Random DNA sequence and text image of a folding

A variety of output types and options are illustrated through the folding of a randomly generated DNA sequence.

It is folded as DNA under default conditions on the regular mfold web server. Six foldings are generated. A text representation of the first folding is given in Figure 1. The sequence name is ``RAN 130299481'', where the number refers to a ``seed'' for a random number generator.

**Figure 1:** The text output of folding 1 of a random DNA. It has 3 stems that touch the exterior loop, and a single multi-branch loop. This figure should be compared with other, easier to interpret drawings of this secondary structure. The | and ^ symbols point to the base pair that was selected for the double traceback to generate this folding.
Structure 1 Folding bases 1 to 200 of RAN 130299481 dG = -18.3 dH = -347.3 dS = -1060.8 Tm = 54.3 10 .-A\| T AA CT CGC G GA GCG C \ -^ T CA 20 30 40 50 .-GGAAAGGCACCATGTA ATATTACATAC TCACG \ AGTGC T \ ---------------- AACTGCGAGAA 60 70 80 90 100 110 120 ATA-- GATA-- .-GG - AA TGATCCGCAAA C CCTGCTG CTGTGT GCCGTG GTG AGTT GCAG \ GGGCGGC GGCACA CGGCGC CAT TCAA TGTC C ACCCA ACGGAA \ -- T G- ----------- C 200 190 180 140 130 150 AAGA ----- G G GCAT CGCA CA \ CGTA GCGT GT T G--- AGTCT - A 170 160

Figure 1: The text output of folding 1 of a random DNA. It has 3 stems that touch the exterior loop, and a single multi-branch loop. This figure should be compared with other, easier to interpret drawings of this secondary structure. The | and ^ symbols point to the base pair that was selected for the double traceback to generate this folding.

Structure    1
 
Folding bases     1 to   200 of RAN   130299481
 dG =    -18.3  dH =   -347.3  dS =  -1060.8  Tm =   54.3
 
 
          10
.-A| T   AA
   CT CGC  G
   GA GCG  C
\ -^ T   CA
 
 
 
   20        30        40        50
  .-GGAAAGGCACCATGTA     ATATTACATAC
                    TCACG           \
                    AGTGC           T
  \ ----------------     AACTGCGAGAA
                           60
 
 
    70          80            90        100       110       120
    ATA--       GATA--      .-GG      -   AA    TGATCCGCAAA    C
         CCTGCTG      CTGTGT    GCCGTG GTG  AGTT           GCAG \
         GGGCGGC      GGCACA    CGGCGC CAT  TCAA           TGTC C
    ACCCA       ACGGAA      \ --      T   G-    -----------    C
  200       190       180       140        130
 
 
                                   150
                              AAGA    -----    G  G
                                  GCAT     CGCA CA \
                                  CGTA     GCGT GT T
                              G---    AGTCT    -  A
                                     170        160

The minimum folding free energy is -18.3 kcal/mole. The default 5% of this number is less than 1 kcal/mole, and so $\delta \delta G$ , the free energy increment, is rounded up to 1 kcal/mole. Figure 2 is the default energy dot plot for this folding.