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
182	0.07944	0.3588	ct_320	nusG	-7.37	0.119406	230 -- 236	81 -- 87	transcription termination/antitermination protein NusG	_____________229_____237\n_____________\|_______\|\n5'-AAC...GUUUU_______CAAGA...UUA-3'\n______________UACGGCU\n______________\|\|\|\|\|\|\|\n______________AUGCCGA\n3'-UUU...CCUCU_______UUGAG...GAA-5'\n_____________\|_______\|\n_____________88______80\n	230 -- 236	81 -- 87	-10.814 kcal/mol	2.34788 kcal/mol	1.09752 kcal/mol	229 237@LB@ \| \|@LB@5'-AAC...GUUUU CAAGA...UUA-3'@LB@ UACGGCU@LB@ \|\|\|\|\|\|\|@LB@ AUGCCGA@LB@3'-UUU...CCUCU UUGAG...GAA-5'@LB@ \| \|@LB@ 88 80@LB@@LB@@LB@Energy -7.37 kcal/mol@LB@Hybridization Energy -10.814 kcal/mol@LB@Unfolding Energy - mRNA 2.34788 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 230 -- 236@LB@Position - sRNA 81 -- 87@LB@Position Seed - mRNA 230 -- 236@LB@Position Seed - sRNA 81 -- 87@LB@
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@
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@
183	0.08019	0.3602	ct_648	N/A	-7.31	0.122948	212 -- 231	14 -- 34		_____________211___________________232\n_____________\|_____________________\|\n5'-ACU...GUAAG________UAAG_________UAUGU...UUA-3'\n______________UAGAAGCU_____AUGGUGUU\n______________:\|\|\|\|\|\|\|_____\|\|\|\|:\|\|\|\n______________GUCUUCGA_____UACCGCAA\n3'-UUU...UCUCA________UAAGG________UCUUA...GAA-5'\n_____________\|_____________________\|\n_____________35____________________13\n	225 -- 231	14 -- 20	-20.6397 kcal/mol	4.879 kcal/mol	8.44924 kcal/mol	211 232@LB@ \| \|@LB@5'-ACU...GUAAG UAAG UAUGU...UUA-3'@LB@ UAGAAGCU AUGGUGUU@LB@ :\|\|\|\|\|\|\| \|\|\|\|:\|\|\|@LB@ GUCUUCGA UACCGCAA@LB@3'-UUU...UCUCA UAAGG UCUUA...GAA-5'@LB@ \| \|@LB@ 35 13@LB@@LB@@LB@Energy -7.31 kcal/mol@LB@Hybridization Energy -20.6397 kcal/mol@LB@Unfolding Energy - mRNA 4.879 kcal/mol@LB@Unfolding Energy - sRNA 8.44924 kcal/mol@LB@@LB@Position - mRNA 212 -- 231@LB@Position - sRNA 14 -- 34@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 14 -- 20@LB@
21	0.0049	0.1918	ct_531	lpxA	-7.30	0.123824	16 -- 37	17 -- 34	acyl-[acyl-carrier-protein]--UDP-N- acetylglucosamine O-acyltransferase	_____________15_____________________38\n_____________\|______________________\|\n5'-UUG...GUAUC___A____AAA_______CA__CUGUU...CGC-3'\n______________CAG_AAGC___AUUCCGU__GC\n______________\|\|\|_\|\|\|\|___\|\|\|\|\|:\|__\|\|\n______________GUC_UUCG___UAAGGUA__CG\n3'-UUU...UCUCA________A_________C___CAAUC...GAA-5'\n_____________\|______________________\|\n_____________35_____________________16\n	27 -- 33	20 -- 26	-14.3796 kcal/mol	2.10386 kcal/mol	4.97809 kcal/mol	15 38@LB@ \| \|@LB@5'-UUG...GUAUC A AAA CA CUGUU...CGC-3'@LB@ CAG AAGC AUUCCGU GC@LB@ \|\|\| \|\|\|\| \|\|\|\|\|:\| \|\|@LB@ GUC UUCG UAAGGUA CG@LB@3'-UUU...UCUCA A C CAAUC...GAA-5'@LB@ \| \|@LB@ 35 16@LB@@LB@@LB@Energy -7.30 kcal/mol@LB@Hybridization Energy -14.3796 kcal/mol@LB@Unfolding Energy - mRNA 2.10386 kcal/mol@LB@Unfolding Energy - sRNA 4.97809 kcal/mol@LB@@LB@Position - mRNA 16 -- 37@LB@Position - sRNA 17 -- 34@LB@Position Seed - mRNA 27 -- 33@LB@Position Seed - sRNA 20 -- 26@LB@
128	0.05098	0.3262	ct_279	nqr3	-7.28	0.125274	283 -- 291	51 -- 59	Na(+)-translocating NADH-quinone reductase subunit C	_____________282_______292\n_____________\|_________\|\n5'-CCG...UGGUA_________CUUCU...UGU-3'\n______________CCCUCCUGU\n______________\|\|\|:\|\|\|\|\|\n______________GGGGGGACA\n3'-UUU...CUGAA_________CAUGU...GAA-5'\n_____________\|_________\|\n_____________60________50\n	285 -- 291	51 -- 57	-15.9842 kcal/mol	0.606269 kcal/mol	8.10291 kcal/mol	282 292@LB@ \| \|@LB@5'-CCG...UGGUA CUUCU...UGU-3'@LB@ CCCUCCUGU@LB@ \|\|\|:\|\|\|\|\|@LB@ GGGGGGACA@LB@3'-UUU...CUGAA CAUGU...GAA-5'@LB@ \| \|@LB@ 60 50@LB@@LB@@LB@Energy -7.28 kcal/mol@LB@Hybridization Energy -15.9842 kcal/mol@LB@Unfolding Energy - mRNA 0.606269 kcal/mol@LB@Unfolding Energy - sRNA 8.10291 kcal/mol@LB@@LB@Position - mRNA 283 -- 291@LB@Position - sRNA 51 -- 59@LB@Position Seed - mRNA 285 -- 291@LB@Position Seed - sRNA 51 -- 57@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@
77	0.02807	0.29	ct_309	N/A	-7.23	0.128520	50 -- 64	17 -- 33		_____________49________________65\n_____________\|_________________\|\n5'-AGA...GCUUA_________GU______UAAAU...UAA-3'\n______________AGGGGCUAU____UGGU\n______________\|\|::\|\|\|\|\|____\|\|\|:\n______________UCUUCGAUA____ACCG\n3'-UUU...CUCAG_________AGGU____CAAUC...GAA-5'\n_____________\|_________________\|\n_____________34________________16\n	52 -- 58	25 -- 31	-14.8286 kcal/mol	2.62564 kcal/mol	4.97804 kcal/mol	49 65@LB@ \| \|@LB@5'-AGA...GCUUA GU UAAAU...UAA-3'@LB@ AGGGGCUAU UGGU@LB@ \|\|::\|\|\|\|\| \|\|\|:@LB@ UCUUCGAUA ACCG@LB@3'-UUU...CUCAG AGGU CAAUC...GAA-5'@LB@ \| \|@LB@ 34 16@LB@@LB@@LB@Energy -7.23 kcal/mol@LB@Hybridization Energy -14.8286 kcal/mol@LB@Unfolding Energy - mRNA 2.62564 kcal/mol@LB@Unfolding Energy - sRNA 4.97804 kcal/mol@LB@@LB@Position - mRNA 50 -- 64@LB@Position - sRNA 17 -- 33@LB@Position Seed - mRNA 52 -- 58@LB@Position Seed - sRNA 25 -- 31@LB@
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@
23	0.006311	0.2093	ct_671	N/A	-7.19	0.130787	265 -- 279	17 -- 34		_____________264_________________280\n_____________\|___________________\|\n5'-CAA...ACGUA________________A__CUAGA...UCC-3'\n______________CAGAGGCU____CAUG_GC\n______________\|\|\|\|:\|\|\|____\|\|\|\|_\|\|\n______________GUCUUCGA____GUAC_CG\n3'-UUU...UCUCA________UAAG_______CAAUC...GAA-5'\n_____________\|___________________\|\n_____________35__________________16\n	266 -- 272	27 -- 33	-15.8996 kcal/mol	3.73088 kcal/mol	4.97809 kcal/mol	264 280@LB@ \| \|@LB@5'-CAA...ACGUA A CUAGA...UCC-3'@LB@ CAGAGGCU CAUG GC@LB@ \|\|\|\|:\|\|\| \|\|\|\| \|\|@LB@ GUCUUCGA GUAC CG@LB@3'-UUU...UCUCA UAAG CAAUC...GAA-5'@LB@ \| \|@LB@ 35 16@LB@@LB@@LB@Energy -7.19 kcal/mol@LB@Hybridization Energy -15.8996 kcal/mol@LB@Unfolding Energy - mRNA 3.73088 kcal/mol@LB@Unfolding Energy - sRNA 4.97809 kcal/mol@LB@@LB@Position - mRNA 265 -- 279@LB@Position - sRNA 17 -- 34@LB@Position Seed - mRNA 266 -- 272@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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usability assessment

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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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