Input and runtime details for job 3429477 (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 3429477 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:26:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:01 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:15:20 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:15:27 CET 2018
	Job Completed		@ Fri Feb 16 20:15:52 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3429477&toolName=CopraRNA ( 30 days expiry )

Description of the job

OxyS

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_000913 Escherichia coli str. K-12 substr. MG1655

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
151	0.02561	0.5485	b4041	plsB	-9.39	0.134646	197 -- 210	74 -- 86	glycerol-3-phosphate O-acyltransferase	_____________196____________211\n_____________\|______________\|\n5'-UCG...ACAUC________CC____GGCCA...UGG-3'\n______________GUUUAUGU__GGCU\n______________\|\|\|:\|:\|\|__\|\|\|\|\n______________CAAGUGCA__CCGA\n3'-CGC...GUUUU________A_____AAUCA...AAG-5'\n_____________\|______________\|\n_____________87_____________73\n	198 -- 204	79 -- 85	-13.0466 kcal/mol	3.14742 kcal/mol	0.513318 kcal/mol	196 211@LB@ \| \|@LB@5'-UCG...ACAUC CC GGCCA...UGG-3'@LB@ GUUUAUGU GGCU@LB@ \|\|\|:\|:\|\| \|\|\|\|@LB@ CAAGUGCA CCGA@LB@3'-CGC...GUUUU A AAUCA...AAG-5'@LB@ \| \|@LB@ 87 73@LB@@LB@@LB@Energy -9.39 kcal/mol@LB@Hybridization Energy -13.0466 kcal/mol@LB@Unfolding Energy - mRNA 3.14742 kcal/mol@LB@Unfolding Energy - sRNA 0.513318 kcal/mol@LB@@LB@Position - mRNA 197 -- 210@LB@Position - sRNA 74 -- 86@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 79 -- 85@LB@
16	0.002981	0.5385	b3428	glgP	-10.45	0.088230	278 -- 289	76 -- 86	glycogen phosphorylase	_____________277__________290\n_____________\|____________\|\n5'-CCA...CUGAU_______A____AAAGG...CGG-3'\n______________GUUUACG_UUGG\n______________\|\|\|:\|\|\|_\|\|\|\|\n______________CAAGUGC_AACC\n3'-CGC...GUUUU____________GAAAU...AAG-5'\n_____________\|____________\|\n_____________87___________75\n	278 -- 284	80 -- 86	-12.981 kcal/mol	2.0211 kcal/mol	0.505081 kcal/mol	277 290@LB@ \| \|@LB@5'-CCA...CUGAU A AAAGG...CGG-3'@LB@ GUUUACG UUGG@LB@ \|\|\|:\|\|\| \|\|\|\|@LB@ CAAGUGC AACC@LB@3'-CGC...GUUUU GAAAU...AAG-5'@LB@ \| \|@LB@ 87 75@LB@@LB@@LB@Energy -10.45 kcal/mol@LB@Hybridization Energy -12.981 kcal/mol@LB@Unfolding Energy - mRNA 2.0211 kcal/mol@LB@Unfolding Energy - sRNA 0.505081 kcal/mol@LB@@LB@Position - mRNA 278 -- 289@LB@Position - sRNA 76 -- 86@LB@Position Seed - mRNA 278 -- 284@LB@Position Seed - sRNA 80 -- 86@LB@
139	0.02326	0.5385	b1651	gloA	-10.25	0.095619	225 -- 233	75 -- 83	glyoxalase I Ni-dependent	_____________224_______234\n_____________\|_________\|\n5'-UGG...UGCUG_________GAUUU...AAA-3'\n______________CGCGUUGGC\n______________\|:\|\|\|\|\|\|\|\n______________GUGCAACCG\n3'-CGC...UUCAA_________AAAUC...AAG-5'\n_____________\|_________\|\n_____________84________74\n	227 -- 233	75 -- 81	-16.4206 kcal/mol	5.67498 kcal/mol	0.492259 kcal/mol	224 234@LB@ \| \|@LB@5'-UGG...UGCUG GAUUU...AAA-3'@LB@ CGCGUUGGC@LB@ \|:\|\|\|\|\|\|\|@LB@ GUGCAACCG@LB@3'-CGC...UUCAA AAAUC...AAG-5'@LB@ \| \|@LB@ 84 74@LB@@LB@@LB@Energy -10.25 kcal/mol@LB@Hybridization Energy -16.4206 kcal/mol@LB@Unfolding Energy - mRNA 5.67498 kcal/mol@LB@Unfolding Energy - sRNA 0.492259 kcal/mol@LB@@LB@Position - mRNA 225 -- 233@LB@Position - sRNA 75 -- 83@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 75 -- 81@LB@
144	0.02429	0.5467	b3156	yhbS	-10.71	0.079718	207 -- 222	50 -- 67	GNAT family putative N-acetyltransferase	_____________206________________223\n_____________\|__________________\|\n5'-CCG...UGCUA__________________CCAUU...AUC-3'\n______________AUUCGAGU__AGAAAUUC\n______________\|\|\|\|\|\|\|\|__\|\|\|\|\|:\|\|\n______________UAAGCUCA__UCUUUGAG\n3'-CGC...AUCAA________AC________AGCUU...AAG-5'\n_____________\|__________________\|\n_____________68_________________49\n	216 -- 222	50 -- 56	-17.6544 kcal/mol	2.73618 kcal/mol	4.21029 kcal/mol	206 223@LB@ \| \|@LB@5'-CCG...UGCUA CCAUU...AUC-3'@LB@ AUUCGAGU AGAAAUUC@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|:\|\|@LB@ UAAGCUCA UCUUUGAG@LB@3'-CGC...AUCAA AC AGCUU...AAG-5'@LB@ \| \|@LB@ 68 49@LB@@LB@@LB@Energy -10.71 kcal/mol@LB@Hybridization Energy -17.6544 kcal/mol@LB@Unfolding Energy - mRNA 2.73618 kcal/mol@LB@Unfolding Energy - sRNA 4.21029 kcal/mol@LB@@LB@Position - mRNA 207 -- 222@LB@Position - sRNA 50 -- 67@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 50 -- 56@LB@
137	0.02312	0.5385	b2153	folE	-12.97	0.031813	230 -- 265	52 -- 87	GTP cyclohydrolase I	_____________229___________________________________266\n_____________\|_____________________________________\|\n5'-CUG...GCCCU________AA___G_______CG____GACU______ACCGC...ACG-3'\n______________GGUUCAUG___GC_UUAGUUG__CGAG____GGAAAC\n______________:\|\|\|\|\|:\|___\|\|_\|\|\|\|\|\|:__\|\|\|\|____:\|\|\|\|\|\n______________UCAAGUGC___CG_AAUCAAU__GCUC____UCUUUG\n3'-CGC...CGUUU________AAC__A_______AA____AAC_______AGAGC...AAG-5'\n_____________\|_____________________________________\|\n_____________88____________________________________51\n	243 -- 249	67 -- 73	-29.7116 kcal/mol	12.3362 kcal/mol	4.40736 kcal/mol	229 266@LB@ \| \|@LB@5'-CUG...GCCCU AA G CG GACU ACCGC...ACG-3'@LB@ GGUUCAUG GC UUAGUUG CGAG GGAAAC@LB@ :\|\|\|\|\|:\| \|\| \|\|\|\|\|\|: \|\|\|\| :\|\|\|\|\|@LB@ UCAAGUGC CG AAUCAAU GCUC UCUUUG@LB@3'-CGC...CGUUU AAC A AA AAC AGAGC...AAG-5'@LB@ \| \|@LB@ 88 51@LB@@LB@@LB@Energy -12.97 kcal/mol@LB@Hybridization Energy -29.7116 kcal/mol@LB@Unfolding Energy - mRNA 12.3362 kcal/mol@LB@Unfolding Energy - sRNA 4.40736 kcal/mol@LB@@LB@Position - mRNA 230 -- 265@LB@Position - sRNA 52 -- 87@LB@Position Seed - mRNA 243 -- 249@LB@Position Seed - sRNA 67 -- 73@LB@
20	0.003438	0.5385	b3093	exuT	-11.51	0.057623	213 -- 228	75 -- 90	hexuronate transporter	_____________212______________229\n_____________\|________________\|\n5'-GGA...AAAUU_____G__________AUAUG...CGC-3'\n______________AAAGG_UUACGUUGGU\n______________\|\|\|:\|_\|:\|\|\|\|\|\|\|:\n______________UUUUC_AGUGCAACCG\n3'-CGC...AGGCG_____A__________AAAUC...AAG-5'\n_____________\|________________\|\n_____________91_______________74\n	222 -- 228	75 -- 81	-17.0017 kcal/mol	4.97243 kcal/mol	0.517251 kcal/mol	212 229@LB@ \| \|@LB@5'-GGA...AAAUU G AUAUG...CGC-3'@LB@ AAAGG UUACGUUGGU@LB@ \|\|\|:\| \|:\|\|\|\|\|\|\|:@LB@ UUUUC AGUGCAACCG@LB@3'-CGC...AGGCG A AAAUC...AAG-5'@LB@ \| \|@LB@ 91 74@LB@@LB@@LB@Energy -11.51 kcal/mol@LB@Hybridization Energy -17.0017 kcal/mol@LB@Unfolding Energy - mRNA 4.97243 kcal/mol@LB@Unfolding Energy - sRNA 0.517251 kcal/mol@LB@@LB@Position - mRNA 213 -- 228@LB@Position - sRNA 75 -- 90@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 75 -- 81@LB@
132	0.0226	0.5385	b2721	hycE	-8.05	0.224194	140 -- 148	71 -- 79	hydrogenase 3 large subunit	_____________139_______149\n_____________\|_________\|\n5'-UUC...UGGGU_________CAUUU...UGA-3'\n______________UUGGCUUUG\n______________\|\|\|\|\|\|\|\|:\n______________AACCGAAAU\n3'-CGC...AGUGC_________CAAUA...AAG-5'\n_____________\|_________\|\n_____________80________70\n	142 -- 148	71 -- 77	-10.5671 kcal/mol	2.29615 kcal/mol	0.222833 kcal/mol	139 149@LB@ \| \|@LB@5'-UUC...UGGGU CAUUU...UGA-3'@LB@ UUGGCUUUG@LB@ \|\|\|\|\|\|\|\|:@LB@ AACCGAAAU@LB@3'-CGC...AGUGC CAAUA...AAG-5'@LB@ \| \|@LB@ 80 70@LB@@LB@@LB@Energy -8.05 kcal/mol@LB@Hybridization Energy -10.5671 kcal/mol@LB@Unfolding Energy - mRNA 2.29615 kcal/mol@LB@Unfolding Energy - sRNA 0.222833 kcal/mol@LB@@LB@Position - mRNA 140 -- 148@LB@Position - sRNA 71 -- 79@LB@Position Seed - mRNA 142 -- 148@LB@Position Seed - sRNA 71 -- 77@LB@
2	0.0001834	0.3	b2729	hypD	-13.53	0.025234	75 -- 91	71 -- 87	hydrogenase maturation protein	_____________74________________92\n_____________\|_________________\|\n5'-CAG...GUACU___A_____________CCAUG...GCC-3'\n______________GGU_CACGUUGGCUUUG\n______________:\|\|_\|\|\|\|\|\|\|\|\|\|\|\|:\n______________UCA_GUGCAACCGAAAU\n3'-CGC...CGUUU___A_____________CAAUA...AAG-5'\n_____________\|_________________\|\n_____________88________________70\n	85 -- 91	71 -- 77	-22.1935 kcal/mol	8.09841 kcal/mol	0.562376 kcal/mol	74 92@LB@ \| \|@LB@5'-CAG...GUACU A CCAUG...GCC-3'@LB@ GGU CACGUUGGCUUUG@LB@ :\|\| \|\|\|\|\|\|\|\|\|\|\|\|:@LB@ UCA GUGCAACCGAAAU@LB@3'-CGC...CGUUU A CAAUA...AAG-5'@LB@ \| \|@LB@ 88 70@LB@@LB@@LB@Energy -13.53 kcal/mol@LB@Hybridization Energy -22.1935 kcal/mol@LB@Unfolding Energy - mRNA 8.09841 kcal/mol@LB@Unfolding Energy - sRNA 0.562376 kcal/mol@LB@@LB@Position - mRNA 75 -- 91@LB@Position - sRNA 71 -- 87@LB@Position Seed - mRNA 85 -- 91@LB@Position Seed - sRNA 71 -- 77@LB@
182	0.03197	0.5559	b0212	gloB	-7.96	0.231442	50 -- 71	56 -- 75	hydroxyacylglutathione hydrolase	_____________49_____________________72\n_____________\|______________________\|\n5'-UUG...AUACA_______GAACCA_________CUGGC...AGC-3'\n______________UUUUAGU______CGGGUUGAG\n______________:\|\|\|\|\|\|______\|\|:\|\|\|\|\|\|\n______________GAAAUCA______GCUCAACUC\n3'-CGC...CAACC_______AUAA___________UUUGA...AAG-5'\n_____________\|______________________\|\n_____________76_____________________55\n	65 -- 71	56 -- 62	-16.3693 kcal/mol	6.6953 kcal/mol	1.71204 kcal/mol	49 72@LB@ \| \|@LB@5'-UUG...AUACA GAACCA CUGGC...AGC-3'@LB@ UUUUAGU CGGGUUGAG@LB@ :\|\|\|\|\|\| \|\|:\|\|\|\|\|\|@LB@ GAAAUCA GCUCAACUC@LB@3'-CGC...CAACC AUAA UUUGA...AAG-5'@LB@ \| \|@LB@ 76 55@LB@@LB@@LB@Energy -7.96 kcal/mol@LB@Hybridization Energy -16.3693 kcal/mol@LB@Unfolding Energy - mRNA 6.6953 kcal/mol@LB@Unfolding Energy - sRNA 1.71204 kcal/mol@LB@@LB@Position - mRNA 50 -- 71@LB@Position - sRNA 56 -- 75@LB@Position Seed - mRNA 65 -- 71@LB@Position Seed - sRNA 56 -- 62@LB@
116	0.01945	0.5385	b1175	minD	-9.10	0.150484	222 -- 240	13 -- 34	inhibitor of FtsZ ring polymerization; chromosome-membrane tethering protein; membrane ATPase of the MinCDEE system	_____________221____________________241\n_____________\|______________________\|\n5'-CUG...UUGUU__________C___________UUGGU...AAA-3'\n______________ACUUC__GGG__AAAGGGGGUG\n______________\|\|\|\|\|__\|\|\|__\|\|\|:\|:\|\|\|\|\n______________UGAAG__CCC__UUUUCUCCAC\n3'-CGC...GUCAC_____UU___AA__________GGCGA...AAG-5'\n_____________\|______________________\|\n_____________35_____________________12\n	234 -- 240	13 -- 19	-19.7427 kcal/mol	7.311 kcal/mol	3.33198 kcal/mol	221 241@LB@ \| \|@LB@5'-CUG...UUGUU C UUGGU...AAA-3'@LB@ ACUUC GGG AAAGGGGGUG@LB@ \|\|\|\|\| \|\|\| \|\|\|:\|:\|\|\|\|@LB@ UGAAG CCC UUUUCUCCAC@LB@3'-CGC...GUCAC UU AA GGCGA...AAG-5'@LB@ \| \|@LB@ 35 12@LB@@LB@@LB@Energy -9.10 kcal/mol@LB@Hybridization Energy -19.7427 kcal/mol@LB@Unfolding Energy - mRNA 7.311 kcal/mol@LB@Unfolding Energy - sRNA 3.33198 kcal/mol@LB@@LB@Position - mRNA 222 -- 240@LB@Position - sRNA 13 -- 34@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 13 -- 19@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)

Job resubmission

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service.

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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