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However, according to our estimations, about 60% of nucleotides are paired in lincRNAs and mRNAs (Shabalina et al. 2006), which is comparable with the base pairing values for some experimentally characterized mRNAs (Kertesz et al. 2010).
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For simplicity, rounded base pair values are used in the text.
Is the read per base pair value adjusted for the total number of reads?
The base-pair probability values for the wildtype RPS17B intron and all of Libri et al.'s [ 8] mutants are given in Table 3.
Expressed in base pairs, genome complexity values for well-studied diploid angiosperms are 82.6 Mb (Arabidopsis thaliana), 290 Mb (Sorghum bicolor), 735 Mb (Solanum lycopersicum) and 955 Mb (Zea mays) [28], [29].
Watson−Crick base pairing is conserved for both the 5′ and 3′ neighboring base pairs.
These custom graphs can be produced from user-defined data in a space or tab-delimited file that either includes; the start and stop positions and the value for that region; or a single value for every base pair, with one value per line.
The values for ΔH, and ΔS for perfect match and mismatch base pairs, initiation/termination GC and AT values, and [Na+] corrections for ΔG calculations come from [ 19, 21- 25].
In contrast, a significant change is observed for the 5′-neighbor A T base pair (Table 2), for which the value of α Kop decreases from 13.8 × 10 to 8.8 × 10 in the presence of the cationic amine at base pair X C.
We give a penalty of 10 for every base pair deleted (other values have been tried with similar results, data not shown).
The number of sequences, N50 values, mean length of the sequences and total base pair length for the contigs, scaffolds and unigenes were also determined (Table 1).
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