Input and runtime details for job 1786318 (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 1786318 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:20:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:20:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:01:46 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:01:53 CET 2018
	Job Completed		@ Fri Feb 16 22:02:22 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1786318&toolName=CopraRNA ( 30 days expiry )

Description of the job

ArcZ

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
59	0.002989	0.1727	b2713	hydN	-12.16	0.053402	276 -- 298	54 -- 76	formate dehydrogenase-H [4Fe-4S] ferredoxin subunit	b3573	_____________275______________________299\n_____________\|________________________\|\n5'-CUU...UUUCU_______A_____A___A______AU-3'\n______________CAUCAGG_AAAUC__GG_CUGUGC\n______________\|\|:\|\|\|\|_\|\|\|\|\|__\|\|_\|\|\|:\|\|\n______________GUGGUCC_UUUAG__CC_GACGCG\n3'-UUU...CGGUU_______C_____AA_________GCAUU...GUG-5'\n_____________\|________________________\|\n_____________77_______________________53\n	276 -- 282	70 -- 76	-25.5609 kcal/mol	4.47784 kcal/mol	8.92391 kcal/mol	275 299@LB@ \| \|@LB@5'-CUU...UUUCU A A A AU-3'@LB@ CAUCAGG AAAUC GG CUGUGC@LB@ \|\|:\|\|\|\| \|\|\|\|\| \|\| \|\|\|:\|\|@LB@ GUGGUCC UUUAG CC GACGCG@LB@3'-UUU...CGGUU C AA GCAUU...GUG-5'@LB@ \| \|@LB@ 77 53@LB@@LB@@LB@Energy -12.16 kcal/mol@LB@Hybridization Energy -25.5609 kcal/mol@LB@Unfolding Energy - mRNA 4.47784 kcal/mol@LB@Unfolding Energy - sRNA 8.92391 kcal/mol@LB@@LB@Position - mRNA 276 -- 298@LB@Position - sRNA 54 -- 76@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 70 -- 76@LB@
104	0.005642	0.1855	b1476	fdnI	-8.74	0.236866	280 -- 291	51 -- 62	formate dehydrogenase-N cytochrome B556 (gamma) subunit nitrate-inducible		_____________279__________292\n_____________\|____________\|\n5'-CGU...CUUCC____G_______CCGGG...UUU-3'\n______________UGGU_GCGCUGU\n______________\|\|\|:_\|\|\|\|:\|\|\n______________ACCG_CGCGGCA\n3'-UUU...UUAGA____A_______UUUAA...GUG-5'\n_____________\|____________\|\n_____________63___________50\n	285 -- 291	51 -- 57	-16.7644 kcal/mol	3.14516 kcal/mol	4.8826 kcal/mol	279 292@LB@ \| \|@LB@5'-CGU...CUUCC G CCGGG...UUU-3'@LB@ UGGU GCGCUGU@LB@ \|\|\|: \|\|\|\|:\|\|@LB@ ACCG CGCGGCA@LB@3'-UUU...UUAGA A UUUAA...GUG-5'@LB@ \| \|@LB@ 63 50@LB@@LB@@LB@Energy -8.74 kcal/mol@LB@Hybridization Energy -16.7644 kcal/mol@LB@Unfolding Energy - mRNA 3.14516 kcal/mol@LB@Unfolding Energy - sRNA 4.8826 kcal/mol@LB@@LB@Position - mRNA 280 -- 291@LB@Position - sRNA 51 -- 62@LB@Position Seed - mRNA 285 -- 291@LB@Position Seed - sRNA 51 -- 57@LB@
165	0.009721	0.2068	b1475	fdnH	-11.62	0.068172	63 -- 98	41 -- 76	formate dehydrogenase-N Fe-S (beta) subunit nitrate-inducible		_____________62_____________________________________99\n_____________\|______________________________________\|\n5'-CGC...CAAUC________CU___GA__G__U___G______G______AUCGC...UUA-3'\n______________CACUGGGG___UU__GG_UG_CGC_CGUAAA__GUUAU\n______________\|\|\|::\|\|\|___\|:__\|\|_\|\|_\|\|\|_\|\|\|\|\|\|__:\|\|\|\|\n______________GUGGUCCC___AG__CC_AC_GCG_GCAUUU__UAAUA\n3'-UUU...CGGUU________UUU__AA__G_____________AA_____CUACU...GUG-5'\n_____________\|______________________________________\|\n_____________77_____________________________________40\n	64 -- 70	69 -- 75	-31.0903 kcal/mol	10.1186 kcal/mol	9.35565 kcal/mol	62 99@LB@ \| \|@LB@5'-CGC...CAAUC CU GA G U G G AUCGC...UUA-3'@LB@ CACUGGGG UU GG UG CGC CGUAAA GUUAU@LB@ \|\|\|::\|\|\| \|: \|\| \|\| \|\|\| \|\|\|\|\|\| :\|\|\|\|@LB@ GUGGUCCC AG CC AC GCG GCAUUU UAAUA@LB@3'-UUU...CGGUU UUU AA G AA CUACU...GUG-5'@LB@ \| \|@LB@ 77 40@LB@@LB@@LB@Energy -11.62 kcal/mol@LB@Hybridization Energy -31.0903 kcal/mol@LB@Unfolding Energy - mRNA 10.1186 kcal/mol@LB@Unfolding Energy - sRNA 9.35565 kcal/mol@LB@@LB@Position - mRNA 63 -- 98@LB@Position - sRNA 41 -- 76@LB@Position Seed - mRNA 64 -- 70@LB@Position Seed - sRNA 69 -- 75@LB@
52	0.002619	0.1727	b2720	hycF	-12.75	0.040951	8 -- 55	44 -- 94	formate hydrogenlyase complex iron-sulfur protein		_____________7______________________________________________________56\n_____________\|______________________________________________________\|\n____5'-CGACCCU____UAC_________GG_________________CCGA_______CU______CGGUA...CAG-3'\n______________GCGC___AUGCUGCGC__CAACACC______GUUU____UGCGCCG__GAUUAU\n______________\|\|\|\|___\|\|:\|\|\|\|\|\|__\|\|\|\|\|\|\|______:\|:\|____\|\|\|\|\|\|\|__:\|\|\|\|\|\n______________CGCG___UAUGACGCG__GUUGUGG______UAGA____ACGCGGC__UUAAUA\n3'-UUU...CCCCA____CU___________________UCCCUU____ACCG_______AU______AUACU...GUG-5'\n_____________\|______________________________________________________\|\n_____________95_____________________________________________________43\n	41 -- 47	52 -- 58	-46.3174 kcal/mol	16.2176 kcal/mol	17.3533 kcal/mol	7 56@LB@ \| \|@LB@ 5'-CGACCCU UAC GG CCGA CU CGGUA...CAG-3'@LB@ GCGC AUGCUGCGC CAACACC GUUU UGCGCCG GAUUAU@LB@ \|\|\|\| \|\|:\|\|\|\|\|\| \|\|\|\|\|\|\| :\|:\| \|\|\|\|\|\|\| :\|\|\|\|\|@LB@ CGCG UAUGACGCG GUUGUGG UAGA ACGCGGC UUAAUA@LB@3'-UUU...CCCCA CU UCCCUU ACCG AU AUACU...GUG-5'@LB@ \| \|@LB@ 95 43@LB@@LB@@LB@Energy -12.75 kcal/mol@LB@Hybridization Energy -46.3174 kcal/mol@LB@Unfolding Energy - mRNA 16.2176 kcal/mol@LB@Unfolding Energy - sRNA 17.3533 kcal/mol@LB@@LB@Position - mRNA 8 -- 55@LB@Position - sRNA 44 -- 94@LB@Position Seed - mRNA 41 -- 47@LB@Position Seed - sRNA 52 -- 58@LB@
126	0.006849	0.1914	b2930	yggF	-13.28	0.032133	176 -- 191	68 -- 83	fructose 1 6 bisphosphatase isozyme		_____________175______________192\n_____________\|________________\|\n5'-AUC...AUUUG________________GGCCG...GCC-3'\n______________GCGUUGAUAUCGGGGA\n______________\|\|\|:::\|:\|:\|:\|\|\|\|\n______________CGCGGUUGUGGUCCCU\n3'-UUU...UAUGA________________UUAGA...GUG-5'\n_____________\|________________\|\n_____________84_______________67\n	185 -- 191	68 -- 74	-24.7766 kcal/mol	4.1491 kcal/mol	7.34657 kcal/mol	175 192@LB@ \| \|@LB@5'-AUC...AUUUG GGCCG...GCC-3'@LB@ GCGUUGAUAUCGGGGA@LB@ \|\|\|:::\|:\|:\|:\|\|\|\|@LB@ CGCGGUUGUGGUCCCU@LB@3'-UUU...UAUGA UUAGA...GUG-5'@LB@ \| \|@LB@ 84 67@LB@@LB@@LB@Energy -13.28 kcal/mol@LB@Hybridization Energy -24.7766 kcal/mol@LB@Unfolding Energy - mRNA 4.1491 kcal/mol@LB@Unfolding Energy - sRNA 7.34657 kcal/mol@LB@@LB@Position - mRNA 176 -- 191@LB@Position - sRNA 68 -- 83@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 68 -- 74@LB@
120	0.006631	0.1913	b0825	fsaA	-14.24	0.020734	15 -- 76	31 -- 86	fructose-6-phosphate aldolase 1	b3946	_____________14_____________________________________________________________77\n_____________\|______________________________________________________________\|\n5'-CUU...AUACG__C____G__________CC___A___G_CGAGUA______AAU____AAAAUCAU______CUCUC...CCG-3'\n______________AC_GUGC_GAUACCGGGG__AUC_UGG_U______GCGCUG___AUUG________AGUUGC\n______________\|\|_\|:\|\|_:\|:\|\|\|:\|\|\|__\|\|\|_\|\|\|_\|______\|\|\|\|:\|___\|\|\|:________\|\|\|\|:\|\n______________UG_CGCG_UUGUGGUCCC__UAG_ACC_A______CGCGGC___UAAU________UCAAUG\n3'-UUU...GCUUA__A____G__________UU___A___G_____________AUU____AAUACUAC______UUCCC...GUG-5'\n_____________\|______________________________________________________________\|\n_____________87_____________________________________________________________30\n	26 -- 32	69 -- 75	-46.4097 kcal/mol	15.1018 kcal/mol	17.0646 kcal/mol	14 77@LB@ \| \|@LB@5'-CUU...AUACG C G CC A G CGAGUA AAU AAAAUCAU CUCUC...CCG-3'@LB@ AC GUGC GAUACCGGGG AUC UGG U GCGCUG AUUG AGUUGC@LB@ \|\| \|:\|\| :\|:\|\|\|:\|\|\| \|\|\| \|\|\| \| \|\|\|\|:\| \|\|\|: \|\|\|\|:\|@LB@ UG CGCG UUGUGGUCCC UAG ACC A CGCGGC UAAU UCAAUG@LB@3'-UUU...GCUUA A G UU A G AUU AAUACUAC UUCCC...GUG-5'@LB@ \| \|@LB@ 87 30@LB@@LB@@LB@Energy -14.24 kcal/mol@LB@Hybridization Energy -46.4097 kcal/mol@LB@Unfolding Energy - mRNA 15.1018 kcal/mol@LB@Unfolding Energy - sRNA 17.0646 kcal/mol@LB@@LB@Position - mRNA 15 -- 76@LB@Position - sRNA 31 -- 86@LB@Position Seed - mRNA 26 -- 32@LB@Position Seed - sRNA 69 -- 75@LB@
192	0.01187	0.2159	b2600	tyrA	-9.34	0.184498	136 -- 155	70 -- 86	fused chorismate mutase T/prephenate dehydrogenase		_____________135__________________156\n_____________\|____________________\|\n5'-UCG...GCCUU_______G__AUU_______AUCUG...UGG-3'\n______________GCUGCGU_AA___CAUCAGG\n______________:\|\|\|\|\|:_\|\|___\|\|:\|\|\|\|\n______________UGACGCG_UU___GUGGUCC\n3'-UUU...GCUUA_______G____________CUUUA...GUG-5'\n_____________\|____________________\|\n_____________87___________________69\n	149 -- 155	70 -- 76	-22.0981 kcal/mol	5.48162 kcal/mol	7.27772 kcal/mol	135 156@LB@ \| \|@LB@5'-UCG...GCCUU G AUU AUCUG...UGG-3'@LB@ GCUGCGU AA CAUCAGG@LB@ :\|\|\|\|\|: \|\| \|\|:\|\|\|\|@LB@ UGACGCG UU GUGGUCC@LB@3'-UUU...GCUUA G CUUUA...GUG-5'@LB@ \| \|@LB@ 87 69@LB@@LB@@LB@Energy -9.34 kcal/mol@LB@Hybridization Energy -22.0981 kcal/mol@LB@Unfolding Energy - mRNA 5.48162 kcal/mol@LB@Unfolding Energy - sRNA 7.27772 kcal/mol@LB@@LB@Position - mRNA 136 -- 155@LB@Position - sRNA 70 -- 86@LB@Position Seed - mRNA 149 -- 155@LB@Position Seed - sRNA 70 -- 76@LB@
88	0.004799	0.1855	b2213	ada	-9.32	0.185618	222 -- 245	63 -- 86	fused DNA-binding transcriptional dual regulator/O6-methylguanine-DNA methyltransferase		_____________221________________________246\n_____________\|__________________________\|\n5'-GGA...GCUUA____A__A__________C_______GUCUU...CCA-3'\n______________ACUG_CG_UCAACGCUGG___AAUCU\n______________\|\|\|\|_\|\|_:\|\|\|\|:\|::\|___\|\|\|\|\|\n______________UGAC_GC_GGUUGUGGUC___UUAGA\n3'-UUU...GCUUA__________________CCU_____ACCGA...GUG-5'\n_____________\|__________________________\|\n_____________87_________________________62\n	233 -- 239	71 -- 77	-21.7615 kcal/mol	5.05104 kcal/mol	7.38602 kcal/mol	221 246@LB@ \| \|@LB@5'-GGA...GCUUA A A C GUCUU...CCA-3'@LB@ ACUG CG UCAACGCUGG AAUCU@LB@ \|\|\|\| \|\| :\|\|\|\|:\|::\| \|\|\|\|\|@LB@ UGAC GC GGUUGUGGUC UUAGA@LB@3'-UUU...GCUUA CCU ACCGA...GUG-5'@LB@ \| \|@LB@ 87 62@LB@@LB@@LB@Energy -9.32 kcal/mol@LB@Hybridization Energy -21.7615 kcal/mol@LB@Unfolding Energy - mRNA 5.05104 kcal/mol@LB@Unfolding Energy - sRNA 7.38602 kcal/mol@LB@@LB@Position - mRNA 222 -- 245@LB@Position - sRNA 63 -- 86@LB@Position Seed - mRNA 233 -- 239@LB@Position Seed - sRNA 71 -- 77@LB@
107	0.005754	0.1855	b3447	ggt	-8.41	0.270031	252 -- 270	52 -- 70	gamma-glutamyltranspeptidase		_____________251_________________271\n_____________\|___________________\|\n5'-GUU...UCUCA_______GUUUUA______CCGCC...CGU-3'\n______________GGAAGUU______GCGCCG\n______________\|\|\|\|:\|:______\|\|\|\|\|\|\n______________CCUUUAG______CGCGGC\n3'-UUU...UGGUC_______AACCGA______AUUUA...GUG-5'\n_____________\|___________________\|\n_____________71__________________51\n	252 -- 258	64 -- 70	-19.4063 kcal/mol	4.14766 kcal/mol	6.84683 kcal/mol	251 271@LB@ \| \|@LB@5'-GUU...UCUCA GUUUUA CCGCC...CGU-3'@LB@ GGAAGUU GCGCCG@LB@ \|\|\|\|:\|: \|\|\|\|\|\|@LB@ CCUUUAG CGCGGC@LB@3'-UUU...UGGUC AACCGA AUUUA...GUG-5'@LB@ \| \|@LB@ 71 51@LB@@LB@@LB@Energy -8.41 kcal/mol@LB@Hybridization Energy -19.4063 kcal/mol@LB@Unfolding Energy - mRNA 4.14766 kcal/mol@LB@Unfolding Energy - sRNA 6.84683 kcal/mol@LB@@LB@Position - mRNA 252 -- 270@LB@Position - sRNA 52 -- 70@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 64 -- 70@LB@
81	0.004478	0.1855	b3327	gspF	-8.77	0.233220	243 -- 251	26 -- 34	general secretory pathway component cryptic		_____________242_______252\n_____________\|_________\|\n5'-AUG...AAAAA_________AUCAU...AAG-3'\n______________UUGCAAGGG\n______________\|\|:\|\|\|\|\|\|\n______________AAUGUUCCC\n3'-UUU...UACUC_________GUGUC...GUG-5'\n_____________\|_________\|\n_____________35________25\n	245 -- 251	26 -- 32	-12.3281 kcal/mol	0.874927 kcal/mol	2.67841 kcal/mol	242 252@LB@ \| \|@LB@5'-AUG...AAAAA AUCAU...AAG-3'@LB@ UUGCAAGGG@LB@ \|\|:\|\|\|\|\|\|@LB@ AAUGUUCCC@LB@3'-UUU...UACUC GUGUC...GUG-5'@LB@ \| \|@LB@ 35 25@LB@@LB@@LB@Energy -8.77 kcal/mol@LB@Hybridization Energy -12.3281 kcal/mol@LB@Unfolding Energy - mRNA 0.874927 kcal/mol@LB@Unfolding Energy - sRNA 2.67841 kcal/mol@LB@@LB@Position - mRNA 243 -- 251@LB@Position - sRNA 26 -- 34@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 26 -- 32@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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service.

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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