Input and runtime details for job 1654565 (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 1654565 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:23:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:24:05 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:25:53 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:26:01 CET 2018
	Job Completed		@ Fri Feb 16 22:26:34 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1654565&toolName=CopraRNA ( 30 days expiry )

Description of the job

FnrS

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
56	0.0007477	0.04704	b2777	queE	-11.99	0.034574	197 -- 232	45 -- 77	7-carboxy-7-deazaguanine synthase; queosine biosynthesis	_____________196___________________________________233\n_____________\|_____________________________________\|\n5'-AAU...GAGAA____________CC____UU__C_A__U__UCC____CCUGC...UUG-3'\n______________UGCUAUGCAGUA___CGA__AA_G_GA_GU___AGAC\n______________\|\|\|\|\|\|\|\|\|\|\|\|___\|:\|__\|\|_\|_\|\|_\|\|___\|\|\|\|\n______________ACGAUACGUCAU___GUU__UU_C_CU_CA___UCUG\n3'-UUU...UUAAC____________UAA___UU_______U__U______UUAUA...ACG-5'\n_____________\|_____________________________________\|\n_____________78____________________________________44\n	202 -- 208	66 -- 72	-23.7263 kcal/mol	6.13303 kcal/mol	5.60521 kcal/mol	196 233@LB@ \| \|@LB@5'-AAU...GAGAA CC UU C A U UCC CCUGC...UUG-3'@LB@ UGCUAUGCAGUA CGA AA G GA GU AGAC@LB@ \|\|\|\|\|\|\|\|\|\|\|\| \|:\| \|\| \| \|\| \|\| \|\|\|\|@LB@ ACGAUACGUCAU GUU UU C CU CA UCUG@LB@3'-UUU...UUAAC UAA UU U U UUAUA...ACG-5'@LB@ \| \|@LB@ 78 44@LB@@LB@@LB@Energy -11.99 kcal/mol@LB@Hybridization Energy -23.7263 kcal/mol@LB@Unfolding Energy - mRNA 6.13303 kcal/mol@LB@Unfolding Energy - sRNA 5.60521 kcal/mol@LB@@LB@Position - mRNA 197 -- 232@LB@Position - sRNA 45 -- 77@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 66 -- 72@LB@
72	0.001523	0.07451	b2296	ackA	-11.55	0.045253	141 -- 168	13 -- 36	acetate kinase A and propionate kinase 2	_____________140__________________________169\n_____________\|____________________________\|\n5'-AUU...AUCAU____U____U____G___CCC_______UUUUU...UAG-3'\n______________GCGC_ACGC_CUAU_GCU___UGACGUU\n______________\|\|\|\|_\|\|\|\|_\|:\|\|_\|\|\|___\|\|\|\|\|\|\|\n______________CGCG_UGCG_GGUA_CGA___ACUGCAA\n3'-UUU...UACCU____U_________G_____________CGUAA...ACG-5'\n_____________\|____________________________\|\n_____________37___________________________12\n	162 -- 168	13 -- 19	-30.8127 kcal/mol	7.01729 kcal/mol	12.2493 kcal/mol	140 169@LB@ \| \|@LB@5'-AUU...AUCAU U U G CCC UUUUU...UAG-3'@LB@ GCGC ACGC CUAU GCU UGACGUU@LB@ \|\|\|\| \|\|\|\| \|:\|\| \|\|\| \|\|\|\|\|\|\|@LB@ CGCG UGCG GGUA CGA ACUGCAA@LB@3'-UUU...UACCU U G CGUAA...ACG-5'@LB@ \| \|@LB@ 37 12@LB@@LB@@LB@Energy -11.55 kcal/mol@LB@Hybridization Energy -30.8127 kcal/mol@LB@Unfolding Energy - mRNA 7.01729 kcal/mol@LB@Unfolding Energy - sRNA 12.2493 kcal/mol@LB@@LB@Position - mRNA 141 -- 168@LB@Position - sRNA 13 -- 36@LB@Position Seed - mRNA 162 -- 168@LB@Position Seed - sRNA 13 -- 19@LB@
111	0.003511	0.1114	b0077	ilvI	-11.05	0.061087	188 -- 206	36 -- 52	acetolactate synthase 3 large subunit	_____________187_________________207\n_____________\|___________________\|\n5'-AAA...CAAAC__________GCC______AUGUU...UUU-3'\n______________AGUGAGGCAG___AUGGAG\n______________\|\|\|:\|\|:\|\|:___\|\|\|\|\|\|\n______________UCAUUCUGUU___UACCUC\n3'-UUU...UUCCU__________A________GCGUU...ACG-5'\n_____________\|___________________\|\n_____________53__________________35\n	191 -- 197	43 -- 49	-19.2253 kcal/mol	4.72052 kcal/mol	3.43382 kcal/mol	187 207@LB@ \| \|@LB@5'-AAA...CAAAC GCC AUGUU...UUU-3'@LB@ AGUGAGGCAG AUGGAG@LB@ \|\|\|:\|\|:\|\|: \|\|\|\|\|\|@LB@ UCAUUCUGUU UACCUC@LB@3'-UUU...UUCCU A GCGUU...ACG-5'@LB@ \| \|@LB@ 53 35@LB@@LB@@LB@Energy -11.05 kcal/mol@LB@Hybridization Energy -19.2253 kcal/mol@LB@Unfolding Energy - mRNA 4.72052 kcal/mol@LB@Unfolding Energy - sRNA 3.43382 kcal/mol@LB@@LB@Position - mRNA 188 -- 206@LB@Position - sRNA 36 -- 52@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 43 -- 49@LB@
80	0.001886	0.08273	b3205	yhbJ	-9.88	0.117656	21 -- 27	1 -- 7	adaptor protein for GlmZ/GlmY sRNA decay glucosamine-6-phosphate-regulated; NTPase	_____________20______28\n_____________\|_______\|\n5'-CGG...AAACG_______AUACU...CCG-3'\n______________CACCUGC\n______________\|\|\|\|\|\|\|\n______________GUGGACG\n3'-UUU...CGUAA_______-5'\n_____________\|______\|\n_____________8______1\n	21 -- 27	1 -- 7	-13.6981 kcal/mol	1.48735 kcal/mol	2.34039 kcal/mol	20 28@LB@ \| \|@LB@5'-CGG...AAACG AUACU...CCG-3'@LB@ CACCUGC@LB@ \|\|\|\|\|\|\|@LB@ GUGGACG@LB@3'-UUU...CGUAA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -9.88 kcal/mol@LB@Hybridization Energy -13.6981 kcal/mol@LB@Unfolding Energy - mRNA 1.48735 kcal/mol@LB@Unfolding Energy - sRNA 2.34039 kcal/mol@LB@@LB@Position - mRNA 21 -- 27@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 21 -- 27@LB@Position Seed - sRNA 1 -- 7@LB@
174	0.007207	0.145	b1034	ycdX	-9.36	0.154134	94 -- 120	35 -- 63	alkaline phosphatase	_____________93_____________________________121\n_____________\|______________________________\|\n5'-GGC...CCAGC__________________G___C__C____AAGUC...AAC-3'\n______________UCGAAAAAGGG___GAGA_GGU_UG_GGGC\n______________\|\|:\|\|\|\|\|\|\|:___:\|\|\|_::\|_\|\|_\|:\|\|\n______________AGUUUUUUCCU___UUCU_UUA_AC_CUCG\n3'-UUU...CAUUA___________UCA____G___U_______CGUUG...ACG-5'\n_____________\|______________________________\|\n_____________64_____________________________34\n	98 -- 104	53 -- 59	-21.9855 kcal/mol	6.52956 kcal/mol	6.08557 kcal/mol	93 121@LB@ \| \|@LB@5'-GGC...CCAGC G C C AAGUC...AAC-3'@LB@ UCGAAAAAGGG GAGA GGU UG GGGC@LB@ \|\|:\|\|\|\|\|\|\|: :\|\|\| ::\| \|\| \|:\|\|@LB@ AGUUUUUUCCU UUCU UUA AC CUCG@LB@3'-UUU...CAUUA UCA G U CGUUG...ACG-5'@LB@ \| \|@LB@ 64 34@LB@@LB@@LB@Energy -9.36 kcal/mol@LB@Hybridization Energy -21.9855 kcal/mol@LB@Unfolding Energy - mRNA 6.52956 kcal/mol@LB@Unfolding Energy - sRNA 6.08557 kcal/mol@LB@@LB@Position - mRNA 94 -- 120@LB@Position - sRNA 35 -- 63@LB@Position Seed - mRNA 98 -- 104@LB@Position Seed - sRNA 53 -- 59@LB@
94	0.002802	0.105	b2905	gcvT	-11.27	0.053451	219 -- 244	68 -- 93	aminomethyltransferase tetrahydrofolate-dependent subunit (T protein) of glycine cleavage complex	_____________218_________________________245\n_____________\|___________________________\|\n5'-CUG...CUCCU_____________CACAC___U_____CGCUC...AAA-3'\n______________UUGUACGAA_CAA_____GCU_UGCGG\n______________\|:\|\|\|\|\|\|\|_\|\|\|_____\|\|\|_\|\|\|:\|\n______________AGCAUGCUU_GUU_____CGA_ACGUC\n3'-UUU...GCCGC_________A___AACA____U_____AUUAA...ACG-5'\n_____________\|___________________________\|\n_____________94__________________________67\n	221 -- 227	85 -- 91	-21.376 kcal/mol	5.42013 kcal/mol	4.68758 kcal/mol	218 245@LB@ \| \|@LB@5'-CUG...CUCCU CACAC U CGCUC...AAA-3'@LB@ UUGUACGAA CAA GCU UGCGG@LB@ \|:\|\|\|\|\|\|\| \|\|\| \|\|\| \|\|\|:\|@LB@ AGCAUGCUU GUU CGA ACGUC@LB@3'-UUU...GCCGC A AACA U AUUAA...ACG-5'@LB@ \| \|@LB@ 94 67@LB@@LB@@LB@Energy -11.27 kcal/mol@LB@Hybridization Energy -21.376 kcal/mol@LB@Unfolding Energy - mRNA 5.42013 kcal/mol@LB@Unfolding Energy - sRNA 4.68758 kcal/mol@LB@@LB@Position - mRNA 219 -- 244@LB@Position - sRNA 68 -- 93@LB@Position Seed - mRNA 221 -- 227@LB@Position Seed - sRNA 85 -- 91@LB@
40	0.000329	0.02897	b2513	yfgM	-16.53	0.001389	180 -- 205	37 -- 63	ancillary SecYEG translocon subunit; putative anti-RcsB factor	_____________179_________________________206\n_____________\|___________________________\|\n5'-GGC...CUGGG_____________A_______C_____AAUUU...UUG-3'\n______________UUAAGGAAGG_AG_AGGACAG_GUGGA\n______________\|:\|\|::\|\|\|\|_\|\|_\|:\|\|\|\|:_:\|\|\|\|\n______________AGUUUUUUCC_UC_UUCUGUU_UACCU\n3'-UUU...CAUUA__________U__A_______A_____CGCGU...ACG-5'\n_____________\|___________________________\|\n_____________64__________________________36\n	193 -- 199	43 -- 49	-25.2652 kcal/mol	3.41523 kcal/mol	5.31676 kcal/mol	179 206@LB@ \| \|@LB@5'-GGC...CUGGG A C AAUUU...UUG-3'@LB@ UUAAGGAAGG AG AGGACAG GUGGA@LB@ \|:\|\|::\|\|\|\| \|\| \|:\|\|\|\|: :\|\|\|\|@LB@ AGUUUUUUCC UC UUCUGUU UACCU@LB@3'-UUU...CAUUA U A A CGCGU...ACG-5'@LB@ \| \|@LB@ 64 36@LB@@LB@@LB@Energy -16.53 kcal/mol@LB@Hybridization Energy -25.2652 kcal/mol@LB@Unfolding Energy - mRNA 3.41523 kcal/mol@LB@Unfolding Energy - sRNA 5.31676 kcal/mol@LB@@LB@Position - mRNA 180 -- 205@LB@Position - sRNA 37 -- 63@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 43 -- 49@LB@
164	0.006461	0.1377	b0864	artP	-11.21	0.055481	74 -- 84	70 -- 80	arginine ABC transporter ATPase	_____________73__________85\n_____________\|___________\|\n5'-AAA...UUAUU___________UUAUU...UAC-3'\n______________UUGUGCUAUGU\n______________\|\|\|\|\|\|\|\|\|\|:\n______________AACACGAUACG\n3'-UUU...UAGUU___________UCAUU...ACG-5'\n_____________\|___________\|\n_____________81__________69\n	78 -- 84	70 -- 76	-15.8897 kcal/mol	2.86206 kcal/mol	1.81863 kcal/mol	73 85@LB@ \| \|@LB@5'-AAA...UUAUU UUAUU...UAC-3'@LB@ UUGUGCUAUGU@LB@ \|\|\|\|\|\|\|\|\|\|:@LB@ AACACGAUACG@LB@3'-UUU...UAGUU UCAUU...ACG-5'@LB@ \| \|@LB@ 81 69@LB@@LB@@LB@Energy -11.21 kcal/mol@LB@Hybridization Energy -15.8897 kcal/mol@LB@Unfolding Energy - mRNA 2.86206 kcal/mol@LB@Unfolding Energy - sRNA 1.81863 kcal/mol@LB@@LB@Position - mRNA 74 -- 84@LB@Position - sRNA 70 -- 80@LB@Position Seed - mRNA 78 -- 84@LB@Position Seed - sRNA 70 -- 76@LB@
39	0.0003198	0.02889	b3960	argH	-9.38	0.152930	179 -- 221	28 -- 64	argininosuccinate lyase	_____________178__________________________________________222\n_____________\|____________________________________________\|\n5'-GCA...UGAAU_______U_____AACAG___UAU____CUU_____________UUUAC...AUA-3'\n______________UUCAAAA_AAGGA_____AGU___GGCA___UGGGGCG_GGCGU\n______________\|\|\|\|\|\|\|_\|\|\|\|\|_____\|\|\|___\|:\|\|___\|\|\|:\|\|\|_::\|\|:\n______________AAGUUUU_UUCCU_____UCA___CUGU___ACCUCGC_UUGCG\n3'-UUU...UCAUU_____________________UU_____UAU_______G_____GGUAG...ACG-5'\n_____________\|____________________________________________\|\n_____________65___________________________________________27\n	210 -- 216	34 -- 40	-30.4591 kcal/mol	8.02766 kcal/mol	13.054 kcal/mol	178 222@LB@ \| \|@LB@5'-GCA...UGAAU U AACAG UAU CUU UUUAC...AUA-3'@LB@ UUCAAAA AAGGA AGU GGCA UGGGGCG GGCGU@LB@ \|\|\|\|\|\|\| \|\|\|\|\| \|\|\| \|:\|\| \|\|\|:\|\|\| ::\|\|:@LB@ AAGUUUU UUCCU UCA CUGU ACCUCGC UUGCG@LB@3'-UUU...UCAUU UU UAU G GGUAG...ACG-5'@LB@ \| \|@LB@ 65 27@LB@@LB@@LB@Energy -9.38 kcal/mol@LB@Hybridization Energy -30.4591 kcal/mol@LB@Unfolding Energy - mRNA 8.02766 kcal/mol@LB@Unfolding Energy - sRNA 13.054 kcal/mol@LB@@LB@Position - mRNA 179 -- 221@LB@Position - sRNA 28 -- 64@LB@Position Seed - mRNA 210 -- 216@LB@Position Seed - sRNA 34 -- 40@LB@
112	0.003634	0.1131	b1473	yddG	-8.08	0.286569	177 -- 226	24 -- 55	aromatic amino acid exporter	_____________176________________________________________________227\n_____________\|__________________________________________________\|\n5'-GCG...UUAAC__C___A_______AACA_C____AUGACACGACAAAAA___________AGGGC...CGG-3'\n______________GG_AAG_GAGACAA____G_GAGC_______________GCAACGCUCAU\n______________\|\|_\|\|\|_:\|\|\|\|\|\|____\|_\|\|\|\|_______________\|\|\|\|\|\|\|:\|\|\|\n______________CC_UUC_UUCUGUU____C_CUCG_______________CGUUGCGGGUA\n3'-UUU...UUUUU______A_______AUA_________________________________GCGAA...ACG-5'\n_____________\|__________________________________________________\|\n_____________56_________________________________________________23\n	216 -- 222	28 -- 34	-30.4707 kcal/mol	9.38627 kcal/mol	13.0079 kcal/mol	176 227@LB@ \| \|@LB@5'-GCG...UUAAC C A AACA C AUGACACGACAAAAA AGGGC...CGG-3'@LB@ GG AAG GAGACAA G GAGC GCAACGCUCAU@LB@ \|\| \|\|\| :\|\|\|\|\|\| \| \|\|\|\| \|\|\|\|\|\|\|:\|\|\|@LB@ CC UUC UUCUGUU C CUCG CGUUGCGGGUA@LB@3'-UUU...UUUUU A AUA GCGAA...ACG-5'@LB@ \| \|@LB@ 56 23@LB@@LB@@LB@Energy -8.08 kcal/mol@LB@Hybridization Energy -30.4707 kcal/mol@LB@Unfolding Energy - mRNA 9.38627 kcal/mol@LB@Unfolding Energy - sRNA 13.0079 kcal/mol@LB@@LB@Position - mRNA 177 -- 226@LB@Position - sRNA 24 -- 55@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 28 -- 34@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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