Input and runtime details for job 6793193 (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 6793193 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:27:03 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:32 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:26:02 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:26:10 CET 2018
	Job Completed		@ Fri Feb 16 21:26:45 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6793193&toolName=CopraRNA ( 30 days expiry )

Description of the job

RprA

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
149	0.006962	0.1638	b0935	ssuD	-8.45	0.421381	102 -- 123	48 -- 71	alkanesulfonate monooxygenase FMNH(2)-dependent		_____________101______________________124\n_____________\|________________________\|\n5'-AAA...CAGCA___A_______A____________GAAAA...AAC-3'\n______________GCA_ACGGCAG_UC__UGUUUUAU\n______________:\|\|_\|\|:\|\|\|:_\|\|__\|\|\|\|\|:\|:\n______________UGU_UGUCGUU_AG__ACAAAGUG\n3'-UUU...UCUGA___G_______A__CA________AGUCC...GCA-5'\n_____________\|________________________\|\n_____________72_______________________47\n	117 -- 123	48 -- 54	-17.2917 kcal/mol	5.19453 kcal/mol	3.65243 kcal/mol	101 124@LB@ \| \|@LB@5'-AAA...CAGCA A A GAAAA...AAC-3'@LB@ GCA ACGGCAG UC UGUUUUAU@LB@ :\|\| \|\|:\|\|\|: \|\| \|\|\|\|\|:\|:@LB@ UGU UGUCGUU AG ACAAAGUG@LB@3'-UUU...UCUGA G A CA AGUCC...GCA-5'@LB@ \| \|@LB@ 72 47@LB@@LB@@LB@Energy -8.45 kcal/mol@LB@Hybridization Energy -17.2917 kcal/mol@LB@Unfolding Energy - mRNA 5.19453 kcal/mol@LB@Unfolding Energy - sRNA 3.65243 kcal/mol@LB@@LB@Position - mRNA 102 -- 123@LB@Position - sRNA 48 -- 71@LB@Position Seed - mRNA 117 -- 123@LB@Position Seed - sRNA 48 -- 54@LB@
8	3.984e-05	0.01752	b2752	cysD	-11.53	0.128779	103 -- 132	45 -- 74	sulfate adenylyltransferase subunit 2		_____________102____________________________133\n_____________\|______________________________\|\n5'-GCC...AAGGA_____U___UC_____G__AA_________UUCUC...UCU-3'\n______________ACUAC_CAU__UAAUU_GU__UUUCAUUCG\n______________\|\|\|\|\|_\|\|:__:\|\|\|\|_\|\|__\|\|\|\|\|:\|\|:\n______________UGAUG_GUG__GUUAA_CA__AAAGUGAGU\n3'-UUU...GUUUC_____U___UC_____G__AC_________CCCCU...GCA-5'\n_____________\|______________________________\|\n_____________75_____________________________44\n	126 -- 132	45 -- 51	-20.8412 kcal/mol	5.57115 kcal/mol	3.74056 kcal/mol	102 133@LB@ \| \|@LB@5'-GCC...AAGGA U UC G AA UUCUC...UCU-3'@LB@ ACUAC CAU UAAUU GU UUUCAUUCG@LB@ \|\|\|\|\| \|\|: :\|\|\|\| \|\| \|\|\|\|\|:\|\|:@LB@ UGAUG GUG GUUAA CA AAAGUGAGU@LB@3'-UUU...GUUUC U UC G AC CCCCU...GCA-5'@LB@ \| \|@LB@ 75 44@LB@@LB@@LB@Energy -11.53 kcal/mol@LB@Hybridization Energy -20.8412 kcal/mol@LB@Unfolding Energy - mRNA 5.57115 kcal/mol@LB@Unfolding Energy - sRNA 3.74056 kcal/mol@LB@@LB@Position - mRNA 103 -- 132@LB@Position - sRNA 45 -- 74@LB@Position Seed - mRNA 126 -- 132@LB@Position Seed - sRNA 45 -- 51@LB@
19	0.0001526	0.02826	b1040	csgD	-18.47	0.001904	103 -- 117	60 -- 74	csgBAC operon transcriptional regulator	b3520	_____________102_____________118\n_____________\|_______________\|\n5'-UUA...UUAUU_______________GCAAC...CGC-3'\n______________ACUACACACAGCAGU\n______________\|\|\|\|\|\|\|\|\|\|\|\|\|:\|\n______________UGAUGUGUGUCGUUA\n3'-UUU...GUUUC_______________AGCAA...GCA-5'\n_____________\|_______________\|\n_____________75______________59\n	111 -- 117	60 -- 66	-23.4761 kcal/mol	1.72592 kcal/mol	3.27997 kcal/mol	102 118@LB@ \| \|@LB@5'-UUA...UUAUU GCAAC...CGC-3'@LB@ ACUACACACAGCAGU@LB@ \|\|\|\|\|\|\|\|\|\|\|\|\|:\|@LB@ UGAUGUGUGUCGUUA@LB@3'-UUU...GUUUC AGCAA...GCA-5'@LB@ \| \|@LB@ 75 59@LB@@LB@@LB@Energy -18.47 kcal/mol@LB@Hybridization Energy -23.4761 kcal/mol@LB@Unfolding Energy - mRNA 1.72592 kcal/mol@LB@Unfolding Energy - sRNA 3.27997 kcal/mol@LB@@LB@Position - mRNA 103 -- 117@LB@Position - sRNA 60 -- 74@LB@Position Seed - mRNA 111 -- 117@LB@Position Seed - sRNA 60 -- 66@LB@
67	0.002719	0.1417	b3454	livF	-11.67	0.120634	106 -- 122	40 -- 58	branched-chain amino acid ABC transporter ATPase		_____________105_________________123\n_____________\|___________________\|\n5'-AGA...AUUUA___GG_____A________CGCCG...UUG-3'\n______________CGU____UCA_UCAGGGGA\n______________\|\|\|____\|\|\|_\|\|\|\|\|\|\|\|\n______________GCA____AGU_AGUCCCCU\n3'-UUU...GUUAA___ACAA___G________AAAGG...GCA-5'\n_____________\|___________________\|\n_____________59__________________39\n	116 -- 122	40 -- 46	-19.8465 kcal/mol	5.75116 kcal/mol	2.42241 kcal/mol	105 123@LB@ \| \|@LB@5'-AGA...AUUUA GG A CGCCG...UUG-3'@LB@ CGU UCA UCAGGGGA@LB@ \|\|\| \|\|\| \|\|\|\|\|\|\|\|@LB@ GCA AGU AGUCCCCU@LB@3'-UUU...GUUAA ACAA G AAAGG...GCA-5'@LB@ \| \|@LB@ 59 39@LB@@LB@@LB@Energy -11.67 kcal/mol@LB@Hybridization Energy -19.8465 kcal/mol@LB@Unfolding Energy - mRNA 5.75116 kcal/mol@LB@Unfolding Energy - sRNA 2.42241 kcal/mol@LB@@LB@Position - mRNA 106 -- 122@LB@Position - sRNA 40 -- 58@LB@Position Seed - mRNA 116 -- 122@LB@Position Seed - sRNA 40 -- 46@LB@
85	0.003677	0.1509	b0813	rhtA	-9.71	0.273689	106 -- 123	34 -- 46	threonine and homoserine efflux system		_____________105________________124\n_____________\|__________________\|\n5'-CAG...CAAAA_______AAAUU______ACAAA...CAC-3'\n______________CGGGGGA_____UUUUCA\n______________\|:\|\|\|\|\|_____\|\|\|:\|\|\n______________GUCCCCU_____AAAGGU\n3'-UUU...AGUGA__________________ACGAA...GCA-5'\n_____________\|__________________\|\n_____________47_________________33\n	106 -- 112	40 -- 46	-14.6812 kcal/mol	3.4305 kcal/mol	1.54427 kcal/mol	105 124@LB@ \| \|@LB@5'-CAG...CAAAA AAAUU ACAAA...CAC-3'@LB@ CGGGGGA UUUUCA@LB@ \|:\|\|\|\|\| \|\|\|:\|\|@LB@ GUCCCCU AAAGGU@LB@3'-UUU...AGUGA ACGAA...GCA-5'@LB@ \| \|@LB@ 47 33@LB@@LB@@LB@Energy -9.71 kcal/mol@LB@Hybridization Energy -14.6812 kcal/mol@LB@Unfolding Energy - mRNA 3.4305 kcal/mol@LB@Unfolding Energy - sRNA 1.54427 kcal/mol@LB@@LB@Position - mRNA 106 -- 123@LB@Position - sRNA 34 -- 46@LB@Position Seed - mRNA 106 -- 112@LB@Position Seed - sRNA 40 -- 46@LB@
92	0.004122	0.1538	b3912	cpxR	-15.13	0.019325	106 -- 130	39 -- 76	response regulator in two-component regulatory system with CpxA		_____________105_____________________________________131\n_____________\|_______________________________________\|\n5'-UGA...GAUUC________A___U__________________________GUAAA...AUG-3'\n______________AGGCUGCA_ACA_GCG______________UCAGGGGGU\n______________\|\|:\|\|:\|\|_\|\|\|_\|\|:______________\|\|\|\|\|\|\|:\|\n______________UCUGAUGU_UGU_CGU______________AGUCCCCUA\n3'-UUU...CCGUU________G_______UAAGCAACAAAGUG_________AAGGU...GCA-5'\n_____________\|_______________________________________\|\n_____________77______________________________________38\n	124 -- 130	39 -- 45	-28.779 kcal/mol	8.86764 kcal/mol	4.77949 kcal/mol	105 131@LB@ \| \|@LB@5'-UGA...GAUUC A U GUAAA...AUG-3'@LB@ AGGCUGCA ACA GCG UCAGGGGGU@LB@ \|\|:\|\|:\|\| \|\|\| \|\|: \|\|\|\|\|\|\|:\|@LB@ UCUGAUGU UGU CGU AGUCCCCUA@LB@3'-UUU...CCGUU G UAAGCAACAAAGUG AAGGU...GCA-5'@LB@ \| \|@LB@ 77 38@LB@@LB@@LB@Energy -15.13 kcal/mol@LB@Hybridization Energy -28.779 kcal/mol@LB@Unfolding Energy - mRNA 8.86764 kcal/mol@LB@Unfolding Energy - sRNA 4.77949 kcal/mol@LB@@LB@Position - mRNA 106 -- 130@LB@Position - sRNA 39 -- 76@LB@Position Seed - mRNA 124 -- 130@LB@Position Seed - sRNA 39 -- 45@LB@
111	0.004903	0.1545	b1735	chbR	-11.17	0.151186	109 -- 138	30 -- 50	repressor of chb operon for N N'-diacetylchitobiose utilization		_____________108____________________________139\n_____________\|______________________________\|\n5'-GAU...GUCCA________AUCAUUUAAU__CG________UGCGC...CUG-3'\n______________CGCUCAGG__________GA__UCCAUGCU\n______________\|:\|\|\|\|\|\|__________\|\|__\|\|\|\|\|\|\|\|\n______________GUGAGUCC__________CU__AGGUACGA\n3'-UUU...ACAAA________C___________AA________AUAUU...GCA-5'\n_____________\|______________________________\|\n_____________51_____________________________29\n	132 -- 138	30 -- 36	-23.5874 kcal/mol	7.28235 kcal/mol	5.13509 kcal/mol	108 139@LB@ \| \|@LB@5'-GAU...GUCCA AUCAUUUAAU CG UGCGC...CUG-3'@LB@ CGCUCAGG GA UCCAUGCU@LB@ \|:\|\|\|\|\|\| \|\| \|\|\|\|\|\|\|\|@LB@ GUGAGUCC CU AGGUACGA@LB@3'-UUU...ACAAA C AA AUAUU...GCA-5'@LB@ \| \|@LB@ 51 29@LB@@LB@@LB@Energy -11.17 kcal/mol@LB@Hybridization Energy -23.5874 kcal/mol@LB@Unfolding Energy - mRNA 7.28235 kcal/mol@LB@Unfolding Energy - sRNA 5.13509 kcal/mol@LB@@LB@Position - mRNA 109 -- 138@LB@Position - sRNA 30 -- 50@LB@Position Seed - mRNA 132 -- 138@LB@Position Seed - sRNA 30 -- 36@LB@
49	0.00161	0.1153	b0655	gltI	-14.54	0.027470	112 -- 169	31 -- 74	glutamate/aspartate periplasmic binding protein		_____________111________________________________________________________170\n_____________\|__________________________________________________________\|\n5'-AUU...ACAAC_______AAUAAAGUU____A____AACAACACAAA______CAAC____A_______GUUCU...UGG-3'\n______________ACUGCAC_________GCAG_CGAU___________CACUCA____GGGU_UCCAUGC\n______________\|\|\|:\|\|\|_________:\|\|\|_\|:\|\|___________\|\|\|\|\|\|____\|\|:\|_\|\|\|\|\|\|\|\n______________UGAUGUG_________UGUC_GUUA___________GUGAGU____CCUA_AGGUACG\n3'-UUU...GUUUC_________________________AGCAACAAA________CC______A_______AAUAU...GCA-5'\n_____________\|__________________________________________________________\|\n_____________75_________________________________________________________30\n	163 -- 169	31 -- 37	-33.5884 kcal/mol	11.7902 kcal/mol	7.26183 kcal/mol	111 170@LB@ \| \|@LB@5'-AUU...ACAAC AAUAAAGUU A AACAACACAAA CAAC A GUUCU...UGG-3'@LB@ ACUGCAC GCAG CGAU CACUCA GGGU UCCAUGC@LB@ \|\|\|:\|\|\| :\|\|\| \|:\|\| \|\|\|\|\|\| \|\|:\| \|\|\|\|\|\|\|@LB@ UGAUGUG UGUC GUUA GUGAGU CCUA AGGUACG@LB@3'-UUU...GUUUC AGCAACAAA CC A AAUAU...GCA-5'@LB@ \| \|@LB@ 75 30@LB@@LB@@LB@Energy -14.54 kcal/mol@LB@Hybridization Energy -33.5884 kcal/mol@LB@Unfolding Energy - mRNA 11.7902 kcal/mol@LB@Unfolding Energy - sRNA 7.26183 kcal/mol@LB@@LB@Position - mRNA 112 -- 169@LB@Position - sRNA 31 -- 74@LB@Position Seed - mRNA 163 -- 169@LB@Position Seed - sRNA 31 -- 37@LB@
191	0.009733	0.1776	b0190	yaeQ	-9.83	0.261410	113 -- 128	45 -- 75	PDDEXK superfamily protein		_____________112_____________________________129\n_____________\|_______________________________\|\n5'-UAC...AAGGU_______________________________UUUCU...CUU-3'\n______________GACUAUAC_CA______________CACUCA\n______________\|\|\|\|\|:\|\|_\|\|______________\|\|\|\|\|\|\n______________CUGAUGUG_GU______________GUGAGU\n3'-UUU...CGUUU________U__CGUUAAGCAACAAA______CCCCU...GCA-5'\n_____________\|_______________________________\|\n_____________76______________________________44\n	114 -- 120	68 -- 74	-15.3898 kcal/mol	1.82074 kcal/mol	3.74078 kcal/mol	112 129@LB@ \| \|@LB@5'-UAC...AAGGU UUUCU...CUU-3'@LB@ GACUAUAC CA CACUCA@LB@ \|\|\|\|\|:\|\| \|\| \|\|\|\|\|\|@LB@ CUGAUGUG GU GUGAGU@LB@3'-UUU...CGUUU U CGUUAAGCAACAAA CCCCU...GCA-5'@LB@ \| \|@LB@ 76 44@LB@@LB@@LB@Energy -9.83 kcal/mol@LB@Hybridization Energy -15.3898 kcal/mol@LB@Unfolding Energy - mRNA 1.82074 kcal/mol@LB@Unfolding Energy - sRNA 3.74078 kcal/mol@LB@@LB@Position - mRNA 113 -- 128@LB@Position - sRNA 45 -- 75@LB@Position Seed - mRNA 114 -- 120@LB@Position Seed - sRNA 68 -- 74@LB@
131	0.005914	0.1577	b2360	yfdQ	-15.68	0.013816	114 -- 143	46 -- 74	CPS-53 (KpLE1) prophage; uncharacterized protein		_____________113____________________________144\n_____________\|______________________________\|\n5'-UCC...GGAAA___C__________G__AUUAAUA______UUAAU...CUG-3'\n______________ACU_CGCGCAGCAG_UC_______UCAUUC\n______________\|\|\|_\|:\|:\|\|\|\|\|:_\|\|_______\|\|\|:\|\|\n______________UGA_GUGUGUCGUU_AG_______AGUGAG\n3'-UUU...GUUUC___U__________A__CAACAA_______UCCCC...GCA-5'\n_____________\|______________________________\|\n_____________75_____________________________45\n	121 -- 127	61 -- 67	-23.4619 kcal/mol	4.06011 kcal/mol	3.72594 kcal/mol	113 144@LB@ \| \|@LB@5'-UCC...GGAAA C G AUUAAUA UUAAU...CUG-3'@LB@ ACU CGCGCAGCAG UC UCAUUC@LB@ \|\|\| \|:\|:\|\|\|\|\|: \|\| \|\|\|:\|\|@LB@ UGA GUGUGUCGUU AG AGUGAG@LB@3'-UUU...GUUUC U A CAACAA UCCCC...GCA-5'@LB@ \| \|@LB@ 75 45@LB@@LB@@LB@Energy -15.68 kcal/mol@LB@Hybridization Energy -23.4619 kcal/mol@LB@Unfolding Energy - mRNA 4.06011 kcal/mol@LB@Unfolding Energy - sRNA 3.72594 kcal/mol@LB@@LB@Position - mRNA 114 -- 143@LB@Position - sRNA 46 -- 74@LB@Position Seed - mRNA 121 -- 127@LB@Position Seed - sRNA 61 -- 67@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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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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