Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007898.1 Hibiscus syriacus cultivar Beakdansim tig00110287_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 546391
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:274229 original size:29 final size:29
Alignment explanation
Indices: 274194--274349 Score: 115
Period size: 29 Copynumber: 5.5 Consensus size: 29
274184 TTATTTTCTC
274194 ATAAATTATAATAAAGACCAAAA-TGTTTA
1 ATAAATTATAATAAAGACCAAAACT-TTTA
* * *
274223 ATGAATTATAATAAAAACCAAAACTTTTT
1 ATAAATTATAATAAAGACCAAAACTTTTA
* ** *
274252 ATAAATTATAATAAAGGCC--ATTTTTTT
1 ATAAATTATAATAAAGACCAAAACTTTTA
* * ** *
274279 ATAAATTACAATAATGGTCAAAACTTTTT
1 ATAAATTATAATAAAGACCAAAACTTTTA
* * *
274308 ATAAATTACAA-AAAGGA-CAAAACTTATC
1 ATAAATTATAATAAA-GACCAAAACTTTTA
*
274336 ATAAATTACAATAA
1 ATAAATTATAATAA
274350 TAACCTATAG
Statistics
Matches: 105, Mismatches: 17, Indels: 10
0.80 0.13 0.08
Matches are distributed among these distances:
27 22 0.21
28 22 0.21
29 60 0.57
30 1 0.01
ACGTcount: A:0.51, C:0.10, G:0.06, T:0.33
Consensus pattern (29 bp):
ATAAATTATAATAAAGACCAAAACTTTTA
Found at i:274329 original size:28 final size:28
Alignment explanation
Indices: 274241--274349 Score: 123
Period size: 28 Copynumber: 3.9 Consensus size: 28
274231 TAATAAAAAC
*
274241 CAAAACTTTTTATAAATTATAATAAAGG
1 CAAAACTTTTTATAAATTACAATAAAGG
* ** *
274269 C-CATTTTTTTATAAATTACAATAATGG
1 CAAAACTTTTTATAAATTACAATAAAGG
274296 TCAAAACTTTTTATAAATTACAA-AAAGG
1 -CAAAACTTTTTATAAATTACAATAAAGG
* *
274324 ACAAAACTTATCATAAATTACAATAA
1 -CAAAACTTTTTATAAATTACAATAA
274350 TAACCTATAG
Statistics
Matches: 66, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
27 21 0.32
28 26 0.39
29 19 0.29
ACGTcount: A:0.49, C:0.11, G:0.06, T:0.35
Consensus pattern (28 bp):
CAAAACTTTTTATAAATTACAATAAAGG
Found at i:274395 original size:28 final size:28
Alignment explanation
Indices: 274338--274407 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
274328 AACTTATCAT
274338 AAATTACAATAATAACCTATAGTTTCTAC
1 AAATTACAATAA-AACCTATAGTTTCTAC
* *
274367 AAATTACAATAAAACCTTGTA-TTTTTAC
1 AAATTACAATAAAACC-TATAGTTTCTAC
274395 AAATTACAATAAA
1 AAATTACAATAAA
274408 GCTCCATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
28 23 0.61
29 15 0.39
ACGTcount: A:0.49, C:0.14, G:0.03, T:0.34
Consensus pattern (28 bp):
AAATTACAATAAAACCTATAGTTTCTAC
Found at i:276185 original size:9 final size:10
Alignment explanation
Indices: 276160--276197 Score: 51
Period size: 9 Copynumber: 3.7 Consensus size: 10
276150 TTTAAATCTT
276160 TTTTTAAATAAA
1 TTTTT-AAT-AA
276172 TTTTTAAT-A
1 TTTTTAATAA
276181 TTTTTAATAA
1 TTTTTAATAA
276191 TTTTTAA
1 TTTTTAA
276198 AAGTTTTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 9 0.36
10 8 0.32
11 3 0.12
12 5 0.20
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (10 bp):
TTTTTAATAA
Found at i:276189 original size:20 final size:20
Alignment explanation
Indices: 276160--276197 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
276150 TTTAAATCTT
276160 TTTTTAAATAAATTTTTAATA
1 TTTTTAAAT-AATTTTTAATA
276181 TTTTT-AATAATTTTTAA
1 TTTTTAAATAATTTTTAA
276198 AAGTTTTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTTTAAATAATTTTTAATA
Found at i:276204 original size:20 final size:21
Alignment explanation
Indices: 276160--276209 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 21
276150 TTTAAATCTT
*
276160 TTTTTAAATAAATTTTTAATA
1 TTTTTAAATAAATTTTTAAAA
276181 TTTTT-AAT-AATTTTTAAAA
1 TTTTTAAATAAATTTTTAAAA
*
276200 GTTTTCAAAT
1 -TTTTTAAAT
276210 GATGTCGTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 10 0.40
20 7 0.28
21 8 0.32
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (21 bp):
TTTTTAAATAAATTTTTAAAA
Found at i:276259 original size:10 final size:9
Alignment explanation
Indices: 276241--276290 Score: 66
Period size: 9 Copynumber: 5.4 Consensus size: 9
276231 ATCTCACATC
276241 AATATTTTT
1 AATATTTTT
276250 AATAATTTTT
1 AAT-ATTTTT
276260 AATATTTTT
1 AATATTTTT
276269 AATATCTTTT
1 AATAT-TTTT
*
276279 -ATCTTTTT
1 AATATTTTT
276287 AATA
1 AATA
276291 ATAGATACTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
8 4 0.11
9 19 0.53
10 13 0.36
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (9 bp):
AATATTTTT
Found at i:276265 original size:19 final size:20
Alignment explanation
Indices: 276241--276292 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
276231 ATCTCACATC
276241 AATATTTTTAATAAT-TTTT
1 AATATTTTTAATAATCTTTT
276260 AATATTTTTAAT-ATCTTTT
1 AATATTTTTAATAATCTTTT
*
276279 -ATCTTTTTAATAAT
1 AATATTTTTAATAAT
276293 AGATACTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 12 0.40
19 18 0.60
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.62
Consensus pattern (20 bp):
AATATTTTTAATAATCTTTT
Found at i:276712 original size:30 final size:30
Alignment explanation
Indices: 276678--276744 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
276668 ATGTTTCTCT
* *
276678 ATATTTTTAATACTATAGAATAATTATGTA
1 ATATTTTTAATACTATAAAATAATTATATA
* * *
276708 ATATTTTTATTATTTTAAAATAATTATATA
1 ATATTTTTAATACTATAAAATAATTATATA
276738 ATATTTT
1 ATATTTT
276745 ATAAATTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (30 bp):
ATATTTTTAATACTATAAAATAATTATATA
Found at i:276753 original size:30 final size:30
Alignment explanation
Indices: 276696--276789 Score: 92
Period size: 30 Copynumber: 3.3 Consensus size: 30
276686 AATACTATAG
* *
276696 AATAATTATGTAATATTTT-TATTATTTTAA
1 AATAATTATATAATATTTTATA-AATTTTAA
276726 AATAATTATATAATATTTTATAAATTTTAA
1 AATAATTATATAATATTTTATAAATTTTAA
* *
276756 AA-AA--ATAT-TTTTTTTAT-AATTTTAA
1 AATAATTATATAATATTTTATAAATTTTAA
276781 TAATAATTA
1 -AATAATTA
276790 ATATTTTGTG
Statistics
Matches: 55, Mismatches: 4, Indels: 11
0.79 0.06 0.16
Matches are distributed among these distances:
25 8 0.15
26 9 0.16
27 6 0.11
29 3 0.05
30 27 0.49
31 2 0.04
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (30 bp):
AATAATTATATAATATTTTATAAATTTTAA
Found at i:278913 original size:29 final size:29
Alignment explanation
Indices: 278880--278972 Score: 79
Period size: 29 Copynumber: 3.2 Consensus size: 29
278870 TATTAGTCTT
278880 TAAACTTTTAATTATTTCAATTTCATCCC
1 TAAACTTTTAATTATTTCAATTTCATCCC
* * *
278909 TAAAC-TATAATTCTCATTTTAATTTC--CCT
1 TAAACTTTTAA-T-T-ATTTCAATTTCATCCC
278938 TAAACTTTTGAA-TA-TTCTAATTTCATCCC
1 TAAACTTTT-AATTATTTC-AATTTCATCCC
278967 TAAACT
1 TAAACT
278973 ATAGCCTTCT
Statistics
Matches: 50, Mismatches: 6, Indels: 16
0.69 0.08 0.22
Matches are distributed among these distances:
26 2 0.04
27 7 0.14
28 5 0.10
29 21 0.42
30 3 0.06
31 12 0.24
ACGTcount: A:0.32, C:0.20, G:0.01, T:0.46
Consensus pattern (29 bp):
TAAACTTTTAATTATTTCAATTTCATCCC
Found at i:278918 original size:60 final size:58
Alignment explanation
Indices: 278848--279026 Score: 188
Period size: 60 Copynumber: 3.0 Consensus size: 58
278838 TCATATGTCT
* *
278848 CTAAATTATAACTTTCATTTTATATTAGTCTTTAAACTTTT-AATTATTTCAATTTCATCC
1 CTAAACTATAACTTTCATTTTA-ATT-GTCCTTAAACTTTTGAA-TATTTCAATTTCATCC
278908 CTAAACTATAA-TTCTCATTTTAATT-TCCCTTAAACTTTTGAATA-TTCTAATTTCATCC
1 CTAAACTATAACTT-TCATTTTAATTGT-CCTTAAACTTTTGAATATTTC-AATTTCATCC
* * * *
278966 CTAAACTATAGCCTTC-TTTCTAAATTTGTCCCTAAACTTTTGAATATTTCAATTTCTTCC
1 CTAAACTATAACTTTCATTT-T-AA-TTGTCCTTAAACTTTTGAATATTTCAATTTCATCC
279026 C
1 C
279027 CAAATTCATC
Statistics
Matches: 103, Mismatches: 6, Indels: 20
0.80 0.05 0.16
Matches are distributed among these distances:
57 7 0.07
58 36 0.35
59 10 0.10
60 46 0.45
61 4 0.04
ACGTcount: A:0.30, C:0.20, G:0.03, T:0.47
Consensus pattern (58 bp):
CTAAACTATAACTTTCATTTTAATTGTCCTTAAACTTTTGAATATTTCAATTTCATCC
Found at i:281181 original size:26 final size:26
Alignment explanation
Indices: 281152--281202 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
281142 AAATAATAAA
*
281152 ATAATATATTTT-ATATGAATTTTTAT
1 ATAA-ATATTTTCATATGAATATTTAT
*
281178 ATAAATATTTTCATTTGAATATTTA
1 ATAAATATTTTCATATGAATATTTA
281203 AAATTCAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (26 bp):
ATAAATATTTTCATATGAATATTTAT
Found at i:281374 original size:28 final size:28
Alignment explanation
Indices: 281342--281395 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
281332 TAACATTCAT
281342 AATAAT-GTATCAGATAATATTATATTTC
1 AATAATCGTATCA-ATAATATTATATTTC
* *
281370 AATAATCTTATTAATAATATTATATT
1 AATAATCGTATCAATAATATTATATT
281396 CCATAAATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 19 0.83
29 4 0.17
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (28 bp):
AATAATCGTATCAATAATATTATATTTC
Found at i:291228 original size:17 final size:18
Alignment explanation
Indices: 291187--291225 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
291177 AACATTAGAT
*
291187 AAAA-GAAAATAACGACTA
1 AAAACGAAAACAACGAC-A
291205 AAAACGAAAACAACGACA
1 AAAACGAAAACAACGACA
291223 AAA
1 AAA
291226 CGACTGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.69, C:0.15, G:0.10, T:0.05
Consensus pattern (18 bp):
AAAACGAAAACAACGACA
Found at i:296109 original size:41 final size:41
Alignment explanation
Indices: 296052--296137 Score: 163
Period size: 41 Copynumber: 2.1 Consensus size: 41
296042 TTCGCGAAGT
*
296052 ACGTTCCTTTATATATGAGAGTTCGCATAGATTTTCAATTC
1 ACGTTCCTTTATATATGAGAGTTCGCATAGATCTTCAATTC
296093 ACGTTCCTTTATATATGAGAGTTCGCATAGATCTTCAATTC
1 ACGTTCCTTTATATATGAGAGTTCGCATAGATCTTCAATTC
296134 ACGT
1 ACGT
296138 CTCTGAAGAT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.40
Consensus pattern (41 bp):
ACGTTCCTTTATATATGAGAGTTCGCATAGATCTTCAATTC
Found at i:301108 original size:34 final size:33
Alignment explanation
Indices: 301064--301151 Score: 90
Period size: 33 Copynumber: 2.6 Consensus size: 33
301054 AATGAGTTTG
*
301064 AAAA-AGTGGGTTAACGGGGGTTTGAGAAGAAGA
1 AAAAGAGTGGGTTAACGGGGGTGTGA-AAGAAGA
*
301097 AAAAGAGTGGGTTTAAC-GGGGTGTGACAGAAGA
1 AAAAGAGTGGG-TTAACGGGGGTGTGAAAGAAGA
* * *
301130 AGAAGAATGGAGTTAATGGGGG
1 AAAAGAGTGG-GTTAACGGGGG
301152 GGGGGGGGGG
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
33 22 0.48
34 19 0.41
35 5 0.11
ACGTcount: A:0.38, C:0.03, G:0.41, T:0.18
Consensus pattern (33 bp):
AAAAGAGTGGGTTAACGGGGGTGTGAAAGAAGA
Found at i:304552 original size:23 final size:24
Alignment explanation
Indices: 304518--304567 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 24
304508 TTATATTTTC
304518 AATTTTGTAAAAAAAAT-TATATA
1 AATTTTGTAAAAAAAATATATATA
*
304541 AATTTT-TAAAAAATATATATATA
1 AATTTTGTAAAAAAAATATATATA
304564 AATT
1 AATT
304568 AATTATAGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 9 0.36
23 16 0.64
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (24 bp):
AATTTTGTAAAAAAAATATATATA
Found at i:314602 original size:59 final size:60
Alignment explanation
Indices: 314529--314664 Score: 159
Period size: 60 Copynumber: 2.3 Consensus size: 60
314519 ATAGTTGAGT
* * * * ** *
314529 GACCATTTTATAACTTTTAATAGTCGAG-GACTCAACAAAGCGACGTCCTATAATTGAAG
1 GACCATTTTGTAACTTTCAATAATCGAGAGACTCAACAAAGCAACACCCTATAATCGAAG
* * *
314588 GACCATTTTGTAACTTTCAATAATCGAGAGACTTAATAAAGCAACACCCTATAATCGATG
1 GACCATTTTGTAACTTTCAATAATCGAGAGACTCAACAAAGCAACACCCTATAATCGAAG
314648 GACCATTTATGT-ACTTT
1 GACCATTT-TGTAACTTT
314665 ACTCTAAAAA
Statistics
Matches: 65, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
59 25 0.38
60 37 0.57
61 3 0.05
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (60 bp):
GACCATTTTGTAACTTTCAATAATCGAGAGACTCAACAAAGCAACACCCTATAATCGAAG
Found at i:314892 original size:12 final size:12
Alignment explanation
Indices: 314875--314954 Score: 90
Period size: 12 Copynumber: 6.7 Consensus size: 12
314865 TTCACGAACA
314875 AGCTCGTTTATG
1 AGCTCGTTTATG
*
314887 AGCTCGTTTATA
1 AGCTCGTTTATG
*
314899 AGTTCGTTTATG
1 AGCTCGTTTATG
* *
314911 AGCTTGTTTATA
1 AGCTCGTTTATG
*
314923 AGTTCGTTTATG
1 AGCTCGTTTATG
*
314935 AGCTCATTTATCG
1 AGCTCGTTTAT-G
314948 A-CTCGTT
1 AGCTCGTT
314955 CGTTTATATT
Statistics
Matches: 55, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
12 53 0.96
13 2 0.04
ACGTcount: A:0.20, C:0.15, G:0.20, T:0.45
Consensus pattern (12 bp):
AGCTCGTTTATG
Found at i:314908 original size:24 final size:24
Alignment explanation
Indices: 314878--314945 Score: 118
Period size: 24 Copynumber: 2.8 Consensus size: 24
314868 ACGAACAAGC
314878 TCGTTTATGAGCTCGTTTATAAGT
1 TCGTTTATGAGCTCGTTTATAAGT
*
314902 TCGTTTATGAGCTTGTTTATAAGT
1 TCGTTTATGAGCTCGTTTATAAGT
*
314926 TCGTTTATGAGCTCATTTAT
1 TCGTTTATGAGCTCGTTTAT
314946 CGACTCGTTC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.21, C:0.12, G:0.19, T:0.49
Consensus pattern (24 bp):
TCGTTTATGAGCTCGTTTATAAGT
Found at i:315899 original size:2 final size:2
Alignment explanation
Indices: 315892--315927 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
315882 GTTTAAGCTA
315892 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
315928 TAAAATTACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:317438 original size:25 final size:25
Alignment explanation
Indices: 317408--317460 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
317398 TTTACTTGTA
317408 AAGAAAGTTCTAATGAAATTGATTT
1 AAGAAAGTTCTAATGAAATTGATTT
317433 AAGAAAGTTCTAATGAAATTGATTT
1 AAGAAAGTTCTAATGAAATTGATTT
317458 AAG
1 AAG
317461 TGATAGGTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.45, C:0.04, G:0.17, T:0.34
Consensus pattern (25 bp):
AAGAAAGTTCTAATGAAATTGATTT
Found at i:321789 original size:24 final size:23
Alignment explanation
Indices: 321762--321827 Score: 105
Period size: 24 Copynumber: 2.8 Consensus size: 23
321752 TTACCCTTGT
*
321762 TTATTTCTAGTGTCAGTTTCACCC
1 TTATTTGTAGTGTCAGTTT-ACCC
321786 TTATTTGTAGTGTCAGTGTTACCC
1 TTATTTGTAGTGTCAGT-TTACCC
321810 TTATTTGTAGTGTCAGTT
1 TTATTTGTAGTGTCAGTT
321828 GTTCTTTAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
23 1 0.03
24 37 0.93
25 2 0.05
ACGTcount: A:0.17, C:0.17, G:0.18, T:0.48
Consensus pattern (23 bp):
TTATTTGTAGTGTCAGTTTACCC
Found at i:325035 original size:50 final size:50
Alignment explanation
Indices: 324981--325141 Score: 234
Period size: 50 Copynumber: 3.2 Consensus size: 50
324971 GAATGGGTTT
* * * *
324981 GTGTTCGTTTATTTATTGTTCGCGAACATGTTCCTTTAATGTTCGAGAAT
1 GTGTTCGTTTATTTATTATTCGCGAATATGTTCATTTAATGTTCGAGAAC
* * *
325031 GTGTTTGTTTATTTATTATTCGCGAATATGTTCGTTTAATGTTCGGGAAC
1 GTGTTCGTTTATTTATTATTCGCGAATATGTTCATTTAATGTTCGAGAAC
*
325081 GTGTTCGTTTATTTATTATTCGTGAATATGTTCATTTAATGTTC-ATGAAC
1 GTGTTCGTTTATTTATTATTCGCGAATATGTTCATTTAATGTTCGA-GAAC
325131 GTGTTCGTTTA
1 GTGTTCGTTTA
325142 ATATTCATGA
Statistics
Matches: 100, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
50 100 1.00
ACGTcount: A:0.20, C:0.11, G:0.20, T:0.48
Consensus pattern (50 bp):
GTGTTCGTTTATTTATTATTCGCGAATATGTTCATTTAATGTTCGAGAAC
Found at i:325041 original size:23 final size:23
Alignment explanation
Indices: 325009--325143 Score: 74
Period size: 23 Copynumber: 5.5 Consensus size: 23
324999 TTCGCGAACA
*
325009 TGTTCCTTTAATGTTCGAGAATG
1 TGTTCGTTTAATGTTCGAGAATG
* * * *
325032 TGTTTGTTTATTTATTATTCGCGAATA
1 TGTTCGTTTA---A-TGTTCGAGAATG
* *
325059 TGTTCGTTTAATGTTCGGGAACG
1 TGTTCGTTTAATGTTCGAGAATG
* * *
325082 TGTTCGTTTATTTATTATTCGTGAATA
1 TGTTCGTTTA---A-TGTTCGAGAATG
* *
325109 TGTTCATTTAATGTTC-ATGAACG
1 TGTTCGTTTAATGTTCGA-GAATG
325132 TGTTCGTTTAAT
1 TGTTCGTTTAAT
325144 ATTCATGAAC
Statistics
Matches: 83, Mismatches: 20, Indels: 18
0.69 0.17 0.15
Matches are distributed among these distances:
23 44 0.53
24 2 0.02
26 2 0.02
27 35 0.42
ACGTcount: A:0.21, C:0.10, G:0.19, T:0.49
Consensus pattern (23 bp):
TGTTCGTTTAATGTTCGAGAATG
Found at i:325052 original size:27 final size:27
Alignment explanation
Indices: 324982--325118 Score: 92
Period size: 27 Copynumber: 5.4 Consensus size: 27
324972 AATGGGTTTG
* * *
324982 TGTTCGTTTATTTATTGTTCGCGAACA
1 TGTTCGTTTATTTATTATTCGAGAATA
* * *
325009 TGTTCCTTTA---A-TGTTCGAGAATG
1 TGTTCGTTTATTTATTATTCGAGAATA
* *
325032 TGTTTGTTTATTTATTATTCGCGAATA
1 TGTTCGTTTATTTATTATTCGAGAATA
* * **
325059 TGTTCGTTTA---A-TGTTCGGGAACG
1 TGTTCGTTTATTTATTATTCGAGAATA
*
325082 TGTTCGTTTATTTATTATTCGTGAATA
1 TGTTCGTTTATTTATTATTCGAGAATA
*
325109 TGTTCATTTA
1 TGTTCGTTTA
325119 ATGTTCATGA
Statistics
Matches: 83, Mismatches: 19, Indels: 16
0.70 0.16 0.14
Matches are distributed among these distances:
23 35 0.42
24 2 0.02
26 2 0.02
27 44 0.53
ACGTcount: A:0.20, C:0.11, G:0.19, T:0.50
Consensus pattern (27 bp):
TGTTCGTTTATTTATTATTCGAGAATA
Found at i:325148 original size:23 final size:23
Alignment explanation
Indices: 325059--325180 Score: 91
Period size: 23 Copynumber: 5.1 Consensus size: 23
325049 TTCGCGAATA
**
325059 TGTTCGTTTAATGTTCGGGAACG
1 TGTTCGTTTAATGTTCATGAACG
* * **
325082 TGTTCGTTTATTTATTATTCGTGAATA
1 TGTTCGTTTA---A-TGTTCATGAACG
*
325109 TGTTCATTTAATGTTCATGAACG
1 TGTTCGTTTAATGTTCATGAACG
* *
325132 TGTTCGTTTAATATTCATGAACA
1 TGTTCGTTTAATGTTCATGAACG
* * *
325155 TATTCATTTATATGTTCACGAACG
1 TGTTCGTTTA-ATGTTCATGAACG
325179 TG
1 TG
325181 CTTATTTAGC
Statistics
Matches: 76, Mismatches: 18, Indels: 9
0.74 0.17 0.09
Matches are distributed among these distances:
23 46 0.61
24 12 0.16
26 1 0.01
27 17 0.22
ACGTcount: A:0.25, C:0.12, G:0.18, T:0.45
Consensus pattern (23 bp):
TGTTCGTTTAATGTTCATGAACG
Found at i:325164 original size:46 final size:48
Alignment explanation
Indices: 324981--325180 Score: 145
Period size: 50 Copynumber: 4.1 Consensus size: 48
324971 GAATGGGTTT
* ** * * *
324981 GTGTTCGTTTATTTATTGTTCGCGAACATGTTCCTTTAATGTTCGA-GAAT
1 GTGTTCGTTTA--TATTATTCATGAACATATTCATTTAATGTTC-ACGAAC
* ** * * * **
325031 GTGTTTGTTTATTTATTATTCGCGAATATGTTCGTTTAATGTTCGGGAAC
1 GTGTTCGTTTA--TATTATTCATGAACATATTCATTTAATGTTCACGAAC
* * * *
325081 GTGTTCGTTTATTTATTATTCGTGAATATGTTCATTTAATGTTCATGAAC
1 GTGTTCGTTTA--TATTATTCATGAACATATTCATTTAATGTTCACGAAC
325131 GTGTTCGTTTA-A-TATTCATGAACATATTCATTTATATGTTCACGAAC
1 GTGTTCGTTTATATTATTCATGAACATATTCATTTA-ATGTTCACGAAC
325178 GTG
1 GTG
325181 CTTATTTAGC
Statistics
Matches: 133, Mismatches: 15, Indels: 7
0.86 0.10 0.05
Matches are distributed among these distances:
46 19 0.14
47 15 0.11
50 99 0.74
ACGTcount: A:0.23, C:0.12, G:0.18, T:0.47
Consensus pattern (48 bp):
GTGTTCGTTTATATTATTCATGAACATATTCATTTAATGTTCACGAAC
Found at i:326143 original size:25 final size:25
Alignment explanation
Indices: 326109--326160 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
326099 GTATATATTT
*
326109 AAAAACTCTTATTCATTTGACAATG
1 AAAAACTCTTAATCATTTGACAATG
326134 AAAAACTCTTAATCATTTGACAATG
1 AAAAACTCTTAATCATTTGACAATG
326159 AA
1 AA
326161 CGTTTATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.33
Consensus pattern (25 bp):
AAAAACTCTTAATCATTTGACAATG
Found at i:328838 original size:74 final size:73
Alignment explanation
Indices: 328758--328966 Score: 255
Period size: 73 Copynumber: 2.8 Consensus size: 73
328748 ATAATATATG
* * *
328758 TATCGATATTTTAACAATTGATCATCTTCATCGACTTTTTCAATATATAAAAGTATCTATCATAA
1 TATCGATATTTTAACATTTGATCATCTT-ATCAACTTTTTCAATATTTAAAAGTATCTATCATAA
328823 TCGCATAAA
65 TCGCATAAA
* * *
328832 TATCGATATTTTAA-ATTTTGATCATTTTATCAACTTTTTCAATATTTAAAAGTATCAATCATTA
1 TATCGATATTTTAACA-TTTGATCATCTTATCAACTTTTTCAATATTTAAAAGTATCTATCATAA
* *
328896 TTGCATTAA
65 TCGCATAAA
* *
328905 TATCGTTTTTTTAAC-TTTCGATCTTATCTT-T-AACTTTTTCAATATTTAAAAGTATCTATCAT
1 TATCGATATTTTAACATTT-GATC--ATCTTATCAACTTTTTCAATATTTAAAAGTATCTATCAT
328967 CATATATCAA
Statistics
Matches: 118, Mismatches: 12, Indels: 11
0.84 0.09 0.08
Matches are distributed among these distances:
72 3 0.03
73 86 0.73
74 25 0.21
75 4 0.03
ACGTcount: A:0.34, C:0.14, G:0.06, T:0.46
Consensus pattern (73 bp):
TATCGATATTTTAACATTTGATCATCTTATCAACTTTTTCAATATTTAAAAGTATCTATCATAAT
CGCATAAA
Found at i:328982 original size:73 final size:70
Alignment explanation
Indices: 328745--328998 Score: 210
Period size: 73 Copynumber: 3.5 Consensus size: 70
328735 AGTGTTTAAC
* * * * *
328745 ATCATAA-TATATGTATCGATATTTTAACAATT-GATCATCTTCATCGACTTTTTCAATATATAA
1 ATCATAATTATA-ATATCGATATTTTAA-ATTTCGATCAT-TTTATCAACTTTTTCAATATTTAA
328808 AAGTATCT
63 AAGTATCT
* *
328816 ATCATAATCGCATAAATATCGATATTTTAAATTTTGATCATTTTATCAACTTTTTCAATATTTAA
1 ATCATAAT--TAT-AATATCGATATTTTAAATTTCGATCATTTTATCAACTTTTTCAATATTTAA
*
328881 AAGTATCA
63 AAGTATCT
* * * * *
328889 ATCATTATTGCATTAATATCGTTTTTTTAACTTTCGATC-TTATCT-TTAACTTTTTCAATATTT
1 ATCATAATT--A-TAATATCGATATTTTAAATTTCGATCATT-T-TATCAACTTTTTCAATATTT
328952 AAAAGTATCT
61 AAAAGTATCT
* * *
328962 ATCATCATATATCAAGTATCGATATTTAAAATATCGA
1 ATCATAAT-TAT-AA-TATCGATATTTTAAATTTCGA
328999 AATGCTTTCT
Statistics
Matches: 149, Mismatches: 21, Indels: 24
0.77 0.11 0.12
Matches are distributed among these distances:
71 8 0.05
72 5 0.03
73 110 0.74
74 25 0.17
75 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.06, T:0.44
Consensus pattern (70 bp):
ATCATAATTATAATATCGATATTTTAAATTTCGATCATTTTATCAACTTTTTCAATATTTAAAAG
TATCT
Found at i:329491 original size:187 final size:182
Alignment explanation
Indices: 329139--329715 Score: 640
Period size: 188 Copynumber: 3.1 Consensus size: 182
329129 AAAGCTAAAG
* * *
329139 TAACATTTTAGGCTCAATCCATTTTATTAATAAAATATTAACATTTCATATCGCAACCTAATTTT
1 TAACATTTTAGGCTCAATCCATTTTATTAATAAAAAATTAACATTTCA-ATCACAACCTTATTTT
* * * * * *
329204 TTAGTTAATTATGACATTCTTGGACGCAACAGTATTTAATATAGATTTTTATAACATTTTTCGC-
65 TTAGTAAACTATGACATTCTTGGGCGCAACAGTA-TTATTATAGATATTCATAACA-TTTTCGCT
* *
329268 -CAACTTATTTTGTTATCGTGAGAAAATCTAAGGTTCCATCAGGTTAAACTCT-A
128 TTAACTTATTTTGTTATCGTGAGAAAATCTAAGGTTCCATCAGCTTAAACTCTGA
* * *
329321 GTAACATTTTAGGCTCAACCCATTTTATTAATAAAAAAGTTAACATTTGAGATCACAACCTTCTT
1 -TAACATTTTAGGCTCAATCCATTTTATTAATAAAAAA-TTAACATTTCA-ATCACAACCTTATT
* * *
329386 TCTTAGTAAACTATGACATTCTTGGGCGCAACCGTATGTATTATAGATATTCATAATATTTTCGG
63 TTTTAGTAAACTATGACATTCTTGGGCGCAACAGTAT-TATTATAGATATTCATAACATTTTC-G
* *
329451 CTTTTAACTTATTTTGTTATCGTGAGAAAATCTAAGGTTCCATTAGCTTAAACTATGA
126 C-TTTAACTTATTTTGTTATCGTGAGAAAATCTAAGGTTCCATCAGCTTAAACTCTGA
* * * * *
329509 TAACATTTTAGGCGCAGTCCATTTTATTATTAAAAATATTAACATTCCAACTCACAACCTATTTT
1 TAACATTTTAGGCTCAATCCATTTTATTAATAAAAA-ATTAACATTTCAA-TCACAACCT-TATT
* * * * *
329574 TTTTAGTGAACCATGATATTATTGGGCGCAACTA-TATTCATTATAGATATTCATTACATTTTCA
63 TTTTAGTAAACTATGACATTCTTGGGCGCAAC-AGTATT-ATTATAGATATTCATAACATTTTC-
* * * * * ** * *
329638 AGATTTAACGTATTTTGTTATGGTGACAAAATTTAAGGTTTTATCAACTTAAATTCTGA
125 -GCTTTAACTTATTTTGTTATCGTGAGAAAATCTAAGGTTCCATCAGCTTAAACTCTGA
329697 TAACATTTTAGGCTCAATC
1 TAACATTTTAGGCTCAATC
329716 TAAAATATTA
Statistics
Matches: 332, Mismatches: 49, Indels: 21
0.83 0.12 0.05
Matches are distributed among these distances:
183 41 0.12
184 70 0.21
186 1 0.00
187 99 0.30
188 120 0.36
189 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (182 bp):
TAACATTTTAGGCTCAATCCATTTTATTAATAAAAAATTAACATTTCAATCACAACCTTATTTTT
TAGTAAACTATGACATTCTTGGGCGCAACAGTATTATTATAGATATTCATAACATTTTCGCTTTA
ACTTATTTTGTTATCGTGAGAAAATCTAAGGTTCCATCAGCTTAAACTCTGA
Found at i:331009 original size:2 final size:2
Alignment explanation
Indices: 331002--331031 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
330992 TAGCAATCAA
331002 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
331032 TGTATTTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:331081 original size:25 final size:25
Alignment explanation
Indices: 331016--331092 Score: 68
Period size: 25 Copynumber: 3.0 Consensus size: 25
331006 ATATATATAT
* *
331016 ATATATATATATATATTGTATTTAAA
1 ATAT-TATATATTTATTTTATTTAAA
*
331042 TTAATT-TAT-TATTATTTTATTTAAA
1 AT-ATTATATAT-TTATTTTATTTAAA
*
331067 ATATTATATATTTATATTTTTTTAAA
1 ATATTATATATTTAT-TTTATTTAAA
331093 TTTGTATAAG
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
24 4 0.10
25 23 0.56
26 12 0.29
27 2 0.05
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (25 bp):
ATATTATATATTTATTTTATTTAAA
Found at i:334788 original size:17 final size:16
Alignment explanation
Indices: 334766--334801 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
334756 ATTTAAAGAT
*
334766 AAAATATTTTAAAATTA
1 AAAATA-TTCAAAATTA
334783 AAAATATTCAAAATTA
1 AAAATATTCAAAATTA
334799 AAA
1 AAA
334802 CACCATTAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAATATTCAAAATTA
Found at i:337120 original size:21 final size:21
Alignment explanation
Indices: 337079--337120 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
337069 ATACATACAA
*
337079 AGATAAAGACCCATATCAATT
1 AGATAAAGACCCAAATCAATT
337100 AGATATAAGACCCAAAT-AATT
1 AGATA-AAGACCCAAATCAATT
337121 TTATTTATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.50, C:0.17, G:0.10, T:0.24
Consensus pattern (21 bp):
AGATAAAGACCCAAATCAATT
Found at i:339826 original size:11 final size:11
Alignment explanation
Indices: 339810--339847 Score: 67
Period size: 11 Copynumber: 3.5 Consensus size: 11
339800 TTTGTGTTGA
339810 TAAAATGTAAG
1 TAAAATGTAAG
339821 TAAAATGTAAG
1 TAAAATGTAAG
*
339832 TAAAATGTAAA
1 TAAAATGTAAG
339843 TAAAA
1 TAAAA
339848 CAAGGGGAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.61, C:0.00, G:0.13, T:0.26
Consensus pattern (11 bp):
TAAAATGTAAG
Found at i:342740 original size:8 final size:8
Alignment explanation
Indices: 342698--342764 Score: 57
Period size: 8 Copynumber: 8.4 Consensus size: 8
342688 TTTACAATTT
342698 ATATATAAA
1 ATAT-TAAA
342707 ATATTCAAA
1 ATATT-AAA
* *
342716 AAATCAAA
1 ATATTAAA
* *
342724 A-AATCAA
1 ATATTAAA
342731 ATATTAAA
1 ATATTAAA
342739 ATATTAAA
1 ATATTAAA
342747 ATATTAAA
1 ATATTAAA
*
342755 A-ATAAAA
1 ATATTAAA
342762 ATA
1 ATA
342765 CTATATATAT
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
7 10 0.21
8 27 0.57
9 10 0.21
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.28
Consensus pattern (8 bp):
ATATTAAA
Found at i:342764 original size:31 final size:33
Alignment explanation
Indices: 342698--342761 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 33
342688 TTTACAATTT
*
342698 ATATATAAAATATTCAAAAAATCAAAAAATCAA
1 ATATATAAAATATTCAAAAAATCAAAAAATAAA
* *
342731 ATAT-TAAAATATT-AAAATAT-TAAAAATAAA
1 ATATATAAAATATTCAAAAAATCAAAAAATAAA
342761 A
1 A
342762 ATACTATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 9 0.32
31 6 0.21
32 9 0.32
33 4 0.14
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (33 bp):
ATATATAAAATATTCAAAAAATCAAAAAATAAA
Found at i:342836 original size:20 final size:21
Alignment explanation
Indices: 342794--342836 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
342784 TGTATATGTA
**
342794 TATTAAAAATGAAAAAGTTAT
1 TATTAAAAATGAAAAAGAAAT
*
342815 TATTAAAAAT-TAAAAGAAAT
1 TATTAAAAATGAAAAAGAAAT
342835 TA
1 TA
342837 AAATACCGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (21 bp):
TATTAAAAATGAAAAAGAAAT
Found at i:343339 original size:2 final size:2
Alignment explanation
Indices: 343332--343358 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
343322 CTTAGCTTAT
343332 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 T
343359 TAAGTTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:343479 original size:16 final size:15
Alignment explanation
Indices: 343458--343496 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
343448 TTATTTTTGG
343458 AATATTTGAATATTTA
1 AATATTT-AATATTTA
*
343474 AATATTTTATATTTA
1 AATATTTAATATTTA
343489 AA-ATTTAA
1 AATATTTAA
343497 AATAATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 5 0.24
15 9 0.43
16 7 0.33
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (15 bp):
AATATTTAATATTTA
Found at i:343499 original size:23 final size:24
Alignment explanation
Indices: 343459--343510 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
343449 TATTTTTGGA
*
343459 ATATTTGAATATTTAAAT-ATTTT
1 ATATTTGAAAATTTAAATAATTTT
343482 ATATTT-AAAATTTAAAATAATTTT
1 ATATTTGAAAATTT-AAATAATTTT
343506 -TATTT
1 ATATTT
343511 TTAAATAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 6 0.23
23 15 0.58
24 5 0.19
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (24 bp):
ATATTTGAAAATTTAAATAATTTT
Found at i:344147 original size:15 final size:15
Alignment explanation
Indices: 344115--344180 Score: 75
Period size: 14 Copynumber: 4.5 Consensus size: 15
344105 TTCTAATTTC
344115 ATTTTTATAAATA-T-
1 ATTTTTA-AAATATTA
344129 ATTTTTAAAATATTA
1 ATTTTTAAAATATTA
* *
344144 A-TTTTAAAATTTTT
1 ATTTTTAAAATATTA
344158 ATTTTTAAAATATATA
1 ATTTTTAAAATAT-TA
344174 ATTTTTA
1 ATTTTTA
344181 TTTTGAATAT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
13 5 0.11
14 20 0.45
15 11 0.25
16 8 0.18
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
ATTTTTAAAATATTA
Found at i:365523 original size:153 final size:153
Alignment explanation
Indices: 365285--365590 Score: 578
Period size: 153 Copynumber: 2.0 Consensus size: 153
365275 TAGCCTACTA
*
365285 TCTTACCTCCCCCTTACCCTATTACATATGGGAACAAGAGATAACCATTTATGCTATAAACTAAC
1 TCTTACCTCCCCCTTACCCTATTACATATGGGAACAAGAGACAACCATTTATGCTATAAACTAAC
365350 ATAAATAGGCATTCTAATTCATGGAGTGGATAGAAAAACACTTTTTACCGGAATCGTTTTTGCCG
66 ATAAATAGGCATTCTAATTCATGGAGTGGATAGAAAAACACTTTTTACCGGAATCGTTTTTGCCG
365415 ACTCATATGTCACATATATAAGAC
131 ACTCATATGTCACATATA-AAGAC
365439 TCTTACCT-CCCCTTACCCTATTACATATGGGAACAAGAGACAACCATTTATGCTATAAACTAAC
1 TCTTACCTCCCCCTTACCCTATTACATATGGGAACAAGAGACAACCATTTATGCTATAAACTAAC
*
365503 ATAAATAGGCATTCTAATTCATGGAGTGGATAGAAAAACACTTTTTACCGGAATCGTTTTTGTCG
66 ATAAATAGGCATTCTAATTCATGGAGTGGATAGAAAAACACTTTTTACCGGAATCGTTTTTGCCG
365568 ACTCATATGTCACATATAAAGAC
131 ACTCATATGTCACATATAAAGAC
365591 GCTTTTTATA
Statistics
Matches: 150, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
152 5 0.03
153 137 0.91
154 8 0.05
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (153 bp):
TCTTACCTCCCCCTTACCCTATTACATATGGGAACAAGAGACAACCATTTATGCTATAAACTAAC
ATAAATAGGCATTCTAATTCATGGAGTGGATAGAAAAACACTTTTTACCGGAATCGTTTTTGCCG
ACTCATATGTCACATATAAAGAC
Found at i:368625 original size:56 final size:56
Alignment explanation
Indices: 368560--368742 Score: 174
Period size: 56 Copynumber: 3.2 Consensus size: 56
368550 AAATTTGCGT
*
368560 GAAGAAGCCTTCACCATATAAAAATACCTCTACATAAAACATCGAGAACTTTGCAC
1 GAAGAAGCCTTCTCCATATAAAAATACCTCTACATAAAACATCGAGAACTTTGCAC
* * * **
368616 GAAGAAGCCTTCTCCACATACCAAATACCT-TAGCATATAAAGCATCGAGAACTATGCTT
1 GAAGAAGCCTTCTCCATATA-AAAATACCTCTA-CATA-AAA-CATCGAGAACTTTGCAC
* * * * * *
368675 GAAAAAACCTTCGTCC-TATAACAATACCTACT-TATAAAACATCAAGAACTTTGCGC
1 GAAGAAGCCTTC-TCCATATAAAAATACCT-CTACATAAAACATCGAGAACTTTGCAC
*
368731 GAAGAGGCCTTC
1 GAAGAAGCCTTC
368743 GCTCTATAAT
Statistics
Matches: 101, Mismatches: 19, Indels: 14
0.75 0.14 0.10
Matches are distributed among these distances:
56 42 0.42
57 15 0.15
58 13 0.13
59 27 0.27
60 4 0.04
ACGTcount: A:0.39, C:0.25, G:0.13, T:0.23
Consensus pattern (56 bp):
GAAGAAGCCTTCTCCATATAAAAATACCTCTACATAAAACATCGAGAACTTTGCAC
Found at i:368750 original size:56 final size:55
Alignment explanation
Indices: 368485--368760 Score: 150
Period size: 56 Copynumber: 4.9 Consensus size: 55
368475 TACATCCACT
* * * * * *
368485 TAAAGCATCAAAAACTTTGTGCGAAGAAACCTTCGCTTTGTAACGAATACCTC-TA
1 TAAAACATCAAGAACTTTGCGCGAAGAAGCCTTCGCTCTATAAC-AATACCTCTTA
* * * * * * * *
368540 -CATA-ATCAATAAATTTGCGTGAAGAAGCCTTCAC-CATATAAAAATACCTCTACA
1 TAAAACATCAAGAACTTTGCGCGAAGAAGCCTTCGCTC-TATAACAATACCTCT-TA
* * * * * *
368594 TAAAACATCGAGAACTTTGCACGAAGAAGCCTTCTC-CACATACCAAATACCTTAGCATA
1 TAAAACATCAAGAACTTTGCGCGAAGAAGCCTTCGCTC-TATAAC-AATACC-T--CTTA
* * * ** * *
368653 TAAAGCATCGAGAACTATGCTTGAAAAAACCTTCG-TCCTATAACAATACCTACTTA
1 TAAAACATCAAGAACTTTGCGCGAAGAAGCCTTCGCT-CTATAACAATACCT-CTTA
* *
368709 TAAAACATCAAGAACTTTGCGCGAAGAGGCCTTCGCTCTATAATGAATACCT
1 TAAAACATCAAGAACTTTGCGCGAAGAAGCCTTCGCTCTATAA-CAATACCT
368761 TCGTACAAAT
Statistics
Matches: 162, Mismatches: 46, Indels: 24
0.70 0.20 0.10
Matches are distributed among these distances:
52 8 0.05
53 28 0.17
54 2 0.01
55 2 0.01
56 65 0.40
57 15 0.09
58 7 0.04
59 33 0.20
60 2 0.01
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.25
Consensus pattern (55 bp):
TAAAACATCAAGAACTTTGCGCGAAGAAGCCTTCGCTCTATAACAATACCTCTTA
Found at i:374198 original size:33 final size:33
Alignment explanation
Indices: 374161--374241 Score: 128
Period size: 33 Copynumber: 2.5 Consensus size: 33
374151 AAAAATAAAT
*
374161 CAACGTATTTGAGTCCTATTGAAATACTAAAAC
1 CAACGTATTTGAGTCCTATTGAAACACTAAAAC
374194 CAACGTATTTGAGTCCTATTGAAACACTAAAAC
1 CAACGTATTTGAGTCCTATTGAAACACTAAAAC
*
374227 CGAA-GCATTTGAGTC
1 C-AACGTATTTGAGTC
374242 TAAGTAGGAC
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
33 43 0.96
34 2 0.04
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (33 bp):
CAACGTATTTGAGTCCTATTGAAACACTAAAAC
Found at i:374300 original size:11 final size:11
Alignment explanation
Indices: 374284--374308 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
374274 GTTTCTTTAA
374284 ACTATAAATAG
1 ACTATAAATAG
374295 ACTATAAATAG
1 ACTATAAATAG
374306 ACT
1 ACT
374309 CAAGCATCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.12, G:0.08, T:0.28
Consensus pattern (11 bp):
ACTATAAATAG
Found at i:374812 original size:16 final size:15
Alignment explanation
Indices: 374789--374838 Score: 77
Period size: 16 Copynumber: 3.4 Consensus size: 15
374779 ATGATAATAC
374789 ATTATTTATTATTTT
1 ATTATTTATTATTTT
374804 ATGTATTTATTATTTT
1 AT-TATTTATTATTTT
374820 ATTA-TTATTA-TTT
1 ATTATTTATTATTTT
374833 ATTATT
1 ATTATT
374839 CATTTTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
13 7 0.21
14 7 0.21
15 4 0.12
16 15 0.45
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (15 bp):
ATTATTTATTATTTT
Found at i:374816 original size:3 final size:3
Alignment explanation
Indices: 374789--374838 Score: 50
Period size: 3 Copynumber: 16.0 Consensus size: 3
374779 ATGATAATAC
374789 ATT ATTT ATT ATT -TT ATGT ATTT ATT ATT -TT ATT ATT ATT ATTT ATT
1 ATT A-TT ATT ATT ATT AT-T A-TT ATT ATT ATT ATT ATT ATT A-TT ATT
374836 ATT
1 ATT
374839 CATTTTTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
2 4 0.10
3 26 0.63
4 10 0.24
5 1 0.02
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (3 bp):
ATT
Found at i:374831 original size:21 final size:21
Alignment explanation
Indices: 374797--374838 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
374787 ACATTATTTA
374797 TTATTTTATGTATTTATTATT
1 TTATTTTATGTATTTATTATT
374818 TTATTATTAT-TATTTATTATT
1 TTATT-TTATGTATTTATTATT
374839 CATTTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (21 bp):
TTATTTTATGTATTTATTATT
Found at i:375365 original size:2 final size:2
Alignment explanation
Indices: 375354--375382 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
375344 CAAACCTAAA
375354 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
375383 TGGTAACATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:376383 original size:29 final size:28
Alignment explanation
Indices: 376341--376401 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 28
376331 TCAATTTACC
376341 CCGAAATACCAAACCCGCCCGCCTTCACA
1 CCGAAATACCAAACCCGCCCG-CTTCACA
376370 CCGAAATACCAAACCCGCCCGCTTCACA
1 CCGAAATACCAAACCCGCCCGCTTCACA
376398 CCGA
1 CCGA
376402 GCGTGACAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 11 0.34
29 21 0.66
ACGTcount: A:0.31, C:0.48, G:0.11, T:0.10
Consensus pattern (28 bp):
CCGAAATACCAAACCCGCCCGCTTCACA
Found at i:381518 original size:23 final size:23
Alignment explanation
Indices: 381492--381549 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
381482 ACAAAGAAAA
* *
381492 ACGTGCTATAAAGGCAGAAGAAG
1 ACGTGCCATAAAAGCAGAAGAAG
* * *
381515 ACGTACCATAAAAGCATAAGAAT
1 ACGTGCCATAAAAGCAGAAGAAG
381538 ACGTGCCATAAA
1 ACGTGCCATAAA
381550 CGTAGAATTA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.16
Consensus pattern (23 bp):
ACGTGCCATAAAAGCAGAAGAAG
Found at i:381849 original size:22 final size:22
Alignment explanation
Indices: 381795--381850 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
381785 ATGAATCATT
* *
381795 TAATAAAATTAATTTAATAGTTA
1 TAATCAAATT-ATTTAATAGTAA
*
381818 TAATTAAATTATTTAAT-GTAA
1 TAATCAAATTATTTAATAGTAA
381839 TAATCATAATTA
1 TAATCA-AATTA
381851 AAATAGAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 8 0.28
22 12 0.41
23 9 0.31
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.45
Consensus pattern (22 bp):
TAATCAAATTATTTAATAGTAA
Found at i:381895 original size:26 final size:27
Alignment explanation
Indices: 381861--381916 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
381851 AAATAGAAAG
* * *
381861 TAAACTTATTAATTTAATTATTATAAT
1 TAAACTTATTAATCTAATGATCATAAT
381888 TAAA-TTATTAATCTAATGATCATAAT
1 TAAACTTATTAATCTAATGATCATAAT
381914 TAA
1 TAA
381917 TAACTTGTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 22 0.85
27 4 0.15
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.46
Consensus pattern (27 bp):
TAAACTTATTAATCTAATGATCATAAT
Found at i:382932 original size:50 final size:45
Alignment explanation
Indices: 382872--382971 Score: 137
Period size: 50 Copynumber: 2.1 Consensus size: 45
382862 CGTTTGTTAA
*
382872 TTAGTTGAGACAAAATACTCTAAAAAAGAATAAAAACCAAAATAACCATT
1 TTAGTCGAGACAAAATACTC--AAAAA-AAT-AAAA-CAAAATAACCATT
*
382922 TTAGTCGAGACAAAATACTCAAAAAAATAAAATAAAATAACCATT
1 TTAGTCGAGACAAAATACTCAAAAAAATAAAACAAAATAACCATT
382967 TTAGT
1 TTAGT
382972 AAACCTTGAC
Statistics
Matches: 48, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
45 17 0.35
46 4 0.08
47 3 0.06
48 5 0.10
50 19 0.40
ACGTcount: A:0.55, C:0.13, G:0.08, T:0.24
Consensus pattern (45 bp):
TTAGTCGAGACAAAATACTCAAAAAAATAAAACAAAATAACCATT
Found at i:386235 original size:31 final size:31
Alignment explanation
Indices: 386197--386286 Score: 153
Period size: 31 Copynumber: 2.9 Consensus size: 31
386187 TAGTAAAGTA
*
386197 AGCCAAAAGCTCTTGTTCCCATTGATATTGG
1 AGCCAAAAGATCTTGTTCCCATTGATATTGG
*
386228 AGCCAAAAGATATTGTTCCCATTGATATTGG
1 AGCCAAAAGATCTTGTTCCCATTGATATTGG
*
386259 AGCCAAAAGATCTTGTTCCCATCGATAT
1 AGCCAAAAGATCTTGTTCCCATTGATAT
386287 CTGTGTACAC
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 55 1.00
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (31 bp):
AGCCAAAAGATCTTGTTCCCATTGATATTGG
Found at i:390852 original size:21 final size:21
Alignment explanation
Indices: 390823--390862 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
390813 GTAAAAAAAT
*
390823 TACCTAAAACATTATTATTTC
1 TACCAAAAACATTATTATTTC
**
390844 TACCAAAAATGTTATTATT
1 TACCAAAAACATTATTATT
390863 GGGCGCTTTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.15, G:0.03, T:0.42
Consensus pattern (21 bp):
TACCAAAAACATTATTATTTC
Found at i:391974 original size:42 final size:40
Alignment explanation
Indices: 391911--391996 Score: 118
Period size: 42 Copynumber: 2.1 Consensus size: 40
391901 TTCGGTTTCC
* * * *
391911 TTTAATATTAGACCATGATAATAAATTTATTATTAATATTCT
1 TTTAAAATTAAACCATAATAATAAATTTATCATTAAT-TT-T
391953 TTTAAAATTAAACCATAATAATAAATTTATCATTAATTTT
1 TTTAAAATTAAACCATAATAATAAATTTATCATTAATTTT
391993 TTTA
1 TTTA
391997 TCATCTAACA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
40 5 0.12
41 2 0.05
42 33 0.82
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (40 bp):
TTTAAAATTAAACCATAATAATAAATTTATCATTAATTTT
Found at i:407010 original size:2 final size:2
Alignment explanation
Indices: 407005--407035 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
406995 TTTATCTCAA
407005 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
407036 ACAAAATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:407136 original size:24 final size:24
Alignment explanation
Indices: 407104--407152 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
407094 TAGCCTCAAT
407104 CTTTTAATAGATTATTATTCCATG
1 CTTTTAATAGATTATTATTCCATG
407128 CTTTTAATAGATTATTATTCCATG
1 CTTTTAATAGATTATTATTCCATG
407152 C
1 C
407153 ATTAACGATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.29, C:0.14, G:0.08, T:0.49
Consensus pattern (24 bp):
CTTTTAATAGATTATTATTCCATG
Found at i:411281 original size:10 final size:9
Alignment explanation
Indices: 411246--411338 Score: 87
Period size: 10 Copynumber: 9.7 Consensus size: 9
411236 GCTGCTGGAA
*
411246 ACCGGTTTA
1 ACCGGTTTG
*
411255 ACCGGTTTTCA
1 ACCGG-TTT-G
411266 ACCGGTTCTG
1 ACCGGTT-TG
411276 ACCGGTTTG
1 ACCGGTTTG
*
411285 ACCGGTTTCA
1 ACCGGTTT-G
*
411295 ACCGGTTCG
1 ACCGGTTTG
411304 AACCGGTTTG
1 -ACCGGTTTG
*
411314 ACCGGTCTG
1 ACCGGTTTG
411323 AACCGGTTTG
1 -ACCGGTTTG
411333 ACCGGT
1 ACCGGT
411339 CAGACCCGAC
Statistics
Matches: 71, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
9 29 0.41
10 35 0.49
11 7 0.10
ACGTcount: A:0.16, C:0.27, G:0.28, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:411290 original size:19 final size:20
Alignment explanation
Indices: 411246--411338 Score: 104
Period size: 19 Copynumber: 4.8 Consensus size: 20
411236 GCTGCTGGAA
* * *
411246 ACCGGTTTAACCGGTTTTCA
1 ACCGGTTTGACCGGTTCTGA
411266 ACCGGTTCTGACCGGTT-TG-
1 ACCGGTT-TGACCGGTTCTGA
*
411285 ACCGGTTTCAACCGGTTC-GA
1 ACCGGTTT-GACCGGTTCTGA
411305 ACCGGTTTGACCGG-TCTGA
1 ACCGGTTTGACCGGTTCTGA
411324 ACCGGTTTGACCGGT
1 ACCGGTTTGACCGGT
411339 CAGACCCGAC
Statistics
Matches: 63, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
18 3 0.05
19 36 0.57
20 16 0.25
21 8 0.13
ACGTcount: A:0.16, C:0.27, G:0.28, T:0.29
Consensus pattern (20 bp):
ACCGGTTTGACCGGTTCTGA
Found at i:411308 original size:29 final size:28
Alignment explanation
Indices: 411246--411338 Score: 123
Period size: 29 Copynumber: 3.2 Consensus size: 28
411236 GCTGCTGGAA
*
411246 ACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 ACCGGTTTGACCGG-TTTCAACCGGTTC-G
411276 ACCGGTTTGACCGGTTTCAACCGGTTCG
1 ACCGGTTTGACCGGTTTCAACCGGTTCG
* * *
411304 AACCGGTTTGACCGGTCTGAACCGGTTTG
1 -ACCGGTTTGACCGGTTTCAACCGGTTCG
411333 ACCGGT
1 ACCGGT
411339 CAGACCCGAC
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
28 7 0.12
29 38 0.66
30 13 0.22
ACGTcount: A:0.16, C:0.27, G:0.28, T:0.29
Consensus pattern (28 bp):
ACCGGTTTGACCGGTTTCAACCGGTTCG
Found at i:411344 original size:9 final size:9
Alignment explanation
Indices: 411266--411344 Score: 52
Period size: 9 Copynumber: 8.3 Consensus size: 9
411256 CCGGTTTTCA
411266 ACCGGTTCTG
1 ACCGG-TCTG
*
411276 ACCGGTTTG
1 ACCGGTCTG
* *
411285 ACCGGTTTCA
1 ACCGGTCT-G
411295 ACCGGT-TCG
1 ACCGGTCT-G
*
411304 AACCGGTTTG
1 -ACCGGTCTG
411314 ACCGGTCTG
1 ACCGGTCTG
*
411323 AACCGGTTTG
1 -ACCGGTCTG
*
411333 ACCGGTCAG
1 ACCGGTCTG
411342 ACC
1 ACC
411345 CGACCCGACC
Statistics
Matches: 58, Mismatches: 7, Indels: 9
0.78 0.09 0.12
Matches are distributed among these distances:
9 31 0.53
10 26 0.45
11 1 0.02
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.25
Consensus pattern (9 bp):
ACCGGTCTG
Found at i:411351 original size:5 final size:5
Alignment explanation
Indices: 411341--411420 Score: 79
Period size: 5 Copynumber: 14.8 Consensus size: 5
411331 TGACCGGTCA
* *
411341 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
*
411390 GACCC GACCGTT GACCC GACCC GACCC GACC
1 GACCC GACC--C GACCC GACCC GACCC GACC
411421 GTTGACCGTT
Statistics
Matches: 63, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
5 51 0.81
7 12 0.19
ACGTcount: A:0.19, C:0.51, G:0.23, T:0.07
Consensus pattern (5 bp):
GACCC
Found at i:411367 original size:22 final size:22
Alignment explanation
Indices: 411341--411427 Score: 174
Period size: 22 Copynumber: 4.0 Consensus size: 22
411331 TGACCGGTCA
411341 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
411363 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
411385 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
411407 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
411428 GTTGACCGTT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 65 1.00
ACGTcount: A:0.18, C:0.49, G:0.23, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:411427 original size:17 final size:15
Alignment explanation
Indices: 411341--411420 Score: 79
Period size: 17 Copynumber: 4.9 Consensus size: 15
411331 TGACCGGTCA
*
411341 GACCCGACCCGACCGTT
1 GACCCGACCCGACC--C
411358 GACCCGACCCGACCC
1 GACCCGACCCGACCC
*
411373 GACCGTTGACCCGACCC
1 GACC--CGACCCGACCC
*
411390 GACCCGACCGTTGACCC
1 GACCCGACC--CGACCC
411407 GACCCGACCCGACC
1 GACCCGACCCGACC
411421 GTTGACCGTT
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
15 12 0.22
17 42 0.78
ACGTcount: A:0.19, C:0.51, G:0.23, T:0.07
Consensus pattern (15 bp):
GACCCGACCCGACCC
Found at i:418634 original size:10 final size:9
Alignment explanation
Indices: 418599--418691 Score: 87
Period size: 10 Copynumber: 9.7 Consensus size: 9
418589 GCTGCTGGAA
*
418599 ACCGGTTTA
1 ACCGGTTTG
*
418608 ACCGGTTTTCA
1 ACCGG-TTT-G
418619 ACCGGTTCTG
1 ACCGGTT-TG
418629 ACCGGTTTG
1 ACCGGTTTG
*
418638 ACCGGTTTCA
1 ACCGGTTT-G
*
418648 ACCGGTTCG
1 ACCGGTTTG
418657 AACCGGTTTG
1 -ACCGGTTTG
*
418667 ACCGGTCTG
1 ACCGGTTTG
418676 AACCGGTTTG
1 -ACCGGTTTG
418686 ACCGGT
1 ACCGGT
418692 CAGACCCGAC
Statistics
Matches: 71, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
9 29 0.41
10 35 0.49
11 7 0.10
ACGTcount: A:0.16, C:0.27, G:0.28, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:418643 original size:19 final size:20
Alignment explanation
Indices: 418599--418691 Score: 104
Period size: 19 Copynumber: 4.8 Consensus size: 20
418589 GCTGCTGGAA
* * *
418599 ACCGGTTTAACCGGTTTTCA
1 ACCGGTTTGACCGGTTCTGA
418619 ACCGGTTCTGACCGGTT-TG-
1 ACCGGTT-TGACCGGTTCTGA
*
418638 ACCGGTTTCAACCGGTTC-GA
1 ACCGGTTT-GACCGGTTCTGA
418658 ACCGGTTTGACCGG-TCTGA
1 ACCGGTTTGACCGGTTCTGA
418677 ACCGGTTTGACCGGT
1 ACCGGTTTGACCGGT
418692 CAGACCCGAC
Statistics
Matches: 63, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
18 3 0.05
19 36 0.57
20 16 0.25
21 8 0.13
ACGTcount: A:0.16, C:0.27, G:0.28, T:0.29
Consensus pattern (20 bp):
ACCGGTTTGACCGGTTCTGA
Found at i:418661 original size:29 final size:28
Alignment explanation
Indices: 418599--418691 Score: 123
Period size: 29 Copynumber: 3.2 Consensus size: 28
418589 GCTGCTGGAA
*
418599 ACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 ACCGGTTTGACCGG-TTTCAACCGGTTC-G
418629 ACCGGTTTGACCGGTTTCAACCGGTTCG
1 ACCGGTTTGACCGGTTTCAACCGGTTCG
* * *
418657 AACCGGTTTGACCGGTCTGAACCGGTTTG
1 -ACCGGTTTGACCGGTTTCAACCGGTTCG
418686 ACCGGT
1 ACCGGT
418692 CAGACCCGAC
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
28 7 0.12
29 38 0.66
30 13 0.22
ACGTcount: A:0.16, C:0.27, G:0.28, T:0.29
Consensus pattern (28 bp):
ACCGGTTTGACCGGTTTCAACCGGTTCG
Found at i:418697 original size:9 final size:9
Alignment explanation
Indices: 418619--418697 Score: 52
Period size: 9 Copynumber: 8.3 Consensus size: 9
418609 CCGGTTTTCA
418619 ACCGGTTCTG
1 ACCGG-TCTG
*
418629 ACCGGTTTG
1 ACCGGTCTG
* *
418638 ACCGGTTTCA
1 ACCGGTCT-G
418648 ACCGGT-TCG
1 ACCGGTCT-G
*
418657 AACCGGTTTG
1 -ACCGGTCTG
418667 ACCGGTCTG
1 ACCGGTCTG
*
418676 AACCGGTTTG
1 -ACCGGTCTG
*
418686 ACCGGTCAG
1 ACCGGTCTG
418695 ACC
1 ACC
418698 CGACCCGACC
Statistics
Matches: 58, Mismatches: 7, Indels: 9
0.78 0.09 0.12
Matches are distributed among these distances:
9 31 0.53
10 26 0.45
11 1 0.02
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.25
Consensus pattern (9 bp):
ACCGGTCTG
Found at i:418704 original size:5 final size:5
Alignment explanation
Indices: 418694--418773 Score: 79
Period size: 5 Copynumber: 14.8 Consensus size: 5
418684 TGACCGGTCA
* *
418694 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
*
418743 GACCC GACCGTT GACCC GACCC GACCC GACC
1 GACCC GACC--C GACCC GACCC GACCC GACC
418774 GTTGACCGTT
Statistics
Matches: 63, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
5 51 0.81
7 12 0.19
ACGTcount: A:0.19, C:0.51, G:0.23, T:0.07
Consensus pattern (5 bp):
GACCC
Found at i:418720 original size:22 final size:22
Alignment explanation
Indices: 418694--418780 Score: 174
Period size: 22 Copynumber: 4.0 Consensus size: 22
418684 TGACCGGTCA
418694 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
418716 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
418738 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
418760 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
418781 GTTGACCGTT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 65 1.00
ACGTcount: A:0.18, C:0.49, G:0.23, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:418780 original size:17 final size:15
Alignment explanation
Indices: 418694--418773 Score: 79
Period size: 17 Copynumber: 4.9 Consensus size: 15
418684 TGACCGGTCA
*
418694 GACCCGACCCGACCGTT
1 GACCCGACCCGACC--C
418711 GACCCGACCCGACCC
1 GACCCGACCCGACCC
*
418726 GACCGTTGACCCGACCC
1 GACC--CGACCCGACCC
*
418743 GACCCGACCGTTGACCC
1 GACCCGACC--CGACCC
418760 GACCCGACCCGACC
1 GACCCGACCCGACC
418774 GTTGACCGTT
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
15 12 0.22
17 42 0.78
ACGTcount: A:0.19, C:0.51, G:0.23, T:0.07
Consensus pattern (15 bp):
GACCCGACCCGACCC
Found at i:428513 original size:19 final size:19
Alignment explanation
Indices: 428489--428525 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
428479 ATAAACTGTG
428489 AAAATGAATTATGAAATTA
1 AAAATGAATTATGAAATTA
*
428508 AAAATGGATTATGAAATT
1 AAAATGAATTATGAAATT
428526 GAATTCTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.14, T:0.32
Consensus pattern (19 bp):
AAAATGAATTATGAAATTA
Found at i:429357 original size:40 final size:40
Alignment explanation
Indices: 429302--429534 Score: 200
Period size: 40 Copynumber: 5.7 Consensus size: 40
429292 ACACGCACTA
* *
429302 TAGTGGCGTTTTTATATAAACGCCGATAAATATTGTACTT
1 TAGTGGCGTTTTTATACAAACGCCGATAAATAATGTACTT
* **
429342 TAGTGGCGTTTTTATACAAACGCCGCTAAA-GGTCGTACTT
1 TAGTGGCGTTTTTATACAAACGCCGATAAATAAT-GTACTT
* * * * * *
429382 TAGTGGCATTTTAAGCACAAGCGCCGATAATTACATGTTCTT
1 TAGTGGCGTTTTTA-TACAAACGCCGATAAATA-ATGTACTT
* * * *
429424 TAGTGGTG-TTTTATTCACAAACGCCGATAATTACACGTACTC
1 TAGTGGCGTTTTTA-T-ACAAACGCCGATAAATA-ATGTACTT
* * * * *
429466 TAGTTGCATTTTTATATAAACGTCGAGAAATAATGTACTT
1 TAGTGGCGTTTTTATACAAACGCCGATAAATAATGTACTT
* *
429506 TAGTGGCGTTTTTATATAAACGCCAATAA
1 TAGTGGCGTTTTTATACAAACGCCGATAA
429535 CGGTCATACT
Statistics
Matches: 151, Mismatches: 36, Indels: 12
0.76 0.18 0.06
Matches are distributed among these distances:
39 1 0.01
40 76 0.50
41 29 0.19
42 39 0.26
43 6 0.04
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (40 bp):
TAGTGGCGTTTTTATACAAACGCCGATAAATAATGTACTT
Found at i:429428 original size:42 final size:42
Alignment explanation
Indices: 429375--429635 Score: 156
Period size: 42 Copynumber: 6.3 Consensus size: 42
429365 CGCTAAAGGT
*
429375 CGTACTTTAGTGGCATTTTAAGCACAAGCGCCGATAATTACA
1 CGTACTTTAGTGGCATTTTAAGCACAAACGCCGATAATTACA
* * ** **
429417 TGTTCTTTAGTGGTGTTTTATTCACAAACGCCGATAATTACA
1 CGTACTTTAGTGGCATTTTAAGCACAAACGCCGATAATTACA
* * * * * * * *
429459 CGTACTCTAGTTGCATTTTTA-TATAAACGTCGAGAAATA-A
1 CGTACTTTAGTGGCATTTTAAGCACAAACGCCGATAATTACA
* * * * * * *
429499 TGTACTTTAGTGGCGTTTTTA-TATAAACGCCAATAACGGT-CA
1 CGTACTTTAGTGGCATTTTAAGCACAAACGCCGATAA--TTACA
* ** *
429541 --TACTTTAGTGGCGTTGCAAGCACAAACGCCGCTAATTACA
1 CGTACTTTAGTGGCATTTTAAGCACAAACGCCGATAATTACA
* *** * * *
429581 CGTACTTTTGTGGTGCTTTACGCACAAATGCCGCTAATTACA
1 CGTACTTTAGTGGCATTTTAAGCACAAACGCCGATAATTACA
*
429623 CATACTTTAGTGG
1 CGTACTTTAGTGG
429636 TGTTTTTAAA
Statistics
Matches: 167, Mismatches: 45, Indels: 14
0.74 0.20 0.06
Matches are distributed among these distances:
39 1 0.01
40 48 0.29
41 24 0.14
42 94 0.56
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (42 bp):
CGTACTTTAGTGGCATTTTAAGCACAAACGCCGATAATTACA
Found at i:429564 original size:164 final size:164
Alignment explanation
Indices: 429287--429652 Score: 455
Period size: 164 Copynumber: 2.2 Consensus size: 164
429277 ATAATGTCGC
* * * *
429287 TAATTACACGCACTATAGTGGCGTTTTTATATAAACGCCGATAAATATTGTACTTTAGTGGCGTT
1 TAATTACACGTACTATAGTGGCATTTTTATATAAACGCCGAGAAATAATGTACTTTAGTGGCGTT
** * ** *
429352 TTTATACAAACGCCGCTAAAGGTCGTACTTTAGTGGCATTTTAAGCACAAGCGCCGATAATTACA
66 TTTATACAAACGCCAATAAAGGTCATACTTTAGTGGCATTGCAAGCACAAACGCCGATAATTACA
* * * **
429417 TGTTCTTTAGTGGTGTTTTATTCACAAACGCCGA
131 CGTACTTTAGTGGTGCTTTACGCACAAACGCCGA
* * *
429451 TAATTACACGTACTCTAGTTGCATTTTTATATAAACGTCGAGAAATAATGTACTTTAGTGGCGTT
1 TAATTACACGTACTATAGTGGCATTTTTATATAAACGCCGAGAAATAATGTACTTTAGTGGCGTT
* * * *
429516 TTTATATAAACGCCAATAACGGTCATACTTTAGTGGCGTTGCAAGCACAAACGCCGCTAATTACA
66 TTTATACAAACGCCAATAAAGGTCATACTTTAGTGGCATTGCAAGCACAAACGCCGATAATTACA
* * *
429581 CGTACTTTTGTGGTGCTTTACGCACAAATGCCGC
131 CGTACTTTAGTGGTGCTTTACGCACAAACGCCGA
* * ** *
429615 TAATTACACATACTTTAGTGGTGTTTTTA-AAAAACGCC
1 TAATTACACGTACTATAGTGGCATTTTTATATAAACGCC
429653 TCTAAACATC
Statistics
Matches: 170, Mismatches: 32, Indels: 1
0.84 0.16 0.00
Matches are distributed among these distances:
163 7 0.04
164 163 0.96
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.34
Consensus pattern (164 bp):
TAATTACACGTACTATAGTGGCATTTTTATATAAACGCCGAGAAATAATGTACTTTAGTGGCGTT
TTTATACAAACGCCAATAAAGGTCATACTTTAGTGGCATTGCAAGCACAAACGCCGATAATTACA
CGTACTTTAGTGGTGCTTTACGCACAAACGCCGA
Found at i:431141 original size:27 final size:29
Alignment explanation
Indices: 431075--431144 Score: 90
Period size: 31 Copynumber: 2.4 Consensus size: 29
431065 TAACACTAGT
* *
431075 TATAAAGGAGTTAACACTGGTACTTTCAAAA
1 TATAAAGGAGTTAACACTAGTA-TAT-AAAA
431106 TATAAAGGAGTTAACACTAGT-TAT-AAA
1 TATAAAGGAGTTAACACTAGTATATAAAA
431133 TATAAAGGAGTT
1 TATAAAGGAGTT
431145 CCATTTGAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
27 15 0.41
29 2 0.05
31 20 0.54
ACGTcount: A:0.44, C:0.09, G:0.17, T:0.30
Consensus pattern (29 bp):
TATAAAGGAGTTAACACTAGTATATAAAA
Found at i:432415 original size:43 final size:42
Alignment explanation
Indices: 432326--432466 Score: 183
Period size: 43 Copynumber: 3.3 Consensus size: 42
432316 ATATCTGACT
* * *
432326 TTTTGCGGCGTTTGTTCAAAAAATGCCTCTATAGATATGACC
1 TTTTGCGGCGTTTGTTCCAAAAATGCCGCTATAGATACGACC
** * **
432368 TTTTGCGGCGTTTGTTCCAAAAGCGCCGCTAAAGATAGCGGTC
1 TTTTGCGGCGTTTGTTCCAAAAATGCCGCTATAGATA-CGACC
432411 TTTTGCGGCGTTTGTTCCAAAAATGCCGCTATAGATAACGACC
1 TTTTGCGGCGTTTGTTCCAAAAATGCCGCTATAGAT-ACGACC
*
432454 TATTGCGGCGTTT
1 TTTTGCGGCGTTT
432467 TTTGTTCTCA
Statistics
Matches: 83, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
42 32 0.39
43 50 0.60
44 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (42 bp):
TTTTGCGGCGTTTGTTCCAAAAATGCCGCTATAGATACGACC
Found at i:432582 original size:20 final size:20
Alignment explanation
Indices: 432559--432619 Score: 113
Period size: 20 Copynumber: 3.0 Consensus size: 20
432549 AAATGCCTCT
432559 ATAGGTAATAAAACGCCGCA
1 ATAGGTAATAAAACGCCGCA
432579 ATAGGTAATAAAACGCCGCA
1 ATAGGTAATAAAACGCCGCA
*
432599 ATAGGTAAAAAAACGCCGCA
1 ATAGGTAATAAAACGCCGCA
432619 A
1 A
432620 ATGTTTTTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.13
Consensus pattern (20 bp):
ATAGGTAATAAAACGCCGCA
Found at i:432911 original size:2 final size:2
Alignment explanation
Indices: 432904--432961 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
432894 GCTTGGGATA
432904 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
432946 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
432962 TAAGCCGAAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:437489 original size:21 final size:22
Alignment explanation
Indices: 437465--437515 Score: 59
Period size: 24 Copynumber: 2.3 Consensus size: 22
437455 AGATTGTTTC
437465 GATTT-TCTTATTTTAATAAAT
1 GATTTATCTTATTTTAATAAAT
* *
437486 GATTTTTATTTTATTTTAATGAAT
1 GA--TTTATCTTATTTTAATAAAT
437510 GATTTA
1 GATTTA
437516 CAAAATAACC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
21 2 0.08
22 4 0.16
23 3 0.12
24 16 0.64
ACGTcount: A:0.31, C:0.02, G:0.08, T:0.59
Consensus pattern (22 bp):
GATTTATCTTATTTTAATAAAT
Found at i:438442 original size:5 final size:5
Alignment explanation
Indices: 438432--438456 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
438422 TTTGGTTGTA
438432 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
438457 TACACTCCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:448020 original size:20 final size:20
Alignment explanation
Indices: 447956--448025 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
447946 TTATATGTAG
* * *
447956 TATTGTTACTATAAGAACAA
1 TATTGATACTTTAATAACAA
*
447976 TATCGATACTGTTAAT-ACAA
1 TATTGATACT-TTAATAACAA
*
447996 CATTGATACTTTAATAACAA
1 TATTGATACTTTAATAACAA
*
448016 TATTGGTACT
1 TATTGATACT
448026 ATTTACCCAA
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 5 0.12
20 32 0.80
21 3 0.08
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.37
Consensus pattern (20 bp):
TATTGATACTTTAATAACAA
Found at i:448281 original size:35 final size:35
Alignment explanation
Indices: 448242--448313 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
448232 AATTTAATTG
448242 TATCCCTACTAAGGACCCCATAAAAAAGATTACTT
1 TATCCCTACTAAGGACCCCATAAAAAAGATTACTT
* *
448277 TATCCCTACTAAGGATCCCATAAAAAATATTACTT
1 TATCCCTACTAAGGACCCCATAAAAAAGATTACTT
448312 TA
1 TA
448314 ATTAATTCTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.40, C:0.24, G:0.07, T:0.29
Consensus pattern (35 bp):
TATCCCTACTAAGGACCCCATAAAAAAGATTACTT
Found at i:453992 original size:37 final size:37
Alignment explanation
Indices: 453916--453992 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 37
453906 TTTTTATATT
*
453916 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * * *
453953 TTTAATTTTTTTAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
453990 TTT
1 TTT
453993 GTAATATTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
36 13 0.38
37 21 0.62
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:455905 original size:2 final size:2
Alignment explanation
Indices: 455900--455935 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
455890 ACACTCACTC
455900 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
455936 TCCTCCATCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:459488 original size:36 final size:36
Alignment explanation
Indices: 459407--459488 Score: 112
Period size: 36 Copynumber: 2.3 Consensus size: 36
459397 TCCTTGAAGT
*
459407 TTTGAGTTCAAACAATTATATATGTAGGATGTATGA
1 TTTGAGTTCAAACAACTATATATGTAGGATGTATGA
* * *
459443 TCT-ATGTTCAAACAACTATATATGTAGGGTGTGTGA
1 TTTGA-GTTCAAACAACTATATATGTAGGATGTATGA
459479 TTTGAGTTCA
1 TTTGAGTTCA
459489 GAAAATTGTA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
35 1 0.03
36 37 0.95
37 1 0.03
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.39
Consensus pattern (36 bp):
TTTGAGTTCAAACAACTATATATGTAGGATGTATGA
Found at i:468560 original size:21 final size:22
Alignment explanation
Indices: 468534--468576 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
468524 GTCTGACTGA
*
468534 CAAAAT-TAAAAAATCGATAAT
1 CAAAATATAAAAAAGCGATAAT
*
468555 CAAAATATAAAAGAGCGATAAT
1 CAAAATATAAAAAAGCGATAAT
468577 TAAATGGTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.60, C:0.09, G:0.09, T:0.21
Consensus pattern (22 bp):
CAAAATATAAAAAAGCGATAAT
Found at i:475246 original size:81 final size:78
Alignment explanation
Indices: 475157--475416 Score: 206
Period size: 81 Copynumber: 3.1 Consensus size: 78
475147 ATATTAAAAA
*
475157 TATTTTTAATATTAAAACAATTATAATTTTGTGTATTTTTTAATTCGTCAAATTATTTTATAACT
1 TATTTTTAATATTAAAACAATTATAATTTT-TGTATTTTTTAATTCATCAAATTATTTTATAA-T
475222 AATTGTTTATGTAAT
64 AATTGTTTATGTAAT
* *
475237 TATTATTTAATTTTTAAAATTAAAA-AAATATAATTTTTGAAATCTAAAATTTTAATT-ATCGAA
1 TATT-TTTAA----T---ATTAAAACAATTATAATTTTTG-TAT-T----TTTTAATTCATC-AA
* * * *
475300 ATTATTTTTTAA-AA--GTATATGAAAAA
51 ATTATTTTATAATAATTGTTTATG-TAAT
* *
475326 TATTTTTAAAATTAAAACAATTATAATTTTATGTATTTTTTAATTCATCAAATTATTTAATAATT
1 TATTTTTAATATTAAAACAATTATAATTTT-TGTATTTTTTAATTCATCAAATTATTTTATAA-T
*
475391 AATTGTTTATTTAAT
64 AATTGTTTATGTAAT
475406 TATTATTTAAT
1 TATT-TTTAAT
475417 TTTTAAAATT
Statistics
Matches: 139, Mismatches: 17, Indels: 47
0.68 0.08 0.23
Matches are distributed among these distances:
77 20 0.14
78 3 0.02
79 2 0.01
80 10 0.07
81 23 0.17
82 13 0.09
83 2 0.01
85 1 0.01
86 2 0.01
87 13 0.09
88 19 0.14
89 6 0.04
90 2 0.01
91 2 0.01
92 21 0.15
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.51
Consensus pattern (78 bp):
TATTTTTAATATTAAAACAATTATAATTTTTGTATTTTTTAATTCATCAAATTATTTTATAATAA
TTGTTTATGTAAT
Found at i:475259 original size:88 final size:85
Alignment explanation
Indices: 475158--475442 Score: 295
Period size: 88 Copynumber: 3.3 Consensus size: 85
475148 TATTAAAAAT
* *
475158 ATTTTTAATATTAAAACAATTATAATTTTGTGTATTTTTTAATTCGTCAAATTATTTTATAACTA
1 ATTTTTAAAATTAAAA-AATTATAATTTT-TGTATTTTTTAATTCATCAAATTATTTTATAA-TA
475223 ATTGTTTATGTAATTATTATTTA
63 ATTGTTTATGTAATTATTATTTA
* * *
475246 ATTTTTAAAATTAAAAAAATATAATTTTTGAAATCTAAAATTTTAATT-ATCGAAATTATTTTTT
1 ATTTTTAAAATTAAAAAATTATAATTTTTG-TAT-T----TTTTAATTCATC-AAATTATTTTAT
* *
475310 AA-AA--GTATATG-AA--A--A-AT-
59 AATAATTGTTTATGTAATTATTATTTA
*
475327 ATTTTTAAAATTAAAACAATTATAATTTTATGTATTTTTTAATTCATCAAATTATTTAATAATTA
1 ATTTTTAAAATTAAAA-AATTATAATTTT-TGTATTTTTTAATTCATCAAATTATTTTATAA-TA
*
475392 ATTGTTTATTTAATTATTATTTA
63 ATTGTTTATGTAATTATTATTTA
475415 ATTTTTAAAATTAAAAAATTATAATTTT
1 ATTTTTAAAATTAAAAAATTATAATTTT
475443 CGAAATCGAA
Statistics
Matches: 162, Mismatches: 14, Indels: 43
0.74 0.06 0.20
Matches are distributed among these distances:
77 20 0.12
78 3 0.02
79 2 0.01
81 22 0.14
82 16 0.10
83 3 0.02
84 1 0.01
85 1 0.01
86 3 0.02
87 28 0.17
88 38 0.23
90 2 0.01
91 2 0.01
92 21 0.13
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (85 bp):
ATTTTTAAAATTAAAAAATTATAATTTTTGTATTTTTTAATTCATCAAATTATTTTATAATAATT
GTTTATGTAATTATTATTTA
Found at i:475327 original size:169 final size:168
Alignment explanation
Indices: 475137--475465 Score: 541
Period size: 169 Copynumber: 2.0 Consensus size: 168
475127 AATTCGTAAC
* * *
475137 TTTTTAAAATATATTAAAAATATTTTTAATATTAAAACAATTATAATTTTGTGTATTTTTTAATT
1 TTTTTAAAATATATGAAAAATATTTTTAAAATTAAAACAATTATAATTTTATGTATTTTTTAATT
* *
475202 CGTCAAATTATTTTATAACTAATTGTTTATGTAATTATTATTTAATTTTTAAAATTAAAAAAATA
66 CATCAAATTATTTAATAACTAATTGTTTATGTAATTATTATTTAATTTTTAAAATTAAAAAAATA
* * *
475267 TAATTTTTGAAATCTAAAATTTTAATTATCGAAATTAT
131 TAATTTTCGAAATCGAAAAATTTAATTATCGAAATTAT
475305 TTTTTAAAAGTATATGAAAAATATTTTTAAAATTAAAACAATTATAATTTTATGTATTTTTTAAT
1 TTTTTAAAA-TATATGAAAAATATTTTTAAAATTAAAACAATTATAATTTTATGTATTTTTTAAT
* * *
475370 TCATCAAATTATTTAATAATTAATTGTTTATTTAATTATTATTTAATTTTTAAAATTAAAAAATT
65 TCATCAAATTATTTAATAACTAATTGTTTATGTAATTATTATTTAATTTTTAAAATTAAAAAAAT
*
475435 ATAATTTTCGAAATCGAAAAATTTATTTATC
130 ATAATTTTCGAAATCGAAAAATTTAATTATC
475466 AAACTATGAA
Statistics
Matches: 148, Mismatches: 12, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
168 9 0.06
169 139 0.94
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.50
Consensus pattern (168 bp):
TTTTTAAAATATATGAAAAATATTTTTAAAATTAAAACAATTATAATTTTATGTATTTTTTAATT
CATCAAATTATTTAATAACTAATTGTTTATGTAATTATTATTTAATTTTTAAAATTAAAAAAATA
TAATTTTCGAAATCGAAAAATTTAATTATCGAAATTAT
Found at i:475448 original size:23 final size:23
Alignment explanation
Indices: 475413--475457 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
475403 AATTATTATT
* *
475413 TAATTTTTAAAATTAAAAAATTA
1 TAATTTTCAAAATCAAAAAATTA
* *
475436 TAATTTTCGAAATCGAAAAATT
1 TAATTTTCAAAATCAAAAAATT
475458 TATTTATCAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.40
Consensus pattern (23 bp):
TAATTTTCAAAATCAAAAAATTA
Found at i:481697 original size:21 final size:23
Alignment explanation
Indices: 481659--481717 Score: 79
Period size: 22 Copynumber: 2.7 Consensus size: 23
481649 CCAAAATAAT
*
481659 AATAAAAATATTATATTT-ATTC
1 AATAAAAATAATATATTTAATTC
*
481681 AATAAAAATAATA-ATTTAATTG
1 AATAAAAATAATATATTTAATTC
481703 AA-AAAAATAATATAT
1 AATAAAAATAATATAT
481718 AGAGGAACAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.42
22 19 0.58
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (23 bp):
AATAAAAATAATATATTTAATTC
Found at i:483404 original size:24 final size:24
Alignment explanation
Indices: 483377--483450 Score: 87
Period size: 24 Copynumber: 3.1 Consensus size: 24
483367 AAACGAAGAT
*
483377 ATCAAAAATCAAAACAGAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* **
483401 ATCAGATATCAGTACAGAA-TCGAG
1 ATCAGAAATCAAAACAGAATTC-AG
*
483425 ATCAGAAATCAAAACAAAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
483449 AT
1 AT
483451 AATGTATCAT
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
23 2 0.05
24 36 0.90
25 2 0.05
ACGTcount: A:0.53, C:0.16, G:0.12, T:0.19
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:483459 original size:48 final size:48
Alignment explanation
Indices: 483377--483468 Score: 125
Period size: 48 Copynumber: 1.9 Consensus size: 48
483367 AAACGAAGAT
* *
483377 ATCAAAAATCAAAACAGAATTCAGATCAGATATCAGT-ACAGAATCGAG
1 ATCAAAAATCAAAACAAAATTCAGATAAGATATCA-TAACAGAATCGAG
*
483425 ATCAGAAATCAAAACAAAATTCAGATAATG-TATCATAACAGAAT
1 ATCAAAAATCAAAACAAAATTCAGATAA-GATATCATAACAGAAT
483469 TCAAGTCGGA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
47 1 0.03
48 37 0.95
49 1 0.03
ACGTcount: A:0.52, C:0.15, G:0.12, T:0.21
Consensus pattern (48 bp):
ATCAAAAATCAAAACAAAATTCAGATAAGATATCATAACAGAATCGAG
Found at i:483481 original size:48 final size:48
Alignment explanation
Indices: 483377--483481 Score: 117
Period size: 48 Copynumber: 2.2 Consensus size: 48
483367 AAACGAAGAT
* * * *
483377 ATCAAAAATCAAAACAGAATTCAGATCAGATATCAGTACAGAATCGAG
1 ATCAGAAATCAAAACAAAATTCAGATAAGATATCAGTACAGAATCAAG
483425 ATCAGAAATCAAAACAAAATTCAGATAATG-TATCA-TAACAGAATTCAAG
1 ATCAGAAATCAAAACAAAATTCAGATAA-GATATCAGT-ACAGAA-TCAAG
*
483474 -TCGGAAAT
1 ATCAGAAAT
483482 AAGATAAAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
47 1 0.02
48 43 0.88
49 5 0.10
ACGTcount: A:0.50, C:0.15, G:0.13, T:0.21
Consensus pattern (48 bp):
ATCAGAAATCAAAACAAAATTCAGATAAGATATCAGTACAGAATCAAG
Found at i:485180 original size:20 final size:20
Alignment explanation
Indices: 485155--485197 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
485145 ACTTCCAGGG
485155 ACAATTCTTGTCATCCTACA
1 ACAATTCTTGTCATCCTACA
485175 ACAATTCTTGTCATCCTACA
1 ACAATTCTTGTCATCCTACA
485195 ACA
1 ACA
485198 TAAGGGTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.33, C:0.30, G:0.05, T:0.33
Consensus pattern (20 bp):
ACAATTCTTGTCATCCTACA
Found at i:488833 original size:12 final size:12
Alignment explanation
Indices: 488811--488884 Score: 78
Period size: 12 Copynumber: 6.2 Consensus size: 12
488801 ATGATACATT
*
488811 ATCTGAATTCTG
1 ATCTGATTTCTG
*
488823 CTCTGATTTCTG
1 ATCTGATTTCTG
488835 ATCTGGA-TTCTG
1 ATCT-GATTTCTG
*
488847 TTCTGATTTCTG
1 ATCTGATTTCTG
*
488859 ATCTGAATTCTG
1 ATCTGATTTCTG
* *
488871 TTTTGATTTCTG
1 ATCTGATTTCTG
488883 AT
1 AT
488885 AAATTCGTTT
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
11 2 0.04
12 46 0.92
13 2 0.04
ACGTcount: A:0.16, C:0.16, G:0.18, T:0.50
Consensus pattern (12 bp):
ATCTGATTTCTG
Found at i:488838 original size:24 final size:24
Alignment explanation
Indices: 488776--488884 Score: 123
Period size: 24 Copynumber: 4.5 Consensus size: 24
488766 AAATATTTTA
*
488776 TCTGATTTCT-AACTTGAATTCTGT
1 TCTGATTTCTGATC-TGAATTCTGT
* * * *
488800 TATGA-TACATTATCTGAATTCTGC
1 TCTGATTTC-TGATCTGAATTCTGT
*
488824 TCTGATTTCTGATCTGGATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
488848 TCTGATTTCTGATCTGAATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
*
488872 TTTGATTTCTGAT
1 TCTGATTTCTGAT
488885 AAATTCGTTT
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
23 2 0.03
24 65 0.92
25 4 0.06
ACGTcount: A:0.19, C:0.16, G:0.16, T:0.50
Consensus pattern (24 bp):
TCTGATTTCTGATCTGAATTCTGT
Found at i:490901 original size:26 final size:26
Alignment explanation
Indices: 490872--490921 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
490862 ACAATGGGCG
490872 ATATACATCGATATGTATCATTAATA
1 ATATACATCGATATGTATCATTAATA
* *
490898 ATATATATTGATATGTATCATTAA
1 ATATACATCGATATGTATCATTAA
490922 ATTTTAATAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (26 bp):
ATATACATCGATATGTATCATTAATA
Found at i:491177 original size:2 final size:2
Alignment explanation
Indices: 491170--491201 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
491160 TGAATTTTAA
491170 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
491202 GATAACAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:492185 original size:15 final size:15
Alignment explanation
Indices: 492147--492196 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
492137 ACAAGAAAGA
492147 TACTAAATTATT-AAT
1 TACT-AATTATTAAAT
* *
492162 AAATAATTATTAAAT
1 TACTAATTATTAAAT
*
492177 TACTAATTATTAATT
1 TACTAATTATTAAAT
492192 TACTA
1 TACTA
492197 GATTTTACAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
14 7 0.24
15 22 0.76
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (15 bp):
TACTAATTATTAAAT
Found at i:492353 original size:67 final size:67
Alignment explanation
Indices: 492256--492435 Score: 191
Period size: 67 Copynumber: 2.6 Consensus size: 67
492246 AGCAATTAGT
* * * * *
492256 CGAGTCGAGTAACAAGTTTTTTTAATGAGCACGAGTCGAGCAAAATTTTGTCGAGCTTAACGAGC
1 CGAGTTGAGTAACAAGTTTTTTTAACGAGCACGAGTCGAGCAAAAATTTATCGAACTTAACGAGC
492321 -A
66 AA
** * *
492322 CGAGTTGAAGTAACAAGTTTTTTTAACGAGCATAAGTCGAGAAAAAATTTATCTAACTTAACGAG
1 CGAGTTG-AGTAACAAGTTTTTTTAACGAGCACGAGTCGAGCAAAAATTTATCGAACTTAACGAG
492387 CAA
65 CAA
* * * *
492390 TGAGTTGAGTCGAACAACAATTTTTATAACGAACACGAGTCGAGCA
1 CGAGTTGAGT--AAC-A-AGTTTTTTTAACGAGCACGAGTCGAGCA
492436 CTACTAAATT
Statistics
Matches: 92, Mismatches: 16, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
66 6 0.07
67 53 0.58
68 7 0.08
69 3 0.03
70 1 0.01
71 22 0.24
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.27
Consensus pattern (67 bp):
CGAGTTGAGTAACAAGTTTTTTTAACGAGCACGAGTCGAGCAAAAATTTATCGAACTTAACGAGC
AA
Found at i:494584 original size:43 final size:42
Alignment explanation
Indices: 494466--494598 Score: 137
Period size: 43 Copynumber: 3.1 Consensus size: 42
494456 TCAATTTTAT
* *
494466 TTTTTATATTTATAATTGAGGCCCCTAATTTTTGTGATCAT-AC
1 TTTTTATATTTATAATTGAGGACCCTAATTTTT-TAATC-TCAC
* * * * *
494509 TTTTTATCTTTATAATCG-GGACCATTAGTTTTTTCCATCTCAC
1 TTTTTATATTTATAATTGAGGACC-CTAATTTTTT-AATCTCAC
*
494552 TTTTTATATTTATAATTGATGACCCTAATTTTTTAAT-TCAC
1 TTTTTATATTTATAATTGAGGACCCTAATTTTTTAATCTCAC
494593 TTTTTA
1 TTTTTA
494599 CCTTTAAAAT
Statistics
Matches: 74, Mismatches: 12, Indels: 10
0.77 0.12 0.10
Matches are distributed among these distances:
41 10 0.14
42 8 0.11
43 52 0.70
44 4 0.05
ACGTcount: A:0.25, C:0.15, G:0.08, T:0.52
Consensus pattern (42 bp):
TTTTTATATTTATAATTGAGGACCCTAATTTTTTAATCTCAC
Found at i:496387 original size:26 final size:26
Alignment explanation
Indices: 496352--496415 Score: 110
Period size: 26 Copynumber: 2.5 Consensus size: 26
496342 AAACATTCAA
*
496352 TTAACTTGACATAACTTATATCCAAT
1 TTAACCTGACATAACTTATATCCAAT
*
496378 TTAACCTGACATAATTTATATCCAAT
1 TTAACCTGACATAACTTATATCCAAT
496404 TTAACCTGACAT
1 TTAACCTGACAT
496416 GACGTAATTC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.38, C:0.20, G:0.05, T:0.38
Consensus pattern (26 bp):
TTAACCTGACATAACTTATATCCAAT
Found at i:507769 original size:5 final size:5
Alignment explanation
Indices: 507759--507783 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
507749 ATGGGGCAAT
507759 TGTGG TGTGG TGTGG TGTGG TGTGG
1 TGTGG TGTGG TGTGG TGTGG TGTGG
507784 GTTTTCTCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.60, T:0.40
Consensus pattern (5 bp):
TGTGG
Found at i:509096 original size:2 final size:2
Alignment explanation
Indices: 509089--509114 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
509079 ATAGAAATAG
509089 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
509115 AATAGAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:541003 original size:38 final size:39
Alignment explanation
Indices: 540951--541030 Score: 135
Period size: 38 Copynumber: 2.1 Consensus size: 39
540941 GAAGGGTTCT
*
540951 TCTTCCTTAACCATCACTCACAAGTA-ATGGTGAAAGCC
1 TCTTCCTCAACCATCACTCACAAGTACATGGTGAAAGCC
*
540989 TCTTCCTCAGCCATCACTCACAAGTACATGGTGAAAGCC
1 TCTTCCTCAACCATCACTCACAAGTACATGGTGAAAGCC
541028 TCT
1 TCT
541031 GTCATTTTAG
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
38 24 0.62
39 15 0.38
ACGTcount: A:0.29, C:0.31, G:0.14, T:0.26
Consensus pattern (39 bp):
TCTTCCTCAACCATCACTCACAAGTACATGGTGAAAGCC
Done.