Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000418.1 Hibiscus syriacus cultivar Beakdansim tig00000765_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: 909013
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 5
Found at i:521448 original size:18 final size:18
Alignment explanation
Indices: 521425--521461 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
521415 CGAAATATAT
521425 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
521443 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
521461 A
1 A
521462 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:521691 original size:23 final size:23
Alignment explanation
Indices: 521665--521729 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
521655 ATGCGAGATA
521665 GATACCTATTACATTATATAAAC
1 GATACCTATTACATTATATAAAC
**
521688 GATACCTATTACATTATATAAGG
1 GATACCTATTACATTATATAAAC
* *
521711 GCTACCTATTACATCATAT
1 GATACCTATTACATTATAT
521730 GTTTACCTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.35
Consensus pattern (23 bp):
GATACCTATTACATTATATAAAC
Found at i:522111 original size:21 final size:20
Alignment explanation
Indices: 522081--522134 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 20
522071 GATAGACACT
*
522081 TTACAATATAACCATTACCTA
1 TTACATTATAACCA-TACCTA
*
522102 TTACATTATATAAACGATACCTA
1 TTACA-T-TAT-AACCATACCTA
522125 TTACATTATA
1 TTACATTATA
522135 TAAGGGCTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
20 1 0.04
21 8 0.29
22 1 0.04
23 14 0.50
24 4 0.14
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.37
Consensus pattern (20 bp):
TTACATTATAACCATACCTA
Found at i:522122 original size:23 final size:23
Alignment explanation
Indices: 522096--522158 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
522086 ATATAACCAT
522096 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
522119 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
522142 TACCTATTACATCATAT
1 TACCTATTACATTATAT
522159 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:522715 original size:184 final size:184
Alignment explanation
Indices: 522428--522779 Score: 677
Period size: 184 Copynumber: 1.9 Consensus size: 184
522418 ATTAATATCT
522428 TAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACC
1 TAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACC
522493 GACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGTATATTTA
66 GACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGTATATTTA
522558 TACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTG
131 TACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTG
*
522612 TAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACC
1 TAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACC
522677 GACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGTATATTTA
66 GACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGTATATTTA
**
522742 TACCGGTTATATTACAAAATTATCTATTTTATTATAAT
131 TACCGGTTATATTACAAAATTATCTATTACATTATAAT
522780 ATGTTGAAAG
Statistics
Matches: 165, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
184 165 1.00
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (184 bp):
TAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACC
GACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGTATATTTA
TACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTG
Found at i:524257 original size:3 final size:3
Alignment explanation
Indices: 524249--524335 Score: 84
Period size: 3 Copynumber: 29.0 Consensus size: 3
524239 ACTTGTTTGG
* * * **
524249 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * * *
524297 AGC TTC ATC GTC ATC ATC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
524336 GTCAGCTTCA
Statistics
Matches: 65, Mismatches: 19, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.24, C:0.34, G:0.06, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:524272 original size:18 final size:18
Alignment explanation
Indices: 524249--524350 Score: 87
Period size: 18 Copynumber: 5.7 Consensus size: 18
524239 ACTTGTTTGG
524249 ATCATCATCTTCATCATC
1 ATCATCATCTTCATCATC
* *
524267 ATCATCATCATCGTCATC
1 ATCATCATCTTCATCATC
* ** * *
524285 ATCTTCATCGCCAGCTTC
1 ATCATCATCTTCATCATC
* *
524303 ATCGTCATCATCATCATC
1 ATCATCATCTTCATCATC
* *
524321 ATCGTCATCTTCATCGTC
1 ATCATCATCTTCATCATC
* *
524339 AGCTTCATCTTC
1 ATCATCATCTTC
524351 TGCGACCGAT
Statistics
Matches: 67, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 67 1.00
ACGTcount: A:0.23, C:0.34, G:0.07, T:0.36
Consensus pattern (18 bp):
ATCATCATCTTCATCATC
Found at i:524316 original size:42 final size:42
Alignment explanation
Indices: 524257--524347 Score: 146
Period size: 42 Copynumber: 2.2 Consensus size: 42
524247 GGATCATCAT
*
524257 CTTCATCATCATCATCATCATCGTCATCATCTTCATCGCCAG
1 CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
* * *
524299 CTTCATCGTCATCATCATCATCATCGTCATCTTCATCGTCAG
1 CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
524341 CTTCATC
1 CTTCATC
524348 TTCTGCGACC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.22, C:0.35, G:0.08, T:0.35
Consensus pattern (42 bp):
CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
Found at i:526371 original size:199 final size:199
Alignment explanation
Indices: 525815--527035 Score: 2311
Period size: 199 Copynumber: 6.1 Consensus size: 199
525805 TTTAAATTAG
* * *
525815 TATCGACACAAAATATA-TAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATT
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
525879 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* * *
525944 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAA
526009 AAAA
196 AAAA
526013 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCAT-AAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
526077 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
526142 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAG
131 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAA
526207 AAAA
196 AAAA
526211 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
526276 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
526341 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAA
526406 AAAA
196 AAAA
* *
526410 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATT
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
526475 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
526540 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAA
526605 AAAA
196 AAAA
*
526609 TATCGACACAAAGTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
526674 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
526739 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAA
526804 AAAA
196 AAAA
526808 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
526873 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
526938 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAA
527003 AAAA
196 AAAA
*
527007 TATCGACACAAACTATATTAGTATCGACA
1 TATCGACACAAACTATATTAGTGTCGACA
527036 TGACCCTTAA
Statistics
Matches: 1003, Mismatches: 18, Indels: 3
0.98 0.02 0.00
Matches are distributed among these distances:
198 208 0.21
199 795 0.79
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.38
Consensus pattern (199 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAA
AAAA
Found at i:527141 original size:19 final size:19
Alignment explanation
Indices: 527119--527157 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
527109 ACATAAAAAA
527119 ATAAATCGTATACAAAATT
1 ATAAATCGTATACAAAATT
*
527138 ATAAATCTTATACAAAATT
1 ATAAATCGTATACAAAATT
527157 A
1 A
527158 ACTCGACATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.54, C:0.10, G:0.03, T:0.33
Consensus pattern (19 bp):
ATAAATCGTATACAAAATT
Found at i:528987 original size:33 final size:33
Alignment explanation
Indices: 528950--529015 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
528940 CATCTTAATA
*
528950 TCACCCCTTAACACCGAAACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
***
528983 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
529016 CCTTCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.45, G:0.02, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCGAAACTTCTTTCACCACT
Found at i:531158 original size:24 final size:24
Alignment explanation
Indices: 531121--531173 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
531111 CCGTTCTATC
531121 TATTTTCAGAGGATAT-TTAGCTTA
1 TATTTTCAGAGGATATGTTA-CTTA
** *
531145 TATTTTCATCGGATATGTTATTTA
1 TATTTTCAGAGGATATGTTACTTA
531169 TATTT
1 TATTT
531174 AATCGATACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.53
Consensus pattern (24 bp):
TATTTTCAGAGGATATGTTACTTA
Found at i:531364 original size:20 final size:19
Alignment explanation
Indices: 531318--531364 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
531308 TCCGGTATCA
*
531318 TTTTACCGTTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
531337 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
531358 TTTTACC
1 TTTTACC
531365 TGTTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.19, C:0.17, G:0.09, T:0.55
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:531512 original size:20 final size:20
Alignment explanation
Indices: 531485--531531 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
531475 ACACTTTTAA
531485 TTTTACCGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
531504 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
531525 TTTTACC
1 TTTTACC
531532 TGGTATATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:532844 original size:3 final size:3
Alignment explanation
Indices: 532836--532874 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
532826 AAATTCATCC
532836 ATT ATT ATT ATT ATT -TT ATT ATT ATT ATT ATT ATT -TT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
532875 CCTAACAAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.12
3 30 0.88
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
ATT
Found at i:532861 original size:20 final size:20
Alignment explanation
Indices: 532836--532874 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
532826 AAATTCATCC
532836 ATTATTATTATTATTTTATT
1 ATTATTATTATTATTTTATT
532856 ATTATTATTATTATTTTAT
1 ATTATTATTATTATTTTAT
532875 CCTAACAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
ATTATTATTATTATTTTATT
Found at i:536930 original size:18 final size:17
Alignment explanation
Indices: 536889--536943 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
536879 CGTTGGCGTT
*
536889 ATATTAACGAATAATTG
1 ATATTAACGAATAAATG
536906 ATATTAACG-ATACAATG
1 ATATTAACGAATA-AATG
*
536923 AGTATTAAATG-ATAAATG
1 A-TATT-AACGAATAAATG
536941 ATA
1 ATA
536944 ACCAAATTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
16 3 0.09
17 15 0.45
18 9 0.27
19 6 0.18
ACGTcount: A:0.49, C:0.05, G:0.13, T:0.33
Consensus pattern (17 bp):
ATATTAACGAATAAATG
Found at i:540196 original size:38 final size:39
Alignment explanation
Indices: 540129--540203 Score: 98
Period size: 38 Copynumber: 1.9 Consensus size: 39
540119 AGGTGTGTTC
* *
540129 AGTTCGTTTATATTCACGAGCAAGCTCGTTTA-TCGACT
1 AGTTCATTTATATTCACGAACAAGCTCGTTTACTCGACT
* * *
540167 AGTTCATTTATGTTCATGAACAAGTTCGTTTACTCGA
1 AGTTCATTTATATTCACGAACAAGCTCGTTTACTCGA
540204 TTCTCCTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
38 27 0.87
39 4 0.13
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.39
Consensus pattern (39 bp):
AGTTCATTTATATTCACGAACAAGCTCGTTTACTCGACT
Found at i:540402 original size:24 final size:24
Alignment explanation
Indices: 540374--540474 Score: 82
Period size: 24 Copynumber: 4.2 Consensus size: 24
540364 AATAAAAAAT
540374 TGAACATATAAACAAACATGTTCG
1 TGAACATATAAACAAACATGTTCG
*** * *
540398 TGAACGGCTAAATGAATACA--TTCA
1 TGAACATATAAA-CAA-ACATGTTCG
* * *
540422 TGAACATATAAACGAACATATTAG
1 TGAACATATAAACAAACATGTTCG
*
540446 TGAATAT-TAAACAAACATGTTCG
1 TGAACATATAAACAAACATGTTCG
540469 TGAACA
1 TGAACA
540475 GTAAATAAAC
Statistics
Matches: 56, Mismatches: 17, Indels: 9
0.68 0.21 0.11
Matches are distributed among these distances:
22 3 0.05
23 19 0.34
24 29 0.52
25 2 0.04
26 3 0.05
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.26
Consensus pattern (24 bp):
TGAACATATAAACAAACATGTTCG
Found at i:543830 original size:34 final size:34
Alignment explanation
Indices: 543787--543859 Score: 128
Period size: 34 Copynumber: 2.1 Consensus size: 34
543777 AGGGTTCATC
*
543787 ATACATACGATCGGGTACGAGATATCACGTTCGG
1 ATACATACGATCGGGTACAAGATATCACGTTCGG
*
543821 ATACATACGATCGGGTACAAGATATTACGTTCGG
1 ATACATACGATCGGGTACAAGATATCACGTTCGG
543855 ATACA
1 ATACA
543860 AGATATCACG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (34 bp):
ATACATACGATCGGGTACAAGATATCACGTTCGG
Found at i:543854 original size:20 final size:20
Alignment explanation
Indices: 543826--543877 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
543816 TTCGGATACA
* *
543826 TACGATCGGGTACAAGATAT
1 TACGTTCGGATACAAGATAT
543846 TACGTTCGGATACAAGATAT
1 TACGTTCGGATACAAGATAT
*
543866 CACGTTCGGATA
1 TACGTTCGGATA
543878 GCAGAACTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (20 bp):
TACGTTCGGATACAAGATAT
Found at i:549902 original size:21 final size:22
Alignment explanation
Indices: 549869--549911 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
549859 ATTTAAAAAT
*
549869 ATTAAAGGAAGTATCGATACTC
1 ATTAAAGGAAGTACCGATACTC
549891 ATTAAA-GAAGTACCGATACTC
1 ATTAAAGGAAGTACCGATACTC
549912 CCTGTCCTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (22 bp):
ATTAAAGGAAGTACCGATACTC
Found at i:552217 original size:12 final size:13
Alignment explanation
Indices: 552193--552228 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
552183 AGTTTTGCCA
552193 AAAATATTTTTTT
1 AAAATATTTTTTT
*
552206 TAAATATTTTTTT
1 AAAATATTTTTTT
552219 AAAATATTTT
1 AAAATATTTT
552229 GTTATATCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
AAAATATTTTTTT
Found at i:552656 original size:22 final size:21
Alignment explanation
Indices: 552628--552670 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
552618 ATTTAAAAAT
552628 ATTAAAGGAAGTACCGATACTC
1 ATTAAAGG-AGTACCGATACTC
*
552650 ATTAAAGGAGTACTGATACTC
1 ATTAAAGGAGTACCGATACTC
552671 CTTGTCCTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.26
Consensus pattern (21 bp):
ATTAAAGGAGTACCGATACTC
Found at i:554292 original size:32 final size:32
Alignment explanation
Indices: 554187--554284 Score: 187
Period size: 32 Copynumber: 3.1 Consensus size: 32
554177 AACTGGTATT
554187 GACCTGAACCTGAGTTGGATCTGGAAATTGTG
1 GACCTGAACCTGAGTTGGATCTGGAAATTGTG
*
554219 GACCTGAACCTGAGTTAGATCTGGAAATTGTG
1 GACCTGAACCTGAGTTGGATCTGGAAATTGTG
554251 GACCTGAACCTGAGTTGGATCTGGAAATTGTG
1 GACCTGAACCTGAGTTGGATCTGGAAATTGTG
554283 GA
1 GA
554285 TATGAACCCG
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 64 1.00
ACGTcount: A:0.27, C:0.15, G:0.31, T:0.28
Consensus pattern (32 bp):
GACCTGAACCTGAGTTGGATCTGGAAATTGTG
Found at i:554665 original size:18 final size:18
Alignment explanation
Indices: 554605--554667 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 18
554595 TTATAATAAA
*
554605 ATATTAATTATGATAATT
1 ATATTAATTATGATTATT
* *
554623 AAATTAATAAATAGATTTATT
1 ATATTAAT-TAT-GA-TTATT
*
554644 ATATTAATTATGATTCTT
1 ATATTAATTATGATTATT
554662 ATATTA
1 ATATTA
554668 TGATTCTTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
18 17 0.47
19 4 0.11
20 4 0.11
21 11 0.31
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (18 bp):
ATATTAATTATGATTATT
Found at i:554669 original size:14 final size:14
Alignment explanation
Indices: 554650--554682 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
554640 TATTATATTA
554650 ATTATGATTCTTAT
1 ATTATGATTCTTAT
554664 ATTATGATTCTTAT
1 ATTATGATTCTTAT
*
554678 GTTAT
1 ATTAT
554683 AAATCTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.27, C:0.06, G:0.09, T:0.58
Consensus pattern (14 bp):
ATTATGATTCTTAT
Found at i:556347 original size:30 final size:30
Alignment explanation
Indices: 556326--556384 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
556316 TGGCAGATCC
*
556326 ACGTAGACTAAATGCTGACGTGGCATGTAT
1 ACGTAGACTAAATACTGACGTGGCATGTAT
*
556356 ACGTAGACTAAATACTGATGTGGCATGTA
1 ACGTAGACTAAATACTGACGTGGCATGTA
556385 CATGTATGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.27
Consensus pattern (30 bp):
ACGTAGACTAAATACTGACGTGGCATGTAT
Found at i:556627 original size:17 final size:18
Alignment explanation
Indices: 556602--556639 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
556592 TTAAATTCAT
*
556602 ATTTAAAATTT-TAATTA
1 ATTTAAAATTTATAACTA
*
556619 ATTTTAAATTTATAACTA
1 ATTTAAAATTTATAACTA
556637 ATT
1 ATT
556640 AATATAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTAAAATTTATAACTA
Found at i:556719 original size:50 final size:50
Alignment explanation
Indices: 556624--556719 Score: 124
Period size: 50 Copynumber: 1.9 Consensus size: 50
556614 AATTAATTTT
** * *
556624 AAATTTATAACTAATTAATATAAATTTATTCATTTGTTTATTTTTATTCA
1 AAATTTATAACTAATTAATATAAATTTATAAATTTGTTAAATTTTATTCA
556674 AAATTTATAACTAATTAATATAAATTTA-AAATTAT-TTAAAATTTTA
1 AAATTTATAACTAATTAATATAAATTTATAAATT-TGTT-AAATTTTA
556720 AATATGAGTC
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
49 5 0.12
50 35 0.88
ACGTcount: A:0.45, C:0.04, G:0.01, T:0.50
Consensus pattern (50 bp):
AAATTTATAACTAATTAATATAAATTTATAAATTTGTTAAATTTTATTCA
Found at i:557053 original size:18 final size:18
Alignment explanation
Indices: 557019--557057 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
557009 AGTTTATATT
*
557019 AATTAGTTATAAATTTAA
1 AATTAATTATAAATTTAA
*
557037 AATTAATTA-AAATTTTA
1 AATTAATTATAAATTTAA
557054 AATT
1 AATT
557058 GACTCAAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (18 bp):
AATTAATTATAAATTTAA
Found at i:559385 original size:2 final size:2
Alignment explanation
Indices: 559378--559454 Score: 133
Period size: 2 Copynumber: 40.0 Consensus size: 2
559368 AATTAAAAAT
559378 TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
559419 TA TA TA TA TA TA TA TA TA -A T- TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
559455 AAGCATATAC
Statistics
Matches: 72, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
1 3 0.04
2 69 0.96
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:560280 original size:100 final size:100
Alignment explanation
Indices: 560147--560384 Score: 250
Period size: 100 Copynumber: 2.3 Consensus size: 100
560137 TTAGTTTTAA
* * *
560147 GTTTTGGGTGTTTGT-AAGGATCAAATAATGGTTTGGGGAAT-AACACGAATGAACAAGGGTTGA
1 GTTTT-GGTGTTTGTGAA-GATCAAATGATGGTTTGGGG-ATGAACACGAATGAAC-ACGATTGA
* *
560210 ATTTTTGGGTATTTGATC-G-AAAAAAGGAATGTGTTTGG
62 AATTTTGGGTATTTGATCGGAAAAAAAGAAATG-GTTTGG
* * * * * *
560248 GTTTTGGTGTTTGTGAAGATCAAATGAGGGTTTTTGTGATGAACATGGATGAACACGATTTAAAT
1 GTTTTGGTGTTTGTGAAGATCAAATGATGG-TTTGGGGATGAACACGAATGAACACGATTGAAAT
*
560313 TTTGGGTGTTTGATCGGAAAAAAAAAAGAAATGGTTTGG
65 TTTGGGTATTTGATCGG---AAAAAAAGAAATGGTTTGG
*
560352 GTTTTGGTGTTTGTGAATATCAAATGATGGTTT
1 GTTTTGGTGTTTGTGAAGATCAAATGATGGTTT
560385 TTGAGATAAA
Statistics
Matches: 115, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
100 43 0.37
101 24 0.21
103 3 0.03
104 34 0.30
105 11 0.10
ACGTcount: A:0.30, C:0.05, G:0.29, T:0.36
Consensus pattern (100 bp):
GTTTTGGTGTTTGTGAAGATCAAATGATGGTTTGGGGATGAACACGAATGAACACGATTGAAATT
TTGGGTATTTGATCGGAAAAAAAGAAATGGTTTGG
Found at i:560784 original size:18 final size:18
Alignment explanation
Indices: 560763--560882 Score: 148
Period size: 18 Copynumber: 7.1 Consensus size: 18
560753 ATTAAATTAA
560763 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
560781 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
*
560799 TA-ATA-ATTATATA-A-
1 TATATAGTTTATATATAC
560813 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
*
560831 TATATATTTTATATATAC
1 TATATAGTTTATATATAC
*
560849 TA-AT-G--AACTATATAC
1 TATATAGTTTA-TATATAC
560864 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
560882 T
1 T
560883 GATGAACTAT
Statistics
Matches: 87, Mismatches: 6, Indels: 18
0.78 0.05 0.16
Matches are distributed among these distances:
14 3 0.03
15 13 0.15
16 16 0.18
17 7 0.08
18 47 0.54
19 1 0.01
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.48
Consensus pattern (18 bp):
TATATAGTTTATATATAC
Found at i:560821 original size:50 final size:51
Alignment explanation
Indices: 560760--560984 Score: 232
Period size: 50 Copynumber: 4.5 Consensus size: 51
560750 ATTATTAAAT
*
560760 TAATATATAGTTTATATATACTATATAGTTTATATATACTAAT-AATTATA
1 TAATATATAGTTTATATATACTATATAGTTTATATATACTAATGAACTATA
*
560810 TAATATATAGTTTATATATACTATATATTTTATATATACTAATGAACTATA
1 TAATATATAGTTTATATATACTATATAGTTTATATATACTAATGAACTATA
* * * * *
560861 TACTATATAGTTTATATATACTGATGA-ACTATATAGTTTA-T-ATAAACTA-A
1 TAATATATAGTTTATATATACT-AT-ATAGTTTATA-TATACTAATGAACTATA
* * * *
560911 TGAACCATAT-G--AACTATATACTCTATAATTTATATATACTAATGAACTATA
1 T-AA-TATATAGTTTA-TATATACTATATAGTTTATATATACTAATGAACTATA
*
560962 TAATATATAATTTATATATACTA
1 TAATATATAGTTTATATATACTA
560985 ATGAACTATA
Statistics
Matches: 142, Mismatches: 19, Indels: 27
0.76 0.10 0.14
Matches are distributed among these distances:
48 4 0.03
49 13 0.09
50 61 0.43
51 46 0.32
52 14 0.10
53 4 0.03
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.44
Consensus pattern (51 bp):
TAATATATAGTTTATATATACTATATAGTTTATATATACTAATGAACTATA
Found at i:560864 original size:33 final size:33
Alignment explanation
Indices: 560824--560996 Score: 215
Period size: 33 Copynumber: 5.2 Consensus size: 33
560814 ATATAGTTTA
*
560824 TATATACTATATATTTTATATATACTAATGAAC
1 TATATACTATATAATTTATATATACTAATGAAC
* *
560857 TATATACTATATAGTTTATATATACTGATGAAC
1 TATATACTATATAATTTATATATACTAATGAAC
* ** *
560890 TATATAGTTTATATAAACTA-ATGA-ACCATATGAAC
1 TATATA--CTATATAATTTATAT-ATACTA-ATGAAC
*
560925 TATATACTCTATAATTTATATATACTAATGAAC
1 TATATACTATATAATTTATATATACTAATGAAC
*
560958 TATATAATATATAATTTATATATACTAATGAAC
1 TATATACTATATAATTTATATATACTAATGAAC
560991 TATATA
1 TATATA
560997 GTTTATTAAT
Statistics
Matches: 119, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
33 89 0.75
34 9 0.08
35 21 0.18
ACGTcount: A:0.44, C:0.09, G:0.05, T:0.42
Consensus pattern (33 bp):
TATATACTATATAATTTATATATACTAATGAAC
Found at i:560879 original size:101 final size:100
Alignment explanation
Indices: 560824--561090 Score: 290
Period size: 101 Copynumber: 2.8 Consensus size: 100
560814 ATATAGTTTA
* *
560824 TATATACTATATATTTTATATATACTAATGAACTATATACTATATAGTTTATATATACTGATGAA
1 TATATACTATATAATTTATATATACTAATGAACTATATAATATATAGTTTATATATACT-ATGAA
*
560889 CTATATAGTTTATATAAACTAATGAACCATATGAAC
65 CTATATAGTATATATAAACTAATGAACCATATGAAC
* *
560925 TATATACTCTATAATTTATATATACTAATGAACTATATAATATATAATTTATATATACTAATGAA
1 TATATACTATATAATTTATATATACTAATGAACTATATAATATATAGTTTATATATACT-ATGAA
* ** * *
560990 CTATATAGT-T-TATTAA-T-AT-AATTATATAAAG
65 CTATATAGTATATATAAACTAATGAACCATATGAAC
* * * *
561021 TATATACTTTATAGTTTAT-TA-A-T-ATAAACTATAT-ATATATAGTCTATAT-TA--ATGAAC
1 TATATACTATATAATTTATATATACTAATGAACTATATAATATATAGTTTATATATACTATGAAC
*
561078 TATAAAGTATATA
66 TATATAGTATATA
561091 GTTTATATAT
Statistics
Matches: 148, Mismatches: 16, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
87 13 0.09
88 1 0.01
89 2 0.01
90 2 0.01
91 13 0.09
92 10 0.07
93 1 0.01
94 1 0.01
95 2 0.01
96 25 0.17
97 2 0.01
98 1 0.01
99 5 0.03
100 1 0.01
101 69 0.47
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.43
Consensus pattern (100 bp):
TATATACTATATAATTTATATATACTAATGAACTATATAATATATAGTTTATATATACTATGAAC
TATATAGTATATATAAACTAATGAACCATATGAAC
Found at i:560943 original size:42 final size:40
Alignment explanation
Indices: 560892--560970 Score: 113
Period size: 42 Copynumber: 1.9 Consensus size: 40
560882 TGATGAACTA
*
560892 TATAGTTTATATAAACTAATGAACCATATGAACTATATACTC
1 TATAATTTATATAAACTAATGAACCATAT-AA-TATATACTC
* *
560934 TATAATTTATATATACTAATGAACTATATAATATATA
1 TATAATTTATATAAACTAATGAACCATATAATATATA
560971 ATTTATATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 6 0.18
41 2 0.06
42 26 0.76
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.39
Consensus pattern (40 bp):
TATAATTTATATAAACTAATGAACCATATAATATATACTC
Found at i:561114 original size:12 final size:12
Alignment explanation
Indices: 561086--561125 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
561076 ACTATAAAGT
561086 ATATAGTTTAT-
1 ATATAGTTTATA
*
561097 ATATAGTATATA
1 ATATAGTTTATA
561109 ATATAGTTTATA
1 ATATAGTTTATA
561121 ATATA
1 ATATA
561126 TAGTAAATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
11 10 0.38
12 16 0.62
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.47
Consensus pattern (12 bp):
ATATAGTTTATA
Found at i:561482 original size:18 final size:18
Alignment explanation
Indices: 561456--561535 Score: 52
Period size: 21 Copynumber: 4.2 Consensus size: 18
561446 AATTAGATTG
561456 CCCAGGGGTACAAATTCC
1 CCCAGGGGTACAAATTCC
* **
561474 CCCATGGGTACCGATTCCC
1 CCCAGGGGTACAAATT-CC
* *
561493 CCCGAGGGGGAACAGATTCCC
1 CCC-A-GGGGTACAAATT-CC
**
561514 CCCAGGGGGTACCGATTCC
1 CCCA-GGGGTACAAATTCC
561533 CCC
1 CCC
561536 TGTCTAACGG
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
18 13 0.25
19 10 0.20
20 13 0.25
21 15 0.29
ACGTcount: A:0.20, C:0.39, G:0.26, T:0.15
Consensus pattern (18 bp):
CCCAGGGGTACAAATTCC
Found at i:561514 original size:20 final size:20
Alignment explanation
Indices: 561486--561535 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
561476 CATGGGTACC
561486 GATTCCCCCCGAGGGGGAACA
1 GATTCCCCCC-AGGGGGAACA
* *
561507 GATTCCCCCCAGGGGGTACC
1 GATTCCCCCCAGGGGGAACA
561527 GATTCCCCC
1 GATTCCCCC
561536 TGTCTAACGG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.18, C:0.40, G:0.28, T:0.14
Consensus pattern (20 bp):
GATTCCCCCCAGGGGGAACA
Found at i:562201 original size:2 final size:2
Alignment explanation
Indices: 562196--562277 Score: 54
Period size: 2 Copynumber: 44.0 Consensus size: 2
562186 CTACATAGTT
* * * *
562196 TA TA TA TA -A TA TA TA -A AA T- TA TA AA TA TA AA CTA TA TA GTT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA
562237 TA TA TA TA T- TA -A TA TA TA TA TA TA TA TA T- TA -A TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
562274 TA TA
1 TA TA
562278 ATTGTTTTAA
Statistics
Matches: 63, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
1 8 0.13
2 53 0.84
3 2 0.03
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (2 bp):
TA
Found at i:563371 original size:13 final size:13
Alignment explanation
Indices: 563349--563395 Score: 69
Period size: 13 Copynumber: 3.6 Consensus size: 13
563339 ATAAAAAATG
*
563349 TAAATTATATATA
1 TAAATAATATATA
563362 TAAATAATATA-A
1 TAAATAATATATA
563374 TATAATAATATATA
1 TA-AATAATATATA
563388 TAAATAAT
1 TAAATAAT
563396 CAGTTGAACT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
12 3 0.10
13 25 0.81
14 3 0.10
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TAAATAATATATA
Found at i:574905 original size:20 final size:21
Alignment explanation
Indices: 574880--574931 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
574870 TTTTCCCAAT
*
574880 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
574900 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
574921 TCGCAATGCGA
1 TCGCAATGCGA
574932 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:574945 original size:20 final size:20
Alignment explanation
Indices: 574920--574993 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
574910 AATTGGGAAA
*
574920 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
574940 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
574961 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
*
574981 TTCGCAACGCGAT
1 ATCGCAACGCGAT
574994 TTACATAGCG
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
19 2 0.05
20 26 0.60
21 13 0.30
22 2 0.05
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:575556 original size:19 final size:19
Alignment explanation
Indices: 575511--575558 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
575501 TTCGAGAATG
*
575511 AAAATCGCAACGCGGAAAT
1 AAAATCGCAACGCGGAAAC
*
575530 AACTATCGCAACGC-GAAACC
1 AA-AATCGCAACGCGGAAA-C
575550 AAAATCGCA
1 AAAATCGCA
575559 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.46, C:0.27, G:0.17, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGGAAAC
Found at i:575576 original size:19 final size:19
Alignment explanation
Indices: 575554--575699 Score: 105
Period size: 19 Copynumber: 8.1 Consensus size: 19
575544 GAAACCAAAA
*
575554 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
575573 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
575592 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
575606 TCTCGTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
575625 TCGCATTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
575639 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
575658 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
575678 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
575698 TC
1 TC
575700 AACCAAAAGA
Statistics
Matches: 99, Mismatches: 16, Indels: 24
0.71 0.12 0.17
Matches are distributed among these distances:
14 18 0.18
16 4 0.04
17 5 0.05
19 40 0.40
20 31 0.31
21 1 0.01
ACGTcount: A:0.13, C:0.25, G:0.20, T:0.42
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:575624 original size:33 final size:33
Alignment explanation
Indices: 575587--575674 Score: 149
Period size: 33 Copynumber: 2.6 Consensus size: 33
575577 GTTGCGATTT
575587 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
* *
575620 TCATTTCGCATTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
575653 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
575675 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 37 0.73
34 14 0.27
ACGTcount: A:0.12, C:0.27, G:0.22, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:575676 original size:20 final size:20
Alignment explanation
Indices: 575642--575699 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
575632 GCGATTCTCT
**
575642 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
575662 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
575682 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
575700 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:577868 original size:21 final size:21
Alignment explanation
Indices: 577844--577952 Score: 55
Period size: 21 Copynumber: 5.2 Consensus size: 21
577834 TCATTCCTCG
577844 AGAGTCCCCTCTCACCGTTCA
1 AGAGTCCCCTCTCACCGTTCA
* * * *
577865 AGAGGCCACTGTCATCC-CTCA
1 AGAGTCCCCTCTCA-CCGTTCA
* * *
577886 AGAGTCCACTC-CTATCGTTGA
1 AGAGTCCCCTCTC-ACCGTTCA
* * *
577907 AGAGGCCCCTATCATTCC--TCG
1 AGAGTCCCCTCTCA--CCGTTCA
*
577928 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCTCACCGTTCA
577949 AGAG
1 AGAG
577953 GCCACTGTCA
Statistics
Matches: 61, Mismatches: 19, Indels: 16
0.64 0.20 0.17
Matches are distributed among these distances:
19 2 0.03
20 2 0.03
21 53 0.87
22 3 0.05
23 1 0.02
ACGTcount: A:0.22, C:0.38, G:0.18, T:0.22
Consensus pattern (21 bp):
AGAGTCCCCTCTCACCGTTCA
Found at i:577868 original size:42 final size:41
Alignment explanation
Indices: 577822--577955 Score: 178
Period size: 42 Copynumber: 3.2 Consensus size: 41
577812 CCTATTGTTA
577822 AAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCTCACCGTTC
1 AAGAGGCCCCTATCATTCCTCGAGAGTCCCCTC-CACCGTTC
* * * * * * *
577864 AAGAGGCCACTGTCATCCCTCAAGAGTCCACTCCTATCGTTG
1 AAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCC-ACCGTTC
577906 AAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCACCGTTC
1 AAGAGGCCCCTATCATTCCTCGAGAGTCCCCT-CCACCGTTC
577948 AAGAGGCC
1 AAGAGGCC
577956 ACTGTCATCG
Statistics
Matches: 76, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
41 1 0.01
42 73 0.96
43 2 0.03
ACGTcount: A:0.22, C:0.38, G:0.19, T:0.22
Consensus pattern (41 bp):
AAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCACCGTTC
Found at i:577967 original size:21 final size:21
Alignment explanation
Indices: 577859--577974 Score: 65
Period size: 21 Copynumber: 5.5 Consensus size: 21
577849 CCCCTCTCAC
577859 CGTTCAAGAGGCCACTGTCAT
1 CGTTCAAGAGGCCACTGTCAT
** * *
577880 CCCTCAAGAGTCCACT-CCTAT
1 CGTTCAAGAGGCCACTGTC-AT
* * *
577901 CGTTGAAGAGGCCCCTATCATT
1 CGTTCAAGAGGCCACTGTCA-T
* * * * ** *
577923 C-CTCGAGAGTCCCCTCCCAC
1 CGTTCAAGAGGCCACTGTCAT
577943 CGTTCAAGAGGCCACTGTCAT
1 CGTTCAAGAGGCCACTGTCAT
*
577964 CGTTGAAGAGG
1 CGTTCAAGAGG
577975 TCCTTCCCAC
Statistics
Matches: 66, Mismatches: 25, Indels: 8
0.67 0.25 0.08
Matches are distributed among these distances:
20 2 0.03
21 61 0.92
22 3 0.05
ACGTcount: A:0.22, C:0.34, G:0.22, T:0.22
Consensus pattern (21 bp):
CGTTCAAGAGGCCACTGTCAT
Found at i:577973 original size:84 final size:84
Alignment explanation
Indices: 577789--577964 Score: 316
Period size: 84 Copynumber: 2.1 Consensus size: 84
577779 CCCGACTCGC
* *
577789 CTGTCATCCCTAAAGAGTCCACTCCTATTGTTAAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTAAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
*
577854 CTCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
*
577873 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTAAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
577938 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
577957 CTGTCATC
1 CTGTCATC
577965 GTTGAAGAGG
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 88 1.00
ACGTcount: A:0.22, C:0.36, G:0.17, T:0.24
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTCCACTCCTATCGTTAAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
CCCACCGTTCAAGAGGCCA
Found at i:577983 original size:42 final size:41
Alignment explanation
Indices: 577789--577994 Score: 146
Period size: 42 Copynumber: 4.9 Consensus size: 41
577779 CCCGACTCGC
* * * ** * *
577789 CTGTCATCCCTAAAGAGTCCACTCCTATTGTTAAAGAGGCCC
1 CTGTCATCCTTGAAGAGTCC-CTCCCACCGTTCAAGAGGCCA
* * *
577831 CTATCATTCCTCG-AGAGTCCCCTCTCACCGTTCAAGAGGCCA
1 CTGTCA-TCCTTGAAGAGT-CCCTCCCACCGTTCAAGAGGCCA
* * * * * *
577873 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCC
1 CTGTCATCCTTGAAGAGTCC-CTCCCACCGTTCAAGAGGCCA
* *
577915 CTATCATTCCTCG-AGAGTCCCCTCCCACCGTTCAAGAGGCCA
1 CTGTCA-TCCTTGAAGAGT-CCCTCCCACCGTTCAAGAGGCCA
* * *
577957 CTGTCATCGTTGAAGAGGTCCTTCCCACCATTCAAGAG
1 CTGTCATCCTTGAAGA-GTCCCTCCCACCGTTCAAGAG
577995 CCCGATTCAC
Statistics
Matches: 124, Mismatches: 32, Indels: 16
0.72 0.19 0.09
Matches are distributed among these distances:
41 9 0.07
42 103 0.83
43 12 0.10
ACGTcount: A:0.23, C:0.35, G:0.18, T:0.24
Consensus pattern (41 bp):
CTGTCATCCTTGAAGAGTCCCTCCCACCGTTCAAGAGGCCA
Found at i:577994 original size:84 final size:84
Alignment explanation
Indices: 577789--577994 Score: 261
Period size: 84 Copynumber: 2.5 Consensus size: 84
577779 CCCGACTCGC
* * *** *
577789 CTGTCATCCCTAAAGAGTCCACTCCTATTGTTAAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
*
577854 CTCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
* * * *
577873 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
577938 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
** * *
577957 CTGTCATCGTTGAAGAGGTCC-TTCCCACCATTCAAGAG
1 CTGTCATCCCTCAAGA-GTCCACTCCCACCATTCAAGAG
577995 CCCGATTCAC
Statistics
Matches: 109, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
84 105 0.96
85 4 0.04
ACGTcount: A:0.23, C:0.35, G:0.18, T:0.24
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
CCCACCGTTCAAGAGGCCA
Found at i:579373 original size:14 final size:14
Alignment explanation
Indices: 579354--579389 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
579344 ATTGTTTAAT
579354 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
579368 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
579382 TGATTTGT
1 TGATTTGT
579390 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:579570 original size:19 final size:19
Alignment explanation
Indices: 579548--579698 Score: 98
Period size: 19 Copynumber: 8.7 Consensus size: 19
579538 CGAAATTAAA
*
579548 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
579567 TTCGCATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
579583 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
579600 TTCGCATTGCGA-----AA
1 TTCGCATTGCGATTTTCAT
* *
579614 TTAGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
579633 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
579649 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
** *
579666 TTCGCATTGCGATAGTAAT
1 TTCGCATTGCGATTTTCAT
579685 TTCCGCATTGCGAT
1 TT-CGCATTGCGAT
579699 AGACATTAAG
Statistics
Matches: 100, Mismatches: 16, Indels: 31
0.68 0.11 0.21
Matches are distributed among these distances:
14 23 0.23
16 13 0.13
17 13 0.13
19 40 0.40
20 11 0.11
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.42
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:579594 original size:33 final size:32
Alignment explanation
Indices: 579552--579678 Score: 193
Period size: 33 Copynumber: 3.9 Consensus size: 32
579542 ATTAAATTCG
579552 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
579585 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
579618 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
579651 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
579679 AGTAATTTCC
Statistics
Matches: 86, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
31 3 0.03
33 80 0.93
35 3 0.03
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:579636 original size:66 final size:66
Alignment explanation
Indices: 579545--579677 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
579535 ACGCGAAATT
*
579545 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
579610 G
66 G
*
579611 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
579676 G
66 G
579677 A
1 A
579678 TAGTAATTTC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.41
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:581313 original size:12 final size:12
Alignment explanation
Indices: 581296--581320 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
581286 TCTTCGGGGA
581296 CTTTTTCTTCTT
1 CTTTTTCTTCTT
581308 CTTTTTCTTCTT
1 CTTTTTCTTCTT
581320 C
1 C
581321 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:581531 original size:24 final size:24
Alignment explanation
Indices: 581504--581550 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
581494 CAAAATCCGA
*
581504 GTATTGACCAATATCAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
581528 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
581551 AATACTGACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGG
Found at i:581559 original size:24 final size:24
Alignment explanation
Indices: 581508--581559 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
581498 ATCCGAGTAT
* ** *
581508 TGACCAATATCAAAGTTCGGGTAT
1 TGACCAAGATCAAAGTTCGAATAC
*
581532 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTTCGAATAC
581556 TGAC
1 TGAC
581560 TAGTACTCAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (24 bp):
TGACCAAGATCAAAGTTCGAATAC
Found at i:582319 original size:20 final size:20
Alignment explanation
Indices: 582290--582340 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
582280 TGTATTATCT
582290 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
*
582310 CGTTGTGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
582330 CGTTGCGAAAG
1 CGTTGCGAAAG
582341 GCAATCATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.29, C:0.18, G:0.31, T:0.22
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGAATCG
Found at i:582610 original size:20 final size:20
Alignment explanation
Indices: 582553--582603 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
582543 ATTCATTTGA
*
582553 CTATCACAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
582573 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
582593 CTATCGCAACG
1 CTATCGCAACG
582604 ACAAAATCGC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.35, C:0.27, G:0.22, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:582670 original size:19 final size:19
Alignment explanation
Indices: 582629--582693 Score: 95
Period size: 19 Copynumber: 3.7 Consensus size: 19
582619 GAAATGAAAA
582629 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
582645 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
582662 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
582681 TCGCATTGCGATT
1 TCGCATTGCGATT
582694 CTCTCGTTGC
Statistics
Matches: 44, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
14 11 0.25
16 3 0.07
17 3 0.07
19 27 0.61
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:582819 original size:14 final size:14
Alignment explanation
Indices: 582800--582836 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
582790 CATCAATTAA
582800 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
582814 ACAAATCATCTTTT
1 ACAAATCAACATTT
582828 ACAAATCAA
1 ACAAATCAA
582837 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:584727 original size:20 final size:20
Alignment explanation
Indices: 584704--584757 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
584694 GAAACTTAAA
584704 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
584724 ATCGCAACAC-AGAAATGGCT
1 ATCGCAACGCGA-AAATGACT
*
584744 ATCGCAATGCGAAA
1 ATCGCAACGCGAAA
584758 TTAAAATCGC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 1 0.04
20 26 0.93
21 1 0.04
ACGTcount: A:0.41, C:0.24, G:0.20, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:584766 original size:19 final size:18
Alignment explanation
Indices: 584744--584839 Score: 64
Period size: 19 Copynumber: 5.7 Consensus size: 18
584734 AGAAATGGCT
584744 ATCGCAATGCGAAATTAAA
1 ATCGCAATGCGAAA-TAAA
*
584763 ATCGCAA--CG--ACAAA
1 ATCGCAATGCGAAATAAA
*
584777 ATCGCAATGCGAAATGAA
1 ATCGCAATGCGAAATAAA
*
584795 ATCGC-A-GCG--ACAAA
1 ATCGCAATGCGAAATAAA
* *
584809 ATCGCAACGCGAAACACAA
1 ATCGCAATGCGAAATA-AA
*
584828 ATCGCATTGCGA
1 ATCGCAATGCGA
584840 TTTTCATTTC
Statistics
Matches: 61, Mismatches: 7, Indels: 18
0.71 0.08 0.21
Matches are distributed among these distances:
14 18 0.30
15 2 0.03
16 8 0.13
17 3 0.05
18 11 0.18
19 19 0.31
ACGTcount: A:0.44, C:0.24, G:0.19, T:0.14
Consensus pattern (18 bp):
ATCGCAATGCGAAATAAA
Found at i:584779 original size:14 final size:14
Alignment explanation
Indices: 584760--584817 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
584750 ATGCGAAATT
584760 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
584774 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
*
584790 ATGAAATCGCAGCGAC
1 A--AAATCGCAACGAC
584806 AAAATCGCAACG
1 AAAATCGCAACG
584818 CGAAACACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 20 0.56
16 8 0.22
18 8 0.22
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:584786 original size:33 final size:32
Alignment explanation
Indices: 584744--584833 Score: 126
Period size: 32 Copynumber: 2.8 Consensus size: 32
584734 AGAAATGGCT
584744 ATCGCAATGCGAAATTAAAATCGCAACGACAAA
1 ATCGCAATGCGAAA-TAAAATCGCAACGACAAA
* *
584777 ATCGCAATGCGAAATGAAATCGCAGCGACAAA
1 ATCGCAATGCGAAATAAAATCGCAACGACAAA
* *
584809 ATCGCAACGCGAAACACAAATCGCA
1 ATCGCAATGCGAAATA-AAATCGCA
584834 TTGCGATTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
32 29 0.57
33 22 0.43
ACGTcount: A:0.46, C:0.24, G:0.18, T:0.12
Consensus pattern (32 bp):
ATCGCAATGCGAAATAAAATCGCAACGACAAA
Found at i:584851 original size:19 final size:19
Alignment explanation
Indices: 584829--584910 Score: 104
Period size: 18 Copynumber: 4.6 Consensus size: 19
584819 GAAACACAAA
584829 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
584848 TCGCGTTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
*
584866 TCGCATTGC-AATTT--TT
1 TCGCATTGCGATTTTCATT
584882 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
584899 TCGCATTGCGAT
1 TCGCATTGCGAT
584911 AGCCATTTTC
Statistics
Matches: 54, Mismatches: 3, Indels: 12
0.78 0.04 0.17
Matches are distributed among these distances:
14 4 0.07
15 4 0.07
16 5 0.09
17 6 0.11
18 18 0.33
19 17 0.31
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:584946 original size:20 final size:20
Alignment explanation
Indices: 584897--584946 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
584887 GCGATTTTCA
*
584897 TTTCGCATTGCGATAGCCAT
1 TTTCGCGTTGCGATAGCCAT
*
584917 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGCCAT
*
584937 TTTCGTGTTG
1 TTTCGCGTTG
584947 TGAAAGTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.14, C:0.20, G:0.24, T:0.42
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGCCAT
Found at i:585457 original size:18 final size:18
Alignment explanation
Indices: 585431--585475 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
585421 GTCGATCAGA
*
585431 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
585449 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
585467 TGATGGCTC
1 TGATGGCTC
585476 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:586820 original size:20 final size:20
Alignment explanation
Indices: 586795--586868 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 20
586785 AATAGTTTCT
*
586795 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACGC
**
586815 GAAAATGACTATCGCAACGC
1 GAAAATGAAAATCGCAACGC
** **
586835 GAATTTGACTATCGCAACGC
1 GAAAATGAAAATCGCAACGC
*
586855 GAAACT-AAAATCGC
1 GAAAATGAAAATCGC
586869 GTTGCGATTT
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 6 0.13
20 39 0.87
ACGTcount: A:0.43, C:0.23, G:0.18, T:0.16
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACGC
Found at i:587129 original size:22 final size:21
Alignment explanation
Indices: 587095--587143 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 21
587085 TCTGAGAGAT
587095 GGAGAT-AGACGGATTTCGCC
1 GGAGATGAGACGGATTTCGCC
*
587115 GGAGATGAGGACGGATTTCGTC
1 GGAGATGA-GACGGATTTCGCC
587137 GGAGATG
1 GGAGATG
587144 GGTGAGAGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 6 0.23
21 1 0.04
22 19 0.73
ACGTcount: A:0.24, C:0.14, G:0.41, T:0.20
Consensus pattern (21 bp):
GGAGATGAGACGGATTTCGCC
Found at i:587419 original size:20 final size:20
Alignment explanation
Indices: 587313--587447 Score: 103
Period size: 20 Copynumber: 6.7 Consensus size: 20
587303 CGCTTTGAAA
*
587313 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
587334 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
587354 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
587374 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
*
587395 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* *
587415 ATCGCATTACGATAGTCATT
1 ATCGCATTGCGATAGTCAGT
587435 ATCGCATTGCGAT
1 ATCGCATTGCGAT
587448 TTTTCCAATT
Statistics
Matches: 93, Mismatches: 17, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
19 5 0.05
20 63 0.68
21 23 0.25
22 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:587419 original size:61 final size:61
Alignment explanation
Indices: 587313--587450 Score: 177
Period size: 61 Copynumber: 2.3 Consensus size: 61
587303 CGCTTTGAAA
* * * * *
587313 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTACGAAAGTCAGT
* * * * * *
587374 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTACGATAGTCATT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTACGAAAGTCAGT
587435 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
587451 TCCAATTCGC
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
61 64 1.00
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTACGAAAGTCAGT
Found at i:587466 original size:61 final size:61
Alignment explanation
Indices: 587313--587468 Score: 163
Period size: 61 Copynumber: 2.6 Consensus size: 61
587303 CGCTTTGAAA
* * * * * *
587313 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTAATATCGCGTTGCGATAGTAAGAATCGCATTACGAAAGTCAGT
* * * * * * *
587374 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTACGATAGTCATT
1 ATCGCATTGCGATTTTGTAATATCGCGTTGCGATAGTAAGAATCGCATTACGAAAGTCAGT
587435 ATCGCATTGCGATTTT-TCCAAT-TCGCGTTGCGAT
1 ATCGCATTGCGATTTTGT--AATATCGCGTTGCGAT
587469 TTACTTATTC
Statistics
Matches: 78, Mismatches: 15, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
60 1 0.01
61 75 0.96
62 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTAATATCGCGTTGCGATAGTAAGAATCGCATTACGAAAGTCAGT
Found at i:587558 original size:21 final size:21
Alignment explanation
Indices: 587518--587558 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
587508 ATTGTAGACC
**
587518 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
587539 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
587559 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:589013 original size:94 final size:94
Alignment explanation
Indices: 588864--589042 Score: 340
Period size: 94 Copynumber: 1.9 Consensus size: 94
588854 AGTGAATCGG
*
588864 TCATTTACATGCTTAATATGTGTTCATGTCCTCTTGGTCTGTAAATTGGCATACTTGTTTCCATC
1 TCATTTACATGCTTAATATGTGTTCATGTCCTCTTGGTCTGTAAATTGACATACTTGTTTCCATC
588929 TGACATTTATTGATATCCAAGTAAATTGA
66 TGACATTTATTGATATCCAAGTAAATTGA
*
588958 TCATTTACATGCTTAATATGTGTTCGTGTCCTCTTGGTCTGTAAATTGACATACTTGTTTCCATC
1 TCATTTACATGCTTAATATGTGTTCATGTCCTCTTGGTCTGTAAATTGACATACTTGTTTCCATC
589023 TGACATTTATTGATATCCAA
66 TGACATTTATTGATATCCAA
589043 CTTTAGGAGT
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
94 83 1.00
ACGTcount: A:0.25, C:0.18, G:0.15, T:0.43
Consensus pattern (94 bp):
TCATTTACATGCTTAATATGTGTTCATGTCCTCTTGGTCTGTAAATTGACATACTTGTTTCCATC
TGACATTTATTGATATCCAAGTAAATTGA
Found at i:590420 original size:15 final size:15
Alignment explanation
Indices: 590400--590429 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
590390 GTTGCTGCAC
590400 CGAAGTTGCAACAGA
1 CGAAGTTGCAACAGA
590415 CGAAGTTGCAACAGA
1 CGAAGTTGCAACAGA
590430 AGTTAATTCT
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:0.40, C:0.20, G:0.27, T:0.13
Consensus pattern (15 bp):
CGAAGTTGCAACAGA
Found at i:593389 original size:29 final size:29
Alignment explanation
Indices: 593315--593396 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
593305 ATAATAAGGT
* *
593315 ATTATAAAATAGTATAGGTTTAGATAATA
1 ATTATAAAATAATATATGTTTAGATAATA
*
593344 ATTATAAAATAATATATGTTTAGATAATG
1 ATTATAAAATAATATATGTTTAGATAATA
*
593373 ATTATAAAATAATATATATTTAGA
1 ATTATAAAATAATATATGTTTAGA
593397 ATATTTATGT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (29 bp):
ATTATAAAATAATATATGTTTAGATAATA
Found at i:599640 original size:18 final size:18
Alignment explanation
Indices: 599613--599664 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
599603 TTTTCTAATC
* *
599613 TTTATAACAGTAGCATTT
1 TTTATTACAGTAGCATTA
*
599631 TTTATTACAGTAACA-TA
1 TTTATTACAGTAGCATTA
* *
599648 TTTATTATAATAGCATT
1 TTTATTACAGTAGCATT
599665 GTGATTTTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
17 13 0.48
18 14 0.52
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.46
Consensus pattern (18 bp):
TTTATTACAGTAGCATTA
Found at i:610864 original size:17 final size:17
Alignment explanation
Indices: 610841--610882 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
610831 ACAATTATTC
610841 TAAAAATAAATAAAACA
1 TAAAAATAAATAAAACA
* * *
610858 TAGAAATACATAAAATA
1 TAAAAATAAATAAAACA
610875 TAAAAATA
1 TAAAAATA
610883 GGCTCCTATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.21
Consensus pattern (17 bp):
TAAAAATAAATAAAACA
Found at i:623829 original size:36 final size:36
Alignment explanation
Indices: 623749--623949 Score: 167
Period size: 36 Copynumber: 5.4 Consensus size: 36
623739 TAATAATTTC
* *
623749 AAAAAC-TATAATATATCGTTTTTGAAAACTTATTTTTAAA
1 AAAAACATATAATATATAGTTTTT-AAAA-TTA-TTTT--G
623789 AAAAACATATAATATATAGTTTTTAAAATTATTTTG
1 AAAAACATATAATATATAGTTTTTAAAATTATTTTG
* *
623825 AAAAACATATAGTATATAGTTTTTTAAAATAATTTTG
1 AAAAACATATAATATATAG-TTTTTAAAATTATTTTG
* * *
623862 -AAAACGTATAGTATATAGTTTTTAAAA-TAGTTTCG
1 AAAAACATATAATATATAGTTTTTAAAATTA-TTTTG
** ** **
623897 -AAAATGTATAATATATAGTTTAAAAAAATGGTTTTG
1 AAAAACATATAATATATAGTTT-TTAAAATTATTTTG
*
623933 AAAACATATATAATATA
1 AAAA-ACATATAATATA
623950 ATGGCTTTGA
Statistics
Matches: 139, Mismatches: 15, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
34 1 0.01
35 32 0.23
36 43 0.31
37 19 0.14
38 15 0.11
39 3 0.02
40 10 0.07
41 16 0.12
ACGTcount: A:0.47, C:0.04, G:0.08, T:0.41
Consensus pattern (36 bp):
AAAAACATATAATATATAGTTTTTAAAATTATTTTG
Found at i:623949 original size:71 final size:72
Alignment explanation
Indices: 623790--623949 Score: 175
Period size: 71 Copynumber: 2.2 Consensus size: 72
623780 ATTTTTAAAA
* * ***
623790 AAAACATATA-ATATATAGTTTTTAAAATTATTTTGAAAAACATATAGTATATAGTTTTTTAAAA
1 AAAACATATATA-ATATAGTTTTTAAAATTATTTCGAAAAACATATAATATATAGTTTAAAAAAA
623854 TAATTTTG
65 TAATTTTG
* **
623862 AAAACGTATAGT-ATATAGTTTTTAAAA-TAGTTTCG-AAAATGTATAATATATAGTTTAAAAAA
1 AAAACATATA-TAATATAGTTTTTAAAATTA-TTTCGAAAAACATATAATATATAGTTTAAAAAA
**
623924 ATGGTTTTG
64 ATAATTTTG
623933 AAAACATATATAATATA
1 AAAACATATATAATATA
623950 ATGGCTTTGA
Statistics
Matches: 73, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
70 1 0.01
71 44 0.60
72 28 0.38
ACGTcount: A:0.47, C:0.03, G:0.09, T:0.41
Consensus pattern (72 bp):
AAAACATATATAATATAGTTTTTAAAATTATTTCGAAAAACATATAATATATAGTTTAAAAAAAT
AATTTTG
Found at i:624023 original size:13 final size:13
Alignment explanation
Indices: 624005--624032 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
623995 TATAATATAG
624005 TTTTGAAAACATA
1 TTTTGAAAACATA
624018 TTTTGAAAACATA
1 TTTTGAAAACATA
624031 TT
1 TT
624033 ATATAGTTTT
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:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (13 bp):
TTTTGAAAACATA
Found at i:624056 original size:20 final size:22
Alignment explanation
Indices: 624018--624057 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
624008 TGAAAACATA
*
624018 TTTTGAAAACATATTATATAGT
1 TTTTGAAAACATATAATATAGT
624040 TTTTG-AAA-ATATAATATA
1 TTTTGAAAACATATAATATA
624058 TGTTACATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 3 0.18
22 5 0.29
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (22 bp):
TTTTGAAAACATATAATATAGT
Found at i:624098 original size:17 final size:19
Alignment explanation
Indices: 624076--624116 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
624066 AGTTTACGTA
624076 TTATA-TTA-TATATTATT
1 TTATATTTATTATATTATT
624093 TTATATTTATTATATTATT
1 TTATATTTATTATATTATT
*
624112 ATATA
1 TTATA
624117 GGTATTCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.24
18 3 0.14
19 13 0.62
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TTATATTTATTATATTATT
Found at i:624122 original size:19 final size:19
Alignment explanation
Indices: 624084--624122 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
624074 TATTATATTA
* **
624084 TATATTATTTTATATTTAT
1 TATATTATTATATAGGTAT
624103 TATATTATTATATAGGTAT
1 TATATTATTATATAGGTAT
624122 T
1 T
624123 CATTTAATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (19 bp):
TATATTATTATATAGGTAT
Found at i:625700 original size:17 final size:18
Alignment explanation
Indices: 625678--625717 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
625668 ATACTAATAA
625678 TATCTTTA-AAAAAACTT
1 TATCTTTATAAAAAACTT
*
625695 TATC-TTATAATAAACTT
1 TATCTTTATAAAAAACTT
625712 TATCTT
1 TATCTT
625718 ATATTAAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 3 0.15
17 16 0.80
18 1 0.05
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.47
Consensus pattern (18 bp):
TATCTTTATAAAAAACTT
Found at i:625851 original size:5 final size:5
Alignment explanation
Indices: 625841--625886 Score: 92
Period size: 5 Copynumber: 9.2 Consensus size: 5
625831 CGATGTCTTA
625841 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT T
625887 ACTTAACTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTCT
Found at i:629016 original size:18 final size:18
Alignment explanation
Indices: 628993--629036 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
628983 ATTACGTTAA
628993 GAAGATAAGGATAAGTTT
1 GAAGATAAGGATAAGTTT
629011 GAAGATAAGGATAAGTTT
1 GAAGATAAGGATAAGTTT
*
629029 GAAAATAA
1 GAAGATAA
629037 ATATTAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (18 bp):
GAAGATAAGGATAAGTTT
Found at i:629974 original size:17 final size:17
Alignment explanation
Indices: 629952--629984 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
629942 TTGAGAGAGA
*
629952 AAAATAGTTGGGTGACC
1 AAAATAGTTGAGTGACC
629969 AAAATAGTTGAGTGAC
1 AAAATAGTTGAGTGAC
629985 TAAATATGTA
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:0.39, C:0.09, G:0.27, T:0.24
Consensus pattern (17 bp):
AAAATAGTTGAGTGACC
Found at i:631521 original size:33 final size:33
Alignment explanation
Indices: 631483--631551 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
631473 CCCCAACACA
* *
631483 GCACGTCCCTAATACCCCAACACAGGTCGCCAT
1 GCACGTCCCCAACACCCCAACACAGGTCGCCAT
*
631516 GCACGTCCCCAACACCCCAACACAGGTCGTCAT
1 GCACGTCCCCAACACCCCAACACAGGTCGCCAT
631549 GCA
1 GCA
631552 GCACTCCCAC
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:0.28, C:0.43, G:0.16, T:0.13
Consensus pattern (33 bp):
GCACGTCCCCAACACCCCAACACAGGTCGCCAT
Found at i:631714 original size:23 final size:23
Alignment explanation
Indices: 631684--631727 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
631674 GTGCATGGGT
631684 TGCATCCATAGCTGGGAGATTCC
1 TGCATCCATAGCTGGGAGATTCC
631707 TGCATCCATAGCTGGGAGATT
1 TGCATCCATAGCTGGGAGATT
631728 GTAGCCAAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (23 bp):
TGCATCCATAGCTGGGAGATTCC
Found at i:632179 original size:27 final size:25
Alignment explanation
Indices: 632149--632204 Score: 94
Period size: 27 Copynumber: 2.2 Consensus size: 25
632139 AATTTAGTTA
632149 ATTAGTTTGTTAGTTTAAGTTAATTAT
1 ATTAGTTTGTTAGTTTAAGTT-A-TAT
632176 ATTAGTTTGTTAGTTTAAGTTATAT
1 ATTAGTTTGTTAGTTTAAGTTATAT
632201 ATTA
1 ATTA
632205 TTATATAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
25 7 0.24
26 1 0.03
27 21 0.72
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.55
Consensus pattern (25 bp):
ATTAGTTTGTTAGTTTAAGTTATAT
Found at i:632508 original size:39 final size:39
Alignment explanation
Indices: 632461--632538 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
632451 TTATATTAGA
632461 TAATTTGTGCGAGATAATTTCTTTTTAAAAAAATATTGT
1 TAATTTGTGCGAGATAATTTCTTTTTAAAAAAATATTGT
632500 TAATTTGTGCGAGATAATTTCTTTTTAAAAAAATATTGT
1 TAATTTGTGCGAGATAATTTCTTTTTAAAAAAATATTGT
632539 GTTTAAAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.36, C:0.05, G:0.13, T:0.46
Consensus pattern (39 bp):
TAATTTGTGCGAGATAATTTCTTTTTAAAAAAATATTGT
Found at i:634803 original size:37 final size:38
Alignment explanation
Indices: 634762--634837 Score: 145
Period size: 37 Copynumber: 2.0 Consensus size: 38
634752 TTCGTAGCGA
634762 GATAGTCAGCATGGGTAAG-TTTATTTTCAAATTTTGT
1 GATAGTCAGCATGGGTAAGTTTTATTTTCAAATTTTGT
634799 GATAGTCAGCATGGGTAAGTTTTATTTTCAAATTTTGT
1 GATAGTCAGCATGGGTAAGTTTTATTTTCAAATTTTGT
634837 G
1 G
634838 CATTTTTTAC
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 19 0.50
38 19 0.50
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.43
Consensus pattern (38 bp):
GATAGTCAGCATGGGTAAGTTTTATTTTCAAATTTTGT
Found at i:635850 original size:60 final size:60
Alignment explanation
Indices: 635774--636759 Score: 788
Period size: 60 Copynumber: 17.2 Consensus size: 60
635764 GTATTTATAA
*
635774 GATTTAGTAATGATTAGTAATGATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
* * *
635834 GATTTAGTAATAATTAGTAGTAATGAAATTATTATTAATATTTAATGATTTGATATTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
*
635894 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
* *
635954 GA-TTAG---T-A--A-TAATAAT----TTATTATTAATATTTAATGATTTTATATTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
* * * ** * ** * *
636002 GATTTAGTAATGATTTGATAGTAAT-AATTTACGACTTGAACAATGAACAATG-TTTGGT--TCA
1 GATTTAGTAATGATTAG-TAATAATGAAATTATTA-TT-AA-TAT--TTAATGATTTGATAGTAA
636063 -
60 T
* ** * * * * * *
636063 -ATTAACCATAT-TTTCGT--TACATAAAATTA-TAATAATGATTTAGT-A-ATGATTAGTAAT
1 GATTTAGTA-ATGATTAGTAATA-ATGAAATTATTATTAAT-ATTTAATGATTTGA-TAGTAAT
* * * * ** * *
636120 -A-AT-GAAATTATTATTAAT-ATTTAATGA-T-TTGATA-TTAATGA-TT--TAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
* * ** * * *
636170 GA-TTAGTAAT-AAT-G-AA-ATTGTTATTAATATT--TA-ATG---ATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
*
636219 GATTTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
*
636279 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
* *
636339 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTAATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
* * *
636399 GA-TTAGTAATGATTAATAATAATGAAATTATTATTAATTTTTAATGATTTAATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
* * * * * *
636458 GA-TTAGTAAT-AAT-GAAATTAT--TATTAATATTTAATGATTTGAT-ATTAATGATTTAGTAA
1 GATTTAGTAATGATTAGTAATAATGAAATTATTA-TTAAT-ATTTAATGATT--TGA--TAGTAA
636517 T
60 T
* *
636518 TA-TTAG---T-A--A-TAAT-A--AAATTGTTATTAATATTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
* * *
636567 GATTTAGTAATGATTAGTAATAATGATATTATTATTAATATTTAATGATTTGATATTATT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
* *
636627 GATTTAGTAATGATTAATAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
* * * *
636687 GA-TTAGTAATGATTAATAATAAT-AATTTATTATTAATATTTAATGATTTAATATTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
636745 GATTTAGTAATGATT
1 GATTTAGTAATGATT
636760 TGATAGTAAT
Statistics
Matches: 753, Mismatches: 103, Indels: 141
0.76 0.10 0.14
Matches are distributed among these distances:
46 1 0.00
47 2 0.00
48 31 0.04
49 31 0.04
50 20 0.03
51 11 0.01
52 23 0.03
53 18 0.02
54 25 0.03
55 21 0.03
56 18 0.02
57 28 0.04
58 41 0.05
59 109 0.14
60 356 0.47
61 4 0.01
62 4 0.01
63 2 0.00
64 4 0.01
65 4 0.01
ACGTcount: A:0.41, C:0.01, G:0.12, T:0.46
Consensus pattern (60 bp):
GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
Found at i:636124 original size:13 final size:12
Alignment explanation
Indices: 636088--636184 Score: 53
Period size: 11 Copynumber: 8.1 Consensus size: 12
636078 GTTACATAAA
636088 ATTATAATAATG
1 ATTATAATAATG
*
636100 ATT-TAGTAATG
1 ATTATAATAATG
636111 ATTAGTAATAATG
1 ATTA-TAATAATG
*
636124 AAATTATTATTAAT-
1 --ATTA-TAATAATG
*
636138 ATT-TAATGAT-
1 ATTATAATAATG
*
636148 -TTGATATTAATG
1 ATT-ATAATAATG
*
636160 ATT-TAGTAATG
1 ATTATAATAATG
636171 ATTAGTAATAATG
1 ATTA-TAATAATG
636184 A
1 A
636185 AATTGTTATT
Statistics
Matches: 65, Mismatches: 10, Indels: 19
0.69 0.11 0.20
Matches are distributed among these distances:
9 2 0.03
10 5 0.08
11 25 0.38
12 6 0.09
13 17 0.26
15 10 0.15
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.44
Consensus pattern (12 bp):
ATTATAATAATG
Found at i:636308 original size:120 final size:120
Alignment explanation
Indices: 636095--636759 Score: 986
Period size: 120 Copynumber: 5.7 Consensus size: 120
636085 AAAATTATAA
636095 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATG
1 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATG
*
636160 ATTTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAG
66 ATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAG
* *
636215 TAATGATTTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATG
1 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATG
*
636280 ATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAT
66 ATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAG
* * *
636335 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTAATAGTAATG
1 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATG
* *
636400 A-TTAGTAATGATTAATAATAATGAAATTATTATTAATTTTTAATGA--T--T--
66 ATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAG
* * *
636448 T-A--A--TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGAT--TTG-ATATTA
1 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAAT-ATT--TAATGATTTGATATTA
* * *
636505 ATGATTTAGTAATTATTAGTAATAATAAAATTGTTATTAATATTTAATGATTTGATAG
63 ATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAG
* *
636563 TAATGATTTAGTAATGATTAGTAATAATGATATTATTATTAATATTTAATGATTTGATATTATTG
1 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATG
* *
636628 ATTTAGTAATGATTAATAATAATGAAATTATTATTAATTTTTAATGATTTGATAG
66 ATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAG
* * *
636683 TAATGA-TTAGTAATGATTAATAATAAT-AATTTATTATTAATATTTAATGATTTAATATTAATG
1 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATG
636746 ATTTAGTAATGATT
66 ATTTAGTAATGATT
636760 TGATAGTAAT
Statistics
Matches: 495, Mismatches: 32, Indels: 38
0.88 0.06 0.07
Matches are distributed among these distances:
108 44 0.09
109 45 0.09
110 1 0.00
111 4 0.01
112 1 0.00
113 2 0.00
115 2 0.00
116 1 0.00
117 4 0.01
118 47 0.09
119 67 0.14
120 277 0.56
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.47
Consensus pattern (120 bp):
TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATG
ATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAG
Found at i:636436 original size:21 final size:21
Alignment explanation
Indices: 636410--636486 Score: 55
Period size: 21 Copynumber: 3.3 Consensus size: 21
636400 ATTAGTAATG
636410 ATTAATAATAATGAAATTATT
1 ATTAATAATAATGAAATTATT
** *
636431 ATTAATTTTTAATGATTTAATAGTAATG
1 ATTAA-TAATAATGA---AAT--T-ATT
*
636459 ATTAGTAATAATGAAATTATT
1 ATTAATAATAATGAAATTATT
636480 ATTAATA
1 ATTAATA
636487 TTTAATGATT
Statistics
Matches: 41, Mismatches: 8, Indels: 14
0.65 0.13 0.22
Matches are distributed among these distances:
21 13 0.32
22 8 0.20
24 3 0.07
25 3 0.07
27 8 0.20
28 6 0.15
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (21 bp):
ATTAATAATAATGAAATTATT
Found at i:636497 original size:288 final size:287
Alignment explanation
Indices: 636163--636755 Score: 1069
Period size: 288 Copynumber: 2.1 Consensus size: 287
636153 ATTAATGATT
*
636163 TAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTTAGTA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTA
*
636228 ATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGAT
66 ATGATTAGTAATAATAAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGAT
*
636293 TAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGATTAGTA
131 TAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGATTAATA
636358 ATAATGAAATTATTATTAATTTTTAATGATTTAATAGTAATGATTAGTAATGATTAATAATAATG
196 ATAATGAAATTATTATTAATTTTTAATGATTTAATAGTAATGATTAGTAATGATTAATAATAAT-
*
636423 AAATTATTATTAATTTTTAATGATTTAA
260 AAATTATTATTAATATTTAATGATTTAA
*
636451 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTA
*
636516 ATTATTAGTAATAATAAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGAT
66 ATGATTAGTAATAATAAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGAT
* *
636581 TAGTAATAATGATATTATTATTAATATTTAATGATTTGATATTATTGATTTAGTAATGATTAATA
131 TAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGATTAATA
*
636646 ATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAATGATTAATAATAATA
196 ATAATGAAATTATTATTAATTTTTAATGATTTAATAGTAATGATTAGTAATGATTAATAATAATA
*
636711 ATTTATTATTAATATTTAATGATTTAA
261 AATTATTATTAATATTTAATGATTTAA
*
636738 TATTAATGATTTAGTAAT
1 TAGTAATGA-TTAGTAAT
636756 GATTTGATAG
Statistics
Matches: 293, Mismatches: 11, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
287 34 0.12
288 259 0.88
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.47
Consensus pattern (287 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTA
ATGATTAGTAATAATAAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGAT
TAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGATTAATA
ATAATGAAATTATTATTAATTTTTAATGATTTAATAGTAATGATTAGTAATGATTAATAATAATA
AATTATTATTAATATTTAATGATTTAA
Found at i:636503 original size:21 final size:20
Alignment explanation
Indices: 636479--636755 Score: 66
Period size: 21 Copynumber: 13.8 Consensus size: 20
636469 ATGAAATTAT
*
636479 TATTAATATTTAATGATTTGA
1 TATTAATATTTAAT-AATTGA
*
636500 TATTAATGATTTAGTAATT-A
1 TATTAAT-ATTTAATAATTGA
* * *
636520 TTAGTAATA-ATAA-AATTGT
1 -TATTAATATTTAATAATTGA
*
636539 TATTAATATTTAATGATTTGA
1 TATTAATATTTAAT-AATTGA
* *
636560 TAGTAATGATTTAGTAA-TGA
1 TATTAAT-ATTTAATAATTGA
* * *
636580 TTAGTAATA-ATGAT-ATT-A
1 -TATTAATATTTAATAATTGA
*
636598 TTATTAATATTTAATGATTTGA
1 -TATTAATATTTAAT-AATTGA
* *
636620 TATTATTGATTTAGTAA-TG-
1 TATTAAT-ATTTAATAATTGA
*
636639 -ATTAATA-ATAATGAAATT-A
1 TATTAATATTTAAT--AATTGA
* *
636658 TTATTAATTTTTAATGATTTGA
1 -TATTAATATTTAAT-AATTGA
* *
636680 TAGTAATGA-TTAGTAA-TG-
1 TATTAAT-ATTTAATAATTGA
* *
636698 -ATTAATA-ATAATAATTTA
1 TATTAATATTTAATAATTGA
* *
636716 TTATTAATATTTAATGATTTAA
1 -TATTAATATTTAAT-AATTGA
*
636738 TATTAATGATTTAGTAAT
1 TATTAAT-ATTTAATAAT
636756 GATTTGATAG
Statistics
Matches: 183, Mismatches: 43, Indels: 60
0.64 0.15 0.21
Matches are distributed among these distances:
16 9 0.05
17 7 0.04
18 28 0.15
19 14 0.08
20 16 0.09
21 75 0.41
22 34 0.19
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.48
Consensus pattern (20 bp):
TATTAATATTTAATAATTGA
Found at i:636743 original size:14 final size:15
Alignment explanation
Indices: 636719--636750 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
636709 TAATTTATTA
636719 TTAATATTTAATGAT
1 TTAATATTTAATGAT
636734 TTAATA-TTAATGAT
1 TTAATATTTAATGAT
636748 TTA
1 TTA
636751 GTAATGATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (15 bp):
TTAATATTTAATGAT
Found at i:636756 original size:25 final size:25
Alignment explanation
Indices: 636727--636775 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
636717 TATTAATATT
* *
636727 TAATGATTTAATATTAATGATTTAG
1 TAATGATTTAATAGTAATAATTTAG
*
636752 TAATGATTTGATAGTAATAATTTA
1 TAATGATTTAATAGTAATAATTTA
636776 CGACTTGAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (25 bp):
TAATGATTTAATAGTAATAATTTAG
Found at i:639007 original size:15 final size:14
Alignment explanation
Indices: 638984--639014 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
638974 TACAACACTA
638984 AACTTTAATATAAT
1 AACTTTAATATAAT
638998 AACTTATAATATAAT
1 AACTT-TAATATAAT
639013 AA
1 AA
639015 ACTAATAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
AACTTTAATATAAT
Found at i:639020 original size:8 final size:8
Alignment explanation
Indices: 639009--639043 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
638999 ACTTATAATA
639009 TAATAAAC
1 TAATAAAC
639017 TAATAAAC
1 TAATAAAC
639025 TAATAAAC
1 TAATAAAC
*
639033 TAACAAAC
1 TAATAAAC
639041 TAA
1 TAA
639044 ACTTTTTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.63, C:0.14, G:0.00, T:0.23
Consensus pattern (8 bp):
TAATAAAC
Found at i:639022 original size:16 final size:16
Alignment explanation
Indices: 638989--639035 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
638979 CACTAAACTT
*
638989 TAATATAAT-AACTTA
1 TAATATAATAAACTAA
639004 TAATATAATAAACTAA
1 TAATATAATAAACTAA
639020 TAA-ACTAATAAACTAA
1 TAATA-TAATAAACTAA
639036 CAAACTAAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 10 0.34
16 19 0.66
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.32
Consensus pattern (16 bp):
TAATATAATAAACTAA
Found at i:639307 original size:27 final size:28
Alignment explanation
Indices: 639270--639323 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
639260 ACGATTAACA
*
639270 AAACAAACTAATT-AATTATTTTTTATC
1 AAACAAACTAATTAAATAATTTTTTATC
*
639297 AAACATACTAATTAAATAATTTTTTAT
1 AAACAAACTAATTAAATAATTTTTTAT
639324 TTATGTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 12 0.50
28 12 0.50
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.44
Consensus pattern (28 bp):
AAACAAACTAATTAAATAATTTTTTATC
Found at i:639357 original size:21 final size:22
Alignment explanation
Indices: 639333--639373 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
639323 TTTATGTATA
639333 ATATAACT-TAAACTAACAATC
1 ATATAACTCTAAACTAACAATC
*
639354 ATATAACTCTAAATTAACAA
1 ATATAACTCTAAACTAACAA
639374 ACTAATTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.54, C:0.17, G:0.00, T:0.29
Consensus pattern (22 bp):
ATATAACTCTAAACTAACAATC
Found at i:639514 original size:13 final size:13
Alignment explanation
Indices: 639475--639521 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
639465 CTCACAAGAG
639475 CCTTATCTCCCTTT
1 CCTT-TCTCCCTTT
* *
639489 CTTCTTCTTCCTTT
1 CCT-TTCTCCCTTT
639503 CCTTTCTCCCTTT
1 CCTTTCTCCCTTT
639516 -CTTTCT
1 CCTTTCT
639522 TTCTCGGCTG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 6 0.21
13 9 0.32
14 12 0.43
15 1 0.04
ACGTcount: A:0.02, C:0.40, G:0.00, T:0.57
Consensus pattern (13 bp):
CCTTTCTCCCTTT
Found at i:639808 original size:18 final size:19
Alignment explanation
Indices: 639775--639810 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
639765 CAGGCATGCA
639775 ACGGGAGCAGGAGGGGAGC
1 ACGGGAGCAGGAGGGGAGC
639794 ACGGGAGCA-GAGGGGAG
1 ACGGGAGCAGGAGGGGAG
639811 GACGTGAAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.28, C:0.14, G:0.58, T:0.00
Consensus pattern (19 bp):
ACGGGAGCAGGAGGGGAGC
Found at i:639871 original size:29 final size:29
Alignment explanation
Indices: 639835--639934 Score: 155
Period size: 29 Copynumber: 3.4 Consensus size: 29
639825 TCGCCGGGAC
*** *
639835 TGCTTGGCGACCTACAAGGTCGCTGGGAG
1 TGCTTGGCGACCTTGTAGGTCGCTAGGAG
*
639864 TGCATGGCGACCTTGTAGGTCGCTAGGAG
1 TGCTTGGCGACCTTGTAGGTCGCTAGGAG
639893 TGCTTGGCGACCTTGTAGGTCGCTAGGAG
1 TGCTTGGCGACCTTGTAGGTCGCTAGGAG
639922 TGCTTGGCGACCT
1 TGCTTGGCGACCT
639935 GTGTTGGGGT
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 65 1.00
ACGTcount: A:0.15, C:0.23, G:0.37, T:0.25
Consensus pattern (29 bp):
TGCTTGGCGACCTTGTAGGTCGCTAGGAG
Found at i:640609 original size:17 final size:17
Alignment explanation
Indices: 640587--640621 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
640577 ACTTTATTAT
640587 TATTATGTAAAAAATAA
1 TATTATGTAAAAAATAA
* *
640604 TATTATGTGAAAAGTAA
1 TATTATGTAAAAAATAA
640621 T
1 T
640622 TATTTTAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.37
Consensus pattern (17 bp):
TATTATGTAAAAAATAA
Found at i:641194 original size:14 final size:15
Alignment explanation
Indices: 641169--641200 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
641159 ATAAATATTA
641169 ATATTATTAAAAAAT
1 ATATTATTAAAAAAT
641184 ATATT-TTAAAAAAT
1 ATATTATTAAAAAAT
641198 ATA
1 ATA
641201 AATTTTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATATTATTAAAAAAT
Found at i:641209 original size:17 final size:17
Alignment explanation
Indices: 641161--641209 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 17
641151 TATAACATAT
*
641161 AAATATTAATATTATTAAA
1 AAATA-TAA-ATTTTTAAA
641180 AAATAT--A-TTTTAAA
1 AAATATAAATTTTTAAA
641194 AAATATAAATTTTTAA
1 AAATATAAATTTTTAA
641210 TATAATTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
14 12 0.46
15 1 0.04
16 1 0.04
17 6 0.23
18 1 0.04
19 5 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AAATATAAATTTTTAAA
Found at i:642082 original size:10 final size:10
Alignment explanation
Indices: 642034--642087 Score: 54
Period size: 10 Copynumber: 5.1 Consensus size: 10
642024 CCAACATGTT
642034 GGGCATCCGA
1 GGGCATCCGA
*
642044 GGCCATCCGA
1 GGGCATCCGA
*
642054 GTGAGCTATGCGA
1 G-G-GC-ATCCGA
*
642067 GAGCATCCGA
1 GGGCATCCGA
642077 GGGCATCCGA
1 GGGCATCCGA
642087 G
1 G
642088 CGATGCCATC
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
10 25 0.71
11 3 0.09
12 1 0.03
13 6 0.17
ACGTcount: A:0.22, C:0.28, G:0.37, T:0.13
Consensus pattern (10 bp):
GGGCATCCGA
Found at i:642099 original size:14 final size:14
Alignment explanation
Indices: 642074--642152 Score: 95
Period size: 14 Copynumber: 5.6 Consensus size: 14
642064 CGAGAGCATC
*
642074 CGAGGGCATCCGAG
1 CGAGGCCATCCGAG
* *
642088 CGATGCCATCCGAC
1 CGAGGCCATCCGAG
*
642102 CGAGGGCATCCGAG
1 CGAGGCCATCCGAG
* *
642116 CGATGCCATCCGAC
1 CGAGGCCATCCGAG
*
642130 CGAGGGCATCCGAG
1 CGAGGCCATCCGAG
642144 CGAGGCCAT
1 CGAGGCCAT
642153 GCACGTCCCA
Statistics
Matches: 52, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 52 1.00
ACGTcount: A:0.22, C:0.34, G:0.34, T:0.10
Consensus pattern (14 bp):
CGAGGCCATCCGAG
Done.