Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399465.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2728.0, 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: 4296
ACGTcount: A:0.24, C:0.08, G:0.08, T:0.23
Warning! 1556 characters in sequence are not A, C, G, or T
Found at i:1193 original size:170 final size:172
Alignment explanation
Indices: 872--1211 Score: 458
Period size: 170 Copynumber: 2.0 Consensus size: 172
862 NNNNNNNNNN
* * * * *
872 ATGAATGTCTTTTTCTTCACATTTCTCACAGTCGACATTCAATTATAATCTATTTTAACTAAAAA
1 ATGAATGTCATTTTCTTCACATTTCTCACAGTAGACATTCAATTACAATATATTTTAACCAAAAA
* * ** *
937 TGTACAAAGAATTTAAGCTAACATCAATTTTGAGATTTGAAAACCATTTAAAGCGAGTAATAAGG
66 TGTACAAAAAATTTAAGCTAAAATCAATTACGAGATTTGAAAACAATTTAAAGCGAGTAATAAGG
* * *
1002 CTTTTAAACGAATGTGTGACTATAAATGGGCTTTTCTTACCA
131 CTTTTAAACGAATGAGTGACTATAAATAGACTTTTCTTACCA
*
1044 ATGAATG-CATTTTCTTCACATTTCTCA-AGGTAGACATTCAATTACAATATGTTTTAACCAAAA
1 ATGAATGTCATTTTCTTCACATTTCTCACA-GTAGACATTCAATTACAATATATTTTAACCAAAA
*
1107 ATGTA-AAAAAATTTAATG-TAAAATCAATTACGAGATTAT-AAAATAATTTAAAGCGAGTAATA
65 ATGTACAAAAAATTTAA-GCTAAAATCAATTACGAGATT-TGAAAACAATTTAAAGCGAGTAATA
*
1169 AGGCTTTT-AAGGAAATGAGTGACTATAAATAGACTTTTCTTAC
128 AGGCTTTTAAACG-AATGAGTGACTATAAATAGACTTTTCTTAC
1212 TAANNNNNNN
Statistics
Matches: 148, Mismatches: 16, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
169 3 0.02
170 83 0.56
171 55 0.37
172 7 0.05
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (172 bp):
ATGAATGTCATTTTCTTCACATTTCTCACAGTAGACATTCAATTACAATATATTTTAACCAAAAA
TGTACAAAAAATTTAAGCTAAAATCAATTACGAGATTTGAAAACAATTTAAAGCGAGTAATAAGG
CTTTTAAACGAATGAGTGACTATAAATAGACTTTTCTTACCA
Found at i:1587 original size:21 final size:21
Alignment explanation
Indices: 1563--1602 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1553 GGATGGGTGA
1563 CAATAAATGAACTTTTTTTAC
1 CAATAAATGAACTTTTTTTAC
* * *
1584 CAATGAATGCATTTTTTTT
1 CAATAAATGAACTTTTTTT
1603 CATGTTTCCC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.12, G:0.07, T:0.47
Consensus pattern (21 bp):
CAATAAATGAACTTTTTTTAC
Found at i:2892 original size:172 final size:170
Alignment explanation
Indices: 2294--3027 Score: 478
Period size: 171 Copynumber: 4.3 Consensus size: 170
2284 TTTTGAGATA
* * * ** * *
2294 ATAAAACCATTTAAAGTGAGTAATGAGGCTTTTAAAGGAATTAGTGACTATAAATAGACCTTGCT
1 ATAAAACCATTTAAAGTGAGTAATAAAGC-TTTGAAGGAATGGGTGACTATAAATAGACTTTTCT
* * * * * * * * * * * * *
2359 AGCCAATGAATGCATTTTTTTTAACGTTTCTTAAGGTAAACATTCAATTGTACTCTGTTTTAACT
65 TGCCAATAAATGCCTTTTTCTTCAGGTTTCTCAAGATAGACATTCAATTATAATCTGCTTTAACC
* * * *
2424 AAAAATGTAAAATAATTCAACTTAAAATCAATTATTA-TATT
130 AAAAATGTAAAACAATTCAAATTAAAATCAACTA-TAGCATT
* * * * * * ** * *
2465 ATATAATCATTTAAAGCGAGTAATAAGGTTTTCGAAGGATTAAGAGAGTATAAATAGACTTTTCT
1 ATAAAACCATTTAAAGTGAGTAATAAAGCTTT-GAAGGAATGGGTGACTATAAATAGACTTTTCT
* * * * * * * **
2530 T-CCAAATGAATGGCTTTGTCTACATGTTCCT-AAGCCA-AG-CATTCAATTATAGTCTAATTTA
65 TGCC-AATAAATGCCTTTTTCTTCAGGTTTCTCAAG--ATAGACATTCAATTATAATCTGCTTTA
* * **********
2591 A-AAAAAATGTAAAACAATTCAACTTANNNNNNNNNNTGAG-ATT
127 ACCAAAAATGTAAAACAATTCAAATTAAAATCAACTAT-AGCATT
* * * * *
2634 AGAAAACTATTTAAAGTGGGTAATAAAACTTTTGAAGGAATGGGTAACTATAAATAGACTTTTCT
1 ATAAAACCATTTAAAGTGAGTAATAAAGC-TTTGAAGGAATGGGTGACTATAAATAGACTTTTCT
** *
2699 TGCCAATAAATGCCTTTTTCTTCAGGTTTCTCAA-AGTTTACGTTCAATTATAATCTGCTTTAAC
65 TGCCAATAAATGCCTTTTTCTTCAGGTTTCTCAAGA-TAGACATTCAATTATAATCTGCTTTAAC
* * * * * * *
2763 CAAAAATGTACAAAGAATTCAAATTAGAAT-TAGTTTTGATATT
129 CAAAAATGTA-AAACAATTCAAATTAAAATCAACTATAG-CATT
* *
2806 ATAAAACCATTTAAAGTGAGTAATAATGCTTCTGAAGGAATGGGTGACTATAAATGGACTTTTCT
1 ATAAAACCATTTAAAGTGAGTAATAAAGCTT-TGAAGGAATGGGTGACTATAAATAGACTTTTCT
********** * * * *
2871 TGCNNNNNNNNNNCTTTTTCTTTATGTTTCTCAAGATAGACATTCAATTATAGTCTGTTTTAACC
65 TGCCAATAAATGCCTTTTTCTTCAGGTTTCTCAAGATAGACATTCAATTATAATCTGCTTTAACC
* *
2936 AAAGATGTAAAACAATTCAACTTAAAATCAACTATAGCATT
130 AAAAATGTAAAACAATTCAAATTAAAATCAACTATAGCATT
* *
2977 ATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAGAGAATGGGTGACTAT
1 ATAAAACCATTTAAAGTGAGTAATAAAGCTTTGAAG-GAATGGGTGACTAT
3028 NNNNNNNNNN
Statistics
Matches: 429, Mismatches: 114, Indels: 40
0.74 0.20 0.07
Matches are distributed among these distances:
167 1 0.00
168 1 0.00
169 95 0.22
170 58 0.14
171 144 0.34
172 129 0.30
173 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.34
Consensus pattern (170 bp):
ATAAAACCATTTAAAGTGAGTAATAAAGCTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTT
GCCAATAAATGCCTTTTTCTTCAGGTTTCTCAAGATAGACATTCAATTATAATCTGCTTTAACCA
AAAATGTAAAACAATTCAAATTAAAATCAACTATAGCATT
Done.