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
140	0.01604	0.3851	b4022	rluF	-13.68	0.046602	82 -- 103	39 -- 60	23S rRNA pseudouridine(2604) synthase	_____________81______________________104\n_____________\|_______________________\|\n5'-UUA...UGCUU____A_______U__________AACGA...UGU-3'\n______________CUGG_AAGUGAU_UGAGCAG_GU\n______________\|\|\|\|_\|\|\|::\|\|_\|\|\|\|\|\|:_\|\|\n______________GACC_UUCGUUA_ACUCGUU_CA\n3'-UUU...AUUAU____________C_______A__GCACG...GCG-5'\n_____________\|_______________________\|\n_____________61______________________38\n	95 -- 101	42 -- 48	-22.0004 kcal/mol	5.021 kcal/mol	3.3001 kcal/mol	81 104@LB@ \| \|@LB@5'-UUA...UGCUU A U AACGA...UGU-3'@LB@ CUGG AAGUGAU UGAGCAG GU@LB@ \|\|\|\| \|\|\|::\|\| \|\|\|\|\|\|: \|\|@LB@ GACC UUCGUUA ACUCGUU CA@LB@3'-UUU...AUUAU C A GCACG...GCG-5'@LB@ \| \|@LB@ 61 38@LB@@LB@@LB@Energy -13.68 kcal/mol@LB@Hybridization Energy -22.0004 kcal/mol@LB@Unfolding Energy - mRNA 5.021 kcal/mol@LB@Unfolding Energy - sRNA 3.3001 kcal/mol@LB@@LB@Position - mRNA 82 -- 103@LB@Position - sRNA 39 -- 60@LB@Position Seed - mRNA 95 -- 101@LB@Position Seed - sRNA 42 -- 48@LB@
133	0.0147	0.3709	b3832	rmuC	-11.93	0.091595	31 -- 71	21 -- 63	DNA recombination protein	_____________30________________________________________________72\n_____________\|_________________________________________________\|\n5'-AAA...AAAUC___G_________________C______CU___GUAA___UC_______UGUCU...AGC-3'\n______________GUG_UGGAAGC______GGCG__GUCGU__GCU____UUC___UUCUCC\n______________:\|:_\|\|\|\|\|\|\|______:\|\|:__\|\|\|\|\|__\|\|\|____\|\|\|___\|\|\|\|\|\|\n______________UAU_ACCUUCG______UCGU__CAGCA__CGA____AAG___AAGAGG\n3'-UUU...UUCAU___G_______UUACAC____UA_________________UCC______CGCUC...GCG-5'\n_____________\|_________________________________________________\|\n_____________64________________________________________________20\n	35 -- 41	53 -- 59	-30.4211 kcal/mol	10.4952 kcal/mol	7.99187 kcal/mol	30 72@LB@ \| \|@LB@5'-AAA...AAAUC G C CU GUAA UC UGUCU...AGC-3'@LB@ GUG UGGAAGC GGCG GUCGU GCU UUC UUCUCC@LB@ :\|: \|\|\|\|\|\|\| :\|\|: \|\|\|\|\| \|\|\| \|\|\| \|\|\|\|\|\|@LB@ UAU ACCUUCG UCGU CAGCA CGA AAG AAGAGG@LB@3'-UUU...UUCAU G UUACAC UA UCC CGCUC...GCG-5'@LB@ \| \|@LB@ 64 20@LB@@LB@@LB@Energy -11.93 kcal/mol@LB@Hybridization Energy -30.4211 kcal/mol@LB@Unfolding Energy - mRNA 10.4952 kcal/mol@LB@Unfolding Energy - sRNA 7.99187 kcal/mol@LB@@LB@Position - mRNA 31 -- 71@LB@Position - sRNA 21 -- 63@LB@Position Seed - mRNA 35 -- 41@LB@Position Seed - sRNA 53 -- 59@LB@
83	0.008249	0.3318	b0183	rnhB	-13.04	0.059790	42 -- 55	44 -- 58	ribonuclease HII degrades RNA of DNA-RNA hybrids	_____________41______________56\n_____________\|_______________\|\n5'-AAU...UUGCA_______________CGCAA...UCC-3'\n______________GGAAG_AGUGUGAGC\n______________\|\|\|\|\|_\|:\|\|\|\|\|\|\|\n______________CCUUC_UUACACUCG\n3'-UUU...UAUGA_____G_________UUACA...GCG-5'\n_____________\|_______________\|\n_____________59______________43\n	49 -- 55	44 -- 50	-21.6429 kcal/mol	5.39444 kcal/mol	3.20799 kcal/mol	41 56@LB@ \| \|@LB@5'-AAU...UUGCA CGCAA...UCC-3'@LB@ GGAAG AGUGUGAGC@LB@ \|\|\|\|\| \|:\|\|\|\|\|\|\|@LB@ CCUUC UUACACUCG@LB@3'-UUU...UAUGA G UUACA...GCG-5'@LB@ \| \|@LB@ 59 43@LB@@LB@@LB@Energy -13.04 kcal/mol@LB@Hybridization Energy -21.6429 kcal/mol@LB@Unfolding Energy - mRNA 5.39444 kcal/mol@LB@Unfolding Energy - sRNA 3.20799 kcal/mol@LB@@LB@Position - mRNA 42 -- 55@LB@Position - sRNA 44 -- 58@LB@Position Seed - mRNA 49 -- 55@LB@Position Seed - sRNA 44 -- 50@LB@
139	0.01578	0.3813	b3386	rpe	-11.91	0.092481	276 -- 300	34 -- 60	D-ribulose-5-phosphate 3-epimerase	_____________275_________________________300\n_____________\|___________________________\|\n5'-CGC...AAGCC____C_________C__U__________-3'\n______________CUGG_AGC__UG_G_GC_GAUGUCGUGC\n______________\|\|\|\|_\|\|\|__\|\|_\|_\|\|_:\|\|\|\|\|\|\|\|\|\n______________GACC_UCG__AC_C_CG_UUACAGCACG\n3'-UUU...AUUAU____U___UU__A_U_____________AAAGU...GCG-5'\n_____________\|____________________________\|\n_____________61___________________________33\n	294 -- 300	34 -- 40	-27.2321 kcal/mol	8.55668 kcal/mol	6.76671 kcal/mol	275 300@LB@ \| \|@LB@5'-CGC...AAGCC C C U -3'@LB@ CUGG AGC UG G GC GAUGUCGUGC@LB@ \|\|\|\| \|\|\| \|\| \| \|\| :\|\|\|\|\|\|\|\|\|@LB@ GACC UCG AC C CG UUACAGCACG@LB@3'-UUU...AUUAU U UU A U AAAGU...GCG-5'@LB@ \| \|@LB@ 61 33@LB@@LB@@LB@Energy -11.91 kcal/mol@LB@Hybridization Energy -27.2321 kcal/mol@LB@Unfolding Energy - mRNA 8.55668 kcal/mol@LB@Unfolding Energy - sRNA 6.76671 kcal/mol@LB@@LB@Position - mRNA 276 -- 300@LB@Position - sRNA 34 -- 60@LB@Position Seed - mRNA 294 -- 300@LB@Position Seed - sRNA 34 -- 40@LB@
179	0.02212	0.4113	b3317	rplB	-11.24	0.118994	191 -- 218	39 -- 68	50S ribosomal subunit protein L2	_____________190____________________________219\n_____________\|______________________________\|\n5'-GCA...CGGAG_________AAU__________UUA_____AAACC...UGC-3'\n______________GAGUAAUAC____GGCAGU_UG___AAUGU\n______________:\|\|\|\|\|\|\|\|____:\|\|\|:\|_\|\|___\|\|\|\|\|\n______________UUCAUUAUG____UCGUUA_AC___UUACA\n3'-UUU...ACCGA_________ACCU______C__UCG_____GCACG...GCG-5'\n_____________\|______________________________\|\n_____________69_____________________________38\n	193 -- 199	60 -- 66	-19.7264 kcal/mol	5.17772 kcal/mol	3.30515 kcal/mol	190 219@LB@ \| \|@LB@5'-GCA...CGGAG AAU UUA AAACC...UGC-3'@LB@ GAGUAAUAC GGCAGU UG AAUGU@LB@ :\|\|\|\|\|\|\|\| :\|\|\|:\| \|\| \|\|\|\|\|@LB@ UUCAUUAUG UCGUUA AC UUACA@LB@3'-UUU...ACCGA ACCU C UCG GCACG...GCG-5'@LB@ \| \|@LB@ 69 38@LB@@LB@@LB@Energy -11.24 kcal/mol@LB@Hybridization Energy -19.7264 kcal/mol@LB@Unfolding Energy - mRNA 5.17772 kcal/mol@LB@Unfolding Energy - sRNA 3.30515 kcal/mol@LB@@LB@Position - mRNA 191 -- 218@LB@Position - sRNA 39 -- 68@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 60 -- 66@LB@
164	0.02028	0.4072	b3295	rpoA	-11.98	0.089862	19 -- 43	66 -- 90	RNA polymerase alpha subunit	_____________18_________________________44\n_____________\|__________________________\|\n5'-GAA...CGCGU__________U__G_A__________CAGCG...GUG-3'\n______________GAAAGCC_GC_CU_G_GCUGGCUGAG\n______________:\|\|\|\|\|\|_\|\|_\|:_\|_\|\|\|\|\|\|\|:\|\|\n______________UUUUCGG_CG_GG_C_CGACCGAUUC\n___________3'-_______U__U__G____________AUUAU...GCG-5'\n______________\|_________________________\|\n______________90________________________65\n	37 -- 43	66 -- 72	-33.5627 kcal/mol	9.82436 kcal/mol	11.7544 kcal/mol	18 44@LB@ \| \|@LB@5'-GAA...CGCGU U G A CAGCG...GUG-3'@LB@ GAAAGCC GC CU G GCUGGCUGAG@LB@ :\|\|\|\|\|\| \|\| \|: \| \|\|\|\|\|\|\|:\|\|@LB@ UUUUCGG CG GG C CGACCGAUUC@LB@ 3'- U U G AUUAU...GCG-5'@LB@ \| \|@LB@ 90 65@LB@@LB@@LB@Energy -11.98 kcal/mol@LB@Hybridization Energy -33.5627 kcal/mol@LB@Unfolding Energy - mRNA 9.82436 kcal/mol@LB@Unfolding Energy - sRNA 11.7544 kcal/mol@LB@@LB@Position - mRNA 19 -- 43@LB@Position - sRNA 66 -- 90@LB@Position Seed - mRNA 37 -- 43@LB@Position Seed - sRNA 66 -- 72@LB@
6	0.0003052	0.1521	b4255	rraB	-18.72	0.006315	136 -- 158	39 -- 61	protein inhibitor of RNase E	_____________135_____________________159\n_____________\|_______________________\|\n5'-GAG...ACAAA_G____________C________GUGAC...CCA-3'\n______________G_UGGAGGCAAUGU_AGUGGUGU\n______________:_\|\|\|\|:\|\|\|\|\|\|\|_\|\|:::\|\|\|\n______________U_ACCUUCGUUACA_UCGUUACA\n3'-UUU...CAUUA_G____________C________GCACG...GCG-5'\n_____________\|_______________________\|\n_____________62______________________38\n	152 -- 158	39 -- 45	-27.5113 kcal/mol	5.49395 kcal/mol	3.30099 kcal/mol	135 159@LB@ \| \|@LB@5'-GAG...ACAAA G C GUGAC...CCA-3'@LB@ G UGGAGGCAAUGU AGUGGUGU@LB@ : \|\|\|\|:\|\|\|\|\|\|\| \|\|:::\|\|\|@LB@ U ACCUUCGUUACA UCGUUACA@LB@3'-UUU...CAUUA G C GCACG...GCG-5'@LB@ \| \|@LB@ 62 38@LB@@LB@@LB@Energy -18.72 kcal/mol@LB@Hybridization Energy -27.5113 kcal/mol@LB@Unfolding Energy - mRNA 5.49395 kcal/mol@LB@Unfolding Energy - sRNA 3.30099 kcal/mol@LB@@LB@Position - mRNA 136 -- 158@LB@Position - sRNA 39 -- 61@LB@Position Seed - mRNA 152 -- 158@LB@Position Seed - sRNA 39 -- 45@LB@
98	0.01017	0.3393	b1234	rssA	-9.29	0.241768	243 -- 258	1 -- 20	putative patatin-like family phospholipase	_____________242___________________259\n_____________\|_____________________\|\n5'-GAU...GCGCG_____A_______________AUAUU...AAA-3'\n______________GCGAG_GGU_____UGGUCGC\n______________\|\|\|\|\|_\|\|\|_____\|\|:\|\|\|\|\n______________CGCUC_CCA_____ACUAGCG\n3'-UUU...AGAGG_________GAAGG_______-5'\n_____________\|____________________\|\n_____________21___________________1\n	252 -- 258	1 -- 7	-21.3571 kcal/mol	5.88093 kcal/mol	6.18231 kcal/mol	242 259@LB@ \| \|@LB@5'-GAU...GCGCG A AUAUU...AAA-3'@LB@ GCGAG GGU UGGUCGC@LB@ \|\|\|\|\| \|\|\| \|\|:\|\|\|\|@LB@ CGCUC CCA ACUAGCG@LB@3'-UUU...AGAGG GAAGG -5'@LB@ \| \|@LB@ 21 1@LB@@LB@@LB@Energy -9.29 kcal/mol@LB@Hybridization Energy -21.3571 kcal/mol@LB@Unfolding Energy - mRNA 5.88093 kcal/mol@LB@Unfolding Energy - sRNA 6.18231 kcal/mol@LB@@LB@Position - mRNA 243 -- 258@LB@Position - sRNA 1 -- 20@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 1 -- 7@LB@
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@
88	0.008994	0.3393	b0721	sdhC	-13.41	0.051766	40 -- 58	43 -- 60	succinate dehydrogenase membrane subunit binds cytochrome b556	_____________39__________________59\n_____________\|___________________\|\n5'-UCC...CGCAU_____________UUU___UGACG...CCG-3'\n______________CUGGAAGCAGUGU___GCA\n______________\|\|\|\|\|\|\|\|\|:\|\|\|___\|\|\|\n______________GACCUUCGUUACA___CGU\n3'-UUU...AUUAU_____________CU____UACAG...GCG-5'\n_____________\|___________________\|\n_____________61__________________42\n	46 -- 52	48 -- 54	-24.0509 kcal/mol	7.34137 kcal/mol	3.29917 kcal/mol	39 59@LB@ \| \|@LB@5'-UCC...CGCAU UUU UGACG...CCG-3'@LB@ CUGGAAGCAGUGU GCA@LB@ \|\|\|\|\|\|\|\|\|:\|\|\| \|\|\|@LB@ GACCUUCGUUACA CGU@LB@3'-UUU...AUUAU CU UACAG...GCG-5'@LB@ \| \|@LB@ 61 42@LB@@LB@@LB@Energy -13.41 kcal/mol@LB@Hybridization Energy -24.0509 kcal/mol@LB@Unfolding Energy - mRNA 7.34137 kcal/mol@LB@Unfolding Energy - sRNA 3.29917 kcal/mol@LB@@LB@Position - mRNA 40 -- 58@LB@Position - sRNA 43 -- 60@LB@Position Seed - mRNA 46 -- 52@LB@Position Seed - sRNA 48 -- 54@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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