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
21	0.000482	0.08173	stm1057	pepN	-18.92	0.026522	201 -- 244	36 -- 81	aminopeptidase N	_____________200______________245\n_____________\|________________\|\n5'-CUU...UUUAU___________C____GCCAA...AAA-3'\n______________GACACAACAGC_ACAA\n______________:\|\|\|\|\|\|\|\|:\|_\|\|\|\|\n______________UUGUGUUGUUG_UGUU\n3'-UUU...AACGU________________GUAGU...UCA-5'\n_____________\|________________\|\n_____________82_______________35\n	207 -- 213	77 -- 83	-17.6161 kcal/mol	1.99149 kcal/mol	3.56182 kcal/mol	200 245@LB@ \| \|@LB@5'-CUU...UUUAU C GCCAA...AAA-3'@LB@ GACACAACAGC ACAA@LB@ :\|\|\|\|\|\|\|\|:\| \|\|\|\|@LB@ UUGUGUUGUUG UGUU@LB@3'-UUU...AACGU GUAGU...UCA-5'@LB@ \| \|@LB@ 82 35@LB@@LB@@LB@Energy -18.92 kcal/mol@LB@Hybridization Energy -17.6161 kcal/mol@LB@Unfolding Energy - mRNA 1.99149 kcal/mol@LB@Unfolding Energy - sRNA 3.56182 kcal/mol@LB@@LB@Position - mRNA 201 -- 244@LB@Position - sRNA 36 -- 81@LB@Position Seed - mRNA 207 -- 213@LB@Position Seed - sRNA 77 -- 83@LB@
22	0.0005859	0.08814	stm1976	fliM	-14.91	0.122150	23 -- 60	38 -- 69	flagellar motor switch protein FliM	_____________22_____________________________________61\n_____________\|______________________________________\|\n5'-AAA...AAGUG_________CU____UUGUUGUUUU_____________CGCCG...GCG-3'\n______________CGCAGCCGU__GCUG__________CCCGUCAGAAUGC\n______________\|:\|\|:\|\|\|\|__\|\|::__________\|\|\|:\|\|\|\|\|\|::\|\n______________GUGUUGGCA__CGGU__________GGGUAGUCUUGUG\n3'-UUU...UUGUA_________UU____UUUC___________________CGUAA...UCA-5'\n_____________\|______________________________________\|\n_____________70_____________________________________37\n	49 -- 55	43 -- 49	-35.5971 kcal/mol	10.3893 kcal/mol	19.1758 kcal/mol	22 61@LB@ \| \|@LB@5'-AAA...AAGUG CU UUGUUGUUUU CGCCG...GCG-3'@LB@ CGCAGCCGU GCUG CCCGUCAGAAUGC@LB@ \|:\|\|:\|\|\|\| \|\|:: \|\|\|:\|\|\|\|\|\|::\|@LB@ GUGUUGGCA CGGU GGGUAGUCUUGUG@LB@3'-UUU...UUGUA UU UUUC CGUAA...UCA-5'@LB@ \| \|@LB@ 70 37@LB@@LB@@LB@Energy -14.91 kcal/mol@LB@Hybridization Energy -35.5971 kcal/mol@LB@Unfolding Energy - mRNA 10.3893 kcal/mol@LB@Unfolding Energy - sRNA 19.1758 kcal/mol@LB@@LB@Position - mRNA 23 -- 60@LB@Position - sRNA 38 -- 69@LB@Position Seed - mRNA 49 -- 55@LB@Position Seed - sRNA 43 -- 49@LB@
23	0.0005914	0.08814	stm3466	crp	-13.97	0.171291	272 -- 288	36 -- 50	transcriptional regulator Crp	_____________271_______________________________289\n_____________\|_________________________________\|\n5'-ACG...CGAAA______CUAAA________________C_____UAAUA...AGG-3'\n______________GCUAUG_____ACAGACA____AGAUG_UACAG\n______________:\|\|\|\|\|_____\|\|\|\|\|\|\|____\|:\|\|\|_\|\|\|\|\|\n______________UGAUAC_____UGUCUGU____UUUAC_AUGUC\n3'-UUU...AUUAG______C___________CCCA___________CUUCA...UCA-5'\n_____________\|_________________________________\|\n_____________51________________________________35\n	21 -- 27	155 -- 161	-20.3438 kcal/mol	4.64329 kcal/mol	5.58455 kcal/mol	271 289@LB@ \| \|@LB@5'-ACG...CGAAA CUAAA C UAAUA...AGG-3'@LB@ GCUAUG ACAGACA AGAUG UACAG@LB@ :\|\|\|\|\| \|\|\|\|\|\|\| \|:\|\|\| \|\|\|\|\|@LB@ UGAUAC UGUCUGU UUUAC AUGUC@LB@3'-UUU...AUUAG C CCCA CUUCA...UCA-5'@LB@ \| \|@LB@ 51 35@LB@@LB@@LB@Energy -13.97 kcal/mol@LB@Hybridization Energy -20.3438 kcal/mol@LB@Unfolding Energy - mRNA 4.64329 kcal/mol@LB@Unfolding Energy - sRNA 5.58455 kcal/mol@LB@@LB@Position - mRNA 272 -- 288@LB@Position - sRNA 36 -- 50@LB@Position Seed - mRNA 21 -- 27@LB@Position Seed - sRNA 155 -- 161@LB@
24	0.000609	0.08814	stm3510	yhgH	-18.34	0.033208	106 -- 153	42 -- 84	DNA utilization protein GntX	_____________105____________________________________154\n_____________\|______________________________________\|\n5'-CCG...UCCGU____________G__G___AUUUCCCUC__________UGCCA...GCG-3'\n______________GCAGCAGCACAA_AU_ACA_________GCCGUAGGUC\n______________:\|\|:\|\|:\|\|\|\|\|_\|\|_\|\|\|_________:\|\|\|\|\|:\|:\|\n______________UGUUGUUGUGUU_UA_UGU_________UGGCAUUCGG\n3'-UUU...GUUUG____________G__G______________________UUUUC...UCA-5'\n_____________\|______________________________________\|\n_____________85_____________________________________41\n	135 -- 141	58 -- 64	-35.7194 kcal/mol	10.0869 kcal/mol	11.5136 kcal/mol	105 154@LB@ \| \|@LB@5'-CCG...UCCGU G G AUUUCCCUC UGCCA...GCG-3'@LB@ GCAGCAGCACAA AU ACA GCCGUAGGUC@LB@ :\|\|:\|\|:\|\|\|\|\| \|\| \|\|\| :\|\|\|\|\|:\|:\|@LB@ UGUUGUUGUGUU UA UGU UGGCAUUCGG@LB@3'-UUU...GUUUG G G UUUUC...UCA-5'@LB@ \| \|@LB@ 85 41@LB@@LB@@LB@Energy -18.34 kcal/mol@LB@Hybridization Energy -35.7194 kcal/mol@LB@Unfolding Energy - mRNA 10.0869 kcal/mol@LB@Unfolding Energy - sRNA 11.5136 kcal/mol@LB@@LB@Position - mRNA 106 -- 153@LB@Position - sRNA 42 -- 84@LB@Position Seed - mRNA 135 -- 141@LB@Position Seed - sRNA 58 -- 64@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@
26	0.0006768	0.08814	stm1365	ydiJ	-17.55	0.045121	78 -- 116	57 -- 91	similar to E. coli putative oxidase (AAC74757.1); Blastp hit to AAC74757.1 (1018 aa) 88% identity in aa 1 - 1017	_____________77_________________________117\n_____________\|__________________________\|\n5'-CUA...AAUGU_________AAUA_____________AACGA...CCA-3'\n______________GAUACAACA____ACGCAACA_CGCA\n______________:\|:\|\|\|\|\|\|____\|\|:\|\|\|\|\|_\|:\|\|\n______________UUGUGUUGU____UGUGUUGU_GUGU\n3'-UUU...AACGU_____________________A____UGGCA...UCA-5'\n_____________\|__________________________\|\n_____________92_________________________56\n	95 -- 101	71 -- 77	-21.9961 kcal/mol	1.97147 kcal/mol	5.98953 kcal/mol	77 117@LB@ \| \|@LB@5'-CUA...AAUGU AAUA AACGA...CCA-3'@LB@ GAUACAACA ACGCAACA CGCA@LB@ :\|:\|\|\|\|\|\| \|\|:\|\|\|\|\| \|:\|\|@LB@ UUGUGUUGU UGUGUUGU GUGU@LB@3'-UUU...AACGU A UGGCA...UCA-5'@LB@ \| \|@LB@ 92 56@LB@@LB@@LB@Energy -17.55 kcal/mol@LB@Hybridization Energy -21.9961 kcal/mol@LB@Unfolding Energy - mRNA 1.97147 kcal/mol@LB@Unfolding Energy - sRNA 5.98953 kcal/mol@LB@@LB@Position - mRNA 78 -- 116@LB@Position - sRNA 57 -- 91@LB@Position Seed - mRNA 95 -- 101@LB@Position Seed - sRNA 71 -- 77@LB@
27	0.0006872	0.08814	stm1806	nhaB	-13.59	0.196266	64 -- 136	66 -- 135	Na+/H+ antiporter NhaB	_____________63___________________________________________________________________________137\n_____________\|____________________________________________________________________________\|\n5'-AGC...AUGAA_________GAUCAAG______AUU______U_____CU______AUC_U____G__UU__UU____U________CUCGC...CAU-3'\n______________GAAAAAGGG_______GC_ACC____UCUGA_AUCGC__GCCAAU___G_UAAG_AC__GC__GCAU__CGUCGCG\n______________\|\|\|\|\|\|\|\|\|_______\|\|_\|\|\|____\|\|\|\|\|_\|\|\|\|\|__:\|\|\|\|\|___\|_:\|\|:_\|\|__:\|__:\|\|:__\|:\|\|:\|:\n______________CUUUUUCCC_______CG_UGG____AGACU_UAGCG__UGGUUA___C_GUUU_UG__UG__UGUG__GUAGUGU\n3'-UUU...CUUCA_________AUCAGAG__A___CACC___________UC______A________G__U___U_____UU_______UGGCA...UCA-5'\n_____________\|____________________________________________________________________________\|\n_____________136__________________________________________________________________________65\n	130 -- 136	66 -- 72	-51.3167 kcal/mol	14.8404 kcal/mol	22.5826 kcal/mol	63 137@LB@ \| \|@LB@5'-AGC...AUGAA GAUCAAG AUU U CU AUC U G UU UU U CUCGC...CAU-3'@LB@ GAAAAAGGG GC ACC UCUGA AUCGC GCCAAU G UAAG AC GC GCAU CGUCGCG@LB@ \|\|\|\|\|\|\|\|\| \|\| \|\|\| \|\|\|\|\| \|\|\|\|\| :\|\|\|\|\| \| :\|\|: \|\| :\| :\|\|: \|:\|\|:\|:@LB@ CUUUUUCCC CG UGG AGACU UAGCG UGGUUA C GUUU UG UG UGUG GUAGUGU@LB@3'-UUU...CUUCA AUCAGAG A CACC UC A G U U UU UGGCA...UCA-5'@LB@ \| \|@LB@ 136 65@LB@@LB@@LB@Energy -13.59 kcal/mol@LB@Hybridization Energy -51.3167 kcal/mol@LB@Unfolding Energy - mRNA 14.8404 kcal/mol@LB@Unfolding Energy - sRNA 22.5826 kcal/mol@LB@@LB@Position - mRNA 64 -- 136@LB@Position - sRNA 66 -- 135@LB@Position Seed - mRNA 130 -- 136@LB@Position Seed - sRNA 66 -- 72@LB@
28	0.0007333	0.08814	stm0376	sbmA	-15.26	0.107034	68 -- 102	55 -- 90	peptide transporter	_____________67______________________________103\n_____________\|_______________________________\|\n5'-GCU...AGAAA_______UA____U______GUAG_______UGCCU...AUU-3'\n______________UGCGAAC__AGCG_CACAAC____GUCACAA\n______________\|\|\|:\|\|\|__\|:\|:_\|\|\|\|\|\|____:\|\|\|\|\|\|\n______________ACGUUUG__UUGU_GUGUUG____UAGUGUU\n3'-UUU...GGUUA_______UG____U_________________GGCAU...UCA-5'\n_____________\|_______________________________\|\n_____________91______________________________54\n	99 -- 105	65 -- 71	-26.4432 kcal/mol	7.11088 kcal/mol	6.59083 kcal/mol	67 103@LB@ \| \|@LB@5'-GCU...AGAAA UA U GUAG UGCCU...AUU-3'@LB@ UGCGAAC AGCG CACAAC GUCACAA@LB@ \|\|\|:\|\|\| \|:\|: \|\|\|\|\|\| :\|\|\|\|\|\|@LB@ ACGUUUG UUGU GUGUUG UAGUGUU@LB@3'-UUU...GGUUA UG U GGCAU...UCA-5'@LB@ \| \|@LB@ 91 54@LB@@LB@@LB@Energy -15.26 kcal/mol@LB@Hybridization Energy -26.4432 kcal/mol@LB@Unfolding Energy - mRNA 7.11088 kcal/mol@LB@Unfolding Energy - sRNA 6.59083 kcal/mol@LB@@LB@Position - mRNA 68 -- 102@LB@Position - sRNA 55 -- 90@LB@Position Seed - mRNA 99 -- 105@LB@Position Seed - sRNA 65 -- 71@LB@
29	0.0007392	0.08814	stm3096	yqgE	-16.45	0.068552	198 -- 251	37 -- 84	DUF179 domain-containing protein	_____________197___________252\n_____________\|_____________\|\n5'-UGG...UAUAU_____________CAGGA...GCG-3'\n______________UUGCGAGCACAAC\n______________\|\|\|\|:\|:\|\|\|\|\|\|\n______________AACGUUUGUGUUG\n3'-UUU...UGGUU_____________UUGUG...UCA-5'\n_____________\|_____________\|\n_____________85____________36\n	284 -- 290	80 -- 86	-18.5161 kcal/mol	2.82597 kcal/mol	3.5889 kcal/mol	197 252@LB@ \| \|@LB@5'-UGG...UAUAU CAGGA...GCG-3'@LB@ UUGCGAGCACAAC@LB@ \|\|\|\|:\|:\|\|\|\|\|\|@LB@ AACGUUUGUGUUG@LB@3'-UUU...UGGUU UUGUG...UCA-5'@LB@ \| \|@LB@ 85 36@LB@@LB@@LB@Energy -16.45 kcal/mol@LB@Hybridization Energy -18.5161 kcal/mol@LB@Unfolding Energy - mRNA 2.82597 kcal/mol@LB@Unfolding Energy - sRNA 3.5889 kcal/mol@LB@@LB@Position - mRNA 198 -- 251@LB@Position - sRNA 37 -- 84@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 80 -- 86@LB@
30	0.0007612	0.08814	stm3909	ilvC	-21.15	0.011132	166 -- 188	66 -- 89	ketol-acid reductoisomerase	_____________165_____________________189\n_____________\|_______________________\|\n5'-CCA...AACAA_______________________GGAGU...GCU-3'\n______________UAAGCGCGAC_ACACAACAUCAC\n______________:\|\|:\|:\|:\|\|_\|\|\|\|\|\|\|\|\|\|\|\|\n______________GUUUGUGUUG_UGUGUUGUAGUG\n3'-UUU...UUAAC__________U____________UUGGC...UCA-5'\n_____________\|_______________________\|\n_____________90______________________65\n	181 -- 187	67 -- 73	-29.859 kcal/mol	2.61707 kcal/mol	5.66809 kcal/mol	165 189@LB@ \| \|@LB@5'-CCA...AACAA GGAGU...GCU-3'@LB@ UAAGCGCGAC ACACAACAUCAC@LB@ :\|\|:\|:\|:\|\| \|\|\|\|\|\|\|\|\|\|\|\|@LB@ GUUUGUGUUG UGUGUUGUAGUG@LB@3'-UUU...UUAAC U UUGGC...UCA-5'@LB@ \| \|@LB@ 90 65@LB@@LB@@LB@Energy -21.15 kcal/mol@LB@Hybridization Energy -29.859 kcal/mol@LB@Unfolding Energy - mRNA 2.61707 kcal/mol@LB@Unfolding Energy - sRNA 5.66809 kcal/mol@LB@@LB@Position - mRNA 166 -- 188@LB@Position - sRNA 66 -- 89@LB@Position Seed - mRNA 181 -- 187@LB@Position Seed - sRNA 67 -- 73@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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