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
93	0.03342	0.2954	ct_815	mrsA_2	-4.95	0.370159	203 -- 227	23 -- 45	phosphoglucosamine mutase	_____________202_______________________228\n_____________\|_________________________\|\n5'-UAC...GCAAU_____GU__U__G___C________GGAAC...AGG-3'\n______________GACAC__GA_GU_AGA_AGCUAUUC\n______________:\|\|\|\|__\|\|_\|\|_\|\|\|_\|\|\|\|\|\|\|\|\n______________UUGUG__CU_CA_UCU_UCGAUAAG\n3'-UUU...CAUGU_____AU_____G____________GUACC...GAA-5'\n_____________\|_________________________\|\n_____________46________________________22\n	221 -- 227	23 -- 29	-22.8159 kcal/mol	6.25755 kcal/mol	11.6121 kcal/mol	202 228@LB@ \| \|@LB@5'-UAC...GCAAU GU U G C GGAAC...AGG-3'@LB@ GACAC GA GU AGA AGCUAUUC@LB@ :\|\|\|\| \|\| \|\| \|\|\| \|\|\|\|\|\|\|\|@LB@ UUGUG CU CA UCU UCGAUAAG@LB@3'-UUU...CAUGU AU G GUACC...GAA-5'@LB@ \| \|@LB@ 46 22@LB@@LB@@LB@Energy -4.95 kcal/mol@LB@Hybridization Energy -22.8159 kcal/mol@LB@Unfolding Energy - mRNA 6.25755 kcal/mol@LB@Unfolding Energy - sRNA 11.6121 kcal/mol@LB@@LB@Position - mRNA 203 -- 227@LB@Position - sRNA 23 -- 45@LB@Position Seed - mRNA 221 -- 227@LB@Position Seed - sRNA 23 -- 29@LB@
108	0.04117	0.3134	ct_817	tyrP_1	-6.29	0.204127	20 -- 34	17 -- 30	tyrosine-specific transport protein	_____________19______________35\n_____________\|_______________\|\n5'-CGA...AUCAU____UACA_______UUUAC...UCC-3'\n______________GGCU____CCAUGGC\n______________:\|\|\|____\|\|\|\|\|\|\|\n______________UCGA____GGUACCG\n3'-UUU...AGUCU____UAA________CAAUC...GAA-5'\n_____________\|_______________\|\n_____________31______________16\n	28 -- 34	17 -- 23	-15.6862 kcal/mol	4.66372 kcal/mol	4.73426 kcal/mol	19 35@LB@ \| \|@LB@5'-CGA...AUCAU UACA UUUAC...UCC-3'@LB@ GGCU CCAUGGC@LB@ :\|\|\| \|\|\|\|\|\|\|@LB@ UCGA GGUACCG@LB@3'-UUU...AGUCU UAA CAAUC...GAA-5'@LB@ \| \|@LB@ 31 16@LB@@LB@@LB@Energy -6.29 kcal/mol@LB@Hybridization Energy -15.6862 kcal/mol@LB@Unfolding Energy - mRNA 4.66372 kcal/mol@LB@Unfolding Energy - sRNA 4.73426 kcal/mol@LB@@LB@Position - mRNA 20 -- 34@LB@Position - sRNA 17 -- 30@LB@Position Seed - mRNA 28 -- 34@LB@Position Seed - sRNA 17 -- 23@LB@
80	0.02888	0.29	ct_821	sucC	-7.97	0.087313	257 -- 264	53 -- 60	succinyl-CoA ligase subunit beta	_____________256______265\n_____________\|________\|\n5'-UCG...CCUAU________AUCAC...CAG-3'\n______________UCCCCCCU\n______________\|\|\|\|\|\|\|\|\n______________AGGGGGGA\n3'-UUU...ACUGA________CACAU...GAA-5'\n_____________\|________\|\n_____________61_______52\n	258 -- 264	53 -- 59	-16.0066 kcal/mol	1.58949 kcal/mol	6.45136 kcal/mol	256 265@LB@ \| \|@LB@5'-UCG...CCUAU AUCAC...CAG-3'@LB@ UCCCCCCU@LB@ \|\|\|\|\|\|\|\|@LB@ AGGGGGGA@LB@3'-UUU...ACUGA CACAU...GAA-5'@LB@ \| \|@LB@ 61 52@LB@@LB@@LB@Energy -7.97 kcal/mol@LB@Hybridization Energy -16.0066 kcal/mol@LB@Unfolding Energy - mRNA 1.58949 kcal/mol@LB@Unfolding Energy - sRNA 6.45136 kcal/mol@LB@@LB@Position - mRNA 257 -- 264@LB@Position - sRNA 53 -- 60@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 53 -- 59@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@
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@
120	0.04883	0.3262	ct_827	nrdA	-5.19	0.334730	7 -- 13	82 -- 88	ribonucleoside-diphosphate reductase subunit alpha	_____________6_______14\n_____________\|_______\|\n_____5'-UUCUAU_______AUACA...CUU-3'\n______________AUAUGGU\n______________\|\|\|:\|\|:\n______________UAUGCCG\n3'-UUU...GCCUC_______AUUGA...GAA-5'\n_____________\|_______\|\n_____________89______81\n	7 -- 13	82 -- 88	-6.89581 kcal/mol	0.608866 kcal/mol	1.09753 kcal/mol	6 14@LB@ \| \|@LB@ 5'-UUCUAU AUACA...CUU-3'@LB@ AUAUGGU@LB@ \|\|\|:\|\|:@LB@ UAUGCCG@LB@3'-UUU...GCCUC AUUGA...GAA-5'@LB@ \| \|@LB@ 89 81@LB@@LB@@LB@Energy -5.19 kcal/mol@LB@Hybridization Energy -6.89581 kcal/mol@LB@Unfolding Energy - mRNA 0.608866 kcal/mol@LB@Unfolding Energy - sRNA 1.09753 kcal/mol@LB@@LB@Position - mRNA 7 -- 13@LB@Position - sRNA 82 -- 88@LB@Position Seed - mRNA 7 -- 13@LB@Position Seed - sRNA 82 -- 88@LB@
180	0.07821	0.3571	ct_831	murB	-7.63	0.104376	230 -- 248	17 -- 33	UDP-N-acetylenolpyruvoylglucosamine reductase	_____________229_________________249\n_____________\|___________________\|\n5'-GUU...GUUCA____U_________UAA__CGCUU...UAA-3'\n______________AGAA_CUGUUCCAU___GC\n______________\|\|\|\|_\|\|:\|\|\|\|\|\|___\|\|\n______________UCUU_GAUAAGGUA___CG\n3'-UUU...CUCAG____C_________C____CAAUC...GAA-5'\n_____________\|___________________\|\n_____________34__________________16\n	237 -- 243	20 -- 26	-14.8604 kcal/mol	2.25495 kcal/mol	4.97804 kcal/mol	229 249@LB@ \| \|@LB@5'-GUU...GUUCA U UAA CGCUU...UAA-3'@LB@ AGAA CUGUUCCAU GC@LB@ \|\|\|\| \|\|:\|\|\|\|\|\| \|\|@LB@ UCUU GAUAAGGUA CG@LB@3'-UUU...CUCAG C C CAAUC...GAA-5'@LB@ \| \|@LB@ 34 16@LB@@LB@@LB@Energy -7.63 kcal/mol@LB@Hybridization Energy -14.8604 kcal/mol@LB@Unfolding Energy - mRNA 2.25495 kcal/mol@LB@Unfolding Energy - sRNA 4.97804 kcal/mol@LB@@LB@Position - mRNA 230 -- 248@LB@Position - sRNA 17 -- 33@LB@Position Seed - mRNA 237 -- 243@LB@Position Seed - sRNA 20 -- 26@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@
131	0.05291	0.3262	ct_842	pnp	-7.97	0.086989	198 -- 205	17 -- 24	polyribonucleotide nucleotidyltransferase	_____________197______206\n_____________\|________\|\n5'-UGA...ACAAC________UUUUG...UCA-3'\n______________UCCAUGGC\n______________\|\|\|\|\|\|\|\|\n______________AGGUACCG\n3'-UUU...CGAUA________CAAUC...GAA-5'\n_____________\|________\|\n_____________25_______16\n	199 -- 205	17 -- 23	-14.0999 kcal/mol	1.64992 kcal/mol	4.47615 kcal/mol	197 206@LB@ \| \|@LB@5'-UGA...ACAAC UUUUG...UCA-3'@LB@ UCCAUGGC@LB@ \|\|\|\|\|\|\|\|@LB@ AGGUACCG@LB@3'-UUU...CGAUA CAAUC...GAA-5'@LB@ \| \|@LB@ 25 16@LB@@LB@@LB@Energy -7.97 kcal/mol@LB@Hybridization Energy -14.0999 kcal/mol@LB@Unfolding Energy - mRNA 1.64992 kcal/mol@LB@Unfolding Energy - sRNA 4.47615 kcal/mol@LB@@LB@Position - mRNA 198 -- 205@LB@Position - sRNA 17 -- 24@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 17 -- 23@LB@
17	0.003987	0.1836	ct_843	rs15	-6.01	0.232273	282 -- 295	22 -- 34	30S ribosomal protein S15	_____________281____________296\n_____________\|______________\|\n5'-AGG...AUGUG____UU________GACUG-3'\n______________CAGA__GCUAUUCU\n______________\|\|\|\|__\|\|\|\|\|\|\|:\n______________GUCU__CGAUAAGG\n3'-UUU...UCUCA____U_________UACCG...GAA-5'\n_____________\|______________\|\n_____________35_____________21\n	288 -- 294	23 -- 29	-14.3687 kcal/mol	3.62939 kcal/mol	4.72608 kcal/mol	281 296@LB@ \| \|@LB@5'-AGG...AUGUG UU GACUG-3'@LB@ CAGA GCUAUUCU@LB@ \|\|\|\| \|\|\|\|\|\|\|:@LB@ GUCU CGAUAAGG@LB@3'-UUU...UCUCA U UACCG...GAA-5'@LB@ \| \|@LB@ 35 21@LB@@LB@@LB@Energy -6.01 kcal/mol@LB@Hybridization Energy -14.3687 kcal/mol@LB@Unfolding Energy - mRNA 3.62939 kcal/mol@LB@Unfolding Energy - sRNA 4.72608 kcal/mol@LB@@LB@Position - mRNA 282 -- 295@LB@Position - sRNA 22 -- 34@LB@Position Seed - mRNA 288 -- 294@LB@Position Seed - sRNA 23 -- 29@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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