Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold8
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: 6381039
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 22487 characters in sequence are not A, C, G, or T
File 3 of 33
Found at i:287005 original size:20 final size:20
Alignment explanation
Indices: 286980--287065 Score: 61
Period size: 20 Copynumber: 4.0 Consensus size: 20
286970 ATATATTTTT
286980 AAATATTATAATTATATTTA
1 AAATATTATAATTATATTTA
287000 AAATATTATATATTTATATATTTTA
1 AAATATTATA-A--T-TATA-TTTA
*
287025 ATATATTAATAATTAATATTATA
1 AAATATT-ATAATT-ATATT-TA
287048 TAAAT-TT-TAA-TATATTTA
1 -AAATATTATAATTATATTTA
287066 TATATTTTTA
Statistics
Matches: 55, Mismatches: 2, Indels: 20
0.71 0.03 0.26
Matches are distributed among these distances:
18 2 0.04
19 5 0.09
20 11 0.20
21 4 0.07
22 3 0.05
23 9 0.16
24 7 0.13
25 11 0.20
26 3 0.05
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
AAATATTATAATTATATTTA
Found at i:287018 original size:8 final size:8
Alignment explanation
Indices: 286967--287098 Score: 62
Period size: 8 Copynumber: 16.2 Consensus size: 8
286957 TTGTATCAAT
286967 TTTATATA
1 TTTATATA
* *
286975 TTTTTAAA
1 TTTATATA
286983 TATTATA-A
1 T-TTATATA
286991 -TTATAT-
1 TTTATATA
* *
286997 TTAAAATA
1 TTTATATA
287005 -TTATATA
1 TTTATATA
287012 TTTATATA
1 TTTATATA
287020 TTT-TAATA
1 TTTAT-ATA
287028 TATTA-ATA
1 T-TTATATA
*
287036 ATTA-ATA
1 TTTATATA
*
287043 TTATATAAA
1 TT-TATATA
287052 TTTTAATATA
1 -TTT-ATATA
287062 TTTATATA
1 TTTATATA
287070 TTTTTATCATA
1 --TTTAT-ATA
*
287081 TTTATATT
1 TTTATATA
*
287089 TTTTTATA
1 TTTATATA
287097 TT
1 TT
287099 ATGTCATATT
Statistics
Matches: 95, Mismatches: 14, Indels: 30
0.68 0.10 0.22
Matches are distributed among these distances:
6 5 0.05
7 17 0.18
8 42 0.44
9 17 0.18
10 11 0.12
11 3 0.03
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (8 bp):
TTTATATA
Found at i:287066 original size:20 final size:18
Alignment explanation
Indices: 286947--287097 Score: 88
Period size: 19 Copynumber: 8.4 Consensus size: 18
286937 ATCTAATTAT
* *
286947 TTTTATAAATTTGTATCAA
1 TTTTATATATTTATAT-AA
*
286966 TTTTATATATTTTTA-AA
1 TTTTATATATTTATATAA
286983 TATTATAATTATATTTA-A-AA
1 T-TT-T-A-TATATTTATATAA
*
287003 TATTATATATTTATAT-A
1 TTTTATATATTTATATAA
287020 TTTTA-ATATATTA-ATAA
1 TTTTATATAT-TTATATAA
287037 --TTA-ATA-TTATATAAA
1 TTTTATATATTTATAT-AA
*
287052 TTTTAATATATTTATATAT
1 TTTT-ATATATTTATATAA
**
287071 TTTTATCATATTTATATTT
1 TTTTAT-ATATTTATATAA
287090 TTTTATAT
1 TTTTATAT
287098 TATGTCATAT
Statistics
Matches: 109, Mismatches: 7, Indels: 33
0.73 0.05 0.22
Matches are distributed among these distances:
13 3 0.03
14 2 0.02
15 8 0.07
16 14 0.13
17 16 0.15
18 8 0.07
19 40 0.37
20 11 0.10
21 7 0.06
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (18 bp):
TTTTATATATTTATATAA
Found at i:287119 original size:26 final size:26
Alignment explanation
Indices: 287076--287126 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
287066 TATATTTTTA
287076 TCATATTTATATTTTTTTATATTATG
1 TCATATTTATATTTTTTTATATTATG
*
287102 TCATATTT-TATTTATTTTTTATTAT
1 TCATATTTATATTT-TTTTATATTAT
287127 ATTTATATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 5 0.22
26 18 0.78
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.69
Consensus pattern (26 bp):
TCATATTTATATTTTTTTATATTATG
Found at i:287128 original size:21 final size:21
Alignment explanation
Indices: 287052--287130 Score: 63
Period size: 21 Copynumber: 3.6 Consensus size: 21
287042 ATTATATAAA
* *
287052 TTTTAATATA-TTTATATA-T
1 TTTTATTATATTTTATTTATT
* *
287071 TTTTATCATATTTATATTTTTT
1 TTTTATTATATTT-TATTTATT
287093 TATATTATGTCATATTTTATTTATT
1 T-T-TTAT-T-ATATTTTATTTATT
287118 TTTTATTATATTT
1 TTTTATTATATTT
287131 ATATCATGTT
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
19 8 0.17
20 2 0.04
21 10 0.21
22 3 0.06
23 5 0.11
24 5 0.11
25 8 0.17
26 6 0.13
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.68
Consensus pattern (21 bp):
TTTTATTATATTTTATTTATT
Found at i:287942 original size:31 final size:31
Alignment explanation
Indices: 287907--287968 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
287897 TTTACATAGT
287907 CGAATATTCGCCTTTTTTTGTACTAAAAACC
1 CGAATATTCGCCTTTTTTTGTACTAAAAACC
*
287938 CGAATATTCTCCTTTTTTTGTACTAAAAACC
1 CGAATATTCGCCTTTTTTTGTACTAAAAACC
287969 TAAAATTTAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.29, C:0.23, G:0.08, T:0.40
Consensus pattern (31 bp):
CGAATATTCGCCTTTTTTTGTACTAAAAACC
Found at i:288454 original size:6 final size:6
Alignment explanation
Indices: 288443--288480 Score: 58
Period size: 6 Copynumber: 6.2 Consensus size: 6
288433 TGAAAGTTAT
*
288443 TTGTAA TTGTAA TTGTAAA TTTTAA TTGTAA TTGTAA T
1 TTGTAA TTGTAA TTGT-AA TTGTAA TTGTAA TTGTAA T
288481 AATTACATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 24 0.83
7 5 0.17
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (6 bp):
TTGTAA
Found at i:288470 original size:19 final size:20
Alignment explanation
Indices: 288441--288479 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
288431 TTTGAAAGTT
288441 ATTTGTAATTGTAATTGTAA
1 ATTTGTAATTGTAATTGTAA
288461 ATTT-TAATTGTAATTGTAA
1 ATTTGTAATTGTAATTGTAA
288480 TAATTACATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (20 bp):
ATTTGTAATTGTAATTGTAA
Found at i:289181 original size:20 final size:20
Alignment explanation
Indices: 289158--289199 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
289148 ATGATTATAA
*
289158 ATATATATTTTAATTATATT
1 ATATATATTATAATTATATT
*
289178 ATATTTATTATAATTATATT
1 ATATATATTATAATTATATT
289198 AT
1 AT
289200 TTCGATGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
ATATATATTATAATTATATT
Found at i:289188 original size:9 final size:11
Alignment explanation
Indices: 289151--289199 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
289141 TAATTTCATG
289151 ATTATAAATATAT
1 ATTAT-AAT-TAT
*
289164 ATTTTAATTAT
1 ATTATAATTAT
289175 ATTAT-ATT-T
1 ATTATAATTAT
289184 ATTATAATTAT
1 ATTATAATTAT
289195 ATTAT
1 ATTAT
289200 TTCGATGAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 6 0.19
10 6 0.19
11 13 0.41
12 3 0.09
13 4 0.12
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
ATTATAATTAT
Found at i:289385 original size:13 final size:13
Alignment explanation
Indices: 289367--289392 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
289357 GGAGAAATAG
289367 AAAAAAAAGAAGA
1 AAAAAAAAGAAGA
289380 AAAAAAAAGAAGA
1 AAAAAAAAGAAGA
289393 TATTCTGGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAAAAGAAGA
Found at i:289721 original size:11 final size:11
Alignment explanation
Indices: 289705--289753 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
289695 AATTATGATT
289705 ATATAAATATA
1 ATATAAATATA
*
289716 ATATAAAAATA
1 ATATAAATATA
289727 AT-TAAAATATA
1 ATAT-AAATATA
289738 ATAT-AATATTA
1 ATATAAATA-TA
289749 ATATA
1 ATATA
289754 TAAATATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
10 5 0.16
11 26 0.81
12 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
ATATAAATATA
Found at i:289750 original size:22 final size:24
Alignment explanation
Indices: 289704--289760 Score: 82
Period size: 22 Copynumber: 2.5 Consensus size: 24
289694 TAATTATGAT
289704 TATATAAATATAATATAAAAATAA
1 TATATAAATATAATATAAAAATAA
* *
289728 T-TA-AAATATAATATAATATTAA
1 TATATAAATATAATATAAAAATAA
289750 TATATAAATAT
1 TATATAAATAT
289761 TTTAAAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 18 0.62
23 4 0.14
24 7 0.24
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
TATATAAATATAATATAAAAATAA
Found at i:289751 original size:33 final size:34
Alignment explanation
Indices: 289705--289806 Score: 101
Period size: 33 Copynumber: 3.2 Consensus size: 34
289695 AATTATGATT
289705 ATATAA-ATATAATATAAAAATA-ATTAAAATATA
1 ATATAATATATAATATAAAAATATATTAAAAT-TA
* * *
289738 ATATAATAT-TAATATATAAATATTTTAAAATTT
1 ATATAATATATAATATAAAAATATATTAAAATTA
* *
289771 ATATAATATAT--TAT--TAATATATTAAAATTT
1 ATATAATATATAATATAAAAATATATTAAAATTA
289801 ATATAA
1 ATATAA
289807 AAATATAAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
30 20 0.33
32 3 0.05
33 28 0.46
34 10 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (34 bp):
ATATAATATATAATATAAAAATATATTAAAATTA
Found at i:289796 original size:30 final size:30
Alignment explanation
Indices: 289703--289806 Score: 109
Period size: 30 Copynumber: 3.3 Consensus size: 30
289693 TTAATTATGA
* *
289703 TTATATAAATATAATATAAAAATAATTAAAAT
1 TTATAT-AATATATTATAAATAT-ATTAAAAT
* *
289735 ATAATATAATATTAATATATAAATATTTTAAAAT
1 -TTATATAATA-T-AT-TATAAATATATTAAAAT
*
289769 TTATATAATATATTATTAATATATTAAAAT
1 TTATATAATATATTATAAATATATTAAAAT
289799 TTATATAA
1 TTATATAA
289807 AAATATAAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
30 23 0.38
31 2 0.03
32 5 0.08
33 15 0.25
34 8 0.13
35 8 0.13
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (30 bp):
TTATATAATATATTATAAATATATTAAAAT
Found at i:289813 original size:38 final size:36
Alignment explanation
Indices: 289730--289814 Score: 100
Period size: 38 Copynumber: 2.2 Consensus size: 36
289720 AAAAATAATT
289730 AAAATATAATATAATATTAATATATAAATATTTTAA
1 AAAATATAATATAATATTAATATATAAATATTTTAA
* *
289766 AATTTATATAATATATTATTAATATATTAAA-ATTTATATA
1 AA--AATATAATATAATATTAATATA-TAAATATTT-TA-A
289806 AAAATATAA
1 AAAATATAA
289815 AATTTTTTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
36 2 0.05
38 30 0.73
39 6 0.15
40 3 0.07
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (36 bp):
AAAATATAATATAATATTAATATATAAATATTTTAA
Found at i:290480 original size:19 final size:19
Alignment explanation
Indices: 290426--290481 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 19
290416 AAATTATTTT
290426 TAATATATTTAATTATAAAA
1 TAATATATTTAA-TATAAAA
*
290446 TATATAAATCTTAATATAAAA
1 TA-ATATAT-TTAATATAAAA
*
290467 TAATTTATTTAATAT
1 TAATATATTTAATAT
290482 TTTAATATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 7 0.23
20 6 0.19
21 14 0.45
22 4 0.13
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (19 bp):
TAATATATTTAATATAAAA
Found at i:290856 original size:11 final size:10
Alignment explanation
Indices: 290828--290862 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
290818 TAAAATTATA
*
290828 ATATATAAAA
1 ATATATAAAT
290838 ATATATAAAT
1 ATATATAAAT
290848 ATGATATAAAT
1 AT-ATATAAAT
290859 ATAT
1 ATAT
290863 GTAATACTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 13 0.57
11 10 0.43
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (10 bp):
ATATATAAAT
Found at i:291905 original size:11 final size:11
Alignment explanation
Indices: 291889--291937 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
291879 TTATTACTTT
291889 TTATTTATAAA
1 TTATTTATAAA
* *
291900 TTATTTTTAAT
1 TTATTTATAAA
291911 TTATTTATAAA
1 TTATTTATAAA
291922 TTA--TATAAA
1 TTATTTATAAA
291931 TTTATTT
1 -TTATTT
291938 TTATTAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
9 6 0.19
10 3 0.10
11 21 0.68
12 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TTATTTATAAA
Found at i:292368 original size:295 final size:297
Alignment explanation
Indices: 291830--292420 Score: 1006
Period size: 295 Copynumber: 2.0 Consensus size: 297
291820 TTCTTTCTGA
*
291830 TATTGTACATGTATTATTTTTATTAAAATTAATTAATATTATGCATGTATTATTACTTTTTATTT
1 TATTATACATGTATTATTTTTATTAAAATTAATTAATATTATGCATGTATTATTAC-TTTTATTT
* *
291895 ATAAATTATTTTTAATTTATTTATAAATTATATAAATTTATTTTTATTAAAATTAATTAATATTG
65 ATAAATTATTTTTAATTTATTTATAAATTATACAAATTTATTTTTATTAAAACTAATTAATATTG
* * **
291960 TATATATATTATTTTTATAATTTATAGAACTTAAATTTATGTTAGCCAACAATATTTTACTTTTT
130 TACATATATTATTTTTATAATTGATAGAACTTAAATTTATGTTAGCCAACAATAAATTACTTTTT
** * * *
292025 TCGATAATTACTTATTTCGGATTTACAGGCGCACACATTTTATTTTTCGGTAACGACTTAAATAT
195 TCGATAACGACTTATTTCGGATTTACAGACGCACACATTTTATTTTTCGGTAACAACTTAAATAC
* *
292090 GAGCTTTCCTTTATTTGTAAAGTGACCAAGAAAAAATT
260 GAGCTTTCCTTTATCTGTAAAATGACCAAGAAAAAATT
*
292128 TATTATACATGTATTATTTTTATTAAAATTAATTAATATTGTGCATGTATTATTA-TTTT-TTTA
1 TATTATACATGTATTATTTTTATTAAAATTAATTAATATTATGCATGTATTATTACTTTTATTTA
*
292191 TAAATTATTTTTAATTTATTTATAAATTATACAAATTTATTTTTATTAAAACTAATTACTATTGT
66 TAAATTATTTTTAATTTATTTATAAATTATACAAATTTATTTTTATTAAAACTAATTAATATTGT
*
292256 ACATGTATTATTTTTATAATTGATAGAACTTAAATTTATGTTAGCCAACAATAAATTACTTTTTT
131 ACATATATTATTTTTATAATTGATAGAACTTAAATTTATGTTAGCCAACAATAAATTACTTTTTT
292321 CGATAACGACTTATTTCGGATTTACAGACGCACACATTTTATTTTTCGGTAACAACTTAAATACG
196 CGATAACGACTTATTTCGGATTTACAGACGCACACATTTTATTTTTCGGTAACAACTTAAATACG
292386 AGCTTTCCTTTATCTGTAAAATGACCAAGAAAAAA
261 AGCTTTCCTTTATCTGTAAAATGACCAAGAAAAAA
292421 ATTTTCCTCA
Statistics
Matches: 276, Mismatches: 17, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
295 219 0.79
296 4 0.01
298 53 0.19
ACGTcount: A:0.36, C:0.09, G:0.08, T:0.47
Consensus pattern (297 bp):
TATTATACATGTATTATTTTTATTAAAATTAATTAATATTATGCATGTATTATTACTTTTATTTA
TAAATTATTTTTAATTTATTTATAAATTATACAAATTTATTTTTATTAAAACTAATTAATATTGT
ACATATATTATTTTTATAATTGATAGAACTTAAATTTATGTTAGCCAACAATAAATTACTTTTTT
CGATAACGACTTATTTCGGATTTACAGACGCACACATTTTATTTTTCGGTAACAACTTAAATACG
AGCTTTCCTTTATCTGTAAAATGACCAAGAAAAAATT
Found at i:296108 original size:91 final size:91
Alignment explanation
Indices: 295937--296345 Score: 461
Period size: 91 Copynumber: 4.5 Consensus size: 91
295927 ATCTTTACAG
* * *
295937 TCTTTCTTTTTTCCTATAAAAAAGAATCTAATTTTTAGATATAATTCATGCATTAGTCTAATCCT
1 TCTTTCTTTTTT-CTATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCCT
* * *
296002 TGTAGCTTAACATTTACAATCAATCAA
65 TGCAGTTTGACATTTACAATCAATCAA
* * * * * *
296029 TCTTTCTTTTTTCTATAAAAAAGAATCCGATTCTCATATGTAATTTATGTATTAGTCTAATCTTT
1 TCTTTCTTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCCTT
** * * *
296094 ATAGTTTGATATTTACAACCAATCAG
66 GCAGTTTGACATTTACAATCAATCAA
* *
296120 TCTTTCTTGTTTTCTGTAAAAAAGAATCTGATTCTCATATATAATTCATGCATTAGTCTAATCCT
1 TCTTTCTT-TTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCCT
296185 TGCAG--T-ACATTTACAATCAATCAA
65 TGCAGTTTGACATTTACAATCAATCAA
* **
296209 CTCTTAT-TTTTTTCTATAAAAAATAAT-TGATTCTCAGATATAATTCATGCATTAGAATAATCC
1 -TCTT-TCTTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCC
* *
296272 TTGCAGTCTGATATTTACAATCAATCAA
64 TTGCAGTTTGACATTTACAATCAATCAA
* * * *
296300 -CTTTTCTTTTTTTTCCATAAAAAAGAATCCGATTTTAAGATATAAT
1 TC-TTTC--TTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAAT
296346 CACATTTTTT
Statistics
Matches: 269, Mismatches: 37, Indels: 21
0.82 0.11 0.06
Matches are distributed among these distances:
88 39 0.14
89 33 0.12
90 10 0.04
91 90 0.33
92 83 0.31
93 14 0.05
ACGTcount: A:0.34, C:0.16, G:0.08, T:0.43
Consensus pattern (91 bp):
TCTTTCTTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCCTT
GCAGTTTGACATTTACAATCAATCAA
Found at i:296871 original size:28 final size:28
Alignment explanation
Indices: 296840--296905 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 28
296830 TTTTTTATAA
296840 ATTAATTAA-ATTTAAAAAATAATAATAT
1 ATTAATTAATATTTAAAAAA-AATAATAT
* *
296868 ATTAATTATTATTTTTAATAAAAATAATAT
1 ATTAATTA--ATATTTAAAAAAAATAATAT
296898 -TTAATTAA
1 ATTAATTAA
296906 CTTAAAGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
27 1 0.03
28 8 0.24
29 7 0.21
30 9 0.27
31 8 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (28 bp):
ATTAATTAATATTTAAAAAAAATAATAT
Found at i:297113 original size:33 final size:33
Alignment explanation
Indices: 297076--297159 Score: 91
Period size: 34 Copynumber: 2.5 Consensus size: 33
297066 GTAAATTTTT
*
297076 AAAAT-TTAATTAATATTATTTTTTATTTTATTA
1 AAAATATTAATTAATATTACTTTTTATTTTA-TA
* * * *
297109 AAAATAATAATAAAAAATACTTTTTATTTTATA
1 AAAATATTAATTAATATTACTTTTTATTTTATA
297142 AAAATATATAA-TAATATT
1 AAAATAT-TAATTAATATT
297160 TTAATTTGTT
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
33 17 0.43
34 23 0.57
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (33 bp):
AAAATATTAATTAATATTACTTTTTATTTTATA
Found at i:297286 original size:12 final size:12
Alignment explanation
Indices: 297246--297337 Score: 71
Period size: 12 Copynumber: 7.2 Consensus size: 12
297236 TAATTAATTT
*
297246 TTATCTTATATA
1 TTATATTATATA
297258 TT-TATTTATTATA
1 TTATA-TTA-TATA
*
297271 TTATATTATATG
1 TTATATTATATA
297283 TTATAAATTCTATATA
1 TTAT--A-T-TATATA
* *
297299 TTATGTTATATG
1 TTATATTATATA
297311 TTATATTATATA
1 TTATATTATATA
297323 -TATATATATATA
1 TTATAT-TATATA
297335 TTA
1 TTA
297338 CTATAAATAT
Statistics
Matches: 64, Mismatches: 7, Indels: 17
0.73 0.08 0.19
Matches are distributed among these distances:
11 6 0.09
12 33 0.52
13 12 0.19
14 3 0.05
15 1 0.02
16 9 0.14
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (12 bp):
TTATATTATATA
Found at i:297300 original size:28 final size:26
Alignment explanation
Indices: 297254--297335 Score: 91
Period size: 28 Copynumber: 3.2 Consensus size: 26
297244 TTTTATCTTA
297254 TATAT-TTAT-TTAT-TATATTATAT
1 TATATGTTATATTATATATATTATAT
* *
297277 TATATGTTATAAATTCTATATATTATGT
1 TATATGTTAT--ATTATATATATTATAT
297305 TATATGTTATATTATATATA-TATAT
1 TATATGTTATATTATATATATTATAT
297330 ATATAT
1 -TATAT
297336 TACTATAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
23 5 0.10
24 4 0.08
25 4 0.08
26 14 0.29
27 3 0.06
28 19 0.39
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.57
Consensus pattern (26 bp):
TATATGTTATATTATATATATTATAT
Found at i:297324 original size:2 final size:2
Alignment explanation
Indices: 297312--297438 Score: 85
Period size: 2 Copynumber: 67.0 Consensus size: 2
297302 TGTTATATGT
* *
297312 TA TA T- TA TA TA TA TA TA TA TA TA T- TA CTA TA AA TA TA TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* ** *
297353 CA GC TA TA TA TA TA -A TT TA TA -A TA TA TA -A TA TA -A TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
297390 TT TA TA TA TA GTA TA TA TA TA -A TA TA -A TC TA TA -A TA CTA TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
297431 TA TA TA TA
1 TA TA TA TA
297439 ACATTAATAT
Statistics
Matches: 98, Mismatches: 14, Indels: 26
0.71 0.10 0.19
Matches are distributed among these distances:
1 10 0.10
2 82 0.84
3 6 0.06
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.45
Consensus pattern (2 bp):
TA
Found at i:297398 original size:37 final size:36
Alignment explanation
Indices: 297317--297438 Score: 115
Period size: 37 Copynumber: 3.3 Consensus size: 36
297307 TATGTTATAT
*
297317 TATATATATATATATATATTACTATAAATATATAA-ACA
1 TATATATATATATATATA-TAATAT-AATATATAATA-A
** *
297355 GCTATATATATA-ATTTATAATAT-ATAATATAATAA
1 TATATATATATATATATATAATATAAT-ATATAATAA
* * *
297390 TTTATATATAGTATATATATAATATAATCTATAATAC
1 TATATATATA-TATATATATAATATAATATATAATAA
297427 TATATATATATA
1 TATATATATATA
297439 ACATTAATAT
Statistics
Matches: 69, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
34 2 0.03
35 15 0.22
36 10 0.14
37 30 0.43
38 12 0.17
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (36 bp):
TATATATATATATATATATAATATAATATATAATAA
Found at i:297531 original size:18 final size:18
Alignment explanation
Indices: 297510--297544 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
297500 AAATCACTAA
297510 TTTATTATATTTTTTTTT
1 TTTATTATATTTTTTTTT
*
297528 TTTATTTTATTTTTTTT
1 TTTATTATATTTTTTTT
297545 AGTTTTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (18 bp):
TTTATTATATTTTTTTTT
Found at i:297537 original size:20 final size:20
Alignment explanation
Indices: 297510--297554 Score: 58
Period size: 18 Copynumber: 2.3 Consensus size: 20
297500 AAATCACTAA
*
297510 TTTATTATA-TTTTTTT-TT
1 TTTATTTTATTTTTTTTATT
297528 TTTATTTTATTTTTTTTAGTT
1 TTTATTTTATTTTTTTTA-TT
297549 TTTATT
1 TTTATT
297555 ATTTTTTAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 8 0.35
19 7 0.30
21 8 0.35
ACGTcount: A:0.16, C:0.00, G:0.02, T:0.82
Consensus pattern (20 bp):
TTTATTTTATTTTTTTTATT
Found at i:297559 original size:17 final size:16
Alignment explanation
Indices: 297519--297565 Score: 64
Period size: 17 Copynumber: 3.1 Consensus size: 16
297509 ATTTATTATA
297519 TTTT-TTTTTTTTA--
1 TTTTATTTTTTTTAGT
297532 TTTTATTTTTTTTAGT
1 TTTTATTTTTTTTAGT
297548 TTTTATTATTTTTTAGT
1 TTTTATT-TTTTTTAGT
297565 T
1 T
297566 AAGTTTCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
13 4 0.13
14 9 0.30
16 7 0.23
17 10 0.33
ACGTcount: A:0.13, C:0.00, G:0.04, T:0.83
Consensus pattern (16 bp):
TTTTATTTTTTTTAGT
Found at i:297559 original size:18 final size:18
Alignment explanation
Indices: 297510--297565 Score: 53
Period size: 17 Copynumber: 3.0 Consensus size: 18
297500 AAATCACTAA
*
297510 TTTATTATATTTTTT-TTT
1 TTTATTAT-TTTTTTAGTT
297528 TTTATTTTATTTTTTTTAGTT
1 TTTA--TTA-TTTTTTTAGTT
297549 TTTATTA-TTTTTTAGTT
1 TTTATTATTTTTTTAGTT
297566 AAGTTTCTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
17 10 0.30
18 4 0.12
19 3 0.09
20 9 0.27
21 7 0.21
ACGTcount: A:0.16, C:0.00, G:0.04, T:0.80
Consensus pattern (18 bp):
TTTATTATTTTTTTAGTT
Found at i:298079 original size:2 final size:2
Alignment explanation
Indices: 298059--298176 Score: 75
Period size: 2 Copynumber: 66.0 Consensus size: 2
298049 AATAAATAAA
*
298059 AT AT AT TT AT -T AT AT -T AT AT AT -T AT -T AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
298096 AT CT AT -T AT AT CT AT TT AT AT -T AA AT -T A- AT -T 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
* *
298133 -T AT AT AT GT -T AT AT A- AT AT AT AT AT AT AT AT -T GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
298171 AT AT AT
1 AT AT AT
298177 TATCCATACA
Statistics
Matches: 90, Mismatches: 12, Indels: 28
0.69 0.09 0.22
Matches are distributed among these distances:
1 14 0.16
2 76 0.84
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (2 bp):
AT
Found at i:298106 original size:42 final size:42
Alignment explanation
Indices: 298060--298139 Score: 119
Period size: 42 Copynumber: 1.9 Consensus size: 42
298050 ATAAATAAAA
*
298060 TATATTTA-TTATATTATATATT-ATTATATATTATATATCTAT
1 TATATCTATTTATATTA-A-ATTAATTATATATTATATATCTAT
298102 TATATCTATTTATATTAAATTAATTATATATTATATAT
1 TATATCTATTTATATTAAATTAATTATATATTATATAT
298140 GTTATATAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
41 3 0.09
42 24 0.69
43 8 0.23
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (42 bp):
TATATCTATTTATATTAAATTAATTATATATTATATATCTAT
Found at i:298138 original size:9 final size:9
Alignment explanation
Indices: 298059--298174 Score: 84
Period size: 9 Copynumber: 12.9 Consensus size: 9
298049 AATAAATAAA
298059 ATATAT-TT
1 ATATATATT
298067 AT-TATATT
1 ATATATATT
298075 ATATATTATT
1 ATATA-TATT
298085 ATATAT-TAT
1 ATATATAT-T
*
298094 ATATCTATT
1 ATATATATT
*
298103 ATATCTATTT
1 ATATATA-TT
*
298113 ATATTAAATT
1 ATA-TATATT
298123 AATTATATATT
1 -A-TATATATT
*
298134 ATATATGTT
1 ATATATATT
298143 ATATA-A-T
1 ATATATATT
298150 ATATATA-T
1 ATATATATT
298158 ATATAT-TGT
1 ATATATAT-T
298167 ATATATAT
1 ATATATAT
298175 ATTATCCATA
Statistics
Matches: 89, Mismatches: 6, Indels: 24
0.75 0.05 0.20
Matches are distributed among these distances:
7 9 0.10
8 15 0.17
9 36 0.40
10 19 0.21
11 8 0.09
12 2 0.02
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (9 bp):
ATATATATT
Found at i:298540 original size:19 final size:19
Alignment explanation
Indices: 298516--298554 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
298506 ATTGATATTA
298516 ATATATATATAATACTATAAC
1 ATATATATAT-ATA-TATAAC
298537 ATATATATATATATATAA
1 ATATATATATATATATAA
298555 TATTAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 3 0.17
21 10 0.56
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (19 bp):
ATATATATATATATATAAC
Found at i:299296 original size:17 final size:17
Alignment explanation
Indices: 299259--299300 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
299249 TTTCAATTTA
*
299259 TTTGAATTCAAATCGTG
1 TTTGAATTCAAATCATG
* *
299276 TTTGAATTCAAATTATT
1 TTTGAATTCAAATCATG
299293 TTTGAATT
1 TTTGAATT
299301 TAGATTAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.31, C:0.07, G:0.12, T:0.50
Consensus pattern (17 bp):
TTTGAATTCAAATCATG
Found at i:303988 original size:32 final size:32
Alignment explanation
Indices: 303947--304010 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
303937 CAAAGCTATA
303947 TTTGCTCCAATTTATGCCAAAGGGCTTATGAT
1 TTTGCTCCAATTTATGCCAAAGGGCTTATGAT
303979 TTTGCTCCAATTTATGCCAAAGGGCTTATGAT
1 TTTGCTCCAATTTATGCCAAAGGGCTTATGAT
304011 AAGTTGCGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.38
Consensus pattern (32 bp):
TTTGCTCCAATTTATGCCAAAGGGCTTATGAT
Found at i:305534 original size:2 final size:2
Alignment explanation
Indices: 305527--305556 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
305517 TTTTCACATT
305527 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
305557 GAAATGAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:308375 original size:2 final size:2
Alignment explanation
Indices: 308362--308406 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
308352 TTAATATACG
*
308362 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
308404 TA T
1 TA T
308407 TTCAGTTTGA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:309221 original size:215 final size:213
Alignment explanation
Indices: 308852--309284 Score: 848
Period size: 215 Copynumber: 2.0 Consensus size: 213
308842 ACTTATTACT
308852 GAAAAAATACAGCAAGAAGATATACATACATATATATATATATATACGAACACTTAACAACGACT
1 GAAAAAATACAGCAAGAAGATATACATACATATATATATATATATACGAACACTTAACAACGACT
308917 TCAAGTGACAGTAATGTACGTGTAACCAAATTCATATATCTTTTTTTTTCTTTTGGACTTTTGGT
66 TCAAGTGACAGTAATGTACGTGTAACCAAATTCATATATCTTTTTTTTTCTTTTGGACTTTTGGT
308982 TGCATTGATTTTTATTTTATCTCACGTTGCAACCAAATGAGTATTTATGTACGTGTAATTGCAAA
131 TGCATTGATTTTTATTTTATCTCACGTTGCAACCAAATGAGTATTTATGTACGTGTAATTGCAAA
309047 AGGTTTTCCTTTTACCAA
196 AGGTTTTCCTTTTACCAA
309065 GAAAAAATACAGCAAGAAGATATACATACATATATATATATATATATACGAACACTTAACAACGA
1 GAAAAAATACAGCAAGAAGATATACATAC--ATATATATATATATATACGAACACTTAACAACGA
309130 CTTCAAGTGACAGTAATGTACGTGTAACCAAATTCATATATCTTTTTTTTTCTTTTGGACTTTTG
64 CTTCAAGTGACAGTAATGTACGTGTAACCAAATTCATATATCTTTTTTTTTCTTTTGGACTTTTG
309195 GTTGCATTGATTTTTATTTTATCTCACGTTGCAACCAAATGAGTATTTATGTACGTGTAATTGCA
129 GTTGCATTGATTTTTATTTTATCTCACGTTGCAACCAAATGAGTATTTATGTACGTGTAATTGCA
309260 AAAGGTTTTCCTTTTACCAA
194 AAAGGTTTTCCTTTTACCAA
309280 GAAAA
1 GAAAA
309285 TTTGAAAATT
Statistics
Matches: 218, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
213 29 0.13
215 189 0.87
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (213 bp):
GAAAAAATACAGCAAGAAGATATACATACATATATATATATATATACGAACACTTAACAACGACT
TCAAGTGACAGTAATGTACGTGTAACCAAATTCATATATCTTTTTTTTTCTTTTGGACTTTTGGT
TGCATTGATTTTTATTTTATCTCACGTTGCAACCAAATGAGTATTTATGTACGTGTAATTGCAAA
AGGTTTTCCTTTTACCAA
Found at i:310985 original size:17 final size:15
Alignment explanation
Indices: 310934--310978 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
310924 AAAATATGTA
*
310934 AAAATTTATATAAATT
1 AAAATTTATA-ATATT
*
310950 AAATTATTATAATATT
1 AAAAT-TTATAATATT
310966 AAAATTTATAATA
1 AAAATTTATAATA
310979 CTTTAAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
15 8 0.32
16 12 0.48
17 5 0.20
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
AAAATTTATAATATT
Found at i:310994 original size:32 final size:33
Alignment explanation
Indices: 310920--310995 Score: 86
Period size: 32 Copynumber: 2.3 Consensus size: 33
310910 AACATCAAAT
310920 ATATAA-AATATGTAAAAATTTATATAAATTAA
1 ATATAATAATATGTAAAAATTTATATAAATTAA
* **
310952 ATTATTATAATAT-T-AAAATTTATAATACTTTAA
1 A-TATAATAATATGTAAAAATTTAT-ATAAATTAA
310985 ATATAATAATA
1 ATATAATAATA
310996 GAAGAGAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
32 19 0.51
33 13 0.35
34 5 0.14
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (33 bp):
ATATAATAATATGTAAAAATTTATATAAATTAA
Found at i:311704 original size:13 final size:13
Alignment explanation
Indices: 311688--311722 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
311678 ATTACACGTG
311688 TATATATTAT-TAT
1 TATAT-TTATGTAT
311701 TATATTTATGTAT
1 TATATTTATGTAT
311714 TATATTTAT
1 TATATTTAT
311723 AAACATCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 4 0.19
13 17 0.81
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (13 bp):
TATATTTATGTAT
Found at i:314059 original size:18 final size:17
Alignment explanation
Indices: 314024--314058 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
314014 ATTAATATTT
314024 TAAAATTTATATAAATA
1 TAAAATTTATATAAATA
*
314041 TAAAATAT-TATAAATA
1 TAAAATTTATATAAATA
314057 TA
1 TA
314059 TGATCGTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAAATTTATATAAATA
Found at i:317377 original size:21 final size:21
Alignment explanation
Indices: 317347--317396 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
317337 CGTAAAAATT
317347 AATATTAAATT-TAATGATTTAA
1 AATA-TAAATTAT-ATGATTTAA
* *
317369 AATATAAATTATTTTATTTAA
1 AATATAAATTATATGATTTAA
317390 AATATAA
1 AATATAA
317397 TAAAAATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 20 0.80
22 5 0.20
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
AATATAAATTATATGATTTAA
Found at i:319438 original size:7 final size:7
Alignment explanation
Indices: 319428--319452 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
319418 TAAAAATAAA
319428 AAATTTT
1 AAATTTT
319435 AAATTTT
1 AAATTTT
319442 AAATTTT
1 AAATTTT
319449 AAAT
1 AAAT
319453 CTTATGACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (7 bp):
AAATTTT
Found at i:320187 original size:21 final size:22
Alignment explanation
Indices: 320161--320208 Score: 89
Period size: 21 Copynumber: 2.2 Consensus size: 22
320151 TGATCCGAAC
320161 TCAAAAAACTCGATTAATTAA-
1 TCAAAAAACTCGATTAATTAAT
320182 TCAAAAAACTCGATTAATTAAT
1 TCAAAAAACTCGATTAATTAAT
320204 TCAAA
1 TCAAA
320209 TTTAAATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 21 0.81
22 5 0.19
ACGTcount: A:0.52, C:0.15, G:0.04, T:0.29
Consensus pattern (22 bp):
TCAAAAAACTCGATTAATTAAT
Found at i:320341 original size:16 final size:16
Alignment explanation
Indices: 320283--320342 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 16
320273 CGAAATAATT
320283 CGAACCTGAAATGATC
1 CGAACCTGAAATGATC
** * *
320299 CTCATCTAAAATGA-C
1 CGAACCTGAAATGATC
320314 TCGAA-CTCGAAATGATC
1 -CGAACCT-GAAATGATC
320331 CGAACCTGAAAT
1 CGAACCTGAAAT
320343 AACCCGAATA
Statistics
Matches: 33, Mismatches: 7, Indels: 8
0.69 0.15 0.17
Matches are distributed among these distances:
15 3 0.09
16 27 0.82
17 3 0.09
ACGTcount: A:0.38, C:0.25, G:0.15, T:0.22
Consensus pattern (16 bp):
CGAACCTGAAATGATC
Found at i:321224 original size:32 final size:32
Alignment explanation
Indices: 321187--321256 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
321177 TGACTCAAAT
* * * *
321187 CTGAAATGACCCGAACCCGAGATGATTCGAAC
1 CTGAAATAACCCGAACCCAAAATGATCCGAAC
*
321219 CTGAAATAACTCGAACCCAAAATGATCCGAAC
1 CTGAAATAACCCGAACCCAAAATGATCCGAAC
*
321251 TTGAAA
1 CTGAAA
321257 ATGATCCAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.40, C:0.26, G:0.17, T:0.17
Consensus pattern (32 bp):
CTGAAATAACCCGAACCCAAAATGATCCGAAC
Found at i:321249 original size:16 final size:16
Alignment explanation
Indices: 321189--321250 Score: 54
Period size: 16 Copynumber: 3.9 Consensus size: 16
321179 ACTCAAATCT
*
321189 GAAATGACCCGAACCC
1 GAAATGATCCGAACCC
* * *
321205 GAGATGATTCGAACCT
1 GAAATGATCCGAACCC
*
321221 GAAAT-AACTCGAACCC
1 GAAATGATC-CGAACCC
*
321237 AAAATGATCCGAAC
1 GAAATGATCCGAAC
321251 TTGAAAATGA
Statistics
Matches: 34, Mismatches: 10, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
15 1 0.03
16 31 0.91
17 2 0.06
ACGTcount: A:0.40, C:0.27, G:0.18, T:0.15
Consensus pattern (16 bp):
GAAATGATCCGAACCC
Found at i:325227 original size:2 final size:2
Alignment explanation
Indices: 325220--325255 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
325210 ACAATTTTCA
325220 AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
325256 ATTACTGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:326456 original size:10 final size:10
Alignment explanation
Indices: 326441--326470 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
326431 AAAGTCATGT
326441 AGAAAGACAA
1 AGAAAGACAA
326451 AGAAAGACAA
1 AGAAAGACAA
*
326461 AGAAAAACAA
1 AGAAAGACAA
326471 GGGACTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.73, C:0.10, G:0.17, T:0.00
Consensus pattern (10 bp):
AGAAAGACAA
Found at i:329366 original size:24 final size:22
Alignment explanation
Indices: 329337--329391 Score: 56
Period size: 24 Copynumber: 2.4 Consensus size: 22
329327 TATTTAAAAT
329337 TAAAAATATTTTGAATAAAATAA
1 TAAAAATATTTT-AATAAAATAA
* *
329360 GTAAAAAAAATTTTATTAAAATAA
1 -T-AAAAATATTTTAATAAAATAA
*
329384 CAAAAATA
1 TAAAAATA
329392 ACCCTTAGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
22 6 0.23
24 10 0.38
25 10 0.38
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.31
Consensus pattern (22 bp):
TAAAAATATTTTAATAAAATAA
Found at i:329493 original size:29 final size:30
Alignment explanation
Indices: 329467--329546 Score: 103
Period size: 30 Copynumber: 2.7 Consensus size: 30
329457 TATAACATCT
329467 AAATAAATTATTAA-CTTTAATTTACATTA
1 AAATAAATTATTAATCTTTAATTTACATTA
* *
329496 AAATAAATTTTTAATTTTTAATTT-CTATTA
1 AAATAAATTATTAATCTTTAATTTAC-ATTA
329526 AAATAAGATT-TTAATCTTTAA
1 AAATAA-ATTATTAATCTTTAA
329547 ATTTTACTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
29 14 0.31
30 28 0.62
31 3 0.07
ACGTcount: A:0.45, C:0.05, G:0.01, T:0.49
Consensus pattern (30 bp):
AAATAAATTATTAATCTTTAATTTACATTA
Found at i:329518 original size:30 final size:30
Alignment explanation
Indices: 329467--329570 Score: 101
Period size: 30 Copynumber: 3.5 Consensus size: 30
329457 TATAACATCT
* *
329467 AAATAAATTATTAA-CTTTAATTTACATTA
1 AAATAAATTTTTAATTTTTAATTTACATTA
329496 AAATAAATTTTTAATTTTTAATTT-CTATTA
1 AAATAAATTTTTAATTTTTAATTTAC-ATTA
*
329526 AAATAAGA-TTTTAATCTTTAAATTTTAC-TT-
1 AAATAA-ATTTTTAAT-TTTTAA-TTTACATTA
*
329556 AAATAAGTTTTTAAT
1 AAATAAATTTTTAAT
329571 AGAAATCAAT
Statistics
Matches: 64, Mismatches: 4, Indels: 13
0.79 0.05 0.16
Matches are distributed among these distances:
29 14 0.22
30 38 0.59
31 8 0.12
32 3 0.05
33 1 0.02
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (30 bp):
AAATAAATTTTTAATTTTTAATTTACATTA
Found at i:331435 original size:17 final size:17
Alignment explanation
Indices: 331406--331468 Score: 51
Period size: 17 Copynumber: 3.8 Consensus size: 17
331396 TGTCAATTAC
*
331406 TTTA-TTATCAAAAATT
1 TTTATTTATTAAAAATT
331422 TTTATTTATT-AAAATT
1 TTTATTTATTAAAAATT
* * *
331438 TCTT-TCATATTAAAGATA
1 T-TTAT-TTATTAAAAATT
331456 TTTATTTATTAAA
1 TTTATTTATTAAA
331469 TAAATTTAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
16 12 0.32
17 19 0.51
18 6 0.16
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.54
Consensus pattern (17 bp):
TTTATTTATTAAAAATT
Found at i:331900 original size:29 final size:31
Alignment explanation
Indices: 331865--331932 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 31
331855 ACATATATTA
*
331865 TTTTATTAATT-TTATTTATAAA-AATT-TAT
1 TTTTATTAATTAATATTTA-AAATAATTATAT
331894 TTTTATT-ATTAATATTTAAAATAATTATAT
1 TTTTATTAATTAATATTTAAAATAATTATAT
*
331924 TTTAATTAA
1 TTTTATTAA
331933 AATTAAATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
28 6 0.18
29 17 0.52
30 9 0.27
31 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (31 bp):
TTTTATTAATTAATATTTAAAATAATTATAT
Found at i:334553 original size:1 final size:1
Alignment explanation
Indices: 334549--334574 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
334539 TATGTTTTTA
334549 GGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGG
334575 TTTGGAAGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:335035 original size:13 final size:13
Alignment explanation
Indices: 334989--335115 Score: 62
Period size: 13 Copynumber: 10.3 Consensus size: 13
334979 TTTTAGATAT
334989 TATATAAAT-TCAA
1 TATATAAATAT-AA
* *
335002 TAAAAAAATATAA
1 TATATAAATATAA
335015 TATA-AAATATAA
1 TATATAAATATAA
335027 TATATAAATAT--
1 TATATAAATATAA
*
335038 T-T-TAAATATGA
1 TATATAAATATAA
*
335049 CATA-AATATATGAA
1 TATATAA-ATAT-AA
*
335063 TATA-AAATTTTTAA
1 TATATAAA--TATAA
*
335077 -ATATAATTATAA
1 TATATAAATATAA
335089 TATAT-AA-A-AA
1 TATATAAATATAA
*
335099 TATATAAAAATAA
1 TATATAAATATAA
335112 TATA
1 TATA
335116 AATTATTAAA
Statistics
Matches: 89, Mismatches: 10, Indels: 30
0.69 0.08 0.23
Matches are distributed among these distances:
9 7 0.08
10 8 0.09
11 4 0.04
12 21 0.24
13 36 0.40
14 11 0.12
15 2 0.02
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (13 bp):
TATATAAATATAA
Found at i:335089 original size:6 final size:7
Alignment explanation
Indices: 335009--335095 Score: 51
Period size: 7 Copynumber: 12.9 Consensus size: 7
334999 CAATAAAAAA
335009 ATATAAT
1 ATATAAT
335016 ATA-AA-
1 ATATAAT
335021 ATATAAT
1 ATATAAT
335028 ATATAAAT
1 ATAT-AAT
*
335036 ATTTTAA-
1 A-TATAAT
* *
335043 ATATGAC
1 ATATAAT
335050 ATA-AAT
1 ATATAAT
335056 ATATGAAT
1 ATAT-AAT
*
335064 ATAAAAT
1 ATATAAT
* *
335071 TTTTAA-
1 ATATAAT
335077 ATATAAT
1 ATATAAT
335084 -TATAAT
1 ATATAAT
335090 ATATAA
1 ATATAA
335096 AAATATATAA
Statistics
Matches: 60, Mismatches: 11, Indels: 18
0.67 0.12 0.20
Matches are distributed among these distances:
5 3 0.05
6 21 0.35
7 22 0.37
8 12 0.20
9 2 0.03
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.40
Consensus pattern (7 bp):
ATATAAT
Found at i:335091 original size:34 final size:34
Alignment explanation
Indices: 335007--335095 Score: 112
Period size: 34 Copynumber: 2.6 Consensus size: 34
334997 TTCAATAAAA
*
335007 AAATATAATATAAAATATAATATATAAATATTTT
1 AAATATAATATAATATATAATATATAAATATTTT
335041 AAATATGACATA-AATATATGAATATA-AAAT-TTTT
1 AAATAT-A-ATATAATATAT-AATATATAAATATTTT
335075 AAATATAATTATAATATATAA
1 AAATATAA-TATAATATATAA
335096 AAATATATAA
Statistics
Matches: 49, Mismatches: 1, Indels: 11
0.80 0.02 0.18
Matches are distributed among these distances:
32 1 0.02
33 5 0.10
34 23 0.47
35 11 0.22
36 9 0.18
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.39
Consensus pattern (34 bp):
AAATATAATATAATATATAATATATAAATATTTT
Found at i:335118 original size:9 final size:10
Alignment explanation
Indices: 335087--335117 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
335077 ATATAATTAT
335087 AATATATAAA
1 AATATATAAA
335097 AATATATAAA
1 AATATATAAA
335107 AATAATATAAA
1 AAT-ATATAAA
335118 TTATTAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 13 0.65
11 7 0.35
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
AATATATAAA
Found at i:335611 original size:27 final size:27
Alignment explanation
Indices: 335563--335615 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
335553 AAAAAATAAA
* **
335563 TTTTAAATAAAGAAAATTTTTAGTATAT
1 TTTTAAATAAACAAAAAATTTA-TATAT
335591 TTTTAAA-AAACAAAAAATTTATATA
1 TTTTAAATAAACAAAAAATTTATATA
335616 AAATCTTCTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 4 0.18
27 11 0.50
28 7 0.32
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.42
Consensus pattern (27 bp):
TTTTAAATAAACAAAAAATTTATATAT
Found at i:336268 original size:19 final size:19
Alignment explanation
Indices: 336247--336284 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
336237 ATTAAAATAA
*
336247 TTTTTGATTTTAATTTTAAT
1 TTTTTAATTTT-ATTTTAAT
336267 TTTTTAATTTTATTTTAA
1 TTTTTAATTTTATTTTAA
336285 AATAATGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (19 bp):
TTTTTAATTTTATTTTAAT
Found at i:337299 original size:19 final size:20
Alignment explanation
Indices: 337273--337319 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
337263 TTGAAATGAA
*
337273 AAAAAAAAGAAAGAAAAAAGG
1 AAAAAAAAG-AGGAAAAAAGG
*
337294 AAAAAAAAGAGGAAAAAGGG
1 AAAAAAAAGAGGAAAAAAGG
337314 AAAAAA
1 AAAAAA
337320 TTATGTGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 15 0.62
21 9 0.38
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (20 bp):
AAAAAAAAGAGGAAAAAAGG
Found at i:337309 original size:11 final size:11
Alignment explanation
Indices: 337270--337310 Score: 55
Period size: 12 Copynumber: 3.5 Consensus size: 11
337260 GATTTGAAAT
*
337270 GAAAAAAAAAA
1 GAAAAAAAAAG
337281 GAAAGAAAAAAG
1 GAAA-AAAAAAG
337293 GAAAAAAAAGAG
1 GAAAAAAAA-AG
337305 GAAAAA
1 GAAAAA
337311 GGGAAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 9 0.33
12 18 0.67
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (11 bp):
GAAAAAAAAAG
Found at i:337374 original size:19 final size:19
Alignment explanation
Indices: 337336--337374 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
337326 GTTTATATTT
*
337336 ATATTATTTTTTATTTTAA
1 ATATTATTTTTTATTATAA
337355 ATATTATATTTTTA-TATAA
1 ATATTAT-TTTTTATTATAA
337374 A
1 A
337375 ATTTTTACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
ATATTATTTTTTATTATAA
Found at i:337376 original size:20 final size:19
Alignment explanation
Indices: 337336--337376 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
337326 GTTTATATTT
* *
337336 ATATTATTTTTTATTTTAA
1 ATATTATTTTTTATATAAA
337355 ATATTATATTTTTATATAAA
1 ATATTAT-TTTTTATATAAA
337375 AT
1 AT
337377 TTTTACATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
ATATTATTTTTTATATAAA
Found at i:337761 original size:22 final size:23
Alignment explanation
Indices: 337733--337779 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
337723 AGAAAGATGG
*
337733 AAAGAAAAAAGAAAA-GAAAGAA
1 AAAGAAAAAAGAAAATAAAAGAA
*
337755 AAAGAAAGAAGAAAATAAAAGAA
1 AAAGAAAAAAGAAAATAAAAGAA
337778 AA
1 AA
337780 TTTAATATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (23 bp):
AAAGAAAAAAGAAAATAAAAGAA
Found at i:338625 original size:14 final size:12
Alignment explanation
Indices: 338584--338630 Score: 60
Period size: 12 Copynumber: 3.9 Consensus size: 12
338574 CATGCCATAT
338584 TTATTTTTTATA
1 TTATTTTTTATA
*
338596 TTATGTTTTA-A
1 TTATTTTTTATA
338607 TTATTTTTTATA
1 TTATTTTTTATA
*
338619 TCATATTTTTAT
1 TTAT-TTTTTAT
338631 TTTCGTATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.33
12 13 0.43
13 7 0.23
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (12 bp):
TTATTTTTTATA
Found at i:338627 original size:23 final size:23
Alignment explanation
Indices: 338584--338627 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
338574 CATGCCATAT
* *
338584 TTATTTTTTATATTATGTTTTAA
1 TTATTTTTTATATCATATTTTAA
338607 TTATTTTTTATATCATATTTT
1 TTATTTTTTATATCATATTTT
338628 TATTTTCGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.70
Consensus pattern (23 bp):
TTATTTTTTATATCATATTTTAA
Found at i:338632 original size:20 final size:21
Alignment explanation
Indices: 338583--338633 Score: 59
Period size: 23 Copynumber: 2.4 Consensus size: 21
338573 TCATGCCATA
* *
338583 TTTATTTTTTATATTATGTTT
1 TTTATTTTTTATATCATGATT
338604 TAATTATTTTTTATATCAT-ATT
1 T--TTATTTTTTATATCATGATT
338626 TTTATTTT
1 TTTATTTT
338634 CGTATATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 7 0.27
21 1 0.04
22 3 0.12
23 15 0.58
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.73
Consensus pattern (21 bp):
TTTATTTTTTATATCATGATT
Found at i:338970 original size:17 final size:17
Alignment explanation
Indices: 338945--339000 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
338935 TTTAAATATA
*
338945 AAAAATTATTATTTAAT
1 AAAATTTATTATTTAAT
338962 AAAATTTATT-TTATAAT
1 AAAATTTATTATT-TAAT
*
338979 TAAATTT-TTA-TTAAT
1 AAAATTTATTATTTAAT
338994 AATAATT
1 AA-AATT
339001 AAAATTTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
15 5 0.15
16 9 0.27
17 19 0.58
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
AAAATTTATTATTTAAT
Found at i:339007 original size:696 final size:679
Alignment explanation
Indices: 337645--338913 Score: 1641
Period size: 696 Copynumber: 1.9 Consensus size: 679
337635 CTATACATAT
* *
337645 ATATAAAATTAACTACATAAATAAATCTATATTGATACATGTTCTGTTTTCGAGTTTTTTTCAGC
1 ATATAAAATTAACTACATAAATAAATCTATATTAACACATGTTCTGTTTTCGAGTTTTTTTCAGC
* ** * *
337710 AATTATAGGAGAGAGAAAGATGGAAAGAAAAAAGAAAAGAAAGAAAAAGAAAGAAGAAAATAAAA
66 AATCATAGGAGAGAGAAAGATACAAAGAAAAAAGAAAAAAAAAAAAAAGAAAGAAGAAAATAAAA
* *
337775 GAAAATTTAATATGTTTATATTTATACCCGTATTATTTTTTTATTGTTTAAAATATTATAAATTT
131 AAAAATTTAATATGTTTATATTTATACCCGTATTATTTTTTTATTATTTAAAATATTATAAATTT
* *
337840 ATATAATATTGTACACATATATATTTATATGTTTTATATTCGTATCATATTCATTTTATATTATG
196 ATATAATATTGTACACATATATATTTATATGTTTTATATTCATACCATATTCATTTTATATTATG
* * *
337905 TTTTAATTATTTTTTATTTAATGTTTTTATTTTTATATAGTTAAAATAATATAAATTTATATAAA
261 TTTTAATTATTTTTTATATAATATTTTTATTTTCATATAGTTAAAATAATATAAATTTATATAAA
*
337970 TTTTTACATATTAATTATTTATATATGTATATTTTGGCATATTAATATAATTAAATAATATATTT
326 TTTTTACATATTAATTATTTATATATGTATA-TTTGGCACATTAATATAATTAAATAATATATTT
* * * *
338035 AAAATGATAGATTCTTAAGTTGATGTACCATCTATTTAAAATTCATACCCTATTCTAAATGTAAA
390 AAAATGATAGAATCTCAAGTTAATGTACCATCTAATTAAAATTCATACCCTATTCTAAATGTAAA
*
338100 TTTAAAGAAATAAATAAATATTATTTAATAAAATTTAATTTTTATTAAAAATAATGAAAAATATA
455 TTT--A-AAATAAATAAATATTATTTAATAAAATTTAACTTTTATTAAAAATAATGAAAAATAT-
* * * * * * **
338165 AAAAATTAAAAATGTCATTATTTATTTTATTTTTAAATGATGTGTTTAAAATAATGAATTTTTGT
516 ----ATTAAAAATATCATTAATTATTTTATTTTTAAATAATATATTTAAAATAATAAATTTTTAC
* * ***
338230 GTTAACTCACAAACCAATTAAATTTTATTTTTAATTTTTTTAAATACAAAATTTAAATACATAAT
577 ATTAAATCACAAACCAATTAAATTTTATTAAAAATTTTTTTAAATACAAAATTTAAATACATAAT
*
338295 TATTATTTAAAAAATTTCAAATTAAATTTTTATTAATA
642 TATTATTTAAAAAATTTAAAATTAAATTTTTATTAATA
*
338333 ATAT-AAATTAACTACATAAATAAATCTAATGTTAACACATG-TCTTGCTTTT-GAGTTTTTTTC
1 ATATAAAATTAACTACATAAATAAATCT-ATATTAACACATGTTC-TG-TTTTCGAGTTTTTTTC
* * * *
338395 GGCAGTCATGGGAGAGAGAAAGATACAAAGAAAAAAATAAAAAAATAAAAGAAAGAAAAAGAGAG
63 AGCAATCATAGGAGAGAGAAAGATACAAAG-AAAAAAGAAAAAAA-AAAA-AAAG--AAAGA-AG
** * *
338460 AGAAA-AATAAAAAAATTTAATATGTTTATATTTATACTTGTGTTA-TTTTTTATTATTTAAAGT
122 A-AAATAA-AAAAAAATTTAATATGTTTATATTTATACCCGTATTATTTTTTTATTATTTAAAAT
* * *
338523 A-TATAAATTTATATAATATTTTACACATATATATTTATATGTTCTTATATTCATGCCATATTTA
185 ATTATAAATTTATATAATATTGTACACATATATATTTATATGTT-TTATATTCATACCATATTCA
* * * * *
338587 TTTTTTATATTATGTTTTAATTATTTTTTATATCATATTTTTATTTTCGTATATTTAAAGTAGTA
249 --TTTTATATTATGTTTTAATTATTTTTTATATAATATTTTTATTTTCATATAGTTAAAATAATA
* * *
338652 TAAATTTATATAAATTTTTACATATTAATTATTTATTTATGTATA-TTGAG-ACATTAGTGTAAT
312 TAAATTTATATAAATTTTTACATATTAATTATTTATATATGTATATTTG-GCACATTAATATAAT
* ** * * *
338715 TAAATAATATATTTAAAATGATA-AATCTGCATGTTAATGTATGATC-AATTAAAATTTATATCT
376 TAAATAATATATTTAAAATGATAGAATCT-CAAGTTAATGTACCATCTAATTAAAATTCATACCC
*
338778 TATTCTAAATGTAGATTT-AAATAAATAAATATTATTTAATAAAATTT-ACTTTTATTAAAAATA
440 TATTCTAAATGTAAATTTAAAATAAATAAATATTATTTAATAAAATTTAACTTTTATTAAAAATA
* *
338841 AT-TAAAAT-T-TTAAAAATATTATTAATTATTTTATTTTTAAATAATATATTTAAAATAATAAA
505 ATGAAAAATATATTAAAAATATCATTAATTATTTTATTTTTAAATAATATATTTAAAATAATAAA
338903 TTTTTACATTA
570 TTTTTACATTA
338914 TAATTAAAAT
Statistics
Matches: 507, Mismatches: 58, Indels: 40
0.84 0.10 0.07
Matches are distributed among these distances:
680 54 0.11
686 1 0.00
687 30 0.06
688 68 0.13
689 45 0.09
690 3 0.01
691 4 0.01
693 80 0.16
694 86 0.17
695 37 0.07
696 99 0.20
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.44
Consensus pattern (679 bp):
ATATAAAATTAACTACATAAATAAATCTATATTAACACATGTTCTGTTTTCGAGTTTTTTTCAGC
AATCATAGGAGAGAGAAAGATACAAAGAAAAAAGAAAAAAAAAAAAAAGAAAGAAGAAAATAAAA
AAAAATTTAATATGTTTATATTTATACCCGTATTATTTTTTTATTATTTAAAATATTATAAATTT
ATATAATATTGTACACATATATATTTATATGTTTTATATTCATACCATATTCATTTTATATTATG
TTTTAATTATTTTTTATATAATATTTTTATTTTCATATAGTTAAAATAATATAAATTTATATAAA
TTTTTACATATTAATTATTTATATATGTATATTTGGCACATTAATATAATTAAATAATATATTTA
AAATGATAGAATCTCAAGTTAATGTACCATCTAATTAAAATTCATACCCTATTCTAAATGTAAAT
TTAAAATAAATAAATATTATTTAATAAAATTTAACTTTTATTAAAAATAATGAAAAATATATTAA
AAATATCATTAATTATTTTATTTTTAAATAATATATTTAAAATAATAAATTTTTACATTAAATCA
CAAACCAATTAAATTTTATTAAAAATTTTTTTAAATACAAAATTTAAATACATAATTATTATTTA
AAAAATTTAAAATTAAATTTTTATTAATA
Found at i:339171 original size:4 final size:4
Alignment explanation
Indices: 339164--339201 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
339154 CGCAGGTGAA
339164 AAAG AAAG AAAG AAAG AACA- AAAG AAAG AAAG -AAG AAA
1 AAAG AAAG AAAG AAAG AA-AG AAAG AAAG AAAG AAAG AAA
339202 ATTTTTTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
3 4 0.13
4 26 0.84
5 1 0.03
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:339189 original size:16 final size:16
Alignment explanation
Indices: 339168--339202 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
339158 GGTGAAAAAG
339168 AAAGAAAGAAAGAACA
1 AAAGAAAGAAAGAACA
*
339184 AAAGAAAGAAAGAAGA
1 AAAGAAAGAAAGAACA
339200 AAA
1 AAA
339203 TTTTTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.77, C:0.03, G:0.20, T:0.00
Consensus pattern (16 bp):
AAAGAAAGAAAGAACA
Found at i:339263 original size:11 final size:11
Alignment explanation
Indices: 339247--339274 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
339237 TTTAAAATAT
339247 TATATTTTTTA
1 TATATTTTTTA
339258 TATATTTTTTA
1 TATATTTTTTA
339269 TATATT
1 TATATT
339275 AATAATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TATATTTTTTA
Found at i:339266 original size:33 final size:35
Alignment explanation
Indices: 339215--339321 Score: 86
Period size: 33 Copynumber: 3.1 Consensus size: 35
339205 TTTTTATATG
*
339215 TTTATATTTATA-AGTTTTTGTAT-TTAA-AATATTA
1 TTTAT-TTTATATAGTTTTTATATATTAATAAT-TTA
*
339249 TATT-TTTTATATATTTTTTATATATTAATAATTTA
1 T-TTATTTTATATAGTTTTTATATATTAATAATTTA
*
339284 TTTATTTTAT-TA-TATTTATATA--AATATATGTTA
1 TTTATTTTATATAGTTTTTATATATTAATA-AT-TTA
339317 TTTAT
1 TTTAT
339322 ATATGGGAGA
Statistics
Matches: 63, Mismatches: 3, Indels: 15
0.78 0.04 0.19
Matches are distributed among these distances:
31 4 0.06
32 2 0.03
33 23 0.37
34 15 0.24
35 16 0.25
36 3 0.05
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.63
Consensus pattern (35 bp):
TTTATTTTATATAGTTTTTATATATTAATAATTTA
Found at i:339294 original size:9 final size:10
Alignment explanation
Indices: 339244--339300 Score: 50
Period size: 9 Copynumber: 6.0 Consensus size: 10
339234 GTATTTAAAA
339244 TATTATATTT
1 TATTATATTT
339254 T-TTATATATT
1 TATTATAT-TT
* *
339264 TTTTATATAT
1 TATTATATTT
*
339274 TA--ATAATT
1 TATTATATTT
339282 TATT-TATTT
1 TATTATATTT
339291 TATTATATTT
1 TATTATATTT
339301 ATATAAATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
8 6 0.16
9 14 0.38
10 11 0.30
11 6 0.16
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TATTATATTT
Found at i:342097 original size:23 final size:23
Alignment explanation
Indices: 342071--342150 Score: 160
Period size: 23 Copynumber: 3.5 Consensus size: 23
342061 TGGACATATT
342071 AAAAATGCATGAAACATAATAAA
1 AAAAATGCATGAAACATAATAAA
342094 AAAAATGCATGAAACATAATAAA
1 AAAAATGCATGAAACATAATAAA
342117 AAAAATGCATGAAACATAATAAA
1 AAAAATGCATGAAACATAATAAA
342140 AAAAATGCATG
1 AAAAATGCATG
342151 GTCAAAGGCT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 57 1.00
ACGTcount: A:0.64, C:0.09, G:0.10, T:0.17
Consensus pattern (23 bp):
AAAAATGCATGAAACATAATAAA
Found at i:343090 original size:20 final size:19
Alignment explanation
Indices: 343065--343135 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
343055 AGACATAATG
343065 TATCGATACATTGAAGAATA
1 TATCGATACATTGAA-AATA
* * *
343085 TATCGATACATTCATACATG
1 TATCGATACATTGA-AAATA
*
343105 TATCGATATATTGAAAAATA
1 TATCGATACATTG-AAAATA
*
343125 TATAGATACAT
1 TATCGATACAT
343136 CTGGGTAAAA
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
20 38 0.95
21 2 0.05
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.34
Consensus pattern (19 bp):
TATCGATACATTGAAAATA
Found at i:343118 original size:40 final size:39
Alignment explanation
Indices: 343058--343135 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
343048 GGTAAAAAGA
* *
343058 CATAATGTATCGATACATTGAAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATAGATACATT
*
343097 CATACATGTATCGATATATTGAAAAATATATAGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATAGATACAT
343136 CTGGGTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.33
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATAGATACATT
Found at i:343397 original size:19 final size:19
Alignment explanation
Indices: 343373--343434 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
343363 ATTTAAAATA
*
343373 TTATATATTTATATATTTT
1 TTATATATTAATATATTTT
343392 TTATATATTAATA-ATTTAT
1 TTATATATTAATATATTT-T
*
343411 TT-TAT-TTCATATATATTT
1 TTATATATTAATATAT-TTT
343429 TTATAT
1 TTATAT
343435 GTACTGTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
17 5 0.14
18 12 0.32
19 20 0.54
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (19 bp):
TTATATATTAATATATTTT
Found at i:348428 original size:2 final size:2
Alignment explanation
Indices: 348421--348452 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
348411 GAATCGAGAA
348421 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
348453 CATTGTTGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:354498 original size:19 final size:19
Alignment explanation
Indices: 354476--354515 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
354466 GAGAATATTC
354476 AAAAAAAATAAGA-AAAGAA
1 AAAAAAAATAA-ATAAAGAA
*
354495 AAAAATAATAAATAAAGAA
1 AAAAAAAATAAATAAAGAA
354514 AA
1 AA
354516 GATATGAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 1 0.05
19 18 0.95
ACGTcount: A:0.82, C:0.00, G:0.07, T:0.10
Consensus pattern (19 bp):
AAAAAAAATAAATAAAGAA
Found at i:355603 original size:18 final size:18
Alignment explanation
Indices: 355582--355616 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
355572 CTTTTATTAC
*
355582 AAAAAAATAATTTAAAAG
1 AAAAAAACAATTTAAAAG
*
355600 AAAATAACAATTTAAAA
1 AAAAAAACAATTTAAAA
355617 AATTTTAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.23
Consensus pattern (18 bp):
AAAAAAACAATTTAAAAG
Found at i:355867 original size:16 final size:16
Alignment explanation
Indices: 355848--355905 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
355838 TTATATTTAA
355848 TTTTAATTTAAATAAT
1 TTTTAATTTAAATAAT
*
355864 TTTTGATTTAAATAA-
1 TTTTAATTTAAATAAT
* *
355879 TTTTATATTCAAATTAT
1 TTTTA-ATTTAAATAAT
*
355896 TTTAAATTTA
1 TTTTAATTTA
355906 TTTTATAATT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 4 0.12
16 26 0.76
17 4 0.12
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (16 bp):
TTTTAATTTAAATAAT
Found at i:355905 original size:32 final size:31
Alignment explanation
Indices: 355845--355905 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
355835 AAATTATATT
* **
355845 TAATTTTAATTTAAATAATTTTTGATTTAAA
1 TAATTTTAATTCAAATAATTTTAAATTTAAA
*
355876 TAATTTTATATTCAAATTATTTTAAATTTA
1 TAATTTTA-ATTCAAATAATTTTAAATTTA
355906 TTTTATAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 8 0.32
32 17 0.68
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (31 bp):
TAATTTTAATTCAAATAATTTTAAATTTAAA
Found at i:355911 original size:27 final size:26
Alignment explanation
Indices: 355870--355920 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
355860 TAATTTTTGA
355870 TTTAAATAATTTTAT-ATTCAAATTAT
1 TTTAAATAATTTTATAATT-AAATTAT
*
355896 TTTAAATTTATTTTATAATTAAATT
1 TTTAAA-TAATTTTATAATTAAATT
355921 TAAATAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 6 0.27
27 13 0.59
28 3 0.14
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (26 bp):
TTTAAATAATTTTATAATTAAATTAT
Found at i:356731 original size:3 final size:3
Alignment explanation
Indices: 356679--356711 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
356669 GAAGTTACTG
356679 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
356712 TTATTATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:356747 original size:2 final size:2
Alignment explanation
Indices: 356736--356789 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
356726 AATAATAAGA
356736 AG AG -G AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
356777 AG AG AG AG AG AG A
1 AG AG AG AG AG AG A
356790 ATGGTTTCAT
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:357039 original size:19 final size:20
Alignment explanation
Indices: 357015--357053 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
357005 TTCAATTATG
357015 TTATTTAAAATTTT-TATTT
1 TTATTTAAAATTTTATATTT
357034 TTATTTAAAATTTTATATTT
1 TTATTTAAAATTTTATATTT
357054 AATATATACT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTTAAAATTTTATATTT
Found at i:357047 original size:18 final size:19
Alignment explanation
Indices: 357015--357054 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
357005 TTCAATTATG
*
357015 TTATTTAAAATTTTTATTT
1 TTATTTAAAATTTTTATAT
357034 TTATTTAAAA-TTTTATAT
1 TTATTTAAAATTTTTATAT
357052 TTA
1 TTA
357055 ATATATACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTATTTAAAATTTTTATAT
Found at i:357068 original size:17 final size:17
Alignment explanation
Indices: 357046--357089 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
357036 ATTTAAAATT
*
357046 TTATATTTAATATATAC
1 TTATATTTAATACATAC
*
357063 TTATATTTAATACATAT
1 TTATATTTAATACATAC
*
357080 TTAAATTTAA
1 TTATATTTAA
357090 ATAAAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (17 bp):
TTATATTTAATACATAC
Found at i:357130 original size:19 final size:20
Alignment explanation
Indices: 357097--357144 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
357087 TAAATAAAAA
*
357097 ATAAAAAT-TTTTAAA-TTT
1 ATAAAAATATTATAAACTTT
357115 ATAAAAATATTATAAACTTT
1 ATAAAAATATTATAAACTTT
*
357135 -TAAATATATT
1 ATAAAAATATT
357145 TATTTTAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 8 0.31
19 15 0.58
20 3 0.12
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (20 bp):
ATAAAAATATTATAAACTTT
Found at i:357135 original size:27 final size:26
Alignment explanation
Indices: 357079--357139 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
357069 TTAATACATA
*
357079 TTTAAATTTAAATAAAAAATAAAAATT
1 TTTAAATTT-AATAAAAAATAAAAACT
*
357106 TTTAAATTT-ATAAAAATATTATAAACT
1 TTTAAATTTAATAAAAA-A-TAAAAACT
357133 TTTAAAT
1 TTTAAAT
357140 ATATTTATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 7 0.23
26 1 0.03
27 22 0.73
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (26 bp):
TTTAAATTTAATAAAAAATAAAAACT
Found at i:357158 original size:17 final size:17
Alignment explanation
Indices: 357133--357180 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
357123 ATTATAAACT
357133 TTTAA-ATATATTTAT-
1 TTTAATATATATTTATA
357148 TTTAAATATATATTTATA
1 TTT-AATATATATTTATA
*
357166 TTTAATATTTATTTA
1 TTTAATATATATTTA
357181 AATTCAGATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 3 0.10
16 2 0.07
17 21 0.72
18 3 0.10
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTAATATATATTTATA
Found at i:357308 original size:2 final size:2
Alignment explanation
Indices: 357301--357348 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
357291 CTCGAAGAGA
* * * *
357301 AT AT AT AT AT AG AT AG GT AT AC 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
357343 AT AT AT
1 AT AT AT
357349 CAGTCTTTTA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (2 bp):
AT
Found at i:359736 original size:106 final size:105
Alignment explanation
Indices: 359552--359762 Score: 395
Period size: 106 Copynumber: 2.0 Consensus size: 105
359542 ACTTTAGTCA
* *
359552 TGGCATTGTGGCCTCAACCTATTCATCTTCACCTAAATTCAGAAAGTGGTCTTCGGGTAGTAAAA
1 TGGCATTATGGCCTCAACCTATTCATCTTCACCTAAATTCAGAAAGTGGCCTTCGGGTAGTAAAA
359617 GTCAATACATATAGCCATGTTATTGTAGCTTCCATCATGT
66 GTCAATACATATAGCCATGTTATTGTAGCTTCCATCATGT
359657 TGGCATTATGGCCTCAACCTATTCATCTTTCACCTAAATTCAGAAAGTGGCCTTCGGGTAGTAAA
1 TGGCATTATGGCCTCAACCTATTCATC-TTCACCTAAATTCAGAAAGTGGCCTTCGGGTAGTAAA
359722 AGTCAATACATATAGCCATGTTATTGTAGCTTCCATCATGT
65 AGTCAATACATATAGCCATGTTATTGTAGCTTCCATCATGT
359763 CATTCAGGAA
Statistics
Matches: 103, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
105 26 0.25
106 77 0.75
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (105 bp):
TGGCATTATGGCCTCAACCTATTCATCTTCACCTAAATTCAGAAAGTGGCCTTCGGGTAGTAAAA
GTCAATACATATAGCCATGTTATTGTAGCTTCCATCATGT
Found at i:362696 original size:28 final size:27
Alignment explanation
Indices: 362643--362711 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 27
362633 TGATTTAAAT
* **
362643 AAAATTTAATATTTATTTTTATATTATA
1 AAAATTTAAT-TTAATTTAAATATTATA
362671 AAAATTTAATTTAATTTAAATAATTATA
1 AAAATTTAATTTAATTTAAAT-ATTATA
**
362699 AATTTTTAATTTA
1 AAAATTTAATTTA
362712 TAAATTAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
27 8 0.23
28 27 0.77
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
AAAATTTAATTTAATTTAAATATTATA
Found at i:362906 original size:16 final size:17
Alignment explanation
Indices: 362877--362917 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
362867 TTTTTTAAAT
*
362877 TAAATTAATTTTAAA-AA
1 TAAATT-ATATTAAATAA
362894 TAAATTATATTAAATAA
1 TAAATTATATTAAATAA
362911 T-AATTAT
1 TAAATTAT
362918 TTATTTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATTATATTAAATAA
Found at i:363660 original size:32 final size:33
Alignment explanation
Indices: 363631--363691 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 33
363621 TGATTATTTT
* *
363631 TGTGTAATTA-GTTGATAGTAATT-GTTTATTA
1 TGTGGAATTAGGTTGAGAGTAATTAGTTTATTA
*
363662 TGTGGAATTAGGTTTAGAGTAATTAGTTTA
1 TGTGGAATTAGGTTGAGAGTAATTAGTTTA
363692 GGGCTAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 9 0.36
32 11 0.44
33 5 0.20
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.48
Consensus pattern (33 bp):
TGTGGAATTAGGTTGAGAGTAATTAGTTTATTA
Found at i:363687 original size:15 final size:15
Alignment explanation
Indices: 363667--363706 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
363657 TATTATGTGG
363667 AATTAGGTTTAGAG-T
1 AATTA-GTTTAGAGCT
*
363682 AATTAGTTTAGGGCT
1 AATTAGTTTAGAGCT
363697 AATTAGTTTA
1 AATTAGTTTA
363707 AAGCCTATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 7 0.30
15 16 0.70
ACGTcount: A:0.33, C:0.03, G:0.23, T:0.42
Consensus pattern (15 bp):
AATTAGTTTAGAGCT
Found at i:369262 original size:75 final size:75
Alignment explanation
Indices: 369083--369397 Score: 470
Period size: 75 Copynumber: 4.2 Consensus size: 75
369073 TGAAATATGT
*
369083 AGATTATCTCGGATTAGTTGTTGATAGTAGTAATGTGAAATATGCAGAAACATTT-TTGATTGTA
1 AGATTATCTCAGATTAGTTGTTGATAGTAGTAATGTGAAATATGCAGAAACATTTGTTGATTGTA
*
369147 GTTATCGTAC
66 GTTATCGTGC
* * * *
369157 AGATTATCTCGGATTAGTTGTTGATAGTAGTACTGTGAAATATGCAGAAACATTTATTAATTGTA
1 AGATTATCTCAGATTAGTTGTTGATAGTAGTAATGTGAAATATGCAGAAACATTTGTTGATTGTA
*
369222 GTTATCATGC
66 GTTATCGTGC
* * * *
369232 ATATTATCTCATATTAGTTATTGATAGTAGTAATGTGAAAAATGCAGAAACATTTGTTGATTGTA
1 AGATTATCTCAGATTAGTTGTTGATAGTAGTAATGTGAAATATGCAGAAACATTTGTTGATTGTA
369297 GTTATCGTGC
66 GTTATCGTGC
* * * *
369307 AGATTATCTCAGATTAGTTGTTGATAATAATACTGTGAAATATGCAGAAATATTTGTTGATTGTA
1 AGATTATCTCAGATTAGTTGTTGATAGTAGTAATGTGAAATATGCAGAAACATTTGTTGATTGTA
*
369372 ATTATCGTGC
66 GTTATCGTGC
*
369382 AGATGATCTCAGATTA
1 AGATTATCTCAGATTA
369398 TTATTTCATC
Statistics
Matches: 217, Mismatches: 23, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
74 54 0.25
75 163 0.75
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.39
Consensus pattern (75 bp):
AGATTATCTCAGATTAGTTGTTGATAGTAGTAATGTGAAATATGCAGAAACATTTGTTGATTGTA
GTTATCGTGC
Found at i:369328 original size:39 final size:38
Alignment explanation
Indices: 369138--369331 Score: 96
Period size: 39 Copynumber: 5.1 Consensus size: 38
369128 AGAAACATTT
* *
369138 TTGATTGTAGTTATCGTACAGATTATCTCGGATTAGTTG
1 TTGATTGTAGTTATCGTGCA-ATTATCTCAGATTAGTTG
* * * ** * *
369177 TTGATAGTAG-TA-CTGTG-AAATAT-GCAGAAACATTTA
1 TTGATTGTAGTTATC-GTGCAATTATCTCAG-ATTAGTTG
* * * *
369213 TTAATTGTAGTTATCATGCATATTATCTCATATTAGTTA
1 TTGATTGTAGTTATCGTGCA-ATTATCTCAGATTAGTTG
* * ** * ** *
369252 TTGATAGTAGTAAT-GTG-AAAAAT-GCAGAAACATTTG
1 TTGATTGTAGTTATCGTGCAATTATCTCAG-ATTAGTTG
369288 TTGATTGTAGTTATCGTGCAGATTATCTCAGATTAGTTG
1 TTGATTGTAGTTATCGTGCA-ATTATCTCAGATTAGTTG
369327 TTGAT
1 TTGAT
369332 AATAATACTG
Statistics
Matches: 105, Mismatches: 38, Indels: 24
0.63 0.23 0.14
Matches are distributed among these distances:
35 4 0.04
36 35 0.33
37 10 0.10
38 9 0.09
39 42 0.40
40 5 0.05
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.41
Consensus pattern (38 bp):
TTGATTGTAGTTATCGTGCAATTATCTCAGATTAGTTG
Found at i:370277 original size:2 final size:2
Alignment explanation
Indices: 370272--370321 Score: 59
Period size: 2 Copynumber: 26.0 Consensus size: 2
370262 AAAAGCATTC
* *
370272 AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AA AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
370313 -T AA AT AT AT
1 AT AT AT AT AT
370322 GATAGTATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:370844 original size:38 final size:36
Alignment explanation
Indices: 370760--370845 Score: 84
Period size: 39 Copynumber: 2.3 Consensus size: 36
370750 TCAGTCTCTC
* * *
370760 CATTACTTTTTTAGGTATTAACTTTTTCAAGTTTGT
1 CATTACTTTTTTAGATATTAACTTTTTCAAATTTAT
* *
370796 CA-TAGCCTTTTTTAAGATATTTGACTTTTTTAAATTTAT
1 CATTA--CTTTTTT-AGATA-TTAACTTTTTCAAATTTAT
370835 CATTACTTTTT
1 CATTACTTTTT
370846 CAAGTTTTCT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
35 2 0.05
36 2 0.05
37 7 0.17
38 10 0.25
39 17 0.43
40 2 0.05
ACGTcount: A:0.24, C:0.12, G:0.08, T:0.56
Consensus pattern (36 bp):
CATTACTTTTTTAGATATTAACTTTTTCAAATTTAT
Found at i:370916 original size:20 final size:20
Alignment explanation
Indices: 370893--370930 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
370883 GTTATTCATT
*
370893 TTTTTTTAGGCTCGTTATAA
1 TTTTTTTAAGCTCGTTATAA
*
370913 TTTTTTTAAGCTCTTTAT
1 TTTTTTTAAGCTCGTTAT
370931 TGCCTTTGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.11, G:0.11, T:0.61
Consensus pattern (20 bp):
TTTTTTTAAGCTCGTTATAA
Found at i:371033 original size:21 final size:20
Alignment explanation
Indices: 371008--371053 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
370998 TATCTATTAC
*
371008 CTTTTCAAGCTTGCTATTTGT
1 CTTTTCAAGCTTGCTA-TAGT
* *
371029 CTTTTTAAGTTTGCTATAGT
1 CTTTTCAAGCTTGCTATAGT
371049 CTTTT
1 CTTTT
371054 AAAATTATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.15, C:0.15, G:0.13, T:0.57
Consensus pattern (20 bp):
CTTTTCAAGCTTGCTATAGT
Found at i:371052 original size:20 final size:21
Alignment explanation
Indices: 370984--371053 Score: 65
Period size: 20 Copynumber: 3.4 Consensus size: 21
370974 AGTCTTGCCA
*
370984 TAGTCTTTTTAGGTTAT-CTAT
1 TAGTCTTTTTAAGTT-TGCTAT
* * *
371005 TA-CCTTTTCAAGCTTGCTAT
1 TAGTCTTTTTAAGTTTGCTAT
*
371025 TTGTCTTTTTAAGTTTGCTA-
1 TAGTCTTTTTAAGTTTGCTAT
371045 TAGTCTTTT
1 TAGTCTTTT
371054 AAAATTATTA
Statistics
Matches: 38, Mismatches: 9, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
19 1 0.03
20 21 0.55
21 16 0.42
ACGTcount: A:0.17, C:0.14, G:0.13, T:0.56
Consensus pattern (21 bp):
TAGTCTTTTTAAGTTTGCTAT
Found at i:373401 original size:2 final size:2
Alignment explanation
Indices: 373394--373423 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
373384 TCCATGATAC
*
373394 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
373424 TTAATTTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:375987 original size:2 final size:2
Alignment explanation
Indices: 375970--376020 Score: 68
Period size: 2 Copynumber: 26.0 Consensus size: 2
375960 TTGGTACTAG
* * *
375970 TA TA TC TA TT TA TA TA TA TA TA TA TA TG T- TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
376011 TA TA TA TA TA
1 TA TA TA TA TA
376021 GATTATTATT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (2 bp):
TA
Found at i:379719 original size:2 final size:2
Alignment explanation
Indices: 379712--379739 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
379702 ACCTCTTTAG
379712 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
379740 GTTGTGCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:381442 original size:22 final size:23
Alignment explanation
Indices: 381414--381457 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
381404 CATAAGGGAA
*
381414 AACAAAAA-ATTAAAAAAAAAAC
1 AACAAAAATAATAAAAAAAAAAC
*
381436 AACAAAAATAATAATAAAAAAA
1 AACAAAAATAATAAAAAAAAAA
381458 TGATAGAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.82, C:0.07, G:0.00, T:0.11
Consensus pattern (23 bp):
AACAAAAATAATAAAAAAAAAAC
Found at i:382443 original size:8 final size:8
Alignment explanation
Indices: 382430--382454 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
382420 TCTACACGCA
382430 CACGCCCG
1 CACGCCCG
382438 CACGCCCG
1 CACGCCCG
382446 CACGCCCG
1 CACGCCCG
382454 C
1 C
382455 CTTTAATCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.64, G:0.24, T:0.00
Consensus pattern (8 bp):
CACGCCCG
Found at i:384332 original size:27 final size:27
Alignment explanation
Indices: 384294--384371 Score: 102
Period size: 27 Copynumber: 2.9 Consensus size: 27
384284 TAAGATATTT
**
384294 TTATCTGAATTTTGAATTTTAAAATTG
1 TTATCTGAATTTTGAATTTTAAAATCA
*
384321 TTATCCGAATTTTGAATTTTAAAAATCA
1 TTATCTGAATTTTGAATTTT-AAAATCA
* *
384349 TTATTTGGATTTTGAATTTTAAA
1 TTATCTGAATTTTGAATTTTAAA
384372 TTTAATATCT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
27 22 0.50
28 22 0.50
ACGTcount: A:0.35, C:0.05, G:0.10, T:0.50
Consensus pattern (27 bp):
TTATCTGAATTTTGAATTTTAAAATCA
Found at i:384360 original size:28 final size:28
Alignment explanation
Indices: 384294--384371 Score: 95
Period size: 28 Copynumber: 2.8 Consensus size: 28
384284 TAAGATATTT
* **
384294 TTATCTGAATTTTGAATTTT-AAAATTG
1 TTATCCGAATTTTGAATTTTAAAAATCA
384321 TTATCCGAATTTTGAATTTTAAAAATCA
1 TTATCCGAATTTTGAATTTTAAAAATCA
** *
384349 TTATTTGGATTTTGAATTTTAAA
1 TTATCCGAATTTTGAATTTTAAA
384372 TTTAATATCT
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 19 0.43
28 25 0.57
ACGTcount: A:0.35, C:0.05, G:0.10, T:0.50
Consensus pattern (28 bp):
TTATCCGAATTTTGAATTTTAAAAATCA
Found at i:385290 original size:2 final size:2
Alignment explanation
Indices: 385283--385308 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
385273 TATCTATTTC
385283 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
385309 TTTAGTCACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:387635 original size:57 final size:57
Alignment explanation
Indices: 387569--387685 Score: 216
Period size: 57 Copynumber: 2.1 Consensus size: 57
387559 GGAGTATGAA
387569 CAATATTGTTTATGGTTAGTTCTTTTTCGAAAGTCATTTTCAACACTTCCTTTCCGT
1 CAATATTGTTTATGGTTAGTTCTTTTTCGAAAGTCATTTTCAACACTTCCTTTCCGT
* *
387626 CAATATTGTTTATGGTTAGTTCTTTTTCGAAAGTCATTTTCAATACTTCCTTTCTGT
1 CAATATTGTTTATGGTTAGTTCTTTTTCGAAAGTCATTTTCAACACTTCCTTTCCGT
387683 CAA
1 CAA
387686 AAACTTTGTA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.22, C:0.18, G:0.12, T:0.48
Consensus pattern (57 bp):
CAATATTGTTTATGGTTAGTTCTTTTTCGAAAGTCATTTTCAACACTTCCTTTCCGT
Found at i:388851 original size:17 final size:17
Alignment explanation
Indices: 388818--388851 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
388808 TAAATAAAAT
**
388818 TAATATATATATTCAAA
1 TAATATATATAAACAAA
388835 TAATATATATAAACAAA
1 TAATATATATAAACAAA
388852 GATTAAAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (17 bp):
TAATATATATAAACAAA
Done.