Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399643.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2892.0, 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: 2869
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.22
Warning! 1124 characters in sequence are not A, C, G, or T
Found at i:1711 original size:171 final size:171
Alignment explanation
Indices: 1413--2127 Score: 554
Period size: 171 Copynumber: 4.2 Consensus size: 171
1403 TTTAACTTAA
* *
1413 AATCAATTATGAAATTATAAAA-ATATTTAAAGTGAGTAATAAGGCTTCTGAAGCAATGGGTGAC
1 AATCAATTATGAGATTATAAAACA-ATTTAAAGTGAGTAATAAGGCTTCTAAAG-AATGGGTGAC
* * * ** *
1477 TATAAA-AGGACTTTTCTTGCTAATTAATAG-CTTTTGCTTCATATTTCTTGAGCTGGACATTCA
64 TATAAATA-GACTTTTCTTGCCAATGAA-AGCCTTTTTCTTCACGTTTCTTGAGCTAGACATTCA
*
1540 ATTATAATTTG-TTTAACCAATAATGTAAAAAAAATTGAACCTAC
127 ATTATAATATGTTTTAACCAATAATGTAAAAAAAATTGAACCTAC
* * * *
1584 AAGCAATTTTGAGATTATAAAACAATTTAAAGTGAGTAATGAGGCTTTTAAAGAAATGGGTGACT
1 AATCAATTATGAGATTATAAAACAATTTAAAGTGAGTAATAAGGCTTCTAAAG-AATGGGTGACT
* ** * *
1649 ATAAATAGACTTTTCTTGCCAATGAAAGCCTTTTTCTTCACGTTTCTCGAAATAAACATTCAACT
65 ATAAATAGACTTTTCTTGCCAATGAAAGCCTTTTTCTTCACGTTTCTTGAGCTAGACATTCAATT
* * * * *
1714 ATAGTCTGTTTTAACCAA-ATATGT-ATAAAAATTCAACTTAC
130 ATAATATGTTTTAACCAATA-ATGTAAAAAAAATTGAACCTAC
* * * *********
1755 AATCAATTATGAGAGTATAAAACCATTTAAAGCGAGTAATAAGNNNNNNNNNNGAATGGGTGACT
1 AATCAATTATGAGATTATAAAACAATTTAAAGTGAGTAATAAG-GCTTCTAAAGAATGGGTGACT
* * * *
1820 ATAAATGGACTTTTCTTACCAATGAATGCCTTTTTCTGCACGTTTCTTGAGCTAGACATTCAATT
65 ATAAATAGACTTTTCTTGCCAATGAAAGCCTTTTTCTTCACGTTTCTTGAGCTAGACATTCAATT
* * * *
1885 ATAATATGTTTTAACTAATAATGTAAAAATATTTGAACCTAA
130 ATAATATGTTTTAACCAATAATGTAAAAAAAATTGAACCTAC
* * ********* ** * * * * *
1927 AATCAATTTTCAGNNNNNNNNNNC-ATTTAAAGCAAGTAATAAGGATTTTGAAGGAAT-AGAGAC
1 AATCAATTATGAG-ATTATAAAACAATTTAAAGTGAGTAATAAGGCTTCT-AAAGAATGGGTGAC
* * * * **
1990 TATAAAT-GAATATTTCTTGCTAATGAATGCTTTTTTCTTCACGTTTCTCAAGGCTAG-CATTCA
64 TATAAATAGACT-TTTCTTGCCAATGAAAGCCTTTTTCTTCACGTTTCTTGA-GCTAGACATTCA
*** ** * * *
2053 ATTATAGCCTGTTTTAATGAAAAATGT-AAAAAAATTTAA-CTAGA
127 ATTATAATATGTTTTAACCAATAATGTAAAAAAAATTGAACCTA-C
*
2097 AATCAATTATGAGATTATAAAACCATTTAAA
1 AATCAATTATGAGATTATAAAACAATTTAAA
2128 NNNNNNNNNN
Statistics
Matches: 424, Mismatches: 106, Indels: 29
0.76 0.19 0.05
Matches are distributed among these distances:
169 4 0.01
170 33 0.08
171 320 0.75
172 66 0.16
173 1 0.00
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.34
Consensus pattern (171 bp):
AATCAATTATGAGATTATAAAACAATTTAAAGTGAGTAATAAGGCTTCTAAAGAATGGGTGACTA
TAAATAGACTTTTCTTGCCAATGAAAGCCTTTTTCTTCACGTTTCTTGAGCTAGACATTCAATTA
TAATATGTTTTAACCAATAATGTAAAAAAAATTGAACCTAC
Found at i:2027 original size:342 final size:331
Alignment explanation
Indices: 1467--2127 Score: 686
Period size: 342 Copynumber: 2.0 Consensus size: 331
1457 CTTCTGAAGC
* * * * * *
1467 AATGGGTGACTATAAAAGGACTTTTCTTGCTAATTAATAGCTTTTGCTTCATATTTCTTGAGCTG
1 AATGGGTGACTATAAAAGGACTTTTCTTACCAATGAATAGCTTTTGCTGCACATTTCTTGAGCTA
* * *
1532 GACATTCAATTATAATTTGTTTAACCAATAATGTAAAAAAAATTGAACCTACAAGCAATTTTGAG
66 GACATTCAATTATAATATGTTTAACCAATAATGTAAAAAAAATTGAACCTAAAAGCAATTTTCAG
** * * * * *
1597 ATTATAAAACAATTTAAAGTGAGTAATGAGGCTTTTAAAGAAATGGGTGACTATAAATAGACTTT
131 ATTATAAAACAATTTAAAGCAAGTAATAAGGATTTTAAAGAAATGAGAGACTATAAATAGAATTT
*
1662 TCTTGCCAATGAAAGCCTTTTTCTTCACGTTTCTCGAA-ATAAACATTCAACTATAGTCTGTTTT
196 TCTTGCCAATGAAAGCCTTTTTCTTCACGTTTCTC-AAGAT-AACATTCAACTATAGCCTGTTTT
* * *
1726 AACCAAATATGTATAAAAATTCAACTTA-CAATCAATTATGAGAGTATAAAACCATTTAAAGCGA
259 AACCAAAAATGTAAAAAAATTCAAC-TAGAAATCAATTATGAGAGTATAAAACCATTTAAAGCGA
1790 GTAATAAGNNNNNNNNNNG
323 GTAATAAG----------G
* * *
1809 AATGGGTGACTATAAATGGACTTTTCTTACCAATGAAT-GCCTTTTTCTGCACGTTTCTTGAGCT
1 AATGGGTGACTATAAAAGGACTTTTCTTACCAATGAATAG-CTTTTGCTGCACATTTCTTGAGCT
* * * *
1873 AGACATTCAATTATAATATGTTTTAACTAATAATGTAAAAATATTTGAACCTAAAATCAATTTTC
65 AGACATTCAATTATAATATG-TTTAACCAATAATGTAAAAAAAATTGAACCTAAAAGCAATTTTC
********* * *
1938 AGNNNNNNNNNNC-ATTTAAAGCAAGTAATAAGGATTTTGAAGGAAT-AGAGACTATAAAT-GAA
129 AG-ATTATAAAACAATTTAAAGCAAGTAATAAGGATTTTAAAGAAATGAGAGACTATAAATAGAA
* * * * * *
2000 TATTTCTTGCTAATGAATGCTTTTTTCTTCACGTTTCTCAAGGCTAGCATTCAATTATAGCCTGT
193 T-TTTCTTGCCAATGAAAGCCTTTTTCTTCACGTTTCTCAA-GATAACATTCAACTATAGCCTGT
** * *
2065 TTTAATGAAAAATGTAAAAAAATTTAACTAGAAATCAATTATGAGATTATAAAACCATTTAAA
256 TTTAACCAAAAATGTAAAAAAATTCAACTAGAAATCAATTATGAGAGTATAAAACCATTTAAA
2128 NNNNNNNNNN
Statistics
Matches: 264, Mismatches: 48, Indels: 14
0.81 0.15 0.04
Matches are distributed among these distances:
341 8 0.03
342 187 0.71
343 68 0.26
344 1 0.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.34
Consensus pattern (331 bp):
AATGGGTGACTATAAAAGGACTTTTCTTACCAATGAATAGCTTTTGCTGCACATTTCTTGAGCTA
GACATTCAATTATAATATGTTTAACCAATAATGTAAAAAAAATTGAACCTAAAAGCAATTTTCAG
ATTATAAAACAATTTAAAGCAAGTAATAAGGATTTTAAAGAAATGAGAGACTATAAATAGAATTT
TCTTGCCAATGAAAGCCTTTTTCTTCACGTTTCTCAAGATAACATTCAACTATAGCCTGTTTTAA
CCAAAAATGTAAAAAAATTCAACTAGAAATCAATTATGAGAGTATAAAACCATTTAAAGCGAGTA
ATAAGG
Done.