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
151	0.06398	0.3424	ct_647	N/A	-6.81	0.158308	265 -- 281	12 -- 34		_____________264_____________________282\n_____________\|_______________________\|\n5'-UAU...UGCAA_______________________CGUCA...AGG-3'\n______________UAGGAGC______AUGGUGUUGG\n______________:\|\|:\|\|\|______\|\|\|\|:\|\|\|:\|\n______________GUCUUCG______UACCGCAAUC\n3'-UUU...UCUCA_______AUAAGG__________UUAUG...GAA-5'\n_____________\|_______________________\|\n_____________35______________________11\n	274 -- 280	13 -- 19	-18.8273 kcal/mol	3.44317 kcal/mol	8.57325 kcal/mol	264 282@LB@ \| \|@LB@5'-UAU...UGCAA CGUCA...AGG-3'@LB@ UAGGAGC AUGGUGUUGG@LB@ :\|\|:\|\|\| \|\|\|\|:\|\|\|:\|@LB@ GUCUUCG UACCGCAAUC@LB@3'-UUU...UCUCA AUAAGG UUAUG...GAA-5'@LB@ \| \|@LB@ 35 11@LB@@LB@@LB@Energy -6.81 kcal/mol@LB@Hybridization Energy -18.8273 kcal/mol@LB@Unfolding Energy - mRNA 3.44317 kcal/mol@LB@Unfolding Energy - sRNA 8.57325 kcal/mol@LB@@LB@Position - mRNA 265 -- 281@LB@Position - sRNA 12 -- 34@LB@Position Seed - mRNA 274 -- 280@LB@Position Seed - sRNA 13 -- 19@LB@
152	0.064	0.3424	ct_749	alaS	-4.53	0.436714	274 -- 290	41 -- 57	alanine--tRNA ligase	_____________273_______________291\n_____________\|_________________\|\n5'-AAA...AUCUU_______UUUCCC____AAUGA...CUU-3'\n______________CUCCUGU______GCAU\n______________\|:\|\|\|\|\|______:\|\|:\n______________GGGGACA______UGUG\n3'-UUU...GAAGG_______CAUGUU____AUCUC...GAA-5'\n_____________\|_________________\|\n_____________58________________40\n	274 -- 280	51 -- 57	-13.0187 kcal/mol	0.670655 kcal/mol	7.82241 kcal/mol	273 291@LB@ \| \|@LB@5'-AAA...AUCUU UUUCCC AAUGA...CUU-3'@LB@ CUCCUGU GCAU@LB@ \|:\|\|\|\|\| :\|\|:@LB@ GGGGACA UGUG@LB@3'-UUU...GAAGG CAUGUU AUCUC...GAA-5'@LB@ \| \|@LB@ 58 40@LB@@LB@@LB@Energy -4.53 kcal/mol@LB@Hybridization Energy -13.0187 kcal/mol@LB@Unfolding Energy - mRNA 0.670655 kcal/mol@LB@Unfolding Energy - sRNA 7.82241 kcal/mol@LB@@LB@Position - mRNA 274 -- 290@LB@Position - sRNA 41 -- 57@LB@Position Seed - mRNA 274 -- 280@LB@Position Seed - sRNA 51 -- 57@LB@
153	0.06453	0.3424	ct_729	serS	-6.28	0.205305	1 -- 23	3 -- 33	serine--tRNA ligase	______________1______________________________24\n______________\|______________________________\|\n___________5'-____C_G_____U__________________CCUCA...UGG-3'\n______________AGAA_C_AUUCC_UG________AUGCCAAC\n______________\|\|\|\|_\|_\|\|\|\|\|_\|\|________\|\|:\|\|\|\|\|\n______________UCUU_G_UAAGG_AC________UAUGGUUG\n3'-UUU...CUCAG____C_A_____U__CGCAAUCU________AA-5'\n_____________\|_______________________________\|\n_____________34______________________________2\n	17 -- 23	3 -- 9	-16.9997 kcal/mol	2.1318 kcal/mol	8.59196 kcal/mol	1 24@LB@ \| \|@LB@ 5'- C G U CCUCA...UGG-3'@LB@ AGAA C AUUCC UG AUGCCAAC@LB@ \|\|\|\| \| \|\|\|\|\| \|\| \|\|:\|\|\|\|\|@LB@ UCUU G UAAGG AC UAUGGUUG@LB@3'-UUU...CUCAG C A U CGCAAUCU AA-5'@LB@ \| \|@LB@ 34 2@LB@@LB@@LB@Energy -6.28 kcal/mol@LB@Hybridization Energy -16.9997 kcal/mol@LB@Unfolding Energy - mRNA 2.1318 kcal/mol@LB@Unfolding Energy - sRNA 8.59196 kcal/mol@LB@@LB@Position - mRNA 1 -- 23@LB@Position - sRNA 3 -- 33@LB@Position Seed - mRNA 17 -- 23@LB@Position Seed - sRNA 3 -- 9@LB@
154	0.06467	0.3424	ct_517	rl24	-3.21	0.671117	143 -- 150	27 -- 34	50S ribosomal protein L24	_____________142______151\n_____________\|________\|\n5'-UAA...CGAGA________UUGUU...AGG-3'\n______________CAGAGGCU\n______________\|\|\|\|:\|\|\|\n______________GUCUUCGA\n3'-UUU...UCUCA________UAAGG...GAA-5'\n_____________\|________\|\n_____________35_______26\n	144 -- 150	27 -- 33	-11.3134 kcal/mol	3.50051 kcal/mol	4.59929 kcal/mol	142 151@LB@ \| \|@LB@5'-UAA...CGAGA UUGUU...AGG-3'@LB@ CAGAGGCU@LB@ \|\|\|\|:\|\|\|@LB@ GUCUUCGA@LB@3'-UUU...UCUCA UAAGG...GAA-5'@LB@ \| \|@LB@ 35 26@LB@@LB@@LB@Energy -3.21 kcal/mol@LB@Hybridization Energy -11.3134 kcal/mol@LB@Unfolding Energy - mRNA 3.50051 kcal/mol@LB@Unfolding Energy - sRNA 4.59929 kcal/mol@LB@@LB@Position - mRNA 143 -- 150@LB@Position - sRNA 27 -- 34@LB@Position Seed - mRNA 144 -- 150@LB@Position Seed - sRNA 27 -- 33@LB@
155	0.06493	0.3424	ct_355	N/A	-6.27	0.205473	16 -- 22	80 -- 86		_____________15______23\n_____________\|_______\|\n5'-GUU...UUCUG_______GGUCC...CCU-3'\n______________ACGGCUG\n______________\|\|\|\|\|\|:\n______________UGCCGAU\n3'-UUU...CUCUA_______UGAGG...GAA-5'\n_____________\|_______\|\n_____________87______79\n	16 -- 22	80 -- 86	-10.68 kcal/mol	3.341 kcal/mol	1.06449 kcal/mol	15 23@LB@ \| \|@LB@5'-GUU...UUCUG GGUCC...CCU-3'@LB@ ACGGCUG@LB@ \|\|\|\|\|\|:@LB@ UGCCGAU@LB@3'-UUU...CUCUA UGAGG...GAA-5'@LB@ \| \|@LB@ 87 79@LB@@LB@@LB@Energy -6.27 kcal/mol@LB@Hybridization Energy -10.68 kcal/mol@LB@Unfolding Energy - mRNA 3.341 kcal/mol@LB@Unfolding Energy - sRNA 1.06449 kcal/mol@LB@@LB@Position - mRNA 16 -- 22@LB@Position - sRNA 80 -- 86@LB@Position Seed - mRNA 16 -- 22@LB@Position Seed - sRNA 80 -- 86@LB@
156	0.06505	0.3424	ct_254	N/A	-6.97	0.146186	84 -- 91	80 -- 87		_____________83_______92\n_____________\|________\|\n5'-GUC...AUCGU________GCGUU...UAC-3'\n______________UAUGGCUG\n______________\|\|:\|\|\|\|:\n______________AUGCCGAU\n3'-UUU...CCUCU________UGAGG...GAA-5'\n_____________\|________\|\n_____________88_______79\n	85 -- 91	80 -- 86	-9.90306 kcal/mol	1.8348 kcal/mol	1.09752 kcal/mol	83 92@LB@ \| \|@LB@5'-GUC...AUCGU GCGUU...UAC-3'@LB@ UAUGGCUG@LB@ \|\|:\|\|\|\|:@LB@ AUGCCGAU@LB@3'-UUU...CCUCU UGAGG...GAA-5'@LB@ \| \|@LB@ 88 79@LB@@LB@@LB@Energy -6.97 kcal/mol@LB@Hybridization Energy -9.90306 kcal/mol@LB@Unfolding Energy - mRNA 1.8348 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 84 -- 91@LB@Position - sRNA 80 -- 87@LB@Position Seed - mRNA 85 -- 91@LB@Position Seed - sRNA 80 -- 86@LB@
157	0.06639	0.3424	ct_213	rpiA	-7.48	0.112460	245 -- 274	28 -- 57	ribose-5-phosphate isomerase A	_____________244____________________________275\n_____________\|______________________________\|\n5'-GAA...UUUUU____AUCAA_____A_____C_C_______AGUAG...UGU-3'\n______________CCCU_____GCAGA_ACUAG_G_UAGAGGC\n______________\|\|\|:_____:\|\|:\|_\|\|\|\|\|_\|_:\|\|\|:\|\|\n______________GGGG_____UGUUU_UGAUC_C_GUCUUCG\n3'-UUU...GAAGG____ACACA_____G_____U_A_______AUAAG...GAA-5'\n_____________\|______________________________\|\n_____________58_____________________________27\n	268 -- 274	28 -- 34	-25.4315 kcal/mol	5.87242 kcal/mol	12.0748 kcal/mol	244 275@LB@ \| \|@LB@5'-GAA...UUUUU AUCAA A C C AGUAG...UGU-3'@LB@ CCCU GCAGA ACUAG G UAGAGGC@LB@ \|\|\|: :\|\|:\| \|\|\|\|\| \| :\|\|\|:\|\|@LB@ GGGG UGUUU UGAUC C GUCUUCG@LB@3'-UUU...GAAGG ACACA G U A AUAAG...GAA-5'@LB@ \| \|@LB@ 58 27@LB@@LB@@LB@Energy -7.48 kcal/mol@LB@Hybridization Energy -25.4315 kcal/mol@LB@Unfolding Energy - mRNA 5.87242 kcal/mol@LB@Unfolding Energy - sRNA 12.0748 kcal/mol@LB@@LB@Position - mRNA 245 -- 274@LB@Position - sRNA 28 -- 57@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 28 -- 34@LB@
158	0.06677	0.3424	ct_770	fabF	-2.81	0.742017	6 -- 13	26 -- 33	3-oxoacyl-ACP synthase	_____________5________14\n_____________\|________\|\n______5'-UAUAG________AAAAA...GUG-3'\n______________AGGAGUUA\n______________\|\|:\|\|:\|\|\n______________UCUUCGAU\n3'-UUU...CUCAG________AAGGU...GAA-5'\n_____________\|________\|\n_____________34_______25\n	7 -- 13	26 -- 32	-8.27201 kcal/mol	0.759487 kcal/mol	4.69868 kcal/mol	5 14@LB@ \| \|@LB@ 5'-UAUAG AAAAA...GUG-3'@LB@ AGGAGUUA@LB@ \|\|:\|\|:\|\|@LB@ UCUUCGAU@LB@3'-UUU...CUCAG AAGGU...GAA-5'@LB@ \| \|@LB@ 34 25@LB@@LB@@LB@Energy -2.81 kcal/mol@LB@Hybridization Energy -8.27201 kcal/mol@LB@Unfolding Energy - mRNA 0.759487 kcal/mol@LB@Unfolding Energy - sRNA 4.69868 kcal/mol@LB@@LB@Position - mRNA 6 -- 13@LB@Position - sRNA 26 -- 33@LB@Position Seed - mRNA 7 -- 13@LB@Position Seed - sRNA 26 -- 32@LB@
159	0.06732	0.3424	ct_663	N/A	-7.57	0.107718	228 -- 234	15 -- 21	type III secretion system chaperone	_____________227_____235\n_____________\|_______\|\n5'-UCU...AUUUU_______AUAUG...GCC-3'\n______________GUGGCGU\n______________:\|\|\|\|\|\|\n______________UACCGCA\n3'-UUU...UAAGG_______AUCUU...GAA-5'\n_____________\|_______\|\n_____________22______14\n	228 -- 234	15 -- 21	-10.4333 kcal/mol	1.67755 kcal/mol	1.18845 kcal/mol	227 235@LB@ \| \|@LB@5'-UCU...AUUUU AUAUG...GCC-3'@LB@ GUGGCGU@LB@ :\|\|\|\|\|\|@LB@ UACCGCA@LB@3'-UUU...UAAGG AUCUU...GAA-5'@LB@ \| \|@LB@ 22 14@LB@@LB@@LB@Energy -7.57 kcal/mol@LB@Hybridization Energy -10.4333 kcal/mol@LB@Unfolding Energy - mRNA 1.67755 kcal/mol@LB@Unfolding Energy - sRNA 1.18845 kcal/mol@LB@@LB@Position - mRNA 228 -- 234@LB@Position - sRNA 15 -- 21@LB@Position Seed - mRNA 228 -- 234@LB@Position Seed - sRNA 15 -- 21@LB@
160	0.06752	0.3424	ct_324	N/A	-4.86	0.383763	195 -- 205	17 -- 27		_____________194_________206\n_____________\|___________\|\n5'-ACA...GUAGA__GG_______CAAAG...UGC-3'\n______________UA__CCAUGGU\n______________\|\|__\|\|\|\|\|\|:\n______________AU__GGUACCG\n3'-UUU...CUUCG__AA_______CAAUC...GAA-5'\n_____________\|___________\|\n_____________28__________16\n	199 -- 205	17 -- 23	-11.7516 kcal/mol	2.4023 kcal/mol	4.49196 kcal/mol	194 206@LB@ \| \|@LB@5'-ACA...GUAGA GG CAAAG...UGC-3'@LB@ UA CCAUGGU@LB@ \|\| \|\|\|\|\|\|:@LB@ AU GGUACCG@LB@3'-UUU...CUUCG AA CAAUC...GAA-5'@LB@ \| \|@LB@ 28 16@LB@@LB@@LB@Energy -4.86 kcal/mol@LB@Hybridization Energy -11.7516 kcal/mol@LB@Unfolding Energy - mRNA 2.4023 kcal/mol@LB@Unfolding Energy - sRNA 4.49196 kcal/mol@LB@@LB@Position - mRNA 195 -- 205@LB@Position - sRNA 17 -- 27@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 17 -- 23@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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