Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401396.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4525.0, 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: 1926
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.29
Warning! 352 characters in sequence are not A, C, G, or T
Found at i:985 original size:172 final size:171
Alignment explanation
Indices: 437--1497 Score: 788
Period size: 171 Copynumber: 6.2 Consensus size: 171
427 NNNNNNNNNN
* * ***
437 ATAAGGCTTTTGAAGGAATGAGTGACTATAAATAGACTTTTCTTGCCAATGAATTTTTTTTTCTT
1 ATAAGGCTTTTGAAAGAATGAGTGACTATAAATGGACTTTTCTTGCCAATGAATACCTTTTTCTT
* * * ** *
502 CACGTTTCTTGAGGTAGACATTCAATTATAATCTGTTTGAGCCAAAAATATAAAACCATTCAACT
66 CATGTTTCTAGAGGTAGACATTCAATTATAATCTGTTTGAACCAAAAATATAAAAAAATTAAACT
* * **
567 TGAAATCAATTATGAGATGATAAAACTATTTAAAGCCAGTA
131 TAAAATCAATTATGAGATTATAAAACTATTTAAAGTGAGTA
* * * * *
608 ATAAGGCTTTTGAAAGAATGAGTGACTATAAATGAACTTTCCATACCAATGAATATCTTTTTCTT
1 ATAAGGCTTTTGAAAGAATGAGTGACTATAAATGGACTTTTCTTGCCAATGAATACCTTTTTCTT
* ** * * *
673 CATGTTTCAAGAAATAGACATTCAATTATAATCTGTTTTAA-TAAAAATATATAAAAAATTGAAC
66 CATGTTTCTAGAGGTAGACATTCAATTATAATCTGTTTGAACCAAAAATATA-AAAAAATTAAAC
* * * *
737 TTAAAATAAATGT-TGAGCTTGTAAAACCATTTAAAGTGAGTA
130 TTAAAATCAAT-TATGAGATTATAAAACTATTTAAAGTGAGTA
********** * *
779 ATAAGGCTTTTNNNNNNNNNNGTGACTATAAATGGACTTTTCTTGCCAATGAATACCGTTTTGTT
1 ATAAGGCTTTTGAAAGAATGAGTGACTATAAATGGACTTTTCTTGCCAATGAATACCTTTTTCTT
** *
844 C-TCGTTTCTCTAGGTAGACATTCAATTATAATCTGTTAT-AACCATAAATATCAAAAAAATTAA
66 CAT-GTTTCTAGAGGTAGACATTCAATTATAATCTGTT-TGAACCAAAAATAT-AAAAAAATTAA
* * *
907 ACTTAAAATCAATTTTGAGATTATAAAACTATATAAAGTGAATA
128 ACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGTGAGTA
* * * * * * * * *
951 ATAAGCCTTTTGAAATAATGGGTGGCTCTAAATGGACTTTTTTTGCTAATGGATGCCTTTTTCTT
1 ATAAGGCTTTTGAAAGAATGAGTGACTATAAATGGACTTTTCTTGCCAATGAATACCTTTTTCTT
* ** ** * * *
1016 CATGTTTCTAGAGGTAAACATTCAATTATTGTCTGTTTGAATAAAAAATATAAGAAAATTTAGCT
66 CATGTTTCTAGAGGTAGACATTCAATTATAATCTGTTTGAACCAAAAATATAAAAAAATTAAACT
********** *
1081 TAAAATCAATTATGAGATTNNNNNNNNNNTTAAAGCGAGTA
131 TAAAATCAATTATGAGATTATAAAACTATTTAAAGTGAGTA
** * * * * * *
1122 ATAAGGCTTTTGAGCGAAGGGGAGACTATAAATGAAATTTTCTTGCCAATGAACTA-TTTTTTCT
1 ATAAGGCTTTTGAAAGAATGAGTGACTATAAATGGACTTTTCTTGCCAATGAA-TACCTTTTTCT
* ** * * * ** * *
1186 TCATGTTTCTTA-AGATAGGTATTTAATTATAATTTGTTTTAACCAGTAATGTAAAAACATTGAA
65 TCATGTTTC-TAGAGGTAGACATTCAATTATAATCTGTTTGAACCAAAAATATAAAAAAATT-AA
* * * * * * *
1250 CCCTAAAATCAATTATGAAATTACAAAACCATTTAAAGCGAATA
128 ACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGTGAGTA
* * * * * * * * ***
1294 ATAAGACTTTTGAATGATTGGGAGACTGTAAATGGACTTTTCTTGTCAATGAAT-GCTTTTNNNN
1 ATAAGGCTTTTGAAAGAATGAGTGACTATAAATGGACTTTTCTTGCCAATGAATACCTTTT-TCT
****** * * * * * * *
1358 NNNNNNTTCTCGAGCTAAACATTCAATTATAGTCTGTTTTAA-GAAAAATATAAAAAAATTTAAC
65 TCATGTTTCTAGAGGTAGACATTCAATTATAATCTGTTTGAACCAAAAATATAAAAAAATTAAAC
* * * ** * *
1422 CTATAATTAATTATGAGATTGCAAAACTTTTTAAAGCGAGTA
130 TTAAAATCAATTATGAGATTATAAAACTATTTAAAGTGAGTA
*
1464 CTAAGGCTTTTGAAAGAATGAGTGACTATAAATG
1 ATAAGGCTTTTGAAAGAATGAGTGACTATAAATG
1498 NNNNNNNNNN
Statistics
Matches: 679, Mismatches: 196, Indels: 31
0.75 0.22 0.03
Matches are distributed among these distances:
170 74 0.11
171 360 0.53
172 243 0.36
173 2 0.00
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.35
Consensus pattern (171 bp):
ATAAGGCTTTTGAAAGAATGAGTGACTATAAATGGACTTTTCTTGCCAATGAATACCTTTTTCTT
CATGTTTCTAGAGGTAGACATTCAATTATAATCTGTTTGAACCAAAAATATAAAAAAATTAAACT
TAAAATCAATTATGAGATTATAAAACTATTTAAAGTGAGTA
Found at i:1151 original size:343 final size:339
Alignment explanation
Indices: 437--1497 Score: 853
Period size: 343 Copynumber: 3.1 Consensus size: 339
427 NNNNNNNNNN
* * *
437 ATAAGGCTTTTGAAGGAATGAGTGACTATAAATAGACTTTTCTTGCCAATGAATTTTTTTTTCTT
1 ATAAGGCTTTTG-AGGAAGGAGTGACTATAAATGGACTTTTCTTGCCAATGAA-TATTTTTTCTT
* * * * * *
502 CACGTTTCTTGAGGTAGACATTCAATTATAATCTGTTTGAGCCAAAAATATAAAACCATTCAACT
64 CTCGTTTCTTAAGGTAGACATTCAATTATAATCTGTTT-AACCATAAATATAAAAACATTAAACT
* * * * * * *
567 TGAAATCAATTATGAGATGATAAAACTATTTAAAGCCAGTAATAAGGCTTTTGAAAGAATGAGTG
128 TAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAATAATAAGACTTTTGAAATAATGGGTG
* * * *
632 ACTATAAATGAACTTTCCATACCAATGAATATCTTTTTCTTCATGTTTCAAGAAATAGACATTCA
193 ACTATAAATGGACTTTTCATACCAATGAATACCTTTTTCTTCATGTTTCAAGAAATAAACATTCA
* *
697 ATTATAATCTGTTTTAATAAAAATATATAAAAAATTGAACTTAAAATAAATGTTGAGCTTGTAAA
258 ATTATAATCTGTTTGAATAAAAATATATAAAAAATTGAACTTAAAATAAATGTTGAGATTGTAAA
*
762 ACCATTTAAAGTGAGTA
323 ACCATTTAAAGCGAGTA
********* ** *
779 ATAAGGCTTTTNNNNNNNNNNGTGACTATAAATGGACTTTTCTTGCCAATGAATACCGTTTTGTT
1 ATAAGGCTTTT-GAGGAAGGAGTGACTATAAATGGACTTTTCTTGCCAATGAATA-TTTTTTCTT
*
844 CTCGTTTCTCT-AGGTAGACATTCAATTATAATCTGTTATAACCATAAATATCAAAAAAATTAAA
64 CTCGTTTCT-TAAGGTAGACATTCAATTATAATCTGTT-TAACCATAAATAT-AAAAACATTAAA
* * * *
908 CTTAAAATCAATTTTGAGATTATAAAACTATATAAAGTGAATAATAAGCCTTTTGAAATAATGGG
126 CTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAATAATAAGACTTTTGAAATAATGGG
* * ** * * * * * **
973 TGGCTCTAAATGGACTTTTTTTGCTAATGGATGCCTTTTTCTTCATGTTTCTAGAGGTAAACATT
191 TGACTATAAATGGACTTTTCATACCAATGAATACCTTTTTCTTCATGTTTCAAGAAATAAACATT
** * * * *
1038 CAATTATTGTCTGTTTGAATAAAAA-ATATAAGAAAATTTAGCTTAAAATCAAT-TATGAGATTN
256 CAATTATAATCTGTTTGAATAAAAATATATAA-AAAATTGAACTTAAAATAAATGT-TGAGATTG
*********
1101 NNNNNNNNNTTAAAGCGAGTA
319 TAAAACCATTTAAAGCGAGTA
* * * *
1122 ATAAGGCTTTTGAGCGAAGGGGAGACTATAAATGAAATTTTCTTGCCAATGAACTATTTTTTCTT
1 ATAAGGCTTTTGAG-GAAGGAGTGACTATAAATGGACTTTTCTTGCCAATGAA-TATTTTTTCTT
* ** * * *
1187 CAT-GTTTCTTAAGATAGGTATTTAATTATAATTTGTTTTAACCAGT-AATGTAAAAACATTGAA
64 C-TCGTTTCTTAAGGTAGACATTCAATTATAATCTG-TTTAACCA-TAAATATAAAAACATT-AA
* * * * * *
1250 CCCTAAAATCAATTATGAAATTACAAAACCATTTAAAGCGAATAATAAGACTTTTG-AATGATTG
125 ACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAATAATAAGACTTTTGAAAT-AATG
* * * ** * ********* ** **
1314 GGAGACTGTAAATGGACTTTTCTTGTCAATGAAT-GCTTTTNNNNNNNNNNTTCTCGAGCTAAAC
189 GGTGACTATAAATGGACTTTTCATACCAATGAATACCTTTT-TCTTCATGTTTCAAGAAATAAAC
* * * * * * *
1378 ATTCAATTATAGTCTGTTTTAAGAAAAATATA-AAAAAATTTAACCTATAATTAAT-TATGAGAT
253 ATTCAATTATAATCTGTTTGAATAAAAATATATAAAAAATTGAACTTAAAATAAATGT-TGAGAT
* **
1441 TGCAAAACTTTTTAAAGCGAGTA
317 TGTAAAACCATTTAAAGCGAGTA
* * *
1464 CTAAGGCTTTTGAAAGAATGAGTGACTATAAATG
1 ATAAGGCTTTTG-AGGAAGGAGTGACTATAAATG
1498 NNNNNNNNNN
Statistics
Matches: 565, Mismatches: 136, Indels: 36
0.77 0.18 0.05
Matches are distributed among these distances:
341 1 0.00
342 181 0.32
343 374 0.66
344 9 0.02
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.35
Consensus pattern (339 bp):
ATAAGGCTTTTGAGGAAGGAGTGACTATAAATGGACTTTTCTTGCCAATGAATATTTTTTCTTCT
CGTTTCTTAAGGTAGACATTCAATTATAATCTGTTTAACCATAAATATAAAAACATTAAACTTAA
AATCAATTATGAGATTATAAAACTATTTAAAGCGAATAATAAGACTTTTGAAATAATGGGTGACT
ATAAATGGACTTTTCATACCAATGAATACCTTTTTCTTCATGTTTCAAGAAATAAACATTCAATT
ATAATCTGTTTGAATAAAAATATATAAAAAATTGAACTTAAAATAAATGTTGAGATTGTAAAACC
ATTTAAAGCGAGTA
Done.