Freiburg RNA Tools
IntaRNA - Results
BIF
IFF
IntaRNA 4627738

Input and runtime details for job 4627738 (precomputed example)

Sequence Parameters

? Query ncRNA (short) in FASTA[.fa]
? Index first query position1
? Target RNA (long) in FASTA[.fa]
? Target NCBI RefSeq IDNC_003210
? All repliconsyes
? Extract sequences aroundstart codon
? nt upstream (1-300)75
? nt downstream (1-300)75
? Index first target position-75

Output Parameters

? Number of interactions per RNA pair1
? Suboptimal interaction overlap can overlap in query
? Max. interaction lengthnot provided
? Max. absolute energy of an interaction0
? Max. delta energy above mfe of an interaction100
? No lonely base pairsyes
? No GU at helix endsyes

Seed Parameters

? Min. number of basepairs in seed7
? Max. Number of mismatches in seed0
? Maximal energy0
? Minimal unpaired probability (per RNA)0
? Seed position (query)not provided
? Seed position (target)not provided
? Ignore seeds with GU base pairsno
? Ignore seeds with GU endsyes

Folding Parameters

? Temperature for energy computation37.0
? Access. query: folding window size150
? Access. query: max. basepair distance100
? Access. target: folding window size150
? Access. target: max. basepair distance100
? Energy parameter set (Vienna package) Turner model, 2004

Job ID 4627738 (server version trunk)

?Job Submitted & Queued@ Mon Jan 27 14:20:43 CET 2020
?Processing Started@ Mon Jan 27 14:22:37 CET 2020
?IntaRNA Finished & Post-Processing@ Mon Jan 27 14:24:00 CET 2020
?Post-Processing Finished@ Mon Jan 27 14:24:55 CET 2020
?Job Completed@ Mon Jan 27 14:25:04 CET 2020
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=4627738&toolName=IntaRNA ( 30 days expiry )

The job description you specified

LhrA2 - Listeria monocytogenes


? Output download complete results [zip]

Downloadable files

[csv]
[png] [pdf]
[png] [pdf]
[txt]
[html] [pdf] [png]


heatmap

? Identified Interactions for NC_003210 Listeria monocytogenes EGD-e

Sort by selecting a column name
Target Start(T) End(T) Query Start(Q) End(Q) Energy p-value fdr gene annotation
lmo0022 -2 42 LhrA2 160 208 -14.13 0.02415 0.9474659 PTS fructose transporter subunit IIB
lmo0057 -22 7 LhrA2 157 181 -16.2 0.0079642 0.863511
lmo0066 -22 6 LhrA2 158 199 -14.3 0.0221203 0.9474659 toxin
lmo0129 -14 15 LhrA2 176 203 -16.42 0.0070414 0.863511 N-acetylmuramoyl-L-alanine amidase
lmo0131 -8 31 LhrA2 165 204 -15.78 0.0100463 0.863511
lmo0137 -20 28 LhrA2 154 207 -13.49 0.0334303 0.9493467 peptide ABC transporter permease
lmo0139 52 72 LhrA2 166 186 -16.03 0.0087531 0.863511 lmo0139
lmo0142a 37 73 LhrA2 119 157 -14.8 0.0170282 0.9082262
lmo0143 -75 -5 LhrA2 92 157 -13.99 0.0259491 0.9474659 lmo0143
lmo0181 -54 -34 LhrA2 158 179 -15.02 0.0151521 0.9011628 sugar ABC transporter substrate-binding protein
lmo0184 -42 10 LhrA2 158 203 -14.64 0.0185255 0.9128702 oligo-16-glucosidase
lmo0191 -75 -47 LhrA2 154 182 -15.56 0.0113293 0.863511 phospho-beta-glucosidase
lmo0194 -20 42 LhrA2 155 212 -15.09 0.0145966 0.9011628 ABC transporter ATP-binding protein
lmo0196 -2 56 LhrA2 156 208 -15.48 0.0118324 0.8692263 regulatory protein SpoVG
lmo0197 -23 48 LhrA2 99 173 -16.05 0.0086566 0.863511 regulatory protein SpoVG
lmo0198 29 59 LhrA2 153 183 -13.57 0.0321135 0.9493467 glmU bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase
lmo0200 -10 14 LhrA2 175 204 -14.21 0.0231743 0.9474659 prfA listeriolysin positive regulatory protein
lmo0205 -28 -2 LhrA2 160 186 -15.42 0.0122233 0.8754939 plcB phospholipase C
lmo0233 38 73 LhrA2 157 198 -16.51 0.0066934 0.863511 DNA repair protein RadA
lmo0292 3 49 LhrA2 155 203 -14.32 0.0218921 0.9474659 heat-shock protein htrA serine protease
lmo0302 -15 26 LhrA2 167 204 -14.58 0.0191177 0.9128702 lmo0302
lmo0383 24 64 LhrA2 151 186 -18.44 0.002162 0.863511 methylmalonate-semialdehyde dehydrogenase
lmo0390 -50 -8 LhrA2 167 211 -13.46 0.0339368 0.9493467 uracil-DNA glycosylase
lmo0397 -23 37 LhrA2 160 211 -18.55 0.0020219 0.863511
lmo0444 5 27 LhrA2 157 181 -13.98 0.0260822 0.9474659
lmo0482 44 69 LhrA2 172 210 -15.99 0.008949 0.863511 ribosomal RNA large subunit methyltransferase N
lmo0551 -68 -3 LhrA2 154 204 -15.63 0.0109054 0.863511 lmo0551
lmo0649 -9 5 LhrA2 190 204 -14.7 0.0179502 0.9128702 transcriptional regulator
lmo0661 46 71 LhrA2 156 186 -14.51 0.0198308 0.9163749
lmo0788 -23 -4 LhrA2 197 212 -14.54 0.0195222 0.9163749 lmo0788
lmo0835 -20 29 LhrA2 146 186 -18.17 0.0025454 0.863511 peptidoglycan binding protein
lmo0850 -49 -18 LhrA2 148 170 -14.84 0.0166718 0.9082262
lmo0851 -12 20 LhrA2 172 200 -17.88 0.0030274 0.863511 lmo0851
lmo0888 -1 37 LhrA2 174 211 -13.9 0.02717 0.9474659
lmo0922 -24 14 LhrA2 154 188 -14.95 0.0157271 0.9011628 pantothenate kinase
lmo0926 56 74 LhrA2 155 175 -15.07 0.0147533 0.9011628 TetR family transcriptional regulator
lmo1018 51 72 LhrA2 158 181 -13.69 0.0302275 0.9493467 copper homeostasis protein CutC
lmo1109 -23 11 LhrA2 141 172 -13.88 0.0274484 0.9474659
lmo1147 -65 10 LhrA2 158 211 -18.08 0.0026867 0.863511 cobalamin biosynthesis protein CopB
lmo1161 -12 36 LhrA2 158 204 -16.94 0.0052414 0.863511 ethanolamine utilization protein EutJ
lmo1187 -62 -29 LhrA2 153 183 -19.53 0.0010984 0.863511 ethanolamine utilization protein EutQ
lmo1203 -27 -2 LhrA2 155 181 -15.88 0.0095091 0.863511 cbiL cobalt-precorrin-2 C(20)-methyltransferase
lmo1217 28 75 LhrA2 167 211 -13.51 0.0330966 0.9493467 endo-14-beta-glucanase and to aminopeptidase
lmo1229 -3 28 LhrA2 147 182 -17.22 0.0044601 0.863511
lmo1246 -20 5 LhrA2 184 206 -13.51 0.0330966 0.9493467 ATP-dependent RNA helicase
lmo1258 24 74 LhrA2 157 207 -15.61 0.011025 0.863511 lmo1258
lmo1278 -16 16 LhrA2 173 203 -13.95 0.0264853 0.9474659 clpQ ATP-dependent protease peptidase subunit
lmo1327 11 40 LhrA2 157 186 -13.94 0.026621 0.9474659 rbfA ribosome-binding factor A
lmo1401 -52 9 LhrA2 155 204 -13.43 0.0344502 0.9493467
lmo1403 -17 22 LhrA2 169 208 -16.71 0.0059768 0.863511 mutS DNA mismatch repair protein MutS
lmo1454 -29 16 LhrA2 154 211 -14.13 0.02415 0.9474659 rpoD RNA polymerase sigma factor RpoD
lmo1481 1 24 LhrA2 151 181 -15.05 0.0149116 0.9011628 holA DNA polymerase III subunit delta
lmo1507 -25 4 LhrA2 147 173 -16.85 0.0055185 0.863511 response regulator
lmo1517 -59 -32 LhrA2 172 198 -14 0.0258166 0.9474659 nitrogen regulatory PII protein
lmo1572 1 26 LhrA2 157 179 -17.19 0.0045383 0.863511 accA acetyl-CoA carboxylase carboxyltransferase subunit alpha
lmo1575 -14 28 LhrA2 150 181 -13.9 0.02717 0.9474659
lmo1584 -2 11 LhrA2 169 181 -15.55 0.0113911 0.863511
lmo1631 -59 -38 LhrA2 148 170 -13.79 0.0287341 0.9493467 trpD anthranilate phosphoribosyltransferase
lmo1659 23 35 LhrA2 169 181 -13.48 0.0335984 0.9493467 lmo1659
lmo1666 -46 7 LhrA2 157 204 -16.3 0.0075316 0.863511 peptidoglycan-linked protein
lmo1689 -16 16 LhrA2 157 186 -15.11 0.0144414 0.9011628 A/G-specific adenine glycosylase
lmo1709 21 41 LhrA2 163 181 -14.62 0.0187209 0.9128702 methionine aminopeptidase
lmo1717 -6 17 LhrA2 147 170 -15.35 0.0126946 0.8870739
lmo1724 -57 12 LhrA2 156 211 -13.58 0.0319523 0.9493467 ABC transporter ATP-binding protein
lmo1767 11 63 LhrA2 158 213 -13.96 0.0263503 0.9474659 purM phosphoribosylaminoimidazole synthetase
lmo1798 21 65 LhrA2 129 169 -13.42 0.034623 0.9493467
lmo1828 11 21 LhrA2 201 211 -16.11 0.0083732 0.863511
lmo1835 -25 28 LhrA2 154 207 -18.61 0.0019491 0.863511 carB carbamoyl-phosphate synthetase
lmo1875 -25 4 LhrA2 150 179 -15.67 0.0106699 0.863511 ABC transporter ATP-binding protein
lmo1883 -5 28 LhrA2 139 173 -25.95 9.7e-06 0.0277905 chitinase
lmo1941 23 69 LhrA2 156 207 -15.29 0.0131118 0.8878302
lmo1952 -9 31 LhrA2 161 204 -15.84 0.0097207 0.863511 lysA diaminopimelate decarboxylase
lmo1984 -14 29 LhrA2 157 201 -15.62 0.0109651 0.863511 ilvB acetolactate synthase
lmo2074 -69 -43 LhrA2 147 173 -18.23 0.0024551 0.863511
lmo2106 -29 22 LhrA2 159 207 -14.28 0.0223506 0.9474659
lmo2121 32 72 LhrA2 153 189 -14.83 0.0167603 0.9082262 maltose phosphorylase
lmo2146 -8 30 LhrA2 172 211 -13.99 0.0259491 0.9474659 LysR family transcriptional regulator
lmo2251 -12 5 LhrA2 149 165 -13.92 0.0268942 0.9474659 amino acid ABC transporter ATP-binding protein
lmo2282 -21 35 LhrA2 157 205 -15.26 0.0133252 0.8878302 protein gp21
lmo2299 37 63 LhrA2 155 181 -15.54 0.0114532 0.863511 portal protein
lmo2308 -14 7 LhrA2 147 170 -16.63 0.0062544 0.863511 single-stranded DNA-binding protein
lmo2314 -15 17 LhrA2 171 207 -14.04 0.0252928 0.9474659 lmo2314
lmo2327 -39 14 LhrA2 155 208 -14.96 0.0156437 0.9011628 lmo2327
lmo2445 -67 -36 LhrA2 157 177 -14.24 0.0228179 0.9474659 internalin
lmo2446 -22 16 LhrA2 154 187 -17.3 0.0042577 0.863511 glycosidase
lmo2486 -27 32 LhrA2 159 195 -15.82 0.0098281 0.863511 lmo2486
lmo2566 -22 16 LhrA2 155 186 -14.16 0.0237797 0.9474659 lmo2566
lmo2596 -36 -21 LhrA2 171 186 -13.45 0.0341071 0.9493467 rpsI 30S ribosomal protein S9
lmo2613 -16 13 LhrA2 177 203 -13.6 0.0316321 0.9493467 rplO 50S ribosomal protein L15
lmo2615 -18 25 LhrA2 155 202 -17.05 0.0049203 0.863511 rpsE 30S ribosomal protein S5
lmo2654 -5 11 LhrA2 167 184 -14.34 0.0216662 0.9474659 fus elongation factor G
lmo2681 -27 4 LhrA2 154 182 -13.49 0.0334303 0.9493467 kdpB potassium-transporting ATPase subunit B
lmo2759 -28 4 LhrA2 141 173 -14.73 0.0176689 0.9128702
lmo2765 -13 18 LhrA2 155 199 -15.86 0.0096143 0.863511 PTS cellbiose transporter subunit IIA
lmo2768 30 51 LhrA2 161 179 -16.16 0.0081436 0.863511 hypothetical membrane protein
lmo2793 -2 47 LhrA2 115 174 -13.69 0.0302275 0.9493467 lmo2793
lmo2797 -16 53 LhrA2 153 209 -13.46 0.0339368 0.9493467 PTS mannitol transporter subunit IIA
lmo2807 -29 7 LhrA2 157 186 -14.79 0.0171184 0.9082262 hypothetical secreted protein
lmo2809 -46 -2 LhrA2 161 211 -13.64 0.0310006 0.9493467 hypothetical secreted protein
lmo2811 -50 -8 LhrA2 160 203 -14.59 0.0190178 0.9128702 trmE tRNA modification GTPase TrmE
Rows: 1-10 11-20 21-30 31-40 41-50 51-60 61-70 71-80 81-90 91-100 all

Details of Selected Interaction Download Interaction Details

Target

Query

		

		

Job resubmission

Use the following button if you want to resubmit the job with altered input or parameterization:
Feeds the job parameters to the input page to resubmit the job.

de.NBI usability assessment

Please support us by filling this short quality survey for evaluating this de.NBI service.

When using IntaRNA please cite :

Results are computed with IntaRNA version 3.1.3 linking Vienna RNA package 2.4.14