Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401461.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4588.0, 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: 2394
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.31
Warning! 236 characters in sequence are not A, C, G, or T
Found at i:1364 original size:339 final size:339
Alignment explanation
Indices: 711--1808 Score: 877
Period size: 339 Copynumber: 3.2 Consensus size: 339
701 CAATGTAGAT
* * *
711 ATTCAATTATAATCTA-TTTAATCAAAGAAGTAAAAA-ATATTGAACTTAAAATCAATTATGAGA
1 ATTCAATTATAGTCTATTTTAATGAAA-AA-CAAAAACA-ATTGAACTTAAAATCAATTATGAGA
* * * **** * * * *
774 TTATTAAACTATTTAAAGCAAGTAATAAAATTTTTGAAAGAATGGGAAACTTTAAATGGACTTTT
63 TTATAAAACCATTTAAAGCAACTAATAAGGCCTTTGAAGGAATGAGAAACTATAAATGAACTTTT
* * * ** * * ** * *
839 CATCCAAATAAATAAATTT-TTCTACATGTTTCCCGAG-GTAGACATTCAATTATAGTTTGTTTG
128 CTTCCAAA-AAATGAGTTTGTTC-ACACATTCCCCAAGCCAAG-CATTCAATTATAGTATGTTTT
* * ********** * * ** *
902 AACAAAAAATGAAAAAAAAATTGAANNNNNNNNNNATTTTGAGAAAATAAAACCATTTAAAGTGA
190 AACAAAAAAT--ATAAAAAATTAAACTTAAAATCAATTATAAGACTATAAAACCATTTAAAGCGA
* * **
967 GTAATAAGGCTTTTGAAGGATTG-GAGACTATAAATGGACTTTTCTTTTAAATAAATGGGTTTTT
253 GTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATAGACTTTTCTTCCAAATAAATGGGTTTTT
* * *
1031 CTATATGTTTCCCAAGGCAAGC
318 CTAGACGTTTACCAAGGCAAGC
* ** *************
1053 ATTCAATTATAGTCTATTTTAGTGAAAAATGTAAAA-AATNNNNNNNNNNNNNAATTATGAGATT
1 ATTCAATTATAGTCTATTTTAATGAAAAA-CAAAAACAATTGAACTTAAAATCAATTATGAGATT
* *
1117 ATAAAACCATTTAAAGCAACTAATAAGGCTTTTGAAGGAATGAGAAACTATAAATGCACTTTT-T
65 ATAAAACCATTTAAAGCAACTAATAAGGCCTTTGAAGGAATGAGAAACTATAAATGAACTTTTCT
* * * *
1181 TCCAAATAAATGGGTTT-TTCCACACATTCCCCAAGGCAGGCATTCAATTATAGTATGTTTTAAT
130 TCCAAA-AAATGAGTTTGTT-CACACATTCCCCAAGCCAAGCATTCAATTATAGTATGTTTTAAC
* * * ** *
1245 AAAAAATA-AAAACAATTCAACTTAAAATCAATTATGAGATTATACGACCATTTAGAGCGAGTAA
193 AAAAAATATAAAA-AATTAAACTTAAAATCAATTATAAGACTATAAAACCATTTAAAGCGAGTAA
* *
1309 TAAGGTTTTTGAAGGAATGAGAGACTATAAATATACTTTTCTTCCAAATAAATGGGTTTTTCTAG
257 TAAGGCTTTTGAAGGAATGAGAGACTATAAATAGACTTTTCTTCCAAATAAATGGGTTTTTCTAG
* *
1374 ACGTTTACTAAGGCAAGT
322 ACGTTTACCAAGGCAAGC
* * *
1392 GTTCAATTATAGTTTGTTTTAATGAAAAACAAAAACAATTGAACTTAAAATCAATTATGAGATTA
1 ATTCAATTATAGTCTATTTTAATGAAAAACAAAAACAATTGAACTTAAAATCAATTATGAGATTA
* * * ** *
1457 TAAAACCATTTAGAGCGATTAATTCGGCCTTTGAAGGAATGAGAGACTATAAATGAACTTTTCTT
66 TAAAACCATTTAAAGCAACTAATAAGGCCTTTGAAGGAATGAGAAACTATAAATGAACTTTTCTT
* * * ** * *
1522 CCAAAAAATTAGTTTGTTTACACTTTTTCCAAGCCAAGCATTCAATTATAGTCTTTTTTAACAAA
131 CCAAAAAATGAGTTTGTTCACACATTCCCCAAGCCAAGCATTCAATTATAGTATGTTTTAACAAA
* * *
1587 AAATATAAAAAATTAAACTTAAAATCAATTTTAAGACTATAAAATCATTTAAAGCAAGTAATAAG
196 AAATATAAAAAATTAAACTTAAAATCAATTATAAGACTATAAAACCATTTAAAGCGAGTAATAAG
* * * * ** ** *
1652 GCTTTTGAAGGAATAAAAAACTATAAATAGACTTTTCTTACC-AATGAATGCCTTTTTCTTCATG
261 GCTTTTGAAGGAATGAGAGACTATAAATAGACTTTTCTT-CCAAATAAATGGGTTTTTCTAGACG
** * * **
1716 TTT-CTTGACGTAAAA
325 TTTAC-CAAGGCAAGC
* * * * * * *
1731 ATTCAATTATAATCTGTTTTAATCAAAAAAATAAAAAAAATTAAACTTAAAATCAATTTTGAGAT
1 ATTCAATTATAGTCTATTTTAAT--GAAAAACAAAAACAATTGAACTTAAAATCAATTATGAGAT
1796 TATAAAACCATTT
64 TATAAAACCATTT
1809 NNNNNNNNNN
Statistics
Matches: 600, Mismatches: 143, Indels: 27
0.78 0.19 0.04
Matches are distributed among these distances:
337 4 0.01
338 56 0.09
339 324 0.54
340 69 0.12
341 117 0.19
342 22 0.04
343 8 0.01
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.33
Consensus pattern (339 bp):
ATTCAATTATAGTCTATTTTAATGAAAAACAAAAACAATTGAACTTAAAATCAATTATGAGATTA
TAAAACCATTTAAAGCAACTAATAAGGCCTTTGAAGGAATGAGAAACTATAAATGAACTTTTCTT
CCAAAAAATGAGTTTGTTCACACATTCCCCAAGCCAAGCATTCAATTATAGTATGTTTTAACAAA
AAATATAAAAAATTAAACTTAAAATCAATTATAAGACTATAAAACCATTTAAAGCGAGTAATAAG
GCTTTTGAAGGAATGAGAGACTATAAATAGACTTTTCTTCCAAATAAATGGGTTTTTCTAGACGT
TTACCAAGGCAAGC
Found at i:1802 original size:172 final size:170
Alignment explanation
Indices: 711--2394 Score: 997
Period size: 169 Copynumber: 9.9 Consensus size: 170
701 CAATGTAGAT
* * * * *
711 ATTCAATTATAATCT-ATTTAATCAAAGAAGTAAAAAATATTGAACTTAAAATCAATTATGAGAT
1 ATTCAATTATAGTCTGTTTTAATCAAA-AAATAAAAAAAATTAAACTTAAAATCAATTATGAGAT
* * *** * * * * *
775 TATTAAACTATTTAAAGCAAGTAATAAAATTTTTGAAAGAATGGGAAACTTTAAATGGACTTTTC
65 TATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATAGACTTTTC
* *** * ** * *
840 ATCCAAATAAATAAATTTTTCTACATGTTTCCCGAGGTAGAC
130 TTCC-AATAAATGCGTTTTTCTACACGTTTCTTGAGGCAAAC
* * * ********** *
882 ATTCAATTATAGTTTGTTTGAA-CAAAAAATGAAAAAAAAATTGAANNNNNNNNNNATTTTGAGA
1 ATTCAATTATAGTCTGTTTTAATCAAAAAAT--AAAAAAAATTAAACTTAAAATCAATTATGAGA
** ** * *
946 AAATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGATTG-GAGACTATAAATGGACTTTT
64 TTATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATAGACTTTT
** * * * *** *
1010 CTTTTAAATAAATGGGTTTTTCTATATGTTTCCCAAGGCAAGC
129 C-TTCCAATAAATGCGTTTTTCTACACGTTTCTTGAGGCAAAC
* * * ** *************
1053 ATTCAATTATAGTCTATTTTAGT-GAAAAATGTAAAAAATNNNNNNNNNNNNNAATTATGAGATT
1 ATTCAATTATAGTCTGTTTTAATCAAAAAATAAAAAAAATTAAACTTAAAATCAATTATGAGATT
* *
1117 ATAAAACCATTTAAAGCAACTAATAAGGCTTTTGAAGGAATGAGAAACTATAAAT-GCACTTTT-
66 ATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATAG-ACTTTTC
* * * * *** **
1180 TTCCAAATAAATGGGTTTTTCCACACATTCCCCAAGGCAGGC
130 TTCC-AATAAATGCGTTTTTCTACACGTTTCTTGAGGCAAAC
* * *
1222 ATTCAATTATAGTATGTTTTAAT-AAAAAATAAAAACAATTCAACTTAAAATCAATTATGAGATT
1 ATTCAATTATAGTCTGTTTTAATCAAAAAATAAAAAAAATTAAACTTAAAATCAATTATGAGATT
** * * * *
1286 ATACGACCATTTAGAGCGAGTAATAAGGTTTTTGAAGGAATGAGAGACTATAAATATACTTTTCT
66 ATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATAGACTTTTCT
* * * **
1351 TCCAAATAAATGGGTTTTTCTAGACGTTTAC-TAAGGCAAGT
131 TCC-AATAAATGCGTTTTTCTACACGTTT-CTTGAGGCAAAC
* * * * * *
1392 GTTCAATTATAGTTTGTTTTAAT-GAAAAACAAAAACAATTGAACTTAAAATCAATTATGAGATT
1 ATTCAATTATAGTCTGTTTTAATCAAAAAATAAAAAAAATTAAACTTAAAATCAATTATGAGATT
* * * ** *
1456 ATAAAACCATTTAGAGCGATTAATTCGGCCTTTGAAGGAATGAGAGACTATAAAT-GAACTTTTC
66 ATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATAG-ACTTTTC
* ** * * *
1520 TTCCAAAAAATTAGTTTGTT-TACAC-TTT-TTCCAAGCCAAGC
130 TTCCAATAAATGCGTTT-TTCTACACGTTTCTT--GAGGCAAAC
* * * * *
1561 ATTCAATTATAGTCTTTTTTAA-CAAAAAATATAAAAAATTAAACTTAAAATCAATTTTAAGACT
1 ATTCAATTATAGTCTGTTTTAATCAAAAAATAAAAAAAATTAAACTTAAAATCAATTATGAGATT
* * * *
1625 ATAAAATCATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATAAAAAACTATAAATAGACTTTTCT
66 ATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATAGACTTTTCT
* * * * * * *
1690 TACCAATGAATGCCTTTTTCTTCATGTTTCTTGACGTAAAA
131 T-CCAATAAATGCGTTTTTCTACACGTTTCTTGAGGCAAAC
* *
1731 ATTCAATTATAATCTGTTTTAATCAAAAAAATAAAAAAAATTAAACTTAAAATCAATTTTGAGAT
1 ATTCAATTATAGTCTGTTTTAATC-AAAAAATAAAAAAAATTAAACTTAAAATCAATTATGAGAT
********** * *
1796 TATAAAACCATTTNNNNNNNNNNATAAGGCTTTTAAAGGAAT-AGGTGACTATAAATAGACTTTT
65 TATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATGA-GAGACTATAAATAGACTTTT
* * * * * * *
1860 CTTACCAATGAATACCTTTTTGTTCACGTTT-TATGAGGTAGAC
129 CTT-CCAATAAATGCGTTTTTCTACACGTTTCT-TGAGGCAAAC
* * * * * *
1903 ATTCAATTATA-ACATGCTTTAATTAAGAAAGTAAAAAAAATTGAA-TTGAAAATCAATTTTGAG
1 ATTCAATTATAGTC-TGTTTTAATCAA-AAAATAAAAAAAATTAAACTT-AAAATCAATTATGAG
* ** * * * *
1966 ATTATAAAATCATTTAAAGTGAGTAATAAGGTTTTTGCAGGAATTG-GTGACTATAAATAGA-AT
63 ATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGAA-TGAGAGACTATAAATAGACTT
* * * * * * * * * *
2029 TTCTTTGCAAATGAATTCATTTTTGTTCTCGTTTCTGGAGGTAAAT
127 TTC-TT-CCAATAAATGCGTTTTTCTACACGTTTCTTGAGGCAAAC
* * * * * *
2075 ATTCATTTATAGTCTATTTTAATC-AAAAATATAAAAAAA-TCAACTAAAAATCAATTATAAGTT
1 ATTCAATTATAGTCTGTTTTAATCAAAAAATA-AAAAAAATTAAACTTAAAATCAATTATGAGAT
* * * * * * * * *
2138 TATAAAATCGTTTAAAGCAAGTAATAAGGCTTTTGAACGAATCAAAGACTGTAAATGGATTTTTT
65 TATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATAGACTTTTC
* * * * * *
2203 TTCAAATAAATG-GGTTTTCTAACACGTTTCCTAAAGCAAGC
130 TTCCAATAAATGCGTTTTTCT-ACACGTTTCTTGAGGCAAAC
** * * **********
2244 ATTCAATTGCAGTCTGTTTTAA-CAAAAAATGTAAAAAAGTT-AANNNNNNNNNNATTATGAGAT
1 ATTCAATTATAGTCTGTTTTAATCAAAAAAT-AAAAAAAATTAAACTTAAAATCAATTATGAGAT
*** * *
2307 TATAAAACCATTTAAAGCGTCTAATAAGGCTTTAGAAGGAATAAGAGACTATAAATAGACTTTTC
65 TATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATAGACTTTTC
* *
2372 TTTCAAATAAATGAGTTTTTCTA
130 -TTCCAATAAATGCGTTTTTCTA
Statistics
Matches: 1188, Mismatches: 281, Indels: 89
0.76 0.18 0.06
Matches are distributed among these distances:
167 1 0.00
168 11 0.01
169 433 0.36
170 294 0.25
171 124 0.10
172 322 0.27
173 3 0.00
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.34
Consensus pattern (170 bp):
ATTCAATTATAGTCTGTTTTAATCAAAAAATAAAAAAAATTAAACTTAAAATCAATTATGAGATT
ATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATAGACTTTTCT
TCCAATAAATGCGTTTTTCTACACGTTTCTTGAGGCAAAC
Done.