Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399606.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_286.0, 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: 4230
ACGTcount: A:0.24, C:0.08, G:0.09, T:0.23
Warning! 1491 characters in sequence are not A, C, G, or T
Found at i:846 original size:171 final size:171
Alignment explanation
Indices: 554--880 Score: 460
Period size: 171 Copynumber: 1.9 Consensus size: 171
544 NNNNNNNNNN
* *
554 AATAAGGCTTTTGAAGGAATGAGTGACTATAAATAGACTTTTCTTGCCATTGAACGCTTTTCTCT
1 AATAAGGCTTTTGAAGGAATGAGTGACTATAAATAGACTTTTCTTGCCAATCAACGCTTTTCTCT
* * * * *
619 TCACGCTTCTCCAGGTAGACATTCAATTATAGTCTGTTTTAAACAAAAATGTAAAAAAATTTAAC
66 TCACGCTTCTCAAGGTAAACATTCAATTATAGTCTGTGTTAAACAAAAAAGTAAAAAAATTCAAC
*
684 TCAAAATTAATGACGAGATTATAAAACAATTTAAAATGACT
131 TCAAAATCAATGACGAGATTATAAAACAATTTAAAATGACT
* * *
725 AATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTGTTT-TTGCCAATCAATGCCTTTT-T
1 AATAAGGCTTTTGAAGGAATGAGTGACTATAAATAGACT-TTTCTTGCCAATCAACG-CTTTTCT
* * * *
788 CTTCATGTTTCTTAAGGTAAACATTCAATTATAGTCTGTGTTAACCAAAAAAGTAAAAAAATTCA
64 CTTCACGCTTCTCAAGGTAAACATTCAATTATAGTCTGTGTTAAACAAAAAAGTAAAAAAATTCA
* * *
853 ACTTAAAATCAATTATGAGATTATAAAA
129 ACTCAAAATCAATGACGAGATTATAAAA
881 TNNNNNNNNN
Statistics
Matches: 136, Mismatches: 18, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
171 128 0.94
172 8 0.06
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (171 bp):
AATAAGGCTTTTGAAGGAATGAGTGACTATAAATAGACTTTTCTTGCCAATCAACGCTTTTCTCT
TCACGCTTCTCAAGGTAAACATTCAATTATAGTCTGTGTTAAACAAAAAAGTAAAAAAATTCAAC
TCAAAATCAATGACGAGATTATAAAACAATTTAAAATGACT
Found at i:1690 original size:171 final size:169
Alignment explanation
Indices: 1334--1897 Score: 413
Period size: 171 Copynumber: 3.3 Consensus size: 169
1324 NNNNNNNNNN
** **
1334 CTTAAAATCAATTATGAGATTAT-AAACCATTTAAAGCGAGTAATAAGGCTTTTGGAGGAATGGG
1 CTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAACCTTTTAAAGGAATGGG
* * ** * * * * * * ** * **
1398 TGACTATCAATACACTTTTTTTGCTAGTGAATGCCTTTTTTTTCACGTTTCTTGAGGTAGATGTT
66 TAACTATAAATGGACTTGTTTTGCCAATGAATGACTTTTTCTTCATGTTTCTCAAGGCAGACATT
********** * *
1463 CAATTATAGTNNNNNNNNNNCAAAAATGTAAA-ACAATTCAC
131 CAATTATAGTCTATTTTAAGCAAAAA--TAAATA-AAATCAA
* * * *
1504 CTTAAAATTAATTATGAGATTATAAAACCATTTAAAGCGAATAATAAATCTTTTAAAGGAATGTG
1 CTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAACCTTTTAAAGGAATGGG
* **
1569 TGACTATAAATGGACTT-TTCTTGCCAATGAAT-ACTTTTTGCTTTC-TGTTTCTTGAGGCAGAC
66 TAACTATAAATGGACTTGTT-TTGCCAATGAATGACTTTTT-C-TTCATGTTTCTCAAGGCAGAC
* *
1631 ATTCAATTATTGTCTATTTTAATG-AAAAATATAA-AAAATTTTAA
128 ATTCAATTATAGTCTATTTTAA-GCAAAAATA-AATAAAA--TCAA
* * *********** ** *
1675 CTTAAAGTCAATTATGAAATTATAAAACTNNNNNNNNNNAGTAATAAGGCTTTTGAAGGAATGGG
1 CTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAACCTTTTAAAGGAATGGG
* * * * *
1740 TAACTCTAAATGGACTTGTTTTGCTAGTGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATT
66 TAACTATAAATGGACTTGTTTTGCCAATGAATGACTTTTTCTTCATGTTTCTCAAGGCAGACATT
* * *
1805 CAGTTATAGTCTGTTTTAAGCAAAAATAAATAAAATCAC
131 CAATTATAGTCTATTTTAAGCAAAAATAAATAAAATCAA
1844 CTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAACCTTTT
1 CTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAACCTTTT
1898 NNNNNNNNNN
Statistics
Matches: 302, Mismatches: 79, Indels: 27
0.74 0.19 0.07
Matches are distributed among these distances:
169 45 0.15
170 39 0.13
171 207 0.69
172 11 0.04
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.35
Consensus pattern (169 bp):
CTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAACCTTTTAAAGGAATGGG
TAACTATAAATGGACTTGTTTTGCCAATGAATGACTTTTTCTTCATGTTTCTCAAGGCAGACATT
CAATTATAGTCTATTTTAAGCAAAAATAAATAAAATCAA
Done.