Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398753.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2036.0, 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: 3733
ACGTcount: A:0.24, C:0.07, G:0.08, T:0.23
Warning! 1427 characters in sequence are not A, C, G, or T
Found at i:324 original size:171 final size:170
Alignment explanation
Indices: 1--1132 Score: 1107
Period size: 171 Copynumber: 6.6 Consensus size: 170
* * * ** * *
1 AGAGGCTATAAATAGACTTTTCTTGTCAATGAATGCCTTTTTCTTCACATTTCTCAAGTTAAACA
1 AGAGACTATAAATGGACTTTTCTTGTCAATGAATGCTTTTTTCTTCATGTTTCTCAAGATAGACA
* * *
66 TTCAATTATAGCCTGTTTTAA-CAAAAAAAGTAAAAATATTCAACTTAAAATCAATTATGAGATT
66 TTCAATTATAGTCTGTTTTAATCAAAAATA-TAAAAAAATTCAACTTAAAATCAATTATGAGATT
* * *
130 ATAAAACCATTTGAAGTGAGTAATATGGCTTTTGAAGAAAA
130 ATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGAAAT
* * *
171 AGATGACTATAAATGGACTTTTCTTGTCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTAAAT
1 AGA-GACTATAAATGGACTTTTCTTGTCAATGAATGCTTTTTTCTTCATGTTTCTCAAGATAGAC
* * *
236 ATTCAATTATAGTCTGTTTTAATCAAAAATATAAAAAAATTCAACCTAAAATTAATTATAAGATT
65 ATTCAATTATAGTCTGTTTTAATCAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATT
* * * *
301 AGAAAATCATTTAAAGCGAGTAATAAGGCTTTTGAAGAATT
130 ATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGAAAT
* * * * * * * * * *
342 GGGCGACTATAAATGGATTTTTCTTATCAACGAATGCTTTTGTCTTTATGTTTTTTAAGATAGAT
1 -AGAGACTATAAATGGACTTTTCTTGTCAATGAATGCTTTTTTCTTCATGTTTCTCAAGATAGAC
* * * *
407 AGTCAATTATTA-TTTGTTTTAATCAAAAATGTTAAAAAAATT-AACTTAAAATCAATTATTAGA
65 ATTCAATTA-TAGTCTGTTTTAATCAAAAAT-ATAAAAAAATTCAACTTAAAATCAATTATGAGA
* * *
470 TT-TGAAAACCATTTAAAATGAAG-AATAAGGCTTTCGAAGGAAT
128 TTAT-AAAACCATTTAAAGTG-AGTAATAAGGCTTTTGAAGAAAT
* * * * * *
513 GGAAGGCTATAAATAGACTTTTCTTGCCAATGAATACTTTTTTCTTCACT-TTTCTTAAGATAGA
1 AG-AGACTATAAATGGACTTTTCTTGTCAATGAATGCTTTTTTCTTCA-TGTTTCTCAAGATAGA
* * * * * *
577 CATTCAATTATAGTCTGTTTTAATGAAAAATGTAAAAAAATTGAACTTAAATTTAATTGTGAGAT
64 CATTCAATTATAGTCTGTTTTAATCAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGAT
* * * * * *
642 TATAAAATCATTTAGAA-TGAGTAAAAAGCCTATTAAAGGAAT
129 TATAAAACCATTTA-AAGTGAGTAATAAGGCTTTTGAAGAAAT
** * * * * *
684 GAGAGGTTATAAATGGACTTTTCTTATCAATGAATGCTTTTCTCTTCATGATTGTCAAGGTAGAC
1 -AGAGACTATAAATGGACTTTTCTTGTCAATGAATGCTTTTTTCTTCATGTTTCTCAAGATAGAC
* * * *
749 ATTCAATTATAGTCTGTTTTAA-CTAAAATTGTTAAAAAATTCAACTTAAAATCAATTATGACAT
65 ATTCAATTATAGTCTGTTTTAATC-AAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGAT
* * * *
813 TATAAAACCATTCAAAGCGTGTAATAAGGCTTTTGAAGGAAT
129 TATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGAAAT
* * * * * * *
855 AGGTGACTATGAATGGAATTTTCATGAT-AATAAAT-ATTTTTTCCTTCACGTTTCTCAAGATAG
1 A-GAGACTATAAATGGACTTTTCTTG-TCAATGAATGCTTTTTT-CTTCATGTTTCTCAAGATAG
* * * * * * * *
918 ACATTGAATTATTGTCTGTTTTAATGAAAAATGTAAAAAAATTTAACTTAAAAACGATTACGAGA
63 ACATTCAATTATAGTCTGTTTTAATCAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGA
* * *
983 TTATAAAACCATTTAAAGTGACTAATAAGGCTTTTGAAGGAGT
128 TTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGAAAT
* * ** * * * *
1026 GGGAGGCTATAAATAAACTTTTCTTGTCAATGAATTCTTTTTTCTTTATATTTCTTGAA-ATAGA
1 -AGAGACTATAAATGGACTTTTCTTGTCAATGAATGCTTTTTTCTTCATGTTTC-TCAAGATAGA
* * * *
1090 CATTCAATTGTTGTCTATTTTAAACAAAAATATAAAAAAATTC
64 CATTCAATTATAGTCTGTTTTAATCAAAAATATAAAAAAATTC
1133 NNNNNNNNNN
Statistics
Matches: 789, Mismatches: 147, Indels: 51
0.80 0.15 0.05
Matches are distributed among these distances:
170 29 0.04
171 723 0.92
172 37 0.05
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (170 bp):
AGAGACTATAAATGGACTTTTCTTGTCAATGAATGCTTTTTTCTTCATGTTTCTCAAGATAGACA
TTCAATTATAGTCTGTTTTAATCAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTA
TAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGAAAT
Found at i:970 original size:513 final size:513
Alignment explanation
Indices: 3--1132 Score: 1373
Period size: 513 Copynumber: 2.2 Consensus size: 513
1 AG
* * * * * *
3 AGGCTATAAATAGACTTTTCTTGTCAATGAATGCCTTTTTCTTCACATTTCTCAAGTTAAACATT
1 AGGCTATAAATAGACTTTTCTTGTCAATGAATACTTTTTTCTTCACTTTTCTTAAGATAGACATT
* *
68 CAATTATAGCCTGTTTTAACAAAAAAA-GTAAAAATATTCAACTTAAAATCAATTATGAGATTAT
66 CAATTATAGTCTGTTTTAA-AAAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTAT
* * * * * *
132 AAAACCATTTGAAGTGAGTAATATGGCTTTTGAAGAAAAAGATGACTATAAATGGACTTTTCTTG
130 AAAACCATTTGAAGTGAGTAAAAAGCCTATTAAAGAAAAAGATGACTATAAATGGACTTTTCTTA
* * *
197 TCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTAAATATTCAATTATAGTCTGTTTTAATCAA
195 TCAATGAATGCTTTTCTCTTCATGATTCTCAAGGTAAACATTCAATTATAGTCTGTTTTAATCAA
* * * *
262 AAATATAAAAAAATTCAACCTAAAATTAATTATAAGATTAGAAAATCATTTAAAGCGAGTAATAA
260 AAATATAAAAAAATTCAACCTAAAATCAATTATAACATTAGAAAACCATTCAAAGCGAGTAATAA
* * * * * * *
327 GGCTTTTGAAGAATTGGGCGACTATAAATGGATTTTTCTTATCAACGAATGCTTTTGTCTTTATG
325 GGCTTTTGAAGAATTAGGCGACTATAAATGGAATTTTCTGATCAACAAATGATTTTGTCTTCACG
* * * *
392 TTTTTTAAGATAGATAGTCAATTATTATTTGTTTTAATCAAAAATGTTAAAAAAATTAACTTAAA
390 TTTCTCAAGATAGACAGTCAATTATTATCTGTTTTAATCAAAAATGTTAAAAAAATTAACTTAAA
* **
457 ATCAATTATTAGATT-TGAAAACCATTTAAAATGAAGAATAAGGCTTTCGAAGGAATGGA
455 AACAATTACGAGATTAT-AAAACCATTTAAAATGAAGAATAAGGCTTTCGAAGGAATGGA
*
516 AGGCTATAAATAGACTTTTCTTGCCAATGAATACTTTTTTCTTCACTTTTCTTAAGATAGACATT
1 AGGCTATAAATAGACTTTTCTTGTCAATGAATACTTTTTTCTTCACTTTTCTTAAGATAGACATT
** * * * *
581 CAATTATAGTCTGTTTTAATGAAAAATGTAAAAAAATTGAACTTAAATTTAATTGTGAGATTATA
66 CAATTATAGTCTGTTTTAAAAAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATA
* ** **
646 AAATCATTTAGAA-TGAGTAAAAAGCCTATTAAAGGAATGAGA-GGTTATAAATGGACTTTTCTT
131 AAACCATTT-GAAGTGAGTAAAAAGCCTATTAAA-GAAAAAGATGACTATAAATGGACTTTTCTT
* *
709 ATCAATGAATGCTTTTCTCTTCATGATTGTCAAGGTAGACATTCAATTATAGTCTGTTTTAA-CT
194 ATCAATGAATGCTTTTCTCTTCATGATTCTCAAGGTAAACATTCAATTATAGTCTGTTTTAATC-
* * * * * * *
773 AAAATTGTTAAAAAATTCAACTTAAAATCAATTATGACATTATAAAACCATTCAAAGCGTGTAAT
258 AAAAATATAAAAAAATTCAACCTAAAATCAATTATAACATTAGAAAACCATTCAAAGCGAGTAAT
* * * *
838 AAGGCTTTTGAAGGAA-TAGGTGACTATGAATGGAATTTTCATGAT-AATAAAT-ATTTTTTCCT
323 AAGGCTTTTGAA-GAATTAGGCGACTATAAATGGAATTTTC-TGATCAACAAATGATTTTGT-CT
* * * *
900 TCACGTTTCTCAAGATAGACATTGAATTATTGTCTGTTTTAATGAAAAATG-TAAAAAAATTTAA
385 TCACGTTTCTCAAGATAGACAGTCAATTATTATCTGTTTTAATCAAAAATGTTAAAAAAA-TTAA
* * ** * * *
964 CTTAAAAACGATTACGAGATTATAAAACCATTTAAAGTGACTAATAAGGCTTTTGAAGGAGTGGG
449 CTTAAAAACAATTACGAGATTATAAAACCATTTAAAATGAAGAATAAGGCTTTCGAAGGAATGGA
* * *
1029 AGGCTATAAATAAACTTTTCTTGTCAATGAATTCTTTTTTCTTTA-TATTTCTTGAA-ATAGACA
1 AGGCTATAAATAGACTTTTCTTGTCAATGAATACTTTTTTCTTCACT-TTTCTT-AAGATAGACA
* * * * *
1092 TTCAATTGTTGTCTATTTTAAACAAAAATATAAAAAAATTC
64 TTCAATTATAGTCTGTTTTAAAAAAAAATGTAAAAAAATTC
1133 NNNNNNNNNN
Statistics
Matches: 524, Mismatches: 82, Indels: 22
0.83 0.13 0.04
Matches are distributed among these distances:
512 20 0.04
513 486 0.93
514 18 0.03
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (513 bp):
AGGCTATAAATAGACTTTTCTTGTCAATGAATACTTTTTTCTTCACTTTTCTTAAGATAGACATT
CAATTATAGTCTGTTTTAAAAAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATA
AAACCATTTGAAGTGAGTAAAAAGCCTATTAAAGAAAAAGATGACTATAAATGGACTTTTCTTAT
CAATGAATGCTTTTCTCTTCATGATTCTCAAGGTAAACATTCAATTATAGTCTGTTTTAATCAAA
AATATAAAAAAATTCAACCTAAAATCAATTATAACATTAGAAAACCATTCAAAGCGAGTAATAAG
GCTTTTGAAGAATTAGGCGACTATAAATGGAATTTTCTGATCAACAAATGATTTTGTCTTCACGT
TTCTCAAGATAGACAGTCAATTATTATCTGTTTTAATCAAAAATGTTAAAAAAATTAACTTAAAA
ACAATTACGAGATTATAAAACCATTTAAAATGAAGAATAAGGCTTTCGAAGGAATGGA
Done.