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
134	0.05433	0.3262	ct_581	thrS	-7.17	0.132364	52 -- 64	21 -- 33	threonine--tRNA ligase	_____________51___________65\n_____________\|____________\|\n5'-AAA...CUAAA_______CC___GAACU...CAG-3'\n______________AGAAGCU__UCC\n______________\|\|\|\|\|\|\|__\|\|\|\n______________UCUUCGA__AGG\n3'-UUU...CUCAG_______UA___UACCG...GAA-5'\n_____________\|____________\|\n_____________34___________20\n	52 -- 58	27 -- 33	-13.855 kcal/mol	1.83194 kcal/mol	4.72509 kcal/mol	51 65@LB@ \| \|@LB@5'-AAA...CUAAA CC GAACU...CAG-3'@LB@ AGAAGCU UCC@LB@ \|\|\|\|\|\|\| \|\|\|@LB@ UCUUCGA AGG@LB@3'-UUU...CUCAG UA UACCG...GAA-5'@LB@ \| \|@LB@ 34 20@LB@@LB@@LB@Energy -7.17 kcal/mol@LB@Hybridization Energy -13.855 kcal/mol@LB@Unfolding Energy - mRNA 1.83194 kcal/mol@LB@Unfolding Energy - sRNA 4.72509 kcal/mol@LB@@LB@Position - mRNA 52 -- 64@LB@Position - sRNA 21 -- 33@LB@Position Seed - mRNA 52 -- 58@LB@Position Seed - sRNA 27 -- 33@LB@
19	0.004244	0.1836	ct_583	gp6D	-9.00	0.049504	83 -- 102	18 -- 35	virulence protein GP6-D	_____________82___________________103\n_____________\|____________________\|\n5'-UAA...CUAUC________CGCUA_______GAAAC...CUC-3'\n______________UCAGAAGC_____UCCAUGG\n______________\|\|\|\|\|\|\|\|_____\|\|\|\|\|\|\|\n______________AGUCUUCG_____AGGUACC\n3'-UUU...AUCUC________AUA_________GCAAU...GAA-5'\n_____________\|____________________\|\n_____________36___________________17\n	96 -- 102	18 -- 24	-22.1713 kcal/mol	8.18904 kcal/mol	4.97803 kcal/mol	82 103@LB@ \| \|@LB@5'-UAA...CUAUC CGCUA GAAAC...CUC-3'@LB@ UCAGAAGC UCCAUGG@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ AGUCUUCG AGGUACC@LB@3'-UUU...AUCUC AUA GCAAU...GAA-5'@LB@ \| \|@LB@ 36 17@LB@@LB@@LB@Energy -9.00 kcal/mol@LB@Hybridization Energy -22.1713 kcal/mol@LB@Unfolding Energy - mRNA 8.18904 kcal/mol@LB@Unfolding Energy - sRNA 4.97803 kcal/mol@LB@@LB@Position - mRNA 83 -- 102@LB@Position - sRNA 18 -- 35@LB@Position Seed - mRNA 96 -- 102@LB@Position Seed - sRNA 18 -- 24@LB@
50	0.01829	0.29	ct_588	rbsU	-10.49	0.021035	31 -- 46	21 -- 34	serine phosphatase RsbU	_____________30_______________47\n_____________\|________________\|\n5'-GUC...GGGUC________CU______AGAUU...UCC-3'\n______________CAGAAGCU__AUUCCA\n______________\|\|\|\|\|\|\|\|__\|\|\|\|\|\|\n______________GUCUUCGA__UAAGGU\n3'-UUU...UCUCA________________ACCGC...GAA-5'\n_____________\|________________\|\n_____________35_______________20\n	32 -- 38	27 -- 33	-17.905 kcal/mol	2.68182 kcal/mol	4.73132 kcal/mol	30 47@LB@ \| \|@LB@5'-GUC...GGGUC CU AGAUU...UCC-3'@LB@ CAGAAGCU AUUCCA@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ GUCUUCGA UAAGGU@LB@3'-UUU...UCUCA ACCGC...GAA-5'@LB@ \| \|@LB@ 35 20@LB@@LB@@LB@Energy -10.49 kcal/mol@LB@Hybridization Energy -17.905 kcal/mol@LB@Unfolding Energy - mRNA 2.68182 kcal/mol@LB@Unfolding Energy - sRNA 4.73132 kcal/mol@LB@@LB@Position - mRNA 31 -- 46@LB@Position - sRNA 21 -- 34@LB@Position Seed - mRNA 32 -- 38@LB@Position Seed - sRNA 27 -- 33@LB@
43	0.01649	0.29	ct_590	N/A	-9.68	0.033714	159 -- 170	17 -- 28		_____________158__________171\n_____________\|____________\|\n5'-AGU...CAAUU____________AAAGG...UCA-3'\n______________UUAUUCCAUGGU\n______________:\|\|\|\|\|\|\|\|\|\|:\n______________GAUAAGGUACCG\n3'-UUU...UCUUC____________CAAUC...GAA-5'\n_____________\|____________\|\n_____________29___________16\n	164 -- 170	17 -- 23	-16.2126 kcal/mol	1.90936 kcal/mol	4.62088 kcal/mol	158 171@LB@ \| \|@LB@5'-AGU...CAAUU AAAGG...UCA-3'@LB@ UUAUUCCAUGGU@LB@ :\|\|\|\|\|\|\|\|\|\|:@LB@ GAUAAGGUACCG@LB@3'-UUU...UCUUC CAAUC...GAA-5'@LB@ \| \|@LB@ 29 16@LB@@LB@@LB@Energy -9.68 kcal/mol@LB@Hybridization Energy -16.2126 kcal/mol@LB@Unfolding Energy - mRNA 1.90936 kcal/mol@LB@Unfolding Energy - sRNA 4.62088 kcal/mol@LB@@LB@Position - mRNA 159 -- 170@LB@Position - sRNA 17 -- 28@LB@Position Seed - mRNA 164 -- 170@LB@Position Seed - sRNA 17 -- 23@LB@
37	0.01294	0.2859	ct_591	sdhB	-7.06	0.139804	161 -- 176	18 -- 34	succinate dehydrogenase iron sulfur subunit	_____________160_______________177\n_____________\|_________________\|\n5'-AAA...AUUUA_____________UG__AAAUA...GGG-3'\n______________UAGAGGC_GUUCC__GG\n______________:\|\|\|:\|\|_:\|\|\|\|__\|\|\n______________GUCUUCG_UAAGG__CC\n3'-UUU...UCUCA_______A_____UA__GCAAU...GAA-5'\n_____________\|_________________\|\n_____________35________________17\n	161 -- 167	28 -- 34	-17.8156 kcal/mol	5.77845 kcal/mol	4.97803 kcal/mol	160 177@LB@ \| \|@LB@5'-AAA...AUUUA UG AAAUA...GGG-3'@LB@ UAGAGGC GUUCC GG@LB@ :\|\|\|:\|\| :\|\|\|\| \|\|@LB@ GUCUUCG UAAGG CC@LB@3'-UUU...UCUCA A UA GCAAU...GAA-5'@LB@ \| \|@LB@ 35 17@LB@@LB@@LB@Energy -7.06 kcal/mol@LB@Hybridization Energy -17.8156 kcal/mol@LB@Unfolding Energy - mRNA 5.77845 kcal/mol@LB@Unfolding Energy - sRNA 4.97803 kcal/mol@LB@@LB@Position - mRNA 161 -- 176@LB@Position - sRNA 18 -- 34@LB@Position Seed - mRNA 161 -- 167@LB@Position Seed - sRNA 28 -- 34@LB@
136	0.05474	0.3262	ct_592	sdhA	-7.43	0.115894	38 -- 56	18 -- 34	succinate dehydrogenase flavoprotein subunit	_____________37__________________57\n_____________\|___________________\|\n5'-UCU...UGUUA___CU_____UU_______GUUUA...UGU-3'\n______________UAG__GCUGU__UCCAUGG\n______________:\|\|__\|\|\|:\|__\|\|\|\|\|\|\|\n______________GUC__CGAUA__AGGUACC\n3'-UUU...UCUCA___UU______________GCAAU...GAA-5'\n_____________\|___________________\|\n_____________35__________________17\n	50 -- 56	18 -- 24	-18.2308 kcal/mol	5.82664 kcal/mol	4.97803 kcal/mol	37 57@LB@ \| \|@LB@5'-UCU...UGUUA CU UU GUUUA...UGU-3'@LB@ UAG GCUGU UCCAUGG@LB@ :\|\| \|\|\|:\| \|\|\|\|\|\|\|@LB@ GUC CGAUA AGGUACC@LB@3'-UUU...UCUCA UU GCAAU...GAA-5'@LB@ \| \|@LB@ 35 17@LB@@LB@@LB@Energy -7.43 kcal/mol@LB@Hybridization Energy -18.2308 kcal/mol@LB@Unfolding Energy - mRNA 5.82664 kcal/mol@LB@Unfolding Energy - sRNA 4.97803 kcal/mol@LB@@LB@Position - mRNA 38 -- 56@LB@Position - sRNA 18 -- 34@LB@Position Seed - mRNA 50 -- 56@LB@Position Seed - sRNA 18 -- 24@LB@
42	0.01617	0.29	ct_610	N/A	-8.69	0.058803	15 -- 22	80 -- 87	virulence protein CADD	_____________14_______23\n_____________\|________\|\n5'-GAU...GCAGU________UUGUU...GGG-3'\n______________UGCGGCUG\n______________\|:\|\|\|\|\|:\n______________AUGCCGAU\n3'-UUU...CCUCU________UGAGG...GAA-5'\n_____________\|________\|\n_____________88_______79\n	16 -- 22	80 -- 86	-11.8172 kcal/mol	2.02516 kcal/mol	1.09752 kcal/mol	14 23@LB@ \| \|@LB@5'-GAU...GCAGU UUGUU...GGG-3'@LB@ UGCGGCUG@LB@ \|:\|\|\|\|\|:@LB@ AUGCCGAU@LB@3'-UUU...CCUCU UGAGG...GAA-5'@LB@ \| \|@LB@ 88 79@LB@@LB@@LB@Energy -8.69 kcal/mol@LB@Hybridization Energy -11.8172 kcal/mol@LB@Unfolding Energy - mRNA 2.02516 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 15 -- 22@LB@Position - sRNA 80 -- 87@LB@Position Seed - mRNA 16 -- 22@LB@Position Seed - sRNA 80 -- 86@LB@
169	0.07086	0.3447	ct_615	sigA	-4.07	0.514760	248 -- 272	10 -- 33	RNA polymerase sigma factor	_____________247________________________273\n_____________\|__________________________\|\n5'-GGU...CAAGA_____AAA_____AAGAAA_______GAGUU...AAG-3'\n______________AGAAG____UCCA______GUUAGAA\n______________\|\|\|\|\|____\|\|\|\|______\|\|\|\|\|\|\|\n______________UCUUC____AGGU______CAAUCUU\n3'-UUU...CUCAG_____GAUA____ACCG_________AUGGU...GAA-5'\n_____________\|__________________________\|\n_____________34_________________________9\n	266 -- 272	10 -- 16	-15.5151 kcal/mol	2.85327 kcal/mol	8.5898 kcal/mol	247 273@LB@ \| \|@LB@5'-GGU...CAAGA AAA AAGAAA GAGUU...AAG-3'@LB@ AGAAG UCCA GUUAGAA@LB@ \|\|\|\|\| \|\|\|\| \|\|\|\|\|\|\|@LB@ UCUUC AGGU CAAUCUU@LB@3'-UUU...CUCAG GAUA ACCG AUGGU...GAA-5'@LB@ \| \|@LB@ 34 9@LB@@LB@@LB@Energy -4.07 kcal/mol@LB@Hybridization Energy -15.5151 kcal/mol@LB@Unfolding Energy - mRNA 2.85327 kcal/mol@LB@Unfolding Energy - sRNA 8.5898 kcal/mol@LB@@LB@Position - mRNA 248 -- 272@LB@Position - sRNA 10 -- 33@LB@Position Seed - mRNA 266 -- 272@LB@Position Seed - sRNA 10 -- 16@LB@
61	0.02387	0.29	ct_628	ispA	-7.51	0.111028	11 -- 52	17 -- 56	farnesyl diphosphate synthase	_____________10__________________________________________53\n_____________\|___________________________________________\|\n5'-UUC...GAGAG_G____AA___A_____GAAAA________________UA___AGAGG...UAG-3'\n______________C_UUGU__UAC_AAACG_____AGUUAGGAGCU_UUCC__GGU\n______________\|_:\|\|\|__\|\|\|_\|\|\|\|:_____\|\|\|:\|\|:\|\|\|\|_\|\|\|\|__\|\|:\n______________G_GACA__AUG_UUUGU_____UCAGUCUUCGA_AAGG__CCG\n3'-UUU...AAGGG_G____C__________GAUC____________U____UA___CAAUC...GAA-5'\n_____________\|___________________________________________\|\n_____________57__________________________________________16\n	36 -- 42	28 -- 34	-30.6817 kcal/mol	10.2369 kcal/mol	12.9359 kcal/mol	10 53@LB@ \| \|@LB@5'-UUC...GAGAG G AA A GAAAA UA AGAGG...UAG-3'@LB@ C UUGU UAC AAACG AGUUAGGAGCU UUCC GGU@LB@ \| :\|\|\| \|\|\| \|\|\|\|: \|\|\|:\|\|:\|\|\|\| \|\|\|\| \|\|:@LB@ G GACA AUG UUUGU UCAGUCUUCGA AAGG CCG@LB@3'-UUU...AAGGG G C GAUC U UA CAAUC...GAA-5'@LB@ \| \|@LB@ 57 16@LB@@LB@@LB@Energy -7.51 kcal/mol@LB@Hybridization Energy -30.6817 kcal/mol@LB@Unfolding Energy - mRNA 10.2369 kcal/mol@LB@Unfolding Energy - sRNA 12.9359 kcal/mol@LB@@LB@Position - mRNA 11 -- 52@LB@Position - sRNA 17 -- 56@LB@Position Seed - mRNA 36 -- 42@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@

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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usability assessment

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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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