Input and runtime details for job 1786318 (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 1786318 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:20:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:20:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:01:46 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:01:53 CET 2018
	Job Completed		@ Fri Feb 16 22:02:22 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1786318&toolName=CopraRNA ( 30 days expiry )

Description of the job

ArcZ

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
189	0.01136	0.2116	b3413	gntX	-9.78	0.152759	211 -- 235	52 -- 76	DNA catabolic protein	_____________210_______________________236\n_____________\|_________________________\|\n5'-CCC...AACAG_______AUU__GC_____A_____AAUGC...AUA-3'\n______________UACCGGG___AU__UGGCU_UGCCG\n______________:\|\|\|:\|\|___\|\|__\|\|\|\|\|_:\|\|\|\|\n______________GUGGUCC___UA__ACCGA_GCGGC\n3'-UUU...CGGUU_______CUU__GA_____C_____AUUUA...GUG-5'\n_____________\|_________________________\|\n_____________77________________________51\n	211 -- 217	70 -- 76	-26.9968 kcal/mol	7.94838 kcal/mol	9.26585 kcal/mol	210 236@LB@ \| \|@LB@5'-CCC...AACAG AUU GC A AAUGC...AUA-3'@LB@ UACCGGG AU UGGCU UGCCG@LB@ :\|\|\|:\|\| \|\| \|\|\|\|\| :\|\|\|\|@LB@ GUGGUCC UA ACCGA GCGGC@LB@3'-UUU...CGGUU CUU GA C AUUUA...GUG-5'@LB@ \| \|@LB@ 77 51@LB@@LB@@LB@Energy -9.78 kcal/mol@LB@Hybridization Energy -26.9968 kcal/mol@LB@Unfolding Energy - mRNA 7.94838 kcal/mol@LB@Unfolding Energy - sRNA 9.26585 kcal/mol@LB@@LB@Position - mRNA 211 -- 235@LB@Position - sRNA 52 -- 76@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 70 -- 76@LB@
60	0.003031	0.1727	b3432	glgB	-10.57	0.108575	114 -- 123	51 -- 60	1 4-alpha-glucan branching enzyme	_____________113________124\n_____________\|__________\|\n5'-CAU...AGAGU__________UCAGG...GAC-3'\n______________GCUGCGCCGU\n______________\|\|\|\|\|\|\|\|\|\|\n______________CGACGCGGCA\n3'-UUU...AGAAC__________UUUAA...GUG-5'\n_____________\|__________\|\n_____________61_________50\n	117 -- 123	51 -- 57	-20.705 kcal/mol	5.26394 kcal/mol	4.87294 kcal/mol	113 124@LB@ \| \|@LB@5'-CAU...AGAGU UCAGG...GAC-3'@LB@ GCUGCGCCGU@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ CGACGCGGCA@LB@3'-UUU...AGAAC UUUAA...GUG-5'@LB@ \| \|@LB@ 61 50@LB@@LB@@LB@Energy -10.57 kcal/mol@LB@Hybridization Energy -20.705 kcal/mol@LB@Unfolding Energy - mRNA 5.26394 kcal/mol@LB@Unfolding Energy - sRNA 4.87294 kcal/mol@LB@@LB@Position - mRNA 114 -- 123@LB@Position - sRNA 51 -- 60@LB@Position Seed - mRNA 117 -- 123@LB@Position Seed - sRNA 51 -- 57@LB@
107	0.005754	0.1855	b3447	ggt	-8.41	0.270031	252 -- 270	52 -- 70	gamma-glutamyltranspeptidase	_____________251_________________271\n_____________\|___________________\|\n5'-GUU...UCUCA_______GUUUUA______CCGCC...CGU-3'\n______________GGAAGUU______GCGCCG\n______________\|\|\|\|:\|:______\|\|\|\|\|\|\n______________CCUUUAG______CGCGGC\n3'-UUU...UGGUC_______AACCGA______AUUUA...GUG-5'\n_____________\|___________________\|\n_____________71__________________51\n	252 -- 258	64 -- 70	-19.4063 kcal/mol	4.14766 kcal/mol	6.84683 kcal/mol	251 271@LB@ \| \|@LB@5'-GUU...UCUCA GUUUUA CCGCC...CGU-3'@LB@ GGAAGUU GCGCCG@LB@ \|\|\|\|:\|: \|\|\|\|\|\|@LB@ CCUUUAG CGCGGC@LB@3'-UUU...UGGUC AACCGA AUUUA...GUG-5'@LB@ \| \|@LB@ 71 51@LB@@LB@@LB@Energy -8.41 kcal/mol@LB@Hybridization Energy -19.4063 kcal/mol@LB@Unfolding Energy - mRNA 4.14766 kcal/mol@LB@Unfolding Energy - sRNA 6.84683 kcal/mol@LB@@LB@Position - mRNA 252 -- 270@LB@Position - sRNA 52 -- 70@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 64 -- 70@LB@
49	0.00252	0.1727	b3452	ugpA	-14.40	0.019328	59 -- 78	52 -- 70	sn-glycerol-3-phosphate ABC transporter permease	_____________58___________________79\n_____________\|____________________\|\n5'-GAG...AGCGU_______AGUU_________CUUUG...CGG-3'\n______________GGAAAUC____GCUGCGCCG\n______________\|\|\|\|\|\|\|____\|\|\|\|\|\|\|\|\|\n______________CCUUUAG____CGACGCGGC\n3'-UUU...UGGUC_______AAC__________AUUUA...GUG-5'\n_____________\|____________________\|\n_____________71___________________51\n	72 -- 78	52 -- 58	-27.9409 kcal/mol	6.69662 kcal/mol	6.84683 kcal/mol	58 79@LB@ \| \|@LB@5'-GAG...AGCGU AGUU CUUUG...CGG-3'@LB@ GGAAAUC GCUGCGCCG@LB@ \|\|\|\|\|\|\| \|\|\|\|\|\|\|\|\|@LB@ CCUUUAG CGACGCGGC@LB@3'-UUU...UGGUC AAC AUUUA...GUG-5'@LB@ \| \|@LB@ 71 51@LB@@LB@@LB@Energy -14.40 kcal/mol@LB@Hybridization Energy -27.9409 kcal/mol@LB@Unfolding Energy - mRNA 6.69662 kcal/mol@LB@Unfolding Energy - sRNA 6.84683 kcal/mol@LB@@LB@Position - mRNA 59 -- 78@LB@Position - sRNA 52 -- 70@LB@Position Seed - mRNA 72 -- 78@LB@Position Seed - sRNA 52 -- 58@LB@
194	0.01194	0.2159	b3454	livF	-10.01	0.138607	25 -- 47	72 -- 86	branched-chain amino acid ABC transporter ATPase	_____________24______________________48\n_____________\|_______________________\|\n5'-AGA...GCCGA_______AAUCAUCA________CUAUC...UUG-3'\n______________ACUGCGC________CAACACCA\n______________\|\|\|\|\|\|\|________\|\|\|\|\|\|\|\|\n______________UGACGCG________GUUGUGGU\n3'-UUU...GCUUA_______________________CCCUU...GUG-5'\n_____________\|_______________________\|\n_____________87______________________71\n	41 -- 47	72 -- 78	-22.1496 kcal/mol	4.90616 kcal/mol	7.23529 kcal/mol	24 48@LB@ \| \|@LB@5'-AGA...GCCGA AAUCAUCA CUAUC...UUG-3'@LB@ ACUGCGC CAACACCA@LB@ \|\|\|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ UGACGCG GUUGUGGU@LB@3'-UUU...GCUUA CCCUU...GUG-5'@LB@ \| \|@LB@ 87 71@LB@@LB@@LB@Energy -10.01 kcal/mol@LB@Hybridization Energy -22.1496 kcal/mol@LB@Unfolding Energy - mRNA 4.90616 kcal/mol@LB@Unfolding Energy - sRNA 7.23529 kcal/mol@LB@@LB@Position - mRNA 25 -- 47@LB@Position - sRNA 72 -- 86@LB@Position Seed - mRNA 41 -- 47@LB@Position Seed - sRNA 72 -- 78@LB@
142	0.00825	0.2033	b3457	livH	-8.25	0.287512	56 -- 64	3 -- 11	branched-chain amino acid ABC transporter permease	_____________55________65\n_____________\|_________\|\n5'-GAU...CGUGA_________UGAAC...ACG-3'\n______________UUGGGCCGC\n______________\|::\|\|\|\|\|\|\n______________AGUCCGGCG\n3'-UUU...CAAAA_________UG-5'\n_____________\|_________\|\n_____________12________2\n	58 -- 64	3 -- 9	-16.0849 kcal/mol	2.23282 kcal/mol	5.54194 kcal/mol	55 65@LB@ \| \|@LB@5'-GAU...CGUGA UGAAC...ACG-3'@LB@ UUGGGCCGC@LB@ \|::\|\|\|\|\|\|@LB@ AGUCCGGCG@LB@3'-UUU...CAAAA UG-5'@LB@ \| \|@LB@ 12 2@LB@@LB@@LB@Energy -8.25 kcal/mol@LB@Hybridization Energy -16.0849 kcal/mol@LB@Unfolding Energy - mRNA 2.23282 kcal/mol@LB@Unfolding Energy - sRNA 5.54194 kcal/mol@LB@@LB@Position - mRNA 56 -- 64@LB@Position - sRNA 3 -- 11@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 3 -- 9@LB@
153	0.009069	0.2059	b3529	yhjK	-8.15	0.299018	186 -- 212	47 -- 74	cyclic-di-GMP phosphodiesterase	_____________185__________________________213\n_____________\|____________________________\|\n5'-AGC...GAUUU_________GACAAU_____________CGCUC...AUC-3'\n______________CCGGGGGGA______UUGCG_CGUAAGU\n______________\|\|:\|\|\|::\|______:\|\|\|\|_\|\|\|\|\|:\|\n______________GGUCCCUUU______GACGC_GCAUUUA\n3'-UUU...GUUGU_________AGAACC_____G_______AUAAU...GUG-5'\n_____________\|____________________________\|\n_____________75___________________________46\n	187 -- 193	67 -- 73	-27.1977 kcal/mol	10.2409 kcal/mol	8.80319 kcal/mol	185 213@LB@ \| \|@LB@5'-AGC...GAUUU GACAAU CGCUC...AUC-3'@LB@ CCGGGGGGA UUGCG CGUAAGU@LB@ \|\|:\|\|\|::\| :\|\|\|\| \|\|\|\|\|:\|@LB@ GGUCCCUUU GACGC GCAUUUA@LB@3'-UUU...GUUGU AGAACC G AUAAU...GUG-5'@LB@ \| \|@LB@ 75 46@LB@@LB@@LB@Energy -8.15 kcal/mol@LB@Hybridization Energy -27.1977 kcal/mol@LB@Unfolding Energy - mRNA 10.2409 kcal/mol@LB@Unfolding Energy - sRNA 8.80319 kcal/mol@LB@@LB@Position - mRNA 186 -- 212@LB@Position - sRNA 47 -- 74@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 67 -- 73@LB@
73	0.003782	0.1804	b3560	glyQ	-10.80	0.098141	7 -- 31	51 -- 74	glycine tRNA synthetase alpha subunit	_____________6__________________________32\n_____________\|__________________________\|\n_____5'-ACAGUU____________A__AAA_____G__UAUAC...UGG-3'\n______________CCAGGGAAG_CU_UG___UGCGC_GU\n______________\|\|\|\|\|\|\|\|:_\|\|_\|\|___\|\|\|\|\|_\|\|\n______________GGUCCCUUU_GA_AC___ACGCG_CA\n3'-UUU...GUUGU_________A_____CG______G__UUUAA...GUG-5'\n_____________\|__________________________\|\n_____________75_________________________50\n	9 -- 15	66 -- 72	-27.2651 kcal/mol	7.67928 kcal/mol	8.78847 kcal/mol	6 32@LB@ \| \|@LB@ 5'-ACAGUU A AAA G UAUAC...UGG-3'@LB@ CCAGGGAAG CU UG UGCGC GU@LB@ \|\|\|\|\|\|\|\|: \|\| \|\| \|\|\|\|\| \|\|@LB@ GGUCCCUUU GA AC ACGCG CA@LB@3'-UUU...GUUGU A CG G UUUAA...GUG-5'@LB@ \| \|@LB@ 75 50@LB@@LB@@LB@Energy -10.80 kcal/mol@LB@Hybridization Energy -27.2651 kcal/mol@LB@Unfolding Energy - mRNA 7.67928 kcal/mol@LB@Unfolding Energy - sRNA 8.78847 kcal/mol@LB@@LB@Position - mRNA 7 -- 31@LB@Position - sRNA 51 -- 74@LB@Position Seed - mRNA 9 -- 15@LB@Position Seed - sRNA 66 -- 72@LB@
158	0.009324	0.2062	b3574	yiaJ	-10.56	0.109206	175 -- 190	70 -- 85	transcriptional repressor for the yiaKLMNO-lyxK-sgbHUE operon	_____________174______________191\n_____________\|________________\|\n5'-CCC...ACACU________C_______ACGCG...UUG-3'\n______________UUGCGCUA_CAUCAGG\n______________:\|\|\|\|\|:\|_\|\|:\|\|\|\|\n______________GACGCGGU_GUGGUCC\n3'-UUU...CUUAU________U_______CUUUA...GUG-5'\n_____________\|________________\|\n_____________86_______________69\n	184 -- 190	70 -- 76	-22.9924 kcal/mol	5.16069 kcal/mol	7.27689 kcal/mol	174 191@LB@ \| \|@LB@5'-CCC...ACACU C ACGCG...UUG-3'@LB@ UUGCGCUA CAUCAGG@LB@ :\|\|\|\|\|:\| \|\|:\|\|\|\|@LB@ GACGCGGU GUGGUCC@LB@3'-UUU...CUUAU U CUUUA...GUG-5'@LB@ \| \|@LB@ 86 69@LB@@LB@@LB@Energy -10.56 kcal/mol@LB@Hybridization Energy -22.9924 kcal/mol@LB@Unfolding Energy - mRNA 5.16069 kcal/mol@LB@Unfolding Energy - sRNA 7.27689 kcal/mol@LB@@LB@Position - mRNA 175 -- 190@LB@Position - sRNA 70 -- 85@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 70 -- 76@LB@
80	0.004451	0.1855	b3578	yiaN	-12.19	0.052777	198 -- 212	52 -- 66	2 3-diketo-L-gulonate TRAP transporter large permease protein	_____________197_____________213\n_____________\|_______________\|\n5'-GGC...GCUUA___A___________AUUUU...UCU-3'\n______________AUC_UGGCUGUGCUG\n______________\|\|\|_\|\|\|\|\|\|:\|\|:\|\n______________UAG_ACCGACGCGGC\n3'-UUU...CCCUU___A___________AUUUA...GUG-5'\n_____________\|_______________\|\n_____________67______________51\n	206 -- 212	52 -- 58	-22.6247 kcal/mol	3.67694 kcal/mol	6.76246 kcal/mol	197 213@LB@ \| \|@LB@5'-GGC...GCUUA A AUUUU...UCU-3'@LB@ AUC UGGCUGUGCUG@LB@ \|\|\| \|\|\|\|\|\|:\|\|:\|@LB@ UAG ACCGACGCGGC@LB@3'-UUU...CCCUU A AUUUA...GUG-5'@LB@ \| \|@LB@ 67 51@LB@@LB@@LB@Energy -12.19 kcal/mol@LB@Hybridization Energy -22.6247 kcal/mol@LB@Unfolding Energy - mRNA 3.67694 kcal/mol@LB@Unfolding Energy - sRNA 6.76246 kcal/mol@LB@@LB@Position - mRNA 198 -- 212@LB@Position - sRNA 52 -- 66@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 52 -- 58@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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