Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397959.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1263.0, 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: 3530
ACGTcount: A:0.29, C:0.10, G:0.11, T:0.28
Warning! 822 characters in sequence are not A, C, G, or T
Found at i:680 original size:171 final size:168
Alignment explanation
Indices: 90--1075 Score: 770
Period size: 171 Copynumber: 5.8 Consensus size: 168
80 TTCCAAGGCC
* * * ** * **
90 GACATTCAATTACAATTTGTTTTAATAAAAAATGTAAAAAATTTTACTTAAAATCAATTATGAGA
1 GACATTCAATTATAATATATTTTAACCAAAAATATAAAAAATTCAACTTAAAATCAATTATGAGA
* * * * *
155 TTATAAAACCATTTAAAGTGAA-CAATAAGGCTTTCGAAGTCTTGAGTGATTACAAATAGACTTT
66 TTATAAAACCATTTAAAGT-AAGTAATAAGGGTTTCGAAG-CTTGAGTGACTATAAATGGACTTT
* * * * * ** *
219 TCCTACCGATGGGTGGCTTTTACTTCACGTTTCTCAAAATA
129 TCTTGCCAATGGATGGCTTTTA-TTCATGTTTCTTGAAGTA
* *** *
260 GACATTGAATTATAATATATTTTGGTCAAAAA-AGTGAAAAAATTCAACTTAAAATTAATTATGA
1 GACATTCAATTATAATATATTTTAACCAAAAATA-T-AAAAAATTCAACTTAAAATCAATTATGA
* * ** * * *
324 GATTATAAAACCATTTAAAGCAAATACGAAGGGTTTCGAAGGTATAAGTGACTATGAATAGG-CT
64 GATTATAAAACCATTTAAAGTAAGTAATAAGGGTTTCGAAGCT-TGAGTGACTATAAAT-GGACT
* * * * * *
388 TTTCTTGTCAATGAATAGCTTTTTTTCATGTTTCTCGAGGTA
127 TTTCTTGCCAATGGATGGCTTTTATTCATGTTTCTTGAAGTA
* * *
430 GACATGT-AAGTATAATCTATTTTAACCCAAAATATAAAAAATTCAA-TCTAAAATCAATTATGA
1 GACAT-TCAATTATAATATATTTTAACCAAAAATATAAAAAATTCAACT-TAAAATCAATTATGA
* * * * *
493 GATTATAATACCATTTAAATTGAGTAATAAGGGTTTCGAAAGCTTGAATGACTCTAAATGGACTT
64 GATTATAAAACCATTTAAAGTAAGTAATAAGGGTTTCG-AAGCTTGAGTGACTATAAATGGACTT
* * *
558 TTCTTGCCGATGGATGGCTTTTGATTCATGTTTTTTGAAATA
128 TTCTTGCCAATGGATGGCTTTT-ATTCATGTTTCTTGAAGTA
*
600 GACATTCAATTATAATAT-TTTTAACCAAAAATTATAAAAAGAGTT-AACTTAAAATCAATTCTG
1 GACATTCAATTATAATATATTTTAACCAAAAA-TATAAAAA-A-TTCAACTTAAAATCAATTATG
* * * *** * *
663 AGATTATAAAACCATTTAAAGCAAGTAAT-AGGTCTTTGGAAGGAAGAGGTGACTATAAATGAAA
63 AGATTATAAAACCATTTAAAGTAAGTAATAAGG-GTTTCGAAGCTTGA-GTGACTATAAATGGAC
* * ** * * * *
727 TTTTCTTTCCAATGAATAGTTTTTTCTTTATGTTTCCT-AAGGCA
126 TTTTCTTGCCAATGGAT-GGCTTTTATTCATGTTTCTTGAA-GTA
* * * * * * * * *
771 AACGTTCAACTATAATCTTTTTTAACTAAAAATGCTAAAATATTCAACTTAAAATGAATTATGAG
1 GACATTCAATTATAATATATTTTAACCAAAAAT-ATAAAAAATTCAACTTAAAATCAATTATGAG
* * * * *
836 ATTATAAAACCATTTAAAGAAAGTAATAATGTTTTCGAAGGCAT-AGGTGACTATAAATTGACTT
65 ATTATAAAACCATTTAAAGTAAGTAATAAGGGTTTCGAA-GCTTGA-GTGACTATAAATGGACTT
** * * *
900 TTCTTTTCAATGGATGGCTTTTGCTTCATGTTTC-TCAAGGCA
128 TTCTTGCCAATGGATGGCTTTT-ATTCATGTTTCTTGAA-GTA
* * * *
942 GAAATTCAAATATAATATATTTAAACCAAAAATATAAAAAAAATTCAACTTAAAATTAATTATGA
1 GACATTCAATTATAATATATTTTAACCAAAAATAT--AAAAAATTCAACTTAAAATCAATTATGA
* * * *** * * *
1007 GATTAAAAAACCATTTAAAGTGAGTAGTAATACTTTCGAAGGTATAAGTGACTATAAATAGACTT
64 GATTATAAAACCATTTAAAGTAAGTAATAAGGGTTTCGAAGCT-TGAGTGACTATAAATGGACTT
1072 TTCT
128 TTCT
1076 CTGGATGGCT
Statistics
Matches: 652, Mismatches: 133, Indels: 60
0.77 0.16 0.07
Matches are distributed among these distances:
168 3 0.00
169 101 0.15
170 127 0.19
171 308 0.47
172 112 0.17
173 1 0.00
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (168 bp):
GACATTCAATTATAATATATTTTAACCAAAAATATAAAAAATTCAACTTAAAATCAATTATGAGA
TTATAAAACCATTTAAAGTAAGTAATAAGGGTTTCGAAGCTTGAGTGACTATAAATGGACTTTTC
TTGCCAATGGATGGCTTTTATTCATGTTTCTTGAAGTA
Found at i:744 original size:340 final size:340
Alignment explanation
Indices: 30--1075 Score: 969
Period size: 340 Copynumber: 3.1 Consensus size: 340
20 AAAGGCATTG
* * * * **
30 GTGACTGTAAATTGACTTTTCTTG-CTAATGAAT-GACTTTTTCTTCATATTTTCC-AAGGCCGA
1 GTGACTATAAATAGAATTTTCTTGTC-AATGAATAG-CTTTTTCTTCAT-GTTTCCTAAGGCAAA
* * * * ** **
92 CATTCAATTACAATTTGTTTTAATAAAAAATG-TAAAAAATTTTACTTAAAATCAATTATGAGAT
63 CATTCAACTATAATCTATTTTAACCAAAAATGATAAAAAATTCAACTTAAAATCAATTATGAGAT
** *
156 TATAAAACCATTTAAAGTGAACAATAAGGCTTTCG-AAGTCTTGAGTGATTAC-AAATAGACTTT
128 TATAAAACCATTTAAAGTGAGTAATAAGGCTTTCGAAAG-CTTGAGTGACT-CTAAATAGACTTT
* * * * * *
219 TCCTACCGATGGGTGGCTTTT-ACTTCACGTTTCTCAAAATAGACATTGAATTATAATATATTTT
191 TCTTACCGATGGATGGCTTTTGA-TTCATGTTTTTTAAAATAGACATTCAATTATAATATATTTT
***
283 GGTCAAAAA-AGTGAAAAAATTCAACTTAAAATTAATTATGAGATTATAAAACCATTTAAAGCAA
255 AACCAAAAATA-T-AAAAAATTCAACTTAAAATTAATTATGAGATTATAAAACCATTTAAAGCAA
* * *
347 ATACGAAGGGTTTCGAAGGTATAA
318 ATAC-AAGGCTTTCGAAGGAAGAA
* ** * * *
371 GTGACTATGAATAGGCTTTTCTTGTCAATGAATAGCTTTTT-TTCATGTTT-CTCGAGGTAGACA
1 GTGACTATAAATAGAATTTTCTTGTCAATGAATAGCTTTTTCTTCATGTTTCCT-AAGGCAAACA
* *
434 TGT-AAGTATAATCTATTTTAACCCAAAAT-ATAAAAAATTCAA-TCTAAAATCAATTATGAGAT
65 T-TCAACTATAATCTATTTTAACCAAAAATGATAAAAAATTCAACT-TAAAATCAATTATGAGAT
* * * * *
496 TATAATACCATTTAAATTGAGTAATAAGGGTTTCGAAAGCTTGAATGACTCTAAATGGACTTTTC
128 TATAAAACCATTTAAAGTGAGTAATAAGGCTTTCGAAAGCTTGAGTGACTCTAAATAGACTTTTC
* *
561 TTGCCGATGGATGGCTTTTGATTCATGTTTTTTGAAATAGACATTCAATTATAATAT-TTTTAAC
193 TTACCGATGGATGGCTTTTGATTCATGTTTTTTAAAATAGACATTCAATTATAATATATTTTAAC
* * *
625 CAAAAATTATAAAAAGAGTT-AACTTAAAATCAATTCTGAGATTATAAAACCATTTAAAGCAAGT
258 CAAAAA-TATAAAAA-A-TTCAACTTAAAATTAATTATGAGATTATAAAACCATTTAAAGCAAAT
* *
689 A-ATAGGTCTTTGGAAGGAAGAG
320 ACA-AGG-CTTTCGAAGGAAGAA
* *
711 GTGACTATAAAT-GAAATTTTCTT-TCCAATGAATAGTTTTTTCTTTATGTTTCCTAAGGCAAAC
1 GTGACTATAAATAG-AATTTTCTTGT-CAATGAATAGCTTTTTCTTCATGTTTCCTAAGGCAAAC
* * * * * *
774 GTTCAACTATAATCTTTTTTAACTAAAAATGCTAAAATATTCAACTTAAAATGAATTATGAGATT
64 ATTCAACTATAATCTATTTTAACCAAAAATGATAAAAAATTCAACTTAAAATCAATTATGAGATT
** * * * * * *
839 ATAAAACCATTTAAAGAAAGTAATAATGTTTTCGAAGGCAT-AGGTGACTATAAATTGACTTTTC
129 ATAAAACCATTTAAAGTGAGTAATAAGGCTTTCGAAAGCTTGA-GTGACTCTAAATAGACTTTTC
** * * * * *** * * *
903 TTTTCAATGGATGGCTTTTGCTTCATGTTTCTCAAGGCAGAAATTCAAATATAATATATTTAAAC
193 TTACCGATGGATGGCTTTTGATTCATGTTTTTTAAAATAGACATTCAATTATAATATATTTTAAC
* ** *
968 CAAAAATATAAAAAAAATTCAACTTAAAATTAATTATGAGATTAAAAAACCATTTAAAGTGAGTA
258 CAAAAATAT--AAAAAATTCAACTTAAAATTAATTATGAGATTATAAAACCATTTAAAGCAAATA
* ** * *
1033 GTAATACTTTCGAAGGTATAA
321 -CAAGGCTTTCGAAGGAAGAA
*
1054 GTGACTATAAATAGACTTTTCT
1 GTGACTATAAATAGAATTTTCT
1076 CTGGATGGCT
Statistics
Matches: 578, Mismatches: 96, Indels: 60
0.79 0.13 0.08
Matches are distributed among these distances:
338 2 0.00
339 25 0.04
340 246 0.43
341 79 0.14
342 134 0.23
343 84 0.15
344 7 0.01
345 1 0.00
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.36
Consensus pattern (340 bp):
GTGACTATAAATAGAATTTTCTTGTCAATGAATAGCTTTTTCTTCATGTTTCCTAAGGCAAACAT
TCAACTATAATCTATTTTAACCAAAAATGATAAAAAATTCAACTTAAAATCAATTATGAGATTAT
AAAACCATTTAAAGTGAGTAATAAGGCTTTCGAAAGCTTGAGTGACTCTAAATAGACTTTTCTTA
CCGATGGATGGCTTTTGATTCATGTTTTTTAAAATAGACATTCAATTATAATATATTTTAACCAA
AAATATAAAAAATTCAACTTAAAATTAATTATGAGATTATAAAACCATTTAAAGCAAATACAAGG
CTTTCGAAGGAAGAA
Done.