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	Additional homologs
81	0.01751	0.6177	b2741	rpoS	-9.52	0.051528	88 -- 101	44 -- 56	RNA polymerase sigma S (sigma 38) factor		_____________87_____________102\n_____________\|______________\|\n5'-CGG...AAAUU_____C________AUCCG...AGG-3'\n______________CGUUA_AAGGGGAA\n______________\|\|\|:\|_\|\|\|:\|\|\|\|\n______________GCAGU_UUCUCCUU\n3'-UUU...ACCGG______________AAAGU...ACA-5'\n_____________\|______________\|\n_____________57_____________43\n	95 -- 101	44 -- 50	-13.0318 kcal/mol	2.56318 kcal/mol	0.948902 kcal/mol	87 102@LB@ \| \|@LB@5'-CGG...AAAUU C AUCCG...AGG-3'@LB@ CGUUA AAGGGGAA@LB@ \|\|\|:\| \|\|\|:\|\|\|\|@LB@ GCAGU UUCUCCUU@LB@3'-UUU...ACCGG AAAGU...ACA-5'@LB@ \| \|@LB@ 57 43@LB@@LB@@LB@Energy -9.52 kcal/mol@LB@Hybridization Energy -13.0318 kcal/mol@LB@Unfolding Energy - mRNA 2.56318 kcal/mol@LB@Unfolding Energy - sRNA 0.948902 kcal/mol@LB@@LB@Position - mRNA 88 -- 101@LB@Position - sRNA 44 -- 56@LB@Position Seed - mRNA 95 -- 101@LB@Position Seed - sRNA 44 -- 50@LB@
82	0.01753	0.6177	b2204	napH	-9.88	0.043521	152 -- 162	42 -- 52	ferredoxin-type protein		_____________151_________163\n_____________\|___________\|\n5'-CAC...UGGCG___________AGGUC...UCU-3'\n______________AAAGGGGAGUU\n______________\|\|\|\|:\|\|\|:\|\|\n______________UUUCUCCUUAA\n3'-UUU...GGCAG___________AGUAA...ACA-5'\n_____________\|___________\|\n_____________53__________41\n	156 -- 162	42 -- 48	-12.4472 kcal/mol	1.70007 kcal/mol	0.866923 kcal/mol	151 163@LB@ \| \|@LB@5'-CAC...UGGCG AGGUC...UCU-3'@LB@ AAAGGGGAGUU@LB@ \|\|\|\|:\|\|\|:\|\|@LB@ UUUCUCCUUAA@LB@3'-UUU...GGCAG AGUAA...ACA-5'@LB@ \| \|@LB@ 53 41@LB@@LB@@LB@Energy -9.88 kcal/mol@LB@Hybridization Energy -12.4472 kcal/mol@LB@Unfolding Energy - mRNA 1.70007 kcal/mol@LB@Unfolding Energy - sRNA 0.866923 kcal/mol@LB@@LB@Position - mRNA 152 -- 162@LB@Position - sRNA 42 -- 52@LB@Position Seed - mRNA 156 -- 162@LB@Position Seed - sRNA 42 -- 48@LB@
83	0.0176	0.6177	b2457	eutM	-9.48	0.052376	185 -- 194	44 -- 53	ethanolamine utilization protein putative carboxysome structural protein		_____________184________195\n_____________\|__________\|\n5'-UAU...CCUGA__________AGCAC...UUA-3'\n______________UAAAGAGGAA\n______________:\|\|\|\|\|\|\|\|\|\n______________GUUUCUCCUU\n3'-UUU...GGGCA__________AAAGU...ACA-5'\n_____________\|__________\|\n_____________54_________43\n	188 -- 194	44 -- 50	-11.8586 kcal/mol	1.44575 kcal/mol	0.927997 kcal/mol	184 195@LB@ \| \|@LB@5'-UAU...CCUGA AGCAC...UUA-3'@LB@ UAAAGAGGAA@LB@ :\|\|\|\|\|\|\|\|\|@LB@ GUUUCUCCUU@LB@3'-UUU...GGGCA AAAGU...ACA-5'@LB@ \| \|@LB@ 54 43@LB@@LB@@LB@Energy -9.48 kcal/mol@LB@Hybridization Energy -11.8586 kcal/mol@LB@Unfolding Energy - mRNA 1.44575 kcal/mol@LB@Unfolding Energy - sRNA 0.927997 kcal/mol@LB@@LB@Position - mRNA 185 -- 194@LB@Position - sRNA 44 -- 53@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 44 -- 50@LB@
84	0.01785	0.6177	b4318	fimF	-9.06	0.063721	96 -- 107	44 -- 55	minor component of type 1 fimbriae	b1504 b0943	_____________95___________108\n_____________\|____________\|\n5'-CAU...AAUGG_GA_________AAUGC...UCA-3'\n______________G__GAAGAGGAA\n______________\|__:\|\|\|\|\|\|\|\|\n______________C__UUUCUCCUU\n3'-UUU...CCGGG_AG_________AAAGU...ACA-5'\n_____________\|____________\|\n_____________56___________43\n	101 -- 107	44 -- 50	-12.9705 kcal/mol	2.96464 kcal/mol	0.941432 kcal/mol	95 108@LB@ \| \|@LB@5'-CAU...AAUGG GA AAUGC...UCA-3'@LB@ G GAAGAGGAA@LB@ \| :\|\|\|\|\|\|\|\|@LB@ C UUUCUCCUU@LB@3'-UUU...CCGGG AG AAAGU...ACA-5'@LB@ \| \|@LB@ 56 43@LB@@LB@@LB@Energy -9.06 kcal/mol@LB@Hybridization Energy -12.9705 kcal/mol@LB@Unfolding Energy - mRNA 2.96464 kcal/mol@LB@Unfolding Energy - sRNA 0.941432 kcal/mol@LB@@LB@Position - mRNA 96 -- 107@LB@Position - sRNA 44 -- 55@LB@Position Seed - mRNA 101 -- 107@LB@Position Seed - sRNA 44 -- 50@LB@
85	0.01786	0.6177	b1427	rimL	-14.01	0.006161	123 -- 133	46 -- 56	ribosomal-protein-L7/L12-serine acetyltransferase		_____________122_________134\n_____________\|___________\|\n5'-GAU...GAGAG___________UGUAA...CCU-3'\n______________CGUCAAAGAGG\n______________\|\|\|\|\|\|\|\|\|\|\|\n______________GCAGUUUCUCC\n3'-UUU...ACCGG___________UUAAA...ACA-5'\n_____________\|___________\|\n_____________57__________45\n	127 -- 133	46 -- 52	-17.3934 kcal/mol	2.45026 kcal/mol	0.93204 kcal/mol	122 134@LB@ \| \|@LB@5'-GAU...GAGAG UGUAA...CCU-3'@LB@ CGUCAAAGAGG@LB@ \|\|\|\|\|\|\|\|\|\|\|@LB@ GCAGUUUCUCC@LB@3'-UUU...ACCGG UUAAA...ACA-5'@LB@ \| \|@LB@ 57 45@LB@@LB@@LB@Energy -14.01 kcal/mol@LB@Hybridization Energy -17.3934 kcal/mol@LB@Unfolding Energy - mRNA 2.45026 kcal/mol@LB@Unfolding Energy - sRNA 0.93204 kcal/mol@LB@@LB@Position - mRNA 123 -- 133@LB@Position - sRNA 46 -- 56@LB@Position Seed - mRNA 127 -- 133@LB@Position Seed - sRNA 46 -- 52@LB@
86	0.01794	0.6177	b3260	dusB	-7.53	0.128932	119 -- 138	38 -- 55	tRNA-dihydrouridine synthase B		_____________118__________________139\n_____________\|____________________\|\n5'-ACU...GAUUG_______UUU__CC______CUCGU...GAG-3'\n______________GUCAAAG___GG__UUUCAU\n______________\|\|\|\|\|\|\|___\|\|__\|\|\|\|\|\|\n______________CAGUUUC___CC__AAAGUA\n3'-UUU...CCGGG_______U____UU______AAAAA...ACA-5'\n_____________\|____________________\|\n_____________56___________________37\n	119 -- 125	49 -- 55	-13.3869 kcal/mol	4.6894 kcal/mol	1.17036 kcal/mol	118 139@LB@ \| \|@LB@5'-ACU...GAUUG UUU CC CUCGU...GAG-3'@LB@ GUCAAAG GG UUUCAU@LB@ \|\|\|\|\|\|\| \|\| \|\|\|\|\|\|@LB@ CAGUUUC CC AAAGUA@LB@3'-UUU...CCGGG U UU AAAAA...ACA-5'@LB@ \| \|@LB@ 56 37@LB@@LB@@LB@Energy -7.53 kcal/mol@LB@Hybridization Energy -13.3869 kcal/mol@LB@Unfolding Energy - mRNA 4.6894 kcal/mol@LB@Unfolding Energy - sRNA 1.17036 kcal/mol@LB@@LB@Position - mRNA 119 -- 138@LB@Position - sRNA 38 -- 55@LB@Position Seed - mRNA 119 -- 125@LB@Position Seed - sRNA 49 -- 55@LB@
87	0.01794	0.6177	b3499	rlmJ	-10.99	0.025859	12 -- 21	46 -- 55	23S rRNA m(6)A2030 methyltransferase SAM-dependent		_____________11_________22\n_____________\|__________\|\n5'-GCG...UCCUG__________UUAAG...AUA-3'\n______________GUUAAAGAGG\n______________\|\|:\|\|\|\|\|\|\|\n______________CAGUUUCUCC\n3'-UUU...CCGGG__________UUAAA...ACA-5'\n_____________\|__________\|\n_____________56_________45\n	15 -- 21	46 -- 52	-14.3615 kcal/mol	2.45195 kcal/mol	0.924411 kcal/mol	11 22@LB@ \| \|@LB@5'-GCG...UCCUG UUAAG...AUA-3'@LB@ GUUAAAGAGG@LB@ \|\|:\|\|\|\|\|\|\|@LB@ CAGUUUCUCC@LB@3'-UUU...CCGGG UUAAA...ACA-5'@LB@ \| \|@LB@ 56 45@LB@@LB@@LB@Energy -10.99 kcal/mol@LB@Hybridization Energy -14.3615 kcal/mol@LB@Unfolding Energy - mRNA 2.45195 kcal/mol@LB@Unfolding Energy - sRNA 0.924411 kcal/mol@LB@@LB@Position - mRNA 12 -- 21@LB@Position - sRNA 46 -- 55@LB@Position Seed - mRNA 15 -- 21@LB@Position Seed - sRNA 46 -- 52@LB@
88	0.01799	0.6177	b0415	ribE	-8.66	0.076826	57 -- 64	47 -- 54	riboflavin synthase beta chain		_____________56_______65\n_____________\|________\|\n5'-CGG...UAAAU________AUACG...GUG-3'\n______________UCAAAGAG\n______________\|\|\|\|\|\|\|\|\n______________AGUUUCUC\n3'-UUU...CGGGC________CUUAA...ACA-5'\n_____________\|________\|\n_____________55_______46\n	58 -- 64	47 -- 53	-10.4141 kcal/mol	0.855178 kcal/mol	0.897871 kcal/mol	56 65@LB@ \| \|@LB@5'-CGG...UAAAU AUACG...GUG-3'@LB@ UCAAAGAG@LB@ \|\|\|\|\|\|\|\|@LB@ AGUUUCUC@LB@3'-UUU...CGGGC CUUAA...ACA-5'@LB@ \| \|@LB@ 55 46@LB@@LB@@LB@Energy -8.66 kcal/mol@LB@Hybridization Energy -10.4141 kcal/mol@LB@Unfolding Energy - mRNA 0.855178 kcal/mol@LB@Unfolding Energy - sRNA 0.897871 kcal/mol@LB@@LB@Position - mRNA 57 -- 64@LB@Position - sRNA 47 -- 54@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 47 -- 53@LB@
89	0.01853	0.6177	b1448	mnaT	-8.57	0.080000	123 -- 134	43 -- 54	methionine N-acyltransferase; L-amino acid N-acyltransferase		_____________122__________135\n_____________\|____________\|\n5'-CGC...UAAUU___UC_______CCGUU...CGG-3'\n______________UCA__GAGGAAU\n______________\|\|\|__\|\|\|\|\|\|\|\n______________AGU__CUCCUUA\n3'-UUU...CGGGC___UU_______AAGUA...ACA-5'\n_____________\|____________\|\n_____________55___________42\n	128 -- 134	43 -- 49	-11.9422 kcal/mol	2.42412 kcal/mol	0.944705 kcal/mol	122 135@LB@ \| \|@LB@5'-CGC...UAAUU UC CCGUU...CGG-3'@LB@ UCA GAGGAAU@LB@ \|\|\| \|\|\|\|\|\|\|@LB@ AGU CUCCUUA@LB@3'-UUU...CGGGC UU AAGUA...ACA-5'@LB@ \| \|@LB@ 55 42@LB@@LB@@LB@Energy -8.57 kcal/mol@LB@Hybridization Energy -11.9422 kcal/mol@LB@Unfolding Energy - mRNA 2.42412 kcal/mol@LB@Unfolding Energy - sRNA 0.944705 kcal/mol@LB@@LB@Position - mRNA 123 -- 134@LB@Position - sRNA 43 -- 54@LB@Position Seed - mRNA 128 -- 134@LB@Position Seed - sRNA 43 -- 49@LB@
90	0.01863	0.6177	b0659	ybeY	-9.29	0.057244	42 -- 51	47 -- 56	ssRNA-specific endoribonuclease; 16S rRNA 3' end maturation and quality control co-endoribonuclease working with RNase R; rRNA transcription antitermination factor		_____________41_________52\n_____________\|__________\|\n5'-ACU...GCCGA__________AUCAG...CGC-3'\n______________UGUCGAAGAG\n______________:\|\|\|:\|\|\|\|\|\n______________GCAGUUUCUC\n3'-UUU...ACCGG__________CUUAA...ACA-5'\n_____________\|__________\|\n_____________57_________46\n	45 -- 51	47 -- 53	-13.0692 kcal/mol	2.86289 kcal/mol	0.911734 kcal/mol	41 52@LB@ \| \|@LB@5'-ACU...GCCGA AUCAG...CGC-3'@LB@ UGUCGAAGAG@LB@ :\|\|\|:\|\|\|\|\|@LB@ GCAGUUUCUC@LB@3'-UUU...ACCGG CUUAA...ACA-5'@LB@ \| \|@LB@ 57 46@LB@@LB@@LB@Energy -9.29 kcal/mol@LB@Hybridization Energy -13.0692 kcal/mol@LB@Unfolding Energy - mRNA 2.86289 kcal/mol@LB@Unfolding Energy - sRNA 0.911734 kcal/mol@LB@@LB@Position - mRNA 42 -- 51@LB@Position - sRNA 47 -- 56@LB@Position Seed - mRNA 45 -- 51@LB@Position Seed - sRNA 47 -- 53@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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