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
142	0.0566	0.3262	ct_284	N/A	-6.95	0.147726	278 -- 292	18 -- 30	phospholipase D	_____________277_____________293\n_____________\|_______________\|\n5'-AUC...ACUAU_________GG____AGACAAAA-3'\n______________AGCUAUUCC__AUGG\n______________\|\|\|\|\|\|\|\|\|__\|\|\|\|\n______________UCGAUAAGG__UACC\n3'-UUU...AGUCU_______________GCAAU...GAA-5'\n_____________\|_______________\|\n_____________31______________17\n	280 -- 286	22 -- 28	-16.5616 kcal/mol	4.87795 kcal/mol	4.73403 kcal/mol	277 293@LB@ \| \|@LB@5'-AUC...ACUAU GG AGACAAAA-3'@LB@ AGCUAUUCC AUGG@LB@ \|\|\|\|\|\|\|\|\| \|\|\|\|@LB@ UCGAUAAGG UACC@LB@3'-UUU...AGUCU GCAAU...GAA-5'@LB@ \| \|@LB@ 31 17@LB@@LB@@LB@Energy -6.95 kcal/mol@LB@Hybridization Energy -16.5616 kcal/mol@LB@Unfolding Energy - mRNA 4.87795 kcal/mol@LB@Unfolding Energy - sRNA 4.73403 kcal/mol@LB@@LB@Position - mRNA 278 -- 292@LB@Position - sRNA 18 -- 30@LB@Position Seed - mRNA 280 -- 286@LB@Position Seed - sRNA 22 -- 28@LB@
195	0.08712	0.3657	ct_704	pcnB_2	-3.31	0.654425	101 -- 107	28 -- 34	poly A polymerase	_____________100_____108\n_____________\|_______\|\n5'-CAA...UACGG_______CAUCC...UGC-3'\n______________UAGAAGC\n______________:\|\|\|\|\|\|\n______________GUCUUCG\n3'-UUU...UCUCA_______AUAAG...GAA-5'\n_____________\|_______\|\n_____________35______27\n	101 -- 107	28 -- 34	-7.75845 kcal/mol	0.338622 kcal/mol	4.11458 kcal/mol	100 108@LB@ \| \|@LB@5'-CAA...UACGG CAUCC...UGC-3'@LB@ UAGAAGC@LB@ :\|\|\|\|\|\|@LB@ GUCUUCG@LB@3'-UUU...UCUCA AUAAG...GAA-5'@LB@ \| \|@LB@ 35 27@LB@@LB@@LB@Energy -3.31 kcal/mol@LB@Hybridization Energy -7.75845 kcal/mol@LB@Unfolding Energy - mRNA 0.338622 kcal/mol@LB@Unfolding Energy - sRNA 4.11458 kcal/mol@LB@@LB@Position - mRNA 101 -- 107@LB@Position - sRNA 28 -- 34@LB@Position Seed - mRNA 101 -- 107@LB@Position Seed - sRNA 28 -- 34@LB@
131	0.05291	0.3262	ct_842	pnp	-7.97	0.086989	198 -- 205	17 -- 24	polyribonucleotide nucleotidyltransferase	_____________197______206\n_____________\|________\|\n5'-UGA...ACAAC________UUUUG...UCA-3'\n______________UCCAUGGC\n______________\|\|\|\|\|\|\|\|\n______________AGGUACCG\n3'-UUU...CGAUA________CAAUC...GAA-5'\n_____________\|________\|\n_____________25_______16\n	199 -- 205	17 -- 23	-14.0999 kcal/mol	1.64992 kcal/mol	4.47615 kcal/mol	197 206@LB@ \| \|@LB@5'-UGA...ACAAC UUUUG...UCA-3'@LB@ UCCAUGGC@LB@ \|\|\|\|\|\|\|\|@LB@ AGGUACCG@LB@3'-UUU...CGAUA CAAUC...GAA-5'@LB@ \| \|@LB@ 25 16@LB@@LB@@LB@Energy -7.97 kcal/mol@LB@Hybridization Energy -14.0999 kcal/mol@LB@Unfolding Energy - mRNA 1.64992 kcal/mol@LB@Unfolding Energy - sRNA 4.47615 kcal/mol@LB@@LB@Position - mRNA 198 -- 205@LB@Position - sRNA 17 -- 24@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 17 -- 23@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@
115	0.04794	0.3262	ct_778	priA	-6.05	0.227860	46 -- 52	54 -- 60	primosomal protein N'	_____________45______53\n_____________\|_______\|\n5'-CGC...GUCAU_______AUCCU...AAA-3'\n______________UCCCCUC\n______________\|\|\|\|\|:\|\n______________AGGGGGG\n3'-UUU...ACUGA_______ACACA...GAA-5'\n_____________\|_______\|\n_____________61______53\n	46 -- 52	54 -- 60	-12.5948 kcal/mol	0.0982726 kcal/mol	6.44182 kcal/mol	45 53@LB@ \| \|@LB@5'-CGC...GUCAU AUCCU...AAA-3'@LB@ UCCCCUC@LB@ \|\|\|\|\|:\|@LB@ AGGGGGG@LB@3'-UUU...ACUGA ACACA...GAA-5'@LB@ \| \|@LB@ 61 53@LB@@LB@@LB@Energy -6.05 kcal/mol@LB@Hybridization Energy -12.5948 kcal/mol@LB@Unfolding Energy - mRNA 0.0982726 kcal/mol@LB@Unfolding Energy - sRNA 6.44182 kcal/mol@LB@@LB@Position - mRNA 46 -- 52@LB@Position - sRNA 54 -- 60@LB@Position Seed - mRNA 46 -- 52@LB@Position Seed - sRNA 54 -- 60@LB@
98	0.03528	0.2959	ct_676	N/A	-6.99	0.144558	38 -- 44	80 -- 86	protein-arginine kinase activator protein	_____________37______45\n_____________\|_______\|\n5'-GGG...GCUCA_______GAGCA...GUU-3'\n______________GCGGUUA\n______________:\|\|\|:\|\|\n______________UGCCGAU\n3'-UUU...CUCUA_______UGAGG...GAA-5'\n_____________\|_______\|\n_____________87______79\n	38 -- 44	80 -- 86	-8.44953 kcal/mol	0.39201 kcal/mol	1.06449 kcal/mol	37 45@LB@ \| \|@LB@5'-GGG...GCUCA GAGCA...GUU-3'@LB@ GCGGUUA@LB@ :\|\|\|:\|\|@LB@ UGCCGAU@LB@3'-UUU...CUCUA UGAGG...GAA-5'@LB@ \| \|@LB@ 87 79@LB@@LB@@LB@Energy -6.99 kcal/mol@LB@Hybridization Energy -8.44953 kcal/mol@LB@Unfolding Energy - mRNA 0.39201 kcal/mol@LB@Unfolding Energy - sRNA 1.06449 kcal/mol@LB@@LB@Position - mRNA 38 -- 44@LB@Position - sRNA 80 -- 86@LB@Position Seed - mRNA 38 -- 44@LB@Position Seed - sRNA 80 -- 86@LB@
69	0.02639	0.29	ct_745	hemG	-5.84	0.251832	282 -- 296	21 -- 34	protoporphyrinogen oxidase	_____________281_____________297\n_____________\|_______________\|\n5'-UUU...AUGUG___CU_U________GAAA-3'\n______________CAG__G_CUAUUCUA\n______________\|\|\|__\|_\|\|\|\|\|\|:\|\n______________GUC__C_GAUAAGGU\n3'-UUU...UCUCA___UU__________ACCGC...GAA-5'\n_____________\|_______________\|\n_____________35______________20\n	290 -- 296	21 -- 27	-11.5957 kcal/mol	1.02702 kcal/mol	4.73132 kcal/mol	281 297@LB@ \| \|@LB@5'-UUU...AUGUG CU U GAAA-3'@LB@ CAG G CUAUUCUA@LB@ \|\|\| \| \|\|\|\|\|\|:\|@LB@ GUC C GAUAAGGU@LB@3'-UUU...UCUCA UU ACCGC...GAA-5'@LB@ \| \|@LB@ 35 20@LB@@LB@@LB@Energy -5.84 kcal/mol@LB@Hybridization Energy -11.5957 kcal/mol@LB@Unfolding Energy - mRNA 1.02702 kcal/mol@LB@Unfolding Energy - sRNA 4.73132 kcal/mol@LB@@LB@Position - mRNA 282 -- 296@LB@Position - sRNA 21 -- 34@LB@Position Seed - mRNA 290 -- 296@LB@Position Seed - sRNA 21 -- 27@LB@
124	0.04963	0.3262	ct_290	ptsN_1	-8.82	0.054773	1 -- 15	18 -- 32	PTS fructose transporter subunit IIA	______________1______________16\n______________\|______________\|\n___________5'-____G__________GAUGC...UUA-3'\n______________GAGG_UAUUUUGUGG\n______________\|\|:\|_\|\|\|\|:::\|\|\|\n______________CUUC_AUAAGGUACC\n3'-UUU...UCAGU____G__________GCAAU...GAA-5'\n_____________\|_______________\|\n_____________33______________17\n	9 -- 15	18 -- 24	-16.4794 kcal/mol	2.69105 kcal/mol	4.96566 kcal/mol	1 16@LB@ \| \|@LB@ 5'- G GAUGC...UUA-3'@LB@ GAGG UAUUUUGUGG@LB@ \|\|:\| \|\|\|\|:::\|\|\|@LB@ CUUC AUAAGGUACC@LB@3'-UUU...UCAGU G GCAAU...GAA-5'@LB@ \| \|@LB@ 33 17@LB@@LB@@LB@Energy -8.82 kcal/mol@LB@Hybridization Energy -16.4794 kcal/mol@LB@Unfolding Energy - mRNA 2.69105 kcal/mol@LB@Unfolding Energy - sRNA 4.96566 kcal/mol@LB@@LB@Position - mRNA 1 -- 15@LB@Position - sRNA 18 -- 32@LB@Position Seed - mRNA 9 -- 15@LB@Position Seed - sRNA 18 -- 24@LB@
139	0.05609	0.3262	ct_291	ptsN_2	-9.13	0.046270	268 -- 291	36 -- 59	PTS fructose transporter subunit IIA	_____________267______________________292\n_____________\|________________________\|\n5'-UGU...AAUCA_______ACAUU____________AAGAU...UCC-3'\n______________CUUUCUU_____CAGAUACUAGAG\n______________\|:::\|:\|_____\|\|:\|:\|\|\|\|\|\|\|\n______________GGGGGGA_____GUUUGUGAUCUC\n3'-UUU...CUGAA_______CACAU____________AGUCU...GAA-5'\n_____________\|________________________\|\n_____________60_______________________35\n	285 -- 291	36 -- 42	-20.1073 kcal/mol	2.01119 kcal/mol	8.97132 kcal/mol	267 292@LB@ \| \|@LB@5'-UGU...AAUCA ACAUU AAGAU...UCC-3'@LB@ CUUUCUU CAGAUACUAGAG@LB@ \|:::\|:\| \|\|:\|:\|\|\|\|\|\|\|@LB@ GGGGGGA GUUUGUGAUCUC@LB@3'-UUU...CUGAA CACAU AGUCU...GAA-5'@LB@ \| \|@LB@ 60 35@LB@@LB@@LB@Energy -9.13 kcal/mol@LB@Hybridization Energy -20.1073 kcal/mol@LB@Unfolding Energy - mRNA 2.01119 kcal/mol@LB@Unfolding Energy - sRNA 8.97132 kcal/mol@LB@@LB@Position - mRNA 268 -- 291@LB@Position - sRNA 36 -- 59@LB@Position Seed - mRNA 285 -- 291@LB@Position Seed - sRNA 36 -- 42@LB@
90	0.03275	0.2942	ct_332	pykF	-4.34	0.468844	109 -- 116	80 -- 87	pyruvate kinase	_____________108______117\n_____________\|________\|\n5'-UUU...GCGAU________CUAAA...GCC-3'\n______________UGCGGUUG\n______________\|:\|\|\|:\|:\n______________AUGCCGAU\n3'-UUU...CCUCU________UGAGG...GAA-5'\n_____________\|________\|\n_____________88_______79\n	110 -- 116	80 -- 86	-9.21836 kcal/mol	3.78563 kcal/mol	1.09752 kcal/mol	108 117@LB@ \| \|@LB@5'-UUU...GCGAU CUAAA...GCC-3'@LB@ UGCGGUUG@LB@ \|:\|\|\|:\|:@LB@ AUGCCGAU@LB@3'-UUU...CCUCU UGAGG...GAA-5'@LB@ \| \|@LB@ 88 79@LB@@LB@@LB@Energy -4.34 kcal/mol@LB@Hybridization Energy -9.21836 kcal/mol@LB@Unfolding Energy - mRNA 3.78563 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 109 -- 116@LB@Position - sRNA 80 -- 87@LB@Position Seed - mRNA 110 -- 116@LB@Position Seed - sRNA 80 -- 86@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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