Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018403028.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_696.0, 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: 1855
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.33
Warning! 168 characters in sequence are not A, C, G, or T
Found at i:329 original size:171 final size:168
Alignment explanation
Indices: 9--627 Score: 687
Period size: 171 Copynumber: 3.6 Consensus size: 168
1 ATGTTGTC
* * *
9 CAAGGTAGACATTCAATTATAATCTGTTTT-ATAAAAAATGTAAAAACATTCAACTTGAAATCAA
1 CAAGGTAGACATTCAATTATAATCTATTTTAATAAAAAATATAAAAAAATTCAACTTGAAATCAA
* *
73 TTATGAGATTATAAAAATAATTAAAGCGAGTAATAAGGCTTCCGAAAGTATAGGTGACTATAAAT
66 TTATGAGATTATAAAAACAATTAAAGCGAGTAATAAGGCTTTC-AAAGTATAGGTGACTATAAAT
**
138 GGACTTTTCT-GGCTAATGAATATCTTTTTTTACACATTTCT
130 GGACTTTTCTCAAC-AATGAATAT-TTTTTTT-CACATTTCT
* * * *
179 CGAGGTGGATATTCAACTATAATCTATTTTAATAAAAAATATAAAAAAATTCAACTTGAAATCAA
1 CAAGGTAGACATTCAATTATAATCTATTTTAATAAAAAATATAAAAAAATTCAACTTGAAATCAA
* * * *
244 TTATGAGATTATAAAAACAATTAAAGCAAGTAATAGGGCTTTCAAAGGTATTGGTGAGTATAAAT
66 TTATGAGATTATAAAAACAATTAAAGCGAGTAATAAGGCTTTCAAA-GTATAGGTGACTATAAAT
*
309 GGACTTTTCTCAACAATGAATGGTATTTTCTTT-ACATTTCT
130 GGACTTTTCTCAACAATGAA---TATTTTTTTTCACATTTCT
* * *
350 TAAGGTAGACATTTAATTATAATCTGA-TTTAAGT-AAAAATAAAAAAAAATTCAACTT-AAAGT
1 CAAGGTAGACATTCAATTATAATCT-ATTTTAA-TAAAAAATATAAAAAAATTCAACTTGAAA-T
** * * * *
412 CAATTATGAGATTATAAAAGTATTTAAAGCGTGTAATAAGGCTTTTGAAAGCATAGGTGACTATA
63 CAATTATGAGATTATAAAAACAATTAAAGCGAGTAATAAGGC-TTTCAAAGTATAGGTGACTATA
* ** **
477 AATGGACTTTTCTTCCA-AATGAATATTGTTTTCTTCATGTTTAA
127 AATGGACTTTTC-TCAACAATGAATATT-TTTT-TTCACATTTCT
* * * * *
521 CAAGATAGACATTTAATTATAATCTGTTTTAATAAAAAATA-AAAAAAATTTAACTTCAAATCAA
1 CAAGGTAGACATTCAATTATAATCTATTTTAATAAAAAATATAAAAAAATTCAACTTGAAATCAA
* * * * *
585 TTATGAGATTATTAAATCAGTTAAAGTGAGTAATAAGCCTTTC
66 TTATGAGATTATAAAAACAATTAAAGCGAGTAATAAGGCTTTC
628 GAAGGCTTGG
Statistics
Matches: 381, Mismatches: 51, Indels: 35
0.82 0.11 0.07
Matches are distributed among these distances:
168 4 0.01
169 6 0.02
170 84 0.22
171 266 0.70
172 12 0.03
173 6 0.02
174 3 0.01
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (168 bp):
CAAGGTAGACATTCAATTATAATCTATTTTAATAAAAAATATAAAAAAATTCAACTTGAAATCAA
TTATGAGATTATAAAAACAATTAAAGCGAGTAATAAGGCTTTCAAAGTATAGGTGACTATAAATG
GACTTTTCTCAACAATGAATATTTTTTTTCACATTTCT
Found at i:1508 original size:341 final size:330
Alignment explanation
Indices: 886--1510 Score: 670
Period size: 341 Copynumber: 1.9 Consensus size: 330
876 CAAAGGCTTG
* * *
886 GGTGACTATAAATAGGCTTTTCTTACCAATGAATGACTTGTTTTTCACGTTTCTCTAAGTAAACA
1 GGTGACTATAAATAGGCTTTTCTTACCAATGAATGACTTGTTCTTCACATTTCTCCAAGTAAACA
* ** * *
951 TTTAATTATTATCTATTTCAATCAAAAATGAAAAAAAATTAACTTAAAGTAAATTACAAGATTAT
66 TTCAATTAAAATCTATTTCAATAAAAAATGAAAAAAAATTAACTTAAAATAAATTACAAGATTAT
* *
1016 AAAACTATTTAAAGTGAGTACTAAGGCTTTTAAAGGCATAAGTGACTATAAATGGACTTTTCTTN
131 AAAACTATTTAAAGCGAGTACTAAGGCTTTTAAAGGCATAAGTGACTATAAATGGACTTTTCTTG
********* *
1081 NNNNNNNNNGGATTTTTCTTCACGTTTCTCAAGGTAGACATTCAATCATAATCTGTTTTTAAAAA
196 TCAATGAATGGATTTTTCTTCACGTTTCTCAAGGTAAACATTCAATCATAATCTGTTTTTAAAAA
* *
1146 AAATGAAAACAATTCAACTTAAAGTCANNNNNNNNNNTATAAAACCATTTAAAATGAGTAATAAG
261 AAATAAAAAAAATTCAACTTAAAGTCA----------TATAAAACCATTTAAAATGAGTAATAAG
1211 GCACTTGAAGGTGTA
316 GCACTTGAAGGTGTA
1226 GGTGACTATAAAT-GGACTTTTCTTACCAATGAAT-ATCCTT-TTCTTCACATTTC-CCAAGGTA
1 GGTGACTATAAATAGG-CTTTTCTTACCAATGAATGA--CTTGTTCTTCACATTTCTCCAA-GTA
* * * * ***
1287 AACATTCAATTAAAATCTATTTTAATAAAAAAT-ATAAAAAATTTCAACTTAAAATCAGTTATGG
62 AACATTCAATTAAAATCTATTTCAATAAAAAATGA-AAAAAAATT-AACTTAAAATAAATTACAA
* ** * * *
1351 GATTATAAAAGC-ATTTAAAGCGAGTACTAAGGCTTTTGAAGGCATGCGTGACTGTAAATGTATT
125 GATTATAAAA-CTATTTAAAGCGAGTACTAAGGCTTTTAAAGGCATAAGTGACTATAAATGGACT
* * * *
1415 TTTGTTGTCAATGAATGGTTTTTTCTTCACGTTTTTCAAGGTAAACATTCAATTATAATCTG-TT
189 TTTCTTGTCAATGAATGGATTTTTCTTCACGTTTCTCAAGGTAAACATTCAATCATAATCTGTTT
* *
1479 TTAACTAAAAATAAAAAAAATTTAACTTAAAG
254 TTAA-AAAAAATAAAAAAAATTCAACTTAAAG
1511 NNNNNNNNNN
Statistics
Matches: 236, Mismatches: 41, Indels: 15
0.81 0.14 0.05
Matches are distributed among these distances:
339 7 0.03
340 87 0.37
341 141 0.60
342 1 0.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.35
Consensus pattern (330 bp):
GGTGACTATAAATAGGCTTTTCTTACCAATGAATGACTTGTTCTTCACATTTCTCCAAGTAAACA
TTCAATTAAAATCTATTTCAATAAAAAATGAAAAAAAATTAACTTAAAATAAATTACAAGATTAT
AAAACTATTTAAAGCGAGTACTAAGGCTTTTAAAGGCATAAGTGACTATAAATGGACTTTTCTTG
TCAATGAATGGATTTTTCTTCACGTTTCTCAAGGTAAACATTCAATCATAATCTGTTTTTAAAAA
AAATAAAAAAAATTCAACTTAAAGTCATATAAAACCATTTAAAATGAGTAATAAGGCACTTGAAG
GTGTA
Done.