Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401062.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4221.0, 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, 960
Length: 1601
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.30
Warning! 175 characters in sequence are not A, C, G, or T
Found at i:287 original size:172 final size:169
Alignment explanation
Indices: 1--460 Score: 448
Period size: 172 Copynumber: 2.7 Consensus size: 169
1 AAATATAAAAAAATTT-AAATTAAAATCAATTATGAGGTTATAAAATCATTT-AAGACGAGTAAT
1 AAATATAAAAAAATTTCAAATTAAAAT-AATTATGAGGTTATAAAATCATTTAAAG-CGAGTAAT
* ** * ********* *
64 AAAGCTTTTGAAGGCATGGGTGACTAGAAATGNNNNNNNNNNGCCAATGGATATCTTTTTCTTCA
64 AAGGCTTTTGAAGGCATCAGTGACTATAAATG-ACTTTTCTTGCCAATGGATATCATTTTCTTCA
* *
129 AGTTTCTTGGAA-AAAACAT-TCAATTATAACCTGTTTTAATAAA
128 AGTTTC-T-CAAGAAAACATGT-AATTATAACCTATTTTAATAAA
172 AAATATAAAAAAATTTCAAATTAAAACTAATTATG-GTGTTATAAAATCATTTAAAGCGAGTAAT
1 AAATATAAAAAAATTTCAAATTAAAA-TAATTATGAG-GTTATAAAATCATTTAAAGCGAGTAAT
* * *
236 AAGGCTTTTGACGGTATCAGTGACTATAAATCGACTTTTCTTGCTAATGGATATCATTTTCTTCA
64 AAGGCTTTTGAAGGCATCAGTGACTATAAAT-GACTTTTCTTGCCAATGGATATCATTTTCTTCA
* * * * *
301 CGTTTCTCAAGGTAAACGTGTAATTATAATCTATTTTAATAAT
128 AGTTTCTCAA-GAAAACATGTAATTATAACCTATTTTAATAAA
* * * * * * *
344 AAATAT-AAAAAAGTTCAACTTAAAAGTAACTATGAGATCA-AAAAACTATTTAAAGCGAGTAAA
1 AAATATAAAAAAATTTCAAATTAAAA-TAATTATGAGGTTATAAAATC-ATTTAAAGCGAGTAAT
** *
407 AAGGCTTTCAAAGGCATTAGTGACTATAAATGGACTTTTCTTGCCAATGGATAT
64 AAGGCTTTTGAAGGCATCAGTGACTATAAAT-GACTTTTCTTGCCAATGGATAT
461 NNNNNNNNNN
Statistics
Matches: 240, Mismatches: 39, Indels: 20
0.80 0.13 0.07
Matches are distributed among these distances:
170 7 0.03
171 106 0.44
172 121 0.50
173 6 0.03
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.33
Consensus pattern (169 bp):
AAATATAAAAAAATTTCAAATTAAAATAATTATGAGGTTATAAAATCATTTAAAGCGAGTAATAA
GGCTTTTGAAGGCATCAGTGACTATAAATGACTTTTCTTGCCAATGGATATCATTTTCTTCAAGT
TTCTCAAGAAAACATGTAATTATAACCTATTTTAATAAA
Found at i:450 original size:171 final size:172
Alignment explanation
Indices: 150--460 Score: 421
Period size: 171 Copynumber: 1.8 Consensus size: 172
140 AAAAACATTC
* * * * * *
150 AATTATAACCTGTTTTAATAAAAAATATAAAAAAATTTCAAATTAAAACTAATTATGGTGTTATA
1 AATTATAACCTATTTTAATAAAAAATATAAAAAAAGTTCAAATTAAAACTAACTATGGTATCAAA
* ** * *
215 AAATCATTTAAAGCGAGTAATAAGGCTTTTGACGGTATCAGTGACTATAAATCGACTTTTCTTGC
66 AAATCATTTAAAGCGAGTAAAAAGGCTTTCAAAGGCATCAGTGACTATAAATCGACTTTTCTTGC
*
280 TAATGGATATCATTTTCTTCACGTTTCTCAAGGTAAACGTGT
131 CAATGGATATCATTTTCTTCACGTTTCTCAAGGTAAACGTGT
* * * *
322 AATTATAATCTATTTTAATAATAAATAT-AAAAAAGTTCAACTTAAAAGTAACTATGAG-ATCAA
1 AATTATAACCTATTTTAATAAAAAATATAAAAAAAGTTCAAATTAAAACTAACTATG-GTATCAA
* *
385 AAAA-CTATTTAAAGCGAGTAAAAAGGCTTTCAAAGGCATTAGTGACTATAAATGGACTTTTCTT
65 AAAATC-ATTTAAAGCGAGTAAAAAGGCTTTCAAAGGCATCAGTGACTATAAATCGACTTTTCTT
449 GCCAATGGATAT
129 GCCAATGGATAT
461 NNNNNNNNNN
Statistics
Matches: 119, Mismatches: 18, Indels: 5
0.84 0.13 0.04
Matches are distributed among these distances:
170 1 0.01
171 92 0.77
172 26 0.22
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.34
Consensus pattern (172 bp):
AATTATAACCTATTTTAATAAAAAATATAAAAAAAGTTCAAATTAAAACTAACTATGGTATCAAA
AAATCATTTAAAGCGAGTAAAAAGGCTTTCAAAGGCATCAGTGACTATAAATCGACTTTTCTTGC
CAATGGATATCATTTTCTTCACGTTTCTCAAGGTAAACGTGT
Found at i:1473 original size:171 final size:162
Alignment explanation
Indices: 1288--1601 Score: 353
Period size: 171 Copynumber: 1.9 Consensus size: 162
1278 TAAAAAATTA
* * * * * *
1288 TTTAAATCGAGTAATAAGGCTTTCGAAGGCATAGGTTACTATAAATGGACTTTTTTTACCAATGG
1 TTTAAATCGAGTAATAAAGCTTTCGAAAGCATAGGTGACGATAAATAGACTTTTCTTACCAATGG
* *
1353 ATATCTTTTTCTTCACATATCTCGAGGCAAACATTCAATTATAGTCTGTCTTAAGAAAAAATAT-
66 ATATATTTTTCTTCACATATCTCGAGGCAAACATTCAATTATAATCTGTCTTAAGAAAAAATATA
1417 AAAAAAATTCAANNNNNNNNNNATTATGAGGTTATAAAATCC
131 AAAAAAATTCAA----------ATTATGAGGTTATAAAATCC
* * **
1459 TTTAAAGT-GAGTAATAAAGCTTTTGAAAGCATGGGTGACGATAAATAGACTTTTCTTGTCAATG
1 TTTAAA-TCGAGTAATAAAGCTTTCGAAAGCATAGGTGACGATAAATAGACTTTTCTTACCAATG
* * * * * *
1523 GATATATTTTTCTTCACCTTTCTTGAGGCAAACATTCAATTATAATCTGTTTTCATAAAAAATAT
65 GATATATTTTTCTTCACATATCTCGAGGCAAACATTCAATTATAATCTGTCTTAAGAAAAAATAT
1588 AAAAAAAATTCAAA
130 AAAAAAAATTCAAA
Statistics
Matches: 123, Mismatches: 18, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
162 1 0.01
171 109 0.89
172 13 0.11
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.34
Consensus pattern (162 bp):
TTTAAATCGAGTAATAAAGCTTTCGAAAGCATAGGTGACGATAAATAGACTTTTCTTACCAATGG
ATATATTTTTCTTCACATATCTCGAGGCAAACATTCAATTATAATCTGTCTTAAGAAAAAATATA
AAAAAAATTCAAATTATGAGGTTATAAAATCC
Done.