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	Additional homologs
45	0.001296	0.1014	b2465	tktB	-16.90	0.006168	210 -- 248	39 -- 78	transketolase 2 thiamine triphosphate-binding		_____________209__________________________________________249\n_____________\|____________________________________________\|\n5'-AGU...CCCGA______CU______AU________CG___________UAU____GCGGU...CUG-3'\n______________AAAGAC__UGC_CA__GCGAUUCG______CACUCAG___GGAU\n______________\|\|\|\|\|\|__\|:\|_\|\|__\|\|:\|\|\|\|\|______\|\|\|\|\|\|\|___\|\|\|\|\n______________UUUCUG__AUG_GU__CGUUAAGC______GUGAGUC___CCUA\n3'-UUU...ACCCG___________U__GU________AACAAA_______C______AAGGU...GCA-5'\n_____________\|____________________________________________\|\n_____________79___________________________________________38\n	235 -- 241	44 -- 50	-32.1578 kcal/mol	10.4844 kcal/mol	4.77966 kcal/mol	209 249@LB@ \| \|@LB@5'-AGU...CCCGA CU AU CG UAU GCGGU...CUG-3'@LB@ AAAGAC UGC CA GCGAUUCG CACUCAG GGAU@LB@ \|\|\|\|\|\| \|:\| \|\| \|\|:\|\|\|\|\| \|\|\|\|\|\|\| \|\|\|\|@LB@ UUUCUG AUG GU CGUUAAGC GUGAGUC CCUA@LB@3'-UUU...ACCCG U GU AACAAA C AAGGU...GCA-5'@LB@ \| \|@LB@ 79 38@LB@@LB@@LB@Energy -16.90 kcal/mol@LB@Hybridization Energy -32.1578 kcal/mol@LB@Unfolding Energy - mRNA 10.4844 kcal/mol@LB@Unfolding Energy - sRNA 4.77966 kcal/mol@LB@@LB@Position - mRNA 210 -- 248@LB@Position - sRNA 39 -- 78@LB@Position Seed - mRNA 235 -- 241@LB@Position Seed - sRNA 44 -- 50@LB@
114	0.005004	0.1545	b0025	ribF	-11.63	0.123109	210 -- 237	43 -- 71	bifunctional riboflavin kinase/FAD synthetase		_____________209___________________________238\n_____________\|_____________________________\|\n5'-UGG...AGCUG__________UACAUAAUC____GC____CCCCG...GCG-3'\n______________AUACGCGGCA__________UCA__CAGG\n______________\|:\|\|:\|:\|\|\|__________\|\|\|__\|\|\|\|\n______________UGUGUGUCGU__________AGU__GUCC\n3'-UUU...UCUGA__________UAAGCAACAA___GA____CCUAA...GCA-5'\n_____________\|_____________________________\|\n_____________72____________________________42\n	213 -- 219	62 -- 68	-21.1915 kcal/mol	5.23887 kcal/mol	4.32409 kcal/mol	209 238@LB@ \| \|@LB@5'-UGG...AGCUG UACAUAAUC GC CCCCG...GCG-3'@LB@ AUACGCGGCA UCA CAGG@LB@ \|:\|\|:\|:\|\|\| \|\|\| \|\|\|\|@LB@ UGUGUGUCGU AGU GUCC@LB@3'-UUU...UCUGA UAAGCAACAA GA CCUAA...GCA-5'@LB@ \| \|@LB@ 72 42@LB@@LB@@LB@Energy -11.63 kcal/mol@LB@Hybridization Energy -21.1915 kcal/mol@LB@Unfolding Energy - mRNA 5.23887 kcal/mol@LB@Unfolding Energy - sRNA 4.32409 kcal/mol@LB@@LB@Position - mRNA 210 -- 237@LB@Position - sRNA 43 -- 71@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 62 -- 68@LB@
160	0.007693	0.1668	b1671	ydhX	-11.21	0.148807	210 -- 235	39 -- 74	putative 4Fe-4S ferridoxin-type protein; FNR Nar NarP-regulated protein; putative subunit of YdhYVWXUT oxidoreductase complex	b4072	_____________209__________________________________236\n_____________\|____________________________________\|\n5'-CAC...CCUUC___CG________________________U______GGGAA...AGG-3'\n______________ACU__ACGCA__AAUUUGU________UC_GGGGAU\n______________\|\|\|__\|\|:\|\|__\|\|\|\|:\|\|________\|\|_\|\|\|\|\|\|\n______________UGA__UGUGU__UUAAGCA________AG_CCCCUA\n3'-UUU...GUUUC___UG_____CG_______ACAAAGUG__U______AAGGU...GCA-5'\n_____________\|____________________________________\|\n_____________75___________________________________38\n	220 -- 226	56 -- 62	-21.5478 kcal/mol	5.56457 kcal/mol	4.77831 kcal/mol	209 236@LB@ \| \|@LB@5'-CAC...CCUUC CG U GGGAA...AGG-3'@LB@ ACU ACGCA AAUUUGU UC GGGGAU@LB@ \|\|\| \|\|:\|\| \|\|\|\|:\|\| \|\| \|\|\|\|\|\|@LB@ UGA UGUGU UUAAGCA AG CCCCUA@LB@3'-UUU...GUUUC UG CG ACAAAGUG U AAGGU...GCA-5'@LB@ \| \|@LB@ 75 38@LB@@LB@@LB@Energy -11.21 kcal/mol@LB@Hybridization Energy -21.5478 kcal/mol@LB@Unfolding Energy - mRNA 5.56457 kcal/mol@LB@Unfolding Energy - sRNA 4.77831 kcal/mol@LB@@LB@Position - mRNA 210 -- 235@LB@Position - sRNA 39 -- 74@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 56 -- 62@LB@
175	0.008768	0.1747	b0658	ybeX	-12.37	0.086971	210 -- 256	35 -- 75	putative ion transport		_____________209_____________________________________________257\n_____________\|_______________________________________________\|\n5'-UUA...GCGAC___AAUU___________GACACGAUAAG__ACA__AA_________CUCCC...ACC-3'\n______________GAC____CACACAGUAGU___________CA___AG__GGGAUUUUU\n______________\|\|\|____\|\|\|\|\|\|\|:\|:\|___________\|\|___\|\|__\|\|\|\|\|\|\|::\n______________CUG____GUGUGUCGUUA___________GU___UC__CCCUAAAGG\n3'-UUU...CGUUU___AU_____________AGCAACAAA____GAG_____________UACGA...GCA-5'\n_____________\|_______________________________________________\|\n_____________76______________________________________________34\n	249 -- 255	36 -- 42	-26.9454 kcal/mol	9.77444 kcal/mol	4.80541 kcal/mol	209 257@LB@ \| \|@LB@5'-UUA...GCGAC AAUU GACACGAUAAG ACA AA CUCCC...ACC-3'@LB@ GAC CACACAGUAGU CA AG GGGAUUUUU@LB@ \|\|\| \|\|\|\|\|\|\|:\|:\| \|\| \|\| \|\|\|\|\|\|\|::@LB@ CUG GUGUGUCGUUA GU UC CCCUAAAGG@LB@3'-UUU...CGUUU AU AGCAACAAA GAG UACGA...GCA-5'@LB@ \| \|@LB@ 76 34@LB@@LB@@LB@Energy -12.37 kcal/mol@LB@Hybridization Energy -26.9454 kcal/mol@LB@Unfolding Energy - mRNA 9.77444 kcal/mol@LB@Unfolding Energy - sRNA 4.80541 kcal/mol@LB@@LB@Position - mRNA 210 -- 256@LB@Position - sRNA 35 -- 75@LB@Position Seed - mRNA 249 -- 255@LB@Position Seed - sRNA 36 -- 42@LB@
186	0.009502	0.1776	b1631	rsxG	-12.74	0.072174	210 -- 253	41 -- 74	SoxR iron-sulfur cluster reduction factor component; putative membrane protein of electron transport complex		_____________209____________________________________________254\n_____________\|______________________________________________\|\n5'-CUG...UGAAA_____CCGAAA________UUA_____G______AUUUG___C___UUCAA...CGA-3'\n______________ACUAU______ACACGGCA___CGUUG___CGCU_____CAG_GGG\n______________\|\|\|\|:______\|\|\|\|:\|\|\|___\|\|\|\|\|___\|:\|\|_____\|\|\|_\|\|\|\n______________UGAUG______UGUGUCGU___GCAAC___GUGA_____GUC_CCC\n3'-UUU...GUUUC___________________UAA_____AAA________________UAAAG...GCA-5'\n_____________\|______________________________________________\|\n_____________75_____________________________________________40\n	222 -- 228	62 -- 68	-28.539 kcal/mol	11.0247 kcal/mol	4.77133 kcal/mol	209 254@LB@ \| \|@LB@5'-CUG...UGAAA CCGAAA UUA G AUUUG C UUCAA...CGA-3'@LB@ ACUAU ACACGGCA CGUUG CGCU CAG GGG@LB@ \|\|\|\|: \|\|\|\|:\|\|\| \|\|\|\|\| \|:\|\| \|\|\| \|\|\|@LB@ UGAUG UGUGUCGU GCAAC GUGA GUC CCC@LB@3'-UUU...GUUUC UAA AAA UAAAG...GCA-5'@LB@ \| \|@LB@ 75 40@LB@@LB@@LB@Energy -12.74 kcal/mol@LB@Hybridization Energy -28.539 kcal/mol@LB@Unfolding Energy - mRNA 11.0247 kcal/mol@LB@Unfolding Energy - sRNA 4.77133 kcal/mol@LB@@LB@Position - mRNA 210 -- 253@LB@Position - sRNA 41 -- 74@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 62 -- 68@LB@
29	0.0004091	0.04965	b0958	sulA	-15.92	0.011809	212 -- 243	48 -- 76	SOS cell division inhibitor		_____________211______________________________244\n_____________\|________________________________\|\n5'-AUA...ACUUC____________UC__UC_____C___C____CCGCA...UCA-3'\n______________AGGCUAUGCACA__GU__UUCGU_GUU_UCAU\n______________\|\|:\|\|\|::\|\|\|\|__\|:__\|\|\|\|\|_\|\|\|_\|\|\|:\n______________UCUGAUGUGUGU__CG__AAGCA_CAA_AGUG\n3'-UUU...CCGUU________________UU_____A________AGUCC...GCA-5'\n_____________\|________________________________\|\n_____________77_______________________________47\n	217 -- 223	65 -- 71	-24.9625 kcal/mol	5.35271 kcal/mol	3.68714 kcal/mol	211 244@LB@ \| \|@LB@5'-AUA...ACUUC UC UC C C CCGCA...UCA-3'@LB@ AGGCUAUGCACA GU UUCGU GUU UCAU@LB@ \|\|:\|\|\|::\|\|\|\| \|: \|\|\|\|\| \|\|\| \|\|\|:@LB@ UCUGAUGUGUGU CG AAGCA CAA AGUG@LB@3'-UUU...CCGUU UU A AGUCC...GCA-5'@LB@ \| \|@LB@ 77 47@LB@@LB@@LB@Energy -15.92 kcal/mol@LB@Hybridization Energy -24.9625 kcal/mol@LB@Unfolding Energy - mRNA 5.35271 kcal/mol@LB@Unfolding Energy - sRNA 3.68714 kcal/mol@LB@@LB@Position - mRNA 212 -- 243@LB@Position - sRNA 48 -- 76@LB@Position Seed - mRNA 217 -- 223@LB@Position Seed - sRNA 65 -- 71@LB@
136	0.006258	0.1605	b0219	yafV	-11.82	0.112632	212 -- 233	61 -- 78	putative NAD(P)-binding C-N hydrolase family amidase		_____________211____________________234\n_____________\|______________________\|\n5'-GUC...GGUUU___________UUUU_______CCACU...CCG-3'\n______________GAAGAUUACGC____GCAGCAA\n______________:\|\|\|\|:\|\|\|:\|____:\|\|\|\|\|\|\n______________UUUCUGAUGUG____UGUCGUU\n3'-UUU...ACCCG______________________AAGCA...GCA-5'\n_____________\|______________________\|\n_____________79_____________________60\n	227 -- 233	61 -- 67	-20.0989 kcal/mol	5.01896 kcal/mol	3.25783 kcal/mol	211 234@LB@ \| \|@LB@5'-GUC...GGUUU UUUU CCACU...CCG-3'@LB@ GAAGAUUACGC GCAGCAA@LB@ :\|\|\|\|:\|\|\|:\| :\|\|\|\|\|\|@LB@ UUUCUGAUGUG UGUCGUU@LB@3'-UUU...ACCCG AAGCA...GCA-5'@LB@ \| \|@LB@ 79 60@LB@@LB@@LB@Energy -11.82 kcal/mol@LB@Hybridization Energy -20.0989 kcal/mol@LB@Unfolding Energy - mRNA 5.01896 kcal/mol@LB@Unfolding Energy - sRNA 3.25783 kcal/mol@LB@@LB@Position - mRNA 212 -- 233@LB@Position - sRNA 61 -- 78@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 61 -- 67@LB@
196	0.01003	0.1776	b0344	lacZ	-8.86	0.369200	215 -- 237	48 -- 76	beta-D-galactosidase		_____________214___________________________238\n_____________\|_____________________________\|\n5'-ACC...AUUAC_____________________C_______AACGU...CUU-3'\n______________GGAUU_CAC_UGGC____CGU_GUUUUAC\n______________:\|\|:\|_\|\|\|_::\|\|____\|\|\|_\|\|\|\|:\|\|\n______________UCUGA_GUG_GUCG____GCA_CAAAGUG\n3'-UUU...CCGUU_____U___U____UUAA___A_______AGUCC...GCA-5'\n_____________\|_____________________________\|\n_____________77____________________________47\n	231 -- 237	48 -- 54	-17.9156 kcal/mol	5.37156 kcal/mol	3.68714 kcal/mol	214 238@LB@ \| \|@LB@5'-ACC...AUUAC C AACGU...CUU-3'@LB@ GGAUU CAC UGGC CGU GUUUUAC@LB@ :\|\|:\| \|\|\| ::\|\| \|\|\| \|\|\|\|:\|\|@LB@ UCUGA GUG GUCG GCA CAAAGUG@LB@3'-UUU...CCGUU U U UUAA A AGUCC...GCA-5'@LB@ \| \|@LB@ 77 47@LB@@LB@@LB@Energy -8.86 kcal/mol@LB@Hybridization Energy -17.9156 kcal/mol@LB@Unfolding Energy - mRNA 5.37156 kcal/mol@LB@Unfolding Energy - sRNA 3.68714 kcal/mol@LB@@LB@Position - mRNA 215 -- 237@LB@Position - sRNA 48 -- 76@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 48 -- 54@LB@
55	0.001955	0.1223	b0840	deoR	-10.34	0.214583	216 -- 260	60 -- 103	deoxyribose-5-phosphate-inducible deoxyribose operon transcriptional repressor; repressor of nupG and tsx		_____________215____________________________________________261\n_____________\|______________________________________________\|\n5'-GUG...GUCGC_______G________C__C__CU_____A____AA__________AAGUU...UUU-3'\n______________GAAGAGC_UAUCG_GG_AG_UG__GCAAG_AUUA__ACGCAGCGAU\n______________:\|\|:\|\|\|_:\|\|\|\|_\|\|_\|\|_\|\|__\|\|\|\|:_\|:\|\|__\|\|:\|\|\|\|:\|\|\n______________UUUUUCG_GUAGC_CC_UC_AC__CGUUU_UGAU__UGUGUCGUUA\n_________3'-UU_______G_____A__C__U__C______C____G___________AGCAA...GCA-5'\n_____________\|______________________________________________\|\n_____________104____________________________________________59\n	254 -- 260	60 -- 66	-39.4084 kcal/mol	12.9673 kcal/mol	16.1071 kcal/mol	215 261@LB@ \| \|@LB@5'-GUG...GUCGC G C C CU A AA AAGUU...UUU-3'@LB@ GAAGAGC UAUCG GG AG UG GCAAG AUUA ACGCAGCGAU@LB@ :\|\|:\|\|\| :\|\|\|\| \|\| \|\| \|\| \|\|\|\|: \|:\|\| \|\|:\|\|\|\|:\|\|@LB@ UUUUUCG GUAGC CC UC AC CGUUU UGAU UGUGUCGUUA@LB@ 3'-UU G A C U C C G AGCAA...GCA-5'@LB@ \| \|@LB@ 104 59@LB@@LB@@LB@Energy -10.34 kcal/mol@LB@Hybridization Energy -39.4084 kcal/mol@LB@Unfolding Energy - mRNA 12.9673 kcal/mol@LB@Unfolding Energy - sRNA 16.1071 kcal/mol@LB@@LB@Position - mRNA 216 -- 260@LB@Position - sRNA 60 -- 103@LB@Position Seed - mRNA 254 -- 260@LB@Position Seed - sRNA 60 -- 66@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@

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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