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
151	0.03043	0.6177	b3081	fadH	-8.56	0.080347	290 -- 297	43 -- 50	2 4-dienoyl-CoA reductase NADH and FMN-linked		_____________289______298\n_____________\|________\|\n5'-UGG...GGGCU________ACC-3'\n______________GGAGGAAU\n______________:\|\|\|\|\|\|\|\n______________UCUCCUUA\n3'-UUU...CAGUU________AAGUA...ACA-5'\n_____________\|________\|\n_____________51_______42\n	291 -- 297	43 -- 49	-10.5858 kcal/mol	1.17616 kcal/mol	0.845564 kcal/mol	289 298@LB@ \| \|@LB@5'-UGG...GGGCU ACC-3'@LB@ GGAGGAAU@LB@ :\|\|\|\|\|\|\|@LB@ UCUCCUUA@LB@3'-UUU...CAGUU AAGUA...ACA-5'@LB@ \| \|@LB@ 51 42@LB@@LB@@LB@Energy -8.56 kcal/mol@LB@Hybridization Energy -10.5858 kcal/mol@LB@Unfolding Energy - mRNA 1.17616 kcal/mol@LB@Unfolding Energy - sRNA 0.845564 kcal/mol@LB@@LB@Position - mRNA 290 -- 297@LB@Position - sRNA 43 -- 50@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 43 -- 49@LB@
139	0.02683	0.6177	b1474	fdnG	-8.74	0.074199	188 -- 196	44 -- 52	formate dehydrogenase-N alpha subunit nitrate-inducible	b3894	_____________187_______197\n_____________\|_________\|\n5'-AUU...UGAAA_________AGCAA...CUC-3'\n______________AAAGAGGAA\n______________\|\|\|\|\|\|\|\|\|\n______________UUUCUCCUU\n3'-UUU...GGCAG_________AAAGU...ACA-5'\n_____________\|_________\|\n_____________53________43\n	190 -- 196	44 -- 50	-11.3772 kcal/mol	1.78024 kcal/mol	0.860683 kcal/mol	187 197@LB@ \| \|@LB@5'-AUU...UGAAA AGCAA...CUC-3'@LB@ AAAGAGGAA@LB@ \|\|\|\|\|\|\|\|\|@LB@ UUUCUCCUU@LB@3'-UUU...GGCAG AAAGU...ACA-5'@LB@ \| \|@LB@ 53 43@LB@@LB@@LB@Energy -8.74 kcal/mol@LB@Hybridization Energy -11.3772 kcal/mol@LB@Unfolding Energy - mRNA 1.78024 kcal/mol@LB@Unfolding Energy - sRNA 0.860683 kcal/mol@LB@@LB@Position - mRNA 188 -- 196@LB@Position - sRNA 44 -- 52@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 44 -- 50@LB@
177	0.03616	0.6177	b1474	fdnG	-8.74	0.074199	188 -- 196	44 -- 52	formate dehydrogenase-N alpha subunit nitrate-inducible	b3894	_____________187_______197\n_____________\|_________\|\n5'-AUU...UGAAA_________AGCAA...CUC-3'\n______________AAAGAGGAA\n______________\|\|\|\|\|\|\|\|\|\n______________UUUCUCCUU\n3'-UUU...GGCAG_________AAAGU...ACA-5'\n_____________\|_________\|\n_____________53________43\n	190 -- 196	44 -- 50	-11.3772 kcal/mol	1.78024 kcal/mol	0.860683 kcal/mol	187 197@LB@ \| \|@LB@5'-AUU...UGAAA AGCAA...CUC-3'@LB@ AAAGAGGAA@LB@ \|\|\|\|\|\|\|\|\|@LB@ UUUCUCCUU@LB@3'-UUU...GGCAG AAAGU...ACA-5'@LB@ \| \|@LB@ 53 43@LB@@LB@@LB@Energy -8.74 kcal/mol@LB@Hybridization Energy -11.3772 kcal/mol@LB@Unfolding Energy - mRNA 1.78024 kcal/mol@LB@Unfolding Energy - sRNA 0.860683 kcal/mol@LB@@LB@Position - mRNA 188 -- 196@LB@Position - sRNA 44 -- 52@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 44 -- 50@LB@
11	0.002274	0.593	b1476	fdnI	-10.73	0.029150	152 -- 175	44 -- 69	formate dehydrogenase-N cytochrome B556 (gamma) subunit nitrate-inducible		_____________151________________________176\n_____________\|__________________________\|\n5'-CGU...ACUAC____G______________UA_____GUGGA...UUU-3'\n______________AUCG_UAUUGGCCCG__AA__AGGAA\n______________\|\|\|\|_\|\|\|\|\|\|\|\|\|\|__\|\|__\|\|\|\|\|\n______________UAGC_AUAACCGGGC__UU__UCCUU\n3'-UUU...GGUUA____G__________AG__UC_____AAAGU...ACA-5'\n_____________\|__________________________\|\n_____________70_________________________43\n	160 -- 166	55 -- 61	-29.2423 kcal/mol	7.20098 kcal/mol	11.3099 kcal/mol	151 176@LB@ \| \|@LB@5'-CGU...ACUAC G UA GUGGA...UUU-3'@LB@ AUCG UAUUGGCCCG AA AGGAA@LB@ \|\|\|\| \|\|\|\|\|\|\|\|\|\| \|\| \|\|\|\|\|@LB@ UAGC AUAACCGGGC UU UCCUU@LB@3'-UUU...GGUUA G AG UC AAAGU...ACA-5'@LB@ \| \|@LB@ 70 43@LB@@LB@@LB@Energy -10.73 kcal/mol@LB@Hybridization Energy -29.2423 kcal/mol@LB@Unfolding Energy - mRNA 7.20098 kcal/mol@LB@Unfolding Energy - sRNA 11.3099 kcal/mol@LB@@LB@Position - mRNA 152 -- 175@LB@Position - sRNA 44 -- 69@LB@Position Seed - mRNA 160 -- 166@LB@Position Seed - sRNA 55 -- 61@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@
33	0.006504	0.6129	b1937	fliE	-6.45	0.207626	119 -- 135	24 -- 40	flagellar basal-body component		_____________118_______________136\n_____________\|_________________\|\n5'-CUG...AAACC_____________C___UUAGC...GUU-3'\n______________CGUUUUUUUGUUG_UAU\n______________\|:\|\|\|\|\|\|\|:\|\|:_\|\|\|\n______________GUAAAAAAAUAAU_AUA\n3'-UUU...UUAAA_____________A___CGGCA...ACA-5'\n_____________\|_________________\|\n_____________41________________23\n	124 -- 130	29 -- 35	-10.2961 kcal/mol	2.85244 kcal/mol	0.998368 kcal/mol	118 136@LB@ \| \|@LB@5'-CUG...AAACC C UUAGC...GUU-3'@LB@ CGUUUUUUUGUUG UAU@LB@ \|:\|\|\|\|\|\|\|:\|\|: \|\|\|@LB@ GUAAAAAAAUAAU AUA@LB@3'-UUU...UUAAA A CGGCA...ACA-5'@LB@ \| \|@LB@ 41 23@LB@@LB@@LB@Energy -6.45 kcal/mol@LB@Hybridization Energy -10.2961 kcal/mol@LB@Unfolding Energy - mRNA 2.85244 kcal/mol@LB@Unfolding Energy - sRNA 0.998368 kcal/mol@LB@@LB@Position - mRNA 119 -- 135@LB@Position - sRNA 24 -- 40@LB@Position Seed - mRNA 124 -- 130@LB@Position Seed - sRNA 29 -- 35@LB@
61	0.01292	0.6177	b4154	frdA	-9.46	0.053105	187 -- 202	38 -- 54	anaerobic fumarate reductase catalytic and NAD/flavoprotein subunit		_____________186_______________203\n_____________\|_________________\|\n5'-UAA...AACAA__U_________G____GCAAA...UCG-3'\n______________UC__GGAGGAAU_UCGU\n______________\|\|__:\|\|\|\|\|\|\|_\|\|:\|\n______________AG__UCUCCUUA_AGUA\n3'-UUU...CGGGC__UU________A____AAAAA...ACA-5'\n_____________\|_________________\|\n_____________55________________37\n	191 -- 197	43 -- 49	-14.1575 kcal/mol	3.5319 kcal/mol	1.17036 kcal/mol	186 203@LB@ \| \|@LB@5'-UAA...AACAA U G GCAAA...UCG-3'@LB@ UC GGAGGAAU UCGU@LB@ \|\| :\|\|\|\|\|\|\| \|\|:\|@LB@ AG UCUCCUUA AGUA@LB@3'-UUU...CGGGC UU A AAAAA...ACA-5'@LB@ \| \|@LB@ 55 37@LB@@LB@@LB@Energy -9.46 kcal/mol@LB@Hybridization Energy -14.1575 kcal/mol@LB@Unfolding Energy - mRNA 3.5319 kcal/mol@LB@Unfolding Energy - sRNA 1.17036 kcal/mol@LB@@LB@Position - mRNA 187 -- 202@LB@Position - sRNA 38 -- 54@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 43 -- 49@LB@
140	0.02703	0.6177	b3447	ggt	-5.41	0.319095	66 -- 81	38 -- 54	gamma-glutamyltranspeptidase		_____________65________________82\n_____________\|_________________\|\n5'-GUU...AAGAA________UC_______CGCGU...CGU-3'\n______________UCAGA_AG__GUUUCAU\n______________\|\|\|:\|_\|\|__:\|\|\|\|\|\|\n______________AGUUU_UC__UAAAGUA\n3'-UUU...CGGGC_____C__CU_______AAAAA...ACA-5'\n_____________\|_________________\|\n_____________55________________37\n	75 -- 81	38 -- 44	-8.61894 kcal/mol	2.03989 kcal/mol	1.17036 kcal/mol	65 82@LB@ \| \|@LB@5'-GUU...AAGAA UC CGCGU...CGU-3'@LB@ UCAGA AG GUUUCAU@LB@ \|\|\|:\| \|\| :\|\|\|\|\|\|@LB@ AGUUU UC UAAAGUA@LB@3'-UUU...CGGGC C CU AAAAA...ACA-5'@LB@ \| \|@LB@ 55 37@LB@@LB@@LB@Energy -5.41 kcal/mol@LB@Hybridization Energy -8.61894 kcal/mol@LB@Unfolding Energy - mRNA 2.03989 kcal/mol@LB@Unfolding Energy - sRNA 1.17036 kcal/mol@LB@@LB@Position - mRNA 66 -- 81@LB@Position - sRNA 38 -- 54@LB@Position Seed - mRNA 75 -- 81@LB@Position Seed - sRNA 38 -- 44@LB@
53	0.01077	0.6177	b3429	glgA	-6.74	0.182373	105 -- 111	44 -- 50	glycogen synthase		_____________104_____112\n_____________\|_______\|\n5'-GUA...AACGC_______GAUGC...ACG-3'\n______________AGAGGAA\n______________\|\|\|\|\|\|\|\n______________UCUCCUU\n3'-UUU...CAGUU_______AAAGU...ACA-5'\n_____________\|_______\|\n_____________51______43\n	105 -- 111	44 -- 50	-9.00959 kcal/mol	1.43957 kcal/mol	0.825028 kcal/mol	104 112@LB@ \| \|@LB@5'-GUA...AACGC GAUGC...ACG-3'@LB@ AGAGGAA@LB@ \|\|\|\|\|\|\|@LB@ UCUCCUU@LB@3'-UUU...CAGUU AAAGU...ACA-5'@LB@ \| \|@LB@ 51 43@LB@@LB@@LB@Energy -6.74 kcal/mol@LB@Hybridization Energy -9.00959 kcal/mol@LB@Unfolding Energy - mRNA 1.43957 kcal/mol@LB@Unfolding Energy - sRNA 0.825028 kcal/mol@LB@@LB@Position - mRNA 105 -- 111@LB@Position - sRNA 44 -- 50@LB@Position Seed - mRNA 105 -- 111@LB@Position Seed - sRNA 44 -- 50@LB@
91	0.01869	0.6177	b3432	glgB	-9.43	0.053684	93 -- 103	45 -- 56	1 4-alpha-glucan branching enzyme		_____________92___________104\n_____________\|____________\|\n5'-CAU...GACGA____________UGCAC...GAC-3'\n______________CG_CAGAGAGGA\n______________\|\|_\|\|:\|\|\|\|\|\|\n______________GC_GUUUCUCCU\n3'-UUU...ACCGG__A_________UAAAG...ACA-5'\n_____________\|____________\|\n_____________57___________44\n	97 -- 103	45 -- 51	-14.5586 kcal/mol	4.18817 kcal/mol	0.938337 kcal/mol	92 104@LB@ \| \|@LB@5'-CAU...GACGA UGCAC...GAC-3'@LB@ CG CAGAGAGGA@LB@ \|\| \|\|:\|\|\|\|\|\|@LB@ GC GUUUCUCCU@LB@3'-UUU...ACCGG A UAAAG...ACA-5'@LB@ \| \|@LB@ 57 44@LB@@LB@@LB@Energy -9.43 kcal/mol@LB@Hybridization Energy -14.5586 kcal/mol@LB@Unfolding Energy - mRNA 4.18817 kcal/mol@LB@Unfolding Energy - sRNA 0.938337 kcal/mol@LB@@LB@Position - mRNA 93 -- 103@LB@Position - sRNA 45 -- 56@LB@Position Seed - mRNA 97 -- 103@LB@Position Seed - sRNA 45 -- 51@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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