Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398796.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2079.0, 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: 2134
ACGTcount: A:0.26, C:0.10, G:0.11, T:0.27
Warning! 539 characters in sequence are not A, C, G, or T
Found at i:893 original size:171 final size:171
Alignment explanation
Indices: 1--960 Score: 971
Period size: 172 Copynumber: 5.6 Consensus size: 171
** * * *
1 TAAGGCTTTTGAAGGAACAGCTGACTATAAATGGACTTTTCTTGCAAATGAATGTC-TTTTTCTT
1 TAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTTC-T
* ** * * * *
65 TACATTTCTTGAGGTAGACATTCAATTGTAGTGTGTTTTAGCCAAAAATATA-AAAAAATTCAAC
65 TACGTTTCTCAAGGTAGACATTCAATTCTAGTCTGTTTTAACCAAAAATGTACAAAAAATTCAAC
* * *
129 TTAAAATCAATTATGGCATTATAAAATCATTTGAAGCGAGTAA
130 TTAAAATCAATTATGG-ATTATAAAACCATTTAAAGTGAGTAA
* ** * *
172 TGAGGCTTTTGAAGTTATGGGTGACTATAAGTGGACTTTTCTTGCCAATGAAT-ACTTTTTTCTT
1 TAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTTCTT
* * * ** * *
236 -CTTGTTTCTCAAGATAGATATCCAATTCTAGTCCATTTTAACCAAAAATGTACAAAGAATTAAA
66 AC--GTTTCTCAAGGTAGACATTCAATTCTAGTCTGTTTTAACCAAAAATGTACAAAAAATTCAA
* * * * *
300 ATTTAAATTAATTTTGAGATTATAAAACCATTTAAAGTGAATAA
129 CTTAAAATCAATTATG-GATTATAAAACCATTTAAAGTGAGTAA
* * * * *
344 CT-AGGCTTTTAAAGGAATGGGTGGCTATAAATGGACTTGTCTTGCAAATGAATGTC-TTTTTCT
1 -TAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTTCT
* * * * * * * * *
407 TCACATTTCTCAAGCTAGACATTCAATTATAATATGTTTTAACTAAAAAGGCTA-AAAAATTTGA
65 T-ACGTTTCTCAAGGTAGACATTCAATTCTAGTCTGTTTTAACCAAAAATG-TACAAAAAATTCA
* *
471 ACTTAAAATCAATTATAAGATTATAAAACCATTTAAGGTGAGTAA
128 ACTTAAAATCAATTAT-GGATTATAAAACCATTTAAAGTGAGTAA
* * *
516 TAAGGCTTTTG-GGGAAATGGATGACTATAAATGGACTTCTT-TTACCAATGAA--CC-TTTTTC
1 TAAGGCTTTTGAAGG-AATGGGTGACTATAAATGGACTT-TTCTTGCCAATGAATGCCTTTTTTC
* ** * * * * * *
576 TTCATGTTTCTTGAGGTTGGCATTCAATTATATTCCGTTTTAACCAAAAATGTACAAAGAATTCA
64 TT-ACGTTTCTCAAGGTAGACATTCAATTCTAGTCTGTTTTAACCAAAAATGTACAAAAAATTCA
* * *
641 AATTTAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAA
128 ACTTAAAATCAATTATG-GATTATAAAACCATTTAAAGTGAGTAA
* *
686 AAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTTGTT
1 TAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTTCTT
* * * *
751 GCGTTTCTCGAGGTAAACA-TCAATTCTAGTATGTTTTAACCAAAAATG-A-AAAAAAGTTCAAC
66 ACGTTTCTCAAGGTAGACATTCAATTCTAGTCTGTTTTAACCAAAAATGTACAAAAAA-TTCAAC
* *
813 TTAAAATCAATTATGGCATTATAAAACCATGTAAAGCGAGTAA
130 TTAAAATCAATTATGG-ATTATAAAACCATTTAAAGTGAGTAA
* * *
856 TAAGGCTTTTTGAAGGTATGGGTGACTATAAATGGACTTCTCTTGCTAATGAATG-CTTTTTTCT
1 TAAGGC-TTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTTCT
* *
920 TCACGTTTCTCAAAGTAAACATTCAATTCTAGTCTGTTTTA
65 T-ACGTTTCTCAAGGTAGACATTCAATTCTAGTCTGTTTTA
961 TAAAACCAAC
Statistics
Matches: 645, Mismatches: 118, Indels: 51
0.79 0.14 0.06
Matches are distributed among these distances:
169 11 0.02
170 195 0.30
171 179 0.28
172 246 0.38
173 13 0.02
174 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (171 bp):
TAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTTCTT
ACGTTTCTCAAGGTAGACATTCAATTCTAGTCTGTTTTAACCAAAAATGTACAAAAAATTCAACT
TAAAATCAATTATGGATTATAAAACCATTTAAAGTGAGTAA
Found at i:2084 original size:171 final size:163
Alignment explanation
Indices: 1689--2134 Score: 353
Period size: 171 Copynumber: 2.6 Consensus size: 163
1679 NNNNNNNNNN
** * *
1689 TGTAAATGAACTTTTCTTGCCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTTGATAGTCAAT
1 TGTAAATGAACTTTTCTTGCCAATGAATGCTTTTTTCTTCATGTTTCTTGAGGTAGACAGTCAAT
** * * * * * * * *
1754 TTAGTTTGTTTTAACTAAAAATGTATAAAGAATTCAAATTTAAATCTATTTTGAGATTACAAAAC
66 TTAGTCCGTTTGAACCAAAAATATATAAAAAATTCAAATTAAAATCAAATATGAGATTACAAAAC
* **
1819 CATTTAAAGTGAGTAATAAGGCTTTTGANNNNNNNNNNGAC
131 CATTTAAAGCGAGTAATAAGGCTTTTGA--------AGGAC
* * * *
1860 TATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCATT-ACT-TTTTTTGAGGTAGACA-TCC
1 TGTAAATGAACTTTTCTTGCCAATGAATGCTTTTTTC-TTCA-TGTTTCTTGAGGTAGACAGT-C
* *
1922 AATTATAGTCCGTTTGAACCAAAAATATA-AAAAAATTCAACTTAAAATCAAATATG-GCATTAT
63 AATT-TAGTCCGTTTGAACCAAAAATATATAAAAAATTCAAATTAAAATCAAATATGAG-ATTAC
* **
1985 AAAACCATTTAAAGCGAGTAATGAGGCTTTTGAAGNNNNNNNNNNC
126 AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAG--------GAC
*
2031 TGTAAATGAACTTTTCTTGCCAATGAATGCTTTTTTCTTCATGTCTCTTGAGGTAGACAGTCAAT
1 TGTAAATGAACTTTTCTTGCCAATGAATGCTTTTTTCTTCATGTTTCTTGAGGTAGACAGTCAAT
* ** * * * * *
2096 TCAGTTTGTTTTAACTAAAAATGTACAAAGAATTCAAAT
66 TTAGTCCGTTTGAACCAAAAATATATAAAAAATTCAAAT
Statistics
Matches: 219, Mismatches: 39, Indels: 34
0.75 0.13 0.12
Matches are distributed among these distances:
170 23 0.11
171 173 0.79
172 23 0.11
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.36
Consensus pattern (163 bp):
TGTAAATGAACTTTTCTTGCCAATGAATGCTTTTTTCTTCATGTTTCTTGAGGTAGACAGTCAAT
TTAGTCCGTTTGAACCAAAAATATATAAAAAATTCAAATTAAAATCAAATATGAGATTACAAAAC
CATTTAAAGCGAGTAATAAGGCTTTTGAAGGAC
Done.