Input and runtime details for job 5172788 (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 5172788 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:22:50 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:35:14 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:35:22 CET 2018
	Job Completed		@ Fri Feb 16 20:35:53 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5172788&toolName=CopraRNA ( 30 days expiry )

Description of the job

CyaR

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
140	0.006493	0.1559	b1916	sdiA	-12.48	0.051059	182 -- 224	1 -- 50	quorum-sensing transcriptional activator		_____________181_________________________________________________225\n_____________\|___________________________________________________\|\n5'-UGU...CUCUC_____C_____G_____U______U___GGAUAA___AU____________UGGCG...AGG-3'\n______________AGGGG___GUU_C_GGU_UA_CUA_GCA_______GG_____UUUUUCAGC\n______________\|\|\|:\|___\|\|\|_\|_\|\|\|_:\|_\|\|\|_\|\|\|_______\|\|_____\|\|\|\|\|\|\|\|\|\n______________UCCUC___CAA_G_CCA_GU_GAU_CGU_______CC_____AAAAAGUCG\n3'-UUU...CCGAU_____CAC___G_A___U__C_______AAAAUAC__AAUAC_________-5'\n_____________\|__________________________________________________\|\n_____________51_________________________________________________1\n	218 -- 224	1 -- 7	-26.3158 kcal/mol	9.17132 kcal/mol	4.6634 kcal/mol	181 225@LB@ \| \|@LB@5'-UGU...CUCUC C G U U GGAUAA AU UGGCG...AGG-3'@LB@ AGGGG GUU C GGU UA CUA GCA GG UUUUUCAGC@LB@ \|\|\|:\| \|\|\| \| \|\|\| :\| \|\|\| \|\|\| \|\| \|\|\|\|\|\|\|\|\|@LB@ UCCUC CAA G CCA GU GAU CGU CC AAAAAGUCG@LB@3'-UUU...CCGAU CAC G A U C AAAAUAC AAUAC -5'@LB@ \| \|@LB@ 51 1@LB@@LB@@LB@Energy -12.48 kcal/mol@LB@Hybridization Energy -26.3158 kcal/mol@LB@Unfolding Energy - mRNA 9.17132 kcal/mol@LB@Unfolding Energy - sRNA 4.6634 kcal/mol@LB@@LB@Position - mRNA 182 -- 224@LB@Position - sRNA 1 -- 50@LB@Position Seed - mRNA 218 -- 224@LB@Position Seed - sRNA 1 -- 7@LB@
99	0.003591	0.1219	b0533	sfmH	-7.90	0.364135	113 -- 140	1 -- 34	FimA homolog function unknown	b3145 b0941	_____________112________________________________141\n_____________\|__________________________________\|\n5'-GAC...AAGCU______A___CGUCACU_________________AGUUU...AUA-3'\n______________UACAGC_AGC_________GUUA____UUUCGGC\n______________\|\|\|\|\|\|_\|\|\|_________\|\|\|\|____\|\|\|\|:\|\|\n______________AUGUCG_UCG_________CAAU____AAAGUCG\n3'-UUU...GGACC______A___UAAAAUACC____ACAA_______-5'\n_____________\|_________________________________\|\n_____________35________________________________1\n	134 -- 140	1 -- 7	-18.6412 kcal/mol	9.24123 kcal/mol	1.49507 kcal/mol	112 141@LB@ \| \|@LB@5'-GAC...AAGCU A CGUCACU AGUUU...AUA-3'@LB@ UACAGC AGC GUUA UUUCGGC@LB@ \|\|\|\|\|\| \|\|\| \|\|\|\| \|\|\|\|:\|\|@LB@ AUGUCG UCG CAAU AAAGUCG@LB@3'-UUU...GGACC A UAAAAUACC ACAA -5'@LB@ \| \|@LB@ 35 1@LB@@LB@@LB@Energy -7.90 kcal/mol@LB@Hybridization Energy -18.6412 kcal/mol@LB@Unfolding Energy - mRNA 9.24123 kcal/mol@LB@Unfolding Energy - sRNA 1.49507 kcal/mol@LB@@LB@Position - mRNA 113 -- 140@LB@Position - sRNA 1 -- 34@LB@Position Seed - mRNA 134 -- 140@LB@Position Seed - sRNA 1 -- 7@LB@
31	0.0004941	0.05357	b1272	sohB	-11.06	0.104388	188 -- 235	1 -- 51	inner membrane protein S49 peptidase family protein		_____________187__________________________________________________236\n_____________\|____________________________________________________\|\n5'-UGU...UAACC____U_____AC__G___A__U____U_UGAA_____UU_____________GAAAA...AAC-3'\n______________AAGG_GG_GG__UC_UGG_AU_GUUG_C____UAUGG____UGUUUUU_GGC\n______________\|\|\|\|_\|\|_\|\|__\|\|_\|\|\|_\|:_\|:\|:_\|____\|\|\|\|\|____\|\|\|\|\|\|\|_:\|\|\n______________UUCC_CC_CC__AG_ACC_UG_CGAU_G____AUACC____ACAAAAA_UCG\n3'-UUU...UCCGA____U__A__A___G___A__U____C_UAAA_____CAAU_______G___-5'\n_____________\|___________________________________________________\|\n_____________52__________________________________________________1\n	226 -- 232	5 -- 11	-30.2617 kcal/mol	14.5124 kcal/mol	4.69283 kcal/mol	187 236@LB@ \| \|@LB@5'-UGU...UAACC U AC G A U U UGAA UU GAAAA...AAC-3'@LB@ AAGG GG GG UC UGG AU GUUG C UAUGG UGUUUUU GGC@LB@ \|\|\|\| \|\| \|\| \|\| \|\|\| \|: \|:\|: \| \|\|\|\|\| \|\|\|\|\|\|\| :\|\|@LB@ UUCC CC CC AG ACC UG CGAU G AUACC ACAAAAA UCG@LB@3'-UUU...UCCGA U A A G A U C UAAA CAAU G -5'@LB@ \| \|@LB@ 52 1@LB@@LB@@LB@Energy -11.06 kcal/mol@LB@Hybridization Energy -30.2617 kcal/mol@LB@Unfolding Energy - mRNA 14.5124 kcal/mol@LB@Unfolding Energy - sRNA 4.69283 kcal/mol@LB@@LB@Position - mRNA 188 -- 235@LB@Position - sRNA 1 -- 51@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 5 -- 11@LB@
60	0.001479	0.08283	b1886	tar	-8.65	0.283085	258 -- 290	4 -- 38	methyl-accepting chemotaxis protein II		_____________257__________________________________291\n_____________\|____________________________________\|\n5'-UGC...UCGCA___U______________CC___CAGUC________UCUUC...UUC-3'\n______________CUG_UACAGCU__UAUUU___GG_____UGUUUUUU\n______________\|\|\|_\|\|\|\|\|\|\|__:\|\|\|\|___\|\|_____\|\|\|\|\|\|\|:\n______________GAC_AUGUCGA__GUAAA___CC_____ACAAAAAG\n3'-UUU...CCAAG___C_______UC_____AUA__CAAU_________UCG-5'\n_____________\|____________________________________\|\n_____________39___________________________________3\n	284 -- 290	4 -- 10	-19.1357 kcal/mol	5.94997 kcal/mol	4.53981 kcal/mol	257 291@LB@ \| \|@LB@5'-UGC...UCGCA U CC CAGUC UCUUC...UUC-3'@LB@ CUG UACAGCU UAUUU GG UGUUUUUU@LB@ \|\|\| \|\|\|\|\|\|\| :\|\|\|\| \|\| \|\|\|\|\|\|\|:@LB@ GAC AUGUCGA GUAAA CC ACAAAAAG@LB@3'-UUU...CCAAG C UC AUA CAAU UCG-5'@LB@ \| \|@LB@ 39 3@LB@@LB@@LB@Energy -8.65 kcal/mol@LB@Hybridization Energy -19.1357 kcal/mol@LB@Unfolding Energy - mRNA 5.94997 kcal/mol@LB@Unfolding Energy - sRNA 4.53981 kcal/mol@LB@@LB@Position - mRNA 258 -- 290@LB@Position - sRNA 4 -- 38@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 4 -- 10@LB@
152	0.007594	0.1679	b3992	thiF	-12.60	0.047865	3 -- 22	24 -- 47	adenylyltransferase modifies ThiS C-terminus		_____________2________________________23\n_____________\|________________________\|\n_________5'-GC_____________A__________CGGCA...UUA-3'\n______________AGG_GG___CUGG_ACAGCUGGCA\n______________\|\|\|_\|\|___\|\|\|\|_\|\|\|\|\|\|:\|\|\|\n______________UCC_CC___GACC_UGUCGAUCGU\n3'-UUU...AUUCC___A__AAG____A__________AAAAU...UCG-5'\n_____________\|________________________\|\n_____________48_______________________23\n	16 -- 22	24 -- 30	-27.3128 kcal/mol	10.1529 kcal/mol	4.55893 kcal/mol	2 23@LB@ \| \|@LB@ 5'-GC A CGGCA...UUA-3'@LB@ AGG GG CUGG ACAGCUGGCA@LB@ \|\|\| \|\| \|\|\|\| \|\|\|\|\|\|:\|\|\|@LB@ UCC CC GACC UGUCGAUCGU@LB@3'-UUU...AUUCC A AAG A AAAAU...UCG-5'@LB@ \| \|@LB@ 48 23@LB@@LB@@LB@Energy -12.60 kcal/mol@LB@Hybridization Energy -27.3128 kcal/mol@LB@Unfolding Energy - mRNA 10.1529 kcal/mol@LB@Unfolding Energy - sRNA 4.55893 kcal/mol@LB@@LB@Position - mRNA 3 -- 22@LB@Position - sRNA 24 -- 47@LB@Position Seed - mRNA 16 -- 22@LB@Position Seed - sRNA 24 -- 30@LB@
82	0.002694	0.1082	b2474	tmcA	-11.34	0.091143	115 -- 147	1 -- 34	elongator methionine tRNA (ac4C34) acetyltransferase		_____________114________________________________148\n_____________\|__________________________________\|\n5'-GAU...AACGC__________UUAAACGU____UCGACAG_____GAUCC...UUG-3'\n______________UACAGCUGGU________GGUU________CGGC\n______________\|\|\|\|\|\|\|:\|:________\|\|\|\|________\|:\|\|\n______________AUGUCGAUCG________CCAA________GUCG\n3'-UUU...GGACC__________UAAAAUAC____UACAAAAA____-5'\n_____________\|_________________________________\|\n_____________35________________________________1\n	118 -- 124	25 -- 31	-23.7384 kcal/mol	10.9014 kcal/mol	1.49507 kcal/mol	114 148@LB@ \| \|@LB@5'-GAU...AACGC UUAAACGU UCGACAG GAUCC...UUG-3'@LB@ UACAGCUGGU GGUU CGGC@LB@ \|\|\|\|\|\|\|:\|: \|\|\|\| \|:\|\|@LB@ AUGUCGAUCG CCAA GUCG@LB@3'-UUU...GGACC UAAAAUAC UACAAAAA -5'@LB@ \| \|@LB@ 35 1@LB@@LB@@LB@Energy -11.34 kcal/mol@LB@Hybridization Energy -23.7384 kcal/mol@LB@Unfolding Energy - mRNA 10.9014 kcal/mol@LB@Unfolding Energy - sRNA 1.49507 kcal/mol@LB@@LB@Position - mRNA 115 -- 147@LB@Position - sRNA 1 -- 34@LB@Position Seed - mRNA 118 -- 124@LB@Position Seed - sRNA 25 -- 31@LB@
73	0.002141	0.09621	b0740	tolB	-11.17	0.098836	117 -- 150	8 -- 46	periplasmic protein		_____________116______________________________________151\n_____________\|________________________________________\|\n5'-UCC...GCCAC______________GUUUUGU___________________AACAU...CCG-3'\n______________GG_GGUU_CUGGUA_______GUAUUUUA___GUU_UGUU\n______________\|\|_\|\|\|\|_\|\|\|\|\|\|_______\|:\|\|\|\|\|\|___\|\|\|_\|\|\|\|\n______________CC_CCAA_GACCAU_______CGUAAAAU___CAA_ACAA\n3'-UUU...UUCCU__A____G______GUCGAU_________ACC___U____AAAGUCG-5'\n_____________\|________________________________________\|\n_____________47_______________________________________7\n	137 -- 143	19 -- 25	-23.6895 kcal/mol	7.90884 kcal/mol	4.60831 kcal/mol	116 151@LB@ \| \|@LB@5'-UCC...GCCAC GUUUUGU AACAU...CCG-3'@LB@ GG GGUU CUGGUA GUAUUUUA GUU UGUU@LB@ \|\| \|\|\|\| \|\|\|\|\|\| \|:\|\|\|\|\|\| \|\|\| \|\|\|\|@LB@ CC CCAA GACCAU CGUAAAAU CAA ACAA@LB@3'-UUU...UUCCU A G GUCGAU ACC U AAAGUCG-5'@LB@ \| \|@LB@ 47 7@LB@@LB@@LB@Energy -11.17 kcal/mol@LB@Hybridization Energy -23.6895 kcal/mol@LB@Unfolding Energy - mRNA 7.90884 kcal/mol@LB@Unfolding Energy - sRNA 4.60831 kcal/mol@LB@@LB@Position - mRNA 117 -- 150@LB@Position - sRNA 8 -- 46@LB@Position Seed - mRNA 137 -- 143@LB@Position Seed - sRNA 19 -- 25@LB@
164	0.008548	0.1748	b0461	tomB	-9.85	0.177976	15 -- 39	9 -- 30	Hha toxicity attenuator; conjugation-related protein		_____________14________________________40\n_____________\|_________________________\|\n5'-UGC...UUAGU________GAAAAA___A__CC___CCCGC...AUC-3'\n______________GCUAGUAU______GUG_GU__UGU\n______________\|\|\|\|\|:\|\|______:\|\|_\|\|__\|\|\|\n______________CGAUCGUA______UAC_CA__ACA\n3'-UUU...CAUGU________AAA______C__AU___AAAAGUCG-5'\n_____________\|_________________________\|\n_____________31________________________8\n	16 -- 22	23 -- 29	-13.2091 kcal/mol	1.89111 kcal/mol	1.4702 kcal/mol	14 40@LB@ \| \|@LB@5'-UGC...UUAGU GAAAAA A CC CCCGC...AUC-3'@LB@ GCUAGUAU GUG GU UGU@LB@ \|\|\|\|\|:\|\| :\|\| \|\| \|\|\|@LB@ CGAUCGUA UAC CA ACA@LB@3'-UUU...CAUGU AAA C AU AAAAGUCG-5'@LB@ \| \|@LB@ 31 8@LB@@LB@@LB@Energy -9.85 kcal/mol@LB@Hybridization Energy -13.2091 kcal/mol@LB@Unfolding Energy - mRNA 1.89111 kcal/mol@LB@Unfolding Energy - sRNA 1.4702 kcal/mol@LB@@LB@Position - mRNA 15 -- 39@LB@Position - sRNA 9 -- 30@LB@Position Seed - mRNA 16 -- 22@LB@Position Seed - sRNA 23 -- 29@LB@
189	0.01085	0.1919	b3606	trmL	-8.64	0.283903	120 -- 126	63 -- 69	tRNA Leu mC34 mU34 2'-O-methyltransferase SAM-dependent		_____________119_____127\n_____________\|_______\|\n5'-UAG...CCUCC_______GGGCC...AAC-3'\n______________GGGGAGA\n______________:\|\|\|\|\|\|\n______________UCCCUCU\n3'-UUU...CACAU_______AAUGU...UCG-5'\n_____________\|_______\|\n_____________70______62\n	120 -- 126	63 -- 69	-10.8913 kcal/mol	1.31422 kcal/mol	0.939295 kcal/mol	119 127@LB@ \| \|@LB@5'-UAG...CCUCC GGGCC...AAC-3'@LB@ GGGGAGA@LB@ :\|\|\|\|\|\|@LB@ UCCCUCU@LB@3'-UUU...CACAU AAUGU...UCG-5'@LB@ \| \|@LB@ 70 62@LB@@LB@@LB@Energy -8.64 kcal/mol@LB@Hybridization Energy -10.8913 kcal/mol@LB@Unfolding Energy - mRNA 1.31422 kcal/mol@LB@Unfolding Energy - sRNA 0.939295 kcal/mol@LB@@LB@Position - mRNA 120 -- 126@LB@Position - sRNA 63 -- 69@LB@Position Seed - mRNA 120 -- 126@LB@Position Seed - sRNA 63 -- 69@LB@
44	0.0009392	0.07174	b3453	ugpB	-12.21	0.059079	239 -- 268	1 -- 32	sn-glycerol-3-phosphate ABC transporter periplasmic binding protein		_____________238_______________________________269\n_____________\|_________________________________\|\n5'-UUC...GCGCU___A________A______GA___CACA_____AGUGA...UGG-3'\n______________CGG_CUGGCGUU__AUGGG__AUG______GGC\n______________\|:\|_\|\|:\|\|:\|\|__\|\|\|\|\|__\|\|\|______:\|\|\n______________GUC_GAUCGUAA__UACCC__UAC______UCG\n3'-UUU...ACCAU____________AA_____AA___AAAAAG___-5'\n_____________\|________________________________\|\n_____________33_______________________________1\n	244 -- 250	22 -- 28	-24.6308 kcal/mol	10.9347 kcal/mol	1.49075 kcal/mol	238 269@LB@ \| \|@LB@5'-UUC...GCGCU A A GA CACA AGUGA...UGG-3'@LB@ CGG CUGGCGUU AUGGG AUG GGC@LB@ \|:\| \|\|:\|\|:\|\| \|\|\|\|\| \|\|\| :\|\|@LB@ GUC GAUCGUAA UACCC UAC UCG@LB@3'-UUU...ACCAU AA AA AAAAAG -5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -12.21 kcal/mol@LB@Hybridization Energy -24.6308 kcal/mol@LB@Unfolding Energy - mRNA 10.9347 kcal/mol@LB@Unfolding Energy - sRNA 1.49075 kcal/mol@LB@@LB@Position - mRNA 239 -- 268@LB@Position - sRNA 1 -- 32@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 22 -- 28@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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