 1 0.05
22 9 0.43
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (22 bp):
TAATTTTTTATCATATTATAAT
Found at i:255605 original size:10 final size:10
Alignment explanation
Indices: 255586--255644 Score: 59
Period size: 10 Copynumber: 5.6 Consensus size: 10
255576 TGATTTTCAC
255586 AAAAAA-ATA
1 AAAAAATATA
255595 AAAAAATATA
1 AAAAAATATA
255605 AAATAAATA-A
1 AAA-AAATATA
255615 AAAGAAAGTATA
1 AAA-AAA-TATA
255627 AAAAAATAATA
1 AAAAAAT-ATA
255638 ATAAAAA
1 A-AAAAA
255645 GTGTTTTCCA
Statistics
Matches: 43, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
9 6 0.14
10 14 0.33
11 14 0.33
12 9 0.21
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (10 bp):
AAAAAATATA
Found at i:255609 original size:15 final size:14
Alignment explanation
Indices: 255588--255644 Score: 53
Period size: 15 Copynumber: 3.8 Consensus size: 14
255578 ATTTTCACAA
255588 AAAAATAAAAAAAT
1 AAAAATAAAAAAAT
255602 ATAAAATAAATAAAA-
1 A-AAAATAAA-AAAAT
255617 AGAAAGTATAAAAAAAT
1 A-AAA--ATAAAAAAAT
*
255634 AATAATAAAAA
1 AAAAATAAAAA
255645 GTGTTTTCCA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 8 0.22
15 12 0.33
16 10 0.28
17 6 0.17
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.18
Consensus pattern (14 bp):
AAAAATAAAAAAAT
Found at i:258284 original size:8 final size:8
Alignment explanation
Indices: 258258--258363 Score: 69
Period size: 8 Copynumber: 12.9 Consensus size: 8
258248 CTTTTATAAT
258258 TATATTTA
1 TATATTTA
* *
258266 AATAATTA
1 TATATTTA
258274 TATATTTA
1 TATATTTA
258282 TATAAATTTTAA
1 TAT--A-TTT-A
*
258294 TATATTAA
1 TATATTTA
258302 TA-ATTTAA
1 TATATTT-A
258310 TATATTTA
1 TATATTTA
258318 TATACTTTTA
1 TATA--TTTA
258328 TTATATTTA
1 -TATATTTA
*
258337 TATAATT-
1 TATATTTA
258344 TAT-TTTA
1 TATATTTA
258351 T-TATTT-
1 TATATTTA
258357 TATATTT
1 TATATTT
258364 TAATTAATTT
Statistics
Matches: 78, Mismatches: 8, Indels: 25
0.70 0.07 0.23
Matches are distributed among these distances:
6 4 0.05
7 15 0.19
8 32 0.41
9 10 0.13
10 6 0.08
11 7 0.09
12 4 0.05
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (8 bp):
TATATTTA
Found at i:258316 original size:26 final size:26
Alignment explanation
Indices: 258258--258345 Score: 74
Period size: 26 Copynumber: 3.3 Consensus size: 26
258248 CTTTTATAAT
258258 TATATTTAAATAATTATATATTTATA
1 TATATTTAAATAATTATATATTTATA
* *
258284 TAAATTTTAATATATTA-ATAATTTA-A
1 TATATTTAAATA-ATTATAT-ATTTATA
* *
258310 TATATTTATATACTTTTATTATATTTATA
1 TATATTTAAATA--ATTA-TATATTTATA
258339 TA-ATTTA
1 TATATTTA
258346 TTTTATTATT
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
26 22 0.44
27 13 0.26
28 10 0.20
29 5 0.10
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (26 bp):
TATATTTAAATAATTATATATTTATA
Found at i:258347 original size:18 final size:18
Alignment explanation
Indices: 258256--258352 Score: 94
Period size: 18 Copynumber: 5.4 Consensus size: 18
258246 TACTTTTATA
*
258256 ATTATATTTAAATAA-TT
1 ATTATATTTATATAATTT
258273 A-TATATTTATATAAATTT
1 ATTATATTTATAT-AATTT
*
258291 -TAATATATTA-ATAATTT
1 ATTATAT-TTATATAATTT
* *
258308 AATATATTTATATACTTTT
1 ATTATATTTATATA-ATTT
258327 ATTATATTTATATAATTT
1 ATTATATTTATATAATTT
*
258345 ATTTTATT
1 ATTATATT
258353 ATTTTATATT
Statistics
Matches: 65, Mismatches: 8, Indels: 13
0.76 0.09 0.15
Matches are distributed among these distances:
16 10 0.15
17 11 0.17
18 25 0.38
19 19 0.29
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTATATTTATATAATTT
Found at i:258358 original size:13 final size:15
Alignment explanation
Indices: 258243--258396 Score: 65
Period size: 14 Copynumber: 9.8 Consensus size: 15
258233 TATATTTTTA
258243 TTATACTTT-TATAA-
1 TTATA-TTTATATAAT
*
258257 TTATATTTAAATAAT
1 TTATATTTATATAAT
258272 TATATATTTATATAAATT
1 T-TATATTTATAT-AA-T
258290 TTAATATATTA-ATAATT
1 TT-ATAT-TTATATAA-T
*
258307 TAATATATTTATATACTTTT
1 T--TATATTTATATA---AT
258327 ATTATATTTATATAAT
1 -TTATATTTATATAAT
*
258343 TTAT-TTTAT-TATT
1 TTATATTTATATAAT
258356 TTATATTT-TAATTAAT
1 TTATATTTAT-A-TAAT
*
258372 TT-TTTATTATATAA-
1 TTATAT-TTATATAAT
258386 TTATA-TTATAT
1 TTATATTTATAT
258397 TAAAAATTAT
Statistics
Matches: 111, Mismatches: 8, Indels: 43
0.69 0.05 0.27
Matches are distributed among these distances:
13 17 0.15
14 19 0.17
15 11 0.10
16 19 0.17
17 12 0.11
18 15 0.14
19 16 0.14
20 1 0.01
21 1 0.01
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (15 bp):
TTATATTTATATAAT
Found at i:258360 original size:20 final size:20
Alignment explanation
Indices: 258331--258394 Score: 58
Period size: 20 Copynumber: 3.1 Consensus size: 20
258321 ACTTTTATTA
* *
258331 TATTTATATAATTTATTTTAT
1 TATTT-TATAATTTAATTAAT
*
258352 TATTTTATATTTTAATTAAT
1 TATTTTATAATTTAATTAAT
* *
258372 T-TTTTATTATATAATTATAT
1 TATTTTATAATTTAATTA-AT
258392 TAT
1 TAT
258395 ATTAAAAATT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
19 13 0.37
20 16 0.46
21 6 0.17
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TATTTTATAATTTAATTAAT
Found at i:258382 original size:63 final size:69
Alignment explanation
Indices: 258251--258406 Score: 168
Period size: 63 Copynumber: 2.3 Consensus size: 69
258241 TATTATACTT
258251 TTATAATTATATTTAAATAATTATATATTTATATAAATTTTAATATATTAATAATTTAATATATT
1 TTAT-ATTATATTTAAATAATTATATATTTATAT-AATTTTAATATATTAATAATTT-ATATATT
*
258316 TATATAC
63 TATATAA
* * * *
258323 TTTTATTATATTTATATAATT-TAT-TTTAT-T-ATTTT-ATATTTTAATTAATTT-TTTA-TTA
1 TTATATTATATTTAAATAATTATATATTTATATAATTTTAATATATTAA-TAATTTATATATTTA
258381 TATAA
65 TATAA
258386 TTATATTATA-TTAAA-AATTAT
1 TTATATTATATTTAAATAATTAT
258407 CAAATTTAAT
Statistics
Matches: 75, Mismatches: 7, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
61 4 0.05
62 5 0.07
63 16 0.21
64 3 0.04
65 8 0.11
66 11 0.15
68 1 0.01
69 5 0.07
70 3 0.04
71 16 0.21
72 3 0.04
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (69 bp):
TTATATTATATTTAAATAATTATATATTTATATAATTTTAATATATTAATAATTTATATATTTAT
ATAA
Found at i:258623 original size:5 final size:5
Alignment explanation
Indices: 258613--258655 Score: 54
Period size: 5 Copynumber: 8.8 Consensus size: 5
258603 CGATTCATGT
*
258613 TATTA TATTA TATT- TA-TA TATTT TATTA TATTA TATTTA TATT
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TA-TTA TATT
258656 TAAAATATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
3 1 0.03
4 4 0.12
5 23 0.70
6 5 0.15
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (5 bp):
TATTA
Found at i:258639 original size:18 final size:18
Alignment explanation
Indices: 258613--258707 Score: 63
Period size: 18 Copynumber: 5.3 Consensus size: 18
258603 CGATTCATGT
*
258613 TATTATATTATATTTATA
1 TATTTTATTATATTTATA
*
258631 TATTTTATTATATTATATT
1 TATTTTATTATATT-TATA
**
258650 TATATTTAAAATATTT-TA
1 TAT-TTTATTATATTTATA
* *
258668 TA-TTTATAAAATTT-TAA
1 TATTTTATTATATTTAT-A
*
258685 TATTTTAATA-ATTTATTA
1 TATTTTATTATATTTA-TA
258703 TATTT
1 TATTT
258708 AATTTTTAAA
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
16 11 0.18
17 7 0.11
18 27 0.44
19 8 0.13
20 9 0.15
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TATTTTATTATATTTATA
Found at i:258667 original size:16 final size:16
Alignment explanation
Indices: 258648--258709 Score: 65
Period size: 16 Copynumber: 3.7 Consensus size: 16
258638 TTATATTATA
258648 TTTATATTTAAAATAT
1 TTTATATTTAAAATAT
258664 TTTATATTTATAAA-AT
1 TTTATATTTA-AAATAT
258680 TTTAATATTTTAATAAT-T
1 TTT-ATA-TTTAA-AATAT
258698 TATTATATTTAA
1 T-TTATATTTAA
258710 TTTTTAAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
16 15 0.38
17 12 0.30
18 11 0.28
19 2 0.05
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTATATTTAAAATAT
Found at i:258671 original size:22 final size:23
Alignment explanation
Indices: 258616--258675 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 23
258606 TTCATGTTAT
** *
258616 TATATTATATTTATATATTTTAT
1 TATATTATATTTATATATTAAAA
258639 TATATTATATTTATAT-TTAAAA
1 TATATTATATTTATATATTAAAA
*
258661 TATTTTATATTTATA
1 TATATTATATTTATA
258676 AAATTTTAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
22 17 0.52
23 16 0.48
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
TATATTATATTTATATATTAAAA
Found at i:258952 original size:18 final size:19
Alignment explanation
Indices: 258932--258972 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
258922 ATGAGTCATT
258932 AAAATATATAAATTTATTAA
1 AAAAT-TATAAATTTATTAA
* *
258952 AAAATTTTAAATTTTTTAA
1 AAAATTATAAATTTATTAA
258971 AA
1 AA
258973 GTAAAGACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
AAAATTATAAATTTATTAA
Found at i:259909 original size:30 final size:32
Alignment explanation
Indices: 259863--259922 Score: 106
Period size: 30 Copynumber: 1.9 Consensus size: 32
259853 AAGTAAATAA
259863 TATATGTAATTTTTAAATTTTAAAATATATTT
1 TATATGTAATTTTTAAATTTTAAAATATATTT
259895 TATAT-TAA-TTTTAAATTTTAAAATATAT
1 TATATGTAATTTTTAAATTTTAAAATATAT
259923 CAATTAGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 20 0.71
31 3 0.11
32 5 0.18
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (32 bp):
TATATGTAATTTTTAAATTTTAAAATATATTT
Found at i:260250 original size:20 final size:20
Alignment explanation
Indices: 260225--260262 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
260215 CAAGCATTTA
260225 AAATTTTGATTTTGAAGTTT
1 AAATTTTGATTTTGAAGTTT
260245 AAATTTTGATTTTGAAGT
1 AAATTTTGATTTTGAAGT
260263 GCTTTTGACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.53
Consensus pattern (20 bp):
AAATTTTGATTTTGAAGTTT
Found at i:261956 original size:16 final size:14
Alignment explanation
Indices: 261918--261960 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
261908 ATTAAAATTT
261918 TATTAAAATATAAAA
1 TATTAAAA-ATAAAA
*
261933 TATAAAAAATAAAGA
1 TATTAAAAATAAA-A
261948 TATTTAAAAATAA
1 TA-TTAAAAATAA
261961 TTGTAGAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 5 0.21
15 10 0.42
16 9 0.38
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (14 bp):
TATTAAAAATAAAA
Found at i:262593 original size:16 final size:17
Alignment explanation
Indices: 262557--262594 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
262547 TATCCGAGTT
*
262557 ATTTTAAATTTTAAATT
1 ATTTTAAATTTTAAATA
*
262574 ATTTTAAA-TTTAAGTA
1 ATTTTAAATTTTAAATA
262590 ATTTT
1 ATTTT
262595 GAGCATGAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
ATTTTAAATTTTAAATA
Found at i:262791 original size:25 final size:25
Alignment explanation
Indices: 262745--262795 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
262735 CGATACACTG
262745 TTATACTTTATCTTAATTTATTATTT
1 TTATACTTTATCTTAATTTATT-TTT
*
262771 TTATATTTTAT-TTAATTTATTTTT
1 TTATACTTTATCTTAATTTATTTTT
262795 T
1 T
262796 GGTATGTTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 4 0.17
25 10 0.42
26 10 0.42
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (25 bp):
TTATACTTTATCTTAATTTATTTTT
Found at i:263168 original size:23 final size:23
Alignment explanation
Indices: 263131--263178 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
263121 AATTAATTAA
*
263131 AATATAATATGATATAAAAA-AT
1 AATATAATATAATATAAAAATAT
263153 AATATAAATATAATATAAAAATAT
1 AATAT-AATATAATATAAAAATAT
263177 AA
1 AA
263179 AATATTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 5 0.22
23 14 0.61
24 4 0.17
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (23 bp):
AATATAATATAATATAAAAATAT
Found at i:263177 original size:19 final size:19
Alignment explanation
Indices: 263153--263219 Score: 55
Period size: 19 Copynumber: 3.4 Consensus size: 19
263143 TATAAAAAAT
263153 AATATAAATATAATATAAA
1 AATATAAATATAATATAAA
* *
263172 AATATAAA-ATATTTTAAA
1 AATATAAATATAATATAAA
* *
263190 ATTTATATAATATAATTATTAA
1 A-ATATA-AATATAA-TATAAA
*
263212 TATATAAA
1 AATATAAA
263220 AAGAATGAAT
Statistics
Matches: 36, Mismatches: 8, Indels: 7
0.71 0.16 0.14
Matches are distributed among these distances:
18 9 0.25
19 12 0.33
20 4 0.11
21 7 0.19
22 4 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AATATAAATATAATATAAA
Found at i:264037 original size:20 final size:20
Alignment explanation
Indices: 264012--264062 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
264002 TCAATATAAA
*
264012 ATTTAAAAATTAATAATTAT
1 ATTTAAAAATTAAAAATTAT
**
264032 ATTTAAAAGGTAAAAATTAT
1 ATTTAAAAATTAAAAATTAT
*
264052 TTTTAAAAATT
1 ATTTAAAAATT
264063 TGAGAAAAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (20 bp):
ATTTAAAAATTAAAAATTAT
Found at i:268998 original size:20 final size:19
Alignment explanation
Indices: 268959--268999 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
268949 TATATAATTT
* *
268959 TTTAAAATTTTTTTATATA
1 TTTAAAATTTTTTAAAATA
268978 TTTAAAAGTTTTTTAAAATA
1 TTTAAAA-TTTTTTAAAATA
268998 TT
1 TT
269000 ATATTTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (19 bp):
TTTAAAATTTTTTAAAATA
Found at i:269162 original size:2 final size:2
Alignment explanation
Indices: 269157--269192 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
269147 AAGCTAATTG
269157 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
269193 CATTTCCACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:272327 original size:18 final size:16
Alignment explanation
Indices: 272299--272333 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
272289 TAAATTGATA
272299 TATTTAATTTTTTATAT
1 TATTTAA-TTTTTATAT
272316 TATTTCAATTTTTATAT
1 TATTT-AATTTTTATAT
272333 T
1 T
272334 GATAGAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.88
18 2 0.12
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.69
Consensus pattern (16 bp):
TATTTAATTTTTATAT
Found at i:275180 original size:16 final size:17
Alignment explanation
Indices: 275155--275196 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
275145 TTTTATTAAA
* *
275155 TAAAATAATAA-ATAAT
1 TAAAAAAATAACATAAC
*
275171 TAAAAAAATAACATTAC
1 TAAAAAAATAACATAAC
275188 TAAAAAAAT
1 TAAAAAAAT
275197 TGTTAATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 10 0.45
17 12 0.55
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (17 bp):
TAAAAAAATAACATAAC
Found at i:276241 original size:20 final size:20
Alignment explanation
Indices: 276218--276342 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
276208 AAGTACCCAG
*
276218 ATGTATCGATCCATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
276238 ATGTATCGATATATGTATGA
1 ATGTATCGATACATTTTTCA
*
276258 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
*
276278 ATATATCGATACATTCTGTCTTTTTACCCA
1 ATGTATCGATACA-------TTTTT---CA
276308 GATGTATCGATACATTTTTCA
1 -ATGTATCGATACATTTTTCA
276329 ATGTATCGATACAT
1 ATGTATCGATACAT
276343 CTAGTTAAAA
Statistics
Matches: 81, Mismatches: 13, Indels: 22
0.70 0.11 0.19
Matches are distributed among these distances:
20 56 0.69
21 2 0.02
24 5 0.06
27 4 0.05
30 2 0.02
31 12 0.15
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:277233 original size:20 final size:21
Alignment explanation
Indices: 277201--277239 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
277191 AGCCTTTGAC
277201 CATGCATTTTTTATTATGTTT
1 CATGCATTTTTTATTATGTTT
277222 CATGCA-TTTTTATTATGT
1 CATGCATTTTTTATTATGT
277240 CCAGCATCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.21, C:0.10, G:0.10, T:0.59
Consensus pattern (21 bp):
CATGCATTTTTTATTATGTTT
Found at i:279877 original size:16 final size:16
Alignment explanation
Indices: 279856--279889 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
279846 AATAATAATT
279856 ATAGCAACATTAAAAC
1 ATAGCAACATTAAAAC
279872 ATAGCAACATTAAAAC
1 ATAGCAACATTAAAAC
279888 AT
1 AT
279890 TTTTAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.56, C:0.18, G:0.06, T:0.21
Consensus pattern (16 bp):
ATAGCAACATTAAAAC
Found at i:280271 original size:19 final size:20
Alignment explanation
Indices: 280247--280289 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
280237 TTTAAATCAA
280247 AATATGATGAATATTTT-AT
1 AATATGATGAATATTTTCAT
**
280266 AATATGATTTATATTTTCAT
1 AATATGATGAATATTTTCAT
280286 AATA
1 AATA
280290 ATATGAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (20 bp):
AATATGATGAATATTTTCAT
Found at i:282438 original size:2 final size:2
Alignment explanation
Indices: 282431--282465 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
282421 ACATATGTAC
282431 AT 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 AT A
282466 AGAGTTCATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:285264 original size:24 final size:23
Alignment explanation
Indices: 285218--285282 Score: 60
Period size: 24 Copynumber: 2.7 Consensus size: 23
285208 TTAAATGAAT
* *
285218 TTTTTATGAATATTAAATAAACA
1 TTTTCATGAATATTAAACAAACA
*
285241 TTTTCATGAATATATAAACGAACA
1 TTTTCATGAATAT-TAAACAAACA
*
285265 TGTTT-ACGAATAATTAAA
1 T-TTTCATGAAT-ATTAAA
285283 AATATGTTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
23 12 0.34
24 18 0.51
25 5 0.14
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (23 bp):
TTTTCATGAATATTAAACAAACA
Found at i:285432 original size:11 final size:11
Alignment explanation
Indices: 285418--285460 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
285408 AATTTAATGA
285418 TAAATAAACTT
1 TAAATAAACTT
*
285429 TAAATAAACTGC
1 TAAATAAACT-T
*
285441 TAAACAAACTT
1 TAAATAAACTT
285452 TAAATAAAC
1 TAAATAAAC
285461 AATAATCTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.56, C:0.14, G:0.02, T:0.28
Consensus pattern (11 bp):
TAAATAAACTT
Found at i:290208 original size:82 final size:82
Alignment explanation
Indices: 290110--290271 Score: 261
Period size: 82 Copynumber: 2.0 Consensus size: 82
290100 ATATATATAT
* * * *
290110 ATTATATTTTTTATTTATTGAATTTTAAATAATAATTTGGGTTTTTGAAAAAATTTATAAATATG
1 ATTATACTTTTAATTTATTAAATTTTAAATAATAATTTAGGTTTTTGAAAAAATTTATAAATATG
*
290175 GGTTAAATCAAATTGGG
66 AGTTAAATCAAATTGGG
* *
290192 ATTATACTTTTAATTTATTAAATTTTAAATAATAATTTAGGTTTTTGAAAAAATTTGTAAATGTG
1 ATTATACTTTTAATTTATTAAATTTTAAATAATAATTTAGGTTTTTGAAAAAATTTATAAATATG
290257 AGTTAAATCAAATTG
66 AGTTAAATCAAATTG
290272 AGCTTTGAAA
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
82 73 1.00
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.47
Consensus pattern (82 bp):
ATTATACTTTTAATTTATTAAATTTTAAATAATAATTTAGGTTTTTGAAAAAATTTATAAATATG
AGTTAAATCAAATTGGG
Found at i:290651 original size:23 final size:24
Alignment explanation
Indices: 290620--290671 Score: 88
Period size: 23 Copynumber: 2.2 Consensus size: 24
290610 TCAAAGAATT
*
290620 TAATAAATTAAAATATATAATATA
1 TAATAAATTAAAATATACAATATA
290644 -AATAAATTAAAATATACAATATA
1 TAATAAATTAAAATATACAATATA
290667 TAATA
1 TAATA
290672 GATAATAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 22 0.85
24 4 0.15
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (24 bp):
TAATAAATTAAAATATACAATATA
Found at i:294052 original size:13 final size:13
Alignment explanation
Indices: 294034--294080 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
294024 GTAAATTAAA
294034 ATTTTATTTATTT
1 ATTTTATTTATTT
*
294047 ATTTTATATATTT
1 ATTTTATTTATTT
* *
294060 ATTTTACTTGTTT
1 ATTTTATTTATTT
294073 A-TTTATTT
1 ATTTTATTT
294081 GTAATTAATA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
12 6 0.21
13 23 0.79
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (13 bp):
ATTTTATTTATTT
Found at i:295184 original size:16 final size:17
Alignment explanation
Indices: 295165--295197 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
295155 GGTTCAAGCC
295165 TTTTCGAGTTC-AGTTT
1 TTTTCGAGTTCGAGTTT
295181 TTTTCGAGTTCGAGTTT
1 TTTTCGAGTTCGAGTTT
295198 GGATTGGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.12, C:0.12, G:0.21, T:0.55
Consensus pattern (17 bp):
TTTTCGAGTTCGAGTTT
Found at i:296330 original size:22 final size:22
Alignment explanation
Indices: 296305--296348 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
296295 AAAGCCCATG
* *
296305 ATATAATTTACTTTTTGATAAA
1 ATATAATTTAATTTTTAATAAA
296327 ATATAATTTAATTTTTAATAAA
1 ATATAATTTAATTTTTAATAAA
296349 TTGTTATTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (22 bp):
ATATAATTTAATTTTTAATAAA
Found at i:296569 original size:16 final size:16
Alignment explanation
Indices: 296550--296617 Score: 57
Period size: 16 Copynumber: 4.2 Consensus size: 16
296540 GGTTTAGAGC
296550 TTTTTGGGTTC-GTGTT
1 TTTTTGGGTTCAG-GTT
*
296566 TTTTCGGGTTCAGGTT
1 TTTTTGGGTTCAGGTT
* * *
296582 CTTTTGGGTTCAAGCT
1 TTTTTGGGTTCAGGTT
* **
296598 ATTTCAGGTTCAGGTT
1 TTTTTGGGTTCAGGTT
296614 TTTT
1 TTTT
296618 ACTTTTTGGT
Statistics
Matches: 40, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
16 39 0.98
17 1 0.03
ACGTcount: A:0.09, C:0.12, G:0.26, T:0.53
Consensus pattern (16 bp):
TTTTTGGGTTCAGGTT
Found at i:296837 original size:3 final size:3
Alignment explanation
Indices: 296829--296855 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
296819 ATCTTTAGAA
296829 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
296856 TTTAATTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:297844 original size:28 final size:29
Alignment explanation
Indices: 297812--297869 Score: 109
Period size: 28 Copynumber: 2.0 Consensus size: 29
297802 TATTTAGTCG
297812 TAATCCTCTCATGCA-TTTTTTTTATTGT
1 TAATCCTCTCATGCATTTTTTTTTATTGT
297840 TAATCCTCTCATGCATTTTTTTTTATTGT
1 TAATCCTCTCATGCATTTTTTTTTATTGT
297869 T
1 T
297870 CGTTTTATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 15 0.52
29 14 0.48
ACGTcount: A:0.17, C:0.17, G:0.07, T:0.59
Consensus pattern (29 bp):
TAATCCTCTCATGCATTTTTTTTTATTGT
Found at i:299235 original size:19 final size:19
Alignment explanation
Indices: 299211--299248 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
299201 GGAGGCAAAG
299211 TGAGTATCTTCTATGAGTT
1 TGAGTATCTTCTATGAGTT
299230 TGAGTATCTTCTATGAGTT
1 TGAGTATCTTCTATGAGTT
299249 GATCTTCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.11, G:0.21, T:0.47
Consensus pattern (19 bp):
TGAGTATCTTCTATGAGTT
Found at i:312895 original size:49 final size:49
Alignment explanation
Indices: 312828--312922 Score: 172
Period size: 49 Copynumber: 1.9 Consensus size: 49
312818 CCAAGCTTCG
*
312828 CATCCCTGAACTATGAAGACCCAGCAAAGCTCCTTTCATGGTTCCATCC
1 CATCCCTGAACTATGAAGACCCAGAAAAGCTCCTTTCATGGTTCCATCC
*
312877 CATCCCTGAACTCTGAAGACCCAGAAAAGCTCCTTTCATGGTTCCA
1 CATCCCTGAACTATGAAGACCCAGAAAAGCTCCTTTCATGGTTCCA
312923 AGTTCTAAAC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.27, C:0.34, G:0.15, T:0.24
Consensus pattern (49 bp):
CATCCCTGAACTATGAAGACCCAGAAAAGCTCCTTTCATGGTTCCATCC
Found at i:320552 original size:7 final size:7
Alignment explanation
Indices: 320540--320564 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
320530 TACAGATTGT
320540 AAAATAA
1 AAAATAA
320547 AAAATAA
1 AAAATAA
320554 AAAATAA
1 AAAATAA
320561 AAAA
1 AAAA
320565 GCAAAATGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAATAA
Found at i:322199 original size:16 final size:17
Alignment explanation
Indices: 322169--322201 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
322159 TTCTGTGTTA
*
322169 ATTTTTAATTTATTAAT
1 ATTTTTAATTAATTAAT
322186 ATTTTT-ATTAATTAAT
1 ATTTTTAATTAATTAAT
322202 TTATATATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTTTTAATTAATTAAT
Found at i:327092 original size:20 final size:22
Alignment explanation
Indices: 327040--327096 Score: 73
Period size: 20 Copynumber: 2.6 Consensus size: 22
327030 TAAAATTTTA
*
327040 ATTTTAATTTTAATATATATAAT
1 ATTTTATTTTTAA-ATATATAAT
327063 ATTTTATTTTTAAAT-TATAAT
1 ATTTTATTTTTAAATATATAAT
*
327084 -TTTTTTTTTTAAA
1 ATTTTATTTTTAAA
327097 AAAAATATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
20 12 0.38
21 6 0.19
22 2 0.06
23 12 0.38
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
ATTTTATTTTTAAATATATAAT
Found at i:327643 original size:16 final size:17
Alignment explanation
Indices: 327622--327653 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
327612 TATTATAATA
327622 TTATAT-ATATAAATTT
1 TTATATAATATAAATTT
327638 TTATATAATATAAATT
1 TTATATAATATAAATT
327654 ATATAATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTATATAATATAAATTT
Found at i:327655 original size:14 final size:14
Alignment explanation
Indices: 327615--327663 Score: 55
Period size: 14 Copynumber: 3.3 Consensus size: 14
327605 TTATTCATAT
327615 TATAATATTATAT-A
1 TATAA-ATTATATAA
327629 TATAAATTTTTATATAA
1 TATAAA---TTATATAA
327646 TATAAATTATATAA
1 TATAAATTATATAA
327660 TATA
1 TATA
327664 TGTAAATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
13 1 0.03
14 17 0.55
16 6 0.19
17 7 0.23
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TATAAATTATATAA
Done.