Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398380.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1677.0, 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: 3372
ACGTcount: A:0.24, C:0.07, G:0.08, T:0.23
Warning! 1290 characters in sequence are not A, C, G, or T
Found at i:1596 original size:171 final size:171
Alignment explanation
Indices: 1302--1629 Score: 440
Period size: 171 Copynumber: 1.9 Consensus size: 171
1292 NNNNNNNNNN
* ** * * * * *
1302 TTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTATCAATGAATGCTTTTGCCTTTACGTTT
1 TTTTGAAGAAATGGACGACTATAAATACACTTTTCTTACCAATAAATACTTTTGCCTTCACGTTT
* *
1367 CTCTAGATAGACAGTAAATTGTTATCTGTTTTAATCAAAAATGTAAAAAAAATTAACTTAAAATC
66 CTCGAGATAGACAGTAAATTATTATCTGTTTTAATCAAAAATGTAAAAAAAATTAACTTAAAATC
*
1432 AATTATTAGATTAGAAAATCATTTAAAATAAGTAATAAGGC
131 AATTATTAGATTAGAAAACCATTTAAAATAAGTAATAAGGC
* * * *
1473 TTTTGAAGAAATGGACGTCTATAAATACACTTTTCTTGCCATTAAATACTTTTGTCTTCACGTTT
1 TTTTGAAGAAATGGACGACTATAAATACACTTTTCTTACCAATAAATACTTTTGCCTTCACGTTT
* * * * * * *
1538 CTCGAGATTGATAGTCAATTATTGTTTGTTTTAATCAAAAATGTAGAAAAATTTAACTTAAAATC
66 CTCGAGATAGACAGTAAATTATTATCTGTTTTAATCAAAAATGTAAAAAAAATTAACTTAAAATC
* *
1603 AATTATTCGATTATAAAACCATTTAAA
131 AATTATTAGATTAGAAAACCATTTAAA
1630 GCAAGTAANN
Statistics
Matches: 133, Mismatches: 24, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
171 133 1.00
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.38
Consensus pattern (171 bp):
TTTTGAAGAAATGGACGACTATAAATACACTTTTCTTACCAATAAATACTTTTGCCTTCACGTTT
CTCGAGATAGACAGTAAATTATTATCTGTTTTAATCAAAAATGTAAAAAAAATTAACTTAAAATC
AATTATTAGATTAGAAAACCATTTAAAATAAGTAATAAGGC
Found at i:2358 original size:171 final size:168
Alignment explanation
Indices: 2012--2618 Score: 475
Period size: 171 Copynumber: 3.6 Consensus size: 168
2002 NNNNNNNNNN
* *
2012 CTATAAATGGACTTTTCTTGCCAATGGATG-TGTTTTTCTTCACGTTTGTTGAGGTCGACATTCA
1 CTATAAATGGACTTTTCTTGCCAATGAATGCT-TTTTTCTTCACGTTTGTTGAGGTAGACATTCA
* * *
2076 GTTATAGTCTATTTTAATAAAGAATGTAAAAAAATTGAACTTAAAATCAATTATGAAATTATAAA
65 ATTATAGCCTATTTTAATAAA-AATATAAAAAAATTGAACTTAAAATCAATTATGAAATTATAAA
* ********* *
2141 ACTATTTAA-AGTGAGTAATAAGGCTNNNNNNNNNNTGGGTGA
129 ACCATTTAACA-TGAGTAATAAGGCT-TTTAAAGAAT-GGAGA
* *
2183 CTATAAATGGACTTTTCTTGCCAATGAATGTTTTTTTCTTCATGTTTGTTGAGGTAGACATTCAA
1 CTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTCTTCACGTTTGTTGAGGTAGACATTCAA
* ********** *
2248 TTATAGCCTATTTTAATGAAAAATGTAAAAAAATTNNNNNNNNNNTCAATTATGACATTATAAAA
66 TTATAGCCTATTTTAAT-AAAAATATAAAAAAATTGAACTTAAAATCAATTATGAAATTATAAAA
2313 CCATTTAACATGAGTAATAAGGCTTTTGAAAGAATGGACGA
130 CCATTTAACATGAGTAATAAGGCTTTT-AAAGAATGGA-GA
* * ** * * * * * *
2354 CTATAAATGTACTTCTCTTGATAATGAATACTTTTTCCTTAACGTTTTTTGAGATAGACATTCTA
1 CTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTCTTCACGTTTGTTGAGGTAGACATTCAA
* * * ********** * *
2419 TTATTGTCCGT-TTTAAACAAAAATATAAAAANNNNNNNNNNAAAATCAATTATTAGATTATAAA
66 TTATAG-CC-TATTTTAATAAAAATATAAAAAAATTGAACTTAAAATCAATTATGAAATTATAAA
* *
2483 ACCATTTAACATGAGTAATAAGGCTTTTAAGGAATGAGAGG
129 ACCATTTAACATGAGTAATAAGGCTTTTAAAGAATG-GAGA
* ** * * * * * * *
2524 CTATAAATAGACTTTTCACGTCAATGAATGCTATTTTCTTCACATTTCTCGAGCTAAACATTCAA
1 CTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTCTTCACGTTTGTTGAGGTAGACATTCAA
2589 TTATAGCCT-TTTTAATAAAAAATATAAAAA
66 TTATAGCCTATTTTAAT-AAAAATATAAAAA
2619 TANNNNNNNN
Statistics
Matches: 352, Mismatches: 75, Indels: 20
0.79 0.17 0.04
Matches are distributed among these distances:
168 6 0.02
169 15 0.04
170 63 0.18
171 255 0.72
172 12 0.03
173 1 0.00
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.35
Consensus pattern (168 bp):
CTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTCTTCACGTTTGTTGAGGTAGACATTCAA
TTATAGCCTATTTTAATAAAAATATAAAAAAATTGAACTTAAAATCAATTATGAAATTATAAAAC
CATTTAACATGAGTAATAAGGCTTTTAAAGAATGGAGA
Found at i:2653 original size:169 final size:159
Alignment explanation
Indices: 2461--2787 Score: 329
Period size: 169 Copynumber: 2.0 Consensus size: 159
2451 NNNNNNNNNA
2461 AAATCAATTATTAGATTATAAAACCATTT-AACATGAGTAATAAGGCTTTT-AAGG-AATGAGAG
1 AAATCAATTATTAGATTATAAAACCATTTGAA-ATGAGTAATAAGGCTTTTGAAGGAAATGAGA-
*
2523 GCTATAAATAGACTTTTCACGTCAATGAATGCTATTTTCTTCACATTTCTCGAGCTAAACATTCA
64 -CTATAAATAGACTTTTCACGTCAATGAATACT-TTTTCTTCACATTTCTCGAGCTAAACATTCA
2588 ATTATAGCCT-TTTTAATAAAAAATATAAAAAT
127 ATTATAGCCTGTTTTAATAAAAAATATAAAAAT
** * * * *
2620 ANNNNNNNNNNAATCAATTATTAGATTATAAAACTGTTTGAAGTTAGTATTATGGCTTTTGAAGG
1 A----------AATCAATTATTAGATTATAAAACCATTTGAAATGAGTAATAAGGCTTTTGAAGG
* * * ** * *
2685 AAAATGTGACTATAAATGGATTTTTCTTGTCAATGAATACTTTTTCTTCACGTTTCTCGAGGTAA
56 -AAATGAGACTATAAATAGACTTTTCACGTCAATGAATACTTTTTCTTCACATTTCTCGAGCTAA
* * * *
2750 ATATTCAATTATTGTCTGTTTTAATAAAAAATGTAAAA
120 ACATTCAATTATAGCCTGTTTTAATAAAAAATATAAAA
2788 CAATTCAACC
Statistics
Matches: 135, Mismatches: 18, Indels: 19
0.78 0.10 0.11
Matches are distributed among these distances:
159 1 0.01
169 76 0.56
170 52 0.39
172 6 0.04
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.37
Consensus pattern (159 bp):
AAATCAATTATTAGATTATAAAACCATTTGAAATGAGTAATAAGGCTTTTGAAGGAAATGAGACT
ATAAATAGACTTTTCACGTCAATGAATACTTTTTCTTCACATTTCTCGAGCTAAACATTCAATTA
TAGCCTGTTTTAATAAAAAATATAAAAAT
Done.