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
85	0.006705	0.2588	bsu28790	araB	-13.91	0.048694	184 -- 192	30 -- 38	ribulokinase	_____________183_______193\n_____________\|_________\|\n5'-GGA...CAAAA_________GAUGU...AAU-3'\n______________GUAGAGGGG\n______________:\|\|\|\|\|\|\|\|\n______________UAUCUCCCC\n3'-UUU...UAGAC_________AACCC...AUA-5'\n_____________\|_________\|\n_____________39________29\n	186 -- 192	30 -- 36	-16.4519 kcal/mol	1.87822 kcal/mol	0.6591 kcal/mol	183 193@LB@ \| \|@LB@5'-GGA...CAAAA GAUGU...AAU-3'@LB@ GUAGAGGGG@LB@ :\|\|\|\|\|\|\|\|@LB@ UAUCUCCCC@LB@3'-UUU...UAGAC AACCC...AUA-5'@LB@ \| \|@LB@ 39 29@LB@@LB@@LB@Energy -13.91 kcal/mol@LB@Hybridization Energy -16.4519 kcal/mol@LB@Unfolding Energy - mRNA 1.87822 kcal/mol@LB@Unfolding Energy - sRNA 0.6591 kcal/mol@LB@@LB@Position - mRNA 184 -- 192@LB@Position - sRNA 30 -- 38@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 30 -- 36@LB@
58	0.003185	0.1832	bsu24100	bkdR	-13.90	0.048953	199 -- 241	21 -- 51	sigma L-dependent transcriptional regulator YqiR	_____________198_________________________________________242\n_____________\|___________________________________________\|\n5'-AAU...UAUCG____GCAAAA___A_______U___UGCC__CAAAA_______GGCGU...ACA-3'\n______________GGAU______GGU_CUGAUAG_AGG____GG_____GGGGAAC\n______________\|\|\|\|______\|:\|_\|\|\|\|\|\|\|_\|\|\|____\|\|_____\|\|\|\|\|\|\|\n______________CCUA______CUA_GACUAUC_UCC____CC_____CCCCUUG\n3'-UUU...AAAAG____GAA________________________AA__________UCUCU...AUA-5'\n_____________\|___________________________________________\|\n_____________52__________________________________________20\n	235 -- 241	21 -- 27	-28.1295 kcal/mol	11.4588 kcal/mol	2.76846 kcal/mol	198 242@LB@ \| \|@LB@5'-AAU...UAUCG GCAAAA A U UGCC CAAAA GGCGU...ACA-3'@LB@ GGAU GGU CUGAUAG AGG GG GGGGAAC@LB@ \|\|\|\| \|:\| \|\|\|\|\|\|\| \|\|\| \|\| \|\|\|\|\|\|\|@LB@ CCUA CUA GACUAUC UCC CC CCCCUUG@LB@3'-UUU...AAAAG GAA AA UCUCU...AUA-5'@LB@ \| \|@LB@ 52 20@LB@@LB@@LB@Energy -13.90 kcal/mol@LB@Hybridization Energy -28.1295 kcal/mol@LB@Unfolding Energy - mRNA 11.4588 kcal/mol@LB@Unfolding Energy - sRNA 2.76846 kcal/mol@LB@@LB@Position - mRNA 199 -- 241@LB@Position - sRNA 21 -- 51@LB@Position Seed - mRNA 235 -- 241@LB@Position Seed - sRNA 21 -- 27@LB@
117	0.0101	0.2881	bsu39670	iolJ	-13.86	0.049938	182 -- 196	29 -- 51	6-phospho-5-dehydro-2-deoxy-D-gluconate aldolase	_____________181_____________________197\n_____________\|_______________________\|\n5'-CCG...GUAAU____AAA________________GAAUA...CGA-3'\n______________GGAU___________GGAGGGGU\n______________\|\|\|\|___________:\|\|\|\|\|\|\|\n______________CCUA___________UCUCCCCA\n3'-UUU...AAAAG____GAACUAGACUA________ACCCC...AUA-5'\n_____________\|_______________________\|\n_____________52______________________28\n	190 -- 196	29 -- 35	-16.9006 kcal/mol	2.07053 kcal/mol	0.974539 kcal/mol	181 197@LB@ \| \|@LB@5'-CCG...GUAAU AAA GAAUA...CGA-3'@LB@ GGAU GGAGGGGU@LB@ \|\|\|\| :\|\|\|\|\|\|\|@LB@ CCUA UCUCCCCA@LB@3'-UUU...AAAAG GAACUAGACUA ACCCC...AUA-5'@LB@ \| \|@LB@ 52 28@LB@@LB@@LB@Energy -13.86 kcal/mol@LB@Hybridization Energy -16.9006 kcal/mol@LB@Unfolding Energy - mRNA 2.07053 kcal/mol@LB@Unfolding Energy - sRNA 0.974539 kcal/mol@LB@@LB@Position - mRNA 182 -- 196@LB@Position - sRNA 29 -- 51@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 29 -- 35@LB@
68	0.004453	0.2184	bsu22580	ypiB	-13.80	0.051176	183 -- 197	21 -- 39	Evidence 4: Homologs of previously reported genes of unknown function; PubMedId: 16847875	_____________182_________________198\n_____________\|___________________\|\n5'-AGC...CGAAC________A__________UACAU...ACU-3'\n______________GAUAGAGG_____GGGAAU\n______________\|\|\|\|\|\|\|\|_____\|\|\|\|\|:\n______________CUAUCUCC_____CCCUUG\n3'-UUU...CUAGA________CCAAC______UCUCU...AUA-5'\n_____________\|___________________\|\n_____________40__________________20\n	184 -- 190	32 -- 38	-18.5124 kcal/mol	2.13446 kcal/mol	2.58006 kcal/mol	182 198@LB@ \| \|@LB@5'-AGC...CGAAC A UACAU...ACU-3'@LB@ GAUAGAGG GGGAAU@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|:@LB@ CUAUCUCC CCCUUG@LB@3'-UUU...CUAGA CCAAC UCUCU...AUA-5'@LB@ \| \|@LB@ 40 20@LB@@LB@@LB@Energy -13.80 kcal/mol@LB@Hybridization Energy -18.5124 kcal/mol@LB@Unfolding Energy - mRNA 2.13446 kcal/mol@LB@Unfolding Energy - sRNA 2.58006 kcal/mol@LB@@LB@Position - mRNA 183 -- 197@LB@Position - sRNA 21 -- 39@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 32 -- 38@LB@
99	0.00842	0.2778	bsu19470	yojF	-13.80	0.051174	184 -- 193	30 -- 39	Evidence 4: Homologs of previously reported genes of unknown function	_____________183________194\n_____________\|__________\|\n5'-GAA...AAGAA__A_______AGCAA...CAG-3'\n______________GA_AGAGGGG\n______________\|\|_\|\|\|\|\|\|\|\n______________CU_UCUCCCC\n3'-UUU...CUAGA__A_______AACCC...AUA-5'\n_____________\|__________\|\n_____________40_________29\n	187 -- 193	30 -- 36	-15.454 kcal/mol	0.87683 kcal/mol	0.779184 kcal/mol	183 194@LB@ \| \|@LB@5'-GAA...AAGAA A AGCAA...CAG-3'@LB@ GA AGAGGGG@LB@ \|\| \|\|\|\|\|\|\|@LB@ CU UCUCCCC@LB@3'-UUU...CUAGA A AACCC...AUA-5'@LB@ \| \|@LB@ 40 29@LB@@LB@@LB@Energy -13.80 kcal/mol@LB@Hybridization Energy -15.454 kcal/mol@LB@Unfolding Energy - mRNA 0.87683 kcal/mol@LB@Unfolding Energy - sRNA 0.779184 kcal/mol@LB@@LB@Position - mRNA 184 -- 193@LB@Position - sRNA 30 -- 39@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 30 -- 36@LB@
40	0.001724	0.1438	bsu18440	gltD	-13.77	0.051762	193 -- 208	22 -- 36	glutamate synthase [NADPH] small chain	_____________192______________209\n_____________\|________________\|\n5'-AGA...AGGGG_____AACA_______ACCAA...CUU-3'\n______________AGAGG____UGGGGAA\n______________\|\|\|\|\|____\|\|\|\|\|\|\|\n______________UCUCC____ACCCCUU\n3'-UUU...GACUA_____CCA________GUCUC...AUA-5'\n_____________\|________________\|\n_____________37_______________21\n	202 -- 208	22 -- 28	-17.8722 kcal/mol	3.06294 kcal/mol	1.03819 kcal/mol	192 209@LB@ \| \|@LB@5'-AGA...AGGGG AACA ACCAA...CUU-3'@LB@ AGAGG UGGGGAA@LB@ \|\|\|\|\| \|\|\|\|\|\|\|@LB@ UCUCC ACCCCUU@LB@3'-UUU...GACUA CCA GUCUC...AUA-5'@LB@ \| \|@LB@ 37 21@LB@@LB@@LB@Energy -13.77 kcal/mol@LB@Hybridization Energy -17.8722 kcal/mol@LB@Unfolding Energy - mRNA 3.06294 kcal/mol@LB@Unfolding Energy - sRNA 1.03819 kcal/mol@LB@@LB@Position - mRNA 193 -- 208@LB@Position - sRNA 22 -- 36@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 22 -- 28@LB@
31	0.001131	0.119	bsu15020	coaD	-13.71	0.053189	186 -- 192	30 -- 36	phosphopantetheine adenylyltransferase	_____________185_____193\n_____________\|_______\|\n5'-UCC...UAAAA_______GUAGU...AUG-3'\n______________AGAGGGG\n______________\|\|\|\|\|\|\|\n______________UCUCCCC\n3'-UUU...GACUA_______AACCC...AUA-5'\n_____________\|_______\|\n_____________37______29\n	186 -- 192	30 -- 36	-14.3069 kcal/mol	0.46648 kcal/mol	0.133643 kcal/mol	185 193@LB@ \| \|@LB@5'-UCC...UAAAA GUAGU...AUG-3'@LB@ AGAGGGG@LB@ \|\|\|\|\|\|\|@LB@ UCUCCCC@LB@3'-UUU...GACUA AACCC...AUA-5'@LB@ \| \|@LB@ 37 29@LB@@LB@@LB@Energy -13.71 kcal/mol@LB@Hybridization Energy -14.3069 kcal/mol@LB@Unfolding Energy - mRNA 0.46648 kcal/mol@LB@Unfolding Energy - sRNA 0.133643 kcal/mol@LB@@LB@Position - mRNA 186 -- 192@LB@Position - sRNA 30 -- 36@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 30 -- 36@LB@
15	0.0002364	0.05257	bsu19290	yozO	-13.57	0.056229	184 -- 195	28 -- 39	Evidence 4: Homologs of previously reported genes of unknown function	_____________183__________196\n_____________\|____________\|\n5'-AAA...AUGCA__A_________CUUCA...UGG-3'\n______________GA_AGAGGGGUU\n______________\|\|_\|\|\|\|\|\|\|\|\|\n______________CU_UCUCCCCAA\n3'-UUU...CUAGA__A_________CCCCU...AUA-5'\n_____________\|____________\|\n_____________40___________27\n	189 -- 195	28 -- 34	-16.9963 kcal/mol	2.64187 kcal/mol	0.77983 kcal/mol	183 196@LB@ \| \|@LB@5'-AAA...AUGCA A CUUCA...UGG-3'@LB@ GA AGAGGGGUU@LB@ \|\| \|\|\|\|\|\|\|\|\|@LB@ CU UCUCCCCAA@LB@3'-UUU...CUAGA A CCCCU...AUA-5'@LB@ \| \|@LB@ 40 27@LB@@LB@@LB@Energy -13.57 kcal/mol@LB@Hybridization Energy -16.9963 kcal/mol@LB@Unfolding Energy - mRNA 2.64187 kcal/mol@LB@Unfolding Energy - sRNA 0.77983 kcal/mol@LB@@LB@Position - mRNA 184 -- 195@LB@Position - sRNA 28 -- 39@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 28 -- 34@LB@
130	0.01149	0.2883	bsu02620	phoD	-13.55	0.056825	174 -- 193	30 -- 50	alkaline phosphatase D	_____________173____________________194\n_____________\|______________________\|\n5'-GCC...GAGAC____AA___G____G_______AUCUU...CGG-3'\n______________GAUC__UGA___GA_AGAGGGG\n______________\|\|\|\|__\|\|\|___\|\|_\|\|\|\|\|\|\|\n______________CUAG__ACU___CU_UCUCCCC\n3'-UUU...AAAGC____A____AGA__A_______AACCC...AUA-5'\n_____________\|______________________\|\n_____________51_____________________29\n	187 -- 193	30 -- 36	-18.9864 kcal/mol	4.46268 kcal/mol	0.974272 kcal/mol	173 194@LB@ \| \|@LB@5'-GCC...GAGAC AA G G AUCUU...CGG-3'@LB@ GAUC UGA GA AGAGGGG@LB@ \|\|\|\| \|\|\| \|\| \|\|\|\|\|\|\|@LB@ CUAG ACU CU UCUCCCC@LB@3'-UUU...AAAGC A AGA A AACCC...AUA-5'@LB@ \| \|@LB@ 51 29@LB@@LB@@LB@Energy -13.55 kcal/mol@LB@Hybridization Energy -18.9864 kcal/mol@LB@Unfolding Energy - mRNA 4.46268 kcal/mol@LB@Unfolding Energy - sRNA 0.974272 kcal/mol@LB@@LB@Position - mRNA 174 -- 193@LB@Position - sRNA 30 -- 50@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 30 -- 36@LB@
50	0.002285	0.1525	bsu22460	ypjH	-13.49	0.058216	160 -- 194	23 -- 52	glycosyltransferase YpjH	_____________159____________________________________195\n_____________\|______________________________________\|\n5'-AAG...CCAAA_____GCUGAUG_______A_____U__C_________CGAAC...AUG-3'\n______________CGGAU_______CUUGAUC_UGAUG__G___UUGGGGG\n______________\|\|\|\|\|_______\|\|\|\|\|\|\|_\|\|\|\|:__\|___\|\|\|\|\|\|:\n______________GCCUA_______GAACUAG_ACUAU__C___AACCCCU\n3'-UUU...AAAAA_________________________CU_CCC_______UGUCU...AUA-5'\n_____________\|______________________________________\|\n_____________53_____________________________________22\n	188 -- 194	23 -- 29	-25.8094 kcal/mol	11.3359 kcal/mol	0.981961 kcal/mol	159 195@LB@ \| \|@LB@5'-AAG...CCAAA GCUGAUG A U C CGAAC...AUG-3'@LB@ CGGAU CUUGAUC UGAUG G UUGGGGG@LB@ \|\|\|\|\| \|\|\|\|\|\|\| \|\|\|\|: \| \|\|\|\|\|\|:@LB@ GCCUA GAACUAG ACUAU C AACCCCU@LB@3'-UUU...AAAAA CU CCC UGUCU...AUA-5'@LB@ \| \|@LB@ 53 22@LB@@LB@@LB@Energy -13.49 kcal/mol@LB@Hybridization Energy -25.8094 kcal/mol@LB@Unfolding Energy - mRNA 11.3359 kcal/mol@LB@Unfolding Energy - sRNA 0.981961 kcal/mol@LB@@LB@Position - mRNA 160 -- 194@LB@Position - sRNA 23 -- 52@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 23 -- 29@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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