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
36	0.01184	0.2704	ct_030	gmk	-11.03	0.015227	49 -- 70	6 -- 34	guanylate kinase	_____________48____________________________71\n_____________\|_____________________________\|\n5'-AUA...UGAUG_____________________________CCGAG...CAC-3'\n______________CGGAAGCU___UCAUG____UAGAGUACC\n______________\|:\|\|\|\|\|\|___:\|\|\|\|____\|\|\|\|:\|\|\|\|\n______________GUCUUCGA___GGUAC____AUCUUAUGG\n3'-UUU...UCUCA________UAA_____CGCA_________UUGAA-5'\n_____________\|_____________________________\|\n_____________35____________________________5\n	64 -- 70	6 -- 12	-24.3478 kcal/mol	4.72233 kcal/mol	8.59183 kcal/mol	48 71@LB@ \| \|@LB@5'-AUA...UGAUG CCGAG...CAC-3'@LB@ CGGAAGCU UCAUG UAGAGUACC@LB@ \|:\|\|\|\|\|\| :\|\|\|\| \|\|\|\|:\|\|\|\|@LB@ GUCUUCGA GGUAC AUCUUAUGG@LB@3'-UUU...UCUCA UAA CGCA UUGAA-5'@LB@ \| \|@LB@ 35 5@LB@@LB@@LB@Energy -11.03 kcal/mol@LB@Hybridization Energy -24.3478 kcal/mol@LB@Unfolding Energy - mRNA 4.72233 kcal/mol@LB@Unfolding Energy - sRNA 8.59183 kcal/mol@LB@@LB@Position - mRNA 49 -- 70@LB@Position - sRNA 6 -- 34@LB@Position Seed - mRNA 64 -- 70@LB@Position Seed - sRNA 6 -- 12@LB@
173	0.07335	0.3448	ct_543	hisS	-6.45	0.189015	1 -- 7	82 -- 88	histidine--tRNA ligase	______________1______8\n______________\|______\|\n___________5'-_______GUAUU...AGC-3'\n______________AUGCGGC\n______________\|\|:\|\|\|\|\n______________UAUGCCG\n3'-UUU...GCCUC_______AUUGA...GAA-5'\n_____________\|_______\|\n_____________89______81\n	1 -- 7	82 -- 88	-9.9342 kcal/mol	2.38776 kcal/mol	1.09753 kcal/mol	1 8@LB@ \| \|@LB@ 5'- GUAUU...AGC-3'@LB@ AUGCGGC@LB@ \|\|:\|\|\|\|@LB@ UAUGCCG@LB@3'-UUU...GCCUC AUUGA...GAA-5'@LB@ \| \|@LB@ 89 81@LB@@LB@@LB@Energy -6.45 kcal/mol@LB@Hybridization Energy -9.9342 kcal/mol@LB@Unfolding Energy - mRNA 2.38776 kcal/mol@LB@Unfolding Energy - sRNA 1.09753 kcal/mol@LB@@LB@Position - mRNA 1 -- 7@LB@Position - sRNA 82 -- 88@LB@Position Seed - mRNA 1 -- 7@LB@Position Seed - sRNA 82 -- 88@LB@
9	0.0008717	0.07962	ct_743	hctA	-7.87	0.092034	214 -- 220	82 -- 88	histone H1-like protein	_____________213_____221\n_____________\|_______\|\n5'-GUU...AAAAG_______AAAAA...AAA-3'\n______________AUACGGC\n______________\|\|\|\|\|\|\|\n______________UAUGCCG\n3'-UUU...GCCUC_______AUUGA...GAA-5'\n_____________\|_______\|\n_____________89______81\n	214 -- 220	82 -- 88	-10.5788 kcal/mol	1.61458 kcal/mol	1.09753 kcal/mol	213 221@LB@ \| \|@LB@5'-GUU...AAAAG AAAAA...AAA-3'@LB@ AUACGGC@LB@ \|\|\|\|\|\|\|@LB@ UAUGCCG@LB@3'-UUU...GCCUC AUUGA...GAA-5'@LB@ \| \|@LB@ 89 81@LB@@LB@@LB@Energy -7.87 kcal/mol@LB@Hybridization Energy -10.5788 kcal/mol@LB@Unfolding Energy - mRNA 1.61458 kcal/mol@LB@Unfolding Energy - sRNA 1.09753 kcal/mol@LB@@LB@Position - mRNA 214 -- 220@LB@Position - sRNA 82 -- 88@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 82 -- 88@LB@
12	0.002873	0.1836	ct_040	ruvB	-8.58	0.062725	112 -- 136	36 -- 60	Holliday junction DNA helicase RuvB	_____________111_______________________137\n_____________\|_________________________\|\n5'-CAG...GGGAA_________ACUU___C________GAUGU...AAG-3'\n______________UCCCUCUUG____CAG_CGCUGGAG\n______________\|\|\|\|:\|:\|\|____\|\|:_\|:\|\|:\|\|\|\n______________AGGGGGGAC____GUU_GUGAUCUC\n3'-UUU...ACUGA_________ACAU___U________AGUCU...GAA-5'\n_____________\|_________________________\|\n_____________61________________________35\n	113 -- 119	53 -- 59	-26.2752 kcal/mol	7.75429 kcal/mol	9.944 kcal/mol	111 137@LB@ \| \|@LB@5'-CAG...GGGAA ACUU C GAUGU...AAG-3'@LB@ UCCCUCUUG CAG CGCUGGAG@LB@ \|\|\|\|:\|:\|\| \|\|: \|:\|\|:\|\|\|@LB@ AGGGGGGAC GUU GUGAUCUC@LB@3'-UUU...ACUGA ACAU U AGUCU...GAA-5'@LB@ \| \|@LB@ 61 35@LB@@LB@@LB@Energy -8.58 kcal/mol@LB@Hybridization Energy -26.2752 kcal/mol@LB@Unfolding Energy - mRNA 7.75429 kcal/mol@LB@Unfolding Energy - sRNA 9.944 kcal/mol@LB@@LB@Position - mRNA 112 -- 136@LB@Position - sRNA 36 -- 60@LB@Position Seed - mRNA 113 -- 119@LB@Position Seed - sRNA 53 -- 59@LB@
58	0.02303	0.29	ct_184	N/A	-4.35	0.465673	5 -- 18	18 -- 35	Holliday junction resolvase	_____________4__________________19\n_____________\|__________________\|\n_______5'-ACGU_______AA_________AUUAA...UGC-3'\n______________UUAGAAG______CAUGG\n______________\|:\|\|\|\|\|______\|\|\|\|\|\n______________AGUCUUC______GUACC\n3'-UUU...AUCUC_______GAUAAG_____GCAAU...GAA-5'\n_____________\|__________________\|\n_____________36_________________17\n	5 -- 11	29 -- 35	-12.193 kcal/mol	2.86148 kcal/mol	4.97803 kcal/mol	4 19@LB@ \| \|@LB@ 5'-ACGU AA AUUAA...UGC-3'@LB@ UUAGAAG CAUGG@LB@ \|:\|\|\|\|\| \|\|\|\|\|@LB@ AGUCUUC GUACC@LB@3'-UUU...AUCUC GAUAAG GCAAU...GAA-5'@LB@ \| \|@LB@ 36 17@LB@@LB@@LB@Energy -4.35 kcal/mol@LB@Hybridization Energy -12.193 kcal/mol@LB@Unfolding Energy - mRNA 2.86148 kcal/mol@LB@Unfolding Energy - sRNA 4.97803 kcal/mol@LB@@LB@Position - mRNA 5 -- 18@LB@Position - sRNA 18 -- 35@LB@Position Seed - mRNA 5 -- 11@LB@Position Seed - sRNA 29 -- 35@LB@
107	0.04107	0.3134	ct_813	N/A	-9.66	0.034154	135 -- 167	17 -- 51	inclusion membrane protein	_____________134_________________________________168\n_____________\|___________________________________\|\n5'-CCA...AAAUU________AA________U___________U____CCAUC...AGG-3'\n______________UGUGCAGA___UAG_GUC_GAGGCUGUUUU_UGGU\n______________\|\|\|:\|\|:\|___\|\|\|_\|\|\|_\|\|:\|\|\|:\|\|::_\|\|\|:\n______________ACAUGUUU___AUC_CAG_CUUCGAUAAGG_ACCG\n3'-UUU...GGGAC________GUG___U___U___________U____CAAUC...GAA-5'\n_____________\|___________________________________\|\n_____________52__________________________________16\n	155 -- 161	23 -- 29	-33.5835 kcal/mol	11.0074 kcal/mol	12.9166 kcal/mol	134 168@LB@ \| \|@LB@5'-CCA...AAAUU AA U U CCAUC...AGG-3'@LB@ UGUGCAGA UAG GUC GAGGCUGUUUU UGGU@LB@ \|\|\|:\|\|:\| \|\|\| \|\|\| \|\|:\|\|\|:\|\|:: \|\|\|:@LB@ ACAUGUUU AUC CAG CUUCGAUAAGG ACCG@LB@3'-UUU...GGGAC GUG U U U CAAUC...GAA-5'@LB@ \| \|@LB@ 52 16@LB@@LB@@LB@Energy -9.66 kcal/mol@LB@Hybridization Energy -33.5835 kcal/mol@LB@Unfolding Energy - mRNA 11.0074 kcal/mol@LB@Unfolding Energy - sRNA 12.9166 kcal/mol@LB@@LB@Position - mRNA 135 -- 167@LB@Position - sRNA 17 -- 51@LB@Position Seed - mRNA 155 -- 161@LB@Position Seed - sRNA 23 -- 29@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@
54	0.02089	0.29	ct_119	incA	-7.14	0.134009	237 -- 243	52 -- 58	inclusion membrane protein A	_____________236_____244\n_____________\|_______\|\n5'-UCC...CAUCU_______CACCU...AGA-3'\n______________CCCCCUG\n______________\|\|\|\|\|\|\|\n______________GGGGGAC\n3'-UUU...UGAAG_______ACAUG...GAA-5'\n_____________\|_______\|\n_____________59______51\n	237 -- 243	52 -- 58	-14.4133 kcal/mol	0.279731 kcal/mol	6.99083 kcal/mol	236 244@LB@ \| \|@LB@5'-UCC...CAUCU CACCU...AGA-3'@LB@ CCCCCUG@LB@ \|\|\|\|\|\|\|@LB@ GGGGGAC@LB@3'-UUU...UGAAG ACAUG...GAA-5'@LB@ \| \|@LB@ 59 51@LB@@LB@@LB@Energy -7.14 kcal/mol@LB@Hybridization Energy -14.4133 kcal/mol@LB@Unfolding Energy - mRNA 0.279731 kcal/mol@LB@Unfolding Energy - sRNA 6.99083 kcal/mol@LB@@LB@Position - mRNA 237 -- 243@LB@Position - sRNA 52 -- 58@LB@Position Seed - mRNA 237 -- 243@LB@Position Seed - sRNA 52 -- 58@LB@
138	0.05554	0.3262	ct_806	ptr	-4.69	0.410459	54 -- 70	19 -- 33	insulinase/protease	_____________53________________71\n_____________\|_________________\|\n5'-GUU...UCCGA________AUAUA____AUAAA...UAA-3'\n______________AGAAGCUG_____CAUG\n______________\|\|\|\|\|\|\|:_____\|\|\|\|\n______________UCUUCGAU_____GUAC\n3'-UUU...CUCAG________AAG______CGCAA...GAA-5'\n_____________\|_________________\|\n_____________34________________18\n	55 -- 61	26 -- 32	-13.627 kcal/mol	3.96302 kcal/mol	4.97702 kcal/mol	53 71@LB@ \| \|@LB@5'-GUU...UCCGA AUAUA AUAAA...UAA-3'@LB@ AGAAGCUG CAUG@LB@ \|\|\|\|\|\|\|: \|\|\|\|@LB@ UCUUCGAU GUAC@LB@3'-UUU...CUCAG AAG CGCAA...GAA-5'@LB@ \| \|@LB@ 34 18@LB@@LB@@LB@Energy -4.69 kcal/mol@LB@Hybridization Energy -13.627 kcal/mol@LB@Unfolding Energy - mRNA 3.96302 kcal/mol@LB@Unfolding Energy - sRNA 4.97702 kcal/mol@LB@@LB@Position - mRNA 54 -- 70@LB@Position - sRNA 19 -- 33@LB@Position Seed - mRNA 55 -- 61@LB@Position Seed - sRNA 26 -- 32@LB@
194	0.08693	0.3657	ct_285	lplA_1	-4.48	0.444512	66 -- 74	27 -- 35	lipoate protein ligase	_____________65________75\n_____________\|_________\|\n5'-CUU...AAUUU_________UUUUU...UUC-3'\n______________UUAGAAGCU\n______________\|:\|\|\|\|\|\|\|\n______________AGUCUUCGA\n3'-UUU...AUCUC_________UAAGG...GAA-5'\n_____________\|_________\|\n_____________36________26\n	68 -- 74	27 -- 33	-10.5389 kcal/mol	1.46011 kcal/mol	4.60001 kcal/mol	65 75@LB@ \| \|@LB@5'-CUU...AAUUU UUUUU...UUC-3'@LB@ UUAGAAGCU@LB@ \|:\|\|\|\|\|\|\|@LB@ AGUCUUCGA@LB@3'-UUU...AUCUC UAAGG...GAA-5'@LB@ \| \|@LB@ 36 26@LB@@LB@@LB@Energy -4.48 kcal/mol@LB@Hybridization Energy -10.5389 kcal/mol@LB@Unfolding Energy - mRNA 1.46011 kcal/mol@LB@Unfolding Energy - sRNA 4.60001 kcal/mol@LB@@LB@Position - mRNA 66 -- 74@LB@Position - sRNA 27 -- 35@LB@Position Seed - mRNA 68 -- 74@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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