Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399819.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3058.0, 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, 853
Length: 1422
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.34
Warning! 51 characters in sequence are not A, C, G, or T
Found at i:449 original size:172 final size:170
Alignment explanation
Indices: 176--1387 Score: 1100
Period size: 171 Copynumber: 7.1 Consensus size: 170
166 NNNNNNNNNN
* * * **
176 TTAACCAAAAATGTAAAAAAAATTGAACTTAGAATCAATTTTGAGATTATAAAATGATTTAAAGT
1 TTAACCAAAAATGT-AAAAAAATTCAACTTAAAATCAATTATG-GATTATAAAACCATTTAAAGT
* * * ** * * *
241 GAGCAATAACGCTACTGAAGGAATGGGTGACTATAAATAGACTTTTCTTGCTAATGAATGCTTTT
64 AAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTT
** *
306 TTCTTTGCGTTTCTCAAGGTAGACATTCAATTATAGTCTATT
129 TTCTTCACGTTTCTCAAGGTAGACATTCAATTATAGTCTGTT
* * *
348 TCAGCCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGGCATTATAAAACCATTCAAAGTA
1 TTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGG-ATTATAAAACCATTTAAAGTA
* *
413 AGTAATAAGGCTTTTTGAAGGTATGAGTGACTATAAATGGACTTTTCTTGCC-ATGAATGTTTTT
65 AGTAATAAGGC-TTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTT
* *
477 TTCTTCACGTTTCTCAAGGTAGACATTCAATTTTGGTCTGTT
129 TTCTTCACGTTTCTCAAGGTAGACATTCAATTATAGTCTGTT
* * * * * *
519 TTAACAAAAAATGTTAAAAAATTTAACTTAAAATCAATTATTAGTTTATAAAACCATTTAAAGCA
1 TTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTA-TGGATTATAAAACCATTTAAAGTA
* ** * * **
584 AGTAATAAGGCTTTCGAAGGCTTGACTGACTATAAATGGACTTTT-TGTGCAAATGGTTGGC-TT
65 AGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCT-TGCCAATGAAT-GCTTT
* * * * * *
647 TTGCTTCACG-TTCCCTATGGCAGGA-ACTCAATTATAGCCT-TT
128 TTTCTTCACGTTTCTC-AAGGTA-GACATTCAATTATAGTCTGTT
* * * *
689 TTGAACCAAAAATGTTAAAATATTCAACTTAAAATCAATTTTGAGATTATAAAGCCATTTAAAGT
1 TT-AACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATG-GATTATAAAACCATTTAAAGT
* ** ** * * * *
754 GAGTAATAAGGCTTTTGAAGGCTTGAGCAACTATAAATGGACTTCTCTTGCCAATGAGTACCTTT
64 AAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTT
* * * * *
819 TTCTTCACATTTC-CAAAGGCAAACACTCAATTATAATCTGTT
129 TTCTTCACGTTTCTC-AAGGTAGACATTCAATTATAGTCTGTT
* ** * *
861 CTAACCAAAAACATCAAAAAATTCAA-TCTAAAATCAATTATGAGGTTATAAAACCATTTAAAGT
1 TTAACCAAAAATGTAAAAAAATTCAACT-TAAAATCAATTATG-GATTATAAAACCATTTAAAGT
* * * *
925 AAGTAATAAGGCTTTTAAAAGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATTCCTTT
64 AAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTGCCAATGAA-TGCTTT
* * * * *
990 TTT-TTCACTTTTCTCAAGGTGGACATTCTATTATAATTTGTT
128 TTTCTTCACGTTTCTCAAGGTAGACATTCAATTATAGTCTGTT
** * * * * ** * *
1032 TTAATGAAAAATATGCAAAGAATTCAAATTTGAATCAATT-TGGAGAATATAAAACCATTTAAAC
1 TTAACCAAAAATGT-AAAAAAATTCAACTTAAAATCAATTAT-G-GATTATAAAACCATTTAAAG
* * * ** * *
1096 TGAGCAATAAGGCTTTTGAAGAAAT-AGGTGACTATAAACAGACTGTTCTTGCCAATGAATGCCT
63 TAAGTAATAAGGCTTTTGAAGGAATGA-GTGACTATAAATGGACTTTTCTTGCCAATGAATGCTT
* * * *
1160 TTTTCTTTATGTATCTCGAGGTAGACATTCAATTATAGTCTGTT
127 TTTTCTTCACGTTTCTCAAGGTAGACATTCAATTATAGTCTGTT
* * * ** * *
1204 TTAACCTAAAATGTAAAAAGCATTCAACCTTAAAATAAATTATGGTATTGCAAAACTATGTAAAG
1 TTAACCAAAAATGTAAAAA-AATTCAA-CTTAAAATCAATTATGG-ATTATAAAACCATTTAAAG
* * * * * * * *
1269 CAAGTAATAAGGCTTTTGAAGGCATGGGTGGCTATTAATGGCCTTTTCTTGCAAATTAATGC--T
63 TAAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTGCCAATGAATGCTTT
** * * *
1332 TTTCTTCATTTTTCTCAAGGTAGGCATTCAATTCTAGTCTATT
128 TTTCTTCACGTTTCTCAAGGTAGACATTCAATTATAGTCTGTT
1375 TTAACCAAAAATG
1 TTAACCAAAAATG
1388 ATGGAAGAAT
Statistics
Matches: 843, Mismatches: 169, Indels: 57
0.79 0.16 0.05
Matches are distributed among these distances:
169 1 0.00
170 46 0.05
171 523 0.62
172 201 0.24
173 71 0.08
174 1 0.00
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (170 bp):
TTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGGATTATAAAACCATTTAAAGTAA
GTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTT
CTTCACGTTTCTCAAGGTAGACATTCAATTATAGTCTGTT
Done.