Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold230
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: 2055625
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 2 of 14
Found at i:87183 original size:20 final size:20
Alignment explanation
Indices: 87144--87183 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
87134 TAATATAATT
*
87144 TTAATTTATTTTATTTTTTA
1 TTAATTTATTTTATTATTTA
87164 TTAATTT-TTTTATATATTTA
1 TTAATTTATTTTAT-TATTTA
87184 AACTAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (20 bp):
TTAATTTATTTTATTATTTA
Found at i:87997 original size:2 final size:2
Alignment explanation
Indices: 87954--87980 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
87944 GATTTAAAAG
87954 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
87981 GAGATCCATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:88619 original size:2 final size:2
Alignment explanation
Indices: 88612--88646 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
88602 CATGTCTTCT
88612 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
88647 TATTTAACCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:89050 original size:15 final size:16
Alignment explanation
Indices: 89016--89050 Score: 56
Period size: 14 Copynumber: 2.3 Consensus size: 16
89006 CTTATTTAAT
89016 TTTAATTATAAAAATA
1 TTTAATTATAAAAATA
89032 -TTAA-TATAAAAATA
1 TTTAATTATAAAAATA
89046 TTTAA
1 TTTAA
89051 AAAATAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TTTAATTATAAAAATA
Found at i:93624 original size:8 final size:8
Alignment explanation
Indices: 93611--93749 Score: 62
Period size: 8 Copynumber: 17.4 Consensus size: 8
93601 ATAATATTAA
*
93611 ATATAATT
1 ATATAAAT
93619 ATATAAAT
1 ATATAAAT
93627 ATAATAAAT
1 AT-ATAAAT
93636 ATA-AAAT
1 ATATAAAT
93643 A-ATTAAA-
1 ATA-TAAAT
93650 ATATAATATT
1 ATATAA-A-T
93660 ATATAAAT
1 ATATAAAT
93668 ATAT--AT
1 ATATAAAT
*
93674 -TTTAAA-
1 ATATAAAT
*
93680 ATTTAAAT
1 ATATAAAT
93688 AATATAAAT
1 -ATATAAAT
*
93697 -TATTAAT
1 ATATAAAT
93704 ATATTCAAATTT
1 ATA-T-AAA--T
*
93716 ATTTAAAT
1 ATATAAAT
*
93724 ATAAAAAT
1 ATATAAAT
*
93732 ATTTAAA-
1 ATATAAAT
*
93739 ATATAATT
1 ATATAAAT
93747 ATA
1 ATA
93750 ATATTATAAA
Statistics
Matches: 101, Mismatches: 12, Indels: 36
0.68 0.08 0.24
Matches are distributed among these distances:
5 2 0.02
6 3 0.03
7 27 0.27
8 37 0.37
9 17 0.17
10 11 0.11
11 1 0.01
12 3 0.03
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (8 bp):
ATATAAAT
Found at i:93651 original size:16 final size:15
Alignment explanation
Indices: 93603--93670 Score: 61
Period size: 14 Copynumber: 4.4 Consensus size: 15
93593 AAAAAATGAT
93603 AATATTAAATATAAT-
1 AATA-TAAATATAATA
*
93618 TATATAAATATAATA
1 AATATAAATATAATA
93633 AATATAAA-ATAATTA
1 AATATAAATATAA-TA
93648 AA-ATATAATATTATATA
1 AATATA-AATA-TA-ATA
93665 AATATA
1 AATATA
93671 TATTTTAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
14 17 0.39
15 16 0.36
16 1 0.02
17 6 0.14
18 4 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AATATAAATATAATA
Found at i:93937 original size:2 final size:2
Alignment explanation
Indices: 93930--93978 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
93920 TCCTTGCATT
93930 TA 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 TA
93972 TA TA TA T
1 TA TA TA T
93979 TAGCCCGATG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:94199 original size:18 final size:16
Alignment explanation
Indices: 94176--94218 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 16
94166 ATAATTAAAT
94176 TTTTAAAAATATATATTA
1 TTTTAAAAA-A-ATATTA
94194 TTTTAATTAAAAATATTA
1 TTTTAA--AAAAATATTA
94212 TTTTAAA
1 TTTTAAA
94219 TTAAATCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 1 0.04
18 18 0.78
19 1 0.04
20 3 0.13
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TTTTAAAAAAATATTA
Found at i:94222 original size:19 final size:18
Alignment explanation
Indices: 94188--94223 Score: 63
Period size: 18 Copynumber: 1.9 Consensus size: 18
94178 TTAAAAATAT
94188 ATATTATTTTAATTAAAA
1 ATATTATTTTAATTAAAA
94206 ATATTATTTTAAATTAAA
1 ATATTATTTT-AATTAAA
94224 TCAAATTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATATTATTTTAATTAAAA
Found at i:94222 original size:23 final size:22
Alignment explanation
Indices: 94165--94222 Score: 57
Period size: 23 Copynumber: 2.7 Consensus size: 22
94155 TATTATATTT
*
94165 TATA-ATTAAATT-TTTAAAAA
1 TATATATTAAATTAATTAAAAA
**
94185 TATATATTATTTTAATTAAAAA
1 TATATATTAAATTAATTAAAAA
*
94207 TATTATTTTAAATTAA
1 TA-TATATTAAATTAA
94223 ATCAAATTAA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
20 4 0.14
21 6 0.21
22 9 0.31
23 10 0.34
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TATATATTAAATTAATTAAAAA
Found at i:94843 original size:18 final size:17
Alignment explanation
Indices: 94806--94850 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
94796 TAATTTGAAT
*
94806 TTAA-ATTTTAATATTT
1 TTAATATTTTAATATTC
94822 TTAATATTTTAATTATTC
1 TTAATATTTTAA-TATTC
*
94840 TTAATTTTTTA
1 TTAATATTTTA
94851 TCTTTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 4 0.16
17 7 0.28
18 14 0.56
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (17 bp):
TTAATATTTTAATATTC
Found at i:95334 original size:19 final size:20
Alignment explanation
Indices: 95297--95335 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
95287 ATAATAAATG
*
95297 TATAATATTTTAAACATAAT
1 TATAATATTGTAAACATAAT
*
95317 TATAATA-TGTAAATATAAT
1 TATAATATTGTAAACATAAT
95336 ATGAACATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (20 bp):
TATAATATTGTAAACATAAT
Found at i:95567 original size:18 final size:18
Alignment explanation
Indices: 95522--95578 Score: 73
Period size: 18 Copynumber: 3.2 Consensus size: 18
95512 TATTATAATT
95522 TATATAAATAT-ATAAAA
1 TATATAAATATGATAAAA
*
95539 TATTTTAAATATGATAAAA
1 TA-TATAAATATGATAAAA
*
95558 TATATGAATATGAT-AAA
1 TATATAAATATGATAAAA
95575 TATA
1 TATA
95579 CGAATTGTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
17 9 0.26
18 18 0.51
19 8 0.23
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (18 bp):
TATATAAATATGATAAAA
Found at i:95577 original size:17 final size:18
Alignment explanation
Indices: 95546--95583 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
95536 AAATATTTTA
*
95546 AATATGATAAAATATATG
1 AATATGATAAAATATACG
95564 AATATGAT-AAATATACG
1 AATATGATAAAATATACG
95581 AAT
1 AAT
95584 TGTCATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.55, C:0.03, G:0.11, T:0.32
Consensus pattern (18 bp):
AATATGATAAAATATACG
Found at i:96414 original size:14 final size:14
Alignment explanation
Indices: 96397--96434 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
96387 TATTTATATA
*
96397 TATTATGTTATTTT
1 TATTATATTATTTT
96411 TATTATATTATTTTT
1 TATTATATTA-TTTT
96426 TATT-TATTA
1 TATTATATTA
96435 AACATATCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 14 0.64
15 8 0.36
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (14 bp):
TATTATATTATTTT
Found at i:96417 original size:19 final size:19
Alignment explanation
Indices: 96387--96434 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
96377 ATATAATAAA
96387 TATTTATATATATTATGTTAT
1 TATTTAT-TATATTAT-TTAT
*
96408 T-TTTATTATATTATTTTT
1 TATTTATTATATTATTTAT
96426 TATTTATTA
1 TATTTATTA
96435 AACATATCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 4 0.16
19 15 0.60
20 5 0.20
21 1 0.04
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (19 bp):
TATTTATTATATTATTTAT
Found at i:99458 original size:2 final size:2
Alignment explanation
Indices: 99451--99475 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
99441 GTTATAATTT
99451 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
99476 TCTCAAATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:100204 original size:19 final size:20
Alignment explanation
Indices: 100175--100212 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
100165 GTTGGATACT
100175 CTTTTTGTTTTATTAATGAG
1 CTTTTTGTTTTATTAATGAG
*
100195 CTTTTT-TTTTATTCATGA
1 CTTTTTGTTTTATTAATGA
100213 ACAAAGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.18, C:0.08, G:0.11, T:0.63
Consensus pattern (20 bp):
CTTTTTGTTTTATTAATGAG
Found at i:103825 original size:2 final size:2
Alignment explanation
Indices: 103818--103843 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
103808 ATATTGAGAA
103818 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
103844 TAAATAATAA
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:104192 original size:22 final size:21
Alignment explanation
Indices: 104153--104222 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 21
104143 TTAATTTATA
* *
104153 TTAAAAATATAATTAATTAAAAG
1 TTAAAAATTTAA-AAATT-AAAG
104176 TTAAAAATTTAAAAATT-AA-
1 TTAAAAATTTAAAAATTAAAG
104195 TTAAATATAATTTAAAAATTAAAG
1 TT-AA-A-AATTTAAAAATTAAAG
104219 TTAA
1 TTAA
104223 GATTTTGTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
19 2 0.05
20 4 0.10
21 1 0.03
22 16 0.40
23 15 0.38
24 2 0.05
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (21 bp):
TTAAAAATTTAAAAATTAAAG
Found at i:104198 original size:30 final size:31
Alignment explanation
Indices: 104153--104214 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
104143 TTAATTTATA
*
104153 TTAAAAATATAATTAATTAAAAGTTAAAAAT
1 TTAAAAATATAATTAAATAAAAGTTAAAAAT
* *
104184 TTAAAAAT-TAATTAAATATAATTTAAAAAT
1 TTAAAAATATAATTAAATAAAAGTTAAAAAT
104214 T
1 T
104215 AAAGTTAAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 20 0.71
31 8 0.29
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (31 bp):
TTAAAAATATAATTAAATAAAAGTTAAAAAT
Found at i:114757 original size:2 final size:2
Alignment explanation
Indices: 114750--114792 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
114740 GCTGCTGCTG
* *
114750 CT CT CT CT TT AT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
114792 C
1 C
114793 CTGACTTAAC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.02, C:0.47, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Found at i:115939 original size:2 final size:2
Alignment explanation
Indices: 115926--115966 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
115916 GTAGTTGGTG
*
115926 CT CT CT CG CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
115967 ACACACACAC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.51, G:0.02, T:0.46
Consensus pattern (2 bp):
CT
Found at i:124337 original size:27 final size:27
Alignment explanation
Indices: 124304--124398 Score: 95
Period size: 27 Copynumber: 3.5 Consensus size: 27
124294 TTAACCATTC
*
124304 ATATATTTATATAATATTTATAATATT
1 ATATATTTATATAATATTTAAAATATT
* * *
124331 TTTTA-TTATAATTATATTTAAAATATT
1 ATATATTTAT-ATAATATTTAAAATATT
* *
124358 ATATATTTAAATAA-ATGTTAATATATCT
1 ATATATTTATATAATAT-TTAAAATAT-T
124386 ATATATTTATATA
1 ATATATTTATATA
124399 CCGTATTGTT
Statistics
Matches: 54, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
26 6 0.11
27 32 0.59
28 16 0.30
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (27 bp):
ATATATTTATATAATATTTAAAATATT
Found at i:132185 original size:19 final size:21
Alignment explanation
Indices: 132138--132189 Score: 63
Period size: 19 Copynumber: 2.5 Consensus size: 21
132128 TCAAACGAAA
*
132138 AATAATTTAACTATAAAAATAT
1 AATATTTTAA-TATAAAAATAT
*
132160 AAAATTTTAATAT-AAAA-AT
1 AATATTTTAATATAAAAATAT
132179 AATATTTTAAT
1 AATATTTTAAT
132190 TTTTTTAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 12 0.44
20 4 0.15
21 3 0.11
22 8 0.30
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
AATATTTTAATATAAAAATAT
Found at i:132677 original size:29 final size:28
Alignment explanation
Indices: 132645--132699 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 28
132635 TTATTATTAT
132645 ATTTAAAATTT-ATCATTTAATAAATTTAA
1 ATTTAAAATTTAAT-ATTT-ATAAATTTAA
*
132674 ATTTAAATTTTAATATTTATAAATTT
1 ATTTAAAATTTAATATTTATAAATTT
132700 TTTGTATCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 8 0.33
29 14 0.58
30 2 0.08
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (28 bp):
ATTTAAAATTTAATATTTATAAATTTAA
Found at i:132700 original size:16 final size:15
Alignment explanation
Indices: 132643--132699 Score: 59
Period size: 14 Copynumber: 3.9 Consensus size: 15
132633 TTTTATTATT
132643 ATATTTA-AAATTT-
1 ATATTTATAAATTTA
132656 ATCATTTAATAAATTTA
1 AT-ATTT-ATAAATTTA
*
132673 A-ATTTA-AATTTTA
1 ATATTTATAAATTTA
132686 ATATTTATAAATTT
1 ATATTTATAAATTT
132700 TTTGTATCTT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
13 9 0.25
14 10 0.28
15 10 0.28
16 6 0.17
17 1 0.03
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (15 bp):
ATATTTATAAATTTA
Found at i:133428 original size:5 final size:5
Alignment explanation
Indices: 133420--133470 Score: 52
Period size: 5 Copynumber: 10.4 Consensus size: 5
133410 ATTTAATAAT
* * *
133420 TTATA TTATA TTATT TTATA TTATAA TTATA TT-TA ATATA TTTTA TT-TA
1 TTATA TTATA TTATA TTATA TTAT-A TTATA TTATA TTATA TTATA TTATA
133469 TT
1 TT
133471 TAAATTTTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
4 7 0.18
5 27 0.69
6 5 0.13
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (5 bp):
TTATA
Found at i:133512 original size:32 final size:33
Alignment explanation
Indices: 133411--133516 Score: 107
Period size: 32 Copynumber: 3.3 Consensus size: 33
133401 AATTTAATAA
*
133411 TTTAATA-ATTT-ATATTATATTATTTTAT--AT
1 TTTAATATATTTAATA-TATTTTATTTTATAAAT
* *
133441 TATAATTATATTTAATATATTTTATTTATTTAAAT
1 TTTAA-TATATTTAATATATTTTATTT-TATAAAT
133476 TTTAATATA-TTAATA-ATTTATATTTTATAAAT
1 TTTAATATATTTAATATATTT-TATTTTATAAAT
133508 TTTAATATA
1 TTTAATATA
133517 CTCTTATATT
Statistics
Matches: 64, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
30 4 0.06
31 2 0.03
32 32 0.50
33 16 0.25
34 4 0.06
35 6 0.09
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (33 bp):
TTTAATATATTTAATATATTTTATTTTATAAAT
Found at i:135445 original size:5 final size:5
Alignment explanation
Indices: 135422--135469 Score: 53
Period size: 5 Copynumber: 9.2 Consensus size: 5
135412 GGATATAATT
*
135422 ATTTA ATTT- ATTGA TATTTA ATTTTAA ATTTA ATTTA ATTTA ATTTA
1 ATTTA ATTTA ATTTA -ATTTA A-TTT-A ATTTA ATTTA ATTTA ATTTA
135469 A
1 A
135470 ATTATTATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
4 3 0.08
5 22 0.59
6 10 0.27
7 2 0.05
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (5 bp):
ATTTA
Found at i:135462 original size:22 final size:22
Alignment explanation
Indices: 135436--135486 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
135426 AATTTATTGA
135436 TATTTAATTTTAAATT-TAATT
1 TATTTAATTTTAAATTATAATT
*
135457 TAATTTAA-TTTAAATTATTATT
1 T-ATTTAATTTTAAATTATAATT
135479 TATTTAAT
1 TATTTAAT
135487 AAAAAATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 15 0.58
22 11 0.42
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TATTTAATTTTAAATTATAATT
Found at i:135479 original size:27 final size:27
Alignment explanation
Indices: 135419--135486 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 27
135409 TACGGATATA
135419 ATTATTTAATTT-ATTGATATTTAATT
1 ATTATTTAATTTAATTGATATTTAATT
*
135445 -TTAAATTTAATTTAATTTA-ATTTAAATT
1 ATT--ATTTAATTTAATTGATATTT-AATT
135473 ATTATTT-ATTTAAT
1 ATTATTTAATTTAAT
135487 AAAAAATTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
25 2 0.06
26 7 0.19
27 17 0.47
28 8 0.22
29 2 0.06
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (27 bp):
ATTATTTAATTTAATTGATATTTAATT
Found at i:135549 original size:31 final size:28
Alignment explanation
Indices: 135488--135566 Score: 86
Period size: 31 Copynumber: 2.7 Consensus size: 28
135478 TTATTTAATA
* * *
135488 AAAAATTAATTTTTTATAATATTAATAT
1 AAAATTTAATTTTTTAAAATATTAAAAT
*
135516 AAATTTTAATTATTTTAAAATATTTTAAAAT
1 AAAATTTAATT-TTTTAAAATA--TTAAAAT
*
135547 AAAATATAATTTTTTAAAAT
1 AAAATTTAATTTTTTAAAAT
135567 CGAATGGAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
28 9 0.21
29 9 0.21
30 9 0.21
31 15 0.36
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (28 bp):
AAAATTTAATTTTTTAAAATATTAAAAT
Found at i:135849 original size:3 final size:3
Alignment explanation
Indices: 135841--135878 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
135831 GTGTTTGAAT
135841 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
135879 CTATTTTCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:139061 original size:16 final size:16
Alignment explanation
Indices: 139040--139096 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
139030 AACGTATAAC
139040 TATATATATTATATAT
1 TATATATATTATATAT
* *
139056 TATATAAATTTTAATAT
1 TATATATATTAT-ATAT
*
139073 GTTTATATATTTATATAT
1 -TATATATA-TTATATAT
139091 TA-ATAT
1 TATATAT
139097 GTTTTGTTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
16 14 0.44
17 5 0.16
18 10 0.31
19 3 0.09
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (16 bp):
TATATATATTATATAT
Found at i:139090 original size:18 final size:17
Alignment explanation
Indices: 139040--139096 Score: 57
Period size: 18 Copynumber: 3.4 Consensus size: 17
139030 AACGTATAAC
139040 TATATATA-TTATATAT
1 TATATATATTTATATAT
*
139056 TATATAAATTT-TAATAT
1 TATATATATTTAT-ATAT
*
139073 GTTTATATATTTATATAT
1 -TATATATATTTATATAT
139091 TA-ATAT
1 TATATAT
139097 GTTTTGTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
16 12 0.36
17 7 0.21
18 13 0.39
19 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
TATATATATTTATATAT
Found at i:139093 original size:24 final size:26
Alignment explanation
Indices: 139048--139100 Score: 74
Period size: 24 Copynumber: 2.1 Consensus size: 26
139038 ACTATATATA
*
139048 TTATATATTATATAAATTTTAATATGT
1 TTATATATTATAT-AATATTAATATGT
139075 TTATATATT-TAT-ATATTAATATGT
1 TTATATATTATATAATATTAATATGT
139099 TT
1 TT
139101 TGTTTATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 13 0.52
26 3 0.12
27 9 0.36
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (26 bp):
TTATATATTATATAATATTAATATGT
Found at i:139904 original size:22 final size:23
Alignment explanation
Indices: 139876--139919 Score: 72
Period size: 22 Copynumber: 1.9 Consensus size: 23
139866 AAATTTAAAA
139876 AATTTTAAAAT-TTTTATATATT
1 AATTTTAAAATATTTTATATATT
139898 AATTTTAAAATAATTTTATATA
1 AATTTTAAAAT-ATTTTATATA
139920 ATAAAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 11 0.55
24 9 0.45
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
AATTTTAAAATATTTTATATATT
Found at i:139922 original size:13 final size:13
Alignment explanation
Indices: 139887--139923 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
139877 ATTTTAAAAT
*
139887 TTTTATATATTAA
1 TTTTATATAATAA
139900 TTTTA-A-AATAA
1 TTTTATATAATAA
139911 TTTTATATAATAA
1 TTTTATATAATAA
139924 AATATAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
11 9 0.43
12 2 0.10
13 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TTTTATATAATAA
Found at i:140313 original size:16 final size:18
Alignment explanation
Indices: 140294--140335 Score: 63
Period size: 16 Copynumber: 2.5 Consensus size: 18
140284 AATTAATTTA
140294 TTTAATAAAAAAT-AT-T
1 TTTAATAAAAAATAATAT
140310 TTTAAT-AAAAATAATAT
1 TTTAATAAAAAATAATAT
140327 TTTAATAAA
1 TTTAATAAA
140336 TATAAATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 6 0.26
16 8 0.35
17 7 0.30
18 2 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TTTAATAAAAAATAATAT
Found at i:140329 original size:17 final size:17
Alignment explanation
Indices: 140294--140345 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
140284 AATTAATTTA
140294 TTTAAT-AAAA-AATATT
1 TTTAATAAAAATAATA-T
140310 TTTAATAAAAATAATAT
1 TTTAATAAAAATAATAT
*
140327 TTTAATAAATATAA-AT
1 TTTAATAAAAATAATAT
140343 TTT
1 TTT
140346 TGTGATAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
16 11 0.33
17 18 0.55
18 4 0.12
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TTTAATAAAAATAATAT
Found at i:140346 original size:17 final size:17
Alignment explanation
Indices: 140253--140346 Score: 63
Period size: 17 Copynumber: 5.6 Consensus size: 17
140243 TTAAATTTTG
* * *
140253 ATAAAATTTTATTAATT
1 ATAAATTTTTAATAAAT
*
140270 ATAAATTATTTGAT-AAT
1 ATAAATT-TTTAATAAAT
*
140287 -TAATTTATTTAATAAA-
1 ATAAATT-TTTAATAAAT
*
140303 A-AATATTTTTAATAAAA
1 ATAA-ATTTTTAATAAAT
140320 AT-AATATTTTAATAAAT
1 ATAAAT-TTTTAATAAAT
140337 ATAAATTTTT
1 ATAAATTTTT
140347 GTGATAAATT
Statistics
Matches: 61, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
16 24 0.39
17 30 0.49
18 7 0.11
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (17 bp):
ATAAATTTTTAATAAAT
Found at i:140562 original size:43 final size:46
Alignment explanation
Indices: 140510--140595 Score: 117
Period size: 43 Copynumber: 1.9 Consensus size: 46
140500 TTACAAATTA
*
140510 TTTATGAAAAAATTTGTAATTTTAT-C-TCAT-AAAAATTATAAGTT
1 TTTATGAAAAAATTTATAATTTTATACGT-ATAAAAAATTATAAGTT
*
140554 TTTA-GAAAATATTTATAATTTTATACGTATAAAAAATTATAA
1 TTTATGAAAAAATTTATAATTTTATACGTATAAAAAATTATAA
140596 ATTTAATTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
43 18 0.49
44 7 0.19
45 12 0.32
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (46 bp):
TTTATGAAAAAATTTATAATTTTATACGTATAAAAAATTATAAGTT
Found at i:140890 original size:2 final size:2
Alignment explanation
Indices: 140883--140941 Score: 84
Period size: 2 Copynumber: 30.0 Consensus size: 2
140873 ACTTTTGCTG
*
140883 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
140924 AT TT AT AT TT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
140942 GTGTGTGTGT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
AT
Found at i:142074 original size:2 final size:2
Alignment explanation
Indices: 142063--142109 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
142053 TTCTAGTTTC
*
142063 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
142104 TA TA TA
1 TA TA TA
142110 AGATCTTCTT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:142389 original size:4 final size:4
Alignment explanation
Indices: 142380--142413 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
142370 GGGATCACAA
142380 GACT GACT GACT GACT GACT GACT GACT GACT GA
1 GACT GACT GACT GACT GACT GACT GACT GACT GA
142414 TGATGATGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (4 bp):
GACT
Found at i:143418 original size:18 final size:18
Alignment explanation
Indices: 143395--143431 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
143385 TAAAAGTAAG
143395 AAATGATAGTTTTTTCAA
1 AAATGATAGTTTTTTCAA
143413 AAATGATAGTTTTTTCAA
1 AAATGATAGTTTTTTCAA
143431 A
1 A
143432 TAAGAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.43
Consensus pattern (18 bp):
AAATGATAGTTTTTTCAA
Found at i:144402 original size:2 final size:2
Alignment explanation
Indices: 144395--144438 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
144385 TCAAAGAGGA
144395 AT AT 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 AT AT
144437 AT
1 AT
144439 GCACACACAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:144474 original size:2 final size:2
Alignment explanation
Indices: 144467--144501 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
144457 GAGGAGAGGA
144467 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
144502 ATAAAAGAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:149341 original size:17 final size:19
Alignment explanation
Indices: 149319--149355 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
149309 TGTACGATCC
149319 CGTTG-CAA-AGCCAAGAA
1 CGTTGCCAACAGCCAAGAA
*
149336 CGTTGCCAACAGCCATGAA
1 CGTTGCCAACAGCCAAGAA
149355 C
1 C
149356 AGTGAGAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 5 0.29
18 3 0.18
19 9 0.53
ACGTcount: A:0.35, C:0.30, G:0.22, T:0.14
Consensus pattern (19 bp):
CGTTGCCAACAGCCAAGAA
Found at i:150738 original size:20 final size:23
Alignment explanation
Indices: 150702--150743 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
150692 AATTGAGTTT
150702 CCGTTGAGAGAAGTGGC-GGTTC
1 CCGTTGAGAGAAGTGGCAGGTTC
150724 CCGTTGA-AG-AGTGGCAGGTT
1 CCGTTGAGAGAAGTGGCAGGTT
150744 AGAGTGTGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.32
21 6 0.32
22 7 0.37
ACGTcount: A:0.19, C:0.17, G:0.40, T:0.24
Consensus pattern (23 bp):
CCGTTGAGAGAAGTGGCAGGTTC
Found at i:151338 original size:18 final size:19
Alignment explanation
Indices: 151296--151338 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
151286 TTTTTTAACA
*
151296 TTATT-ATATATAATAATT
1 TTATTAATATATAATAAAT
*
151314 TTTTTAATATA-AATAAAT
1 TTATTAATATATAATAAAT
151332 TTATTAA
1 TTATTAA
151339 CTATTTCATA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTATTAATATATAATAAAT
Found at i:151472 original size:53 final size:51
Alignment explanation
Indices: 151411--151510 Score: 130
Period size: 53 Copynumber: 1.9 Consensus size: 51
151401 TTTATTAATA
* *
151411 AATTTAATTT-ATACAAATTAAATTTTAAATAAAATTTTTATAAAATAAAAAT
1 AATTTAATTTAAT-CAAATTAAAATTTAAATAAAAATTTT-TAAAATAAAAAT
**
151463 AATTATAATTTAATTTAATTAAAATTTAAATAAAAATTTTTAAAATAA
1 AATT-TAATTTAATCAAATTAAAATTTAAATAAAAATTTTTAAAATAA
151511 TTAATTTATG
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
52 12 0.29
53 28 0.67
54 2 0.05
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (51 bp):
AATTTAATTTAATCAAATTAAAATTTAAATAAAAATTTTTAAAATAAAAAT
Found at i:152164 original size:53 final size:53
Alignment explanation
Indices: 152097--152212 Score: 155
Period size: 53 Copynumber: 2.2 Consensus size: 53
152087 TAAATAAGTG
* * * *
152097 AATAA-TAGATTTAAATATTTAAATTTATT-TTTTATAAAAATAATGTAAATTTG
1 AATAATTA-ATTTAAATATCTAAATTAATTATTTT-TAAAAATAATATAAATTTA
*
152150 TATAATTAATTTAAATATCTAAATTAATTATTTTTAAAAATAATATAAATTTA
1 AATAATTAATTTAAATATCTAAATTAATTATTTTTAAAAATAATATAAATTTA
152203 AATAATTAAT
1 AATAATTAAT
152213 ATTTAAAATT
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
53 49 0.89
54 6 0.11
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.47
Consensus pattern (53 bp):
AATAATTAATTTAAATATCTAAATTAATTATTTTTAAAAATAATATAAATTTA
Found at i:152205 original size:15 final size:15
Alignment explanation
Indices: 152187--152219 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
152177 TTATTTTTAA
152187 AAATAATATAA-ATTT
1 AAATAAT-TAATATTT
152202 AAATAATTAATATTT
1 AAATAATTAATATTT
152217 AAA
1 AAA
152220 ATTTTATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 3 0.18
15 14 0.82
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AAATAATTAATATTT
Found at i:153129 original size:53 final size:52
Alignment explanation
Indices: 153064--153178 Score: 144
Period size: 53 Copynumber: 2.2 Consensus size: 52
153054 TAAATAAGTG
* * * *
153064 AATAA-TAGATTTAAATATTTAAATTTATT-TTTTATAAAAATAATGTAAATTTG
1 AATAATTA-ATTTAAATATCTAAATTAATTATTTT-TAAAAATAATAT-AATTTA
*
153117 TATAATTAATTTAAATATCTAAATTAATTATTTTTAAAAATAATATAATTTA
1 AATAATTAATTTAAATATCTAAATTAATTATTTTTAAAAATAATATAATTTA
153169 AATAATTAAT
1 AATAATTAAT
153179 ATTTAAAATT
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
52 14 0.26
53 34 0.63
54 6 0.11
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.47
Consensus pattern (52 bp):
AATAATTAATTTAAATATCTAAATTAATTATTTTTAAAAATAATATAATTTA
Found at i:153187 original size:16 final size:15
Alignment explanation
Indices: 153131--153197 Score: 50
Period size: 16 Copynumber: 4.5 Consensus size: 15
153121 ATTAATTTAA
* *
153131 ATATCTAAATTAATT
1 ATATTTAAAATAATT
*
153146 ATTTTTAAAAATAA-T
1 ATATTT-AAAATAATT
153161 ATAATTT-AAATAATT
1 AT-ATTTAAAATAATT
*
153176 AATATTTAAAAT-TTT
1 -ATATTTAAAATAATT
153191 ATATTTA
1 ATATTTA
153198 CGTTTACTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
14 13 0.31
15 14 0.33
16 15 0.36
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (15 bp):
ATATTTAAAATAATT
Found at i:153355 original size:966 final size:967
Alignment explanation
Indices: 152085--154008 Score: 3775
Period size: 966 Copynumber: 2.0 Consensus size: 967
152075 TTTTTTATAT
152085 TTTAAATAAGTGAATAATAGATTTAAATATTTAAATTTATTTTTTATAAAAATAATGTAAATTTG
1 TTTAAATAAGTGAATAATAGATTTAAATATTTAAATTTATTTTTTATAAAAATAATGTAAATTTG
152150 TATAATTAATTTAAATATCTAAATTAATTATTTTTAAAAATAATATAAATTTAAATAATTAATAT
66 TATAATTAATTTAAATATCTAAATTAATTATTTTTAAAAATAATATAAATTTAAATAATTAATAT
152215 TTAAAATTTTATATTTACGTTTACTAAATAATAATTATAATATTTAAATTCACGTTCACTTAAAA
131 TTAAAATTTTATATTTACGTTTACTAAATAATAATTATAATATTTAAATTCACGTTCACTTAAAA
152280 TCTTTATAAATAAAATTAGATAATTATAAATATCTAAATTCATATTATATATCACTATTTTTAGA
196 TCTTTATAAATAAAATTAGATAATTATAAATATCTAAATTCATATTATATATCACTATTTTTAGA
152345 AATTAGCCATGATTGACGATGATAAAATAGTGATGTTCGAGATTACAGATCTAAAAACAACCATT
261 AATTAGCCATGATTGACGATGATAAAATAGTGATGTTCGAGATTACAGATCTAAAAACAACCATT
152410 ACATAAAAGAAATTTATGAAACACCTTTTTAATTAACCCTTCATTAACGCATAAAATAAATTTTT
326 ACATAAAAGAAATTTATGAAACACCTTTTTAATTAACCCTTCATTAACGCATAAAATAAATTTTT
*
152475 ATTTTAAATGTAAAGAGTTCATTAACGTTAATTTTACGGATAGAATTATTATAATTCAGTTAATT
391 ATTTTAAATGTAAAGAGTTAATTAACGTTAATTTTACGGATAGAATTATTATAATTCAGTTAATT
152540 TATATGGATACACTAATATTTGTTGAATCTAACCAACTCAAGTATGACTATAAATAGTCATTCAA
456 TATATGGATACACTAATATTTGTTGAATCTAACCAACTCAAGTATGACTATAAATAGTCATTCAA
152605 GTTCATTCGTTTAAGTATCCCACAAGAAGTGAGAGAAAAACAAAATAAAATCCTTTATCTTTACT
521 GTTCATTCGTTTAAGTATCCCACAAGAAGTGAGAGAAAAACAAAATAAAATCCTTTATCTTTACT
152670 CGTGGACGTAGACTTTTTGCTGAACTACGTAATTTCTTTTGTGTCTTCTATTTTGTGCTTGTTCT
586 CGTGGACGTAGACTTTTTGCTGAACTACGTAATTTCTTTTGTGTCTTCTATTTTGTGCTTGTTCT
152735 TCATTTTTCTTATTTCATTTAGTTGTGGTCATGCTCTTCCCATCGATGCTCTAACAGTGGTATCA
651 TCATTTTTCTTATTTCATTTAGTTGTGGTCATGCTCTTCCCATCGATGCTCTAACAGTGGTATCA
152800 GAGCTATT-AGTTATCGAGGTACTATTTACATATATAGGTGCCATTCATATATATGGGCACTATT
716 GAGCTATTGA-TTATCGAGGTACTATTTACATATATAGGTGCCATTCATATATATGGGCACTATT
152864 CACGTATACGATACTGTACACGTAAAATAGTGAGAACAAATTTTGAATTTATGGAGGGAAAACAA
780 CACGTATACGATACTGTACACGTAAAATAGTGAGAACAAATTTTGAATTTATGGAGGGAAAACAA
152929 TGGCGATAAAATATGAAATTGAGAAGTTCAACGGAAACAAATTCACGTTGCGGAAAATGAAGATG
845 TGGCGATAAAATATGAAATTGAGAAGTTCAACGGAAACAAATTCACGTTGCGGAAAATGAAGATG
152994 AAAGCTGTTTTAAAGAAAAATAATTGCTTGGCAGCAATTGGAGAGAGACAAAATTTAA
910 AAAGCTGTTTTAAAGAAAAATAATTGCTTGGCAGCAATTGGAGAGAGACAAAATTTAA
153052 TTTAAATAAGTGAATAATAGATTTAAATATTTAAATTTATTTTTTATAAAAATAATGTAAATTTG
1 TTTAAATAAGTGAATAATAGATTTAAATATTTAAATTTATTTTTTATAAAAATAATGTAAATTTG
153117 TATAATTAATTTAAATATCTAAATTAATTATTTTTAAAAATAATAT-AATTTAAATAATTAATAT
66 TATAATTAATTTAAATATCTAAATTAATTATTTTTAAAAATAATATAAATTTAAATAATTAATAT
153181 TTAAAATTTTATATTTACGTTTACTATAAATAATAATTATAATATTTAAATTCACGTTCACTTAA
131 TTAAAATTTTATATTTACGTTTAC--TAAATAATAATTATAATATTTAAATTCACGTTCACTTAA
153246 AATCTTTATAAATAAAATTAGATAATTATAAATATCTAAATTCATA-T-TATATCACTATTTTTA
194 AATCTTTATAAATAAAATTAGATAATTATAAATATCTAAATTCATATTATATATCACTATTTTTA
*
153309 GAAATTAGCCATGATTGACGATGATAAAATAGTGATGTTTGAGATTACAGATCTAAAAACAACCA
259 GAAATTAGCCATGATTGACGATGATAAAATAGTGATGTTCGAGATTACAGATCTAAAAACAACCA
153374 TTACATAAAAGAAATTTATGAAACACCTTTTTAATTAACCCTTCATTAACGCATAAAATAAATTT
324 TTACATAAAAGAAATTTATGAAACACCTTTTTAATTAACCCTTCATTAACGCATAAAATAAATTT
153439 TTATTTTAAATGTAAAGAGTTAATTAACGTTAATTTTACGGATAGAATTATTATAATTCAGTTAA
389 TTATTTTAAATGTAAAGAGTTAATTAACGTTAATTTTACGGATAGAATTATTATAATTCAGTTAA
153504 TTTATATGGATACACTAATATTTGTTGAATCTAACCAACTCAAGTATGACTATAAATAGTCATTC
454 TTTATATGGATACACTAATATTTGTTGAATCTAACCAACTCAAGTATGACTATAAATAGTCATTC
153569 AAGTTCATTCGTTTAAGTATCCCACAAGAAGTGAGAGAAAAACAAAATAAAATCCTTTATCTTTA
519 AAGTTCATTCGTTTAAGTATCCCACAAGAAGTGAGAGAAAAACAAAATAAAATCCTTTATCTTTA
153634 CTCGTGGACGTAGACTTTTTGCTGAACTACGTAATTTCTTTTGTGTCTTCTATTTTGTGCTTGTT
584 CTCGTGGACGTAGACTTTTTGCTGAACTACGTAATTTCTTTTGTGTCTTCTATTTTGTGCTTGTT
153699 CTTCATTTTTCTTATTTCATTTAGTTGTGGTCATGCTCTTCCCATCGATGCTCTAACAGTGGTAT
649 CTTCATTTTTCTTATTTCATTTAGTTGTGGTCATGCTCTTCCCATCGATGCTCTAACAGTGGTAT
153764 CAGAGCTATTGATTATCGAGGTACTATTTACATATATAGGTGCCATTCATATATATGGGCACTAT
714 CAGAGCTATTGATTATCGAGGTACTATTTACATATATAGGTGCCATTCATATATATGGGCACTAT
153829 TCACGTATACGATACTGTACACGTAAAATAGTGAGAACAAATTTTGAATTTATGGAGGGAAAACA
779 TCACGTATACGATACTGTACACGTAAAATAGTGAGAACAAATTTTGAATTTATGGAGGGAAAACA
153894 ATGGCGATAAAATATGAAATTGAGAAGTTCAACGGAAACAAATTCACGTTGCGGAAAATGAAGAT
844 ATGGCGATAAAATATGAAATTGAGAAGTTCAACGGAAACAAATTCACGTTGCGGAAAATGAAGAT
153959 GAAAGCTGTTTTAAAGAAAAATAATTGCTTGGCAGCAATTGGAGAGAGAC
909 GAAAGCTGTTTTAAAGAAAAATAATTGCTTGGCAGCAATTGGAGAGAGAC
154009 CGAGTGAGAT
Statistics
Matches: 952, Mismatches: 2, Indels: 7
0.99 0.00 0.01
Matches are distributed among these distances:
966 754 0.79
967 113 0.12
968 85 0.09
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (967 bp):
TTTAAATAAGTGAATAATAGATTTAAATATTTAAATTTATTTTTTATAAAAATAATGTAAATTTG
TATAATTAATTTAAATATCTAAATTAATTATTTTTAAAAATAATATAAATTTAAATAATTAATAT
TTAAAATTTTATATTTACGTTTACTAAATAATAATTATAATATTTAAATTCACGTTCACTTAAAA
TCTTTATAAATAAAATTAGATAATTATAAATATCTAAATTCATATTATATATCACTATTTTTAGA
AATTAGCCATGATTGACGATGATAAAATAGTGATGTTCGAGATTACAGATCTAAAAACAACCATT
ACATAAAAGAAATTTATGAAACACCTTTTTAATTAACCCTTCATTAACGCATAAAATAAATTTTT
ATTTTAAATGTAAAGAGTTAATTAACGTTAATTTTACGGATAGAATTATTATAATTCAGTTAATT
TATATGGATACACTAATATTTGTTGAATCTAACCAACTCAAGTATGACTATAAATAGTCATTCAA
GTTCATTCGTTTAAGTATCCCACAAGAAGTGAGAGAAAAACAAAATAAAATCCTTTATCTTTACT
CGTGGACGTAGACTTTTTGCTGAACTACGTAATTTCTTTTGTGTCTTCTATTTTGTGCTTGTTCT
TCATTTTTCTTATTTCATTTAGTTGTGGTCATGCTCTTCCCATCGATGCTCTAACAGTGGTATCA
GAGCTATTGATTATCGAGGTACTATTTACATATATAGGTGCCATTCATATATATGGGCACTATTC
ACGTATACGATACTGTACACGTAAAATAGTGAGAACAAATTTTGAATTTATGGAGGGAAAACAAT
GGCGATAAAATATGAAATTGAGAAGTTCAACGGAAACAAATTCACGTTGCGGAAAATGAAGATGA
AAGCTGTTTTAAAGAAAAATAATTGCTTGGCAGCAATTGGAGAGAGACAAAATTTAA
Found at i:165049 original size:23 final size:22
Alignment explanation
Indices: 164989--165053 Score: 78
Period size: 22 Copynumber: 2.9 Consensus size: 22
164979 ATTAATTAAA
* *
164989 AAATATTTATATTATTAAATTT
1 AAATATTTTTATAATTAAATTT
*
165011 ATATATTTTTATAATTAAATTT
1 AAATATTTTTATAATTAAATTT
165033 AAATAATTTTT-TAAATTAAAT
1 AAAT-ATTTTTAT-AATTAAAT
165054 AATATAGTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 23 0.62
23 14 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
AAATATTTTTATAATTAAATTT
Found at i:165162 original size:9 final size:9
Alignment explanation
Indices: 165148--165236 Score: 60
Period size: 9 Copynumber: 9.8 Consensus size: 9
165138 TTTATTTTAA
*
165148 AAATTAGTT
1 AAATTAATT
165157 AAATTAATT
1 AAATTAATT
165166 AAA--AATT
1 AAATTAATT
165173 AAATTAAATT
1 AAATT-AATT
*
165183 AAATTATTTT
1 AAATTA-ATT
*
165193 ATATTAATTTT
1 AAATTAA--TT
165204 AAA-TAATTT
1 AAATTAA-TT
*
165213 TAATT-ATT
1 AAATTAATT
*
165221 AAATAAATT
1 AAATTAATT
165230 AAATTAA
1 AAATTAA
165237 ATTATTTTAT
Statistics
Matches: 63, Mismatches: 9, Indels: 16
0.72 0.10 0.18
Matches are distributed among these distances:
7 7 0.11
8 5 0.08
9 27 0.43
10 20 0.32
11 4 0.06
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (9 bp):
AAATTAATT
Found at i:165163 original size:5 final size:5
Alignment explanation
Indices: 165155--165240 Score: 56
Period size: 5 Copynumber: 17.6 Consensus size: 5
165145 TAAAAATTAG
** * *
165155 TTAAA TT-AA TTAAAAA TTAAA TTAAA TTAAA TTATT TTATA TTAATT
1 TTAAA TTAAA TT--AAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAA-A
* *
165202 TTAAA -TAAT TTTAA TT--A TTAAA -TAAA TTAAA TTAAA TTA
1 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTA
165241 TTTTATATTT
Statistics
Matches: 64, Mismatches: 9, Indels: 16
0.72 0.10 0.18
Matches are distributed among these distances:
3 3 0.05
4 11 0.17
5 42 0.66
6 4 0.06
7 4 0.06
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (5 bp):
TTAAA
Found at i:165179 original size:21 final size:20
Alignment explanation
Indices: 165144--165184 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
165134 AATATTTATT
*
165144 TTAAAAATTAGTTAAATTAA
1 TTAAAAATTAATTAAATTAA
165164 TTAAAAATTAAATTAAATTAA
1 TTAAAAATT-AATTAAATTAA
165185 ATTATTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (20 bp):
TTAAAAATTAATTAAATTAA
Found at i:165335 original size:26 final size:28
Alignment explanation
Indices: 165281--165343 Score: 78
Period size: 26 Copynumber: 2.3 Consensus size: 28
165271 ATAATTAATT
*
165281 TTTTTAATTATATTTAATAAAATTTTTA
1 TTTTTAATTATATTCAATAAAATTTTTA
165309 TTTTTAATTA-ATGTCAA-AAAA-TTTTA
1 TTTTTAATTATAT-TCAATAAAATTTTTA
*
165335 TTTTAAATT
1 TTTTTAATT
165344 TGAGTTAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 13 0.41
27 6 0.19
28 13 0.41
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (28 bp):
TTTTTAATTATATTCAATAAAATTTTTA
Found at i:165422 original size:19 final size:19
Alignment explanation
Indices: 165351--165434 Score: 60
Period size: 25 Copynumber: 3.9 Consensus size: 19
165341 ATTTGAGTTA
165351 AATTATAAATAATTAAATTT
1 AATTA-AAATAATTAAATTT
165371 AAAATTAAATATAAAAATTAAATTT
1 --AATTAAA-AT---AATTAAATTT
*
165396 ATTTTTAAAATAATTAAATTT
1 A--ATTAAAATAATTAAATTT
*
165417 AATTAAATTAATTTAAAT
1 AATTAAAATAA-TTAAAT
165435 AATTTAAATT
Statistics
Matches: 52, Mismatches: 3, Indels: 16
0.73 0.04 0.23
Matches are distributed among these distances:
19 8 0.15
20 6 0.12
21 13 0.25
22 7 0.13
23 1 0.02
24 2 0.04
25 15 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
AATTAAAATAATTAAATTT
Found at i:165427 original size:9 final size:9
Alignment explanation
Indices: 165400--165457 Score: 55
Period size: 9 Copynumber: 6.0 Consensus size: 9
165390 AAATTTATTT
*
165400 TTAAAATAA
1 TTAAATTAA
165409 TTAAATTTAA
1 TTAAA-TTAA
165419 TTAAATTAA
1 TTAAATTAA
165428 TTTAAA-TAA
1 -TTAAATTAA
165437 TTTAAATTTATA
1 -TTAAA-TTA-A
165449 TTAAATTAA
1 TTAAATTAA
165458 ATATTAATTT
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
9 19 0.44
10 16 0.37
11 7 0.16
12 1 0.02
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
TTAAATTAA
Found at i:165456 original size:35 final size:33
Alignment explanation
Indices: 165413--165516 Score: 120
Period size: 35 Copynumber: 3.0 Consensus size: 33
165403 AAATAATTAA
*
165413 ATTT-AATTAAATTAATTTAAATAATTTAAATTT
1 ATTTAAATTAAATTAATTTTAA-AATTTAAATTT
*
165446 ATATTAAATTAAATATTAATTTTAAAATTAAAATTT
1 AT-TTAAATT-AA-ATTAATTTTAAAATTTAAATTT
*
165482 ATTTAAATTTAAATTAAATTTTAAACTTTAAATTT
1 ATTTAAA-TTAAATT-AATTTTAAAATTTAAATTT
165517 TGAATTCAAC
Statistics
Matches: 61, Mismatches: 4, Indels: 10
0.81 0.05 0.13
Matches are distributed among these distances:
33 2 0.03
34 5 0.08
35 28 0.46
36 16 0.26
37 10 0.16
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (33 bp):
ATTTAAATTAAATTAATTTTAAAATTTAAATTT
Found at i:165479 original size:25 final size:23
Alignment explanation
Indices: 165361--165516 Score: 94
Period size: 25 Copynumber: 6.7 Consensus size: 23
165351 AATTATAAAT
* *
165361 AATTAAATTTAAAATTAAATATAA
1 AATTAAATTTAAATTTAAA-ATTA
**
165385 AAATTAAATTTATTTTTAAAA-T-
1 A-ATTAAATTTAAATTTAAAATTA
165407 AATTAAATTT-AA-TT-AAATTA
1 AATTAAATTTAAATTTAAAATTA
* *
165427 ATTTAAATAATTTAAATTT-ATATTA
1 AATT--A-AATTTAAATTTAAAATTA
*
165452 AATTAAATATTAATTTTAAAATTAA
1 AATTAAAT-TTAAATTTAAAATT-A
*
165477 AATT-TATTTAAATTT-AAATTA
1 AATTAAATTTAAATTTAAAATTA
165498 AATTTTAAACTTTAAATTT
1 AA--TTAAA-TTTAAATTT
165517 TGAATTCAAC
Statistics
Matches: 103, Mismatches: 14, Indels: 29
0.71 0.10 0.20
Matches are distributed among these distances:
18 3 0.03
19 3 0.03
20 3 0.03
21 12 0.12
22 10 0.10
23 22 0.21
24 11 0.11
25 39 0.38
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (23 bp):
AATTAAATTTAAATTTAAAATTA
Found at i:165484 original size:22 final size:22
Alignment explanation
Indices: 165407--165504 Score: 71
Period size: 22 Copynumber: 4.5 Consensus size: 22
165397 TTTTTAAAAT
*
165407 AATT-AAATTTAATTAAA-TT-
1 AATTAAAATTTATTTAAATTTA
* *
165426 AATTTAAA-TAATTTAAATTTA
1 AATTAAAATTTATTTAAATTTA
* * *
165447 TATT-AAATTAAATATTAATTTTAA
1 AATTAAAATT-TAT-TTAAATTT-A
165471 AATTAAAATTTATTTAAATTTA
1 AATTAAAATTTATTTAAATTTA
*
165493 AATTAAATTTTA
1 AATTAAAATTTA
165505 AACTTTAAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
19 11 0.17
20 8 0.13
21 4 0.06
22 15 0.24
23 14 0.22
24 6 0.10
25 5 0.08
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
AATTAAAATTTATTTAAATTTA
Found at i:165500 original size:5 final size:5
Alignment explanation
Indices: 165407--165501 Score: 57
Period size: 5 Copynumber: 17.8 Consensus size: 5
165397 TTTTTAAAAT
* * * *
165407 AATTA AATTT AATTA AATTA ATTTA AA-TA ATTTA AATTTA TATTA AATTAA
1 AATTA AATTA AATTA AATTA AATTA AATTA AATTA AA-TTA AATTA AATT-A
* * *
165458 ATATTA ATTTTAA AATTAA AATTT ATTTA AATTTA AATTA AATT
1 A-ATTA A-ATT-A AATT-A AATTA AATTA AA-TTA AATTA AATT
165502 TTAAACTTTA
Statistics
Matches: 70, Mismatches: 14, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
4 3 0.04
5 38 0.54
6 24 0.34
7 5 0.07
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (5 bp):
AATTA
Found at i:165511 original size:7 final size:6
Alignment explanation
Indices: 165348--165516 Score: 83
Period size: 6 Copynumber: 28.3 Consensus size: 6
165338 TAAATTTGAG
* * * **
165348 TTAAAT TATAAAT AATTAAAT TTAAAA TTAAAT ATAAAAA TTAAAT TTATTT
1 TTAAAT T-TAAAT --TTAAAT TTAAAT TTAAAT -TTAAAT TTAAAT TTAAAT
165400 TTAAAAT AATTAAAT TT-AA- TTAAA- TT-AAT TTAAA- -T-AAT TTAAAT
1 TT-AAAT --TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* * *
165444 TTATA- TTAAA- TTAAAT ATTAATT TTAAAAT TAAAAT TT--AT TTAAAT
1 TTAAAT TTAAAT TTAAAT -TTAAAT TT-AAAT TTAAAT TTAAAT TTAAAT
165490 TTAAA- TTAAATT TTAAACT TTAAAT TT
1 TTAAAT TTAAA-T TTAAA-T TTAAAT TT
165517 TGAATTCAAC
Statistics
Matches: 126, Mismatches: 17, Indels: 40
0.69 0.09 0.22
Matches are distributed among these distances:
3 2 0.02
4 9 0.07
5 23 0.18
6 49 0.39
7 31 0.25
8 9 0.07
9 3 0.02
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (6 bp):
TTAAAT
Found at i:166845 original size:18 final size:19
Alignment explanation
Indices: 166806--166849 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
166796 TTATTGTATG
166806 AATATAACTAAAAAAATTAA
1 AATATAACTAAAAAAA-TAA
166826 AATATAA-TAAAAATAA-AA
1 AATATAACTAAAAA-AATAA
166844 AATATA
1 AATATA
166850 TATATATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 8 0.35
19 6 0.26
20 9 0.39
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (19 bp):
AATATAACTAAAAAAATAA
Found at i:166863 original size:22 final size:20
Alignment explanation
Indices: 166824--166880 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 20
166814 TAAAAAAATT
166824 AAAATATA-ATA-AAAATAA
1 AAAATATATATATAAAATAA
166842 AAAATATATATATATAATATAA
1 AAAATATATATATA-AA-ATAA
*
166864 ATGAATATGATATATAA
1 A-AAATAT-ATATATAA
166881 TGACAATTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
18 8 0.25
19 3 0.09
20 1 0.03
21 2 0.06
22 5 0.16
23 6 0.19
24 7 0.22
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.32
Consensus pattern (20 bp):
AAAATATATATATAAAATAA
Found at i:167136 original size:12 final size:12
Alignment explanation
Indices: 167121--167154 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
167111 TTTTATGATA
167121 AAAATTATTATT
1 AAAATTATTATT
*
167133 AAAATTATAATT
1 AAAATTATTATT
167145 AAAATGTATT
1 AAAAT-TATT
167155 TAAAATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 16 0.84
13 3 0.16
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (12 bp):
AAAATTATTATT
Found at i:167333 original size:24 final size:25
Alignment explanation
Indices: 167303--167352 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
167293 TATTCTTAAT
* *
167303 TTTTTAA-TACTGTTTAATATAAAA
1 TTTTTAATTAATGTATAATATAAAA
167327 TTTTTAATTAATGTATAATATAAAA
1 TTTTTAATTAATGTATAATATAAAA
167352 T
1 T
167353 AATAAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.30
25 16 0.70
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (25 bp):
TTTTTAATTAATGTATAATATAAAA
Found at i:168079 original size:21 final size:20
Alignment explanation
Indices: 168055--168113 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
168045 AAATATTTGT
168055 ATAATATAAAATTATATTTCA
1 ATAA-ATAAAATTATATTTCA
*
168076 ATAAATAATTATTAT-TTTCA
1 ATAAATAA-AATTATATTTCA
*
168096 ACTGAATAAAA-TATATTT
1 A-TAAATAAAATTATATTT
168114 ACGTGCAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
19 3 0.09
20 14 0.44
21 15 0.47
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (20 bp):
ATAAATAAAATTATATTTCA
Found at i:168399 original size:14 final size:14
Alignment explanation
Indices: 168382--168413 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
168372 TAAATAATTT
168382 GTTTAATTTAATAA
1 GTTTAATTTAATAA
*
168396 GTTTAATTTATTAA
1 GTTTAATTTAATAA
168410 GTTT
1 GTTT
168414 GTGTTTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.56
Consensus pattern (14 bp):
GTTTAATTTAATAA
Found at i:168510 original size:22 final size:21
Alignment explanation
Indices: 168479--168519 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
168469 TATTTTTATT
*
168479 TAAATTTAATTTAAAAATATA
1 TAAATTTAATATAAAAATATA
168500 TAAATATTAATATAAAAATA
1 TAAAT-TTAATATAAAAATA
168520 ATTTTTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
TAAATTTAATATAAAAATATA
Found at i:168934 original size:21 final size:20
Alignment explanation
Indices: 168908--168946 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
168898 AAAAAATAAT
168908 ATATAAGAAATTTTAATTTAA
1 ATATAA-AAATTTTAATTTAA
*
168929 ATATAAATATTTTAATTT
1 ATATAAAAATTTTAATTT
168947 TTTTTCTATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
ATATAAAAATTTTAATTTAA
Found at i:169555 original size:26 final size:26
Alignment explanation
Indices: 169525--169584 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
169515 TAATTTTAGG
*
169525 TTAAATTAATTTAAATTTTTAAAAT-T
1 TTAAATTAATTTAAA-ATTTAAAATAT
169551 TTAAATTAATTTAAAATTTAAAATAAT
1 TTAAATTAATTTAAAATTTAAAAT-AT
169578 TTAAATT
1 TTAAATT
169585 TTAATTAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
25 8 0.26
26 15 0.48
27 8 0.26
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
TTAAATTAATTTAAAATTTAAAATAT
Found at i:169572 original size:17 final size:16
Alignment explanation
Indices: 169532--169602 Score: 76
Period size: 16 Copynumber: 4.4 Consensus size: 16
169522 AGGTTAAATT
169532 AATTTAAATT--TTTAA
1 AATTTAAATTAATTT-A
169547 AATTTTAAATTAATTTAA
1 AA-TTTAAATTAATTT-A
*
169565 AATTTAAAATAATTTA
1 AATTTAAATTAATTTA
*
169581 AATTTTAATTAA-TTA
1 AATTTAAATTAATTTA
169596 AATTTAA
1 AATTTAA
169603 TTTTTTTATT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
15 11 0.22
16 19 0.39
17 12 0.24
18 7 0.14
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AATTTAAATTAATTTA
Found at i:169803 original size:16 final size:16
Alignment explanation
Indices: 169752--169805 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
169742 GGTCATATCG
*
169752 AATTTAAATTATTTTA
1 AATTCAAATTATTTTA
* * * **
169768 TATTGAATTTATTTCG
1 AATTCAAATTATTTTA
169784 AATTCAAATTATTTTA
1 AATTCAAATTATTTTA
169800 AATTCA
1 AATTCA
169806 GATTTATCCA
Statistics
Matches: 28, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.39, C:0.06, G:0.04, T:0.52
Consensus pattern (16 bp):
AATTCAAATTATTTTA
Found at i:170406 original size:14 final size:14
Alignment explanation
Indices: 170362--170411 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
170352 TTTGTATTTG
170362 AAATAATTTAAATAA
1 AAATAATTT-AATAA
*
170377 AAAT-ATTAAATTTAA
1 AAATAATTTAA--TAA
170392 AAATAATTTAATAA
1 AAATAATTTAATAA
170406 AAATAA
1 AAATAA
170412 AACTTTACTT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
13 2 0.07
14 12 0.40
15 11 0.37
16 5 0.17
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
AAATAATTTAATAA
Found at i:171881 original size:24 final size:23
Alignment explanation
Indices: 171835--171927 Score: 77
Period size: 24 Copynumber: 4.0 Consensus size: 23
171825 TTACTTTATT
* * *
171835 ATTTAAAATAATATTAAAAAATTA
1 ATTTTAAATAATATT-TATAATTA
*
171859 ATTTTATATTAATATTTATAATTA
1 ATTTTA-AATAATATTTATAATTA
*
171883 AATTTAAATAA-ATTT-T-ATTA
1 ATTTTAAATAATATTTATAATTA
171903 ATATTTAAATAATAATTTA-AATTA
1 AT-TTTAAATAAT-ATTTATAATTA
171927 A
1 A
171928 ATTAAACTTA
Statistics
Matches: 56, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
20 5 0.09
21 10 0.18
22 4 0.07
23 8 0.14
24 21 0.38
25 8 0.14
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
ATTTTAAATAATATTTATAATTA
Found at i:171905 original size:33 final size:34
Alignment explanation
Indices: 171853--171930 Score: 106
Period size: 33 Copynumber: 2.3 Consensus size: 34
171843 TAATATTAAA
* *
171853 AAATTAATTTTATATTAATATTTATAATTA-AATTT
1 AAATTAAATTT-TATTAATATTTA-AATAATAATTT
171888 AAA-TAAATTTTATTAATATTTAAATAATAATTT
1 AAATTAAATTTTATTAATATTTAAATAATAATTT
171921 AAATTAAATT
1 AAATTAAATT
171931 AAACTTATTC
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
32 4 0.10
33 20 0.51
34 12 0.31
35 3 0.08
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (34 bp):
AAATTAAATTTTATTAATATTTAAATAATAATTT
Found at i:171908 original size:11 final size:12
Alignment explanation
Indices: 171855--171927 Score: 59
Period size: 11 Copynumber: 6.4 Consensus size: 12
171845 ATATTAAAAA
171855 ATTAAT-TTTAT
1 ATTAATATTTAT
171866 ATTAATATTTAT
1 ATTAATATTTAT
171878 AATTAA-ATTTA-
1 -ATTAATATTTAT
*
171889 AATAA-ATTT-T
1 ATTAATATTTAT
171899 ATTAATATTTA-
1 ATTAATATTTAT
* *
171910 AATAATAATTTAA
1 ATTAAT-ATTTAT
171923 ATTAA
1 ATTAA
171928 ATTAAACTTA
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
10 12 0.24
11 15 0.29
12 15 0.29
13 9 0.18
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
ATTAATATTTAT
Found at i:172359 original size:14 final size:15
Alignment explanation
Indices: 172337--172365 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
172327 ATTTTAATTT
172337 TATTATTTAAAATAA
1 TATTATTTAAAATAA
172352 TATT-TTTAAAATAA
1 TATTATTTAAAATAA
172366 AAAATTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TATTATTTAAAATAA
Found at i:172434 original size:19 final size:17
Alignment explanation
Indices: 172391--172442 Score: 52
Period size: 19 Copynumber: 2.9 Consensus size: 17
172381 ATTAATATTT
172391 ATAA-TTAAATTTAAATA
1 ATAATTTAAA-TTAAATA
**
172408 ATTTTTTATTAATTAAATA
1 ATAATTTA--AATTAAATA
172427 ATAATTTAAATTAAAT
1 ATAATTTAAATTAAAT
172443 TTAAAAATCA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
17 10 0.36
18 3 0.11
19 13 0.46
20 2 0.07
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
ATAATTTAAATTAAATA
Found at i:172443 original size:11 final size:11
Alignment explanation
Indices: 172376--172447 Score: 51
Period size: 12 Copynumber: 6.5 Consensus size: 11
172366 AAAATTATTT
*
172376 TTTATATTAATA
1 TTTAAATTAA-A
172388 TTTATAATTAAA
1 TTTA-AATTAAA
*
172400 TTTAAA-TAAT
1 TTTAAATTAAA
**
172410 TTTTTATT-AA
1 TTTAAATTAAA
*
172420 -TTAAATAATAA
1 TTTAAATTA-AA
172431 TTTAAATTAAA
1 TTTAAATTAAA
172442 TTTAAA
1 TTTAAA
172448 AATCAAGTCA
Statistics
Matches: 46, Mismatches: 9, Indels: 11
0.70 0.14 0.17
Matches are distributed among these distances:
9 4 0.09
10 8 0.17
11 13 0.28
12 16 0.35
13 5 0.11
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
TTTAAATTAAA
Found at i:173053 original size:2 final size:2
Alignment explanation
Indices: 173042--173079 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
173032 TATTAAATAA
173042 AT AT AT -T AT AT AT -T 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 AT
173080 TTGCCTTCAC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:173508 original size:21 final size:22
Alignment explanation
Indices: 173484--173527 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
173474 ATTCGACTTC
*
173484 ATTTTTA-ATATAATATATATT
1 ATTTTTATATATAACATATATT
*
173505 A-TTTTATATTTAACATATATT
1 ATTTTTATATATAACATATATT
173526 AT
1 AT
173528 GTAATTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
ATTTTTATATATAACATATATT
Found at i:173564 original size:12 final size:13
Alignment explanation
Indices: 173545--173573 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
173535 ATATAAATCT
173545 TAAAAAAATTAAG
1 TAAAAAAATTAAG
173558 TAAAAAAATTAAG
1 TAAAAAAATTAAG
173571 TAA
1 TAA
173574 TTTATATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (13 bp):
TAAAAAAATTAAG
Found at i:173823 original size:17 final size:16
Alignment explanation
Indices: 173801--173857 Score: 55
Period size: 16 Copynumber: 3.5 Consensus size: 16
173791 TTCATAAACT
173801 ATATAAATTTAAATATA
1 ATATAAATTT-AATATA
173818 ATATAAATTATTAA-ATA
1 ATATAAA-T-TTAATATA
*
173835 A-ATAAATATAATATA
1 ATATAAATTTAATATA
*
173850 TTATAAAT
1 ATATAAAT
173858 ATTATTATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
14 3 0.09
15 4 0.12
16 11 0.32
17 11 0.32
18 3 0.09
19 2 0.06
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
ATATAAATTTAATATA
Found at i:173855 original size:16 final size:17
Alignment explanation
Indices: 173802--173869 Score: 63
Period size: 17 Copynumber: 4.1 Consensus size: 17
173792 TCATAAACTA
*
173802 TATAAAT-TTAAATATAA
1 TATAAATATT-AATATAT
173819 TATAAATTATTAA-ATA-
1 TATAAA-TATTAATATAT
*
173835 AATAAATA-TAATATAT
1 TATAAATATTAATATAT
*
173851 TATAAATATTATTATAT
1 TATAAATATTAATATAT
173868 TA
1 TA
173870 ATTATATTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
14 3 0.07
15 5 0.12
16 12 0.28
17 18 0.42
18 3 0.07
19 2 0.05
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TATAAATATTAATATAT
Found at i:174620 original size:26 final size:26
Alignment explanation
Indices: 174568--174621 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
174558 ATTTTTATTT
* *
174568 TATATTTATTTAAATATAGATATAAA
1 TATATTTATTTAAATATAGAAAAAAA
*
174594 TATATATT-TTTAAATATATAAAAAAA
1 TATAT-TTATTTAAATATAGAAAAAAA
174620 TA
1 TA
174622 ATTAAGTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 22 0.92
27 2 0.08
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (26 bp):
TATATTTATTTAAATATAGAAAAAAA
Found at i:175196 original size:25 final size:22
Alignment explanation
Indices: 175150--175209 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 22
175140 ATTATATTAA
*
175150 TTTAATTTATAAATTAAAAAAT
1 TTTAATTTTTAAATTAAAAAAT
175172 TTTAATTATTTAAATTAAATTAAAT
1 TTTAATT-TTTAAATTAAA--AAAT
*
175197 TTTATTTTTTAAA
1 TTTAATTTTTAAA
175210 ATTTATACTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 7 0.21
23 10 0.30
24 6 0.18
25 10 0.30
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTAATTTTTAAATTAAAAAAT
Found at i:175211 original size:25 final size:24
Alignment explanation
Indices: 175154--175212 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 24
175144 TATTAATTTA
175154 ATTTATAAATTAAAAAATTTTAATT
1 ATTTA-AAATTAAAAAATTTTAATT
175179 ATTT-AAATTAAATTAAATTTT-ATT
1 ATTTAAAATTAAA--AAATTTTAATT
*
175203 TTTTAAAATT
1 ATTTAAAATT
175213 TATACTATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
23 8 0.27
24 6 0.20
25 16 0.53
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
ATTTAAAATTAAAAAATTTTAATT
Found at i:175576 original size:2 final size:2
Alignment explanation
Indices: 175558--175596 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
175548 ATGGTGTAAG
* *
175558 TA TA TA TC TA TA CA TA TA TA TA TA TA TA TA -A 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
175597 GTCAAAAGGA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:179022 original size:3 final size:3
Alignment explanation
Indices: 179014--179042 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
179004 GACGAATATA
179014 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
179043 ACTTAAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:179083 original size:6 final size:6
Alignment explanation
Indices: 179074--179157 Score: 65
Period size: 6 Copynumber: 14.7 Consensus size: 6
179064 TAATTATCTT
179074 TATAAA TATAAA T-TAAA -AT-AA TATAAA T-TAAA -AT-AA TATAAA
1 TATAAA TATAAA TATAAA TATAAA TATAAA TATAAA TATAAA TATAAA
* * *
179116 TTATTAAA TA-AAT TAAAAA TAAAAA TATAAA TATAATA TATA
1 -TA-TAAA TATAAA TATAAA TATAAA TATAAA TATAA-A TATA
179158 TGAAATATAT
Statistics
Matches: 65, Mismatches: 3, Indels: 19
0.75 0.03 0.22
Matches are distributed among these distances:
4 4 0.06
5 18 0.28
6 30 0.46
7 9 0.14
8 4 0.06
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
TATAAA
Found at i:179098 original size:15 final size:15
Alignment explanation
Indices: 179078--179155 Score: 85
Period size: 15 Copynumber: 5.4 Consensus size: 15
179068 TATCTTTATA
179078 AATATAAATTAAAAT
1 AATATAAATTAAAAT
179093 AATATAAATTAAAAT
1 AATATAAATTAAAAT
*
179108 AATATAAATT--ATT
1 AATATAAATTAAAAT
179121 AA-ATAAATT-AAA-
1 AATATAAATTAAAAT
*
179133 AATAAAAATATAAATAT
1 AATATAAAT-TAAA-AT
179150 AATATA
1 AATATA
179156 TATGAAATAT
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
12 9 0.17
13 10 0.19
14 1 0.02
15 27 0.51
16 1 0.02
17 5 0.09
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AATATAAATTAAAAT
Found at i:179174 original size:53 final size:55
Alignment explanation
Indices: 179077--179189 Score: 135
Period size: 53 Copynumber: 2.1 Consensus size: 55
179067 TTATCTTTAT
*
179077 AAATATAAATTAAAATAATATAAATTAAAATAATATAAATTATTAAATAAATTAA
1 AAATAAAAATTAAAATAATATAAATTAAAATAATATAAATTATTAAATAAATTAA
* * * *
179132 AAATAAAAATATAAATATAATATATA-TGAAAT-ATAT-AA-TATTAATTATATTAA
1 AAATAAAAAT-TAAA-ATAATATAAATTAAAATAATATAAATTATTAAATAAATTAA
179185 AAATA
1 AAATA
179190 TCATATCATA
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
53 18 0.35
54 2 0.04
55 13 0.25
56 9 0.18
57 9 0.18
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (55 bp):
AAATAAAAATTAAAATAATATAAATTAAAATAATATAAATTATTAAATAAATTAA
Found at i:179206 original size:24 final size:24
Alignment explanation
Indices: 179135--179208 Score: 80
Period size: 23 Copynumber: 3.1 Consensus size: 24
179125 AAATTAAAAA
179135 TAAAAATATAAATATAATA-TATAT
1 TAAAAATAT-AATATAATATTATAT
* * *
179159 GAAATATATAATATTA-ATTATAT
1 TAAAAATATAATATAATATTATAT
* *
179182 TAAAAATATCATATCATATTATAT
1 TAAAAATATAATATAATATTATAT
179206 TAA
1 TAA
179209 TTTTCTGTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
22 1 0.02
23 23 0.56
24 17 0.41
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (24 bp):
TAAAAATATAATATAATATTATAT
Found at i:180637 original size:20 final size:21
Alignment explanation
Indices: 180612--180654 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
180602 AGAATCTGGT
180612 TTGTTTAAAAATT-TAAATTA
1 TTGTTTAAAAATTATAAATTA
*
180632 TTGTTTATAAATTAATAAATTA
1 TTGTTTAAAAATT-ATAAATTA
180654 T
1 T
180655 ATATTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 12 0.60
22 8 0.40
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (21 bp):
TTGTTTAAAAATTATAAATTA
Found at i:180984 original size:21 final size:21
Alignment explanation
Indices: 180926--180986 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 21
180916 AATACTAAAT
*
180926 ATTAATTATAATTTTTTAAAC
1 ATTAATTATAATTTTTTTAAC
* ***
180947 A--AATAATTAACCCTTTTAAC
1 ATTAATTA-TAATTTTTTTAAC
180967 ATTAATTATAATTTTTTTAA
1 ATTAATTATAATTTTTTTAA
180987 AAAATCAAAT
Statistics
Matches: 28, Mismatches: 9, Indels: 6
0.65 0.21 0.14
Matches are distributed among these distances:
19 4 0.14
20 10 0.36
21 10 0.36
22 4 0.14
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (21 bp):
ATTAATTATAATTTTTTTAAC
Found at i:181287 original size:2 final size:2
Alignment explanation
Indices: 181280--181314 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
181270 GTAAGTATGC
*
181280 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
181315 GTCAAAAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:182066 original size:19 final size:18
Alignment explanation
Indices: 182029--182067 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
182019 TAAATTATTG
*
182029 ATTTGTTTAAATTTAAAA
1 ATTTATTTAAATTTAAAA
182047 ATTTATTTAATATTTTAAAA
1 ATTTATTTAA-A-TTTAAAA
182067 A
1 A
182068 GATTTAAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
19 1 0.06
20 8 0.44
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
ATTTATTTAAATTTAAAA
Found at i:182559 original size:2 final size:2
Alignment explanation
Indices: 182548--182590 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
182538 TAACTTGATC
182548 TA TA -A 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 TA
182589 TA
1 TA
182591 AAAGGAAGAA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:183320 original size:20 final size:20
Alignment explanation
Indices: 183287--183325 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
183277 TAGATTAAGG
183287 TTAAAAAATATTTAATTGAA
1 TTAAAAAATATTTAATTGAA
183307 TTAATAAAAT-TTTAATTGA
1 TTAA-AAAATATTTAATTGA
183326 GTTTTTAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (20 bp):
TTAAAAAATATTTAATTGAA
Found at i:184790 original size:14 final size:15
Alignment explanation
Indices: 184771--184804 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
184761 TTCTACTTTT
*
184771 TATTTATCTTAAA-A
1 TATTTATATTAAATA
184785 TATTTATATTAAATA
1 TATTTATATTAAATA
184800 TATTT
1 TATTT
184805 TTAAATATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (15 bp):
TATTTATATTAAATA
Found at i:186499 original size:16 final size:16
Alignment explanation
Indices: 186461--186515 Score: 60
Period size: 16 Copynumber: 3.3 Consensus size: 16
186451 TACAAATGAC
186461 ATATATATTACATTATATT
1 ATATAT-TTA-ATT-TATT
186480 -TATATTTAATTTATT
1 ATATATTTAATTTATT
186495 ATATATTT-ATATTATT
1 ATATATTTAAT-TTATT
186511 ATATA
1 ATATA
186516 ATAATTGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
15 6 0.18
16 20 0.59
17 3 0.09
18 5 0.15
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (16 bp):
ATATATTTAATTTATT
Found at i:186915 original size:11 final size:12
Alignment explanation
Indices: 186890--186929 Score: 55
Period size: 11 Copynumber: 3.3 Consensus size: 12
186880 TTTTTATTAA
186890 ATTATATTTTAT
1 ATTATATTTTAT
*
186902 ATTA-ATTTTTT
1 ATTATATTTTAT
186913 ATTATATTTATAT
1 ATTATATTT-TAT
186926 ATTA
1 ATTA
186930 AAATTATCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 10 0.42
12 8 0.33
13 6 0.25
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
ATTATATTTTAT
Found at i:190558 original size:17 final size:17
Alignment explanation
Indices: 190531--190577 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
190521 AATATATAAA
190531 TATTAAT-ATAAAATTAT
1 TATTAATAATAAAA-TAT
* *
190548 TATT-TTAATAATATAT
1 TATTAATAATAAAATAT
190564 TATTAATAATAAAA
1 TATTAATAATAAAA
190578 ATTTAAGTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
16 8 0.33
17 16 0.67
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TATTAATAATAAAATAT
Found at i:190561 original size:36 final size:36
Alignment explanation
Indices: 190474--190580 Score: 89
Period size: 36 Copynumber: 3.1 Consensus size: 36
190464 ATAAAGTTAT
* * *
190474 ATTATTA-TTTAGTAATA-A-AAATATTATTATTTAA
1 ATTATTATTTTAATAATATATAAATATTAATA-TAAA
* * *
190508 ATT-TAATTTAAAAAATATATAAATATTAATATAAA
1 ATTATTATTTTAATAATATATAAATATTAATATAAA
* * *
190543 ATTATTATTTTAATAATATATTATTAATAATA-AAA
1 ATTATTATTTTAATAATATATAAATATTAATATAAA
190578 ATT
1 ATT
190581 TAAGTTTTGT
Statistics
Matches: 57, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
33 2 0.04
34 10 0.18
35 13 0.23
36 32 0.56
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (36 bp):
ATTATTATTTTAATAATATATAAATATTAATATAAA
Found at i:193956 original size:21 final size:20
Alignment explanation
Indices: 193927--193979 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
193917 TAATAAAAAA
*
193927 TAATATTTTATTGATTTAATT
1 TAATATTTTATT-AATTAATT
*
193948 TAATTTTTTATTAATTAATT
1 TAATATTTTATTAATTAATT
* *
193968 AAATAATTTATT
1 TAATATTTTATT
193980 CTTCAATATA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
TAATATTTTATTAATTAATT
Found at i:194944 original size:17 final size:17
Alignment explanation
Indices: 194919--194959 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
194909 TATTTCTTTT
* *
194919 TTAATTTTTTATTTAAA
1 TTAAATTTTAATTTAAA
194936 TTAAATTTTAATTTAAA
1 TTAAATTTTAATTTAAA
*
194953 TTGAATT
1 TTAAATT
194960 ATTTTAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (17 bp):
TTAAATTTTAATTTAAA
Found at i:196689 original size:27 final size:27
Alignment explanation
Indices: 196669--196736 Score: 83
Period size: 22 Copynumber: 2.7 Consensus size: 27
196659 TTAATATTAG
*
196669 ATATTATATAAAAATAATTAAAATATA
1 ATATGATATAAAAATAATTAAAATATA
196696 ATATGATATAAAAATAA-T---ATA-A
1 ATATGATATAAAAATAATTAAAATATA
*
196718 ATATGATATAAATATAATT
1 ATATGATATAAAAATAATT
196737 TTTTTAAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
22 17 0.45
23 4 0.11
26 1 0.03
27 16 0.42
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (27 bp):
ATATGATATAAAAATAATTAAAATATA
Found at i:196694 original size:22 final size:25
Alignment explanation
Indices: 196669--196736 Score: 63
Period size: 27 Copynumber: 2.8 Consensus size: 25
196659 TTAATATTAG
196669 ATATTATATAAAAATAATTAA-AAT
1 ATATTATATAAAAATAATTAATAAT
196693 ATAATATGATATAAAAATAA-T-ATAA-
1 AT-AT-T-ATATAAAAATAATTAATAAT
* *
196718 ATATGATATAAATATAATT
1 ATATTATATAAAAATAATT
196737 TTTTTAAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
22 11 0.30
23 1 0.03
24 4 0.11
25 5 0.14
26 4 0.11
27 12 0.32
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (25 bp):
ATATTATATAAAAATAATTAATAAT
Found at i:196715 original size:11 final size:11
Alignment explanation
Indices: 196690--196735 Score: 58
Period size: 11 Copynumber: 4.3 Consensus size: 11
196680 AAATAATTAA
196690 AATAT-AATAT
1 AATATAAATAT
* *
196700 GATATAAAAAT
1 AATATAAATAT
196711 AATATAAATAT
1 AATATAAATAT
*
196722 GATATAAATAT
1 AATATAAATAT
196733 AAT
1 AAT
196736 TTTTTTAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
10 4 0.14
11 25 0.86
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (11 bp):
AATATAAATAT
Found at i:199726 original size:17 final size:16
Alignment explanation
Indices: 199699--199740 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
199689 TATCTAAATT
199699 ATTTTATA-TTTATATA
1 ATTTTATATTTTA-ATA
199715 ATTTTAATATTTTAATA
1 ATTTT-ATATTTTAATA
199732 A-TTTATATT
1 ATTTTATATT
199741 ATATATCTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 5 0.21
16 8 0.33
17 7 0.29
18 4 0.17
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTTTATATTTTAATA
Found at i:199751 original size:22 final size:22
Alignment explanation
Indices: 199721--199784 Score: 53
Period size: 22 Copynumber: 3.0 Consensus size: 22
199711 TATAATTTTA
*
199721 ATATTTTAATAATTTATATTAT
1 ATATATTAATAATTTATATTAT
* * *
199743 ATATCTTAAAAATATT-TATTTT
1 ATATATTAATAAT-TTATATTAT
*
199765 TTATATT-AT-ATTTATATTAT
1 ATATATTAATAATTTATATTAT
199785 TTTTTATGTC
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
19 2 0.06
20 7 0.21
21 1 0.03
22 21 0.64
23 2 0.06
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (22 bp):
ATATATTAATAATTTATATTAT
Done.