Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402910.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5959.0, 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, 825
Length: 1375
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.35
Warning! 20 characters in sequence are not A, C, G, or T
Found at i:715 original size:170 final size:169
Alignment explanation
Indices: 1--1371 Score: 898
Period size: 171 Copynumber: 8.0 Consensus size: 169
** *
1 TAAGGCTTTTGAAGGAATGGGAGACTATAAATAGACTTTTC-TTGCTAATGAATATTTTTTTCTC
1 TAAGGCTTTTGAAGGAATGGGAGACTATAAATAGACTTTTCTTTGC-AATGAAT-GCTTTTTCTT
* * * * *
65 CACGTTTCTGAAGGTAGACATTCAATTATTA-TGTGTTTTTACTAAAAATGCAAAAAAATGAACA
64 CACGTTTCTGAAGGTAGACATTCAATTA-TAGTCTGTTTTAACCAAAAATGTAAAAAATTGAACA
* *
129 TAAAATCAATTTTGAGAT-ATAAAACTATTTAAAGCGGGTAA
128 TAAAATCAATTATGAGATAATAAAACTATTTAAAGCGAGTAA
* * * * * * * *
170 TAAAGCTTTTAAAAGAATGGGTGACTATAAATAAACTTTTCTTTCCAATGAATACTTTTTTTTTT
1 TAAGGCTTTTGAAGGAATGGGAGACTATAAATAGACTTTTCTTTGCAATGAATGC--TTTTTCTT
** * * * *
235 TGCGTTTCTTG-AGGTAGACATTCAATTATAGTCTGTTTTAACCAAGAATGGAAAAAAATTAAAA
64 CACGTTTC-TGAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAAT-GTAAAAAATTGAAC
*
299 ATAAAATCAA-TATTTAGATAATAAAACTATTTAAAGTCGA-TAA
127 ATAAAATCAATTA-TGAGATAATAAAACTATTTAAAG-CGAGTAA
* * * * *
342 TAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTCTCCTATTG--ATGAATGCCTTTTCTT
1 TAAGGCTTTTGAAGGAATGGGAGACTATAAATAGACTT-TTCT-TTGCAATGAATGCTTTTTC-T
* * * * * **
405 TCACATTTCTCAATGTAGACATTCAATTATAATCTGTTTTAACCAAAAAAGTAAAAACTATTGTG
63 TCACGTTTCTGAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAA--ATTGAA
* * * *
470 CCTAAAATCAATTATGAGATTATAAAA-TCATTTAAAGCAAATAA
126 CATAAAATCAATTATGAGATAATAAAACT-ATTTAAAGCGAGTAA
* * *
514 TTAGGCTTTTAAAGGAATGGGAGACTATAAATAGACTTTTCTTGGCAATGAATGCTTTTTCTTCA
1 TAAGGCTTTTGAAGGAATGGGAGACTATAAATAGACTTTTCTTTGCAATGAATGCTTTTTCTTCA
* * * ** * * * *
579 TGTTTTTGAAGGTCA-ACATTTAATTATAGTCTGTTCAAATCAAAAGTGTAAATAAATTCAACTT
66 CGTTTCTGAAGGT-AGACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAA-AAATTGAACAT
*
643 AAAATCAATTATAAGATAATAAAAAC-ATTTAAAGCGAGTAA
129 AAAATCAATTATGAGATAAT-AAAACTATTTAAAGCGAGTAA
* * * * * * **
684 TAAGGCTTTTGAAGGATTGAGAGATTATAAATGGACTTTTC-CTACTAATGAATATTTTTTCTTC
1 TAAGGCTTTTGAAGGAATGGGAGACTATAAATAGACTTTTCTTTGC-AATGAATGCTTTTTCTTC
* ** * * * *
748 ACATTTCATG-AGGTAGACATTCAATTATAACCTATTTTAACTAAAAATATTAAAAAAATTAAAC
65 ACGTTTC-TGAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAAT-GT-AAAAAATTGAAC
* ***********
812 ATAAAATCAATTATGAGATTATAAAGNNNNNNNNNNCGAGTAA
127 ATAAAATCAATTATGAGATAATAAAACTATTTAAAGCGAGTAA
* * * * * **
855 TAAGGCTTTTGAAAGAACGAGAGAGTATAAATGGACTTTTC-TTGCCAATGAATTTTTTTTCTTC
1 TAAGGCTTTTGAAGGAATGGGAGACTATAAATAGACTTTTCTTTG-CAATGAATGCTTTTTCTTC
* * * * * *
919 ATGTTTTTTG-AGGTAAACATTCAATTATGGTCTATTTTAACTAAAAATGTAAAAAAAAAATTGA
65 ACG-TTTCTGAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGT----AAAAAATTGA
* ********** *
983 ACTTAAAATCAANNNNNNNNNNATAAAA-TCATTTAAAGCAAGTAA
125 ACATAAAATCAATTATGAGATAATAAAACT-ATTTAAAGCGAGTAA
* ** * * * * *
1028 TAAGGCTTTCGAAGGAATAAGAGACCATAAATGGA-TTTTTTTTGCCAATAAATACCTTTTT-TT
1 TAAGGCTTTTGAAGGAATGGGAGACTATAAATAGACTTTTCTTTG-CAATGAAT-GCTTTTTCTT
* * * * * ** * *
1091 CACGTTTCTCAAGGCAAAAATTCAATTATAGTCTTTTTTAAATAAATATGTAAAAAGA-TGAATA
64 CACGTTTCTGAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAA-ATTGAACA
* * * * *
1155 TAAAATCAATTTTGAGATTATAAAACCACTTAAATTCG-GTAA
128 TAAAATCAATTATGAGATAATAAAACTATTTAAA-GCGAGTAA
* * * * * *
1197 TAAGGCTTTTAAAGGAATGAGTA-ACTATAAATGGAC-GTT-TTTGCCAATAAATGCCTTTGTCT
1 TAAGGCTTTTGAAGGAATG-GGAGACTATAAATAGACTTTTCTTTG-CAATGAATG-CTTTTTCT
* * * * * ** * * * **
1259 TCATGTTTCTTAATGTACATACCCAATTATAATCTGTTTTAACAAAAAAAGTCAAAAAAATAAAA
63 TCACGTTTCTGAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGT--AAAAAATTGAA
* * *
1324 CTTAAAATTAATTATGAGATTATAAAACTATTTAAAGCGAGTAA
126 CATAAAATCAATTATGAGATAATAAAACTATTTAAAGCGAGTAA
1368 TAAG
1 TAAG
1372 ACTT
Statistics
Matches: 930, Mismatches: 222, Indels: 98
0.74 0.18 0.08
Matches are distributed among these distances:
168 18 0.02
169 149 0.16
170 188 0.20
171 294 0.32
172 156 0.17
173 118 0.13
174 7 0.01
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.35
Consensus pattern (169 bp):
TAAGGCTTTTGAAGGAATGGGAGACTATAAATAGACTTTTCTTTGCAATGAATGCTTTTTCTTCA
CGTTTCTGAAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAATTGAACATAA
AATCAATTATGAGATAATAAAACTATTTAAAGCGAGTAA
Found at i:895 original size:341 final size:337
Alignment explanation
Indices: 1--1266 Score: 1016
Period size: 341 Copynumber: 3.7 Consensus size: 337
* * * * *
1 TAAGGCTTTTGAAGGAATGGGAGACTATAAATAGACTTTTCTTGCTAATGAATATTTTTTTCTCC
1 TAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTTCCTACTAATGAATA-TTTTTTCTTC
* * * * *
66 ACGTTTCTGAAGGTAGACATTCAATTATTATGTGTTTTTACTAAAAAT-GCAAAAAAA-TGAACA
65 ACATTTCTG-AGGTAGACATTCAATTATAATCTGTTTTAACTAAAAATAGTAAAAAAATTGAACA
* * * * *
129 TAAAATCAATTTTGAGA-TATAAAACTATTTAAAGCGGGTAATAAAGCTTTTAAAAGAATGGGTG
129 TAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTT-AAAGAATGGGAG
* * * **
193 ACTATAAATAAACTTTTCTTTCCAATGAATACTTTTTTTTTTTGCGTTTCTTGAGGTAGACATTC
193 ACTATAAATAGACTTTTCTTGCCAATGAATACTTTTTCTTCAT--GTTT-TTGAGGTA-ACATTC
** *
258 AATTATAGTCTGTTTTAACCAAGAATGGAAAAAAATTAAAAATAAAATCAATATTTAGATAATAA
254 AATTATAGTCTGTTCAAACCAAGAATGGAAAAAAATTAAAAATAAAATCAATATTAAGATAATAA
323 AACTATTTAAAGTCGATAA
319 AACTATTTAAAGTCGATAA
* * * * ***
342 TAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTCTCCTATTGATGAATGCCTTTTCTTTC
1 TAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTTCCTACTAATGAATATTTTTTC-TTC
* * * * **
407 ACATTTCTCAATGTAGACATTCAATTATAATCTGTTTTAACCAAAAA-AGTAAAAACTATTGTGC
65 ACATTTCT-GAGGTAGACATTCAATTATAATCTGTTTTAACTAAAAATAGTAAAAA-AATTGAAC
* * * * *
471 CTAAAATCAATTATGAGATTATAAAATCATTTAAAGCAAATAATTAGGCTTTTAAAGGAATGGGA
128 ATAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTAAA-GAATGGGA
* * *
536 GACTATAAATAGACTTTTCTTGGCAATGAATGCTTTTTCTTCATGTTTTTGAAGGTCAACATTTA
192 GACTATAAATAGACTTTTCTTGCCAATGAATACTTTTTCTTCATGTTTTTG-AGGT-AACATTCA
* * * * **
601 ATTATAGTCTGTTCAAATCAA-AAGTGTAAATAAATTCAACTTAAAATCAAT-TATAAGATAATA
255 ATTATAGTCTGTTCAAACCAAGAA-TGGAAAAAAATTAAAAATAAAATCAATAT-TAAGATAAT-
664 AAAAC-ATTTAAAG-CGAGTAA
317 AAAACTATTTAAAGTCGA-TAA
* *
684 TAAGGCTTTTGAAGGATTGAGAGATTATAAATGGACTTTTCCTACTAATGAATATTTTTTCTTCA
1 TAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTTCCTACTAATGAATATTTTTTCTTCA
* * * *
749 CATTTCATGAGGTAGACATTCAATTATAACCTATTTTAACTAAAAATATTAAAAAAATTAAACAT
66 CATTTC-TGAGGTAGACATTCAATTATAATCTGTTTTAACTAAAAATAGTAAAAAAATTGAACAT
*********** * *
814 AAAATCAATTATGAGATTATAAAGNNNNNNNNNNCGAGTAATAAGGCTTTTGAAAGAACGAGAGA
130 AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTT-AAAGAATGGGAGA
* * **
879 GTATAAATGGACTTTTCTTGCCAATGAATTTTTTTTCTTCATGTTTTTTGAGGTAAACATTCAAT
194 CTATAAATAGACTTTTCTTGCCAATGAATACTTTTTCTTCATG-TTTTTGAGGT-AACATTCAAT
* * ** * * * * ** **********
944 TATGGTCTATTTTAACTAAAAATGTAAAAAAAAAATTGAACTTAAAATCAANNNNNNNNNNATAA
257 TATAGTCTGTTCAAACCAAGAATG---GAAAAAAATTAAAAATAAAATCAATATTAAGATAATAA
*
1009 AA-TCATTTAAAG-CAAGTAA
319 AACT-ATTTAAAGTCGA-TAA
* * * * ** * * * *
1028 TAAGGCTTTCGAAGGAATAAGAGACCATAAATGGATTTTTTTTGCCAATAAATACCTTTTT-TTC
1 TAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTTCCTACTAATGAATA-TTTTTTCTTC
* * * * * * * * * * *
1092 ACGTTTCTCAAGGCAAAAATTCAATTATAGTCTTTTTTAAATAAATAT-GTAAAAAGA-TGAATA
65 ACATTTCT-GAGGTAGACATTCAATTATAATCTGTTTTAACTAAAAATAGTAAAAAAATTGAACA
* * * *
1155 TAAAATCAATTTTGAGATTATAAAACCACTTAAATTCG-GTAATAAGGCTTTTAAAGGAATGAGT
129 TAAAATCAATTATGAGATTATAAAACCATTTAAA-GCGAGTAATAAGGCTTTTAAA-GAATG-GG
* * * * *
1219 A-ACTATAAATGGACGTTT-TTGCCAATAAATGCCTTTGTCTTCATGTTT
191 AGACTATAAATAGACTTTTCTTGCCAATGAAT-ACTTTTTCTTCATGTTT
1267 CTTAATGTAC
Statistics
Matches: 736, Mismatches: 159, Indels: 60
0.77 0.17 0.06
Matches are distributed among these distances:
340 5 0.01
341 277 0.38
342 216 0.29
343 43 0.06
344 190 0.26
345 5 0.01
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.35
Consensus pattern (337 bp):
TAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTTCCTACTAATGAATATTTTTTCTTCA
CATTTCTGAGGTAGACATTCAATTATAATCTGTTTTAACTAAAAATAGTAAAAAAATTGAACATA
AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTAAAGAATGGGAGACT
ATAAATAGACTTTTCTTGCCAATGAATACTTTTTCTTCATGTTTTTGAGGTAACATTCAATTATA
GTCTGTTCAAACCAAGAATGGAAAAAAATTAAAAATAAAATCAATATTAAGATAATAAAACTATT
TAAAGTCGATAA
Done.