Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402925.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5972.0, 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, 670
Length: 1118
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Found at i:759 original size:341 final size:337
Alignment explanation
Indices: 1--1105 Score: 1133
Period size: 341 Copynumber: 3.2 Consensus size: 337
* **
1 ATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTCGAAGGTTTGAATGACTATAAA
1 ATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTCGAAGGCTTGGGTGACTATAAA
* * *
66 T-AGACTTTTCTTGTC-AATGAATGACTTTTTCTTCACGTTTTTTGAGGCAGATAGTT-AATTAT
66 TGAG-CTTTTCTTG-CAAATGAATGAGTTTTTCTTCACGTTTCTTGAGGCAAATA-TTCAATTAT
* * * * * * * *
128 AATTTGGTTTAACTAAAAATCTAAAGATATTCAACCTAAAATTAATTATAAGATTATAAAACCAT
128 AATATGTTTTAACAAAAAATATAAA-AAATTCAACTTAAAATCAATTATGAGATTATAAAA-CAT
* * * * *
193 TTAAAGCAAGCAATAAGGCTTTCGAAA-GCTTGGGTGACTATAAATGG-CTTTTTTTTTCTAATG
191 TTAAAG-AAGTAATAAGGCTTTC-AAAGGCTTGAGTGACTATAAAAGGAC-TTTTTTTACCAATG
* * * * * *
256 GATGGATTTTTCTTCACATTTCCCAAGGAAAACTTTCAATTACAATCTGTTTTATTCAAAAATAT
253 GATGGCTTTTTCTTCACATTTCTCAAGG-AAACATTCAATTATAAT-TATTTTAATCAAAAATA-
* *
321 AAAAAACATTCAACTTAAAATTA
315 AAAAAATATTCAACTTAAAATCA
* * ** *
344 ATTATGAGTTTATAAAACTATTTAAAGTGAGTAGGAAGGCTTAT-GAAGGCTTGGGTGACTCTAA
1 ATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTT-TCGAAGGCTTGGGTGACTATAA
* * *
408 ATGGGCTTTTCTTGCAAATGAATGAGTTTTTGTTCATGTTTCTTGAGGCAAATATTCAATTATAA
65 ATGAGCTTTTCTTGCAAATGAATGAGTTTTTCTTCACGTTTCTTGAGGCAAATATTCAATTATAA
* * * *
473 TATGTTTTAACCAAAAATATAAAACAATTTAACTTAAAATCAATTATGAGATTAAAAAATCATTA
130 TATGTTTTAACAAAAAATATAAAA-AATTCAACTTAAAATCAATTATGAGATTATAAAA-CATTT
* *
538 AAAGTAAGTAATAAGGCTTTCAAAGGCTTGAGTGA-TAATAAAAGGACTTTTTATCCCAATGGAT
193 AAAG-AAGTAATAAGGCTTTCAAAGGCTTGAGTGACT-ATAAAAGGACTTTTTTTACCAATGGAT
** * *
602 GGCTTTCAC-TCACATTTCTCAAGGTATACATTCAATTATAATATATTTTAATCAAAAATACAAA
256 GGCTTTTTCTTCACATTTCTCAAGG-AAACATTCAATTATAAT-TATTTTAATCAAAAATAAAAA
*
666 AATATTGAACTTAAAATCA
319 AATATTCAACTTAAAATCA
* * * *
685 ATTATGAGATTATAAATCCATATAAAGTGAGTAAT-AGAGTTTTTGAAGGCTTGGGTGACTATAA
1 ATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAG-GCTTTCGAAGGCTTGGGTGACTATAA
* * * * * * *
749 CTGAGCTTTTCTTGCATATAAATG-GCTTTTTCTTCACGTTTGC--CAAGCTAAACATTCATTTA
65 ATGAGCTTTTCTTGCAAATGAATGAG-TTTTTCTTCACGTTT-CTTGAGGC-AAATATTCAATTA
* * * * ** *
811 TAATCTATTTTAATAAAAAATATAAAAAGGTTCAACTTAAAATCTTTTATGCGATTATAAAACTA
127 TAATATGTTTTAACAAAAAATATAAAAA-ATTCAACTTAAAATCAATTATGAGATTATAAAAC-A
* *
876 TTTAAAGAGAGTAATAAGGCTTTTAAAGGCATGAGTGACTATAAATA-GACTTTTTTTACCAATG
190 TTTAAAGA-AGTAATAAGGCTTTCAAAGGCTTGAGTGACTATAAA-AGGACTTTTTTTACCAATG
* * * * * * *
940 AATGGCTTTTTCTTCACGTTTCTCAAGGCAAGCATAT-GATTATAATTTTTTTAA-CTACAAATG
253 GATGGCTTTTTCTTCACATTTCTCAAGG-AAACAT-TCAATTATAATTATTTTAATC-AAAAATA
*
1003 TAAAAATATTCAACTTAAAATCA
315 AAAAAATATTCAACTTAAAATCA
** * *
1026 ATTATGAGATTATAAAACTTTTTTAAAGCGAGTAATAAGGCTTTCGAAGGCTTGGGTGATTATAA
1 ATTATGAGATTATAAAAC-CATTTAAAGTGAGTAATAAGGCTTTCGAAGGCTTGGGTGACTATAA
1091 ATGAGCTTTTCTTGC
65 ATGAGCTTTTCTTGC
1106 CAATAAAAGG
Statistics
Matches: 636, Mismatches: 103, Indels: 47
0.81 0.13 0.06
Matches are distributed among these distances:
340 11 0.02
341 277 0.44
342 130 0.20
343 215 0.34
344 3 0.00
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (337 bp):
ATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTCGAAGGCTTGGGTGACTATAAA
TGAGCTTTTCTTGCAAATGAATGAGTTTTTCTTCACGTTTCTTGAGGCAAATATTCAATTATAAT
ATGTTTTAACAAAAAATATAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACATTTAAA
GAAGTAATAAGGCTTTCAAAGGCTTGAGTGACTATAAAAGGACTTTTTTTACCAATGGATGGCTT
TTTCTTCACATTTCTCAAGGAAACATTCAATTATAATTATTTTAATCAAAAATAAAAAAATATTC
AACTTAAAATCA
Found at i:869 original size:171 final size:167
Alignment explanation
Indices: 1--1112 Score: 888
Period size: 171 Copynumber: 6.5 Consensus size: 167
* * * * **
1 ATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTCGAAGGTTTGAATGACTATAAA
1 ATTATGAGATTATAAAACTATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGGGTGACTATAAA
* * * ** * * *
66 T-AGACTTTTCTTGTCAATGAATGACTTTTTCTTCACGTTTTTTGAGGCAGATAGTTAATTATAA
66 TGAG-CTTTTCTTG-CAATAAATGGCTTTTTCTTCACGTTTCTCAAGGCAAACA-TTCATTATAA
* * * *
130 TT-TGGTTTAACTAAAAATCTAAAGATATTCAACCTAAAATTA
128 TTAT--TTTAA-TAAAAATATAAAAATATTCAACTTAAAATCA
* * * * *
172 ATTATAAGATTATAAAACCATTTAAAGCA-AGCAATAAGGCTTTCGAAAGCTTGGGTGACTATAA
1 ATTATGAGATTATAAAACTATTTAAAG-AGAGTAATAAGGCTTTTGAAGGCTTGGGTGACTATAA
* * ** * * * * * *
236 ATG-GCTTTTTTTTTCTAATGGATGGATTTTTCTTCACATTTCCCAAGGAAAACTTTCAATTACA
65 ATGAGC-TTTTCTTGC-AATAAATGGCTTTTTCTTCACGTTTCTCAAGGCAAACATTC-ATTATA
* * * *
300 ATCTGTTTTATTCAAAAATATAAAAAACATTCAACTTAAAATTA
127 AT-TATTTTAAT-AAAAATAT-AAAAATATTCAACTTAAAATCA
* * ** * *
344 ATTATGAGTTTATAAAACTATTTAAAGTGAGTAGGAAGGCTTATGAAGGCTTGGGTGACTCTAAA
1 ATTATGAGATTATAAAACTATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGGGTGACTATAAA
* * * * ** *
409 TGGGCTTTTCTTGCAAATGAATGAG-TTTTTGTTCATGTTTCTTGAGGCAAATATTCAATTATAA
66 TGAGCTTTTCTTGC-AATAAATG-GCTTTTTCTTCACGTTTCTCAAGGCAAACATTC-ATTATAA
* * *
473 TATGTTTTAACCAAAAATATAAAACA-ATTTAACTTAAAATCA
128 T-TATTTTAA-TAAAAATATAAAA-ATATTCAACTTAAAATCA
* * ** *
515 ATTATGAGATTA-AAAAATCATTAAAAGTA-AGTAATAAGGCTTTCAAAGGCTTGAGTGA-TAAT
1 ATTATGAGATTATAAAACT-ATTTAAAG-AGAGTAATAAGGCTTTTGAAGGCTTGGGTGACT-AT
* * ** ** * * *
577 AAAAG-GACTTTT-TATCCCAATGGATGGCTTTCAC-TCACATTTCTCAAGGTATACATTCAATT
63 AAATGAG-CTTTTCT-T-GCAATAAATGGCTTTTTCTTCACGTTTCTCAAGGCAAACATTC-ATT
* *
639 ATAATATATTTTAATCAAAAATACAAAAATATTGAACTTAAAATCA
124 ATAAT-TATTTTAAT-AAAAATATAAAAATATTCAACTTAAAATCA
* * * * *
685 ATTATGAGATTATAAATCCATATAAAGTGAGTAAT-AGAGTTTTTGAAGGCTTGGGTGACTATAA
1 ATTATGAGATTATAAAACTATTTAAAGAGAGTAATAAG-GCTTTTGAAGGCTTGGGTGACTATAA
*
749 CTGAGCTTTTCTTGCATATAAATGGCTTTTTCTTCACGTTTGC-CAA-GCTAAACATTCATTTAT
65 ATGAGCTTTTCTTGCA-ATAAATGGCTTTTTCTTCACGTTT-CTCAAGGC-AAACATTCA-TTAT
** *
812 AATCTATTTTAATAAAAAATATAAAAAGGTTCAACTTAAAATCT
126 AAT-TATTTTAAT-AAAAATATAAAAATATTCAACTTAAAATCA
* * * * *
856 TTTATGCGATTATAAAACTATTTAAAGAGAGTAATAAGGCTTTTAAAGGCATGAGTGACTATAAA
1 ATTATGAGATTATAAAACTATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGGGTGACTATAAA
* * * * *
921 T-AGACTTTTTTTACCAATGAATGGCTTTTTCTTCACGTTTCTCAAGGCAAGCATATGATTATAA
66 TGAG-CTTTTCTT-GCAATAAATGGCTTTTTCTTCACGTTTCTCAAGGCAAACAT-TCATTATAA
* * *
985 TTTTTTTAACTACAAATGTAAAAATATTCAACTTAAAATCA
128 TTATTTTAA-TAAAAATATAAAAATATTCAACTTAAAATCA
* * * *
1026 ATTATGAGATTATAAAACTTTTTTAAAGCGAGTAATAAGGCTTTCGAAGGCTTGGGTGATTATAA
1 ATTATGAGATTATAAAAC-TATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGGGTGACTATAA
1091 ATGAGCTTTTCTTGCCAATAAA
65 ATGAGCTTTTCTTG-CAATAAA
1113 AGGGTT
Statistics
Matches: 750, Mismatches: 147, Indels: 88
0.76 0.15 0.09
Matches are distributed among these distances:
169 5 0.01
170 189 0.25
171 405 0.54
172 147 0.20
173 4 0.01
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (167 bp):
ATTATGAGATTATAAAACTATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGGGTGACTATAAA
TGAGCTTTTCTTGCAATAAATGGCTTTTTCTTCACGTTTCTCAAGGCAAACATTCATTATAATTA
TTTTAATAAAAATATAAAAATATTCAACTTAAAATCA
Done.