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
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@
159	0.01439	0.3008	bsu00560	spoVT	-10.85	0.160189	242 -- 254	41 -- 53	stage V sporulation protein T	_____________241___________255\n_____________\|_____________\|\n5'-ACA...UUAGG_______G_____CCUAA...CGC-3'\n______________UCGGGUC_UGAUU\n______________\|\|\|\|:\|\|_\|\|\|\|:\n______________AGCCUAG_ACUAG\n3'-UUU...AAAAA_______A_____ACUAU...AUA-5'\n_____________\|_____________\|\n_____________54____________40\n	242 -- 248	47 -- 53	-14.0147 kcal/mol	2.18551 kcal/mol	0.979862 kcal/mol	241 255@LB@ \| \|@LB@5'-ACA...UUAGG G CCUAA...CGC-3'@LB@ UCGGGUC UGAUU@LB@ \|\|\|\|:\|\| \|\|\|\|:@LB@ AGCCUAG ACUAG@LB@3'-UUU...AAAAA A ACUAU...AUA-5'@LB@ \| \|@LB@ 54 40@LB@@LB@@LB@Energy -10.85 kcal/mol@LB@Hybridization Energy -14.0147 kcal/mol@LB@Unfolding Energy - mRNA 2.18551 kcal/mol@LB@Unfolding Energy - sRNA 0.979862 kcal/mol@LB@@LB@Position - mRNA 242 -- 254@LB@Position - sRNA 41 -- 53@LB@Position Seed - mRNA 242 -- 248@LB@Position Seed - sRNA 47 -- 53@LB@
195	0.01942	0.3269	bsu00690	ftsH	-11.53	0.125763	258 -- 269	21 -- 33	ATP-dependent zinc metalloprotease FtsH	_____________257___________270\n_____________\|_____________\|\n5'-AGU...UAAUC_______U_____UACUU...AAA-3'\n______________GGGGUUG__GAGC\n______________\|\|\|\|\|\|\|__\|\|:\|\n______________CCCCAAC__CUUG\n3'-UUU...UAUCU_______CC____UCUCU...AUA-5'\n_____________\|_____________\|\n_____________34____________20\n	258 -- 264	27 -- 33	-15.4755 kcal/mol	2.12746 kcal/mol	1.8225 kcal/mol	257 270@LB@ \| \|@LB@5'-AGU...UAAUC U UACUU...AAA-3'@LB@ GGGGUUG GAGC@LB@ \|\|\|\|\|\|\| \|\|:\|@LB@ CCCCAAC CUUG@LB@3'-UUU...UAUCU CC UCUCU...AUA-5'@LB@ \| \|@LB@ 34 20@LB@@LB@@LB@Energy -11.53 kcal/mol@LB@Hybridization Energy -15.4755 kcal/mol@LB@Unfolding Energy - mRNA 2.12746 kcal/mol@LB@Unfolding Energy - sRNA 1.8225 kcal/mol@LB@@LB@Position - mRNA 258 -- 269@LB@Position - sRNA 21 -- 33@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 27 -- 33@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@
177	0.01681	0.3152	bsu00910	ispF	-14.14	0.044127	219 -- 247	31 -- 51	2-D-methyl-D-erythritol 2 4-cyclodiphosphate synthase	_____________218____________________________248\n_____________\|______________________________\|\n5'-UCG...GACAA__________G__CAUCAAUUA________CCGUC...UUG-3'\n______________GGAUU_UGAU_UG_________GUGGAGGG\n______________\|\|\|\|:_\|\|\|\|_\|\|_________:\|:\|\|\|\|\|\n______________CCUAG_ACUA_AC_________UAUCUCCC\n3'-UUU...AAAAG_____A____G___________________CAACC...AUA-5'\n_____________\|______________________________\|\n_____________52_____________________________30\n	241 -- 247	31 -- 37	-21.3343 kcal/mol	6.22033 kcal/mol	0.970589 kcal/mol	218 248@LB@ \| \|@LB@5'-UCG...GACAA G CAUCAAUUA CCGUC...UUG-3'@LB@ GGAUU UGAU UG GUGGAGGG@LB@ \|\|\|\|: \|\|\|\| \|\| :\|:\|\|\|\|\|@LB@ CCUAG ACUA AC UAUCUCCC@LB@3'-UUU...AAAAG A G CAACC...AUA-5'@LB@ \| \|@LB@ 52 30@LB@@LB@@LB@Energy -14.14 kcal/mol@LB@Hybridization Energy -21.3343 kcal/mol@LB@Unfolding Energy - mRNA 6.22033 kcal/mol@LB@Unfolding Energy - sRNA 0.970589 kcal/mol@LB@@LB@Position - mRNA 219 -- 247@LB@Position - sRNA 31 -- 51@LB@Position Seed - mRNA 241 -- 247@LB@Position Seed - sRNA 31 -- 37@LB@
23	0.0004941	0.06638	bsu00930	cysE	-16.71	0.013304	161 -- 195	22 -- 53	serine acetyltransferase	_____________160_________________________________196\n_____________\|___________________________________\|\n5'-CCU...UUUUA______AGAG__AA__A_______AAACG______AGCAU...UAC-3'\n______________UUGGGU____GA__UC_GAUAGAG_____GGGGGA\n______________\|:\|\|:\|____\|\|__\|\|_\|\|\|\|\|\|\|_____\|\|\|\|:\|\n______________AGCCUA____CU__AG_CUAUCUC_____CCCCUU\n3'-UUU...AAAAA______GAA_______A_______CCCAA______GUCUC...AUA-5'\n_____________\|___________________________________\|\n_____________54__________________________________21\n	178 -- 184	33 -- 39	-24.9399 kcal/mol	6.34776 kcal/mol	1.88616 kcal/mol	160 196@LB@ \| \|@LB@5'-CCU...UUUUA AGAG AA A AAACG AGCAU...UAC-3'@LB@ UUGGGU GA UC GAUAGAG GGGGGA@LB@ \|:\|\|:\| \|\| \|\| \|\|\|\|\|\|\| \|\|\|\|:\|@LB@ AGCCUA CU AG CUAUCUC CCCCUU@LB@3'-UUU...AAAAA GAA A CCCAA GUCUC...AUA-5'@LB@ \| \|@LB@ 54 21@LB@@LB@@LB@Energy -16.71 kcal/mol@LB@Hybridization Energy -24.9399 kcal/mol@LB@Unfolding Energy - mRNA 6.34776 kcal/mol@LB@Unfolding Energy - sRNA 1.88616 kcal/mol@LB@@LB@Position - mRNA 161 -- 195@LB@Position - sRNA 22 -- 53@LB@Position Seed - mRNA 178 -- 184@LB@Position Seed - sRNA 33 -- 39@LB@
43	0.00194	0.1492	bsu01370	adk	-12.74	0.079154	128 -- 149	32 -- 52	adenylate kinase	_____________127____________________150\n_____________\|______________________\|\n5'-UUU...UACCG_______A___AAAAC______AAAUG...AUA-3'\n______________UGGAUUU_UGA_____UAGAGG\n______________:\|\|\|\|:\|_\|\|\|_____\|\|\|\|\|\|\n______________GCCUAGA_ACU_____AUCUCC\n3'-UUU...AAAAA___________AGACU______CCAAC...AUA-5'\n_____________\|______________________\|\n_____________53_____________________31\n	128 -- 134	46 -- 52	-16.4639 kcal/mol	2.75066 kcal/mol	0.976384 kcal/mol	127 150@LB@ \| \|@LB@5'-UUU...UACCG A AAAAC AAAUG...AUA-3'@LB@ UGGAUUU UGA UAGAGG@LB@ :\|\|\|\|:\| \|\|\| \|\|\|\|\|\|@LB@ GCCUAGA ACU AUCUCC@LB@3'-UUU...AAAAA AGACU CCAAC...AUA-5'@LB@ \| \|@LB@ 53 31@LB@@LB@@LB@Energy -12.74 kcal/mol@LB@Hybridization Energy -16.4639 kcal/mol@LB@Unfolding Energy - mRNA 2.75066 kcal/mol@LB@Unfolding Energy - sRNA 0.976384 kcal/mol@LB@@LB@Position - mRNA 128 -- 149@LB@Position - sRNA 32 -- 52@LB@Position Seed - mRNA 128 -- 134@LB@Position Seed - sRNA 46 -- 52@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@
134	0.01184	0.2883	bsu01450	cbiO	-8.85	0.304208	221 -- 231	32 -- 43	energy-coupling factor transporter ATP-binding protein EcfA1	_____________220__________232\n_____________\|____________\|\n5'-AUA...UUGAU____________AUAUC...AUG-3'\n______________AUC_GGUAGAGG\n______________\|\|\|_\|:\|\|\|\|\|\|\n______________UAG_CUAUCUCC\n3'-UUU...AGAAC___A________CCAAC...AUA-5'\n_____________\|____________\|\n_____________44___________31\n	225 -- 231	32 -- 38	-12.7681 kcal/mol	2.95776 kcal/mol	0.959872 kcal/mol	220 232@LB@ \| \|@LB@5'-AUA...UUGAU AUAUC...AUG-3'@LB@ AUC GGUAGAGG@LB@ \|\|\| \|:\|\|\|\|\|\|@LB@ UAG CUAUCUCC@LB@3'-UUU...AGAAC A CCAAC...AUA-5'@LB@ \| \|@LB@ 44 31@LB@@LB@@LB@Energy -8.85 kcal/mol@LB@Hybridization Energy -12.7681 kcal/mol@LB@Unfolding Energy - mRNA 2.95776 kcal/mol@LB@Unfolding Energy - sRNA 0.959872 kcal/mol@LB@@LB@Position - mRNA 221 -- 231@LB@Position - sRNA 32 -- 43@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 32 -- 38@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@

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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