Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold348
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: 425534
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
File 2 of 3
Found at i:167698 original size:23 final size:23
Alignment explanation
Indices: 167672--167725 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
167662 TTTTATATAA
167672 TATAAATT-AT-TAAATAATTATTT
1 TATAAATTAATATAAATAA--ATTT
*
167695 TATATATTAATAATAAATAAATTT
1 TATAAATTAAT-ATAAATAAATTT
167719 TATAAAT
1 TATAAAT
167726 AAATTCATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 7 0.27
24 12 0.46
26 7 0.27
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TATAAATTAATATAAATAAATTT
Found at i:172276 original size:14 final size:14
Alignment explanation
Indices: 172239--172268 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
172229 GTTCGATTTG
*
172239 TAATAAAATAAAAT
1 TAATAAAATTAAAT
172253 TAATAAAATTAAAT
1 TAATAAAATTAAAT
172267 TA
1 TA
172269 TTGAAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
TAATAAAATTAAAT
Found at i:172618 original size:22 final size:21
Alignment explanation
Indices: 172589--172631 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
172579 TTATATATGC
**
172589 TTATTATTTATACGATATAAA
1 TTATTATTTATAAAATATAAA
172610 TTATATATTTATAAAATATAAA
1 TTAT-TATTTATAAAATATAAA
172632 AATAATATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (21 bp):
TTATTATTTATAAAATATAAA
Found at i:173700 original size:12 final size:11
Alignment explanation
Indices: 173687--173728 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
173677 AATTAAATTA
173687 AAATATAATAT
1 AAATATAATAT
*
173698 AAAAAATAATAT
1 -AAATATAATAT
173710 AAATACT-ATAT
1 AAATA-TAATAT
173721 AAATATAA
1 AAATATAA
173729 AACATATCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 1 0.04
11 14 0.54
12 11 0.42
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (11 bp):
AAATATAATAT
Found at i:174831 original size:24 final size:23
Alignment explanation
Indices: 174804--174848 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
174794 AAGTTAGATC
*
174804 AAATTAAGTTATTATAAATTTTTA
1 AAATTAAATTATT-TAAATTTTTA
*
174828 AAATTAAATTATTTTAATTTT
1 AAATTAAATTATTTAAATTTT
174849 AAATTATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
AAATTAAATTATTTAAATTTTTA
Found at i:174863 original size:16 final size:15
Alignment explanation
Indices: 174818--174867 Score: 57
Period size: 16 Copynumber: 3.3 Consensus size: 15
174808 TAAGTTATTA
* *
174818 TAAATT-TTTAAAAT
1 TAAATTATTTTAATT
174832 TAAATTATTTTAATTT
1 TAAATTATTTTAA-TT
*
174848 TAAATTATTTTGATT
1 TAAATTATTTTAATT
174863 TAAAT
1 TAAAT
174868 AGATGTAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
14 6 0.19
15 12 0.39
16 13 0.42
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (15 bp):
TAAATTATTTTAATT
Found at i:174866 original size:15 final size:16
Alignment explanation
Indices: 174831--174867 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
174821 ATTTTTAAAA
174831 TTAAATTATTTTAATT
1 TTAAATTATTTTAATT
*
174847 TTAAATTATTTTGA-T
1 TTAAATTATTTTAATT
174862 TTAAAT
1 TTAAAT
174868 AGATGTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (16 bp):
TTAAATTATTTTAATT
Found at i:176518 original size:23 final size:23
Alignment explanation
Indices: 176463--176518 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
176453 TAATTAATTC
*
176463 ATATTAATTTTATAATAATAAAA
1 ATATTTATTTTATAATAATAAAA
* *
176486 ATGATATATTTTGTAA-AATAAAA
1 AT-ATTTATTTTATAATAATAAAA
176509 TATATTTATT
1 -ATATTTATT
176519 GCATATTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
23 15 0.56
24 12 0.44
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (23 bp):
ATATTTATTTTATAATAATAAAA
Found at i:179347 original size:38 final size:36
Alignment explanation
Indices: 179271--179347 Score: 84
Period size: 38 Copynumber: 2.1 Consensus size: 36
179261 TTTCTCCTCC
* * *
179271 TTTTTTAATTAAAATTTAAATTATTATTGTAAATAT
1 TTTTTTAATTAAAATTTAAATAAATATTGTAAACAT
*
179307 TTTTTTAATTATATAGATTT-AATAAATATTGTATACAT
1 TTTTTTAATTA-A-A-ATTTAAATAAATATTGTAAACAT
179345 TTT
1 TTT
179348 ATGAGTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
36 11 0.32
37 1 0.03
38 18 0.53
39 4 0.12
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (36 bp):
TTTTTTAATTAAAATTTAAATAAATATTGTAAACAT
Found at i:183006 original size:18 final size:19
Alignment explanation
Indices: 182983--183018 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
182973 ATAATCAGAT
182983 TAAAA-TTAATATTATAAG
1 TAAAATTTAATATTATAAG
*
183001 TAAAATTTATTATTATAA
1 TAAAATTTAATATTATAA
183019 AGTATTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (19 bp):
TAAAATTTAATATTATAAG
Found at i:185286 original size:2 final size:2
Alignment explanation
Indices: 185274--185310 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
185264 TTCCAATTCC
* *
185274 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
185311 GAAAAGAAAA
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:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:186327 original size:2 final size:2
Alignment explanation
Indices: 186320--186348 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
186310 AAATTTCTCT
186320 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
186349 TATATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:187946 original size:27 final size:27
Alignment explanation
Indices: 187901--188009 Score: 71
Period size: 27 Copynumber: 3.8 Consensus size: 27
187891 TGCTATTCGT
*
187901 ATATTTTAT-TATATAATAATATTTAAA
1 ATATTTTATATTTAT-ATAATATTTAAA
*
187928 ATATTTTATATTTATATAA-ATTT-TA
1 ATATTTTATATTTATATAATATTTAAA
* *
187953 TTATATTAATAATTCATATTATATATATTTTAAA
1 ATAT-TTTAT-ATT--TA-TATA-ATA-TTTAAA
*
187987 ATATTTATATATTTATATTATAT
1 ATATTT-TATATTTATATAATAT
188010 CATGTATTAA
Statistics
Matches: 63, Mismatches: 8, Indels: 21
0.68 0.09 0.23
Matches are distributed among these distances:
25 4 0.06
26 8 0.13
27 16 0.25
28 5 0.08
29 5 0.08
30 7 0.11
31 3 0.05
32 1 0.02
33 8 0.13
34 6 0.10
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (27 bp):
ATATTTTATATTTATATAATATTTAAA
Found at i:187976 original size:32 final size:33
Alignment explanation
Indices: 187939--188009 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 33
187929 TATTTTATAT
**
187939 TTATATAAATTTTATTATATTAATA-ATTCATA
1 TTATATAAATTTTAAAATATTAATATATTCATA
* * *
187971 TTATATATATTTTAAAATATTTATATATTTATA
1 TTATATAAATTTTAAAATATTAATATATTCATA
188004 TTATAT
1 TTATAT
188010 CATGTATTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
32 21 0.64
33 12 0.36
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.56
Consensus pattern (33 bp):
TTATATAAATTTTAAAATATTAATATATTCATA
Found at i:187995 original size:18 final size:18
Alignment explanation
Indices: 187922--188000 Score: 63
Period size: 18 Copynumber: 4.1 Consensus size: 18
187912 TATAATAATA
187922 TTTAAAATATTT-TATAT
1 TTTAAAATATTTATATAT
187939 TTATATAAAT-TTTATTATAT
1 TT-TA-AAATATTTA-TATAT
* *
187959 TAATAATTCATATTATATATAT
1 T-TTAA--AATATT-TATATAT
187981 TTTAAAATATTTATATAT
1 TTTAAAATATTTATATAT
187999 TT
1 TT
188001 ATATTATATC
Statistics
Matches: 49, Mismatches: 4, Indels: 17
0.70 0.06 0.24
Matches are distributed among these distances:
17 2 0.04
18 14 0.29
19 10 0.20
20 8 0.16
21 5 0.10
22 8 0.16
23 2 0.04
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTAAAATATTTATATAT
Found at i:188018 original size:58 final size:62
Alignment explanation
Indices: 187907--188021 Score: 150
Period size: 59 Copynumber: 1.9 Consensus size: 62
187897 TCGTATATTT
* *
187907 TATTATATAATAATATTTAAAATATTTTATATTTATATAAATTTTATTATATTAATAATTCA
1 TATTATATAATAATATTTAAAATATTTTATATTTATATAAATATCATTATATTAATAATTCA
* *
187969 TATTATAT-AT-AT-TTTAAAATATTTATATATTTATAT-TATATCA-TGTATTAATA
1 TATTATATAATAATATTTAAAATATTT-TATATTTATATAAATATCATTATATTAATA
188022 TTTTTTACAT
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
58 9 0.19
59 16 0.33
60 13 0.27
61 2 0.04
62 8 0.17
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.54
Consensus pattern (62 bp):
TATTATATAATAATATTTAAAATATTTTATATTTATATAAATATCATTATATTAATAATTCA
Found at i:188311 original size:19 final size:20
Alignment explanation
Indices: 188283--188325 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
188273 TATAATTTAA
*
188283 TTTAATTTAAAACAATAT-T
1 TTTAAATTAAAACAATATAT
*
188302 TTTAAATTAAAATAATATAT
1 TTTAAATTAAAACAATATAT
188322 TTTA
1 TTTA
188326 TTTAAATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
TTTAAATTAAAACAATATAT
Found at i:188330 original size:19 final size:19
Alignment explanation
Indices: 188282--188331 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
188272 TTATAATTTA
*
188282 ATTTAATTTAAAACAATAT
1 ATTTTATTTAAAACAATAT
* *
188301 -TTTTAAATTAAAATAATAT
1 ATTTT-ATTTAAAACAATAT
188320 ATTTTATTTAAA
1 ATTTTATTTAAA
188332 TTTAATTATA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 3 0.12
19 18 0.72
20 4 0.16
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (19 bp):
ATTTTATTTAAAACAATAT
Found at i:191052 original size:3 final size:3
Alignment explanation
Indices: 191044--191091 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
191034 ATGATAAAAA
191044 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
191092 ATAATTTCAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:191535 original size:2 final size:2
Alignment explanation
Indices: 191528--191556 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
191518 CATGATCAAA
191528 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
191557 AAGGACAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:194694 original size:12 final size:12
Alignment explanation
Indices: 194677--194701 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
194667 AAAGAAAGAA
194677 GATAAATGAAAT
1 GATAAATGAAAT
194689 GATAAATGAAAT
1 GATAAATGAAAT
194701 G
1 G
194702 GAATTAAGAT
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:0.56, C:0.00, G:0.20, T:0.24
Consensus pattern (12 bp):
GATAAATGAAAT
Found at i:195175 original size:21 final size:21
Alignment explanation
Indices: 195151--195190 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
195141 TTTTAATATT
*
195151 TAAAAATTTTAGTTAAATTGA
1 TAAAAATGTTAGTTAAATTGA
* *
195172 TAAATATGTTATTTAAATT
1 TAAAAATGTTAGTTAAATT
195191 AAATCATATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.47
Consensus pattern (21 bp):
TAAAAATGTTAGTTAAATTGA
Found at i:196347 original size:22 final size:22
Alignment explanation
Indices: 196322--196365 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
196312 TAAGAAATAA
*
196322 TAAA-AATAAATATTTTATAAAT
1 TAAATAAT-AATATTATATAAAT
*
196344 TAAATAATATTATTATATAAAT
1 TAAATAATAATATTATATAAAT
196366 ATTTATATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TAAATAATAATATTATATAAAT
Found at i:197612 original size:21 final size:20
Alignment explanation
Indices: 197582--197621 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
197572 TTTTGTTAAA
197582 TAAAATTATTTTAA-ATAATT
1 TAAAATTA-TTTAATATAATT
197602 TAAATATTATTTAATATAAT
1 TAAA-ATTATTTAATATAAT
197622 AAATAAACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TAAAATTATTTAATATAATT
Found at i:197624 original size:19 final size:19
Alignment explanation
Indices: 197580--197626 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 19
197570 TATTTTGTTA
197580 AATAAA-ATTATTTTAAAT
1 AATAAATATTATTTTAAAT
197598 AATTTAAATATTA-TTTAATAT
1 AA--TAAATATTATTTTAA-AT
197619 AATAAATA
1 AATAAATA
197627 AACTTATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
18 2 0.08
19 6 0.24
20 9 0.36
21 8 0.32
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
AATAAATATTATTTTAAAT
Found at i:199667 original size:24 final size:23
Alignment explanation
Indices: 199640--199687 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
199630 AAGACTTTCA
* *
199640 AAATTAAATTCAATTTATATAATT
1 AAATCAAATTCAA-TTATAAAATT
*
199664 AAATCAAGTTCAATTATAAAATT
1 AAATCAAATTCAATTATAAAATT
199687 A
1 A
199688 TCTTATAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (23 bp):
AAATCAAATTCAATTATAAAATT
Found at i:199759 original size:20 final size:20
Alignment explanation
Indices: 199727--199764 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
199717 TATGTAATCG
199727 TATAATATCTTAAATTATCA
1 TATAATATCTTAAATTATCA
199747 TATATATAT-TTAAATTAT
1 TATA-ATATCTTAAATTAT
199765 TTATTTTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (20 bp):
TATAATATCTTAAATTATCA
Found at i:199981 original size:21 final size:22
Alignment explanation
Indices: 199941--199982 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
199931 ACTTCTTTTT
199941 ATTTTGTCTTACTAATTCTTAA
1 ATTTTGTCTTACTAATTCTTAA
199963 ATTTTAGTCTTA-T-ATTCTTA
1 ATTTT-GTCTTACTAATTCTTA
199983 TTTATTCTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.37
22 6 0.32
23 6 0.32
ACGTcount: A:0.26, C:0.12, G:0.05, T:0.57
Consensus pattern (22 bp):
ATTTTGTCTTACTAATTCTTAA
Found at i:200113 original size:21 final size:23
Alignment explanation
Indices: 200078--200127 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 23
200068 TATATGTTAA
200078 AATTTAAATTCATCAA-ATTAATT
1 AATTTAAATTCATCAATA-TAATT
*
200101 ATTTTAAA-T-ATCAATATAATT
1 AATTTAAATTCATCAATATAATT
200122 AATTTA
1 AATTTA
200128 TAAAATTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 15 0.62
22 2 0.08
23 7 0.29
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (23 bp):
AATTTAAATTCATCAATATAATT
Found at i:200532 original size:19 final size:21
Alignment explanation
Indices: 200508--200546 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
200498 CTCTTCCAAA
*
200508 ATTAT-ATCTAAT-TAATTAT
1 ATTATAATCAAATCTAATTAT
200527 ATTATAATCAAATCTAATTA
1 ATTATAATCAAATCTAATTA
200547 AAATCTCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (21 bp):
ATTATAATCAAATCTAATTAT
Found at i:201390 original size:22 final size:21
Alignment explanation
Indices: 201356--201402 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
201346 TTTATATTTT
201356 TATTTATTATTTAAATATAAC
1 TATTTATTATTTAAATATAAC
* *
201377 TATTTATTTATTTAAATTTAAT
1 TATTTA-TTATTTAAATATAAC
201399 TATT
1 TATT
201403 AGTATACACT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTTATTATTTAAATATAAC
Found at i:201768 original size:16 final size:15
Alignment explanation
Indices: 201749--201862 Score: 59
Period size: 15 Copynumber: 6.9 Consensus size: 15
201739 AATTTGAACA
**
201749 TAAATTTAAAATATTT
1 TAAATTTAAAA-AAAT
201765 TAAATTTTAAAAAAAT
1 TAAA-TTTAAAAAAAT
201781 TAAATTTAAATTTAAAATGAT
1 TAAATTT-AA---AAAA--AT
* *
201802 TAAAAATTAAAAAGAT
1 T-AAATTTAAAAAAAT
201818 TAAA-TTAAAAAAACT
1 TAAATTTAAAAAAA-T
* *
201833 CAAATTCAAAAAAAAAT
1 TAAATT--TAAAAAAAT
201850 TAAATTTAAAAAA
1 TAAATTTAAAAAA
201863 GCTCGAATGA
Statistics
Matches: 77, Mismatches: 9, Indels: 25
0.69 0.08 0.23
Matches are distributed among these distances:
14 8 0.10
15 16 0.21
16 16 0.21
17 13 0.17
18 10 0.13
19 4 0.05
21 5 0.06
22 5 0.06
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (15 bp):
TAAATTTAAAAAAAT
Found at i:201811 original size:22 final size:22
Alignment explanation
Indices: 201764--201812 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
201754 TTAAAATATT
*
201764 TTAAATTTTAAAAAAATTAAAT
1 TTAAATTTTAAAAAAATTAAAA
**
201786 TTAAA-TTTAAAATGATTAAAAA
1 TTAAATTTTAAAAAAATT-AAAA
201808 TTAAA
1 TTAAA
201813 AAGATTAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (22 bp):
TTAAATTTTAAAAAAATTAAAA
Found at i:201814 original size:37 final size:37
Alignment explanation
Indices: 201749--201823 Score: 98
Period size: 37 Copynumber: 2.0 Consensus size: 37
201739 AATTTGAACA
**
201749 TAAATTTAAAATATTTTAAATTTTAAAAAAATTAAATT
1 TAAATTTAAAATA-TTTAAAAATTAAAAAAATTAAATT
*
201787 TAAATTTAAAATGA-TTAAAAATTAAAAAGATTAAATT
1 TAAATTTAAAAT-ATTTAAAAATTAAAAAAATTAAATT
201824 AAAAAAACTC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
37 20 0.61
38 12 0.36
39 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (37 bp):
TAAATTTAAAATATTTAAAAATTAAAAAAATTAAATT
Found at i:201830 original size:17 final size:16
Alignment explanation
Indices: 201810--201862 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
201800 ATTAAAAATT
*
201810 AAAAAGATTAAATT-A
1 AAAAAAATTAAATTAA
* *
201825 AAAAAACTCAAATTCAA
1 AAAAAAATTAAATT-AA
201842 AAAAAAATTAAATTTAA
1 AAAAAAATTAAA-TTAA
201859 AAAA
1 AAAA
201863 GCTCGAATGA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
15 11 0.37
17 17 0.57
18 2 0.07
ACGTcount: A:0.70, C:0.06, G:0.02, T:0.23
Consensus pattern (16 bp):
AAAAAAATTAAATTAA
Found at i:206057 original size:6 final size:6
Alignment explanation
Indices: 206039--206069 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
206029 CCCTTTTTTG
*
206039 TTTCTC TTCCTC TTTCTC TTTCTC TTTCTC T
1 TTTCTC TTTCTC TTTCTC TTTCTC TTTCTC T
206070 CGACTCTCCG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (6 bp):
TTTCTC
Found at i:208603 original size:36 final size:36
Alignment explanation
Indices: 208528--208611 Score: 109
Period size: 36 Copynumber: 2.3 Consensus size: 36
208518 TAGTAAAGAT
**
208528 ATTATATTAAAAATATATATATATATAAATATATTA
1 ATTATATTAAAAATATATATATATATAAATATAAAA
*
208564 ATTA-ATTAAAAAGTATATTTATAT-TAAATAATAAAA
1 ATTATATTAAAAA-TATATATATATATAAAT-ATAAAA
208600 ATTATATTAAAA
1 ATTATATTAAAA
208612 TGAAATAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
35 13 0.31
36 22 0.52
37 7 0.17
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (36 bp):
ATTATATTAAAAATATATATATATATAAATATAAAA
Found at i:208605 original size:25 final size:26
Alignment explanation
Indices: 208557--208607 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
208547 TATATATAAA
*
208557 TATATTAATTAATTAAAAAGTATATT
1 TATATTAAATAATTAAAAAGTATATT
*
208583 TATATTAAATAA-TAAAAATTATATT
1 TATATTAAATAATTAAAAAGTATATT
208608 AAAATGAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 12 0.52
26 11 0.48
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (26 bp):
TATATTAAATAATTAAAAAGTATATT
Found at i:208617 original size:25 final size:25
Alignment explanation
Indices: 208570--208619 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
208560 ATTAATTAAT
* * *
208570 TAAAAAGTATATTTATATTAAATAA
1 TAAAAAGTATATTAAAATGAAATAA
*
208595 TAAAAATTATATTAAAATGAAATAA
1 TAAAAAGTATATTAAAATGAAATAA
208620 ATATTAAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (25 bp):
TAAAAAGTATATTAAAATGAAATAA
Found at i:208693 original size:16 final size:17
Alignment explanation
Indices: 208662--208703 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
208652 TTAATAAAAT
*
208662 AAATATAAAAAGTTAAC
1 AAATATAAAAAGTTAAA
*
208679 AAATA-AAAAATTTAAA
1 AAATATAAAAAGTTAAA
*
208695 AAATTTAAA
1 AAATATAAA
208704 TAATTAGAGG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.26
Consensus pattern (17 bp):
AAATATAAAAAGTTAAA
Found at i:209063 original size:28 final size:28
Alignment explanation
Indices: 209032--209128 Score: 85
Period size: 34 Copynumber: 3.3 Consensus size: 28
209022 TATAATAATA
209032 ATAATATTTAAAATATTTTATATTTTAT
1 ATAATATTTAAAATATTTTATATTTTAT
*
209060 ATAA-ATTTTAATAAATTAATAATTTATATTATAT
1 ATAATA-TTT-A-AAA-T-AT--TTTATATTTTAT
209094 A-AAT-TTTAAAATA-TTTATATATTTAT
1 ATAATATTTAAAATATTTTATAT-TTTAT
209120 ATAATATTT
1 ATAATATTT
209129 TATATGATAA
Statistics
Matches: 56, Mismatches: 2, Indels: 22
0.70 0.03 0.28
Matches are distributed among these distances:
25 7 0.12
26 5 0.09
27 4 0.07
28 11 0.20
29 2 0.04
30 6 0.11
31 2 0.04
32 5 0.09
33 2 0.04
34 12 0.21
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
ATAATATTTAAAATATTTTATATTTTAT
Found at i:209096 original size:32 final size:33
Alignment explanation
Indices: 209043--209126 Score: 102
Period size: 32 Copynumber: 2.5 Consensus size: 33
209033 TAATATTTAA
209043 AATAT-TTTATATTTTATATAAATTTTAATAA-ATT
1 AATATATTTATA--TTATATAAATTTTAA-AATATT
209077 AATA-ATTTATATTATATAAATTTTAAAATATT
1 AATATATTTATATTATATAAATTTTAAAATATT
* *
209109 TATATATTTATATAATAT
1 AATATATTTATATTATAT
209127 TTTATATGAT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
31 2 0.04
32 21 0.47
33 12 0.27
34 10 0.22
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (33 bp):
AATATATTTATATTATATAAATTTTAAAATATT
Found at i:209147 original size:28 final size:26
Alignment explanation
Indices: 209077--209147 Score: 72
Period size: 28 Copynumber: 2.6 Consensus size: 26
209067 TTAATAAATT
209077 AATAATTTATATTATATAAATTTTAA
1 AATAATTTATATTATATAAATTTTAA
*
209103 AATATTTATATATTTATATAATATTTTATA
1 AATAATT-TATA-TTATATAA-ATTTTA-A
*
209133 TGATAATTTA-ATTAT
1 -AATAATTTATATTAT
209148 TTTTATATCA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
26 6 0.16
27 4 0.11
28 12 0.32
29 7 0.19
30 3 0.08
31 5 0.14
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (26 bp):
AATAATTTATATTATATAAATTTTAA
Found at i:209306 original size:2 final size:2
Alignment explanation
Indices: 209299--209333 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
209289 TAAGAAGTGA
209299 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
209334 ATAAGAGTTT
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:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:210190 original size:36 final size:36
Alignment explanation
Indices: 210150--210249 Score: 105
Period size: 38 Copynumber: 2.8 Consensus size: 36
210140 TTATTAAAGT
*
210150 TATATTTATGTTAAATAATAAAATATAAATTAAAAA
1 TATATTTATATTAAATAATAAAATATAAATTAAAAA
* * *
210186 TATATTTATCTTGAATAATAATAAAATAT-TATTAAAAT
1 TATATTTATATT--A-AATAATAAAATATAAATTAAAAA
* *
210224 TATACTTATATTAAAGAAT-AAATATA
1 TATATTTATATTAAATAATAAAATATA
210250 GAAGAAATAA
Statistics
Matches: 54, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
34 6 0.11
35 5 0.09
36 12 0.22
38 18 0.33
39 13 0.24
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.41
Consensus pattern (36 bp):
TATATTTATATTAAATAATAAAATATAAATTAAAAA
Found at i:210244 original size:38 final size:36
Alignment explanation
Indices: 210134--210238 Score: 115
Period size: 36 Copynumber: 2.9 Consensus size: 36
210124 AATAAATAGT
* *
210134 TAAAA-ATTATTAAAGTTATATTTATGTT-AAATAA
1 TAAAATATTATTAAAATTATATTTATATTAAAATAA
* * *
210168 TAAAATATAAATTAAAAATATATTTATCTTGAATAATAA
1 TAAAATAT-TATTAAAATTATATTTATATT-AA-AATAA
*
210207 TAAAATATTATTAAAATTATACTTATATTAAA
1 TAAAATATTATTAAAATTATATTTATATTAAA
210239 GAATAAATAT
Statistics
Matches: 58, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
34 5 0.09
35 2 0.03
36 18 0.31
37 2 0.03
38 18 0.31
39 13 0.22
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (36 bp):
TAAAATATTATTAAAATTATATTTATATTAAAATAA
Found at i:211330 original size:24 final size:24
Alignment explanation
Indices: 211303--211350 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
211293 TATAAAATTT
211303 TAAAAT-TTTTCTTTA-ATTTATAAA
1 TAAAATATTTT-TTTATA-TTATAAA
211327 TAAAATATTTTTTTATATTATAAA
1 TAAAATATTTTTTTATATTATAAA
211351 AATTTAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (24 bp):
TAAAATATTTTTTTATATTATAAA
Found at i:211560 original size:1 final size:1
Alignment explanation
Indices: 211554--211578 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
211544 TTTGGTGGGG
211554 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
211579 CCCCCTCAAG
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:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:211827 original size:6 final size:6
Alignment explanation
Indices: 211816--211841 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
211806 AAGGTAAAAC
211816 AAATAA AAATAA AAATAA AAATAA AA
1 AAATAA AAATAA AAATAA AAATAA AA
211842 CTTGTTCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:212412 original size:11 final size:11
Alignment explanation
Indices: 212283--212415 Score: 60
Period size: 11 Copynumber: 12.0 Consensus size: 11
212273 TAAAAAATTG
*
212283 ATATGAATATA
1 ATATAAATATA
* *
212294 ATAAAAATATT
1 ATATAAATATA
* * *
212305 TTATAAAAATT
1 ATATAAATATA
*
212316 ATATAAATTTA
1 ATATAAATATA
*
212327 ATTATTAAAATATT
1 A-TA-T-AAATATA
**
212341 ATGATTTATATAA
1 AT-ATAAATAT-A
212354 ATATATAATAT-
1 ATATA-AATATA
*
212365 -TTTAAATATA
1 ATATAAATATA
212375 ATAT---TATA
1 ATATAAATATA
*
212383 ATATAAAAATA
1 ATATAAATATA
*
212394 AAATAAATATA
1 ATATAAATATA
212405 ATATAAATATA
1 ATATAAATATA
212416 TACATGGTAA
Statistics
Matches: 88, Mismatches: 23, Indels: 22
0.66 0.17 0.17
Matches are distributed among these distances:
8 8 0.09
9 5 0.06
10 3 0.03
11 48 0.55
12 8 0.09
13 9 0.10
14 7 0.08
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (11 bp):
ATATAAATATA
Found at i:218615 original size:25 final size:26
Alignment explanation
Indices: 218574--218624 Score: 70
Period size: 24 Copynumber: 2.0 Consensus size: 26
218564 AAAGTTAAAA
218574 ATATTTAAAAATAAAAA-T-ATTTAT
1 ATATTTAAAAATAAAAAGTAATTTAT
*
218598 ATATTTTAAAATAAAAAAGTAATTTAT
1 ATATTTAAAAAT-AAAAAGTAATTTAT
218625 TTATAATAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 11 0.48
25 5 0.22
26 1 0.04
27 6 0.26
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (26 bp):
ATATTTAAAAATAAAAAGTAATTTAT
Found at i:221362 original size:49 final size:49
Alignment explanation
Indices: 221313--221407 Score: 113
Period size: 49 Copynumber: 2.0 Consensus size: 49
221303 TTATATTTTA
* * * * *
221313 AAATAACATTAAA-ATTTTATTTTTATATTAAT-ATTTATAATTAAATTT
1 AAATAAAAATAAATATTTTATTATTAAAATAATAATTT-TAATTAAATTT
*
221361 AAATAAAAATAAATTTTTTATTATTAAAATAATAATTTTAATTAAAT
1 AAATAAAAATAAATATTTTATTATTAAAATAATAATTTTAATTAAAT
221408 CAAACTTGTC
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
48 11 0.28
49 24 0.62
50 4 0.10
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (49 bp):
AAATAAAAATAAATATTTTATTATTAAAATAATAATTTTAATTAAATTT
Found at i:221399 original size:21 final size:20
Alignment explanation
Indices: 221366--221404 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
221356 AATTTAAATA
* *
221366 AAAATAAATTTTTTATTATT
1 AAAATAAAATTTTAATTATT
221386 AAAATAATAATTTTAATTA
1 AAAATAA-AATTTTAATTA
221405 AATCAAACTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AAAATAAAATTTTAATTATT
Found at i:228153 original size:2 final size:2
Alignment explanation
Indices: 228146--228171 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
228136 CGTTACTTTG
228146 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
228172 TTACAGATAG
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:229113 original size:37 final size:38
Alignment explanation
Indices: 229038--229140 Score: 100
Period size: 37 Copynumber: 2.7 Consensus size: 38
229028 ATGTTTCTAG
* * * *
229038 ATAAAATGCTGCTAAATCAAACCATAGAGCGATATTTT
1 ATAAAACGTTGCTAAATCAAACCATACAGCGACATTTT
* * *
229076 A-AAAACGTTGCTAAATCAAATCATACAGTGACGTTTT
1 ATAAAACGTTGCTAAATCAAACCATACAGCGACATTTT
*
229113 ATTTGTAAACGTTGCTAAATCAAACCAT
1 A--T-AAAACGTTGCTAAATCAAACCAT
229141 GTAATAACGT
Statistics
Matches: 52, Mismatches: 9, Indels: 5
0.79 0.14 0.08
Matches are distributed among these distances:
37 30 0.58
38 1 0.02
41 21 0.40
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.30
Consensus pattern (38 bp):
ATAAAACGTTGCTAAATCAAACCATACAGCGACATTTT
Found at i:230688 original size:28 final size:27
Alignment explanation
Indices: 230596--230688 Score: 84
Period size: 28 Copynumber: 3.4 Consensus size: 27
230586 TGATATAAAT
* *
230596 TATTATTTAATAATAAAATAATTTTTA
1 TATTATTTAATAATAAAATAAATTTAA
* * *
230623 TTTTAATTTAATCATAAAA-ATA-TTAA
1 TATT-ATTTAATAATAAAATAAATTTAA
230649 TA-TATTTAAATAATAAAATAAATTATAA
1 TATTATTT-AATAATAAAATAAATT-TAA
*
230677 AATTATTTAATA
1 TATTATTTAATA
230689 TTTAATTCTA
Statistics
Matches: 51, Mismatches: 9, Indels: 11
0.72 0.13 0.15
Matches are distributed among these distances:
24 4 0.08
25 10 0.20
26 6 0.12
27 5 0.10
28 21 0.41
29 5 0.10
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (27 bp):
TATTATTTAATAATAAAATAAATTTAA
Found at i:233915 original size:18 final size:19
Alignment explanation
Indices: 233879--233918 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
233869 GATCAGCATC
*
233879 AATCACAGATTTTTTTAAG
1 AATCACAGATTTTTCTAAG
233898 AATCACAGA-TTTTCTAAG
1 AATCACAGATTTTTCTAAG
233916 AAT
1 AAT
233919 TACAATTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (19 bp):
AATCACAGATTTTTCTAAG
Found at i:234730 original size:17 final size:17
Alignment explanation
Indices: 234635--234754 Score: 77
Period size: 18 Copynumber: 6.9 Consensus size: 17
234625 ACCCTTTTGT
*
234635 AATCGCAGATTTTCAAAG
1 AATCACAGATTTTC-AAG
234653 AATCACAGATTTTC-AG
1 AATCACAGATTTTCAAG
* * *
234669 CATCAATCAAGATATT-AGG
1 AATC-A-C-AGATTTTCAAG
* *
234688 AATCACAGATTTTTTAAA
1 AATCACAGA-TTTTCAAG
234706 AATCACAGATTTTCAAG
1 AATCACAGATTTTCAAG
* * *
234723 AATTACAGA-TAT-ATAT
1 AATCACAGATTTTCA-AG
234739 AATCACAGATTTTCAA
1 AATCACAGATTTTCAA
234755 CCCCAATAAT
Statistics
Matches: 78, Mismatches: 15, Indels: 19
0.70 0.13 0.17
Matches are distributed among these distances:
15 1 0.01
16 19 0.24
17 22 0.28
18 26 0.33
19 10 0.13
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.32
Consensus pattern (17 bp):
AATCACAGATTTTCAAG
Found at i:238282 original size:20 final size:18
Alignment explanation
Indices: 238241--238285 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
238231 TTTTTTATAT
238241 AAATATATTTAATTTTTA
1 AAATATATTTAATTTTTA
* *
238259 AAATATTTTTATATATTTTG
1 AAATATATTTA-AT-TTTTA
238279 AAATATA
1 AAATATA
238286 AATCTCTCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 10 0.45
19 2 0.09
20 10 0.45
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (18 bp):
AAATATATTTAATTTTTA
Found at i:240075 original size:16 final size:16
Alignment explanation
Indices: 240054--240084 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
240044 ATTTTTTTTC
*
240054 TTTTTTTCACCCATAA
1 TTTTTTCCACCCATAA
240070 TTTTTTCCACCCATA
1 TTTTTTCCACCCATA
240085 CAATGGGTGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.29, G:0.00, T:0.48
Consensus pattern (16 bp):
TTTTTTCCACCCATAA
Found at i:240381 original size:31 final size:32
Alignment explanation
Indices: 240346--240406 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
240336 AAATTTAGTC
240346 ATAAAGAGATT-AAGTTCTTTATAACTCTTTT
1 ATAAAGAGATTAAAGTTCTTTATAACTCTTTT
* *
240377 ATAAAGAGATTAAATTTCTTTATATCTCTT
1 ATAAAGAGATTAAAGTTCTTTATAACTCTT
240407 GCTTACCTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 11 0.41
32 16 0.59
ACGTcount: A:0.36, C:0.10, G:0.08, T:0.46
Consensus pattern (32 bp):
ATAAAGAGATTAAAGTTCTTTATAACTCTTTT
Found at i:240837 original size:22 final size:22
Alignment explanation
Indices: 240791--240841 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
240781 AAAAATTATT
* *
240791 TTATAA-TAATATTTATATATT
1 TTATAATTAATATTTAAATATA
240812 TTATAATTAA-ATATTAAATATA
1 TTATAATTAATAT-TTAAATATA
240834 TTATAATT
1 TTATAATT
240842 TATAAAAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 8 0.31
22 18 0.69
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TTATAATTAATATTTAAATATA
Found at i:244758 original size:7 final size:7
Alignment explanation
Indices: 244746--244771 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
244736 TCCAAACAAG
244746 CAGAGAC
1 CAGAGAC
244753 CAGAGAC
1 CAGAGAC
244760 CAGAGAC
1 CAGAGAC
244767 CAGAG
1 CAGAG
244772 GAGGGATGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.27, G:0.31, T:0.00
Consensus pattern (7 bp):
CAGAGAC
Found at i:245759 original size:122 final size:121
Alignment explanation
Indices: 245618--245839 Score: 327
Period size: 122 Copynumber: 1.8 Consensus size: 121
245608 CCACCCACTC
* * * * * *
245618 ATTTTATTATAATAGTTATAATTTTATTATATTAGTTGTTGGCTTGTAAAATCAAAATTATGATT
1 ATTTTATTATAATAATTATAATTTTATTATATTAGTTGTTGACTTATAAAATCAAAACTATAATA
* *
245683 TACATTTTAAAAAAAATTAATAAAGAAATTTAATAATAAGCTCAATCCAACTCATGA
66 TACACTTT-AAAAAAATTAATAAAAAAATTTAATAATAAGCTCAATCCAACTCATGA
* *
245740 ATTTTATTATAATAATTATAATTTTATTTTATTAGTTGTTGACTTATAAAATCAAAGCTATAATA
1 ATTTTATTATAATAATTATAATTTTATTATATTAGTTGTTGACTTATAAAATCAAAACTATAATA
* *
245805 TGCACTTTAAAAAAATTAGTAAAAAAATTTAATAA
66 TACACTTTAAAAAAATTAATAAAAAAATTTAATAA
245840 AATTATATTA
Statistics
Matches: 88, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
121 25 0.28
122 63 0.72
ACGTcount: A:0.45, C:0.06, G:0.07, T:0.42
Consensus pattern (121 bp):
ATTTTATTATAATAATTATAATTTTATTATATTAGTTGTTGACTTATAAAATCAAAACTATAATA
TACACTTTAAAAAAATTAATAAAAAAATTTAATAATAAGCTCAATCCAACTCATGA
Found at i:245853 original size:32 final size:30
Alignment explanation
Indices: 245817--245893 Score: 77
Period size: 32 Copynumber: 2.5 Consensus size: 30
245807 CACTTTAAAA
*
245817 AAATTAGTAAAAAAATTTAATAAAAT-TATATT
1 AAATTAATAAAAAAA-TTAA-AAAATATAT-TT
*
245849 AAATTATTAAAATTAAATTAAAAAATATATTT
1 AAATTAATAAAA--AAATTAAAAAATATATTT
245881 AAA-TAATAAAAAA
1 AAATTAATAAAAAA
245894 TATAATATGA
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
29 2 0.05
31 7 0.17
32 21 0.52
33 7 0.17
34 3 0.08
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (30 bp):
AAATTAATAAAAAAATTAAAAAATATATTT
Found at i:245884 original size:18 final size:19
Alignment explanation
Indices: 245861--245897 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
245851 ATTATTAAAA
245861 TTAAAT-TAAAAAATATAT
1 TTAAATATAAAAAATATAT
245879 TTAAATAATAAAAAATATA
1 TTAAAT-ATAAAAAATATA
245898 ATATGAACAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TTAAATATAAAAAATATAT
Found at i:245963 original size:21 final size:22
Alignment explanation
Indices: 245937--245982 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
245927 ACATATTTAC
*
245937 AAATATAAATATATTT-AAATA
1 AAATATAAATATATTTCAAACA
*
245958 AAATATAATTATATTTCAAACA
1 AAATATAAATATATTTCAAACA
245980 AAA
1 AAA
245983 GCATATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (22 bp):
AAATATAAATATATTTCAAACA
Found at i:246331 original size:24 final size:23
Alignment explanation
Indices: 246276--246332 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 23
246266 TTTTGAGTTA
* *
246276 ATTTGATTTAATTTAAAATAATT
1 ATTTTATTTAAATTAAAATAATT
246299 -TTTTA---AAATTAAAATAATAT
1 ATTTTATTTAAATTAAAATAAT-T
246319 ATTTTATTTAAATT
1 ATTTTATTTAAATT
246333 TAATTATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 9
0.71 0.05 0.24
Matches are distributed among these distances:
19 12 0.44
20 1 0.04
21 5 0.19
22 4 0.15
24 5 0.19
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
ATTTTATTTAAATTAAAATAATT
Found at i:247865 original size:2 final size:2
Alignment explanation
Indices: 247858--247893 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
247848 GCTGCTTAAG
* *
247858 AT AT AT AT AT AT AT AT AT AT AC AT AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
247894 CATTCTCTGC
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:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:248016 original size:5 final size:5
Alignment explanation
Indices: 248002--248031 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
247992 TCTTGTTAGT
*
248002 GAAAA AAAAA GAAAA GAAAA GAAAA GAAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA
248032 CACTACAGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:248548 original size:33 final size:33
Alignment explanation
Indices: 248511--248584 Score: 89
Period size: 33 Copynumber: 2.2 Consensus size: 33
248501 TTTATGTTAT
248511 TATATAA-AAATAATTATACATT-ATATAATATAA
1 TATATAATAAATAA-TAT-CATTGATATAATATAA
* * *
248544 TATATAATATATAATATCATTGATATATTATAT
1 TATATAATAAATAATATCATTGATATAATATAA
248577 TATATAAT
1 TATATAAT
248585 TTTAAATTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
32 4 0.11
33 27 0.75
34 5 0.14
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (33 bp):
TATATAATAAATAATATCATTGATATAATATAA
Found at i:248549 original size:21 final size:19
Alignment explanation
Indices: 248509--248585 Score: 75
Period size: 21 Copynumber: 3.8 Consensus size: 19
248499 CATTTATGTT
*
248509 ATTATATAAAAATAATTATA
1 ATTATAT-AATATAATTATA
248529 CATTATATAATATAATATATA
1 -ATTATATAATATAAT-TATA
*
248550 A-TATATAATATCATTGATA
1 ATTATATAATATAATT-ATA
*
248569 TATTATATTATATAATT
1 -ATTATATAATATAATT
248586 TTAAATTATT
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
18 1 0.02
19 15 0.31
20 9 0.19
21 23 0.48
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (19 bp):
ATTATATAATATAATTATA
Found at i:249655 original size:2 final size:2
Alignment explanation
Indices: 249602--249636 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
249592 TGGACGATAA
*
249602 AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
249637 GAGAGAAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:249972 original size:2 final size:2
Alignment explanation
Indices: 249967--250003 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
249957 ACACACACAC
*
249967 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
250004 GATCAGAAGC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:252117 original size:21 final size:18
Alignment explanation
Indices: 252087--252126 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
252077 TATTTTTATT
252087 TAAATTTAATTATAAATATA
1 TAAATTTAA-TATAAA-ATA
252107 TAAATATTAATATAAAATA
1 TAAAT-TTAATATAAAATA
252126 T
1 T
252127 TTTTAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 11 0.58
21 4 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TAAATTTAATATAAAATA
Found at i:252135 original size:7 final size:7
Alignment explanation
Indices: 252125--252158 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
252115 AATATAAAAT
252125 ATTTTTA
1 ATTTTTA
252132 ATTTTTA
1 ATTTTTA
252139 ATTTTTA
1 ATTTTTA
252146 ATTTTTA
1 ATTTTTA
252153 ATTTTT
1 ATTTTT
252159 TAAATAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
ATTTTTA
Found at i:255044 original size:15 final size:16
Alignment explanation
Indices: 255006--255047 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
254996 TAATATTATA
*
255006 TGTGAATTCTCATGCT
1 TGTGAATTCTTATGCT
255022 TGTGAATTCTTATGCT
1 TGTGAATTCTTATGCT
255038 T-TGAATTCTT
1 TGTGAATTCTT
255048 TTGAATATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 9 0.36
16 16 0.64
ACGTcount: A:0.19, C:0.14, G:0.17, T:0.50
Consensus pattern (16 bp):
TGTGAATTCTTATGCT
Found at i:255672 original size:17 final size:17
Alignment explanation
Indices: 255650--255684 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
255640 TTGCATGTTT
255650 ATAATAAGTAGTCATAA
1 ATAATAAGTAGTCATAA
255667 ATAATAAGTAGTCATAA
1 ATAATAAGTAGTCATAA
255684 A
1 A
255685 CAAACTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.54, C:0.06, G:0.11, T:0.29
Consensus pattern (17 bp):
ATAATAAGTAGTCATAA
Found at i:256439 original size:20 final size:20
Alignment explanation
Indices: 256411--256485 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
256401 TTTTACCTTG
256411 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
256431 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
256451 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
256471 ATGTATCGATACATT
1 ATGTATCGATACATT
256486 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:256478 original size:40 final size:39
Alignment explanation
Indices: 256411--256488 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
256401 TTTTACCTTG
* *
256411 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
256451 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
256489 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:257433 original size:22 final size:22
Alignment explanation
Indices: 257399--257452 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
257389 AGCCTTTGAC
257399 CATGCA-TTTTTTATTATGTTT
1 CATGCATTTTTTTATTATGTTT
257420 CATGCATTTTTTTATTATGTTT
1 CATGCATTTTTTTATTATGTTT
257442 CATGCATTTTT
1 CATGCATTTTT
257453 AACATGTACA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 6 0.19
22 26 0.81
ACGTcount: A:0.19, C:0.11, G:0.09, T:0.61
Consensus pattern (22 bp):
CATGCATTTTTTTATTATGTTT
Found at i:263920 original size:12 final size:12
Alignment explanation
Indices: 263889--263921 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
263879 ACCCAATCCT
263889 AAAAAAAA-CAA
1 AAAAAAAACCAA
263900 AAAAAAAACCAA
1 AAAAAAAACCAA
263912 AAAAAAAACC
1 AAAAAAAACC
263922 TTTTCACCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.38
12 13 0.62
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAACCAA
Found at i:265139 original size:28 final size:27
Alignment explanation
Indices: 264935--265455 Score: 656
Period size: 27 Copynumber: 19.0 Consensus size: 27
264925 GTGTGACCTC
264935 TTTAAGTCCACAACTCCGTGGCACCCT
1 TTTAAGTCCACAACTCCGTGGCACCCT
*
264962 TTTAAGTCCATAACTCCGTGGCATCCC-
1 TTTAAGTCCACAACTCCGTGGCA-CCCT
*
264989 TTTAAGCGGTACCAC-ACTCCGTGGAACCCT
1 TTTAA---GT-CCACAACTCCGTGGCACCCT
* *
265019 TTTAAGTCCACAAATCCGTGGAACCC-
1 TTTAAGTCCACAACTCCGTGGCACCCT
265045 TTTAAGTCCACAACTCCGTGGCACCCTT
1 TTTAAGTCCACAACTCCGTGGCACCC-T
* *
265073 TTATAAGTCCATAACTCCCGTGGCATCTCT
1 TT-TAAGTCCACAACT-CCGTGGCA-CCCT
* *
265103 TTTAAGTCCACAAACTCTGTGGCACTCT
1 TTTAAGTCCAC-AACTCCGTGGCACCCT
*
265131 TTTTAGTCCACAACTCCGTGGCACCCT
1 TTTAAGTCCACAACTCCGTGGCACCCT
265158 TTTAAGTCCACAACTCCGTGGCACCCT
1 TTTAAGTCCACAACTCCGTGGCACCCT
265185 TTTAAGTCCACAACT-C-TGGCACCCT
1 TTTAAGTCCACAACTCCGTGGCACCCT
*
265210 TTTAAGTCCACAACTCTGTGGCACCCT
1 TTTAAGTCCACAACTCCGTGGCACCCT
265237 TTTAAGTCCACAACTCCGTGGCACCCT
1 TTTAAGTCCACAACTCCGTGGCACCCT
* *
265264 TTTAAGTCCACAAATCCGTGGCATCCT
1 TTTAAGTCCACAACTCCGTGGCACCCT
* *
265291 TTTAAGACCACAACTCCGTGGCATCTCT
1 TTTAAGTCCACAACTCCGTGGCA-CCCT
* *
265319 TTTGAGTCCACAACTCTGTGGCACCCT
1 TTTAAGTCCACAACTCCGTGGCACCCT
* *
265346 TTTGAGTCCACAACTCCCTGGCACCCT
1 TTTAAGTCCACAACTCCGTGGCACCCT
* * *
265373 TTTAAAATCCACAACTCTGTGGCACTCT
1 TTT-AAGTCCACAACTCCGTGGCACCCT
* *
265401 TTTAAAATCCACAACTCCGTGGCACTCT
1 TTT-AAGTCCACAACTCCGTGGCACCCT
* *
265429 TTTAAAATCCACAACTCTGTGGCACCC
1 TTT-AAGTCCACAACTCCGTGGCACCC
265456 ATTTCAAAGC
Statistics
Matches: 441, Mismatches: 36, Indels: 33
0.86 0.07 0.06
Matches are distributed among these distances:
25 24 0.05
26 29 0.07
27 209 0.47
28 112 0.25
29 30 0.07
30 32 0.07
31 5 0.01
ACGTcount: A:0.24, C:0.34, G:0.14, T:0.28
Consensus pattern (27 bp):
TTTAAGTCCACAACTCCGTGGCACCCT
Found at i:265638 original size:28 final size:28
Alignment explanation
Indices: 265009--266559 Score: 1157
Period size: 28 Copynumber: 54.2 Consensus size: 28
264999 ACCACACTCC
* * * *
265009 GTGGAACCCTTTT-AAGTCCACAAATCC
1 GTGGCACCCTTTTAAAGCCCACAAGTCA
* * * *
265036 GTGGAACCC-TTT-AAGTCCACAACTCC
1 GTGGCACCCTTTTAAAGCCCACAAGTCA
* * * *
265062 GTGGCACCCTTTTATAAGTCCATAACTCCC
1 GTGGCACCCTTTTA-AAGCCCACAAGT-CA
* * * *
265092 GTGGCATCTCTTTT-AAGTCCACAAACTCT
1 GTGGCA-CCCTTTTAAAGCCCAC-AAGTCA
* * * * *
265121 GTGGCACTCTTTT-TAGTCCACAACTCC
1 GTGGCACCCTTTTAAAGCCCACAAGTCA
* * *
265148 GTGGCACCCTTTT-AAGTCCACAACTCC
1 GTGGCACCCTTTTAAAGCCCACAAGTCA
* *
265175 GTGGCACCCTTTT-AAGTCCACAACTC-
1 GTGGCACCCTTTTAAAGCCCACAAGTCA
* * *
265201 -TGGCACCCTTTT-AAGTCCACAACTCT
1 GTGGCACCCTTTTAAAGCCCACAAGTCA
* * *
265227 GTGGCACCCTTTT-AAGTCCACAACTCC
1 GTGGCACCCTTTTAAAGCCCACAAGTCA
* * *
265254 GTGGCACCCTTTT-AAGTCCACAAATCC
1 GTGGCACCCTTTTAAAGCCCACAAGTCA
* * * *
265281 GTGGCATCCTTTT-AAGACCACAACTCC
1 GTGGCACCCTTTTAAAGCCCACAAGTCA
* * * * *
265308 GTGGCATCTCTTTT-GAGTCCACAACTCT
1 GTGGCA-CCCTTTTAAAGCCCACAAGTCA
* * * *
265336 GTGGCACCCTTTT-GAGTCCACAACTCC
1 GTGGCACCCTTTTAAAGCCCACAAGTCA
* ** * *
265363 CTGGCACCCTTTTAAAATCCACAACTCT
1 GTGGCACCCTTTTAAAGCCCACAAGTCA
* ** * *
265391 GTGGCACTCTTTTAAAATCCACAACTCC
1 GTGGCACCCTTTTAAAGCCCACAAGTCA
* ** * *
265419 GTGGCACTCTTTTAAAATCCACAACTCT
1 GTGGCACCCTTTTAAAGCCCACAAGTCA
* **
265447 GTGGCACCCATTTCAAAGCCCACACAAGTTG
1 GTGGCACCC-TTTTAAAG-CC-CACAAGTCA
* * *
265478 GTGGTAACCTATTTCAAAGCCCACACAAGTCG
1 GTGGCACCCT-TTT-AAAG-CC-CACAAGTCA
* *
265510 GTGGCAACCCATTTCAAAGCCCACACAAGTCG
1 GTGGC-ACCC-TTTTAAAG-CC-CACAAGTCA
*
265542 GTGGCAACCCCTTTCAAAGCCCACACAAGTCA
1 GTGGC-A-CCCTTTTAAAG-CC-CACAAGTCA
* *
265574 GTGGCACCCCTTTCAAAGCCCACGCAAGTTA
1 GTGGCA-CCCTTTTAAAGCCCA--CAAGTCA
*
265605 GTGGCACCCTTTTAAAGCCCACAAGTTA
1 GTGGCACCCTTTTAAAGCCCACAAGTCA
*
265633 GTGGCACTCTTTTCAAAGCCCACAAGTCA
1 GTGGCACCCTTTT-AAAGCCCACAAGTCA
* *
265662 GTGGCACCCTTTCAAAGCCCACAAGTTA
1 GTGGCACCCTTTTAAAGCCCACAAGTCA
*
265690 GTGGCACCTTTTTCAAAGCCCACGCAAGTCA
1 GTGGCACCCTTTT-AAAGCCCA--CAAGTCA
*
265721 GTGGCACCCTTTTGAAGCCCACAAGTCA
1 GTGGCACCCTTTTAAAGCCCACAAGTCA
* *** *
265749 GTGGCACCATTGCGAAGCCCACAATTCA
1 GTGGCACCCTTTTAAAGCCCACAAGTCA
** *
265777 GTGGCACTGTTTCAAAGCCCACAAGTCA
1 GTGGCACCCTTTTAAAGCCCACAAGTCA
265805 GTGGCACCCTTTTAAAGCCCACACAAGTCA
1 GTGGCACCCTTTTAAAG-CC-CACAAGTCA
* * *
265835 GTGACACTCCTTTCAAAGCTCACAAGTCA
1 GTGGCAC-CCTTTTAAAGCCCACAAGTCA
*
265864 GTGGCACTCCTTTCAAAGCCCACAAGTCA
1 GTGGCAC-CCTTTTAAAGCCCACAAGTCA
* *
265893 GTGGCACTCTTTTCAAAGCCCACAAATCA
1 GTGGCACCCTTTT-AAAGCCCACAAGTCA
** *
265922 GTGGCACTTTTTTCAAAGCCCACAAGTTA
1 GTGGCACCCTTTT-AAAGCCCACAAGTCA
* *
265951 GTGGCACCCTTTCAAAGCCCACAAGTTA
1 GTGGCACCCTTTTAAAGCCCACAAGTCA
* * *
265979 GTGGCACCCTTTCAGAGCCCACAAGTTA
1 GTGGCACCCTTTTAAAGCCCACAAGTCA
**
266007 GTGGCACCCTTTCGAAGCCCACAAGTCA
1 GTGGCACCCTTTTAAAGCCCACAAGTCA
* *** * * * *
266035 GTGGCACCATTGCGAAGCCTATAATTTA
1 GTGGCACCCTTTTAAAGCCCACAAGTCA
* *
266063 GTGGCACTCTTTCAAAGCCCACAAGTCA
1 GTGGCACCCTTTTAAAGCCCACAAGTCA
266091 GTGGCACCCTTTTAAAGCCCACACAAGTCA
1 GTGGCACCCTTTTAAAG-CC-CACAAGTCA
*
266121 GTGGCACTCCTTTTAAAGCTCACGCAAGTCA
1 GTGGCAC-CCTTTTAAAGC-C-CACAAGTCA
* *
266152 GTGGTA-CCTTTTCAAAGCCCACGAGTCA
1 GTGGCACCCTTTT-AAAGCCCACAAGTCA
* *
266180 GTGGCACTCTTTCAAAGCCCACAAGTCA
1 GTGGCACCCTTTTAAAGCCCACAAGTCA
* ** *
266208 GTGGCACCCTTTCAAAGCCCATGAGTTA
1 GTGGCACCCTTTTAAAGCCCACAAGTCA
*
266236 GTGGCACCCTTTCAAAGCCCACACAAGTCA
1 GTGGCACCCTTTTAAAG-CC-CACAAGTCA
*
266266 GTGGCACTCCTTTCAAAGCCCACGCAAGTCA
1 GTGGCAC-CCTTTTAAAGCCCA--CAAGTCA
* * * *
266297 GTAGTA-CCTTTTCAAAGCCCACGAGTTA
1 GTGGCACCCTTTT-AAAGCCCACAAGTCA
* *
266325 GTGGCACTCTTTCAAAGCCCACAAGTCA
1 GTGGCACCCTTTTAAAGCCCACAAGTCA
* *
266353 GTGGCACCC-TTTCAAGCCCACGAGTCA
1 GTGGCACCCTTTTAAAGCCCACAAGTCA
* *
266380 GTGGTA-CCTTTTCAAAGCCCACGAGTCA
1 GTGGCACCCTTTT-AAAGCCCACAAGTCA
**
266408 GTGGCA-CC-TTGCAAGCCCACAAGTCA
1 GTGGCACCCTTTTAAAGCCCACAAGTCA
* * *
266434 GTGGCACTCTTTCAAAGCCCACGAGTCA
1 GTGGCACCCTTTTAAAGCCCACAAGTCA
* *
266462 GTGGCATCCTTTCAAAGCCCACGTAAGTCA
1 GTGGCACCCTTTTAAAGCCCAC--AAGTCA
266492 GTGGCACCCTTTTAAAGCCCACGCAAGTCA
1 GTGGCACCCTTTTAAAGCCCA--CAAGTCA
** *
266522 GTAACACTCTTTTCAAAGCCTACACAAG-CTA
1 GTGGCACCCTTTT-AAAGCC--CACAAGTC-A
266553 GTGGCAC
1 GTGGCAC
266560 ATTTTTTTTA
Statistics
Matches: 1318, Mismatches: 153, Indels: 102
0.84 0.10 0.06
Matches are distributed among these distances:
25 25 0.02
26 45 0.03
27 206 0.16
28 500 0.38
29 187 0.14
30 139 0.11
31 135 0.10
32 70 0.05
33 10 0.01
34 1 0.00
ACGTcount: A:0.27, C:0.32, G:0.17, T:0.24
Consensus pattern (28 bp):
GTGGCACCCTTTTAAAGCCCACAAGTCA
Found at i:266211 original size:145 final size:144
Alignment explanation
Indices: 265489--266559 Score: 1194
Period size: 145 Copynumber: 7.4 Consensus size: 144
265479 TGGTAACCTA
* *
265489 TTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCCT
1 TTTCAAAG-CC-CACAAGTCAGTGGC-ACCC-TTTCAAAGCCCACACAAGTCAGTGGC-A-CCCT
* * * *
265554 TTCAAAGCCCACACAAGTCAGTGGCACCCCTTTCAAAGCCCACGCAAGTTAGTGGCACCCTTTTA
60 TTCAAAGCCCACACAAGTCAGTGGCA-CCTTTTCAAAGCCCACG--AGTCAGTGGCACTCTTTCA
*
265619 AAGCCCACAAGTTAGTGGCACTC
122 AAGCCCACAAGTCAGTGGCACTC
* *
265642 TTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAG-CC-CACAAGTTAGTGGCACCTTTTTCA
1 -TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACACAAGTCAGTGGCACC-CTTTCA
* * * * *
265705 AAGCCCACGCAAGTCAGTGGCACCCTTTT-GAAGCCCACAAGTCAGTGGCAC-CATTGCGAAGCC
64 AAGCCCACACAAGTCAGTGGCA-CCTTTTCAAAGCCCACGAGTCAGTGGCACTC-TTTCAAAGCC
* *
265768 CACAATTCAGTGGCACTG
127 CACAAGTCAGTGGCACTC
* *
265786 TTTCAAAGCCCACAAGTCAGTGGCACCCTTTTAAAGCCCACACAAGTCAGTGACACTCCTTTCAA
1 TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACACAAGTCAGTGGCAC-CCTTTCAA
* * *
265851 AG--CTCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCC
65 AGCCCACACAAGTCAGTGGCAC-CTTTTCAAAGCCCACGAGTCAGTGGCACTC-TTTCAAAGCCC
* *
265914 ACAAATCAGTGGCACTTT
128 ACAAGTCAGTGGCAC-TC
* * *
265932 TTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAG-CC-CACAAGTTAGTGGCACCCTTTCAGA
1 TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACACAAGTCAGTGGCACCCTTTCAAA
* * * * * * * *
265995 G-CC-CACAAGTTAGTGGCACCCTTTCGAAGCCCACAAGTCAGTGGCAC-CATTGCGAAGCCTAT
66 GCCCACACAAGTCAGTGGCACCTTTTCAAAGCCCACGAGTCAGTGGCACTC-TTTCAAAGCCCAC
* *
266057 AATTTAGTGGCACTC
130 AAGTCAGTGGCACTC
* *
266072 TTTCAAAGCCCACAAGTCAGTGGCACCCTTTTAAAGCCCACACAAGTCAGTGGCACTCCTTTTAA
1 TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACACAAGTCAGTGGCAC-CCTTTCAA
* * *
266137 AGCTCACGCAAGTCAGTGGTACCTTTTCAAAGCCCACGAGTCAGTGGCACTCTTTCAAAGCCCAC
65 AGCCCACACAAGTCAGTGGCACCTTTTCAAAGCCCACGAGTCAGTGGCACTCTTTCAAAGCCCAC
*
266202 AAGTCAGTGGCACCC
130 AAGTCAGTGGCACTC
** *
266217 TTTCAAAGCCCATGAGTTAGTGGCACCCTTTCAAAGCCCACACAAGTCAGTGGCACTCCTTTCAA
1 TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACACAAGTCAGTGGCAC-CCTTTCAA
* * * *
266282 AGCCCACGCAAGTCAGTAGTACCTTTTCAAAGCCCACGAGTTAGTGGCACTCTTTCAAAGCCCAC
65 AGCCCACACAAGTCAGTGGCACCTTTTCAAAGCCCACGAGTCAGTGGCACTCTTTCAAAGCCCAC
*
266347 AAGTCAGTGGCACCC
130 AAGTCAGTGGCACTC
* * * * *
266362 TTTC-AAGCCCACGAGTCAGTGGTACCTTTTCAAAG-CC-CACGAGTCAGTGGCA-CCTTGC-AA
1 TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACACAAGTCAGTGGCACCCTTTCAAA
266422 G-CC-CACAAGTCAGTGGCA-CTCTTTCAAAGCCCACGAGTCAGTGGCA-TCCTTTCAAAGCCCA
66 GCCCACACAAGTCAGTGGCACCT-TTTCAAAGCCCACGAGTCAGTGGCACT-CTTTCAAAGCCCA
*
266483 CGTAAGTCAGTGGCACCC
129 C--AAGTCAGTGGCACTC
* ** * *
266501 TTTTAAAGCCCACGCAAGTCAGTAACACTCTTTTCAAAGCCTACACAAG-CTAGTGGCAC
1 TTTCAAAGCCCA--CAAGTCAGTGGCAC-CCTTTCAAAGCCCACACAAGTC-AGTGGCAC
266560 ATTTTTTTTA
Statistics
Matches: 802, Mismatches: 87, Indels: 64
0.84 0.09 0.07
Matches are distributed among these distances:
136 3 0.00
137 50 0.06
138 2 0.00
139 21 0.03
140 47 0.06
141 23 0.03
142 67 0.08
143 99 0.12
144 101 0.13
145 260 0.32
146 47 0.06
147 33 0.04
148 12 0.01
149 2 0.00
150 8 0.01
151 4 0.00
152 13 0.02
153 2 0.00
154 8 0.01
ACGTcount: A:0.28, C:0.32, G:0.19, T:0.22
Consensus pattern (144 bp):
TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACACAAGTCAGTGGCACCCTTTCAAA
GCCCACACAAGTCAGTGGCACCTTTTCAAAGCCCACGAGTCAGTGGCACTCTTTCAAAGCCCACA
AGTCAGTGGCACTC
Found at i:267142 original size:20 final size:20
Alignment explanation
Indices: 267114--267188 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
267104 TTTTACCTTG
267114 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
267134 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * * *
267154 ATGCATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
267174 ATGTATCGATACATT
1 ATGTATCGATACATT
267189 ATGTCTTTTT
Statistics
Matches: 41, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:268987 original size:29 final size:28
Alignment explanation
Indices: 268955--269010 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
268945 ATTAATCTCA
268955 ATTTAAATTAATATTTAATAATAAAAAAT
1 ATTTAAATTAA-ATTTAATAATAAAAAAT
* * *
268984 ATTTTATTTAAATTTAATTATAAAAAA
1 ATTTAAATTAAATTTAATAATAAAAAA
269011 AAAATAGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 15 0.62
29 9 0.38
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (28 bp):
ATTTAAATTAAATTTAATAATAAAAAAT
Found at i:269543 original size:16 final size:17
Alignment explanation
Indices: 269522--269554 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
269512 AAATTTATAT
*
269522 TTTTTATTTTA-ATTCA
1 TTTTTAATTTAGATTCA
269538 TTTTTAATTTAGATTCA
1 TTTTTAATTTAGATTCA
269555 CTTATTTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.27, C:0.06, G:0.03, T:0.64
Consensus pattern (17 bp):
TTTTTAATTTAGATTCA
Found at i:271961 original size:29 final size:27
Alignment explanation
Indices: 271921--271994 Score: 89
Period size: 29 Copynumber: 2.7 Consensus size: 27
271911 TATTGATAAA
*
271921 AATATAATTAAAATATATAAAATTTATAT
1 AATATATTTAAAATAT-TAAAATTT-TAT
271950 AATATATTTAAAATATTAAAATTTTAT
1 AATATATTTAAAATATTAAAATTTTAT
*
271977 -ATAGTATTTATAAT-TTAA
1 AATA-TATTTAAAATATTAA
271995 TGATAATAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
26 7 0.17
27 12 0.29
28 8 0.19
29 15 0.36
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (27 bp):
AATATATTTAAAATATTAAAATTTTAT
Found at i:272108 original size:6 final size:6
Alignment explanation
Indices: 272097--272124 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
272087 TACGATAAAC
272097 AAAGCG AAAGCG AAAGCG AAAGCG AAAG
1 AAAGCG AAAGCG AAAGCG AAAGCG AAAG
272125 TTGCCGTCAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.54, C:0.14, G:0.32, T:0.00
Consensus pattern (6 bp):
AAAGCG
Found at i:273721 original size:28 final size:28
Alignment explanation
Indices: 273681--273739 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
273671 AGTGGAACGA
273681 CTTTATTTATATCATCATATATAATTAG
1 CTTTATTTATATCATCATATATAATTAG
273709 CTTTATTTATATCATCATATATAATTAG
1 CTTTATTTATATCATCATATATAATTAG
273737 CTT
1 CTT
273740 GGGTTCTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.34, C:0.12, G:0.03, T:0.51
Consensus pattern (28 bp):
CTTTATTTATATCATCATATATAATTAG
Found at i:276478 original size:54 final size:54
Alignment explanation
Indices: 276396--276503 Score: 207
Period size: 54 Copynumber: 2.0 Consensus size: 54
276386 ACCAATTAAA
*
276396 AACATCTTTATTGGCATGATTAATTGATCCAAGATTTTGATTAGTTGGAATAAG
1 AACATCTTCATTGGCATGATTAATTGATCCAAGATTTTGATTAGTTGGAATAAG
276450 AACATCTTCATTGGCATGATTAATTGATCCAAGATTTTGATTAGTTGGAATAAG
1 AACATCTTCATTGGCATGATTAATTGATCCAAGATTTTGATTAGTTGGAATAAG
276504 CTCAAGCCTT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (54 bp):
AACATCTTCATTGGCATGATTAATTGATCCAAGATTTTGATTAGTTGGAATAAG
Found at i:278182 original size:2 final size:2
Alignment explanation
Indices: 278177--278212 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
278167 TTTCCTTTTT
278177 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
278213 AACGCGCACT
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:280275 original size:21 final size:21
Alignment explanation
Indices: 280229--280284 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 21
280219 TTTATTATAT
280229 ATTATATT-TATATTT-A-AA
1 ATTATATTATATATTTAATAA
280247 ATT-T-TTATATATTTAATAA
1 ATTATATTATATATTTAATAA
* *
280266 ATTATATTATGTTTTTAAT
1 ATTATATTATATATTTAAT
280285 TACATGGTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
16 2 0.06
17 8 0.26
18 4 0.13
19 5 0.16
20 1 0.03
21 11 0.35
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
ATTATATTATATATTTAATAA
Found at i:284553 original size:12 final size:13
Alignment explanation
Indices: 284531--284562 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
284521 GAATTTTTTA
284531 AAAATATTAAATT
1 AAAATATTAAATT
284544 AAAA-ATTAAATT
1 AAAATATTAAATT
284556 AAAATAT
1 AAAATAT
284563 GGGGACCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
AAAATATTAAATT
Found at i:284963 original size:2 final size:2
Alignment explanation
Indices: 284956--284992 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
284946 TTCTTGATGA
284956 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 A
284993 GTACTGACTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:286143 original size:12 final size:12
Alignment explanation
Indices: 286126--286164 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
286116 AAATTCATTT
286126 TATTATTTATAA
1 TATTATTTATAA
286138 TATTATTTA-AA
1 TATTATTTATAA
* *
286149 TATAATTTTTAA
1 TATTATTTATAA
286161 TATT
1 TATT
286165 TATATATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
11 9 0.39
12 14 0.61
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TATTATTTATAA
Found at i:286164 original size:20 final size:21
Alignment explanation
Indices: 286141--286218 Score: 58
Period size: 20 Copynumber: 3.8 Consensus size: 21
286131 TTTATAATAT
286141 TATTTAAAT-ATAATTTTTAA
1 TATTTAAATAATAATTTTTAA
*
286161 TATTT--AT-ATATTTTTATAA
1 TATTTAAATAATAATTTT-TAA
* *
286180 TTAAATTTAAATAAAAATTTTTAT
1 -T--ATTTAAATAATAATTTTTAA
286204 TA-TTAAATAATAATT
1 TATTTAAATAATAATT
286219 AAAAATAAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 14
0.71 0.08 0.22
Matches are distributed among these distances:
18 9 0.20
19 3 0.07
20 18 0.39
21 1 0.02
22 4 0.09
23 1 0.02
24 4 0.09
25 6 0.13
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TATTTAAATAATAATTTTTAA
Found at i:286222 original size:26 final size:26
Alignment explanation
Indices: 286170--286224 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
286160 ATATTTATAT
*
286170 ATTTTTATAATTAAATTTAAATAAAA
1 ATTTTTATAATTAAATATAAATAAAA
* *
286196 ATTTTTATTATTAAATAATAATTAAAA
1 ATTTTTATAATTAAAT-ATAAATAAAA
286223 AT
1 AT
286225 AAATTTATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 15 0.60
27 10 0.40
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
ATTTTTATAATTAAATATAAATAAAA
Found at i:291568 original size:15 final size:17
Alignment explanation
Indices: 291534--291568 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
291524 CATCATAAAA
291534 TATTTAATATTTTAACT
1 TATTTAATATTTTAACT
291551 TATTTAA-ATTTT-ACT
1 TATTTAATATTTTAACT
291566 TAT
1 TAT
291569 CATCAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.33
16 5 0.28
17 7 0.39
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (17 bp):
TATTTAATATTTTAACT
Found at i:291616 original size:14 final size:14
Alignment explanation
Indices: 291583--291609 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
291573 AATTATTCTT
291583 AATAAAATATTATA
1 AATAAAATATTATA
291597 AATAAAATATTAT
1 AATAAAATATTAT
291610 GTTTAAATAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AATAAAATATTATA
Found at i:291683 original size:18 final size:18
Alignment explanation
Indices: 291651--291693 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
291641 ATCTTTTTAA
291651 ATATGAATATATTAAA-ATT
1 ATAT-AATATATTAAATA-T
*
291670 ATATAATATTTTAAATAT
1 ATATAATATATTAAATAT
291688 ATATAA
1 ATATAA
291694 CGGGATAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (18 bp):
ATATAATATATTAAATAT
Found at i:292170 original size:2 final size:2
Alignment explanation
Indices: 292163--292211 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
292153 GGGTTAAAGC
292163 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
292205 CT CT CT C
1 CT CT CT C
292212 ACTCATATTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:292408 original size:16 final size:16
Alignment explanation
Indices: 292389--292420 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
292379 TCATATTTAA
*
292389 ATTATTTTTTAATTAT
1 ATTATATTTTAATTAT
292405 ATTATATTTTAATTAT
1 ATTATATTTTAATTAT
292421 TTTTTATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
ATTATATTTTAATTAT
Found at i:292411 original size:27 final size:28
Alignment explanation
Indices: 292368--292435 Score: 95
Period size: 27 Copynumber: 2.4 Consensus size: 28
292358 TAAAAAATTA
292368 TTATATT-TATCTCATATTTAAATTATTTT
1 TTATATTATAT-T-ATATTTAAATTATTTT
*
292397 TTA-ATTATATTATATTTTAATTATTTT
1 TTATATTATATTATATTTAAATTATTTT
292424 TTATATTATATT
1 TTATATTATATT
292436 CTTCTTATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
27 18 0.50
28 12 0.33
29 6 0.17
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (28 bp):
TTATATTATATTATATTTAAATTATTTT
Found at i:295286 original size:16 final size:16
Alignment explanation
Indices: 295261--295299 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
295251 TTTTTATTTT
295261 AATTAAATTTAAATTA
1 AATTAAATTTAAATTA
*
295277 AATTAGATTTAAATTA
1 AATTAAATTTAAATTA
*
295293 ATTTAAA
1 AATTAAA
295300 AATTTATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (16 bp):
AATTAAATTTAAATTA
Found at i:295319 original size:31 final size:30
Alignment explanation
Indices: 295283--295381 Score: 89
Period size: 31 Copynumber: 3.3 Consensus size: 30
295273 ATTAAATTAG
295283 ATTTAAATTAATTTAAAAATTTATTTTATT
1 ATTTAAATTAATTTAAAAATTTATTTTATT
*
295313 ATTTTAAA-AAATATTAAAAATTTTAATTTTA-T
1 A-TTTAAATTAAT-TTAAAAA-TTT-ATTTTATT
* * *
295345 AATTAAATTTAA-ATAAAAATAT-TTTTATT
1 ATTTAAA-TTAATTTAAAAATTTATTTTATT
295374 ATTTAAAT
1 ATTTAAAT
295382 AATAAAAAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 16
0.72 0.08 0.21
Matches are distributed among these distances:
28 6 0.11
29 7 0.12
30 6 0.11
31 24 0.43
32 5 0.09
33 8 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (30 bp):
ATTTAAATTAATTTAAAAATTTATTTTATT
Found at i:295403 original size:61 final size:60
Alignment explanation
Indices: 295296--295412 Score: 141
Period size: 60 Copynumber: 1.9 Consensus size: 60
295286 TAAATTAATT
*
295296 TAAAAATTTATTTTATTATTTTAAAAAATATTAAAAATTTTAATTTTATAATTAAATTTAAA
1 TAAAAATATATTTTATTATTTTAAAAAATA-TAAAAATTTTAATTTT-TAATTAAATTTAAA
* *
295358 TAAAAATAT-TTTTATTA-TTTAAATAATA-AAAAATCATATTAATTTTTATTTAAAT
1 TAAAAATATATTTTATTATTTTAAAAAATATAAAAAT--T-TTAATTTTTAATTAAAT
295413 CAAATATAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
58 6 0.12
60 19 0.39
61 16 0.33
62 8 0.16
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.50
Consensus pattern (60 bp):
TAAAAATATATTTTATTATTTTAAAAAATATAAAAATTTTAATTTTTAATTAAATTTAAA
Found at i:295841 original size:14 final size:14
Alignment explanation
Indices: 295822--295882 Score: 104
Period size: 14 Copynumber: 4.4 Consensus size: 14
295812 CAGCCACAAT
295822 ATATATATATATAA
1 ATATATATATATAA
295836 ATATATATATATAA
1 ATATATATATATAA
* *
295850 ATATATAAATATAT
1 ATATATATATATAA
295864 ATATATATATATAA
1 ATATATATATATAA
295878 ATATA
1 ATATA
295883 GTAATTGAGA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 43 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
ATATATATATATAA
Found at i:295902 original size:2 final size:2
Alignment explanation
Indices: 295820--295882 Score: 90
Period size: 2 Copynumber: 31.5 Consensus size: 2
295810 AACAGCCACA
* * *
295820 AT AT AT AT AT AT AT AA AT AT AT AT AT AT AA AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
295862 AT AT AT AT AT AT AT AA AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
295883 GTAATTGAGA
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:299780 original size:15 final size:14
Alignment explanation
Indices: 299757--299786 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
299747 TTAATTGGAC
299757 AAAATTTAAAAAAT
1 AAAATTTAAAAAAT
299771 AAAATATTAAAAAAT
1 AAAAT-TTAAAAAAT
299786 A
1 A
299787 TTTTATATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
AAAATTTAAAAAAT
Found at i:300631 original size:13 final size:13
Alignment explanation
Indices: 300613--300637 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
300603 TTTTAATTCA
300613 TAAAATTTAAAAT
1 TAAAATTTAAAAT
300626 TAAAATTTAAAA
1 TAAAATTTAAAA
300638 AAATTAAATT
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TAAAATTTAAAAT
Found at i:301605 original size:13 final size:15
Alignment explanation
Indices: 301573--301606 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
301563 TTTATTTATT
301573 TAAAATTTGACGTAA
1 TAAAATTTGACGTAA
301588 TAAAATTT-ACGT-A
1 TAAAATTTGACGTAA
301601 TAAAAT
1 TAAAAT
301607 ATAATAATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.37
14 4 0.21
15 8 0.42
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.35
Consensus pattern (15 bp):
TAAAATTTGACGTAA
Found at i:301862 original size:2 final size:2
Alignment explanation
Indices: 301855--301896 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
301845 ACTACCTACC
* *
301855 TA TA TA TA TG TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
301897 AAATAAAGGA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:307469 original size:14 final size:14
Alignment explanation
Indices: 307450--307477 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
307440 GAACAACCAT
307450 AACTGTTGTGCTAA
1 AACTGTTGTGCTAA
307464 AACTGTTGTGCTAA
1 AACTGTTGTGCTAA
307478 CACACAAAAA
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:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (14 bp):
AACTGTTGTGCTAA
Found at i:308235 original size:20 final size:19
Alignment explanation
Indices: 308210--308276 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 19
308200 ATTTTTTTAT
308210 TTATTTAAATAATGTTATAA
1 TTATTTAAATAAT-TTATAA
*
308230 TTATTTATATAA-TTATAA
1 TTATTTAAATAATTTATAA
308248 TT-TTAAATAAATAATTTATATA
1 TTATT---TAAATAATTTATA-A
308270 TTATTTA
1 TTATTTA
308277 TTTTAATTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
17 2 0.05
18 8 0.21
20 19 0.49
21 5 0.13
22 3 0.08
23 2 0.05
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (19 bp):
TTATTTAAATAATTTATAA
Found at i:308303 original size:29 final size:28
Alignment explanation
Indices: 308237--308307 Score: 90
Period size: 29 Copynumber: 2.5 Consensus size: 28
308227 TAATTATTTA
*
308237 TATAATTA-TAATTTTAAATAAATAATT
1 TATAATTATTTATTTTAAATAAATAATT
*
308264 TATATATTATTTATTTTAATTTAAATAATT
1 TATA-ATTATTTATTTTAA-ATAAATAATT
*
308294 TTTAATTATTTATT
1 TATAATTATTTATT
308308 AACTTTTAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 4 0.11
28 4 0.11
29 18 0.47
30 12 0.32
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (28 bp):
TATAATTATTTATTTTAAATAAATAATT
Found at i:309801 original size:19 final size:18
Alignment explanation
Indices: 309760--309803 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 18
309750 TACAAAAAAT
309760 ATTTTAATCTTATATTTA
1 ATTTTAATCTTATATTTA
309778 A-TTTAAT-TATATATATTA
1 ATTTTAATCT-TATAT-TTA
309796 ATTTTAAT
1 ATTTTAAT
309804 ATGAATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 1 0.04
17 11 0.48
18 5 0.22
19 6 0.26
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (18 bp):
ATTTTAATCTTATATTTA
Found at i:310408 original size:29 final size:28
Alignment explanation
Indices: 310371--310427 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
310361 TGTTTTTAGC
*
310371 TAAATATTAAGA-AGTAAATGGATATTTTT
1 TAAACATTAAGAGAGTAAAT-G-TATTTTT
310400 TAAACATTAAGAGAGTAAATGTATTTTT
1 TAAACATTAAGAGAGTAAATGTATTTTT
310428 CATAAAGATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 7 0.27
29 12 0.46
30 7 0.27
ACGTcount: A:0.44, C:0.02, G:0.14, T:0.40
Consensus pattern (28 bp):
TAAACATTAAGAGAGTAAATGTATTTTT
Found at i:317039 original size:15 final size:16
Alignment explanation
Indices: 316999--317039 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
316989 GAGAGAAATC
316999 AGAAAAAAGAAACGAAT
1 AGAAAAAAG-AACGAAT
*
317016 -GATAAAAGAAC-AAT
1 AGAAAAAAGAACGAAT
317030 AGAAAAAAGA
1 AGAAAAAAGA
317040 CGCAAGTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
14 3 0.14
15 11 0.52
16 7 0.33
ACGTcount: A:0.71, C:0.05, G:0.17, T:0.07
Consensus pattern (16 bp):
AGAAAAAAGAACGAAT
Done.