Input and runtime details for job 5774122 (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 5774122 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:30:38 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:16:08 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 23:32:42 CET 2018
	Post-Processing Finished		@ Fri Feb 16 23:32:50 CET 2018
	Job Completed		@ Fri Feb 16 23:33:10 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5774122&toolName=CopraRNA ( 30 days expiry )

Description of the job

FsrA

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_000964 Bacillus subtilis subsp. subtilis str. 168

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	Additional homologs
77	0.005688	0.2441	bsu35180	csbA	-19.97	0.002143	87 -- 126	11 -- 50	general stress protein CsbA		_____________86__________________________________________127\n_____________\|___________________________________________\|\n5'-UGA...UGAUU_____________AA_______A___U_U__G___________GAAUG...CAG-3'\n______________GAUUUUGG_CUGA___AGGGGU_UGG_G_AA_UAGAGGG_AGC\n______________\|\|\|:\|\|\|:_\|\|\|\|___\|\|\|\|\|\|_\|\|\|_\|_\|\|_:\|\|\|\|:\|_\|\|\|\n______________CUAGAACU_GACU___UCCCCA_ACC_C_UU_GUCUCUC_UCG\n3'-UUU...AAAGC________A____AUC____________C__________A___AAGAG...AUA-5'\n_____________\|___________________________________________\|\n_____________51__________________________________________10\n	117 -- 123	15 -- 21	-37.9995 kcal/mol	8.07502 kcal/mol	9.95602 kcal/mol	86 127@LB@ \| \|@LB@5'-UGA...UGAUU AA A U U G GAAUG...CAG-3'@LB@ GAUUUUGG CUGA AGGGGU UGG G AA UAGAGGG AGC@LB@ \|\|\|:\|\|\|: \|\|\|\| \|\|\|\|\|\| \|\|\| \| \|\| :\|\|\|\|:\| \|\|\|@LB@ CUAGAACU GACU UCCCCA ACC C UU GUCUCUC UCG@LB@3'-UUU...AAAGC A AUC C A AAGAG...AUA-5'@LB@ \| \|@LB@ 51 10@LB@@LB@@LB@Energy -19.97 kcal/mol@LB@Hybridization Energy -37.9995 kcal/mol@LB@Unfolding Energy - mRNA 8.07502 kcal/mol@LB@Unfolding Energy - sRNA 9.95602 kcal/mol@LB@@LB@Position - mRNA 87 -- 126@LB@Position - sRNA 11 -- 50@LB@Position Seed - mRNA 117 -- 123@LB@Position Seed - sRNA 15 -- 21@LB@
69	0.004753	0.2298	bsu24850	glcK	-6.97	0.496286	33 -- 46	15 -- 29	glucokinase		_____________32______________47\n_____________\|_______________\|\n5'-GCU...UUAUU____A__________CUUGA...UUC-3'\n______________UUGG__GACAGAGAG\n______________\|\|\|\|__:\|\|\|\|\|\|\|\|\n______________AACC__UUGUCUCUC\n3'-UUU...UCCCC____CC_________AUCGA...AUA-5'\n_____________\|_______________\|\n_____________30______________14\n	40 -- 46	15 -- 21	-16.6304 kcal/mol	3.64593 kcal/mol	6.01316 kcal/mol	32 47@LB@ \| \|@LB@5'-GCU...UUAUU A CUUGA...UUC-3'@LB@ UUGG GACAGAGAG@LB@ \|\|\|\| :\|\|\|\|\|\|\|\|@LB@ AACC UUGUCUCUC@LB@3'-UUU...UCCCC CC AUCGA...AUA-5'@LB@ \| \|@LB@ 30 14@LB@@LB@@LB@Energy -6.97 kcal/mol@LB@Hybridization Energy -16.6304 kcal/mol@LB@Unfolding Energy - mRNA 3.64593 kcal/mol@LB@Unfolding Energy - sRNA 6.01316 kcal/mol@LB@@LB@Position - mRNA 33 -- 46@LB@Position - sRNA 15 -- 29@LB@Position Seed - mRNA 40 -- 46@LB@Position Seed - sRNA 15 -- 21@LB@
40	0.001724	0.1438	bsu18440	gltD	-13.77	0.051762	193 -- 208	22 -- 36	glutamate synthase [NADPH] small chain		_____________192______________209\n_____________\|________________\|\n5'-AGA...AGGGG_____AACA_______ACCAA...CUU-3'\n______________AGAGG____UGGGGAA\n______________\|\|\|\|\|____\|\|\|\|\|\|\|\n______________UCUCC____ACCCCUU\n3'-UUU...GACUA_____CCA________GUCUC...AUA-5'\n_____________\|________________\|\n_____________37_______________21\n	202 -- 208	22 -- 28	-17.8722 kcal/mol	3.06294 kcal/mol	1.03819 kcal/mol	192 209@LB@ \| \|@LB@5'-AGA...AGGGG AACA ACCAA...CUU-3'@LB@ AGAGG UGGGGAA@LB@ \|\|\|\|\| \|\|\|\|\|\|\|@LB@ UCUCC ACCCCUU@LB@3'-UUU...GACUA CCA GUCUC...AUA-5'@LB@ \| \|@LB@ 37 21@LB@@LB@@LB@Energy -13.77 kcal/mol@LB@Hybridization Energy -17.8722 kcal/mol@LB@Unfolding Energy - mRNA 3.06294 kcal/mol@LB@Unfolding Energy - sRNA 1.03819 kcal/mol@LB@@LB@Position - mRNA 193 -- 208@LB@Position - sRNA 22 -- 36@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 22 -- 28@LB@
26	0.0005174	0.06638	bsu28170	hemA	-17.53	0.008676	171 -- 186	24 -- 36	glutamyl-tRNA reductase		_____________170______________187\n_____________\|________________\|\n5'-AUG...AAUUA___UU___U_______GUGUA...UGC-3'\n______________AGA__GGG_GUUGGGG\n______________\|\|\|__\|\|\|_\|\|\|\|\|\|\|\n______________UCU__CCC_CAACCCC\n3'-UUU...GACUA________________UUGUC...AUA-5'\n_____________\|________________\|\n_____________37_______________23\n	180 -- 186	24 -- 30	-19.8849 kcal/mol	2.21391 kcal/mol	0.138435 kcal/mol	170 187@LB@ \| \|@LB@5'-AUG...AAUUA UU U GUGUA...UGC-3'@LB@ AGA GGG GUUGGGG@LB@ \|\|\| \|\|\| \|\|\|\|\|\|\|@LB@ UCU CCC CAACCCC@LB@3'-UUU...GACUA UUGUC...AUA-5'@LB@ \| \|@LB@ 37 23@LB@@LB@@LB@Energy -17.53 kcal/mol@LB@Hybridization Energy -19.8849 kcal/mol@LB@Unfolding Energy - mRNA 2.21391 kcal/mol@LB@Unfolding Energy - sRNA 0.138435 kcal/mol@LB@@LB@Position - mRNA 171 -- 186@LB@Position - sRNA 24 -- 36@LB@Position Seed - mRNA 180 -- 186@LB@Position Seed - sRNA 24 -- 30@LB@
115	0.009897	0.2871	bsu22830	gpsA	-18.23	0.005947	227 -- 241	21 -- 34	glycerol-3-phosphate dehydrogenase		_____________226_____________242\n_____________\|_______________\|\n5'-GGU...GGAGC____A__________AGCAC...GUG-3'\n______________GGGG_GUUGGGGAAC\n______________:\|\|\|_\|\|\|\|\|\|\|\|\|\|\n______________UCCC_CAACCCCUUG\n3'-UUU...CUAUC_______________UCUCU...AUA-5'\n_____________\|_______________\|\n_____________35______________20\n	235 -- 241	21 -- 27	-24.3947 kcal/mol	4.254 kcal/mol	1.91139 kcal/mol	226 242@LB@ \| \|@LB@5'-GGU...GGAGC A AGCAC...GUG-3'@LB@ GGGG GUUGGGGAAC@LB@ :\|\|\| \|\|\|\|\|\|\|\|\|\|@LB@ UCCC CAACCCCUUG@LB@3'-UUU...CUAUC UCUCU...AUA-5'@LB@ \| \|@LB@ 35 20@LB@@LB@@LB@Energy -18.23 kcal/mol@LB@Hybridization Energy -24.3947 kcal/mol@LB@Unfolding Energy - mRNA 4.254 kcal/mol@LB@Unfolding Energy - sRNA 1.91139 kcal/mol@LB@@LB@Position - mRNA 227 -- 241@LB@Position - sRNA 21 -- 34@LB@Position Seed - mRNA 235 -- 241@LB@Position Seed - sRNA 21 -- 27@LB@
116	0.01008	0.2881	bsu32800	yusH	-9.74	0.231897	187 -- 194	31 -- 38	glycine cleavage system H protein		_____________186______195\n_____________\|________\|\n5'-AUC...AAAAA________AUUCA...CCG-3'\n______________AUGGAGGG\n______________\|\|:\|\|\|\|\|\n______________UAUCUCCC\n3'-UUU...UAGAC________CAACC...AUA-5'\n_____________\|________\|\n_____________39_______30\n	188 -- 194	31 -- 37	-12.574 kcal/mol	2.17853 kcal/mol	0.65488 kcal/mol	186 195@LB@ \| \|@LB@5'-AUC...AAAAA AUUCA...CCG-3'@LB@ AUGGAGGG@LB@ \|\|:\|\|\|\|\|@LB@ UAUCUCCC@LB@3'-UUU...UAGAC CAACC...AUA-5'@LB@ \| \|@LB@ 39 30@LB@@LB@@LB@Energy -9.74 kcal/mol@LB@Hybridization Energy -12.574 kcal/mol@LB@Unfolding Energy - mRNA 2.17853 kcal/mol@LB@Unfolding Energy - sRNA 0.65488 kcal/mol@LB@@LB@Position - mRNA 187 -- 194@LB@Position - sRNA 31 -- 38@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 31 -- 37@LB@
139	0.01217	0.2883	bsu30960	glgD	-11.28	0.137516	171 -- 191	30 -- 50	glycogen biosynthesis protein GlgD		_____________170____________________192\n_____________\|______________________\|\n5'-ACU...GAAUU_____AAUUA____________GCAGA...UUG-3'\n______________GAUUU_____CUGA_AGAGGGG\n______________\|\|\|:\|_____\|\|\|\|_\|\|\|\|\|\|\|\n______________CUAGA_____GACU_UCUCCCC\n3'-UUU...AAAGC_____ACUA_____A_______AACCC...AUA-5'\n_____________\|______________________\|\n_____________51_____________________29\n	185 -- 191	30 -- 36	-19.1028 kcal/mol	6.84884 kcal/mol	0.974272 kcal/mol	170 192@LB@ \| \|@LB@5'-ACU...GAAUU AAUUA GCAGA...UUG-3'@LB@ GAUUU CUGA AGAGGGG@LB@ \|\|\|:\| \|\|\|\| \|\|\|\|\|\|\|@LB@ CUAGA GACU UCUCCCC@LB@3'-UUU...AAAGC ACUA A AACCC...AUA-5'@LB@ \| \|@LB@ 51 29@LB@@LB@@LB@Energy -11.28 kcal/mol@LB@Hybridization Energy -19.1028 kcal/mol@LB@Unfolding Energy - mRNA 6.84884 kcal/mol@LB@Unfolding Energy - sRNA 0.974272 kcal/mol@LB@@LB@Position - mRNA 171 -- 191@LB@Position - sRNA 30 -- 50@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 30 -- 36@LB@
50	0.002285	0.1525	bsu22460	ypjH	-13.49	0.058216	160 -- 194	23 -- 52	glycosyltransferase YpjH		_____________159____________________________________195\n_____________\|______________________________________\|\n5'-AAG...CCAAA_____GCUGAUG_______A_____U__C_________CGAAC...AUG-3'\n______________CGGAU_______CUUGAUC_UGAUG__G___UUGGGGG\n______________\|\|\|\|\|_______\|\|\|\|\|\|\|_\|\|\|\|:__\|___\|\|\|\|\|\|:\n______________GCCUA_______GAACUAG_ACUAU__C___AACCCCU\n3'-UUU...AAAAA_________________________CU_CCC_______UGUCU...AUA-5'\n_____________\|______________________________________\|\n_____________53_____________________________________22\n	188 -- 194	23 -- 29	-25.8094 kcal/mol	11.3359 kcal/mol	0.981961 kcal/mol	159 195@LB@ \| \|@LB@5'-AAG...CCAAA GCUGAUG A U C CGAAC...AUG-3'@LB@ CGGAU CUUGAUC UGAUG G UUGGGGG@LB@ \|\|\|\|\| \|\|\|\|\|\|\| \|\|\|\|: \| \|\|\|\|\|\|:@LB@ GCCUA GAACUAG ACUAU C AACCCCU@LB@3'-UUU...AAAAA CU CCC UGUCU...AUA-5'@LB@ \| \|@LB@ 53 22@LB@@LB@@LB@Energy -13.49 kcal/mol@LB@Hybridization Energy -25.8094 kcal/mol@LB@Unfolding Energy - mRNA 11.3359 kcal/mol@LB@Unfolding Energy - sRNA 0.981961 kcal/mol@LB@@LB@Position - mRNA 160 -- 194@LB@Position - sRNA 23 -- 52@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 23 -- 29@LB@
190	0.01911	0.3269	bsu05370	ydfD	-12.16	0.099313	269 -- 294	11 -- 36	GntR family transcriptional regulator	bsu10880	_____________268________________________295\n_____________\|__________________________\|\n5'-AAA...AUUAA____AAAAUA__A_____________CGAUUG-3'\n______________AGAG______GG_AAUGGAGAGUGGC\n______________\|\|\|\|______\|\|_\|\|::\|\|\|\|\|\|:\|\|\n______________UCUC______CC_UUGUCUCUCAUCG\n3'-UUU...GACUA____CCCAAC__C_____________AAGAG...AUA-5'\n_____________\|__________________________\|\n_____________37_________________________10\n	288 -- 294	11 -- 17	-24.9379 kcal/mol	3.68177 kcal/mol	9.10067 kcal/mol	268 295@LB@ \| \|@LB@5'-AAA...AUUAA AAAAUA A CGAUUG-3'@LB@ AGAG GG AAUGGAGAGUGGC@LB@ \|\|\|\| \|\| \|\|::\|\|\|\|\|\|:\|\|@LB@ UCUC CC UUGUCUCUCAUCG@LB@3'-UUU...GACUA CCCAAC C AAGAG...AUA-5'@LB@ \| \|@LB@ 37 10@LB@@LB@@LB@Energy -12.16 kcal/mol@LB@Hybridization Energy -24.9379 kcal/mol@LB@Unfolding Energy - mRNA 3.68177 kcal/mol@LB@Unfolding Energy - sRNA 9.10067 kcal/mol@LB@@LB@Position - mRNA 269 -- 294@LB@Position - sRNA 11 -- 36@LB@Position Seed - mRNA 288 -- 294@LB@Position Seed - sRNA 11 -- 17@LB@
90	0.006982	0.2588	bsu40920	yyaF	-12.87	0.074972	6 -- 31	25 -- 50	GTP-dependent nucleic acid-binding protein EngD		_____________5___________________________32\n_____________\|___________________________\|\n______5'-CAAAU___ACAAAU_______AU__AA_____AAGUA...CGU-3'\n______________GAU______UCUGAUA__GG___UGGG\n______________\|\|\|______\|\|\|\|\|\|\|__\|\|___\|\|\|\|\n______________CUA______AGACUAU__CC___ACCC\n3'-UUU...AAAGC___GAACU________CU__CCA____CUUGU...AUA-5'\n_____________\|___________________________\|\n_____________51__________________________24\n	15 -- 21	36 -- 42	-17.5884 kcal/mol	3.73957 kcal/mol	0.976057 kcal/mol	5 32@LB@ \| \|@LB@ 5'-CAAAU ACAAAU AU AA AAGUA...CGU-3'@LB@ GAU UCUGAUA GG UGGG@LB@ \|\|\| \|\|\|\|\|\|\| \|\| \|\|\|\|@LB@ CUA AGACUAU CC ACCC@LB@3'-UUU...AAAGC GAACU CU CCA CUUGU...AUA-5'@LB@ \| \|@LB@ 51 24@LB@@LB@@LB@Energy -12.87 kcal/mol@LB@Hybridization Energy -17.5884 kcal/mol@LB@Unfolding Energy - mRNA 3.73957 kcal/mol@LB@Unfolding Energy - sRNA 0.976057 kcal/mol@LB@@LB@Position - mRNA 6 -- 31@LB@Position - sRNA 25 -- 50@LB@Position Seed - mRNA 15 -- 21@LB@Position Seed - sRNA 36 -- 42@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

Use the following button if you want to resubmit the job with altered input or parameterization:

usability assessment

Please support us by filling this short quality survey for evaluating this

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

Main Menu

Freiburg RNA Tools

Interaction Prediction

Seq-Str Alignment

CRISPR

Sequence Design

Splicing

SNP & Mutation

Classification

Gene set extension

MoDPepInt Server

CPSP-Tools Server

Galaxy-FR

CMV server

Teaching