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
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@
94	0.004209	0.1538	b1798	leuE	-8.23	0.450453	21 -- 61	47 -- 73	leucine efflux protein	_____________20_________________________________________62\n_____________\|__________________________________________\|\n5'-UGC...AAUUU____________U____CC_AGCACUACCCGAAUU_______GGAGC...AAA-3'\n______________UUACGC_CAGUA_UUUG__G_______________UUUCACU\n______________:\|\|\|:\|_\|\|\|:\|_\|\|:\|__\|_______________\|\|\|\|\|\|\|\n______________GAUGUG_GUCGU_AAGC__C_______________AAAGUGA\n3'-UUU...UUUCU______U_____U____AA_______________________GUCCC...GCA-5'\n_____________\|__________________________________________\|\n_____________74_________________________________________46\n	55 -- 61	47 -- 53	-16.3548 kcal/mol	4.43937 kcal/mol	3.69006 kcal/mol	20 62@LB@ \| \|@LB@5'-UGC...AAUUU U CC AGCACUACCCGAAUU GGAGC...AAA-3'@LB@ UUACGC CAGUA UUUG G UUUCACU@LB@ :\|\|\|:\| \|\|\|:\| \|\|:\| \| \|\|\|\|\|\|\|@LB@ GAUGUG GUCGU AAGC C AAAGUGA@LB@3'-UUU...UUUCU U U AA GUCCC...GCA-5'@LB@ \| \|@LB@ 74 46@LB@@LB@@LB@Energy -8.23 kcal/mol@LB@Hybridization Energy -16.3548 kcal/mol@LB@Unfolding Energy - mRNA 4.43937 kcal/mol@LB@Unfolding Energy - sRNA 3.69006 kcal/mol@LB@@LB@Position - mRNA 21 -- 61@LB@Position - sRNA 47 -- 73@LB@Position Seed - mRNA 55 -- 61@LB@Position Seed - sRNA 47 -- 53@LB@
10	6.564e-05	0.0231	b3458	livK	-17.14	0.005196	153 -- 196	35 -- 71	leucine transporter subunit	_____________152____________________________________________197\n_____________\|______________________________________________\|\n5'-UGU...UGUUA______AAAAACAA_____CACAACA______GAAU__________GACUA...CGA-3'\n______________ACACAU________AGCAA_________UCAC____GGGGAUUUUU\n______________\|\|\|\|\|:________\|\|\|\|\|_________\|\|\|\|____\|\|\|\|\|\|\|\|::\n______________UGUGUG________UCGUU_________AGUG____CCCCUAAAGG\n3'-UUU...UCUGA___________________AAGCAACAA____AGU___________UACGA...GCA-5'\n_____________\|______________________________________________\|\n_____________72_____________________________________________34\n	190 -- 196	35 -- 41	-26.3585 kcal/mol	4.43917 kcal/mol	4.78171 kcal/mol	152 197@LB@ \| \|@LB@5'-UGU...UGUUA AAAAACAA CACAACA GAAU GACUA...CGA-3'@LB@ ACACAU AGCAA UCAC GGGGAUUUUU@LB@ \|\|\|\|\|: \|\|\|\|\| \|\|\|\| \|\|\|\|\|\|\|\|::@LB@ UGUGUG UCGUU AGUG CCCCUAAAGG@LB@3'-UUU...UCUGA AAGCAACAA AGU UACGA...GCA-5'@LB@ \| \|@LB@ 72 34@LB@@LB@@LB@Energy -17.14 kcal/mol@LB@Hybridization Energy -26.3585 kcal/mol@LB@Unfolding Energy - mRNA 4.43917 kcal/mol@LB@Unfolding Energy - sRNA 4.78171 kcal/mol@LB@@LB@Position - mRNA 153 -- 196@LB@Position - sRNA 35 -- 71@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 35 -- 41@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@
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@
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@
163	0.007762	0.1668	b0394	mak	-14.23	0.032787	242 -- 265	40 -- 75	manno(fructo)kinase	_____________241__________________________________266\n_____________\|____________________________________\|\n5'-GUU...GAAGU________UG______G___________________GCAGU...GUG-3'\n______________GAUUGCAC__GGCGAU_____________CAGGGGA\n______________\|\|:\|:\|\|\|__:\|\|:\|\|_____________\|\|\|\|\|\|\|\n______________CUGAUGUG__UCGUUA_____________GUCCCCU\n3'-UUU...CGUUU________UG______AGCAACAAAGUGA_______AAAGG...GCA-5'\n_____________\|____________________________________\|\n_____________76___________________________________39\n	259 -- 265	40 -- 46	-27.5886 kcal/mol	8.58508 kcal/mol	4.77786 kcal/mol	241 266@LB@ \| \|@LB@5'-GUU...GAAGU UG G GCAGU...GUG-3'@LB@ GAUUGCAC GGCGAU CAGGGGA@LB@ \|\|:\|:\|\|\| :\|\|:\|\| \|\|\|\|\|\|\|@LB@ CUGAUGUG UCGUUA GUCCCCU@LB@3'-UUU...CGUUU UG AGCAACAAAGUGA AAAGG...GCA-5'@LB@ \| \|@LB@ 76 39@LB@@LB@@LB@Energy -14.23 kcal/mol@LB@Hybridization Energy -27.5886 kcal/mol@LB@Unfolding Energy - mRNA 8.58508 kcal/mol@LB@Unfolding Energy - sRNA 4.77786 kcal/mol@LB@@LB@Position - mRNA 242 -- 265@LB@Position - sRNA 40 -- 75@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 40 -- 46@LB@
97	0.004509	0.1538	b0465	mscK	-15.00	0.020897	217 -- 248	49 -- 74	mechanosensitive channel protein intermediate conductance K+ regulated	_____________216______________________________249\n_____________\|________________________________\|\n5'-CGA...CCAGU______AACGAU_______U______U_____GCAUU...CGC-3'\n______________AUUACA______CACGGCA_UUUGUU_UUUCA\n______________\|:\|\|\|\|______\|\|\|:\|\|\|_\|\|:\|\|\|_\|\|\|\|\|\n______________UGAUGU______GUGUCGU_AAGCAA_AAAGU\n3'-UUU...GUUUC___________________U______C_____GAGUC...GCA-5'\n_____________\|________________________________\|\n_____________75_______________________________48\n	229 -- 235	62 -- 68	-21.8954 kcal/mol	3.22234 kcal/mol	3.67122 kcal/mol	216 249@LB@ \| \|@LB@5'-CGA...CCAGU AACGAU U U GCAUU...CGC-3'@LB@ AUUACA CACGGCA UUUGUU UUUCA@LB@ \|:\|\|\|\| \|\|\|:\|\|\| \|\|:\|\|\| \|\|\|\|\|@LB@ UGAUGU GUGUCGU AAGCAA AAAGU@LB@3'-UUU...GUUUC U C GAGUC...GCA-5'@LB@ \| \|@LB@ 75 48@LB@@LB@@LB@Energy -15.00 kcal/mol@LB@Hybridization Energy -21.8954 kcal/mol@LB@Unfolding Energy - mRNA 3.22234 kcal/mol@LB@Unfolding Energy - sRNA 3.67122 kcal/mol@LB@@LB@Position - mRNA 217 -- 248@LB@Position - sRNA 49 -- 74@LB@Position Seed - mRNA 229 -- 235@LB@Position Seed - sRNA 62 -- 68@LB@
89	0.003963	0.1538	b1252	tonB	-10.58	0.194225	25 -- 43	64 -- 82	membrane spanning protein in TonB-ExbB-ExbD transport complex	_____________24___________________44\n_____________\|____________________\|\n5'-AGU...UGAAA_________U__________AAAGA...AUC-3'\n______________GGGCGAAGA_CUGCA_ACGG\n______________\|\|\|\|:\|\|\|\|_\|\|:\|\|_\|\|:\|\n______________CCCGUUUCU_GAUGU_UGUC\n3'-UUU...CUCUA_______________G____GUUAA...GCA-5'\n_____________\|____________________\|\n_____________83___________________63\n	25 -- 31	76 -- 82	-25.6168 kcal/mol	4.83236 kcal/mol	10.2054 kcal/mol	24 44@LB@ \| \|@LB@5'-AGU...UGAAA U AAAGA...AUC-3'@LB@ GGGCGAAGA CUGCA ACGG@LB@ \|\|\|\|:\|\|\|\| \|\|:\|\| \|\|:\|@LB@ CCCGUUUCU GAUGU UGUC@LB@3'-UUU...CUCUA G GUUAA...GCA-5'@LB@ \| \|@LB@ 83 63@LB@@LB@@LB@Energy -10.58 kcal/mol@LB@Hybridization Energy -25.6168 kcal/mol@LB@Unfolding Energy - mRNA 4.83236 kcal/mol@LB@Unfolding Energy - sRNA 10.2054 kcal/mol@LB@@LB@Position - mRNA 25 -- 43@LB@Position - sRNA 64 -- 82@LB@Position Seed - mRNA 25 -- 31@LB@Position Seed - sRNA 76 -- 82@LB@
80	0.003376	0.1462	b3098	yqjD	-10.12	0.233597	155 -- 204	31 -- 75	membrane-anchored ribosome-binding protein	_____________154_________________________________________________205\n_____________\|___________________________________________________\|\n5'-UCA...CGCGC______UA__UCA____A___CACUAC_______CCU__A__AAA______CGAAA...AAG-3'\n______________GACUAC__AC___CAAU__GU______UUACUCA___GG_GA___CUAUGU\n______________\|\|\|\|\|\|__\|\|___\|\|\|\|__\|\|______\|:\|\|\|\|\|___\|\|_\|\|___\|:\|\|\|:\n______________CUGAUG__UG___GUUA__CA______AGUGAGU___CC_CU___GGUACG\n3'-UUU...CGUUU______UG__UC_____AG__ACAA_________C_______AAA______AAUAU...GCA-5'\n_____________\|___________________________________________________\|\n_____________76__________________________________________________30\n	181 -- 187	45 -- 51	-24.4421 kcal/mol	7.05998 kcal/mol	7.26183 kcal/mol	154 205@LB@ \| \|@LB@5'-UCA...CGCGC UA UCA A CACUAC CCU A AAA CGAAA...AAG-3'@LB@ GACUAC AC CAAU GU UUACUCA GG GA CUAUGU@LB@ \|\|\|\|\|\| \|\| \|\|\|\| \|\| \|:\|\|\|\|\| \|\| \|\| \|:\|\|\|:@LB@ CUGAUG UG GUUA CA AGUGAGU CC CU GGUACG@LB@3'-UUU...CGUUU UG UC AG ACAA C AAA AAUAU...GCA-5'@LB@ \| \|@LB@ 76 30@LB@@LB@@LB@Energy -10.12 kcal/mol@LB@Hybridization Energy -24.4421 kcal/mol@LB@Unfolding Energy - mRNA 7.05998 kcal/mol@LB@Unfolding Energy - sRNA 7.26183 kcal/mol@LB@@LB@Position - mRNA 155 -- 204@LB@Position - sRNA 31 -- 75@LB@Position Seed - mRNA 181 -- 187@LB@Position Seed - sRNA 45 -- 51@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

Use the following button if you want to resubmit the job with altered input or parameterization:

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service.

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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