Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167849.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_12, 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: 22966848
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 129000 characters in sequence are not A, C, G, or T
File 108 of 129
Found at i:18023545 original size:14 final size:15
Alignment explanation
Indices: 18023521--18023549 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
18023511 AAATAGAGTT
18023521 AATTGAAATATAAAA
1 AATTGAAATATAAAA
18023536 AATT-AAATATAAAA
1 AATTGAAATATAAAA
18023550 CTAAAAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (15 bp):
AATTGAAATATAAAA
Found at i:18033015 original size:150 final size:150
Alignment explanation
Indices: 18032732--18033330 Score: 857
Period size: 150 Copynumber: 4.0 Consensus size: 150
18032722 CTGTAGAAAT
* * *
18032732 AAGCCAAATGATATGGCTTATGTACAGCATGGGAAGAAACCACCTAAGTTAGTTTATAAACGGCG
1 AAGCCAAATGATATGGTTTATGTACAGCCTGGAAAGAAACCACCTAAGTTAGTTTATAAACGGCG
* *
18032797 GAAAAAGCACAGTGAATCCCAGGAAAAGTCTGGTGCCGAAATAGGAATGAAGGAGAAAGAAGAAA
66 GAAAAAGCACAGTGAATCCCAGGAAAAGTCTGGTGCTGAAATAGGAATGAAGGAGAAAGAAGAGA
*
18032862 ACTGTTGTAGTGTGTTGTCA
131 ACTGTTGTAGTTTGTTGTCA
18032882 AAGCCAAATGATATGGTTTATGTACAGCCTGGAAAGAAACCACCTAAGTTAGTTTATAAACGGCG
1 AAGCCAAATGATATGGTTTATGTACAGCCTGGAAAGAAACCACCTAAGTTAGTTTATAAACGGCG
* * * * ** * *
18032947 GAAAAATCTCAGTGAACCCCAGGAAAAGACTGGTTTTGAAATAGGAATGAAGGAGAGAGAGGAGA
66 GAAAAAGCACAGTGAATCCCAGGAAAAGTCTGGTGCTGAAATAGGAATGAAGGAGAAAGAAGAGA
*
18033012 ACTGTTGTAGTTTGTTGTTA
131 ACTGTTGTAGTTTGTTGTCA
* ** * *
18033032 AAGCCAAATGATATGCTTTACATACAGCGTGGAAAGAAACCACCTAAGTTAATTTATAAACGGCG
1 AAGCCAAATGATATGGTTTATGTACAGCCTGGAAAGAAACCACCTAAGTTAGTTTATAAACGGCG
* * * *
18033097 GAAAAAGCACAGCGAATCCCAGGAAAAGTCTGGTGCTGAAATAAGAAT---GGAGAGAGTAGAGA
66 GAAAAAGCACAGTGAATCCCAGGAAAAGTCTGGTGCTGAAATAGGAATGAAGGAGAAAGAAGAGA
18033159 ACTGTTGTAGTTTGTTGTCA
131 ACTGTTGTAGTTTGTTGTCA
* *
18033179 AAGCCAAATGATATGGTTTATGCACAG-CAGGTAAAGAAACCACCTAAGTTAGTTTATAAACGGC
1 AAGCCAAATGATATGGTTTATGTACAGCCTGG-AAAGAAACCACCTAAGTTAGTTTATAAACGGC
* ** * * *
18033243 TGAAAAAGCATGGTGAATCCCAGGAAAA-TTTGGGTGTTGGAATAGGAATGAAGGAGAAAGAAGA
65 GGAAAAAGCACAGTGAATCCCAGGAAAAGTCT-GGTGCTGAAATAGGAATGAAGGAGAAAGAAGA
18033307 GAACTGTTGTAGTTTGTTGTCA
129 GAACTGTTGTAGTTTGTTGTCA
18033329 AA
1 AA
18033331 CTCAAGTGTG
Statistics
Matches: 396, Mismatches: 48, Indels: 10
0.87 0.11 0.02
Matches are distributed among these distances:
146 4 0.01
147 123 0.31
150 269 0.68
ACGTcount: A:0.38, C:0.13, G:0.26, T:0.23
Consensus pattern (150 bp):
AAGCCAAATGATATGGTTTATGTACAGCCTGGAAAGAAACCACCTAAGTTAGTTTATAAACGGCG
GAAAAAGCACAGTGAATCCCAGGAAAAGTCTGGTGCTGAAATAGGAATGAAGGAGAAAGAAGAGA
ACTGTTGTAGTTTGTTGTCA
Found at i:18033269 original size:297 final size:298
Alignment explanation
Indices: 18032732--18033326 Score: 885
Period size: 297 Copynumber: 2.0 Consensus size: 298
18032722 CTGTAGAAAT
** * *
18032732 AAGCCAAATGATATGGCTTATGTACAGCATGGGAAGAAACCACCTAAGTTAGTTTATAAACGGCG
1 AAGCCAAATGATATGGCTTACATACAGCATGGAAAGAAACCACCTAAGTTAATTTATAAACGGCG
* *
18032797 GAAAAAGCACAGTGAATCCCAGGAAAAGTCTGGTGCCGAAATAGGAATGAAGGAGAAAGAAGAAA
66 GAAAAAGCACAGCGAATCCCAGGAAAAGTCTGGTGCCGAAATAAGAAT--AGGAGAAAGAAGAAA
* *
18032862 ACTGTTGTAGTGTGTTGTCAAAGCCAAATGATATGGTTTATGTACAGCCTGGAAAGAAACCACCT
129 ACTGTTGTAGTGTGTTGTCAAAGCCAAATGATATGGTTTATGCACAGCCAGGAAAGAAACCACCT
* *
18032927 AAGTTAGTTTATAAACGGCGGAAAAATCTCAGTGAACCCCAGGAAAAGACT-GGTTTTGAAATAG
194 AAGTTAGTTTATAAACGGCGGAAAAAGCTCAGTGAACCCCAGGAAAA-ACTGGGTGTTGAAATAG
* *
18032991 GAATGAAGGAGAGAGAGGAGAACTGTTGTAGTTTGTTGTTA
258 GAATGAAGGAGAAAGAAGAGAACTGTTGTAGTTTGTTGTTA
*
18033032 AAGCCAAATGATAT-GCTTTACATACAGCGTGGAAAGAAACCACCTAAGTTAATTTATAAACGGC
1 AAGCCAAATGATATGGC-TTACATACAGCATGGAAAGAAACCACCTAAGTTAATTTATAAACGGC
* * * *
18033096 GGAAAAAGCACAGCGAATCCCAGGAAAAGTCTGGTGCTGAAATAAGAAT-GGAGAGAGTAGAGAA
65 GGAAAAAGCACAGCGAATCCCAGGAAAAGTCTGGTGCCGAAATAAGAATAGGAGAAAGAAGAAAA
*
18033160 CTGTTGTAGTTTGTTGTCAAAGCCAAATGATATGGTTTATGCACAG-CAGGTAAAGAAACCACCT
130 CTGTTGTAGTGTGTTGTCAAAGCCAAATGATATGGTTTATGCACAGCCAGG-AAAGAAACCACCT
* * * ** *
18033224 AAGTTAGTTTATAAACGGCTGAAAAAGCAT-GGTGAATCCCAGGAAAATTTGGGTGTTGGAATAG
194 AAGTTAGTTTATAAACGGCGGAAAAAGC-TCAGTGAACCCCAGGAAAAACTGGGTGTTGAAATAG
18033288 GAATGAAGGAGAAAGAAGAGAACTGTTGTAGTTTGTTGT
258 GAATGAAGGAGAAAGAAGAGAACTGTTGTAGTTTGTTGT
18033327 CAAACTCAAG
Statistics
Matches: 267, Mismatches: 24, Indels: 11
0.88 0.08 0.04
Matches are distributed among these distances:
296 4 0.01
297 158 0.59
298 1 0.00
299 2 0.01
300 102 0.38
ACGTcount: A:0.38, C:0.13, G:0.26, T:0.23
Consensus pattern (298 bp):
AAGCCAAATGATATGGCTTACATACAGCATGGAAAGAAACCACCTAAGTTAATTTATAAACGGCG
GAAAAAGCACAGCGAATCCCAGGAAAAGTCTGGTGCCGAAATAAGAATAGGAGAAAGAAGAAAAC
TGTTGTAGTGTGTTGTCAAAGCCAAATGATATGGTTTATGCACAGCCAGGAAAGAAACCACCTAA
GTTAGTTTATAAACGGCGGAAAAAGCTCAGTGAACCCCAGGAAAAACTGGGTGTTGAAATAGGAA
TGAAGGAGAAAGAAGAGAACTGTTGTAGTTTGTTGTTA
Found at i:18037560 original size:28 final size:29
Alignment explanation
Indices: 18037511--18037580 Score: 74
Period size: 28 Copynumber: 2.5 Consensus size: 29
18037501 ATCTTAAATT
* * *
18037511 AAAATAT-TAAATA-ATAATTTAATTAAT
1 AAAATATATAAATATATAAATTAAATAAA
*
18037538 ATAATATATAAATATA-AAATTAAATAAA
1 AAAATATATAAATATATAAATTAAATAAA
*
18037566 AAAATATATATATAT
1 AAAATATATAAATAT
18037581 TATATATCAT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
27 6 0.17
28 28 0.80
29 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (29 bp):
AAAATATATAAATATATAAATTAAATAAA
Found at i:18038910 original size:3 final size:3
Alignment explanation
Indices: 18038902--18038933 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
18038892 ACAATATTAC
18038902 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
18038934 TTTTATTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:18044400 original size:10 final size:10
Alignment explanation
Indices: 18044385--18044413 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
18044375 GTATGAAATG
18044385 AATATTCATA
1 AATATTCATA
18044395 AATATTCATA
1 AATATTCATA
18044405 AATATTCAT
1 AATATTCAT
18044414 TAATGAGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.41
Consensus pattern (10 bp):
AATATTCATA
Found at i:18045838 original size:9 final size:9
Alignment explanation
Indices: 18045824--18045849 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
18045814 ATGTTTAAGG
18045824 GTTTGGTTT
1 GTTTGGTTT
18045833 GTTTGGTTT
1 GTTTGGTTT
18045842 GTTTGGTT
1 GTTTGGTT
18045850 GAATAACATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.35, T:0.65
Consensus pattern (9 bp):
GTTTGGTTT
Found at i:18046905 original size:357 final size:353
Alignment explanation
Indices: 18046229--18047421 Score: 1491
Period size: 357 Copynumber: 3.3 Consensus size: 353
18046219 TTTTTTTTTT
* * *
18046229 AAATCATTGAAGGCATTGTTATCTGCAATCATCTTCAGTAATTATATACAAACTATGATAAAAAT
1 AAATTATTGAAGGCATTGTTATCTGCAAT-ACCTTCAGTAATTATATACAAACTATGATAAGAAT
* * * * *
18046294 TATTAAAGGCATTTTTCTTGGATATACGCCTTTAATAATAGTGTTAGAATTTGTGTGACGGTCTA
65 TATTAAAGGCATCTTTCTTGGATATACGCCTTCAATAACAGTGTTAAAATTTGTGTGACGGTATA
* * *
18046359 TAGAAGGTATTTTACAGTAGAAGATACCTTTAATAATTCTCAAAATATTTAGT-AAGAAAATTTT
130 TAGAAGGTATTTTATAGTAGAAGATGCCTTTAATAATTCT-AAAATTTTTAGTGAA-AAAATTTT
* *
18046423 GAAGGCATCTGTTATTAACAAACGCCTTCAGTAATGGATTACTAAGTTTAAAGGTATATT-AAAG
193 GAAGGCATCTATTATTAACAAACGCTTTCAGTAATGGATTACTAAGTTTAAAGGTATATTGAAA-
* ** * *
18046487 GTGCC-TTTTCTAATAAACACCTTCCATTACCATCGTGGTATATTAAAGGCCTGTCATAATAAAA
257 --GCCTTTTTTTAATAAATGCCTTCCATTACCATCGTGGTATATTGAAGGCGTGTCATAATAAAA
*
18046551 GACGCCTTTAATAATCTGAGAAAAGTTTTTTAGAA
320 GACGCCTTTAATAATCTGAGAAAAATTTTTT-GAA
* * * *
18046586 AAATTATTGAAGGCATTGTTATCTGCAACTACCTTTAGTAATTGTCTACAAACTGTGATAAGAAT
1 AAATTATTGAAGGCATTGTTATCTGCAA-TACCTTCAGTAATTATATACAAACTATGATAAGAAT
* * ** * * *
18046651 GATTAAATGTGTCTTTCTTGGATATACACTTTCAATAATAGTGTTAAAATTTGTGTGACGGTATA
65 TATTAAAGGCATCTTTCTTGGATATACGCCTTCAATAACAGTGTTAAAATTTGTGTGACGGTATA
**
18046716 TAGAATATATTTTATAGTAGAAGATGCCTTTAATAATTTCTAAAATTTTTAGTGAAAAAATTTTG
130 TAGAAGGTATTTTATAGTAGAAGATGCCTTTAATAA-TTCTAAAATTTTTAGTGAAAAAATTTTG
* *
18046781 AAGGCTTTTATTATTAACAAACGCTTTCAGTAATGGATTACTAAGTTTAAAGGTATATTGAAAGC
194 AAGGCATCTATTATTAACAAACGCTTTCAGTAATGGATTACTAAGTTTAAAGGTATATTGAAAGC
* * * * *
18046846 CTTTTTTTTAATAAATGTCATCCATTACCATCGTGGTATATTGAAGGCGTGTTATAATAAAATAT
259 C-TTTTTTTAATAAATGCCTTCCATTACCATCGTGGTATATTGAAGGCGTGTCATAATAAAAGAC
* *
18046911 GCCTTTAATAATCTGAAAAAAAAAATTTTT-AA
323 GCCTTTAATAATCTG--AGAAAAATTTTTTGAA
* * *
18046943 AAATTATTGAAGGCGTTGTTATCTGTAAT-CGCATTCAGTAATTATATACAAACTATGATATGAA
1 AAATTATTGAAGGCATTGTTATCTGCAATAC-C-TTCAGTAATTATATACAAACTATGATAAGAA
* * * * *
18047007 TTATTAAAAGCGTCTTTCTTGGATATATGCCTTCAATAACAGTGTTAGAATTTGTGTGACAGTAT
64 TTATTAAAGGCATCTTTCTTGGATATACGCCTTCAATAACAGTGTTAAAATTTGTGTGACGGTAT
* * * * *
18047072 ATAAAAGGTATTTTGTAGTAGAAGACGCTTTTAATAATTCTTAAAATTTTTAGTGAGAAAATTTT
129 ATAGAAGGTATTTTATAGTAGAAGATGCCTTTAATAATTC-TAAAATTTTTAGTGAAAAAATTTT
* * *
18047137 GAAGGCGTCTATTATTAACAAATGCTTTCAGTAATGGATTACTAAGTTTAAAGGTATATTGAAGG
193 GAAGGCATCTATTATTAACAAACGCTTTCAGTAATGGATTACTAAGTTTAAAGGTATATTGAAAG
* * ***
18047202 TGCTTTTTTTAATAAATGCCTTCTATTACCATTAAGGTATATTGAAGGCGTGTCATAATAAAAGA
258 -CCTTTTTTTAATAAATGCCTTCCATTACCATCGTGGTATATTGAAGGCGTGTCATAATAAAAGA
* * *
18047267 CGTCTTTAATAATCCGAGAAAATTTTTTTTGAA
322 CGCCTTTAATAATCTGAGAAAA-ATTTTTTGAA
* * ** * * *
18047300 AAATTATTGAAGCCGTTGTTATCTGCAACCGCCTTTACTAATTATATACAAACAATGAT-AGAAA
1 AAATTATTGAAGGCATTGTTATCTGCAA-TACCTTCAGTAATTATATACAAACTATGATAAG-AA
* *
18047364 TTATTAAAGGCATTTTTCTTGGATATACGCCTTCAATAACCA-TGTTAAAATTTATGTG
64 TTATTAAAGGCATCTTTCTTGGATATACGCCTTCAATAA-CAGTGTTAAAATTTGTGTG
18047422 GCGATATGTT
Statistics
Matches: 724, Mismatches: 94, Indels: 36
0.85 0.11 0.04
Matches are distributed among these distances:
355 9 0.01
356 11 0.02
357 679 0.94
358 14 0.02
359 11 0.02
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (353 bp):
AAATTATTGAAGGCATTGTTATCTGCAATACCTTCAGTAATTATATACAAACTATGATAAGAATT
ATTAAAGGCATCTTTCTTGGATATACGCCTTCAATAACAGTGTTAAAATTTGTGTGACGGTATAT
AGAAGGTATTTTATAGTAGAAGATGCCTTTAATAATTCTAAAATTTTTAGTGAAAAAATTTTGAA
GGCATCTATTATTAACAAACGCTTTCAGTAATGGATTACTAAGTTTAAAGGTATATTGAAAGCCT
TTTTTTAATAAATGCCTTCCATTACCATCGTGGTATATTGAAGGCGTGTCATAATAAAAGACGCC
TTTAATAATCTGAGAAAAATTTTTTGAA
Found at i:18057066 original size:21 final size:22
Alignment explanation
Indices: 18057042--18057096 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
18057032 CTTATGATAT
18057042 AATTTTGATAATCT-TTAATAA
1 AATTTTGATAATCTCTTAATAA
* **
18057063 AATTTTGATAAACTCTTAATGC
1 AATTTTGATAATCTCTTAATAA
18057085 AATTTTGATAAT
1 AATTTTGATAAT
18057097 TTATAACATA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 13 0.45
22 16 0.55
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.45
Consensus pattern (22 bp):
AATTTTGATAATCTCTTAATAA
Found at i:18057536 original size:22 final size:22
Alignment explanation
Indices: 18057418--18057561 Score: 67
Period size: 22 Copynumber: 6.6 Consensus size: 22
18057408 ATATTGTCAA
* * * *
18057418 TCATTTACAACTATATTGTAAT
1 TCATTTACTACTAAATTATTAT
* *
18057440 TTATTTATTACTAAATTATTAT
1 TCATTTACTACTAAATTATTAT
* * **
18057462 GCATTTACTATTATGTTA-TAT
1 TCATTTACTACTAAATTATTAT
* ** * * *
18057483 TAATTTGTTATTAAGTTATCAAT
1 TCATTTACTACTAAATTAT-TAT
*
18057506 T-ATTGACTACTAAATTATTAT
1 TCATTTACTACTAAATTATTAT
* * *
18057527 TCATTTACTATTAAGTTATTAC
1 TCATTTACTACTAAATTATTAT
* *
18057549 TAATTTATTACTA
1 TCATTTACTACTA
18057562 CGTTAACCAT
Statistics
Matches: 88, Mismatches: 31, Indels: 6
0.70 0.25 0.05
Matches are distributed among these distances:
21 19 0.22
22 66 0.75
23 3 0.03
ACGTcount: A:0.35, C:0.09, G:0.05, T:0.51
Consensus pattern (22 bp):
TCATTTACTACTAAATTATTAT
Found at i:18060483 original size:15 final size:14
Alignment explanation
Indices: 18060455--18060496 Score: 52
Period size: 15 Copynumber: 3.1 Consensus size: 14
18060445 TTTGTAAATT
18060455 AATT-AAAACAAAA
1 AATTGAAAACAAAA
18060468 AATTGAAAAGCAAAA
1 AATTGAAAA-CAAAA
*
18060483 AATAGAAAA-AAAA
1 AATTGAAAACAAAA
18060496 A
1 A
18060497 CAAATTTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
13 9 0.35
14 4 0.15
15 13 0.50
ACGTcount: A:0.76, C:0.05, G:0.07, T:0.12
Consensus pattern (14 bp):
AATTGAAAACAAAA
Found at i:18072150 original size:18 final size:18
Alignment explanation
Indices: 18072124--18072248 Score: 105
Period size: 18 Copynumber: 6.9 Consensus size: 18
18072114 CTTTGTTCTT
18072124 GATACATTTGAGGTGGAG
1 GATACATTTGAGGTGGAG
* *
18072142 GATATATTTGA---GGAT
1 GATACATTTGAGGTGGAG
*
18072157 GATACATTTGTGGTGGAG
1 GATACATTTGAGGTGGAG
* * * *
18072175 GGTACATTTGTGGT-AACT
1 GATACATTTGAGGTGGA-G
18072193 GATACATTTGAGGTGGAG
1 GATACATTTGAGGTGGAG
* *
18072211 GATATATTTGAAGAGGTTGAG
1 GATACATTT---GAGGTGGAG
18072232 GATACATTTGAGGTGGA
1 GATACATTTGAGGTGGA
18072249 TAATAACCAT
Statistics
Matches: 83, Mismatches: 16, Indels: 16
0.72 0.14 0.14
Matches are distributed among these distances:
15 12 0.14
17 1 0.01
18 53 0.64
19 1 0.01
21 16 0.19
ACGTcount: A:0.28, C:0.05, G:0.34, T:0.33
Consensus pattern (18 bp):
GATACATTTGAGGTGGAG
Found at i:18072165 original size:33 final size:35
Alignment explanation
Indices: 18072123--18072221 Score: 139
Period size: 33 Copynumber: 2.9 Consensus size: 35
18072113 CCTTTGTTCT
18072123 TGATACATTTGAGGTGGAGGATATATTTGAGG-A-
1 TGATACATTTGAGGTGGAGGATATATTTGAGGAAC
* * * *
18072156 TGATACATTTGTGGTGGAGGGTACATTTGTGGTAAC
1 TGATACATTTGAGGTGGAGGATATATTTGAGG-AAC
18072192 TGATACATTTGAGGTGGAGGATATATTTGA
1 TGATACATTTGAGGTGGAGGATATATTTGA
18072222 AGAGGTTGAG
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
33 28 0.51
35 1 0.02
36 26 0.47
ACGTcount: A:0.27, C:0.05, G:0.32, T:0.35
Consensus pattern (35 bp):
TGATACATTTGAGGTGGAGGATATATTTGAGGAAC
Found at i:18072226 original size:21 final size:21
Alignment explanation
Indices: 18072202--18072242 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
18072192 TGATACATTT
*
18072202 GAGGTGGAGGATATATTTGAA
1 GAGGTGGAGGATACATTTGAA
*
18072223 GAGGTTGAGGATACATTTGA
1 GAGGTGGAGGATACATTTGA
18072243 GGTGGATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.02, G:0.37, T:0.29
Consensus pattern (21 bp):
GAGGTGGAGGATACATTTGAA
Found at i:18076032 original size:26 final size:26
Alignment explanation
Indices: 18075983--18076031 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
18075973 TTTCAAAAAT
*
18075983 TAAAAGTTTTCAAACTTATATTTTAA
1 TAAAAGTTTTCAAACCTATATTTTAA
18076009 TAAAA-TTTTCAAACCTATATTTT
1 TAAAAGTTTTCAAACCTATATTTT
18076032 TTATTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.41, C:0.10, G:0.02, T:0.47
Consensus pattern (26 bp):
TAAAAGTTTTCAAACCTATATTTTAA
Found at i:18076279 original size:19 final size:20
Alignment explanation
Indices: 18076257--18076294 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
18076247 AAACAACAAA
*
18076257 AAAATTA-AAATTCATATAC
1 AAAATTATAAATTAATATAC
18076276 AAAATTATAAATTAATATA
1 AAAATTATAAATTAATATA
18076295 TAACACAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (20 bp):
AAAATTATAAATTAATATAC
Found at i:18076544 original size:39 final size:38
Alignment explanation
Indices: 18076500--18076595 Score: 147
Period size: 39 Copynumber: 2.5 Consensus size: 38
18076490 CATACACTCT
18076500 ACCACACCCAATCCCTCCCCACCTTCCCCCCAACGCCCC
1 ACCACACCCAAT-CCTCCCCACCTTCCCCCCAACGCCCC
* * *
18076539 ACCACACCCAATCTTCCCCCACTTTCCCCCCAATGCCCC
1 ACCACACCCAATCCT-CCCCACCTTCCCCCCAACGCCCC
18076578 ACCACACCCAATCCTCCC
1 ACCACACCCAATCCTCCC
18076596 TACCCCATCC
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
38 5 0.10
39 47 0.90
ACGTcount: A:0.22, C:0.62, G:0.02, T:0.14
Consensus pattern (38 bp):
ACCACACCCAATCCTCCCCACCTTCCCCCCAACGCCCC
Found at i:18078987 original size:22 final size:21
Alignment explanation
Indices: 18078943--18078987 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
18078933 ATTTATCTTA
**
18078943 TTATTTTTTTATTTCTAGGAT
1 TTATTTTTTTATTTCTAAAAT
18078964 TTATTTTTGTTATTTCTAAAAT
1 TTATTTTT-TTATTTCTAAAAT
18078986 TT
1 TT
18078988 TCTAATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.22, C:0.04, G:0.07, T:0.67
Consensus pattern (21 bp):
TTATTTTTTTATTTCTAAAAT
Found at i:18080128 original size:160 final size:159
Alignment explanation
Indices: 18079850--18080142 Score: 381
Period size: 160 Copynumber: 1.8 Consensus size: 159
18079840 CAGTATAAAC
*
18079850 TTATATGTTTTAATTTTTCTTATCTATACTGACAGTTAATACCTGCCAGTATAAACTTGTAATTC
1 TTATATGTTTTAATTTTTCTTACCTATACTGACAGTTAATACCTGCCAGTATAAACTTGTAATTC
* ** * * * * *
18079915 TTTTTACCTATATTGATGCTTAAAGCCCGTCAGTATAGATTTGTATGTTTTAATTTTCTCACTTA
66 TTTTTACCAATACCGACGCTT-AAGCCCATCAGTATAGACTTATATGTTTTAATTTTCTCACCTA
18079980 TATTGATTGCTAGCGCCCGTTAGTACAGAT
130 TATTGATTGCTAGCGCCCGTTAGTACAGAT
** * ** * *
18080010 TTATATGTTTTAATTTTTCTTACCTATACTGATGGTTAATACTTGTTAGTATAGACTTGTAATTT
1 TTATATGTTTTAATTTTTCTTACCTATACTGACAGTTAATACCTGCCAGTATAAACTTGTAATTC
* * *
18080075 TTTTTACCAATACCGACGCTT-AGCATCCATCGGTATAGACTTATATTTTTTAATTTTCTTACCT
66 TTTTTACCAATACCGACGCTTAAGC--CCATCAGTATAGACTTATATGTTTTAATTTTCTCACCT
18080139 ATAT
129 ATAT
18080143 CGACAATTAG
Statistics
Matches: 112, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
158 3 0.03
160 109 0.97
ACGTcount: A:0.26, C:0.16, G:0.12, T:0.46
Consensus pattern (159 bp):
TTATATGTTTTAATTTTTCTTACCTATACTGACAGTTAATACCTGCCAGTATAAACTTGTAATTC
TTTTTACCAATACCGACGCTTAAGCCCATCAGTATAGACTTATATGTTTTAATTTTCTCACCTAT
ATTGATTGCTAGCGCCCGTTAGTACAGAT
Found at i:18080167 original size:55 final size:55
Alignment explanation
Indices: 18080108--18080241 Score: 151
Period size: 55 Copynumber: 2.4 Consensus size: 55
18080098 CATCCATCGG
*
18080108 TATAGACTTATATTTTTTAATTTTCTTACCTATATCGACAATTAGAGACTGTCAA
1 TATAGACTTATATATTTTAATTTTCTTACCTATATCGACAATTAGAGACTGTCAA
* * * * * *** * *
18080163 TATAGAATTGTGTATTTTAATTTTCTTGCCTATATTGATGGTTAGAGATTGTTAA
1 TATAGACTTATATATTTTAATTTTCTTACCTATATCGACAATTAGAGACTGTCAA
* *
18080218 TGTAGACTTATATGTTTTAATTTT
1 TATAGACTTATATATTTTAATTTT
18080242 TTTATTATAT
Statistics
Matches: 63, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
55 63 1.00
ACGTcount: A:0.29, C:0.09, G:0.13, T:0.49
Consensus pattern (55 bp):
TATAGACTTATATATTTTAATTTTCTTACCTATATCGACAATTAGAGACTGTCAA
Found at i:18080379 original size:24 final size:24
Alignment explanation
Indices: 18080347--18080393 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
18080337 TTTTTTTAAA
* *
18080347 AATTATATTTTTAATTATTAATATT
1 AATTATATTTATAATCA-TAATATT
18080372 AATT-TATTTATAATCATAATAT
1 AATTATATTTATAATCATAATAT
18080394 GATATATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 6 0.30
24 10 0.50
25 4 0.20
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (24 bp):
AATTATATTTATAATCATAATATT
Found at i:18080560 original size:15 final size:15
Alignment explanation
Indices: 18080525--18080553 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
18080515 TACCAAGTCT
18080525 AATAAAACAAACATC
1 AATAAAACAAACATC
18080540 AATAAAACAAACAT
1 AATAAAACAAACAT
18080554 AGATAAAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.69, C:0.17, G:0.00, T:0.14
Consensus pattern (15 bp):
AATAAAACAAACATC
Found at i:18083034 original size:54 final size:58
Alignment explanation
Indices: 18082952--18083118 Score: 189
Period size: 60 Copynumber: 2.9 Consensus size: 58
18082942 ATCCTTTTTC
* ** *
18082952 AAAATTGATACTTTTAACTTTACCTTAAAGCA-TT-TGGA-AATTTTTA-TTTTAAGG
1 AAAATTGATACTTTCAACTTTTTCTTAAAACATTTCTGGATAATTTTTATTTTTAAGG
* *
18083006 AAAATTGATACTTTCAACTTTTTCTTAAAATATTTTTCTTGATAATTTTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTTCTTAAAACA--TTTCTGGATAATTTTTATTTTTAAGG
* * * * *
18083066 AAAATTGGTACTTTCAACTTTTTCTCAAAATATTTTTTGATAATTTTTATTTT
1 AAAATTGATACTTTCAACTTTTTCTTAAAACATTTCTGGATAATTTTTATTTT
18083119 AAAAATTTTA
Statistics
Matches: 98, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
54 27 0.28
57 2 0.02
58 23 0.23
59 8 0.08
60 38 0.39
ACGTcount: A:0.32, C:0.09, G:0.08, T:0.51
Consensus pattern (58 bp):
AAAATTGATACTTTCAACTTTTTCTTAAAACATTTCTGGATAATTTTTATTTTTAAGG
Found at i:18083069 original size:60 final size:58
Alignment explanation
Indices: 18082990--18083367 Score: 229
Period size: 58 Copynumber: 6.2 Consensus size: 58
18082980 AGCATTTGGA
*
18082990 AATTTTTA-TTTTAAGGAAAATTGATACTTTCAACTTTTTCTTAAAATATTTTTCTTGAT
1 AATTTTTATTTTTAAGGAAAATTGATACTTTCAACTTTTTCTCAAAATA-TTTT-TTGAT
*
18083049 AATTTTTATTTTTAAGGAAAATTGGTACTTTCAACTTTTTCTCAAAATATTTTTTGAT
1 AATTTTTATTTTTAAGGAAAATTGATACTTTCAACTTTTTCTCAAAATATTTTTTGAT
* * * *
18083107 AATTTTTA-TTTT-A--AAAATT-TTACTTTAAGGAAAATTGATACTTTCAACTTTTCCTCAAAG
1 AATTTTTATTTTTAAGGAAAATTGATACTTT-----CAACT--T--TTT---------CTCAAAA
*
18083167 CATTTTTTAGA-
48 TATTTTTT-GAT
** * *
18083178 AAAATTTATTTTTAAGGAAAATTGATACTTTCAACTTTTTCCTAAAAATATTTTTT-AA
1 AATTTTTATTTTTAAGGAAAATTGATACTTTCAACTTTTT-CTCAAAATATTTTTTGAT
* * * *
18083236 AAATTTTATTTTCAAGAAAAATTGATACTTTCAA-TTTTTCTCCAAAAATATATTTTTCA-
1 AATTTTTATTTTTAAGGAAAATTGATACTTTCAACTTTTTCT-C-AAAATAT-TTTTTGAT
* * * * * *
18083295 AATCTTTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCTTTAAAAATA-CTTTTGAAA
1 AA--TTTTTATTTTTAAGGAAAATTGATACTTTCAACTTTT-TCTCAAAATATTTTTTG-AT
18083356 AATTTTTATTTT
1 AATTTTTATTTT
18083368 AGAAATTTTA
Statistics
Matches: 259, Mismatches: 24, Indels: 72
0.73 0.07 0.20
Matches are distributed among these distances:
53 6 0.02
54 6 0.02
56 3 0.01
57 10 0.04
58 54 0.21
59 46 0.18
60 41 0.16
61 39 0.15
62 7 0.03
63 2 0.01
67 3 0.01
69 1 0.00
71 22 0.08
72 6 0.02
73 1 0.00
75 6 0.02
76 6 0.02
ACGTcount: A:0.35, C:0.10, G:0.06, T:0.49
Consensus pattern (58 bp):
AATTTTTATTTTTAAGGAAAATTGATACTTTCAACTTTTTCTCAAAATATTTTTTGAT
Found at i:18083324 original size:61 final size:58
Alignment explanation
Indices: 18083115--18083367 Score: 287
Period size: 58 Copynumber: 4.3 Consensus size: 58
18083105 ATAATTTTTA
* * * * **
18083115 TTTTAAAAATTTTACTTT-AAGGAAAATTGATACTTTCAACTTTTC-CTCAAAGCATT
1 TTTTAAAAATTTTATTTTCAAGAAAAATTGATACTTTCAATTTTTCTCTAAAAATATT
* * *
18083171 TTTTAGAAAAATTTATTTTTAAGGAAAATTGATACTTTCAACTTTTTC-CTAAAAATATT
1 TTTTA-AAAATTTTATTTTCAAGAAAAATTGATACTTTCAA-TTTTTCTCTAAAAATATT
*
18083230 TTTTAAAAATTTTATTTTCAAGAAAAATTGATACTTTCAATTTTTCTCCAAAAATATAT
1 TTTTAAAAATTTTATTTTCAAGAAAAATTGATACTTTCAATTTTTCTCTAAAAATAT-T
** * * *
18083289 TTTTCAAATCTTTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCTTTAAAAATACT
1 TTTT-AAA-AATTTTATTTTCAAGAAAAATTGATACTTTCAATTTTTCTCTAAAAATATT
*
18083349 TTTGAAAAATTTTTATTTT
1 TTTTAAAAA-TTTTATTTT
18083368 AGAAATTTTA
Statistics
Matches: 170, Mismatches: 19, Indels: 13
0.84 0.09 0.06
Matches are distributed among these distances:
56 5 0.03
57 17 0.10
58 62 0.36
59 35 0.21
60 7 0.04
61 44 0.26
ACGTcount: A:0.37, C:0.11, G:0.05, T:0.47
Consensus pattern (58 bp):
TTTTAAAAATTTTATTTTCAAGAAAAATTGATACTTTCAATTTTTCTCTAAAAATATT
Found at i:18083532 original size:3 final size:3
Alignment explanation
Indices: 18083524--18083561 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
18083514 CTAATCAATA
18083524 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
18083562 ATATATATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:18084265 original size:19 final size:19
Alignment explanation
Indices: 18084241--18084339 Score: 75
Period size: 19 Copynumber: 5.3 Consensus size: 19
18084231 TTGATCAAGA
18084241 AAAATAATAAAATAAA-AAT
1 AAAATAAT-AAATAAATAAT
*
18084260 AAAATAATAGATAAATAAT
1 AAAATAATAAATAAATAAT
18084279 AAAATATATTAAA-AAAT-AT
1 AAAATA-A-TAAATAAATAAT
*
18084298 -TAATAGATAAAT-AATAAT
1 AAAATA-ATAAATAAATAAT
*
18084316 AATAATAATGAA-AAATAAT
1 AA-AATAATAAATAAATAAT
*
18084335 TAAAT
1 AAAAT
18084340 TAAAAAAATG
Statistics
Matches: 65, Mismatches: 7, Indels: 17
0.73 0.08 0.19
Matches are distributed among these distances:
17 7 0.11
18 16 0.25
19 30 0.46
20 9 0.14
21 3 0.05
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (19 bp):
AAAATAATAAATAAATAAT
Found at i:18084268 original size:3 final size:3
Alignment explanation
Indices: 18084243--18084334 Score: 61
Period size: 3 Copynumber: 31.0 Consensus size: 3
18084233 GATCAAGAAA
*
18084243 AAT AAT AA- AAT AAA AAT AA- AAT AAT AGAT AAAT AAT AA- AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT -AAT AAT AAT AAT AAT
* * *
18084286 ATT AA- AA- AAT ATT AAT AGAT AAAT AAT AAT AAT AAT AAT GAAA AAT
1 AAT AAT AAT AAT AAT AAT A-AT -AAT AAT AAT AAT AAT AAT -AAT AAT
18084332 AAT
1 AAT
18084335 TAAATTAAAA
Statistics
Matches: 71, Mismatches: 8, Indels: 20
0.72 0.08 0.20
Matches are distributed among these distances:
2 12 0.17
3 47 0.66
4 10 0.14
5 2 0.03
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:18084278 original size:30 final size:30
Alignment explanation
Indices: 18084242--18084334 Score: 98
Period size: 34 Copynumber: 2.9 Consensus size: 30
18084232 TGATCAAGAA
18084242 AAATAATAAAATAAAAATAAAATAATAGAT
1 AAATAATAAAATAAAAATAAAATAATAGAT
18084272 AAATAATAAAATATATTAAA-AAATATTAATAGAT
1 AAATAATAAAATA-A--AAATAAA-A-TAATAGAT
*
18084306 AAATAATAATAATAATAATGAAAAATAAT
1 AAATAATAA-AATAAAAAT--AAAATAAT
18084335 TAAATTAAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 15
0.77 0.01 0.22
Matches are distributed among these distances:
30 13 0.25
31 1 0.02
32 5 0.09
33 8 0.15
34 19 0.36
35 7 0.13
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (30 bp):
AAATAATAAAATAAAAATAAAATAATAGAT
Found at i:18084307 original size:34 final size:33
Alignment explanation
Indices: 18084242--18084323 Score: 102
Period size: 34 Copynumber: 2.5 Consensus size: 33
18084232 TGATCAAGAA
18084242 AAATAATAAAATA-A-AAATAAA-A-TAATAGAT
1 AAATAATAAAATATATAAA-AAATATTAATAGAT
18084272 AAATAATAAAATATATTAAAAAATATTAATAGAT
1 AAATAATAAAATATA-TAAAAAATATTAATAGAT
18084306 AAATAATAATAATA-ATAA
1 AAATAATAA-AATATATAA
18084324 TGAAAAATAA
Statistics
Matches: 46, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
30 13 0.28
31 1 0.02
32 3 0.07
33 7 0.15
34 18 0.39
35 4 0.09
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (33 bp):
AAATAATAAAATATATAAAAAATATTAATAGAT
Found at i:18084339 original size:30 final size:29
Alignment explanation
Indices: 18084239--18084339 Score: 93
Period size: 30 Copynumber: 3.5 Consensus size: 29
18084229 AATTGATCAA
*
18084239 GAAAAATAATAAAATAAAAATAAAATAAT
1 GAAAAATAATAAAATAATAATAAAATAAT
* *
18084268 AGATAAATAATAAAAT-ATATTAAAA-AAT
1 -GAAAAATAATAAAATAATAATAAAATAAT
**
18084296 -ATTAATAGAT-AAATAATAATAATAATAAT
1 GAAAAATA-ATAAAATAATAATAA-AATAAT
*
18084325 GAAAAATAATTAAAT
1 GAAAAATAATAAAAT
18084340 TAAAAAAATG
Statistics
Matches: 58, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
26 10 0.17
27 8 0.14
28 5 0.09
29 12 0.21
30 23 0.40
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (29 bp):
GAAAAATAATAAAATAATAATAAAATAAT
Found at i:18084716 original size:41 final size:43
Alignment explanation
Indices: 18084656--18084807 Score: 175
Period size: 45 Copynumber: 3.5 Consensus size: 43
18084646 GCTTAACAAT
*
18084656 TTTTGAAGAAATAAA-TGCTCATCTAAATAGAGGC-TCCATGAC
1 TTTTGAA-AAATAAATTGCTCATCTAAATAGAGGCAACCATGAC
*
18084698 -TTTGAAAAATAAATTGCTCCTCTAAATAGAGGCAACCATGAC
1 TTTTGAAAAATAAATTGCTCATCTAAATAGAGGCAACCATGAC
* ** * * *
18084740 TTTTGAAAAAAATAAATTGCTTATCTAAGCAAAGGCAACCACGGC
1 TTTTG--AAAAATAAATTGCTCATCTAAATAGAGGCAACCATGAC
18084785 TTTTAGAAAAATAAATTGCTCAT
1 TTTT-GAAAAATAAATTGCTCAT
18084808 TTAAGCAGCC
Statistics
Matches: 94, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
40 7 0.07
41 24 0.26
42 7 0.07
43 4 0.04
44 16 0.17
45 35 0.37
46 1 0.01
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.28
Consensus pattern (43 bp):
TTTTGAAAAATAAATTGCTCATCTAAATAGAGGCAACCATGAC
Found at i:18084759 original size:45 final size:45
Alignment explanation
Indices: 18084656--18084891 Score: 171
Period size: 45 Copynumber: 5.2 Consensus size: 45
18084646 GCTTAACAAT
* *
18084656 TTTTG-AAGAAATAAA-TGCTCATCTAAATAGAGGC-TCCATGAC
1 TTTTGAAAAAAATAAATTGCTCATCTAAATAGAGGCAACCATGAC
*
18084698 -TTTG--AAAAATAAATTGCTCCTCTAAATAGAGGCAACCATGAC
1 TTTTGAAAAAAATAAATTGCTCATCTAAATAGAGGCAACCATGAC
* ** * * *
18084740 TTTTGAAAAAAATAAATTGCTTATCTAAGCAAAGGCAACCACGGC
1 TTTTGAAAAAAATAAATTGCTCATCTAAATAGAGGCAACCATGAC
* * *
18084785 TTTT-AGAAAAATAAATTGCTCATTTAAGCAGCCTAAGCAGAGGCAACCACGAC
1 TTTTGAAAAAAATAAATTGCTCATCTAA--A---T----AGAGGCAACCATGAC
* * * * * *
18084838 TTTTGGAAAAAATAAACTGTTCTTCTAAACAAAGGCAACCATGAC
1 TTTTGAAAAAAATAAATTGCTCATCTAAATAGAGGCAACCATGAC
18084883 TTTTTGAAA
1 -TTTTGAAA
18084892 GTAAATTACT
Statistics
Matches: 151, Mismatches: 27, Indels: 28
0.73 0.13 0.14
Matches are distributed among these distances:
40 8 0.05
41 22 0.15
42 7 0.05
43 4 0.03
44 20 0.13
45 48 0.32
46 7 0.05
52 1 0.01
53 17 0.11
54 17 0.11
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.27
Consensus pattern (45 bp):
TTTTGAAAAAAATAAATTGCTCATCTAAATAGAGGCAACCATGAC
Found at i:18096575 original size:59 final size:59
Alignment explanation
Indices: 18096515--18096625 Score: 145
Period size: 59 Copynumber: 1.9 Consensus size: 59
18096505 TTTTAGAAAT
* *
18096515 TTTA-CTTTAAAAAAAATTGATACTTTCAAC-TTTTCCTCAAAAGCATTTTTTACAAAAA
1 TTTATCTTTAAAAAAAATTAATACTTTCAACTTTTTCCT-AAAAACATTTTTTACAAAAA
* ** *
18096573 TTTATTTTTAAGGAAAATTAATACTTTCAACTTTTTCCTAAAAATATTTTTTA
1 TTTATCTTTAAAAAAAATTAATACTTTCAACTTTTTCCTAAAAACATTTTTTA
18096626 GAAATTTAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
58 4 0.09
59 34 0.76
60 7 0.16
ACGTcount: A:0.39, C:0.13, G:0.04, T:0.45
Consensus pattern (59 bp):
TTTATCTTTAAAAAAAATTAATACTTTCAACTTTTTCCTAAAAACATTTTTTACAAAAA
Found at i:18096598 original size:130 final size:132
Alignment explanation
Indices: 18096392--18096632 Score: 337
Period size: 131 Copynumber: 1.8 Consensus size: 132
18096382 GCTTGTGTAC
* * * * ** **
18096392 AAAAAAAATTGATATTTTTAACTTTTCCTTAAAATATTTTTCTTGATAATTTTTATTTTTAAGAA
1 AAAAAAAATTGATACTTTCAACTTTTCCTCAAAACATTTTTCTACATAAAATTTATTTTTAAGAA
* *
18096457 AAATTAGTACTTTCAACTTTTT-CTCAAAATATTTTTT-GATAATTTTTATTTTAGAAATTTTAC
66 AAATTAATACTTTCAACTTTTTCCTAAAAATATTTTTTAGA-AATTTTTATTTTAGAAATTTTAC
18096520 TTT
130 TTT
*
18096523 AAAAAAAATTGATACTTTCAACTTTTCCTCAAAAGCATTTTT-TACA-AAAATTTATTTTTAAGG
1 AAAAAAAATTGATACTTTCAACTTTTCCTCAAAA-CATTTTTCTACATAAAATTTATTTTTAAGA
18096586 AAAATTAATACTTTCAACTTTTTCCTAAAAATATTTTTTAGAAATTT
65 AAAATTAATACTTTCAACTTTTTCCTAAAAATATTTTTTAGAAATTT
18096633 AATTTTCAAG
Statistics
Matches: 96, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
130 36 0.38
131 52 0.54
132 8 0.08
ACGTcount: A:0.38, C:0.10, G:0.05, T:0.48
Consensus pattern (132 bp):
AAAAAAAATTGATACTTTCAACTTTTCCTCAAAACATTTTTCTACATAAAATTTATTTTTAAGAA
AAATTAATACTTTCAACTTTTTCCTAAAAATATTTTTTAGAAATTTTTATTTTAGAAATTTTACT
TT
Found at i:18096770 original size:15 final size:15
Alignment explanation
Indices: 18096737--18096769 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
18096727 CTAAAAATAC
18096737 TTTTAAAAATTTTTA
1 TTTTAAAAATTTTTA
*
18096752 TTTTAGAAA-TTTTA
1 TTTTAAAAATTTTTA
18096766 TTTT
1 TTTT
18096770 TCAAGAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (15 bp):
TTTTAAAAATTTTTA
Found at i:18096866 original size:73 final size:74
Alignment explanation
Indices: 18096678--18096892 Score: 296
Period size: 73 Copynumber: 2.9 Consensus size: 74
18096668 TGAAAATATT
* * ** *
18096678 TTTTA-AAATTTTTTTATTTCCAATGGAAATTGATACTTTCAACTTTCCCCTAAAAATAC--TTT
1 TTTTAGAAATTTTATT-TTT-CAA-GAAAATTGATACTTTCAACTTTTTCTTAAAAATACTTTTT
*
18096740 TAAAAATTTTTA
63 TTAAAATTTTTA
18096752 TTTTAGAAATTTTATTTTTCAAGAAAATTGATACTTTCAACTTTTTCTTAAAAATACTTTTTTTA
1 TTTTAGAAATTTTATTTTTCAAGAAAATTGATACTTTCAACTTTTTCTTAAAAATACTTTTTTTA
18096817 AAA-TTTTA
66 AAATTTTTA
*
18096825 TTTTAGAACTTTTA-TTTTCAAGAAAAATTGATACTTTCAACTTTTTCTTAAAAATACTTTTTTT
1 TTTTAGAAATTTTATTTTTCAAG-AAAATTGATACTTTCAACTTTTTCTTAAAAATACTTTTTTT
18096889 AAAA
65 AAAA
18096893 AAATATATAT
Statistics
Matches: 130, Mismatches: 7, Indels: 9
0.89 0.05 0.06
Matches are distributed among these distances:
72 39 0.30
73 66 0.51
74 16 0.12
75 9 0.07
ACGTcount: A:0.36, C:0.11, G:0.04, T:0.49
Consensus pattern (74 bp):
TTTTAGAAATTTTATTTTTCAAGAAAATTGATACTTTCAACTTTTTCTTAAAAATACTTTTTTTA
AAATTTTTA
Found at i:18096894 original size:16 final size:16
Alignment explanation
Indices: 18096864--18096893 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
18096854 GATACTTTCA
18096864 ACTTTTTCTTAAAAAT
1 ACTTTTTCTTAAAAAT
18096880 ACTTTTT-TTAAAAA
1 ACTTTTTCTTAAAAA
18096894 AATATATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (16 bp):
ACTTTTTCTTAAAAAT
Found at i:18096960 original size:11 final size:11
Alignment explanation
Indices: 18096938--18096966 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
18096928 GAAAAATTAT
18096938 TAAAAT-AAAA
1 TAAAATAAAAA
18096948 TAAAATAAAAA
1 TAAAATAAAAA
18096959 TAAAATAA
1 TAAAATAA
18096967 GGAATACCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.33
11 12 0.67
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (11 bp):
TAAAATAAAAA
Found at i:18097741 original size:4 final size:4
Alignment explanation
Indices: 18097724--18097797 Score: 62
Period size: 4 Copynumber: 18.5 Consensus size: 4
18097714 GATCAAGAAA
* * * *
18097724 AAAT AAAT ATAT AAAT -AA- AAAT AAAA ATAAT AGAT AAAT AAAA AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAAT
* *
18097771 ATAAT AAAA AAAT AAAT AGAT AAAT AA
1 A-AAT AAAT AAAT AAAT AAAT AAAT AA
18097798 CAATAATAAT
Statistics
Matches: 54, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
3 4 0.07
4 43 0.80
5 7 0.13
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:18097794 original size:33 final size:33
Alignment explanation
Indices: 18097736--18097822 Score: 115
Period size: 33 Copynumber: 2.7 Consensus size: 33
18097726 ATAAATATAT
*
18097736 AAATAAAAATAAAAAT-AATAGATAAATAAAAA
1 AAATAATAATAAAAATAAATAGATAAATAAAAA
*
18097768 AATATAATAA-AAAAATAAATAGATAAATAACAA
1 AA-ATAATAATAAAAATAAATAGATAAATAAAAA
* *
18097801 TAATAATAATAAAAGTAAATAG
1 AAATAATAATAAAAATAAATAG
18097823 TATATTTTGT
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
32 15 0.31
33 33 0.69
ACGTcount: A:0.72, C:0.01, G:0.05, T:0.22
Consensus pattern (33 bp):
AAATAATAATAAAAATAAATAGATAAATAAAAA
Found at i:18097795 original size:12 final size:11
Alignment explanation
Indices: 18097724--18097813 Score: 61
Period size: 12 Copynumber: 8.6 Consensus size: 11
18097714 GATCAAGAAA
18097724 AAATAAATATAT
1 AAATAAATA-AT
18097736 AAATAAA-AAT
1 AAATAAATAAT
18097746 -AA-AAATAAT
1 AAATAAATAAT
*
18097755 AGATAAATAA-
1 AAATAAATAAT
18097765 AAA-AATATAAT
1 AAATAA-ATAAT
*
18097776 AAAAAAATAAAT
1 AAATAAAT-AAT
*
18097788 AGATAAATAA-
1 AAATAAATAAT
*
18097798 CAAT-AATAAT
1 AAATAAATAAT
18097808 -AATAAA
1 AAATAAA
18097814 AGTAAATAGT
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
8 3 0.05
9 15 0.24
10 13 0.21
11 14 0.22
12 18 0.29
ACGTcount: A:0.73, C:0.01, G:0.02, T:0.23
Consensus pattern (11 bp):
AAATAAATAAT
Found at i:18098494 original size:23 final size:23
Alignment explanation
Indices: 18098468--18098512 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
18098458 TACATAGAAA
*
18098468 AATTACATGTAAAGAAA-GTAATG
1 AATTACAT-TAAAAAAATGTAATG
*
18098491 AATTTCATTAAAAAAATGTAAT
1 AATTACATTAAAAAAATGTAAT
18098513 TGTACAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.53, C:0.04, G:0.11, T:0.31
Consensus pattern (23 bp):
AATTACATTAAAAAAATGTAATG
Found at i:18099826 original size:16 final size:16
Alignment explanation
Indices: 18099805--18099860 Score: 69
Period size: 16 Copynumber: 3.4 Consensus size: 16
18099795 CATGTCCTTA
18099805 GGATTTTTAGGAGTTT
1 GGATTTTTAGGAGTTT
*
18099821 GGA-TTTTAGGGGATTTT
1 GGATTTTTA--GGAGTTT
*
18099838 GGATTTTTAGAAGTTT
1 GGATTTTTAGGAGTTT
18099854 GGATTTT
1 GGATTTT
18099861 AGAGGTTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
15 5 0.15
16 15 0.44
17 9 0.26
18 5 0.15
ACGTcount: A:0.20, C:0.00, G:0.30, T:0.50
Consensus pattern (16 bp):
GGATTTTTAGGAGTTT
Found at i:18099863 original size:15 final size:15
Alignment explanation
Indices: 18099809--18099868 Score: 57
Period size: 15 Copynumber: 3.8 Consensus size: 15
18099799 TCCTTAGGAT
*
18099809 TTTTAGGAGTTTGGA
1 TTTTAGAAGTTTGGA
* *
18099824 TTTTAGGGGATTTTGGA
1 TTTTA--GAAGTTTGGA
18099841 TTTTTAGAAGTTTGGA
1 -TTTTAGAAGTTTGGA
*
18099857 TTTTAGAGGTTT
1 TTTTAGAAGTTT
18099869 TAGAAACCTA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
15 16 0.42
16 8 0.21
17 9 0.24
18 5 0.13
ACGTcount: A:0.20, C:0.00, G:0.30, T:0.50
Consensus pattern (15 bp):
TTTTAGAAGTTTGGA
Found at i:18099894 original size:10 final size:10
Alignment explanation
Indices: 18099879--18099914 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
18099869 TAGAAACCTA
18099879 GGATTTTGGG
1 GGATTTTGGG
18099889 GGATTTT---
1 GGATTTTGGG
18099896 GGATTTTGGG
1 GGATTTTGGG
18099906 GGATTTTGG
1 GGATTTTGG
18099915 ATTTTTAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
7 7 0.30
10 16 0.70
ACGTcount: A:0.11, C:0.00, G:0.44, T:0.44
Consensus pattern (10 bp):
GGATTTTGGG
Found at i:18099949 original size:92 final size:92
Alignment explanation
Indices: 18099835--18100069 Score: 384
Period size: 92 Copynumber: 2.6 Consensus size: 92
18099825 TTTAGGGGAT
*
18099835 TTTGGATTTTTA-GA-AGTTTGGATTTTAGAGGTTTTAGAAACCTAGGATTTTGGGGGATTTTGG
1 TTTGGA-TTTTAGGAGATTTTGGATTTTAGAGGTTTTAGAAACCTAGGATTTTGGGGGATTTTGG
* * *
18099898 ATTTTGGGGGATTTTGGATTTTTAAGAG
65 ATCTTAGGAGATTTTGGATTTTTAAGAG
*
18099926 TTTGGATTTTAGGAGATTTTGGATTTTAGAGGTTTTAGAAACCTAGGATTTGGGGGGATTTTGGA
1 TTTGGATTTTAGGAGATTTTGGATTTTAGAGGTTTTAGAAACCTAGGATTTTGGGGGATTTTGGA
18099991 TCTTAGGAGATTTTGGATTTTTAAGAG
66 TCTTAGGAGATTTTGGATTTTTAAGAG
* *
18100018 TTTGGATTTTAGGAGATTTTGGATTTTAGGGGTTCTAGAAACCTAGGATTTT
1 TTTGGATTTTAGGAGATTTTGGATTTTAGAGGTTTTAGAAACCTAGGATTTT
18100070 AAGGTTTAGA
Statistics
Matches: 134, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
90 5 0.04
91 8 0.06
92 121 0.90
ACGTcount: A:0.23, C:0.03, G:0.30, T:0.44
Consensus pattern (92 bp):
TTTGGATTTTAGGAGATTTTGGATTTTAGAGGTTTTAGAAACCTAGGATTTTGGGGGATTTTGGA
TCTTAGGAGATTTTGGATTTTTAAGAG
Found at i:18100045 original size:17 final size:17
Alignment explanation
Indices: 18099879--18100047 Score: 105
Period size: 17 Copynumber: 9.6 Consensus size: 17
18099869 TAGAAACCTA
* *
18099879 GGATTTTGGGGGATTTT
1 GGATTTTAGGAGATTTT
* *
18099896 GGATTTTGGGGGATTTT
1 GGATTTTAGGAGATTTT
*
18099913 GGATTTTTA--AGAGTTT
1 GGA-TTTTAGGAGATTTT
18099929 GGATTTTAGGAGATTTT
1 GGATTTTAGGAGATTTT
*
18099946 GGATTTTA-GAGGTTTTAGAAACCT
1 GGATTTTAGGA-GATTT-------T
** *
18099970 AGGATTTGGGGGGATTTT
1 -GGATTTTAGGAGATTTT
*
18099988 GGATCTTAGGAGATTTT
1 GGATTTTAGGAGATTTT
*
18100005 GGATTTTTA--AGAGTTT
1 GGA-TTTTAGGAGATTTT
18100021 GGATTTTAGGAGATTTT
1 GGATTTTAGGAGATTTT
18100038 GGATTTTAGG
1 GGATTTTAGG
18100048 GGTTCTAGAA
Statistics
Matches: 120, Mismatches: 16, Indels: 32
0.71 0.10 0.19
Matches are distributed among these distances:
15 10 0.08
16 19 0.16
17 70 0.58
18 9 0.08
24 1 0.01
25 10 0.08
26 1 0.01
ACGTcount: A:0.21, C:0.02, G:0.33, T:0.44
Consensus pattern (17 bp):
GGATTTTAGGAGATTTT
Found at i:18100136 original size:16 final size:16
Alignment explanation
Indices: 18100115--18100213 Score: 92
Period size: 16 Copynumber: 6.1 Consensus size: 16
18100105 CAGATTTTGG
18100115 GGGGTTTTGGATTTTA
1 GGGGTTTTGGATTTTA
* *
18100131 GGGGTTTCGAATTTTA
1 GGGGTTTTGGATTTTA
*
18100147 TGGGG-TTTGGATTTAA
1 -GGGGTTTTGGATTTTA
* *
18100163 GGGATTTGGGATTTTTA
1 GGGGTTTTGGA-TTTTA
* * *
18100180 GGGGTTTCGAATTTAA
1 GGGGTTTTGGATTTTA
*
18100196 GGGATTTTGGATTTTA
1 GGGGTTTTGGATTTTA
18100212 GG
1 GG
18100214 AAGTTTTAGA
Statistics
Matches: 64, Mismatches: 16, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
15 3 0.05
16 45 0.70
17 16 0.25
ACGTcount: A:0.18, C:0.02, G:0.35, T:0.44
Consensus pattern (16 bp):
GGGGTTTTGGATTTTA
Found at i:18100177 original size:32 final size:33
Alignment explanation
Indices: 18100098--18100211 Score: 108
Period size: 33 Copynumber: 3.5 Consensus size: 33
18100088 TTTAAGATTT
* ** *
18100098 GGGATTTCAGATTTT-GGGGGGTTTTGGATTTTA
1 GGGATTTCGGATTTTATAGGGG-TTTGGATTTAA
* *
18100131 GGGGTTTCGAATTTTAT-GGGGTTTGGATTTAA
1 GGGATTTCGGATTTTATAGGGGTTTGGATTTAA
* *
18100163 GGGATTTGGGATTTT-TAGGGGTTTCGAATTTAA
1 GGGATTTCGGATTTTATAGGGGTTT-GGATTTAA
*
18100196 GGGATTTTGGATTTTA
1 GGGATTTCGGATTTTA
18100212 GGAAGTTTTA
Statistics
Matches: 67, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
31 1 0.01
32 29 0.43
33 37 0.55
ACGTcount: A:0.18, C:0.03, G:0.34, T:0.45
Consensus pattern (33 bp):
GGGATTTCGGATTTTATAGGGGTTTGGATTTAA
Found at i:18101638 original size:3 final size:3
Alignment explanation
Indices: 18101606--18101652 Score: 55
Period size: 3 Copynumber: 16.7 Consensus size: 3
18101596 TTTATTAATA
* *
18101606 ATT ATT -TT ATT -TT ATT TTT ATT A-A ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
18101651 AT
1 AT
18101653 AGTGAAATGA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
2 5 0.14
3 32 0.86
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:18105588 original size:21 final size:23
Alignment explanation
Indices: 18105541--18105588 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 23
18105531 TGTTGCAAAA
*
18105541 AATTGAACTTGATGATTTTTATT
1 AATTGAACTTGATGATTTCTATT
*
18105564 -ATTG-ACTTG-TGCTTTCTATT
1 AATTGAACTTGATGATTTCTATT
18105584 AATTG
1 AATTG
18105589 TTAGAACTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 9 0.41
21 9 0.41
22 4 0.18
ACGTcount: A:0.25, C:0.08, G:0.15, T:0.52
Consensus pattern (23 bp):
AATTGAACTTGATGATTTCTATT
Found at i:18106813 original size:22 final size:22
Alignment explanation
Indices: 18106764--18106822 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 22
18106754 AAAGTACCCA
*
18106764 AAGGTTTTTAAAAGATCATACCTC
1 AAGG-TTTTATAA-ATCATACCTC
* *
18106788 AAGGTTTTATAAATCATGCCTT
1 AAGGTTTTATAAATCATACCTC
18106810 AAGGTATTT-TAAA
1 AAGGT-TTTATAAA
18106823 ATTATATCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
22 17 0.55
23 10 0.32
24 4 0.13
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (22 bp):
AAGGTTTTATAAATCATACCTC
Found at i:18108366 original size:6 final size:6
Alignment explanation
Indices: 18108355--18108395 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
18108345 AACATGCCTT
18108355 TTTTTC TTTTTCC TTTTT- TGTTTTC TTTTT- TTTTTC TTTTT
1 TTTTTC TTTTT-C TTTTTC T-TTTTC TTTTTC TTTTTC TTTTT
18108396 TTTCTACTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
5 6 0.19
6 18 0.58
7 7 0.23
ACGTcount: A:0.00, C:0.12, G:0.02, T:0.85
Consensus pattern (6 bp):
TTTTTC
Found at i:18108389 original size:11 final size:11
Alignment explanation
Indices: 18108355--18108398 Score: 61
Period size: 11 Copynumber: 3.7 Consensus size: 11
18108345 AACATGCCTT
18108355 TTTTTCTTTTTCC
1 TTTTT-TTTTT-C
18108368 TTTTTTGTTTTC
1 TTTTTT-TTTTC
18108380 TTTTTTTTTTC
1 TTTTTTTTTTC
18108391 TTTTTTTT
1 TTTTTTTT
18108399 CTACTTGCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 13 0.43
12 8 0.27
13 9 0.30
ACGTcount: A:0.00, C:0.11, G:0.02, T:0.86
Consensus pattern (11 bp):
TTTTTTTTTTC
Found at i:18108752 original size:12 final size:13
Alignment explanation
Indices: 18108735--18108764 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
18108725 CTCTTTCACT
18108735 TTTTTG-TTTTTA
1 TTTTTGTTTTTTA
18108747 TTTTTGTTTTTTA
1 TTTTTGTTTTTTA
18108760 TTTTT
1 TTTTT
18108765 TATTTTGGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.07, C:0.00, G:0.07, T:0.87
Consensus pattern (13 bp):
TTTTTGTTTTTTA
Found at i:18114683 original size:19 final size:20
Alignment explanation
Indices: 18114647--18114684 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
18114637 AGGATTACAT
*
18114647 TTTTTTATTTTTGTAAATTA
1 TTTTTTATATTTGTAAATTA
18114667 TTTTTTATATTTG-AAATT
1 TTTTTTATATTTGTAAATT
18114685 TTCTTCTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.68
Consensus pattern (20 bp):
TTTTTTATATTTGTAAATTA
Found at i:18118936 original size:22 final size:22
Alignment explanation
Indices: 18118895--18118941 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 22
18118885 CCGTTTGTTT
18118895 ATTTGAATATTAAAAGTTTATTA
1 ATTTGAATATTAAAAGTTTA-TA
18118918 ATTT-AATAATTAAAA-TTTATA
1 ATTTGAAT-ATTAAAAGTTTATA
18118939 ATT
1 ATT
18118942 ACTTTCTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 5 0.22
22 7 0.30
23 11 0.48
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (22 bp):
ATTTGAATATTAAAAGTTTATA
Found at i:18119354 original size:22 final size:22
Alignment explanation
Indices: 18119329--18119373 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
18119319 TGAGAACTTC
*
18119329 AATATTAATAAGAAAATAAATA
1 AATATTAATAAAAAAATAAATA
* *
18119351 AATATTAGTAAAAAAATATATA
1 AATATTAATAAAAAAATAAATA
18119373 A
1 A
18119374 TTAGTTATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (22 bp):
AATATTAATAAAAAAATAAATA
Found at i:18119952 original size:16 final size:16
Alignment explanation
Indices: 18119931--18119967 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
18119921 TAGATAAAAA
*
18119931 TAAAATTTTTTAATAT
1 TAAAATTTTTGAATAT
18119947 TAAAA--TTTGAATAT
1 TAAAATTTTTGAATAT
18119961 TAAAATT
1 TAAAATT
18119968 ATTAAATATC
Statistics
Matches: 18, Mismatches: 1, Indels: 4
0.78 0.04 0.17
Matches are distributed among these distances:
14 13 0.72
16 5 0.28
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (16 bp):
TAAAATTTTTGAATAT
Found at i:18119965 original size:30 final size:31
Alignment explanation
Indices: 18119931--18119989 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
18119921 TAGATAAAAA
* * *
18119931 TAAAATTTTTTAATATTA-AAATTTGAATAT
1 TAAAATTATTAAATATCACAAATTTGAATAT
18119961 TAAAATTATTAAATATCACAAATTTGAAT
1 TAAAATTATTAAATATCACAAATTTGAAT
18119990 TGTTATGGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 15 0.60
31 10 0.40
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.44
Consensus pattern (31 bp):
TAAAATTATTAAATATCACAAATTTGAATAT
Found at i:18120206 original size:15 final size:15
Alignment explanation
Indices: 18120182--18120228 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
18120172 GAAATGTAAT
18120182 AAAATAATTATAATTA
1 AAAAT-ATTATAATTA
18120198 AAAATATTAT-ATTA
1 AAAATATTATAATTA
*
18120212 AAATTTATATATAATTA
1 AAA-ATAT-TATAATTA
18120229 TTGAATAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 7 0.26
15 8 0.30
16 8 0.30
17 4 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AAAATATTATAATTA
Found at i:18120211 original size:14 final size:16
Alignment explanation
Indices: 18120182--18120228 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 16
18120172 GAAATGTAAT
18120182 AAAATAATTATAATTA
1 AAAATAATTATAATTA
18120198 AAAAT-ATTAT-ATTA
1 AAAATAATTATAATTA
* *
18120212 AAATTTATATATAATTA
1 AAAATAAT-TATAATTA
18120229 TTGAATAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 8 0.30
15 7 0.26
16 8 0.30
17 4 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AAAATAATTATAATTA
Found at i:18121473 original size:14 final size:16
Alignment explanation
Indices: 18121448--18121491 Score: 88
Period size: 16 Copynumber: 2.8 Consensus size: 16
18121438 GCTAATATGT
18121448 AAATAAATATATAACA
1 AAATAAATATATAACA
18121464 AAATAAATATATAACA
1 AAATAAATATATAACA
18121480 AAATAAATATAT
1 AAATAAATATAT
18121492 TCAACATGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (16 bp):
AAATAAATATATAACA
Found at i:18123981 original size:12 final size:12
Alignment explanation
Indices: 18123964--18123988 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
18123954 TAATAAAATA
18123964 TAAAAATATTAT
1 TAAAAATATTAT
18123976 TAAAAATATTAT
1 TAAAAATATTAT
18123988 T
1 T
18123989 TATAATTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAAAAATATTAT
Found at i:18124153 original size:17 final size:15
Alignment explanation
Indices: 18124128--18124162 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
18124118 TATAAAAAAA
18124128 TTTTTAATT--TTAT
1 TTTTTAATTAATTAT
18124141 TTTTTAATTAATTAT
1 TTTTTAATTAATTAT
18124156 TTTTTAA
1 TTTTTAA
18124163 AAAAATTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 9 0.45
15 11 0.55
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTTAATTAATTAT
Found at i:18134940 original size:24 final size:21
Alignment explanation
Indices: 18134893--18134935 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
18134883 TTTAAAATAA
18134893 AAATAAATAAATAAATAATTT
1 AAATAAATAAATAAATAATTT
18134914 AAATAAA-AAATAAATATATTT
1 AAATAAATAAATAAATA-ATTT
18134935 A
1 A
18134936 CTAAACAAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
AAATAAATAAATAAATAATTT
Found at i:18138920 original size:12 final size:12
Alignment explanation
Indices: 18138878--18138923 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
18138868 CATAGAATAA
18138878 AAATCATGCAAT
1 AAATCATGCAAT
* *
18138890 AAACCAT--AAA
1 AAATCATGCAAT
18138900 AACATCATGCAAT
1 AA-ATCATGCAAT
18138913 AAATCATGCAA
1 AAATCATGCAA
18138924 ATGACATGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
10 4 0.15
11 4 0.15
12 15 0.56
13 4 0.15
ACGTcount: A:0.54, C:0.20, G:0.07, T:0.20
Consensus pattern (12 bp):
AAATCATGCAAT
Found at i:18138967 original size:20 final size:20
Alignment explanation
Indices: 18138928--18139081 Score: 125
Period size: 20 Copynumber: 7.8 Consensus size: 20
18138918 ATGCAAATGA
* * *
18138928 CATGAAAATAAATCAATAAT
1 CATGCAAATATATAAATAAT
* *
18138948 CATGCAAACATATAAGTAAT
1 CATGCAAATATATAAATAAT
* * * *
18138968 AATGCAATTA-ATAAGTAAC
1 CATGCAAATATATAAATAAT
* * *
18138987 CATGCAATTAACATTAATAAT
1 CATGCAAAT-ATATAAATAAT
* *
18139008 CATACAAGTATATAAACT-AT
1 CATGCAAATATATAAA-TAAT
18139028 CATGCAAATATATAAATAAT
1 CATGCAAATATATAAATAAT
*
18139048 CATACAAATA-ATAAATAAT
1 CATGCAAATATATAAATAAT
*
18139067 CATGAAAATATATAA
1 CATGCAAATATATAA
18139082 TTCTGCAATA
Statistics
Matches: 107, Mismatches: 22, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
19 34 0.32
20 59 0.55
21 14 0.13
ACGTcount: A:0.55, C:0.12, G:0.06, T:0.28
Consensus pattern (20 bp):
CATGCAAATATATAAATAAT
Found at i:18138983 original size:19 final size:19
Alignment explanation
Indices: 18138959--18138997 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
18138949 ATGCAAACAT
*
18138959 ATAAGTAATAATGCAATTA
1 ATAAGTAACAATGCAATTA
*
18138978 ATAAGTAACCATGCAATTA
1 ATAAGTAACAATGCAATTA
18138997 A
1 A
18138998 CATTAATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.28
Consensus pattern (19 bp):
ATAAGTAACAATGCAATTA
Found at i:18140872 original size:43 final size:43
Alignment explanation
Indices: 18140779--18140889 Score: 118
Period size: 43 Copynumber: 2.6 Consensus size: 43
18140769 ATAATTGAGC
* * **
18140779 CATTGAAACTTTTTGAAAAATAAAATGTTCTTTCACCATTAAGG
1 CATTGAAAC-TTTTGAAAAATAAAATGTTCTCTCACAACCAAGG
*
18140823 CATTGAAACTTTTGAAAAATAAAGTGTT-TCTCTACAACCAAGG
1 CATTGAAACTTTTGAAAAATAAAATGTTCTCTC-ACAACCAAGG
**
18140866 GTTTGAAACTTTT-AGAAAATAAAA
1 CATTGAAACTTTTGA-AAAATAAAA
18140890 GTATTCTTTC
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
42 4 0.07
43 44 0.77
44 9 0.16
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (43 bp):
CATTGAAACTTTTGAAAAATAAAATGTTCTCTCACAACCAAGG
Found at i:18140964 original size:37 final size:36
Alignment explanation
Indices: 18140872--18141112 Score: 175
Period size: 37 Copynumber: 6.4 Consensus size: 36
18140862 AAGGGTTTGA
* *
18140872 AACTTTTAGAAAATAAAAGTATTCTTTCATTGAGGCTTC
1 AACTTTGA-AAAATAAAA-TATT-TTTCATTAAGGCTTC
* *
18140911 AACGTTGGAAAAATAAAATATTTTTCTATTTAGGCTTC
1 AAC-TTTGAAAAATAAAATATTTTTC-ATTAAGGCTTC
*
18140949 AACTTTGAAAAATAAAGA-ATTCTTTCATTAAGGCTTT
1 AACTTTGAAAAATAAA-ATATT-TTTCATTAAGGCTTC
*
18140986 AACTTTGAAAAAAATAAAATA--TTTCATTGAGGCTTC
1 AACTTTG--AAAAATAAAATATTTTTCATTAAGGCTTC
* * * * * *
18141022 AACTTTTGAAAAAATAAAAAACTATTCCACTAAAGCTTA
1 AAC-TTTG-AAAAATAAAATA-TTTTTCATTAAGGCTTC
* ** *
18141061 AACTTTGAAAAATAAAGA-ATTCTATCATCGAGGTTTC
1 AACTTTGAAAAATAAA-ATATT-TTTCATTAAGGCTTC
*
18141098 AATTTTGAAAAATAA
1 AACTTTGAAAAATAA
18141113 GGTACTACTC
Statistics
Matches: 165, Mismatches: 24, Indels: 28
0.76 0.11 0.13
Matches are distributed among these distances:
36 29 0.18
37 70 0.42
38 28 0.17
39 35 0.21
40 3 0.02
ACGTcount: A:0.43, C:0.12, G:0.11, T:0.35
Consensus pattern (36 bp):
AACTTTGAAAAATAAAATATTTTTCATTAAGGCTTC
Found at i:18140975 original size:75 final size:73
Alignment explanation
Indices: 18140872--18141039 Score: 203
Period size: 75 Copynumber: 2.2 Consensus size: 73
18140862 AAGGGTTTGA
* * * *
18140872 AACTTTTAGAAAATAAAAGTATTCTTTCATTGAGGCTTCAACGTTG-GAAAAATAAAATATTTTT
1 AACTTTGA-AAAAT-AAAGAATTCTTTCATTAAGGCTTCAACGTTGAAAAAAATAAAATA--TTT
*
18140936 CTATTTAGGCTTC
62 C-ATTGAGGCTTC
* *
18140949 AACTTTGAAAAATAAAGAATTCTTTCATTAAGGCTTTAACTTTGAAAAAAATAAAATATTTCATT
1 AACTTTGAAAAATAAAGAATTCTTTCATTAAGGCTTCAACGTTGAAAAAAATAAAATATTTCATT
18141014 GAGGCTTC
66 GAGGCTTC
18141022 AACTTTTGAAAAAATAAA
1 AAC-TTTG-AAAAATAAA
18141040 AAACTATTCC
Statistics
Matches: 81, Mismatches: 7, Indels: 8
0.84 0.07 0.08
Matches are distributed among these distances:
73 13 0.16
74 8 0.10
75 36 0.44
76 17 0.21
77 7 0.09
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (73 bp):
AACTTTGAAAAATAAAGAATTCTTTCATTAAGGCTTCAACGTTGAAAAAAATAAAATATTTCATT
GAGGCTTC
Found at i:18141065 original size:75 final size:75
Alignment explanation
Indices: 18140919--18141072 Score: 195
Period size: 75 Copynumber: 2.0 Consensus size: 75
18140909 TCAACGTTGG
* * * * * * *
18140919 AAAAATAAAATATTTTTCTATTTAGGCTTCAACTTTGAAAAATAAAGAATTCTTTCATTAAGGCT
1 AAAAATAAAATA-TTTTCTATTGAGGCTTCAACTTTGAAAAATAAAAAACTATTCCACTAAAGCT
*
18140984 TTAACTTTGAA
65 TAAACTTTGAA
18140995 AAAAATAAAATA-TTTC-ATTGAGGCTTCAACTTTTGAAAAAATAAAAAACTATTCCACTAAAGC
1 AAAAATAAAATATTTTCTATTGAGGCTTCAAC-TTTG-AAAAATAAAAAACTATTCCACTAAAGC
18141058 TTAAACTTTGAA
64 TTAAACTTTGAA
18141070 AAA
1 AAA
18141073 TAAAGAATTC
Statistics
Matches: 68, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
73 13 0.19
74 8 0.12
75 35 0.51
76 12 0.18
ACGTcount: A:0.45, C:0.12, G:0.08, T:0.34
Consensus pattern (75 bp):
AAAAATAAAATATTTTCTATTGAGGCTTCAACTTTGAAAAATAAAAAACTATTCCACTAAAGCTT
AAACTTTGAA
Found at i:18141105 original size:112 final size:111
Alignment explanation
Indices: 18140896--18141109 Score: 277
Period size: 112 Copynumber: 1.9 Consensus size: 111
18140886 AAAAGTATTC
* * * * * * * * *
18140896 TTTCATTGAGGCTTCAACGTTGGAAAAATAAAATATTTTTCTATTTAGGCTTCAACTTTGAAAAA
1 TTTCATTGAGGCTTCAACGTTGAAAAAATAAAAAACTATTCCACTAAAGCTTAAACTTTGAAAAA
* *
18140961 TAAAGAATTCTTTCATTAAGGCTTTAACTTTGAAAAAAATAAAATA
66 TAAAGAATTCTATCATCAAGGCTTTAACTTTGAAAAAAATAAAATA
*
18141007 TTTCATTGAGGCTTCAACTTTTGAAAAAATAAAAAACTATTCCACTAAAGCTTAAACTTTGAAAA
1 TTTCATTGAGGCTTCAAC-GTTGAAAAAATAAAAAACTATTCCACTAAAGCTTAAACTTTGAAAA
* *
18141072 ATAAAGAATTCTATCATCGAGG-TTTCAATTTTGAAAAA
65 ATAAAGAATTCTATCATCAAGGCTTT-AACTTTGAAAAA
18141110 TAAGGTACTA
Statistics
Matches: 87, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
111 21 0.24
112 66 0.76
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.35
Consensus pattern (111 bp):
TTTCATTGAGGCTTCAACGTTGAAAAAATAAAAAACTATTCCACTAAAGCTTAAACTTTGAAAAA
TAAAGAATTCTATCATCAAGGCTTTAACTTTGAAAAAAATAAAATA
Found at i:18141147 original size:112 final size:112
Alignment explanation
Indices: 18140944--18141151 Score: 251
Period size: 112 Copynumber: 1.9 Consensus size: 112
18140934 TTCTATTTAG
* * * * *
18140944 GCTTCAACTTTGAAAAATAAAGAATTCTTTCATTAAGGCTTTAACTTTGAAAAAAATAAAATATT
1 GCTTAAACTTTGAAAAATAAAGAATTCTATCATCAAGGCTTTAACTTTGAAAAAAAGAAAATACT
* *
18141009 TCATTGAGGCTTCAACTTTTGAAAAAATAAAAAACTATTCCACTAAA
66 CCACTGAGGCTTCAACTTTTGAAAAAATAAAAAACTATTCCACTAAA
* * ** *
18141056 GCTTAAACTTTGAAAAATAAAGAATTCTATCATCGAGG-TTTCAATTTTGAAAAATAAGGTACTA
1 GCTTAAACTTTGAAAAATAAAGAATTCTATCATCAAGGCTTT-AACTTTGAAAAA-AAGAAAATA
*
18141120 CTCCACTGAGTC-TCTAACTTTTG-AAAAATAAA
64 CTCCACTGAGGCTTC-AACTTTTGAAAAAATAAA
18141152 GTATTCATCC
Statistics
Matches: 80, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
111 3 0.04
112 56 0.70
113 21 0.26
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.33
Consensus pattern (112 bp):
GCTTAAACTTTGAAAAATAAAGAATTCTATCATCAAGGCTTTAACTTTGAAAAAAAGAAAATACT
CCACTGAGGCTTCAACTTTTGAAAAAATAAAAAACTATTCCACTAAA
Found at i:18141309 original size:48 final size:48
Alignment explanation
Indices: 18141235--18141329 Score: 147
Period size: 48 Copynumber: 2.0 Consensus size: 48
18141225 TAAAATCATG
*
18141235 TCCAAGAAAGCTCATTTTCAATAAAAGCTTGAAAC-TTAAAGATTCTCA
1 TCCAAGAAAGCTCATTTTCAACAAAAGCTTGAAACTTTAAA-ATTCTCA
* *
18141283 TCCAAGGAAGCTCCTTTTCAACAAAAGCTTGAAACTTTAAAATTCTC
1 TCCAAGAAAGCTCATTTTCAACAAAAGCTTGAAACTTTAAAATTCTC
18141330 GGAAACCCCT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
48 38 0.88
49 5 0.12
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.29
Consensus pattern (48 bp):
TCCAAGAAAGCTCATTTTCAACAAAAGCTTGAAACTTTAAAATTCTCA
Found at i:18143991 original size:44 final size:44
Alignment explanation
Indices: 18143893--18144137 Score: 198
Period size: 44 Copynumber: 5.6 Consensus size: 44
18143883 GTAGAGGCTT
** * * *
18143893 ACAACTTTTGAAAAAATAAATATGGCTCATTTAAACAGAA-GCTCA
1 ACAA-TTTTGAAAAAATAAATAAAGCTCCTATAATCA-AAGGCTCA
** * * *
18143938 ATGACTTTGAAAAAATATATAAAGCTCCTATAATCAAAGGCTTA
1 ACAATTTTGAAAAAATAAATAAAGCTCCTATAATCAAAGGCTCA
* *
18143982 ACAATTTTGAAAAAATAAATAATA-CTCCTCTAAGCAAAGGCTCA
1 ACAATTTTGAAAAAATAAATAA-AGCTCCTATAATCAAAGGCTCA
*
18144026 ACAATTTTGAAAAAATAAATAATGCTCCTCAT-ATCAAAGGCTCA
1 ACAATTTTGAAAAAATAAATAAAGCTCCT-ATAATCAAAGGCTCA
* * * * * * *
18144070 ATAATTTT-AGAAAGTAAATAAAGTTCATCTAAACAAAGG-TACA
1 ACAATTTTGAAAAAATAAATAAAGCTCCTATAATCAAAGGCT-CA
* *
18144113 ACAACTTTG--GAAATAAATAAAGCTC
1 ACAATTTTGAAAAAATAAATAAAGCTC
18144138 ATCTAAACAC
Statistics
Matches: 160, Mismatches: 33, Indels: 17
0.76 0.16 0.08
Matches are distributed among these distances:
42 15 0.09
43 32 0.20
44 109 0.68
45 4 0.03
ACGTcount: A:0.47, C:0.15, G:0.11, T:0.27
Consensus pattern (44 bp):
ACAATTTTGAAAAAATAAATAAAGCTCCTATAATCAAAGGCTCA
Found at i:18144036 original size:88 final size:88
Alignment explanation
Indices: 18143887--18144137 Score: 232
Period size: 88 Copynumber: 2.9 Consensus size: 88
18143877 CCCTAAGTAG
* * **
18143887 AGGCTT-ACAACTTTTGAAAAAATAAATATGGCTCATTTAAACAGAAGCTCAATGACTTTGAAAA
1 AGGCTTAACAA-TTTTGAAAAAATAAATATGACTCATCTAAACAGAAGCTCAACAACTTTGAAAA
*
18143951 AATATATAAAGCTCCT-ATAATCAA
65 AATAAATAAAGCTCCTCAT-ATCAA
* * *
18143975 AGGCTTAACAATTTTGAAAAAATAAATAAT-ACTCCTCTAAGCA-AAGGCTCAACAATTTTGAAA
1 AGGCTTAACAATTTTGAAAAAATAAAT-ATGACTCATCTAAACAGAA-GCTCAACAACTTTGAAA
*
18144038 AAATAAATAATGCTCCTCATATCAA
64 AAATAAATAAAGCTCCTCATATCAA
* * * * * * * *
18144063 AGGCTCAATAATTTT-AGAAAGTAAATA-AAGTTCATCTAAACA-AAGGTACAACAACTTTG--G
1 AGGCTTAACAATTTTGAAAAAATAAATATGA-CTCATCTAAACAGAAGCT-CAACAACTTTGAAA
18144123 AAATAAATAAAGCTC
64 AAATAAATAAAGCTC
18144138 ATCTAAACAC
Statistics
Matches: 136, Mismatches: 20, Indels: 17
0.79 0.12 0.10
Matches are distributed among these distances:
85 14 0.10
86 4 0.03
87 32 0.24
88 78 0.57
89 8 0.06
ACGTcount: A:0.47, C:0.15, G:0.11, T:0.27
Consensus pattern (88 bp):
AGGCTTAACAATTTTGAAAAAATAAATATGACTCATCTAAACAGAAGCTCAACAACTTTGAAAAA
ATAAATAAAGCTCCTCATATCAA
Found at i:18144107 original size:43 final size:44
Alignment explanation
Indices: 18143905--18144216 Score: 166
Period size: 44 Copynumber: 7.2 Consensus size: 44
18143895 AACTTTTGAA
** * ** *
18143905 AAAATAAATATGGCTCATTTAAACAGAA-GCT-CAATGACTTTGAA
1 AAAATAAATAAAGCTCATCTAAACA-AAGGCTACAACAACTTT-AG
* * * * * * *
18143949 AAAATATATAAAGCTCCTATAATCAAAGGCT-TAACAATTTTGAA
1 AAAATAAATAAAGCTCATCTAAACAAAGGCTACAACAACTTT-AG
* * * *
18143993 AAAATAAATAATA-CTCCTCTAAGCAAAGGCT-CAACAATTTTGAA
1 AAAATAAATAA-AGCTCATCTAAACAAAGGCTACAACAACTTT-AG
* * * * *
18144037 AAAATAAATAATGCTCCTC-ATATCAAAGGCT-CAATAATTTTAG
1 AAAATAAATAAAGCTCATCTA-AACAAAGGCTACAACAACTTTAG
* *
18144080 AAAGTAAATAAAGTTCATCTAAACAAAGG-TACAACAACTTT-G
1 AAAATAAATAAAGCTCATCTAAACAAAGGCTACAACAACTTTAG
* * * *
18144122 GAAATAAATAAAGCTCATCTAAACACA-GATACAATAACTTTAG
1 AAAATAAATAAAGCTCATCTAAACAAAGGCTACAACAACTTTAG
* * * * *
18144165 AAAAT--A-AAAGCTCCTCTAAATAGAGGCT-CAACAAATTTAAA
1 AAAATAAATAAAGCTCATCTAAACAAAGGCTACAACAACTTT-AG
18144206 AAAATAAATAA
1 AAAATAAATAA
18144217 GACTCCTCTA
Statistics
Matches: 217, Mismatches: 38, Indels: 26
0.77 0.14 0.09
Matches are distributed among these distances:
40 23 0.11
41 10 0.05
42 36 0.17
43 40 0.18
44 107 0.49
45 1 0.00
ACGTcount: A:0.49, C:0.15, G:0.10, T:0.26
Consensus pattern (44 bp):
AAAATAAATAAAGCTCATCTAAACAAAGGCTACAACAACTTTAG
Found at i:18144133 original size:42 final size:43
Alignment explanation
Indices: 18144075--18144172 Score: 128
Period size: 42 Copynumber: 2.3 Consensus size: 43
18144065 GCTCAATAAT
* *
18144075 TTTA-GAAAGTAAATAAAGTTCATCTAAACAAAGGTACAACAAC
1 TTTAGGAAA-TAAATAAAGCTCATCTAAACAAAGATACAACAAC
* *
18144118 TTT-GGAAATAAATAAAGCTCATCTAAACACAGATACAATAAC
1 TTTAGGAAATAAATAAAGCTCATCTAAACAAAGATACAACAAC
*
18144160 TTTAGAAAATAAA
1 TTTAGGAAATAAA
18144173 AGCTCCTCTA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
42 33 0.69
43 15 0.31
ACGTcount: A:0.52, C:0.13, G:0.10, T:0.24
Consensus pattern (43 bp):
TTTAGGAAATAAATAAAGCTCATCTAAACAAAGATACAACAAC
Found at i:18144697 original size:21 final size:21
Alignment explanation
Indices: 18144668--18144744 Score: 91
Period size: 21 Copynumber: 3.6 Consensus size: 21
18144658 ATCTAAATTT
* *
18144668 AAAGGTTCTTATTAGAAACTC
1 AAAGATTCTCATTAGAAACTC
*
18144689 AAAGATTCTCATTTGAAACTC
1 AAAGATTCTCATTAGAAACTC
* *
18144710 AAATATTCTCATTTAAAAACTC
1 AAAGATTCTCA-TTAGAAACTC
*
18144732 AAAAATTCTCATT
1 AAAGATTCTCATT
18144745 TAAGGATACA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
21 30 0.62
22 18 0.38
ACGTcount: A:0.42, C:0.17, G:0.06, T:0.35
Consensus pattern (21 bp):
AAAGATTCTCATTAGAAACTC
Found at i:18144732 original size:22 final size:22
Alignment explanation
Indices: 18144683--18144747 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
18144673 TTCTTATTAG
* *
18144683 AAACTCAAAGATTCTCATTT-G
1 AAACTCAAAAATTCTCATTTAA
*
18144704 AAACTCAAATATTCTCATTTAA
1 AAACTCAAAAATTCTCATTTAA
18144726 AAACTCAAAAATTCTCATTTAA
1 AAACTCAAAAATTCTCATTTAA
18144748 GGATACATAA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
21 19 0.47
22 21 0.52
ACGTcount: A:0.45, C:0.18, G:0.03, T:0.34
Consensus pattern (22 bp):
AAACTCAAAAATTCTCATTTAA
Found at i:18145812 original size:28 final size:32
Alignment explanation
Indices: 18145779--18145856 Score: 110
Period size: 28 Copynumber: 2.5 Consensus size: 32
18145769 CATTTTTTCA
18145779 TCTTTCATTTTCTCATTCTCTTTTTT-T-T-T
1 TCTTTCATTTTCTCATTCTCTTTTTTCTATAT
*
18145808 T-TTTCATTTTTTCATTCTCTTTTTTCTACTAT
1 TCTTTCATTTTCTCATTCTCTTTTTTCTA-TAT
18145840 TCTTTCATTTTCTCATT
1 TCTTTCATTTTCTCATT
18145857 TTTTCATTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
28 23 0.55
29 2 0.05
31 1 0.02
32 2 0.05
33 14 0.33
ACGTcount: A:0.10, C:0.21, G:0.00, T:0.69
Consensus pattern (32 bp):
TCTTTCATTTTCTCATTCTCTTTTTTCTATAT
Found at i:18145867 original size:8 final size:8
Alignment explanation
Indices: 18145763--18145868 Score: 57
Period size: 8 Copynumber: 13.8 Consensus size: 8
18145753 CTTTTCTCTC
*
18145763 TTTTTACA
1 TTTTTTCA
18145771 TTTTTTCA
1 TTTTTTCA
*
18145779 -TCTTTCA
1 TTTTTTCA
*
18145786 TTTTCTCA
1 TTTTTTCA
*
18145794 --TTCTC-
1 TTTTTTCA
*
18145799 TTTTTT-T
1 TTTTTTCA
18145806 TTTTTTCA
1 TTTTTTCA
18145814 TTTTTTCA
1 TTTTTTCA
*
18145822 --TTCTC-
1 TTTTTTCA
18145827 TTTTTTCTA
1 TTTTTTC-A
18145836 CTATTCTTTCA
1 -T-TT-TTTCA
*
18145847 TTTTCTCA
1 TTTTTTCA
18145855 TTTTTTCA
1 TTTTTTCA
18145863 TTTTTT
1 TTTTTT
18145869 TCTTCATTAT
Statistics
Matches: 76, Mismatches: 10, Indels: 24
0.69 0.09 0.22
Matches are distributed among these distances:
6 9 0.12
7 19 0.25
8 37 0.49
9 2 0.03
10 2 0.03
11 3 0.04
12 4 0.05
ACGTcount: A:0.11, C:0.18, G:0.00, T:0.71
Consensus pattern (8 bp):
TTTTTTCA
Found at i:18150541 original size:191 final size:192
Alignment explanation
Indices: 18150197--18150542 Score: 455
Period size: 191 Copynumber: 1.8 Consensus size: 192
18150187 AAAAGAATAC
* * * **
18150197 AATTACTTTTATTGAAATTTTATTTAAATTATTCCATCAATCGGGACAAATTTGGAGAAATTTCT
1 AATTACTTTTATTGAAACTTTATCTAAATTATTCCATCAATCGAGACAAATTCAGAGAAATTTCT
* * * * * *
18150262 CACCTAGAGATTTCTTAGGAATTTATCATTTGAAATTTTTAAGAATCTCATCCTTAGGTAATTAG
66 CACCTAGAAATTTCTTAGAAATTTACCATTTAAAATTTTTAAAAATCTCATCCTTAGATAATTAG
* ***
18150327 AATTTTTTCAAAATTTTTATTTTTTATTTTTTTGGTTTTTTTATTGTTTGAAAATAAATATT
131 AATTTATTCAAAATAAATATTTTTTATTTTTTTGGTTTTTTTATTGTTTGAAAATAAATATT
* * *
18150389 AATTA-TTGTTATTGAAACTTTATCTAAATTATT-CATCATTTGAGACAAATTCAGATAAATTTC
1 AATTACTT-TTATTGAAACTTTATCTAAATTATTCCATCAATCGAGACAAATTCAGAGAAATTTC
* *
18150452 TCACCTAGAAATTTTTTAGAAATTTACCATTTAAAATTTTTAAAAATTTCATCCTTAGATAATTA
65 TCACCTAGAAATTTCTTAGAAATTTACCATTTAAAATTTTTAAAAATCTCATCCTTAGATAATTA
**
18150517 TTATTTATTCTAAAA-AAATATTTTTT
130 GAATTTATTC-AAAATAAATATTTTTT
18150543 TATTATTATT
Statistics
Matches: 130, Mismatches: 22, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
191 98 0.75
192 32 0.25
ACGTcount: A:0.35, C:0.10, G:0.08, T:0.47
Consensus pattern (192 bp):
AATTACTTTTATTGAAACTTTATCTAAATTATTCCATCAATCGAGACAAATTCAGAGAAATTTCT
CACCTAGAAATTTCTTAGAAATTTACCATTTAAAATTTTTAAAAATCTCATCCTTAGATAATTAG
AATTTATTCAAAATAAATATTTTTTATTTTTTTGGTTTTTTTATTGTTTGAAAATAAATATT
Found at i:18151533 original size:13 final size:14
Alignment explanation
Indices: 18151504--18151551 Score: 50
Period size: 13 Copynumber: 3.7 Consensus size: 14
18151494 AATTAACTAA
18151504 AAATATAAAAAATC
1 AAATATAAAAAATC
*
18151518 AAATAT-AAACATC
1 AAATATAAAAAATC
*
18151531 AAA-GTAAAAAAT-
1 AAATATAAAAAATC
18151543 AAA-ATAAAA
1 AAATATAAAA
18151552 TAGAAAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 9 0.31
13 14 0.48
14 6 0.21
ACGTcount: A:0.73, C:0.06, G:0.02, T:0.19
Consensus pattern (14 bp):
AAATATAAAAAATC
Found at i:18151759 original size:6 final size:7
Alignment explanation
Indices: 18151741--18151774 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
18151731 TTTTGCTTTG
18151741 TATTTTA
1 TATTTTA
18151748 TATTTT-
1 TATTTTA
18151754 TATTTT-
1 TATTTTA
18151760 TATTTTA
1 TATTTTA
18151767 TATTTTA
1 TATTTTA
18151774 T
1 T
18151775 GTATATATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 12 0.46
7 14 0.54
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (7 bp):
TATTTTA
Found at i:18151817 original size:4 final size:4
Alignment explanation
Indices: 18151796--18151921 Score: 63
Period size: 4 Copynumber: 33.2 Consensus size: 4
18151786 CCTTTGTACC
* * *
18151796 TTAT GTAT TTAT TT-T TTAT TTAT TTA- TTAT TACTAT TTAT TAAT ATAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT T--TAT TTAT TTAT TTAT
* * * * * *
18151844 ATCT TTA- TTA- TTAT TT-T TTAT ATAT GTA- TT-T TTAT TTAT CTAG
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
* * *
18151887 TTAT ATAT TTA- TTA- TTAT TTAT TCAT TTAT ATAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT T
18151922 ATAATTTATC
Statistics
Matches: 92, Mismatches: 21, Indels: 18
0.70 0.16 0.14
Matches are distributed among these distances:
3 24 0.26
4 64 0.70
6 4 0.04
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (4 bp):
TTAT
Found at i:18151817 original size:11 final size:11
Alignment explanation
Indices: 18151796--18151923 Score: 88
Period size: 10 Copynumber: 11.6 Consensus size: 11
18151786 CCTTTGTACC
18151796 TTATGTATTTAT
1 TTAT-TATTTAT
*
18151808 TTTTTATTTAT
1 TTATTATTTAT
18151819 TTATTATTACTAT
1 TTATTATT--TAT
*
18151832 TTATTA-ATAT
1 TTATTATTTAT
* *
18151842 ATA-TCTTTA-
1 TTATTATTTAT
18151851 TTATTATTT-T
1 TTATTATTTAT
*
18151861 TTATATATGTAT
1 TTAT-TATTTAT
18151873 TT-TTATTTAT
1 TTATTATTTAT
* *
18151883 CTAGTTATATAT
1 TTA-TTATTTAT
18151895 TTATTA-TTAT
1 TTATTATTTAT
18151905 TTATTCATTTAT
1 TTATT-ATTTAT
*
18151917 ATATTAT
1 TTATTAT
18151924 AATTTATCTG
Statistics
Matches: 90, Mismatches: 15, Indels: 23
0.70 0.12 0.18
Matches are distributed among these distances:
9 3 0.03
10 30 0.33
11 25 0.28
12 23 0.26
13 9 0.10
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (11 bp):
TTATTATTTAT
Found at i:18151825 original size:26 final size:25
Alignment explanation
Indices: 18151796--18151921 Score: 105
Period size: 26 Copynumber: 4.9 Consensus size: 25
18151786 CCTTTGTACC
*
18151796 TTATGTATTTATTTTTTATTTATTTA
1 TTAT-TATTTATTTTTTATATATTTA
* *
18151822 TTATTA-CTATTTATTAATATATATCT-
1 TTATTATTTATTT-TT--TATATATTTA
*
18151848 TTATTA-TTATTTTTTATATATGTA
1 TTATTATTTATTTTTTATATATTTA
* **
18151872 TTTTTATTTATCTAGTTATATATTTA
1 TTATTATTTAT-TTTTTATATATTTA
*
18151898 TTATTATTTATTCATTTATATATT
1 TTATTATTTATT-TTTTATATATT
18151922 ATAATTTATC
Statistics
Matches: 82, Mismatches: 11, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
23 8 0.10
24 10 0.12
25 11 0.13
26 46 0.56
27 7 0.09
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (25 bp):
TTATTATTTATTTTTTATATATTTA
Found at i:18151882 original size:47 final size:49
Alignment explanation
Indices: 18151804--18151932 Score: 133
Period size: 47 Copynumber: 2.7 Consensus size: 49
18151794 CCTTATGTAT
* * *
18151804 TTATTTTTTATTTATTTATTATTACTATTTAT-TAATATATATCTTTATTA
1 TTATTTTTTATATATGTATTATTA-TATTTATCTAAT-TATATATTTATTA
*
18151854 TTATTTTTTATATATGTATT-TT-TATTTATCTAGTTATATATTTATTA
1 TTATTTTTTATATATGTATTATTATATTTATCTAATTATATATTTATTA
* * *
18151901 TTATTTATTCATTTATATATTA-TA-ATTTATCT
1 TTATTT-TTTATATATGTATTATTATATTTATCT
18151933 GTTATTATTA
Statistics
Matches: 68, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
47 25 0.37
48 23 0.34
49 2 0.03
50 18 0.26
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (49 bp):
TTATTTTTTATATATGTATTATTATATTTATCTAATTATATATTTATTA
Found at i:18151930 original size:26 final size:26
Alignment explanation
Indices: 18151860--18151930 Score: 76
Period size: 26 Copynumber: 2.7 Consensus size: 26
18151850 ATTATTATTT
18151860 TTTATATATGTAT-TTTTATTTATCTA
1 TTTATATAT-TATATTTTATTTATCTA
*
18151886 GTTATATATT-TATTATTATTTAT-TCA
1 TTTATATATTATATT-TTATTTATCT-A
*
18151912 TTTATATATTATAATTTAT
1 TTTATATATTATATTTTAT
18151931 CTGTTATTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
24 1 0.03
25 4 0.11
26 30 0.79
27 3 0.08
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (26 bp):
TTTATATATTATATTTTATTTATCTA
Found at i:18151988 original size:20 final size:19
Alignment explanation
Indices: 18151937--18151988 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
18151927 TTATCTGTTA
18151937 TTATTATTCTTTTATTTATC
1 TTATTATT-TTTTATTTATC
* * *
18151957 TTGTAATATTTTGATTTATC
1 TTATTAT-TTTTTATTTATC
18151977 TTATTATTTTTT
1 TTATTATTTTTT
18151989 TCTAATTATC
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
19 4 0.16
20 20 0.80
21 1 0.04
ACGTcount: A:0.21, C:0.06, G:0.04, T:0.69
Consensus pattern (19 bp):
TTATTATTTTTTATTTATC
Found at i:18151998 original size:22 final size:22
Alignment explanation
Indices: 18151972--18152034 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 22
18151962 ATATTTTGAT
18151972 TTATCTTATTATTTTTTTCTAA
1 TTATCTTATTATTTTTTTCTAA
*
18151994 TTATC-TATTAATATTTTTT-TAT
1 TTATCTTATT-AT-TTTTTTCTAA
*
18152016 TTATCTGATT-TTTTTTTCT
1 TTATCTTATTATTTTTTTCT
18152035 TTTTTTTTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
20 6 0.17
21 6 0.17
22 14 0.40
23 9 0.26
ACGTcount: A:0.21, C:0.08, G:0.02, T:0.70
Consensus pattern (22 bp):
TTATCTTATTATTTTTTTCTAA
Found at i:18152920 original size:18 final size:19
Alignment explanation
Indices: 18152887--18152922 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
18152877 CCAAATTTTT
*
18152887 TTTTGTTTTCTTTTTATTA
1 TTTTGATTTCTTTTTATTA
18152906 TTTTGATTT-TTTTTATT
1 TTTTGATTTCTTTTTATT
18152923 TTATTTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.11, C:0.03, G:0.06, T:0.81
Consensus pattern (19 bp):
TTTTGATTTCTTTTTATTA
Found at i:18152928 original size:14 final size:14
Alignment explanation
Indices: 18152883--18152941 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
18152873 CGTTCCAAAT
* *
18152883 TTTTTTTTGTTTTC
1 TTTTTTTTATTTTA
*
18152897 TTTTTATTATTTTGA
1 TTTTTTTTATTTT-A
18152912 TTTTTTTTATTTTA
1 TTTTTTTTATTTTA
*
18152926 -TTTATTTATTGTTA
1 TTTTTTTTATT-TTA
18152940 TT
1 TT
18152942 ATATTAGGGT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
13 9 0.24
14 15 0.41
15 13 0.35
ACGTcount: A:0.14, C:0.02, G:0.05, T:0.80
Consensus pattern (14 bp):
TTTTTTTTATTTTA
Found at i:18152991 original size:19 final size:19
Alignment explanation
Indices: 18152962--18153018 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
18152952 TGTTTAATAT
18152962 TTTTTTCTATTTTTTATTTA
1 TTTTTT-TATTTTTTATTTA
18152982 TTTTTTTA-TTTTTATTTTA
1 TTTTTTTATTTTTTA-TTTA
* * *
18153001 TTCTTATATATTTTATTT
1 TTTTTTTATTTTTTATTT
18153019 GTTTCATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
18 6 0.19
19 15 0.47
20 11 0.34
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTTTTATTTTTTATTTA
Found at i:18153217 original size:59 final size:58
Alignment explanation
Indices: 18153056--18153519 Score: 413
Period size: 59 Copynumber: 7.7 Consensus size: 58
18153046 AAACAAAAAA
* * * * *
18153056 CAAAAAAACATTTTT-GAGGAAAAGTTGAAAGTATTAATTTTTTTTAAGAA-TAAATTTT
1 CAAAAAAAAATTTTTAG-GGAAAAGTTGAAAGTATCAATTTTTCTCAA-AATTAAAATTT
* *
18153114 CAAAAAAAGATTTTCTTTTTTA-GAAAAAGTTGAAAGTATCAATTTTTCTCAAAATTAAAAATTT
1 CAAAAAAA-A-----ATTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTCAAAATT-AAAATTT
* * * * *
18153178 -AAAAAATATATTTTTAGGGAAAAGTTGAAAGTATTAATTTTCCTCGAAATTAAGAATTC
1 CAAAAAA-AAATTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTCAAAATTAA-AATTT
* * * *
18153237 CAAAAAAAAAAATTTTTAGAGAAAAGTTGAAAGTATCAATTTTCCTTAAGAA-TAAATTTT
1 C--AAAAAAAAATTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTCAA-AATTAAAATTT
** * * * *
18153297 CAAAAAAAGTTTTTTTGAGGAAAAGTCGAAAGTATCAATTTTCCTCGAAATTAAAATTTT
1 CAAAAAAAAATTTTTAG-GGAAAAGTTGAAAGTATCAATTTTTCTCAAAATTAAAA-TTT
* *
18153357 C-AAAAAAAATTTTT-GGAAAAAAGTTGAAAGTATCAATTTTTCTTAAAGA-TAAAATTT
1 CAAAAAAAAATTTTTAGG-GAAAAGTTGAAAGTATCAATTTTTCTCAAA-ATTAAAATTT
* *
18153414 CAAAAAAAAAGGTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTCAAAATTAAAGTTT
1 CAAAAAAAAA---TTTTTAG-GGAAAAGTTGAAAGTATCAATTTTTCTCAAAATTAAAATTT
*
18153476 CCAAAAAAAAATATTTTGGGGAAAAGTTGAAAGTATCAATTTTT
1 -CAAAAAAAAAT-TTTTAGGGAAAAGTTGAAAGTATCAATTTTT
18153520 TCTTGTACAA
Statistics
Matches: 336, Mismatches: 40, Indels: 58
0.77 0.09 0.13
Matches are distributed among these distances:
57 5 0.01
58 70 0.21
59 76 0.23
60 34 0.10
61 49 0.15
62 46 0.14
63 44 0.13
64 12 0.04
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.36
Consensus pattern (58 bp):
CAAAAAAAAATTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTCAAAATTAAAATTT
Found at i:18153276 original size:120 final size:118
Alignment explanation
Indices: 18153130--18153519 Score: 472
Period size: 120 Copynumber: 3.3 Consensus size: 118
18153120 AAGATTTTCT
*
18153130 TTTTTAGA-AAAAGTTGAAAGTATCAATTTTTCTCAAAATTAAAAATTT-AAAAAATATATTTTT
1 TTTTTAGAGAAAAGTTGAAAGTATCAATTTTTCTTAAAA-T-AAAATTTCAAAAAA-ATATTTTT
* *
18153193 AG-GGAAAAGTTGAAAGTATTAATTTTCCTCGAAATTAAGAATTCCAAAAAAAAAAA
63 TGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAA-AATTCCAAAAAAAAAAA
* *
18153249 TTTTTAGAGAAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAATTTTCAAAAAAAGT-TTTTTT
1 TTTTTAGAGAAAAGTTGAAAGTATCAATTTTTCTTAA-AATAAAATTTCAAAAAAA-TATTTTTT
* *
18153313 GAGGAAAAGTCGAAAGTATCAATTTTCCTCGAAATTAAAATTTTC---AAAAAAAA
64 GAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAA-TTCCAAAAAAAAAAA
* * *
18153366 TTTTTGGAAAAAAGTTGAAAGTATCAATTTTTCTTAAAGATAAAATTTCAAAAAAAAAGGTTTTT
1 TTTTTAGAGAAAAGTTGAAAGTATCAATTTTTCTTAAA-ATAAAATTTCAAAAAAATA---TTTT
* * * *
18153431 TTGAGGAAAAGTTGAAAGTATCAATTTTTCTCAAAATTAAAGTTTCCAAAAAAAAATA
62 TTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAA-ATTCCAAAAAAAAAAA
* *
18153489 -TTTTGGGGAAAAGTTGAAAGTATCAATTTTT
1 TTTTTAGAGAAAAGTTGAAAGTATCAATTTTT
18153520 TCTTGTACAA
Statistics
Matches: 236, Mismatches: 20, Indels: 27
0.83 0.07 0.10
Matches are distributed among these distances:
116 1 0.00
117 58 0.25
119 23 0.10
120 116 0.49
121 2 0.01
122 29 0.12
123 7 0.03
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.35
Consensus pattern (118 bp):
TTTTTAGAGAAAAGTTGAAAGTATCAATTTTTCTTAAAATAAAATTTCAAAAAAATATTTTTTGA
GGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAATTCCAAAAAAAAAAA
Found at i:18155346 original size:22 final size:23
Alignment explanation
Indices: 18155321--18155363 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
18155311 TAATTTAAAT
18155321 CTTTT-TTTCTTTTTTTTTTTGC
1 CTTTTGTTTCTTTTTTTTTTTGC
*
18155343 CTTTTGTTTTTTTTTTTTTTT
1 CTTTTGTTTCTTTTTTTTTTT
18155364 TTTGCACATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.00, C:0.09, G:0.05, T:0.86
Consensus pattern (23 bp):
CTTTTGTTTCTTTTTTTTTTTGC
Found at i:18158282 original size:17 final size:19
Alignment explanation
Indices: 18158255--18158290 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
18158245 TTCATATATA
18158255 TATATTAAAAATAA-AATT
1 TATATTAAAAATAACAATT
18158273 TATA-TAAAAATAACAATT
1 TATATTAAAAATAACAATT
18158291 AAGTTTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (19 bp):
TATATTAAAAATAACAATT
Found at i:18158345 original size:31 final size:30
Alignment explanation
Indices: 18158303--18158383 Score: 99
Period size: 31 Copynumber: 2.7 Consensus size: 30
18158293 GTTTAATAAA
* * * *
18158303 ATATATATAATTTATTTTTAATTTATATAT
1 ATATAAATAATTTATATATAATTCATATAT
* *
18158333 ATGTGAATTAATTTATATATAATTCATATAT
1 ATAT-AAATAATTTATATATAATTCATATAT
18158364 ATATAAATAATTTATATATA
1 ATATAAATAATTTATATATA
18158384 TGTGAATTCA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
30 18 0.43
31 24 0.57
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.52
Consensus pattern (30 bp):
ATATAAATAATTTATATATAATTCATATAT
Found at i:18158364 original size:15 final size:15
Alignment explanation
Indices: 18158321--18158383 Score: 63
Period size: 15 Copynumber: 4.1 Consensus size: 15
18158311 AATTTATTTT
* *
18158321 TAATTTATATATATG
1 TAATTAATATATATA
*
18158336 TGAATTAATTTATATA
1 T-AATTAATATATATA
*
18158352 TAATTCATATATATA
1 TAATTAATATATATA
* *
18158367 TAAATAATTTATATA
1 TAATTAATATATATA
18158382 TA
1 TA
18158384 TGTGAATTCA
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
15 27 0.69
16 12 0.31
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (15 bp):
TAATTAATATATATA
Found at i:18158373 original size:19 final size:19
Alignment explanation
Indices: 18158346--18158384 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
18158336 TGAATTAATT
*
18158346 TATATATAATTCATATATA
1 TATAAATAATTCATATATA
*
18158365 TATAAATAATTTATATATA
1 TATAAATAATTCATATATA
18158384 T
1 T
18158385 GTGAATTCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (19 bp):
TATAAATAATTCATATATA
Found at i:18160448 original size:18 final size:17
Alignment explanation
Indices: 18160416--18160449 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
18160406 GTGCTTAGGT
18160416 TAGTCGACCTATCAACA
1 TAGTCGACCTATCAACA
*
18160433 TAGTCTACCATATCAAC
1 TAGTCGACC-TATCAAC
18160450 TTAAACCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.35, C:0.29, G:0.09, T:0.26
Consensus pattern (17 bp):
TAGTCGACCTATCAACA
Found at i:18161634 original size:56 final size:56
Alignment explanation
Indices: 18161499--18161634 Score: 148
Period size: 56 Copynumber: 2.4 Consensus size: 56
18161489 AATGGTCAAT
** * *
18161499 CTAAGCCTTTATAAAAGTAATTTATTAAAACAAGCTTTTAGGTCGAGGTGACCGAG
1 CTAAGCCTTTATAAAAGTAATTTGCTAAAACAAGCTTTTAGGTCAAAGTGACCGAG
* * * * * * *
18161555 CTGAGCCTTTATGAAAGCAATTTGCTGAGACAAGCCTTTT-GGTCAAAGTGACTGTG
1 CTAAGCCTTTATAAAAGTAATTTGCTAAAACAAG-CTTTTAGGTCAAAGTGACCGAG
*
18161611 CTAAGCCTTTTTAAAAGTAATTTG
1 CTAAGCCTTTATAAAAGTAATTTG
18161635 TCAAGATAAG
Statistics
Matches: 64, Mismatches: 15, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
56 59 0.92
57 5 0.08
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (56 bp):
CTAAGCCTTTATAAAAGTAATTTGCTAAAACAAGCTTTTAGGTCAAAGTGACCGAG
Found at i:18162564 original size:32 final size:32
Alignment explanation
Indices: 18162528--18162590 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
18162518 TATAACACAT
* *
18162528 AATTTTTATATAAAATATAATATAAATATATA
1 AATTTTAATATAAAATATAATACAAATATATA
***
18162560 AATTTTAATATTTTATATAATACAAATATAT
1 AATTTTAATATAAAATATAATACAAATATAT
18162591 GAAACGTCAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (32 bp):
AATTTTAATATAAAATATAATACAAATATATA
Found at i:18170705 original size:20 final size:19
Alignment explanation
Indices: 18170677--18170717 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
18170667 TAACAACAAG
*
18170677 AAAGCAACAGAGAAACTTGA
1 AAAGAAACAGAGAAAC-TGA
*
18170697 AAAGAAACAGAGTAACTGA
1 AAAGAAACAGAGAAACTGA
18170716 AA
1 AA
18170718 GATATGGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.59, C:0.12, G:0.20, T:0.10
Consensus pattern (19 bp):
AAAGAAACAGAGAAACTGA
Found at i:18173380 original size:2 final size:2
Alignment explanation
Indices: 18173373--18173414 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
18173363 GAATATTCAA
18173373 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
18173415 ACACACACAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:18173419 original size:2 final size:2
Alignment explanation
Indices: 18173414--18173443 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
18173404 CTCTCTCTCT
18173414 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
18173444 TGCTATTTCT
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:18179854 original size:7 final size:7
Alignment explanation
Indices: 18179844--18179871 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
18179834 ACGAACCTTA
18179844 AACCTCG
1 AACCTCG
18179851 AACCTCG
1 AACCTCG
18179858 AACCTCG
1 AACCTCG
18179865 AACCTCG
1 AACCTCG
18179872 CTCTGATACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.43, G:0.14, T:0.14
Consensus pattern (7 bp):
AACCTCG
Found at i:18179854 original size:14 final size:14
Alignment explanation
Indices: 18179835--18179870 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
18179825 CTTGGACCCA
*
18179835 CGAACCTTAAACCT
1 CGAACCTCAAACCT
*
18179849 CGAACCTCGAACCT
1 CGAACCTCAAACCT
18179863 CGAACCTC
1 CGAACCTC
18179871 GCTCTGATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.42, G:0.11, T:0.17
Consensus pattern (14 bp):
CGAACCTCAAACCT
Found at i:18192911 original size:16 final size:15
Alignment explanation
Indices: 18192872--18192908 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
18192862 ACCCAAATGG
*
18192872 TAAAAAATTTAGAAA
1 TAAAAAATTAAGAAA
*
18192887 TAAAAAATTAATAAA
1 TAAAAAATTAAGAAA
18192902 TAAAAAA
1 TAAAAAA
18192909 ATTTTCTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (15 bp):
TAAAAAATTAAGAAA
Found at i:18196622 original size:12 final size:12
Alignment explanation
Indices: 18196601--18196632 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
18196591 TATCAAAAAG
18196601 TAAAAA-AATTT
1 TAAAAATAATTT
18196612 TAAAAATAATTT
1 TAAAAATAATTT
18196624 TAAAAATAA
1 TAAAAATAA
18196633 AAACACCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
TAAAAATAATTT
Found at i:18204146 original size:18 final size:18
Alignment explanation
Indices: 18204112--18204145 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
18204102 TAACACACAC
18204112 AAAAAAATAAAATAAAAT
1 AAAAAAATAAAATAAAAT
18204130 AAAAAAAT-AAATAAAA
1 AAAAAAATAAAATAAAA
18204146 ACTAGAGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (18 bp):
AAAAAAATAAAATAAAAT
Found at i:18213757 original size:12 final size:13
Alignment explanation
Indices: 18213742--18213770 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
18213732 ATTTTAATAT
18213742 AATT-TATTTTAA
1 AATTGTATTTTAA
18213754 AATTGTATTTTAA
1 AATTGTATTTTAA
18213767 AATT
1 AATT
18213771 AATTCAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.25
13 12 0.75
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.55
Consensus pattern (13 bp):
AATTGTATTTTAA
Found at i:18215996 original size:10 final size:10
Alignment explanation
Indices: 18215981--18216009 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
18215971 TGTGTTTGAA
18215981 GTCGAGCCGC
1 GTCGAGCCGC
18215991 GTCGAGCCGC
1 GTCGAGCCGC
18216001 GTCGAGCCG
1 GTCGAGCCG
18216010 TTTCATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.10, C:0.38, G:0.41, T:0.10
Consensus pattern (10 bp):
GTCGAGCCGC
Found at i:18216198 original size:22 final size:20
Alignment explanation
Indices: 18216144--18216198 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 20
18216134 ATCCAATGAT
18216144 GAAATTTATAAAAATTTTAATG
1 GAAATTTAT--AAATTTTAATG
*
18216166 GAACATATATAAATTTTAAATG
1 GAA-ATTTATAAATTTT-AATG
18216188 GTAAATTTATA
1 G-AAATTTATA
18216199 TAAATTCTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
21 7 0.25
22 14 0.50
23 7 0.25
ACGTcount: A:0.49, C:0.02, G:0.09, T:0.40
Consensus pattern (20 bp):
GAAATTTATAAATTTTAATG
Found at i:18222802 original size:14 final size:15
Alignment explanation
Indices: 18222769--18222810 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
18222759 ATTAACACTT
*
18222769 CTTTTTTCTTTTCTA
1 CTTTTTTATTTTCTA
*
18222784 ATTTTTTATTTT-TA
1 CTTTTTTATTTTCTA
18222798 CTTTTTTAATTTT
1 CTTTTTT-ATTTT
18222811 GAACAATTGG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 8 0.35
15 15 0.65
ACGTcount: A:0.14, C:0.10, G:0.00, T:0.76
Consensus pattern (15 bp):
CTTTTTTATTTTCTA
Done.