Input and runtime details for job 3202356 (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 3202356 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:24:02 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:24:35 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 02:03:47 CET 2018
	Post-Processing Finished		@ Sat Feb 17 02:03:55 CET 2018
	Job Completed		@ Sat Feb 17 02:04:28 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3202356&toolName=CopraRNA ( 30 days expiry )

Description of the job

GcvB

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_003197 NC_003277 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

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
130	0.00652	0.1774	stm4228	malF	-14.47	0.143021	162 -- 175	1 -- 15	maltose ABC transporter permease MalF		_____________161_____________176\n_____________\|_______________\|\n5'-AAC...ACAUC_______________UUCAA...UAA-3'\n______________UCCGGC_CAGGAAGU\n______________\|\|\|\|\|\|_\|\|\|\|\|\|\|\|\n______________AGGCCG_GUCCUUCA\n3'-UUU...AAGCA______A________-5'\n_____________\|______________\|\n_____________16_____________1\n	169 -- 175	1 -- 7	-25.2779 kcal/mol	6.67863 kcal/mol	4.81264 kcal/mol	161 176@LB@ \| \|@LB@5'-AAC...ACAUC UUCAA...UAA-3'@LB@ UCCGGC CAGGAAGU@LB@ \|\|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ AGGCCG GUCCUUCA@LB@3'-UUU...AAGCA A -5'@LB@ \| \|@LB@ 16 1@LB@@LB@@LB@Energy -14.47 kcal/mol@LB@Hybridization Energy -25.2779 kcal/mol@LB@Unfolding Energy - mRNA 6.67863 kcal/mol@LB@Unfolding Energy - sRNA 4.81264 kcal/mol@LB@@LB@Position - mRNA 162 -- 175@LB@Position - sRNA 1 -- 15@LB@Position Seed - mRNA 169 -- 175@LB@Position Seed - sRNA 1 -- 7@LB@
25	0.0006298	0.08814	stm3161	metC	-13.21	0.223681	190 -- 249	35 -- 90	cystathionine beta-lyase		_____________189__________________250\n_____________\|____________________\|\n5'-CAA...AACUG_________G__________AAAAA...CAC-3'\n______________GUAAACGCA__GACGCAGCA\n______________\|:\|\|\|\|:\|\|__:\|\|:\|\|:\|\|\n______________CGUUUGUGU__UUGUGUUGU\n3'-UUU...GUUAA_________UG_________AGUGU...UCA-5'\n_____________\|____________________\|\n_____________91___________________34\n	243 -- 249	71 -- 77	-21.5854 kcal/mol	5.07977 kcal/mol	3.80671 kcal/mol	189 250@LB@ \| \|@LB@5'-CAA...AACUG G AAAAA...CAC-3'@LB@ GUAAACGCA GACGCAGCA@LB@ \|:\|\|\|\|:\|\| :\|\|:\|\|:\|\|@LB@ CGUUUGUGU UUGUGUUGU@LB@3'-UUU...GUUAA UG AGUGU...UCA-5'@LB@ \| \|@LB@ 91 34@LB@@LB@@LB@Energy -13.21 kcal/mol@LB@Hybridization Energy -21.5854 kcal/mol@LB@Unfolding Energy - mRNA 5.07977 kcal/mol@LB@Unfolding Energy - sRNA 3.80671 kcal/mol@LB@@LB@Position - mRNA 190 -- 249@LB@Position - sRNA 35 -- 90@LB@Position Seed - mRNA 243 -- 249@LB@Position Seed - sRNA 71 -- 77@LB@
59	0.00232	0.14	stm4105	metF	-16.51	0.066936	223 -- 245	40 -- 59	methylenetetrahydrofolate reductase [NAD(P)H]		_____________222__________________246\n_____________\|____________________\|\n5'-AAG...UUUAC__________AUA_______GCGAU...GCA-3'\n______________AACACAACAA___AUAACAU\n______________\|\|\|\|\|\|\|\|\|\|___\|:\|\|\|\|\|\n______________UUGUGUUGUU___UGUUGUA\n3'-UUU...AACGU__________G_________GUGUU...UCA-5'\n_____________\|____________________\|\n_____________60___________________39\n	175 -- 181	70 -- 76	-16.6304 kcal/mol	0.675865 kcal/mol	3.87174 kcal/mol	222 246@LB@ \| \|@LB@5'-AAG...UUUAC AUA GCGAU...GCA-3'@LB@ AACACAACAA AUAACAU@LB@ \|\|\|\|\|\|\|\|\|\| \|:\|\|\|\|\|@LB@ UUGUGUUGUU UGUUGUA@LB@3'-UUU...AACGU G GUGUU...UCA-5'@LB@ \| \|@LB@ 60 39@LB@@LB@@LB@Energy -16.51 kcal/mol@LB@Hybridization Energy -16.6304 kcal/mol@LB@Unfolding Energy - mRNA 0.675865 kcal/mol@LB@Unfolding Energy - sRNA 3.87174 kcal/mol@LB@@LB@Position - mRNA 223 -- 245@LB@Position - sRNA 40 -- 59@LB@Position Seed - mRNA 175 -- 181@LB@Position Seed - sRNA 70 -- 76@LB@
155	0.008213	0.1845	stm3112	mltC	-21.66	0.009126	170 -- 198	62 -- 90	murein transglycosylase C		_____________169____________________________199\n_____________\|______________________________\|\n5'-UAA...ACAUG___UA________________G___UC___GAAUG...UCA-3'\n______________GCA___ACGACAACACAACAU_CAC__CCG\n______________\|\|\|___\|\|:\|\|\|\|\|\|\|\|\|\|\|\|_\|\|\|__\|\|\|\n______________CGU___UGUUGUUGUGUUGUA_GUG__GGC\n3'-UUU...GUUAA___UUG___________________UU___AUUCG...UCA-5'\n_____________\|______________________________\|\n_____________91_____________________________61\n	183 -- 189	70 -- 76	-33.7206 kcal/mol	4.25464 kcal/mol	8.62576 kcal/mol	169 199@LB@ \| \|@LB@5'-UAA...ACAUG UA G UC GAAUG...UCA-3'@LB@ GCA ACGACAACACAACAU CAC CCG@LB@ \|\|\| \|\|:\|\|\|\|\|\|\|\|\|\|\|\| \|\|\| \|\|\|@LB@ CGU UGUUGUUGUGUUGUA GUG GGC@LB@3'-UUU...GUUAA UUG UU AUUCG...UCA-5'@LB@ \| \|@LB@ 91 61@LB@@LB@@LB@Energy -21.66 kcal/mol@LB@Hybridization Energy -33.7206 kcal/mol@LB@Unfolding Energy - mRNA 4.25464 kcal/mol@LB@Unfolding Energy - sRNA 8.62576 kcal/mol@LB@@LB@Position - mRNA 170 -- 198@LB@Position - sRNA 62 -- 90@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 70 -- 76@LB@
172	0.009395	0.1945	stm3373	mreC	-15.91	0.084075	179 -- 229	45 -- 87	rod shape-determining protein MreC		_____________178____________230\n_____________\|______________\|\n5'-UGA...UGUUA_____AG_______CAUUC...GGA-3'\n______________AUGGA__AGACGGG\n______________\|\|\|\|\|__\|\|\|\|:\|\|\n______________UACCU__UCUGUCC\n3'-UUU...AGUGA_____G________CAUUU...UCA-5'\n_____________\|______________\|\n_____________88_____________44\n	21 -- 27	153 -- 159	-16.2478 kcal/mol	4.60826 kcal/mol	2.82582 kcal/mol	178 230@LB@ \| \|@LB@5'-UGA...UGUUA AG CAUUC...GGA-3'@LB@ AUGGA AGACGGG@LB@ \|\|\|\|\| \|\|\|\|:\|\|@LB@ UACCU UCUGUCC@LB@3'-UUU...AGUGA G CAUUU...UCA-5'@LB@ \| \|@LB@ 88 44@LB@@LB@@LB@Energy -15.91 kcal/mol@LB@Hybridization Energy -16.2478 kcal/mol@LB@Unfolding Energy - mRNA 4.60826 kcal/mol@LB@Unfolding Energy - sRNA 2.82582 kcal/mol@LB@@LB@Position - mRNA 179 -- 229@LB@Position - sRNA 45 -- 87@LB@Position Seed - mRNA 21 -- 27@LB@Position Seed - sRNA 153 -- 159@LB@
107	0.00529	0.1728	stm0994	mukB	-11.10	0.440174	5 -- 20	154 -- 167	cell division protein MukB		_____________4_________________________21\n_____________\|_________________________\|\n5'-UGG...UCAGC_______U__________G______AAUAA...CCG-3'\n______________CGGACAG_GG_______A_AGGAAG\n______________\|:\|\|\|\|\|_\|\|_______\|_\|\|\|\|\|\|\n______________GUCUGUC_CC_______U_UCCUUC\n3'-UUU...UACCU__________AUUUACA_G______ACUUU...UCA-5'\n_____________\|_________________________\|\n_____________168_______________________153\n	179 -- 185	154 -- 160	-19.4251 kcal/mol	3.58038 kcal/mol	5.99227 kcal/mol	4 21@LB@ \| \|@LB@5'-UGG...UCAGC U G AAUAA...CCG-3'@LB@ CGGACAG GG A AGGAAG@LB@ \|:\|\|\|\|\| \|\| \| \|\|\|\|\|\|@LB@ GUCUGUC CC U UCCUUC@LB@3'-UUU...UACCU AUUUACA G ACUUU...UCA-5'@LB@ \| \|@LB@ 168 153@LB@@LB@@LB@Energy -11.10 kcal/mol@LB@Hybridization Energy -19.4251 kcal/mol@LB@Unfolding Energy - mRNA 3.58038 kcal/mol@LB@Unfolding Energy - sRNA 5.99227 kcal/mol@LB@@LB@Position - mRNA 5 -- 20@LB@Position - sRNA 154 -- 167@LB@Position Seed - mRNA 179 -- 185@LB@Position Seed - sRNA 154 -- 160@LB@
17	0.0003055	0.06194	stm2694	N/A	-22.95	0.005498	261 -- 295	52 -- 90	Fels-2 prophage protein		_____________260_____________________________________296\n_____________\|_______________________________________\|\n5'-ACG...UAUCA_____________A_G____________AGU________UAUAA-3'\n______________GC___UACGACAA_A_AACGUUACAACC____GCCAAAA\n______________\|\|___:\|\|:\|\|\|\|_\|_\|\|\|:\|:\|\|\|\|\|\|____\|\|\|\|\|\|\|\n______________CG___GUGUUGUU_U_UUGUAGUGUUGG____CGGUUUU\n3'-UUU...GUUAA__UUU________G_G____________CAUU_______CGGGU...UCA-5'\n_____________\|_______________________________________\|\n_____________91______________________________________51\n	289 -- 295	52 -- 58	-35.4487 kcal/mol	2.51857 kcal/mol	14.0353 kcal/mol	260 296@LB@ \| \|@LB@5'-ACG...UAUCA A G AGU UAUAA-3'@LB@ GC UACGACAA A AACGUUACAACC GCCAAAA@LB@ \|\| :\|\|:\|\|\|\| \| \|\|\|:\|:\|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ CG GUGUUGUU U UUGUAGUGUUGG CGGUUUU@LB@3'-UUU...GUUAA UUU G G CAUU CGGGU...UCA-5'@LB@ \| \|@LB@ 91 51@LB@@LB@@LB@Energy -22.95 kcal/mol@LB@Hybridization Energy -35.4487 kcal/mol@LB@Unfolding Energy - mRNA 2.51857 kcal/mol@LB@Unfolding Energy - sRNA 14.0353 kcal/mol@LB@@LB@Position - mRNA 261 -- 295@LB@Position - sRNA 52 -- 90@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 52 -- 58@LB@
32	0.001017	0.1132	stm1874	N/A	-30.35	0.000300	5 -- 53	36 -- 83	putative inner membrane protein		_____________4__________________________________________________54\n_____________\|__________________________________________________\|\n_______5'-GGUU___________C______U____CUC________________A_______CCGGC...CCG-3'\n______________CAGCGGCGCAA_CAUUAC_GGCC___AG_CAAGAGCUCAUCA_AACGCGC\n______________\|\|:\|::\|:\|\|\|_\|\|\|:\|\|_::\|\|___\|\|_\|\|\|:\|\|\|:\|\|\|\|\|_\|\|\|:\|\|\|\n______________GUUGUUGUGUU_GUAGUG_UUGG___UC_GUUUUCGGGUAGU_UUGUGCG\n3'-UUU...UUUGU_______________________CAU__G_____________C_______UAAGG...UCA-5'\n_____________\|__________________________________________________\|\n_____________84_________________________________________________35\n	47 -- 53	36 -- 42	-54.7325 kcal/mol	11.1988 kcal/mol	22.0738 kcal/mol	4 54@LB@ \| \|@LB@ 5'-GGUU C U CUC A CCGGC...CCG-3'@LB@ CAGCGGCGCAA CAUUAC GGCC AG CAAGAGCUCAUCA AACGCGC@LB@ \|\|:\|::\|:\|\|\| \|\|\|:\|\| ::\|\| \|\| \|\|\|:\|\|\|:\|\|\|\|\| \|\|\|:\|\|\|@LB@ GUUGUUGUGUU GUAGUG UUGG UC GUUUUCGGGUAGU UUGUGCG@LB@3'-UUU...UUUGU CAU G C UAAGG...UCA-5'@LB@ \| \|@LB@ 84 35@LB@@LB@@LB@Energy -30.35 kcal/mol@LB@Hybridization Energy -54.7325 kcal/mol@LB@Unfolding Energy - mRNA 11.1988 kcal/mol@LB@Unfolding Energy - sRNA 22.0738 kcal/mol@LB@@LB@Position - mRNA 5 -- 53@LB@Position - sRNA 36 -- 83@LB@Position Seed - mRNA 47 -- 53@LB@Position Seed - sRNA 36 -- 42@LB@
34	0.001111	0.1164	stm2746	N/A	-14.94	0.120804	53 -- 101	36 -- 90	putative excinuclease ATPase subunit	stm4494 stm3753	_____________52_____________________102\n_____________\|______________________\|\n5'-GGA...UUGAA____UA_________U______UCAAG...AUG-3'\n______________GCAA__ACAACAACG__ACAUU\n______________\|\|\|\|__\|\|\|\|\|\|\|\|:__\|\|\|\|:\n______________CGUU__UGUUGUUGU__UGUAG\n3'-UUU...GUUAA____UG_________GU_____UGUUG...UCA-5'\n_____________\|______________________\|\n_____________91_____________________35\n	61 -- 67	76 -- 82	-20.4267 kcal/mol	3.3222 kcal/mol	4.33922 kcal/mol	52 102@LB@ \| \|@LB@5'-GGA...UUGAA UA U UCAAG...AUG-3'@LB@ GCAA ACAACAACG ACAUU@LB@ \|\|\|\| \|\|\|\|\|\|\|\|: \|\|\|\|:@LB@ CGUU UGUUGUUGU UGUAG@LB@3'-UUU...GUUAA UG GU UGUUG...UCA-5'@LB@ \| \|@LB@ 91 35@LB@@LB@@LB@Energy -14.94 kcal/mol@LB@Hybridization Energy -20.4267 kcal/mol@LB@Unfolding Energy - mRNA 3.3222 kcal/mol@LB@Unfolding Energy - sRNA 4.33922 kcal/mol@LB@@LB@Position - mRNA 53 -- 101@LB@Position - sRNA 36 -- 90@LB@Position Seed - mRNA 61 -- 67@LB@Position Seed - sRNA 76 -- 82@LB@
49	0.001802	0.1291	stm1787	N/A	-18.29	0.033902	137 -- 202	34 -- 90	[Ni/Fe] hydrogenase large subunit		_____________136__________________203\n_____________\|____________________\|\n5'-GGC...CCAAC________C___________GUUAG...GCG-3'\n______________GUAAACGC_ACAA_ACAACA\n______________\|:\|\|\|\|:\|_\|\|\|\|_\|\|\|\|\|\|\n______________CGUUUGUG_UGUU_UGUUGU\n3'-UUU...GUUAA________U____G______AGUGU...UCA-5'\n_____________\|____________________\|\n_____________91___________________33\n	138 -- 144	83 -- 89	-18.7581 kcal/mol	1.39906 kcal/mol	3.80671 kcal/mol	136 203@LB@ \| \|@LB@5'-GGC...CCAAC C GUUAG...GCG-3'@LB@ GUAAACGC ACAA ACAACA@LB@ \|:\|\|\|\|:\| \|\|\|\| \|\|\|\|\|\|@LB@ CGUUUGUG UGUU UGUUGU@LB@3'-UUU...GUUAA U G AGUGU...UCA-5'@LB@ \| \|@LB@ 91 33@LB@@LB@@LB@Energy -18.29 kcal/mol@LB@Hybridization Energy -18.7581 kcal/mol@LB@Unfolding Energy - mRNA 1.39906 kcal/mol@LB@Unfolding Energy - sRNA 3.80671 kcal/mol@LB@@LB@Position - mRNA 137 -- 202@LB@Position - sRNA 34 -- 90@LB@Position Seed - mRNA 138 -- 144@LB@Position Seed - sRNA 83 -- 89@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

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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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