Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399250.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2519.0, 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: 1755
ACGTcount: A:0.32, C:0.09, G:0.12, T:0.29
Warning! 329 characters in sequence are not A, C, G, or T
Found at i:1009 original size:171 final size:170
Alignment explanation
Indices: 460--1014 Score: 483
Period size: 172 Copynumber: 3.2 Consensus size: 170
450 NNNNNNNNNN
* * * * *
460 CTTTTGAAGGAATGAGTGACTATAAATAGACTTTTGTTACCAATG-AATGTCTTTTTCTTCACGT
1 CTTTTGAAGGAATGAGAGACTATAAATAGACTTTTCTT-GC--TGAAATGCCTTTCTCTTCACGT
* *
524 TTCAAGAGGTAGACATTCAATTCTAAACTATTTT-AGAAAAAAATGT-AAAAAAAATTGAACTTT
63 TTCATGAGGTAGACATTCAATTATAAACTATTTTAAG-AAAAAATGTAAAAAAAAATTGAAC-TT
* ***
587 AAATCAATTTTGAGATTATAAACCCATTTAAAATGTGTAATAAGG
126 AAATCAATTTTGAGATTATAAAACCATTTAAAACAAGTAATAAGG
* * ********
632 CTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTGCT-AANNNNNNNNNNNCTCTTCACGT
1 CTTTTGAAGGAATGAGAGACTATAAATAGACTTTTCTTGCTGAA---ATGCCTTTCTCTTCACGT
* * * *
696 TTCATGAGGTAGACATTTAATTATAAACTGTTTTAACAAAAAA--TACAAATAAAATTGAACTTA
63 TTCATGAGGTAGACATTCAATTATAAACTATTTTAAGAAAAAATGTA-AAAAAAAATTGAACTT-
* * * *****
759 AAACCAATTGTGAGATTATAAAACCATTTAAAGCAAGTAANNNNN
126 AAATCAATTTTGAGATTATAAAACCATTTAAAACAAGTAATAAGG
***** *
804 NNNNNGAAGGAATGAGAGACTATAAATGGACTTTTCTTGCTGAAATGCCTTTCTCTTCACGTTTC
1 CTTTTGAAGGAATGAGAGACTATAAATAGACTTTTCTTGCTGAAATGCCTTTCTCTTCACGTTTC
* *
869 ATGAGGTAGACATTCAATTATAATCTATTTTAAGAAAAAATGTAAAAAAAAATTGAACTCAAATT
66 ATGAGGTAGACATTCAATTATAAACTATTTTAAGAAAAAATGTAAAAAAAAATTGAACTTAAA-T
* **********
934 TAATTTTGAGATTATAAAACCATNNNNNNNNNNTAATAAGG
130 CAATTTTGAGATTATAAAACCATTTAAAACAAGTAATAAGG
* *
975 CTTTTGAAGGAATGAGAGACTATGAATAGACTTTTTTTGC
1 CTTTTGAAGGAATGAGAGACTATAAATAGACTTTTCTTGC
1015 CAATGAATGC
Statistics
Matches: 293, Mismatches: 78, Indels: 25
0.74 0.20 0.06
Matches are distributed among these distances:
169 2 0.01
170 53 0.18
171 73 0.25
172 162 0.55
173 3 0.01
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.32
Consensus pattern (170 bp):
CTTTTGAAGGAATGAGAGACTATAAATAGACTTTTCTTGCTGAAATGCCTTTCTCTTCACGTTTC
ATGAGGTAGACATTCAATTATAAACTATTTTAAGAAAAAATGTAAAAAAAAATTGAACTTAAATC
AATTTTGAGATTATAAAACCATTTAAAACAAGTAATAAGG
Found at i:1709 original size:169 final size:170
Alignment explanation
Indices: 1305--1755 Score: 422
Period size: 169 Copynumber: 2.6 Consensus size: 170
1295 NATTTAAAGT
* * * *
1305 GAGTAATAAGGCTTTTGAAGGAACGAGAAACTATAAATAGAATTTTCTTTCAAATAAATGAGTTT
1 GAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATAGACTTTTCTTCCAAA-AAATGAGTTT
* * * *
1370 TTCTACACGTTTCTC-ACTGCAGGCATTCAATTACAATCTATTTTAATAAAAAAATATAAAAAAG
65 TTCTACACGTTTCTCGA-TGCAAGCATTCAATTATAGTCTAGTTTAATAAAAAAATATAAAAAAG
*
1434 TAAACTTAAAATCAATTATGAGAGTATAAATCCTTTTAAAAC
129 TAAACTTAAAATCAATTATGAGAGTATAAAACCTTTTAAAAC
* * ** *********
1476 GACTAATGAGGCTTTTGAAAAAATGAGAGACTATAAATAGACTTTTCTNNNNNNNNNNTGAGTTT
1 GAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATAGACTTTTCT-TCCAAAAAATGAGTTT
* * * *
1541 TT-TACACGTTTCTCGAGGCAAGCATTCAATTATAGTGT-GTTTAATTAAAAAATATAAAAAATT
65 TTCTACACGTTTCTCGATGCAAGCATTCAATTATAGTCTAGTTTAATAAAAAAATATAAAAAAGT
* * *********
1604 CAACTTAAAATCAATTATGAGATTATAAAACCNNNNNNNNN
130 AAACTTAAAATCAATTATGAGAGTATAAAACCTTTTAAAAC
* * * *
1645 NAGTAATAAGGCTTTTGAAGGAATGGGAGATTATAAATGGACTTTTCTTCCAAAAATATGAGTTT
1 GAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATAGACTTTTCTTCCAAAAA-ATGAGTTT
* * * * * *
1710 TTCTATAGGTTTCTTGATGCATGGATTCAATTATAGTCTATTTTAA
65 TTCTACACGTTTCTCGATGCAAGCATTCAATTATAGTCTAGTTTAA
Statistics
Matches: 214, Mismatches: 61, Indels: 10
0.75 0.21 0.04
Matches are distributed among these distances:
169 100 0.47
170 58 0.27
171 56 0.26
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.33
Consensus pattern (170 bp):
GAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATAGACTTTTCTTCCAAAAAATGAGTTTT
TCTACACGTTTCTCGATGCAAGCATTCAATTATAGTCTAGTTTAATAAAAAAATATAAAAAAGTA
AACTTAAAATCAATTATGAGAGTATAAAACCTTTTAAAAC
Done.