Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398957.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2239.0, 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: 9309
ACGTcount: A:0.32, C:0.09, G:0.12, T:0.31
Warning! 1491 characters in sequence are not A, C, G, or T
Found at i:872 original size:172 final size:160
Alignment explanation
Indices: 660--969 Score: 284
Period size: 172 Copynumber: 1.9 Consensus size: 160
650 NNNNNNNNGA
* * **
660 GACTATAAATAGACTTTTTTTGCCAATGAATACTTTTTTCT-TCACATTTCTTGAGGCAGACATT
1 GACTATAAATAGACTTTTCTTGCCAATAAATACTTTTTTCTAT-ACATTTCTCAAGGCAGACATT
* * *
724 CAATTATTGTCTATTTTAACCAAAAATGTAAAAAAAATTGAAATTAAAATCAATTAAGAGATTAT
65 CAATTATAGTCT-GTTTAACCAAAAATG-AAAAAAAATTGAAATTAAAATCAATTAAGAGATCAT
*
789 AAAACTATTTAAAGTGAGTNNNNNNNNNNTTGAAGGATTGGGT
128 AAAACCATTTAAAGTGAGT----------TTGAAGGATTGGGT
* * **
832 GACTATAAATAGACTTTTCTT-CTTAATAAATGGC-TTTTTCTATAGGTTTCTCAAGGCAGACAT
1 GACTATAAATAGACTTTTCTTGC-CAATAAAT-ACTTTTTTCTATACATTTCTCAAGGCAGACAT
** * * * * * *
895 TCAATTATAGTCTGTTTAATGAATAATGGAAATAAATTTAACTTAAAATCAATTATGAGATCATA
64 TCAATTATAGTCTGTTTAACCAAAAATGAAAAAAAATTGAAATTAAAATCAATTAAGAGATCATA
960 AAACCATTTA
129 AAACCATTTA
970 NNNNNNNNNN
Statistics
Matches: 115, Mismatches: 20, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
170 40 0.35
171 12 0.10
172 61 0.53
173 2 0.02
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.36
Consensus pattern (160 bp):
GACTATAAATAGACTTTTCTTGCCAATAAATACTTTTTTCTATACATTTCTCAAGGCAGACATTC
AATTATAGTCTGTTTAACCAAAAATGAAAAAAAATTGAAATTAAAATCAATTAAGAGATCATAAA
ACCATTTAAAGTGAGTTTGAAGGATTGGGT
Found at i:2039 original size:172 final size:161
Alignment explanation
Indices: 1825--2161 Score: 313
Period size: 172 Copynumber: 2.0 Consensus size: 161
1815 TAAAACTATT
* ** * * * *
1825 TAAAGTGAGTAATAAGGTTTTTAAAGGAGTGGGTGACTATAAATGGT-CTTGT-CTCACCAATGA
1 TAAAGCGAGTAATAAGGCCTTTAAAGGAATGAGAGACTATAAAT-ATACTTGTCCT-ACCAATGA
* * * * * *
1888 ATG-TCTTTTTCTTCATGTTTCTTGAGGTAGAC-CTCGAATTATAATTTGTTTTAACCAATAATG
64 ATGCT-TTTTTCTTCATGTTTCATAAGGTACACAATC-AATTATAATTTGTTTTAACCAAAAATA
* * *
1951 TAAAAAATATTGAACCTGAAATCAATTATGGGATTA
127 TAAAAAAAATT-AACCTAAAATCAATTATGAGATTA
* *
1987 TAAANNNNNNNNNNGCGAGTAATAAGGCCTTTGAAGGAATGAGAGACTATAAATATACTTTTCCT
1 TAAA----------GCGAGTAATAAGGCCTTTAAAGGAATGAGAGACTATAAATATACTTGTCCT
* *
2052 ACCAGTGAATGCTTTTTTCTTCATGTTTCATAAGGTACACAATCAATTATAGTTTGTTTTAACCA
56 ACCAATGAATGCTTTTTTCTTCATGTTTCATAAGGTACACAATCAATTATAATTTGTTTTAACCA
* *
2117 AAAATATAAAAAAAATTAACTTAAAATTAATTATGAGATTA
121 AAAATATAAAAAAAATTAACCTAAAATCAATTATGAGATTA
2158 TAAA
1 TAAA
2162 ACCATTTANN
Statistics
Matches: 139, Mismatches: 22, Indels: 19
0.77 0.12 0.11
Matches are distributed among these distances:
162 4 0.03
171 25 0.18
172 105 0.76
173 5 0.04
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.35
Consensus pattern (161 bp):
TAAAGCGAGTAATAAGGCCTTTAAAGGAATGAGAGACTATAAATATACTTGTCCTACCAATGAAT
GCTTTTTTCTTCATGTTTCATAAGGTACACAATCAATTATAATTTGTTTTAACCAAAAATATAAA
AAAAATTAACCTAAAATCAATTATGAGATTA
Found at i:5973 original size:171 final size:171
Alignment explanation
Indices: 5553--6415 Score: 516
Period size: 171 Copynumber: 5.1 Consensus size: 171
5543 NNNNNNNAAC
* * * * * * * *
5553 AAATTGAACCTAAAATCAATTATGAGATTATAAAACTATTTAGAA-CGAGTAATAAGTCTTTTGA
1 AAATTCAACTTAAAATCTATTATGAGATTAAAAAATTATTTA-AAGCAAGTAATAAGGCGTTTGA
* * * *** * * *** *
5617 AAGAAT--GAGACTATAAATGGCCTTTTCTTGC-CAATGAATATTTTTTTCTTCACGTTTTTTAA
65 AGGAATGAGAGACTATAAATAGACTTTTCTT-CTCAATGAATGGCTTTTTCTACATGTTCCATGA
* * * *
5679 GGT-AGACATTCAA-TATAGTGTGTTTTAACT-AAAAATATAAAA
129 GGTAAG-CATTCAATTATAATATGTTTTAA-TGAAGAATGTAAAA
* ** *
5721 AAATTCAGCTTAAAATCTATTATGAGA-TAATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGA
1 AAATTCAACTTAAAATCTATTATGAGATTAA-AAAATTATTTAAAGCAAGTAATAAGGCGTTTGA
********** *
5785 ANNNNNNNNNNACTATAAATAGACTTTTCTTCTTAATGAATGGCTTTTTCTACATGTTCCATGAG
65 AGGAATGAGAGACTATAAATAGACTTTTCTTCTCAATGAATGGCTTTTTCTACATGTTCCATGAG
* * * * *
5850 GTAAACATTCAATTATAGTCTATTTTAATAAAGAATGTAAAA
130 GTAAGCATTCAATTATAATATGTTTTAATGAAGAATGTAAAA
**********
5892 AAATTCAACTTANNNNNNNNNNTGAGATTAAAAAATTATTTAAAGCAAGTAATAAGGCGTTTGAA
1 AAATTCAACTTAAAATCTATTATGAGATTAAAAAATTATTTAAAGCAAGTAATAAGGCGTTTGAA
* * * *
5957 GGAATGGGAGACTATAAATGGACTTTTTTTCTCAATGAATGGCTTTTTCTACACGTTTTCCA--A
66 GGAATGAGAGACTATAAATAGACTTTTCTTCTCAATGAATGGCTTTTTCTACA--TGTTCCATGA
* *
6020 -GTCAAGTATTCAATTATATTATGTTTTAATGAAGAATGTAAAA
129 GGT-AAGCATTCAATTATAATATGTTTTAATGAAGAATGTAAAA
* * ** **********
6063 AACTTCAGCTTAAAATCTATTATGAGATTGTAANNNNNNNNNNAGCAAGTAATAAGGCGTTTGAA
1 AAATTCAACTTAAAATCTATTATGAGATTAAAAAATTATTTAAAGCAAGTAATAAGGCGTTTGAA
* * * * * *
6128 GGAATGAGAGACTATAAATAAACTTTTCTTCTCGATGAATGGATTTTTCTACATGTTTCTTGAGC
66 GGAATGAGAGACTATAAATAGACTTTTCTTCTCAATGAATGGCTTTTTCTACATGTTCCATGAGG
*
6193 CAAGCATTCAATTATAATATGTTTTAATGAAGAATGTAAAA
131 TAAGCATTCAATTATAATATGTTTTAATGAAGAATGTAAAA
********** * ** * *** *
6234 AAATTCAACNNNNNNNNNNTTATGAGATTATAAAACCATTAAAAGTGTGTAATAAGGCTTTTGAA
1 AAATTCAACTTAAAATCTATTATGAGATTAAAAAATTATTTAAAGCAAGTAATAAGGCGTTTGAA
* * **
6299 -GATATGAGAAACTATAAATTGACTTTTCTTAC-CAATGAAT-GCTTTTTTCTTTATGTTTCTC-
66 GGA-ATGAGAGACTATAAATAGACTTTTCTT-CTCAATGAATGGC-TTTTTCTACATG-TTC-CA
* * * * * *
6360 T-AGGTAAACATTCAATTATAGTCTGCTTTAATGAAAAATATAAAA
126 TGAGGTAAGCATTCAATTATAATATGTTTTAATGAAGAATGTAAAA
6405 AAATTCAACTT
1 AAATTCAACTT
6416 NNNNNNNNNN
Statistics
Matches: 526, Mismatches: 149, Indels: 37
0.74 0.21 0.05
Matches are distributed among these distances:
167 4 0.01
168 51 0.10
169 5 0.01
170 55 0.10
171 397 0.75
172 7 0.01
173 7 0.01
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.35
Consensus pattern (171 bp):
AAATTCAACTTAAAATCTATTATGAGATTAAAAAATTATTTAAAGCAAGTAATAAGGCGTTTGAA
GGAATGAGAGACTATAAATAGACTTTTCTTCTCAATGAATGGCTTTTTCTACATGTTCCATGAGG
TAAGCATTCAATTATAATATGTTTTAATGAAGAATGTAAAA
Done.