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
167	0.01619	0.3152	bsu31500	yuxK	-13.98	0.047449	182 -- 199	26 -- 51	Evidence 4: Homologs of previously reported genes of unknown function		_____________181__________________________200\n_____________\|____________________________\|\n5'-UAC...UUAAA______________________AUA___AGUGA...ACG-3'\n______________GGAUC__________GGAGGGG___UGG\n______________\|\|\|\|\|__________:\|\|\|\|\|\|___\|\|\|\n______________CCUAG__________UCUCCCC___ACC\n3'-UUU...AAAAG_____AACUAGACUA_______A_____CCUUG...AUA-5'\n_____________\|____________________________\|\n_____________52___________________________25\n	187 -- 193	30 -- 36	-20.9361 kcal/mol	5.98517 kcal/mol	0.975822 kcal/mol	181 200@LB@ \| \|@LB@5'-UAC...UUAAA AUA AGUGA...ACG-3'@LB@ GGAUC GGAGGGG UGG@LB@ \|\|\|\|\| :\|\|\|\|\|\| \|\|\|@LB@ CCUAG UCUCCCC ACC@LB@3'-UUU...AAAAG AACUAGACUA A CCUUG...AUA-5'@LB@ \| \|@LB@ 52 25@LB@@LB@@LB@Energy -13.98 kcal/mol@LB@Hybridization Energy -20.9361 kcal/mol@LB@Unfolding Energy - mRNA 5.98517 kcal/mol@LB@Unfolding Energy - sRNA 0.975822 kcal/mol@LB@@LB@Position - mRNA 182 -- 199@LB@Position - sRNA 26 -- 51@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 30 -- 36@LB@
173	0.01667	0.3152	bsu28970	ytxB	-13.17	0.066474	182 -- 201	13 -- 34	tvp38/tmem64 family membrane protein YtxB		_____________181____________________202\n_____________\|______________________\|\n5'-UGC...UUCAA_____AA_______U_______UGAAA...AAA-3'\n______________AGGGG____GGAAC_GAGGGUA\n______________\|\|\|\|\|____\|\|\|\|\|_\|\|\|:\|\|\|\n______________UCCCC____CCUUG_CUCUCAU\n3'-UUU...CUAUC_____AACC_____U_______CGAAG...AUA-5'\n_____________\|______________________\|\n_____________35_____________________12\n	195 -- 201	13 -- 19	-25.067 kcal/mol	2.85387 kcal/mol	9.04315 kcal/mol	181 202@LB@ \| \|@LB@5'-UGC...UUCAA AA U UGAAA...AAA-3'@LB@ AGGGG GGAAC GAGGGUA@LB@ \|\|\|\|\| \|\|\|\|\| \|\|\|:\|\|\|@LB@ UCCCC CCUUG CUCUCAU@LB@3'-UUU...CUAUC AACC U CGAAG...AUA-5'@LB@ \| \|@LB@ 35 12@LB@@LB@@LB@Energy -13.17 kcal/mol@LB@Hybridization Energy -25.067 kcal/mol@LB@Unfolding Energy - mRNA 2.85387 kcal/mol@LB@Unfolding Energy - sRNA 9.04315 kcal/mol@LB@@LB@Position - mRNA 182 -- 201@LB@Position - sRNA 13 -- 34@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 13 -- 19@LB@
178	0.01684	0.3152	bsu09460	ctrA	-17.20	0.010320	182 -- 213	20 -- 50	amino acid permease		_____________181_________________________________214\n_____________\|___________________________________\|\n5'-CAA...UAGAU____GG__G____________AA__AAA_______UUUUU...UAA-3'\n______________GAUC__GA_UUGA___AGGGG__UG___GGGAGCG\n______________\|\|\|\|__\|\|_:\|\|\|___\|\|\|\|\|__\|\|___\|\|\|\|:\|:\n______________CUAG__CU_GACU___UCCCC__AC___CCCUUGU\n3'-UUU...AAAGC____AA__A____AUC_____A_____________CUCUC...AUA-5'\n_____________\|___________________________________\|\n_____________51__________________________________19\n	207 -- 213	20 -- 26	-25.5851 kcal/mol	4.15406 kcal/mol	4.22897 kcal/mol	181 214@LB@ \| \|@LB@5'-CAA...UAGAU GG G AA AAA UUUUU...UAA-3'@LB@ GAUC GA UUGA AGGGG UG GGGAGCG@LB@ \|\|\|\| \|\| :\|\|\| \|\|\|\|\| \|\| \|\|\|\|:\|:@LB@ CUAG CU GACU UCCCC AC CCCUUGU@LB@3'-UUU...AAAGC AA A AUC A CUCUC...AUA-5'@LB@ \| \|@LB@ 51 19@LB@@LB@@LB@Energy -17.20 kcal/mol@LB@Hybridization Energy -25.5851 kcal/mol@LB@Unfolding Energy - mRNA 4.15406 kcal/mol@LB@Unfolding Energy - sRNA 4.22897 kcal/mol@LB@@LB@Position - mRNA 182 -- 213@LB@Position - sRNA 20 -- 50@LB@Position Seed - mRNA 207 -- 213@LB@Position Seed - sRNA 20 -- 26@LB@
27	0.0005687	0.07027	bsu32550	yurJ	-13.20	0.065709	183 -- 191	31 -- 39	ABC transporter ATP-binding protein		_____________182_______192\n_____________\|_________\|\n5'-AAC...CAAAA_________ACUUU...UGC-3'\n______________GAUAGGGGG\n______________\|\|\|\|\|:\|\|\|\n______________CUAUCUCCC\n3'-UUU...CUAGA_________CAACC...AUA-5'\n_____________\|_________\|\n_____________40________30\n	185 -- 191	31 -- 37	-15.8488 kcal/mol	1.87568 kcal/mol	0.774822 kcal/mol	182 192@LB@ \| \|@LB@5'-AAC...CAAAA ACUUU...UGC-3'@LB@ GAUAGGGGG@LB@ \|\|\|\|\|:\|\|\|@LB@ CUAUCUCCC@LB@3'-UUU...CUAGA CAACC...AUA-5'@LB@ \| \|@LB@ 40 30@LB@@LB@@LB@Energy -13.20 kcal/mol@LB@Hybridization Energy -15.8488 kcal/mol@LB@Unfolding Energy - mRNA 1.87568 kcal/mol@LB@Unfolding Energy - sRNA 0.774822 kcal/mol@LB@@LB@Position - mRNA 183 -- 191@LB@Position - sRNA 31 -- 39@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 31 -- 37@LB@
68	0.004453	0.2184	bsu22580	ypiB	-13.80	0.051176	183 -- 197	21 -- 39	Evidence 4: Homologs of previously reported genes of unknown function; PubMedId: 16847875		_____________182_________________198\n_____________\|___________________\|\n5'-AGC...CGAAC________A__________UACAU...ACU-3'\n______________GAUAGAGG_____GGGAAU\n______________\|\|\|\|\|\|\|\|_____\|\|\|\|\|:\n______________CUAUCUCC_____CCCUUG\n3'-UUU...CUAGA________CCAAC______UCUCU...AUA-5'\n_____________\|___________________\|\n_____________40__________________20\n	184 -- 190	32 -- 38	-18.5124 kcal/mol	2.13446 kcal/mol	2.58006 kcal/mol	182 198@LB@ \| \|@LB@5'-AGC...CGAAC A UACAU...ACU-3'@LB@ GAUAGAGG GGGAAU@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|:@LB@ CUAUCUCC CCCUUG@LB@3'-UUU...CUAGA CCAAC UCUCU...AUA-5'@LB@ \| \|@LB@ 40 20@LB@@LB@@LB@Energy -13.80 kcal/mol@LB@Hybridization Energy -18.5124 kcal/mol@LB@Unfolding Energy - mRNA 2.13446 kcal/mol@LB@Unfolding Energy - sRNA 2.58006 kcal/mol@LB@@LB@Position - mRNA 183 -- 197@LB@Position - sRNA 21 -- 39@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 32 -- 38@LB@
94	0.007849	0.2778	bsu27000	yraB	-9.14	0.279232	183 -- 193	29 -- 39	MerR family transcriptional regulator		_____________182_________194\n_____________\|___________\|\n5'-AGU...UACAG_______A___GAAGA...ACA-3'\n______________GAUAGAG_GGU\n______________\|\|\|\|\|\|\|_\|\|\|\n______________CUAUCUC_CCA\n3'-UUU...CUAGA_______C___ACCCC...AUA-5'\n_____________\|___________\|\n_____________40__________28\n	183 -- 189	33 -- 39	-13.977 kcal/mol	4.05751 kcal/mol	0.779471 kcal/mol	182 194@LB@ \| \|@LB@5'-AGU...UACAG A GAAGA...ACA-3'@LB@ GAUAGAG GGU@LB@ \|\|\|\|\|\|\| \|\|\|@LB@ CUAUCUC CCA@LB@3'-UUU...CUAGA C ACCCC...AUA-5'@LB@ \| \|@LB@ 40 28@LB@@LB@@LB@Energy -9.14 kcal/mol@LB@Hybridization Energy -13.977 kcal/mol@LB@Unfolding Energy - mRNA 4.05751 kcal/mol@LB@Unfolding Energy - sRNA 0.779471 kcal/mol@LB@@LB@Position - mRNA 183 -- 193@LB@Position - sRNA 29 -- 39@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 33 -- 39@LB@
103	0.008788	0.2778	bsu06070	ydiP	-8.66	0.321247	183 -- 194	27 -- 44	BsuMI modification methylase subunit YdiP	bsu20250	_____________182________________195\n_____________\|__________________\|\n5'-GGA...AAAAA__________________AUAUC...UGG-3'\n______________GAUUUGA______GGUUG\n______________\|\|\|:\|\|\|______\|\|\|\|\|\n______________CUAGACU______CCAAC\n3'-UUU...UAGAA_______AUCUCC_____CCCUU...AUA-5'\n_____________\|__________________\|\n_____________45_________________26\n	183 -- 189	38 -- 44	-12.3729 kcal/mol	2.73997 kcal/mol	0.971452 kcal/mol	182 195@LB@ \| \|@LB@5'-GGA...AAAAA AUAUC...UGG-3'@LB@ GAUUUGA GGUUG@LB@ \|\|\|:\|\|\| \|\|\|\|\|@LB@ CUAGACU CCAAC@LB@3'-UUU...UAGAA AUCUCC CCCUU...AUA-5'@LB@ \| \|@LB@ 45 26@LB@@LB@@LB@Energy -8.66 kcal/mol@LB@Hybridization Energy -12.3729 kcal/mol@LB@Unfolding Energy - mRNA 2.73997 kcal/mol@LB@Unfolding Energy - sRNA 0.971452 kcal/mol@LB@@LB@Position - mRNA 183 -- 194@LB@Position - sRNA 27 -- 44@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 38 -- 44@LB@
118	0.01022	0.2883	bsu19370	sucA	-9.59	0.243554	183 -- 190	23 -- 30	2-oxoglutarate dehydrogenase subunit E1		_____________182______191\n_____________\|________\|\n5'-UUU...UUUAA________UAAUA...AUC-3'\n______________GUUGGGGG\n______________\|\|\|\|\|\|\|:\n______________CAACCCCU\n3'-UUU...CUCCC________UGUCU...AUA-5'\n_____________\|________\|\n_____________31_______22\n	184 -- 190	23 -- 29	-13.0923 kcal/mol	3.48895 kcal/mol	0.018115 kcal/mol	182 191@LB@ \| \|@LB@5'-UUU...UUUAA UAAUA...AUC-3'@LB@ GUUGGGGG@LB@ \|\|\|\|\|\|\|:@LB@ CAACCCCU@LB@3'-UUU...CUCCC UGUCU...AUA-5'@LB@ \| \|@LB@ 31 22@LB@@LB@@LB@Energy -9.59 kcal/mol@LB@Hybridization Energy -13.0923 kcal/mol@LB@Unfolding Energy - mRNA 3.48895 kcal/mol@LB@Unfolding Energy - sRNA 0.018115 kcal/mol@LB@@LB@Position - mRNA 183 -- 190@LB@Position - sRNA 23 -- 30@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 23 -- 29@LB@
15	0.0002364	0.05257	bsu19290	yozO	-13.57	0.056229	184 -- 195	28 -- 39	Evidence 4: Homologs of previously reported genes of unknown function		_____________183__________196\n_____________\|____________\|\n5'-AAA...AUGCA__A_________CUUCA...UGG-3'\n______________GA_AGAGGGGUU\n______________\|\|_\|\|\|\|\|\|\|\|\|\n______________CU_UCUCCCCAA\n3'-UUU...CUAGA__A_________CCCCU...AUA-5'\n_____________\|____________\|\n_____________40___________27\n	189 -- 195	28 -- 34	-16.9963 kcal/mol	2.64187 kcal/mol	0.77983 kcal/mol	183 196@LB@ \| \|@LB@5'-AAA...AUGCA A CUUCA...UGG-3'@LB@ GA AGAGGGGUU@LB@ \|\| \|\|\|\|\|\|\|\|\|@LB@ CU UCUCCCCAA@LB@3'-UUU...CUAGA A CCCCU...AUA-5'@LB@ \| \|@LB@ 40 27@LB@@LB@@LB@Energy -13.57 kcal/mol@LB@Hybridization Energy -16.9963 kcal/mol@LB@Unfolding Energy - mRNA 2.64187 kcal/mol@LB@Unfolding Energy - sRNA 0.77983 kcal/mol@LB@@LB@Position - mRNA 184 -- 195@LB@Position - sRNA 28 -- 39@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 28 -- 34@LB@
85	0.006705	0.2588	bsu28790	araB	-13.91	0.048694	184 -- 192	30 -- 38	ribulokinase		_____________183_______193\n_____________\|_________\|\n5'-GGA...CAAAA_________GAUGU...AAU-3'\n______________GUAGAGGGG\n______________:\|\|\|\|\|\|\|\|\n______________UAUCUCCCC\n3'-UUU...UAGAC_________AACCC...AUA-5'\n_____________\|_________\|\n_____________39________29\n	186 -- 192	30 -- 36	-16.4519 kcal/mol	1.87822 kcal/mol	0.6591 kcal/mol	183 193@LB@ \| \|@LB@5'-GGA...CAAAA GAUGU...AAU-3'@LB@ GUAGAGGGG@LB@ :\|\|\|\|\|\|\|\|@LB@ UAUCUCCCC@LB@3'-UUU...UAGAC AACCC...AUA-5'@LB@ \| \|@LB@ 39 29@LB@@LB@@LB@Energy -13.91 kcal/mol@LB@Hybridization Energy -16.4519 kcal/mol@LB@Unfolding Energy - mRNA 1.87822 kcal/mol@LB@Unfolding Energy - sRNA 0.6591 kcal/mol@LB@@LB@Position - mRNA 184 -- 192@LB@Position - sRNA 30 -- 38@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 30 -- 36@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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