Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398344.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1643.0, 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: 3218
ACGTcount: A:0.27, C:0.09, G:0.10, T:0.26
Warning! 906 characters in sequence are not A, C, G, or T
Found at i:1214 original size:170 final size:169
Alignment explanation
Indices: 1038--1581 Score: 452
Period size: 171 Copynumber: 3.2 Consensus size: 169
1028 NNNNNNNNNN
* * * *
1038 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACAATAAATGAACTTTTTTTGCTAATAA
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGAACTTTTCTTGCTAATGA
*
1103 ATGCCTTTTCTTCATGTTTTTCAAGGTAGACATTCAATTACT-GTCTGTTTTAACCAGAAATGAA
66 ATGCCTTTTCTTCATGTTTTTCAAGCTAGACATTCAATTA-TAGTCTGTTTTAACCA-AAATGAA
*
1167 AAAAAATTGAACCTAAAATCAATTTTGAGAATATAAAATCA
129 AAAAAATTGAACCTAAAATCAATTTTGAGAATATAAAACCA
*********** * * * * *
1208 TTTAAAGCGAGTAANNNNNNNNNNAAAGGAATAAGAGACTATAAATAAACTTTTGTTGCCAATGA
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGAACTTTTCTTGCTAATGA
* * * *
1273 ATGCCTTTTTCTTCATGTTTCTT-TAGCTAGACATTCAATTATAAT-TATTTTAACCAATTATGC
66 ATGCC-TTTTCTTCATGTTT-TTCAAGCTAGACATTCAATTATAGTCTGTTTTAACCAA-AATG-
* *
1336 AATAAAAATTGAACCTAAAATCGATTTTGAG-ATGATAAAACCA
127 AAAAAAAATTGAACCTAAAATCAATTTTGAGAAT-ATAAAACCA
********** * * *
1379 TTTAAAGCGAGTAATAAGGNNNNNNNNNNAATGAGTGACTATAAATGGAGTTTTCTTG-TCCATG
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGAACTTTTCTTGCT-AATG
* * * * **
1443 AATGCTTTTTTCTTTATGTTTCTCAAGTTAGACATTCAATTATAGTCTGTTTTGATTCAAAAT-A
65 AATGC-CTTTTCTTCATGTTTTTCAAGCTAGACATTCAATTATAGTCTGTTTT-AACCAAAATGA
* * * * * * *
1507 TAAAAAAATTTAACTTAAAATCAAATGTCAGATTATAAAAGCA
128 -AAAAAAATTGAACCTAAAATCAATTTTGAGAATATAAAACCA
*
1550 TTAAAAGCGAGTAATAAGGCTTTTGAAGGAAT
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAAT
1582 ACGAGGCCGT
Statistics
Matches: 286, Mismatches: 75, Indels: 25
0.74 0.19 0.06
Matches are distributed among these distances:
169 1 0.00
170 69 0.24
171 202 0.71
172 10 0.03
173 4 0.01
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.34
Consensus pattern (169 bp):
TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGAACTTTTCTTGCTAATGA
ATGCCTTTTCTTCATGTTTTTCAAGCTAGACATTCAATTATAGTCTGTTTTAACCAAAATGAAAA
AAAATTGAACCTAAAATCAATTTTGAGAATATAAAACCA
Found at i:2833 original size:170 final size:171
Alignment explanation
Indices: 2482--3074 Score: 509
Period size: 172 Copynumber: 3.5 Consensus size: 171
2472 NNNNNNNNNA
* * * * **
2482 GACTATAAATGGACTTTTTTTTGCCAACGAAT-GCTTGTTTCTTCACATTTCTTG-AGCTAGAA-
1 GACTATAAATGGAC-TTTTCTTGTCAATGAATACCTT-TTTCTTCATGTTTCTTGAAG-TA-AAC
* * * * * ** *
2544 AATCAATTACAGTCT-TTTTAACCAATAATCTAATTAAAATTGAACCTAAAATCAAATATGAGAT
62 AATCAATTATAATATGTTTTAACCAAAAATGTAAAAAAAATTGAACCTAAAATCAATTA-GAGAT
**********
2608 TATAAAATCATTTAAAGCGAGTAATAAGNNNNNNNNNNGAATGGGT
126 TATAAAATCATTTAAAGCGAGTAATAAGGCTCTTGAAGGAATGGGT
* * ** * * **
2654 GATTATAAATGGACTTTTCTTCTCAATGAATTTCTTTTGCTACATGTTTGC-T-AAGGTAGGCAA
1 GACTATAAATGGACTTTTCTTGTCAATGAATACCTTTTTCTTCATGTTT-CTTGAA-GTAAACAA
* * *** * * *
2717 TCAATTATAGTTTGTTTTAGTGAAAAATGT-AAAACAATTAAACTTAAAATCAATTAGAGATTAT
64 TCAATTATAATATGTTTTAACCAAAAATGTAAAAAAAATTGAACCTAAAATCAATTAGAGATTAT
*
2781 AAAATCATTTAAAGCGAGTAATAAGGCTCTTGAAGGAATGAGT
129 AAAATCATTTAAAGCGAGTAATAAGGCTCTTGAAGGAATGGGT
* * * *
2824 GAGTATAAATGGACTTTTCTTGTCAATGTATACCTTTTTCTTCATGTTTCTTGAATTAAACATTC
1 GACTATAAATGGACTTTTCTTGTCAATGAATACCTTTTTCTTCATGTTTCTTGAAGTAAACAATC
* * * * * *
2889 AATTATAATATGTTTTAACCAATAATGTAAAAAAAAATTGAACCAAAAATCAGTTTTGGGATTGT
66 AATTATAATATGTTTTAACCAAAAATGT-AAAAAAAATTGAACCTAAAATCA-ATTAGAGATTAT
* * * *
2954 AAAACCATTTAAAGCGAATAATAATGCTTTTGAAGGAATGGGT
129 AAAATCATTTAAAGCGAGTAATAAGGCTCTTGAAGGAATGGGT
* * * * *
2997 GACT-TAAATGGACTTTTCTTGTCCATGAATCCCTTTTTCTTCATGTTTCTTGAACTAGACATTC
1 GACTATAAATGGACTTTTCTTGTCAATGAATACCTTTTTCTTCATGTTTCTTGAAGTAAACAATC
3061 AATTATAATATGTT
66 AATTATAATATGTT
3075 NNNNNNNNNN
Statistics
Matches: 338, Mismatches: 72, Indels: 22
0.78 0.17 0.05
Matches are distributed among these distances:
169 1 0.00
170 111 0.33
171 61 0.18
172 116 0.34
173 49 0.14
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.36
Consensus pattern (171 bp):
GACTATAAATGGACTTTTCTTGTCAATGAATACCTTTTTCTTCATGTTTCTTGAAGTAAACAATC
AATTATAATATGTTTTAACCAAAAATGTAAAAAAAATTGAACCTAAAATCAATTAGAGATTATAA
AATCATTTAAAGCGAGTAATAAGGCTCTTGAAGGAATGGGT
Done.