Input and runtime details for job 5172788 (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 5172788 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:22:50 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:35:14 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:35:22 CET 2018
	Job Completed		@ Fri Feb 16 20:35:53 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5172788&toolName=CopraRNA ( 30 days expiry )

Description of the job

CyaR

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
70	0.00193	0.09081	b1823	cspC	-11.95	0.067388	30 -- 62	1 -- 36	stress protein member of the CspA-family		_____________29___________________________________63\n_____________\|____________________________________\|\n5'-UAU...AACGA____________UG______U__GGCA_________AAAGA...UCU-3'\n______________GGUACAGUU__C__UUUAUG_GU_____UUUUCAGU\n______________\|\|\|\|\|\|\|:\|__\|__\|\|\|\|\|\|_\|\|_____\|\|\|\|\|\|\|:\n______________CCAUGUCGA__G__AAAUAC_CA_____AAAAGUCG\n3'-UUU...AAGGA_________UC_UA______C__AUACA________-5'\n_____________\|___________________________________\|\n_____________37__________________________________1\n	56 -- 62	1 -- 7	-24.9618 kcal/mol	11.5162 kcal/mol	1.49509 kcal/mol	29 63@LB@ \| \|@LB@5'-UAU...AACGA UG U GGCA AAAGA...UCU-3'@LB@ GGUACAGUU C UUUAUG GU UUUUCAGU@LB@ \|\|\|\|\|\|\|:\| \| \|\|\|\|\|\| \|\| \|\|\|\|\|\|\|:@LB@ CCAUGUCGA G AAAUAC CA AAAAGUCG@LB@3'-UUU...AAGGA UC UA C AUACA -5'@LB@ \| \|@LB@ 37 1@LB@@LB@@LB@Energy -11.95 kcal/mol@LB@Hybridization Energy -24.9618 kcal/mol@LB@Unfolding Energy - mRNA 11.5162 kcal/mol@LB@Unfolding Energy - sRNA 1.49509 kcal/mol@LB@@LB@Position - mRNA 30 -- 62@LB@Position - sRNA 1 -- 36@LB@Position Seed - mRNA 56 -- 62@LB@Position Seed - sRNA 1 -- 7@LB@
82	0.002694	0.1082	b2474	tmcA	-11.34	0.091143	115 -- 147	1 -- 34	elongator methionine tRNA (ac4C34) acetyltransferase		_____________114________________________________148\n_____________\|__________________________________\|\n5'-GAU...AACGC__________UUAAACGU____UCGACAG_____GAUCC...UUG-3'\n______________UACAGCUGGU________GGUU________CGGC\n______________\|\|\|\|\|\|\|:\|:________\|\|\|\|________\|:\|\|\n______________AUGUCGAUCG________CCAA________GUCG\n3'-UUU...GGACC__________UAAAAUAC____UACAAAAA____-5'\n_____________\|_________________________________\|\n_____________35________________________________1\n	118 -- 124	25 -- 31	-23.7384 kcal/mol	10.9014 kcal/mol	1.49507 kcal/mol	114 148@LB@ \| \|@LB@5'-GAU...AACGC UUAAACGU UCGACAG GAUCC...UUG-3'@LB@ UACAGCUGGU GGUU CGGC@LB@ \|\|\|\|\|\|\|:\|: \|\|\|\| \|:\|\|@LB@ AUGUCGAUCG CCAA GUCG@LB@3'-UUU...GGACC UAAAAUAC UACAAAAA -5'@LB@ \| \|@LB@ 35 1@LB@@LB@@LB@Energy -11.34 kcal/mol@LB@Hybridization Energy -23.7384 kcal/mol@LB@Unfolding Energy - mRNA 10.9014 kcal/mol@LB@Unfolding Energy - sRNA 1.49507 kcal/mol@LB@@LB@Position - mRNA 115 -- 147@LB@Position - sRNA 1 -- 34@LB@Position Seed - mRNA 118 -- 124@LB@Position Seed - sRNA 25 -- 31@LB@
85	0.002796	0.1082	b4536	yobH	-12.68	0.045962	237 -- 287	1 -- 38	uncharacterized protein		_____________236__________________________________________________288\n_____________\|____________________________________________________\|\n5'-CAA...UAGCA_________AUAGGAUUAUUA__C____GA______C___U__A__GGA___AAAGA...CCG-3'\n______________CUGGUAUGG____________CU_AGCG___UAUGG_GUU_UG_UU___AGC\n______________\|\|\|\|\|\|::\|____________\|\|_\|\|\|:___\|\|\|\|\|_\|\|\|_\|\|_\|\|___\|\|\|\n______________GACCAUGUC____________GA_UCGU___AUACC_CAA_AC_AA___UCG\n3'-UUU...CCAAG____________________________AAA_________U__A__AAG___-5'\n_____________\|___________________________________________________\|\n_____________39__________________________________________________1\n	239 -- 245	30 -- 36	-25.5821 kcal/mol	8.3664 kcal/mol	4.54019 kcal/mol	236 288@LB@ \| \|@LB@5'-CAA...UAGCA AUAGGAUUAUUA C GA C U A GGA AAAGA...CCG-3'@LB@ CUGGUAUGG CU AGCG UAUGG GUU UG UU AGC@LB@ \|\|\|\|\|\|::\| \|\| \|\|\|: \|\|\|\|\| \|\|\| \|\| \|\| \|\|\|@LB@ GACCAUGUC GA UCGU AUACC CAA AC AA UCG@LB@3'-UUU...CCAAG AAA U A AAG -5'@LB@ \| \|@LB@ 39 1@LB@@LB@@LB@Energy -12.68 kcal/mol@LB@Hybridization Energy -25.5821 kcal/mol@LB@Unfolding Energy - mRNA 8.3664 kcal/mol@LB@Unfolding Energy - sRNA 4.54019 kcal/mol@LB@@LB@Position - mRNA 237 -- 287@LB@Position - sRNA 1 -- 38@LB@Position Seed - mRNA 239 -- 245@LB@Position Seed - sRNA 30 -- 36@LB@
88	0.002837	0.1082	b4377	yjjU	-10.09	0.160689	120 -- 144	1 -- 33	putative patatin-like family phospholipase		_____________119________________________________145\n_____________\|__________________________________\|\n5'-AGG...GUCCA____A___________C_________________GAAUA...GAC-3'\n______________GCGG_CUGGC_UUUUG_GG________UUUUAGC\n______________:\|:\|_\|\|:\|\|_\|\|\|\|:_\|\|________\|\|\|:\|\|\|\n______________UGUC_GAUCG_AAAAU_CC________AAAGUCG\n3'-UUU...GACCA__________U_____A__CAAUACAA_______-5'\n_____________\|_________________________________\|\n_____________34________________________________1\n	138 -- 144	1 -- 7	-20.956 kcal/mol	9.37145 kcal/mol	1.49313 kcal/mol	119 145@LB@ \| \|@LB@5'-AGG...GUCCA A C GAAUA...GAC-3'@LB@ GCGG CUGGC UUUUG GG UUUUAGC@LB@ :\|:\| \|\|:\|\| \|\|\|\|: \|\| \|\|\|:\|\|\|@LB@ UGUC GAUCG AAAAU CC AAAGUCG@LB@3'-UUU...GACCA U A CAAUACAA -5'@LB@ \| \|@LB@ 34 1@LB@@LB@@LB@Energy -10.09 kcal/mol@LB@Hybridization Energy -20.956 kcal/mol@LB@Unfolding Energy - mRNA 9.37145 kcal/mol@LB@Unfolding Energy - sRNA 1.49313 kcal/mol@LB@@LB@Position - mRNA 120 -- 144@LB@Position - sRNA 1 -- 33@LB@Position Seed - mRNA 138 -- 144@LB@Position Seed - sRNA 1 -- 7@LB@
99	0.003591	0.1219	b0533	sfmH	-7.90	0.364135	113 -- 140	1 -- 34	FimA homolog function unknown	b3145 b0941	_____________112________________________________141\n_____________\|__________________________________\|\n5'-GAC...AAGCU______A___CGUCACU_________________AGUUU...AUA-3'\n______________UACAGC_AGC_________GUUA____UUUCGGC\n______________\|\|\|\|\|\|_\|\|\|_________\|\|\|\|____\|\|\|\|:\|\|\n______________AUGUCG_UCG_________CAAU____AAAGUCG\n3'-UUU...GGACC______A___UAAAAUACC____ACAA_______-5'\n_____________\|_________________________________\|\n_____________35________________________________1\n	134 -- 140	1 -- 7	-18.6412 kcal/mol	9.24123 kcal/mol	1.49507 kcal/mol	112 141@LB@ \| \|@LB@5'-GAC...AAGCU A CGUCACU AGUUU...AUA-3'@LB@ UACAGC AGC GUUA UUUCGGC@LB@ \|\|\|\|\|\| \|\|\| \|\|\|\| \|\|\|\|:\|\|@LB@ AUGUCG UCG CAAU AAAGUCG@LB@3'-UUU...GGACC A UAAAAUACC ACAA -5'@LB@ \| \|@LB@ 35 1@LB@@LB@@LB@Energy -7.90 kcal/mol@LB@Hybridization Energy -18.6412 kcal/mol@LB@Unfolding Energy - mRNA 9.24123 kcal/mol@LB@Unfolding Energy - sRNA 1.49507 kcal/mol@LB@@LB@Position - mRNA 113 -- 140@LB@Position - sRNA 1 -- 34@LB@Position Seed - mRNA 134 -- 140@LB@Position Seed - sRNA 1 -- 7@LB@
101	0.003756	0.123	b2972	pppA	-13.47	0.029286	211 -- 222	1 -- 12	bifunctional prepilin leader peptidase/ methylase		_____________210__________223\n_____________\|____________\|\n5'-UAA...UUUUG____________AAUAC...GGC-3'\n______________AUGUUUUUCAGC\n______________\|\|\|\|\|\|\|\|\|\|\|\|\n______________UACAAAAAGUCG\n3'-UUU...CCCAA____________-5'\n_____________\|___________\|\n_____________13__________1\n	216 -- 222	1 -- 7	-17.018 kcal/mol	2.64154 kcal/mol	0.904394 kcal/mol	210 223@LB@ \| \|@LB@5'-UAA...UUUUG AAUAC...GGC-3'@LB@ AUGUUUUUCAGC@LB@ \|\|\|\|\|\|\|\|\|\|\|\|@LB@ UACAAAAAGUCG@LB@3'-UUU...CCCAA -5'@LB@ \| \|@LB@ 13 1@LB@@LB@@LB@Energy -13.47 kcal/mol@LB@Hybridization Energy -17.018 kcal/mol@LB@Unfolding Energy - mRNA 2.64154 kcal/mol@LB@Unfolding Energy - sRNA 0.904394 kcal/mol@LB@@LB@Position - mRNA 211 -- 222@LB@Position - sRNA 1 -- 12@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 1 -- 7@LB@
109	0.004204	0.1296	b1384	feaR	-11.47	0.085662	210 -- 231	1 -- 26	transcriptional activator for tynA and feaB		_____________209________________________232\n_____________\|__________________________\|\n5'-UGU...ACCCC___________AUA___AG_______AAUGG...CGG-3'\n______________GCA____GUGG___AUG__UUUCAGC\n______________\|\|\|____:\|\|\|___\|\|\|__\|\|\|\|\|\|\|\n______________CGU____UACC___UAC__AAAGUCG\n3'-UUU...UCGAU___AAAA____CAA___AA_______-5'\n_____________\|_________________________\|\n_____________27________________________1\n	225 -- 231	1 -- 7	-17.3605 kcal/mol	4.42522 kcal/mol	1.46544 kcal/mol	209 232@LB@ \| \|@LB@5'-UGU...ACCCC AUA AG AAUGG...CGG-3'@LB@ GCA GUGG AUG UUUCAGC@LB@ \|\|\| :\|\|\| \|\|\| \|\|\|\|\|\|\|@LB@ CGU UACC UAC AAAGUCG@LB@3'-UUU...UCGAU AAAA CAA AA -5'@LB@ \| \|@LB@ 27 1@LB@@LB@@LB@Energy -11.47 kcal/mol@LB@Hybridization Energy -17.3605 kcal/mol@LB@Unfolding Energy - mRNA 4.42522 kcal/mol@LB@Unfolding Energy - sRNA 1.46544 kcal/mol@LB@@LB@Position - mRNA 210 -- 231@LB@Position - sRNA 1 -- 26@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 1 -- 7@LB@
113	0.004738	0.1404	b3197	kdsD	-14.34	0.017174	210 -- 240	1 -- 35	D-arabinose 5-phosphate isomerase		_____________209_________________________________241\n_____________\|___________________________________\|\n5'-AGG...CGCAC___G________ACC________U__AC_______AAGCA...ACA-3'\n______________GUA_AGUUA_CA______GGGUU_UG__UUUCAGC\n______________\|\|\|_\|\|:\|\|_\|\|______\|\|\|\|\|_\|\|__\|\|\|\|\|\|\|\n______________CAU_UCGAU_GU______CCCAA_AC__AAAGUCG\n3'-UUU...AGGAC___G_____C__AAAAUA_____U__AA_______-5'\n_____________\|__________________________________\|\n_____________36_________________________________1\n	234 -- 240	1 -- 7	-24.924 kcal/mol	9.08416 kcal/mol	1.49508 kcal/mol	209 241@LB@ \| \|@LB@5'-AGG...CGCAC G ACC U AC AAGCA...ACA-3'@LB@ GUA AGUUA CA GGGUU UG UUUCAGC@LB@ \|\|\| \|\|:\|\| \|\| \|\|\|\|\| \|\| \|\|\|\|\|\|\|@LB@ CAU UCGAU GU CCCAA AC AAAGUCG@LB@3'-UUU...AGGAC G C AAAAUA U AA -5'@LB@ \| \|@LB@ 36 1@LB@@LB@@LB@Energy -14.34 kcal/mol@LB@Hybridization Energy -24.924 kcal/mol@LB@Unfolding Energy - mRNA 9.08416 kcal/mol@LB@Unfolding Energy - sRNA 1.49508 kcal/mol@LB@@LB@Position - mRNA 210 -- 240@LB@Position - sRNA 1 -- 35@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 1 -- 7@LB@
114	0.004808	0.1404	b2372	yfdV	-9.14	0.236047	240 -- 266	1 -- 35	putative transporter		_____________239____________________________________267\n_____________\|______________________________________\|\n5'-UUC...UUAUC___AU__U______________________________GGCAG...CUC-3'\n______________GUA__CA_GCU_GU______UGGGUUAU____UUUAGC\n______________\|\|\|__\|\|_\|\|\|_\|:______\|\|\|\|\|\|\|\|____\|\|:\|\|\|\n______________CAU__GU_CGA_CG______ACCCAAUA____AAGUCG\n3'-UUU...AGGAC___________U__UAAAAU________CAAA______-5'\n_____________\|_____________________________________\|\n_____________36____________________________________1\n	254 -- 260	11 -- 17	-17.7969 kcal/mol	7.16419 kcal/mol	1.49508 kcal/mol	239 267@LB@ \| \|@LB@5'-UUC...UUAUC AU U GGCAG...CUC-3'@LB@ GUA CA GCU GU UGGGUUAU UUUAGC@LB@ \|\|\| \|\| \|\|\| \|: \|\|\|\|\|\|\|\| \|\|:\|\|\|@LB@ CAU GU CGA CG ACCCAAUA AAGUCG@LB@3'-UUU...AGGAC U UAAAAU CAAA -5'@LB@ \| \|@LB@ 36 1@LB@@LB@@LB@Energy -9.14 kcal/mol@LB@Hybridization Energy -17.7969 kcal/mol@LB@Unfolding Energy - mRNA 7.16419 kcal/mol@LB@Unfolding Energy - sRNA 1.49508 kcal/mol@LB@@LB@Position - mRNA 240 -- 266@LB@Position - sRNA 1 -- 35@LB@Position Seed - mRNA 254 -- 260@LB@Position Seed - sRNA 11 -- 17@LB@
127	0.005388	0.142	b2721	hycE	-10.66	0.125013	137 -- 158	1 -- 36	hydrogenase 3 large subunit		_____________136___________________________________159\n_____________\|_____________________________________\|\n5'-UUC...GGCUG___UU____UU__________________________GUUCG...UGA-3'\n______________GGU__GGCU__GCAU_______________UUUUAGC\n______________\|\|\|__:\|\|\|__\|\|\|\|_______________\|\|\|:\|\|\|\n______________CCA__UCGA__CGUA_______________AAAGUCG\n3'-UUU...AAGGA___UG____U_____AAAUACCCAAUACAA_______-5'\n_____________\|____________________________________\|\n_____________37___________________________________1\n	152 -- 158	1 -- 7	-16.3373 kcal/mol	4.17778 kcal/mol	1.49509 kcal/mol	136 159@LB@ \| \|@LB@5'-UUC...GGCUG UU UU GUUCG...UGA-3'@LB@ GGU GGCU GCAU UUUUAGC@LB@ \|\|\| :\|\|\| \|\|\|\| \|\|\|:\|\|\|@LB@ CCA UCGA CGUA AAAGUCG@LB@3'-UUU...AAGGA UG U AAAUACCCAAUACAA -5'@LB@ \| \|@LB@ 37 1@LB@@LB@@LB@Energy -10.66 kcal/mol@LB@Hybridization Energy -16.3373 kcal/mol@LB@Unfolding Energy - mRNA 4.17778 kcal/mol@LB@Unfolding Energy - sRNA 1.49509 kcal/mol@LB@@LB@Position - mRNA 137 -- 158@LB@Position - sRNA 1 -- 36@LB@Position Seed - mRNA 152 -- 158@LB@Position Seed - sRNA 1 -- 7@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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