Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399856.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3090.0, 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, 679
Length: 1133
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.33
Warning! 73 characters in sequence are not A, C, G, or T
Found at i:807 original size:342 final size:342
Alignment explanation
Indices: 138--833 Score: 731
Period size: 342 Copynumber: 2.0 Consensus size: 342
128 NNNNNAATAA
* *
138 AAAAATATAAAAAAATTCAACTTAAAATCAATTATCAGATTATAAAACCATTTCAAACGAGTAAT
1 AAAAATATAAAAAAATTCAACTTAAAATCAACTATCAGATTATAAAACCATTTCAAACGAGCAAT
* ** * *
203 AAGACTTTCAAAGGTAAGGGTGACTATAAAGGGACTTTTCTTGCTAATGATAGCCTTTTTCTTCA
66 AAGACTTTCAAAGGTAAGAGTGACTATAAAAAGACTTTTCTTACCAATGATAGCCTTTTTCTTCA
268 TGTTTCCTAAGGCAAACATTCAACTATAATCCGTTTTAACAAAAAATGTAAAACAATTCAACTTA
131 TGTTTCCTAAGGCAAACATTCAACTATAATCCGTTTTAACAAAAAATGTAAAACAATTCAACTTA
* ********** * * * * *
333 AAATCNNNNNNNNNNTTATAAAACCTTTTAAAGCGAGCAATAAGGCTTTTAAATGCTTGAGTGAC
196 AAACCAATTATGAGATTATAAAACCATTTAAAGCGAGCAATAAGGATTTTAAAAGCATGAGTAAC
* * ** * **********
398 TATAAATAGGCTTTTCTTACCAATGAATGACTTTTTCTTTATGTTTTCANNNNNNNNNNTCCAAT
261 TATAAATAGACTTTTCTTACCAATGAATGACTTTTTCTTGACATCTTCATGGGCAGACATCCAAT
463 TATAATCTGTTTTAACC
326 TATAATCTGTTTTAACC
* * * ** *
480 AAAAATATAAAAAAATTCAACTTAAAATTAACTATGAGGTTATAAAA-TTTTTTAAAGCGAGCAA
1 AAAAATATAAAAAAATTCAACTTAAAATCAACTATCAGATTATAAAACCATTTCAAA-CGAGCAA
* * * *
544 TAAGGCTTTTAAAGGCT-TGAGTGACTATAAATAAG-CTTTTCTTACCAATGA-ATGGCTTTTTC
65 TAAGACTTTCAAAGG-TAAGAGTGACTATAAA-AAGACTTTTCTTACCAATGATA-GCCTTTTTC
* * * * *
606 TTTATGTTT-CTAAAGGCAAACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAACGATTCA
127 TTCATGTTTCCT-AAGGCAAACATTCAACTATAATCCGTTTTAACAAAAAATGTAAAACAATTCA
* *
670 A-TCTAAAACCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATTAGGATTTTAAAAGCATG
191 ACT-TAAAACCAATTATGAGATTATAAAACCATTTAAAGCGAGCAATAAGGATTTTAAAAGCATG
* *
734 AGTAACTATAAAT-GAACTTTTCTTGCCAATGAATGACTTTTTCTTGACATCTTCCTGGGCAGAC
255 AGTAACTATAAATAG-ACTTTTCTTACCAATGAATGACTTTTTCTTGACATCTTCATGGGCAGAC
* * *
798 ATTCAATTATAATTTTTTTTAACC
319 ATCCAATTATAATCTGTTTTAACC
*
822 AAAAATGTAAAA
1 AAAAATATAAAA
834 NNNNNNNNNN
Statistics
Matches: 286, Mismatches: 61, Indels: 14
0.79 0.17 0.04
Matches are distributed among these distances:
341 11 0.04
342 273 0.95
343 2 0.01
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.34
Consensus pattern (342 bp):
AAAAATATAAAAAAATTCAACTTAAAATCAACTATCAGATTATAAAACCATTTCAAACGAGCAAT
AAGACTTTCAAAGGTAAGAGTGACTATAAAAAGACTTTTCTTACCAATGATAGCCTTTTTCTTCA
TGTTTCCTAAGGCAAACATTCAACTATAATCCGTTTTAACAAAAAATGTAAAACAATTCAACTTA
AAACCAATTATGAGATTATAAAACCATTTAAAGCGAGCAATAAGGATTTTAAAAGCATGAGTAAC
TATAAATAGACTTTTCTTACCAATGAATGACTTTTTCTTGACATCTTCATGGGCAGACATCCAAT
TATAATCTGTTTTAACC
Found at i:856 original size:171 final size:170
Alignment explanation
Indices: 1--951 Score: 635
Period size: 171 Copynumber: 5.6 Consensus size: 170
* * * * * * * *
1 GAGATAATAAAACCATTTAAAGTGAGTAATTAGGCTTTTGAAGGCATGGGTAACCATAAATGGAC
1 GAGATTATAAAACCATTTAAAGCGAGTAATTAGGATTTTAAAAGCATGAGTAACTATAAATGAAC
* * * * ********
66 TTTACTTGCCAATGAATGGCTTTTTCTTCATGTTTCTCAAGGTAAACATTCAATTATNNNNNNNN
66 TTTTCTTGCCAATGAATGGCTTTTTCTTCATCTTCCT-AAGGCAAACATTCAATTATAATCTGTT
** ** * **
131 NNAATAAAAAAATATAAAAAAATTCAA-CTTAAAATCAATTAT
130 TTAA-CCAAAAATGTAAAACGATTCAATC-TAAAATCAATTAT
* * * * * * * * * *
173 CAGATTATAAAACCATTTCAAA-CGAGTAA-TAAGACTTTCAAAGGTAAGGGTGACTATAAAGGG
1 GAGATTATAAAACCATTT-AAAGCGAGTAATTAGGA-TTTTAAAAGCATGAGTAACTATAAATGA
* * * * *
236 ACTTTTCTTGCTAATG-ATAGCCTTTTTCTTCATGTTTCCTAAGGCAAACATTCAACTATAATCC
64 ACTTTTCTTGCCAATGAAT-GGCTTTTTCTTCAT-CTTCCTAAGGCAAACATTCAATTATAATCT
* * ******
300 GTTTTAACAAAAAATGTAAAACAATTCAA-CTTAAAATCNNNNNN
127 GTTTTAACCAAAAATGTAAAACGATTCAATC-TAAAATCAATTAT
**** * * * * * * * *
344 NNNNTTATAAAACCTTTTAAAGCGAGCAATAAGGCTTTTAAATGCTTGAGTGACTATAAAT-AGG
1 GAGATTATAAAACCATTTAAAGCGAGTAATTAGGATTTTAAAAGCATGAGTAACTATAAATGA-A
* * * * * ********* *
408 CTTTTCTTACCAATGAATGACTTTTTCTTTATGTT-TTCANNNNNNNNNNTCCAATTATAATCTG
65 CTTTTCTTGCCAATGAATGGCTTTTTCTTCATCTTCCT-A-AGGCAAACATTCAATTATAATCTG
* ** * *
472 TTTTAACCAAAAATATAAAAAAATTCAA-CTTAAAATTAACTAT
128 TTTTAACCAAAAATGTAAAACGATTCAATC-TAAAATCAATTAT
* *** * * * * * *
515 GAGGTTATAAAATTTTTTAAAGCGAGCAATAAGGCTTTTAAAGGCTTGAGTGACTATAAAT-AAG
1 GAGATTATAAAACCATTTAAAGCGAGTAATTAGGATTTTAAAAGCATGAGTAACTATAAATGAA-
* * * *
579 CTTTTCTTACCAATGAATGGCTTTTTCTTTATGTTTCTAAAGGCAAACATTCAATTATAATCTGT
65 CTTTTCTTGCCAATGAATGGCTTTTTCTTCATCTTCCT-AAGGCAAACATTCAATTATAATCTGT
*
644 TTTAACCAAAAATGTAAAACGATTCAATCTAAAACCAATTAT
129 TTTAACCAAAAATGTAAAACGATTCAATCTAAAATCAATTAT
686 GAGATTATAAAACCATTTAAAGCGAGTAATTAGGATTTTAAAAGCATGAGTAACTATAAATGAAC
1 GAGATTATAAAACCATTTAAAGCGAGTAATTAGGATTTTAAAAGCATGAGTAACTATAAATGAAC
* * * * *
751 TTTTCTTGCCAATGAATGACTTTTTCTTGACATCTTCCT-GGGCAGACATTCAATTATAATTTTT
66 TTTTCTTGCCAATGAATGGCTTTTTCTT--CATCTTCCTAAGGCAAACATTCAATTATAATCTGT
**********
815 TTTAACCAAAAATGTAAAANNNNNNNNNNTAAAATCAATTAT
129 TTTAACCAAAAATGTAAAACGATTCAATCTAAAATCAATTAT
* * * *
857 GAGATTATAAAACCATTTAAAACAAGTAATTAGGATTTTAAAAGCATGAGTAATTATAAATGGAC
1 GAGATTATAAAACCATTTAAAGCGAGTAATTAGGATTTTAAAAGCATGAGTAACTATAAATGAAC
*
922 TTTTCTTGTCAATGAATGGCTTTTTCTTCA
66 TTTTCTTGCCAATGAATGGCTTTTTCTTCA
952 CGNNNNNNNN
Statistics
Matches: 616, Mismatches: 147, Indels: 35
0.77 0.18 0.04
Matches are distributed among these distances:
169 3 0.00
170 6 0.01
171 496 0.81
172 98 0.16
173 13 0.02
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.33
Consensus pattern (170 bp):
GAGATTATAAAACCATTTAAAGCGAGTAATTAGGATTTTAAAAGCATGAGTAACTATAAATGAAC
TTTTCTTGCCAATGAATGGCTTTTTCTTCATCTTCCTAAGGCAAACATTCAATTATAATCTGTTT
TAACCAAAAATGTAAAACGATTCAATCTAAAATCAATTAT
Done.