Input and runtime details for job 6527768 (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 6527768 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:24:51 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:20 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:38:58 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:39:05 CET 2018
	Job Completed		@ Fri Feb 16 20:39:38 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6527768&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicA

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
119	0.01215	0.3104	b3691	dgoT	-8.17	0.239341	58 -- 68	8 -- 21	D-galactonate transporter	_____________57_____________69\n_____________\|______________\|\n5'-GUG...AUGAA______________AGCAG...CCA-3'\n______________GAUAACA___GCGU\n______________\|\|\|\|\|\|\|___\|\|\|:\n______________CUAUUGU___CGCG\n3'-UUU...UACUA_______UUA____CAGAAAG-5'\n_____________\|______________\|\n_____________22_____________7\n	58 -- 64	15 -- 21	-12.2033 kcal/mol	2.79285 kcal/mol	1.23638 kcal/mol	57 69@LB@ \| \|@LB@5'-GUG...AUGAA AGCAG...CCA-3'@LB@ GAUAACA GCGU@LB@ \|\|\|\|\|\|\| \|\|\|:@LB@ CUAUUGU CGCG@LB@3'-UUU...UACUA UUA CAGAAAG-5'@LB@ \| \|@LB@ 22 7@LB@@LB@@LB@Energy -8.17 kcal/mol@LB@Hybridization Energy -12.2033 kcal/mol@LB@Unfolding Energy - mRNA 2.79285 kcal/mol@LB@Unfolding Energy - sRNA 1.23638 kcal/mol@LB@@LB@Position - mRNA 58 -- 68@LB@Position - sRNA 8 -- 21@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 15 -- 21@LB@
168	0.01645	0.3104	b3720	bglH	-8.64	0.202347	15 -- 28	9 -- 22	carbohydrate-specific outer membrane porin cryptic	_____________14_____________29\n_____________\|______________\|\n5'-AUU...GAUCG_________UG___AAGGA...GCC-3'\n______________UGAUGAUAA__GCG\n______________\|\|\|\|:\|:\|\|__\|\|\|\n______________ACUAUUGUU__CGC\n3'-UUU...CUACU_________UA___GCAGAAAG-5'\n_____________\|______________\|\n_____________23_____________8\n	17 -- 23	14 -- 20	-13.7208 kcal/mol	3.8428 kcal/mol	1.23827 kcal/mol	14 29@LB@ \| \|@LB@5'-AUU...GAUCG UG AAGGA...GCC-3'@LB@ UGAUGAUAA GCG@LB@ \|\|\|\|:\|:\|\| \|\|\|@LB@ ACUAUUGUU CGC@LB@3'-UUU...CUACU UA GCAGAAAG-5'@LB@ \| \|@LB@ 23 8@LB@@LB@@LB@Energy -8.64 kcal/mol@LB@Hybridization Energy -13.7208 kcal/mol@LB@Unfolding Energy - mRNA 3.8428 kcal/mol@LB@Unfolding Energy - sRNA 1.23827 kcal/mol@LB@@LB@Position - mRNA 15 -- 28@LB@Position - sRNA 9 -- 22@LB@Position Seed - mRNA 17 -- 23@LB@Position Seed - sRNA 14 -- 20@LB@
189	0.01853	0.3104	b3743	asnC	-7.74	0.278830	255 -- 266	5 -- 18	transcriptional activator of asnA; autorepressor	_____________254____________267\n_____________\|______________\|\n5'-AUU...UAAUG______________ACCGC...GCG-3'\n______________GGC_AAUGCGCG_C\n______________::\|_\|\|\|\|\|\|\|\|_\|\n______________UUG_UUACGCGC_G\n3'-UUU...UACUA___U________A_AAAG-5'\n_____________\|______________\|\n_____________19_____________4\n	259 -- 265	7 -- 13	-14.4034 kcal/mol	5.44099 kcal/mol	1.2243 kcal/mol	254 267@LB@ \| \|@LB@5'-AUU...UAAUG ACCGC...GCG-3'@LB@ GGC AAUGCGCG C@LB@ ::\| \|\|\|\|\|\|\|\| \|@LB@ UUG UUACGCGC G@LB@3'-UUU...UACUA U A AAAG-5'@LB@ \| \|@LB@ 19 4@LB@@LB@@LB@Energy -7.74 kcal/mol@LB@Hybridization Energy -14.4034 kcal/mol@LB@Unfolding Energy - mRNA 5.44099 kcal/mol@LB@Unfolding Energy - sRNA 1.2243 kcal/mol@LB@@LB@Position - mRNA 255 -- 266@LB@Position - sRNA 5 -- 18@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 7 -- 13@LB@
53	0.004896	0.3024	b3790	wecD	-9.15	0.167607	125 -- 139	7 -- 21	TDP-fucosamine acetyltransferase	_____________124_____________140\n_____________\|_______________\|\n5'-CUG...GGCUC_________G_____AAGCG...UGA-3'\n______________GAUGACGAG_GUGUG\n______________\|\|\|:\|\|:\|:_\|:\|:\|\n______________CUAUUGUUU_CGCGC\n3'-UUU...UACUA_________A_____AGAAAG-5'\n_____________\|_______________\|\n_____________22______________6\n	126 -- 132	14 -- 20	-15.9636 kcal/mol	5.57309 kcal/mol	1.24179 kcal/mol	124 140@LB@ \| \|@LB@5'-CUG...GGCUC G AAGCG...UGA-3'@LB@ GAUGACGAG GUGUG@LB@ \|\|\|:\|\|:\|: \|:\|:\|@LB@ CUAUUGUUU CGCGC@LB@3'-UUU...UACUA A AGAAAG-5'@LB@ \| \|@LB@ 22 6@LB@@LB@@LB@Energy -9.15 kcal/mol@LB@Hybridization Energy -15.9636 kcal/mol@LB@Unfolding Energy - mRNA 5.57309 kcal/mol@LB@Unfolding Energy - sRNA 1.24179 kcal/mol@LB@@LB@Position - mRNA 125 -- 139@LB@Position - sRNA 7 -- 21@LB@Position Seed - mRNA 126 -- 132@LB@Position Seed - sRNA 14 -- 20@LB@
105	0.01074	0.3104	b3791	wecE	-13.91	0.024834	1 -- 12	7 -- 18	TDP-4-oxo-6-deoxy-D-glucose transaminase	______________1___________13\n______________\|___________\|\n___________5'-____________AAUUG...CCC-3'\n______________GACAGAUGCGCG\n______________:\|\|\|:\|\|\|\|\|\|\|\n______________UUGUUUACGCGC\n3'-UUU...UACUA____________AGAAAG-5'\n_____________\|____________\|\n_____________19___________6\n	6 -- 12	7 -- 13	-19.4696 kcal/mol	4.34626 kcal/mol	1.20891 kcal/mol	1 13@LB@ \| \|@LB@ 5'- AAUUG...CCC-3'@LB@ GACAGAUGCGCG@LB@ :\|\|\|:\|\|\|\|\|\|\|@LB@ UUGUUUACGCGC@LB@3'-UUU...UACUA AGAAAG-5'@LB@ \| \|@LB@ 19 6@LB@@LB@@LB@Energy -13.91 kcal/mol@LB@Hybridization Energy -19.4696 kcal/mol@LB@Unfolding Energy - mRNA 4.34626 kcal/mol@LB@Unfolding Energy - sRNA 1.20891 kcal/mol@LB@@LB@Position - mRNA 1 -- 12@LB@Position - sRNA 7 -- 18@LB@Position Seed - mRNA 6 -- 12@LB@Position Seed - sRNA 7 -- 13@LB@
93	0.009444	0.3104	b3822	recQ	-7.42	0.310549	176 -- 212	9 -- 45	ATP-dependent DNA helicase	_____________175____________________________________213\n_____________\|______________________________________\|\n5'-CGC...CUGUU________A__CAA__________AU______CAG___GAAGU...UUA-3'\n______________UUUAUUUC_GG___UC_GGGGUGA__GUGGCG___GCG\n______________\|\|:\|\|:\|\|_\|:___\|\|_\|\|\|:\|\|\|__:\|::\|:___\|\|\|\n______________AAGUAGAG_CU___AG_CCCUACU__UAUUGU___CGC\n3'-UUU...UUUUA________A__UA___U_______AC______UUA___GCAGAAAG-5'\n_____________\|______________________________________\|\n_____________46_____________________________________8\n	192 -- 198	23 -- 29	-25.6556 kcal/mol	8.78202 kcal/mol	9.45193 kcal/mol	175 213@LB@ \| \|@LB@5'-CGC...CUGUU A CAA AU CAG GAAGU...UUA-3'@LB@ UUUAUUUC GG UC GGGGUGA GUGGCG GCG@LB@ \|\|:\|\|:\|\| \|: \|\| \|\|\|:\|\|\| :\|::\|: \|\|\|@LB@ AAGUAGAG CU AG CCCUACU UAUUGU CGC@LB@3'-UUU...UUUUA A UA U AC UUA GCAGAAAG-5'@LB@ \| \|@LB@ 46 8@LB@@LB@@LB@Energy -7.42 kcal/mol@LB@Hybridization Energy -25.6556 kcal/mol@LB@Unfolding Energy - mRNA 8.78202 kcal/mol@LB@Unfolding Energy - sRNA 9.45193 kcal/mol@LB@@LB@Position - mRNA 176 -- 212@LB@Position - sRNA 9 -- 45@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 23 -- 29@LB@
146	0.01406	0.3104	b3831	udp	-7.35	0.318150	153 -- 161	1 -- 9	uridine phosphorylase	_____________152_______162\n_____________\|_________\|\n5'-AUC...GUAAA_________UGCUU...AGA-3'\n______________GUGUCUUUU\n______________\|:\|\|\|\|\|\|:\n______________CGCAGAAAG\n3'-UUU...UUACG_________-5'\n_____________\|________\|\n_____________10_______1\n	155 -- 161	1 -- 7	-10.4616 kcal/mol	1.99462 kcal/mol	1.11751 kcal/mol	152 162@LB@ \| \|@LB@5'-AUC...GUAAA UGCUU...AGA-3'@LB@ GUGUCUUUU@LB@ \|:\|\|\|\|\|\|:@LB@ CGCAGAAAG@LB@3'-UUU...UUACG -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -7.35 kcal/mol@LB@Hybridization Energy -10.4616 kcal/mol@LB@Unfolding Energy - mRNA 1.99462 kcal/mol@LB@Unfolding Energy - sRNA 1.11751 kcal/mol@LB@@LB@Position - mRNA 153 -- 161@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 155 -- 161@LB@Position Seed - sRNA 1 -- 7@LB@
63	0.0059	0.3087	b3834	ubiJ	-8.76	0.193647	289 -- 295	4 -- 10	aerobic ubiquinone synthesis protein SCP2 family protein	_____________288_____296\n_____________\|_______\|\n5'-GCU...CCGCU_______GCUGG-3'\n______________CGCGUCU\n______________\|\|\|\|\|\|\|\n______________GCGCAGA\n3'-UUU...UUUAC_______AAG-5'\n_____________\|_______\|\n_____________11______3\n	289 -- 295	4 -- 10	-11.2085 kcal/mol	1.2993 kcal/mol	1.14958 kcal/mol	288 296@LB@ \| \|@LB@5'-GCU...CCGCU GCUGG-3'@LB@ CGCGUCU@LB@ \|\|\|\|\|\|\|@LB@ GCGCAGA@LB@3'-UUU...UUUAC AAG-5'@LB@ \| \|@LB@ 11 3@LB@@LB@@LB@Energy -8.76 kcal/mol@LB@Hybridization Energy -11.2085 kcal/mol@LB@Unfolding Energy - mRNA 1.2993 kcal/mol@LB@Unfolding Energy - sRNA 1.14958 kcal/mol@LB@@LB@Position - mRNA 289 -- 295@LB@Position - sRNA 4 -- 10@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 4 -- 10@LB@
39	0.002561	0.2224	b3845	fadA	-14.30	0.021162	112 -- 126	5 -- 20	3-ketoacyl-CoA thiolase (thiolase I)	_____________111______________127\n_____________\|________________\|\n5'-UCC...UCUGC________________AUAAC...AUU-3'\n______________GUAAUAAA_GCGCGUC\n______________:\|\|\|:\|\|\|_\|\|\|\|\|\|\|\n______________UAUUGUUU_CGCGCAG\n3'-UUU...ACUAC________A_______AAAG-5'\n_____________\|________________\|\n_____________21_______________4\n	120 -- 126	5 -- 11	-19.3309 kcal/mol	3.78617 kcal/mol	1.24804 kcal/mol	111 127@LB@ \| \|@LB@5'-UCC...UCUGC AUAAC...AUU-3'@LB@ GUAAUAAA GCGCGUC@LB@ :\|\|\|:\|\|\| \|\|\|\|\|\|\|@LB@ UAUUGUUU CGCGCAG@LB@3'-UUU...ACUAC A AAAG-5'@LB@ \| \|@LB@ 21 4@LB@@LB@@LB@Energy -14.30 kcal/mol@LB@Hybridization Energy -19.3309 kcal/mol@LB@Unfolding Energy - mRNA 3.78617 kcal/mol@LB@Unfolding Energy - sRNA 1.24804 kcal/mol@LB@@LB@Position - mRNA 112 -- 126@LB@Position - sRNA 5 -- 20@LB@Position Seed - mRNA 120 -- 126@LB@Position Seed - sRNA 5 -- 11@LB@
44	0.003062	0.2325	b3847	pepQ	-9.98	0.122201	144 -- 157	8 -- 21	proline dipeptidase	_____________143____________158\n_____________\|______________\|\n5'-UUG...CUCUG_____AC_______UAAGA...UUC-3'\n______________GAUGA__GAUGUGC\n______________\|\|\|:\|__:\|\|\|:\|\|\n______________CUAUU__UUACGCG\n3'-UUU...UACUA_____GU_______CAGAAAG-5'\n_____________\|______________\|\n_____________22_____________7\n	151 -- 157	8 -- 14	-13.3112 kcal/mol	2.09686 kcal/mol	1.23638 kcal/mol	143 158@LB@ \| \|@LB@5'-UUG...CUCUG AC UAAGA...UUC-3'@LB@ GAUGA GAUGUGC@LB@ \|\|\|:\| :\|\|\|:\|\|@LB@ CUAUU UUACGCG@LB@3'-UUU...UACUA GU CAGAAAG-5'@LB@ \| \|@LB@ 22 7@LB@@LB@@LB@Energy -9.98 kcal/mol@LB@Hybridization Energy -13.3112 kcal/mol@LB@Unfolding Energy - mRNA 2.09686 kcal/mol@LB@Unfolding Energy - sRNA 1.23638 kcal/mol@LB@@LB@Position - mRNA 144 -- 157@LB@Position - sRNA 8 -- 21@LB@Position Seed - mRNA 151 -- 157@LB@Position Seed - sRNA 8 -- 14@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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service.

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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