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
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@
163	0.06794	0.3424	ct_661	N/A	-2.85	0.735752	184 -- 191	21 -- 28	DNA topoisomerase IV subunit B	_____________183______192\n_____________\|________\|\n5'-AAA...UUGCC________CACAC...GCG-3'\n______________UUAUUCCA\n______________:\|\|\|\|\|\|\|\n______________GAUAAGGU\n3'-UUU...UCUUC________ACCGC...GAA-5'\n_____________\|________\|\n_____________29_______20\n	185 -- 191	21 -- 27	-7.6538 kcal/mol	0.450062 kcal/mol	4.35509 kcal/mol	183 192@LB@ \| \|@LB@5'-AAA...UUGCC CACAC...GCG-3'@LB@ UUAUUCCA@LB@ :\|\|\|\|\|\|\|@LB@ GAUAAGGU@LB@3'-UUU...UCUUC ACCGC...GAA-5'@LB@ \| \|@LB@ 29 20@LB@@LB@@LB@Energy -2.85 kcal/mol@LB@Hybridization Energy -7.6538 kcal/mol@LB@Unfolding Energy - mRNA 0.450062 kcal/mol@LB@Unfolding Energy - sRNA 4.35509 kcal/mol@LB@@LB@Position - mRNA 184 -- 191@LB@Position - sRNA 21 -- 28@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 21 -- 27@LB@
188	0.08401	0.363	ct_024	N/A	-5.57	0.284242	184 -- 199	20 -- 35	release factor glutamine methyltransferase	_____________183______________200\n_____________\|________________\|\n5'-AGA...GUACA____C________G__CAUGA...AGA-3'\n______________UCGG_AGCUAUUC_GU\n______________\|\|:\|_\|\|\|\|\|\|\|\|_:\|\n______________AGUC_UCGAUAAG_UA\n3'-UUU...AUCUC____U________G__CCGCA...GAA-5'\n_____________\|________________\|\n_____________36_______________19\n	190 -- 196	23 -- 29	-16.0617 kcal/mol	5.57694 kcal/mol	4.91708 kcal/mol	183 200@LB@ \| \|@LB@5'-AGA...GUACA C G CAUGA...AGA-3'@LB@ UCGG AGCUAUUC GU@LB@ \|\|:\| \|\|\|\|\|\|\|\| :\|@LB@ AGUC UCGAUAAG UA@LB@3'-UUU...AUCUC U G CCGCA...GAA-5'@LB@ \| \|@LB@ 36 19@LB@@LB@@LB@Energy -5.57 kcal/mol@LB@Hybridization Energy -16.0617 kcal/mol@LB@Unfolding Energy - mRNA 5.57694 kcal/mol@LB@Unfolding Energy - sRNA 4.91708 kcal/mol@LB@@LB@Position - mRNA 184 -- 199@LB@Position - sRNA 20 -- 35@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 23 -- 29@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@
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@
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@
92	0.03292	0.2942	ct_558	lipA	-15.60	0.000793	187 -- 244	3 -- 58	lipoyl synthase	_____________186_________________________________________________________245\n_____________\|___________________________________________________________\|\n5'-ACU...AUAUG_______CUAAA_____ACC__U______UCUC_______UAAAAAAUCU______C__CAGAU...AAA-3'\n______________CCCCCUG_____AAAUG___GA_UCAGAA____CUAUUCC___________AUACC_GC\n______________\|\|\|\|\|\|\|_____\|\|\|::___\|\|_\|\|\|\|\|\|____\|\|\|\|\|\|\|___________\|\|\|\|\|_:\|\n______________GGGGGAC_____UUUGU___CU_AGUCUU____GAUAAGG___________UAUGG_UG\n3'-UUU...UGAAG_______ACAUG_____GAU__C______C__________UACCGCAAUCU_____U__AA-5'\n_____________\|___________________________________________________________\|\n_____________59__________________________________________________________2\n	220 -- 226	22 -- 28	-35.9268 kcal/mol	3.77883 kcal/mol	16.5523 kcal/mol	186 245@LB@ \| \|@LB@5'-ACU...AUAUG CUAAA ACC U UCUC UAAAAAAUCU C CAGAU...AAA-3'@LB@ CCCCCUG AAAUG GA UCAGAA CUAUUCC AUACC GC@LB@ \|\|\|\|\|\|\| \|\|\|:: \|\| \|\|\|\|\|\| \|\|\|\|\|\|\| \|\|\|\|\| :\|@LB@ GGGGGAC UUUGU CU AGUCUU GAUAAGG UAUGG UG@LB@3'-UUU...UGAAG ACAUG GAU C C UACCGCAAUCU U AA-5'@LB@ \| \|@LB@ 59 2@LB@@LB@@LB@Energy -15.60 kcal/mol@LB@Hybridization Energy -35.9268 kcal/mol@LB@Unfolding Energy - mRNA 3.77883 kcal/mol@LB@Unfolding Energy - sRNA 16.5523 kcal/mol@LB@@LB@Position - mRNA 187 -- 244@LB@Position - sRNA 3 -- 58@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 22 -- 28@LB@
1	6.997e-05	0.03358	ct_198	oppA_3	-8.59	0.062291	189 -- 206	17 -- 33	oligopeptide ABC transporter substrate-binding protein	_____________188________________207\n_____________\|__________________\|\n5'-AAA...UCUAA______C________C__AAGAU...CUC-3'\n______________GGAGGU_AUUCCAUG_GC\n______________:\|\|:\|:_\|\|\|\|\|\|\|\|_\|\|\n______________UCUUCG_UAAGGUAC_CG\n3'-UUU...CUCAG______A___________CAAUC...GAA-5'\n_____________\|__________________\|\n_____________34_________________16\n	197 -- 203	19 -- 25	-19.6111 kcal/mol	6.04348 kcal/mol	4.97804 kcal/mol	188 207@LB@ \| \|@LB@5'-AAA...UCUAA C C AAGAU...CUC-3'@LB@ GGAGGU AUUCCAUG GC@LB@ :\|\|:\|: \|\|\|\|\|\|\|\| \|\|@LB@ UCUUCG UAAGGUAC CG@LB@3'-UUU...CUCAG A CAAUC...GAA-5'@LB@ \| \|@LB@ 34 16@LB@@LB@@LB@Energy -8.59 kcal/mol@LB@Hybridization Energy -19.6111 kcal/mol@LB@Unfolding Energy - mRNA 6.04348 kcal/mol@LB@Unfolding Energy - sRNA 4.97804 kcal/mol@LB@@LB@Position - mRNA 189 -- 206@LB@Position - sRNA 17 -- 33@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 19 -- 25@LB@
85	0.03073	0.29	ct_522	rs3	-5.11	0.345416	189 -- 204	18 -- 34	30S ribosomal protein S3	_____________188_______________205\n_____________\|_________________\|\n5'-UGU...GGCAG_______AAGG______GUCAA...UCA-3'\n______________UAGGAGU_____UAUGG\n______________:\|\|:\|\|:_____:\|\|\|\|\n______________GUCUUCG_____GUACC\n3'-UUU...UCUCA_______AUAAG_____GCAAU...GAA-5'\n_____________\|_________________\|\n_____________35________________17\n	189 -- 195	28 -- 34	-12.0284 kcal/mol	1.93617 kcal/mol	4.97803 kcal/mol	188 205@LB@ \| \|@LB@5'-UGU...GGCAG AAGG GUCAA...UCA-3'@LB@ UAGGAGU UAUGG@LB@ :\|\|:\|\|: :\|\|\|\|@LB@ GUCUUCG GUACC@LB@3'-UUU...UCUCA AUAAG GCAAU...GAA-5'@LB@ \| \|@LB@ 35 17@LB@@LB@@LB@Energy -5.11 kcal/mol@LB@Hybridization Energy -12.0284 kcal/mol@LB@Unfolding Energy - mRNA 1.93617 kcal/mol@LB@Unfolding Energy - sRNA 4.97803 kcal/mol@LB@@LB@Position - mRNA 189 -- 204@LB@Position - sRNA 18 -- 34@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 28 -- 34@LB@
8	0.0008373	0.07962	ct_066	N/A	-11.14	0.014316	190 -- 205	17 -- 33		_____________189_______________206\n_____________\|_________________\|\n5'-UUU...CACUA_________________UACGG...GUU-3'\n______________AGGAGCUAUUC_AUGGC\n______________\|\|:\|\|\|\|\|\|\|\|_\|\|\|\|\|\n______________UCUUCGAUAAG_UACCG\n3'-UUU...CUCAG___________G_____CAAUC...GAA-5'\n_____________\|_________________\|\n_____________34________________16\n	194 -- 200	23 -- 29	-22.6652 kcal/mol	6.55112 kcal/mol	4.97804 kcal/mol	189 206@LB@ \| \|@LB@5'-UUU...CACUA UACGG...GUU-3'@LB@ AGGAGCUAUUC AUGGC@LB@ \|\|:\|\|\|\|\|\|\|\| \|\|\|\|\|@LB@ UCUUCGAUAAG UACCG@LB@3'-UUU...CUCAG G CAAUC...GAA-5'@LB@ \| \|@LB@ 34 16@LB@@LB@@LB@Energy -11.14 kcal/mol@LB@Hybridization Energy -22.6652 kcal/mol@LB@Unfolding Energy - mRNA 6.55112 kcal/mol@LB@Unfolding Energy - sRNA 4.97804 kcal/mol@LB@@LB@Position - mRNA 190 -- 205@LB@Position - sRNA 17 -- 33@LB@Position Seed - mRNA 194 -- 200@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)

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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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