Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A12
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: 103038859
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4950000 characters in sequence are not A, C, G, or T
File 275 of 320
Found at i:88725828 original size:15 final size:15
Alignment explanation
Indices: 88725808--88725837 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
88725798 CATTTTATTT
*
88725808 ATATTAGGATAATTA
1 ATATTAAGATAATTA
88725823 ATATTAAGATAATTA
1 ATATTAAGATAATTA
88725838 TTAGGATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (15 bp):
ATATTAAGATAATTA
Found at i:88732001 original size:33 final size:33
Alignment explanation
Indices: 88731959--88732025 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
88731949 TATTTCCAGG
*
88731959 TAAGCTTCGATCTCGGTGGCAAGGACCTTTTAT
1 TAAGCTTCGATCTCGGTGGCAAAGACCTTTTAT
88731992 TAAGCTTCGATCTCGGTGGCAAAGACCTTTTAT
1 TAAGCTTCGATCTCGGTGGCAAAGACCTTTTAT
88732025 T
1 T
88732026 GTGACTGAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.34
Consensus pattern (33 bp):
TAAGCTTCGATCTCGGTGGCAAAGACCTTTTAT
Found at i:88732235 original size:5 final size:5
Alignment explanation
Indices: 88732225--88732279 Score: 55
Period size: 5 Copynumber: 11.4 Consensus size: 5
88732215 GCAACCCAAT
*
88732225 TTTTA TTTTA TTTTA -TTTA TTTTTA TTTT- TATTTA TTTTA TCTTA --TTA
1 TTTTA TTTTA TTTTA TTTTA -TTTTA TTTTA T-TTTA TTTTA TTTTA TTTTA
88732273 TTTTA TT
1 TTTTA TT
88732280 ATTTATTATT
Statistics
Matches: 43, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
3 3 0.07
4 5 0.12
5 30 0.70
6 5 0.12
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:88732284 original size:20 final size:19
Alignment explanation
Indices: 88732223--88732286 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 19
88732213 AGGCAACCCA
88732223 ATTTTTATTTTATTTTATTT
1 ATTTTTATTTTA-TTTATTT
88732243 ATTTTTATTTTTATTTATTTT
1 ATTTTTA-TTTTATTTA-TTT
88732264 ATCTTATTATTTTA-TTATTT
1 AT-TT-TTATTTTATTTATTT
88732284 ATT
1 ATT
88732287 ATTTTCAGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
19 1 0.03
20 16 0.40
21 13 0.32
22 7 0.17
23 3 0.08
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.77
Consensus pattern (19 bp):
ATTTTTATTTTATTTATTT
Found at i:88733841 original size:15 final size:15
Alignment explanation
Indices: 88733821--88733850 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
88733811 CATTTTATTT
*
88733821 ATATTAGGATAATTA
1 ATATTAAGATAATTA
88733836 ATATTAAGATAATTA
1 ATATTAAGATAATTA
88733851 TTAGGATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (15 bp):
ATATTAAGATAATTA
Found at i:88733894 original size:10 final size:10
Alignment explanation
Indices: 88733875--88733906 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
88733865 ATTTAGGATT
88733875 TTAT-TTTAA
1 TTATCTTTAA
88733884 TTATCTTTAA
1 TTATCTTTAA
88733894 TTATCTTTAA
1 TTATCTTTAA
88733904 TTA
1 TTA
88733907 AATGTATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.62
Consensus pattern (10 bp):
TTATCTTTAA
Found at i:88738093 original size:34 final size:34
Alignment explanation
Indices: 88738055--88738122 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
88738045 GACAAAGAGT
88738055 AAGTGAGACACCGTAAGACTCCCATGGCAAATAA
1 AAGTGAGACACCGTAAGACTCCCATGGCAAATAA
88738089 AAGTGAGACACCGTAAGACTCCCATGGCAAATAA
1 AAGTGAGACACCGTAAGACTCCCATGGCAAATAA
88738123 CGATCCCATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.41, C:0.24, G:0.21, T:0.15
Consensus pattern (34 bp):
AAGTGAGACACCGTAAGACTCCCATGGCAAATAA
Found at i:88739431 original size:2 final size:2
Alignment explanation
Indices: 88739424--88739487 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
88739414 TTTTCACACG
88739424 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
88739466 CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT
88739488 TTGCGGAGAG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:88743645 original size:2 final size:2
Alignment explanation
Indices: 88743633--88743664 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
88743623 AGAAGGCTTT
88743633 TA TA T- 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 T
88743665 GTAAAGTACC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:88766533 original size:35 final size:34
Alignment explanation
Indices: 88766485--88766557 Score: 119
Period size: 35 Copynumber: 2.1 Consensus size: 34
88766475 ACAGATCCAT
*
88766485 TCTCTTCGCAATATCTGGATGGTTTTGAACTAAA
1 TCTCTTCACAATATCTGGATGGTTTTGAACTAAA
*
88766519 CTCTCTTCATAATATCTGGATGGTTTTGAACTAAA
1 -TCTCTTCACAATATCTGGATGGTTTTGAACTAAA
88766554 TCTC
1 TCTC
88766558 GTAGAGAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
34 4 0.11
35 32 0.89
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (34 bp):
TCTCTTCACAATATCTGGATGGTTTTGAACTAAA
Found at i:88767243 original size:22 final size:23
Alignment explanation
Indices: 88767218--88767263 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
88767208 CAACCAAATC
88767218 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
88767240 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
88767263 A
1 A
88767264 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:88767269 original size:23 final size:23
Alignment explanation
Indices: 88767225--88767269 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
88767215 ATCAATTCAA
*
88767225 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
88767248 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
88767270 CACATATCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:88771557 original size:30 final size:29
Alignment explanation
Indices: 88771523--88771579 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
88771513 TAGAATAAAA
*
88771523 AATAACA-ATAATATTAATATATACACGAAT
1 AATAACAGA-AATAATAATA-ATACACGAAT
88771553 AATAACAGAAATAATAATAATACACGA
1 AATAACAGAAATAATAATAATACACGA
88771580 CAAGTCAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 8 0.32
30 16 0.64
31 1 0.04
ACGTcount: A:0.60, C:0.11, G:0.05, T:0.25
Consensus pattern (29 bp):
AATAACAGAAATAATAATAATACACGAAT
Found at i:88771793 original size:12 final size:12
Alignment explanation
Indices: 88771776--88771810 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
88771766 AAAATAATAC
88771776 TATATGTATAAA
1 TATATGTATAAA
*
88771788 TATATGTATATA
1 TATATGTATAAA
*
88771800 TACATGTATAA
1 TATATGTATAA
88771811 TGGAAACATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.43
Consensus pattern (12 bp):
TATATGTATAAA
Found at i:88771832 original size:3 final size:3
Alignment explanation
Indices: 88771824--88771985 Score: 66
Period size: 3 Copynumber: 55.0 Consensus size: 3
88771814 AAACATACAC
* * ** *
88771824 TAA TAA TAA TAA TAA TAA TAA TAA TACG TAT TAAA TGG TAA -AA GAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA T-AA TAA TAA TAA TAA
* * * ** * * *
88771870 TAA TAG TAA CAA T-G TTT TAA -AA TGA TAA TAG TAA TAA AAA TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * *
88771915 -AA TAA GAG TGA TAA TAA TAG TAA TAA TAA TAA TAG TAA TAG TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
88771962 -AA GTAA AAA TAA TAG TAA TAA TAA
1 TAA -TAA TAA TAA TAA TAA TAA TAA
88771986 CGGTAAATAC
Statistics
Matches: 113, Mismatches: 38, Indels: 16
0.68 0.23 0.10
Matches are distributed among these distances:
2 11 0.10
3 96 0.85
4 6 0.05
ACGTcount: A:0.59, C:0.01, G:0.10, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:88772191 original size:3 final size:3
Alignment explanation
Indices: 88772183--88772229 Score: 53
Period size: 3 Copynumber: 16.0 Consensus size: 3
88772173 AAAGGAAAAT
* *
88772183 ATA ATA ATA ATA GCT- ATA AT- ACA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
88772227 ATA
1 ATA
88772230 CATTGGATAG
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
2 2 0.05
3 34 0.92
4 1 0.03
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:88772221 original size:20 final size:21
Alignment explanation
Indices: 88772183--88772223 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
88772173 AAAGGAAAAT
88772183 ATAATAATAATAGCTATAATACA
1 ATAATAATAATA-C-ATAATACA
88772206 ATAATAATAATA-ATAATA
1 ATAATAATAATACATAATA
88772224 ATAATACATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
23 12 0.67
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (21 bp):
ATAATAATAATACATAATACA
Found at i:88772430 original size:143 final size:146
Alignment explanation
Indices: 88772265--88772537 Score: 401
Period size: 143 Copynumber: 1.9 Consensus size: 146
88772255 TAATATGGTG
* *
88772265 ATAATAGTAATAATATTGAAATACAAAAAGCATATATAATATAATAAAAATATCAAAATAAAGTA
1 ATAATAGTAATAATATTGAAATACAAAAAGCAAATATAACATAATAAAAATATCAAAATAAAGTA
* * * *
88772330 ATAAAAAATAATACTATATATA-A-ATATGTATACATATACATACA-TA-TATAATAAAAATAAT
66 ATAAAAAATAATACTAGATATACATATATATATAAATAAACATACACTACTAT-ATAAAAATAAT
88772391 ATGCACTAATATTAATA
130 ATGCACTAATATTAATA
* * * *
88772408 ATAATAGTAATAATATTGAAATACAAAAAGTAAATATAACATAATAATAATGTTAAAATAAAGTA
1 ATAATAGTAATAATATTGAAATACAAAAAGCAAATATAACATAATAAAAATATCAAAATAAAGTA
* *
88772473 ATTAAAAATAATACTAGATATACATATATATATAAATAAACATACACTACTATATAATAATAATA
66 ATAAAAAATAATACTAGATATACATATATATATAAATAAACATACACTACTATATAAAAATAATA
88772538 ATAATATAGA
Statistics
Matches: 114, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
143 79 0.69
144 1 0.01
145 18 0.16
146 13 0.11
147 3 0.03
ACGTcount: A:0.59, C:0.06, G:0.04, T:0.31
Consensus pattern (146 bp):
ATAATAGTAATAATATTGAAATACAAAAAGCAAATATAACATAATAAAAATATCAAAATAAAGTA
ATAAAAAATAATACTAGATATACATATATATATAAATAAACATACACTACTATATAAAAATAATA
TGCACTAATATTAATA
Found at i:88774594 original size:10 final size:10
Alignment explanation
Indices: 88774579--88774606 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
88774569 ATTAGGGAAA
88774579 AAAGTAAAAC
1 AAAGTAAAAC
88774589 AAAGTAAAAC
1 AAAGTAAAAC
88774599 AAAGTAAA
1 AAAGTAAA
88774607 CATGTAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.71, C:0.07, G:0.11, T:0.11
Consensus pattern (10 bp):
AAAGTAAAAC
Found at i:88775281 original size:25 final size:25
Alignment explanation
Indices: 88775253--88775304 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
88775243 TTTGGCTTGA
**
88775253 CATTTACTAAGCAATATCGGATATT
1 CATTTACTAAGCAATATCAAATATT
* *
88775278 CATTTATTAGGCAATATCAAATATT
1 CATTTACTAAGCAATATCAAATATT
88775303 CA
1 CA
88775305 AATTAATCTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (25 bp):
CATTTACTAAGCAATATCAAATATT
Found at i:88780633 original size:21 final size:21
Alignment explanation
Indices: 88780587--88780633 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
88780577 CATATTAGAT
88780587 CAATAAAATTTTTTAATAAGTA
1 CAATAAAATTTTTT-ATAAGTA
*
88780609 -AATAAAATTATTTT-TATGTA
1 CAATAAAATT-TTTTATAAGTA
88780629 CAATA
1 CAATA
88780634 CAAAAATGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
20 5 0.23
21 13 0.59
22 4 0.18
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (21 bp):
CAATAAAATTTTTTATAAGTA
Found at i:88783220 original size:21 final size:21
Alignment explanation
Indices: 88783188--88783242 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
88783178 AAAGTTAAAT
* *
88783188 AGAAGCTCGTAAGAGCTGGAC
1 AGAAGCTTGTAAGAGCTGAAC
*
88783209 AGAATCTTGTAAGAGCTGAAC
1 AGAAGCTTGTAAGAGCTGAAC
88783230 AGAAGCTTGTAAG
1 AGAAGCTTGTAAG
88783243 TGTAATGCCC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.36, C:0.15, G:0.29, T:0.20
Consensus pattern (21 bp):
AGAAGCTTGTAAGAGCTGAAC
Found at i:88786460 original size:30 final size:30
Alignment explanation
Indices: 88786426--88786489 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 30
88786416 ATAATAAAAT
88786426 AATAATAAATATCTT-ATTAAAT-ATTAATAA
1 AATAAT-AATATCTTAATTAAATAATT-ATAA
* *
88786456 AATAATAATTTTTTAATTAAATAATTATAA
1 AATAATAATATCTTAATTAAATAATTATAA
88786486 AATA
1 AATA
88786490 TCATCAACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 6 0.20
30 21 0.70
31 3 0.10
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (30 bp):
AATAATAATATCTTAATTAAATAATTATAA
Found at i:88793228 original size:7 final size:7
Alignment explanation
Indices: 88793205--88793245 Score: 50
Period size: 7 Copynumber: 5.9 Consensus size: 7
88793195 TATATATATA
88793205 TATTATAT
1 TATTA-AT
88793213 TATT-A-
1 TATTAAT
88793218 TATTAAT
1 TATTAAT
88793225 TATTAAT
1 TATTAAT
88793232 TATTAAT
1 TATTAAT
88793239 TAATTAA
1 T-ATTAA
88793246 AATATAAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
5 4 0.13
6 2 0.07
7 15 0.50
8 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TATTAAT
Found at i:88794462 original size:10 final size:11
Alignment explanation
Indices: 88794430--88794463 Score: 54
Period size: 10 Copynumber: 3.3 Consensus size: 11
88794420 CTGGACAATT
88794430 AATTGATATTG
1 AATTGATATTG
88794441 -ATTGATATTG
1 AATTGATATTG
88794451 AATTGA-ATTG
1 AATTGATATTG
88794461 AAT
1 AAT
88794464 AGTTCTTTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 17 0.77
11 5 0.23
ACGTcount: A:0.38, C:0.00, G:0.18, T:0.44
Consensus pattern (11 bp):
AATTGATATTG
Found at i:88799355 original size:40 final size:40
Alignment explanation
Indices: 88799311--88799422 Score: 172
Period size: 40 Copynumber: 2.8 Consensus size: 40
88799301 TTAAGTTACC
* *
88799311 ATAGTGAATCAGGAACAAATCCTATCCACTTTATATAT-TT
1 ATAGTGAATCAGGAATAAATCCTATTCACTTTA-ATATCTT
*
88799351 ATAGTGAATCAGGAATAAATCCTATTCACTTTAATTTCTT
1 ATAGTGAATCAGGAATAAATCCTATTCACTTTAATATCTT
*
88799391 TTAGTGAATCAGGAATAAATCCTATTCACTTT
1 ATAGTGAATCAGGAATAAATCCTATTCACTTT
88799423 TAATTCTCGA
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
39 3 0.04
40 64 0.96
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.38
Consensus pattern (40 bp):
ATAGTGAATCAGGAATAAATCCTATTCACTTTAATATCTT
Found at i:88805205 original size:40 final size:41
Alignment explanation
Indices: 88805089--88805205 Score: 175
Period size: 40 Copynumber: 2.9 Consensus size: 41
88805079 CCTTCTCGAG
88805089 AATTAAAAGTGAATAGGATTTATTCCTGATTCACTA-AAAGA
1 AATT-AAAGTGAATAGGATTTATTCCTGATTCACTATAAAGA
*
88805130 AATTAAAGTGAATAGGATTTATTCCTGATTCACTATAAATA
1 AATTAAAGTGAATAGGATTTATTCCTGATTCACTATAAAGA
* * *
88805171 TA-TAAAGTGGATAGGATTTGTTCCTGATTCACTAT
1 AATTAAAGTGAATAGGATTTATTCCTGATTCACTAT
88805206 GGTAACTTAA
Statistics
Matches: 71, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
40 62 0.87
41 9 0.13
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.36
Consensus pattern (41 bp):
AATTAAAGTGAATAGGATTTATTCCTGATTCACTATAAAGA
Found at i:88805225 original size:40 final size:38
Alignment explanation
Indices: 88805089--88805229 Score: 165
Period size: 40 Copynumber: 3.5 Consensus size: 38
88805079 CCTTCTCGAG
*
88805089 AATTAAAAGTGAATAGGATTTATTCCTGATTCACTAAAAGA
1 AATT-AAAGTGAATAGGATTTATTCCTGATTCACT--ATGA
*
88805130 AATTAAAGTGAATAGGATTTATTCCTGATTCACTATAA
1 AATTAAAGTGAATAGGATTTATTCCTGATTCACTATGA
* *
88805168 ATATATAAAGTGGATAGGATTTGTTCCTGATTCACTATGGTA
1 A-AT-TAAAGTGAATAGGATTTATTCCTGATTCACTAT-G-A
* *
88805210 ACTTAAGGTGAATAGGATTT
1 AATTAAAGTGAATAGGATTT
88805230 TCCCTAAAAT
Statistics
Matches: 88, Mismatches: 8, Indels: 9
0.84 0.08 0.09
Matches are distributed among these distances:
38 3 0.03
39 2 0.02
40 76 0.86
41 5 0.06
42 2 0.02
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.35
Consensus pattern (38 bp):
AATTAAAGTGAATAGGATTTATTCCTGATTCACTATGA
Found at i:88810061 original size:10 final size:11
Alignment explanation
Indices: 88810046--88810079 Score: 54
Period size: 10 Copynumber: 3.3 Consensus size: 11
88810036 GCAAAGAACT
88810046 ATTCAAT-TCA
1 ATTCAATATCA
88810056 ATTCAATATCA
1 ATTCAATATCA
88810067 A-TCAATATCA
1 ATTCAATATCA
88810077 ATT
1 ATT
88810080 AATTGTCCAG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 17 0.77
11 5 0.23
ACGTcount: A:0.44, C:0.18, G:0.00, T:0.38
Consensus pattern (11 bp):
ATTCAATATCA
Found at i:88811276 original size:7 final size:7
Alignment explanation
Indices: 88811261--88811301 Score: 50
Period size: 7 Copynumber: 5.9 Consensus size: 7
88811251 CTTTTATATT
88811261 TTAATTAA
1 TTAA-TAA
88811269 TTAATAA
1 TTAATAA
88811276 TTAATAA
1 TTAATAA
88811283 TTAAT-A
1 TTAATAA
88811289 -TAATAA
1 TTAATAA
88811295 TATAATA
1 T-TAATA
88811302 TATATATAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
5 4 0.13
6 2 0.07
7 15 0.50
8 9 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
TTAATAA
Found at i:88817721 original size:25 final size:24
Alignment explanation
Indices: 88817693--88817757 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 24
88817683 GATGTTGATG
*
88817693 TATTTTATATTATTTATTAAATTAT
1 TATTTTAT-TTATTTAATAAATTAT
*
88817718 TATTTTATTATATTTAATAGATTAT
1 TATTTTATT-TATTTAATAAATTAT
88817743 TATTTTATTTTATTT
1 TATTTTA-TTTATTT
88817758 TATTTAGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
24 1 0.03
25 33 0.92
26 2 0.06
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (24 bp):
TATTTTATTTATTTAATAAATTAT
Found at i:88817772 original size:30 final size:30
Alignment explanation
Indices: 88817693--88817772 Score: 83
Period size: 30 Copynumber: 2.6 Consensus size: 30
88817683 GATGTTGATG
88817693 TATTTTATATTATTTATTA-AATTATTATTT
1 TATTTTAT-TTATTTATTATAATTATTATTT
* ** *
88817723 TATTATATTTAATAGATTATTATT-TTATTT
1 TATTTTATTT-ATTTATTATAATTATTATTT
88817753 TATTTTATTTAGTTTATTAT
1 TATTTTATTTA-TTTATTAT
88817773 GTGTGTGTAT
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
29 3 0.08
30 34 0.85
31 3 0.08
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (30 bp):
TATTTTATTTATTTATTATAATTATTATTT
Found at i:88830077 original size:10 final size:11
Alignment explanation
Indices: 88830045--88830078 Score: 54
Period size: 10 Copynumber: 3.3 Consensus size: 11
88830035 CTGGACAATT
88830045 AATTGATATTG
1 AATTGATATTG
88830056 -ATTGATATTG
1 AATTGATATTG
88830066 AATTGA-ATTG
1 AATTGATATTG
88830076 AAT
1 AAT
88830079 AGTTCTTTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 17 0.77
11 5 0.23
ACGTcount: A:0.38, C:0.00, G:0.18, T:0.44
Consensus pattern (11 bp):
AATTGATATTG
Found at i:88834970 original size:40 final size:40
Alignment explanation
Indices: 88834926--88835037 Score: 172
Period size: 40 Copynumber: 2.8 Consensus size: 40
88834916 TTAAGTTACC
* *
88834926 ATAGTGAATCAGGAACAAATCCTATCCACTTTATATAT-TT
1 ATAGTGAATCAGGAATAAATCCTATTCACTTTA-ATATCTT
*
88834966 ATAGTGAATCAGGAATAAATCCTATTCACTTTAATTTCTT
1 ATAGTGAATCAGGAATAAATCCTATTCACTTTAATATCTT
*
88835006 TTAGTGAATCAGGAATAAATCCTATTCACTTT
1 ATAGTGAATCAGGAATAAATCCTATTCACTTT
88835038 TAATTCTCGA
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
39 3 0.04
40 64 0.96
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.38
Consensus pattern (40 bp):
ATAGTGAATCAGGAATAAATCCTATTCACTTTAATATCTT
Found at i:88838504 original size:44 final size:43
Alignment explanation
Indices: 88838385--88839006 Score: 586
Period size: 44 Copynumber: 14.1 Consensus size: 43
88838375 TGCCATCGTC
* * * *
88838385 GATCGGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAA
1 GATCTGCTATCTTCGATCTACTT--CCACCAATATAGGAAGACAA
* * *
88838430 GATCTGC-ATCGTCGATCCACTTCCTACCAATATAGGAAGACAG
1 GATCTGCTATCTTCGATCTACTTCC-ACCAATATAGGAAGACAA
* * * * * *
88838473 GACCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGATAA
1 GATCTGCTATCTTCGATCTACTTC-CACCAATATAGGAAGACAA
* * *
88838517 GATCTGCTTTCTGCGATCTACTTTGCCACCAATATGGGAAGACAA
1 GATCTGCTATCTTCGATCTAC-TT-CCACCAATATAGGAAGACAA
* * * *
88838562 GATCTGTTTTCTGCGATCTACTTTGCCACCAATATGGGAAGACAA
1 GATCTGCTATCTTCGATCTAC-TT-CCACCAATATAGGAAGACAA
* * *
88838607 GATCTGC-ATCTTCGATCCACTTCCTACCAATATAGGAAGATAG
1 GATCTGCTATCTTCGATCTACTTCC-ACCAATATAGGAAGACAA
* * * *
88838650 GATCTGATATCTTCGATCTACTTCACGCCAATACATGAAGACAA
1 GATCTGCTATCTTCGATCTACTTC-CACCAATATAGGAAGACAA
* *
88838694 GATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAA
1 GATCTGCTATCTTCGATCTACTT--CCACCAATATAGGAAGACAA
* * * *
88838739 GATCTGTTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAA
1 GATCTGCTATCTTCGATCTACTT--CCACCAATATAGGAAGACAA
* * *
88838784 GATCTGC-ATCTTCGATCCACTTCCTACCAATATAGGAAGATAG
1 GATCTGCTATCTTCGATCTACTTCC-ACCAATATAGGAAGACAA
* * * *
88838827 GATCTGATATCTTCGATCTACTTCACGCCAATACATGAAGACAA
1 GATCTGCTATCTTCGATCTACTTC-CACCAATATAGGAAGACAA
* * * *
88838871 GATCTGCTTTCTTCGATCTACTTCGCGCCAATACATGAAGACAA
1 GATCTGCTATCTTCGATCTACTTC-CACCAATATAGGAAGACAA
* * *
88838915 GATCTGC-ATCTTCGATCCACTTCCTACCAATATAGGAAGATAG
1 GATCTGCTATCTTCGATCTACTTCC-ACCAATATAGGAAGACAA
* * * *
88838958 GATCTGATATCTTCGATCTACTTCACGCCAATACATGAAGACAA
1 GATCTGCTATCTTCGATCTACTTC-CACCAATATAGGAAGACAA
88839002 GATCT
1 GATCT
88839007 ACTTTAATGA
Statistics
Matches: 482, Mismatches: 79, Indels: 33
0.81 0.13 0.06
Matches are distributed among these distances:
42 7 0.01
43 98 0.20
44 235 0.49
45 140 0.29
46 2 0.00
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (43 bp):
GATCTGCTATCTTCGATCTACTTCCACCAATATAGGAAGACAA
Found at i:88838698 original size:177 final size:177
Alignment explanation
Indices: 88838392--88838981 Score: 916
Period size: 177 Copynumber: 3.3 Consensus size: 177
88838382 GTCGATCGGC
* * * *
88838392 TTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCATCGTCGATCCACTTCCTAC
1 TTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTAC
* * * * *
88838457 CAATATAGGAAGACAGGACCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGATAAGATCT
66 CAATATAGGAAGATAGGATCTGATATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCT
* *
88838522 GCTTTCTGCGATCTACTTTGCCACCAATATGGGAAGACAAGATCTGT
131 GCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGT
*
88838569 TTTCTGCGATCTACTTTGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTAC
1 TTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTAC
88838634 CAATATAGGAAGATAGGATCTGATATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCT
66 CAATATAGGAAGATAGGATCTGATATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCT
88838699 GCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGT
131 GCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGT
88838746 TTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTAC
1 TTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTAC
88838811 CAATATAGGAAGATAGGATCTGATATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCT
66 CAATATAGGAAGATAGGATCTGATATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCT
* ***
88838876 GCTTTCTTCGATCTACTTCG-CGCCAATACATGAAGACAAGATCTG-
131 GCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGT
** * * * * * * * *
88838921 CATCTTCGATCCACTTC-CTACCAATATAGGAAGATAGGATCTGATATCTTCGATCTACTTC
1 TTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTG-CATCTTCGATCCACTTC
88838982 ACGCCAATAC
Statistics
Matches: 385, Mismatches: 27, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
174 22 0.06
175 28 0.07
176 21 0.05
177 314 0.82
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (177 bp):
TTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTAC
CAATATAGGAAGATAGGATCTGATATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCT
GCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGT
Found at i:88855168 original size:51 final size:51
Alignment explanation
Indices: 88855100--88855250 Score: 226
Period size: 51 Copynumber: 3.1 Consensus size: 51
88855090 ATCACATTTA
88855100 TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTG
1 TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTG
88855151 TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCA----
1 TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTG
* * *
88855198 T---TTGTCACTGATCAGATAAGTGTAGCTGAGGCTACCACTCATCACTTG
1 TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTG
88855246 TCACT
1 TCACT
88855251 GATCATAAGT
Statistics
Matches: 90, Mismatches: 3, Indels: 14
0.84 0.03 0.13
Matches are distributed among these distances:
44 40 0.44
47 1 0.01
48 1 0.01
51 48 0.53
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (51 bp):
TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTG
Found at i:88855193 original size:44 final size:44
Alignment explanation
Indices: 88855097--88855255 Score: 219
Period size: 44 Copynumber: 3.5 Consensus size: 44
88855087 CTGATCACAT
88855097 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
88855141 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
1 -T-T-A----TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
* * *
88855192 TTATCATTTGTCACTGATCAGATAAGTGTAGCTGAGGCTACCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
*
88855236 TCATCACTTGTCACTGATCA
1 TTATCACTTGTCACTGATCA
88855256 TAAGTACTCA
Statistics
Matches: 103, Mismatches: 5, Indels: 13
0.85 0.04 0.11
Matches are distributed among these distances:
44 56 0.54
45 1 0.01
46 1 0.01
47 1 0.01
48 1 0.01
49 1 0.01
50 1 0.01
51 41 0.40
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.31
Consensus pattern (44 bp):
TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
Found at i:88857842 original size:29 final size:29
Alignment explanation
Indices: 88857800--88857857 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
88857790 AAGTGAGTGA
88857800 ATGTACCGTAAGGCCGGAGAGAGATAAGT
1 ATGTACCGTAAGGCCGGAGAGAGATAAGT
*
88857829 ATGTACCGTAAGGCCGGGGAGAGATAAGT
1 ATGTACCGTAAGGCCGGAGAGAGATAAGT
88857858 CTTCTTCTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.33, C:0.14, G:0.36, T:0.17
Consensus pattern (29 bp):
ATGTACCGTAAGGCCGGAGAGAGATAAGT
Found at i:88874809 original size:44 final size:43
Alignment explanation
Indices: 88874669--88874826 Score: 153
Period size: 44 Copynumber: 3.7 Consensus size: 43
88874659 AGCATATACA
* * * * *
88874669 ATGCCAACGTCCCAGACGTAGTCTTACATGT-AATCAAACATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAAAACAAA-ATCG
* * * * *
88874712 ATGCTACTGTCCCAAATAGGGTCTTACAC--AAAATC-AAATACG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAAAA-CAAAAT-CG
88874754 ATGCCAATGTCCCAGACATGGTCTTACACGTAAAACAAAAGTCG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAAAACAAAA-TCG
*
88874798 ATGCCAATGTCCCAGACGTGGTCTTACAC
1 ATGCCAATGTCCCAGACATGGTCTTACAC
88874827 AATATCACAT
Statistics
Matches: 92, Mismatches: 16, Indels: 13
0.76 0.13 0.11
Matches are distributed among these distances:
41 2 0.02
42 30 0.33
43 22 0.24
44 37 0.40
45 1 0.01
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.23
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGTAAAACAAAATCG
Found at i:88874826 original size:86 final size:85
Alignment explanation
Indices: 88874664--88874833 Score: 200
Period size: 86 Copynumber: 2.0 Consensus size: 85
88874654 CGGAAAGCAT
* * * * *
88874664 ATACAATGCCAACGTCCCAGACGTAGTCTTACATGTAATCAAACATCGATGCTACTGTCCCAAAT
1 ATACAATGCCAACGTCCCAGACATAGTCTTACACGTAAACAAACATCGATGCCAATGTCCCAAAT
88874729 AGGGTCTTACACAAAATCAA
66 AGGGTCTTACACAAAATCAA
* * * *
88874749 ATACGATGCCAATGTCCCAGACATGGTCTTACACGTAAAACAAA-AGTCGATGCCAATGTCCCAG
1 ATACAATGCCAACGTCCCAGACATAGTCTTACACGT-AAACAAACA-TCGATGCCAATGTCCCAA
* *
88874813 A-CGTGGTCTTACACAATATCA
64 ATAG-GGTCTTACACAAAATCA
88874834 CATATCGGAA
Statistics
Matches: 71, Mismatches: 11, Indels: 5
0.82 0.13 0.06
Matches are distributed among these distances:
85 33 0.46
86 38 0.54
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.23
Consensus pattern (85 bp):
ATACAATGCCAACGTCCCAGACATAGTCTTACACGTAAACAAACATCGATGCCAATGTCCCAAAT
AGGGTCTTACACAAAATCAA
Found at i:88886638 original size:5 final size:5
Alignment explanation
Indices: 88886628--88886656 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
88886618 TATAGTGAGA
88886628 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
88886657 AGAACACACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:88894508 original size:21 final size:22
Alignment explanation
Indices: 88894482--88894541 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 22
88894472 AAAATTAATT
88894482 AATATTTATATA-ATTAAAATA
1 AATATTTATATATATTAAAATA
88894503 AATA-TTATA-ATATT-AAATA
1 AATATTTATATATATTAAAATA
88894522 ATTATATTTAGTATATATTA
1 A--ATATTTA-TATATATTA
88894542 TATTATAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
19 7 0.22
20 8 0.25
21 7 0.22
22 3 0.09
23 2 0.06
24 5 0.16
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
AATATTTATATATATTAAAATA
Found at i:88895272 original size:21 final size:20
Alignment explanation
Indices: 88895248--88895291 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
88895238 TATAATAGCG
88895248 AAACGATAGCAAAACAATGAA
1 AAACGATAGCAAAACAAT-AA
*
88895269 AAAC-AGTGGCAAAACAATAA
1 AAACGA-TAGCAAAACAATAA
88895289 AAA
1 AAA
88895292 TGTAGCAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.64, C:0.14, G:0.14, T:0.09
Consensus pattern (20 bp):
AAACGATAGCAAAACAATAA
Found at i:88896191 original size:42 final size:42
Alignment explanation
Indices: 88896132--88896215 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
88896122 TGAATGGTTT
*
88896132 TTATAACGTCCCCAACCCGGTCTAGACGTTAGACCCGAATTC
1 TTATAACGTCCCCAACCCGGTCTAGACGTTAGACCCAAATTC
*
88896174 TTATAACGTCTCCAACCCGGTCTAGACGTTAGACCCAAATTC
1 TTATAACGTCCCCAACCCGGTCTAGACGTTAGACCCAAATTC
88896216 GAGATATTAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.27, C:0.32, G:0.15, T:0.25
Consensus pattern (42 bp):
TTATAACGTCCCCAACCCGGTCTAGACGTTAGACCCAAATTC
Found at i:88899095 original size:28 final size:29
Alignment explanation
Indices: 88899061--88899122 Score: 90
Period size: 28 Copynumber: 2.1 Consensus size: 29
88899051 ATTGGGATGG
* *
88899061 AAGGAGTAAAAGTTTT-GGGGAAAGTAGA
1 AAGGAGTAAAAGTTTTAGGGAAAAGTAAA
88899089 AAGGAGTAAAAGTTTTAAGGGAAAAGTAAA
1 AAGGAGTAAAAGTTTT-AGGGAAAAGTAAA
88899119 AAGG
1 AAGG
88899123 TTGGGGAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 16 0.53
30 14 0.47
ACGTcount: A:0.48, C:0.00, G:0.32, T:0.19
Consensus pattern (29 bp):
AAGGAGTAAAAGTTTTAGGGAAAAGTAAA
Found at i:88900265 original size:26 final size:26
Alignment explanation
Indices: 88900236--88900421 Score: 150
Period size: 26 Copynumber: 7.4 Consensus size: 26
88900226 AAACGAAACA
* * * *
88900236 AAATAATTTATAAAGCAATTTGAAGT
1 AAATAATATATAAAACAATTTAAAAT
* * *
88900262 AAAT-A-AGATAAAATAATTTGAAAT
1 AAATAATATATAAAACAATTTAAAAT
**
88900286 AAATAATACGTAAAACAATTTAAAAT
1 AAATAATATATAAAACAATTTAAAAT
* *
88900312 AAATAATATACAAAGCAATTTAAAAT
1 AAATAATATATAAAACAATTTAAAAT
** * *
88900338 AAATAATATATATGATACTTT---A-
1 AAATAATATATAAAACAATTTAAAAT
* * *
88900360 AAATAACATATAAAAGAGTTTAAAAT
1 AAATAATATATAAAACAATTTAAAAT
* *
88900386 AAATAATATGTAAAAAAATTTAAAAT
1 AAATAATATATAAAACAATTTAAAAT
88900412 AAATAATATA
1 AAATAATATA
88900422 CATAAATATA
Statistics
Matches: 125, Mismatches: 29, Indels: 12
0.75 0.17 0.07
Matches are distributed among these distances:
22 16 0.13
23 1 0.01
24 18 0.14
25 3 0.02
26 87 0.70
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.31
Consensus pattern (26 bp):
AAATAATATATAAAACAATTTAAAAT
Found at i:88900291 original size:50 final size:52
Alignment explanation
Indices: 88900236--88900423 Score: 165
Period size: 50 Copynumber: 3.7 Consensus size: 52
88900226 AAACGAAACA
* * * * * *
88900236 AAATAATTTATAAAGCAATTTGAAGTAAATAAGATA-AAA-TAATTTGAAAT
1 AAATAATATATAAAACAATTTAAAATAAATAAGATACAAAGCAATTTAAAAT
** *
88900286 AAATAATACGTAAAACAATTTAAAATAAATAATATACAAAGCAATTTAAAAT
1 AAATAATATATAAAACAATTTAAAATAAATAAGATACAAAGCAATTTAAAAT
** * * *
88900338 AAATAATATATATGATACTTTAAAATAACAT---ATA-AAAG-AGTTTAAAAT
1 AAATAATATATAAAACAATTTAAAATAA-ATAAGATACAAAGCAATTTAAAAT
* * *
88900386 AAATAATATGTAAAAAAATTTAAAATAAATAATATACA
1 AAATAATATATAAAACAATTTAAAATAAATAAGATACA
88900424 TAAATATATA
Statistics
Matches: 110, Mismatches: 21, Indels: 13
0.76 0.15 0.09
Matches are distributed among these distances:
47 2 0.02
48 32 0.29
49 4 0.04
50 35 0.32
51 4 0.04
52 31 0.28
53 2 0.02
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.30
Consensus pattern (52 bp):
AAATAATATATAAAACAATTTAAAATAAATAAGATACAAAGCAATTTAAAAT
Found at i:88900408 original size:48 final size:51
Alignment explanation
Indices: 88900276--88900423 Score: 167
Period size: 48 Copynumber: 2.9 Consensus size: 51
88900266 AAGATAAAAT
* * *
88900276 AATTTGAAATAAATAATACGTAAAACAATTTAAAATAAATAATATACAAAGC
1 AATTTAAAATAAATAATATGTAAAAAAATTTAAAAT-AATAATATACAAAGC
* ** * * *
88900328 AATTTAAAATAAATAATATATATGATACTTTAAAATAA-CATATA-AAAG-
1 AATTTAAAATAAATAATATGTAAAAAAATTTAAAATAATAATATACAAAGC
*
88900376 AGTTTAAAATAAATAATATGTAAAAAAATTTAAAATAAATAATATACA
1 AATTTAAAATAAATAATATGTAAAAAAATTTAAAAT-AATAATATACA
88900424 TAAATATATA
Statistics
Matches: 78, Mismatches: 15, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
48 30 0.38
49 6 0.08
50 10 0.13
51 3 0.04
52 29 0.37
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.30
Consensus pattern (51 bp):
AATTTAAAATAAATAATATGTAAAAAAATTTAAAATAATAATATACAAAGC
Found at i:88900719 original size:25 final size:24
Alignment explanation
Indices: 88900670--88900720 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
88900660 AGAACTTAAA
*
88900670 AATAGATAATATATAAAATAATTT
1 AATAGATAATATATAAAACAATTT
*
88900694 AATATGAT-ATATAATAAAACAGTTT
1 AATA-GATAATAT-ATAAAACAATTT
88900719 AA
1 AA
88900721 AGTAAAAGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 8 0.35
25 15 0.65
ACGTcount: A:0.57, C:0.02, G:0.06, T:0.35
Consensus pattern (24 bp):
AATAGATAATATATAAAACAATTT
Found at i:88902503 original size:13 final size:14
Alignment explanation
Indices: 88902482--88902510 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
88902472 TGAAAAATGG
88902482 ATTAGAAAATATTT
1 ATTAGAAAATATTT
88902496 ATTA-AAAATATTT
1 ATTAGAAAATATTT
88902509 AT
1 AT
88902511 GAAGTTAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (14 bp):
ATTAGAAAATATTT
Found at i:88903073 original size:31 final size:32
Alignment explanation
Indices: 88903024--88903087 Score: 87
Period size: 31 Copynumber: 2.0 Consensus size: 32
88903014 ATATTAAATA
*
88903024 AGATATTTATTAATTAAATA-ATTATATTATG
1 AGATATTTATTAATTAAATATATTAAATTATG
*
88903055 AGATTTTTATGTAA-TAAATATATTAAATTATG
1 AGATATTTAT-TAATTAAATATATTAAATTATG
88903087 A
1 A
88903088 CAAATGTATG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 15 0.52
32 14 0.48
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (32 bp):
AGATATTTATTAATTAAATATATTAAATTATG
Found at i:88903591 original size:15 final size:15
Alignment explanation
Indices: 88903568--88903615 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
88903558 TATCAAATTT
88903568 ATATTGATTGAAATC
1 ATATTGATTGAAATC
* * *
88903583 ATTTTGATTGAATTT
1 ATATTGATTGAAATC
88903598 ATATTGATTGAAAT-
1 ATATTGATTGAAATC
88903612 ATAT
1 ATAT
88903616 ATATGATTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
14 4 0.14
15 24 0.86
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (15 bp):
ATATTGATTGAAATC
Found at i:88905415 original size:38 final size:37
Alignment explanation
Indices: 88905332--88905420 Score: 124
Period size: 38 Copynumber: 2.4 Consensus size: 37
88905322 TAAGGGGTGT
*
88905332 TACAGTAGACATGTTTAATATGTATTCGGTTCAACAG
1 TACAGTAGACATGTTTAACATGTATTCGGTTCAACAG
* * *
88905369 TAGTAGTAGGCATGTTTAACATGTATTCGGTTCAACCG
1 TA-CAGTAGACATGTTTAACATGTATTCGGTTCAACAG
88905407 TGACAGTAGACATG
1 T-ACAGTAGACATG
88905421 CAACTAATAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
37 2 0.05
38 41 0.93
39 1 0.02
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (37 bp):
TACAGTAGACATGTTTAACATGTATTCGGTTCAACAG
Found at i:88909053 original size:53 final size:53
Alignment explanation
Indices: 88908897--88909062 Score: 212
Period size: 53 Copynumber: 3.1 Consensus size: 53
88908887 GACGAAAAAT
* **
88908897 ATGTGATAAGTGTG-C-CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCA
1 ATGTGATAA-TGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
88908949 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
1 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
* * * *
88909002 ATGTGATAATGTGATTCCGTATAAGACTAT-GTCTGGGATATGGCTTCGGTATGA
1 ATGTGATAATGTGACTCCGTATAAGACCATAG-CTGGGCTATGGCATCGGTAT-A
88909056 TATGTGA
1 -ATGTGA
88909063 ACTGTGTAAG
Statistics
Matches: 102, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
51 4 0.04
52 11 0.11
53 80 0.78
54 1 0.01
55 6 0.06
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (53 bp):
ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
Found at i:88916481 original size:53 final size:53
Alignment explanation
Indices: 88916400--88916548 Score: 205
Period size: 53 Copynumber: 2.8 Consensus size: 53
88916390 GACGAAAAAT
* *
88916400 ATGTGATAAGTGTG-C-CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCA
1 ATGTGATAA-TGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTACA
*
88916452 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
1 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTACA
* * *
88916505 ATGTGATAATGTGATTCCATATAAGACCAT-GTCTGGGATATGGC
1 ATGTGATAATGTGACTCCGTATAAGACCATAG-CTGGGCTATGGC
88916549 TTCGCTATGA
Statistics
Matches: 88, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
51 4 0.05
52 11 0.12
53 73 0.83
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.29
Consensus pattern (53 bp):
ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTACA
Found at i:88919178 original size:41 final size:41
Alignment explanation
Indices: 88919121--88919200 Score: 160
Period size: 41 Copynumber: 2.0 Consensus size: 41
88919111 CAATGAGTAA
88919121 GTTTTGTCAAATGATGTTATTTCAAATCTGTAACTTGTTAG
1 GTTTTGTCAAATGATGTTATTTCAAATCTGTAACTTGTTAG
88919162 GTTTTGTCAAATGATGTTATTTCAAATCTGTAACTTGTT
1 GTTTTGTCAAATGATGTTATTTCAAATCTGTAACTTGTT
88919201 TCTAAGATTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.26, C:0.10, G:0.16, T:0.47
Consensus pattern (41 bp):
GTTTTGTCAAATGATGTTATTTCAAATCTGTAACTTGTTAG
Found at i:88922703 original size:20 final size:19
Alignment explanation
Indices: 88922674--88922721 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
88922664 ATAGTATTTT
*
88922674 ATTTTATTTTCTATATTATA
1 ATTTTTTTTTCTA-ATTATA
* *
88922694 ATTTTTTTTTGTAATTATG
1 ATTTTTTTTTCTAATTATA
88922713 ATTTTTTTT
1 ATTTTTTTT
88922722 ATTTTATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.71
Consensus pattern (19 bp):
ATTTTTTTTTCTAATTATA
Found at i:88923036 original size:22 final size:22
Alignment explanation
Indices: 88923008--88923053 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
88922998 GACATGTTTA
88923008 ACGATATAGGTATGAACAGATT
1 ACGATATAGGTATGAACAGATT
88923030 ACGATATAGGTATGAACAGATT
1 ACGATATAGGTATGAACAGATT
88923052 AC
1 AC
88923054 CTACAAATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.41, C:0.11, G:0.22, T:0.26
Consensus pattern (22 bp):
ACGATATAGGTATGAACAGATT
Found at i:88945311 original size:33 final size:33
Alignment explanation
Indices: 88945239--88945315 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 33
88945229 AACATTTATA
* * *
88945239 AGTAAGACCATAGTTGGGCTATGACATTCTAAT
1 AGTAAGACCATAATTGGGCTATGACATACAAAT
* *
88945272 AATAAGACCATAATTGGGTTATGACACTACAAAT
1 AGTAAGACCATAATTGGGCTATGACA-TACAAAT
88945306 -GTAAGACCAT
1 AGTAAGACCAT
88945316 GGCCGAGCCA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
33 32 0.86
34 5 0.14
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (33 bp):
AGTAAGACCATAATTGGGCTATGACATACAAAT
Found at i:88947086 original size:52 final size:54
Alignment explanation
Indices: 88947016--88947157 Score: 157
Period size: 52 Copynumber: 2.7 Consensus size: 54
88947006 TGATATATGT
* *
88947016 TTCC-GTATAAGGCCATAGCTGGGCTATAGCATCGGTACAATGTGAT-ACGTG-
1 TTCCAGTATAAGACCATAGCTGGGCTATGGCATCGGTACAATGTGATAACGTGA
* * *** *
88947067 TTCCAGTATAAGACTATAGCTGGGCTATGGCGTCGGTGTGATGTGATAATGTGA
1 TTCCAGTATAAGACCATAGCTGGGCTATGGCATCGGTACAATGTGATAACGTGA
* * *
88947121 TTCTA-TATAAGACCATATCTGGGATATGGCATCGGTA
1 TTCCAGTATAAGACCATAGCTGGGCTATGGCATCGGTA
88947158 TTATATGTGA
Statistics
Matches: 74, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
51 4 0.05
52 35 0.47
53 31 0.42
54 4 0.05
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.30
Consensus pattern (54 bp):
TTCCAGTATAAGACCATAGCTGGGCTATGGCATCGGTACAATGTGATAACGTGA
Found at i:88947684 original size:31 final size:31
Alignment explanation
Indices: 88947649--88947710 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
88947639 AATGAATAAG
88947649 TATGCAAAGTAAGTTGAATGTGATGTTTTGT
1 TATGCAAAGTAAGTTGAATGTGATGTTTTGT
88947680 TATGCAAAGTAAGTTGAATGTGATGTTTTGT
1 TATGCAAAGTAAGTTGAATGTGATGTTTTGT
88947711 GTTTGAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.29, C:0.03, G:0.26, T:0.42
Consensus pattern (31 bp):
TATGCAAAGTAAGTTGAATGTGATGTTTTGT
Found at i:88949669 original size:28 final size:28
Alignment explanation
Indices: 88949637--88949694 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
88949627 TATTTATTAG
88949637 AAATATTTACAAAGCTAATAGTATAGTT
1 AAATATTTACAAAGCTAATAGTATAGTT
**
88949665 AAATATTTACGGAGCTAATAGTATAGTT
1 AAATATTTACAAAGCTAATAGTATAGTT
88949693 AA
1 AA
88949695 TTAGACTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.34
Consensus pattern (28 bp):
AAATATTTACAAAGCTAATAGTATAGTT
Found at i:88949944 original size:17 final size:16
Alignment explanation
Indices: 88949922--88949955 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
88949912 AAATAATGTT
88949922 ATATTATAATTATATTA
1 ATATTATAA-TATATTA
88949939 ATATTATAATATATTA
1 ATATTATAATATATTA
88949955 A
1 A
88949956 GTGAATAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATATTATAATATATTA
Found at i:88950912 original size:6 final size:6
Alignment explanation
Indices: 88950892--88950947 Score: 67
Period size: 6 Copynumber: 9.2 Consensus size: 6
88950882 ATAAGGTACT
* * * *
88950892 CTGTGTA CTGATA CTGCTA CTGTTA CTGTTA CTATTA TTGTTA CTGTTA
1 CTGT-TA CTGTTA CTGTTA CTGTTA CTGTTA CTGTTA CTGTTA CTGTTA
88950941 CTGTTA C
1 CTGTTA C
88950948 AGAGTATTCT
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
6 39 0.93
7 3 0.07
ACGTcount: A:0.20, C:0.18, G:0.16, T:0.46
Consensus pattern (6 bp):
CTGTTA
Found at i:88952745 original size:13 final size:13
Alignment explanation
Indices: 88952727--88952751 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
88952717 TAATGGTATA
88952727 TTGAATCCATGAT
1 TTGAATCCATGAT
88952740 TTGAATCCATGA
1 TTGAATCCATGA
88952752 AAATTTAGTA
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TTGAATCCATGAT
Found at i:88954078 original size:47 final size:47
Alignment explanation
Indices: 88954009--88954601 Score: 776
Period size: 47 Copynumber: 12.3 Consensus size: 47
88953999 CTCGTAGTGA
88954009 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
1 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
* *
88954056 ATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATAT
1 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TAT
*
88954105 ATATGTGATAAGTCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
1 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
* ** * *
88954152 ATATGTGATAAGGCCGAATCACCAATGTGATGAATGTGAAAGAGTATAT
1 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG-AA-AGTGTAT
88954201 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--T
1 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
* *
88954246 ATATGTGATAAGGCCTAATAGCCGATGTGATAAATGTGAAAGTGTAT
1 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
* *
88954293 ATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATAT
1 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TAT
88954342 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
1 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
*
88954389 ATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTAT
1 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
*
88954436 ATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTAT
1 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
* *
88954483 ATATGTGGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
1 ATA--T-GTG-ATA-A---G----GCCT-AATGGCCGATGTGATGAATGTGAAAGTGTAT
* * * * * * * *
88954543 ATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTAC
1 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
*
88954590 AAATGTGATAAG
1 ATATGTGATAAG
88954602 TCCCGAAGGG
Statistics
Matches: 485, Mismatches: 40, Indels: 42
0.86 0.07 0.07
Matches are distributed among these distances:
45 43 0.09
47 256 0.53
48 6 0.01
49 130 0.27
50 3 0.01
51 3 0.01
52 2 0.00
55 1 0.00
56 2 0.00
57 3 0.01
58 1 0.00
59 2 0.00
60 33 0.07
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (47 bp):
ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
Found at i:88954177 original size:96 final size:96
Alignment explanation
Indices: 88954009--88954601 Score: 783
Period size: 96 Copynumber: 6.1 Consensus size: 96
88953999 CTCGTAGTGA
88954009 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAA
1 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAA
*
88954074 TGGCCAATGTGATGAATGTGAAAGTGTATAT
66 TGACCAATGTGATGAATGTGAAAGTGTATAT
*
88954105 ATATGTGATAAGTCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAA
1 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAA
* *
88954170 TCACCAATGTGATGAATGTGAAAGAGTATAT
66 TGACCAATGTGATGAATGTGAAAGTGTATAT
*
88954201 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATGTGATAAGGCCTAA
1 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAA
* *
88954264 T-AGCCGATGTGATAAATGTGAAAGTG--TAT
66 TGA-CCAATGTGATGAATGTGAAAGTGTATAT
* * *
88954293 ATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCT
1 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCG
* *
88954358 AATGGCCGATGTGATGAATGTGAAAGTG--TAT
64 AATGACCAATGTGATGAATGTGAAAGTGTATAT
* *
88954389 ATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAA
1 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAA
*
88954454 T-AGCCGATGTGATGAATGTGAAAGTGTATATATGTGGTGTAT
66 TGA-CCAATGTGATGAATGTGAAAGTG----TA-------TAT
* * *
88954496 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAG
1 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAA
* * * *
88954561 TGGCCAACGTGATGGATGTGAAAGTGTACA-
66 TGACCAATGTGATGAATGTGAAAGTGTATAT
88954591 A-ATGTGATAAG
1 ATATGTGATAAG
88954602 TCCCGAAGGG
Statistics
Matches: 449, Mismatches: 27, Indels: 44
0.86 0.05 0.08
Matches are distributed among these distances:
92 45 0.10
93 1 0.00
94 94 0.21
95 1 0.00
96 222 0.49
103 2 0.00
107 84 0.19
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (96 bp):
ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAA
TGACCAATGTGATGAATGTGAAAGTGTATAT
Found at i:88954424 original size:237 final size:240
Alignment explanation
Indices: 88954003--88954601 Score: 899
Period size: 237 Copynumber: 2.5 Consensus size: 240
88953993 AAGCAGCTCG
*
88954003 TAGTGAATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
1 TAGTGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
*
88954068 GCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGTCCTAATGGCCGATGT
66 GCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGT
88954133 GATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATCACCAATGTGATGAATGTGAAAGAGTA
131 GATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATCACCAATGTGATGAATGTG-AA-AGTA
*
88954198 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAA-T-GTG-A-A
194 TATATATGTGATAAGGCCTAATAGCCGATGTGATGAAGTAGTGTATA
* *
88954241 -AGTGTATATGTGATAAGGCCTAATAGCCGATGTGATAAATGTGAAAGTGTATATATGTGATAAG
1 TAGTGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
88954305 GCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGT
66 GCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGT
* * *
88954370 GATGAATGTGAAAGTGTATATATGTGATAAGGCCTAAT-AGCCGATGTGATGAATGTGAAAGTGT
131 GATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATCA-CCAATGTGATGAATGTGAAAGTAT
88954434 ATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATA
195 ATATATGTGATAAGGCCTAATAGCCGATGTGATGAA-GT---AGTGTATA
88954484 TATGTGGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGT
1 TA----GTG--TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGT
* * * * * *
88954549 GACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTACA-A-ATGTGATAAG
60 GATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAG
88954602 TCCCGAAGGG
Statistics
Matches: 329, Mismatches: 16, Indels: 22
0.90 0.04 0.06
Matches are distributed among these distances:
235 39 0.12
236 3 0.01
237 179 0.54
241 3 0.01
242 1 0.00
243 1 0.00
244 1 0.00
248 13 0.04
249 1 0.00
250 88 0.27
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (240 bp):
TAGTGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
GCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGT
GATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATCACCAATGTGATGAATGTGAAAGTATA
TATATGTGATAAGGCCTAATAGCCGATGTGATGAAGTAGTGTATA
Found at i:88954495 original size:13 final size:13
Alignment explanation
Indices: 88954477--88954502 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
88954467 GAATGTGAAA
88954477 GTGTATATATGTG
1 GTGTATATATGTG
88954490 GTGTATATATGTG
1 GTGTATATATGTG
88954503 ATAAGGCCTA
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:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (13 bp):
GTGTATATATGTG
Found at i:88954500 original size:60 final size:60
Alignment explanation
Indices: 88954430--88954549 Score: 231
Period size: 60 Copynumber: 2.0 Consensus size: 60
88954420 GAATGTGAAA
88954430 GTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTG
1 GTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTG
*
88954490 GTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTG
1 GTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTG
88954550 ACAGGGCCGA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.31, C:0.07, G:0.29, T:0.33
Consensus pattern (60 bp):
GTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTG
Found at i:88954506 original size:107 final size:107
Alignment explanation
Indices: 88954383--88954588 Score: 331
Period size: 107 Copynumber: 1.9 Consensus size: 107
88954373 GAATGTGAAA
*
88954383 GTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
1 GTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAAG
* * *
88954448 GCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTG
66 GCCGAATAGCCAACGTGATGAATGTGAAAGTGTATATATGTG
* *
88954490 GTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAGG
1 GTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAAG
* * *
88954555 GCCGAGTGGCCAACGTGATGGATGTGAAAGTGTA
66 GCCGAATAGCCAACGTGATGAATGTGAAAGTGTA
88954589 CAAATGTGAT
Statistics
Matches: 90, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
107 90 1.00
ACGTcount: A:0.31, C:0.09, G:0.31, T:0.30
Consensus pattern (107 bp):
GTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAAG
GCCGAATAGCCAACGTGATGAATGTGAAAGTGTATATATGTG
Found at i:88954533 original size:31 final size:31
Alignment explanation
Indices: 88954438--88954534 Score: 89
Period size: 31 Copynumber: 3.2 Consensus size: 31
88954428 AAGTGTATAT
*
88954438 ATGTGATAAGGCCTAATAGCCGATGTGATGA
1 ATGTGATAAGGCCTAATGGCCGATGTGATGA
**
88954469 ATGTGA-AAGTGTATATATGTG--G-TGT-AT-A
1 ATGTGATAAG-GCCTA-ATG-GCCGATGTGATGA
88954497 TATGTGATAAGGCCTAATGGCCGATGTGATGA
1 -ATGTGATAAGGCCTAATGGCCGATGTGATGA
88954529 ATGTGA
1 ATGTGA
88954535 AAGTGTATAT
Statistics
Matches: 51, Mismatches: 5, Indels: 20
0.67 0.07 0.26
Matches are distributed among these distances:
27 1 0.02
28 4 0.08
29 12 0.24
30 12 0.24
31 18 0.35
32 3 0.06
33 1 0.02
ACGTcount: A:0.31, C:0.08, G:0.30, T:0.31
Consensus pattern (31 bp):
ATGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:88956376 original size:40 final size:40
Alignment explanation
Indices: 88956065--88956364 Score: 429
Period size: 40 Copynumber: 7.5 Consensus size: 40
88956055 TGAAATGTCT
* *
88956065 GGGCTAAATCTCGAAGAGCATTCGTGCTAGTGATGTATCC
1 GGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCC
* *
88956105 GGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCC
1 GGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCC
* * *
88956145 GGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATATATCC
1 GGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCC
88956185 GGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCC
1 GGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCC
*
88956225 GGGCTAAGTCTCGAAGAGCATTCGTGCTAGTGATGTATCC
1 GGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCC
* * *
88956265 GGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATATATCC
1 GGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCC
* ** * * * *
88956305 GTGCTAAACCCCGAAGAGCATTTGTGCTGGTGTTTTATCC
1 GGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCC
*
88956345 GGGCTAGGTCCCGAAGAGCA
1 GGGCTAAGTCCCGAAGAGCA
88956365 ATCATGCTGG
Statistics
Matches: 232, Mismatches: 28, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 232 1.00
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCC
Found at i:88958560 original size:13 final size:13
Alignment explanation
Indices: 88958542--88958566 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
88958532 TAATGGTATA
88958542 TTGAATCCATGAT
1 TTGAATCCATGAT
88958555 TTGAATCCATGA
1 TTGAATCCATGA
88958567 AAATTTAGTA
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TTGAATCCATGAT
Found at i:88959895 original size:47 final size:47
Alignment explanation
Indices: 88959826--88960371 Score: 745
Period size: 47 Copynumber: 11.3 Consensus size: 47
88959816 CTCGTAGTGA
*
88959826 ATATGTGATAAGGCCTAATGGCCGATGTGATAAATGTGAAAGTGTAT
1 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
* *
88959873 ATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATAT
1 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TAT
88959922 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
1 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
88959969 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TAT
88960018 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--T
1 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
*
88960063 ATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTAT
1 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
* * *
88960110 ATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTCTATAT
1 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG--TGTAT
88960159 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
1 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
*
88960206 ATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTAT
1 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
* *
88960253 ATATGTGGTGTATACATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
1 ATA--T-GTG-ATA-A---G----GCCT-AATGGCCGATGTGATGAATGTGAAAGTGTAT
* * * * * * *
88960313 ATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTAT
1 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
*
88960360 AAATGTGATAAG
1 ATATGTGATAAG
88960372 TCCCGAAGGG
Statistics
Matches: 450, Mismatches: 28, Indels: 42
0.87 0.05 0.08
Matches are distributed among these distances:
45 44 0.10
47 217 0.48
48 2 0.00
49 137 0.30
50 3 0.01
51 3 0.01
52 2 0.00
55 1 0.00
56 2 0.00
57 3 0.01
58 1 0.00
59 2 0.00
60 33 0.07
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (47 bp):
ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
Found at i:88959990 original size:96 final size:94
Alignment explanation
Indices: 88959826--88960371 Score: 763
Period size: 96 Copynumber: 5.6 Consensus size: 94
88959816 CTCGTAGTGA
* *
88959826 ATATGTGATAAGGCCTAATGGCCGATGTGATAAATGTGAAAGTGTATATATGTGATAAGGCCGAA
1 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAA
*
88959891 TGGCCAATGTGATGAATGTGAAAGTGTATAT
66 TGGCCGATGTGATGAATGTGAAAGTG--TAT
88959922 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAA
1 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAA
88959987 TGGCCGATGTGATGAATGTGAAAGTGTATAT
66 TGGCCGATGTGATGAATGTGAAAGTG--TAT
88960018 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATGTGATAAGGCCTAA
1 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAA
*
88960081 TAGCCGATGTGATGAATGTGAAAGTGTAT
66 TGGCCGATGTGATGAATGTGAAAGTGTAT
* * *
88960110 ATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTCTATATATATGTGATAAGGCCT
1 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG--TGTATATATGTGATAAGGCCT
88960175 AATGGCCGATGTGATGAATGTGAAAGTGTAT
64 AATGGCCGATGTGATGAATGTGAAAGTGTAT
*
88960206 ATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGGTGTATACATG
1 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG----TA-------TAT--ATG
88960271 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
53 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
* * * * * * * *
88960313 ATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
88960372 TCCCGAAGGG
Statistics
Matches: 412, Mismatches: 21, Indels: 36
0.88 0.04 0.08
Matches are distributed among these distances:
92 43 0.10
94 56 0.14
96 225 0.55
98 2 0.00
103 2 0.00
105 3 0.01
107 81 0.20
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (94 bp):
ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAA
TGGCCGATGTGATGAATGTGAAAGTGTAT
Found at i:88960241 original size:237 final size:240
Alignment explanation
Indices: 88959821--88960371 Score: 874
Period size: 237 Copynumber: 2.3 Consensus size: 240
88959811 AACAGCTCGT
* *
88959821 AGTGAATATGTGATAAGGCCTAATGGCCGATGTGATAAATGTGAAAGTGTATATATGTGATAAGG
1 AGTGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGG
*
88959886 CCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTG
66 CCGAATGGCCAATGTGATGAATGTGAAAGTCTATATATATGTGATAAGGCCTAATGGCCGATGTG
*
88959951 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG-TA
131 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGATA
88960015 TA-TAT-ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
196 TAGTATAATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
88960058 AGTGTATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGG
1 AGTGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGG
88960123 CCGAATGGCCAATGTGATGAATGTGAAAGTCTATATATATGTGATAAGGCCTAATGGCCGATGTG
66 CCGAATGGCCAATGTGATGAATGTGAAAGTCTATATATATGTGATAAGGCCTAATGGCCGATGTG
88960188 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTAT
131 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG-AT
88960253 ATATGTGGTGTATACATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
195 ATA------GTATA-ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* * * * * * * *
88960306 AGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGATAA
1 AGTG--TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
88960371 G
64 G
88960372 TCCCGAAGGG
Statistics
Matches: 287, Mismatches: 14, Indels: 13
0.91 0.04 0.04
Matches are distributed among these distances:
237 187 0.65
239 4 0.01
246 3 0.01
248 42 0.15
250 51 0.18
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (240 bp):
AGTGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGG
CCGAATGGCCAATGTGATGAATGTGAAAGTCTATATATATGTGATAAGGCCTAATGGCCGATGTG
ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGATA
TAGTATAATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
Found at i:88960272 original size:60 final size:60
Alignment explanation
Indices: 88960200--88960319 Score: 222
Period size: 60 Copynumber: 2.0 Consensus size: 60
88960190 GAATGTGAAA
*
88960200 GTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTG
1 GTGTATACATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTG
*
88960260 GTGTATACATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTG
1 GTGTATACATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTG
88960320 ACAGGGCCGA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.31, C:0.07, G:0.29, T:0.33
Consensus pattern (60 bp):
GTGTATACATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTG
Found at i:88960283 original size:107 final size:107
Alignment explanation
Indices: 88960156--88960366 Score: 332
Period size: 107 Copynumber: 2.0 Consensus size: 107
88960146 TGAAAGTCTA
* *
88960156 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
1 TATACATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAAGGCC
* * * *
88960221 TAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGGTG
66 GAATAGCCAACGTGATGAATGTGAAAGTGTATAAATGTGGTG
*
88960263 TATACATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCC
1 TATACATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAAGGCC
* * *
88960328 GAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTG
66 GAATAGCCAACGTGATGAATGTGAAAGTGTATAAATGTG
88960367 ATAAGTCCCG
Statistics
Matches: 94, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
107 94 1.00
ACGTcount: A:0.31, C:0.09, G:0.30, T:0.29
Consensus pattern (107 bp):
TATACATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAAGGCC
GAATAGCCAACGTGATGAATGTGAAAGTGTATAAATGTGGTG
Found at i:88960303 original size:31 final size:31
Alignment explanation
Indices: 88960208--88960304 Score: 89
Period size: 31 Copynumber: 3.2 Consensus size: 31
88960198 AAGTGTATAT
*
88960208 ATGTGATAAGGCCTAATAGCCGATGTGATGA
1 ATGTGATAAGGCCTAATGGCCGATGTGATGA
**
88960239 ATGTGA-AAGTGTATATATGTG--G-TGT-AT-A
1 ATGTGATAAG-GCCTA-ATG-GCCGATGTGATGA
88960267 CATGTGATAAGGCCTAATGGCCGATGTGATGA
1 -ATGTGATAAGGCCTAATGGCCGATGTGATGA
88960299 ATGTGA
1 ATGTGA
88960305 AAGTGTATAT
Statistics
Matches: 51, Mismatches: 5, Indels: 20
0.67 0.07 0.26
Matches are distributed among these distances:
27 1 0.02
28 4 0.08
29 12 0.24
30 12 0.24
31 18 0.35
32 3 0.06
33 1 0.02
ACGTcount: A:0.31, C:0.09, G:0.30, T:0.30
Consensus pattern (31 bp):
ATGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:88963994 original size:28 final size:28
Alignment explanation
Indices: 88963932--88963995 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 28
88963922 AATTTAATTT
** * *
88963932 AATTTAATAATAATTAATATGTTATATA
1 AATTTAATAATAAACAATATCTAATATA
*
88963960 AACTTAATAATAAACAATATCTAAT-TA
1 AATTTAATAATAAACAATATCTAATATA
88963987 CAATTTAAT
1 -AATTTAAT
88963996 TTGAAATTAC
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
27 2 0.07
28 27 0.93
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.41
Consensus pattern (28 bp):
AATTTAATAATAAACAATATCTAATATA
Found at i:88970910 original size:31 final size:31
Alignment explanation
Indices: 88970874--88970934 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
88970864 TAAAAACCAG
*
88970874 TGACTTCAATAAAAGCTATCGAATAGTTCAA
1 TGACTTAAATAAAAGCTATCGAATAGTTCAA
* * *
88970905 TGACTTAAATGAAAGCTTTTGAATAGTTCA
1 TGACTTAAATAAAAGCTATCGAATAGTTCA
88970935 GTAATATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (31 bp):
TGACTTAAATAAAAGCTATCGAATAGTTCAA
Found at i:88975062 original size:31 final size:31
Alignment explanation
Indices: 88974996--88975063 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
88974986 TTCGGTTCAC
*
88974996 TTAAAATTTAATTTAAATAATAAAAATATTT
1 TTAAAATTTAATTTAAATAATAAAAATATTA
*
88975027 TTAAAATTTAAATTT-AATTAT-AAAATATTAA
1 TTAAAATTT-AATTTAAATAATAAAAATATT-A
88975058 TTAAAA
1 TTAAAA
88975064 ATATATTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 8 0.24
31 20 0.61
32 5 0.15
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (31 bp):
TTAAAATTTAATTTAAATAATAAAAATATTA
Found at i:88975465 original size:12 final size:12
Alignment explanation
Indices: 88975448--88975473 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
88975438 TTTTTCTGAA
88975448 TTTTTATAATTT
1 TTTTTATAATTT
88975460 TTTTTATAATTT
1 TTTTTATAATTT
88975472 TT
1 TT
88975474 GAGTACTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTTATAATTT
Found at i:88976817 original size:61 final size:60
Alignment explanation
Indices: 88976703--88976818 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 60
88976693 ACCTTGACAC
* * * *
88976703 TTTTTTTAATTTGGTATCTAAACTTTTTTTAGGCCCAATTTGGTACTTGAATTTAATATT
1 TTTTTTTAATTTGGTACCTAAAATTTTTTTAAGCCCAATTTGGTACTTAAATTTAATATT
**
88976763 TTTTTCTTAATTTGGTACCTAAAATTTTTTTAAGTTCAATTTGGTA-TCTAAATTTA
1 TTTTT-TTAATTTGGTACCTAAAATTTTTTTAAGCCCAATTTGGTACT-TAAATTTA
88976819 CTAAATATTA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
60 6 0.12
61 42 0.88
ACGTcount: A:0.27, C:0.09, G:0.10, T:0.53
Consensus pattern (60 bp):
TTTTTTTAATTTGGTACCTAAAATTTTTTTAAGCCCAATTTGGTACTTAAATTTAATATT
Found at i:88977289 original size:31 final size:31
Alignment explanation
Indices: 88977252--88977327 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
88977242 CTCCAAAAAA
* *
88977252 TTTAAGTACCAACTTA-AGAAAAAGTGTCAAG
1 TTTAAGTACCAAATTAGA-AAAAAGTGACAAG
* *
88977283 TTTAAGTATCAAATTAGAAAAAAGTGAGAAG
1 TTTAAGTACCAAATTAGAAAAAAGTGACAAG
*
88977314 TTCAAGTACCAAAT
1 TTTAAGTACCAAAT
88977328 GTTATATTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
31 37 0.97
32 1 0.03
ACGTcount: A:0.47, C:0.11, G:0.16, T:0.26
Consensus pattern (31 bp):
TTTAAGTACCAAATTAGAAAAAAGTGACAAG
Found at i:88992072 original size:8 final size:8
Alignment explanation
Indices: 88992059--88992083 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
88992049 ATATATACTA
88992059 AATAAAAT
1 AATAAAAT
88992067 AATAAAAT
1 AATAAAAT
88992075 AATAAAAT
1 AATAAAAT
88992083 A
1 A
88992084 TCATTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AATAAAAT
Found at i:88995319 original size:25 final size:25
Alignment explanation
Indices: 88995291--88995373 Score: 96
Period size: 25 Copynumber: 3.3 Consensus size: 25
88995281 CAACTCACAT
* *
88995291 GAGCTTACTGTTACTCAGTTCGGAG
1 GAGCTTACTGTTATTCAGCTCGGAG
* *
88995316 GAGCTTATTGTTATTCAACTCGGAG
1 GAGCTTACTGTTATTCAGCTCGGAG
* *
88995341 GAGCTTA-TCGTTATTCAGCTCGAAA
1 GAGCTTACT-GTTATTCAGCTCGGAG
88995366 GAGCTTAC
1 GAGCTTAC
88995374 CATTTACAGC
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
24 1 0.02
25 48 0.98
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (25 bp):
GAGCTTACTGTTATTCAGCTCGGAG
Found at i:88999994 original size:14 final size:14
Alignment explanation
Indices: 88999977--89000011 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
88999967 AATCACATCT
*
88999977 TATTCATTTGTTCA
1 TATTCATTTGTACA
88999991 TATTTCATTTGTACA
1 TA-TTCATTTGTACA
89000006 TATTCA
1 TATTCA
89000012 CATTTCATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.26, C:0.14, G:0.06, T:0.54
Consensus pattern (14 bp):
TATTCATTTGTACA
Found at i:88999999 original size:15 final size:15
Alignment explanation
Indices: 88999979--89000009 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
88999969 TCACATCTTA
*
88999979 TTCATTTGTTCATAT
1 TTCATTTGTACATAT
88999994 TTCATTTGTACATAT
1 TTCATTTGTACATAT
89000009 T
1 T
89000010 CACATTTCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.13, G:0.06, T:0.58
Consensus pattern (15 bp):
TTCATTTGTACATAT
Found at i:89000276 original size:43 final size:41
Alignment explanation
Indices: 89000198--89000355 Score: 138
Period size: 43 Copynumber: 3.7 Consensus size: 41
89000188 AGCTCGTACA
* *
89000198 ATGCCAATGTCCTAGACATGGTCTTACATGTAATCAAACATCG
1 ATGCC-ATGTCCTAGACATGGTCTTACACGAAATCAAACA-CG
* * * *
89000241 ATGCCACTGTCCCAGACAGGGTCTTACACGAAATCATATACG
1 ATGCCA-TGTCCTAGACATGGTCTTACACGAAATCAAACACG
* **
89000283 ATACCGATGTCCTAGACATGGTCTTACACGTAAATCTCAAA-TTG
1 ATGCC-ATGTCCTAGACATGGTCTTACACG-AAA--TCAAACACG
* *
89000327 ATGTCGATGTCCAAGACATGGTCTTACAC
1 ATG-CCATGTCCTAGACATGGTCTTACAC
89000356 AATATCACAT
Statistics
Matches: 94, Mismatches: 15, Indels: 11
0.78 0.12 0.09
Matches are distributed among these distances:
42 28 0.30
43 36 0.38
44 25 0.27
45 5 0.05
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.27
Consensus pattern (41 bp):
ATGCCATGTCCTAGACATGGTCTTACACGAAATCAAACACG
Found at i:89005910 original size:19 final size:18
Alignment explanation
Indices: 89005862--89005916 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
89005852 TGCTCATCCA
*
89005862 TGTTTTGAATGTTAATGT
1 TGTTTTGAATGTTAAGGT
* *
89005880 TGCTTTGTATGTTAAGGT
1 TGTTTTGAATGTTAAGGT
* *
89005898 TGATTTTGCATGTCAAGGT
1 TG-TTTTGAATGTTAAGGT
89005917 CGAAAAAGGC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
18 17 0.57
19 13 0.43
ACGTcount: A:0.20, C:0.05, G:0.25, T:0.49
Consensus pattern (18 bp):
TGTTTTGAATGTTAAGGT
Found at i:89014941 original size:26 final size:22
Alignment explanation
Indices: 89014911--89014962 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 22
89014901 TATCGAAAAA
89014911 TAAATTTTTAAATAACTTTTTATTCT
1 TAAATTTTTAAA-AA--TTTTATT-T
89014937 TAAATTTTTAAAAATTTTATTT
1 TAAATTTTTAAAAATTTTATTT
89014959 TAAA
1 TAAA
89014963 AATCAAGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
22 5 0.19
23 7 0.27
25 2 0.08
26 12 0.46
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (22 bp):
TAAATTTTTAAAAATTTTATTT
Found at i:89018523 original size:14 final size:14
Alignment explanation
Indices: 89018496--89018534 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
89018486 TACAATATCT
*
89018496 AAATAATAAAAATA
1 AAATAGTAAAAATA
*
89018510 AAATAGTAACAATA
1 AAATAGTAAAAATA
*
89018524 TAATAGTAAAA
1 AAATAGTAAAA
89018535 CGATAGGAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.69, C:0.03, G:0.05, T:0.23
Consensus pattern (14 bp):
AAATAGTAAAAATA
Found at i:89024170 original size:21 final size:21
Alignment explanation
Indices: 89024146--89024354 Score: 186
Period size: 21 Copynumber: 10.0 Consensus size: 21
89024136 TAAGCTGAAT
* *
89024146 AGAAACTCTTAAGAGTTAAAC
1 AGAAACTCATAAGAGCTAAAC
* *
89024167 AGAAGCTCATAAGAGCTGAAC
1 AGAAACTCATAAGAGCTAAAC
* *
89024188 AGAAACTCATAAGAGTTGAAC
1 AGAAACTCATAAGAGCTAAAC
* * *
89024209 AGAAGCTCGTGAGAGCTAAAC
1 AGAAACTCATAAGAGCTAAAC
* * *
89024230 AGAAACTCGTATGAGTTAAAC
1 AGAAACTCATAAGAGCTAAAC
* *
89024251 A-AAAGCTCGTAAGAGCTGAAC
1 AGAAA-CTCATAAGAGCTAAAC
* * * *
89024272 GGAAACTCATAAGAGTTGAAT
1 AGAAACTCATAAGAGCTAAAC
*
89024293 AGAAACTCAAAAGAGCTAAAC
1 AGAAACTCATAAGAGCTAAAC
* * *
89024314 GGAAACTAATAAGAGTTAAAC
1 AGAAACTCATAAGAGCTAAAC
* *
89024335 AGAAGCTCGTAAGAGCTAAA
1 AGAAACTCATAAGAGCTAAA
89024355 TATAAAGTAA
Statistics
Matches: 150, Mismatches: 36, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
20 3 0.02
21 144 0.96
22 3 0.02
ACGTcount: A:0.46, C:0.15, G:0.21, T:0.18
Consensus pattern (21 bp):
AGAAACTCATAAGAGCTAAAC
Found at i:89024287 original size:84 final size:84
Alignment explanation
Indices: 89024146--89024351 Score: 295
Period size: 84 Copynumber: 2.5 Consensus size: 84
89024136 TAAGCTGAAT
* *
89024146 AGAAACTCTTAAGAGTTAAACAGAAGCTCATAAGAGCTGAACAGAAACTCATAAGAGTTGAACAG
1 AGAAACTCATAAGAGTTAAACAGAAGCTCGTAAGAGCTGAACAGAAACTCATAAGAGTTGAACAG
* ***
89024211 AAGCTCGTGAGAGCTAAAC
66 AAACTCAAAAGAGCTAAAC
* * * * *
89024230 AGAAACTCGTATGAGTTAAACAAAAGCTCGTAAGAGCTGAACGGAAACTCATAAGAGTTGAATAG
1 AGAAACTCATAAGAGTTAAACAGAAGCTCGTAAGAGCTGAACAGAAACTCATAAGAGTTGAACAG
89024295 AAACTCAAAAGAGCTAAAC
66 AAACTCAAAAGAGCTAAAC
* *
89024314 GGAAACTAATAAGAGTTAAACAGAAGCTCGTAAGAGCT
1 AGAAACTCATAAGAGTTAAACAGAAGCTCGTAAGAGCT
89024352 AAATATAAAG
Statistics
Matches: 107, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
84 107 1.00
ACGTcount: A:0.45, C:0.16, G:0.21, T:0.18
Consensus pattern (84 bp):
AGAAACTCATAAGAGTTAAACAGAAGCTCGTAAGAGCTGAACAGAAACTCATAAGAGTTGAACAG
AAACTCAAAAGAGCTAAAC
Found at i:89024352 original size:42 final size:42
Alignment explanation
Indices: 89024146--89024354 Score: 265
Period size: 42 Copynumber: 5.0 Consensus size: 42
89024136 TAAGCTGAAT
* * *
89024146 AGAAACTCTTAAGAGTTAAACAGAAGCTCATAAGAGCTGAAC
1 AGAAACTCATAAGAGTTAAACAGAAGCTCGTAAGAGCTAAAC
* *
89024188 AGAAACTCATAAGAGTTGAACAGAAGCTCGTGAGAGCTAAAC
1 AGAAACTCATAAGAGTTAAACAGAAGCTCGTAAGAGCTAAAC
* * * *
89024230 AGAAACTCGTATGAGTTAAACAAAAGCTCGTAAGAGCTGAAC
1 AGAAACTCATAAGAGTTAAACAGAAGCTCGTAAGAGCTAAAC
* * * * **
89024272 GGAAACTCATAAGAGTTGAATAGAAACTCAAAAGAGCTAAAC
1 AGAAACTCATAAGAGTTAAACAGAAGCTCGTAAGAGCTAAAC
* *
89024314 GGAAACTAATAAGAGTTAAACAGAAGCTCGTAAGAGCTAAA
1 AGAAACTCATAAGAGTTAAACAGAAGCTCGTAAGAGCTAAA
89024355 TATAAAGTAA
Statistics
Matches: 140, Mismatches: 27, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 140 1.00
ACGTcount: A:0.46, C:0.15, G:0.21, T:0.18
Consensus pattern (42 bp):
AGAAACTCATAAGAGTTAAACAGAAGCTCGTAAGAGCTAAAC
Found at i:89026304 original size:146 final size:148
Alignment explanation
Indices: 89026114--89026412 Score: 530
Period size: 146 Copynumber: 2.0 Consensus size: 148
89026104 ACTTTGGTTA
* *
89026114 ATATTCATCATTATCTTTCTCTTTCTCTTTCAGAGTATTTCAAGATAATTAATAGAATAGAATCA
1 ATATTCATCATTATCTTTCTCTCTCTCTTTCAGAATATTTCAAGATAATTAATAGAATAGAATCA
89026179 ACTTTTAAATGAGTGTTTCAAGGCTATTAAAGCAGTGCTAGTTGATCACTTAAAGAGGCAAATAA
66 ACTTTTAAATGAGTGTTTCAAGGCTATTAAAGCAGTGCTAGTTGATCACTTAAAGAGGCAAATAA
*
89026244 ACAAGTTTTTTGTGTCAC
131 ACAAGTTGTTTGTGTCAC
89026262 ATATTCATCATTAT-TTT-TCTCTCTCTTTCAGAATATTTCAAGATAATTAATAGAATAGAATCA
1 ATATTCATCATTATCTTTCTCTCTCTCTTTCAGAATATTTCAAGATAATTAATAGAATAGAATCA
* * *
89026325 ACTTTTAAATGAGTGTTTCAAGGCTGTTAAAGTAGTGCTGGTTGATCACTTAAAGAGGCAAATAA
66 ACTTTTAAATGAGTGTTTCAAGGCTATTAAAGCAGTGCTAGTTGATCACTTAAAGAGGCAAATAA
89026390 ACAAGTTGTTTGTGTCAC
131 ACAAGTTGTTTGTGTCAC
89026408 ATATT
1 ATATT
89026413 ATTTTGTAGT
Statistics
Matches: 145, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
146 128 0.88
147 3 0.02
148 14 0.10
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (148 bp):
ATATTCATCATTATCTTTCTCTCTCTCTTTCAGAATATTTCAAGATAATTAATAGAATAGAATCA
ACTTTTAAATGAGTGTTTCAAGGCTATTAAAGCAGTGCTAGTTGATCACTTAAAGAGGCAAATAA
ACAAGTTGTTTGTGTCAC
Found at i:89027625 original size:29 final size:29
Alignment explanation
Indices: 89027593--89027648 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
89027583 TTGCAGAAGA
* *
89027593 GTAAATACT-AAAAATTTGAAGGGCTAAAT
1 GTAAATA-TGAAAAAGTTGAAGGACTAAAT
89027622 GTAAATATGAAAAAGTTGAAGGACTAA
1 GTAAATATGAAAAAGTTGAAGGACTAA
89027649 TAGTGAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 1 0.04
29 23 0.96
ACGTcount: A:0.50, C:0.05, G:0.20, T:0.25
Consensus pattern (29 bp):
GTAAATATGAAAAAGTTGAAGGACTAAAT
Found at i:89027916 original size:13 final size:13
Alignment explanation
Indices: 89027898--89027931 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
89027888 TATTTTATTA
89027898 ATATTTTAATAAG
1 ATATTTTAATAAG
89027911 ATATTTTAATAAG
1 ATATTTTAATAAG
89027924 ATATTTTA
1 ATATTTTA
89027932 TTAATTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (13 bp):
ATATTTTAATAAG
Found at i:89027941 original size:13 final size:13
Alignment explanation
Indices: 89027888--89027935 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
89027878 AGATAAATAT
89027888 TATTTTATT-A-A
1 TATTTTATTAAGA
*
89027899 TATTTTAATAAGA
1 TATTTTATTAAGA
*
89027912 TATTTTAATAAGA
1 TATTTTATTAAGA
89027925 TATTTTATTAA
1 TATTTTATTAA
89027936 TTTATTATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
11 8 0.24
12 1 0.03
13 24 0.73
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (13 bp):
TATTTTATTAAGA
Found at i:89029597 original size:33 final size:33
Alignment explanation
Indices: 89029523--89029635 Score: 113
Period size: 33 Copynumber: 3.4 Consensus size: 33
89029513 TTCAGTGATC
*
89029523 AGTGTAAGACCATATCTAGGATATGGTATC-C-
1 AGTGTAAGACCATATCTAGGATATGGTAACACA
* *
89029554 TGATGATAAGACCATATCTAGGATATGGTACCACA
1 AG-TG-TAAGACCATATCTAGGATATGGTAACACA
* ** * *
89029589 AGTGTAAGACCATAGCTAGGCCATGGCAATACA
1 AGTGTAAGACCATATCTAGGATATGGTAACACA
*
89029622 CGTGTAAGACCATA
1 AGTGTAAGACCATA
89029636 GTTGGACTAT
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
31 1 0.01
32 2 0.03
33 61 0.90
34 3 0.04
35 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (33 bp):
AGTGTAAGACCATATCTAGGATATGGTAACACA
Found at i:89029764 original size:46 final size:46
Alignment explanation
Indices: 89029711--89029882 Score: 254
Period size: 46 Copynumber: 3.7 Consensus size: 46
89029701 TTCAAATGTG
89029711 TAAGACCATGGTTGAAAGATACCATGGCAACATGATAGGAAATGAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGATAGGAAATGAA
* *
89029757 TAAGACCATGGTTGAAAGATACCATGGCAACGTGATAAGAAATGAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGATAGGAAATGAA
* * * *
89029803 TAAGACCATGGTTGAAAGATACCATGGAAACATGAAAGAAAATGAG
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGATAGGAAATGAA
* * * *
89029849 TAAGACCATAGTTGAAAGACACTATGGCATCATG
1 TAAGACCATGGTTGAAAGATACCATGGCAACATG
89029883 TCGAAGATAA
Statistics
Matches: 113, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 113 1.00
ACGTcount: A:0.44, C:0.13, G:0.23, T:0.20
Consensus pattern (46 bp):
TAAGACCATGGTTGAAAGATACCATGGCAACATGATAGGAAATGAA
Found at i:89030287 original size:174 final size:174
Alignment explanation
Indices: 89029997--89030345 Score: 698
Period size: 174 Copynumber: 2.0 Consensus size: 174
89029987 TACAAAATGG
89029997 TTGTGTGGAATGTTTACACGAATTGGTCATATAAAAATATATGTACAAAAAAATTGCATGAAATA
1 TTGTGTGGAATGTTTACACGAATTGGTCATATAAAAATATATGTACAAAAAAATTGCATGAAATA
89030062 ATTATGAAGATAGATAAACGAAATAAGTATAGTTACATGGAATATAATTTATGTTAAGTTTGATA
66 ATTATGAAGATAGATAAACGAAATAAGTATAGTTACATGGAATATAATTTATGTTAAGTTTGATA
89030127 TGAACTATTACCGGAATAAATATACATAAAATATATAGAAATAA
131 TGAACTATTACCGGAATAAATATACATAAAATATATAGAAATAA
89030171 TTGTGTGGAATGTTTACACGAATTGGTCATATAAAAATATATGTACAAAAAAATTGCATGAAATA
1 TTGTGTGGAATGTTTACACGAATTGGTCATATAAAAATATATGTACAAAAAAATTGCATGAAATA
89030236 ATTATGAAGATAGATAAACGAAATAAGTATAGTTACATGGAATATAATTTATGTTAAGTTTGATA
66 ATTATGAAGATAGATAAACGAAATAAGTATAGTTACATGGAATATAATTTATGTTAAGTTTGATA
89030301 TGAACTATTACCGGAATAAATATACATAAAATATATAGAAATAA
131 TGAACTATTACCGGAATAAATATACATAAAATATATAGAAATAA
89030345 T
1 T
89030346 GGTGCATGGA
Statistics
Matches: 175, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
174 175 1.00
ACGTcount: A:0.46, C:0.06, G:0.15, T:0.32
Consensus pattern (174 bp):
TTGTGTGGAATGTTTACACGAATTGGTCATATAAAAATATATGTACAAAAAAATTGCATGAAATA
ATTATGAAGATAGATAAACGAAATAAGTATAGTTACATGGAATATAATTTATGTTAAGTTTGATA
TGAACTATTACCGGAATAAATATACATAAAATATATAGAAATAA
Found at i:89032121 original size:25 final size:25
Alignment explanation
Indices: 89032081--89032152 Score: 74
Period size: 25 Copynumber: 2.9 Consensus size: 25
89032071 TTGGCTTTCT
* *
89032081 TGAGCTTCCCGATAAATGGCTCACCA
1 TGAGTTTCCCGTTAAATGGCTCA-CA
* **
89032107 -GAGTTTTCCGTTAAACAGCTCACA
1 TGAGTTTCCCGTTAAATGGCTCACA
*
89032131 TGAGTTTCCCGTTATATGGCTC
1 TGAGTTTCCCGTTAAATGGCTC
89032153 GAAAGAGCTT
Statistics
Matches: 36, Mismatches: 9, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
24 2 0.06
25 34 0.94
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (25 bp):
TGAGTTTCCCGTTAAATGGCTCACA
Found at i:89032533 original size:14 final size:14
Alignment explanation
Indices: 89032514--89032543 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
89032504 TTAAACCTAG
89032514 ACCAATCCAAATCA
1 ACCAATCCAAATCA
*
89032528 ACCAATCCAATTCA
1 ACCAATCCAAATCA
89032542 AC
1 AC
89032544 ATATTTTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.37, G:0.00, T:0.17
Consensus pattern (14 bp):
ACCAATCCAAATCA
Found at i:89035782 original size:26 final size:26
Alignment explanation
Indices: 89035746--89035853 Score: 173
Period size: 26 Copynumber: 4.2 Consensus size: 26
89035736 TGAAATTCCA
89035746 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAAACCATT
*
89035772 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAAACCATT
* *
89035798 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAAACCATT
89035824 ATCATGGAACATTTACCT-AACCTATT
1 ATCATGGAACATTTACCTAAACC-ATT
89035850 ATCA
1 ATCA
89035854 ATTTGTATCA
Statistics
Matches: 76, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
25 3 0.04
26 73 0.96
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAAACCATT
Found at i:89053466 original size:30 final size:30
Alignment explanation
Indices: 89053427--89053487 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 30
89053417 CACCTATCAT
*
89053427 AATAAAATATATTA-ATTCAATATTTT-TAA
1 AATAAAA-ATATTACATTAAATATTTTATAA
89053456 AATAAAAATATTACATTAAATATTTTATAA
1 AATAAAAATATTACATTAAATATTTTATAA
89053486 AA
1 AA
89053488 ATAGATAATG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 6 0.21
29 18 0.62
30 5 0.17
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (30 bp):
AATAAAAATATTACATTAAATATTTTATAA
Found at i:89053969 original size:18 final size:18
Alignment explanation
Indices: 89053946--89053987 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
89053936 ATTTCAAGTC
*
89053946 TTTAATTGTTATAATAT-T
1 TTTAATTATT-TAATATAT
89053964 TTTAATTATTTAATATAT
1 TTTAATTATTTAATATAT
89053982 TTTAAT
1 TTTAAT
89053988 AGATTCAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (18 bp):
TTTAATTATTTAATATAT
Found at i:89055938 original size:16 final size:15
Alignment explanation
Indices: 89055910--89055961 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
89055900 AAGTAATTAA
89055910 AAATAGTACTATATAT
1 AAATA-TACTATATAT
89055926 AAATATACATATATAT
1 AAATATAC-TATATAT
*
89055942 ACATATA-TA-ATA-
1 AAATATACTATATAT
89055954 AAATATAC
1 AAATATAC
89055962 ACTAGTATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
12 6 0.19
13 3 0.09
14 2 0.06
15 3 0.09
16 18 0.56
ACGTcount: A:0.56, C:0.08, G:0.02, T:0.35
Consensus pattern (15 bp):
AAATATACTATATAT
Found at i:89055959 original size:12 final size:13
Alignment explanation
Indices: 89055944--89056004 Score: 58
Period size: 12 Copynumber: 5.0 Consensus size: 13
89055934 ATATATATAC
89055944 ATATATAATAA-A
1 ATATATAATAATA
* * *
89055956 ATATACACTAGTA
1 ATATATAATAATA
*
89055969 TTA-ATAATAATA
1 ATATATAATAATA
89055981 ATA-ATAATAATA
1 ATATATAATAATA
89055993 ATA-ATAATAATA
1 ATATATAATAATA
89056005 TTGAAATACA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
12 37 0.93
13 3 0.08
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (13 bp):
ATATATAATAATA
Found at i:89055978 original size:3 final size:3
Alignment explanation
Indices: 89055970--89056004 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
89055960 ACACTAGTAT
89055970 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
89056005 TTGAAATACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:89056002 original size:154 final size:149
Alignment explanation
Indices: 89055844--89056305 Score: 561
Period size: 151 Copynumber: 3.1 Consensus size: 149
89055834 TAAAACTAGC
89055844 AATAATAATGAAATACAAAAAAAAAGCAAATATAATATAATAATAATGTTAAAATAAAGTAATTA
1 AATAATAATGAAATAC----AAAAAGCAAATATAATATAATAATAAT-TTAAAATAAAGTAATTA
* *
89055909 AAAATAGTACTATATATAAATATACATATATATACATATATAAT-AAAATATACACTAGTATTAA
61 AAAATAATACTATATATAAATATATATATATATACATATATAATAAAAATATACACTA-TATTAA
89055973 TAATAATAATAATAATAATAATAAT
125 TAATAATAATAATAATAATAATAAT
* *
89055998 AATAATATTGAAATACAAAAAGCAAATATAATATAATAAAAATATTAAAATAAAGTAATTAAAAA
1 AATAATAATGAAATACAAAAAGCAAATATAATATAATAATAAT-TTAAAATAAAGTAATT--AAA
* *
89056063 AATAATACTATGTATAAATATATATACGTATACATACATATACAATAAAAATATACACTA-A-T-
63 AATAATACTATATATAAATATATATA--TAT--ATACATATATAATAAAAATATACACTATATTA
* *
89056125 AT--TAATAATAATAATGATAATAGT
124 ATAATAATAATAATAATAATAATAAT
* *
89056149 AATAATATTGAAATACAAAAAGCAAATATAATA-AA-AAT-A-TTAAAATAAAGTAATAAAAAAT
1 AATAATAATGAAATACAAAAAGCAAATATAATATAATAATAATTTAAAATAAAGTAATTAAAAAT
89056210 AATACTATATATAAATATATATATCCATATACATATATAATAAAAAATATACACTAATATATAA-
66 AATACTATATATAAATATATATAT--ATATACATATATAAT-AAAAATATACACT-ATAT-TAAT
* *
89056274 AAAAAT-ATAATAATAGTAATAAT
126 AATAATAATAATAATAATAATAAT
*
89056297 ATTAATAAT
1 AATAATAAT
89056306 ATTAGAAATA
Statistics
Matches: 272, Mismatches: 19, Indels: 40
0.82 0.06 0.12
Matches are distributed among these distances:
142 13 0.05
143 13 0.05
144 31 0.11
145 1 0.00
146 15 0.06
147 1 0.00
148 23 0.08
149 5 0.02
150 44 0.16
151 53 0.19
152 26 0.10
153 2 0.01
154 19 0.07
155 1 0.00
156 12 0.04
157 13 0.05
ACGTcount: A:0.60, C:0.05, G:0.04, T:0.31
Consensus pattern (149 bp):
AATAATAATGAAATACAAAAAGCAAATATAATATAATAATAATTTAAAATAAAGTAATTAAAAAT
AATACTATATATAAATATATATATATATACATATATAATAAAAATATACACTATATTAATAATAA
TAATAATAATAATAATAAT
Found at i:89056295 original size:9 final size:8
Alignment explanation
Indices: 89056242--89056322 Score: 50
Period size: 7 Copynumber: 10.5 Consensus size: 8
89056232 ATCCATATAC
89056242 ATAT-ATA
1 ATATAATA
*
89056249 ATA-AAAA
1 ATATAATA
89056256 ATATACACTA
1 ATATA-A-TA
89056266 ATAT-ATA
1 ATATAATA
89056273 A-A-AA-A
1 ATATAATA
89056278 ATATAATA
1 ATATAATA
89056286 ATAGTAATA
1 ATA-TAATA
89056295 ATATTAATA
1 ATA-TAATA
* *
89056304 ATATTAGA
1 ATATAATA
89056312 A-ATAATA
1 ATATAATA
89056319 ATAT
1 ATAT
89056323 TTAATAAAGA
Statistics
Matches: 57, Mismatches: 7, Indels: 19
0.69 0.08 0.23
Matches are distributed among these distances:
5 2 0.04
6 3 0.05
7 18 0.32
8 12 0.21
9 17 0.30
10 5 0.09
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (8 bp):
ATATAATA
Found at i:89056295 original size:22 final size:23
Alignment explanation
Indices: 89056236--89056295 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 23
89056226 ATATATATCC
89056236 ATATACA-T-ATATAAT-AAAAA
1 ATATACACTAATATAATAAAAAA
89056256 ATATACACTAATAT-ATAAAAAA
1 ATATACACTAATATAATAAAAAA
89056278 ATATA-A-TAATAGTAATAA
1 ATATACACTAATA-TAATAA
89056296 TATTAATAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
20 12 0.34
21 5 0.14
22 18 0.51
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (23 bp):
ATATACACTAATATAATAAAAAA
Found at i:89056333 original size:21 final size:23
Alignment explanation
Indices: 89056290--89056334 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
89056280 ATAATAATAG
*
89056290 TAATAATATTAATAATATTAGAAA
1 TAATAATATT-ATAATATAAGAAA
89056314 TAATAATATT-TAATA-AAGAAA
1 TAATAATATTATAATATAAGAAA
89056335 CGAAAATAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 5 0.25
24 10 0.50
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (23 bp):
TAATAATATTATAATATAAGAAA
Found at i:89059272 original size:42 final size:41
Alignment explanation
Indices: 89059218--89059337 Score: 127
Period size: 41 Copynumber: 2.9 Consensus size: 41
89059208 ATTTTTTTTT
*
89059218 AGCTCTCATGAGCTTCAGTTTAACCCTTCTAGGTTTCAGTTC
1 AGCTCTTATGAGCTTCAGTTTAACCCTT-TAGGTTTCAGTTC
* *
89059260 AGCTCTTTTGAGCTTCAGTTTAA-CC-TTAGGAGTTTCCGTTC
1 AGCTCTTATGAGCTTCAGTTTAACCCTTTA-G-GTTTCAGTTC
* * * *
89059301 AGCTCTTACGAGCTTCCGTTCAACCCTTATGGGTTTC
1 AGCTCTTATGAGCTTCAGTTTAACCCTT-TAGGTTTC
89059338 CATTTAGTAC
Statistics
Matches: 65, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
39 2 0.03
40 2 0.03
41 30 0.46
42 28 0.43
43 2 0.03
44 1 0.02
ACGTcount: A:0.17, C:0.26, G:0.18, T:0.38
Consensus pattern (41 bp):
AGCTCTTATGAGCTTCAGTTTAACCCTTTAGGTTTCAGTTC
Found at i:89059307 original size:41 final size:41
Alignment explanation
Indices: 89059218--89059338 Score: 138
Period size: 42 Copynumber: 2.9 Consensus size: 41
89059208 ATTTTTTTTT
* *
89059218 AGCTCTCATGAGCTTCAGTTTAACCCTTCTA-GGTTTCAGTTC
1 AGCTCTTATGAGCTTCAGTTTAACCC-T-TAGGGTTTCCGTTC
*
89059260 AGCTCTTTTGAGCTTCAGTTTAA-CCTTAGGAGTTTCCGTTC
1 AGCTCTTATGAGCTTCAGTTTAACCCTTAGG-GTTTCCGTTC
* * *
89059301 AGCTCTTACGAGCTTCCGTTCAACCCTTATGGGTTTCC
1 AGCTCTTATGAGCTTCAGTTTAACCCTTA-GGGTTTCC
89059339 ATTTAGTACT
Statistics
Matches: 68, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
39 2 0.03
40 2 0.03
41 30 0.44
42 32 0.47
43 2 0.03
ACGTcount: A:0.17, C:0.26, G:0.18, T:0.38
Consensus pattern (41 bp):
AGCTCTTATGAGCTTCAGTTTAACCCTTAGGGTTTCCGTTC
Found at i:89059317 original size:21 final size:21
Alignment explanation
Indices: 89059256--89059322 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
89059246 CTAGGTTTCA
** *
89059256 GTTCAGCTCTTTTGAGCTTCA
1 GTTCAGCTCTTACGAGCTTCC
* * * *
89059277 GTTTAAC-CTTAGGAGTTTCC
1 GTTCAGCTCTTACGAGCTTCC
89059297 GTTCAGCTCTTACGAGCTTCC
1 GTTCAGCTCTTACGAGCTTCC
89059318 GTTCA
1 GTTCA
89059323 ACCCTTATGG
Statistics
Matches: 35, Mismatches: 10, Indels: 2
0.74 0.21 0.04
Matches are distributed among these distances:
20 14 0.40
21 21 0.60
ACGTcount: A:0.16, C:0.25, G:0.19, T:0.39
Consensus pattern (21 bp):
GTTCAGCTCTTACGAGCTTCC
Done.