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
62	0.02417	0.29	ct_705	clpX	-8.32	0.072096	259 -- 275	17 -- 33	ATP-dependent Clp protease ATP-binding subunit ClpX	_____________258_______________276\n_____________\|_________________\|\n5'-CUG...UGUUG________A__GC____CCAUC...AUU-3'\n______________AGAAGCUA_UC__UGGU\n______________\|\|\|\|\|\|\|\|_\|\|__\|\|\|:\n______________UCUUCGAU_AG__ACCG\n3'-UUU...CUCAG________A__GU____CAAUC...GAA-5'\n_____________\|_________________\|\n_____________34________________16\n	260 -- 266	26 -- 32	-18.4351 kcal/mol	5.13531 kcal/mol	4.97804 kcal/mol	258 276@LB@ \| \|@LB@5'-CUG...UGUUG A GC CCAUC...AUU-3'@LB@ AGAAGCUA UC UGGU@LB@ \|\|\|\|\|\|\|\| \|\| \|\|\|:@LB@ UCUUCGAU AG ACCG@LB@3'-UUU...CUCAG A GU CAAUC...GAA-5'@LB@ \| \|@LB@ 34 16@LB@@LB@@LB@Energy -8.32 kcal/mol@LB@Hybridization Energy -18.4351 kcal/mol@LB@Unfolding Energy - mRNA 5.13531 kcal/mol@LB@Unfolding Energy - sRNA 4.97804 kcal/mol@LB@@LB@Position - mRNA 259 -- 275@LB@Position - sRNA 17 -- 33@LB@Position Seed - mRNA 260 -- 266@LB@Position Seed - sRNA 26 -- 32@LB@
119	0.04857	0.3262	ct_706	clpP_2	-8.60	0.061801	14 -- 27	22 -- 35	ATP-dependent Clp protease proteolytic subunit	_____________13_____________28\n_____________\|______________\|\n5'-CGA...AAGAU______________UUCUU...GGC-3'\n______________UUAGAGGUUGUUCC\n______________\|:\|\|\|:\|:\|:\|\|\|\|\n______________AGUCUUCGAUAAGG\n3'-UUU...AUCUC______________UACCG...GAA-5'\n_____________\|______________\|\n_____________36_____________21\n	16 -- 22	27 -- 33	-17.9181 kcal/mol	4.58788 kcal/mol	4.72627 kcal/mol	13 28@LB@ \| \|@LB@5'-CGA...AAGAU UUCUU...GGC-3'@LB@ UUAGAGGUUGUUCC@LB@ \|:\|\|\|:\|:\|:\|\|\|\|@LB@ AGUCUUCGAUAAGG@LB@3'-UUU...AUCUC UACCG...GAA-5'@LB@ \| \|@LB@ 36 21@LB@@LB@@LB@Energy -8.60 kcal/mol@LB@Hybridization Energy -17.9181 kcal/mol@LB@Unfolding Energy - mRNA 4.58788 kcal/mol@LB@Unfolding Energy - sRNA 4.72627 kcal/mol@LB@@LB@Position - mRNA 14 -- 27@LB@Position - sRNA 22 -- 35@LB@Position Seed - mRNA 16 -- 22@LB@Position Seed - sRNA 27 -- 33@LB@
71	0.027	0.29	ct_712	N/A	-6.32	0.201489	257 -- 263	81 -- 87	type III secretion system effector protein	_____________256_____264\n_____________\|_______\|\n5'-CAG...GAGAC_______CCUCG...CAG-3'\n______________UGCGGCU\n______________\|:\|\|\|\|\|\n______________AUGCCGA\n3'-UUU...CCUCU_______UUGAG...GAA-5'\n_____________\|_______\|\n_____________88______80\n	257 -- 263	81 -- 87	-10.8048 kcal/mol	3.3916 kcal/mol	1.09752 kcal/mol	256 264@LB@ \| \|@LB@5'-CAG...GAGAC CCUCG...CAG-3'@LB@ UGCGGCU@LB@ \|:\|\|\|\|\|@LB@ AUGCCGA@LB@3'-UUU...CCUCU UUGAG...GAA-5'@LB@ \| \|@LB@ 88 80@LB@@LB@@LB@Energy -6.32 kcal/mol@LB@Hybridization Energy -10.8048 kcal/mol@LB@Unfolding Energy - mRNA 3.3916 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 257 -- 263@LB@Position - sRNA 81 -- 87@LB@Position Seed - mRNA 257 -- 263@LB@Position Seed - sRNA 81 -- 87@LB@
164	0.06834	0.3424	ct_716	N/A	-9.26	0.042990	10 -- 57	2 -- 60		_____________9____________________________________________________________58\n_____________\|____________________________________________________________\|\n5'-UCA...GAGCU________UACU_____GC_________U_________GAUAUCAU______________AGGAG...UAG-3'\n______________UCUCUCCU_____CAAA__CUA___UCA_GAAGCUAUU________________CCAACU\n______________\|\|:\|:\|\|\|_____\|\|\|\|__\|\|\|___\|\|\|_\|\|\|\|\|\|\|\|\|________________\|\|\|\|\|\|\n______________AGGGGGGA_____GUUU__GAU___AGU_CUUCGAUAA________________GGUUGA\n3'-UUU...ACUGA________CACAU____GU___CUC_____________GGUACCGCAAUCUUAU______A-5'\n_____________\|____________________________________________________________\|\n_____________61___________________________________________________________1\n	37 -- 43	24 -- 30	-32.8059 kcal/mol	5.03112 kcal/mol	18.5194 kcal/mol	9 58@LB@ \| \|@LB@5'-UCA...GAGCU UACU GC U GAUAUCAU AGGAG...UAG-3'@LB@ UCUCUCCU CAAA CUA UCA GAAGCUAUU CCAACU@LB@ \|\|:\|:\|\|\| \|\|\|\| \|\|\| \|\|\| \|\|\|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ AGGGGGGA GUUU GAU AGU CUUCGAUAA GGUUGA@LB@3'-UUU...ACUGA CACAU GU CUC GGUACCGCAAUCUUAU A-5'@LB@ \| \|@LB@ 61 1@LB@@LB@@LB@Energy -9.26 kcal/mol@LB@Hybridization Energy -32.8059 kcal/mol@LB@Unfolding Energy - mRNA 5.03112 kcal/mol@LB@Unfolding Energy - sRNA 18.5194 kcal/mol@LB@@LB@Position - mRNA 10 -- 57@LB@Position - sRNA 2 -- 60@LB@Position Seed - mRNA 37 -- 43@LB@Position Seed - sRNA 24 -- 30@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@
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@
84	0.03042	0.29	ct_726	N/A	-6.32	0.200732	30 -- 36	81 -- 87	cell division protein	_____________29______37\n_____________\|_______\|\n5'-AGG...CCCCC_______UGCUG...AUC-3'\n______________UAUGGCU\n______________\|\|:\|\|\|\|\n______________AUGCCGA\n3'-UUU...CCUCU_______UUGAG...GAA-5'\n_____________\|_______\|\n_____________88______80\n	30 -- 36	81 -- 87	-8.84564 kcal/mol	1.42457 kcal/mol	1.09752 kcal/mol	29 37@LB@ \| \|@LB@5'-AGG...CCCCC UGCUG...AUC-3'@LB@ UAUGGCU@LB@ \|\|:\|\|\|\|@LB@ AUGCCGA@LB@3'-UUU...CCUCU UUGAG...GAA-5'@LB@ \| \|@LB@ 88 80@LB@@LB@@LB@Energy -6.32 kcal/mol@LB@Hybridization Energy -8.84564 kcal/mol@LB@Unfolding Energy - mRNA 1.42457 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 30 -- 36@LB@Position - sRNA 81 -- 87@LB@Position Seed - mRNA 30 -- 36@LB@Position Seed - sRNA 81 -- 87@LB@
153	0.06453	0.3424	ct_729	serS	-6.28	0.205305	1 -- 23	3 -- 33	serine--tRNA ligase	______________1______________________________24\n______________\|______________________________\|\n___________5'-____C_G_____U__________________CCUCA...UGG-3'\n______________AGAA_C_AUUCC_UG________AUGCCAAC\n______________\|\|\|\|_\|_\|\|\|\|\|_\|\|________\|\|:\|\|\|\|\|\n______________UCUU_G_UAAGG_AC________UAUGGUUG\n3'-UUU...CUCAG____C_A_____U__CGCAAUCU________AA-5'\n_____________\|_______________________________\|\n_____________34______________________________2\n	17 -- 23	3 -- 9	-16.9997 kcal/mol	2.1318 kcal/mol	8.59196 kcal/mol	1 24@LB@ \| \|@LB@ 5'- C G U CCUCA...UGG-3'@LB@ AGAA C AUUCC UG AUGCCAAC@LB@ \|\|\|\| \| \|\|\|\|\| \|\| \|\|:\|\|\|\|\|@LB@ UCUU G UAAGG AC UAUGGUUG@LB@3'-UUU...CUCAG C A U CGCAAUCU AA-5'@LB@ \| \|@LB@ 34 2@LB@@LB@@LB@Energy -6.28 kcal/mol@LB@Hybridization Energy -16.9997 kcal/mol@LB@Unfolding Energy - mRNA 2.1318 kcal/mol@LB@Unfolding Energy - sRNA 8.59196 kcal/mol@LB@@LB@Position - mRNA 1 -- 23@LB@Position - sRNA 3 -- 33@LB@Position Seed - mRNA 17 -- 23@LB@Position Seed - sRNA 3 -- 9@LB@
49	0.01821	0.29	ct_733	N/A	-8.44	0.067485	96 -- 102	80 -- 86		_____________95______103\n_____________\|_______\|\n5'-AUG...UGCCA_______UUGAU...CUA-3'\n______________GCGGCUA\n______________:\|\|\|\|\|\|\n______________UGCCGAU\n3'-UUU...CUCUA_______UGAGG...GAA-5'\n_____________\|_______\|\n_____________87______79\n	96 -- 102	80 -- 86	-11.4095 kcal/mol	1.90152 kcal/mol	1.06449 kcal/mol	95 103@LB@ \| \|@LB@5'-AUG...UGCCA UUGAU...CUA-3'@LB@ GCGGCUA@LB@ :\|\|\|\|\|\|@LB@ UGCCGAU@LB@3'-UUU...CUCUA UGAGG...GAA-5'@LB@ \| \|@LB@ 87 79@LB@@LB@@LB@Energy -8.44 kcal/mol@LB@Hybridization Energy -11.4095 kcal/mol@LB@Unfolding Energy - mRNA 1.90152 kcal/mol@LB@Unfolding Energy - sRNA 1.06449 kcal/mol@LB@@LB@Position - mRNA 96 -- 102@LB@Position - sRNA 80 -- 86@LB@Position Seed - mRNA 96 -- 102@LB@Position Seed - sRNA 80 -- 86@LB@
175	0.07342	0.3448	ct_738	yycJ	-7.78	0.096435	160 -- 204	18 -- 50	Zn-dependent hydrolase	_____________159____________________________________________205\n_____________\|______________________________________________\|\n5'-CAU...ACCGC_____________UCCAAUUAUCAAA______C_A___A_______AAGGU...AAC-3'\n______________GU_CAAAUACUAG_____________UCAGGA_G_UUA_UCCAUGG\n______________\|\|_\|\|\|\|:\|\|\|\|\|_____________\|\|\|\|:\|_\|_:\|\|_\|\|\|\|\|\|\|\n______________CA_GUUUGUGAUC_____________AGUCUU_C_GAU_AGGUACC\n3'-UUU...GGACA__U__________UC_______________________A_______GCAAU...GAA-5'\n_____________\|______________________________________________\|\n_____________51_____________________________________________17\n	198 -- 204	18 -- 24	-28.1471 kcal/mol	7.4527 kcal/mol	12.9164 kcal/mol	159 205@LB@ \| \|@LB@5'-CAU...ACCGC UCCAAUUAUCAAA C A A AAGGU...AAC-3'@LB@ GU CAAAUACUAG UCAGGA G UUA UCCAUGG@LB@ \|\| \|\|\|\|:\|\|\|\|\| \|\|\|\|:\| \| :\|\| \|\|\|\|\|\|\|@LB@ CA GUUUGUGAUC AGUCUU C GAU AGGUACC@LB@3'-UUU...GGACA U UC A GCAAU...GAA-5'@LB@ \| \|@LB@ 51 17@LB@@LB@@LB@Energy -7.78 kcal/mol@LB@Hybridization Energy -28.1471 kcal/mol@LB@Unfolding Energy - mRNA 7.4527 kcal/mol@LB@Unfolding Energy - sRNA 12.9164 kcal/mol@LB@@LB@Position - mRNA 160 -- 204@LB@Position - sRNA 18 -- 50@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 18 -- 24@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)

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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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