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
55	0.02093	0.29	ct_785	rl34	-4.69	0.410747	264 -- 270	80 -- 86	50S ribosomal protein L34	_____________263_____271\n_____________\|_______\|\n5'-ACA...CUCGC_______CAAAA...GCC-3'\n______________AUGGCUA\n______________\|:\|\|\|\|\|\n______________UGCCGAU\n3'-UUU...CUCUA_______UGAGG...GAA-5'\n_____________\|_______\|\n_____________87______79\n	264 -- 270	80 -- 86	-8.67787 kcal/mol	2.92801 kcal/mol	1.06449 kcal/mol	263 271@LB@ \| \|@LB@5'-ACA...CUCGC CAAAA...GCC-3'@LB@ AUGGCUA@LB@ \|:\|\|\|\|\|@LB@ UGCCGAU@LB@3'-UUU...CUCUA UGAGG...GAA-5'@LB@ \| \|@LB@ 87 79@LB@@LB@@LB@Energy -4.69 kcal/mol@LB@Hybridization Energy -8.67787 kcal/mol@LB@Unfolding Energy - mRNA 2.92801 kcal/mol@LB@Unfolding Energy - sRNA 1.06449 kcal/mol@LB@@LB@Position - mRNA 264 -- 270@LB@Position - sRNA 80 -- 86@LB@Position Seed - mRNA 264 -- 270@LB@Position Seed - sRNA 80 -- 86@LB@
189	0.0841	0.363	ct_792	mutS	-5.18	0.336119	140 -- 151	22 -- 33	DNA mismatch repair protein MutS	_____________139__________152\n_____________\|____________\|\n5'-AUA...ACAUA____C_______CCUAC...AAG-3'\n______________AGAG_CUGUUCC\n______________\|\|\|:_\|\|:\|\|\|\|\n______________UCUU_GAUAAGG\n3'-UUU...CUCAG____C_______UACCG...GAA-5'\n_____________\|____________\|\n_____________34___________21\n	145 -- 151	22 -- 28	-12.2041 kcal/mol	2.29966 kcal/mol	4.72509 kcal/mol	139 152@LB@ \| \|@LB@5'-AUA...ACAUA C CCUAC...AAG-3'@LB@ AGAG CUGUUCC@LB@ \|\|\|: \|\|:\|\|\|\|@LB@ UCUU GAUAAGG@LB@3'-UUU...CUCAG C UACCG...GAA-5'@LB@ \| \|@LB@ 34 21@LB@@LB@@LB@Energy -5.18 kcal/mol@LB@Hybridization Energy -12.2041 kcal/mol@LB@Unfolding Energy - mRNA 2.29966 kcal/mol@LB@Unfolding Energy - sRNA 4.72509 kcal/mol@LB@@LB@Position - mRNA 140 -- 151@LB@Position - sRNA 22 -- 33@LB@Position Seed - mRNA 145 -- 151@LB@Position Seed - sRNA 22 -- 28@LB@
60	0.02363	0.29	ct_796	glyQ	-6.44	0.189870	236 -- 248	21 -- 33	glycine--tRNA ligase	_____________235___________249\n_____________\|_____________\|\n5'-UAG...AUGAU__C__________AACUU...AAG-3'\n______________GG_AGCUAUUCUA\n______________:\|_\|\|\|\|\|\|\|\|:\|\n______________UC_UCGAUAAGGU\n3'-UUU...CUCAG__U__________ACCGC...GAA-5'\n_____________\|_____________\|\n_____________34____________20\n	241 -- 247	22 -- 28	-13.5001 kcal/mol	2.33043 kcal/mol	4.73034 kcal/mol	235 249@LB@ \| \|@LB@5'-UAG...AUGAU C AACUU...AAG-3'@LB@ GG AGCUAUUCUA@LB@ :\| \|\|\|\|\|\|\|\|:\|@LB@ UC UCGAUAAGGU@LB@3'-UUU...CUCAG U ACCGC...GAA-5'@LB@ \| \|@LB@ 34 20@LB@@LB@@LB@Energy -6.44 kcal/mol@LB@Hybridization Energy -13.5001 kcal/mol@LB@Unfolding Energy - mRNA 2.33043 kcal/mol@LB@Unfolding Energy - sRNA 4.73034 kcal/mol@LB@@LB@Position - mRNA 236 -- 248@LB@Position - sRNA 21 -- 33@LB@Position Seed - mRNA 241 -- 247@LB@Position Seed - sRNA 22 -- 28@LB@
18	0.004135	0.1836	ct_799	N/A	-8.26	0.074627	30 -- 52	17 -- 35	50S ribosomal protein L25/general stress protein Ctc	_____________29______________________53\n_____________\|_______________________\|\n5'-AUC...AAUAA_________GCAA__A_______AGACG...GAA-3'\n______________UCAGAGGCU____GU_CCAUGGU\n______________\|\|\|\|\|:\|\|\|____:\|_\|\|\|\|\|\|:\n______________AGUCUUCGA____UA_GGUACCG\n3'-UUU...AUCUC_______________A_______CAAUC...GAA-5'\n_____________\|_______________________\|\n_____________36______________________16\n	46 -- 52	17 -- 23	-22.1109 kcal/mol	8.8748 kcal/mol	4.9781 kcal/mol	29 53@LB@ \| \|@LB@5'-AUC...AAUAA GCAA A AGACG...GAA-3'@LB@ UCAGAGGCU GU CCAUGGU@LB@ \|\|\|\|\|:\|\|\| :\| \|\|\|\|\|\|:@LB@ AGUCUUCGA UA GGUACCG@LB@3'-UUU...AUCUC A CAAUC...GAA-5'@LB@ \| \|@LB@ 36 16@LB@@LB@@LB@Energy -8.26 kcal/mol@LB@Hybridization Energy -22.1109 kcal/mol@LB@Unfolding Energy - mRNA 8.8748 kcal/mol@LB@Unfolding Energy - sRNA 4.9781 kcal/mol@LB@@LB@Position - mRNA 30 -- 52@LB@Position - sRNA 17 -- 35@LB@Position Seed - mRNA 46 -- 52@LB@Position Seed - sRNA 17 -- 23@LB@
2	8.171e-05	0.03358	ct_802	rs18	-7.95	0.088258	66 -- 79	21 -- 34	30S ribosomal protein S18	_____________65_____________80\n_____________\|______________\|\n5'-GUU...AGCCC__________CG__GAGUU...UUA-3'\n______________CAGAAGCUAU__CA\n______________\|\|\|\|\|\|\|\|\|\|__\|\|\n______________GUCUUCGAUA__GU\n3'-UUU...UCUCA__________AG__ACCGC...GAA-5'\n_____________\|______________\|\n_____________35_____________20\n	68 -- 74	26 -- 32	-17.0234 kcal/mol	4.34679 kcal/mol	4.73132 kcal/mol	65 80@LB@ \| \|@LB@5'-GUU...AGCCC CG GAGUU...UUA-3'@LB@ CAGAAGCUAU CA@LB@ \|\|\|\|\|\|\|\|\|\| \|\|@LB@ GUCUUCGAUA GU@LB@3'-UUU...UCUCA AG ACCGC...GAA-5'@LB@ \| \|@LB@ 35 20@LB@@LB@@LB@Energy -7.95 kcal/mol@LB@Hybridization Energy -17.0234 kcal/mol@LB@Unfolding Energy - mRNA 4.34679 kcal/mol@LB@Unfolding Energy - sRNA 4.73132 kcal/mol@LB@@LB@Position - mRNA 66 -- 79@LB@Position - sRNA 21 -- 34@LB@Position Seed - mRNA 68 -- 74@LB@Position Seed - sRNA 26 -- 32@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@
127	0.0509	0.3262	ct_808	cafE	-7.80	0.095102	169 -- 204	18 -- 57	ribonuclease E	_____________168_________________________________________205\n_____________\|___________________________________________\|\n5'-GUU...GAGGA_______A______________CAU______ACG_________AAAAC...AAA-3'\n______________CUCCUGU____GAGCGC_AGAG___UUAGGA______CCAUGG\n______________\|:\|\|\|\|\|____:\|:\|:\|_\|\|\|\|___\|:\|\|:\|______\|\|\|\|\|\|\n______________GGGGACA____UUUGUG_UCUC___AGUCUU______GGUACC\n3'-UUU...GAAGG_______CAUG______A_____________CGAUAA______GCAAU...GAA-5'\n_____________\|___________________________________________\|\n_____________58__________________________________________17\n	169 -- 175	51 -- 57	-30.1775 kcal/mol	9.43695 kcal/mol	12.9362 kcal/mol	168 205@LB@ \| \|@LB@5'-GUU...GAGGA A CAU ACG AAAAC...AAA-3'@LB@ CUCCUGU GAGCGC AGAG UUAGGA CCAUGG@LB@ \|:\|\|\|\|\| :\|:\|:\| \|\|\|\| \|:\|\|:\| \|\|\|\|\|\|@LB@ GGGGACA UUUGUG UCUC AGUCUU GGUACC@LB@3'-UUU...GAAGG CAUG A CGAUAA GCAAU...GAA-5'@LB@ \| \|@LB@ 58 17@LB@@LB@@LB@Energy -7.80 kcal/mol@LB@Hybridization Energy -30.1775 kcal/mol@LB@Unfolding Energy - mRNA 9.43695 kcal/mol@LB@Unfolding Energy - sRNA 12.9362 kcal/mol@LB@@LB@Position - mRNA 169 -- 204@LB@Position - sRNA 18 -- 57@LB@Position Seed - mRNA 169 -- 175@LB@Position Seed - sRNA 51 -- 57@LB@
99	0.03647	0.3007	ct_810	rl32	-4.11	0.507281	35 -- 46	46 -- 58	50S ribosomal protein L32	_____________34____________47\n_____________\|_____________\|\n5'-UUC...CAAGU_____________CGUUU...GCA-3'\n______________CUUCCUG_GUAUA\n______________\|::\|\|\|\|_\|\|\|:\|\n______________GGGGGAC_CAUGU\n3'-UUU...UGAAG_______A_____UUGUG...GAA-5'\n_____________\|_____________\|\n_____________59____________45\n	35 -- 41	52 -- 58	-13.0221 kcal/mol	1.6119 kcal/mol	7.29598 kcal/mol	34 47@LB@ \| \|@LB@5'-UUC...CAAGU CGUUU...GCA-3'@LB@ CUUCCUG GUAUA@LB@ \|::\|\|\|\| \|\|\|:\|@LB@ GGGGGAC CAUGU@LB@3'-UUU...UGAAG A UUGUG...GAA-5'@LB@ \| \|@LB@ 59 45@LB@@LB@@LB@Energy -4.11 kcal/mol@LB@Hybridization Energy -13.0221 kcal/mol@LB@Unfolding Energy - mRNA 1.6119 kcal/mol@LB@Unfolding Energy - sRNA 7.29598 kcal/mol@LB@@LB@Position - mRNA 35 -- 46@LB@Position - sRNA 46 -- 58@LB@Position Seed - mRNA 35 -- 41@LB@Position Seed - sRNA 52 -- 58@LB@
186	0.08332	0.363	ct_811	plsX	-5.83	0.252304	163 -- 171	79 -- 87	phosphate acyltransferase	_____________162_______172\n_____________\|_________\|\n5'-GGC...GUUAU_________GAAGU...AAC-3'\n______________UACGGUUGA\n______________\|\|\|\|\|:\|:\|\n______________AUGCCGAUU\n3'-UUU...CCUCU_________GAGGU...GAA-5'\n_____________\|_________\|\n_____________88________78\n	165 -- 171	79 -- 85	-10.158 kcal/mol	3.22704 kcal/mol	1.09752 kcal/mol	162 172@LB@ \| \|@LB@5'-GGC...GUUAU GAAGU...AAC-3'@LB@ UACGGUUGA@LB@ \|\|\|\|\|:\|:\|@LB@ AUGCCGAUU@LB@3'-UUU...CCUCU GAGGU...GAA-5'@LB@ \| \|@LB@ 88 78@LB@@LB@@LB@Energy -5.83 kcal/mol@LB@Hybridization Energy -10.158 kcal/mol@LB@Unfolding Energy - mRNA 3.22704 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 163 -- 171@LB@Position - sRNA 79 -- 87@LB@Position Seed - mRNA 165 -- 171@LB@Position Seed - sRNA 79 -- 85@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@

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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