Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398042.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1350.0, 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: 4492
ACGTcount: A:0.24, C:0.07, G:0.09, T:0.22
Warning! 1696 characters in sequence are not A, C, G, or T
Found at i:3611 original size:172 final size:171
Alignment explanation
Indices: 3192--3891 Score: 626
Period size: 172 Copynumber: 4.1 Consensus size: 171
3182 NNNNNNNNNN
* * * * *
3192 CAATTATGAGATTACAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAAGAATGGGTGATTATA
1 CAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATGAGTGACTAAA
* * * * * *
3257 AATGGATTTTTCTAGCCAATGAATGCCTTTTTCTTCACATTACATGAGGTAGACAATAAATTATA
66 AATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCACGTTTCATGAGGTAGACATTCAATTATA
* * ** *
3322 ATCTGTTTTAATAAAAAATACAAAAAAACTCAACTTAAAAT
131 ATCTATTTTAAAAAAAAATGTAAAAAAATTCAACTTAAAAT
********** * * * *
3363 CAATTNNNNNNNNNNAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAACGAATGGGTGACCATA
1 CAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATGAGTGACTAAA
* * * * * *
3428 AATGCACTTTTCTTGCCAATGAATGCTTTTTTCTTTACGTTTCTTGAGGTCGACATTTAATTATA
66 AATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCACGTTTCATGAGGTAGACATTCAATTATA
* * * *
3493 GTCTGTTTTAACAAAAAAATGTAAGACAATTCAACTTAAAAT
131 ATCTATTTTAA-AAAAAAATGTAAAAAAATTCAACTTAAAAT
* * * * * *
3535 CAATTATGACATTATAAAACTATTTAAAGCGAGTAATGACGCTTTTGGAGGAATGAGTGACTAAA
1 CAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATGAGTGACTAAA
* * *
3600 AATGGACTTTTCTTACCAATGAATGCCTTTTTCTCCATGTTTCATGAGGTAGACATTCAATTATA
66 AATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCACGTTTCATGAGGTAGACATTCAATTATA
* *
3665 ATCTATTTT--AAGAAAATGTAAAAGAAATTAAACTTAAAAT
131 ATCTATTTTAAAAAAAAATGTAAAA-AAATTCAACTTAAAAT
* * * * * * *
3705 TAATTTTAAAATTATAAAATCATTTAAAGCGAGTAA-AAGGGGTTTTGAAGGAATGAGTGACTAT
1 CAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAA-GGCTTTTGAAGGAATGAGTGACTA-
* * ** * * *** *
3769 AACA--GACTTTTCTT-CCAAATAAATGAGTTTTTC-TAAGTGTTTCCCAAGGCA-AGCATTCAA
64 AAAATGGACTTTTCTTGCC-AATGAATGCCTTTTTCTTCA-CGTTTCATGAGGTAGA-CATTCAA
* * *
3829 TTATAGTCTATTTTAAGAAAAAATGAAAAAAAAATT-AACTTAAAAT
126 TTATAATCTATTTTAAAAAAAAATG-TAAAAAAATTCAACTTAAAAT
3875 CAATTATGAGATTATAA
1 CAATTATGAGATTATAA
3892 NNNNNNNNNN
Statistics
Matches: 426, Mismatches: 93, Indels: 21
0.79 0.17 0.04
Matches are distributed among these distances:
168 4 0.01
169 66 0.15
170 88 0.21
171 131 0.31
172 137 0.32
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.33
Consensus pattern (171 bp):
CAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATGAGTGACTAAA
AATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCACGTTTCATGAGGTAGACATTCAATTATA
ATCTATTTTAAAAAAAAATGTAAAAAAATTCAACTTAAAAT
Found at i:3891 original size:170 final size:170
Alignment explanation
Indices: 3479--3891 Score: 430
Period size: 170 Copynumber: 2.4 Consensus size: 170
3469 TCTTGAGGTC
* * * * * * *
3479 GACATTTAATTATAGTCTGTTTTAACAAAAAAATGTAAGACAATTCAACTTAAAATCAATTATGA
1 GACATTCAATTATAGTCTATTTTAA-GAAAAAATGAAAAAAAATTAAACTTAAAATCAATTATGA
* * *
3544 CATTATAAAACTATTTAAAGCGAGTAATGACGCTTTTGGAGGAATGAGTGACTAAAAATGGACTT
65 AATTATAAAACTATTTAAAGCGAGTAAAGACGCTTTTGAAGGAATGAGTGACTAAAAA-GGACTT
* * * ** *
3609 TTCTTACCAATGAATGCCTTTTTCTCCATGTTTCATGAGGTA
129 TTCTTACCAATAAATGACTTTTTCTCAATGTTTCACAAGGAA
* * * * *
3651 GACATTCAATTATAATCTATTTTAAG--AAAATGTAAAAGAAATTAAACTTAAAATTAATTTTAA
1 GACATTCAATTATAGTCTATTTTAAGAAAAAATG-AAAAAAAATTAAACTTAAAATCAATTATGA
* * *
3714 AATTATAAAA-TCATTTAAAGCGAGTAAA-AGGGGTTTTGAAGGAATGAGTGACTATAACA-GAC
65 AATTATAAAACT-ATTTAAAGCGAGTAAAGA-CGCTTTTGAAGGAATGAGTGACTA-AAAAGGAC
* *
3776 TTTTCTT-CCAAATAAATGAGTTTTTCT-AAGTGTTTCCCAAGGCAA
127 TTTTCTTACC-AATAAATGACTTTTTCTCAA-TGTTTCACAAGG-AA
3821 G-CATTCAATTATAGTCTATTTTAAGAAAAAATGAAAAAAAAATT-AACTTAAAATCAATTATGA
1 GACATTCAATTATAGTCTATTTTAAGAAAAAATG-AAAAAAAATTAAACTTAAAATCAATTATGA
*
3884 GATTATAA
65 AATTATAA
3892 NNNNNNNNNN
Statistics
Matches: 199, Mismatches: 33, Indels: 20
0.79 0.13 0.08
Matches are distributed among these distances:
168 3 0.02
169 64 0.32
170 92 0.46
171 18 0.09
172 22 0.11
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.34
Consensus pattern (170 bp):
GACATTCAATTATAGTCTATTTTAAGAAAAAATGAAAAAAAATTAAACTTAAAATCAATTATGAA
ATTATAAAACTATTTAAAGCGAGTAAAGACGCTTTTGAAGGAATGAGTGACTAAAAAGGACTTTT
CTTACCAATAAATGACTTTTTCTCAATGTTTCACAAGGAA
Done.