Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009570.1 Hibiscus syriacus cultivar Beakdansim tig00116932_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: 102255
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:5664 original size:19 final size:19
Alignment explanation
Indices: 5640--5679 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
5630 AGAAATCCCA
5640 ATACATAAGTAAGGGTCCT
1 ATACATAAGTAAGGGTCCT
5659 ATACATAAGTAAGGGTCCT
1 ATACATAAGTAAGGGTCCT
5678 AT
1 AT
5680 GAATACGCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.28
Consensus pattern (19 bp):
ATACATAAGTAAGGGTCCT
Found at i:15463 original size:228 final size:229
Alignment explanation
Indices: 15097--16204 Score: 1392
Period size: 228 Copynumber: 4.9 Consensus size: 229
15087 TAGGTGGAGA
* * * * * * * * *
15097 GTGGATTCC-TTCTGGATGTTGTAGTCCG-CAAGAGTCCTGCCATCCTCCAGCTGCTTCCCTGCA
1 GTGGACTCCTTTCTGGATGTTGTAGTCAGCCAAG-GTGCGGCCATCCTCGAGTTGTTTACCGGCA
* * * * * *
15160 AAGATCAGCCTCTGCTGGTCCGGAGGGATACCTTCCTTATCCTGGATCTTAGCCTTGACATTATC
65 AAGATCAACCTCTGCTGGTCTGGGGGGATACCCTCCTTATCTTGAATCTTAGCCTTGACATTATC
* * *
15225 AATGGTGTCCGAGCTCTCAACCTCCAAGGTGATGGTCTTCCCAGTCAGTGTCTTCACAAAAATCT
130 AATGGTGTCCGAGCTCTCAACCTCCAAGGTGATGGTCTTCCCAGTAAGTGTCTTCACAAAGATTT
15290 GCATACCACCACGGAGACGAAGCACCAAGTGAAGG
195 GCATACCACCACGGAGACGAAGCACCAAGTGAAGG
*
15325 GTCGACT-CTTTCTGGATGTTGTAGTCAGCCAAGGTGCGGCCATCCTCGAGTTGTTTACCGGCAA
1 GTGGACTCCTTTCTGGATGTTGTAGTCAGCCAAGGTGCGGCCATCCTCGAGTTGTTTACCGGCAA
* * *
15389 ATATCAACCTCTGCTGGTCTGGGGGGATACCCTCCTTATCTTGAATTTTAGCCTTGACATTGTCA
66 AGATCAACCTCTGCTGGTCTGGGGGGATACCCTCCTTATCTTGAATCTTAGCCTTGACATTATCA
* *
15454 ATAGTGTCCGAGCTCTCAACCTCCAAGGTGATGGTCTTCCCAGTGAGTGTCTTCACAAAGATTTG
131 ATGGTGTCCGAGCTCTCAACCTCCAAGGTGATGGTCTTCCCAGTAAGTGTCTTCACAAAGATTTG
*
15519 CATACCACCACGGAGACGGAGCACCAAGTGAAGG
196 CATACCACCACGGAGACGAAGCACCAAGTGAAGG
*
15553 GTGGATTCCTTT-TGGATGTTGTAGTCAGCCAAGGTGCGGCCATCCTCGAGTTGTTTACCGGCAA
1 GTGGACTCCTTTCTGGATGTTGTAGTCAGCCAAGGTGCGGCCATCCTCGAGTTGTTTACCGGCAA
* * * *
15617 ATATCAATCTCTGCTGGTCT-GGGGGATACCCTCCTTATCTTGAATTTTAGCCTTGACATTGTCA
66 AGATCAACCTCTGCTGGTCTGGGGGGATACCCTCCTTATCTTGAATCTTAGCCTTGACATTATCA
* *
15681 ATAGTGTCCGAGCTCTCAACCTCCAAGGTGATGGTCTTCCCAGTGAGTGTCTTCACAAAGATTTG
131 ATGGTGTCCGAGCTCTCAACCTCCAAGGTGATGGTCTTCCCAGTAAGTGTCTTCACAAAGATTTG
* *
15746 CATACCACCGCGGAGACGGAGCACCAAGTGAAGG
196 CATACCACCACGGAGACGAAGCACCAAGTGAAGG
*
15780 GTGGATTCCTTT-TGGATGTTGTAGTCAGCCAAGGTGCGGCCATCCTCGAGTTGTTTACCGGCAA
1 GTGGACTCCTTTCTGGATGTTGTAGTCAGCCAAGGTGCGGCCATCCTCGAGTTGTTTACCGGCAA
* * * * *
15844 AGATCAATCTCTGCTGGTCTGGGGGGAT-CCCTTCCTTGTCTTGAATCTTGGCCTTAACGTTATC
66 AGATCAACCTCTGCTGGTCTGGGGGGATACCC-TCCTTATCTTGAATCTTAGCCTTGACATTATC
* * * * * * * *
15908 AATGGTGTCGGAGCTTTCCACCTCGAGGGTGATGGTCTTGCCAGTAAGGGTCTTAACAAAGATTT
130 AATGGTGTCCGAGCTCTCAACCTCCAAGGTGATGGTCTTCCCAGTAAGTGTCTTCACAAAGATTT
* ** * * *
15973 GCATACCACCCCTCAAACGAAGGACCAAGTGGAGG
195 GCATACCACCACGGAGACGAAGCACCAAGTGAAGG
* * * * * * * *
16008 GTGGACTCC-TTCTGAATGTTGTAGTCTG-CAAGGGTACGGCCATCCTCCAGCTGTTTTCCAGCG
1 GTGGACTCCTTTCTGGATGTTGTAGTCAGCCAA-GGTGCGGCCATCCTCGAGTTGTTTACCGGCA
* * * * * * * * *
16071 AAGAT-AAGCCTCTGTTGGTCTGGTGGGATTCCTTCCTTGTCCTGGATCTTGGCCTTGACGTTAT
65 AAGATCAA-CCTCTGCTGGTCTGGGGGGATACCCTCCTTATCTTGAATCTTAGCCTTGACATTAT
* * * * * * *
16135 CAATGGTGTCGGAGCTTTCCACCT-CAAGGGTGATGGTCTTGCCAGTAAGGGTCTTGACGAAGAT
129 CAATGGTGTCCGAGCTCTCAACCTCCAA-GGTGATGGTCTTCCCAGTAAGTGTCTTCACAAAGAT
16199 TTGCAT
193 TTGCAT
16205 CTATTTTCAA
Statistics
Matches: 798, Mismatches: 72, Indels: 20
0.90 0.08 0.02
Matches are distributed among these distances:
227 237 0.30
228 551 0.69
229 10 0.01
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.28
Consensus pattern (229 bp):
GTGGACTCCTTTCTGGATGTTGTAGTCAGCCAAGGTGCGGCCATCCTCGAGTTGTTTACCGGCAA
AGATCAACCTCTGCTGGTCTGGGGGGATACCCTCCTTATCTTGAATCTTAGCCTTGACATTATCA
ATGGTGTCCGAGCTCTCAACCTCCAAGGTGATGGTCTTCCCAGTAAGTGTCTTCACAAAGATTTG
CATACCACCACGGAGACGAAGCACCAAGTGAAGG
Found at i:16050 original size:455 final size:456
Alignment explanation
Indices: 15090--16204 Score: 1477
Period size: 455 Copynumber: 2.4 Consensus size: 456
15080 GGAGGACTAG
* * * * * * *
15090 GTGGAGAGTGGATTCCTTCTGGATGTTGTAGTCCGCAAGAGTCCTGCCATCCTCCAGCTGCTTCC
1 GTGGAGGGTGGATTCCTTCTGGATGTTGTAGTCAGCAAGGGTACGGCCATCCTCCAGCTGTTTAC
* * *
15155 CTGCAAAGATCAGCCTCTGCTGGTCCGGAGGGATACCTTCCTTATCCTGGATCTTAGCCTTGACA
66 CAGCAAAGATCAACCTCTGCTGGTCTGGAGGGATACCTTCCTTATCCTGGATCTTAGCCTTGACA
*
15220 TTATCAATGGTGTCCGAGCTCTCAACCTCCAAGGTGATGGTCTTCCCAGTCAGTGTCTTCACAAA
131 TTATCAATGGTGTCCGAGCTCTCAACCTCCAAGGTGATGGTCTTCCCAGTAAGTGTCTTCACAAA
* *
15285 AATCTGCATACCACCACGGAGACGAAGCACCAAGTGAAGGGTCGACTCTTTCTGGATGTTGTAGT
196 GATTTGCATACCACCACGGAGACGAAGCACCAAGTGAAGGGTCGACTCTTTCTGGATGTTGTAGT
*
15350 CAGCCAAGGTGCGGCCATCCTCGAGTTGTTTACCGGCAAATATCAACCTCTGCTGGTCTGGGGGG
261 CAGCCAAGGTGCGGCCATCCTCGAGTTGTTTACCGGCAAAGATCAACCTCTGCTGGTCTGGGGGG
* * *
15415 ATACCCTCCTTATCTTGAATTTTAGCCTTGACATTGTCAATAGTGTCCGAGCTCTCAACCTCCAA
326 ATACCCTCCTTATCTTGAATCTTAGCCTTAACATTATCAATAGTGTCCGAGCTCTCAACCTCCAA
* * * * * *
15480 GGTGATGGTCTTCCCAGTGAGTGTCTTCACAAAGATTTGCATACCACCACGGAGACGGAGCACCA
391 GGTGATGGTCTTCCCAGTAAGGGTCTTAACAAAGATTTGCATACCACCACGCAAACGAAGCACCA
15545 A
456 A
* * * * *
15546 GTGAAGGGTGGATTCCTTTTGGATGTTGTAGTCAGCCAA-GGTGCGGCCATCCTCGAGTTGTTTA
1 GTGGAGGGTGGATTCCTTCTGGATGTTGTAGTCAG-CAAGGGTACGGCCATCCTCCAGCTGTTTA
* * * * * * *
15610 CCGGCAAATATCAATCTCTGCTGGTCTGG-GGGATACCCTCCTTATCTTGAATTTTAGCCTTGAC
65 CCAGCAAAGATCAACCTCTGCTGGTCTGGAGGGATACCTTCCTTATCCTGGATCTTAGCCTTGAC
* * *
15674 ATTGTCAATAGTGTCCGAGCTCTCAACCTCCAAGGTGATGGTCTTCCCAGTGAGTGTCTTCACAA
130 ATTATCAATGGTGTCCGAGCTCTCAACCTCCAAGGTGATGGTCTTCCCAGTAAGTGTCTTCACAA
* * * *
15739 AGATTTGCATACCACCGCGGAGACGGAGCACCAAGTGAAGGGTGGATTCCTTT-TGGATGTTGTA
195 AGATTTGCATACCACCACGGAGACGAAGCACCAAGTGAAGGGTCGACT-CTTTCTGGATGTTGTA
*
15803 GTCAGCCAAGGTGCGGCCATCCTCGAGTTGTTTACCGGCAAAGATCAATCTCTGCTGGTCTGGGG
259 GTCAGCCAAGGTGCGGCCATCCTCGAGTTGTTTACCGGCAAAGATCAACCTCTGCTGGTCTGGGG
* * * * * * *
15868 GGAT-CCCTTCCTTGTCTTGAATCTTGGCCTTAACGTTATCAATGGTGTCGGAGCTTTCCACCTC
324 GGATACCC-TCCTTATCTTGAATCTTAGCCTTAACATTATCAATAGTGTCCGAGCTCTCAACCTC
* * * * * *
15932 GAGGGTGATGGTCTTGCCAGTAAGGGTCTTAACAAAGATTTGCATACCACCCCTCAAACGAAGGA
388 CAAGGTGATGGTCTTCCCAGTAAGGGTCTTAACAAAGATTTGCATACCACCACGCAAACGAAGCA
15997 CCAA
453 CCAA
* * * *
16001 GTGGAGGGTGGACTCCTTCTGAATGTTGTAGTCTGCAAGGGTACGGCCATCCTCCAGCTGTTTTC
1 GTGGAGGGTGGATTCCTTCTGGATGTTGTAGTCAGCAAGGGTACGGCCATCCTCCAGCTGTTTAC
* * * * * *
16066 CAGCGAAGAT-AAGCCTCTGTTGGTCTGGTGGGATTCCTTCCTTGTCCTGGATCTTGGCCTTGAC
66 CAGCAAAGATCAA-CCTCTGCTGGTCTGGAGGGATACCTTCCTTATCCTGGATCTTAGCCTTGAC
* * * * * * * *
16130 GTTATCAATGGTGTCGGAGCTTTCCACCT-CAAGGGTGATGGTCTTGCCAGTAAGGGTCTTGACG
130 ATTATCAATGGTGTCCGAGCTCTCAACCTCCAA-GGTGATGGTCTTCCCAGTAAGTGTCTTCACA
16194 AAGATTTGCAT
194 AAGATTTGCAT
16205 CTATTTTCAA
Statistics
Matches: 567, Mismatches: 85, Indels: 14
0.85 0.13 0.02
Matches are distributed among these distances:
454 8 0.01
455 391 0.69
456 165 0.29
457 3 0.01
ACGTcount: A:0.21, C:0.25, G:0.26, T:0.28
Consensus pattern (456 bp):
GTGGAGGGTGGATTCCTTCTGGATGTTGTAGTCAGCAAGGGTACGGCCATCCTCCAGCTGTTTAC
CAGCAAAGATCAACCTCTGCTGGTCTGGAGGGATACCTTCCTTATCCTGGATCTTAGCCTTGACA
TTATCAATGGTGTCCGAGCTCTCAACCTCCAAGGTGATGGTCTTCCCAGTAAGTGTCTTCACAAA
GATTTGCATACCACCACGGAGACGAAGCACCAAGTGAAGGGTCGACTCTTTCTGGATGTTGTAGT
CAGCCAAGGTGCGGCCATCCTCGAGTTGTTTACCGGCAAAGATCAACCTCTGCTGGTCTGGGGGG
ATACCCTCCTTATCTTGAATCTTAGCCTTAACATTATCAATAGTGTCCGAGCTCTCAACCTCCAA
GGTGATGGTCTTCCCAGTAAGGGTCTTAACAAAGATTTGCATACCACCACGCAAACGAAGCACCA
A
Found at i:17290 original size:17 final size:17
Alignment explanation
Indices: 17265--17303 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
17255 GTCAGTGACG
*
17265 TCACTAACGTGGTTACC
1 TCACCAACGTGGTTACC
17282 TCACCAACGTGGTTACC
1 TCACCAACGTGGTTACC
17299 TCACC
1 TCACC
17304 CAAATAACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.23, C:0.36, G:0.15, T:0.26
Consensus pattern (17 bp):
TCACCAACGTGGTTACC
Found at i:19133 original size:22 final size:20
Alignment explanation
Indices: 19101--19142 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
19091 ATATAAAAAA
19101 TTATTTTTTATTAAATATTTT
1 TTATTTTTTATTAAAT-TTTT
*
19122 TTATATTTTTATTTAATTTTT
1 TTAT-TTTTTATTAAATTTTT
19143 AAATAAGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (20 bp):
TTATTTTTTATTAAATTTTT
Found at i:20090 original size:20 final size:20
Alignment explanation
Indices: 20061--20098 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
20051 ATTTAGGCAC
*
20061 ATATTCAAAATTTAAATAAA
1 ATATTCAAAATTAAAATAAA
*
20081 ATATTTAAAATTAAAATA
1 ATATTCAAAATTAAAATA
20099 TTATAATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (20 bp):
ATATTCAAAATTAAAATAAA
Found at i:21678 original size:12 final size:12
Alignment explanation
Indices: 21661--21740 Score: 61
Period size: 12 Copynumber: 6.2 Consensus size: 12
21651 CTACACACCG
21661 CACGCACACACA
1 CACGCACACACA
*
21673 CACGCACGCACGCA
1 CACGCA--CACACA
* *
21687 TGCACGCACGCACG
1 --CACGCACACACA
* *
21701 CACGCACGCACG
1 CACGCACACACA
21713 CACGCACACACTA
1 CACGCACACAC-A
*
21726 CATGCACACACA
1 CACGCACACACA
21738 CAC
1 CAC
21741 ACACTACATG
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
12 31 0.56
13 10 0.18
14 8 0.15
16 6 0.11
ACGTcount: A:0.33, C:0.47, G:0.16, T:0.04
Consensus pattern (12 bp):
CACGCACACACA
Found at i:21680 original size:4 final size:4
Alignment explanation
Indices: 21659--21719 Score: 95
Period size: 4 Copynumber: 15.2 Consensus size: 4
21649 ACCTACACAC
* * *
21659 CGCA CGCA CACA CACA CGCA CGCA CGCA TGCA CGCA CGCA CGCA CGCA
1 CGCA CGCA CGCA CGCA CGCA CGCA CGCA CGCA CGCA CGCA CGCA CGCA
21707 CGCA CGCA CGCA C
1 CGCA CGCA CGCA C
21720 ACACTACATG
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 53 1.00
ACGTcount: A:0.28, C:0.49, G:0.21, T:0.02
Consensus pattern (4 bp):
CGCA
Found at i:21741 original size:21 final size:21
Alignment explanation
Indices: 21708--21752 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
21698 ACGCACGCAC
* *
21708 GCACGCACGCACACACTACAT
1 GCACACACACACACACTACAT
21729 GCACACACACACACACTACAT
1 GCACACACACACACACTACAT
21750 GCA
1 GCA
21753 TACATGCCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.38, C:0.42, G:0.11, T:0.09
Consensus pattern (21 bp):
GCACACACACACACACTACAT
Found at i:21785 original size:4 final size:4
Alignment explanation
Indices: 21745--23693 Score: 3607
Period size: 4 Copynumber: 490.0 Consensus size: 4
21735 ACACACACAC
* * * *
21745 TACA TGCA TACA TGCCA TACA TGCA TACA TGCA TACA TACA TACA TACA
1 TACA TACA TACA T-ACA TACA TACA TACA TACA TACA TACA TACA TACA
21794 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
21842 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * * * * * *
21890 TACA TACA GACA TACA TACA CACA CACA CACA TACA TGCA TGCA TGCA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
*
21938 TACA TACA TACA TACA TACA TATA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
21986 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
22034 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
22082 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
22130 TACA TACA TAC- -ACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* *
22176 TACA TACA TACA TACA TACA TGCA TACA TACA TGCA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* *
22224 TGCA TACA TACA TACA T--A TACA TACA TACA TGCA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
22270 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
22318 TACA TAC- -ACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
22364 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
22412 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
22460 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
22508 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
22556 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
22604 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TAC-
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
22651 -ACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
22698 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
22746 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
22794 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
22842 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
22890 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
22938 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
22986 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
23034 TACA T--A TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
23080 TACA TACA T--A TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
23126 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
23174 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
23222 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
23270 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * * *
23318 GACA TACA TACA TACA TACA TACA TACA TACA TATA CATA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
23366 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
23414 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
**
23462 TACA TACA TACA TACA TACA TACA TACA CGCA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
23510 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
23558 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
23606 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
23654 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
23694 CGCATATCAC
Statistics
Matches: 1898, Mismatches: 34, Indels: 26
0.97 0.02 0.01
Matches are distributed among these distances:
2 12 0.01
4 1883 0.99
5 3 0.00
ACGTcount: A:0.49, C:0.25, G:0.01, T:0.25
Consensus pattern (4 bp):
TACA
Found at i:24416 original size:13 final size:13
Alignment explanation
Indices: 24398--24425 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
24388 TGCAATTTCA
24398 AAAGCTTTTCATG
1 AAAGCTTTTCATG
24411 AAAGCTTTTCATG
1 AAAGCTTTTCATG
24424 AA
1 AA
24426 CACTTCTACA
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:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (13 bp):
AAAGCTTTTCATG
Found at i:24993 original size:2 final size:2
Alignment explanation
Indices: 24988--25060 Score: 132
Period size: 2 Copynumber: 37.5 Consensus size: 2
24978 TCTCTCTCTC
24988 TA TA TA TA TA TA TA TA TA TA TA TA TA T- 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
25029 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
25061 TTCTATTAAT
Statistics
Matches: 69, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
1 2 0.03
2 67 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:27002 original size:41 final size:41
Alignment explanation
Indices: 26827--27282 Score: 436
Period size: 41 Copynumber: 11.1 Consensus size: 41
26817 TAACGGCATT
* * ** * *
26827 TTTAGCGGCGTTTTTAGAACAAACGTTGCTAAATACTTGTAC
1 TTTAGTGGCGTTTTTA-TACAAACGCCGCTAAAGACTCGTAC
26869 TTTAGTGGCGTTTTT-TACAAACGCCGCTAAAGACT-GT-C
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTAC
* * * * *
26907 TTTAGTGGCATATTTAGAACAAACGCCGCTAAATACTCATAC
1 TTTAGTGGCGTTTTTA-TACAAACGCCGCTAAAGACTCGTAC
* *
26949 TTTAATGGCGTTTTTAATACAAACGCCGATAAAGACT-GTAC
1 TTTAGTGGCGTTTTT-ATACAAACGCCGCTAAAGACTCGTAC
* * * * *
26990 TTTAGCGACGTTTTTATACAAACACCGTTATAGACTCGTAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTAC
* *
27031 TTTAGTGGTGTTTTTATACAAACGCCGCTAAAGACTCATAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTAC
* * * * *
27072 TTTAGTGGCGTTTTTATATAAATGTCGCTAAAGACTCATAT
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTAC
* * * * *
27113 TTTAGTGGCGTTTTAATACAAACGTCGCTATAGACTAGTCC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTAC
* * *
27154 TTTAGTGGAGTTTTTATATAAACGCCGCTATAGACTC-TAAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGT-AC
* * * ** * * *
27195 TTTAGTGGCATTTTTTTACAAACACCGCTGTACACTCATGC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTAC
* * * *
27236 TTTAGTGGCATTTTTATACAAACGCCGTTATAGACTCGTGC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTAC
27277 TTTAGT
1 TTTAGT
27283 TGGAGCCCCT
Statistics
Matches: 343, Mismatches: 63, Indels: 17
0.81 0.15 0.04
Matches are distributed among these distances:
38 14 0.04
39 2 0.01
40 53 0.15
41 228 0.66
42 45 0.13
43 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (41 bp):
TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTAC
Found at i:29698 original size:2 final size:2
Alignment explanation
Indices: 29691--29737 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
29681 TATTACGATA
*
29691 AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29733 AT AT A
1 AT AT A
29738 ATGTAGAGAG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:31147 original size:43 final size:42
Alignment explanation
Indices: 31065--31368 Score: 266
Period size: 43 Copynumber: 7.2 Consensus size: 42
31055 AAGGTAATTA
* * *
31065 GCGGCGTTT-TT-CAATAACGCCGCTATAGATAT-ACTCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAAATCTGAC-CTTTT
* * *
31105 GCGGCGTTTGATTCCAAAAACGCCACAATAAATCTGTCCTTTT
1 GCGGCGTTTG-TTCCAAAAACGCCGCTATAAATCTGACCTTTT
* * * *
31148 GCGGCGTTTATATCCAAAAACACCAC--TAGATCTGACCTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAAATCTGACCTTTT
* *
31189 GCGACGTTTGTATCCAAAAACGCCGCTATAGATCTCGACCTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAAATCT-GACCTTTT
*
31233 G-TGCGTTTGTTCC-AAAACGCCGCTATAGATATC-GACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATA-A-ATCTGACCTTTT
* * *
31274 GCAGCGTTTGTTCCAAAGACGCCGCGATAGATAT-TGACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATA-A-ATCTGACCTTTT
* * * * *
31317 GCGGCGTTTGTTCCTAAAACGTCGCGATAGATCTTGACCTATT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAAATC-TGACCTTTT
31360 GCGGCGTTT
1 GCGGCGTTT
31369 TTTGTTCTCA
Statistics
Matches: 223, Mismatches: 26, Indels: 27
0.81 0.09 0.10
Matches are distributed among these distances:
40 9 0.04
41 60 0.27
42 17 0.08
43 127 0.57
44 10 0.04
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.32
Consensus pattern (42 bp):
GCGGCGTTTGTTCCAAAAACGCCGCTATAAATCTGACCTTTT
Found at i:31197 original size:84 final size:83
Alignment explanation
Indices: 31100--31336 Score: 232
Period size: 84 Copynumber: 2.8 Consensus size: 83
31090 TAGATATACT
* * *
31100 CTTTTGCGGCGTTTGATTCCAAAAACGCCACAATAAATCTGTCCTTTTGCGGCGTTTATATCCAA
1 CTTTTGCGACGTTTG-TTCCAAAAACGCCGCAATAAATCTGACCTTTTGCGGCGTTTAT-TCC-A
*
31165 AAACACCAC-TAGATCT-GAC
63 AAACACCACATAGATATCGAC
* * * *
31184 CTTTTGCGACGTTTGTATCCAAAAACGCCGCTATAGATCTCGACCTTTTG-TGCGTTTGTTCCAA
1 CTTTTGCGACGTTTGT-TCCAAAAACGCCGCAATAAATCT-GACCTTTTGCGGCGTTTATTCCAA
* *
31248 AACGCCGCTATAGATATCGAC
64 AACACCAC-ATAGATATCGAC
* * *
31269 CTTTTGC-AGCGTTTGTTCCAAAGACGCCGCGATAGATAT-TGACCTTTTGCGGCGTTTGTTCCT
1 CTTTTGCGA-CGTTTGTTCCAAAAACGCCGCAATA-A-ATCTGACCTTTTGCGGCGTTTATTCC-
31332 AAAAC
62 AAAAC
31337 GTCGCGATAG
Statistics
Matches: 129, Mismatches: 14, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
82 8 0.06
83 4 0.03
84 73 0.57
85 37 0.29
86 7 0.05
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (83 bp):
CTTTTGCGACGTTTGTTCCAAAAACGCCGCAATAAATCTGACCTTTTGCGGCGTTTATTCCAAAA
CACCACATAGATATCGAC
Found at i:58411 original size:9 final size:9
Alignment explanation
Indices: 58399--58425 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
58389 CAGCAGGGAT
58399 TGCAGGTGG
1 TGCAGGTGG
58408 TGCAGGTGG
1 TGCAGGTGG
58417 TGCAGGTGG
1 TGCAGGTGG
58426 CATGAAGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.11, C:0.11, G:0.56, T:0.22
Consensus pattern (9 bp):
TGCAGGTGG
Found at i:70389 original size:15 final size:15
Alignment explanation
Indices: 70352--70392 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
70342 GCACAGACAT
70352 CACATGCTCCACCAG
1 CACATGCTCCACCAG
* *
70367 CGCATGCTCCACCTG
1 CACATGCTCCACCAG
*
70382 CACCTGCTCCA
1 CACATGCTCCA
70393 TCAACCGATG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.20, C:0.49, G:0.15, T:0.17
Consensus pattern (15 bp):
CACATGCTCCACCAG
Found at i:70942 original size:96 final size:96
Alignment explanation
Indices: 70778--70963 Score: 336
Period size: 96 Copynumber: 1.9 Consensus size: 96
70768 TATGCGGATA
70778 GCCCATGTGCTGCTCCATTTCAGCGTGTTTCTTCAACACATGGTGACGAAACTCATGGGACCACA
1 GCCCATGTGCTGCTCCATTTCAGCGTGTTTCTTCAACACATGGTGACGAAACTCATGGGACCACA
70843 TCAACTAGTACGCAAGTGGAAGCTGGAACTT
66 TCAACTAGTACGCAAGTGGAAGCTGGAACTT
* * *
70874 GCCCATTTGCTGCTTCATTTCAGCGTGTTTCTTCAACGCATGGTGACGAAACTCATGGGACCACA
1 GCCCATGTGCTGCTCCATTTCAGCGTGTTTCTTCAACACATGGTGACGAAACTCATGGGACCACA
*
70939 TCAACTAGTGCGCAAGTGGAAGCTG
66 TCAACTAGTACGCAAGTGGAAGCTG
70964 TTTCAGTGCA
Statistics
Matches: 86, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
96 86 1.00
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.26
Consensus pattern (96 bp):
GCCCATGTGCTGCTCCATTTCAGCGTGTTTCTTCAACACATGGTGACGAAACTCATGGGACCACA
TCAACTAGTACGCAAGTGGAAGCTGGAACTT
Found at i:73707 original size:12 final size:11
Alignment explanation
Indices: 73683--73713 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
73673 ACCGTATTGT
73683 AAAATATAAAA
1 AAAATATAAAA
73694 AAAATATAAAA
1 AAAATATAAAA
73705 AAAA-ATAAA
1 AAAATATAAA
73714 TAAAGTTTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.25
11 15 0.75
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAATATAAAA
Found at i:75000 original size:21 final size:21
Alignment explanation
Indices: 74976--75093 Score: 114
Period size: 21 Copynumber: 5.7 Consensus size: 21
74966 ACGTTGCATT
*
74976 TCGCATTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
** ** **
74997 TCGCGTTGCG-TTTTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
75017 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
75038 TCGCGTTGCGAT-TTTTCATT
1 TCGCGTTGCGATAGTTGAAAA
75058 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
75079 TCGCGTTGCGATAGT
1 TCGCGTTGCGATAGT
75094 CTGCAGTTGT
Statistics
Matches: 72, Mismatches: 23, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
20 29 0.40
21 43 0.60
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.36
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:75017 original size:41 final size:41
Alignment explanation
Indices: 74972--75090 Score: 213
Period size: 41 Copynumber: 2.9 Consensus size: 41
74962 TTTCACGTTG
*
74972 CATTTCGCATTGCGATAGTTGAAAATCGCGTTGCG-TTTTT
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTT
75012 CCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTT
1 -CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTT
75054 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGAT
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGAT
75091 AGTCTGCAGT
Statistics
Matches: 76, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
41 71 0.93
42 5 0.07
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.37
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTT
Found at i:75022 original size:20 final size:20
Alignment explanation
Indices: 74997--75069 Score: 76
Period size: 20 Copynumber: 3.6 Consensus size: 20
74987 TAGTTGAAAA
74997 TCGCGTTGCG-TTTTTCCATT
1 TCGCGTTGCGATTTTT-CATT
* ** **
75017 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTTCATT
75038 TCGCGTTGCGATTTTTCATT
1 TCGCGTTGCGATTTTTCATT
75058 TCGCGTTGCGAT
1 TCGCGTTGCGAT
75070 AGTTGAAAAT
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
20 25 0.61
21 14 0.34
22 2 0.05
ACGTcount: A:0.14, C:0.21, G:0.25, T:0.41
Consensus pattern (20 bp):
TCGCGTTGCGATTTTTCATT
Found at i:75755 original size:6 final size:6
Alignment explanation
Indices: 75746--75777 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
75736 GCCGTCCGTC
75746 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TC
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TC
75778 ATACGTGTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.19, G:0.47, T:0.34
Consensus pattern (6 bp):
TCGTGG
Found at i:75937 original size:21 final size:21
Alignment explanation
Indices: 75894--75937 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
75884 ACAACTGTAG
** *
75894 ACTATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
75915 ACTATCGCAACGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
75936 AC
1 AC
75938 GCGAATTTAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.30, G:0.16, T:0.20
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:77062 original size:27 final size:27
Alignment explanation
Indices: 77032--77095 Score: 110
Period size: 27 Copynumber: 2.4 Consensus size: 27
77022 GATCGTATCA
77032 AATGTCTTCACACCATTGAACCAACAG
1 AATGTCTTCACACCATTGAACCAACAG
77059 AATGTCTTCACACCATTGAACCAACAG
1 AATGTCTTCACACCATTGAACCAACAG
* *
77086 AGTTTCTTCA
1 AATGTCTTCA
77096 TCTGGTGTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.34, C:0.28, G:0.11, T:0.27
Consensus pattern (27 bp):
AATGTCTTCACACCATTGAACCAACAG
Found at i:79775 original size:35 final size:36
Alignment explanation
Indices: 79726--79795 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 36
79716 CTGAAGTTGA
**
79726 GCTTAGCTTAAAACCAACAAAGTAGTTTTTCTTTTG
1 GCTTAGCTTAAAACCAACAAAGTAGCATTTCTTTTG
* **
79762 GCTTA-CTTGAAACCATGAAAGTAGCATTTCTTTT
1 GCTTAGCTTAAAACCAACAAAGTAGCATTTCTTTT
79796 AGATTGCTGA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
35 24 0.83
36 5 0.17
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (36 bp):
GCTTAGCTTAAAACCAACAAAGTAGCATTTCTTTTG
Found at i:85947 original size:21 final size:21
Alignment explanation
Indices: 85899--85949 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
85889 TTCTGCAGCC
* *
85899 ATTTCAGATGGCACCGTAGCT
1 ATTTCAGATGACACCATAGCT
**
85920 ACATCAGATGACACCATAGCT
1 ATTTCAGATGACACCATAGCT
85941 ATTTCAGAT
1 ATTTCAGAT
85950 ATCACCACAG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (21 bp):
ATTTCAGATGACACCATAGCT
Found at i:85955 original size:21 final size:20
Alignment explanation
Indices: 85899--85956 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 20
85889 TTCTGCAGCC
* *
85899 ATTTCAGATGGCACCGTAGCT
1 ATTTCAGAT-ACACCATAGCT
**
85920 ACATCAGATGACACCATAGCT
1 ATTTCAGAT-ACACCATAGCT
85941 ATTTCAGATATCACCA
1 ATTTCAGATA-CACCA
85957 CAGCCGAGTC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
20 1 0.03
21 29 0.97
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.26
Consensus pattern (20 bp):
ATTTCAGATACACCATAGCT
Found at i:85989 original size:63 final size:63
Alignment explanation
Indices: 85922--86041 Score: 170
Period size: 63 Copynumber: 1.9 Consensus size: 63
85912 CCGTAGCTAC
* *
85922 ATCAGATGACACCAT-AGCTATTTCAGATATCACCACAGCCGAGTCAAACGCCACCGTTTCCAT
1 ATCAGATGACACCATAAG-TATATCAGATACCACCACAGCCGAGTCAAACGCCACCGTTTCCAT
* * * *
85985 ATCAGATGCCACCATAAGTATATCAGATACCACCACAGCCGGGTCAGATGCCACCGT
1 ATCAGATGACACCATAAGTATATCAGATACCACCACAGCCGAGTCAAACGCCACCGT
86042 CGCAGGGTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
63 48 0.96
64 2 0.04
ACGTcount: A:0.32, C:0.32, G:0.17, T:0.20
Consensus pattern (63 bp):
ATCAGATGACACCATAAGTATATCAGATACCACCACAGCCGAGTCAAACGCCACCGTTTCCAT
Found at i:86515 original size:23 final size:24
Alignment explanation
Indices: 86489--86545 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 24
86479 TTGTAAAGTT
*
86489 TTTATTTAATTATGGA-ATTTTTA
1 TTTATTTAATTATGAATATTTTTA
** *
86512 TTTATTTTTTTATTAATATTTTTA
1 TTTATTTAATTATGAATATTTTTA
86536 -TTATTTAATT
1 TTTATTTAATT
86546 GTTAGAATTG
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
23 20 0.74
24 7 0.26
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (24 bp):
TTTATTTAATTATGAATATTTTTA
Found at i:89717 original size:17 final size:18
Alignment explanation
Indices: 89683--89717 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
89673 AATCCAAAAA
89683 AATTTAAAAAATCACAAT
1 AATTTAAAAAATCACAAT
*
89701 AATTTAAATAA-CACAAT
1 AATTTAAAAAATCACAAT
89718 TTCATATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.29
Consensus pattern (18 bp):
AATTTAAAAAATCACAAT
Found at i:89854 original size:16 final size:15
Alignment explanation
Indices: 89824--89860 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
89814 AAATTTGTTC
*
89824 AAATAATTAAATATA
1 AAATAAATAAATATA
89839 AAATAAATATAATATA
1 AAATAAATA-AATATA
89855 AAATAA
1 AAATAA
89861 TTTTACCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AAATAAATAAATATA
Found at i:92408 original size:29 final size:29
Alignment explanation
Indices: 92323--92395 Score: 128
Period size: 29 Copynumber: 2.5 Consensus size: 29
92313 CCCTTTTTGA
*
92323 AATGAACATTCCAAGATTTTACCTTTACC
1 AATGAACAATCCAAGATTTTACCTTTACC
*
92352 AATTAACAATCCAAGATTTTACCTTTACC
1 AATGAACAATCCAAGATTTTACCTTTACC
92381 AATGAACAATCCAAG
1 AATGAACAATCCAAG
92396 CCTTTTTCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.40, C:0.23, G:0.07, T:0.30
Consensus pattern (29 bp):
AATGAACAATCCAAGATTTTACCTTTACC
Found at i:95614 original size:6 final size:6
Alignment explanation
Indices: 95603--95855 Score: 506
Period size: 6 Copynumber: 42.2 Consensus size: 6
95593 AACCAACGAT
95603 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
95651 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
95699 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
95747 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
95795 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
95843 ATATAC ATATAC A
1 ATATAC ATATAC A
95856 GTGTTGGATT
Statistics
Matches: 247, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 247 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (6 bp):
ATATAC
Found at i:97447 original size:23 final size:23
Alignment explanation
Indices: 97417--97460 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
97407 TCCTTATAAT
97417 TGGAGGGCAACCAATAAAAAAAC
1 TGGAGGGCAACCAATAAAAAAAC
97440 TGGAGGGCAACCAATAAAAAA
1 TGGAGGGCAACCAATAAAAAA
97461 GTTAACTTTT
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:0.52, C:0.16, G:0.23, T:0.09
Consensus pattern (23 bp):
TGGAGGGCAACCAATAAAAAAAC
Done.