Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402624.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5695.0, 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: 2336
ACGTcount: A:0.25, C:0.08, G:0.08, T:0.23
Warning! 838 characters in sequence are not A, C, G, or T
Found at i:1233 original size:171 final size:167
Alignment explanation
Indices: 948--2336 Score: 1332
Period size: 171 Copynumber: 8.1 Consensus size: 167
938 NNNNNNNNNN
* * * * *
948 AATGGACTTTTCTTACCAATGGATATCTTTTTCTTCACATTTCTCGAGGTAG-ACTTCCATTATA
1 AATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTTTCT-GAAGTAGAAATT-AATTATA
* *
1012 ATCTGTTTTAATTAAAAATATAAAAAAATTCAACTAAAAATCAATTATGAGATTACAAAAGCATT
64 ATCTGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAA-CAATTATGAGATTA-AAAAGCATT
* *
1077 TAAAGAGAATAATAAGGCTTTCGAAGGCATGGGTGACTATA
127 TAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATA
* * *
1118 TATGGACTTTTTTTGCCAATGGATATCTTTTTCTTCATGTTTCCTGAAGTAGATAATTAATTATA
1 AATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTTT-CTGAAGTAGA-AATTAATTATA
* * * *
1183 ATATGTTTTAATAAAAAATATAAAAAAGTTCTACTTAAAACAAATTATGAGATTAAAAAAGCTTT
64 ATCTGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAAC-AATTATGAGATT-AAAAAGCATT
* * * * * * * * *
1248 TAAAGTGAGTAAAAAGGCTATCGAAAGAATGGGTAATTCTG
127 TAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATA
* * * * * *
1289 AATAGACTTTTCTTGCCAATGGATATCCTCTTCTTCACTTTTCTCGACGCA-AACATTTAATTAT
1 AATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTTTCT-GAAGTAGAA-A-TTAATTAT
* **
1353 AATCTGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGGTTATAAAAATAT
63 AATCTGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAA-CAATTATGAGATTA-AAAAGCAT
* *
1418 TTAAAGCGAGTAATAAGGCTCTCGAAGGCATGGGTTACTATA
126 TTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATA
* * * * * *
1460 AATGGATTTTTTTTGTCAATGGATATCTTTTTTTTCACGTTTCTCAAGATA-AACATACAATTAT
1 AATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTTTCTGAAG-TAGAA-AT-TAATTAT
* * * * * *
1524 AATCTGCTTTAATAATAAATATAAAAAAATT-AAGCTAAAAATTAAGTATGAGATTAAAAAACTA
63 AATCTGTTTTAATAAAAAATATAAAAAAATTCAA-CTTAAAA-CAATTATGAGATTAAAAAGC-A
* * *
1588 TTTAAAGCGAGTAGTAAGGCTTTCAAAGGCATTGGTGACTATA
125 TTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATA
* * * * * *
1631 AATGAACTTTTCTTGTCAATGGATATCTTTTTCTTTATGTTTCTCATAGTAGACATTCAATTATA
1 AATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTTTCTGA-AGTAGAAATT-AATTATA
* * * *
1696 ATCTGTTTTAATAAAAAATATAAAAAAGTTCAGCTTACAACTAATTAT-AAATTAAAAATGCATT
64 ATCTGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAAC-AATTATGAGATTAAAAA-GCATT
* *
1760 TAAAGCGAGAAATAAGGCTTTCGAAGGCATGGGTTACTATA
127 TAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATA
* * * * *
1801 AATGGACTTTTCTTACCAATGGATATCTTTTTCTTCATGTTTCTTGAGGCAGACATTCAATTATA
1 AATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTTTC-TGAAGTAGAAATT-AATTATA
* * * *
1866 ATCTATTTTAATAAAAAATATAAAAAAATTCAAATTAAAATCAATTATGAGGTTATAAAATCATT
64 ATCTGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAA-CAATTATGAGATTA-AAAAGCATT
* * * *
1931 TAAAGCGAGTAATAAAGCTTTTGTAGGTATGGGTGACTATA
127 TAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATA
* * *
1972 ATTGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTTTCTCAAGGTAGACATTCAATTATA
1 AATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTTTCTGAA-GTAGAAATT-AATTATA
* * * * * ********* * * *
2037 ATATATTGTAGTAAAAAATATAAAAAAATTCAAATTNNNNNNNNNNATTAGGTTATAAAATCATT
64 ATCTGTTTTAATAAAAAATATAAAAAAATTCAACTT-AAAACAATTATGAGATTA-AAAAGCATT
* * * *** *
2102 TAAAGCAAGTAATAAAGCTTTTGAAGGCACAAGTGACTCTA
127 TAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATA
* * ********
2143 AATGGACTTTTCTTACCAATGGATATCTTTTTCTTCACGTTTCTTGAAGCA-ANNNNNNNNNNAT
1 AATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTTTC-TGAAGTAGA--AATTAATTAT
* * *
2207 AATCTGTTTTAATAAAAAATATAAAAAAGTTCAACTTAAAACTAATTATAAAATTAAAAATGCAT
63 AATCTGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAAC-AATTATGAGATTAAAAA-GCAT
* * *
2272 TTAAAGCGAGAAATAAGGCTTTCGAAGGCATGAGTTACTATA
126 TTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATA
*
2314 AATGAACTTTTCTTGCCAATGGA
1 AATGGACTTTTCTTGCCAATGGA
Statistics
Matches: 1004, Mismatches: 184, Indels: 61
0.80 0.15 0.05
Matches are distributed among these distances:
169 1 0.00
170 210 0.21
171 777 0.77
172 16 0.02
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.35
Consensus pattern (167 bp):
AATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTTTCTGAAGTAGAAATTAATTATAAT
CTGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAACAATTATGAGATTAAAAAGCATTTAAA
GCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATA
Found at i:2265 original size:683 final size:683
Alignment explanation
Indices: 948--2336 Score: 1609
Period size: 683 Copynumber: 2.0 Consensus size: 683
938 NNNNNNNNNN
* * * *
948 AATGGACTTTTCTTACCAATGGATATCTTTTTCTTCACATTTCTCGAGGTAGACTTCCATTATAA
1 AATGAACTTTTCTTGCCAATGGATATCTTTTTCTTCACATTTCTCGAAGTAGACTTCAATTATAA
* *
1013 TCTGTTTTAATTAAAAATATAAAAAAATTCAACTAAAAATCAATTATGAGATTACAAAAGCATTT
66 TCTGTTTTAATAAAAAATATAAAAAAATTCAACTAAAAATCAATTATGAAATTACAAAAGCATTT
* * *
1078 AAAGAGAATAATAAGGCTTTCGAAGGCATGGGTGACTATATATGGACTTTTTTTGCCAATGGATA
131 AAAGAGAATAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTACCAATGGATA
* *
1143 TCTTTTTCTTCATGTTTCCTGAAGTAGATAATTAATTATAATATGTTTTAATAAAAAATATAAAA
196 TCTTTTTCTTCATGTTTCCTGAAGCAGATAATTAATTATAATATATTTTAATAAAAAATATAAAA
* * * * *
1208 AAGTTCTACTTAAAACAAATTATGAGATTAAAAAAGCTTTTAAAGTGAGTAAAAAGGCTATCGAA
261 AAATTCAAATTAAAACAAATTATGAGATTAAAAAAGCATTTAAAGCGAGTAAAAAGGCTATCGAA
* * * *
1273 AGAATGGGTAATTCTGAATAGACTTTTCTTGCCAATGGATATCCTCTTCTTCACTTTTCTCGACG
326 AGAATGGGTAACTATGAATAGACTTTTCTTGCCAATGGATATCCTCTTCTTCACGTTTCTCAACG
* * * * *
1338 CAAACATTTAATTATAATCTGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAATTATG
391 CAAACATTCAATTATAATATATTGTAATAAAAAATATAAAAAAATTCAAATTAAAATCAATTATG
* * *** * *
1403 AGGTTATAAAAATATTTAAAGCGAGTAATAAGGCTCTCGAAGGCATGGGTTACTATAAATGGATT
456 AGGTTATAAAAATATTTAAAGCAAGTAATAAAGCTCTCGAAGGCACAAGTGACTATAAATGGACT
* ** * *
1468 TTTTTTGTCAATGGATATCTTTTTTTTCACGTTTCTCAAGATAAACATACAATTATAATCTGCTT
521 TTTCTTACCAATGGATATCTTTTTCTTCACGTTTCTCAAGACAAACATACAATTATAATCTGCTT
* * * *
1533 TAATAATAAATATAAAAAAATTAAGCTAAAAATTAAGTATGAGATTAAAAA-ACTATTTAAAGCG
586 TAATAAAAAATATAAAAAAATTAAGCTAAAAACTAAGTATAAAATTAAAAATAC-ATTTAAAGCG
* *
1597 AGTAGTAAGGCTTTCAAAGGCATTG-GTGACTATA
650 AGAAATAAGGCTTTCAAAGGCA-TGAGTGACTATA
* * **
1631 AATGAACTTTTCTTGTCAATGGATATCTTTTTCTTTATGTTTCTC-ATAGTAGACATTCAATTAT
1 AATGAACTTTTCTTGCCAATGGATATCTTTTTCTTCACATTTCTCGA-AGTAGAC-TTCAATTAT
* * * *
1695 AATCTGTTTTAATAAAAAATATAAAAAAGTTCAGCTTACAA-CTAATTAT-AAATTA-AAAATGC
64 AATCTGTTTTAATAAAAAATATAAAAAAATTCAACTAAAAATC-AATTATGAAATTACAAAA-GC
* *
1757 ATTTAAAGCGAGA-AATAAGGCTTTCGAAGGCATGGGTTACTATAAATGGACTTTTCTTACCAAT
127 ATTTAAAGAGA-ATAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTACCAAT
* * * *
1821 GGATATCTTTTTCTTCATGTTTCTTGAGGCAGA-CATTCAATTATAATCTATTTTAATAAAAAAT
191 GGATATCTTTTTCTTCATGTTTCCTGAAGCAGATAATT-AATTATAATATATTTTAATAAAAAAT
* * *
1885 ATAAAAAAATTCAAATTAAAATC-AATTATGAGGTTATAAAATCATTTAAAGCGAGTAATAAA-G
255 ATAAAAAAATTCAAATTAAAA-CAAATTATGAGATTAAAAAAGCATTTAAAGCGAGTAA-AAAGG
* * * * * * * * *
1948 CTTTTGTAGGTATGGGTGACTAT-AATTGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGT
318 CTATCGAAAGAATGGGTAACTATGAA-TAGACTTTTCTTGCCAATGGATATCCTCTTCTTCACGT
* * * * ****
2012 TTCTCAAGGTAGACATTCAATTATAATATATTGTAGTAAAAAATATAAAAAAATTCAAATTNNNN
382 TTCTCAACGCAAACATTCAATTATAATATATTGTAATAAAAAATATAAAAAAATTCAAATTAAAA
****** * * * *
2077 NNNNNNATTAGGTTAT-AAAATCATTTAAAGCAAGTAATAAAGCTTTTGAAGGCACAAGTGACTC
447 TCAATTATGAGGTTATAAAAAT-ATTTAAAGCAAGTAATAAAGCTCTCGAAGGCACAAGTGACTA
* **********
2141 TAAATGGACTTTTCTTACCAATGGATATCTTTTTCTTCACGTTTCTTGAAG-CAANNNNNNNNNN
511 TAAATGGACTTTTCTTACCAATGGATATCTTTTTCTTCACGTTTC-TCAAGACAAACATACAATT
* * * * *
2205 ATAATCTGTTTTAATAAAAAATATAAAAAAGTTCAA-CTTAAAACTAATTATAAAATTAAAAATG
575 ATAATCTGCTTTAATAAAAAATATAAAAAAATT-AAGCTAAAAACTAAGTATAAAATTAAAAATA
* *
2269 CATTTAAAGCGAGAAATAAGGCTTTCGAAGGCATGAGTTACTATA
639 CATTTAAAGCGAGAAATAAGGCTTTCAAAGGCATGAGTGACTATA
2314 AATGAACTTTTCTTGCCAATGGA
1 AATGAACTTTTCTTGCCAATGGA
Statistics
Matches: 586, Mismatches: 106, Indels: 28
0.81 0.15 0.04
Matches are distributed among these distances:
682 17 0.03
683 507 0.87
684 62 0.11
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.35
Consensus pattern (683 bp):
AATGAACTTTTCTTGCCAATGGATATCTTTTTCTTCACATTTCTCGAAGTAGACTTCAATTATAA
TCTGTTTTAATAAAAAATATAAAAAAATTCAACTAAAAATCAATTATGAAATTACAAAAGCATTT
AAAGAGAATAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTACCAATGGATA
TCTTTTTCTTCATGTTTCCTGAAGCAGATAATTAATTATAATATATTTTAATAAAAAATATAAAA
AAATTCAAATTAAAACAAATTATGAGATTAAAAAAGCATTTAAAGCGAGTAAAAAGGCTATCGAA
AGAATGGGTAACTATGAATAGACTTTTCTTGCCAATGGATATCCTCTTCTTCACGTTTCTCAACG
CAAACATTCAATTATAATATATTGTAATAAAAAATATAAAAAAATTCAAATTAAAATCAATTATG
AGGTTATAAAAATATTTAAAGCAAGTAATAAAGCTCTCGAAGGCACAAGTGACTATAAATGGACT
TTTCTTACCAATGGATATCTTTTTCTTCACGTTTCTCAAGACAAACATACAATTATAATCTGCTT
TAATAAAAAATATAAAAAAATTAAGCTAAAAACTAAGTATAAAATTAAAAATACATTTAAAGCGA
GAAATAAGGCTTTCAAAGGCATGAGTGACTATA
Done.