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
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@
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@
190	0.08414	0.363	ct_503	N/A	-6.17	0.215667	244 -- 250	81 -- 87		_____________243_____251\n_____________\|_______\|\n5'-UGG...UUUGU_______UCGCA...CUC-3'\n______________UACGGUU\n______________\|\|\|\|\|:\|\n______________AUGCCGA\n3'-UUU...CCUCU_______UUGAG...GAA-5'\n_____________\|_______\|\n_____________88______80\n	244 -- 250	81 -- 87	-7.94334 kcal/mol	0.67364 kcal/mol	1.09752 kcal/mol	243 251@LB@ \| \|@LB@5'-UGG...UUUGU UCGCA...CUC-3'@LB@ UACGGUU@LB@ \|\|\|\|\|:\|@LB@ AUGCCGA@LB@3'-UUU...CCUCU UUGAG...GAA-5'@LB@ \| \|@LB@ 88 80@LB@@LB@@LB@Energy -6.17 kcal/mol@LB@Hybridization Energy -7.94334 kcal/mol@LB@Unfolding Energy - mRNA 0.67364 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 244 -- 250@LB@Position - sRNA 81 -- 87@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 81 -- 87@LB@
193	0.08525	0.3631	ct_196	N/A	-5.32	0.316248	140 -- 149	20 -- 29	inclusion membrane protein	_____________139________150\n_____________\|__________\|\n5'-UUU...AUAAU__________UUCUU...AAC-3'\n______________GCUAUUUCAU\n______________\|\|\|\|\|\|:\|\|\|\n______________CGAUAAGGUA\n3'-UUU...GUCUU__________CCGCA...GAA-5'\n_____________\|__________\|\n_____________30_________19\n	141 -- 147	22 -- 28	-11.6207 kcal/mol	1.68905 kcal/mol	4.60882 kcal/mol	139 150@LB@ \| \|@LB@5'-UUU...AUAAU UUCUU...AAC-3'@LB@ GCUAUUUCAU@LB@ \|\|\|\|\|\|:\|\|\|@LB@ CGAUAAGGUA@LB@3'-UUU...GUCUU CCGCA...GAA-5'@LB@ \| \|@LB@ 30 19@LB@@LB@@LB@Energy -5.32 kcal/mol@LB@Hybridization Energy -11.6207 kcal/mol@LB@Unfolding Energy - mRNA 1.68905 kcal/mol@LB@Unfolding Energy - sRNA 4.60882 kcal/mol@LB@@LB@Position - mRNA 140 -- 149@LB@Position - sRNA 20 -- 29@LB@Position Seed - mRNA 141 -- 147@LB@Position Seed - sRNA 22 -- 28@LB@
196	0.08741	0.3657	ct_698	N/A	-4.23	0.486304	280 -- 292	22 -- 34	tRNA modification GTPase	_____________279___________293\n_____________\|_____________\|\n5'-AAA...CGGAC____U________UAUUUCUG-3'\n______________CGGA_GCUAUUUC\n______________\|:\|\|_\|\|\|\|\|\|:\|\n______________GUCU_CGAUAAGG\n3'-UUU...UCUCA____U________UACCG...GAA-5'\n_____________\|_____________\|\n_____________35____________21\n	285 -- 291	23 -- 29	-13.8571 kcal/mol	4.89721 kcal/mol	4.72608 kcal/mol	279 293@LB@ \| \|@LB@5'-AAA...CGGAC U UAUUUCUG-3'@LB@ CGGA GCUAUUUC@LB@ \|:\|\| \|\|\|\|\|\|:\|@LB@ GUCU CGAUAAGG@LB@3'-UUU...UCUCA U UACCG...GAA-5'@LB@ \| \|@LB@ 35 21@LB@@LB@@LB@Energy -4.23 kcal/mol@LB@Hybridization Energy -13.8571 kcal/mol@LB@Unfolding Energy - mRNA 4.89721 kcal/mol@LB@Unfolding Energy - sRNA 4.72608 kcal/mol@LB@@LB@Position - mRNA 280 -- 292@LB@Position - sRNA 22 -- 34@LB@Position Seed - mRNA 285 -- 291@LB@Position Seed - sRNA 23 -- 29@LB@
198	0.08843	0.3671	ct_257	N/A	-6.39	0.194258	76 -- 83	79 -- 86		_____________75_______84\n_____________\|________\|\n5'-CUA...GGCGG________CAGAA...UCA-3'\n______________AUGGCUGA\n______________\|:\|\|\|\|:\|\n______________UGCCGAUU\n3'-UUU...CUCUA________GAGGU...GAA-5'\n_____________\|________\|\n_____________87_______78\n	77 -- 83	79 -- 85	-9.5904 kcal/mol	2.10083 kcal/mol	1.09752 kcal/mol	75 84@LB@ \| \|@LB@5'-CUA...GGCGG CAGAA...UCA-3'@LB@ AUGGCUGA@LB@ \|:\|\|\|\|:\|@LB@ UGCCGAUU@LB@3'-UUU...CUCUA GAGGU...GAA-5'@LB@ \| \|@LB@ 87 78@LB@@LB@@LB@Energy -6.39 kcal/mol@LB@Hybridization Energy -9.5904 kcal/mol@LB@Unfolding Energy - mRNA 2.10083 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 76 -- 83@LB@Position - sRNA 79 -- 86@LB@Position Seed - mRNA 77 -- 83@LB@Position Seed - sRNA 79 -- 85@LB@
140	0.05617	0.3262	ct_759	nlpD	-2.72	0.757894	26 -- 32	51 -- 57	muramidase	_____________25______33\n_____________\|_______\|\n5'-GAG...AGAGU_______AACCG...AGU-3'\n______________UCCCUGU\n______________:\|\|\|\|\|\|\n______________GGGGACA\n3'-UUU...GAAGG_______CAUGU...GAA-5'\n_____________\|_______\|\n_____________58______50\n	26 -- 32	51 -- 57	-10.8083 kcal/mol	0.989353 kcal/mol	7.09845 kcal/mol	25 33@LB@ \| \|@LB@5'-GAG...AGAGU AACCG...AGU-3'@LB@ UCCCUGU@LB@ :\|\|\|\|\|\|@LB@ GGGGACA@LB@3'-UUU...GAAGG CAUGU...GAA-5'@LB@ \| \|@LB@ 58 50@LB@@LB@@LB@Energy -2.72 kcal/mol@LB@Hybridization Energy -10.8083 kcal/mol@LB@Unfolding Energy - mRNA 0.989353 kcal/mol@LB@Unfolding Energy - sRNA 7.09845 kcal/mol@LB@@LB@Position - mRNA 26 -- 32@LB@Position - sRNA 51 -- 57@LB@Position Seed - mRNA 26 -- 32@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@
6	0.000543	0.07439	ct_280	nqr4	-8.45	0.067322	89 -- 131	2 -- 35	Na(+)-translocating NADH-quinone reductase subunit D	_____________88___________________________________________132\n_____________\|____________________________________________\|\n5'-GAC...GAAUU__________C___GACUUGUA_________CC_______UU__CUCAU...CGG-3'\n______________UCAGGAGCUA_UUU________AUGGUGUUA__GAAU_CC__CU\n______________\|\|\|\|:\|\|\|\|\|_\|::________\|\|\|\|:\|\|\|\|__\|\|\|\|_\|\|__\|\|\n______________AGUCUUCGAU_AGG________UACCGCAAU__CUUA_GG__GA\n3'-UUU...AUCUC__________A__________________________U__UU__A-5'\n_____________\|____________________________________________\|\n_____________36___________________________________________1\n	113 -- 119	13 -- 19	-28.603 kcal/mol	11.5634 kcal/mol	8.59199 kcal/mol	88 132@LB@ \| \|@LB@5'-GAC...GAAUU C GACUUGUA CC UU CUCAU...CGG-3'@LB@ UCAGGAGCUA UUU AUGGUGUUA GAAU CC CU@LB@ \|\|\|\|:\|\|\|\|\| \|:: \|\|\|\|:\|\|\|\| \|\|\|\| \|\| \|\|@LB@ AGUCUUCGAU AGG UACCGCAAU CUUA GG GA@LB@3'-UUU...AUCUC A U UU A-5'@LB@ \| \|@LB@ 36 1@LB@@LB@@LB@Energy -8.45 kcal/mol@LB@Hybridization Energy -28.603 kcal/mol@LB@Unfolding Energy - mRNA 11.5634 kcal/mol@LB@Unfolding Energy - sRNA 8.59199 kcal/mol@LB@@LB@Position - mRNA 89 -- 131@LB@Position - sRNA 2 -- 35@LB@Position Seed - mRNA 113 -- 119@LB@Position Seed - sRNA 13 -- 19@LB@
120	0.04883	0.3262	ct_827	nrdA	-5.19	0.334730	7 -- 13	82 -- 88	ribonucleoside-diphosphate reductase subunit alpha	_____________6_______14\n_____________\|_______\|\n_____5'-UUCUAU_______AUACA...CUU-3'\n______________AUAUGGU\n______________\|\|\|:\|\|:\n______________UAUGCCG\n3'-UUU...GCCUC_______AUUGA...GAA-5'\n_____________\|_______\|\n_____________89______81\n	7 -- 13	82 -- 88	-6.89581 kcal/mol	0.608866 kcal/mol	1.09753 kcal/mol	6 14@LB@ \| \|@LB@ 5'-UUCUAU AUACA...CUU-3'@LB@ AUAUGGU@LB@ \|\|\|:\|\|:@LB@ UAUGCCG@LB@3'-UUU...GCCUC AUUGA...GAA-5'@LB@ \| \|@LB@ 89 81@LB@@LB@@LB@Energy -5.19 kcal/mol@LB@Hybridization Energy -6.89581 kcal/mol@LB@Unfolding Energy - mRNA 0.608866 kcal/mol@LB@Unfolding Energy - sRNA 1.09753 kcal/mol@LB@@LB@Position - mRNA 7 -- 13@LB@Position - sRNA 82 -- 88@LB@Position Seed - mRNA 7 -- 13@LB@Position Seed - sRNA 82 -- 88@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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