Input and runtime details for job 5344133 (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 5344133 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:28:43 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:36:11 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 02:15:51 CET 2018
	Post-Processing Finished		@ Sat Feb 17 02:15:58 CET 2018
	Job Completed		@ Sat Feb 17 02:16:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5344133&toolName=CopraRNA ( 30 days expiry )

Description of the job

RybB

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_000913 Escherichia coli str. K-12 substr. MG1655

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
136	0.00981	0.2504	b4063	soxR	-14.24	0.041834	39 -- 60	1 -- 21	redox-sensitive transcriptional activator of soxS; autorepressor	_____________38_____________________61\n_____________\|______________________\|\n5'-GCA...CGACU_______U_UU______C____CAAUA...GUA-3'\n______________ACAUCAA_G__AAGCGG_UGGU\n______________\|\|\|\|\|\|\|_\|__\|\|\|\|:\|_\|\|\|:\n______________UGUAGUU_C__UUCGUC_ACCG\n3'-UUU...ACCCC_______U_UU___________-5'\n_____________\|_____________________\|\n_____________22____________________1\n	39 -- 45	15 -- 21	-21.0533 kcal/mol	5.29766 kcal/mol	1.51103 kcal/mol	38 61@LB@ \| \|@LB@5'-GCA...CGACU U UU C CAAUA...GUA-3'@LB@ ACAUCAA G AAGCGG UGGU@LB@ \|\|\|\|\|\|\| \| \|\|\|\|:\| \|\|\|:@LB@ UGUAGUU C UUCGUC ACCG@LB@3'-UUU...ACCCC U UU -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -14.24 kcal/mol@LB@Hybridization Energy -21.0533 kcal/mol@LB@Unfolding Energy - mRNA 5.29766 kcal/mol@LB@Unfolding Energy - sRNA 1.51103 kcal/mol@LB@@LB@Position - mRNA 39 -- 60@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 39 -- 45@LB@Position Seed - sRNA 15 -- 21@LB@
145	0.01066	0.2504	b2153	folE	-11.37	0.162147	44 -- 68	1 -- 21	GTP cyclohydrolase I	_____________43________________________69\n_____________\|_________________________\|\n5'-CUG...UUUUA_____UGCU__U_________C___AAUUA...ACG-3'\n______________ACAUC____GA_GAAAGGCAG_GGC\n______________\|\|\|\|\|____:\|_\|\|\|\|:\|\|\|\|_\|\|\|\n______________UGUAG____UU_CUUUUCGUC_CCG\n3'-UUU...ACCCC___________U_________A___-5'\n_____________\|________________________\|\n_____________22_______________________1\n	58 -- 64	5 -- 11	-23.5216 kcal/mol	10.6442 kcal/mol	1.51103 kcal/mol	43 69@LB@ \| \|@LB@5'-CUG...UUUUA UGCU U C AAUUA...ACG-3'@LB@ ACAUC GA GAAAGGCAG GGC@LB@ \|\|\|\|\| :\| \|\|\|\|:\|\|\|\| \|\|\|@LB@ UGUAG UU CUUUUCGUC CCG@LB@3'-UUU...ACCCC U A -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -11.37 kcal/mol@LB@Hybridization Energy -23.5216 kcal/mol@LB@Unfolding Energy - mRNA 10.6442 kcal/mol@LB@Unfolding Energy - sRNA 1.51103 kcal/mol@LB@@LB@Position - mRNA 44 -- 68@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 5 -- 11@LB@
187	0.01374	0.2529	b1344	ttcA	-15.51	0.020761	46 -- 73	1 -- 29	tRNA s(2)C32 thioltransferase iron sulfur cluster protein	_____________45_____________________________74\n_____________\|______________________________\|\n5'-GCU...CAGCC____________G___CUGC_____A____GUAUG...UCA-3'\n______________AAAUGGGG_CAU_AAA_____GCAG_UGGU\n______________\|\|\|\|\|\|\|\|_\|\|\|_\|\|\|_____\|\|\|\|_\|\|\|:\n______________UUUACCCC_GUA_UUU_____CGUC_ACCG\n3'-UUU...GGUGU________U___G___CUUUU_________-5'\n_____________\|_____________________________\|\n_____________30____________________________1\n	47 -- 53	22 -- 28	-26.0543 kcal/mol	8.02666 kcal/mol	2.51907 kcal/mol	45 74@LB@ \| \|@LB@5'-GCU...CAGCC G CUGC A GUAUG...UCA-3'@LB@ AAAUGGGG CAU AAA GCAG UGGU@LB@ \|\|\|\|\|\|\|\| \|\|\| \|\|\| \|\|\|\| \|\|\|:@LB@ UUUACCCC GUA UUU CGUC ACCG@LB@3'-UUU...GGUGU U G CUUUU -5'@LB@ \| \|@LB@ 30 1@LB@@LB@@LB@Energy -15.51 kcal/mol@LB@Hybridization Energy -26.0543 kcal/mol@LB@Unfolding Energy - mRNA 8.02666 kcal/mol@LB@Unfolding Energy - sRNA 2.51907 kcal/mol@LB@@LB@Position - mRNA 46 -- 73@LB@Position - sRNA 1 -- 29@LB@Position Seed - mRNA 47 -- 53@LB@Position Seed - sRNA 22 -- 28@LB@
119	0.008338	0.2459	b0123	cueO	-14.31	0.040489	47 -- 61	9 -- 24	multicopper oxidase (laccase)	_____________46_______________62\n_____________\|________________\|\n5'-CUG...UACCA________________UAAAC...CGU-3'\n______________GGGGC_UUAAAGAAGA\n______________\|\|\|:\|_\|:\|\|\|\|\|\|:\|\n______________CCCUG_AGUUUCUUUU\n3'-UUU...UUUAC_____U__________CGUCACCG-5'\n_____________\|________________\|\n_____________25_______________8\n	55 -- 61	9 -- 15	-17.0719 kcal/mol	2.10565 kcal/mol	0.659805 kcal/mol	46 62@LB@ \| \|@LB@5'-CUG...UACCA UAAAC...CGU-3'@LB@ GGGGC UUAAAGAAGA@LB@ \|\|\|:\| \|:\|\|\|\|\|\|:\|@LB@ CCCUG AGUUUCUUUU@LB@3'-UUU...UUUAC U CGUCACCG-5'@LB@ \| \|@LB@ 25 8@LB@@LB@@LB@Energy -14.31 kcal/mol@LB@Hybridization Energy -17.0719 kcal/mol@LB@Unfolding Energy - mRNA 2.10565 kcal/mol@LB@Unfolding Energy - sRNA 0.659805 kcal/mol@LB@@LB@Position - mRNA 47 -- 61@LB@Position - sRNA 9 -- 24@LB@Position Seed - mRNA 55 -- 61@LB@Position Seed - sRNA 9 -- 15@LB@
140	0.01029	0.2504	b3247	rng	-10.20	0.255190	49 -- 63	1 -- 14	ribonuclease G	_____________48______________64\n_____________\|_______________\|\n5'-GUU...CCGUU___U_______GU__AUACG...CGC-3'\n______________AGA_AAAGCAG__GC\n______________\|\|\|_\|\|\|\|\|\|\|__\|\|\n______________UCU_UUUCGUC__CG\n3'-UUU...UAGUU___________AC__-5'\n_____________\|______________\|\n_____________15_____________1\n	53 -- 59	5 -- 11	-13.7724 kcal/mol	2.22711 kcal/mol	1.34059 kcal/mol	48 64@LB@ \| \|@LB@5'-GUU...CCGUU U GU AUACG...CGC-3'@LB@ AGA AAAGCAG GC@LB@ \|\|\| \|\|\|\|\|\|\| \|\|@LB@ UCU UUUCGUC CG@LB@3'-UUU...UAGUU AC -5'@LB@ \| \|@LB@ 15 1@LB@@LB@@LB@Energy -10.20 kcal/mol@LB@Hybridization Energy -13.7724 kcal/mol@LB@Unfolding Energy - mRNA 2.22711 kcal/mol@LB@Unfolding Energy - sRNA 1.34059 kcal/mol@LB@@LB@Position - mRNA 49 -- 63@LB@Position - sRNA 1 -- 14@LB@Position Seed - mRNA 53 -- 59@LB@Position Seed - sRNA 5 -- 11@LB@
79	0.004643	0.2062	b2264	menD	-12.62	0.093644	52 -- 86	1 -- 30	2-succinyl-5-enolpyruvyl-6-hydroxy-3- cyclohexene-1-carboxylate synthase; SEPHCHC synthase	_____________51_____________________________________87\n_____________\|______________________________________\|\n5'-CGU...GAGCA_______CAGGAAAUC____A_____C___________UGCGU...GUU-3'\n______________AGAGUGG_________GACA_CAAAG___GGCAG_GGC\n______________\|:\|:\|\|\|_________\|\|\|\|_\|\|\|\|\|___:\|\|\|\|_\|\|\|\n______________UUUUACC_________CUGU_GUUUC___UCGUC_CCG\n3'-UUU...AGGUG_______C____________A_____UUU_____A___-5'\n_____________\|_____________________________________\|\n_____________31____________________________________1\n	52 -- 58	24 -- 30	-24.8101 kcal/mol	9.6737 kcal/mol	2.51911 kcal/mol	51 87@LB@ \| \|@LB@5'-CGU...GAGCA CAGGAAAUC A C UGCGU...GUU-3'@LB@ AGAGUGG GACA CAAAG GGCAG GGC@LB@ \|:\|:\|\|\| \|\|\|\| \|\|\|\|\| :\|\|\|\| \|\|\|@LB@ UUUUACC CUGU GUUUC UCGUC CCG@LB@3'-UUU...AGGUG C A UUU A -5'@LB@ \| \|@LB@ 31 1@LB@@LB@@LB@Energy -12.62 kcal/mol@LB@Hybridization Energy -24.8101 kcal/mol@LB@Unfolding Energy - mRNA 9.6737 kcal/mol@LB@Unfolding Energy - sRNA 2.51911 kcal/mol@LB@@LB@Position - mRNA 52 -- 86@LB@Position - sRNA 1 -- 30@LB@Position Seed - mRNA 52 -- 58@LB@Position Seed - sRNA 24 -- 30@LB@
127	0.009277	0.2491	b2781	mazG	-12.70	0.090074	53 -- 69	8 -- 24	nucleoside triphosphate pyrophosphohydrolase	_____________52________________70\n_____________\|_________________\|\n5'-UGA...CAAGA__A___A__________AACAG...CGC-3'\n______________GG_GCA_CGAAGAAAGG\n______________\|\|_:\|\|_\|:\|\|\|\|\|\|:\|\n______________CC_UGU_GUUUCUUUUC\n3'-UUU...UUUAC__C___A__________GUCACCG-5'\n_____________\|_________________\|\n_____________25________________7\n	63 -- 69	8 -- 14	-16.258 kcal/mol	2.86814 kcal/mol	0.688982 kcal/mol	52 70@LB@ \| \|@LB@5'-UGA...CAAGA A A AACAG...CGC-3'@LB@ GG GCA CGAAGAAAGG@LB@ \|\| :\|\| \|:\|\|\|\|\|\|:\|@LB@ CC UGU GUUUCUUUUC@LB@3'-UUU...UUUAC C A GUCACCG-5'@LB@ \| \|@LB@ 25 7@LB@@LB@@LB@Energy -12.70 kcal/mol@LB@Hybridization Energy -16.258 kcal/mol@LB@Unfolding Energy - mRNA 2.86814 kcal/mol@LB@Unfolding Energy - sRNA 0.688982 kcal/mol@LB@@LB@Position - mRNA 53 -- 69@LB@Position - sRNA 8 -- 24@LB@Position Seed - mRNA 63 -- 69@LB@Position Seed - sRNA 8 -- 14@LB@
47	0.002271	0.1648	b3169	nusA	-13.61	0.058009	55 -- 79	4 -- 28	transcription termination/antitermination L factor	_____________54__________________________80\n_____________\|___________________________\|\n5'-UUG...UCGUA_____CA________UC__________AGACG...CAG-3'\n______________AAUGG__GGGCGUUA____AAAGCGGU\n______________\|\|\|\|\|__\|\|:\|:\|:\|____\|\|\|\|\|:\|\|\n______________UUACC__CCUGUAGU____UUUCGUCA\n3'-UUU...GUGUU_______________UUCU________CCG-5'\n_____________\|___________________________\|\n_____________29__________________________3\n	73 -- 79	4 -- 10	-21.8237 kcal/mol	5.69952 kcal/mol	2.51457 kcal/mol	54 80@LB@ \| \|@LB@5'-UUG...UCGUA CA UC AGACG...CAG-3'@LB@ AAUGG GGGCGUUA AAAGCGGU@LB@ \|\|\|\|\| \|\|:\|:\|:\| \|\|\|\|\|:\|\|@LB@ UUACC CCUGUAGU UUUCGUCA@LB@3'-UUU...GUGUU UUCU CCG-5'@LB@ \| \|@LB@ 29 3@LB@@LB@@LB@Energy -13.61 kcal/mol@LB@Hybridization Energy -21.8237 kcal/mol@LB@Unfolding Energy - mRNA 5.69952 kcal/mol@LB@Unfolding Energy - sRNA 2.51457 kcal/mol@LB@@LB@Position - mRNA 55 -- 79@LB@Position - sRNA 4 -- 28@LB@Position Seed - mRNA 73 -- 79@LB@Position Seed - sRNA 4 -- 10@LB@
83	0.005101	0.2147	b2610	ffh	-14.32	0.040245	57 -- 74	4 -- 21	Signal Recognition Particle (SRP) component with 4.5S RNA (ffs)	_____________56_________________75\n_____________\|__________________\|\n5'-AGG...GAGCA___AG_____________AUAGC...AAG-3'\n______________AUA__AAAGAGAAGCAGU\n______________\|:\|__\|\|\|\|\|:\|\|\|\|\|\|\|\n______________UGU__UUUCUUUUCGUCA\n3'-UUU...ACCCC___AG_____________CCG-5'\n_____________\|__________________\|\n_____________22_________________3\n	68 -- 74	4 -- 10	-18.2522 kcal/mol	2.42435 kcal/mol	1.51 kcal/mol	56 75@LB@ \| \|@LB@5'-AGG...GAGCA AG AUAGC...AAG-3'@LB@ AUA AAAGAGAAGCAGU@LB@ \|:\| \|\|\|\|\|:\|\|\|\|\|\|\|@LB@ UGU UUUCUUUUCGUCA@LB@3'-UUU...ACCCC AG CCG-5'@LB@ \| \|@LB@ 22 3@LB@@LB@@LB@Energy -14.32 kcal/mol@LB@Hybridization Energy -18.2522 kcal/mol@LB@Unfolding Energy - mRNA 2.42435 kcal/mol@LB@Unfolding Energy - sRNA 1.51 kcal/mol@LB@@LB@Position - mRNA 57 -- 74@LB@Position - sRNA 4 -- 21@LB@Position Seed - mRNA 68 -- 74@LB@Position Seed - sRNA 4 -- 10@LB@
200	0.01506	0.259	b0404	acpH	-14.03	0.046767	57 -- 80	6 -- 28	acyl carrier protein (ACP) phosphodiesterase; ACP hydrolyase	_____________56________________________81\n_____________\|_________________________\|\n5'-GCC...GGGAU______CA_________UUC_____AUUCA...GUU-3'\n______________AGUGGG___AUCAGGGA___GGGCA\n______________\|:\|\|\|\|___\|\|\|\|::\|\|___::\|\|\|\n______________UUACCC___UAGUUUCU___UUCGU\n3'-UUU...GUGUU______CUG________U_______CACCG-5'\n_____________\|_________________________\|\n_____________29________________________5\n	66 -- 72	12 -- 18	-19.5231 kcal/mol	4.78501 kcal/mol	0.706454 kcal/mol	56 81@LB@ \| \|@LB@5'-GCC...GGGAU CA UUC AUUCA...GUU-3'@LB@ AGUGGG AUCAGGGA GGGCA@LB@ \|:\|\|\|\| \|\|\|\|::\|\| ::\|\|\|@LB@ UUACCC UAGUUUCU UUCGU@LB@3'-UUU...GUGUU CUG U CACCG-5'@LB@ \| \|@LB@ 29 5@LB@@LB@@LB@Energy -14.03 kcal/mol@LB@Hybridization Energy -19.5231 kcal/mol@LB@Unfolding Energy - mRNA 4.78501 kcal/mol@LB@Unfolding Energy - sRNA 0.706454 kcal/mol@LB@@LB@Position - mRNA 57 -- 80@LB@Position - sRNA 6 -- 28@LB@Position Seed - mRNA 66 -- 72@LB@Position Seed - sRNA 12 -- 18@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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