Identification and characterization of microRNAs from Phaeodactylum tricornutum by high-throughput sequencing and bioinformatics analysis

Table 4 Characteristics of P. tricornutum pre-miRNA sequences.

miRNA name	location^a	mfe^b	len^c	P-value^d	total reads and 5' homogeneity^e			hairpin characteristics^f
					PT1	PT2	PT3	bulges	mismatched
pti-miR5471	chr_1:1604545:1604822:-	-78.8	278	0.172	0/0	9/9	0/0	0	5
pti-miR5472	chr_10:761305:761625:-	-85.9	321	0.355	64/88	23/30	145/213	0	5
pti-miR5473	chr_11:35406:35506:-	-30.4	101	0.019	6/9	0	9/15	0	4
pti-miR5474	chr_15:663006:663165:+	-42.7	160	0.801	22/23	69/71	20/22	0	6
pti-miR5475	chr_18:415320:415541:-	-62	222	0.44	0/0	226/230	383/385	0	4
pti-miR5476	chr_19:299730:299870:-	-52.8	141	0.043	0/0	0/0	9/15	0	3
pti-miR5477	chr_1:2137385:2137503:-	-26.1	119	0.025	0/0	0/0	6/9	0	6
pti-miR5478	chr_23:97534:97765:+	-76.1	232	0.029	0/0	0/0	5/7	0	4
pti-miR5479	chr_25:444580:444846:+	-79.6	267	0.1	0/0	0/0	18/19	0	4
pti-miR5480	chr_26:278601:278960:+	-105	360	0.146	0/0	0/0	6/8	0	6
pti-miR5481	chr_2:1365749:1366009:+	-70.8	261	0.213	0/0	0/0	5/5	0	4
pti-miR5482	chr_9:128204:128523:+	-101	320	0.561	0/0	0/0	5/6	0	3
pti-miR5483	chr_9:523733:524013:+	-67.6	281	0.126	0/0	0/0	10/12	0	5

^aIndicated the chromosome number, start and end site and sense (+) or antisense strand (-) that the pre-miRNAs located.
^bMinimum Free Energy (cal/mol) of pre-miRNAs, predicted by mfold.
^clength of pre-miRNAs.
^dcomputed P-values of miRNA precursors.
^enumber of reads that had the same 5' end as the mature miRNA and the total number reads mapped to the precursors.
^fasymmetric bulges larger than 2 nt and mismatched miRNA bases in the miRNA region.

ISSN: 1471-2164