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
137	0.006825	0.1774	stm1196	acpP	-14.14	0.161333	197 -- 223	36 -- 60	acyl carrier protein	_____________196___________________________________________224\n_____________\|_____________________________________________\|\n5'-ACU...AGAAC_______GAAA_____C____A____CU__GCGUUAA________AAGUA...UGG-3'\n______________GCGUUAA____AUUAU_GGCG_ACAG__GG_______GCAGGAAG\n______________:\|:\|\|\|\|____\|:\|\|\|_\|:\|:_\|\|\|\|__\|\|_______:\|\|\|\|\|\|\|\n______________UGUAAUU____UGAUA_CUGU_UGUC__CC_______UGUCCUUC\n3'-UUU...CACGA_______AG_______C____C________AUUUACA________ACUUU...UCA-5'\n_____________\|_____________________________________________\|\n_____________61____________________________________________35\n	258 -- 264	137 -- 143	-28.6095 kcal/mol	10.3633 kcal/mol	7.13805 kcal/mol	196 224@LB@ \| \|@LB@5'-ACU...AGAAC GAAA C A CU GCGUUAA AAGUA...UGG-3'@LB@ GCGUUAA AUUAU GGCG ACAG GG GCAGGAAG@LB@ :\|:\|\|\|\| \|:\|\|\| \|:\|: \|\|\|\| \|\| :\|\|\|\|\|\|\|@LB@ UGUAAUU UGAUA CUGU UGUC CC UGUCCUUC@LB@3'-UUU...CACGA AG C C AUUUACA ACUUU...UCA-5'@LB@ \| \|@LB@ 61 35@LB@@LB@@LB@Energy -14.14 kcal/mol@LB@Hybridization Energy -28.6095 kcal/mol@LB@Unfolding Energy - mRNA 10.3633 kcal/mol@LB@Unfolding Energy - sRNA 7.13805 kcal/mol@LB@@LB@Position - mRNA 197 -- 223@LB@Position - sRNA 36 -- 60@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 137 -- 143@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@
143	0.007336	0.182	stm2276	ubiG	-14.65	0.134291	225 -- 278	36 -- 81	2-octaprenyl-6-hydroxy phenol methylase	_____________224_________________279\n_____________\|___________________\|\n5'-CAC...CGGCA____________CA_____UUUGC...AAU-3'\n______________GUAGAUAUAACG__GCGAC\n______________\|:\|:\|:\|:\|\|\|:__:\|:\|\|\n______________CGUUUGUGUUGU__UGUUG\n3'-UUU...GUUAA____________UG_____UAGUG...UCA-5'\n_____________\|___________________\|\n_____________82__________________35\n	134 -- 140	80 -- 86	-18.0681 kcal/mol	5.41873 kcal/mol	3.80362 kcal/mol	224 279@LB@ \| \|@LB@5'-CAC...CGGCA CA UUUGC...AAU-3'@LB@ GUAGAUAUAACG GCGAC@LB@ \|:\|:\|:\|:\|\|\|: :\|:\|\|@LB@ CGUUUGUGUUGU UGUUG@LB@3'-UUU...GUUAA UG UAGUG...UCA-5'@LB@ \| \|@LB@ 82 35@LB@@LB@@LB@Energy -14.65 kcal/mol@LB@Hybridization Energy -18.0681 kcal/mol@LB@Unfolding Energy - mRNA 5.41873 kcal/mol@LB@Unfolding Energy - sRNA 3.80362 kcal/mol@LB@@LB@Position - mRNA 225 -- 278@LB@Position - sRNA 36 -- 81@LB@Position Seed - mRNA 134 -- 140@LB@Position Seed - sRNA 80 -- 86@LB@
149	0.007892	0.1845	stm2071	hisG	-15.61	0.094042	166 -- 245	36 -- 100	ATP phosphoribosyltransferase	_____________165________________________246\n_____________\|__________________________\|\n5'-UUU...AGACC__UU________A________G____ACGCA...AUU-3'\n______________GG__CAGACAGG_UAA____A_AGGA\n______________\|\|__\|\|\|\|\|\|\|\|_\|\|\|____\|_\|\|\|\|\n______________CC__GUCUGUCC_AUU____U_UCCU\n3'-UUU...UGAUA__U_________C___UACA_G____UCACU...UCA-5'\n_____________\|__________________________\|\n_____________101________________________35\n	177 -- 183	153 -- 159	-19.7047 kcal/mol	3.01127 kcal/mol	3.70983 kcal/mol	165 246@LB@ \| \|@LB@5'-UUU...AGACC UU A G ACGCA...AUU-3'@LB@ GG CAGACAGG UAA A AGGA@LB@ \|\| \|\|\|\|\|\|\|\| \|\|\| \| \|\|\|\|@LB@ CC GUCUGUCC AUU U UCCU@LB@3'-UUU...UGAUA U C UACA G UCACU...UCA-5'@LB@ \| \|@LB@ 101 35@LB@@LB@@LB@Energy -15.61 kcal/mol@LB@Hybridization Energy -19.7047 kcal/mol@LB@Unfolding Energy - mRNA 3.01127 kcal/mol@LB@Unfolding Energy - sRNA 3.70983 kcal/mol@LB@@LB@Position - mRNA 166 -- 245@LB@Position - sRNA 36 -- 100@LB@Position Seed - mRNA 177 -- 183@LB@Position Seed - sRNA 153 -- 159@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@
165	0.008886	0.1918	stm0281	N/A	-13.47	0.204933	267 -- 289	36 -- 56	type VI secretion system-associated protein	_____________266______________________________________________290\n_____________\|________________________________________________\|\n5'-UGA...UAAUU____A_____A______A__UAU___C_____UGACC_C_______G_AGUGA...ACC-3'\n______________ACGG_ACGGG_UAAAUG_AU___GAG_UGGAA_____G_GUAGUCU_G\n______________\|\|:\|_\|\|:\|\|_\|\|\|\|\|\|_\|:___:\|\|_\|\|:\|\|_____\|_\|\|\|\|\|\|\|_\|\n______________UGUC_UGUCC_AUUUAC_UG___UUC_ACUUU_____C_CAUCAGA_C\n3'-UUU...AUACC__________C______A__UCC_________UUC___________G_GAUGG...UCA-5'\n_____________\|________________________________________________\|\n_____________57_______________________________________________35\n	219 -- 225	121 -- 127	-29.4304 kcal/mol	8.43831 kcal/mol	11.9516 kcal/mol	266 290@LB@ \| \|@LB@5'-UGA...UAAUU A A A UAU C UGACC C G AGUGA...ACC-3'@LB@ ACGG ACGGG UAAAUG AU GAG UGGAA G GUAGUCU G@LB@ \|\|:\| \|\|:\|\| \|\|\|\|\|\| \|: :\|\| \|\|:\|\| \| \|\|\|\|\|\|\| \|@LB@ UGUC UGUCC AUUUAC UG UUC ACUUU C CAUCAGA C@LB@3'-UUU...AUACC C A UCC UUC G GAUGG...UCA-5'@LB@ \| \|@LB@ 57 35@LB@@LB@@LB@Energy -13.47 kcal/mol@LB@Hybridization Energy -29.4304 kcal/mol@LB@Unfolding Energy - mRNA 8.43831 kcal/mol@LB@Unfolding Energy - sRNA 11.9516 kcal/mol@LB@@LB@Position - mRNA 267 -- 289@LB@Position - sRNA 36 -- 56@LB@Position Seed - mRNA 219 -- 225@LB@Position Seed - sRNA 121 -- 127@LB@
178	0.009774	0.1951	stm2667	pheA	-14.20	0.157815	177 -- 228	36 -- 93	chorismate mutase	_____________176__________________229\n_____________\|____________________\|\n5'-GAC...ACAAA___G______C_________GGAAA...UUG-3'\n______________AAA_GCAACA_UAUGACAUC\n______________\|\|\|_:\|\|\|\|\|_:\|::\|\|\|\|\|\n______________UUU_UGUUGU_GUGUUGUAG\n3'-UUU...UAACG___G______U_________UGUUG...UCA-5'\n_____________\|____________________\|\n_____________94___________________35\n	202 -- 208	69 -- 75	-17.8987 kcal/mol	1.45353 kcal/mol	4.11387 kcal/mol	176 229@LB@ \| \|@LB@5'-GAC...ACAAA G C GGAAA...UUG-3'@LB@ AAA GCAACA UAUGACAUC@LB@ \|\|\| :\|\|\|\|\| :\|::\|\|\|\|\|@LB@ UUU UGUUGU GUGUUGUAG@LB@3'-UUU...UAACG G U UGUUG...UCA-5'@LB@ \| \|@LB@ 94 35@LB@@LB@@LB@Energy -14.20 kcal/mol@LB@Hybridization Energy -17.8987 kcal/mol@LB@Unfolding Energy - mRNA 1.45353 kcal/mol@LB@Unfolding Energy - sRNA 4.11387 kcal/mol@LB@@LB@Position - mRNA 177 -- 228@LB@Position - sRNA 36 -- 93@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 69 -- 75@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@
192	0.01067	0.197	stm2650	yfiP	-13.22	0.223534	188 -- 232	36 -- 90	DTW domain-containing protein	_____________187_________________________233\n_____________\|___________________________\|\n5'-UCA...UCUCC________UUUCUAUGACC________UGUCC...GCU-3'\n______________GCAAACGC___________AAUAACGC\n______________\|\|\|\|\|\|:\|___________\|\|:\|\|\|:\|\n______________CGUUUGUG___________UUGUUGUG\n3'-UUU...GUUAA___________________________UUGUA...UCA-5'\n_____________\|___________________________\|\n_____________91__________________________35\n	208 -- 214	75 -- 81	-16.7007 kcal/mol	3.95203 kcal/mol	3.72363 kcal/mol	187 233@LB@ \| \|@LB@5'-UCA...UCUCC UUUCUAUGACC UGUCC...GCU-3'@LB@ GCAAACGC AAUAACGC@LB@ \|\|\|\|\|\|:\| \|\|:\|\|\|:\|@LB@ CGUUUGUG UUGUUGUG@LB@3'-UUU...GUUAA UUGUA...UCA-5'@LB@ \| \|@LB@ 91 35@LB@@LB@@LB@Energy -13.22 kcal/mol@LB@Hybridization Energy -16.7007 kcal/mol@LB@Unfolding Energy - mRNA 3.95203 kcal/mol@LB@Unfolding Energy - sRNA 3.72363 kcal/mol@LB@@LB@Position - mRNA 188 -- 232@LB@Position - sRNA 36 -- 90@LB@Position Seed - mRNA 208 -- 214@LB@Position Seed - sRNA 75 -- 81@LB@
197	0.01093	0.197	stm2924	rpoS	-16.80	0.060020	191 -- 216	36 -- 60	RNA polymerase sigma factor RpoS	_____________190________________________________217\n_____________\|__________________________________\|\n___5'-CGGGAACA_________U____C___GCAAAAAA________AUGGG...AGG-3'\n______________ACAGGAAGU_AAGG_GGG________UCGCUACU\n______________\|\|\|\|\|\|\|\|\|_\|\|::_\|\|\|________\|\|\|\|\|\|\|:\n______________UGUCCUUCA_UUUU_CCC________AGCGAUGG\n3'-UUU...UUACA_________C____U___AUCAG___________CACCA...UCA-5'\n_____________\|__________________________________\|\n_____________61_________________________________35\n	36 -- 42	114 -- 120	-31.3768 kcal/mol	8.74888 kcal/mol	8.99738 kcal/mol	190 217@LB@ \| \|@LB@ 5'-CGGGAACA U C GCAAAAAA AUGGG...AGG-3'@LB@ ACAGGAAGU AAGG GGG UCGCUACU@LB@ \|\|\|\|\|\|\|\|\| \|\|:: \|\|\| \|\|\|\|\|\|\|:@LB@ UGUCCUUCA UUUU CCC AGCGAUGG@LB@3'-UUU...UUACA C U AUCAG CACCA...UCA-5'@LB@ \| \|@LB@ 61 35@LB@@LB@@LB@Energy -16.80 kcal/mol@LB@Hybridization Energy -31.3768 kcal/mol@LB@Unfolding Energy - mRNA 8.74888 kcal/mol@LB@Unfolding Energy - sRNA 8.99738 kcal/mol@LB@@LB@Position - mRNA 191 -- 216@LB@Position - sRNA 36 -- 60@LB@Position Seed - mRNA 36 -- 42@LB@Position Seed - sRNA 114 -- 120@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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