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
2	8.171e-05	0.03358	ct_802	rs18	-7.95	0.088258	66 -- 79	21 -- 34	30S ribosomal protein S18	_____________65_____________80\n_____________\|______________\|\n5'-GUU...AGCCC__________CG__GAGUU...UUA-3'\n______________CAGAAGCUAU__CA\n______________\|\|\|\|\|\|\|\|\|\|__\|\|\n______________GUCUUCGAUA__GU\n3'-UUU...UCUCA__________AG__ACCGC...GAA-5'\n_____________\|______________\|\n_____________35_____________20\n	68 -- 74	26 -- 32	-17.0234 kcal/mol	4.34679 kcal/mol	4.73132 kcal/mol	65 80@LB@ \| \|@LB@5'-GUU...AGCCC CG GAGUU...UUA-3'@LB@ CAGAAGCUAU CA@LB@ \|\|\|\|\|\|\|\|\|\| \|\|@LB@ GUCUUCGAUA GU@LB@3'-UUU...UCUCA AG ACCGC...GAA-5'@LB@ \| \|@LB@ 35 20@LB@@LB@@LB@Energy -7.95 kcal/mol@LB@Hybridization Energy -17.0234 kcal/mol@LB@Unfolding Energy - mRNA 4.34679 kcal/mol@LB@Unfolding Energy - sRNA 4.73132 kcal/mol@LB@@LB@Position - mRNA 66 -- 79@LB@Position - sRNA 21 -- 34@LB@Position Seed - mRNA 68 -- 74@LB@Position Seed - sRNA 26 -- 32@LB@
194	0.08693	0.3657	ct_285	lplA_1	-4.48	0.444512	66 -- 74	27 -- 35	lipoate protein ligase	_____________65________75\n_____________\|_________\|\n5'-CUU...AAUUU_________UUUUU...UUC-3'\n______________UUAGAAGCU\n______________\|:\|\|\|\|\|\|\|\n______________AGUCUUCGA\n3'-UUU...AUCUC_________UAAGG...GAA-5'\n_____________\|_________\|\n_____________36________26\n	68 -- 74	27 -- 33	-10.5389 kcal/mol	1.46011 kcal/mol	4.60001 kcal/mol	65 75@LB@ \| \|@LB@5'-CUU...AAUUU UUUUU...UUC-3'@LB@ UUAGAAGCU@LB@ \|:\|\|\|\|\|\|\|@LB@ AGUCUUCGA@LB@3'-UUU...AUCUC UAAGG...GAA-5'@LB@ \| \|@LB@ 36 26@LB@@LB@@LB@Energy -4.48 kcal/mol@LB@Hybridization Energy -10.5389 kcal/mol@LB@Unfolding Energy - mRNA 1.46011 kcal/mol@LB@Unfolding Energy - sRNA 4.60001 kcal/mol@LB@@LB@Position - mRNA 66 -- 74@LB@Position - sRNA 27 -- 35@LB@Position Seed - mRNA 68 -- 74@LB@Position Seed - sRNA 27 -- 33@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@
174	0.07335	0.3448	ct_777	bioF	-7.25	0.126962	76 -- 92	19 -- 34	8-amino-7-oxononanoate synthase	_____________75________________93\n_____________\|_________________\|\n5'-CUG...UCAGG_______G_____U___UUGGG...UUU-3'\n______________UAGAAGC_AUUCC_AUG\n______________:\|\|\|\|\|\|_\|\|\|\|\|_\|\|\|\n______________GUCUUCG_UAAGG_UAC\n3'-UUU...UCUCA_______A_________CGCAA...GAA-5'\n_____________\|_________________\|\n_____________35________________18\n	76 -- 82	28 -- 34	-16.4612 kcal/mol	4.23516 kcal/mol	4.97732 kcal/mol	75 93@LB@ \| \|@LB@5'-CUG...UCAGG G U UUGGG...UUU-3'@LB@ UAGAAGC AUUCC AUG@LB@ :\|\|\|\|\|\| \|\|\|\|\| \|\|\|@LB@ GUCUUCG UAAGG UAC@LB@3'-UUU...UCUCA A CGCAA...GAA-5'@LB@ \| \|@LB@ 35 18@LB@@LB@@LB@Energy -7.25 kcal/mol@LB@Hybridization Energy -16.4612 kcal/mol@LB@Unfolding Energy - mRNA 4.23516 kcal/mol@LB@Unfolding Energy - sRNA 4.97732 kcal/mol@LB@@LB@Position - mRNA 76 -- 92@LB@Position - sRNA 19 -- 34@LB@Position Seed - mRNA 76 -- 82@LB@Position Seed - sRNA 28 -- 34@LB@
176	0.07518	0.3511	ct_481	N/A	-6.18	0.214715	76 -- 94	18 -- 35		_____________75__________________95\n_____________\|___________________\|\n5'-AUA...CCAUU__U___AU___________AAACA...AUU-3'\n______________UC_GAA__CUGUUCUAUGG\n______________\|\|_\|\|\|__\|\|:\|\|\|:\|\|\|\|\n______________AG_CUU__GAUAAGGUACC\n3'-UUU...AUCUC__U___C____________GCAAU...GAA-5'\n_____________\|___________________\|\n_____________36__________________17\n	88 -- 94	18 -- 24	-16.4052 kcal/mol	5.24588 kcal/mol	4.97803 kcal/mol	75 95@LB@ \| \|@LB@5'-AUA...CCAUU U AU AAACA...AUU-3'@LB@ UC GAA CUGUUCUAUGG@LB@ \|\| \|\|\| \|\|:\|\|\|:\|\|\|\|@LB@ AG CUU GAUAAGGUACC@LB@3'-UUU...AUCUC U C GCAAU...GAA-5'@LB@ \| \|@LB@ 36 17@LB@@LB@@LB@Energy -6.18 kcal/mol@LB@Hybridization Energy -16.4052 kcal/mol@LB@Unfolding Energy - mRNA 5.24588 kcal/mol@LB@Unfolding Energy - sRNA 4.97803 kcal/mol@LB@@LB@Position - mRNA 76 -- 94@LB@Position - sRNA 18 -- 35@LB@Position Seed - mRNA 88 -- 94@LB@Position Seed - sRNA 18 -- 24@LB@
198	0.08843	0.3671	ct_257	N/A	-6.39	0.194258	76 -- 83	79 -- 86		_____________75_______84\n_____________\|________\|\n5'-CUA...GGCGG________CAGAA...UCA-3'\n______________AUGGCUGA\n______________\|:\|\|\|\|:\|\n______________UGCCGAUU\n3'-UUU...CUCUA________GAGGU...GAA-5'\n_____________\|________\|\n_____________87_______78\n	77 -- 83	79 -- 85	-9.5904 kcal/mol	2.10083 kcal/mol	1.09752 kcal/mol	75 84@LB@ \| \|@LB@5'-CUA...GGCGG CAGAA...UCA-3'@LB@ AUGGCUGA@LB@ \|:\|\|\|\|:\|@LB@ UGCCGAUU@LB@3'-UUU...CUCUA GAGGU...GAA-5'@LB@ \| \|@LB@ 87 78@LB@@LB@@LB@Energy -6.39 kcal/mol@LB@Hybridization Energy -9.5904 kcal/mol@LB@Unfolding Energy - mRNA 2.10083 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 76 -- 83@LB@Position - sRNA 79 -- 86@LB@Position Seed - mRNA 77 -- 83@LB@Position Seed - sRNA 79 -- 85@LB@
172	0.07285	0.3448	ct_090	lcrD	-6.84	0.155915	81 -- 102	18 -- 39	low calcium response protein D	_____________80______________________103\n_____________\|_______________________\|\n5'-AUU...GGAAA___________U________GA_ACCAC...UGU-3'\n______________AGAGUU_GAAG_UUAUUCCA__G\n______________\|\|\|\|\|:_\|\|\|\|_:\|\|\|\|\|\|\|__\|\n______________UCUCAG_CUUC_GAUAAGGU__C\n3'-UUU...UGUGA______U_____________AC_GCAAU...GAA-5'\n_____________\|_______________________\|\n_____________40______________________17\n	93 -- 99	21 -- 27	-20.344 kcal/mol	3.91171 kcal/mol	9.59078 kcal/mol	80 103@LB@ \| \|@LB@5'-AUU...GGAAA U GA ACCAC...UGU-3'@LB@ AGAGUU GAAG UUAUUCCA G@LB@ \|\|\|\|\|: \|\|\|\| :\|\|\|\|\|\|\| \|@LB@ UCUCAG CUUC GAUAAGGU C@LB@3'-UUU...UGUGA U AC GCAAU...GAA-5'@LB@ \| \|@LB@ 40 17@LB@@LB@@LB@Energy -6.84 kcal/mol@LB@Hybridization Energy -20.344 kcal/mol@LB@Unfolding Energy - mRNA 3.91171 kcal/mol@LB@Unfolding Energy - sRNA 9.59078 kcal/mol@LB@@LB@Position - mRNA 81 -- 102@LB@Position - sRNA 18 -- 39@LB@Position Seed - mRNA 93 -- 99@LB@Position Seed - sRNA 21 -- 27@LB@
88	0.03104	0.29	ct_766	miaA	-2.38	0.813549	82 -- 88	27 -- 33	tRNA dimethylallyltransferase	_____________81______89\n_____________\|_______\|\n5'-AUA...UAAUG_______UUGUA...UGU-3'\n______________GGAAGCU\n______________:\|\|\|\|\|\|\n______________UCUUCGA\n3'-UUU...CUCAG_______UAAGG...GAA-5'\n_____________\|_______\|\n_____________34______26\n	82 -- 88	27 -- 33	-8.83329 kcal/mol	1.86027 kcal/mol	4.59825 kcal/mol	81 89@LB@ \| \|@LB@5'-AUA...UAAUG UUGUA...UGU-3'@LB@ GGAAGCU@LB@ :\|\|\|\|\|\|@LB@ UCUUCGA@LB@3'-UUU...CUCAG UAAGG...GAA-5'@LB@ \| \|@LB@ 34 26@LB@@LB@@LB@Energy -2.38 kcal/mol@LB@Hybridization Energy -8.83329 kcal/mol@LB@Unfolding Energy - mRNA 1.86027 kcal/mol@LB@Unfolding Energy - sRNA 4.59825 kcal/mol@LB@@LB@Position - mRNA 82 -- 88@LB@Position - sRNA 27 -- 33@LB@Position Seed - mRNA 82 -- 88@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@
156	0.06505	0.3424	ct_254	N/A	-6.97	0.146186	84 -- 91	80 -- 87		_____________83_______92\n_____________\|________\|\n5'-GUC...AUCGU________GCGUU...UAC-3'\n______________UAUGGCUG\n______________\|\|:\|\|\|\|:\n______________AUGCCGAU\n3'-UUU...CCUCU________UGAGG...GAA-5'\n_____________\|________\|\n_____________88_______79\n	85 -- 91	80 -- 86	-9.90306 kcal/mol	1.8348 kcal/mol	1.09752 kcal/mol	83 92@LB@ \| \|@LB@5'-GUC...AUCGU GCGUU...UAC-3'@LB@ UAUGGCUG@LB@ \|\|:\|\|\|\|:@LB@ AUGCCGAU@LB@3'-UUU...CCUCU UGAGG...GAA-5'@LB@ \| \|@LB@ 88 79@LB@@LB@@LB@Energy -6.97 kcal/mol@LB@Hybridization Energy -9.90306 kcal/mol@LB@Unfolding Energy - mRNA 1.8348 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 84 -- 91@LB@Position - sRNA 80 -- 87@LB@Position Seed - mRNA 85 -- 91@LB@Position Seed - sRNA 80 -- 86@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:

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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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