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 3 of 14
Found at i:204668 original size:29 final size:29
Alignment explanation
Indices: 204635--204715 Score: 101
Period size: 30 Copynumber: 2.8 Consensus size: 29
204625 TTTATTATTT
204635 TATTTAAATAAATTTTTATATTTT-TGTTA
1 TATTTAAATAAATTTTTA-ATTTTATGTTA
* *
204664 TATTTAAATAAATTTTAAATTTTAATTTTA
1 TATTTAAATAAATTTTTAATTTT-ATGTTA
* *
204694 TATCTAAATAAATTATTAATTT
1 TATTTAAATAAATTTTTAATTT
204716 ATATTTAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
28 5 0.11
29 17 0.38
30 23 0.51
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (29 bp):
TATTTAAATAAATTTTTAATTTTATGTTA
Found at i:204702 original size:30 final size:29
Alignment explanation
Indices: 204618--204712 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 29
204608 AAAAAAAGCC
204618 TTTAAATTTTATTATTTTAT-TTAAATAAATT
1 TTTAAATTTTA--ATTTTATATTAAATAAA-T
* *
204649 TTTATATTTT--TGTTATATTTAAATAAAT
1 TTTAAATTTTAATTTTATA-TTAAATAAAT
204677 TTTAAATTTTAATTTTATATCTAAATAAAT
1 TTTAAATTTTAATTTTATAT-TAAATAAAT
204707 TATTAA
1 T-TTAA
204713 TTTATATTTA
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
27 5 0.09
28 10 0.19
29 10 0.19
30 16 0.30
31 13 0.24
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (29 bp):
TTTAAATTTTAATTTTATATTAAATAAAT
Found at i:204705 original size:23 final size:23
Alignment explanation
Indices: 204679--204737 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
204669 AAATAAATTT
204679 TAAATT-TTAATTTTATATCTAAA
1 TAAATTATTAA-TTTATATCTAAA
*
204702 TAAATTATTAATTTATATTTAAA
1 TAAATTATTAATTTATATCTAAA
* *
204725 -AAAGTATTTATTT
1 TAAATTATTAATTT
204738 GAGTATAAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 11 0.34
23 17 0.53
24 4 0.12
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (23 bp):
TAAATTATTAATTTATATCTAAA
Found at i:204737 original size:22 final size:23
Alignment explanation
Indices: 204685--204737 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
204675 ATTTTAAATT
*
204685 TTAATTTTATATCTAAATAAATTA
1 TTAA-TTTATATCTAAATAAAGTA
*
204709 TTAATTTATATTTAAA-AAAGTA
1 TTAATTTATATCTAAATAAAGTA
*
204731 TTTATTT
1 TTAATTT
204738 GAGTATAAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 11 0.42
23 11 0.42
24 4 0.15
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (23 bp):
TTAATTTATATCTAAATAAAGTA
Found at i:207737 original size:13 final size:13
Alignment explanation
Indices: 207709--207763 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
207699 AAGAGAAAAG
*
207709 TTAAATATTAAAAT
1 TTAAA-ATTTAAAT
207723 TTAAAATTTAAAT
1 TTAAAATTTAAAT
*
207736 TTATTAA-TTAAAT
1 TTA-AAATTTAAAT
*
207749 TTAAATTTTAAAT
1 TTAAAATTTAAAT
207762 TT
1 TT
207764 TATTACAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
12 1 0.03
13 27 0.77
14 7 0.20
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
TTAAAATTTAAAT
Found at i:210878 original size:26 final size:23
Alignment explanation
Indices: 210849--210896 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
210839 ATTACACATT
210849 TTTATTTATTTATATTATTATTTTAA
1 TTTATTT-TTT-T-TTATTATTTTAA
*
210875 TTTATTTTTTTTTGTTATTTTA
1 TTTATTTTTTTTTATTATTTTA
210897 GTTACTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 10 0.48
24 1 0.05
25 3 0.14
26 7 0.33
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (23 bp):
TTTATTTTTTTTTATTATTTTAA
Found at i:211775 original size:16 final size:16
Alignment explanation
Indices: 211754--211798 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
211744 ATTTAATAAT
* *
211754 TAAATTTTTTTATTAG
1 TAAATTTATTTATGAG
211770 TAAATTTATTTATGAG
1 TAAATTTATTTATGAG
211786 TCAAA-TTATTTAT
1 T-AAATTTATTTAT
211799 TTATTTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 23 0.88
17 3 0.12
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.56
Consensus pattern (16 bp):
TAAATTTATTTATGAG
Found at i:211919 original size:21 final size:23
Alignment explanation
Indices: 211893--211937 Score: 76
Period size: 21 Copynumber: 2.0 Consensus size: 23
211883 AATAATATTT
211893 TTATTTAAAT-TTAAT-TAAAAA
1 TTATTTAAATATTAATATAAAAA
211914 TTATTTAAATATTAATATAAAAA
1 TTATTTAAATATTAATATAAAAA
211937 T
1 T
211938 AATATTATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 10 0.45
22 5 0.23
23 7 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TTATTTAAATATTAATATAAAAA
Found at i:213444 original size:17 final size:17
Alignment explanation
Indices: 213425--213458 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
213415 ATTTAATTAT
213425 AAAATATATATTAATATA
1 AAAAT-TATATTAATATA
*
213443 AAAATTATTTTAATAT
1 AAAATTATATTAATAT
213459 TATTAAAATA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AAAATTATATTAATATA
Found at i:213444 original size:29 final size:29
Alignment explanation
Indices: 213386--213444 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
213376 TTAAATCACT
* * * *
213386 ATTTACTTATAAAAATATTTTTTATTTAA
1 ATTTAATTATAAAAATATTATTAATATAA
213415 ATTTAATTAT-AAAATATATATTAATATAA
1 ATTTAATTATAAAAATAT-TATTAATATAA
213444 A
1 A
213445 AATTATTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
28 7 0.28
29 18 0.72
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (29 bp):
ATTTAATTATAAAAATATTATTAATATAA
Found at i:216034 original size:22 final size:23
Alignment explanation
Indices: 215999--216054 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
215989 AATAATATTT
215999 TATT-TAAAT-TTAAT-TATAAAA
1 TATTATAAATATTAATATA-AAAA
216020 TA-TATAAATATTAATATAAAAA
1 TATTATAAATATTAATATAAAAA
*
216042 TATTTTAAATATT
1 TATTATAAATATT
216055 TTAATATATT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
20 1 0.03
21 7 0.23
22 11 0.37
23 11 0.37
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
TATTATAAATATTAATATAAAAA
Found at i:216054 original size:23 final size:22
Alignment explanation
Indices: 215999--216102 Score: 80
Period size: 21 Copynumber: 5.0 Consensus size: 22
215989 AATAATATTT
215999 TATTTAAAT-TTAATTATAAAA
1 TATTTAAATATTAATTATAAAA
*
216020 TATATAAATATTAA-TATAAAAA
1 TATTTAAATATTAATTAT-AAAA
*
216042 TATTTTAAATA-T--TT-TAATA
1 TA-TTTAAATATTAATTATAAAA
* *
216061 TATTTAAATAATAATT-TAAAC
1 TATTTAAATATTAATTATAAAA
*
216082 TATATTAAAT-TTAAATATAAA
1 TAT-TTAAATATTAATTATAAA
216103 TTTAAATAGG
Statistics
Matches: 67, Mismatches: 7, Indels: 17
0.74 0.08 0.19
Matches are distributed among these distances:
18 8 0.12
19 6 0.09
20 1 0.01
21 24 0.36
22 21 0.31
23 7 0.10
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (22 bp):
TATTTAAATATTAATTATAAAA
Found at i:216079 original size:12 final size:13
Alignment explanation
Indices: 216056--216110 Score: 60
Period size: 12 Copynumber: 4.2 Consensus size: 13
216046 TTAAATATTT
*
216056 TAATATATTTAAA
1 TAATAAATTTAAA
216069 TAAT-AATTTAAA
1 TAATAAATTTAAA
216081 CTATATTAAATTTAAA
1 -TA-A-TAAATTTAAA
216097 T-ATAAATTTAAA
1 TAATAAATTTAAA
216109 TA
1 TA
216111 GGTCTACTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
12 18 0.50
13 7 0.19
14 1 0.03
15 2 0.06
16 8 0.22
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (13 bp):
TAATAAATTTAAA
Found at i:216324 original size:16 final size:16
Alignment explanation
Indices: 216303--216387 Score: 50
Period size: 16 Copynumber: 5.1 Consensus size: 16
216293 TTATTCATTG
216303 TAAATTTAATTAAAAT
1 TAAATTTAATTAAAAT
*
216319 TAAATTTTAA-AAAATAT
1 TAAA-TTTAATTAAA-AT
216336 TATACATTTAAATT-AAAT
1 TA-A-ATTT-AATTAAAAT
* **
216354 TAAATTAAATTATTAT
1 TAAATTTAATTAAAAT
*
216370 TTAA-TTAATTAATAAT
1 TAAATTTAATTAA-AAT
216386 TA
1 TA
216388 TTTTTATTTA
Statistics
Matches: 51, Mismatches: 10, Indels: 16
0.66 0.13 0.21
Matches are distributed among these distances:
15 10 0.20
16 18 0.35
17 10 0.20
18 8 0.16
19 5 0.10
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (16 bp):
TAAATTTAATTAAAAT
Found at i:222858 original size:14 final size:14
Alignment explanation
Indices: 222841--222869 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
222831 AAAAAATACT
222841 ATTAACATAATATG
1 ATTAACATAATATG
222855 ATTAACATAATATG
1 ATTAACATAATATG
222869 A
1 A
222870 ATATATGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.34
Consensus pattern (14 bp):
ATTAACATAATATG
Found at i:222885 original size:19 final size:18
Alignment explanation
Indices: 222861--222901 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 18
222851 TATGATTAAC
222861 ATAATATGAATATATGA-AT
1 ATAATATG-AT-TATGATAT
222880 ATAATATGATTATGATAT
1 ATAATATGATTATGATAT
222898 ATAA
1 ATAA
222902 AGATAATATG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 5 0.24
18 8 0.38
19 8 0.38
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.39
Consensus pattern (18 bp):
ATAATATGATTATGATAT
Found at i:222899 original size:24 final size:25
Alignment explanation
Indices: 222865--222912 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
222855 ATTAACATAA
* *
222865 TATGAATATATGAATATAATATGAT
1 TATGAATATATAAAGATAATATGAT
222890 TATG-ATATATAAAGATAATATGA
1 TATGAATATATAAAGATAATATGA
222913 ATAAGATTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (25 bp):
TATGAATATATAAAGATAATATGAT
Found at i:224803 original size:2 final size:2
Alignment explanation
Indices: 224796--224824 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
224786 AAATTGCCTC
224796 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 A
224825 AGATGCATGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:225540 original size:18 final size:18
Alignment explanation
Indices: 225513--225549 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
225503 CTTCCAGCTG
225513 TGGACAAGTCCGGAGAAA
1 TGGACAAGTCCGGAGAAA
* *
225531 TGGACGAGTCCTGAGAAA
1 TGGACAAGTCCGGAGAAA
225549 T
1 T
225550 TAACGGGAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.32, T:0.16
Consensus pattern (18 bp):
TGGACAAGTCCGGAGAAA
Found at i:225683 original size:2 final size:2
Alignment explanation
Indices: 225676--225704 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
225666 AAAAATGGTT
225676 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
225705 TTTCTGATGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:228013 original size:31 final size:31
Alignment explanation
Indices: 227975--228038 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
227965 AGTTGATCAG
227975 TTAGGTGCCAGCTGTATTAGCTACTGAATAA
1 TTAGGTGCCAGCTGTATTAGCTACTGAATAA
228006 TTAGGTGCCAGCTGTATTAGCTACTGAATAA
1 TTAGGTGCCAGCTGTATTAGCTACTGAATAA
228037 TT
1 TT
228039 TTATTCTCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (31 bp):
TTAGGTGCCAGCTGTATTAGCTACTGAATAA
Found at i:232804 original size:69 final size:70
Alignment explanation
Indices: 232700--232839 Score: 237
Period size: 69 Copynumber: 2.0 Consensus size: 70
232690 TTGTTTATTT
* *
232700 TGTTATTAGTGTGAAAAAAAAAATGAAAAAGATACCATTGAATGCCACGTGTTAAAGCGGAATTA
1 TGTTATTAATGTG-AAAAAAAAATCAAAAAGATACCATTGAATGCCACGTGTTAAAGCGGAATTA
232765 TTAACA
65 TTAACA
*
232771 TGTTATTAATGTG-AAAAAAAATCAAAAAGATACCATTGAATGCCACGTGTTAAAGTGGAATTAT
1 TGTTATTAATGTGAAAAAAAAATCAAAAAGATACCATTGAATGCCACGTGTTAAAGCGGAATTAT
232835 TAACA
66 TAACA
232840 ACAATTAATA
Statistics
Matches: 66, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
69 54 0.82
71 12 0.18
ACGTcount: A:0.45, C:0.10, G:0.17, T:0.28
Consensus pattern (70 bp):
TGTTATTAATGTGAAAAAAAAATCAAAAAGATACCATTGAATGCCACGTGTTAAAGCGGAATTAT
TAACA
Found at i:234862 original size:17 final size:17
Alignment explanation
Indices: 234816--234863 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
234806 GGAATTATGA
*
234816 TTATTA-AATAATAATT
1 TTATTACAAAAATAATT
* *
234832 TTA-AACATAAATAATT
1 TTATTACAAAAATAATT
234848 TTATTACAAAAATAAT
1 TTATTACAAAAATAAT
234864 AAATTAATAA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
15 1 0.04
16 14 0.56
17 10 0.40
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (17 bp):
TTATTACAAAAATAATT
Found at i:238829 original size:9 final size:9
Alignment explanation
Indices: 238815--238844 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
238805 AATCTCTTAT
238815 CACTAGAAC
1 CACTAGAAC
238824 CACTAGAAC
1 CACTAGAAC
238833 CACTAGAAC
1 CACTAGAAC
238842 CAC
1 CAC
238845 GTTGGATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.43, C:0.37, G:0.10, T:0.10
Consensus pattern (9 bp):
CACTAGAAC
Found at i:240224 original size:24 final size:22
Alignment explanation
Indices: 240175--240225 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
240165 TATAATATAA
*
240175 ATATATAAATATTTTAAAATTT
1 ATATATAAATATATTAAAATTT
240197 ATATA-AAATAATATTAAAATTT
1 ATATATAAAT-ATATTAAAATTT
*
240219 AGATATA
1 ATATATA
240226 TATAAAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 4 0.16
22 20 0.80
23 1 0.04
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
ATATATAAATATATTAAAATTT
Found at i:240229 original size:50 final size:48
Alignment explanation
Indices: 240130--240250 Score: 120
Period size: 50 Copynumber: 2.4 Consensus size: 48
240120 GACTTTTGTT
* * *
240130 TAAATATGTTAATATTACATATAAAAAAATTAAAATATAATATAAATATA
1 TAAATATCTTAAAATT-TATATAAAAAAATTAAAATATAATAT-AATATA
* *
240180 TAAATATTTTAAAATTTATATAAAATAATATTAAAATTTAGATAT-ATATA
1 TAAATATCTTAAAATTTATATAAAA-AA-ATTAAAATATA-ATATAATATA
*
240230 -AAATATCATAAATATTTATAT
1 TAAATATCTTAAA-ATTTATAT
240251 GATAAAATAC
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
49 18 0.30
50 29 0.48
51 10 0.16
52 4 0.07
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (48 bp):
TAAATATCTTAAAATTTATATAAAAAAATTAAAATATAATATAATATA
Found at i:240246 original size:28 final size:27
Alignment explanation
Indices: 240148--240247 Score: 87
Period size: 28 Copynumber: 3.6 Consensus size: 27
240138 TTAATATTAC
* * *
240148 ATATAAAAAAATTAAAATATA-ATATAA
1 ATATATAAATATTTAAATATATATA-AA
*
240175 ATATATAAATATTTTAAAATTTATATAAA
1 ATATATAAATA-TTT-AAATATATATAAA
*
240204 ATAATATTAAA-ATTTAGATATATATAAA
1 AT-ATA-TAAATATTTAAATATATATAAA
240232 ATATCATAAATATTTA
1 ATAT-ATAAATATTTA
240248 TATGATAAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
27 15 0.25
28 21 0.35
29 13 0.22
30 7 0.12
31 4 0.07
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (27 bp):
ATATATAAATATTTAAATATATATAAA
Found at i:240250 original size:26 final size:26
Alignment explanation
Indices: 240196--240259 Score: 62
Period size: 28 Copynumber: 2.4 Consensus size: 26
240186 TTTTAAAATT
240196 TATATAAAATAATATTAAAATTTAGATA
1 TATATAAAAT-ATATTAAAATTTA-ATA
240224 TATATAAAATATCA-TAAATATTT-ATA
1 TATATAAAATAT-ATTAAA-ATTTAATA
*
240250 T-GATAAAATA
1 TATATAAAATA
240260 CACCAATTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
25 8 0.24
26 4 0.12
27 6 0.18
28 15 0.45
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (26 bp):
TATATAAAATATATTAAAATTTAATA
Found at i:240623 original size:18 final size:19
Alignment explanation
Indices: 240585--240625 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
240575 ATTTATTTTA
*
240585 TTTAAAATTATTATATAAT
1 TTTAAAATTATTAAATAAT
*
240604 TTTAAATTTATTAAAT-AT
1 TTTAAAATTATTAAATAAT
240622 TTTA
1 TTTA
240626 TTAATACGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTAAAATTATTAAATAAT
Found at i:241478 original size:20 final size:21
Alignment explanation
Indices: 241428--241478 Score: 52
Period size: 20 Copynumber: 2.4 Consensus size: 21
241418 TAACTAGATT
241428 AATTTAATTTAATTTAAATTTA
1 AATTTAATTT-ATTTAAATTTA
**
241450 AATAAAATTT-TTTAAA-TTA
1 AATTTAATTTATTTAAATTTA
241469 CAATTTAATT
1 -AATTTAATT
241479 CAATTCTTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
19 3 0.12
20 13 0.54
22 8 0.33
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
AATTTAATTTATTTAAATTTA
Found at i:243257 original size:12 final size:12
Alignment explanation
Indices: 243237--243292 Score: 60
Period size: 12 Copynumber: 4.7 Consensus size: 12
243227 TATATATTAT
243237 TATTTAAAATAA
1 TATTTAAAATAA
*
243249 TATTAAAAATAA
1 TATTTAAAATAA
* *
243261 TTTTTAAATTAA
1 TATTTAAAATAA
*
243273 TATTTATAATTAA
1 TATTTA-AAATAA
243286 -ATTTAAA
1 TATTTAAA
243293 TTAAAAAATA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
11 2 0.05
12 30 0.79
13 6 0.16
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
TATTTAAAATAA
Found at i:245145 original size:16 final size:16
Alignment explanation
Indices: 245120--245150 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
245110 ATAAGTTTAA
*
245120 TATATGAATATATTTT
1 TATATAAATATATTTT
245136 TATATAAATATATTT
1 TATATAAATATATTT
245151 AATTTTTTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
TATATAAATATATTTT
Found at i:251651 original size:11 final size:11
Alignment explanation
Indices: 251635--251660 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
251625 ACTGGGTCCT
251635 TGATCACCTTG
1 TGATCACCTTG
251646 TGATCACCTTG
1 TGATCACCTTG
251657 TGAT
1 TGAT
251661 ACTTAATGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.38
Consensus pattern (11 bp):
TGATCACCTTG
Found at i:257373 original size:38 final size:39
Alignment explanation
Indices: 257322--257402 Score: 146
Period size: 38 Copynumber: 2.1 Consensus size: 39
257312 TTTGATACCC
257322 AAAGACAGTTTAAGCAGTAAAAAA-TTAAAAAAAAAAAA
1 AAAGACAGTTTAAGCAGTAAAAAATTTAAAAAAAAAAAA
*
257360 AAAGATAGTTTAAGCAGTAAAAAATTTAAAAAAAAAAAA
1 AAAGACAGTTTAAGCAGTAAAAAATTTAAAAAAAAAAAA
257399 AAAG
1 AAAG
257403 TTTGACTTCA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
38 23 0.56
39 18 0.44
ACGTcount: A:0.68, C:0.04, G:0.11, T:0.17
Consensus pattern (39 bp):
AAAGACAGTTTAAGCAGTAAAAAATTTAAAAAAAAAAAA
Found at i:258106 original size:4 final size:4
Alignment explanation
Indices: 258099--258168 Score: 61
Period size: 4 Copynumber: 17.2 Consensus size: 4
258089 TCGGTAGGAG
* * * *
258099 AGAA AGAA AGAA AGAA AGAAA AAAA AGAAA AAAA AGAA AGGA GGAA A-AA
1 AGAA AGAA AGAA AGAA AG-AA AGAA AG-AA AGAA AGAA AGAA AGAA AGAA
* *
258148 AGAA AAAA AGAA AAAA AGAA A
1 AGAA AGAA AGAA AGAA AGAA A
258169 AATATTTGTA
Statistics
Matches: 51, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
3 3 0.06
4 42 0.82
5 6 0.12
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:258112 original size:8 final size:8
Alignment explanation
Indices: 258099--258170 Score: 74
Period size: 8 Copynumber: 8.9 Consensus size: 8
258089 TCGGTAGGAG
*
258099 AGAAAGAA
1 AGAAAAAA
*
258107 AGAAAGAA
1 AGAAAAAA
258115 AGAAAAAAA
1 AG-AAAAAA
258124 AGAAAAAA
1 AGAAAAAA
**
258132 A-AGAAAGG
1 AGA-AAAAA
*
258140 AGGAAAAA
1 AGAAAAAA
258148 AGAAAAAA
1 AGAAAAAA
258156 AGAAAAAA
1 AGAAAAAA
258164 AGAAAAA
1 AGAAAAA
258171 TATTTGTATT
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
7 1 0.02
8 46 0.85
9 7 0.13
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (8 bp):
AGAAAAAA
Found at i:258127 original size:9 final size:9
Alignment explanation
Indices: 258113--258170 Score: 55
Period size: 9 Copynumber: 6.0 Consensus size: 9
258103 AGAAAGAAAG
258113 AAAGAAAAA
1 AAAGAAAAA
258122 AAAGAAAAA
1 AAAGAAAAA
258131 AAAGAAAGGAGGA
1 AAAGAAA--A--A
*
258144 AAAAAGAAAA
1 AAAGA-AAAA
258154 AAAG-AAAA
1 AAAGAAAAA
258162 AAAGAAAAA
1 AAAGAAAAA
258171 TATTTGTATT
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
8 8 0.20
9 20 0.49
10 4 0.10
11 1 0.02
12 1 0.02
13 5 0.12
14 2 0.05
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (9 bp):
AAAGAAAAA
Found at i:258459 original size:4 final size:4
Alignment explanation
Indices: 258452--258514 Score: 60
Period size: 4 Copynumber: 16.2 Consensus size: 4
258442 TCAGCCGGAG
* * *
258452 AGAA AGAA AGAA AGAA AGAAA AAAA AGAA A-AA A-AA AGAA AGGA GGAA
1 AGAA AGAA AGAA AGAA AG-AA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
*
258499 A-AA AGAA AAAA AGAA A
1 AGAA AGAA AGAA AGAA A
258515 AATATTTGTA
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
3 9 0.19
4 36 0.75
5 3 0.06
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:258489 original size:27 final size:25
Alignment explanation
Indices: 258458--258510 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 25
258448 GGAGAGAAAG
258458 AAAGAAAGAAAGAAAAAAAAGAAAAAA
1 AAAGAAAG-AAG-AAAAAAAGAAAAAA
* *
258485 AAAGAAAGGAGGAAAAAAGAAAAAA
1 AAAGAAAGAAGAAAAAAAGAAAAAA
258510 A
1 A
258511 GAAAAATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 14 0.58
26 2 0.08
27 8 0.33
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (25 bp):
AAAGAAAGAAGAAAAAAAGAAAAAA
Found at i:258805 original size:4 final size:4
Alignment explanation
Indices: 258798--258867 Score: 61
Period size: 4 Copynumber: 17.2 Consensus size: 4
258788 TCAGCCGGAG
* * * *
258798 AGAA AGAA AGAA AGAA AGAAA AAAA AGAAA AAAA AGAA AGGA GGAA A-AA
1 AGAA AGAA AGAA AGAA AG-AA AGAA AG-AA AGAA AGAA AGAA AGAA AGAA
* *
258847 AGAA AAAA AGAA AAAA AGAA A
1 AGAA AGAA AGAA AGAA AGAA A
258868 AATATTTGTA
Statistics
Matches: 51, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
3 3 0.06
4 42 0.82
5 6 0.12
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:258811 original size:8 final size:8
Alignment explanation
Indices: 258798--258869 Score: 74
Period size: 8 Copynumber: 8.9 Consensus size: 8
258788 TCAGCCGGAG
*
258798 AGAAAGAA
1 AGAAAAAA
*
258806 AGAAAGAA
1 AGAAAAAA
258814 AGAAAAAAA
1 AG-AAAAAA
258823 AGAAAAAA
1 AGAAAAAA
**
258831 A-AGAAAGG
1 AGA-AAAAA
*
258839 AGGAAAAA
1 AGAAAAAA
258847 AGAAAAAA
1 AGAAAAAA
258855 AGAAAAAA
1 AGAAAAAA
258863 AGAAAAA
1 AGAAAAA
258870 TATTTGTATT
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
7 1 0.02
8 46 0.85
9 7 0.13
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (8 bp):
AGAAAAAA
Found at i:258826 original size:9 final size:9
Alignment explanation
Indices: 258812--258869 Score: 55
Period size: 9 Copynumber: 6.0 Consensus size: 9
258802 AGAAAGAAAG
258812 AAAGAAAAA
1 AAAGAAAAA
258821 AAAGAAAAA
1 AAAGAAAAA
258830 AAAGAAAGGAGGA
1 AAAGAAA--A--A
*
258843 AAAAAGAAAA
1 AAAGA-AAAA
258853 AAAG-AAAA
1 AAAGAAAAA
258861 AAAGAAAAA
1 AAAGAAAAA
258870 TATTTGTATT
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
8 8 0.20
9 20 0.49
10 4 0.10
11 1 0.02
12 1 0.02
13 5 0.12
14 2 0.05
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (9 bp):
AAAGAAAAA
Found at i:258847 original size:699 final size:682
Alignment explanation
Indices: 258023--259407 Score: 2391
Period size: 699 Copynumber: 2.0 Consensus size: 682
258013 ATCTATACGT
* ** *
258023 AATACTAAAATTAACTACACAAATGCATGAGGTGTTGACATGTAATATTTTTTTTGGTTTTTTTT
1 AATACTAAAATTAACTACACAAATGCATGAGGTGTTGACATGGAATATTCCTTTGGGTTTTTTTT
* *
258088 TTCGGTAGGAGAGAAAGAAAGAAAGAAAGAAAAAAAAGAAAAAAAAGAAAGGAGGAAAAAAGAAA
66 TTCAGCAGGAGAGAAAGAAAGAAAGAAAGAAAAAAAAGAAAAAAAAGAAAGGAGGAAAAAAGAAA
258153 AAAAGAAAAAAAGAAAAATATTTGTATTTATATTTATGTTATTTTTTATATGTAAAATATTATAT
131 AAAAGAAAAAAAGAAAAATATTTGTATTTATATTTATGTTATTTTTTATATGTAAAATATTATAT
258218 TTTTGTATTTTTTATATATGAATAATTCGTTTTATTTCATATATATTTTTATATGTACGTGTATT
196 TTTTGTATTTTTTATATATGAATAATTCGTTTTATTTCATATATATTTTTATATGTACGTGTATT
258283 CGTGTTATGTGTATATTATTTTTAAGTTATGTTTTAAATATTTTTTATAAATATTATGTTTATAT
261 CGTGTTATGTGTATATTATTTTTAAGTTATGTTTTAAATATTTTTTATAAATATTATGTTTATAT
258348 TTTTTTATGTTTAAAATAAAATAAAATACTAAAATTAACTACACAAATGCATGAGGTGTTGACGC
326 TTTTTTATGTTTAAAATAAAATAAAATACTAAAATTAACTACACAAATGCATGAGGTGTTGACGC
258413 ATGGCACTTCCTTTGGG-TTTTTTTTTTTTTCAGCCGGAGAGAAAGAAAGAAAGAAAGAAAAAAA
391 ATGGCACTTCCTTTGGGTTTTTTTTTTTTTTCAGCC-G-GAG--AGAAAGAAAGAAAG-----AA
258477 AGAAAAAAAAAGAAAGGAGGAAAAAAGAAAAAAAGAAAAATATTTGTATTTATATTTATGTTATT
447 AG-AAAAAAAAGAAAGGAGG--AAAAG--AAAAA-AAAAATATTTGTATTTATATTTATGTTATT
258542 TTTTATATGTAAAATATTATATTTTTGTA-TTTTTTATATATGAATAATTCGTTTTATTTCATAT
506 TTTTATATGTAAAATATTATATTTTT-TATTTTTTTATATATGAATAATTCGTTTTATTTCATAT
* *
258606 ATATTTTTATATGTACGTGTATTCGTGTTATGTGTATATTATTTTTAAGTTATGTTTTAAATATT
570 ATATTTTTATATATACGTATATTCGTGTTATGTGTATATTATTTTTAAGTTATGTTTTAAATATT
*
258671 TTTTATAAATATTATGTTTAT-ATTTTTTTATGTTTAAAATAAAATAA
635 TTTTATAAATATCATGTTTATGATTTTTTTATGTTTAAAATAAAATAA
* *
258718 AATACTAAAATTAACTACACAAATGCATGAGGTGTTGACGCATGGCA-CTTCCTTTGGGTTTTTT
1 AATACTAAAATTAACTACACAAATGCATGAGGTGTTGA--CATGGAATATTCCTTTGGG---TTT
*
258782 TTTTTTTCAGCCGGAGAGAAAGAAAGAAAGAAAGAAAAAAAAGAAAAAAAAGAAAGGAGGAAAAA
61 TTTTTTTCAGCAGGAGAGAAAGAAAGAAAGAAAGAAAAAAAAGAAAAAAAAGAAAGGAGGAAAAA
258847 AGAAAAAAAGAAAAAAAGAAAAATATTTGTATTTATATTTATGTTATTTTTTATATGTAAAATAT
126 AGAAAAAAAGAAAAAAAGAAAAATATTTGTATTTATATTTATGTTATTTTTTATATGTAAAATAT
258912 TATATTTTTGTATTTTTTATATATGAATAATTCGTTTTATTTCATATATATTTTTATATGTACGT
191 TATATTTTTGTATTTTTTATATATGAATAATTCGTTTTATTTCATATATATTTTTATATGTACGT
258977 GTATTCGTGTTATGTGTATATTATTTTTAAGTTATGTTTTAAATATTTTTTATAAATATTATGTT
256 GTATTCGTGTTATGTGTATATTATTTTTAAGTTATGTTTTAAATATTTTTTATAAATATTATGTT
259042 TATATTTTTTTATGTTTAAAATAAAATAAAATACTAAAATTAACTACACAAATGCATGAGGTGTT
321 TATATTTTTTTATGTTTAAAATAAAATAAAATACTAAAATTAACTACACAAATGCATGAGGTGTT
* *
259107 GATGCATGGCACTTCCTTTGGGTTTTTTTTTTTTTTCAGTCGGAGAGAAAGAAAGAAAGAAAGAA
386 GACGCATGGCACTTCCTTTGGGTTTTTTTTTTTTTTCAGCCGGAGAGAAAGAAAGAAAGAAAGAA
*
259172 AAAAAAGAAAGGAGGAAAAGAGAAAAAAAATATTTGTATTTATATTTATGTTATTTTTTATATGT
451 AAAAAAGAAAGGAGGAAAAGAAAAAAAAAATATTTGTATTTATATTTATGTTATTTTTTATATGT
259237 AAAATATTATATTTTTTATTTTTTTATATATGAATAATTCGTTTTATTTCATATATATTTTTATA
516 AAAATATTATATTTTTTATTTTTTTATATATGAATAATTCGTTTTATTTCATATATATTTTTATA
* *
259302 TATACGTATATTCGTGTTGTGTGTATATTATTTTTATGTTATGTTTTAAATATTTTTTATAAATA
581 TATACGTATATTCGTGTTATGTGTATATTATTTTTAAGTTATGTTTTAAATATTTTTTATAAATA
*
259367 TCATGTTTATGTTTTTTTTATGTTTAAAATAAAATAA
646 TCATGTTTATGATTTTTTTATGTTTAAAATAAAATAA
259404 AATA
1 AATA
259408 AATTTATATA
Statistics
Matches: 664, Mismatches: 18, Indels: 25
0.94 0.03 0.04
Matches are distributed among these distances:
684 2 0.00
685 172 0.26
686 33 0.05
688 5 0.01
690 17 0.03
691 4 0.01
695 38 0.06
696 21 0.03
697 5 0.01
698 3 0.00
699 347 0.52
700 17 0.03
ACGTcount: A:0.39, C:0.05, G:0.13, T:0.43
Consensus pattern (682 bp):
AATACTAAAATTAACTACACAAATGCATGAGGTGTTGACATGGAATATTCCTTTGGGTTTTTTTT
TTCAGCAGGAGAGAAAGAAAGAAAGAAAGAAAAAAAAGAAAAAAAAGAAAGGAGGAAAAAAGAAA
AAAAGAAAAAAAGAAAAATATTTGTATTTATATTTATGTTATTTTTTATATGTAAAATATTATAT
TTTTGTATTTTTTATATATGAATAATTCGTTTTATTTCATATATATTTTTATATGTACGTGTATT
CGTGTTATGTGTATATTATTTTTAAGTTATGTTTTAAATATTTTTTATAAATATTATGTTTATAT
TTTTTTATGTTTAAAATAAAATAAAATACTAAAATTAACTACACAAATGCATGAGGTGTTGACGC
ATGGCACTTCCTTTGGGTTTTTTTTTTTTTTCAGCCGGAGAGAAAGAAAGAAAGAAAGAAAAAAA
AGAAAGGAGGAAAAGAAAAAAAAAATATTTGTATTTATATTTATGTTATTTTTTATATGTAAAAT
ATTATATTTTTTATTTTTTTATATATGAATAATTCGTTTTATTTCATATATATTTTTATATATAC
GTATATTCGTGTTATGTGTATATTATTTTTAAGTTATGTTTTAAATATTTTTTATAAATATCATG
TTTATGATTTTTTTATGTTTAAAATAAAATAA
Found at i:259176 original size:353 final size:350
Alignment explanation
Indices: 258023--259407 Score: 2308
Period size: 346 Copynumber: 4.0 Consensus size: 350
258013 ATCTATACGT
** * ** *
258023 AATACTAAAATTAACTACACAAATGCATGAGGTGTTGA--CATGTAATATTTTTTTTGG---TTT
1 AATACTAAAATTAACTACACAAATGCATGAGGTGTTGACGCATGGCA-CTTCCTTTGGGTTTTTT
* **
258083 TTTTTTTCGGTAGGAGAGAAAGAAAGAAAGAAAGAAAAAAAAGAAAAAAAAGAAAGGAGGAAAAA
65 TTTTTTTCAGCCGGAGAGAAAGAAAGAAAGAAAGAAAAAAAAGAAAAAAAAGAAAGGAGG--AAA
258148 AGAAAAAAAGAAAAAAAGAAAAATATTTGTATTTATATTTATGTTATTTTTTATATGTAAAATAT
128 AG-AAAAAAGAAAAAAAGAAAAATATTTGTATTTATATTTATGTTATTTTTTATATGTAAAATAT
258213 TATATTTTTGTATTTTTTATATATGAATAATTCGTTTTATTTCATATATATTTTTATATGTACGT
192 TATATTTTTGTATTTTTTATATATGAATAATTCGTTTTATTTCATATATATTTTTATATGTACGT
258278 GTATTCGTGTTATGTGTATATTATTTTTAAGTTATGTTTTAAATATTTTTTATAAATATTATGTT
257 GTATTCGTGTTATGTGTATATTATTTTTAAGTTATGTTTTAAATATTTTTTATAAATATTATGTT
258343 TATATTTTTTTATGTTTAAAATAAAATAA
322 TATATTTTTTTATGTTTAAAATAAAATAA
258372 AATACTAAAATTAACTACACAAATGCATGAGGTGTTGACGCATGGCACTTCCTTTGGGTTTTTTT
1 AATACTAAAATTAACTACACAAATGCATGAGGTGTTGACGCATGGCACTTCCTTTGGGTTTTTTT
258437 TTTTTTCAGCCGGAGAGAAAGAAAGAAAGAAAGAAAAAAAAGAAAAAAAAAGAAAGGA-G----G
66 TTTTTTCAGCCGGAGAGAAAGAAAGAAAGAAAGAAAAAAAAG-AAAAAAAAGAAAGGAGGAAAAG
258497 AAAAAAGAAAAAAAGAAAAATATTTGTATTTATATTTATGTTATTTTTTATATGTAAAATATTAT
130 AAAAAAGAAAAAAAGAAAAATATTTGTATTTATATTTATGTTATTTTTTATATGTAAAATATTAT
258562 ATTTTTGTATTTTTTATATATGAATAATTCGTTTTATTTCATATATATTTTTATATGTACGTGTA
195 ATTTTTGTATTTTTTATATATGAATAATTCGTTTTATTTCATATATATTTTTATATGTACGTGTA
258627 TTCGTGTTATGTGTATATTATTTTTAAGTTATGTTTTAAATATTTTTTATAAATATTATGTTTAT
260 TTCGTGTTATGTGTATATTATTTTTAAGTTATGTTTTAAATATTTTTTATAAATATTATGTTTAT
258692 ATTTTTTTATGTTTAAAATAAAATAA
325 ATTTTTTTATGTTTAAAATAAAATAA
258718 AATACTAAAATTAACTACACAAATGCATGAGGTGTTGACGCATGGCACTTCCTTTGGGTTTTTTT
1 AATACTAAAATTAACTACACAAATGCATGAGGTGTTGACGCATGGCACTTCCTTTGGGTTTTTTT
258783 TTTTTTCAGCCGGAGAGAAAGAAAGAAAGAAAGAAAAAAAAGAAAAAAAAGAAAGGAGGAAAAAA
66 TTTTTTCAGCCGGAGAGAAAGAAAGAAAGAAAGAAAAAAAAGAAAAAAAAGAAAGGAGG--AAAA
258848 GAAAAAAAGAAAAAAAGAAAAATATTTGTATTTATATTTATGTTATTTTTTATATGTAAAATATT
129 G-AAAAAAGAAAAAAAGAAAAATATTTGTATTTATATTTATGTTATTTTTTATATGTAAAATATT
258913 ATATTTTTGTATTTTTTATATATGAATAATTCGTTTTATTTCATATATATTTTTATATGTACGTG
193 ATATTTTTGTATTTTTTATATATGAATAATTCGTTTTATTTCATATATATTTTTATATGTACGTG
258978 TATTCGTGTTATGTGTATATTATTTTTAAGTTATGTTTTAAATATTTTTTATAAATATTATGTTT
258 TATTCGTGTTATGTGTATATTATTTTTAAGTTATGTTTTAAATATTTTTTATAAATATTATGTTT
259043 ATATTTTTTTATGTTTAAAATAAAATAA
323 ATATTTTTTTATGTTTAAAATAAAATAA
*
259071 AATACTAAAATTAACTACACAAATGCATGAGGTGTTGATGCATGGCACTTCCTTTGGGTTTTTTT
1 AATACTAAAATTAACTACACAAATGCATGAGGTGTTGACGCATGGCACTTCCTTTGGG-TTTTTT
*
259136 TTTTTTTCAGTC-G-GAG--AGAAAGAAAGAAAG-----AAAGAAAAAAAAGAAAGGAGGAAAAG
65 TTTTTTTCAGCCGGAGAGAAAGAAAGAAAGAAAGAAAAAAAAGAAAAAAAAGAAAGGAGGAAAAG
259192 -----AG----AAA-AAAAATATTTGTATTTATATTTATGTTATTTTTTATATGTAAAATATTAT
130 AAAAAAGAAAAAAAGAAAAATATTTGTATTTATATTTATGTTATTTTTTATATGTAAAATATTAT
* *
259247 ATTTTT-TATTTTTTTATATATGAATAATTCGTTTTATTTCATATATATTTTTATATATACGTAT
195 ATTTTTGTA-TTTTTTATATATGAATAATTCGTTTTATTTCATATATATTTTTATATGTACGTGT
* * *
259311 ATTCGTGTTGTGTGTATATTATTTTTATGTTATGTTTTAAATATTTTTTATAAATATCATGTTTA
259 ATTCGTGTTATGTGTATATTATTTTTAAGTTATGTTTTAAATATTTTTTATAAATATTATGTTTA
*
259376 TGTTTTTTTTATGTTTAAAATAAAATAA
324 T-ATTTTTTTATGTTTAAAATAAAATAA
259404 AATA
1 AATA
259408 AATTTATATA
Statistics
Matches: 1002, Mismatches: 17, Indels: 50
0.94 0.02 0.05
Matches are distributed among these distances:
331 2 0.00
332 172 0.17
333 32 0.03
337 2 0.00
343 5 0.00
345 36 0.04
346 329 0.33
347 1 0.00
349 38 0.04
350 21 0.02
351 5 0.00
352 4 0.00
353 323 0.32
354 32 0.03
ACGTcount: A:0.39, C:0.05, G:0.13, T:0.43
Consensus pattern (350 bp):
AATACTAAAATTAACTACACAAATGCATGAGGTGTTGACGCATGGCACTTCCTTTGGGTTTTTTT
TTTTTTCAGCCGGAGAGAAAGAAAGAAAGAAAGAAAAAAAAGAAAAAAAAGAAAGGAGGAAAAGA
AAAAAGAAAAAAAGAAAAATATTTGTATTTATATTTATGTTATTTTTTATATGTAAAATATTATA
TTTTTGTATTTTTTATATATGAATAATTCGTTTTATTTCATATATATTTTTATATGTACGTGTAT
TCGTGTTATGTGTATATTATTTTTAAGTTATGTTTTAAATATTTTTTATAAATATTATGTTTATA
TTTTTTTATGTTTAAAATAAAATAA
Found at i:259180 original size:21 final size:23
Alignment explanation
Indices: 259154--259200 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 23
259144 AGTCGGAGAG
259154 AAAGAAAGAAAG-AAAGA-AAAA
1 AAAGAAAGAAAGAAAAGAGAAAA
* *
259175 AAAGAAAGGAGGAAAAGAGAAAA
1 AAAGAAAGAAAGAAAAGAGAAAA
259198 AAA
1 AAA
259201 ATATTTGTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 10 0.45
22 5 0.23
23 7 0.32
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (23 bp):
AAAGAAAGAAAGAAAAGAGAAAA
Found at i:259189 original size:25 final size:24
Alignment explanation
Indices: 259152--259201 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
259142 TCAGTCGGAG
259152 AGAAAGAAAGAAAGAAAGAAAAAAA
1 AGAAAGAAAGAAA-AAAGAAAAAAA
* * *
259177 AGAAAGGAGGAAAAGAGAAAAAAA
1 AGAAAGAAAGAAAAAAGAAAAAAA
259201 A
1 A
259202 TATTTGTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (24 bp):
AGAAAGAAAGAAAAAAGAAAAAAA
Found at i:260525 original size:23 final size:25
Alignment explanation
Indices: 260498--260558 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 25
260488 GTATTCTTAC
260498 TGTGTTTATATTATTTT-T-TATGT
1 TGTGTTTATATTATTTTATATATGT
260521 TGTGTTT-TAATT-TTTTATATATGT
1 TGTGTTTAT-ATTATTTTATATATGT
* *
260545 TGAGTTTATGTTAT
1 TGTGTTTATATTAT
260559 ATCTCAATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
22 5 0.16
23 11 0.35
24 13 0.42
25 2 0.06
ACGTcount: A:0.20, C:0.00, G:0.15, T:0.66
Consensus pattern (25 bp):
TGTGTTTATATTATTTTATATATGT
Found at i:261504 original size:20 final size:20
Alignment explanation
Indices: 261482--261520 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
261472 ATAATGAATT
261482 TTTTAAAATT-TTTTATTAA
1 TTTTAAAATTATTTTATTAA
*
261501 TTTTAAATTTATTTTATTAA
1 TTTTAAAATTATTTTATTAA
261521 AAATAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTAAAATTATTTTATTAA
Found at i:261508 original size:50 final size:53
Alignment explanation
Indices: 261454--261567 Score: 132
Period size: 51 Copynumber: 2.2 Consensus size: 53
261444 GGTGGTTAGG
261454 TAAATATT-TTTTA-AAAAAATAATGAAT-TTTTTAAAATT-T-TTTATTAATTT
1 TAAAT-TTATTTTATAAAAAATAAT-AATATTTTTAAAATTATATTTATTAATTT
* * *
261504 TAAATTTATTTTATTAAAAATAATAATATTTTTAAATTTATATTTATTAA-TA
1 TAAATTTATTTTATAAAAAATAATAATATTTTTAAAATTATATTTATTAATTT
261556 TAAATTTTATTT
1 TAAA-TTTATTT
261568 AATATTTTAA
Statistics
Matches: 55, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
49 2 0.04
50 13 0.24
51 19 0.35
52 6 0.11
53 15 0.27
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (53 bp):
TAAATTTATTTTATAAAAAATAATAATATTTTTAAAATTATATTTATTAATTT
Found at i:261842 original size:23 final size:23
Alignment explanation
Indices: 261797--261842 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
261787 TCGATAAATT
* *
261797 TAAATATTAAAAATATATTTTAA
1 TAAATATTAAAAATAAATATTAA
261820 TAAAT-TTAAAAATAAATAATTAA
1 TAAATATTAAAAATAAAT-ATTAA
261843 ATAGTTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
TAAATATTAAAAATAAATATTAA
Found at i:266868 original size:21 final size:22
Alignment explanation
Indices: 266827--266871 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
266817 AAAATAATAT
*
266827 ATTTTTAAATTTAATTTTAAAA
1 ATTTTTAAATTTAATTATAAAA
266849 ATTTTT-AATATTAA-TATAAAA
1 ATTTTTAAAT-TTAATTATAAAA
266870 AT
1 AT
266872 AATTTTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
ATTTTTAAATTTAATTATAAAA
Found at i:267425 original size:23 final size:21
Alignment explanation
Indices: 267377--267421 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
267367 AACTAAGAAC
*
267377 TTTA-TATAAAATTTTAAAAA
1 TTTATTATAAAATTATAAAAA
*
267397 ATTATTATAATAATTATAAAAA
1 TTTATTATAA-AATTATAAAAA
267419 TTT
1 TTT
267422 TATTTATTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
20 3 0.15
21 5 0.25
22 12 0.60
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TTTATTATAAAATTATAAAAA
Found at i:267429 original size:4 final size:4
Alignment explanation
Indices: 267420--267445 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
267410 TTATAAAAAT
267420 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
267446 GAGTAATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:267841 original size:29 final size:30
Alignment explanation
Indices: 267809--267892 Score: 77
Period size: 29 Copynumber: 2.9 Consensus size: 30
267799 ATGCAATAAA
267809 AAAATATAATATTAATAT-AATAATAAATT
1 AAAATATAATATTAATATAAATAATAAATT
* * *
267838 AAAA-ATTATATAAATATAAATAAT-ATTT
1 AAAATATAATATTAATATAAATAATAAATT
* * * *
267866 TAAATATGATTTTAATATGAAT-ATAAA
1 AAAATATAATATTAATATAAATAATAAA
267893 ATATATGAAT
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
28 19 0.44
29 24 0.56
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.39
Consensus pattern (30 bp):
AAAATATAATATTAATATAAATAATAAATT
Found at i:272239 original size:2 final size:2
Alignment explanation
Indices: 272232--272264 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
272222 GATATTTAAA
272232 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 A
272265 ACTTACTGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:273521 original size:14 final size:14
Alignment explanation
Indices: 273488--273543 Score: 51
Period size: 14 Copynumber: 4.1 Consensus size: 14
273478 TCATATTTTG
* *
273488 AAATATTTATATTT
1 AAATATTTAAATAT
* *
273502 ACATATTTAATTAT
1 AAATATTTAAATAT
*
273516 AAATA-TAAAATAT
1 AAATATTTAAATAT
*
273529 AAATTTTTAAATAT
1 AAATATTTAAATAT
273543 A
1 A
273544 TAAAAAATTT
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
13 10 0.31
14 22 0.69
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (14 bp):
AAATATTTAAATAT
Found at i:275018 original size:26 final size:27
Alignment explanation
Indices: 274973--275046 Score: 84
Period size: 24 Copynumber: 2.8 Consensus size: 27
274963 ATTGGTAAGA
274973 AAAATTTATTTTATTAATTAAAATTTAAT
1 AAAATTT-TTTTATT-ATTAAAATTTAAT
*
275002 AAAATTTTTTTA-TATT--AATTTTAT
1 AAAATTTTTTTATTATTAAAATTTAAT
*
275026 -ATATTTTTTTATTATTAAAAT
1 AAAATTTTTTTATTATTAAAAT
275047 ATTAGTTTAC
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
23 10 0.25
24 11 0.28
26 6 0.15
27 1 0.03
28 5 0.12
29 7 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (27 bp):
AAAATTTTTTTATTATTAAAATTTAAT
Found at i:275753 original size:4 final size:4
Alignment explanation
Indices: 275744--275770 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
275734 TCTGCTTGTA
275744 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
275771 GATCAACTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:277102 original size:21 final size:23
Alignment explanation
Indices: 277057--277107 Score: 70
Period size: 21 Copynumber: 2.3 Consensus size: 23
277047 TTTAAAAGTA
277057 AAATAAATATTACATATAAATTTT
1 AAAT-AATATTACATATAAATTTT
*
277081 AAATAATATTA-A-ATATATTTT
1 AAATAATATTACATATAAATTTT
277102 AAATAA
1 AAATAA
277108 AATAAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 14 0.54
22 1 0.04
23 7 0.27
24 4 0.15
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (23 bp):
AAATAATATTACATATAAATTTT
Found at i:277115 original size:21 final size:21
Alignment explanation
Indices: 277076--277115 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
277066 TTACATATAA
* *
277076 ATTTTAAATAATATTAAATAT
1 ATTTTAAATAAAATAAAATAT
277097 ATTTTAAATAAAATAAAAT
1 ATTTTAAATAAAATAAAAT
277116 TATAAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
ATTTTAAATAAAATAAAATAT
Found at i:277127 original size:23 final size:23
Alignment explanation
Indices: 277101--277161 Score: 72
Period size: 23 Copynumber: 2.6 Consensus size: 23
277091 AAATATATTT
277101 TAAATAAAATAAAATTATAAAAA
1 TAAATAAAATAAAATTATAAAAA
*
277124 TAAAT-AAATAATAATTTTAAAAA
1 TAAATAAAATAA-AATTATAAAAA
277147 TATAA-AAAATTAAAA
1 TA-AATAAAA-TAAAA
277162 ATAAATTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
22 6 0.18
23 17 0.52
24 7 0.21
25 3 0.09
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (23 bp):
TAAATAAAATAAAATTATAAAAA
Found at i:277498 original size:3 final size:3
Alignment explanation
Indices: 277490--277517 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
277480 ATTTATATAT
277490 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
277518 TAAAGTCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:277505 original size:32 final size:31
Alignment explanation
Indices: 277443--277507 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
277433 TATTAAATTA
* * *
277443 AAATATAATTTATATTTAATGTATTGATAAT
1 AAATATAATTTATATTTAATATAATAATAAT
277474 AAATA-AATTTATATATTAATAATAATAATAAT
1 AAATATAATTTATAT-TTAAT-ATAATAATAAT
277506 AA
1 AA
277508 TAATAATAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 9 0.31
31 10 0.34
32 10 0.34
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (31 bp):
AAATATAATTTATATTTAATATAATAATAAT
Found at i:280597 original size:37 final size:40
Alignment explanation
Indices: 280525--280601 Score: 106
Period size: 37 Copynumber: 2.0 Consensus size: 40
280515 ATATTTATAT
280525 AAAATTTAATATATTAATAATTAATATTAAATATTTTTTA
1 AAAATTTAATATATTAATAATTAATATTAAATATTTTTTA
* * *
280565 AAAATTT-ATATATTTATAA-T-ATTTTAATTATTTTTTA
1 AAAATTTAATATATTAATAATTAATATTAAATATTTTTTA
280602 TTTTATTTGT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
37 15 0.44
38 1 0.03
39 11 0.32
40 7 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (40 bp):
AAAATTTAATATATTAATAATTAATATTAAATATTTTTTA
Found at i:281076 original size:37 final size:35
Alignment explanation
Indices: 281005--281098 Score: 109
Period size: 37 Copynumber: 2.7 Consensus size: 35
280995 TTTTATTAAA
* ** *
281005 TAAAAAT-TTAAATAAAATTAAACTTATTTGAATT
1 TAAAAATATTAAATTAAATTAATGTTATTTAAATT
*
281039 TAAAAATATTTATATTAAATATAATGTTATTTAAATT
1 TAAAAATA-TTAAATTAAAT-TAATGTTATTTAAATT
*
281076 TAAATATATTAAATTAAATTAAT
1 TAAAAATATTAAATTAAATTAAT
281099 ATTTTATTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
34 7 0.14
35 4 0.08
36 19 0.38
37 20 0.40
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (35 bp):
TAAAAATATTAAATTAAATTAATGTTATTTAAATT
Found at i:282174 original size:15 final size:16
Alignment explanation
Indices: 282153--282207 Score: 60
Period size: 15 Copynumber: 3.4 Consensus size: 16
282143 ATATTTATTT
282153 TTAAATTTATATAATA
1 TTAAATTTATATAATA
*
282169 -TAAATTTTTA-ATATA
1 TTAAATTTATATA-ATA
282184 TTAAAATTTATATAAATA
1 TT-AAATTTATAT-AATA
282202 TTAAAT
1 TTAAAT
282208 ATTTTAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
14 1 0.03
15 12 0.38
16 1 0.03
17 12 0.38
18 5 0.16
19 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TTAAATTTATATAATA
Found at i:282196 original size:32 final size:35
Alignment explanation
Indices: 282155--282240 Score: 106
Period size: 37 Copynumber: 2.5 Consensus size: 35
282145 ATTTATTTTT
*
282155 AAATTTATATAATATAAAT-TTTT-AAT-ATATTA
1 AAATTTATATAATATAAATATTTTAAATAAAATTA
282187 AAATTTATATAAATATTAAATATTTTAAATAAAATTA
1 AAATTTATAT-AATA-TAAATATTTTAAATAAAATTA
*
282224 AAATTTAATAAAATATA
1 AAATTT-ATATAATATA
282241 TAAATATGAT
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
32 10 0.22
33 4 0.09
34 5 0.11
35 4 0.09
36 5 0.11
37 15 0.33
38 3 0.07
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (35 bp):
AAATTTATATAATATAAATATTTTAAATAAAATTA
Found at i:282201 original size:20 final size:21
Alignment explanation
Indices: 282178--282258 Score: 56
Period size: 18 Copynumber: 4.2 Consensus size: 21
282168 ATAAATTTTT
282178 AATATATTAAAAT-TTATAT-
1 AATATATTAAAATATTATATA
282197 AA-ATATT-AAATATT-T-TA
1 AATATATTAAAATATTATATA
*
282214 AATAAAATTAAAAT-TTA-ATA
1 AAT-ATATTAAAATATTATATA
*
282234 AA-ATA-TATAAATATGATATA
1 AATATATTA-AAATATTATATA
282254 AATAT
1 AATAT
282259 TTTTACTATT
Statistics
Matches: 48, Mismatches: 3, Indels: 20
0.68 0.04 0.28
Matches are distributed among these distances:
16 1 0.02
17 9 0.19
18 13 0.27
19 10 0.21
20 13 0.27
21 2 0.04
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (21 bp):
AATATATTAAAATATTATATA
Found at i:282233 original size:16 final size:16
Alignment explanation
Indices: 282183--282237 Score: 65
Period size: 16 Copynumber: 3.1 Consensus size: 16
282173 TTTTTAATAT
282183 ATTAAAATTTATATAAA
1 ATTAAAATTTA-ATAAA
282200 TATTAAATATTTTAAATAAA
1 -ATTAAA-A-TTT-AATAAA
282220 ATTAAAATTTAATAAA
1 ATTAAAATTTAATAAA
282236 AT
1 AT
282238 ATATAAATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
16 8 0.24
17 3 0.09
18 7 0.21
19 7 0.21
20 8 0.24
21 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTAAAATTTAATAAA
Found at i:282571 original size:22 final size:23
Alignment explanation
Indices: 282544--282594 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
282534 TGAAGATTAA
* *
282544 TTAAATTAAATT-TATTTTATAT
1 TTAAATTAAATTAAATTTAATAT
282566 TTAAA-TAAATTAAATTTAATAT
1 TTAAATTAAATTAAATTTAATAT
282588 TTAAATT
1 TTAAATT
282595 TATTATAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 6 0.24
22 18 0.72
23 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
TTAAATTAAATTAAATTTAATAT
Found at i:282599 original size:22 final size:23
Alignment explanation
Indices: 282544--282613 Score: 65
Period size: 22 Copynumber: 3.1 Consensus size: 23
282534 TGAAGATTAA
*
282544 TTAAATTAAATT-T-ATTTTATAT
1 TTAAA-TAAATTATAATTTAATAT
282566 TTAAATAAATTA-AATTTAATAT
1 TTAAATAAATTATAATTTAATAT
** *
282588 TTAAATTTATTATAATTAAATTAT
1 TTAAATAAATTATAATTTAA-TAT
282612 TT
1 TT
282614 TTAATTTAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
21 6 0.15
22 23 0.57
23 6 0.15
24 5 0.12
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
TTAAATAAATTATAATTTAATAT
Found at i:282624 original size:16 final size:16
Alignment explanation
Indices: 282586--282660 Score: 86
Period size: 16 Copynumber: 4.8 Consensus size: 16
282576 TAAATTTAAT
282586 ATTTAAATTTATTA-TA
1 ATTTAAA-TTATTATTA
*
282602 A-TTAAATTATTTTTA
1 ATTTAAATTATTATTA
*
282617 ATTTAAATTATTATGA
1 ATTTAAATTATTATTA
282633 ATTTAAATTA--ATTA
1 ATTTAAATTATTATTA
282647 ATTTTAAATTATTA
1 A-TTTAAATTATTA
282661 ATTTTTTAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
14 9 0.18
15 17 0.34
16 23 0.46
17 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (16 bp):
ATTTAAATTATTATTA
Found at i:282653 original size:31 final size:29
Alignment explanation
Indices: 282541--282660 Score: 97
Period size: 31 Copynumber: 4.0 Consensus size: 29
282531 ATATGAAGAT
*
282541 TAATTAAATTAAATTTATTTT--A-TATT-
1 TAATTAAATT-AATTAATTTTAAATTATTA
*
282567 TAAATAAATTAAATTTAATATTTAAATTTATTA
1 TAATTAAATT-AA-TTAAT-TTTAAA-TTATTA
*
282600 TAATTAAATTATTTTTAA-TTTAAATTATTA
1 TAATTAAATTA--ATTAATTTTAAATTATTA
282630 TGAATTTAAATTAATTAATTTTAAATTATTA
1 T-AA-TTAAATTAATTAATTTTAAATTATTA
282661 ATTTTTTAAT
Statistics
Matches: 77, Mismatches: 5, Indels: 19
0.76 0.05 0.19
Matches are distributed among these distances:
26 12 0.16
27 4 0.05
28 3 0.04
30 12 0.16
31 20 0.26
32 13 0.17
33 13 0.17
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (29 bp):
TAATTAAATTAATTAATTTTAAATTATTA
Found at i:282654 original size:15 final size:15
Alignment explanation
Indices: 282634--282682 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
282624 TTATTATGAA
282634 TTTAAATTAATTAAT
1 TTTAAATTAATTAAT
282649 TTTAAATT-ATTAAT
1 TTTAAATTAATTAAT
*
282663 TTT---TTAATTAAA
1 TTTAAATTAATTAAT
282675 TTTAAATT
1 TTTAAATT
282683 TTAATAAAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
11 2 0.07
12 8 0.28
14 9 0.31
15 10 0.34
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTAAATTAATTAAT
Found at i:282660 original size:14 final size:14
Alignment explanation
Indices: 282614--282665 Score: 61
Period size: 15 Copynumber: 3.6 Consensus size: 14
282604 TAAATTATTT
282614 TTAA-TTTAAATTA
1 TTAATTTTAAATTA
*
282627 TTATGAATTTAAATTAA
1 TTA--ATTTTAAATT-A
282644 TTAATTTTAAATTA
1 TTAATTTTAAATTA
282658 TTAATTTT
1 TTAATTTT
282666 TTAATTAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
13 3 0.09
14 9 0.26
15 10 0.29
16 8 0.24
17 4 0.12
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (14 bp):
TTAATTTTAAATTA
Found at i:287344 original size:22 final size:22
Alignment explanation
Indices: 287319--287366 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
287309 AAATATTACT
*
287319 TAAAAAAAAT-TAAAATATAATA
1 TAAAAAAAATAT-AAATAAAATA
*
287341 TAAAAATAATATAAATAAAATA
1 TAAAAAAAATATAAATAAAATA
287363 TAAA
1 TAAA
287367 TACGTAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 22 0.96
23 1 0.04
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (22 bp):
TAAAAAAAATATAAATAAAATA
Found at i:287353 original size:16 final size:16
Alignment explanation
Indices: 287332--287365 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
287322 AAAAAATTAA
287332 AATATAATATAAAA-AT
1 AATATAA-ATAAAATAT
287348 AATATAAATAAAATAT
1 AATATAAATAAAATAT
287364 AA
1 AA
287366 ATACGTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AATATAAATAAAATAT
Found at i:287361 original size:33 final size:33
Alignment explanation
Indices: 287298--287366 Score: 79
Period size: 33 Copynumber: 2.1 Consensus size: 33
287288 TGATAATTTT
*
287298 AAATATAATAAAAATATTACTTAAAAAAAAT-TA
1 AAATATAATAAAAATAATAC-TAAAAAAAATATA
*
287331 AAATATAATATAAAAATAATA-TAAATAAAATATA
1 AAATAT-A-ATAAAAATAATACTAAAAAAAATATA
287365 AA
1 AA
287367 TACGTAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
33 15 0.48
34 5 0.16
35 11 0.35
ACGTcount: A:0.70, C:0.01, G:0.00, T:0.29
Consensus pattern (33 bp):
AAATATAATAAAAATAATACTAAAAAAAATATA
Found at i:287810 original size:24 final size:22
Alignment explanation
Indices: 287783--287842 Score: 70
Period size: 24 Copynumber: 2.7 Consensus size: 22
287773 AATAAACATG
287783 ATATAATATATTTAAATATGATT
1 ATATAATATATTTAAATAT-ATT
* *
287806 AATATAATAAATTTATATATATT
1 -ATATAATATATTTAAATATATT
287829 ATAT--TATATTTAAA
1 ATATAATATATTTAAA
287843 ATTTTAATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 8 0.25
22 4 0.12
23 3 0.09
24 17 0.53
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
ATATAATATATTTAAATATATT
Found at i:288475 original size:16 final size:15
Alignment explanation
Indices: 288456--288488 Score: 50
Period size: 14 Copynumber: 2.2 Consensus size: 15
288446 GTTGAAAGTT
288456 TTAAACAAAATTATAA
1 TTAAA-AAAATTATAA
288472 TT-AAAAAATTATAA
1 TTAAAAAAATTATAA
288486 TTA
1 TTA
288489 CTACATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 3
0.84 0.00 0.16
Matches are distributed among these distances:
14 12 0.75
15 2 0.12
16 2 0.12
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (15 bp):
TTAAAAAAATTATAA
Found at i:288481 original size:14 final size:14
Alignment explanation
Indices: 288462--288488 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
288452 AGTTTTAAAC
288462 AAAATTATAATTAA
1 AAAATTATAATTAA
288476 AAAATTATAATTA
1 AAAATTATAATTA
288489 CTACATAATA
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:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AAAATTATAATTAA
Found at i:293824 original size:17 final size:17
Alignment explanation
Indices: 293788--293833 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
293778 TTAACGTATG
** *
293788 AAATAAAATATTATATA
1 AAATAAAATAAAATAAA
293805 AAATAAAATAAAATAAA
1 AAATAAAATAAAATAAA
*
293822 AAATAATATAAA
1 AAATAAAATAAA
293834 TATTTTAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
AAATAAAATAAAATAAA
Found at i:295587 original size:7 final size:7
Alignment explanation
Indices: 295577--295604 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
295567 TATAAATACA
295577 AAATTTT
1 AAATTTT
295584 AAATTTT
1 AAATTTT
295591 AAATTTT
1 AAATTTT
295598 AAATTTT
1 AAATTTT
295605 TTAAATATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
AAATTTT
Found at i:295620 original size:23 final size:23
Alignment explanation
Indices: 295580--295623 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
295570 AAATACAAAA
*
295580 TTTTAAATTTTAAATTTTAAATT
1 TTTTAAATATTAAATTTTAAATT
**
295603 TTTTAAATATTATTTTTTAAA
1 TTTTAAATATTAAATTTTAAA
295624 AATCATTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
TTTTAAATATTAAATTTTAAATT
Found at i:295716 original size:35 final size:34
Alignment explanation
Indices: 295677--295747 Score: 106
Period size: 35 Copynumber: 2.1 Consensus size: 34
295667 ACATAGTTTC
* * *
295677 TCTAAACCATTAAAAAATTATACTCTTTCTTTGCT
1 TCTAAACCATTAAAAAA-TATAATCTTGCTTTACT
295712 TCTAAACCATTAAAAAATATAATCTTGCTTTACT
1 TCTAAACCATTAAAAAATATAATCTTGCTTTACT
295746 TC
1 TC
295748 ACAAAGTTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
34 16 0.48
35 17 0.52
ACGTcount: A:0.37, C:0.20, G:0.03, T:0.41
Consensus pattern (34 bp):
TCTAAACCATTAAAAAATATAATCTTGCTTTACT
Found at i:296231 original size:14 final size:14
Alignment explanation
Indices: 296212--296262 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
296202 CATCTAATGA
296212 TTATATTTATTCAT
1 TTATATTTATTCAT
*
296226 TTATATTTATTAAAT
1 TTATATTTATT-CAT
296241 TTAT-TATTATTCAT
1 TTATAT-TTATTCAT
*
296255 TTGTATTT
1 TTATATTT
296263 TGATATTAGC
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 19 0.61
15 12 0.39
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (14 bp):
TTATATTTATTCAT
Found at i:296581 original size:20 final size:20
Alignment explanation
Indices: 296556--296617 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
296546 ATTTATGTAA
*
296556 TAATTTTTTTATATATTTTT
1 TAATTTATTTATATATTTTT
*
296576 TAATTTATTTATGTATTTATTT
1 TAATTTATTTATATA-TT-TTT
296598 TATATTTATATTA-ATATTTT
1 TA-ATTTAT-TTATATATTTT
296618 ATATTATATT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
20 13 0.37
21 4 0.11
22 7 0.20
23 8 0.23
24 3 0.09
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (20 bp):
TAATTTATTTATATATTTTT
Found at i:296615 original size:23 final size:23
Alignment explanation
Indices: 296573--296638 Score: 66
Period size: 23 Copynumber: 2.9 Consensus size: 23
296563 TTTATATATT
*
296573 TTTTA-ATTTAT-TTATGTATTTA
1 TTTTATATTTATATTA-ATATTTA
296595 TTTTATATTTATATTAATATTTTA
1 TTTTATATTTATATTAATA-TTTA
* *
296619 TATTATA-TTATATTTATATT
1 TTTTATATTTATATTAATATT
296639 ATATATTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
22 7 0.18
23 18 0.47
24 13 0.34
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (23 bp):
TTTTATATTTATATTAATATTTA
Found at i:296633 original size:29 final size:29
Alignment explanation
Indices: 296592--296653 Score: 99
Period size: 29 Copynumber: 2.1 Consensus size: 29
296582 ATTTATGTAT
*
296592 TTATTTTATATTTATATTA-ATATTTTATA
1 TTATATTATATTTATATTATATATTTT-TA
296621 TTATATTATATTTATATTATATATTTTTA
1 TTATATTATATTTATATTATATATTTTTA
296650 TTAT
1 TTAT
296654 CTTTAAAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 24 0.77
30 7 0.23
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (29 bp):
TTATATTATATTTATATTATATATTTTTA
Found at i:296638 original size:11 final size:11
Alignment explanation
Indices: 296589--296642 Score: 62
Period size: 11 Copynumber: 5.3 Consensus size: 11
296579 TTTATTTATG
*
296589 TATTTATTTTA
1 TATTTATATTA
296600 TATTTATATTA
1 TATTTATATTA
*
296611 -A--TATTTTA
1 TATTTATATTA
296619 TA-TTATATTA
1 TATTTATATTA
296629 TATTTATATTA
1 TATTTATATTA
296640 TAT
1 TAT
296643 ATTTTTATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
8 6 0.16
9 1 0.03
10 9 0.24
11 21 0.57
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TATTTATATTA
Found at i:296641 original size:5 final size:5
Alignment explanation
Indices: 296592--296642 Score: 52
Period size: 5 Copynumber: 10.2 Consensus size: 5
296582 ATTTATGTAT
* *
296592 TTATT TTATA TTTATA TTA-A -TATT TTATA TTATA TTATA TTTATA TTATA
1 TTATA TTATA -TTATA TTATA TTATA TTATA TTATA TTATA -TTATA TTATA
296642 T
1 T
296643 ATTTTTATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
3 2 0.05
4 1 0.03
5 26 0.67
6 10 0.26
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (5 bp):
TTATA
Found at i:296643 original size:23 final size:23
Alignment explanation
Indices: 296589--296645 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 23
296579 TTTATTTATG
*
296589 TATTTATTTTATATTTATATTAA
1 TATTTATATTATATTTATATTAA
*
296612 TATTTTATATTATA-TTATATTTA
1 TA-TTTATATTATATTTATATTAA
296635 TATTATATATT
1 TATT-TATATT
296646 TTTATTATCT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 2 0.07
23 18 0.60
24 10 0.33
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
TATTTATATTATATTTATATTAA
Found at i:296652 original size:13 final size:13
Alignment explanation
Indices: 296558--296653 Score: 70
Period size: 13 Copynumber: 6.8 Consensus size: 13
296548 TTATGTAATA
296558 ATTTTT-TTATAT
1 ATTTTTATTATAT
*
296570 ATTTTTTAATTTATTT
1 A-TTTTT-A-TTATAT
*
296586 ATGTATTTATTTTAT
1 AT-T-TTTATTATAT
*
296601 ATTTATATTA-AT
1 ATTTTTATTATAT
296613 ATTTTATATTATATT
1 ATTTT-TATTATA-T
296628 ATATTTATATTATAT
1 AT-TTT-TATTATAT
296643 ATTTTTATTAT
1 ATTTTTATTAT
296654 CTTTAAAATA
Statistics
Matches: 68, Mismatches: 6, Indels: 19
0.73 0.06 0.20
Matches are distributed among these distances:
12 7 0.10
13 21 0.31
14 5 0.07
15 13 0.19
16 19 0.28
17 3 0.04
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.68
Consensus pattern (13 bp):
ATTTTTATTATAT
Found at i:301297 original size:26 final size:27
Alignment explanation
Indices: 301267--301352 Score: 85
Period size: 26 Copynumber: 3.4 Consensus size: 27
301257 ACCCTTTGTG
301267 TTTGTCAAAAATGA-TAGTTCCTTTTT-
1 TTTGTCAAAAATGAGTAGTT-CTTTTTA
*
301293 TTTGTCAAAAAT-AGTGGTTCTTTTTA
1 TTTGTCAAAAATGAGTAGTTCTTTTTA
* * *
301319 TTTATCAAAAATG-GTA--ACTTGTTA
1 TTTGTCAAAAATGAGTAGTTCTTTTTA
301343 TTTGTCAAAA
1 TTTGTCAAAA
301353 TTGGTGACTA
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
24 15 0.29
25 7 0.14
26 29 0.57
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.47
Consensus pattern (27 bp):
TTTGTCAAAAATGAGTAGTTCTTTTTA
Found at i:302788 original size:12 final size:13
Alignment explanation
Indices: 302771--302803 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
302761 CGTTGATCAA
302771 TAAATTTTAAT-T
1 TAAATTTTAATAT
302783 TAAATTTTAATAT
1 TAAATTTTAATAT
*
302796 TATATTTT
1 TAAATTTT
302804 GTTATCTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TAAATTTTAATAT
Found at i:305220 original size:16 final size:16
Alignment explanation
Indices: 305199--305284 Score: 64
Period size: 16 Copynumber: 5.2 Consensus size: 16
305189 AAACTGATCA
305199 ATTTAAATTTAAAATG
1 ATTTAAATTTAAAATG
* ** *
305215 ATTTAAAATCGAAATA
1 ATTTAAATTTAAAATG
* * *
305231 AATCAAATTTAAAATA
1 ATTTAAATTTAAAATG
*
305247 ATTTAAACCATTCAAAATG
1 ATTT-AA--ATTTAAAATG
*
305266 ATTTAAATCTAAAATG
1 ATTTAAATTTAAAATG
305282 ATT
1 ATT
305285 GAATCTGTTA
Statistics
Matches: 52, Mismatches: 15, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
16 36 0.69
17 2 0.04
18 2 0.04
19 12 0.23
ACGTcount: A:0.52, C:0.07, G:0.05, T:0.36
Consensus pattern (16 bp):
ATTTAAATTTAAAATG
Found at i:305347 original size:22 final size:22
Alignment explanation
Indices: 305291--305347 Score: 55
Period size: 22 Copynumber: 2.5 Consensus size: 22
305281 GATTGAATCT
*
305291 GTTATATTAAAAAATTAAAATTA
1 GTTA-ATTAAAATATTAAAATTA
*
305314 ATTAATCT-AAATATTAAACA-TA
1 GTTAAT-TAAAATATTAAA-ATTA
305336 GTTAATTAAAAT
1 GTTAATTAAAAT
305348 CTAAAATAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
21 1 0.04
22 22 0.79
23 5 0.18
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.39
Consensus pattern (22 bp):
GTTAATTAAAATATTAAAATTA
Found at i:305370 original size:16 final size:17
Alignment explanation
Indices: 305341--305372 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
305331 ACATAGTTAA
305341 TTAAAATCTAAAATAAC
1 TTAAAATCTAAAATAAC
305358 TTAAAAT-TAAAATAA
1 TTAAAATCTAAAATAA
305373 TCCAAACTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.31
Consensus pattern (17 bp):
TTAAAATCTAAAATAAC
Found at i:305654 original size:2 final size:2
Alignment explanation
Indices: 305637--305683 Score: 78
Period size: 2 Copynumber: 23.5 Consensus size: 2
305627 TTTCTCTATC
305637 AT AT AT GAT AT A- 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
305679 AT AT A
1 AT AT A
305684 CAAAAACTGA
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.02
2 40 0.93
3 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:306978 original size:25 final size:26
Alignment explanation
Indices: 306950--306999 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
306940 ATACCGACTC
306950 AATTAAAAAAAAAAT-TTAAAATTTA
1 AATTAAAAAAAAAATATTAAAATTTA
** *
306975 AATTATTATAAAAATATTAAAATTT
1 AATTAAAAAAAAAATATTAAAATTT
307000 TATAATATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (26 bp):
AATTAAAAAAAAAATATTAAAATTTA
Found at i:310510 original size:76 final size:76
Alignment explanation
Indices: 310384--310687 Score: 599
Period size: 76 Copynumber: 4.0 Consensus size: 76
310374 CGCAATCCCT
310384 TAACACAAAGTAAACCAATACAAGTTAAAGAAGAACTAAAAGCAATAAGTTATAAACCCCAAAAG
1 TAACACAAAGTAAACCAATACAAGTTAAAGAAGAACTAAAAGCAATAAGTTATAAACCCCAAAAG
310449 GGTTAAACATG
66 GGTTAAACATG
310460 TAACACAAAGTAAACCAATACAAGTTAAAGAAGAACTAAAAGCAATAAGTTATAAACCCCAAAAG
1 TAACACAAAGTAAACCAATACAAGTTAAAGAAGAACTAAAAGCAATAAGTTATAAACCCCAAAAG
310525 GGTTAAACATG
66 GGTTAAACATG
310536 TAACACAAAGTAAACCAATACAAGTTAAAGAAGAACTAAAAGCAATAAGTTATAAACCCCAAAAG
1 TAACACAAAGTAAACCAATACAAGTTAAAGAAGAACTAAAAGCAATAAGTTATAAACCCCAAAAG
310601 GGTTAAACATG
66 GGTTAAACATG
*
310612 TAACACAAAGTAAACCAATACAAGTTAAAGAAGAACTAAGAGCAATAAGTTATAAACCCCAAAAG
1 TAACACAAAGTAAACCAATACAAGTTAAAGAAGAACTAAAAGCAATAAGTTATAAACCCCAAAAG
310677 GGTTAAACATG
66 GGTTAAACATG
310688 CCAAAAAAAA
Statistics
Matches: 227, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 227 1.00
ACGTcount: A:0.54, C:0.16, G:0.13, T:0.17
Consensus pattern (76 bp):
TAACACAAAGTAAACCAATACAAGTTAAAGAAGAACTAAAAGCAATAAGTTATAAACCCCAAAAG
GGTTAAACATG
Found at i:311759 original size:175 final size:176
Alignment explanation
Indices: 311476--311820 Score: 629
Period size: 175 Copynumber: 2.0 Consensus size: 176
311466 ACGTTTTTTT
311476 TTTTATTTTTTGTTGAATTTTACCTATAAACATATTTAAAAATAGATTTCAAAGACGTAATGGAC
1 TTTTATTTTTTGTTGAATTTTACCTATAAACATATTTAAAAATAGATTTCAAAGACGTAATGGAC
*
311541 CAGATCAAACTTTGGGTAGTATTTGGACATGATTCTATCCGATCAATGAACAGCTTTAACGTGAA
66 CAGATCAAACTTTGGGTAGTATCTGGACATGATTCTATCCGATCAATGAACAGCTTTAACGTGAA
*
311606 ATAGCCAATGGGGAGGGGTGGTCAGATAACCAAGAACTGGCTGAAC
131 ATAGCCAATGGGGAGGGGTGGTCAGATAACCAAAAACTGGCTGAAC
**
311652 TTTT-TTTTTTGTTGAATTTTACCTATAAATGTATTTAAAAATAGATTTCAAAGACGTAATGGAC
1 TTTTATTTTTTGTTGAATTTTACCTATAAACATATTTAAAAATAGATTTCAAAGACGTAATGGAC
311716 CAGATCAAACTTTGGGTAGTATCTGGACATGATTCTATCCGATCAATGAACAGCTTTAACGTGAA
66 CAGATCAAACTTTGGGTAGTATCTGGACATGATTCTATCCGATCAATGAACAGCTTTAACGTGAA
* *
311781 ATGGCCAATGGTGAGGGGTGGTCAGATAACCAAAAACTGG
131 ATAGCCAATGGGGAGGGGTGGTCAGATAACCAAAAACTGG
311821 TTTGCTTTAT
Statistics
Matches: 163, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
175 159 0.98
176 4 0.02
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.32
Consensus pattern (176 bp):
TTTTATTTTTTGTTGAATTTTACCTATAAACATATTTAAAAATAGATTTCAAAGACGTAATGGAC
CAGATCAAACTTTGGGTAGTATCTGGACATGATTCTATCCGATCAATGAACAGCTTTAACGTGAA
ATAGCCAATGGGGAGGGGTGGTCAGATAACCAAAAACTGGCTGAAC
Found at i:313233 original size:18 final size:18
Alignment explanation
Indices: 313206--313245 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
313196 ATTATTTGTG
313206 TATTAATATAATTA-ATGA
1 TATTAATAT-ATTATATGA
*
313224 TATTATTATATTATATGA
1 TATTAATATATTATATGA
313242 TATT
1 TATT
313246 TAACATATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (18 bp):
TATTAATATATTATATGA
Found at i:313283 original size:12 final size:12
Alignment explanation
Indices: 313266--313291 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
313256 AAGTAAAAAA
313266 TTAATTAATTTT
1 TTAATTAATTTT
313278 TTAATTAATTTT
1 TTAATTAATTTT
313290 TT
1 TT
313292 TATTTTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTAATTAATTTT
Found at i:314940 original size:18 final size:20
Alignment explanation
Indices: 314896--314940 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 20
314886 TTTTTTTAAA
*
314896 AATATTTTATATAAATAATT
1 AATATTTTAAATAAATAATT
314916 AA-A-TTTAAATAAA-AA-T
1 AATATTTTAAATAAATAATT
314932 AATATTTTA
1 AATATTTTA
314941 TTATTTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
16 3 0.14
17 3 0.14
18 13 0.59
19 1 0.05
20 2 0.09
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AATATTTTAAATAAATAATT
Found at i:314952 original size:19 final size:17
Alignment explanation
Indices: 314928--314972 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
314918 ATTTAAATAA
*
314928 AAATAATATTTTATTATTT
1 AAATAATAATTTA--ATTT
314947 AAATAATAATTTAATTT
1 AAATAATAATTTAATTT
*
314964 AAATTATAA
1 AAATAATAA
314973 AATTTTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 12 0.50
19 12 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
AAATAATAATTTAATTT
Found at i:314965 original size:17 final size:18
Alignment explanation
Indices: 314890--314972 Score: 57
Period size: 19 Copynumber: 4.7 Consensus size: 18
314880 ATTTGATTTT
314890 TTTAAA-AAT-ATTT-TA
1 TTTAAATAATAATTTATA
* *
314905 TATAAATAATTAAATTTAAA
1 TTTAAATAA-T-AATTTATA
** *
314925 TAAAAATAATATTTTATTA
1 TTTAAATAATAATTTA-TA
314944 TTTAAATAATAATTTA-A
1 TTTAAATAATAATTTATA
*
314961 TTTAAATTATAA
1 TTTAAATAATAA
314973 AATTTTTTAT
Statistics
Matches: 53, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
15 5 0.09
16 2 0.04
17 13 0.25
18 5 0.09
19 19 0.36
20 9 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTTAAATAATAATTTATA
Found at i:316661 original size:32 final size:32
Alignment explanation
Indices: 316604--316688 Score: 102
Period size: 32 Copynumber: 2.6 Consensus size: 32
316594 TATTTTATGG
316604 TATT-ATAATATTATATTTATATAAATTTTAATAA
1 TATTAATAAT-TTATA-TTATATAAATTTTAA-AA
316638 -ATTAATAATTTATATTATATAAATTTTAAAA
1 TATTAATAATTTATATTATATAAATTTTAAAA
* *
316669 TATTTATATATTTACATTAT
1 TATTAATA-ATTTATATTAT
316689 TTTTTATATT
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
31 2 0.04
32 21 0.46
33 18 0.39
34 5 0.11
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (32 bp):
TATTAATAATTTATATTATATAAATTTTAAAA
Found at i:318913 original size:4 final size:4
Alignment explanation
Indices: 318904--318934 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
318894 CAACTAGCAA
*
318904 ATAC ATAC ATAC ATAC ATAC ATAT ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
318935 ATAGAGATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.52, C:0.19, G:0.00, T:0.29
Consensus pattern (4 bp):
ATAC
Found at i:322886 original size:15 final size:14
Alignment explanation
Indices: 322835--322891 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 14
322825 TTTAATATTT
322835 AAATTAAT-AAAAA
1 AAATTAATAAAAAA
*
322848 AATTTAAATAAAAAA
1 AAATT-AATAAAAAA
322863 AGAGA-TAATAAAATAA
1 A-A-ATTAATAAAA-AA
322879 AAATTAATAAAAA
1 AAATTAATAAAAA
322892 TTAAATTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
13 4 0.11
14 5 0.14
15 22 0.61
16 5 0.14
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.23
Consensus pattern (14 bp):
AAATTAATAAAAAA
Found at i:324459 original size:12 final size:12
Alignment explanation
Indices: 324444--324475 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
324434 TTATAATTTT
324444 AAATATAAATAA
1 AAATATAAATAA
324456 AAATATAAATAA
1 AAATATAAATAA
324468 ATAATATA
1 A-AATATA
324476 TTTTTAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.68
13 6 0.32
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (12 bp):
AAATATAAATAA
Found at i:324795 original size:4 final size:4
Alignment explanation
Indices: 324779--324822 Score: 79
Period size: 4 Copynumber: 11.0 Consensus size: 4
324769 CCAGGAAAGC
*
324779 ATTT ATTT GTTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
324823 TCTCTTCTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:325761 original size:25 final size:25
Alignment explanation
Indices: 325724--325775 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 25
325714 AAGATGGATA
** *
325724 TAAAAAATATAAATTTTAAATATAT
1 TAAAAAATATAAAAATAAAATATAT
* *
325749 TAAAAATTTTAAAAATAAAATATAT
1 TAAAAAATATAAAAATAAAATATAT
325774 TA
1 TA
325776 GACATATATT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (25 bp):
TAAAAAATATAAAAATAAAATATAT
Found at i:326563 original size:21 final size:21
Alignment explanation
Indices: 326539--326598 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
326529 TATTAAAAGT
*
326539 TACATTTTTTCATCCAAAAAA
1 TACATTATTTCATCCAAAAAA
* **
326560 TACATTCTTTCATCCAACCAA
1 TACATTATTTCATCCAAAAAA
*
326581 TGCATTATTTCATCCAAA
1 TACATTATTTCATCCAAA
326599 GATACCTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.37
Consensus pattern (21 bp):
TACATTATTTCATCCAAAAAA
Found at i:329956 original size:1 final size:1
Alignment explanation
Indices: 329921--329945 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
329911 ACTTGCTTAG
329921 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
329946 CCAAACTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:330903 original size:26 final size:23
Alignment explanation
Indices: 330867--330915 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 23
330857 CGATAATTTT
330867 AAAAATATTATAATTATATAATATA
1 AAAAATATTATAA-TATA-AATATA
330892 AAAAATAATTATAATATAAATATA
1 AAAAAT-ATTATAATATAAATATA
330916 TTAATATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 6 0.26
25 10 0.43
26 7 0.30
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (23 bp):
AAAAATATTATAATATAAATATA
Found at i:330922 original size:14 final size:14
Alignment explanation
Indices: 330903--330991 Score: 63
Period size: 14 Copynumber: 5.9 Consensus size: 14
330893 AAAATAATTA
330903 TAATATAAATATAT
1 TAATATAAATATAT
*
330917 TAATATTTTAAAATTTATT
1 TAATA---T-AAATATA-T
330936 TAATATAAAT-TAT
1 TAATATAAATATAT
**
330949 TAATATATTTATAT
1 TAATATAAATATAT
*
330963 TAATATATTATATAT
1 TAATATA-AATATAT
*
330978 TATATATAATTATA
1 TA-ATATAAATATA
330992 ACAAATAAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 15
0.74 0.07 0.18
Matches are distributed among these distances:
13 9 0.15
14 17 0.28
15 16 0.26
16 6 0.10
17 1 0.02
18 6 0.10
19 6 0.10
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TAATATAAATATAT
Found at i:330987 original size:21 final size:21
Alignment explanation
Indices: 330938--330990 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
330928 AATTTATTTA
330938 ATATA-AATTATTAATATATT
1 ATATATAATTATTAATATATT
330958 -TATATTAATATATT-ATATATT
1 ATATA-TAAT-TATTAATATATT
330979 ATATATAATTAT
1 ATATATAATTAT
330991 AACAAATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
19 4 0.14
20 3 0.10
21 14 0.48
22 8 0.28
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATATATAATTATTAATATATT
Found at i:331774 original size:24 final size:25
Alignment explanation
Indices: 331740--331802 Score: 64
Period size: 24 Copynumber: 2.7 Consensus size: 25
331730 ATAAACTTTA
*
331740 TAAT-TAT-TAAATTATTAATATTT
1 TAATATATATAAATTATTAATATAT
331763 TAA-ATATATAAA-TA-TAATATAT
1 TAATATATATAAATTATTAATATAT
*
331785 TAATTATATTTAAATTAT
1 TAA-TATATATAAATTAT
331803 CGATTCATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
22 10 0.31
23 8 0.25
24 12 0.38
25 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
TAATATATATAAATTATTAATATAT
Found at i:332331 original size:24 final size:25
Alignment explanation
Indices: 332277--332335 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 25
332267 ACTAAATTAA
*
332277 ATTTTATAT--TTATAATGTTTTAT
1 ATTTTATATAATTATAATATTTTAT
*
332300 ATTTTATATAATTATATTATTTT-T
1 ATTTTATATAATTATAATATTTTAT
332324 ATTTTATATAAT
1 ATTTTATATAAT
332336 ATTTTAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
23 9 0.28
24 13 0.41
25 10 0.31
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (25 bp):
ATTTTATATAATTATAATATTTTAT
Done.