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
95	0.005813	0.2147	b3450	ugpC	-12.76	0.087557	84 -- 111	1 -- 34	sn-glycerol-3-phosphate ABC transporter ATPase	_____________83_________________________________112\n_____________\|__________________________________\|\n5'-GUG...AGGCA___________A________U_____________GAUGU...UCG-3'\n______________CCACGGAAUGG__AC_UCAG_GA____UGGUGGC\n______________\|\|\|\|::\|\|\|\|\|__\|\|_\|\|\|:_\|\|____::\|\|\|\|\|\n______________GGUGUUUUACC__UG_AGUU_CU____GUCACCG\n3'-UUU...CCCGA___________CC__U____U__UUUC_______-5'\n_____________\|_________________________________\|\n_____________35________________________________1\n	105 -- 111	1 -- 7	-27.9886 kcal/mol	10.9582 kcal/mol	4.26884 kcal/mol	83 112@LB@ \| \|@LB@5'-GUG...AGGCA A U GAUGU...UCG-3'@LB@ CCACGGAAUGG AC UCAG GA UGGUGGC@LB@ \|\|\|\|::\|\|\|\|\| \|\| \|\|\|: \|\| ::\|\|\|\|\|@LB@ GGUGUUUUACC UG AGUU CU GUCACCG@LB@3'-UUU...CCCGA CC U U UUUC -5'@LB@ \| \|@LB@ 35 1@LB@@LB@@LB@Energy -12.76 kcal/mol@LB@Hybridization Energy -27.9886 kcal/mol@LB@Unfolding Energy - mRNA 10.9582 kcal/mol@LB@Unfolding Energy - sRNA 4.26884 kcal/mol@LB@@LB@Position - mRNA 84 -- 111@LB@Position - sRNA 1 -- 34@LB@Position Seed - mRNA 105 -- 111@LB@Position Seed - sRNA 1 -- 7@LB@
198	0.01428	0.2531	b4393	trpR	-20.45	0.000581	86 -- 104	16 -- 34	transcriptional repressor tryptophan-binding	_____________85__________________105\n_____________\|___________________\|\n5'-GAG...GAGCG___________________UUACU...AUC-3'\n______________CCACGGAAUGGGGACGUCG\n______________\|\|\|\|::\|\|\|\|\|\|\|\|\|:\|\|:\n______________GGUGUUUUACCCCUGUAGU\n3'-UUU...CCCGA___________________UUCUU...CCG-5'\n_____________\|___________________\|\n_____________35__________________15\n	98 -- 104	16 -- 22	-32.2935 kcal/mol	7.91935 kcal/mol	3.92811 kcal/mol	85 105@LB@ \| \|@LB@5'-GAG...GAGCG UUACU...AUC-3'@LB@ CCACGGAAUGGGGACGUCG@LB@ \|\|\|\|::\|\|\|\|\|\|\|\|\|:\|\|:@LB@ GGUGUUUUACCCCUGUAGU@LB@3'-UUU...CCCGA UUCUU...CCG-5'@LB@ \| \|@LB@ 35 15@LB@@LB@@LB@Energy -20.45 kcal/mol@LB@Hybridization Energy -32.2935 kcal/mol@LB@Unfolding Energy - mRNA 7.91935 kcal/mol@LB@Unfolding Energy - sRNA 3.92811 kcal/mol@LB@@LB@Position - mRNA 86 -- 104@LB@Position - sRNA 16 -- 34@LB@Position Seed - mRNA 98 -- 104@LB@Position Seed - sRNA 16 -- 22@LB@
15	0.0006403	0.1243	b0178	skp	-17.37	0.006465	90 -- 106	1 -- 17	periplasmic chaperone	_____________89________________107\n_____________\|_________________\|\n5'-CUC...CUCCA________U________AGUGU...UCC-3'\n______________CAAAGGAA_GUAGUGGU\n______________\|\|\|\|\|:\|\|_\|:\|\|\|\|\|:\n______________GUUUCUUU_CGUCACCG\n3'-UUU...CUGUA________U________-5'\n_____________\|________________\|\n_____________18_______________1\n	100 -- 106	1 -- 7	-21.6829 kcal/mol	2.87621 kcal/mol	1.43853 kcal/mol	89 107@LB@ \| \|@LB@5'-CUC...CUCCA U AGUGU...UCC-3'@LB@ CAAAGGAA GUAGUGGU@LB@ \|\|\|\|\|:\|\| \|:\|\|\|\|\|:@LB@ GUUUCUUU CGUCACCG@LB@3'-UUU...CUGUA U -5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -17.37 kcal/mol@LB@Hybridization Energy -21.6829 kcal/mol@LB@Unfolding Energy - mRNA 2.87621 kcal/mol@LB@Unfolding Energy - sRNA 1.43853 kcal/mol@LB@@LB@Position - mRNA 90 -- 106@LB@Position - sRNA 1 -- 17@LB@Position Seed - mRNA 100 -- 106@LB@Position Seed - sRNA 1 -- 7@LB@
155	0.01136	0.2504	b2168	fruK	-7.75	0.545043	91 -- 105	7 -- 22	fructose-1-phosphate kinase	_____________90_______________106\n_____________\|________________\|\n5'-AAA...CACUU________________CAUCG...CCA-3'\n______________GGCGUU_AAGAAAGGU\n______________\|:\|:\|:_\|\|\|\|\|\|:\|:\n______________CUGUAG_UUCUUUUCG\n3'-UUU...UACCC______U_________UCACCG-5'\n_____________\|________________\|\n_____________23_______________6\n	99 -- 105	7 -- 13	-14.0922 kcal/mol	5.75103 kcal/mol	0.590875 kcal/mol	90 106@LB@ \| \|@LB@5'-AAA...CACUU CAUCG...CCA-3'@LB@ GGCGUU AAGAAAGGU@LB@ \|:\|:\|: \|\|\|\|\|\|:\|:@LB@ CUGUAG UUCUUUUCG@LB@3'-UUU...UACCC U UCACCG-5'@LB@ \| \|@LB@ 23 6@LB@@LB@@LB@Energy -7.75 kcal/mol@LB@Hybridization Energy -14.0922 kcal/mol@LB@Unfolding Energy - mRNA 5.75103 kcal/mol@LB@Unfolding Energy - sRNA 0.590875 kcal/mol@LB@@LB@Position - mRNA 91 -- 105@LB@Position - sRNA 7 -- 22@LB@Position Seed - mRNA 99 -- 105@LB@Position Seed - sRNA 7 -- 13@LB@
105	0.007004	0.2333	b4034	malE	-12.62	0.093531	92 -- 123	2 -- 32	maltose transporter subunit	_____________91_________________________________124\n_____________\|__________________________________\|\n5'-AGG...ACAAA____C_________________C___G__GA___AAAGA...UGG-3'\n______________GCGA_GGUGGGG_CGU_AGGGG_AAG_AG__UGG\n______________:\|:\|_::\|\|\|\|\|_\|:\|_\|::\|:_\|\|\|_\|\|__\|\|\|\n______________UGUU_UUACCCC_GUA_UUUCU_UUC_UC__ACC\n3'-UUU...CGAGG____________U___G_____U___G_______G-5'\n_____________\|__________________________________\|\n_____________33_________________________________1\n	97 -- 103	22 -- 28	-24.1065 kcal/mol	8.94734 kcal/mol	2.53929 kcal/mol	91 124@LB@ \| \|@LB@5'-AGG...ACAAA C C G GA AAAGA...UGG-3'@LB@ GCGA GGUGGGG CGU AGGGG AAG AG UGG@LB@ :\|:\| ::\|\|\|\|\| \|:\| \|::\|: \|\|\| \|\| \|\|\|@LB@ UGUU UUACCCC GUA UUUCU UUC UC ACC@LB@3'-UUU...CGAGG U G U G G-5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -12.62 kcal/mol@LB@Hybridization Energy -24.1065 kcal/mol@LB@Unfolding Energy - mRNA 8.94734 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 92 -- 123@LB@Position - sRNA 2 -- 32@LB@Position Seed - mRNA 97 -- 103@LB@Position Seed - sRNA 22 -- 28@LB@
164	0.01206	0.2504	b0882	clpA	-9.12	0.369525	95 -- 107	48 -- 60	ATPase and specificity subunit of ClpA-ClpP ATP-dependent serine protease chaperone activity	_____________94____________108\n_____________\|_____________\|\n5'-UUU...GCAGA____A________AUGGU...CGC-3'\n______________AACC_AAGUGGCG\n______________\|\|\|\|_\|\|:\|\|\|\|\|\n______________UUGG_UUUACCGC\n3'-UUU...GGAAC____C________CCCAA...CCG-5'\n_____________\|_____________\|\n_____________61____________47\n	101 -- 107	48 -- 54	-16.8445 kcal/mol	3.76103 kcal/mol	3.96136 kcal/mol	94 108@LB@ \| \|@LB@5'-UUU...GCAGA A AUGGU...CGC-3'@LB@ AACC AAGUGGCG@LB@ \|\|\|\| \|\|:\|\|\|\|\|@LB@ UUGG UUUACCGC@LB@3'-UUU...GGAAC C CCCAA...CCG-5'@LB@ \| \|@LB@ 61 47@LB@@LB@@LB@Energy -9.12 kcal/mol@LB@Hybridization Energy -16.8445 kcal/mol@LB@Unfolding Energy - mRNA 3.76103 kcal/mol@LB@Unfolding Energy - sRNA 3.96136 kcal/mol@LB@@LB@Position - mRNA 95 -- 107@LB@Position - sRNA 48 -- 60@LB@Position Seed - mRNA 101 -- 107@LB@Position Seed - sRNA 48 -- 54@LB@
39	0.001912	0.1648	b2532	trmJ	-14.54	0.035636	97 -- 121	1 -- 23	tRNA mC32 mU32 2'-O-methyltransferase SAM-dependent	_____________96________________________122\n_____________\|_________________________\|\n5'-CGU...UCACU_____________C__G_AAAC___GCAGA...UGU-3'\n______________GGAUGUUAAAGAA_GG_A____GGC\n______________\|\|\|::\|:\|\|\|\|\|\|_:\|_\|____\|\|\|\n______________CCUGUAGUUUCUU_UC_U____CCG\n3'-UUU...UUACC_____________U__G_CA_____-5'\n_____________\|________________________\|\n_____________24_______________________1\n	103 -- 109	11 -- 17	-19.8008 kcal/mol	3.67656 kcal/mol	1.57928 kcal/mol	96 122@LB@ \| \|@LB@5'-CGU...UCACU C G AAAC GCAGA...UGU-3'@LB@ GGAUGUUAAAGAA GG A GGC@LB@ \|\|\|::\|:\|\|\|\|\|\| :\| \| \|\|\|@LB@ CCUGUAGUUUCUU UC U CCG@LB@3'-UUU...UUACC U G CA -5'@LB@ \| \|@LB@ 24 1@LB@@LB@@LB@Energy -14.54 kcal/mol@LB@Hybridization Energy -19.8008 kcal/mol@LB@Unfolding Energy - mRNA 3.67656 kcal/mol@LB@Unfolding Energy - sRNA 1.57928 kcal/mol@LB@@LB@Position - mRNA 97 -- 121@LB@Position - sRNA 1 -- 23@LB@Position Seed - mRNA 103 -- 109@LB@Position Seed - sRNA 11 -- 17@LB@
183	0.01318	0.2504	b4483	tatD	-12.95	0.080004	100 -- 117	8 -- 25	quality control of Tat-exported FeS proteins; Mg-dependent cytoplasmic DNase	_____________99__________________118\n_____________\|___________________\|\n5'-CUG...GUAAA___C__A____________GAAAA...UCA-3'\n______________GGG_GA_AUC_GGGAAGAG\n______________\|\|\|_\|\|_\|\|\|_::\|\|\|:\|\|\n______________CCC_CU_UAG_UUCUUUUC\n3'-UUU...UUUUA______G___U________GUCACCG-5'\n_____________\|___________________\|\n_____________26__________________7\n	111 -- 117	8 -- 14	-16.1661 kcal/mol	2.51597 kcal/mol	0.697717 kcal/mol	99 118@LB@ \| \|@LB@5'-CUG...GUAAA C A GAAAA...UCA-3'@LB@ GGG GA AUC GGGAAGAG@LB@ \|\|\| \|\| \|\|\| ::\|\|\|:\|\|@LB@ CCC CU UAG UUCUUUUC@LB@3'-UUU...UUUUA G U GUCACCG-5'@LB@ \| \|@LB@ 26 7@LB@@LB@@LB@Energy -12.95 kcal/mol@LB@Hybridization Energy -16.1661 kcal/mol@LB@Unfolding Energy - mRNA 2.51597 kcal/mol@LB@Unfolding Energy - sRNA 0.697717 kcal/mol@LB@@LB@Position - mRNA 100 -- 117@LB@Position - sRNA 8 -- 25@LB@Position Seed - mRNA 111 -- 117@LB@Position Seed - sRNA 8 -- 14@LB@
147	0.01091	0.2504	b2720	hycF	-14.84	0.030299	116 -- 133	1 -- 16	formate hydrogenlyase complex iron-sulfur protein	_____________115________________134\n_____________\|__________________\|\n5'-CGA...CGUAA___________AA_____GCCGU...CAG-3'\n______________GAAGAAGAGCA__GUGGU\n______________:\|\|\|\|\|:\|\|\|\|__\|\|\|\|:\n______________UUUCUUUUCGU__CACCG\n3'-UUU...UGUAG__________________-5'\n_____________\|_________________\|\n_____________17________________1\n	120 -- 126	6 -- 12	-19.8629 kcal/mol	3.67538 kcal/mol	1.34555 kcal/mol	115 134@LB@ \| \|@LB@5'-CGA...CGUAA AA GCCGU...CAG-3'@LB@ GAAGAAGAGCA GUGGU@LB@ :\|\|\|\|\|:\|\|\|\| \|\|\|\|:@LB@ UUUCUUUUCGU CACCG@LB@3'-UUU...UGUAG -5'@LB@ \| \|@LB@ 17 1@LB@@LB@@LB@Energy -14.84 kcal/mol@LB@Hybridization Energy -19.8629 kcal/mol@LB@Unfolding Energy - mRNA 3.67538 kcal/mol@LB@Unfolding Energy - sRNA 1.34555 kcal/mol@LB@@LB@Position - mRNA 116 -- 133@LB@Position - sRNA 1 -- 16@LB@Position Seed - mRNA 120 -- 126@LB@Position Seed - sRNA 6 -- 12@LB@
121	0.008566	0.2484	b3466	yhhL	-13.33	0.066537	119 -- 150	1 -- 32	DUF1145 family protein	_____________118_________________________________151\n_____________\|___________________________________\|\n5'-GUU...UUCCA_____C___UCAUU_____________________GGGUC...UUA-3'\n______________GCAAA_UGG_____ACAUC_GGGAAAA__AGUGGC\n______________:\|\|\|\|_\|\|\|_____\|\|\|\|\|_::\|\|\|\|\|__\|\|\|\|\|\|\n______________UGUUU_ACC_____UGUAG_UUCUUUU__UCACCG\n3'-UUU...CGAGG_____U___CC________U_______CG______-5'\n_____________\|__________________________________\|\n_____________33_________________________________1\n	138 -- 144	9 -- 15	-23.4834 kcal/mol	7.61069 kcal/mol	2.53929 kcal/mol	118 151@LB@ \| \|@LB@5'-GUU...UUCCA C UCAUU GGGUC...UUA-3'@LB@ GCAAA UGG ACAUC GGGAAAA AGUGGC@LB@ :\|\|\|\| \|\|\| \|\|\|\|\| ::\|\|\|\|\| \|\|\|\|\|\|@LB@ UGUUU ACC UGUAG UUCUUUU UCACCG@LB@3'-UUU...CGAGG U CC U CG -5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -13.33 kcal/mol@LB@Hybridization Energy -23.4834 kcal/mol@LB@Unfolding Energy - mRNA 7.61069 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 119 -- 150@LB@Position - sRNA 1 -- 32@LB@Position Seed - mRNA 138 -- 144@LB@Position Seed - sRNA 9 -- 15@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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