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
34	0.01043	0.2518	ct_642	N/A	-9.37	0.040224	239 -- 246	53 -- 60		_____________238______247\n_____________\|________\|\n5'-AGG...UCUUC________CUUCG...CUG-3'\n______________UCCCCCCU\n______________\|\|\|\|\|\|\|\|\n______________AGGGGGGA\n3'-UUU...ACUGA________CACAU...GAA-5'\n_____________\|________\|\n_____________61_______52\n	240 -- 246	53 -- 59	-15.9954 kcal/mol	0.170944 kcal/mol	6.45136 kcal/mol	238 247@LB@ \| \|@LB@5'-AGG...UCUUC CUUCG...CUG-3'@LB@ UCCCCCCU@LB@ \|\|\|\|\|\|\|\|@LB@ AGGGGGGA@LB@3'-UUU...ACUGA CACAU...GAA-5'@LB@ \| \|@LB@ 61 52@LB@@LB@@LB@Energy -9.37 kcal/mol@LB@Hybridization Energy -15.9954 kcal/mol@LB@Unfolding Energy - mRNA 0.170944 kcal/mol@LB@Unfolding Energy - sRNA 6.45136 kcal/mol@LB@@LB@Position - mRNA 239 -- 246@LB@Position - sRNA 53 -- 60@LB@Position Seed - mRNA 240 -- 246@LB@Position Seed - sRNA 53 -- 59@LB@
72	0.02709	0.29	ct_530	fmt	-6.32	0.201483	239 -- 246	80 -- 87	methionyl-tRNA formyltransferase	_____________238______247\n_____________\|________\|\n5'-UAA...CAAUU________CUGUU...CGC-3'\n______________UGCGGCUA\n______________\|:\|\|\|\|\|\|\n______________AUGCCGAU\n3'-UUU...CCUCU________UGAGG...GAA-5'\n_____________\|________\|\n_____________88_______79\n	240 -- 246	80 -- 86	-12.3749 kcal/mol	4.96164 kcal/mol	1.09752 kcal/mol	238 247@LB@ \| \|@LB@5'-UAA...CAAUU CUGUU...CGC-3'@LB@ UGCGGCUA@LB@ \|:\|\|\|\|\|\|@LB@ AUGCCGAU@LB@3'-UUU...CCUCU UGAGG...GAA-5'@LB@ \| \|@LB@ 88 79@LB@@LB@@LB@Energy -6.32 kcal/mol@LB@Hybridization Energy -12.3749 kcal/mol@LB@Unfolding Energy - mRNA 4.96164 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 239 -- 246@LB@Position - sRNA 80 -- 87@LB@Position Seed - mRNA 240 -- 246@LB@Position Seed - sRNA 80 -- 86@LB@
53	0.01942	0.29	ct_580	N/A	-10.14	0.025883	244 -- 280	22 -- 57	S-adenosylmethionine/S-adenosylhomocysteine transporter	_____________243___________________________________281\n_____________\|_____________________________________\|\n5'-GUU...ACAAA___G_____U_____C___UU__GACAU_________CUUAA...CUU-3'\n______________CCU_UGUGU_UAAAC_CUG__GU_____GGCUAUUUU\n______________\|\|:_\|\|\|\|\|_:\|\|\|\|_\|\|:__\|\|_____:\|\|\|\|\|\|::\n______________GGG_ACACA_GUUUG_GAU__CA_____UCGAUAAGG\n3'-UUU...GAAGG___G_____U_____U___CU__GUCU__________UACCG...GAA-5'\n_____________\|_____________________________________\|\n_____________58____________________________________21\n	273 -- 279	23 -- 29	-28.6785 kcal/mol	5.85369 kcal/mol	12.6861 kcal/mol	243 281@LB@ \| \|@LB@5'-GUU...ACAAA G U C UU GACAU CUUAA...CUU-3'@LB@ CCU UGUGU UAAAC CUG GU GGCUAUUUU@LB@ \|\|: \|\|\|\|\| :\|\|\|\| \|\|: \|\| :\|\|\|\|\|\|::@LB@ GGG ACACA GUUUG GAU CA UCGAUAAGG@LB@3'-UUU...GAAGG G U U CU GUCU UACCG...GAA-5'@LB@ \| \|@LB@ 58 21@LB@@LB@@LB@Energy -10.14 kcal/mol@LB@Hybridization Energy -28.6785 kcal/mol@LB@Unfolding Energy - mRNA 5.85369 kcal/mol@LB@Unfolding Energy - sRNA 12.6861 kcal/mol@LB@@LB@Position - mRNA 244 -- 280@LB@Position - sRNA 22 -- 57@LB@Position Seed - mRNA 273 -- 279@LB@Position Seed - sRNA 23 -- 29@LB@
167	0.06963	0.3427	ct_724	N/A	-5.10	0.346834	244 -- 255	24 -- 35		_____________243__________256\n_____________\|____________\|\n5'-ACC...GUUAU____________GUCGC...GAC-3'\n______________UCGGGGGUUAUU\n______________\|\|:\|::\|:\|\|\|\|\n______________AGUCUUCGAUAA\n3'-UUU...AUCUC____________GGUAC...GAA-5'\n_____________\|____________\|\n_____________36___________23\n	245 -- 251	28 -- 34	-12.4512 kcal/mol	2.62645 kcal/mol	4.72035 kcal/mol	243 256@LB@ \| \|@LB@5'-ACC...GUUAU GUCGC...GAC-3'@LB@ UCGGGGGUUAUU@LB@ \|\|:\|::\|:\|\|\|\|@LB@ AGUCUUCGAUAA@LB@3'-UUU...AUCUC GGUAC...GAA-5'@LB@ \| \|@LB@ 36 23@LB@@LB@@LB@Energy -5.10 kcal/mol@LB@Hybridization Energy -12.4512 kcal/mol@LB@Unfolding Energy - mRNA 2.62645 kcal/mol@LB@Unfolding Energy - sRNA 4.72035 kcal/mol@LB@@LB@Position - mRNA 244 -- 255@LB@Position - sRNA 24 -- 35@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 28 -- 34@LB@
190	0.08414	0.363	ct_503	N/A	-6.17	0.215667	244 -- 250	81 -- 87		_____________243_____251\n_____________\|_______\|\n5'-UGG...UUUGU_______UCGCA...CUC-3'\n______________UACGGUU\n______________\|\|\|\|\|:\|\n______________AUGCCGA\n3'-UUU...CCUCU_______UUGAG...GAA-5'\n_____________\|_______\|\n_____________88______80\n	244 -- 250	81 -- 87	-7.94334 kcal/mol	0.67364 kcal/mol	1.09752 kcal/mol	243 251@LB@ \| \|@LB@5'-UGG...UUUGU UCGCA...CUC-3'@LB@ UACGGUU@LB@ \|\|\|\|\|:\|@LB@ AUGCCGA@LB@3'-UUU...CCUCU UUGAG...GAA-5'@LB@ \| \|@LB@ 88 80@LB@@LB@@LB@Energy -6.17 kcal/mol@LB@Hybridization Energy -7.94334 kcal/mol@LB@Unfolding Energy - mRNA 0.67364 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 244 -- 250@LB@Position - sRNA 81 -- 87@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 81 -- 87@LB@
157	0.06639	0.3424	ct_213	rpiA	-7.48	0.112460	245 -- 274	28 -- 57	ribose-5-phosphate isomerase A	_____________244____________________________275\n_____________\|______________________________\|\n5'-GAA...UUUUU____AUCAA_____A_____C_C_______AGUAG...UGU-3'\n______________CCCU_____GCAGA_ACUAG_G_UAGAGGC\n______________\|\|\|:_____:\|\|:\|_\|\|\|\|\|_\|_:\|\|\|:\|\|\n______________GGGG_____UGUUU_UGAUC_C_GUCUUCG\n3'-UUU...GAAGG____ACACA_____G_____U_A_______AUAAG...GAA-5'\n_____________\|______________________________\|\n_____________58_____________________________27\n	268 -- 274	28 -- 34	-25.4315 kcal/mol	5.87242 kcal/mol	12.0748 kcal/mol	244 275@LB@ \| \|@LB@5'-GAA...UUUUU AUCAA A C C AGUAG...UGU-3'@LB@ CCCU GCAGA ACUAG G UAGAGGC@LB@ \|\|\|: :\|\|:\| \|\|\|\|\| \| :\|\|\|:\|\|@LB@ GGGG UGUUU UGAUC C GUCUUCG@LB@3'-UUU...GAAGG ACACA G U A AUAAG...GAA-5'@LB@ \| \|@LB@ 58 27@LB@@LB@@LB@Energy -7.48 kcal/mol@LB@Hybridization Energy -25.4315 kcal/mol@LB@Unfolding Energy - mRNA 5.87242 kcal/mol@LB@Unfolding Energy - sRNA 12.0748 kcal/mol@LB@@LB@Position - mRNA 245 -- 274@LB@Position - sRNA 28 -- 57@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 28 -- 34@LB@
169	0.07086	0.3447	ct_615	sigA	-4.07	0.514760	248 -- 272	10 -- 33	RNA polymerase sigma factor	_____________247________________________273\n_____________\|__________________________\|\n5'-GGU...CAAGA_____AAA_____AAGAAA_______GAGUU...AAG-3'\n______________AGAAG____UCCA______GUUAGAA\n______________\|\|\|\|\|____\|\|\|\|______\|\|\|\|\|\|\|\n______________UCUUC____AGGU______CAAUCUU\n3'-UUU...CUCAG_____GAUA____ACCG_________AUGGU...GAA-5'\n_____________\|__________________________\|\n_____________34_________________________9\n	266 -- 272	10 -- 16	-15.5151 kcal/mol	2.85327 kcal/mol	8.5898 kcal/mol	247 273@LB@ \| \|@LB@5'-GGU...CAAGA AAA AAGAAA GAGUU...AAG-3'@LB@ AGAAG UCCA GUUAGAA@LB@ \|\|\|\|\| \|\|\|\| \|\|\|\|\|\|\|@LB@ UCUUC AGGU CAAUCUU@LB@3'-UUU...CUCAG GAUA ACCG AUGGU...GAA-5'@LB@ \| \|@LB@ 34 9@LB@@LB@@LB@Energy -4.07 kcal/mol@LB@Hybridization Energy -15.5151 kcal/mol@LB@Unfolding Energy - mRNA 2.85327 kcal/mol@LB@Unfolding Energy - sRNA 8.5898 kcal/mol@LB@@LB@Position - mRNA 248 -- 272@LB@Position - sRNA 10 -- 33@LB@Position Seed - mRNA 266 -- 272@LB@Position Seed - sRNA 10 -- 16@LB@
102	0.03801	0.3036	ct_001	N/A	-7.82	0.094515	254 -- 277	28 -- 49		_____________253______________________278\n_____________\|________________________\|\n5'-CUU...GGAGC_____________AUU________AACAG...UAC-3'\n______________UAUAAACACUGGA___UUAGGAGU\n______________\|\|:\|\|\|\|\|\|\|:\|\|___\|:\|\|:\|\|:\n______________AUGUUUGUGAUCU___AGUCUUCG\n3'-UUU...GACAC_____________C__________AUAAG...GAA-5'\n_____________\|________________________\|\n_____________50_______________________27\n	271 -- 277	28 -- 34	-23.2003 kcal/mol	3.96195 kcal/mol	11.4222 kcal/mol	253 278@LB@ \| \|@LB@5'-CUU...GGAGC AUU AACAG...UAC-3'@LB@ UAUAAACACUGGA UUAGGAGU@LB@ \|\|:\|\|\|\|\|\|\|:\|\| \|:\|\|:\|\|:@LB@ AUGUUUGUGAUCU AGUCUUCG@LB@3'-UUU...GACAC C AUAAG...GAA-5'@LB@ \| \|@LB@ 50 27@LB@@LB@@LB@Energy -7.82 kcal/mol@LB@Hybridization Energy -23.2003 kcal/mol@LB@Unfolding Energy - mRNA 3.96195 kcal/mol@LB@Unfolding Energy - sRNA 11.4222 kcal/mol@LB@@LB@Position - mRNA 254 -- 277@LB@Position - sRNA 28 -- 49@LB@Position Seed - mRNA 271 -- 277@LB@Position Seed - sRNA 28 -- 34@LB@
123	0.04914	0.3262	ct_754	icc	-7.18	0.131374	254 -- 264	47 -- 57		_____________253_________265\n_____________\|___________\|\n5'-AUU...AUUCA___________UCCCU...GCU-3'\n______________CUUCUGUGUAC\n______________\|::\|\|\|\|\|\|\|\|\n______________GGGGACACAUG\n3'-UUU...GAAGG___________UUUGU...GAA-5'\n_____________\|___________\|\n_____________58__________46\n	258 -- 264	47 -- 53	-16.923 kcal/mol	2.45356 kcal/mol	7.2877 kcal/mol	253 265@LB@ \| \|@LB@5'-AUU...AUUCA UCCCU...GCU-3'@LB@ CUUCUGUGUAC@LB@ \|::\|\|\|\|\|\|\|\|@LB@ GGGGACACAUG@LB@3'-UUU...GAAGG UUUGU...GAA-5'@LB@ \| \|@LB@ 58 46@LB@@LB@@LB@Energy -7.18 kcal/mol@LB@Hybridization Energy -16.923 kcal/mol@LB@Unfolding Energy - mRNA 2.45356 kcal/mol@LB@Unfolding Energy - sRNA 7.2877 kcal/mol@LB@@LB@Position - mRNA 254 -- 264@LB@Position - sRNA 47 -- 57@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 47 -- 53@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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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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