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
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@
22	0.005311	0.1984	ct_111	groES	-5.40	0.305537	269 -- 283	17 -- 33	co-chaperonin GroES	_____________268_______________284\n_____________\|_________________\|\n5'-AGC...GAAGA_____________CU__AAGAG...UUC-3'\n______________AGAAGCU__UCCA__GC\n______________\|\|\|\|\|\|\|__\|\|\|\|__\|\|\n______________UCUUCGA__AGGU__CG\n3'-UUU...CUCAG_______UA____AC__CAAUC...GAA-5'\n_____________\|_________________\|\n_____________34________________16\n	269 -- 275	27 -- 33	-15.094 kcal/mol	4.71335 kcal/mol	4.97804 kcal/mol	268 284@LB@ \| \|@LB@5'-AGC...GAAGA CU AAGAG...UUC-3'@LB@ AGAAGCU UCCA GC@LB@ \|\|\|\|\|\|\| \|\|\|\| \|\|@LB@ UCUUCGA AGGU CG@LB@3'-UUU...CUCAG UA AC CAAUC...GAA-5'@LB@ \| \|@LB@ 34 16@LB@@LB@@LB@Energy -5.40 kcal/mol@LB@Hybridization Energy -15.094 kcal/mol@LB@Unfolding Energy - mRNA 4.71335 kcal/mol@LB@Unfolding Energy - sRNA 4.97804 kcal/mol@LB@@LB@Position - mRNA 269 -- 283@LB@Position - sRNA 17 -- 33@LB@Position Seed - mRNA 269 -- 275@LB@Position Seed - sRNA 27 -- 33@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@
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@
25	0.00654	0.2093	ct_672	N/A	-9.75	0.032384	176 -- 205	17 -- 33	type III secretion system protein	_____________175____________________________206\n_____________\|______________________________\|\n5'-AUC...GUAGA_______CAUAUAUAAGGU___C_______AGUUG...CUG-3'\n______________AGAAGCU____________AUU_CCAUGGC\n______________\|\|\|\|\|\|\|____________\|\|\|_\|\|\|\|\|\|\|\n______________UCUUCGA____________UAA_GGUACCG\n3'-UUU...CUCAG______________________________CAAUC...GAA-5'\n_____________\|______________________________\|\n_____________34_____________________________16\n	199 -- 205	17 -- 23	-19.3096 kcal/mol	4.57941 kcal/mol	4.97804 kcal/mol	175 206@LB@ \| \|@LB@5'-AUC...GUAGA CAUAUAUAAGGU C AGUUG...CUG-3'@LB@ AGAAGCU AUU CCAUGGC@LB@ \|\|\|\|\|\|\| \|\|\| \|\|\|\|\|\|\|@LB@ UCUUCGA UAA GGUACCG@LB@3'-UUU...CUCAG CAAUC...GAA-5'@LB@ \| \|@LB@ 34 16@LB@@LB@@LB@Energy -9.75 kcal/mol@LB@Hybridization Energy -19.3096 kcal/mol@LB@Unfolding Energy - mRNA 4.57941 kcal/mol@LB@Unfolding Energy - sRNA 4.97804 kcal/mol@LB@@LB@Position - mRNA 176 -- 205@LB@Position - sRNA 17 -- 33@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 17 -- 23@LB@
26	0.006621	0.2093	ct_267	ihfA	-8.59	0.062448	193 -- 205	17 -- 31	DNA-binding protein HU	_____________192_____________206\n_____________\|_______________\|\n5'-UAA...GCAAC_______________AACGA...AUA-3'\n______________AAGCUA__CCAUGGC\n______________\|\|\|\|\|\|__\|\|\|\|\|\|\|\n______________UUCGAU__GGUACCG\n3'-UUU...CAGUC______AA_______CAAUC...GAA-5'\n_____________\|_______________\|\n_____________32______________16\n	199 -- 205	17 -- 23	-17.4173 kcal/mol	3.97125 kcal/mol	4.86101 kcal/mol	192 206@LB@ \| \|@LB@5'-UAA...GCAAC AACGA...AUA-3'@LB@ AAGCUA CCAUGGC@LB@ \|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ UUCGAU GGUACCG@LB@3'-UUU...CAGUC AA CAAUC...GAA-5'@LB@ \| \|@LB@ 32 16@LB@@LB@@LB@Energy -8.59 kcal/mol@LB@Hybridization Energy -17.4173 kcal/mol@LB@Unfolding Energy - mRNA 3.97125 kcal/mol@LB@Unfolding Energy - sRNA 4.86101 kcal/mol@LB@@LB@Position - mRNA 193 -- 205@LB@Position - sRNA 17 -- 31@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 17 -- 23@LB@
27	0.007389	0.2199	ct_855	fumC	-7.16	0.132975	201 -- 207	82 -- 88	fumarate hydratase	_____________200_____208\n_____________\|_______\|\n5'-AUA...AGCAU_______AAGAG...GUA-3'\n______________AUGCGGC\n______________\|\|:\|\|\|\|\n______________UAUGCCG\n3'-UUU...GCCUC_______AUUGA...GAA-5'\n_____________\|_______\|\n_____________89______81\n	201 -- 207	82 -- 88	-10.3037 kcal/mol	2.04792 kcal/mol	1.09753 kcal/mol	200 208@LB@ \| \|@LB@5'-AUA...AGCAU AAGAG...GUA-3'@LB@ AUGCGGC@LB@ \|\|:\|\|\|\|@LB@ UAUGCCG@LB@3'-UUU...GCCUC AUUGA...GAA-5'@LB@ \| \|@LB@ 89 81@LB@@LB@@LB@Energy -7.16 kcal/mol@LB@Hybridization Energy -10.3037 kcal/mol@LB@Unfolding Energy - mRNA 2.04792 kcal/mol@LB@Unfolding Energy - sRNA 1.09753 kcal/mol@LB@@LB@Position - mRNA 201 -- 207@LB@Position - sRNA 82 -- 88@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 82 -- 88@LB@
28	0.007489	0.2199	ct_755	groEL_3	-5.45	0.299165	283 -- 296	17 -- 33	chaperonin GroEL	_____________282_______________297\n_____________\|_________________\|\n5'-CAC...AGUAA_________________CCCG-3'\n______________AGGGGU___UUUAUGGC\n______________\|\|::\|:___\|::\|\|\|\|\|\n______________UCUUCG___AGGUACCG\n3'-UUU...CUCAG______AUA________CAAUC...GAA-5'\n_____________\|_________________\|\n_____________34________________16\n	290 -- 296	17 -- 23	-13.7025 kcal/mol	3.27337 kcal/mol	4.97804 kcal/mol	282 297@LB@ \| \|@LB@5'-CAC...AGUAA CCCG-3'@LB@ AGGGGU UUUAUGGC@LB@ \|\|::\|: \|::\|\|\|\|\|@LB@ UCUUCG AGGUACCG@LB@3'-UUU...CUCAG AUA CAAUC...GAA-5'@LB@ \| \|@LB@ 34 16@LB@@LB@@LB@Energy -5.45 kcal/mol@LB@Hybridization Energy -13.7025 kcal/mol@LB@Unfolding Energy - mRNA 3.27337 kcal/mol@LB@Unfolding Energy - sRNA 4.97804 kcal/mol@LB@@LB@Position - mRNA 283 -- 296@LB@Position - sRNA 17 -- 33@LB@Position Seed - mRNA 290 -- 296@LB@Position Seed - sRNA 17 -- 23@LB@
29	0.008327	0.236	ct_722	pgm	-9.49	0.037543	218 -- 230	17 -- 29	2 3-bisphosphoglycerate-dependent phosphoglycerate mutase	_____________217___________231\n_____________\|_____________\|\n5'-CUU...AUCUU____CG_______CAAUC...UUC-3'\n______________GCUA__CCAUGGC\n______________\|\|\|\|__\|\|\|\|\|\|\|\n______________CGAU__GGUACCG\n3'-UUU...GUCUU____AA_______CAAUC...GAA-5'\n_____________\|_____________\|\n_____________30____________16\n	224 -- 230	17 -- 23	-17.8075 kcal/mol	3.64492 kcal/mol	4.66832 kcal/mol	217 231@LB@ \| \|@LB@5'-CUU...AUCUU CG CAAUC...UUC-3'@LB@ GCUA CCAUGGC@LB@ \|\|\|\| \|\|\|\|\|\|\|@LB@ CGAU GGUACCG@LB@3'-UUU...GUCUU AA CAAUC...GAA-5'@LB@ \| \|@LB@ 30 16@LB@@LB@@LB@Energy -9.49 kcal/mol@LB@Hybridization Energy -17.8075 kcal/mol@LB@Unfolding Energy - mRNA 3.64492 kcal/mol@LB@Unfolding Energy - sRNA 4.66832 kcal/mol@LB@@LB@Position - mRNA 218 -- 230@LB@Position - sRNA 17 -- 29@LB@Position Seed - mRNA 224 -- 230@LB@Position Seed - sRNA 17 -- 23@LB@
30	0.009028	0.2474	ct_455	murA	-8.03	0.084305	255 -- 264	26 -- 35	UDP-N-acetylglucosamine 1-carboxyvinyltransferase	_____________254________265\n_____________\|__________\|\n5'-AAA...GCGUG__________AAAAU...UAC-3'\n______________UCAGGAGCUA\n______________\|\|\|\|:\|\|\|\|\|\n______________AGUCUUCGAU\n3'-UUU...AUCUC__________AAGGU...GAA-5'\n_____________\|__________\|\n_____________36_________25\n	258 -- 264	26 -- 32	-13.9898 kcal/mol	1.25877 kcal/mol	4.69985 kcal/mol	254 265@LB@ \| \|@LB@5'-AAA...GCGUG AAAAU...UAC-3'@LB@ UCAGGAGCUA@LB@ \|\|\|\|:\|\|\|\|\|@LB@ AGUCUUCGAU@LB@3'-UUU...AUCUC AAGGU...GAA-5'@LB@ \| \|@LB@ 36 25@LB@@LB@@LB@Energy -8.03 kcal/mol@LB@Hybridization Energy -13.9898 kcal/mol@LB@Unfolding Energy - mRNA 1.25877 kcal/mol@LB@Unfolding Energy - sRNA 4.69985 kcal/mol@LB@@LB@Position - mRNA 255 -- 264@LB@Position - sRNA 26 -- 35@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 26 -- 32@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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