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
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@
170	0.009347	0.1945	stm0477	acrR	-17.70	0.042454	229 -- 246	74 -- 91	DNA-binding transcriptional repressor AcrR	_____________228________________247\n_____________\|__________________\|\n5'-AAG...AGCGC__G_______________UCCUG...CGC-3'\n______________UG_AGACACGACAACACA\n______________\|\|_\|:\|\|\|\|:\|\|\|\|\|\|\|\|\n______________AC_UUUGUGUUGUUGUGU\n3'-UUU...GGUUA__G_______________UGUAG...UCA-5'\n_____________\|__________________\|\n_____________92_________________73\n	240 -- 246	74 -- 80	-24.9092 kcal/mol	3.16809 kcal/mol	3.73631 kcal/mol	228 247@LB@ \| \|@LB@5'-AAG...AGCGC G UCCUG...CGC-3'@LB@ UG AGACACGACAACACA@LB@ \|\| \|:\|\|\|\|:\|\|\|\|\|\|\|\|@LB@ AC UUUGUGUUGUUGUGU@LB@3'-UUU...GGUUA G UGUAG...UCA-5'@LB@ \| \|@LB@ 92 73@LB@@LB@@LB@Energy -17.70 kcal/mol@LB@Hybridization Energy -24.9092 kcal/mol@LB@Unfolding Energy - mRNA 3.16809 kcal/mol@LB@Unfolding Energy - sRNA 3.73631 kcal/mol@LB@@LB@Position - mRNA 229 -- 246@LB@Position - sRNA 74 -- 91@LB@Position Seed - mRNA 240 -- 246@LB@Position Seed - sRNA 74 -- 80@LB@
132	0.006673	0.1774	stm2677	ffh	-17.54	0.045291	232 -- 275	38 -- 86	4.5S-RNP protein	_____________231_________________________________________________________________________________________________276\n_____________\|___________________________________________________________________________________________________\|\n5'-UAG...CAAAA_______UA__U_____CG____UU__CC__________A_A____A___A__G___UACG___C______CU____CC__U____________AA___GGCUU...AAG-3'\n______________ACGGGCA__GU__GUGU__ACAG__GA__AGUGAGAAAG_G_AG_C__GU_UA_CGU____UGA__CGCAG__CCAA__GU__GCAUAACAACA__GAC\n______________\|\|:\|:\|\|__\|\|__:\|\|\|__\|\|\|\|__\|\|__\|\|\|\|\|:\|\|\|\|_\|_\|\|_\|__\|:_\|\|_\|\|\|____\|\|\|__\|\|\|\|\|__\|\|\|\|__\|:__:\|\|:\|\|\|\|\|\|\|__:\|\|\n______________UGUCUGU__CA__UACA__UGUC__CU__UCACUUUUUC_C_UC_G__CG_AU_GCA____ACU__GCGUC__GGUU__CG__UGUGUUGUUGU__UUG\n3'-UUU...AUACC_______CC__UU__________________________C_A__A_AG_____G___CCAG___UA_____U_____AA__UU___________G____UAGUG...UCA-5'\n_____________\|___________________________________________________________________________________________________\|\n_____________87__________________________________________________________________________________________________37\n	110 -- 116	76 -- 82	-60.3799 kcal/mol	23.7315 kcal/mol	24.6218 kcal/mol	231 276@LB@ \| \|@LB@5'-UAG...CAAAA UA U CG UU CC A A A A G UACG C CU CC U AA GGCUU...AAG-3'@LB@ ACGGGCA GU GUGU ACAG GA AGUGAGAAAG G AG C GU UA CGU UGA CGCAG CCAA GU GCAUAACAACA GAC@LB@ \|\|:\|:\|\| \|\| :\|\|\| \|\|\|\| \|\| \|\|\|\|\|:\|\|\|\| \| \|\| \| \|: \|\| \|\|\| \|\|\| \|\|\|\|\| \|\|\|\| \|: :\|\|:\|\|\|\|\|\|\| :\|\|@LB@ UGUCUGU CA UACA UGUC CU UCACUUUUUC C UC G CG AU GCA ACU GCGUC GGUU CG UGUGUUGUUGU UUG@LB@3'-UUU...AUACC CC UU C A A AG G CCAG UA U AA UU G UAGUG...UCA-5'@LB@ \| \|@LB@ 87 37@LB@@LB@@LB@Energy -17.54 kcal/mol@LB@Hybridization Energy -60.3799 kcal/mol@LB@Unfolding Energy - mRNA 23.7315 kcal/mol@LB@Unfolding Energy - sRNA 24.6218 kcal/mol@LB@@LB@Position - mRNA 232 -- 275@LB@Position - sRNA 38 -- 86@LB@Position Seed - mRNA 110 -- 116@LB@Position Seed - sRNA 76 -- 82@LB@
139	0.007115	0.182	stm0826	ybiN	-18.61	0.029895	232 -- 282	36 -- 90	23S rRNA (adenine(1618)-N(6))-methyltransferase	_____________231___________________283\n_____________\|_____________________\|\n5'-CUC...GAGCC_____AACGAGCG________AAUUC...UUC-3'\n______________GAUCA________AGGCAGGG\n______________:\|\|\|\|________\|\|:\|\|\|\|\|\n______________UUAGU________UCUGUCCC\n3'-UUU...UGUAA_____GAUACCUG________AUUUA...UCA-5'\n_____________\|_____________________\|\n_____________91____________________35\n	124 -- 130	152 -- 158	-17.5433 kcal/mol	4.82059 kcal/mol	3.53427 kcal/mol	231 283@LB@ \| \|@LB@5'-CUC...GAGCC AACGAGCG AAUUC...UUC-3'@LB@ GAUCA AGGCAGGG@LB@ :\|\|\|\| \|\|:\|\|\|\|\|@LB@ UUAGU UCUGUCCC@LB@3'-UUU...UGUAA GAUACCUG AUUUA...UCA-5'@LB@ \| \|@LB@ 91 35@LB@@LB@@LB@Energy -18.61 kcal/mol@LB@Hybridization Energy -17.5433 kcal/mol@LB@Unfolding Energy - mRNA 4.82059 kcal/mol@LB@Unfolding Energy - sRNA 3.53427 kcal/mol@LB@@LB@Position - mRNA 232 -- 282@LB@Position - sRNA 36 -- 90@LB@Position Seed - mRNA 124 -- 130@LB@Position Seed - sRNA 152 -- 158@LB@
118	0.005761	0.1738	stm1840	yobG	-17.14	0.052758	234 -- 267	153 -- 188	PhoP regulon feedback inhibition protein MgrB	_____________233____________________________________________________________________________________268\n_____________\|______________________________________________________________________________________\|\n5'-ACA...AGAGU___________AUUUCGAU____C_U_____GC________GGUA______U___U_____UGU________GUGUU_________GUGCG...AAU-3'\n______________GGAGUGAAAAA________GGGU_G_UCUCG__AUCGUGGU_______GUA_GCC_GUUGC___GGGCGCAG_____UAAUAUCAU\n______________\|:\|\|\|\|\|\|\|\|\|________\|\|\|\|_\|_\|\|\|\|\|__\|:\|\|\|\|\|\|_______\|:\|_:\|\|_:\|\|\|\|___:::\|:\|\|:_____:\|\|:\|\|\|\|:\n______________CUUCACUUUUU________CCCA_C_AGAGC__UGGCACCA_______CGU_UGG_UAACG___UUUGUGUU_____GUUGUAGUG\n3'-UUU...AUGUC_______________________U_______GA________GACUUAG___C___U________________GUUGU_________UUGGC...UCA-5'\n_____________\|______________________________________________________________________________________\|\n_____________189____________________________________________________________________________________152\n	274 -- 280	67 -- 73	-62.0847 kcal/mol	28.922 kcal/mol	22.0106 kcal/mol	233 268@LB@ \| \|@LB@5'-ACA...AGAGU AUUUCGAU C U GC GGUA U U UGU GUGUU GUGCG...AAU-3'@LB@ GGAGUGAAAAA GGGU G UCUCG AUCGUGGU GUA GCC GUUGC GGGCGCAG UAAUAUCAU@LB@ \|:\|\|\|\|\|\|\|\|\| \|\|\|\| \| \|\|\|\|\| \|:\|\|\|\|\|\| \|:\| :\|\| :\|\|\|\| :::\|:\|\|: :\|\|:\|\|\|\|:@LB@ CUUCACUUUUU CCCA C AGAGC UGGCACCA CGU UGG UAACG UUUGUGUU GUUGUAGUG@LB@3'-UUU...AUGUC U GA GACUUAG C U GUUGU UUGGC...UCA-5'@LB@ \| \|@LB@ 189 152@LB@@LB@@LB@Energy -17.14 kcal/mol@LB@Hybridization Energy -62.0847 kcal/mol@LB@Unfolding Energy - mRNA 28.922 kcal/mol@LB@Unfolding Energy - sRNA 22.0106 kcal/mol@LB@@LB@Position - mRNA 234 -- 267@LB@Position - sRNA 153 -- 188@LB@Position Seed - mRNA 274 -- 280@LB@Position Seed - sRNA 67 -- 73@LB@
60	0.002585	0.1534	stm0758	ybgR	-11.90	0.345594	235 -- 293	32 -- 91	cation transporter	_____________234_________________________294\n_____________\|___________________________\|\n5'-GGU...ACACC___CG___G__________U_______CUGCU...UCC-3'\n______________UGC__AAA_AUAAUAAUGC__CGUCGC\n______________\|\|\|__\|\|\|_\|:\|\|:\|\|::\|__\|:\|\|:\|\n______________ACG__UUU_UGUUGUUGUG__GUAGUG\n3'-UUU...GGUUA________G__________UU______UUGGC...UCA-5'\n_____________\|___________________________\|\n_____________92__________________________31\n	247 -- 253	75 -- 81	-19.147 kcal/mol	4.2306 kcal/mol	5.6854 kcal/mol	234 294@LB@ \| \|@LB@5'-GGU...ACACC CG G U CUGCU...UCC-3'@LB@ UGC AAA AUAAUAAUGC CGUCGC@LB@ \|\|\| \|\|\| \|:\|\|:\|\|::\| \|:\|\|:\|@LB@ ACG UUU UGUUGUUGUG GUAGUG@LB@3'-UUU...GGUUA G UU UUGGC...UCA-5'@LB@ \| \|@LB@ 92 31@LB@@LB@@LB@Energy -11.90 kcal/mol@LB@Hybridization Energy -19.147 kcal/mol@LB@Unfolding Energy - mRNA 4.2306 kcal/mol@LB@Unfolding Energy - sRNA 5.6854 kcal/mol@LB@@LB@Position - mRNA 235 -- 293@LB@Position - sRNA 32 -- 91@LB@Position Seed - mRNA 247 -- 253@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@
196	0.01089	0.197	stm3904	ilvD	-14.14	0.161583	237 -- 253	179 -- 194	dihydroxy-acid dehydratase	_____________236___________254\n_____________\|_____________\|\n5'-CGA...UGAAG___AA________AGUAA...GCA-3'\n______________GGA__AGAUGGGG\n______________\|\|\|__\|\|\|::\|\|\|\n______________CCU__UCUGUCCC\n3'-UUU...UGAUA___G_________AUUUA...UCA-5'\n_____________\|_____________\|\n_____________195___________178\n	182 -- 188	152 -- 158	-15.6614 kcal/mol	1.17371 kcal/mol	3.10307 kcal/mol	236 254@LB@ \| \|@LB@5'-CGA...UGAAG AA AGUAA...GCA-3'@LB@ GGA AGAUGGGG@LB@ \|\|\| \|\|\|::\|\|\|@LB@ CCU UCUGUCCC@LB@3'-UUU...UGAUA G AUUUA...UCA-5'@LB@ \| \|@LB@ 195 178@LB@@LB@@LB@Energy -14.14 kcal/mol@LB@Hybridization Energy -15.6614 kcal/mol@LB@Unfolding Energy - mRNA 1.17371 kcal/mol@LB@Unfolding Energy - sRNA 3.10307 kcal/mol@LB@@LB@Position - mRNA 237 -- 253@LB@Position - sRNA 179 -- 194@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 152 -- 158@LB@
164	0.008796	0.191	stm2932	ygbE	-13.54	0.199482	240 -- 279	44 -- 82	putative inner membrane protein	_____________239________________280\n_____________\|__________________\|\n5'-CGC...GCGUA__________________UUUCA...CCA-3'\n______________AUAGC__CAUAACAUUAC\n______________\|:\|:\|__\|\|:\|\|\|\|\|:\|\|\n______________UGUUG__GUGUUGUAGUG\n3'-UUU...GUUUG_____UU___________UUGGC...UCA-5'\n_____________\|__________________\|\n_____________83_________________43\n	250 -- 256	67 -- 73	-14.8194 kcal/mol	1.59581 kcal/mol	5.25507 kcal/mol	239 280@LB@ \| \|@LB@5'-CGC...GCGUA UUUCA...CCA-3'@LB@ AUAGC CAUAACAUUAC@LB@ \|:\|:\| \|\|:\|\|\|\|\|:\|\|@LB@ UGUUG GUGUUGUAGUG@LB@3'-UUU...GUUUG UU UUGGC...UCA-5'@LB@ \| \|@LB@ 83 43@LB@@LB@@LB@Energy -13.54 kcal/mol@LB@Hybridization Energy -14.8194 kcal/mol@LB@Unfolding Energy - mRNA 1.59581 kcal/mol@LB@Unfolding Energy - sRNA 5.25507 kcal/mol@LB@@LB@Position - mRNA 240 -- 279@LB@Position - sRNA 44 -- 82@LB@Position Seed - mRNA 250 -- 256@LB@Position Seed - sRNA 67 -- 73@LB@
145	0.007435	0.1826	stm1822	yoaB	-15.17	0.110813	243 -- 269	162 -- 185	similar to E. coli orf hypothetical protein (AAC74879.1); Blastp hit to AAC74879.1 (130 aa) 92% identity in aa 17 - 130	_____________242______________________270\n_____________\|________________________\|\n5'-GUG...AUUUG___AG_____UAU_U_________AAGGC...CCG-3'\n______________CAC___GGAU___G_CAGGGUAGA\n______________\|\|\|___\|\|\|:___\|_\|\|\|\|\|\|\|:\|\n______________GUG___CCUG___C_GUCCCAUUU\n3'-UUU...AAUUA___AUA____U___U_________ACAUG...UCA-5'\n_____________\|________________________\|\n_____________186______________________161\n	106 -- 112	148 -- 154	-19.875 kcal/mol	5.9246 kcal/mol	4.20228 kcal/mol	242 270@LB@ \| \|@LB@5'-GUG...AUUUG AG UAU U AAGGC...CCG-3'@LB@ CAC GGAU G CAGGGUAGA@LB@ \|\|\| \|\|\|: \| \|\|\|\|\|\|\|:\|@LB@ GUG CCUG C GUCCCAUUU@LB@3'-UUU...AAUUA AUA U U ACAUG...UCA-5'@LB@ \| \|@LB@ 186 161@LB@@LB@@LB@Energy -15.17 kcal/mol@LB@Hybridization Energy -19.875 kcal/mol@LB@Unfolding Energy - mRNA 5.9246 kcal/mol@LB@Unfolding Energy - sRNA 4.20228 kcal/mol@LB@@LB@Position - mRNA 243 -- 269@LB@Position - sRNA 162 -- 185@LB@Position Seed - mRNA 106 -- 112@LB@Position Seed - sRNA 148 -- 154@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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