Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402744.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5804.0, 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, 677
Length: 1129
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.36
Found at i:325 original size:172 final size:171
Alignment explanation
Indices: 1--1129 Score: 1023
Period size: 172 Copynumber: 6.6 Consensus size: 171
* * * * * * *
1 TTCAACTCAAAATAAATTATG-GCATTACAAAACCATTTAAAGCGAATAATACA-GCTTTTGAAG
1 TTCAACTTAAAATCAATTTTGAG-ATTATAAAATCATTTAAAGTGAGTAATA-AGGCTTTTGAA-
* * * * * *
64 GC-ATGGGTGACCACAAATAGACTTTTCTTGTCAATGAATGCATTTTTCTTCATGATTCTCATGG
63 GCAATGGGTAACTATAAATAGACTTCTCTTGCCAATGAATGC-TTTTTCTTCATGTTTCTCATGG
* ** * * * *
128 TAGACATTCGATCCTAGTCTGTTTTAACTAAAAATGTGCAAAGAA
127 TAGACATTCAATTATAATATGTTTTAACTAAAAATGTGAAAAAAA
** * *
173 TTCAACTTTTAATCAATTTTGAGATTATAAAACCATTTAAAGTGCGTAATAAGGCTTTTGAA-CA
1 TTCAACTTAAAATCAATTTTGAGATTATAAAATCATTTAAAGTGAGTAATAAGGCTTTTGAAGCA
* * * *
237 AGTGGGTCACTATAAATGGACTTCTCTTGCTAATGAATGCTCTTTTCTTTATGTTTCTCGA-GGT
66 A-TGGGTAACTATAAATAGACTTCTCTTGCCAATGAATGCT-TTTTCTTCATGTTTCTC-ATGGT
* * * * *
301 AAACGTTCAATTATAATATGTTTTAACTAGAAAA-CT-AAAGAAT
128 AGACATTCAATTATAATATGTTTTAACTA-AAAATGTGAAAAAAA
* * * * * * * *
344 TTGAACTTAAAATAAATTTTGAGAATATAAAATCATTTAAAGAGATTAATTAGGCTTTTCAAGTA
1 TTCAACTTAAAATCAATTTTGAGATTATAAAATCATTTAAAGTGAGTAATAAGGCTTTTGAAGCA
* * * *
409 ATAGGTGACTATAAATAGACTTTTCTTGCCAATGAATACTTTTTCTTCATGTTTCTCATGGTAGA
66 ATGGGTAACTATAAATAGACTTCTCTTGCCAATGAATGCTTTTTCTTCATGTTTCTCATGGTAGA
* * * * *
474 CATTCAATTCTAGTCTG-TTTAACCAAAAATAT-AAAACAAA
131 CATTCAATTATAATATGTTTTAACTAAAAATGTGAAAA-AAA
* ** * * * * **
514 TTCATCTTAAAATCAATTACGATATTACAAAATCATTTAAAGCGAGTAATAATGCTTTTGAAGGT
1 TTCAACTTAAAATCAATTTTGAGATTATAAAATCATTTAAAGTGAGTAATAAGGCTTTTGAAGCA
* * *
579 ATGGATAACTATAAATAGACTTTTCTTACCAATGAATGCTTATTTCTTCATGTTTCTCATGGTAG
66 ATGGGTAACTATAAATAGACTTCTCTTGCCAATGAATGCTT-TTTCTTCATGTTTCTCATGGTAG
* * *
644 ACATTCAATTCTAGTCTGTTTTAACTAAAAATGTAGAAAAAAA
130 ACATTCAATTATAATATGTTTTAACTAAAAATGT-GAAAAAAA
* * * * *
687 TT-ATA-TTTAAATCAATTTTGAGATTAAAAAATCTTTTAAAGTGAGTAATAAGGCTTTTAAAGG
1 TTCA-ACTTAAAATCAATTTTGAGATTATAAAATCATTTAAAGTGAGTAATAAGGCTTTTGAAGC
* * * *
750 AATGGGTAACTATAAATGGACTTCTCTTGCCAATGAATGCTCTCTTCTTTATGTTTCTTA-GAGT
65 AATGGGTAACTATAAATAGACTTCTCTTGCCAATGAATGCT-TTTTCTTCATGTTTCTCATG-GT
* * *
814 AGATATTCAATTATAAAATGTTTTAACTAGAAAA-G-CAAAAAAA
128 AGACATTCAATTATAATATGTTTTAACTA-AAAATGTGAAAAAAA
* * * * *
857 TTTGAGCTTAAAATCAATTTTAAGATTATAAAACCATTTAAAGTGATTAATAAGGCTTTTGAAGC
1 -TTCAACTTAAAATCAATTTTGAGATTATAAAATCATTTAAAGTGAGTAATAAGGCTTTTGAAGC
* * * * * * * *
922 AATGAGTGACTATAAATAGAATTTTCTTACCAATAAATACCTTTTTCTTCATGTCTCTCATGGTA
65 AATGGGTAACTATAAATAGACTTCTCTTGCCAATGAAT-GCTTTTTCTTCATGTTTCTCATGGTA
* * * *
987 GACATTCAATTCTAGTCTG-TTTAACTAAAAATAT-AAAATAAA
129 GACATTCAATTATAATATGTTTTAACTAAAAATGTGAAAA-AAA
** * * * * *
1029 TTCAACTTAAAATCAATTACG-GTATTACAAAATTATTTCAAGTGAGTAATAATGCTTTTGAAGG
1 TTCAACTTAAAATCAATTTTGAG-ATTATAAAATCATTTAAAGTGAGTAATAAGGCTTTTGAAGC
* ** *
1093 TATGGGCGACTATAAATAGACTTTTCTTGCCAATGAA
65 AATGGGTAACTATAAATAGACTTCTCTTGCCAATGAA
Statistics
Matches: 780, Mismatches: 149, Indels: 57
0.79 0.15 0.06
Matches are distributed among these distances:
168 4 0.01
169 12 0.02
170 135 0.17
171 227 0.29
172 379 0.49
173 19 0.02
174 4 0.01
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.36
Consensus pattern (171 bp):
TTCAACTTAAAATCAATTTTGAGATTATAAAATCATTTAAAGTGAGTAATAAGGCTTTTGAAGCA
ATGGGTAACTATAAATAGACTTCTCTTGCCAATGAATGCTTTTTCTTCATGTTTCTCATGGTAGA
CATTCAATTATAATATGTTTTAACTAAAAATGTGAAAAAAA
Done.