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
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@
109	0.04235	0.3194	ct_002	gatC	-8.76	0.056639	255 -- 282	18 -- 44	aspartyl/glutamyl-tRNA amidotransferase subunit C	_____________254__________________________283\n_____________\|____________________________\|\n5'-GAC...AUGCU________________AUGCCCA_____AAGAG...CUA-3'\n______________GCAUUGGAGUUGGAAG_______CGUGG\n______________:\|\|:\|:\|\|\|\|::\|\|\|\|_______\|:\|\|\|\n______________UGUGAUCUCAGUCUUC_______GUACC\n3'-UUU...AUGUU________________GAUAAG______GCAAU...GAA-5'\n_____________\|____________________________\|\n_____________45___________________________17\n	261 -- 267	32 -- 38	-28.0671 kcal/mol	6.54471 kcal/mol	12.7603 kcal/mol	254 283@LB@ \| \|@LB@5'-GAC...AUGCU AUGCCCA AAGAG...CUA-3'@LB@ GCAUUGGAGUUGGAAG CGUGG@LB@ :\|\|:\|:\|\|\|\|::\|\|\|\| \|:\|\|\|@LB@ UGUGAUCUCAGUCUUC GUACC@LB@3'-UUU...AUGUU GAUAAG GCAAU...GAA-5'@LB@ \| \|@LB@ 45 17@LB@@LB@@LB@Energy -8.76 kcal/mol@LB@Hybridization Energy -28.0671 kcal/mol@LB@Unfolding Energy - mRNA 6.54471 kcal/mol@LB@Unfolding Energy - sRNA 12.7603 kcal/mol@LB@@LB@Position - mRNA 255 -- 282@LB@Position - sRNA 18 -- 44@LB@Position Seed - mRNA 261 -- 267@LB@Position Seed - sRNA 32 -- 38@LB@
11	0.002752	0.1836	ct_015	phoH	-12.12	0.007844	167 -- 186	33 -- 60	ATPase	_____________166__________________________187\n_____________\|____________________________\|\n5'-CCA...CUAUC_____________________U______UUUAG...UAA-3'\n______________UCCCCCUU________ACACU_GAGUCA\n______________\|\|\|\|\|\|:\|________\|\|\|\|\|_\|\|\|\|\|\|\n______________AGGGGGGA________UGUGA_CUCAGU\n3'-UUU...ACUGA________CACAUGUU_____U______CUUCG...GAA-5'\n_____________\|____________________________\|\n_____________61___________________________32\n	168 -- 174	53 -- 59	-26.4608 kcal/mol	2.95889 kcal/mol	11.3851 kcal/mol	166 187@LB@ \| \|@LB@5'-CCA...CUAUC U UUUAG...UAA-3'@LB@ UCCCCCUU ACACU GAGUCA@LB@ \|\|\|\|\|\|:\| \|\|\|\|\| \|\|\|\|\|\|@LB@ AGGGGGGA UGUGA CUCAGU@LB@3'-UUU...ACUGA CACAUGUU U CUUCG...GAA-5'@LB@ \| \|@LB@ 61 32@LB@@LB@@LB@Energy -12.12 kcal/mol@LB@Hybridization Energy -26.4608 kcal/mol@LB@Unfolding Energy - mRNA 2.95889 kcal/mol@LB@Unfolding Energy - sRNA 11.3851 kcal/mol@LB@@LB@Position - mRNA 167 -- 186@LB@Position - sRNA 33 -- 60@LB@Position Seed - mRNA 168 -- 174@LB@Position Seed - sRNA 53 -- 59@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@
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@
20	0.004812	0.1918	ct_026	rs16	-8.27	0.073959	26 -- 51	3 -- 33	30S ribosomal protein S16	_____________25______________________________52\n_____________\|_______________________________\|\n5'-CUG...ACGAA________________AA_________G___CGGAU...AUA-3'\n______________AGGAGUUA____GUGG__UU_GAGUAU_AGC\n______________\|\|:\|\|:\|\|____:\|\|\|__\|\|_\|\|:\|\|:_\|:\|\n______________UCUUCGAU____UACC__AA_CUUAUG_UUG\n3'-UUU...CUCAG________AAGG____GC__U______G___AA-5'\n_____________\|_______________________________\|\n_____________34______________________________2\n	27 -- 33	26 -- 32	-20.5759 kcal/mol	3.70935 kcal/mol	8.59196 kcal/mol	25 52@LB@ \| \|@LB@5'-CUG...ACGAA AA G CGGAU...AUA-3'@LB@ AGGAGUUA GUGG UU GAGUAU AGC@LB@ \|\|:\|\|:\|\| :\|\|\| \|\| \|\|:\|\|: \|:\|@LB@ UCUUCGAU UACC AA CUUAUG UUG@LB@3'-UUU...CUCAG AAGG GC U G AA-5'@LB@ \| \|@LB@ 34 2@LB@@LB@@LB@Energy -8.27 kcal/mol@LB@Hybridization Energy -20.5759 kcal/mol@LB@Unfolding Energy - mRNA 3.70935 kcal/mol@LB@Unfolding Energy - sRNA 8.59196 kcal/mol@LB@@LB@Position - mRNA 26 -- 51@LB@Position - sRNA 3 -- 33@LB@Position Seed - mRNA 27 -- 33@LB@Position Seed - sRNA 26 -- 32@LB@
36	0.01184	0.2704	ct_030	gmk	-11.03	0.015227	49 -- 70	6 -- 34	guanylate kinase	_____________48____________________________71\n_____________\|_____________________________\|\n5'-AUA...UGAUG_____________________________CCGAG...CAC-3'\n______________CGGAAGCU___UCAUG____UAGAGUACC\n______________\|:\|\|\|\|\|\|___:\|\|\|\|____\|\|\|\|:\|\|\|\|\n______________GUCUUCGA___GGUAC____AUCUUAUGG\n3'-UUU...UCUCA________UAA_____CGCA_________UUGAA-5'\n_____________\|_____________________________\|\n_____________35____________________________5\n	64 -- 70	6 -- 12	-24.3478 kcal/mol	4.72233 kcal/mol	8.59183 kcal/mol	48 71@LB@ \| \|@LB@5'-AUA...UGAUG CCGAG...CAC-3'@LB@ CGGAAGCU UCAUG UAGAGUACC@LB@ \|:\|\|\|\|\|\| :\|\|\|\| \|\|\|\|:\|\|\|\|@LB@ GUCUUCGA GGUAC AUCUUAUGG@LB@3'-UUU...UCUCA UAA CGCA UUGAA-5'@LB@ \| \|@LB@ 35 5@LB@@LB@@LB@Energy -11.03 kcal/mol@LB@Hybridization Energy -24.3478 kcal/mol@LB@Unfolding Energy - mRNA 4.72233 kcal/mol@LB@Unfolding Energy - sRNA 8.59183 kcal/mol@LB@@LB@Position - mRNA 49 -- 70@LB@Position - sRNA 6 -- 34@LB@Position Seed - mRNA 64 -- 70@LB@Position Seed - sRNA 6 -- 12@LB@
12	0.002873	0.1836	ct_040	ruvB	-8.58	0.062725	112 -- 136	36 -- 60	Holliday junction DNA helicase RuvB	_____________111_______________________137\n_____________\|_________________________\|\n5'-CAG...GGGAA_________ACUU___C________GAUGU...AAG-3'\n______________UCCCUCUUG____CAG_CGCUGGAG\n______________\|\|\|\|:\|:\|\|____\|\|:_\|:\|\|:\|\|\|\n______________AGGGGGGAC____GUU_GUGAUCUC\n3'-UUU...ACUGA_________ACAU___U________AGUCU...GAA-5'\n_____________\|_________________________\|\n_____________61________________________35\n	113 -- 119	53 -- 59	-26.2752 kcal/mol	7.75429 kcal/mol	9.944 kcal/mol	111 137@LB@ \| \|@LB@5'-CAG...GGGAA ACUU C GAUGU...AAG-3'@LB@ UCCCUCUUG CAG CGCUGGAG@LB@ \|\|\|\|:\|:\|\| \|\|: \|:\|\|:\|\|\|@LB@ AGGGGGGAC GUU GUGAUCUC@LB@3'-UUU...ACUGA ACAU U AGUCU...GAA-5'@LB@ \| \|@LB@ 61 35@LB@@LB@@LB@Energy -8.58 kcal/mol@LB@Hybridization Energy -26.2752 kcal/mol@LB@Unfolding Energy - mRNA 7.75429 kcal/mol@LB@Unfolding Energy - sRNA 9.944 kcal/mol@LB@@LB@Position - mRNA 112 -- 136@LB@Position - sRNA 36 -- 60@LB@Position Seed - mRNA 113 -- 119@LB@Position Seed - sRNA 53 -- 59@LB@
187	0.08358	0.363	ct_041	N/A	-5.64	0.274890	141 -- 160	41 -- 59		_____________140__________________161\n_____________\|____________________\|\n5'-UUU...UGCAA________GCA_________CUUAA...CUA-3'\n______________CCCCUUUG___UAUGAACAU\n______________\|\|\|\|::\|\|___\|\|::\|\|\|\|:\n______________GGGGGGAC___AUGUUUGUG\n3'-UUU...CUGAA________AC__________AUCUC...GAA-5'\n_____________\|____________________\|\n_____________60___________________40\n	142 -- 148	52 -- 58	-19.5521 kcal/mol	5.08593 kcal/mol	8.82318 kcal/mol	140 161@LB@ \| \|@LB@5'-UUU...UGCAA GCA CUUAA...CUA-3'@LB@ CCCCUUUG UAUGAACAU@LB@ \|\|\|\|::\|\| \|\|::\|\|\|\|:@LB@ GGGGGGAC AUGUUUGUG@LB@3'-UUU...CUGAA AC AUCUC...GAA-5'@LB@ \| \|@LB@ 60 40@LB@@LB@@LB@Energy -5.64 kcal/mol@LB@Hybridization Energy -19.5521 kcal/mol@LB@Unfolding Energy - mRNA 5.08593 kcal/mol@LB@Unfolding Energy - sRNA 8.82318 kcal/mol@LB@@LB@Position - mRNA 141 -- 160@LB@Position - sRNA 41 -- 59@LB@Position Seed - mRNA 142 -- 148@LB@Position Seed - sRNA 52 -- 58@LB@
64	0.02465	0.29	ct_045	pepA	-6.49	0.184926	191 -- 205	17 -- 33	cytosol aminopeptidase	_____________190_______________206\n_____________\|_________________\|\n5'-UUU...AACAA_________________AUUAC...CUG-3'\n______________AGAGGUUAUU__GUGGU\n______________\|\|\|:\|:\|\|\|\|__:\|\|\|:\n______________UCUUCGAUAA__UACCG\n3'-UUU...CUCAG__________GG_____CAAUC...GAA-5'\n_____________\|_________________\|\n_____________34________________16\n	191 -- 197	27 -- 33	-15.0477 kcal/mol	3.57571 kcal/mol	4.97804 kcal/mol	190 206@LB@ \| \|@LB@5'-UUU...AACAA AUUAC...CUG-3'@LB@ AGAGGUUAUU GUGGU@LB@ \|\|\|:\|:\|\|\|\| :\|\|\|:@LB@ UCUUCGAUAA UACCG@LB@3'-UUU...CUCAG GG CAAUC...GAA-5'@LB@ \| \|@LB@ 34 16@LB@@LB@@LB@Energy -6.49 kcal/mol@LB@Hybridization Energy -15.0477 kcal/mol@LB@Unfolding Energy - mRNA 3.57571 kcal/mol@LB@Unfolding Energy - sRNA 4.97804 kcal/mol@LB@@LB@Position - mRNA 191 -- 205@LB@Position - sRNA 17 -- 33@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 27 -- 33@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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