Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398770.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2053.0, 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, 987
Length: 1646
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.30
Warning! 234 characters in sequence are not A, C, G, or T
Found at i:380 original size:170 final size:170
Alignment explanation
Indices: 2--1084 Score: 993
Period size: 170 Copynumber: 6.3 Consensus size: 170
1 T
* ** * * * * * *
2 GTTTCCTAAGGCAAACATTCAGTTGTAATTTATTTCAATAAAATATGTAAAAACAATTCAACGTA
1 GTTTCCTAAGGTAAACATTCAAATATAATCTATTTTAATAAAAAATAT-AAAA-AATTCAACTTA
* *********** *
67 AAATCAATTATGAGATTATAAAACCATTTAAAGCTAGTAATANNNNNNNNNNTGGCTTAAGTGAC
64 AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCTTGAGTGAC
* * * * * *
132 TATAAATGAACTTTTCTT-ACTAATGGATAGTTTTTGCTTTAA
129 TATAAATGGACTTTTCTTGTC-AATGGATGGCTTTTGCTTCAC
* * * *
174 GTTTACTGAA-GTAGACTTTCAAATATAATCTATTTTAATAAAAAATATAAAAAATTTAACTTAA
1 GTTTCCT-AAGGTAAACATTCAAATATAATCTATTTTAATAAAAAATATAAAAAATTCAACTTAA
* * **
238 AATCAATAATGCGATTATAAAATTATTTAAAGCGAGTAATAAGG-TTATCGAAGGCTTGAGTGAC
65 AATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTT-TCGAAGGCTTGAGTGAC
* *
302 TATAAATGGACTTTTCTTGTCAATGGATAGCTTTTGCTTCAT
129 TATAAATGGACTTTTCTTGTCAATGGATGGCTTTTGCTTCAC
* ** * ** *
344 GTTTCCTGAGGTAAACATTCAGTTATAATTTATTTTAACCAAATATATAAAAAACTTCAACTTAA
1 GTTTCCTAAGGTAAACATTCAAATATAATCTATTTTAATAAAAAATATAAAAAA-TTCAACTTAA
* *
409 AATC-ATT-TGAGATTATAAAACTATTTAAAAG-GAGTAATAAGGCTTTCAAAGGCTT-ATGTGA
65 AATCAATTATGAGATTATAAAACCATTT-AAAGCGAGTAATAAGGCTTTCGAAGGCTTGA-GTGA
* *
470 CTATAAATGGACTTTTCTTATCAATGGATGGCTTTTACTTCAC
128 CTATAAATGGACTTTTCTTGTCAATGGATGGCTTTTGCTTCAC
* ** * * * * *
513 GTTTCTTGAA-GTGGACATTGAAATATAATCTGTTTTATTGAAAAATATAAAAAAATTCAACTTC
1 GTTTCCT-AAGGTAAACATTCAAATATAATCTATTTTAATAAAAAATAT-AAAAAATTCAACTTA
* * * * * *
577 AAGTCAATAATGAGATTATAAAACCATTTAAAGCCAGTAATAAGACTTTCAAAAGCTTGAGTGAC
64 AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCTTGAGTGAC
* * *
642 TATAAATGGACTCTTCTTGTCAATGAATGACTTTTGC-TCACC
129 TATAAATGGACTTTTCTTGTCAATGGATGGCTTTTGCTTCA-C
* * * * * ** *
684 TTTTTCT-AGGCAAAGATTCAATTATAATAGATTTTAATGAAAAATGCA-AAAAAATTCAACTTA
1 GTTTCCTAAGGTAAACATTCAAATATAATCTATTTTAATAAAAAAT--ATAAAAAATTCAACTTA
* * * * * * ** *
747 AAATCAATTATTAGACTATAGAACCATTTAAAACGAGTAATAAGGCTTCCGAAGGCTTAAGCAAT
64 AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCTTGAGTGAC
** *
812 TATAAATGGACTTTTCTTGTCAATGGATGGCTTTTTTTTTAC
129 TATAAATGGACTTTTCTTGTCAATGGATGGCTTTTGCTTCAC
* * * * * * * *
854 GTTTCCTAAGGCAAACAGTCAAATATAATTTGTTTTCACT-AGAAATACAAGAAAAATCAACTTA
1 GTTTCCTAAGGTAAACATTCAAATATAATCTATTTT-AATAAAAAATATAA-AAAATTCAACTTA
* * *
918 AAATCAATTATAAGATTATCAAACCATTTAAAGCGAGTATTAAGGCTTTCGAAGGCTTGAGTGAC
64 AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCTTGAGTGAC
* * *
983 AATAAATGGACTTTTCTTGGCAATGGATGGCTTTTGCCTCAC
129 TATAAATGGACTTTTCTTGTCAATGGATGGCTTTTGCTTCAC
* ** * *
1025 GTTTCTTAAGGTTGACATTCAAATATAATCTATTTTAACAAAAAATGTAAAAAAATTCAA
1 GTTTCCTAAGGTAAACATTCAAATATAATCTATTTTAATAAAAAATAT-AAAAAATTCAA
1085 TGCAAACTAA
Statistics
Matches: 732, Mismatches: 154, Indels: 51
0.78 0.16 0.05
Matches are distributed among these distances:
168 1 0.00
169 128 0.17
170 289 0.39
171 272 0.37
172 40 0.05
173 2 0.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (170 bp):
GTTTCCTAAGGTAAACATTCAAATATAATCTATTTTAATAAAAAATATAAAAAATTCAACTTAAA
ATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAGGCTTGAGTGACTA
TAAATGGACTTTTCTTGTCAATGGATGGCTTTTGCTTCAC
Found at i:916 original size:341 final size:339
Alignment explanation
Indices: 120--1084 Score: 991
Period size: 341 Copynumber: 2.8 Consensus size: 339
110 NNNNNNNNNT
** * * * * * * *
120 GGCTTAAGTGACTATAAATGAACTTTTCTTA-CTAATGGATAGTTTTTGCTTTAAGTTTACTGAA
1 GGCTTAAGCAACTATAAATGGACTTTTCTTATC-AATGGATGGCTTTTACTTCACGTTTCCTGAA
** * * * * *
184 GT-AGACTTTCAAATATAATCTATTTTAATAAAAAATA-TAAAAAATTTAACTTAAAATCAATAA
65 GTGA-ACAGTCAAATATAATCTGTTTTACTGAAAAATACAAAAAAATTCAACTTAAAATCAATAA
* ** *
247 TGCGATTATAAAATTATTTAAAGCGAGTAATAAGGTTATCGAAGGCTTGAGTGACTATAAATGGA
129 TGAGATTATAAAACCATTTAAAGCGAGTAATAAGCTT-TCGAAGGCTTGAGTGACTATAAATGGA
* * **
312 CTTTTCTTGTCAATGGAT-AGCTTTTGCTTCA-TGTTTCCTGAGGTAAACATTCAGTTATAATTT
193 CTTTTCTTGTCAATGGATGA-CTTTTGC-TCACTGTTTCCTGAGGCAAACATTCAATTATAATAG
* * * * * *
375 ATTTTAACCAAATATATAAAAAACTTCAACTTAAAATCATTTGAGATTATAAAACTATTTAAAAG
256 ATTTTAACCAAAAATACAAAAAAATTCAACTTAAAATCATTTGAGACTATAAAACCATTTAAAAC
*
440 GAGTAATAAGGCTTTCAAA
321 GAGTAATAAGGCTTCCAAA
* ** *
459 GGCTTATGTGACTATAAATGGACTTTTCTTATCAATGGATGGCTTTTACTTCACGTTTCTTGAAG
1 GGCTTAAGCAACTATAAATGGACTTTTCTTATCAATGGATGGCTTTTACTTCACGTTTCCTGAAG
* * * * * * *
524 TGGACATTGAAATATAATCTGTTTTATTGAAAAATATAAAAAAATTCAACTTCAAGTCAATAATG
66 TGAACAGTCAAATATAATCTGTTTTACTGAAAAATACAAAAAAATTCAACTTAAAATCAATAATG
* * *
589 AGATTATAAAACCATTTAAAGCCAGTAATAAGACTTTCAAAAGCTTGAGTGACTATAAATGGACT
131 AGATTATAAAACCATTTAAAGCGAGTAATAAG-CTTTCGAAGGCTTGAGTGACTATAAATGGACT
* * * *
654 CTTCTTGTCAATGAATGACTTTTGCTCACCT-TTTTCT-AGGCAAAGATTCAATTATAATAGATT
195 TTTCTTGTCAATGGATGACTTTTGCTCA-CTGTTTCCTGAGGCAAACATTCAATTATAATAGATT
** * * *
717 TTAATGAAAAATGCAAAAAAATTCAACTTAAAATCAATTATTAGACTATAGAACCATTTAAAACG
259 TTAACCAAAAATACAAAAAAATTCAACTTAAAATC-ATT-TGAGACTATAAAACCATTTAAAACG
*
782 AGTAATAAGGCTTCCGAA
322 AGTAATAAGGCTTCCAAA
* * ** *
800 GGCTTAAGCAATTATAAATGGACTTTTCTTGTCAATGGATGGCTTTTTTTTTACGTTTCCT-AAG
1 GGCTTAAGCAACTATAAATGGACTTTTCTTATCAATGGATGGCTTTTACTTCACGTTTCCTGAAG
* *
864 -GCAAACAGTCAAATATAATTTGTTTTCACT-AGAAATACAAGAAAAA-TCAACTTAAAATCAAT
66 TG--AACAGTCAAATATAATCTGTTTT-ACTGAAAAATACAA-AAAAATTCAACTTAAAATCAAT
* * * * *
926 TATAAGATTATCAAACCATTTAAAGCGAGTATTAAGGCTTTCGAAGGCTTGAGTGACAATAAATG
127 AATGAGATTATAAAACCATTTAAAGCGAGTAATAA-GCTTTCGAAGGCTTGAGTGACTATAAATG
* * * * *** * *
991 GACTTTTCTTGGCAATGGATGGCTTTTGCCTCAC-GTTTCTTAAGGTTGACATTCAAATATAATC
191 GACTTTTCTTGTCAATGGATGACTTTTG-CTCACTGTTTCCTGAGGCAAACATTCAATTATAATA
* * **
1055 TATTTTAACAAAAAATGTAAAAAAATTCAA
255 GATTTTAACCAAAAATACAAAAAAATTCAA
1085 TGCAAACTAA
Statistics
Matches: 520, Mismatches: 89, Indels: 31
0.81 0.14 0.05
Matches are distributed among these distances:
339 137 0.26
340 112 0.22
341 217 0.42
342 54 0.10
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (339 bp):
GGCTTAAGCAACTATAAATGGACTTTTCTTATCAATGGATGGCTTTTACTTCACGTTTCCTGAAG
TGAACAGTCAAATATAATCTGTTTTACTGAAAAATACAAAAAAATTCAACTTAAAATCAATAATG
AGATTATAAAACCATTTAAAGCGAGTAATAAGCTTTCGAAGGCTTGAGTGACTATAAATGGACTT
TTCTTGTCAATGGATGACTTTTGCTCACTGTTTCCTGAGGCAAACATTCAATTATAATAGATTTT
AACCAAAAATACAAAAAAATTCAACTTAAAATCATTTGAGACTATAAAACCATTTAAAACGAGTA
ATAAGGCTTCCAAA
Done.