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
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@
28	0.007489	0.2199	ct_755	groEL_3	-5.45	0.299165	283 -- 296	17 -- 33	chaperonin GroEL	_____________282_______________297\n_____________\|_________________\|\n5'-CAC...AGUAA_________________CCCG-3'\n______________AGGGGU___UUUAUGGC\n______________\|\|::\|:___\|::\|\|\|\|\|\n______________UCUUCG___AGGUACCG\n3'-UUU...CUCAG______AUA________CAAUC...GAA-5'\n_____________\|_________________\|\n_____________34________________16\n	290 -- 296	17 -- 23	-13.7025 kcal/mol	3.27337 kcal/mol	4.97804 kcal/mol	282 297@LB@ \| \|@LB@5'-CAC...AGUAA CCCG-3'@LB@ AGGGGU UUUAUGGC@LB@ \|\|::\|: \|::\|\|\|\|\|@LB@ UCUUCG AGGUACCG@LB@3'-UUU...CUCAG AUA CAAUC...GAA-5'@LB@ \| \|@LB@ 34 16@LB@@LB@@LB@Energy -5.45 kcal/mol@LB@Hybridization Energy -13.7025 kcal/mol@LB@Unfolding Energy - mRNA 3.27337 kcal/mol@LB@Unfolding Energy - sRNA 4.97804 kcal/mol@LB@@LB@Position - mRNA 283 -- 296@LB@Position - sRNA 17 -- 33@LB@Position Seed - mRNA 290 -- 296@LB@Position Seed - sRNA 17 -- 23@LB@
22	0.005311	0.1984	ct_111	groES	-5.40	0.305537	269 -- 283	17 -- 33	co-chaperonin GroES	_____________268_______________284\n_____________\|_________________\|\n5'-AGC...GAAGA_____________CU__AAGAG...UUC-3'\n______________AGAAGCU__UCCA__GC\n______________\|\|\|\|\|\|\|__\|\|\|\|__\|\|\n______________UCUUCGA__AGGU__CG\n3'-UUU...CUCAG_______UA____AC__CAAUC...GAA-5'\n_____________\|_________________\|\n_____________34________________16\n	269 -- 275	27 -- 33	-15.094 kcal/mol	4.71335 kcal/mol	4.97804 kcal/mol	268 284@LB@ \| \|@LB@5'-AGC...GAAGA CU AAGAG...UUC-3'@LB@ AGAAGCU UCCA GC@LB@ \|\|\|\|\|\|\| \|\|\|\| \|\|@LB@ UCUUCGA AGGU CG@LB@3'-UUU...CUCAG UA AC CAAUC...GAA-5'@LB@ \| \|@LB@ 34 16@LB@@LB@@LB@Energy -5.40 kcal/mol@LB@Hybridization Energy -15.094 kcal/mol@LB@Unfolding Energy - mRNA 4.71335 kcal/mol@LB@Unfolding Energy - sRNA 4.97804 kcal/mol@LB@@LB@Position - mRNA 269 -- 283@LB@Position - sRNA 17 -- 33@LB@Position Seed - mRNA 269 -- 275@LB@Position Seed - sRNA 27 -- 33@LB@
105	0.03879	0.3036	ct_546	N/A	-8.76	0.056849	221 -- 228	80 -- 87	contains leader (17) peptide	_____________220______229\n_____________\|________\|\n5'-CGC...UUUAU________UUUUU...ACG-3'\n______________UGCGGCUA\n______________\|:\|\|\|\|\|\|\n______________AUGCCGAU\n3'-UUU...CCUCU________UGAGG...GAA-5'\n_____________\|________\|\n_____________88_______79\n	222 -- 228	80 -- 86	-12.4581 kcal/mol	2.60487 kcal/mol	1.09752 kcal/mol	220 229@LB@ \| \|@LB@5'-CGC...UUUAU UUUUU...ACG-3'@LB@ UGCGGCUA@LB@ \|:\|\|\|\|\|\|@LB@ AUGCCGAU@LB@3'-UUU...CCUCU UGAGG...GAA-5'@LB@ \| \|@LB@ 88 79@LB@@LB@@LB@Energy -8.76 kcal/mol@LB@Hybridization Energy -12.4581 kcal/mol@LB@Unfolding Energy - mRNA 2.60487 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 221 -- 228@LB@Position - sRNA 80 -- 87@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 80 -- 86@LB@
95	0.03456	0.2959	ct_073	N/A	-12.13	0.007785	261 -- 279	41 -- 58	contains leader (19) peptide	_____________260_________________280\n_____________\|___________________\|\n5'-GAC...CUGAU_________AUU_______UGACA...GGG-3'\n______________CCCUCUGUG___CAAACAU\n______________\|\|\|:\|\|\|\|\|___\|\|\|\|\|\|:\n______________GGGGGACAC___GUUUGUG\n3'-UUU...UGAAG_________AU________AUCUC...GAA-5'\n_____________\|___________________\|\n_____________59__________________40\n	263 -- 269	50 -- 56	-22.185 kcal/mol	2.22773 kcal/mol	7.82865 kcal/mol	260 280@LB@ \| \|@LB@5'-GAC...CUGAU AUU UGACA...GGG-3'@LB@ CCCUCUGUG CAAACAU@LB@ \|\|\|:\|\|\|\|\| \|\|\|\|\|\|:@LB@ GGGGGACAC GUUUGUG@LB@3'-UUU...UGAAG AU AUCUC...GAA-5'@LB@ \| \|@LB@ 59 40@LB@@LB@@LB@Energy -12.13 kcal/mol@LB@Hybridization Energy -22.185 kcal/mol@LB@Unfolding Energy - mRNA 2.22773 kcal/mol@LB@Unfolding Energy - sRNA 7.82865 kcal/mol@LB@@LB@Position - mRNA 261 -- 279@LB@Position - sRNA 41 -- 58@LB@Position Seed - mRNA 263 -- 269@LB@Position Seed - sRNA 50 -- 56@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@
177	0.07605	0.3532	ct_428	ubiE	-3.67	0.587989	9 -- 17	20 -- 28	demethylmenaquinone methyltransferase	_____________8_________18\n_____________\|_________\|\n___5'-UUCUUCAA_________UUCAG...AUA-3'\n______________CUAUUUCAU\n______________\|\|\|\|\|:\|\|\|\n______________GAUAAGGUA\n3'-UUU...UCUUC_________CCGCA...GAA-5'\n_____________\|_________\|\n_____________29________19\n	10 -- 16	21 -- 27	-8.26525 kcal/mol	0.050804 kcal/mol	4.54807 kcal/mol	8 18@LB@ \| \|@LB@ 5'-UUCUUCAA UUCAG...AUA-3'@LB@ CUAUUUCAU@LB@ \|\|\|\|\|:\|\|\|@LB@ GAUAAGGUA@LB@3'-UUU...UCUUC CCGCA...GAA-5'@LB@ \| \|@LB@ 29 19@LB@@LB@@LB@Energy -3.67 kcal/mol@LB@Hybridization Energy -8.26525 kcal/mol@LB@Unfolding Energy - mRNA 0.050804 kcal/mol@LB@Unfolding Energy - sRNA 4.54807 kcal/mol@LB@@LB@Position - mRNA 9 -- 17@LB@Position - sRNA 20 -- 28@LB@Position Seed - mRNA 10 -- 16@LB@Position Seed - sRNA 21 -- 27@LB@
189	0.0841	0.363	ct_792	mutS	-5.18	0.336119	140 -- 151	22 -- 33	DNA mismatch repair protein MutS	_____________139__________152\n_____________\|____________\|\n5'-AUA...ACAUA____C_______CCUAC...AAG-3'\n______________AGAG_CUGUUCC\n______________\|\|\|:_\|\|:\|\|\|\|\n______________UCUU_GAUAAGG\n3'-UUU...CUCAG____C_______UACCG...GAA-5'\n_____________\|____________\|\n_____________34___________21\n	145 -- 151	22 -- 28	-12.2041 kcal/mol	2.29966 kcal/mol	4.72509 kcal/mol	139 152@LB@ \| \|@LB@5'-AUA...ACAUA C CCUAC...AAG-3'@LB@ AGAG CUGUUCC@LB@ \|\|\|: \|\|:\|\|\|\|@LB@ UCUU GAUAAGG@LB@3'-UUU...CUCAG C UACCG...GAA-5'@LB@ \| \|@LB@ 34 21@LB@@LB@@LB@Energy -5.18 kcal/mol@LB@Hybridization Energy -12.2041 kcal/mol@LB@Unfolding Energy - mRNA 2.29966 kcal/mol@LB@Unfolding Energy - sRNA 4.72509 kcal/mol@LB@@LB@Position - mRNA 140 -- 151@LB@Position - sRNA 22 -- 33@LB@Position Seed - mRNA 145 -- 151@LB@Position Seed - sRNA 22 -- 28@LB@
75	0.02725	0.29	ct_536	dnaQ_2	-6.54	0.180881	173 -- 186	18 -- 31	DNA polymerase III subunit epsilon	_____________172____________187\n_____________\|______________\|\n5'-AGA...GAUUU_____U________AGAAC...GGU-3'\n______________GAGCU_UUUUAUGG\n______________:\|\|\|\|_\|\|::\|\|\|\|\n______________UUCGA_AAGGUACC\n3'-UUU...CAGUC_____U________GCAAU...GAA-5'\n_____________\|______________\|\n_____________32_____________17\n	180 -- 186	18 -- 24	-14.3298 kcal/mol	2.92947 kcal/mol	4.86077 kcal/mol	172 187@LB@ \| \|@LB@5'-AGA...GAUUU U AGAAC...GGU-3'@LB@ GAGCU UUUUAUGG@LB@ :\|\|\|\| \|\|::\|\|\|\|@LB@ UUCGA AAGGUACC@LB@3'-UUU...CAGUC U GCAAU...GAA-5'@LB@ \| \|@LB@ 32 17@LB@@LB@@LB@Energy -6.54 kcal/mol@LB@Hybridization Energy -14.3298 kcal/mol@LB@Unfolding Energy - mRNA 2.92947 kcal/mol@LB@Unfolding Energy - sRNA 4.86077 kcal/mol@LB@@LB@Position - mRNA 173 -- 186@LB@Position - sRNA 18 -- 31@LB@Position Seed - mRNA 180 -- 186@LB@Position Seed - sRNA 18 -- 24@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@

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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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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