Input and runtime details for job 7743500 (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 7743500 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:35:00 CET 2018
	CopraRNA Started		@ Fri Feb 16 21:27:12 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 06:56:30 CET 2018
	Post-Processing Finished		@ Sat Feb 17 06:56:38 CET 2018
	Job Completed		@ Sat Feb 17 06:57:11 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=7743500&toolName=CopraRNA ( 30 days expiry )

Description of the job

PrrF1

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_002516 Pseudomonas aeruginosa PAO1

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
189	0.005044	0.1227	pa4284	recB	-12.92	0.038081	40 -- 56	70 -- 89	exodeoxyribonuclease V subunit beta	_____________39___________________57\n_____________\|____________________\|\n5'-CCC...ACGAG____________A_______GGGCG...UCA-3'\n______________GGAGGGUUCGGC____UGGG\n______________\|:\|\|:\|\|:\|\|:\|____\|\|\|\|\n______________CUUCUCAGGCUG____ACCC\n3'-UUU...UUAGA____________ACGC____AGAGA...GUU-5'\n_____________\|____________________\|\n_____________90___________________69\n	45 -- 51	78 -- 84	-22.2148 kcal/mol	3.43278 kcal/mol	5.86471 kcal/mol	39 57@LB@ \| \|@LB@5'-CCC...ACGAG A GGGCG...UCA-3'@LB@ GGAGGGUUCGGC UGGG@LB@ \|:\|\|:\|\|:\|\|:\| \|\|\|\|@LB@ CUUCUCAGGCUG ACCC@LB@3'-UUU...UUAGA ACGC AGAGA...GUU-5'@LB@ \| \|@LB@ 90 69@LB@@LB@@LB@Energy -12.92 kcal/mol@LB@Hybridization Energy -22.2148 kcal/mol@LB@Unfolding Energy - mRNA 3.43278 kcal/mol@LB@Unfolding Energy - sRNA 5.86471 kcal/mol@LB@@LB@Position - mRNA 40 -- 56@LB@Position - sRNA 70 -- 89@LB@Position Seed - mRNA 45 -- 51@LB@Position Seed - sRNA 78 -- 84@LB@
193	0.005243	0.1243	pa3725	recJ	-10.65	0.130688	184 -- 203	102 -- 119	single-stranded-DNA-specific exonuclease RecJ	_____________183__________________204\n_____________\|____________________\|\n5'-CGU...GUCGA____AAC__GUGA_______CGUAU...GCG-3'\n______________GCCG___GA____CCUGAUG\n______________:\|\|\|___\|\|____\|\|\|\|\|\|\|\n______________UGGC___CU____GGACUAC\n3'-UUU...GUUUU____A____AAUC_______UCCUC...GUU-5'\n_____________\|____________________\|\n_____________120__________________101\n	197 -- 203	102 -- 108	-15.7224 kcal/mol	2.82992 kcal/mol	2.24274 kcal/mol	183 204@LB@ \| \|@LB@5'-CGU...GUCGA AAC GUGA CGUAU...GCG-3'@LB@ GCCG GA CCUGAUG@LB@ :\|\|\| \|\| \|\|\|\|\|\|\|@LB@ UGGC CU GGACUAC@LB@3'-UUU...GUUUU A AAUC UCCUC...GUU-5'@LB@ \| \|@LB@ 120 101@LB@@LB@@LB@Energy -10.65 kcal/mol@LB@Hybridization Energy -15.7224 kcal/mol@LB@Unfolding Energy - mRNA 2.82992 kcal/mol@LB@Unfolding Energy - sRNA 2.24274 kcal/mol@LB@@LB@Position - mRNA 184 -- 203@LB@Position - sRNA 102 -- 119@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 102 -- 108@LB@
119	0.002082	0.07999	pa4053	ribE	-9.84	0.193218	284 -- 298	103 -- 117	6 7-dimethyl-8-ribityllumazine synthase	_____________283_____________299\n_____________\|_______________\|\n5'-UGC...UUCGU_____AA________CA-3'\n______________CGUGG__AGCCUGGU\n______________\|\|\|\|:__\|\|\|\|\|\|:\|\n______________GCACU__UCGGACUA\n3'-UUU...UUUUG_____AA________CUCCU...GUU-5'\n_____________\|_______________\|\n_____________118_____________102\n	292 -- 298	103 -- 109	-17.5695 kcal/mol	5.50648 kcal/mol	2.23013 kcal/mol	283 299@LB@ \| \|@LB@5'-UGC...UUCGU AA CA-3'@LB@ CGUGG AGCCUGGU@LB@ \|\|\|\|: \|\|\|\|\|\|:\|@LB@ GCACU UCGGACUA@LB@3'-UUU...UUUUG AA CUCCU...GUU-5'@LB@ \| \|@LB@ 118 102@LB@@LB@@LB@Energy -9.84 kcal/mol@LB@Hybridization Energy -17.5695 kcal/mol@LB@Unfolding Energy - mRNA 5.50648 kcal/mol@LB@Unfolding Energy - sRNA 2.23013 kcal/mol@LB@@LB@Position - mRNA 284 -- 298@LB@Position - sRNA 103 -- 117@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 103 -- 109@LB@
15	2.583e-05	0.007914	pa3049	rmf	-22.33	0.000014	230 -- 282	40 -- 88	ribosome modulation factor	_____________229____________________________________________________283\n_____________\|______________________________________________________\|\n5'-CGA...UUGGA________UU_U_______UUA__AGAA____AUA______AA___________UUUGU...AUC-3'\n______________AAGAG_CC__C_UGCGUGG___UC____CGGC___ACCGGU__AUCUCGUGAUC\n______________\|\|\|\|\|_\|\|__\|_\|\|\|\|\|\|\|___\|\|____\|:\|\|___\|\|\|\|\|:__\|\|\|\|\|\|:\|\|:\|\n______________UUCUC_GG__G_ACGCACC___AG____GUCG___UGGCCG__UAGAGCGCUGG\n3'-UUU...UAGAC_____A__CU_________CAG__A_______AA_______AC___________UCAAC...GUU-5'\n_____________\|______________________________________________________\|\n_____________89_____________________________________________________39\n	276 -- 282	40 -- 46	-52.7199 kcal/mol	11.3783 kcal/mol	19.0139 kcal/mol	229 283@LB@ \| \|@LB@5'-CGA...UUGGA UU U UUA AGAA AUA AA UUUGU...AUC-3'@LB@ AAGAG CC C UGCGUGG UC CGGC ACCGGU AUCUCGUGAUC@LB@ \|\|\|\|\| \|\| \| \|\|\|\|\|\|\| \|\| \|:\|\| \|\|\|\|\|: \|\|\|\|\|\|:\|\|:\|@LB@ UUCUC GG G ACGCACC AG GUCG UGGCCG UAGAGCGCUGG@LB@3'-UUU...UAGAC A CU CAG A AA AC UCAAC...GUU-5'@LB@ \| \|@LB@ 89 39@LB@@LB@@LB@Energy -22.33 kcal/mol@LB@Hybridization Energy -52.7199 kcal/mol@LB@Unfolding Energy - mRNA 11.3783 kcal/mol@LB@Unfolding Energy - sRNA 19.0139 kcal/mol@LB@@LB@Position - mRNA 230 -- 282@LB@Position - sRNA 40 -- 88@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 40 -- 46@LB@
31	8.059e-05	0.01177	pa5164	rmlC	-15.78	0.005968	187 -- 204	101 -- 122	dTDP-4-dehydrorhamnose 3 5-epimerase	_____________186____________________205\n_____________\|______________________\|\n5'-ACC...UGACC_________UA___________AAGCG...GCG-3'\n______________GAGACCGUG______CUGAUGA\n______________:\|:\|\|\|\|\|\|______\|\|\|\|\|\|\|\n______________UUUUGGCAC______GACUACU\n3'-UUU...CCAGU_________UAAUCG_______CCUCU...GUU-5'\n_____________\|______________________\|\n_____________123____________________100\n	198 -- 204	101 -- 107	-20.9444 kcal/mol	2.92213 kcal/mol	2.24427 kcal/mol	186 205@LB@ \| \|@LB@5'-ACC...UGACC UA AAGCG...GCG-3'@LB@ GAGACCGUG CUGAUGA@LB@ :\|:\|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ UUUUGGCAC GACUACU@LB@3'-UUU...CCAGU UAAUCG CCUCU...GUU-5'@LB@ \| \|@LB@ 123 100@LB@@LB@@LB@Energy -15.78 kcal/mol@LB@Hybridization Energy -20.9444 kcal/mol@LB@Unfolding Energy - mRNA 2.92213 kcal/mol@LB@Unfolding Energy - sRNA 2.24427 kcal/mol@LB@@LB@Position - mRNA 187 -- 204@LB@Position - sRNA 101 -- 122@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 101 -- 107@LB@
100	0.001607	0.07384	pa0607	rpe	-12.76	0.041806	177 -- 194	99 -- 118	ribulose-phosphate 3-epimerase	_____________176__________________195\n_____________\|____________________\|\n5'-CCG...GCCUU_______CC____U______UGCGC...UUC-3'\n______________CCGUGAU___CCU__UGAGG\n______________\|\|\|\|\|\|\|___\|\|\|__\|\|\|\|\|\n______________GGCACUA___GGA__ACUCC\n3'-UUU...UUUUU_______AUC___CU_____UCUAU...GUU-5'\n_____________\|____________________\|\n_____________119__________________98\n	177 -- 183	112 -- 118	-19.2108 kcal/mol	4.20353 kcal/mol	2.24947 kcal/mol	176 195@LB@ \| \|@LB@5'-CCG...GCCUU CC U UGCGC...UUC-3'@LB@ CCGUGAU CCU UGAGG@LB@ \|\|\|\|\|\|\| \|\|\| \|\|\|\|\|@LB@ GGCACUA GGA ACUCC@LB@3'-UUU...UUUUU AUC CU UCUAU...GUU-5'@LB@ \| \|@LB@ 119 98@LB@@LB@@LB@Energy -12.76 kcal/mol@LB@Hybridization Energy -19.2108 kcal/mol@LB@Unfolding Energy - mRNA 4.20353 kcal/mol@LB@Unfolding Energy - sRNA 2.24947 kcal/mol@LB@@LB@Position - mRNA 177 -- 194@LB@Position - sRNA 99 -- 118@LB@Position Seed - mRNA 177 -- 183@LB@Position Seed - sRNA 112 -- 118@LB@
78	0.000864	0.05078	pa4263	rplC	-13.85	0.021626	50 -- 71	101 -- 122	50S ribosomal protein L3	_____________49_______________________72\n_____________\|________________________\|\n5'-CGA...CGGAU________C_______G_______AGCUC...AUC-3'\n______________AAAACCGU_GAU__GC_CUGAUGA\n______________\|\|\|\|\|\|\|\|_\|\|\|__\|\|_\|\|\|\|\|\|\|\n______________UUUUGGCA_CUA__CG_GACUACU\n3'-UUU...CCAGU____________AU__________CCUCU...GUU-5'\n_____________\|________________________\|\n_____________123______________________100\n	65 -- 71	101 -- 107	-22.5702 kcal/mol	6.47727 kcal/mol	2.24427 kcal/mol	49 72@LB@ \| \|@LB@5'-CGA...CGGAU C G AGCUC...AUC-3'@LB@ AAAACCGU GAU GC CUGAUGA@LB@ \|\|\|\|\|\|\|\| \|\|\| \|\| \|\|\|\|\|\|\|@LB@ UUUUGGCA CUA CG GACUACU@LB@3'-UUU...CCAGU AU CCUCU...GUU-5'@LB@ \| \|@LB@ 123 100@LB@@LB@@LB@Energy -13.85 kcal/mol@LB@Hybridization Energy -22.5702 kcal/mol@LB@Unfolding Energy - mRNA 6.47727 kcal/mol@LB@Unfolding Energy - sRNA 2.24427 kcal/mol@LB@@LB@Position - mRNA 50 -- 71@LB@Position - sRNA 101 -- 122@LB@Position Seed - mRNA 65 -- 71@LB@Position Seed - sRNA 101 -- 107@LB@
5	7.253e-07	0.0006667	pa5351	rubA1	-17.51	0.001615	172 -- 222	71 -- 121	rubredoxin	_____________171___________________________________________________223\n_____________\|_____________________________________________________\|\n5'-CGG...GCGCU__________AAC__GCCC____UAAACAA_______AG_____AA_______UGUGU...UGC-3'\n______________GAACCGUGGU___CC____GAGG________UGAAGA___UGGC__UGCGUGG\n______________:\|\|\|\|\|\|\|:\|___\|\|____\|\|\|\|________\|\|\|\|\|\|___:\|:\|__\|\|\|\|\|\|\|\n______________UUUGGCACUA___GG____CUCC________ACUUCU___GCUG__ACGCACC\n3'-UUU...CAGUU__________AUC__ACUA____UCUAUUAG______CAG_____________CAGAG...GUU-5'\n_____________\|_____________________________________________________\|\n_____________122___________________________________________________70\n	216 -- 222	71 -- 77	-42.807 kcal/mol	11.4444 kcal/mol	13.8582 kcal/mol	171 223@LB@ \| \|@LB@5'-CGG...GCGCU AAC GCCC UAAACAA AG AA UGUGU...UGC-3'@LB@ GAACCGUGGU CC GAGG UGAAGA UGGC UGCGUGG@LB@ :\|\|\|\|\|\|\|:\| \|\| \|\|\|\| \|\|\|\|\|\| :\|:\| \|\|\|\|\|\|\|@LB@ UUUGGCACUA GG CUCC ACUUCU GCUG ACGCACC@LB@3'-UUU...CAGUU AUC ACUA UCUAUUAG CAG CAGAG...GUU-5'@LB@ \| \|@LB@ 122 70@LB@@LB@@LB@Energy -17.51 kcal/mol@LB@Hybridization Energy -42.807 kcal/mol@LB@Unfolding Energy - mRNA 11.4444 kcal/mol@LB@Unfolding Energy - sRNA 13.8582 kcal/mol@LB@@LB@Position - mRNA 172 -- 222@LB@Position - sRNA 71 -- 121@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 71 -- 77@LB@
4	5.154e-07	0.0005922	pa1581	sdhC	-15.05	0.009907	206 -- 221	108 -- 123	succinate dehydrogenase subunit C	_____________205______________222\n_____________\|________________\|\n5'-ACG...GUGAA___________A____AAACG...CUG-3'\n______________AAAAGCCGUGA_UAGC\n______________\|\|\|\|:\|\|\|\|\|\|_\|\|\|\|\n______________UUUUUGGCACU_AUCG\n3'-UUU...CCCAG___________A____GACUA...GUU-5'\n_____________\|________________\|\n_____________124______________107\n	210 -- 216	113 -- 119	-19.67 kcal/mol	2.45872 kcal/mol	2.16544 kcal/mol	205 222@LB@ \| \|@LB@5'-ACG...GUGAA A AAACG...CUG-3'@LB@ AAAAGCCGUGA UAGC@LB@ \|\|\|\|:\|\|\|\|\|\| \|\|\|\|@LB@ UUUUUGGCACU AUCG@LB@3'-UUU...CCCAG A GACUA...GUU-5'@LB@ \| \|@LB@ 124 107@LB@@LB@@LB@Energy -15.05 kcal/mol@LB@Hybridization Energy -19.67 kcal/mol@LB@Unfolding Energy - mRNA 2.45872 kcal/mol@LB@Unfolding Energy - sRNA 2.16544 kcal/mol@LB@@LB@Position - mRNA 206 -- 221@LB@Position - sRNA 108 -- 123@LB@Position Seed - mRNA 210 -- 216@LB@Position Seed - sRNA 113 -- 119@LB@
47	0.0003012	0.02946	pa1776	sigX	-11.73	0.074706	90 -- 102	103 -- 115	RNA polymerase sigma factor SigX	_____________89____________103\n_____________\|_____________\|\n5'-CGU...CGAUA___C_________CUCAC...UGU-3'\n______________UGA_UGGCCUGAU\n______________\|\|\|_\|:\|\|\|\|\|\|\|\n______________ACU_AUCGGACUA\n3'-UUU...UUGGC___A_________CUCCU...GUU-5'\n_____________\|_____________\|\n_____________116___________102\n	96 -- 102	103 -- 109	-16.1519 kcal/mol	2.30076 kcal/mol	2.12156 kcal/mol	89 103@LB@ \| \|@LB@5'-CGU...CGAUA C CUCAC...UGU-3'@LB@ UGA UGGCCUGAU@LB@ \|\|\| \|:\|\|\|\|\|\|\|@LB@ ACU AUCGGACUA@LB@3'-UUU...UUGGC A CUCCU...GUU-5'@LB@ \| \|@LB@ 116 102@LB@@LB@@LB@Energy -11.73 kcal/mol@LB@Hybridization Energy -16.1519 kcal/mol@LB@Unfolding Energy - mRNA 2.30076 kcal/mol@LB@Unfolding Energy - sRNA 2.12156 kcal/mol@LB@@LB@Position - mRNA 90 -- 102@LB@Position - sRNA 103 -- 115@LB@Position Seed - mRNA 96 -- 102@LB@Position Seed - sRNA 103 -- 109@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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