Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398918.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_22.0, 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: 2948
ACGTcount: A:0.25, C:0.10, G:0.11, T:0.28
Warning! 767 characters in sequence are not A, C, G, or T
Found at i:1368 original size:171 final size:162
Alignment explanation
Indices: 1152--1477 Score: 304
Period size: 171 Copynumber: 2.0 Consensus size: 162
1142 TATAAAGCCA
*
1152 TTTAAAGTGAGTAATAAGGCTTTTGAAGGAACAAGTGTATATAAATGGACTTTTCTTG-CAAATG
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAACAAGTGTATATAAATGGACTTTTCTTGTC-AATG
** * * *
1216 AATG-TCTTTCTCTT-TATGTTTCTTGAGCTAAACATTCAATTGTAGTCTATTTTAGCAAAAAAT
65 AATGCT-TTTCTCTTCT-TGTTTCTCAAGCTAAACATTCAATTCTAGTCTATTTTAACAAAAAAC
*
1279 AT-AAAAAAATTCAACTTAAAATCAATTATGGCAT
128 ATGAAAAAAATTCAAATTAAAATCAATTATGGCAT
* ** *
1313 TNNNNNNNNNNTTAAAGCGAGTAATAAGGCTTTTGAAGGTA-TGGATG-ACTATAAATGGAGTTT
1 T----------TTAAAGCGAGTAATAAGGCTTTTGAAGGAACAAG-TGTA-TATAAATGGACTTT
* * * *
1376 TCTTGTCAATGAATGCTTTTTTCTTCTTGTTTCTCAAGGTAGACATTCAATTCTAGTCTTTTTTA
54 TCTTGTCAATGAATGCTTTTCTCTTCTTGTTTCTCAAGCTAAACATTCAATTCTAGTCTATTTTA
* * * *
1441 ACTAAAAACATGCAAAGAATTCAAATTTAAATCAATT
119 ACAAAAAACATGAAAAAAATTCAAATTAAAATCAATT
1478 TTGAGATTAT
Statistics
Matches: 130, Mismatches: 19, Indels: 21
0.76 0.11 0.12
Matches are distributed among these distances:
161 1 0.01
170 2 0.02
171 103 0.79
172 24 0.18
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.37
Consensus pattern (162 bp):
TTTAAAGCGAGTAATAAGGCTTTTGAAGGAACAAGTGTATATAAATGGACTTTTCTTGTCAATGA
ATGCTTTTCTCTTCTTGTTTCTCAAGCTAAACATTCAATTCTAGTCTATTTTAACAAAAAACATG
AAAAAAATTCAAATTAAAATCAATTATGGCAT
Found at i:1984 original size:342 final size:332
Alignment explanation
Indices: 1135--1952 Score: 689
Period size: 342 Copynumber: 2.4 Consensus size: 332
1125 NNNNNNNNNN
* * * * * ***
1135 TTGAGATTATAAAGCCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAACAAGTGTA-TATAAATG
1 TTGAGATTATAAAACCATTTAAACTGAATAACAAGGCTTTTCAAGGAATGGGTG-ACTATAAATG
* * * * * * * * *
1199 GACTTTTCTTGCAAATGAATGTC-TTTCTCTTTATGTTTCTTGAGCTAAACATTCAATTGTAGTC
65 GACTTTTCTTGCCAATGAATGCCATTTGTC-TTACGTTTCTTAAGGTAGACA-TCAATTCTAATC
* * * * * * *
1263 TATTTTAGCAAAAAA-TATAAAAAAATTCAACTTAAAATCAATTATGGCATTNNNNNNNNNNTTA
128 TGTTTT-GAAAAAAATTGTAAAAATATTCAAGTTAAAATTAATTATGGCATT----------ATA
* * * * * * ** * ****
1327 AAGCGAGTAATAAGGCTTTTGAAGGTATGGATGACTATAAATGGAGTTTTCTTGTCAATGAATGC
182 AAACCATTTATGAGGCTTTTGAAGGCATGGATGACTATAAATAAACTTTTCACACCAATGAATGC
* *
1392 TTTTTTCTTCTTGTTTCTCAAGGTAGACATTCAATTCTAGTCTTTTTTAACTAAAAACATGCAAA
247 TTTTTTCTTCTTGTTTCTCAAGGTAGACATTCAATTCTAGTCTTTTTTAACTAAAAAAATACAAA
1457 GAATTCAAATTTAAATCAATT
312 GAATTCAAATTTAAATCAATT
* **********
1478 TTGAGATTATAAAATCATTTAAACTGAATAACAAGGCTTTTCAAGGAATGGGTNNNNNNNNNNGG
1 TTGAGATTATAAAACCATTTAAACTGAATAACAAGGCTTTTCAAGGAATGGGTGACTATAAATGG
* * * *
1543 ACTTTTCTTGCCAATGAATGCCTTTTGTGTTACGTTTCTTGAGGTTGACATCAATTCTAATCTGT
66 ACTTTTCTTGCCAATGAATGCCATTTGTCTTACGTTTCTTAAGGTAGACATCAATTCTAATCTGT
1608 TTTGAAAAAAATTGTAAAAATATTCAAGTTAAAATTAATTATGGCATTATAAAACCATTTNNNNN
131 TTTGAAAAAAATTGTAAAAATATTCAAGTTAAAATTAATTATGGCATTATAAAACCATTT-----
*
1673 NNNNNATGAGGCTTTTGAAGGCATGGGTGACTATAAATAAACTTTTCACACCAATGAATGCTTTT
191 -----ATGAGGCTTTTGAAGGCATGGATGACTATAAATAAACTTTTCACACCAATGAATGCTTTT
*
1738 TTCTTCATT-TTTGTCAAGGTAGACATTCAATTC-AGT-TTGTTTTAA-TAAAAAAAGTACAAAG
251 TTCTTC-TTGTTTCTCAAGGTAGACATTCAATTCTAGTCTT-TTTTAACTAAAAAAA-TACAAAG
*
1799 AATTCAAATTTAAGTCAATT
313 AATTCAAATTTAAATCAATT
* ********** *
1819 TTGAGATTATAAAACCATTTAAAGTGNNNNNNNNNNCTTTTGAAGGAATGGGTGACTATAAATGG
1 TTGAGATTATAAAACCATTTAAACTGAATAACAAGGCTTTTCAAGGAATGGGTGACTATAAATGG
*
1884 ACTTTTCTTGCCAATGAATG-CATTTGTCTTAACGTTTCTTAAGGTAGACATTCAATTCTAGTCT
66 ACTTTTCTTGCCAATGAATGCCATTTGTCTT-ACGTTTCTTAAGGTAGACA-TCAATTCTAATCT
1948 GTTTT
129 GTTTT
1953 AACCAAAAAT
Statistics
Matches: 376, Mismatches: 81, Indels: 37
0.76 0.16 0.07
Matches are distributed among these distances:
332 7 0.02
340 17 0.05
341 120 0.32
342 143 0.38
343 85 0.23
344 4 0.01
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.36
Consensus pattern (332 bp):
TTGAGATTATAAAACCATTTAAACTGAATAACAAGGCTTTTCAAGGAATGGGTGACTATAAATGG
ACTTTTCTTGCCAATGAATGCCATTTGTCTTACGTTTCTTAAGGTAGACATCAATTCTAATCTGT
TTTGAAAAAAATTGTAAAAATATTCAAGTTAAAATTAATTATGGCATTATAAAACCATTTATGAG
GCTTTTGAAGGCATGGATGACTATAAATAAACTTTTCACACCAATGAATGCTTTTTTCTTCTTGT
TTCTCAAGGTAGACATTCAATTCTAGTCTTTTTTAACTAAAAAAATACAAAGAATTCAAATTTAA
ATCAATT
Done.