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
200	0.01989	0.3269	bsu30150	ytdP	-13.03	0.070310	188 -- 210	28 -- 52	AraC family transcriptional regulator		_____________187________________________211\n_____________\|__________________________\|\n5'-UUU...UGAAG_____G_UA______AAU________UUAUG...UAU-3'\n______________UGGAU_U_____UGA___GGGGGGUU\n______________:\|\|\|\|_\|_____\|\|\|___\|:\|\|\|\|\|\|\n______________GCCUA_A_____ACU___CUCCCCAA\n3'-UUU...AAAAA_____G_ACUAG___AU_________CCCCU...AUA-5'\n_____________\|__________________________\|\n_____________53_________________________27\n	204 -- 210	28 -- 34	-18.7355 kcal/mol	4.72292 kcal/mol	0.980555 kcal/mol	187 211@LB@ \| \|@LB@5'-UUU...UGAAG G UA AAU UUAUG...UAU-3'@LB@ UGGAU U UGA GGGGGGUU@LB@ :\|\|\|\| \| \|\|\| \|:\|\|\|\|\|\|@LB@ GCCUA A ACU CUCCCCAA@LB@3'-UUU...AAAAA G ACUAG AU CCCCU...AUA-5'@LB@ \| \|@LB@ 53 27@LB@@LB@@LB@Energy -13.03 kcal/mol@LB@Hybridization Energy -18.7355 kcal/mol@LB@Unfolding Energy - mRNA 4.72292 kcal/mol@LB@Unfolding Energy - sRNA 0.980555 kcal/mol@LB@@LB@Position - mRNA 188 -- 210@LB@Position - sRNA 28 -- 52@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 28 -- 34@LB@
11	0.0001235	0.03747	bsu15610	sumT	-12.35	0.092299	189 -- 208	22 -- 34	uroporphyrinogen-iii C-methyltransferase		_____________188__________________209\n_____________\|____________________\|\n5'-GAA...AGAUC_____AAAUACGA_______AGUAU...AUG-3'\n______________GGGGG________UGGGGAA\n______________:\|\|\|\|________\|\|\|\|\|\|\|\n______________UCCCC________ACCCCUU\n3'-UUU...CUAUC_____A______________GUCUC...AUA-5'\n_____________\|____________________\|\n_____________35___________________21\n	202 -- 208	22 -- 28	-16.2617 kcal/mol	2.89451 kcal/mol	1.02154 kcal/mol	188 209@LB@ \| \|@LB@5'-GAA...AGAUC AAAUACGA AGUAU...AUG-3'@LB@ GGGGG UGGGGAA@LB@ :\|\|\|\| \|\|\|\|\|\|\|@LB@ UCCCC ACCCCUU@LB@3'-UUU...CUAUC A GUCUC...AUA-5'@LB@ \| \|@LB@ 35 21@LB@@LB@@LB@Energy -12.35 kcal/mol@LB@Hybridization Energy -16.2617 kcal/mol@LB@Unfolding Energy - mRNA 2.89451 kcal/mol@LB@Unfolding Energy - sRNA 1.02154 kcal/mol@LB@@LB@Position - mRNA 189 -- 208@LB@Position - sRNA 22 -- 34@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 22 -- 28@LB@
28	0.0009752	0.1113	bsu00830	ctsR	-15.39	0.025224	189 -- 206	23 -- 36	transcriptional regulator CtsR		_____________188________________207\n_____________\|__________________\|\n5'-UGG...GUAAA___G_______AGU____CAUAA...CAG-3'\n______________GGA_GGGGUUG___GGGA\n______________:\|\|_\|\|\|\|\|\|\|___\|\|\|\|\n______________UCU_CCCCAAC___CCCU\n3'-UUU...GACUA__________________UGUCU...AUA-5'\n_____________\|__________________\|\n_____________37_________________22\n	193 -- 199	27 -- 33	-19.308 kcal/mol	3.78136 kcal/mol	0.139628 kcal/mol	188 207@LB@ \| \|@LB@5'-UGG...GUAAA G AGU CAUAA...CAG-3'@LB@ GGA GGGGUUG GGGA@LB@ :\|\| \|\|\|\|\|\|\| \|\|\|\|@LB@ UCU CCCCAAC CCCU@LB@3'-UUU...GACUA UGUCU...AUA-5'@LB@ \| \|@LB@ 37 22@LB@@LB@@LB@Energy -15.39 kcal/mol@LB@Hybridization Energy -19.308 kcal/mol@LB@Unfolding Energy - mRNA 3.78136 kcal/mol@LB@Unfolding Energy - sRNA 0.139628 kcal/mol@LB@@LB@Position - mRNA 189 -- 206@LB@Position - sRNA 23 -- 36@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 27 -- 33@LB@
122	0.01077	0.2883	bsu18910	rapK	-11.72	0.116857	189 -- 197	28 -- 36	response regulator aspartate phosphatase K		_____________188_______198\n_____________\|_________\|\n5'-UAU...CAGAA_________UAAAU...CAG-3'\n______________AGAGGGGUU\n______________\|\|\|\|\|\|\|\|\|\n______________UCUCCCCAA\n3'-UUU...GACUA_________CCCCU...AUA-5'\n_____________\|_________\|\n_____________37________27\n	191 -- 197	28 -- 34	-15.633 kcal/mol	3.77416 kcal/mol	0.134381 kcal/mol	188 198@LB@ \| \|@LB@5'-UAU...CAGAA UAAAU...CAG-3'@LB@ AGAGGGGUU@LB@ \|\|\|\|\|\|\|\|\|@LB@ UCUCCCCAA@LB@3'-UUU...GACUA CCCCU...AUA-5'@LB@ \| \|@LB@ 37 27@LB@@LB@@LB@Energy -11.72 kcal/mol@LB@Hybridization Energy -15.633 kcal/mol@LB@Unfolding Energy - mRNA 3.77416 kcal/mol@LB@Unfolding Energy - sRNA 0.134381 kcal/mol@LB@@LB@Position - mRNA 189 -- 197@LB@Position - sRNA 28 -- 36@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 28 -- 34@LB@
184	0.01795	0.3254	bsu30470	ytzC	-13.40	0.060457	189 -- 197	28 -- 36	Evidence 4: Homologs of previously reported genes of unknown function		_____________188_______198\n_____________\|_________\|\n5'-UUC...CAAGA_________ACUGU...AUU-3'\n______________GGAGGGGUU\n______________:\|\|\|\|\|\|\|\|\n______________UCUCCCCAA\n3'-UUU...GACUA_________CCCCU...AUA-5'\n_____________\|_________\|\n_____________37________27\n	191 -- 197	28 -- 34	-16.1349 kcal/mol	2.59994 kcal/mol	0.134381 kcal/mol	188 198@LB@ \| \|@LB@5'-UUC...CAAGA ACUGU...AUU-3'@LB@ GGAGGGGUU@LB@ :\|\|\|\|\|\|\|\|@LB@ UCUCCCCAA@LB@3'-UUU...GACUA CCCCU...AUA-5'@LB@ \| \|@LB@ 37 27@LB@@LB@@LB@Energy -13.40 kcal/mol@LB@Hybridization Energy -16.1349 kcal/mol@LB@Unfolding Energy - mRNA 2.59994 kcal/mol@LB@Unfolding Energy - sRNA 0.134381 kcal/mol@LB@@LB@Position - mRNA 189 -- 197@LB@Position - sRNA 28 -- 36@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 28 -- 34@LB@
198	0.0197	0.3269	bsu08980	yhbH	-11.85	0.111658	189 -- 195	30 -- 36	stress response UPF0229 protein YhbH		_____________188_____196\n_____________\|_______\|\n5'-GGC...GUUAA_______AAUUC...UGC-3'\n______________GGAGGGG\n______________:\|\|\|\|\|\|\n______________UCUCCCC\n3'-UUU...GACUA_______AACCC...AUA-5'\n_____________\|_______\|\n_____________37______29\n	189 -- 195	30 -- 36	-13.8096 kcal/mol	1.82966 kcal/mol	0.133643 kcal/mol	188 196@LB@ \| \|@LB@5'-GGC...GUUAA AAUUC...UGC-3'@LB@ GGAGGGG@LB@ :\|\|\|\|\|\|@LB@ UCUCCCC@LB@3'-UUU...GACUA AACCC...AUA-5'@LB@ \| \|@LB@ 37 29@LB@@LB@@LB@Energy -11.85 kcal/mol@LB@Hybridization Energy -13.8096 kcal/mol@LB@Unfolding Energy - mRNA 1.82966 kcal/mol@LB@Unfolding Energy - sRNA 0.133643 kcal/mol@LB@@LB@Position - mRNA 189 -- 195@LB@Position - sRNA 30 -- 36@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 30 -- 36@LB@
6	3.166e-05	0.01761	bsu12160	yjgC	-18.77	0.004394	190 -- 206	10 -- 27	oxidoreductase	bsu27220 bsu03310	_____________189________________207\n_____________\|__________________\|\n5'-UAA...AGAAA__________________GGCAA...UGC-3'\n______________GGGGAAUGGAGA_UGGCU\n______________\|\|\|\|\|\|::\|\|\|\|_\|:\|\|\|\n______________CCCCUUGUCUCU_AUCGA\n3'-UUU...CCCAA____________C_____AGAGA...AUA-5'\n_____________\|__________________\|\n_____________28_________________9\n	192 -- 198	19 -- 25	-27.0798 kcal/mol	2.28534 kcal/mol	6.0284 kcal/mol	189 207@LB@ \| \|@LB@5'-UAA...AGAAA GGCAA...UGC-3'@LB@ GGGGAAUGGAGA UGGCU@LB@ \|\|\|\|\|\|::\|\|\|\| \|:\|\|\|@LB@ CCCCUUGUCUCU AUCGA@LB@3'-UUU...CCCAA C AGAGA...AUA-5'@LB@ \| \|@LB@ 28 9@LB@@LB@@LB@Energy -18.77 kcal/mol@LB@Hybridization Energy -27.0798 kcal/mol@LB@Unfolding Energy - mRNA 2.28534 kcal/mol@LB@Unfolding Energy - sRNA 6.0284 kcal/mol@LB@@LB@Position - mRNA 190 -- 206@LB@Position - sRNA 10 -- 27@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 19 -- 25@LB@
60	0.003464	0.1926	bsu03300	nasD	-15.33	0.025906	190 -- 205	34 -- 52	nitrite reductase		_____________189_________________206\n_____________\|___________________\|\n5'-UUU...AGGAG___________________AAAAA...CAA-3'\n______________CGGAUC___AUCUGAUGGG\n______________\|\|\|\|\|\|___\|\|\|\|\|\|\|:\|:\n______________GCCUAG___UAGACUAUCU\n3'-UUU...AAAAA______AAC__________CCCCA...AUA-5'\n_____________\|___________________\|\n_____________53__________________33\n	199 -- 205	34 -- 40	-21.0079 kcal/mol	4.70189 kcal/mol	0.976339 kcal/mol	189 206@LB@ \| \|@LB@5'-UUU...AGGAG AAAAA...CAA-3'@LB@ CGGAUC AUCUGAUGGG@LB@ \|\|\|\|\|\| \|\|\|\|\|\|\|:\|:@LB@ GCCUAG UAGACUAUCU@LB@3'-UUU...AAAAA AAC CCCCA...AUA-5'@LB@ \| \|@LB@ 53 33@LB@@LB@@LB@Energy -15.33 kcal/mol@LB@Hybridization Energy -21.0079 kcal/mol@LB@Unfolding Energy - mRNA 4.70189 kcal/mol@LB@Unfolding Energy - sRNA 0.976339 kcal/mol@LB@@LB@Position - mRNA 190 -- 205@LB@Position - sRNA 34 -- 52@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 34 -- 40@LB@
73	0.005255	0.2402	bsu21750	scuA	-12.63	0.082513	190 -- 220	28 -- 51	SCO1 protein		_____________189_____________________________221\n_____________\|_______________________________\|\n5'-GGG...GGAAA____GGAU___A___A__UUAUCA_______AACGG...AGC-3'\n______________GGAU____GUC_UGA_GG______AGGGGUU\n______________\|\|\|\|____:\|\|_\|\|\|_:\|______\|\|\|\|\|\|\|\n______________CCUA____UAG_ACU_UC______UCCCCAA\n3'-UUU...AAAAG____GAAC_______A_______________CCCCU...AUA-5'\n_____________\|_______________________________\|\n_____________52______________________________27\n	214 -- 220	28 -- 34	-18.667 kcal/mol	5.06013 kcal/mol	0.974859 kcal/mol	189 221@LB@ \| \|@LB@5'-GGG...GGAAA GGAU A A UUAUCA AACGG...AGC-3'@LB@ GGAU GUC UGA GG AGGGGUU@LB@ \|\|\|\| :\|\| \|\|\| :\| \|\|\|\|\|\|\|@LB@ CCUA UAG ACU UC UCCCCAA@LB@3'-UUU...AAAAG GAAC A CCCCU...AUA-5'@LB@ \| \|@LB@ 52 27@LB@@LB@@LB@Energy -12.63 kcal/mol@LB@Hybridization Energy -18.667 kcal/mol@LB@Unfolding Energy - mRNA 5.06013 kcal/mol@LB@Unfolding Energy - sRNA 0.974859 kcal/mol@LB@@LB@Position - mRNA 190 -- 220@LB@Position - sRNA 28 -- 51@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 28 -- 34@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@

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

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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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