Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007713.1 Hibiscus syriacus cultivar Beakdansim tig00109937_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: 584604
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:453143 original size:33 final size:33
Alignment explanation
Indices: 453102--453176 Score: 98
Period size: 33 Copynumber: 2.3 Consensus size: 33
453092 GCGACCTACC
* * *
453102 CTCGCTCGGCTT-CCCTCGGATTCCCTCGCATAG
1 CTCGCTCGG-TTGCCCTAGGATGCCCTCACATAG
453135 CTCGCTCGGTTGCCCTAGGATGCCCTCACATAG
1 CTCGCTCGGTTGCCCTAGGATGCCCTCACATAG
*
453168 CTCGTTCGG
1 CTCGCTCGG
453177 ATGGCCTCGG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
32 2 0.05
33 35 0.95
ACGTcount: A:0.11, C:0.39, G:0.24, T:0.27
Consensus pattern (33 bp):
CTCGCTCGGTTGCCCTAGGATGCCCTCACATAG
Found at i:453226 original size:14 final size:14
Alignment explanation
Indices: 453207--453246 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
453197 TCGGATGCTC
*
453207 TCGGATGGCCTCGG
1 TCGGATGGCCTCGA
453221 TCGGATGGCCTCGA
1 TCGGATGGCCTCGA
*
453235 TCGGATAGCCTC
1 TCGGATGGCCTC
453247 AGATGCCCAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.12, C:0.30, G:0.35, T:0.23
Consensus pattern (14 bp):
TCGGATGGCCTCGA
Found at i:453328 original size:29 final size:29
Alignment explanation
Indices: 453291--453348 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
453281 GCAATCTCTT
*
453291 GTAGCTCGCCGGGAAGACATGGCGACCTA
1 GTAGCTCGCCCGGAAGACATGGCGACCTA
* *
453320 GTAGGTCGCCCGGAAGGCATGGCGACCTA
1 GTAGCTCGCCCGGAAGACATGGCGACCTA
453349 CGGCCAACAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.22, C:0.28, G:0.36, T:0.14
Consensus pattern (29 bp):
GTAGCTCGCCCGGAAGACATGGCGACCTA
Found at i:458306 original size:17 final size:18
Alignment explanation
Indices: 458284--458320 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
458274 ATAAAAAAAA
458284 TATTATAATTTTTTA-TT
1 TATTATAATTTTTTAGTT
458301 TATTATAATTTTTTAGTT
1 TATTATAATTTTTTAGTT
458319 TA
1 TA
458321 GAGAGGTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (18 bp):
TATTATAATTTTTTAGTT
Found at i:461256 original size:14 final size:14
Alignment explanation
Indices: 461237--461267 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
461227 ATAAAATTAA
461237 ATGTTGAATGCTTG
1 ATGTTGAATGCTTG
*
461251 ATGTTGAATGTTTG
1 ATGTTGAATGCTTG
461265 ATG
1 ATG
461268 ATTTAGATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.03, G:0.29, T:0.45
Consensus pattern (14 bp):
ATGTTGAATGCTTG
Found at i:461344 original size:3 final size:3
Alignment explanation
Indices: 461336--461360 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
461326 GTATCTTGAA
461336 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
461361 TATGTATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:461707 original size:15 final size:15
Alignment explanation
Indices: 461687--461716 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
461677 TTAAAAAATT
461687 TAATAGAAACTATTG
1 TAATAGAAACTATTG
461702 TAATAGAAACTATTG
1 TAATAGAAACTATTG
461717 ATGTGTCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.07, G:0.13, T:0.33
Consensus pattern (15 bp):
TAATAGAAACTATTG
Found at i:462259 original size:14 final size:14
Alignment explanation
Indices: 462240--462267 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
462230 AATACGCAAT
462240 TAAAGGTAATCAAC
1 TAAAGGTAATCAAC
462254 TAAAGGTAATCAAC
1 TAAAGGTAATCAAC
462268 ACGCACCCGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.14, G:0.14, T:0.21
Consensus pattern (14 bp):
TAAAGGTAATCAAC
Found at i:466843 original size:3 final size:3
Alignment explanation
Indices: 466835--466861 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
466825 TCCCTTCTTT
466835 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
466862 ATTTTTGTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:468878 original size:33 final size:33
Alignment explanation
Indices: 468836--468933 Score: 108
Period size: 33 Copynumber: 3.0 Consensus size: 33
468826 CGAAGGCGAC
* * *
468836 GAAGAAATCGATTTTGTGGGCTGCTTT-GGCGTA
1 GAAGAAATCGATTTTCT-GGCCGCTTTCGGCGGA
* * *
468869 GAAGAAATCGATTGTCTGGCCGGTTTCGGCGGC
1 GAAGAAATCGATTTTCTGGCCGCTTTCGGCGGA
* *
468902 GAAGAAATCGATTTTCTGGCCGATTTCAGCGG
1 GAAGAAATCGATTTTCTGGCCGCTTTCGGCGG
468934 CGAAAGGAAG
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
32 7 0.13
33 48 0.87
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (33 bp):
GAAGAAATCGATTTTCTGGCCGCTTTCGGCGGA
Found at i:468934 original size:33 final size:33
Alignment explanation
Indices: 468869--468937 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
468859 CTTTGGCGTA
* *
468869 GAAGAAATCGATTGTCTGGCCGGTTTCGGCGGC
1 GAAGAAATCGATTGTCTGGCCGATTTCAGCGGC
*
468902 GAAGAAATCGATTTTCTGGCCGATTTCAGCGGC
1 GAAGAAATCGATTGTCTGGCCGATTTCAGCGGC
468935 GAA
1 GAA
468938 AGGAAGACCC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.25
Consensus pattern (33 bp):
GAAGAAATCGATTGTCTGGCCGATTTCAGCGGC
Found at i:469732 original size:18 final size:18
Alignment explanation
Indices: 469705--469746 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
469695 TTTTTTAAGG
*
469705 GAATTAGAATCCCCGATA
1 GAATTGGAATCCCCGATA
* *
469723 GAATTGGAATCCCTGATG
1 GAATTGGAATCCCCGATA
469741 GAATTG
1 GAATTG
469747 AATTCCATCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (18 bp):
GAATTGGAATCCCCGATA
Found at i:470317 original size:216 final size:212
Alignment explanation
Indices: 469868--470646 Score: 1049
Period size: 216 Copynumber: 3.7 Consensus size: 212
469858 CTTATTCATA
* * *
469868 TATTGAATAAAAATATTTTTTTATTA-TT---TCGGGTCGGGTCGGGTTTCTAATTCATATATTC
1 TATTAAATAAAAATAATTTTTTATTATTTCGGTCGGGTCGGGTCGGATTTCTAATTCATATATTC
* * **
469929 GGGTC--G--GG-TGAAACTTTATTTTAATCTGGTCGAATCGGGTTTTTTTAAGTGTGATATTCT
66 GGGTCGGGTCGGATGAAACTTTATTTT-GTTTGGTCGGGTCGGG-TTTTTTAAGTGTGATATTC-
469989 GGTTGGGTCGGGTCAGGTTCGGGTTTAGGGTG-AAAAAACCGGACCGA-CCGAAAATATATATAA
128 ----GGGTC--G---GGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATAA
470052 TTCAGATC-GGTCGGATTAAGTCACTGTTTT
184 TTC-G-TCGGGTCGGATTAAGTCACTGTTTT
** *
470082 TATTAAATAAAAATAATTTTTTATTATTTCGGATCGGGTCGGGTTTGATTTCTAATTTATATATT
1 TATTAAATAAAAATAATTTTTTATTATTTCGG-TCGGGTCGGGTCGGATTTCTAATTCATATATT
*
470147 CGGGTCGGGTCGGATGAAACTTTATTTTGTTTGGGTCGGGTCGGGTTTTTTAATTGTGATATTCG
65 CGGGTCGGGTCGGATGAAACTTTATTTTGTTT-GGTCGGGTCGGGTTTTTTAAGTGTGATATTCG
*
470212 GGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCTACCCGAAAATATATATAATTCGGGTCGG
129 GGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATTC--GTCGG
470277 GTCGGATTAAGTCACTGTTTT
192 GTCGGATTAAGTCACTGTTTT
470298 TATTAAATAAAAATAATTTTTTATTATTTCGTGTCGGGTCGGGTCGGATTTCTAATTCATATATT
1 TATTAAATAAAAATAATTTTTTATTATTTCG-GTCGGGTCGGGTCGGATTTCTAATTCATATATT
* * * *
470363 TGGGTTGGGTCGGGTGAAACTTTATTTTGTTCAGGTCGGGTCGGGTTTTTTAAGTGTGATATTCG
65 CGGGTCGGGTCGGATGAAACTTTATTTTGTT-TGGTCGGGTCGGGTTTTTTAAGTGTGATATTCG
470428 GGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATAA-T--TCGGGT
129 GGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATTCGTCGGGT
470490 CGGATTAAGTCACTGTTTT
194 CGGATTAAGTCACTGTTTT
470509 TATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGGTCGGGTCGGATTTCTAATTCATATATT
1 TATTAAATAAAAATAATTTTTTATTATTTC-GGTCGGGTCGGGTCGGATTTCTAATTCATATATT
* * *
470574 CAGGTCGGGTCGGATGAAGCTTTATTTTG--T--TCGGGTCGGGTTTTTTAAGTGTGATATTCGA
65 CGGGTCGGGTCGGATGAAACTTTATTTTGTTTGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGG
*
470635 GTCGAG-TCGGGT
130 GTCGGGTTCGGGT
470647 CGGGTTTTTT
Statistics
Matches: 517, Mismatches: 30, Indels: 45
0.87 0.05 0.08
Matches are distributed among these distances:
205 6 0.01
206 35 0.07
211 112 0.22
212 1 0.00
213 17 0.03
214 38 0.07
215 24 0.05
216 197 0.38
217 1 0.00
218 5 0.01
219 34 0.07
221 1 0.00
223 22 0.04
224 24 0.05
ACGTcount: A:0.24, C:0.12, G:0.26, T:0.38
Consensus pattern (212 bp):
TATTAAATAAAAATAATTTTTTATTATTTCGGTCGGGTCGGGTCGGATTTCTAATTCATATATTC
GGGTCGGGTCGGATGAAACTTTATTTTGTTTGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGG
TCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATTCGTCGGGTCG
GATTAAGTCACTGTTTT
Found at i:470665 original size:38 final size:38
Alignment explanation
Indices: 470604--470690 Score: 135
Period size: 38 Copynumber: 2.3 Consensus size: 38
470594 TTTATTTTGT
470604 TCGGGTCGGG-TTTTTTAAGTGTGATATTC-GAGTC-GAG
1 TCGGGTCGGGTTTTTTTAAGTGTGATATTCAG-GTCAG-G
470641 TCGGGTCGGGTTTTTTTAAGTGTGATATTCAGGTCAGG
1 TCGGGTCGGGTTTTTTTAAGTGTGATATTCAGGTCAGG
470679 TCGGGTCGGGTT
1 TCGGGTCGGGTT
470691 CCATATTGAA
Statistics
Matches: 47, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
37 10 0.21
38 35 0.74
39 2 0.04
ACGTcount: A:0.14, C:0.11, G:0.37, T:0.38
Consensus pattern (38 bp):
TCGGGTCGGGTTTTTTTAAGTGTGATATTCAGGTCAGG
Found at i:471663 original size:33 final size:33
Alignment explanation
Indices: 471621--471691 Score: 142
Period size: 33 Copynumber: 2.2 Consensus size: 33
471611 TCTCTGACTC
471621 ATCTCTTCGAATGACACCATTTCAATGCATTAA
1 ATCTCTTCGAATGACACCATTTCAATGCATTAA
471654 ATCTCTTCGAATGACACCATTTCAATGCATTAA
1 ATCTCTTCGAATGACACCATTTCAATGCATTAA
471687 ATCTC
1 ATCTC
471692 GATATTCATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.32, C:0.25, G:0.08, T:0.34
Consensus pattern (33 bp):
ATCTCTTCGAATGACACCATTTCAATGCATTAA
Found at i:472637 original size:43 final size:44
Alignment explanation
Indices: 472544--472750 Score: 210
Period size: 43 Copynumber: 4.8 Consensus size: 44
472534 AAACAAAAAG
* * * ** *
472544 CGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTTTAGATAAA
1 CGCCGCAGTAGGTGTTGATGTTTAGCGGCGTTTTTCTCCACAAA
* * * *
472588 TGCCGCAATA-GTTTATGATGTTTAGCGGCGTTTTTCTCTA-AAA
1 CGCCGCAGTAGGTGT-TGATGTTTAGCGGCGTTTTTCTCCACAAA
*
472631 CGCCGCAGTAGGTGTTGATGTTTTGCGGCG-TTTTC-CCACAAA
1 CGCCGCAGTAGGTGTTGATGTTTAGCGGCGTTTTTCTCCACAAA
*
472673 CGCCGCAGTAGGTGTTGATGTTTTA-CGACGTTTTT-TCCACAAA
1 CGCCGCAGTAGGTGTTGATG-TTTAGCGGCGTTTTTCTCCACAAA
* * * *
472716 CGCCGTAGTAGGTTTTGATGTTTTGCAGCGTTTTT
1 CGCCGCAGTAGGTGTTGATGTTTAGCGGCGTTTTT
472751 GCTAAAAACG
Statistics
Matches: 138, Mismatches: 18, Indels: 15
0.81 0.11 0.09
Matches are distributed among these distances:
41 2 0.01
42 35 0.25
43 68 0.49
44 33 0.24
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (44 bp):
CGCCGCAGTAGGTGTTGATGTTTAGCGGCGTTTTTCTCCACAAA
Found at i:473159 original size:21 final size:21
Alignment explanation
Indices: 473121--473173 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
473111 CTGCTGATAT
*
473121 GCTGCTTCTCTTTGTGCTGCC
1 GCTGCTTCTCTTTCTGCTGCC
*
473142 GCTGCTTCT-TTCTCTGCTTCC
1 GCTGCTTCTCTT-TCTGCTGCC
* *
473163 ACTGCTACTCT
1 GCTGCTTCTCT
473174 GGTTGCTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 2 0.08
21 23 0.88
22 1 0.04
ACGTcount: A:0.04, C:0.36, G:0.17, T:0.43
Consensus pattern (21 bp):
GCTGCTTCTCTTTCTGCTGCC
Found at i:473188 original size:21 final size:21
Alignment explanation
Indices: 473155--473224 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
473145 GCTTCTTTCT
** *
473155 CTGCTTCCACTGCTACTCTGG
1 CTGCTTCTGCTGCTGCTCTGG
* *
473176 TTGCTTTTGCTGCTGCTCTGG
1 CTGCTTCTGCTGCTGCTCTGG
**
473197 CTGCTTCTGCTGCTGCTCTCT
1 CTGCTTCTGCTGCTGCTCTGG
473218 CTGCTTC
1 CTGCTTC
473225 CCTTGCTTCA
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.03, C:0.34, G:0.21, T:0.41
Consensus pattern (21 bp):
CTGCTTCTGCTGCTGCTCTGG
Found at i:478981 original size:21 final size:23
Alignment explanation
Indices: 478951--479002 Score: 65
Period size: 21 Copynumber: 2.4 Consensus size: 23
478941 TATCACACAT
*
478951 AAAATATAAATGTATA-ATA-TA
1 AAAATATAAATATATATATATTA
*
478972 AAAATTTAAATATATATATATTA
1 AAAATATAAATATATATATATTA
478995 AAAA-ATAA
1 AAAATATAA
479003 TCATCAGTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 14 0.54
22 6 0.23
23 6 0.23
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (23 bp):
AAAATATAAATATATATATATTA
Found at i:480172 original size:30 final size:30
Alignment explanation
Indices: 480136--480199 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
480126 CTCATAATTT
480136 TGGGTTCAATTTTGTGTAGCTGGTGAGCCC
1 TGGGTTCAATTTTGTGTAGCTGGTGAGCCC
480166 TGGGTTCAATTTTGTGTAGCTGGTGAGCCC
1 TGGGTTCAATTTTGTGTAGCTGGTGAGCCC
480196 TGGG
1 TGGG
480200 GCATGGTTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.12, C:0.16, G:0.36, T:0.36
Consensus pattern (30 bp):
TGGGTTCAATTTTGTGTAGCTGGTGAGCCC
Found at i:482256 original size:41 final size:41
Alignment explanation
Indices: 482211--482288 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 41
482201 GCATTTTTCT
* *
482211 ACAAACGCC-GCTAAAGTACATGGATATTGCGGCGTTTGATC
1 ACAAACGCCAGAT-AAGTACAAGGATATTGCGGCGTTTGATC
*
482252 ACAAACGCCAGATAAGTACAAGGCTATTGCGGCGTTT
1 ACAAACGCCAGATAAGTACAAGGATATTGCGGCGTTT
482289 TCGCACAACA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
41 31 0.94
42 2 0.06
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.23
Consensus pattern (41 bp):
ACAAACGCCAGATAAGTACAAGGATATTGCGGCGTTTGATC
Found at i:482612 original size:82 final size:82
Alignment explanation
Indices: 482514--482700 Score: 214
Period size: 82 Copynumber: 2.3 Consensus size: 82
482504 TTTGTTTGAT
** * * * * *
482514 AAACGCCGCTAAATTACTTCTCAATAGTGTCGTTTGTTGAACAAATGACTCTATAAACAACACTA
1 AAACGCCGCTAAATTACCACTCAATAGCGGCGTTTGTTGAAAAAACGACACTATAAACAACACTA
*
482579 TCGTGGCGTTTGTA-TAA
66 TCGCGGCGTTTG-ACTAA
* * * *
482596 AAACGCCGCTAAATTACCACTCTATTGCGGCGTTTGTTGAAAAAACGCCACTATAAACAACTCTA
1 AAACGCCGCTAAATTACCACTCAATAGCGGCGTTTGTTGAAAAAACGACACTATAAACAACACTA
* * *
482661 TTGCGTCGTTTGAGCTAT
66 TCGCGGCGTTTGA-CTAA
482679 AAACGCCGCTAAATTACCACTC
1 AAACGCCGCTAAATTACCACTC
482701 TATTGCGGTG
Statistics
Matches: 88, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 1 0.01
82 63 0.72
83 24 0.27
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.29
Consensus pattern (82 bp):
AAACGCCGCTAAATTACCACTCAATAGCGGCGTTTGTTGAAAAAACGACACTATAAACAACACTA
TCGCGGCGTTTGACTAA
Found at i:482628 original size:41 final size:41
Alignment explanation
Indices: 482583--482732 Score: 155
Period size: 41 Copynumber: 3.6 Consensus size: 41
482573 ACACTATCGT
*
482583 GGCGTTTGTATAAAAACGCCGCTAAATTACCACTCTATTGC
1 GGCGTTTGTATAAAAACGCCACTAAATTACCACTCTATTGC
*
482624 GGCGTTTGT-TGAAAAAACGCCACTATAA--ACAACTCTATTGC
1 GGCGTTTGTAT--AAAAACGCCACTA-AATTACCACTCTATTGC
* * *
482665 GTCGTTTG-AGCTATAAACGCCGCTAAATTACCACTCTATTGC
1 GGCGTTTGTA--TAAAAACGCCACTAAATTACCACTCTATTGC
* * *
482707 GGTGTTTATTTAAAAACGCCACTAAA
1 GGCGTTTGTATAAAAACGCCACTAAA
482733 GTATCATTTT
Statistics
Matches: 88, Mismatches: 12, Indels: 18
0.75 0.10 0.15
Matches are distributed among these distances:
40 3 0.03
41 53 0.60
42 29 0.33
43 3 0.03
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (41 bp):
GGCGTTTGTATAAAAACGCCACTAAATTACCACTCTATTGC
Found at i:482724 original size:82 final size:81
Alignment explanation
Indices: 482387--482730 Score: 282
Period size: 83 Copynumber: 4.2 Consensus size: 81
482377 GGCGTTTTTA
* * * * * * **
482387 TAAAAACGACACGATAAACAA-TGTATTGCGGCGTTTGTGGGACAAACGCCGCTAAATTATTACT
1 TAAAAACGCCACTATAAACAACTCTATTGCGGCGTTTG-AGTATAAACGCCGCTAAATTACCACT
* *
482451 CTATTACGGTGTTTTTT
65 CTATTGCGGTGTTTGTT
* * * ** *
482468 TACAGAAACACCACTATAAACAAAC-CTTTTGCGACGTTTGTTTGATAAACGCCGCTAAATTACT
1 TA-A-AAACGCCACTATAAAC-AACTCTATTGCGGCGTTTGAGT-ATAAACGCCGCTAAATTACC
* * * *
482532 TCTCAATAG-TGTCGTTTGTT
62 ACTCTATTGCGGT-GTTTGTT
* * * * * * * *
482552 GAACAAATGACTCTATAAACAACACTATCGTGGCGTTTGTA-TAAAAACGCCGCTAAATTACCAC
1 TAA-AAACGCCACTATAAACAACTCTATTGCGGCGTTTG-AGTATAAACGCCGCTAAATTACCAC
*
482616 TCTATTGCGGCGTTTGTT
64 TCTATTGCGGTGTTTGTT
* *
482634 GAAAAAACGCCACTATAAACAACTCTATTGCGTCGTTTGAGCTATAAACGCCGCTAAATTACCAC
1 -TAAAAACGCCACTATAAACAACTCTATTGCGGCGTTTGAG-TATAAACGCCGCTAAATTACCAC
*
482699 TCTATTGCGGTGTTTATT
64 TCTATTGCGGTGTTTGTT
482717 TAAAAACGCCACTA
1 TAAAAACGCCACTA
482731 AAGTATCATT
Statistics
Matches: 204, Mismatches: 47, Indels: 23
0.74 0.17 0.08
Matches are distributed among these distances:
81 3 0.01
82 76 0.37
83 81 0.40
84 44 0.22
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (81 bp):
TAAAAACGCCACTATAAACAACTCTATTGCGGCGTTTGAGTATAAACGCCGCTAAATTACCACTC
TATTGCGGTGTTTGTT
Found at i:486000 original size:23 final size:22
Alignment explanation
Indices: 485940--486008 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 22
485930 CATTTTAGTA
*
485940 AAAATATTAACTATTAAAATATTT
1 AAAATA-TAA-TATTAAAATTTTT
*
485964 AAAATATATTTATTAAAATTTTT
1 AAAATATA-ATATTAAAATTTTT
*
485987 AATAATATAATATTATAATTTT
1 AA-AATATAATATTAAAATTTT
486009 AGTATAATAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
23 27 0.69
24 12 0.31
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (22 bp):
AAAATATAATATTAAAATTTTT
Found at i:486008 original size:22 final size:22
Alignment explanation
Indices: 485942--486024 Score: 69
Period size: 23 Copynumber: 3.5 Consensus size: 22
485932 TTTTAGTAAA
485942 AATATTAACTATTAAAATATTTAA-
1 AATA-TAA-TATTAAAAT-TTTAAT
*
485966 AATATATTTATTAAAATTTTTAAT
1 AATATA-ATATTAAAA-TTTTAAT
*
485990 AATATAATATTATAATTTTAGTAT
1 AATATAATATTAAAATTTTA--AT
486014 AATAATAATAT
1 AAT-ATAATAT
486025 ATTCAATTAT
Statistics
Matches: 50, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
22 5 0.10
23 22 0.44
24 16 0.32
25 7 0.14
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (22 bp):
AATATAATATTAAAATTTTAAT
Found at i:488703 original size:23 final size:23
Alignment explanation
Indices: 488673--488747 Score: 102
Period size: 23 Copynumber: 3.3 Consensus size: 23
488663 GTCGAGGGTT
488673 CTATGTGGTCCTT-AGGGACAAAA
1 CTATGTGGTCCTTCA-GGACAAAA
*
488696 CTATGTGGTCCTTCAGGATAAAA
1 CTATGTGGTCCTTCAGGACAAAA
*
488719 CTATGTGGTCTTTCAGGAC-AAA
1 CTATGTGGTCCTTCAGGACAAAA
488741 -TATGTGG
1 CTATGTGG
488748 CACTTCGGTG
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
21 7 0.15
22 3 0.06
23 37 0.77
24 1 0.02
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (23 bp):
CTATGTGGTCCTTCAGGACAAAA
Found at i:491689 original size:17 final size:17
Alignment explanation
Indices: 491669--491715 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
491659 TTCTCATCAA
491669 TTTTATTCA-TTATTTAT
1 TTTTATT-ATTTATTTAT
491686 TTTTATTATTTATTTAT
1 TTTTATTATTTATTTAT
*
491703 TTTCATTATTTAT
1 TTTTATTATTTAT
491716 AAATCATCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
16 1 0.04
17 27 0.96
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTATTATTTATTTAT
Found at i:496913 original size:27 final size:27
Alignment explanation
Indices: 496867--496925 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
496857 ATTTCTTAAA
496867 AATAATATTATTGAATTA-TTAATACTG
1 AATAATATTATTGAATTATTTAATA-TG
*
496894 AATAATATTATT-TATGTATTTAATATG
1 AATAATATTATTGAAT-TATTTAATATG
496921 -ATAAT
1 AATAAT
496926 TTAATAATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 7 0.24
27 16 0.55
28 6 0.21
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (27 bp):
AATAATATTATTGAATTATTTAATATG
Found at i:497236 original size:16 final size:18
Alignment explanation
Indices: 497215--497248 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
497205 TTGAAAAATA
497215 ATAAT-AATAA-ATTATT
1 ATAATAAATAATATTATT
497231 ATAATAAATAATATTATT
1 ATAATAAATAATATTATT
497249 TATTGTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 5 0.31
18 6 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATAATAAATAATATTATT
Found at i:503903 original size:59 final size:58
Alignment explanation
Indices: 503735--503915 Score: 185
Period size: 59 Copynumber: 3.2 Consensus size: 58
503725 AATAACTAGG
*
503735 TGATCATTTTGTAACTTTTAGTGGTCGATGGACTCAATAGAGCAACA-CTATCAAT---
1 TGATCATTTTGTAACTTTTAGTAGTCGATGGACTCAATAGAGCAACATCTAT-AATCGA
* * * * * * * **
503790 T-ATCATTTTATAAATTTTAATAGTCAAT-AACTCAATAAAACATTATCCTATAATCGA
1 TGATCATTTTGTAACTTTTAGTAGTCGATGGACTCAATAGAGCAACAT-CTATAATCGA
* *
503847 TGATCATTTTGTAACTTTTGGTAGTCGATGGACTCAACAGAGCAACATCTTATAATCGA
1 TGATCATTTTGTAACTTTTAGTAGTCGATGGACTCAATAGAGCAACATC-TATAATCGA
503906 TGATCATTTT
1 TGATCATTTT
503916 AATAGCCAAA
Statistics
Matches: 97, Mismatches: 21, Indels: 12
0.75 0.16 0.09
Matches are distributed among these distances:
53 12 0.12
54 25 0.26
55 5 0.05
57 1 0.01
58 23 0.24
59 31 0.32
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.37
Consensus pattern (58 bp):
TGATCATTTTGTAACTTTTAGTAGTCGATGGACTCAATAGAGCAACATCTATAATCGA
Found at i:505074 original size:14 final size:14
Alignment explanation
Indices: 505055--505082 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
505045 GCACACACAG
505055 ACGACATTTTAGAT
1 ACGACATTTTAGAT
505069 ACGACATTTTAGAT
1 ACGACATTTTAGAT
505083 GCACATGCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (14 bp):
ACGACATTTTAGAT
Found at i:508652 original size:95 final size:95
Alignment explanation
Indices: 508489--508663 Score: 296
Period size: 95 Copynumber: 1.8 Consensus size: 95
508479 AACTAACAAC
* * *
508489 AGGCCCAATCCGATCTCATCAAAATGTCACAACCCTAAGCATAATTGAGTTGTATTCCTTTAAGC
1 AGGCCCAATCCAATCTCATCAAAATATCACAACCCTAAGCATAATTGAGTTCTATTCCTTTAAGC
508554 CCTTTAATTAAGTACACTCCTGCTTACGTA
66 CCTTTAATTAAGTACACTCCTGCTTACGTA
* *
508584 AGGCCCAATCCAATCTCATCAAAATATCACATCCCTAAGCCTAATTGAGTTCTATTCCTTTAAGC
1 AGGCCCAATCCAATCTCATCAAAATATCACAACCCTAAGCATAATTGAGTTCTATTCCTTTAAGC
*
508649 CCTTTATTTAAGTAC
66 CCTTTAATTAAGTAC
508664 GACCCGAACC
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
95 74 1.00
ACGTcount: A:0.31, C:0.27, G:0.11, T:0.31
Consensus pattern (95 bp):
AGGCCCAATCCAATCTCATCAAAATATCACAACCCTAAGCATAATTGAGTTCTATTCCTTTAAGC
CCTTTAATTAAGTACACTCCTGCTTACGTA
Found at i:512359 original size:81 final size:79
Alignment explanation
Indices: 512256--512440 Score: 214
Period size: 79 Copynumber: 2.3 Consensus size: 79
512246 CGATTTGACC
* * * * *
512256 GTTCGATTAACGGTTAAAGAAAAAAAAATTTATTTTATTCTGT-TAAT-AATTTTGGGTGCGATT
1 GTTCGATTAATGGTTAAAGAAAAAAAAAGTTA-ATGATT-T-TCAAATAAATTTT-GGTGCGATT
512319 AACAGTCAAATAATTTCG
62 AACAGTCAAATAATTTCG
* *** * *
512337 GTTCGATCAATGGTTAAAGAAAAAATCGGTTAATGATTTTCAAATAAATTTTGGTTCGATTAACG
1 GTTCGATTAATGGTTAAAGAAAAAAAAAGTTAATGATTTTCAAATAAATTTTGGTGCGATTAACA
512402 GTCAAATAATTTCG
66 GTCAAATAATTTCG
512416 GTTCGATTAAT-GTTAAAGAAAAAAA
1 GTTCGATTAATGGTTAAAGAAAAAAA
512441 TTTCGGTTAA
Statistics
Matches: 89, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
78 14 0.16
79 39 0.44
80 10 0.11
81 26 0.29
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.36
Consensus pattern (79 bp):
GTTCGATTAATGGTTAAAGAAAAAAAAAGTTAATGATTTTCAAATAAATTTTGGTGCGATTAACA
GTCAAATAATTTCG
Found at i:512538 original size:25 final size:26
Alignment explanation
Indices: 512471--512542 Score: 76
Period size: 26 Copynumber: 2.8 Consensus size: 26
512461 TTAATAATTT
512471 TCAAATAAATTTCGGTTCAATTAACGG
1 TCAAA-AAATTTCGGTTCAATTAACGG
* * *
512498 TCAAATAATTTCGGTTCGATTAA-TG
1 TCAAAAAATTTCGGTTCAATTAACGG
* *
512523 TTAAAAAATTTTGGTT-AATT
1 TCAAAAAATTTCGGTTCAATT
512543 TCGTTCGGTT
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
24 3 0.08
25 14 0.37
26 16 0.42
27 5 0.13
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.40
Consensus pattern (26 bp):
TCAAAAAATTTCGGTTCAATTAACGG
Found at i:512585 original size:90 final size:91
Alignment explanation
Indices: 512362--512571 Score: 332
Period size: 95 Copynumber: 2.3 Consensus size: 91
512352 AAAGAAAAAA
* *
512362 TCGGTTAATGATTTTCAAATAAATTTTGGTTCGATTAACGGTCAAATAATTTCGGTTCGATTAAT
1 TCGGTTAATAATTTTCAAATAAATTTTGGTTCAATTAACGGTCAAATAATTTCGGTTCGATTAAT
*
512427 GTTAAAGAAAAAAATTTCGGTTAATTTGGT
66 GTT----AAAAAAATTTCGGTTAATTTCGT
*
512457 TCGGTTAATAATTTTCAAATAAATTTCGGTTCAATTAACGGTCAAATAATTTCGGTTCGATTAAT
1 TCGGTTAATAATTTTCAAATAAATTTTGGTTCAATTAACGGTCAAATAATTTCGGTTCGATTAAT
*
512522 GTT-AAAAAATTTTGGTTAATTTCGT
66 GTTAAAAAAATTTCGGTTAATTTCGT
512547 TCGGTTAATAATTTTCAAATAAATT
1 TCGGTTAATAATTTTCAAATAAATT
512572 ATTTTTTCCT
Statistics
Matches: 110, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
90 45 0.41
95 65 0.59
ACGTcount: A:0.34, C:0.09, G:0.15, T:0.41
Consensus pattern (91 bp):
TCGGTTAATAATTTTCAAATAAATTTTGGTTCAATTAACGGTCAAATAATTTCGGTTCGATTAAT
GTTAAAAAAATTTCGGTTAATTTCGT
Found at i:514778 original size:28 final size:29
Alignment explanation
Indices: 514713--514778 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
514703 ACTGATTAAG
* * *
514713 TATATTTTGATTTTATTTATATTTTTAAA
1 TATATTTTAATTTTATTTATATCTTCAAA
514742 TATATTTTAATTTTATCTTA-A-CTTCAAA
1 TATATTTTAATTTTAT-TTATATCTTCAAA
514770 TATATTTTA
1 TATATTTTA
514779 TTCTTTTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 14 0.42
29 16 0.48
30 3 0.09
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.61
Consensus pattern (29 bp):
TATATTTTAATTTTATTTATATCTTCAAA
Found at i:514790 original size:28 final size:28
Alignment explanation
Indices: 514713--514793 Score: 76
Period size: 28 Copynumber: 2.9 Consensus size: 28
514703 ACTGATTAAG
* * *
514713 TATATTTTGATTTTAT-TTATATTTTTAAA
1 TATATTTTAATTTTATATTA-A-CTTCAAA
*
514742 TATATTTTAATTTTATCTTAACTTCAAA
1 TATATTTTAATTTTATATTAACTTCAAA
*
514770 TATATTTT-ATTCTTTTATTAACTT
1 TATATTTTAATT-TTATATTAACTT
514794 AAAAAAATTA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
27 3 0.07
28 23 0.51
29 16 0.36
30 3 0.07
ACGTcount: A:0.31, C:0.06, G:0.01, T:0.62
Consensus pattern (28 bp):
TATATTTTAATTTTATATTAACTTCAAA
Found at i:514902 original size:23 final size:24
Alignment explanation
Indices: 514854--514921 Score: 68
Period size: 23 Copynumber: 2.8 Consensus size: 24
514844 TATTGGAATA
** *
514854 TAAGTTAATAATAAAATCTATTTT
1 TAAGTTAATAATAAAAAATATATT
514878 TAAGTTAA-AATAAAAAATATATT
1 TAAGTTAATAATAAAAAATATATT
*
514901 TAA-TAAATTGAATAAAAAATA
1 TAAGTTAA-T-AATAAAAAATA
514922 AAATATATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
22 3 0.08
23 15 0.41
24 8 0.22
25 11 0.30
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.37
Consensus pattern (24 bp):
TAAGTTAATAATAAAAAATATATT
Found at i:517766 original size:26 final size:28
Alignment explanation
Indices: 517724--517791 Score: 70
Period size: 26 Copynumber: 2.5 Consensus size: 28
517714 GATGATGATG
*
517724 ATTAGAAATGTTT-TATA-ATTT-AAAAA
1 ATTATAAAT-TTTATATATATTTGAAAAA
*
517750 ATTATAAATTTTATATATTTTTGAAAAA
1 ATTATAAATTTTATATATATTTGAAAAA
*
517778 ATTATTGAATTTTA
1 ATTA-TAAATTTTA
517792 AAATTAATTG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
25 3 0.09
26 12 0.34
27 3 0.09
28 9 0.26
29 8 0.23
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (28 bp):
ATTATAAATTTTATATATATTTGAAAAA
Found at i:522871 original size:29 final size:28
Alignment explanation
Indices: 522838--522918 Score: 92
Period size: 29 Copynumber: 2.8 Consensus size: 28
522828 TGACATAAAC
*
522838 TTAAAGGTCTAAATTGAAAAAATAGAAAG
1 TTAAAGGACTAAA-TGAAAAAATAGAAAG
*
522867 TTAAAGGACTAAA-AAACTAAAATAGAAAG
1 TTAAAGGACTAAATGAA--AAAATAGAAAG
522896 TTAAAGGACTTAAATAGAAAAAA
1 TTAAAGGAC-TAAAT-GAAAAAA
522919 AAAATTTGAA
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
27 2 0.05
29 32 0.73
30 8 0.18
32 2 0.05
ACGTcount: A:0.59, C:0.05, G:0.15, T:0.21
Consensus pattern (28 bp):
TTAAAGGACTAAATGAAAAAATAGAAAG
Found at i:522900 original size:21 final size:21
Alignment explanation
Indices: 522876--522915 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
522866 GTTAAAGGAC
522876 TAAAAAACTAAAATAGAAAGT
1 TAAAAAACTAAAATAGAAAGT
** *
522897 TAAAGGACTTAAATAGAAA
1 TAAAAAACTAAAATAGAAA
522916 AAAAAAATTT
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:0.62, C:0.05, G:0.12, T:0.20
Consensus pattern (21 bp):
TAAAAAACTAAAATAGAAAGT
Found at i:524019 original size:27 final size:27
Alignment explanation
Indices: 523989--524075 Score: 86
Period size: 27 Copynumber: 3.1 Consensus size: 27
523979 TCTTCTGTGA
523989 TTTGTCTTCTCTTTGATATTTTTTTAT
1 TTTGTCTTCTCTTTGATATTTTTTTAT
** * ** *
524016 TTTGGGTTTTCTTTGAT-TTGCTTGAGT
1 TTTGTCTTCTCTTTGATATTTTTTTA-T
524043 GATTTGTCTTCTCTTTGATATTTTTTTAT
1 --TTTGTCTTCTCTTTGATATTTTTTTAT
524072 TTTG
1 TTTG
524076 AGTTTTCTTT
Statistics
Matches: 44, Mismatches: 12, Indels: 8
0.69 0.19 0.12
Matches are distributed among these distances:
26 5 0.11
27 19 0.43
29 15 0.34
30 5 0.11
ACGTcount: A:0.10, C:0.09, G:0.15, T:0.66
Consensus pattern (27 bp):
TTTGTCTTCTCTTTGATATTTTTTTAT
Found at i:524027 original size:29 final size:28
Alignment explanation
Indices: 523995--524083 Score: 76
Period size: 29 Copynumber: 3.1 Consensus size: 28
523985 GTGATTTGTC
*
523995 TTCTCTTTGATATTTTTTTATTTTGGGT
1 TTCTCTTTGATATTTTTTTATTTTGGTT
** * *
524023 TT-TCTTTGAT-TTGCTTGAGTGATTT-GTC
1 TTCTCTTTGATATTTTTTTA-T--TTTGGTT
524051 TTCTCTTTGATATTTTTTTATTTTGAGTT
1 TTCTCTTTGATATTTTTTTATTTTG-GTT
524080 TTCT
1 TTCT
524084 TTGATTTGCT
Statistics
Matches: 45, Mismatches: 9, Indels: 13
0.67 0.13 0.19
Matches are distributed among these distances:
26 5 0.11
27 12 0.27
28 5 0.11
29 18 0.40
30 5 0.11
ACGTcount: A:0.11, C:0.09, G:0.15, T:0.65
Consensus pattern (28 bp):
TTCTCTTTGATATTTTTTTATTTTGGTT
Found at i:524053 original size:56 final size:56
Alignment explanation
Indices: 523985--524105 Score: 233
Period size: 56 Copynumber: 2.2 Consensus size: 56
523975 CTTTTCTTCT
*
523985 GTGATTTGTCTTCTCTTTGATATTTTTTTATTTTGGGTTTTCTTTGATTTGCTTGA
1 GTGATTTGTCTTCTCTTTGATATTTTTTTATTTTGAGTTTTCTTTGATTTGCTTGA
524041 GTGATTTGTCTTCTCTTTGATATTTTTTTATTTTGAGTTTTCTTTGATTTGCTTGA
1 GTGATTTGTCTTCTCTTTGATATTTTTTTATTTTGAGTTTTCTTTGATTTGCTTGA
524097 GTGATTTGT
1 GTGATTTGT
524106 GGCAGGCGAC
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 64 1.00
ACGTcount: A:0.12, C:0.08, G:0.18, T:0.62
Consensus pattern (56 bp):
GTGATTTGTCTTCTCTTTGATATTTTTTTATTTTGAGTTTTCTTTGATTTGCTTGA
Found at i:524084 original size:27 final size:27
Alignment explanation
Indices: 523998--524088 Score: 85
Period size: 27 Copynumber: 3.3 Consensus size: 27
523988 ATTTGTCTTC
*
523998 TCTTTGATATTTTTTTATTTTGGGTTT
1 TCTTTGATATTTTTTTATTTTGAGTTT
** * ** *
524025 TCTTTGAT-TTGCTTGAGTGATTTGTCTTC
1 TCTTTGATATTTTTTTA-T--TTTGAGTTT
524054 TCTTTGATATTTTTTTATTTTGAGTTT
1 TCTTTGATATTTTTTTATTTTGAGTTT
524081 TCTTTGAT
1 TCTTTGAT
524089 TTGCTTGAGT
Statistics
Matches: 48, Mismatches: 12, Indels: 8
0.71 0.18 0.12
Matches are distributed among these distances:
26 5 0.10
27 23 0.48
29 15 0.31
30 5 0.10
ACGTcount: A:0.12, C:0.08, G:0.15, T:0.65
Consensus pattern (27 bp):
TCTTTGATATTTTTTTATTTTGAGTTT
Found at i:524104 original size:29 final size:29
Alignment explanation
Indices: 524016--524104 Score: 85
Period size: 29 Copynumber: 3.1 Consensus size: 29
524006 ATTTTTTTAT
*
524016 TTTGGGTTTTCTTTGATTTGCTTGAGTGA
1 TTTGAGTTTTCTTTGATTTGCTTGAGTGA
** * ** *
524045 TTTGTCTTCTCTTTGATATTTTTTTA-T--
1 TTTGAGTTTTCTTTGAT-TTGCTTGAGTGA
524072 TTTGAGTTTTCTTTGATTTGCTTGAGTGA
1 TTTGAGTTTTCTTTGATTTGCTTGAGTGA
524101 TTTG
1 TTTG
524105 TGGCAGGCGA
Statistics
Matches: 44, Mismatches: 12, Indels: 8
0.69 0.19 0.12
Matches are distributed among these distances:
26 5 0.11
27 15 0.34
29 19 0.43
30 5 0.11
ACGTcount: A:0.11, C:0.08, G:0.20, T:0.61
Consensus pattern (29 bp):
TTTGAGTTTTCTTTGATTTGCTTGAGTGA
Found at i:530269 original size:30 final size:30
Alignment explanation
Indices: 530235--530297 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
530225 AAAAGTTATG
530235 TATTTAGTCATTCACTTACATTCGTCGTTA
1 TATTTAGTCATTCACTTACATTCGTCGTTA
530265 TATTTAGTCATTCACTTACATTCGTCGTTA
1 TATTTAGTCATTCACTTACATTCGTCGTTA
530295 TAT
1 TAT
530298 ACCATTAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.24, C:0.19, G:0.10, T:0.48
Consensus pattern (30 bp):
TATTTAGTCATTCACTTACATTCGTCGTTA
Found at i:536724 original size:17 final size:18
Alignment explanation
Indices: 536687--536727 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
536677 ATATTATGTA
*
536687 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
536705 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
536722 TTTACT
1 TTTACT
536728 AATATAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:538437 original size:18 final size:18
Alignment explanation
Indices: 538410--538449 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
538400 ACAGCAGCCA
*
538410 CCGCAGCCATTTATGATG
1 CCGCAACCATTTATGATG
538428 CCGCAACCATTTATGATG
1 CCGCAACCATTTATGATG
538446 CCGC
1 CCGC
538450 CATCGCCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.33, G:0.20, T:0.25
Consensus pattern (18 bp):
CCGCAACCATTTATGATG
Found at i:541059 original size:22 final size:22
Alignment explanation
Indices: 541016--541060 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
541006 TTATTTGATT
** *
541016 ATTTAAAATATAATTATTTTAA
1 ATTTAAAATATAAAAATATTAA
541038 ATTTAAAATATAAAAATATTAA
1 ATTTAAAATATAAAAATATTAA
541060 A
1 A
541061 AAATTATATA
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:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
ATTTAAAATATAAAAATATTAA
Found at i:541142 original size:16 final size:14
Alignment explanation
Indices: 541100--541145 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
541090 TAGTATTATT
541100 TATT-AAATA-AAA
1 TATTAAAATATAAA
*
541112 CATTAAAATATAAA
1 TATTAAAATATAAA
541126 TATTAAAATTAATAAA
1 TATTAAAA-T-ATAAA
541142 TATT
1 TATT
541146 TACTATAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 3 0.11
13 5 0.18
14 10 0.36
15 1 0.04
16 9 0.32
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (14 bp):
TATTAAAATATAAA
Found at i:545077 original size:202 final size:200
Alignment explanation
Indices: 544721--545223 Score: 696
Period size: 202 Copynumber: 2.5 Consensus size: 200
544711 GCCACGTAAA
* * *
544721 GAATCTCTAAAGAACTCATGTTCTGCAAAACACGAG-T--TTGCCACATCACCTCAAGAATCTTT
1 GAATCTCTGAAGAACTCATGTTCTGCAAAA-ACAAGTTGCTTGCCACGTCACCTCAAGAATCTTT
* * * *
544783 GCAGGCCCATATCTCTTCCATATCATGTTAAAA-ATC--TATTTTTTGAAAAAAAAAATGAGACT
65 GCAGGCCCATGTCCCTTCCATATCACGTTAAAATCTCTTTATTTTTTGAAAAAAAAAATGAGACT
* **
544845 TTCATTCGAATCCTTATTTCAAGCAAGTGAAGGTAAACAAGCAAACCATACAAAACTGAAATGAA
130 TTCATTCGAATACTTATTTCAAAAAAGTGAAGGTAAACAAGCAAACCATACAAAACTGAAATGAA
544910 CGTTAG
195 CGTTAG
*
544916 GAATCTCTGAAGAACTCATGTTATGCAAAAAGCAAGTTGCTTGCCACGTCACCTCAAGAATCTTT
1 GAATCTCTGAAGAACTCATGTTCTGCAAAAA-CAAGTTGCTTGCCACGTCACCTCAAGAATCTTT
* * * ***
544981 GTAGGCCCATGTCCCTTTCATATCACGTTAAGAATCTCTTTCTTTTTTTTTAAAAAAAATGAGAC
65 GCAGGCCCATGTCCCTTCCATATCACGTTAA-AATCTCTTTATTTTTTGAAAAAAAAAATGAGAC
* *
545046 TTTCATTCGAATACTTATTTTAAAAAAGTGAAGGTAAACAAGCAAACCATACAGAACTGAAATGA
129 TTTCATTCGAATACTTATTTCAAAAAAGTGAAGGTAAACAAGCAAACCATACAAAACTGAAATGA
*
545111 ACGTTAT
194 ACGTTAG
* *
545118 GAATCTCTGAATAACTCATGTTCTG-AAAAACACGAGTTGCTTGCCACGTCCCCTCAAGAATCTT
1 GAATCTCTGAAGAACTCATGTTCTGCAAAAACA--AGTTGCTTGCCACGTCACCTCAAGAATCTT
*
545182 TGCAGACCCATGTCCCTTCCATATCACGTTAATAATCTCTTT
64 TGCAGGCCCATGTCCCTTCCATATCACGTTAA-AATCTCTTT
545224 TTTGAAAAAA
Statistics
Matches: 271, Mismatches: 27, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
194 1 0.00
195 31 0.11
196 1 0.00
198 50 0.18
199 2 0.01
200 4 0.01
201 5 0.02
202 177 0.65
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (200 bp):
GAATCTCTGAAGAACTCATGTTCTGCAAAAACAAGTTGCTTGCCACGTCACCTCAAGAATCTTTG
CAGGCCCATGTCCCTTCCATATCACGTTAAAATCTCTTTATTTTTTGAAAAAAAAAATGAGACTT
TCATTCGAATACTTATTTCAAAAAAGTGAAGGTAAACAAGCAAACCATACAAAACTGAAATGAAC
GTTAG
Found at i:565321 original size:13 final size:13
Alignment explanation
Indices: 565303--565329 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
565293 ATAGTTGAAG
565303 AGTCTTCATATGC
1 AGTCTTCATATGC
565316 AGTCTTCATATGC
1 AGTCTTCATATGC
565329 A
1 A
565330 CGTGTGTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (13 bp):
AGTCTTCATATGC
Found at i:566310 original size:13 final size:13
Alignment explanation
Indices: 566292--566319 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
566282 TGGCAACAAT
566292 AAAAAAAAAAAAG
1 AAAAAAAAAAAAG
566305 AAAAAAAAAAAAG
1 AAAAAAAAAAAAG
566318 AA
1 AA
566320 GGTATGGGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAG
Found at i:571352 original size:17 final size:17
Alignment explanation
Indices: 571330--571362 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
571320 AACATTCAAT
*
571330 AAATAATTAGTTATAAA
1 AAATAATTAGGTATAAA
571347 AAATAATTAGGTATAA
1 AAATAATTAGGTATAA
571363 TTGAGGGGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (17 bp):
AAATAATTAGGTATAAA
Found at i:572620 original size:3 final size:3
Alignment explanation
Indices: 572612--572659 Score: 71
Period size: 3 Copynumber: 16.3 Consensus size: 3
572602 TTCTTCACTT
* *
572612 TAA TAA TAA TAA TAA TAC TAA TAC TAA T-A TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
572659 T
1 T
572660 TAAGGAGACG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:580141 original size:33 final size:33
Alignment explanation
Indices: 580094--580188 Score: 81
Period size: 32 Copynumber: 2.9 Consensus size: 33
580084 TGAAATTGAA
* * *
580094 TTAACCTGAACCGAAAGA-AACTTGAACCA-AAT
1 TTAACCCGATCCGAAAGACAACTCGAA-CATAAT
580126 TGTAACCCGATCCGAAA-ACAACTCGAACATAAT
1 T-TAACCCGATCCGAAAGACAACTCGAACATAAT
* * * *
580159 TTATCCCGATCCAAAAG-CAACCCGAGCATA
1 TTAACCCGATCCGAAAGACAACTCGAACATA
580189 TTGAAATTGA
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
32 28 0.54
33 24 0.46
ACGTcount: A:0.42, C:0.27, G:0.13, T:0.18
Consensus pattern (33 bp):
TTAACCCGATCCGAAAGACAACTCGAACATAAT
Found at i:583568 original size:37 final size:36
Alignment explanation
Indices: 583527--583603 Score: 91
Period size: 37 Copynumber: 2.1 Consensus size: 36
583517 AGGTGGTAAC
* * *
583527 ATTTATAACATTAGATAGCTGAATAATTCAAAAAATA
1 ATTTATAACATTAAAAACCTGAATAATT-AAAAAATA
* * *
583564 ATTTATAAGATTAAAAACCTGAATCATTTAAAAATA
1 ATTTATAACATTAAAAACCTGAATAATTAAAAAATA
583600 ATTT
1 ATTT
583604 TATATACCAA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
36 11 0.32
37 23 0.68
ACGTcount: A:0.51, C:0.08, G:0.06, T:0.35
Consensus pattern (36 bp):
ATTTATAACATTAAAAACCTGAATAATTAAAAAATA
Found at i:584271 original size:21 final size:21
Alignment explanation
Indices: 584247--584286 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
584237 TAAGGTAAAA
*
584247 TTATTTTTTATTAAATTATGT
1 TTATTTTATATTAAATTATGT
*
584268 TTATTTTATATTTAATTAT
1 TTATTTTATATTAAATTAT
584287 TTAACTAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (21 bp):
TTATTTTATATTAAATTATGT
Done.