Input and runtime details for job 5882223 (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 5882223 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:39:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 03:02:39 CET 2018
	Post-Processing Finished		@ Sat Feb 17 03:02:47 CET 2018
	Job Completed		@ Sat Feb 17 03:03:15 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5882223&toolName=CopraRNA ( 30 days expiry )

Description of the job

Spot42

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
191	0.008587	0.1558	b0823	ybiW	-9.49	0.063221	47 -- 54	1 -- 8	putative pyruvate formate lyase	b3951	_____________46_______55\n_____________\|________\|\n5'-ACC...UUUUC________CACAC...CGC-3'\n______________UGCCCUAC\n______________\|:\|\|\|\|\|\|\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	48 -- 54	1 -- 7	-12.4662 kcal/mol	0.878635 kcal/mol	2.11603 kcal/mol	46 55@LB@ \| \|@LB@5'-ACC...UUUUC CACAC...CGC-3'@LB@ UGCCCUAC@LB@ \|:\|\|\|\|\|\|@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -9.49 kcal/mol@LB@Hybridization Energy -12.4662 kcal/mol@LB@Unfolding Energy - mRNA 0.878635 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 47 -- 54@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 48 -- 54@LB@Position Seed - sRNA 1 -- 7@LB@
192	0.008619	0.1558	b2561	yfhH	-12.96	0.004772	194 -- 222	4 -- 32	putative DNA-binding transcriptional regulator		_____________193____________________________223\n_____________\|______________________________\|\n5'-CCU...GCGAG________U_____G_______________GUCAG...GCC-3'\n______________GAAAGAUA_GAACG_CUUACUUC_GUAUCC\n______________\|\|\|\|\|\|\|\|_\|\|\|\|:_\|\|\|\|\|:\|\|_\|\|\|:\|\|\n______________CUUUCUAU_CUUGU_GAAUGGAG_CAUGGG\n3'-AUU...CCAGA______________A________A______AUG-5'\n_____________\|______________________________\|\n_____________33_____________________________3\n	195 -- 201	25 -- 31	-31.2741 kcal/mol	9.51226 kcal/mol	8.82263 kcal/mol	193 223@LB@ \| \|@LB@5'-CCU...GCGAG U G GUCAG...GCC-3'@LB@ GAAAGAUA GAACG CUUACUUC GUAUCC@LB@ \|\|\|\|\|\|\|\| \|\|\|\|: \|\|\|\|\|:\|\| \|\|\|:\|\|@LB@ CUUUCUAU CUUGU GAAUGGAG CAUGGG@LB@3'-AUU...CCAGA A A AUG-5'@LB@ \| \|@LB@ 33 3@LB@@LB@@LB@Energy -12.96 kcal/mol@LB@Hybridization Energy -31.2741 kcal/mol@LB@Unfolding Energy - mRNA 9.51226 kcal/mol@LB@Unfolding Energy - sRNA 8.82263 kcal/mol@LB@@LB@Position - mRNA 194 -- 222@LB@Position - sRNA 4 -- 32@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 25 -- 31@LB@
193	0.008653	0.1558	b1677	lpp	-9.16	0.078007	273 -- 298	53 -- 76	murein lipoprotein		_____________272________________________299\n_____________\|__________________________\|\n5'-UCA...GCAAC________CGA______GUCU_____CG-3'\n______________GCUAAAAU___UCAGCU____UCUGA\n______________\|\|\|\|\|\|\|\|___\|\|\|\|\|:____\|\|:\|\|\n______________CGAUUUUA___AGUCGG____AGGCU\n3'-AUU...CCCGC________UA_______UUU______AAUGC...AUG-5'\n_____________\|__________________________\|\n_____________77_________________________52\n	273 -- 279	70 -- 76	-19.09 kcal/mol	3.58418 kcal/mol	6.36489 kcal/mol	272 299@LB@ \| \|@LB@5'-UCA...GCAAC CGA GUCU CG-3'@LB@ GCUAAAAU UCAGCU UCUGA@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|: \|\|:\|\|@LB@ CGAUUUUA AGUCGG AGGCU@LB@3'-AUU...CCCGC UA UUU AAUGC...AUG-5'@LB@ \| \|@LB@ 77 52@LB@@LB@@LB@Energy -9.16 kcal/mol@LB@Hybridization Energy -19.09 kcal/mol@LB@Unfolding Energy - mRNA 3.58418 kcal/mol@LB@Unfolding Energy - sRNA 6.36489 kcal/mol@LB@@LB@Position - mRNA 273 -- 298@LB@Position - sRNA 53 -- 76@LB@Position Seed - mRNA 273 -- 279@LB@Position Seed - sRNA 70 -- 76@LB@
194	0.008663	0.1558	b0213	yafS	-5.39	0.521143	17 -- 34	51 -- 73	putative S-adenosyl-L-methionine-dependent methyltransferase		_____________16______________________35\n_____________\|_______________________\|\n5'-UGG...GGUGA_______________________GCCAG...UCA-3'\n______________GAAAUAU__GGCC___UCCGGUU\n______________:\|\|\|\|\|\|__:\|\|\|___\|\|\|\|:\|\|\n______________UUUUAUA__UCGG___AGGCUAA\n3'-AUU...GCCGA_______AG____UUU_______UGCAC...AUG-5'\n_____________\|_______________________\|\n_____________74______________________50\n	28 -- 34	51 -- 57	-15.2768 kcal/mol	3.69768 kcal/mol	6.213 kcal/mol	16 35@LB@ \| \|@LB@5'-UGG...GGUGA GCCAG...UCA-3'@LB@ GAAAUAU GGCC UCCGGUU@LB@ :\|\|\|\|\|\| :\|\|\| \|\|\|\|:\|\|@LB@ UUUUAUA UCGG AGGCUAA@LB@3'-AUU...GCCGA AG UUU UGCAC...AUG-5'@LB@ \| \|@LB@ 74 50@LB@@LB@@LB@Energy -5.39 kcal/mol@LB@Hybridization Energy -15.2768 kcal/mol@LB@Unfolding Energy - mRNA 3.69768 kcal/mol@LB@Unfolding Energy - sRNA 6.213 kcal/mol@LB@@LB@Position - mRNA 17 -- 34@LB@Position - sRNA 51 -- 73@LB@Position Seed - mRNA 28 -- 34@LB@Position Seed - sRNA 51 -- 57@LB@
195	0.008707	0.1558	b3318	rplW	-7.58	0.194751	202 -- 213	43 -- 55	50S ribosomal subunit protein L23		_____________201___________214\n_____________\|_____________\|\n5'-GCA...UGGCA_____________AACGU...AAG-3'\n______________UGAUU_CGUGAAG\n______________:\|\|\|\|_\|\|\|\|\|\|\|\n______________GCUAA_GCACUUC\n3'-AUU...UUUAG_____U_______AUUUU...AUG-5'\n_____________\|_____________\|\n_____________56____________42\n	207 -- 213	43 -- 49	-13.4464 kcal/mol	2.60751 kcal/mol	3.2693 kcal/mol	201 214@LB@ \| \|@LB@5'-GCA...UGGCA AACGU...AAG-3'@LB@ UGAUU CGUGAAG@LB@ :\|\|\|\| \|\|\|\|\|\|\|@LB@ GCUAA GCACUUC@LB@3'-AUU...UUUAG U AUUUU...AUG-5'@LB@ \| \|@LB@ 56 42@LB@@LB@@LB@Energy -7.58 kcal/mol@LB@Hybridization Energy -13.4464 kcal/mol@LB@Unfolding Energy - mRNA 2.60751 kcal/mol@LB@Unfolding Energy - sRNA 3.2693 kcal/mol@LB@@LB@Position - mRNA 202 -- 213@LB@Position - sRNA 43 -- 55@LB@Position Seed - mRNA 207 -- 213@LB@Position Seed - sRNA 43 -- 49@LB@
196	0.008709	0.1558	b2498	upp	-7.14	0.244299	249 -- 259	45 -- 56	uracil phosphoribosyltransferase		_____________248__________260\n_____________\|____________\|\n5'-GGC...UGGGA____________GCAAG...CCG-3'\n______________CUGA_UGCGUGA\n______________\|:\|\|_\|:\|\|\|\|\|\n______________GGCU_AUGCACU\n3'-AUU...GUUUA____A_______UCAUU...AUG-5'\n_____________\|____________\|\n_____________57___________44\n	253 -- 259	45 -- 51	-12.6155 kcal/mol	3.20986 kcal/mol	2.27945 kcal/mol	248 260@LB@ \| \|@LB@5'-GGC...UGGGA GCAAG...CCG-3'@LB@ CUGA UGCGUGA@LB@ \|:\|\| \|:\|\|\|\|\|@LB@ GGCU AUGCACU@LB@3'-AUU...GUUUA A UCAUU...AUG-5'@LB@ \| \|@LB@ 57 44@LB@@LB@@LB@Energy -7.14 kcal/mol@LB@Hybridization Energy -12.6155 kcal/mol@LB@Unfolding Energy - mRNA 3.20986 kcal/mol@LB@Unfolding Energy - sRNA 2.27945 kcal/mol@LB@@LB@Position - mRNA 249 -- 259@LB@Position - sRNA 45 -- 56@LB@Position Seed - mRNA 253 -- 259@LB@Position Seed - sRNA 45 -- 51@LB@
197	0.00873	0.1558	b2324	mnmC	-9.11	0.080832	111 -- 120	52 -- 61	fused 5-methylaminomethyl-2-thiouridine-forming enzyme methyltransferase and FAD-dependent demodification enzyme		_____________110________121\n_____________\|__________\|\n5'-GCU...CCGAA__________CAGCC...ACG-3'\n______________CAAGUCCGAU\n______________\|\|\|:\|\|\|\|\|\|\n______________GUUUAGGCUA\n3'-AUU...AGUCG__________AUGCA...AUG-5'\n_____________\|__________\|\n_____________62_________51\n	114 -- 120	52 -- 58	-12.6788 kcal/mol	1.38997 kcal/mol	2.20422 kcal/mol	110 121@LB@ \| \|@LB@5'-GCU...CCGAA CAGCC...ACG-3'@LB@ CAAGUCCGAU@LB@ \|\|\|:\|\|\|\|\|\|@LB@ GUUUAGGCUA@LB@3'-AUU...AGUCG AUGCA...AUG-5'@LB@ \| \|@LB@ 62 51@LB@@LB@@LB@Energy -9.11 kcal/mol@LB@Hybridization Energy -12.6788 kcal/mol@LB@Unfolding Energy - mRNA 1.38997 kcal/mol@LB@Unfolding Energy - sRNA 2.20422 kcal/mol@LB@@LB@Position - mRNA 111 -- 120@LB@Position - sRNA 52 -- 61@LB@Position Seed - mRNA 114 -- 120@LB@Position Seed - sRNA 52 -- 58@LB@
198	0.008802	0.1558	b1905	ftnA	-8.07	0.149574	234 -- 260	3 -- 24	ferritin iron storage protein (cytoplasmic)		_____________233_________________________261\n_____________\|___________________________\|\n5'-CAU...UUAAU_____GA_GA____GGAA_________UCACU...AUC-3'\n______________GAGCA__U__ACCU____CUGUACUCU\n______________\|\|:\|\|__\|__\|\|\|\|____\|\|\|\|\|\|:\|\|\n______________CUUGU__A__UGGA____GACAUGGGA\n3'-AUU...UCUAU_____AG_A__________________UG-5'\n_____________\|___________________________\|\n_____________25__________________________2\n	254 -- 260	3 -- 9	-20.546 kcal/mol	4.48094 kcal/mol	8.02061 kcal/mol	233 261@LB@ \| \|@LB@5'-CAU...UUAAU GA GA GGAA UCACU...AUC-3'@LB@ GAGCA U ACCU CUGUACUCU@LB@ \|\|:\|\| \| \|\|\|\| \|\|\|\|\|\|:\|\|@LB@ CUUGU A UGGA GACAUGGGA@LB@3'-AUU...UCUAU AG A UG-5'@LB@ \| \|@LB@ 25 2@LB@@LB@@LB@Energy -8.07 kcal/mol@LB@Hybridization Energy -20.546 kcal/mol@LB@Unfolding Energy - mRNA 4.48094 kcal/mol@LB@Unfolding Energy - sRNA 8.02061 kcal/mol@LB@@LB@Position - mRNA 234 -- 260@LB@Position - sRNA 3 -- 24@LB@Position Seed - mRNA 254 -- 260@LB@Position Seed - sRNA 3 -- 9@LB@
199	0.008811	0.1558	b4515	cydX	-11.13	0.020449	151 -- 184	5 -- 31	cytochrome d (bd-I) ubiquinol oxidase subunit X		_____________150________________________________185\n_____________\|__________________________________\|\n5'-ACC...CCAAA_______UU______AAC___CACUC________AAGUA...GUC-3'\n______________GAAGAUA__GAACGU___ACC_____UCUGUACU\n______________:\|\|\|\|\|\|__\|\|\|\|:\|___\|\|\|_____\|\|\|\|\|\|\|:\n______________UUUCUAU__CUUGUA___UGG_____AGACAUGG\n3'-AUU...CAGAC_______________GAA________________GAUG-5'\n_____________\|__________________________________\|\n_____________32_________________________________4\n	178 -- 184	5 -- 11	-22.8813 kcal/mol	3.72257 kcal/mol	8.05162 kcal/mol	150 185@LB@ \| \|@LB@5'-ACC...CCAAA UU AAC CACUC AAGUA...GUC-3'@LB@ GAAGAUA GAACGU ACC UCUGUACU@LB@ :\|\|\|\|\|\| \|\|\|\|:\| \|\|\| \|\|\|\|\|\|\|:@LB@ UUUCUAU CUUGUA UGG AGACAUGG@LB@3'-AUU...CAGAC GAA GAUG-5'@LB@ \| \|@LB@ 32 4@LB@@LB@@LB@Energy -11.13 kcal/mol@LB@Hybridization Energy -22.8813 kcal/mol@LB@Unfolding Energy - mRNA 3.72257 kcal/mol@LB@Unfolding Energy - sRNA 8.05162 kcal/mol@LB@@LB@Position - mRNA 151 -- 184@LB@Position - sRNA 5 -- 31@LB@Position Seed - mRNA 178 -- 184@LB@Position Seed - sRNA 5 -- 11@LB@
200	0.009019	0.1567	b3343	tusB	-6.18	0.382258	145 -- 152	1 -- 8	mnm(5)-s(2)U34-tRNA synthesis 2-thiolation protein		_____________144______153\n_____________\|________\|\n5'-GCU...GCAGA________GCCGC...GCG-3'\n______________UGCCUUAC\n______________\|:\|\|:\|\|\|\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	146 -- 152	1 -- 7	-9.97017 kcal/mol	1.6972 kcal/mol	2.11603 kcal/mol	144 153@LB@ \| \|@LB@5'-GCU...GCAGA GCCGC...GCG-3'@LB@ UGCCUUAC@LB@ \|:\|\|:\|\|\|@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -6.18 kcal/mol@LB@Hybridization Energy -9.97017 kcal/mol@LB@Unfolding Energy - mRNA 1.6972 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 145 -- 152@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 146 -- 152@LB@Position Seed - sRNA 1 -- 7@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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