Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400101.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_332.0, 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: 5901
ACGTcount: A:0.20, C:0.07, G:0.08, T:0.20
Warning! 2741 characters in sequence are not A, C, G, or T
Found at i:1659 original size:513 final size:511
Alignment explanation
Indices: 713--1885 Score: 1444
Period size: 513 Copynumber: 2.3 Consensus size: 511
703 TTCTTGTGGC
* *
713 AAACATTCAATTATAGTCTGTTTTAATGAGAAATGTAAAAAGAATTGAACTTAAAATTAATTATT
1 AAACATTCAATTATAGTCTGTTTTAATGAGAAATGTAAAAA-AATTGAAATTAAAA-TAATTATG
* * *
778 AGCTTATAAAACTATTTAGAACGAGTAAAAAGGCTGTTGAAGGACTGAGAGGCTATAAATAGACT
64 AGATTAAAAAACCATTTAGAACGAGTAAAAAGGCTGTTGAAGGACTGAGAGGCTATAAATAGACT
* * *
843 TTTATTATCAATGAATGCTTTTTTCTTCACGGTTCTTGAGGCAGACATTCAATTATAGCCTGTTT
129 TTTATCATCAATGAATGCTTTTTTCTTCACGGTTCTCGAGGCAAACATTCAATTATAGCCTGTTT
* * ** * *
908 TAAGGAAAAATGTAAAAAAATTCAACTCAAAATAAATTATTAGATTATAAACTATTTAAAGCGAG
194 TAAGAAAAAACGTAAAAAAATTCAACTCAAAATAAATTACAAGATTAAAAACCATTTAAAGCGAG
* *
973 TAATAAGACTTTTGAAAGAATGGGTGACTATAAATGGACTTTTCTTGCCAATAAATATGTTTTTC
259 TAACAAGACTTTTGAAAGAATGGGTGACTATAAATGAACTTTTCTTGCCAATAAATATGTTTTTC
* * * * * *
1038 TTCATGTTTCTTGAGATAGACATTCAATTATATTCTGTTTTAATGAAAAATATAAACAAACTCAA
324 TTCACGTTTCTCGAGATAAACAGTCAATTATATTCTGTTTTAATCAAAAATATAAAAAAACTCAA
* * *
1103 CTTAAAATCAATTATGACATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGG
389 CTTAAAATCAATTATGACATTAGAAAACCATTTAAAATGAGTAATAAGGCTTTCGAAGGAATGGG
* * *
1168 TGACTATAAATGGACTTTTCTTGAAAATAAATACTTTTTTCTTCA-TGTTTCTCAAGAT
454 AGACTATAAATAGACTTTTCTTGAAAATAAATACTTTGTTCTTCACT-TTTCTCAAGAT
* * * * *
1226 AAACATTCAATTATTGTCTGTTTTAATCAAAAATGTAAAAAAATTCAAGTTAAAATCAATTATGA
1 AAACATTCAATTATAGTCTGTTTTAATGAGAAATGTAAAAAAATTGAAATTAAAAT-AATTATGA
* * * * *
1291 GATTAGAAAAACCATTTA-AAGTGAGTAATAAGGCTTTTGAAGGAGTGGGAGGCTAT-AAT-GAA
65 GATTA-AAAAACCATTTAGAA-CGAGTAAAAAGGCTGTTGAAGGACTGAGAGGCTATAAATAG-A
* * * * * *
1353 CTTTTCTCATCAATGAATGCTTTTTTCTTCACGTTTGTCGAGGTAAATATTCAATTATAGTCTGT
127 CTTTTATCATCAATGAATGCTTTTTTCTTCACGGTTCTCGAGGCAAACATTCAATTATAGCCTGT
* * * *
1418 TTTAATAAAAAACGTAAAAAAATTTAGC-CTAAAATTAATTACAAGATTAGAAAACCATTTAAAG
192 TTTAAGAAAAAACGTAAAAAAATTCAACTC-AAAATAAATTACAAGATTA-AAAACCATTTAAAG
* * * **
1482 CGAGTAACAAGGCTTTTGAAGGAATGGGTGACTATAAATGAACTTTTCTTGTC-ATTGA-ATGCT
255 CGAGTAACAAGACTTTTGAAAGAATGGGTGACTATAAATGAACTTTTCTTGCCAATAAATATG-T
* *
1545 TTTGTCTTCACGTTTCTCGAGGTAAACAGTCAATTAT-TGTCTGTTTTAATCAAAAATGTAAAAA
319 TTT-TCTTCACGTTTCTCGAGATAAACAGTCAATTATAT-TCTGTTTTAATCAAAAATATAAAAA
* * *
1609 AATTCAACTTAAAATCAATTATTAGATTAGAAAACCATTTAAAATGAGTAATAAGGCTTTCGAAG
382 AACTCAACTTAAAATCAATTATGACATTAGAAAACCATTTAAAATGAGTAATAAGGCTTTCGAAG
* * * ** * * *
1674 GAATGTGAGGCTCTAAATAGACTTTTCTTGCCAATGAATGCTTTGTTCTTCACTTTTCTCAAGGT
447 GAATGGGAGACTATAAATAGACTTTTCTTGAAAATAAATACTTTGTTCTTCACTTTTCTCAAGAT
* * *
1739 AGACATTTAATTATAGTCTGTTTTAATGAGAAATGTAAAAAAATTGAAATTAAAAGTAATTTTGA
1 AAACATTCAATTATAGTCTGTTTTAATGAGAAATGTAAAAAAATTGAAATTAAAA-TAATTATGA
* * * ** * * * * *
1804 GATTATAAAATCTTTTAGAACGAGTAAAAAGGCAATTAAAGAAATAAGAGGCTATAAATGGACTT
65 GATTAAAAAACCATTTAGAACGAGTAAAAAGGCTGTTGAAGGACTGAGAGGCTATAAATAGACTT
* *
1869 TTTTTATCAATGAATGC
130 TTATCATCAATGAATGC
1886 CTTTNNNNNN
Statistics
Matches: 559, Mismatches: 87, Indels: 28
0.83 0.13 0.04
Matches are distributed among these distances:
511 6 0.01
512 167 0.30
513 383 0.69
514 3 0.01
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (511 bp):
AAACATTCAATTATAGTCTGTTTTAATGAGAAATGTAAAAAAATTGAAATTAAAATAATTATGAG
ATTAAAAAACCATTTAGAACGAGTAAAAAGGCTGTTGAAGGACTGAGAGGCTATAAATAGACTTT
TATCATCAATGAATGCTTTTTTCTTCACGGTTCTCGAGGCAAACATTCAATTATAGCCTGTTTTA
AGAAAAAACGTAAAAAAATTCAACTCAAAATAAATTACAAGATTAAAAACCATTTAAAGCGAGTA
ACAAGACTTTTGAAAGAATGGGTGACTATAAATGAACTTTTCTTGCCAATAAATATGTTTTTCTT
CACGTTTCTCGAGATAAACAGTCAATTATATTCTGTTTTAATCAAAAATATAAAAAAACTCAACT
TAAAATCAATTATGACATTAGAAAACCATTTAAAATGAGTAATAAGGCTTTCGAAGGAATGGGAG
ACTATAAATAGACTTTTCTTGAAAATAAATACTTTGTTCTTCACTTTTCTCAAGAT
Found at i:1882 original size:171 final size:170
Alignment explanation
Indices: 688--1885 Score: 1226
Period size: 171 Copynumber: 7.0 Consensus size: 170
678 NNNNNNNNNN
* * * *
688 CTTTTTTCTTCACTTTTCTTGTGGCAAACATTCAATTATAGTCTGTTTTAATGAGAAATGTAAAA
1 CTTTTTTCTTCACTTTTCTCGAGGTAAACATTCAATTATAGTCTGTTTTAATGAAAAATGTAAAA
* * * * * *
753 AGAATTGAACTTAAAATTAATTATTAGCTTATAAAACTATTTAGAA-CGAGTAAAAAGGCTGTTG
66 A-AATTCAACTTAAAATCAATT-TTAGATTATAAAACCATTTA-AAGCGAGTAATAAGGCTTTTG
* * * *
817 AAGGACTGAGAGGCTATAAATAGACTTTTATTATCAATGAATG
128 AAGGAATGGGAGGCTATAAATGGACTTTTCTTATCAATGAATG
** * * * * *
860 CTTTTTTCTTCACGGTTCTTGAGGCAGACATTCAATTATAGCCTGTTTTAAGGAAAAATGTAAAA
1 CTTTTTTCTTCACTTTTCTCGAGGTAAACATTCAATTATAGTCTGTTTTAATGAAAAATGTAAAA
* * * *
925 AAATTCAACTCAAAATAAATTATTAGATTAT-AAACTATTTAAAGCGAGTAATAAGACTTTTGAA
66 AAATTCAACTTAAAATCAATT-TTAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAA
* * * ** *
989 AGAATGGGTGACTATAAATGGACTTTTCTTGCCAATAAAT-
130 GGAATGGGAGGCTATAAATGGACTTTTCTTATCAATGAATG
* * * * * *
1029 ATGTTTTTCTTCA-TGTTTCTTGAGATAGACATTCAATTATATTCTGTTTTAATGAAAAATATAA
1 CT-TTTTTCTTCACT-TTTCTCGAGGTAAACATTCAATTATAGTCTGTTTTAATGAAAAATGTAA
* * * * *
1093 ACAAACTCAACTTAAAATCAATTATGACATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTG
64 AAAAATTCAACTTAAAATCAATT-TTAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTG
* * * * *
1158 AAGGAATGGGTGACTATAAATGGACTTTTCTTGA-AAATAAATA
128 AAGGAATGGGAGGCTATAAATGGACTTTTCTT-ATCAATGAATG
* * * *
1201 CTTTTTTCTTCA-TGTTTCTCAAGATAAACATTCAATTATTGTCTGTTTTAATCAAAAATGTAAA
1 CTTTTTTCTTCACT-TTTCTCGAGGTAAACATTCAATTATAGTCTGTTTTAATGAAAAATGTAAA
* * * *
1265 AAAATTCAAGTTAAAATCAATTATGAGATTAGAAAAACCATTTAAAGTGAGTAATAAGGCTTTTG
65 AAAATTCAACTTAAAATCAATT-TTAGATTA-TAAAACCATTTAAAGCGAGTAATAAGGCTTTTG
* * *
1330 AAGGAGTGGGAGGCTAT-AATGAACTTTTCTCATCAATGAATG
128 AAGGAATGGGAGGCTATAAATGGACTTTTCTTATCAATGAATG
* * * * *
1372 CTTTTTTCTTCACGTTTGTCGAGGTAAATATTCAATTATAGTCTGTTTTAATAAAAAACGTAAAA
1 CTTTTTTCTTCACTTTTCTCGAGGTAAACATTCAATTATAGTCTGTTTTAATGAAAAATGTAAAA
* * * * ** * *
1437 AAATTTAGCCTAAAATTAATTACAAGATTAGAAAACCATTTAAAGCGAGTAACAAGGCTTTTGAA
66 AAATTCAACTTAAAATCAATT-TTAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAA
* * * * *
1502 GGAATGGGTGACTATAAATGAACTTTTCTTGTCATTGAATG
130 GGAATGGGAGGCTATAAATGGACTTTTCTTATCAATGAATG
* * * * *
1543 CTTTTGTCTTCACGTTTCTCGAGGTAAACAGTCAATTATTGTCTGTTTTAATCAAAAATGTAAAA
1 CTTTTTTCTTCACTTTTCTCGAGGTAAACATTCAATTATAGTCTGTTTTAATGAAAAATGTAAAA
* ** *
1608 AAATTCAACTTAAAATCAATTATTAGATTAGAAAACCATTTAAAATGAGTAATAAGGCTTTCGAA
66 AAATTCAACTTAAAATCAATT-TTAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAA
* * * **
1673 GGAATGTGAGGCTCTAAATAGACTTTTCTTGCCAATGAATG
130 GGAATGGGAGGCTATAAATGGACTTTTCTTATCAATGAATG
* * * * *
1714 CTTTGTTCTTCACTTTTCTCAAGGTAGACATTTAATTATAGTCTGTTTTAATGAGAAATGTAAAA
1 CTTTTTTCTTCACTTTTCTCGAGGTAAACATTCAATTATAGTCTGTTTTAATGAAAAATGTAAAA
* * * * * ** *
1779 AAATTGAAATTAAAAGT-AATTTTGAGATTATAAAATCTTTTAGAA-CGAGTAAAAAGGCAATTA
66 AAATTCAACTTAAAA-TCAATTTT-AGATTATAAAACCATTTA-AAGCGAGTAATAAGGCTTTTG
* ** *
1842 AAGAAATAAGAGGCTATAAATGGACTTTTTTTATCAATGAATG
128 AAGGAATGGGAGGCTATAAATGGACTTTTCTTATCAATGAATG
1885 C
1 C
1886 CTTTNNNNNN
Statistics
Matches: 869, Mismatches: 144, Indels: 27
0.84 0.14 0.03
Matches are distributed among these distances:
169 3 0.00
170 183 0.21
171 574 0.66
172 109 0.13
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (170 bp):
CTTTTTTCTTCACTTTTCTCGAGGTAAACATTCAATTATAGTCTGTTTTAATGAAAAATGTAAAA
AAATTCAACTTAAAATCAATTTTAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAG
GAATGGGAGGCTATAAATGGACTTTTCTTATCAATGAATG
Found at i:4875 original size:171 final size:171
Alignment explanation
Indices: 4413--4876 Score: 434
Period size: 171 Copynumber: 2.7 Consensus size: 171
4403 CTTGATGCAG
* * * * *
4413 ACATTCAAATAT-AGTCTGTTTTAATAAAAGATGTAAAAAACTTAACTTAAAATCAATTATGATA
1 ACATTCAATTATGA-TCTGTTTTAACAAAAAATGTAAAAAACTTAACTTAAAATCAATTACGAGA
* * * *
4477 TTATAAAATCATTTAAAGTGAGTACTAAGGCTTTTGAAGGATTGGGCGACTATAAATAAACTTTT
65 TTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATAAACTTTT
*
4542 CTTGAAAAATGAATACTTTTCCCTTCACATTTCTCAAGATAG
130 CTTGAAAAATGAATACTTTTCCCTTCACATTTCTCAAGATAA
* * * * **********
4584 AGATTCAATTGTTATCTGTTTTAATC-AAAAATGTAAAAAAACTCAACTTAAANNNNNNNNNNAG
1 ACATTCAATTATGATCTGTTTTAA-CAAAAAATGT-AAAAAACTTAACTTAAAATCAATTACGAG
* * * * * *
4648 ATTATAAAACCATTTAAAGCGACTAATAAGGCTTTCGAAGGAATGAGAGGCTATAAATAGACTTC
64 ATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATAAACTT-
*** * ** * *
4713 TT-TT-ACCCATGAATGCTTTTTTCTTCACATTTCTCGAGCTAA
128 TTCTTGAAAAATGAATACTTTTCCCTTCACATTTCTCAAGATAA
* *
4755 ACATTCAATTATG-GCTTGTTTTAACAAAAAATGTAAAAATATTTAACTTAAAATCAATTACGAG
1 ACATTCAATTATGATC-TGTTTTAACAAAAAATGTAAAAA-ACTTAACTTAAAATCAATTACGAG
* * * * *
4819 ATTGTAAAACCATTTGAAGTGAGTAATATGGCTTTTGAAGGAAAGGGTGACTATAAAT
64 ATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAAT
4877 NNNNNNNNNN
Statistics
Matches: 224, Mismatches: 62, Indels: 14
0.75 0.21 0.05
Matches are distributed among these distances:
170 7 0.03
171 141 0.63
172 74 0.33
173 2 0.01
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.33
Consensus pattern (171 bp):
ACATTCAATTATGATCTGTTTTAACAAAAAATGTAAAAAACTTAACTTAAAATCAATTACGAGAT
TATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGAGACTATAAATAAACTTTTC
TTGAAAAATGAATACTTTTCCCTTCACATTTCTCAAGATAA
Done.