Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400124.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3340.0, 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: 2225
ACGTcount: A:0.21, C:0.07, G:0.08, T:0.20
Warning! 978 characters in sequence are not A, C, G, or T
Found at i:1593 original size:171 final size:171
Alignment explanation
Indices: 1302--2036 Score: 729
Period size: 171 Copynumber: 4.3 Consensus size: 171
1292 TGAGTGACTA
* * * *
1302 TAAATAGACTTTTCTTCTTAATGAATGGCTT-TTT-TTGCACGTTGCT-TAGGATAGACATTCAA
1 TAAATGGACTTTTCTTCTCAATGAAT-GCTTGTTTCTT-CACGTTTCTCAAGG-TAGACATTCAA
* *
1364 TTATAGTATGTTTTAATAAAAAATGTAAACAAATTCAACTTAAAATCAATTATGAGATTATAAAA
63 TTATAGTATGTTTTAATAAAAAATGTAAAAAAATTCAACTTAAAATCAATGATGAGATTATAAAA
1429 CTATTTAAAGCGAGTAATAAGCCTTTTAAAGGAATGGATGGCTC
128 CTATTTAAAGCGAGTAATAAGCCTTTTAAAGGAATGGATGGCTC
* * * *
1473 TAAGTGGACTTTTCTTGTCAATGAATTCTTGTTTCTTCACGTTTCAT-GAGGTAGACATTCAATT
1 TAAATGGACTTTTCTTCTCAATGAATGCTTGTTTCTTCACGTTTC-TCAAGGTAGACATTCAATT
* * **
1537 ATAGTATTTTTTAATCACCAATGTAAAAAAATTCAACTTAAAATCAATGATGAGATTATAAAAAC
65 ATAGTATGTTTTAATAAAAAATGTAAAAAAATTCAACTTAAAATCAATGATGAGATTAT-AAAAC
* * * * * * **
1602 -ATTTAATGTGAGTAAAAAGCTTTTTGAAGAAAT-GAGTGATTC
129 TATTTAAAGCGAGTAATAAGCCTTTTAAAGGAATGGA-TGGCTC
* * * * *
1644 TAAATGGACTTCTCTTGTCAATGAATGCTTGTTTCTTTACGTTTCTCAAGGTAGATATTCAACTA
1 TAAATGGACTTTTCTTCTCAATGAATGCTTGTTTCTTCACGTTTCTCAAGGTAGACATTCAATTA
* **
1709 TAGTATGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAA-GTATGAGATTATAAAGTT
66 TAGTATGTTTTAATAAAAAATGTAAAAAAATTCAACTTAAAATCAATG-ATGAGATTATAAAACT
** * *
1773 ATTTAAAATGAGTAATAAGCCTTTTGAAGGAATAGG-TGGCTA
130 ATTTAAAGCGAGTAATAAGCCTTTTAAAGGAAT-GGATGGCTC
** * * * *
1815 TAAATAAACTTTTCTTCTCAATCAATGGCTT-TTACTGCACGTTTCTCAAGTTAGACATTCAATT
1 TAAATGGACTTTTCTTCTCAATGAAT-GCTTGTTTCTTCACGTTTCTCAAGGTAGACATTCAATT
* ** * * * * ** * *
1879 TTTCTCTATTTTCAA-GAAAAATGTAAAAAAATTCAACCTAATTTCAATTATGAGATTATAAAAT
65 ATAGTATGTTTT-AATAAAAAATGTAAAAAAATTCAACTTAAAATCAATGATGAGATTATAAAAC
* * * * *
1943 TATTTTAATCGAGTAATAAGGCTTTTGAAA-GAATGGGTGGCTG
129 TATTTAAAGCGAGTAATAAGCCTTTT-AAAGGAATGGATGGCTC
* * * *
1986 TAAATGGACTTTTGTTCTCAATCGATAAGCTT-TTTCTACACGTTTCCCAAG
1 TAAATGGACTTTTCTTCTCAAT-GA-ATGCTTGTTTCTTCACGTTTCTCAAG
2037 ATACATTTTC
Statistics
Matches: 467, Mismatches: 80, Indels: 33
0.81 0.14 0.06
Matches are distributed among these distances:
170 12 0.03
171 413 0.88
172 40 0.09
173 2 0.00
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.37
Consensus pattern (171 bp):
TAAATGGACTTTTCTTCTCAATGAATGCTTGTTTCTTCACGTTTCTCAAGGTAGACATTCAATTA
TAGTATGTTTTAATAAAAAATGTAAAAAAATTCAACTTAAAATCAATGATGAGATTATAAAACTA
TTTAAAGCGAGTAATAAGCCTTTTAAAGGAATGGATGGCTC
Found at i:1992 original size:342 final size:342
Alignment explanation
Indices: 1291--1996 Score: 811
Period size: 342 Copynumber: 2.1 Consensus size: 342
1281 NNNNNNNNNN
* * * * * * * *
1291 ATGAGTGACTATAAATAGACTTTTCTTCTTAATGAATGGCTT-TTT-TTGCACGTTGCT-TAGGA
1 ATGAGTGACTCTAAATGGACTTCTCTTGTCAATGAAT-GCTTGTTTCTT-TACGTTTCTCAAGG-
* * * *
1353 TAGACATTCAATTATAGTATGTTTTAATAAAAAATGTAAACAAATTCAACTTAAAATCAATTATG
63 TAGACATTCAACTATAGTATGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAAGTATG
* * * **
1418 AGATTATAAAACTATTTAAAGCGAGTAATAAGCCTTTTAAAGGAATGGATGGCTCTAAGTGGACT
128 AGATTATAAAACTATTTAAAACGAGTAATAAGCCTTTTAAAGGAATGGATGGCTATAAATAAACT
* * * * * * *
1483 TTTCTTGTCAATGAATTCTTGTTTCTTCACGTTTCATGAGGTAGACATTCAATTATAGTATTTTT
193 TTTCTTCTCAATCAATGCTTGTTACTGCACGTTTCATAAGGTAGACATTCAATTATACTATTTTT
* ** * *
1548 TAATCACCAATGTAAAAAAATTCAACTTAAAATCAATGATGAGATTATAAAAACATTTAATGTGA
258 CAATCAAAAATGTAAAAAAATTCAACCTAAAATCAATGATGAGATTATAAAAACATTTAATGCGA
1613 GTAAAAAGCTTTTTGAAGAA
323 GTAAAAAGCTTTTTGAAGAA
*
1633 ATGAGTGATTCTAAATGGACTTCTCTTGTCAATGAATGCTTGTTTCTTTACGTTTCTCAAGGTAG
1 ATGAGTGACTCTAAATGGACTTCTCTTGTCAATGAATGCTTGTTTCTTTACGTTTCTCAAGGTAG
*
1698 ATATTCAACTATAGTATGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAAGTATGAGA
66 ACATTCAACTATAGTATGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAAGTATGAGA
** * *
1763 TTATAAAGTTATTTAAAATGAGTAATAAGCCTTTTGAAGGAATAGG-TGGCTATAAATAAACTTT
131 TTATAAAACTATTTAAAACGAGTAATAAGCCTTTTAAAGGAAT-GGATGGCTATAAATAAACTTT
* * * *
1827 TCTTCTCAATCAATGGCTT-TTACTGCACGTTTC-TCAAGTTAGACATTCAATTTTTCTCTATTT
195 TCTTCTCAATCAAT-GCTTGTTACTGCACGTTTCAT-AAGGTAGACATTCAATTATACTAT-TTT
* ** * **
1890 TCAA-GAAAAATGTAAAAAAATTCAACCTAATTTCAATTATGAGATTATAAAATTATTTTAAT-C
257 TCAATCAAAAATGTAAAAAAATTCAACCTAAAATCAATGATGAGATTATAAAAACA-TTTAATGC
*
1953 GAGTAATAAGGC-TTTTGAA-AGA
321 GAGTAA-AAAGCTTTTTGAAGA-A
* * *
1975 ATGGGTGGCTGTAAATGGACTT
1 ATGAGTGACTCTAAATGGACTT
1997 TTGTTCTCAA
Statistics
Matches: 304, Mismatches: 50, Indels: 20
0.81 0.13 0.05
Matches are distributed among these distances:
341 6 0.02
342 272 0.89
343 26 0.09
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (342 bp):
ATGAGTGACTCTAAATGGACTTCTCTTGTCAATGAATGCTTGTTTCTTTACGTTTCTCAAGGTAG
ACATTCAACTATAGTATGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAAGTATGAGA
TTATAAAACTATTTAAAACGAGTAATAAGCCTTTTAAAGGAATGGATGGCTATAAATAAACTTTT
CTTCTCAATCAATGCTTGTTACTGCACGTTTCATAAGGTAGACATTCAATTATACTATTTTTCAA
TCAAAAATGTAAAAAAATTCAACCTAAAATCAATGATGAGATTATAAAAACATTTAATGCGAGTA
AAAAGCTTTTTGAAGAA
Done.