Input and runtime details for job 6756176 (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 6756176 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:58 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:23:17 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:01:55 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:02:03 CET 2018
	Job Completed		@ Fri Feb 16 20:02:30 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6756176&toolName=CopraRNA ( 30 days expiry )

Description of the job

DsrA

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_000913 Escherichia coli str. K-12 substr. MG1655

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
180	0.02111	0.3768	b2753	iap	-4.77	0.357003	164 -- 179	25 -- 40	aminopeptidase in alkaline phosphatase isozyme conversion	_____________163______________180\n_____________\|________________\|\n5'-UAG...CUAUG___G_A__________CAUGG...CUA-3'\n______________GCG_U_AAAAAAUUUG\n______________\|\|:_\|_\|\|\|\|\|\|\|\|:\|\n______________CGU_A_UUUUUUAAGC\n3'-UUU...UUCUU___G_A__________AAUGU...CAA-5'\n_____________\|________________\|\n_____________41_______________24\n	170 -- 176	28 -- 34	-8.71545 kcal/mol	2.29678 kcal/mol	1.64821 kcal/mol	163 180@LB@ \| \|@LB@5'-UAG...CUAUG G A CAUGG...CUA-3'@LB@ GCG U AAAAAAUUUG@LB@ \|\|: \| \|\|\|\|\|\|\|\|:\|@LB@ CGU A UUUUUUAAGC@LB@3'-UUU...UUCUU G A AAUGU...CAA-5'@LB@ \| \|@LB@ 41 24@LB@@LB@@LB@Energy -4.77 kcal/mol@LB@Hybridization Energy -8.71545 kcal/mol@LB@Unfolding Energy - mRNA 2.29678 kcal/mol@LB@Unfolding Energy - sRNA 1.64821 kcal/mol@LB@@LB@Position - mRNA 164 -- 179@LB@Position - sRNA 25 -- 40@LB@Position Seed - mRNA 170 -- 176@LB@Position Seed - sRNA 28 -- 34@LB@
199	0.02405	0.3893	b2412	zipA	-4.86	0.342002	121 -- 136	25 -- 40	FtsZ stabilizer	_____________120______________137\n_____________\|________________\|\n5'-CAG...CACUU__________UAA___GCAAA...CUU-3'\n______________GCACUUGAGG___UCG\n______________\|\|\|\|\|\|:\|::___\|\|\|\n______________CGUGAAUUUU___AGC\n3'-UUU...UUCUU__________UUA___AAUGU...CAA-5'\n_____________\|________________\|\n_____________41_______________24\n	124 -- 130	31 -- 37	-13.2366 kcal/mol	6.7246 kcal/mol	1.64821 kcal/mol	120 137@LB@ \| \|@LB@5'-CAG...CACUU UAA GCAAA...CUU-3'@LB@ GCACUUGAGG UCG@LB@ \|\|\|\|\|\|:\|:: \|\|\|@LB@ CGUGAAUUUU AGC@LB@3'-UUU...UUCUU UUA AAUGU...CAA-5'@LB@ \| \|@LB@ 41 24@LB@@LB@@LB@Energy -4.86 kcal/mol@LB@Hybridization Energy -13.2366 kcal/mol@LB@Unfolding Energy - mRNA 6.7246 kcal/mol@LB@Unfolding Energy - sRNA 1.64821 kcal/mol@LB@@LB@Position - mRNA 121 -- 136@LB@Position - sRNA 25 -- 40@LB@Position Seed - mRNA 124 -- 130@LB@Position Seed - sRNA 31 -- 37@LB@
2	4.936e-07	0.0007949	b1237	hns	-13.24	0.001473	195 -- 222	26 -- 57	global DNA-binding transcriptional dual regulator H-NS	_____________194______________________________223\n_____________\|________________________________\|\n5'-CUC...AGAUU___ACAA_________________________UGAAC...UAG-3'\n______________ACU____UGAGC__GAAGCACUUAAA__AUUC\n______________\|\|\|____\|:\|\|\|__\|\|\|\|\|\|\|\|\|\|\|\|__\|\|\|\|\n______________UGA____AUUCG__CUUCGUGAAUUU__UAAG\n3'-UUU...UACUU___ACGA_____UU____________UU____CAAUG...CAA-5'\n_____________\|________________________________\|\n_____________58_______________________________25\n	212 -- 218	32 -- 38	-22.6274 kcal/mol	3.10903 kcal/mol	6.27605 kcal/mol	194 223@LB@ \| \|@LB@5'-CUC...AGAUU ACAA UGAAC...UAG-3'@LB@ ACU UGAGC GAAGCACUUAAA AUUC@LB@ \|\|\| \|:\|\|\| \|\|\|\|\|\|\|\|\|\|\|\| \|\|\|\|@LB@ UGA AUUCG CUUCGUGAAUUU UAAG@LB@3'-UUU...UACUU ACGA UU UU CAAUG...CAA-5'@LB@ \| \|@LB@ 58 25@LB@@LB@@LB@Energy -13.24 kcal/mol@LB@Hybridization Energy -22.6274 kcal/mol@LB@Unfolding Energy - mRNA 3.10903 kcal/mol@LB@Unfolding Energy - sRNA 6.27605 kcal/mol@LB@@LB@Position - mRNA 195 -- 222@LB@Position - sRNA 26 -- 57@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 32 -- 38@LB@
11	0.0001294	0.03789	b3687	ibpA	-8.25	0.051487	69 -- 81	26 -- 38	heat shock chaperone	_____________68____________82\n_____________\|_____________\|\n5'-AAC...AUAAG_____________AUUUC...GCU-3'\n______________GCUUGAAAAGUUC\n______________:\|\|\|:\|\|\|\|:\|\|\|\n______________UGAAUUUUUUAAG\n3'-UUU...CUUCG_____________CAAUG...CAA-5'\n_____________\|_____________\|\n_____________39____________25\n	75 -- 81	26 -- 32	-13.0918 kcal/mol	3.40592 kcal/mol	1.43364 kcal/mol	68 82@LB@ \| \|@LB@5'-AAC...AUAAG AUUUC...GCU-3'@LB@ GCUUGAAAAGUUC@LB@ :\|\|\|:\|\|\|\|:\|\|\|@LB@ UGAAUUUUUUAAG@LB@3'-UUU...CUUCG CAAUG...CAA-5'@LB@ \| \|@LB@ 39 25@LB@@LB@@LB@Energy -8.25 kcal/mol@LB@Hybridization Energy -13.0918 kcal/mol@LB@Unfolding Energy - mRNA 3.40592 kcal/mol@LB@Unfolding Energy - sRNA 1.43364 kcal/mol@LB@@LB@Position - mRNA 69 -- 81@LB@Position - sRNA 26 -- 38@LB@Position Seed - mRNA 75 -- 81@LB@Position Seed - sRNA 26 -- 32@LB@
34	0.001265	0.1198	b0826	moeB	-10.82	0.009172	276 -- 295	26 -- 46	molybdopterin synthase sulfurylase	_____________275___________________296\n_____________\|_____________________\|\n5'-CUU...ACGGC_____________________UCGCG-3'\n______________CAGGAGGCGC_UGAAAGAUUC\n______________\|\|:\|\|:\|\|:\|_\|:\|\|\|:\|\|\|\|\n______________GUUCUUCGUG_AUUUUUUAAG\n3'-UUU...AAUUC__________A__________CAAUG...CAA-5'\n_____________\|_____________________\|\n_____________47____________________25\n	289 -- 295	26 -- 32	-23.0973 kcal/mol	6.15128 kcal/mol	6.13041 kcal/mol	275 296@LB@ \| \|@LB@5'-CUU...ACGGC UCGCG-3'@LB@ CAGGAGGCGC UGAAAGAUUC@LB@ \|\|:\|\|:\|\|:\| \|:\|\|\|:\|\|\|\|@LB@ GUUCUUCGUG AUUUUUUAAG@LB@3'-UUU...AAUUC A CAAUG...CAA-5'@LB@ \| \|@LB@ 47 25@LB@@LB@@LB@Energy -10.82 kcal/mol@LB@Hybridization Energy -23.0973 kcal/mol@LB@Unfolding Energy - mRNA 6.15128 kcal/mol@LB@Unfolding Energy - sRNA 6.13041 kcal/mol@LB@@LB@Position - mRNA 276 -- 295@LB@Position - sRNA 26 -- 46@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 26 -- 32@LB@
35	0.001338	0.121	b0405	queA	-9.92	0.017135	73 -- 106	26 -- 60	S-adenosylmethionine:tRNA ribosyltransferase-isomerase	_____________72____________________________________107\n_____________\|_____________________________________\|\n5'-GGG...UCCGC_____GG___A__U_____U_________________AUCGA...GGC-3'\n______________GAGAU__GCU_AA_GCAGG_GAGC___UAAAAAAUUC\n______________\|\|:\|:__\|\|\|_\|\|_\|\|\|:\|_:\|\|\|___\|\|\|\|\|\|\|\|\|\|\n______________CUUUG__CGA_UU_CGUUC_UUCG___AUUUUUUAAG\n3'-UUU...CCCUA_____AA___A_____________UGA__________CAAUG...CAA-5'\n_____________\|_____________________________________\|\n_____________61____________________________________25\n	100 -- 106	26 -- 32	-25.4572 kcal/mol	9.25896 kcal/mol	6.27609 kcal/mol	72 107@LB@ \| \|@LB@5'-GGG...UCCGC GG A U U AUCGA...GGC-3'@LB@ GAGAU GCU AA GCAGG GAGC UAAAAAAUUC@LB@ \|\|:\|: \|\|\| \|\| \|\|\|:\| :\|\|\| \|\|\|\|\|\|\|\|\|\|@LB@ CUUUG CGA UU CGUUC UUCG AUUUUUUAAG@LB@3'-UUU...CCCUA AA A UGA CAAUG...CAA-5'@LB@ \| \|@LB@ 61 25@LB@@LB@@LB@Energy -9.92 kcal/mol@LB@Hybridization Energy -25.4572 kcal/mol@LB@Unfolding Energy - mRNA 9.25896 kcal/mol@LB@Unfolding Energy - sRNA 6.27609 kcal/mol@LB@@LB@Position - mRNA 73 -- 106@LB@Position - sRNA 26 -- 60@LB@Position Seed - mRNA 100 -- 106@LB@Position Seed - sRNA 26 -- 32@LB@
47	0.002119	0.1452	b0694	kdpE	-6.96	0.113004	177 -- 189	26 -- 38	response regulator in two-component regulatory system with KdpD	_____________176___________190\n_____________\|_____________\|\n5'-ACG...CCUGA_____________CAUGA...CGC-3'\n______________ACUUGAAGAAUUU\n______________\|\|\|\|:\|\|:\|\|\|\|:\n______________UGAAUUUUUUAAG\n3'-UUU...CUUCG_____________CAAUG...CAA-5'\n_____________\|_____________\|\n_____________39____________25\n	179 -- 185	30 -- 36	-10.6038 kcal/mol	2.21135 kcal/mol	1.43364 kcal/mol	176 190@LB@ \| \|@LB@5'-ACG...CCUGA CAUGA...CGC-3'@LB@ ACUUGAAGAAUUU@LB@ \|\|\|\|:\|\|:\|\|\|\|:@LB@ UGAAUUUUUUAAG@LB@3'-UUU...CUUCG CAAUG...CAA-5'@LB@ \| \|@LB@ 39 25@LB@@LB@@LB@Energy -6.96 kcal/mol@LB@Hybridization Energy -10.6038 kcal/mol@LB@Unfolding Energy - mRNA 2.21135 kcal/mol@LB@Unfolding Energy - sRNA 1.43364 kcal/mol@LB@@LB@Position - mRNA 177 -- 189@LB@Position - sRNA 26 -- 38@LB@Position Seed - mRNA 179 -- 185@LB@Position Seed - sRNA 30 -- 36@LB@
78	0.004685	0.1935	b3905	rhaS	-7.96	0.061746	70 -- 86	26 -- 40	transcriptional activator of rhaBAD and rhaT	_____________69________________87\n_____________\|_________________\|\n5'-UGG...UCACC______CCU________ACGCU...AUG-3'\n______________GCAUUU___GAAAAUUC\n______________\|\|\|:\|\|___:\|\|\|\|\|\|\|\n______________CGUGAA___UUUUUAAG\n3'-UUU...UUCUU______U__________CAAUG...CAA-5'\n_____________\|_________________\|\n_____________41________________25\n	80 -- 86	26 -- 32	-11.6625 kcal/mol	2.05222 kcal/mol	1.64811 kcal/mol	69 87@LB@ \| \|@LB@5'-UGG...UCACC CCU ACGCU...AUG-3'@LB@ GCAUUU GAAAAUUC@LB@ \|\|\|:\|\| :\|\|\|\|\|\|\|@LB@ CGUGAA UUUUUAAG@LB@3'-UUU...UUCUU U CAAUG...CAA-5'@LB@ \| \|@LB@ 41 25@LB@@LB@@LB@Energy -7.96 kcal/mol@LB@Hybridization Energy -11.6625 kcal/mol@LB@Unfolding Energy - mRNA 2.05222 kcal/mol@LB@Unfolding Energy - sRNA 1.64811 kcal/mol@LB@@LB@Position - mRNA 70 -- 86@LB@Position - sRNA 26 -- 40@LB@Position Seed - mRNA 80 -- 86@LB@Position Seed - sRNA 26 -- 32@LB@
85	0.005692	0.2157	b4052	dnaB	-8.38	0.047402	89 -- 103	26 -- 40	replicative DNA helicase	_____________88______________104\n_____________\|_______________\|\n5'-UGC...CCACC_______U_______AAUUC...CGG-3'\n______________GUGCUUG_GAAAUUC\n______________\|::\|\|\|:_:\|\|\|\|\|\|\n______________CGUGAAU_UUUUAAG\n3'-UUU...UUCUU_______U_______CAAUG...CAA-5'\n_____________\|_______________\|\n_____________41______________25\n	97 -- 103	26 -- 32	-13.045 kcal/mol	3.01413 kcal/mol	1.64811 kcal/mol	88 104@LB@ \| \|@LB@5'-UGC...CCACC U AAUUC...CGG-3'@LB@ GUGCUUG GAAAUUC@LB@ \|::\|\|\|: :\|\|\|\|\|\|@LB@ CGUGAAU UUUUAAG@LB@3'-UUU...UUCUU U CAAUG...CAA-5'@LB@ \| \|@LB@ 41 25@LB@@LB@@LB@Energy -8.38 kcal/mol@LB@Hybridization Energy -13.045 kcal/mol@LB@Unfolding Energy - mRNA 3.01413 kcal/mol@LB@Unfolding Energy - sRNA 1.64811 kcal/mol@LB@@LB@Position - mRNA 89 -- 103@LB@Position - sRNA 26 -- 40@LB@Position Seed - mRNA 97 -- 103@LB@Position Seed - sRNA 26 -- 32@LB@
110	0.009505	0.2693	b0632	dacA	-12.82	0.002052	146 -- 175	26 -- 57	D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 5)	_____________145______________________________176\n_____________\|________________________________\|\n5'-CCU...AGUGC_______AU______________UUUU_____CAUCA...AUA-3'\n______________AUUUGCU__AGUAGG__GCACUU____AAUUC\n______________\|:\|\|\|\|\|__\|\|:\|:\|__\|\|\|\|\|\|____\|\|\|\|\|\n______________UGAACGA__UCGUUC__CGUGAA____UUAAG\n3'-UUU...UACUU_______AU______UU______UUUU_____CAAUG...CAA-5'\n_____________\|________________________________\|\n_____________58_______________________________25\n	146 -- 152	51 -- 57	-23.8315 kcal/mol	4.73353 kcal/mol	6.27605 kcal/mol	145 176@LB@ \| \|@LB@5'-CCU...AGUGC AU UUUU CAUCA...AUA-3'@LB@ AUUUGCU AGUAGG GCACUU AAUUC@LB@ \|:\|\|\|\|\| \|\|:\|:\| \|\|\|\|\|\| \|\|\|\|\|@LB@ UGAACGA UCGUUC CGUGAA UUAAG@LB@3'-UUU...UACUU AU UU UUUU CAAUG...CAA-5'@LB@ \| \|@LB@ 58 25@LB@@LB@@LB@Energy -12.82 kcal/mol@LB@Hybridization Energy -23.8315 kcal/mol@LB@Unfolding Energy - mRNA 4.73353 kcal/mol@LB@Unfolding Energy - sRNA 6.27605 kcal/mol@LB@@LB@Position - mRNA 146 -- 175@LB@Position - sRNA 26 -- 57@LB@Position Seed - mRNA 146 -- 152@LB@Position Seed - sRNA 51 -- 57@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)

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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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