Input and runtime details for job 1765463 (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 1765463 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:41:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:42:13 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 19:57:45 CET 2018
	Post-Processing Finished		@ Fri Feb 16 19:57:53 CET 2018
	Job Completed		@ Fri Feb 16 19:58:19 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1765463&toolName=CopraRNA ( 30 days expiry )

Description of the job

5 ChiX sequences

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
64	0.01382	0.6177	b3250	mreC	-10.24	0.036759	206 -- 229	53 -- 75	cell wall structural complex MreBCD transmembrane component MreC	_____________205_______________________230\n_____________\|_________________________\|\n5'-GAC...AUGAA______UUUUA__CG__________GCUAC...GGA-3'\n______________GCCAAU_____GC___UGGCCCGUC\n______________\|\|\|\|\|\|_____\|\|___\|\|\|\|\|\|\|\|\|\n______________CGGUUA_____CG___ACCGGGCAG\n3'-UUU...UUUAC______UAG____AUA_________UUUCU...ACA-5'\n_____________\|_________________________\|\n_____________76________________________52\n	223 -- 229	53 -- 59	-27.5071 kcal/mol	5.94491 kcal/mol	11.3228 kcal/mol	205 230@LB@ \| \|@LB@5'-GAC...AUGAA UUUUA CG GCUAC...GGA-3'@LB@ GCCAAU GC UGGCCCGUC@LB@ \|\|\|\|\|\| \|\| \|\|\|\|\|\|\|\|\|@LB@ CGGUUA CG ACCGGGCAG@LB@3'-UUU...UUUAC UAG AUA UUUCU...ACA-5'@LB@ \| \|@LB@ 76 52@LB@@LB@@LB@Energy -10.24 kcal/mol@LB@Hybridization Energy -27.5071 kcal/mol@LB@Unfolding Energy - mRNA 5.94491 kcal/mol@LB@Unfolding Energy - sRNA 11.3228 kcal/mol@LB@@LB@Position - mRNA 206 -- 229@LB@Position - sRNA 53 -- 75@LB@Position Seed - mRNA 223 -- 229@LB@Position Seed - sRNA 53 -- 59@LB@
65	0.01408	0.6177	b3176	glmM	-9.74	0.046438	133 -- 141	48 -- 56	phosphoglucosamine mutase	_____________132_______142\n_____________\|_________\|\n5'-GUU...CAUGA_________AACCG...CGG-3'\n______________CGUCAAAGA\n______________\|\|\|\|\|\|\|\|\|\n______________GCAGUUUCU\n3'-UUU...ACCGG_________CCUUA...ACA-5'\n_____________\|_________\|\n_____________57________47\n	135 -- 141	48 -- 54	-11.8395 kcal/mol	1.20122 kcal/mol	0.896433 kcal/mol	132 142@LB@ \| \|@LB@5'-GUU...CAUGA AACCG...CGG-3'@LB@ CGUCAAAGA@LB@ \|\|\|\|\|\|\|\|\|@LB@ GCAGUUUCU@LB@3'-UUU...ACCGG CCUUA...ACA-5'@LB@ \| \|@LB@ 57 47@LB@@LB@@LB@Energy -9.74 kcal/mol@LB@Hybridization Energy -11.8395 kcal/mol@LB@Unfolding Energy - mRNA 1.20122 kcal/mol@LB@Unfolding Energy - sRNA 0.896433 kcal/mol@LB@@LB@Position - mRNA 133 -- 141@LB@Position - sRNA 48 -- 56@LB@Position Seed - mRNA 135 -- 141@LB@Position Seed - sRNA 48 -- 54@LB@
66	0.01414	0.6177	b0440	hupB	-10.30	0.035643	184 -- 193	44 -- 53	HU DNA-binding transcriptional regulator beta subunit	_____________183________194\n_____________\|__________\|\n5'-CGC...AAUUA__________GAGAA...CUG-3'\n______________UAAAGAGGAA\n______________:\|\|\|\|\|\|\|\|\|\n______________GUUUCUCCUU\n3'-UUU...GGGCA__________AAAGU...ACA-5'\n_____________\|__________\|\n_____________54_________43\n	187 -- 193	44 -- 50	-11.552 kcal/mol	0.319105 kcal/mol	0.927997 kcal/mol	183 194@LB@ \| \|@LB@5'-CGC...AAUUA GAGAA...CUG-3'@LB@ UAAAGAGGAA@LB@ :\|\|\|\|\|\|\|\|\|@LB@ GUUUCUCCUU@LB@3'-UUU...GGGCA AAAGU...ACA-5'@LB@ \| \|@LB@ 54 43@LB@@LB@@LB@Energy -10.30 kcal/mol@LB@Hybridization Energy -11.552 kcal/mol@LB@Unfolding Energy - mRNA 0.319105 kcal/mol@LB@Unfolding Energy - sRNA 0.927997 kcal/mol@LB@@LB@Position - mRNA 184 -- 193@LB@Position - sRNA 44 -- 53@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 44 -- 50@LB@
67	0.01414	0.6177	b0474	adk	-7.17	0.151538	186 -- 198	39 -- 51	adenylate kinase	_____________185___________199\n_____________\|_____________\|\n5'-ACC...AUUUU_______U_____CAAUG...AUA-3'\n______________AAGGGGA_UUUCG\n______________\|\|\|:\|\|\|_\|\|\|\|:\n______________UUCUCCU_AAAGU\n3'-UUU...GCAGU_______U_____AAAAA...ACA-5'\n_____________\|_____________\|\n_____________52____________38\n	186 -- 192	45 -- 51	-12.5937 kcal/mol	4.3836 kcal/mol	1.04441 kcal/mol	185 199@LB@ \| \|@LB@5'-ACC...AUUUU U CAAUG...AUA-3'@LB@ AAGGGGA UUUCG@LB@ \|\|\|:\|\|\| \|\|\|\|:@LB@ UUCUCCU AAAGU@LB@3'-UUU...GCAGU U AAAAA...ACA-5'@LB@ \| \|@LB@ 52 38@LB@@LB@@LB@Energy -7.17 kcal/mol@LB@Hybridization Energy -12.5937 kcal/mol@LB@Unfolding Energy - mRNA 4.3836 kcal/mol@LB@Unfolding Energy - sRNA 1.04441 kcal/mol@LB@@LB@Position - mRNA 186 -- 198@LB@Position - sRNA 39 -- 51@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 45 -- 51@LB@
68	0.01422	0.6177	b3826	yigL	-7.04	0.159921	44 -- 50	49 -- 55	pyridoxal phosphate phosphatase	_____________43______51\n_____________\|_______\|\n5'-GCA...AUCCU_______GAGGA...CGC-3'\n______________GUCGAAG\n______________\|\|\|:\|\|\|\n______________CAGUUUC\n3'-UUU...CCGGG_______UCCUU...ACA-5'\n_____________\|_______\|\n_____________56______48\n	44 -- 50	49 -- 55	-7.68974 kcal/mol	0.331193 kcal/mol	0.314364 kcal/mol	43 51@LB@ \| \|@LB@5'-GCA...AUCCU GAGGA...CGC-3'@LB@ GUCGAAG@LB@ \|\|\|:\|\|\|@LB@ CAGUUUC@LB@3'-UUU...CCGGG UCCUU...ACA-5'@LB@ \| \|@LB@ 56 48@LB@@LB@@LB@Energy -7.04 kcal/mol@LB@Hybridization Energy -7.68974 kcal/mol@LB@Unfolding Energy - mRNA 0.331193 kcal/mol@LB@Unfolding Energy - sRNA 0.314364 kcal/mol@LB@@LB@Position - mRNA 44 -- 50@LB@Position - sRNA 49 -- 55@LB@Position Seed - mRNA 44 -- 50@LB@Position Seed - sRNA 49 -- 55@LB@
69	0.01434	0.6177	b0551	quuD	-6.03	0.248082	117 -- 124	48 -- 55	DLP12 prophage; putative antitermination protein	_____________116______125\n_____________\|________\|\n5'-ACU...AUGAA________UAACA...GAU-3'\n______________GUCAGAGA\n______________\|\|\|\|:\|\|\|\n______________CAGUUUCU\n3'-UUU...CCGGG________CCUUA...ACA-5'\n_____________\|________\|\n_____________56_______47\n	118 -- 124	48 -- 54	-9.27195 kcal/mol	2.92769 kcal/mol	0.318869 kcal/mol	116 125@LB@ \| \|@LB@5'-ACU...AUGAA UAACA...GAU-3'@LB@ GUCAGAGA@LB@ \|\|\|\|:\|\|\|@LB@ CAGUUUCU@LB@3'-UUU...CCGGG CCUUA...ACA-5'@LB@ \| \|@LB@ 56 47@LB@@LB@@LB@Energy -6.03 kcal/mol@LB@Hybridization Energy -9.27195 kcal/mol@LB@Unfolding Energy - mRNA 2.92769 kcal/mol@LB@Unfolding Energy - sRNA 0.318869 kcal/mol@LB@@LB@Position - mRNA 117 -- 124@LB@Position - sRNA 48 -- 55@LB@Position Seed - mRNA 118 -- 124@LB@Position Seed - sRNA 48 -- 54@LB@
70	0.01448	0.6177	b4012	yjaB	-8.12	0.098308	234 -- 242	44 -- 52	GNAT-family putative N-acetyltransferase; acetyl coenzyme A-binding protein	_____________233_______243\n_____________\|_________\|\n5'-AAG...AUGAG_________GAACU...CAG-3'\n______________GAAGGGGAG\n______________:\|\|\|:\|\|\|:\n______________UUUCUCCUU\n3'-UUU...GGCAG_________AAAGU...ACA-5'\n_____________\|_________\|\n_____________53________43\n	236 -- 242	44 -- 50	-9.78668 kcal/mol	0.80114 kcal/mol	0.860683 kcal/mol	233 243@LB@ \| \|@LB@5'-AAG...AUGAG GAACU...CAG-3'@LB@ GAAGGGGAG@LB@ :\|\|\|:\|\|\|:@LB@ UUUCUCCUU@LB@3'-UUU...GGCAG AAAGU...ACA-5'@LB@ \| \|@LB@ 53 43@LB@@LB@@LB@Energy -8.12 kcal/mol@LB@Hybridization Energy -9.78668 kcal/mol@LB@Unfolding Energy - mRNA 0.80114 kcal/mol@LB@Unfolding Energy - sRNA 0.860683 kcal/mol@LB@@LB@Position - mRNA 234 -- 242@LB@Position - sRNA 44 -- 52@LB@Position Seed - mRNA 236 -- 242@LB@Position Seed - sRNA 44 -- 50@LB@
71	0.01472	0.6177	b0846	rcdA	-10.28	0.035999	187 -- 195	44 -- 52	transcriptional regulator of csgD and ybiJI; autoregulator	_____________186_______196\n_____________\|_________\|\n5'-GCG...UGCAG_________AUGAC...AAA-3'\n______________AGAGAGGAA\n______________\|:\|\|\|\|\|\|\|\n______________UUUCUCCUU\n3'-UUU...GGCAG_________AAAGU...ACA-5'\n_____________\|_________\|\n_____________53________43\n	189 -- 195	44 -- 50	-11.6116 kcal/mol	0.46711 kcal/mol	0.860683 kcal/mol	186 196@LB@ \| \|@LB@5'-GCG...UGCAG AUGAC...AAA-3'@LB@ AGAGAGGAA@LB@ \|:\|\|\|\|\|\|\|@LB@ UUUCUCCUU@LB@3'-UUU...GGCAG AAAGU...ACA-5'@LB@ \| \|@LB@ 53 43@LB@@LB@@LB@Energy -10.28 kcal/mol@LB@Hybridization Energy -11.6116 kcal/mol@LB@Unfolding Energy - mRNA 0.46711 kcal/mol@LB@Unfolding Energy - sRNA 0.860683 kcal/mol@LB@@LB@Position - mRNA 187 -- 195@LB@Position - sRNA 44 -- 52@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 44 -- 50@LB@
72	0.015	0.6177	b2513	yfgM	-10.40	0.034106	179 -- 190	45 -- 55	ancillary SecYEG translocon subunit; putative anti-RcsB factor	_____________178__________191\n_____________\|____________\|\n5'-GGC...ACUGG________A___GAAGG...UUG-3'\n______________GUUAAGGA_GGA\n______________\|\|:\|\|:\|\|_\|\|\|\n______________CAGUUUCU_CCU\n3'-UUU...CCGGG____________UAAAG...ACA-5'\n_____________\|____________\|\n_____________56___________44\n	180 -- 186	48 -- 54	-12.2699 kcal/mol	0.940443 kcal/mol	0.930875 kcal/mol	178 191@LB@ \| \|@LB@5'-GGC...ACUGG A GAAGG...UUG-3'@LB@ GUUAAGGA GGA@LB@ \|\|:\|\|:\|\| \|\|\|@LB@ CAGUUUCU CCU@LB@3'-UUU...CCGGG UAAAG...ACA-5'@LB@ \| \|@LB@ 56 44@LB@@LB@@LB@Energy -10.40 kcal/mol@LB@Hybridization Energy -12.2699 kcal/mol@LB@Unfolding Energy - mRNA 0.940443 kcal/mol@LB@Unfolding Energy - sRNA 0.930875 kcal/mol@LB@@LB@Position - mRNA 179 -- 190@LB@Position - sRNA 45 -- 55@LB@Position Seed - mRNA 180 -- 186@LB@Position Seed - sRNA 48 -- 54@LB@
73	0.01516	0.6177	b0619	citA	-15.44	0.003129	164 -- 175	46 -- 57	sensory histidine kinase in two-component regulatory system with CitB	_____________163__________176\n_____________\|____________\|\n5'-CAU...UACAU____________CUCGG...UCA-3'\n______________CCGUCAAAGAGG\n______________\|\|\|\|\|\|\|\|\|\|\|\|\n______________GGCAGUUUCUCC\n3'-UUU...AACCG____________UUAAA...ACA-5'\n_____________\|____________\|\n_____________58___________45\n	169 -- 175	46 -- 52	-20.3901 kcal/mol	2.21322 kcal/mol	2.7365 kcal/mol	163 176@LB@ \| \|@LB@5'-CAU...UACAU CUCGG...UCA-3'@LB@ CCGUCAAAGAGG@LB@ \|\|\|\|\|\|\|\|\|\|\|\|@LB@ GGCAGUUUCUCC@LB@3'-UUU...AACCG UUAAA...ACA-5'@LB@ \| \|@LB@ 58 45@LB@@LB@@LB@Energy -15.44 kcal/mol@LB@Hybridization Energy -20.3901 kcal/mol@LB@Unfolding Energy - mRNA 2.21322 kcal/mol@LB@Unfolding Energy - sRNA 2.7365 kcal/mol@LB@@LB@Position - mRNA 164 -- 175@LB@Position - sRNA 46 -- 57@LB@Position Seed - mRNA 169 -- 175@LB@Position Seed - sRNA 46 -- 52@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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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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