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
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@
24	0.006504	0.2093	ct_534	cutE	-7.36	0.119875	40 -- 61	34 -- 57	apolipoprotein N-acyltransferase	_____________39_______________________62\n_____________\|________________________\|\n5'-CAG...CAAUU________GAAGUU__________AAUCC...GCG-3'\n______________CCCCUGUG______C_C_AGAGUU\n______________\|\|\|\|\|\|\|\|______\|_\|_\|\|\|\|\|:\n______________GGGGACAC______G_G_UCUCAG\n3'-UUU...GAAGG________AUGUUU_U_A______UCUUC...GAA-5'\n_____________\|________________________\|\n_____________58_______________________33\n	41 -- 47	50 -- 56	-22.0571 kcal/mol	6.72142 kcal/mol	7.97509 kcal/mol	39 62@LB@ \| \|@LB@5'-CAG...CAAUU GAAGUU AAUCC...GCG-3'@LB@ CCCCUGUG C C AGAGUU@LB@ \|\|\|\|\|\|\|\| \| \| \|\|\|\|\|:@LB@ GGGGACAC G G UCUCAG@LB@3'-UUU...GAAGG AUGUUU U A UCUUC...GAA-5'@LB@ \| \|@LB@ 58 33@LB@@LB@@LB@Energy -7.36 kcal/mol@LB@Hybridization Energy -22.0571 kcal/mol@LB@Unfolding Energy - mRNA 6.72142 kcal/mol@LB@Unfolding Energy - sRNA 7.97509 kcal/mol@LB@@LB@Position - mRNA 40 -- 61@LB@Position - sRNA 34 -- 57@LB@Position Seed - mRNA 41 -- 47@LB@Position Seed - sRNA 50 -- 56@LB@
70	0.02698	0.29	ct_381	artJ	-6.76	0.162330	168 -- 194	31 -- 57	arginine ABC transporter substrate-binding protein ArtJ	_____________167__________________________195\n_____________\|____________________________\|\n5'-AUU...UAUAG______CC__UA__C_____________GUGAG...GUG-3'\n______________UCCCUG__GU__GA_CAUU_GAGUCGGA\n______________:\|\|\|\|\|__\|\|__:\|_\|\|:\|_\|\|\|\|\|:\|\|\n______________GGGGAC__CA__UU_GUGA_CUCAGUCU\n3'-UUU...GAAGG______A___UG__U____U________UCGAU...GAA-5'\n_____________\|____________________________\|\n_____________58___________________________30\n	188 -- 194	31 -- 37	-25.975 kcal/mol	9.18513 kcal/mol	10.0297 kcal/mol	167 195@LB@ \| \|@LB@5'-AUU...UAUAG CC UA C GUGAG...GUG-3'@LB@ UCCCUG GU GA CAUU GAGUCGGA@LB@ :\|\|\|\|\| \|\| :\| \|\|:\| \|\|\|\|\|:\|\|@LB@ GGGGAC CA UU GUGA CUCAGUCU@LB@3'-UUU...GAAGG A UG U U UCGAU...GAA-5'@LB@ \| \|@LB@ 58 30@LB@@LB@@LB@Energy -6.76 kcal/mol@LB@Hybridization Energy -25.975 kcal/mol@LB@Unfolding Energy - mRNA 9.18513 kcal/mol@LB@Unfolding Energy - sRNA 10.0297 kcal/mol@LB@@LB@Position - mRNA 168 -- 194@LB@Position - sRNA 31 -- 57@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 31 -- 37@LB@
109	0.04235	0.3194	ct_002	gatC	-8.76	0.056639	255 -- 282	18 -- 44	aspartyl/glutamyl-tRNA amidotransferase subunit C	_____________254__________________________283\n_____________\|____________________________\|\n5'-GAC...AUGCU________________AUGCCCA_____AAGAG...CUA-3'\n______________GCAUUGGAGUUGGAAG_______CGUGG\n______________:\|\|:\|:\|\|\|\|::\|\|\|\|_______\|:\|\|\|\n______________UGUGAUCUCAGUCUUC_______GUACC\n3'-UUU...AUGUU________________GAUAAG______GCAAU...GAA-5'\n_____________\|____________________________\|\n_____________45___________________________17\n	261 -- 267	32 -- 38	-28.0671 kcal/mol	6.54471 kcal/mol	12.7603 kcal/mol	254 283@LB@ \| \|@LB@5'-GAC...AUGCU AUGCCCA AAGAG...CUA-3'@LB@ GCAUUGGAGUUGGAAG CGUGG@LB@ :\|\|:\|:\|\|\|\|::\|\|\|\| \|:\|\|\|@LB@ UGUGAUCUCAGUCUUC GUACC@LB@3'-UUU...AUGUU GAUAAG GCAAU...GAA-5'@LB@ \| \|@LB@ 45 17@LB@@LB@@LB@Energy -8.76 kcal/mol@LB@Hybridization Energy -28.0671 kcal/mol@LB@Unfolding Energy - mRNA 6.54471 kcal/mol@LB@Unfolding Energy - sRNA 12.7603 kcal/mol@LB@@LB@Position - mRNA 255 -- 282@LB@Position - sRNA 18 -- 44@LB@Position Seed - mRNA 261 -- 267@LB@Position Seed - sRNA 32 -- 38@LB@
62	0.02417	0.29	ct_705	clpX	-8.32	0.072096	259 -- 275	17 -- 33	ATP-dependent Clp protease ATP-binding subunit ClpX	_____________258_______________276\n_____________\|_________________\|\n5'-CUG...UGUUG________A__GC____CCAUC...AUU-3'\n______________AGAAGCUA_UC__UGGU\n______________\|\|\|\|\|\|\|\|_\|\|__\|\|\|:\n______________UCUUCGAU_AG__ACCG\n3'-UUU...CUCAG________A__GU____CAAUC...GAA-5'\n_____________\|_________________\|\n_____________34________________16\n	260 -- 266	26 -- 32	-18.4351 kcal/mol	5.13531 kcal/mol	4.97804 kcal/mol	258 276@LB@ \| \|@LB@5'-CUG...UGUUG A GC CCAUC...AUU-3'@LB@ AGAAGCUA UC UGGU@LB@ \|\|\|\|\|\|\|\| \|\| \|\|\|:@LB@ UCUUCGAU AG ACCG@LB@3'-UUU...CUCAG A GU CAAUC...GAA-5'@LB@ \| \|@LB@ 34 16@LB@@LB@@LB@Energy -8.32 kcal/mol@LB@Hybridization Energy -18.4351 kcal/mol@LB@Unfolding Energy - mRNA 5.13531 kcal/mol@LB@Unfolding Energy - sRNA 4.97804 kcal/mol@LB@@LB@Position - mRNA 259 -- 275@LB@Position - sRNA 17 -- 33@LB@Position Seed - mRNA 260 -- 266@LB@Position Seed - sRNA 26 -- 32@LB@
79	0.0288	0.29	ct_431	clpP_1	-3.71	0.580570	128 -- 134	79 -- 85	ATP-dependent Clp protease proteolytic subunit	_____________127_____135\n_____________\|_______\|\n5'-GAA...ACGUG_______UUUAU...AAA-3'\n______________UGGCUGA\n______________:\|\|\|\|:\|\n______________GCCGAUU\n3'-UUU...UCUAU_______GAGGU...GAA-5'\n_____________\|_______\|\n_____________86______78\n	128 -- 134	79 -- 85	-7.88567 kcal/mol	3.08 kcal/mol	1.09751 kcal/mol	127 135@LB@ \| \|@LB@5'-GAA...ACGUG UUUAU...AAA-3'@LB@ UGGCUGA@LB@ :\|\|\|\|:\|@LB@ GCCGAUU@LB@3'-UUU...UCUAU GAGGU...GAA-5'@LB@ \| \|@LB@ 86 78@LB@@LB@@LB@Energy -3.71 kcal/mol@LB@Hybridization Energy -7.88567 kcal/mol@LB@Unfolding Energy - mRNA 3.08 kcal/mol@LB@Unfolding Energy - sRNA 1.09751 kcal/mol@LB@@LB@Position - mRNA 128 -- 134@LB@Position - sRNA 79 -- 85@LB@Position Seed - mRNA 128 -- 134@LB@Position Seed - sRNA 79 -- 85@LB@
119	0.04857	0.3262	ct_706	clpP_2	-8.60	0.061801	14 -- 27	22 -- 35	ATP-dependent Clp protease proteolytic subunit	_____________13_____________28\n_____________\|______________\|\n5'-CGA...AAGAU______________UUCUU...GGC-3'\n______________UUAGAGGUUGUUCC\n______________\|:\|\|\|:\|:\|:\|\|\|\|\n______________AGUCUUCGAUAAGG\n3'-UUU...AUCUC______________UACCG...GAA-5'\n_____________\|______________\|\n_____________36_____________21\n	16 -- 22	27 -- 33	-17.9181 kcal/mol	4.58788 kcal/mol	4.72627 kcal/mol	13 28@LB@ \| \|@LB@5'-CGA...AAGAU UUCUU...GGC-3'@LB@ UUAGAGGUUGUUCC@LB@ \|:\|\|\|:\|:\|:\|\|\|\|@LB@ AGUCUUCGAUAAGG@LB@3'-UUU...AUCUC UACCG...GAA-5'@LB@ \| \|@LB@ 36 21@LB@@LB@@LB@Energy -8.60 kcal/mol@LB@Hybridization Energy -17.9181 kcal/mol@LB@Unfolding Energy - mRNA 4.58788 kcal/mol@LB@Unfolding Energy - sRNA 4.72627 kcal/mol@LB@@LB@Position - mRNA 14 -- 27@LB@Position - sRNA 22 -- 35@LB@Position Seed - mRNA 16 -- 22@LB@Position Seed - sRNA 27 -- 33@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@
11	0.002752	0.1836	ct_015	phoH	-12.12	0.007844	167 -- 186	33 -- 60	ATPase	_____________166__________________________187\n_____________\|____________________________\|\n5'-CCA...CUAUC_____________________U______UUUAG...UAA-3'\n______________UCCCCCUU________ACACU_GAGUCA\n______________\|\|\|\|\|\|:\|________\|\|\|\|\|_\|\|\|\|\|\|\n______________AGGGGGGA________UGUGA_CUCAGU\n3'-UUU...ACUGA________CACAUGUU_____U______CUUCG...GAA-5'\n_____________\|____________________________\|\n_____________61___________________________32\n	168 -- 174	53 -- 59	-26.4608 kcal/mol	2.95889 kcal/mol	11.3851 kcal/mol	166 187@LB@ \| \|@LB@5'-CCA...CUAUC U UUUAG...UAA-3'@LB@ UCCCCCUU ACACU GAGUCA@LB@ \|\|\|\|\|\|:\| \|\|\|\|\| \|\|\|\|\|\|@LB@ AGGGGGGA UGUGA CUCAGU@LB@3'-UUU...ACUGA CACAUGUU U CUUCG...GAA-5'@LB@ \| \|@LB@ 61 32@LB@@LB@@LB@Energy -12.12 kcal/mol@LB@Hybridization Energy -26.4608 kcal/mol@LB@Unfolding Energy - mRNA 2.95889 kcal/mol@LB@Unfolding Energy - sRNA 11.3851 kcal/mol@LB@@LB@Position - mRNA 167 -- 186@LB@Position - sRNA 33 -- 60@LB@Position Seed - mRNA 168 -- 174@LB@Position Seed - sRNA 53 -- 59@LB@
130	0.05252	0.3262	ct_826	pssA	-5.40	0.306560	126 -- 136	23 -- 33	CDP-diacylglycerol--serine O-phosphatidyltransferase	_____________125_________137\n_____________\|___________\|\n5'-AUA...UAAAA_______UC__AACAA...UCA-3'\n______________AGAAGCU__UC\n______________\|\|\|\|\|\|\|__\|\|\n______________UCUUCGA__AG\n3'-UUU...CUCAG_______UA__GUACC...GAA-5'\n_____________\|___________\|\n_____________34__________22\n	126 -- 132	27 -- 33	-11.4676 kcal/mol	1.34949 kcal/mol	4.72321 kcal/mol	125 137@LB@ \| \|@LB@5'-AUA...UAAAA UC AACAA...UCA-3'@LB@ AGAAGCU UC@LB@ \|\|\|\|\|\|\| \|\|@LB@ UCUUCGA AG@LB@3'-UUU...CUCAG UA GUACC...GAA-5'@LB@ \| \|@LB@ 34 22@LB@@LB@@LB@Energy -5.40 kcal/mol@LB@Hybridization Energy -11.4676 kcal/mol@LB@Unfolding Energy - mRNA 1.34949 kcal/mol@LB@Unfolding Energy - sRNA 4.72321 kcal/mol@LB@@LB@Position - mRNA 126 -- 136@LB@Position - sRNA 23 -- 33@LB@Position Seed - mRNA 126 -- 132@LB@Position Seed - sRNA 27 -- 33@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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