Table 1 The P-value of features considered in this study that can contribute to tRF-mRNA interaction

Sequence feature of target sites

Type of seed match

Position 8 match

2.87E−28

Position 1 match

7.28E−13

Position 1 A

0.34

Bases identity immediately flanking seed match (2nt)

Base identity of position 2 upstream

0.80

Base identity of position 1 upstream

2.88E−03

Base identity of position 1 downstream

7.67E−07

Base identity of position 2 downstream

0.43

Bases component in the vicinity of seed match

GC percentage 35 nt upstream

5.89E−13

GC percentage 25 nt upstream(excluding 10 nts immediately upstream)

4.28E−14

GC percentage 15 nt downstream

2.18E−11

Score 35 nt upstream

7.51E−03

Score 25 nt Upstream (excluding 10 nts immediately upstream)

2.61E−16

Score downstream

7.49E−12

Base component 35 nt upstream

See Additional files 1, 2, 3: Table

Base component 15 nt downstream

See Additional file 1, 2, 3: Table

Dinucleotide component 35  nt upstream

See Additional file 1, 2, 3: Table

Dinucleotide component 15 nt downstream

See Additional file 1, 2, 3: Table

Distance to the end of tRF

Distance to the 5′ end

2.37E−08

Distance to the 3′ end

1.90E−03

Distance to the nearest end

2.12E−03

Sequence feature of transcripts

3′-UTR properties

Length of 3′-UTR

4.80E−08

GC percentage of 3′-UTR

5.40E−06

frequency of seed matches in 3′-UTR

0.08

Base component(AGCT) of 3′-UTR

See Additional file 1, 2, 3: Table

Dinucleotide component of 3′-UTR

See Additional file 1, 2, 3: Table

CDS properties

Length of CDS

1.95E−04

GC percentage of CDS

2.33E−03

Frequency of seed matches in CDS

6.51E−06

5′-UTR properties

length of 5′-UTR

0.40

GC percentage of 5′-UTR

0.08

Frequency of seed matches in 5′-UTR

0.02

Sequence feature of tRFs

tRF sequence properties

Length of tRF

2.77E−21

GC percentage of tRF

2.46E−11

TA

Target abundance in genome

7.19E−03

Target abundance in 3′-UTR

0.09

SPS

GC percentage of seed

8.69E−18

Stability and thermodynamics of tRF-mRNA interaction

Secondary structure of target mRNA

Nucleotides exposed at seed match

7.49E−03

Nucleotides exposed surrounding seed match

0.99

Energy to free base-pairing interactions of target site

3.51E−06

Secondary structure of tRF-mRNA

Number of bases paired in duplex

1.53E−20

MFE

1.36E−57