Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398818.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2102.0, 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: 6469
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.23
Warning! 2439 characters in sequence are not A, C, G, or T
Found at i:1816 original size:172 final size:172
Alignment explanation
Indices: 1638--2003 Score: 437
Period size: 172 Copynumber: 2.1 Consensus size: 172
1628 NNNTAATCTT
* *
1638 AAAATTGATTTAAATTTTAATTCTTTGTACATTTTTCGTTAAAACATACTAGGATTTAATGTCTA
1 AAAATTGATTTAAATTTTAATTCTTTATACATTTTTCGTTAAAACAGACTAGGATTTAATGTCTA
* * **
1703 CCTTCAGAAACATGAAGAAAAA-AGTATTCATTAGAAAGAAAAGTGTATTTATAGTCACCCATAC
66 CCTTCAGAAACATAAAGAAAAAGA-CATTCATTAGAAAGAAAAGTCCATTTATAGTCACCCATAC
* *
1767 CTTCAAAAACCTCATTACTCGCTTTAAATGGTTTTATAATATC
130 CTTCAAAAACCTCACTACTCGCTTTAAATGGTTTTATAATACC
* * **********
1810 AAAATTGATTTAAATTTTAATTCTTTATACATTTTTGGTTAAAATAGACTAGNNNNNNNNNNCTA
1 AAAATTGATTTAAATTTTAATTCTTTATACATTTTTCGTTAAAACAGACTAGGATTTAATGTCTA
* * *
1875 CCTTGAGAAACATAAAGAAAAAGACATTCATTGGAATGAAAAGTCCATTTATAGTCACCCATACC
66 CCTTCAGAAACATAAAGAAAAAGACATTCATTAGAAAGAAAAGTCCATTTATAGTCACCCATACC
* ** * *
1940 TTCAAAAGCCTTGCTACTCGCTTTAAATGGTTTTGTAATGCC
131 TTCAAAAACCTCACTACTCGCTTTAAATGGTTTTATAATACC
* * *
1982 ATAATTGATTTTAAGTTTAATT
1 AAAATTGATTTAAATTTTAATT
2004 TTTTTTTTAT
Statistics
Matches: 162, Mismatches: 31, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
172 161 0.99
173 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.36
Consensus pattern (172 bp):
AAAATTGATTTAAATTTTAATTCTTTATACATTTTTCGTTAAAACAGACTAGGATTTAATGTCTA
CCTTCAGAAACATAAAGAAAAAGACATTCATTAGAAAGAAAAGTCCATTTATAGTCACCCATACC
TTCAAAAACCTCACTACTCGCTTTAAATGGTTTTATAATACC
Found at i:4641 original size:172 final size:171
Alignment explanation
Indices: 4352--5779 Score: 1499
Period size: 172 Copynumber: 8.3 Consensus size: 171
4342 NNNNNNNNNN
* * * * * * * * * * *
4352 TCTCTAGGTAGACATTCAATTATAATTTG-TTTAACTAAACATATAAAAAAATTCTACTTAAAAT
1 TCTCAAGGTAGACATTCAATTCTAGTCTGTTTTAACCAAAAATGTACAAAAATTCAAATTTAAAT
* ** * * * *
4416 CAATTATG-GCATTCCAAAACCATTTAAAGC-AAGTAGTAAGGCTTTTGAAGGTATGGGTGACTA
66 CAATTTTGAG-ATTATAAAACTATTTAAA-CTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTA
* * *
4479 TAAATAGATTTTTCTTGCCAATGAATGCTTTTTTCTTCATGTT
129 TAAATGGACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTT
* * *
4522 TCTCAAGGTAGATATTCAATTCTAGTTTGTTTTAACCAAAAATGCACAAAACATTCAAATTTAAA
1 TCTCAAGGTAGACATTCAATTCTAGTCTGTTTTAACCAAAAATGTACAAAA-ATTCAAATTTAAA
* * *
4587 TCAATTTTGAGATTATAAAACTATTTAAACTGAGTAATAAGGCTCTTGAAGGTATGAGTGACTAT
65 TCAATTTTGAGATTATAAAACTATTTAAACTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTAT
* *
4652 AAATGGACTTTTTTTGCTAATGAATACTTTTTTCTTCATGTT
130 AAATGGACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTT
* * * * *
4694 TCTGAAGGTAGACATTCAATCCTAGTCTGTTTTAACCAAAAATGTTCGAAGAATTCAAA-CTAAA
1 TCTCAAGGTAGACATTCAATTCTAGTCTGTTTTAACCAAAAATGTAC-AAAAATTCAAATTTAAA
* ** * * * *
4758 TCAATTTTGAGATTATAAAACCATTTGGAGTGAGTAAGAAGGCTTTAGAAGGAATTGGTGACTAT
65 TCAATTTTGAGATTATAAAACTATTTAAACTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTAT
* ** *
4823 AAATGGACTTCTCTTGCCAAAAAATAAC-TTTTTCTAT-ACGTT
130 AAATGGACTTTTCTTGCCAATGAAT-ACTTTTTTCT-TCATGTT
* * * *
4865 TCTCAAGGTAGACAATT-AATTATAGTCCG-TTTAACCAAAAA--TACAAAACAATTCAACTTAA
1 TCTCAAGGTAGAC-ATTCAATTCTAGTCTGTTTTAACCAAAAATGTAC-AAA-AATTCAAATTTA
* * ** *
4926 AATCAATTAT-AGCATTATAAAACCATTTAAAGC-GAGTAATAAGGCTTTTGAAGCTATGGGTAA
63 AATCAATTTTGAG-ATTATAAAACTATTTAAA-CTGAGTAATAAGGCTTTTGAAGGAATGGGTGA
* ** * *
4989 CTATAAATAGACTTTTCTTTTCAATGAATGCTTTTTTCGTCATGTT
126 CTATAAATGGACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTT
* * * * * *
5035 TCTGAAGGTAGACATTCAATTCTAGTCTATTTAAATCAAAAGTGTACAAAGAATTCATATTTAAA
1 TCTCAAGGTAGACATTCAATTCTAGTCTGTTTTAACCAAAAATGTACAAA-AATTCAAATTTAAA
* *
5100 TCAATTTTGAGATTATAAAA-TCATTTAAACTGAGTACTAAGG-TTCTTAAAGGAATGGGTGACT
65 TCAATTTTGAGATTATAAAACT-ATTTAAACTGAGTAATAAGGCTT-TTGAAGGAATGGGTGACT
* *
5163 ATAAATGGACTTTTTTTCCCAATGAATACTTTTTTCTTCATGTT
128 ATAAATGGACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTT
* * * * * *
5207 TCTAAAGGTAGAGATTCAA-TCGTAGTTTGTTTTAACTAAAAATGTACAAAGAGTTCAAATTTCA
1 TCTCAAGGTAGACATTCAATTC-TAGTCTGTTTTAACCAAAAATGTACAAA-AATTCAAATTTAA
* * *
5271 ATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGTGACTA
64 ATCAATTTTGAGATTATAAAACTATTTAAACTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTA
* * *
5336 TAAATGAACTTTTCTTGCCAATGAATGCTTTCTTCTTCATGTT
129 TAAATGGACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTT
* * *
5379 TCTCAGGGTAGACATTCAATTCTAGTCTGTTTTAACTAAAAATGTATAAAGAATTCAAATTTAAA
1 TCTCAAGGTAGACATTCAATTCTAGTCTGTTTTAACCAAAAATGTACAAA-AATTCAAATTTAAA
* *
5444 TCAATTTTGAGATTATAAAACTATTTAAAGC-GAGTAATAAGTCTTTTGAATGTAA-GGGTGACT
65 TCAATTTTGAGATTATAAAACTATTTAAA-CTGAGTAATAAGGCTTTTGAA-GGAATGGGTGACT
** *
5507 ATAAATAAACTTTTCTTGCTAATGAATACTTTTTTCTTCATGTT
128 ATAAATGGACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTT
* * * * *
5551 TCTGAAGGTAGACATTCAATCCTAGTCTGTTTTAACCAAAAATGTACAAATCATTTAAACTTAAA
1 TCTCAAGGTAGACATTCAATTCTAGTCTGTTTTAACCAAAAATGTACAAA-AATTCAAATTTAAA
* * * *
5616 TCAATTTTGAGATTATAAAA-TCATTTAAAGTGAGTAATAAGGCTTTTGAATGAATGGATGGCTA
65 TCAATTTTGAGATTATAAAACT-ATTTAAACTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTA
* * * * * * * * **
5680 TAAATGGAATTCTCTAGACAATAAATGCCTTTTTCTTTACATT
129 TAAATGGACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTT
** * * * *
5723 TCTTGAGGTAGACATTCAATTATAGTTTG-TTTAACCAAAAATATAAAAAAAATTCAA
1 TCTCAAGGTAGACATTCAATTCTAGTCTGTTTTAACCAAAAATGT-ACAAAAATTCAA
5780 CNNNNNNNNN
Statistics
Matches: 1050, Mismatches: 176, Indels: 63
0.81 0.14 0.05
Matches are distributed among these distances:
168 4 0.00
169 14 0.01
170 141 0.13
171 164 0.16
172 711 0.68
173 16 0.02
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.37
Consensus pattern (171 bp):
TCTCAAGGTAGACATTCAATTCTAGTCTGTTTTAACCAAAAATGTACAAAAATTCAAATTTAAAT
CAATTTTGAGATTATAAAACTATTTAAACTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATA
AATGGACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTT
Done.