Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402383.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5462.0, 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, 915
Length: 1526
ACGTcount: A:0.26, C:0.07, G:0.10, T:0.25
Warning! 479 characters in sequence are not A, C, G, or T
Found at i:293 original size:171 final size:171
Alignment explanation
Indices: 5--712 Score: 540
Period size: 171 Copynumber: 4.1 Consensus size: 171
1 AGCG
* ** * *
5 AGTAATAAGGCATTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTCTGAATGAATTACTTTT
1 AGTAATAAGGCTTTTGAAGGAATGAATGACTATAAATGGACTTTTCTTCTGAATAAATGACTTTT
* * *
70 TCTACACATTTCTTAAAGCAGGCATTCAATGATAGTCTGTTTTAACTAAAAATGTTAAAAAATTT
66 TCTACACATTTCTTAAAGCAAGCATTCAATGATAGTCTGTTTTAACTAAAAATGTAAAAAAATTC
**
135 AACTT-AAAATCAATTATTAGATTATAAAATAATTTAAAGCC
131 AA-TTCAAAATCAATTAGGAGATTATAAAATAATTTAAAGCC
** *
176 AGTAATAAGGCTTTTGAAGGAATGAATGACTATAAATGGACTTTTCTTCTTTATAAATGGCTTTT
1 AGTAATAAGGCTTTTGAAGGAATGAATGACTATAAATGGACTTTTCTTCTGAATAAATGACTTTT
* * * * *
241 TCTACACATTTCTTGAGGCAAGTATTTAATTG-TAGTCTGTTTTAAGTAAAAATGTAAAAAAATT
66 TCTACACATTTCTTAAAGCAAGCATTCAA-TGATAGTCTGTTTTAACTAAAAATGTAAAAAAATT
* *
305 CAATTCAAAATCAATTAGGAGATTATAAAATAATTTGAAGCG
130 CAATTCAAAATCAATTAGGAGATTATAAAATAATTTAAAGCC
* ** *********** * * *
347 AGTAATAAGGCTTTTGAAGAAATGGGTGACTANNNNNNNNNNNTTCTTGC-CAATGAATGCCTTT
1 AGTAATAAGGCTTTTGAAGGAATGAATGACTATAAATGGACTTTTCTT-CTGAATAAATGACTTT
* * * * * ** *
411 TTCTTCATATTTCTT-GAGCTAGACATTCAATTATAGTAAGTTTTAACCAAAAATGT-AAAAAAT
65 TTCTACACATTTCTTAAAGCAAG-CATTCAATGATAGTCTGTTTTAACTAAAAATGTAAAAAAAT
* * **
474 TAAAACTT-AAAATCAATTATGAGATTATAAAATAATTTAAAGTG
129 T-CAA-TTCAAAATCAATTAGGAGATTATAAAATAATTTAAAGCC
* * * * * * * * *
518 AGCAACACGACTTTTGAAGAAATGAGTGACTGTAAATGAAATTTTCTTACT-AATAAATG-CGTT
1 AGTAATAAGGCTTTTGAAGGAATGAATGACTATAAATGGACTTTTCTT-CTGAATAAATGAC-TT
* ** * * * * * *
581 TTTCTTCATGTTTCTCAAAG-TAGACATTCAATTATTA-TATGGTTTTAGC-AAAAATATAAAAA
64 TTTCTACACATTTCTTAAAGCAAG-CATTCAATGA-TAGTCT-GTTTTAACTAAAAATGTAAAAA
* ** ** **
643 AATTTAACTT-AAAATCAATTATAAGATTATAAAGCAATTTAAAGAG
126 AATTCAA-TTCAAAATCAATTAGGAGATTATAAAATAATTTAAAGCC
* *
689 AGCAATAAGGGTTTTGAAGGAATG
1 AGTAATAAGGCTTTTGAAGGAATG
713 GGTGACTANN
Statistics
Matches: 435, Mismatches: 89, Indels: 26
0.79 0.16 0.05
Matches are distributed among these distances:
170 16 0.04
171 395 0.91
172 24 0.06
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.35
Consensus pattern (171 bp):
AGTAATAAGGCTTTTGAAGGAATGAATGACTATAAATGGACTTTTCTTCTGAATAAATGACTTTT
TCTACACATTTCTTAAAGCAAGCATTCAATGATAGTCTGTTTTAACTAAAAATGTAAAAAAATTC
AATTCAAAATCAATTAGGAGATTATAAAATAATTTAAAGCC
Found at i:744 original size:342 final size:330
Alignment explanation
Indices: 56--814 Score: 695
Period size: 342 Copynumber: 2.2 Consensus size: 330
46 TTTTCTTCTG
** * * * *
56 AATGAATTACTTTTTCTACACATTTCTTAAAGC-AGGCATTCAATGATAGTCTGTTTTAACTAAA
1 AATGAATGCCTTTTTCTTCA-ATTTCTT-AAGCTAGACATTCAATTATAGTCTGTTTTAACAAAA
* * * *
120 AATGTTAAAAAATTTAACTTAAAATCAATTATTAGATTATAAAATAATTTAAAGCCAGTAATAAG
64 AATG-TAAAAAATTAAACTTAAAATCAATTATGAGATTATAAAATAATTTAAAGCCAGCAACAAG
* * * * *
185 GCTTTTGAAGGAATGAATGACTATAAATGGACTTTTCTTCTTTATAAATGGCTTTTTCTACACAT
128 ACTTTTGAAGAAATGAATGACTATAAATGAAATTTTCTTCTTAATAAATGGCTTTTTCTACACAT
** * * * * * *
250 TTCTTGAGGCAAGTATTTAATTGTAGTCTGTTTTAAGTAAAAATGTAAAAAAATTCAATTCAAAA
193 TTCTCAAAGCAAGCATTCAATTGTAGTATGTTTTAAGCAAAAATATAAAAAAATTCAATTCAAAA
* * * * *
315 TCAATTAGGAGATTATAAAATAATTTGAAGCGAGTAATAAGGCTTTTGAAGAAATGGGTGACTAN
258 TCAATTAGAAGATTATAAAACAATTTAAAGAGAGCAATAAGGCTTTTGAAGAAATGGGTGACTA-
* *
380 NNNNNNNNNNTTCTTGCC
322 ---------TTTCTTACC
* ** *
398 AATGAATGCCTTTTTCTTCATATTTCTTGAGCTAGACATTCAATTATAGTAAGTTTTAACCAAAA
1 AATGAATGCCTTTTTCTTCA-ATTTCTTAAGCTAGACATTCAATTATAGTCTGTTTTAACAAAAA
** *
463 ATGTAAAAAATTAAAACTTAAAATCAATTATGAGATTATAAAATAATTTAAAGTGAGCAACACGA
65 ATGTAAAAAATT-AAACTTAAAATCAATTATGAGATTATAAAATAATTTAAAGCCAGCAACAAGA
* * * **
528 CTTTTGAAGAAATGAGTGACTGTAAATGAAATTTTCTTAC-TAATAAAT-GCGTTTTTCTTCATG
129 CTTTTGAAGAAATGAATGACTATAAATGAAATTTTCTT-CTTAATAAATGGC-TTTTTCTACACA
* * *
591 TTTCTCAAAG-TAGACATTCAATTATTA-TATGGTTTT-AGCAAAAATATAAAAAAATTTAACTT
192 TTTCTCAAAGCAAG-CATTCAATT-GTAGTAT-GTTTTAAGCAAAAATATAAAAAAATTCAA-TT
* * * *
653 -AAAATCAATTATAAGATTATAAAGCAATTTAAAGAGAGCAATAAGGGTTTTGAAGGAATGGGTG
253 CAAAATCAATTAGAAGATTATAAAACAATTTAAAGAGAGCAATAAGGCTTTTGAAGAAATGGGTG
717 ACTANNNNNNNNNNTTTCTTACC
318 ACTA----------TTTCTTACC
* * * * *
740 AATGAATGCATTTTTCTTCAAGTTTCTCAAGGTAGACATTCAATTATTGTCTGTTTTATCAAAAA
1 AATGAATGCCTTTTTCTTCAA-TTTCTTAAGCTAGACATTCAATTATAGTCTGTTTTAACAAAAA
805 ATGTAAAAAA
65 ATGTAAAAAA
815 ATTTAGCTTA
Statistics
Matches: 350, Mismatches: 58, Indels: 18
0.82 0.14 0.04
Matches are distributed among these distances:
341 17 0.05
342 323 0.92
343 10 0.03
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.35
Consensus pattern (330 bp):
AATGAATGCCTTTTTCTTCAATTTCTTAAGCTAGACATTCAATTATAGTCTGTTTTAACAAAAAA
TGTAAAAAATTAAACTTAAAATCAATTATGAGATTATAAAATAATTTAAAGCCAGCAACAAGACT
TTTGAAGAAATGAATGACTATAAATGAAATTTTCTTCTTAATAAATGGCTTTTTCTACACATTTC
TCAAAGCAAGCATTCAATTGTAGTATGTTTTAAGCAAAAATATAAAAAAATTCAATTCAAAATCA
ATTAGAAGATTATAAAACAATTTAAAGAGAGCAATAAGGCTTTTGAAGAAATGGGTGACTATTTC
TTACC
Done.