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: https://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
151	0.00796	0.1845	stm2365	folC	-10.71	0.491716	269 -- 300	50 -- 78	bifunctional tetrahydrofolate synthase/dihydrofolate synthase	_____________268__________301\n_____________\|____________\|\n5'-CCG...CGGCG____A_______UCUGA...AGC-3'\n______________CCGG_UCAGGAG\n______________\|\|\|\|_\|\|\|\|\|\|:\n______________GGCC_AGUCCUU\n3'-UUU...AGCAA____G_______CA-5'\n_____________\|____________\|\n_____________79___________49\n	115 -- 121	3 -- 9	-17.3652 kcal/mol	5.30633 kcal/mol	4.72771 kcal/mol	268 301@LB@ \| \|@LB@5'-CCG...CGGCG A UCUGA...AGC-3'@LB@ CCGG UCAGGAG@LB@ \|\|\|\| \|\|\|\|\|\|:@LB@ GGCC AGUCCUU@LB@3'-UUU...AGCAA G CA-5'@LB@ \| \|@LB@ 79 49@LB@@LB@@LB@Energy -10.71 kcal/mol@LB@Hybridization Energy -17.3652 kcal/mol@LB@Unfolding Energy - mRNA 5.30633 kcal/mol@LB@Unfolding Energy - sRNA 4.72771 kcal/mol@LB@@LB@Position - mRNA 269 -- 300@LB@Position - sRNA 50 -- 78@LB@Position Seed - mRNA 115 -- 121@LB@Position Seed - sRNA 3 -- 9@LB@
152	0.008087	0.1845	stm0213	dapD	-12.65	0.271269	222 -- 289	49 -- 104	2 3 4 5-tetrahydropyridine-2 6-dicarboxylate N-succinyltransferase	_____________221______________________290\n_____________\|________________________\|\n5'-UUU...UUAAC_________GUU___G________UGAGA...AGG-3'\n______________AAUGCAGCA___ACA_AACGUUAU\n______________\|\|::\|\|:\|\|___\|\|\|_\|\|\|:\|:\|:\n______________UUGUGUUGU___UGU_UUGUAGUG\n3'-UUU...AACGU_______________G________UUGGC...UCA-5'\n_____________\|________________________\|\n_____________105______________________48\n	202 -- 208	79 -- 85	-17.6746 kcal/mol	3.78795 kcal/mol	5.3513 kcal/mol	221 290@LB@ \| \|@LB@5'-UUU...UUAAC GUU G UGAGA...AGG-3'@LB@ AAUGCAGCA ACA AACGUUAU@LB@ \|\|::\|\|:\|\| \|\|\| \|\|\|:\|:\|:@LB@ UUGUGUUGU UGU UUGUAGUG@LB@3'-UUU...AACGU G UUGGC...UCA-5'@LB@ \| \|@LB@ 105 48@LB@@LB@@LB@Energy -12.65 kcal/mol@LB@Hybridization Energy -17.6746 kcal/mol@LB@Unfolding Energy - mRNA 3.78795 kcal/mol@LB@Unfolding Energy - sRNA 5.3513 kcal/mol@LB@@LB@Position - mRNA 222 -- 289@LB@Position - sRNA 49 -- 104@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 79 -- 85@LB@
153	0.008123	0.1845	stm2512	xseA	-14.57	0.138273	215 -- 252	42 -- 82	exodeoxyribonuclease VII large subunit	_____________214________253\n_____________\|__________\|\n5'-CGU...UUUUU__________GCCUU...GCG-3'\n______________ACCGUAAGCC\n______________\|\|\|\|\|\|\|\|\|\|\n______________UGGCAUUCGG\n3'-UUU...AGUGU__________UUUUC...UCA-5'\n_____________\|__________\|\n_____________83_________41\n	234 -- 240	56 -- 62	-17.1871 kcal/mol	1.1981 kcal/mol	7.48121 kcal/mol	214 253@LB@ \| \|@LB@5'-CGU...UUUUU GCCUU...GCG-3'@LB@ ACCGUAAGCC@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ UGGCAUUCGG@LB@3'-UUU...AGUGU UUUUC...UCA-5'@LB@ \| \|@LB@ 83 41@LB@@LB@@LB@Energy -14.57 kcal/mol@LB@Hybridization Energy -17.1871 kcal/mol@LB@Unfolding Energy - mRNA 1.1981 kcal/mol@LB@Unfolding Energy - sRNA 7.48121 kcal/mol@LB@@LB@Position - mRNA 215 -- 252@LB@Position - sRNA 42 -- 82@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 56 -- 62@LB@
154	0.008185	0.1845	stm3738	yigC	-11.16	0.433331	228 -- 246	55 -- 74	similar to E. coli orf hypothetical protein (AAC76670.1); Blastp hit to AAC76670.1 (223 aa) 94% identity in aa 19 - 223	_____________227__________________247\n_____________\|____________________\|\n5'-UAA...ACCUC_____________AC_____AAAUG...UUA-3'\n______________GCA__UACAAUAA__CACAA\n______________\|\|\|__:\|\|\|\|:\|\|__\|\|\|\|\|\n______________CGU__GUGUUGUU__GUGUU\n3'-UUU...GUUAA___UU_______________GUAGU...UCA-5'\n_____________\|____________________\|\n_____________75___________________54\n	27 -- 33	78 -- 84	-12.6647 kcal/mol	0.985902 kcal/mol	3.77104 kcal/mol	227 247@LB@ \| \|@LB@5'-UAA...ACCUC AC AAAUG...UUA-3'@LB@ GCA UACAAUAA CACAA@LB@ \|\|\| :\|\|\|\|:\|\| \|\|\|\|\|@LB@ CGU GUGUUGUU GUGUU@LB@3'-UUU...GUUAA UU GUAGU...UCA-5'@LB@ \| \|@LB@ 75 54@LB@@LB@@LB@Energy -11.16 kcal/mol@LB@Hybridization Energy -12.6647 kcal/mol@LB@Unfolding Energy - mRNA 0.985902 kcal/mol@LB@Unfolding Energy - sRNA 3.77104 kcal/mol@LB@@LB@Position - mRNA 228 -- 246@LB@Position - sRNA 55 -- 74@LB@Position Seed - mRNA 27 -- 33@LB@Position Seed - sRNA 78 -- 84@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@
156	0.008228	0.1845	stm1715	yciN	-28.69	0.000575	104 -- 163	36 -- 90	similar to E. coli orf hypothetical protein (AAC74355.1); Blastp hit to AAC74355.1 (83 aa) 92% identity in aa 1 - 83	_____________103___________________________________________________________164\n_____________\|_____________________________________________________________\|\n5'-UCG...UGCCA____________UG____AUC_____AUUUC_______AAUAUUU___________G____UCAGC...CCA-3'\n______________GUGAACGCAACA__ACAA___CAUCA_____CUGUGAG_______GCCCAUCAGAA__UGC\n______________\|::\|\|\|:\|\|\|\|\|__\|\|\|\|___\|\|\|\|\|_____\|:\|\|:\|\|_______\|\|\|\|\|\|\|\|\|\|\|__:\|\|\n______________CGUUUGUGUUGU__UGUU___GUAGU_____GGCAUUC_______CGGGUAGUCUU__GCG\n3'-UUU...GUUAA____________UG____________GUU_________GGUUUU____________GU___UAAGG...UCA-5'\n_____________\|_____________________________________________________________\|\n_____________91____________________________________________________________35\n	152 -- 158	42 -- 48	-53.6458 kcal/mol	9.96696 kcal/mol	22.5 kcal/mol	103 164@LB@ \| \|@LB@5'-UCG...UGCCA UG AUC AUUUC AAUAUUU G UCAGC...CCA-3'@LB@ GUGAACGCAACA ACAA CAUCA CUGUGAG GCCCAUCAGAA UGC@LB@ \|::\|\|\|:\|\|\|\|\| \|\|\|\| \|\|\|\|\| \|:\|\|:\|\| \|\|\|\|\|\|\|\|\|\|\| :\|\|@LB@ CGUUUGUGUUGU UGUU GUAGU GGCAUUC CGGGUAGUCUU GCG@LB@3'-UUU...GUUAA UG GUU GGUUUU GU UAAGG...UCA-5'@LB@ \| \|@LB@ 91 35@LB@@LB@@LB@Energy -28.69 kcal/mol@LB@Hybridization Energy -53.6458 kcal/mol@LB@Unfolding Energy - mRNA 9.96696 kcal/mol@LB@Unfolding Energy - sRNA 22.5 kcal/mol@LB@@LB@Position - mRNA 104 -- 163@LB@Position - sRNA 36 -- 90@LB@Position Seed - mRNA 152 -- 158@LB@Position Seed - sRNA 42 -- 48@LB@
157	0.008234	0.1845	stm0693	fur	-16.04	0.080078	199 -- 253	31 -- 90	ferric iron uptake transcriptional regulator	_____________198________________________254\n_____________\|__________________________\|\n5'-GCA...AUUCC___U___UG__________C______AAGAA...ACG-3'\n______________GCA_GAC__ACAACAAUAC_GCAUUA\n______________\|\|\|_:\|\|__\|\|\|\|\|\|\|:\|\|_:\|\|\|:\|\n______________CGU_UUG__UGUUGUUGUG_UGUAGU\n3'-UUU...GUUAA___________________U______GUUGG...UCA-5'\n_____________\|__________________________\|\n_____________91_________________________30\n	211 -- 217	75 -- 81	-20.9388 kcal/mol	2.89423 kcal/mol	5.29697 kcal/mol	198 254@LB@ \| \|@LB@5'-GCA...AUUCC U UG C AAGAA...ACG-3'@LB@ GCA GAC ACAACAAUAC GCAUUA@LB@ \|\|\| :\|\| \|\|\|\|\|\|\|:\|\| :\|\|\|:\|@LB@ CGU UUG UGUUGUUGUG UGUAGU@LB@3'-UUU...GUUAA U GUUGG...UCA-5'@LB@ \| \|@LB@ 91 30@LB@@LB@@LB@Energy -16.04 kcal/mol@LB@Hybridization Energy -20.9388 kcal/mol@LB@Unfolding Energy - mRNA 2.89423 kcal/mol@LB@Unfolding Energy - sRNA 5.29697 kcal/mol@LB@@LB@Position - mRNA 199 -- 253@LB@Position - sRNA 31 -- 90@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 75 -- 81@LB@
158	0.00827	0.1845	stm1712	acnA	-14.47	0.143385	236 -- 294	48 -- 104	aconitate hydratase 1	_____________235_________________295\n_____________\|___________________\|\n5'-AUC...CAACC_______G_AU________CGCAA...GCG-3'\n______________CUGUGGA_A__CAGGGUAA\n______________\|\|:\|\|\|\|_\|__\|\|\|\|\|\|\|\|\n______________GAUACCU_U__GUCCCAUU\n3'-UUU...UUAGU_______G_CU________UACAU...UCA-5'\n_____________\|___________________\|\n_____________105_________________47\n	167 -- 173	149 -- 155	-24.0869 kcal/mol	10.3759 kcal/mol	4.11594 kcal/mol	235 295@LB@ \| \|@LB@5'-AUC...CAACC G AU CGCAA...GCG-3'@LB@ CUGUGGA A CAGGGUAA@LB@ \|\|:\|\|\|\| \| \|\|\|\|\|\|\|\|@LB@ GAUACCU U GUCCCAUU@LB@3'-UUU...UUAGU G CU UACAU...UCA-5'@LB@ \| \|@LB@ 105 47@LB@@LB@@LB@Energy -14.47 kcal/mol@LB@Hybridization Energy -24.0869 kcal/mol@LB@Unfolding Energy - mRNA 10.3759 kcal/mol@LB@Unfolding Energy - sRNA 4.11594 kcal/mol@LB@@LB@Position - mRNA 236 -- 294@LB@Position - sRNA 48 -- 104@LB@Position Seed - mRNA 167 -- 173@LB@Position Seed - sRNA 149 -- 155@LB@
159	0.008305	0.1845	stm3625	yhjV	-13.06	0.235438	203 -- 240	55 -- 86	transporter	_____________202________________________241\n_____________\|__________________________\|\n5'-UUA...UAUUU_____________CUCUA________CGACA...UCU-3'\n______________UGGGCAG__GGGG______UGCAGGA\n______________\|\|\|:\|\|\|__:\|\|\|______\|:\|\|\|\|\|\n______________ACCUGUC__UCCC______AUGUCCU\n3'-UUU...GUGAU_______UG____AUUUAC_______UCACU...UCA-5'\n_____________\|__________________________\|\n_____________87_________________________54\n	202 -- 208	139 -- 145	-24.2103 kcal/mol	7.6176 kcal/mol	3.71206 kcal/mol	202 241@LB@ \| \|@LB@5'-UUA...UAUUU CUCUA CGACA...UCU-3'@LB@ UGGGCAG GGGG UGCAGGA@LB@ \|\|\|:\|\|\| :\|\|\| \|:\|\|\|\|\|@LB@ ACCUGUC UCCC AUGUCCU@LB@3'-UUU...GUGAU UG AUUUAC UCACU...UCA-5'@LB@ \| \|@LB@ 87 54@LB@@LB@@LB@Energy -13.06 kcal/mol@LB@Hybridization Energy -24.2103 kcal/mol@LB@Unfolding Energy - mRNA 7.6176 kcal/mol@LB@Unfolding Energy - sRNA 3.71206 kcal/mol@LB@@LB@Position - mRNA 203 -- 240@LB@Position - sRNA 55 -- 86@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 139 -- 145@LB@
160	0.008331	0.1845	stm0002	thrA	-15.10	0.113872	18 -- 81	44 -- 90	bifunctional aspartate kinase/homoserine dehydrogenase I	_____________17______________________82\n_____________\|_______________________\|\n5'-CCA...UACAA________AAUAA__________AGUAC...UAG-3'\n______________GACAGACA_____AAAUG_ACAG\n______________\|\|\|\|\|\|\|\|_____\|\|\|\|\|_\|\|\|\|\n______________CUGUCUGU_____UUUAC_UGUC\n3'-UUU...GAUAC________CCCA______A____CUUCA...UCA-5'\n_____________\|_______________________\|\n_____________91______________________43\n	19 -- 25	155 -- 161	-19.4516 kcal/mol	0.236149 kcal/mol	3.68511 kcal/mol	17 82@LB@ \| \|@LB@5'-CCA...UACAA AAUAA AGUAC...UAG-3'@LB@ GACAGACA AAAUG ACAG@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\| \|\|\|\|@LB@ CUGUCUGU UUUAC UGUC@LB@3'-UUU...GAUAC CCCA A CUUCA...UCA-5'@LB@ \| \|@LB@ 91 43@LB@@LB@@LB@Energy -15.10 kcal/mol@LB@Hybridization Energy -19.4516 kcal/mol@LB@Unfolding Energy - mRNA 0.236149 kcal/mol@LB@Unfolding Energy - sRNA 3.68511 kcal/mol@LB@@LB@Position - mRNA 18 -- 81@LB@Position - sRNA 44 -- 90@LB@Position Seed - mRNA 19 -- 25@LB@Position Seed - sRNA 155 -- 161@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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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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