Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399558.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2813.0, 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, 775
Length: 1293
ACGTcount: A:0.30, C:0.10, G:0.13, T:0.31
Warning! 216 characters in sequence are not A, C, G, or T
Found at i:1021 original size:170 final size:169
Alignment explanation
Indices: 722--1293 Score: 422
Period size: 170 Copynumber: 3.4 Consensus size: 169
712 NNNNNNNNNN
* * * * *
722 TGAATGGCTTTTTCTGTATGTTTTCTGAGGTAGACATTCAATTATAGCCTGTTTTAACCAAATAT
1 TGAAT-GCTTTTTCTATATGTTTCCTAAGGTAGACATTCAATTATAGCATGTTTTAACCAAAAAT
** * *
787 GTAAAAAAATTCGACTTAAAATCAATTATGATTTTATAAAATAATTTAAAGCGAGTAGTAAGGC-
65 GTAAAAAAATTCGACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCT
* * * *
851 TTGAAAGGAATGGGTGACAATAAATTGGCTTTTCTT-CTCAA
130 TTGAAA-GAATAGGAGACAATAAATAGACTTTTCTTGC-CAA
* *
892 TGAATAGCTTTTTCTATATGTTTCCTAAGGTAGACATTCAATTATAGTATGTTTTAGCCAAAAAT
1 TGAAT-GCTTTTTCTATATGTTTCCTAAGGTAGACATTCAATTATAGCATGTTTTAACCAAAAAT
********** *
957 GTAAAANNNNNNNNNNTAAAATCAATTATGAGATTATAAAACAATTTAAAGTGAGTAATAAGGCT
65 GTAAAAAAATTCGACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCT
**
1022 TTGAAAGAATAGGAGACTGTAAATAGACTTTTCTTGCCAA
130 TTGAAAGAATAGGAGACAATAAATAGACTTTTCTTGCCAA
* * * * * * * **
1062 TGAATGTTTTTTCT-TACGTTT-TTGAAGGCAAACATTTAATTATAGTC-TATTTTAATAAAAAA
1 TGAATGCTTTTTCTATATGTTTCCT-AAGGTAGACATTCAATTATAG-CATGTTTTAACCAAAAA
* * ********** * * * *
1124 TCTAAAAACATTCNNNNNNNNNNCAATTATGAGATTATAAAACCATTTCAAGTGAGTAATAAGTC
64 TGTAAAAAAATTCGACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGC
* * * * * * *
1189 TTTTG-AAGAATGGGTGACTATAAATGGACTTTTGTTACCAG
129 -TTTGAAAGAATAGGAGACAATAAATAGACTTTTCTTGCCAA
** * *
1230 TGAATGTCTTTTTCT-TCATGTTTTTTGAGGTAGACCTTCAATTATAGTC-TGTTTTAACCAAAA
1 TGAATG-CTTTTTCTAT-ATGTTTCCTAAGGTAGACATTCAATTATAG-CATGTTTTAACCAAAA
1293 A
63 A
Statistics
Matches: 321, Mismatches: 73, Indels: 16
0.78 0.18 0.04
Matches are distributed among these distances:
167 1 0.00
168 119 0.37
169 20 0.06
170 172 0.54
171 9 0.03
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.36
Consensus pattern (169 bp):
TGAATGCTTTTTCTATATGTTTCCTAAGGTAGACATTCAATTATAGCATGTTTTAACCAAAAATG
TAAAAAAATTCGACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTT
TGAAAGAATAGGAGACAATAAATAGACTTTTCTTGCCAA
Found at i:1179 original size:168 final size:160
Alignment explanation
Indices: 979--1286 Score: 336
Period size: 168 Copynumber: 1.9 Consensus size: 160
969 NNNNTAAAAT
*
979 CAATTATGAGATTATAAAACAATTTAAAGTGAGTAATAAGGC-TTTGAAAGAATAGGAGACTGTA
1 CAATTATGAGATTATAAAACAATTTAAAGTGAGTAATAAGGCTTTTG-AAGAATAGGAGACTATA
* *
1043 AATAGACTTTTCTTGCCAATGAATGT-TTTTTCTT-ACG-TTTTTGAAGGCAAACATTTAATTAT
65 AATAGACTTTTCTTACCAATGAATGTCTTTTTCTTCACGTTTTTTG-AGGCAAACATTCAATTAT
1105 AGTCTATTTTAATAAAAAATCTAAAAACATTC
129 AGTCTATTTTAATAAAAAATCTAAAAACATTC
* * * *
1137 NNNNNNNNNNCAATTATGAGATTATAAAACCATTTCAAGTGAGTAATAAGTCTTTTGAAGAATGG
1 ----------CAATTATGAGATTATAAAACAATTTAAAGTGAGTAATAAGGCTTTTGAAGAATAG
* * * * * * * *
1202 GTGACTATAAATGGACTTTTGTTACCAGTGAATGTCTTTTTCTTCATGTTTTTTGAGGTAGACCT
56 GAGACTATAAATAGACTTTTCTTACCAATGAATGTCTTTTTCTTCACGTTTTTTGAGGCAAACAT
*
1267 TCAATTATAGTCTGTTTTAA
121 TCAATTATAGTCTATTTTAA
1287 CCAAAAA
Statistics
Matches: 120, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
168 75 0.62
169 12 0.10
170 27 0.22
171 6 0.05
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.37
Consensus pattern (160 bp):
CAATTATGAGATTATAAAACAATTTAAAGTGAGTAATAAGGCTTTTGAAGAATAGGAGACTATAA
ATAGACTTTTCTTACCAATGAATGTCTTTTTCTTCACGTTTTTTGAGGCAAACATTCAATTATAG
TCTATTTTAATAAAAAATCTAAAAACATTC
Done.