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
51	0.002362	0.1545	bsu28450	sdhC	-14.17	0.043697	178 -- 219	14 -- 47	succinate dehydrogenase cytochrome b558 subunit	_____________177_________________________________________220\n_____________\|___________________________________________\|\n5'-AAA...UCGCA_______AAAC______UAAAGUAAU__CU_____________UUUAU...AGU-3'\n______________CUU_AUC____AGGGGG_________GU__GGGAACAGAGAGU\n______________\|\|\|_\|\|\|____\|\|:\|\|\|_________\|\|__\|\|\|\|\|\|\|\|\|\|\|\|\|\n______________GAA_UAG____UCUCCC_________CA__CCCUUGUCUCUCA\n3'-UUU...GCCUA___C___ACUA_________________AC_____________UCGAA...AUA-5'\n_____________\|___________________________________________\|\n_____________48__________________________________________13\n	213 -- 219	14 -- 20	-33.4599 kcal/mol	9.41028 kcal/mol	9.88362 kcal/mol	177 220@LB@ \| \|@LB@5'-AAA...UCGCA AAAC UAAAGUAAU CU UUUAU...AGU-3'@LB@ CUU AUC AGGGGG GU GGGAACAGAGAGU@LB@ \|\|\| \|\|\| \|\|:\|\|\| \|\| \|\|\|\|\|\|\|\|\|\|\|\|\|@LB@ GAA UAG UCUCCC CA CCCUUGUCUCUCA@LB@3'-UUU...GCCUA C ACUA AC UCGAA...AUA-5'@LB@ \| \|@LB@ 48 13@LB@@LB@@LB@Energy -14.17 kcal/mol@LB@Hybridization Energy -33.4599 kcal/mol@LB@Unfolding Energy - mRNA 9.41028 kcal/mol@LB@Unfolding Energy - sRNA 9.88362 kcal/mol@LB@@LB@Position - mRNA 178 -- 219@LB@Position - sRNA 14 -- 47@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 14 -- 20@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@
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@
54	0.002747	0.1697	bsu35790	yvyI	-14.15	0.043919	186 -- 197	25 -- 36	mannose-6-phosphate isomerase YvyI	_____________185__________198\n_____________\|____________\|\n5'-UCU...ACAGG________AC__AUCAU...AAU-3'\n______________GGAGGGGU__GG\n______________:\|\|\|\|\|\|\|__\|\|\n______________UCUCCCCA__CC\n3'-UUU...GACUA________AC__CUUGU...AUA-5'\n_____________\|____________\|\n_____________37___________24\n	187 -- 193	29 -- 35	-17.2174 kcal/mol	2.92719 kcal/mol	0.135926 kcal/mol	185 198@LB@ \| \|@LB@5'-UCU...ACAGG AC AUCAU...AAU-3'@LB@ GGAGGGGU GG@LB@ :\|\|\|\|\|\|\| \|\|@LB@ UCUCCCCA CC@LB@3'-UUU...GACUA AC CUUGU...AUA-5'@LB@ \| \|@LB@ 37 24@LB@@LB@@LB@Energy -14.15 kcal/mol@LB@Hybridization Energy -17.2174 kcal/mol@LB@Unfolding Energy - mRNA 2.92719 kcal/mol@LB@Unfolding Energy - sRNA 0.135926 kcal/mol@LB@@LB@Position - mRNA 186 -- 197@LB@Position - sRNA 25 -- 36@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 29 -- 35@LB@
55	0.002845	0.1725	bsu40380	yycI	-20.10	0.001970	172 -- 209	12 -- 51	two-component system YycFG regulatory protein	_____________171_________________________________________210\n_____________\|___________________________________________\|\n5'-CAG...ACAAA_____UA____G____A_______GCU________U_______AAUAA...GCA-3'\n______________GGAUU__UUGA___GA_GGAGGGG______AACAG_GGAGUGG\n______________\|\|\|\|:__\|\|\|\|___\|\|_:\|\|\|\|\|\|______\|\|\|\|\|_:\|\|\|\|:\|\n______________CCUAG__AACU___CU_UCUCCCC______UUGUC_UCUCAUC\n3'-UUU...AAAAG___________AGA__A_______AACCCC_____________GAAGA...AUA-5'\n_____________\|___________________________________________\|\n_____________52__________________________________________11\n	203 -- 209	12 -- 18	-35.1528 kcal/mol	5.09356 kcal/mol	9.95619 kcal/mol	171 210@LB@ \| \|@LB@5'-CAG...ACAAA UA G A GCU U AAUAA...GCA-3'@LB@ GGAUU UUGA GA GGAGGGG AACAG GGAGUGG@LB@ \|\|\|\|: \|\|\|\| \|\| :\|\|\|\|\|\| \|\|\|\|\| :\|\|\|\|:\|@LB@ CCUAG AACU CU UCUCCCC UUGUC UCUCAUC@LB@3'-UUU...AAAAG AGA A AACCCC GAAGA...AUA-5'@LB@ \| \|@LB@ 52 11@LB@@LB@@LB@Energy -20.10 kcal/mol@LB@Hybridization Energy -35.1528 kcal/mol@LB@Unfolding Energy - mRNA 5.09356 kcal/mol@LB@Unfolding Energy - sRNA 9.95619 kcal/mol@LB@@LB@Position - mRNA 172 -- 209@LB@Position - sRNA 12 -- 51@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 12 -- 18@LB@
56	0.002918	0.1738	bsu04390	ydbA	-13.95	0.047884	245 -- 258	25 -- 39	Evidence 4: Homologs of previously reported genes of unknown function	_____________244_____________259\n_____________\|_______________\|\n5'-UUC...AAAGA_______AAA_____AAAAA...GCC-3'\n______________GAUAGAG____UGGG\n______________\|\|\|\|\|\|\|____\|\|\|\|\n______________CUAUCUC____ACCC\n3'-UUU...CUAGA_______CCCA____CUUGU...AUA-5'\n_____________\|_______________\|\n_____________40______________24\n	245 -- 251	33 -- 39	-15.533 kcal/mol	0.795684 kcal/mol	0.783603 kcal/mol	244 259@LB@ \| \|@LB@5'-UUC...AAAGA AAA AAAAA...GCC-3'@LB@ GAUAGAG UGGG@LB@ \|\|\|\|\|\|\| \|\|\|\|@LB@ CUAUCUC ACCC@LB@3'-UUU...CUAGA CCCA CUUGU...AUA-5'@LB@ \| \|@LB@ 40 24@LB@@LB@@LB@Energy -13.95 kcal/mol@LB@Hybridization Energy -15.533 kcal/mol@LB@Unfolding Energy - mRNA 0.795684 kcal/mol@LB@Unfolding Energy - sRNA 0.783603 kcal/mol@LB@@LB@Position - mRNA 245 -- 258@LB@Position - sRNA 25 -- 39@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 33 -- 39@LB@
57	0.003091	0.1809	bsu19720	yodR	-13.42	0.059995	155 -- 217	11 -- 51	coenzyme A transferase subunit beta	_____________154_________________________________________________________________218\n_____________\|___________________________________________________________________\|\n5'-GCU...ACCGG_______UG________________UACGAAGCGA____GUGAAGUGGAAAUGG__UU_________AGAAA...CCU-3'\n______________GGGUUUU___UUGA___GGGGGUUG__________GGGA_______________GC__GGGAGUAGC\n______________\|\|:\|:\|\|___:\|\|\|___:\|\|\|\|\|\|\|__________\|\|\|\|_______________:\|__\|:\|\|\|\|\|\|\|\n______________CCUAGAA___GACU___UCCCCAAC__________CCCU_______________UG__CUCUCAUCG\n3'-UUU...AAAAG_______CUA____AUC_______________________________________U__________AAGAG...AUA-5'\n_____________\|___________________________________________________________________\|\n_____________52__________________________________________________________________10\n	211 -- 217	11 -- 17	-37.5623 kcal/mol	14.1868 kcal/mol	9.95641 kcal/mol	154 218@LB@ \| \|@LB@5'-GCU...ACCGG UG UACGAAGCGA GUGAAGUGGAAAUGG UU AGAAA...CCU-3'@LB@ GGGUUUU UUGA GGGGGUUG GGGA GC GGGAGUAGC@LB@ \|\|:\|:\|\| :\|\|\| :\|\|\|\|\|\|\| \|\|\|\| :\| \|:\|\|\|\|\|\|\|@LB@ CCUAGAA GACU UCCCCAAC CCCU UG CUCUCAUCG@LB@3'-UUU...AAAAG CUA AUC U AAGAG...AUA-5'@LB@ \| \|@LB@ 52 10@LB@@LB@@LB@Energy -13.42 kcal/mol@LB@Hybridization Energy -37.5623 kcal/mol@LB@Unfolding Energy - mRNA 14.1868 kcal/mol@LB@Unfolding Energy - sRNA 9.95641 kcal/mol@LB@@LB@Position - mRNA 155 -- 217@LB@Position - sRNA 11 -- 51@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 11 -- 17@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@
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@
60	0.003464	0.1926	bsu03300	nasD	-15.33	0.025906	190 -- 205	34 -- 52	nitrite reductase	_____________189_________________206\n_____________\|___________________\|\n5'-UUU...AGGAG___________________AAAAA...CAA-3'\n______________CGGAUC___AUCUGAUGGG\n______________\|\|\|\|\|\|___\|\|\|\|\|\|\|:\|:\n______________GCCUAG___UAGACUAUCU\n3'-UUU...AAAAA______AAC__________CCCCA...AUA-5'\n_____________\|___________________\|\n_____________53__________________33\n	199 -- 205	34 -- 40	-21.0079 kcal/mol	4.70189 kcal/mol	0.976339 kcal/mol	189 206@LB@ \| \|@LB@5'-UUU...AGGAG AAAAA...CAA-3'@LB@ CGGAUC AUCUGAUGGG@LB@ \|\|\|\|\|\| \|\|\|\|\|\|\|:\|:@LB@ GCCUAG UAGACUAUCU@LB@3'-UUU...AAAAA AAC CCCCA...AUA-5'@LB@ \| \|@LB@ 53 33@LB@@LB@@LB@Energy -15.33 kcal/mol@LB@Hybridization Energy -21.0079 kcal/mol@LB@Unfolding Energy - mRNA 4.70189 kcal/mol@LB@Unfolding Energy - sRNA 0.976339 kcal/mol@LB@@LB@Position - mRNA 190 -- 205@LB@Position - sRNA 34 -- 52@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 34 -- 40@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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