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
147	0.05913	0.3307	ct_243	lpxD	-5.18	0.335797	179 -- 192	18 -- 32	UDP-3-O-acylglucosamine N-acyltransferase	_____________178_____________193\n_____________\|_______________\|\n5'-UCA...CAUGC_______G____A__AGUGC...UCG-3'\n______________GAAGCUA__CCG_GG\n______________\|\|\|\|\|\|\|__\|\|:_\|\|\n______________CUUCGAU__GGU_CC\n3'-UUU...UCAGU_______AA___A__GCAAU...GAA-5'\n_____________\|_______________\|\n_____________33______________17\n	179 -- 185	26 -- 32	-15.005 kcal/mol	4.85774 kcal/mol	4.96566 kcal/mol	178 193@LB@ \| \|@LB@5'-UCA...CAUGC G A AGUGC...UCG-3'@LB@ GAAGCUA CCG GG@LB@ \|\|\|\|\|\|\| \|\|: \|\|@LB@ CUUCGAU GGU CC@LB@3'-UUU...UCAGU AA A GCAAU...GAA-5'@LB@ \| \|@LB@ 33 17@LB@@LB@@LB@Energy -5.18 kcal/mol@LB@Hybridization Energy -15.005 kcal/mol@LB@Unfolding Energy - mRNA 4.85774 kcal/mol@LB@Unfolding Energy - sRNA 4.96566 kcal/mol@LB@@LB@Position - mRNA 179 -- 192@LB@Position - sRNA 18 -- 32@LB@Position Seed - mRNA 179 -- 185@LB@Position Seed - sRNA 26 -- 32@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@
85	0.03073	0.29	ct_522	rs3	-5.11	0.345416	189 -- 204	18 -- 34	30S ribosomal protein S3	_____________188_______________205\n_____________\|_________________\|\n5'-UGU...GGCAG_______AAGG______GUCAA...UCA-3'\n______________UAGGAGU_____UAUGG\n______________:\|\|:\|\|:_____:\|\|\|\|\n______________GUCUUCG_____GUACC\n3'-UUU...UCUCA_______AUAAG_____GCAAU...GAA-5'\n_____________\|_________________\|\n_____________35________________17\n	189 -- 195	28 -- 34	-12.0284 kcal/mol	1.93617 kcal/mol	4.97803 kcal/mol	188 205@LB@ \| \|@LB@5'-UGU...GGCAG AAGG GUCAA...UCA-3'@LB@ UAGGAGU UAUGG@LB@ :\|\|:\|\|: :\|\|\|\|@LB@ GUCUUCG GUACC@LB@3'-UUU...UCUCA AUAAG GCAAU...GAA-5'@LB@ \| \|@LB@ 35 17@LB@@LB@@LB@Energy -5.11 kcal/mol@LB@Hybridization Energy -12.0284 kcal/mol@LB@Unfolding Energy - mRNA 1.93617 kcal/mol@LB@Unfolding Energy - sRNA 4.97803 kcal/mol@LB@@LB@Position - mRNA 189 -- 204@LB@Position - sRNA 18 -- 34@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 28 -- 34@LB@
145	0.05831	0.3298	ct_635	N/A	-5.11	0.346704	276 -- 282	53 -- 59		_____________275_____283\n_____________\|_______\|\n5'-AUC...UCGAA_______UUGGA...CUG-3'\n______________CCCUCCU\n______________\|\|\|:\|\|\|\n______________GGGGGGA\n3'-UUU...CUGAA_______CACAU...GAA-5'\n_____________\|_______\|\n_____________60______52\n	276 -- 282	53 -- 59	-11.2032 kcal/mol	0.619026 kcal/mol	5.47887 kcal/mol	275 283@LB@ \| \|@LB@5'-AUC...UCGAA UUGGA...CUG-3'@LB@ CCCUCCU@LB@ \|\|\|:\|\|\|@LB@ GGGGGGA@LB@3'-UUU...CUGAA CACAU...GAA-5'@LB@ \| \|@LB@ 60 52@LB@@LB@@LB@Energy -5.11 kcal/mol@LB@Hybridization Energy -11.2032 kcal/mol@LB@Unfolding Energy - mRNA 0.619026 kcal/mol@LB@Unfolding Energy - sRNA 5.47887 kcal/mol@LB@@LB@Position - mRNA 276 -- 282@LB@Position - sRNA 53 -- 59@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 53 -- 59@LB@
167	0.06963	0.3427	ct_724	N/A	-5.10	0.346834	244 -- 255	24 -- 35		_____________243__________256\n_____________\|____________\|\n5'-ACC...GUUAU____________GUCGC...GAC-3'\n______________UCGGGGGUUAUU\n______________\|\|:\|::\|:\|\|\|\|\n______________AGUCUUCGAUAA\n3'-UUU...AUCUC____________GGUAC...GAA-5'\n_____________\|____________\|\n_____________36___________23\n	245 -- 251	28 -- 34	-12.4512 kcal/mol	2.62645 kcal/mol	4.72035 kcal/mol	243 256@LB@ \| \|@LB@5'-ACC...GUUAU GUCGC...GAC-3'@LB@ UCGGGGGUUAUU@LB@ \|\|:\|::\|:\|\|\|\|@LB@ AGUCUUCGAUAA@LB@3'-UUU...AUCUC GGUAC...GAA-5'@LB@ \| \|@LB@ 36 23@LB@@LB@@LB@Energy -5.10 kcal/mol@LB@Hybridization Energy -12.4512 kcal/mol@LB@Unfolding Energy - mRNA 2.62645 kcal/mol@LB@Unfolding Energy - sRNA 4.72035 kcal/mol@LB@@LB@Position - mRNA 244 -- 255@LB@Position - sRNA 24 -- 35@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 28 -- 34@LB@
52	0.01886	0.29	ct_784	rnpA	-5.05	0.354130	114 -- 120	80 -- 86	ribonuclease P protein component	_____________113_____121\n_____________\|_______\|\n5'-UCU...CUCGC_______CAAAA...UGA-3'\n______________AUGGCUA\n______________\|:\|\|\|\|\|\n______________UGCCGAU\n3'-UUU...CUCUA_______UGAGG...GAA-5'\n_____________\|_______\|\n_____________87______79\n	114 -- 120	80 -- 86	-8.53572 kcal/mol	2.4168 kcal/mol	1.06449 kcal/mol	113 121@LB@ \| \|@LB@5'-UCU...CUCGC CAAAA...UGA-3'@LB@ AUGGCUA@LB@ \|:\|\|\|\|\|@LB@ UGCCGAU@LB@3'-UUU...CUCUA UGAGG...GAA-5'@LB@ \| \|@LB@ 87 79@LB@@LB@@LB@Energy -5.05 kcal/mol@LB@Hybridization Energy -8.53572 kcal/mol@LB@Unfolding Energy - mRNA 2.4168 kcal/mol@LB@Unfolding Energy - sRNA 1.06449 kcal/mol@LB@@LB@Position - mRNA 114 -- 120@LB@Position - sRNA 80 -- 86@LB@Position Seed - mRNA 114 -- 120@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@
192	0.08479	0.363	ct_293	accD	-5.01	0.360945	270 -- 276	79 -- 85	acetyl-CoA carboxylase carboxyltransferase subunit beta	_____________269_____277\n_____________\|_______\|\n5'-GUA...GUGGC_______AAUGU...UGA-3'\n______________UGGCUAA\n______________:\|\|\|\|\|\|\n______________GCCGAUU\n3'-UUU...UCUAU_______GAGGU...GAA-5'\n_____________\|_______\|\n_____________86______78\n	270 -- 276	79 -- 85	-7.87376 kcal/mol	1.76808 kcal/mol	1.09751 kcal/mol	269 277@LB@ \| \|@LB@5'-GUA...GUGGC AAUGU...UGA-3'@LB@ UGGCUAA@LB@ :\|\|\|\|\|\|@LB@ GCCGAUU@LB@3'-UUU...UCUAU GAGGU...GAA-5'@LB@ \| \|@LB@ 86 78@LB@@LB@@LB@Energy -5.01 kcal/mol@LB@Hybridization Energy -7.87376 kcal/mol@LB@Unfolding Energy - mRNA 1.76808 kcal/mol@LB@Unfolding Energy - sRNA 1.09751 kcal/mol@LB@@LB@Position - mRNA 270 -- 276@LB@Position - sRNA 79 -- 85@LB@Position Seed - mRNA 270 -- 276@LB@Position Seed - sRNA 79 -- 85@LB@
93	0.03342	0.2954	ct_815	mrsA_2	-4.95	0.370159	203 -- 227	23 -- 45	phosphoglucosamine mutase	_____________202_______________________228\n_____________\|_________________________\|\n5'-UAC...GCAAU_____GU__U__G___C________GGAAC...AGG-3'\n______________GACAC__GA_GU_AGA_AGCUAUUC\n______________:\|\|\|\|__\|\|_\|\|_\|\|\|_\|\|\|\|\|\|\|\|\n______________UUGUG__CU_CA_UCU_UCGAUAAG\n3'-UUU...CAUGU_____AU_____G____________GUACC...GAA-5'\n_____________\|_________________________\|\n_____________46________________________22\n	221 -- 227	23 -- 29	-22.8159 kcal/mol	6.25755 kcal/mol	11.6121 kcal/mol	202 228@LB@ \| \|@LB@5'-UAC...GCAAU GU U G C GGAAC...AGG-3'@LB@ GACAC GA GU AGA AGCUAUUC@LB@ :\|\|\|\| \|\| \|\| \|\|\| \|\|\|\|\|\|\|\|@LB@ UUGUG CU CA UCU UCGAUAAG@LB@3'-UUU...CAUGU AU G GUACC...GAA-5'@LB@ \| \|@LB@ 46 22@LB@@LB@@LB@Energy -4.95 kcal/mol@LB@Hybridization Energy -22.8159 kcal/mol@LB@Unfolding Energy - mRNA 6.25755 kcal/mol@LB@Unfolding Energy - sRNA 11.6121 kcal/mol@LB@@LB@Position - mRNA 203 -- 227@LB@Position - sRNA 23 -- 45@LB@Position Seed - mRNA 221 -- 227@LB@Position Seed - sRNA 23 -- 29@LB@
160	0.06752	0.3424	ct_324	N/A	-4.86	0.383763	195 -- 205	17 -- 27		_____________194_________206\n_____________\|___________\|\n5'-ACA...GUAGA__GG_______CAAAG...UGC-3'\n______________UA__CCAUGGU\n______________\|\|__\|\|\|\|\|\|:\n______________AU__GGUACCG\n3'-UUU...CUUCG__AA_______CAAUC...GAA-5'\n_____________\|___________\|\n_____________28__________16\n	199 -- 205	17 -- 23	-11.7516 kcal/mol	2.4023 kcal/mol	4.49196 kcal/mol	194 206@LB@ \| \|@LB@5'-ACA...GUAGA GG CAAAG...UGC-3'@LB@ UA CCAUGGU@LB@ \|\| \|\|\|\|\|\|:@LB@ AU GGUACCG@LB@3'-UUU...CUUCG AA CAAUC...GAA-5'@LB@ \| \|@LB@ 28 16@LB@@LB@@LB@Energy -4.86 kcal/mol@LB@Hybridization Energy -11.7516 kcal/mol@LB@Unfolding Energy - mRNA 2.4023 kcal/mol@LB@Unfolding Energy - sRNA 4.49196 kcal/mol@LB@@LB@Position - mRNA 195 -- 205@LB@Position - sRNA 17 -- 27@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 17 -- 23@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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