Input and runtime details for job 1765463 (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 1765463 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:41:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:42:13 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 19:57:45 CET 2018
	Post-Processing Finished		@ Fri Feb 16 19:57:53 CET 2018
	Job Completed		@ Fri Feb 16 19:58:19 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1765463&toolName=CopraRNA ( 30 days expiry )

Description of the job

5 ChiX sequences

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
62	0.01306	0.6177	b4034	malE	-9.62	0.049140	112 -- 120	45 -- 53	maltose transporter subunit	_____________111_______121\n_____________\|_________\|\n5'-AGG...AGGGG_________UGGAA...UGG-3'\n______________CAAGGAGGA\n______________\|\|\|:\|\|\|\|\|\n______________GUUUCUCCU\n3'-UUU...GGGCA_________UAAAG...ACA-5'\n_____________\|_________\|\n_____________54________44\n	114 -- 120	45 -- 51	-12.5673 kcal/mol	2.02865 kcal/mol	0.917553 kcal/mol	111 121@LB@ \| \|@LB@5'-AGG...AGGGG UGGAA...UGG-3'@LB@ CAAGGAGGA@LB@ \|\|\|:\|\|\|\|\|@LB@ GUUUCUCCU@LB@3'-UUU...GGGCA UAAAG...ACA-5'@LB@ \| \|@LB@ 54 44@LB@@LB@@LB@Energy -9.62 kcal/mol@LB@Hybridization Energy -12.5673 kcal/mol@LB@Unfolding Energy - mRNA 2.02865 kcal/mol@LB@Unfolding Energy - sRNA 0.917553 kcal/mol@LB@@LB@Position - mRNA 112 -- 120@LB@Position - sRNA 45 -- 53@LB@Position Seed - mRNA 114 -- 120@LB@Position Seed - sRNA 45 -- 51@LB@
166	0.03384	0.6177	b4035	malK	-4.35	0.473183	186 -- 196	44 -- 53	maltose ABC transportor ATPase	_____________185_________197\n_____________\|___________\|\n5'-CGC...UGUUA_______A___GGGCA...UGU-3'\n______________CAAAGGG_GAA\n______________\|\|\|\|\|:\|_\|\|\|\n______________GUUUCUC_CUU\n3'-UUU...GGGCA___________AAAGU...ACA-5'\n_____________\|___________\|\n_____________54__________43\n	186 -- 192	47 -- 53	-9.12531 kcal/mol	3.84302 kcal/mol	0.927997 kcal/mol	185 197@LB@ \| \|@LB@5'-CGC...UGUUA A GGGCA...UGU-3'@LB@ CAAAGGG GAA@LB@ \|\|\|\|\|:\| \|\|\|@LB@ GUUUCUC CUU@LB@3'-UUU...GGGCA AAAGU...ACA-5'@LB@ \| \|@LB@ 54 43@LB@@LB@@LB@Energy -4.35 kcal/mol@LB@Hybridization Energy -9.12531 kcal/mol@LB@Unfolding Energy - mRNA 3.84302 kcal/mol@LB@Unfolding Energy - sRNA 0.927997 kcal/mol@LB@@LB@Position - mRNA 186 -- 196@LB@Position - sRNA 44 -- 53@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 47 -- 53@LB@
187	0.03882	0.6177	b0403	malZ	-7.79	0.114240	189 -- 197	42 -- 50	maltodextrin glucosidase	_____________188_______198\n_____________\|_________\|\n5'-UUU...AUCAC_________AUGAU...AGC-3'\n______________AGGGGAAUU\n______________\|\|:\|\|\|\|\|\|\n______________UCUCCUUAA\n3'-UUU...CAGUU_________AGUAA...ACA-5'\n_____________\|_________\|\n_____________51________41\n	191 -- 197	42 -- 48	-10.7884 kcal/mol	2.13721 kcal/mol	0.856185 kcal/mol	188 198@LB@ \| \|@LB@5'-UUU...AUCAC AUGAU...AGC-3'@LB@ AGGGGAAUU@LB@ \|\|:\|\|\|\|\|\|@LB@ UCUCCUUAA@LB@3'-UUU...CAGUU AGUAA...ACA-5'@LB@ \| \|@LB@ 51 41@LB@@LB@@LB@Energy -7.79 kcal/mol@LB@Hybridization Energy -10.7884 kcal/mol@LB@Unfolding Energy - mRNA 2.13721 kcal/mol@LB@Unfolding Energy - sRNA 0.856185 kcal/mol@LB@@LB@Position - mRNA 189 -- 197@LB@Position - sRNA 42 -- 50@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 42 -- 48@LB@
16	0.003381	0.593	b0956	matP	-12.11	0.015217	269 -- 280	42 -- 53	Ter macrodomain organizer matS-binding protein	_____________268__________281\n_____________\|____________\|\n5'-UUU...CAUCG____________AAUCA...AAG-3'\n______________CGAAGGGGAGUU\n______________\|:\|\|\|:\|\|\|:\|\|\n______________GUUUCUCCUUAA\n3'-UUU...GGGCA____________AGUAA...ACA-5'\n_____________\|____________\|\n_____________54___________41\n	274 -- 280	42 -- 48	-15.3716 kcal/mol	2.33274 kcal/mol	0.933904 kcal/mol	268 281@LB@ \| \|@LB@5'-UUU...CAUCG AAUCA...AAG-3'@LB@ CGAAGGGGAGUU@LB@ \|:\|\|\|:\|\|\|:\|\|@LB@ GUUUCUCCUUAA@LB@3'-UUU...GGGCA AGUAA...ACA-5'@LB@ \| \|@LB@ 54 41@LB@@LB@@LB@Energy -12.11 kcal/mol@LB@Hybridization Energy -15.3716 kcal/mol@LB@Unfolding Energy - mRNA 2.33274 kcal/mol@LB@Unfolding Energy - sRNA 0.933904 kcal/mol@LB@@LB@Position - mRNA 269 -- 280@LB@Position - sRNA 42 -- 53@LB@Position Seed - mRNA 274 -- 280@LB@Position Seed - sRNA 42 -- 48@LB@
21	0.004054	0.5992	b2076	mdtC	-11.67	0.018717	158 -- 193	45 -- 78	multidrug efflux system subunit C	_____________157____________________________________194\n_____________\|______________________________________\|\n5'-CUC...GCAUU____A____AAGC____UU__________UG_______GGCGU...CGG-3'\n______________GUGG_CCAA____CGCU____GCCCGUCA__AAGAGGA\n______________:\|\|\|_\|\|\|\|____\|\|\|\|____\|\|\|\|\|\|\|\|__\|\|\|\|\|\|\|\n______________UACC_GGUU____GCGA____CGGGCAGU__UUCUCCU\n_____3'-UUUUUU_________AUA_____UAAC_________________UAAAG...ACA-5'\n_____________\|______________________________________\|\n_____________79_____________________________________44\n	187 -- 193	45 -- 51	-37.8051 kcal/mol	12.6053 kcal/mol	13.5316 kcal/mol	157 194@LB@ \| \|@LB@5'-CUC...GCAUU A AAGC UU UG GGCGU...CGG-3'@LB@ GUGG CCAA CGCU GCCCGUCA AAGAGGA@LB@ :\|\|\| \|\|\|\| \|\|\|\| \|\|\|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ UACC GGUU GCGA CGGGCAGU UUCUCCU@LB@ 3'-UUUUUU AUA UAAC UAAAG...ACA-5'@LB@ \| \|@LB@ 79 44@LB@@LB@@LB@Energy -11.67 kcal/mol@LB@Hybridization Energy -37.8051 kcal/mol@LB@Unfolding Energy - mRNA 12.6053 kcal/mol@LB@Unfolding Energy - sRNA 13.5316 kcal/mol@LB@@LB@Position - mRNA 158 -- 193@LB@Position - sRNA 45 -- 78@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 45 -- 51@LB@
36	0.007218	0.6129	b3938	metJ	-9.22	0.059290	181 -- 189	45 -- 53	transcriptional repressor S-adenosylmethionine-binding	_____________180_______190\n_____________\|_________\|\n5'-UCU...AUUGA_________UUAAG...UGU-3'\n______________CGAAGAGGA\n______________\|:\|\|\|\|\|\|\|\n______________GUUUCUCCU\n3'-UUU...GGGCA_________UAAAG...ACA-5'\n_____________\|_________\|\n_____________54________44\n	183 -- 189	45 -- 51	-12.478 kcal/mol	2.34125 kcal/mol	0.917553 kcal/mol	180 190@LB@ \| \|@LB@5'-UCU...AUUGA UUAAG...UGU-3'@LB@ CGAAGAGGA@LB@ \|:\|\|\|\|\|\|\|@LB@ GUUUCUCCU@LB@3'-UUU...GGGCA UAAAG...ACA-5'@LB@ \| \|@LB@ 54 44@LB@@LB@@LB@Energy -9.22 kcal/mol@LB@Hybridization Energy -12.478 kcal/mol@LB@Unfolding Energy - mRNA 2.34125 kcal/mol@LB@Unfolding Energy - sRNA 0.917553 kcal/mol@LB@@LB@Position - mRNA 181 -- 189@LB@Position - sRNA 45 -- 53@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 45 -- 51@LB@
12	0.002398	0.593	b1114	mfd	-13.52	0.007793	210 -- 241	45 -- 73	transcription-repair coupling factor	_____________209______________________________242\n_____________\|________________________________\|\n5'-UUC...CUGAA____________ACGCU___________C___UGAGC...AAA-3'\n______________CAAUAUCGUUAU_____GCCCGUCAAAG_GGG\n______________\|\|\|\|\|\|\|\|:\|\|\|_____\|\|\|\|\|\|\|\|\|\|\|_\|\|:\n______________GUUAUAGCGAUA_____CGGGCAGUUUC_CCU\n3'-UUU...UACCG____________AC______________U___UAAAG...ACA-5'\n_____________\|________________________________\|\n_____________74_______________________________44\n	231 -- 237	49 -- 55	-37.142 kcal/mol	12.2919 kcal/mol	11.3343 kcal/mol	209 242@LB@ \| \|@LB@5'-UUC...CUGAA ACGCU C UGAGC...AAA-3'@LB@ CAAUAUCGUUAU GCCCGUCAAAG GGG@LB@ \|\|\|\|\|\|\|\|:\|\|\| \|\|\|\|\|\|\|\|\|\|\| \|\|:@LB@ GUUAUAGCGAUA CGGGCAGUUUC CCU@LB@3'-UUU...UACCG AC U UAAAG...ACA-5'@LB@ \| \|@LB@ 74 44@LB@@LB@@LB@Energy -13.52 kcal/mol@LB@Hybridization Energy -37.142 kcal/mol@LB@Unfolding Energy - mRNA 12.2919 kcal/mol@LB@Unfolding Energy - sRNA 11.3343 kcal/mol@LB@@LB@Position - mRNA 210 -- 241@LB@Position - sRNA 45 -- 73@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 49 -- 55@LB@
49	0.009604	0.6129	b1175	minD	-8.49	0.083180	191 -- 199	40 -- 48	inhibitor of FtsZ ring polymerization; chromosome-membrane tethering protein; membrane ATPase of the MinCDEE system	_____________190_______200\n_____________\|_________\|\n5'-CUG...UAACA_________UAUGG...AAA-3'\n______________AGGAAUUUC\n______________\|\|\|\|\|\|\|\|\|\n______________UCCUUAAAG\n3'-UUU...GUUUC_________UAAAA...ACA-5'\n_____________\|_________\|\n_____________49________39\n	193 -- 199	40 -- 46	-11.0161 kcal/mol	1.62901 kcal/mol	0.898161 kcal/mol	190 200@LB@ \| \|@LB@5'-CUG...UAACA UAUGG...AAA-3'@LB@ AGGAAUUUC@LB@ \|\|\|\|\|\|\|\|\|@LB@ UCCUUAAAG@LB@3'-UUU...GUUUC UAAAA...ACA-5'@LB@ \| \|@LB@ 49 39@LB@@LB@@LB@Energy -8.49 kcal/mol@LB@Hybridization Energy -11.0161 kcal/mol@LB@Unfolding Energy - mRNA 1.62901 kcal/mol@LB@Unfolding Energy - sRNA 0.898161 kcal/mol@LB@@LB@Position - mRNA 191 -- 199@LB@Position - sRNA 40 -- 48@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 40 -- 46@LB@
89	0.01853	0.6177	b1448	mnaT	-8.57	0.080000	123 -- 134	43 -- 54	methionine N-acyltransferase; L-amino acid N-acyltransferase	_____________122__________135\n_____________\|____________\|\n5'-CGC...UAAUU___UC_______CCGUU...CGG-3'\n______________UCA__GAGGAAU\n______________\|\|\|__\|\|\|\|\|\|\|\n______________AGU__CUCCUUA\n3'-UUU...CGGGC___UU_______AAGUA...ACA-5'\n_____________\|____________\|\n_____________55___________42\n	128 -- 134	43 -- 49	-11.9422 kcal/mol	2.42412 kcal/mol	0.944705 kcal/mol	122 135@LB@ \| \|@LB@5'-CGC...UAAUU UC CCGUU...CGG-3'@LB@ UCA GAGGAAU@LB@ \|\|\| \|\|\|\|\|\|\|@LB@ AGU CUCCUUA@LB@3'-UUU...CGGGC UU AAGUA...ACA-5'@LB@ \| \|@LB@ 55 42@LB@@LB@@LB@Energy -8.57 kcal/mol@LB@Hybridization Energy -11.9422 kcal/mol@LB@Unfolding Energy - mRNA 2.42412 kcal/mol@LB@Unfolding Energy - sRNA 0.944705 kcal/mol@LB@@LB@Position - mRNA 123 -- 134@LB@Position - sRNA 43 -- 54@LB@Position Seed - mRNA 128 -- 134@LB@Position Seed - sRNA 43 -- 49@LB@
7	0.001184	0.5444	b0817	mntR	-11.99	0.016054	285 -- 294	46 -- 55	Mn(2+)-responsive manganese regulon transcriptional regulator	_____________284________295\n_____________\|__________\|\n5'-CUU...GCCAG__________CGCAUC-3'\n______________GUCAGAGAGG\n______________\|\|\|\|:\|\|\|\|\|\n______________CAGUUUCUCC\n3'-UUU...CCGGG__________UUAAA...ACA-5'\n_____________\|__________\|\n_____________56_________45\n	288 -- 294	46 -- 52	-16.1275 kcal/mol	3.21103 kcal/mol	0.924411 kcal/mol	284 295@LB@ \| \|@LB@5'-CUU...GCCAG CGCAUC-3'@LB@ GUCAGAGAGG@LB@ \|\|\|\|:\|\|\|\|\|@LB@ CAGUUUCUCC@LB@3'-UUU...CCGGG UUAAA...ACA-5'@LB@ \| \|@LB@ 56 45@LB@@LB@@LB@Energy -11.99 kcal/mol@LB@Hybridization Energy -16.1275 kcal/mol@LB@Unfolding Energy - mRNA 3.21103 kcal/mol@LB@Unfolding Energy - sRNA 0.924411 kcal/mol@LB@@LB@Position - mRNA 285 -- 294@LB@Position - sRNA 46 -- 55@LB@Position Seed - mRNA 288 -- 294@LB@Position Seed - sRNA 46 -- 52@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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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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