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
9	0.0004314	0.161	b1647	ydhF	-17.39	0.010703	25 -- 48	37 -- 61	putative oxidoreductase	_____________24________________________49\n_____________\|_________________________\|\n5'-UUC...UUUUA___________AA_________G__AAAAA...AGC-3'\n______________ACUGGAA_UAA__UGAGCGAUG_CG\n______________\|\|\|\|\|\|\|_:\|\|__\|\|\|\|\|:\|\|\|_\|\|\n______________UGACCUU_GUU__ACUCGUUAC_GC\n3'-UUU...CAUUA_______C___AC_________A__ACGAA...GCG-5'\n_____________\|_________________________\|\n_____________62________________________36\n	39 -- 45	40 -- 46	-25.2966 kcal/mol	4.60014 kcal/mol	3.30158 kcal/mol	24 49@LB@ \| \|@LB@5'-UUC...UUUUA AA G AAAAA...AGC-3'@LB@ ACUGGAA UAA UGAGCGAUG CG@LB@ \|\|\|\|\|\|\| :\|\| \|\|\|\|\|:\|\|\| \|\|@LB@ UGACCUU GUU ACUCGUUAC GC@LB@3'-UUU...CAUUA C AC A ACGAA...GCG-5'@LB@ \| \|@LB@ 62 36@LB@@LB@@LB@Energy -17.39 kcal/mol@LB@Hybridization Energy -25.2966 kcal/mol@LB@Unfolding Energy - mRNA 4.60014 kcal/mol@LB@Unfolding Energy - sRNA 3.30158 kcal/mol@LB@@LB@Position - mRNA 25 -- 48@LB@Position - sRNA 37 -- 61@LB@Position Seed - mRNA 39 -- 45@LB@Position Seed - sRNA 40 -- 46@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@
154	0.01903	0.4072	b2823	ppdC	-17.47	0.010387	242 -- 260	40 -- 58	putative prepilin peptidase-dependent protein	_____________241_________________261\n_____________\|___________________\|\n5'-ACG...CUGCC___________U_______GUGUU...UCC-3'\n______________GGAGGUAAUGU_GGCGAUG\n______________\|\|\|:\|:\|\|\|\|\|_:\|\|:\|\|\|\n______________CCUUCGUUACA_UCGUUAC\n3'-UUU...UAUGA___________C_______AGCAC...GCG-5'\n_____________\|___________________\|\n_____________59__________________39\n	254 -- 260	40 -- 46	-26.2879 kcal/mol	5.60197 kcal/mol	3.21578 kcal/mol	241 261@LB@ \| \|@LB@5'-ACG...CUGCC U GUGUU...UCC-3'@LB@ GGAGGUAAUGU GGCGAUG@LB@ \|\|\|:\|:\|\|\|\|\| :\|\|:\|\|\|@LB@ CCUUCGUUACA UCGUUAC@LB@3'-UUU...UAUGA C AGCAC...GCG-5'@LB@ \| \|@LB@ 59 39@LB@@LB@@LB@Energy -17.47 kcal/mol@LB@Hybridization Energy -26.2879 kcal/mol@LB@Unfolding Energy - mRNA 5.60197 kcal/mol@LB@Unfolding Energy - sRNA 3.21578 kcal/mol@LB@@LB@Position - mRNA 242 -- 260@LB@Position - sRNA 40 -- 58@LB@Position Seed - mRNA 254 -- 260@LB@Position Seed - sRNA 40 -- 46@LB@
72	0.00645	0.301	b2125	yehT	-9.24	0.246554	1 -- 8	14 -- 21	putative response regulator in two-component system withYehU	______________1_______9\n______________\|_______\|\n___________5'-________GCAAC...GUU-3'\n______________CGUGAGGG\n______________\|\|:\|\|\|\|\|\n______________GCGCUCCC\n3'-UUU...AAGAG________AGAAG...GCG-5'\n_____________\|________\|\n_____________22_______13\n	2 -- 8	14 -- 20	-15.432 kcal/mol	1.85513 kcal/mol	4.33947 kcal/mol	1 9@LB@ \| \|@LB@ 5'- GCAAC...GUU-3'@LB@ CGUGAGGG@LB@ \|\|:\|\|\|\|\|@LB@ GCGCUCCC@LB@3'-UUU...AAGAG AGAAG...GCG-5'@LB@ \| \|@LB@ 22 13@LB@@LB@@LB@Energy -9.24 kcal/mol@LB@Hybridization Energy -15.432 kcal/mol@LB@Unfolding Energy - mRNA 1.85513 kcal/mol@LB@Unfolding Energy - sRNA 4.33947 kcal/mol@LB@@LB@Position - mRNA 1 -- 8@LB@Position - sRNA 14 -- 21@LB@Position Seed - mRNA 2 -- 8@LB@Position Seed - sRNA 14 -- 20@LB@
134	0.01479	0.3709	b1930	yedF	-8.51	0.315187	12 -- 23	55 -- 66	putative TusA family sulfurtransferase	_____________11___________24\n_____________\|____________\|\n5'-ACG...CUGGC___U________UGAUU...AAG-3'\n______________GUA_UACUGGGA\n______________\|\|\|_\|\|\|\|\|\|:\|\n______________CAU_AUGACCUU\n3'-UUU...CGAUU___U________CGUUA...GCG-5'\n_____________\|____________\|\n_____________67___________54\n	17 -- 23	55 -- 61	-12.6769 kcal/mol	2.14533 kcal/mol	2.01956 kcal/mol	11 24@LB@ \| \|@LB@5'-ACG...CUGGC U UGAUU...AAG-3'@LB@ GUA UACUGGGA@LB@ \|\|\| \|\|\|\|\|\|:\|@LB@ CAU AUGACCUU@LB@3'-UUU...CGAUU U CGUUA...GCG-5'@LB@ \| \|@LB@ 67 54@LB@@LB@@LB@Energy -8.51 kcal/mol@LB@Hybridization Energy -12.6769 kcal/mol@LB@Unfolding Energy - mRNA 2.14533 kcal/mol@LB@Unfolding Energy - sRNA 2.01956 kcal/mol@LB@@LB@Position - mRNA 12 -- 23@LB@Position - sRNA 55 -- 66@LB@Position Seed - mRNA 17 -- 23@LB@Position Seed - sRNA 55 -- 61@LB@
81	0.008086	0.3318	b3114	tdcE	-10.99	0.130865	237 -- 290	38 -- 86	pyruvate formate-lyase 4/2-ketobutyrate formate-lyase	_____________236_____________________________________________________291\n_____________\|_______________________________________________________\|\n5'-AGA...UGUAC____A___A____U_____UUAA_____CGG_______AAACGAAAU________CGCGA...UUA-3'\n______________GCCG_CGC_UGGC_UGGCU____AGGUA___ACUGGAA__________UAAUGUC\n______________\|\|\|:_\|:\|_:\|\|\|_\|\|\|\|\|____\|:\|\|\|___\|\|\|\|\|\|\|__________:\|\|\|\|\|\|\n______________CGGU_GUG_GCCG_ACCGA____UUCAU___UGACCUU__________GUUACAG\n_______3'-UUUU____C___G___________________UA________CGUUACACUC_______CACGA...GCG-5'\n_____________\|_______________________________________________________\|\n_____________87______________________________________________________37\n	284 -- 290	38 -- 44	-39.8415 kcal/mol	13.9412 kcal/mol	14.9106 kcal/mol	236 291@LB@ \| \|@LB@5'-AGA...UGUAC A A U UUAA CGG AAACGAAAU CGCGA...UUA-3'@LB@ GCCG CGC UGGC UGGCU AGGUA ACUGGAA UAAUGUC@LB@ \|\|\|: \|:\| :\|\|\| \|\|\|\|\| \|:\|\|\| \|\|\|\|\|\|\| :\|\|\|\|\|\|@LB@ CGGU GUG GCCG ACCGA UUCAU UGACCUU GUUACAG@LB@ 3'-UUUU C G UA CGUUACACUC CACGA...GCG-5'@LB@ \| \|@LB@ 87 37@LB@@LB@@LB@Energy -10.99 kcal/mol@LB@Hybridization Energy -39.8415 kcal/mol@LB@Unfolding Energy - mRNA 13.9412 kcal/mol@LB@Unfolding Energy - sRNA 14.9106 kcal/mol@LB@@LB@Position - mRNA 237 -- 290@LB@Position - sRNA 38 -- 86@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 38 -- 44@LB@
39	0.003417	0.2776	b4469	ygiQ	-15.58	0.022035	190 -- 206	44 -- 60	Radical SAM superfamily protein	_____________189_______________207\n_____________\|_________________\|\n5'-GCG...CAUUU__________AA_____UCUAU...CUC-3'\n______________CUGGAAGCAA__UGAGC\n______________\|\|\|\|\|\|\|\|\|\|__\|\|\|\|\|\n______________GACCUUCGUU__ACUCG\n3'-UUU...AUUAU__________AC_____UUACA...GCG-5'\n_____________\|_________________\|\n_____________61________________43\n	193 -- 199	51 -- 57	-24.5566 kcal/mol	5.6787 kcal/mol	3.2985 kcal/mol	189 207@LB@ \| \|@LB@5'-GCG...CAUUU AA UCUAU...CUC-3'@LB@ CUGGAAGCAA UGAGC@LB@ \|\|\|\|\|\|\|\|\|\| \|\|\|\|\|@LB@ GACCUUCGUU ACUCG@LB@3'-UUU...AUUAU AC UUACA...GCG-5'@LB@ \| \|@LB@ 61 43@LB@@LB@@LB@Energy -15.58 kcal/mol@LB@Hybridization Energy -24.5566 kcal/mol@LB@Unfolding Energy - mRNA 5.6787 kcal/mol@LB@Unfolding Energy - sRNA 3.2985 kcal/mol@LB@@LB@Position - mRNA 190 -- 206@LB@Position - sRNA 44 -- 60@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 51 -- 57@LB@
84	0.008296	0.3318	b0892	rarA	-13.69	0.046473	183 -- 215	37 -- 66	recombination intermediate processing DNA-dependent ATPase	_____________182_________________________________216\n_____________\|___________________________________\|\n5'-CAA...UCAAC____GUA________CCUGA________UC_____CUCGA...AUU-3'\n______________GUAA_____GAGGCA_____GUGAGCAA__UGUCG\n______________\|\|\|\|_____\|\|:\|\|\|_____\|\|\|\|\|\|\|\|__\|\|\|\|\|\n______________CAUU_____CUUCGU_____CACUCGUU__ACAGC\n3'-UUU...CGAUU____AUGAC______UA__________________ACGAA...GCG-5'\n_____________\|___________________________________\|\n_____________67__________________________________36\n	202 -- 208	42 -- 48	-25.9915 kcal/mol	8.99953 kcal/mol	3.30551 kcal/mol	182 216@LB@ \| \|@LB@5'-CAA...UCAAC GUA CCUGA UC CUCGA...AUU-3'@LB@ GUAA GAGGCA GUGAGCAA UGUCG@LB@ \|\|\|\| \|\|:\|\|\| \|\|\|\|\|\|\|\| \|\|\|\|\|@LB@ CAUU CUUCGU CACUCGUU ACAGC@LB@3'-UUU...CGAUU AUGAC UA ACGAA...GCG-5'@LB@ \| \|@LB@ 67 36@LB@@LB@@LB@Energy -13.69 kcal/mol@LB@Hybridization Energy -25.9915 kcal/mol@LB@Unfolding Energy - mRNA 8.99953 kcal/mol@LB@Unfolding Energy - sRNA 3.30551 kcal/mol@LB@@LB@Position - mRNA 183 -- 215@LB@Position - sRNA 37 -- 66@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 42 -- 48@LB@
137	0.01545	0.379	b0881	clpS	-11.92	0.091960	57 -- 82	37 -- 62	regulatory protein for ClpA substrate specificity	_____________56_________________________83\n_____________\|__________________________\|\n5'-GCA...AACGC_____AC__G_______CA_______CUGAU...UCA-3'\n______________UAUUG__AG_AAUGUGA__GAUGUCG\n______________\|\|:\|\|__\|\|_\|\|\|\|\|\|\|__:\|\|\|\|\|\|\n______________AUGAC__UC_UUACACU__UUACAGC\n3'-UUU...UCAUU_____CU__G_______CG_______ACGAA...GCG-5'\n_____________\|__________________________\|\n_____________63_________________________36\n	76 -- 82	37 -- 43	-23.3317 kcal/mol	8.10565 kcal/mol	3.3026 kcal/mol	56 83@LB@ \| \|@LB@5'-GCA...AACGC AC G CA CUGAU...UCA-3'@LB@ UAUUG AG AAUGUGA GAUGUCG@LB@ \|\|:\|\| \|\| \|\|\|\|\|\|\| :\|\|\|\|\|\|@LB@ AUGAC UC UUACACU UUACAGC@LB@3'-UUU...UCAUU CU G CG ACGAA...GCG-5'@LB@ \| \|@LB@ 63 36@LB@@LB@@LB@Energy -11.92 kcal/mol@LB@Hybridization Energy -23.3317 kcal/mol@LB@Unfolding Energy - mRNA 8.10565 kcal/mol@LB@Unfolding Energy - sRNA 3.3026 kcal/mol@LB@@LB@Position - mRNA 57 -- 82@LB@Position - sRNA 37 -- 62@LB@Position Seed - mRNA 76 -- 82@LB@Position Seed - sRNA 37 -- 43@LB@
95	0.009964	0.3393	b3902	rhaD	-16.21	0.017174	243 -- 283	43 -- 89	rhamnulose-1-phosphate aldolase	_____________242_______________________________________________284\n_____________\|_________________________________________________\|\n5'-AGA...UGAUC_______C____GA__C________AAG_____________________CAACG...UGA-3'\n______________AAAGCCA_CACC__CG_CUGGCUGA_____GCUGGGA______UGAGCG\n______________\|\|\|\|\|\|\|_\|\|\|\|__\|\|_\|\|\|\|\|\|:\|_____:\|\|\|\|:\|______\|\|\|\|\|:\n______________UUUCGGU_GUGG__GC_GACCGAUU_____UGACCUU______ACUCGU\n__________3'-U_______C________C________CAUUA_______CGUUAC______UACAG...GCG-5'\n_____________\|_________________________________________________\|\n_____________90________________________________________________42\n	271 -- 277	55 -- 61	-44.1539 kcal/mol	13.0365 kcal/mol	14.9102 kcal/mol	242 284@LB@ \| \|@LB@5'-AGA...UGAUC C GA C AAG CAACG...UGA-3'@LB@ AAAGCCA CACC CG CUGGCUGA GCUGGGA UGAGCG@LB@ \|\|\|\|\|\|\| \|\|\|\| \|\| \|\|\|\|\|\|:\| :\|\|\|\|:\| \|\|\|\|\|:@LB@ UUUCGGU GUGG GC GACCGAUU UGACCUU ACUCGU@LB@ 3'-U C C CAUUA CGUUAC UACAG...GCG-5'@LB@ \| \|@LB@ 90 42@LB@@LB@@LB@Energy -16.21 kcal/mol@LB@Hybridization Energy -44.1539 kcal/mol@LB@Unfolding Energy - mRNA 13.0365 kcal/mol@LB@Unfolding Energy - sRNA 14.9102 kcal/mol@LB@@LB@Position - mRNA 243 -- 283@LB@Position - sRNA 43 -- 89@LB@Position Seed - mRNA 271 -- 277@LB@Position Seed - sRNA 55 -- 61@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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