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
178	0.008884	0.1747	b0051	rsmA	-9.94	0.250586	2 -- 32	30 -- 58	16S rRNA m(6)A1518 m(6)A1519 dimethyltransferase SAM-dependent	_____________1_______________________________33\n_____________\|_______________________________\|\n__________5'-G__A___AC___GA______UC__C_______AAAAU...UUA-3'\n______________CG_UGU__CAC__UCAGGG__UU_CCGUGCU\n______________\|\|_\|\|\|__\|\|\|__\|\|\|\|\|\|__\|\|_\|\|:\|\|\|\|\n______________GC_ACA__GUG__AGUCCC__AA_GGUACGA\n3'-UUU...GUUAA__A___AA___________CU__A_______AUAUU...GCA-5'\n_____________\|_______________________________\|\n_____________59______________________________29\n	26 -- 32	30 -- 36	-26.3106 kcal/mol	10.5715 kcal/mol	5.79877 kcal/mol	1 33@LB@ \| \|@LB@ 5'-G A AC GA UC C AAAAU...UUA-3'@LB@ CG UGU CAC UCAGGG UU CCGUGCU@LB@ \|\| \|\|\| \|\|\| \|\|\|\|\|\| \|\| \|\|:\|\|\|\|@LB@ GC ACA GUG AGUCCC AA GGUACGA@LB@3'-UUU...GUUAA A AA CU A AUAUU...GCA-5'@LB@ \| \|@LB@ 59 29@LB@@LB@@LB@Energy -9.94 kcal/mol@LB@Hybridization Energy -26.3106 kcal/mol@LB@Unfolding Energy - mRNA 10.5715 kcal/mol@LB@Unfolding Energy - sRNA 5.79877 kcal/mol@LB@@LB@Position - mRNA 2 -- 32@LB@Position - sRNA 30 -- 58@LB@Position Seed - mRNA 26 -- 32@LB@Position Seed - sRNA 30 -- 36@LB@
142	0.006549	0.1605	b3902	rhaD	-9.93	0.251242	192 -- 218	44 -- 69	rhamnulose-1-phosphate aldolase	_____________191_________________________219\n_____________\|___________________________\|\n5'-AGA...CAGGA______AACAUGCAAAACA________UCCUG...UGA-3'\n______________ACACAG_____________UUACUCAG\n______________\|\|\|\|\|\|_____________\|:\|\|\|\|\|\|\n______________UGUGUC_____________AGUGAGUC\n3'-UUU...UGAUG______GUUAAGCAACAA_________CCCUA...GCA-5'\n_____________\|___________________________\|\n_____________70__________________________43\n	212 -- 218	44 -- 50	-16.231 kcal/mol	2.20309 kcal/mol	4.09554 kcal/mol	191 219@LB@ \| \|@LB@5'-AGA...CAGGA AACAUGCAAAACA UCCUG...UGA-3'@LB@ ACACAG UUACUCAG@LB@ \|\|\|\|\|\| \|:\|\|\|\|\|\|@LB@ UGUGUC AGUGAGUC@LB@3'-UUU...UGAUG GUUAAGCAACAA CCCUA...GCA-5'@LB@ \| \|@LB@ 70 43@LB@@LB@@LB@Energy -9.93 kcal/mol@LB@Hybridization Energy -16.231 kcal/mol@LB@Unfolding Energy - mRNA 2.20309 kcal/mol@LB@Unfolding Energy - sRNA 4.09554 kcal/mol@LB@@LB@Position - mRNA 192 -- 218@LB@Position - sRNA 44 -- 69@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 44 -- 50@LB@
158	0.007677	0.1668	b1267	yciO	-9.92	0.252655	228 -- 242	61 -- 75	putative RNA binding protein	_____________227_____________243\n_____________\|_______________\|\n5'-GCG...AUCCU___A__C________CGUCU...CAA-3'\n______________GAU_AC_CACAGCAA\n______________\|\|:_\|\|_\|\|\|\|\|\|\|\|\n______________CUG_UG_GUGUCGUU\n3'-UUU...CGUUU___A__U________AAGCA...GCA-5'\n_____________\|_______________\|\n_____________76______________60\n	236 -- 242	61 -- 67	-14.6343 kcal/mol	1.46218 kcal/mol	3.25399 kcal/mol	227 243@LB@ \| \|@LB@5'-GCG...AUCCU A C CGUCU...CAA-3'@LB@ GAU AC CACAGCAA@LB@ \|\|: \|\| \|\|\|\|\|\|\|\|@LB@ CUG UG GUGUCGUU@LB@3'-UUU...CGUUU A U AAGCA...GCA-5'@LB@ \| \|@LB@ 76 60@LB@@LB@@LB@Energy -9.92 kcal/mol@LB@Hybridization Energy -14.6343 kcal/mol@LB@Unfolding Energy - mRNA 1.46218 kcal/mol@LB@Unfolding Energy - sRNA 3.25399 kcal/mol@LB@@LB@Position - mRNA 228 -- 242@LB@Position - sRNA 61 -- 75@LB@Position Seed - mRNA 236 -- 242@LB@Position Seed - sRNA 61 -- 67@LB@
191	0.009733	0.1776	b0190	yaeQ	-9.83	0.261410	113 -- 128	45 -- 75	PDDEXK superfamily protein	_____________112_____________________________129\n_____________\|_______________________________\|\n5'-UAC...AAGGU_______________________________UUUCU...CUU-3'\n______________GACUAUAC_CA______________CACUCA\n______________\|\|\|\|\|:\|\|_\|\|______________\|\|\|\|\|\|\n______________CUGAUGUG_GU______________GUGAGU\n3'-UUU...CGUUU________U__CGUUAAGCAACAAA______CCCCU...GCA-5'\n_____________\|_______________________________\|\n_____________76______________________________44\n	114 -- 120	68 -- 74	-15.3898 kcal/mol	1.82074 kcal/mol	3.74078 kcal/mol	112 129@LB@ \| \|@LB@5'-UAC...AAGGU UUUCU...CUU-3'@LB@ GACUAUAC CA CACUCA@LB@ \|\|\|\|\|:\|\| \|\| \|\|\|\|\|\|@LB@ CUGAUGUG GU GUGAGU@LB@3'-UUU...CGUUU U CGUUAAGCAACAAA CCCCU...GCA-5'@LB@ \| \|@LB@ 76 44@LB@@LB@@LB@Energy -9.83 kcal/mol@LB@Hybridization Energy -15.3898 kcal/mol@LB@Unfolding Energy - mRNA 1.82074 kcal/mol@LB@Unfolding Energy - sRNA 3.74078 kcal/mol@LB@@LB@Position - mRNA 113 -- 128@LB@Position - sRNA 45 -- 75@LB@Position Seed - mRNA 114 -- 120@LB@Position Seed - sRNA 68 -- 74@LB@
85	0.003677	0.1509	b0813	rhtA	-9.71	0.273689	106 -- 123	34 -- 46	threonine and homoserine efflux system	_____________105________________124\n_____________\|__________________\|\n5'-CAG...CAAAA_______AAAUU______ACAAA...CAC-3'\n______________CGGGGGA_____UUUUCA\n______________\|:\|\|\|\|\|_____\|\|\|:\|\|\n______________GUCCCCU_____AAAGGU\n3'-UUU...AGUGA__________________ACGAA...GCA-5'\n_____________\|__________________\|\n_____________47_________________33\n	106 -- 112	40 -- 46	-14.6812 kcal/mol	3.4305 kcal/mol	1.54427 kcal/mol	105 124@LB@ \| \|@LB@5'-CAG...CAAAA AAAUU ACAAA...CAC-3'@LB@ CGGGGGA UUUUCA@LB@ \|:\|\|\|\|\| \|\|\|:\|\|@LB@ GUCCCCU AAAGGU@LB@3'-UUU...AGUGA ACGAA...GCA-5'@LB@ \| \|@LB@ 47 33@LB@@LB@@LB@Energy -9.71 kcal/mol@LB@Hybridization Energy -14.6812 kcal/mol@LB@Unfolding Energy - mRNA 3.4305 kcal/mol@LB@Unfolding Energy - sRNA 1.54427 kcal/mol@LB@@LB@Position - mRNA 106 -- 123@LB@Position - sRNA 34 -- 46@LB@Position Seed - mRNA 106 -- 112@LB@Position Seed - sRNA 40 -- 46@LB@
77	0.003184	0.1452	b4406	yaeP	-9.70	0.274250	222 -- 254	40 -- 71	UPF0253 family protein	_____________221________________________________255\n_____________\|__________________________________\|\n5'-ACC...AGUUA_______A_____A__CG_AAA________C___GACUU...UGC-3'\n______________AUACGCA_GCGGU_CG__G___UCGC_CAG_GGA\n______________\|:\|\|:\|\|_\|\|::\|_\|\|__\|___\|\|:\|_\|\|\|_\|\|\|\n______________UGUGUGU_CGUUA_GC__C___AGUG_GUC_CCU\n3'-UUU...UCUGA_____________A__AA_AA_____A___C___AAAGG...GCA-5'\n_____________\|__________________________________\|\n_____________72_________________________________39\n	222 -- 228	65 -- 71	-25.8836 kcal/mol	11.435 kcal/mol	4.74818 kcal/mol	221 255@LB@ \| \|@LB@5'-ACC...AGUUA A A CG AAA C GACUU...UGC-3'@LB@ AUACGCA GCGGU CG G UCGC CAG GGA@LB@ \|:\|\|:\|\| \|\|::\| \|\| \| \|\|:\| \|\|\| \|\|\|@LB@ UGUGUGU CGUUA GC C AGUG GUC CCU@LB@3'-UUU...UCUGA A AA AA A C AAAGG...GCA-5'@LB@ \| \|@LB@ 72 39@LB@@LB@@LB@Energy -9.70 kcal/mol@LB@Hybridization Energy -25.8836 kcal/mol@LB@Unfolding Energy - mRNA 11.435 kcal/mol@LB@Unfolding Energy - sRNA 4.74818 kcal/mol@LB@@LB@Position - mRNA 222 -- 254@LB@Position - sRNA 40 -- 71@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 65 -- 71@LB@
164	0.007775	0.1668	b2097	fbaB	-9.67	0.277966	247 -- 265	48 -- 68	fructose-bisphosphate aldolase class I	_____________246___________________266\n_____________\|_____________________\|\n5'-AAU...CCUUU_______C________A_G__AAUUC...AUG-3'\n______________UACAGCA___CGUUGU_U_AC\n______________:\|\|\|\|\|\|___\|\|\|\|\|\|_\|_\|\|\n______________GUGUCGU___GCAACA_A_UG\n3'-UUU...GAUGU_______UAA______A_G__AGUCC...GCA-5'\n_____________\|_____________________\|\n_____________69____________________47\n	247 -- 253	62 -- 68	-18.0796 kcal/mol	4.78239 kcal/mol	3.63277 kcal/mol	246 266@LB@ \| \|@LB@5'-AAU...CCUUU C A G AAUUC...AUG-3'@LB@ UACAGCA CGUUGU U AC@LB@ :\|\|\|\|\|\| \|\|\|\|\|\| \| \|\|@LB@ GUGUCGU GCAACA A UG@LB@3'-UUU...GAUGU UAA A G AGUCC...GCA-5'@LB@ \| \|@LB@ 69 47@LB@@LB@@LB@Energy -9.67 kcal/mol@LB@Hybridization Energy -18.0796 kcal/mol@LB@Unfolding Energy - mRNA 4.78239 kcal/mol@LB@Unfolding Energy - sRNA 3.63277 kcal/mol@LB@@LB@Position - mRNA 247 -- 265@LB@Position - sRNA 48 -- 68@LB@Position Seed - mRNA 247 -- 253@LB@Position Seed - sRNA 62 -- 68@LB@
113	0.004991	0.1545	b0888	trxB	-9.59	0.285839	209 -- 223	61 -- 75	thioredoxin reductase FAD/NAD(P)-binding	_____________208_____________224\n_____________\|_______________\|\n5'-AAC...GGCAC___CAA_________ACUGC...UGC-3'\n______________GAC___ACACAGUAA\n______________\|\|\|___\|\|\|\|\|\|:\|\|\n______________CUG___UGUGUCGUU\n3'-UUU...CGUUU___AUG_________AAGCA...GCA-5'\n_____________\|_______________\|\n_____________76______________60\n	217 -- 223	61 -- 67	-15.4977 kcal/mol	2.65453 kcal/mol	3.25399 kcal/mol	208 224@LB@ \| \|@LB@5'-AAC...GGCAC CAA ACUGC...UGC-3'@LB@ GAC ACACAGUAA@LB@ \|\|\| \|\|\|\|\|\|:\|\|@LB@ CUG UGUGUCGUU@LB@3'-UUU...CGUUU AUG AAGCA...GCA-5'@LB@ \| \|@LB@ 76 60@LB@@LB@@LB@Energy -9.59 kcal/mol@LB@Hybridization Energy -15.4977 kcal/mol@LB@Unfolding Energy - mRNA 2.65453 kcal/mol@LB@Unfolding Energy - sRNA 3.25399 kcal/mol@LB@@LB@Position - mRNA 209 -- 223@LB@Position - sRNA 61 -- 75@LB@Position Seed - mRNA 217 -- 223@LB@Position Seed - sRNA 61 -- 67@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@
148	0.006951	0.1638	b3995	rsd	-9.56	0.289012	16 -- 28	58 -- 70	stationary phase protein binds sigma 70 RNA polymerase subunit	_____________15____________29\n_____________\|_____________\|\n5'-AAU...UUCGC_____________UCCCU...ACU-3'\n______________CAUAUGGCAAUUC\n______________\|\|:\|::\|\|\|\|\|\|\|\n______________GUGUGUCGUUAAG\n3'-UUU...CUGAU_____________CAACA...GCA-5'\n_____________\|_____________\|\n_____________71____________57\n	22 -- 28	58 -- 64	-15.8606 kcal/mol	3.09015 kcal/mol	3.21169 kcal/mol	15 29@LB@ \| \|@LB@5'-AAU...UUCGC UCCCU...ACU-3'@LB@ CAUAUGGCAAUUC@LB@ \|\|:\|::\|\|\|\|\|\|\|@LB@ GUGUGUCGUUAAG@LB@3'-UUU...CUGAU CAACA...GCA-5'@LB@ \| \|@LB@ 71 57@LB@@LB@@LB@Energy -9.56 kcal/mol@LB@Hybridization Energy -15.8606 kcal/mol@LB@Unfolding Energy - mRNA 3.09015 kcal/mol@LB@Unfolding Energy - sRNA 3.21169 kcal/mol@LB@@LB@Position - mRNA 16 -- 28@LB@Position - sRNA 58 -- 70@LB@Position Seed - mRNA 22 -- 28@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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