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	Additional homologs
161	0.01751	0.3504	b3394	hofN	-4.92	0.333288	275 -- 286	18 -- 29	DNA catabolic putative fimbrial assembly protein		_____________274__________287\n_____________\|____________\|\n5'-UGG...CUGAU____________UCUGC...CCG-3'\n______________GUUCGUUGCGCC\n______________:\|\|\|\|\|\|:\|:\|\|\n______________UAAGCAAUGUGG\n3'-UUU...UUUUU____________UCCUU...CAA-5'\n_____________\|____________\|\n_____________30___________17\n	275 -- 281	23 -- 29	-17.9024 kcal/mol	4.53191 kcal/mol	8.4513 kcal/mol	274 287@LB@ \| \|@LB@5'-UGG...CUGAU UCUGC...CCG-3'@LB@ GUUCGUUGCGCC@LB@ :\|\|\|\|\|\|:\|:\|\|@LB@ UAAGCAAUGUGG@LB@3'-UUU...UUUUU UCCUU...CAA-5'@LB@ \| \|@LB@ 30 17@LB@@LB@@LB@Energy -4.92 kcal/mol@LB@Hybridization Energy -17.9024 kcal/mol@LB@Unfolding Energy - mRNA 4.53191 kcal/mol@LB@Unfolding Energy - sRNA 8.4513 kcal/mol@LB@@LB@Position - mRNA 275 -- 286@LB@Position - sRNA 18 -- 29@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 23 -- 29@LB@
162	0.01764	0.3508	b0654	gltJ	-6.81	0.123116	18 -- 45	15 -- 42	glutamate/aspartate ABC transporter permease		_____________17___________________________46\n_____________\|____________________________\|\n5'-CAA...UGACA_______GAACU____ACAAGA______GGCGG...UCG-3'\n______________AGGCACU_____AAUU______ACCAGG\n______________\|:\|\|\|\|\|_____\|\|\|\|______\|\|\|\|\|\|\n______________UUCGUGA_____UUAA______UGGUCC\n3'-UUU...CGUUC_______AUUUU____GCAAUG______UUUAG...CAA-5'\n_____________\|____________________________\|\n_____________43___________________________14\n	18 -- 24	36 -- 42	-19.3193 kcal/mol	3.30421 kcal/mol	9.20431 kcal/mol	17 46@LB@ \| \|@LB@5'-CAA...UGACA GAACU ACAAGA GGCGG...UCG-3'@LB@ AGGCACU AAUU ACCAGG@LB@ \|:\|\|\|\|\| \|\|\|\| \|\|\|\|\|\|@LB@ UUCGUGA UUAA UGGUCC@LB@3'-UUU...CGUUC AUUUU GCAAUG UUUAG...CAA-5'@LB@ \| \|@LB@ 43 14@LB@@LB@@LB@Energy -6.81 kcal/mol@LB@Hybridization Energy -19.3193 kcal/mol@LB@Unfolding Energy - mRNA 3.30421 kcal/mol@LB@Unfolding Energy - sRNA 9.20431 kcal/mol@LB@@LB@Position - mRNA 18 -- 45@LB@Position - sRNA 15 -- 42@LB@Position Seed - mRNA 18 -- 24@LB@Position Seed - sRNA 36 -- 42@LB@
163	0.0182	0.3566	b0397	sbcC	-8.10	0.056577	196 -- 210	26 -- 43	exonuclease dsDNA ATP-dependent		_____________195________________211\n_____________\|__________________\|\n5'-GAA...AACAC__________________UCAGC...UUG-3'\n______________GAAGCAU___GAAAAUUC\n______________\|\|\|\|\|\|:___:\|\|\|\|\|\|\|\n______________CUUCGUG___UUUUUAAG\n3'-UUU...UCGUU_______AAU________CAAUG...CAA-5'\n_____________\|__________________\|\n_____________44_________________25\n	204 -- 210	26 -- 32	-13.6528 kcal/mol	1.79109 kcal/mol	3.75931 kcal/mol	195 211@LB@ \| \|@LB@5'-GAA...AACAC UCAGC...UUG-3'@LB@ GAAGCAU GAAAAUUC@LB@ \|\|\|\|\|\|: :\|\|\|\|\|\|\|@LB@ CUUCGUG UUUUUAAG@LB@3'-UUU...UCGUU AAU CAAUG...CAA-5'@LB@ \| \|@LB@ 44 25@LB@@LB@@LB@Energy -8.10 kcal/mol@LB@Hybridization Energy -13.6528 kcal/mol@LB@Unfolding Energy - mRNA 1.79109 kcal/mol@LB@Unfolding Energy - sRNA 3.75931 kcal/mol@LB@@LB@Position - mRNA 196 -- 210@LB@Position - sRNA 26 -- 43@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 26 -- 32@LB@
164	0.01824	0.3566	b1854	pykA	-7.33	0.090768	1 -- 31	25 -- 60	pyruvate kinase II		______________1___________________________________32\n______________\|___________________________________\|\n___________5'-_____GG__CA_____________________A___CGUUU...ACG-3'\n______________GAAGC__GU______AAGAAGCGCU_GAAGGA_UCG\n______________\|\|\|:\|__\|:______\|\|\|\|\|\|\|:\|\|_:\|\|::\|_\|\|\|\n______________CUUUG__CG______UUCUUCGUGA_UUUUUU_AGC\n3'-UUU...CCCUA_____AA__AAUUCG__________A______A___AAUGU...CAA-5'\n_____________\|____________________________________\|\n_____________61___________________________________24\n	15 -- 21	36 -- 42	-23.5606 kcal/mol	9.95433 kcal/mol	6.27609 kcal/mol	1 32@LB@ \| \|@LB@ 5'- GG CA A CGUUU...ACG-3'@LB@ GAAGC GU AAGAAGCGCU GAAGGA UCG@LB@ \|\|\|:\| \|: \|\|\|\|\|\|\|:\|\| :\|\|::\| \|\|\|@LB@ CUUUG CG UUCUUCGUGA UUUUUU AGC@LB@3'-UUU...CCCUA AA AAUUCG A A AAUGU...CAA-5'@LB@ \| \|@LB@ 61 24@LB@@LB@@LB@Energy -7.33 kcal/mol@LB@Hybridization Energy -23.5606 kcal/mol@LB@Unfolding Energy - mRNA 9.95433 kcal/mol@LB@Unfolding Energy - sRNA 6.27609 kcal/mol@LB@@LB@Position - mRNA 1 -- 31@LB@Position - sRNA 25 -- 60@LB@Position Seed - mRNA 15 -- 21@LB@Position Seed - sRNA 36 -- 42@LB@
165	0.01827	0.3566	b2937	speB	-7.30	0.092452	5 -- 22	25 -- 41	agmatinase		_____________4__________________23\n_____________\|__________________\|\n_______5'-CAAC___UC_____________AGGCA...CAG-3'\n______________AGU__CUUGAAGAGUUCG\n______________\|\|:__\|\|\|:\|\|:\|:\|\|\|\|\n______________UCG__GAAUUUUUUAAGC\n3'-UUU...GUUCU___U______________AAUGU...CAA-5'\n_____________\|__________________\|\n_____________42_________________24\n	16 -- 22	25 -- 31	-14.9284 kcal/mol	5.98061 kcal/mol	1.64839 kcal/mol	4 23@LB@ \| \|@LB@ 5'-CAAC UC AGGCA...CAG-3'@LB@ AGU CUUGAAGAGUUCG@LB@ \|\|: \|\|\|:\|\|:\|:\|\|\|\|@LB@ UCG GAAUUUUUUAAGC@LB@3'-UUU...GUUCU U AAUGU...CAA-5'@LB@ \| \|@LB@ 42 24@LB@@LB@@LB@Energy -7.30 kcal/mol@LB@Hybridization Energy -14.9284 kcal/mol@LB@Unfolding Energy - mRNA 5.98061 kcal/mol@LB@Unfolding Energy - sRNA 1.64839 kcal/mol@LB@@LB@Position - mRNA 5 -- 22@LB@Position - sRNA 25 -- 41@LB@Position Seed - mRNA 16 -- 22@LB@Position Seed - sRNA 25 -- 31@LB@
166	0.01873	0.3614	b0473	htpG	-6.61	0.137913	119 -- 133	26 -- 39	protein refolding molecular co-chaperone Hsp90 Hsp70-dependent; heat-shock protein; ATPase		_____________118_____________134\n_____________\|_______________\|\n5'-UCA...GCUCU_________UU____UCCCU...GUG-3'\n______________CGCUUGAAA__AUUC\n______________\|:\|\|\|:\|\|\|__\|\|\|\|\n______________GUGAAUUUU__UAAG\n3'-UUU...UCUUC_________U_____CAAUG...CAA-5'\n_____________\|_______________\|\n_____________40______________25\n	121 -- 127	31 -- 37	-10.0825 kcal/mol	1.82368 kcal/mol	1.64668 kcal/mol	118 134@LB@ \| \|@LB@5'-UCA...GCUCU UU UCCCU...GUG-3'@LB@ CGCUUGAAA AUUC@LB@ \|:\|\|\|:\|\|\| \|\|\|\|@LB@ GUGAAUUUU UAAG@LB@3'-UUU...UCUUC U CAAUG...CAA-5'@LB@ \| \|@LB@ 40 25@LB@@LB@@LB@Energy -6.61 kcal/mol@LB@Hybridization Energy -10.0825 kcal/mol@LB@Unfolding Energy - mRNA 1.82368 kcal/mol@LB@Unfolding Energy - sRNA 1.64668 kcal/mol@LB@@LB@Position - mRNA 119 -- 133@LB@Position - sRNA 26 -- 39@LB@Position Seed - mRNA 121 -- 127@LB@Position Seed - sRNA 31 -- 37@LB@
167	0.01879	0.3614	b4383	deoB	-8.94	0.033088	90 -- 118	37 -- 59	phosphopentomutase		_____________89____________________________119\n_____________\|_____________________________\|\n5'-AGG...CAAUU________CGAUA_____CC__A______ACCAA...AUA-3'\n______________AAACUUGC_____AAGCA__GG_AAGCAC\n______________\|\|\|\|\|\|\|\|_____\|\|\|\|\|__:\|_\|\|\|\|\|\|\n______________UUUGAACG_____UUCGU__UC_UUCGUG\n3'-UUU...CCUAC________AA___________________AAUUU...CAA-5'\n_____________\|_____________________________\|\n_____________60____________________________36\n	91 -- 97	52 -- 58	-21.3309 kcal/mol	6.14475 kcal/mol	6.24627 kcal/mol	89 119@LB@ \| \|@LB@5'-AGG...CAAUU CGAUA CC A ACCAA...AUA-3'@LB@ AAACUUGC AAGCA GG AAGCAC@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\| :\| \|\|\|\|\|\|@LB@ UUUGAACG UUCGU UC UUCGUG@LB@3'-UUU...CCUAC AA AAUUU...CAA-5'@LB@ \| \|@LB@ 60 36@LB@@LB@@LB@Energy -8.94 kcal/mol@LB@Hybridization Energy -21.3309 kcal/mol@LB@Unfolding Energy - mRNA 6.14475 kcal/mol@LB@Unfolding Energy - sRNA 6.24627 kcal/mol@LB@@LB@Position - mRNA 90 -- 118@LB@Position - sRNA 37 -- 59@LB@Position Seed - mRNA 91 -- 97@LB@Position Seed - sRNA 52 -- 58@LB@
168	0.01885	0.3614	b1792	yeaO	-5.97	0.195997	133 -- 142	25 -- 34	DUF488 family protein		_____________132________143\n_____________\|__________\|\n5'-UGU...AGACA__________CUAAU...CCG-3'\n______________AAGAAAUUCG\n______________\|\|:\|\|\|\|\|\|\|\n______________UUUUUUAAGC\n3'-UUU...GUGAA__________AAUGU...CAA-5'\n_____________\|__________\|\n_____________35_________24\n	136 -- 142	25 -- 31	-8.43117 kcal/mol	1.28773 kcal/mol	1.16883 kcal/mol	132 143@LB@ \| \|@LB@5'-UGU...AGACA CUAAU...CCG-3'@LB@ AAGAAAUUCG@LB@ \|\|:\|\|\|\|\|\|\|@LB@ UUUUUUAAGC@LB@3'-UUU...GUGAA AAUGU...CAA-5'@LB@ \| \|@LB@ 35 24@LB@@LB@@LB@Energy -5.97 kcal/mol@LB@Hybridization Energy -8.43117 kcal/mol@LB@Unfolding Energy - mRNA 1.28773 kcal/mol@LB@Unfolding Energy - sRNA 1.16883 kcal/mol@LB@@LB@Position - mRNA 133 -- 142@LB@Position - sRNA 25 -- 34@LB@Position Seed - mRNA 136 -- 142@LB@Position Seed - sRNA 25 -- 31@LB@
169	0.01902	0.3625	b0858	ybjO	-5.59	0.239654	140 -- 156	25 -- 43	DUF2593 family inner membrane protein		_____________139__________________157\n_____________\|____________________\|\n5'-AUG...UGGCU____A_______________CCAAC...UUA-3'\n______________GAAG_CACU___AAAAUUUG\n______________\|\|\|\|_\|\|\|\|___\|\|\|\|\|\|:\|\n______________CUUC_GUGA___UUUUAAGC\n3'-UUU...UCGUU_________AUU________AAUGU...CAA-5'\n_____________\|____________________\|\n_____________44___________________24\n	150 -- 156	25 -- 31	-11.6219 kcal/mol	2.26879 kcal/mol	3.76226 kcal/mol	139 157@LB@ \| \|@LB@5'-AUG...UGGCU A CCAAC...UUA-3'@LB@ GAAG CACU AAAAUUUG@LB@ \|\|\|\| \|\|\|\| \|\|\|\|\|\|:\|@LB@ CUUC GUGA UUUUAAGC@LB@3'-UUU...UCGUU AUU AAUGU...CAA-5'@LB@ \| \|@LB@ 44 24@LB@@LB@@LB@Energy -5.59 kcal/mol@LB@Hybridization Energy -11.6219 kcal/mol@LB@Unfolding Energy - mRNA 2.26879 kcal/mol@LB@Unfolding Energy - sRNA 3.76226 kcal/mol@LB@@LB@Position - mRNA 140 -- 156@LB@Position - sRNA 25 -- 43@LB@Position Seed - mRNA 150 -- 156@LB@Position Seed - sRNA 25 -- 31@LB@
170	0.01916	0.363	b1202	ycgV	-6.78	0.125661	82 -- 88	39 -- 45	putative adhesin	b2647	_____________81______89\n_____________\|_______\|\n5'-ACU...UCUCU_______UCAUC...UUG-3'\n______________GAGAAGC\n______________:\|\|\|\|\|\|\n______________UUCUUCG\n3'-UUU...AUUCG_______UGAAU...CAA-5'\n_____________\|_______\|\n_____________46______38\n	82 -- 88	39 -- 45	-7.60605 kcal/mol	0.31609 kcal/mol	0.514773 kcal/mol	81 89@LB@ \| \|@LB@5'-ACU...UCUCU UCAUC...UUG-3'@LB@ GAGAAGC@LB@ :\|\|\|\|\|\|@LB@ UUCUUCG@LB@3'-UUU...AUUCG UGAAU...CAA-5'@LB@ \| \|@LB@ 46 38@LB@@LB@@LB@Energy -6.78 kcal/mol@LB@Hybridization Energy -7.60605 kcal/mol@LB@Unfolding Energy - mRNA 0.31609 kcal/mol@LB@Unfolding Energy - sRNA 0.514773 kcal/mol@LB@@LB@Position - mRNA 82 -- 88@LB@Position - sRNA 39 -- 45@LB@Position Seed - mRNA 82 -- 88@LB@Position Seed - sRNA 39 -- 45@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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