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
146	0.0246	0.5467	b2813	mltA	-8.67	0.177423	203 -- 222	69 -- 90	membrane-bound lytic murein transglycosylase A	_____________202____________________223\n_____________\|______________________\|\n5'-UGC...ACAAU_____G_________G_AA___ACCUU...AAG-3'\n______________GAAAG___ACGUUGG_U__AGU\n______________:\|\|\|\|___\|\|\|\|\|\|\|_\|__\|\|\|\n______________UUUUC___UGCAACC_A__UCA\n3'-CGC...AGGCG_____AAG_______G_AA___AUAAG...AAG-5'\n_____________\|______________________\|\n_____________91_____________________68\n	209 -- 215	76 -- 82	-14.1188 kcal/mol	4.87564 kcal/mol	0.572281 kcal/mol	202 223@LB@ \| \|@LB@5'-UGC...ACAAU G G AA ACCUU...AAG-3'@LB@ GAAAG ACGUUGG U AGU@LB@ :\|\|\|\| \|\|\|\|\|\|\| \| \|\|\|@LB@ UUUUC UGCAACC A UCA@LB@3'-CGC...AGGCG AAG G AA AUAAG...AAG-5'@LB@ \| \|@LB@ 91 68@LB@@LB@@LB@Energy -8.67 kcal/mol@LB@Hybridization Energy -14.1188 kcal/mol@LB@Unfolding Energy - mRNA 4.87564 kcal/mol@LB@Unfolding Energy - sRNA 0.572281 kcal/mol@LB@@LB@Position - mRNA 203 -- 222@LB@Position - sRNA 69 -- 90@LB@Position Seed - mRNA 209 -- 215@LB@Position Seed - sRNA 76 -- 82@LB@
138	0.02324	0.5385	b1826	mgrB	-8.64	0.179438	205 -- 238	60 -- 90	regulatory peptide for PhoPQ feedback inhibition	_____________204__________________________________239\n_____________\|____________________________________\|\n5'-UAC...AGUGA___________A___G_CGUUC__________U___GUUGG...AAU-3'\n______________AAAAGUUU_CG_UGG_U_____UGGUUGU_CG_GGU\n______________\|\|\|\|\|\|\|:_\|\|_\|\|\|_\|_____\|:\|\|\|:\|_\|\|_:\|\|\n______________UUUUCAAG_GC_ACC_A_____AUCAAUA_GC_UCA\n3'-CGC...AGGCG________U__A___G_A___________A______ACUCU...AAG-5'\n_____________\|____________________________________\|\n_____________91___________________________________59\n	226 -- 232	66 -- 72	-16.3224 kcal/mol	5.97183 kcal/mol	1.70935 kcal/mol	204 239@LB@ \| \|@LB@5'-UAC...AGUGA A G CGUUC U GUUGG...AAU-3'@LB@ AAAAGUUU CG UGG U UGGUUGU CG GGU@LB@ \|\|\|\|\|\|\|: \|\| \|\|\| \| \|:\|\|\|:\| \|\| :\|\|@LB@ UUUUCAAG GC ACC A AUCAAUA GC UCA@LB@3'-CGC...AGGCG U A G A A ACUCU...AAG-5'@LB@ \| \|@LB@ 91 59@LB@@LB@@LB@Energy -8.64 kcal/mol@LB@Hybridization Energy -16.3224 kcal/mol@LB@Unfolding Energy - mRNA 5.97183 kcal/mol@LB@Unfolding Energy - sRNA 1.70935 kcal/mol@LB@@LB@Position - mRNA 205 -- 238@LB@Position - sRNA 60 -- 90@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 66 -- 72@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@
29	0.005218	0.5385	b3433	asd	-11.22	0.064904	208 -- 219	71 -- 82	aspartate-semialdehyde dehydrogenase NAD(P)-binding	_____________207__________220\n_____________\|____________\|\n5'-UCA...GAAAA____________UCGGC...UCU-3'\n______________AUGUUGGUUUUA\n______________\|:\|\|\|\|\|:\|\|\|\|\n______________UGCAACCGAAAU\n3'-CGC...UCAAG____________CAAUA...AAG-5'\n_____________\|____________\|\n_____________83___________70\n	213 -- 219	71 -- 77	-13.9075 kcal/mol	2.30708 kcal/mol	0.38228 kcal/mol	207 220@LB@ \| \|@LB@5'-UCA...GAAAA UCGGC...UCU-3'@LB@ AUGUUGGUUUUA@LB@ \|:\|\|\|\|\|:\|\|\|\|@LB@ UGCAACCGAAAU@LB@3'-CGC...UCAAG CAAUA...AAG-5'@LB@ \| \|@LB@ 83 70@LB@@LB@@LB@Energy -11.22 kcal/mol@LB@Hybridization Energy -13.9075 kcal/mol@LB@Unfolding Energy - mRNA 2.30708 kcal/mol@LB@Unfolding Energy - sRNA 0.38228 kcal/mol@LB@@LB@Position - mRNA 208 -- 219@LB@Position - sRNA 71 -- 82@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 71 -- 77@LB@
6	0.001078	0.5385	b0849	grxA	-11.19	0.065759	209 -- 232	58 -- 81	glutaredoxin 1 redox coenzyme for ribonucleotide reductase (RNR1a)	_____________208______________________233\n_____________\|________________________\|\n5'-AGU...CAAAC____AU_______C__________CCCUU...AUC-3'\n______________CGUU__UUUUGGU_GUUCGGGUUG\n______________\|\|\|\|__:\|\|\|:\|\|_:\|\|\|\|:\|\|\|\|\n______________GCAA__GAAAUCA_UAAGCUCAAC\n3'-CGC...CAAGU____CC_______A__________UCUUU...AAG-5'\n_____________\|________________________\|\n_____________82_______________________57\n	226 -- 232	58 -- 64	-21.2762 kcal/mol	8.79419 kcal/mol	1.29619 kcal/mol	208 233@LB@ \| \|@LB@5'-AGU...CAAAC AU C CCCUU...AUC-3'@LB@ CGUU UUUUGGU GUUCGGGUUG@LB@ \|\|\|\| :\|\|\|:\|\| :\|\|\|\|:\|\|\|\|@LB@ GCAA GAAAUCA UAAGCUCAAC@LB@3'-CGC...CAAGU CC A UCUUU...AAG-5'@LB@ \| \|@LB@ 82 57@LB@@LB@@LB@Energy -11.19 kcal/mol@LB@Hybridization Energy -21.2762 kcal/mol@LB@Unfolding Energy - mRNA 8.79419 kcal/mol@LB@Unfolding Energy - sRNA 1.29619 kcal/mol@LB@@LB@Position - mRNA 209 -- 232@LB@Position - sRNA 58 -- 81@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 58 -- 64@LB@
25	0.004715	0.5385	b0009	mog	-11.66	0.054310	209 -- 227	68 -- 85	molybdochelatase incorporating molybdenum into molybdopterin	_____________208__________________228\n_____________\|____________________\|\n5'-UGG...AAUAC_______AU___________UCCAU...CAU-3'\n______________UUUACGU__UGGC_UUAGUU\n______________\|\|:\|\|\|\|__\|\|\|\|_\|\|\|\|\|\|\n______________AAGUGCA__ACCG_AAUCAA\n3'-CGC...UUUUC_____________A______UAAGC...AAG-5'\n_____________\|____________________\|\n_____________86___________________67\n	209 -- 215	79 -- 85	-16.6663 kcal/mol	4.44065 kcal/mol	0.567776 kcal/mol	208 228@LB@ \| \|@LB@5'-UGG...AAUAC AU UCCAU...CAU-3'@LB@ UUUACGU UGGC UUAGUU@LB@ \|\|:\|\|\|\| \|\|\|\| \|\|\|\|\|\|@LB@ AAGUGCA ACCG AAUCAA@LB@3'-CGC...UUUUC A UAAGC...AAG-5'@LB@ \| \|@LB@ 86 67@LB@@LB@@LB@Energy -11.66 kcal/mol@LB@Hybridization Energy -16.6663 kcal/mol@LB@Unfolding Energy - mRNA 4.44065 kcal/mol@LB@Unfolding Energy - sRNA 0.567776 kcal/mol@LB@@LB@Position - mRNA 209 -- 227@LB@Position - sRNA 68 -- 85@LB@Position Seed - mRNA 209 -- 215@LB@Position Seed - sRNA 79 -- 85@LB@
185	0.03283	0.5559	b1937	fliE	-12.05	0.046361	209 -- 229	14 -- 35	flagellar basal-body component	_____________208____________________230\n_____________\|______________________\|\n5'-CUG...UCAGC___A_______AUU________UAUCA...GUU-3'\n______________GAU__CAGGGG___GAAGGGGU\n______________\|\|:__\|\|:\|\|\|___:\|\|\|:\|\|\|\n______________CUG__GUUCCC___UUUCUCCA\n3'-CGC...CGUCA___AA______AAU________CGGCG...AAG-5'\n_____________\|______________________\|\n_____________36_____________________13\n	223 -- 229	14 -- 20	-20.5154 kcal/mol	5.13678 kcal/mol	3.33183 kcal/mol	208 230@LB@ \| \|@LB@5'-CUG...UCAGC A AUU UAUCA...GUU-3'@LB@ GAU CAGGGG GAAGGGGU@LB@ \|\|: \|\|:\|\|\| :\|\|\|:\|\|\|@LB@ CUG GUUCCC UUUCUCCA@LB@3'-CGC...CGUCA AA AAU CGGCG...AAG-5'@LB@ \| \|@LB@ 36 13@LB@@LB@@LB@Energy -12.05 kcal/mol@LB@Hybridization Energy -20.5154 kcal/mol@LB@Unfolding Energy - mRNA 5.13678 kcal/mol@LB@Unfolding Energy - sRNA 3.33183 kcal/mol@LB@@LB@Position - mRNA 209 -- 229@LB@Position - sRNA 14 -- 35@LB@Position Seed - mRNA 223 -- 229@LB@Position Seed - sRNA 14 -- 20@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@
184	0.03259	0.5559	b0811	glnH	-9.61	0.123139	215 -- 230	74 -- 90	glutamine transporter subunit	_____________214________________231\n_____________\|__________________\|\n5'-AUC...GUAUU_______U__________GCACU...CCG-3'\n______________AAAAGUU_CAC__UGGCU\n______________\|\|\|\|\|\|\|_\|\|\|__\|\|\|\|\|\n______________UUUUCAA_GUG__ACCGA\n3'-CGC...AGGCG___________CA_____AAUCA...AAG-5'\n_____________\|__________________\|\n_____________91_________________73\n	215 -- 221	84 -- 90	-14.2101 kcal/mol	4.07847 kcal/mol	0.517587 kcal/mol	214 231@LB@ \| \|@LB@5'-AUC...GUAUU U GCACU...CCG-3'@LB@ AAAAGUU CAC UGGCU@LB@ \|\|\|\|\|\|\| \|\|\| \|\|\|\|\|@LB@ UUUUCAA GUG ACCGA@LB@3'-CGC...AGGCG CA AAUCA...AAG-5'@LB@ \| \|@LB@ 91 73@LB@@LB@@LB@Energy -9.61 kcal/mol@LB@Hybridization Energy -14.2101 kcal/mol@LB@Unfolding Energy - mRNA 4.07847 kcal/mol@LB@Unfolding Energy - sRNA 0.517587 kcal/mol@LB@@LB@Position - mRNA 215 -- 230@LB@Position - sRNA 74 -- 90@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 84 -- 90@LB@
198	0.03475	0.5559	b1249	clsA	-8.08	0.221640	216 -- 230	57 -- 82	cardiolipin synthase 1	_____________215________________________231\n_____________\|__________________________\|\n5'-GUC...UUUAU__________________________UUGGC...CAG-3'\n______________ACGUUGGU___________GAGUUGG\n______________\|\|\|\|\|\|\|:___________\|\|\|\|\|\|:\n______________UGCAACCG___________CUCAACU\n3'-CGC...UCAAG________AAAUCAAUAAG_______CUUUG...AAG-5'\n_____________\|__________________________\|\n_____________83_________________________56\n	224 -- 230	57 -- 63	-16.5635 kcal/mol	7.18735 kcal/mol	1.29708 kcal/mol	215 231@LB@ \| \|@LB@5'-GUC...UUUAU UUGGC...CAG-3'@LB@ ACGUUGGU GAGUUGG@LB@ \|\|\|\|\|\|\|: \|\|\|\|\|\|:@LB@ UGCAACCG CUCAACU@LB@3'-CGC...UCAAG AAAUCAAUAAG CUUUG...AAG-5'@LB@ \| \|@LB@ 83 56@LB@@LB@@LB@Energy -8.08 kcal/mol@LB@Hybridization Energy -16.5635 kcal/mol@LB@Unfolding Energy - mRNA 7.18735 kcal/mol@LB@Unfolding Energy - sRNA 1.29708 kcal/mol@LB@@LB@Position - mRNA 216 -- 230@LB@Position - sRNA 57 -- 82@LB@Position Seed - mRNA 224 -- 230@LB@Position Seed - sRNA 57 -- 63@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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