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
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@
142	0.0566	0.3262	ct_284	N/A	-6.95	0.147726	278 -- 292	18 -- 30	phospholipase D	_____________277_____________293\n_____________\|_______________\|\n5'-AUC...ACUAU_________GG____AGACAAAA-3'\n______________AGCUAUUCC__AUGG\n______________\|\|\|\|\|\|\|\|\|__\|\|\|\|\n______________UCGAUAAGG__UACC\n3'-UUU...AGUCU_______________GCAAU...GAA-5'\n_____________\|_______________\|\n_____________31______________17\n	280 -- 286	22 -- 28	-16.5616 kcal/mol	4.87795 kcal/mol	4.73403 kcal/mol	277 293@LB@ \| \|@LB@5'-AUC...ACUAU GG AGACAAAA-3'@LB@ AGCUAUUCC AUGG@LB@ \|\|\|\|\|\|\|\|\| \|\|\|\|@LB@ UCGAUAAGG UACC@LB@3'-UUU...AGUCU GCAAU...GAA-5'@LB@ \| \|@LB@ 31 17@LB@@LB@@LB@Energy -6.95 kcal/mol@LB@Hybridization Energy -16.5616 kcal/mol@LB@Unfolding Energy - mRNA 4.87795 kcal/mol@LB@Unfolding Energy - sRNA 4.73403 kcal/mol@LB@@LB@Position - mRNA 278 -- 292@LB@Position - sRNA 18 -- 30@LB@Position Seed - mRNA 280 -- 286@LB@Position Seed - sRNA 22 -- 28@LB@
143	0.05698	0.3262	ct_451	cdsA	-5.69	0.268983	146 -- 169	3 -- 34	phosphatidate cytidylyltransferase	_____________145______________________________170\n_____________\|________________________________\|\n5'-GAC...CUUGC_______G___AAAAC________________AACGA...GUA-3'\n______________UAGAAGC_AUU_____________AUACCAAC\n______________:\|\|\|\|\|\|_\|\|\|_____________\|\|\|\|\|\|\|\|\n______________GUCUUCG_UAA_____________UAUGGUUG\n3'-UUU...UCUCA_______A___GGUACCGCAAUCU________AA-5'\n_____________\|________________________________\|\n_____________35_______________________________2\n	163 -- 169	3 -- 9	-16.5797 kcal/mol	2.2962 kcal/mol	8.59197 kcal/mol	145 170@LB@ \| \|@LB@5'-GAC...CUUGC G AAAAC AACGA...GUA-3'@LB@ UAGAAGC AUU AUACCAAC@LB@ :\|\|\|\|\|\| \|\|\| \|\|\|\|\|\|\|\|@LB@ GUCUUCG UAA UAUGGUUG@LB@3'-UUU...UCUCA A GGUACCGCAAUCU AA-5'@LB@ \| \|@LB@ 35 2@LB@@LB@@LB@Energy -5.69 kcal/mol@LB@Hybridization Energy -16.5797 kcal/mol@LB@Unfolding Energy - mRNA 2.2962 kcal/mol@LB@Unfolding Energy - sRNA 8.59197 kcal/mol@LB@@LB@Position - mRNA 146 -- 169@LB@Position - sRNA 3 -- 34@LB@Position Seed - mRNA 163 -- 169@LB@Position Seed - sRNA 3 -- 9@LB@
144	0.05714	0.3262	ct_392	yprS	-4.10	0.509599	238 -- 247	22 -- 33		_____________237__________248\n_____________\|____________\|\n5'-AGG...CCCUG____________CAAUU...GUC-3'\n______________AGAGGCU__UCC\n______________\|\|\|:\|\|\|__\|\|\|\n______________UCUUCGA__AGG\n3'-UUU...CUCAG_______UA___UACCG...GAA-5'\n_____________\|____________\|\n_____________34___________21\n	238 -- 244	27 -- 33	-11.7781 kcal/mol	2.9519 kcal/mol	4.72509 kcal/mol	237 248@LB@ \| \|@LB@5'-AGG...CCCUG CAAUU...GUC-3'@LB@ AGAGGCU UCC@LB@ \|\|\|:\|\|\| \|\|\|@LB@ UCUUCGA AGG@LB@3'-UUU...CUCAG UA UACCG...GAA-5'@LB@ \| \|@LB@ 34 21@LB@@LB@@LB@Energy -4.10 kcal/mol@LB@Hybridization Energy -11.7781 kcal/mol@LB@Unfolding Energy - mRNA 2.9519 kcal/mol@LB@Unfolding Energy - sRNA 4.72509 kcal/mol@LB@@LB@Position - mRNA 238 -- 247@LB@Position - sRNA 22 -- 33@LB@Position Seed - mRNA 238 -- 244@LB@Position Seed - sRNA 27 -- 33@LB@
145	0.05831	0.3298	ct_635	N/A	-5.11	0.346704	276 -- 282	53 -- 59		_____________275_____283\n_____________\|_______\|\n5'-AUC...UCGAA_______UUGGA...CUG-3'\n______________CCCUCCU\n______________\|\|\|:\|\|\|\n______________GGGGGGA\n3'-UUU...CUGAA_______CACAU...GAA-5'\n_____________\|_______\|\n_____________60______52\n	276 -- 282	53 -- 59	-11.2032 kcal/mol	0.619026 kcal/mol	5.47887 kcal/mol	275 283@LB@ \| \|@LB@5'-AUC...UCGAA UUGGA...CUG-3'@LB@ CCCUCCU@LB@ \|\|\|:\|\|\|@LB@ GGGGGGA@LB@3'-UUU...CUGAA CACAU...GAA-5'@LB@ \| \|@LB@ 60 52@LB@@LB@@LB@Energy -5.11 kcal/mol@LB@Hybridization Energy -11.2032 kcal/mol@LB@Unfolding Energy - mRNA 0.619026 kcal/mol@LB@Unfolding Energy - sRNA 5.47887 kcal/mol@LB@@LB@Position - mRNA 276 -- 282@LB@Position - sRNA 53 -- 59@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 53 -- 59@LB@
146	0.05858	0.3298	ct_655	kdsA	-5.70	0.267824	236 -- 245	48 -- 57	2-dehydro-3-deoxyphosphooctonate aldolase	_____________235________246\n_____________\|__________\|\n5'-GCU...GCAGG__________AUUGA...CUC-3'\n______________CCCUUGUGUA\n______________\|\|\|:\|\|\|\|\|\|\n______________GGGGACACAU\n3'-UUU...GAAGG__________GUUUG...GAA-5'\n_____________\|__________\|\n_____________58_________47\n	237 -- 243	50 -- 56	-16.3498 kcal/mol	3.37377 kcal/mol	7.27486 kcal/mol	235 246@LB@ \| \|@LB@5'-GCU...GCAGG AUUGA...CUC-3'@LB@ CCCUUGUGUA@LB@ \|\|\|:\|\|\|\|\|\|@LB@ GGGGACACAU@LB@3'-UUU...GAAGG GUUUG...GAA-5'@LB@ \| \|@LB@ 58 47@LB@@LB@@LB@Energy -5.70 kcal/mol@LB@Hybridization Energy -16.3498 kcal/mol@LB@Unfolding Energy - mRNA 3.37377 kcal/mol@LB@Unfolding Energy - sRNA 7.27486 kcal/mol@LB@@LB@Position - mRNA 236 -- 245@LB@Position - sRNA 48 -- 57@LB@Position Seed - mRNA 237 -- 243@LB@Position Seed - sRNA 50 -- 56@LB@
147	0.05913	0.3307	ct_243	lpxD	-5.18	0.335797	179 -- 192	18 -- 32	UDP-3-O-acylglucosamine N-acyltransferase	_____________178_____________193\n_____________\|_______________\|\n5'-UCA...CAUGC_______G____A__AGUGC...UCG-3'\n______________GAAGCUA__CCG_GG\n______________\|\|\|\|\|\|\|__\|\|:_\|\|\n______________CUUCGAU__GGU_CC\n3'-UUU...UCAGU_______AA___A__GCAAU...GAA-5'\n_____________\|_______________\|\n_____________33______________17\n	179 -- 185	26 -- 32	-15.005 kcal/mol	4.85774 kcal/mol	4.96566 kcal/mol	178 193@LB@ \| \|@LB@5'-UCA...CAUGC G A AGUGC...UCG-3'@LB@ GAAGCUA CCG GG@LB@ \|\|\|\|\|\|\| \|\|: \|\|@LB@ CUUCGAU GGU CC@LB@3'-UUU...UCAGU AA A GCAAU...GAA-5'@LB@ \| \|@LB@ 33 17@LB@@LB@@LB@Energy -5.18 kcal/mol@LB@Hybridization Energy -15.005 kcal/mol@LB@Unfolding Energy - mRNA 4.85774 kcal/mol@LB@Unfolding Energy - sRNA 4.96566 kcal/mol@LB@@LB@Position - mRNA 179 -- 192@LB@Position - sRNA 18 -- 32@LB@Position Seed - mRNA 179 -- 185@LB@Position Seed - sRNA 26 -- 32@LB@
148	0.06134	0.3407	ct_434	ygbB	-10.66	0.019089	186 -- 200	41 -- 57	2-C-methyl-D-erythritol 2 4-cyclodiphosphate synthase	_____________185_______________201\n_____________\|_________________\|\n5'-GGU...CCUGU_____U___________AUGAC...AUC-3'\n______________CCCCU___UGCAAGCAC\n______________\|\|\|\|\|___\|:\|\|\|:\|\|\|\n______________GGGGA___AUGUUUGUG\n3'-UUU...GAAGG_____CAC_________AUCUC...GAA-5'\n_____________\|_________________\|\n_____________58________________40\n	194 -- 200	41 -- 47	-19.7128 kcal/mol	1.2348 kcal/mol	7.82241 kcal/mol	185 201@LB@ \| \|@LB@5'-GGU...CCUGU U AUGAC...AUC-3'@LB@ CCCCU UGCAAGCAC@LB@ \|\|\|\|\| \|:\|\|\|:\|\|\|@LB@ GGGGA AUGUUUGUG@LB@3'-UUU...GAAGG CAC AUCUC...GAA-5'@LB@ \| \|@LB@ 58 40@LB@@LB@@LB@Energy -10.66 kcal/mol@LB@Hybridization Energy -19.7128 kcal/mol@LB@Unfolding Energy - mRNA 1.2348 kcal/mol@LB@Unfolding Energy - sRNA 7.82241 kcal/mol@LB@@LB@Position - mRNA 186 -- 200@LB@Position - sRNA 41 -- 57@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 41 -- 47@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@
150	0.06394	0.3424	ct_208	gseA	-4.42	0.454874	290 -- 300	19 -- 29	3-deoxy-D-manno-octulosonic acid transferase	_____________289________300\n_____________\|__________\|\n5'-UUG...AAAGU___U_______-3'\n______________GUU_UUCCAUG\n______________\|:\|_\|\|\|\|\|\|\|\n______________CGA_AAGGUAC\n3'-UUU...GUCUU___U_______CGCAA...GAA-5'\n_____________\|___________\|\n_____________30__________18\n	294 -- 300	19 -- 25	-10.2082 kcal/mol	1.1238 kcal/mol	4.66719 kcal/mol	289 300@LB@ \| \|@LB@5'-UUG...AAAGU U -3'@LB@ GUU UUCCAUG@LB@ \|:\| \|\|\|\|\|\|\|@LB@ CGA AAGGUAC@LB@3'-UUU...GUCUU U CGCAA...GAA-5'@LB@ \| \|@LB@ 30 18@LB@@LB@@LB@Energy -4.42 kcal/mol@LB@Hybridization Energy -10.2082 kcal/mol@LB@Unfolding Energy - mRNA 1.1238 kcal/mol@LB@Unfolding Energy - sRNA 4.66719 kcal/mol@LB@@LB@Position - mRNA 290 -- 300@LB@Position - sRNA 19 -- 29@LB@Position Seed - mRNA 294 -- 300@LB@Position Seed - sRNA 19 -- 25@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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