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
24	0.006504	0.2093	ct_534	cutE	-7.36	0.119875	40 -- 61	34 -- 57	apolipoprotein N-acyltransferase	_____________39_______________________62\n_____________\|________________________\|\n5'-CAG...CAAUU________GAAGUU__________AAUCC...GCG-3'\n______________CCCCUGUG______C_C_AGAGUU\n______________\|\|\|\|\|\|\|\|______\|_\|_\|\|\|\|\|:\n______________GGGGACAC______G_G_UCUCAG\n3'-UUU...GAAGG________AUGUUU_U_A______UCUUC...GAA-5'\n_____________\|________________________\|\n_____________58_______________________33\n	41 -- 47	50 -- 56	-22.0571 kcal/mol	6.72142 kcal/mol	7.97509 kcal/mol	39 62@LB@ \| \|@LB@5'-CAG...CAAUU GAAGUU AAUCC...GCG-3'@LB@ CCCCUGUG C C AGAGUU@LB@ \|\|\|\|\|\|\|\| \| \| \|\|\|\|\|:@LB@ GGGGACAC G G UCUCAG@LB@3'-UUU...GAAGG AUGUUU U A UCUUC...GAA-5'@LB@ \| \|@LB@ 58 33@LB@@LB@@LB@Energy -7.36 kcal/mol@LB@Hybridization Energy -22.0571 kcal/mol@LB@Unfolding Energy - mRNA 6.72142 kcal/mol@LB@Unfolding Energy - sRNA 7.97509 kcal/mol@LB@@LB@Position - mRNA 40 -- 61@LB@Position - sRNA 34 -- 57@LB@Position Seed - mRNA 41 -- 47@LB@Position Seed - sRNA 50 -- 56@LB@
75	0.02725	0.29	ct_536	dnaQ_2	-6.54	0.180881	173 -- 186	18 -- 31	DNA polymerase III subunit epsilon	_____________172____________187\n_____________\|______________\|\n5'-AGA...GAUUU_____U________AGAAC...GGU-3'\n______________GAGCU_UUUUAUGG\n______________:\|\|\|\|_\|\|::\|\|\|\|\n______________UUCGA_AAGGUACC\n3'-UUU...CAGUC_____U________GCAAU...GAA-5'\n_____________\|______________\|\n_____________32_____________17\n	180 -- 186	18 -- 24	-14.3298 kcal/mol	2.92947 kcal/mol	4.86077 kcal/mol	172 187@LB@ \| \|@LB@5'-AGA...GAUUU U AGAAC...GGU-3'@LB@ GAGCU UUUUAUGG@LB@ :\|\|\|\| \|\|::\|\|\|\|@LB@ UUCGA AAGGUACC@LB@3'-UUU...CAGUC U GCAAU...GAA-5'@LB@ \| \|@LB@ 32 17@LB@@LB@@LB@Energy -6.54 kcal/mol@LB@Hybridization Energy -14.3298 kcal/mol@LB@Unfolding Energy - mRNA 2.92947 kcal/mol@LB@Unfolding Energy - sRNA 4.86077 kcal/mol@LB@@LB@Position - mRNA 173 -- 186@LB@Position - sRNA 18 -- 31@LB@Position Seed - mRNA 180 -- 186@LB@Position Seed - sRNA 18 -- 24@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@
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@
105	0.03879	0.3036	ct_546	N/A	-8.76	0.056849	221 -- 228	80 -- 87	contains leader (17) peptide	_____________220______229\n_____________\|________\|\n5'-CGC...UUUAU________UUUUU...ACG-3'\n______________UGCGGCUA\n______________\|:\|\|\|\|\|\|\n______________AUGCCGAU\n3'-UUU...CCUCU________UGAGG...GAA-5'\n_____________\|________\|\n_____________88_______79\n	222 -- 228	80 -- 86	-12.4581 kcal/mol	2.60487 kcal/mol	1.09752 kcal/mol	220 229@LB@ \| \|@LB@5'-CGC...UUUAU UUUUU...ACG-3'@LB@ UGCGGCUA@LB@ \|:\|\|\|\|\|\|@LB@ AUGCCGAU@LB@3'-UUU...CCUCU UGAGG...GAA-5'@LB@ \| \|@LB@ 88 79@LB@@LB@@LB@Energy -8.76 kcal/mol@LB@Hybridization Energy -12.4581 kcal/mol@LB@Unfolding Energy - mRNA 2.60487 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 221 -- 228@LB@Position - sRNA 80 -- 87@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 80 -- 86@LB@
96	0.03475	0.2959	ct_548	N/A	-8.10	0.081484	276 -- 282	54 -- 60		_____________275_____283\n_____________\|_______\|\n5'-ACA...UGCUC_______ACUAU...AAU-3'\n______________UCCCCCC\n______________\|\|\|\|\|\|\|\n______________AGGGGGG\n3'-UUU...ACUGA_______ACACA...GAA-5'\n_____________\|_______\|\n_____________61______53\n	276 -- 282	54 -- 60	-15.7273 kcal/mol	1.19056 kcal/mol	6.44182 kcal/mol	275 283@LB@ \| \|@LB@5'-ACA...UGCUC ACUAU...AAU-3'@LB@ UCCCCCC@LB@ \|\|\|\|\|\|\|@LB@ AGGGGGG@LB@3'-UUU...ACUGA ACACA...GAA-5'@LB@ \| \|@LB@ 61 53@LB@@LB@@LB@Energy -8.10 kcal/mol@LB@Hybridization Energy -15.7273 kcal/mol@LB@Unfolding Energy - mRNA 1.19056 kcal/mol@LB@Unfolding Energy - sRNA 6.44182 kcal/mol@LB@@LB@Position - mRNA 276 -- 282@LB@Position - sRNA 54 -- 60@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 54 -- 60@LB@
92	0.03292	0.2942	ct_558	lipA	-15.60	0.000793	187 -- 244	3 -- 58	lipoyl synthase	_____________186_________________________________________________________245\n_____________\|___________________________________________________________\|\n5'-ACU...AUAUG_______CUAAA_____ACC__U______UCUC_______UAAAAAAUCU______C__CAGAU...AAA-3'\n______________CCCCCUG_____AAAUG___GA_UCAGAA____CUAUUCC___________AUACC_GC\n______________\|\|\|\|\|\|\|_____\|\|\|::___\|\|_\|\|\|\|\|\|____\|\|\|\|\|\|\|___________\|\|\|\|\|_:\|\n______________GGGGGAC_____UUUGU___CU_AGUCUU____GAUAAGG___________UAUGG_UG\n3'-UUU...UGAAG_______ACAUG_____GAU__C______C__________UACCGCAAUCU_____U__AA-5'\n_____________\|___________________________________________________________\|\n_____________59__________________________________________________________2\n	220 -- 226	22 -- 28	-35.9268 kcal/mol	3.77883 kcal/mol	16.5523 kcal/mol	186 245@LB@ \| \|@LB@5'-ACU...AUAUG CUAAA ACC U UCUC UAAAAAAUCU C CAGAU...AAA-3'@LB@ CCCCCUG AAAUG GA UCAGAA CUAUUCC AUACC GC@LB@ \|\|\|\|\|\|\| \|\|\|:: \|\| \|\|\|\|\|\| \|\|\|\|\|\|\| \|\|\|\|\| :\|@LB@ GGGGGAC UUUGU CU AGUCUU GAUAAGG UAUGG UG@LB@3'-UUU...UGAAG ACAUG GAU C C UACCGCAAUCU U AA-5'@LB@ \| \|@LB@ 59 2@LB@@LB@@LB@Energy -15.60 kcal/mol@LB@Hybridization Energy -35.9268 kcal/mol@LB@Unfolding Energy - mRNA 3.77883 kcal/mol@LB@Unfolding Energy - sRNA 16.5523 kcal/mol@LB@@LB@Position - mRNA 187 -- 244@LB@Position - sRNA 3 -- 58@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 22 -- 28@LB@
116	0.04833	0.3262	ct_570	gspF	-8.17	0.078365	199 -- 207	80 -- 88	type II secretion system protein F	_____________198_______208\n_____________\|_________\|\n5'-AUC...AGGGG_________GGUUU...CUG-3'\n______________AUAUGGCUA\n______________\|\|\|:\|\|\|\|\|\n______________UAUGCCGAU\n3'-UUU...GCCUC_________UGAGG...GAA-5'\n_____________\|_________\|\n_____________89________79\n	201 -- 207	80 -- 86	-11.0443 kcal/mol	1.77912 kcal/mol	1.09753 kcal/mol	198 208@LB@ \| \|@LB@5'-AUC...AGGGG GGUUU...CUG-3'@LB@ AUAUGGCUA@LB@ \|\|\|:\|\|\|\|\|@LB@ UAUGCCGAU@LB@3'-UUU...GCCUC UGAGG...GAA-5'@LB@ \| \|@LB@ 89 79@LB@@LB@@LB@Energy -8.17 kcal/mol@LB@Hybridization Energy -11.0443 kcal/mol@LB@Unfolding Energy - mRNA 1.77912 kcal/mol@LB@Unfolding Energy - sRNA 1.09753 kcal/mol@LB@@LB@Position - mRNA 199 -- 207@LB@Position - sRNA 80 -- 88@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 80 -- 86@LB@
47	0.01707	0.29	ct_577	N/A	-4.79	0.394783	124 -- 141	41 -- 59		_____________123_________________142\n_____________\|___________________\|\n5'-GAU...CAAGC_______CCUAA_______AAAAG...AAU-3'\n______________CUCCUCU______AAACAC\n______________\|:\|\|:\|\|______\|\|\|\|\|\|\n______________GGGGGGA______UUUGUG\n3'-UUU...CUGAA_______CACAUG______AUCUC...GAA-5'\n_____________\|___________________\|\n_____________60__________________40\n	124 -- 130	53 -- 59	-14.9438 kcal/mol	1.33474 kcal/mol	8.82318 kcal/mol	123 142@LB@ \| \|@LB@5'-GAU...CAAGC CCUAA AAAAG...AAU-3'@LB@ CUCCUCU AAACAC@LB@ \|:\|\|:\|\| \|\|\|\|\|\|@LB@ GGGGGGA UUUGUG@LB@3'-UUU...CUGAA CACAUG AUCUC...GAA-5'@LB@ \| \|@LB@ 60 40@LB@@LB@@LB@Energy -4.79 kcal/mol@LB@Hybridization Energy -14.9438 kcal/mol@LB@Unfolding Energy - mRNA 1.33474 kcal/mol@LB@Unfolding Energy - sRNA 8.82318 kcal/mol@LB@@LB@Position - mRNA 124 -- 141@LB@Position - sRNA 41 -- 59@LB@Position Seed - mRNA 124 -- 130@LB@Position Seed - sRNA 53 -- 59@LB@
53	0.01942	0.29	ct_580	N/A	-10.14	0.025883	244 -- 280	22 -- 57	S-adenosylmethionine/S-adenosylhomocysteine transporter	_____________243___________________________________281\n_____________\|_____________________________________\|\n5'-GUU...ACAAA___G_____U_____C___UU__GACAU_________CUUAA...CUU-3'\n______________CCU_UGUGU_UAAAC_CUG__GU_____GGCUAUUUU\n______________\|\|:_\|\|\|\|\|_:\|\|\|\|_\|\|:__\|\|_____:\|\|\|\|\|\|::\n______________GGG_ACACA_GUUUG_GAU__CA_____UCGAUAAGG\n3'-UUU...GAAGG___G_____U_____U___CU__GUCU__________UACCG...GAA-5'\n_____________\|_____________________________________\|\n_____________58____________________________________21\n	273 -- 279	23 -- 29	-28.6785 kcal/mol	5.85369 kcal/mol	12.6861 kcal/mol	243 281@LB@ \| \|@LB@5'-GUU...ACAAA G U C UU GACAU CUUAA...CUU-3'@LB@ CCU UGUGU UAAAC CUG GU GGCUAUUUU@LB@ \|\|: \|\|\|\|\| :\|\|\|\| \|\|: \|\| :\|\|\|\|\|\|::@LB@ GGG ACACA GUUUG GAU CA UCGAUAAGG@LB@3'-UUU...GAAGG G U U CU GUCU UACCG...GAA-5'@LB@ \| \|@LB@ 58 21@LB@@LB@@LB@Energy -10.14 kcal/mol@LB@Hybridization Energy -28.6785 kcal/mol@LB@Unfolding Energy - mRNA 5.85369 kcal/mol@LB@Unfolding Energy - sRNA 12.6861 kcal/mol@LB@@LB@Position - mRNA 244 -- 280@LB@Position - sRNA 22 -- 57@LB@Position Seed - mRNA 273 -- 279@LB@Position Seed - sRNA 23 -- 29@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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