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
31	0.009434	0.2502	ct_824	N/A	-6.02	0.231369	20 -- 32	21 -- 33	Zn-dependent peptidase	_____________19____________33\n_____________\|_____________\|\n5'-GUC...UUUUA________G____GUAUG...CCG-3'\n______________GGAAGCUA_UCUA\n______________:\|\|\|\|\|\|\|_\|\|:\|\n______________UCUUCGAU_AGGU\n3'-UUU...CUCAG________A____ACCGC...GAA-5'\n_____________\|_____________\|\n_____________34____________20\n	21 -- 27	26 -- 32	-13.8347 kcal/mol	3.08274 kcal/mol	4.73034 kcal/mol	19 33@LB@ \| \|@LB@5'-GUC...UUUUA G GUAUG...CCG-3'@LB@ GGAAGCUA UCUA@LB@ :\|\|\|\|\|\|\| \|\|:\|@LB@ UCUUCGAU AGGU@LB@3'-UUU...CUCAG A ACCGC...GAA-5'@LB@ \| \|@LB@ 34 20@LB@@LB@@LB@Energy -6.02 kcal/mol@LB@Hybridization Energy -13.8347 kcal/mol@LB@Unfolding Energy - mRNA 3.08274 kcal/mol@LB@Unfolding Energy - sRNA 4.73034 kcal/mol@LB@@LB@Position - mRNA 20 -- 32@LB@Position - sRNA 21 -- 33@LB@Position Seed - mRNA 21 -- 27@LB@Position Seed - sRNA 26 -- 32@LB@
32	0.009822	0.2518	ct_649	ygfA	-6.64	0.172247	22 -- 28	80 -- 86	5-formyltetrahydrofolate cyclo-ligase	_____________21______29\n_____________\|_______\|\n5'-UAC...AAGUG_______CCGAG...AGC-3'\n______________AUGGCUA\n______________\|:\|\|\|\|\|\n______________UGCCGAU\n3'-UUU...CUCUA_______UGAGG...GAA-5'\n_____________\|_______\|\n_____________87______79\n	22 -- 28	80 -- 86	-8.81528 kcal/mol	1.11082 kcal/mol	1.06449 kcal/mol	21 29@LB@ \| \|@LB@5'-UAC...AAGUG CCGAG...AGC-3'@LB@ AUGGCUA@LB@ \|:\|\|\|\|\|@LB@ UGCCGAU@LB@3'-UUU...CUCUA UGAGG...GAA-5'@LB@ \| \|@LB@ 87 79@LB@@LB@@LB@Energy -6.64 kcal/mol@LB@Hybridization Energy -8.81528 kcal/mol@LB@Unfolding Energy - mRNA 1.11082 kcal/mol@LB@Unfolding Energy - sRNA 1.06449 kcal/mol@LB@@LB@Position - mRNA 22 -- 28@LB@Position - sRNA 80 -- 86@LB@Position Seed - mRNA 22 -- 28@LB@Position Seed - sRNA 80 -- 86@LB@
33	0.01042	0.2518	ct_780	N/A	-7.85	0.092931	30 -- 50	15 -- 34		_____________29____________________51\n_____________\|_____________________\|\n5'-UGU...AAAAA___C____GAA_G________GUCAA...UCA-3'\n______________CAG_AAGU___U_CAUGGCGU\n______________\|\|\|_\|\|\|:___\|_\|\|\|\|\|\|\|\|\n______________GUC_UUCG___A_GUACCGCA\n3'-UUU...UCUCA________AUA_G________AUCUU...GAA-5'\n_____________\|_____________________\|\n_____________35____________________14\n	44 -- 50	15 -- 21	-20.7959 kcal/mol	4.71518 kcal/mol	8.23265 kcal/mol	29 51@LB@ \| \|@LB@5'-UGU...AAAAA C GAA G GUCAA...UCA-3'@LB@ CAG AAGU U CAUGGCGU@LB@ \|\|\| \|\|\|: \| \|\|\|\|\|\|\|\|@LB@ GUC UUCG A GUACCGCA@LB@3'-UUU...UCUCA AUA G AUCUU...GAA-5'@LB@ \| \|@LB@ 35 14@LB@@LB@@LB@Energy -7.85 kcal/mol@LB@Hybridization Energy -20.7959 kcal/mol@LB@Unfolding Energy - mRNA 4.71518 kcal/mol@LB@Unfolding Energy - sRNA 8.23265 kcal/mol@LB@@LB@Position - mRNA 30 -- 50@LB@Position - sRNA 15 -- 34@LB@Position Seed - mRNA 44 -- 50@LB@Position Seed - sRNA 15 -- 21@LB@
34	0.01043	0.2518	ct_642	N/A	-9.37	0.040224	239 -- 246	53 -- 60		_____________238______247\n_____________\|________\|\n5'-AGG...UCUUC________CUUCG...CUG-3'\n______________UCCCCCCU\n______________\|\|\|\|\|\|\|\|\n______________AGGGGGGA\n3'-UUU...ACUGA________CACAU...GAA-5'\n_____________\|________\|\n_____________61_______52\n	240 -- 246	53 -- 59	-15.9954 kcal/mol	0.170944 kcal/mol	6.45136 kcal/mol	238 247@LB@ \| \|@LB@5'-AGG...UCUUC CUUCG...CUG-3'@LB@ UCCCCCCU@LB@ \|\|\|\|\|\|\|\|@LB@ AGGGGGGA@LB@3'-UUU...ACUGA CACAU...GAA-5'@LB@ \| \|@LB@ 61 52@LB@@LB@@LB@Energy -9.37 kcal/mol@LB@Hybridization Energy -15.9954 kcal/mol@LB@Unfolding Energy - mRNA 0.170944 kcal/mol@LB@Unfolding Energy - sRNA 6.45136 kcal/mol@LB@@LB@Position - mRNA 239 -- 246@LB@Position - sRNA 53 -- 60@LB@Position Seed - mRNA 240 -- 246@LB@Position Seed - sRNA 53 -- 59@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@
36	0.01184	0.2704	ct_030	gmk	-11.03	0.015227	49 -- 70	6 -- 34	guanylate kinase	_____________48____________________________71\n_____________\|_____________________________\|\n5'-AUA...UGAUG_____________________________CCGAG...CAC-3'\n______________CGGAAGCU___UCAUG____UAGAGUACC\n______________\|:\|\|\|\|\|\|___:\|\|\|\|____\|\|\|\|:\|\|\|\|\n______________GUCUUCGA___GGUAC____AUCUUAUGG\n3'-UUU...UCUCA________UAA_____CGCA_________UUGAA-5'\n_____________\|_____________________________\|\n_____________35____________________________5\n	64 -- 70	6 -- 12	-24.3478 kcal/mol	4.72233 kcal/mol	8.59183 kcal/mol	48 71@LB@ \| \|@LB@5'-AUA...UGAUG CCGAG...CAC-3'@LB@ CGGAAGCU UCAUG UAGAGUACC@LB@ \|:\|\|\|\|\|\| :\|\|\|\| \|\|\|\|:\|\|\|\|@LB@ GUCUUCGA GGUAC AUCUUAUGG@LB@3'-UUU...UCUCA UAA CGCA UUGAA-5'@LB@ \| \|@LB@ 35 5@LB@@LB@@LB@Energy -11.03 kcal/mol@LB@Hybridization Energy -24.3478 kcal/mol@LB@Unfolding Energy - mRNA 4.72233 kcal/mol@LB@Unfolding Energy - sRNA 8.59183 kcal/mol@LB@@LB@Position - mRNA 49 -- 70@LB@Position - sRNA 6 -- 34@LB@Position Seed - mRNA 64 -- 70@LB@Position Seed - sRNA 6 -- 12@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@
38	0.01345	0.2859	ct_769	ybeB	-11.98	0.008536	76 -- 102	17 -- 43	ribosome silencing factor	_____________75___________________________103\n_____________\|____________________________\|\n5'-CUU...GAUCU________GAA_________________AAAGA...CCC-3'\n______________CGCUAGAG___AGAGGCUAUUUU_UGGU\n______________\|:\|\|\|\|\|\|___\|\|\|:\|\|\|\|\|\|::_\|\|\|:\n______________GUGAUCUC___UCUUCGAUAAGG_ACCG\n3'-UUU...UGUUU________AG_____________U____CAAUC...GAA-5'\n_____________\|____________________________\|\n_____________44___________________________16\n	91 -- 97	23 -- 29	-31.1732 kcal/mol	6.53125 kcal/mol	12.6613 kcal/mol	75 103@LB@ \| \|@LB@5'-CUU...GAUCU GAA AAAGA...CCC-3'@LB@ CGCUAGAG AGAGGCUAUUUU UGGU@LB@ \|:\|\|\|\|\|\| \|\|\|:\|\|\|\|\|\|:: \|\|\|:@LB@ GUGAUCUC UCUUCGAUAAGG ACCG@LB@3'-UUU...UGUUU AG U CAAUC...GAA-5'@LB@ \| \|@LB@ 44 16@LB@@LB@@LB@Energy -11.98 kcal/mol@LB@Hybridization Energy -31.1732 kcal/mol@LB@Unfolding Energy - mRNA 6.53125 kcal/mol@LB@Unfolding Energy - sRNA 12.6613 kcal/mol@LB@@LB@Position - mRNA 76 -- 102@LB@Position - sRNA 17 -- 43@LB@Position Seed - mRNA 91 -- 97@LB@Position Seed - sRNA 23 -- 29@LB@
39	0.01357	0.2859	ct_401	gltT	-7.80	0.095127	36 -- 47	44 -- 55	sodium:dicarboxylate symport protein	_____________35___________48\n_____________\|____________\|\n5'-UGU...GGUAU____________AAAGG...AUA-3'\n______________CCUGUGUACAGA\n______________\|\|\|\|\|\|\|\|\|\|:\|\n______________GGACACAUGUUU\n3'-UUU...AGGGG____________GUGAU...GAA-5'\n_____________\|____________\|\n_____________56___________43\n	41 -- 47	44 -- 50	-17.8988 kcal/mol	2.58215 kcal/mol	7.51272 kcal/mol	35 48@LB@ \| \|@LB@5'-UGU...GGUAU AAAGG...AUA-3'@LB@ CCUGUGUACAGA@LB@ \|\|\|\|\|\|\|\|\|\|:\|@LB@ GGACACAUGUUU@LB@3'-UUU...AGGGG GUGAU...GAA-5'@LB@ \| \|@LB@ 56 43@LB@@LB@@LB@Energy -7.80 kcal/mol@LB@Hybridization Energy -17.8988 kcal/mol@LB@Unfolding Energy - mRNA 2.58215 kcal/mol@LB@Unfolding Energy - sRNA 7.51272 kcal/mol@LB@@LB@Position - mRNA 36 -- 47@LB@Position - sRNA 44 -- 55@LB@Position Seed - mRNA 41 -- 47@LB@Position Seed - sRNA 44 -- 50@LB@
40	0.01393	0.2859	ct_695	N/A	-4.73	0.403172	160 -- 166	82 -- 88		_____________159_____167\n_____________\|_______\|\n5'-AUU...AAGGU_______GUUCG...AGG-3'\n______________AUGCGGU\n______________\|\|:\|\|\|:\n______________UAUGCCG\n3'-UUU...GCCUC_______AUUGA...GAA-5'\n_____________\|_______\|\n_____________89______81\n	160 -- 166	82 -- 88	-8.16543 kcal/mol	2.33498 kcal/mol	1.09753 kcal/mol	159 167@LB@ \| \|@LB@5'-AUU...AAGGU GUUCG...AGG-3'@LB@ AUGCGGU@LB@ \|\|:\|\|\|:@LB@ UAUGCCG@LB@3'-UUU...GCCUC AUUGA...GAA-5'@LB@ \| \|@LB@ 89 81@LB@@LB@@LB@Energy -4.73 kcal/mol@LB@Hybridization Energy -8.16543 kcal/mol@LB@Unfolding Energy - mRNA 2.33498 kcal/mol@LB@Unfolding Energy - sRNA 1.09753 kcal/mol@LB@@LB@Position - mRNA 160 -- 166@LB@Position - sRNA 82 -- 88@LB@Position Seed - mRNA 160 -- 166@LB@Position Seed - sRNA 82 -- 88@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

Use the following button if you want to resubmit the job with altered input or parameterization:

usability assessment

Please support us by filling this short quality survey for evaluating this

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

Main Menu

Freiburg RNA Tools

Interaction Prediction

Seq-Str Alignment

CRISPR

Sequence Design

Splicing

SNP & Mutation

Classification

Gene set extension

MoDPepInt Server

CPSP-Tools Server

Galaxy-FR

CMV server

Teaching