Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402610.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5681.0, 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: 1706
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.29
Warning! 317 characters in sequence are not A, C, G, or T
Found at i:323 original size:172 final size:169
Alignment explanation
Indices: 4--1001 Score: 895
Period size: 172 Copynumber: 5.7 Consensus size: 169
1 TAG
** * * * *
4 TCTGTTTTAACCAAAAATGTAATAATATTCAACTTAAAATCAATTATGGGAATATAAAACCATTT
1 TCTGTTTTAATGAAAAATGTAA-AAAATTCAAATTAAAATCAATTATGAGATTATAAAACCATTT
* * * ** *
69 AAAGCGAGTAATATGGCTTTTGAAA-TAATGGGAGACCGTAAATGAACTTTTCTTGCCAATGAAT
65 AAAGAGAGTAATAAGGCTTTT-AAAGGAATGGGAGACTATAAATGGACTTTTCTTGCCAATGAAT
* *
133 GCTTTTTTCTTGATGTTTCTCAAGGTAGACATTCAATTATAA
129 GCCTTTTTCTTCATGTTTC-CAAGGTAGACATTCAATTATAA
** * *
175 TCTAATTTAACT-AAAAATGTACAAACAATTCAAATTAAAATCAATTTTGAGATTATAAAACCGT
1 TCTGTTTTAA-TGAAAAATGTA-AAA-AATTCAAATTAAAATCAATTATGAGATTATAAAACCAT
* *
239 TTAAAGAGAGTATTAAGGCTTTTAAAGGAATGGGAGACTATAAATTGACTTTTCTTGCCAATGAA
63 TTAAAGAGAGTAATAAGGCTTTTAAAGGAATGGGAGACTATAAATGGACTTTTCTTGCCAATGAA
* *
304 TGCCTTTTTCTTCATGTTTCCTAAGGTAGGCATTCAATTATAG
128 TGCCTTTTTCTTCATGTTTCC-AAGGTAGACATTCAATTATAA
* * *
347 TCTGTTTTAATCAAAAATATAAAAAAGATTCAACTTAAAATCAATTATGAGATTATAAAACCATT
1 TCTGTTTTAATGAAAAATGT-AAAAA-ATTCAAATTAAAATCAATTATGAGATTATAAAACCATT
* * * *
412 TAAAGAGAGTAATAAGGCTTTTGACA-GAATGGAAAACTATAAATGGCCTTTTCTTGCCAATGAA
64 TAAAGAGAGTAATAAGGCTTTT-AAAGGAATGGGAGACTATAAATGGACTTTTCTTGCCAATGAA
* * *
476 TGCTTTTTTCTTCATGTTTCTCTAGGTAGACATTCGATTATAA
128 TGCCTTTTTCTTCATGTTTC-CAAGGTAGACATTCAATTATAA
* * * *
519 TCTGTTTTAATGAAAAATGAATAAAAAATTCAACTTAAAATCAATTAT-AAACTTA-AAATCAAT
1 TCTGTTTTAATGAAAAATG--TAAAAAATTCAAATTAAAATCAATTATGAGA-TTATAAAACCAT
* * * * *** * *
582 TATAAGCTTAAAAAGTCATTTAAAGCAAGTAGTAAGCCTCGTAAAAGAACAGGACACTATAAATG
63 T-TAA----AGAGAGT-A-ATAAGGCTTTTA--AAG----G--AATG----GGAGACTATAAATG
* * * *
647 GACTTTTCTTTCCATTGAATGCATTTTTC-TCTATGTTTCCGAAGGTAGACATTCAATTAAAA
109 GACTTTTCTTGCCAATGAATGCCTTTTTCTTC-ATGTTTCC-AAGGTAGACATTCAATTATAA
* * *
709 TCTATTTTAACT-AAAAAAGTACAAAGAATTCAAA-TATAAATCAATTTTGAGATTATAAAACCA
1 TCTGTTTTAA-TGAAAAATGTA-AAA-AATTCAAATTA-AAATCAATTATGAGATTATAAAACCA
* * * * **
772 TTTAAAGTGAGTAATACGGCTTTTAAAGTAATGAGAGACTATAAATTCACTTTTCTTG-CAATGA
62 TTTAAAGAGAGTAATAAGGCTTTTAAAGGAATGGGAGACTATAAATGGACTTTTCTTGCCAATGA
** * * *
836 ATG-CTTTTGTCTTCACCTTTCCCAAGGTAGTCATTCGATTATAG
127 ATGCCTTTT-TCTTCATGTTT-CCAAGGTAGACATTCAATTATAA
* * *
880 TCTGTTTTAATGCAAAATGTAAGAAAA-TC-AACTAACAATCAATTATGAGATTATAAAACTATT
1 TCTGTTTTAATGAAAAATGTAA-AAAATTCAAATTAA-AATCAATTATGAGATTATAAAACCATT
* * * *
943 TAAAGCGAGCAATAAAGCTTTTAAAGGAATGAGAGACTATAAATGGACTTTTCTTGCCA
64 TAAAGAGAGTAATAAGGCTTTTAAAGGAATGGGAGACTATAAATGGACTTTTCTTGCCA
1002 GNNNNNNNNN
Statistics
Matches: 674, Mismatches: 104, Indels: 99
0.77 0.12 0.11
Matches are distributed among these distances:
168 3 0.00
169 78 0.12
170 10 0.01
171 83 0.12
172 335 0.50
173 9 0.01
174 1 0.00
176 8 0.01
177 2 0.00
178 6 0.01
179 1 0.00
182 3 0.00
184 7 0.01
185 1 0.00
186 7 0.01
188 2 0.00
189 8 0.01
190 100 0.15
191 10 0.01
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (169 bp):
TCTGTTTTAATGAAAAATGTAAAAAATTCAAATTAAAATCAATTATGAGATTATAAAACCATTTA
AAGAGAGTAATAAGGCTTTTAAAGGAATGGGAGACTATAAATGGACTTTTCTTGCCAATGAATGC
CTTTTTCTTCATGTTTCCAAGGTAGACATTCAATTATAA
Found at i:573 original size:18 final size:18
Alignment explanation
Indices: 550--594 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
540 TAAAAAATTC
550 AACTTAAAATCAATTATA
1 AACTTAAAATCAATTATA
568 AACTTAAAATCAATTATA
1 AACTTAAAATCAATTATA
*
586 AGCTTAAAA
1 AACTTAAAA
595 AGTCATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.56, C:0.11, G:0.02, T:0.31
Consensus pattern (18 bp):
AACTTAAAATCAATTATA
Found at i:968 original size:362 final size:361
Alignment explanation
Indices: 275--925 Score: 876
Period size: 362 Copynumber: 1.8 Consensus size: 361
265 GGAATGGGAG
* * * *
275 ACTATAAATTGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCCTAAGGTAGGCATTCA
1 ACTATAAATGGACTTTTCTTGCCAATGAATGCATTTTTCTTCATGTTTCCGAAGGTAGACATTCA
* * * *
340 ATTATAGTCTGTTTTAATCAAAAATATAAAAAAGATTCAACTTAAAATCAATTATGAGATTATAA
66 ATTAAAATCTATTTTAATCAAAAATATAAAAAAGATTCAAATTAAAATCAATTATGAGATTATAA
*
405 AACCATTTAAAGAGAGTAATAAGGCTTTTGACAGAATGGAAAACTATAAATGGCCTTTTCTTGCC
131 AACCATTTAAAGAGAGTAATAAGGCTTTTGAAAGAATGGAAAACTATAAATGGCCTTTTCTTGCC
* ** * *
470 AATGAATGCTTTTTTCTTCATGTTTCTCTAGGTAGACATTCGATTATAATCTGTTTTAATGAAAA
196 AATGAATGCTTTTGTCTTCACCTTTCCCAAGGTAGACATTCGATTATAATCTGTTTTAATGAAAA
**
535 ATGAATAAAAAATTCAACTTAAAATCAATTATAAACTTAAAATCAATTATAAGCTTAAAAAGTCA
261 ATG-ATAAAAAATTCAACTTAAAATCAATTATAAACTTAAAATCAATTATAAGCGCAAAAAGTCA
600 TTTAAAGCAAGTAGTAAGCCTCGTAAAAGAACAGGAC
325 TTTAAAGCAAGTAGTAAGCCTCGTAAAAGAACAGGAC
* *
637 ACTATAAATGGACTTTTCTTTCCATTGAATGCATTTTTC-TCTATGTTTCCGAAGGTAGACATTC
1 ACTATAAATGGACTTTTCTTGCCAATGAATGCATTTTTCTTC-ATGTTTCCGAAGGTAGACATTC
* *
701 AATTAAAATCTATTTTAA-CTAAAAA-AGT-ACAAAGAATTCAAA-TATAAATCAATTTTGAGAT
65 AATTAAAATCTATTTTAATC-AAAAATA-TAAAAAAG-ATTCAAATTA-AAATCAATTATGAGAT
* * * *
762 TATAAAACCATTTAAAGTGAGTAATACGGCTTTT-AAAGTAAT-GAGAGACTATAAAT-TCACTT
126 TATAAAACCATTTAAAGAGAGTAATAAGGCTTTTGAAAG-AATGGA-AAACTATAAATGGC-CTT
* *
824 TTCTTG-CAATGAATGCTTTTGTCTTCACCTTTCCCAAGGTAGTCATTCGATTATAGTCTGTTTT
188 TTCTTGCCAATGAATGCTTTTGTCTTCACCTTTCCCAAGGTAGACATTCGATTATAATCTGTTTT
*
888 AATGCAAAATG-TAAGAAAA-TCAAC-TAACAATCAATTAT
253 AATGAAAAATGATAA-AAAATTCAACTTAA-AATCAATTAT
926 GAGATTATAA
Statistics
Matches: 254, Mismatches: 25, Indels: 23
0.84 0.08 0.08
Matches are distributed among these distances:
358 3 0.01
359 18 0.07
360 4 0.02
361 78 0.31
362 151 0.59
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.35
Consensus pattern (361 bp):
ACTATAAATGGACTTTTCTTGCCAATGAATGCATTTTTCTTCATGTTTCCGAAGGTAGACATTCA
ATTAAAATCTATTTTAATCAAAAATATAAAAAAGATTCAAATTAAAATCAATTATGAGATTATAA
AACCATTTAAAGAGAGTAATAAGGCTTTTGAAAGAATGGAAAACTATAAATGGCCTTTTCTTGCC
AATGAATGCTTTTGTCTTCACCTTTCCCAAGGTAGACATTCGATTATAATCTGTTTTAATGAAAA
ATGATAAAAAATTCAACTTAAAATCAATTATAAACTTAAAATCAATTATAAGCGCAAAAAGTCAT
TTAAAGCAAGTAGTAAGCCTCGTAAAAGAACAGGAC
Done.