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
175	0.01672	0.3152	bsu04630	ydcC	-11.64	0.120416	196 -- 203	27 -- 34	sporulation protein YdcC		_____________195______204\n_____________\|________\|\n5'-CCG...GAAAA________AAAAA...UGG-3'\n______________AGGGGUUG\n______________\|\|\|\|\|\|\|\|\n______________UCCCCAAC\n3'-UUU...CUAUC________CCCUU...AUA-5'\n_____________\|________\|\n_____________35_______26\n	197 -- 203	27 -- 33	-14.5305 kcal/mol	2.76844 kcal/mol	0.118612 kcal/mol	195 204@LB@ \| \|@LB@5'-CCG...GAAAA AAAAA...UGG-3'@LB@ AGGGGUUG@LB@ \|\|\|\|\|\|\|\|@LB@ UCCCCAAC@LB@3'-UUU...CUAUC CCCUU...AUA-5'@LB@ \| \|@LB@ 35 26@LB@@LB@@LB@Energy -11.64 kcal/mol@LB@Hybridization Energy -14.5305 kcal/mol@LB@Unfolding Energy - mRNA 2.76844 kcal/mol@LB@Unfolding Energy - sRNA 0.118612 kcal/mol@LB@@LB@Position - mRNA 196 -- 203@LB@Position - sRNA 27 -- 34@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 27 -- 33@LB@
190	0.01911	0.3269	bsu05370	ydfD	-12.16	0.099313	269 -- 294	11 -- 36	GntR family transcriptional regulator	bsu10880	_____________268________________________295\n_____________\|__________________________\|\n5'-AAA...AUUAA____AAAAUA__A_____________CGAUUG-3'\n______________AGAG______GG_AAUGGAGAGUGGC\n______________\|\|\|\|______\|\|_\|\|::\|\|\|\|\|\|:\|\|\n______________UCUC______CC_UUGUCUCUCAUCG\n3'-UUU...GACUA____CCCAAC__C_____________AAGAG...AUA-5'\n_____________\|__________________________\|\n_____________37_________________________10\n	288 -- 294	11 -- 17	-24.9379 kcal/mol	3.68177 kcal/mol	9.10067 kcal/mol	268 295@LB@ \| \|@LB@5'-AAA...AUUAA AAAAUA A CGAUUG-3'@LB@ AGAG GG AAUGGAGAGUGGC@LB@ \|\|\|\| \|\| \|\|::\|\|\|\|\|\|:\|\|@LB@ UCUC CC UUGUCUCUCAUCG@LB@3'-UUU...GACUA CCCAAC C AAGAG...AUA-5'@LB@ \| \|@LB@ 37 10@LB@@LB@@LB@Energy -12.16 kcal/mol@LB@Hybridization Energy -24.9379 kcal/mol@LB@Unfolding Energy - mRNA 3.68177 kcal/mol@LB@Unfolding Energy - sRNA 9.10067 kcal/mol@LB@@LB@Position - mRNA 269 -- 294@LB@Position - sRNA 11 -- 36@LB@Position Seed - mRNA 288 -- 294@LB@Position Seed - sRNA 11 -- 17@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@
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@
102	0.008773	0.2778	bsu06170	ydjE	-10.58	0.175640	264 -- 284	30 -- 50	sugar kinase YdjE		_____________263___________________285\n_____________\|_____________________\|\n5'-GGG...AUGUU__CG_______A_____A___CGCCA...AAA-3'\n______________GA__UUGAUUU_AUGGA_GGG\n______________\|\|__\|\|\|\|\|:\|_\|\|:\|\|_\|\|\|\n______________CU__AACUAGA_UAUCU_CCC\n3'-UUU...AAAGC__AG_______C_____C___AACCC...AUA-5'\n_____________\|_____________________\|\n_____________51____________________29\n	268 -- 274	40 -- 46	-17.5575 kcal/mol	6.00068 kcal/mol	0.974272 kcal/mol	263 285@LB@ \| \|@LB@5'-GGG...AUGUU CG A A CGCCA...AAA-3'@LB@ GA UUGAUUU AUGGA GGG@LB@ \|\| \|\|\|\|\|:\| \|\|:\|\| \|\|\|@LB@ CU AACUAGA UAUCU CCC@LB@3'-UUU...AAAGC AG C C AACCC...AUA-5'@LB@ \| \|@LB@ 51 29@LB@@LB@@LB@Energy -10.58 kcal/mol@LB@Hybridization Energy -17.5575 kcal/mol@LB@Unfolding Energy - mRNA 6.00068 kcal/mol@LB@Unfolding Energy - sRNA 0.974272 kcal/mol@LB@@LB@Position - mRNA 264 -- 284@LB@Position - sRNA 30 -- 50@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 40 -- 46@LB@
81	0.005945	0.2448	bsu06390	yebD	-16.11	0.017881	267 -- 291	30 -- 53	Evidence 5: No homology to any previously reported sequences		_____________266_______________________292\n_____________\|_________________________\|\n5'-UUU...UGCUC_____A___U___AA__A_______AACAG...UUG-3'\n______________UCGGA_UUU_AUC__GG_AGAGGGG\n______________\|\|\|\|\|_:\|\|_\|\|\|__\|:_\|\|\|\|\|\|\|\n______________AGCCU_GAA_UAG__CU_UCUCCCC\n3'-UUU...AAAAA_____A___C___A___A_______AACCC...AUA-5'\n_____________\|_________________________\|\n_____________54________________________29\n	285 -- 291	30 -- 36	-22.0812 kcal/mol	4.98677 kcal/mol	0.985344 kcal/mol	266 292@LB@ \| \|@LB@5'-UUU...UGCUC A U AA A AACAG...UUG-3'@LB@ UCGGA UUU AUC GG AGAGGGG@LB@ \|\|\|\|\| :\|\| \|\|\| \|: \|\|\|\|\|\|\|@LB@ AGCCU GAA UAG CU UCUCCCC@LB@3'-UUU...AAAAA A C A A AACCC...AUA-5'@LB@ \| \|@LB@ 54 29@LB@@LB@@LB@Energy -16.11 kcal/mol@LB@Hybridization Energy -22.0812 kcal/mol@LB@Unfolding Energy - mRNA 4.98677 kcal/mol@LB@Unfolding Energy - sRNA 0.985344 kcal/mol@LB@@LB@Position - mRNA 267 -- 291@LB@Position - sRNA 30 -- 53@LB@Position Seed - mRNA 285 -- 291@LB@Position Seed - sRNA 30 -- 36@LB@
53	0.002724	0.1697	bsu06970	yesO	-13.13	0.067695	188 -- 199	26 -- 36	ABC transporter substrate-binding protein		_____________187__________200\n_____________\|____________\|\n5'-CGA...AUUAA_______A____UUUGA...UUA-3'\n______________AGGGGGG_UUGG\n______________\|\|:\|\|\|\|_\|\|\|\|\n______________UCUCCCC_AACC\n3'-UUU...GACUA____________CCUUG...AUA-5'\n_____________\|____________\|\n_____________37___________25\n	188 -- 194	30 -- 36	-17.5942 kcal/mol	4.33325 kcal/mol	0.135623 kcal/mol	187 200@LB@ \| \|@LB@5'-CGA...AUUAA A UUUGA...UUA-3'@LB@ AGGGGGG UUGG@LB@ \|\|:\|\|\|\| \|\|\|\|@LB@ UCUCCCC AACC@LB@3'-UUU...GACUA CCUUG...AUA-5'@LB@ \| \|@LB@ 37 25@LB@@LB@@LB@Energy -13.13 kcal/mol@LB@Hybridization Energy -17.5942 kcal/mol@LB@Unfolding Energy - mRNA 4.33325 kcal/mol@LB@Unfolding Energy - sRNA 0.135623 kcal/mol@LB@@LB@Position - mRNA 188 -- 199@LB@Position - sRNA 26 -- 36@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 30 -- 36@LB@
61	0.003607	0.1972	bsu06860	yezE	-12.02	0.104394	226 -- 262	26 -- 52	TetR family transcriptional regulator		_____________225___________________________________263\n_____________\|_____________________________________\|\n5'-AGG...UGAUA___CG____U___UCACAGGGC________UUU____AGAGU...UGC-3'\n______________CGG__CUUG_UCU_________GAUAGAGG___UUGG\n______________\|\|\|__\|\|\|\|_\|\|\|_________\|\|\|\|\|\|\|\|___\|\|\|\|\n______________GCC__GAAC_AGA_________CUAUCUCC___AACC\n3'-UUU...AAAAA___UA____U____________________CC_____CCUUG...AUA-5'\n_____________\|_____________________________________\|\n_____________53____________________________________25\n	249 -- 255	32 -- 38	-24.4528 kcal/mol	11.4473 kcal/mol	0.980817 kcal/mol	225 263@LB@ \| \|@LB@5'-AGG...UGAUA CG U UCACAGGGC UUU AGAGU...UGC-3'@LB@ CGG CUUG UCU GAUAGAGG UUGG@LB@ \|\|\| \|\|\|\| \|\|\| \|\|\|\|\|\|\|\| \|\|\|\|@LB@ GCC GAAC AGA CUAUCUCC AACC@LB@3'-UUU...AAAAA UA U CC CCUUG...AUA-5'@LB@ \| \|@LB@ 53 25@LB@@LB@@LB@Energy -12.02 kcal/mol@LB@Hybridization Energy -24.4528 kcal/mol@LB@Unfolding Energy - mRNA 11.4473 kcal/mol@LB@Unfolding Energy - sRNA 0.980817 kcal/mol@LB@@LB@Position - mRNA 226 -- 262@LB@Position - sRNA 26 -- 52@LB@Position Seed - mRNA 249 -- 255@LB@Position Seed - sRNA 32 -- 38@LB@
109	0.009307	0.2778	bsu07880	yfkJ	-15.70	0.021808	288 -- 299	30 -- 51	low molecular weight protein-tyrosine-phosphatase YfkJ		_____________287____________________300\n_____________\|______________________\|\n5'-GGU...AAAAA______________________A-3'\n______________GGAU__________UAGAGGGG\n______________\|\|\|\|__________\|\|\|\|\|\|\|\|\n______________CCUA__________AUCUCCCC\n3'-UUU...AAAAG____GAACUAGACU________AACCC...AUA-5'\n_____________\|______________________\|\n_____________52_____________________29\n	293 -- 299	30 -- 36	-17.0834 kcal/mol	0.412933 kcal/mol	0.974282 kcal/mol	287 300@LB@ \| \|@LB@5'-GGU...AAAAA A-3'@LB@ GGAU UAGAGGGG@LB@ \|\|\|\| \|\|\|\|\|\|\|\|@LB@ CCUA AUCUCCCC@LB@3'-UUU...AAAAG GAACUAGACU AACCC...AUA-5'@LB@ \| \|@LB@ 52 29@LB@@LB@@LB@Energy -15.70 kcal/mol@LB@Hybridization Energy -17.0834 kcal/mol@LB@Unfolding Energy - mRNA 0.412933 kcal/mol@LB@Unfolding Energy - sRNA 0.974282 kcal/mol@LB@@LB@Position - mRNA 288 -- 299@LB@Position - sRNA 30 -- 51@LB@Position Seed - mRNA 293 -- 299@LB@Position Seed - sRNA 30 -- 36@LB@
169	0.01639	0.3152	bsu07850	yfkM	-11.33	0.135062	186 -- 208	22 -- 34	general stress protein 18		_____________185_____________________209\n_____________\|_______________________\|\n5'-UGU...AAAGC___A___UAUGAAUCA_______AAAAA...CUG-3'\n______________GGG_GGU_________UGGGGAA\n______________:\|\|_\|\|\|_________\|\|\|\|\|\|\|\n______________UCC_CCA_________ACCCCUU\n3'-UUU...CUAUC_______________________GUCUC...AUA-5'\n_____________\|_______________________\|\n_____________35______________________21\n	202 -- 208	22 -- 28	-15.0114 kcal/mol	2.66027 kcal/mol	1.02154 kcal/mol	185 209@LB@ \| \|@LB@5'-UGU...AAAGC A UAUGAAUCA AAAAA...CUG-3'@LB@ GGG GGU UGGGGAA@LB@ :\|\| \|\|\| \|\|\|\|\|\|\|@LB@ UCC CCA ACCCCUU@LB@3'-UUU...CUAUC GUCUC...AUA-5'@LB@ \| \|@LB@ 35 21@LB@@LB@@LB@Energy -11.33 kcal/mol@LB@Hybridization Energy -15.0114 kcal/mol@LB@Unfolding Energy - mRNA 2.66027 kcal/mol@LB@Unfolding Energy - sRNA 1.02154 kcal/mol@LB@@LB@Position - mRNA 186 -- 208@LB@Position - sRNA 22 -- 34@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)

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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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