Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402760.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5819.0, 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: 2749
ACGTcount: A:0.27, C:0.09, G:0.11, T:0.27
Warning! 720 characters in sequence are not A, C, G, or T
Found at i:311 original size:172 final size:170
Alignment explanation
Indices: 2--1060 Score: 1139
Period size: 171 Copynumber: 6.2 Consensus size: 170
1 A
* * * *
2 AAGGAATGGATGACTATAAATGGACTTTTCTTG-TCAATGAATGCCTTTTTCTTCAGGTCTCTTA
1 AAGGAATGGGTGACTATAAATGGACTTTTCTTGCT-AATGAATGCCTTTTTCTTCATGTTTCTTG
* * * * *
66 AGTTAGACATTCAATTATAGTATGTTTTAACTAAAAATGTAAAAAAAAATGAACTTAAAATCAAT
65 AGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGT--AAAAAATTCAACTTAAAATCAAT
* *
131 TATGAGATTATAAAACTATTTAAAGTGTGTAATAAGGCTTTTG
128 TATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTG
* *
174 AAGGAATGGGTGACTATTAATGGACTTTTCTTGCTAATGAATG-CTTTTTCCTTCACGTTTCTTG
1 AAGGAATGGGTGACTATAAATGGACTTTTCTTGCTAATGAATGCCTTTTT-CTTCATGTTTCTTG
* * * * * * *
238 AGGTTGATATTCAATTATAATCTTTTTTAACCAAAAATGTACAAAGAATTCAAATTTAAATCAGT
65 AGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTA-AAA-AATTCAACTTAAAATCAAT
* *
303 TTTGAGATTATAAAATCATTTAAAGTGAGTAATAAGGCTTTTG
128 TATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTG
** * **
346 AAGCCATGGGTGACTATAAATAGACTTTTCTTGGC-AATGAATGCCTTTTTCTTTGTGTTTCTTG
1 AAGGAATGGGTGACTATAAATGGACTTTTCTT-GCTAATGAATGCCTTTTTCTTCATGTTTCTTG
* * * *
410 AGGTAGACATCCAATTATAGTCCGTTTTAACCAAAAAATGTAAGAAACTCAACTTAAAATCAATT
65 AGGTAGACATTCAATTATAGTCTGTTTTAACC-AAAAATGTAAAAAATTCAACTTAAAATCAATT
*
475 ATG-GCATTCTAAAACCATTTAAAGTGAGTAATAAGGCTTTTG
129 ATGAG-ATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTG
* * * * * * * *
517 AAGGTATAGTTGACTATAAATGGACTTTTCTTCCAAATGAATGCTTTTTTCTTCATATTTC-TCA
1 AAGGAATGGGTGACTATAAATGGACTTTTCTTGCTAATGAATGCCTTTTTCTTCATGTTTCTTGA
* * * * * *
581 TGGTAGATATTCAATT-CAGTTTGTTTTAACCAAAAATGTACAAACAATTCAAATTTAAGTCAAT
66 -GGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTA-AAA-AATTCAACTTAAAATCAAT
* * * * *
645 TTTGAGATTATAAAATCATTTAAAGTGAGCAATAAGGCATTTA
128 TATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTG
*
688 AAGGAATGGGTGACTATAAATGGACTTTTCTTG-TAAATGAATGCCTTTTTCTTTATGTTTCTTG
1 AAGGAATGGGTGACTATAAATGGACTTTTCTTGCT-AATGAATGCCTTTTTCTTCATGTTTCTTG
** **
752 AGGTAGACAACCAATTATAGTCCATTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATT
65 AGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGT-AAAAAATTCAACTTAAAATCAATT
*** * *
817 ATGCCTTTGTAAAACCATTTAAAGCGAGTAATGAA-GCTTTT-
129 ATGAGATTATAAAACCATTTAAAGTGAGTAAT-AAGGCTTTTG
* * * * * * *** **
858 AAAGATATGAGTGACTATAAATGAACTTTTCTTGCCAATGAATGCTTTTTTATTTGCGTTTCTCA
1 AAGGA-ATGGGTGACTATAAATGGACTTTTCTTGCTAATGAATGCCTTTTTCTTCATGTTTCTTG
* * * * * *
923 AGATAGACATTCAATTATAGTATGTTTTAACTAAAAATATAAAAAACTTTAACCTAAAATCAATT
65 AGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAA-TTCAACTTAAAATCAATT
* ** *
988 ATG-GCATTATAAAACCATCTAAAACGAGTAATGAGGCTTTTG
129 ATGAG-ATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTG
*
1030 AAGGAATGGGTGACTATAAATGGATTTTTCT
1 AAGGAATGGGTGACTATAAATGGACTTTTCT
1061 NNNNNNNNNN
Statistics
Matches: 736, Mismatches: 127, Indels: 49
0.81 0.14 0.05
Matches are distributed among these distances:
169 9 0.01
170 30 0.04
171 436 0.59
172 242 0.33
173 19 0.03
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (170 bp):
AAGGAATGGGTGACTATAAATGGACTTTTCTTGCTAATGAATGCCTTTTTCTTCATGTTTCTTGA
GGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAATTCAACTTAAAATCAATTAT
GAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTG
Found at i:716 original size:342 final size:339
Alignment explanation
Indices: 1--1060 Score: 1290
Period size: 342 Copynumber: 3.1 Consensus size: 339
* * *
1 AAAGGAATGGATGACTATAAATGGACTTTTCTTGTCAATGAATGCCTTTTTCTTCAG-GTCTCTT
1 AAAGGAATGGGTGACTATAAATGGACTTTTCTTGTCAATGAATGCCTTTTTCTT-TGTGTTTCTT
* * * ** * *
65 AAGTTAGACATTCAATTATAGTATGTTTTAACTAAAAATGTAAAAAAAAATGAACTTAAAATCAA
65 GAGGTAGACATCCAATTATAGTCCGTTTTAACCAAAAATGT-AAAAAAAATCAACTTAAAATCAA
* * * * *
130 TTATGAG-ATTATAAAACTATTTAAAGTGTGTAATAAGGCTTTTGAAGGAATGGGTGACTATTAA
129 TTATG-GCATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGTAT-AGTGACTATAAA
* * * * *
194 TGGACTTTTCTTGCTAATGAATGCTTTTTCCTTCACGTTTCTTGAGGTTGATATTCAATTATAAT
192 TGGACTTTTCTT-CCAATGAATGCTTTTTTCTTCACGTTTC-TCAGGTAGATATTCAATTATAGT
*
259 CTT-TTTTAACCAAAAATGTACAAAGAATTCAAATTTAAATCAGTTTTGAGATTATAAAATCATT
255 -TTGTTTTAACCAAAAATGTACAAA-AATTCAAATTTAAATCAATTTTGAGATTATAAAATCATT
323 TAAAGTGAGTAATAAGGCTTTT
318 TAAAGTGAGTAATAAGGCTTTT
* ** * *
345 GAAGCCATGGGTGACTATAAATAGACTTTTCTTGGCAATGAATGCCTTTTTCTTTGTGTTTCTTG
1 AAAGGAATGGGTGACTATAAATGGACTTTTCTTGTCAATGAATGCCTTTTTCTTTGTGTTTCTTG
* *
410 AGGTAGACATCCAATTATAGTCCGTTTTAACCAAAAAATGT-AAGAAACTCAACTTAAAATCAAT
66 AGGTAGACATCCAATTATAGTCCGTTTTAACC-AAAAATGTAAAAAAAATCAACTTAAAATCAAT
*
474 TATGGCATTCTAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGTATAGTTGACTATAAATG
130 TATGGCATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGTATAG-TGACTATAAATG
** *
539 GACTTTTCTTCCAAATGAATGCTTTTTTCTTCATATTTCTCATGGTAGATATTCAATT-CAGTTT
194 GACTTTTCTTCC-AATGAATGCTTTTTTCTTCACGTTTCTCA-GGTAGATATTCAATTATAGTTT
*
603 GTTTTAACCAAAAATGTACAAACAATTCAAATTTAAGTCAATTTTGAGATTATAAAATCATTTAA
257 GTTTTAACCAAAAATGTACAAA-AATTCAAATTTAAATCAATTTTGAGATTATAAAATCATTTAA
* *
668 AGTGAGCAATAAGGCATTT
321 AGTGAGTAATAAGGCTTTT
* *
687 AAAGGAATGGGTGACTATAAATGGACTTTTCTTGTAAATGAATGCCTTTTTCTTTATGTTTCTTG
1 AAAGGAATGGGTGACTATAAATGGACTTTTCTTGTCAATGAATGCCTTTTTCTTTGTGTTTCTTG
* * *
752 AGGTAGACAACCAATTATAGTCCATTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATT
66 AGGTAGACATCCAATTATAGTCCGTTTTAACCAAAAATGTAAAAAAAATCAACTTAAAATCAATT
* * * * * *
817 ATGCCTTTGTAAAACCATTTAAAGCGAGTAATGAA-GCTTTTAAAGATATGAGTGACTATAAATG
131 ATGGCATTATAAAACCATTTAAAGTGAGTAAT-AAGGCTTTTGAAGGTAT-AGTGACTATAAATG
* * ** * * *
881 AACTTTTCTTGCCAATGAATGCTTTTTTATTTGCGTTTCTCAAGATAGACATTCAATTATAGTAT
194 GACTTTTCTT-CCAATGAATGCTTTTTTCTTCACGTTTCTC-AGGTAGATATTCAATTATAGTTT
* * * ** * * * *
946 GTTTTAACTAAAAATATA-AAAAACTTTAACCTAAAATCAATTATG-GCATTATAAAACCATCTA
257 GTTTTAACCAAAAATGTACAAAAA-TTCAAATTTAAATCAATTTTGAG-ATTATAAAATCATTTA
** *
1009 AAACGAGTAATGAGGCTTTT
320 AAGTGAGTAATAAGGCTTTT
* *
1029 GAAGGAATGGGTGACTATAAATGGATTTTTCT
1 AAAGGAATGGGTGACTATAAATGGACTTTTCT
1061 NNNNNNNNNN
Statistics
Matches: 621, Mismatches: 80, Indels: 32
0.85 0.11 0.04
Matches are distributed among these distances:
341 13 0.02
342 369 0.59
343 150 0.24
344 81 0.13
345 8 0.01
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (339 bp):
AAAGGAATGGGTGACTATAAATGGACTTTTCTTGTCAATGAATGCCTTTTTCTTTGTGTTTCTTG
AGGTAGACATCCAATTATAGTCCGTTTTAACCAAAAATGTAAAAAAAATCAACTTAAAATCAATT
ATGGCATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGTATAGTGACTATAAATGGA
CTTTTCTTCCAATGAATGCTTTTTTCTTCACGTTTCTCAGGTAGATATTCAATTATAGTTTGTTT
TAACCAAAAATGTACAAAAATTCAAATTTAAATCAATTTTGAGATTATAAAATCATTTAAAGTGA
GTAATAAGGCTTTT
Done.