Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399527.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2787.0, 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: 1927
ACGTcount: A:0.24, C:0.08, G:0.09, T:0.24
Warning! 678 characters in sequence are not A, C, G, or T
Found at i:632 original size:171 final size:171
Alignment explanation
Indices: 246--1001 Score: 478
Period size: 171 Copynumber: 4.4 Consensus size: 171
236 NNNNGCAATG
* * *
246 GGTGACTATAAATAGACTTTTCTTACCAATGAAAACTTTTTTCTTCATGTTTCTGAAGGTAGACA
1 GGTGACTATAAATAGACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTCAAGGTAGACA
* * * * * * *
311 TTCAAAGTTAGTCTATTTTAACCAAAACTATGCGAAGAATTCAAATTTAAATCAATTTTGAGATT
66 TTCAAAGTTAGTATATTTTAACAAAAAATATGCAAAAAATTCAAATTAAAATCAATTATGAGATT
* * * *
376 ATAAAACTATTTACAGTGAGTAATAAGGCTCTTGAAGTAAT
131 ACAAAACTATTTAAAGTGACTAATAAGACTCTTGAAGTAAT
* * * * *
417 GAGTGACTATAAATAGACTTTTCTTGCCAACGAATGCATTTTTCTTTATGTTTCTCTAGGTAGAC
1 G-GTGACTATAAATAGACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTCAAGGTAGAC
* * ** *
482 ATTC-AATTATAGTATGTTTTAACAAAAAAT-TTTAAAAAATTCAACTTAAAATCAATTATG-GC
65 ATTCAAAGT-TAGTATATTTTAACAAAAAATATGCAAAAAATTCAAATTAAAATCAATTATGAG-
* * *
544 ATTACAAAACTGTTTAAAGTGACTAGTAAGACTTTTGAAGGT-AT
128 ATTACAAAACTATTTAAAGTGACTAATAAGACTCTTGAA-GTAAT
* * **********
588 AGGTGACTATAAA-CGAACTTTTCGTGCCAATGAATACTTTTTTCTTCATGTTTCNNNNNNNNNN
1 -GGTGACTATAAATAG-ACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTCAAGGTAGA
* * * * * * * * * * *
652 CATTC-AATTCTAGTCTGTTTTAACTAAAAGTGTACAAAGATTTCAAATTTAAATCAATTTTGAG
64 CATTCAAAGT-TAGTATATTTTAACAAAAAATATGCAAAAAATTCAAATTAAAATCAATTATGAG
* * * * * ****
716 ATTATAAAAAC-GTTTAAAGTGAGTAATAA-AGCTTTTAAAGNNNNN
128 ATTA-CAAAACTATTTAAAGTGACTAATAAGA-CTCTTGAAG-TAAT
***** * * ** * * *
761 NNNNNCTATAAATGGACTTCTCTTGCCAATGAATGTTTTTTTCTTTATATTTCTCAAGCTAGACA
1 GGTGACTATAAATAGACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTCAAGGTAGACA
* * * * * * * * * *
826 ATC-AATTATAATATGTTTTAATCGGAGAAGTA---AAAAAATTTGAACTTAAAATTAATT-TGA
66 TTCAAAGT-TAGTATATTTTAA-C-AAAAAATATGCAAAAAA-TTCAAATTAAAATCAATTATGA
* * * *
886 GATTATAAAACCATTTAAAGTGATTAATAATG-CTTTTGAAGTAAT
127 GATTACAAAACTATTTAAAGTGACTAATAA-GACTCTTGAAGTAAT
* * *
931 GGGTGACTATAAAAAGACTTTTCTTGCTAATGAATACTTTTTTCTTCATGTTTCTCAAGGTAGAT
1 -GGTGACTATAAATAGACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTCAAGGTAGAC
996 ATTCAA
65 ATTCAA
1002 TTCTAGTCTA
Statistics
Matches: 444, Mismatches: 120, Indels: 41
0.73 0.20 0.07
Matches are distributed among these distances:
170 7 0.02
171 222 0.50
172 202 0.45
173 8 0.02
174 5 0.01
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.37
Consensus pattern (171 bp):
GGTGACTATAAATAGACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTCAAGGTAGACA
TTCAAAGTTAGTATATTTTAACAAAAAATATGCAAAAAATTCAAATTAAAATCAATTATGAGATT
ACAAAACTATTTAAAGTGACTAATAAGACTCTTGAAGTAAT
Found at i:703 original size:343 final size:333
Alignment explanation
Indices: 6--984 Score: 718
Period size: 343 Copynumber: 2.9 Consensus size: 333
1 AAAGT
* * * * *
6 TTCAAATTTAAATCAATTTTGAGATTATAGAACCATTTAAAGTGAGTAATAAAGCTTTTCAAGGA
1 TTCAAATTTAAATCAATTTTGAGATTATAAAAACATTTAAAGTGAGTAATAAAGCTCTTAAAGTA
* * ********** * *
71 ATGCA-TGACTATAAATGGACTTCTCTTGCCAATGAATGCNNNNNNNNNNATGTTTCTCAGGCTA
66 ATG-AGTGACTATAAATAGACTTCTCTTGCCAACGAATGCATTTTTCTTTATATTTCTCAAGCTA
** * * * *
135 GACGTTCAATTATAATATATTTTAACCAGAGAAA-TAAAAAAATTTGAACTTAAAATCAATTTTG
130 GACAATCAATTATAATATGTTTTAATCA-AAAAAGTAAAAAAATTTCAACTTAAAATCAA-TTTG
* ****************** * * *
199 AGATTATAAAACCATTTAAAGTGNNNNNNNNNNNNNNNNNNGCAATGGGTGACTATAAATAGACT
193 AGATTACAAAACCATTTAAAGTGACTAATAATGCTTTTGAAGTAATAGGTGACTATAAAAAGACT
* * * * *
264 TTTCTTACCAATGAAAACTTTTTTCTTCATGTTTCTGAAGGTAGACATTCAAAGT-TAGTCTATT
258 TTTCGTGCCAATGAATACTTTTTTCTTCATGTTTC----------CATTC-AATTCTAGTCTGTT
* * * * *
328 TTAACCAAAACTATGCGAAGAA
312 TTAACTAAAAGTGTACAAAGAA
* * *
350 TTCAAATTTAAATCAATTTTGAGATTAT-AAAACTATTTACAGTGAGTAATAAGGCTCTTGAAGT
1 TTCAAATTTAAATCAATTTTGAGATTATAAAAAC-ATTTAAAGTGAGTAATAAAGCTCTTAAAGT
* * * *
414 AATGAGTGACTATAAATAGACTTTTCTTGCCAACGAATGCATTTTTCTTTATGTTTCTCTAGGTA
65 AATGAGTGACTATAAATAGACTTCTCTTGCCAACGAATGCATTTTTCTTTATATTTCTCAAGCTA
* * * *
479 GACATTCAATTATAGTATGTTTTAA-CAAAAAATTTTAAAAAA-TTCAACTTAAAATCAATTATG
130 GACAATCAATTATAATATGTTTTAATCAAAAAA-GTAAAAAAATTTCAACTTAAAATCAATT-TG
** * *
542 -GCATTACAAAACTGTTTAAAGTGACTAGTAA-GACTTTTGAAGGT-ATAGGTGACTAT-AAACG
193 AG-ATTACAAAACCATTTAAAGTGACTAATAATG-CTTTTGAA-GTAATAGGTGACTATAAAAAG
603 AACTTTTCGTGCCAATGAATACTTTTTTCTTCATGTTTCNNNNNNNNNNCATTCAATTCTAGTCT
255 -ACTTTTCGTGCCAATGAATACTTTTTTCTTCATGTTTC----------CATTCAATTCTAGTCT
*
668 GTTTTAACTAAAAGTGTACAAAGAT
309 GTTTTAACTAAAAGTGTACAAAGAA
* * **
693 TTCAAATTTAAATCAATTTTGAGATTATAAAAACGTTTAAAGTGAGTAATAAAGCTTTTAAAGNN
1 TTCAAATTTAAATCAATTTTGAGATTATAAAAACATTTAAAGTGAGTAATAAAGCTCTTAAAGTA
******** * * **
758 NNNNNNNNCTATAAATGGACTTCTCTTGCCAATGAATGTTTTTTTCTTTATATTTCTCAAGCTAG
66 ATGAGTGACTATAAATAGACTTCTCTTGCCAACGAATGCATTTTTCTTTATATTTCTCAAGCTAG
** * * *
823 ACAATCAATTATAATATGTTTTAATCGGAGAAGTAAAAAAATTTGAACTTAAAATTAATTTGAGA
131 ACAATCAATTATAATATGTTTTAATCAAAAAAGTAAAAAAATTTCAACTTAAAATCAATTTGAGA
* * *
888 TTATAAAACCATTTAAAGTGATTAATAATGCTTTTGAAGTAATGGGTGACTATAAAAAGACTTTT
196 TTACAAAACCATTTAAAGTGACTAATAATGCTTTTGAAGTAATAGGTGACTATAAAAAGACTTTT
* *
953 CTTGCTAATGAATACTTTTTTCTTCATGTTTC
261 CGTGCCAATGAATACTTTTTTCTTCATGTTTC
985 TCAAGGTAGA
Statistics
Matches: 503, Mismatches: 115, Indels: 35
0.77 0.18 0.05
Matches are distributed among these distances:
342 15 0.03
343 327 0.65
344 161 0.32
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.35
Consensus pattern (333 bp):
TTCAAATTTAAATCAATTTTGAGATTATAAAAACATTTAAAGTGAGTAATAAAGCTCTTAAAGTA
ATGAGTGACTATAAATAGACTTCTCTTGCCAACGAATGCATTTTTCTTTATATTTCTCAAGCTAG
ACAATCAATTATAATATGTTTTAATCAAAAAAGTAAAAAAATTTCAACTTAAAATCAATTTGAGA
TTACAAAACCATTTAAAGTGACTAATAATGCTTTTGAAGTAATAGGTGACTATAAAAAGACTTTT
CGTGCCAATGAATACTTTTTTCTTCATGTTTCCATTCAATTCTAGTCTGTTTTAACTAAAAGTGT
ACAAAGAA
Found at i:1002 original size:343 final size:344
Alignment explanation
Indices: 242--1012 Score: 840
Period size: 343 Copynumber: 2.2 Consensus size: 344
232 NNNNNNNNGC
* * * *
242 AATGGGTGACTATAAATAGACTTTTCTTACCAATGAAAACTTTTTTCTTCATGTTTCTGAAGGTA
1 AATGGGTGACTATAAAAAGACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTCAAGGTA
* * *
307 GACATTCAAAGT-TAGTCTATTTTAACCAAAACTATGCGAAGAATTCAAATTTAAATCAATTTTG
66 GACATTC-AATTCTAGTCTATTTTAACCAAAACTATACAAAGAATTCAAATTTAAATCAATTTTG
* * *
371 AGATTATAAAACTATTTACAGTGAGTAATAAGGCTCTTGAAGTAATGAGTGACTATAAATAGACT
130 AGATTATAAAACTATTTAAAGTGAGTAATAAAGCTCTTAAAGTAATGAGTGACTATAAATAGACT
* * * * * *
436 TTTCTTGCCAACGAATGCATTTTTCTTTATGTTTCTCTAGGTAGACATTCAATTATAGTATGTTT
195 TCTCTTGCCAACGAATGCATTTTTCTTTATATTTCTCAAGCTAGACAATCAATTATAATATGTTT
* * **
501 TAACAAAAAATTTTAAAAAATTCAACTTAAAATCAATTATGGCATTACAAAACTGTTTAAAGTGA
260 TAACAAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGGCATTACAAAACCATTTAAAGTGA
*
566 CTAGTAAGACTTTTGAAGGT
325 CTAATAAGACTTTTGAAGGT
* * * *******
586 -ATAGGTGACTAT-AAACGAACTTTTCGTGCCAATGAATACTTTTTTCTTCATGTTTCNNNNNNN
1 AATGGGTGACTATAAAAAG-ACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTCAAGGT
*** * * * * *
649 NNNCATTCAATTCTAGTCTGTTTTAACTAAAAGTGTACAAAGATTTCAAATTTAAATCAATTTTG
65 AGACATTCAATTCTAGTCTATTTTAACCAAAACTATACAAAGAATTCAAATTTAAATCAATTTTG
* * ********** *
714 AGATTATAAAAAC-GTTTAAAGTGAGTAATAAAGCTTTTAAAGNNNNNNNNNNCTATAAATGGAC
130 AGATTAT-AAAACTATTTAAAGTGAGTAATAAAGCTCTTAAAGTAATGAGTGACTATAAATAGAC
* **
778 TTCTCTTGCCAATGAATGTTTTTTTCTTTATATTTCTCAAGCTAGACAATCAATTATAATATGTT
194 TTCTCTTGCCAACGAATGCATTTTTCTTTATATTTCTCAAGCTAGACAATCAATTATAATATGTT
** * * * *
843 TTAATCGGAGAA-GTAAAAAAATTTGAACTTAAAATTAATT-TGAG-ATTATAAAACCATTTAAA
259 TTAA-CAAAAAATGTAAAAAAA-TTCAACTTAAAATCAATTATG-GCATTACAAAACCATTTAAA
*
905 GTGATTAATAATG-CTTTTGAA-GT
321 GTGACTAATAA-GACTTTTGAAGGT
*
928 AATGGGTGACTATAAAAAGACTTTTCTTGCTAATGAATACTTTTTTCTTCATGTTTCTCAAGGTA
1 AATGGGTGACTATAAAAAGACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTCAAGGTA
*
993 GATATTCAATTCTAGTCTAT
66 GACATTCAATTCTAGTCTAT
1013 NNNNNNNNNN
Statistics
Matches: 341, Mismatches: 77, Indels: 19
0.78 0.18 0.04
Matches are distributed among these distances:
342 8 0.02
343 302 0.89
344 31 0.09
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.37
Consensus pattern (344 bp):
AATGGGTGACTATAAAAAGACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTCAAGGTA
GACATTCAATTCTAGTCTATTTTAACCAAAACTATACAAAGAATTCAAATTTAAATCAATTTTGA
GATTATAAAACTATTTAAAGTGAGTAATAAAGCTCTTAAAGTAATGAGTGACTATAAATAGACTT
CTCTTGCCAACGAATGCATTTTTCTTTATATTTCTCAAGCTAGACAATCAATTATAATATGTTTT
AACAAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGGCATTACAAAACCATTTAAAGTGAC
TAATAAGACTTTTGAAGGT
Done.