Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold24
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: 3006277
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.30
Warning! 383161 characters in sequence are not A, C, G, or T
File 3 of 19
Found at i:285307 original size:28 final size:28
Alignment explanation
Indices: 285232--285335 Score: 81
Period size: 29 Copynumber: 3.6 Consensus size: 28
285222 AATATTTAAA
*
285232 ATATTTTATATTTATATAAATTTTAATAAATT
1 ATATTTTATATAT-TAT-AA-TTTAAT-AATT
*
285264 AATAATTTATATTATT-TAAATTTAA-AATAT
1 -ATATTTTATA-TATTAT-AATTTAATAAT-T
*
285294 ATATTTTATATATTATATTTTAATAATT
1 ATATTTTATATATTATAATTTAATAATT
285322 ATA-TTTA-ATATTAT
1 ATATTTTATATATTAT
285336 GGTATTCAAT
Statistics
Matches: 63, Mismatches: 4, Indels: 15
0.77 0.05 0.18
Matches are distributed among these distances:
26 7 0.11
27 4 0.06
28 14 0.22
29 16 0.25
30 1 0.02
31 5 0.08
32 4 0.06
33 10 0.16
34 2 0.03
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
ATATTTTATATATTATAATTTAATAATT
Found at i:285307 original size:71 final size:72
Alignment explanation
Indices: 285171--285319 Score: 159
Period size: 71 Copynumber: 2.1 Consensus size: 72
285161 CTTTGAGGTA
* * *
285171 TTTAAT-AA-TTTAATAATTTATATTATATTTATATTTTTATTATATTATAATAATATTTAAAAT
1 TTTAATAAATTTTAATAAATTATATTATATTTATATTTTTATAATATTAAAATAATATTTAAAAT
*
285234 ATTTTAT
66 ATTATAT
*
285241 ATTTATATAAATTTTAATAAATTA-A-TA-ATTTATATTATTTA-AAT-TTAAAATATATATTTT
1 -TTTA-ATAAATTTTAATAAATTATATTATATTTATATT-TTTATAATATTAAAATA-ATATTTA
*
285301 ATATATTATAT
62 AAATATTATAT
285312 TTTAATAA
1 TTTAATAA
285320 TTATATTTAA
Statistics
Matches: 67, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
69 4 0.06
70 11 0.16
71 30 0.45
72 8 0.12
73 3 0.04
74 11 0.16
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (72 bp):
TTTAATAAATTTTAATAAATTATATTATATTTATATTTTTATAATATTAAAATAATATTTAAAAT
ATTATAT
Found at i:285328 original size:27 final size:27
Alignment explanation
Indices: 285179--285335 Score: 97
Period size: 28 Copynumber: 5.9 Consensus size: 27
285169 TATTTAATAA
285179 TTTAATAATT-TATATTATAT-TTATAT
1 TTTAATAATTATAT-TTATATATTATAT
*
285205 TTT--T-ATTATA-TTATA-ATAATAT
1 TTTAATAATTATATTTATATATTATAT
* *
285227 TTAAAATATTTTATATTTATATA--A-AT
1 TT-TAATA-ATTATATTTATATATTATAT
*
285253 TTTAATAAATTAATAATTTATATTATT-TAAA
1 TTTAAT-AATT-AT-ATTTATA-TATTAT-AT
285284 TTTAA-AATATATATTTTATATATTATAT
1 TTTAATAAT-TATA-TTTATATATTATAT
285312 TTTAATAATTATATTTA-ATATTAT
1 TTTAATAATTATATTTATATATTAT
285336 GGTATTCAAT
Statistics
Matches: 103, Mismatches: 7, Indels: 42
0.68 0.05 0.28
Matches are distributed among these distances:
22 12 0.12
23 3 0.03
24 3 0.03
25 6 0.06
26 17 0.17
27 17 0.17
28 22 0.21
29 16 0.16
30 1 0.01
31 6 0.06
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
TTTAATAATTATATTTATATATTATAT
Found at i:285511 original size:22 final size:22
Alignment explanation
Indices: 285483--285526 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
285473 GATGCCTTCC
285483 TGTCTTGAGAACATAAATCCAA
1 TGTCTTGAGAACATAAATCCAA
285505 TGTCTTGAGAACATAAATCCAA
1 TGTCTTGAGAACATAAATCCAA
285527 CAGACGAGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.27
Consensus pattern (22 bp):
TGTCTTGAGAACATAAATCCAA
Found at i:285675 original size:13 final size:13
Alignment explanation
Indices: 285659--285694 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
285649 ATTTTAATTT
*
285659 TTTATTATTAATA
1 TTTATTATAAATA
285672 TTTATTATAAATA
1 TTTATTATAAATA
285685 TTTATTATAA
1 TTTATTATAA
285695 TTTATGAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
TTTATTATAAATA
Found at i:285679 original size:16 final size:16
Alignment explanation
Indices: 285643--285692 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 16
285633 TGATAGTTAT
285643 TTTATTATT-TTAAT-
1 TTTATTATTATTAATA
285657 TTT-TTATTATTAATA
1 TTTATTATTATTAATA
285672 TTTATTA-TA--AATA
1 TTTATTATTATTAATA
285685 TTTATTAT
1 TTTATTAT
285693 AATTTATGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
13 16 0.50
14 8 0.25
15 5 0.16
16 3 0.09
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTATTATTATTAATA
Found at i:286876 original size:21 final size:22
Alignment explanation
Indices: 286850--286899 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
286840 AAATTAATTT
*
286850 ATTTAAAT-ATAAATTAATAAA
1 ATTTAAATAAAAAATTAATAAA
* *
286871 ATTTAATTAAAAAATTAATAAT
1 ATTTAAATAAAAAATTAATAAA
286893 A-TTAAAT
1 ATTTAAAT
286900 TATCAATTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
ATTTAAATAAAAAATTAATAAA
Found at i:286889 original size:22 final size:22
Alignment explanation
Indices: 286824--286901 Score: 68
Period size: 22 Copynumber: 3.4 Consensus size: 22
286814 TGATTTTAAT
*
286824 TTTAATTTAAAAAATTAA-ATTAA
1 TTTAA-TTAAAAAATTAATA-AAA
*
286847 TTTATTTAAATATAAATTAATAAAA
1 TTTAATT-AA-A-AAATTAATAAAA
*
286872 TTTAATTAAAAAATTAATAATA
1 TTTAATTAAAAAATTAATAAAA
*
286894 TTAAATTA
1 TTTAATTA
286902 TCAATTTAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
22 20 0.43
23 7 0.15
24 3 0.07
25 15 0.33
26 1 0.02
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TTTAATTAAAAAATTAATAAAA
Found at i:286907 original size:21 final size:21
Alignment explanation
Indices: 286852--286907 Score: 60
Period size: 22 Copynumber: 2.7 Consensus size: 21
286842 ATTAATTTAT
286852 TTAAA-TATAAATTAATAAAA
1 TTAAATTATAAATTAATAAAA
* * *
286872 TTTAATTAAAAAATTAATAATA
1 TTAAATT-ATAAATTAATAAAA
*
286894 TTAAATTATCAATT
1 TTAAATTATAAATT
286908 TAAATTAAAA
Statistics
Matches: 28, 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 18 0.64
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
TTAAATTATAAATTAATAAAA
Found at i:287004 original size:10 final size:10
Alignment explanation
Indices: 286962--287040 Score: 60
Period size: 9 Copynumber: 7.9 Consensus size: 10
286952 AATCTGAGCA
286962 TAAA-TTAAT
1 TAAATTTAAT
*
286971 AAAATTTAA-
1 TAAATTTAAT
286980 TAAATTTAAATAT
1 TAAATTT--A-AT
286993 TAAATTTAAT
1 TAAATTTAAT
287003 T-AATTTAAAT
1 TAAATTT-AAT
*
287013 TTAA-TTAATT
1 TAAATTTAA-T
287023 TAAATTTAAT
1 TAAATTTAAT
287033 T-AATTTAA
1 TAAATTTAA
287041 ATATTAAATT
Statistics
Matches: 58, Mismatches: 3, Indels: 18
0.73 0.04 0.23
Matches are distributed among these distances:
9 23 0.40
10 19 0.33
11 8 0.14
12 1 0.02
13 7 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (10 bp):
TAAATTTAAT
Found at i:287010 original size:5 final size:5
Alignment explanation
Indices: 286973--287040 Score: 54
Period size: 5 Copynumber: 13.4 Consensus size: 5
286963 AAATTAATAA
*
286973 AATTT AA-TA AATTT AAATATT AAATTT AA-TT AATTT AAATTT AA-TT
1 AATTT AATTT AATTT -AAT-TT -AATTT AATTT AATTT -AATTT AATTT
287019 AATTT AAATTT AA-TT AATTT AA
1 AATTT -AATTT AATTT AATTT AA
287041 ATATTAAATT
Statistics
Matches: 53, Mismatches: 2, Indels: 16
0.75 0.03 0.23
Matches are distributed among these distances:
4 15 0.28
5 17 0.32
6 15 0.28
7 6 0.11
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (5 bp):
AATTT
Found at i:287012 original size:15 final size:15
Alignment explanation
Indices: 286980--287127 Score: 117
Period size: 15 Copynumber: 9.6 Consensus size: 15
286970 TAAAATTTAA
*
286980 TAAATTTAAAT-A-T
1 TAAATTTAATTAATT
286993 TAAATTTAATTAATT
1 TAAATTTAATTAATT
287008 TAAATTTAATTAATT
1 TAAATTTAATTAATT
287023 TAAATTTAATTAATT
1 TAAATTTAATTAATT
287038 TAAATATTAAATTAA--
1 TAAAT-TT-AATTAATT
* *
287053 -AAATTAAAATAATT
1 TAAATTTAATTAATT
* *
287067 TAAATTCAAAATAATT
1 TAAATT-TAATTAATT
*
287083 TAATTTGATTAATTTTAATAT
1 TAA-AT--TTAA--TTAAT-T
*
287104 TAAATCTAATTAATT
1 TAAATTTAATTAATT
287119 TAAATTTAA
1 TAAATTTAA
287128 AATGATACAA
Statistics
Matches: 112, Mismatches: 9, Indels: 26
0.76 0.06 0.18
Matches are distributed among these distances:
12 5 0.04
13 11 0.10
14 5 0.04
15 50 0.45
16 19 0.17
17 7 0.06
18 5 0.04
19 1 0.01
20 5 0.04
21 4 0.04
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (15 bp):
TAAATTTAATTAATT
Found at i:287051 original size:5 final size:5
Alignment explanation
Indices: 286991--287072 Score: 56
Period size: 5 Copynumber: 15.6 Consensus size: 5
286981 AAATTTAAAT
* * * * * *
286991 ATTAA ATTTA ATTAA TTTAA ATTTA ATTAA TTTAA ATTTA ATTAA TTTAAA
1 ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA ATT-AA
* *
287042 TATTAA ATTAAAA ATTAA AATAA TTTAA ATT
1 -ATTAA ATT--AA ATTAA ATTAA ATTAA ATT
287073 CAAAATAATT
Statistics
Matches: 57, Mismatches: 16, Indels: 8
0.70 0.20 0.10
Matches are distributed among these distances:
5 46 0.81
6 4 0.07
7 7 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (5 bp):
ATTAA
Found at i:287066 original size:59 final size:59
Alignment explanation
Indices: 286994--287108 Score: 160
Period size: 59 Copynumber: 1.9 Consensus size: 59
286984 TTTAAATATT
* * * *
286994 AAATTTAATTAATTTAAATT-TAATTAATTTAAATTTAATTAATTTAAATATTAAATTAA
1 AAATTAAAATAATTTAAATTCAAAATAATTT-AATTTAATTAATTTAAATATTAAATTAA
* *
287053 AAATTAAAATAATTTAAATTCAAAATAATTTAATTTGATTAATTTTAATATTAAAT
1 AAATTAAAATAATTTAAATTCAAAATAATTTAATTTAATTAATTTAAATATTAAAT
287109 CTAATTAATT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
59 41 0.84
60 8 0.16
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (59 bp):
AAATTAAAATAATTTAAATTCAAAATAATTTAATTTAATTAATTTAAATATTAAATTAA
Found at i:287410 original size:26 final size:25
Alignment explanation
Indices: 287368--287416 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
287358 ATTTACATTC
* *
287368 ATATATAATATATTTTTAAATATAA
1 ATATAAAATATAATTTTAAATATAA
287393 ATATAAAATTATAATTTTAAATAT
1 ATATAAAA-TATAATTTTAAATAT
287417 TTTTTAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
ATATAAAATATAATTTTAAATATAA
Found at i:287450 original size:38 final size:37
Alignment explanation
Indices: 287374--287462 Score: 94
Period size: 37 Copynumber: 2.4 Consensus size: 37
287364 ATTCATATAT
* *
287374 AATATATTTTTAAATATAAATATAAAATTATAATTTTA
1 AATAT-TTTTTAAATATAAATATAAAATTAAAAATTTA
287412 AATATTTTTTAAATATAAA-A-AAATATTAAAAAAATTTA
1 AATATTTTTTAAATATAAATATAAA-ATT--AAAAATTTA
*
287450 AATA-TATTTAAAT
1 AATATTTTTTAAAT
287463 TATATACATA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
35 3 0.07
36 4 0.09
37 22 0.49
38 16 0.36
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (37 bp):
AATATTTTTTAAATATAAATATAAAATTAAAAATTTA
Found at i:288149 original size:134 final size:134
Alignment explanation
Indices: 287978--288230 Score: 389
Period size: 134 Copynumber: 1.9 Consensus size: 134
287968 AAATATTAAA
* * *
287978 ATTAAAATTTTAAATTTATTAAATATTTTCAACAATTATTACGTAAATAAACTTAATTAAATTTA
1 ATTAAAATTTTAAATTTATTAAATATTTTCAACAATTATTACATAAACAAACTTAATTAAACTTA
* * *
288043 ATATTTAATTATTTCTCAACAACTATATTTATATGCTTTTAAGAAGGTTGAATAGGGTTAAACAT
66 AAATTCAATTATTTCTCAACAACTATATTTATATGCTCTTAAGAAGGTTGAATAGGGTTAAACAT
288108 TGAG
131 TGAG
* * **
288112 ATTAAAATTTTAAATTTATTAAATATTTTTAAGAATTATTACATAAACAAACTTGGTTAAACTTA
1 ATTAAAATTTTAAATTTATTAAATATTTTCAACAATTATTACATAAACAAACTTAATTAAACTTA
* * *
288177 AAATTCAATTATTTCTCAATAACTGTATTTATATGCTCTTAAGAAGTTTGAATA
66 AAATTCAATTATTTCTCAACAACTATATTTATATGCTCTTAAGAAGGTTGAATA
288231 AGATTAGATA
Statistics
Matches: 106, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
134 106 1.00
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.43
Consensus pattern (134 bp):
ATTAAAATTTTAAATTTATTAAATATTTTCAACAATTATTACATAAACAAACTTAATTAAACTTA
AAATTCAATTATTTCTCAACAACTATATTTATATGCTCTTAAGAAGGTTGAATAGGGTTAAACAT
TGAG
Found at i:288267 original size:134 final size:132
Alignment explanation
Indices: 287974--288273 Score: 320
Period size: 134 Copynumber: 2.2 Consensus size: 132
287964 TTATAAATAT
* * *
287974 TAAA-ATTAAAATTTTAAATTTATTAAATATTTTCAACAATTATTACGTAAATAAACTTAATTAA
1 TAAAGATTAAAATATTAAA--TATTAAATATTTTCAACAATTATTACATAAACAAACTTAATTAA
* * * * * *
288038 ATTTAATATTTAATTATTTCTCAACAACTATATTTATATGCTTTTAAGAAGGTTGAATAGGGTTA
64 ACTTAAAATTCAATTATTTCTCAACAACTATATTTATATGCTCTTAAGAAGGTTGAATAAGATTA
288103 AACA
129 AACA
** * * * **
288107 TTGAGATTAAAATTTTAAATTTATTAAATATTTTTAAGAATTATTACATAAACAAACTTGGTTAA
1 TAAAGATTAAAATATTAAA--TATTAAATATTTTCAACAATTATTACATAAACAAACTTAATTAA
* * *
288172 ACTTAAAATTCAATTATTTCTCAATAACTGTATTTATATGCTCTTAAGAAGTTTGAATAAGATTA
64 ACTTAAAATTCAATTATTTCTCAACAACTATATTTATATGCTCTTAAGAAGGTTGAATAAGATTA
*
288237 GATAGA
129 -A-ACA
288243 -AAAGATTTATAAATATTAAA-ATTAAA-ATTTT
1 TAAAGA-TTA-AAATATTAAATATTAAATATTTT
288274 AAATTTATTA
Statistics
Matches: 141, Mismatches: 21, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
133 7 0.05
134 116 0.82
135 4 0.03
136 5 0.04
137 9 0.06
ACGTcount: A:0.44, C:0.07, G:0.08, T:0.42
Consensus pattern (132 bp):
TAAAGATTAAAATATTAAATATTAAATATTTTCAACAATTATTACATAAACAAACTTAATTAAAC
TTAAAATTCAATTATTTCTCAACAACTATATTTATATGCTCTTAAGAAGGTTGAATAAGATTAAA
CA
Found at i:288387 original size:151 final size:151
Alignment explanation
Indices: 288112--288387 Score: 365
Period size: 151 Copynumber: 1.8 Consensus size: 151
288102 AAACATTGAG
* * * *
288112 ATTAAAATTTTAAATTTATTAAATATTTTTAAGAATTATTACATAAACAAACTTGGTTAAACTTA
1 ATTAAAATTTTAAATTTATTAAATATTCTCAAGAATAATTACATAAACAAACTTGGTTAAACTCA
* * * * ****
288177 AAATTCAATTATTTCTCAATAACTGTATTTATATGCTCTTAAGAAGTTTGAATAAGATTAGATAG
66 AAATTCAATTATTCCTCAACAACTGCATTTATATGCTATTAAGAAGAACCAATAAGATTAGATAG
288242 AAAAGATTTATAAATATTAAA
131 AAAAGATTTATAAATATTAAA
* ** *
288263 ATTAAAATTTTAAATTTATTAAATATTCTCAAGAGTAATTATGTAAACAAGCTTGGTTAAACTCA
1 ATTAAAATTTTAAATTTATTAAATATTCTCAAGAATAATTACATAAACAAACTTGGTTAAACTCA
* * *
288328 AGATTCAATTGTTCCTCAACAACTGCATTTATATGCTATTAAGAA-AACCAAGTAGGATTA
66 AAATTCAATTATTCCTCAACAACTGCATTTATATGCTATTAAGAAGAACCAA-TAAGATTA
288388 AACCCTAAAT
Statistics
Matches: 105, Mismatches: 19, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
150 2 0.02
151 103 0.98
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.38
Consensus pattern (151 bp):
ATTAAAATTTTAAATTTATTAAATATTCTCAAGAATAATTACATAAACAAACTTGGTTAAACTCA
AAATTCAATTATTCCTCAACAACTGCATTTATATGCTATTAAGAAGAACCAATAAGATTAGATAG
AAAAGATTTATAAATATTAAA
Found at i:289798 original size:25 final size:28
Alignment explanation
Indices: 289756--289814 Score: 79
Period size: 26 Copynumber: 2.2 Consensus size: 28
289746 ATTTAAAATA
* *
289756 TATTAAAGTATTAAAT-AAATTA-TTTT
1 TATTAAAATATTAAATAAAATAATTTTT
289782 TATTAAAATA-TAAATAAAATAATTTTT
1 TATTAAAATATTAAATAAAATAATTTTT
289809 TATTAA
1 TATTAA
289815 TTAAATAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 5 0.17
26 14 0.48
27 10 0.34
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (28 bp):
TATTAAAATATTAAATAAAATAATTTTT
Found at i:290184 original size:15 final size:14
Alignment explanation
Indices: 290166--290228 Score: 54
Period size: 14 Copynumber: 4.3 Consensus size: 14
290156 TTTTAAAAAA
290166 ATAATATTTATAATT
1 ATAATATTTA-AATT
290181 ATAATATTTAAATT
1 ATAATATTTAAATT
* * **
290195 TTAGTATACAAATTTT
1 ATAATATTTAAA--TT
*
290211 TTAATATTTAAATT
1 ATAATATTTAAATT
290225 ATAA
1 ATAA
290229 AAAATAATTT
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
14 17 0.45
15 10 0.26
16 11 0.29
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (14 bp):
ATAATATTTAAATT
Found at i:290489 original size:24 final size:22
Alignment explanation
Indices: 290445--290490 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
290435 GTGACTGATA
**
290445 TTTTATTTTTAAAATTTTTATT
1 TTTTATTTTTAAAATAATTATT
290467 TTTTATTTATTAAAAATAATTATT
1 TTTTATTT-TT-AAAATAATTATT
290491 GATCATTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 8 0.40
23 2 0.10
24 10 0.50
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
TTTTATTTTTAAAATAATTATT
Found at i:291971 original size:2 final size:2
Alignment explanation
Indices: 291920--291955 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
291910 AATATATGAC
*
291920 AT AT AT AT AT AA 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
291956 GAGATTAACA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:292208 original size:32 final size:31
Alignment explanation
Indices: 292128--292209 Score: 83
Period size: 31 Copynumber: 2.6 Consensus size: 31
292118 TTTCTTCTTC
* *
292128 TTTCTTCTCTTGCTTCCTTATACCTTTTTTT
1 TTTCTTATCTTGCTTCCTCATACCTTTTTTT
* *** **
292159 TTTCTTTTCTCATTTCCTCATTTCTTTTTTT
1 TTTCTTATCTTGCTTCCTCATACCTTTTTTT
292190 TTTCCTTATCTTGCTTCCTC
1 TTT-CTTATCTTGCTTCCTC
292210 CAACCTAGCT
Statistics
Matches: 39, Mismatches: 11, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
31 27 0.69
32 12 0.31
ACGTcount: A:0.06, C:0.27, G:0.02, T:0.65
Consensus pattern (31 bp):
TTTCTTATCTTGCTTCCTCATACCTTTTTTT
Found at i:293177 original size:316 final size:316
Alignment explanation
Indices: 292593--293296 Score: 713
Period size: 316 Copynumber: 2.2 Consensus size: 316
292583 AAGTAAGGTG
* * * * * *
292593 CATTAATCCTACATTGGACAATAAAGGGAAGATCTTTAGGCATATAAACGGGTACGCTGCATATC
1 CATTAATCCCACATCGGACAAGAAAGGGAAGATCTTTGGGCATATAAACGAGTACGCTGCACATC
* * * *
292658 TTATCAGACATGCCTTTTGGGAAGAGGGTAATGGCCCCGTGACAAGTGGTATCAGAGCCAACACT
66 CTATCAAACATGCCTTTTGGGAAGAGGGTAATGACCCCGTGACAAGTAGTATCAGAGCCAACACT
* * * * *
292723 TAACTATCCAATTTCATGCCAAGCATTCCAACGAGTGGGGTAAATAGGGTGGATCAATTGTGACT
131 TAACGATCCAATTTCACGCCAAGCATCCCAACGAGTGGGGTAAATAGGATGGACCAATTGTGACT
* * * * * * * *
292788 TCACACCGAACATCCTGAGGATGAGGTTTGTAAAAATTAAGGAGAAGCCCGTGATAGGGGCGTCA
196 CCACACCAAACATCCCGAGGATGAGGTTCGAAAAAAATAAGGAGAAGCCCGCGATAGGGGCATCA
* ** * **
292853 CGAGATTGGTTGGGAGAGAATGTCATGCCAAATGCTCTAAAAAAGTAGACAGGGTA
261 CGAGATTGGATGGGAGAGAATGTCATGCCAAACACTATAAAAAAGTAGACAAAGTA
* * * **
292909 CATTAATCCCACATCGGACAAGAAAGGGAAGATCTTTGGGCATATAAATGAGTGCGTTGTGCATC
1 CATTAATCCCACATCGGACAAGAAAGGGAAGATCTTTGGGCATATAAACGAGTACGCTGCACATC
* * *
292974 CTATCAAACATGTCTTTTGGGAATGA-GGTAATGACCCCGTGACAAGTAGTATTAGAGCCAACCC
66 CTATCAAACATGCCTTTTGGGAA-GAGGGTAATGACCCCGTGACAAGTAGTATCAGAGCCAACAC
* * * * * * * **
293038 TTGACGGTTCGATTTTACGCTAAGCA-CCCAACGGGTGGGGTAGGTAGGATGGACCAACTT-TGA
130 TTAACGATCCAATTTCACGCCAAGCATCCCAACGAGTGGGGTAAATAGGATGGACCAA-TTGTGA
** * *
293101 CTCCACGTCAAACATCCCGAGGGTGGAGG-TCGAAAAAAAT-AGTGAAGAAGCCTGCGAT-GGGG
194 CTCCACACCAAACATCCCGAGGAT-GAGGTTCGAAAAAAATAAG-G-AGAAGCCCGCGATAGGGG
* * * * * * *
293163 TTATCAGGAGATTGGATGTGAGAGAATGTCATGCTAAGCACTATAAAAAAGTAGGCAAAGTG
256 -CATCACGAGATTGGATGGGAGAGAATGTCATGCCAAACACTATAAAAAAGTAGACAAAGTA
* * * * * *
293225 CATTAATCACACATTC-AACAAGAAA-GGAATGATTTTTGGGCATAGAAGCGGGTACGCTGCACA
1 CATTAATCCCACA-TCGGACAAGAAAGGGAA-GATCTTTGGGCATATAAACGAGTACGCTGCACA
293288 TCCTATCAA
64 TCCTATCAA
293297 TTTTTTTTTA
Statistics
Matches: 312, Mismatches: 68, Indels: 16
0.79 0.17 0.04
Matches are distributed among these distances:
314 2 0.01
315 63 0.20
316 243 0.78
317 4 0.01
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.23
Consensus pattern (316 bp):
CATTAATCCCACATCGGACAAGAAAGGGAAGATCTTTGGGCATATAAACGAGTACGCTGCACATC
CTATCAAACATGCCTTTTGGGAAGAGGGTAATGACCCCGTGACAAGTAGTATCAGAGCCAACACT
TAACGATCCAATTTCACGCCAAGCATCCCAACGAGTGGGGTAAATAGGATGGACCAATTGTGACT
CCACACCAAACATCCCGAGGATGAGGTTCGAAAAAAATAAGGAGAAGCCCGCGATAGGGGCATCA
CGAGATTGGATGGGAGAGAATGTCATGCCAAACACTATAAAAAAGTAGACAAAGTA
Found at i:294618 original size:78 final size:78
Alignment explanation
Indices: 294488--294643 Score: 267
Period size: 78 Copynumber: 2.0 Consensus size: 78
294478 TATAAATGTC
* *
294488 TTCATCGACATCTTCGTGAACCCATTGAACTCCGATACTAGTACTAGGGATATTCTCATCCAAGT
1 TTCATCGACATCTTCATGAACCCATTGAACTCCGATACTAGTACTAGAGATATTCTCATCCAAGT
294553 TTTGATTGGCAAA
66 TTTGATTGGCAAA
* * *
294566 TTCATCGACATCTTCATGAACCCATTGAACTTCGATACTAGTACTAGAGATATTTTCTTCCAAGT
1 TTCATCGACATCTTCATGAACCCATTGAACTCCGATACTAGTACTAGAGATATTCTCATCCAAGT
294631 TTTGATTGGCAAA
66 TTTGATTGGCAAA
294644 AAGTAAGCAT
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
78 73 1.00
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (78 bp):
TTCATCGACATCTTCATGAACCCATTGAACTCCGATACTAGTACTAGAGATATTCTCATCCAAGT
TTTGATTGGCAAA
Found at i:301109 original size:17 final size:17
Alignment explanation
Indices: 301087--301158 Score: 69
Period size: 17 Copynumber: 4.3 Consensus size: 17
301077 TATATAATTT
*
301087 TTTATATATAAATTATA
1 TTTATATATATATTATA
*
301104 TTTATAT-TATTTTATA
1 TTTATATATATATTATA
*
301120 TATTAT-TTTATATTATA
1 T-TTATATATATATTATA
301137 TTT-TATATTATATTATA
1 TTTATATA-TATATTATA
*
301154 ATTAT
1 TTTAT
301159 TTTTTAATTG
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
15 1 0.02
16 12 0.27
17 31 0.69
18 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTATATATATATTATA
Found at i:301129 original size:22 final size:22
Alignment explanation
Indices: 301093--301161 Score: 86
Period size: 22 Copynumber: 3.0 Consensus size: 22
301083 ATTTTTTATA
*
301093 TATAAATTATATTTATATTATTT
1 TATATATTAT-TTTATATTATTT
301116 TATATATTATTTTATATTATATT
1 TATATATTATTTTATATTAT-TT
*
301139 T-TATATTATATTATAATTATTT
1 TATATATTATTTTAT-ATTATTT
301161 T
1 T
301162 TTAATTGTGT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
22 25 0.60
23 17 0.40
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TATATATTATTTTATATTATTT
Found at i:301135 original size:27 final size:26
Alignment explanation
Indices: 301075--301152 Score: 81
Period size: 27 Copynumber: 3.0 Consensus size: 26
301065 GTATTACACA
*
301075 TTTATA-TA-ATTTTTTATATA-TAA
1 TTTATATTATATTTTTTATATATTAT
*
301098 ATTATATTTATATTATTTTATATATTAT
1 TTTATA-TTATATT-TTTTATATATTAT
*
301126 TTTATATTATATTTTATATTATATTAT
1 TTTATATTATATTTTTTA-TATATTAT
301153 AATTATTTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
23 5 0.11
25 2 0.04
26 7 0.16
27 24 0.53
28 7 0.16
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (26 bp):
TTTATATTATATTTTTTATATATTAT
Found at i:301145 original size:12 final size:12
Alignment explanation
Indices: 301098--301164 Score: 72
Period size: 12 Copynumber: 5.9 Consensus size: 12
301088 TTATATATAA
301098 ATTATA-TTTAT
1 ATTATATTTTAT
301109 A-T-TATTTTAT
1 ATTATATTTTAT
301119 A-TATTATTTTAT
1 ATTA-TATTTTAT
301131 ATTATATTTTAT
1 ATTATATTTTAT
*
301143 ATTATATTATA-
1 ATTATATTTTAT
*
301154 ATTATTTTTTA
1 ATTATATTTTA
301165 ATTGTGTTTG
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
9 2 0.04
10 8 0.16
11 10 0.20
12 27 0.55
13 2 0.04
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
ATTATATTTTAT
Found at i:301153 original size:5 final size:5
Alignment explanation
Indices: 301088--301158 Score: 58
Period size: 5 Copynumber: 13.8 Consensus size: 5
301078 ATATAATTTT
* *
301088 TTATA TATAAA TTATA TTTATA TTAT- TT-TA -TATA TTATT TTATA TTATA
1 TTATA T-TATA TTATA -TTATA TTATA TTATA TTATA TTATA TTATA TTATA
301137 TTTTATA TTATA TTATAA TTAT
1 --TTATA TTATA TTAT-A TTAT
301159 TTTTTAATTG
Statistics
Matches: 54, Mismatches: 4, Indels: 15
0.74 0.05 0.21
Matches are distributed among these distances:
3 2 0.04
4 4 0.07
5 29 0.54
6 14 0.26
7 5 0.09
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTATA
Found at i:306007 original size:2 final size:2
Alignment explanation
Indices: 306000--306024 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
305990 GTCATATAAT
306000 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
306025 CATCTCCTGA
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:306024 original size:48 final size:48
Alignment explanation
Indices: 305950--306049 Score: 175
Period size: 48 Copynumber: 2.1 Consensus size: 48
305940 ACGGCAACAC
305950 TTATCATATATATATATATATATATATCATCCCCTGAAATGTCATATAA
1 TTATCATATATATATATATATATATATCATCCCCTGAAATGTCATA-AA
*
305999 TTAT-ATATATATATATATATATATATCATCTCCTGAAATGTCATAAA
1 TTATCATATATATATATATATATATATCATCCCCTGAAATGTCATAAA
306046 TTAT
1 TTAT
306050 TAAGGGCATC
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
47 6 0.12
48 40 0.80
49 4 0.08
ACGTcount: A:0.41, C:0.12, G:0.04, T:0.43
Consensus pattern (48 bp):
TTATCATATATATATATATATATATATCATCCCCTGAAATGTCATAAA
Found at i:306351 original size:20 final size:19
Alignment explanation
Indices: 306306--306352 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
306296 TTGATAAAAA
306306 AATTTATAAAAAAAATATTC
1 AATTT-TAAAAAAAATATTC
* *
306326 ATTTTTAAAAAAATATATTT
1 AATTTTAAAAAAA-ATATTC
306346 AATTTTA
1 AATTTTA
306353 TACGAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (19 bp):
AATTTTAAAAAAAATATTC
Found at i:313126 original size:18 final size:18
Alignment explanation
Indices: 313103--313137 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
313093 ATTATAACTA
313103 TTAAAATTTAAATTTAAT
1 TTAAAATTTAAATTTAAT
313121 TTAAAATTTAAATTTAA
1 TTAAAATTTAAATTTAA
313138 AATTATTGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTAAAATTTAAATTTAAT
Found at i:313141 original size:7 final size:6
Alignment explanation
Indices: 313106--313138 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
313096 ATAACTATTA
313106 AAATTT AAATTT -AATTT AAAATTT AAATTT AAA
1 AAATTT AAATTT AAATTT -AAATTT AAATTT AAA
313139 ATTATTGGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 5 0.20
6 15 0.60
7 5 0.20
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (6 bp):
AAATTT
Found at i:321360 original size:20 final size:20
Alignment explanation
Indices: 321335--321378 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
321325 CACAAAACCC
*
321335 AAAATTGAAGCTTTGCAAC-T
1 AAAATT-AAGCTCTGCAACTT
*
321355 AAAATTTAGCTCTGCAACTT
1 AAAATTAAGCTCTGCAACTT
321375 AAAA
1 AAAA
321379 AAAATGGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.43, C:0.16, G:0.11, T:0.30
Consensus pattern (20 bp):
AAAATTAAGCTCTGCAACTT
Found at i:322294 original size:2 final size:2
Alignment explanation
Indices: 322243--322285 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
322233 CCTTTGCTGA
322243 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
322285 C
1 C
322286 CCCCTCTCTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:322596 original size:12 final size:12
Alignment explanation
Indices: 322573--322623 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
322563 ATTAGATAAT
322573 ATAAAT-TTAAA
1 ATAAATATTAAA
322584 ATAAATATTAAA
1 ATAAATATTAAA
** *
322596 ATTTACATTAAAA
1 ATAAATATT-AAA
322609 ATAAATTATTAAA
1 ATAAA-TATTAAA
322622 AT
1 AT
322624 TTTATAAATT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
11 6 0.19
12 11 0.35
13 11 0.35
14 3 0.10
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (12 bp):
ATAAATATTAAA
Found at i:322630 original size:18 final size:17
Alignment explanation
Indices: 322609--322644 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
322599 TACATTAAAA
322609 ATAAATTATTAAAATTTT
1 ATAAATTA-TAAAATTTT
*
322627 ATAAATTATAATATTTT
1 ATAAATTATAAAATTTT
322644 A
1 A
322645 AATATAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATAAATTATAAAATTTT
Found at i:322927 original size:3 final size:3
Alignment explanation
Indices: 322919--322947 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
322909 ATGCTTTACC
322919 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
322948 CCACTTTTGT
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:323235 original size:14 final size:14
Alignment explanation
Indices: 323216--323267 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
323206 TTTAATTTTA
323216 AATAAATATTATAT
1 AATAAATATTATAT
323230 AATAAATAATTAATAT
1 AATAAAT-ATT-ATAT
* *
323246 AAAATAAATTTTATTT
1 --AATAAATATTATAT
323262 AATAAA
1 AATAAA
323268 ATAATTTTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
14 13 0.41
15 3 0.09
16 7 0.22
17 2 0.06
18 7 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AATAAATATTATAT
Found at i:323237 original size:18 final size:18
Alignment explanation
Indices: 323214--323254 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
323204 ATTTTAATTT
* *
323214 TAAATAAATATTATATAA
1 TAAATAAATAATATAAAA
*
323232 TAAATAATTAATATAAAA
1 TAAATAAATAATATAAAA
323250 TAAAT
1 TAAAT
323255 TTTATTTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TAAATAAATAATATAAAA
Found at i:323285 original size:19 final size:18
Alignment explanation
Indices: 323197--323285 Score: 57
Period size: 19 Copynumber: 5.2 Consensus size: 18
323187 TTAAATATTT
*
323197 TAAAAT-AATTTTA-ATT
1 TAAAATAAATTTTATATA
* *
323213 TTAAATAAATATTATATA
1 TAAAATAAATTTTATATA
323231 -ATAAAT-AA--TTA-ATA
1 TA-AAATAAATTTTATATA
*
323245 TAAAATAAATTTTATTTAA
1 TAAAATAAATTTTATAT-A
*
323264 TAAAATAATTTTTGATATA
1 TAAAATAAATTTT-ATATA
323283 TAA
1 TAA
323286 CTTTAGAGGT
Statistics
Matches: 56, Mismatches: 7, Indels: 17
0.70 0.09 0.21
Matches are distributed among these distances:
14 7 0.12
15 6 0.11
16 5 0.09
17 11 0.20
18 7 0.12
19 17 0.30
20 3 0.05
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (18 bp):
TAAAATAAATTTTATATA
Found at i:323722 original size:14 final size:15
Alignment explanation
Indices: 323703--323777 Score: 68
Period size: 15 Copynumber: 5.1 Consensus size: 15
323693 TTAAAAAATT
323703 TAATATT-TATATTA
1 TAATATTATATATTA
323717 TAATATTATATATT-
1 TAATATTATATATTA
*
323731 TATTCATTATATGA-TA
1 TAAT-ATTATAT-ATTA
*
323747 TAA-ATTATATAATA
1 TAATATTATATATTA
* *
323761 TAAAATAATATATTA
1 TAATATTATATATTA
323776 TA
1 TA
323778 TAATTAAAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
13 1 0.02
14 22 0.43
15 25 0.49
16 3 0.06
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (15 bp):
TAATATTATATATTA
Found at i:325017 original size:21 final size:20
Alignment explanation
Indices: 324987--325032 Score: 67
Period size: 21 Copynumber: 2.3 Consensus size: 20
324977 GGTACTATTG
324987 ATATTTTAATAAAATAATTA
1 ATATTTTAATAAAATAATTA
*
325007 ATATATTTAATAATATAATT-
1 ATAT-TTTAATAAAATAATTA
325027 ATATTT
1 ATATTT
325033 ATTATATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 2 0.08
20 8 0.33
21 14 0.58
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATTTTAATAAAATAATTA
Found at i:325048 original size:18 final size:18
Alignment explanation
Indices: 324999--325050 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
324989 ATTTTAATAA
324999 AATAAT-TAAT-ATATTT
1 AATAATATAATAATATTT
*
325015 AATAATATAATTATATTT
1 AATAATATAATAATATTT
*
325033 -ATTATATATATAATATTT
1 AATAATATA-ATAATATTT
325051 TTAAATCGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 6 0.19
17 11 0.35
18 14 0.45
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
AATAATATAATAATATTT
Found at i:325230 original size:19 final size:19
Alignment explanation
Indices: 325181--325240 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
325171 ATATATATGA
*
325181 ATAAAATATA-AAATAAA-
1 ATAAATTATATAAATAAAT
*
325198 ATAATTTA-ATTAAATAAAT
1 ATAAATTATA-TAAATAAAT
325217 ATAAATTATATAAA-AAATT
1 ATAAATTATATAAATAAA-T
325236 ATAAA
1 ATAAA
325241 ATTAAATCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
16 1 0.03
17 6 0.17
18 10 0.29
19 17 0.49
20 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
ATAAATTATATAAATAAAT
Found at i:325630 original size:3 final size:3
Alignment explanation
Indices: 325622--325651 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
325612 GACTTCATAT
325622 ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
325652 GTTTGATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:325644 original size:14 final size:14
Alignment explanation
Indices: 325625--325651 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
325615 TTCATATATA
325625 ATAATAATAATAAT
1 ATAATAATAATAAT
325639 ATAATAATAATAA
1 ATAATAATAATAA
325652 GTTTGATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
ATAATAATAATAAT
Found at i:325989 original size:15 final size:14
Alignment explanation
Indices: 325969--326013 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
325959 GATTATTTTA
325969 AAAAATTTATATTT
1 AAAAATTTATATTT
*
325983 AATAAATTTAAATTT
1 AA-AAATTTATATTT
*
325998 TAAAATTTAATATTT
1 AAAAATTT-ATATTT
326013 A
1 A
326014 TAATATTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
14 8 0.32
15 17 0.68
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
AAAAATTTATATTT
Found at i:327038 original size:11 final size:11
Alignment explanation
Indices: 327024--327102 Score: 59
Period size: 11 Copynumber: 6.6 Consensus size: 11
327014 GTTAAATCTC
327024 TATAATATAAA
1 TATAATATAAA
*
327035 TATAAAATAAATA
1 TATAATAT-AA-A
327048 TATAATATAAA
1 TATAATATAAA
327059 TTATTAATATATTAA
1 -TA-TAATATA--AA
**
327074 TATAATATATT
1 TATAATATAAA
* *
327085 TAAAATATAAT
1 TATAATATAAA
327096 TATAATA
1 TATAATA
327103 CGATAAAATT
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
11 23 0.42
12 6 0.11
13 22 0.40
14 2 0.04
15 2 0.04
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
TATAATATAAA
Found at i:327066 original size:13 final size:12
Alignment explanation
Indices: 327026--327082 Score: 55
Period size: 13 Copynumber: 4.6 Consensus size: 12
327016 TAAATCTCTA
327026 TAATATAAATA-
1 TAATATAAATAT
*
327037 TAAAATAAATAT
1 TAATATAAATAT
327049 ATAATATAAATTAT
1 -TAATATAAA-TAT
327063 TAATATATTAATA-
1 TAATATA--AATAT
327076 TAATATA
1 TAATATA
327083 TTTAAAATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
11 10 0.26
13 22 0.56
14 5 0.13
15 2 0.05
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
TAATATAAATAT
Found at i:327067 original size:24 final size:26
Alignment explanation
Indices: 327024--327126 Score: 74
Period size: 24 Copynumber: 4.0 Consensus size: 26
327014 GTTAAATCTC
327024 TATAATATAAATATAAAATA-AAT-A
1 TATAATATAAATATAAAATATAATAA
* *
327048 TATAATATAAAT-TATTAATATATTAA
1 TATAATATAAATATA-AAATATAATAA
* *
327074 TATAATAT--ATTTAAAATATAATTA
1 TATAATATAAATATAAAATATAATAA
*
327098 TAATACGATA-AAATTTATAAATATAATAA
1 T-ATA--ATATAAATATA-AAATATAATAA
327127 GTGATTTTGT
Statistics
Matches: 63, Mismatches: 6, Indels: 15
0.75 0.07 0.18
Matches are distributed among these distances:
23 2 0.03
24 27 0.43
25 7 0.11
26 9 0.14
27 3 0.05
28 5 0.08
29 10 0.16
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (26 bp):
TATAATATAAATATAAAATATAATAA
Found at i:327071 original size:8 final size:7
Alignment explanation
Indices: 327024--327102 Score: 57
Period size: 6 Copynumber: 12.0 Consensus size: 7
327014 GTTAAATCTC
327024 TATAATA
1 TATAATA
327031 TA-AATA
1 TATAATA
327037 TA-AA-A
1 TATAATA
327042 TA-AATA
1 TATAATA
327048 TATAATA
1 TATAATA
327055 TA-AAT-
1 TATAATA
327060 TATTAATA
1 TA-TAATA
327068 TATTAATA
1 TA-TAATA
327076 TA-ATATA
1 TATA-ATA
* *
327083 TTTAAAA
1 TATAATA
327090 TATAAT-
1 TATAATA
327096 TATAATA
1 TATAATA
327103 CGATAAAATT
Statistics
Matches: 60, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
5 7 0.12
6 21 0.35
7 21 0.35
8 11 0.18
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
TATAATA
Found at i:327084 original size:21 final size:19
Alignment explanation
Indices: 327024--327102 Score: 71
Period size: 18 Copynumber: 4.4 Consensus size: 19
327014 GTTAAATCTC
*
327024 TATAATATA-AATATAAAA
1 TATAATATATAATATAAAT
327042 TA-AATATATAATATAAAT
1 TATAATATATAATATAAAT
327060 TATTAATATATTAATAT-AA-
1 TA-TAATATA-TAATATAAAT
* *
327079 TAT-ATTTAAAATAT-AAT
1 TATAATATATAATATAAAT
327096 TATAATA
1 TATAATA
327103 CGATAAAATT
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
16 7 0.14
17 13 0.25
18 15 0.29
19 2 0.04
20 8 0.16
21 6 0.12
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TATAATATATAATATAAAT
Found at i:327087 original size:22 final size:21
Alignment explanation
Indices: 327044--327102 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 21
327034 ATATAAAATA
327044 AATATATAATATAA-ATTATT
1 AATATATAATATAATATTATT
327064 AATATATTAATATAATA-TATTT
1 AATATA-TAATATAATATTA-TT
*
327086 AAAATATAATTATAATA
1 AATATATAA-TATAATA
327103 CGATAAAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
20 6 0.18
21 13 0.38
22 15 0.44
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AATATATAATATAATATTATT
Found at i:327500 original size:12 final size:12
Alignment explanation
Indices: 327477--327508 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
327467 CTTTAAGCAC
327477 TATAAT-TAAAA
1 TATAATATAAAA
327488 TATAATATAAAA
1 TATAATATAAAA
327500 TATAATATA
1 TATAATATA
327509 TTATAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
TATAATATAAAA
Found at i:327518 original size:30 final size:32
Alignment explanation
Indices: 327484--327543 Score: 97
Period size: 30 Copynumber: 1.9 Consensus size: 32
327474 CACTATAATT
327484 AAAATATAATATAAA-ATAT-AATATATTATA
1 AAAATATAATATAAATATATAAATATATTATA
*
327514 AAAATATGATATAAATATATAAATATATTA
1 AAAATATAATATAAATATATAAATATATTA
327544 AAATTTTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 14 0.52
31 4 0.15
32 9 0.33
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (32 bp):
AAAATATAATATAAATATATAAATATATTATA
Found at i:327537 original size:19 final size:17
Alignment explanation
Indices: 327486--327540 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 17
327476 CTATAATTAA
327486 AATATAATATAAAATAT
1 AATATAATATAAAATAT
*
327503 AATATATTATAAAAATAT
1 AATATAATAT-AAAATAT
*
327521 GATATAAATATATAAATAT
1 AATAT-AATATA-AAATAT
327540 A
1 A
327541 TTAAAATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
17 9 0.29
18 12 0.39
19 10 0.32
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (17 bp):
AATATAATATAAAATAT
Found at i:327576 original size:31 final size:30
Alignment explanation
Indices: 327492--327580 Score: 83
Period size: 31 Copynumber: 2.9 Consensus size: 30
327482 TTAAAATATA
* * *
327492 ATAT-AAAATAT-AATATATTATAAAAATATG
1 ATATAAAAATATAAATATA-T-TAAAATTTTT
*
327522 ATATAAATATATAAATATATTAAAATTTTT
1 ATATAAAAATATAAATATATTAAAATTTTT
* *
327552 ATATAAAAATTATTAATTTATTAAAATTT
1 ATATAAAAA-TATAAATATATTAAAATTT
327581 ATTTAAATAA
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
30 19 0.39
31 24 0.49
32 6 0.12
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (30 bp):
ATATAAAAATATAAATATATTAAAATTTTT
Found at i:329341 original size:32 final size:32
Alignment explanation
Indices: 329299--329367 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 32
329289 TTTCACTTCA
*
329299 AGTCACTTCGAATTTAGATTACTTTAATTTTG
1 AGTCACTTCGAATTTAGATCACTTTAATTTTG
* * * * *
329331 AGTCATTTCGATTTTTGATCATTTTATTTTTG
1 AGTCACTTCGAATTTAGATCACTTTAATTTTG
329363 AGTCA
1 AGTCA
329368 AATGGATTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.25, C:0.12, G:0.13, T:0.51
Consensus pattern (32 bp):
AGTCACTTCGAATTTAGATCACTTTAATTTTG
Found at i:329361 original size:15 final size:16
Alignment explanation
Indices: 329321--329367 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
329311 TTTAGATTAC
*
329321 TTTAATTTTGAGTCAT
1 TTTATTTTTGAGTCAT
*
329337 TTCGATTTTTGA-TCAT
1 TT-TATTTTTGAGTCAT
329353 TTTATTTTTGAGTCA
1 TTTATTTTTGAGTCA
329368 AATGGATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 8 0.31
16 11 0.42
17 7 0.27
ACGTcount: A:0.21, C:0.09, G:0.13, T:0.57
Consensus pattern (16 bp):
TTTATTTTTGAGTCAT
Found at i:330927 original size:17 final size:19
Alignment explanation
Indices: 330893--330930 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
330883 TTAAAACAAA
330893 ATATAAACATTGAAATAAT
1 ATATAAACATTGAAATAAT
*
330912 ATATAAA-ATT-AGATAAT
1 ATATAAACATTGAAATAAT
330929 AT
1 AT
330931 GAATCATGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 8 0.44
18 3 0.17
19 7 0.39
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34
Consensus pattern (19 bp):
ATATAAACATTGAAATAAT
Found at i:332223 original size:14 final size:15
Alignment explanation
Indices: 332196--332225 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
332186 TTTTATATTA
332196 ATATTTATATATTTT
1 ATATTTATATATTTT
332211 ATATTTA-ATATTTT
1 ATATTTATATATTTT
332225 A
1 A
332226 AAAATTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
ATATTTATATATTTT
Found at i:332254 original size:19 final size:20
Alignment explanation
Indices: 332219--332257 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
332209 TTATATTTAA
*
332219 TATTTTAAAAATTATAATTT
1 TATTTTAAAAATAATAATTT
332239 TATTTT-AAAATAATAATTT
1 TATTTTAAAAATAATAATTT
332258 AGATCGGATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TATTTTAAAAATAATAATTT
Found at i:333275 original size:14 final size:15
Alignment explanation
Indices: 333253--333300 Score: 55
Period size: 14 Copynumber: 3.3 Consensus size: 15
333243 TAACTATAAT
*
333253 AATTATATATAATTT
1 AATTATATATAATTC
*
333268 AA-TATATA-AAATC
1 AATTATATATAATTC
*
333281 AATTATATATAATGC
1 AATTATATATAATTC
333296 AATTA
1 AATTA
333301 AATAAAATGA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
13 5 0.19
14 12 0.44
15 10 0.37
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (15 bp):
AATTATATATAATTC
Found at i:333275 original size:25 final size:27
Alignment explanation
Indices: 333233--333293 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
333223 TTAATTTATT
*
333233 TATATAATTATAACTAT-AAT-AATTA
1 TATATAATTATAAATATAAATCAATTA
333258 TATATAATT-TAATATATAAAATCAATTA
1 TATATAATTATAA-ATAT-AAATCAATTA
333286 TATATAAT
1 TATATAAT
333294 GCAATTAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
24 3 0.10
25 12 0.39
27 3 0.10
28 13 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (27 bp):
TATATAATTATAAATATAAATCAATTA
Found at i:333331 original size:26 final size:25
Alignment explanation
Indices: 333299--333353 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
333289 ATAATGCAAT
*
333299 TAAATAAAATGAAATAAT-TAATATTA
1 TAAAT-AAATAAAATAATATAATA-TA
*
333325 TAAATAAATAAAATATTATAATATA
1 TAAATAAATAAAATAATATAATATA
333350 TAAA
1 TAAA
333354 ATTTCATTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 16 0.62
26 10 0.38
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (25 bp):
TAAATAAATAAAATAATATAATATA
Found at i:333352 original size:17 final size:18
Alignment explanation
Indices: 333318--333355 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
333308 TGAAATAATT
333318 AATATTATAAATAAATAA
1 AATATTATAAATAAATAA
*
333336 AATATTAT-AATATATAA
1 AATATTATAAATAAATAA
333353 AAT
1 AAT
333356 TTCATTGAAA
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:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
AATATTATAAATAAATAA
Found at i:334101 original size:27 final size:26
Alignment explanation
Indices: 334071--334148 Score: 70
Period size: 27 Copynumber: 2.9 Consensus size: 26
334061 TATAATTATA
334071 TTTAAAATATTATATATTTATATAAAT
1 TTTAAAATATTATATATTTATAT-AAT
* *
334098 TTTAATATATTA-ATTATTTAT-TTAT
1 TTTAAAATATTATA-TATTTATATAAT
*
334123 TTTAAATTATATAATTATATTTATAT
1 TTTAAA--ATATTA-TATATTTATAT
334149 TATAATATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
25 7 0.17
26 2 0.05
27 23 0.56
28 7 0.17
29 2 0.05
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (26 bp):
TTTAAAATATTATATATTTATATAAT
Found at i:334132 original size:18 final size:19
Alignment explanation
Indices: 334060--334152 Score: 74
Period size: 18 Copynumber: 5.2 Consensus size: 19
334050 TTATTATATC
*
334060 ATATAATTATATTTAAAAT
1 ATATAATTATATTTAAATT
*
334079 ATTATATATT-TATATAAATT
1 A-TATA-ATTATATTTAAATT
334099 -T-TAA-TATA-TT-AATT
1 ATATAATTATATTTAAATT
* *
334113 ATTTATTTAT-TTTAAATT
1 ATATAATTATATTTAAATT
*
334131 ATATAATTATATTTATATT
1 ATATAATTATATTTAAATT
334150 ATA
1 ATA
334153 ATATATTGAG
Statistics
Matches: 58, Mismatches: 7, Indels: 18
0.70 0.08 0.22
Matches are distributed among these distances:
14 4 0.07
15 3 0.05
16 5 0.09
17 7 0.12
18 13 0.22
19 11 0.19
20 12 0.21
21 3 0.05
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
ATATAATTATATTTAAATT
Found at i:335378 original size:29 final size:29
Alignment explanation
Indices: 335322--335402 Score: 83
Period size: 29 Copynumber: 2.7 Consensus size: 29
335312 GACAATTTTA
**
335322 AATAATAATTAATAAATAAATAAAATATATTT
1 AATAATAATTAAT--AT-AATATGATATATTT
*
335354 AATAAATAA-TAATATTATATGATATATTT
1 AAT-AATAATTAATATAATATGATATATTT
*
335383 AATTATAATTAATATAATAT
1 AATAATAATTAATATAATAT
335403 ATTTAACTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
28 4 0.10
29 24 0.57
30 2 0.05
32 7 0.17
33 5 0.12
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (29 bp):
AATAATAATTAATATAATATGATATATTT
Found at i:335791 original size:19 final size:20
Alignment explanation
Indices: 335747--335791 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
335737 TATTACATTT
*
335747 AATACTTATTTAATATTAAA
1 AATATTTATTTAATATTAAA
* *
335767 ATTATTTATTTTATA-TAAA
1 AATATTTATTTAATATTAAA
335786 AATATT
1 AATATT
335792 AAAATTAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (20 bp):
AATATTTATTTAATATTAAA
Found at i:336749 original size:37 final size:37
Alignment explanation
Indices: 336697--336780 Score: 116
Period size: 37 Copynumber: 2.3 Consensus size: 37
336687 GAAATTGATT
* *
336697 TAATATAATATATAAATTTTATTAGTT-TATAATAAAA
1 TAATATAATAAATAAATTTTATCA-TTATATAATAAAA
*
336734 TAATATAATAAATAAATTTTATCATTATATATTAAAA
1 TAATATAATAAATAAATTTTATCATTATATAATAAAA
*
336771 TAAGATAATA
1 TAATATAATA
336781 TATTTTAATT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
36 2 0.05
37 40 0.95
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.43
Consensus pattern (37 bp):
TAATATAATAAATAAATTTTATCATTATATAATAAAA
Found at i:337605 original size:2 final size:2
Alignment explanation
Indices: 337598--337631 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
337588 AGGAATGTAT
337598 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
337632 AACAACTATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:339662 original size:27 final size:29
Alignment explanation
Indices: 339632--339699 Score: 77
Period size: 32 Copynumber: 2.3 Consensus size: 29
339622 TTAAAGAATA
*
339632 ATAAAATAAA-TA-AATATATTAAAATTT
1 ATAAAATAAATTATAATATATCAAAATTT
339659 ATAAAATATAAATTATTAATATATCAAAATTT
1 AT-AAA-ATAAATTA-TAATATATCAAAATTT
339691 ATATAAATA
1 ATA-AAATA
339700 TATATTTTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
27 2 0.06
28 3 0.09
29 5 0.15
30 2 0.06
31 4 0.12
32 18 0.53
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38
Consensus pattern (29 bp):
ATAAAATAAATTATAATATATCAAAATTT
Found at i:339713 original size:33 final size:33
Alignment explanation
Indices: 339642--339714 Score: 105
Period size: 32 Copynumber: 2.2 Consensus size: 33
339632 ATAAAATAAA
*
339642 TAAATATATTAAAATTTATAAAATATAAATTAT
1 TAAATATATCAAAATTTATAAAATATAAATTAT
*
339675 T-AATATATCAAAATTTATATAAATATATATT-T
1 TAAATATATCAAAATTTATA-AAATATAAATTAT
339707 TAAATATA
1 TAAATATA
339715 ATTATAATAC
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
32 19 0.53
33 17 0.47
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (33 bp):
TAAATATATCAAAATTTATAAAATATAAATTAT
Found at i:340669 original size:13 final size:14
Alignment explanation
Indices: 340641--340672 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
340631 AGAAAGATAA
340641 ATAAATTATGTAAT
1 ATAAATTATGTAAT
340655 ATAAATTAT-TAAT
1 ATAAATTATGTAAT
340668 ATAAA
1 ATAAA
340673 AAAAATTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (14 bp):
ATAAATTATGTAAT
Found at i:343315 original size:14 final size:13
Alignment explanation
Indices: 343291--343320 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
343281 TAAATCATGT
343291 TATTTTTTTATTA
1 TATTTTTTTATTA
343304 TATTTTTATTATTA
1 TATTTTT-TTATTA
343318 TAT
1 TAT
343321 AATAAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (13 bp):
TATTTTTTTATTA
Found at i:343548 original size:13 final size:14
Alignment explanation
Indices: 343509--343550 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
343499 AAGTTTTATT
343509 ATATATACATATTTTA
1 ATATATA-AT-TTTTA
*
343525 ATATATTATTTTTA
1 ATATATAATTTTTA
343539 ATA-ATAATTTTT
1 ATATATAATTTTT
343551 TTATCTCATC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 8 0.33
15 2 0.08
16 6 0.25
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (14 bp):
ATATATAATTTTTA
Found at i:346890 original size:23 final size:23
Alignment explanation
Indices: 346864--346908 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
346854 AATCACTAAC
346864 AATATATAAATTTATATAATAAT
1 AATATATAAATTTATATAATAAT
* *
346887 AATATATAATTTTGTATAATAA
1 AATATATAAATTTATATAATAA
346909 CAATGTAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
AATATATAAATTTATATAATAAT
Found at i:347402 original size:27 final size:28
Alignment explanation
Indices: 347341--347411 Score: 92
Period size: 27 Copynumber: 2.6 Consensus size: 28
347331 AAACAAGCCT
*
347341 CCATATTTGACAAATC-CAAAGAAAACCA
1 CCATTTTTGACAAA-CACAAAGAAAACCA
*
347369 CCATTTTTGACAAACACAAA-ATAACCA
1 CCATTTTTGACAAACACAAAGAAAACCA
*
347396 CCATTTTTGATAAACA
1 CCATTTTTGACAAACA
347412 AATGGGTGGC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
27 22 0.56
28 17 0.44
ACGTcount: A:0.46, C:0.24, G:0.06, T:0.24
Consensus pattern (28 bp):
CCATTTTTGACAAACACAAAGAAAACCA
Found at i:349329 original size:21 final size:22
Alignment explanation
Indices: 349291--349336 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
349281 ATTTGTTGAA
* **
349291 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
349312 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
349334 ACT
1 ACT
349337 TGTCTGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:351813 original size:20 final size:20
Alignment explanation
Indices: 351788--351833 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
351778 AAGAATTGAA
*
351788 GAGGGATACAAGAGAGGGAT
1 GAGGGATACAAGAGAGGGAG
* **
351808 GAGGGATGCTTGAGAGGGAG
1 GAGGGATACAAGAGAGGGAG
351828 GAGGGA
1 GAGGGA
351834 ACCTCTATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.04, G:0.52, T:0.11
Consensus pattern (20 bp):
GAGGGATACAAGAGAGGGAG
Found at i:352036 original size:21 final size:22
Alignment explanation
Indices: 352003--352045 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
351993 ACTCTCACAC
* *
352003 TTGTTTGAAAAG-AGAATTAAA
1 TTGTTTCAAAAGAAAAATTAAA
*
352024 TTGTTTCATAAGAAAAATTAAA
1 TTGTTTCAAAAGAAAAATTAAA
352046 ATTAGGTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.49, C:0.02, G:0.14, T:0.35
Consensus pattern (22 bp):
TTGTTTCAAAAGAAAAATTAAA
Found at i:352084 original size:2 final size:2
Alignment explanation
Indices: 352077--352121 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
352067 GCTTATTATC
352077 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
352119 AT A
1 AT A
352122 CAATTAAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:352929 original size:22 final size:22
Alignment explanation
Indices: 352904--352945 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
352894 AAATTATATT
352904 ATTAAAAT-TTTATAATTAATAA
1 ATTAAAATATTTAT-ATTAATAA
*
352926 ATTAAATTATTTATATTAAT
1 ATTAAAATATTTATATTAAT
352946 TTTGTTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATTAAAATATTTATATTAATAA
Found at i:362580 original size:12 final size:12
Alignment explanation
Indices: 362558--362608 Score: 57
Period size: 12 Copynumber: 3.9 Consensus size: 12
362548 AACTGTGCCG
362558 TCAATTTTGAAAT
1 TCAA-TTTGAAAT
362571 TCAATTTGAAAT
1 TCAATTTGAAAT
*
362583 AGTAAATGTTGAAAT
1 --TCAAT-TTGAAAT
362598 TCAATTTGAAA
1 TCAATTTGAAA
362609 CAGTGAAGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
12 14 0.42
13 8 0.24
14 4 0.12
15 7 0.21
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.39
Consensus pattern (12 bp):
TCAATTTGAAAT
Found at i:362620 original size:27 final size:27
Alignment explanation
Indices: 362564--362620 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
362554 GCCGTCAATT
* *
362564 TTGAAATTCAATTTGAAATAGTAAATG
1 TTGAAATTCAATTTGAAACAGTAAAGG
*
362591 TTGAAATTCAATTTGAAACAGTGAAGG
1 TTGAAATTCAATTTGAAACAGTAAAGG
362618 TTG
1 TTG
362621 CATAGTACCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.35
Consensus pattern (27 bp):
TTGAAATTCAATTTGAAACAGTAAAGG
Found at i:365563 original size:202 final size:202
Alignment explanation
Indices: 365210--365612 Score: 797
Period size: 202 Copynumber: 2.0 Consensus size: 202
365200 AAATATTCGA
365210 TGATACAAATGAGGTTGTGGAGGTCTTTATTTACAGTTGAATCCTCCTTACATCAATGGCTTATA
1 TGATACAAATGAGGTTGTGGAGGTCTTTATTTACAGTTGAATCCTCCTTACATCAATGGCTTATA
365275 TTAAATTTAATGGACGGTTATGATTAATACTTATTAATAAAATCTAGAACCCCAGATAAGTTTAA
66 TTAAATTTAATGGACGGTTATGATTAATACTTATTAATAAAATCTAGAACCCCAGATAAGTTTAA
365340 ACTTTATCACTCTATCTCTATAGAGTTCTAATTAAGCTGAAGTAATTGTAATTCACTGACTTTCT
131 ACTTTATCACTCTATCTCTATAGAGTTCTAATTAAGCTGAAGTAATTGTAATTCACTGACTTTCT
365405 AAGTTTT
196 AAGTTTT
*
365412 TGATACGAATGAGGTTGTGGAGGTCTTTATTTACAGTTGAATCCTCCTTACATCAATGGCTTATA
1 TGATACAAATGAGGTTGTGGAGGTCTTTATTTACAGTTGAATCCTCCTTACATCAATGGCTTATA
365477 TTAAATTTAATGGACGGTTATGATTAATACTTATTAATAAAATCTAGAACCCCAGATAAGTTTAA
66 TTAAATTTAATGGACGGTTATGATTAATACTTATTAATAAAATCTAGAACCCCAGATAAGTTTAA
365542 ACTTTATCACTCTATCTCTATAGAGTTCTAATTAAGCTGAAGTAATTGTAATTCACTGACTTTCT
131 ACTTTATCACTCTATCTCTATAGAGTTCTAATTAAGCTGAAGTAATTGTAATTCACTGACTTTCT
365607 AAGTTT
196 AAGTTT
365613 CTAAAAACTT
Statistics
Matches: 200, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
202 200 1.00
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (202 bp):
TGATACAAATGAGGTTGTGGAGGTCTTTATTTACAGTTGAATCCTCCTTACATCAATGGCTTATA
TTAAATTTAATGGACGGTTATGATTAATACTTATTAATAAAATCTAGAACCCCAGATAAGTTTAA
ACTTTATCACTCTATCTCTATAGAGTTCTAATTAAGCTGAAGTAATTGTAATTCACTGACTTTCT
AAGTTTT
Found at i:374389 original size:18 final size:17
Alignment explanation
Indices: 374357--374399 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
374347 ATATTAAAAA
374357 ATATTAAAAATATTTTT
1 ATATTAAAAATATTTTT
*
374374 ATATTAATATATATTTTT
1 ATATTAA-AAATATTTTT
*
374392 AAATTAAA
1 ATATTAAA
374400 TTTATATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATATTAAAAATATTTTT
Found at i:380661 original size:27 final size:27
Alignment explanation
Indices: 380606--380661 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
380596 CTGTGTAACT
* *
380606 TTTATTATTTCAAATTGAATTTCATAA
1 TTTACTATTTCAAATTGAATTTCAAAA
* *
380633 TTTACTATTTTAAATTGAATTTTAAAA
1 TTTACTATTTCAAATTGAATTTCAAAA
380660 TT
1 TT
380662 GACGATTGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.38, C:0.05, G:0.04, T:0.54
Consensus pattern (27 bp):
TTTACTATTTCAAATTGAATTTCAAAA
Found at i:381594 original size:22 final size:21
Alignment explanation
Indices: 381558--381599 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
381548 TTCAATTAAA
381558 AAATTATATAAAAATTAAATTT
1 AAATTATATAAAAA-TAAATTT
381580 AAATTATA-ATAAAATAAATT
1 AAATTATATA-AAAATAAATT
381600 AAGGGTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AAATTATATAAAAATAAATTT
Found at i:381714 original size:21 final size:21
Alignment explanation
Indices: 381690--381730 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
381680 TTTTAACTTT
* *
381690 TTTTTATATATAATAGTTTTC
1 TTTTTAAAAATAATAGTTTTC
*
381711 TTTTTAAAAATAATATTTTT
1 TTTTTAAAAATAATAGTTTT
381731 AACTAACAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (21 bp):
TTTTTAAAAATAATAGTTTTC
Found at i:382054 original size:2 final size:2
Alignment explanation
Indices: 382047--382081 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
382037 TTGGAAAAAG
382047 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
382082 CATGAAATAT
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:382487 original size:45 final size:47
Alignment explanation
Indices: 382423--382512 Score: 157
Period size: 45 Copynumber: 2.0 Consensus size: 47
382413 AAAAAACAAA
382423 TATCACTTTAAGTGTATAAATA-T-ATATCTATTACATATTTTCTAT
1 TATCACTTTAAGTGTATAAATATTAATATCTATTACATATTTTCTAT
*
382468 TATCACTTTAAGTTTATAAATATTAATATCTATTACATATTTTCT
1 TATCACTTTAAGTGTATAAATATTAATATCTATTACATATTTTCT
382513 TGTTTCAATA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
45 21 0.50
46 1 0.02
47 20 0.48
ACGTcount: A:0.36, C:0.11, G:0.03, T:0.50
Consensus pattern (47 bp):
TATCACTTTAAGTGTATAAATATTAATATCTATTACATATTTTCTAT
Found at i:383141 original size:3 final size:3
Alignment explanation
Indices: 383133--383164 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
383123 AAAATTGAGT
383133 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
383165 TATTATTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:383169 original size:3 final size:3
Alignment explanation
Indices: 383163--383223 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
383153 AATAATAATA
383163 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
383211 ATT ATT ATT ATT A
1 ATT ATT ATT ATT A
383224 ACCTTATCAT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:384679 original size:19 final size:19
Alignment explanation
Indices: 384657--384695 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
384647 AGTATTTAAG
384657 TTTTTTA-ATTTTTAAATT
1 TTTTTTATATTTTTAAATT
*
384675 TTTTTTATTTTTTTAAATT
1 TTTTTTATATTTTTAAATT
384694 TT
1 TT
384696 AATTTGTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTTTTATATTTTTAAATT
Found at i:384686 original size:26 final size:26
Alignment explanation
Indices: 384657--384711 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
384647 AGTATTTAAG
*
384657 TTTTTTAATTTTTAAATTT-TTTTTAT
1 TTTTTTAAATTTT-AATTTGTTTTTAT
*
384683 TTTTTTAAATTTTAATTTGTTTTTCT
1 TTTTTTAAATTTTAATTTGTTTTTAT
384709 TTT
1 TTT
384712 AAAATATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 5 0.19
26 21 0.81
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (26 bp):
TTTTTTAAATTTTAATTTGTTTTTAT
Found at i:384705 original size:19 final size:19
Alignment explanation
Indices: 384665--384706 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
384655 AGTTTTTTAA
* *
384665 TTTTTAAATTTTTTTTATT
1 TTTTTAAATTTTATTTAGT
384684 TTTTTAAATTTTAATTT-GT
1 TTTTTAAATTTT-ATTTAGT
384703 TTTT
1 TTTT
384707 CTTTTAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 17 0.85
20 3 0.15
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.76
Consensus pattern (19 bp):
TTTTTAAATTTTATTTAGT
Found at i:385009 original size:17 final size:17
Alignment explanation
Indices: 384989--385045 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
384979 TAACTTTTAC
384989 TTTTTCATTGATAATTT
1 TTTTTCATTGATAATTT
* * ***
385006 TTTTT-TTTGAAAAAAC
1 TTTTTCATTGATAATTT
385022 TTTTTCATTGATAATTT
1 TTTTTCATTGATAATTT
*
385039 ATTTTCA
1 TTTTTCA
385046 AAACATTTCA
Statistics
Matches: 28, Mismatches: 11, Indels: 2
0.68 0.27 0.05
Matches are distributed among these distances:
16 11 0.39
17 17 0.61
ACGTcount: A:0.28, C:0.07, G:0.05, T:0.60
Consensus pattern (17 bp):
TTTTTCATTGATAATTT
Found at i:385465 original size:21 final size:20
Alignment explanation
Indices: 385443--385495 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
385433 AAAAATTTAT
385443 TTATTTAATTTTTAAATTAA
1 TTATTTAATTTTTAAATTAA
* **
385463 TT-TTTATTTTTTATCTTAA
1 TTATTTAATTTTTAAATTAA
385482 TTATTTTAATTTTT
1 TTA-TTTAATTTTT
385496 TTATAGCAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 16 0.59
20 2 0.07
21 9 0.33
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (20 bp):
TTATTTAATTTTTAAATTAA
Found at i:385645 original size:14 final size:14
Alignment explanation
Indices: 385591--385648 Score: 62
Period size: 15 Copynumber: 4.0 Consensus size: 14
385581 TATGATAGAG
* *
385591 TTATTTTTAAAATT
1 TTATATTTAAAAAT
* *
385605 TTAAATATTAAATAT
1 TTATAT-TTAAAAAT
385620 TTATATTTTAAAAAT
1 TTATA-TTTAAAAAT
385635 TTATATTTAAAAAT
1 TTATATTTAAAAAT
385649 AAATTATAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
14 13 0.36
15 22 0.61
16 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TTATATTTAAAAAT
Found at i:390628 original size:27 final size:25
Alignment explanation
Indices: 390592--390676 Score: 75
Period size: 27 Copynumber: 3.3 Consensus size: 25
390582 ATTATGTATT
390592 TTTAA-TTTTAAATAAATTAAAAATA
1 TTTAATTTTTAAATAAA-TAAAAATA
** *
390617 TTTAATTATTTATTTAAAATAAAAAAA
1 TTTAATT-TTTAAAT-AAATAAAAATA
*
390644 TTATAATTTTTAAATATAT-AAAATAA
1 TT-TAATTTTTAAATAAATAAAAAT-A
390670 TTTAATT
1 TTTAATT
390677 GACATAATAA
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
25 14 0.29
26 7 0.15
27 19 0.40
28 8 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
TTTAATTTTTAAATAAATAAAAATA
Found at i:391782 original size:17 final size:18
Alignment explanation
Indices: 391760--391793 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
391750 ATATATATAT
391760 ATATATATAAT-TCATTA
1 ATATATATAATATCATTA
*
391777 ATATATTTAATATCATT
1 ATATATATAATATCATT
391794 CATGTATATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (18 bp):
ATATATATAATATCATTA
Found at i:391802 original size:22 final size:22
Alignment explanation
Indices: 391753--391802 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
391743 GATTCATATA
391753 TATATATATATATATAATTCAT
1 TATATATATATATATAATTCAT
* *
391775 TA-ATATATTTAATATCATTCAT
1 TATATATATAT-ATATAATTCAT
391797 GTATAT
1 -TATAT
391803 CCATAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 7 0.30
22 12 0.52
23 2 0.09
24 2 0.09
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.50
Consensus pattern (22 bp):
TATATATATATATATAATTCAT
Found at i:396984 original size:29 final size:28
Alignment explanation
Indices: 396934--396988 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
396924 TATATTCATA
*
396934 TCATATTCATATAATTTTTTTATATTACG
1 TCATATTCATATAATTATTTTA-ATTACG
*
396963 TCATATTTTATATAA-TATTTTAATTA
1 TCATA-TTCATATAATTATTTTAATTA
396989 TTTTTTTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 4 0.17
29 11 0.48
30 8 0.35
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.56
Consensus pattern (28 bp):
TCATATTCATATAATTATTTTAATTACG
Found at i:397263 original size:8 final size:8
Alignment explanation
Indices: 397252--397337 Score: 52
Period size: 8 Copynumber: 10.4 Consensus size: 8
397242 TATAAATATA
397252 ATATAAAT
1 ATATAAAT
397260 ATATAAAT
1 ATATAAAT
* *
397268 AAATAAAA
1 ATATAAAT
* *
397276 ATCTATAT
1 ATATAAAT
397284 AATATAAAT
1 -ATATAAAT
397293 -TATTAACAT
1 ATA-TAA-AT
*
397302 AT-TAAAA
1 ATATAAAT
397309 ATTATATAAT
1 A-TATA-AAT
397319 ATATAACA-
1 ATATAA-AT
397327 ATATAAAT
1 ATATAAAT
397335 ATA
1 ATA
397338 ATTCTAATAA
Statistics
Matches: 59, Mismatches: 10, Indels: 18
0.68 0.11 0.21
Matches are distributed among these distances:
7 5 0.08
8 35 0.59
9 15 0.25
10 4 0.07
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.36
Consensus pattern (8 bp):
ATATAAAT
Found at i:397285 original size:16 final size:17
Alignment explanation
Indices: 397247--397331 Score: 63
Period size: 16 Copynumber: 5.1 Consensus size: 17
397237 AATTATATAA
*
397247 ATATAATATAAATATAT
1 ATATAATATAAAAATAT
* *
397264 AAATAA-ATAAAAATCT
1 ATATAATATAAAAATAT
*
397280 ATATAATAT-AAATTAT
1 ATATAATATAAAAATAT
397296 -TA-ACATATTAAAAAT-T
1 ATATA-ATA-TAAAAATAT
397312 ATATAATATATAACAATAT
1 ATATAATATA-AA-AATAT
397331 A
1 A
397332 AATATAATTC
Statistics
Matches: 52, Mismatches: 7, Indels: 16
0.69 0.09 0.21
Matches are distributed among these distances:
14 1 0.02
15 5 0.10
16 22 0.42
17 18 0.35
18 4 0.08
19 2 0.04
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (17 bp):
ATATAATATAAAAATAT
Found at i:397320 original size:32 final size:33
Alignment explanation
Indices: 397247--397335 Score: 103
Period size: 33 Copynumber: 2.7 Consensus size: 33
397237 AATTATATAA
397247 ATATAATATAAATATATAAATAAATAAAAATCT
1 ATATAATATAAATATATAAATAAATAAAAATCT
*
397280 ATATAATATAAAT-TATTAACAT-ATTAAAAAT-T
1 ATATAATATAAATATA-TAA-ATAAATAAAAATCT
*
397312 ATATAATATATAACAATATAAATA
1 ATATAATATA-AA-TATATAAATA
397336 TAATTCTAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
32 13 0.27
33 28 0.58
34 5 0.10
35 2 0.04
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (33 bp):
ATATAATATAAATATATAAATAAATAAAAATCT
Found at i:397740 original size:21 final size:21
Alignment explanation
Indices: 397714--397757 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
397704 TCGATAAAAT
397714 ATTAAATTTTTAA-TTTTAATA
1 ATTAAA-TTTTAATTTTTAATA
397735 ATTAAATTTTAATTTTTAATA
1 ATTAAATTTTAATTTTTAATA
397756 AT
1 AT
397758 CTCAAATACA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTAAATTTTAATTTTTAATA
Found at i:398180 original size:8 final size:8
Alignment explanation
Indices: 398167--398238 Score: 58
Period size: 8 Copynumber: 8.4 Consensus size: 8
398157 TAAAGAAGTG
398167 ATATTTAT
1 ATATTTAT
398175 ATATTTGTATT
1 ATA-TT-TA-T
398186 ATATTTAT
1 ATATTTAT
398194 ATATTTAT
1 ATATTTAT
398202 ATA-TTAT
1 ATATTTAT
398209 A-ATTGTATT
1 ATATT-TA-T
*
398218 AAAATATTAT
1 -ATAT-TTAT
398228 ATATTTAT
1 ATATTTAT
398236 ATA
1 ATA
398239 AATTTTAATA
Statistics
Matches: 54, Mismatches: 1, Indels: 18
0.74 0.01 0.25
Matches are distributed among these distances:
6 1 0.02
7 6 0.11
8 24 0.44
9 8 0.15
10 6 0.11
11 8 0.15
12 1 0.02
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (8 bp):
ATATTTAT
Found at i:398215 original size:32 final size:34
Alignment explanation
Indices: 398174--398238 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
398164 GTGATATTTA
* *
398174 TATATTTGTATT-ATAT-TTATATATTTATATAT
1 TATAATTGTATTAAAATATTATATATTTATATAT
398206 TATAATTGTATTAAAATATTATATATTTATATA
1 TATAATTGTATTAAAATATTATATATTTATATA
398239 AATTTTAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 11 0.38
33 3 0.10
34 15 0.52
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (34 bp):
TATAATTGTATTAAAATATTATATATTTATATAT
Found at i:398217 original size:27 final size:27
Alignment explanation
Indices: 398167--398233 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 27
398157 TAAAGAAGTG
* * *
398167 ATATTTATATATTTGTATTATATTTAT
1 ATATTTATATATTTGAATTATATTAAA
*
398194 ATATTTATATATTAT-AATTGTATTAAA
1 ATATTTATATATT-TGAATTATATTAAA
398221 ATA-TTATATATTT
1 ATATTTATATATTT
398234 ATATAAATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
25 1 0.03
26 9 0.26
27 24 0.69
28 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (27 bp):
ATATTTATATATTTGAATTATATTAAA
Found at i:398241 original size:19 final size:19
Alignment explanation
Indices: 398202--398240 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
398192 ATATATTTAT
398202 ATATTATA-ATTGTATTAAA
1 ATATTATATATT-TATTAAA
398221 ATATTATATATTTATATAAA
1 ATATTATATATTTAT-TAAA
398241 TTTTAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (19 bp):
ATATTATATATTTATTAAA
Found at i:398251 original size:18 final size:18
Alignment explanation
Indices: 398228--398276 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
398218 AAAATATTAT
398228 ATATTTATATAAATTTTA
1 ATATTTATATAAATTTTA
398246 ATATTT-TAATAAA--TTA
1 ATATTTAT-ATAAATTTTA
398262 A-A-TTATATAAATTTT
1 ATATTTATATAAATTTT
398277 TAAAACTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
14 7 0.26
15 2 0.07
16 6 0.22
17 1 0.04
18 11 0.41
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATATTTATATAAATTTTA
Found at i:398294 original size:42 final size:43
Alignment explanation
Indices: 398215--398303 Score: 101
Period size: 42 Copynumber: 2.1 Consensus size: 43
398205 TTATAATTGT
* *
398215 ATTAAAATATTATATATTTATATAAATTTTAATATTTTAATAA
1 ATTAAAATATTATAAATTTATATAAATTTTAAAATTTTAATAA
* * * *
398258 ATTAAATTA-TATAAATTTTTA-AAACTTTTAAAATTTTTATAT
1 ATTAAAATATTATAAATTTATATAAA-TTTTAAAATTTTAATAA
398300 ATTA
1 ATTA
398304 TTTTATACCA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
41 3 0.08
42 28 0.72
43 8 0.21
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (43 bp):
ATTAAAATATTATAAATTTATATAAATTTTAAAATTTTAATAA
Found at i:405964 original size:17 final size:17
Alignment explanation
Indices: 405944--405995 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
405934 TATTATGCAC
405944 ATTCATAAATTATATAA-
1 ATTCATAAATTATA-AAT
*
405961 ATTCATGAATT-TAAAT
1 ATTCATAAATTATAAAT
*
405977 ATTTATAAATTATAAAT
1 ATTCATAAATTATAAAT
405994 AT
1 AT
405996 ACATGAATGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 2 0.07
16 11 0.37
17 17 0.57
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (17 bp):
ATTCATAAATTATAAAT
Done.