Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402360.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_544.0, 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: 4387
ACGTcount: A:0.22, C:0.08, G:0.07, T:0.24
Warning! 1738 characters in sequence are not A, C, G, or T
Found at i:291 original size:169 final size:169
Alignment explanation
Indices: 1--811 Score: 868
Period size: 170 Copynumber: 4.8 Consensus size: 169
* *
1 TAATCTCATAATTGATTTTACGTTGAATTTTTTTACATTTTTTGTTAAAATAGACTATAATTGAA
1 TAATCTCATAATTGATTTTAAGTTGAA-TTTTTTACATTTTTT-TTAAAACAGACTATAATTGAA
* * * * * * * *
66 TATCTACCTAGGGAAACGTGCAAAAAAAGTCATTCATTGAGAAGAAAAACTCATTTTTAATCACC
64 TGTCTATCTCGAGAAACATGCAGAAAAAGCCATTCATTGAGAAGAAAAATTCATTTTTAATCACC
*
131 CATTCTTTC-GAAGCCTTATTACTCGGTTTAAATGATTTTA
129 CATTCTTTCAAAAGCCTTATTACTCGGTTTAAATGATTTTA
* * * *
171 TAATCTCATAATTGATTTTAAGTTAAACTTTTTTATATATTTTTTAAAACAGACAATAATTGAAT
1 TAATCTCATAATTGATTTTAAGTTGAA-TTTTTTACATTTTTTTTAAAACAGACTATAATTGAAT
* * * * *
236 GTCTATCTCGAGAAACATGTAGAAAAAGACATTGATTGAGAAGAAAAGTTCA-TTTTAATCACCA
65 GTCTATCTCGAGAAACATGCAGAAAAAGCCATTCATTGAGAAGAAAAATTCATTTTTAATCACCC
* * **
300 ATTATTTCAAAAGTCTTATTACTCATTTTAAAT-AGTTTTA
130 ATTCTTTCAAAAGCCTTATTACTCGGTTTAAATGA-TTTTA
* * *
340 TAATCTTATAATTGATTTTAAATT-AAATTTTTACATTTTTTGTTAAAACAGACTATAATTGAAT
1 TAATCTCATAATTGATTTTAAGTTGAATTTTTTACATTTTTT-TTAAAACAGACTATAATTGAAT
* ** * * * * * * *
404 ATCTGCCTCGAGAAACATGCAAAAAAAGTCATTCATTAAGAAGAAAAAATCTATTTATAGTCACT
65 GTCTATCTCGAGAAACATGCAGAAAAAGCCATTCATTGAGAAGAAAAATTC-ATTTTTAATCACC
* * * * * *
469 CATTCCTTCAAAATCCTTATTACCCGCTTTAAATGGTTTTG
129 CATTCTTTCAAAAGCCTTATTACTCGGTTTAAATGATTTTA
* *
510 TAAT-TAATAATTGATTTTAAGTTGAATTTTTTACATTTTTCTTTAAAACAGACTATAATTGAAA
1 TAATCTCATAATTGATTTTAAGTTGAATTTTTTACATTTTT-TTTAAAACAGACTATAATTGAAT
* * * *
574 G-CT-TGC-CTTAGAAA-AGGTGTAGAAAAAGCCATTCATTGAGAAGAAAAATCCATTTTTATTC
65 GTCTAT-CTC-GAGAAACA--TGCAGAAAAAGCCATTCATTGAGAAGAAAAATTCATTTTTAATC
* * *
635 ACCCATTCTTTC-AAAGCCTTATTACTTGGTTTCAATGATTTAA
126 ACCCATTCTTTCAAAAGCCTTATTACTCGGTTTAAATGATTTTA
* * * *
678 TAATCTCATAATTGATTTTAAGTTGAAGTTTTTTACATTTTTCTTTGAAATAGACAATAATTAAA
1 TAATCTCATAATTGATTTTAAGTTGAA-TTTTTTACATTTTT-TTTAAAACAGACTATAATTGAA
* * * * * * *
743 TGTCTATCTTGAGAGACATGCAGAAAAAGCCATTGATTGAGAAGAAAAGTCCATTTATAGTCACC
64 TGTCTATCTCGAGAAACATGCAGAAAAAGCCATTCATTGAGAAGAAAAATTCATTTTTAATCACC
808 CATT
129 CATT
812 NNNNNNNNNN
Statistics
Matches: 531, Mismatches: 92, Indels: 36
0.81 0.14 0.05
Matches are distributed among these distances:
167 12 0.02
168 112 0.21
169 173 0.33
170 224 0.42
171 8 0.02
172 2 0.00
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (169 bp):
TAATCTCATAATTGATTTTAAGTTGAATTTTTTACATTTTTTTTAAAACAGACTATAATTGAATG
TCTATCTCGAGAAACATGCAGAAAAAGCCATTCATTGAGAAGAAAAATTCATTTTTAATCACCCA
TTCTTTCAAAAGCCTTATTACTCGGTTTAAATGATTTTA
Found at i:683 original size:338 final size:339
Alignment explanation
Indices: 1--811 Score: 962
Period size: 338 Copynumber: 2.4 Consensus size: 339
* *
1 TAATCTCATAATTGATTTTACGTTGAATTTTTTTACATTTTTTGTTAAAATAGACTATAATTGAA
1 TAATCTCATAATTGATTTTAAGTTGAAGTTTTTTACATTTTTTGTTAAAATAGACTATAATTGAA
* * * * *
66 TATCTACCTAGGGAAACGTGCAAAAAAAGTCATTCATTGAGAAGAAAAACTCATTTTTAATCACC
66 TATCTACCTAGAGAAACATGCAAAAAAAGTCATTCATTGAGAAGAAAAAATCATTTATAGTCACC
* * * * *
131 CATTCTTTCGAAGCCTTATTACTCGGTTTAAATGATTTTATAATCTCATAATTGATTTTAAGTTA
131 CATTCCTTCAAAGCCTTATTACCCGCTTTAAATGATTTTATAATCTAATAATTGATTTTAAGTTA
* *
196 AACTTTTTTATATATTTTTTAAAACAGACAATAATTGAATGTCTATCTCGAGAAACATGTAGAAA
196 AACTTTTTTACATATTTTTTAAAACAGACAATAATTGAAAGTCTATCTCGAGAAACATGTAGAAA
* * * * *
261 AAGACATTGATTGAGAAGAAAAGTTCATTTTAATCACCAATTATTTCAAAAGTCTTATTACTCAT
261 AAGACATTCATTGAGAAGAAAAATCCATTTTAATCACCAATTATTTCAAAAGCCTTATTACTCAG
*
326 TTTAAATAGTTTTA
326 TTTAAATAGTTTAA
* * * *
340 TAATCTTATAATTGATTTTAAATT-AA-ATTTTTACATTTTTTGTTAAAACAGACTATAATTGAA
1 TAATCTCATAATTGATTTTAAGTTGAAGTTTTTTACATTTTTTGTTAAAATAGACTATAATTGAA
* * *
403 TATCTGCCTCGAGAAACATGCAAAAAAAGTCATTCATTAAGAAGAAAAAATCTATTTATAGTCAC
66 TATCTACCTAGAGAAACATGCAAAAAAAGTCATTCATTGAGAAGAAAAAATC-ATTTATAGTCAC
* * * *
468 TCATTCCTTCAAAATCCTTATTACCCGCTTTAAATGGTTTTGTAAT-TAATAATTGATTTTAAGT
130 CCATTCCTTC-AAAGCCTTATTACCCGCTTTAAATGATTTTATAATCTAATAATTGATTTTAAGT
* * * *
532 TGAA-TTTTTTACATTTTTCTTTAAAACAGACTATAATTGAAAG-CT-TGC-CTTAGAAA-AGGT
194 TAAACTTTTTTACATATTT-TTTAAAACAGACAATAATTGAAAGTCTAT-CTC-GAGAAACA--T
* * * *
592 GTAGAAAAAGCCATTCATTGAGAAGAAAAATCCATTTTTATTCACCCATTCTTTC-AAAGCCTTA
254 GTAGAAAAAGACATTCATTGAGAAGAAAAATCCA-TTTTAATCACCAATTATTTCAAAAGCCTTA
** *
656 TTACTTGGTTTCAAT-GATTTAA
318 TTACTCAGTTTAAATAG-TTTAA
* * *
678 TAATCTCATAATTGATTTTAAGTTGAAGTTTTTTACATTTTTCT-TTGAAATAGACAATAATTAA
1 TAATCTCATAATTGATTTTAAGTTGAAGTTTTTTACATTTTT-TGTTAAAATAGACTATAATTGA
* * * * * * * *
742 ATGTCTATCTTGAGAGACATGCAGAAAAAGCCATTGATTGAGAAG-AAAAGTCCATTTATAGTCA
65 ATATCTACCTAGAGAAACATGCAAAAAAAGTCATTCATTGAGAAGAAAAAAT-CATTTATAGTCA
806 CCCATT
129 CCCATT
812 NNNNNNNNNN
Statistics
Matches: 400, Mismatches: 59, Indels: 26
0.82 0.12 0.05
Matches are distributed among these distances:
336 3 0.01
337 102 0.25
338 138 0.34
339 90 0.22
340 66 0.17
341 1 0.00
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (339 bp):
TAATCTCATAATTGATTTTAAGTTGAAGTTTTTTACATTTTTTGTTAAAATAGACTATAATTGAA
TATCTACCTAGAGAAACATGCAAAAAAAGTCATTCATTGAGAAGAAAAAATCATTTATAGTCACC
CATTCCTTCAAAGCCTTATTACCCGCTTTAAATGATTTTATAATCTAATAATTGATTTTAAGTTA
AACTTTTTTACATATTTTTTAAAACAGACAATAATTGAAAGTCTATCTCGAGAAACATGTAGAAA
AAGACATTCATTGAGAAGAAAAATCCATTTTAATCACCAATTATTTCAAAAGCCTTATTACTCAG
TTTAAATAGTTTAA
Done.