Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400200.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3413.0, 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: 5847
ACGTcount: A:0.22, C:0.08, G:0.08, T:0.22
Warning! 2402 characters in sequence are not A, C, G, or T
Found at i:4127 original size:171 final size:171
Alignment explanation
Indices: 3659--4605 Score: 1012
Period size: 171 Copynumber: 5.5 Consensus size: 171
3649 NNNNNNNNNN
** ** * *
3659 TCAATTATAGTCTGTTTTAATTAAAAATGCT-AAAAAATTTGACTTAAGATCAATTACGAGATTA
1 TCAATTATAGTCTGTTTTAACAAAAAATG-TAAAAAAATTCAACTTAAAATCAATTATGAGATTA
* * ** *
3723 TAAAATCATTTGAAGCGAGTAATATCGCTTTTGAAAGAATGGGTGACTATAAATGGGA-TTTTCC
65 TAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAAT-GGACTTTT-C
* * * * * * *
3787 TAG-CAATGAATGTCTT-TTTCTTCACGTCTATAGAGCTAAACAT
128 TTGCCAATGAATG-CTTGTTTCTTCATGTTTCTCGAGGTAGACAT
* * * * * * * *
3830 TCAATTATAATTTGTTTTAACCAATAATGTAAAAACAATTGAACTTAAAATCAATTTTAAGACTA
1 TCAATTATAGTCTGTTTTAACAAAAAATGTAAAAA-AATTCAACTTAAAATCAATTATGAGATTA
* * *
3895 TAAAACCATTTAAAACGAGTAATAAGGCTTTTGAAGGAATAGGAGACTATAAATGGACTTTTCTT
65 TAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTT
* * * *
3960 GTCAATGAATGCTTGTTTCTTCACGTTGCTCGAGGTAGAGAT
130 GCCAATGAATGCTTGTTTCTTCATGTTTCTCGAGGTAGACAT
*
4002 TCAATTATAGTCTGTTTTAACAAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTAC
1 TCAATTATAGTCTGTTTTAACAAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTAT
* * * *
4067 AAAACCATTTAAAGTGAGTAAGAAGGCTTTTTAAGGAATGGGTGACTATAAATAGACTTTTCTTG
66 AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTG
* * *
4132 CCAATGAATGCTTGTTTCTACATGTTTCT-GAAGAAGACAT
131 CCAATGAATGCTTGTTTCTTCATGTTTCTCGAGGTAGACAT
* * * *
4172 TCAATTATACTGTGTTTTAA-ACAAAAATAG-AAAAAAATTCAGCTTCAAATCAATTATGAGATT
1 TCAATTATAGTCTGTTTTAACA-AAAAAT-GTAAAAAAATTCAACTTAAAATCAATTATGAGATT
* * * ** * *
4235 ACAAAACCATTTAAAGTGAGCAATAAAACTTTTTAAGGAATAGGTGACTATAAATGGACTTTTCT
64 ATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCT
* *
4300 TGCCAATGAATGCTTGTTTCTTCATGTTTCTCAAGCTAGACAT
129 TGCCAATGAATGCTTGTTTCTTCATGTTTCTCGAGGTAGACAT
* * * ** * * * *
4343 TCAATTATAGTGTGTTTTAGCCAAAAATACAAAATAAGTCAACTTAAAATCAATTATTAGATCAT
1 TCAATTATAGTCTGTTTTAACAAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTAT
* ** * * * * *
4408 AAAATCATTTAAAGTAAGGAATAAGGCTTTTAAAAGAATGGGTGACTATAAGTAGACCTTTT-TT
66 AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGA-CTTTTCTT
* * * *
4472 GCCAATGAATGCGTT-TTTCTTTATGTTTCTCGAGGGAAACAG
130 GCCAATGAATGC-TTGTTTCTTCATGTTTCTCGAGGTAGACAT
* * * * * *
4514 TCAATTATAGTCTGTTTTAACAAAAAATATAAAACAATTCTACCTAAAAACGATTATGAGATTAT
1 TCAATTATAGTCTGTTTTAACAAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTAT
*
4579 AAAATCATTTAAAGCGAGTAATAAGGC
66 AAAACCATTTAAAGCGAGTAATAAGGC
4606 NNNNNNNNNN
Statistics
Matches: 656, Mismatches: 108, Indels: 24
0.83 0.14 0.03
Matches are distributed among these distances:
169 1 0.00
170 153 0.23
171 363 0.55
172 139 0.21
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (171 bp):
TCAATTATAGTCTGTTTTAACAAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTAT
AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTG
CCAATGAATGCTTGTTTCTTCATGTTTCTCGAGGTAGACAT
Found at i:4347 original size:341 final size:339
Alignment explanation
Indices: 3659--4602 Score: 1067
Period size: 341 Copynumber: 2.8 Consensus size: 339
3649 NNNNNNNNNN
** ** * *
3659 TCAATTATAGTCTGTTTTAATTAAAAATGCT-AAAAAATTTGACTTAAGATCAATTACGAGATTA
1 TCAATTATAGTCTGTTTTAACAAAAAATG-TAAAAAAATTCAACTTAAAATCAATTATGAGATTA
* * ** * *
3723 TAAAATCATTTGAAGCGAGTAATATCGCTTTTGAAAGAATGGGTGACTATAAATGGGA-TTTTCC
65 TAAAATCATTTAAAGTGAGTAATAAGGCTTTTAAAAGAATGGGTGACTATAAAT-AGACTTTT-C
* * * * *
3787 TAG-CAATGAATGTCTTTTTCTTCACGTCTAT-AGAGCTAAACATTCAATTATAATTTGTTTTAA
128 TTGCCAATGAATG-CTTTTTCTTCATGTTTCTGAGAG--AAACATTCAATTATAATCTGTTTTAA
* * * * * * *
3850 CCAATAAT-GTAAAAACAATTGAACTTAAAATCAATTTTAAGACTATAAAACCATTTAAAACGAG
190 ACAAAAATAG-AAAAA-AATT-CACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAG
** *
3914 TAATAAGGCTTTTGAAGGAATAGGAGACTATAAATGGACTTTTCTTGTCAATGAATGCTTGTTTC
252 TAATAAAACTTTTGAAGGAATAGGAGACTATAAATGGACTTTTCTTGCCAATGAATGCTTGTTTC
* * *
3979 TTCACGTTGCTCGAGGTAGAGAT
317 TTCACGTTGCTCAAGCTAGACAT
*
4002 TCAATTATAGTCTGTTTTAACAAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTAC
1 TCAATTATAGTCTGTTTTAACAAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTAT
* * * *
4067 AAAACCATTTAAAGTGAGTAAGAAGGCTTTTTAAGGAATGGGTGACTATAAATAGACTTTTCTTG
66 AAAATCATTTAAAGTGAGTAATAAGGCTTTTAAAAGAATGGGTGACTATAAATAGACTTTTCTTG
* * *
4132 CCAATGAATGCTTGTTTCTACATGTTTCTGA-AGAAGACATTCAATTATACTGTGTTTTAAACAA
131 CCAATGAATGCTT-TTTCTTCATGTTTCTGAGAGAA-ACATTCAATTATAATCTGTTTTAAACAA
* * * *
4196 AAATAGAAAAAAATTCAGCTTCAAATCAATTATGAGATTACAAAACCATTTAAAGTGAGCAATAA
194 AAATAGAAAAAAATTCA-CTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAA
* * *
4261 AACTTTTTAAGGAATAGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCTTGTTTCTTCATG
258 AACTTTTGAAGGAATAGGAGACTATAAATGGACTTTTCTTGCCAATGAATGCTTGTTTCTTCACG
*
4326 TTTCTCAAGCTAGACAT
323 TTGCTCAAGCTAGACAT
* * * ** * * * *
4343 TCAATTATAGTGTGTTTTAGCCAAAAATACAAAATAAGTCAACTTAAAATCAATTATTAGATCAT
1 TCAATTATAGTCTGTTTTAACAAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTAT
* * *
4408 AAAATCATTTAAAGTAAGGAATAAGGCTTTTAAAAGAATGGGTGACTATAAGTAGACCTTTT-TT
66 AAAATCATTTAAAGTGAGTAATAAGGCTTTTAAAAGAATGGGTGACTATAAATAGA-CTTTTCTT
* * * *
4472 GCCAATGAATGCGTTTTTCTTTATGTTTCTCGAGGGAAACAGTCAATTATAGTCTGTTTT-AACA
130 GCCAATGAATGC-TTTTTCTTCATGTTTCT-GAGAGAAACATTCAATTATAATCTGTTTTAAAC-
* * * * * *
4536 AAAAATATAAAACAATTCTACCTAAAAACGATTATGAGATTATAAAATCATTTAAAGCGAGTAAT
192 AAAAATAGAAAAAAATTC-ACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAAT
4601 AA
256 AA
4603 GGCNNNNNNN
Statistics
Matches: 510, Mismatches: 77, Indels: 29
0.83 0.12 0.05
Matches are distributed among these distances:
340 1 0.00
341 251 0.49
342 125 0.25
343 132 0.26
344 1 0.00
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (339 bp):
TCAATTATAGTCTGTTTTAACAAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTAT
AAAATCATTTAAAGTGAGTAATAAGGCTTTTAAAAGAATGGGTGACTATAAATAGACTTTTCTTG
CCAATGAATGCTTTTTCTTCATGTTTCTGAGAGAAACATTCAATTATAATCTGTTTTAAACAAAA
ATAGAAAAAAATTCACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAAAC
TTTTGAAGGAATAGGAGACTATAAATGGACTTTTCTTGCCAATGAATGCTTGTTTCTTCACGTTG
CTCAAGCTAGACAT
Done.