Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold392
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: 803515
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
File 3 of 6
Found at i:238001 original size:2 final size:2
Alignment explanation
Indices: 237994--238024 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
237984 AACTAAGGTG
237994 TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
238025 AGCAGAAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:238015 original size:13 final size:13
Alignment explanation
Indices: 237997--238022 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
237987 TAAGGTGTAT
237997 ATATATATATATA
1 ATATATATATATA
238010 ATATATATATATA
1 ATATATATATATA
238023 TAAGCAGAAA
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATATATATATA
Found at i:238015 original size:15 final size:15
Alignment explanation
Indices: 237995--238025 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
237985 ACTAAGGTGT
237995 ATATATATATATATA
1 ATATATATATATATA
238010 ATATATATATATATA
1 ATATATATATATATA
238025 A
1 A
238026 GCAGAAACAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATATATATATATATA
Found at i:242714 original size:2 final size:2
Alignment explanation
Indices: 242707--242739 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
242697 AACTAAATCT
*
242707 TA TA TA TA TA TG TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
242740 TTGACTCGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:243356 original size:16 final size:15
Alignment explanation
Indices: 243295--243357 Score: 63
Period size: 15 Copynumber: 4.1 Consensus size: 15
243285 TATTAATTAT
*
243295 AAATTGTAAATATAAA
1 AAATT-TAAATAAAAA
* *
243311 AAATATAAATAAATA
1 AAATTTAAATAAAAA
* *
243326 AAATTTAATTGAAAAT
1 AAATTTAAAT-AAAAA
243342 AAATTTAAATAAAAA
1 AAATTTAAATAAAAA
243357 A
1 A
243358 TTTTAAAATT
Statistics
Matches: 37, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
15 21 0.57
16 16 0.43
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (15 bp):
AAATTTAAATAAAAA
Found at i:243469 original size:14 final size:15
Alignment explanation
Indices: 243446--243475 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
243436 TAAAGTTTAC
243446 AAAAACAAAAAAAGG
1 AAAAACAAAAAAAGG
243461 AAAAA-AAAAAAAGG
1 AAAAACAAAAAAAGG
243475 A
1 A
243476 GTGGAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.83, C:0.03, G:0.13, T:0.00
Consensus pattern (15 bp):
AAAAACAAAAAAAGG
Found at i:243619 original size:23 final size:21
Alignment explanation
Indices: 243593--243638 Score: 65
Period size: 23 Copynumber: 2.1 Consensus size: 21
243583 AATGTATATA
*
243593 TATTTAAATTATAATTTAAAATT
1 TATTTAAATT-TAACTT-AAATT
243616 TATTTAAATTTAACTTAAATT
1 TATTTAAATTTAACTTAAATT
243637 TA
1 TA
243639 AATTATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.32
22 5 0.23
23 10 0.45
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
TATTTAAATTTAACTTAAATT
Found at i:243639 original size:11 final size:11
Alignment explanation
Indices: 243594--243639 Score: 58
Period size: 11 Copynumber: 4.1 Consensus size: 11
243584 ATGTATATAT
243594 ATTTAAATTATA
1 ATTTAAATT-TA
243606 ATTTAAAATTT-
1 ATTT-AAATTTA
243617 ATTTAAATTTA
1 ATTTAAATTTA
*
243628 ACTTAAATTTA
1 ATTTAAATTTA
243639 A
1 A
243640 ATTATTTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
10 6 0.19
11 15 0.48
12 5 0.16
13 5 0.16
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (11 bp):
ATTTAAATTTA
Found at i:243905 original size:24 final size:24
Alignment explanation
Indices: 243834--243906 Score: 69
Period size: 24 Copynumber: 3.0 Consensus size: 24
243824 TTTATTTTTA
* *
243834 TTTTAAATTTTTAA-GATAATTAAT
1 TTTTAAA-TTTAAATGATAATAAAT
* *
243858 TATTTAAA-TTAATATTATATTAAAT
1 T-TTTAAATTTAA-ATGATAATAAAT
243883 TTTTAAATTTAAATGATAATAAAT
1 TTTTAAATTTAAATGATAATAAAT
243907 AATTCTTTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
23 3 0.08
24 18 0.46
25 18 0.46
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.51
Consensus pattern (24 bp):
TTTTAAATTTAAATGATAATAAAT
Found at i:244153 original size:22 final size:22
Alignment explanation
Indices: 244113--244154 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
244103 ATAATAATAT
*
244113 TATTTTTATTTTAATATTTATA
1 TATTTTTATATTAATATTTATA
244135 TATTTTTATAATTAA-ATTTA
1 TATTTTTAT-ATTAATATTTA
244155 AATAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TATTTTTATATTAATATTTATA
Found at i:244181 original size:32 final size:30
Alignment explanation
Indices: 244131--244193 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 30
244121 TTTTAATATT
244131 TATATATTTTTATAATTAAATTTAAATAAAAA
1 TATATATTTTTATAATTAAATTT--ATAAAAA
*
244163 TATAT-TTTATTATTATTAAATTTATAAAAA
1 TATATATTT-TTATAATTAAATTTATAAAAA
244193 T
1 T
244194 TTTATTTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 8 0.28
31 3 0.10
32 18 0.62
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (30 bp):
TATATATTTTTATAATTAAATTTATAAAAA
Found at i:245090 original size:2 final size:2
Alignment explanation
Indices: 245083--245112 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
245073 TTTTGGTTGA
245083 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
245113 TGTTATGGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:245434 original size:19 final size:20
Alignment explanation
Indices: 245402--245441 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
245392 CTATTACTGA
245402 TTTAAAATTAAAAA-TATTT
1 TTTAAAATTAAAAATTATTT
* *
245421 TTTAATATTTAAAATTATTT
1 TTTAAAATTAAAAATTATTT
245441 T
1 T
245442 AATTTAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTAAAATTAAAAATTATTT
Found at i:249627 original size:12 final size:13
Alignment explanation
Indices: 249610--249665 Score: 62
Period size: 12 Copynumber: 4.3 Consensus size: 13
249600 ATCGCATCAA
249610 ATTTGA-TTATAT
1 ATTTGATTTATAT
249622 ATTTGATTTGAATAT
1 ATTTGATTT--ATAT
*
249637 ATTTAATTTATAT
1 ATTTGATTTATAT
*
249650 ATTT-TTTTATAT
1 ATTTGATTTATAT
249662 ATTT
1 ATTT
249666 AAATATAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
12 17 0.44
13 10 0.26
15 12 0.31
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.62
Consensus pattern (13 bp):
ATTTGATTTATAT
Found at i:249638 original size:15 final size:13
Alignment explanation
Indices: 249616--249667 Score: 61
Period size: 15 Copynumber: 3.9 Consensus size: 13
249606 TCAAATTTGA
*
249616 TTATATATTTGAT
1 TTATATATTTAAT
249629 TTGAATATATTTAAT
1 TT--ATATATTTAAT
*
249644 TTATATATTT-TT
1 TTATATATTTAAT
249656 TTATATATTTAA
1 TTATATATTTAA
249668 ATATAATTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
12 11 0.33
13 10 0.30
15 12 0.36
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (13 bp):
TTATATATTTAAT
Found at i:249928 original size:44 final size:44
Alignment explanation
Indices: 249878--249967 Score: 135
Period size: 44 Copynumber: 2.0 Consensus size: 44
249868 AGTCCTCGTG
* *
249878 AAATGTTAAATTGTAAATGTAAACTAATGTCGTCGTTCAGAGTT
1 AAATGTTAAAATGTAAATGTAAACTAATGTCATCGTTCAGAGTT
* * *
249922 AAATGTTAAAATGTAGATGTTAACTAATGTCATCGTTGAGAGTT
1 AAATGTTAAAATGTAAATGTAAACTAATGTCATCGTTCAGAGTT
249966 AA
1 AA
249968 CCATATTAGC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.36
Consensus pattern (44 bp):
AAATGTTAAAATGTAAATGTAAACTAATGTCATCGTTCAGAGTT
Found at i:250431 original size:75 final size:72
Alignment explanation
Indices: 250344--250501 Score: 178
Period size: 75 Copynumber: 2.2 Consensus size: 72
250334 TATATTTTTA
* *
250344 TTTAATAAATTTATATCAGTTAAATATG-ACAT-TAAAAATATATATT-TTTAATTTTATATTTA
1 TTTAATAAATTTATATCAGTTAAAT-TGTA-ATATAAAAATA-A-ATTATTT-ATTTTATAATAA
250406 TAATAAATTATTT
61 T-ATAAATTATTT
* * * * *
250419 TTTATTAAATTTATATTATTTAACTTGTAATATTAAAATAAATTATTTATTTTATAATAATATAA
1 TTTAATAAATTTATATCAGTTAAATTGTAATATAAAAATAAATTATTTATTTTATAATAATATAA
250484 ATTATTT
66 ATTATTT
250491 TTTAATAAATT
1 TTTAATAAATT
250502 CGATGTTATG
Statistics
Matches: 72, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
72 21 0.29
73 14 0.19
74 8 0.11
75 29 0.40
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (72 bp):
TTTAATAAATTTATATCAGTTAAATTGTAATATAAAAATAAATTATTTATTTTATAATAATATAA
ATTATTT
Found at i:250440 original size:18 final size:17
Alignment explanation
Indices: 250382--250440 Score: 52
Period size: 16 Copynumber: 3.6 Consensus size: 17
250372 ACATTAAAAA
* *
250382 TATATATTT-TTAATTT
1 TATATTTTTATTAAATT
* *
250398 TATATTTATAATAAA-T
1 TATATTTTTATTAAATT
250414 TAT-TTTTTATTAAATT
1 TATATTTTTATTAAATT
250430 TATATTATTTA
1 TATATT-TTTA
250441 ACTTGTAATA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
15 9 0.27
16 15 0.45
17 5 0.15
18 4 0.12
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TATATTTTTATTAAATT
Found at i:251292 original size:10 final size:10
Alignment explanation
Indices: 251255--251296 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
251245 AAATTAAAGA
251255 ATATAAATAAT
1 ATATAAA-AAT
*
251266 ATATACAAAT
1 ATATAAAAAT
251276 -TATTAAAAAT
1 ATA-TAAAAAT
251286 ATATAAAAAT
1 ATATAAAAAT
251296 A
1 A
251297 ATTTAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
9 2 0.07
10 17 0.63
11 8 0.30
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (10 bp):
ATATAAAAAT
Found at i:261568 original size:18 final size:18
Alignment explanation
Indices: 261545--261583 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
261535 ATTCAATCCG
*
261545 ATTAATATGATGTTTAAT
1 ATTAATAAGATGTTTAAT
261563 ATTAATAAGATGTTTAAT
1 ATTAATAAGATGTTTAAT
261581 ATT
1 ATT
261584 CAATCAGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (18 bp):
ATTAATAAGATGTTTAAT
Found at i:270310 original size:2 final size:2
Alignment explanation
Indices: 270297--270333 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
270287 ATACACATCC
*
270297 AG AG AA AG 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 AG AG AG AG A
270334 CGTCATACTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:270995 original size:36 final size:37
Alignment explanation
Indices: 270918--270995 Score: 86
Period size: 36 Copynumber: 2.1 Consensus size: 37
270908 TTTGTTTGAT
* * * **
270918 ATATATTAAAATATAAATATAAAATATAATCTTTTAA
1 ATATATAAAAATAAAAATATAAAATATAATATCATAA
* *
270955 ATATATAAAAATAAAAATA-AAAATTTAATATCATAC
1 ATATATAAAAATAAAAATATAAAATATAATATCATAA
270991 ATATA
1 ATATA
270996 CTCATATTAT
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
36 17 0.50
37 17 0.50
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (37 bp):
ATATATAAAAATAAAAATATAAAATATAATATCATAA
Found at i:272214 original size:10 final size:10
Alignment explanation
Indices: 272201--272276 Score: 50
Period size: 10 Copynumber: 7.3 Consensus size: 10
272191 ATATTATTAA
272201 AAATTAAAAT
1 AAATTAAAAT
272211 AAA-TATAAAT
1 AAATTA-AAAT
*
272221 ATTATTAAAA-
1 A-AATTAAAAT
*
272231 AATATTAAATT
1 AA-ATTAAAAT
*
272242 AAATACAAATAT
1 AAAT-TAAA-AT
272254 AAATTAAAA-
1 AAATTAAAAT
272263 ATAATTAAAAT
1 A-AATTAAAAT
272274 AAA
1 AAA
272277 ATATAAAAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 18
0.68 0.08 0.24
Matches are distributed among these distances:
9 3 0.06
10 28 0.55
11 13 0.25
12 7 0.14
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (10 bp):
AAATTAAAAT
Found at i:272229 original size:16 final size:16
Alignment explanation
Indices: 272210--272401 Score: 58
Period size: 16 Copynumber: 11.6 Consensus size: 16
272200 AAAATTAAAA
272210 TAAATATAAATATTAT
1 TAAATATAAATATTAT
272226 T-AA-A-AAATATTAAAT
1 TAAATATAAATATT--AT
* *
272241 TAAATACAAATATAAAT
1 TAAATATAAATAT-TAT
* * **
272258 TAAAAATAATTAAAAT
1 TAAATATAAATATTAT
* *
272274 AAAATATAAAAATATAT
1 TAAATATAAATAT-TAT
*
272291 TATATTATATAAATAATAT
1 TA-A--ATATAAATATTAT
* * *
272310 AAAATATATATATCAAT
1 TAAATATAAATAT-TAT
272327 TATAGTATATTAAA-ATTTAT
1 TA-A--ATA-TAAATA-TTAT
272347 ATAAATATAAATTATT-T
1 -TAAATATAAA-TATTAT
* *
272364 TAAATATAATTATAAT
1 TAAATATAAATATTAT
*
272380 TTAATA-AAATA-TA-
1 TAAATATAAATATTAT
272393 TAAATATAA
1 TAAATATAA
272402 TTAAATTATC
Statistics
Matches: 128, Mismatches: 27, Indels: 44
0.64 0.14 0.22
Matches are distributed among these distances:
13 12 0.09
14 4 0.03
15 12 0.09
16 37 0.29
17 23 0.18
18 14 0.11
19 5 0.04
20 15 0.12
21 6 0.05
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (16 bp):
TAAATATAAATATTAT
Found at i:272238 original size:31 final size:31
Alignment explanation
Indices: 272189--272292 Score: 117
Period size: 31 Copynumber: 3.4 Consensus size: 31
272179 TTAGTGAAAA
272189 AAATAT-TATT-AAAA-ATTAAAATAAATAT
1 AAATATATATTAAAAATATTAAAATAAATAT
* *
272217 AAATAT-TATTAAAAAATATTAAATTAAATAC
1 AAATATATATT-AAAAATATTAAAATAAATAT
*
272248 AAATATAAATTAAAAATAATTAAAATAAAATAT
1 AAATATATATTAAAAAT-ATTAAAAT-AAATAT
*
272281 AAAAATATATTA
1 AAATATATATTA
272293 TATTATATAA
Statistics
Matches: 63, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
28 10 0.16
30 4 0.06
31 24 0.38
32 10 0.16
33 15 0.24
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (31 bp):
AAATATATATTAAAAATATTAAAATAAATAT
Found at i:272256 original size:27 final size:26
Alignment explanation
Indices: 272226--272318 Score: 73
Period size: 27 Copynumber: 3.4 Consensus size: 26
272216 TAAATATTAT
272226 TAAAAAATATTAAATTAAATACAAATA
1 TAAAAAATATTAAATTAAATA-AAATA
*
272253 TAAATTAAA-AAT-AATTAAAATAAAATA
1 TAAA--AAATATTAAATT-AAATAAAATA
* *
272280 TAAAAATATATTATATTATATAAATAATA
1 TAAAAA-ATATTAAATTAAAT-AA-AATA
*
272309 TAAAATATAT
1 TAAAAAATAT
272319 ATATCAATTA
Statistics
Matches: 53, Mismatches: 5, Indels: 15
0.73 0.07 0.21
Matches are distributed among these distances:
25 2 0.04
26 1 0.02
27 22 0.42
28 16 0.30
29 12 0.23
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (26 bp):
TAAAAAATATTAAATTAAATAAAATA
Found at i:272258 original size:53 final size:56
Alignment explanation
Indices: 272201--272312 Score: 133
Period size: 54 Copynumber: 2.1 Consensus size: 56
272191 ATATTATTAA
** *
272201 AAATT-AAAATAAATATAAATATTAT-TAAAAA-ATATTAAATTAAATACA-AATAT
1 AAATTAAAAATAAATA-AAATAAAATATAAAAATATATTAAATTAAATAAATAATAT
* * *
272254 AAATTAAAAATAATTAAAATAAAATATAAAAATATATTATATTATATAAATAATAT
1 AAATTAAAAATAAATAAAATAAAATATAAAAATATATTAAATTAAATAAATAATAT
272310 AAA
1 AAA
272313 ATATATATAT
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
53 12 0.24
54 15 0.31
55 14 0.29
56 8 0.16
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (56 bp):
AAATTAAAAATAAATAAAATAAAATATAAAAATATATTAAATTAAATAAATAATAT
Found at i:272273 original size:22 final size:23
Alignment explanation
Indices: 272203--272292 Score: 70
Period size: 22 Copynumber: 4.2 Consensus size: 23
272193 ATTATTAAAA
*
272203 ATTAAAAT-AAATATAAATAT-T
1 ATTAAAATAAAATATAAAAATAT
* *
272224 ATT--AA-AAAATATTAAATTA-
1 ATTAAAATAAAATATAAAAATAT
*
272243 AATACAAATATAAAT-TAAAAATA-
1 ATTA-AAATA-AAATATAAAAATAT
272266 ATTAAAATAAAATATAAAAATAT
1 ATTAAAATAAAATATAAAAATAT
272289 ATTA
1 ATTA
272293 TATTATATAA
Statistics
Matches: 53, Mismatches: 7, Indels: 16
0.70 0.09 0.21
Matches are distributed among these distances:
19 13 0.25
21 7 0.13
22 15 0.28
23 14 0.26
24 4 0.08
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (23 bp):
ATTAAAATAAAATATAAAAATAT
Found at i:272317 original size:18 final size:17
Alignment explanation
Indices: 272213--272319 Score: 55
Period size: 18 Copynumber: 6.3 Consensus size: 17
272203 ATTAAAATAA
*
272213 ATATAAATATTATTAAAAA
1 ATATAAATA-TA-TAAAAT
* *
272232 ATATTAAATTAAATACAA-
1 ATA-TAAA-TATATAAAAT
272250 ATATAAAT-TA-AAAAT
1 ATATAAATATATAAAAT
*
272265 A-ATTAA-A-ATAAAAT
1 ATATAAATATATAAAAT
* * *
272279 ATAAAAATATATTATATT
1 ATATAAATATA-TAAAAT
272297 ATATAAATAATATAAAAT
1 ATATAAAT-ATATAAAAT
272315 ATATA
1 ATATA
272320 TATCAATTAT
Statistics
Matches: 66, Mismatches: 12, Indels: 21
0.67 0.12 0.21
Matches are distributed among these distances:
13 1 0.02
14 13 0.20
15 5 0.08
16 2 0.03
17 5 0.08
18 23 0.35
19 10 0.15
20 5 0.08
21 2 0.03
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.36
Consensus pattern (17 bp):
ATATAAATATATAAAAT
Found at i:272329 original size:36 final size:36
Alignment explanation
Indices: 272263--272336 Score: 87
Period size: 36 Copynumber: 2.1 Consensus size: 36
272253 TAAATTAAAA
* *
272263 ATAATTAAAATAAAATATAAAAATATATTATATTAT
1 ATAAATAAAATAAAATATAAAAATATATTATAGTAT
* * *
272299 ATAAATAATATAAAATATATATATCA-ATTATAGTAT
1 ATAAATAAAATAAAATATAAAAAT-ATATTATAGTAT
272335 AT
1 AT
272337 TAAAATTTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
36 31 0.97
37 1 0.03
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (36 bp):
ATAAATAAAATAAAATATAAAAATATATTATAGTAT
Found at i:272336 original size:41 final size:40
Alignment explanation
Indices: 272261--272338 Score: 95
Period size: 41 Copynumber: 1.9 Consensus size: 40
272251 TATAAATTAA
*
272261 AAATAATTAAAATAAAATATAAAAATATATTATATTATAT
1 AAATAATTAAAATAAAATATAAAAATATAGTATATTATAT
* * *
272301 AAATAATATAAAAT-ATATATATCAATTATAGTATATTA
1 AAATAAT-TAAAATAAAATATA-AAAATATAGTATATTA
272339 AAATTTATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
40 13 0.41
41 19 0.59
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (40 bp):
AAATAATTAAAATAAAATATAAAAATATAGTATATTATAT
Found at i:272673 original size:21 final size:21
Alignment explanation
Indices: 272631--272673 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
272621 TTCTATCTCC
*
272631 TTCTCCGCCGTCTCGAGCCCT
1 TTCTCCGCCGTCTCGAACCCT
* *
272652 TTCTCCGCTGTCTCGAATCCT
1 TTCTCCGCCGTCTCGAACCCT
272673 T
1 T
272674 CCTTCACGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.07, C:0.42, G:0.16, T:0.35
Consensus pattern (21 bp):
TTCTCCGCCGTCTCGAACCCT
Found at i:276248 original size:28 final size:28
Alignment explanation
Indices: 276212--276265 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
276202 AGATACATTT
276212 AAATTAAATGTTAACATAGCATATATTC
1 AAATTAAATGTTAACATAGCATATATTC
*
276240 AAATTAAATGTTAGCATAGCATATAT
1 AAATTAAATGTTAACATAGCATATAT
276266 CGGCATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.35
Consensus pattern (28 bp):
AAATTAAATGTTAACATAGCATATATTC
Found at i:276911 original size:14 final size:15
Alignment explanation
Indices: 276894--276932 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
276884 TTAATTTTTT
276894 AATTTTA-TATTAAA
1 AATTTTATTATTAAA
*
276908 AATTATATTATTAAA
1 AATTTTATTATTAAA
276923 AA-TTTATTAT
1 AATTTTATTAT
276933 ATTTAATACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
AATTTTATTATTAAA
Found at i:276921 original size:15 final size:14
Alignment explanation
Indices: 276897--276932 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
276887 ATTTTTTAAT
276897 TTTA-TATTAAAAA
1 TTTATTATTAAAAA
276910 TTATATTATTAAAAA
1 TT-TATTATTAAAAA
276925 TTTATTAT
1 TTTATTAT
276933 ATTTAATACA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 2 0.10
14 8 0.38
15 11 0.52
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TTTATTATTAAAAA
Found at i:277990 original size:17 final size:17
Alignment explanation
Indices: 277968--278001 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
277958 CATCCACGTC
277968 AAATATATACTCATATT
1 AAATATATACTCATATT
*
277985 AAATATATATTCATATT
1 AAATATATACTCATATT
278002 CGTATCAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (17 bp):
AAATATATACTCATATT
Found at i:278355 original size:17 final size:17
Alignment explanation
Indices: 278330--278363 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
278320 GTGAGCCTAG
*
278330 TGTTAGATATGAGTATA
1 TGTTAGATATAAGTATA
*
278347 TGTTTGATATAAGTATA
1 TGTTAGATATAAGTATA
278364 CTTAACTTTT
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:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (17 bp):
TGTTAGATATAAGTATA
Found at i:280246 original size:4 final size:4
Alignment explanation
Indices: 280239--280269 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
280229 TAACTATATA
280239 TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TAT
280270 CCAAACAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:284292 original size:12 final size:12
Alignment explanation
Indices: 284275--284299 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
284265 CTTACCATGC
284275 TTTATATAAATT
1 TTTATATAAATT
284287 TTTATATAAATT
1 TTTATATAAATT
284299 T
1 T
284300 CTAAGGTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTATATAAATT
Found at i:285633 original size:2 final size:2
Alignment explanation
Indices: 285626--285674 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
285616 ATTCTAATCA
285626 TC TC TC TC TC TC TC 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 TC TC TC TC TC TC TC
285668 TC TC TC T
1 TC TC TC T
285675 TTGTATCCCT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:287423 original size:20 final size:21
Alignment explanation
Indices: 287400--287452 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
287390 ATATATAATA
**
287400 AATTTAAATTTTTTTTAAA-T
1 AATTTAAATTTTTAATAAATT
*
287420 AATTAAAATTTTTAATAAATT
1 AATTTAAATTTTTAATAAATT
*
287441 AAATTAAATTTT
1 AATTTAAATTTT
287453 AAAATCGATA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
AATTTAAATTTTTAATAAATT
Found at i:287436 original size:16 final size:18
Alignment explanation
Indices: 287411--287443 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
287401 ATTTAAATTT
287411 TTTTTAAAT-AATTAAAA
1 TTTTTAAATAAATTAAAA
287428 TTTTT-AATAAATTAAA
1 TTTTTAAATAAATTAAA
287444 TTAAATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TTTTTAAATAAATTAAAA
Found at i:287534 original size:2 final size:2
Alignment explanation
Indices: 287527--287560 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
287517 GGAGGGTGTC
*
287527 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AC AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
287561 GGTATTAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:288970 original size:21 final size:21
Alignment explanation
Indices: 288932--288971 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
288922 TTTAAAAAAT
*
288932 TATTTTATATTAATATTTATA
1 TATTTTATAATAATATTTATA
288953 TATTTTATAAATAA-ATTTA
1 TATTTTAT-AATAATATTTA
288972 AATAAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TATTTTATAATAATATTTATA
Found at i:292447 original size:15 final size:16
Alignment explanation
Indices: 292427--292459 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
292417 AAATTATTAA
*
292427 AAAAAGAGAAA-AAAG
1 AAAAAGAAAAACAAAG
292442 AAAAAGAAAAACAAAG
1 AAAAAGAAAAACAAAG
292458 AA
1 AA
292460 TTTGAGTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAAACAAAG
Found at i:292654 original size:25 final size:24
Alignment explanation
Indices: 292619--292667 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
292609 ACGACATATC
*
292619 AAAAAATAAAATAAAA-ATTAATTT
1 AAAAAATAAAA-AAAATAATAATTT
292643 AAAAAATAAAAAAAAATAATAATTT
1 AAAAAAT-AAAAAAAATAATAATTT
292668 TTTAATTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (24 bp):
AAAAAATAAAAAAAATAATAATTT
Found at i:293486 original size:13 final size:15
Alignment explanation
Indices: 293470--293559 Score: 62
Period size: 14 Copynumber: 6.1 Consensus size: 15
293460 AAAATATTAA
293470 TATATTA-AT-AATT
1 TATATTATATAAATT
293483 TATATTATATAAATT
1 TATATTATATAAATT
* *
293498 TATA-TATATACATA
1 TATATTATATAAATT
*
293512 TATATTTATATTATATT
1 TATA-TTATA-TAAATT
* * *
293529 CATGTTAT-TAATTT
1 TATATTATATAAATT
*
293543 TATATCATATAATATT
1 TATATTATATAA-ATT
293559 T
1 T
293560 TAATTATTTT
Statistics
Matches: 58, Mismatches: 12, Indels: 11
0.72 0.15 0.14
Matches are distributed among these distances:
13 7 0.12
14 23 0.40
15 11 0.19
16 11 0.19
17 6 0.10
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.54
Consensus pattern (15 bp):
TATATTATATAAATT
Found at i:293537 original size:20 final size:21
Alignment explanation
Indices: 293489--293559 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 21
293479 AATTTATATT
*
293489 ATATAAATTTATA-TATATAC
1 ATATATATTTATATTATATAC
*
293509 ATATATATTTATATTATATTC
1 ATATATATTTATATTATATAC
* * *
293530 ATGT-TATTAATTTTATAT-C
1 ATATATATTTATATTATATAC
293549 ATATAATATTT
1 ATAT-ATATTT
293560 TAATTATTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
19 4 0.10
20 24 0.59
21 13 0.32
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.54
Consensus pattern (21 bp):
ATATATATTTATATTATATAC
Found at i:293732 original size:17 final size:17
Alignment explanation
Indices: 293692--293734 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
293682 TTTGAATAAG
*
293692 TTTTTTATCAATTTAAA
1 TTTTTTATCAATTAAAA
293709 TTATTTTGAT-AATTAAAA
1 TT-TTTT-ATCAATTAAAA
293727 TTTTTTAT
1 TTTTTTAT
293735 TTAAATTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
16 2 0.09
17 6 0.26
18 13 0.57
19 2 0.09
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (17 bp):
TTTTTTATCAATTAAAA
Found at i:293819 original size:13 final size:13
Alignment explanation
Indices: 293801--293843 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
293791 ATTAATTATG
*
293801 AATAATAAATATA
1 AATAATAAAAATA
293814 AATAATATAAAATA
1 AATAATA-AAAATA
*
293828 AATGAATAAAATTA
1 AAT-AATAAAAATA
293842 AA
1 AA
293844 AACGAACTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 7 0.27
14 15 0.58
15 4 0.15
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (13 bp):
AATAATAAAAATA
Found at i:293826 original size:52 final size:51
Alignment explanation
Indices: 293724--293830 Score: 146
Period size: 52 Copynumber: 2.1 Consensus size: 51
293714 TTGATAATTA
*
293724 AAATTTTTTATTTAAATTAATTATAAAATATATAAATATTAATATAAAAAT
1 AAATTTTTTATTTAAATTAATTATAAAATATATAAATATAAATATAAAAAT
* *
293775 AAATTTTTTATTTTTAATTAATTAT-GAATA-ATAAATATAAATAATATAAAAT
1 AAATTTTTTA-TTTAAATTAATTATAAAATATATAAATATAAAT-ATA-AAAAT
293827 AAAT
1 AAAT
293831 GAATAAAATT
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
50 11 0.22
51 17 0.34
52 22 0.44
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (51 bp):
AAATTTTTTATTTAAATTAATTATAAAATATATAAATATAAATATAAAAAT
Found at i:294229 original size:28 final size:28
Alignment explanation
Indices: 294198--294275 Score: 77
Period size: 32 Copynumber: 2.6 Consensus size: 28
294188 ATTGAATTAA
294198 AAATTAAATTAATTAGATTTTTAATTTT
1 AAATTAAATTAATTAGATTTTTAATTTT
* *
294226 AAATTTAATCAATTAATTAAATTTTTTATTTTT
1 AAA-TT-A--AATTAATTAGA-TTTTTAATTTT
*
294259 AATTTAAA-TAATTAGAT
1 AAATTAAATTAATTAGAT
294276 CGTTTAGTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
27 1 0.02
28 10 0.24
29 4 0.10
30 1 0.02
31 1 0.02
32 12 0.29
33 12 0.29
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.53
Consensus pattern (28 bp):
AAATTAAATTAATTAGATTTTTAATTTT
Found at i:294272 original size:32 final size:32
Alignment explanation
Indices: 294204--294265 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
294194 TTAAAAATTA
*
294204 AATTAATTAGATTTTTAATTTTAAATTTAATC
1 AATTAATTAAATTTTTAATTTTAAATTTAATC
* *
294236 AATTAATTAAATTTTTTATTTTTAATTTAA
1 AATTAATTAAATTTTTAATTTTAAATTTAA
294266 ATAATTAGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (32 bp):
AATTAATTAAATTTTTAATTTTAAATTTAATC
Found at i:294516 original size:20 final size:20
Alignment explanation
Indices: 294491--294528 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
294481 AAATTTCATG
294491 AATTGAATTGATT-TCTAACT
1 AATTGAATT-ATTATCTAACT
294511 AATTGAATTATTATCTAA
1 AATTGAATTATTATCTAA
294529 TTCTTATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.45
Consensus pattern (20 bp):
AATTGAATTATTATCTAACT
Found at i:295883 original size:17 final size:18
Alignment explanation
Indices: 295848--295886 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
295838 TAATTAAATA
*
295848 TTTTTTTAAAATTTTTTAT
1 TTTTTTTAAAA-TTATTAT
295867 TTTTTTTAAAA-TATTAT
1 TTTTTTTAAAATTATTAT
295884 TTT
1 TTT
295887 GTTCAACTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
19 11 0.58
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTTTTAAAATTATTAT
Found at i:295944 original size:3 final size:3
Alignment explanation
Indices: 295936--295967 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
295926 CTTTCTTCGT
295936 TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
295968 ATTTTTTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:295956 original size:14 final size:14
Alignment explanation
Indices: 295937--295965 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
295927 TTTCTTCGTT
295937 TATTATTATTATTA
1 TATTATTATTATTA
295951 TATTATTATTATTA
1 TATTATTATTATTA
295965 T
1 T
295966 TAATTTTTTG
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TATTATTATTATTA
Found at i:300504 original size:12 final size:12
Alignment explanation
Indices: 300487--300513 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
300477 TTTAATAATA
300487 TAATAATAAAAT
1 TAATAATAAAAT
300499 TAATAATAAAAT
1 TAATAATAAAAT
300511 TAA
1 TAA
300514 ATTTTTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
TAATAATAAAAT
Found at i:300554 original size:38 final size:37
Alignment explanation
Indices: 300512--300588 Score: 93
Period size: 38 Copynumber: 2.0 Consensus size: 37
300502 TAATAAAATT
*
300512 AAATTTTTAATT-AATTTAAATTTAAATTAAATAAATAA
1 AAATTTTAAATTAAATTT-AATTTAAATT-AATAAATAA
* *
300550 AAATTTTAAATTAAAATTTAATTTAACTTAATTAATAA
1 AAATTTTAAATT-AAATTTAATTTAAATTAATAAATAA
300588 A
1 A
300589 TAAATTTGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
38 20 0.59
39 9 0.26
40 5 0.15
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (37 bp):
AAATTTTAAATTAAATTTAATTTAAATTAATAAATAA
Found at i:300608 original size:13 final size:12
Alignment explanation
Indices: 300581--300638 Score: 52
Period size: 13 Copynumber: 4.9 Consensus size: 12
300571 TTTAACTTAA
300581 TTAATAAATAAAT
1 TTAAT-AATAAAT
*
300594 TTGAATAATACAT
1 TT-AATAATAAAT
300607 TTAATAA-AAA-
1 TTAATAATAAAT
300617 -T-ATAATAAAT
1 TTAATAATAAAT
300627 ATTAATAATAAA
1 -TTAATAATAAA
300639 AAATAAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
8 4 0.11
9 4 0.11
11 2 0.05
12 6 0.16
13 18 0.49
14 3 0.08
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (12 bp):
TTAATAATAAAT
Found at i:300657 original size:23 final size:24
Alignment explanation
Indices: 300608--300660 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
300598 ATAATACATT
*
300608 TAATAAAAATATAATAAATATTAA
1 TAATAAAAATATAATAAATATGAA
*
300632 TAATAAAAA-ATAA-AATTATGACA
1 TAATAAAAATATAATAAATATGA-A
300655 TAATAA
1 TAATAA
300661 TCATAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 6 0.23
23 11 0.42
24 9 0.35
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (24 bp):
TAATAAAAATATAATAAATATGAA
Found at i:300675 original size:27 final size:26
Alignment explanation
Indices: 300629--300680 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
300619 TAATAAATAT
300629 TAATAATAAAAAATAAAATTATGACA
1 TAATAATAAAAAATAAAATTATGACA
* *
300655 TAATAATCATAAAATTAAATTATGAC
1 TAATAAT-AAAAAATAAAATTATGAC
300681 TCTATTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.60, C:0.06, G:0.04, T:0.31
Consensus pattern (26 bp):
TAATAATAAAAAATAAAATTATGACA
Found at i:301043 original size:12 final size:12
Alignment explanation
Indices: 300990--301089 Score: 58
Period size: 11 Copynumber: 8.8 Consensus size: 12
300980 AAAAATTCGT
300990 TTAA-ATTTAAA
1 TTAATATTTAAA
301001 TTAA-ATTT-AA
1 TTAATATTTAAA
*
301011 TATAAT-TTT-AT
1 T-TAATATTTAAA
*
301022 TTAAAAATTTAAA
1 TT-AATATTTAAA
*
301035 TTATTATTTAAAA
1 TTAATATTT-AAA
*
301048 TTAAT-TTTATA
1 TTAATATTTAAA
301059 TTAATATTTAAA
1 TTAATATTTAAA
301071 --AAT-TTTATAA
1 TTAATATTTA-AA
301081 TTAA-ATTTA
1 TTAATATTTA
301090 TAAATTTATT
Statistics
Matches: 70, Mismatches: 8, Indels: 21
0.71 0.08 0.21
Matches are distributed among these distances:
9 4 0.06
10 9 0.13
11 25 0.36
12 22 0.31
13 10 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTAATATTTAAA
Found at i:301060 original size:18 final size:19
Alignment explanation
Indices: 301013--301062 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
301003 AAATTTAATA
301013 TAATTTTAT-TTAAAAATT
1 TAATTTTATATTAAAAATT
301031 TAAATTATTAT-TT-AAAA-T
1 T-AATT-TTATATTAAAAATT
301049 TAATTTTATATTAA
1 TAATTTTATATTAA
301063 TATTTAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
16 4 0.14
17 6 0.21
18 4 0.14
19 8 0.29
20 6 0.21
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TAATTTTATATTAAAAATT
Found at i:301074 original size:21 final size:21
Alignment explanation
Indices: 301019--301096 Score: 79
Period size: 21 Copynumber: 3.6 Consensus size: 21
301009 AATATAATTT
* *
301019 TATTTAAAAA-TTTAAATTAT
1 TATTTAAAAATTTTATATTAA
301039 TATTTAAAATTAATTTTATATTAA
1 TATTT-AAA--AATTTTATATTAA
301063 TATTTAAAAATTTTATAATTAA
1 TATTTAAAAATTTTAT-ATTAA
*
301085 -ATTTATAAATTT
1 TATTTAAAAATTT
301097 ATTGTTACTA
Statistics
Matches: 50, Mismatches: 3, Indels: 9
0.81 0.05 0.15
Matches are distributed among these distances:
20 5 0.10
21 22 0.44
22 5 0.10
23 5 0.10
24 13 0.26
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TATTTAAAAATTTTATATTAA
Found at i:302320 original size:21 final size:21
Alignment explanation
Indices: 302288--302335 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
302278 GGCTAGATTC
* **
302288 TCTTTAAGAAGGATCGAT-AA
1 TCTTTTAGAAGGAAAGATCAA
302308 TCTTTTAGAAAGGAAAGATCAA
1 TCTTTTAG-AAGGAAAGATCAA
302330 TCTTTT
1 TCTTTT
302336 TATATATAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 7 0.30
21 8 0.35
22 8 0.35
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (21 bp):
TCTTTTAGAAGGAAAGATCAA
Found at i:302571 original size:11 final size:11
Alignment explanation
Indices: 302520--302581 Score: 56
Period size: 11 Copynumber: 5.6 Consensus size: 11
302510 ATCAATAAAC
302520 AAAT-TTATTT
1 AAATATTATTT
*
302530 ATAGATATTAATT
1 A-A-ATATTATTT
*
302543 AAAAATTATTT
1 AAATATTATTT
*
302554 AATTATTATTT
1 AAATATTATTT
302565 AAATATT-TTT
1 AAATATTATTT
*
302575 ATATATT
1 AAATATT
302582 TAATACATTA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
10 10 0.24
11 23 0.55
12 3 0.07
13 6 0.14
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (11 bp):
AAATATTATTT
Found at i:303601 original size:8 final size:8
Alignment explanation
Indices: 303574--303643 Score: 65
Period size: 8 Copynumber: 8.5 Consensus size: 8
303564 TTAATCGATA
303574 ATTTATAT
1 ATTTATAT
303582 ATTTTATCAT
1 A-TTTAT-AT
303592 ATTTATAT
1 ATTTATAT
303600 ATTT-TAT
1 ATTTATAT
303607 AATATTATA-
1 -AT-TTATAT
303616 A-TTATAT
1 ATTTATAT
303623 ATTTTATAT
1 A-TTTATAT
*
303632 TTTTATAT
1 ATTTATAT
303640 ATTT
1 ATTT
303644 TAATAAATTA
Statistics
Matches: 52, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
6 5 0.10
7 4 0.08
8 20 0.38
9 18 0.35
10 5 0.10
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (8 bp):
ATTTATAT
Found at i:303637 original size:23 final size:23
Alignment explanation
Indices: 303574--303638 Score: 76
Period size: 23 Copynumber: 2.7 Consensus size: 23
303564 TTAATCGATA
*
303574 ATTTATATATTTTATCATATTTATAT
1 ATTT-TATATTTT-T-ATAATTATAT
* *
303600 ATTTTATAATATTATAATTATAT
1 ATTTTATATTTTTATAATTATAT
303623 ATTTTATATTTTTATA
1 ATTTTATATTTTTATA
303639 TATTTTAATA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
23 23 0.68
24 1 0.03
25 6 0.18
26 4 0.12
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (23 bp):
ATTTTATATTTTTATAATTATAT
Found at i:303644 original size:9 final size:9
Alignment explanation
Indices: 303575--303645 Score: 82
Period size: 9 Copynumber: 8.4 Consensus size: 9
303565 TAATCGATAA
303575 TTTATATAT
1 TTTATATAT
303584 TTTATCATA-
1 TTTAT-ATAT
303593 TTTATATAT
1 TTTATATAT
303602 TTTATA-AT
1 TTTATATAT
*
303610 ATTATA-A-
1 TTTATATAT
303617 -TTATATAT
1 TTTATATAT
303625 TTTATAT-T
1 TTTATATAT
303633 TTTATATAT
1 TTTATATAT
303642 TTTA
1 TTTA
303646 ATAAATTAAC
Statistics
Matches: 55, Mismatches: 1, Indels: 12
0.81 0.01 0.18
Matches are distributed among these distances:
6 5 0.09
7 1 0.02
8 19 0.35
9 27 0.49
10 3 0.05
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.63
Consensus pattern (9 bp):
TTTATATAT
Found at i:303668 original size:38 final size:40
Alignment explanation
Indices: 303577--303670 Score: 104
Period size: 38 Copynumber: 2.4 Consensus size: 40
303567 ATCGATAATT
* * *
303577 TATATATTTTATCATATTTATATATTTTATAATATTATAAT
1 TATATATATTAT-ATTTTTATATATTTTATAATATTATAAC
*
303618 TATATATTTTATATTTTTATATATTTTAATAA-A-T-TAAC
1 TATATATATTATATTTTTATATATTTT-ATAATATTATAAC
*
303656 TATTTATATTATATT
1 TATATATATTATATT
303671 AATTTTAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
38 16 0.33
39 1 0.02
40 15 0.31
41 16 0.33
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (40 bp):
TATATATATTATATTTTTATATATTTTATAATATTATAAC
Found at i:303988 original size:19 final size:19
Alignment explanation
Indices: 303961--303999 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
303951 TTAACTTTTA
303961 TTTTTATTTTTT-ATTGAT
1 TTTTTATTTTTTAATTGAT
303979 TTTTTGATTTTTTAATTGAT
1 TTTTT-ATTTTTTAATTGAT
303999 T
1 T
304000 ATTATATTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.26
19 7 0.37
20 7 0.37
ACGTcount: A:0.18, C:0.00, G:0.08, T:0.74
Consensus pattern (19 bp):
TTTTTATTTTTTAATTGAT
Found at i:304335 original size:2 final size:2
Alignment explanation
Indices: 304328--304353 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
304318 GCCCTGAAAA
304328 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
304354 GATACAGGCT
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:305182 original size:2 final size:2
Alignment explanation
Indices: 305171--305203 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
305161 CAAGATTAAG
305171 TA TA TA -A 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
305204 GGTTTTAATC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:305722 original size:22 final size:23
Alignment explanation
Indices: 305687--305763 Score: 76
Period size: 22 Copynumber: 3.5 Consensus size: 23
305677 ATATTTTATT
305687 TAAATTTAATTATAAAAAT-ATA
1 TAAATTTAATTATAAAAATAATA
305709 TAAATATTAA-TATAAAAATAATA
1 TAAAT-TTAATTATAAAAATAATA
*
305732 T-AATTTAAATA-ATAAAATAA-A
1 TAAATTTAATTATA-AAAATAATA
*
305753 TTAA-TTAATTA
1 TAAATTTAATTA
305764 AAATTAAATT
Statistics
Matches: 49, Mismatches: 1, Indels: 11
0.80 0.02 0.18
Matches are distributed among these distances:
21 13 0.27
22 28 0.57
23 8 0.16
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
TAAATTTAATTATAAAAATAATA
Found at i:305745 original size:17 final size:17
Alignment explanation
Indices: 305711--305761 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
305701 AAAATATATA
*
305711 AATATTAATATAAA-AAT
1 AATA-TAATTTAAATAAT
305728 AATATAATTTAAATAAT
1 AATATAATTTAAATAAT
* * *
305745 AAAATAAATTAATTAAT
1 AATATAATTTAAATAAT
305762 TAAAATTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
16 8 0.28
17 21 0.72
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
AATATAATTTAAATAAT
Found at i:312438 original size:6 final size:6
Alignment explanation
Indices: 312427--312466 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
312417 AGAATTTACG
* * *
312427 GGTGGA GGTGGA GGTGAA GCTGGA GGTGGA GGTGGC GGTG
1 GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGTG
312467 AAGGCACCGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.15, C:0.05, G:0.62, T:0.17
Consensus pattern (6 bp):
GGTGGA
Found at i:313924 original size:20 final size:20
Alignment explanation
Indices: 313899--313939 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
313889 TCTTGATTCG
313899 AATCAAAAATCTTTCCTTTA
1 AATCAAAAATCTTTCCTTTA
*
313919 AATCAAAGATCTTTCCTTTA
1 AATCAAAAATCTTTCCTTTA
313939 A
1 A
313940 CCCTGGTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.39, C:0.20, G:0.02, T:0.39
Consensus pattern (20 bp):
AATCAAAAATCTTTCCTTTA
Found at i:320516 original size:18 final size:19
Alignment explanation
Indices: 320475--320532 Score: 68
Period size: 18 Copynumber: 3.2 Consensus size: 19
320465 TTCAATTATT
320475 AATTTAATTATTTTAATAT-
1 AATTTAA-TATTTTAATATA
* *
320494 -TTTTAATA-TTTAATTTA
1 AATTTAATATTTTAATATA
320511 AATTTAATATTTTAATATA
1 AATTTAATATTTTAATATA
320530 AAT
1 AAT
320533 AATAATTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
16 7 0.22
17 2 0.06
18 12 0.38
19 11 0.34
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
AATTTAATATTTTAATATA
Found at i:321079 original size:10 final size:10
Alignment explanation
Indices: 321064--321107 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
321054 TATAAATAGT
321064 TTTATTTTTA
1 TTTATTTTTA
321074 TTTATTTTTA
1 TTTATTTTTA
*
321084 -TT-TGTTTA
1 TTTATTTTTA
321092 -TTATTTTTA
1 TTTATTTTTA
321101 TTT-TTTT
1 TTTATTTT
321108 AAAAAAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
8 7 0.23
9 11 0.37
10 12 0.40
ACGTcount: A:0.16, C:0.00, G:0.02, T:0.82
Consensus pattern (10 bp):
TTTATTTTTA
Found at i:321097 original size:17 final size:18
Alignment explanation
Indices: 321070--321108 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
321060 TAGTTTTATT
321070 TTTATTTATTTTTATTTG
1 TTTATTTATTTTTATTTG
*
321088 TTTA-TTATTTTTATTTT
1 TTTATTTATTTTTATTTG
321105 TTTA
1 TTTA
321109 AAAAAATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (18 bp):
TTTATTTATTTTTATTTG
Found at i:321206 original size:114 final size:114
Alignment explanation
Indices: 320999--321208 Score: 266
Period size: 114 Copynumber: 1.8 Consensus size: 114
320989 TTGCTAGAAG
* *
320999 AATATATCAATATTTATAATTAAAATAGTAAATAATTGAGTATTGATAAATTATTTATAAATAGT
1 AATATATCAATATTTATAATTAAAATAGTAAATAAATGAGTATTGATAAATTATTGATAAATAGT
* * ** *
321064 TTTATTTTTATTTATTTTTATTTGTTTATTATTTTTATTTTTTTAAAAA
66 TATATTTTTACTTATTTGAATTTATTTATTATTTTTATTTTTTTAAAAA
*
321113 AATATATTC-ATATTTATAATTAAAATCGTAAATAAATGA-TCATTCGATAAA-TAGTTGATAAA
1 AATATA-TCAATATTTATAATTAAAATAGTAAATAAATGAGT-ATT-GATAAATTA-TTGATAAA
* *
321175 TAGTTAT-TTTTTGCTTGTTTGAATTTATTTATTA
62 TAGTTATATTTTTACTTATTTGAATTTATTTATTA
321209 AGCTAAATAA
Statistics
Matches: 82, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
113 1 0.01
114 60 0.73
115 21 0.26
ACGTcount: A:0.39, C:0.03, G:0.07, T:0.51
Consensus pattern (114 bp):
AATATATCAATATTTATAATTAAAATAGTAAATAAATGAGTATTGATAAATTATTGATAAATAGT
TATATTTTTACTTATTTGAATTTATTTATTATTTTTATTTTTTTAAAAA
Found at i:321384 original size:16 final size:16
Alignment explanation
Indices: 321363--321423 Score: 54
Period size: 16 Copynumber: 3.6 Consensus size: 16
321353 TAATAATTAT
321363 TATTTATATATTTTTA
1 TATTTATATATTTTTA
321379 TATTTATAATATAATTTATAA
1 TATTTAT-ATAT--TTT-T-A
321400 TATTTATAT-TTTATTA
1 TATTTATATATTT-TTA
321416 T-TTTATAT
1 TATTTATAT
321424 TTAGAACTAG
Statistics
Matches: 39, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
15 7 0.18
16 9 0.23
17 7 0.18
18 1 0.03
19 4 0.10
20 3 0.08
21 8 0.21
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TATTTATATATTTTTA
Found at i:321410 original size:43 final size:42
Alignment explanation
Indices: 321342--321426 Score: 111
Period size: 44 Copynumber: 2.0 Consensus size: 42
321332 TATTCGATTG
321342 TAATATAATAATAATAATTATTA-TTTATATATTTTTATATTTA
1 TAATATAATAATAATAATTATTATTTTAT-TA-TTTTATATTTA
* *
321385 TAATATAATTTATAATATTTA-TATTTTATTATTTTATATTTA
1 TAATATAA-TAATAATAATTATTATTTTATTATTTTATATTTA
321427 GAACTAGTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
42 11 0.29
43 12 0.32
44 15 0.39
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (42 bp):
TAATATAATAATAATAATTATTATTTTATTATTTTATATTTA
Found at i:321412 original size:28 final size:29
Alignment explanation
Indices: 321355--321413 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 29
321345 TATAATAATA
* *
321355 ATAATTATTATTTATATATTTTTATATTT
1 ATAATTATAATTTATATATTTATATATTT
321384 ATAA-TATAATTTATAATATTTATAT-TTT
1 ATAATTATAATTTAT-ATATTTATATATTT
321412 AT
1 AT
321414 TATTTTATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 14 0.52
29 13 0.48
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (29 bp):
ATAATTATAATTTATATATTTATATATTT
Found at i:321423 original size:21 final size:20
Alignment explanation
Indices: 321363--321426 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 20
321353 TAATAATTAT
321363 TATTTATATATTTTTATATTTA
1 TATTTAT-TA-TTTTATATTTA
* *
321385 TA-ATATAATTTATAATATTTA
1 TATTTATTATTT-T-ATATTTA
321406 TATTTTATTATTTTATATTTA
1 TA-TTTATTATTTTATATTTA
321427 GAACTAGTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
19 3 0.09
20 2 0.06
21 19 0.56
22 3 0.09
23 7 0.21
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TATTTATTATTTTATATTTA
Found at i:324385 original size:30 final size:30
Alignment explanation
Indices: 324349--324408 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
324339 GGGAAATAGA
*
324349 AAGCCGACAGAAGTA-AGAAGATAGGATTTT
1 AAGCCGACAGAACTACA-AAGATAGGATTTT
324379 AAGCCGACAGAACTACAAAGATAGGATTTT
1 AAGCCGACAGAACTACAAAGATAGGATTTT
324409 GGTATTAAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 27 0.96
31 1 0.04
ACGTcount: A:0.43, C:0.13, G:0.23, T:0.20
Consensus pattern (30 bp):
AAGCCGACAGAACTACAAAGATAGGATTTT
Found at i:324690 original size:24 final size:26
Alignment explanation
Indices: 324663--324717 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 26
324653 TTATTGTATG
*
324663 TATTATAATTAT-AAATATAAT-TAA
1 TATTATAATTATCAAATATAATAAAA
* *
324687 TATTATTATTATCAATTATAATAAAA
1 TATTATAATTATCAAATATAATAAAA
324713 TATTA
1 TATTA
324718 ATATTGATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 11 0.42
25 8 0.31
26 7 0.27
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (26 bp):
TATTATAATTATCAAATATAATAAAA
Found at i:324890 original size:22 final size:22
Alignment explanation
Indices: 324845--324889 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
324835 TAATTTGAAA
324845 ATAAATATAATATTTTATAAAT
1 ATAAATATAATATTTTATAAAT
*
324867 ATAAATATAA-ATTAT-TAAAT
1 ATAAATATAATATTTTATAAAT
324887 ATA
1 ATA
324890 TTATATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.36
21 4 0.18
22 10 0.45
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
ATAAATATAATATTTTATAAAT
Found at i:325213 original size:17 final size:18
Alignment explanation
Indices: 325185--325234 Score: 54
Period size: 17 Copynumber: 3.0 Consensus size: 18
325175 GCTGAACCCT
*
325185 AATTTGAAATTTTATTTA
1 AATTTGAAATTTAATTTA
325203 AATTT-AAATTTAATTT-
1 AATTTGAAATTTAATTTA
*
325219 TATTTG--ATTTAATTTA
1 AATTTGAAATTTAATTTA
325235 TAAATTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
15 9 0.32
16 4 0.14
17 10 0.36
18 5 0.18
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (18 bp):
AATTTGAAATTTAATTTA
Found at i:325242 original size:22 final size:22
Alignment explanation
Indices: 325185--325242 Score: 55
Period size: 22 Copynumber: 2.5 Consensus size: 22
325175 GCTGAACCCT
325185 AATTTGAAATTTTATTTAAATTTA
1 AATTT-AAA-TTTATTTAAATTTA
* *
325209 AATTTAATTTTATTT-GATTTA
1 AATTTAAATTTATTTAAATTTA
*
325230 ATTTATAAATTTA
1 AATT-TAAATTTA
325243 AATTATCATT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 8 0.28
22 14 0.48
23 2 0.07
24 5 0.17
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (22 bp):
AATTTAAATTTATTTAAATTTA
Found at i:325248 original size:27 final size:27
Alignment explanation
Indices: 325193--325248 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
325183 CTAATTTGAA
* *
325193 ATTTTATTTAAATTTAAATTTAATTTT
1 ATTTGATTTAAATTTAAATTTAATATT
*
325220 ATTTGATTTAATTTATAAATTTAA-ATT
1 ATTTGATTTAAATT-TAAATTTAATATT
325247 AT
1 AT
325249 CATTAAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 16 0.64
28 9 0.36
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (27 bp):
ATTTGATTTAAATTTAAATTTAATATT
Found at i:325284 original size:40 final size:39
Alignment explanation
Indices: 325198--325306 Score: 98
Period size: 40 Copynumber: 2.7 Consensus size: 39
325188 TTGAAATTTT
** * *
325198 ATTTAAATTTAAATTTAATTTTATTTGATT-TAATTTATAA
1 ATTTAAATTTAAATAAAATATT-TTT-ATTATATTTTATAA
* *
325238 ATTTAAATTATCATTAAAAATATTTTATATTATATTTTAT-A
1 ATTTAAATT-TAAAT-AAAATATTTT-TATTATATTTTATAA
325279 A-TTAAATTTAAATAAAATATTTTTATTA
1 ATTTAAATTTAAATAAAATATTTTTATTA
325307 ATTAACTTGT
Statistics
Matches: 57, Mismatches: 8, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
37 5 0.09
38 10 0.18
39 3 0.05
40 16 0.28
41 10 0.18
42 13 0.23
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (39 bp):
ATTTAAATTTAAATAAAATATTTTTATTATATTTTATAA
Found at i:325711 original size:11 final size:11
Alignment explanation
Indices: 325695--325721 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
325685 ATTTTTAATT
325695 AATTAAATATA
1 AATTAAATATA
325706 AATTAAATATA
1 AATTAAATATA
325717 AATTA
1 AATTA
325722 TTAAATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
AATTAAATATA
Found at i:325726 original size:14 final size:14
Alignment explanation
Indices: 325691--325730 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
325681 TATTATTTTT
325691 AATTAATTAAATAT-
1 AATT-ATTAAATATA
325705 AA--ATTAAATATA
1 AATTATTAAATATA
325717 AATTATTAAATATA
1 AATTATTAAATATA
325731 TTATTTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
11 9 0.39
12 2 0.09
14 12 0.52
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AATTATTAAATATA
Found at i:325804 original size:21 final size:23
Alignment explanation
Indices: 325780--325822 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
325770 CATGTCATAT
*
325780 TTATTATA-TTATTTTT-TATAA
1 TTATTAAATTTATTTTTATATAA
325801 TTATTAAATTTATTTTTATATA
1 TTATTAAATTTATTTTTATATA
325823 TATTTAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
22 8 0.42
23 4 0.21
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
TTATTAAATTTATTTTTATATAA
Found at i:325812 original size:15 final size:15
Alignment explanation
Indices: 325794--325846 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
325784 TATATTATTT
325794 TTTATAATTATTAAA
1 TTTATAATTATTAAA
** *
325809 TTTATTTTTATATATA
1 TTTATAATTAT-TAAA
* *
325825 TTTAAAATTATCAAA
1 TTTATAATTATTAAA
325840 TTTATAA
1 TTTATAA
325847 AAATAATTTT
Statistics
Matches: 28, Mismatches: 9, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
15 17 0.61
16 11 0.39
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTATAATTATTAAA
Found at i:325826 original size:21 final size:22
Alignment explanation
Indices: 325787--325835 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
325777 TATTTATTAT
325787 ATTATTTTTTATAATTA-TTAAA
1 ATTA-TTTTTATAATTATTTAAA
*
325809 TTTATTTTTAT-ATATATTTAAA
1 ATTATTTTTATAAT-TATTTAAA
325831 ATTAT
1 ATTAT
325836 CAAATTTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 2 0.09
21 9 0.39
22 12 0.52
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
ATTATTTTTATAATTATTTAAA
Found at i:325832 original size:23 final size:22
Alignment explanation
Indices: 325788--325833 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
325778 ATTTATTATA
*
325788 TTATTTTTTATAATTATTAAAT
1 TTATTTTTTATAATTATAAAAT
325810 TTATTTTTATATATATT-TAAAAT
1 TTATTTTT-TATA-ATTATAAAAT
325833 T
1 T
325834 ATCAAATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 8 0.38
23 10 0.48
24 3 0.14
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TTATTTTTTATAATTATAAAAT
Found at i:325882 original size:13 final size:13
Alignment explanation
Indices: 325866--325895 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
325856 TATAATATTT
*
325866 TAATATATTTAAA
1 TAATATATTAAAA
325879 TAATATATTAAAA
1 TAATATATTAAAA
325892 TAAT
1 TAAT
325896 CACACTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
TAATATATTAAAA
Found at i:325966 original size:17 final size:17
Alignment explanation
Indices: 325940--325978 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
325930 TTTAAAATTT
325940 TTTAAATTAT-AATATAA
1 TTTAAATTATAAATA-AA
*
325957 TTTAACTTATAAATAAA
1 TTTAAATTATAAATAAA
325974 TTTAA
1 TTTAA
325979 TTAAAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (17 bp):
TTTAAATTATAAATAAA
Found at i:329870 original size:2 final size:2
Alignment explanation
Indices: 329863--329909 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
329853 AGAAGGTGCT
329863 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
329905 TA TA T
1 TA TA T
329910 TCTTTGATGG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:331560 original size:27 final size:26
Alignment explanation
Indices: 331493--331560 Score: 66
Period size: 27 Copynumber: 2.5 Consensus size: 26
331483 TATTTTATTA
* **
331493 TATTATAATTATATTTAAAATATTTTT
1 TATTATTATTAT-TTTAAAATATTAAT
331520 TATT-TATATTTATTTTAAAATATTAAT
1 TATTAT-TA-TTATTTTAAAATATTAAT
331547 TATTATTATGTATT
1 TATTATTAT-TATT
331561 ATACCTTAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
26 2 0.06
27 27 0.79
28 5 0.15
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (26 bp):
TATTATTATTATTTTAAAATATTAAT
Found at i:332457 original size:2 final size:2
Alignment explanation
Indices: 332452--332478 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
332442 TAGAAAAATA
332452 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 A
332479 AAGTGGGTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:332986 original size:16 final size:16
Alignment explanation
Indices: 332965--333014 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
332955 TTTATATTAT
* *
332965 TATTAATTATAATAAA
1 TATTAATAATAAAAAA
332981 TATTAATAATAAAAAA
1 TATTAATAATAAAAAA
*
332997 TA--AAAAATAAAAAA
1 TATTAATAATAAAAAA
333011 -ATTA
1 TATTA
333015 TTTTAATTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 1 0.03
14 11 0.38
15 1 0.03
16 16 0.55
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
TATTAATAATAAAAAA
Found at i:334224 original size:163 final size:165
Alignment explanation
Indices: 333964--334261 Score: 363
Period size: 163 Copynumber: 1.8 Consensus size: 165
333954 TATTTCTGTT
** * *
333964 TCTTTGTTAAACAATACTAAAAAGTATTATTATTGTACGAAAAACAATAATAAAAAACTTAATTT
1 TCTTTGTTAAACAATAC-AAAAAAAACTATTATTGTACGAAAAACAAAAATAAAAAACTTAATTT
* * * * * * *
334029 ATTTAATTTATATAATTTATTATTTTTAAAATATAATATTTAGTAAAGT-TAAAAATTAAAATTT
65 ATTCAATGTATATAATTTATAATTGTTAAAATATAACATTCAAT-AAGTATAAAAATTAAAATTT
334093 AATATTTATTATCTTTTCTCTACCTTCAACCCGGTTA
129 AATATTTATTATCTTTTCTCTACCTTCAACCCGGTTA
* * *
334130 TCTTTGTTAAACAATA-AAAAAAAACTATTATTGTAC-TAAAACAAAAATAAAAAGTATTTATTT
1 TCTTTGTTAAACAATACAAAAAAAACTATTATTGTACGAAAAACAAAAATAAAAA--ACTTAATT
* * * *
334193 TA-TCCATGTA-ATTATTTATAATTGTTAAAATATAACATTCAATGAGTATAAAATTTAAAATTT
64 TATTCAATGTATATAATTTATAATTGTTAAAATATAACATTCAATAAGTATAAAAATTAAAATTT
334256 AATATT
129 AATATT
334262 ATAATTTTTT
Statistics
Matches: 111, Mismatches: 18, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
162 3 0.03
163 62 0.56
164 22 0.20
165 8 0.07
166 16 0.14
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (165 bp):
TCTTTGTTAAACAATACAAAAAAAACTATTATTGTACGAAAAACAAAAATAAAAAACTTAATTTA
TTCAATGTATATAATTTATAATTGTTAAAATATAACATTCAATAAGTATAAAAATTAAAATTTAA
TATTTATTATCTTTTCTCTACCTTCAACCCGGTTA
Found at i:335761 original size:21 final size:21
Alignment explanation
Indices: 335735--335776 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
335725 TTAATATTTT
335735 TATATAAAT-TTAATTATAAAA
1 TATATAAATATTAA-TATAAAA
335756 TATATAAATATTAATATAAAA
1 TATATAAATATTAATATAAAA
335777 ATAATATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TATATAAATATTAATATAAAA
Found at i:335821 original size:37 final size:34
Alignment explanation
Indices: 335738--335822 Score: 82
Period size: 37 Copynumber: 2.4 Consensus size: 34
335728 ATATTTTTAT
* *
335738 ATAAATTTA-ATTATAAAATATATAAATATTAAT
1 ATAAATTTATATTATAAAATATATAAATAATAAA
* * *
335771 ATAAAAATAATATTTTAATAATATAATAAATAATAAA
1 AT-AAATTTATATTATAA-AATAT-ATAAATAATAAA
335808 ATAAATTTTATATTA
1 ATAAA-TTTATATTA
335823 AATCAGAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
33 2 0.05
34 5 0.13
35 6 0.15
36 8 0.21
37 18 0.46
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (34 bp):
ATAAATTTATATTATAAAATATATAAATAATAAA
Found at i:336057 original size:2 final size:2
Alignment explanation
Indices: 336052--336076 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
336042 CATAGAGAGT
336052 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
336077 TAGGATTGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:338361 original size:13 final size:13
Alignment explanation
Indices: 338343--338367 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
338333 TTAATAAGAT
338343 AATATATATTTTG
1 AATATATATTTTG
338356 AATATATATTTT
1 AATATATATTTT
338368 AAAAAATAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (13 bp):
AATATATATTTTG
Found at i:338662 original size:13 final size:13
Alignment explanation
Indices: 338641--338689 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
338631 TTCCTTATTT
*
338641 AAGAGAGAAAAAA
1 AAGAAAGAAAAAA
338654 AAGAAAGAAAAAA
1 AAGAAAGAAAAAA
* *
338667 CAA-TAAGAAAAAG
1 -AAGAAAGAAAAAA
338680 AAGAAAGAAA
1 AAGAAAGAAA
338690 GAGAAAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
12 2 0.07
13 26 0.87
14 2 0.07
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (13 bp):
AAGAAAGAAAAAA
Found at i:341656 original size:35 final size:35
Alignment explanation
Indices: 341617--341683 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
341607 ATCATATCCA
*
341617 AATGTATTGTTTCATGTTCATTATAATAATTTAAC
1 AATGTATTATTTCATGTTCATTATAATAATTTAAC
*
341652 AATGTGTTATTTCATGTTCATTATAATAATTT
1 AATGTATTATTTCATGTTCATTATAATAATTT
341684 TATGTTAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.33, C:0.07, G:0.09, T:0.51
Consensus pattern (35 bp):
AATGTATTATTTCATGTTCATTATAATAATTTAAC
Found at i:341738 original size:22 final size:22
Alignment explanation
Indices: 341693--341739 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
341683 TTATGTTAAA
*
341693 TTATTAAATGTGTTATATCGTG
1 TTATTAAATGTGTTATAACGTG
*
341715 TTATTAAAT-TGTCTATAACTTG
1 TTATTAAATGTGT-TATAACGTG
341737 TTA
1 TTA
341740 GAGCTCCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 3 0.14
22 19 0.86
ACGTcount: A:0.30, C:0.06, G:0.13, T:0.51
Consensus pattern (22 bp):
TTATTAAATGTGTTATAACGTG
Found at i:343775 original size:19 final size:19
Alignment explanation
Indices: 343744--343793 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
343734 AGGTATTTGA
*
343744 TATATTAATTATTTATAGATT
1 TATATT-ATTATTAATA-ATT
343765 TATA-TATTATTAATAATT
1 TATATTATTATTAATAATT
343783 TATATTATTAT
1 TATATTATTAT
343794 ATTTATTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 7 0.26
19 15 0.56
20 1 0.04
21 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (19 bp):
TATATTATTATTAATAATT
Found at i:343783 original size:26 final size:28
Alignment explanation
Indices: 343746--343805 Score: 79
Period size: 26 Copynumber: 2.2 Consensus size: 28
343736 GTATTTGATA
*
343746 TATTAATTATTTATA-GATT-TATATAT
1 TATTAATAATTTATATGATTATATATAT
* *
343772 TATTAATAATTTATATTATTATATTTAT
1 TATTAATAATTTATATGATTATATATAT
343800 TATTAA
1 TATTAA
343806 CTAAATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 14 0.48
27 3 0.10
28 12 0.41
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (28 bp):
TATTAATAATTTATATGATTATATATAT
Found at i:343984 original size:10 final size:11
Alignment explanation
Indices: 343980--344021 Score: 52
Period size: 10 Copynumber: 3.9 Consensus size: 11
343970 CCCTTCTCTT
343980 TCCTTTCCTTC
1 TCCTTTCCTTC
343991 -CCTTTCCTTCC
1 TCCTTTCCTT-C
*
344002 TGCTTTCC-TC
1 TCCTTTCCTTC
344012 TCCTTTCCTT
1 TCCTTTCCTT
344022 TTTAAGACAG
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
10 17 0.65
11 3 0.12
12 6 0.23
ACGTcount: A:0.00, C:0.45, G:0.02, T:0.52
Consensus pattern (11 bp):
TCCTTTCCTTC
Found at i:344506 original size:22 final size:22
Alignment explanation
Indices: 344469--344532 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
344459 ATAGTGGTGT
344469 TAAATTTTATAA-TTATATTTA
1 TAAATTTTATAATTTATATTTA
*
344490 -AAATATTTATAATTTATATTAA
1 TAAAT-TTTATAATTTATATTTA
* *
344512 TAAATTTTAAAATATATATTT
1 TAAATTTTATAATTTATATTT
344533 GTATCCTGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
20 4 0.11
21 7 0.19
22 21 0.58
23 4 0.11
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TAAATTTTATAATTTATATTTA
Found at i:348824 original size:39 final size:41
Alignment explanation
Indices: 348775--348861 Score: 108
Period size: 42 Copynumber: 2.1 Consensus size: 41
348765 TATATCATAT
* * *
348775 AAATATAAATTTTAAA-ATT-TTATA-ACATAAATTATTAAC
1 AAATAAAAATTTTAAATATTATTATATA-ATAAATTATAAAA
348814 AAATAAAAATTTTAAATATTATTATATTAATAAATTATAAAA
1 AAATAAAAATTTTAAATATTATTATA-TAATAAATTATAAAA
348856 AAATAA
1 AAATAA
348862 TACCAATGCA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
39 15 0.37
40 3 0.07
41 5 0.12
42 17 0.41
43 1 0.02
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (41 bp):
AAATAAAAATTTTAAATATTATTATATAATAAATTATAAAA
Found at i:351177 original size:18 final size:18
Alignment explanation
Indices: 351156--351205 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
351146 TATAATATAA
*
351156 ATTATTAATATATTAAAT
1 ATTATTAATATATAAAAT
351174 ATTATATAA-ATATAAAAT
1 ATTAT-TAATATATAAAAT
351192 -TTA-TAATATGATAA
1 ATTATTAATAT-ATAA
351206 TGATCGTCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
15 3 0.11
16 2 0.07
17 7 0.25
18 13 0.46
19 3 0.11
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (18 bp):
ATTATTAATATATAAAAT
Found at i:351196 original size:15 final size:15
Alignment explanation
Indices: 351138--351197 Score: 52
Period size: 15 Copynumber: 3.7 Consensus size: 15
351128 AATTTTTTTA
351138 AAAATTTATATAATAT
1 AAAATTTATA-AATAT
351154 -AAA-TTATTAATATATT
1 AAAATTTA-TAA-ATA-T
351170 AAATATTATATAAATAT
1 AAA-ATT-TATAAATAT
351187 AAAATTTATAA
1 AAAATTTATAA
351198 TATGATAATG
Statistics
Matches: 37, Mismatches: 0, Indels: 15
0.71 0.00 0.29
Matches are distributed among these distances:
14 4 0.11
15 13 0.35
16 4 0.11
17 6 0.16
18 4 0.11
19 4 0.11
20 2 0.05
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AAAATTTATAAATAT
Done.