Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399169.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2441.0, 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: 5298
ACGTcount: A:0.27, C:0.08, G:0.09, T:0.24
Warning! 1678 characters in sequence are not A, C, G, or T
Found at i:1662 original size:171 final size:171
Alignment explanation
Indices: 1127--2925 Score: 1620
Period size: 171 Copynumber: 10.5 Consensus size: 171
1117 NNNNNNNNNN
* * * * * *
1127 AGTCTGTTTTAACCAAAAGTGT-TAAAAATTCAATTTAAAATTAATTATAAGATTCTAAAACCAT
1 AGTCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCAT
* * * * * * * *
1191 TTAAAGCAAGTAATAAGGCCTTTGAAGGAATGAGTGACTATAAATAGA-ATTTATTACTAATGAA
66 TTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATAGACTTTTCTTGCCAATGAA
* * * * * * *
1255 TGCCGTTTTC-TT-CATATTTCTTAATGTAGAAATTCAATTAC
131 TG-CTTTTTCTTTACATGTTTC-CAAGGCAGACATTCAATTAT
* * * * * * * *
1296 AATCTATTTTAACCAAAAATATAAAAAAAATAAACTTAAAATTAATAATGAGATTATAAAACTAT
1 AGTCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCAT
* * ** * *
1361 TTAAAGCGACTAATAAGGC-TTTGAAAGAATTAGAGACGATAAAT-GAACTTTT-TTTCTCAATG
66 TTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATAG-ACTTTTCTTGC-CAATG
* ** * *
1423 AATGACTTTTTCTATA-A-GTTTTCTGAGACAGGCATTCAATTAT
129 AATG-CTTTTTCTTTACATG-TTTCCAAGGCAGACATTCAATTAT
** *
1466 AGTCTGTTTTAATAAAAAATGTAAAAAAATTCAACTTAGAATCAATTATGAGATTATAAAACCAT
1 AGTCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCAT
* * * *
1531 TTAAAGTGAATAATAAGGCTTTTGAAGGAATAGGAGACTATAAATGGACTTTTCTTGCCAATGAA
66 TTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATAGACTTTTCTTGCCAATGAA
* *
1596 TGCTTTTTTCTTTACAT-TTTCCAAGGCAAACATTTAATTAT
131 TGC-TTTTTCTTTACATGTTTCCAAGGCAGACATTCAATTAT
* * * * *
1637 AGTCTGTTTTAACCAAAAGTGTAAAAACATTCAACTTAAAATCAATTAT-AGGACTGTAAAACTA
1 AGTCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGA-GATTATAAAACCA
* * *
1701 TTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATAGACTTTTCTTGCTAATGA
65 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATAGACTTTTCTTGCCAATGA
* ** *
1766 ATGCCTTTTTC-TT-CACGTTTCTTAGGATAGACATTCAATTAT
130 ATG-CTTTTTCTTTACATGTTTCCAAGG-CAGACATTCAATTAT
* * * *
1808 AGTCTATTTTAACCAAAAATTTAGAAAACTTCAACTTAAAATCAATTATGAGATTATAAAACCAT
1 AGTCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCAT
** *
1873 TTAAATTGAGTAATAAGGCTTTTAAAGGAATGGGTA-ACTATAAATAGACTTTTCTTGCCAATGA
66 TTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGG-AGACTATAAATAGACTTTTCTTGCCAATGA
* * ** *
1937 ATGGCTTTTTCATCACAT-TTGT-TGAGGTAGACATTCAATTAT
130 AT-GCTTTTTCTTTACATGTT-TCCAAGGCAGACATTCAATTAT
* * * * * *
1979 AATCTGTTTTAA-AAAATAATATAAAAATAATTGAAC-CAATAATCAATTATTAGATTATAAAAC
1 AGTCTGTTTTAACCAAA-AATGTAAAAA-AATTCAACTTAA-AATCAATTATGAGATTATAAAAC
* * ** * * *
2042 TATTTAAAGCAAAAAATAAGG-TCTTTAAAGGAATGGGTGACTATAAAT-GTACTTTTCCTT-TC
63 CATTTAAAGCGAGTAATAAGGCT-TTTGAAGGAATGGGAGACTATAAATAG-ACTTTT-CTTGCC
* * * * *
2104 AATGAATAGCTCTTTC--TACATGGTTCTCGAGGCATG-CATACAATTGT
125 AATGAAT-GCTTTTTCTTTACATGTTTC-CAAGGCA-GACATTCAATTAT
* * * *
2151 AGTCTATTTTAACCAAAAATGCAAAAAAATTCAACTTAAAATAAATTATGAGATTATAAAACCAC
1 AGTCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCAT
* * * * * *
2216 TTAAAGCGAGTAACAAGGCTTTTGAAGGAATGAGAGGCTATAAATGGACTTTTCTTACTAATGAA
66 TTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATAGACTTTTCTTGCCAATGAA
* * * ** *
2281 TACCTTTTTC--CATATGTTTCTTGAGGTAGACATTCAATTAT
131 T-GCTTTTTCTTTACATGTTTC-CAAGGCAGACATTCAATTAT
* ** * * *
2322 AGTATGTTTTAATGAATAATGTAAAAATAATTGAACCTAAAATCAATTATGAGATTATAAAACTC
1 AGTCTGTTTTAACCAAAAATGTAAAAA-AATTCAACTTAAAATCAATTATGAGATTATAAAAC-C
* * * *
2387 -TTTAAAGCGAGTAATAAAGCTTTTGAAAGAATGGGTGACTATAAATAGACATTTCTT-CTCAAT
64 ATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATAGACTTTTCTTGC-CAAT
* *
2450 GAATGGCTTTTTC--TCCATGTTTCCTAAGACAGACATTCAATTAT
128 GAAT-GCTTTTTCTTTACATGTTTCC-AAGGCAGACATTCAATTAT
** * *
2494 AACCTGTTTTAACTAAAAATGTAAAAAAAATTGAACTTAAAATCAATT-TGAGATTATAAAACCA
1 AGTCTGTTTTAACCAAAAATGT-AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCA
* *
2558 TTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATGGACTTTTCTTGCCAATGA
65 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATAGACTTTTCTTGCCAATGA
* * * *
2623 ATACTTTTTTCTTTATACT-TTT-CAAGGTAGACATTGAATTAT
130 ATGC-TTTTTCTTTACA-TGTTTCCAAGGCAGACATTCAATTAT
* * * * **
2665 AGTCTATCTTAACCAAAAGTGTAAAAACAATTTAACTTAAAATCAATTATGAGATTATAAAATAA
1 AGTCTGTTTTAACCAAAAATGTAAAAA-AATTCAACTTAAAATCAATTATGAGATTATAAAACCA
* * * ** * ***
2730 TTGAAAGCGAGTAATAAGGCCTTTAAAGGTGTGGGTA-ACTATAAATATACTTTTCTTTTTTAAT
65 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGG-AGACTATAAATAGACTTTTC-TTGCCAAT
2794 GAATGGC-TTTT-TTTACATGTTTCCCAAGGCATG-CATTCAATTAT
128 GAAT-GCTTTTTCTTTACATGTTT-CCAAGGCA-GACATTCAATTAT
* * * * ** * *
2838 ATTTTGTTTTAACTAAAAATGCAAAAAAATTCAGTTTAAAATCAATTATGAGAATATAAAACTAT
1 AGTCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCAT
*
2903 TTATAGCGAGTAATAAGGCTTTT
66 TTAAAGCGAGTAATAAGGCTTTT
2926 NNNNNNNNNN
Statistics
Matches: 1332, Mismatches: 238, Indels: 117
0.79 0.14 0.07
Matches are distributed among these distances:
168 1 0.00
169 45 0.03
170 183 0.14
171 626 0.47
172 407 0.31
173 67 0.05
174 3 0.00
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (171 bp):
AGTCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCAT
TTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATAGACTTTTCTTGCCAATGAA
TGCTTTTTCTTTACATGTTTCCAAGGCAGACATTCAATTAT
Found at i:2187 original size:343 final size:336
Alignment explanation
Indices: 1127--2925 Score: 1823
Period size: 343 Copynumber: 5.3 Consensus size: 336
1117 NNNNNNNNNN
* ** * * * *
1127 AGTCTGTTTTAACCAAAAGTG-TTAAAAATTCAATTTAAAATTAATTATAAGATTCTAAAACCAT
1 AGTCTGTTTTAACCAAAAATGCAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCAT
* * * * * * * * *
1191 TTAAAGCAAGTAATAAGGCCTTTGAAGGAATGAGTGACTATAAATAGA-ATTTATTACTAATGAA
66 TTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATGGACTTTTCTTGCCAATGAA
* * * * * * *
1255 TGCCGTTTTCTTCATATTTCTTAATGTAGAAATTCAATTACAATCTATTTTAACCAAAAATATAA
131 T-CCTTTTTCTTCATATTT-TTAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTAA
* * * * *
1320 AAAAAATAAACTTAAAATTAATAATGAGATTATAAAACTATTTAAAGCGACTAATAAGGCTTTGA
194 AAAAATTGAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTGA
** * * * * * *
1385 AAGAATTAGAGACGATAAATGAACTTTTTTTCTCAATGAATGACTTTTTCTATAAGTTT-TCTGA
259 AAGAATGGGTGACTATAAATG-ACTTTTCTT-TCAATGAATG-CTTTTTCTACATGTTTCTC-AA
* *
1449 GACAGGCATTCAATTAT
320 GGCATGCATTCAATTAT
** * *
1466 AGTCTGTTTTAATAAAAAATGTAAAAAAATTCAACTTAGAATCAATTATGAGATTATAAAACCAT
1 AGTCTGTTTTAACCAAAAATGCAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCAT
* * *
1531 TTAAAGTGAATAATAAGGCTTTTGAAGGAATAGGAGACTATAAATGGACTTTTCTTGCCAATGAA
66 TTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATGGACTTTTCTTGCCAATGAA
* * * * * * * *
1596 TGCTTTTTTCTTTACATTTTCCAAGGCAAACATTTAATTATAGTCTGTTTTAACCAAAAGTGTAA
131 T-CCTTTTTCTTCATATTTT-TAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTAA
* * * *
1661 AAACATTCAACTTAAAATCAATTAT-AGGACTGTAAAACTATTTAAAGCGAGTAATAAGGCTTTT
194 AAAAATTGAACTTAAAATCAATTATGA-GATTATAAAACTATTTAAAGCGAGTAATAAGGC-TTT
* * * *
1725 GAAAGAATGGGTGACTATAAATAGACTTTTCTTGCTAATGAATGCCTTTTTCTTCACGTTTCT-T
257 GAAAGAATGGGTGACTATAAAT-GACTTTTCTTTC-AATGAATG-CTTTTTCTACATGTTTCTCA
1789 AGG-ATAGACATTCAATTAT
319 AGGCAT-G-CATTCAATTAT
* ** * *
1808 AGTCTATTTTAACCAAAAATTTAGAAAACTTCAACTTAAAATCAATTATGAGATTATAAAACCAT
1 AGTCTGTTTTAACCAAAAATGCAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCAT
** * *
1873 TTAAATTGAGTAATAAGGCTTTTAAAGGAATGGGTA-ACTATAAATAGACTTTTCTTGCCAATGA
66 TTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGG-AGACTATAAATGGACTTTTCTTGCCAATGA
* * * * * * *
1937 ATGGCTTTTTCATCACATTTGTTGAGGTAGACATTCAATTATAATCTGTTTTAA-AAAATAATAT
130 AT-CCTTTTTCTTCATATTT-TTAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAA-AATGT
* * * **
2001 AAAAATAATTGAAC-CAATAATCAATTATTAGATTATAAAACTATTTAAAGCAAAAAATAAGGTC
192 AAAAA-AATTGAACTTAA-AATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGG-C
* *
2065 TTT-AAAGGAATGGGTGACTATAAATGTACTTTTCCTTTCAATGAATAGCTCTTTCTACATGGTT
254 TTTGAAA-GAATGGGTGACTATAAATG-ACTTTT-CTTTCAATGAAT-GCTTTTTCTACATGTTT
* * *
2129 CTCGAGGCATGCATACAATTGT
315 CTCAAGGCATGCATTCAATTAT
* * *
2151 AGTCTATTTTAACCAAAAATGCAAAAAAATTCAACTTAAAATAAATTATGAGATTATAAAACCAC
1 AGTCTGTTTTAACCAAAAATGCAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCAT
* * * * *
2216 TTAAAGCGAGTAACAAGGCTTTTGAAGGAATGAGAGGCTATAAATGGACTTTTCTTACTAATGAA
66 TTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATGGACTTTTCTTGCCAATGAA
* * ** *
2281 TACCTTTTTC--CATATGTTTCTTGAGGTAGACATTCAATTATAGTATGTTTTAATGAATAATGT
131 T-CCTTTTTCTTCATA--TTT-TTAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGT
* * *
2344 AAAAATAATTGAACCTAAAATCAATTATGAGATTATAAAACTCTTTAAAGCGAGTAATAAAGCTT
192 AAAAA-AATTGAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGC-T
* *
2409 TTGAAAGAATGGGTGACTATAAATAGACATTTCTTCTCAATGAATGGCTTTTTCTCCATGTTTC-
255 TTGAAAGAATGGGTGACTATAAAT-GACTTTTCTT-TCAATGAAT-GCTTTTTCTACATGTTTCT
*
2473 CTAAGACA-GACATTCAATTAT
317 C-AAGGCATG-CATTCAATTAT
** * * *
2494 AACCTGTTTTAACTAAAAATGTAAAAAAAATTGAACTTAAAATCAATT-TGAGATTATAAAACCA
1 AGTCTGTTTTAACCAAAAATG-CAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCA
*
2558 TTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATGGACTTTTCTTGCCAATGA
65 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATGGACTTTTCTTGCCAATGA
* * * * * * *
2623 ATACTTTTTTCTTTATACTTTTCAAGGTAGACATTGAATTATAGTCTATCTTAACCAAAAGTGTA
130 AT-CCTTTTTCTTCATA-TTTTTAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTA
* *
2688 AAAACAATTTAACTTAAAATCAATTATGAGATTATAAAA-TAATTGAAAGCGAGTAATAAGGCCT
193 AAAA-AATTGAACTTAAAATCAATTATGAGATTATAAAACT-ATTTAAAGCGAGTAATAAGG-CT
** * * * *
2752 TT-AAAGGTGTGGGTAACTATAAATATACTTTTCTTTTTTAATGAATGGCTTTTTTTACATGTTT
255 TTGAAA-GAATGGGTGACTATAAAT-GACTTTTC--TTTCAATGAAT-GCTTTTTCTACATGTTT
*
2816 CCCAAGGCATGCATTCAATTAT
315 CTCAAGGCATGCATTCAATTAT
* * * ** * *
2838 ATTTTGTTTTAACTAAAAATGCAAAAAAATTCAGTTTAAAATCAATTATGAGAATATAAAACTAT
1 AGTCTGTTTTAACCAAAAATGCAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCAT
*
2903 TTATAGCGAGTAATAAGGCTTTT
66 TTAAAGCGAGTAATAAGGCTTTT
2926 NNNNNNNNNN
Statistics
Matches: 1223, Mismatches: 192, Indels: 85
0.82 0.13 0.06
Matches are distributed among these distances:
339 18 0.01
340 79 0.06
341 120 0.10
342 243 0.20
343 613 0.50
344 141 0.12
345 9 0.01
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (336 bp):
AGTCTGTTTTAACCAAAAATGCAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCAT
TTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATGGACTTTTCTTGCCAATGAA
TCCTTTTTCTTCATATTTTTAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAA
AAATTGAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTGAAA
GAATGGGTGACTATAAATGACTTTTCTTTCAATGAATGCTTTTTCTACATGTTTCTCAAGGCATG
CATTCAATTAT
Found at i:3952 original size:172 final size:170
Alignment explanation
Indices: 3562--4011 Score: 442
Period size: 172 Copynumber: 2.6 Consensus size: 170
3552 GCCTTTGAAG
* * *
3562 GAATGGGTGACTATAAATGTACTTTTCCTT-TCAATGAATAGATTTTTCTACATGTTTCTCTAGG
1 GAATGGGTGACTATAAATGAACTTTT-CTTCTCAATGAATAGCTTTTTCCACATGTTTCT-TAGG
* * ******
3626 CATGCATA--CAATTATAGTCTATTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATNNNNNN
64 CA-G-ATATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAAATTCAACCTAAAATCAATTA
**** * * * *
3689 NNNNATTATAAAACCATTTAAAGCGAGTAACAAGGCTTTTGAAG
127 TGAGATTATAAAACCATTTAAAGCGAATAACAAAGCTTTTAAAA
* * * *
3733 GAATGAGAGGCTATAAATGAACTTTTCTTACT-AATGAATACCTTTTTCCACATGTTTCTTGAGG
1 GAATGGGTGACTATAAATGAACTTTTCTT-CTCAATGAATAGCTTTTTCCACATGTTTCTT-AGG
* * * *
3797 TAGATATTCAATTATAGTCTGTTTTAACGAATAATGTAAAAATAATTGAACCTAAAATCAATTAT
64 CAGATATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAA-AATTCAACCTAAAATCAATTAT
* *
3862 GAGATTATAAAACCCTTTAAAGCGAATAATAAAGCTTTTAAAA
128 GAGATTATAAAACCATTTAAAGCGAATAACAAAGCTTTTAAAA
* * * * *
3905 GAATGGGTGACTATAAATGGACATTTCTTCTCAATGAATAGCTTTTTCTC-CACGTTTCCTAAGA
1 GAATGGGTGACTATAAATGAACTTTTCTTCTCAATGAATAGCTTTTTC-CACATGTTT-CTTAGG
* ** *
3969 CAGACATTCAATTATAACCTGTTTTAACTAAAAATGTAAAAAA
64 CAGATATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAA
4012 NNNNNNNNNN
Statistics
Matches: 226, Mismatches: 44, Indels: 18
0.78 0.15 0.06
Matches are distributed among these distances:
169 3 0.01
170 5 0.02
171 84 0.37
172 131 0.58
173 3 0.01
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.34
Consensus pattern (170 bp):
GAATGGGTGACTATAAATGAACTTTTCTTCTCAATGAATAGCTTTTTCCACATGTTTCTTAGGCA
GATATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAAATTCAACCTAAAATCAATTATGAG
ATTATAAAACCATTTAAAGCGAATAACAAAGCTTTTAAAA
Done.