Input and runtime details for job 6756176 (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 6756176 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:58 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:23:17 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:01:55 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:02:03 CET 2018
	Job Completed		@ Fri Feb 16 20:02:30 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6756176&toolName=CopraRNA ( 30 days expiry )

Description of the job

DsrA

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
161	0.01751	0.3504	b3394	hofN	-4.92	0.333288	275 -- 286	18 -- 29	DNA catabolic putative fimbrial assembly protein	_____________274__________287\n_____________\|____________\|\n5'-UGG...CUGAU____________UCUGC...CCG-3'\n______________GUUCGUUGCGCC\n______________:\|\|\|\|\|\|:\|:\|\|\n______________UAAGCAAUGUGG\n3'-UUU...UUUUU____________UCCUU...CAA-5'\n_____________\|____________\|\n_____________30___________17\n	275 -- 281	23 -- 29	-17.9024 kcal/mol	4.53191 kcal/mol	8.4513 kcal/mol	274 287@LB@ \| \|@LB@5'-UGG...CUGAU UCUGC...CCG-3'@LB@ GUUCGUUGCGCC@LB@ :\|\|\|\|\|\|:\|:\|\|@LB@ UAAGCAAUGUGG@LB@3'-UUU...UUUUU UCCUU...CAA-5'@LB@ \| \|@LB@ 30 17@LB@@LB@@LB@Energy -4.92 kcal/mol@LB@Hybridization Energy -17.9024 kcal/mol@LB@Unfolding Energy - mRNA 4.53191 kcal/mol@LB@Unfolding Energy - sRNA 8.4513 kcal/mol@LB@@LB@Position - mRNA 275 -- 286@LB@Position - sRNA 18 -- 29@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 23 -- 29@LB@
34	0.001265	0.1198	b0826	moeB	-10.82	0.009172	276 -- 295	26 -- 46	molybdopterin synthase sulfurylase	_____________275___________________296\n_____________\|_____________________\|\n5'-CUU...ACGGC_____________________UCGCG-3'\n______________CAGGAGGCGC_UGAAAGAUUC\n______________\|\|:\|\|:\|\|:\|_\|:\|\|\|:\|\|\|\|\n______________GUUCUUCGUG_AUUUUUUAAG\n3'-UUU...AAUUC__________A__________CAAUG...CAA-5'\n_____________\|_____________________\|\n_____________47____________________25\n	289 -- 295	26 -- 32	-23.0973 kcal/mol	6.15128 kcal/mol	6.13041 kcal/mol	275 296@LB@ \| \|@LB@5'-CUU...ACGGC UCGCG-3'@LB@ CAGGAGGCGC UGAAAGAUUC@LB@ \|\|:\|\|:\|\|:\| \|:\|\|\|:\|\|\|\|@LB@ GUUCUUCGUG AUUUUUUAAG@LB@3'-UUU...AAUUC A CAAUG...CAA-5'@LB@ \| \|@LB@ 47 25@LB@@LB@@LB@Energy -10.82 kcal/mol@LB@Hybridization Energy -23.0973 kcal/mol@LB@Unfolding Energy - mRNA 6.15128 kcal/mol@LB@Unfolding Energy - sRNA 6.13041 kcal/mol@LB@@LB@Position - mRNA 276 -- 295@LB@Position - sRNA 26 -- 46@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 26 -- 32@LB@
80	0.005376	0.2146	b1520	yneE	-6.66	0.134465	278 -- 284	34 -- 40	bestrophin family putative inner membrane protein	_____________277_____285\n_____________\|_______\|\n5'-CGU...UCCUC_______CUACU...UCU-3'\n______________GCGCUUA\n______________\|\|:\|\|\|\|\n______________CGUGAAU\n3'-UUU...UUCUU_______UUUUU...CAA-5'\n_____________\|_______\|\n_____________41______33\n	278 -- 284	34 -- 40	-8.65652 kcal/mol	0.386276 kcal/mol	1.61352 kcal/mol	277 285@LB@ \| \|@LB@5'-CGU...UCCUC CUACU...UCU-3'@LB@ GCGCUUA@LB@ \|\|:\|\|\|\|@LB@ CGUGAAU@LB@3'-UUU...UUCUU UUUUU...CAA-5'@LB@ \| \|@LB@ 41 33@LB@@LB@@LB@Energy -6.66 kcal/mol@LB@Hybridization Energy -8.65652 kcal/mol@LB@Unfolding Energy - mRNA 0.386276 kcal/mol@LB@Unfolding Energy - sRNA 1.61352 kcal/mol@LB@@LB@Position - mRNA 278 -- 284@LB@Position - sRNA 34 -- 40@LB@Position Seed - mRNA 278 -- 284@LB@Position Seed - sRNA 34 -- 40@LB@
12	0.0001753	0.04706	b3676	yidH	-12.46	0.002725	279 -- 300	7 -- 26	DUF202 family inner membrane protein	_____________278___________________300\n_____________\|_____________________\|\n5'-GCC...GGAUC___AC__________UU_____-3'\n______________CGU__UGCACUAGGA__UCUGG\n______________\|\|\|__\|:\|\|\|:\|\|\|\|__\|\|\|\|:\n______________GCA__AUGUGGUCCU__AGACU\n3'-UUU...UUUAA_______________UU_____ACACAA-5'\n_____________\|______________________\|\n_____________27_____________________6\n	286 -- 292	15 -- 21	-23.8048 kcal/mol	2.98352 kcal/mol	8.36616 kcal/mol	278 300@LB@ \| \|@LB@5'-GCC...GGAUC AC UU -3'@LB@ CGU UGCACUAGGA UCUGG@LB@ \|\|\| \|:\|\|\|:\|\|\|\| \|\|\|\|:@LB@ GCA AUGUGGUCCU AGACU@LB@3'-UUU...UUUAA UU ACACAA-5'@LB@ \| \|@LB@ 27 6@LB@@LB@@LB@Energy -12.46 kcal/mol@LB@Hybridization Energy -23.8048 kcal/mol@LB@Unfolding Energy - mRNA 2.98352 kcal/mol@LB@Unfolding Energy - sRNA 8.36616 kcal/mol@LB@@LB@Position - mRNA 279 -- 300@LB@Position - sRNA 7 -- 26@LB@Position Seed - mRNA 286 -- 292@LB@Position Seed - sRNA 15 -- 21@LB@
56	0.002803	0.1597	b2514	hisS	-5.93	0.201249	279 -- 295	24 -- 41	histidyl tRNA synthetase	_____________278_________________296\n_____________\|___________________\|\n5'-AUG...UUGAA_____AC____________GCUCG-3'\n______________GGCAC__UGAAAAA__CGU\n______________:\|\|\|\|__\|:\|\|\|\|\|__\|\|\|\n______________UCGUG__AUUUUUU__GCA\n3'-UUU...GUUCU_____A________AA___AUGUG...CAA-5'\n_____________\|___________________\|\n_____________42__________________23\n	286 -- 292	29 -- 35	-10.1195 kcal/mol	2.54562 kcal/mol	1.64881 kcal/mol	278 296@LB@ \| \|@LB@5'-AUG...UUGAA AC GCUCG-3'@LB@ GGCAC UGAAAAA CGU@LB@ :\|\|\|\| \|:\|\|\|\|\| \|\|\|@LB@ UCGUG AUUUUUU GCA@LB@3'-UUU...GUUCU A AA AUGUG...CAA-5'@LB@ \| \|@LB@ 42 23@LB@@LB@@LB@Energy -5.93 kcal/mol@LB@Hybridization Energy -10.1195 kcal/mol@LB@Unfolding Energy - mRNA 2.54562 kcal/mol@LB@Unfolding Energy - sRNA 1.64881 kcal/mol@LB@@LB@Position - mRNA 279 -- 295@LB@Position - sRNA 24 -- 41@LB@Position Seed - mRNA 286 -- 292@LB@Position Seed - sRNA 29 -- 35@LB@
15	0.0003116	0.06692	b2149	mglA	-7.01	0.109495	281 -- 289	33 -- 41	methyl-galactoside ABC transporter ATPase	_____________280_______290\n_____________\|_________\|\n5'-CGA...GUUAA_________UAACG...AUU-3'\n______________GGCACUUGA\n______________:\|\|\|\|\|\|:\|\n______________UCGUGAAUU\n3'-UUU...GUUCU_________UUUUA...CAA-5'\n_____________\|_________\|\n_____________42________32\n	283 -- 289	33 -- 39	-11.227 kcal/mol	2.59529 kcal/mol	1.6188 kcal/mol	280 290@LB@ \| \|@LB@5'-CGA...GUUAA UAACG...AUU-3'@LB@ GGCACUUGA@LB@ :\|\|\|\|\|\|:\|@LB@ UCGUGAAUU@LB@3'-UUU...GUUCU UUUUA...CAA-5'@LB@ \| \|@LB@ 42 32@LB@@LB@@LB@Energy -7.01 kcal/mol@LB@Hybridization Energy -11.227 kcal/mol@LB@Unfolding Energy - mRNA 2.59529 kcal/mol@LB@Unfolding Energy - sRNA 1.6188 kcal/mol@LB@@LB@Position - mRNA 281 -- 289@LB@Position - sRNA 33 -- 41@LB@Position Seed - mRNA 283 -- 289@LB@Position Seed - sRNA 33 -- 39@LB@
179	0.02107	0.3768	b3226	nanR	-7.22	0.096643	281 -- 296	26 -- 41	sialic acid-inducible nan operon repressor	_____________280______________297\n_____________\|________________\|\n5'-AUU...CCGCU_____G_______C__UCCG-3'\n______________GGCGC_UAAAAAA_UC\n______________:\|\|:\|_\|\|\|\|\|\|\|_\|\|\n______________UCGUG_AUUUUUU_AG\n3'-UUU...GUUCU_____A_______A__CAAUG...CAA-5'\n_____________\|________________\|\n_____________42_______________25\n	287 -- 293	29 -- 35	-11.6683 kcal/mol	2.7952 kcal/mol	1.64829 kcal/mol	280 297@LB@ \| \|@LB@5'-AUU...CCGCU G C UCCG-3'@LB@ GGCGC UAAAAAA UC@LB@ :\|\|:\| \|\|\|\|\|\|\| \|\|@LB@ UCGUG AUUUUUU AG@LB@3'-UUU...GUUCU A A CAAUG...CAA-5'@LB@ \| \|@LB@ 42 25@LB@@LB@@LB@Energy -7.22 kcal/mol@LB@Hybridization Energy -11.6683 kcal/mol@LB@Unfolding Energy - mRNA 2.7952 kcal/mol@LB@Unfolding Energy - sRNA 1.64829 kcal/mol@LB@@LB@Position - mRNA 281 -- 296@LB@Position - sRNA 26 -- 41@LB@Position Seed - mRNA 287 -- 293@LB@Position Seed - sRNA 29 -- 35@LB@
66	0.003432	0.1645	b0882	clpA	-7.45	0.084488	282 -- 290	34 -- 42	ATPase and specificity subunit of ClpA-ClpP ATP-dependent serine protease chaperone activity	_____________281_______291\n_____________\|_________\|\n5'-UUU...CCGUC_________UUACU...CGC-3'\n______________GAGCACUUG\n______________:\|\|\|\|\|\|\|:\n______________UUCGUGAAU\n3'-UUU...CGUUC_________UUUUU...CAA-5'\n_____________\|_________\|\n_____________43________33\n	284 -- 290	34 -- 40	-10.5586 kcal/mol	1.49281 kcal/mol	1.61613 kcal/mol	281 291@LB@ \| \|@LB@5'-UUU...CCGUC UUACU...CGC-3'@LB@ GAGCACUUG@LB@ :\|\|\|\|\|\|\|:@LB@ UUCGUGAAU@LB@3'-UUU...CGUUC UUUUU...CAA-5'@LB@ \| \|@LB@ 43 33@LB@@LB@@LB@Energy -7.45 kcal/mol@LB@Hybridization Energy -10.5586 kcal/mol@LB@Unfolding Energy - mRNA 1.49281 kcal/mol@LB@Unfolding Energy - sRNA 1.61613 kcal/mol@LB@@LB@Position - mRNA 282 -- 290@LB@Position - sRNA 34 -- 42@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 34 -- 40@LB@
96	0.007122	0.239	b2060	wzc	-5.51	0.249431	285 -- 291	37 -- 43	colanic acid production tyrosine-protein kinase; autokinase; Ugd phosphorylase	_____________284_____292\n_____________\|_______\|\n5'-GAA...UCAUU_______GCUGG...GGG-3'\n______________GAAGCGC\n______________\|\|\|\|\|:\|\n______________CUUCGUG\n3'-UUU...UCGUU_______AAUUU...CAA-5'\n_____________\|_______\|\n_____________44______36\n	285 -- 291	37 -- 43	-9.9751 kcal/mol	0.803081 kcal/mol	3.6595 kcal/mol	284 292@LB@ \| \|@LB@5'-GAA...UCAUU GCUGG...GGG-3'@LB@ GAAGCGC@LB@ \|\|\|\|\|:\|@LB@ CUUCGUG@LB@3'-UUU...UCGUU AAUUU...CAA-5'@LB@ \| \|@LB@ 44 36@LB@@LB@@LB@Energy -5.51 kcal/mol@LB@Hybridization Energy -9.9751 kcal/mol@LB@Unfolding Energy - mRNA 0.803081 kcal/mol@LB@Unfolding Energy - sRNA 3.6595 kcal/mol@LB@@LB@Position - mRNA 285 -- 291@LB@Position - sRNA 37 -- 43@LB@Position Seed - mRNA 285 -- 291@LB@Position Seed - sRNA 37 -- 43@LB@
183	0.02165	0.3768	b4201	priB	-4.41	0.419305	289 -- 298	45 -- 54	primosomal protein N	_____________288________299\n_____________\|__________\|\n5'-AGG...GUUCG__________UC-3'\n______________UGCUUGAGCA\n______________\|\|\|\|\|:\|\|\|\|\n______________ACGAAUUCGU\n3'-UUU...UUUGA__________UCUUC...CAA-5'\n_____________\|__________\|\n_____________55_________44\n	290 -- 296	47 -- 53	-14.7774 kcal/mol	4.46723 kcal/mol	5.90361 kcal/mol	288 299@LB@ \| \|@LB@5'-AGG...GUUCG UC-3'@LB@ UGCUUGAGCA@LB@ \|\|\|\|\|:\|\|\|\|@LB@ ACGAAUUCGU@LB@3'-UUU...UUUGA UCUUC...CAA-5'@LB@ \| \|@LB@ 55 44@LB@@LB@@LB@Energy -4.41 kcal/mol@LB@Hybridization Energy -14.7774 kcal/mol@LB@Unfolding Energy - mRNA 4.46723 kcal/mol@LB@Unfolding Energy - sRNA 5.90361 kcal/mol@LB@@LB@Position - mRNA 289 -- 298@LB@Position - sRNA 45 -- 54@LB@Position Seed - mRNA 290 -- 296@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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