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
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@
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@
45	0.01671	0.29	ct_469	N/A	-9.81	0.031394	4 -- 20	17 -- 35		_____________3___________________21\n_____________\|___________________\|\n________5'-AUU___________________AACCU...UCU-3'\n______________UCAGAAGCU_UUUC_UGGU\n______________\|\|\|\|\|\|\|\|\|_\|\|:\|_\|\|\|:\n______________AGUCUUCGA_AAGG_ACCG\n3'-UUU...AUCUC_________U____U____CAAUC...GAA-5'\n_____________\|___________________\|\n_____________36__________________16\n	6 -- 12	27 -- 33	-19.4129 kcal/mol	4.62874 kcal/mol	4.9781 kcal/mol	3 21@LB@ \| \|@LB@ 5'-AUU AACCU...UCU-3'@LB@ UCAGAAGCU UUUC UGGU@LB@ \|\|\|\|\|\|\|\|\| \|\|:\| \|\|\|:@LB@ AGUCUUCGA AAGG ACCG@LB@3'-UUU...AUCUC U U CAAUC...GAA-5'@LB@ \| \|@LB@ 36 16@LB@@LB@@LB@Energy -9.81 kcal/mol@LB@Hybridization Energy -19.4129 kcal/mol@LB@Unfolding Energy - mRNA 4.62874 kcal/mol@LB@Unfolding Energy - sRNA 4.9781 kcal/mol@LB@@LB@Position - mRNA 4 -- 20@LB@Position - sRNA 17 -- 35@LB@Position Seed - mRNA 6 -- 12@LB@Position Seed - sRNA 27 -- 33@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@
62	0.02417	0.29	ct_705	clpX	-8.32	0.072096	259 -- 275	17 -- 33	ATP-dependent Clp protease ATP-binding subunit ClpX	_____________258_______________276\n_____________\|_________________\|\n5'-CUG...UGUUG________A__GC____CCAUC...AUU-3'\n______________AGAAGCUA_UC__UGGU\n______________\|\|\|\|\|\|\|\|_\|\|__\|\|\|:\n______________UCUUCGAU_AG__ACCG\n3'-UUU...CUCAG________A__GU____CAAUC...GAA-5'\n_____________\|_________________\|\n_____________34________________16\n	260 -- 266	26 -- 32	-18.4351 kcal/mol	5.13531 kcal/mol	4.97804 kcal/mol	258 276@LB@ \| \|@LB@5'-CUG...UGUUG A GC CCAUC...AUU-3'@LB@ AGAAGCUA UC UGGU@LB@ \|\|\|\|\|\|\|\| \|\| \|\|\|:@LB@ UCUUCGAU AG ACCG@LB@3'-UUU...CUCAG A GU CAAUC...GAA-5'@LB@ \| \|@LB@ 34 16@LB@@LB@@LB@Energy -8.32 kcal/mol@LB@Hybridization Energy -18.4351 kcal/mol@LB@Unfolding Energy - mRNA 5.13531 kcal/mol@LB@Unfolding Energy - sRNA 4.97804 kcal/mol@LB@@LB@Position - mRNA 259 -- 275@LB@Position - sRNA 17 -- 33@LB@Position Seed - mRNA 260 -- 266@LB@Position Seed - sRNA 26 -- 32@LB@
64	0.02465	0.29	ct_045	pepA	-6.49	0.184926	191 -- 205	17 -- 33	cytosol aminopeptidase	_____________190_______________206\n_____________\|_________________\|\n5'-UUU...AACAA_________________AUUAC...CUG-3'\n______________AGAGGUUAUU__GUGGU\n______________\|\|\|:\|:\|\|\|\|__:\|\|\|:\n______________UCUUCGAUAA__UACCG\n3'-UUU...CUCAG__________GG_____CAAUC...GAA-5'\n_____________\|_________________\|\n_____________34________________16\n	191 -- 197	27 -- 33	-15.0477 kcal/mol	3.57571 kcal/mol	4.97804 kcal/mol	190 206@LB@ \| \|@LB@5'-UUU...AACAA AUUAC...CUG-3'@LB@ AGAGGUUAUU GUGGU@LB@ \|\|\|:\|:\|\|\|\| :\|\|\|:@LB@ UCUUCGAUAA UACCG@LB@3'-UUU...CUCAG GG CAAUC...GAA-5'@LB@ \| \|@LB@ 34 16@LB@@LB@@LB@Energy -6.49 kcal/mol@LB@Hybridization Energy -15.0477 kcal/mol@LB@Unfolding Energy - mRNA 3.57571 kcal/mol@LB@Unfolding Energy - sRNA 4.97804 kcal/mol@LB@@LB@Position - mRNA 191 -- 205@LB@Position - sRNA 17 -- 33@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 27 -- 33@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@
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@
107	0.04107	0.3134	ct_813	N/A	-9.66	0.034154	135 -- 167	17 -- 51	inclusion membrane protein	_____________134_________________________________168\n_____________\|___________________________________\|\n5'-CCA...AAAUU________AA________U___________U____CCAUC...AGG-3'\n______________UGUGCAGA___UAG_GUC_GAGGCUGUUUU_UGGU\n______________\|\|\|:\|\|:\|___\|\|\|_\|\|\|_\|\|:\|\|\|:\|\|::_\|\|\|:\n______________ACAUGUUU___AUC_CAG_CUUCGAUAAGG_ACCG\n3'-UUU...GGGAC________GUG___U___U___________U____CAAUC...GAA-5'\n_____________\|___________________________________\|\n_____________52__________________________________16\n	155 -- 161	23 -- 29	-33.5835 kcal/mol	11.0074 kcal/mol	12.9166 kcal/mol	134 168@LB@ \| \|@LB@5'-CCA...AAAUU AA U U CCAUC...AGG-3'@LB@ UGUGCAGA UAG GUC GAGGCUGUUUU UGGU@LB@ \|\|\|:\|\|:\| \|\|\| \|\|\| \|\|:\|\|\|:\|\|:: \|\|\|:@LB@ ACAUGUUU AUC CAG CUUCGAUAAGG ACCG@LB@3'-UUU...GGGAC GUG U U U CAAUC...GAA-5'@LB@ \| \|@LB@ 52 16@LB@@LB@@LB@Energy -9.66 kcal/mol@LB@Hybridization Energy -33.5835 kcal/mol@LB@Unfolding Energy - mRNA 11.0074 kcal/mol@LB@Unfolding Energy - sRNA 12.9166 kcal/mol@LB@@LB@Position - mRNA 135 -- 167@LB@Position - sRNA 17 -- 51@LB@Position Seed - mRNA 155 -- 161@LB@Position Seed - sRNA 23 -- 29@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