Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167960.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_22, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 19587844
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 68000 characters in sequence are not A, C, G, or T
File 101 of 105
Found at i:18474295 original size:8 final size:8
Alignment explanation
Indices: 18474282--18474310 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
18474272 ATCCTGTGAT
18474282 TGGTTGAA
1 TGGTTGAA
18474290 TGGTTGAA
1 TGGTTGAA
18474298 TGGTTGAA
1 TGGTTGAA
18474306 TGGTT
1 TGGTT
18474311 TTAATTTATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.21, C:0.00, G:0.38, T:0.41
Consensus pattern (8 bp):
TGGTTGAA
Found at i:18477601 original size:3 final size:3
Alignment explanation
Indices: 18477587--18477620 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
18477577 AATTCAAACA
*
18477587 CTT CTT CGT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
18477621 ACCATCCTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.35, G:0.03, T:0.62
Consensus pattern (3 bp):
CTT
Found at i:18485516 original size:18 final size:18
Alignment explanation
Indices: 18485471--18485520 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
18485461 GAGAGACCGT
*
18485471 GGTCGTGATCGTGATCGA
1 GGTCGTGATCGTGATAGA
**
18485489 GCACGTGATCGTGATAGA
1 GGTCGTGATCGTGATAGA
*
18485507 GGTCGGGATCGTGA
1 GGTCGTGATCGTGA
18485521 GCGTGATAGA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (18 bp):
GGTCGTGATCGTGATAGA
Found at i:18496362 original size:11 final size:12
Alignment explanation
Indices: 18496346--18496374 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
18496336 ATATATATAT
18496346 ATTAAA-TTTGA
1 ATTAAATTTTGA
18496357 ATTAAATTTTGA
1 ATTAAATTTTGA
18496369 ATTAAA
1 ATTAAA
18496375 AAATAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 6 0.35
12 11 0.65
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (12 bp):
ATTAAATTTTGA
Found at i:18498145 original size:23 final size:23
Alignment explanation
Indices: 18498107--18498154 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
18498097 TTTATGAAAA
**
18498107 ATTATTATTAAAAAAATTAATTT
1 ATTATTATTAAAAAAAAAAATTT
**
18498130 ATTATTATTATTAAAAAAAATTT
1 ATTATTATTAAAAAAAAAAATTT
18498153 AT
1 AT
18498155 ATAATTCTCT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
ATTATTATTAAAAAAAAAAATTT
Found at i:18498426 original size:7 final size:7
Alignment explanation
Indices: 18498395--18498437 Score: 50
Period size: 7 Copynumber: 5.6 Consensus size: 7
18498385 AATAAAATTC
18498395 AAAATAA
1 AAAATAA
18498402 CAAAATAA
1 -AAAATAA
18498410 TAATATATAA
1 -AA-A-ATAA
18498420 AAAATAA
1 AAAATAA
18498427 AAAATAA
1 AAAATAA
18498434 AAAA
1 AAAA
18498438 AATTTTTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
7 15 0.47
8 10 0.31
9 3 0.09
10 4 0.12
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (7 bp):
AAAATAA
Found at i:18498437 original size:16 final size:17
Alignment explanation
Indices: 18498403--18498440 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
18498393 TCAAAATAAC
* *
18498403 AAAATAATAATATATAA
1 AAAATAATAAAATAAAA
18498420 AAAATAA-AAAATAAAA
1 AAAATAATAAAATAAAA
18498436 AAAAT
1 AAAAT
18498441 TTTTTTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (17 bp):
AAAATAATAAAATAAAA
Found at i:18502644 original size:2 final size:2
Alignment explanation
Indices: 18502637--18502672 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
18502627 TTTGAAATCA
18502637 AT AT AT AT AT AT A- 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
18502673 CACATTATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:18505774 original size:7 final size:7
Alignment explanation
Indices: 18505764--18505798 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
18505754 ACGAACCTTA
18505764 AACCTCG
1 AACCTCG
18505771 AACCTCG
1 AACCTCG
18505778 AACCTCG
1 AACCTCG
18505785 AACCTCG
1 AACCTCG
18505792 AACCTCG
1 AACCTCG
18505799 CTCTGATACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.29, C:0.43, G:0.14, T:0.14
Consensus pattern (7 bp):
AACCTCG
Found at i:18505774 original size:14 final size:14
Alignment explanation
Indices: 18505755--18505798 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
18505745 CTTGGACCCA
*
18505755 CGAACCTTAAACCT
1 CGAACCTCAAACCT
*
18505769 CGAACCTCGAACCT
1 CGAACCTCAAACCT
*
18505783 CGAACCTCGAACCT
1 CGAACCTCAAACCT
18505797 CG
1 CG
18505799 CTCTGATACC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.30, C:0.41, G:0.14, T:0.16
Consensus pattern (14 bp):
CGAACCTCAAACCT
Found at i:18505781 original size:21 final size:21
Alignment explanation
Indices: 18505755--18505798 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
18505745 CTTGGACCCA
*
18505755 CGAACCTTAAACCTCGAACCT
1 CGAACCTCAAACCTCGAACCT
*
18505776 CGAACCTCGAACCTCGAACCT
1 CGAACCTCAAACCTCGAACCT
18505797 CG
1 CG
18505799 CTCTGATACC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.41, G:0.14, T:0.16
Consensus pattern (21 bp):
CGAACCTCAAACCTCGAACCT
Found at i:18507736 original size:28 final size:28
Alignment explanation
Indices: 18507683--18507737 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
18507673 TCAAAATCTA
* **
18507683 ATTAACTAAATTATTTTATTTTATTTTT
1 ATTAACTAAATTAATTTATTGAATTTTT
18507711 ATTAACTAAATTAAATTTA-TGAATTTT
1 ATTAACTAAATT-AATTTATTGAATTTT
18507738 AAAAATTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 18 0.78
29 5 0.22
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (28 bp):
ATTAACTAAATTAATTTATTGAATTTTT
Found at i:18509423 original size:14 final size:14
Alignment explanation
Indices: 18509404--18509441 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
18509394 ATAAATATTA
18509404 TATTAAATTAAATT
1 TATTAAATTAAATT
18509418 TATTAAATT-AA-T
1 TATTAAATTAAATT
18509430 T-TTAAATTAAAT
1 TATTAAATTAAAT
18509442 CAATTATGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
11 7 0.32
12 4 0.18
13 2 0.09
14 9 0.41
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TATTAAATTAAATT
Found at i:18510668 original size:15 final size:15
Alignment explanation
Indices: 18510645--18510678 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
18510635 GGTTTGATTA
*
18510645 ATTTTAAATTAAATT
1 ATTTAAAATTAAATT
18510660 ATTTAAAATTAAATT
1 ATTTAAAATTAAATT
18510675 ATTT
1 ATTT
18510679 TATTTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATTTAAAATTAAATT
Found at i:18511685 original size:21 final size:22
Alignment explanation
Indices: 18511647--18511690 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
18511637 ACAATTTGAT
* *
18511647 AATTATGAATAGATAATTAATG
1 AATTATGAATAAAAAATTAATG
*
18511669 AATT-TGAATAAAAAATTTATG
1 AATTATGAATAAAAAATTAATG
18511690 A
1 A
18511691 TTCACATATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.36
Consensus pattern (22 bp):
AATTATGAATAAAAAATTAATG
Found at i:18511956 original size:18 final size:18
Alignment explanation
Indices: 18511933--18511973 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
18511923 TTTAAATAAA
* *
18511933 TAAATATTTTAACGGATT
1 TAAATATTTAAACGAATT
18511951 TAAATATTTAAACGAATT
1 TAAATATTTAAACGAATT
18511969 TAAAT
1 TAAAT
18511974 TTGGATAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.41
Consensus pattern (18 bp):
TAAATATTTAAACGAATT
Found at i:18512004 original size:47 final size:47
Alignment explanation
Indices: 18511953--18512049 Score: 140
Period size: 47 Copynumber: 2.1 Consensus size: 47
18511943 AACGGATTTA
* *
18511953 AATATTTAAACGAATTTAAATTTGGATAATGATATTAAATTTAAATG
1 AATATTTAAACGAATTTAAATTTGGAAAATAATATTAAATTTAAATG
* * * *
18512000 AATATTTAAATGGATTTGAATTTTGAAAATAATATTAAATTTAAATG
1 AATATTTAAACGAATTTAAATTTGGAAAATAATATTAAATTTAAATG
18512047 AAT
1 AAT
18512050 TCAGATATCA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.47, C:0.01, G:0.10, T:0.41
Consensus pattern (47 bp):
AATATTTAAACGAATTTAAATTTGGAAAATAATATTAAATTTAAATG
Found at i:18513514 original size:19 final size:21
Alignment explanation
Indices: 18513472--18513516 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
18513462 TATTGAGAAA
18513472 AAAATGGAAGAGAGGAAAAGG
1 AAAATGGAAGAGAGGAAAAGG
18513493 AAAAT-GAAG-GAGGGAAAA-G
1 AAAATGGAAGAGA-GGAAAAGG
18513512 AAAAT
1 AAAAT
18513517 AATTCAGAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 8 0.35
20 10 0.43
21 5 0.22
ACGTcount: A:0.60, C:0.00, G:0.33, T:0.07
Consensus pattern (21 bp):
AAAATGGAAGAGAGGAAAAGG
Found at i:18517062 original size:13 final size:12
Alignment explanation
Indices: 18517034--18517079 Score: 58
Period size: 13 Copynumber: 3.8 Consensus size: 12
18517024 CATCGATTCA
18517034 AAATTTAAT-TT
1 AAATTTAATATT
18517045 AAATTTAATATAT
1 AAATTTAATAT-T
18517058 AAATTTAATATCT
1 AAATTTAATAT-T
*
18517071 TAATTTAAT
1 AAATTTAAT
18517080 TTTTTAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
11 9 0.29
12 1 0.03
13 21 0.68
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (12 bp):
AAATTTAATATT
Found at i:18520268 original size:23 final size:24
Alignment explanation
Indices: 18520234--18520282 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
18520224 AAATTTTAAA
*
18520234 ATTTGATTTGAA-AATAAAATTTT
1 ATTTGATCTGAACAATAAAATTTT
*
18520257 ATTTGATCTGAATCAATTAAATTTT
1 ATTTGATCTGAA-CAATAAAATTTT
18520282 A
1 A
18520283 CAATTAAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 11 0.50
25 11 0.50
ACGTcount: A:0.41, C:0.04, G:0.08, T:0.47
Consensus pattern (24 bp):
ATTTGATCTGAACAATAAAATTTT
Found at i:18520348 original size:13 final size:13
Alignment explanation
Indices: 18520326--18520364 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
18520316 TTAATTTTTA
*
18520326 ATTTTTATATATT
1 ATTTTAATATATT
**
18520339 ATTTTAATATAAA
1 ATTTTAATATATT
18520352 ATTTTAATATATT
1 ATTTTAATATATT
18520365 TAAGTAGATT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
ATTTTAATATATT
Found at i:18520355 original size:33 final size:33
Alignment explanation
Indices: 18520318--18520398 Score: 80
Period size: 33 Copynumber: 2.5 Consensus size: 33
18520308 TCGATTTATT
*
18520318 AATTTTTAATTTTTATA-TATTATTTTAATATAA
1 AATTTTTAATTTTTATAGTA-GATTTTAATATAA
*
18520351 AA-TTTTAATATATTTA-AGTAGATTTTCATATAA
1 AATTTTTAAT-T-TTTATAGTAGATTTTAATATAA
*
18520384 AATTATT-ATTTTTAT
1 AATTTTTAATTTTTAT
18520399 TTTACAAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
31 4 0.10
32 8 0.20
33 19 0.47
34 9 0.22
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (33 bp):
AATTTTTAATTTTTATAGTAGATTTTAATATAA
Found at i:18530012 original size:18 final size:18
Alignment explanation
Indices: 18529982--18530016 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
18529972 CAAGTTATAA
18529982 AGCAAAAGCAACAGCAAG
1 AGCAAAAGCAACAGCAAG
18530000 AGCAACAAG-AACAGCAA
1 AGCAA-AAGCAACAGCAA
18530017 CTCCACCGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.57, C:0.23, G:0.20, T:0.00
Consensus pattern (18 bp):
AGCAAAAGCAACAGCAAG
Found at i:18534662 original size:21 final size:21
Alignment explanation
Indices: 18534616--18534671 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 21
18534606 TTAATTTATT
*
18534616 AATTTATTATATTATTTTAATAA
1 AATTT-TTATA-TATTTAAATAA
18534639 AATTTTTAATATATTTAAAT-A
1 AATTTTT-ATATATTTAAATAA
18534660 AATTTTTATATA
1 AATTTTTATATA
18534672 ATAATTATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
20 5 0.16
21 8 0.26
22 10 0.32
23 8 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
AATTTTTATATATTTAAATAA
Found at i:18534864 original size:28 final size:29
Alignment explanation
Indices: 18534801--18534864 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 29
18534791 TATGTATATT
* *
18534801 TAATATTTAATTTTAATATAAATCAAATA
1 TAATAATTAATTTAAATATAAATCAAATA
*
18534830 -AAAAATTAATTTAAAT-TAAATCAAATA
1 TAATAATTAATTTAAATATAAATCAAATA
18534857 TAATAATT
1 TAATAATT
18534865 TGGAATCAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 11 0.37
28 19 0.63
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (29 bp):
TAATAATTAATTTAAATATAAATCAAATA
Found at i:18535546 original size:26 final size:27
Alignment explanation
Indices: 18535503--18535570 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 27
18535493 GATACAATAA
* *
18535503 AATTTTCAAATTTGATTTAAAATT-TATT
1 AATTTT-AAATTTTATTT-AAATTCGATT
*
18535531 -ATTTTAAATTTTATTTGAATTCGATT
1 AATTTTAAATTTTATTTAAATTCGATT
18535557 AATTTTAAATTTTA
1 AATTTTAAATTTTA
18535571 AATTCGAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
25 4 0.11
26 13 0.37
27 18 0.51
ACGTcount: A:0.37, C:0.03, G:0.04, T:0.56
Consensus pattern (27 bp):
AATTTTAAATTTTATTTAAATTCGATT
Found at i:18535662 original size:13 final size:13
Alignment explanation
Indices: 18535644--18535703 Score: 61
Period size: 13 Copynumber: 4.6 Consensus size: 13
18535634 AATAAAAATA
18535644 ATTTAATTTTTAT
1 ATTTAATTTTTAT
18535657 ATTTAA-TTTTA-
1 ATTTAATTTTTAT
*
18535668 AGTTTAATTATTTAA
1 A-TTTAATT-TTTAT
*
18535683 ATTTAAATTTTAT
1 ATTTAATTTTTAT
*
18535696 ATATAATT
1 ATTTAATT
18535704 AAAATAATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
11 1 0.03
12 10 0.26
13 17 0.44
14 10 0.26
15 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (13 bp):
ATTTAATTTTTAT
Found at i:18535673 original size:12 final size:12
Alignment explanation
Indices: 18535644--18535703 Score: 50
Period size: 12 Copynumber: 4.7 Consensus size: 12
18535634 AATAAAAATA
18535644 ATTTAATTTTTAT
1 ATTTAA-TTTTAT
18535657 ATTTAATTTTA-
1 ATTTAATTTTAT
*
18535668 AGTTTAATTATTTAA
1 A-TTTAA-T-TTTAT
18535683 ATTTAAATTTTAT
1 ATTT-AATTTTAT
*
18535696 ATATAATT
1 ATTTAATT
18535704 AAAATAATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
11 1 0.03
12 14 0.35
13 14 0.35
14 8 0.20
15 3 0.08
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (12 bp):
ATTTAATTTTAT
Found at i:18535691 original size:15 final size:14
Alignment explanation
Indices: 18535643--18535688 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 14
18535633 AAATAAAAAT
18535643 AATTTAATT-TTTA
1 AATTTAATTATTTA
*
18535656 TATTTAA-T-TTTA
1 AATTTAATTATTTA
*
18535668 AGTTTAATTATTTA
1 AATTTAATTATTTA
18535682 AATTTAA
1 AATTTAA
18535689 ATTTTATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
12 10 0.37
13 7 0.26
14 10 0.37
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (14 bp):
AATTTAATTATTTA
Found at i:18535702 original size:27 final size:26
Alignment explanation
Indices: 18535647--18535704 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 26
18535637 AAAAATAATT
* *
18535647 TAATT-TTTATATTTAATTTTAAGTT
1 TAATTATTTAAATTTAATTTTAAGTA
18535672 TAATTATTTAAATTTAAATTTTATA-TA
1 TAATTATTTAAATTT-AATTTTA-AGTA
18535699 TAATTA
1 TAATTA
18535705 AAATAATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 5 0.18
26 8 0.29
27 14 0.50
28 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (26 bp):
TAATTATTTAAATTTAATTTTAAGTA
Found at i:18537237 original size:25 final size:27
Alignment explanation
Indices: 18537199--18537248 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
18537189 TATATTTTTA
*
18537199 ATATTTTTAATATAAA-ATTAAAAAAT
1 ATATTTTTAATATAAATAATAAAAAAT
18537225 ATATTTTT-ATATAAATAATAAAAA
1 ATATTTTTAATATAAATAATAAAAA
18537249 TTATCCAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (27 bp):
ATATTTTTAATATAAATAATAAAAAAT
Found at i:18539029 original size:12 final size:12
Alignment explanation
Indices: 18539012--18539054 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
18539002 GGATGCATGA
18539012 CCAACATCATCG
1 CCAACATCATCG
*
18539024 CCAACATCATCA
1 CCAACATCATCG
* * *
18539036 TCATCATCGTCG
1 CCAACATCATCG
18539048 CCAACAT
1 CCAACAT
18539055 GGAATAATAA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.33, C:0.40, G:0.07, T:0.21
Consensus pattern (12 bp):
CCAACATCATCG
Found at i:18541361 original size:20 final size:20
Alignment explanation
Indices: 18541336--18541375 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
18541326 GTTCAAGTAA
18541336 TTTGATTCATCAATTAAGTT
1 TTTGATTCATCAATTAAGTT
18541356 TTTGATTCATCAATTAAGTT
1 TTTGATTCATCAATTAAGTT
18541376 GAGTGTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (20 bp):
TTTGATTCATCAATTAAGTT
Found at i:18541561 original size:23 final size:24
Alignment explanation
Indices: 18541501--18541569 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 24
18541491 TTTAAGTATG
*
18541501 AATAATTAAATTTTTGTTGAATAT
1 AATAATTAAATTTATGTTGAATAT
* *
18541525 AATAATTGAGTTTAT-TT-ATATAT
1 AATAATTAAATTTATGTTGA-ATAT
* *
18541548 ATTAATTAAATTTA-ATTGAATA
1 AATAATTAAATTTATGTTGAATA
18541570 AGTTTAAGTA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
22 1 0.03
23 22 0.61
24 13 0.36
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.49
Consensus pattern (24 bp):
AATAATTAAATTTATGTTGAATAT
Found at i:18541717 original size:15 final size:14
Alignment explanation
Indices: 18541699--18541728 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
18541689 TTTAAATTCG
18541699 ATTAATTATATTTTT
1 ATTAATTAT-TTTTT
18541714 ATTAATTATTTTTT
1 ATTAATTATTTTTT
18541728 A
1 A
18541729 GTGGCATGCG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
ATTAATTATTTTTT
Found at i:18541938 original size:16 final size:16
Alignment explanation
Indices: 18541917--18541947 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18541907 ATATGTTTAC
18541917 TTTATTTTCAAAATAT
1 TTTATTTTCAAAATAT
*
18541933 TTTATTTTTAAAATA
1 TTTATTTTCAAAATA
18541948 CGATTTTTTT
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:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTATTTTCAAAATAT
Found at i:18543133 original size:13 final size:13
Alignment explanation
Indices: 18543117--18543150 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
18543107 AGATGATACA
*
18543117 ATAAAAATATAAT
1 ATAAAAATAAAAT
18543130 ATAAAAATAAAAT
1 ATAAAAATAAAAT
*
18543143 TTAAAAAT
1 ATAAAAAT
18543151 GATATAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
ATAAAAATAAAAT
Found at i:18543264 original size:30 final size:31
Alignment explanation
Indices: 18543212--18543278 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 31
18543202 TATATTTTAT
**
18543212 ATTTTATATAATTTAAATTAT-AATACATAA
1 ATTTTATATAAAATAAATTATAAATACATAA
* *
18543242 TTTTTATATAAAATATAA-TATAAATATATAA
1 ATTTTATATAAAATA-AATTATAAATACATAA
18543273 ATTTTA
1 ATTTTA
18543279 ATATTTTATA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
30 15 0.50
31 15 0.50
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (31 bp):
ATTTTATATAAAATAAATTATAAATACATAA
Found at i:18543295 original size:37 final size:36
Alignment explanation
Indices: 18543196--18543296 Score: 91
Period size: 37 Copynumber: 2.7 Consensus size: 36
18543186 AGTGTAATAA
*
18543196 AAATTTT-ATATTTTATATTTTATATAATTTAAATTAT
1 AAATTTTAATATTTTATA--TTATATAATATAAATTAT
** *
18543233 -AATACATAAT-TTTTATATAAAATATAATATAAATATAT
1 AAAT-TTTAATATTTTATAT--TATATAATATAAAT-TAT
18543271 AAATTTTAATATTTTATATTATATAA
1 AAATTTTAATATTTTATATTATATAA
18543297 ATTTACAAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
35 1 0.02
36 3 0.06
37 26 0.52
38 9 0.18
39 11 0.22
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (36 bp):
AAATTTTAATATTTTATATTATATAATATAAATTAT
Found at i:18544307 original size:20 final size:19
Alignment explanation
Indices: 18544279--18544339 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 19
18544269 TGTAAAATAT
*
18544279 TTAAATTTATATATTTATA
1 TTAATTTTATATATTTATA
18544298 TTATATTTTATATAATCTTA-A
1 TTA-ATTTTATAT-AT-TTATA
*
18544319 TTAATTTTATTAAATTTATA
1 TTAATTTTA-TATATTTATA
18544339 T
1 T
18544340 ATTATTATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
19 6 0.17
20 18 0.51
21 8 0.23
22 3 0.09
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (19 bp):
TTAATTTTATATATTTATA
Found at i:18544362 original size:19 final size:20
Alignment explanation
Indices: 18544321--18544367 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
18544311 AATCTTAATT
18544321 AATT-TTATT-AAATTTATA
1 AATTATTATTAAAATTTATA
*
18544339 TATTATTATTAAAATTT-TA
1 AATTATTATTAAAATTTATA
18544358 AATTA-TATTA
1 AATTATTATTA
18544368 TTTTTATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 8 0.32
19 11 0.44
20 6 0.24
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
AATTATTATTAAAATTTATA
Found at i:18545042 original size:20 final size:20
Alignment explanation
Indices: 18544993--18545042 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
18544983 TTCTGTTGAT
18544993 TTGTTT-TTATTTTTAATTTA
1 TTGTTTATT-TTTTTAATTTA
* *
18545013 TTATTAATTTTTTT-ATCTTA
1 TTGTTTATTTTTTTAAT-TTA
18545033 TTGTTTATTT
1 TTGTTTATTT
18545043 GATTGAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
19 2 0.08
20 20 0.83
21 2 0.08
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.74
Consensus pattern (20 bp):
TTGTTTATTTTTTTAATTTA
Found at i:18555474 original size:21 final size:22
Alignment explanation
Indices: 18555450--18555501 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
18555440 TTTTAATATT
18555450 TTTTTATAT-TATTT-AATAAA
1 TTTTTATATATATTTAAATAAA
18555470 GTTTTTA-ATATATTTAAATAAA
1 -TTTTTATATATATTTAAATAAA
*
18555492 TTTATATATA
1 TTTTTATATA
18555502 AAATAATTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 2 0.07
21 16 0.59
22 9 0.33
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
TTTTTATATATATTTAAATAAA
Found at i:18555480 original size:22 final size:22
Alignment explanation
Indices: 18555449--18555491 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
18555439 ATTTTAATAT
*
18555449 TTTTTTATATTATTT-AATAAAG
1 TTTTTAATA-TATTTAAATAAAG
18555471 TTTTTAATATATTTAAATAAA
1 TTTTTAATATATTTAAATAAA
18555492 TTTATATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
TTTTTAATATATTTAAATAAAG
Found at i:18557236 original size:16 final size:17
Alignment explanation
Indices: 18557212--18557247 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
18557202 GGAATCAATG
*
18557212 ATCACTTATTTTGTGTC
1 ATCACTTATTTTGTGCC
18557229 ATCA-TTATTTTGTGCC
1 ATCACTTATTTTGTGCC
18557245 ATC
1 ATC
18557248 CATCTTAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.19, C:0.19, G:0.11, T:0.50
Consensus pattern (17 bp):
ATCACTTATTTTGTGCC
Found at i:18560099 original size:26 final size:27
Alignment explanation
Indices: 18560069--18560119 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
18560059 ATGTTTATAA
*
18560069 TTATAAAATACTAATAATA-AAATTAG
1 TTATAAAATAATAATAATATAAATTAG
**
18560095 TTATAATCTAATAATAATATAAATT
1 TTATAAAATAATAATAATATAAATT
18560120 GTAATTATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 16 0.76
27 5 0.24
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (27 bp):
TTATAAAATAATAATAATATAAATTAG
Found at i:18560124 original size:23 final size:23
Alignment explanation
Indices: 18560079--18560124 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
18560069 TTATAAAATA
* *
18560079 CTAATAATAAAATTAGTTATAAT
1 CTAATAATAAAATAAATTATAAT
* *
18560102 CTAATAATAATATAAATTGTAAT
1 CTAATAATAAAATAAATTATAAT
18560125 TATTAATCTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.39
Consensus pattern (23 bp):
CTAATAATAAAATAAATTATAAT
Found at i:18560127 original size:29 final size:26
Alignment explanation
Indices: 18560066--18560134 Score: 66
Period size: 26 Copynumber: 2.5 Consensus size: 26
18560056 TGAATGTTTA
** *
18560066 TAATTATAAAATACTAATAATAAAAT
1 TAATTATAATCTAATAATAATAAAAT
*
18560092 TAGTTATAATCTAATAATAATATAAATT
1 TAATTATAATCTAATAATAATA-AAA-T
18560120 GTAATTATTAATCTA
1 -TAATTA-TAATCTA
18560135 GAAAAATGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
26 18 0.53
27 3 0.09
28 1 0.03
29 5 0.15
30 7 0.21
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.41
Consensus pattern (26 bp):
TAATTATAATCTAATAATAATAAAAT
Found at i:18560252 original size:52 final size:52
Alignment explanation
Indices: 18560184--18560341 Score: 262
Period size: 52 Copynumber: 3.0 Consensus size: 52
18560174 TTTAAAATAC
* *
18560184 AATTATTAATTGTAATAATAACTGATAAATTATAAATATATTTATGTATTTATT
1 AATTA-TAATT-TAATAATAATTGATAAATTGTAAATATATTTATGTATTTATT
*
18560238 AATTATAATTTAATAATAATTGACAAATTGTAAATATATTTATGTATTTATT
1 AATTATAATTTAATAATAATTGATAAATTGTAAATATATTTATGTATTTATT
*
18560290 AATTATAATTTAATAATAATTGATAAATTGTAAACATATTTATGTATTTATT
1 AATTATAATTTAATAATAATTGATAAATTGTAAATATATTTATGTATTTATT
18560342 TTTAATTATT
Statistics
Matches: 99, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
52 89 0.90
53 5 0.05
54 5 0.05
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (52 bp):
AATTATAATTTAATAATAATTGATAAATTGTAAATATATTTATGTATTTATT
Found at i:18560410 original size:12 final size:13
Alignment explanation
Indices: 18560395--18560429 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
18560385 ATTGTATCAG
18560395 TAATTATTAAA-T
1 TAATTATTAAATT
18560407 TAATTATTAAATT
1 TAATTATTAAATT
*
18560420 TAATAATTAA
1 TAATTATTAA
18560430 TAATTGTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
TAATTATTAAATT
Found at i:18560429 original size:7 final size:7
Alignment explanation
Indices: 18560404--18560474 Score: 53
Period size: 7 Copynumber: 10.7 Consensus size: 7
18560394 GTAATTATTA
18560404 AATTAAT
1 AATTAAT
*
18560411 TATTAA-
1 AATTAAT
*
18560417 ATTTAAT
1 AATTAAT
18560424 AATTAAT
1 AATTAAT
**
18560431 AATTGTT
1 AATTAAT
18560438 AA-T-AT
1 AATTAAT
*
18560443 AATTCTAT
1 AATT-AAT
18560451 AATTAAT
1 AATTAAT
18560458 AATTAAT
1 AATTAAT
18560465 -ATTAA-
1 AATTAAT
18560470 AATTA
1 AATTA
18560475 CTATAAAAAT
Statistics
Matches: 51, Mismatches: 8, Indels: 11
0.73 0.11 0.16
Matches are distributed among these distances:
5 3 0.06
6 15 0.29
7 27 0.53
8 6 0.12
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (7 bp):
AATTAAT
Found at i:18560473 original size:27 final size:27
Alignment explanation
Indices: 18560395--18560480 Score: 77
Period size: 27 Copynumber: 3.1 Consensus size: 27
18560385 ATTGTATCAG
*
18560395 TAATTATTAAATTAATTATT-AAATT-TAA
1 TAATTAAT-AATTAA-TATTAAAATTCT-A
** * *
18560423 TAATTAATAATTGTTAATATAATTCTA
1 TAATTAATAATTAATATTAAAATTCTA
18560450 TAATTAATAATTAATATTAAAATTACTA
1 TAATTAATAATTAATATTAAAATT-CTA
18560478 TAA
1 TAA
18560481 AAATTATTAT
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
26 3 0.07
27 29 0.63
28 14 0.30
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (27 bp):
TAATTAATAATTAATATTAAAATTCTA
Found at i:18564647 original size:12 final size:12
Alignment explanation
Indices: 18564616--18564650 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
18564606 ATTTATTATT
* *
18564616 AATTAAAATTGA
1 AATTAAATTTTA
18564628 AATTAAATTTTA
1 AATTAAATTTTA
18564640 AATTAAATTTT
1 AATTAAATTTT
18564651 TATTTATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (12 bp):
AATTAAATTTTA
Found at i:18564693 original size:34 final size:32
Alignment explanation
Indices: 18564655--18564726 Score: 83
Period size: 34 Copynumber: 2.2 Consensus size: 32
18564645 AATTTTTATT
*
18564655 TATTTTATATT-TTAATAAAATTTAAATAAATAGA
1 TATTTTA-ATTATTAA-AAAATTTAAACAAATA-A
*
18564689 TATTTTAATTGATTAAAATATTTAAACAAATAA
1 TATTTTAATT-ATTAAAAAATTTAAACAAATAA
18564722 TATTT
1 TATTT
18564727 ATTTAAATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
33 9 0.26
34 21 0.62
35 4 0.12
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (32 bp):
TATTTTAATTATTAAAAAATTTAAACAAATAA
Found at i:18564818 original size:26 final size:27
Alignment explanation
Indices: 18564768--18564819 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
18564758 TTAAACTTAA
* **
18564768 ATAAATATTTAAATTAATTTTAATATT
1 ATAAATATTTAAATAAATTCAAATATT
18564795 ATAAATA-TTAAATAAATTCAAATAT
1 ATAAATATTTAAATAAATTCAAATAT
18564820 AAATATCTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (27 bp):
ATAAATATTTAAATAAATTCAAATATT
Found at i:18565249 original size:16 final size:16
Alignment explanation
Indices: 18565230--18565267 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
18565220 AAAATTTGAT
*
18565230 TTAATTTAATTTAAAA
1 TTAATTAAATTTAAAA
18565246 TTAATTAAATTTAAAA
1 TTAATTAAATTTAAAA
18565262 -TAATTA
1 TTAATTA
18565268 TCAAATATCG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 6 0.29
16 15 0.71
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAATTAAATTTAAAA
Found at i:18567701 original size:14 final size:15
Alignment explanation
Indices: 18567682--18567711 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
18567672 TATATTTACC
18567682 AATTTTA-TAAATAA
1 AATTTTATTAAATAA
18567696 AATTTTATTAAATAA
1 AATTTTATTAAATAA
18567711 A
1 A
18567712 TATATATACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AATTTTATTAAATAA
Found at i:18569761 original size:22 final size:24
Alignment explanation
Indices: 18569720--18569770 Score: 70
Period size: 22 Copynumber: 2.2 Consensus size: 24
18569710 CTTTTATGAA
* *
18569720 ATTAAAAAATTATTTTATTAGTTT
1 ATTAAAAAATTATTTAATTAATTT
18569744 ATTAAAAAA-T-TTTAATTAATTT
1 ATTAAAAAATTATTTAATTAATTT
18569766 ATTAA
1 ATTAA
18569771 CAATTCATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 15 0.60
23 1 0.04
24 9 0.36
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (24 bp):
ATTAAAAAATTATTTAATTAATTT
Found at i:18572200 original size:20 final size:20
Alignment explanation
Indices: 18572171--18572218 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
18572161 TATTTAAACT
* *
18572171 TTATTTATATGTATTAAATTA
1 TTATTAATAT-TATTAAAATA
*
18572192 TT-TTAATATTTTTAAAATA
1 TTATTAATATTATTAAAATA
18572211 TTATTAAT
1 TTATTAAT
18572219 GTGACATTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 10 0.43
20 11 0.48
21 2 0.09
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (20 bp):
TTATTAATATTATTAAAATA
Found at i:18574677 original size:4 final size:4
Alignment explanation
Indices: 18574668--18574715 Score: 50
Period size: 4 Copynumber: 12.5 Consensus size: 4
18574658 TCAAAATTCG
18574668 TTGT TTGT TTGT TTGT TTGT TT-T TT-T TT-T TTGCT TT-T TTAGT TTGT
1 TTGT TTGT TTGT TTGT TTGT TTGT TTGT TTGT TTG-T TTGT TT-GT TTGT
18574714 TT
1 TT
18574716 CCTTTGTCTC
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
3 12 0.30
4 22 0.55
5 6 0.15
ACGTcount: A:0.02, C:0.02, G:0.17, T:0.79
Consensus pattern (4 bp):
TTGT
Found at i:18575181 original size:3 final size:3
Alignment explanation
Indices: 18575173--18575200 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
18575163 GAGAGAAGTA
18575173 GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT G
18575201 GGTTCATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:18575989 original size:10 final size:11
Alignment explanation
Indices: 18575965--18576007 Score: 54
Period size: 10 Copynumber: 4.0 Consensus size: 11
18575955 TATATATTAT
*
18575965 TTTAATATGAA
1 TTTAATATAAA
18575976 TTTAATAT-AA
1 TTTAATATAAA
18575986 TTTAA-ATAAA
1 TTTAATATAAA
18575996 TTTATATATAAA
1 TTTA-ATATAAA
18576008 ATAATTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
9 2 0.07
10 13 0.45
11 9 0.31
12 5 0.17
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (11 bp):
TTTAATATAAA
Found at i:18587104 original size:31 final size:31
Alignment explanation
Indices: 18587037--18587108 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
18587027 CATCTTATAA
* *
18587037 AATATTAAAATTATATATTCATAAAATATTT
1 AATATAAAAATTATATATTCACAAAATATTT
* **
18587068 TATATAAAAATTATATA-TCACAATTTATATT
1 AATATAAAAATTATATATTCACAAAATAT-TT
18587099 AATATAAAAA
1 AATATAAAAA
18587109 ATTAAATTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
30 8 0.24
31 26 0.76
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (31 bp):
AATATAAAAATTATATATTCACAAAATATTT
Found at i:18588764 original size:18 final size:18
Alignment explanation
Indices: 18588743--18588834 Score: 70
Period size: 18 Copynumber: 5.2 Consensus size: 18
18588733 TTTTACATAG
18588743 AAATATTATTATATTAAT
1 AAATATTATTATATTAAT
*
18588761 AAATAATATTATATT-AT
1 AAATATTATTATATTAAT
*
18588778 -AATA-TATTA-ATAAAT
1 AAATATTATTATATTAAT
* *
18588793 AGGATATTATTA-A-TAAA
1 A-AATATTATTATATTAAT
18588810 AATATATTATAATATATTAAT
1 AA-ATATTAT--TATATTAAT
18588831 AAAT
1 AAAT
18588835 GGTAGTAATA
Statistics
Matches: 58, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
14 2 0.03
15 7 0.12
16 4 0.07
17 15 0.26
18 20 0.34
19 2 0.03
20 3 0.05
21 5 0.09
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (18 bp):
AAATATTATTATATTAAT
Found at i:18588771 original size:13 final size:13
Alignment explanation
Indices: 18588753--18588985 Score: 106
Period size: 13 Copynumber: 18.3 Consensus size: 13
18588743 AAATATTATT
18588753 ATATTAATAAATA
1 ATATTAATAAATA
18588766 ATATTATATTATAAT-
1 ATATTA-A-TA-AATA
18588781 ATATTAATAAATAGGA
1 ATATTAATAAAT---A
18588797 TATTATTAATAAA-A
1 -A-TATTAATAAATA
*
18588811 ATA-TATTATAAT-
1 ATATTAATA-AATA
*
18588823 ATATTAATAAATG
1 ATATTAATAAATA
* *
18588836 GTAGTAATATAAT-
1 ATATTAATA-AATA
*
18588849 ATTTTAATAAATA
1 ATATTAATAAATA
*
18588862 ATATTAAGAAATA
1 ATATTAATAAATA
*
18588875 ACATT-AT-AAT-
1 ATATTAATAAATA
18588885 ATATTAATAAATA
1 ATATTAATAAATA
*
18588898 GTATATT-ATTAATA
1 --ATATTAATAAATA
18588912 A-A-TAAT--ATA
1 ATATTAATAAATA
* *
18588921 CTATTAATATGAT-
1 ATATTAATA-AATA
*
18588934 ATATT-AGAAATA
1 ATATTAATAAATA
*
18588946 TTATTAATAAATA
1 ATATTAATAAATA
*
18588959 TTATT-AT-AAT-
1 ATATTAATAAATA
18588969 ATATTAATAAATA
1 ATATTAATAAATA
18588982 ATAT
1 ATAT
18588986 AAAGAATAAT
Statistics
Matches: 169, Mismatches: 20, Indels: 62
0.67 0.08 0.25
Matches are distributed among these distances:
9 3 0.02
10 10 0.06
11 23 0.14
12 32 0.19
13 60 0.36
14 14 0.08
15 13 0.08
16 3 0.02
17 1 0.01
18 10 0.06
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.42
Consensus pattern (13 bp):
ATATTAATAAATA
Found at i:18588862 original size:15 final size:15
Alignment explanation
Indices: 18588756--18588866 Score: 57
Period size: 18 Copynumber: 7.0 Consensus size: 15
18588746 TATTATTATA
18588756 TTAATAAATAATATT
1 TTAATAAATAATATT
* * *
18588771 AT-AT-TATAATATA
1 TTAATAAATAATATT
18588784 TTAATAAATAGGATATT
1 TTAATAAATA--ATATT
18588801 ATTAATAAA-AATATAT
1 -TTAATAAATAATAT-T
* *
18588817 TATAATATATTAATAAATG
1 T-TAATA-AATAAT--ATT
* *
18588836 GTAGTAATATAATATT
1 TTAATAA-ATAATATT
18588852 TTAATAAATAATATT
1 TTAATAAATAATATT
18588867 AAGAAATAAC
Statistics
Matches: 70, Mismatches: 14, Indels: 24
0.65 0.13 0.22
Matches are distributed among these distances:
13 8 0.11
14 4 0.06
15 17 0.24
16 13 0.19
17 7 0.10
18 19 0.27
20 2 0.03
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (15 bp):
TTAATAAATAATATT
Found at i:18588909 original size:18 final size:18
Alignment explanation
Indices: 18588886--18588929 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
18588876 CATTATAATA
* *
18588886 TATTAATAAATAGTATAT
1 TATTAATAAATAATATAC
18588904 TATTAATAAATAATATAC
1 TATTAATAAATAATATAC
18588922 TATTAATA
1 TATTAATA
18588930 TGATATATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (18 bp):
TATTAATAAATAATATAC
Found at i:18589044 original size:19 final size:18
Alignment explanation
Indices: 18589017--18589060 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
18589007 TTTTAAGTAT
*
18589017 TTTTTATATTAACATAATA
1 TTTTAATATTAA-ATAATA
*
18589036 TTTTAATATTAAATATTA
1 TTTTAATATTAAATAATA
18589054 TTATTAA
1 TT-TTAA
18589061 AATATAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (18 bp):
TTTTAATATTAAATAATA
Found at i:18589102 original size:16 final size:16
Alignment explanation
Indices: 18589064--18589111 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
18589054 TTATTAAAAT
*
18589064 ATAATTACTTTTGAAT-
1 ATAAATACTTTT-AATA
*
18589080 ATTAATACTTTTAATA
1 ATAAATACTTTTAATA
*
18589096 ATAAATAATTTTAATA
1 ATAAATACTTTTAATA
18589112 TATTTTAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 3 0.11
16 24 0.89
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (16 bp):
ATAAATACTTTTAATA
Found at i:18589110 original size:25 final size:25
Alignment explanation
Indices: 18589081--18589142 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 25
18589071 CTTTTGAATA
18589081 TTAATACTTTTAATAATAAATA-ATT
1 TTAATA-TTTTAATAATAAATATATT
*
18589106 TTAATATATTTTAATAATAAATATTTT
1 TT-A-ATATTTTAATAATAAATATATT
18589133 TTAATATTTT
1 TTAATATTTT
18589143 GACAGTTAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
25 9 0.27
26 17 0.52
27 7 0.21
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (25 bp):
TTAATATTTTAATAATAAATATATT
Found at i:18589117 original size:26 final size:27
Alignment explanation
Indices: 18589088--18589139 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 27
18589078 ATATTAATAC
18589088 TTTTAATAATAAATA-ATTTTAATATA
1 TTTTAATAATAAATATATTTTAATATA
*
18589114 TTTTAATAATAAATATTTTTTAATAT
1 TTTTAATAATAAATATATTTTAATAT
18589140 TTTGACAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 15 0.62
27 9 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
TTTTAATAATAAATATATTTTAATATA
Found at i:18589284 original size:14 final size:14
Alignment explanation
Indices: 18589265--18589312 Score: 87
Period size: 14 Copynumber: 3.4 Consensus size: 14
18589255 AAATGTAAAC
*
18589265 ATTTTTTAAAAATT
1 ATTTTTCAAAAATT
18589279 ATTTTTCAAAAATT
1 ATTTTTCAAAAATT
18589293 ATTTTTCAAAAATT
1 ATTTTTCAAAAATT
18589307 ATTTTT
1 ATTTTT
18589313 TGCGAAACAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (14 bp):
ATTTTTCAAAAATT
Found at i:18599544 original size:21 final size:21
Alignment explanation
Indices: 18599520--18599594 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 21
18599510 AAAAATGCAA
18599520 TATTTACATTAATAAATTAGT
1 TATTTACATTAATAAATTAGT
**
18599541 TATTTTA-ATTTAACAATAAAAAATGT
1 TA-TTTACA-TT---AATAAATTA-GT
18599567 AATATTTACATTAATAAATTAGT
1 --TATTTACATTAATAAATTAGT
18599590 TATTT
1 TATTT
18599595 TAATTTAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 18
0.65 0.06 0.29
Matches are distributed among these distances:
21 8 0.20
22 6 0.15
23 2 0.05
24 7 0.17
25 7 0.17
26 2 0.05
27 6 0.15
28 3 0.07
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (21 bp):
TATTTACATTAATAAATTAGT
Found at i:18599544 original size:49 final size:49
Alignment explanation
Indices: 18599487--18599606 Score: 222
Period size: 49 Copynumber: 2.4 Consensus size: 49
18599477 TTTATAACAC
18599487 TTAGTTATTTTAATTTAATAATAAAAAATGCAATATTTACATTAATAAA
1 TTAGTTATTTTAATTTAATAATAAAAAATGCAATATTTACATTAATAAA
* *
18599536 TTAGTTATTTTAATTTAACAATAAAAAATGTAATATTTACATTAATAAA
1 TTAGTTATTTTAATTTAATAATAAAAAATGCAATATTTACATTAATAAA
18599585 TTAGTTATTTTAATTTAATAAT
1 TTAGTTATTTTAATTTAATAAT
18599607 TAATAAATTT
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 68 1.00
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.46
Consensus pattern (49 bp):
TTAGTTATTTTAATTTAATAATAAAAAATGCAATATTTACATTAATAAA
Found at i:18599553 original size:22 final size:22
Alignment explanation
Indices: 18599528--18599605 Score: 68
Period size: 22 Copynumber: 3.3 Consensus size: 22
18599518 AATATTTACA
18599528 TTAATAAATTAGTTATTTTAAT
1 TTAATAAATTAGTTATTTTAAT
** *
18599550 TTAACAATAAAAAATGTAATATTTACA-
1 TT---AATAAATTA-GTTAT-TTTA-AT
18599577 TTAATAAATTAGTTATTTTAAT
1 TTAATAAATTAGTTATTTTAAT
18599599 TTAATAA
1 TTAATAA
18599606 TTAATAAATT
Statistics
Matches: 43, Mismatches: 6, Indels: 14
0.68 0.10 0.22
Matches are distributed among these distances:
21 1 0.02
22 13 0.30
23 4 0.09
24 7 0.16
25 7 0.16
26 4 0.09
27 6 0.14
28 1 0.02
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.46
Consensus pattern (22 bp):
TTAATAAATTAGTTATTTTAAT
Found at i:18599823 original size:27 final size:27
Alignment explanation
Indices: 18599773--18599825 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
18599763 GTATAAGTAA
* * *
18599773 ATTTTGATAATTTTTTATATAATTTTG
1 ATTTTGATAATTTGTAATAAAATTTTG
18599800 ATTTTGATAATTTGTAATAAAATTTT
1 ATTTTGATAATTTGTAATAAAATTTT
18599826 AACAACTTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (27 bp):
ATTTTGATAATTTGTAATAAAATTTTG
Found at i:18600189 original size:22 final size:22
Alignment explanation
Indices: 18600164--18600427 Score: 147
Period size: 22 Copynumber: 12.0 Consensus size: 22
18600154 GTTATTGATA
*
18600164 ATTAAGTTATTATTGATTTACT
1 ATTAAGTTATTAATGATTTACT
* * *
18600186 ATTATGTTATCAGTGATTTACT
1 ATTAAGTTATTAATGATTTACT
** * * *
18600208 ATTAAACTATCAATGATATATT
1 ATTAAGTTATTAATGATTTACT
* *
18600230 ACTAAATTATTAATGATTTACT
1 ATTAAGTTATTAATGATTTACT
* ** *
18600252 ATTAAATTAACATTGATTTACT
1 ATTAAGTTATTAATGATTTACT
* * *
18600274 GTTAATTTATTAATTATTTACT
1 ATTAAGTTATTAATGATTTACT
* * * *
18600296 ACTAAGTTATAAATAATTTATT
1 ATTAAGTTATTAATGATTTACT
* * * *
18600318 ACTAAATTGTTGATGATTTACT
1 ATTAAGTTATTAATGATTTACT
* * *
18600340 ACTAAGTTATTGATAATTT-CTT
1 ATTAAGTTATTAATGATTTAC-T
** *
18600362 ACAAAGTT-GTAATTGA-TTACT
1 ATTAAGTTATTAA-TGATTTACT
* * *
18600383 ATTAATTTATCAATGTTTTACT
1 ATTAAGTTATTAATGATTTACT
* * *
18600405 ATAAAGTTATTAATAATTAACT
1 ATTAAGTTATTAATGATTTACT
18600427 A
1 A
18600428 ATTTATTACT
Statistics
Matches: 182, Mismatches: 55, Indels: 10
0.74 0.22 0.04
Matches are distributed among these distances:
21 13 0.07
22 169 0.93
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.47
Consensus pattern (22 bp):
ATTAAGTTATTAATGATTTACT
Found at i:18600247 original size:44 final size:44
Alignment explanation
Indices: 18600199--18600596 Score: 164
Period size: 44 Copynumber: 8.9 Consensus size: 44
18600189 ATGTTATCAG
* *
18600199 TGATTTACTATTAAACTATCAATGATATATTACTAAATTATTAA
1 TGATTTACTATTAAATTATCAATGATTTATTACTAAATTATTAA
* * * ** *
18600243 TGATTTACTATTAAATTAACATTGATTTACTGTTAATTTATTAA
1 TGATTTACTATTAAATTATCAATGATTTATTACTAAATTATTAA
* * * * * * *
18600287 TTATTTACTACTAAGTTATAAATAATTTATTACTAAATTGTTGA
1 TGATTTACTATTAAATTATCAATGATTTATTACTAAATTATTAA
* * ** * * *
18600331 TGATTTACTACTAAGTTATTGATAATTTCTTAC-AAAGTT-GTAA
1 TGATTTACTATTAAATTATCAATGATTTATTACTAAA-TTATTAA
* * *
18600374 TTGA-TTACTATTAATTTATCAATGTTTTACTA-TAAAGTTATTAA
1 -TGATTTACTATTAAATTATCAATGATTTATTACTAAA-TTATTAA
* * * ** * *
18600418 TAATTAACTAATTTATTACTAAATTATCATTGATTTACAATTAAATTATTAG
1 TGATT---T-A-CTA-T--TAAATTATCAATGATTTATTACTAAATTATTAA
* * * * * * **
18600470 TAATTTACTACTAAGTTATCAATAATTTGTTATTATGTTATT-A
1 TGATTTACTATTAAATTATCAATGATTTATTACTAAATTATTAA
* ** * *
18600513 TACATTTACTATTATGTTATCATTGATTTACTACT-AATT-TTCAA
1 T-GATTTACTATTAAATTATCAATGATTTATTACTAAATTATT-AA
* * ** *
18600557 TTATCTACTACAAAATTATCACA-AATTTATTACTAAATTA
1 TGATTTACTATTAAATTATCA-ATGATTTATTACTAAATTA
18600597 ACCATCATTC
Statistics
Matches: 261, Mismatches: 73, Indels: 39
0.70 0.20 0.10
Matches are distributed among these distances:
42 2 0.01
43 59 0.23
44 159 0.61
47 3 0.01
48 2 0.01
49 3 0.01
50 1 0.00
52 28 0.11
53 4 0.02
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (44 bp):
TGATTTACTATTAAATTATCAATGATTTATTACTAAATTATTAA
Found at i:18600467 original size:52 final size:54
Alignment explanation
Indices: 18600371--18600479 Score: 125
Period size: 52 Copynumber: 2.0 Consensus size: 54
18600361 TACAAAGTTG
* *
18600371 TAATTGATTACTATTAATTTATCAATGTTTTACTATAAAGTTATTAATAATTAAC
1 TAATTGATTACTA-TAATTTATCAATGATTTACAATAAAGTTATTAATAATTAAC
* * * *
18600426 TAATTTATTACTA-AA-TTATCATTGATTTACAATTAAA-TTATTAGTAATTTAC
1 TAATTGATTACTATAATTTATCAATGATTTACAA-TAAAGTTATTAATAATTAAC
18600478 TA
1 TA
18600480 CTAAGTTATC
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
52 29 0.62
53 6 0.13
55 12 0.26
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.48
Consensus pattern (54 bp):
TAATTGATTACTATAATTTATCAATGATTTACAATAAAGTTATTAATAATTAAC
Found at i:18600488 original size:22 final size:22
Alignment explanation
Indices: 18600426--18600592 Score: 79
Period size: 22 Copynumber: 7.6 Consensus size: 22
18600416 AATAATTAAC
* *
18600426 TAATTTATTACTAAATTATCAT
1 TAATTTACTACTAAGTTATCAT
* * * * * *
18600448 TGATTTACAATTAAATTATTAG
1 TAATTTACTACTAAGTTATCAT
*
18600470 TAATTTACTACTAAGTTATCAA
1 TAATTTACTACTAAGTTATCAT
** * * *
18600492 TAATTTGTTATTATGTTATTA-
1 TAATTTACTACTAAGTTATCAT
* *
18600513 TACATTTACTATTATGTTATCAT
1 TA-ATTTACTACTAAGTTATCAT
* *
18600536 TGATTTACTACTAA-TTTTCAAT
1 TAATTTACTACTAAGTTATC-AT
* * * *
18600558 T-ATCTACTACAAAATTATCAC
1 TAATTTACTACTAAGTTATCAT
* *
18600579 AAATTTATTACTAA
1 TAATTTACTACTAA
18600593 ATTAACCATC
Statistics
Matches: 108, Mismatches: 32, Indels: 10
0.72 0.21 0.07
Matches are distributed among these distances:
21 17 0.16
22 90 0.83
23 1 0.01
ACGTcount: A:0.38, C:0.11, G:0.04, T:0.47
Consensus pattern (22 bp):
TAATTTACTACTAAGTTATCAT
Found at i:18600850 original size:22 final size:22
Alignment explanation
Indices: 18600805--18600861 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
18600795 ATTGATTTAT
* *
18600805 TATTAAGTTATCACTAATTTAC
1 TATTAAGTTATCAATAATTGAC
* *
18600827 TATTAAATTATCAATGATTGAC
1 TATTAAGTTATCAATAATTGAC
*
18600849 TACTAAGTTATCA
1 TATTAAGTTATCA
18600862 TTTGTTATTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42
Consensus pattern (22 bp):
TATTAAGTTATCAATAATTGAC
Found at i:18601024 original size:13 final size:12
Alignment explanation
Indices: 18601004--18601029 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
18600994 TTGAAAATTA
18601004 GATTTTTTTATT
1 GATTTTTTTATT
18601016 GATTTTTTTATT
1 GATTTTTTTATT
18601028 GA
1 GA
18601030 ATAAGTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.19, C:0.00, G:0.12, T:0.69
Consensus pattern (12 bp):
GATTTTTTTATT
Found at i:18601209 original size:22 final size:22
Alignment explanation
Indices: 18601153--18601210 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
18601143 GATAGTTACT
* * *
18601153 TTATCAGTTATTTAATACTAAG
1 TTATCAATAATTTAATACTAAA
* * *
18601175 TTGTTAATGATTTAATACTAAA
1 TTATCAATAATTTAATACTAAA
18601197 TTATCAATAATTTA
1 TTATCAATAATTTA
18601211 TTTTTAATTT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (22 bp):
TTATCAATAATTTAATACTAAA
Found at i:18601239 original size:22 final size:22
Alignment explanation
Indices: 18601214--18601275 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
18601204 TAATTTATTT
*
18601214 TTAATTTATGAATAATTTACCA
1 TTAAGTTATGAATAATTTACCA
* * *
18601236 TTAAGTTGTGAATGATTTATCA
1 TTAAGTTATGAATAATTTACCA
*
18601258 TTAAGTTATTAATAATTT
1 TTAAGTTATGAATAATTT
18601276 TTATTAAATT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.37, C:0.05, G:0.10, T:0.48
Consensus pattern (22 bp):
TTAAGTTATGAATAATTTACCA
Found at i:18601491 original size:22 final size:22
Alignment explanation
Indices: 18601466--18601527 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
18601456 TGATTTATCG
18601466 TTATATTTTTATATATTTACTA-
1 TTATATTTTTAT-TATTTACTAC
* * *
18601488 TTATGTTATCATTGATTTACTAC
1 TTATATTTTTATT-ATTTACTAC
18601511 TTA-ATTTTTATTATTTA
1 TTATATTTTTATTATTTA
18601528 TTACAAAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
21 6 0.19
22 23 0.72
23 3 0.09
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.61
Consensus pattern (22 bp):
TTATATTTTTATTATTTACTAC
Found at i:18601622 original size:22 final size:21
Alignment explanation
Indices: 18601589--18601864 Score: 116
Period size: 22 Copynumber: 12.9 Consensus size: 21
18601579 GTTATTACCA
18601589 ATTTA-TATTAAATTATGCATG
1 ATTTATTATTAAATTAT-CATG
18601610 ATTTATTATTAAATTATCACTG
1 ATTTATTATTAAATTATCA-TG
* ** *
18601632 ATTAATTATTATGTTATCGATT
1 ATTTATTATTAAATTATC-ATG
*
18601654 ATTTATTATTAAGTTAT-ATTG
1 ATTTATTATTAAATTATCA-TG
* * * *
18601675 TTTTACTT-TTAAGTTCTTAATG
1 ATTTA-TTATTAAATT-ATCATG
* * *
18601697 ATTAACTATTAAATTATCAATT
1 ATTTATTATTAAATTATC-ATG
* *
18601719 ATTTATTACTAATTTATCATTG
1 ATTTATTATTAAATTATCA-TG
* * * *
18601741 ACTTACTATTAAATTATTTATA
1 ATTTATTATTAAATTA-TCATG
* * *
18601763 ATTTACTACT--ATTA--ATT
1 ATTTATTATTAAATTATCATG
* * **
18601780 AATTATTATTAAACTAAAACTG
1 ATTTATTATTAAATTATCA-TG
** * *
18601802 ATTTACCATTAAATTATTACTA
1 ATTTATTATTAAATTATCA-TG
18601824 ATTTATTATTAAATTATCATTG
1 ATTTATTATTAAATTATCA-TG
* *
18601846 ATTTATTACTAAGTTATCA
1 ATTTATTATTAAATTATCA
18601865 ATAATTAACT
Statistics
Matches: 190, Mismatches: 49, Indels: 31
0.70 0.18 0.11
Matches are distributed among these distances:
17 9 0.05
19 3 0.02
20 5 0.03
21 23 0.12
22 146 0.77
23 4 0.02
ACGTcount: A:0.37, C:0.08, G:0.05, T:0.50
Consensus pattern (21 bp):
ATTTATTATTAAATTATCATG
Found at i:18601772 original size:25 final size:25
Alignment explanation
Indices: 18601730--18601785 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 25
18601720 TTTATTACTA
*
18601730 ATTTATCATTGACTTACTATTAAATT
1 ATTTATAATTGACTTACTATT-AATT
*
18601756 ATTTATAATTTAC-TACTATTAATT
1 ATTTATAATTGACTTACTATTAATT
*
18601780 AATTAT
1 ATTTAT
18601786 TATTAAACTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 9 0.33
25 7 0.26
26 11 0.41
ACGTcount: A:0.38, C:0.09, G:0.02, T:0.52
Consensus pattern (25 bp):
ATTTATAATTGACTTACTATTAATT
Found at i:18601795 original size:25 final size:25
Alignment explanation
Indices: 18601744--18601791 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
18601734 ATCATTGACT
* *
18601744 TACTATTAAATTATTTATAATTTAC
1 TACTATTAAATTAATTATAATTAAC
*
18601769 TACTATT-AATTAATTATTATTAA
1 TACTATTAAATTAATTATAATTAA
18601792 ACTAAAACTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (25 bp):
TACTATTAAATTAATTATAATTAAC
Found at i:18601870 original size:44 final size:44
Alignment explanation
Indices: 18601610--18601886 Score: 140
Period size: 44 Copynumber: 6.4 Consensus size: 44
18601600 ATTATGCATG
* * * * * *
18601610 ATTTATTATTAAATTATCACTGATTAATTATTATGTTATCGATT
1 ATTTATTATTAAATTATCATTGATTTATTACTAAGTTATCAATA
* * * * * *
18601654 ATTTATTATTAAGTTAT-ATTGTTTTACTT-TTAAGTTCTTAATG
1 ATTTATTATTAAATTATCATTGATTTA-TTACTAAGTTATCAATA
* * * * *
18601697 ATTAACTATTAAATTATCAATT-ATTTATTACTAATTTATCATTG
1 ATTTATTATTAAATTATC-ATTGATTTATTACTAAGTTATCAATA
* * * * * *
18601741 ACTTACTATTAAATTAT-TTATAATTTACTACT-A-TTA--ATTA
1 ATTTATTATTAAATTATCAT-TGATTTATTACTAAGTTATCAATA
* ** * ** * * * *
18601781 A-TTATTATTAAACTAAAACTGATTTACCATTAAATTATTACTA
1 ATTTATTATTAAATTATCATTGATTTATTACTAAGTTATCAATA
18601824 ATTTATTATTAAATTATCATTGATTTATTACTAAGTTATCAATA
1 ATTTATTATTAAATTATCATTGATTTATTACTAAGTTATCAATA
* * *
18601868 ATTAACTACTAAATTATCA
1 ATTTATTATTAAATTATCA
18601887 CTTATTTTTT
Statistics
Matches: 176, Mismatches: 45, Indels: 24
0.72 0.18 0.10
Matches are distributed among these distances:
39 21 0.12
40 5 0.03
41 3 0.02
42 4 0.02
43 37 0.21
44 103 0.59
45 3 0.02
ACGTcount: A:0.38, C:0.09, G:0.04, T:0.49
Consensus pattern (44 bp):
ATTTATTATTAAATTATCATTGATTTATTACTAAGTTATCAATA
Found at i:18602063 original size:22 final size:21
Alignment explanation
Indices: 18602016--18602077 Score: 61
Period size: 22 Copynumber: 2.9 Consensus size: 21
18602006 AATTTCAATT
* * *
18602016 ATTTACTACTAAATTATTATTC
1 ATTTACTA-TAAATTATCACTA
18602038 ATTTACTATTAAATTATCACTA
1 ATTTACTA-TAAATTATCACTA
* *
18602060 ATTTAATATAAGTTATCA
1 ATTTACTATAAATTATCA
18602078 ATGATTACTA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
21 9 0.26
22 25 0.74
ACGTcount: A:0.40, C:0.11, G:0.02, T:0.47
Consensus pattern (21 bp):
ATTTACTATAAATTATCACTA
Found at i:18604511 original size:13 final size:13
Alignment explanation
Indices: 18604493--18604519 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
18604483 CCGAATTCAA
18604493 ATATATATAAATT
1 ATATATATAAATT
18604506 ATATATATAAATT
1 ATATATATAAATT
18604519 A
1 A
18604520 AGTTTAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATATATATAAATT
Found at i:18606929 original size:11 final size:11
Alignment explanation
Indices: 18606913--18606937 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
18606903 TGCTATAAAA
18606913 TATAATAATGG
1 TATAATAATGG
18606924 TATAATAATGG
1 TATAATAATGG
18606935 TAT
1 TAT
18606938 TATGGTATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (11 bp):
TATAATAATGG
Found at i:18607652 original size:17 final size:17
Alignment explanation
Indices: 18607619--18607655 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
18607609 TGTCTCATTG
**
18607619 ATAAATAAATTTTATAT
1 ATAAATAAATTGGATAT
18607636 ATAAATAAATTGGATAT
1 ATAAATAAATTGGATAT
18607653 ATA
1 ATA
18607656 TATGTTATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (17 bp):
ATAAATAAATTGGATAT
Found at i:18611142 original size:25 final size:25
Alignment explanation
Indices: 18611113--18611166 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
18611103 ATATGAAGGT
*
18611113 AATTATTGTGAATTTAATATTTTA-A
1 AATTATTGTCAATTTAAT-TTTTATA
*
18611138 AATTATTGTCTATTTAATTTTTATA
1 AATTATTGTCAATTTAATTTTTATA
18611163 AATT
1 AATT
18611167 TTATTTTGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 5 0.19
25 21 0.81
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.56
Consensus pattern (25 bp):
AATTATTGTCAATTTAATTTTTATA
Found at i:18611392 original size:2 final size:2
Alignment explanation
Indices: 18611385--18611410 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
18611375 GCCTATTTTA
18611385 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
18611411 TTTACCATGA
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:18611792 original size:42 final size:43
Alignment explanation
Indices: 18611713--18611803 Score: 105
Period size: 41 Copynumber: 2.1 Consensus size: 43
18611703 GATAATTAAT
18611713 AACTTAGTAATTAATCATTAAAAACTTAAAAGTAATTAGT-AC
1 AACTTAGTAATTAATCATTAAAAACTTAAAAGTAATTAGTGAC
* * * * * *
18611755 AACTTAGTAA-TAATGATTGATAACTTAATATTAAATTAGTGAT
1 AACTTAGTAATTAATCATTAAAAACTTAAAAGT-AATTAGTGAC
18611798 AACTTA
1 AACTTA
18611804 ATAGTAAATG
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
41 17 0.41
42 17 0.41
43 7 0.17
ACGTcount: A:0.47, C:0.08, G:0.09, T:0.36
Consensus pattern (43 bp):
AACTTAGTAATTAATCATTAAAAACTTAAAAGTAATTAGTGAC
Found at i:18611821 original size:22 final size:22
Alignment explanation
Indices: 18611774--18611821 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
18611764 ATAATGATTG
* * * *
18611774 ATAACTTAATATTAAATTAGTG
1 ATAACTTAATAGTAAATGAATA
18611796 ATAACTTAATAGTAAATGAATA
1 ATAACTTAATAGTAAATGAATA
18611818 ATAA
1 ATAA
18611822 TTGATAGCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.52, C:0.04, G:0.08, T:0.35
Consensus pattern (22 bp):
ATAACTTAATAGTAAATGAATA
Found at i:18611850 original size:11 final size:11
Alignment explanation
Indices: 18611834--18612038 Score: 80
Period size: 11 Copynumber: 18.7 Consensus size: 11
18611824 GATAGCTTTT
*
18611834 TAATAAATCAA
1 TAATAAATTAA
18611845 TAAT-AATATAA
1 TAATAAAT-TAA
*
18611856 TAATATA-TACA
1 TAATAAATTA-A
**
18611867 TAATACCTTAA
1 TAATAAATTAA
* *
18611878 TGATAAATCAA
1 TAATAAATTAA
* *
18611889 TTAT-AATATAG
1 TAATAAAT-TAA
*
18611900 TTATAAA-TACA
1 TAATAAATTA-A
*
18611911 TAATAAA-TAG
1 TAATAAATTAA
* *
18611921 TATTAAATCAA
1 TAATAAATTAA
*
18611932 TAATAACTTAA
1 TAATAAATTAA
* *
18611943 CAA-AAAATAA
1 TAATAAATTAA
* * *
18611953 TTGATAATTTTA
1 -TAATAAATTAA
* *
18611965 TAATTAATTAT
1 TAATAAATTAA
* *
18611976 TGATAAATTAG
1 TAATAAATTAA
*
18611987 TAATAAATCAA
1 TAATAAATTAA
* *
18611998 TGATAACTTAA
1 TAATAAATTAA
18612009 TAATAAATTAA
1 TAATAAATTAA
*
18612020 TAATAATTTAA
1 TAATAAATTAA
*
18612031 TAGTAAAT
1 TAATAAAT
18612039 CAATTTCAGT
Statistics
Matches: 137, Mismatches: 47, Indels: 20
0.67 0.23 0.10
Matches are distributed among these distances:
10 21 0.15
11 107 0.78
12 9 0.07
ACGTcount: A:0.54, C:0.05, G:0.04, T:0.37
Consensus pattern (11 bp):
TAATAAATTAA
Found at i:18612002 original size:44 final size:44
Alignment explanation
Indices: 18611924--18612042 Score: 114
Period size: 44 Copynumber: 2.7 Consensus size: 44
18611914 TAAATAGTAT
* * * * * *
18611924 TAAATCAATAATAACTTAACAAAAAAT-AATTGATAATTTTATAA
1 TAAATTAATAATAAATTAATAATAAATCAA-TGATAACTTAATAA
* * * *
18611968 TTAATTATTGATAAATTAGTAATAAATCAATGATAACTTAATAA
1 TAAATTAATAATAAATTAATAATAAATCAATGATAACTTAATAA
* *
18612012 TAAATTAATAATAATTTAATAGTAAATCAAT
1 TAAATTAATAATAAATTAATAATAAATCAAT
18612043 TTCAGTTTAA
Statistics
Matches: 58, Mismatches: 16, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
44 56 0.97
45 2 0.03
ACGTcount: A:0.54, C:0.05, G:0.04, T:0.37
Consensus pattern (44 bp):
TAAATTAATAATAAATTAATAATAAATCAATGATAACTTAATAA
Found at i:18612157 original size:22 final size:22
Alignment explanation
Indices: 18612070--18612272 Score: 105
Period size: 22 Copynumber: 9.3 Consensus size: 22
18612060 TAGTTGATAG
** *
18612070 TAGTAAATC-ATGAATAGTTTAG
1 TAGTAAATCAATG-ATAACTTAA
* * *
18612092 TAGCAAATCAATGATAAATTAG
1 TAGTAAATCAATGATAACTTAA
* * *
18612114 CACTAAAT-AATTGATAATTTAA
1 TAGTAAATCAA-TGATAACTTAA
* * * *
18612136 TAGTTAATCATTAAAAACTTAA
1 TAGTAAATCAATGATAACTTAA
* *
18612158 AAGTAAATCAAT-ATAATTTAA
1 TAGTAAATCAATGATAACTTAA
18612179 TAGTAAATC-ATCGATAA-TATAA
1 TAGTAAATCAAT-GATAACT-TAA
*
18612201 TAGTTAATCAATGATAACTTAA
1 TAGTAAATCAATGATAACTTAA
* * *
18612223 TAATAAAT-TATGCATAATTTAA
1 TAGTAAATCAATG-ATAACTTAA
* * * *
18612245 TA-TAAATTAGTAATAACTTGA
1 TAGTAAATCAATGATAACTTAA
18612266 TAGTAAA
1 TAGTAAA
18612273 AAGATTTACT
Statistics
Matches: 139, Mismatches: 31, Indels: 22
0.72 0.16 0.11
Matches are distributed among these distances:
20 2 0.01
21 35 0.25
22 95 0.68
23 7 0.05
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (22 bp):
TAGTAAATCAATGATAACTTAA
Found at i:18612210 original size:43 final size:44
Alignment explanation
Indices: 18612117--18612230 Score: 117
Period size: 43 Copynumber: 2.6 Consensus size: 44
18612107 AAATTAGCAC
* *
18612117 TAAAT-AATTGATAATTTAATAGTTAATCATTAAAAACTTAAAAG
1 TAAATCAA-TGATAATTTAATAGTAAATCATCAAAAACTTAAAAG
* * *
18612161 TAAATCAAT-ATAATTTAATAGTAAATCATCGATAA-TATAATAG
1 TAAATCAATGATAATTTAATAGTAAATCATCAAAAACT-TAAAAG
* * *
18612204 TTAATCAATGATAACTTAATAATAAAT
1 TAAATCAATGATAATTTAATAGTAAAT
18612231 TATGCATAAT
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
42 1 0.02
43 35 0.59
44 21 0.36
45 2 0.03
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.36
Consensus pattern (44 bp):
TAAATCAATGATAATTTAATAGTAAATCATCAAAAACTTAAAAG
Found at i:18612220 original size:65 final size:64
Alignment explanation
Indices: 18612117--18612251 Score: 157
Period size: 65 Copynumber: 2.1 Consensus size: 64
18612107 AAATTAGCAC
* * *
18612117 TAAATAATTGATAATTTAATAGTTAATCATTAAAAACTTAA-AAGTAAATCAAT-ATAATTTAAT
1 TAAATAATCGATAATATAATAGTTAATCAATAAAAACTTAATAA-TAAAT-AATCATAATTTAAT
18612180 A
64 A
* * * *
18612181 GTAAATCATCGATAATATAATAGTTAATCAATGATAACTTAATAATAAATTATGCATAATTTAAT
1 -TAAATAATCGATAATATAATAGTTAATCAATAAAAACTTAATAATAAATAAT-CATAATTTAAT
18612246 A
64 A
18612247 TAAAT
1 TAAAT
18612252 TAGTAATAAC
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
64 2 0.03
65 45 0.75
66 13 0.22
ACGTcount: A:0.51, C:0.06, G:0.06, T:0.37
Consensus pattern (64 bp):
TAAATAATCGATAATATAATAGTTAATCAATAAAAACTTAATAATAAATAATCATAATTTAATA
Found at i:18612260 original size:21 final size:22
Alignment explanation
Indices: 18612214--18612272 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 22
18612204 TTAATCAATG
*
18612214 ATAACTTAATAATAAATTATGC
1 ATAACTTAATAATAAATTATGA
*
18612236 ATAATTTAAT-ATAAATTA-GTA
1 ATAACTTAATAATAAATTATG-A
* *
18612257 ATAACTTGATAGTAAA
1 ATAACTTAATAATAAA
18612273 AAGATTTACT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
20 1 0.03
21 16 0.53
22 13 0.43
ACGTcount: A:0.51, C:0.05, G:0.07, T:0.37
Consensus pattern (22 bp):
ATAACTTAATAATAAATTATGA
Found at i:18615581 original size:7 final size:7
Alignment explanation
Indices: 18615569--18615599 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
18615559 CATGAGTCCC
18615569 GCAGCTT
1 GCAGCTT
18615576 GCAGCTT
1 GCAGCTT
18615583 GCAGCTT
1 GCAGCTT
*
18615590 GCAACTT
1 GCAGCTT
18615597 GCA
1 GCA
18615600 TGTGGGAGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.19, C:0.29, G:0.26, T:0.26
Consensus pattern (7 bp):
GCAGCTT
Found at i:18616644 original size:16 final size:16
Alignment explanation
Indices: 18616625--18616674 Score: 66
Period size: 16 Copynumber: 3.1 Consensus size: 16
18616615 ATAATAGTTT
18616625 TAAATAAAAATATATA
1 TAAATAAAAATATATA
*
18616641 TAAATAAAGAAT-TAAA
1 TAAATAAA-AATATATA
18616657 TAAATAACAAATATATA
1 TAAATAA-AAATATATA
18616674 T
1 T
18616675 TTTTATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
16 21 0.72
17 8 0.28
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (16 bp):
TAAATAAAAATATATA
Found at i:18616661 original size:26 final size:26
Alignment explanation
Indices: 18616597--18616662 Score: 62
Period size: 28 Copynumber: 2.5 Consensus size: 26
18616587 ATATGAATTT
* * *
18616597 ATTAAATTAAGATATTAAATAATAGT
1 ATTAAATAAATATATTAAATAATAGA
*
18616623 TTTAAATAAAAATATATATAAATAA-AGA
1 ATTAAAT--AAATATAT-TAAATAATAGA
18616651 ATTAAATAAATA
1 ATTAAATAAATA
18616663 ACAAATATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
26 11 0.34
28 14 0.44
29 7 0.22
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.35
Consensus pattern (26 bp):
ATTAAATAAATATATTAAATAATAGA
Found at i:18617493 original size:22 final size:19
Alignment explanation
Indices: 18617452--18617507 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 19
18617442 ATAATATAAA
*
18617452 AATAATAATTTAAAATTTT
1 AATAATAATTTAAAAATTT
18617471 AATAATAATTATATATAAATTT
1 AATAATAATT-TA-A-AAATTT
18617493 AATAA-AATTTAAAAA
1 AATAATAATTTAAAAA
18617508 ATATATTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
18 3 0.09
19 11 0.33
20 4 0.12
21 5 0.15
22 10 0.30
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AATAATAATTTAAAAATTT
Found at i:18617562 original size:20 final size:22
Alignment explanation
Indices: 18617539--18617586 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
18617529 CAATACGAAT
18617539 TATAATA-TATAAT-TTTTATA
1 TATAATATTATAATATTTTATA
*
18617559 TATAA-ATTTTAATATTTTATA
1 TATAATATTATAATATTTTATA
*
18617580 TAAAATA
1 TATAATA
18617587 AATACACAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 1 0.04
20 10 0.43
21 11 0.48
22 1 0.04
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TATAATATTATAATATTTTATA
Found at i:18618086 original size:28 final size:29
Alignment explanation
Indices: 18618053--18618118 Score: 75
Period size: 28 Copynumber: 2.3 Consensus size: 29
18618043 TCCTTTCAAT
*
18618053 TAAAATAAAAATTT-TATTTTTTAATT-CA
1 TAAAATAAAAATTTATATATTTT-ATTACA
* *
18618081 TAAAAT-TAAATTTATATATTTTATTATA
1 TAAAATAAAAATTTATATATTTTATTACA
18618109 TAAAATAAAA
1 TAAAATAAAA
18618119 TAATATTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
27 9 0.29
28 20 0.65
29 2 0.06
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (29 bp):
TAAAATAAAAATTTATATATTTTATTACA
Found at i:18619842 original size:27 final size:27
Alignment explanation
Indices: 18619812--18619864 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
18619802 GAAAATAAAA
* *
18619812 ATAATAAT-ATTATTAAGATTAATTATT
1 ATAATAATGA-TATTAAAATCAATTATT
18619839 ATAATAATGATATTAAAATCAATTAT
1 ATAATAATGATATTAAAATCAATTAT
18619865 CGGATGTGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (27 bp):
ATAATAATGATATTAAAATCAATTATT
Found at i:18628882 original size:2 final size:2
Alignment explanation
Indices: 18628870--18628903 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
18628860 TCCTTTTCTT
*
18628870 TA TA TA AA 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
18628904 CTTGCAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:18632342 original size:13 final size:13
Alignment explanation
Indices: 18632324--18632360 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
18632314 AAATACGTTA
18632324 AAATAAATAATAT
1 AAATAAATAATAT
*
18632337 AAATAAAAAATAT
1 AAATAAATAATAT
18632350 -AA-AAATAATAT
1 AAATAAATAATAT
18632361 GAATTTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 8 0.36
12 2 0.09
13 12 0.55
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (13 bp):
AAATAAATAATAT
Found at i:18632476 original size:18 final size:18
Alignment explanation
Indices: 18632453--18632487 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
18632443 ATATAATATA
18632453 AGAATATTCGAAAAACCG
1 AGAATATTCGAAAAACCG
18632471 AGAATATTCGAAAAACC
1 AGAATATTCGAAAAACC
18632488 TGTTAACCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.17, G:0.14, T:0.17
Consensus pattern (18 bp):
AGAATATTCGAAAAACCG
Found at i:18638852 original size:25 final size:23
Alignment explanation
Indices: 18638823--18638875 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 23
18638813 ATATATATAT
* *
18638823 AATAAAATAATAATTTTTTAATTAA
1 AATAAAATAA-AAATATTT-ATTAA
18638848 AAT--AATAAAAATATTTATTAA
1 AATAAAATAAAAATATTTATTAA
18638869 AATAAAA
1 AATAAAA
18638876 AAATTCGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
21 8 0.33
22 6 0.25
23 7 0.29
25 3 0.12
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
AATAAAATAAAAATATTTATTAA
Found at i:18639827 original size:18 final size:18
Alignment explanation
Indices: 18639797--18639837 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
18639787 ATTTTTTAAT
*
18639797 TTTAA-AAATATATAAAA
1 TTTAATAAAAATATAAAA
*
18639814 TTTAATAAAAATATATAA
1 TTTAATAAAAATATAAAA
18639832 TTTAAT
1 TTTAAT
18639838 TCAATTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TTTAATAAAAATATAAAA
Found at i:18646401 original size:24 final size:26
Alignment explanation
Indices: 18646344--18646404 Score: 81
Period size: 26 Copynumber: 2.3 Consensus size: 26
18646334 TAATTAAAAG
*
18646344 TAATATATTTTTATTAAAAAATATAT
1 TAATATATATTTATTAAAAAATATAT
18646370 TAATATATATTTA-TAAAAAAT-TATT
1 TAATATATATTTATTAAAAAATATA-T
18646395 TAAATATATA
1 T-AATATATA
18646405 AAATATAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 2 0.06
25 10 0.31
26 20 0.62
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
TAATATATATTTATTAAAAAATATAT
Found at i:18646421 original size:33 final size:34
Alignment explanation
Indices: 18646362--18646429 Score: 86
Period size: 33 Copynumber: 2.0 Consensus size: 34
18646352 TTTTATTAAA
* *
18646362 AAATATATTAATATATATTTATAAAAAAT-TATTT
1 AAATATATAAATATATAATT-TAAAAAATATATTT
*
18646396 AAATATATAAA-ATATAAATTAAAAAATATATTT
1 AAATATATAAATATATAATTTAAAAAATATATTT
18646429 A
1 A
18646430 TTTTTATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
32 8 0.27
33 12 0.40
34 10 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (34 bp):
AAATATATAAATATATAATTTAAAAAATATATTT
Found at i:18646459 original size:57 final size:55
Alignment explanation
Indices: 18646356--18646464 Score: 130
Period size: 57 Copynumber: 1.9 Consensus size: 55
18646346 ATATATTTTT
18646356 ATTAAAAAATATATTAATATATATTTATAAAAAATTATTTAAATATATAAAATATAA
1 ATTAAAAAATATATTAATATATATTTATAAAAAATTA-TTAAATATA-AAAATATAA
* * * * *
18646413 ATTAAAAAATATATTTATTTTTATTTTTTTAAAAAATTA-TAGATATAAAAAT
1 ATTAAAAAATATA-TTA-ATATATATTTATAAAAAATTATTAAATATAAAAAT
18646465 TATTTATATC
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
56 5 0.11
57 20 0.44
58 3 0.07
59 17 0.38
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (55 bp):
ATTAAAAAATATATTAATATATATTTATAAAAAATTATTAAATATAAAAATATAA
Found at i:18652161 original size:181 final size:178
Alignment explanation
Indices: 18651838--18652193 Score: 606
Period size: 181 Copynumber: 2.0 Consensus size: 178
18651828 TTCCTTTTGT
* *
18651838 GAATCTTTTGCAGATATACTTTATCAGCTCATTTGAGGATTTAGCATAAATAATTTCATGATTAC
1 GAATCTTTTGCAGATATACTTTAGCAGCTCATTTGAGGATTTAGCATAAATAATTTCATGATCAC
*
18651903 TGAAAAAATAAATAAAAGATATTATTCAAATTCTTGCCTGTACTAATTCTCCTTTGGAGAGCATG
66 TGAAAAAATAAAAAAAAGATATTATTCAAATTCTTGCCTGTACTAATTCTCCTTTGGAGAGCATG
*
18651968 GTATTCTCCCAGAAGCTAGCATGAAAGGATTCATGGAGCCAACCCACA
131 GTATTCTCCCAGAAGCTAGCATGAAACGATTCATGGAGCCAACCCACA
18652016 GAATCTTTTGCAGATATACTTACTTTAGCAGCTCATTTGAGGATTTAGCATAAATAATTTCATGA
1 GAATCTTTTGCAG--ATA--TACTTTAGCAGCTCATTTGAGGATTTAGCATAAATAATTTCATGA
18652081 TCACTGAAAAAA-AAAAAAAAGATATTATTCAAATTCTTGCCTGTACTAATTCTCCTTTGGAGAG
62 TCACTGAAAAAATAAAAAAAAGATATTATTCAAATTCTTGCCTGTACTAATTCTCCTTTGGAGAG
* * *
18652145 CATGTTATTGTCCCAGAAGCTAGCATGAAACGATTCATGTAGCCAACCC
127 CATGGTATTCTCCCAGAAGCTAGCATGAAACGATTCATGGAGCCAACCC
18652194 GAAGAACTTC
Statistics
Matches: 167, Mismatches: 7, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
178 13 0.08
180 3 0.02
181 96 0.57
182 55 0.33
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (178 bp):
GAATCTTTTGCAGATATACTTTAGCAGCTCATTTGAGGATTTAGCATAAATAATTTCATGATCAC
TGAAAAAATAAAAAAAAGATATTATTCAAATTCTTGCCTGTACTAATTCTCCTTTGGAGAGCATG
GTATTCTCCCAGAAGCTAGCATGAAACGATTCATGGAGCCAACCCACA
Found at i:18660114 original size:30 final size:30
Alignment explanation
Indices: 18660080--18660222 Score: 100
Period size: 30 Copynumber: 4.8 Consensus size: 30
18660070 GAATGAAAAG
* *
18660080 TTTATTTAGATATTAATTAAAAATTAATGA
1 TTTATTTAAATATAAATTAAAAATTAATGA
*
18660110 TTTATTTAAATATAAATTAAAAATTAA-AA
1 TTTATTTAAATATAAATTAAAAATTAATGA
** * *
18660139 GTTTATTTAAATGCAAACTAAATAA-TAATAA
1 -TTTATTTAAATATAAATTAAA-AATTAATGA
* * * *
18660170 CTTATTTAAATGT-AA-TAATAATATAA-AA
1 TTTATTTAAATATAAATTAAAAAT-TAATGA
*
18660198 TTTATTTAAATA-AAATGATAAAATT
1 TTTATTTAAATATAAATTA-AAAATT
18660223 CAAATATTTT
Statistics
Matches: 92, Mismatches: 13, Indels: 17
0.75 0.11 0.14
Matches are distributed among these distances:
27 2 0.02
28 17 0.18
29 8 0.09
30 61 0.66
31 4 0.04
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.41
Consensus pattern (30 bp):
TTTATTTAAATATAAATTAAAAATTAATGA
Done.