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
43	0.00107	0.08759	b4036	lamB	-10.48	0.202041	185 -- 197	39 -- 51	maltose outer membrane porin (maltoporin)	_____________184___________198\n_____________\|_____________\|\n5'-CGC...AGCAA_G_______A___AGAAU...GUU-3'\n______________U_ACUCAGG_GAU\n______________\|_\|\|\|\|\|\|\|_\|\|\|\n______________A_UGAGUCC_CUA\n3'-UUU...AACAA_G_______C___AAGGU...GCA-5'\n_____________\|_____________\|\n_____________52____________38\n	187 -- 193	43 -- 49	-14.6452 kcal/mol	2.36402 kcal/mol	1.79807 kcal/mol	184 198@LB@ \| \|@LB@5'-CGC...AGCAA G A AGAAU...GUU-3'@LB@ U ACUCAGG GAU@LB@ \| \|\|\|\|\|\|\| \|\|\|@LB@ A UGAGUCC CUA@LB@3'-UUU...AACAA G C AAGGU...GCA-5'@LB@ \| \|@LB@ 52 38@LB@@LB@@LB@Energy -10.48 kcal/mol@LB@Hybridization Energy -14.6452 kcal/mol@LB@Unfolding Energy - mRNA 2.36402 kcal/mol@LB@Unfolding Energy - sRNA 1.79807 kcal/mol@LB@@LB@Position - mRNA 185 -- 197@LB@Position - sRNA 39 -- 51@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 43 -- 49@LB@
82	0.00343	0.1462	b4043	lexA	-10.80	0.176998	163 -- 196	40 -- 72	transcriptional repressor of SOS regulon	_____________162________________________________197\n_____________\|__________________________________\|\n5'-CGC...GUAUA___U_______UAAC___AUAUA___C_______CGGAA...AGC-3'\n______________UAC_CACAGCA____UGU_____CAC_CAGGGGG\n______________\|\|\|_\|\|\|\|\|\|\|____:\|\|_____\|\|\|_\|\|\|\|\|\|:\n______________AUG_GUGUCGU____GCA_____GUG_GUCCCCU\n3'-UUU...UUCUG___U_______UAA____ACAAA___A_______AAAGG...GCA-5'\n_____________\|__________________________________\|\n_____________73_________________________________39\n	190 -- 196	40 -- 46	-30.123 kcal/mol	14.5591 kcal/mol	4.76217 kcal/mol	162 197@LB@ \| \|@LB@5'-CGC...GUAUA U UAAC AUAUA C CGGAA...AGC-3'@LB@ UAC CACAGCA UGU CAC CAGGGGG@LB@ \|\|\| \|\|\|\|\|\|\| :\|\| \|\|\| \|\|\|\|\|\|:@LB@ AUG GUGUCGU GCA GUG GUCCCCU@LB@3'-UUU...UUCUG U UAA ACAAA A AAAGG...GCA-5'@LB@ \| \|@LB@ 73 39@LB@@LB@@LB@Energy -10.80 kcal/mol@LB@Hybridization Energy -30.123 kcal/mol@LB@Unfolding Energy - mRNA 14.5591 kcal/mol@LB@Unfolding Energy - sRNA 4.76217 kcal/mol@LB@@LB@Position - mRNA 163 -- 196@LB@Position - sRNA 40 -- 72@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 40 -- 46@LB@
14	0.0001025	0.0245	b4051	qorA	-14.73	0.024599	192 -- 224	48 -- 76	quinone oxidoreductase NADPH-dependent	_____________191_______________________________225\n_____________\|_________________________________\|\n5'-CGC...GUUCU___GG___________CA__AA___AA______AAGCA...UCG-3'\n______________GGA__ACACAUGGCAA__CG__UUG__UUUCAC\n______________:\|\|__\|\|\|\|\|::\|\|\|\|__\|\|__\|\|\|__\|\|\|\|\|\|\n______________UCU__UGUGUGUCGUU__GC__AAC__AAAGUG\n3'-UUU...CCGUU___GA___________AA_______________AGUCC...GCA-5'\n_____________\|_________________________________\|\n_____________77________________________________47\n	201 -- 207	61 -- 67	-23.6874 kcal/mol	5.27405 kcal/mol	3.68714 kcal/mol	191 225@LB@ \| \|@LB@5'-CGC...GUUCU GG CA AA AA AAGCA...UCG-3'@LB@ GGA ACACAUGGCAA CG UUG UUUCAC@LB@ :\|\| \|\|\|\|\|::\|\|\|\| \|\| \|\|\| \|\|\|\|\|\|@LB@ UCU UGUGUGUCGUU GC AAC AAAGUG@LB@3'-UUU...CCGUU GA AA AGUCC...GCA-5'@LB@ \| \|@LB@ 77 47@LB@@LB@@LB@Energy -14.73 kcal/mol@LB@Hybridization Energy -23.6874 kcal/mol@LB@Unfolding Energy - mRNA 5.27405 kcal/mol@LB@Unfolding Energy - sRNA 3.68714 kcal/mol@LB@@LB@Position - mRNA 192 -- 224@LB@Position - sRNA 48 -- 76@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 61 -- 67@LB@
25	0.0002079	0.02926	b4064	ghxP	-13.58	0.046769	115 -- 151	38 -- 73	guanine/hypoxanthine permease high affinity; guanine/hypoxanthine:H+ symporter	_____________114____________________________________152\n_____________\|______________________________________\|\n5'-UCG...CAAAC___GA_____G__GAUAAC________GG_________GUCCG...UAA-3'\n______________CUG___GCAG_AA______GUUUCGCU__CAGGGGAUU\n______________\|\|:___:\|\|\|_\|\|______\|\|\|\|\|:\|\|__\|\|\|\|\|\|\|\|\|\n______________GAU___UGUC_UU______CAAAGUGA__GUCCCCUAA\n3'-UUU...UUUCU___GUG____G__AAGCAA___________________AGGUA...GCA-5'\n_____________\|______________________________________\|\n_____________74_____________________________________37\n	145 -- 151	38 -- 44	-32.2199 kcal/mol	13.8672 kcal/mol	4.77333 kcal/mol	114 152@LB@ \| \|@LB@5'-UCG...CAAAC GA G GAUAAC GG GUCCG...UAA-3'@LB@ CUG GCAG AA GUUUCGCU CAGGGGAUU@LB@ \|\|: :\|\|\| \|\| \|\|\|\|\|:\|\| \|\|\|\|\|\|\|\|\|@LB@ GAU UGUC UU CAAAGUGA GUCCCCUAA@LB@3'-UUU...UUUCU GUG G AAGCAA AGGUA...GCA-5'@LB@ \| \|@LB@ 74 37@LB@@LB@@LB@Energy -13.58 kcal/mol@LB@Hybridization Energy -32.2199 kcal/mol@LB@Unfolding Energy - mRNA 13.8672 kcal/mol@LB@Unfolding Energy - sRNA 4.77333 kcal/mol@LB@@LB@Position - mRNA 115 -- 151@LB@Position - sRNA 38 -- 73@LB@Position Seed - mRNA 145 -- 151@LB@Position Seed - sRNA 38 -- 44@LB@
32	0.0005139	0.05552	b4070	nrfA	-17.83	0.003136	66 -- 107	41 -- 78	nitrite reductase formate-dependent cytochrome	_____________65_________________________________________108\n_____________\|__________________________________________\|\n5'-UGU...UGAUU______A___UU_______UG___AU_____A___A______CGAGC...CAA-3'\n______________AAAGAC_ACA__CACAGUG__GUU__UUGUU_CAC_UAGGGG\n______________\|\|\|\|\|\|_\|\|\|__\|\|\|\|\|::__:\|\|__\|\|\|\|\|_\|\|\|_:\|\|\|\|\|\n______________UUUCUG_UGU__GUGUCGU__UAA__AACAA_GUG_GUCCCC\n3'-UUU...ACCCG______A_________________GC_____A___A______UAAAG...GCA-5'\n_____________\|__________________________________________\|\n_____________79_________________________________________40\n	78 -- 84	62 -- 68	-32.7887 kcal/mol	10.1881 kcal/mol	4.77302 kcal/mol	65 108@LB@ \| \|@LB@5'-UGU...UGAUU A UU UG AU A A CGAGC...CAA-3'@LB@ AAAGAC ACA CACAGUG GUU UUGUU CAC UAGGGG@LB@ \|\|\|\|\|\| \|\|\| \|\|\|\|\|:: :\|\| \|\|\|\|\| \|\|\| :\|\|\|\|\|@LB@ UUUCUG UGU GUGUCGU UAA AACAA GUG GUCCCC@LB@3'-UUU...ACCCG A GC A A UAAAG...GCA-5'@LB@ \| \|@LB@ 79 40@LB@@LB@@LB@Energy -17.83 kcal/mol@LB@Hybridization Energy -32.7887 kcal/mol@LB@Unfolding Energy - mRNA 10.1881 kcal/mol@LB@Unfolding Energy - sRNA 4.77302 kcal/mol@LB@@LB@Position - mRNA 66 -- 107@LB@Position - sRNA 41 -- 78@LB@Position Seed - mRNA 78 -- 84@LB@Position Seed - sRNA 62 -- 68@LB@
190	0.009703	0.1776	b4125	dcuS	-9.98	0.246838	251 -- 265	60 -- 75	sensory histidine kinase in two-component regulatory system with DcuR regulator of anaerobic fumarate respiration	_____________250______________266\n_____________\|________________\|\n5'-UCC...AAAUU__G_____________CUUAA...UAU-3'\n______________GA_UAC_CACAGUGAU\n______________\|\|_\|\|\|_\|\|\|\|\|::\|\|\n______________CU_AUG_GUGUCGUUA\n3'-UUU...CGUUU__G___U_________AGCAA...GCA-5'\n_____________\|________________\|\n_____________76_______________59\n	259 -- 265	60 -- 66	-16.3548 kcal/mol	3.08747 kcal/mol	3.28851 kcal/mol	250 266@LB@ \| \|@LB@5'-UCC...AAAUU G CUUAA...UAU-3'@LB@ GA UAC CACAGUGAU@LB@ \|\| \|\|\| \|\|\|\|\|::\|\|@LB@ CU AUG GUGUCGUUA@LB@3'-UUU...CGUUU G U AGCAA...GCA-5'@LB@ \| \|@LB@ 76 59@LB@@LB@@LB@Energy -9.98 kcal/mol@LB@Hybridization Energy -16.3548 kcal/mol@LB@Unfolding Energy - mRNA 3.08747 kcal/mol@LB@Unfolding Energy - sRNA 3.28851 kcal/mol@LB@@LB@Position - mRNA 251 -- 265@LB@Position - sRNA 60 -- 75@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 60 -- 66@LB@
115	0.005088	0.155	b4131	cadA	-16.57	0.007707	197 -- 237	37 -- 75	lysine decarboxylase acid-inducible	_____________196__________________________________________238\n_____________\|____________________________________________\|\n5'-CUC...GAUAU______GA___UUAUU_____A_____AA____AU_________AUUUU...UUG-3'\n______________GACUAU__ACG_____GCAAU___UUG__UCAC___GGGGGUUU\n______________\|\|\|\|\|:__\|\|:_____\|\|\|\|\|___\|\|\|__\|\|\|\|___\|\|\|\|:\|\|\|\n______________CUGAUG__UGU_____CGUUA___AAC__AGUG___CCCCUAAA\n3'-UUU...CGUUU______UG_____________AGC___AA____AGU________GGUAC...GCA-5'\n_____________\|____________________________________________\|\n_____________76___________________________________________36\n	231 -- 237	37 -- 43	-27.1465 kcal/mol	5.79755 kcal/mol	4.77966 kcal/mol	196 238@LB@ \| \|@LB@5'-CUC...GAUAU GA UUAUU A AA AU AUUUU...UUG-3'@LB@ GACUAU ACG GCAAU UUG UCAC GGGGGUUU@LB@ \|\|\|\|\|: \|\|: \|\|\|\|\| \|\|\| \|\|\|\| \|\|\|\|:\|\|\|@LB@ CUGAUG UGU CGUUA AAC AGUG CCCCUAAA@LB@3'-UUU...CGUUU UG AGC AA AGU GGUAC...GCA-5'@LB@ \| \|@LB@ 76 36@LB@@LB@@LB@Energy -16.57 kcal/mol@LB@Hybridization Energy -27.1465 kcal/mol@LB@Unfolding Energy - mRNA 5.79755 kcal/mol@LB@Unfolding Energy - sRNA 4.77966 kcal/mol@LB@@LB@Position - mRNA 197 -- 237@LB@Position - sRNA 37 -- 75@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 37 -- 43@LB@
70	0.002881	0.1417	b4144	yjeI	-14.17	0.033933	177 -- 235	31 -- 99	DUF4156 family lipoprotein	_____________176______________________________________________________________________236\n_____________\|________________________________________________________________________\|\n5'-GCA...CGUCC_________AUU________G__UA______________AA_______________CA______G__G____CGCGC...GCA-3'\n______________AGCUCAUUG______AUGGG_AA__AC_AUGCAC_GUAA__________UACUUAG__GGGAUU_UC_GUGC\n______________\|\|\|:\|\|\|:\|______\|\|\|\|\|_\|\|__\|\|_\|::\|\|\|_\|:\|\|__________:\|\|\|:\|\|__\|\|\|\|\|\|_\|\|_:\|\|\|\n______________UCGGGUAGC______UACCC_UU__UG_UGUGUG_CGUU__________GUGAGUC__CCCUAA_AG_UACG\n_____3'-UUUUUU_________ACCCUC_____G__UC__A______U____AAGCAACAAA__________________G____AAUAU...GCA-5'\n_____________\|________________________________________________________________________\|\n_____________100______________________________________________________________________30\n	213 -- 219	44 -- 50	-46.9384 kcal/mol	12.7048 kcal/mol	20.0691 kcal/mol	176 236@LB@ \| \|@LB@5'-GCA...CGUCC AUU G UA AA CA G G CGCGC...GCA-3'@LB@ AGCUCAUUG AUGGG AA AC AUGCAC GUAA UACUUAG GGGAUU UC GUGC@LB@ \|\|\|:\|\|\|:\| \|\|\|\|\| \|\| \|\| \|::\|\|\| \|:\|\| :\|\|\|:\|\| \|\|\|\|\|\| \|\| :\|\|\|@LB@ UCGGGUAGC UACCC UU UG UGUGUG CGUU GUGAGUC CCCUAA AG UACG@LB@ 3'-UUUUUU ACCCUC G UC A U AAGCAACAAA G AAUAU...GCA-5'@LB@ \| \|@LB@ 100 30@LB@@LB@@LB@Energy -14.17 kcal/mol@LB@Hybridization Energy -46.9384 kcal/mol@LB@Unfolding Energy - mRNA 12.7048 kcal/mol@LB@Unfolding Energy - sRNA 20.0691 kcal/mol@LB@@LB@Position - mRNA 177 -- 235@LB@Position - sRNA 31 -- 99@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 44 -- 50@LB@
20	0.0001757	0.02926	b4175	hflC	-15.67	0.013919	175 -- 193	40 -- 75	HflB protease modulator specific for phage lambda cII repressor	_____________174__________________________________194\n_____________\|____________________________________\|\n5'-UUA...GUAAC____________________________________AAUAA...GUU-3'\n______________GACUAC___CAGCG______________UCAGGGGG\n______________\|\|\|\|\|\|___\|\|\|\|:______________\|\|\|\|\|\|\|:\n______________CUGAUG___GUCGU______________AGUCCCCU\n3'-UUU...CGUUU______UGU_____UAAGCAACAAAGUG________AAAGG...GCA-5'\n_____________\|____________________________________\|\n_____________76___________________________________39\n	187 -- 193	40 -- 46	-24.7611 kcal/mol	4.31935 kcal/mol	4.77786 kcal/mol	174 194@LB@ \| \|@LB@5'-UUA...GUAAC AAUAA...GUU-3'@LB@ GACUAC CAGCG UCAGGGGG@LB@ \|\|\|\|\|\| \|\|\|\|: \|\|\|\|\|\|\|:@LB@ CUGAUG GUCGU AGUCCCCU@LB@3'-UUU...CGUUU UGU UAAGCAACAAAGUG AAAGG...GCA-5'@LB@ \| \|@LB@ 76 39@LB@@LB@@LB@Energy -15.67 kcal/mol@LB@Hybridization Energy -24.7611 kcal/mol@LB@Unfolding Energy - mRNA 4.31935 kcal/mol@LB@Unfolding Energy - sRNA 4.77786 kcal/mol@LB@@LB@Position - mRNA 175 -- 193@LB@Position - sRNA 40 -- 75@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 40 -- 46@LB@
162	0.007731	0.1668	b4202	rpsR	-9.58	0.287294	60 -- 77	62 -- 76	30S ribosomal subunit protein S18	_____________59_________________78\n_____________\|__________________\|\n5'-CGG...AAACC____CAU___U_______UAACG...UCA-3'\n______________AGGC___UAC_CACAGUA\n______________\|\|:\|___\|\|\|_\|\|\|\|\|:\|\n______________UCUG___AUG_GUGUCGU\n3'-UUU...CCGUU__________U_______UAAGC...GCA-5'\n_____________\|__________________\|\n_____________77_________________61\n	71 -- 77	62 -- 68	-14.2281 kcal/mol	1.39912 kcal/mol	3.25371 kcal/mol	59 78@LB@ \| \|@LB@5'-CGG...AAACC CAU U UAACG...UCA-3'@LB@ AGGC UAC CACAGUA@LB@ \|\|:\| \|\|\| \|\|\|\|\|:\|@LB@ UCUG AUG GUGUCGU@LB@3'-UUU...CCGUU U UAAGC...GCA-5'@LB@ \| \|@LB@ 77 61@LB@@LB@@LB@Energy -9.58 kcal/mol@LB@Hybridization Energy -14.2281 kcal/mol@LB@Unfolding Energy - mRNA 1.39912 kcal/mol@LB@Unfolding Energy - sRNA 3.25371 kcal/mol@LB@@LB@Position - mRNA 60 -- 77@LB@Position - sRNA 62 -- 76@LB@Position Seed - mRNA 71 -- 77@LB@Position Seed - sRNA 62 -- 68@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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