Input and runtime details for job 6038639 (precomputed example)

Sequence input

	sRNA sequences		[.fa]
	Putative target sequences (organism of interest)		[.fa]
	Extract sequences around		start codon
	nt up (1-300)		200
	nt down (1-300)		100

CopraRNA parameters

	Consensus prediction		off
	p-value combination		no
	p-value filtering (0=off)		0

IntaRNA parameters

	Target folding window size		150
	Target max. basepair distance		100

Job ID 6038639 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:35:57 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:19:35 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:35:30 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:35:37 CET 2018
	Job Completed		@ Fri Feb 16 21:35:51 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6038639&toolName=CopraRNA ( 30 days expiry )

Description of the job

IhtA

Output download complete results [zip]

Downloadable files

	CopraRNA result table:		[csv]
	Functional enrichment file		[txt]
	Auxiliary enrichment file		[csv]
	mRNA regions plot		[png] [pdf] [ps]
	sRNA regions plot		[png] [pdf] [ps]
	Functional annotation chart		[html] [pdf]
	Phylogenetic conservation		[png] [pdf]
	16S rDNA tree		[txt] [svg]

mRNA region plot

sRNA region plot

Annot. chart

Conserved, identified interactions for NC_000117 Chlamydia trachomatis D/UW-3/CX

Select: 1-10 11-20 21-30 31-40 41-50 51-60 61-70 71-80 81-90 91-100 101-110 111-120 121-130 131-140 141-150 151-160 161-170 171-180 181-190 191-200 all

Sort by selecting a column name:

Rank	CopraRNA p-value	CopraRNA fdr value	Locus Tag	Gene Name	Energy [kcal/mol]	IntaRNA p-value	Position mRNA	Position sRNA	Annotation
94	0.03394	0.2959	ct_249	N/A	-6.52	0.182571	223 -- 229	80 -- 86		_____________222_____230\n_____________\|_______\|\n5'-UUG...UGAUC_______UUGGG...CUG-3'\n______________AUGGCUG\n______________\|:\|\|\|\|:\n______________UGCCGAU\n3'-UUU...CUCUA_______UGAGG...GAA-5'\n_____________\|_______\|\n_____________87______79\n	223 -- 229	80 -- 86	-8.72307 kcal/mol	1.13798 kcal/mol	1.06449 kcal/mol	222 230@LB@ \| \|@LB@5'-UUG...UGAUC UUGGG...CUG-3'@LB@ AUGGCUG@LB@ \|:\|\|\|\|:@LB@ UGCCGAU@LB@3'-UUU...CUCUA UGAGG...GAA-5'@LB@ \| \|@LB@ 87 79@LB@@LB@@LB@Energy -6.52 kcal/mol@LB@Hybridization Energy -8.72307 kcal/mol@LB@Unfolding Energy - mRNA 1.13798 kcal/mol@LB@Unfolding Energy - sRNA 1.06449 kcal/mol@LB@@LB@Position - mRNA 223 -- 229@LB@Position - sRNA 80 -- 86@LB@Position Seed - mRNA 223 -- 229@LB@Position Seed - sRNA 80 -- 86@LB@
156	0.06505	0.3424	ct_254	N/A	-6.97	0.146186	84 -- 91	80 -- 87		_____________83_______92\n_____________\|________\|\n5'-GUC...AUCGU________GCGUU...UAC-3'\n______________UAUGGCUG\n______________\|\|:\|\|\|\|:\n______________AUGCCGAU\n3'-UUU...CCUCU________UGAGG...GAA-5'\n_____________\|________\|\n_____________88_______79\n	85 -- 91	80 -- 86	-9.90306 kcal/mol	1.8348 kcal/mol	1.09752 kcal/mol	83 92@LB@ \| \|@LB@5'-GUC...AUCGU GCGUU...UAC-3'@LB@ UAUGGCUG@LB@ \|\|:\|\|\|\|:@LB@ AUGCCGAU@LB@3'-UUU...CCUCU UGAGG...GAA-5'@LB@ \| \|@LB@ 88 79@LB@@LB@@LB@Energy -6.97 kcal/mol@LB@Hybridization Energy -9.90306 kcal/mol@LB@Unfolding Energy - mRNA 1.8348 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 84 -- 91@LB@Position - sRNA 80 -- 87@LB@Position Seed - mRNA 85 -- 91@LB@Position Seed - sRNA 80 -- 86@LB@
198	0.08843	0.3671	ct_257	N/A	-6.39	0.194258	76 -- 83	79 -- 86		_____________75_______84\n_____________\|________\|\n5'-CUA...GGCGG________CAGAA...UCA-3'\n______________AUGGCUGA\n______________\|:\|\|\|\|:\|\n______________UGCCGAUU\n3'-UUU...CUCUA________GAGGU...GAA-5'\n_____________\|________\|\n_____________87_______78\n	77 -- 83	79 -- 85	-9.5904 kcal/mol	2.10083 kcal/mol	1.09752 kcal/mol	75 84@LB@ \| \|@LB@5'-CUA...GGCGG CAGAA...UCA-3'@LB@ AUGGCUGA@LB@ \|:\|\|\|\|:\|@LB@ UGCCGAUU@LB@3'-UUU...CUCUA GAGGU...GAA-5'@LB@ \| \|@LB@ 87 78@LB@@LB@@LB@Energy -6.39 kcal/mol@LB@Hybridization Energy -9.5904 kcal/mol@LB@Unfolding Energy - mRNA 2.10083 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 76 -- 83@LB@Position - sRNA 79 -- 86@LB@Position Seed - mRNA 77 -- 83@LB@Position Seed - sRNA 79 -- 85@LB@
185	0.083	0.363	ct_260	N/A	-8.27	0.074080	87 -- 93	53 -- 59		_____________86______94\n_____________\|_______\|\n5'-GUU...CCCCC_______CCCAU...UCA-3'\n______________CCCCCCU\n______________\|\|\|\|\|\|\|\n______________GGGGGGA\n3'-UUU...CUGAA_______CACAU...GAA-5'\n_____________\|_______\|\n_____________60______52\n	87 -- 93	53 -- 59	-14.3095 kcal/mol	0.558947 kcal/mol	5.47887 kcal/mol	86 94@LB@ \| \|@LB@5'-GUU...CCCCC CCCAU...UCA-3'@LB@ CCCCCCU@LB@ \|\|\|\|\|\|\|@LB@ GGGGGGA@LB@3'-UUU...CUGAA CACAU...GAA-5'@LB@ \| \|@LB@ 60 52@LB@@LB@@LB@Energy -8.27 kcal/mol@LB@Hybridization Energy -14.3095 kcal/mol@LB@Unfolding Energy - mRNA 0.558947 kcal/mol@LB@Unfolding Energy - sRNA 5.47887 kcal/mol@LB@@LB@Position - mRNA 87 -- 93@LB@Position - sRNA 53 -- 59@LB@Position Seed - mRNA 87 -- 93@LB@Position Seed - sRNA 53 -- 59@LB@
26	0.006621	0.2093	ct_267	ihfA	-8.59	0.062448	193 -- 205	17 -- 31	DNA-binding protein HU	_____________192_____________206\n_____________\|_______________\|\n5'-UAA...GCAAC_______________AACGA...AUA-3'\n______________AAGCUA__CCAUGGC\n______________\|\|\|\|\|\|__\|\|\|\|\|\|\|\n______________UUCGAU__GGUACCG\n3'-UUU...CAGUC______AA_______CAAUC...GAA-5'\n_____________\|_______________\|\n_____________32______________16\n	199 -- 205	17 -- 23	-17.4173 kcal/mol	3.97125 kcal/mol	4.86101 kcal/mol	192 206@LB@ \| \|@LB@5'-UAA...GCAAC AACGA...AUA-3'@LB@ AAGCUA CCAUGGC@LB@ \|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ UUCGAU GGUACCG@LB@3'-UUU...CAGUC AA CAAUC...GAA-5'@LB@ \| \|@LB@ 32 16@LB@@LB@@LB@Energy -8.59 kcal/mol@LB@Hybridization Energy -17.4173 kcal/mol@LB@Unfolding Energy - mRNA 3.97125 kcal/mol@LB@Unfolding Energy - sRNA 4.86101 kcal/mol@LB@@LB@Position - mRNA 193 -- 205@LB@Position - sRNA 17 -- 31@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 17 -- 23@LB@
89	0.03269	0.2942	ct_269	murE	-8.94	0.051230	172 -- 183	46 -- 57	UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2 6-diaminopimelate ligase	_____________171__________184\n_____________\|____________\|\n5'-AUC...UGAAG____________UGUCU...UUG-3'\n______________CCCUUGUGUGCG\n______________\|\|\|:\|\|\|\|\|:\|:\n______________GGGGACACAUGU\n3'-UUU...GAAGG____________UUGUG...GAA-5'\n_____________\|____________\|\n_____________58___________45\n	176 -- 182	47 -- 53	-19.7508 kcal/mol	3.51628 kcal/mol	7.29173 kcal/mol	171 184@LB@ \| \|@LB@5'-AUC...UGAAG UGUCU...UUG-3'@LB@ CCCUUGUGUGCG@LB@ \|\|\|:\|\|\|\|\|:\|:@LB@ GGGGACACAUGU@LB@3'-UUU...GAAGG UUGUG...GAA-5'@LB@ \| \|@LB@ 58 45@LB@@LB@@LB@Energy -8.94 kcal/mol@LB@Hybridization Energy -19.7508 kcal/mol@LB@Unfolding Energy - mRNA 3.51628 kcal/mol@LB@Unfolding Energy - sRNA 7.29173 kcal/mol@LB@@LB@Position - mRNA 172 -- 183@LB@Position - sRNA 46 -- 57@LB@Position Seed - mRNA 176 -- 182@LB@Position Seed - sRNA 47 -- 53@LB@
63	0.02436	0.29	ct_270	pbp3	-9.04	0.048476	131 -- 156	5 -- 34	penicillin-binding protein	_____________130_____________________________157\n_____________\|_______________________________\|\n5'-UAA...UGUUG____U____U____UCC______________GUAUC...GAG-3'\n______________CAGA_AGCU_UUCU________AGAAUACCA\n______________\|\|\|\|_\|\|\|\|_\|\|\|:________\|\|\|\|\|\|\|\|\|\n______________GUCU_UCGA_AAGG________UCUUAUGGU\n3'-UUU...UCUCA_________U____UACCGCAA_________UGAA-5'\n_____________\|_______________________________\|\n_____________35______________________________4\n	149 -- 155	6 -- 12	-21.654 kcal/mol	4.02029 kcal/mol	8.59194 kcal/mol	130 157@LB@ \| \|@LB@5'-UAA...UGUUG U U UCC GUAUC...GAG-3'@LB@ CAGA AGCU UUCU AGAAUACCA@LB@ \|\|\|\| \|\|\|\| \|\|\|: \|\|\|\|\|\|\|\|\|@LB@ GUCU UCGA AAGG UCUUAUGGU@LB@3'-UUU...UCUCA U UACCGCAA UGAA-5'@LB@ \| \|@LB@ 35 4@LB@@LB@@LB@Energy -9.04 kcal/mol@LB@Hybridization Energy -21.654 kcal/mol@LB@Unfolding Energy - mRNA 4.02029 kcal/mol@LB@Unfolding Energy - sRNA 8.59194 kcal/mol@LB@@LB@Position - mRNA 131 -- 156@LB@Position - sRNA 5 -- 34@LB@Position Seed - mRNA 149 -- 155@LB@Position Seed - sRNA 6 -- 12@LB@
128	0.05098	0.3262	ct_279	nqr3	-7.28	0.125274	283 -- 291	51 -- 59	Na(+)-translocating NADH-quinone reductase subunit C	_____________282_______292\n_____________\|_________\|\n5'-CCG...UGGUA_________CUUCU...UGU-3'\n______________CCCUCCUGU\n______________\|\|\|:\|\|\|\|\|\n______________GGGGGGACA\n3'-UUU...CUGAA_________CAUGU...GAA-5'\n_____________\|_________\|\n_____________60________50\n	285 -- 291	51 -- 57	-15.9842 kcal/mol	0.606269 kcal/mol	8.10291 kcal/mol	282 292@LB@ \| \|@LB@5'-CCG...UGGUA CUUCU...UGU-3'@LB@ CCCUCCUGU@LB@ \|\|\|:\|\|\|\|\|@LB@ GGGGGGACA@LB@3'-UUU...CUGAA CAUGU...GAA-5'@LB@ \| \|@LB@ 60 50@LB@@LB@@LB@Energy -7.28 kcal/mol@LB@Hybridization Energy -15.9842 kcal/mol@LB@Unfolding Energy - mRNA 0.606269 kcal/mol@LB@Unfolding Energy - sRNA 8.10291 kcal/mol@LB@@LB@Position - mRNA 283 -- 291@LB@Position - sRNA 51 -- 59@LB@Position Seed - mRNA 285 -- 291@LB@Position Seed - sRNA 51 -- 57@LB@
6	0.000543	0.07439	ct_280	nqr4	-8.45	0.067322	89 -- 131	2 -- 35	Na(+)-translocating NADH-quinone reductase subunit D	_____________88___________________________________________132\n_____________\|____________________________________________\|\n5'-GAC...GAAUU__________C___GACUUGUA_________CC_______UU__CUCAU...CGG-3'\n______________UCAGGAGCUA_UUU________AUGGUGUUA__GAAU_CC__CU\n______________\|\|\|\|:\|\|\|\|\|_\|::________\|\|\|\|:\|\|\|\|__\|\|\|\|_\|\|__\|\|\n______________AGUCUUCGAU_AGG________UACCGCAAU__CUUA_GG__GA\n3'-UUU...AUCUC__________A__________________________U__UU__A-5'\n_____________\|____________________________________________\|\n_____________36___________________________________________1\n	113 -- 119	13 -- 19	-28.603 kcal/mol	11.5634 kcal/mol	8.59199 kcal/mol	88 132@LB@ \| \|@LB@5'-GAC...GAAUU C GACUUGUA CC UU CUCAU...CGG-3'@LB@ UCAGGAGCUA UUU AUGGUGUUA GAAU CC CU@LB@ \|\|\|\|:\|\|\|\|\| \|:: \|\|\|\|:\|\|\|\| \|\|\|\| \|\| \|\|@LB@ AGUCUUCGAU AGG UACCGCAAU CUUA GG GA@LB@3'-UUU...AUCUC A U UU A-5'@LB@ \| \|@LB@ 36 1@LB@@LB@@LB@Energy -8.45 kcal/mol@LB@Hybridization Energy -28.603 kcal/mol@LB@Unfolding Energy - mRNA 11.5634 kcal/mol@LB@Unfolding Energy - sRNA 8.59199 kcal/mol@LB@@LB@Position - mRNA 89 -- 131@LB@Position - sRNA 2 -- 35@LB@Position Seed - mRNA 113 -- 119@LB@Position Seed - sRNA 13 -- 19@LB@
135	0.05472	0.3262	ct_283	N/A	-6.89	0.152000	262 -- 284	14 -- 35		_____________261______________________285\n_____________\|________________________\|\n5'-UAC...GUUUA_____CU________GC_______UGUUU...UUG-3'\n______________UCGGA__AGUUA_UC__UGGCGUU\n______________\|\|:\|\|__\|\|:\|\|_\|\|__\|\|\|\|\|\|\|\n______________AGUCU__UCGAU_AG__ACCGCAA\n3'-UUU...AUCUC____________A__GU_______UCUUA...GAA-5'\n_____________\|________________________\|\n_____________36_______________________13\n	278 -- 284	14 -- 20	-19.9844 kcal/mol	4.64246 kcal/mol	8.44936 kcal/mol	261 285@LB@ \| \|@LB@5'-UAC...GUUUA CU GC UGUUU...UUG-3'@LB@ UCGGA AGUUA UC UGGCGUU@LB@ \|\|:\|\| \|\|:\|\| \|\| \|\|\|\|\|\|\|@LB@ AGUCU UCGAU AG ACCGCAA@LB@3'-UUU...AUCUC A GU UCUUA...GAA-5'@LB@ \| \|@LB@ 36 13@LB@@LB@@LB@Energy -6.89 kcal/mol@LB@Hybridization Energy -19.9844 kcal/mol@LB@Unfolding Energy - mRNA 4.64246 kcal/mol@LB@Unfolding Energy - sRNA 8.44936 kcal/mol@LB@@LB@Position - mRNA 262 -- 284@LB@Position - sRNA 14 -- 35@LB@Position Seed - mRNA 278 -- 284@LB@Position Seed - sRNA 14 -- 20@LB@

Details of Selected Interaction Download Interaction Details

mRNA

sRNA

Energy

Hybridization Energy

Unfolding Energy - mRNA

Unfolding Energy - sRNA

Position - mRNA

Position - sRNA

Position Seed - mRNA

Position Seed - sRNA

Evolutionary conservation of mRNA targets (alignment generated with Jalview)

Evolutionary conservation of sRNA (alignment generated with Jalview)

Job resubmission

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

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service.

When using CopraRNA please cite :

Patrick R. Wright, Jens Georg, Martin Mann, Dragos A. Sorescu, Andreas S. Richter, Steffen Lott, Robert Kleinkauf, Wolfgang R. Hess, and Rolf Backofen
CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains
Nucleic Acids Research, 2014, 42 (W1), W119-W123.
Patrick R. Wright, Andreas S. Richter, Kai Papenfort, Martin Mann, Joerg Vogel, Wolfgang R. Hess, Rolf Backofen and Jens Georg
Comparative genomics boosts target prediction for bacterial small RNAs
Proc Natl Acad Sci USA, 2013, 110 (37), E3487-E3496.
Martin Raden, Syed M Ali, Omer S Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu, Robert Kleinkauf, Steffen C Lott, Mostafa M Mohamed, Alexander Mattheis, Milad Miladi, Andreas S Richter, Sebastian Will, Joachim Wolff, Patrick R Wright, and Rolf Backofen
Freiburg RNA tools: a central online resource for RNA-focused research and teaching
Nucleic Acids Research, 46(W1), W25-W29, 2018.

Results are computed with CopraRNA version 2.1.2

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