Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400786.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3962.0, 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: 2404
ACGTcount: A:0.31, C:0.10, G:0.11, T:0.29
Warning! 452 characters in sequence are not A, C, G, or T
Found at i:1174 original size:171 final size:170
Alignment explanation
Indices: 755--2404 Score: 1532
Period size: 171 Copynumber: 9.6 Consensus size: 170
745 NNNNNNNNNN
* * *
755 TATAAATGAACTTTTCTTGCCAATGAATGCCTTTTTCTTCACATTTCT-TGAGGTAGACAATCAA
1 TATAAATG-ACTTTTCTTGCCAATGAATGCCTTTTTCTTCACGTTTCTCT-AAGTAGACATTCAA
* * * * ** * *
819 TAAGAATCTTTTTTTGACCAAAAATGTAAAAAAA-AAAACTTAAAATCAATTTTGAGACTATAAA
64 TTATAATC-TGTTTTAACCAAAAATGTAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAA
* * * * *
883 ACCATTTAACGTGAGTAATAAGGCTTCTGAAGGAATTGGTGAC
128 ACAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGAC
** * *
926 TAT-AATAGACTTTTCTTGCTGATGAATGCATTTTTCTTCACGTTTCTCAAAGTAGACATGT-AA
1 TATAAAT-GACTTTTCTTGCCAATGAATGCCTTTTTCTTCACGTTTCTCTAAGTAGACAT-TCAA
* * * *
989 TTATTATCTGTTTTAACCAAATATGTAAAAAAATTTAACTTCAAATCAATTATGGGATTATAAAA
64 TTATAATCTGTTTTAACCAAAAATGTAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAA
1054 CAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGAC
129 CAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGAC
* * * *
1096 TATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTCTAACTAGGCAATCAAT
1 TATAAAT-GACTTTTCTTGCCAATGAATGCCTTTTTCTTCACGTTTCTCTAAGTAGACATTCAAT
* * *
1161 TATAATCTGTTTTAACCAAAAAGGTAAAAAAATTTAACTTAAAATCAATTATTAGATTATAAAAT
65 TATAATCTGTTTTAACCAAAAATGTAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAAC
* * * **
1226 AATTTAAAGCTAGTAATAAGGCTTTTCAAAGAATCAGTGAC
130 AATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGAC
* * *
1267 TATAAATTGACTTTTCTTGCCAATGAATGACTTTTTTTTCATC-TTTCTC-AAGGTAGACATTCG
1 TATAAA-TGACTTTTCTTGCCAATGAATGCCTTTTTCTTCA-CGTTTCTCTAA-GTAGACATTCA
* * *
1330 ATTATAGTCTGTTTTAACC-AAAATG-CAAAAAATTTCAACTTAAAATCAATTATCAGATTATAA
63 ATTATAATCTGTTTTAACCAAAAATGTAAAAAAATTT-AACTTAAAATCAATTATGAGATTATAA
* *
1393 AACAATTTAAAGTGAGTAATAAGGTTTTTGAAGGAATGGGTGAC
127 AACAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGAC
* * * * * *
1437 TATAAATGTACTTATT-TTTCTAAATGAATGGCC-TTTTCCTCACATTTCT-TGACGTAGGCATT
1 TATAAATG-ACTT-TTCTTGC-CAATGAAT-GCCTTTTTCTTCACGTTTCTCT-AAGTAGACATT
* * * * * *
1499 CAATTATAGTTTGTTTTATCCAAAAATGTAAAAAAATTAAACTTAAAATCAATTATGAGATAAAA
61 CAATTATAATCTGTTTTAACCAAAAATGTAAAAAAATTTAACTTAAAATCAATTATGAGATTATA
* * *
1564 AAATC-GTTTAAAGCGAGTAATAAGGCTTTTGGAGGAATGGGTGAT
126 AAA-CAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGAC
* * * *
1609 TATAAATGGACTTTTCTTGCCAATGAAAGCCTTTTTC-TCTAAGTTTCTCAAAGTAGACATTGAA
1 TATAAAT-GACTTTTCTTGCCAATGAATGCCTTTTTCTTC-ACGTTTCTCTAAGTAGACATTCAA
** * *
1673 TTATAGCCTGTTTGAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAA
64 TTATAATCTGTTTTAACCAAAAATGTAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAA
*
1738 CTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGAC
129 CAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGAC
** * * *
1780 TATAAATAGACTTTTCTT-ATAGATGAATG-CTTGTTTCTTTATGTTTCTCTAGGCT-GACATTC
1 TATAAAT-GACTTTTCTTGCCA-ATGAATGCCTT-TTTCTTCACGTTTCTCTAAG-TAGACATTC
* * * * * * * * * *
1842 AATTATTATTTATTTTAATCAAAAATGTAAAAAAGTTTAGCTTCAAATCAATTATGGGAATACAA
62 AATTATAATCTGTTTTAACCAAAAATGTAAAAAAATTTAACTTAAAATCAATTATGAGATTATAA
* * ** * * * * * *
1907 AACCATTTGAAGTAAATAATAAAGCTTTTAAAGAAATAGGTAAC
127 AACAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGAC
* * * * * * *
1951 TATAAATGGACTTTTCTT-CTCATTGAATGGCTTTTTCTACATGTTTC-CCAAGACAGGCATTCA
1 TATAAAT-GACTTTTCTTGC-CAATGAATGCCTTTTTCTTCACGTTTCTCTAAG-TAGACATTCA
* * ** * *
2014 ATTATAGTATGTTTTAATAAAAAATGTAAAAAAATTCAACTTAAAATCATTTATGAGATTATAAA
63 ATTATAATCTGTTTTAACCAAAAATGTAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAA
*
2079 ACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGAC
128 ACAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGAC
* * * * *
2122 TATAAATGAACCTTTCTTGCCAATGAATG-CTTGTTTCTTTACATTTCTC-AAGGTTGACGTTCA
1 TATAAATG-ACTTTTCTTGCCAATGAATGCCTT-TTTCTTCACGTTTCTCTAA-GTAGACATTCA
* * * * **********
2185 GTTACT-ATCTATTTGAACCAAAAATGTAAAAAAATTTAACTTCAAATCANNNNNNNNNNTATAA
63 ATTA-TAATCTGTTTTAACCAAAAATGTAAAAAAATTTAACTTAAAATCAATTATGAGATTATAA
** ** * *
2249 AATTATTTAAAGTAAGTAATAAGGCTTTTAGAA-GAGTGGGTAAC
127 AACAATTTAAAGCGAGTAATAAGGCTTTT-GAAGGAATGGGTGAC
* * * *
2293 TTTAAATGGACTTTTCTTCCCAATGAATGACTTTTTCTAT-ACGTTT-TCTAAAGTA-AGTATTC
1 TATAAAT-GACTTTTCTTGCCAATGAATGCCTTTTTCT-TCACGTTTCTCT-AAGTAGA-CATTC
* * ** * *
2355 AATTATAATTTATTTTAAAGAAAAAAAGTAAAAAAATTGAACTTAAAATC
62 AATTATAATCTGTTTT-AACCAAAAATGTAAAAAAATTTAACTTAAAATC
Statistics
Matches: 1213, Mismatches: 218, Indels: 95
0.79 0.14 0.06
Matches are distributed among these distances:
169 33 0.03
170 223 0.18
171 814 0.67
172 133 0.11
173 10 0.01
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (170 bp):
TATAAATGACTTTTCTTGCCAATGAATGCCTTTTTCTTCACGTTTCTCTAAGTAGACATTCAATT
ATAATCTGTTTTAACCAAAAATGTAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAACA
ATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGAC
Done.