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
20	0.004812	0.1918	ct_026	rs16	-8.27	0.073959	26 -- 51	3 -- 33	30S ribosomal protein S16	_____________25______________________________52\n_____________\|_______________________________\|\n5'-CUG...ACGAA________________AA_________G___CGGAU...AUA-3'\n______________AGGAGUUA____GUGG__UU_GAGUAU_AGC\n______________\|\|:\|\|:\|\|____:\|\|\|__\|\|_\|\|:\|\|:_\|:\|\n______________UCUUCGAU____UACC__AA_CUUAUG_UUG\n3'-UUU...CUCAG________AAGG____GC__U______G___AA-5'\n_____________\|_______________________________\|\n_____________34______________________________2\n	27 -- 33	26 -- 32	-20.5759 kcal/mol	3.70935 kcal/mol	8.59196 kcal/mol	25 52@LB@ \| \|@LB@5'-CUG...ACGAA AA G CGGAU...AUA-3'@LB@ AGGAGUUA GUGG UU GAGUAU AGC@LB@ \|\|:\|\|:\|\| :\|\|\| \|\| \|\|:\|\|: \|:\|@LB@ UCUUCGAU UACC AA CUUAUG UUG@LB@3'-UUU...CUCAG AAGG GC U G AA-5'@LB@ \| \|@LB@ 34 2@LB@@LB@@LB@Energy -8.27 kcal/mol@LB@Hybridization Energy -20.5759 kcal/mol@LB@Unfolding Energy - mRNA 3.70935 kcal/mol@LB@Unfolding Energy - sRNA 8.59196 kcal/mol@LB@@LB@Position - mRNA 26 -- 51@LB@Position - sRNA 3 -- 33@LB@Position Seed - mRNA 27 -- 33@LB@Position Seed - sRNA 26 -- 32@LB@
185	0.083	0.363	ct_260	N/A	-8.27	0.074080	87 -- 93	53 -- 59		_____________86______94\n_____________\|_______\|\n5'-GUU...CCCCC_______CCCAU...UCA-3'\n______________CCCCCCU\n______________\|\|\|\|\|\|\|\n______________GGGGGGA\n3'-UUU...CUGAA_______CACAU...GAA-5'\n_____________\|_______\|\n_____________60______52\n	87 -- 93	53 -- 59	-14.3095 kcal/mol	0.558947 kcal/mol	5.47887 kcal/mol	86 94@LB@ \| \|@LB@5'-GUU...CCCCC CCCAU...UCA-3'@LB@ CCCCCCU@LB@ \|\|\|\|\|\|\|@LB@ GGGGGGA@LB@3'-UUU...CUGAA CACAU...GAA-5'@LB@ \| \|@LB@ 60 52@LB@@LB@@LB@Energy -8.27 kcal/mol@LB@Hybridization Energy -14.3095 kcal/mol@LB@Unfolding Energy - mRNA 0.558947 kcal/mol@LB@Unfolding Energy - sRNA 5.47887 kcal/mol@LB@@LB@Position - mRNA 87 -- 93@LB@Position - sRNA 53 -- 59@LB@Position Seed - mRNA 87 -- 93@LB@Position Seed - sRNA 53 -- 59@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@
122	0.04895	0.3262	ct_683	N/A	-8.21	0.076506	46 -- 53	80 -- 87		_____________45_______54\n_____________\|________\|\n5'-AAG...GUACU________GGAGA...AAG-3'\n______________UACGGCUA\n______________\|\|\|\|\|\|\|\|\n______________AUGCCGAU\n3'-UUU...CCUCU________UGAGG...GAA-5'\n_____________\|________\|\n_____________88_______79\n	47 -- 53	80 -- 86	-12.375 kcal/mol	3.06531 kcal/mol	1.09752 kcal/mol	45 54@LB@ \| \|@LB@5'-AAG...GUACU GGAGA...AAG-3'@LB@ UACGGCUA@LB@ \|\|\|\|\|\|\|\|@LB@ AUGCCGAU@LB@3'-UUU...CCUCU UGAGG...GAA-5'@LB@ \| \|@LB@ 88 79@LB@@LB@@LB@Energy -8.21 kcal/mol@LB@Hybridization Energy -12.375 kcal/mol@LB@Unfolding Energy - mRNA 3.06531 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 46 -- 53@LB@Position - sRNA 80 -- 87@LB@Position Seed - mRNA 47 -- 53@LB@Position Seed - sRNA 80 -- 86@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@
35	0.01072	0.2518	ct_483	N/A	-8.14	0.079674	97 -- 146	5 -- 57		_____________96______________________________________________________147\n_____________\|_______________________________________________________\|\n5'-UAG...GUCUU____GAC_______G_GAAAU_____UC____________AAAAAAA________AGGUA...GCG-3'\n______________CUCC____UACAGA_A_____GAGUC_____CUAUUCCAU________AAUACCA\n______________\|:\|\|____\|\|\|\|:\|_\|_____\|\|\|\|\|_____\|\|\|\|\|\|\|\|\|________\|\|\|\|\|\|\|\n______________GGGG____AUGUUU_U_____CUCAG_____GAUAAGGUA________UUAUGGU\n3'-UUU...GAAGG____ACAC______G_GAU_______UCUUC_________CCGCAAUC_______UGAA-5'\n_____________\|_______________________________________________________\|\n_____________58______________________________________________________4\n	140 -- 146	5 -- 11	-33.404 kcal/mol	8.71732 kcal/mol	16.5501 kcal/mol	96 147@LB@ \| \|@LB@5'-UAG...GUCUU GAC G GAAAU UC AAAAAAA AGGUA...GCG-3'@LB@ CUCC UACAGA A GAGUC CUAUUCCAU AAUACCA@LB@ \|:\|\| \|\|\|\|:\| \| \|\|\|\|\| \|\|\|\|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ GGGG AUGUUU U CUCAG GAUAAGGUA UUAUGGU@LB@3'-UUU...GAAGG ACAC G GAU UCUUC CCGCAAUC UGAA-5'@LB@ \| \|@LB@ 58 4@LB@@LB@@LB@Energy -8.14 kcal/mol@LB@Hybridization Energy -33.404 kcal/mol@LB@Unfolding Energy - mRNA 8.71732 kcal/mol@LB@Unfolding Energy - sRNA 16.5501 kcal/mol@LB@@LB@Position - mRNA 97 -- 146@LB@Position - sRNA 5 -- 57@LB@Position Seed - mRNA 140 -- 146@LB@Position Seed - sRNA 5 -- 11@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@
30	0.009028	0.2474	ct_455	murA	-8.03	0.084305	255 -- 264	26 -- 35	UDP-N-acetylglucosamine 1-carboxyvinyltransferase	_____________254________265\n_____________\|__________\|\n5'-AAA...GCGUG__________AAAAU...UAC-3'\n______________UCAGGAGCUA\n______________\|\|\|\|:\|\|\|\|\|\n______________AGUCUUCGAU\n3'-UUU...AUCUC__________AAGGU...GAA-5'\n_____________\|__________\|\n_____________36_________25\n	258 -- 264	26 -- 32	-13.9898 kcal/mol	1.25877 kcal/mol	4.69985 kcal/mol	254 265@LB@ \| \|@LB@5'-AAA...GCGUG AAAAU...UAC-3'@LB@ UCAGGAGCUA@LB@ \|\|\|\|:\|\|\|\|\|@LB@ AGUCUUCGAU@LB@3'-UUU...AUCUC AAGGU...GAA-5'@LB@ \| \|@LB@ 36 25@LB@@LB@@LB@Energy -8.03 kcal/mol@LB@Hybridization Energy -13.9898 kcal/mol@LB@Unfolding Energy - mRNA 1.25877 kcal/mol@LB@Unfolding Energy - sRNA 4.69985 kcal/mol@LB@@LB@Position - mRNA 255 -- 264@LB@Position - sRNA 26 -- 35@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 26 -- 32@LB@
59	0.02324	0.29	ct_106	yceC	-7.97	0.086897	139 -- 180	3 -- 31	tRNA pseudouridine synthase A	_____________138__________________________________________181\n_____________\|____________________________________________\|\n5'-CUC...GAAAA__________UAUCA______AAUUCUCGUAAAAUC________ACACU...CCG-3'\n______________AAGCUGUUCU_______UAGA_______________GUACCAAC\n______________\|\|\|\|\|:\|\|\|:_______\|\|\|\|_______________:\|\|\|\|\|\|\|\n______________UUCGAUAAGG_______AUCU_______________UAUGGUUG\n3'-UUU...CAGUC__________UACCGCA___________________________AA-5'\n_____________\|____________________________________________\|\n_____________32___________________________________________2\n	174 -- 180	3 -- 9	-21.8491 kcal/mol	5.39956 kcal/mol	8.47511 kcal/mol	138 181@LB@ \| \|@LB@5'-CUC...GAAAA UAUCA AAUUCUCGUAAAAUC ACACU...CCG-3'@LB@ AAGCUGUUCU UAGA GUACCAAC@LB@ \|\|\|\|\|:\|\|\|: \|\|\|\| :\|\|\|\|\|\|\|@LB@ UUCGAUAAGG AUCU UAUGGUUG@LB@3'-UUU...CAGUC UACCGCA AA-5'@LB@ \| \|@LB@ 32 2@LB@@LB@@LB@Energy -7.97 kcal/mol@LB@Hybridization Energy -21.8491 kcal/mol@LB@Unfolding Energy - mRNA 5.39956 kcal/mol@LB@Unfolding Energy - sRNA 8.47511 kcal/mol@LB@@LB@Position - mRNA 139 -- 180@LB@Position - sRNA 3 -- 31@LB@Position Seed - mRNA 174 -- 180@LB@Position Seed - sRNA 3 -- 9@LB@
131	0.05291	0.3262	ct_842	pnp	-7.97	0.086989	198 -- 205	17 -- 24	polyribonucleotide nucleotidyltransferase	_____________197______206\n_____________\|________\|\n5'-UGA...ACAAC________UUUUG...UCA-3'\n______________UCCAUGGC\n______________\|\|\|\|\|\|\|\|\n______________AGGUACCG\n3'-UUU...CGAUA________CAAUC...GAA-5'\n_____________\|________\|\n_____________25_______16\n	199 -- 205	17 -- 23	-14.0999 kcal/mol	1.64992 kcal/mol	4.47615 kcal/mol	197 206@LB@ \| \|@LB@5'-UGA...ACAAC UUUUG...UCA-3'@LB@ UCCAUGGC@LB@ \|\|\|\|\|\|\|\|@LB@ AGGUACCG@LB@3'-UUU...CGAUA CAAUC...GAA-5'@LB@ \| \|@LB@ 25 16@LB@@LB@@LB@Energy -7.97 kcal/mol@LB@Hybridization Energy -14.0999 kcal/mol@LB@Unfolding Energy - mRNA 1.64992 kcal/mol@LB@Unfolding Energy - sRNA 4.47615 kcal/mol@LB@@LB@Position - mRNA 198 -- 205@LB@Position - sRNA 17 -- 24@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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