Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398605.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1895.0, 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: 3096
ACGTcount: A:0.27, C:0.10, G:0.11, T:0.26
Warning! 790 characters in sequence are not A, C, G, or T
Found at i:1881 original size:512 final size:501
Alignment explanation
Indices: 1005--1951 Score: 964
Period size: 512 Copynumber: 1.9 Consensus size: 501
995 NNNNNNNNNN
*
1005 TCTTGCCAATGAATGCCTTTTCTTCATGTTTCCTAAGGTAGACATTCAATTCTAGTCTGTTTTAA
1 TCTTACCAATGAATGCCTTTTCTTCATGTTTCCTAAGGTAGACATTCAATTCTAGTCTGTTTTAA
* *********** * *
1070 CTAAAAATGTAAAAATACTTNNNNNNNNNNCAATTATTAGTTTATAAAACCATTTAAACGAAGTA
66 CCAAAAATGTAAAAATACTCAACTTAAAAACAATTATTAGTTTATAAAACCATTTAAACAAAGCA
** * * * **
1135 ATAACGCTTTTGAATGCTTGAGTGACTAGAAATGAACTTTTCGTGCTGATGGTTGGCTTTTGCTT
131 ATAACGCTTTCAAAGGCTTAAGTGACTACAAATGAACTTTTCGTGCCAATGGTTGGCTTTTGCTT
** * * *
1200 CATGTTTTCCAAGGCAAACATTCAATTGTAGCCTTTTTTAACCAAAAATGTAAAAAGATTCTACT
196 CATGTTCCCCAAGGCAAACATTCAATTGTAGCCTTTTTTAACCAAAAATATAAAAAGAGTCAACT
**
1265 CAAAATCAATTTTGAGATTATTTAACCATTTAAGGTGAGTAATAAGGCTTTTGAAAGAATGGGTG
261 CAAAATCAATTTTGAGATTATAAAACCATTTAAGGTGAGTAATAAGGCTTTTGAAAGAATGGGTG
* ********** * * *
1330 ACTATAAATGGACTTTTCNNNNNNNNNNATACCTTTTCTTCATGTTTTTTGAGGTAGACATGCAA
326 ACTATAAATAGACTTTTCATTGCCGATGATACCTTTTCTTAATGTTTCTTGAGGTAAACATGCAA
* * *
1395 TTATAATCT-GTTTGAACCAAAAATGTGAAAAGATTCAACTTAAAATCAAATATCACATCATAAA
391 TTATAATCTAATTT-AACCAAAAATGTAAAAAGACTCAACTTAAAATCAAATATCACATCATAAA
1459 ACTATTTAAAGTGAGCAATAAGACATTTGAGGGTATGGNNNNNNNNNNATGGACTTT
455 ACTATTTAAAGTGAGCAATAAGACATTTGAGGGTATGG----------ATGGACTTT
* * * * *
1516 TCTTACCAATGAATTTCTTTTTCTTCATGTTTCTTGAGGTAGACATTCAATTCTAGTCTGTTTTT
1 TCTTACCAATGAA-TGCCTTTTCTTCATGTTTCCTAAGGTAGACATTCAATTCTAGTCTGTTTTA
*
1581 ACCAAAAATGTGAAAATACTCAACTTAAAAACAATTATTAGTTTATAAAACCATTTAAACAAAGC
65 ACCAAAAATGTAAAAATACTCAACTTAAAAACAATTATTAGTTTATAAAACCATTTAAACAAAGC
* * ***
1646 AATAACGCTTTCAAAGGTTTAAGTGACTACAAATGGACTTTTCGTGCCAATGGTTGGCTTTTNNN
130 AATAACGCTTTCAAAGGCTTAAGTGACTACAAATGAACTTTTCGTGCCAATGGTTGGCTTTTGCT
******* *
1711 NNNNNNNCCCCAAGGCAGACATTCAATTGTAGCC-TTTTTAACCAAAAATATAAAAAGAGTCAAC
195 TCATGTTCCCCAAGGCAAACATTCAATTGTAGCCTTTTTTAACCAAAAATATAAAAAGAGTCAAC
* * ********** * *
1775 TTATAATCAATTTTGAGATTATAAAACCATNNNNNNNNNNTGATAAGGCTTTTGAAGGAATGGGT
260 TCAAAATCAATTTTGAGATTATAAAACCATTTAAGGTGAGTAATAAGGCTTTTGAAAGAATGGGT
* * * *
1840 GTCTATAAATAGCCTTTTC-TTGCCGATGAGTGCCTTTTTCTTAATGTTTCTTGAGGTAAACATT
325 GACTATAAATAGACTTTTCATTGCCGATGA-TACC-TTTTCTTAATGTTTCTTGAGGTAAACATG
* * * *
1904 CAATTCTAGTCTAATTTAACCAAAAATGTAAAAATACTGAACTTAAAA
388 CAATTATAATCTAATTTAACCAAAAATGTAAAAAGACTCAACTTAAAA
1952 ATAATTATTA
Statistics
Matches: 346, Mismatches: 86, Indels: 7
0.79 0.20 0.02
Matches are distributed among these distances:
510 1 0.00
511 107 0.31
512 235 0.68
513 3 0.01
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.34
Consensus pattern (501 bp):
TCTTACCAATGAATGCCTTTTCTTCATGTTTCCTAAGGTAGACATTCAATTCTAGTCTGTTTTAA
CCAAAAATGTAAAAATACTCAACTTAAAAACAATTATTAGTTTATAAAACCATTTAAACAAAGCA
ATAACGCTTTCAAAGGCTTAAGTGACTACAAATGAACTTTTCGTGCCAATGGTTGGCTTTTGCTT
CATGTTCCCCAAGGCAAACATTCAATTGTAGCCTTTTTTAACCAAAAATATAAAAAGAGTCAACT
CAAAATCAATTTTGAGATTATAAAACCATTTAAGGTGAGTAATAAGGCTTTTGAAAGAATGGGTG
ACTATAAATAGACTTTTCATTGCCGATGATACCTTTTCTTAATGTTTCTTGAGGTAAACATGCAA
TTATAATCTAATTTAACCAAAAATGTAAAAAGACTCAACTTAAAATCAAATATCACATCATAAAA
CTATTTAAAGTGAGCAATAAGACATTTGAGGGTATGGATGGACTTT
Done.