Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400580.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3773.0, 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, 768
Length: 1281
ACGTcount: A:0.27, C:0.11, G:0.14, T:0.29
Warning! 251 characters in sequence are not A, C, G, or T
Found at i:510 original size:172 final size:171
Alignment explanation
Indices: 5--801 Score: 874
Period size: 172 Copynumber: 4.6 Consensus size: 171
1 AAGA
* * * * * *
5 CTTTTGAAGGAATGGGTGACTATAAGTCGACTTTTCTTGCTAATGCATGCCTTTTTC-TCTACGT
1 CTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATACCTTTTTCTTC-ATGT
* * * * * *
69 TTCTTAAGGTAGACGTTCAATTATAGTCTGTTATAACCAAAAATGTAAAA-ACATTCAACTTGAA
65 TTCTTGAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAAGA-ATTCAAATTTAA
* *
133 ATCAATTATG-GCATTATAAAACAATTTAAAGTGTGTAATAAGG
129 ATCAATTATGAG-ATTATAAAACTATTTAAAGTGAGTAATAAGG
* * * * *
176 CTTTTGAGGGAATAGGTGACTATAAATGGACTCTTCTTGCCAATGAAGAATGCC-TTTTCGTTCG
1 CTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAAT---GAATACCTTTTTC-TTCA
* ** * *
240 TGTTTCTTGAGGTTGACATTCAATTATAATCCCTTTCAACCAAAAATGTGCAAAGAATTCAAATT
62 TGTTTCTTGAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGT-AAAAGAATTCAAATT
* * * * **
305 TCAATCAATTTTGGGTTTACGAAACTATTTAAAGTGAGTAATAAGG
126 TAAATCAATTATGAGATTATAAAACTATTTAAAGTGAGTAATAAGG
* * * *
351 CTTTTAAAGAAATGGGTGGCTATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCATGTT
1 CTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATACCTTTTTCTTCATGTT
* * * * * * *
416 TCTCGAGCTAGACATTCAATTATAATATGTTTTAACCAAAAATGTAAAACAATTTGAACTTAAAA
66 TCTTGAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAAGAA-TTCAAATTTAAA
*
481 TCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGG
130 TCAATTATGAGATTATAAAACTATTTAAAGTGAGTAATAAGG
* *
523 CTTTTGAAGGAATGGGTGACTATAAATGGACTTCTCTTG-CAATG-A-ACCTTTTTCTTCACGTT
1 CTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATACCTTTTTCTTCATGTT
* *
585 TCTTGAGGTTGACGATTCAATTATAATCTGTTTTAACAAAAAATGTACAAAGAATTCAAATTTAA
66 TCTTGAGGTAGAC-ATTCAATTATAATCTGTTTTAACCAAAAATGTA-AAAGAATTCAAATTTAA
* * * * *
650 ATAAATTTTAAGATTAT-AAATTATTTAAAGTGAGTAATGAGG
129 ATCAATTATGAGATTATAAAACTATTTAAAGTGAGTAATAAGG
* * * * * *
692 CTTTTGAAGGTATGGGTGACTATAAATTGACTTTCCTTGCCAATGAAT-GCTTTTGACTTCGTGT
1 CTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATACCTTTT-TCTTCATGT
** * *
756 TTCTCAAGGTAGACATTCAATTCTAGTCTGTTTTAACCAAAAATGT
65 TTCTTGAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGT
802 NNNNNNNNNN
Statistics
Matches: 520, Mismatches: 90, Indels: 32
0.81 0.14 0.05
Matches are distributed among these distances:
169 82 0.16
170 59 0.11
171 88 0.17
172 146 0.28
173 10 0.02
174 46 0.09
175 87 0.17
176 2 0.00
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.36
Consensus pattern (171 bp):
CTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATACCTTTTTCTTCATGTT
TCTTGAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAAGAATTCAAATTTAAAT
CAATTATGAGATTATAAAACTATTTAAAGTGAGTAATAAGG
Found at i:736 original size:341 final size:342
Alignment explanation
Indices: 5--801 Score: 1018
Period size: 341 Copynumber: 2.3 Consensus size: 342
1 AAGA
* * * *
5 CTTTTGAAGGAATGGGTGACTATAAGTCGACTTTTCTTGCTAATGCATGCCTTTTTC-TCTACGT
1 CTTTTGAAGGAATGGGTGACTATAAATCGACTTTTCTTGCCAATGAAT-CCTTTTTCTTC-ATGT
* * * *
69 TTCTTAAGGTAGACGTTCAATTATAGTCTGTTATAACCAAAAATGTAAAAACATTCAACTTGAAA
64 TTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAACATTCAACTTAAAA
* *
134 TCAATTATGGCATTATAAAACAATTTAAAGTGTGTAATAAGGCTTTTGAGGGAATAGGTGACTAT
129 TCAATTATGGCATTATAAAACAATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGTGACTAT
**
199 AAATGGACTCTTCTTGCCAATGAAGAATGCCTTTTCGTTCGTGTTTCTTGAGGTTGACATTCAAT
194 AAATGGACTCTTCTTGCCAAT--AGAA-GCCTTTTCGTTCACGTTTCTTGAGGTTGACATTCAAT
* * * * ** *
264 TATAATCCCTTTCAACCAAAAATGTGCAAAGAATTCAAATTTCAATCAATTTTGGGTTTACGAAA
256 TATAATCCCTTTCAACAAAAAATGTACAAAGAATTCAAATTTAAATAAATTTTAAGATTACGAAA
329 CTATTTAAAGTGAGTAATAAGG
321 CTATTTAAAGTGAGTAATAAGG
* * * * *
351 CTTTTAAAGAAATGGGTGGCTATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCATGTT
1 CTTTTGAAGGAATGGGTGACTATAAATCGACTTTTCTTGCCAATGAAT-CCTTTTTCTTCATGTT
* * * * *
416 TCTCGAGCTAGACATTCAATTATAATATGTTTTAACCAAAAATGT-AAAACAATTTGAACTTAAA
65 TCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAC-A-TTCAACTTAAA
* *
480 ATCAATTATGAG-ATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACT
128 ATCAATTATG-GCATTATAAAACAATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGTGACT
544 ATAAATGGACT-TCTCTTG-CAAT-GAA-CCTTTTTC-TTCACGTTTCTTGAGGTTGACGATTCA
192 ATAAATGGACTCT-TCTTGCCAATAGAAGCC-TTTTCGTTCACGTTTCTTGAGGTTGAC-ATTCA
** * *
604 ATTATAATCTGTTTTAACAAAAAATGTACAAAGAATTCAAATTTAAATAAATTTTAAGATTA-TA
254 ATTATAATCCCTTTCAACAAAAAATGTACAAAGAATTCAAATTTAAATAAATTTTAAGATTACGA
* *
668 AATTATTTAAAGTGAGTAATGAGG
319 AACTATTTAAAGTGAGTAATAAGG
* * * * * *
692 CTTTTGAAGGTATGGGTGACTATAAATTGACTTTCCTTGCCAATGAATGCTTTTGACTTCGTGTT
1 CTTTTGAAGGAATGGGTGACTATAAATCGACTTTTCTTGCCAATGAATCCTTTT-TCTTCATGTT
*
757 TCTCAAGGTAGACATTCAATTCTAGTCTGTTTTAACCAAAAATGT
65 TCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGT
802 NNNNNNNNNN
Statistics
Matches: 391, Mismatches: 52, Indels: 21
0.84 0.11 0.05
Matches are distributed among these distances:
340 5 0.01
341 134 0.34
342 62 0.16
343 3 0.01
345 5 0.01
346 96 0.25
347 85 0.22
348 1 0.00
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.36
Consensus pattern (342 bp):
CTTTTGAAGGAATGGGTGACTATAAATCGACTTTTCTTGCCAATGAATCCTTTTTCTTCATGTTT
CTCAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAACATTCAACTTAAAATC
AATTATGGCATTATAAAACAATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAA
ATGGACTCTTCTTGCCAATAGAAGCCTTTTCGTTCACGTTTCTTGAGGTTGACATTCAATTATAA
TCCCTTTCAACAAAAAATGTACAAAGAATTCAAATTTAAATAAATTTTAAGATTACGAAACTATT
TAAAGTGAGTAATAAGG
Done.