Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401323.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4461.0, 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, 647
Length: 1079
ACGTcount: A:0.30, C:0.09, G:0.10, T:0.28
Warning! 248 characters in sequence are not A, C, G, or T
Found at i:283 original size:170 final size:170
Alignment explanation
Indices: 1--352 Score: 394
Period size: 170 Copynumber: 2.1 Consensus size: 170
* * * * *
1 TATAAAACCATTTATAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAATGGATTTTTCT
1 TATAAAACCATTTAAAATGAGTAACAAGGCTTTTGAAAGAATGGGTAACTATAATGGATTTTTCT
* * * * * *** *
66 TGTCAATGAATATGTTTTTTTTCATGTTTCTTGAGATAGACATTCAATTACTA-TCTGTTTTAAC
66 TCTCAATGAATATGCTTTTCTACACGTTTCCCAAGATAGACATTCAATTA-TAGTCTATTTTAA-
* ** *
130 T-AAAAATGTAAAAAAATTCAACTTCAAATCAATTATGGGAT
129 TGAAAAATATAAAAAAATTCAACTAAAAATCAATTATGAGAT
*
171 TATAAAACTATTTAAAATGAGTAACAAGGCTTTTGAAAGAATGGGTAACTATAAATGGATTTTT-
1 TATAAAACCATTTAAAATGAGTAACAAGGCTTTTGAAAGAATGGGTAACTAT-AATGGATTTTTC
*
235 TTCTCAAT-AA-ATGACCTTTTCTACACGTTTCCCAAGGCA-AG-CATTCAATTATAGTTTATTT
65 TTCTCAATGAATATG--CTTTTCTACACGTTTCCCAA-G-ATAGACATTCAATTATAGTCTATTT
* *
296 TAATGAAAAATATAAAGAAATTCAACTAAAAATTAATTATGAGAT
126 TAATGAAAAATATAAAAAAATTCAACTAAAAATCAATTATGAGAT
341 TATAAAACCATT
1 TATAAAACCATT
353 NNNNNNNNNN
Statistics
Matches: 152, Mismatches: 23, Indels: 14
0.80 0.12 0.07
Matches are distributed among these distances:
168 3 0.02
169 5 0.03
170 129 0.85
171 14 0.09
172 1 0.01
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (170 bp):
TATAAAACCATTTAAAATGAGTAACAAGGCTTTTGAAAGAATGGGTAACTATAATGGATTTTTCT
TCTCAATGAATATGCTTTTCTACACGTTTCCCAAGATAGACATTCAATTATAGTCTATTTTAATG
AAAAATATAAAAAAATTCAACTAAAAATCAATTATGAGAT
Found at i:883 original size:171 final size:161
Alignment explanation
Indices: 591--916 Score: 325
Period size: 171 Copynumber: 2.0 Consensus size: 161
581 NNNNNNNNNN
* *
591 TTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTAAAGAAATGAGTCACTATAAAT
1 TTATGAGATTATAAAACCATTTAAAGCAACTAATAAGGCTTTTAAAGAAATGAGTCACTATAAAT
* ** * * * * * * *
656 GGACTTTTCTTCTAAATGAATGACTTTTTCTACACTTTTTTTTAGGCAGGCATTCAATTATAGTC
66 GAACTTTTCTTAGAAATGAAAGACTTTTTCTACACTGTTTCTCAAGCAGACATTCAATTATAATC
*
721 TATTTTAACAAA-AAATATAAAAAAATTCNNNNNNNNNNCAA
131 TATTGTAA-AAACAAATATAAAAAAATTC----------CAA
* * * * *
762 TTATGAGATTATAAAACCATTTAAAGTAACTAATAAGGCTTTTGAAGGAATGGGTGACTATAAAT
1 TTATGAGATTATAAAACCATTTAAAGCAACTAATAAGGCTTTTAAAGAAATGAGTCACTATAAAT
* * *
827 GAAAC-TTTCTTAGCAATGAAAGCCTTTTTCTTCA-TGTTTCTCAAGCTAGACATTCAATTATAA
66 G-AACTTTTCTTAGAAATGAAAGACTTTTTCTACACTGTTTCTCAAGC-AGACATTCAATTATAA
890 TCTATTGTAAAAACAAATATAAAAAAA
129 TCTATTGTAAAAACAAATATAAAAAAA
917 ATTAAATTTA
Statistics
Matches: 131, Mismatches: 21, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
170 11 0.08
171 118 0.90
172 2 0.02
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.34
Consensus pattern (161 bp):
TTATGAGATTATAAAACCATTTAAAGCAACTAATAAGGCTTTTAAAGAAATGAGTCACTATAAAT
GAACTTTTCTTAGAAATGAAAGACTTTTTCTACACTGTTTCTCAAGCAGACATTCAATTATAATC
TATTGTAAAAACAAATATAAAAAAATTCCAA
Done.