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
131	0.006551	0.1774	stm3217	aer	-17.88	0.039631	254 -- 298	36 -- 77	senses cellular redox state or proton motive force; similar to E. coli aerotaxis sensor receptor flavoprotein (AAC76107.1); Blastp hit to AAC76107.1 (506 aa) 83% identity in aa 1 - 506	_____________253____________________________________________________________________________________299\n_____________\|______________________________________________________________________________________\|\n5'-UUU...AAGGC______UGA_____________________ACAAA____AA__AUU____________________UC__G______UUUA_____UAAAG...CCA-3'\n______________GCAGGA___GGUGAAAA_________UCGU_____UAUU__GG____AAUCGCA____AAUUGCGA__CA_AGCAAU____ACAAC\n______________:\|\|\|\|\|___:\|\|\|\|\|\|\|_________\|\|\|:_____\|\|::__\|\|____\|\|\|\|\|\|\|____\|\|\|\|\|\|:\|__\|\|_\|:\|\|\|:____\|\|\|\|\|\n______________UGUCCU___UCACUUUU_________AGCG_____AUGG__CC____UUAGCGU____UUAACGUU__GU_UUGUUG____UGUUG\n3'-UUU...UUACA_________________UCCCAUCAG_____________CA__AGAC_______CUGG________U___G_______________UAGUG...UCA-5'\n_____________\|______________________________________________________________________________________\|\n_____________78_____________________________________________________________________________________35\n	89 -- 95	99 -- 105	-43.6348 kcal/mol	13.4466 kcal/mol	20.9633 kcal/mol	253 299@LB@ \| \|@LB@5'-UUU...AAGGC UGA ACAAA AA AUU UC G UUUA UAAAG...CCA-3'@LB@ GCAGGA GGUGAAAA UCGU UAUU GG AAUCGCA AAUUGCGA CA AGCAAU ACAAC@LB@ :\|\|\|\|\| :\|\|\|\|\|\|\| \|\|\|: \|\|:: \|\| \|\|\|\|\|\|\| \|\|\|\|\|\|:\| \|\| \|:\|\|\|: \|\|\|\|\|@LB@ UGUCCU UCACUUUU AGCG AUGG CC UUAGCGU UUAACGUU GU UUGUUG UGUUG@LB@3'-UUU...UUACA UCCCAUCAG CA AGAC CUGG U G UAGUG...UCA-5'@LB@ \| \|@LB@ 78 35@LB@@LB@@LB@Energy -17.88 kcal/mol@LB@Hybridization Energy -43.6348 kcal/mol@LB@Unfolding Energy - mRNA 13.4466 kcal/mol@LB@Unfolding Energy - sRNA 20.9633 kcal/mol@LB@@LB@Position - mRNA 254 -- 298@LB@Position - sRNA 36 -- 77@LB@Position Seed - mRNA 89 -- 95@LB@Position Seed - sRNA 99 -- 105@LB@
150	0.007945	0.1845	stm2555	glyA	-15.42	0.100951	252 -- 282	137 -- 168	serine hydroxymethyltransferase	_____________251_________________________________283\n_____________\|___________________________________\|\n5'-CAC...GGCAG________________AA________GUC______AGCAC...UCG-3'\n______________GCUAUGGA___GCAGG__AAA_GUAC___AGGAAG\n______________:\|\|\|\|\|\|\|___:\|\|\|\|__\|\|\|_\|\|\|\|___\|\|\|\|\|\|\n______________UGAUACCU___UGUCC__UUU_CAUG___UCCUUC\n3'-UUU...AUUAG________GUC_____CA___A_____________ACUUU...UCA-5'\n_____________\|___________________________________\|\n_____________169_________________________________136\n	253 -- 259	161 -- 167	-28.2568 kcal/mol	5.17684 kcal/mol	6.91101 kcal/mol	251 283@LB@ \| \|@LB@5'-CAC...GGCAG AA GUC AGCAC...UCG-3'@LB@ GCUAUGGA GCAGG AAA GUAC AGGAAG@LB@ :\|\|\|\|\|\|\| :\|\|\|\| \|\|\| \|\|\|\| \|\|\|\|\|\|@LB@ UGAUACCU UGUCC UUU CAUG UCCUUC@LB@3'-UUU...AUUAG GUC CA A ACUUU...UCA-5'@LB@ \| \|@LB@ 169 136@LB@@LB@@LB@Energy -15.42 kcal/mol@LB@Hybridization Energy -28.2568 kcal/mol@LB@Unfolding Energy - mRNA 5.17684 kcal/mol@LB@Unfolding Energy - sRNA 6.91101 kcal/mol@LB@@LB@Position - mRNA 252 -- 282@LB@Position - sRNA 137 -- 168@LB@Position Seed - mRNA 253 -- 259@LB@Position Seed - sRNA 161 -- 167@LB@
47	0.001676	0.127	stm0637	dacA	-17.91	0.039191	14 -- 64	37 -- 92	serine-type D-Ala-D-Ala carboxypeptidase	_____________13____________________65\n_____________\|_____________________\|\n5'-GUU...AACGU_________GA__________UACAG...AUA-3'\n______________UUGCAAACA____AGCACAAU\n______________\|\|\|\|\|\|\|\|\|____\|:\|\|\|\|\|:\n______________AACGUUUGU____UUGUGUUG\n3'-UUU...UGGUU_________GUUG________UAGUG...UCA-5'\n_____________\|_____________________\|\n_____________93____________________36\n	26 -- 32	72 -- 78	-19.7119 kcal/mol	3.03223 kcal/mol	3.80821 kcal/mol	13 65@LB@ \| \|@LB@5'-GUU...AACGU GA UACAG...AUA-3'@LB@ UUGCAAACA AGCACAAU@LB@ \|\|\|\|\|\|\|\|\| \|:\|\|\|\|\|:@LB@ AACGUUUGU UUGUGUUG@LB@3'-UUU...UGGUU GUUG UAGUG...UCA-5'@LB@ \| \|@LB@ 93 36@LB@@LB@@LB@Energy -17.91 kcal/mol@LB@Hybridization Energy -19.7119 kcal/mol@LB@Unfolding Energy - mRNA 3.03223 kcal/mol@LB@Unfolding Energy - sRNA 3.80821 kcal/mol@LB@@LB@Position - mRNA 14 -- 64@LB@Position - sRNA 37 -- 92@LB@Position Seed - mRNA 26 -- 32@LB@Position Seed - sRNA 72 -- 78@LB@
71	0.003339	0.1596	stm0105	yabI	-14.10	0.163814	151 -- 168	141 -- 162	similar to E. coli orf hypothetical protein (AAC73176.1); Blastp hit to AAC73176.1 (254 aa) 89% identity in aa 1 - 253	_____________150____________________169\n_____________\|______________________\|\n5'-UGA...ACGAA__G___________________AAUCC...GGU-3'\n______________GG_GGACGGGGUAA____GCAG\n______________\|:_:\|\|\|:\|\|\|\|\|\|____:\|\|\|\n______________CU_UCUGUCCCAUU____UGUC\n3'-UUU...GAUAC__G___________UACA____CUUCA...UCA-5'\n_____________\|______________________\|\n_____________163____________________140\n	158 -- 164	149 -- 155	-23.8591 kcal/mol	5.26969 kcal/mol	3.68511 kcal/mol	150 169@LB@ \| \|@LB@5'-UGA...ACGAA G AAUCC...GGU-3'@LB@ GG GGACGGGGUAA GCAG@LB@ \|: :\|\|\|:\|\|\|\|\|\| :\|\|\|@LB@ CU UCUGUCCCAUU UGUC@LB@3'-UUU...GAUAC G UACA CUUCA...UCA-5'@LB@ \| \|@LB@ 163 140@LB@@LB@@LB@Energy -14.10 kcal/mol@LB@Hybridization Energy -23.8591 kcal/mol@LB@Unfolding Energy - mRNA 5.26969 kcal/mol@LB@Unfolding Energy - sRNA 3.68511 kcal/mol@LB@@LB@Position - mRNA 151 -- 168@LB@Position - sRNA 141 -- 162@LB@Position Seed - mRNA 158 -- 164@LB@Position Seed - sRNA 149 -- 155@LB@
91	0.004202	0.1596	stm0387	yaiI	-16.26	0.073758	5 -- 45	23 -- 58	similar to E. coli orf hypothetical protein (AAC73490.1); Blastp hit to AAC73490.1 (192 aa) 89% identity in aa 41 - 191	_____________4____________________________________________46\n_____________\|____________________________________________\|\n_______5'-GUCC_______AUAGCCUU______AUU________G___A_______CGAUU...CCA-3'\n______________GCCAAGA________GCCCAU____AC_CGCA__CC_AUAAAAC\n______________\|\|\|\|\|:\|________\|\|\|\|\|\|____\|\|_\|\|\|\|__\|\|_\|\|\|\|\|\|\|\n______________CGGUUUU________CGGGUA____UG_GCGU__GG_UAUUUUG\n3'-UUU...GCAUU_____________________GUCU__U____AA__C_______AAAAG...UCA-5'\n_____________\|____________________________________________\|\n_____________59___________________________________________22\n	5 -- 11	52 -- 58	-32.2087 kcal/mol	3.21436 kcal/mol	17.1718 kcal/mol	4 46@LB@ \| \|@LB@ 5'-GUCC AUAGCCUU AUU G A CGAUU...CCA-3'@LB@ GCCAAGA GCCCAU AC CGCA CC AUAAAAC@LB@ \|\|\|\|\|:\| \|\|\|\|\|\| \|\| \|\|\|\| \|\| \|\|\|\|\|\|\|@LB@ CGGUUUU CGGGUA UG GCGU GG UAUUUUG@LB@3'-UUU...GCAUU GUCU U AA C AAAAG...UCA-5'@LB@ \| \|@LB@ 59 22@LB@@LB@@LB@Energy -16.26 kcal/mol@LB@Hybridization Energy -32.2087 kcal/mol@LB@Unfolding Energy - mRNA 3.21436 kcal/mol@LB@Unfolding Energy - sRNA 17.1718 kcal/mol@LB@@LB@Position - mRNA 5 -- 45@LB@Position - sRNA 23 -- 58@LB@Position Seed - mRNA 5 -- 11@LB@Position Seed - sRNA 52 -- 58@LB@
99	0.004942	0.1728	stm0604	ybdM	-18.77	0.028138	203 -- 249	36 -- 81	similar to E. coli orf hypothetical protein (AAC73702.1); Blastp hit to AAC73702.1 (209 aa) 77% identity in aa 5 - 209	_____________202___________________250\n_____________\|_____________________\|\n5'-AAA...CUUAU______C______________AAAUA...AUA-3'\n______________GCAACA_CGAC_UCACAACCG\n______________:\|\|\|\|\|_\|:\|\|_\|\|\|\|\|\|\|\|\|\n______________UGUUGU_GUUG_AGUGUUGGC\n3'-UUU...UGUGU___________U_________AUUCG...UCA-5'\n_____________\|_____________________\|\n_____________82____________________35\n	216 -- 222	62 -- 68	-25.0091 kcal/mol	1.37283 kcal/mol	7.72388 kcal/mol	202 250@LB@ \| \|@LB@5'-AAA...CUUAU C AAAUA...AUA-3'@LB@ GCAACA CGAC UCACAACCG@LB@ :\|\|\|\|\| \|:\|\| \|\|\|\|\|\|\|\|\|@LB@ UGUUGU GUUG AGUGUUGGC@LB@3'-UUU...UGUGU U AUUCG...UCA-5'@LB@ \| \|@LB@ 82 35@LB@@LB@@LB@Energy -18.77 kcal/mol@LB@Hybridization Energy -25.0091 kcal/mol@LB@Unfolding Energy - mRNA 1.37283 kcal/mol@LB@Unfolding Energy - sRNA 7.72388 kcal/mol@LB@@LB@Position - mRNA 203 -- 249@LB@Position - sRNA 36 -- 81@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 62 -- 68@LB@
183	0.01015	0.1966	stm0813	ybhP	-18.40	0.032407	2 -- 54	36 -- 90	similar to E. coli orf hypothetical protein (AAC73877.1); Blastp hit to AAC73877.1 (253 aa) 86% identity in aa 1 - 253	_____________1____________________________________55\n_____________\|____________________________________\|\n__________5'-A____________UA__CU__CA______________GGUUG...UGC-3'\n______________GUAAAUGCAACA__AU__GC___ACAACCG_AGGCC\n______________\|:\|\|\|::\|\|\|\|\|__\|:__:\|___\|\|\|\|\|\|\|_\|:\|\|\|\n______________CGUUUGUGUUGU__UG__UG___UGUUGGC_UUCGG\n3'-UUU...GUUAA____________UG__U___UAG_______A_____UUUUC...UCA-5'\n_____________\|____________________________________\|\n_____________91___________________________________35\n	24 -- 30	62 -- 68	-32.6929 kcal/mol	6.87264 kcal/mol	11.8287 kcal/mol	1 55@LB@ \| \|@LB@ 5'-A UA CU CA GGUUG...UGC-3'@LB@ GUAAAUGCAACA AU GC ACAACCG AGGCC@LB@ \|:\|\|\|::\|\|\|\|\| \|: :\| \|\|\|\|\|\|\| \|:\|\|\|@LB@ CGUUUGUGUUGU UG UG UGUUGGC UUCGG@LB@3'-UUU...GUUAA UG U UAG A UUUUC...UCA-5'@LB@ \| \|@LB@ 91 35@LB@@LB@@LB@Energy -18.40 kcal/mol@LB@Hybridization Energy -32.6929 kcal/mol@LB@Unfolding Energy - mRNA 6.87264 kcal/mol@LB@Unfolding Energy - sRNA 11.8287 kcal/mol@LB@@LB@Position - mRNA 2 -- 54@LB@Position - sRNA 36 -- 90@LB@Position Seed - mRNA 24 -- 30@LB@Position Seed - sRNA 62 -- 68@LB@
189	0.01049	0.1967	stm0871	ybjM	-13.57	0.197684	34 -- 53	71 -- 89	similar to E. coli orf hypothetical protein (AAC73935.1); Blastp hit to AAC73935.1 (125 aa) 72% identity in aa 1 - 125	_____________33___________________54\n_____________\|____________________\|\n5'-AAU...GCAUC______AA____________AUAUA...GCG-3'\n______________CAAAUA__AACAACACAACA\n______________\|\|\|\|:\|__\|\|\|\|\|\|\|\|\|\|\|\|\n______________GUUUGU__UUGUUGUGUUGU\n3'-UUU...UUAAC______G_____________AGUGU...UCA-5'\n_____________\|____________________\|\n_____________90___________________70\n	47 -- 53	71 -- 77	-19.7565 kcal/mol	2.01075 kcal/mol	3.79866 kcal/mol	33 54@LB@ \| \|@LB@5'-AAU...GCAUC AA AUAUA...GCG-3'@LB@ CAAAUA AACAACACAACA@LB@ \|\|\|\|:\| \|\|\|\|\|\|\|\|\|\|\|\|@LB@ GUUUGU UUGUUGUGUUGU@LB@3'-UUU...UUAAC G AGUGU...UCA-5'@LB@ \| \|@LB@ 90 70@LB@@LB@@LB@Energy -13.57 kcal/mol@LB@Hybridization Energy -19.7565 kcal/mol@LB@Unfolding Energy - mRNA 2.01075 kcal/mol@LB@Unfolding Energy - sRNA 3.79866 kcal/mol@LB@@LB@Position - mRNA 34 -- 53@LB@Position - sRNA 71 -- 89@LB@Position Seed - mRNA 47 -- 53@LB@Position Seed - sRNA 71 -- 77@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@
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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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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