Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold263
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: 1338270
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 3 of 10
Found at i:386269 original size:13 final size:13
Alignment explanation
Indices: 386251--386276 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
386241 AATACATGAA
386251 AATATAAAAATAT
1 AATATAAAAATAT
386264 AATATAAAAATAT
1 AATATAAAAATAT
386277 TAATTATTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AATATAAAAATAT
Found at i:386406 original size:16 final size:17
Alignment explanation
Indices: 386380--386413 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
386370 TTATAATTAA
386380 ATTTGAATTAAAAAAAT
1 ATTTGAATTAAAAAAAT
*
386397 ATTT-AATTAAATAAAT
1 ATTTGAATTAAAAAAAT
386413 A
1 A
386414 ATAATTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
ATTTGAATTAAAAAAAT
Found at i:386721 original size:15 final size:14
Alignment explanation
Indices: 386694--386728 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
386684 AAAAAAATTT
*
386694 AAATATAATA-AAA
1 AAATATAACATAAA
386707 AAATATAACATAAA
1 AAATATAACATAAA
386721 AAATATAA
1 AAATATAA
386729 ATATCAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (14 bp):
AAATATAACATAAA
Found at i:386741 original size:11 final size:10
Alignment explanation
Indices: 386683--386780 Score: 53
Period size: 11 Copynumber: 9.6 Consensus size: 10
386673 TTAAATTTTT
* *
386683 TAAAAAAATT
1 TAAATAAATA
386693 TAAATATAATA
1 TAAATA-AATA
386704 -AAA-AAATA
1 TAAATAAATA
386712 TAACATAAA-A
1 TAA-ATAAATA
386722 -AATATAAATA
1 TAA-ATAAATA
386732 TCAAATAAATTA
1 T-AAATAAA-TA
386744 TAAATAAAT-
1 TAAATAAATA
**
386753 TAAAATTTATA
1 T-AAATAAATA
386764 TAATATAAATA
1 TAA-ATAAATA
*
386775 TTAATA
1 TAAATA
386781 TATTAATTTT
Statistics
Matches: 69, Mismatches: 8, Indels: 22
0.70 0.08 0.22
Matches are distributed among these distances:
8 4 0.06
9 11 0.16
10 23 0.33
11 26 0.38
12 5 0.07
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (10 bp):
TAAATAAATA
Found at i:386800 original size:18 final size:19
Alignment explanation
Indices: 386777--386812 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
386767 TATAAATATT
*
386777 AATATATTA-ATTTTAATA
1 AATATATAATATTTTAATA
386795 AATATATAATATTTTAAT
1 AATATATAATATTTTAAT
386813 TTTTAAATGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
AATATATAATATTTTAATA
Found at i:386811 original size:25 final size:24
Alignment explanation
Indices: 386768--386815 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
386758 TTTATATAAT
386768 ATAAATATTAATATATTAATTTTA
1 ATAAATATTAATATATTAATTTTA
*
386792 ATAAATATATAATATTTTAATTTT
1 ATAAATAT-TAATATATTAATTTT
386816 TAAATGCAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
ATAAATATTAATATATTAATTTTA
Found at i:387232 original size:29 final size:30
Alignment explanation
Indices: 387173--387262 Score: 110
Period size: 30 Copynumber: 3.0 Consensus size: 30
387163 AATATGCATG
*
387173 AAATTTTAGTATTT-TATCTAAATAAATTTT
1 AAATTTTA-TATTTATATTTAAATAAATTTT
* *
387203 TACTTTTATATTTATATTTAAATAAATTTT
1 AAATTTTATATTTATATTTAAATAAATTTT
* * *
387233 AAATTTTAAATTTATATTCAAATAATTTTT
1 AAATTTTATATTTATATTTAAATAAATTTT
387263 TAATCATTTA
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
29 5 0.10
30 46 0.90
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (30 bp):
AAATTTTATATTTATATTTAAATAAATTTT
Found at i:387447 original size:30 final size:29
Alignment explanation
Indices: 387413--387469 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
387403 ATTATTAATT
387413 TTTAACTTGTACTAAAATAAGCTTTTAAAC
1 TTTAACTTGTA-TAAAATAAGCTTTTAAAC
* * * *
387443 TTTAATTTTTATTAAATAATCTTTTAA
1 TTTAACTTGTATAAAATAAGCTTTTAA
387470 CATAAATTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 14 0.61
30 9 0.39
ACGTcount: A:0.39, C:0.09, G:0.04, T:0.49
Consensus pattern (29 bp):
TTTAACTTGTATAAAATAAGCTTTTAAAC
Found at i:387492 original size:17 final size:17
Alignment explanation
Indices: 387444--387492 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
387434 CTTTTAAACT
387444 TTAA-TTTTTA-TTAAA
1 TTAATTTTTTACTTAAA
* *
387459 -TAATCTTTTAACATAAA
1 TTAAT-TTTTTACTTAAA
387476 TTAATTTTTTACTTAAA
1 TTAATTTTTTACTTAAA
387493 ATAAAATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
14 3 0.12
16 5 0.19
17 14 0.54
18 4 0.15
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAATTTTTTACTTAAA
Found at i:387852 original size:8 final size:9
Alignment explanation
Indices: 387839--387876 Score: 53
Period size: 8 Copynumber: 4.3 Consensus size: 9
387829 TCAGGTATAA
387839 AAAT-AAAT
1 AAATAAAAT
387847 AAAT-AAAT
1 AAATAAAAT
387855 AAATAAAAT
1 AAATAAAAT
387864 AAAATAAAAT
1 -AAATAAAAT
387874 AAA
1 AAA
387877 AACTATGTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 12 0.43
9 7 0.25
10 9 0.32
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
AAATAAAAT
Found at i:387865 original size:5 final size:5
Alignment explanation
Indices: 387838--387877 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
387828 TTCAGGTATA
387838 AAAAT -AAAT -AAAT -AAAT -AAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
387878 ACTATGTGGT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 16 0.47
5 18 0.53
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:389683 original size:4 final size:4
Alignment explanation
Indices: 389674--389699 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
389664 CATAAAAAAA
389674 TATT TATT TATT TATT TATT TATT TA
1 TATT TATT TATT TATT TATT TATT TA
389700 AATTTTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:390607 original size:18 final size:18
Alignment explanation
Indices: 390584--390618 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
390574 AAAAATTTAA
*
390584 TTTTTTGAATATATAATT
1 TTTTTTGAAAATATAATT
*
390602 TTTTTTTAAAATATAAT
1 TTTTTTGAAAATATAAT
390619 AATATTGAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (18 bp):
TTTTTTGAAAATATAATT
Found at i:391055 original size:32 final size:33
Alignment explanation
Indices: 391019--391084 Score: 80
Period size: 32 Copynumber: 2.0 Consensus size: 33
391009 ATATGACACA
*
391019 AAATTATGAATATATCAAAATTTATAT-AATAT
1 AAATTATGAATATATCAAAATATATATAAATAT
* * * *
391051 AAATTATTAATTTGTCAATATATATATAAATAT
1 AAATTATGAATATATCAAAATATATATAAATAT
391084 A
1 A
391085 TAATATTTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
32 22 0.79
33 6 0.21
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (33 bp):
AAATTATGAATATATCAAAATATATATAAATAT
Found at i:391098 original size:28 final size:27
Alignment explanation
Indices: 391041--391115 Score: 80
Period size: 28 Copynumber: 2.7 Consensus size: 27
391031 TATCAAAATT
*
391041 TATATAATATAAAT-TATTAATTTGTCAA
1 TATAT-ATATAAATATA-TAATTTGTAAA
*
391069 TATATATATAAATATATAATATTTTAAA
1 TATATATATAAATATATAAT-TTGTAAA
* *
391097 TATATATAAAAATACATAA
1 TATATATATAAATATATAA
391116 AGAAGATACG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
27 12 0.29
28 29 0.71
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (27 bp):
TATATATATAAATATATAATTTGTAAA
Found at i:394894 original size:21 final size:22
Alignment explanation
Indices: 394857--394900 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
394847 AAATTAATTT
394857 TTATATAATTAAAATAT-AAAA
1 TTATATAATTAAAATATCAAAA
*
394878 TTATAT-ATCTAATATATCAAAA
1 TTATATAAT-TAAAATATCAAAA
394900 T
1 T
394901 CAATAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 2 0.10
21 13 0.65
22 5 0.25
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (22 bp):
TTATATAATTAAAATATCAAAA
Found at i:395670 original size:19 final size:19
Alignment explanation
Indices: 395614--395670 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
395604 CTACATATAT
395614 ATATATAGGATAAGTTCAC
1 ATATATAGGATAAGTTCAC
* *
395633 ATATGATA-TAT-A--T-AT
1 ATAT-ATAGGATAAGTTCAC
395648 ATATATAGGATAAGTTCAC
1 ATATATAGGATAAGTTCAC
395667 ATAT
1 ATAT
395671 GCTCTCTAGG
Statistics
Matches: 28, Mismatches: 4, Indels: 12
0.64 0.09 0.27
Matches are distributed among these distances:
14 3 0.11
15 7 0.25
16 2 0.07
18 2 0.07
19 11 0.39
20 3 0.11
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.37
Consensus pattern (19 bp):
ATATATAGGATAAGTTCAC
Found at i:396092 original size:19 final size:19
Alignment explanation
Indices: 396068--396132 Score: 64
Period size: 19 Copynumber: 3.5 Consensus size: 19
396058 TTGATATTGA
396068 TTTAAATATATATTTTTAT
1 TTTAAATATATATTTTTAT
* *
396087 TTTAAAT-TGATATAATTAAT
1 TTTAAATAT-ATAT-TTTTAT
*
396107 TTTAAATAT-TA-TTTTAA
1 TTTAAATATATATTTTTAT
396124 TTTAAATAT
1 TTTAAATAT
396133 TAATATATAT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
17 12 0.32
18 1 0.03
19 13 0.34
20 11 0.29
21 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (19 bp):
TTTAAATATATATTTTTAT
Found at i:396115 original size:39 final size:40
Alignment explanation
Indices: 396068--396146 Score: 108
Period size: 39 Copynumber: 2.0 Consensus size: 40
396058 TTGATATTGA
* * *
396068 TTTAAATATATATTTTTATTTTAA-ATTGATATA-ATTAAT
1 TTTAAATAT-TATTTTAATTTAAATATTAATATATATTAAT
396107 TTTAAATATTATTTTAATTTAAATATTAATATATATTAAT
1 TTTAAATATTATTTTAATTTAAATATTAATATATATTAAT
396147 ATTATATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
38 12 0.34
39 17 0.49
40 6 0.17
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (40 bp):
TTTAAATATTATTTTAATTTAAATATTAATATATATTAAT
Found at i:399327 original size:17 final size:19
Alignment explanation
Indices: 399288--399330 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
399278 ACTAAGATGG
**
399288 TATATTTAATATATGTTTT
1 TATATTTAATATATGTTGA
399307 TATATTTAATAT-T-TTGA
1 TATATTTAATATATGTTGA
399324 TATATTT
1 TATATTT
399331 TTAATTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 9 0.41
18 1 0.05
19 12 0.55
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.63
Consensus pattern (19 bp):
TATATTTAATATATGTTGA
Found at i:399985 original size:16 final size:16
Alignment explanation
Indices: 399966--400046 Score: 66
Period size: 16 Copynumber: 5.2 Consensus size: 16
399956 ATTAAATTCA
399966 ATAATTTTAAAATAAT
1 ATAATTTTAAAATAAT
399982 ATAATTATT-AAATAAT
1 ATAATT-TTAAAATAAT
*
399998 ATAA-TGT--AATAA-
1 ATAATTTTAAAATAAT
*
400010 ATAA-TTAAAATATAAT
1 ATAATTTTAAA-ATAAT
*
400026 ATAATATTAAAAATAAT
1 ATAAT-TTTAAAATAAT
400043 ATAA
1 ATAA
400047 ATATATTAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 13
0.77 0.04 0.18
Matches are distributed among these distances:
12 5 0.09
13 5 0.09
14 2 0.04
15 5 0.09
16 21 0.38
17 11 0.20
18 6 0.11
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (16 bp):
ATAATTTTAAAATAAT
Found at i:400024 original size:28 final size:29
Alignment explanation
Indices: 399976--400052 Score: 79
Period size: 28 Copynumber: 2.6 Consensus size: 29
399966 ATAATTTTAA
*
399976 AATAATATAATTATTAA-ATAATATAAT-GT
1 AATAA-ATAATTA-AAATATAATATAATAGT
*
400005 AATAAATAATTAAAATATAATATAATATT
1 AATAAATAATTAAAATATAATATAATAGT
400034 AA-AAATAATATAAATATAT
1 AATAAATAAT-TAAA-ATAT
400053 TAAATTTATT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
27 2 0.05
28 24 0.57
29 12 0.29
30 4 0.10
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (29 bp):
AATAAATAATTAAAATATAATATAATAGT
Found at i:400034 original size:18 final size:18
Alignment explanation
Indices: 400004--400056 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
399994 TAATATAATG
400004 TAATA-AATAATTAAAATA
1 TAATATAATAATTAAAA-A
400022 TAATATAAT-ATTAAAAA
1 TAATATAATAATTAAAAA
400039 TAATATAAATATATTAAA
1 TAATAT-AATA-ATTAAA
400057 TTTATTTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
17 7 0.23
18 15 0.48
19 3 0.10
20 6 0.19
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
TAATATAATAATTAAAAA
Found at i:400054 original size:20 final size:21
Alignment explanation
Indices: 400006--400056 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
399996 ATATAATGTA
400006 ATAAATA-ATTAAAATATAAT
1 ATAAATATATTAAAATATAAT
400026 AT--A-ATATTAAAA-ATAAT
1 ATAAATATATTAAAATATAAT
400043 ATAAATATATTAAA
1 ATAAATATATTAAA
400057 TTTATTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 8 0.30
19 1 0.04
20 10 0.37
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
ATAAATATATTAAAATATAAT
Found at i:400057 original size:18 final size:16
Alignment explanation
Indices: 399975--400057 Score: 61
Period size: 17 Copynumber: 5.2 Consensus size: 16
399965 AATAATTTTA
399975 AAATAATATAAT-TATT
1 AAATAATATAATATA-T
*
399991 AAATAATATAATGTAAT
1 AAATAATATAATAT-AT
400008 AAATAAT-TAA-A-AT
1 AAATAATATAATATAT
*
400021 --ATAATATAATATTAA
1 AAATAATATAATA-TAT
400036 AAATAATATAAATATATT
1 AAATAATAT-AATATA-T
400054 AAAT
1 AAAT
400058 TTATTTTTAT
Statistics
Matches: 54, Mismatches: 3, Indels: 18
0.72 0.04 0.24
Matches are distributed among these distances:
11 5 0.09
12 3 0.06
13 3 0.06
15 1 0.02
16 15 0.28
17 18 0.33
18 9 0.17
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (16 bp):
AAATAATATAATATAT
Found at i:400586 original size:17 final size:18
Alignment explanation
Indices: 400548--400589 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
400538 TTGATTAAGT
400548 TAATTAA-TTTAATTAAAA
1 TAATTAATTTTAA-TAAAA
400566 -AATTAATTTTAA-AAAA
1 TAATTAATTTTAATAAAA
400582 TAATTAAT
1 TAATTAAT
400590 AAAAAGTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 4 0.18
17 13 0.59
18 5 0.23
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAATTAATTTTAATAAAA
Found at i:400592 original size:14 final size:15
Alignment explanation
Indices: 400549--400594 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
400539 TGATTAAGTT
400549 AATTAATTTAATTAAAA
1 AATTAA-TTAA-TAAAA
*
400566 AATTAATT-TTAAAA
1 AATTAATTAATAAAA
400580 AA-TAATTAATAAAA
1 AATTAATTAATAAAA
400594 A
1 A
400595 GTTCATTTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 5 0.19
14 13 0.50
16 2 0.08
17 6 0.23
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AATTAATTAATAAAA
Found at i:414074 original size:30 final size:30
Alignment explanation
Indices: 414027--414099 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 30
414017 TCAATACGTG
*
414027 TATAATTTATA-TAAATAAAATATAAAAT-T
1 TATAATTTAAATTAAAT-AAATATAAAATAT
*
414056 TATAATTTAAATTAAATAAATATAAATTAT
1 TATAATTTAAATTAAATAAATATAAAATAT
414086 TAT-ATATTAAATTA
1 TATAAT-TTAAATTA
414100 TGAATGTTAG
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
29 22 0.56
30 17 0.44
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (30 bp):
TATAATTTAAATTAAATAAATATAAAATAT
Found at i:416221 original size:12 final size:12
Alignment explanation
Indices: 416204--416228 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
416194 ATTCTAAGAG
416204 GAAGAAAAATTC
1 GAAGAAAAATTC
416216 GAAGAAAAATTC
1 GAAGAAAAATTC
416228 G
1 G
416229 GAACTAAGTG
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:0.08, G:0.20, T:0.16
Consensus pattern (12 bp):
GAAGAAAAATTC
Found at i:416724 original size:32 final size:32
Alignment explanation
Indices: 416688--416752 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
416678 AATTCACTGC
*
416688 AGATTTCAGTTAGTATTTCTCACACTGATTCA
1 AGATTTCAGTTAGTATTTCTCACACTAATTCA
* *
416720 AGATTTCATTTAGTATTTCTCACATTAATTCA
1 AGATTTCAGTTAGTATTTCTCACACTAATTCA
416752 A
1 A
416753 CTAAGTGTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.31, C:0.17, G:0.09, T:0.43
Consensus pattern (32 bp):
AGATTTCAGTTAGTATTTCTCACACTAATTCA
Found at i:419629 original size:21 final size:21
Alignment explanation
Indices: 419594--419634 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
419584 TTGCTATAAG
*
419594 TTTCCTTATCACTTTTTTTTT
1 TTTCCTTATCACTTTATTTTT
* *
419615 TTTCCTTTTCCCTTTATTTT
1 TTTCCTTATCACTTTATTTT
419635 CAAGTATAAT
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:0.07, C:0.22, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTCCTTATCACTTTATTTTT
Found at i:423837 original size:35 final size:37
Alignment explanation
Indices: 423773--423852 Score: 101
Period size: 37 Copynumber: 2.2 Consensus size: 37
423763 ATTTTATATC
* *
423773 ATAAAATATATATACATATAATATTTTAAATATAATT
1 ATAAAATATAAATACATATAATATATTAAATATAATT
*
423810 ATAATATATAAATACATA-AAT-TATTAAATATAATGT
1 ATAAAATATAAATACATATAATATATTAAATATAAT-T
423846 ATTAAAA
1 A-TAAAA
423853 AGTTTTATAC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
35 12 0.32
36 5 0.14
37 20 0.54
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (37 bp):
ATAAAATATAAATACATATAATATATTAAATATAATT
Found at i:431534 original size:2 final size:2
Alignment explanation
Indices: 431527--431558 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
431517 ATAAAACAAC
431527 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
431559 GTGGATAATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:442069 original size:14 final size:15
Alignment explanation
Indices: 442039--442078 Score: 55
Period size: 14 Copynumber: 2.6 Consensus size: 15
442029 ATATGCAAGA
442039 TCCTTTTCTTTTCTTT
1 TCCTTTT-TTTTCTTT
442055 TCCTTTTTTTT-TTT
1 TCCTTTTTTTTCTTT
442069 TCCTTATTTT
1 TCCTT-TTTT
442079 CCAGAAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.35
15 8 0.35
16 7 0.30
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.78
Consensus pattern (15 bp):
TCCTTTTTTTTCTTT
Found at i:451828 original size:40 final size:40
Alignment explanation
Indices: 451775--451851 Score: 93
Period size: 40 Copynumber: 1.9 Consensus size: 40
451765 TGTATAAATT
* * *
451775 ATAATTAAATTTAAATTTAAATAAAATAATTTATTTAATAA
1 ATAATTAAATTTAAAATAAAATAAAATAA-ATATTTAATAA
* *
451816 ATAA-TAATTTTAAAATAAAATAATATAAATATTTAA
1 ATAATTAAATTTAAAATAAAATAAAATAAATATTTAA
451852 ATTGCAATAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
39 7 0.23
40 20 0.65
41 4 0.13
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (40 bp):
ATAATTAAATTTAAAATAAAATAAAATAAATATTTAATAA
Found at i:451837 original size:16 final size:17
Alignment explanation
Indices: 451793--451839 Score: 51
Period size: 19 Copynumber: 2.7 Consensus size: 17
451783 ATTTAAATTT
*
451793 AAATAAAATAATTTATT
1 AAATAAAATAATTTATA
*
451810 TAATAAATAATAATTT-TA
1 AAAT-AA-AATAATTTATA
451828 AAATAAAATAAT
1 AAATAAAATAAT
451840 ATAAATATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
16 6 0.24
17 5 0.20
18 6 0.24
19 8 0.32
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AAATAAAATAATTTATA
Found at i:454094 original size:2 final size:2
Alignment explanation
Indices: 454089--454139 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
454079 CTGACATATA
454089 TG TG TG 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 TG TG TG
454131 TG TG TG TG T
1 TG TG TG TG T
454140 ATATATGTAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:457259 original size:32 final size:31
Alignment explanation
Indices: 457211--457292 Score: 85
Period size: 32 Copynumber: 2.6 Consensus size: 31
457201 AATAAAATTT
* * *
457211 TATATAAAAATAATATAGTAT-AATAATATAAA
1 TATATAAAATTTATATAATATGAAT--TATAAA
*
457243 TATATAAAATTTATATAATATGAATTATTAA
1 TATATAAAATTTATATAATATGAATTATAAA
*
457274 TATATTAAAATTTTTATAA
1 TATA-TAAAATTTATATAA
457293 ATATAAATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
31 9 0.21
32 31 0.72
33 3 0.07
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (31 bp):
TATATAAAATTTATATAATATGAATTATAAA
Found at i:457296 original size:18 final size:17
Alignment explanation
Indices: 457244--457313 Score: 51
Period size: 15 Copynumber: 4.4 Consensus size: 17
457234 TAATATAAAT
*
457244 ATATAAAATTTATAT-A
1 ATATAAAATTTTTATAA
* * *
457260 ATAT-GAATTATTA-AT
1 ATATAAAATTTTTATAA
457275 ATATTAAAATTTTTATAA
1 ATA-TAAAATTTTTATAA
*
457293 ATAT-AAATATTT-TAA
1 ATATAAAATTTTTATAA
457308 ATATAA
1 ATATAA
457314 TTATAATAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
15 16 0.39
16 13 0.32
17 8 0.20
18 4 0.10
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (17 bp):
ATATAAAATTTTTATAA
Found at i:457395 original size:4 final size:4
Alignment explanation
Indices: 457386--457422 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
457376 ATGTAAACGG
457386 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT T
457423 AGACTAGCAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:458258 original size:2 final size:2
Alignment explanation
Indices: 458251--458275 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
458241 TATCTCCCAA
458251 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
458276 GTGATTGGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:459767 original size:16 final size:16
Alignment explanation
Indices: 459746--459776 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
459736 GCATTGCCAA
459746 ATCTCTCAATCACAAT
1 ATCTCTCAATCACAAT
459762 ATCTCTCAATCACAA
1 ATCTCTCAATCACAA
459777 AATCACAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.32, G:0.00, T:0.29
Consensus pattern (16 bp):
ATCTCTCAATCACAAT
Found at i:459836 original size:21 final size:21
Alignment explanation
Indices: 459812--459857 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
459802 AGTGAGTTAC
459812 AAATATTAAAATTCGAATTTA
1 AAATATTAAAATTCGAATTTA
*
459833 AAATATTAAGATTCGAATTTA
1 AAATATTAAAATTCGAATTTA
459854 AAAT
1 AAAT
459858 TTGTTGGATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.52, C:0.04, G:0.07, T:0.37
Consensus pattern (21 bp):
AAATATTAAAATTCGAATTTA
Found at i:460767 original size:2 final size:2
Alignment explanation
Indices: 460760--460797 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
460750 GGAGTTATTT
460760 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
460798 AACACAGCGA
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:461529 original size:2 final size:2
Alignment explanation
Indices: 461522--461546 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
461512 ACCAGAATAC
461522 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 A
461547 TGTACAGAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:466632 original size:150 final size:151
Alignment explanation
Indices: 466282--466881 Score: 912
Period size: 150 Copynumber: 4.0 Consensus size: 151
466272 AGAAAGATTC
* * *
466282 AAAACTTAAGTCAAAAACACGCCAAGAATCGAAACAAACAAGAAATTATCTAATCACGTTCAATT
1 AAAACTTAAGCCAAAAACACGCCAAGAATCAAAACAAACAAGAAATTATCTAATCACATTCAATT
* * * *
466347 TCTTTATTGCGTTAATCCAAGCTAAGTAGCAGATAAAGCTGTTACATG-AA---ACAATGCTGTC
66 TCTTTATTGCGTTAATCCAAGCAAAGTAGCAGATAAAGCTATTACACGAAATTTACAATTCTGTC
* *
466408 ACATTCAATATATTTTCCTTT
131 ACACTCAATATATTTTCTTTT
*
466429 AAAACTTAAGCCAAAAACATGCCAAGAATCAAAACAAACAAGAAATTATCTAATCACATTCAATT
1 AAAACTTAAGCCAAAAACACGCCAAGAATCAAAACAAACAAGAAATTATCTAATCACATTCAATT
* *
466494 TCTTTATTGCGTTAATCCAAGCTAAGTAGCAGATAAAGCTATTCCACGAAATTTACAATTCTGTC
66 TCTTTATTGCGTTAATCCAAGCAAAGTAGCAGATAAAGCTATTACACGAAATTTACAATTCTGTC
*
466559 ACACTCAATA-AATTTCTTTT
131 ACACTCAATATATTTTCTTTT
* *
466579 AAAACTTAAGCCAAAAACACGCCAAGAATCAAAACAAACAAGAAAATATCTAATTACATTCAA-T
1 AAAACTTAAGCCAAAAACACGCCAAGAATCAAAACAAACAAGAAATTATCTAATCACATTCAATT
* *
466643 TCTTTATTGCATTAATCCAAGCAAAGTCGCAGATAAAGCTATTACACGAAATTTACAATTCTGTC
66 TCTTTATTGCGTTAATCCAAGCAAAGTAGCAGATAAAGCTATTACACGAAATTTACAATTCTGTC
466708 ACACTCAATATATTTTCTTTT
131 ACACTCAATATATTTTCTTTT
* * *
466729 AAAACTTAAGCCAAAAACACGCCAAGATTCGAAACAAACAAGAAATTATCTAATTACATTCAATT
1 AAAACTTAAGCCAAAAACACGCCAAGAATCAAAACAAACAAGAAATTATCTAATCACATTCAATT
* * *
466794 TCTTTATTGCGTTAATCCAAGCAAAGTTGCAGATAAAGCTATTGCACAAAATTTACAATTCTGT-
66 TCTTTATTGCGTTAATCCAAGCAAAGTAGCAGATAAAGCTATTACACGAAATTTACAATTCTGTC
*
466858 -CACTACAA-ATATTTCCTTTT
131 ACACT-CAATATATTTTCTTTT
466878 AAAA
1 AAAA
466882 GGAAATTAAG
Statistics
Matches: 419, Mismatches: 27, Indels: 12
0.91 0.06 0.03
Matches are distributed among these distances:
147 106 0.25
148 2 0.00
149 91 0.22
150 140 0.33
151 80 0.19
ACGTcount: A:0.42, C:0.20, G:0.09, T:0.29
Consensus pattern (151 bp):
AAAACTTAAGCCAAAAACACGCCAAGAATCAAAACAAACAAGAAATTATCTAATCACATTCAATT
TCTTTATTGCGTTAATCCAAGCAAAGTAGCAGATAAAGCTATTACACGAAATTTACAATTCTGTC
ACACTCAATATATTTTCTTTT
Found at i:467741 original size:33 final size:32
Alignment explanation
Indices: 467679--467743 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 32
467669 TTTAATTCAA
**
467679 ATAAATATTTATATTATAATTTTAGTAAATAT
1 ATAAATATTTATATTATAATGATAGTAAATAT
*
467711 ATAAATATTTTATATTGAT-ATGATATTAAATAT
1 ATAAATA-TTTATATT-ATAATGATAGTAAATAT
467744 CAAATGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 7 0.25
33 19 0.68
34 2 0.07
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (32 bp):
ATAAATATTTATATTATAATGATAGTAAATAT
Found at i:468404 original size:5 final size:5
Alignment explanation
Indices: 468394--468428 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
468384 AAAAAATTAA
*
468394 AATTT AATTT AATTT AAATTT ACTTT AATTT AATT
1 AATTT AATTT AATTT -AATTT AATTT AATTT AATT
468429 CAGCTCGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (5 bp):
AATTT
Found at i:468412 original size:16 final size:16
Alignment explanation
Indices: 468388--468426 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
468378 GTAATAAAAA
*
468388 AATTAAAATTTAATTT
1 AATTTAAATTTAATTT
*
468404 AATTTAAATTTACTTT
1 AATTTAAATTTAATTT
468420 AATTTAA
1 AATTTAA
468427 TTCAGCTCGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (16 bp):
AATTTAAATTTAATTT
Found at i:468896 original size:28 final size:26
Alignment explanation
Indices: 468831--468896 Score: 62
Period size: 27 Copynumber: 2.4 Consensus size: 26
468821 TAAAGTAAAT
*
468831 TTATATATTTTTATTGTATTTGAATAA
1 TTAT-TATTTTTATTGTATATGAATAA
*
468858 TTTTTAGTTTTTGATT-TATATGTAATAA
1 TTATTA-TTTTT-ATTGTATATG-AATAA
468886 GTTATTATTTT
1 -TTATTATTTT
468897 AAATAAATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
26 2 0.06
27 13 0.41
28 12 0.38
29 5 0.16
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.62
Consensus pattern (26 bp):
TTATTATTTTTATTGTATATGAATAA
Found at i:468901 original size:17 final size:17
Alignment explanation
Indices: 468881--468914 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
468871 ATTTATATGT
* *
468881 AATAAGTTATTATTTTA
1 AATAAATTATTAATTTA
468898 AATAAATTATTAATTTA
1 AATAAATTATTAATTTA
468915 TGTTAAGATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
AATAAATTATTAATTTA
Found at i:470105 original size:21 final size:21
Alignment explanation
Indices: 470056--470113 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
470046 ATGTTTTTTA
*
470056 ATTTTTAATTAAATTTGATAAT
1 ATTTTTAA-TAAATTTGAAAAT
*
470078 -TTATTTAATAAATTTTAAAAT
1 ATT-TTTAATAAATTTGAAAAT
*
470099 ATTTTTAAAAAATTT
1 ATTTTTAATAAATTT
470114 AATATTAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 24 0.77
22 7 0.23
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
ATTTTTAATAAATTTGAAAAT
Found at i:470660 original size:21 final size:20
Alignment explanation
Indices: 470621--470673 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
470611 ACTAATATAT
*
470621 AATATACATTAATCATATTTA
1 AATATATATTAATCATA-TTA
**
470642 AATATATATTAATTTTATTA
1 AATATATATTAATCATATTA
*
470662 ATTTATATATTA
1 A-ATATATATTA
470674 TTAAATTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 4 0.15
21 23 0.85
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (20 bp):
AATATATATTAATCATATTA
Found at i:472773 original size:6 final size:6
Alignment explanation
Indices: 472764--472793 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
472754 TATATACATA
*
472764 TATATG TATATG TATATG TATATG TCTATG
1 TATATG TATATG TATATG TATATG TATATG
472794 CGTATATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.30, C:0.03, G:0.17, T:0.50
Consensus pattern (6 bp):
TATATG
Found at i:472803 original size:18 final size:18
Alignment explanation
Indices: 472761--472819 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 18
472751 TGATATATAC
*
472761 ATATATATGTATATGTAT
1 ATATATATGTATATGCAT
* * *
472779 ATGTATATGTCTATGCGT
1 ATATATATGTATATGCAT
* *
472797 ATATATATATATATACAT
1 ATATATATGTATATGCAT
472815 ATATA
1 ATATA
472820 CAAAGTGGAA
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.39, C:0.05, G:0.10, T:0.46
Consensus pattern (18 bp):
ATATATATGTATATGCAT
Found at i:474445 original size:19 final size:20
Alignment explanation
Indices: 474423--474471 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 20
474413 TTATTAAAAA
*
474423 ATATTAAAATAA-TTATTTT
1 ATATTAAAACAATTTATTTT
*
474442 ATATTAATACAATTTTATTTT
1 ATATTAAAACAA-TTTATTTT
474463 ATAATTAAA
1 AT-ATTAAA
474472 TTTTTTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 10 0.42
21 9 0.38
22 5 0.21
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATTAAAACAATTTATTTT
Found at i:474617 original size:27 final size:27
Alignment explanation
Indices: 474585--474636 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
474575 GTATATAATT
474585 TATATTTAATAT-ATATTTAAATATAAA
1 TATA-TTAATATAATATTTAAATATAAA
*
474612 TATATTAATATAATTTTTAAATATA
1 TATATTAATATAATATTTAAATATA
474637 TAAAAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (27 bp):
TATATTAATATAATATTTAAATATAAA
Found at i:477485 original size:91 final size:91
Alignment explanation
Indices: 477330--477500 Score: 270
Period size: 91 Copynumber: 1.9 Consensus size: 91
477320 TTGTGTTGTG
* *
477330 TTAAGCATATTCGTATTTTGTGCACATTTGCACCGACTAAATGTTATATATTCGATATTAAGCAT
1 TTAAGCATATTCGTATTTTGTGCACATCTGCACCGACTAAATGTTATATACTCGATATTAAGCAT
477395 GTTTATGTAAGACCTATTAGAACTTA
66 GTTTATGTAAGACCTATTAGAACTTA
* * * * *
477421 TTAAGCATATTCGTGTTTTGTGCACATCTGTACTGGCTAATTGTTATATACTCGATATTAAGCAT
1 TTAAGCATATTCGTATTTTGTGCACATCTGCACCGACTAAATGTTATATACTCGATATTAAGCAT
*
477486 GTTTATGTAGGACCT
66 GTTTATGTAAGACCT
477501 CTTAAGCATA
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
91 72 1.00
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.40
Consensus pattern (91 bp):
TTAAGCATATTCGTATTTTGTGCACATCTGCACCGACTAAATGTTATATACTCGATATTAAGCAT
GTTTATGTAAGACCTATTAGAACTTA
Found at i:481242 original size:20 final size:21
Alignment explanation
Indices: 481219--481316 Score: 59
Period size: 20 Copynumber: 4.9 Consensus size: 21
481209 TTATTTTATT
*
481219 ATATTATAA-TTATATTTAAA
1 ATATTATAATTTATATATAAA
*
481239 ATATTTTAATTTATATAT-AA
1 ATATTATAATTTATATATAAA
*
481259 AT-TT-TAATTTAT-TA-ACA
1 ATATTATAATTTATATATAAA
* *
481276 AT-TTAT-ATTATATATTTTAAT
1 ATATTATAATT-TATA-TATAAA
481297 ATATTTATATATTTATATAT
1 ATA-TTATA-ATTTATATAT
481317 TATATAAAAT
Statistics
Matches: 60, Mismatches: 7, Indels: 19
0.70 0.08 0.22
Matches are distributed among these distances:
17 10 0.17
18 12 0.20
19 2 0.03
20 13 0.22
21 10 0.17
23 6 0.10
24 4 0.07
25 3 0.05
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (21 bp):
ATATTATAATTTATATATAAA
Found at i:481295 original size:30 final size:29
Alignment explanation
Indices: 481246--481316 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 29
481236 AAAATATTTT
*
481246 AATTTATATATAAATTTTAATTTATTAAC
1 AATTTATATATAAATTTTAATATATTAAC
* * *
481275 AATTTATATTATATATTTTAATATATTTAT
1 AATTTATA-TATAAATTTTAATATATTAAC
481305 ATATTTATATAT
1 A-ATTTATATAT
481317 TATATAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 8 0.22
30 21 0.58
31 7 0.19
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.56
Consensus pattern (29 bp):
AATTTATATATAAATTTTAATATATTAAC
Found at i:484847 original size:40 final size:40
Alignment explanation
Indices: 484803--484962 Score: 275
Period size: 40 Copynumber: 4.0 Consensus size: 40
484793 GATAGGTGTG
* *
484803 AAGGATTAAAACCGCGGCGTTGATTTACATGCGGCGCTCC
1 AAGGATTAAAACCGCGGCGTTGATTTACATGCGGCGCACA
* *
484843 AAGGATTAAAACCGCAGCGTTGATTTACATGTGGCGCACA
1 AAGGATTAAAACCGCGGCGTTGATTTACATGCGGCGCACA
*
484883 AAGGATTAAAACCGCGGCGTTGATTTACATGTGGCGCACA
1 AAGGATTAAAACCGCGGCGTTGATTTACATGCGGCGCACA
484923 AAGGATTAAAACCGCGGCGTTGATTTACATGCGGCGCACA
1 AAGGATTAAAACCGCGGCGTTGATTTACATGCGGCGCACA
484963 CTGTTTTAGT
Statistics
Matches: 114, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 114 1.00
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (40 bp):
AAGGATTAAAACCGCGGCGTTGATTTACATGCGGCGCACA
Found at i:487743 original size:79 final size:79
Alignment explanation
Indices: 487612--487772 Score: 295
Period size: 79 Copynumber: 2.0 Consensus size: 79
487602 AGATGTTCTC
* *
487612 GATCCTATTTCAAGCAAGTTAAGCAGTCATGAGCAGAGTGATTGACCTTAAACATTAAATAAACT
1 GATCCTATTTCAAGCAAGTTAAGCAATCATGAGCAGAGTGATGGACCTTAAACATTAAATAAACT
487677 TACTTTTATCCATT
66 TACTTTTATCCATT
*
487691 GATCCTATTTCAAGCAAGTTAAGCAATCATGAGCAGAGTGATGGATCTTAAACATTAAATAAACT
1 GATCCTATTTCAAGCAAGTTAAGCAATCATGAGCAGAGTGATGGACCTTAAACATTAAATAAACT
487756 TACTTTTATCCATT
66 TACTTTTATCCATT
487770 GAT
1 GAT
487773 ACGCCAGGAA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
79 79 1.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (79 bp):
GATCCTATTTCAAGCAAGTTAAGCAATCATGAGCAGAGTGATGGACCTTAAACATTAAATAAACT
TACTTTTATCCATT
Found at i:491846 original size:32 final size:32
Alignment explanation
Indices: 491799--491894 Score: 122
Period size: 32 Copynumber: 3.0 Consensus size: 32
491789 TAAATTTAAT
*
491799 AAATTAGATATAATTACTCATAAATTTGATAA
1 AAATTAAATATAATTACTCATAAATTTGATAA
*
491831 AAATTAAATAAAATTACTCATAAATTT-AGTAA
1 AAATTAAATATAATTACTCATAAATTTGA-TAA
* * * *
491863 ATATTAAACATAATTACTTAAAAATTTGATAA
1 AAATTAAATATAATTACTCATAAATTTGATAA
491895 TCATTAAAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
31 1 0.02
32 53 0.96
33 1 0.02
ACGTcount: A:0.53, C:0.06, G:0.04, T:0.36
Consensus pattern (32 bp):
AAATTAAATATAATTACTCATAAATTTGATAA
Found at i:491901 original size:32 final size:31
Alignment explanation
Indices: 491788--491902 Score: 108
Period size: 32 Copynumber: 3.6 Consensus size: 31
491778 ATATAACATT
* * *
491788 ATAAATTTAATAA-ATTAGATATAATTACTC
1 ATAAATTTGATAATATTAAACATAATTACTC
* * *
491818 ATAAATTTGATAAAAATTAAATAAAATTACTC
1 ATAAATTTGAT-AATATTAAACATAATTACTC
*
491850 ATAAATTT-AGTAAATATTAAACATAATTACTT
1 ATAAATTTGA-T-AATATTAAACATAATTACTC
*
491882 AAAAATTTGATAATCATTAAA
1 ATAAATTTGATAAT-ATTAAA
491903 AAGTTTTAAC
Statistics
Matches: 72, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
30 10 0.14
31 6 0.08
32 55 0.76
33 1 0.01
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.37
Consensus pattern (31 bp):
ATAAATTTGATAATATTAAACATAATTACTC
Found at i:492471 original size:22 final size:19
Alignment explanation
Indices: 492436--492484 Score: 53
Period size: 22 Copynumber: 2.4 Consensus size: 19
492426 TTAAATAAGA
*
492436 TTTAGATTTAAATTTTCATAT
1 TTTAAATTTAAATTTT-A-AT
*
492457 TTATAAATTTTAATTTTAAT
1 TT-TAAATTTAAATTTTAAT
492477 TTTAAATT
1 TTTAAATT
492485 GATTTATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 6 0.24
20 4 0.16
21 3 0.12
22 12 0.48
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (19 bp):
TTTAAATTTAAATTTTAAT
Found at i:492812 original size:26 final size:26
Alignment explanation
Indices: 492782--492849 Score: 127
Period size: 26 Copynumber: 2.6 Consensus size: 26
492772 TATTTAAAAT
*
492782 TTTAATTTTTATTTTTATAATTCGAG
1 TTTAATTTTAATTTTTATAATTCGAG
492808 TTTAATTTTAATTTTTATAATTCGAG
1 TTTAATTTTAATTTTTATAATTCGAG
492834 TTTAATTTTAATTTTT
1 TTTAATTTTAATTTTT
492850 TTTGTTAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.28, C:0.03, G:0.06, T:0.63
Consensus pattern (26 bp):
TTTAATTTTAATTTTTATAATTCGAG
Found at i:493232 original size:2 final size:2
Alignment explanation
Indices: 493225--493259 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
493215 TGTCAATCTA
493225 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
493260 ATATATATAT
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:493264 original size:2 final size:2
Alignment explanation
Indices: 493259--493283 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
493249 TCTCTCTCTC
493259 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
493284 TCCTTTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:496666 original size:14 final size:16
Alignment explanation
Indices: 496647--496679 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
496637 TGAGATAAAT
496647 AAAAAATA-G-CAAAA
1 AAAAAATATGTCAAAA
496661 AAAAAATATGTCAAAA
1 AAAAAATATGTCAAAA
496677 AAA
1 AAA
496680 GAAAAGAAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 1 0.06
16 8 0.47
ACGTcount: A:0.76, C:0.06, G:0.06, T:0.12
Consensus pattern (16 bp):
AAAAAATATGTCAAAA
Found at i:508330 original size:12 final size:12
Alignment explanation
Indices: 508315--508371 Score: 57
Period size: 12 Copynumber: 5.0 Consensus size: 12
508305 CCATATTGTA
508315 ACCCATCTGACC
1 ACCCATCTGACC
* *
508327 ACCCATTTGACG
1 ACCCATCTGACC
*
508339 ACCCATGTG---
1 ACCCATCTGACC
508348 ACCCATCTGACC
1 ACCCATCTGACC
*
508360 ACCCATTTGACC
1 ACCCATCTGACC
508372 CATCTGCCCC
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
9 8 0.22
12 29 0.78
ACGTcount: A:0.25, C:0.42, G:0.12, T:0.21
Consensus pattern (12 bp):
ACCCATCTGACC
Found at i:508332 original size:33 final size:32
Alignment explanation
Indices: 508295--508374 Score: 83
Period size: 33 Copynumber: 2.4 Consensus size: 32
508285 TCCCATTTGG
*
508295 CCCATATGGCCCATATTGTAACCCATCTGACCA
1 CCCATTTGGCCCATA-TGTAACCCATCTGACCA
*
508328 CCCATTTGACGACCC--ATGTGACCCATCTGACCA
1 CCCATTTG--G-CCCATATGTAACCCATCTGACCA
*
508361 CCCATTTGACCCAT
1 CCCATTTGGCCCAT
508375 CTGCCCCATA
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
30 3 0.08
33 31 0.79
34 1 0.03
35 1 0.03
36 3 0.08
ACGTcount: A:0.25, C:0.39, G:0.12, T:0.24
Consensus pattern (32 bp):
CCCATTTGGCCCATATGTAACCCATCTGACCA
Found at i:508353 original size:21 final size:21
Alignment explanation
Indices: 508327--508377 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
508317 CCATCTGACC
* *
508327 ACCCATTTGACGACCCATGTG
1 ACCCATCTGACCACCCATGTG
*
508348 ACCCATCTGACCACCCATTTG
1 ACCCATCTGACCACCCATGTG
508369 ACCCATCTG
1 ACCCATCTG
508378 CCCCATATTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.24, C:0.39, G:0.14, T:0.24
Consensus pattern (21 bp):
ACCCATCTGACCACCCATGTG
Found at i:508958 original size:6 final size:6
Alignment explanation
Indices: 508934--508972 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
508924 CATTTGATGC
* * *
508934 CCATGG CCATGT CCCTGA CCATGA CCATGA CCATGA CCA
1 CCATGA CCATGA CCATGA CCATGA CCATGA CCATGA CCA
508973 AATTCCTCCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.26, C:0.38, G:0.18, T:0.18
Consensus pattern (6 bp):
CCATGA
Found at i:508999 original size:12 final size:12
Alignment explanation
Indices: 508981--509059 Score: 110
Period size: 12 Copynumber: 6.8 Consensus size: 12
508971 CAAATTCCTC
508981 CTCATCATCAAA
1 CTCATCATCAAA
*
508993 TTCATCATCAAA
1 CTCATCATCAAA
509005 CTCATCATCAAA
1 CTCATCATCAAA
*
509017 TTCATCATCAAA
1 CTCATCATCAAA
*
509029 CTCATCACCAAA
1 CTCATCATCAAA
509041 CTCATCAT--AA
1 CTCATCATCAAA
509051 -TCATCATCA
1 CTCATCATCA
509060 CTTTCACCAA
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
9 7 0.12
10 2 0.03
12 50 0.85
ACGTcount: A:0.41, C:0.32, G:0.00, T:0.28
Consensus pattern (12 bp):
CTCATCATCAAA
Found at i:510366 original size:2 final size:2
Alignment explanation
Indices: 510359--510393 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
510349 CACATGCTGT
510359 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
510394 GTTGATTTGT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:511190 original size:19 final size:19
Alignment explanation
Indices: 511150--511195 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
511140 AACATAAAAT
* *
511150 AAAATTT-ACAAATCTATC
1 AAAATTTAACAAATATATA
*
511168 AAAATTTAATAAATATATA
1 AAAATTTAACAAATATATA
511187 AAAATTTAA
1 AAAATTTAA
511196 AATTCAATAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 7 0.29
19 17 0.71
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAATTTAACAAATATATA
Found at i:513737 original size:21 final size:21
Alignment explanation
Indices: 513713--513769 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
513703 AATTCAATTA
*
513713 TAAAAATATAATAAT-AATTTT
1 TAAAAAT-TAAAAATAAATTTT
*
513734 TAAACATTAAAAATAAATTTT
1 TAAAAATTAAAAATAAATTTT
* *
513755 TTAAATTTAATAAAT
1 TAAAAATTAA-AAAT
513770 TATATCAAAC
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 6 0.21
21 19 0.66
22 4 0.14
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
TAAAAATTAAAAATAAATTTT
Found at i:515078 original size:18 final size:18
Alignment explanation
Indices: 515037--515084 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 18
515027 ATATTATAAT
*
515037 TTTAAAATTATTAAAAATA
1 TTTAAAA-TATTAAAAAAA
515056 TTTAAAAT-TTAAATAAAA
1 TTTAAAATATTAAA-AAAA
515074 TTTAAAATATT
1 TTTAAAATATT
515085 CTTTGATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 5 0.19
18 12 0.46
19 9 0.35
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TTTAAAATATTAAAAAAA
Found at i:515412 original size:6 final size:6
Alignment explanation
Indices: 515401--515457 Score: 53
Period size: 6 Copynumber: 8.8 Consensus size: 6
515391 CTATTTAAAA
*
515401 TAAATT TAAATT TAAATT TAAATT TATTATT TATATATTT TATAA-T TAAATT
1 TAAATT TAAATT TAAATT TAAATT TA-AATT TA-A-A-TT TA-AATT TAAATT
515453 TAAAT
1 TAAAT
515458 AAAAATATTA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
5 2 0.04
6 29 0.64
7 6 0.13
8 2 0.04
9 6 0.13
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
TAAATT
Found at i:515901 original size:16 final size:16
Alignment explanation
Indices: 515857--515906 Score: 59
Period size: 14 Copynumber: 3.2 Consensus size: 16
515847 TATTGTAAAA
515857 AAAATTAATAAAAATTT
1 AAAA-TAATAAAAATTT
* *
515874 AAAAT-GT-TAAATTT
1 AAAATAATAAAAATTT
515888 AAAATAATAAAAATTT
1 AAAATAATAAAAATTT
515904 AAA
1 AAA
515907 TATGTGAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
14 11 0.41
15 2 0.07
16 10 0.37
17 4 0.15
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (16 bp):
AAAATAATAAAAATTT
Found at i:516164 original size:15 final size:16
Alignment explanation
Indices: 516144--516173 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
516134 TCGTATATTA
516144 ACAGTAAAAA-AAAAT
1 ACAGTAAAAATAAAAT
516159 ACAGTAAAAATAAAA
1 ACAGTAAAAATAAAA
516174 GAAGTTATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.73, C:0.07, G:0.07, T:0.13
Consensus pattern (16 bp):
ACAGTAAAAATAAAAT
Found at i:516885 original size:23 final size:23
Alignment explanation
Indices: 516822--516890 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 23
516812 TATTAGTATT
* *
516822 TATATATATTTAAATATAT-ATA
1 TATATATATATACATATATCATA
* *
516844 -AAATATATAGTTACTTATATCATA
1 TATATATATA--TACATATATCATA
516868 TATATATATATACATATA-CATA
1 TATATATATATACATATATCATA
516890 T
1 T
516891 TCATATGTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
21 7 0.19
22 5 0.14
23 14 0.38
24 3 0.08
25 8 0.22
ACGTcount: A:0.48, C:0.06, G:0.01, T:0.45
Consensus pattern (23 bp):
TATATATATATACATATATCATA
Found at i:517975 original size:18 final size:18
Alignment explanation
Indices: 517949--517992 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
517939 TCTTTCATAG
* * *
517949 ATAATAATAATAATAGTA
1 ATAAAAATAAAAATAATA
*
517967 ATAAAAATAAAAATAATC
1 ATAAAAATAAAAATAATA
517985 ATAAAAAT
1 ATAAAAAT
517993 TTACATAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (18 bp):
ATAAAAATAAAAATAATA
Found at i:523717 original size:17 final size:17
Alignment explanation
Indices: 523697--523731 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
523687 TATTTTTATG
*
523697 TAATATAATAAAAATAT
1 TAATATAACAAAAATAT
523714 TAATATAACAAAAATAT
1 TAATATAACAAAAATAT
523731 T
1 T
523732 TATCGATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (17 bp):
TAATATAACAAAAATAT
Found at i:523877 original size:30 final size:29
Alignment explanation
Indices: 523841--523897 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 29
523831 ATTTAGCTAA
*
523841 GTTATACTATAATTATTGGCAAAAAAAAAG
1 GTTATACTATAATTA-TGACAAAAAAAAAG
523871 GTTATACTATAATTATGACAAAAAAAA
1 GTTATACTATAATTATGACAAAAAAAA
523898 CTATACTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 11 0.42
30 15 0.58
ACGTcount: A:0.53, C:0.07, G:0.11, T:0.30
Consensus pattern (29 bp):
GTTATACTATAATTATGACAAAAAAAAAG
Found at i:523902 original size:26 final size:29
Alignment explanation
Indices: 523843--523910 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 29
523833 TTAGCTAAGT
* *
523843 TATACTATAATTATTGGCAAAAAAAAAGGT
1 TATACTATAATTATTGACAAAAAAAAA-GC
523873 TATACTATAATTA-TGAC-AAAAAAAA-C
1 TATACTATAATTATTGACAAAAAAAAAGC
523899 TATACTATAATT
1 TATACTATAATT
523911 TATAAATCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
26 12 0.33
28 8 0.22
29 3 0.08
30 13 0.36
ACGTcount: A:0.51, C:0.09, G:0.07, T:0.32
Consensus pattern (29 bp):
TATACTATAATTATTGACAAAAAAAAAGC
Found at i:528762 original size:14 final size:15
Alignment explanation
Indices: 528743--528774 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
528733 TAAAAATATA
528743 TTTAAAATTT-TAAT
1 TTTAAAATTTATAAT
528757 TTTAAAATTTATAAT
1 TTTAAAATTTATAAT
528772 TTT
1 TTT
528775 TACAATATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTTAAAATTTATAAT
Found at i:528928 original size:29 final size:31
Alignment explanation
Indices: 528896--528953 Score: 84
Period size: 29 Copynumber: 1.9 Consensus size: 31
528886 TGAAAGAAGC
528896 TTAGATTTTATA-TTATTAAATT-TAATATT
1 TTAGATTTTATATTTATTAAATTATAATATT
* *
528925 TTAGTTTTTATATTTTTTAAATTATAATA
1 TTAGATTTTATATTTATTAAATTATAATA
528954 AATAAATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 11 0.44
30 9 0.36
31 5 0.20
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.60
Consensus pattern (31 bp):
TTAGATTTTATATTTATTAAATTATAATATT
Found at i:528937 original size:14 final size:14
Alignment explanation
Indices: 528896--528940 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
528886 TGAAAGAAGC
528896 TTAGATTTTATATT
1 TTAGATTTTATATT
* *
528910 ATTAAATTTAATATT
1 -TTAGATTTTATATT
*
528925 TTAGTTTTTATATT
1 TTAGATTTTATATT
528939 TT
1 TT
528941 TTAAATTATA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 13 0.52
15 12 0.48
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.64
Consensus pattern (14 bp):
TTAGATTTTATATT
Found at i:529674 original size:32 final size:32
Alignment explanation
Indices: 529633--529699 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
529623 TCCATTTCTT
529633 TTCTTTTCTTTTTGAAAATCACTAATAATTAA
1 TTCTTTTCTTTTTGAAAATCACTAATAATTAA
529665 TTCTTTTCTTTTTGAAAATCACTAATAATTAA
1 TTCTTTTCTTTTTGAAAATCACTAATAATTAA
529697 TTC
1 TTC
529700 CTTTAAGTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.33, C:0.13, G:0.03, T:0.51
Consensus pattern (32 bp):
TTCTTTTCTTTTTGAAAATCACTAATAATTAA
Found at i:530878 original size:15 final size:15
Alignment explanation
Indices: 530837--530881 Score: 65
Period size: 15 Copynumber: 3.0 Consensus size: 15
530827 TTTGATCATA
*
530837 AATATTTAATAAATTT
1 AATATTTAA-AATTTT
530853 AA-ATTTAAAATTTT
1 AATATTTAAAATTTT
530867 AATATTTAAAATTTT
1 AATATTTAAAATTTT
530882 TTTCAATCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 7 0.26
15 18 0.67
16 2 0.07
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
AATATTTAAAATTTT
Found at i:531290 original size:202 final size:197
Alignment explanation
Indices: 530644--531349 Score: 551
Period size: 204 Copynumber: 3.5 Consensus size: 197
530634 TATCAATTAC
* * * * * * * ** *
530644 ATTTAAATTTTAAAATTTAATAATTATAATTTTTTTATTTTTTTAAATTACAAATATATGTAATT
1 ATTTAAA-TTTAAATTTTAATATTTATAATTTTTTT-TATCTTCAAACTACGAGCATATATAATT
* * *
530709 ATTTGTTTAGTTACAATGACAATGCCAATTATGTAATTAGTTAGCTTTTTGTT-ATGTGCAAAAT
64 A-TTG-TCAGTTACAATGACAATGCCAATTA-CTAATGAGTTAG-TTTTT-TTCATGTGCAAAAT
* * * * * * ** * **
530773 CATTAGATGTTATCTCAATTCAGAATTTAATTTAAATTATTTATTAAATTATCTTTTGATCATAA
124 CA-TACATCTCATCTCAATTTAGAATTTAATTTAATTTATTTATTTAACAATCTTTTAAAAAT-A
530838 ATATTTAATAA
187 ATATTTAATAA
* * ** *
530849 ATTTAAATTTAAAATTTTAATATTTAAAATTTTTTTCAATCAACAAACTACGAGCATATGTAATT
1 ATTTAAATTT-AAATTTTAATATTTATAATTTTTTT-TATCTTCAAACTACGAGCATATATAATT
* * * * *
530914 ATTGGATCA-TGTACAATGGCAATGCCAACTGCTAATGAGTTAATTTTTTGTCAAGTGCAAAATC
64 ATT-G-TCAGT-TACAATGACAATGCCAATTACTAATGAGTTAGTTTTTT-TCATGTGCAAAATC
* * * * * * * * *
530978 ATAGCTTTTCATCTCAATTTGGAATTTAAGTTAGTTAAATAATTTAATCAATTTTTTTAAAAA-A
125 ATA-CATCTCATCTCAATTTAGAATTTAATTTAATTTATTTATTTAA-CAA-TCTTTTAAAAATA
531042 ATATTTAATAA
187 ATATTTAATAA
* * * * *
531053 ATTTAAAATTTAAATTTTTATATCTATAA-TTTTTTTATCTTCAAATTACCAGTGTATACTATAA
1 ATTT-AAATTTAAATTTTAATATTTATAATTTTTTTTATCTTCAAACTA-C-GAGCATA-TAT-A
*
531117 ATTA-T-TCAGTTACAATGACAATGCCAATTACATAATGAGTTAGTTTTTTTCATGTGTAAAATC
61 ATTATTGTCAGTTACAATGACAATGCCAATTAC-TAATGAGTTAGTTTTTTTCATGTGCAAAATC
* *
531180 ATGACATCTCATCTCAATTTAAAATTTAATTTAATTTATTTATTTAACAATCTTTAAAAAATAAT
125 AT-ACATCTCATCTCAATTTAGAATTTAATTTAATTTATTTATTTAACAATCTTTTAAAAATAAT
* *
531245 ATCTAATAT
189 ATTTAATAA
* * * * *
531254 ATCTAGAATTTAAATTTTAATATTTATAATTTTTTTTTAATCTTCAAACTATGAGTATTTACAAT
1 ATTTA-AATTTAAATTTTAATATTTATAA-TTTTTTTT-ATCTTCAAACTACGAGCATATATAAT
* **
531319 TACTTATTTGATTACAATGACAATGCCAATT
63 TA-TTGTCAG-TTACAATGACAATGCCAATT
531350 GTATGTCATG
Statistics
Matches: 395, Mismatches: 81, Indels: 51
0.75 0.15 0.10
Matches are distributed among these distances:
200 15 0.04
201 39 0.10
202 85 0.22
203 42 0.11
204 124 0.31
205 78 0.20
206 12 0.03
ACGTcount: A:0.38, C:0.09, G:0.07, T:0.45
Consensus pattern (197 bp):
ATTTAAATTTAAATTTTAATATTTATAATTTTTTTTATCTTCAAACTACGAGCATATATAATTAT
TGTCAGTTACAATGACAATGCCAATTACTAATGAGTTAGTTTTTTTCATGTGCAAAATCATACAT
CTCATCTCAATTTAGAATTTAATTTAATTTATTTATTTAACAATCTTTTAAAAATAATATTTAAT
AA
Found at i:535115 original size:19 final size:18
Alignment explanation
Indices: 535044--535121 Score: 63
Period size: 19 Copynumber: 4.2 Consensus size: 18
535034 AAAAAATCAA
*
535044 ATATTTTTATCATATTTAT
1 ATATTTTTATAAT-TTTAT
*
535063 ATATTTTTAT-TTTTTAT
1 ATATTTTTATAATTTTAT
*
535080 A-ATTAAATTTAAAATTTTAT
1 ATATT---TTTATAATTTTAT
535100 ATATTTTTATAAATTTTA-
1 ATATTTTTAT-AATTTTAT
535118 ATAT
1 ATAT
535122 GTTAGTAATT
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
16 3 0.06
17 6 0.12
18 9 0.18
19 21 0.43
20 7 0.14
21 3 0.06
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (18 bp):
ATATTTTTATAATTTTAT
Found at i:535121 original size:18 final size:18
Alignment explanation
Indices: 535087--535121 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
535077 TATAATTAAA
535087 TTTAAAATTTTATATATT
1 TTTAAAATTTTATATATT
535105 TTTATAAATTTTA-ATAT
1 TTTA-AAATTTTATATAT
535122 GTTAGTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTAAAATTTTATATATT
Found at i:535187 original size:28 final size:24
Alignment explanation
Indices: 535149--535203 Score: 65
Period size: 28 Copynumber: 2.1 Consensus size: 24
535139 ACAATATCAC
535149 ATAAATTTTAATAAATTTATATATTTAT
1 ATAAATTTTAAT---TTTAT-TATTTAT
*
535177 ATAATTTTTAATTTTATTATTTAT
1 ATAAATTTTAATTTTATTATTTAT
535201 ATA
1 ATA
535204 TATAATTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 10 0.38
25 5 0.19
28 11 0.42
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
ATAAATTTTAATTTTATTATTTAT
Found at i:535413 original size:18 final size:18
Alignment explanation
Indices: 535387--535427 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
535377 TTATTATTTA
535387 AAATA-TATTATAATATT
1 AAATATTATTATAATATT
* *
535404 AAATATTATTTTTATATT
1 AAATATTATTATAATATT
535422 -AATATT
1 AAATATT
535428 TAAATTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
AAATATTATTATAATATT
Found at i:535437 original size:14 final size:14
Alignment explanation
Indices: 535420--535453 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
535410 TATTTTTATA
535420 TTAATATTTAAATT
1 TTAATATTTAAATT
*
535434 TTAAAATTTAAATT
1 TTAATATTTAAATT
*
535448 TAAATA
1 TTAATA
535454 AAATTTTAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTAATATTTAAATT
Found at i:536370 original size:11 final size:12
Alignment explanation
Indices: 536354--536409 Score: 64
Period size: 11 Copynumber: 4.7 Consensus size: 12
536344 TATATTTAAA
536354 TTTAAATAT-AT
1 TTTAAATATAAT
536365 TTTAAATATAAT
1 TTTAAATATAAT
536377 TATTAAATATAAAT
1 T-TTAAATAT-AAT
536391 ATTTAAA-A-AAT
1 -TTTAAATATAAT
536402 TTTAAATA
1 TTTAAATA
536410 ATATAATACT
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
10 6 0.15
11 13 0.32
12 3 0.08
13 9 0.22
14 8 0.20
15 1 0.03
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
TTTAAATATAAT
Found at i:536406 original size:24 final size:23
Alignment explanation
Indices: 536336--536409 Score: 62
Period size: 24 Copynumber: 3.1 Consensus size: 23
536326 CATCTATGAT
* * *
536336 TATATTATTATATTTAAATTTAAA
1 TATATT-TTAAATATAATTTTAAA
536360 TATATTTTAAATATAATTATTAAA
1 TATATTTTAAATATAATT-TTAAA
536384 TATAAATATTTAAA-A-AATTTTAAA
1 TAT--AT-TTTAAATATAATTTTAAA
536408 TA
1 TA
536410 ATATAATACT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
23 9 0.21
24 21 0.49
25 4 0.09
26 3 0.07
27 6 0.14
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TATATTTTAAATATAATTTTAAA
Found at i:536699 original size:6 final size:6
Alignment explanation
Indices: 536690--536723 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
536680 TAATAAAAAA
536690 TATATT TATATT TAATATT TAATATT TATATT TA
1 TATATT TATATT T-ATATT T-ATATT TATATT TA
536724 AATATCATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 14 0.52
7 13 0.48
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (6 bp):
TATATT
Found at i:536707 original size:7 final size:7
Alignment explanation
Indices: 536691--536724 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
536681 AATAAAAAAT
536691 ATATTT-
1 ATATTTA
536697 ATATTTA
1 ATATTTA
536704 ATATTTA
1 ATATTTA
536711 ATATTT-
1 ATATTTA
536717 ATATTTA
1 ATATTTA
536724 A
1 A
536725 ATATCATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 12 0.46
7 14 0.54
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
ATATTTA
Found at i:536728 original size:14 final size:14
Alignment explanation
Indices: 536691--536724 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
536681 AATAAAAAAT
536691 ATATTT-ATATTTA
1 ATATTTAATATTTA
536704 ATATTTAATATTT-
1 ATATTTAATATTTA
536717 ATATTTAA
1 ATATTTAA
536725 ATATCATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 14 0.70
14 6 0.30
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
ATATTTAATATTTA
Found at i:536758 original size:22 final size:22
Alignment explanation
Indices: 536733--536774 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
536723 AAATATCATA
536733 AATTTTTGTAA-AATTTATTTTT
1 AATTTTT-TAACAATTTATTTTT
*
536755 AATTTTTTAACTATTTATTT
1 AATTTTTTAACAATTTATTT
536775 ATTTTATTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (22 bp):
AATTTTTTAACAATTTATTTTT
Found at i:540121 original size:18 final size:17
Alignment explanation
Indices: 540087--540138 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 17
540077 TTGATAATTG
*
540087 ATTAAAAATATAAAATAA
1 ATTAAAAAT-TATAATAA
540105 ATTTAAAAATTATAAT-A
1 A-TTAAAAATTATAATAA
*
540122 ATTCAAAATT-TAATAA
1 ATTAAAAATTATAATAA
540138 A
1 A
540139 CACGAAATGA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
15 4 0.13
16 10 0.33
17 2 0.07
18 6 0.20
19 8 0.27
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (17 bp):
ATTAAAAATTATAATAA
Found at i:541708 original size:15 final size:16
Alignment explanation
Indices: 541690--541757 Score: 63
Period size: 15 Copynumber: 4.2 Consensus size: 16
541680 TTATCTATAA
541690 AAATAATATAA-ATTT
1 AAATAATATAATATTT
541705 AAATAATA-AATATTT
1 AAATAATATAATATTT
541720 AAA-AAT-TAATATTT
1 AAATAATATAATATTT
*
541734 ATGTAGTAATTATAATATTT
1 A---AATAA-TATAATATTT
541754 AAAT
1 AAAT
541758 TTTTGATTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 14
0.73 0.03 0.24
Matches are distributed among these distances:
14 13 0.30
15 15 0.35
17 3 0.07
18 2 0.05
19 1 0.02
20 9 0.21
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (16 bp):
AAATAATATAATATTT
Found at i:542592 original size:22 final size:21
Alignment explanation
Indices: 542566--542638 Score: 74
Period size: 22 Copynumber: 3.2 Consensus size: 21
542556 TATTAATCTT
542566 AAATATAATATAAAAATAATTA
1 AAATATAATATAAAAA-AATTA
542588 AAATATAATATAAAAAATATATA
1 AAATATAATATAAAAAA-AT-TA
* *
542611 TAATATAAATATATAAACGAATTA
1 AAATAT-AATATA-AAA-AAATTA
542635 AAAT
1 AAAT
542639 TTTAAAATTA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
21 1 0.02
22 18 0.42
23 7 0.16
24 11 0.26
25 5 0.12
26 1 0.02
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (21 bp):
AAATATAATATAAAAAAATTA
Found at i:542622 original size:11 final size:11
Alignment explanation
Indices: 542565--542623 Score: 65
Period size: 11 Copynumber: 5.7 Consensus size: 11
542555 TTATTAATCT
542565 TAAATATAATA
1 TAAATATAATA
*
542576 TAAAAATAAT-
1 TAAATATAATA
542586 TAAAATATAATA
1 T-AAATATAATA
542598 TAAA-A-AATA
1 TAAATATAATA
542607 T--ATATAATA
1 TAAATATAATA
542616 TAAATATA
1 TAAATATA
542624 TAAACGAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
7 1 0.03
8 1 0.03
9 10 0.25
10 2 0.05
11 25 0.62
12 1 0.03
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
TAAATATAATA
Found at i:542671 original size:15 final size:15
Alignment explanation
Indices: 542653--542707 Score: 65
Period size: 15 Copynumber: 3.5 Consensus size: 15
542643 AAATTATTAT
542653 AATATAAAATATTTA
1 AATATAAAATATTTA
542668 AATAATAAAATCTATTTA
1 AAT-ATAAAA--TATTTA
* *
542686 AATATATAATATATA
1 AATATAAAATATTTA
542701 AATATAA
1 AATATAA
542708 TTATAATATA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
15 14 0.41
16 6 0.18
17 5 0.15
18 9 0.26
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (15 bp):
AATATAAAATATTTA
Found at i:542674 original size:18 final size:18
Alignment explanation
Indices: 542651--542699 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
542641 TAAAATTATT
542651 ATAATATAAAATATTTAA
1 ATAATATAAAATATTTAA
*
542669 ATAATA-AAATCTATTTAA
1 ATAATATAAA-ATATTTAA
*
542687 AT-ATATAATATAT
1 ATAATATAAAATAT
542700 AAATATAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
17 9 0.35
18 17 0.65
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (18 bp):
ATAATATAAAATATTTAA
Found at i:542690 original size:33 final size:32
Alignment explanation
Indices: 542641--542728 Score: 87
Period size: 33 Copynumber: 2.8 Consensus size: 32
542631 ATTAAAATTT
*
542641 TAAAATTATTATAATATAAAATATTTAAATAA
1 TAAAATTATTATAATATAAAATATATAAATAA
*
542673 TAAAATCTATT-TAAATATATAATATATAAAT-A
1 TAAAAT-TATTAT-AATATAAAATATATAAATAA
*
542705 T--AATTATAAT-ATATAAAAATATAT
1 TAAAATTATTATAATAT-AAAATATAT
542729 TATCGATCTA
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
28 4 0.08
29 11 0.23
30 4 0.08
32 9 0.19
33 20 0.42
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (32 bp):
TAAAATTATTATAATATAAAATATATAAATAA
Found at i:542712 original size:19 final size:20
Alignment explanation
Indices: 542690--542731 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
542680 TATTTAAATA
*
542690 TATAATATATAAATATA-AT
1 TATAATATATAAAAATATAT
542709 TATAATATATAAAAATATAT
1 TATAATATATAAAAATATAT
542729 TAT
1 TAT
542732 CGATCTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TATAATATATAAAAATATAT
Found at i:543582 original size:26 final size:24
Alignment explanation
Indices: 543552--543617 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 24
543542 ACTTTTTAAA
*
543552 AAAAATATGATTTATTTTTATAATTTT
1 AAAAA-AT-ATTTATTATT-TAATTTT
*
543579 AAAAAATATTTTAATATTTAATTTT
1 AAAAAATA-TTTATTATTTAATTTT
543604 AAAAAATAATTTAT
1 AAAAAAT-ATTTAT
543618 GGTTTTCACA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
25 19 0.56
26 10 0.29
27 5 0.15
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (24 bp):
AAAAAATATTTATTATTTAATTTT
Found at i:543613 original size:13 final size:13
Alignment explanation
Indices: 543571--543615 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
543561 ATTTATTTTT
543571 ATAATTTTAAAAA
1 ATAATTTTAAAAA
* *
543584 AT-ATTTTAATAT
1 ATAATTTTAAAAA
*
543596 TTAATTTTAAAAA
1 ATAATTTTAAAAA
543609 ATAATTT
1 ATAATTT
543616 ATGGTTTTCA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
12 9 0.36
13 16 0.64
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
ATAATTTTAAAAA
Found at i:546283 original size:19 final size:18
Alignment explanation
Indices: 546256--546293 Score: 67
Period size: 19 Copynumber: 2.1 Consensus size: 18
546246 GTTATTTTTA
546256 TTTTTTAAAATATTTATT
1 TTTTTTAAAATATTTATT
546274 TTTTTGTAAAATATTTATT
1 TTTTT-TAAAATATTTATT
546293 T
1 T
546294 AAATATAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (18 bp):
TTTTTTAAAATATTTATT
Found at i:546601 original size:17 final size:17
Alignment explanation
Indices: 546551--546601 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
546541 AAAAATATAA
*
546551 ATATAAA-AATTTAAAT
1 ATATAAATAAATTAAAT
*
546567 TTATTAAATATTAATTAAAT
1 ATA-TAAATA--AATTAAAT
546587 ATATAAATAAATTAA
1 ATATAAATAAATTAA
546602 TTTAAATTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
16 2 0.07
17 10 0.36
18 1 0.04
19 6 0.21
20 9 0.32
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATATAAATAAATTAAAT
Found at i:546822 original size:17 final size:16
Alignment explanation
Indices: 546802--546838 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
546792 ATTTATATTC
*
546802 TATATTTATATATAACA
1 TATATTTAAATATAA-A
546819 TATATTTAAATATAAA
1 TATATTTAAATATAAA
546835 TATA
1 TATA
546839 AATTATAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (16 bp):
TATATTTAAATATAAA
Found at i:546882 original size:15 final size:15
Alignment explanation
Indices: 546864--546904 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
546854 AATATATAAA
* *
546864 ATATAAAATATATTT
1 ATATATAATATATTC
*
546879 ATATTTAATATATTC
1 ATATATAATATATTC
546894 ATATATAATAT
1 ATATATAATAT
546905 TTACCTAAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (15 bp):
ATATATAATATATTC
Found at i:547656 original size:19 final size:19
Alignment explanation
Indices: 547634--547677 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
547624 TTATTGATTC
547634 AATAAAATATATTTTTAAA-
1 AATAAAATAT-TTTTTAAAT
**
547653 AATAATTTATTTTTTAAAT
1 AATAAAATATTTTTTAAAT
547672 AATAAA
1 AATAAA
547678 TAAATTTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
AATAAAATATTTTTTAAAT
Found at i:548004 original size:20 final size:19
Alignment explanation
Indices: 547956--548004 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
547946 AAATAAATAT
547956 AAATTATATAAAAATTATAA
1 AAATT-TATAAAAATTATAA
* * *
547976 AAATATATAAAATTTTATAC
1 AAATTTATAAAA-ATTATAA
547996 AAATTTATA
1 AAATTTATA
548005 TAGACCTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (19 bp):
AAATTTATAAAAATTATAA
Found at i:548006 original size:12 final size:11
Alignment explanation
Indices: 547959--548006 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
547949 TAAATATAAA
*
547959 TTATATAAAAA
1 TTATATAAAAT
547970 TTATA-AAAA-
1 TTATATAAAAT
547979 -TATATAAAAT
1 TTATATAAAAT
547989 TT-TATACAAAT
1 TTATATA-AAAT
548000 TTATATA
1 TTATATA
548007 GACCTTTTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
8 4 0.12
9 4 0.12
10 8 0.25
11 12 0.38
12 4 0.12
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (11 bp):
TTATATAAAAT
Done.