Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401760.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4873.0, 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: 2063
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.34
Warning! 182 characters in sequence are not A, C, G, or T
Found at i:328 original size:170 final size:161
Alignment explanation
Indices: 119--435 Score: 320
Period size: 171 Copynumber: 1.9 Consensus size: 161
109 CTTTTACAAT
* * *
119 GAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACGTTTT-TTGCCAATGAATATCCT
1 GAGTAATAAGGCTTTTGAAGGAACGGATGACTATAAATGGAC-TTTTCTTGCCAATGAAT-GCCT
* * *
183 TTTT-TTCA-TGTTCTTGAGGTAGACATTCAATTATAATATATTTTAACTAAAAATGTAAAAA-A
64 TTTTCTTCATTGTTCTGGAGGTAAACATTCAATTATAATATATTTTAACGAAAAATGTAAAAATA
* *
245 TTTCAACTTAAAATTAATNNNNNNNNNNTAAAACTATTTAAAGC
129 -TTCAACTGAAAAATAAT----------TAAAACTATTTAAAGC
* * *
289 GAGTAATAAGGCTTTT-AAGGGTACGGATGACTGTAAATGGACTTTTCTTGCCAATGAATGCTTT
1 GAGTAATAAGGCTTTTGAA-GGAACGGATGACTATAAATGGACTTTTCTTGCCAATGAATGCCTT
* * * * * *
353 TTTCTTCATTTTTCTGGAGGTAAACATTCAATTCTAGTCTATTTTAACGAATAATGTTAAAATAT
65 TTTCTTCATTGTTCTGGAGGTAAACATTCAATTATAATATATTTTAACGAAAAATGTAAAAATAT
418 TCAACTGAAAAATAATTA
130 TCAACTGAAAAATAATTA
436 TTAGTTTATG
Statistics
Matches: 125, Mismatches: 17, Indels: 19
0.78 0.11 0.12
Matches are distributed among these distances:
161 2 0.02
169 12 0.10
170 51 0.41
171 59 0.47
172 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.37
Consensus pattern (161 bp):
GAGTAATAAGGCTTTTGAAGGAACGGATGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTT
TTCTTCATTGTTCTGGAGGTAAACATTCAATTATAATATATTTTAACGAAAAATGTAAAAATATT
CAACTGAAAAATAATTAAAACTATTTAAAGC
Found at i:1140 original size:172 final size:167
Alignment explanation
Indices: 810--2061 Score: 803
Period size: 172 Copynumber: 7.3 Consensus size: 167
800 NNNNNNNNNN
* * * *
810 TAATAAGGCTTTTGAAGGAATGAGT-AGTTATAAATGGACTTTTCTTGTTC-ATTAATGACCTTT
1 TAATAAGGCTTTTGAAGGAATGGGTGA-CTATAAATGG-CTTTTCTTG-CCAATGAATG-CCTTT
* * * * *
873 TT-TT-ACGTTTCTTAATG-TAGGCATTCAATTATAATCTATTTTAACTAAAAATGTATAAAGAA
62 TTCTTCA-TTTTCTCAA-GCTAGACATTCAATTATAATCTGTTTTAAC-AAAAA--TATAAAAAA
* * * * * *
935 TTCAAATTTAAATCAAATTTGTGATTATAAAACTATTTAAAGCGAG
122 TTGAACTTAAAATCAATTTTGAGATTATAAAACTATTTAAAGTGAG
* * *
981 TAATAAGACTTTTGAAGGGATGGGTGACTATAAATGTGCTTTTCTTGCCAACGAATGCCTTTTTC
1 TAATAAGGCTTTTGAAGGAATGGGTGACTATAAATG-GCTTTTCTTGCCAATGAATGCCTTTTTC
* * *
1046 TTCATGTTTCTCCACCTAGACATTCAATTATAATCTGTTTTAATGAAAAATATAAATAAATTTGA
65 TTCAT-TTTCTCAAGCTAGACATTCAATTATAATCTGTTTTAA-CAAAAATATAAA-AAA-TTGA
* *
1111 ACTTAAAATCAATTTTGAAATTATAAAACTATTTAAAGTTAG
126 ACTTAAAATCAATTTTGAGATTATAAAACTATTTAAAGTGAG
* * * * * * *
1153 CAATAAGGCTTGTAAAGCAATGGGTGACTATAAATAGACTTTTCTTACCAATGAATGCCTTTTAC
1 TAATAAGGCTTTTGAAGGAATGGGTGACTATAAAT-GGCTTTTCTTGCCAATGAATGCCTTTTTC
* * * * * * *
1218 TTGAAATTTCT-AGAGATAGACATTCAATTATAATTTGCTTTAACAAAAAATGTACAAAGAATTC
65 TT-CATTTTCTCA-AGCTAGACATTCAATTATAATCTGTTTTAAC-AAAAATATA-AAA-AATTG
* * **********
1282 AAATTTAAATCAATTTTGAGATNNNNNNNNNNTTTAAAGTGAG
125 AACTTAAAATCAATTTTGAGATTATAAAACTATTTAAAGTGAG
* ** * ** **
1325 TAATAAGGATTTTGAAGGAATAAGTGACTATAAATGGGCTTTTCTTACCAACCAATATCTTTTTC
1 TAATAAGGCTTTTGAAGGAATGGGTGACTATAAAT-GGCTTTTCTTGCCAATGAATGCCTTTTTC
* * * *
1390 TTCACGTTTCTCAAGTTAGACATTCAATTATAATATGTTTTCACCAAAAATATAAATAAATTTGA
65 TTCA-TTTTCTCAAGCTAGACATTCAATTATAATCTGTTTT-AACAAAAATATAAA-AAA-TTGA
* **********
1455 ACTTAAAATCGATTTTGAGATTATAANNNNNNNNNNAGTGAG
126 ACTTAAAATCAATTTTGAGATTATAAAACTATTTAAAGTGAG
* * * * * *
1497 CAATAAGGCTTTTGAAGTAATGGGTGACTAGAAATAGACTTTTCTTGCTAATGAATGTCTTTTTC
1 TAATAAGGCTTTTGAAGGAATGGGTGACTATAAAT-GGCTTTTCTTGCCAATGAATGCCTTTTTC
* * * * * *
1562 TTGACATTTT-TCAAGGTAAACATTCAATTATAATCTATTTTCACAAAAAATTTAAAACAATTCA
65 TT--CATTTTCTCAAGCTAGACATTCAATTATAATCTGTTTTAAC-AAAAATATAAAA-AATTGA
* ********* *
1626 ACTTAAAATCAATTATGAGNNNNNNNNNNCT-TTTAAAGTAAG
126 ACTTAAAATCAATTTTGAG-ATTATAAAACTATTTAAAGTGAG
* *** * * *
1668 TAATAAGGCTTTTGAAATG-ATGGGTGACTATAAATGGACTTTTCTTTTTATTGAATGTCATTTT
1 TAATAAGGCTTTTG-AAGGAATGGGTGACTATAAATGG-CTTTTCTTGCCAATGAATGCCTTTTT
* * * * * * *
1732 CTTCACTTTTCTCGAGGTAGATATTAAATTATAATCTATTTGAACAAAAATGTACAAAGAATTGA
64 CTTCA-TTTTCTCAAGCTAGACATTCAATTATAATCTGTTTTAACAAAAATATA-AAA-AATTGA
*********** * * *
1797 AANNNNNNNNNNTTTTGAGATTATAAAACCATTTAATGAGAG
126 ACTTAAAATCAATTTTGAGATTATAAAACTATTTAAAGTGAG
* * * * **
1839 TAATAAGGCTTTTAAAAGAATGGATGATTATAAATGGGCTTTTCTTGCCAATGAATGCCTAATTC
1 TAATAAGGCTTTTGAAGGAATGGGTGACTATAAAT-GGCTTTTCTTGCCAATGAATGCCTTTTTC
* * * * * * *
1904 TTCACATTTCTTAAGCTAGACATTCAACTATAATATGTTTGAACTAAAAATGTACATAAATTTGA
65 TTCA-TTTTCTCAAGCTAGACATTCAATTATAATCTGTTTTAAC-AAAAATATA-A-AAAATTGA
* * *
1969 ACTTAAAATTAATTTTGAGATTAGAAAACTATTTAAAGTGCG
126 ACTTAAAATCAATTTTGAGATTATAAAACTATTTAAAGTGAG
*
2011 TAATAAGGCTTTTGAAGTAATGGGTGACTATAAATGGACTTTTCTTGCCAA
1 TAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGG-CTTTTCTTGCCAA
2062 CG
Statistics
Matches: 827, Mismatches: 217, Indels: 73
0.74 0.19 0.07
Matches are distributed among these distances:
169 2 0.00
170 31 0.04
171 267 0.32
172 511 0.62
173 14 0.02
174 2 0.00
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.36
Consensus pattern (167 bp):
TAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGCTTTTCTTGCCAATGAATGCCTTTTTCT
TCATTTTCTCAAGCTAGACATTCAATTATAATCTGTTTTAACAAAAATATAAAAAATTGAACTTA
AAATCAATTTTGAGATTATAAAACTATTTAAAGTGAG
Done.