Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401241.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4388.0, 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: 2085
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.26
Warning! 522 characters in sequence are not A, C, G, or T
Found at i:784 original size:171 final size:171
Alignment explanation
Indices: 565--926 Score: 439
Period size: 171 Copynumber: 2.1 Consensus size: 171
555 NNNNNNNNNN
* * * *
565 TGAGATTATAAAACCATTTAAAGCTAGTAATAAGGCTTTTGAAGGAATGGGTGGA-TATAAATA-
1 TGAGATTATAAAACCATTTAAAGCGAATAATAAGGCTTTTGAAGGAATGAG-AGACTATAAA-AG
*** * * * * *
628 GACTTTTCTTGTCAATGAATGCCTATTTCTTGATGTTT-CTCAAGGTACACATTAAATTATAATC
64 GACTTTTCTCACCAATGAATGCCTATTTCATCATGTTTCCCCAA-GCACACATTAAATTAAAATC
* *
692 TATTTAAA-CAAAAAATATAAAACA-AATTCAACTTGAAATCAATTA
128 TATTCAAATC-AAAAATATAAAA-ATAA-TCAACTTAAAATCAATTA
* *
737 TGAGATTGTGAAA-CATTTAAAGCGAATAATAAGGCTTTTGAAGGAATGAGAGACTATAAAAGGA
1 TGAGATTATAAAACCATTTAAAGCGAATAATAAGGCTTTTGAAGGAATGAGAGACTATAAAAGGA
* * * *
801 CTTTTCTCACCAATGAATGTCTTTTTCATCATGTTTCCCCAAGCAGACATTCAATTAAAATCTAT
66 CTTTTCTCACCAATGAATGCCTATTTCATCATGTTTCCCCAAGCACACATTAAATTAAAATCTAT
*
866 TCAAATCAAAAATGTAAAAATAATCAACTTAAAATCAATTA
131 TCAAATCAAAAATATAAAAATAATCAACTTAAAATCAATTA
907 TGAGATTATAAAACCATTTA
1 TGAGATTATAAAACCATTTA
927 NNNNNNNNNN
Statistics
Matches: 161, Mismatches: 23, Indels: 13
0.82 0.12 0.07
Matches are distributed among these distances:
170 32 0.20
171 113 0.70
172 16 0.10
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (171 bp):
TGAGATTATAAAACCATTTAAAGCGAATAATAAGGCTTTTGAAGGAATGAGAGACTATAAAAGGA
CTTTTCTCACCAATGAATGCCTATTTCATCATGTTTCCCCAAGCACACATTAAATTAAAATCTAT
TCAAATCAAAAATATAAAAATAATCAACTTAAAATCAATTA
Found at i:1735 original size:171 final size:172
Alignment explanation
Indices: 1430--1792 Score: 398
Period size: 171 Copynumber: 2.1 Consensus size: 172
1420 NNNNNNNNNN
* * *
1430 ATCAATTATGAGATTATAAAACCATTTAAAGTGAGCAATAAGGGTTTCGAAAGAATGGGTGACTA
1 ATCAATTATGAGATTATAAAACCATTTAAAGCGAGCAATAAGGCTTTCGAAAGAATGGGTGAATA
* * *
1495 TAAATGGACTTTTCTTGCTAAGGACTATCTTTTTTTTCATGTTTCTCGAGATAAATAGTCAAATA
66 TAAATGGACTTTTCTTGCTAAGGAATAGCTTTTTTTTCATGTTTCTCGAGATAAACAGTCAAATA
*
1560 TAATCGATGTTAAA-TAAAAATTTAAAA-AAATGT-AACTTCAA
131 TAATCGAT-TTAAACTAAAAATATAAAACAAAT-TCAACTTCAA
* * * *
1601 ATCAATTATCAGATTATAAAACCATTTAAAGCGCGTAATAAGGCTTTTGAAAGAATGGGTGAATA
1 ATCAATTATGAGATTATAAAACCATTTAAAGCGAGCAATAAGGCTTTCGAAAGAATGGGTGAATA
* * ** * * * * * * * *
1666 TAAATGG-TTTTTTTTTATCAATGAATGGCTTTTTCTTT-ATGTTTCTTGAGGTACACATTTAAT
66 TAAATGGACTTTTCTTGCT-AAGGAATAGCTTTTT-TTTCATGTTTCTCGAGATAAACAGTCAAA
* * *
1729 TATAATCTATTTAAACTAAAACTATAAAACCAATTCAACTTCAA
129 TATAATCGATTTAAACTAAAAATATAAAACAAATTCAACTTCAA
*
1773 A--AATTTTGAGATTATAAAAC
1 ATCAATTATGAGATTATAAAAC
1793 TATTNNNNNN
Statistics
Matches: 159, Mismatches: 28, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
170 29 0.18
171 115 0.72
172 15 0.09
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.36
Consensus pattern (172 bp):
ATCAATTATGAGATTATAAAACCATTTAAAGCGAGCAATAAGGCTTTCGAAAGAATGGGTGAATA
TAAATGGACTTTTCTTGCTAAGGAATAGCTTTTTTTTCATGTTTCTCGAGATAAACAGTCAAATA
TAATCGATTTAAACTAAAAATATAAAACAAATTCAACTTCAA
Done.