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. Author manuscript; available in PMC: 2009 Jan 1.
Published in final edited form as: Genomics. 2007 Nov 14;91(1):108–117. doi: 10.1016/j.ygeno.2007.09.004

Table 1.

Sequence parameters and algorithms used in the present analysis.

Sequence
characteristics		 Computer program Specifications
GC-content Perl script Relative GC-content [%]
Tandem
repeats		 Tandem Repeat Finder
(Benson 1999)		 Default parameters, score threshold 50, unit
length ≥ 2 nt; Analyzed for presence/absence
Poly-A
stretches		 Tandem Repeat Finder
(Benson 1999)		 Default parameters, score threshold 50,
unit=mono-nucleotide “A” ≥ 25 [nt]
Poly-T
stretches		 Tandem Repeat Finder
(Benson 1999)		 Default parameters, score threshold 50,
unit=mono-nucleotide “T” ≥ 25 [nt]
Folding energy RNAfold (Hofacker 2003) Default parameters [Kcal/mol]
Normalized
folding energy
(Z-score)		 RNAfold (Hofacker 2003) Z-score: each sequence was shuffled 1000
times by maintaining the di-nucleotide
frequency to avoid composition biases, and
the folding energy was calculated. The
average of resulting energies was subtracted
from the folding energy of the real sequence
and divided by the standard deviation.
Number of
hairpins		 RNAfold (Hofacker 2003) Number of hairpins were determined from
RNAfold output
Maximum
length of
hairpins		 RNAfold (Hofacker 2003) Length of the longest hairpin was extracted
from RNAfold output [nt]
GC-skew Perl script (G+C)/(G−C) (Perna & Kocher 1995)
AT-skew Perl script (A+T)/(A−T) (Perna & Kocher 1995)