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
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@
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@
132	0.05402	0.3262	ct_150	rl33	-5.54	0.287166	186 -- 205	17 -- 33	50S ribosomal protein L33	_____________185__________________206\n_____________\|____________________\|\n5'-CUC...UCUUG___AAA____CA________CAGCA...UAG-3'\n______________AGA___GGUU__UUCAUGGC\n______________\|\|\|___:\|:\|__\|:\|\|\|\|\|\|\n______________UCU___UCGA__AGGUACCG\n3'-UUU...CUCAG__________UA________CAAUC...GAA-5'\n_____________\|____________________\|\n_____________34___________________16\n	199 -- 205	17 -- 23	-14.3817 kcal/mol	3.85921 kcal/mol	4.97804 kcal/mol	185 206@LB@ \| \|@LB@5'-CUC...UCUUG AAA CA CAGCA...UAG-3'@LB@ AGA GGUU UUCAUGGC@LB@ \|\|\| :\|:\| \|:\|\|\|\|\|\|@LB@ UCU UCGA AGGUACCG@LB@3'-UUU...CUCAG UA CAAUC...GAA-5'@LB@ \| \|@LB@ 34 16@LB@@LB@@LB@Energy -5.54 kcal/mol@LB@Hybridization Energy -14.3817 kcal/mol@LB@Unfolding Energy - mRNA 3.85921 kcal/mol@LB@Unfolding Energy - sRNA 4.97804 kcal/mol@LB@@LB@Position - mRNA 186 -- 205@LB@Position - sRNA 17 -- 33@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 17 -- 23@LB@
141	0.05655	0.3262	ct_645	N/A	-6.85	0.155161	266 -- 276	17 -- 28		_____________265__________277\n_____________\|____________\|\n5'-GAG...GUUCU____________UGCCA...AGU-3'\n______________UUGUUCC_UGGC\n______________:\|:\|\|\|\|_\|\|\|\|\n______________GAUAAGG_ACCG\n3'-UUU...UCUUC_______U____CAAUC...GAA-5'\n_____________\|____________\|\n_____________29___________16\n	266 -- 272	22 -- 28	-12.7306 kcal/mol	1.25811 kcal/mol	4.62088 kcal/mol	265 277@LB@ \| \|@LB@5'-GAG...GUUCU UGCCA...AGU-3'@LB@ UUGUUCC UGGC@LB@ :\|:\|\|\|\| \|\|\|\|@LB@ GAUAAGG ACCG@LB@3'-UUU...UCUUC U CAAUC...GAA-5'@LB@ \| \|@LB@ 29 16@LB@@LB@@LB@Energy -6.85 kcal/mol@LB@Hybridization Energy -12.7306 kcal/mol@LB@Unfolding Energy - mRNA 1.25811 kcal/mol@LB@Unfolding Energy - sRNA 4.62088 kcal/mol@LB@@LB@Position - mRNA 266 -- 276@LB@Position - sRNA 17 -- 28@LB@Position Seed - mRNA 266 -- 272@LB@Position Seed - sRNA 22 -- 28@LB@
149	0.06369	0.3424	ct_124	accC	-5.62	0.277702	171 -- 193	17 -- 31	acetyl-CoA carboxylase biotin carboxylase subunit	_____________170_____________________194\n_____________\|_______________________\|\n5'-CUC...GUUCU____________AUAGUUAA___UUAGU...UGG-3'\n______________AAGUUAUUCCGU________GGC\n______________\|\|\|:\|\|\|\|\|\|:\|________\|\|\|\n______________UUCGAUAAGGUA________CCG\n3'-UUU...CAGUC_______________________CAAUC...GAA-5'\n_____________\|_______________________\|\n_____________32______________________16\n	176 -- 182	20 -- 26	-15.1557 kcal/mol	4.67447 kcal/mol	4.86101 kcal/mol	170 194@LB@ \| \|@LB@5'-CUC...GUUCU AUAGUUAA UUAGU...UGG-3'@LB@ AAGUUAUUCCGU GGC@LB@ \|\|\|:\|\|\|\|\|\|:\| \|\|\|@LB@ UUCGAUAAGGUA CCG@LB@3'-UUU...CAGUC CAAUC...GAA-5'@LB@ \| \|@LB@ 32 16@LB@@LB@@LB@Energy -5.62 kcal/mol@LB@Hybridization Energy -15.1557 kcal/mol@LB@Unfolding Energy - mRNA 4.67447 kcal/mol@LB@Unfolding Energy - sRNA 4.86101 kcal/mol@LB@@LB@Position - mRNA 171 -- 193@LB@Position - sRNA 17 -- 31@LB@Position Seed - mRNA 176 -- 182@LB@Position Seed - sRNA 20 -- 26@LB@
160	0.06752	0.3424	ct_324	N/A	-4.86	0.383763	195 -- 205	17 -- 27		_____________194_________206\n_____________\|___________\|\n5'-ACA...GUAGA__GG_______CAAAG...UGC-3'\n______________UA__CCAUGGU\n______________\|\|__\|\|\|\|\|\|:\n______________AU__GGUACCG\n3'-UUU...CUUCG__AA_______CAAUC...GAA-5'\n_____________\|___________\|\n_____________28__________16\n	199 -- 205	17 -- 23	-11.7516 kcal/mol	2.4023 kcal/mol	4.49196 kcal/mol	194 206@LB@ \| \|@LB@5'-ACA...GUAGA GG CAAAG...UGC-3'@LB@ UA CCAUGGU@LB@ \|\| \|\|\|\|\|\|:@LB@ AU GGUACCG@LB@3'-UUU...CUUCG AA CAAUC...GAA-5'@LB@ \| \|@LB@ 28 16@LB@@LB@@LB@Energy -4.86 kcal/mol@LB@Hybridization Energy -11.7516 kcal/mol@LB@Unfolding Energy - mRNA 2.4023 kcal/mol@LB@Unfolding Energy - sRNA 4.49196 kcal/mol@LB@@LB@Position - mRNA 195 -- 205@LB@Position - sRNA 17 -- 27@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 17 -- 23@LB@
166	0.06935	0.3427	ct_700	N/A	-9.45	0.038462	185 -- 207	17 -- 35		_____________184_____________________208\n_____________\|_______________________\|\n5'-UGG...AAAAC___________GCAUUA______UAAUC...AUC-3'\n______________UCAGAAGUUGU______UGUGGC\n______________\|\|\|\|\|\|\|:\|:\|______::\|\|\|\|\n______________AGUCUUCGAUA______GUACCG\n3'-UUU...AUCUC___________AG__________CAAUC...GAA-5'\n_____________\|_______________________\|\n_____________36______________________16\n	187 -- 193	27 -- 33	-18.7157 kcal/mol	4.28595 kcal/mol	4.9781 kcal/mol	184 208@LB@ \| \|@LB@5'-UGG...AAAAC GCAUUA UAAUC...AUC-3'@LB@ UCAGAAGUUGU UGUGGC@LB@ \|\|\|\|\|\|\|:\|:\| ::\|\|\|\|@LB@ AGUCUUCGAUA GUACCG@LB@3'-UUU...AUCUC AG CAAUC...GAA-5'@LB@ \| \|@LB@ 36 16@LB@@LB@@LB@Energy -9.45 kcal/mol@LB@Hybridization Energy -18.7157 kcal/mol@LB@Unfolding Energy - mRNA 4.28595 kcal/mol@LB@Unfolding Energy - sRNA 4.9781 kcal/mol@LB@@LB@Position - mRNA 185 -- 207@LB@Position - sRNA 17 -- 35@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 27 -- 33@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@
3	0.0003482	0.07439	ct_023	prfA	-10.22	0.024627	158 -- 204	18 -- 56	peptide chain release factor	_____________157_____________________________________________205\n_____________\|_______________________________________________\|\n5'-GAA...CUGGU______UAG_G____________AAAGG______AAGUCG_______AAAUA...CGC-3'\n______________CUUUGU___A_AGAUACUAGAGU_____CAGAAG______UUCAUGG\n______________\|::\|\|\|___\|_\|:\|:\|\|\|\|\|\|\|\|_____\|\|\|\|\|\|______\|:\|\|\|\|\|\n______________GGGACA___U_UUUGUGAUCUCA_____GUCUUC______AGGUACC\n3'-UUU...AAGGG______CA__G_______________________GAUA_________GCAAU...GAA-5'\n_____________\|_______________________________________________\|\n_____________57______________________________________________17\n	198 -- 204	18 -- 24	-35.7937 kcal/mol	12.6341 kcal/mol	12.9359 kcal/mol	157 205@LB@ \| \|@LB@5'-GAA...CUGGU UAG G AAAGG AAGUCG AAAUA...CGC-3'@LB@ CUUUGU A AGAUACUAGAGU CAGAAG UUCAUGG@LB@ \|::\|\|\| \| \|:\|:\|\|\|\|\|\|\|\| \|\|\|\|\|\| \|:\|\|\|\|\|@LB@ GGGACA U UUUGUGAUCUCA GUCUUC AGGUACC@LB@3'-UUU...AAGGG CA G GAUA GCAAU...GAA-5'@LB@ \| \|@LB@ 57 17@LB@@LB@@LB@Energy -10.22 kcal/mol@LB@Hybridization Energy -35.7937 kcal/mol@LB@Unfolding Energy - mRNA 12.6341 kcal/mol@LB@Unfolding Energy - sRNA 12.9359 kcal/mol@LB@@LB@Position - mRNA 158 -- 204@LB@Position - sRNA 18 -- 56@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 18 -- 24@LB@
19	0.004244	0.1836	ct_583	gp6D	-9.00	0.049504	83 -- 102	18 -- 35	virulence protein GP6-D	_____________82___________________103\n_____________\|____________________\|\n5'-UAA...CUAUC________CGCUA_______GAAAC...CUC-3'\n______________UCAGAAGC_____UCCAUGG\n______________\|\|\|\|\|\|\|\|_____\|\|\|\|\|\|\|\n______________AGUCUUCG_____AGGUACC\n3'-UUU...AUCUC________AUA_________GCAAU...GAA-5'\n_____________\|____________________\|\n_____________36___________________17\n	96 -- 102	18 -- 24	-22.1713 kcal/mol	8.18904 kcal/mol	4.97803 kcal/mol	82 103@LB@ \| \|@LB@5'-UAA...CUAUC CGCUA GAAAC...CUC-3'@LB@ UCAGAAGC UCCAUGG@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ AGUCUUCG AGGUACC@LB@3'-UUU...AUCUC AUA GCAAU...GAA-5'@LB@ \| \|@LB@ 36 17@LB@@LB@@LB@Energy -9.00 kcal/mol@LB@Hybridization Energy -22.1713 kcal/mol@LB@Unfolding Energy - mRNA 8.18904 kcal/mol@LB@Unfolding Energy - sRNA 4.97803 kcal/mol@LB@@LB@Position - mRNA 83 -- 102@LB@Position - sRNA 18 -- 35@LB@Position Seed - mRNA 96 -- 102@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)

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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