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
66	0.004158	0.2071	bsu22770	mtrB	-14.22	0.042769	173 -- 192	31 -- 51	transcription attenuation protein MtrB	_____________172___________________193\n_____________\|_____________________\|\n5'-UAG...CGCCA______AAUAAA_________UGCUA...ACC-3'\n______________GGA_CU______GAUAGAGGG\n______________\|\|\|_\|\|______\|\|\|\|\|\|\|\|\|\n______________CCU_GA______CUAUCUCCC\n3'-UUU...AAAAG___A__ACUAGA_________CAACC...AUA-5'\n_____________\|_____________________\|\n_____________52____________________30\n	186 -- 192	31 -- 37	-18.8398 kcal/mol	3.65373 kcal/mol	0.970589 kcal/mol	172 193@LB@ \| \|@LB@5'-UAG...CGCCA AAUAAA UGCUA...ACC-3'@LB@ GGA CU GAUAGAGGG@LB@ \|\|\| \|\| \|\|\|\|\|\|\|\|\|@LB@ CCU GA CUAUCUCCC@LB@3'-UUU...AAAAG A ACUAGA CAACC...AUA-5'@LB@ \| \|@LB@ 52 30@LB@@LB@@LB@Energy -14.22 kcal/mol@LB@Hybridization Energy -18.8398 kcal/mol@LB@Unfolding Energy - mRNA 3.65373 kcal/mol@LB@Unfolding Energy - sRNA 0.970589 kcal/mol@LB@@LB@Position - mRNA 173 -- 192@LB@Position - sRNA 31 -- 51@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 31 -- 37@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@
106	0.009109	0.2778	bsu01390	infA	-12.86	0.075307	175 -- 189	30 -- 45	translation initiation factor IF-1	_____________174______________190\n_____________\|________________\|\n5'-CCA...GUUAC____________A___AGAAC...UGG-3'\n______________UGAUUUGA_AGA_GGG\n______________\|\|\|\|:\|\|\|_\|\|\|_\|\|\|\n______________ACUAGACU_UCU_CCC\n3'-UUU...CUAGA________A___C___AACCC...AUA-5'\n_____________\|________________\|\n_____________46_______________29\n	176 -- 182	38 -- 44	-16.3452 kcal/mol	2.51395 kcal/mol	0.969561 kcal/mol	174 190@LB@ \| \|@LB@5'-CCA...GUUAC A AGAAC...UGG-3'@LB@ UGAUUUGA AGA GGG@LB@ \|\|\|\|:\|\|\| \|\|\| \|\|\|@LB@ ACUAGACU UCU CCC@LB@3'-UUU...CUAGA A C AACCC...AUA-5'@LB@ \| \|@LB@ 46 29@LB@@LB@@LB@Energy -12.86 kcal/mol@LB@Hybridization Energy -16.3452 kcal/mol@LB@Unfolding Energy - mRNA 2.51395 kcal/mol@LB@Unfolding Energy - sRNA 0.969561 kcal/mol@LB@@LB@Position - mRNA 175 -- 189@LB@Position - sRNA 30 -- 45@LB@Position Seed - mRNA 176 -- 182@LB@Position Seed - sRNA 38 -- 44@LB@
131	0.01151	0.2883	bsu03110	ycgH	-12.02	0.104581	161 -- 192	27 -- 50	transporter	_____________160______________________________193\n_____________\|________________________________\|\n5'-UUU...GGACA____ACA____AACCUUA____AA________AAUAA...UCG-3'\n______________GAUC___AUCU_______GAUA__AGGGGUUG\n______________\|\|\|\|___\|\|\|\|_______\|\|\|\|__\|\|\|\|\|\|\|\|\n______________CUAG___UAGA_______CUAU__UCCCCAAC\n3'-UUU...AAAGC____AAC_______________C_________CCCUU...AUA-5'\n_____________\|________________________________\|\n_____________51_______________________________26\n	186 -- 192	27 -- 33	-20.341 kcal/mol	7.34553 kcal/mol	0.975523 kcal/mol	160 193@LB@ \| \|@LB@5'-UUU...GGACA ACA AACCUUA AA AAUAA...UCG-3'@LB@ GAUC AUCU GAUA AGGGGUUG@LB@ \|\|\|\| \|\|\|\| \|\|\|\| \|\|\|\|\|\|\|\|@LB@ CUAG UAGA CUAU UCCCCAAC@LB@3'-UUU...AAAGC AAC C CCCUU...AUA-5'@LB@ \| \|@LB@ 51 26@LB@@LB@@LB@Energy -12.02 kcal/mol@LB@Hybridization Energy -20.341 kcal/mol@LB@Unfolding Energy - mRNA 7.34553 kcal/mol@LB@Unfolding Energy - sRNA 0.975523 kcal/mol@LB@@LB@Position - mRNA 161 -- 192@LB@Position - sRNA 27 -- 50@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 27 -- 33@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@
55	0.002845	0.1725	bsu40380	yycI	-20.10	0.001970	172 -- 209	12 -- 51	two-component system YycFG regulatory protein	_____________171_________________________________________210\n_____________\|___________________________________________\|\n5'-CAG...ACAAA_____UA____G____A_______GCU________U_______AAUAA...GCA-3'\n______________GGAUU__UUGA___GA_GGAGGGG______AACAG_GGAGUGG\n______________\|\|\|\|:__\|\|\|\|___\|\|_:\|\|\|\|\|\|______\|\|\|\|\|_:\|\|\|\|:\|\n______________CCUAG__AACU___CU_UCUCCCC______UUGUC_UCUCAUC\n3'-UUU...AAAAG___________AGA__A_______AACCCC_____________GAAGA...AUA-5'\n_____________\|___________________________________________\|\n_____________52__________________________________________11\n	203 -- 209	12 -- 18	-35.1528 kcal/mol	5.09356 kcal/mol	9.95619 kcal/mol	171 210@LB@ \| \|@LB@5'-CAG...ACAAA UA G A GCU U AAUAA...GCA-3'@LB@ GGAUU UUGA GA GGAGGGG AACAG GGAGUGG@LB@ \|\|\|\|: \|\|\|\| \|\| :\|\|\|\|\|\| \|\|\|\|\| :\|\|\|\|:\|@LB@ CCUAG AACU CU UCUCCCC UUGUC UCUCAUC@LB@3'-UUU...AAAAG AGA A AACCCC GAAGA...AUA-5'@LB@ \| \|@LB@ 52 11@LB@@LB@@LB@Energy -20.10 kcal/mol@LB@Hybridization Energy -35.1528 kcal/mol@LB@Unfolding Energy - mRNA 5.09356 kcal/mol@LB@Unfolding Energy - sRNA 9.95619 kcal/mol@LB@@LB@Position - mRNA 172 -- 209@LB@Position - sRNA 12 -- 51@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 12 -- 18@LB@
129	0.01144	0.2883	bsu36230	ywqF	-11.45	0.129133	185 -- 195	31 -- 41	UDP-glucose 6-dehydrogenase YwqF	_____________184_________196\n_____________\|___________\|\n5'-UUU...UUUAA___U_______AAACA...CUC-3'\n______________CUG_UGGAGGG\n______________\|\|\|_\|:\|\|\|\|\|\n______________GAC_AUCUCCC\n3'-UUU...AACUA___U_______CAACC...AUA-5'\n_____________\|___________\|\n_____________42__________30\n	189 -- 195	31 -- 37	-16.042 kcal/mol	3.66073 kcal/mol	0.928126 kcal/mol	184 196@LB@ \| \|@LB@5'-UUU...UUUAA U AAACA...CUC-3'@LB@ CUG UGGAGGG@LB@ \|\|\| \|:\|\|\|\|\|@LB@ GAC AUCUCCC@LB@3'-UUU...AACUA U CAACC...AUA-5'@LB@ \| \|@LB@ 42 30@LB@@LB@@LB@Energy -11.45 kcal/mol@LB@Hybridization Energy -16.042 kcal/mol@LB@Unfolding Energy - mRNA 3.66073 kcal/mol@LB@Unfolding Energy - sRNA 0.928126 kcal/mol@LB@@LB@Position - mRNA 185 -- 195@LB@Position - sRNA 31 -- 41@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 31 -- 37@LB@
145	0.01267	0.2913	bsu36760	murAA	-10.92	0.156018	188 -- 194	30 -- 36	UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1	_____________187_____195\n_____________\|_______\|\n5'-UAG...GACGC_______AAUAC...UAU-3'\n______________GGAGGGG\n______________:\|\|\|\|\|\|\n______________UCUCCCC\n3'-UUU...GACUA_______AACCC...AUA-5'\n_____________\|_______\|\n_____________37______29\n	188 -- 194	30 -- 36	-13.3986 kcal/mol	2.34028 kcal/mol	0.133643 kcal/mol	187 195@LB@ \| \|@LB@5'-UAG...GACGC AAUAC...UAU-3'@LB@ GGAGGGG@LB@ :\|\|\|\|\|\|@LB@ UCUCCCC@LB@3'-UUU...GACUA AACCC...AUA-5'@LB@ \| \|@LB@ 37 29@LB@@LB@@LB@Energy -10.92 kcal/mol@LB@Hybridization Energy -13.3986 kcal/mol@LB@Unfolding Energy - mRNA 2.34028 kcal/mol@LB@Unfolding Energy - sRNA 0.133643 kcal/mol@LB@@LB@Position - mRNA 188 -- 194@LB@Position - sRNA 30 -- 36@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 30 -- 36@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@
46	0.002102	0.1496	bsu35160	uvrA	-18.29	0.005742	210 -- 232	21 -- 44	UvrABC system protein A	_____________209______________________233\n_____________\|________________________\|\n5'-CAC...CUAUG____G________UGAA_______CAGGG...GUU-3'\n______________GAUC_GAUAGAGG_____GGGAGC\n______________\|\|\|\|_\|\|\|\|\|\|\|\|_____\|\|\|\|:\|\n______________CUAG_CUAUCUCC_____CCCUUG\n3'-UUU...UAGAA____A________CCAAC______UCUCU...AUA-5'\n_____________\|________________________\|\n_____________45_______________________20\n	216 -- 222	32 -- 38	-26.4443 kcal/mol	5.3846 kcal/mol	2.7671 kcal/mol	209 233@LB@ \| \|@LB@5'-CAC...CUAUG G UGAA CAGGG...GUU-3'@LB@ GAUC GAUAGAGG GGGAGC@LB@ \|\|\|\| \|\|\|\|\|\|\|\| \|\|\|\|:\|@LB@ CUAG CUAUCUCC CCCUUG@LB@3'-UUU...UAGAA A CCAAC UCUCU...AUA-5'@LB@ \| \|@LB@ 45 20@LB@@LB@@LB@Energy -18.29 kcal/mol@LB@Hybridization Energy -26.4443 kcal/mol@LB@Unfolding Energy - mRNA 5.3846 kcal/mol@LB@Unfolding Energy - sRNA 2.7671 kcal/mol@LB@@LB@Position - mRNA 210 -- 232@LB@Position - sRNA 21 -- 44@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 32 -- 38@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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