Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400965.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4125.0, 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: 1710
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.31
Warning! 248 characters in sequence are not A, C, G, or T
Found at i:866 original size:171 final size:169
Alignment explanation
Indices: 348--1709 Score: 1044
Period size: 171 Copynumber: 7.9 Consensus size: 169
338 NNNNNNNNNN
** * *
348 TGCCAATGAATGCCTTTTTCTTTACAGCTCTCAAGG-ACGACATTCAAATATAGTCTGTTTTAAT
1 TGCCAATGAATGCCTTTTTCTTT--ATTTCTCAAGGTA-GACATTCAATTATAGTCTGTTTTAAC
* * * * * *
412 CTAAAATGTAAAAACAATTCAACCTTAAAATCAATTATGGCATTACAAAACTATTTAAAGCAAGT
63 CAAAAATG-AAAAAAAATTCAA-CTTAAAATCAATTATGGCAATATAAAACCATTTAAAGCGAGT
********** * * * *
477 NNNNNNNNNNTTGAAGGTATGAGTGGCTATAAATGGACATTTCT
126 AATGAGGCTTTTGAAGGTATGGGTGACTATAAATAGACTTTTCT
* * * * * *
521 TGCAAATTAATG-CTTTTGACTTCATTTTTCTCAAGGTAGGCATTCAATTCTAGTCTGTTTTAAC
1 TGCCAATGAATGCCTTTT-TCTT--TATTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAAC
** * * * * * * ********** *
585 TGAAAATCATAGAAGAATTCAAATTTAAATCAATTTTNNNNNNNNNNAACCATTTAAAGTGAGTA
63 CAAAAATGA-AAAAAAATTCAACTTAAAATCAATTATGGCAATATAAAACCATTTAAAGCGAGTA
* * * * * * *
650 ATAAAGCTTTTAAAGGAATGAGTGACTGTAAATTGACTTTTCT
127 ATGAGGCTTTTGAAGGTATGGGTGACTATAAATAGACTTTTCT
*
693 TGCCAATGAATGCCTTTTTCTTTGCATTTCTCAAGGTAGACATTCAATTATAGTCTATTTTAACC
1 TGCCAATGAATGCCTTTTTCTTT--ATTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACC
* *** *
758 AAAAATGAAAAAAAAATCAACTTAAAATCAATTACAACAATATAAAATCATTTAAAGCGAGTAAT
64 AAAAATGAAAAAAAATTCAACTTAAAATCAATTATGGCAATATAAAACCATTTAAAGCGAGTAAT
*
823 GATGCTTTTGAAGGCT-TGGGTGACTATAAATAGACTTTTCT
129 GAGGCTTTTGAAGG-TATGGGTGACTATAAATAGACTTTTCT
* * ** * **
864 TGCCAATGAATG-CTTTTT-TTTATGTTTCTAAAGGTAGACATTCAATTCTAGAATGTTTTGATA
1 TGCCAATGAATGCCTTTTTCTTTA--TTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACC
* * * * * * * * * *
927 AAAAATGACCAAAGAATTCAAATTTAAATCAATTTTGAG-ATTACAAAACTATTTGAAGTGAGTA
64 AAAAATGA-AAAAAAATTCAACTTAAAATCAATTATG-GCAATATAAAACCATTTAAAGCGAGTA
* * *
991 AT-ACGGCTTTT-ACAAGAATGGGTGACTATAAATGGACTTTTCT
127 ATGA-GGCTTTTGA-AGGTATGGGTGACTATAAATAGACTTTTCT
* * *
1034 TGCCAATGAATTCCTTTTTCATTATTGTTCTCAAGGTGGACATTCAATTATAGTCTGTTTTAA-C
1 TGCCAATGAATGCCTTTTTCTTTA-T-TTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACC
* * * * * *
1098 ATGAAATGTAAAAAAAATTCAATCTTAAAATCAATTATGGCATTGTAAAATCATTTAACGCAAGT
64 A-AAAATG-AAAAAAAATTCAA-CTTAAAATCAATTATGGCAATATAAAACCATTTAAAGCGAGT
** * * * * *
1163 GGTAAGGCTTTTGAAGGTATAGGTGATTATAAATTGGCTTTTCT
126 AATGAGGCTTTTGAAGGTATGGGTGACTATAAATAGACTTTTCT
* * * * * *
1207 TGCCAATAAATTCTTTTTTCTTCTTATTTCTCAAGGTGGACATTCAATTATAATTTGTTTTAACC
1 TGCCAATGAATGCCTTTTTC-T-TTATTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACC
* * * *
1272 AAAAATGTAGAAAAATTTAACTTAAAATCAATTATGGC-ATCATAAAACCATGTAAAGCGAGTAA
64 AAAAATGAAAAAAAATTCAACTTAAAATCAATTATGGCAAT-ATAAAACCATTTAAAGCGAGTAA
1336 TGAGGCTTTTGAAGGTATGGGTGACTATAAATAGACTTTTCT
128 TGAGGCTTTTGAAGGTATGGGTGACTATAAATAGACTTTTCT
* * *
1378 TGCCAATGAATG-CTTTTCTCTTCACGTTTCTCAAGGTAGACATCCAATTCTAGTCTGTTTTAAC
1 TGCCAATGAATGCCTTTT-TCTTTA--TTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAAC
* * * * * *
1442 TAAAAATGTAAAAAAATTCAACTTGAAATCAATTATGGC-ATCTTAAAACCATTTAAACCAAGTA
63 CAAAAATGAAAAAAAATTCAACTTAAAATCAATTATGGCAAT-ATAAAACCATTTAAAGCGAGTA
* * *
1506 ATGAGGCTTCTAAAGGTATAGGTGACTATAAATAGACTTTTCT
127 ATGAGGCTTTTGAAGGTATGGGTGACTATAAATAGACTTTTCT
* * * * * * *
1549 TGCCAATGAAT-CTTTTTTCTTTATATTTCTAAAAGTAGGCATTCAATTCTAGTCTATTTTAATC
1 TGCCAATGAATGCCTTTTTC-TT-TATTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACC
** * * * * * * * *
1613 AAAAATGACCGAAGAATTCAAATTTAAATCCATTTTGAG-ATTACAAAACCATTTAAAGTGAGTA
64 AAAAATGA-AAAAAAATTCAACTTAAAATCAATTATG-GCAATATAAAACCATTTAAAGCGAGTA
* *
1677 AT-ATGGCTTTTAAAGGAATGGGTGACTATAAAT
127 ATGA-GGCTTTTGAAGGTATGGGTGACTATAAAT
1710 G
Statistics
Matches: 940, Mismatches: 210, Indels: 80
0.76 0.17 0.07
Matches are distributed among these distances:
167 1 0.00
169 46 0.05
170 139 0.15
171 386 0.41
172 176 0.19
173 182 0.19
174 6 0.01
175 4 0.00
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.35
Consensus pattern (169 bp):
TGCCAATGAATGCCTTTTTCTTTATTTCTCAAGGTAGACATTCAATTATAGTCTGTTTTAACCAA
AAATGAAAAAAAATTCAACTTAAAATCAATTATGGCAATATAAAACCATTTAAAGCGAGTAATGA
GGCTTTTGAAGGTATGGGTGACTATAAATAGACTTTTCT
Found at i:1359 original size:514 final size:514
Alignment explanation
Indices: 678--1610 Score: 1244
Period size: 514 Copynumber: 1.8 Consensus size: 514
668 TGAGTGACTG
*
678 TAAATTGACTTTTCTTGCCAATGAATGCCTTTTTCTTTGCATTTCTCAAGGTAGACATTCAATTA
1 TAAATTGACTTTTCTTGCCAATAAATGCCTTTTTCTTTGCATTTCTCAAGGTAGACATTCAATTA
* *
743 TAGTCTATTTTAACCAAAAATGAAAAAAAAATCAACTTAAAATCAATTACAACAATATAAAATCA
66 TAATCTATTTTAACCAAAAATGAAAAAAAAATCAACTTAAAATCAATTACAACAATATAAAACCA
* *
808 TTTAAAGCGAGTAATGATGCTTTTGAAGGCTTGGGTGACTATAAATAGACTTTTCTTGCCAATGA
131 TGTAAAGCGAGTAATGAGGCTTTTGAAGGCTTGGGTGACTATAAATAGACTTTTCTTGCCAATGA
* * * *
873 ATGCTTTT-T-TTTATGTTTCTAAAGGTAGACATTCAATTCTAGAATGTTTTGA-TAAAAAATG-
196 ATGCTTTTCTCTTCACGTTTCTAAAGGTAGACATCCAATTCTAGAATGTTTTAACT-AAAAATGT
* * * * * ***
934 ACCAAAGAATTCAAATTTAAATCAATTTTGAG-AT-TACAAAACTATTTGAAGTGAGTAAT-ACG
260 A--AAAAAATTCAAATTGAAATCAATTATG-GCATCT-CAAAACCATTTAAACCAAGTAATGA-G
* * *
996 GCTTTTACAA-GAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATTCCTTTTTCATTAT-
320 GCTTCTA-AAGGAATAGGTGACTATAAATAGACTTTTCTTGCCAATGAA-TCCTTTTTCATTATA
* * *
1059 TGTTCTCAAGGT-GGACATTCAATTATAGTCTGTTTTAACATGAAATGTAAAAAAAATTCAATCT
383 T-TTCTAAAAGTAGG-CATTCAATTATAGTCTATTTTAACATGAAATGTAAAAAAAATTCAATCT
1123 TAAAATCAATTATGGCATTGTAAAATCATTTAACGCAAGTGGTAAGGCTTTTGAAGGTATAGGTG
446 TAAAATCAATTATGGCATTGTAAAATCATTTAACGCAAGTGGTAAGGCTTTTGAAGGTATAGGTG
1188 ATTA
511 ATTA
* * * * *
1192 TAAATTGGCTTTTCTTGCCAATAAATTCTTTTTTCTTCT-TATTTCTCAAGGTGGACATTCAATT
1 TAAATTGACTTTTCTTGCCAATAAATGCCTTTTTCTT-TGCATTTCTCAAGGTAGACATTCAATT
* * * * * * ***
1256 ATAATTTGTTTTAACCAAAAATGTAGAAAAATTTAACTTAAAATCAATTATGGC-ATCATAAAAC
65 ATAATCTATTTTAACCAAAAATGAAAAAAAAATCAACTTAAAATCAATTACAACAAT-ATAAAAC
1320 CATGTAAAGCGAGTAATGAGGCTTTTGAAGG-TATGGGTGACTATAAATAGACTTTTCTTGCCAA
129 CATGTAAAGCGAGTAATGAGGCTTTTGAAGGCT-TGGGTGACTATAAATAGACTTTTCTTGCCAA
* **
1384 TGAATGCTTTTCTCTTCACGTTTCTCAAGGTAGACATCCAATTCTAGTCTGTTTTAACTAAAAAT
193 TGAATGCTTTTCTCTTCACGTTTCTAAAGGTAGACATCCAATTCTAGAATGTTTTAACTAAAAAT
* *
1449 GTAAAAAAATTCAACTTGAAATCAATTATGGCATCTTAAAACCATTTAAACCAAGTAATGAGGCT
258 GTAAAAAAATTCAAATTGAAATCAATTATGGCATCTCAAAACCATTTAAACCAAGTAATGAGGCT
* * *
1514 TCTAAAGGTATAGGTGACTATAAATAGACTTTTCTTGCCAATGAATCTTTTTTCTTTATATTTCT
323 TCTAAAGGAATAGGTGACTATAAATAGACTTTTCTTGCCAATGAATCCTTTTTCATTATATTTCT
*
1579 AAAAGTAGGCATTCAATTCTAGTCTATTTTAA
388 AAAAGTAGGCATTCAATTATAGTCTATTTTAA
1611 TCAAAAATGA
Statistics
Matches: 360, Mismatches: 46, Indels: 26
0.83 0.11 0.06
Matches are distributed among these distances:
513 3 0.01
514 221 0.61
515 89 0.25
516 45 0.12
517 2 0.01
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (514 bp):
TAAATTGACTTTTCTTGCCAATAAATGCCTTTTTCTTTGCATTTCTCAAGGTAGACATTCAATTA
TAATCTATTTTAACCAAAAATGAAAAAAAAATCAACTTAAAATCAATTACAACAATATAAAACCA
TGTAAAGCGAGTAATGAGGCTTTTGAAGGCTTGGGTGACTATAAATAGACTTTTCTTGCCAATGA
ATGCTTTTCTCTTCACGTTTCTAAAGGTAGACATCCAATTCTAGAATGTTTTAACTAAAAATGTA
AAAAAATTCAAATTGAAATCAATTATGGCATCTCAAAACCATTTAAACCAAGTAATGAGGCTTCT
AAAGGAATAGGTGACTATAAATAGACTTTTCTTGCCAATGAATCCTTTTTCATTATATTTCTAAA
AGTAGGCATTCAATTATAGTCTATTTTAACATGAAATGTAAAAAAAATTCAATCTTAAAATCAAT
TATGGCATTGTAAAATCATTTAACGCAAGTGGTAAGGCTTTTGAAGGTATAGGTGATTA
Done.