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
108	0.04117	0.3134	ct_817	tyrP_1	-6.29	0.204127	20 -- 34	17 -- 30	tyrosine-specific transport protein	_____________19______________35\n_____________\|_______________\|\n5'-CGA...AUCAU____UACA_______UUUAC...UCC-3'\n______________GGCU____CCAUGGC\n______________:\|\|\|____\|\|\|\|\|\|\|\n______________UCGA____GGUACCG\n3'-UUU...AGUCU____UAA________CAAUC...GAA-5'\n_____________\|_______________\|\n_____________31______________16\n	28 -- 34	17 -- 23	-15.6862 kcal/mol	4.66372 kcal/mol	4.73426 kcal/mol	19 35@LB@ \| \|@LB@5'-CGA...AUCAU UACA UUUAC...UCC-3'@LB@ GGCU CCAUGGC@LB@ :\|\|\| \|\|\|\|\|\|\|@LB@ UCGA GGUACCG@LB@3'-UUU...AGUCU UAA CAAUC...GAA-5'@LB@ \| \|@LB@ 31 16@LB@@LB@@LB@Energy -6.29 kcal/mol@LB@Hybridization Energy -15.6862 kcal/mol@LB@Unfolding Energy - mRNA 4.66372 kcal/mol@LB@Unfolding Energy - sRNA 4.73426 kcal/mol@LB@@LB@Position - mRNA 20 -- 34@LB@Position - sRNA 17 -- 30@LB@Position Seed - mRNA 28 -- 34@LB@Position Seed - sRNA 17 -- 23@LB@
51	0.01855	0.29	ct_758	murD	-8.46	0.066834	21 -- 39	25 -- 51	UDP-N-acetylmuramoylalanine--D-glutamate ligase	_____________20__________________________40\n_____________\|___________________________\|\n5'-CUG...GUGAU___________________________AAAUU...ACA-3'\n______________UGUACA________AGUCGGAAGUUAU\n______________\|\|\|\|\|\|________\|\|\|\|:\|\|\|\|:\|\|\|\n______________ACAUGU________UCAGUCUUCGAUA\n3'-UUU...GGGAC______UUGUGAUC_____________AGGUA...GAA-5'\n_____________\|___________________________\|\n_____________52__________________________24\n	33 -- 39	25 -- 31	-21.2974 kcal/mol	1.17475 kcal/mol	11.6617 kcal/mol	20 40@LB@ \| \|@LB@5'-CUG...GUGAU AAAUU...ACA-3'@LB@ UGUACA AGUCGGAAGUUAU@LB@ \|\|\|\|\|\| \|\|\|\|:\|\|\|\|:\|\|\|@LB@ ACAUGU UCAGUCUUCGAUA@LB@3'-UUU...GGGAC UUGUGAUC AGGUA...GAA-5'@LB@ \| \|@LB@ 52 24@LB@@LB@@LB@Energy -8.46 kcal/mol@LB@Hybridization Energy -21.2974 kcal/mol@LB@Unfolding Energy - mRNA 1.17475 kcal/mol@LB@Unfolding Energy - sRNA 11.6617 kcal/mol@LB@@LB@Position - mRNA 21 -- 39@LB@Position - sRNA 25 -- 51@LB@Position Seed - mRNA 33 -- 39@LB@Position Seed - sRNA 25 -- 31@LB@
32	0.009822	0.2518	ct_649	ygfA	-6.64	0.172247	22 -- 28	80 -- 86	5-formyltetrahydrofolate cyclo-ligase	_____________21______29\n_____________\|_______\|\n5'-UAC...AAGUG_______CCGAG...AGC-3'\n______________AUGGCUA\n______________\|:\|\|\|\|\|\n______________UGCCGAU\n3'-UUU...CUCUA_______UGAGG...GAA-5'\n_____________\|_______\|\n_____________87______79\n	22 -- 28	80 -- 86	-8.81528 kcal/mol	1.11082 kcal/mol	1.06449 kcal/mol	21 29@LB@ \| \|@LB@5'-UAC...AAGUG CCGAG...AGC-3'@LB@ AUGGCUA@LB@ \|:\|\|\|\|\|@LB@ UGCCGAU@LB@3'-UUU...CUCUA UGAGG...GAA-5'@LB@ \| \|@LB@ 87 79@LB@@LB@@LB@Energy -6.64 kcal/mol@LB@Hybridization Energy -8.81528 kcal/mol@LB@Unfolding Energy - mRNA 1.11082 kcal/mol@LB@Unfolding Energy - sRNA 1.06449 kcal/mol@LB@@LB@Position - mRNA 22 -- 28@LB@Position - sRNA 80 -- 86@LB@Position Seed - mRNA 22 -- 28@LB@Position Seed - sRNA 80 -- 86@LB@
7	0.0007305	0.07962	ct_505	gapA	-11.17	0.013986	23 -- 47	19 -- 39	glyceraldehyde-3-phosphate dehydrogenase	_____________22________________________48\n_____________\|_________________________\|\n5'-GUC...AUAGA______AUUG___________G___UGUUA...AUU-3'\n______________AGAGUC____GGAAGUUAUUU_AUG\n______________\|\|\|\|\|\|____:\|\|\|\|:\|\|\|\|:_\|\|\|\n______________UCUCAG____UCUUCGAUAAG_UAC\n3'-UUU...UGUGA_____________________G___CGCAA...GAA-5'\n_____________\|_________________________\|\n_____________40________________________18\n	34 -- 40	26 -- 32	-23.0041 kcal/mol	2.2627 kcal/mol	9.5668 kcal/mol	22 48@LB@ \| \|@LB@5'-GUC...AUAGA AUUG G UGUUA...AUU-3'@LB@ AGAGUC GGAAGUUAUUU AUG@LB@ \|\|\|\|\|\| :\|\|\|\|:\|\|\|\|: \|\|\|@LB@ UCUCAG UCUUCGAUAAG UAC@LB@3'-UUU...UGUGA G CGCAA...GAA-5'@LB@ \| \|@LB@ 40 18@LB@@LB@@LB@Energy -11.17 kcal/mol@LB@Hybridization Energy -23.0041 kcal/mol@LB@Unfolding Energy - mRNA 2.2627 kcal/mol@LB@Unfolding Energy - sRNA 9.5668 kcal/mol@LB@@LB@Position - mRNA 23 -- 47@LB@Position - sRNA 19 -- 39@LB@Position Seed - mRNA 34 -- 40@LB@Position Seed - sRNA 26 -- 32@LB@
4	0.0004436	0.07439	ct_864	xerD	-16.31	0.000480	24 -- 38	17 -- 31	site-specific tyrosine recombinase XerD	_____________23______________39\n_____________\|_______________\|\n5'-CAU...AUGGA_______________ACCUU...AUU-3'\n______________GAGCUAUUCCAUGGU\n______________:\|\|\|\|\|\|\|\|\|\|\|\|\|:\n______________UUCGAUAAGGUACCG\n3'-UUU...CAGUC_______________CAAUC...GAA-5'\n_____________\|_______________\|\n_____________32______________16\n	32 -- 38	17 -- 23	-24.2689 kcal/mol	3.09995 kcal/mol	4.86101 kcal/mol	23 39@LB@ \| \|@LB@5'-CAU...AUGGA ACCUU...AUU-3'@LB@ GAGCUAUUCCAUGGU@LB@ :\|\|\|\|\|\|\|\|\|\|\|\|\|:@LB@ UUCGAUAAGGUACCG@LB@3'-UUU...CAGUC CAAUC...GAA-5'@LB@ \| \|@LB@ 32 16@LB@@LB@@LB@Energy -16.31 kcal/mol@LB@Hybridization Energy -24.2689 kcal/mol@LB@Unfolding Energy - mRNA 3.09995 kcal/mol@LB@Unfolding Energy - sRNA 4.86101 kcal/mol@LB@@LB@Position - mRNA 24 -- 38@LB@Position - sRNA 17 -- 31@LB@Position Seed - mRNA 32 -- 38@LB@Position Seed - sRNA 17 -- 23@LB@
170	0.07264	0.3448	ct_415	yebL	-4.69	0.409849	24 -- 30	22 -- 28	metal ABC transporter substrate-binding protein	_____________23______31\n_____________\|_______\|\n5'-AUU...AAAAA_______UCACC...CCU-3'\n______________CUGUUCC\n______________\|\|:\|\|\|\|\n______________GAUAAGG\n3'-UUU...UCUUC_______UACCG...GAA-5'\n_____________\|_______\|\n_____________29______21\n	24 -- 30	22 -- 28	-9.14166 kcal/mol	0.102316 kcal/mol	4.35007 kcal/mol	23 31@LB@ \| \|@LB@5'-AUU...AAAAA UCACC...CCU-3'@LB@ CUGUUCC@LB@ \|\|:\|\|\|\|@LB@ GAUAAGG@LB@3'-UUU...UCUUC UACCG...GAA-5'@LB@ \| \|@LB@ 29 21@LB@@LB@@LB@Energy -4.69 kcal/mol@LB@Hybridization Energy -9.14166 kcal/mol@LB@Unfolding Energy - mRNA 0.102316 kcal/mol@LB@Unfolding Energy - sRNA 4.35007 kcal/mol@LB@@LB@Position - mRNA 24 -- 30@LB@Position - sRNA 22 -- 28@LB@Position Seed - mRNA 24 -- 30@LB@Position Seed - sRNA 22 -- 28@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@
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@
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@
171	0.07267	0.3448	ct_057	gcpE	-5.03	0.358241	27 -- 78	18 -- 60	4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (flavodoxin)	_____________26____________________________________________________79\n_____________\|_____________________________________________________\|\n5'-AGA...GAACA____UCAA_______AAUU________AUUUUUAAAG_______UC_______AGACC...AAU-3'\n______________UCCC____CCC_GUG____UAUAAACA__________GGAAGUU__UCCAUGG\n______________\|\|\|\|____\|\|\|_\|\|\|____\|\|:\|\|\|\|\|__________:\|\|\|\|:\|__\|\|\|\|\|\|\|\n______________AGGG____GGG_CAC____AUGUUUGU__________UCUUCGA__AGGUACC\n3'-UUU...ACUGA___________A_______________GAUCUCAG_________UA_______GCAAU...GAA-5'\n_____________\|_____________________________________________________\|\n_____________61____________________________________________________17\n	72 -- 78	18 -- 24	-36.1086 kcal/mol	16.1769 kcal/mol	14.9054 kcal/mol	26 79@LB@ \| \|@LB@5'-AGA...GAACA UCAA AAUU AUUUUUAAAG UC AGACC...AAU-3'@LB@ UCCC CCC GUG UAUAAACA GGAAGUU UCCAUGG@LB@ \|\|\|\| \|\|\| \|\|\| \|\|:\|\|\|\|\| :\|\|\|\|:\| \|\|\|\|\|\|\|@LB@ AGGG GGG CAC AUGUUUGU UCUUCGA AGGUACC@LB@3'-UUU...ACUGA A GAUCUCAG UA GCAAU...GAA-5'@LB@ \| \|@LB@ 61 17@LB@@LB@@LB@Energy -5.03 kcal/mol@LB@Hybridization Energy -36.1086 kcal/mol@LB@Unfolding Energy - mRNA 16.1769 kcal/mol@LB@Unfolding Energy - sRNA 14.9054 kcal/mol@LB@@LB@Position - mRNA 27 -- 78@LB@Position - sRNA 18 -- 60@LB@Position Seed - mRNA 72 -- 78@LB@Position Seed - sRNA 18 -- 24@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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