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
137	0.01211	0.2883	bsu27850	nadA	-8.79	0.309443	168 -- 191	32 -- 52	quinolinate synthase A		_____________167_______________________192\n_____________\|_________________________\|\n5'-UAC...UGUUA__UU___AAA__A____________AAUGC...UUA-3'\n______________CG__AUC___UG_AUCU_GUGGAGG\n______________\|\|__\|\|\|___\|\|_\|\|\|\|_:\|:\|\|\|\|\n______________GC__UAG___AC_UAGA_UAUCUCC\n3'-UUU...AAAAA__C____A_________C_______CCAAC...AUA-5'\n_____________\|_________________________\|\n_____________53________________________31\n	185 -- 191	32 -- 38	-13.8724 kcal/mol	4.10431 kcal/mol	0.976384 kcal/mol	167 192@LB@ \| \|@LB@5'-UAC...UGUUA UU AAA A AAUGC...UUA-3'@LB@ CG AUC UG AUCU GUGGAGG@LB@ \|\| \|\|\| \|\| \|\|\|\| :\|:\|\|\|\|@LB@ GC UAG AC UAGA UAUCUCC@LB@3'-UUU...AAAAA C A C CCAAC...AUA-5'@LB@ \| \|@LB@ 53 31@LB@@LB@@LB@Energy -8.79 kcal/mol@LB@Hybridization Energy -13.8724 kcal/mol@LB@Unfolding Energy - mRNA 4.10431 kcal/mol@LB@Unfolding Energy - sRNA 0.976384 kcal/mol@LB@@LB@Position - mRNA 168 -- 191@LB@Position - sRNA 32 -- 52@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 32 -- 38@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@
59	0.003314	0.1874	bsu01560	kbaA	-8.60	0.327174	11 -- 30	33 -- 52	kinB-signaling pathway activation protein		_____________10___________________31\n_____________\|____________________\|\n5'-AGU...AUAUC__CUG________UU_____CGCAA...AUA-3'\n______________CG___CUUGGUCU__UGGAG\n______________\|\|___\|\|\|\|:\|\|\|__\|:\|\|\|\n______________GC___GAACUAGA__AUCUC\n3'-UUU...AAAAA__CUA________CU_____CCCAA...AUA-5'\n_____________\|____________________\|\n_____________53___________________32\n	17 -- 23	40 -- 46	-17.5678 kcal/mol	7.9942 kcal/mol	0.976367 kcal/mol	10 31@LB@ \| \|@LB@5'-AGU...AUAUC CUG UU CGCAA...AUA-3'@LB@ CG CUUGGUCU UGGAG@LB@ \|\| \|\|\|\|:\|\|\| \|:\|\|\|@LB@ GC GAACUAGA AUCUC@LB@3'-UUU...AAAAA CUA CU CCCAA...AUA-5'@LB@ \| \|@LB@ 53 32@LB@@LB@@LB@Energy -8.60 kcal/mol@LB@Hybridization Energy -17.5678 kcal/mol@LB@Unfolding Energy - mRNA 7.9942 kcal/mol@LB@Unfolding Energy - sRNA 0.976367 kcal/mol@LB@@LB@Position - mRNA 11 -- 30@LB@Position - sRNA 33 -- 52@LB@Position Seed - mRNA 17 -- 23@LB@Position Seed - sRNA 40 -- 46@LB@
42	0.001862	0.1479	bsu40320	argI	-8.56	0.330283	1 -- 17	32 -- 48	arginase		______________1_________________18\n______________\|_________________\|\n___________5'-_____C_______CC___AGCAG...UGA-3'\n______________UCUUG_AUUUGAU___GG\n______________\|\|\|\|\|_\|\|:\|\|\|\|___\|\|\n______________AGAAC_UAGACUA___CC\n3'-UUU...AGCCU_____________UCU__CCAAC...AUA-5'\n_____________\|__________________\|\n_____________49_________________31\n	7 -- 13	37 -- 43	-12.1859 kcal/mol	2.6521 kcal/mol	0.970016 kcal/mol	1 18@LB@ \| \|@LB@ 5'- C CC AGCAG...UGA-3'@LB@ UCUUG AUUUGAU GG@LB@ \|\|\|\|\| \|\|:\|\|\|\| \|\|@LB@ AGAAC UAGACUA CC@LB@3'-UUU...AGCCU UCU CCAAC...AUA-5'@LB@ \| \|@LB@ 49 31@LB@@LB@@LB@Energy -8.56 kcal/mol@LB@Hybridization Energy -12.1859 kcal/mol@LB@Unfolding Energy - mRNA 2.6521 kcal/mol@LB@Unfolding Energy - sRNA 0.970016 kcal/mol@LB@@LB@Position - mRNA 1 -- 17@LB@Position - sRNA 32 -- 48@LB@Position Seed - mRNA 7 -- 13@LB@Position Seed - sRNA 37 -- 43@LB@
166	0.01583	0.3152	bsu38190	galT	-8.42	0.343831	170 -- 181	16 -- 26	galactose-1-phosphate uridylyltransferase		_____________169__________182\n_____________\|____________\|\n5'-GGG...GGAGA_______A____ACUAA...AUG-3'\n______________GGGAGCG_GAGA\n______________\|\|\|\|:\|:_\|\|\|\|\n______________CCCUUGU_CUCU\n3'-UUU...CCAAC____________CAUCG...AUA-5'\n_____________\|____________\|\n_____________27___________15\n	170 -- 176	20 -- 26	-15.5563 kcal/mol	1.12924 kcal/mol	6.00672 kcal/mol	169 182@LB@ \| \|@LB@5'-GGG...GGAGA A ACUAA...AUG-3'@LB@ GGGAGCG GAGA@LB@ \|\|\|\|:\|: \|\|\|\|@LB@ CCCUUGU CUCU@LB@3'-UUU...CCAAC CAUCG...AUA-5'@LB@ \| \|@LB@ 27 15@LB@@LB@@LB@Energy -8.42 kcal/mol@LB@Hybridization Energy -15.5563 kcal/mol@LB@Unfolding Energy - mRNA 1.12924 kcal/mol@LB@Unfolding Energy - sRNA 6.00672 kcal/mol@LB@@LB@Position - mRNA 170 -- 181@LB@Position - sRNA 16 -- 26@LB@Position Seed - mRNA 170 -- 176@LB@Position Seed - sRNA 20 -- 26@LB@
52	0.002415	0.1549	bsu03320	nasB	-8.41	0.344801	188 -- 199	36 -- 51	assimilatory nitrate reductase electron transfer subunit		_____________187______________200\n_____________\|________________\|\n5'-UUU...CCAAA________________CAUGA...UCA-3'\n______________GGA____GGUCUGAUA\n______________\|\|\|____\|:\|\|\|\|\|\|\|\n______________CCU____CUAGACUAU\n3'-UUU...AAAAG___AGAA_________CUCCC...AUA-5'\n_____________\|________________\|\n_____________52_______________35\n	193 -- 199	36 -- 42	-13.3061 kcal/mol	3.93547 kcal/mol	0.960469 kcal/mol	187 200@LB@ \| \|@LB@5'-UUU...CCAAA CAUGA...UCA-3'@LB@ GGA GGUCUGAUA@LB@ \|\|\| \|:\|\|\|\|\|\|\|@LB@ CCU CUAGACUAU@LB@3'-UUU...AAAAG AGAA CUCCC...AUA-5'@LB@ \| \|@LB@ 52 35@LB@@LB@@LB@Energy -8.41 kcal/mol@LB@Hybridization Energy -13.3061 kcal/mol@LB@Unfolding Energy - mRNA 3.93547 kcal/mol@LB@Unfolding Energy - sRNA 0.960469 kcal/mol@LB@@LB@Position - mRNA 188 -- 199@LB@Position - sRNA 36 -- 51@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 36 -- 42@LB@
146	0.01275	0.2913	bsu00450	sspF	-8.40	0.345478	283 -- 295	24 -- 38	small acid-soluble spore protein SspF		_____________282_____________296\n_____________\|_______________\|\n5'-UGA...AAAAA_______C_______UGAAA-3'\n______________AUGGAGG___UGGGG\n______________\|\|:\|\|\|\|___\|\|\|\|\|\n______________UAUCUCC___ACCCC\n3'-UUU...UAGAC_______CCA_____UUGUC...AUA-5'\n_____________\|_______________\|\n_____________39______________23\n	283 -- 289	32 -- 38	-17.1295 kcal/mol	8.05792 kcal/mol	0.668509 kcal/mol	282 296@LB@ \| \|@LB@5'-UGA...AAAAA C UGAAA-3'@LB@ AUGGAGG UGGGG@LB@ \|\|:\|\|\|\| \|\|\|\|\|@LB@ UAUCUCC ACCCC@LB@3'-UUU...UAGAC CCA UUGUC...AUA-5'@LB@ \| \|@LB@ 39 23@LB@@LB@@LB@Energy -8.40 kcal/mol@LB@Hybridization Energy -17.1295 kcal/mol@LB@Unfolding Energy - mRNA 8.05792 kcal/mol@LB@Unfolding Energy - sRNA 0.668509 kcal/mol@LB@@LB@Position - mRNA 283 -- 295@LB@Position - sRNA 24 -- 38@LB@Position Seed - mRNA 283 -- 289@LB@Position Seed - sRNA 32 -- 38@LB@
185	0.01858	0.3269	bsu27560	hisS	-8.40	0.345340	122 -- 132	25 -- 38	histidine--tRNA ligase		_____________121____________133\n_____________\|______________\|\n5'-GCG...GUAUA_______C______AGUUU...CUU-3'\n______________GUAGGGG____GGG\n______________:\|\|\|:\|\|____\|\|\|\n______________UAUCUCC____CCC\n3'-UUU...UAGAC_______CCAA___CUUGU...AUA-5'\n_____________\|______________\|\n_____________39_____________24\n	122 -- 128	32 -- 38	-11.8618 kcal/mol	2.79445 kcal/mol	0.662893 kcal/mol	121 133@LB@ \| \|@LB@5'-GCG...GUAUA C AGUUU...CUU-3'@LB@ GUAGGGG GGG@LB@ :\|\|\|:\|\| \|\|\|@LB@ UAUCUCC CCC@LB@3'-UUU...UAGAC CCAA CUUGU...AUA-5'@LB@ \| \|@LB@ 39 24@LB@@LB@@LB@Energy -8.40 kcal/mol@LB@Hybridization Energy -11.8618 kcal/mol@LB@Unfolding Energy - mRNA 2.79445 kcal/mol@LB@Unfolding Energy - sRNA 0.662893 kcal/mol@LB@@LB@Position - mRNA 122 -- 132@LB@Position - sRNA 25 -- 38@LB@Position Seed - mRNA 122 -- 128@LB@Position Seed - sRNA 32 -- 38@LB@
170	0.0164	0.3152	bsu13090	ykkC	-8.27	0.358617	162 -- 212	23 -- 55	multidrug resistance protein		_____________161__________________________________________________213\n_____________\|____________________________________________________\|\n5'-UCA...UUUGU_______GAA____A__A_______AA__AAUGACUCAAAAU_AAA______UUGGU...CCA-3'\n______________UUUCGGA___UCUU_AU__GAUAGA__GG_____________G___UGGGGA\n______________\|\|\|\|\|\|\|___\|\|\|\|_\|\|__\|\|\|\|\|\|__\|\|_____________\|___\|\|\|\|\|\|\n______________AAAGCCU___AGAA_UA__CUAUCU__CC_____________C___ACCCCU\n3'-UUU...UCAAA______________C__GA______C_________________A________UGUCU...AUA-5'\n_____________\|____________________________________________________\|\n_____________56___________________________________________________22\n	162 -- 168	49 -- 55	-21.902 kcal/mol	11.1231 kcal/mol	2.51158 kcal/mol	161 213@LB@ \| \|@LB@5'-UCA...UUUGU GAA A A AA AAUGACUCAAAAU AAA UUGGU...CCA-3'@LB@ UUUCGGA UCUU AU GAUAGA GG G UGGGGA@LB@ \|\|\|\|\|\|\| \|\|\|\| \|\| \|\|\|\|\|\| \|\| \| \|\|\|\|\|\|@LB@ AAAGCCU AGAA UA CUAUCU CC C ACCCCU@LB@3'-UUU...UCAAA C GA C A UGUCU...AUA-5'@LB@ \| \|@LB@ 56 22@LB@@LB@@LB@Energy -8.27 kcal/mol@LB@Hybridization Energy -21.902 kcal/mol@LB@Unfolding Energy - mRNA 11.1231 kcal/mol@LB@Unfolding Energy - sRNA 2.51158 kcal/mol@LB@@LB@Position - mRNA 162 -- 212@LB@Position - sRNA 23 -- 55@LB@Position Seed - mRNA 162 -- 168@LB@Position Seed - sRNA 49 -- 55@LB@
91	0.007102	0.2604	bsu36520	glnK	-7.98	0.387566	247 -- 267	32 -- 49	nitrogen regulatory PII-like protein		_____________246____________________268\n_____________\|______________________\|\n5'-GGU...GGCAA_______AAAG_______C___AACUC...CUU-3'\n______________AUUUUGA____CUGA_AG_AGG\n______________\|\|:\|\|\|\|____\|\|\|\|_\|\|_\|\|\|\n______________UAGAACU____GACU_UC_UCC\n3'-UUU...AAGCC_______A_______A______CCAAC...AUA-5'\n_____________\|______________________\|\n_____________50_____________________31\n	247 -- 253	43 -- 49	-11.0905 kcal/mol	2.14263 kcal/mol	0.970192 kcal/mol	246 268@LB@ \| \|@LB@5'-GGU...GGCAA AAAG C AACUC...CUU-3'@LB@ AUUUUGA CUGA AG AGG@LB@ \|\|:\|\|\|\| \|\|\|\| \|\| \|\|\|@LB@ UAGAACU GACU UC UCC@LB@3'-UUU...AAGCC A A CCAAC...AUA-5'@LB@ \| \|@LB@ 50 31@LB@@LB@@LB@Energy -7.98 kcal/mol@LB@Hybridization Energy -11.0905 kcal/mol@LB@Unfolding Energy - mRNA 2.14263 kcal/mol@LB@Unfolding Energy - sRNA 0.970192 kcal/mol@LB@@LB@Position - mRNA 247 -- 267@LB@Position - sRNA 32 -- 49@LB@Position Seed - mRNA 247 -- 253@LB@Position Seed - sRNA 43 -- 49@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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