Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400209.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3420.1, 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: 2080
ACGTcount: A:0.29, C:0.10, G:0.11, T:0.27
Warning! 461 characters in sequence are not A, C, G, or T
Found at i:447 original size:170 final size:169
Alignment explanation
Indices: 14--780 Score: 631
Period size: 170 Copynumber: 4.5 Consensus size: 169
4 TTTTGTTACA
* **
14 TTTCTCGAGGTAGACATTTAATTATAGTCTATTTAACTAAAAATATAAAAAAATTCAACTTAAAA
1 TTTCTCGAGGTAGACATTCAATTATAGTCT-TTTAACTAAAAATATCGAAAAATTCAACTTAAAA
* *
79 TCAATTACGGCATTACAAAACCATTTAGAGCGAGTAATAAGGCTTTTGAATGTATGGGTGACTA-
65 TCAATTATGGCATTACAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAATGTATGGGTGACTAT
* ** *
143 AAATGGACCTTTCTTGCCAATGAATGTTTTTTTCTTCATG
130 AAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCACG
* * * * *
183 TTTCTCAAGGTAG-CATTCAATTCTAGTCTATTTTAACTAAAAATGCA-CGAAGAATTCAAATTT
1 TTTCTCGAGGTAGACATTCAATTATAGTC--TTTTAACTAAAAAT--ATCGAAAAATTCAACTTA
* * * * ** ** * * *
246 AAATCGATTTTAAG-ATTATAAAAATATTTAAAGTAAGTAATAAGGTTTTTGAAGGAATGGGTGA
62 AAATCAATTAT-GGCATTACAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAATGTATGGGTGA
310 CTATAAATGGACTTTTCTTAG-CAATGAATGCCTTTTTCTAT-ACG
126 CTATAAATGGACTTTTCTT-GCCAATGAATGCCTTTTTCT-TCACG
* * *
354 TTTTTTGAGGTAGACATTCAATTATAGTCTTTT-ACATAAAAAATATCGAAAAATTGAACTTAAA
1 TTTCTCGAGGTAGACATTCAATTATAGTCTTTTAAC-T-AAAAATATCGAAAAATTCAACTTAAA
* * * * * *
418 ATAAATTATGGCATTACAAAACGATTTAAAGCGAGTAATACGGCTTTTAAATGTATAGGCGACTA
64 ATCAATTATGGCATTACAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAATGTATGGGTGACTA
* * * *
483 TAAATGGACTTTTCTTGCCAATAAATGCATTTATCTTCATG
129 TAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCACG
* * * * * *
524 ATTCTCAAGGTAGACATTCAATTCA-AGCCTATTTTAACCAAAAATGTAC-AAAGAATTCAAATT
1 TTTCTCGAGGTAGACATTCAATT-ATAG--TCTTTTAACTAAAAATAT-CGAAA-AATTCAACTT
* * * * * ** * * * * *
587 CAAATCAATTTTGAG-ATTATAACATC-TTTTGAGCTGAGTAAAAAGGCTCTTGAAGGAATGCGT
61 AAAATCAATTATG-GCATTACAAAACCATTTAAAGC-GAGTAATAAGGCTTTTGAATGTATGGGT
* * * *
650 CACTATAAATGGACTTTTCTTGCCCATGAATGCCTTTCTCTTTACG
124 GACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCACG
* ** * * * * * * **
696 TTTC-AGAATATAGATATTGAATTAAAGTCTATTTTAACCAAAATTGTAAAAAAATTCAACTTAA
1 TTTCTCG-AGGTAGACATTCAATTATAGTC--TTTTAACTAAAAATATCGAAAAATTCAACTTAA
760 AATCAATTATGGCATTACAAA
63 AATCAATTATGGCATTACAAA
781 NNNNNNNNNN
Statistics
Matches: 467, Mismatches: 102, Indels: 56
0.75 0.16 0.09
Matches are distributed among these distances:
168 13 0.03
169 31 0.07
170 186 0.40
171 94 0.20
172 140 0.30
173 3 0.01
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (169 bp):
TTTCTCGAGGTAGACATTCAATTATAGTCTTTTAACTAAAAATATCGAAAAATTCAACTTAAAAT
CAATTATGGCATTACAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAATGTATGGGTGACTATA
AATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCACG
Found at i:681 original size:342 final size:340
Alignment explanation
Indices: 20--780 Score: 956
Period size: 342 Copynumber: 2.2 Consensus size: 340
10 TACATTTCTC
* *
20 GAGGTAGACATTTAATTATAGTCTATTTAACTAAAAATATAAAAAAATTCAACTTAAAATCAATT
1 GAGGTAGACATTCAATTATAGTCTATTTAACTAAAAATATAAAAAAATTCAACTTAAAATAAATT
* * * *
85 ACGGCATTACAAAACCATTTAGAGCGAGTAATAAGGCTTTTGAATGTATGGGTGACTAAAATGGA
66 ACGGCATTACAAAACCATTTAAAGCGAGTAATAAGGCTTTTAAATGTATAGGCGACTAAAATGGA
* ** * * * *
150 CCTTTCTTGCCAATGAATGTTTTTTTCTTCATGTTTCTCAAGGTAGCATTCAATTCTAGTCTATT
131 CCTTTCTTGCCAATAAATGCATTTATCTTCATGATTCTCAAGGTAGCATTCAATTCAAGCCTATT
* * * *
215 TTAACTAAAAATGCACGAAGAATTCAAATTTAAATCGATTTTAAGATTATAAAAATATTTAAAGT
196 TTAACCAAAAATGCACAAAGAATTCAAATTCAAATCAATTTTAAGATTATAAAAATATTTAAAGT
* * * * *
280 AAGTAATAAGGTTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTAGCAATGAATGCCTTT
261 AAGTAAAAAGGCTCTTGAAGGAATGCGTCACTATAAATGGACTTTTCTTAGCAATGAATGCCTTT
*
345 TTCTATACGTTTTTT
326 CTCTATACGTTTTTT
** *
360 GAGGTAGACATTCAATTATAGTCT-TTT-ACATAAAAAATATCGAAAAATTGAACTTAAAATAAA
1 GAGGTAGACATTCAATTATAGTCTATTTAAC-T-AAAAATATAAAAAAATTCAACTTAAAATAAA
* * *
423 TTATGGCATTACAAAACGATTTAAAGCGAGTAATACGGCTTTTAAATGTATAGGCGACTATAAAT
64 TTACGGCATTACAAAACCATTTAAAGCGAGTAATAAGGCTTTTAAATGTATAGGCGACTA-AAAT
*
488 GGACTTTTCTTGCCAATAAATGCATTTATCTTCATGATTCTCAAGGTAGACATTCAATTCAAGCC
128 GGACCTTTCTTGCCAATAAATGCATTTATCTTCATGATTCTCAAGGTAG-CATTCAATTCAAGCC
* * * * *
553 TATTTTAACCAAAAATGTACAAAGAATTCAAATTCAAATCAATTTTGAGATTAT-AACATCTTTT
192 TATTTTAACCAAAAATGCACAAAGAATTCAAATTCAAATCAATTTTAAGATTATAAAAATATTTA
* * *
617 GAGCTGAGTAAAAAGGCTCTTGAAGGAATGCGTCACTATAAATGGACTTTTCTT-GCCCATGAAT
257 AAG-TAAGTAAAAAGGCTCTTGAAGGAATGCGTCACTATAAATGGACTTTTCTTAG-CAATGAAT
* **
681 GCCTTTCTCTTTACG-TTTCA
320 GCCTTTCTCTATACGTTTTTT
** * * * * * * *
701 GAATATAGATATTGAATTAAAGTCTATTTTAACCAAAATTGTAAAAAAATTCAACTTAAAATCAA
1 G-AGGTAGACATTCAATTATAGTCTA-TTTAACTAAAAATATAAAAAAATTCAACTTAAAATAAA
*
766 TTATGGCATTACAAA
64 TTACGGCATTACAAA
781 NNNNNNNNNN
Statistics
Matches: 358, Mismatches: 53, Indels: 17
0.84 0.12 0.04
Matches are distributed among these distances:
338 2 0.01
339 4 0.01
340 103 0.29
341 61 0.17
342 143 0.40
343 40 0.11
344 3 0.01
345 2 0.01
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (340 bp):
GAGGTAGACATTCAATTATAGTCTATTTAACTAAAAATATAAAAAAATTCAACTTAAAATAAATT
ACGGCATTACAAAACCATTTAAAGCGAGTAATAAGGCTTTTAAATGTATAGGCGACTAAAATGGA
CCTTTCTTGCCAATAAATGCATTTATCTTCATGATTCTCAAGGTAGCATTCAATTCAAGCCTATT
TTAACCAAAAATGCACAAAGAATTCAAATTCAAATCAATTTTAAGATTATAAAAATATTTAAAGT
AAGTAAAAAGGCTCTTGAAGGAATGCGTCACTATAAATGGACTTTTCTTAGCAATGAATGCCTTT
CTCTATACGTTTTTT
Done.