Input and runtime details for job 6793193 (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 6793193 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:27:03 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:32 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:26:02 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:26:10 CET 2018
	Job Completed		@ Fri Feb 16 21:26:45 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6793193&toolName=CopraRNA ( 30 days expiry )

Description of the job

RprA

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
100	0.004525	0.1538	b2550	yphH	-8.03	0.477033	31 -- 47	39 -- 54	putative DNA-binding transcriptional regulator	_____________30_________________48\n_____________\|__________________\|\n5'-AGG...GCCCG_______A___UC_____CUCAA...UGG-3'\n______________GUUUCAU__GG__GGGAU\n______________\|\|\|\|\|\|:__:\|__\|\|\|\|\|\n______________CAAAGUG__UC__CCCUA\n3'-UUU...AGCAA_______AG_________AAGGU...GCA-5'\n_____________\|__________________\|\n_____________55_________________38\n	31 -- 37	48 -- 54	-12.873 kcal/mol	2.94673 kcal/mol	1.89674 kcal/mol	30 48@LB@ \| \|@LB@5'-AGG...GCCCG A UC CUCAA...UGG-3'@LB@ GUUUCAU GG GGGAU@LB@ \|\|\|\|\|\|: :\| \|\|\|\|\|@LB@ CAAAGUG UC CCCUA@LB@3'-UUU...AGCAA AG AAGGU...GCA-5'@LB@ \| \|@LB@ 55 38@LB@@LB@@LB@Energy -8.03 kcal/mol@LB@Hybridization Energy -12.873 kcal/mol@LB@Unfolding Energy - mRNA 2.94673 kcal/mol@LB@Unfolding Energy - sRNA 1.89674 kcal/mol@LB@@LB@Position - mRNA 31 -- 47@LB@Position - sRNA 39 -- 54@LB@Position Seed - mRNA 31 -- 37@LB@Position Seed - sRNA 48 -- 54@LB@
194	0.009812	0.1776	b2687	luxS	-7.90	0.495572	99 -- 106	42 -- 49	S-ribosylhomocysteine lyase	_____________98_______107\n_____________\|________\|\n5'-GAA...UCUGA________AUGAU...UCA-3'\n______________AUUCAGGG\n______________\|:\|\|\|\|\|\|\n______________UGAGUCCC\n3'-UUU...CAAAG________CUAAA...GCA-5'\n_____________\|________\|\n_____________50_______41\n	100 -- 106	42 -- 48	-12.5942 kcal/mol	3.05922 kcal/mol	1.63991 kcal/mol	98 107@LB@ \| \|@LB@5'-GAA...UCUGA AUGAU...UCA-3'@LB@ AUUCAGGG@LB@ \|:\|\|\|\|\|\|@LB@ UGAGUCCC@LB@3'-UUU...CAAAG CUAAA...GCA-5'@LB@ \| \|@LB@ 50 41@LB@@LB@@LB@Energy -7.90 kcal/mol@LB@Hybridization Energy -12.5942 kcal/mol@LB@Unfolding Energy - mRNA 3.05922 kcal/mol@LB@Unfolding Energy - sRNA 1.63991 kcal/mol@LB@@LB@Position - mRNA 99 -- 106@LB@Position - sRNA 42 -- 49@LB@Position Seed - mRNA 100 -- 106@LB@Position Seed - sRNA 42 -- 48@LB@
121	0.005439	0.1553	b1640	anmK	-7.89	0.496680	290 -- 297	63 -- 70	anhydro-N-acetylmuramic acid kinase	_____________289______298\n_____________\|________\|\n5'-CCA...CGGGU________UGG-3'\n______________CGCACAGC\n______________\|:\|\|\|\|\|\|\n______________GUGUGUCG\n3'-UUU...CUGAU________UUAAG...GCA-5'\n_____________\|________\|\n_____________71_______62\n	291 -- 297	63 -- 69	-13.0848 kcal/mol	2.06561 kcal/mol	3.13161 kcal/mol	289 298@LB@ \| \|@LB@5'-CCA...CGGGU UGG-3'@LB@ CGCACAGC@LB@ \|:\|\|\|\|\|\|@LB@ GUGUGUCG@LB@3'-UUU...CUGAU UUAAG...GCA-5'@LB@ \| \|@LB@ 71 62@LB@@LB@@LB@Energy -7.89 kcal/mol@LB@Hybridization Energy -13.0848 kcal/mol@LB@Unfolding Energy - mRNA 2.06561 kcal/mol@LB@Unfolding Energy - sRNA 3.13161 kcal/mol@LB@@LB@Position - mRNA 290 -- 297@LB@Position - sRNA 63 -- 70@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 63 -- 69@LB@
84	0.003656	0.1509	b0827	moeA	-7.84	0.503176	157 -- 203	32 -- 75	molybdopterin molybdenumtransferase; molybdopterin biosynthesis protein	_____________156_______________________________________________204\n_____________\|_________________________________________________\|\n5'-AUU...UUUCU_______AUA___A______AUU___CC____G____A_U_________GAAUU...UAC-3'\n______________GAC_AUA___GGC_AAUUCG___UUG__UC_C_CAGG_G_GUUUUCAUG\n______________\|\|\|_\|:\|___:\|\|_\|\|\|\|\|\|___\|\|\|__\|\|_\|_\|\|\|\|_\|_:\|\|\|:\|\|\|\|\n______________CUG_UGU___UCG_UUAAGC___AAC__AG_G_GUCC_C_UAAAGGUAC\n3'-UUU...CGUUU___A___GUG________________AA__U_A______C_________GAAUA...GCA-5'\n_____________\|_________________________________________________\|\n_____________76________________________________________________31\n	197 -- 203	32 -- 38	-28.9008 kcal/mol	13.8106 kcal/mol	7.24967 kcal/mol	156 204@LB@ \| \|@LB@5'-AUU...UUUCU AUA A AUU CC G A U GAAUU...UAC-3'@LB@ GAC AUA GGC AAUUCG UUG UC C CAGG G GUUUUCAUG@LB@ \|\|\| \|:\| :\|\| \|\|\|\|\|\| \|\|\| \|\| \| \|\|\|\| \| :\|\|\|:\|\|\|\|@LB@ CUG UGU UCG UUAAGC AAC AG G GUCC C UAAAGGUAC@LB@3'-UUU...CGUUU A GUG AA U A C GAAUA...GCA-5'@LB@ \| \|@LB@ 76 31@LB@@LB@@LB@Energy -7.84 kcal/mol@LB@Hybridization Energy -28.9008 kcal/mol@LB@Unfolding Energy - mRNA 13.8106 kcal/mol@LB@Unfolding Energy - sRNA 7.24967 kcal/mol@LB@@LB@Position - mRNA 157 -- 203@LB@Position - sRNA 32 -- 75@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 32 -- 38@LB@
138	0.006392	0.1605	b0345	lacI	-7.62	0.533808	7 -- 17	61 -- 71	lactose-inducible lac operon transcriptional repressor	_____________6___________18\n_____________\|___________\|\n_____5'-CAUUGA___G_______AAAAG...AAA-3'\n______________ACA_GCAGCGG\n______________\|\|\|_:\|\|\|\|::\n______________UGU_UGUCGUU\n3'-UUU...UCUGA___G_______AAGCA...GCA-5'\n_____________\|___________\|\n_____________72__________60\n	11 -- 17	61 -- 67	-13.1569 kcal/mol	2.35774 kcal/mol	3.17655 kcal/mol	6 18@LB@ \| \|@LB@ 5'-CAUUGA G AAAAG...AAA-3'@LB@ ACA GCAGCGG@LB@ \|\|\| :\|\|\|\|::@LB@ UGU UGUCGUU@LB@3'-UUU...UCUGA G AAGCA...GCA-5'@LB@ \| \|@LB@ 72 60@LB@@LB@@LB@Energy -7.62 kcal/mol@LB@Hybridization Energy -13.1569 kcal/mol@LB@Unfolding Energy - mRNA 2.35774 kcal/mol@LB@Unfolding Energy - sRNA 3.17655 kcal/mol@LB@@LB@Position - mRNA 7 -- 17@LB@Position - sRNA 61 -- 71@LB@Position Seed - mRNA 11 -- 17@LB@Position Seed - sRNA 61 -- 67@LB@
174	0.008627	0.1745	b1926	fliT	-7.57	0.540698	180 -- 211	31 -- 53	putative flagellar synthesis and assembly chaperone	_____________179______________________________212\n_____________\|________________________________\|\n5'-GUG...CCUUC___G_______ACCCAGUCU___GAA______ACCGC...UCA-3'\n______________UUU_AUUCAGG_________GAU___CCAUGC\n______________\|\|\|_\|:\|\|\|\|\|_________\|\|\|___\|\|\|\|\|\|\n______________AAA_UGAGUCC_________CUA___GGUACG\n3'-UUU...GCAAC___G_______C___________AA_______AAUAU...GCA-5'\n_____________\|________________________________\|\n_____________54_______________________________30\n	184 -- 190	43 -- 49	-18.5651 kcal/mol	6.60729 kcal/mol	4.38339 kcal/mol	179 212@LB@ \| \|@LB@5'-GUG...CCUUC G ACCCAGUCU GAA ACCGC...UCA-3'@LB@ UUU AUUCAGG GAU CCAUGC@LB@ \|\|\| \|:\|\|\|\|\| \|\|\| \|\|\|\|\|\|@LB@ AAA UGAGUCC CUA GGUACG@LB@3'-UUU...GCAAC G C AA AAUAU...GCA-5'@LB@ \| \|@LB@ 54 30@LB@@LB@@LB@Energy -7.57 kcal/mol@LB@Hybridization Energy -18.5651 kcal/mol@LB@Unfolding Energy - mRNA 6.60729 kcal/mol@LB@Unfolding Energy - sRNA 4.38339 kcal/mol@LB@@LB@Position - mRNA 180 -- 211@LB@Position - sRNA 31 -- 53@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 43 -- 49@LB@
40	0.0008945	0.07693	b0525	ppiB	-7.31	0.578113	284 -- 298	61 -- 76	peptidyl-prolyl cis-trans isomerase B (rotamase B)	_____________283______________299\n_____________\|________________\|\n5'-UGU...UUCCU___________C____AG-3'\n______________GGACUAC_UGC_GCGA\n______________:\|\|\|\|\|\|_::\|_\|\|:\|\n______________UCUGAUG_GUG_CGUU\n3'-UUU...CCGUU_______U___U____AAGCA...GCA-5'\n_____________\|________________\|\n_____________77_______________60\n	284 -- 290	70 -- 76	-14.2171 kcal/mol	3.65067 kcal/mol	3.25604 kcal/mol	283 299@LB@ \| \|@LB@5'-UGU...UUCCU C AG-3'@LB@ GGACUAC UGC GCGA@LB@ :\|\|\|\|\|\| ::\| \|\|:\|@LB@ UCUGAUG GUG CGUU@LB@3'-UUU...CCGUU U U AAGCA...GCA-5'@LB@ \| \|@LB@ 77 60@LB@@LB@@LB@Energy -7.31 kcal/mol@LB@Hybridization Energy -14.2171 kcal/mol@LB@Unfolding Energy - mRNA 3.65067 kcal/mol@LB@Unfolding Energy - sRNA 3.25604 kcal/mol@LB@@LB@Position - mRNA 284 -- 298@LB@Position - sRNA 61 -- 76@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 70 -- 76@LB@
108	0.004771	0.1538	b2594	rluD	-7.24	0.588975	189 -- 206	62 -- 78	23S rRNA pseudouridine(1911 1915 1917) synthase	_____________188________________207\n_____________\|__________________\|\n5'-CCC...ACGAA____C_G___________CAACG...GUU-3'\n______________GAAG_A_UAUAUAUGGCA\n______________:\|\|\|_\|_\|\|:\|:\|::\|\|\|\n______________UUUC_U_AUGUGUGUCGU\n3'-UUU...ACCCG______G___________UAAGC...GCA-5'\n_____________\|__________________\|\n_____________79_________________61\n	200 -- 206	62 -- 68	-13.9289 kcal/mol	3.43926 kcal/mol	3.2555 kcal/mol	188 207@LB@ \| \|@LB@5'-CCC...ACGAA C G CAACG...GUU-3'@LB@ GAAG A UAUAUAUGGCA@LB@ :\|\|\| \| \|\|:\|:\|::\|\|\|@LB@ UUUC U AUGUGUGUCGU@LB@3'-UUU...ACCCG G UAAGC...GCA-5'@LB@ \| \|@LB@ 79 61@LB@@LB@@LB@Energy -7.24 kcal/mol@LB@Hybridization Energy -13.9289 kcal/mol@LB@Unfolding Energy - mRNA 3.43926 kcal/mol@LB@Unfolding Energy - sRNA 3.2555 kcal/mol@LB@@LB@Position - mRNA 189 -- 206@LB@Position - sRNA 62 -- 78@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 62 -- 68@LB@
165	0.007934	0.1692	b3355	prkB	-7.13	0.603515	287 -- 294	63 -- 70	putative phosphoribulokinase	_____________286______295\n_____________\|________\|\n5'-GGC...AUAUU________UAAAUC-3'\n______________CGCGCAGU\n______________\|:\|:\|\|\|:\n______________GUGUGUCG\n3'-UUU...CUGAU________UUAAG...GCA-5'\n_____________\|________\|\n_____________71_______62\n	288 -- 294	63 -- 69	-11.0055 kcal/mol	0.741841 kcal/mol	3.13161 kcal/mol	286 295@LB@ \| \|@LB@5'-GGC...AUAUU UAAAUC-3'@LB@ CGCGCAGU@LB@ \|:\|:\|\|\|:@LB@ GUGUGUCG@LB@3'-UUU...CUGAU UUAAG...GCA-5'@LB@ \| \|@LB@ 71 62@LB@@LB@@LB@Energy -7.13 kcal/mol@LB@Hybridization Energy -11.0055 kcal/mol@LB@Unfolding Energy - mRNA 0.741841 kcal/mol@LB@Unfolding Energy - sRNA 3.13161 kcal/mol@LB@@LB@Position - mRNA 287 -- 294@LB@Position - sRNA 63 -- 70@LB@Position Seed - mRNA 288 -- 294@LB@Position Seed - sRNA 63 -- 69@LB@
119	0.005328	0.1553	b3417	malP	-6.58	0.680720	220 -- 257	42 -- 71	maltodextrin phosphorylase	_____________219____________________________________258\n_____________\|______________________________________\|\n5'-ACA...UUUUA___AUA________CAG_AAGCGC______G____U__CAGCG...GCC-3'\n______________ACG___AGCAAUUU___G______UUUCAC_UCAG_GG\n______________\|\|:___\|\|\|\|\|\|\|:___\|______\|\|\|\|\|\|_\|\|\|\|_\|\|\n______________UGU___UCGUUAAG___C______AAAGUG_AGUC_CC\n3'-UUU...UCUGA___GUG________CAA_____________________CUAAA...GCA-5'\n_____________\|______________________________________\|\n_____________72_____________________________________41\n	227 -- 233	58 -- 64	-19.6486 kcal/mol	8.3321 kcal/mol	4.73391 kcal/mol	219 258@LB@ \| \|@LB@5'-ACA...UUUUA AUA CAG AAGCGC G U CAGCG...GCC-3'@LB@ ACG AGCAAUUU G UUUCAC UCAG GG@LB@ \|\|: \|\|\|\|\|\|\|: \| \|\|\|\|\|\| \|\|\|\| \|\|@LB@ UGU UCGUUAAG C AAAGUG AGUC CC@LB@3'-UUU...UCUGA GUG CAA CUAAA...GCA-5'@LB@ \| \|@LB@ 72 41@LB@@LB@@LB@Energy -6.58 kcal/mol@LB@Hybridization Energy -19.6486 kcal/mol@LB@Unfolding Energy - mRNA 8.3321 kcal/mol@LB@Unfolding Energy - sRNA 4.73391 kcal/mol@LB@@LB@Position - mRNA 220 -- 257@LB@Position - sRNA 42 -- 71@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 58 -- 64@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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