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
89	0.009246	0.3393	b1279	yciS	-12.08	0.086714	189 -- 204	46 -- 61	DUF1049 family inner membrane protein function unknown	_____________188______________205\n_____________\|________________\|\n5'-ACC...ACAUA__G_____________AAUAU...UGU-3'\n______________AC_GGAAGUAAUGUGA\n______________\|\|_\|\|\|\|\|:\|\|\|\|\|\|\|\n______________UG_CCUUCGUUACACU\n3'-UUU...CAUUA__A_____________CGUUA...GCG-5'\n_____________\|________________\|\n_____________62_______________45\n	198 -- 204	46 -- 52	-21.4875 kcal/mol	6.16612 kcal/mol	3.24422 kcal/mol	188 205@LB@ \| \|@LB@5'-ACC...ACAUA G AAUAU...UGU-3'@LB@ AC GGAAGUAAUGUGA@LB@ \|\| \|\|\|\|\|:\|\|\|\|\|\|\|@LB@ UG CCUUCGUUACACU@LB@3'-UUU...CAUUA A CGUUA...GCG-5'@LB@ \| \|@LB@ 62 45@LB@@LB@@LB@Energy -12.08 kcal/mol@LB@Hybridization Energy -21.4875 kcal/mol@LB@Unfolding Energy - mRNA 6.16612 kcal/mol@LB@Unfolding Energy - sRNA 3.24422 kcal/mol@LB@@LB@Position - mRNA 189 -- 204@LB@Position - sRNA 46 -- 61@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 46 -- 52@LB@
59	0.005518	0.2905	b3663	yicN	-20.80	0.002740	224 -- 256	26 -- 61	DUF1198 family protein	_____________223__________________________________257\n_____________\|____________________________________\|\n5'-CUU...GCCAC_____C________UU__G_________________GCUGA...AUC-3'\n______________GCUGG_GGUAGUGU__GU___GUUG_GUUUUCGGGU\n______________:\|\|\|\|_:\|:\|:\|\|\|__\|:___\|\|:\|_\|:\|\|\|\|:\|\|\|\n______________UGACC_UCGUUACA__CG___CAGC_CGAAAGUCCA\n3'-UUU...CAUUA_____U________CU__UUA____A__________AGAGG...GCG-5'\n_____________\|____________________________________\|\n_____________62___________________________________25\n	250 -- 256	26 -- 32	-36.0496 kcal/mol	7.2648 kcal/mol	7.98122 kcal/mol	223 257@LB@ \| \|@LB@5'-CUU...GCCAC C UU G GCUGA...AUC-3'@LB@ GCUGG GGUAGUGU GU GUUG GUUUUCGGGU@LB@ :\|\|\|\| :\|:\|:\|\|\| \|: \|\|:\| \|:\|\|\|\|:\|\|\|@LB@ UGACC UCGUUACA CG CAGC CGAAAGUCCA@LB@3'-UUU...CAUUA U CU UUA A AGAGG...GCG-5'@LB@ \| \|@LB@ 62 25@LB@@LB@@LB@Energy -20.80 kcal/mol@LB@Hybridization Energy -36.0496 kcal/mol@LB@Unfolding Energy - mRNA 7.2648 kcal/mol@LB@Unfolding Energy - sRNA 7.98122 kcal/mol@LB@@LB@Position - mRNA 224 -- 256@LB@Position - sRNA 26 -- 61@LB@Position Seed - mRNA 250 -- 256@LB@Position Seed - sRNA 26 -- 32@LB@
178	0.02201	0.4113	b4176	yjeT	-16.79	0.013635	217 -- 249	54 -- 87	DUF2065 family protein	_____________216_________________________________250\n_____________\|___________________________________\|\n5'-UCA...AAUCU____________CC______U______________GUUUA...CGA-3'\n______________GGCUGGCGCUUG__CUGGUU___UGGUACUGGAAG\n______________:\|\|::\|\|:\|::\|__\|\|\|\|:\|___\|::\|\|\|\|\|\|\|\|\|\n______________UCGGUCGUGGGC__GACCGA___AUUAUGACCUUC\n________3'-UUU____________C_______UUC____________GUUAC...GCG-5'\n_____________\|___________________________________\|\n_____________88__________________________________53\n	243 -- 249	54 -- 60	-41.1583 kcal/mol	10.0538 kcal/mol	14.3172 kcal/mol	216 250@LB@ \| \|@LB@5'-UCA...AAUCU CC U GUUUA...CGA-3'@LB@ GGCUGGCGCUUG CUGGUU UGGUACUGGAAG@LB@ :\|\|::\|\|:\|::\| \|\|\|\|:\| \|::\|\|\|\|\|\|\|\|\|@LB@ UCGGUCGUGGGC GACCGA AUUAUGACCUUC@LB@ 3'-UUU C UUC GUUAC...GCG-5'@LB@ \| \|@LB@ 88 53@LB@@LB@@LB@Energy -16.79 kcal/mol@LB@Hybridization Energy -41.1583 kcal/mol@LB@Unfolding Energy - mRNA 10.0538 kcal/mol@LB@Unfolding Energy - sRNA 14.3172 kcal/mol@LB@@LB@Position - mRNA 217 -- 249@LB@Position - sRNA 54 -- 87@LB@Position Seed - mRNA 243 -- 249@LB@Position Seed - sRNA 54 -- 60@LB@
45	0.00394	0.2905	b4551	yheV	-11.41	0.111890	172 -- 193	40 -- 61	DUF2387 family putative metal-binding protein	_____________171____________________194\n_____________\|______________________\|\n5'-AUC...GGACG_______UG___U_______A_GGUAA...UUG-3'\n______________GCUGGGA__AAU_UGAGUAG_G\n______________:\|\|\|\|:\|__\|\|\|_\|\|\|\|:\|:_\|\n______________UGACCUU__UUA_ACUCGUU_C\n3'-UUU...CAUUA_______CG___C_______A_AGCAC...GCG-5'\n_____________\|______________________\|\n_____________62_____________________39\n	185 -- 191	42 -- 48	-20.0831 kcal/mol	5.37544 kcal/mol	3.30075 kcal/mol	171 194@LB@ \| \|@LB@5'-AUC...GGACG UG U A GGUAA...UUG-3'@LB@ GCUGGGA AAU UGAGUAG G@LB@ :\|\|\|\|:\| \|\|\| \|\|\|\|:\|: \|@LB@ UGACCUU UUA ACUCGUU C@LB@3'-UUU...CAUUA CG C A AGCAC...GCG-5'@LB@ \| \|@LB@ 62 39@LB@@LB@@LB@Energy -11.41 kcal/mol@LB@Hybridization Energy -20.0831 kcal/mol@LB@Unfolding Energy - mRNA 5.37544 kcal/mol@LB@Unfolding Energy - sRNA 3.30075 kcal/mol@LB@@LB@Position - mRNA 172 -- 193@LB@Position - sRNA 40 -- 61@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 42 -- 48@LB@
160	0.02006	0.4072	b1205	ychH	-13.92	0.042333	252 -- 283	22 -- 60	DUF2583 family putative inner membrane protein	_____________251_____________________________________284\n_____________\|_______________________________________\|\n5'-CAA...UGGGU____U____________G_________G__G____A___AAUCC...UAC-3'\n______________CUGG_GGUAAUG___GU___GUCG_GC__U_GGGU_UUC\n______________\|\|\|\|_:\|:\|\|\|\|___\|:___\|\|\|\|_\|\|__\|_:\|\|\|_:\|\|\n______________GACC_UCGUUAC___CG___CAGC_CG__A_UCCA_GAG\n3'-UUU...AUUAU____U_______ACU__UUA____A__AA_G____A___GCGCU...GCG-5'\n_____________\|_______________________________________\|\n_____________61______________________________________21\n	257 -- 263	49 -- 55	-28.0186 kcal/mol	6.10632 kcal/mol	7.98777 kcal/mol	251 284@LB@ \| \|@LB@5'-CAA...UGGGU U G G G A AAUCC...UAC-3'@LB@ CUGG GGUAAUG GU GUCG GC U GGGU UUC@LB@ \|\|\|\| :\|:\|\|\|\| \|: \|\|\|\| \|\| \| :\|\|\| :\|\|@LB@ GACC UCGUUAC CG CAGC CG A UCCA GAG@LB@3'-UUU...AUUAU U ACU UUA A AA G A GCGCU...GCG-5'@LB@ \| \|@LB@ 61 21@LB@@LB@@LB@Energy -13.92 kcal/mol@LB@Hybridization Energy -28.0186 kcal/mol@LB@Unfolding Energy - mRNA 6.10632 kcal/mol@LB@Unfolding Energy - sRNA 7.98777 kcal/mol@LB@@LB@Position - mRNA 252 -- 283@LB@Position - sRNA 22 -- 60@LB@Position Seed - mRNA 257 -- 263@LB@Position Seed - sRNA 49 -- 55@LB@
77	0.00734	0.3134	b1793	yoaF	-12.59	0.071143	233 -- 250	68 -- 86	DUF333 family outer membrane lipoprotein	_____________232_________________251\n_____________\|___________________\|\n5'-GAU...UGCUU___________________UUCAA...UGG-3'\n______________GCUGGU_CCUGGCUGGUUG\n______________\|\|::\|:_\|\|:\|\|\|\|\|\|:\|:\n______________CGGUCG_GGGCCGACCGAU\n_______3'-UUUU______U____________UCAUU...GCG-5'\n_____________\|___________________\|\n_____________87__________________67\n	243 -- 249	69 -- 75	-29.581 kcal/mol	5.32768 kcal/mol	11.6617 kcal/mol	232 251@LB@ \| \|@LB@5'-GAU...UGCUU UUCAA...UGG-3'@LB@ GCUGGU CCUGGCUGGUUG@LB@ \|\|::\|: \|\|:\|\|\|\|\|\|:\|:@LB@ CGGUCG GGGCCGACCGAU@LB@ 3'-UUUU U UCAUU...GCG-5'@LB@ \| \|@LB@ 87 67@LB@@LB@@LB@Energy -12.59 kcal/mol@LB@Hybridization Energy -29.581 kcal/mol@LB@Unfolding Energy - mRNA 5.32768 kcal/mol@LB@Unfolding Energy - sRNA 11.6617 kcal/mol@LB@@LB@Position - mRNA 233 -- 250@LB@Position - sRNA 68 -- 86@LB@Position Seed - mRNA 243 -- 249@LB@Position Seed - sRNA 69 -- 75@LB@
116	0.01242	0.3585	b0468	ybaN	-14.97	0.028033	230 -- 260	44 -- 78	DUF454 family inner membrane protein	_____________229___________________________________261\n_____________\|_____________________________________\|\n5'-GUC...AUUGG_______________________UAC___________GUGGU...UGC-3'\n______________CUGGCUGGC__GGUAGUGCUGGG___GC____UGGGC\n______________\|:\|\|\|\|\|\|\|__:\|\|\|:\|:\|\|\|\|:___\|\|____\|\|:\|\|\n______________GGCCGACCG__UCAUUAUGACCU___CG____ACUCG\n3'-UUU...UCGUG_________AU____________U____UUAC_____UUACA...GCG-5'\n_____________\|_____________________________________\|\n_____________79____________________________________43\n	244 -- 250	56 -- 62	-40.2392 kcal/mol	12.5705 kcal/mol	12.6976 kcal/mol	229 261@LB@ \| \|@LB@5'-GUC...AUUGG UAC GUGGU...UGC-3'@LB@ CUGGCUGGC GGUAGUGCUGGG GC UGGGC@LB@ \|:\|\|\|\|\|\|\| :\|\|\|:\|:\|\|\|\|: \|\| \|\|:\|\|@LB@ GGCCGACCG UCAUUAUGACCU CG ACUCG@LB@3'-UUU...UCGUG AU U UUAC UUACA...GCG-5'@LB@ \| \|@LB@ 79 43@LB@@LB@@LB@Energy -14.97 kcal/mol@LB@Hybridization Energy -40.2392 kcal/mol@LB@Unfolding Energy - mRNA 12.5705 kcal/mol@LB@Unfolding Energy - sRNA 12.6976 kcal/mol@LB@@LB@Position - mRNA 230 -- 260@LB@Position - sRNA 44 -- 78@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 56 -- 62@LB@
93	0.009691	0.3393	b2959	yggL	-10.23	0.172987	12 -- 59	38 -- 83	DUF469 family protein	_____________11_________________________________________________60\n_____________\|__________________________________________________\|\n5'-GUA...CAUAU___GA___A____GAACCUU____________U___CU__A_________UUCUA...CAU-3'\n______________GGC__CCG_CUGG_______AUGC_GGAA_CA_AUG__UG_AGUGAUGUC\n______________:\|\|__\|\|\|_\|\|\|\|_______\|\|:\|_\|\|\|\|_\|\|_\|\|\|__\|\|_\|\|::\|\|\|\|\|\n______________UCG__GGC_GACC_______UAUG_CCUU_GU_UAC__AC_UCGUUACAG\n____3'-UUUUCGG___UG___C____GAUUCAU____A____C____________________CACGA...GCG-5'\n_____________\|__________________________________________________\|\n_____________84_________________________________________________37\n	53 -- 59	38 -- 44	-35.0381 kcal/mol	9.91615 kcal/mol	14.8888 kcal/mol	11 60@LB@ \| \|@LB@5'-GUA...CAUAU GA A GAACCUU U CU A UUCUA...CAU-3'@LB@ GGC CCG CUGG AUGC GGAA CA AUG UG AGUGAUGUC@LB@ :\|\| \|\|\| \|\|\|\| \|\|:\| \|\|\|\| \|\| \|\|\| \|\| \|\|::\|\|\|\|\|@LB@ UCG GGC GACC UAUG CCUU GU UAC AC UCGUUACAG@LB@ 3'-UUUUCGG UG C GAUUCAU A C CACGA...GCG-5'@LB@ \| \|@LB@ 84 37@LB@@LB@@LB@Energy -10.23 kcal/mol@LB@Hybridization Energy -35.0381 kcal/mol@LB@Unfolding Energy - mRNA 9.91615 kcal/mol@LB@Unfolding Energy - sRNA 14.8888 kcal/mol@LB@@LB@Position - mRNA 12 -- 59@LB@Position - sRNA 38 -- 83@LB@Position Seed - mRNA 53 -- 59@LB@Position Seed - sRNA 38 -- 44@LB@
143	0.01687	0.3964	b3103	yhaH	-11.09	0.125996	208 -- 287	3 -- 67	DUF805 family inner membrane protein	_____________207_________________________________________________________________________________288\n_____________\|___________________________________________________________________________________\|\n5'-AUU...GGACU____U_____A_____CUAAAAAAUU___________C____G__G_G_____CGCAAAGAGUACU__AU____A________AACAU...UUA-3'\n______________GGUA___CUG_AAGUA__________AUGUCG_GUUU_CGGG_UC_U_CGCGG_____________GG__GUUU_UUCUGGUC\n______________:\|\|\|___\|\|\|_\|\|\|:\|__________\|\|\|\|\|\|_\|:\|\|_\|:\|\|_\|\|_\|_\|\|\|\|:_____________\|\|__\|\|:\|_\|:\|\|\|:\|\|\n______________UCAU___GAC_UUCGU__________UACAGC_CGAA_GUCC_AG_A_GCGCU_____________CC__CAGA_AGGACUAG\n3'-UUU...CCGAU____UAU___C_____UACACUCGU_______A____A____A____G___________________________________CG-5'\n_____________\|___________________________________________________________________________________\|\n_____________68__________________________________________________________________________________2\n	281 -- 287	3 -- 9	-42.8726 kcal/mol	17.657 kcal/mol	14.1245 kcal/mol	207 288@LB@ \| \|@LB@5'-AUU...GGACU U A CUAAAAAAUU C G G G CGCAAAGAGUACU AU A AACAU...UUA-3'@LB@ GGUA CUG AAGUA AUGUCG GUUU CGGG UC U CGCGG GG GUUU UUCUGGUC@LB@ :\|\|\| \|\|\| \|\|\|:\| \|\|\|\|\|\| \|:\|\| \|:\|\| \|\| \| \|\|\|\|: \|\| \|\|:\| \|:\|\|\|:\|\|@LB@ UCAU GAC UUCGU UACAGC CGAA GUCC AG A GCGCU CC CAGA AGGACUAG@LB@3'-UUU...CCGAU UAU C UACACUCGU A A A G CG-5'@LB@ \| \|@LB@ 68 2@LB@@LB@@LB@Energy -11.09 kcal/mol@LB@Hybridization Energy -42.8726 kcal/mol@LB@Unfolding Energy - mRNA 17.657 kcal/mol@LB@Unfolding Energy - sRNA 14.1245 kcal/mol@LB@@LB@Position - mRNA 208 -- 287@LB@Position - sRNA 3 -- 67@LB@Position Seed - mRNA 281 -- 287@LB@Position Seed - sRNA 3 -- 9@LB@
49	0.004671	0.2905	b3184	yhbE	-14.90	0.028775	284 -- 299	49 -- 64	EamA family inner membrane putative transporter	_____________283______________300\n_____________\|________________\|\n5'-AAG...AAGCA________________G-3'\n______________GGUGCUGGAGGUGAUG\n______________::\|:\|\|\|\|\|:\|::\|\|\|\n______________UUAUGACCUUCGUUAC\n3'-UUU...AUUCA________________ACUCG...GCG-5'\n_____________\|________________\|\n_____________65_______________48\n	293 -- 299	49 -- 55	-22.6177 kcal/mol	4.70237 kcal/mol	3.01036 kcal/mol	283 300@LB@ \| \|@LB@5'-AAG...AAGCA G-3'@LB@ GGUGCUGGAGGUGAUG@LB@ ::\|:\|\|\|\|\|:\|::\|\|\|@LB@ UUAUGACCUUCGUUAC@LB@3'-UUU...AUUCA ACUCG...GCG-5'@LB@ \| \|@LB@ 65 48@LB@@LB@@LB@Energy -14.90 kcal/mol@LB@Hybridization Energy -22.6177 kcal/mol@LB@Unfolding Energy - mRNA 4.70237 kcal/mol@LB@Unfolding Energy - sRNA 3.01036 kcal/mol@LB@@LB@Position - mRNA 284 -- 299@LB@Position - sRNA 49 -- 64@LB@Position Seed - mRNA 293 -- 299@LB@Position Seed - sRNA 49 -- 55@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)

Job resubmission

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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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