Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402955.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_616.0, 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: 4513
ACGTcount: A:0.26, C:0.10, G:0.09, T:0.26
Warning! 1363 characters in sequence are not A, C, G, or T
Found at i:410 original size:172 final size:171
Alignment explanation
Indices: 62--1115 Score: 1032
Period size: 172 Copynumber: 6.1 Consensus size: 171
52 TTAGCTTGAC
* * *
62 AAACATAAAG-AAAAAGACATTCATTGGCAAGAGAAGTTCATTTATAGTCACCCATTCCTTCAAA
1 AAACATGAAGAAAAAAG-CATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAA
* * * *
126 AGCCTTATTACTCATTTTAAATGGTTTTGTAATCTCAAAATTGATTTAAATTTGAATTCTTCGCA
65 AGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTAAATTTGAATT-TTTGTA
** * * * * * *
191 CATTTTTTATTAAAATAGAGTAGGATTGAATTTTTACCTTCAG
129 CATTTTTGGTTAAAATAGACTAGAATTGAATGTCTACCATGAG
* * * *
234 AAACATGAAGAAAAAAGTATTCATTGGTAAGAAAAGTCCATTTATAGTCACTCATTCCTTCAAGA
1 AAACATGAAGAAAAAAGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAA
*** *
299 GCCTTATTACTTTGTTTAAATGGTTTTATAATTTCAAAATTGATTTAAATTTGAATGTTTTGTAC
66 GCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTAAATTTGAAT-TTTTGTAC
* * * *
364 ATTTCTGGTTAGAATAGACTAGAATTAAATGTTTACCATGAG
130 ATTTTTGGTTAAAATAGACTAGAATTGAATGTCTACCATGAG
* * * *
406 AAACATGAAGAAAAAGGTATTCATTGGCAAGAAAAGTCTATTTATAGTCCCCCATTGCC-TCAAA
1 AAACATGAAGAAAAAAGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATT-CCTTCAAA
* * * * * *
470 AGTCTTATTAATCACTTTAAA-GAGTTTTATAATCTCAAAATTGATTTTAAGTTCAATTTTTTTT
65 AGCCTTATTACTCACTTTAAATG-GTTTTATAATCTCAAAATTGATTTAAATTTGAA--TTTTTG
*** * * * *
534 TGTTTTTTTGGTTAAAAGATATTATAATTGAATGTCTACCATGAG
127 TACATTTTTGGTTAAAATAGACTAGAATTGAATGTCTACCATGAG
* * * * * *
579 AAACATTAATAAGAGAA-CATTCATTGGCCAGAAAAGCCCATTTATCGTCACCCATTCCTTCAAA
1 AAACATGAAGAA-AAAAGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAA
* * * * *
643 AGCTTTATTACTCACTTTAAAT-GTCATAATAATCTCCAAATTGATTTAAATTTGAATTCTTTAT
65 AGCCTTATTACTCACTTTAAATGGT-TTTATAATCTCAAAATTGATTTAAATTTGAATT-TTTGT
*
707 ACATTTTTGGTTAAAATTGACTAGAATAT-AATGTCTACCATGAG
128 ACATTTTTGGTTAAAATAGACTAGAAT-TGAATGTCTACCATGAG
* * *
751 AAACATGAAGAAAAAAGTATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATACCTTAAAAA
1 AAACATGAAGAAAAAAGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAA
* * * * ** * * * * *
816 GCATTATTACTCGCTTTAAATAGTTTTGTAAT-TCCGTAATTAATTTTAAGTTAAATTTTTTTTA
66 GCCTTATTACTCACTTTAAATGGTTTTATAATCT-CAAAATTGATTTAAATTTGAA-TTTTTGTA
* * * * * *
880 TATATTTT-GTT-AAACAGACTATAATTGAATGTGTAGC-TCGAT
129 CAT-TTTTGGTTAAAATAGACTAGAATTGAATGTCTACCAT-GAG
* * * * *
922 AAACATAAAG-AAAAAGACATTTATTGGCAAGAGACGTCCATTTATAGTCGCCCATTCCTTCAAA
1 AAACATGAAGAAAAAAG-CATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAA
* ***
986 AGCCTTATTACTCACTTTAAATTGTTTTATAATCTCAAAATTGATTTAAATTTGAATTCTTCACA
65 AGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTAAATTTGAATT-TTTGTA
* * * * * * *
1051 CATTTTTGATCAAAACAAACTAGGATTGAATGTCTACCTTCAG
129 CATTTTTGGTTAAAATAGACTAGAATTGAATGTCTACCATGAG
* *
1094 AAACATGAAGAGAAAAGTATTC
1 AAACATGAAGAAAAAAGCATTC
1116 NNNNNNNNNN
Statistics
Matches: 714, Mismatches: 142, Indels: 52
0.79 0.16 0.06
Matches are distributed among these distances:
170 14 0.02
171 127 0.18
172 417 0.58
173 153 0.21
174 3 0.00
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (171 bp):
AAACATGAAGAAAAAAGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAA
GCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTAAATTTGAATTTTTGTACA
TTTTTGGTTAAAATAGACTAGAATTGAATGTCTACCATGAG
Found at i:699 original size:345 final size:338
Alignment explanation
Indices: 62--1115 Score: 1100
Period size: 345 Copynumber: 3.1 Consensus size: 338
52 TTAGCTTGAC
* ** *
62 AAACATAAAGAAAAAGACATTCATTGGCAAGAGAAGT-TCATTTATAGTCACCCATTCCTTCAAA
1 AAACATGAAGAAAAAGGTATTCATTGGCAAGAAAAGTCT-ATTTATAGTCACCCATTCCTTCAAA
* * * * ***
126 AGCCTTATTACTCATTTTAAATG-GTTTTGTAATCTCAAAATTGATTTAAATTTGAATTCTTCGC
65 AG-CTTATTACTCACTTTAAA-GAGTTTTGTAATCTCAAAATTGATTTTAAGTTAAATT-TTTTT
** * * * ** * * * * *
190 ACATTTTTTATTAAAATAGAGTAGGATTGAATTTTTACCTTCAGAAACATGAAGAAAAAAGTATT
127 TTATTTTTTGTTAAAAGA-ACTATAATTGAATGTCTACC-TGAGAAACATAAAGAAAAAA-CATT
* * * ***
255 CATTGGTAAGAAAAGTCCATTTATAGTCACTCATTCCTTCAAGAGCCTTATTACTTTGTTTAAAT
189 CATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAAT
* * *
320 GGTTTTATAATTTCAAAATTGATTTAAATTTGAATGT-TTTGTACATTTCTGGTTAGAATAGACT
254 -GTTTTATAATCTCAAAATTGATTTAAATTTGAAT-TCTTTATACATTTCTGGTTAAAATAGACT
*
384 AGAAT-TAAATGTTTACCATGAG
317 AGAATAT-AATGTCTACCATGAG
*
406 AAACATGAAGAAAAAGGTATTCATTGGCAAGAAAAGTCTATTTATAGTCCCCCATTGCC-TCAAA
1 AAACATGAAGAAAAAGGTATTCATTGGCAAGAAAAGTCTATTTATAGTCACCCATT-CCTTCAAA
* * *
470 AGTCTTATTAATCACTTTAAAGAGTTTTATAATCTCAAAATTGATTTTAAGTTCAATTTTTTTTT
65 AG-CTTATTACTCACTTTAAAGAGTTTTGTAATCTCAAAATTGATTTTAAGTTAAATTTTTTTTT
* * * * *
535 GTTTTTTTGGTTAAAAGATATTATAATTGAATGTCTACCATGAGAAACATTAATAAGAGAACATT
129 -ATTTTTT-GTTAAAAGA-ACTATAATTGAATGTCTACC-TGAGAAACATAAAGAA-AAAACATT
* * * *
600 CATTGGCCAGAAAAGCCCATTTATCGTCACCCATTCCTTCAAAAGCTTTATTACTCACTTTAAAT
189 CATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAAT
* * * * *
665 GTCATAATAATCTCCAAATTGATTTAAATTTGAATTCTTTATACATTTTTGGTTAAAATTGACTA
254 GT-TTTATAATCTCAAAATTGATTTAAATTTGAATTCTTTATACATTTCTGGTTAAAATAGACTA
730 GAATATAATGTCTACCATGAG
318 GAATATAATGTCTACCATGAG
* * * *
751 AAACATGAAGAAAAAAGTATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATACCTTAAAAA
1 AAACATGAAGAAAAAGGTATTCATTGGCAAGAAAAGTCTATTTATAGTCACCCATTCCTTCAAAA
* * ** *
816 GCATTATTACTCGCTTTAAATAGTTTTGTAAT-TCCGTAATTAATTTTAAGTTAAATTTTTTTTA
66 GC-TTATTACTCACTTTAAAGAGTTTTGTAATCT-CAAAATTGATTTTAAGTTAAATTTTTTTT-
* * * * *
880 TATATTTTGTTAAACAG-ACTATAATTGAATGTGTAGCTCGATAAACATAAAGAAAAAGACATTT
128 TATTTTTTGTTAAA-AGAACTATAATTGAATGTCTACCT-GAGAAACATAAAGAAAAA-ACATTC
* * *
944 ATTGGCAAGAGACGTCCATTTATAGTCGCCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATT
190 ATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAA-T
* * * * * * *
1009 GTTTTATAATCTCAAAATTGATTTAAATTTGAATTCTTCACACATTTTTGATCAAAACAAACTAG
254 GTTTTATAATCTCAAAATTGATTTAAATTTGAATTCTTTATACATTTCTGGTTAAAATAGACTAG
* * *
1074 GAT-TGAATGTCTACCTTCAG
319 AATAT-AATGTCTACCATGAG
1094 AAACATGAAGAGAAAA-GTATTC
1 AAACATGAAGA-AAAAGGTATTC
1116 NNNNNNNNNN
Statistics
Matches: 597, Mismatches: 94, Indels: 39
0.82 0.13 0.05
Matches are distributed among these distances:
342 4 0.01
343 178 0.30
344 129 0.22
345 281 0.47
346 5 0.01
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (338 bp):
AAACATGAAGAAAAAGGTATTCATTGGCAAGAAAAGTCTATTTATAGTCACCCATTCCTTCAAAA
GCTTATTACTCACTTTAAAGAGTTTTGTAATCTCAAAATTGATTTTAAGTTAAATTTTTTTTTAT
TTTTTGTTAAAAGAACTATAATTGAATGTCTACCTGAGAAACATAAAGAAAAAACATTCATTGGC
AAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGTTTTAT
AATCTCAAAATTGATTTAAATTTGAATTCTTTATACATTTCTGGTTAAAATAGACTAGAATATAA
TGTCTACCATGAG
Done.