Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398340.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_164.0, 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: 3332
ACGTcount: A:0.28, C:0.10, G:0.09, T:0.26
Warning! 885 characters in sequence are not A, C, G, or T
Found at i:1350 original size:171 final size:170
Alignment explanation
Indices: 1009--1378 Score: 442
Period size: 170 Copynumber: 2.2 Consensus size: 170
999 NNNNNNNNNN
* * * * **
1009 AAGTGAGTAATAAGGCTTTTGAAGGAATGTG-TAACTATAAATGGACTTTTCTTGTCAATGAATG
1 AAGTGAGTAATAAGGCCTTTAAAAGAATG-GATGACTATAAATGGACCGTTCTTGTCAATGAATG
* * *
1073 CCTTCTTCTTCACATTTGTCAAGGTAGACATTTAATTATTATCTATTTTAAAAAAATGCAAAAAG
65 CCTTCTTCATCACATTTCTCAAGGTAGACATTTAATTACTATCTATTTTAAAAAAATGCAAAAAG
1138 AATTCAAATTTAAATCAATTTTGAGATTATAAAACTATTTA
130 AATTCAAATTTAAATCAATTTTGAGATTATAAAACTATTTA
* *
1179 AAGTTG-GTAATGAGGCCTTTAAAAGAATGGATGACTATAAATGGACCGTTCTTGTCAATGAGTG
1 AAG-TGAGTAATAAGGCCTTTAAAAGAATGGATGACTATAAATGGACCGTTCTTGTCAATGAATG
* * ** * * * *
1243 CTTTTTTCATCATGTTTCTCAAGGTAGACA-TTGATT-CTAGTCTGTTTTAACTAAAAATGTATA
65 CCTTCTTCATCACATTTCTCAAGGTAGACATTTAATTACTA-TCTATTTTAA--AAAAATGCAAA
* * * *
1306 GAGAATTTAAATTTAAATTAATTTTGAGATTATAAAATTATTTA
127 AAGAATTCAAATTTAAATCAATTTTGAGATTATAAAACTATTTA
* *
1350 AAGTGAGTAATAAGGCTTTTAAAGGAATG
1 AAGTGAGTAATAAGGCCTTTAAAAGAATG
1379 NNNNNNNNNN
Statistics
Matches: 168, Mismatches: 26, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
168 2 0.01
169 15 0.09
170 77 0.46
171 74 0.44
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.38
Consensus pattern (170 bp):
AAGTGAGTAATAAGGCCTTTAAAAGAATGGATGACTATAAATGGACCGTTCTTGTCAATGAATGC
CTTCTTCATCACATTTCTCAAGGTAGACATTTAATTACTATCTATTTTAAAAAAATGCAAAAAGA
ATTCAAATTTAAATCAATTTTGAGATTATAAAACTATTTA
Found at i:2327 original size:172 final size:172
Alignment explanation
Indices: 2112--2657 Score: 613
Period size: 172 Copynumber: 3.2 Consensus size: 172
2102 NNNNNNATTT
* * * *
2112 AAATCAATTTTGAGATTATAAAACCATTTAGAGTGACTAATAAGTCTTTTAAAGGAATGGGTGAC
1 AAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGCAATGGGTGAC
* * * * *
2177 TATAAATAGACTTTTT-GTGCTAATAAATGCCTTTTTCTTC-ACCTTTCTC-AAGCTTGACATTC
66 TATAAATAGA-TTTTTCTTGCTAATAAATGCCTTTTTCTCCTACATTTCTCAAAG-TAGACATTT
* * * *
2239 AATTATAATTTGTTTTAACCAAAAATATAAAAACATTTAAACTTT
129 AATTATAATATGTTTTAACCAAAAATATAAAAA-ATCTGAACTTA
* * **********
2284 AAACCAATTTTGAGATTATAAAACCATTTAAAGAGAGTAATAAGGCTNNNNNNNNNNTGGGTGAC
1 AAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGCAATGGGTGAC
* *
2349 TATAAATAGATTTTTCTTGCCAATGAATGCCTTTTT-TCCTACATTTCTCAAAGTAGACATTTAA
66 TATAAATAGATTTTTCTTGCTAATAAATGCCTTTTTCTCCTACATTTCTCAAAGTAGACATTTAA
2413 TTATAATATGTTTTAACCAAAAA-AGTAAAAAAATCTGAACTTA
131 TTATAATATGTTTTAACCAAAAATA-T-AAAAAATCTGAACTTA
********** *
2456 AAATCAATTTTGAGATTATAAAANNNNNNNNNNTGAGTAATAAGGCTTTTGAAGCAATGGGTGAC
1 AAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGCAATGGGTGAC
*
2521 TATAAATAGATTTTTCTTG-TCAATAAATGCCTTTTTC-CCTACATTTCTCAAAGTAGATATTTA
66 TATAAATAGATTTTTCTTGCT-AATAAATGCCTTTTTCTCCTACATTTCTCAAAGTAGACATTTA
2584 ATTATAATATGTTTTAACCCAAAAAGTA-AAAAAATCTGAACTTA
130 ATTATAATATGTTTTAA-CCAAAAA-TATAAAAAATCTGAACTTA
2628 AAATCAATTTTGAGATTATAAAACCATTTA
1 AAATCAATTTTGAGATTATAAAACCATTTA
2658 NNNNNNNNNN
Statistics
Matches: 306, Mismatches: 58, Indels: 20
0.80 0.15 0.05
Matches are distributed among these distances:
171 8 0.03
172 282 0.92
173 15 0.05
175 1 0.00
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.35
Consensus pattern (172 bp):
AAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGCAATGGGTGAC
TATAAATAGATTTTTCTTGCTAATAAATGCCTTTTTCTCCTACATTTCTCAAAGTAGACATTTAA
TTATAATATGTTTTAACCAAAAATATAAAAAATCTGAACTTA
Done.