Input and runtime details for job 6038639 (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 6038639 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:35:57 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:19:35 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:35:30 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:35:37 CET 2018
	Job Completed		@ Fri Feb 16 21:35:51 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6038639&toolName=CopraRNA ( 30 days expiry )

Description of the job

IhtA

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_000117 Chlamydia trachomatis D/UW-3/CX

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
106	0.04101	0.3134	ct_445	gltX	-7.36	0.119711	199 -- 233	6 -- 32	glutamate--tRNA ligase	_____________198__________________________________234\n_____________\|____________________________________\|\n5'-UUU...GUAGC___U_A________AAA__UAC__________A___CCUUC...CAA-3'\n______________GAA_G_CUG_UCCA___UG___GCGUUAGAGU_GCC\n______________\|\|\|_\|_\|\|:_\|\|\|\|___\|\|___\|\|\|\|\|\|\|\|:\|_:\|\|\n______________CUU_C_GAU_AGGU___AC___CGCAAUCUUA_UGG\n3'-UUU...UCAGU_________A__________________________UUGAA-5'\n_____________\|____________________________________\|\n_____________33___________________________________5\n	220 -- 226	12 -- 18	-22.1489 kcal/mol	6.20636 kcal/mol	8.57923 kcal/mol	198 234@LB@ \| \|@LB@5'-UUU...GUAGC U A AAA UAC A CCUUC...CAA-3'@LB@ GAA G CUG UCCA UG GCGUUAGAGU GCC@LB@ \|\|\| \| \|\|: \|\|\|\| \|\| \|\|\|\|\|\|\|\|:\| :\|\|@LB@ CUU C GAU AGGU AC CGCAAUCUUA UGG@LB@3'-UUU...UCAGU A UUGAA-5'@LB@ \| \|@LB@ 33 5@LB@@LB@@LB@Energy -7.36 kcal/mol@LB@Hybridization Energy -22.1489 kcal/mol@LB@Unfolding Energy - mRNA 6.20636 kcal/mol@LB@Unfolding Energy - sRNA 8.57923 kcal/mol@LB@@LB@Position - mRNA 199 -- 233@LB@Position - sRNA 6 -- 32@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 12 -- 18@LB@
116	0.04833	0.3262	ct_570	gspF	-8.17	0.078365	199 -- 207	80 -- 88	type II secretion system protein F	_____________198_______208\n_____________\|_________\|\n5'-AUC...AGGGG_________GGUUU...CUG-3'\n______________AUAUGGCUA\n______________\|\|\|:\|\|\|\|\|\n______________UAUGCCGAU\n3'-UUU...GCCUC_________UGAGG...GAA-5'\n_____________\|_________\|\n_____________89________79\n	201 -- 207	80 -- 86	-11.0443 kcal/mol	1.77912 kcal/mol	1.09753 kcal/mol	198 208@LB@ \| \|@LB@5'-AUC...AGGGG GGUUU...CUG-3'@LB@ AUAUGGCUA@LB@ \|\|\|:\|\|\|\|\|@LB@ UAUGCCGAU@LB@3'-UUU...GCCUC UGAGG...GAA-5'@LB@ \| \|@LB@ 89 79@LB@@LB@@LB@Energy -8.17 kcal/mol@LB@Hybridization Energy -11.0443 kcal/mol@LB@Unfolding Energy - mRNA 1.77912 kcal/mol@LB@Unfolding Energy - sRNA 1.09753 kcal/mol@LB@@LB@Position - mRNA 199 -- 207@LB@Position - sRNA 80 -- 88@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 80 -- 86@LB@
76	0.02744	0.29	ct_510	secY	-5.37	0.309530	200 -- 207	80 -- 87	preprotein translocase subunit SecY	_____________199______208\n_____________\|________\|\n5'-GAU...AAGUU________CAUUG...UCC-3'\n______________UAUGGCUA\n______________\|\|:\|\|\|\|\|\n______________AUGCCGAU\n3'-UUU...CCUCU________UGAGG...GAA-5'\n_____________\|________\|\n_____________88_______79\n	201 -- 207	80 -- 86	-9.93483 kcal/mol	3.46443 kcal/mol	1.09752 kcal/mol	199 208@LB@ \| \|@LB@5'-GAU...AAGUU CAUUG...UCC-3'@LB@ UAUGGCUA@LB@ \|\|:\|\|\|\|\|@LB@ AUGCCGAU@LB@3'-UUU...CCUCU UGAGG...GAA-5'@LB@ \| \|@LB@ 88 79@LB@@LB@@LB@Energy -5.37 kcal/mol@LB@Hybridization Energy -9.93483 kcal/mol@LB@Unfolding Energy - mRNA 3.46443 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 200 -- 207@LB@Position - sRNA 80 -- 87@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 80 -- 86@LB@
113	0.04597	0.3262	ct_841	ftsH	-6.80	0.159029	200 -- 207	80 -- 87	ATP-dependent zinc metalloprotease FtsH	_____________199______208\n_____________\|________\|\n5'-GGU...AGUUU________AAGAU...UUC-3'\n______________UAUGGCUA\n______________\|\|:\|\|\|\|\|\n______________AUGCCGAU\n3'-UUU...CCUCU________UGAGG...GAA-5'\n_____________\|________\|\n_____________88_______79\n	200 -- 206	81 -- 87	-10.6438 kcal/mol	2.74436 kcal/mol	1.09752 kcal/mol	199 208@LB@ \| \|@LB@5'-GGU...AGUUU AAGAU...UUC-3'@LB@ UAUGGCUA@LB@ \|\|:\|\|\|\|\|@LB@ AUGCCGAU@LB@3'-UUU...CCUCU UGAGG...GAA-5'@LB@ \| \|@LB@ 88 79@LB@@LB@@LB@Energy -6.80 kcal/mol@LB@Hybridization Energy -10.6438 kcal/mol@LB@Unfolding Energy - mRNA 2.74436 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 200 -- 207@LB@Position - sRNA 80 -- 87@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 81 -- 87@LB@
133	0.05414	0.3262	ct_059	fer	-7.78	0.096344	200 -- 207	80 -- 87	ferredoxin	_____________199______208\n_____________\|________\|\n5'-UUC...AGUCC________AGCUC...CUU-3'\n______________UAUGGCUA\n______________\|\|:\|\|\|\|\|\n______________AUGCCGAU\n3'-UUU...CCUCU________UGAGG...GAA-5'\n_____________\|________\|\n_____________88_______79\n	200 -- 206	81 -- 87	-10.7757 kcal/mol	1.8981 kcal/mol	1.09752 kcal/mol	199 208@LB@ \| \|@LB@5'-UUC...AGUCC AGCUC...CUU-3'@LB@ UAUGGCUA@LB@ \|\|:\|\|\|\|\|@LB@ AUGCCGAU@LB@3'-UUU...CCUCU UGAGG...GAA-5'@LB@ \| \|@LB@ 88 79@LB@@LB@@LB@Energy -7.78 kcal/mol@LB@Hybridization Energy -10.7757 kcal/mol@LB@Unfolding Energy - mRNA 1.8981 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 200 -- 207@LB@Position - sRNA 80 -- 87@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 81 -- 87@LB@
27	0.007389	0.2199	ct_855	fumC	-7.16	0.132975	201 -- 207	82 -- 88	fumarate hydratase	_____________200_____208\n_____________\|_______\|\n5'-AUA...AGCAU_______AAGAG...GUA-3'\n______________AUGCGGC\n______________\|\|:\|\|\|\|\n______________UAUGCCG\n3'-UUU...GCCUC_______AUUGA...GAA-5'\n_____________\|_______\|\n_____________89______81\n	201 -- 207	82 -- 88	-10.3037 kcal/mol	2.04792 kcal/mol	1.09753 kcal/mol	200 208@LB@ \| \|@LB@5'-AUA...AGCAU AAGAG...GUA-3'@LB@ AUGCGGC@LB@ \|\|:\|\|\|\|@LB@ UAUGCCG@LB@3'-UUU...GCCUC AUUGA...GAA-5'@LB@ \| \|@LB@ 89 81@LB@@LB@@LB@Energy -7.16 kcal/mol@LB@Hybridization Energy -10.3037 kcal/mol@LB@Unfolding Energy - mRNA 2.04792 kcal/mol@LB@Unfolding Energy - sRNA 1.09753 kcal/mol@LB@@LB@Position - mRNA 201 -- 207@LB@Position - sRNA 82 -- 88@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 82 -- 88@LB@
181	0.07898	0.3587	ct_186	devB	-5.59	0.281766	201 -- 207	80 -- 86	6-phosphogluconolactonase	_____________200_____208\n_____________\|_______\|\n5'-GAA...UAUAC_______CCCUU...CAG-3'\n______________AUGGCUA\n______________\|:\|\|\|\|\|\n______________UGCCGAU\n3'-UUU...CUCUA_______UGAGG...GAA-5'\n_____________\|_______\|\n_____________87______79\n	201 -- 207	80 -- 86	-9.11344 kcal/mol	2.46127 kcal/mol	1.06449 kcal/mol	200 208@LB@ \| \|@LB@5'-GAA...UAUAC CCCUU...CAG-3'@LB@ AUGGCUA@LB@ \|:\|\|\|\|\|@LB@ UGCCGAU@LB@3'-UUU...CUCUA UGAGG...GAA-5'@LB@ \| \|@LB@ 87 79@LB@@LB@@LB@Energy -5.59 kcal/mol@LB@Hybridization Energy -9.11344 kcal/mol@LB@Unfolding Energy - mRNA 2.46127 kcal/mol@LB@Unfolding Energy - sRNA 1.06449 kcal/mol@LB@@LB@Position - mRNA 201 -- 207@LB@Position - sRNA 80 -- 86@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 80 -- 86@LB@
93	0.03342	0.2954	ct_815	mrsA_2	-4.95	0.370159	203 -- 227	23 -- 45	phosphoglucosamine mutase	_____________202_______________________228\n_____________\|_________________________\|\n5'-UAC...GCAAU_____GU__U__G___C________GGAAC...AGG-3'\n______________GACAC__GA_GU_AGA_AGCUAUUC\n______________:\|\|\|\|__\|\|_\|\|_\|\|\|_\|\|\|\|\|\|\|\|\n______________UUGUG__CU_CA_UCU_UCGAUAAG\n3'-UUU...CAUGU_____AU_____G____________GUACC...GAA-5'\n_____________\|_________________________\|\n_____________46________________________22\n	221 -- 227	23 -- 29	-22.8159 kcal/mol	6.25755 kcal/mol	11.6121 kcal/mol	202 228@LB@ \| \|@LB@5'-UAC...GCAAU GU U G C GGAAC...AGG-3'@LB@ GACAC GA GU AGA AGCUAUUC@LB@ :\|\|\|\| \|\| \|\| \|\|\| \|\|\|\|\|\|\|\|@LB@ UUGUG CU CA UCU UCGAUAAG@LB@3'-UUU...CAUGU AU G GUACC...GAA-5'@LB@ \| \|@LB@ 46 22@LB@@LB@@LB@Energy -4.95 kcal/mol@LB@Hybridization Energy -22.8159 kcal/mol@LB@Unfolding Energy - mRNA 6.25755 kcal/mol@LB@Unfolding Energy - sRNA 11.6121 kcal/mol@LB@@LB@Position - mRNA 203 -- 227@LB@Position - sRNA 23 -- 45@LB@Position Seed - mRNA 221 -- 227@LB@Position Seed - sRNA 23 -- 29@LB@
110	0.04403	0.3262	ct_742	ygcA	-7.58	0.107160	204 -- 253	23 -- 59	rRNA methyltransferse	_____________203__________________________________________________254\n_____________\|____________________________________________________\|\n5'-AAC...AGUUG________CUAUCGUAAC___________UU___C___UGU___________AUCUC...UUG-3'\n______________CUCUCCUG__________UGUA__AACAU__UGG_GUC___GGAGGCUGUUC\n______________\|:\|:\|\|\|\|__________\|\|\|\|__\|\|\|\|:__\|:\|_\|\|\|___:\|\|:\|\|\|:\|\|\|\n______________GGGGGGAC__________ACAU__UUGUG__AUC_CAG___UCUUCGAUAAG\n3'-UUU...CUGAA______________________GU__________U_________________GUACC...GAA-5'\n_____________\|____________________________________________________\|\n_____________60___________________________________________________22\n	247 -- 253	23 -- 29	-33.6475 kcal/mol	12.386 kcal/mol	13.6844 kcal/mol	203 254@LB@ \| \|@LB@5'-AAC...AGUUG CUAUCGUAAC UU C UGU AUCUC...UUG-3'@LB@ CUCUCCUG UGUA AACAU UGG GUC GGAGGCUGUUC@LB@ \|:\|:\|\|\|\| \|\|\|\| \|\|\|\|: \|:\| \|\|\| :\|\|:\|\|\|:\|\|\|@LB@ GGGGGGAC ACAU UUGUG AUC CAG UCUUCGAUAAG@LB@3'-UUU...CUGAA GU U GUACC...GAA-5'@LB@ \| \|@LB@ 60 22@LB@@LB@@LB@Energy -7.58 kcal/mol@LB@Hybridization Energy -33.6475 kcal/mol@LB@Unfolding Energy - mRNA 12.386 kcal/mol@LB@Unfolding Energy - sRNA 13.6844 kcal/mol@LB@@LB@Position - mRNA 204 -- 253@LB@Position - sRNA 23 -- 59@LB@Position Seed - mRNA 247 -- 253@LB@Position Seed - sRNA 23 -- 29@LB@
199	0.0896	0.3683	ct_774	cysQ	-5.35	0.311933	207 -- 214	53 -- 60	3'(2') 5'-bisphosphate nucleotidase	_____________206______215\n_____________\|________\|\n5'-UCA...UGUUC________CAAUG...UUC-3'\n______________UCCCUCCU\n______________\|\|\|\|:\|\|\|\n______________AGGGGGGA\n3'-UUU...ACUGA________CACAU...GAA-5'\n_____________\|________\|\n_____________61_______52\n	208 -- 214	53 -- 59	-13.0073 kcal/mol	1.20108 kcal/mol	6.45136 kcal/mol	206 215@LB@ \| \|@LB@5'-UCA...UGUUC CAAUG...UUC-3'@LB@ UCCCUCCU@LB@ \|\|\|\|:\|\|\|@LB@ AGGGGGGA@LB@3'-UUU...ACUGA CACAU...GAA-5'@LB@ \| \|@LB@ 61 52@LB@@LB@@LB@Energy -5.35 kcal/mol@LB@Hybridization Energy -13.0073 kcal/mol@LB@Unfolding Energy - mRNA 1.20108 kcal/mol@LB@Unfolding Energy - sRNA 6.45136 kcal/mol@LB@@LB@Position - mRNA 207 -- 214@LB@Position - sRNA 53 -- 60@LB@Position Seed - mRNA 208 -- 214@LB@Position Seed - sRNA 53 -- 59@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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