Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398778.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2061.0, 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: 1760
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.27
Warning! 354 characters in sequence are not A, C, G, or T
Found at i:94 original size:60 final size:60
Alignment explanation
Indices: 1--118 Score: 218
Period size: 60 Copynumber: 2.0 Consensus size: 60
* *
1 TTAAAGCGAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATGGACATTTCATGCAT
1 TTAAAGCGAGTAATAAGGCTTTTGAAAGAATGGGTAACTATAAATGGACATTTAATGCAT
61 TTAAAGCGAGTAATAAGGCTTTTGAAAGAATGGGTAACTATAAATGGACATTTAATGC
1 TTAAAGCGAGTAATAAGGCTTTTGAAAGAATGGGTAACTATAAATGGACATTTAATGC
119 CAATGAATGC
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.38, C:0.09, G:0.23, T:0.30
Consensus pattern (60 bp):
TTAAAGCGAGTAATAAGGCTTTTGAAAGAATGGGTAACTATAAATGGACATTTAATGCAT
Found at i:355 original size:171 final size:170
Alignment explanation
Indices: 58--1165 Score: 723
Period size: 171 Copynumber: 6.5 Consensus size: 170
48 ACATTTCATG
* * * * **
58 CATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGGGTAACTATAAATGGACATTTAATGCCAAT
1 CATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTGCCAAT
* * ** * * *
123 GAATGCCTTCTTCATCATGTTTCTCTAGATAGACATTCAAGTATAATCTATTTACACCAAAAATT
66 GAATG-CTTTTTCTTCACATTTCTCGAGATAGACAATCAAGTATAATCTGTTTACACCAAAAATT
188 TAAAATAATTCAACTTAAAAATAATTTTGAGATTATAAAAC
130 TAAAATAATTCAACTTAAAAATAATTTTGAGATTATAAAAC
* * * * *
229 CATTTAAACCGAGTAATAAGACTTTTGAAGGGATG-GATGACTATAAACGGACTTTTCTTGCTAA
1 CATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAG-TGACTATAAATGGACTTTTCTTGCCAA
* * * * *
293 TGAATGAATTTTTCTTTACATTTCTCGAGGTAGACAATAAATTATAAAT-TGTTTTA-ACCAAAA
65 TGAATG-CTTTTTCTTCACATTTCTCGAGATAGACAATCAAGTAT-AATCTG-TTTACACCAAAA
* * ** * *
356 ATCTACAAACAATTCGGCTT-ATAATCAATTATGAGATTATAAAAC
127 ATTTA-AAATAATTCAACTTAAAAAT-AATTTTGAGATTATAAAAC
* *********** * *
401 TATTTAANNNNNNNNNNGAGGCTTTTGAAGGAAT-AGGTGGCTATAAATGGACTCTTCTTGCCAA
1 CATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGA-GTGACTATAAATGGACTTTTCTTGCCAA
* ** * * * * * *
465 TGAATGCCTTTTCTTCATGTTTCTCGAGACAGACATTCAATTGTAGTCTATTTTA-A--AGAAAA
65 TGAATGCTTTTTCTTCACATTTCTCGAGATAGACAATCAAGTATAATCT-GTTTACACCA-AAAA
* * * **********
527 TGTAAAAAAAATCAACTT-AAAATCAATNNNNNNNNNNTAAAAC
128 TTTAAAATAATTCAACTTAAAAAT-AATTTTGAGATTATAAAAC
* * * * *
570 TATTGAAAGCGAGTAATAAGGCTTTTGAAGGAATAAGTGACTATAAGTGGACTTTTCATGCCAAT
1 CATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTGCCAAT
** * * * * *
635 GAATGCTTCTTTCTTCATGTTTCTTGAGGTAAAC-ATCCAAGTATAGTCTGTTTACATCAAAAAT
66 GAATGCTT-TTTCTTCACATTTCTCGAGATAGACAAT-CAAGTATAATCTGTTTACACCAAAAAT
* * *
699 TTAAAATAATTCAACTTAAAAACAATTTTGGGATTATAAAAT
129 TTAAAATAATTCAACTTAAAAATAATTTTGAGATTATAAAAC
** * * * *
741 CATTTAAAGTAAGTAATAACGCTTTTGAAGGAATGAGTAACTATAAATGGATTTTTCCTGCCAAT
1 CATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTGCCAAT
* ** * * **
806 GAGTGCCTTTTTAATCACATTTCTCTAGATAGACATTCAAGTATAATCTGTTTACAGTAAAAATT
66 GAATG-CTTTTTCTTCACATTTCTCGAGATAGACAATCAAGTATAATCTGTTTACACCAAAAATT
*
871 TAAAATAATTCAACTTAAAATTAATTTT-AGGATTATAAAAC
130 TAAAATAATTCAACTTAAAAATAATTTTGA-GATTATAAAAC
********** * *
912 CATTTAAAGCGAGTAATAAGGCNNNNNNNNNNATGGGTGACTATAAATGGAC-TTTCTTGTCAAT
1 CATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTGCCAAT
* ** * * *
976 GAATGCCTTTTTCTACATGTTTACT-GAG-TATGACATTCAATTATAA-CTTGTTTTA-ACTAAA
66 GAATG-CTTTTTCTTCACATTT-CTCGAGATA-GACAATCAAGTATAATC-TG-TTTACACCAAA
* * * *
1037 AATATAAAA-AA---AA--T-ATAATCAATTATAAGATTATAAAAC
126 AATTTAAAATAATTCAACTTAAAAAT-AATTTTGAGATTATAAAAC
* * * * * ***
1076 CATTTAAAGTGAGTAGTAAGGCTTTTGAAGGTATGAGTGGCTATAAATAGACTTTTCTTATAAAT
1 CATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTGCCAAT
* *
1141 GAATGCCTTTTGCTTCACGTTTCTC
66 GAATG-CTTTTTCTTCACATTTCTC
1166 AAGGCGACAT
Statistics
Matches: 716, Mismatches: 193, Indels: 62
0.74 0.20 0.06
Matches are distributed among these distances:
163 3 0.00
164 56 0.08
165 30 0.04
166 2 0.00
169 89 0.12
170 100 0.14
171 341 0.48
172 94 0.13
173 1 0.00
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.34
Consensus pattern (170 bp):
CATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTGCCAAT
GAATGCTTTTTCTTCACATTTCTCGAGATAGACAATCAAGTATAATCTGTTTACACCAAAAATTT
AAAATAATTCAACTTAAAAATAATTTTGAGATTATAAAAC
Found at i:1047 original size:512 final size:502
Alignment explanation
Indices: 63--1050 Score: 985
Period size: 512 Copynumber: 1.9 Consensus size: 502
53 TCATGCATTT
**
63 AAAGCGAGTAATAAGGCTTTTGAAAGAATGGGTAACTATAAATGGACATTTAATGCCAATGAATG
1 AAAGCGAGTAATAAGGCTTTTGAAAGAATAAGTAACTATAAATGGACATTTAATGCCAATGAATG
* *
128 CCTTCTTCATCATGTTTCTCTAGATAGACATTCAAGTATAATCTATTTACACCAAAAATTTAAAA
66 CCTTCTTCATCATGTTTCTCTAGATAAACATCCAAGTATAATCTATTTACACCAAAAATTTAAAA
* *
193 TAATTCAACTTAAAAATAATTTTGAGATTATAAAACCATTTAAACCGAGTAATAAGACTTTTGAA
131 TAATTCAACTTAAAAACAATTTTGAGATTATAAAACCATTTAAACCAAGTAATAAGACTTTTGAA
* * * * ** * *
258 GGGATGGATGACTATAAACGGACTTTTCTTGCTAATGAATGAATTTTTCTTTACATTTCTCGAGG
196 GGAATGGATAACTATAAACGGACTTTTCCTGCCAATGAATGAATTTTTAATCACATTTCTCGAGA
* ** *
323 TAGACAATAAATTATAAATTGTTTTAACCAAAAATCTACAAACAATTCGGCTTATAATCAATTAT
261 TAGACAATAAAGTATAAATTGTTTTAACCAAAAATCTACAAACAATTCAACTTAAAATCAATTAT
* *********** *
388 GAGATTATAAAACTATTTAANNNNNNNNNNGAGGCTTTTGAAGGAATAGGTGGCTATAAATGGAC
326 GAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATGGAC
* * *
453 TCTTCTTGCCAATGAATGCCTTTTCTTCATGTTTCTCGAGACAGACATTCAATTGTAGTCTATTT
391 TCTTCTTGCCAATGAATGCCTTTTCTACATGTTTCTCGAGACAGACATTCAATTATACTCTATTT
*
518 TAAAGAAAATGTAAAAAAAATCAACTTAAAATCAATNNNNNNNNNNTAAAACTATTG
456 TAAAGAAAATATAAAAAAAATCAACTTAAAATCAAT----------TAAAACTATTG
* * * * *
575 AAAGCGAGTAATAAGGCTTTTGAAGGAATAAGTGACTATAAGTGGACTTTTCATGCCAATGAATG
1 AAAGCGAGTAATAAGGCTTTTGAAAGAATAAGTAACTATAAATGGACATTTAATGCCAATGAATG
* * * * *
640 -CTTCTTTCTTCATGTTTCT-TGAGGTAAACATCCAAGTATAGTCTGTTTACATCAAAAATTTAA
66 CCTTC-TTCATCATGTTTCTCT-AGATAAACATCCAAGTATAATCTATTTACACCAAAAATTTAA
* * **
703 AATAATTCAACTTAAAAACAATTTTGGGATTATAAAATCATTTAAAGTAAGTAATAACG-CTTTT
129 AATAATTCAACTTAAAAACAATTTTGAGATTATAAAACCATTTAAACCAAGTAATAA-GACTTTT
* * * **
767 GAAGGAAT-GAGTAACTATAAATGGATTTTTCCTGCCAATGAGTGCCTTTTTAATCACATTTCTC
193 GAAGGAATGGA-TAACTATAAACGGACTTTTCCTGCCAATGAATGAATTTTTAATCACATTTCTC
* * * ** * * *
831 TAGATAGACATTCAAGTAT-AATCTG-TTTACAGTAAAAATTTA-AAATAATTCAACTTAAAATT
257 GAGATAGACAATAAAGTATAAAT-TGTTTTA-ACCAAAAATCTACAAACAATTCAACTTAAAATC
* ********** *
893 AATT-TTAGGATTATAAAACCATTTAAAGCGAGTAATAAGGCNNNNNNNNNNATGGGTGACTATA
320 AATTATGA-GATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATA
* *
957 AATGGACT-TTCTTGTCAATGAATGCCTTTTTCTACATGTTTACT-GAGTA-TGACATTCAATTA
384 AATGGACTCTTCTTGCCAATGAATGCC-TTTTCTACATGTTT-CTCGAG-ACAGACATTCAATTA
*
1019 TAACT-TGTTTTAACTA-AAAATATAAAAAAAAT
446 T-ACTCTATTTTAA--AGAAAATATAAAAAAAAT
1051 ATAATCAATT
Statistics
Matches: 386, Mismatches: 77, Indels: 26
0.79 0.16 0.05
Matches are distributed among these distances:
510 19 0.05
511 108 0.28
512 257 0.67
513 2 0.01
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.34
Consensus pattern (502 bp):
AAAGCGAGTAATAAGGCTTTTGAAAGAATAAGTAACTATAAATGGACATTTAATGCCAATGAATG
CCTTCTTCATCATGTTTCTCTAGATAAACATCCAAGTATAATCTATTTACACCAAAAATTTAAAA
TAATTCAACTTAAAAACAATTTTGAGATTATAAAACCATTTAAACCAAGTAATAAGACTTTTGAA
GGAATGGATAACTATAAACGGACTTTTCCTGCCAATGAATGAATTTTTAATCACATTTCTCGAGA
TAGACAATAAAGTATAAATTGTTTTAACCAAAAATCTACAAACAATTCAACTTAAAATCAATTAT
GAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATGGAC
TCTTCTTGCCAATGAATGCCTTTTCTACATGTTTCTCGAGACAGACATTCAATTATACTCTATTT
TAAAGAAAATATAAAAAAAATCAACTTAAAATCAATTAAAACTATTG
Done.