Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401180.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4330.0, 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, 808
Length: 1347
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Found at i:371 original size:170 final size:171
Alignment explanation
Indices: 12--1344 Score: 1062
Period size: 170 Copynumber: 7.8 Consensus size: 171
2 ATGAATAGGT
* * * * * *
12 GACTATAAATAGACTTTTCTTGCAAATGAATTCATTTTTCTTTACGTTTCTCAAGG-TAGACATT
1 GACTATAAATAGACTTTTCTTCCAAATAAATACATTTTTCTTCATGTTTCTCTAGGCTAGACATT
* * * * * * *
76 CAATTATAGTCTATTTTAAACAAAAATGTAAAAACAATTCAACTTAAAATCAGTTATGAGATTCT
66 CAATTATAATTTGTTTTAAAGAAAAATAT-AAAA-AATTCAACTTAAAATCAATTATGAGATTAT
141 AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGA
129 AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGA
* ** * * *
184 GACTATAAATGGACTTTTCTTCCAAATAAATGGATTTTTCTAT-ACGTTTCCCTA-GCTAGGCAT
1 GACTATAAATAGACTTTTCTTCCAAATAAATACATTTTTCT-TCATGTTTCTCTAGGCTAGACAT
* * * *
247 TCAATTATAGTTTGTTTTAAAGAAAAATATAAAAAATTTAACCTAAAATTAATTATGAGATTATA
65 TCAATTATAATTTGTTTTAAAGAAAAATATAAAAAATTCAACTTAAAATCAATTATGAGATTATA
* * * *
312 AAACCCTTTAAAGCGAGTAATAAAGCTTTTGAATGAATGGGT
130 AAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGA
* * * * * * *
354 GA-TCAGAAATAGACTTTTCTTGTC-AATGAATACCTTTTTCTTCATGTTTCTCGA-GATAGATA
1 GACT-ATAAATAGACTTTTCTT-CCAAATAAATACATTTTTCTTCATGTTTCTCTAGGCTAGACA
** * * * ** *
416 TTCAATTATAATCTT-TTTTAACCAAAAATGTAAAAAAAATGAACTTAAAATTGATTACGAGATT
64 TTCAATTATAAT-TTGTTTTAAAGAAAAATAT-AAAAAATTCAACTTAAAATCAATTATGAGATT
* * * *
480 ATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAACGAGA
127 ATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGA
* * * * * * ** *
525 GAATATGAATGGACTTTTCCTGCTAATAAATATTTTTTTCTTCATGTTTGTC-AGGAC-AGACAT
1 GACTATAAATAGACTTTTCTTCCAAATAAATACATTTTTCTTCATGTTTCTCTAGG-CTAGACAT
* * * ** * * * * * *
588 TAAATTATAGTCTGTTTTAACTAAAAATGTAAAAAAAATTTAACATAAAATCAATTTTTAGATAA
65 TCAATTATAATTTGTTTTAAAGAAAAA--TATAAAAAATTCAACTTAAAATCAATTATGAGATTA
** * * * * *
653 TAAAATTATTTAAAGTGAGTAATAAGGTTTTTCACA-GATTAGGA
128 TAAAACCATTTAAAGCGAGTAATAAGGCTTTTGA-AGGAATGGGA
* * ** * * * * *
697 GACTATAAAT-GAATTTTTCTTGTC-AACGAATACCTTTCTCTTCATGTCTCTCGATG-TAGACA
1 GACTATAAATAG-ACTTTTCTT-CCAAATAAATACATTTTTCTTCATGTTTCTCTAGGCTAGACA
* * * *
759 TTCAATTATAATATGTTTTACTCA-AAAAATA-AAAACAATTGAA-TTAAAATCAATTTTGAGAT
64 TTCAATTATAATTTGTTTTA--AAGAAAAATATAAAA-AATTCAACTTAAAATCAATTATGAGAT
* * *
821 TATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGTGT
126 TATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGA
* * * * * * *
867 GACAATAAATAGGCTTTTATTGCAAATGAATTCATTTTTTTTCATGTTTCT-TGAGG-TAGACAT
1 GACTATAAATAGACTTTTCTTCCAAATAAATACATTTTTCTTCATGTTTCTCT-AGGCTAGACAT
**
930 TCAATTATAATTTGTTTTAATA-AAAAATATTAAAAAATTCAACACAAAATCAATTATGAGATTA
65 TCAATTATAATTTGTTTTAA-AGAAAAATA-TAAAAAATTCAACTTAAAATCAATTATGAGATTA
* * * * *
994 TAAACCCATTTAAAGCAAGTAATAAGACTTTTAAAGGAATGAGA
128 TAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGA
* *** * * * *
1038 GACTATAAATAGACTTTTTTTCCAAATAAATGGGTTTTTCTAT-ACGTTTCTCAATGC-ATG-TA
1 GACTATAAATAGACTTTTCTTCCAAATAAATACATTTTTCT-TCATGTTTCTCTAGGCTA-GACA
* * * * *
1100 TTCAATTATTATCTATTTTAATGAAAAATATAAAAAATTTAACTTAAAATCAATTATGAGATTAT
64 TTCAATTATAATTTGTTTTAAAGAAAAATATAAAAAATTCAACTTAAAATCAATTATGAGATTAT
* * * * *
1165 AAATCTATTTAAAGCAACTAATAAGGCTTTTGAAAGAATGGGA
129 AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGA
* *** * * *
1208 GACTATAAATAGACTTTTCTTCTAAATAAATGGGTTTTTCTGCATGGTTC-CTAAGGCAAG-CAT
1 GACTATAAATAGACTTTTCTTCCAAATAAATACATTTTTCTTCATGTTTCTCT-AGGCTAGACAT
* * * * *
1271 TTAATAAT-ATTCTTTTTTAATTG-AAAATGTAAAAAATTCAACTTAAAATCAATTATGAGATTA
65 TCAATTATAATT-TGTTTTAA-AGAAAAATATAAAAAATTCAACTTAAAATCAATTATGAGATTA
*
1334 TAAAACTATTT
128 TAAAACCATTT
1345 CAA
Statistics
Matches: 939, Mismatches: 182, Indels: 82
0.78 0.15 0.07
Matches are distributed among these distances:
169 15 0.02
170 438 0.47
171 278 0.30
172 197 0.21
173 11 0.01
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.37
Consensus pattern (171 bp):
GACTATAAATAGACTTTTCTTCCAAATAAATACATTTTTCTTCATGTTTCTCTAGGCTAGACATT
CAATTATAATTTGTTTTAAAGAAAAATATAAAAAATTCAACTTAAAATCAATTATGAGATTATAA
AACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGA
Found at i:1068 original size:513 final size:513
Alignment explanation
Indices: 12--1238 Score: 1232
Period size: 513 Copynumber: 2.4 Consensus size: 513
2 ATGAATAGGT
* * * *
12 GACTATAAATAGACTTTTCTTGCAAATGAATTCATTTTTCTTTACGTTTCTCAAGGTAGACATTC
1 GACTATAAATAGACTTTTCTTGCAAATAAATTCATTTTTCTTCACGTTTCTCAAGGCAGACATTA
* * * **
77 AATTATAGTCTATTTTAAACAAAAATGTAAAAACAATTCAACTTAAAATCAGTTATGAGATTCTA
66 AATTATAGTCTATTTTAAACAAAAATGTAAAAAAAATTCAACATAAAATCAATTATGAGATAATA
* * *
142 AAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATGGACTTTTCTTCC
131 AAACCATTTAAAGCGAGTAATAAGGCTTTTCAAGGAATAGGAGACTATAAATGAACTTTTCTTCC
* ** * * * * * *
207 AAATAAATGGATTTTTCTATACGTTTCCCTAGCTAGGCATTCAATTATAGTTTGTTTTAAAGAAA
196 AAACAAATACATTTCTCTATACGTCTCCCGAGCTAGACATTCAATTATAATATGTTTTAAAGAAA
* * *
272 AATATAAAAAATTTAACCTAAAATTAATTATGAGATTATAAAACCCTTTAAAGCGAGTAATAAAG
261 AATATAAAAAATTGAACCTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAAG
* * *
337 CTTTTGAATGAATGGGTGATCAGAAATAGACTTTTCTTGTCAATGAATACCTTTTTCTTCATGTT
326 CTTTTGAAGGAATGGGTGATCAGAAATAGACTTTTATTGTCAATGAATACATTTTTCTTCATGTT
* * * * **
402 TCTCGAGATAGATATTCAATTATAATCTTTTTTAACCAAAAATGTAAAAAAAATGAACTTAAAAT
391 TCTCGAGATAGACATTCAATTATAATCTTTTTTAACAAAAAATATAAAAAAAATCAACACAAAAT
** * ** * *
467 TGATTACGAGATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAACGAGA
456 CAATTACGAGATTATAAAACCATTTAAAGCAAGTAATAAGACTTTTAAAGGAACGAGA
* * * * * * * *
525 GAATATGAATGGACTTTTCCTGCTAATAAATAT-TTTTTTCTTCATGTTTGTC-AGGACAGACAT
1 GACTATAAATAGACTTTTCTTGCAAATAAAT-TCATTTTTCTTCACGTTTCTCAAGG-CAGACAT
* * * *
588 TAAATTATAGTCTGTTTT-AACTAAAAATGTAAAAAAAATTTAACATAAAATCAATTTTTAGATA
64 TAAATTATAGTCTATTTTAAAC-AAAAATGTAAAAAAAATTCAACATAAAATCAATTATGAGATA
** * * * *
652 ATAAAATTATTTAAAGTGAGTAATAAGGTTTTTCACA-GATTAGGAGACTATAAATGAATTTTTC
128 ATAAAACCATTTAAAGCGAGTAATAAGGCTTTTCA-AGGAATAGGAGACTATAAATGAACTTTTC
* * * * *
716 TTGTC-AACGAATACCTTTCTCT-TCATGTCTCTCGATG-TAGACATTCAATTATAATATGTTTT
192 TT-CCAAACAAATACATTTCTCTAT-ACGTCTCCCGA-GCTAGACATTCAATTATAATATGTTTT
* * * *
778 ACTCA-AAAAATA-AAAACAATTGAA-TTAAAATCAATTTTGAGATTATAAAACCATTTAAAGTG
254 A--AAGAAAAATATAAAA-AATTGAACCTAAAATCAATTATGAGATTATAAAACCATTTAAAGCG
* * * * *
840 AGTAATAAGGCTTTTGAAGGAATGTGTGA-CAATAAATAGGCTTTTATTG-CAAATGAATTCATT
316 AGTAATAAAGCTTTTGAAGGAATGGGTGATC-AGAAATAGACTTTTATTGTC-AATGAATACATT
* * * * *
903 TTTTTTCATGTTTCTTGAGGTAGACATTCAATTATAAT-TTGTTTTAATAAAAAATATTAAAAAA
379 TTTCTTCATGTTTCTCGAGATAGACATTCAATTATAATCTT-TTTTAACAAAAAATATAAAAAAA
* * *
967 TTCAACACAAAATCAATTATGAGATTATAAACCCATTTAAAGCAAGTAATAAGACTTTTAAAGGA
443 ATCAACACAAAATCAATTACGAGATTATAAAACCATTTAAAGCAAGTAATAAGACTTTTAAAGGA
*
1032 ATGAGA
508 ACGAGA
* * *** * *
1038 GACTATAAATAGACTTTTTTTCCAAATAAATGGGTTTTTCTAT-ACGTTTCTCAATGCATG-TAT
1 GACTATAAATAGACTTTTCTTGCAAATAAATTCATTTTTCT-TCACGTTTCTCAAGGCA-GACAT
* ** * * * *
1101 TCAATTATTA-TCTATTTTAATGAAAAA--TATAAAAAATTTAACTTAAAATCAATTATGAGATT
64 TAAATTA-TAGTCTATTTTAAACAAAAATGTAAAAAAAATTCAACATAAAATCAATTATGAGATA
* * * * * * *
1163 ATAAATCTATTTAAAGCAACTAATAAGGCTTTTGAAAGAATGGGAGACTATAAAT-AGACTTTTC
128 ATAAAACCATTTAAAGCGAGTAATAAGGCTTTTCAAGGAATAGGAGACTATAAATGA-ACTTTTC
* *
1227 TTCTAAATAAAT
192 TTCCAAACAAAT
1239 GGGTTTTTCT
Statistics
Matches: 575, Mismatches: 117, Indels: 46
0.78 0.16 0.06
Matches are distributed among these distances:
510 2 0.00
511 87 0.15
512 11 0.02
513 450 0.78
514 24 0.04
515 1 0.00
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (513 bp):
GACTATAAATAGACTTTTCTTGCAAATAAATTCATTTTTCTTCACGTTTCTCAAGGCAGACATTA
AATTATAGTCTATTTTAAACAAAAATGTAAAAAAAATTCAACATAAAATCAATTATGAGATAATA
AAACCATTTAAAGCGAGTAATAAGGCTTTTCAAGGAATAGGAGACTATAAATGAACTTTTCTTCC
AAACAAATACATTTCTCTATACGTCTCCCGAGCTAGACATTCAATTATAATATGTTTTAAAGAAA
AATATAAAAAATTGAACCTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAAG
CTTTTGAAGGAATGGGTGATCAGAAATAGACTTTTATTGTCAATGAATACATTTTTCTTCATGTT
TCTCGAGATAGACATTCAATTATAATCTTTTTTAACAAAAAATATAAAAAAAATCAACACAAAAT
CAATTACGAGATTATAAAACCATTTAAAGCAAGTAATAAGACTTTTAAAGGAACGAGA
Found at i:1177 original size:341 final size:337
Alignment explanation
Indices: 12--1337 Score: 1127
Period size: 341 Copynumber: 3.9 Consensus size: 337
2 ATGAATAGGT
* * * * *
12 GACTATAAATAGACTTTTCTTGCAAATGAATTCATTTTTCTTTACGTTTCTCAAGGTAGACATTC
1 GACTATAAATAGACTTTT-TTTC-AATGAATACCTTTTTCTTCACGTTTCTCAATGTAGACATTC
* * * * * *
77 AATTATAGTCTATTTTAAACAAAAATGTAAAAACAATTCAACTTAAAATCAGTTATGAGATTCTA
64 AATTATAATCTATTTTAATCAAAAATATAAAAACAATTGAACTTAAAATCAATTATGAGATTATA
* *
142 AAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATGGACTTTTCTTCC
129 AAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGAGACAATAAATGGACTTTTCTTGC
* * * * *
207 AAATAAATGGATTTTTCTAT-ACGTTTCCCTAGCTAGGCATTCAATTATAGTTTGTTTTAA-AGA
194 AAAT-AAT-TATTTTT-TTTCATGTTT-CCTAGGTAGACATTCAATTATAGTTTGTTTTAATA-A
*
270 AAAATA-TAAAAAATTTAAC-CTAAAATTAATTATGAGATTATAAAACCC-TTTAAAGCGAGTAA
254 AAAATATTAAAAAATTTAACAC-AAAATCAATTATGAGATTAT-AAACCCATTTAAAGCGAGTAA
* * *
332 TAA-AGCTTTTGAATGAATGGGT
317 TAAGA-CTTTT-AAAGAATGAGA
* * * *
354 GA-TCAGAAATAGACTTTTCTTGTCAATGAATACCTTTTTCTTCATGTTTCTCGA-GATAGATAT
1 GACT-ATAAATAGACTTTT-TT-TCAATGAATACCTTTTTCTTCACGTTTCTCAATG-TAGACAT
* * * * ** *
417 TCAATTATAATCTTTTTTAACCAAAAATGTAAAAA-AAATGAACTTAAAATTGATTACGAGATTA
62 TCAATTATAATCTATTTTAATCAAAAATATAAAAACAATTGAACTTAAAATCAATTATGAGATTA
* * * * * *
481 TAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGGAACGAGAGA-ATATGAATGGACTTTTCC
127 TAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGAGACA-ATAAATGGACTTTTCT
* * * * * *
545 TGCTAATAAATATTTTTTTCTTCATGTTT-GTCAGGACAGACATTAAATTATAGTCTGTTTTAAC
191 TGCAAATAATTA-TTTTTT-TTCATGTTTCCT-AGG-TAGACATTCAATTATAGTTTGTTTTAA-
* * * * * * *** *
609 T-AAAAATGTAAAAAAAATTTAACATAAAATCAATTTTTAGATAATAAAATTATTTAAAGTGAGT
251 TAAAAAATAT-TAAAAAATTTAACACAAAATCAATTATGAGATTATAAACCCATTTAAAGCGAGT
** * *
673 AATAAGGTTTTTCACAG-ATTAGGA
315 AATAAGACTTTT-AAAGAATGA-GA
* * * * * *
697 GACTATAAAT-GAATTTTTCTTGTCAACGAATACCTTTCTCTTCATGTCTCTCGATGTAGACATT
1 GACTATAAATAG-ACTTTT-TT-TCAATGAATACCTTTTTCTTCACGTTTCTCAATGTAGACATT
* * * *
761 CAATTATAATATGTTTTACTCAAAAA-ATAAAAACAATTGAA-TTAAAATCAATTTTGAGATTAT
63 CAATTATAATCTATTTTAATCAAAAATATAAAAACAATTGAACTTAAAATCAATTATGAGATTAT
* * * *
824 AAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGTGTGACAATAAATAGG-CTTTTATT
128 AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGAGACAATAAAT-GGACTTTTCTT
* *
888 GCAAATGAATTCATTTTTTTTCATGTTTCTTGAGGTAGACATTCAATTATAATTTGTTTTAATAA
192 GCAAAT-AATT-ATTTTTTTTCATGTTTCCT-AGGTAGACATTCAATTATAGTTTGTTTTAATAA
* *
953 AAAATATTAAAAAATTCAACACAAAATCAATTATGAGATTATAAACCCATTTAAAGCAAGTAATA
254 AAAATATTAAAAAATTTAACACAAAATCAATTATGAGATTATAAACCCATTTAAAGCGAGTAATA
1018 AGACTTTTAAAGGAATGAGA
319 AGACTTTTAAA-GAATGAGA
* *** * *
1038 GACTATAAATAGACTTTTTTTCCAAATAAATGGGTTTTTCTAT-ACGTTTCTCAATGCATG-TAT
1 GACTATAAATAGACTTTTTTT-C-AATGAATACCTTTTTCT-TCACGTTTCTCAATGTA-GACAT
* * *
1101 TCAATTATTATCTATTTTAATGAAAAATAT-AAAA-AATTTAACTTAAAATCAATTATGAGATTA
62 TCAATTATAATCTATTTTAATCAAAAATATAAAAACAATTGAACTTAAAATCAATTATGAGATTA
* * * * * * *
1164 TAAATCTATTTAAAGCAACTAATAAGGCTTTTGAAAGAATGGGAGACTATAAATAGACTTTTCTT
127 TAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGAGACAATAAATGGACTTTTCTT
** * * * * * * *
1229 -CTAAATAAATGGGTTTTTCTGCATGGTTCCTAAGGCA-AGCATTTAATAATA-TTCTTTTTTAA
192 GC-AAAT-AAT-TATTTTTTTTCATGTTTCCT-AGGTAGA-CATTCAATTATAGTT-TGTTTTAA
** * * **
1291 TTGAAAAT-GTAAAAAATTCAACTTAAAATCAATTATGAGATTATAAA
251 TAAAAAATATTAAAAAATTTAACACAAAATCAATTATGAGATTATAAA
1338 ACTATTTCAA
Statistics
Matches: 793, Mismatches: 150, Indels: 84
0.77 0.15 0.08
Matches are distributed among these distances:
339 4 0.01
340 62 0.08
341 361 0.46
342 215 0.27
343 148 0.19
344 3 0.00
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.37
Consensus pattern (337 bp):
GACTATAAATAGACTTTTTTTCAATGAATACCTTTTTCTTCACGTTTCTCAATGTAGACATTCAA
TTATAATCTATTTTAATCAAAAATATAAAAACAATTGAACTTAAAATCAATTATGAGATTATAAA
ACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGAGACAATAAATGGACTTTTCTTGCAA
ATAATTATTTTTTTTCATGTTTCCTAGGTAGACATTCAATTATAGTTTGTTTTAATAAAAAATAT
TAAAAAATTTAACACAAAATCAATTATGAGATTATAAACCCATTTAAAGCGAGTAATAAGACTTT
TAAAGAATGAGA
Done.