Input and runtime details for job 8257533 (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 8257533 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:34:31 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:34:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:30:38 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:30:45 CET 2018
	Job Completed		@ Fri Feb 16 22:31:01 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=8257533&toolName=CopraRNA ( 30 days expiry )

Description of the job

LhrA2

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_003210 Listeria monocytogenes EGD-e

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
105	0.02711	0.6733	lmo0347	N/A	-16.41	0.053410	62 -- 87	160 -- 186	dihydroxyacetone kinase	_____________61____________________________88\n_____________\|_____________________________\|\n5'-AUC...GUUGG__________ACU________________UUGGU...AUU-3'\n______________GAACUACGCG___UCGAUG_GAU__AUGA\n______________\|\|\|\|\|\|\|:\|\|___:\|:\|\|\|_\|\|\|__\|\|\|\|\n______________CUUGAUGUGC___GGUUAC_CUA__UACU\n3'-GUU...CUGUA__________C________U___CU____UUUGU...GGA-5'\n_____________\|_____________________________\|\n_____________187___________________________159\n	65 -- 71	177 -- 183	-23.7931 kcal/mol	4.23572 kcal/mol	9.57505 kcal/mol	61 88@LB@ \| \|@LB@5'-AUC...GUUGG ACU UUGGU...AUU-3'@LB@ GAACUACGCG UCGAUG GAU AUGA@LB@ \|\|\|\|\|\|\|:\|\| :\|:\|\|\| \|\|\| \|\|\|\|@LB@ CUUGAUGUGC GGUUAC CUA UACU@LB@3'-GUU...CUGUA C U CU UUUGU...GGA-5'@LB@ \| \|@LB@ 187 159@LB@@LB@@LB@Energy -16.41 kcal/mol@LB@Hybridization Energy -23.7931 kcal/mol@LB@Unfolding Energy - mRNA 4.23572 kcal/mol@LB@Unfolding Energy - sRNA 9.57505 kcal/mol@LB@@LB@Position - mRNA 62 -- 87@LB@Position - sRNA 160 -- 186@LB@Position Seed - mRNA 65 -- 71@LB@Position Seed - sRNA 177 -- 183@LB@
106	0.02722	0.6733	lmo1616	N/A	-15.61	0.075454	67 -- 108	167 -- 211		_____________66______________________109\n_____________\|_______________________\|\n5'-AAG...AUAAC_____U_____GACU________AGGGC...UUU-3'\n______________GAACA_AUGUU____UGACUAGU\n______________:\|\|\|\|_\|\|\|\|:____\|\|\|\|\|\|\|\|\n______________UUUGU_UACAG____ACUGAUCA\n3'-GUU...ACAGA_____C_________________ACGGU...GGA-5'\n_____________\|_______________________\|\n_____________212_____________________166\n	90 -- 96	117 -- 123	-17.5219 kcal/mol	5.32799 kcal/mol	5.058 kcal/mol	66 109@LB@ \| \|@LB@5'-AAG...AUAAC U GACU AGGGC...UUU-3'@LB@ GAACA AUGUU UGACUAGU@LB@ :\|\|\|\| \|\|\|\|: \|\|\|\|\|\|\|\|@LB@ UUUGU UACAG ACUGAUCA@LB@3'-GUU...ACAGA C ACGGU...GGA-5'@LB@ \| \|@LB@ 212 166@LB@@LB@@LB@Energy -15.61 kcal/mol@LB@Hybridization Energy -17.5219 kcal/mol@LB@Unfolding Energy - mRNA 5.32799 kcal/mol@LB@Unfolding Energy - sRNA 5.058 kcal/mol@LB@@LB@Position - mRNA 67 -- 108@LB@Position - sRNA 167 -- 211@LB@Position Seed - mRNA 90 -- 96@LB@Position Seed - sRNA 117 -- 123@LB@
107	0.02737	0.6733	lmo1575	N/A	-17.23	0.037041	80 -- 118	156 -- 205		_____________79______119\n_____________\|_______\|\n5'-GUA...UCACA_______C-3'\n______________AAUGGGG\n______________\|\|:\|\|\|:\n______________UUGCCCU\n3'-GUU...ACGUA_______ACUCC...GGA-5'\n_____________\|_______\|\n_____________206_____155\n	293 -- 299	201 -- 207	-8.20946 kcal/mol	0.611387 kcal/mol	0.326294 kcal/mol	79 119@LB@ \| \|@LB@5'-GUA...UCACA C-3'@LB@ AAUGGGG@LB@ \|\|:\|\|\|:@LB@ UUGCCCU@LB@3'-GUU...ACGUA ACUCC...GGA-5'@LB@ \| \|@LB@ 206 155@LB@@LB@@LB@Energy -17.23 kcal/mol@LB@Hybridization Energy -8.20946 kcal/mol@LB@Unfolding Energy - mRNA 0.611387 kcal/mol@LB@Unfolding Energy - sRNA 0.326294 kcal/mol@LB@@LB@Position - mRNA 80 -- 118@LB@Position - sRNA 156 -- 205@LB@Position Seed - mRNA 293 -- 299@LB@Position Seed - sRNA 201 -- 207@LB@
108	0.02743	0.6733	lmo2330	N/A	-16.53	0.050546	195 -- 214	191 -- 207		_____________194_________215\n_____________\|___________\|\n5'-ACG...GAGAA___________CAAGU...UUU-3'\n______________AGCGGGAUGAG\n______________\|:\|\|\|\|\|\|\|\|\|\n______________UUGCCCUACUC\n3'-GUU...ACGUA___________CGUAU...GGA-5'\n_____________\|___________\|\n_____________208_________190\n	199 -- 205	197 -- 203	-18.6004 kcal/mol	2.16538 kcal/mol	0.386761 kcal/mol	194 215@LB@ \| \|@LB@5'-ACG...GAGAA CAAGU...UUU-3'@LB@ AGCGGGAUGAG@LB@ \|:\|\|\|\|\|\|\|\|\|@LB@ UUGCCCUACUC@LB@3'-GUU...ACGUA CGUAU...GGA-5'@LB@ \| \|@LB@ 208 190@LB@@LB@@LB@Energy -16.53 kcal/mol@LB@Hybridization Energy -18.6004 kcal/mol@LB@Unfolding Energy - mRNA 2.16538 kcal/mol@LB@Unfolding Energy - sRNA 0.386761 kcal/mol@LB@@LB@Position - mRNA 195 -- 214@LB@Position - sRNA 191 -- 207@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 197 -- 203@LB@
109	0.02745	0.6733	lmo0843	N/A	-19.30	0.014041	79 -- 127	106 -- 151		_____________78____________________________________________________128\n_____________\|_____________________________________________________\|\n5'-CCG...GUCCA____C_________________________AUAAUUU__U_____________CCCUG...CUG-3'\n______________AGUG_UUUUGGUG_CU_GAC_GAUGUUUGA_______CU__UUGCCAUUUUAU\n______________\|:\|\|_\|\|\|\|\|\|\|\|_\|\|_:\|\|_\|\|\|\|\|:\|\|\|_______\|\|__\|\|\|\|\|\|\|\|:\|\|\|\n______________UUAC_AAAACCAC_GA_UUG_CUACAGACU_______GA__AACGGUAAGAUA\n3'-GUU...GUUUA____U________A__U___U__________________UC____________ACCUU...GGA-5'\n_____________\|_____________________________________________________\|\n_____________152___________________________________________________105\n	118 -- 124	109 -- 115	-38.6588 kcal/mol	9.72702 kcal/mol	18.7291 kcal/mol	78 128@LB@ \| \|@LB@5'-CCG...GUCCA C AUAAUUU U CCCUG...CUG-3'@LB@ AGUG UUUUGGUG CU GAC GAUGUUUGA CU UUGCCAUUUUAU@LB@ \|:\|\| \|\|\|\|\|\|\|\| \|\| :\|\| \|\|\|\|\|:\|\|\| \|\| \|\|\|\|\|\|\|\|:\|\|\|@LB@ UUAC AAAACCAC GA UUG CUACAGACU GA AACGGUAAGAUA@LB@3'-GUU...GUUUA U A U U UC ACCUU...GGA-5'@LB@ \| \|@LB@ 152 105@LB@@LB@@LB@Energy -19.30 kcal/mol@LB@Hybridization Energy -38.6588 kcal/mol@LB@Unfolding Energy - mRNA 9.72702 kcal/mol@LB@Unfolding Energy - sRNA 18.7291 kcal/mol@LB@@LB@Position - mRNA 79 -- 127@LB@Position - sRNA 106 -- 151@LB@Position Seed - mRNA 118 -- 124@LB@Position Seed - sRNA 109 -- 115@LB@
110	0.02752	0.6733	lmo0057	N/A	-17.32	0.035592	178 -- 213	150 -- 185		_____________177_________________214\n_____________\|___________________\|\n5'-AAA...GCGGG_______CA__________AAGUA...AAG-3'\n______________AGUGGGA__UGAAUGAAGA\n______________\|:\|\|:\|\|__\|\|\|\|\|\|\|\|:\|\n______________UUACUCU__ACUUACUUUU\n3'-GUU...GCCGG___________________GUUUA...GGA-5'\n_____________\|___________________\|\n_____________186_________________149\n	201 -- 207	157 -- 163	-16.939 kcal/mol	2.5385 kcal/mol	0.930085 kcal/mol	177 214@LB@ \| \|@LB@5'-AAA...GCGGG CA AAGUA...AAG-3'@LB@ AGUGGGA UGAAUGAAGA@LB@ \|:\|\|:\|\| \|\|\|\|\|\|\|\|:\|@LB@ UUACUCU ACUUACUUUU@LB@3'-GUU...GCCGG GUUUA...GGA-5'@LB@ \| \|@LB@ 186 149@LB@@LB@@LB@Energy -17.32 kcal/mol@LB@Hybridization Energy -16.939 kcal/mol@LB@Unfolding Energy - mRNA 2.5385 kcal/mol@LB@Unfolding Energy - sRNA 0.930085 kcal/mol@LB@@LB@Position - mRNA 178 -- 213@LB@Position - sRNA 150 -- 185@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 157 -- 163@LB@
111	0.02805	0.6801	lmo2841	N/A	-15.50	0.078879	184 -- 209	152 -- 178	sucrose phosphorylase	_____________183_______________________210\n_____________\|_________________________\|\n5'-UUU...AGGUA_____U__C____UUAA________CUUUC...AAC-3'\n______________AAUGA_GA_GAAU____GAAAACGA\n______________\|\|\|\|\|_\|\|_\|\|\|\|____\|\|\|\|\|\|:\|\n______________UUACU_CU_CUUA____CUUUUGUU\n3'-GUU...GCCGG________A________________UAUUA...GGA-5'\n_____________\|_________________________\|\n_____________179_______________________151\n	215 -- 221	154 -- 160	-12.3618 kcal/mol	2.60591 kcal/mol	0.959215 kcal/mol	183 210@LB@ \| \|@LB@5'-UUU...AGGUA U C UUAA CUUUC...AAC-3'@LB@ AAUGA GA GAAU GAAAACGA@LB@ \|\|\|\|\| \|\| \|\|\|\| \|\|\|\|\|\|:\|@LB@ UUACU CU CUUA CUUUUGUU@LB@3'-GUU...GCCGG A UAUUA...GGA-5'@LB@ \| \|@LB@ 179 151@LB@@LB@@LB@Energy -15.50 kcal/mol@LB@Hybridization Energy -12.3618 kcal/mol@LB@Unfolding Energy - mRNA 2.60591 kcal/mol@LB@Unfolding Energy - sRNA 0.959215 kcal/mol@LB@@LB@Position - mRNA 184 -- 209@LB@Position - sRNA 152 -- 178@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 154 -- 160@LB@
112	0.029	0.6968	lmo0191	N/A	-14.99	0.097641	103 -- 160	154 -- 212	phospho-beta-glucosidase	_____________102__________161\n_____________\|____________\|\n5'-UGU...CCAUG____________GAACG...CGC-3'\n______________GAGUGAAGGCGA\n______________\|\|:\|\|\|\|::\|:\|\n______________CUUACUUUUGUU\n3'-GUU...CUCUA____________UAUUA...GGA-5'\n_____________\|____________\|\n_____________213__________153\n	148 -- 154	154 -- 160	-12.5182 kcal/mol	1.90916 kcal/mol	0.857742 kcal/mol	102 161@LB@ \| \|@LB@5'-UGU...CCAUG GAACG...CGC-3'@LB@ GAGUGAAGGCGA@LB@ \|\|:\|\|\|\|::\|:\|@LB@ CUUACUUUUGUU@LB@3'-GUU...CUCUA UAUUA...GGA-5'@LB@ \| \|@LB@ 213 153@LB@@LB@@LB@Energy -14.99 kcal/mol@LB@Hybridization Energy -12.5182 kcal/mol@LB@Unfolding Energy - mRNA 1.90916 kcal/mol@LB@Unfolding Energy - sRNA 0.857742 kcal/mol@LB@@LB@Position - mRNA 103 -- 160@LB@Position - sRNA 154 -- 212@LB@Position Seed - mRNA 148 -- 154@LB@Position Seed - sRNA 154 -- 160@LB@
114	0.02972	0.6968	lmo2166	N/A	-15.48	0.079589	75 -- 119	153 -- 198	lmo2166	_____________74_________________________________________________120\n_____________\|__________________________________________________\|\n5'-GGA...UAUUC___U_____UG___U______CAU________________AA________ACCCA...AAA-3'\n______________AGG_CAUGG__AUG_AACUAC___CGGUCA______UGAA__GAAGACAA\n______________\|\|\|_\|\|\|:\|__\|\|\|_\|\|\|\|\|\|___\|\|\|:\|\|______\|\|\|\|__\|\|\|:\|\|\|\|\n______________UCC_GUAUC__UAC_UUGAUG___GCCGGU______ACUU__CUUUUGUU\n3'-GUU...CCUAC_________UG__________U________UACUCU____A_________UAUUA...GGA-5'\n_____________\|__________________________________________________\|\n_____________199________________________________________________152\n	112 -- 118	154 -- 160	-33.2648 kcal/mol	10.6544 kcal/mol	13.9801 kcal/mol	74 120@LB@ \| \|@LB@5'-GGA...UAUUC U UG U CAU AA ACCCA...AAA-3'@LB@ AGG CAUGG AUG AACUAC CGGUCA UGAA GAAGACAA@LB@ \|\|\| \|\|\|:\| \|\|\| \|\|\|\|\|\| \|\|\|:\|\| \|\|\|\| \|\|\|:\|\|\|\|@LB@ UCC GUAUC UAC UUGAUG GCCGGU ACUU CUUUUGUU@LB@3'-GUU...CCUAC UG U UACUCU A UAUUA...GGA-5'@LB@ \| \|@LB@ 199 152@LB@@LB@@LB@Energy -15.48 kcal/mol@LB@Hybridization Energy -33.2648 kcal/mol@LB@Unfolding Energy - mRNA 10.6544 kcal/mol@LB@Unfolding Energy - sRNA 13.9801 kcal/mol@LB@@LB@Position - mRNA 75 -- 119@LB@Position - sRNA 153 -- 198@LB@Position Seed - mRNA 112 -- 118@LB@Position Seed - sRNA 154 -- 160@LB@
115	0.03087	0.6968	lmo0059	N/A	-17.38	0.034592	142 -- 189	155 -- 211		_____________141_______________________________________________190\n_____________\|_________________________________________________\|\n5'-AAG...UUAGC____G_____UU___U________________UUUU_____A_______GGGAG...CAU-3'\n______________AGGC__GGAU__AUG_GGCUGCGCG__CAAUG____UGAAU_GAAAGCG\n______________\|\|\|\|__:\|\|:__\|\|\|_::\|\|:\|:\|\|__\|\|\|\|\|____\|\|\|\|\|_\|\|\|\|:\|:\n______________UCCG__UCUG__UAC_UUGAUGUGC__GUUAC____ACUUA_CUUUUGU\n3'-GUU...CCUAC____UA___________________CG_____UCU______________UUAUU...GGA-5'\n_____________\|_________________________________________________\|\n_____________212_______________________________________________154\n	183 -- 189	155 -- 161	-35.3318 kcal/mol	12.9952 kcal/mol	13.976 kcal/mol	141 190@LB@ \| \|@LB@5'-AAG...UUAGC G UU U UUUU A GGGAG...CAU-3'@LB@ AGGC GGAU AUG GGCUGCGCG CAAUG UGAAU GAAAGCG@LB@ \|\|\|\| :\|\|: \|\|\| ::\|\|:\|:\|\| \|\|\|\|\| \|\|\|\|\| \|\|\|\|:\|:@LB@ UCCG UCUG UAC UUGAUGUGC GUUAC ACUUA CUUUUGU@LB@3'-GUU...CCUAC UA CG UCU UUAUU...GGA-5'@LB@ \| \|@LB@ 212 154@LB@@LB@@LB@Energy -17.38 kcal/mol@LB@Hybridization Energy -35.3318 kcal/mol@LB@Unfolding Energy - mRNA 12.9952 kcal/mol@LB@Unfolding Energy - sRNA 13.976 kcal/mol@LB@@LB@Position - mRNA 142 -- 189@LB@Position - sRNA 155 -- 211@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 155 -- 161@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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