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	Additional homologs
120	0.006002	0.1758	stm2925	nlpD	-17.26	0.050371	258 -- 274	153 -- 170	lipoprotein NlpD		_____________257________________275\n_____________\|__________________\|\n5'-GUU...UGGUU___________U______UUGUA...CGG-3'\n______________UCACUAUGG_C_GGCAGG\n______________\|\|\|\|\|\|\|\|\|_\|_\|:\|\|\|\|\n______________AGUGAUACC_G_CUGUCC\n3'-UUU...UAAUU_________U_U______CAUUU...UCA-5'\n_____________\|__________________\|\n_____________171________________152\n	260 -- 266	162 -- 168	-24.411 kcal/mol	4.59255 kcal/mol	3.4766 kcal/mol	257 275@LB@ \| \|@LB@5'-GUU...UGGUU U UUGUA...CGG-3'@LB@ UCACUAUGG C GGCAGG@LB@ \|\|\|\|\|\|\|\|\| \| \|:\|\|\|\|@LB@ AGUGAUACC G CUGUCC@LB@3'-UUU...UAAUU U U CAUUU...UCA-5'@LB@ \| \|@LB@ 171 152@LB@@LB@@LB@Energy -17.26 kcal/mol@LB@Hybridization Energy -24.411 kcal/mol@LB@Unfolding Energy - mRNA 4.59255 kcal/mol@LB@Unfolding Energy - sRNA 3.4766 kcal/mol@LB@@LB@Position - mRNA 258 -- 274@LB@Position - sRNA 153 -- 170@LB@Position Seed - mRNA 260 -- 266@LB@Position Seed - sRNA 162 -- 168@LB@
194	0.01081	0.197	stm1954	fliY	-13.82	0.181182	183 -- 228	153 -- 193	cystine ABC transporter substrate-binding protein		_____________182________________________229\n_____________\|__________________________\|\n5'-CAG...GUCUA_________AC____AUAUU______UACUA...UGC-3'\n______________UGGUCAUUA__GGCA_____CGGGGU\n______________\|::\|\|\|:\|\|__\|:\|\|_____\|:\|\|\|\|\n______________AUUAGUGAU__CUGU_____GUCCCA\n3'-UUU...AUGUA_________AC____CU_________UUUAC...UCA-5'\n_____________\|__________________________\|\n_____________194________________________152\n	173 -- 179	165 -- 171	-18.5851 kcal/mol	4.12345 kcal/mol	4.10259 kcal/mol	182 229@LB@ \| \|@LB@5'-CAG...GUCUA AC AUAUU UACUA...UGC-3'@LB@ UGGUCAUUA GGCA CGGGGU@LB@ \|::\|\|\|:\|\| \|:\|\| \|:\|\|\|\|@LB@ AUUAGUGAU CUGU GUCCCA@LB@3'-UUU...AUGUA AC CU UUUAC...UCA-5'@LB@ \| \|@LB@ 194 152@LB@@LB@@LB@Energy -13.82 kcal/mol@LB@Hybridization Energy -18.5851 kcal/mol@LB@Unfolding Energy - mRNA 4.12345 kcal/mol@LB@Unfolding Energy - sRNA 4.10259 kcal/mol@LB@@LB@Position - mRNA 183 -- 228@LB@Position - sRNA 153 -- 193@LB@Position Seed - mRNA 173 -- 179@LB@Position Seed - sRNA 165 -- 171@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@
52	0.001934	0.1324	stm0653	ybeL	-17.18	0.051878	262 -- 299	155 -- 188	similar to E. coli putative alpha helical protein (AAC73744.1); Blastp hit to AAC73744.1 (160 aa) 91% identity in aa 1 - 160		_____________261________________________300\n_____________\|__________________________\|\n5'-AUU...GCGCG________G____G_____G______C-3'\n______________ACAUUGAU_CGCU_GUGGA_CAGGCG\n______________\|\|\|\|\|:\|\|_\|:\|\|_:\|\|\|\|_\|\|\|:\|:\n______________UGUAAUUA_GUGA_UACCU_GUCUGU\n3'-UUU...CACGA__________________________CCCAU...UCA-5'\n_____________\|__________________________\|\n_____________189________________________154\n	275 -- 281	170 -- 176	-23.9532 kcal/mol	9.91713 kcal/mol	4.10825 kcal/mol	261 300@LB@ \| \|@LB@5'-AUU...GCGCG G G G C-3'@LB@ ACAUUGAU CGCU GUGGA CAGGCG@LB@ \|\|\|\|\|:\|\| \|:\|\| :\|\|\|\| \|\|\|:\|:@LB@ UGUAAUUA GUGA UACCU GUCUGU@LB@3'-UUU...CACGA CCCAU...UCA-5'@LB@ \| \|@LB@ 189 154@LB@@LB@@LB@Energy -17.18 kcal/mol@LB@Hybridization Energy -23.9532 kcal/mol@LB@Unfolding Energy - mRNA 9.91713 kcal/mol@LB@Unfolding Energy - sRNA 4.10825 kcal/mol@LB@@LB@Position - mRNA 262 -- 299@LB@Position - sRNA 155 -- 188@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 170 -- 176@LB@
96	0.004303	0.1596	stm4243	yjbN	-11.74	0.363864	272 -- 280	155 -- 163	tRNA dihydrouridine(20/20a) synthase DusA		_____________271______________________________281\n_____________\|________________________________\|\n5'-UUA...UUAAU___AC_________C____A_____CCU____GGCAG...GUU-3'\n______________GGG____UGUACGG_GAAG_UGAAA___GGGG\n______________\|\|\|____\|\|\|\|\|:\|_\|\|\|\|_\|\|\|\|\|___:\|\|\|\n______________CCC____ACAUGUC_CUUC_ACUUU___UCCC\n3'-UUU...UCUGU___AUUU__________________U______AUCAG...UCA-5'\n_____________\|________________________________\|\n_____________164______________________________154\n	58 -- 64	141 -- 147	-26.0653 kcal/mol	8.12251 kcal/mol	7.07058 kcal/mol	271 281@LB@ \| \|@LB@5'-UUA...UUAAU AC C A CCU GGCAG...GUU-3'@LB@ GGG UGUACGG GAAG UGAAA GGGG@LB@ \|\|\| \|\|\|\|\|:\| \|\|\|\| \|\|\|\|\| :\|\|\|@LB@ CCC ACAUGUC CUUC ACUUU UCCC@LB@3'-UUU...UCUGU AUUU U AUCAG...UCA-5'@LB@ \| \|@LB@ 164 154@LB@@LB@@LB@Energy -11.74 kcal/mol@LB@Hybridization Energy -26.0653 kcal/mol@LB@Unfolding Energy - mRNA 8.12251 kcal/mol@LB@Unfolding Energy - sRNA 7.07058 kcal/mol@LB@@LB@Position - mRNA 272 -- 280@LB@Position - sRNA 155 -- 163@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 141 -- 147@LB@
195	0.01085	0.197	stm0549	fimZ	-13.17	0.226725	219 -- 235	155 -- 171	DNA-binding response regulator		_____________218___________236\n_____________\|_____________\|\n5'-CAG...CUGUU_____________AACAC...UGA-3'\n______________AUCAUUAUGGACG\n______________\|\|\|\|:\|\|\|\|\|\|\|:\n______________UAGUGAUACCUGU\n3'-UUU...GUAAU_____________CUGUC...UCA-5'\n_____________\|_____________\|\n_____________172___________154\n	225 -- 231	159 -- 165	-17.3187 kcal/mol	3.33371 kcal/mol	3.42647 kcal/mol	218 236@LB@ \| \|@LB@5'-CAG...CUGUU AACAC...UGA-3'@LB@ AUCAUUAUGGACG@LB@ \|\|\|\|:\|\|\|\|\|\|\|:@LB@ UAGUGAUACCUGU@LB@3'-UUU...GUAAU CUGUC...UCA-5'@LB@ \| \|@LB@ 172 154@LB@@LB@@LB@Energy -13.17 kcal/mol@LB@Hybridization Energy -17.3187 kcal/mol@LB@Unfolding Energy - mRNA 3.33371 kcal/mol@LB@Unfolding Energy - sRNA 3.42647 kcal/mol@LB@@LB@Position - mRNA 219 -- 235@LB@Position - sRNA 155 -- 171@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 159 -- 165@LB@
41	0.001426	0.1215	stm3718	rfaI	-15.09	0.114319	193 -- 209	157 -- 173	lipopolysaccharide 1 3-galactosyltransferase	stm3717	_____________192_______________210\n_____________\|_________________\|\n5'-AUG...AAAAG___________A_____AAAUA...GGA-3'\n______________UGAUCACUAUG_GCAGA\n______________\|:\|\|\|\|\|\|\|\|\|_:\|\|\|\|\n______________AUUAGUGAUAC_UGUCU\n3'-UUU...AUGUA___________C_____GUCCC...UCA-5'\n_____________\|_________________\|\n_____________174_______________156\n	197 -- 203	163 -- 169	-20.9664 kcal/mol	2.81615 kcal/mol	3.98136 kcal/mol	192 210@LB@ \| \|@LB@5'-AUG...AAAAG A AAAUA...GGA-3'@LB@ UGAUCACUAUG GCAGA@LB@ \|:\|\|\|\|\|\|\|\|\| :\|\|\|\|@LB@ AUUAGUGAUAC UGUCU@LB@3'-UUU...AUGUA C GUCCC...UCA-5'@LB@ \| \|@LB@ 174 156@LB@@LB@@LB@Energy -15.09 kcal/mol@LB@Hybridization Energy -20.9664 kcal/mol@LB@Unfolding Energy - mRNA 2.81615 kcal/mol@LB@Unfolding Energy - sRNA 3.98136 kcal/mol@LB@@LB@Position - mRNA 193 -- 209@LB@Position - sRNA 157 -- 173@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 163 -- 169@LB@
133	0.006689	0.1774	stm0831	dps	-13.05	0.236755	141 -- 176	159 -- 184	DNA starvation/stationary phase protection protein Dps		_____________140________________________177\n_____________\|__________________________\|\n5'-CAU...UUACC___CA_______AACU__________AAUUG...UUA-3'\n______________CAC__AACAGCA____CGUC_UAACC\n______________\|\|\|__\|\|\|\|:\|\|____\|:\|\|_:\|\|\|\|\n______________GUG__UUGUUGU____GUAG_GUUGG\n3'-UUU...CGUUU____________GUU_____U_____CAUUC...UCA-5'\n_____________\|__________________________\|\n_____________185________________________158\n	37 -- 43	76 -- 82	-18.4678 kcal/mol	1.39739 kcal/mol	8.25195 kcal/mol	140 177@LB@ \| \|@LB@5'-CAU...UUACC CA AACU AAUUG...UUA-3'@LB@ CAC AACAGCA CGUC UAACC@LB@ \|\|\| \|\|\|\|:\|\| \|:\|\| :\|\|\|\|@LB@ GUG UUGUUGU GUAG GUUGG@LB@3'-UUU...CGUUU GUU U CAUUC...UCA-5'@LB@ \| \|@LB@ 185 158@LB@@LB@@LB@Energy -13.05 kcal/mol@LB@Hybridization Energy -18.4678 kcal/mol@LB@Unfolding Energy - mRNA 1.39739 kcal/mol@LB@Unfolding Energy - sRNA 8.25195 kcal/mol@LB@@LB@Position - mRNA 141 -- 176@LB@Position - sRNA 159 -- 184@LB@Position Seed - mRNA 37 -- 43@LB@Position Seed - sRNA 76 -- 82@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@
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@

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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