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
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@
199	0.01101	0.197	stm3346	yhcM	-12.83	0.254909	186 -- 228	33 -- 82	cell division protein ZapE	_____________185____________________229\n_____________\|______________________\|\n5'-CAG...UUCAA_G__UA__________UAU___AAGCC...AAA-3'\n______________G_AA__ACAAUAACAU___GCA\n______________\|_\|\|__\|\|\|\|:\|\|\|\|:___:\|\|\n______________C_UU__UGUUGUUGUG___UGU\n3'-UUU...GUUAA_G__UG__________U_____AGUGU...UCA-5'\n_____________\|______________________\|\n_____________83_____________________32\n	193 -- 199	75 -- 81	-14.0954 kcal/mol	2.45302 kcal/mol	3.80671 kcal/mol	185 229@LB@ \| \|@LB@5'-CAG...UUCAA G UA UAU AAGCC...AAA-3'@LB@ G AA ACAAUAACAU GCA@LB@ \| \|\| \|\|\|\|:\|\|\|\|: :\|\|@LB@ C UU UGUUGUUGUG UGU@LB@3'-UUU...GUUAA G UG U AGUGU...UCA-5'@LB@ \| \|@LB@ 83 32@LB@@LB@@LB@Energy -12.83 kcal/mol@LB@Hybridization Energy -14.0954 kcal/mol@LB@Unfolding Energy - mRNA 2.45302 kcal/mol@LB@Unfolding Energy - sRNA 3.80671 kcal/mol@LB@@LB@Position - mRNA 186 -- 228@LB@Position - sRNA 33 -- 82@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 75 -- 81@LB@
110	0.005337	0.1728	stm1920	cheW	-12.58	0.277263	149 -- 192	51 -- 90	chemotaxis protein CheW	_____________148__________193\n_____________\|____________\|\n5'-GUC...UGAUU____________AAUAA...UCC-3'\n______________GAGUGAGAAGGG\n______________:\|\|\|\|\|:\|\|:\|\|\n______________UUCACUUUUUCC\n3'-UUU...UGUCC____________CAUCA...UCA-5'\n_____________\|____________\|\n_____________91___________50\n	188 -- 194	128 -- 134	-15.4894 kcal/mol	2.64754 kcal/mol	3.77328 kcal/mol	148 193@LB@ \| \|@LB@5'-GUC...UGAUU AAUAA...UCC-3'@LB@ GAGUGAGAAGGG@LB@ :\|\|\|\|\|:\|\|:\|\|@LB@ UUCACUUUUUCC@LB@3'-UUU...UGUCC CAUCA...UCA-5'@LB@ \| \|@LB@ 91 50@LB@@LB@@LB@Energy -12.58 kcal/mol@LB@Hybridization Energy -15.4894 kcal/mol@LB@Unfolding Energy - mRNA 2.64754 kcal/mol@LB@Unfolding Energy - sRNA 3.77328 kcal/mol@LB@@LB@Position - mRNA 149 -- 192@LB@Position - sRNA 51 -- 90@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 128 -- 134@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@
20	0.0004512	0.08034	stm2384	aroC	-21.00	0.011794	171 -- 223	39 -- 90	chorismate synthase	_____________170___________________224\n_____________\|_____________________\|\n5'-GUU...AACAC______G________G_____GGAGC...GCA-3'\n______________GCAAAC_ACAACAAC_AUAAC\n______________\|\|\|\|\|\|_\|\|\|\|\|\|\|\|_\|:\|\|\|\n______________CGUUUG_UGUUGUUG_UGUUG\n3'-UUU...GUUAA_____________________UAGUG...UCA-5'\n_____________\|_____________________\|\n_____________91____________________38\n	179 -- 185	77 -- 83	-22.4295 kcal/mol	1.97696 kcal/mol	3.80362 kcal/mol	170 224@LB@ \| \|@LB@5'-GUU...AACAC G G GGAGC...GCA-3'@LB@ GCAAAC ACAACAAC AUAAC@LB@ \|\|\|\|\|\| \|\|\|\|\|\|\|\| \|:\|\|\|@LB@ CGUUUG UGUUGUUG UGUUG@LB@3'-UUU...GUUAA UAGUG...UCA-5'@LB@ \| \|@LB@ 91 38@LB@@LB@@LB@Energy -21.00 kcal/mol@LB@Hybridization Energy -22.4295 kcal/mol@LB@Unfolding Energy - mRNA 1.97696 kcal/mol@LB@Unfolding Energy - sRNA 3.80362 kcal/mol@LB@@LB@Position - mRNA 171 -- 223@LB@Position - sRNA 39 -- 90@LB@Position Seed - mRNA 179 -- 185@LB@Position Seed - sRNA 77 -- 83@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@
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@
108	0.005311	0.1728	stm2183	cdd	-16.35	0.071230	31 -- 68	151 -- 187	cytidine deaminase	_____________30_________________69\n_____________\|__________________\|\n5'-UGG...AGAUC_____UUAA_________GGCCC...UGA-3'\n______________ACAUA____GACAUAGCA\n______________\|\|\|:\|____:\|\|\|:\|:\|\|\n______________UGUGU____UUGUGUUGU\n3'-UUU...ACGUU_____UG___________AGUGU...UCA-5'\n_____________\|__________________\|\n_____________188________________150\n	150 -- 156	71 -- 77	-12.389 kcal/mol	1.12571 kcal/mol	3.50787 kcal/mol	30 69@LB@ \| \|@LB@5'-UGG...AGAUC UUAA GGCCC...UGA-3'@LB@ ACAUA GACAUAGCA@LB@ \|\|\|:\| :\|\|\|:\|:\|\|@LB@ UGUGU UUGUGUUGU@LB@3'-UUU...ACGUU UG AGUGU...UCA-5'@LB@ \| \|@LB@ 188 150@LB@@LB@@LB@Energy -16.35 kcal/mol@LB@Hybridization Energy -12.389 kcal/mol@LB@Unfolding Energy - mRNA 1.12571 kcal/mol@LB@Unfolding Energy - sRNA 3.50787 kcal/mol@LB@@LB@Position - mRNA 31 -- 68@LB@Position - sRNA 151 -- 187@LB@Position Seed - mRNA 150 -- 156@LB@Position Seed - sRNA 71 -- 77@LB@
33	0.001058	0.1142	stm0380	ddlA	-21.71	0.008945	31 -- 67	39 -- 76	D-alanine--D-alanine ligase A	_____________30____________________68\n_____________\|_____________________\|\n5'-AGC...GCCAA___C___C_____________AUCAG...AAA-3'\n______________UGC__GC_CAACAGCACAAUA\n______________\|\|\|__:\|_\|\|\|\|\|:\|\|\|\|\|:\|\n______________ACG__UG_GUUGUUGUGUUGU\n3'-UUU...GGUUA___UU__U_____________AGUGU...UCA-5'\n_____________\|_____________________\|\n_____________77____________________38\n	64 -- 70	71 -- 77	-20.6082 kcal/mol	2.86044 kcal/mol	3.80854 kcal/mol	30 68@LB@ \| \|@LB@5'-AGC...GCCAA C C AUCAG...AAA-3'@LB@ UGC GC CAACAGCACAAUA@LB@ \|\|\| :\| \|\|\|\|\|:\|\|\|\|\|:\|@LB@ ACG UG GUUGUUGUGUUGU@LB@3'-UUU...GGUUA UU U AGUGU...UCA-5'@LB@ \| \|@LB@ 77 38@LB@@LB@@LB@Energy -21.71 kcal/mol@LB@Hybridization Energy -20.6082 kcal/mol@LB@Unfolding Energy - mRNA 2.86044 kcal/mol@LB@Unfolding Energy - sRNA 3.80854 kcal/mol@LB@@LB@Position - mRNA 31 -- 67@LB@Position - sRNA 39 -- 76@LB@Position Seed - mRNA 64 -- 70@LB@Position Seed - sRNA 71 -- 77@LB@
7	8.283e-05	0.04123	stm1953	yedO	-23.64	0.004188	172 -- 228	31 -- 88	D-cysteine desulfhydrase	_____________171__________________________________________________________229\n_____________\|____________________________________________________________\|\n5'-UAA...AAAAA___________________________GA___U___U____ACUA_____CUU_______UUCCC...GUG-3'\n______________GAACAC_AC__CACAACGUU___ACCG__GGC_CAA__GCC____CAUCA___AACGCGC\n______________:\|\|\|\|\|_\|\|__\|\|\|\|\|\|:\|:___\|\|\|\|__:\|\|_\|\|\|__\|\|\|____\|\|\|\|\|___\|\|\|:\|\|\|\n______________UUUGUG_UG__GUGUUGUAG___UGGC__UCG_GUU__CGG____GUAGU___UUGUGCG\n3'-UUU...UAACG______U__UU_________UGU____AU_______UU____________C_________UAAGG...UCA-5'\n_____________\|____________________________________________________________\|\n_____________89___________________________________________________________30\n	218 -- 224	36 -- 42	-46.0183 kcal/mol	9.00749 kcal/mol	22.3196 kcal/mol	171 229@LB@ \| \|@LB@5'-UAA...AAAAA GA U U ACUA CUU UUCCC...GUG-3'@LB@ GAACAC AC CACAACGUU ACCG GGC CAA GCC CAUCA AACGCGC@LB@ :\|\|\|\|\| \|\| \|\|\|\|\|\|:\|: \|\|\|\| :\|\| \|\|\| \|\|\| \|\|\|\|\| \|\|\|:\|\|\|@LB@ UUUGUG UG GUGUUGUAG UGGC UCG GUU CGG GUAGU UUGUGCG@LB@3'-UUU...UAACG U UU UGU AU UU C UAAGG...UCA-5'@LB@ \| \|@LB@ 89 30@LB@@LB@@LB@Energy -23.64 kcal/mol@LB@Hybridization Energy -46.0183 kcal/mol@LB@Unfolding Energy - mRNA 9.00749 kcal/mol@LB@Unfolding Energy - sRNA 22.3196 kcal/mol@LB@@LB@Position - mRNA 172 -- 228@LB@Position - sRNA 31 -- 88@LB@Position Seed - mRNA 218 -- 224@LB@Position Seed - sRNA 36 -- 42@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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