Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401693.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4807.0, 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, 901
Length: 1502
ACGTcount: A:0.23, C:0.09, G:0.08, T:0.23
Warning! 558 characters in sequence are not A, C, G, or T
Found at i:324 original size:172 final size:172
Alignment explanation
Indices: 1--806 Score: 919
Period size: 172 Copynumber: 4.7 Consensus size: 172
* * * * *
1 ACCTTGAGAAACATAAAG-AAAAAGACAATCATTGGCAAGAAAAGTCCATTCATAGACACCCATT
1 ACCTTGAGAAACATGAAGAAAAAAG-TATTCATTGGCAAGAAAAGTCTATTCATAGTCACCCATT
* * * *
65 CCTTCAAAAG-TCTTATTACCCAG-TTTAAATAGTTTTATAATCTCAAAATTGATTCAAACTGGA
65 CCTTCAAAAGCT-TTATT-CCTAGCTTTAAATAGTTTTATAATCTCAAAATTGATTTAAATTTGA
* * * * *
128 ATTTTTTATACATTTTTGGTTAAAATATACTAGAATTGAATGTCT
128 ATTCTTTGTACATTTTTAGTTAAAACAGACTAGAATTGAATGTCT
* * * * * * *
173 ACCATGAGCAACTTGAAGAAAAAAGTATTTATTGGCAAGAAAAGTATATTCGTAGTCACTCATTC
1 ACCTTGAGAAACATGAAGAAAAAAGTATTCATTGGCAAGAAAAGTCTATTCATAGTCACCCATTC
238 CTT-ATAAAGCTTTATTCCTAGCTTTAAATAGTTTTATAATCTCAAAATTGATTTAAATTTGAAT
66 CTTCA-AAAGCTTTATTCCTAGCTTTAAATAGTTTTATAATCTCAAAATTGATTTAAATTTGAAT
*
302 TCTTTGTATATTTTTAGTTAAAACAGACTAGAATTGAATGTCT
130 TCTTTGTACATTTTTAGTTAAAACAGACTAGAATTGAATGTCT
* * *
345 ACCTTGAGAAACATGAAGAAAAAAGCT-TTCATTGGTAAGAAAAGTCTATTTATAGTCACCCATA
1 ACCTTGAGAAACATGAAGAAAAAAG-TATTCATTGGCAAGAAAAGTCTATTCATAGTCACCCATT
* * * * * * *
409 CCTTCAAAAGCTTTATTGCTCGCTTTAAATGGTTTTGTAATGC-CATAATTGATTTCAAGTTGAA
65 CCTTCAAAAGCTTTATTCCTAGCTTTAAATAGTTTTATAAT-CTCAAAATTGATTTAAATTTGAA
* * * *
473 TTATTTTTACATTTTTGGTT-AAACAGACTATAATTGAATGTCT
129 TTCTTTGTACATTTTTAGTTAAAACAGACTAGAATTGAATGTCT
* * * * * * *
516 ACCTTGAGAAACGTAAAGAAAAAGGCATTCATTGGCAATAAAAGTCTATTTATAGTCACCTATTC
1 ACCTTGAGAAACATGAAGAAAAAAGTATTCATTGGCAAGAAAAGTCTATTCATAGTCACCCATTC
* * * * *
581 CTTCAAAAGCCTTATTACTCA-ATTTAAATGGTTTTATAATCTCACAATTGATTTAAATTTGAAT
66 CTTCAAAAGCTTTATTCCT-AGCTTTAAATAGTTTTATAATCTCAAAATTGATTTAAATTTGAAT
* *
645 TCTTTGTACATTTTTAGTTAAAACAGACTAGGATTGATTGTCT
130 TCTTTGTACATTTTTAGTTAAAACAGACTAGAATTGAATGTCT
* * * *
688 ACCTTCAGAAACATGAAGAAAAAAGTATTCATTGGCAAGAAAAGTCTATTTATTGTCACCCATAC
1 ACCTTGAGAAACATGAAGAAAAAAGTATTCATTGGCAAGAAAAGTCTATTCATAGTCACCCATTC
* * * * * * * *
753 TTTCAAAAGCCTTATTACTCGCTTTCAATGGTTTTGTAATGC-CATAATTGATTT
66 CTTCAAAAGCTTTATTCCTAGCTTTAAATAGTTTTATAAT-CTCAAAATTGATTT
807 NNNNNNNNNN
Statistics
Matches: 540, Mismatches: 81, Indels: 26
0.83 0.13 0.04
Matches are distributed among these distances:
170 1 0.00
171 152 0.28
172 376 0.70
173 11 0.02
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (172 bp):
ACCTTGAGAAACATGAAGAAAAAAGTATTCATTGGCAAGAAAAGTCTATTCATAGTCACCCATTC
CTTCAAAAGCTTTATTCCTAGCTTTAAATAGTTTTATAATCTCAAAATTGATTTAAATTTGAATT
CTTTGTACATTTTTAGTTAAAACAGACTAGAATTGAATGTCT
Found at i:646 original size:343 final size:345
Alignment explanation
Indices: 1--806 Score: 1069
Period size: 343 Copynumber: 2.3 Consensus size: 345
* ** * * * *
1 ACCTTGAGAAACATAAAG-AAAAAGACAATCATTGGCAAGAAAAGTCCATTCATAGACACCCATT
1 ACCTTGAGAAACATGAAGAAAAAAG-CTTTCATTGGCAAGAAAAGTCTATTTATAGTCACCCATA
* * * *
65 CCTTCAAAAG-TCTTATTACCCAG-TTTAAATAGTTTTATAAT-CTCAAAATTGA-TTCAAACTG
65 CCTTCAAAAGCT-TTATTACTC-GCTTTAAATGGTTTTGTAATGC-CATAATTGATTTCAAACTG
* * * * *
126 GAATTTTTTATACATTTTTGGTTAAAATATACTAGAATTGAATGTCTACCATGAGCAACTTGAAG
127 GAATTTTTTATACATTTTTGGTTAAAACAGACTAGAATTGAATGTCTACCATGAGAAACGTAAAG
* * * * *
191 AAAAAAGTATTTATTGGCAAGAAAAGTATATTCGTAGTCACTCATTCCTTATAAAGCTTTATTCC
192 AAAAAAGCATTCATTGGCAAGAAAAGTATATTCATAGTCACTCATTCCTTATAAAGCCTTATTAC
* *
256 TAGCTTTAAATAGTTTTATAATCTCAAAATTGATTTAAATTTGAATTCTTTGTATATTTTTAGTT
257 TAGATTTAAATAGTTTTATAATCTCAAAATTGATTTAAATTTGAATTCTTTGTACATTTTTAGTT
321 AAAACAGACTAGAATTGAATGTCT
322 AAAACAGACTAGAATTGAATGTCT
*
345 ACCTTGAGAAACATGAAGAAAAAAGCTTTCATTGGTAAGAAAAGTCTATTTATAGTCACCCATAC
1 ACCTTGAGAAACATGAAGAAAAAAGCTTTCATTGGCAAGAAAAGTCTATTTATAGTCACCCATAC
* * *
410 CTTCAAAAGCTTTATTGCTCGCTTTAAATGGTTTTGTAATGCCATAATTGATTTC-AAGTTGAAT
66 CTTCAAAAGCTTTATTACTCGCTTTAAATGGTTTTGTAATGCCATAATTGATTTCAAACTGGAAT
* *
474 TATTTT-TACATTTTTGGTT-AAACAGACTATAATTGAATGTCTACCTTGAGAAACGTAAAGAAA
131 T-TTTTATACATTTTTGGTTAAAACAGACTAGAATTGAATGTCTACCATGAGAAACGTAAAGAAA
* * * *
537 AAGGCATTCATTGGCAATAAAAGTCTATTTATAGTCAC-CTATTCCTTCA-AAAGCCTTATTACT
195 AAAGCATTCATTGGCAAGAAAAGTATATTCATAGTCACTC-ATTCCTT-ATAAAGCCTTATTACT
* *
600 CA-ATTTAAATGGTTTTATAATCTCACAATTGATTTAAATTTGAATTCTTTGTACATTTTTAGTT
258 -AGATTTAAATAGTTTTATAATCTCAAAATTGATTTAAATTTGAATTCTTTGTACATTTTTAGTT
* *
664 AAAACAGACTAGGATTGATTGTCT
322 AAAACAGACTAGAATTGAATGTCT
* *
688 ACCTTCAGAAACATGAAGAAAAAAG-TATTCATTGGCAAGAAAAGTCTATTTATTGTCACCCATA
1 ACCTTGAGAAACATGAAGAAAAAAGCT-TTCATTGGCAAGAAAAGTCTATTTATAGTCACCCATA
* * *
752 CTTTCAAAAGCCTTATTACTCGCTTTCAATGGTTTTGTAATGCCATAATTGATTT
65 CCTTCAAAAGCTTTATTACTCGCTTTAAATGGTTTTGTAATGCCATAATTGATTT
807 NNNNNNNNNN
Statistics
Matches: 408, Mismatches: 44, Indels: 21
0.86 0.09 0.04
Matches are distributed among these distances:
342 2 0.00
343 278 0.68
344 113 0.28
345 15 0.04
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (345 bp):
ACCTTGAGAAACATGAAGAAAAAAGCTTTCATTGGCAAGAAAAGTCTATTTATAGTCACCCATAC
CTTCAAAAGCTTTATTACTCGCTTTAAATGGTTTTGTAATGCCATAATTGATTTCAAACTGGAAT
TTTTTATACATTTTTGGTTAAAACAGACTAGAATTGAATGTCTACCATGAGAAACGTAAAGAAAA
AAGCATTCATTGGCAAGAAAAGTATATTCATAGTCACTCATTCCTTATAAAGCCTTATTACTAGA
TTTAAATAGTTTTATAATCTCAAAATTGATTTAAATTTGAATTCTTTGTACATTTTTAGTTAAAA
CAGACTAGAATTGAATGTCT
Done.