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
21	0.0003947	0.0627	bsu28260	leuC	-16.01	0.018761	166 -- 191	26 -- 52	3-isopropylmalate dehydratase large subunit	_____________165___________________________192\n_____________\|_____________________________\|\n5'-GAA...UUAAG________A_C___A_________A____AAAUA...UUC-3'\n______________CGG_UCUU_G_UCU_GGUAGAGGG___GG\n______________\|\|\|_\|\|\|\|_\|_\|\|\|_\|:\|\|\|\|\|\|\|___\|\|\n______________GCC_AGAA_C_AGA_CUAUCUCCC___CC\n3'-UUU...AAAAA___U______U_____________CAA__CCUUG...AUA-5'\n_____________\|_____________________________\|\n_____________53____________________________25\n	182 -- 188	31 -- 37	-26.3594 kcal/mol	9.36849 kcal/mol	0.980817 kcal/mol	165 192@LB@ \| \|@LB@5'-GAA...UUAAG A C A A AAAUA...UUC-3'@LB@ CGG UCUU G UCU GGUAGAGGG GG@LB@ \|\|\| \|\|\|\| \| \|\|\| \|:\|\|\|\|\|\|\| \|\|@LB@ GCC AGAA C AGA CUAUCUCCC CC@LB@3'-UUU...AAAAA U U CAA CCUUG...AUA-5'@LB@ \| \|@LB@ 53 25@LB@@LB@@LB@Energy -16.01 kcal/mol@LB@Hybridization Energy -26.3594 kcal/mol@LB@Unfolding Energy - mRNA 9.36849 kcal/mol@LB@Unfolding Energy - sRNA 0.980817 kcal/mol@LB@@LB@Position - mRNA 166 -- 191@LB@Position - sRNA 26 -- 52@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 31 -- 37@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@
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@
24	0.0005065	0.06638	bsu23150	resA	-19.55	0.002768	169 -- 191	24 -- 44	thiol-disulfide oxidoreductase ResA	_____________168_____________________192\n_____________\|_______________________\|\n5'-GUU...GAAUG______CA________AAG____CAGUG...AAG-3'\n______________GAUCUG__AUAGGGGG___GGGG\n______________\|\|\|\|\|\|__\|\|\|\|:\|\|\|___\|\|\|\|\n______________CUAGAC__UAUCUCCC___CCCC\n3'-UUU...UAGAA________________CAA____UUGUC...AUA-5'\n_____________\|_______________________\|\n_____________45______________________23\n	178 -- 184	31 -- 37	-27.4404 kcal/mol	6.91177 kcal/mol	0.977523 kcal/mol	168 192@LB@ \| \|@LB@5'-GUU...GAAUG CA AAG CAGUG...AAG-3'@LB@ GAUCUG AUAGGGGG GGGG@LB@ \|\|\|\|\|\| \|\|\|\|:\|\|\| \|\|\|\|@LB@ CUAGAC UAUCUCCC CCCC@LB@3'-UUU...UAGAA CAA UUGUC...AUA-5'@LB@ \| \|@LB@ 45 23@LB@@LB@@LB@Energy -19.55 kcal/mol@LB@Hybridization Energy -27.4404 kcal/mol@LB@Unfolding Energy - mRNA 6.91177 kcal/mol@LB@Unfolding Energy - sRNA 0.977523 kcal/mol@LB@@LB@Position - mRNA 169 -- 191@LB@Position - sRNA 24 -- 44@LB@Position Seed - mRNA 178 -- 184@LB@Position Seed - sRNA 31 -- 37@LB@
25	0.0005172	0.06638	bsu30210	bioD	-10.94	0.155183	179 -- 210	28 -- 53	ATP-dependent dethiobiotin synthetase BioD	_____________178_______________________________211\n_____________\|_________________________________\|\n5'-GUC...UUCAA_____AAG___G___CACAUCAUUU________UUUUU...UCG-3'\n______________UCGGA____GA_CUG__________GAGGGGUU\n______________\|\|\|\|\|____\|\|_\|\|\|__________\|\|\|\|\|\|\|\|\n______________AGCCU____CU_GAC__________CUCCCCAA\n3'-UUU...AAAAA_____AGAA__A___UAU_______________CCCCU...AUA-5'\n_____________\|_________________________________\|\n_____________54________________________________27\n	204 -- 210	28 -- 34	-21.1469 kcal/mol	9.22099 kcal/mol	0.985925 kcal/mol	178 211@LB@ \| \|@LB@5'-GUC...UUCAA AAG G CACAUCAUUU UUUUU...UCG-3'@LB@ UCGGA GA CUG GAGGGGUU@LB@ \|\|\|\|\| \|\| \|\|\| \|\|\|\|\|\|\|\|@LB@ AGCCU CU GAC CUCCCCAA@LB@3'-UUU...AAAAA AGAA A UAU CCCCU...AUA-5'@LB@ \| \|@LB@ 54 27@LB@@LB@@LB@Energy -10.94 kcal/mol@LB@Hybridization Energy -21.1469 kcal/mol@LB@Unfolding Energy - mRNA 9.22099 kcal/mol@LB@Unfolding Energy - sRNA 0.985925 kcal/mol@LB@@LB@Position - mRNA 179 -- 210@LB@Position - sRNA 28 -- 53@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 28 -- 34@LB@
26	0.0005174	0.06638	bsu28170	hemA	-17.53	0.008676	171 -- 186	24 -- 36	glutamyl-tRNA reductase	_____________170______________187\n_____________\|________________\|\n5'-AUG...AAUUA___UU___U_______GUGUA...UGC-3'\n______________AGA__GGG_GUUGGGG\n______________\|\|\|__\|\|\|_\|\|\|\|\|\|\|\n______________UCU__CCC_CAACCCC\n3'-UUU...GACUA________________UUGUC...AUA-5'\n_____________\|________________\|\n_____________37_______________23\n	180 -- 186	24 -- 30	-19.8849 kcal/mol	2.21391 kcal/mol	0.138435 kcal/mol	170 187@LB@ \| \|@LB@5'-AUG...AAUUA UU U GUGUA...UGC-3'@LB@ AGA GGG GUUGGGG@LB@ \|\|\| \|\|\| \|\|\|\|\|\|\|@LB@ UCU CCC CAACCCC@LB@3'-UUU...GACUA UUGUC...AUA-5'@LB@ \| \|@LB@ 37 23@LB@@LB@@LB@Energy -17.53 kcal/mol@LB@Hybridization Energy -19.8849 kcal/mol@LB@Unfolding Energy - mRNA 2.21391 kcal/mol@LB@Unfolding Energy - sRNA 0.138435 kcal/mol@LB@@LB@Position - mRNA 171 -- 186@LB@Position - sRNA 24 -- 36@LB@Position Seed - mRNA 180 -- 186@LB@Position Seed - sRNA 24 -- 30@LB@
27	0.0005687	0.07027	bsu32550	yurJ	-13.20	0.065709	183 -- 191	31 -- 39	ABC transporter ATP-binding protein	_____________182_______192\n_____________\|_________\|\n5'-AAC...CAAAA_________ACUUU...UGC-3'\n______________GAUAGGGGG\n______________\|\|\|\|\|:\|\|\|\n______________CUAUCUCCC\n3'-UUU...CUAGA_________CAACC...AUA-5'\n_____________\|_________\|\n_____________40________30\n	185 -- 191	31 -- 37	-15.8488 kcal/mol	1.87568 kcal/mol	0.774822 kcal/mol	182 192@LB@ \| \|@LB@5'-AAC...CAAAA ACUUU...UGC-3'@LB@ GAUAGGGGG@LB@ \|\|\|\|\|:\|\|\|@LB@ CUAUCUCCC@LB@3'-UUU...CUAGA CAACC...AUA-5'@LB@ \| \|@LB@ 40 30@LB@@LB@@LB@Energy -13.20 kcal/mol@LB@Hybridization Energy -15.8488 kcal/mol@LB@Unfolding Energy - mRNA 1.87568 kcal/mol@LB@Unfolding Energy - sRNA 0.774822 kcal/mol@LB@@LB@Position - mRNA 183 -- 191@LB@Position - sRNA 31 -- 39@LB@Position Seed - mRNA 185 -- 191@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@
29	0.0009972	0.1113	bsu38140	qoxD	-9.49	0.251109	150 -- 190	24 -- 51	quinol oxidase subunit 4	_____________149_______________________________________191\n_____________\|_________________________________________\|\n5'-UUU...UGUAU_______C____UUAC___UGUCUAUCUCAU___A______GGUCU...CAG-3'\n______________GGAUUUU_AUCU____AGG____________GGG_UUGGGG\n______________\|\|\|\|:\|\|_\|\|\|\|____\|\|:____________\|\|\|_\|\|\|\|\|\|\n______________CCUAGAA_UAGA____UCU____________CCC_AACCCC\n3'-UUU...AAAAG_______C____CUA___________________C______UUGUC...AUA-5'\n_____________\|_________________________________________\|\n_____________52________________________________________23\n	150 -- 156	45 -- 51	-23.5355 kcal/mol	13.0692 kcal/mol	0.978921 kcal/mol	149 191@LB@ \| \|@LB@5'-UUU...UGUAU C UUAC UGUCUAUCUCAU A GGUCU...CAG-3'@LB@ GGAUUUU AUCU AGG GGG UUGGGG@LB@ \|\|\|\|:\|\| \|\|\|\| \|\|: \|\|\| \|\|\|\|\|\|@LB@ CCUAGAA UAGA UCU CCC AACCCC@LB@3'-UUU...AAAAG C CUA C UUGUC...AUA-5'@LB@ \| \|@LB@ 52 23@LB@@LB@@LB@Energy -9.49 kcal/mol@LB@Hybridization Energy -23.5355 kcal/mol@LB@Unfolding Energy - mRNA 13.0692 kcal/mol@LB@Unfolding Energy - sRNA 0.978921 kcal/mol@LB@@LB@Position - mRNA 150 -- 190@LB@Position - sRNA 24 -- 51@LB@Position Seed - mRNA 150 -- 156@LB@Position Seed - sRNA 45 -- 51@LB@
30	0.001001	0.1113	bsu08780	ygaJ	-16.90	0.012052	218 -- 231	24 -- 39	peptidase YgaJ	_____________217______________232\n_____________\|________________\|\n5'-UGU...AUUGC_________C______GUUUU...AGC-3'\n______________GAUGGGGGG___GGGG\n______________\|\|\|:\|:\|\|\|___\|\|\|\|\n______________CUAUCUCCC___CCCC\n3'-UUU...CUAGA_________CAA____UUGUC...AUA-5'\n_____________\|________________\|\n_____________40_______________23\n	220 -- 226	31 -- 37	-22.0746 kcal/mol	4.38344 kcal/mol	0.790436 kcal/mol	217 232@LB@ \| \|@LB@5'-UGU...AUUGC C GUUUU...AGC-3'@LB@ GAUGGGGGG GGGG@LB@ \|\|\|:\|:\|\|\| \|\|\|\|@LB@ CUAUCUCCC CCCC@LB@3'-UUU...CUAGA CAA UUGUC...AUA-5'@LB@ \| \|@LB@ 40 23@LB@@LB@@LB@Energy -16.90 kcal/mol@LB@Hybridization Energy -22.0746 kcal/mol@LB@Unfolding Energy - mRNA 4.38344 kcal/mol@LB@Unfolding Energy - sRNA 0.790436 kcal/mol@LB@@LB@Position - mRNA 218 -- 231@LB@Position - sRNA 24 -- 39@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 31 -- 37@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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