Input and runtime details for job 6860187 (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 6860187 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:33 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:58 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 01:36:19 CET 2018
	Post-Processing Finished		@ Sat Feb 17 01:36:26 CET 2018
	Job Completed		@ Sat Feb 17 01:36:50 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6860187&toolName=CopraRNA ( 30 days expiry )

Description of the job

SgrS

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
123	0.01344	0.3575	b2615	nadK	-10.03	0.271821	99 -- 122	57 -- 77	NAD kinase	_____________98____________123\n_____________\|_____________\|\n5'-CUC...CCCAC________AC___ACUGA...AAG-3'\n______________GGCACCCC__UGC\n______________\|\|\|\|\|\|\|\|__\|\|\|\n______________CCGUGGGG__ACG\n3'-UUU...GUACC________GA___AAGUAG-5'\n_____________\|_____________\|\n_____________78____________56\n	245 -- 251	12 -- 18	-21.986 kcal/mol	5.26387 kcal/mol	8.16826 kcal/mol	98 123@LB@ \| \|@LB@5'-CUC...CCCAC AC ACUGA...AAG-3'@LB@ GGCACCCC UGC@LB@ \|\|\|\|\|\|\|\| \|\|\|@LB@ CCGUGGGG ACG@LB@3'-UUU...GUACC GA AAGUAG-5'@LB@ \| \|@LB@ 78 56@LB@@LB@@LB@Energy -10.03 kcal/mol@LB@Hybridization Energy -21.986 kcal/mol@LB@Unfolding Energy - mRNA 5.26387 kcal/mol@LB@Unfolding Energy - sRNA 8.16826 kcal/mol@LB@@LB@Position - mRNA 99 -- 122@LB@Position - sRNA 57 -- 77@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 12 -- 18@LB@
168	0.01937	0.3812	b4354	yjiY	-11.43	0.145336	99 -- 125	132 -- 159	putative transporter	_____________98__________________________________________________126\n_____________\|___________________________________________________\|\n5'-CUU...UACCU_____UACG_______AACUCU_____CA______A_______A_______AUUUA...ACA-3'\n______________UACUU____CGCGCGU______GGCAA__UC_ACU__CAGGAU_GCGGUCA\n______________\|\|\|\|:____\|:\|:\|:\|______\|\|\|\|\|__\|\|_\|\|\|__\|\|\|:\|\|_\|\|\|\|\|\|\|\n______________AUGAG____GUGUGUA______CCGUU__AG_UGA__GUCUUA_CGCCAGU\n3'-UUU...UGGUU_____UCA________CUACGU_____C___U___AA______A_______AGGGU...UAG-5'\n_____________\|___________________________________________________\|\n_____________160_________________________________________________131\n	119 -- 125	132 -- 138	-39.8751 kcal/mol	13.2469 kcal/mol	12.8104 kcal/mol	98 126@LB@ \| \|@LB@5'-CUU...UACCU UACG AACUCU CA A A AUUUA...ACA-3'@LB@ UACUU CGCGCGU GGCAA UC ACU CAGGAU GCGGUCA@LB@ \|\|\|\|: \|:\|:\|:\| \|\|\|\|\| \|\| \|\|\| \|\|\|:\|\| \|\|\|\|\|\|\|@LB@ AUGAG GUGUGUA CCGUU AG UGA GUCUUA CGCCAGU@LB@3'-UUU...UGGUU UCA CUACGU C U AA A AGGGU...UAG-5'@LB@ \| \|@LB@ 160 131@LB@@LB@@LB@Energy -11.43 kcal/mol@LB@Hybridization Energy -39.8751 kcal/mol@LB@Unfolding Energy - mRNA 13.2469 kcal/mol@LB@Unfolding Energy - sRNA 12.8104 kcal/mol@LB@@LB@Position - mRNA 99 -- 125@LB@Position - sRNA 132 -- 159@LB@Position Seed - mRNA 119 -- 125@LB@Position Seed - sRNA 132 -- 138@LB@
125	0.01377	0.3575	b2827	thyA	-14.98	0.027366	100 -- 109	16 -- 25	thymidylate synthetase	_____________99_____________________110\n_____________\|______________________\|\n5'-CAG...AAACA________A_____________AAAAG...AGA-3'\n______________GUAUUUAG__AC___UGAUGCA\n______________:\|\|:\|:\|\|__\|\|___\|\|\|\|\|\|\|\n______________UAUGAGUC__UG___ACUACGU\n3'-UUU...GUGGU________AG__UGU_______CCGUU...UAG-5'\n_____________\|______________________\|\n_____________26_____________________15\n	220 -- 226	160 -- 166	-15.3976 kcal/mol	3.04146 kcal/mol	4.80633 kcal/mol	99 110@LB@ \| \|@LB@5'-CAG...AAACA A AAAAG...AGA-3'@LB@ GUAUUUAG AC UGAUGCA@LB@ :\|\|:\|:\|\| \|\| \|\|\|\|\|\|\|@LB@ UAUGAGUC UG ACUACGU@LB@3'-UUU...GUGGU AG UGU CCGUU...UAG-5'@LB@ \| \|@LB@ 26 15@LB@@LB@@LB@Energy -14.98 kcal/mol@LB@Hybridization Energy -15.3976 kcal/mol@LB@Unfolding Energy - mRNA 3.04146 kcal/mol@LB@Unfolding Energy - sRNA 4.80633 kcal/mol@LB@@LB@Position - mRNA 100 -- 109@LB@Position - sRNA 16 -- 25@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 160 -- 166@LB@
126	0.01383	0.3575	b1843	yobB	-8.48	0.503741	101 -- 118	168 -- 185	C-N hydrolase family protein	_____________100____________119\n_____________\|______________\|\n5'-CCU...AACUU____AG________UUUCU...CCA-3'\n______________AUAC__AGUUACAC\n______________\|\|\|\|__\|\|\|:\|\|\|\|\n______________UAUG__UCAGUGUG\n3'-UUU...GUGGU____AG________UACUA...UAG-5'\n_____________\|______________\|\n_____________186____________167\n	112 -- 118	168 -- 174	-13.9608 kcal/mol	3.09724 kcal/mol	0.286881 kcal/mol	100 119@LB@ \| \|@LB@5'-CCU...AACUU AG UUUCU...CCA-3'@LB@ AUAC AGUUACAC@LB@ \|\|\|\| \|\|\|:\|\|\|\|@LB@ UAUG UCAGUGUG@LB@3'-UUU...GUGGU AG UACUA...UAG-5'@LB@ \| \|@LB@ 186 167@LB@@LB@@LB@Energy -8.48 kcal/mol@LB@Hybridization Energy -13.9608 kcal/mol@LB@Unfolding Energy - mRNA 3.09724 kcal/mol@LB@Unfolding Energy - sRNA 0.286881 kcal/mol@LB@@LB@Position - mRNA 101 -- 118@LB@Position - sRNA 168 -- 185@LB@Position Seed - mRNA 112 -- 118@LB@Position Seed - sRNA 168 -- 174@LB@
146	0.01559	0.358	b4394	yjjX	-8.60	0.483218	101 -- 114	123 -- 137	non-canonical purine NTP phosphatase ITPase/XTPase	_____________100__________________________________115\n_____________\|____________________________________\|\n5'-UGC...AAUCC______A______________UC________UU___CGAGA...CAU-3'\n______________CGCUAA_AUUCAG__GC_CAU__UGCAGGCA__UCA\n______________\|:\|:\|\|_\|:\|\|\|\|__:\|_\|\|\|__\|\|\|\|\|\|\|\|__\|\|\|\n______________GUGGUU_UGAGUC__UG_GUA__ACGUCCGU__AGU\n3'-UUU...AAAAU______A______AG__U___CU________UC___UGAAA...UAG-5'\n_____________\|____________________________________\|\n_____________138__________________________________122\n	254 -- 260	156 -- 162	-32.2061 kcal/mol	8.98762 kcal/mol	12.5635 kcal/mol	100 115@LB@ \| \|@LB@5'-UGC...AAUCC A UC UU CGAGA...CAU-3'@LB@ CGCUAA AUUCAG GC CAU UGCAGGCA UCA@LB@ \|:\|:\|\| \|:\|\|\|\| :\| \|\|\| \|\|\|\|\|\|\|\| \|\|\|@LB@ GUGGUU UGAGUC UG GUA ACGUCCGU AGU@LB@3'-UUU...AAAAU A AG U CU UC UGAAA...UAG-5'@LB@ \| \|@LB@ 138 122@LB@@LB@@LB@Energy -8.60 kcal/mol@LB@Hybridization Energy -32.2061 kcal/mol@LB@Unfolding Energy - mRNA 8.98762 kcal/mol@LB@Unfolding Energy - sRNA 12.5635 kcal/mol@LB@@LB@Position - mRNA 101 -- 114@LB@Position - sRNA 123 -- 137@LB@Position Seed - mRNA 254 -- 260@LB@Position Seed - sRNA 156 -- 162@LB@
179	0.02059	0.3833	b2535	csiE	-10.55	0.216292	103 -- 142	58 -- 90	stationary phase inducible protein	_____________102___________143\n_____________\|_____________\|\n5'-GCA...GAUUA__________C__CAUUU...UGG-3'\n______________GCAUUCCCUU_GC\n______________\|\|\|::\|\|\|\|\|_\|\|\n______________CGUGGGGGAA_CG\n3'-UUU...UACCC_____________AAGUAG-5'\n_____________\|_____________\|\n_____________91____________57\n	133 -- 139	9 -- 15	-16.9052 kcal/mol	2.85301 kcal/mol	6.64496 kcal/mol	102 143@LB@ \| \|@LB@5'-GCA...GAUUA C CAUUU...UGG-3'@LB@ GCAUUCCCUU GC@LB@ \|\|\|::\|\|\|\|\| \|\|@LB@ CGUGGGGGAA CG@LB@3'-UUU...UACCC AAGUAG-5'@LB@ \| \|@LB@ 91 57@LB@@LB@@LB@Energy -10.55 kcal/mol@LB@Hybridization Energy -16.9052 kcal/mol@LB@Unfolding Energy - mRNA 2.85301 kcal/mol@LB@Unfolding Energy - sRNA 6.64496 kcal/mol@LB@@LB@Position - mRNA 103 -- 142@LB@Position - sRNA 58 -- 90@LB@Position Seed - mRNA 133 -- 139@LB@Position Seed - sRNA 9 -- 15@LB@
99	0.01084	0.3575	b0872	hcr	-12.58	0.084706	106 -- 121	192 -- 205	HCP oxidoreductase NADH-dependent	_____________105______________122\n_____________\|________________\|\n5'-UCC...CAGAC__________U_C___ACGAG...AUU-3'\n______________CUGCUGGCGG_G_UGA\n______________\|\|\|\|\|\|\|\|\|\|_\|_\|\|\|\n______________GACGACCGCC_C_ACU\n3'-UUU...UAUUA________________AAAAU...UAG-5'\n_____________\|________________\|\n_____________206______________191\n	109 -- 115	196 -- 202	-24.2797 kcal/mol	6.55023 kcal/mol	9.06563 kcal/mol	105 122@LB@ \| \|@LB@5'-UCC...CAGAC U C ACGAG...AUU-3'@LB@ CUGCUGGCGG G UGA@LB@ \|\|\|\|\|\|\|\|\|\| \| \|\|\|@LB@ GACGACCGCC C ACU@LB@3'-UUU...UAUUA AAAAU...UAG-5'@LB@ \| \|@LB@ 206 191@LB@@LB@@LB@Energy -12.58 kcal/mol@LB@Hybridization Energy -24.2797 kcal/mol@LB@Unfolding Energy - mRNA 6.55023 kcal/mol@LB@Unfolding Energy - sRNA 9.06563 kcal/mol@LB@@LB@Position - mRNA 106 -- 121@LB@Position - sRNA 192 -- 205@LB@Position Seed - mRNA 109 -- 115@LB@Position Seed - sRNA 196 -- 202@LB@
137	0.01486	0.3575	b3967	murI	-16.98	0.010727	107 -- 167	42 -- 96	glutamate racemase	_____________106__________________________168\n_____________\|____________________________\|\n5'-GUU...GACUG________ACU_____________G___UCGCU...GGU-3'\n______________GGGU_AUU___UAUCAGUAUUUAG_CAC\n______________\|\|\|\|_\|\|\|___:\|:\|\|:\|\|:\|:\|\|_\|\|\|\n______________CCCA_UAA___GUGGUUAUGAGUC_GUG\n3'-UUU...GACCG____C___AAU_____________A___UGUAC...UAG-5'\n_____________\|____________________________\|\n_____________97___________________________41\n	35 -- 41	174 -- 180	-22.1424 kcal/mol	5.45848 kcal/mol	5.03792 kcal/mol	106 168@LB@ \| \|@LB@5'-GUU...GACUG ACU G UCGCU...GGU-3'@LB@ GGGU AUU UAUCAGUAUUUAG CAC@LB@ \|\|\|\| \|\|\| :\|:\|\|:\|\|:\|:\|\| \|\|\|@LB@ CCCA UAA GUGGUUAUGAGUC GUG@LB@3'-UUU...GACCG C AAU A UGUAC...UAG-5'@LB@ \| \|@LB@ 97 41@LB@@LB@@LB@Energy -16.98 kcal/mol@LB@Hybridization Energy -22.1424 kcal/mol@LB@Unfolding Energy - mRNA 5.45848 kcal/mol@LB@Unfolding Energy - sRNA 5.03792 kcal/mol@LB@@LB@Position - mRNA 107 -- 167@LB@Position - sRNA 42 -- 96@LB@Position Seed - mRNA 35 -- 41@LB@Position Seed - sRNA 174 -- 180@LB@
23	0.00185	0.2633	b3492	yhiN	-11.85	0.119629	108 -- 154	124 -- 161	putative oxidoreductase	_____________107_______________________________________155\n_____________\|_________________________________________\|\n5'-CGG...GGAAA_____G______U____AUAG____________________AUGUU...AUA-3'\n______________GGUUU_AUGCCA_UAUU_____GCGC_UGGUGC_GGCGGGU\n______________\|:\|\|\|_\|::\|\|\|_\|\|:\|_____:\|:\|_\|\|:\|\|\|_\|\|\|::\|\|\n______________CUAAA_UGUGGU_AUGA_____UGUG_ACUACG_CCGUUCA\n3'-UUU...GCCCA_____A______U____GUCAG____U______U_______GUUGA...UAG-5'\n_____________\|_________________________________________\|\n_____________162_______________________________________123\n	239 -- 245	153 -- 159	-35.0652 kcal/mol	11.4478 kcal/mol	11.9045 kcal/mol	107 155@LB@ \| \|@LB@5'-CGG...GGAAA G U AUAG AUGUU...AUA-3'@LB@ GGUUU AUGCCA UAUU GCGC UGGUGC GGCGGGU@LB@ \|:\|\|\| \|::\|\|\| \|\|:\| :\|:\| \|\|:\|\|\| \|\|\|::\|\|@LB@ CUAAA UGUGGU AUGA UGUG ACUACG CCGUUCA@LB@3'-UUU...GCCCA A U GUCAG U U GUUGA...UAG-5'@LB@ \| \|@LB@ 162 123@LB@@LB@@LB@Energy -11.85 kcal/mol@LB@Hybridization Energy -35.0652 kcal/mol@LB@Unfolding Energy - mRNA 11.4478 kcal/mol@LB@Unfolding Energy - sRNA 11.9045 kcal/mol@LB@@LB@Position - mRNA 108 -- 154@LB@Position - sRNA 124 -- 161@LB@Position Seed - mRNA 239 -- 245@LB@Position Seed - sRNA 153 -- 159@LB@
13	0.0007116	0.1842	b3052	hldE	-13.53	0.054228	111 -- 134	141 -- 169	heptose 7-phosphate kinase and heptose 1-phosphate adenyltransferase	_____________110______________135\n_____________\|________________\|\n5'-GCG...CGUGA________________CUGGC...CGC-3'\n______________AC_UGGUGCGGGCAAG\n______________\|\|_\|\|:\|\|\|:\|\|\|\|\|\|\n______________UG_ACUACGUCCGUUC\n3'-UUU...CAGUG__U_____________AGUUG...UAG-5'\n_____________\|________________\|\n_____________170______________140\n	119 -- 125	154 -- 160	-22.7709 kcal/mol	5.4675 kcal/mol	7.07904 kcal/mol	110 135@LB@ \| \|@LB@5'-GCG...CGUGA CUGGC...CGC-3'@LB@ AC UGGUGCGGGCAAG@LB@ \|\| \|\|:\|\|\|:\|\|\|\|\|\|@LB@ UG ACUACGUCCGUUC@LB@3'-UUU...CAGUG U AGUUG...UAG-5'@LB@ \| \|@LB@ 170 140@LB@@LB@@LB@Energy -13.53 kcal/mol@LB@Hybridization Energy -22.7709 kcal/mol@LB@Unfolding Energy - mRNA 5.4675 kcal/mol@LB@Unfolding Energy - sRNA 7.07904 kcal/mol@LB@@LB@Position - mRNA 111 -- 134@LB@Position - sRNA 141 -- 169@LB@Position Seed - mRNA 119 -- 125@LB@Position Seed - sRNA 154 -- 160@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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