Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399711.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2957.0, 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: 1809
ACGTcount: A:0.29, C:0.09, G:0.10, T:0.28
Warning! 447 characters in sequence are not A, C, G, or T
Found at i:1120 original size:171 final size:168
Alignment explanation
Indices: 820--1806 Score: 1000
Period size: 171 Copynumber: 5.8 Consensus size: 168
810 TTAAAACTAT
* * * *
820 GGAATGGGTGACTTTAAATGGACTTTTCTTGTCAATGAATG-CTTGTTTCTTCACGTTTCTTGAG
1 GGAATGAGTGACTCTAAATGGACTTTTCTTCTCAATGAATGACTT-TTTCTACACGTTTCTTGAG
* * *
884 GTAGACATTCAATTATAGTATGTTTTAATAAAAAATGTAAAGAAATTCTACTTAAAATCAATTAT
65 GTAGACATTCAATTATAGTATGTTTTAA-AAAAAATATAAAAAAATTC-AATTAAAATCAATTAT
949 GAGATTATAAAACCATTTAAAGCGAGTAATAAGCTTTTTGAA
128 GAGATTATAAAACCATTTAAAGCGAGTAATAAGC-TTTTGAA
* * * * *
991 GGAGTGGGTGACTCTAAATGGACTTTTCTTCTCAATCAATGACTTTTTCTACATGTTTCTTGAGT
1 GGAATGAGTGACTCTAAATGGACTTTTCTTCTCAATGAATGACTTTTTCTACACGTTTCTTGAGG
** * *
1056 TAGACATTCAATTATTTTCTGTTTTAAAGAAAAATATAAAAAAATTCAATTAAAAATTAATTATG
66 TAGACATTCAATTATAGTATGTTTTAAA-AAAAATATAAAAAAATTCAATT-AAAATCAATTATG
**
1121 AGATTATAAAATGATTTAAA-CAGAGTAATAAGGCTTTTGAA
129 AGATTATAAAACCATTTAAAGC-GAGTAATAA-GCTTTTGAA
* ** ** * * * * *
1162 AGAATTCGTGACTAAAAATGGATTTTTCTTCTCAATGAATGGCTTTTTCAACACATTTCCTGAGG
1 GGAATGAGTGACTCTAAATGGACTTTTCTTCTCAATGAATGACTTTTTCTACACGTTTCTTGAGG
* ** * * * * * * *
1227 CAGGTATTTAATTATAATTTGTTTTTAAAAAAAATATTAAAAAATTTAATTTCAAATCAATTAGG
66 TAGACATTCAATTATAGTATG-TTTTAAAAAAAATATAAAAAAATTCAA-TTAAAATCAATTATG
1292 AGATTATAAAACCATTTAAAGCCG-GTAATAAGACTTTTGATA
129 AGATTATAAAACCATTTAAAG-CGAGTAATAAG-CTTTTGA-A
* * *
1334 -GAATGAGTGACTATAAATGGACTTTTCTTCTCAATGAAT-AGCTTTTTCTACATGTTTCCTGAG
1 GGAATGAGTGACTCTAAATGGACTTTTCTTCTCAATGAATGA-CTTTTTCTACACGTTTCTTGAG
* * * *
1397 GCACACAATCAATTATAGTCTGTTTTAACAAAAAATATAAAAAAATTCAACTTAAAATCAATTAT
65 GTAGACATTCAATTATAGTATGTTTTAA-AAAAAATATAAAAAAATTCAA-TTAAAATCAATTAT
* *
1462 GAGATTATAAAACTATTTTAAGCGAGTAATAAGCCTTTTGAA
128 GAGATTATAAAACCATTTAAAGCGAGTAATAAG-CTTTTGAA
** * * * * * * *
1504 GGAATGAGTGACTCTAAAAAGACTTTTTTTTATCAATGAATGCCTGTTTCTTCACGTTTCTTTAT
1 GGAATGAGTGACTCTAAATGGAC-TTTTCTTCTCAATGAATGACTTTTTCTACACGTTTCTTGAG
* * * * * *
1569 ATAGACATTCAGTTATAGTATGTTTTAATCAAAAATGTTAAACAATTCAACTTAAAATCAATTAT
65 GTAGACATTCAATTATAGTATGTTTTAA-AAAAAATATAAAAAAATTCAA-TTAAAATCAATTAT
* *
1634 GAGATTATAAAACCATTTAAAGTGAGTAATAAGCTTTTTAAA
128 GAGATTATAAAACCATTTAAAGCGAGTAATAAGC-TTTTGAA
* * * * **
1676 GGAA-CATGTGACTCTAAATGGACTTTTCTTGTCAATGAATG-CTTGTTTTTTC-CAGTTTCTCA
1 GGAATGA-GTGACTCTAAATGGACTTTTCTTCTCAATGAATGACTT-TTTCTACAC-GTTTCTTG
* * * * * *
1738 AAGTAGGCATTCAATTATAGTATGTTTTAATTAAAATTGTAAAACAATTCAACTTAAAATCAATT
63 AGGTAGACATTCAATTATAGTATGTTTTAA-AAAAAATATAAAAAAATTCAA-TTAAAATCAATT
1803 ATGA
126 ATGA
1807 AAT
Statistics
Matches: 685, Mismatches: 110, Indels: 42
0.82 0.13 0.05
Matches are distributed among these distances:
170 18 0.03
171 511 0.75
172 155 0.23
173 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (168 bp):
GGAATGAGTGACTCTAAATGGACTTTTCTTCTCAATGAATGACTTTTTCTACACGTTTCTTGAGG
TAGACATTCAATTATAGTATGTTTTAAAAAAAATATAAAAAAATTCAATTAAAATCAATTATGAG
ATTATAAAACCATTTAAAGCGAGTAATAAGCTTTTGAA
Done.