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
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@
97	0.03496	0.2959	ct_539	trxA	-6.38	0.195495	87 -- 94	80 -- 87	thioredoxin	_____________86_______95\n_____________\|________\|\n5'-AUG...GAGGU________ACUGG...UGC-3'\n______________UAUGGCUA\n______________\|\|:\|\|\|\|\|\n______________AUGCCGAU\n3'-UUU...CCUCU________UGAGG...GAA-5'\n_____________\|________\|\n_____________88_______79\n	88 -- 94	80 -- 86	-10.4005 kcal/mol	2.9242 kcal/mol	1.09752 kcal/mol	86 95@LB@ \| \|@LB@5'-AUG...GAGGU ACUGG...UGC-3'@LB@ UAUGGCUA@LB@ \|\|:\|\|\|\|\|@LB@ AUGCCGAU@LB@3'-UUU...CCUCU UGAGG...GAA-5'@LB@ \| \|@LB@ 88 79@LB@@LB@@LB@Energy -6.38 kcal/mol@LB@Hybridization Energy -10.4005 kcal/mol@LB@Unfolding Energy - mRNA 2.9242 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 87 -- 94@LB@Position - sRNA 80 -- 87@LB@Position Seed - mRNA 88 -- 94@LB@Position Seed - sRNA 80 -- 86@LB@
185	0.083	0.363	ct_260	N/A	-8.27	0.074080	87 -- 93	53 -- 59		_____________86______94\n_____________\|_______\|\n5'-GUU...CCCCC_______CCCAU...UCA-3'\n______________CCCCCCU\n______________\|\|\|\|\|\|\|\n______________GGGGGGA\n3'-UUU...CUGAA_______CACAU...GAA-5'\n_____________\|_______\|\n_____________60______52\n	87 -- 93	53 -- 59	-14.3095 kcal/mol	0.558947 kcal/mol	5.47887 kcal/mol	86 94@LB@ \| \|@LB@5'-GUU...CCCCC CCCAU...UCA-3'@LB@ CCCCCCU@LB@ \|\|\|\|\|\|\|@LB@ GGGGGGA@LB@3'-UUU...CUGAA CACAU...GAA-5'@LB@ \| \|@LB@ 60 52@LB@@LB@@LB@Energy -8.27 kcal/mol@LB@Hybridization Energy -14.3095 kcal/mol@LB@Unfolding Energy - mRNA 0.558947 kcal/mol@LB@Unfolding Energy - sRNA 5.47887 kcal/mol@LB@@LB@Position - mRNA 87 -- 93@LB@Position - sRNA 53 -- 59@LB@Position Seed - mRNA 87 -- 93@LB@Position Seed - sRNA 53 -- 59@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@
49	0.01821	0.29	ct_733	N/A	-8.44	0.067485	96 -- 102	80 -- 86		_____________95______103\n_____________\|_______\|\n5'-AUG...UGCCA_______UUGAU...CUA-3'\n______________GCGGCUA\n______________:\|\|\|\|\|\|\n______________UGCCGAU\n3'-UUU...CUCUA_______UGAGG...GAA-5'\n_____________\|_______\|\n_____________87______79\n	96 -- 102	80 -- 86	-11.4095 kcal/mol	1.90152 kcal/mol	1.06449 kcal/mol	95 103@LB@ \| \|@LB@5'-AUG...UGCCA UUGAU...CUA-3'@LB@ GCGGCUA@LB@ :\|\|\|\|\|\|@LB@ UGCCGAU@LB@3'-UUU...CUCUA UGAGG...GAA-5'@LB@ \| \|@LB@ 87 79@LB@@LB@@LB@Energy -8.44 kcal/mol@LB@Hybridization Energy -11.4095 kcal/mol@LB@Unfolding Energy - mRNA 1.90152 kcal/mol@LB@Unfolding Energy - sRNA 1.06449 kcal/mol@LB@@LB@Position - mRNA 96 -- 102@LB@Position - sRNA 80 -- 86@LB@Position Seed - mRNA 96 -- 102@LB@Position Seed - sRNA 80 -- 86@LB@
35	0.01072	0.2518	ct_483	N/A	-8.14	0.079674	97 -- 146	5 -- 57		_____________96______________________________________________________147\n_____________\|_______________________________________________________\|\n5'-UAG...GUCUU____GAC_______G_GAAAU_____UC____________AAAAAAA________AGGUA...GCG-3'\n______________CUCC____UACAGA_A_____GAGUC_____CUAUUCCAU________AAUACCA\n______________\|:\|\|____\|\|\|\|:\|_\|_____\|\|\|\|\|_____\|\|\|\|\|\|\|\|\|________\|\|\|\|\|\|\|\n______________GGGG____AUGUUU_U_____CUCAG_____GAUAAGGUA________UUAUGGU\n3'-UUU...GAAGG____ACAC______G_GAU_______UCUUC_________CCGCAAUC_______UGAA-5'\n_____________\|_______________________________________________________\|\n_____________58______________________________________________________4\n	140 -- 146	5 -- 11	-33.404 kcal/mol	8.71732 kcal/mol	16.5501 kcal/mol	96 147@LB@ \| \|@LB@5'-UAG...GUCUU GAC G GAAAU UC AAAAAAA AGGUA...GCG-3'@LB@ CUCC UACAGA A GAGUC CUAUUCCAU AAUACCA@LB@ \|:\|\| \|\|\|\|:\| \| \|\|\|\|\| \|\|\|\|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ GGGG AUGUUU U CUCAG GAUAAGGUA UUAUGGU@LB@3'-UUU...GAAGG ACAC G GAU UCUUC CCGCAAUC UGAA-5'@LB@ \| \|@LB@ 58 4@LB@@LB@@LB@Energy -8.14 kcal/mol@LB@Hybridization Energy -33.404 kcal/mol@LB@Unfolding Energy - mRNA 8.71732 kcal/mol@LB@Unfolding Energy - sRNA 16.5501 kcal/mol@LB@@LB@Position - mRNA 97 -- 146@LB@Position - sRNA 5 -- 57@LB@Position Seed - mRNA 140 -- 146@LB@Position Seed - sRNA 5 -- 11@LB@
195	0.08712	0.3657	ct_704	pcnB_2	-3.31	0.654425	101 -- 107	28 -- 34	poly A polymerase	_____________100_____108\n_____________\|_______\|\n5'-CAA...UACGG_______CAUCC...UGC-3'\n______________UAGAAGC\n______________:\|\|\|\|\|\|\n______________GUCUUCG\n3'-UUU...UCUCA_______AUAAG...GAA-5'\n_____________\|_______\|\n_____________35______27\n	101 -- 107	28 -- 34	-7.75845 kcal/mol	0.338622 kcal/mol	4.11458 kcal/mol	100 108@LB@ \| \|@LB@5'-CAA...UACGG CAUCC...UGC-3'@LB@ UAGAAGC@LB@ :\|\|\|\|\|\|@LB@ GUCUUCG@LB@3'-UUU...UCUCA AUAAG...GAA-5'@LB@ \| \|@LB@ 35 27@LB@@LB@@LB@Energy -3.31 kcal/mol@LB@Hybridization Energy -7.75845 kcal/mol@LB@Unfolding Energy - mRNA 0.338622 kcal/mol@LB@Unfolding Energy - sRNA 4.11458 kcal/mol@LB@@LB@Position - mRNA 101 -- 107@LB@Position - sRNA 28 -- 34@LB@Position Seed - mRNA 101 -- 107@LB@Position Seed - sRNA 28 -- 34@LB@
197	0.08765	0.3657	ct_851	map	-5.60	0.279866	107 -- 113	81 -- 87	methionine aminopeptidase	_____________106_____114\n_____________\|_______\|\n5'-GCU...CUUUC_______UUCAA...AAC-3'\n______________UACGGCU\n______________\|\|\|\|\|\|\|\n______________AUGCCGA\n3'-UUU...CCUCU_______UUGAG...GAA-5'\n_____________\|_______\|\n_____________88______80\n	107 -- 113	81 -- 87	-10.6361 kcal/mol	3.93565 kcal/mol	1.09752 kcal/mol	106 114@LB@ \| \|@LB@5'-GCU...CUUUC UUCAA...AAC-3'@LB@ UACGGCU@LB@ \|\|\|\|\|\|\|@LB@ AUGCCGA@LB@3'-UUU...CCUCU UUGAG...GAA-5'@LB@ \| \|@LB@ 88 80@LB@@LB@@LB@Energy -5.60 kcal/mol@LB@Hybridization Energy -10.6361 kcal/mol@LB@Unfolding Energy - mRNA 3.93565 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 107 -- 113@LB@Position - sRNA 81 -- 87@LB@Position Seed - mRNA 107 -- 113@LB@Position Seed - sRNA 81 -- 87@LB@
90	0.03275	0.2942	ct_332	pykF	-4.34	0.468844	109 -- 116	80 -- 87	pyruvate kinase	_____________108______117\n_____________\|________\|\n5'-UUU...GCGAU________CUAAA...GCC-3'\n______________UGCGGUUG\n______________\|:\|\|\|:\|:\n______________AUGCCGAU\n3'-UUU...CCUCU________UGAGG...GAA-5'\n_____________\|________\|\n_____________88_______79\n	110 -- 116	80 -- 86	-9.21836 kcal/mol	3.78563 kcal/mol	1.09752 kcal/mol	108 117@LB@ \| \|@LB@5'-UUU...GCGAU CUAAA...GCC-3'@LB@ UGCGGUUG@LB@ \|:\|\|\|:\|:@LB@ AUGCCGAU@LB@3'-UUU...CCUCU UGAGG...GAA-5'@LB@ \| \|@LB@ 88 79@LB@@LB@@LB@Energy -4.34 kcal/mol@LB@Hybridization Energy -9.21836 kcal/mol@LB@Unfolding Energy - mRNA 3.78563 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 109 -- 116@LB@Position - sRNA 80 -- 87@LB@Position Seed - mRNA 110 -- 116@LB@Position Seed - sRNA 80 -- 86@LB@
162	0.06757	0.3424	ct_083	N/A	-6.28	0.205297	111 -- 125	18 -- 33		_____________110______________126\n_____________\|________________\|\n5'-GCU...CAAGA________CAG_____AAAUC...UUU-3'\n______________AGAAGCUG____GUGG\n______________\|\|\|\|\|\|\|:____:\|\|\|\n______________UCUUCGAU____UACC\n3'-UUU...CUCAG________AAGG____GCAAU...GAA-5'\n_____________\|________________\|\n_____________34_______________17\n	112 -- 118	26 -- 32	-15.1014 kcal/mol	3.84734 kcal/mol	4.97798 kcal/mol	110 126@LB@ \| \|@LB@5'-GCU...CAAGA CAG AAAUC...UUU-3'@LB@ AGAAGCUG GUGG@LB@ \|\|\|\|\|\|\|: :\|\|\|@LB@ UCUUCGAU UACC@LB@3'-UUU...CUCAG AAGG GCAAU...GAA-5'@LB@ \| \|@LB@ 34 17@LB@@LB@@LB@Energy -6.28 kcal/mol@LB@Hybridization Energy -15.1014 kcal/mol@LB@Unfolding Energy - mRNA 3.84734 kcal/mol@LB@Unfolding Energy - sRNA 4.97798 kcal/mol@LB@@LB@Position - mRNA 111 -- 125@LB@Position - sRNA 18 -- 33@LB@Position Seed - mRNA 112 -- 118@LB@Position Seed - sRNA 26 -- 32@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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