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IntaRNA 7119295

Input and runtime details for job 7119295 (precomputed example)

Sequence Parameters

? Query ncRNA (short) in FASTA[.fa]
? Index first query position1
? Target RNA (long) in FASTA[.fa]
? Target NCBI RefSeq IDNC_005072
? 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 7119295 (server version trunk)

?Job Submitted & Queued@ Mon Jan 27 14:23:26 CET 2020
?Processing Started@ Mon Jan 27 14:25:03 CET 2020
?IntaRNA Finished & Post-Processing@ Mon Jan 27 14:25:25 CET 2020
?Post-Processing Finished@ Mon Jan 27 14:26:09 CET 2020
?Job Completed@ Mon Jan 27 14:26:17 CET 2020
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=7119295&toolName=IntaRNA ( 30 days expiry )

The job description you specified

Yfr1 - Prochlorococcus marinus


? Output download complete results [zip]

Downloadable files

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[txt]
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heatmap

? Identified Interactions for NC_005072 Prochlorococcus marinus subsp. pastoris str. CCMP1986

Sort by selecting a column name
Target Start(T) End(T) Query Start(Q) End(Q) Energy p-value fdr gene annotation
PMM0224 54 72 Yfr1 12 29 -6.64 0.13353 0.8751146 aroC chorismate synthase
PMM0712 -72 -65 Yfr1 12 19 -5.54 0.2352719 0.8751146 major facilitator superfamily multidrug-efflux transporter
PMM1561 35 42 Yfr1 12 19 -4.72 0.3380285 0.8751146
PMM1405 68 75 Yfr1 12 19 -4.34 0.3928103 0.8909401
PMM0021 -74 -68 Yfr1 14 20 -6.53 0.141895 0.8751146 murB UDP-N-acetylenolpyruvoylglucosamine reductase
PMM0665 -1 6 Yfr1 14 20 -4.34 0.3928103 0.8909401 hslO heat shock protein 33
PMM1647 17 23 Yfr1 14 20 -4.25 0.4063526 0.8909401 DNA polymerase III subunit delta
PMM0913 -47 -41 Yfr1 14 20 -4.18 0.4170203 0.8909401 ABC transporter
PMM1443 61 75 Yfr1 19 31 -5.46 0.2442923 0.8751146
PMM1069 -35 -21 Yfr1 19 33 -4.67 0.3449996 0.8751146 folD bifunctional 510-methylene-tetrahydrofolate dehydrogenase/ 510-methylene-tetrahydrofolate cyclohydrolase
PMM1107 2 18 Yfr1 19 34 -4.63 0.3506303 0.8751146 pdxJ pyridoxine 5'-phosphate synthase
PMM0173 41 68 Yfr1 20 38 -10.31 0.0097181 0.8607323
PMM0464 64 70 Yfr1 20 26 -8.22 0.0502434 0.8607323 Tat family protein secretion protein
PMM0937 -35 -28 Yfr1 20 27 -6.88 0.1165771 0.8751146 umuC UmuC protein
PMM1096 -75 -69 Yfr1 20 26 -6.25 0.1649446 0.8751146 lipA,lip lipoyl synthase
PMM1312 -61 -55 Yfr1 20 26 -6.14 0.1747091 0.8751146 PIN domain superfamily protein
PMM0648 50 56 Yfr1 20 26 -6.12 0.1765282 0.8751146 glucose-methanol-choline (GMC) oxidoreductase:NAD binding site
PMM0992 -42 -33 Yfr1 20 28 -6.01 0.1867767 0.8751146
PMM1689 24 32 Yfr1 20 29 -5.58 0.2308453 0.8751146 pyrG CTP synthetase
PMM1707 36 44 Yfr1 20 29 -5.26 0.2678137 0.8751146 argG argininosuccinate synthase
PMM0876 -43 -36 Yfr1 20 27 -5.23 0.2714606 0.8751146
PMM0483 68 74 Yfr1 20 26 -4.77 0.3311335 0.8751146 hemL glutamate-1-semialdehyde aminotransferase
PMM0538 2 9 Yfr1 20 27 -4.7 0.3408079 0.8751146
PMM1593 -24 -18 Yfr1 20 26 -4.7 0.3408079 0.8751146 pebA dihydrobiliverdin:ferredoxin oxidoreductase
PMM1605 -52 -46 Yfr1 20 26 -4.62 0.3520454 0.8751146 rimM 16S rRNA-processing protein RimM
PMM1021 12 18 Yfr1 21 27 -8.47 0.0422349 0.8607323 pili assembly chaperone
PMM1448 62 68 Yfr1 21 27 -8.28 0.0482169 0.8607323
PMM0835 -64 -58 Yfr1 21 27 -7.8 0.0664486 0.8607323
PMM0670 51 61 Yfr1 21 31 -7.28 0.0920548 0.8607323 possible role in phosphonate metabolism
PMM0503 -73 -67 Yfr1 21 27 -6.83 0.1199653 0.8751146 precorrin-6x reductase
PMM1613 59 65 Yfr1 21 27 -6.69 0.1298531 0.8751146 zinc metallopeptidase
PMM1466 60 73 Yfr1 21 33 -6.56 0.1395757 0.8751146 fumC fumarate hydratase
PMM1627 27 33 Yfr1 21 27 -6.26 0.164077 0.8751146 carbohydrate kinase
PMM1604 -72 -66 Yfr1 21 27 -6.15 0.1738046 0.8751146
PMM1332 57 75 Yfr1 21 37 -5.83 0.204443 0.8751146 leucyl aminopeptidase
PMM0702 60 66 Yfr1 21 27 -5.66 0.2221596 0.8751146
PMM0396 -40 -34 Yfr1 21 27 -4.84 0.3216106 0.8751146 proC Delta 1-pyrroline-5-carboxylate reductase
PMM1480 -65 -49 Yfr1 21 38 -4.76 0.3325064 0.8751146
PMM0792 57 63 Yfr1 21 27 -4.64 0.3492182 0.8751146
PMM1119 -3 7 Yfr1 22 31 -11.27 0.0038187 0.7904709 som porin
PMM1634 5 11 Yfr1 22 28 -9.17 0.0251876 0.8607323 gyrB DNA gyrase subunit B
PMM0494 -36 -28 Yfr1 22 30 -9.16 0.0253828 0.8607323 ppa inorganic pyrophosphatase
PMM0384 -48 -42 Yfr1 22 28 -8.55 0.0399051 0.8607323 spnII-interrupted-C
PMM0229 -75 -67 Yfr1 22 31 -7.62 0.0745694 0.8607323 dfp p-pantothenate cysteine ligase and p-pantothenenoylcysteine decarboxylase
PMM0408 1 7 Yfr1 22 28 -7.47 0.0819251 0.8607323 cystathionine gamma-synthase
PMM1120 -75 -69 Yfr1 22 28 -7.05 0.1056045 0.8607323 TPR repeat-containing sulfotransferase
PMM0833 48 55 Yfr1 22 29 -6.17 0.1720057 0.8751146
PMM0120 28 40 Yfr1 22 33 -5.7 0.2179004 0.8751146 cell division inhibitor
PMM0285 -70 -64 Yfr1 22 28 -5.21 0.2739089 0.8751146 phr DNA photolyase
PMM1174 21 36 Yfr1 22 38 -4.93 0.3095948 0.8751146
PMM1121 -3 6 Yfr1 23 31 -8.64 0.0374112 0.8607323 som porin
PMM1166 -58 -52 Yfr1 23 29 -5.42 0.248886 0.8751146
PMM0131 37 43 Yfr1 23 29 -5.11 0.2863537 0.8751146 P-type ATPase transporter for copper
PMM1607 -27 -21 Yfr1 23 29 -4.65 0.347809 0.8751146 psaC photosystem I subunit VII
PMM0137 -62 -51 Yfr1 24 36 -7.35 0.0882142 0.8607323 fabD malonyl CoA-ACP transacylase
PMM0709 -14 -7 Yfr1 25 32 -7.79 0.0668803 0.8607323 som porin
PMM1538 29 35 Yfr1 25 31 -7.18 0.0977678 0.8607323 rpmJ 50S ribosomal protein L36
PMM0387 -68 -62 Yfr1 25 31 -5.21 0.2739089 0.8751146 aroD 3-dehydroquinate dehydratase
PMM0797 45 54 Yfr1 27 36 -6.32 0.1589414 0.8751146 mRNA binding protein
PMM0296 -67 -58 Yfr1 27 37 -4.7 0.3408079 0.8751146 similar to Arabidopsis thaliana photosystem II assembly protein
PMM0417 -71 -63 Yfr1 28 36 -9.92 0.0136924 0.8607323
PMM1278 60 70 Yfr1 28 38 -7.49 0.0809124 0.8607323 circadian phase modifier CpmA-like protein
PMM1083 42 51 Yfr1 28 38 -7.24 0.0943077 0.8607323 kinase
PMM1151 15 21 Yfr1 28 34 -5.12 0.285094 0.8751146 infA translation initiation factor IF-1
PMM1485 49 58 Yfr1 28 38 -4.87 0.3175766 0.8751146 rpoB DNA-directed RNA polymerase subunit beta
PMM1137 -5 4 Yfr1 29 37 -7.17 0.098354 0.8607323 cytochrome b(C-terminal)/b6/petD
PMM1526 11 17 Yfr1 29 35 -7.01 0.1081113 0.8607323 hisB imidazoleglycerol-phosphate dehydratase
PMM0693 -39 -31 Yfr1 29 37 -6.63 0.1342748 0.8751146
PMM0687 62 68 Yfr1 29 35 -6.35 0.1564181 0.8751146
PMM1678 26 32 Yfr1 29 35 -5.87 0.2004204 0.8751146
PMM0657 -57 -49 Yfr1 29 37 -5.79 0.2085211 0.8751146 vanadium/alternative nitrogenase delt
PMM1430 68 74 Yfr1 29 35 -4.71 0.3394167 0.8751146
PMM0017 23 29 Yfr1 29 35 -4.48 0.3721584 0.8754181 dnaJ molecular chaperone DnaJ
PMM0389 68 74 Yfr1 29 35 -4.36 0.3898285 0.8909401 cobI/cbiL precorrin-2 C20-methyltransferase
PMM1592 -72 -66 Yfr1 30 36 -5.87 0.2004204 0.8751146 pebB phycoerythrobilin:ferredoxin oxidoreductase
PMM1454 19 25 Yfr1 30 36 -5.35 0.2570582 0.8751146 atpG ATP synthase F0F1 subunit B'
PMM0303 -70 -64 Yfr1 30 36 -4.75 0.3338823 0.8751146 tRNA nucleotidyltransferase/poly(A) polymerase
PMM0843 35 43 Yfr1 30 38 -4.56 0.3605969 0.8751146 tldD modulator of DNA gyrase TldD
PMM1518 58 65 Yfr1 30 37 -4.51 0.3678018 0.8751146
PMM1144 -58 -52 Yfr1 30 36 -4 0.4449483 0.8909401 hydrolase of the alpha/beta-hydrolase fold
PMM1091 59 66 Yfr1 31 38 -7.76 0.0681888 0.8607323
PMM0388 -68 -61 Yfr1 31 38 -7.08 0.1037542 0.8607323 tRNA-(MS[2]IO[6]A)-hydroxylase
PMM0668 -30 -23 Yfr1 31 38 -4.94 0.3082757 0.8751146 16S ribosomal RNA methyltransferase RsmE
PMM0446 45 51 Yfr1 31 37 -4.54 0.3634704 0.8751146 ctaC cytochrome c oxidase subunit 2
PMM0135 52 58 Yfr1 31 37 -4.27 0.403326 0.8909401 plsX glycerol-3-phosphate acyltransferase PlsX
PMM0484 -13 -7 Yfr1 31 37 -4.22 0.4109104 0.8909401 xthA exodeoxyribonuclease III
PMM1423 36 42 Yfr1 31 37 -4.08 0.4324518 0.8909401
PMM0951 69 75 Yfr1 31 37 -4.03 0.4402471 0.8909401 carA carbamoyl phosphate synthase small subunit
PMM1335 -75 -69 Yfr1 32 38 -7.58 0.0764774 0.8607323 lpxA UDP-N-acetylglucosamine acyltransferase
PMM1685 47 53 Yfr1 32 38 -5.83 0.204443 0.8751146 speE spermidine synthase
PMM1319 52 58 Yfr1 32 38 -5.6 0.228653 0.8751146 beta-lactamase
PMM1180 3 9 Yfr1 32 38 -5.59 0.2297474 0.8751146 sppA signal peptide peptidase SppA (protease IV)
PMM0933 32 38 Yfr1 32 38 -5.33 0.2594242 0.8751146 ksgA dimethyladenosine transferase
PMM1346 18 34 Yfr1 32 51 -5.29 0.2641976 0.8751146
PMM0487 67 73 Yfr1 32 38 -4.95 0.3069599 0.8751146
PMM0080 -65 -59 Yfr1 32 38 -4.75 0.3338823 0.8751146
PMM1216 37 43 Yfr1 32 38 -4.53 0.3649114 0.8751146 sugar-phosphate nucleotidyl transferase
PMM1264 38 44 Yfr1 32 38 -4.16 0.420089 0.8909401 ftsH3 cell division protein FtsH3
PMM1193 -63 -43 Yfr1 36 58 -9.03 0.0280368 0.8607323 tetrapyrrole methylase family protein
PMM1030 10 17 Yfr1 49 56 -4.09 0.4308989 0.8909401 ferric uptake regulator family protein
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

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