Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398973.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2255.0, 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: 6623
ACGTcount: A:0.18, C:0.06, G:0.06, T:0.17
Warning! 3461 characters in sequence are not A, C, G, or T
Found at i:6330 original size:171 final size:160
Alignment explanation
Indices: 5973--6621 Score: 432
Period size: 171 Copynumber: 3.8 Consensus size: 160
5963 NNNNNNNNNN
* * * * *
5973 CATTTAAGGCAAGTAATAAGGCTTTCGAAGGCATGGGTGACTCTAAGTGGACTTTTCTTGTCAAT
1 CATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGAC-TTTCTTGCCAAT
* * ** * * * * * *
6038 GGATATC-ATTTCTTTATGTTTTTTTGAGGCAGACAATCAATTATAATCTATTTTAATAAAATAT
65 -GATATCTTTTTCTTCA-CATTTTCTGATGTAGACATTCAATTATAATCTGTTTTAATAAAAAAT
* * * *
6102 GTTAAAAAGTTTAACTTAAAACTAATTATGNNNNNNNNNNAC
128 ATAAAAAAGTTCAACTTAAAACTAATTATG---------AAC
* * * ** *
6144 TATTTCAAGCGAGTAATAAGGCTTTCGAAGACATGGGTGACTATAAAAAGACCTTTCTTGCCCAT
1 CATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGA-CTTTCTTGCCAAT
* *
6209 GCATATCTTTTTCTTCACATTTTCTGATGTAGACATTCAATTATAATCTGTTTTAAAAAAAAATG
65 G-ATATCTTTTTCTTCACATTTTCTGATGTAGACATTCAATTATAATCTGTTTTAATAAAAAATA
* **
6274 TAAAGAAA-TTTAACTTAAAA-TCAATTATGANNNNNNNNNNT
129 TAAA-AAAGTTCAACTTAAAACT-AATTATGA---------AC
** * *
6315 CATTTAATTCGAGTAATAAGGCTTTTGAAGGCATGGGAT-ACTATAAATGGACTTCTGTTGCCAA
1 CATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGG-TGACTATAAATGGACTT-TCTTGCCAA
* * * * * *
6379 TAGATATCATTTTCTT--TATGTTTCTTGAGGCAAACATTCAATAATAATCTGTTTTAATAAAAA
64 T-GATATCTTTTTCTTCACAT-TTTC-TGATGTAGACATTCAATTATAATCTGTTTTAATAAAAA
*
6442 ATATAAAAAAGTTCAACTTAAAACTAATTATGNNNNNNNNNNAC
126 ATATAAAAAAGTTCAACTTAAAACTAATTATG---------AAC
* * *
6486 CATTTAAAGCGAGTAATAAGGCTTTCGAAGGTATGAGTGACTATAAATGGAATTTTCTTGCCAAT
1 CATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGG-ACTTTCTTGCCAAT
* * * *
6551 GGATATCTTTTTCTTCACA-TTTCTCAATATAGATATTCAATTATAATCTATTTTAAT-AAAAAT
65 -GATATCTTTTTCTTCACATTTTCT-GATGTAGACATTCAATTATAATCTGTTTTAATAAAAAAT
6614 ATAAAAAA
128 ATAAAAAA
6622 TT
Statistics
Matches: 377, Mismatches: 66, Indels: 71
0.73 0.13 0.14
Matches are distributed among these distances:
169 2 0.01
170 28 0.07
171 329 0.87
172 17 0.05
173 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.35
Consensus pattern (160 bp):
CATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTCTTGCCAATG
ATATCTTTTTCTTCACATTTTCTGATGTAGACATTCAATTATAATCTGTTTTAATAAAAAATATA
AAAAAGTTCAACTTAAAACTAATTATGAAC
Found at i:6598 original size:342 final size:322
Alignment explanation
Indices: 5984--6612 Score: 652
Period size: 342 Copynumber: 1.9 Consensus size: 322
5974 ATTTAAGGCA
* * * * *
5984 AGTAATAAGGCTTTCGAAGGCATGGGTGACTCTAAGTGGACTTTTCTTGTCAATGGATATCATTT
1 AGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTCTCTTGCCAATAGATATCATTT
* * * * * * *
6049 CTTTATGTTTTTTTGAGGCAGACAATCAATTATAATCTATTTTAATAAAATATGTTAAAAAGTTT
66 CTTTATGTTTTCTTGAGGCAAACAATCAATAATAATCTATTTTAATAAAAAATATAAAAAAGTTC
* *
6114 AACTTAAAACTAATTATGNNNNNNNNNNACTATTTCAAGCGAGTAATAAGGCTTTCGAAGACATG
131 AACTTAAAACTAATTATG----------ACCATTTAAAGCGAGTAATAAGGCTTTCGAAGACATG
* * * * *
6179 GGTGACTATAAAAAGACCTTTCTTGCCCATGCATATCTTTTTCTTCACATTTTCTGATGTAGACA
186 AGTGACTATAAAAAGAACTTTCTTGCCAATGCATATCTTTTTCTTCACATTTTCTAATATAGACA
*
6244 TTCAATTATAATCTGTTTTAAAAAAAAATGTAAAGAAATTTAACTTAAAATCAATTATGANNNNN
251 TTCAATTATAATCTATTTTAAAAAAAAATGTAAAGAAATTTAACTTAAAATCAATTATGA-----
6309 NNNNNTCATTTAATTCG
311 -----TCATTTAATTCG
* *
6326 AGTAATAAGGCTTTTGAAGGCATGGGAT-ACTATAAATGGACTTCTGTTGCCAATAGATATCATT
1 AGTAATAAGGCTTTCGAAGGCATGGG-TGACTATAAATGGACTTCTCTTGCCAATAGATATCA-T
* *
6390 TTCTTTATG-TTTCTTGAGGCAAACATTCAATAATAATCTGTTTTAATAAAAAATATAAAAAAGT
64 TTCTTTATGTTTTCTTGAGGCAAACAATCAATAATAATCTATTTTAATAAAAAATATAAAAAAGT
**
6454 TCAACTTAAAACTAATTATGNNNNNNNNNNACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGTA
129 TCAACTTAAAACTAATTATG----------ACCATTTAAAGCGAGTAATAAGGCTTTCGAAGACA
** * *
6519 TGAGTGACTATAAATGGAATTTTCTTGCCAATGGATATCTTTTTCTTCACA-TTTCTCAATATAG
184 TGAGTGACTATAAAAAGAACTTTCTTGCCAATGCATATCTTTTTCTTCACATTTTCT-AATATAG
* *
6583 ATATTCAATTATAATCTATTTTAATAAAAA
248 ACATTCAATTATAATCTATTTTAAAAAAAA
6613 TATAAAAAAT
Statistics
Matches: 252, Mismatches: 32, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
341 5 0.02
342 236 0.94
343 11 0.04
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.35
Consensus pattern (322 bp):
AGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTCTCTTGCCAATAGATATCATTT
CTTTATGTTTTCTTGAGGCAAACAATCAATAATAATCTATTTTAATAAAAAATATAAAAAAGTTC
AACTTAAAACTAATTATGACCATTTAAAGCGAGTAATAAGGCTTTCGAAGACATGAGTGACTATA
AAAAGAACTTTCTTGCCAATGCATATCTTTTTCTTCACATTTTCTAATATAGACATTCAATTATA
ATCTATTTTAAAAAAAAATGTAAAGAAATTTAACTTAAAATCAATTATGATCATTTAATTCG
Done.