Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397805.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1105.0, 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: 3781
ACGTcount: A:0.15, C:0.06, G:0.06, T:0.15
Warning! 2191 characters in sequence are not A, C, G, or T
Found at i:2387 original size:170 final size:158
Alignment explanation
Indices: 2154--2477 Score: 309
Period size: 170 Copynumber: 2.0 Consensus size: 158
2144 AAAGCTAGTA
* * *
2154 ATAAGGCTTTTGAAGGCATAGGTGACTATAAATGAACTTTTCTTACCGATGAATGGCTTTTTCTT
1 ATAAGGCTTTTGAAGGCATAGGTGACTATAAATGAACTTTGCTTACCAATGAATAGCTTTTTCTT
* * * *
2219 -CATGTTCTCAATG-TAGACATTTAATTATATTTTG-TTTTAAGCA-AACTTATAAAACAAA-TG
66 ACAT-TTCTCAA-GATAGACATTTAATTATA-ATCGATTTTAACCATAA---ATAAAA-AAATTC
*
2279 AACTTAAAATCAATTATGATATTATAAAACTATTT
124 AACTTAAAATCAATTATGACATTATAAAACTATTT
* * *
2314 NNNNNNNNNNATAAGGCTTTTGAAGGTAT-GGCTGACTATAAATGGACTTTGCTTGCCAATGAAT
1 ----------ATAAGGCTTTTGAAGGCATAGG-TGACTATAAATGAACTTTGCTTACCAATGAAT
* *
2378 AGTTTTTTCTTCACATTTCTCGAGATAGACATTTAATTATAATCGATTTTAACCATAAATAAAAA
55 AGCTTTTTCTT-ACATTTCTCAAGATAGACATTTAATTATAATCGATTTTAACCATAAATAAAAA
*
2443 AATTCAACTTAAAGTCAATTATGACATTATAAAAC
119 AATTCAACTTAAAATCAATTATGACATTATAAAAC
2478 CTTTTAAAGC
Statistics
Matches: 133, Mismatches: 14, Indels: 15
0.82 0.09 0.09
Matches are distributed among these distances:
168 3 0.02
169 37 0.28
170 58 0.44
171 30 0.23
172 5 0.04
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.36
Consensus pattern (158 bp):
ATAAGGCTTTTGAAGGCATAGGTGACTATAAATGAACTTTGCTTACCAATGAATAGCTTTTTCTT
ACATTTCTCAAGATAGACATTTAATTATAATCGATTTTAACCATAAATAAAAAAATTCAACTTAA
AATCAATTATGACATTATAAAACTATTT
Found at i:2502 original size:169 final size:168
Alignment explanation
Indices: 2098--2560 Score: 456
Period size: 169 Copynumber: 2.7 Consensus size: 168
2088 NNNNNNNATG
* ** * * *
2098 AAAAACAATTCAACTCAAAATCAATTATGAGGTTGTAAAATCATTTAAAGCTAGTAATAAGGCTT
1 AAAAA-AATTCAACTTAAAATCAATTATGACATTATAAAA-CTTTTAAAGCGAGTAATAAGGCTT
* * * * *
2163 TTGAAGGCATAGGTGACTATAAATGAACTTTTCTTACCGATGAATGGCTTTTTCTT--CATGTTC
64 TTGAAGGCAT-GGTGACTATAAATGGACTTTTCTTGCCAATGAATAGTTTTTTCTTCACATGTTC
* * *
2226 TCAATGTAGACATTTAATTATATTTTGTTTTAAGCAAACTTAT
128 TCAATGTAGACATTTAATTATATATCGTTTTAACCAAA--TAT
* * **********
2269 AAAACAAA-TGAACTTAAAATCAATTATGATATTATAAAACTATTTNNNNNNNNNNATAAGGCTT
1 AAAA-AAATTCAACTTAAAATCAATTATGACATTATAAAACT-TTTAAAGCGAGTAATAAGGCTT
* *
2333 TTGAAGGTATGGCTGACTATAAATGGACTTTGCTTGCCAATGAATAGTTTTTTCTTCACAT-TTC
64 TTGAAGGCATGG-TGACTATAAATGGACTTTTCTTGCCAATGAATAGTTTTTTCTTCACATGTTC
*
2397 TCGA-GATAGACATTTAATTATA-ATCGATTTTAACCATAA-AT
128 TCAATG-TAGACATTTAATTATATATCG-TTTTAACCA-AATAT
*
2438 AAAAAAATTCAACTTAAAGTCAATTATGACATTATAAAACCTTTTAAAGCGAGTAATAAGGCTTT
1 AAAAAAATTCAACTTAAAATCAATTATGACATTATAAAA-CTTTTAAAGCGAGTAATAAGGCTTT
* *
2503 TCAAGGCATGGGTGACCATAAATGGACTTTTCTTGCCAATGAATA-TCTTTTTCTTCAC
65 TGAAGGCAT-GGTGACTATAAATGGACTTTTCTTGCCAATGAATAGT-TTTTTCTTCAC
2561 GTTNNNNNNN
Statistics
Matches: 236, Mismatches: 44, Indels: 26
0.77 0.14 0.08
Matches are distributed among these distances:
168 4 0.02
169 99 0.42
170 91 0.39
171 36 0.15
172 6 0.03
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.35
Consensus pattern (168 bp):
AAAAAAATTCAACTTAAAATCAATTATGACATTATAAAACTTTTAAAGCGAGTAATAAGGCTTTT
GAAGGCATGGTGACTATAAATGGACTTTTCTTGCCAATGAATAGTTTTTTCTTCACATGTTCTCA
ATGTAGACATTTAATTATATATCGTTTTAACCAAATAT
Done.