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
121	0.04894	0.3262	ct_310	atpE	-7.64	0.103947	27 -- 34	80 -- 87	V-type ATP synthase subunit E	_____________26_______35\n_____________\|________\|\n5'-GCA...CCUUC________CCUUC...UUC-3'\n______________UACGGCUG\n______________\|\|\|\|\|\|\|:\n______________AUGCCGAU\n3'-UUU...CCUCU________UGAGG...GAA-5'\n_____________\|________\|\n_____________88_______79\n	28 -- 34	80 -- 86	-11.9035 kcal/mol	3.17039 kcal/mol	1.09752 kcal/mol	26 35@LB@ \| \|@LB@5'-GCA...CCUUC CCUUC...UUC-3'@LB@ UACGGCUG@LB@ \|\|\|\|\|\|\|:@LB@ AUGCCGAU@LB@3'-UUU...CCUCU UGAGG...GAA-5'@LB@ \| \|@LB@ 88 79@LB@@LB@@LB@Energy -7.64 kcal/mol@LB@Hybridization Energy -11.9035 kcal/mol@LB@Unfolding Energy - mRNA 3.17039 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 27 -- 34@LB@Position - sRNA 80 -- 87@LB@Position Seed - mRNA 28 -- 34@LB@Position Seed - sRNA 80 -- 86@LB@
122	0.04895	0.3262	ct_683	N/A	-8.21	0.076506	46 -- 53	80 -- 87		_____________45_______54\n_____________\|________\|\n5'-AAG...GUACU________GGAGA...AAG-3'\n______________UACGGCUA\n______________\|\|\|\|\|\|\|\|\n______________AUGCCGAU\n3'-UUU...CCUCU________UGAGG...GAA-5'\n_____________\|________\|\n_____________88_______79\n	47 -- 53	80 -- 86	-12.375 kcal/mol	3.06531 kcal/mol	1.09752 kcal/mol	45 54@LB@ \| \|@LB@5'-AAG...GUACU GGAGA...AAG-3'@LB@ UACGGCUA@LB@ \|\|\|\|\|\|\|\|@LB@ AUGCCGAU@LB@3'-UUU...CCUCU UGAGG...GAA-5'@LB@ \| \|@LB@ 88 79@LB@@LB@@LB@Energy -8.21 kcal/mol@LB@Hybridization Energy -12.375 kcal/mol@LB@Unfolding Energy - mRNA 3.06531 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 46 -- 53@LB@Position - sRNA 80 -- 87@LB@Position Seed - mRNA 47 -- 53@LB@Position Seed - sRNA 80 -- 86@LB@
123	0.04914	0.3262	ct_754	icc	-7.18	0.131374	254 -- 264	47 -- 57		_____________253_________265\n_____________\|___________\|\n5'-AUU...AUUCA___________UCCCU...GCU-3'\n______________CUUCUGUGUAC\n______________\|::\|\|\|\|\|\|\|\|\n______________GGGGACACAUG\n3'-UUU...GAAGG___________UUUGU...GAA-5'\n_____________\|___________\|\n_____________58__________46\n	258 -- 264	47 -- 53	-16.923 kcal/mol	2.45356 kcal/mol	7.2877 kcal/mol	253 265@LB@ \| \|@LB@5'-AUU...AUUCA UCCCU...GCU-3'@LB@ CUUCUGUGUAC@LB@ \|::\|\|\|\|\|\|\|\|@LB@ GGGGACACAUG@LB@3'-UUU...GAAGG UUUGU...GAA-5'@LB@ \| \|@LB@ 58 46@LB@@LB@@LB@Energy -7.18 kcal/mol@LB@Hybridization Energy -16.923 kcal/mol@LB@Unfolding Energy - mRNA 2.45356 kcal/mol@LB@Unfolding Energy - sRNA 7.2877 kcal/mol@LB@@LB@Position - mRNA 254 -- 264@LB@Position - sRNA 47 -- 57@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 47 -- 53@LB@
124	0.04963	0.3262	ct_290	ptsN_1	-8.82	0.054773	1 -- 15	18 -- 32	PTS fructose transporter subunit IIA	______________1______________16\n______________\|______________\|\n___________5'-____G__________GAUGC...UUA-3'\n______________GAGG_UAUUUUGUGG\n______________\|\|:\|_\|\|\|\|:::\|\|\|\n______________CUUC_AUAAGGUACC\n3'-UUU...UCAGU____G__________GCAAU...GAA-5'\n_____________\|_______________\|\n_____________33______________17\n	9 -- 15	18 -- 24	-16.4794 kcal/mol	2.69105 kcal/mol	4.96566 kcal/mol	1 16@LB@ \| \|@LB@ 5'- G GAUGC...UUA-3'@LB@ GAGG UAUUUUGUGG@LB@ \|\|:\| \|\|\|\|:::\|\|\|@LB@ CUUC AUAAGGUACC@LB@3'-UUU...UCAGU G GCAAU...GAA-5'@LB@ \| \|@LB@ 33 17@LB@@LB@@LB@Energy -8.82 kcal/mol@LB@Hybridization Energy -16.4794 kcal/mol@LB@Unfolding Energy - mRNA 2.69105 kcal/mol@LB@Unfolding Energy - sRNA 4.96566 kcal/mol@LB@@LB@Position - mRNA 1 -- 15@LB@Position - sRNA 18 -- 32@LB@Position Seed - mRNA 9 -- 15@LB@Position Seed - sRNA 18 -- 24@LB@
125	0.05005	0.3262	ct_644	yohI	-5.25	0.326074	256 -- 262	53 -- 59	tRNA-dihydrouridine synthase	_____________255_____263\n_____________\|_______\|\n5'-CUG...CUACG_______AGCGG...CGG-3'\n______________CCCCCUU\n______________\|\|\|\|\|:\|\n______________GGGGGGA\n3'-UUU...CUGAA_______CACAU...GAA-5'\n_____________\|_______\|\n_____________60______52\n	256 -- 262	53 -- 59	-11.5527 kcal/mol	0.822659 kcal/mol	5.47887 kcal/mol	255 263@LB@ \| \|@LB@5'-CUG...CUACG AGCGG...CGG-3'@LB@ CCCCCUU@LB@ \|\|\|\|\|:\|@LB@ GGGGGGA@LB@3'-UUU...CUGAA CACAU...GAA-5'@LB@ \| \|@LB@ 60 52@LB@@LB@@LB@Energy -5.25 kcal/mol@LB@Hybridization Energy -11.5527 kcal/mol@LB@Unfolding Energy - mRNA 0.822659 kcal/mol@LB@Unfolding Energy - sRNA 5.47887 kcal/mol@LB@@LB@Position - mRNA 256 -- 262@LB@Position - sRNA 53 -- 59@LB@Position Seed - mRNA 256 -- 262@LB@Position Seed - sRNA 53 -- 59@LB@
126	0.05087	0.3262	ct_474	N/A	-6.92	0.149609	150 -- 156	15 -- 21		_____________149_____157\n_____________\|_______\|\n5'-AAA...ACGAA_______GUAUA...UAU-3'\n______________GUGGCGU\n______________:\|\|\|\|\|\|\n______________UACCGCA\n3'-UUU...UAAGG_______AUCUU...GAA-5'\n_____________\|_______\|\n_____________22______14\n	150 -- 156	15 -- 21	-10.3963 kcal/mol	2.28336 kcal/mol	1.18845 kcal/mol	149 157@LB@ \| \|@LB@5'-AAA...ACGAA GUAUA...UAU-3'@LB@ GUGGCGU@LB@ :\|\|\|\|\|\|@LB@ UACCGCA@LB@3'-UUU...UAAGG AUCUU...GAA-5'@LB@ \| \|@LB@ 22 14@LB@@LB@@LB@Energy -6.92 kcal/mol@LB@Hybridization Energy -10.3963 kcal/mol@LB@Unfolding Energy - mRNA 2.28336 kcal/mol@LB@Unfolding Energy - sRNA 1.18845 kcal/mol@LB@@LB@Position - mRNA 150 -- 156@LB@Position - sRNA 15 -- 21@LB@Position Seed - mRNA 150 -- 156@LB@Position Seed - sRNA 15 -- 21@LB@
127	0.0509	0.3262	ct_808	cafE	-7.80	0.095102	169 -- 204	18 -- 57	ribonuclease E	_____________168_________________________________________205\n_____________\|___________________________________________\|\n5'-GUU...GAGGA_______A______________CAU______ACG_________AAAAC...AAA-3'\n______________CUCCUGU____GAGCGC_AGAG___UUAGGA______CCAUGG\n______________\|:\|\|\|\|\|____:\|:\|:\|_\|\|\|\|___\|:\|\|:\|______\|\|\|\|\|\|\n______________GGGGACA____UUUGUG_UCUC___AGUCUU______GGUACC\n3'-UUU...GAAGG_______CAUG______A_____________CGAUAA______GCAAU...GAA-5'\n_____________\|___________________________________________\|\n_____________58__________________________________________17\n	169 -- 175	51 -- 57	-30.1775 kcal/mol	9.43695 kcal/mol	12.9362 kcal/mol	168 205@LB@ \| \|@LB@5'-GUU...GAGGA A CAU ACG AAAAC...AAA-3'@LB@ CUCCUGU GAGCGC AGAG UUAGGA CCAUGG@LB@ \|:\|\|\|\|\| :\|:\|:\| \|\|\|\| \|:\|\|:\| \|\|\|\|\|\|@LB@ GGGGACA UUUGUG UCUC AGUCUU GGUACC@LB@3'-UUU...GAAGG CAUG A CGAUAA GCAAU...GAA-5'@LB@ \| \|@LB@ 58 17@LB@@LB@@LB@Energy -7.80 kcal/mol@LB@Hybridization Energy -30.1775 kcal/mol@LB@Unfolding Energy - mRNA 9.43695 kcal/mol@LB@Unfolding Energy - sRNA 12.9362 kcal/mol@LB@@LB@Position - mRNA 169 -- 204@LB@Position - sRNA 18 -- 57@LB@Position Seed - mRNA 169 -- 175@LB@Position Seed - sRNA 51 -- 57@LB@
128	0.05098	0.3262	ct_279	nqr3	-7.28	0.125274	283 -- 291	51 -- 59	Na(+)-translocating NADH-quinone reductase subunit C	_____________282_______292\n_____________\|_________\|\n5'-CCG...UGGUA_________CUUCU...UGU-3'\n______________CCCUCCUGU\n______________\|\|\|:\|\|\|\|\|\n______________GGGGGGACA\n3'-UUU...CUGAA_________CAUGU...GAA-5'\n_____________\|_________\|\n_____________60________50\n	285 -- 291	51 -- 57	-15.9842 kcal/mol	0.606269 kcal/mol	8.10291 kcal/mol	282 292@LB@ \| \|@LB@5'-CCG...UGGUA CUUCU...UGU-3'@LB@ CCCUCCUGU@LB@ \|\|\|:\|\|\|\|\|@LB@ GGGGGGACA@LB@3'-UUU...CUGAA CAUGU...GAA-5'@LB@ \| \|@LB@ 60 50@LB@@LB@@LB@Energy -7.28 kcal/mol@LB@Hybridization Energy -15.9842 kcal/mol@LB@Unfolding Energy - mRNA 0.606269 kcal/mol@LB@Unfolding Energy - sRNA 8.10291 kcal/mol@LB@@LB@Position - mRNA 283 -- 291@LB@Position - sRNA 51 -- 59@LB@Position Seed - mRNA 285 -- 291@LB@Position Seed - sRNA 51 -- 57@LB@
129	0.0523	0.3262	ct_872	pmpH	-6.76	0.162049	85 -- 103	18 -- 34	outer membrane protein PmpH	_____________84__________________104\n_____________\|___________________\|\n5'-AGA...CAAUA_______A___GG______AAGAU...AUG-3'\n______________UAGAAGU_UAU__CCAUGG\n______________:\|\|\|\|\|:_\|\|\|__\|\|\|\|\|\|\n______________GUCUUCG_AUA__GGUACC\n3'-UUU...UCUCA___________A_______GCAAU...GAA-5'\n_____________\|___________________\|\n_____________35__________________17\n	85 -- 91	28 -- 34	-16.9306 kcal/mol	5.18888 kcal/mol	4.97803 kcal/mol	84 104@LB@ \| \|@LB@5'-AGA...CAAUA A GG AAGAU...AUG-3'@LB@ UAGAAGU UAU CCAUGG@LB@ :\|\|\|\|\|: \|\|\| \|\|\|\|\|\|@LB@ GUCUUCG AUA GGUACC@LB@3'-UUU...UCUCA A GCAAU...GAA-5'@LB@ \| \|@LB@ 35 17@LB@@LB@@LB@Energy -6.76 kcal/mol@LB@Hybridization Energy -16.9306 kcal/mol@LB@Unfolding Energy - mRNA 5.18888 kcal/mol@LB@Unfolding Energy - sRNA 4.97803 kcal/mol@LB@@LB@Position - mRNA 85 -- 103@LB@Position - sRNA 18 -- 34@LB@Position Seed - mRNA 85 -- 91@LB@Position Seed - sRNA 28 -- 34@LB@
130	0.05252	0.3262	ct_826	pssA	-5.40	0.306560	126 -- 136	23 -- 33	CDP-diacylglycerol--serine O-phosphatidyltransferase	_____________125_________137\n_____________\|___________\|\n5'-AUA...UAAAA_______UC__AACAA...UCA-3'\n______________AGAAGCU__UC\n______________\|\|\|\|\|\|\|__\|\|\n______________UCUUCGA__AG\n3'-UUU...CUCAG_______UA__GUACC...GAA-5'\n_____________\|___________\|\n_____________34__________22\n	126 -- 132	27 -- 33	-11.4676 kcal/mol	1.34949 kcal/mol	4.72321 kcal/mol	125 137@LB@ \| \|@LB@5'-AUA...UAAAA UC AACAA...UCA-3'@LB@ AGAAGCU UC@LB@ \|\|\|\|\|\|\| \|\|@LB@ UCUUCGA AG@LB@3'-UUU...CUCAG UA GUACC...GAA-5'@LB@ \| \|@LB@ 34 22@LB@@LB@@LB@Energy -5.40 kcal/mol@LB@Hybridization Energy -11.4676 kcal/mol@LB@Unfolding Energy - mRNA 1.34949 kcal/mol@LB@Unfolding Energy - sRNA 4.72321 kcal/mol@LB@@LB@Position - mRNA 126 -- 136@LB@Position - sRNA 23 -- 33@LB@Position Seed - mRNA 126 -- 132@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)

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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