Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008609.1 Hibiscus syriacus cultivar Beakdansim tig00111565_pilon, whole genome shotgun sequence
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: 282724
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
File 2 of 2
Found at i:182760 original size:40 final size:42
Alignment explanation
Indices: 182684--182762 Score: 110
Period size: 40 Copynumber: 1.9 Consensus size: 42
182674 TTTTATTAGA
*
182684 TTATATAAAATTAATTTAAATATTTATAAATTTAATTTATTT
1 TTATATAAAATTAATTTAAATATTTATAAATATAATTTATTT
*
182726 TTATGTAATAATTAA-TT-AATATTT-TAAATATAATTTA
1 TTATATAA-AATTAATTTAAATATTTATAAATATAATTTA
182763 ACATAAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
40 12 0.35
41 7 0.21
42 9 0.26
43 6 0.18
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (42 bp):
TTATATAAAATTAATTTAAATATTTATAAATATAATTTATTT
Found at i:183330 original size:2 final size:2
Alignment explanation
Indices: 183318--183377 Score: 95
Period size: 2 Copynumber: 30.5 Consensus size: 2
183308 CTTTATATTT
*
183318 TA TA TA AA 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
*
183360 TA TA TA TA T- TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA T
183378 GTTATAAATA
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:183527 original size:18 final size:17
Alignment explanation
Indices: 183504--183542 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
183494 TATTCAGTCT
* *
183504 ATTTTACAATTTTTTCA
1 ATTTTAAAATTATTTCA
183521 CATTTTAAAATTATTTCA
1 -ATTTTAAAATTATTTCA
183539 ATTT
1 ATTT
183543 AATCCCTCTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTTAAAATTATTTCA
Found at i:185226 original size:13 final size:13
Alignment explanation
Indices: 185182--185226 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
185172 TATTTTCTAT
185182 ATTAATTATAATC
1 ATTAATTATAATC
*
185195 CTTATATTATAAATC
1 ATTA-ATTAT-AATC
185210 -TTAATTATAATC
1 ATTAATTATAATC
185222 ATTAA
1 ATTAA
185227 ATTAATTTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
12 4 0.14
13 12 0.43
14 8 0.29
15 4 0.14
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (13 bp):
ATTAATTATAATC
Found at i:185861 original size:15 final size:14
Alignment explanation
Indices: 185837--185877 Score: 59
Period size: 15 Copynumber: 3.0 Consensus size: 14
185827 GTCACTCATG
185837 TTTA-ATTATATAC
1 TTTATATTATATAC
185850 TTATATATTATATAC
1 TT-TATATTATATAC
185865 TTTATA-TATATAC
1 TTTATATTATATAC
185878 ACACATGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 9 0.35
14 6 0.23
15 11 0.42
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (14 bp):
TTTATATTATATAC
Found at i:186000 original size:8 final size:8
Alignment explanation
Indices: 185984--186029 Score: 58
Period size: 8 Copynumber: 5.8 Consensus size: 8
185974 ATAGCATGAG
*
185984 TATACAAA
1 TATATAAA
185992 TATATAAA
1 TATATAAA
186000 TATAT-AA
1 TATATAAA
*
186007 TATATAAG
1 TATATAAA
186015 TATATAAA
1 TATATAAA
186023 CTATATA
1 -TATATA
186030 GTATATAGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
7 7 0.21
8 20 0.61
9 6 0.18
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (8 bp):
TATATAAA
Found at i:186008 original size:15 final size:15
Alignment explanation
Indices: 185990--186021 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
185980 TGAGTATACA
185990 AATATATAAATATAT
1 AATATATAAATATAT
*
186005 AATATATAAGTATAT
1 AATATATAAATATAT
186020 AA
1 AA
186022 ACTATATAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (15 bp):
AATATATAAATATAT
Found at i:186280 original size:16 final size:16
Alignment explanation
Indices: 186256--186346 Score: 73
Period size: 16 Copynumber: 5.8 Consensus size: 16
186246 TTTATATACT
*
186256 TATACTTTATACTTTA
1 TATATTTTATACTTTA
186272 TATATTTTATACTTTA
1 TATATTTTATACTTTA
*
186288 TATATATATATATA-TATA
1 TATAT-T-T-TATACTTTA
* *
186306 TATATATTATTC-TTA
1 TATATTTTATACTTTA
*
186321 TATA-TATATAC-TTA
1 TATATTTTATACTTTA
*
186335 TATATTATATAC
1 TATATTTTATAC
186347 ATATATTATA
Statistics
Matches: 62, Mismatches: 8, Indels: 11
0.77 0.10 0.14
Matches are distributed among these distances:
14 11 0.18
15 16 0.26
16 21 0.34
17 1 0.02
18 9 0.15
19 4 0.06
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (16 bp):
TATATTTTATACTTTA
Found at i:186291 original size:2 final size:2
Alignment explanation
Indices: 186286--186356 Score: 73
Period size: 2 Copynumber: 38.0 Consensus size: 2
186276 TTTTATACTT
*
186286 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA T- TC T- 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
*
186325 TA TA TA CT- TA TA TA T- TA TA TA CA TA TA T- TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
186357 AGTATAATGT
Statistics
Matches: 60, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
1 6 0.10
2 53 0.88
3 1 0.02
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:186295 original size:29 final size:29
Alignment explanation
Indices: 186238--186346 Score: 87
Period size: 31 Copynumber: 3.5 Consensus size: 29
186228 CATTGGCATG
*
186238 TTATATAGTTTATATAC-TTATACTTTATACT
1 TTATATA-TTT-TATACTTTATA-TATATACT
*
186269 TTATATATTTTATACTTTATATATATATAT
1 TTATATATTTTATACTTTATATATATA-CT
*
186299 ATATATATATATATTATTCTTATATATATATAC-
1 -T-TATATAT-T-TTATACTT-TATATATATACT
*
186332 TTATATATTATATAC
1 TTATATATTTTATAC
186347 ATATATTATA
Statistics
Matches: 65, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
29 14 0.22
30 10 0.15
31 15 0.23
32 8 0.12
33 1 0.02
34 7 0.11
35 10 0.15
ACGTcount: A:0.38, C:0.06, G:0.01, T:0.55
Consensus pattern (29 bp):
TTATATATTTTATACTTTATATATATACT
Found at i:186322 original size:21 final size:22
Alignment explanation
Indices: 186285--186352 Score: 75
Period size: 25 Copynumber: 3.0 Consensus size: 22
186275 ATTTTATACT
186285 TTATATA-TATATATATATATA
1 TTATATATTATATATATATATA
*
186306 TATATATTATTCTTATATATATATA
1 T-TATA-TATT-ATATATATATATA
*
186331 CTTATATATTATATACATATAT
1 -TTATATATTATATATATATAT
186353 TATAAGTATA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
21 1 0.03
22 4 0.10
23 12 0.31
24 5 0.13
25 16 0.41
26 1 0.03
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (22 bp):
TTATATATTATATATATATATA
Found at i:186387 original size:24 final size:24
Alignment explanation
Indices: 186342--186387 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
186332 TTATATATTA
*
186342 TATACATATATTATAAGTATAATG
1 TATACATATATTATAAGCATAATG
* * *
186366 TATACTTATATTGTATGCATAA
1 TATACATATATTATAAGCATAA
186388 GTACAATGTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (24 bp):
TATACATATATTATAAGCATAATG
Found at i:186525 original size:19 final size:18
Alignment explanation
Indices: 186501--186541 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
186491 ATATTTAGTC
*
186501 TATTTTACAACTTTTTTCA
1 TATTTTACAA-TTATTTCA
186520 TATTTTACAATTATTTCA
1 TATTTTACAATTATTTCA
186538 -ATTT
1 TATTT
186542 GATATCTCTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 4 0.19
18 7 0.33
19 10 0.48
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.59
Consensus pattern (18 bp):
TATTTTACAATTATTTCA
Found at i:187388 original size:2 final size:2
Alignment explanation
Indices: 187383--187412 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
187373 ACACACACAC
187383 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
187413 TCCCATTACA
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:192303 original size:13 final size:13
Alignment explanation
Indices: 192285--192309 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
192275 ATTTATTTTC
192285 TATATTATAAATT
1 TATATTATAAATT
192298 TATATTATAAAT
1 TATATTATAAAT
192310 AAATTAATTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TATATTATAAATT
Found at i:192364 original size:21 final size:21
Alignment explanation
Indices: 192340--192407 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
192330 TTTATTATTG
192340 AATTTATTATTATATAAAATT
1 AATTTATTATTATATAAAATT
* *
192361 AATTTAAATATT-TATAAATTT
1 AATTT-ATTATTATATAAAATT
* *
192382 AATTTATTTTTATGTAATAATT
1 AATTTATTATTATATAA-AATT
192404 AATT
1 AATT
192408 AATATTTTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
20 4 0.11
21 22 0.58
22 12 0.32
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (21 bp):
AATTTATTATTATATAAAATT
Found at i:192386 original size:42 final size:42
Alignment explanation
Indices: 192321--192427 Score: 123
Period size: 42 Copynumber: 2.6 Consensus size: 42
192311 AATTAATTTC
* *
192321 ATTAAATAATTTAT-TATTGAATTTATTATTATATAA-AATTA
1 ATTAAAT-ATTTATAAATTTAATTTATTATTATATAATAATTA
* *
192362 ATTTAAATATTTATAAATTTAATTTATTTTTATGTAATAATTA
1 A-TTAAATATTTATAAATTTAATTTATTATTATATAATAATTA
*
192405 ATT-AATATTT-TAAATATAATTTA
1 ATTAAATATTTATAAATTTAATTTA
192428 ACATAAAATT
Statistics
Matches: 58, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
40 12 0.21
41 14 0.24
42 26 0.45
43 6 0.10
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (42 bp):
ATTAAATATTTATAAATTTAATTTATTATTATATAATAATTA
Found at i:192987 original size:2 final size:2
Alignment explanation
Indices: 192975--193143 Score: 196
Period size: 2 Copynumber: 88.5 Consensus size: 2
192965 CTTTATATTT
*
192975 TA TA TA AA 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
193017 TA TA TA TA T- TA TA TA TA TA TA TA TA TA -A 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
*
193057 TA TA TA TA TA TA TA -A TA TA TA TA TA TG TA TA -A TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
193096 T- TA TA T- TA T- TA TG TCA TA TA CA TA TA CA TA T- TA TCA TA -A
1 TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA T-A TA TA
*
193135 CA TA TA TA T
1 TA TA TA TA T
193144 TTATTATGTA
Statistics
Matches: 144, Mismatches: 11, Indels: 24
0.80 0.06 0.13
Matches are distributed among these distances:
1 10 0.07
2 131 0.91
3 3 0.02
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (2 bp):
TA
Found at i:193190 original size:18 final size:17
Alignment explanation
Indices: 193167--193205 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
193157 TATTCAGTCT
* *
193167 ATTTTACAATTTTTTCA
1 ATTTTAAAATTATTTCA
193184 CATTTTAAAATTATTTCA
1 -ATTTTAAAATTATTTCA
193202 ATTT
1 ATTT
193206 AATCCCTCTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTTAAAATTATTTCA
Found at i:195907 original size:22 final size:23
Alignment explanation
Indices: 195877--195924 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
195867 TGGCATGTTA
*
195877 TATAGTTTATATA-CTTATACTT
1 TATACTTTATATATCTTATACTT
*
195899 TATACTTTATATATTTTATACTT
1 TATACTTTATATATCTTATACTT
195922 TAT
1 TAT
195925 TATATATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.31, C:0.08, G:0.02, T:0.58
Consensus pattern (23 bp):
TATACTTTATATATCTTATACTT
Found at i:195916 original size:16 final size:16
Alignment explanation
Indices: 195883--195968 Score: 74
Period size: 16 Copynumber: 5.5 Consensus size: 16
195873 GTTATATAGT
*
195883 TTATATAC-TTATA-C
1 TTATATACTTTATATA
195897 TT-TATACTTTATATA
1 TTATATACTTTATATA
*
195912 TTTTATACTTTATTATA
1 TTATATACTTTA-TATA
* *
195929 TATATATA-TATATTTA
1 T-TATATACTTTATATA
195945 TATATATAC-TTATATA
1 T-TATATACTTTATATA
195961 TTATATAC
1 TTATATAC
195969 ATATATAAGT
Statistics
Matches: 60, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
13 5 0.08
14 7 0.12
15 9 0.15
16 26 0.43
17 8 0.13
18 5 0.08
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (16 bp):
TTATATACTTTATATA
Found at i:195930 original size:2 final size:2
Alignment explanation
Indices: 195925--196121 Score: 100
Period size: 2 Copynumber: 102.5 Consensus size: 2
195915 TATACTTTAT
*
195925 TA TA TA TA TA TA TA TA TT TA TA TA TA TA CT- TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* * * * *
195966 TA CA TA TA TA -A GTA TA -A TG TA TA CT- TA T- TG TA TG CA TA -A
1 TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
* * * *
196005 GTA CA -A TG TA CA T- TA TA TA TA TA TA CA TA TA T- TA TCA TA -A
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
* * * *
196045 CA T- TCA TCA TA CA TA T- TA TA TA CA TA TA TA T- TA T- TA TG TA
1 TA TA T-A T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
196085 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
196122 TTAGTCTATT
Statistics
Matches: 149, Mismatches: 25, Indels: 42
0.69 0.12 0.19
Matches are distributed among these distances:
1 15 0.10
2 124 0.83
3 10 0.07
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.46
Consensus pattern (2 bp):
TA
Found at i:196152 original size:19 final size:18
Alignment explanation
Indices: 196128--196168 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
196118 ATATTTAGTC
*
196128 TATTTTACAACTTTTTTCA
1 TATTTTACAA-TTATTTCA
196147 TATTTTACAATTATTTCA
1 TATTTTACAATTATTTCA
196165 -ATTT
1 TATTT
196169 GATATCTCTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 4 0.19
18 7 0.33
19 10 0.48
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.59
Consensus pattern (18 bp):
TATTTTACAATTATTTCA
Found at i:206670 original size:14 final size:13
Alignment explanation
Indices: 206648--206685 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
206638 ATTTTCTATA
206648 TTAATTATAATTC
1 TTAATTATAATTC
*
206661 TTATATTATAAATC
1 TTA-ATTATAATTC
206675 TTAATTATAAT
1 TTAATTATAAT
206686 CATTAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (13 bp):
TTAATTATAATTC
Found at i:206691 original size:13 final size:12
Alignment explanation
Indices: 206648--206691 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 12
206638 ATTTTCTATA
206648 TTAATTATAATTC
1 TTAATTATAA-TC
206661 TTATATTATAAATC
1 TTA-ATTAT-AATC
206675 TTAATTATAATC
1 TTAATTATAATC
206687 ATTAA
1 -TTAA
206692 ATTAATTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 4 0.14
13 12 0.43
14 10 0.36
15 2 0.07
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (12 bp):
TTAATTATAATC
Found at i:207371 original size:2 final size:2
Alignment explanation
Indices: 207359--207412 Score: 83
Period size: 2 Copynumber: 27.5 Consensus size: 2
207349 CTTTATATTT
*
207359 TA TA TA AA 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
*
207401 TA T- TA TA CA TA T
1 TA TA TA TA TA TA T
207413 GTTATAAATA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:207554 original size:18 final size:17
Alignment explanation
Indices: 207531--207569 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
207521 TATTCAGTCT
* *
207531 ATTTTACAATTTTTTCA
1 ATTTTAAAATTATTTCA
207548 CATTTTAAAATTATTTCA
1 -ATTTTAAAATTATTTCA
207566 ATTT
1 ATTT
207570 AATCCCTCTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTTAAAATTATTTCA
Found at i:209897 original size:13 final size:15
Alignment explanation
Indices: 209868--209900 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
209858 TGTTTAATTG
209868 TATACTTATATATTA
1 TATACTTATATATTA
209883 TATACTT-TATA-TA
1 TATACTTATATATTA
209896 TATAC
1 TATAC
209901 CCACATGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
14 4 0.22
15 7 0.39
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (15 bp):
TATACTTATATATTA
Found at i:209984 original size:8 final size:8
Alignment explanation
Indices: 209968--210013 Score: 58
Period size: 8 Copynumber: 5.8 Consensus size: 8
209958 ATAGCATGAG
*
209968 TATACAAA
1 TATATAAA
209976 TATATAAA
1 TATATAAA
209984 TATAT-AA
1 TATATAAA
*
209991 TATATAAG
1 TATATAAA
209999 TATATAAA
1 TATATAAA
210007 CTATATA
1 -TATATA
210014 GTATATAGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
7 7 0.21
8 20 0.61
9 6 0.18
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (8 bp):
TATATAAA
Found at i:209992 original size:15 final size:15
Alignment explanation
Indices: 209974--210005 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
209964 TGAGTATACA
209974 AATATATAAATATAT
1 AATATATAAATATAT
*
209989 AATATATAAGTATAT
1 AATATATAAATATAT
210004 AA
1 AA
210006 ACTATATAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (15 bp):
AATATATAAATATAT
Found at i:210262 original size:16 final size:16
Alignment explanation
Indices: 210238--210274 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
210228 TTTATATACT
*
210238 TATACTTTATACTTTA
1 TATATTTTATACTTTA
210254 TATATTTTATACTTTA
1 TATATTTTATACTTTA
210270 TATAT
1 TATAT
210275 ATATATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.59
Consensus pattern (16 bp):
TATATTTTATACTTTA
Found at i:210265 original size:29 final size:28
Alignment explanation
Indices: 210220--210327 Score: 96
Period size: 29 Copynumber: 3.8 Consensus size: 28
210210 CATTGGCATG
210220 TTATATAGTTTATATACTTATACTTTATACT
1 TTATATA-TTT-TATACTTATA-TTTATACT
*
210251 TTATATATTTTATACTT-TATATATA-T
1 TTATATATTTTATACTTATATTTATACT
* * *
210277 ATATATATATTATTCTTATATATATATAC-
1 TTATATATTTTATACTTATAT-T-TATACT
* *
210306 TTATATATTATATACATATATT
1 TTATATATTTTATACTTATATT
210328 ATAAGTCTAA
Statistics
Matches: 63, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
26 15 0.24
27 8 0.13
28 3 0.05
29 27 0.43
30 3 0.05
31 7 0.11
ACGTcount: A:0.37, C:0.06, G:0.01, T:0.56
Consensus pattern (28 bp):
TTATATATTTTATACTTATATTTATACT
Found at i:210273 original size:2 final size:2
Alignment explanation
Indices: 210268--210330 Score: 57
Period size: 2 Copynumber: 34.0 Consensus size: 2
210258 TTTTATACTT
*
210268 TA TA TA TA TA TA TA TA TA T- TA T- TC T- TA TA TA TA TA TA CT-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
*
210307 TA TA TA T- TA TA TA CA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
210331 AGTCTAATGT
Statistics
Matches: 52, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
1 6 0.12
2 45 0.87
3 1 0.02
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:210317 original size:13 final size:13
Alignment explanation
Indices: 210232--210367 Score: 81
Period size: 13 Copynumber: 10.3 Consensus size: 13
210222 ATATAGTTTA
210232 TATACTTATACT-T
1 TATACTTATA-TAT
210245 TATACTTTATATATTT
1 TATAC-TTATATA--T
210261 TATACTT-TATAT
1 TATACTTATATAT
210273 ATATA-TATATATAT
1 -TATACT-TATATAT
*
210287 TATTCTTATATAT
1 TATACTTATATAT
210300 ATATACTTATATAT
1 -TATACTTATATAT
*
210314 TATA-TACATATAT
1 TATACT-TATATAT
** *
210327 TATAAGTCTA-AT
1 TATACTTATATAT
210339 GTATACTTATAT-T
1 -TATACTTATATAT
210352 GTATAC--ATATAT
1 -TATACTTATATAT
210364 TATA
1 TATA
210368 TATTATTCTT
Statistics
Matches: 100, Mismatches: 9, Indels: 30
0.72 0.06 0.22
Matches are distributed among these distances:
11 8 0.08
12 6 0.06
13 51 0.51
14 27 0.27
15 2 0.02
16 6 0.06
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.52
Consensus pattern (13 bp):
TATACTTATATAT
Found at i:215190 original size:24 final size:24
Alignment explanation
Indices: 215173--215222 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
215163 ATCCTTGAAT
215173 ATTTTAGTTTAACCATCCAAGAAG
1 ATTTTAGTTTAACCATCCAAGAAG
215197 ATTTTAGTTTAACCATCCAAGAAG
1 ATTTTAGTTTAACCATCCAAGAAG
215221 AT
1 AT
215223 ATATATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (24 bp):
ATTTTAGTTTAACCATCCAAGAAG
Found at i:216415 original size:19 final size:20
Alignment explanation
Indices: 216391--216431 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 20
216381 CGAAAAATGT
216391 TATATTTTTA-ATTAAAAAA
1 TATATTTTTATATTAAAAAA
216410 TATATTTTTATTATTAAAAAA
1 TATATTTTTA-TATTAAAAAA
216431 T
1 T
216432 TAAAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 10 0.50
21 10 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TATATTTTTATATTAAAAAA
Found at i:220829 original size:13 final size:13
Alignment explanation
Indices: 220811--220835 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
220801 CATAAAAATA
220811 ATTAAATACAAAC
1 ATTAAATACAAAC
220824 ATTAAATACAAA
1 ATTAAATACAAA
220836 ACGATACAAT
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:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (13 bp):
ATTAAATACAAAC
Found at i:230282 original size:18 final size:19
Alignment explanation
Indices: 230259--230295 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
230249 CTGCGCTTAT
230259 TTTTCAAAATCAAA-ATAG
1 TTTTCAAAATCAAAGATAG
230277 TTTTCAAAATCAAAGATAG
1 TTTTCAAAATCAAAGATAG
230296 ACTTTGGTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.49, C:0.11, G:0.08, T:0.32
Consensus pattern (19 bp):
TTTTCAAAATCAAAGATAG
Found at i:252450 original size:36 final size:33
Alignment explanation
Indices: 252406--252472 Score: 82
Period size: 34 Copynumber: 1.9 Consensus size: 33
252396 TATAAGAATT
252406 ACAATCTCTCTCGATCTAACAAG-GAGAAAACAATG
1 ACAATCTCTCTCGA--TAA-AAGAGAGAAAACAATG
*
252441 ACAATTCTCTCTTGATAAAAGAGAGAAAACAA
1 ACAA-TCTCTCTCGATAAAAGAGAGAAAACAA
252473 CTCTCAAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
33 3 0.10
34 13 0.45
35 4 0.14
36 9 0.31
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.21
Consensus pattern (33 bp):
ACAATCTCTCTCGATAAAAGAGAGAAAACAATG
Found at i:260695 original size:5 final size:5
Alignment explanation
Indices: 260671--260713 Score: 50
Period size: 5 Copynumber: 8.0 Consensus size: 5
260661 CCGTCTAGTC
*
260671 TCGTC TCGTG TCGTG TCGTG TCGTGG TCGTGG TCGTGG TCGTG
1 TCGTG TCGTG TCGTG TCGTG TCGT-G TCGT-G TCGT-G TCGTG
260714 GTAATACGTG
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
5 19 0.53
6 17 0.47
ACGTcount: A:0.00, C:0.21, G:0.42, T:0.37
Consensus pattern (5 bp):
TCGTG
Found at i:260701 original size:6 final size:6
Alignment explanation
Indices: 260676--260715 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
260666 TAGTCTCGTC
260676 TCGT-G TCGT-G TCGT-G TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
260716 AATACGTGTC
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 14 0.41
6 20 0.59
ACGTcount: A:0.00, C:0.17, G:0.45, T:0.38
Consensus pattern (6 bp):
TCGTGG
Found at i:263072 original size:111 final size:110
Alignment explanation
Indices: 262875--263167 Score: 410
Period size: 111 Copynumber: 2.6 Consensus size: 110
262865 AACTTTCAAA
* ** * *
262875 AAAGTATCGATCATTTTTATAAAAAGTATTTATACTTTCAACATATTAGATAAA-TTTACCGGTT
1 AAAGTATCGATCATTTTTAT-AAAAGGATCGATACTTTCAACATATAAGGTAAATTTTACC-GTT
* *
262939 TTGTAATAATGAAACTGATTTTGTCATATTTTTACCTGTTATACTGT
64 TTGTCATAATGAAACTGATTTTGTCATATTTTTACCTGTTATACTAT
* * * *
262986 AAAGTATCTATCTTTTTTATAAAAGGATCGATATTTTCAACATATAAGGTAAATTTTATCGTTTT
1 AAAGTATCGATCATTTTTATAAAAGGATCGATACTTTCAACATATAAGGTAAATTTTACCG-TTT
* * *
263051 TGTCATAATGAAACTGGTTTTGTCATATTTTTACTTGTTATATTAT
65 TGTCATAATGAAACTGATTTTGTCATATTTTTACCTGTTATACTAT
263097 AAAGTATCGATCATTTTTATAAAAGGATCGATACTTTCAACATATCAA-GTAAATTTTACCGTTT
1 AAAGTATCGATCATTTTTATAAAAGGATCGATACTTTCAACATAT-AAGGTAAATTTTACCGTTT
263161 TGTCATA
65 TGTCATA
263168 TTTTTACTTG
Statistics
Matches: 161, Mismatches: 18, Indels: 7
0.87 0.10 0.04
Matches are distributed among these distances:
110 38 0.24
111 121 0.75
112 2 0.01
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.44
Consensus pattern (110 bp):
AAAGTATCGATCATTTTTATAAAAGGATCGATACTTTCAACATATAAGGTAAATTTTACCGTTTT
GTCATAATGAAACTGATTTTGTCATATTTTTACCTGTTATACTAT
Found at i:264006 original size:111 final size:111
Alignment explanation
Indices: 263717--264006 Score: 406
Period size: 111 Copynumber: 2.6 Consensus size: 111
263707 AAATTTTACC
* * *
263717 GGTTTTGTCATATTTTTACCTGTTTTATTATAAAGTATCTATCTTTTTTATAAAAGGATCGATAC
1 GGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCTATCATTTTTATAAAAGGATCGATAC
263782 TTTCAACATATAAGGTAAATTTTACCCTTTTTATCATAATGAAACT
66 TTTCAACATATAAGGTAAATTTTACCCTTTTTATCATAATGAAACT
* * * * * *
263828 GATTTTGTCATATTTTTACCTGGTATATTGTAAAGTGTTTATCCTTTTTATAAAAGGATCGAAAC
1 GGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCTATCATTTTTATAAAAGGATCGATAC
*
263893 TTTCAACATATTAA-GTAAATTTTACCCTTTTTGTCATAATGAAACT
66 TTTCAACATA-TAAGGTAAATTTTACCCTTTTTATCATAATGAAACT
* * * *
263939 GGTTTTGTCATATTTTTACCTATTATATTGTATAA-TATCGATACATTTTTAT-AAAGTATTGAT
1 GGTTTTGTCATATTTTTACCTGTTATATTGTA-AAGTATCTAT-CATTTTTATAAAAGGATCGAT
264002 ACTTT
64 ACTTT
264007 ATATACGCTA
Statistics
Matches: 157, Mismatches: 19, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
111 144 0.92
112 13 0.08
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.47
Consensus pattern (111 bp):
GGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCTATCATTTTTATAAAAGGATCGATAC
TTTCAACATATAAGGTAAATTTTACCCTTTTTATCATAATGAAACT
Found at i:264223 original size:783 final size:763
Alignment explanation
Indices: 262551--264698 Score: 3154
Period size: 783 Copynumber: 2.7 Consensus size: 763
262541 TGTTCATACT
* *
262551 TATTTCACTGTGAACAACATTAATTTAAGGTTATCTTTTGTGTGAGATTTAAGATATTAATTTAG
1 TATTTCACTGTGAAAAACATTAATTTAAGGTTATCTTTTGAGTGAGATTTAAGATATTAATTTAG
* *
262616 TAATTATACGCTTCTAATGATTTATTTTTTATGTTATGGTATATATTATTATTAAATTAAAAACA
66 TAATTATACGCGTCTAATGATTTATTTTTTATGTTATGGTATATACTATTATTAAATTAAAAACA
*
262681 ATAAACATAGATATTACATATTTATCATTATCTTTGGTTAAAATTGTTAAATTTAAATTCTAAAT
131 ATAAACATAGATATTACATATTTATTATTATCTTTGGTTAAAATTGTTAAATTTAAATTCTAAAT
*
262746 AATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAAATAAAATTATTAAATTAATA
196 AATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATA
262811 TTGTAGGTGGAAAACATGAAACACTATT-AAAAATTGTTGAAACATAAATTACATAACTTTCAAA
261 TTGTAGGTGGAAAACATGAAACACTATTAAAAAATT-TTGAAACATAAATTACATAACTTTCAAA
*
262875 AAAGTATCGATCATTTTTATAAAAAGTATTTATACTTTCAACATATTAGATAAA-TTTACCGGTT
325 AAAGTATCGATCATTTTTATAAAAAGTATTTATACTTTCAACATATCAGATAAATTTTACC----
*
262939 TTGTAATAATGAAACTGATTTTGTCATATTTTTACCTGTTATACTGTAAAGTATCTATCTTTTTT
386 ---------TG-----G-TTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCTATCTTTTTT
* * *
263004 ATAAAAGGATCGATATTTTCAACATATAAGGTAAATTTTATCGTTTTTGTCATAATGAAACTGGT
436 ATAAAAGGATCGATACTTTCAACATATAAGGTAAATTTTACCATTTTTGTCATAATGAAACTGGT
* * *
263069 TTTGTCATATTTTTACTTGTTATATTATAAAGTATCGATCATTTTTATAAAAGGATCGATACTTT
501 TTTGTCATATTTTTACCTGTTATATTGTAAAGTATCGATCATTTTTATAAAAGGATCGAAACTTT
* *
263134 CAACATATCAAGTAAATTTTACCGTTTTGTCATATTTTTACTTGTTATATTGTAAAATATCGATA
566 CAACATATCAAGTAAATTTTACCGTTTTGTCATATTTTTACCTATTATATTGTAAAATATCGATA
**
263199 CATTTTTATAAAGTATCGATACTTTATAGGTGCTATTACTCCTTTTCTTTTAAATTCCAAAAGTG
631 CATTTTTATAAAGTATCGATACTTTATAGACGCTATTACTCCTTTTCTTTTAAATTCCAAAAGTG
263264 TCGATACTTATTTAAATGGAATCGATACTTTCAACATATCTGGTAGGTAGTTTAATGTAATAGGT
696 TCGATACTTATTTAAATGGAATCGATACTTTCAACATATCTGGTAGGTAGTTTAATGTAATAGGT
263329 AAG
761 AAG
* *
263332 TATTTCACTGTGAAAAATATTAATTTAAGGTTATCTTTTGAGTGATATTTAAGATATTAATTTAG
1 TATTTCACTGTGAAAAACATTAATTTAAGGTTATCTTTTGAGTGAGATTTAAGATATTAATTTAG
*
263397 TAATTATACGCGTTTAATGATTTATTTTTTATGTTATGGTATATACTATTATTAAATTAAAAACA
66 TAATTATACGCGTCTAATGATTTATTTTTTATGTTATGGTATATACTATTATTAAATTAAAAACA
263462 ATAAACATAGATATTACATATTTATTATTATCTTTGGTTAAAATTGTTAAATTTAAATTCTAAAT
131 ATAAACATAGATATTACATATTTATTATTATCTTTGGTTAAAATTGTTAAATTTAAATTCTAAAT
* *
263527 AATATTTTATAAAATATCAAAATAATCAAATAATTTGTTGTGTAAATGAAATTATTAAATTAATA
196 AATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATA
* *
263592 TTGTATGTGGAAAACATGAAACACTATTAAAAAATTTTGAAACTTAAATTACATAACTTTCAAAA
261 TTGTAGGTGGAAAACATGAAACACTATTAAAAAATTTTGAAACATAAATTACATAACTTTCAAAA
* * * *
263657 AAATATCGATCTTTTTTATAAAAAGTATTTATACTTTCAATATATCAGGTAAATTTTACC-GGTT
326 AAGTATCGATCATTTTTATAAAAAGTATTTATACTTTCAACATATCAGATAAATTTTACCTGGTT
* *
263721 TTGTCATATTTTTACCTGTTTTATTATAAAGTATCTATCTTTTTTATAAAAGGATCGATACTTTC
391 TTGTCATATTTTTACCTGTTATATTGTAAAGTATCTATCTTTTTTATAAAAGGATCGATACTTTC
* * * *
263786 AACATATAAGGTAAATTTTACCCTTTTTATCATAATGAAACTGATTTTGTCATATTTTTACCTGG
456 AACATATAAGGTAAATTTTACCATTTTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGT
* ** * *
263851 TATATTGTAAAGTGTTTATCCTTTTTATAAAAGGATCGAAACTTTCAACATATTAAGTAAATTTT
521 TATATTGTAAAGTATCGATCATTTTTATAAAAGGATCGAAACTTTCAACATATCAAGTAAATTTT
*
263916 ACCCTTTTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTATTATATTGTATAATATCGAT
586 A----------C---------C--GTTTTGTCATATTTTTACCTATTATATTGTAAAATATCGAT
* * *
263981 ACATTTTTATAAAGTATTGATACTTTATATACGCTATTACTGCTTTT-TTTATAAATTCCAAAAG
630 ACATTTTTATAAAGTATCGATACTTTATAGACGCTATTACTCCTTTTCTTT-TAAATTCCAAAAG
264045 TGTCGATACTTATTTAAATGGAATCGATACTTTCAACATATCTGGTAGGTAGTTTAATGTAATAG
694 TGTCGATACTTATTTAAATGGAATCGATACTTTCAACATATCTGGTAGGTAGTTTAATGTAATAG
264110 GTAAG
759 GTAAG
* *
264115 TATTTCACTGTGAAAAACATTAATTTATGGTTATCTTTTGAGTGAGATTTAAGATATTAGTTTAG
1 TATTTCACTGTGAAAAACATTAATTTAAGGTTATCTTTTGAGTGAGATTTAAGATATTAATTTAG
* *
264180 TAATTATACGCGTCTAATGATTTATTTTGTATGTTACGGTATATACTATTATTAAATTAAAAACA
66 TAATTATACGCGTCTAATGATTTATTTTTTATGTTATGGTATATACTATTATTAAATTAAAAACA
264245 ATAAACATAGATATTACATATTTATTATTATCTTTGGTTAAAATTGTTAAATTTAAATTCTAAAT
131 ATAAACATAGATATTACATATTTATTATTATCTTTGGTTAAAATTGTTAAATTTAAATTCTAAAT
* * *
264310 AATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTATTA
196 AATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATA
* *
264375 TTGTAGGTGGAAAATATGAAACACTATTAAAAAATTTTAAAACATAAATTACATAACTTTCAAAA
261 TTGTAGGTGGAAAACATGAAACACTATTAAAAAATTTTGAAACATAAATTACATAACTTTCAAAA
* *
264440 AAGTATCGATCATTTTTATAAAAAGTATCTATAGTTTCAACATATCAGATAAATTTTACCGGTTT
326 AAGTATCGATCATTTTTATAAAAAGTATTTATACTTTCAACATATCAGAT-AA----A----TTT
* *
264505 TATCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTTTCTATCCTTTTTA
382 TA-C---------CTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCTATCTTTTTTA
*
264570 TAAAAGGATCGATACTTTCAACATATAAGGTAAATTTTACTATTTTTGTCATAATGAAACTGGTT
437 TAAAAGGATCGATACTTTCAACATATAAGGTAAATTTTACCATTTTTGTCATAATGAAACTGGTT
* * *
264635 TTGTCATATTTTTACCTGTTATATTGTAAAATATCGATACATTTTTAT-AAAGTATCGATACTTT
502 TTGTCATATTTTTACCTGTTATATTGTAAAGTATCGAT-CATTTTTATAAAAGGATCGAAACTTT
264699 ATAGGCACTA
Statistics
Matches: 1241, Mismatches: 81, Indels: 68
0.89 0.06 0.05
Matches are distributed among these distances:
762 181 0.15
763 1 0.00
768 1 0.00
772 1 0.00
781 353 0.28
782 16 0.01
783 516 0.42
784 2 0.00
788 1 0.00
792 5 0.00
793 1 0.00
802 1 0.00
803 154 0.12
804 8 0.01
ACGTcount: A:0.37, C:0.09, G:0.11, T:0.43
Consensus pattern (763 bp):
TATTTCACTGTGAAAAACATTAATTTAAGGTTATCTTTTGAGTGAGATTTAAGATATTAATTTAG
TAATTATACGCGTCTAATGATTTATTTTTTATGTTATGGTATATACTATTATTAAATTAAAAACA
ATAAACATAGATATTACATATTTATTATTATCTTTGGTTAAAATTGTTAAATTTAAATTCTAAAT
AATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATA
TTGTAGGTGGAAAACATGAAACACTATTAAAAAATTTTGAAACATAAATTACATAACTTTCAAAA
AAGTATCGATCATTTTTATAAAAAGTATTTATACTTTCAACATATCAGATAAATTTTACCTGGTT
TTGTCATATTTTTACCTGTTATATTGTAAAGTATCTATCTTTTTTATAAAAGGATCGATACTTTC
AACATATAAGGTAAATTTTACCATTTTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGT
TATATTGTAAAGTATCGATCATTTTTATAAAAGGATCGAAACTTTCAACATATCAAGTAAATTTT
ACCGTTTTGTCATATTTTTACCTATTATATTGTAAAATATCGATACATTTTTATAAAGTATCGAT
ACTTTATAGACGCTATTACTCCTTTTCTTTTAAATTCCAAAAGTGTCGATACTTATTTAAATGGA
ATCGATACTTTCAACATATCTGGTAGGTAGTTTAATGTAATAGGTAAG
Found at i:264634 original size:111 final size:112
Alignment explanation
Indices: 264438--264698 Score: 366
Period size: 111 Copynumber: 2.3 Consensus size: 112
264428 TAACTTTCAA
* * * *
264438 AAAAGTATCGAT-CATTTTTATAAAAAGTATCTATAGTTTCAACATATCAGATAAATTTTACCGG
1 AAAA-TATCGATACATTTTTAT-AAAAGTATCGATACTTTCAACATATAAGATAAATTTTACCAG
264502 TTTTATCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
64 TTTTATCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
* * * * * * * *
264551 AAAGTTTCTAT-CCTTTTTATAAAAGGATCGATACTTTCAACATATAAGGTAAATTTTACTATTT
1 AAAATATCGATACATTTTTATAAAAGTATCGATACTTTCAACATATAAGATAAATTTTACCAGTT
*
264615 TTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
66 TTATCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
264662 AAAATATCGATACATTTTTAT-AAAGTATCGATACTTT
1 AAAATATCGATACATTTTTATAAAAGTATCGATACTTT
264699 ATAGGCACTA
Statistics
Matches: 129, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
111 105 0.81
112 21 0.16
113 3 0.02
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44
Consensus pattern (112 bp):
AAAATATCGATACATTTTTATAAAAGTATCGATACTTTCAACATATAAGATAAATTTTACCAGTT
TTATCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
Found at i:265112 original size:692 final size:690
Alignment explanation
Indices: 263748--265372 Score: 2585
Period size: 692 Copynumber: 2.4 Consensus size: 690
263738 GTTTTATTAT
* * * * *
263748 AAAGTATCTATCTTTTTTAT-AAAAGGATCGATACTTTCAACATATAAGGTAAATTTTACCCTTT
1 AAAGTATCGATCATTTTTATAAAAAGTATCTATACTTTCAACATATCAGGTAAATTTTA-CC-TT
* *
263812 TTATCATAATGAAACTGATTTTGTCATATTTTTACCTGGTATATTGTAAAGTGTT-TATCCTTTT
64 TTATCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGT-TTCTATCCTTTT
* *
263876 TATAAAAGGATCGAAACTTTCAACATATTAA-GTAAATTTTACCCTTTTTGTCATAATGAAACTG
128 TATAAAAGGATCGATACTTTCAACATA-TAAGGTAAATTTTACCATTTTTGTCATAATGAAACTG
* * *
263940 GTTTTGTCATATTTTTACCTATTATATTGTATAATATCGATACATTTTTATAAAGTATTGATACT
192 GTTTTGTCATATTTTTACCTGTTATATTGTAAAATATCGATACATTTTTATAAAGTATCGATACT
* * *
264005 TTATATACGCTATTACTGCTTTTTTTATAAATTCCAAAAGTGTCGATACTTATTTAAATGGAATC
257 TTATAGACACTATTACTGCTTTTTTTATAAATTCCAAAAGTGTCGATACTTATTTAAATGAAATC
*
264070 GATACTTTCAACATATCTGGTAGGTAGTTTAATGTAATAGGTAAGTATTTCACTGTGAAAAACAT
322 GATACTTTCAACATATCTGGTAGGTAGTTTAATGTAATAGGTAAGTATTTCACTGTAAAAAACAT
*
264135 TAATTTATGGTTATCTTTTGAGTGAGATTTAAGATATTAGTTTAGTAATTATACGCGTCTAATGA
387 TAATTTAAGGTTATCTTTTGAGTGAGATTTAAGATATTAGTTTAGTAATTATACGCGTCTAATGA
264200 TTTATTTTGTATGTTACGGTATATACTATTATTAAATTAAAAACAATAAACATAGATATTACATA
452 TTTATTTTGTATGTTACGGTATATACTATTATTAAATTAAAAACAATAAACATAGATATTACATA
* * *
264265 TTTATTATTATCTTTGGTTAAAATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATAAA
517 TTTATTATTATATTTGGTTAAAATTATTAAATTTAAATTATAAATAATATTTTATAAAATATAAA
* *
264330 AACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTATTATTGTAGGTGGAAAATATGAA
582 AACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAA
264395 ACACTATTAAAAAATTTTAAAACATAAATTACATAACTTTCAAA
647 ACACTATTAAAAAATTTTAAAACATAAATTACATAACTTTCAAA
* *
264439 AAAGTATCGATCATTTTTATAAAAAGTATCTATAGTTTCAACATATCAGATAAATTTTACCGGTT
1 AAAGTATCGATCATTTTTATAAAAAGTATCTATACTTTCAACATATCAGGTAAATTTTACC--TT
264504 TTATCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTTTCTATCCTTTTT
64 TTATCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTTTCTATCCTTTTT
*
264569 ATAAAAGGATCGATACTTTCAACATATAAGGTAAATTTTACTATTTTTGTCATAATGAAACTGGT
129 ATAAAAGGATCGATACTTTCAACATATAAGGTAAATTTTACCATTTTTGTCATAATGAAACTGGT
264634 TTTGTCATATTTTTACCTGTTATATTGTAAAATATCGATACATTTTTATAAAGTATCGATACTTT
194 TTTGTCATATTTTTACCTGTTATATTGTAAAATATCGATACATTTTTATAAAGTATCGATACTTT
*
264699 ATAGGCACTATTACTGCTTTTCTTT-TAAATTCCAAAAGTGTCGATACTTATTTAAATGAAATCG
259 ATAGACACTATTACTGCTTTT-TTTATAAATTCCAAAAGTGTCGATACTTATTTAAATGAAATCG
*
264763 ATACTTTCAACATATCTGGTAGGTAGTTTAATGTAATAGGTAAGTATTTCACTGTAAAAAATATT
323 ATACTTTCAACATATCTGGTAGGTAGTTTAATGTAATAGGTAAGTATTTCACTGTAAAAAACATT
* * *
264828 AATTTAAGGTTATCTTTTTAGTGATATTTAAGATATTATTTTAGTAATTATACGCGTCTAATGAT
388 AATTTAAGGTTATCTTTTGAGTGAGATTTAAGATATTAGTTTAGTAATTATACGCGTCTAATGAT
* *
264893 TTATTTTTTATGTTACGGTATATACTATTATTAAATTAAAAACAATAAACTTAGATATTACATAT
453 TTATTTTGTATGTTACGGTATATACTATTATTAAATTAAAAACAATAAACATAGATATTACATAT
*
264958 TTATTATTATATTTGGTTAAAATTATTAAATTTAAATTATAAATAATATTTTATAAAATATCAAA
518 TTATTATTATATTTGGTTAAAATTATTAAATTTAAATTATAAATAATATTTTATAAAATATAAAA
*
265023 ACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAA
583 ACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAA
* *
265088 CACTATTAAAAATTTTTGAAACATAAATTACATAACTTTCAAA
648 CACTATTAAAAAATTTTAAAACATAAATTACATAACTTTCAAA
265131 AAAGTATCGATCATTTTTATAAAAAAGTATCTATACTTTCAACATATCAGGT-AA----A--TTT
1 AAAGTATCGATCATTTTTAT-AAAAAGTATCTATACTTTCAACATATCAGGTAAATTTTACCTTT
* *
265189 TATC--------A---GTTTTGTCATATTTTTACATGTTATATTGTAAAGTATCTATCCTTTTTT
65 TATCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTTTCTATCC-TTTTT
* *
265243 ATAAAAGGATCGATACTTTCAATATATAAGGTAAATTTTACCGTTTTTGTCATAATGAAACTGGT
129 ATAAAAGGATCGATACTTTCAACATATAAGGTAAATTTTACCATTTTTGTCATAATGAAACTGGT
* * * * * *
265308 TTTATCATATTTTTACATGTTATATTGTAAAGTATCTAT-CCTTTTTATAAAAGGATCGATACTT
194 TTTGTCATATTTTTACCTGTTATATTGTAAAATATCGATACATTTTTAT-AAAGTATCGATACTT
265372 T
258 T
265373 CAACATATCA
Statistics
Matches: 876, Mismatches: 50, Indels: 33
0.91 0.05 0.03
Matches are distributed among these distances:
673 49 0.06
674 117 0.13
676 1 0.00
684 7 0.01
688 1 0.00
691 25 0.03
692 644 0.74
693 32 0.04
ACGTcount: A:0.37, C:0.10, G:0.11, T:0.43
Consensus pattern (690 bp):
AAAGTATCGATCATTTTTATAAAAAGTATCTATACTTTCAACATATCAGGTAAATTTTACCTTTT
ATCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTTTCTATCCTTTTTAT
AAAAGGATCGATACTTTCAACATATAAGGTAAATTTTACCATTTTTGTCATAATGAAACTGGTTT
TGTCATATTTTTACCTGTTATATTGTAAAATATCGATACATTTTTATAAAGTATCGATACTTTAT
AGACACTATTACTGCTTTTTTTATAAATTCCAAAAGTGTCGATACTTATTTAAATGAAATCGATA
CTTTCAACATATCTGGTAGGTAGTTTAATGTAATAGGTAAGTATTTCACTGTAAAAAACATTAAT
TTAAGGTTATCTTTTGAGTGAGATTTAAGATATTAGTTTAGTAATTATACGCGTCTAATGATTTA
TTTTGTATGTTACGGTATATACTATTATTAAATTAAAAACAATAAACATAGATATTACATATTTA
TTATTATATTTGGTTAAAATTATTAAATTTAAATTATAAATAATATTTTATAAAATATAAAAACA
ATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACAC
TATTAAAAAATTTTAAAACATAAATTACATAACTTTCAAA
Found at i:265401 original size:111 final size:112
Alignment explanation
Indices: 265194--265454 Score: 470
Period size: 111 Copynumber: 2.3 Consensus size: 112
265184 AATTTTATCA
265194 GTTTTGTCATATTTTTACATGTTATATTGTAAAGTATCTATCCTTTTTTATAAAAGGATCGATAC
1 GTTTTGTCATATTTTTACATGTTATATTGTAAAGTATCTATCCTTTTTTATAAAAGGATCGATAC
*
265259 TTTCAATATATAAGGTAAATTTTACCGTTTTTGTCATAATGAAACTG
66 TTTCAACATATAAGGTAAATTTTACCGTTTTTGTCATAATGAAACTG
*
265306 GTTTTATCATATTTTTACATGTTATATTGTAAAGTATCTATCC-TTTTTATAAAAGGATCGATAC
1 GTTTTGTCATATTTTTACATGTTATATTGTAAAGTATCTATCCTTTTTTATAAAAGGATCGATAC
*
265370 TTTCAACATATCAGGTAAATTTTACCGTTTTTGTCATAATGAAACTG
66 TTTCAACATATAAGGTAAATTTTACCGTTTTTGTCATAATGAAACTG
* *
265417 GTTTTGTCATATTTTTACCTGTTATATTGTAAAATATC
1 GTTTTGTCATATTTTTACATGTTATATTGTAAAGTATC
265455 GATATATTTT
Statistics
Matches: 143, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
111 101 0.71
112 42 0.29
ACGTcount: A:0.31, C:0.11, G:0.12, T:0.46
Consensus pattern (112 bp):
GTTTTGTCATATTTTTACATGTTATATTGTAAAGTATCTATCCTTTTTTATAAAAGGATCGATAC
TTTCAACATATAAGGTAAATTTTACCGTTTTTGTCATAATGAAACTG
Found at i:266197 original size:111 final size:112
Alignment explanation
Indices: 265916--266287 Score: 547
Period size: 112 Copynumber: 3.3 Consensus size: 112
265906 AACTTTCAAA
* * *
265916 AAAGTATCGATCATTTTTATAAAAAGTATCTATACTTTCAACATATCAGGTAAATTTTACTGGTT
1 AAAGTATCGATCATTTTTATAAAAAGTATCGATACTTTCAACATATCAGGTAAATTTTACCGTTT
*
265981 TTGTCATAATGAAACTGGTTTTGTCATATTTTTACTTGTTATATTGT
66 TTGTCATAATGAATCTGGTTTTGTCATATTTTTACTTGTTATATTGT
* * * *
266028 AAAGTATCTATTCTTTTTTATCAAATG-ATCGATACTTTCAACATATCAGGTAAATTTTACCGTT
1 AAAGTATCGA-TCATTTTTATAAAAAGTATCGATACTTTCAACATATCAGGTAAATTTTACCGTT
*
266092 TTTGTCATAATGAATCTGGTTTTGTCATATTTTTACTTGTTATATTAT
65 TTTGTCATAATGAATCTGGTTTTGTCATATTTTTACTTGTTATATTGT
* * *
266140 AAAGTATCTATCATTTTTATAAAAAG-ATCGATACTTTCAACATATCATGTAAATTTTACCCTTT
1 AAAGTATCGATCATTTTTATAAAAAGTATCGATACTTTCAACATATCAGGTAAATTTTACCGTTT
* *
266204 TTGTCATAATGAAAT-TGGTTTTGTCATATTTGTACATGTTATATTGT
66 TTGTCATAATG-AATCTGGTTTTGTCATATTTTTACTTGTTATATTGT
*
266251 AAAATATCGATACATTTTTAT--AAAGTATCGATACTTT
1 AAAGTATCGAT-CATTTTTATAAAAAGTATCGATACTTT
266288 ATAGGCGCTA
Statistics
Matches: 237, Mismatches: 19, Indels: 9
0.89 0.07 0.03
Matches are distributed among these distances:
110 4 0.02
111 109 0.46
112 111 0.47
113 13 0.05
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.46
Consensus pattern (112 bp):
AAAGTATCGATCATTTTTATAAAAAGTATCGATACTTTCAACATATCAGGTAAATTTTACCGTTT
TTGTCATAATGAATCTGGTTTTGTCATATTTTTACTTGTTATATTGT
Found at i:266364 original size:804 final size:785
Alignment explanation
Indices: 264439--266393 Score: 3153
Period size: 785 Copynumber: 2.5 Consensus size: 785
264429 AACTTTCAAA
* * * * * *
264439 AAAGTATCGA-TCATTTTTATAAAAAGTATCTATAGTTTCAACATATCAGATAAATTTTACCGGT
1 AAAGTATCTATTCTTTTTTATAAAAAG-ATCGATACTTTCAACATATCAGGTAAATTTTACCGTT
* * *
264503 TTTATCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTTTCTATCCTTTT
65 TTTGTCATAATGAAACTGGTTTTGTCATATTTTTACATGTTATATTGTAAAGTATCTATCCTTTT
* *
264568 TATAAAAGGATCGATACTTTCAACATATAAGGTAAATTTTACTATTTTTGTCATAATGAAACTGG
130 TATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCATTTTTGTCATAATGAAACTGG
264633 TTTTGTCATATTTTTACCTGTTATATTGTAAAATATCGATACATTTTTATAAAGTATCGATACTT
195 TTTTGTCATATTTTTACCTGTTATATTGTAAAATATCGATACATTTTTATAAAGTATCGATACTT
* *
264698 TATAGGCACTATTACTGCTTTTCTTTTAAATTCCAAAAGTGTCGATACTTATTTAAATGAAATCG
260 TATAGGCGCTATTACTGCTTTTCTTTTAAATTCCAAAAGTGTCGATACTTATTTAAATGGAATCG
*
264763 ATACTTTCAACATATCTGGTAGGTAGTTTAATGTAATAGGTAAGTATTTCACTGTAAAAAATATT
325 ATACTTTCAACATATCTGGTAGGTAGTTTAATGTAATAGGTAAGTATTTCACTGTAAAAAACATT
* * * * *
264828 AATTTAAGGTTATCTTTTTAGTGATATTTAAGATATTATTTTAGTAATTATACGCGTCTAATGAT
390 AATTTAAAGTTATCTTTTGAGTAAGATTTAAGATATTAATTTAGTAATTATACGCGTCTAATGAT
* *
264893 TTATTTTTTATGTTACGGTATATACTATTATTAAATTAAAAACAATAAACTTAGATATTACATAT
455 TTATTTTTTATGTTACGATATATACTATTATTAAATTAAAAACAATAAACATAGATATTACATAT
* * *
264958 TTATTATTATATTTGGTTAAAATTATTAAATTTAAATTATAAATAATATTTTATAAAATATCAAA
520 TTATTATTATATTCGGTCAAAATTATTAAATTTAAATTATAAATAATATTTTAAAAAATATCAAA
* *
265023 ACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAA
585 ACAATCAAATAATTTTTTGTGAAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAA
* *
265088 CACTATTAAAAATTTTTGAAACATAAATTACATAACTTTCAAAAAAGTATCGATCATTTTTATAA
650 CACTATAAAAAATGTTTGAAACATAAATTACATAACTTTCAAAAAAGTATCGATCATTTTTATAA
265153 AAAAGTATCTATACTTTCAACATATCAGGTAAATTTTATCAGTTTTGTCATATTTTTACATGTTA
715 AAAAGTATCTATACTTTCAACATATCAGGTAAATTTTATCAGTTTTGTCATATTTTTACATGTTA
265218 TATTGT
780 TATTGT
* * * *
265224 AAAGTATCTATCCTTTTTTATAAAAGGATCGATACTTTCAATATATAAGGTAAATTTTACCGTTT
1 AAAGTATCTATTCTTTTTTATAAAAAGATCGATACTTTCAACATATCAGGTAAATTTTACCGTTT
*
265289 TTGTCATAATGAAACTGGTTTTATCATATTTTTACATGTTATATTGTAAAGTATCTATCCTTTTT
66 TTGTCATAATGAAACTGGTTTTGTCATATTTTTACATGTTATATTGTAAAGTATCTATCCTTTTT
*
265354 ATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGTTTTTGTCATAATGAAACTGGT
131 ATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCATTTTTGTCATAATGAAACTGGT
*
265419 TTTGTCATATTTTTACCTGTTATATTGTAAAATATCGATATATTTTTATAAAGTA-CTGATACTT
196 TTTGTCATATTTTTACCTGTTATATTGTAAAATATCGATACATTTTTATAAAGTATC-GATACTT
*
265483 TATAGGCGCTATTACTG-TTTCTCTTTTAAATTCCAAAAGTTTCGATACTTATTTAAATGGAATC
260 TATAGGCGCTATTACTGCTTT-TCTTTTAAATTCCAAAAGTGTCGATACTTATTTAAATGGAATC
* *
265547 GATACTTTCAACATATCCGGTAGGTAGTTTAATGTAATAGGTAAGTATTTCACTGTGAAAAACAT
324 GATACTTTCAACATATCTGGTAGGTAGTTTAATGTAATAGGTAAGTATTTCACTGTAAAAAACAT
* *
265612 TAATTTAAATTTATCTTTTGAGTAAGATTTAAGATATTAATTTAGTAATTATACGTGTCTAATGA
389 TAATTTAAAGTTATCTTTTGAGTAAGATTTAAGATATTAATTTAGTAATTATACGCGTCTAATGA
265677 TTTATTTTTTATGTTACGATATATACTATTATTAAATTAAAAACAATAAACATAGATATTACATA
454 TTTATTTTTTATGTTACGATATATACTATTATTAAATTAAAAACAATAAACATAGATATTACATA
* * *
265742 TTTATTATTATCTTCGGTCAAAATTGTTAAATTTAAATTCTAAATAATATTTTAAAAAATATCAA
519 TTTATTATTATATTCGGTCAAAATTATTAAATTTAAATTATAAATAATATTTTAAAAAATATCAA
*
265807 AACAATCAAATAATTTTTTGTGAAAATGAAATTATTAAATTAATATTGTAGGTGGAAAATATAAA
584 AACAATCAAATAATTTTTTGTGAAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAA
265872 ACACTATAAAAAATGTTTGAAACATAAATTACATAACTTTCAAAAAAGTATCGATCATTTTTAT-
649 ACACTATAAAAAATGTTTGAAACATAAATTACATAACTTTCAAAAAAGTATCGATCATTTTTATA
265936 AAAAAGTATCTATACTTTCAACATATCAGGTAAATTTTACTGGTTTTGTCATAATGAAACTGGTT
714 AAAAAGTATCTATACTTTCAACATATCAGGTAAATTTTA---------TC--------A---GTT
*
266001 TTGTCATATTTTTACTTGTTATATTGT
759 TTGTCATATTTTTACATGTTATATTGT
* *
266028 AAAGTATCTATTCTTTTTTATCAAATGATCGATACTTTCAACATATCAGGTAAATTTTACCGTTT
1 AAAGTATCTATTCTTTTTTATAAAAAGATCGATACTTTCAACATATCAGGTAAATTTTACCGTTT
* * * *
266093 TTGTCATAATGAATCTGGTTTTGTCATATTTTTACTTGTTATATTATAAAGTATCTATCATTTTT
66 TTGTCATAATGAAACTGGTTTTGTCATATTTTTACATGTTATATTGTAAAGTATCTATCCTTTTT
* * * *
266158 ATAAAAAGATCGATACTTTCAACATATCATGTAAATTTTACCCTTTTTGTCATAATGAAATTGGT
131 ATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCATTTTTGTCATAATGAAACTGGT
* *
266223 TTTGTCATATTTGTACATGTTATATTGTAAAATATCGATACATTTTTATAAAGTATCGATACTTT
196 TTTGTCATATTTTTACCTGTTATATTGTAAAATATCGATACATTTTTATAAAGTATCGATACTTT
*
266288 ATAGGCGCTATTACTGCTTTTCTTTTAAATTCCAAAAGTGTCGATTCTTATTTAAATGGAATCGA
261 ATAGGCGCTATTACTGCTTTTCTTTTAAATTCCAAAAGTGTCGATACTTATTTAAATGGAATCGA
266353 TACTTTCAACATATCTGGTAGGTAGTTTAATGTAATAGGTA
326 TACTTTCAACATATCTGGTAGGTAGTTTAATGTAATAGGTA
266394 GCGCCTATTT
Statistics
Matches: 1080, Mismatches: 65, Indels: 31
0.92 0.06 0.03
Matches are distributed among these distances:
784 43 0.04
785 648 0.60
786 13 0.01
793 2 0.00
801 1 0.00
804 369 0.34
805 4 0.00
ACGTcount: A:0.36, C:0.10, G:0.11, T:0.43
Consensus pattern (785 bp):
AAAGTATCTATTCTTTTTTATAAAAAGATCGATACTTTCAACATATCAGGTAAATTTTACCGTTT
TTGTCATAATGAAACTGGTTTTGTCATATTTTTACATGTTATATTGTAAAGTATCTATCCTTTTT
ATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCATTTTTGTCATAATGAAACTGGT
TTTGTCATATTTTTACCTGTTATATTGTAAAATATCGATACATTTTTATAAAGTATCGATACTTT
ATAGGCGCTATTACTGCTTTTCTTTTAAATTCCAAAAGTGTCGATACTTATTTAAATGGAATCGA
TACTTTCAACATATCTGGTAGGTAGTTTAATGTAATAGGTAAGTATTTCACTGTAAAAAACATTA
ATTTAAAGTTATCTTTTGAGTAAGATTTAAGATATTAATTTAGTAATTATACGCGTCTAATGATT
TATTTTTTATGTTACGATATATACTATTATTAAATTAAAAACAATAAACATAGATATTACATATT
TATTATTATATTCGGTCAAAATTATTAAATTTAAATTATAAATAATATTTTAAAAAATATCAAAA
CAATCAAATAATTTTTTGTGAAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAAC
ACTATAAAAAATGTTTGAAACATAAATTACATAACTTTCAAAAAAGTATCGATCATTTTTATAAA
AAAGTATCTATACTTTCAACATATCAGGTAAATTTTATCAGTTTTGTCATATTTTTACATGTTAT
ATTGT
Found at i:266624 original size:23 final size:23
Alignment explanation
Indices: 266589--266639 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
266579 CTAGTAATTA
** * *
266589 ACCTATTTTATTATATATGCGTT
1 ACCTATTACATTATATAAGCGGT
266612 ACCTATTACATTATATAAGCGGT
1 ACCTATTACATTATATAAGCGGT
266635 ACCTA
1 ACCTA
266640 ATATGTTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.31, C:0.18, G:0.10, T:0.41
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCGGT
Found at i:268689 original size:220 final size:220
Alignment explanation
Indices: 268339--269159 Score: 1155
Period size: 220 Copynumber: 3.8 Consensus size: 220
268329 GAGAAAATTG
* * * * * * *
268339 GGTCAATCTGGAAAAAACTTGGTTTTGAAGACGACTCTGCTCATCCGTGTTGAATAGATCTGGTC
1 GGTCAATCTGGAGATAATTTGGTGTTGAAGACGACTCTACTCATCCGTGTTGAAGAGATATGGTC
* * * * * *
268404 GCTTTCAAATAAATTGTTTGTTGGAGATGACATTGTTCCCTCTCGTTGAGGAAGTCAGGTCAATC
66 TCTTTCAGATAAATTGTTTGTTGAAGATGACATTGTTTCTTCTCGTTGAGGAAGTCGGGTCAATC
* *
268469 TGGAGATAATTTGGAGACAACACGGTTCCTTCGCATTGAGGAAGTCTGATTGTCTGAGGATGACA
131 TGGAGATAATTTGGAGACAACACGATTCCTTCGCGTTGAGGAAGTCTGATTGTCTGAGGATGACA
*
268534 CTGCTCATTCGTGTTGAGGAGATCA
196 CTGCTCCTTCGTGTTGAGGAGATCA
*
268559 GGTCAATCTGGAGACAATTTGGTGTTGAAGACGACTCTACTCATCCGTGTTGAAGAGATATGGTC
1 GGTCAATCTGGAGATAATTTGGTGTTGAAGACGACTCTACTCATCCGTGTTGAAGAGATATGGTC
*
268624 GT-TTTCAGATAAATTGTTTGTTGGAGATGACATTGTTTCTTCTCGTTGAGGAAGTCGGGTCAAT
66 -TCTTTCAGATAAATTGTTTGTTGAAGATGACATTGTTTCTTCTCGTTGAGGAAGTCGGGTCAAT
* * * *
268688 CTGGAGATAATTTGGAGACAACATGATTTCTTCGCGTTGAGGAAGTTTGATTGTCTGATGATGAC
130 CTGGAGATAATTTGGAGACAACACGATTCCTTCGCGTTGAGGAAGTCTGATTGTCTGAGGATGAC
* * *
268753 ACTACTCCTTCATGTTGAGGAGATTA
195 ACTGCTCCTTCGTGTTGAGGAGATCA
* * * *
268779 GGTCAATCTGGAGATAATTTGTTGTTGAAGATGACTCTGCTCATCCGTGTTGAAGAGATCTGGTC
1 GGTCAATCTGGAGATAATTTGGTGTTGAAGACGACTCTACTCATCCGTGTTGAAGAGATATGGTC
* * *
268844 TCTTTCAGATAAATTGTTTGTTGAAGATGACGTTGTTTCTTTTCGTTGAGGAAGTC--G--AGTC
66 TCTTTCAGATAAATTGTTTGTTGAAGATGACATTGTTTCTTCTCGTTGAGGAAGTCGGGTCAATC
*
268905 -------AATTTGGAGACAACATGATTCCTTCGCGTTGAGGAAGTCTGATTGTCTGAGGATGACA
131 TGGAGATAATTTGGAGACAACACGATTCCTTCGCGTTGAGGAAGTCTGATTGTCTGAGGATGACA
268963 CTGCTCCTTCGTGTTGAGGAGATCA
196 CTGCTCCTTCGTGTTGAGGAGATCA
* * **
268988 GGTCAATCTGGAGATAATTTGGTGTTGAAGACAACTATACTCATATGTGTTGAAGAGATATGGTC
1 GGTCAATCTGGAGATAATTTGGTGTTGAAGACGACTCTACTCATCCGTGTTGAAGAGATATGGTC
* *
269053 TCTTTCAGATAAATTGTTTGTTGAAGATGACGTTGTTTCTT-TTGATTGAGGAAGTCGGGTCAAT
66 TCTTTCAGATAAATTGTTTGTTGAAGATGACATTGTTTCTTCTCG-TTGAGGAAGTCGGGTCAAT
* * *
269117 ATGGAGATAATTTGGAGATAACACGATTCCTTCGTGTTGAGGA
130 CTGGAGATAATTTGGAGACAACACGATTCCTTCGCGTTGAGGA
269160 GATAGGGTTA
Statistics
Matches: 536, Mismatches: 51, Indels: 28
0.87 0.08 0.05
Matches are distributed among these distances:
208 2 0.00
209 186 0.35
211 1 0.00
213 2 0.00
216 3 0.01
218 1 0.00
219 1 0.00
220 340 0.63
ACGTcount: A:0.25, C:0.14, G:0.26, T:0.34
Consensus pattern (220 bp):
GGTCAATCTGGAGATAATTTGGTGTTGAAGACGACTCTACTCATCCGTGTTGAAGAGATATGGTC
TCTTTCAGATAAATTGTTTGTTGAAGATGACATTGTTTCTTCTCGTTGAGGAAGTCGGGTCAATC
TGGAGATAATTTGGAGACAACACGATTCCTTCGCGTTGAGGAAGTCTGATTGTCTGAGGATGACA
CTGCTCCTTCGTGTTGAGGAGATCA
Found at i:269056 original size:209 final size:209
Alignment explanation
Indices: 268696--269123 Score: 696
Period size: 209 Copynumber: 2.0 Consensus size: 209
268686 ATCTGGAGAT
* * *
268696 AATTTGGAGACAACATGATTTCTTCGCGTTGAGGAAGTTTGATTGTCTGATGATGACACTACTCC
1 AATTTGGAGACAACATGATTCCTTCGCGTTGAGGAAGTCTGATTGTCTGAGGATGACACTACTCC
* * ** * * *
268761 TTCATGTTGAGGAGATTAGGTCAATCTGGAGATAATTTGTTGTTGAAGATGACTCTGCTCATCCG
66 TTCATGTTGAGGAGATCAGGTCAATCTGGAGATAATTTGGTGTTGAAGACAACTATACTCATACG
*
268826 TGTTGAAGAGATCTGGTCTCTTTCAGATAAATTGTTTGTTGAAGATGACGTTGTTTCTTTTCG-T
131 TGTTGAAGAGATATGGTCTCTTTCAGATAAATTGTTTGTTGAAGATGACGTTGTTTCTTTT-GAT
268890 TGAGGAAGTCGAGTC
195 TGAGGAAGTCGAGTC
*
268905 AATTTGGAGACAACATGATTCCTTCGCGTTGAGGAAGTCTGATTGTCTGAGGATGACACTGCTCC
1 AATTTGGAGACAACATGATTCCTTCGCGTTGAGGAAGTCTGATTGTCTGAGGATGACACTACTCC
* *
268970 TTCGTGTTGAGGAGATCAGGTCAATCTGGAGATAATTTGGTGTTGAAGACAACTATACTCATATG
66 TTCATGTTGAGGAGATCAGGTCAATCTGGAGATAATTTGGTGTTGAAGACAACTATACTCATACG
269035 TGTTGAAGAGATATGGTCTCTTTCAGATAAATTGTTTGTTGAAGATGACGTTGTTTCTTTTGATT
131 TGTTGAAGAGATATGGTCTCTTTCAGATAAATTGTTTGTTGAAGATGACGTTGTTTCTTTTGATT
*
269100 GAGGAAGTCGGGTC
196 GAGGAAGTCGAGTC
*
269114 AATATGGAGA
1 AATTTGGAGA
269124 TAATTTGGAG
Statistics
Matches: 202, Mismatches: 16, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
208 1 0.00
209 201 1.00
ACGTcount: A:0.25, C:0.13, G:0.26, T:0.35
Consensus pattern (209 bp):
AATTTGGAGACAACATGATTCCTTCGCGTTGAGGAAGTCTGATTGTCTGAGGATGACACTACTCC
TTCATGTTGAGGAGATCAGGTCAATCTGGAGATAATTTGGTGTTGAAGACAACTATACTCATACG
TGTTGAAGAGATATGGTCTCTTTCAGATAAATTGTTTGTTGAAGATGACGTTGTTTCTTTTGATT
GAGGAAGTCGAGTC
Found at i:269124 original size:429 final size:432
Alignment explanation
Indices: 268339--269159 Score: 1231
Period size: 429 Copynumber: 1.9 Consensus size: 432
268329 GAGAAAATTG
*
268339 GGTCAATCTGGAAAAAACTTGGTTTTGAAGACGACTCTGCTCATCCGTGTTGAATAGATCTGGTC
1 GGTCAATCTGGAAAAAACTTGGTTTTGAAGACGACTCTGCTCATCCGTGTTGAAGAGATCTGGTC
*
268404 GCTTTCAAATAAATTGTTTGTTGGAGATGACATTGTTCCCTCTCGTTGAGGAAGTCAGGTCAATC
66 GCTTTCAAATAAATTGTTTGTTGAAGATGACATTGTTCCCTCTCGTTGAGGAAGTCA-G-CAATC
*
268469 TGGAGATAATTTGGAGACAACACGGTTCCTTCGCATTGAGGAAGTCTGATTGTCTGAGGATGACA
129 ----G--AATTTGGAGACAACACGATTCCTTCGCATTGAGGAAGTCTGATTGTCTGAGGATGACA
* *
268534 CTGCTCATTCGTGTTGAGGAGATCAGGTCAATCTGGAGACAATTTGGTGTTGAAGACGACTCTAC
188 CTGCTCATTCGTGTTGAGGAGATCAGGTCAATCTGGAGACAATTTGGTGTTGAAGACAACTATAC
* *
268599 TCATCCGTGTTGAAGAGATATGGTCGTTTTCAGATAAATTGTTTGTTGGAGATGACATTGTTTCT
253 TCATACGTGTTGAAGAGATATGGTCGTTTTCAGATAAATTGTTTGTTGAAGATGACATTGTTTCT
* * *
268664 TCTCGTTGAGGAAGTCGGGTCAATCTGGAGATAATTTGGAGACAACATGATTTCTTCGCGTTGAG
318 TCTCGTTGAGGAAGTCGGGTCAATATGGAGATAATTTGGAGACAACACGATTCCTTCGCGTTGAG
268729 GAAGTTTGATTGTCTGATGATGACACTACTCCTTCATGTTGAGGAGATTA
383 GAAGTTTGATTGTCTGATGATGACACTACTCCTTCATGTTGAGGAGATTA
* * * *
268779 GGTCAATCTGGAGATAA-TTTGTTGTTGAAGATGACTCTGCTCATCCGTGTTGAAGAGATCTGGT
1 GGTCAATCTGGAAAAAACTTGGTT-TTGAAGACGACTCTGCTCATCCGTGTTGAAGAGATCTGGT
* * * * * * *
268843 CTCTTTCAGATAAATTGTTTGTTGAAGATGACGTTGTTTCTTTTCGTTGAGGAAGTC-G-AGTC-
65 CGCTTTCAAATAAATTGTTTGTTGAAGATGACATTGTTCCCTCTCGTTGAGGAAGTCAGCAATCG
* * *
268905 AATTTGGAGACAACATGATTCCTTCGCGTTGAGGAAGTCTGATTGTCTGAGGATGACACTGCTCC
130 AATTTGGAGACAACACGATTCCTTCGCATTGAGGAAGTCTGATTGTCTGAGGATGACACTGCTCA
* *
268970 TTCGTGTTGAGGAGATCAGGTCAATCTGGAGATAATTTGGTGTTGAAGACAACTATACTCATATG
195 TTCGTGTTGAGGAGATCAGGTCAATCTGGAGACAATTTGGTGTTGAAGACAACTATACTCATACG
* *
269035 TGTTGAAGAGATATGGTC-TCTTTCAGATAAATTGTTTGTTGAAGATGACGTTGTTTCTT-TTGA
260 TGTTGAAGAGATATGGTCGT-TTTCAGATAAATTGTTTGTTGAAGATGACATTGTTTCTTCTCG-
* *
269098 TTGAGGAAGTCGGGTCAATATGGAGATAATTTGGAGATAACACGATTCCTTCGTGTTGAGGA
323 TTGAGGAAGTCGGGTCAATATGGAGATAATTTGGAGACAACACGATTCCTTCGCGTTGAGGA
269160 GATAGGGTTA
Statistics
Matches: 348, Mismatches: 30, Indels: 17
0.88 0.08 0.04
Matches are distributed among these distances:
428 3 0.01
429 233 0.67
436 3 0.01
438 1 0.00
439 5 0.01
440 103 0.30
ACGTcount: A:0.25, C:0.14, G:0.26, T:0.34
Consensus pattern (432 bp):
GGTCAATCTGGAAAAAACTTGGTTTTGAAGACGACTCTGCTCATCCGTGTTGAAGAGATCTGGTC
GCTTTCAAATAAATTGTTTGTTGAAGATGACATTGTTCCCTCTCGTTGAGGAAGTCAGCAATCGA
ATTTGGAGACAACACGATTCCTTCGCATTGAGGAAGTCTGATTGTCTGAGGATGACACTGCTCAT
TCGTGTTGAGGAGATCAGGTCAATCTGGAGACAATTTGGTGTTGAAGACAACTATACTCATACGT
GTTGAAGAGATATGGTCGTTTTCAGATAAATTGTTTGTTGAAGATGACATTGTTTCTTCTCGTTG
AGGAAGTCGGGTCAATATGGAGATAATTTGGAGACAACACGATTCCTTCGCGTTGAGGAAGTTTG
ATTGTCTGATGATGACACTACTCCTTCATGTTGAGGAGATTA
Found at i:269677 original size:103 final size:103
Alignment explanation
Indices: 269537--269766 Score: 234
Period size: 103 Copynumber: 2.3 Consensus size: 103
269527 GGTGAGATAA
* *
269537 AATTTTGTTTCGAGTGAAAC-ATTT-CAAAATTTATGTTTCAAGGGAAAACTATCTCAA-TCGGG
1 AATTTTGTTTCAAGTGAAACAATTTCCAAAATTTATGTTTCAAGGGAAAACTATCTCAAGT-GAG
* * *
269599 AAGAAATTTGCTTTTAAGAAAAACAATCTCAAATGTCATC
65 AAGAAATTAGCTTTTAAGAAAAA-AATCTCAAACGACATC
*** * ** * *
269639 -ATTTTGTTTCAAGTGAAACAATTTCCAGTTTTTGTGTTTTGAGGGAAAATTGTCTCAAGTGAGA
1 AATTTTGTTTCAAGTGAAACAATTTCCAAAATTTATGTTTCAAGGGAAAACTATCTCAAGTGAGA
* * * * * *
269703 CGAAATTAGTTTTTAGGAAAAATATCTCAAGCGAGATC
66 AGAAATTAGCTTTTAAGAAAAAAATCTCAAACGACATC
*
269741 AATTTTGTTTCAAGTGAATCAATTTC
1 AATTTTGTTTCAAGTGAAACAATTTC
269767 AAATTTTGAG
Statistics
Matches: 104, Mismatches: 20, Indels: 7
0.79 0.15 0.05
Matches are distributed among these distances:
101 18 0.17
102 15 0.14
103 70 0.67
104 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (103 bp):
AATTTTGTTTCAAGTGAAACAATTTCCAAAATTTATGTTTCAAGGGAAAACTATCTCAAGTGAGA
AGAAATTAGCTTTTAAGAAAAAAATCTCAAACGACATC
Found at i:269946 original size:37 final size:36
Alignment explanation
Indices: 269834--269949 Score: 106
Period size: 37 Copynumber: 3.2 Consensus size: 36
269824 CAAGGATTTG
* * *
269834 TGTTTCAAGAGAAATTGTCTCAAGCGAGAAAAAATT
1 TGTTTCAAGAAAAATTATCTCAAGCGAGATAAAATT
** ** * * *
269870 TGTTTTTAGAAGAAACAATCTCAAGTGAGATTAATTT
1 TGTTTCAAGAA-AAATTATCTCAAGCGAGATAAAATT
* *
269907 TGTTTCAAGAAAAATTATCTCAAACGAGATGAAACTT
1 TGTTTCAAGAAAAATTATCTCAAGCGAGAT-AAAATT
269944 TGTTTC
1 TGTTTC
269950 GGGATAAACA
Statistics
Matches: 60, Mismatches: 18, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
36 23 0.38
37 37 0.62
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (36 bp):
TGTTTCAAGAAAAATTATCTCAAGCGAGATAAAATT
Found at i:277729 original size:2 final size:2
Alignment explanation
Indices: 277722--277775 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
277712 ATTACGTGGA
277722 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
277764 AT AT AT AT AT AT
1 AT AT AT AT AT AT
277776 TAATATTCAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:279431 original size:27 final size:27
Alignment explanation
Indices: 279401--279455 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
279391 GGATGAAACT
* *
279401 ATGATAGGGAGAGCACAGGTGAAGGGA
1 ATGACAGGGAGAGCACAGGCGAAGGGA
* *
279428 ATGACGGGGAGAGCACCGGCGAAGGGA
1 ATGACAGGGAGAGCACAGGCGAAGGGA
279455 A
1 A
279456 AGGGTAATGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.35, C:0.13, G:0.45, T:0.07
Consensus pattern (27 bp):
ATGACAGGGAGAGCACAGGCGAAGGGA
Done.