Input and runtime details for job 2727377 (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 2727377 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:09 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:28 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:18:35 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:18:43 CET 2018
	Job Completed		@ Fri Feb 16 20:19:11 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=2727377&toolName=CopraRNA ( 30 days expiry )

Description of the job

RyhB

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
30	0.002864	0.2776	b1863	ruvC	-10.04	0.185852	89 -- 98	54 -- 63	component of RuvABC resolvasome endonuclease	_____________88_________99\n_____________\|__________\|\n5'-AGC...UCGAU__________AUUGC...GCA-3'\n______________AUGCUGGAAG\n______________\|\|:\|\|\|\|\|\|\|\n______________UAUGACCUUC\n3'-UUU...UUCAU__________GUUAC...GCG-5'\n_____________\|__________\|\n_____________64_________53\n	92 -- 98	54 -- 60	-14.3659 kcal/mol	1.62427 kcal/mol	2.70635 kcal/mol	88 99@LB@ \| \|@LB@5'-AGC...UCGAU AUUGC...GCA-3'@LB@ AUGCUGGAAG@LB@ \|\|:\|\|\|\|\|\|\|@LB@ UAUGACCUUC@LB@3'-UUU...UUCAU GUUAC...GCG-5'@LB@ \| \|@LB@ 64 53@LB@@LB@@LB@Energy -10.04 kcal/mol@LB@Hybridization Energy -14.3659 kcal/mol@LB@Unfolding Energy - mRNA 1.62427 kcal/mol@LB@Unfolding Energy - sRNA 2.70635 kcal/mol@LB@@LB@Position - mRNA 89 -- 98@LB@Position - sRNA 54 -- 63@LB@Position Seed - mRNA 92 -- 98@LB@Position Seed - sRNA 54 -- 60@LB@
2	1.064e-05	0.01787	b1683	sufB	-21.37	0.002185	208 -- 233	38 -- 66	component of SufBCD Fe-S cluster assembly scaffold	_____________207___________________________234\n_____________\|_____________________________\|\n5'-GUU...GUCUC________________C____________AAAAC...AGC-3'\n______________GUAAUACU_GAAGCAA__UGA_CGAUGUC\n______________\|\|\|\|\|\|\|\|_\|\|\|\|\|\|\|__\|\|\|_\|:\|\|\|\|\|\n______________CAUUAUGA_CUUCGUU__ACU_GUUACAG\n3'-UUU...CGAUU________C_______AC___C_______CACGA...GCG-5'\n_____________\|_____________________________\|\n_____________67____________________________37\n	227 -- 233	38 -- 44	-29.4313 kcal/mol	4.7571 kcal/mol	3.30527 kcal/mol	207 234@LB@ \| \|@LB@5'-GUU...GUCUC C AAAAC...AGC-3'@LB@ GUAAUACU GAAGCAA UGA CGAUGUC@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|\|\| \|\|\| \|:\|\|\|\|\|@LB@ CAUUAUGA CUUCGUU ACU GUUACAG@LB@3'-UUU...CGAUU C AC C CACGA...GCG-5'@LB@ \| \|@LB@ 67 37@LB@@LB@@LB@Energy -21.37 kcal/mol@LB@Hybridization Energy -29.4313 kcal/mol@LB@Unfolding Energy - mRNA 4.7571 kcal/mol@LB@Unfolding Energy - sRNA 3.30527 kcal/mol@LB@@LB@Position - mRNA 208 -- 233@LB@Position - sRNA 38 -- 66@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 38 -- 44@LB@
54	0.00511	0.2905	b0487	cueR	-8.71	0.294876	81 -- 102	6 -- 25	copper-responsive regulon transcriptional regulator	_____________80_____________________103\n_____________\|______________________\|\n5'-GUU...ACAUC________C_CA__A_______UAUUA...AAA-3'\n______________UCUCUGUG_G__GU_CUUCCUG\n______________\|\|\|\|:\|:\|_\|__\|\|_\|\|\|\|\|\|\|\n______________AGAGGCGC_C__CA_GAAGGAC\n3'-UUU...GUCCA________U_C___________UAGCG-5'\n_____________\|______________________\|\n_____________26_____________________5\n	96 -- 102	6 -- 12	-22.4921 kcal/mol	6.07455 kcal/mol	7.70509 kcal/mol	80 103@LB@ \| \|@LB@5'-GUU...ACAUC C CA A UAUUA...AAA-3'@LB@ UCUCUGUG G GU CUUCCUG@LB@ \|\|\|\|:\|:\| \| \|\| \|\|\|\|\|\|\|@LB@ AGAGGCGC C CA GAAGGAC@LB@3'-UUU...GUCCA U C UAGCG-5'@LB@ \| \|@LB@ 26 5@LB@@LB@@LB@Energy -8.71 kcal/mol@LB@Hybridization Energy -22.4921 kcal/mol@LB@Unfolding Energy - mRNA 6.07455 kcal/mol@LB@Unfolding Energy - sRNA 7.70509 kcal/mol@LB@@LB@Position - mRNA 81 -- 102@LB@Position - sRNA 6 -- 25@LB@Position Seed - mRNA 96 -- 102@LB@Position Seed - sRNA 6 -- 12@LB@
4	0.0001495	0.1256	b3867	hemN	-18.37	0.007265	188 -- 239	3 -- 58	coproporphyrinogen III oxidase SAM and NAD(P)H dependent oxygen-independent	_____________187_________________________________________________________240\n_____________\|___________________________________________________________\|\n5'-CGG...CCAUC_____G___________________A_____CAAA____ACU___A___GGC_______CAGAA...CAG-3'\n______________GGAAG_A__GUGAGC_AUGUC_UGU___CAG_____UCG___GGG_UCU___CCUGAUC\n______________\|\|\|\|\|_\|__\|\|\|\|\|\|_\|\|\|\|\|_\|\|:___\|\|\|_____:\|\|___\|\|\|_\|\|\|___\|\|\|\|\|\|\|\n______________CCUUC_U__CACUCG_UACAG_ACG___GUC_____GGC___CCC_AGA___GGACUAG\n3'-UUU...UAUGA_____G_UA______U_____C___AAA___CAAGA___GCU_______A_________CG-5'\n_____________\|___________________________________________________________\|\n_____________59__________________________________________________________2\n	233 -- 239	3 -- 9	-47.0013 kcal/mol	14.5919 kcal/mol	14.0436 kcal/mol	187 240@LB@ \| \|@LB@5'-CGG...CCAUC G A CAAA ACU A GGC CAGAA...CAG-3'@LB@ GGAAG A GUGAGC AUGUC UGU CAG UCG GGG UCU CCUGAUC@LB@ \|\|\|\|\| \| \|\|\|\|\|\| \|\|\|\|\| \|\|: \|\|\| :\|\| \|\|\| \|\|\| \|\|\|\|\|\|\|@LB@ CCUUC U CACUCG UACAG ACG GUC GGC CCC AGA GGACUAG@LB@3'-UUU...UAUGA G UA U C AAA CAAGA GCU A CG-5'@LB@ \| \|@LB@ 59 2@LB@@LB@@LB@Energy -18.37 kcal/mol@LB@Hybridization Energy -47.0013 kcal/mol@LB@Unfolding Energy - mRNA 14.5919 kcal/mol@LB@Unfolding Energy - sRNA 14.0436 kcal/mol@LB@@LB@Position - mRNA 188 -- 239@LB@Position - sRNA 3 -- 58@LB@Position Seed - mRNA 233 -- 239@LB@Position Seed - sRNA 3 -- 9@LB@
74	0.006788	0.3082	b3525	yhjH	-16.42	0.015793	272 -- 288	44 -- 60	cyclic-di-GMP phosphodiesterase FlhDC-regulated	_____________271_______________289\n_____________\|_________________\|\n5'-UUA...CGUUU____UU___________GUGCU...CCU-3'\n______________UUGG__GCAGUGUGAGC\n______________:\|\|\|__\|\|\|:\|\|\|\|\|\|\|\n______________GACC__CGUUACACUCG\n3'-UUU...AUUAU____UU___________UUACA...GCG-5'\n_____________\|_________________\|\n_____________61________________43\n	279 -- 285	47 -- 53	-25.6078 kcal/mol	5.89114 kcal/mol	3.2985 kcal/mol	271 289@LB@ \| \|@LB@5'-UUA...CGUUU UU GUGCU...CCU-3'@LB@ UUGG GCAGUGUGAGC@LB@ :\|\|\| \|\|\|:\|\|\|\|\|\|\|@LB@ GACC CGUUACACUCG@LB@3'-UUU...AUUAU UU UUACA...GCG-5'@LB@ \| \|@LB@ 61 43@LB@@LB@@LB@Energy -16.42 kcal/mol@LB@Hybridization Energy -25.6078 kcal/mol@LB@Unfolding Energy - mRNA 5.89114 kcal/mol@LB@Unfolding Energy - sRNA 3.2985 kcal/mol@LB@@LB@Position - mRNA 272 -- 288@LB@Position - sRNA 44 -- 60@LB@Position Seed - mRNA 279 -- 285@LB@Position Seed - sRNA 47 -- 53@LB@
87	0.008915	0.3393	b2530	iscS	-12.30	0.079567	175 -- 203	40 -- 68	cysteine desulfurase (tRNA sulfurtransferase) PLP-dependent	_____________174___________________________204\n_____________\|_____________________________\|\n5'-AAG...GCAUU________UAC_____UUAUA________AAAUU...UUG-3'\n______________GAGUGAUG___GGAGU_____GAGCAAUG\n______________:\|\|\|:\|\|:___\|:\|\|:_____\|\|\|\|\|\|\|\|\n______________UUCAUUAU___CUUCG_____CUCGUUAC\n3'-UUU...ACCGA________GAC_____UUACA________AGCAC...GCG-5'\n_____________\|_____________________________\|\n_____________69____________________________39\n	197 -- 203	40 -- 46	-22.6486 kcal/mol	7.04226 kcal/mol	3.30507 kcal/mol	174 204@LB@ \| \|@LB@5'-AAG...GCAUU UAC UUAUA AAAUU...UUG-3'@LB@ GAGUGAUG GGAGU GAGCAAUG@LB@ :\|\|\|:\|\|: \|:\|\|: \|\|\|\|\|\|\|\|@LB@ UUCAUUAU CUUCG CUCGUUAC@LB@3'-UUU...ACCGA GAC UUACA AGCAC...GCG-5'@LB@ \| \|@LB@ 69 39@LB@@LB@@LB@Energy -12.30 kcal/mol@LB@Hybridization Energy -22.6486 kcal/mol@LB@Unfolding Energy - mRNA 7.04226 kcal/mol@LB@Unfolding Energy - sRNA 3.30507 kcal/mol@LB@@LB@Position - mRNA 175 -- 203@LB@Position - sRNA 40 -- 68@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 40 -- 46@LB@
36	0.00312	0.2776	b1418	cybB	-18.82	0.006053	229 -- 299	21 -- 85	cytochrome b561	_____________228__________________________________________________________________________300\n_____________\|____________________________________________________________________________\|\n5'-AAC...ACAAA_______UCA_________CUUUU________UUAUC____C__AUU_C______GA_________U__U______C-3'\n______________UCAGCAU___CUGGCUGGU_______UACUGG_____GCAG_GU___G_GCAAUG__GU___UUCG_GG_UUCUUC\n______________:\|\|\|\|\|:___\|:\|\|\|\|\|\|:_______\|\|\|\|\|\|_____\|\|\|:_\|\|___\|_\|\|\|\|\|\|__\|\|___\|\|\|:_\|\|_\|\|\|\|:\|\n______________GGUCGUG___GGCCGACCG_______AUGACC_____CGUU_CA___C_CGUUAC__CA___AAGU_CC_AAGAGG\n______3'-UUUUC___________________AUUCAUU______UU_______A______U______AG__CGA______________CGCUC...GCG-5'\n_____________\|____________________________________________________________________________\|\n_____________86___________________________________________________________________________20\n	241 -- 247	70 -- 76	-54.3818 kcal/mol	15.9593 kcal/mol	19.6 kcal/mol	228 300@LB@ \| \|@LB@5'-AAC...ACAAA UCA CUUUU UUAUC C AUU C GA U U C-3'@LB@ UCAGCAU CUGGCUGGU UACUGG GCAG GU G GCAAUG GU UUCG GG UUCUUC@LB@ :\|\|\|\|\|: \|:\|\|\|\|\|\|: \|\|\|\|\|\| \|\|\|: \|\| \| \|\|\|\|\|\| \|\| \|\|\|: \|\| \|\|\|\|:\|@LB@ GGUCGUG GGCCGACCG AUGACC CGUU CA C CGUUAC CA AAGU CC AAGAGG@LB@ 3'-UUUUC AUUCAUU UU A U AG CGA CGCUC...GCG-5'@LB@ \| \|@LB@ 86 20@LB@@LB@@LB@Energy -18.82 kcal/mol@LB@Hybridization Energy -54.3818 kcal/mol@LB@Unfolding Energy - mRNA 15.9593 kcal/mol@LB@Unfolding Energy - sRNA 19.6 kcal/mol@LB@@LB@Position - mRNA 229 -- 299@LB@Position - sRNA 21 -- 85@LB@Position Seed - mRNA 241 -- 247@LB@Position Seed - sRNA 70 -- 76@LB@
166	0.02064	0.4072	b0429	cyoD	-11.77	0.097498	188 -- 206	44 -- 59	cytochrome o ubiquinol oxidase subunit IV	_____________187_________________207\n_____________\|___________________\|\n5'-UUC...UCUGA____________AAU____CAUUC...UCU-3'\n______________UGGGGGCGAUGU___GAGU\n______________\|\|\|::\|\|:\|\|\|\|___\|\|\|:\n______________ACCUUCGUUACA___CUCG\n3'-UUU...UUAUG___________________UUACA...GCG-5'\n_____________\|___________________\|\n_____________60__________________43\n	193 -- 199	48 -- 54	-20.4312 kcal/mol	5.39053 kcal/mol	3.27056 kcal/mol	187 207@LB@ \| \|@LB@5'-UUC...UCUGA AAU CAUUC...UCU-3'@LB@ UGGGGGCGAUGU GAGU@LB@ \|\|\|::\|\|:\|\|\|\| \|\|\|:@LB@ ACCUUCGUUACA CUCG@LB@3'-UUU...UUAUG UUACA...GCG-5'@LB@ \| \|@LB@ 60 43@LB@@LB@@LB@Energy -11.77 kcal/mol@LB@Hybridization Energy -20.4312 kcal/mol@LB@Unfolding Energy - mRNA 5.39053 kcal/mol@LB@Unfolding Energy - sRNA 3.27056 kcal/mol@LB@@LB@Position - mRNA 188 -- 206@LB@Position - sRNA 44 -- 59@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 48 -- 54@LB@
144	0.01729	0.3998	b2913	serA	-13.50	0.049990	182 -- 221	55 -- 90	D-3-phosphoglycerate dehydrogenase	_____________181______________________________________222\n_____________\|________________________________________\|\n5'-UGU...AUUUC_____A___G___G___AAA____AA_____UC_______AAAGA...CCA-3'\n______________AAAAG_CAG_AUU_GGU___UGGC__AGGUA__GCUGGAG\n______________\|\|\|\|\|_\|\|\|_\|::_\|\|:___\|\|\|\|__\|:\|\|\|__:\|\|\|\|\|:\n______________UUUUC_GUC_UGG_CCG___ACCG__UUCAU__UGACCUU\n___________3'-_____G___G___G__________A______UA_______CGUUA...GCG-5'\n______________\|_______________________________________\|\n______________90______________________________________54\n	215 -- 221	55 -- 61	-33.5694 kcal/mol	6.44391 kcal/mol	13.6256 kcal/mol	181 222@LB@ \| \|@LB@5'-UGU...AUUUC A G G AAA AA UC AAAGA...CCA-3'@LB@ AAAAG CAG AUU GGU UGGC AGGUA GCUGGAG@LB@ \|\|\|\|\| \|\|\| \|:: \|\|: \|\|\|\| \|:\|\|\| :\|\|\|\|\|:@LB@ UUUUC GUC UGG CCG ACCG UUCAU UGACCUU@LB@ 3'- G G G A UA CGUUA...GCG-5'@LB@ \| \|@LB@ 90 54@LB@@LB@@LB@Energy -13.50 kcal/mol@LB@Hybridization Energy -33.5694 kcal/mol@LB@Unfolding Energy - mRNA 6.44391 kcal/mol@LB@Unfolding Energy - sRNA 13.6256 kcal/mol@LB@@LB@Position - mRNA 182 -- 221@LB@Position - sRNA 55 -- 90@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 55 -- 61@LB@
190	0.02395	0.4226	b1189	dadA	-13.37	0.052568	210 -- 233	43 -- 66	D-amino acid dehydrogenase	_____________209_______________________234\n_____________\|_________________________\|\n5'-CCG...GAGUU__C_____G________________GGCGU...CGG-3'\n______________GU_AUACU_GGAAGUGGUGUG_GUA\n______________\|\|_\|\|\|\|\|_\|\|\|\|\|:::\|\|\|\|_\|:\|\n______________CA_UAUGA_CCUUCGUUACAC_CGU\n3'-UUU...CGAUU__U__________________U___UACAG...GCG-5'\n_____________\|_________________________\|\n_____________67________________________42\n	219 -- 225	52 -- 58	-24.725 kcal/mol	8.04945 kcal/mol	3.30463 kcal/mol	209 234@LB@ \| \|@LB@5'-CCG...GAGUU C G GGCGU...CGG-3'@LB@ GU AUACU GGAAGUGGUGUG GUA@LB@ \|\| \|\|\|\|\| \|\|\|\|\|:::\|\|\|\| \|:\|@LB@ CA UAUGA CCUUCGUUACAC CGU@LB@3'-UUU...CGAUU U U UACAG...GCG-5'@LB@ \| \|@LB@ 67 42@LB@@LB@@LB@Energy -13.37 kcal/mol@LB@Hybridization Energy -24.725 kcal/mol@LB@Unfolding Energy - mRNA 8.04945 kcal/mol@LB@Unfolding Energy - sRNA 3.30463 kcal/mol@LB@@LB@Position - mRNA 210 -- 233@LB@Position - sRNA 43 -- 66@LB@Position Seed - mRNA 219 -- 225@LB@Position Seed - sRNA 52 -- 58@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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