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
165	0.06872	0.3424	ct_859	lytB	-7.21	0.129268	10 -- 22	19 -- 31	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	_____________9_____________23\n_____________\|_____________\|\n5'-UCG...UAUAA___________A_UAUCU...CUA-3'\n______________AGGCUAUUCCG_G\n______________\|:\|\|\|\|\|\|\|\|:_\|\n______________UUCGAUAAGGU_C\n3'-UUU...CAGUC___________A_CGCAA...GAA-5'\n_____________\|_____________\|\n_____________32____________18\n	14 -- 20	21 -- 27	-14.969 kcal/mol	2.89565 kcal/mol	4.85984 kcal/mol	9 23@LB@ \| \|@LB@5'-UCG...UAUAA A UAUCU...CUA-3'@LB@ AGGCUAUUCCG G@LB@ \|:\|\|\|\|\|\|\|\|: \|@LB@ UUCGAUAAGGU C@LB@3'-UUU...CAGUC A CGCAA...GAA-5'@LB@ \| \|@LB@ 32 18@LB@@LB@@LB@Energy -7.21 kcal/mol@LB@Hybridization Energy -14.969 kcal/mol@LB@Unfolding Energy - mRNA 2.89565 kcal/mol@LB@Unfolding Energy - sRNA 4.85984 kcal/mol@LB@@LB@Position - mRNA 10 -- 22@LB@Position - sRNA 19 -- 31@LB@Position Seed - mRNA 14 -- 20@LB@Position Seed - sRNA 21 -- 27@LB@
174	0.07335	0.3448	ct_777	bioF	-7.25	0.126962	76 -- 92	19 -- 34	8-amino-7-oxononanoate synthase	_____________75________________93\n_____________\|_________________\|\n5'-CUG...UCAGG_______G_____U___UUGGG...UUU-3'\n______________UAGAAGC_AUUCC_AUG\n______________:\|\|\|\|\|\|_\|\|\|\|\|_\|\|\|\n______________GUCUUCG_UAAGG_UAC\n3'-UUU...UCUCA_______A_________CGCAA...GAA-5'\n_____________\|_________________\|\n_____________35________________18\n	76 -- 82	28 -- 34	-16.4612 kcal/mol	4.23516 kcal/mol	4.97732 kcal/mol	75 93@LB@ \| \|@LB@5'-CUG...UCAGG G U UUGGG...UUU-3'@LB@ UAGAAGC AUUCC AUG@LB@ :\|\|\|\|\|\| \|\|\|\|\| \|\|\|@LB@ GUCUUCG UAAGG UAC@LB@3'-UUU...UCUCA A CGCAA...GAA-5'@LB@ \| \|@LB@ 35 18@LB@@LB@@LB@Energy -7.25 kcal/mol@LB@Hybridization Energy -16.4612 kcal/mol@LB@Unfolding Energy - mRNA 4.23516 kcal/mol@LB@Unfolding Energy - sRNA 4.97732 kcal/mol@LB@@LB@Position - mRNA 76 -- 92@LB@Position - sRNA 19 -- 34@LB@Position Seed - mRNA 76 -- 82@LB@Position Seed - sRNA 28 -- 34@LB@
73	0.02714	0.29	ct_211	N/A	-9.30	0.041995	126 -- 170	20 -- 59		_____________125____________________________________________171\n_____________\|______________________________________________\|\n5'-AGA...UCAAG_____AUUCU_______AAGUC____UUUGAU_________C____ACGAA...UUU-3'\n______________CCCCU_____CUGUGUG_____CAUU_______GAAGCUAU_CCAU\n______________\|\|\|\|:_____\|\|\|\|\|\|:_____\|\|:\|_______\|\|\|\|\|\|\|\|_\|\|\|\|\n______________GGGGG_____GACACAU_____GUGA_______CUUCGAUA_GGUA\n3'-UUU...CUGAA_________________GUUU_____UCUCAGU________A____CCGCA...GAA-5'\n_____________\|______________________________________________\|\n_____________60_____________________________________________19\n	159 -- 165	25 -- 31	-32.2967 kcal/mol	9.12092 kcal/mol	13.8789 kcal/mol	125 171@LB@ \| \|@LB@5'-AGA...UCAAG AUUCU AAGUC UUUGAU C ACGAA...UUU-3'@LB@ CCCCU CUGUGUG CAUU GAAGCUAU CCAU@LB@ \|\|\|\|: \|\|\|\|\|\|: \|\|:\| \|\|\|\|\|\|\|\| \|\|\|\|@LB@ GGGGG GACACAU GUGA CUUCGAUA GGUA@LB@3'-UUU...CUGAA GUUU UCUCAGU A CCGCA...GAA-5'@LB@ \| \|@LB@ 60 19@LB@@LB@@LB@Energy -9.30 kcal/mol@LB@Hybridization Energy -32.2967 kcal/mol@LB@Unfolding Energy - mRNA 9.12092 kcal/mol@LB@Unfolding Energy - sRNA 13.8789 kcal/mol@LB@@LB@Position - mRNA 126 -- 170@LB@Position - sRNA 20 -- 59@LB@Position Seed - mRNA 159 -- 165@LB@Position Seed - sRNA 25 -- 31@LB@
177	0.07605	0.3532	ct_428	ubiE	-3.67	0.587989	9 -- 17	20 -- 28	demethylmenaquinone methyltransferase	_____________8_________18\n_____________\|_________\|\n___5'-UUCUUCAA_________UUCAG...AUA-3'\n______________CUAUUUCAU\n______________\|\|\|\|\|:\|\|\|\n______________GAUAAGGUA\n3'-UUU...UCUUC_________CCGCA...GAA-5'\n_____________\|_________\|\n_____________29________19\n	10 -- 16	21 -- 27	-8.26525 kcal/mol	0.050804 kcal/mol	4.54807 kcal/mol	8 18@LB@ \| \|@LB@ 5'-UUCUUCAA UUCAG...AUA-3'@LB@ CUAUUUCAU@LB@ \|\|\|\|\|:\|\|\|@LB@ GAUAAGGUA@LB@3'-UUU...UCUUC CCGCA...GAA-5'@LB@ \| \|@LB@ 29 19@LB@@LB@@LB@Energy -3.67 kcal/mol@LB@Hybridization Energy -8.26525 kcal/mol@LB@Unfolding Energy - mRNA 0.050804 kcal/mol@LB@Unfolding Energy - sRNA 4.54807 kcal/mol@LB@@LB@Position - mRNA 9 -- 17@LB@Position - sRNA 20 -- 28@LB@Position Seed - mRNA 10 -- 16@LB@Position Seed - sRNA 21 -- 27@LB@
188	0.08401	0.363	ct_024	N/A	-5.57	0.284242	184 -- 199	20 -- 35	release factor glutamine methyltransferase	_____________183______________200\n_____________\|________________\|\n5'-AGA...GUACA____C________G__CAUGA...AGA-3'\n______________UCGG_AGCUAUUC_GU\n______________\|\|:\|_\|\|\|\|\|\|\|\|_:\|\n______________AGUC_UCGAUAAG_UA\n3'-UUU...AUCUC____U________G__CCGCA...GAA-5'\n_____________\|________________\|\n_____________36_______________19\n	190 -- 196	23 -- 29	-16.0617 kcal/mol	5.57694 kcal/mol	4.91708 kcal/mol	183 200@LB@ \| \|@LB@5'-AGA...GUACA C G CAUGA...AGA-3'@LB@ UCGG AGCUAUUC GU@LB@ \|\|:\| \|\|\|\|\|\|\|\| :\|@LB@ AGUC UCGAUAAG UA@LB@3'-UUU...AUCUC U G CCGCA...GAA-5'@LB@ \| \|@LB@ 36 19@LB@@LB@@LB@Energy -5.57 kcal/mol@LB@Hybridization Energy -16.0617 kcal/mol@LB@Unfolding Energy - mRNA 5.57694 kcal/mol@LB@Unfolding Energy - sRNA 4.91708 kcal/mol@LB@@LB@Position - mRNA 184 -- 199@LB@Position - sRNA 20 -- 35@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 23 -- 29@LB@
193	0.08525	0.3631	ct_196	N/A	-5.32	0.316248	140 -- 149	20 -- 29	inclusion membrane protein	_____________139________150\n_____________\|__________\|\n5'-UUU...AUAAU__________UUCUU...AAC-3'\n______________GCUAUUUCAU\n______________\|\|\|\|\|\|:\|\|\|\n______________CGAUAAGGUA\n3'-UUU...GUCUU__________CCGCA...GAA-5'\n_____________\|__________\|\n_____________30_________19\n	141 -- 147	22 -- 28	-11.6207 kcal/mol	1.68905 kcal/mol	4.60882 kcal/mol	139 150@LB@ \| \|@LB@5'-UUU...AUAAU UUCUU...AAC-3'@LB@ GCUAUUUCAU@LB@ \|\|\|\|\|\|:\|\|\|@LB@ CGAUAAGGUA@LB@3'-UUU...GUCUU CCGCA...GAA-5'@LB@ \| \|@LB@ 30 19@LB@@LB@@LB@Energy -5.32 kcal/mol@LB@Hybridization Energy -11.6207 kcal/mol@LB@Unfolding Energy - mRNA 1.68905 kcal/mol@LB@Unfolding Energy - sRNA 4.60882 kcal/mol@LB@@LB@Position - mRNA 140 -- 149@LB@Position - sRNA 20 -- 29@LB@Position Seed - mRNA 141 -- 147@LB@Position Seed - sRNA 22 -- 28@LB@
2	8.171e-05	0.03358	ct_802	rs18	-7.95	0.088258	66 -- 79	21 -- 34	30S ribosomal protein S18	_____________65_____________80\n_____________\|______________\|\n5'-GUU...AGCCC__________CG__GAGUU...UUA-3'\n______________CAGAAGCUAU__CA\n______________\|\|\|\|\|\|\|\|\|\|__\|\|\n______________GUCUUCGAUA__GU\n3'-UUU...UCUCA__________AG__ACCGC...GAA-5'\n_____________\|______________\|\n_____________35_____________20\n	68 -- 74	26 -- 32	-17.0234 kcal/mol	4.34679 kcal/mol	4.73132 kcal/mol	65 80@LB@ \| \|@LB@5'-GUU...AGCCC CG GAGUU...UUA-3'@LB@ CAGAAGCUAU CA@LB@ \|\|\|\|\|\|\|\|\|\| \|\|@LB@ GUCUUCGAUA GU@LB@3'-UUU...UCUCA AG ACCGC...GAA-5'@LB@ \| \|@LB@ 35 20@LB@@LB@@LB@Energy -7.95 kcal/mol@LB@Hybridization Energy -17.0234 kcal/mol@LB@Unfolding Energy - mRNA 4.34679 kcal/mol@LB@Unfolding Energy - sRNA 4.73132 kcal/mol@LB@@LB@Position - mRNA 66 -- 79@LB@Position - sRNA 21 -- 34@LB@Position Seed - mRNA 68 -- 74@LB@Position Seed - sRNA 26 -- 32@LB@
31	0.009434	0.2502	ct_824	N/A	-6.02	0.231369	20 -- 32	21 -- 33	Zn-dependent peptidase	_____________19____________33\n_____________\|_____________\|\n5'-GUC...UUUUA________G____GUAUG...CCG-3'\n______________GGAAGCUA_UCUA\n______________:\|\|\|\|\|\|\|_\|\|:\|\n______________UCUUCGAU_AGGU\n3'-UUU...CUCAG________A____ACCGC...GAA-5'\n_____________\|_____________\|\n_____________34____________20\n	21 -- 27	26 -- 32	-13.8347 kcal/mol	3.08274 kcal/mol	4.73034 kcal/mol	19 33@LB@ \| \|@LB@5'-GUC...UUUUA G GUAUG...CCG-3'@LB@ GGAAGCUA UCUA@LB@ :\|\|\|\|\|\|\| \|\|:\|@LB@ UCUUCGAU AGGU@LB@3'-UUU...CUCAG A ACCGC...GAA-5'@LB@ \| \|@LB@ 34 20@LB@@LB@@LB@Energy -6.02 kcal/mol@LB@Hybridization Energy -13.8347 kcal/mol@LB@Unfolding Energy - mRNA 3.08274 kcal/mol@LB@Unfolding Energy - sRNA 4.73034 kcal/mol@LB@@LB@Position - mRNA 20 -- 32@LB@Position - sRNA 21 -- 33@LB@Position Seed - mRNA 21 -- 27@LB@Position Seed - sRNA 26 -- 32@LB@
50	0.01829	0.29	ct_588	rbsU	-10.49	0.021035	31 -- 46	21 -- 34	serine phosphatase RsbU	_____________30_______________47\n_____________\|________________\|\n5'-GUC...GGGUC________CU______AGAUU...UCC-3'\n______________CAGAAGCU__AUUCCA\n______________\|\|\|\|\|\|\|\|__\|\|\|\|\|\|\n______________GUCUUCGA__UAAGGU\n3'-UUU...UCUCA________________ACCGC...GAA-5'\n_____________\|________________\|\n_____________35_______________20\n	32 -- 38	27 -- 33	-17.905 kcal/mol	2.68182 kcal/mol	4.73132 kcal/mol	30 47@LB@ \| \|@LB@5'-GUC...GGGUC CU AGAUU...UCC-3'@LB@ CAGAAGCU AUUCCA@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ GUCUUCGA UAAGGU@LB@3'-UUU...UCUCA ACCGC...GAA-5'@LB@ \| \|@LB@ 35 20@LB@@LB@@LB@Energy -10.49 kcal/mol@LB@Hybridization Energy -17.905 kcal/mol@LB@Unfolding Energy - mRNA 2.68182 kcal/mol@LB@Unfolding Energy - sRNA 4.73132 kcal/mol@LB@@LB@Position - mRNA 31 -- 46@LB@Position - sRNA 21 -- 34@LB@Position Seed - mRNA 32 -- 38@LB@Position Seed - sRNA 27 -- 33@LB@
60	0.02363	0.29	ct_796	glyQ	-6.44	0.189870	236 -- 248	21 -- 33	glycine--tRNA ligase	_____________235___________249\n_____________\|_____________\|\n5'-UAG...AUGAU__C__________AACUU...AAG-3'\n______________GG_AGCUAUUCUA\n______________:\|_\|\|\|\|\|\|\|\|:\|\n______________UC_UCGAUAAGGU\n3'-UUU...CUCAG__U__________ACCGC...GAA-5'\n_____________\|_____________\|\n_____________34____________20\n	241 -- 247	22 -- 28	-13.5001 kcal/mol	2.33043 kcal/mol	4.73034 kcal/mol	235 249@LB@ \| \|@LB@5'-UAG...AUGAU C AACUU...AAG-3'@LB@ GG AGCUAUUCUA@LB@ :\| \|\|\|\|\|\|\|\|:\|@LB@ UC UCGAUAAGGU@LB@3'-UUU...CUCAG U ACCGC...GAA-5'@LB@ \| \|@LB@ 34 20@LB@@LB@@LB@Energy -6.44 kcal/mol@LB@Hybridization Energy -13.5001 kcal/mol@LB@Unfolding Energy - mRNA 2.33043 kcal/mol@LB@Unfolding Energy - sRNA 4.73034 kcal/mol@LB@@LB@Position - mRNA 236 -- 248@LB@Position - sRNA 21 -- 33@LB@Position Seed - mRNA 241 -- 247@LB@Position Seed - sRNA 22 -- 28@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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