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
89	0.00694	0.2588	bsu06230	iolT	-9.37	0.260314	174 -- 193	31 -- 49	major myo-inositol transporter IolT		_____________173__________________194\n_____________\|____________________\|\n5'-AAA...UACGC_______AAAA__CU_____AAACA...AUG-3'\n______________AUUUUGA____GA__GGGGG\n______________\|\|:\|\|\|\|____\|\|__\|:\|\|\|\n______________UAGAACU____CU__CUCCC\n3'-UUU...AAGCC_______AGA___AU_____CAACC...AUA-5'\n_____________\|____________________\|\n_____________50___________________30\n	174 -- 180	43 -- 49	-14.1903 kcal/mol	3.84886 kcal/mol	0.970571 kcal/mol	173 194@LB@ \| \|@LB@5'-AAA...UACGC AAAA CU AAACA...AUG-3'@LB@ AUUUUGA GA GGGGG@LB@ \|\|:\|\|\|\| \|\| \|:\|\|\|@LB@ UAGAACU CU CUCCC@LB@3'-UUU...AAGCC AGA AU CAACC...AUA-5'@LB@ \| \|@LB@ 50 30@LB@@LB@@LB@Energy -9.37 kcal/mol@LB@Hybridization Energy -14.1903 kcal/mol@LB@Unfolding Energy - mRNA 3.84886 kcal/mol@LB@Unfolding Energy - sRNA 0.970571 kcal/mol@LB@@LB@Position - mRNA 174 -- 193@LB@Position - sRNA 31 -- 49@LB@Position Seed - mRNA 174 -- 180@LB@Position Seed - sRNA 43 -- 49@LB@
22	0.0004167	0.06318	bsu07570	yflS	-5.44	0.672400	163 -- 208	8 -- 27	malate transporter YflS		_____________162____________________________________________209\n_____________\|______________________________________________\|\n5'-AUG...GAAAA_____U____AAACAAGUAUAUAG___GAGACCUAUUUA_______AGAAA...CUC-3'\n______________GGGGA_CGGA______________GAG____________UGGCUUC\n______________\|\|\|\|\|_\|:\|\|______________\|\|\|____________\|:\|\|\|\|\|\n______________CCCCU_GUCU______________CUC____________AUCGAAG\n3'-UUU...CCCAA_____U________________________________________AGAGAUA-5'\n_____________\|______________________________________________\|\n_____________28_____________________________________________7\n	202 -- 208	8 -- 14	-21.2785 kcal/mol	9.2406 kcal/mol	6.59627 kcal/mol	162 209@LB@ \| \|@LB@5'-AUG...GAAAA U AAACAAGUAUAUAG GAGACCUAUUUA AGAAA...CUC-3'@LB@ GGGGA CGGA GAG UGGCUUC@LB@ \|\|\|\|\| \|:\|\| \|\|\| \|:\|\|\|\|\|@LB@ CCCCU GUCU CUC AUCGAAG@LB@3'-UUU...CCCAA U AGAGAUA-5'@LB@ \| \|@LB@ 28 7@LB@@LB@@LB@Energy -5.44 kcal/mol@LB@Hybridization Energy -21.2785 kcal/mol@LB@Unfolding Energy - mRNA 9.2406 kcal/mol@LB@Unfolding Energy - sRNA 6.59627 kcal/mol@LB@@LB@Position - mRNA 163 -- 208@LB@Position - sRNA 8 -- 27@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 8 -- 14@LB@
54	0.002747	0.1697	bsu35790	yvyI	-14.15	0.043919	186 -- 197	25 -- 36	mannose-6-phosphate isomerase YvyI		_____________185__________198\n_____________\|____________\|\n5'-UCU...ACAGG________AC__AUCAU...AAU-3'\n______________GGAGGGGU__GG\n______________:\|\|\|\|\|\|\|__\|\|\n______________UCUCCCCA__CC\n3'-UUU...GACUA________AC__CUUGU...AUA-5'\n_____________\|____________\|\n_____________37___________24\n	187 -- 193	29 -- 35	-17.2174 kcal/mol	2.92719 kcal/mol	0.135926 kcal/mol	185 198@LB@ \| \|@LB@5'-UCU...ACAGG AC AUCAU...AAU-3'@LB@ GGAGGGGU GG@LB@ :\|\|\|\|\|\|\| \|\|@LB@ UCUCCCCA CC@LB@3'-UUU...GACUA AC CUUGU...AUA-5'@LB@ \| \|@LB@ 37 24@LB@@LB@@LB@Energy -14.15 kcal/mol@LB@Hybridization Energy -17.2174 kcal/mol@LB@Unfolding Energy - mRNA 2.92719 kcal/mol@LB@Unfolding Energy - sRNA 0.135926 kcal/mol@LB@@LB@Position - mRNA 186 -- 197@LB@Position - sRNA 25 -- 36@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 29 -- 35@LB@
7	4.152e-05	0.01979	bsu05670	ydgJ	-17.13	0.010734	234 -- 258	25 -- 49	MarR family transcriptional regulator		_____________233_______________________259\n_____________\|_________________________\|\n5'-AAG...UAAUA_______CAG__A___A___A____UUUUG...AUC-3'\n______________GUUUUGA___GA_AGA_GGG_UGGG\n______________:\|:\|\|\|\|___\|\|_\|\|\|_\|\|\|_\|\|\|\|\n______________UAGAACU___CU_UCU_CCC_ACCC\n3'-UUU...AAGCC_______AGA__A___C___A____CUUGU...AUA-5'\n_____________\|_________________________\|\n_____________50________________________24\n	234 -- 240	43 -- 49	-20.9262 kcal/mol	2.82407 kcal/mol	0.976049 kcal/mol	233 259@LB@ \| \|@LB@5'-AAG...UAAUA CAG A A A UUUUG...AUC-3'@LB@ GUUUUGA GA AGA GGG UGGG@LB@ :\|:\|\|\|\| \|\| \|\|\| \|\|\| \|\|\|\|@LB@ UAGAACU CU UCU CCC ACCC@LB@3'-UUU...AAGCC AGA A C A CUUGU...AUA-5'@LB@ \| \|@LB@ 50 24@LB@@LB@@LB@Energy -17.13 kcal/mol@LB@Hybridization Energy -20.9262 kcal/mol@LB@Unfolding Energy - mRNA 2.82407 kcal/mol@LB@Unfolding Energy - sRNA 0.976049 kcal/mol@LB@@LB@Position - mRNA 234 -- 258@LB@Position - sRNA 25 -- 49@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 43 -- 49@LB@
5	2.545e-05	0.01698	bsu22540	qcrC	-19.98	0.002129	169 -- 196	23 -- 48	menaquinol-cytochrome c reductase cytochrome b/c subunit		_____________168____________________________197\n_____________\|______________________________\|\n5'-AAC...UAAAC__________CGA___AA____A_______UGACA...AAA-3'\n______________UCUUGAUCUG___AUA__AGGG___GGGGA\n______________\|\|\|\|\|\|\|\|\|\|___\|\|\|__\|\|\|\|___\|\|\|\|\|\n______________AGAACUAGAC___UAU__UCCC___CCCCU\n3'-UUU...AGCCU________________C_____CAA_____UGUCU...AUA-5'\n_____________\|______________________________\|\n_____________49_____________________________22\n	172 -- 178	39 -- 45	-27.164 kcal/mol	6.20558 kcal/mol	0.979889 kcal/mol	168 197@LB@ \| \|@LB@5'-AAC...UAAAC CGA AA A UGACA...AAA-3'@LB@ UCUUGAUCUG AUA AGGG GGGGA@LB@ \|\|\|\|\|\|\|\|\|\| \|\|\| \|\|\|\| \|\|\|\|\|@LB@ AGAACUAGAC UAU UCCC CCCCU@LB@3'-UUU...AGCCU C CAA UGUCU...AUA-5'@LB@ \| \|@LB@ 49 22@LB@@LB@@LB@Energy -19.98 kcal/mol@LB@Hybridization Energy -27.164 kcal/mol@LB@Unfolding Energy - mRNA 6.20558 kcal/mol@LB@Unfolding Energy - sRNA 0.979889 kcal/mol@LB@@LB@Position - mRNA 169 -- 196@LB@Position - sRNA 23 -- 48@LB@Position Seed - mRNA 172 -- 178@LB@Position Seed - sRNA 39 -- 45@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@
71	0.005061	0.2378	bsu02170	ybfB	-12.87	0.075045	244 -- 269	24 -- 48	MFS transporter	bsu03530	_____________243__________________________270\n_____________\|____________________________\|\n5'-CUU...CACCU_____________UU__C____CA____GUGCG...AGC-3'\n______________UUUUGAUCU__UA__GG_GGUU__GGGG\n______________\|:\|\|\|\|\|\|\|__\|\|__\|\|_\|\|\|\|__\|\|\|\|\n______________AGAACUAGA__AU__CC_CCAA__CCCC\n3'-UUU...AGCCU_________CU__CU_____________UUGUC...AUA-5'\n_____________\|____________________________\|\n_____________49___________________________23\n	246 -- 252	40 -- 46	-21.3597 kcal/mol	7.5105 kcal/mol	0.978761 kcal/mol	243 270@LB@ \| \|@LB@5'-CUU...CACCU UU C CA GUGCG...AGC-3'@LB@ UUUUGAUCU UA GG GGUU GGGG@LB@ \|:\|\|\|\|\|\|\| \|\| \|\| \|\|\|\| \|\|\|\|@LB@ AGAACUAGA AU CC CCAA CCCC@LB@3'-UUU...AGCCU CU CU UUGUC...AUA-5'@LB@ \| \|@LB@ 49 23@LB@@LB@@LB@Energy -12.87 kcal/mol@LB@Hybridization Energy -21.3597 kcal/mol@LB@Unfolding Energy - mRNA 7.5105 kcal/mol@LB@Unfolding Energy - sRNA 0.978761 kcal/mol@LB@@LB@Position - mRNA 244 -- 269@LB@Position - sRNA 24 -- 48@LB@Position Seed - mRNA 246 -- 252@LB@Position Seed - sRNA 40 -- 46@LB@
119	0.01041	0.2883	bsu11480	yjbB	-12.30	0.094041	10 -- 19	22 -- 31	MFS transporter	bsu07460	_____________9__________20\n_____________\|__________\|\n5'-UCA...UUAAA__A_______ACGAU...GGA-3'\n______________GG_UGGGGAA\n______________\|\|_\|\|\|\|\|\|\|\n______________CC_ACCCCUU\n3'-UUU...UCUCC__A_______GUCUC...AUA-5'\n_____________\|__________\|\n_____________32_________21\n	13 -- 19	22 -- 28	-13.9571 kcal/mol	0.741777 kcal/mol	0.918006 kcal/mol	9 20@LB@ \| \|@LB@5'-UCA...UUAAA A ACGAU...GGA-3'@LB@ GG UGGGGAA@LB@ \|\| \|\|\|\|\|\|\|@LB@ CC ACCCCUU@LB@3'-UUU...UCUCC A GUCUC...AUA-5'@LB@ \| \|@LB@ 32 21@LB@@LB@@LB@Energy -12.30 kcal/mol@LB@Hybridization Energy -13.9571 kcal/mol@LB@Unfolding Energy - mRNA 0.741777 kcal/mol@LB@Unfolding Energy - sRNA 0.918006 kcal/mol@LB@@LB@Position - mRNA 10 -- 19@LB@Position - sRNA 22 -- 31@LB@Position Seed - mRNA 13 -- 19@LB@Position Seed - sRNA 22 -- 28@LB@
132	0.01159	0.2883	bsu33140	yvqJ	-14.19	0.043338	185 -- 204	31 -- 52	MFS transporter		_____________184____________________205\n_____________\|______________________\|\n5'-GAC...GGCAA____GG___C_________U__UGAAU...UUA-3'\n______________CGGG____G_UCUGAUGGA_GG\n______________\|\|\|:____\|_\|\|\|\|\|\|:\|\|_\|\|\n______________GCCU____C_AGACUAUCU_CC\n3'-UUU...AAAAA____AGAA_U_________C__CAACC...AUA-5'\n_____________\|______________________\|\n_____________53_____________________30\n	195 -- 201	34 -- 40	-19.4408 kcal/mol	4.27934 kcal/mol	0.976414 kcal/mol	184 205@LB@ \| \|@LB@5'-GAC...GGCAA GG C U UGAAU...UUA-3'@LB@ CGGG G UCUGAUGGA GG@LB@ \|\|\|: \| \|\|\|\|\|\|:\|\| \|\|@LB@ GCCU C AGACUAUCU CC@LB@3'-UUU...AAAAA AGAA U C CAACC...AUA-5'@LB@ \| \|@LB@ 53 30@LB@@LB@@LB@Energy -14.19 kcal/mol@LB@Hybridization Energy -19.4408 kcal/mol@LB@Unfolding Energy - mRNA 4.27934 kcal/mol@LB@Unfolding Energy - sRNA 0.976414 kcal/mol@LB@@LB@Position - mRNA 185 -- 204@LB@Position - sRNA 31 -- 52@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 34 -- 40@LB@
140	0.01224	0.2883	bsu36480	ywoD	-6.33	0.569704	31 -- 37	66 -- 72	MFS transporter		_____________30______38\n_____________\|_______\|\n5'-AUU...AUAUC_______AAAGC...AUA-3'\n______________GGGGUGG\n______________\|\|\|\|\|:\|\n______________CCCCAUC\n3'-UUU...ACCGC_______GCGGU...AUA-5'\n_____________\|_______\|\n_____________73______65\n	31 -- 37	66 -- 72	-11.1749 kcal/mol	4.83937 kcal/mol	0.00366414 kcal/mol	30 38@LB@ \| \|@LB@5'-AUU...AUAUC AAAGC...AUA-3'@LB@ GGGGUGG@LB@ \|\|\|\|\|:\|@LB@ CCCCAUC@LB@3'-UUU...ACCGC GCGGU...AUA-5'@LB@ \| \|@LB@ 73 65@LB@@LB@@LB@Energy -6.33 kcal/mol@LB@Hybridization Energy -11.1749 kcal/mol@LB@Unfolding Energy - mRNA 4.83937 kcal/mol@LB@Unfolding Energy - sRNA 0.00366414 kcal/mol@LB@@LB@Position - mRNA 31 -- 37@LB@Position - sRNA 66 -- 72@LB@Position Seed - mRNA 31 -- 37@LB@Position Seed - sRNA 66 -- 72@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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