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
71	0.027	0.29	ct_712	N/A	-6.32	0.201489	257 -- 263	81 -- 87	type III secretion system effector protein	_____________256_____264\n_____________\|_______\|\n5'-CAG...GAGAC_______CCUCG...CAG-3'\n______________UGCGGCU\n______________\|:\|\|\|\|\|\n______________AUGCCGA\n3'-UUU...CCUCU_______UUGAG...GAA-5'\n_____________\|_______\|\n_____________88______80\n	257 -- 263	81 -- 87	-10.8048 kcal/mol	3.3916 kcal/mol	1.09752 kcal/mol	256 264@LB@ \| \|@LB@5'-CAG...GAGAC CCUCG...CAG-3'@LB@ UGCGGCU@LB@ \|:\|\|\|\|\|@LB@ AUGCCGA@LB@3'-UUU...CCUCU UUGAG...GAA-5'@LB@ \| \|@LB@ 88 80@LB@@LB@@LB@Energy -6.32 kcal/mol@LB@Hybridization Energy -10.8048 kcal/mol@LB@Unfolding Energy - mRNA 3.3916 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 257 -- 263@LB@Position - sRNA 81 -- 87@LB@Position Seed - mRNA 257 -- 263@LB@Position Seed - sRNA 81 -- 87@LB@
72	0.02709	0.29	ct_530	fmt	-6.32	0.201483	239 -- 246	80 -- 87	methionyl-tRNA formyltransferase	_____________238______247\n_____________\|________\|\n5'-UAA...CAAUU________CUGUU...CGC-3'\n______________UGCGGCUA\n______________\|:\|\|\|\|\|\|\n______________AUGCCGAU\n3'-UUU...CCUCU________UGAGG...GAA-5'\n_____________\|________\|\n_____________88_______79\n	240 -- 246	80 -- 86	-12.3749 kcal/mol	4.96164 kcal/mol	1.09752 kcal/mol	238 247@LB@ \| \|@LB@5'-UAA...CAAUU CUGUU...CGC-3'@LB@ UGCGGCUA@LB@ \|:\|\|\|\|\|\|@LB@ AUGCCGAU@LB@3'-UUU...CCUCU UGAGG...GAA-5'@LB@ \| \|@LB@ 88 79@LB@@LB@@LB@Energy -6.32 kcal/mol@LB@Hybridization Energy -12.3749 kcal/mol@LB@Unfolding Energy - mRNA 4.96164 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 239 -- 246@LB@Position - sRNA 80 -- 87@LB@Position Seed - mRNA 240 -- 246@LB@Position Seed - sRNA 80 -- 86@LB@
73	0.02714	0.29	ct_211	N/A	-9.30	0.041995	126 -- 170	20 -- 59		_____________125____________________________________________171\n_____________\|______________________________________________\|\n5'-AGA...UCAAG_____AUUCU_______AAGUC____UUUGAU_________C____ACGAA...UUU-3'\n______________CCCCU_____CUGUGUG_____CAUU_______GAAGCUAU_CCAU\n______________\|\|\|\|:_____\|\|\|\|\|\|:_____\|\|:\|_______\|\|\|\|\|\|\|\|_\|\|\|\|\n______________GGGGG_____GACACAU_____GUGA_______CUUCGAUA_GGUA\n3'-UUU...CUGAA_________________GUUU_____UCUCAGU________A____CCGCA...GAA-5'\n_____________\|______________________________________________\|\n_____________60_____________________________________________19\n	159 -- 165	25 -- 31	-32.2967 kcal/mol	9.12092 kcal/mol	13.8789 kcal/mol	125 171@LB@ \| \|@LB@5'-AGA...UCAAG AUUCU AAGUC UUUGAU C ACGAA...UUU-3'@LB@ CCCCU CUGUGUG CAUU GAAGCUAU CCAU@LB@ \|\|\|\|: \|\|\|\|\|\|: \|\|:\| \|\|\|\|\|\|\|\| \|\|\|\|@LB@ GGGGG GACACAU GUGA CUUCGAUA GGUA@LB@3'-UUU...CUGAA GUUU UCUCAGU A CCGCA...GAA-5'@LB@ \| \|@LB@ 60 19@LB@@LB@@LB@Energy -9.30 kcal/mol@LB@Hybridization Energy -32.2967 kcal/mol@LB@Unfolding Energy - mRNA 9.12092 kcal/mol@LB@Unfolding Energy - sRNA 13.8789 kcal/mol@LB@@LB@Position - mRNA 126 -- 170@LB@Position - sRNA 20 -- 59@LB@Position Seed - mRNA 159 -- 165@LB@Position Seed - sRNA 25 -- 31@LB@
74	0.02719	0.29	ct_114	N/A	-7.65	0.102976	115 -- 129	17 -- 32		_____________114______________130\n_____________\|________________\|\n5'-AGG...GCGGU______UA________AAAAG...AAA-3'\n______________GGAGCU___CUAUGGC\n______________\|:\|\|\|\|___\|:\|\|\|\|\|\n______________CUUCGA___GGUACCG\n3'-UUU...UCAGU______UAA_______CAAUC...GAA-5'\n_____________\|________________\|\n_____________33_______________16\n	123 -- 129	17 -- 23	-17.2748 kcal/mol	4.65579 kcal/mol	4.96575 kcal/mol	114 130@LB@ \| \|@LB@5'-AGG...GCGGU UA AAAAG...AAA-3'@LB@ GGAGCU CUAUGGC@LB@ \|:\|\|\|\| \|:\|\|\|\|\|@LB@ CUUCGA GGUACCG@LB@3'-UUU...UCAGU UAA CAAUC...GAA-5'@LB@ \| \|@LB@ 33 16@LB@@LB@@LB@Energy -7.65 kcal/mol@LB@Hybridization Energy -17.2748 kcal/mol@LB@Unfolding Energy - mRNA 4.65579 kcal/mol@LB@Unfolding Energy - sRNA 4.96575 kcal/mol@LB@@LB@Position - mRNA 115 -- 129@LB@Position - sRNA 17 -- 32@LB@Position Seed - mRNA 123 -- 129@LB@Position Seed - sRNA 17 -- 23@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@
76	0.02744	0.29	ct_510	secY	-5.37	0.309530	200 -- 207	80 -- 87	preprotein translocase subunit SecY	_____________199______208\n_____________\|________\|\n5'-GAU...AAGUU________CAUUG...UCC-3'\n______________UAUGGCUA\n______________\|\|:\|\|\|\|\|\n______________AUGCCGAU\n3'-UUU...CCUCU________UGAGG...GAA-5'\n_____________\|________\|\n_____________88_______79\n	201 -- 207	80 -- 86	-9.93483 kcal/mol	3.46443 kcal/mol	1.09752 kcal/mol	199 208@LB@ \| \|@LB@5'-GAU...AAGUU CAUUG...UCC-3'@LB@ UAUGGCUA@LB@ \|\|:\|\|\|\|\|@LB@ AUGCCGAU@LB@3'-UUU...CCUCU UGAGG...GAA-5'@LB@ \| \|@LB@ 88 79@LB@@LB@@LB@Energy -5.37 kcal/mol@LB@Hybridization Energy -9.93483 kcal/mol@LB@Unfolding Energy - mRNA 3.46443 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 200 -- 207@LB@Position - sRNA 80 -- 87@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 80 -- 86@LB@
77	0.02807	0.29	ct_309	N/A	-7.23	0.128520	50 -- 64	17 -- 33		_____________49________________65\n_____________\|_________________\|\n5'-AGA...GCUUA_________GU______UAAAU...UAA-3'\n______________AGGGGCUAU____UGGU\n______________\|\|::\|\|\|\|\|____\|\|\|:\n______________UCUUCGAUA____ACCG\n3'-UUU...CUCAG_________AGGU____CAAUC...GAA-5'\n_____________\|_________________\|\n_____________34________________16\n	52 -- 58	25 -- 31	-14.8286 kcal/mol	2.62564 kcal/mol	4.97804 kcal/mol	49 65@LB@ \| \|@LB@5'-AGA...GCUUA GU UAAAU...UAA-3'@LB@ AGGGGCUAU UGGU@LB@ \|\|::\|\|\|\|\| \|\|\|:@LB@ UCUUCGAUA ACCG@LB@3'-UUU...CUCAG AGGU CAAUC...GAA-5'@LB@ \| \|@LB@ 34 16@LB@@LB@@LB@Energy -7.23 kcal/mol@LB@Hybridization Energy -14.8286 kcal/mol@LB@Unfolding Energy - mRNA 2.62564 kcal/mol@LB@Unfolding Energy - sRNA 4.97804 kcal/mol@LB@@LB@Position - mRNA 50 -- 64@LB@Position - sRNA 17 -- 33@LB@Position Seed - mRNA 52 -- 58@LB@Position Seed - sRNA 25 -- 31@LB@
78	0.0282	0.29	ct_131	N/A	-9.30	0.042003	199 -- 219	17 -- 35		_____________198___________________220\n_____________\|_____________________\|\n5'-GAG...UGAAU___U_____GUUC________AUAAA...AAU-3'\n______________UCA_GAAGC____UCCAUGGU\n______________\|\|\|_\|\|\|\|\|____\|\|\|\|\|\|\|:\n______________AGU_CUUCG____AGGUACCG\n3'-UUU...AUCUC_________AUA_________CAAUC...GAA-5'\n_____________\|_____________________\|\n_____________36____________________16\n	213 -- 219	17 -- 23	-20.9121 kcal/mol	6.63751 kcal/mol	4.9781 kcal/mol	198 220@LB@ \| \|@LB@5'-GAG...UGAAU U GUUC AUAAA...AAU-3'@LB@ UCA GAAGC UCCAUGGU@LB@ \|\|\| \|\|\|\|\| \|\|\|\|\|\|\|:@LB@ AGU CUUCG AGGUACCG@LB@3'-UUU...AUCUC AUA CAAUC...GAA-5'@LB@ \| \|@LB@ 36 16@LB@@LB@@LB@Energy -9.30 kcal/mol@LB@Hybridization Energy -20.9121 kcal/mol@LB@Unfolding Energy - mRNA 6.63751 kcal/mol@LB@Unfolding Energy - sRNA 4.9781 kcal/mol@LB@@LB@Position - mRNA 199 -- 219@LB@Position - sRNA 17 -- 35@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 17 -- 23@LB@
79	0.0288	0.29	ct_431	clpP_1	-3.71	0.580570	128 -- 134	79 -- 85	ATP-dependent Clp protease proteolytic subunit	_____________127_____135\n_____________\|_______\|\n5'-GAA...ACGUG_______UUUAU...AAA-3'\n______________UGGCUGA\n______________:\|\|\|\|:\|\n______________GCCGAUU\n3'-UUU...UCUAU_______GAGGU...GAA-5'\n_____________\|_______\|\n_____________86______78\n	128 -- 134	79 -- 85	-7.88567 kcal/mol	3.08 kcal/mol	1.09751 kcal/mol	127 135@LB@ \| \|@LB@5'-GAA...ACGUG UUUAU...AAA-3'@LB@ UGGCUGA@LB@ :\|\|\|\|:\|@LB@ GCCGAUU@LB@3'-UUU...UCUAU GAGGU...GAA-5'@LB@ \| \|@LB@ 86 78@LB@@LB@@LB@Energy -3.71 kcal/mol@LB@Hybridization Energy -7.88567 kcal/mol@LB@Unfolding Energy - mRNA 3.08 kcal/mol@LB@Unfolding Energy - sRNA 1.09751 kcal/mol@LB@@LB@Position - mRNA 128 -- 134@LB@Position - sRNA 79 -- 85@LB@Position Seed - mRNA 128 -- 134@LB@Position Seed - sRNA 79 -- 85@LB@
80	0.02888	0.29	ct_821	sucC	-7.97	0.087313	257 -- 264	53 -- 60	succinyl-CoA ligase subunit beta	_____________256______265\n_____________\|________\|\n5'-UCG...CCUAU________AUCAC...CAG-3'\n______________UCCCCCCU\n______________\|\|\|\|\|\|\|\|\n______________AGGGGGGA\n3'-UUU...ACUGA________CACAU...GAA-5'\n_____________\|________\|\n_____________61_______52\n	258 -- 264	53 -- 59	-16.0066 kcal/mol	1.58949 kcal/mol	6.45136 kcal/mol	256 265@LB@ \| \|@LB@5'-UCG...CCUAU AUCAC...CAG-3'@LB@ UCCCCCCU@LB@ \|\|\|\|\|\|\|\|@LB@ AGGGGGGA@LB@3'-UUU...ACUGA CACAU...GAA-5'@LB@ \| \|@LB@ 61 52@LB@@LB@@LB@Energy -7.97 kcal/mol@LB@Hybridization Energy -16.0066 kcal/mol@LB@Unfolding Energy - mRNA 1.58949 kcal/mol@LB@Unfolding Energy - sRNA 6.45136 kcal/mol@LB@@LB@Position - mRNA 257 -- 264@LB@Position - sRNA 53 -- 60@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 53 -- 59@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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