Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401148.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4301.0, 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: 3369
ACGTcount: A:0.26, C:0.08, G:0.09, T:0.24
Warning! 1073 characters in sequence are not A, C, G, or T
Found at i:1253 original size:171 final size:171
Alignment explanation
Indices: 752--1771 Score: 980
Period size: 171 Copynumber: 6.0 Consensus size: 171
742 NNNNNNNNNG
* * * * * *
752 TACTTTCAAAGGTATAGGTGACTATAAATGAACTTTTCTTGGC-AAT-AAATG-GTTTCCTCCTC
1 TACTTTCGAAGGTATGGGTGACTATAAATGGACTTTTCTT-GCTAATGAAA-GCCTTT-TTCTTC
* ** * * * * * **** * *
814 ATGTTTCTTGAGTCGGACAATCAATTATAATCTATTATAACCCGAAACATAAAAAAATTCAATTT
63 ACGTTTCTCAAGACAGACATTCAATTATAATATATTTTAATAAAAAATATAAAAAAATTCAACTT
* **
879 AAAATGAATTATGAGATTAT-AAACCTATTTAAAATGAGTAATAA
128 AAAATCAATTATGAGATTATAAAACC-ATTTAAAGCGAGTAATAA
* * * * * * * *
923 TGCTTTCAAAGGCATGGTTGACTGTAAATGCACTTTTCTTGCTAAT-AAATCATTTTTTCTTCAC
1 TACTTTCGAAGGTATGGGTGACTATAAATGGACTTTTCTTGCTAATGAAAGC-CTTTTTCTTCAC
* * * * *
987 ATTTCTCAAGACAAACATTCAATTATAATATATTTTAATGAAAAATAT-AAAAAATTTAACTGAA
65 GTTTCTCAAGACAGACATTCAATTATAATATATTTTAATAAAAAATATAAAAAAATTCAACTTAA
1051 AATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAA
130 AATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAA
* * * *
1093 TACTTTCGAAGGTATGGCTGACTATAAATGGACTTTACCTGCCAATGAAAGCCTTTTTCTTCACG
1 TACTTTCGAAGGTATGGGTGACTATAAATGGACTTTTCTTGCTAATGAAAGCCTTTTTCTTCACG
* ** * * * * * *
1158 TTTCTTAAGGTAGACATGCAATTATAATCTGTTTTAATAAAAAATGTAAAAAAATTTAACTTGAA
66 TTTCTCAAGACAGACATTCAATTATAATATATTTTAATAAAAAATATAAAAAAATTCAACTTAAA
* **
1223 ATCAATTATGAGATTATAAAATCATTTAAAGCCTGTAATAA
131 ATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAA
* ** * * * *
1264 TACCTTCGAAGGTATGGGTGACTATAAATATACTTTTCTTGCTAATGAATGGCTTTATCTTTACG
1 TACTTTCGAAGGTATGGGTGACTATAAATGGACTTTTCTTGCTAATGAAAGCCTTTTTCTTCACG
* * * *
1329 TTTCTCAAGAGA-AGCATTCAATTATAATATATTTTAATGAAAAATAT-AAAACATTCAACATAA
66 TTTCTCAAGACAGA-CATTCAATTATAATATATTTTAATAAAAAATATAAAAAAATTCAACTTAA
* * *
1392 AATCAATTATGAGATTATAAAATCATGTGAAGCGAGTAATAA
130 AATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAA
* * ** * ** *
1434 TTCTTTCTAAGGTATGGGTGACTATAAATGGACTTGACCTG-TCAATGAAAGGTTTTTTCTTCAT
1 TACTTTCGAAGGTATGGGTGACTATAAATGGACTTTTCTTGCT-AATGAAAGCCTTTTTCTTCAC
* * * * * ** * *
1498 ATTTCTCAAGATAGACGTTCAATTATAATTTATTTTAATCAAAAATGCAAAAAACTTTAACTTAA
65 GTTTCTCAAGACAGACATTCAATTATAATATATTTTAATAAAAAATATAAAAAAATTCAACTTAA
* * * *
1563 AATTAATTATGAGATTATAAAACCATTTAAAGCGTGTAGTGA
130 AATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAA
* ** * * * * *
1605 TGCTTTCGAAGGCGTGGGTGACTATAAATGTACTTTTCTTTCTAATGAATAG-CTTTCTCTTTAT
1 TACTTTCGAAGGTATGGGTGACTATAAATGGACTTTTCTTGCTAATGAA-AGCCTTTTTCTTCAC
* * * *
1669 GTTTTTCAAGACAAACATTCAATTATAATATATTTCAATAAAAAATATAAAAAAAATTCAACTTC
65 GTTTCTCAAGACAGACATTCAATTATAATATATTTTAATAAAAAATAT-AAAAAAATTCAACTTA
* *
1734 AAATCAATTATAAGATTATAAAACTATTTAAAGCGAGT
129 AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGT
1772 NNNNNNNNNN
Statistics
Matches: 692, Mismatches: 144, Indels: 25
0.80 0.17 0.03
Matches are distributed among these distances:
169 1 0.00
170 273 0.39
171 365 0.53
172 53 0.08
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.36
Consensus pattern (171 bp):
TACTTTCGAAGGTATGGGTGACTATAAATGGACTTTTCTTGCTAATGAAAGCCTTTTTCTTCACG
TTTCTCAAGACAGACATTCAATTATAATATATTTTAATAAAAAATATAAAAAAATTCAACTTAAA
ATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAA
Found at i:1375 original size:341 final size:340
Alignment explanation
Indices: 863--1771 Score: 1192
Period size: 341 Copynumber: 2.7 Consensus size: 340
853 ACCCGAAACA
* * * ** *
863 TAAAAAAATTCAATTTAAAATGAATTATGAGATTAT-AAACCTATTTAAAATGAGTAATAATGCT
1 TAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAACC-ATTTAAAGCGTGTAATAATGCT
* * * * * * * * *
927 TTCAAAGGCATGGTTGACTGTAAATGCACTTTTCTTGCTAATAAATCA-TTTTTTCTTCACATTT
65 TTCGAAGGCATGGGTGACTATAAATGTACTTTTCTTGCTAATGAAT-AGCTTTATCTTTACGTTT
*
991 CTCAAGACAAACATTCAATTATAATATATTTTAATGAAAAATATAAAAAATTTAACTGAAAATCA
129 CTCAAGACAAACATTCAATTATAATATATTTTAATGAAAAATATAAAAAATTCAACT-AAAATCA
1056 ATTATGAGATTATAAAACCATTTAAAGCGAGTAATAATACTTTCGAAGGTATGGCTGACTATAAA
193 ATTATGAGATTATAAAACCATTTAAAGCGAGTAATAATACTTTCGAAGGTATGGCTGACTATAAA
* * * *
1121 TGGACTTTACCTGCCAATGAAAGCCTTTTTCTTCACGTTTCTTAAGGTAGACATGCAATTATAAT
258 TGGACTTGACCTGCCAATGAAAGCCTTTTTCTTCACATTTCTCAAGATAGACATGCAATTATAAT
*
1186 CTGTTTTAATAAAAAATG
323 CTATTTTAATAAAAAATG
* * * * *
1204 TAAAAAAATTTAACTTGAAATCAATTATGAGATTATAAAATCATTTAAAGCCTGTAATAATACCT
1 TAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGTGTAATAATGCTT
* * *
1269 TCGAAGGTATGGGTGACTATAAATATACTTTTCTTGCTAATGAATGGCTTTATCTTTACGTTTCT
66 TCGAAGGCATGGGTGACTATAAATGTACTTTTCTTGCTAATGAATAGCTTTATCTTTACGTTTCT
* * *
1334 CAAGAGAAGCATTCAATTATAATATATTTTAATGAAAAATATAAAACATTCAACATAAAATCAAT
131 CAAGACAAACATTCAATTATAATATATTTTAATGAAAAATATAAAAAATTCAAC-TAAAATCAAT
* * * * * *
1399 TATGAGATTATAAAATCATGTGAAGCGAGTAATAATTCTTTCTAAGGTATGGGTGACTATAAATG
195 TATGAGATTATAAAACCATTTAAAGCGAGTAATAATACTTTCGAAGGTATGGCTGACTATAAATG
* ** * * * *
1464 GACTTGACCTGTCAATGAAAGGTTTTTTCTTCATATTTCTCAAGATAGACGTTCAATTATAATTT
260 GACTTGACCTGCCAATGAAAGCCTTTTTCTTCACATTTCTCAAGATAGACATGCAATTATAATCT
*
1529 ATTTTAATCAAAAATG
325 ATTTTAATAAAAAATG
* * * * *
1545 CAAAAAACTTTAACTTAAAATTAATTATGAGATTATAAAACCATTTAAAGCGTGTAGTGATGCTT
1 TAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGTGTAATAATGCTT
* * * * *
1610 TCGAAGGCGTGGGTGACTATAAATGTACTTTTCTTTCTAATGAATAGCTTTCTCTTTATGTTTTT
66 TCGAAGGCATGGGTGACTATAAATGTACTTTTCTTGCTAATGAATAGCTTTATCTTTACGTTTCT
* * *
1675 CAAGACAAACATTCAATTATAATATATTTCAATAAAAAATATAAAAAAAATTCAACTTCAAATCA
131 CAAGACAAACATTCAATTATAATATATTTTAATGAAAAATAT--AAAAAATTCAAC-TAAAATCA
* *
1740 ATTATAAGATTATAAAACTATTTAAAGCGAGT
193 ATTATGAGATTATAAAACCATTTAAAGCGAGT
1772 NNNNNNNNNN
Statistics
Matches: 487, Mismatches: 76, Indels: 8
0.85 0.13 0.01
Matches are distributed among these distances:
341 437 0.90
342 5 0.01
343 45 0.09
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (340 bp):
TAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGTGTAATAATGCTT
TCGAAGGCATGGGTGACTATAAATGTACTTTTCTTGCTAATGAATAGCTTTATCTTTACGTTTCT
CAAGACAAACATTCAATTATAATATATTTTAATGAAAAATATAAAAAATTCAACTAAAATCAATT
ATGAGATTATAAAACCATTTAAAGCGAGTAATAATACTTTCGAAGGTATGGCTGACTATAAATGG
ACTTGACCTGCCAATGAAAGCCTTTTTCTTCACATTTCTCAAGATAGACATGCAATTATAATCTA
TTTTAATAAAAAATG
Done.