Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401181.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4331.0, 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: 2786
ACGTcount: A:0.31, C:0.10, G:0.11, T:0.28
Warning! 578 characters in sequence are not A, C, G, or T
Found at i:760 original size:170 final size:170
Alignment explanation
Indices: 462--1248 Score: 660
Period size: 170 Copynumber: 4.6 Consensus size: 170
452 GAATATCTTT
* * *
462 AATTTAAAATAAATTATGAGATTATAAAAATATTTAAAGAGAGTAATAAGGCCTTT-GAAGTCAT
1 AATTTAAAATCAATTATGAGATTATAAAAACATTTAAAGAGAGTAATAAGG-CTTTCGAAGGCAT
* * * * *
526 GGGTAACTATAAATGAATTTTTCTTACCAATGGATATCTTTTTCTTCATGTTTCAT-GAGGCAGA
65 GGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCATGTTTCCTAG-GGCAGA
*
590 CATTCAATAATTATCTATTTTAATCAAAATCTAAAAAAATTC
129 CATTCAATTATTATCTATTTTAATCAAAATCTAAAAAAATTC
* * * * * *
632 ATTTTAAAATCAATTATGAGATTATAAAAGCATTTAAGGCGAGTAATAAGGCTTTTGAAGTCATG
1 AATTTAAAATCAATTATGAGATTATAAAAACATTTAAAGAGAGTAATAAGGCTTTCGAAGGCATG
* * * * *
697 GGTGACTATAAATGGACCTTTCTCGGCAACGGATATCTTTTTCTTCATGATTCCTAGGGCAGACA
66 GGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCATGTTTCCTAGGGCAGACA
* * * *
762 TTCAATTATAATCTCTTTTAATAAAAAATATAAAAAAA-TC
131 TTCAATTATTATCTATTTTAAT-CAAAATCTAAAAAAATTC
*** * * *
802 AACACAAAATCAATTAT-ATGATTATAAAACCATTTAAAGAGAGTAATAAGGATTCCGAAGGCAT
1 AATTTAAAATCAATTATGA-GATTATAAAAACATTTAAAGAGAGTAATAAGGCTTTCGAAGGCAT
* * ** * * * *
866 GGGTGACTAGAGATGGACTTTTCTTGCCAATAAATATCTTTTTTTTCACGTTTCCTAAGGCAAAC
65 GGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCATGTTTCCTAGGGCAGAC
** * * *
931 CGTCAATTATTATCTGTTTTAA-CAAAAAACGTATAAAAATTC
130 ATTCAATTATTATCTATTTTAATC-AAAATC-TAAAAAAATTC
* * * * * * * *
973 AAGTTAAAATCAATTACGAGATT-TAAAAACCTTTTAGGCACA-AAATAAAGCTTTCGAAGGCAT
1 AATTTAAAATCAATTATGAGATTATAAAAACATTTAAAG-AGAGTAATAAGGCTTTCGAAGGCAT
* ** * * * * ** * *
1036 GGGTGATTATAAATAAACAATTT-TTACTAATGAATGGCTTTTTTTTCA-GATTTTCTTA-GGCA
65 GGGTGACTATAAATGGAC-TTTTCTTGCCAATGGATATCTTTTTCTTCATG--TTTCCTAGGGCA
* * * * * *
1098 AACATTCAGTTATTATTTGTTTTAATTAAAAATATAAAAAAA-TC
127 GACATTCAATTATTATCTATTTTAA-TCAAAATCTAAAAAAATTC
** * * * * * * * *
1142 AGCTTGAAATCAATTATGAAATTATAAAACCATTTAAAGTGAATAATAAGGCTTTCAAAGGTATA
1 AATTTAAAATCAATTATGAGATTATAAAAACATTTAAAGAGAGTAATAAGGCTTTCGAAGGCATG
* * * *
1207 GGTGACTATAATTGGGCTTTTCTTCCCAATGAATATCTTTTT
66 GGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTT
1249 TNNNNNNNNN
Statistics
Matches: 488, Mismatches: 112, Indels: 34
0.77 0.18 0.05
Matches are distributed among these distances:
169 34 0.07
170 405 0.83
171 48 0.10
172 1 0.00
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (170 bp):
AATTTAAAATCAATTATGAGATTATAAAAACATTTAAAGAGAGTAATAAGGCTTTCGAAGGCATG
GGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCATGTTTCCTAGGGCAGACA
TTCAATTATTATCTATTTTAATCAAAATCTAAAAAAATTC
Found at i:2248 original size:171 final size:169
Alignment explanation
Indices: 1774--2786 Score: 658
Period size: 170 Copynumber: 5.9 Consensus size: 169
1764 NNNNNNNNNN
* * * * * * *
1774 TTTAAAGCGAGTAATAAGGCTTTTAAAGGCATGGGTGACTATAAATGGGCTTTTGTTAACGATGA
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGTCATGGGTGACTATAAATGGACTTTTCTTACCAATGG
* * * * *
1839 ATATCTTTTTCTTCGTATTTCCTGAGGCAGACATTCAATCATTATCTATTTTAACCGAAAACAT-
66 ATATCTTTTTCTTCATGTTTCCTGAGGCAGACATTCAATAATTATCTATTTTAA-CAAAAATATA
* *
1903 AAAAAAATTAATTTAAAATAAATTATGAGATTATAAAAATA
130 AAAAAAATCAA-TTAAAATCAATTATGAGATTATAAAAATA
* * * *
1944 TTTAAAGAGAGTAATAAGGCTTTTGAAGTCATGGGT-ACTGTAAATGGACTTTTTTTGCCAATGG
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGTCATGGGTGACTATAAATGGACTTTTCTTACCAATGG
* * * * * *
2008 ATATCTTTTTCTTCATGGTTCATGAAGCAGACATTCAATAATTATCTGTTTTAACCAAAATCGTA
66 ATATCTTTTTCTTCATGTTTCCTGAGGCAGACATTCAATAATTATCTATTTTAACAAAAAT-ATA
*****
2073 AAAAAAATCAATTCAAAATCAATTATGAGATTATAANNNNN
130 AAAAAAATCAATT-AAAATCAATTATGAGATTATAAAAATA
***** * * *
2114 NNNNNAGCGAGTAATAAGGCTTTTGAAGTTATGGGTGACTATAAATGGACCTTTCTTACCAACGG
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGTCATGGGTGACTATAAATGGACTTTTCTTACCAATGG
* * * * * *
2179 ATATCTTTTTCTTCATGTTTCCTGGGGTAGACATTCAATTATAATCTTTTTTAATAAAAAATATA
66 ATATCTTTTTCTTCATGTTTCCTGAGGCAGACATTCAATAATTATCTATTTTAA-CAAAAATATA
* *
2244 AAAAAAATCAACATAAAATCAATTAT-AGGATTATAAAACTA
130 AAAAAAATCAA-TTAAAATCAATTATGA-GATTATAAAAATA
* ** * * * ** * **
2285 TTTAAAGCGAGTAATAAGGATTCCGAAGGCATGGATGACTAGACGTAGACTTTTCTTACCAATAA
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGTCATGGGTGACTATAAATGGACTTTTCTTACCAATGG
* * ** ** * * * * * *
2350 ATATCTTTTTCTGCACGTTTCCCAAACCAAATAGTCAATTATTATCTGTTTTAACAAAAAATGTA
66 ATATCTTTTTCTTCATGTTTCCTGAGGCAGACATTCAATAATTATCTATTTTAAC-AAAAATATA
* * * * *
2415 TAAAAATTCAAGTTAAAATCAATTAGGATATT-TAAAAACA
130 AAAAAAATCAA-TTAAAATCAATTATGAGATTATAAAAATA
* * ** * ** * * * * *
2455 TTTTAGGC-ACAAAATAAGGCTTTCGAAGGAATGGGTGATTATAAATAGACTTTTTTTGCTAATG
1 TTTAAAGCGA-GTAATAAGGCTTTTGAAGTCATGGGTGACTATAAATGGACTTTTCTTACCAATG
* ** * * * * * * *
2519 AATGGCTTTTTCTTCAGGTTTCCTTAGGCAAACATTCAGTTATTAT-TATTTTTAATTAAAAATG
65 GATATCTTTTTCTTCATGTTTCCTGAGGCAGACATTCAATAATTATCTA-TTTTAA-CAAAAATA
* * * ********** *
2583 T-AAAAAATTCAGCTTGAAATCAATTATNNNNNNNNNNAAACA
128 TAAAAAAAATCA-ATTAAAATCAATTATGAGATTATAAAAATA
* ** * * * * *
2625 TTTAAAGCGAGTAATAAGACTTTCAAAGGCATAGGTGACTATAATTAGG-CTTTTCTTGCCGATG
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGTCATGGGTGACTATAAAT-GGACTTTTCTTACCAATG
* * * * * * * * *
2689 AATATCTTTTTTTTCACG-TTACTCAAGGCAAACAATCAATTATTATCTGTTTTAACCAAAAATA
65 GATATCTTTTTCTTCATGTTTCCT-GAGGCAGACATTCAATAATTATCTATTTTAA-CAAAAATA
* *
2753 TAAAAAAATTCAACTTAAAGTCAATTATGAGATT
128 TAAAAAAAATCAA-TTAAAATCAATTATGAGATT
Statistics
Matches: 648, Mismatches: 175, Indels: 39
0.75 0.20 0.05
Matches are distributed among these distances:
168 5 0.01
169 98 0.15
170 292 0.45
171 246 0.38
172 7 0.01
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.35
Consensus pattern (169 bp):
TTTAAAGCGAGTAATAAGGCTTTTGAAGTCATGGGTGACTATAAATGGACTTTTCTTACCAATGG
ATATCTTTTTCTTCATGTTTCCTGAGGCAGACATTCAATAATTATCTATTTTAACAAAAATATAA
AAAAAATCAATTAAAATCAATTATGAGATTATAAAAATA
Done.