Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168381.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_6, 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: 26551601
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 64000 characters in sequence are not A, C, G, or T
File 110 of 130
Found at i:21449223 original size:26 final size:26
Alignment explanation
Indices: 21449173--21449243 Score: 101
Period size: 26 Copynumber: 2.8 Consensus size: 26
21449163 TTAATATAAC
*
21449173 TATTAAAATAT-TAAAAATTATTTAT
1 TATTAAAATATATTAAAATTATTTAT
*
21449198 TATTAAAATATATTTAAATTATTTAT
1 TATTAAAATATATTAAAATTATTTAT
*
21449224 TATTAAAAT-TATTAATATTA
1 TATTAAAATATATTAAAATTA
21449244 AAAAATAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
25 20 0.49
26 21 0.51
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
TATTAAAATATATTAAAATTATTTAT
Found at i:21449247 original size:16 final size:16
Alignment explanation
Indices: 21449179--21449303 Score: 66
Period size: 19 Copynumber: 7.7 Consensus size: 16
21449169 TAACTATTAA
21449179 AATATTAAAAATTATTT
1 AATATT-AAAATTATTT
*
21449196 ATTATTAAAA-TA--T
1 AATATTAAAATTATTT
21449209 -AT-TT-AAATTATTT
1 AATATTAAAATTATTT
*
21449222 ATTATTAAAATTA-TT
1 AATATTAAAATTATTT
* *
21449237 AATATTAAAAAATAATT
1 AATATT-AAAATTATTT
*
21449254 ATATTTTAATAATAATATTT
1 A-ATATTAA-AAT--TATTT
21449274 AATATTAAAATAATATGTT
1 AATATTAAAAT--TAT-TT
*
21449293 AATATAAAAAT
1 AATATTAAAAT
21449304 ACTTAACATA
Statistics
Matches: 85, Mismatches: 10, Indels: 24
0.71 0.08 0.20
Matches are distributed among these distances:
10 3 0.04
11 4 0.05
12 1 0.01
13 2 0.02
14 1 0.01
15 11 0.13
16 16 0.19
17 10 0.12
18 14 0.16
19 18 0.21
20 5 0.06
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (16 bp):
AATATTAAAATTATTT
Found at i:21449350 original size:15 final size:15
Alignment explanation
Indices: 21449332--21449614 Score: 155
Period size: 18 Copynumber: 18.3 Consensus size: 15
21449322 TATTATTCTT
21449332 TATATTATTTATTAA
1 TATATTATTTATTAA
*
21449347 TATATTATAATATTAA
1 TATATTAT-TTATTAA
*
21449363 CTATTAATATATTATTTAATA
1 -TA-TATTAT-TTA-TT-A-A
21449384 GTATATTATTTATTAA
1 -TATATTATTTATTAA
*
21449400 TAATGTATTATTTATTCA
1 T-A--TATTATTTATTAA
21449418 TATATTA-TTA-TAA
1 TATATTATTTATTAA
21449431 TAT-TTATTTATTAAA
1 TATATTATTTATT-AA
*
21449446 TTAATAATATTTATT-A
1 -T-ATATTATTTATTAA
21449462 TATTATTATTTATTAAAA
1 TA-TATTATTTATT--AA
21449480 TAATATTATTTA-TAA
1 T-ATATTATTTATTAA
*
21449495 TATATGATTTATTATA
1 TATATTATTTATTA-A
21449511 TAATATTATTTATTAA
1 T-ATATTATTTATTAA
* * *
21449527 TAT-TAATATATTAG
1 TATATTATTTATTAA
*
21449541 TATAATATTT-TT-A
1 TATATTATTTATTAA
*
21449554 TAATAATATTTA-TAA
1 T-ATATTATTTATTAA
21449569 TA-A-TA-TTA-T-A
1 TATATTATTTATTAA
21449579 -ATATTATTTATTAATA
1 TATATTATTTATT-A-A
21449595 GTATATTATTTATTAA
1 -TATATTATTTATTAA
21449611 TATA
1 TATA
21449615 ATACTATCTA
Statistics
Matches: 214, Mismatches: 18, Indels: 72
0.70 0.06 0.24
Matches are distributed among these distances:
9 1 0.00
10 2 0.01
11 6 0.03
12 8 0.04
13 11 0.05
14 38 0.18
15 43 0.20
16 16 0.07
17 20 0.09
18 54 0.25
19 6 0.03
20 6 0.03
21 3 0.01
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.55
Consensus pattern (15 bp):
TATATTATTTATTAA
Found at i:21449469 original size:21 final size:21
Alignment explanation
Indices: 21449418--21449609 Score: 91
Period size: 21 Copynumber: 9.1 Consensus size: 21
21449408 TATTTATTCA
21449418 TATATTATT-ATAATATTTAT
1 TATATTATTAATAATATTTAT
21449438 T-TATTAAATTAATAATATTTAT
1 TATATT--ATTAATAATATTTAT
* *
21449460 TATATTATT-AT-TTATTAAAAT
1 TATATTATTAATAATATT--TAT
* * *
21449481 AATATTATTTATAATATATGAT
1 TATATTATTAATAATAT-TTAT
*
21449503 T-TATTATATAATATTATTTAT
1 TATATTAT-TAATAATATTTAT
21449524 TA-A-TATTAAT-ATATTAGTAT
1 TATATTATTAATAATATT--TAT
* *
21449544 AATATTTTTATAATAATATTTAT
1 TATA-TTAT-TAATAATATTTAT
* *
21449567 AATAATATT-ATAATA-TTAT
1 TATATTATTAATAATATTTAT
* *
21449586 T-TATTAATAGTATATTATTTAT
1 TATATTATTA--ATAATATTTAT
21449608 TA
1 TA
21449610 ATATAATACT
Statistics
Matches: 131, Mismatches: 18, Indels: 43
0.68 0.09 0.22
Matches are distributed among these distances:
18 9 0.07
19 16 0.12
20 16 0.12
21 34 0.26
22 30 0.23
23 16 0.12
24 5 0.04
25 5 0.04
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
TATATTATTAATAATATTTAT
Found at i:21449476 original size:52 final size:48
Alignment explanation
Indices: 21449405--21449548 Score: 134
Period size: 52 Copynumber: 2.9 Consensus size: 48
21449395 ATTAATAATG
* *
21449405 TATTAT-TTATTCATATATTATTATAATATTTATTTATTAAATTAATAAT-ATT
1 TATTATATTATT-ATTTATTAATATAATATTTATTTA-T-AA-T-AT-ATGATT
*
21449457 TATTATATTATTATTTATTAAAATAATA-TTATTTATAATATATGATT
1 TATTATATTATTATTTATTAATATAATATTTATTTATAATATATGATT
*
21449504 TATTATATAATATTATTTATTAATATTAATATATTA-GTATAATAT
1 TATTATAT--TATTATTTATTAATA-TAATAT-TTATTTATAATAT
21449549 TTTTATAATA
Statistics
Matches: 80, Mismatches: 5, Indels: 15
0.80 0.05 0.15
Matches are distributed among these distances:
46 2 0.03
47 13 0.16
48 1 0.01
49 16 0.20
50 6 0.08
51 15 0.19
52 22 0.28
53 5 0.06
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (48 bp):
TATTATATTATTATTTATTAATATAATATTTATTTATAATATATGATT
Found at i:21449576 original size:115 final size:109
Alignment explanation
Indices: 21449337--21449614 Score: 305
Period size: 115 Copynumber: 2.5 Consensus size: 109
21449327 TTCTTTATAT
** * *
21449337 TATTTATTAAT-ATATTATAATATTAACTATT--AATATATTATTTAATAGTATATTATTTATTA
1 TATTTA-TAATAATATTATAATATTATTTATTAAAATATATTATTT-ATAATATATGATTTATTA
* * *
21449399 ATAATGTATTATTTATTCATATATTATTATAATATTTATTTATTAA
64 ATAATGTATTATTTATTAATATATTAGTATAATATTTATTTAATAA
* * *
21449445 -ATTAATAATATTTATTATATTATTATTTATTAAAATAATATTATTTATAATATATGATTTATTA
1 TATTTATAATA-ATATTATAATATTATTTATTAAAAT-ATATTATTTATAATATATGATTTATTA
*
21449509 TATAATATTATTTATTAATATTAATATATTAGTATAATATTT-TTATAATAA
64 -ATAAT-GTA-TTATT--TATTAATATATTAGTATAATATTTATT-TAATAA
*
21449560 TATTTATAATAATATTATAATATTATTTATTAATAGTATATTATTTATTAATATA
1 TATTTATAATAATATTATAATATTATTTATTAA-AATATATTATTTA-TAATATA
21449615 ATACTATCTA
Statistics
Matches: 141, Mismatches: 15, Indels: 20
0.80 0.09 0.11
Matches are distributed among these distances:
106 4 0.03
107 4 0.03
108 16 0.11
110 19 0.13
111 14 0.10
112 2 0.01
113 5 0.04
114 2 0.01
115 57 0.40
116 18 0.13
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.55
Consensus pattern (109 bp):
TATTTATAATAATATTATAATATTATTTATTAAAATATATTATTTATAATATATGATTTATTAAT
AATGTATTATTTATTAATATATTAGTATAATATTTATTTAATAA
Found at i:21449605 original size:55 final size:59
Alignment explanation
Indices: 21449457--21449614 Score: 172
Period size: 55 Copynumber: 2.7 Consensus size: 59
21449447 TAATAATATT
21449457 TATTATATTATTATTTATTAA-A--ATAATATTATTTATAATATATGATTTATTATATAA
1 TATTATATTATTATTTATTAATAGTATAATATT-TTTATAATATATGATTTATTATATAA
*
21449514 TATTAT-TTATTAATATTAATATATTAGTATAATATTTTTATAATA-AT-ATTTA-TA-ATAA
1 TATTATATTATT-AT-TT-AT-TAATAGTATAATATTTTTATAATATATGATTTATTATATAA
* * *
21449572 TATTATAATATTATTTATTAATAGTATATTATTTAT-TAATATA
1 TATTATATTATTATTTATTAATAGTATAATATTTTTATAATATA
21449615 ATACTATCTA
Statistics
Matches: 87, Mismatches: 5, Indels: 20
0.78 0.04 0.18
Matches are distributed among these distances:
54 5 0.06
55 16 0.18
56 7 0.08
57 10 0.11
58 14 0.16
59 8 0.09
60 7 0.08
61 3 0.03
62 9 0.10
63 8 0.09
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (59 bp):
TATTATATTATTATTTATTAATAGTATAATATTTTTATAATATATGATTTATTATATAA
Found at i:21450186 original size:2 final size:2
Alignment explanation
Indices: 21450179--21450223 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
21450169 ACACAAAGGC
*
21450179 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA TA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
21450221 GA G
1 GA G
21450224 TTAGGTTTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.49, T:0.02
Consensus pattern (2 bp):
GA
Found at i:21457706 original size:20 final size:19
Alignment explanation
Indices: 21457683--21457739 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 19
21457673 TTAACTGTTA
21457683 ATTTGATGATATAGATATTG
1 ATTTGATGATAT-GATATTG
* *
21457703 ATTTTATTGATACGATATTG
1 ATTTGA-TGATATGATATTG
*
21457723 ATTTTGTTGATATGATA
1 A-TTTGATGATATGATA
21457740 ATATAAATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
20 22 0.73
21 8 0.27
ACGTcount: A:0.32, C:0.02, G:0.18, T:0.49
Consensus pattern (19 bp):
ATTTGATGATATGATATTG
Found at i:21458411 original size:20 final size:19
Alignment explanation
Indices: 21458349--21458411 Score: 54
Period size: 20 Copynumber: 3.2 Consensus size: 19
21458339 TTTGGAAGTT
21458349 TTTAGATTTTTTTAAAAATA
1 TTTA-ATTTTTTTAAAAATA
* ***
21458369 TTAAATTTATTTTTTCAATA
1 TTTAATTT-TTTTAAAAATA
*
21458389 TTTAATTTTTTTGAAAATCA
1 TTTAATTTTTTTAAAAAT-A
21458409 TTT
1 TTT
21458412 TTTACACAAC
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
19 11 0.33
20 22 0.67
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (19 bp):
TTTAATTTTTTTAAAAATA
Found at i:21459491 original size:2 final size:2
Alignment explanation
Indices: 21459484--21459513 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
21459474 AAGTATGTGA
21459484 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
21459514 TTGTATAGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21460561 original size:22 final size:22
Alignment explanation
Indices: 21460536--21460588 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
21460526 GAGACTAAAA
* *
21460536 AAATTTTTTTTTAATTTTTGTC
1 AAATTTTTATATAATTTTTGTC
* *
21460558 AAATTTATATATAATTTTTTTC
1 AAATTTTTATATAATTTTTGTC
*
21460580 AAAATTTTA
1 AAATTTTTA
21460589 AATTATATCA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (22 bp):
AAATTTTTATATAATTTTTGTC
Found at i:21461295 original size:21 final size:20
Alignment explanation
Indices: 21461251--21461307 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
21461241 GACCCATTAA
*
21461251 TATTTTTTAAAAATTTTAGT
1 TATTTTTTAAAAAATTTAGT
*
21461271 TATTTTTTAAAAAATTTCGT
1 TATTTTTTAAAAAATTTAGT
*
21461291 CTATTATTATAAAAAAT
1 -TATT-TTTTAAAAAAT
21461308 AACATCATGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
20 18 0.56
21 4 0.12
22 10 0.31
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.53
Consensus pattern (20 bp):
TATTTTTTAAAAAATTTAGT
Found at i:21461934 original size:23 final size:23
Alignment explanation
Indices: 21461888--21461934 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
21461878 ATATATATGT
***
21461888 TATAACTTTGAAAATTCTGATAA
1 TATAACTTTGAAAAAAATGATAA
*
21461911 TATAACTTTGAAAAAAATGTTAA
1 TATAACTTTGAAAAAAATGATAA
21461934 T
1 T
21461935 TTATTTTTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (23 bp):
TATAACTTTGAAAAAAATGATAA
Found at i:21467724 original size:6 final size:6
Alignment explanation
Indices: 21467681--21467740 Score: 59
Period size: 6 Copynumber: 9.3 Consensus size: 6
21467671 AACCTAAAAT
*
21467681 AATTTA AATTGTA ATATTTA TAATTT- AATTTA ATTTTA AATTTAA TAATTTA
1 AATTTA AATT-TA A-ATTTA -AATTTA AATTTA AATTTA AATTT-A -AATTTA
21467733 AATTTA AA
1 AATTTA AA
21467741 ATGATTTGAG
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
5 5 0.11
6 21 0.46
7 11 0.24
8 9 0.20
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (6 bp):
AATTTA
Found at i:21470450 original size:14 final size:14
Alignment explanation
Indices: 21470431--21470475 Score: 65
Period size: 14 Copynumber: 3.2 Consensus size: 14
21470421 CGAAAGTAAC
21470431 TAAC-TTAACTAAAG
1 TAACTTTAA-TAAAG
21470445 TAACTTTAATAAAG
1 TAACTTTAATAAAG
*
21470459 TATCTTTAATAAAG
1 TAACTTTAATAAAG
21470473 TAA
1 TAA
21470476 ATGTAAGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 24 0.86
15 4 0.14
ACGTcount: A:0.49, C:0.09, G:0.07, T:0.36
Consensus pattern (14 bp):
TAACTTTAATAAAG
Found at i:21484522 original size:13 final size:12
Alignment explanation
Indices: 21484481--21484523 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
21484471 AATTTTTATC
*
21484481 TTTTTTAGATTT
1 TTTTTTAAATTT
* *
21484493 TATTTTAAATAT
1 TTTTTTAAATTT
21484505 TTTTTTAACATTT
1 TTTTTTAA-ATTT
21484518 TTTTTT
1 TTTTTT
21484524 GTAAAAACTA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 16 0.64
13 9 0.36
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (12 bp):
TTTTTTAAATTT
Found at i:21485263 original size:20 final size:20
Alignment explanation
Indices: 21485240--21485277 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
21485230 TTAGACTTCC
21485240 TAAATCTTAAATAGATATTT
1 TAAATCTTAAATAGATATTT
* *
21485260 TAAATTTTAAGTAGATAT
1 TAAATCTTAAATAGATAT
21485278 AATCCAACAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.45
Consensus pattern (20 bp):
TAAATCTTAAATAGATATTT
Found at i:21485426 original size:3 final size:3
Alignment explanation
Indices: 21485413--21485446 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
21485403 ATGCTAAACC
21485413 TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
21485447 AATTTAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.14
3 25 0.86
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:21490856 original size:2 final size:2
Alignment explanation
Indices: 21490849--21490876 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
21490839 CCTCCATATA
21490849 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
21490877 TAGTGTGTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:21502351 original size:10 final size:10
Alignment explanation
Indices: 21502332--21502364 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
21502322 ATTTCACATC
*
21502332 ATATTATTTT
1 ATATTTTTTT
21502342 ATATTTTTTT
1 ATATTTTTTT
21502352 ATATTTTTTT
1 ATATTTTTTT
21502362 ATA
1 ATA
21502365 GTATAACATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (10 bp):
ATATTTTTTT
Found at i:21502529 original size:21 final size:19
Alignment explanation
Indices: 21502494--21502534 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
21502484 TATAATTTAA
21502494 AATTTTAATAAAAATCATAT
1 AATTTTAATAAAAAT-ATAT
21502514 AATTTTAATAAAAAATATAT
1 AATTTTAAT-AAAAATATAT
21502534 A
1 A
21502535 TTTCGTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (19 bp):
AATTTTAATAAAAATATAT
Found at i:21503452 original size:22 final size:25
Alignment explanation
Indices: 21503406--21503452 Score: 64
Period size: 22 Copynumber: 2.0 Consensus size: 25
21503396 AATAATTATT
*
21503406 ATAATTATAAGTATAATTTAATAAA
1 ATAATTATAAGTATAATATAATAAA
21503431 ATAA-TATAA-TAT-ATATAATAAA
1 ATAATTATAAGTATAATATAATAAA
21503453 TTTTATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 9 0.43
23 3 0.14
24 5 0.24
25 4 0.19
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (25 bp):
ATAATTATAAGTATAATATAATAAA
Found at i:21508981 original size:48 final size:48
Alignment explanation
Indices: 21508910--21509003 Score: 143
Period size: 48 Copynumber: 2.0 Consensus size: 48
21508900 TGCACAAGGG
* *
21508910 TATCAATCTTTAAATTCACAAAAAATAAACAATCAAGAGTTGAATTTC
1 TATCAATCTTTAAATTCACAAAAAATAAACAATAAAAAGTTGAATTTC
* * *
21508958 TATCATTCTTTAAATTCACAAAAAATATACAGTAAAAAGTTGAATT
1 TATCAATCTTTAAATTCACAAAAAATAAACAATAAAAAGTTGAATT
21509004 CAAAATCAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.48, C:0.13, G:0.06, T:0.33
Consensus pattern (48 bp):
TATCAATCTTTAAATTCACAAAAAATAAACAATAAAAAGTTGAATTTC
Found at i:21511028 original size:13 final size:13
Alignment explanation
Indices: 21511012--21511039 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
21511002 AATTGAAAAA
21511012 TTAAATTAAATAT
1 TTAAATTAAATAT
21511025 TTAAATTAAATAT
1 TTAAATTAAATAT
21511038 TT
1 TT
21511040 TTTTATTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TTAAATTAAATAT
Found at i:21511335 original size:35 final size:34
Alignment explanation
Indices: 21511293--21511381 Score: 103
Period size: 34 Copynumber: 2.6 Consensus size: 34
21511283 GACGTATATG
21511293 AAGAACCAAAGATTTATTATGTAAGTT-TGAGAAAA-A
1 AAGAACCAAAGATTTATTAT-T-A-TTGTGA-AAAAGA
*
21511329 AA-AACCAAAGATTTACTATTATTGTGAAAAAGA
1 AAGAACCAAAGATTTATTATTATTGTGAAAAAGA
*
21511362 AAGAATCAAAGATTTATTAT
1 AAGAACCAAAGATTTATTAT
21511382 ATATGCATGA
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
32 6 0.13
33 7 0.15
34 16 0.34
35 16 0.34
36 2 0.04
ACGTcount: A:0.51, C:0.07, G:0.13, T:0.29
Consensus pattern (34 bp):
AAGAACCAAAGATTTATTATTATTGTGAAAAAGA
Found at i:21512685 original size:2 final size:2
Alignment explanation
Indices: 21512680--21512732 Score: 58
Period size: 2 Copynumber: 27.5 Consensus size: 2
21512670 TATGTCTGTT
* *
21512680 TA TA TA TT TA TA TA TA TA TA TA TA TA T- TA TA -A CTA -A TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
21512720 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
21512733 TAGATTATTC
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
1 3 0.07
2 39 0.91
3 1 0.02
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:21514652 original size:27 final size:27
Alignment explanation
Indices: 21514612--21514664 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
21514602 TTAATTAAAG
* * * *
21514612 ATAAATAATCAAAAATAAAAACAACAA
1 ATAAAAAATAAAAAAAAAAAAAAACAA
21514639 ATAAAAAATAAAAAAAAAAAAAAACA
1 ATAAAAAATAAAAAAAAAAAAAAACA
21514665 TGTCAAACAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.81, C:0.08, G:0.00, T:0.11
Consensus pattern (27 bp):
ATAAAAAATAAAAAAAAAAAAAAACAA
Found at i:21515139 original size:12 final size:12
Alignment explanation
Indices: 21515122--21515146 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
21515112 ATACTTTTGA
21515122 AAATATATATAT
1 AAATATATATAT
21515134 AAATATATATAT
1 AAATATATATAT
21515146 A
1 A
21515147 TTTTTTATCA
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAATATATATAT
Found at i:21520492 original size:15 final size:15
Alignment explanation
Indices: 21520472--21520503 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
21520462 AGTAAATAGC
21520472 TTATTGTTATTATTA
1 TTATTGTTATTATTA
*
21520487 TTATTGTTATTGTTA
1 TTATTGTTATTATTA
21520502 TT
1 TT
21520504 TTCATTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.22, C:0.00, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATTGTTATTATTA
Found at i:21522130 original size:19 final size:19
Alignment explanation
Indices: 21522106--21522149 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
21522096 TAAGTTTGAA
*
21522106 ATTATTTTAT-TCTTTTTTT
1 ATTATTTTATATC-TGTTTT
21522125 ATTA-TTTATATCTGTTTT
1 ATTATTTTATATCTGTTTT
21522143 ATTATTT
1 ATTATTT
21522150 ATTTTTCTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (19 bp):
ATTATTTTATATCTGTTTT
Found at i:21524507 original size:86 final size:87
Alignment explanation
Indices: 21524361--21524537 Score: 311
Period size: 86 Copynumber: 2.0 Consensus size: 87
21524351 ATGAATAAAA
* *
21524361 AAATATGTTAGAACCCCTCACGAAAAGGCAAAAAGAGTTATCCTATCAAGTAGAATCCAATTGAA
1 AAATATGTCAGAACCCCTCACAAAAAGGCAAAAAGAGTTATCCTATCAAGTAGAATCCAATTGAA
*
21524426 ATTAAACTAGAGCAGTCCCCTT
66 ATTAAACTAGAGCAATCCCCTT
21524448 AAATATGTCAGAA-CCCTCACAAAAAGGCAAAAAGAGTTATCCTATCAAGTAGAATCCAATTGAA
1 AAATATGTCAGAACCCCTCACAAAAAGGCAAAAAGAGTTATCCTATCAAGTAGAATCCAATTGAA
*
21524512 ATTAAACTAGAGCAATCCTCTT
66 ATTAAACTAGAGCAATCCCCTT
21524534 AAAT
1 AAAT
21524538 TCAAACTCTA
Statistics
Matches: 86, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
86 74 0.86
87 12 0.14
ACGTcount: A:0.44, C:0.20, G:0.14, T:0.23
Consensus pattern (87 bp):
AAATATGTCAGAACCCCTCACAAAAAGGCAAAAAGAGTTATCCTATCAAGTAGAATCCAATTGAA
ATTAAACTAGAGCAATCCCCTT
Found at i:21525562 original size:13 final size:13
Alignment explanation
Indices: 21525544--21525573 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
21525534 ATGGTAAATT
21525544 TTGTATTTGATTA
1 TTGTATTTGATTA
21525557 TTGTATTTGATTA
1 TTGTATTTGATTA
21525570 TTGT
1 TTGT
21525574 GAATTTGACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.20, C:0.00, G:0.17, T:0.63
Consensus pattern (13 bp):
TTGTATTTGATTA
Found at i:21526533 original size:33 final size:33
Alignment explanation
Indices: 21526447--21526594 Score: 99
Period size: 33 Copynumber: 4.5 Consensus size: 33
21526437 TGGACTAAGC
* * * * *
21526447 CGAAGTTTAAAAGTACGATTACCTAGTTTGAAC
1 CGAAGTTTAAAAATACAATGACCTAGATTGAAT
* *
21526480 CCAA-TTCTAAAAATGA-AATGACCTAGACTGAAT
1 CGAAGTT-TAAAAAT-ACAATGACCTAGATTGAAT
**
21526513 CGAAGTTTAAAAATACAATGATTTAGATTGAA-
1 CGAAGTTTAAAAATACAATGACCTAGATTGAAT
* * *
21526545 CTGAAGTCT-AAAATA-AATTGACCTGGATTGAGT
1 C-GAAGTTTAAAAATACAA-TGACCTAGATTGAAT
* *
21526578 TGAAGTTTGAAAATACA
1 CGAAGTTTAAAAATACA
21526595 TTGTTCTGAA
Statistics
Matches: 88, Mismatches: 18, Indels: 17
0.72 0.15 0.14
Matches are distributed among these distances:
31 2 0.02
32 26 0.30
33 56 0.64
34 4 0.05
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (33 bp):
CGAAGTTTAAAAATACAATGACCTAGATTGAAT
Found at i:21526544 original size:66 final size:66
Alignment explanation
Indices: 21526398--21526594 Score: 177
Period size: 65 Copynumber: 3.0 Consensus size: 66
21526388 CAAAATATGT
* * * * * *
21526398 AATGACTTAGATTGAACCGAATT-AAAAAAAGATATGACTTGGACT-AAGCCGAAGTTTAAAAGT
1 AATGACTTAGATTGAACCGAATTCTAAAAATGAAATGACCTGGACTGAA-TCGAAGTTTAAAAAT
21526461 AC
65 AC
* * * * * *
21526463 GATTACCTAGTTTGAACCCAATTCTAAAAATGAAATGACCTAGACTGAATCGAAGTTTAAAAATA
1 AATGACTTAGATTGAACCGAATTCTAAAAATGAAATGACCTGGACTGAATCGAAGTTTAAAAATA
21526528 C
66 C
* * * * * * *
21526529 AATGATTTAGATTGAACTGAAGTCT-AAAAT-AAATTGACCTGGATTGAGTTGAAGTTTGAAAAT
1 AATGACTTAGATTGAACCGAATTCTAAAAATGAAA-TGACCTGGACTGAATCGAAGTTTAAAAAT
21526592 AC
65 AC
21526594 A
1 A
21526595 TTGTTCTGAA
Statistics
Matches: 104, Mismatches: 25, Indels: 6
0.77 0.19 0.04
Matches are distributed among these distances:
64 3 0.03
65 50 0.48
66 49 0.47
67 2 0.02
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.28
Consensus pattern (66 bp):
AATGACTTAGATTGAACCGAATTCTAAAAATGAAATGACCTGGACTGAATCGAAGTTTAAAAATA
C
Found at i:21526818 original size:33 final size:33
Alignment explanation
Indices: 21526721--21526840 Score: 118
Period size: 33 Copynumber: 3.6 Consensus size: 33
21526711 GAAATAAATG
* * **
21526721 ACTTGGATTAAGCCAAAGTCTATGAATGAAATG
1 ACTTGGACTAAGCCAAAGTCTAAGAATGAAACA
* * * *
21526754 ACTTTGACTGAGCTAAAATCTGAA-AATGAAACA
1 ACTTGGACTAAGCCAAAGTCT-AAGAATGAAACA
*
21526787 ACTTGGATTAAGCCAAAGTCTAAGAATGAAACA
1 ACTTGGACTAAGCCAAAGTCTAAGAATGAAACA
*
21526820 AATTGGACTAAGCTC-AAGTCT
1 ACTTGGACTAAGC-CAAAGTCT
21526841 GAAAATGCAA
Statistics
Matches: 69, Mismatches: 15, Indels: 6
0.77 0.17 0.07
Matches are distributed among these distances:
32 2 0.03
33 65 0.94
34 2 0.03
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.25
Consensus pattern (33 bp):
ACTTGGACTAAGCCAAAGTCTAAGAATGAAACA
Found at i:21526842 original size:66 final size:66
Alignment explanation
Indices: 21526721--21526847 Score: 182
Period size: 66 Copynumber: 1.9 Consensus size: 66
21526711 GAAATAAATG
* ** * * *
21526721 ACTTGGATTAAGCCAAAGTCTATGAATGAAATGACTTTGACTGAGCTAAAATCTGAAAATGAAAC
1 ACTTGGATTAAGCCAAAGTCTAAGAATGAAACAAATTGGACTAAGCTAAAATCTGAAAATGAAAC
21526786 A
66 A
* *
21526787 ACTTGGATTAAGCCAAAGTCTAAGAATGAAACAAATTGGACTAAGCTCAAGTCTGAAAATG
1 ACTTGGATTAAGCCAAAGTCTAAGAATGAAACAAATTGGACTAAGCTAAAATCTGAAAATG
21526848 CAATCTTAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
66 53 1.00
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.24
Consensus pattern (66 bp):
ACTTGGATTAAGCCAAAGTCTAAGAATGAAACAAATTGGACTAAGCTAAAATCTGAAAATGAAAC
A
Found at i:21527094 original size:39 final size:39
Alignment explanation
Indices: 21527002--21527446 Score: 141
Period size: 39 Copynumber: 11.5 Consensus size: 39
21526992 ATTCGAAGGC
* * **
21527002 TAAAATCTTA-TCTTTGAAAAATTTTTCTCAATTAAGGAT
1 TAAAATCTCATTCTTTGAAAAA-TTTCCTCAACCAAGGAT
* * * **
21527041 T-AAAGCT-TTTTTCTTGAAAAGATTTCCTCAACTGAGGAT
1 TAAAATCTCATTCT-TTGAAAA-ATTTCCTCAACCAAGGAT
* * *
21527080 TAAAATCTCATTCTTTGAAAACTTTCCTTAACCAATGAT
1 TAAAATCTCATTCTTTGAAAAATTTCCTCAACCAAGGAT
* * * * *
21527119 TAAAATCTTATTCTTTGAAAACTTTTCTTAAACGAA--AT
1 TAAAATCTCATTCTTTGAAAA-ATTTCCTCAACCAAGGAT
* * * * ** * *
21527157 CAAAGTTTTA-TC-TCAAAAAATTTTTCTC-ACTCAAAGAT
1 TAAAATCTCATTCTTTGAAAAA-TTTCCTCAAC-CAAGGAT
* * **
21527195 TAAAATCTTA-TC-TTGAAAAACATTCCTCAACTTAGGAT
1 TAAAATCTCATTCTTTGAAAAA-TTTCCTCAACCAAGGAT
** * * * * *
21527233 CGATATCTCAATCTTTGAAAACTTTTCGT-AACCAATGAT
1 TAAAATCTCATTCTTTGAAAA-ATTTCCTCAACCAAGGAT
* * * * *
21527272 TAAAATCTTATTCTTTGAAAACTTTTCTTAAACGAA-GAT
1 TAAAATCTCATTCTTTGAAAA-ATTTCCTCAACCAAGGAT
* * * * * *
21527311 CAAAGTCTTA-T-TTCGAAAAATTTTTCTC-ACTCAAAGAT
1 TAAAATCTCATTCTTTGAAAAA-TTTCCTCAAC-CAAGGAT
* * * **
21527349 TAAAATCTTA-TC-TTAAAAAACATTCCTCAACTGAGGAT
1 TAAAATCTCATTCTTTGAAAAA-TTTCCTCAACCAAGGAT
* * * * *
21527387 CAAAATCTCAATCTTTGAAAACTTTCCTTAACCAATGAT
1 TAAAATCTCATTCTTTGAAAAATTTCCTCAACCAAGGAT
*
21527426 TAAAATCTTATTCTTTGAAAA
1 TAAAATCTCATTCTTTGAAAA
21527447 CTTTTCTTAA
Statistics
Matches: 297, Mismatches: 87, Indels: 44
0.69 0.20 0.10
Matches are distributed among these distances:
35 2 0.01
36 13 0.04
37 15 0.05
38 84 0.28
39 135 0.45
40 45 0.15
41 3 0.01
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.38
Consensus pattern (39 bp):
TAAAATCTCATTCTTTGAAAAATTTCCTCAACCAAGGAT
Found at i:21527277 original size:77 final size:77
Alignment explanation
Indices: 21527064--21527536 Score: 316
Period size: 77 Copynumber: 6.2 Consensus size: 77
21527054 TTGAAAAGAT
* * *
21527064 TTCCTCAACTGAGGATTAAAATCTCATTCTTTGAAAACTTTCCTTAACCAATGATTAAAATCTTA
1 TTCCTCAACTGAGGA-TCAAATCTCAATCTTTGAAAACTTTTC-TAACCAATGATTAAAATCTTA
*
21527129 TTCTTTG-AAAACTT
64 TTCTTTGAAAAAC-A
* * * ** *** * * *
21527143 TTCTTAAAC-GA-AATCAAAGT-TTTATCTCAAAAAATTTTTCTCACTCAAAGATTAAAATCTTA
1 TTCCTCAACTGAGGATCAAA-TCTCAATCTTTGAAAACTTTTCTAAC-CAATGATTAAAATCTTA
21527205 -TC-TTGAAAAACA
64 TTCTTTGAAAAACA
* *
21527217 TTCCTCAACTTAGGATCGATATCTCAATCTTTGAAAACTTTTCGTAACCAATGATTAAAATCTTA
1 TTCCTCAACTGAGGATC-AAATCTCAATCTTTGAAAACTTTTC-TAACCAATGATTAAAATCTTA
*
21527282 TTCTTTG-AAAACTT
64 TTCTTTGAAAAAC-A
* * * * * * * *
21527296 TTCTTAAAC-GAAGATCAAAGTCT-TAT-TTCGAAAAATTTTTCTCACTCAAAGATTAAAATCTT
1 TTCCTCAACTGAGGATCAAA-TCTCAATCTTTG-AAAACTTTTCTAAC-CAATGATTAAAATCTT
*
21527358 A-TC-TTAAAAAACA
63 ATTCTTTGAAAAACA
*
21527371 TTCCTCAACTGAGGATCAAAATCTCAATCTTTGAAAACTTTCCTTAACCAATGATTAAAATCTTA
1 TTCCTCAACTGAGGATC-AAATCTCAATCTTTGAAAACTTTTC-TAACCAATGATTAAAATCTTA
*
21527436 TTCTTTG-AAAACTT
64 TTCTTTGAAAAAC-A
* * * * * * * * *
21527450 TTCTTAAAC-GAAGATCAAAGC-CTTATC-TTGAAAATTTTTGTCACTCAAAGATTAAAATCTTA
1 TTCCTCAACTGAGGATCAAATCTC-AATCTTTGAAAACTTTTCTAAC-CAATGATTAAAATCTTA
*
21527512 -TC-TTAAAAAACA
64 TTCTTTGAAAAACA
*
21527524 TTCATCAACTGAG
1 TTCCTCAACTGAG
21527537 AATTAACAAG
Statistics
Matches: 300, Mismatches: 67, Indels: 58
0.71 0.16 0.14
Matches are distributed among these distances:
74 19 0.06
75 32 0.11
76 85 0.28
77 99 0.33
78 39 0.13
79 26 0.09
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (77 bp):
TTCCTCAACTGAGGATCAAATCTCAATCTTTGAAAACTTTTCTAACCAATGATTAAAATCTTATT
CTTTGAAAAACA
Found at i:21527395 original size:154 final size:154
Alignment explanation
Indices: 21527064--21527536 Score: 790
Period size: 154 Copynumber: 3.1 Consensus size: 154
21527054 TTGAAAAGAT
* *
21527064 TTCCTCAACTGAGGATTAAAATCTCATTCTTTGAAAACTTTCCTTAACCAATGATTAAAATCTTA
1 TTCCTCAACTGAGGATCAAAATCTCAATCTTTGAAAACTTTCCTTAACCAATGATTAAAATCTTA
* * *
21527129 TTCTTTGAAAACTTTTCTTAAACGAA-ATCAAAGTTTTATCTCAAAAAATTTTTCTCACTCAAAG
66 TTCTTTGAAAACTTTTCTTAAACGAAGATCAAAGTCTTATTTCGAAAAATTTTTCTCACTCAAAG
*
21527193 ATTAAAATCTTATCTTGAAAAACA
131 ATTAAAATCTTATCTTAAAAAACA
* * * * *
21527217 TTCCTCAACTTAGGATCGATATCTCAATCTTTGAAAACTTTTCGTAACCAATGATTAAAATCTTA
1 TTCCTCAACTGAGGATCAAAATCTCAATCTTTGAAAACTTTCCTTAACCAATGATTAAAATCTTA
21527282 TTCTTTGAAAACTTTTCTTAAACGAAGATCAAAGTCTTATTTCGAAAAATTTTTCTCACTCAAAG
66 TTCTTTGAAAACTTTTCTTAAACGAAGATCAAAGTCTTATTTCGAAAAATTTTTCTCACTCAAAG
21527347 ATTAAAATCTTATCTTAAAAAACA
131 ATTAAAATCTTATCTTAAAAAACA
21527371 TTCCTCAACTGAGGATCAAAATCTCAATCTTTGAAAACTTTCCTTAACCAATGATTAAAATCTTA
1 TTCCTCAACTGAGGATCAAAATCTCAATCTTTGAAAACTTTCCTTAACCAATGATTAAAATCTTA
* *
21527436 TTCTTTGAAAACTTTTCTTAAACGAAGATCAAAGCCTTATCTT-G-AAAATTTTTGTCACTCAAA
66 TTCTTTGAAAACTTTTCTTAAACGAAGATCAAAGTCTTAT-TTCGAAAAATTTTTCTCACTCAAA
21527499 GATTAAAATCTTATCTTAAAAAACA
130 GATTAAAATCTTATCTTAAAAAACA
*
21527524 TTCATCAACTGAG
1 TTCCTCAACTGAG
21527537 AATTAACAAG
Statistics
Matches: 299, Mismatches: 19, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
153 139 0.46
154 158 0.53
155 2 0.01
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (154 bp):
TTCCTCAACTGAGGATCAAAATCTCAATCTTTGAAAACTTTCCTTAACCAATGATTAAAATCTTA
TTCTTTGAAAACTTTTCTTAAACGAAGATCAAAGTCTTATTTCGAAAAATTTTTCTCACTCAAAG
ATTAAAATCTTATCTTAAAAAACA
Found at i:21527447 original size:39 final size:38
Alignment explanation
Indices: 21527077--21527515 Score: 243
Period size: 39 Copynumber: 11.4 Consensus size: 38
21527067 CTCAACTGAG
* *
21527077 GATTAAAATCTCATTCTTTGAAAACTTTCCTTAACCAAT
1 GATTAAAATCTTA-TCTTTGAAAACTTTTCTTAACCAAT
*
21527116 GATTAAAATCTTATTCTTTGAAAACTTTTCTTAAACGAA-
1 GATTAAAATCTTA-TCTTTGAAAACTTTTCTT-AACCAAT
* * * *** * * *
21527155 -ATCAAAGTTTTATCTCAAAAAATTTTTC-TCACTCAAA
1 GATTAAAATCTTATCTTTGAAAACTTTTCTTAAC-CAAT
* * * ** *
21527192 GATTAAAATCTTATC-TTGAAAAACATTCCTCAACTTAG
1 GATTAAAATCTTATCTTTG-AAAACTTTTCTTAACCAAT
** * * *
21527230 GATCGATATCTCAATCTTTGAAAACTTTTCGTAACCAAT
1 GATTAAAATCT-TATCTTTGAAAACTTTTCTTAACCAAT
*
21527269 GATTAAAATCTTATTCTTTGAAAACTTTTCTTAAACGAA-
1 GATTAAAATCTTA-TCTTTGAAAACTTTTCTT-AACCAAT
* * * * * *
21527308 GATCAAAGTCTTAT-TTCGAAAAATTTT-TCTCACTCAAA
1 GATTAAAATCTTATCTTTGAAAACTTTTCT-TAAC-CAAT
** * * * ** *
21527346 GATTAAAATCTTATCTTAAAAAACATTCCTCAACTGAG
1 GATTAAAATCTTATCTTTGAAAACTTTTCTTAACCAAT
* * *
21527384 GATCAAAATCTCAATCTTTGAAAACTTTCCTTAACCAAT
1 GATTAAAATCT-TATCTTTGAAAACTTTTCTTAACCAAT
*
21527423 GATTAAAATCTTATTCTTTGAAAACTTTTCTTAAACGAA-
1 GATTAAAATCTTA-TCTTTGAAAACTTTTCTT-AACCAAT
* ** * *
21527462 GATCAAAGCCTTATC-TTGAAAA-TTTT-TGTCACTCAAA
1 GATTAAAATCTTATCTTTGAAAACTTTTCT-TAAC-CAAT
21527499 GATTAAAATCTTATCTT
1 GATTAAAATCTTATCTT
21527516 AAAAAACATT
Statistics
Matches: 296, Mismatches: 82, Indels: 45
0.70 0.19 0.11
Matches are distributed among these distances:
35 5 0.02
36 13 0.04
37 45 0.15
38 65 0.22
39 149 0.50
40 19 0.06
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.37
Consensus pattern (38 bp):
GATTAAAATCTTATCTTTGAAAACTTTTCTTAACCAAT
Found at i:21529757 original size:16 final size:16
Alignment explanation
Indices: 21529738--21529771 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
21529728 TCTCTTTTGC
*
21529738 TTTTTAATTTTTTTAA
1 TTTTTAATTTATTTAA
*
21529754 TTTTTCATTTATTTAA
1 TTTTTAATTTATTTAA
21529770 TT
1 TT
21529772 AATAAAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTAATTTATTTAA
Found at i:21530500 original size:14 final size:14
Alignment explanation
Indices: 21530481--21530510 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
21530471 TTAATTTTTT
21530481 TTTTGTATTTTATA
1 TTTTGTATTTTATA
*
21530495 TTTTGTATTTTTTA
1 TTTTGTATTTTATA
21530509 TT
1 TT
21530511 AGATCAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.77
Consensus pattern (14 bp):
TTTTGTATTTTATA
Found at i:21535566 original size:58 final size:57
Alignment explanation
Indices: 21535443--21535639 Score: 177
Period size: 60 Copynumber: 3.3 Consensus size: 57
21535433 TTATAAAAAA
* * * **
21535443 ATTATTTAAGATATTTTTGTATA-AAAAATATCTTACATAATTTTTTATATTTTTACCAATAG
1 ATTATTTAAGATA-TTTT-TATAGAAACAT-T-TTAAATAATTTTTTATTTTTTTA--AGGAG
21535505 ATTATTTAAGATATTTTTATAGAAACATTTTAAATAATTTTTTTATTTTTTTAAGGAG
1 ATTATTTAAGATATTTTTATAGAAACATTTTAAATAA-TTTTTTATTTTTTTAAGGAG
* * * *
21535563 ATTATTTAATG-TGTTTTTAAAGAAAAAACACTTTAAATAATTTTTTATTTTTTAAAGG-G
1 ATTATTTAA-GATATTTTTATAG---AAACATTTTAAATAATTTTTTATTTTTTTAAGGAG
21535622 TATTATTTAA-ATATTTTT
1 -ATTATTTAAGATATTTTT
21535640 GGATAAAAAA
Statistics
Matches: 117, Mismatches: 10, Indels: 19
0.80 0.07 0.13
Matches are distributed among these distances:
58 21 0.18
59 15 0.13
60 45 0.38
61 23 0.20
62 13 0.11
ACGTcount: A:0.38, C:0.04, G:0.07, T:0.52
Consensus pattern (57 bp):
ATTATTTAAGATATTTTTATAGAAACATTTTAAATAATTTTTTATTTTTTTAAGGAG
Found at i:21535648 original size:59 final size:58
Alignment explanation
Indices: 21535443--21535668 Score: 201
Period size: 59 Copynumber: 3.8 Consensus size: 58
21535433 TTATAAAAAA
* * **
21535443 ATTATTTAAGATATTTTTGTATAAAAAATA-TCTTACATAATTTTTTATATTTTTACCAATAG
1 ATTATTTAAGATATTTTTG-ATAAAAAACACT-TTAAATAATTTTTTAT-TTTTTA--AAGGG
* * *
21535505 ATTATTTAAGATATTTTT-AT-AGAAACATTTTAAATAATTTTTTTATTTTTTTAAGGAG
1 ATTATTTAAGATATTTTTGATAAAAAACACTTTAAATAA-TTTTTTATTTTTTAAAGG-G
* * *
21535563 ATTATTTAATG-TGTTTTTAAAGAAAAAACACTTTAAATAATTTTTTATTTTTTAAAGGG
1 ATTATTTAA-GATATTTTT-GATAAAAAACACTTTAAATAATTTTTTATTTTTTAAAGGG
* *
21535622 TATTATTTAA-ATATTTTTGGATAAAAAATACCTTAAATAATATTTTT
1 -ATTATTTAAGATATTTTT-GATAAAAAACACTTTAAATAAT-TTTTT
21535669 TAAAAAATAT
Statistics
Matches: 137, Mismatches: 17, Indels: 22
0.78 0.10 0.12
Matches are distributed among these distances:
57 2 0.01
58 16 0.12
59 43 0.31
60 43 0.31
61 15 0.11
62 18 0.13
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.50
Consensus pattern (58 bp):
ATTATTTAAGATATTTTTGATAAAAAACACTTTAAATAATTTTTTATTTTTTAAAGGG
Found at i:21536500 original size:2 final size:2
Alignment explanation
Indices: 21536493--21536548 Score: 67
Period size: 2 Copynumber: 28.0 Consensus size: 2
21536483 CATTTCTCAA
* * * * *
21536493 AT AT AT AT AT AT AT AT AT AT AT AC AC AC AC AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21536535 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
21536549 GTACATTATA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (2 bp):
AT
Found at i:21543130 original size:137 final size:136
Alignment explanation
Indices: 21542971--21543248 Score: 443
Period size: 137 Copynumber: 2.0 Consensus size: 136
21542961 CTTAAGGATT
*
21542971 TAACAAATTTTTAAATTTAAATTTTAATATTTATAATCTCTTTTATTAGCTTT-ATTTTTTTTGT
1 TAACAAATTTTTAAATTTAAATTTCAATATTTATAATCTCTTTTATTAGCTTTAATTTTTTTTGT
* *
21543035 AAGAAAAATTTAAAGATAGATAAATTATTCAATCCCTCAAATCAAGATAAAATATGCTATACCTG
66 AAGAAAAATTTAAA-ATAAATAAATTATTCAATCCCTCAAATCAAGA-AAAAAATGCTATA-CTG
21543100 ACAGTCTAA
128 ACAGTCTAA
21543109 -AACAAATTTTTAAATTTAAATTTCAATATTTATAATCTCTTTTATTAGCTTTAATTTTTTTTGT
1 TAACAAATTTTTAAATTTAAATTTCAATATTTATAATCTCTTTTATTAGCTTTAATTTTTTTTGT
* * * * *
21543173 AAGAAAAATTTTAAATAAATAAATTATTCAGTCTCTCAAATCAGGAAAAAAATGCTATATTGACA
66 AAGAAAAATTTAAAATAAATAAATTATTCAATCCCTCAAATCAAGAAAAAAATGCTATACTGACA
21543238 GTCTAA
131 GTCTAA
21543244 TAACA
1 TAACA
21543249 GATTCGAGAT
Statistics
Matches: 130, Mismatches: 8, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
135 11 0.08
136 16 0.12
137 79 0.61
138 24 0.18
ACGTcount: A:0.41, C:0.10, G:0.06, T:0.42
Consensus pattern (136 bp):
TAACAAATTTTTAAATTTAAATTTCAATATTTATAATCTCTTTTATTAGCTTTAATTTTTTTTGT
AAGAAAAATTTAAAATAAATAAATTATTCAATCCCTCAAATCAAGAAAAAAATGCTATACTGACA
GTCTAA
Found at i:21545108 original size:34 final size:34
Alignment explanation
Indices: 21545070--21545147 Score: 138
Period size: 34 Copynumber: 2.3 Consensus size: 34
21545060 CCGATTATTT
*
21545070 AATGTAGTAGGTATCACTTCAATGGGACCCATTC
1 AATGTCGTAGGTATCACTTCAATGGGACCCATTC
*
21545104 AATGTCGTAGGTGTCACTTCAATGGGACCCATTC
1 AATGTCGTAGGTATCACTTCAATGGGACCCATTC
21545138 AATGTCGTAG
1 AATGTCGTAG
21545148 TAATGTGTAG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (34 bp):
AATGTCGTAGGTATCACTTCAATGGGACCCATTC
Found at i:21545439 original size:12 final size:12
Alignment explanation
Indices: 21545399--21545439 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
21545389 TTTTAAAATT
21545399 TATAATTTTTT-
1 TATAATTTTTTA
*
21545410 TATTATCTTTTTA
1 TATAAT-TTTTTA
21545423 T-TAATTTTTTA
1 TATAATTTTTTA
21545434 TATAAT
1 TATAAT
21545440 ACAAAAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
11 12 0.48
12 12 0.48
13 1 0.04
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (12 bp):
TATAATTTTTTA
Found at i:21545722 original size:3 final size:3
Alignment explanation
Indices: 21545714--21545748 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
21545704 ACATTTTCAC
*
21545714 AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
21545749 AAGAAGTAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:21560837 original size:9 final size:9
Alignment explanation
Indices: 21560823--21560852 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
21560813 TCACAAATAA
21560823 TTTTTTATT
1 TTTTTTATT
21560832 TTTTTTATT
1 TTTTTTATT
21560841 TTTATTTATT
1 TTT-TTTATT
21560851 TT
1 TT
21560853 CAATCAGGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.60
10 8 0.40
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (9 bp):
TTTTTTATT
Found at i:21561029 original size:18 final size:18
Alignment explanation
Indices: 21561006--21561040 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
21560996 AAATGTAATA
* *
21561006 TGATAATAAAGTAAAATT
1 TGATAAAAAAATAAAATT
21561024 TGATAAAAAAATAAAAT
1 TGATAAAAAAATAAAAT
21561041 GATTATTAAA
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:0.63, C:0.00, G:0.09, T:0.29
Consensus pattern (18 bp):
TGATAAAAAAATAAAATT
Found at i:21561240 original size:22 final size:23
Alignment explanation
Indices: 21561215--21561266 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 23
21561205 AATAGTTTAG
21561215 AAAATAATTATAA-T-TTTATATC
1 AAAATAATTATAATTATTTAT-TC
*
21561237 AAAATAATTATTATTATTTATTC
1 AAAATAATTATAATTATTTATTC
21561260 AAAATAA
1 AAAATAA
21561267 AGTTTAAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 12 0.44
23 10 0.37
24 5 0.19
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (23 bp):
AAAATAATTATAATTATTTATTC
Found at i:21561774 original size:20 final size:20
Alignment explanation
Indices: 21561737--21561775 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
21561727 TAACTTTGTT
*
21561737 TTTTTATATATTTAATAAAA
1 TTTTTACATATTTAATAAAA
* *
21561757 TTTTTACATTTTTTATAAA
1 TTTTTACATATTTAATAAA
21561776 TGATACTCGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTTACATATTTAATAAAA
Found at i:21562193 original size:17 final size:17
Alignment explanation
Indices: 21562159--21562206 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
21562149 TTTATTGATT
*
21562159 AATATAATCA-TTATTAA
1 AATATAAT-ATTTAATAA
21562176 AATATAATATTTAATAA
1 AATATAATATTTAATAA
*
21562193 AATTTAAT-TTTAAT
1 AATATAATATTTAAT
21562207 TTCTAATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 7 0.25
17 21 0.75
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (17 bp):
AATATAATATTTAATAA
Found at i:21563886 original size:2 final size:2
Alignment explanation
Indices: 21563879--21563904 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
21563869 TGTTGTACAA
21563879 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
21563905 TGCAAAGTCT
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:21565400 original size:22 final size:22
Alignment explanation
Indices: 21565374--21565421 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
21565364 GTTGAAAGTT
21565374 TTTTATTA-TTAAGATATTAAAA
1 TTTTATTATTTAA-ATATTAAAA
*
21565396 TTTTATTATTTAAATATTAATA
1 TTTTATTATTTAAATATTAAAA
21565418 TTTT
1 TTTT
21565422 TTTAAAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (22 bp):
TTTTATTATTTAAATATTAAAA
Found at i:21573668 original size:2 final size:2
Alignment explanation
Indices: 21573661--21573688 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
21573651 TGAAGGAGTA
21573661 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
21573689 TACTTAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21579578 original size:13 final size:13
Alignment explanation
Indices: 21579558--21579592 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
21579548 AATTTAATTC
21579558 AAATTTAATATAT
1 AAATTTAATATAT
* *
21579571 ACATTTAATATTT
1 AAATTTAATATAT
21579584 AAATTTAAT
1 AAATTTAAT
21579593 TTTAACTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (13 bp):
AAATTTAATATAT
Found at i:21584479 original size:12 final size:12
Alignment explanation
Indices: 21584464--21584506 Score: 54
Period size: 11 Copynumber: 3.8 Consensus size: 12
21584454 AATATAATTT
21584464 AAAATTTTAATA
1 AAAATTTTAATA
*
21584476 AAAATTAT-ATA
1 AAAATTTTAATA
*
21584487 TAAA-TTTAATA
1 AAAATTTTAATA
21584498 AAAATTTTA
1 AAAATTTTA
21584507 TATTTAATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
10 2 0.08
11 12 0.48
12 11 0.44
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
AAAATTTTAATA
Found at i:21584532 original size:37 final size:39
Alignment explanation
Indices: 21584479--21584565 Score: 103
Period size: 38 Copynumber: 2.3 Consensus size: 39
21584469 TTTAATAAAA
21584479 ATTATATATAAATTTAATA-AA-AA-TTTTATATTTA-ATAT
1 ATTA-ATATAAATTTAA-ACAATAATTTTTAT-TTTACATAT
*
21584517 ATTAATATAATTTTAAACAATAATTTTTATTTTACATAT
1 ATTAATATAAATTTAAACAATAATTTTTATTTTACATAT
21584556 -TTAATATAAA
1 ATTAATATAAA
21584566 ATAGATACAA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
36 1 0.02
37 13 0.30
38 19 0.44
39 10 0.23
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.49
Consensus pattern (39 bp):
ATTAATATAAATTTAAACAATAATTTTTATTTTACATAT
Found at i:21587271 original size:17 final size:18
Alignment explanation
Indices: 21587245--21587278 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
21587235 CGTAATTTTA
21587245 AATATGA-TTTTAATTAT
1 AATATGATTTTTAATTAT
*
21587262 AATATTATTTTTAATTA
1 AATATGATTTTTAATTA
21587279 CATAATTACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (18 bp):
AATATGATTTTTAATTAT
Found at i:21588267 original size:17 final size:18
Alignment explanation
Indices: 21588240--21588275 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
21588230 TTAATTTAAA
21588240 TTTGAATCATTTTGATTT
1 TTTGAATCATTTTGATTT
21588258 TTTG-ATCATTTTGATTT
1 TTTGAATCATTTTGATTT
21588275 T
1 T
21588276 GAATTATTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.19, C:0.06, G:0.11, T:0.64
Consensus pattern (18 bp):
TTTGAATCATTTTGATTT
Found at i:21588443 original size:18 final size:18
Alignment explanation
Indices: 21588420--21588459 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
21588410 ATTTAAAAGC
* *
21588420 AATTTATTAATAATATAA
1 AATTTACTAAAAATATAA
21588438 AATTTACTAAAAATATAA
1 AATTTACTAAAAATATAA
21588456 AATT
1 AATT
21588460 ATGACACGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (18 bp):
AATTTACTAAAAATATAA
Found at i:21588534 original size:13 final size:13
Alignment explanation
Indices: 21588516--21588545 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
21588506 GTTTTTATAG
21588516 ATTTATATTTAAT
1 ATTTATATTTAAT
*
21588529 ATTTATTTTTAAT
1 ATTTATATTTAAT
21588542 ATTT
1 ATTT
21588546 CATACATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
ATTTATATTTAAT
Found at i:21588827 original size:15 final size:17
Alignment explanation
Indices: 21588805--21588843 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
21588795 TATTGAGAAG
*
21588805 ATAATTTTAA-AATTTA
1 ATAATTTTAATAATATA
21588821 A-AATTTTAATAATATA
1 ATAATTTTAATAATATA
21588837 ATAATTT
1 ATAATTT
21588844 ATGTTATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 8 0.40
16 7 0.35
17 5 0.25
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATAATTTTAATAATATA
Found at i:21596233 original size:20 final size:19
Alignment explanation
Indices: 21596208--21596256 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 19
21596198 ATGTGAATGG
*
21596208 TTTAAATTTA-CAATTAATTT
1 TTTAAATTTATC-ATT-ATAT
21596228 TTTAAAATTTATCATTATAT
1 TTT-AAATTTATCATTATAT
21596248 TTTAAATTT
1 TTTAAATTT
21596257 TAAAAATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 6 0.23
20 9 0.35
21 10 0.38
22 1 0.04
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTAAATTTATCATTATAT
Found at i:21596237 original size:21 final size:21
Alignment explanation
Indices: 21596211--21596268 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 21
21596201 TGAATGGTTT
21596211 AAATTTACAATTAATTTTTTA
1 AAATTTACAATTAATTTTTTA
*
21596232 AAATTTATC-ATT-ATATTTTA
1 AAATTTA-CAATTAATTTTTTA
* * *
21596252 AATTTTAAAAATAATTT
1 AAATTTACAATTAATTT
21596269 ATTATCATAC
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
20 15 0.52
21 13 0.45
22 1 0.03
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (21 bp):
AAATTTACAATTAATTTTTTA
Found at i:21602691 original size:5 final size:5
Alignment explanation
Indices: 21602676--21602706 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
21602666 CCTCCATGGC
*
21602676 AGAAA AAAAA AGAAA AGAAA AGAAA AGAAA A
1 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA A
21602707 AGGAAAGTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:21604841 original size:22 final size:22
Alignment explanation
Indices: 21604816--21604859 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
21604806 ATTTTTTTTC
**
21604816 CTTAATTCTAGGGATACAAATA
1 CTTAATTCTAGAAATACAAATA
21604838 CTTAATTCTAGAAATACAAATA
1 CTTAATTCTAGAAATACAAATA
21604860 TAGATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.32
Consensus pattern (22 bp):
CTTAATTCTAGAAATACAAATA
Found at i:21612773 original size:28 final size:28
Alignment explanation
Indices: 21612726--21612794 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 28
21612716 TAGTAAAATA
* *
21612726 TTTAATATAATAAATGAATT-TAAAATTT
1 TTTAATATGATAAATAAATTAT-AAATTT
*
21612754 TTTAATATGATACATAAATTATAAATTT
1 TTTAATATGATAAATAAATTATAAATTT
21612782 TAATTAATATGAT
1 T--TTAATATGAT
21612795 TATTTATCTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 24 0.69
29 1 0.03
30 10 0.29
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.46
Consensus pattern (28 bp):
TTTAATATGATAAATAAATTATAAATTT
Found at i:21626966 original size:23 final size:24
Alignment explanation
Indices: 21626940--21626988 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
21626930 ATGTTATAAA
*
21626940 TTTGTTG-AGATTTGTTAGGTTTT
1 TTTGTTGTAGATTTGTTAAGTTTT
*
21626963 TTTGTTGTATATTTGTTAAGTTTT
1 TTTGTTGTAGATTTGTTAAGTTTT
21626987 TT
1 TT
21626989 GTTAGGTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.14, C:0.00, G:0.20, T:0.65
Consensus pattern (24 bp):
TTTGTTGTAGATTTGTTAAGTTTT
Found at i:21628903 original size:18 final size:17
Alignment explanation
Indices: 21628868--21628913 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
21628858 TAGTAGTTTG
* *
21628868 TTTATTTATTTTTTATA
1 TTTATATATTTTTCATA
21628885 TTTATATATATTTTCATA
1 TTTATATAT-TTTTCATA
*
21628903 TTTATGTATTT
1 TTTATATATTT
21628914 ATTTTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 10 0.40
18 15 0.60
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (17 bp):
TTTATATATTTTTCATA
Found at i:21629692 original size:4 final size:4
Alignment explanation
Indices: 21629683--21629725 Score: 52
Period size: 4 Copynumber: 10.8 Consensus size: 4
21629673 CTTTAGGTAT
**
21629683 TTTA TTTA TTTA -TTA TTTA TTTA ACTA TTTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA TTT
21629726 GATTATCTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
3 3 0.09
4 28 0.85
5 2 0.06
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:21634274 original size:18 final size:18
Alignment explanation
Indices: 21634243--21634281 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
21634233 TTTTTTTTTG
* * *
21634243 AAAAATAATGAAAAATGA
1 AAAAAAAATAAAAAAAGA
21634261 AAAAAAAATAAAAAAAGA
1 AAAAAAAATAAAAAAAGA
21634279 AAA
1 AAA
21634282 GAAATTGATG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.82, C:0.00, G:0.08, T:0.10
Consensus pattern (18 bp):
AAAAAAAATAAAAAAAGA
Found at i:21634583 original size:14 final size:14
Alignment explanation
Indices: 21634573--21634608 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
21634563 GAAAAAATGT
21634573 GCAAAAAAAAAAAA
1 GCAAAAAAAAAAAA
*
21634587 GCAAAAAAAAAAGA
1 GCAAAAAAAAAAAA
21634601 G-AAAAAAA
1 GCAAAAAAA
21634609 GAATACCTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 7 0.33
14 14 0.67
ACGTcount: A:0.83, C:0.06, G:0.11, T:0.00
Consensus pattern (14 bp):
GCAAAAAAAAAAAA
Found at i:21636007 original size:17 final size:17
Alignment explanation
Indices: 21635985--21636086 Score: 107
Period size: 17 Copynumber: 6.0 Consensus size: 17
21635975 GAATTTATTA
*
21635985 CAAATCTAAAATTCTTG
1 CAAATCTTAAATTCTTG
* *
21636002 CGAATCTTAGATTCTTG
1 CAAATCTTAAATTCTTG
*
21636019 CAAACCTTAAATTCTTG
1 CAAATCTTAAATTCTTG
**
21636036 TGAATCTTAAATTCTTG
1 CAAATCTTAAATTCTTG
* *
21636053 CAAATCTGAAGTTCTTG
1 CAAATCTTAAATTCTTG
*
21636070 CAAA-CATGAAATTCTTG
1 CAAATC-TTAAATTCTTG
21636087 AAAACTTGAA
Statistics
Matches: 70, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
16 1 0.01
17 69 0.99
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (17 bp):
CAAATCTTAAATTCTTG
Found at i:21636048 original size:51 final size:51
Alignment explanation
Indices: 21635987--21636086 Score: 139
Period size: 51 Copynumber: 2.0 Consensus size: 51
21635977 ATTTATTACA
* * * *
21635987 AATCTAAAATTCTTGCGAATCT-TAGATTCTTGCAAACCTTAAATTCTTGTG
1 AATCTAAAATTCTTGCAAATCTGAAG-TTCTTGCAAACATGAAATTCTTGTG
*
21636038 AATCTTAAATTCTTGCAAATCTGAAGTTCTTGCAAACATGAAATTCTTG
1 AATCTAAAATTCTTGCAAATCTGAAGTTCTTGCAAACATGAAATTCTTG
21636087 AAAACTTGAA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
51 41 0.95
52 2 0.05
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (51 bp):
AATCTAAAATTCTTGCAAATCTGAAGTTCTTGCAAACATGAAATTCTTGTG
Found at i:21636068 original size:34 final size:34
Alignment explanation
Indices: 21635985--21636070 Score: 118
Period size: 34 Copynumber: 2.5 Consensus size: 34
21635975 GAATTTATTA
*
21635985 CAAATCTAAAATTCTTGCGAATCTTAGATTCTTG
1 CAAATCTAAAATTCTTGCGAATCTTAAATTCTTG
* * *
21636019 CAAACCTTAAATTCTTGTGAATCTTAAATTCTTG
1 CAAATCTAAAATTCTTGCGAATCTTAAATTCTTG
* *
21636053 CAAATCTGAAGTTCTTGC
1 CAAATCTAAAATTCTTGC
21636071 AAACATGAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 44 1.00
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (34 bp):
CAAATCTAAAATTCTTGCGAATCTTAAATTCTTG
Found at i:21636096 original size:17 final size:17
Alignment explanation
Indices: 21636012--21636096 Score: 59
Period size: 17 Copynumber: 5.0 Consensus size: 17
21636002 CGAATCTTAG
*
21636012 ATTCTTGCAAACCTT-AA
1 ATTCTTG-AAAACTTGAA
* *
21636029 ATTCTTGTGAATCTT-AA
1 ATTCTTG-AAAACTTGAA
*
21636046 ATTCTTGCAAA-TCTGAA
1 ATTCTTGAAAACT-TGAA
* * *
21636063 GTTCTTGCAAACATGAA
1 ATTCTTGAAAACTTGAA
21636080 ATTCTTGAAAACTTGAA
1 ATTCTTGAAAACTTGAA
21636097 GCTCTTGTGA
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
15 1 0.02
16 3 0.05
17 51 0.93
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.36
Consensus pattern (17 bp):
ATTCTTGAAAACTTGAA
Found at i:21636141 original size:17 final size:17
Alignment explanation
Indices: 21636059--21636141 Score: 76
Period size: 17 Copynumber: 4.9 Consensus size: 17
21636049 CTTGCAAATC
** *
21636059 TGAAGTTCTTGCAAACA
1 TGAAGTTCTTGTGAACT
* **
21636076 TGAAATTCTTGAAAACT
1 TGAAGTTCTTGTGAACT
*
21636093 TGAAGCTCTTGTGAACT
1 TGAAGTTCTTGTGAACT
* *
21636110 TGAAGTTATTGTGAATT
1 TGAAGTTCTTGTGAACT
*
21636127 TGAAGTTCTTATGAA
1 TGAAGTTCTTGTGAA
21636142 ACTTAGATCT
Statistics
Matches: 54, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 54 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (17 bp):
TGAAGTTCTTGTGAACT
Found at i:21636501 original size:17 final size:17
Alignment explanation
Indices: 21636473--21636532 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
21636463 CTGCAAAACT
*
21636473 TAAAATTTTTATGAATC
1 TAAAACTTTTATGAATC
* *
21636490 TGAAACTTTTATGAAAC
1 TAAAACTTTTATGAATC
*
21636507 TTAAAA-TCTTTGTGAATC
1 -TAAAACT-TTTATGAATC
21636525 TAAAACTT
1 TAAAACTT
21636533 CTGAGAATCT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
17 21 0.62
18 13 0.38
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (17 bp):
TAAAACTTTTATGAATC
Found at i:21636891 original size:43 final size:43
Alignment explanation
Indices: 21636810--21637051 Score: 256
Period size: 43 Copynumber: 5.6 Consensus size: 43
21636800 TATTTAAAGT
* *
21636810 TTTTAAAGTTG-TTAGCCTCTGTATAAAGAAGCTCATTTCTTA
1 TTTTAAAGTTGTTTAGCCTCTATATAAAAAAGCTCATTTCTTA
* ** *
21636852 CTTTAAAGTTGTTTAGTGTCTATATAAAAAAGCTTATTTCTTA
1 TTTTAAAGTTGTTTAGCCTCTATATAAAAAAGCTCATTTCTTA
* * * *
21636895 TTTTAAAGTTGTTTAGCCTTTATTTAAAAGAGCGCATTT-TCTA
1 TTTTAAAGTTGTTTAGCCTCTATATAAAAAAGCTCATTTCT-TA
* *
21636938 TTTTTAAGTTGTTTTAGCCTCTATATAAAAAAGCTCATTTATTAA
1 TTTTAAAGTTG-TTTAGCCTCTATATAAAAAAGCTCATTTCTT-A
* * * *
21636983 TTTTAAAGTTGTTTAGCCTTTGTATAGAGAAGC-CTATTTCTTA
1 TTTTAAAGTTGTTTAGCCTCTATATAAAAAAGCTC-ATTTCTTA
* * *
21637026 TTTTAAAATTATTTAGCCTCTTTATA
1 TTTTAAAGTTGTTTAGCCTCTATATA
21637052 GAAGAGTCTA
Statistics
Matches: 165, Mismatches: 29, Indels: 11
0.80 0.14 0.05
Matches are distributed among these distances:
42 11 0.07
43 93 0.56
44 49 0.30
45 12 0.07
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.47
Consensus pattern (43 bp):
TTTTAAAGTTGTTTAGCCTCTATATAAAAAAGCTCATTTCTTA
Found at i:21636962 original size:87 final size:87
Alignment explanation
Indices: 21636810--21637051 Score: 269
Period size: 88 Copynumber: 2.8 Consensus size: 87
21636800 TATTTAAAGT
* * * **
21636810 TTTTAAAGTTG-TTAGCCTCTGTATAAAGAAGCTCATTTCTTACTTTAAAGTTGTTTAGTGTCTA
1 TTTTAAAGTTGTTTAGCCTTTATATAAAGAAGCGCATTTCTTACTTTAAAGTTGTTTAGCCTCTA
* *
21636874 TATAAAAAAGCTTATTTCTT-A
66 TATAAAAAAGCTCATTTATTAA
* * *
21636895 TTTTAAAGTTGTTTAGCCTTTATTTAAA-AGAGCGCATTT-TCTATTTTTAAGTTGTTTTAGCCT
1 TTTTAAAGTTGTTTAGCCTTTATATAAAGA-AGCGCATTTCT-TACTTTAAAGTTG-TTTAGCCT
21636958 CTATATAAAAAAGCTCATTTATTAA
63 CTATATAAAAAAGCTCATTTATTAA
* * * * *
21636983 TTTTAAAGTTGTTTAGCCTTTGTATAGAGAAGC-CTATTTCTTATTTTAAAATTATTTAGCCTCT
1 TTTTAAAGTTGTTTAGCCTTTATATAAAGAAGCGC-ATTTCTTACTTTAAAGTTGTTTAGCCTCT
*
21637047 TTATA
65 ATATA
21637052 GAAGAGTCTA
Statistics
Matches: 132, Mismatches: 17, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
85 13 0.10
86 32 0.24
87 42 0.32
88 43 0.33
89 2 0.02
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.47
Consensus pattern (87 bp):
TTTTAAAGTTGTTTAGCCTTTATATAAAGAAGCGCATTTCTTACTTTAAAGTTGTTTAGCCTCTA
TATAAAAAAGCTCATTTATTAA
Found at i:21637074 original size:43 final size:43
Alignment explanation
Indices: 21636984--21637100 Score: 105
Period size: 43 Copynumber: 2.7 Consensus size: 43
21636974 ATTTATTAAT
* * * * *
21636984 TTTAAAGTTGTTTAGCCT-TTGTATAG-AGAAGCCTATTTCTTAT
1 TTTAAAATTATTTAGCCTCTT-TATAGAAG-AGTCTATTTCTCAA
21637027 TTTAAAATTATTTAGCCTCTTTATAGAAGAGTCTATTTCTCAA
1 TTTAAAATTATTTAGCCTCTTTATAGAAGAGTCTATTTCTCAA
* * * * *
21637070 TTT-AATTTTTTTTGCCTCTGTATAGAGGAGT
1 TTTAAAATTATTTAGCCTCTTTATAGAAGAGT
21637101 TTCATTTGTT
Statistics
Matches: 62, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
42 23 0.37
43 35 0.56
44 4 0.06
ACGTcount: A:0.26, C:0.12, G:0.15, T:0.47
Consensus pattern (43 bp):
TTTAAAATTATTTAGCCTCTTTATAGAAGAGTCTATTTCTCAA
Found at i:21637889 original size:15 final size:15
Alignment explanation
Indices: 21637865--21637903 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
21637855 TACGTTATGA
21637865 TATTACCGACAGAAT
1 TATTACCGACAGAAT
*
21637880 TATTATCGACAGAA-
1 TATTACCGACAGAAT
21637894 T-TTACCGACA
1 TATTACCGACA
21637904 AAAAATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 8 0.36
14 1 0.05
15 13 0.59
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.28
Consensus pattern (15 bp):
TATTACCGACAGAAT
Found at i:21639147 original size:44 final size:44
Alignment explanation
Indices: 21639097--21639187 Score: 146
Period size: 44 Copynumber: 2.1 Consensus size: 44
21639087 CCAACCCATT
21639097 TTAATCATAAAAAATTTTATAAAATTTTCAACTCAAAATCAAAA
1 TTAATCATAAAAAATTTTATAAAATTTTCAACTCAAAATCAAAA
* * * *
21639141 TTAATCATAAAAAGTTTTATAAAATTTTTAATTCAAACTCAAAA
1 TTAATCATAAAAAATTTTATAAAATTTTCAACTCAAAATCAAAA
21639185 TTA
1 TTA
21639188 CCTAATTCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.52, C:0.10, G:0.01, T:0.37
Consensus pattern (44 bp):
TTAATCATAAAAAATTTTATAAAATTTTCAACTCAAAATCAAAA
Found at i:21639261 original size:26 final size:25
Alignment explanation
Indices: 21639231--21639283 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 25
21639221 AAAAAAAAGT
** *
21639231 AAATTATTCGAATTTAAAATTAACTC
1 AAATTATTAAAATCTAAAA-TAACTC
*
21639257 AAATTTTTAAAATCTAAAATAACTC
1 AAATTATTAAAATCTAAAATAACTC
21639282 AA
1 AA
21639284 TCTAAATCTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 8 0.35
26 15 0.65
ACGTcount: A:0.51, C:0.11, G:0.02, T:0.36
Consensus pattern (25 bp):
AAATTATTAAAATCTAAAATAACTC
Found at i:21639503 original size:26 final size:25
Alignment explanation
Indices: 21639469--21639522 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 25
21639459 TATTTTATTG
*
21639469 TAATTAATTAATTATAGAATTACAA
1 TAATTAATTAATTATAAAATTACAA
*
21639494 TAATATAATTAATTATAAAATTATAA
1 TAAT-TAATTAATTATAAAATTACAA
21639520 TAA
1 TAA
21639523 AAAATTATAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 4 0.15
26 22 0.85
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (25 bp):
TAATTAATTAATTATAAAATTACAA
Found at i:21642191 original size:6 final size:6
Alignment explanation
Indices: 21642180--21642344 Score: 62
Period size: 6 Copynumber: 27.8 Consensus size: 6
21642170 TAATATAATA
*
21642180 TTAAAT TTAAAT TT-AA- TTAAATT TTATAT TTAAAT TTAAAT TT-AAT
1 TTAAAT TTAAAT TTAAAT TTAAA-T TTAAAT TTAAAT TTAAAT TTAAAT
** * *
21642226 TTAATAT AAAAAT TAAATTAT TTAAAT TT--AT TT-AA- TTAAAT TT-GA-
1 TTAA-AT TTAAAT TTAA--AT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* * * * * **
21642271 TTAATAT ATAAAA ATAAAT TTAATTT TTATAT TT-AAT AAAAAT TTAATTAT
1 TTAA-AT TTAAAT TTAAAT TTAA-AT TTAAAT TTAAAT TTAAAT TTAA--AT
**
21642322 TTATGT TTAAAT TTAAAT TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAA
21642345 ATATTTTATC
Statistics
Matches: 118, Mismatches: 24, Indels: 34
0.67 0.14 0.19
Matches are distributed among these distances:
4 10 0.08
5 15 0.13
6 68 0.58
7 15 0.13
8 10 0.08
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (6 bp):
TTAAAT
Found at i:21642228 original size:23 final size:23
Alignment explanation
Indices: 21642175--21642343 Score: 87
Period size: 24 Copynumber: 7.1 Consensus size: 23
21642165 CAAATTAATA
*
21642175 TAATATTAAATTTAAATTT-AATT
1 TAAT-TTATATTTAAATTTAAATT
*
21642198 AAATTTTATATTTAAATTTAAATT
1 TAA-TTTATATTTAAATTTAAATT
** *
21642222 TAATTTAATATAAAAATTAAATTATT
1 TAATTT-ATATTTAAATTTAA--ATT
*
21642248 TAAATT-TATTT-AA-TTAAATT
1 TAATTTATATTTAAATTTAAATT
* * * **
21642268 TGATTAATATATAAAAATAAATT
1 TAATTTATATTTAAATTTAAATT
**
21642291 TAATTTTTATATTT-AATAAAAATT
1 TAA--TTTATATTTAAATTTAAATT
*
21642315 TAATTATTTATGTTTAAATTTAAATT
1 T-A--ATTTATATTTAAATTTAAATT
21642341 TAA
1 TAA
21642344 AATATTTTAT
Statistics
Matches: 109, Mismatches: 23, Indels: 28
0.68 0.14 0.17
Matches are distributed among these distances:
20 6 0.06
21 4 0.04
22 5 0.05
23 29 0.27
24 30 0.28
25 17 0.16
26 17 0.16
27 1 0.01
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (23 bp):
TAATTTATATTTAAATTTAAATT
Found at i:21642231 original size:52 final size:47
Alignment explanation
Indices: 21642169--21642295 Score: 132
Period size: 52 Copynumber: 2.6 Consensus size: 47
21642159 TGAGTTCAAA
* *
21642169 TTAATATAATATTAAATTTAAATTTAATTAAATTTTATATTTAAATTTAAAT
1 TTAATTTAATATTAAAATTAAATTTAATTAAA--TT-TATTT-AA-TTAAAT
* *
21642221 TTAATTTAATATAAAAATTAAA-TTATTTAAATTTATTTAATTAAAT
1 TTAATTTAATATTAAAATTAAATTTAATTAAATTTATTTAATTAAAT
* *
21642267 TTGA-TTAATATATAAAAATAAATTTAATT
1 TTAATTTAATAT-TAAAATTAAATTTAATT
21642296 TTTATATTTA
Statistics
Matches: 65, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
45 7 0.11
46 17 0.26
47 7 0.11
48 5 0.08
49 2 0.03
51 8 0.12
52 19 0.29
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.50
Consensus pattern (47 bp):
TTAATTTAATATTAAAATTAAATTTAATTAAATTTATTTAATTAAAT
Found at i:21642274 original size:10 final size:10
Alignment explanation
Indices: 21642186--21642260 Score: 50
Period size: 10 Copynumber: 7.4 Consensus size: 10
21642176 AATATTAAAT
21642186 TTAAATTTAA
1 TTAAATTTAA
21642196 TTAAATTTTATA
1 TTAAA-TTTA-A
21642208 TTTAAATTTAAA
1 -TTAAATTT-AA
*
21642220 TTTAATTTAA
1 TTAAATTTAA
21642230 TATAAA---AA
1 T-TAAATTTAA
*
21642238 TTAAA-TTAT
1 TTAAATTTAA
*
21642247 TTAAATTTAT
1 TTAAATTTAA
21642257 TTAA
1 TTAA
21642261 TTAAATTTGA
Statistics
Matches: 54, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
7 4 0.07
8 3 0.06
9 6 0.11
10 16 0.30
11 14 0.26
12 5 0.09
13 6 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
TTAAATTTAA
Found at i:21642381 original size:10 final size:10
Alignment explanation
Indices: 21642356--21642385 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
21642346 TATTTTATCA
21642356 ATTAAAATAT
1 ATTAAAATAT
21642366 -TTAAAATAT
1 ATTAAAATAT
21642375 ATTAAAATAT
1 ATTAAAATAT
21642385 A
1 A
21642386 AAAATTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
ATTAAAATAT
Found at i:21642387 original size:26 final size:25
Alignment explanation
Indices: 21642336--21642394 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 25
21642326 GTTTAAATTT
* *
21642336 AAATTTAAAATATTTTATCAATTAA
1 AAATTTAAAATATATTATAAATTAA
21642361 AATATTTAAAATATATTA-AAATATAA
1 AA-ATTTAAAATATATTATAAAT-TAA
21642387 AAATTTAA
1 AAATTTAA
21642395 TTAAATTCGT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 11 0.37
26 19 0.63
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (25 bp):
AAATTTAAAATATATTATAAATTAA
Found at i:21642397 original size:19 final size:20
Alignment explanation
Indices: 21642355--21642399 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
21642345 ATATTTTATC
*
21642355 AATTAAAATATTTAAAATAT
1 AATTAAAATATTAAAAATAT
*
21642375 -ATTAAAATA-TAAAAATTT
1 AATTAAAATATTAAAAATAT
21642393 AATTAAA
1 AATTAAA
21642400 TTCGTAAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AATTAAAATATTAAAAATAT
Found at i:21651710 original size:3 final size:3
Alignment explanation
Indices: 21651702--21651732 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
21651692 ATTCATAGTA
21651702 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
21651733 TAGCTAGTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:21655243 original size:26 final size:27
Alignment explanation
Indices: 21655203--21655259 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 27
21655193 TTTTCTTAAA
* * *
21655203 TTCAAAAAATTAAAAGTTAAAACTATT
1 TTCAAAAAATTAAAAATGAAAAATATT
21655230 TTCAAAAAA-TAAAAATGAAAAATATT
1 TTCAAAAAATTAAAAATGAAAAATATT
21655256 TTCA
1 TTCA
21655260 TTAACTAATC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 18 0.67
27 9 0.33
ACGTcount: A:0.58, C:0.07, G:0.04, T:0.32
Consensus pattern (27 bp):
TTCAAAAAATTAAAAATGAAAAATATT
Found at i:21662199 original size:12 final size:12
Alignment explanation
Indices: 21662182--21662233 Score: 56
Period size: 12 Copynumber: 4.5 Consensus size: 12
21662172 GATAGAGTAA
21662182 ATATAGTATTAC
1 ATATAGTATTAC
21662194 ATATAGTATTAC
1 ATATAGTATTAC
**
21662206 ACGTCAGTA--A-
1 ATAT-AGTATTAC
21662216 ATATAGTATTAC
1 ATATAGTATTAC
21662228 ATATAG
1 ATATAG
21662234 CATATTCCAG
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
9 4 0.12
10 2 0.06
11 2 0.06
12 20 0.62
13 4 0.12
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.37
Consensus pattern (12 bp):
ATATAGTATTAC
Found at i:21663804 original size:6 final size:6
Alignment explanation
Indices: 21663793--21663819 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
21663783 TTTTGATCTG
21663793 GCAGGT GCAGGT GCAGGT GCAGGT GCA
1 GCAGGT GCAGGT GCAGGT GCAGGT GCA
21663820 AGGGCAGGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.48, T:0.15
Consensus pattern (6 bp):
GCAGGT
Found at i:21672807 original size:49 final size:48
Alignment explanation
Indices: 21672678--21672816 Score: 147
Period size: 49 Copynumber: 2.9 Consensus size: 48
21672668 AAGTTAGACC
* * * *
21672678 TGTATAAATGA-AAAATTTTGAAATTATATAAATGAAAAACTTTGAACT
1 TGTATAAATCATAAAA-TTTGAAATTGTATAAATAAAAAATTTTGAACT
* * *
21672726 TGTATAAATCATAAAATTTGGACA-TGTTTAAATAAAAAAATTTTGGACT
1 TGTATAAATCATAAAATTT-GAAATTGTATAAAT-AAAAAATTTTGAACT
* *
21672775 TGTATTAATCATAAAATTTGAATTTGTATAAATGAAAAAATT
1 TGTATAAATCATAAAATTTGAAATTGTATAAAT-AAAAAATT
21672817 ATTTACATTG
Statistics
Matches: 75, Mismatches: 12, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
48 22 0.29
49 53 0.71
ACGTcount: A:0.47, C:0.04, G:0.11, T:0.37
Consensus pattern (48 bp):
TGTATAAATCATAAAATTTGAAATTGTATAAATAAAAAATTTTGAACT
Found at i:21672814 original size:24 final size:24
Alignment explanation
Indices: 21672660--21672816 Score: 136
Period size: 24 Copynumber: 6.5 Consensus size: 24
21672650 GTCATTTATG
* *
21672660 AATGAAAAAAGTT-AGACCTGTATA
1 AATGAAAAAATTTGA-ACTTGTATA
* * *
21672684 AATGAAAAATTTTGAAATTATATA
1 AATGAAAAAATTTGAACTTGTATA
*
21672708 AATGAAAAACTTTGAACTTGTATA
1 AATGAAAAAATTTGAACTTGTATA
* * * * *
21672732 AATCATAAAATTTGGACATGTTTA
1 AATGAAAAAATTTGAACTTGTATA
* * *
21672756 AATAAAAAAATTTTGGACTTGTATT
1 AATGAAAAAA-TTTGAACTTGTATA
* * *
21672781 AATCATAAAATTTGAATTTGTATA
1 AATGAAAAAATTTGAACTTGTATA
21672805 AATGAAAAAATT
1 AATGAAAAAATT
21672817 ATTTACATTG
Statistics
Matches: 105, Mismatches: 26, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
24 85 0.81
25 20 0.19
ACGTcount: A:0.48, C:0.05, G:0.11, T:0.35
Consensus pattern (24 bp):
AATGAAAAAATTTGAACTTGTATA
Found at i:21673070 original size:36 final size:36
Alignment explanation
Indices: 21673030--21673102 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
21673020 CCAATCAATA
**
21673030 TGCAATTCATAATTGTGTTTAAGTTAGAAACATGTT
1 TGCAATTCATAATTGTGTTTAAGGGAGAAACATGTT
*
21673066 TGCAATTCATAATTGTGTTTAGGGGAGAAACATGTT
1 TGCAATTCATAATTGTGTTTAAGGGAGAAACATGTT
21673102 T
1 T
21673103 ATGTACTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.32, C:0.08, G:0.21, T:0.40
Consensus pattern (36 bp):
TGCAATTCATAATTGTGTTTAAGGGAGAAACATGTT
Found at i:21673921 original size:25 final size:26
Alignment explanation
Indices: 21673888--21673937 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
21673878 AATACCGATA
*
21673888 TATACTATATATGAATGAATATATAT
1 TATACTATATATAAATGAATATATAT
*
21673914 TATA-TATATTTAAATGAATATATA
1 TATACTATATATAAATGAATATATA
21673938 AGGGAACTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (26 bp):
TATACTATATATAAATGAATATATAT
Found at i:21675365 original size:42 final size:41
Alignment explanation
Indices: 21675307--21675393 Score: 129
Period size: 42 Copynumber: 2.1 Consensus size: 41
21675297 TATAAAGAAC
*
21675307 AAATTAAAACATATGAACAAGGCAGTGTAATTGCATTCCAT
1 AAATTAAAACATATGAACAAGGCAGTGCAATTGCATTCCAT
* * *
21675348 AAATTAAAAACATATGAATAAGGTAGTGCAATTGCATTTCAT
1 AAATT-AAAACATATGAACAAGGCAGTGCAATTGCATTCCAT
21675390 AAAT
1 AAAT
21675394 AATAGACATT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 5 0.12
42 36 0.88
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.29
Consensus pattern (41 bp):
AAATTAAAACATATGAACAAGGCAGTGCAATTGCATTCCAT
Found at i:21676208 original size:55 final size:55
Alignment explanation
Indices: 21676115--21676475 Score: 282
Period size: 55 Copynumber: 6.5 Consensus size: 55
21676105 AACAACAACA
* * *
21676115 AAAGGCTACGTTTCTA-ATTCATAAA-GATAATGATTGTAAATTTTTTTTTCAATC
1 AAAGACTACATTTCTACTTTCATAAATG-TAATGATTGTAAATTTTTTTTTCAATC
* * * *
21676169 AAATATTATATTTCTACTTTCATAAATGTAATGATTGTAATTTTTTTTTTCAATC
1 AAAGACTACATTTCTACTTTCATAAATGTAATGATTGTAAATTTTTTTTTCAATC
* * * * * * * *
21676224 AAGGACTACGTTTATTCTTTCATAAACG-AAGTGACTATAAATTTTTGTTTTC-ATA
1 AAAGACTACATTTCTACTTTCATAAATGTAA-TGATTGTAAATTTTT-TTTTCAATC
* * * * *
21676279 AAAGACTACATTTTTACTTTCCTAAATGTAACGATTGTCAATTTTTTTTTCAAAC
1 AAAGACTACATTTCTACTTTCATAAATGTAATGATTGTAAATTTTTTTTTCAATC
* * * *
21676334 AAAGAAAACTACATTTCTACTTTTATAAAAGTAGTGATTGTAAAATTTTTTTTCAATC
1 AAAG---ACTACATTTCTACTTTCATAAATGTAATGATTGTAAATTTTTTTTTCAATC
* ** ** ** * *
21676392 AAAGATTATGTAACTACTTTCATAAACATAGTGATTGTAAA-TTTTTTTTCAACC
1 AAAGACTACATTTCTACTTTCATAAATGTAATGATTGTAAATTTTTTTTTCAATC
* * ** * *
21676446 AAATATTATGTTTATATTTTCATAAATGTA
1 AAAGACTACATTTCTACTTTCATAAATGTA
21676476 GTTTCTACTT
Statistics
Matches: 242, Mismatches: 56, Indels: 18
0.77 0.18 0.06
Matches are distributed among these distances:
54 53 0.22
55 135 0.56
56 8 0.03
58 46 0.19
ACGTcount: A:0.35, C:0.11, G:0.09, T:0.44
Consensus pattern (55 bp):
AAAGACTACATTTCTACTTTCATAAATGTAATGATTGTAAATTTTTTTTTCAATC
Found at i:21676410 original size:113 final size:110
Alignment explanation
Indices: 21676132--21676448 Score: 316
Period size: 110 Copynumber: 2.9 Consensus size: 110
21676122 ACGTTTCTAA
* *
21676132 TTCAT-AAAGATAATGATTGTAAATTTTTTTTTCAATCAAATATTATATTTCTACTTTCATAAAT
1 TTCATAAAAGA-AGTGATTGTAAATTTTTTTTTCAATCAAAGATTATATTTCTACTTTCATAAAT
* * * *
21676196 GTAATGATTGTAATTTTTTTTTTCAATC-AAGGACTACGTTTATTCT
65 GTAATGATTGTAA-TTTTTTTTTCAAACAAAGAACTACATTTATACT
* * * * * * * *
21676242 TTCATAAACGAAGTGACTATAAATTTTTGTTTTC-ATAAAAGACTACATTTTTACTTTCCTAAAT
1 TTCATAAAAGAAGTGATTGTAAATTTTT-TTTTCAATCAAAGATTATATTTCTACTTTCATAAAT
* *
21676306 GTAACGATTGTCAATTTTTTTTTCAAACAAAGAAAACTACATTTCTACT
65 GTAATGATTGT-AATTTTTTTTTCAAACAAAG--AACTACATTTATACT
* * * * ** **
21676355 TTTATAAAAGTAGTGATTGTAAAATTTTTTTTCAATCAAAGATTATGTAACTACTTTCATAAACA
1 TTCATAAAAGAAGTGATTGTAAATTTTTTTTTCAATCAAAGATTATATTTCTACTTTCATAAATG
* * *
21676420 TAGTGATTGTAAATTTTTTTTCAACCAAA
66 TAATGATTGTAATTTTTTTTTCAAACAAA
21676449 TATTATGTTT
Statistics
Matches: 164, Mismatches: 36, Indels: 12
0.77 0.17 0.06
Matches are distributed among these distances:
110 66 0.40
111 14 0.09
112 22 0.13
113 62 0.38
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.44
Consensus pattern (110 bp):
TTCATAAAAGAAGTGATTGTAAATTTTTTTTTCAATCAAAGATTATATTTCTACTTTCATAAATG
TAATGATTGTAATTTTTTTTTCAAACAAAGAACTACATTTATACT
Found at i:21678484 original size:22 final size:24
Alignment explanation
Indices: 21678438--21678482 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
21678428 ATATTACAGT
21678438 AAAAAAAATATTACAACTAATTTG
1 AAAAAAAATATTACAACTAATTTG
21678462 AAAAAAAAT-TT-CTAACTAATT
1 AAAAAAAATATTAC-AACTAATT
21678483 GAGTGAATAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 1 0.05
23 10 0.50
24 9 0.45
ACGTcount: A:0.58, C:0.09, G:0.02, T:0.31
Consensus pattern (24 bp):
AAAAAAAATATTACAACTAATTTG
Found at i:21679328 original size:230 final size:227
Alignment explanation
Indices: 21678726--21679407 Score: 872
Period size: 230 Copynumber: 3.0 Consensus size: 227
21678716 TAGGGTTTTC
* * * *
21678726 TTGAAATTGTTTTGGTATTTATTTTTTTTTTTCACATTTCCTTTGTGAAATATATTTAAAAATTG
1 TTGAAGTTGTTTTGGTATTTA--TATTTTTTTCACATTTTCTTTGTGAAATATATTTAAAAACTG
* * * * *
21678791 AAGATAATGCAACAATTATTTATAAAAATATTAAAGATGA-TAAAAAATATTTTTAAAAATTGTG
64 AAGATAATGTAATAATTATTTATAAAAAAATTAAAGAT-ATTAAATAATATTTTTAAAAGTTGTG
* *
21678855 ATAAATTTAAATACTTATGTTAACTGTAGATAAATTG-AAAAAA-AAA-TTTTTAAAATTAATTT
128 ATAAATTTAAATACTCATGTTAACTATAGATAAATTGAAAAAAATAAATTTTTTAAAATTAATTT
* * * * * *
21678917 TAAATTAAGATAAGGTAATGTATAGGAGAAATTTC
193 TAAATTGAGATGAGATAAGGTATAAGAGAAATTTA
* * * * *
21678952 CTAAAGTTATTTTGGTATTTATATATTTTTTTTACATTTTCTTTGCGAAATATATTTAAAAACTG
1 TTGAAGTTGTTTTGGTA-TT-TATATTTTTTTCACATTTTCTTTGTGAAATATATTTAAAAACTG
* *
21679017 AAGATAATGTAATAATTATTTATAAAAAAAATTAAATATATTAAATAATATTTTTAAAAGTTGTA
64 AAGATAATGTAATAATTATTTAT-AAAAAAATTAAAGATATTAAATAATATTTTTAAAAGTTGTG
*
21679082 ATAAATTTAAATACTCATGTTAACTATAAATAAATTGAAAAAAATAAATTGTTTTAAAATTAATT
128 ATAAATTTAAATACTCATGTTAACTATAGATAAATTGAAAAAAATAAATT-TTTTAAAATTAATT
* *
21679147 TTAAATTGAGATGATATGAGGTATAAGAGAAACTTTA
192 TTAAATTGAGATGAGATAAGGTATAAGAGAAA-TTTA
* * * * * *
21679184 TTGAAGTTGTTCTGGTATTTATATTTTTTTCATATTTATTTTTGTAAAATATATTTAAAAGCTAA
1 TTGAAGTTGTTTTGGTATTTATATTTTTTTCACATTT-TCTTTGTGAAATATATTTAAAAACTGA
*
21679249 AGATAATGTAATAATTATTTATAAAAAAATTAAAGATATTAAATAATATTTTTAAAAGTTATGAT
65 AGATAATGTAATAATTATTTATAAAAAAATTAAAGATATTAAATAATATTTTTAAAAGTTGTGAT
* * *
21679314 AAATTTAAATACTCATGTTAACTTTAGATAAATT-AAAAAAATAAATTACTTTAAAATTAGTTTT
130 AAATTTAAATACTCATGTTAACTATAGATAAATTGAAAAAAATAAATT-TTTTAAAATTAATTTT
* *
21679378 AAATTGAGATGA-AGTAATGTATAGGAGAAA
194 AAATTGAGATGAGA-TAAGGTATAAGAGAAA
21679408 GAAATTTGAT
Statistics
Matches: 396, Mismatches: 49, Indels: 19
0.85 0.11 0.04
Matches are distributed among these distances:
226 72 0.18
227 70 0.18
228 9 0.02
229 55 0.14
230 89 0.22
231 85 0.21
232 16 0.04
ACGTcount: A:0.44, C:0.04, G:0.10, T:0.42
Consensus pattern (227 bp):
TTGAAGTTGTTTTGGTATTTATATTTTTTTCACATTTTCTTTGTGAAATATATTTAAAAACTGAA
GATAATGTAATAATTATTTATAAAAAAATTAAAGATATTAAATAATATTTTTAAAAGTTGTGATA
AATTTAAATACTCATGTTAACTATAGATAAATTGAAAAAAATAAATTTTTTAAAATTAATTTTAA
ATTGAGATGAGATAAGGTATAAGAGAAATTTA
Found at i:21679851 original size:28 final size:31
Alignment explanation
Indices: 21679817--21679887 Score: 112
Period size: 28 Copynumber: 2.4 Consensus size: 31
21679807 ATTAATAAAT
*
21679817 TTATAATTTAAATATTATATTAAA-ATTTT-
1 TTATAATTTAAATAGTATATTAAATATTTTA
21679846 TT-TAATTTAAATAGTATATTAAATATTTTA
1 TTATAATTTAAATAGTATATTAAATATTTTA
21679876 TTATAATTTAAA
1 TTATAATTTAAA
21679888 AATCATTCTT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
28 20 0.53
29 7 0.18
30 2 0.05
31 9 0.24
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (31 bp):
TTATAATTTAAATAGTATATTAAATATTTTA
Found at i:21680069 original size:2 final size:2
Alignment explanation
Indices: 21680062--21680099 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
21680052 ATTCCCTCCA
21680062 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21680100 TAGTATTATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21680553 original size:22 final size:22
Alignment explanation
Indices: 21680527--21680568 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
21680517 ATAAATGATC
* *
21680527 ATTAATAAAATTTAAATTTTTT
1 ATTAAAAAAATATAAATTTTTT
21680549 ATTAAAAAAATATAAATTTT
1 ATTAAAAAAATATAAATTTT
21680569 AATTAATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATTAAAAAAATATAAATTTTTT
Found at i:21680573 original size:21 final size:22
Alignment explanation
Indices: 21680527--21680574 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
21680517 ATAAATGATC
* * *
21680527 ATTAATAAAATTTAAATTTTTT
1 ATTAAAAAAATATAAATTTTTA
21680549 ATTAAAAAAATATAAA-TTTTA
1 ATTAAAAAAATATAAATTTTTA
21680570 ATTAA
1 ATTAA
21680575 TTATAATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
ATTAAAAAAATATAAATTTTTA
Found at i:21681487 original size:21 final size:21
Alignment explanation
Indices: 21681439--21681487 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
21681429 TTAAAAAATG
*
21681439 ATAATAATAATAAAATTAATT
1 ATAATAATAATAAAATTAAGT
* * *
21681460 ATTATAATATTAAAATTGAGT
1 ATAATAATAATAAAATTAAGT
21681481 ATAATAA
1 ATAATAA
21681488 CGATGAAAGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (21 bp):
ATAATAATAATAAAATTAAGT
Found at i:21682467 original size:26 final size:26
Alignment explanation
Indices: 21682398--21682467 Score: 70
Period size: 26 Copynumber: 2.7 Consensus size: 26
21682388 GATTTAAACA
* * *
21682398 TATTTT-ATAATTCGTGTCGTGTTCG
1 TATTTTAATAATTCGTATCGTATTAG
* ** *
21682423 TGTTTTAATAATTTATATCGTATTAT
1 TATTTTAATAATTCGTATCGTATTAG
21682449 TATTTTAATAATTCGTATC
1 TATTTTAATAATTCGTATC
21682468 ATTATACGTG
Statistics
Matches: 34, Mismatches: 10, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
25 5 0.15
26 29 0.85
ACGTcount: A:0.26, C:0.09, G:0.11, T:0.54
Consensus pattern (26 bp):
TATTTTAATAATTCGTATCGTATTAG
Found at i:21695658 original size:15 final size:14
Alignment explanation
Indices: 21695629--21695677 Score: 62
Period size: 15 Copynumber: 3.4 Consensus size: 14
21695619 GCTGCTCTTT
*
21695629 TTCTTTTCCTTTTC
1 TTCTTTTTCTTTTC
21695643 TTCTTTTTCTTCTTC
1 TTCTTTTTCTT-TTC
*
21695658 TTCTTATTCTTTCTC
1 TTCTTTTTCTTT-TC
21695673 TTCTT
1 TTCTT
21695678 CTTGGGTTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
14 11 0.35
15 20 0.65
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.71
Consensus pattern (14 bp):
TTCTTTTTCTTTTC
Found at i:21697120 original size:2 final size:2
Alignment explanation
Indices: 21697113--21697152 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
21697103 AGTTTGCACT
21697113 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
21697153 AGAACAATGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:21697524 original size:1 final size:1
Alignment explanation
Indices: 21697518--21697542 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
21697508 CCCACCACCG
21697518 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
21697543 GCCTCCCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:21699159 original size:28 final size:30
Alignment explanation
Indices: 21699072--21699222 Score: 131
Period size: 30 Copynumber: 5.2 Consensus size: 30
21699062 AAATAAAAAA
* *
21699072 AAAT-AATTCTAAACTTTATTATTT-TATTT
1 AAATAAATTCTTAACTTT-TAATTTATATTT
* *
21699101 AAATAAATT-TTATA-TTTT-A-TTACATTC
1 AAATAAATTCTTA-ACTTTTAATTTATATTT
*
21699128 AAATAAAAAT-TTAACTTTTAA-TT-TATTT
1 AAAT-AAATTCTTAACTTTTAATTTATATTT
* * *
21699156 AAATAAACTCTTAAATTTTAATTTGTATTT
1 AAATAAATTCTTAACTTTTAATTTATATTT
*
21699186 ACATAAATTCTTAACTTTTAATTTATATTT
1 AAATAAATTCTTAACTTTTAATTTATATTT
21699216 AAATAAA
1 AAATAAA
21699223 CTTTTAATAT
Statistics
Matches: 100, Mismatches: 13, Indels: 17
0.77 0.10 0.13
Matches are distributed among these distances:
26 2 0.02
27 13 0.13
28 29 0.29
29 14 0.14
30 42 0.42
ACGTcount: A:0.42, C:0.07, G:0.01, T:0.50
Consensus pattern (30 bp):
AAATAAATTCTTAACTTTTAATTTATATTT
Found at i:21699245 original size:30 final size:29
Alignment explanation
Indices: 21699093--21699245 Score: 111
Period size: 30 Copynumber: 5.3 Consensus size: 29
21699083 AACTTTATTA
21699093 TTTTATTTAAATAAA-TTTTATATTTT-A-
1 TTTTATTTAAATAAACTTTTA-ATTTTAAT
** * **
21699120 TTACATTCAAATAAAAATTTAACTTTTAA-
1 TTTTATTTAAATAAACTTTTAA-TTTTAAT
*
21699149 -TTTATTTAAATAAACTCTTAAATTTTAAT
1 TTTTATTTAAATAAACT-TTTAATTTTAAT
* *
21699178 TTGTATTTACATAAA-TTCTTAACTTTTAAT
1 TTTTATTTAAATAAACTT-TTAA-TTTTAAT
* * *
21699208 TTATATTTAAATAAACTTTTAATATAAAT
1 TTTTATTTAAATAAACTTTTAATTTTAAT
21699237 TATTTATTT
1 T-TTTATTT
21699246 GAAAAAAGTA
Statistics
Matches: 98, Mismatches: 18, Indels: 17
0.74 0.14 0.13
Matches are distributed among these distances:
27 13 0.13
28 26 0.27
29 15 0.15
30 42 0.43
31 2 0.02
ACGTcount: A:0.41, C:0.06, G:0.01, T:0.53
Consensus pattern (29 bp):
TTTTATTTAAATAAACTTTTAATTTTAAT
Done.