Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402806.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5862.0, 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, 640
Length: 1068
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Found at i:289 original size:172 final size:171
Alignment explanation
Indices: 1--1068 Score: 1046
Period size: 172 Copynumber: 6.3 Consensus size: 171
* * * *
1 TATGAGATTATAAAACTATTTAAAGGGAGTAATAAGGCTTTTGAAGGAATGGGTAACTAGAAATG
1 TATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGAAACTATAAATG
* * *
66 GAGTTTTCTTGTCAATGAATGCCTTTTTCTTCACATTTCTCAAGGTAGACATTCAATTATAATCT
66 GACTTTTCTTGCCAATGAATGCCTTTTTCTTCACGTTTCTCAAGGTAGACATTCAATTATAATCT
* * *
131 GTTTTAACCAATAATATAAAAAAAATTGAACCTAAAATCAAT
131 GTTTTAACCAAAAATAT-AAAAAAATTCAACTTAAAATCAAT
* * * *
173 TTTGAGATTATAAAACTATTTAAAGCGAGTAACAAAGCTTTTGAAGGAATAGGAAACTATAAATT
1 TATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGAAACTATAAATG
* * * * * * *
238 AACTTTTCTTGCCAATGAATTCTTTTTTCCTCACGTTTCTCGATGTAGACATTCAATTAT-A-GT
66 GACTTTTCTTGCCAATGAATGCCTTTTTCTTCACGTTTCTCAAGGTAGACATTCAATTATAATCT
* *
301 GTATTTGACCAAAAATATAAACAAATTCAACTTAAAATCAAT
131 GT-TTTAACCAAAAATATAAAAAAATTCAACTTAAAATCAAT
* ** * * *
343 CATGAGATTATAAAACTATTTAAAGTTAGTAATAAGGCCTTT-AAGGAAT-GGATGATTATAAAT
1 TATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGA-AACTATAAAT
* * * *
406 GGACTTTTTTTTACCAATGAATGCCTTTGTCTTCACGTTTCTCAA-ATAGACATTCAATTATAAT
65 GGAC-TTTTCTTGCCAATGAATGCCTTTTTCTTCACGTTTCTCAAGGTAGACATTCAATTATAAT
* * * *
470 CTGTTTTAACCAGAAATGA-AAAAAATTTTAACTTAAAATTAAT
129 CTGTTTTAACCAAAAAT-ATAAAAAAATTCAACTTAAAATCAAT
* * * * * * *
513 TATGAGATTATAAAACCATTTAAAGAGAGCAATAAAGCTTTTGAAAGAATAGGTAACTACAAATG
1 TATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGAAACTATAAATG
** ** * *
578 GACTTTTCTT-CCTAGCGAATGCCTTTTGGTTCATGTTTCTCAAGGTA-AGCATTCAATTGTAAT
66 GACTTTTCTTGCC-AATGAATGCCTTTTTCTTCACGTTTCTCAAGGTAGA-CATTCAATTATAAT
* * * * * *
641 ATGTTTTTACCAAAAATGTTAAAAAATTTAAACTAAAAATCAAT
129 CTGTTTTAACCAAAAAT-ATAAAAAAATTCAACTTAAAATCAAT
* * * * * ** * *
685 TTTGACATTATAAAACCATTTAAAGCGAGTAATAAGGCTTAT-ACAGGAATAAGTGACCACAAAT
1 TATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGA-AGGAATAGGAAACTATAAAT
* *** * * * **
749 GGACTTTGCTTGCCAATGAATATGTTTTTCTTCATGTTTTTCAAGGTAGACATTCAATAATTCTC
65 GGACTTTTCTTGCCAATGAATGCCTTTTTCTTCACGTTTCTCAAGGTAGACATTCAATTATAATC
* *
814 TGTTTTAACTAAAAATATAAAAAAAATT-GACTTAAAATCAAT
130 TGTTTTAACCAAAAATAT-AAAAAAATTCAACTTAAAATCAAT
* * * *
856 TATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAAGAAT-GAGAGACTATAAAT
1 TATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAG-GAAACTATAAAT
* * * * ** * * * ** * *
920 GAACTTTTCTTACCAACGAAAGGTTTTTTCTACACGTCTCTCGAGACA-AGCATTTAATTATAGT
65 GGACTTTTCTTGCCAATGAATGCCTTTTTCTTCACGTTTCTCAAGGTAGA-CATTCAATTATAAT
* * *
984 CTATTTTAA-TAAAAATATAAAAAAATACAACTTAAAATCAAT
129 CTGTTTTAACCAAAAATATAAAAAAATTCAACTTAAAATCAAT
* * *
1026 TATCAGATTATAAAATTATTTAAAGTGAGTAATAAGGCTTTTG
1 TATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTG
Statistics
Matches: 733, Mismatches: 143, Indels: 42
0.80 0.16 0.05
Matches are distributed among these distances:
168 3 0.00
169 42 0.06
170 251 0.34
171 182 0.25
172 252 0.34
173 3 0.00
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (171 bp):
TATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGAAACTATAAATG
GACTTTTCTTGCCAATGAATGCCTTTTTCTTCACGTTTCTCAAGGTAGACATTCAATTATAATCT
GTTTTAACCAAAAATATAAAAAAATTCAACTTAAAATCAAT
Found at i:425 original size:170 final size:169
Alignment explanation
Indices: 1--1068 Score: 983
Period size: 170 Copynumber: 6.3 Consensus size: 169
* * *
1 TATGAGATTATAAAACTATTTAAAGGGAGTAATAAGGCTTTTGAAGGAATGGGTAACTAGAAATG
1 TATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGATAACTATAAATG
* * *
66 GAGTTTTCTTGTCAATGAATGCCTTTTTCTTCACATTTCTCAAGGTAGACATTCAATTATAATCT
66 GACTTTTCTT-CCAATGAATGCCTTTTTCTTCACGTTTCTCAAGGTAGACATTCAATTATAA-CT
* * *
131 GTTTTAACCAATAATATAAAAAAAATTGAACCTAAAATCAAT
129 GTTTTAACCAAAAATAT-AAAAAAATTCAACTTAAAATCAAT
* * *
173 TTTGAGATTATAAAACTATTTAAAGCGAGTAACAAAGCTTTTGAAGGAATAGGA-AACTATAAAT
1 TATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAAT-GGATAACTATAAAT
** * * * * * *
237 TAACTTTTCTTGCCAATGAATTCTTTTTTCCTCACGTTTCTCGATGTAGACATTCAATTAT-AGT
65 GGACTTTTCTT-CCAATGAATGCCTTTTTCTTCACGTTTCTCAAGGTAGACATTCAATTATAACT
* *
301 GTATTTGACCAAAAATATAAACAAATTCAACTTAAAATCAAT
129 GT-TTTAACCAAAAATATAAAAAAATTCAACTTAAAATCAAT
* ** * * *
343 CATGAGATTATAAAACTATTTAAAGTTAGTAATAAGGCCTTT-AAGGAATGGATGATTATAAATG
1 TATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGATAACTATAAATG
* * *
407 GACTTTTTTTTACCAATGAATGCCTTTGTCTTCACGTTTCTCAA-ATAGACATTCAATTATAATC
66 GAC-TTTTCTT-CCAATGAATGCCTTTTTCTTCACGTTTCTCAAGGTAGACATTCAATTATAA-C
* * * *
471 TGTTTTAACCAGAAATGA-AAAAAATTTTAACTTAAAATTAAT
128 TGTTTTAACCAAAAAT-ATAAAAAAATTCAACTTAAAATCAAT
* * * * * *
513 TATGAGATTATAAAACCATTTAAAGAGAGCAATAAAGCTTTTGAAAGAATAGG-TAACTACAAAT
1 TATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAAT-GGATAACTATAAAT
** ** * *
577 GGACTTTTCTTCCTAGCGAATGCCTTTTGGTTCATGTTTCTCAAGGTA-AGCATTCAATTGTAAT
65 GGACTTTTCTTCC-AATGAATGCCTTTTTCTTCACGTTTCTCAAGGTAGA-CATTCAATTATAA-
* * * * * *
641 ATGTTTTTACCAAAAATGTTAAAAAATTTAAACTAAAAATCAAT
127 CTGTTTTAACCAAAAAT-ATAAAAAAATTCAACTTAAAATCAAT
* * * * * * * *
685 TTTGACATTATAAAACCATTTAAAGCGAGTAATAAGGCTTAT-ACAGGAAT-AAGTGACCACAAA
1 TATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGA-AGGAATGGA-TAACTATAAA
* *** * * * **
748 TGGACTTTGCTTGCCAATGAATATGTTTTTCTTCATGTTTTTCAAGGTAGACATTCAATAATTCT
64 TGGACTTTTCTT-CCAATGAATGCCTTTTTCTTCACGTTTCTCAAGGTAGACATTCAATTA-TAA
* *
813 CTGTTTTAACTAAAAATATAAAAAAAATT-GACTTAAAATCAAT
127 CTGTTTTAACCAAAAATAT-AAAAAAATTCAACTTAAAATCAAT
* * * *
856 TATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAAGAATGAGA-GACTATAAAT
1 TATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATG-GATAACTATAAAT
* * * ** * * * ** * *
920 GAACTTTTCTTACCAACGAAAGGTTTTTTCTACACGTCTCTCGAGACA-AGCATTTAATTATAGT
65 GGACTTTTCTT-CCAATGAATGCCTTTTTCTTCACGTTTCTCAAGGTAGA-CATTCAATTATA-A
* * *
984 CTATTTTAA-TAAAAATATAAAAAAATACAACTTAAAATCAAT
127 CTGTTTTAACCAAAAATATAAAAAAATTCAACTTAAAATCAAT
* * *
1026 TATCAGATTATAAAATTATTTAAAGTGAGTAATAAGGCTTTTG
1 TATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTG
Statistics
Matches: 731, Mismatches: 139, Indels: 54
0.79 0.15 0.06
Matches are distributed among these distances:
168 3 0.00
169 42 0.06
170 252 0.34
171 181 0.25
172 246 0.34
173 7 0.01
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (169 bp):
TATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGATAACTATAAATG
GACTTTTCTTCCAATGAATGCCTTTTTCTTCACGTTTCTCAAGGTAGACATTCAATTATAACTGT
TTTAACCAAAAATATAAAAAAATTCAACTTAAAATCAAT
Done.