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
67	0.02533	0.29	ct_395	grpE	-6.02	0.231793	191 -- 203	19 -- 33	stress response protein GrpE	_____________190_____________204\n_____________\|_______________\|\n5'-CCU...CGCUA_______________ACAGA...UAA-3'\n______________AGGAGCUAU__CAUG\n______________\|\|:\|\|\|\|\|\|__\|\|\|\|\n______________UCUUCGAUA__GUAC\n3'-UUU...CUCAG_________AG____CGCAA...GAA-5'\n_____________\|_______________\|\n_____________34______________18\n	192 -- 198	26 -- 32	-14.6636 kcal/mol	3.66894 kcal/mol	4.97702 kcal/mol	190 204@LB@ \| \|@LB@5'-CCU...CGCUA ACAGA...UAA-3'@LB@ AGGAGCUAU CAUG@LB@ \|\|:\|\|\|\|\|\| \|\|\|\|@LB@ UCUUCGAUA GUAC@LB@3'-UUU...CUCAG AG CGCAA...GAA-5'@LB@ \| \|@LB@ 34 18@LB@@LB@@LB@Energy -6.02 kcal/mol@LB@Hybridization Energy -14.6636 kcal/mol@LB@Unfolding Energy - mRNA 3.66894 kcal/mol@LB@Unfolding Energy - sRNA 4.97702 kcal/mol@LB@@LB@Position - mRNA 191 -- 203@LB@Position - sRNA 19 -- 33@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 26 -- 32@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@
111	0.04436	0.3262	ct_405	ribC	-3.97	0.532190	3 -- 10	49 -- 56	riboflavin synthase	_____________2________11\n_____________\|________\|\n_________5'-AA________CUUGU...AUG-3'\n______________UCCUGUGU\n______________:\|\|\|\|\|\|\|\n______________GGGACACA\n3'-UUU...AAGGG________UGUUU...GAA-5'\n_____________\|________\|\n_____________57_______48\n	4 -- 10	49 -- 55	-11.4476 kcal/mol	0.227857 kcal/mol	7.24525 kcal/mol	2 11@LB@ \| \|@LB@ 5'-AA CUUGU...AUG-3'@LB@ UCCUGUGU@LB@ :\|\|\|\|\|\|\|@LB@ GGGACACA@LB@3'-UUU...AAGGG UGUUU...GAA-5'@LB@ \| \|@LB@ 57 48@LB@@LB@@LB@Energy -3.97 kcal/mol@LB@Hybridization Energy -11.4476 kcal/mol@LB@Unfolding Energy - mRNA 0.227857 kcal/mol@LB@Unfolding Energy - sRNA 7.24525 kcal/mol@LB@@LB@Position - mRNA 3 -- 10@LB@Position - sRNA 49 -- 56@LB@Position Seed - mRNA 4 -- 10@LB@Position Seed - sRNA 49 -- 55@LB@
170	0.07264	0.3448	ct_415	yebL	-4.69	0.409849	24 -- 30	22 -- 28	metal ABC transporter substrate-binding protein	_____________23______31\n_____________\|_______\|\n5'-AUU...AAAAA_______UCACC...CCU-3'\n______________CUGUUCC\n______________\|\|:\|\|\|\|\n______________GAUAAGG\n3'-UUU...UCUUC_______UACCG...GAA-5'\n_____________\|_______\|\n_____________29______21\n	24 -- 30	22 -- 28	-9.14166 kcal/mol	0.102316 kcal/mol	4.35007 kcal/mol	23 31@LB@ \| \|@LB@5'-AUU...AAAAA UCACC...CCU-3'@LB@ CUGUUCC@LB@ \|\|:\|\|\|\|@LB@ GAUAAGG@LB@3'-UUU...UCUUC UACCG...GAA-5'@LB@ \| \|@LB@ 29 21@LB@@LB@@LB@Energy -4.69 kcal/mol@LB@Hybridization Energy -9.14166 kcal/mol@LB@Unfolding Energy - mRNA 0.102316 kcal/mol@LB@Unfolding Energy - sRNA 4.35007 kcal/mol@LB@@LB@Position - mRNA 24 -- 30@LB@Position - sRNA 22 -- 28@LB@Position Seed - mRNA 24 -- 30@LB@Position Seed - sRNA 22 -- 28@LB@
46	0.01681	0.29	ct_425	N/A	-8.97	0.050526	259 -- 284	2 -- 23		_____________258_________________________285\n_____________\|___________________________\|\n5'-CUU...UUCUA__________UC_____UUCU______AAUUU...AAG-3'\n______________CC_UGGCGUU__GAAUA____UCAGCU\n______________\|\|_\|\|\|\|\|\|\|__\|\|\|\|\|____:\|\|:\|\|\n______________GG_ACCGCAA__CUUAU____GGUUGA\n3'-UUU...GAUAA__U_______U________________A-5'\n_____________\|___________________________\|\n_____________24__________________________1\n	261 -- 267	14 -- 20	-21.0816 kcal/mol	4.01638 kcal/mol	8.09761 kcal/mol	258 285@LB@ \| \|@LB@5'-CUU...UUCUA UC UUCU AAUUU...AAG-3'@LB@ CC UGGCGUU GAAUA UCAGCU@LB@ \|\| \|\|\|\|\|\|\| \|\|\|\|\| :\|\|:\|\|@LB@ GG ACCGCAA CUUAU GGUUGA@LB@3'-UUU...GAUAA U U A-5'@LB@ \| \|@LB@ 24 1@LB@@LB@@LB@Energy -8.97 kcal/mol@LB@Hybridization Energy -21.0816 kcal/mol@LB@Unfolding Energy - mRNA 4.01638 kcal/mol@LB@Unfolding Energy - sRNA 8.09761 kcal/mol@LB@@LB@Position - mRNA 259 -- 284@LB@Position - sRNA 2 -- 23@LB@Position Seed - mRNA 261 -- 267@LB@Position Seed - sRNA 14 -- 20@LB@
177	0.07605	0.3532	ct_428	ubiE	-3.67	0.587989	9 -- 17	20 -- 28	demethylmenaquinone methyltransferase	_____________8_________18\n_____________\|_________\|\n___5'-UUCUUCAA_________UUCAG...AUA-3'\n______________CUAUUUCAU\n______________\|\|\|\|\|:\|\|\|\n______________GAUAAGGUA\n3'-UUU...UCUUC_________CCGCA...GAA-5'\n_____________\|_________\|\n_____________29________19\n	10 -- 16	21 -- 27	-8.26525 kcal/mol	0.050804 kcal/mol	4.54807 kcal/mol	8 18@LB@ \| \|@LB@ 5'-UUCUUCAA UUCAG...AUA-3'@LB@ CUAUUUCAU@LB@ \|\|\|\|\|:\|\|\|@LB@ GAUAAGGUA@LB@3'-UUU...UCUUC CCGCA...GAA-5'@LB@ \| \|@LB@ 29 19@LB@@LB@@LB@Energy -3.67 kcal/mol@LB@Hybridization Energy -8.26525 kcal/mol@LB@Unfolding Energy - mRNA 0.050804 kcal/mol@LB@Unfolding Energy - sRNA 4.54807 kcal/mol@LB@@LB@Position - mRNA 9 -- 17@LB@Position - sRNA 20 -- 28@LB@Position Seed - mRNA 10 -- 16@LB@Position Seed - sRNA 21 -- 27@LB@
79	0.0288	0.29	ct_431	clpP_1	-3.71	0.580570	128 -- 134	79 -- 85	ATP-dependent Clp protease proteolytic subunit	_____________127_____135\n_____________\|_______\|\n5'-GAA...ACGUG_______UUUAU...AAA-3'\n______________UGGCUGA\n______________:\|\|\|\|:\|\n______________GCCGAUU\n3'-UUU...UCUAU_______GAGGU...GAA-5'\n_____________\|_______\|\n_____________86______78\n	128 -- 134	79 -- 85	-7.88567 kcal/mol	3.08 kcal/mol	1.09751 kcal/mol	127 135@LB@ \| \|@LB@5'-GAA...ACGUG UUUAU...AAA-3'@LB@ UGGCUGA@LB@ :\|\|\|\|:\|@LB@ GCCGAUU@LB@3'-UUU...UCUAU GAGGU...GAA-5'@LB@ \| \|@LB@ 86 78@LB@@LB@@LB@Energy -3.71 kcal/mol@LB@Hybridization Energy -7.88567 kcal/mol@LB@Unfolding Energy - mRNA 3.08 kcal/mol@LB@Unfolding Energy - sRNA 1.09751 kcal/mol@LB@@LB@Position - mRNA 128 -- 134@LB@Position - sRNA 79 -- 85@LB@Position Seed - mRNA 128 -- 134@LB@Position Seed - sRNA 79 -- 85@LB@
148	0.06134	0.3407	ct_434	ygbB	-10.66	0.019089	186 -- 200	41 -- 57	2-C-methyl-D-erythritol 2 4-cyclodiphosphate synthase	_____________185_______________201\n_____________\|_________________\|\n5'-GGU...CCUGU_____U___________AUGAC...AUC-3'\n______________CCCCU___UGCAAGCAC\n______________\|\|\|\|\|___\|:\|\|\|:\|\|\|\n______________GGGGA___AUGUUUGUG\n3'-UUU...GAAGG_____CAC_________AUCUC...GAA-5'\n_____________\|_________________\|\n_____________58________________40\n	194 -- 200	41 -- 47	-19.7128 kcal/mol	1.2348 kcal/mol	7.82241 kcal/mol	185 201@LB@ \| \|@LB@5'-GGU...CCUGU U AUGAC...AUC-3'@LB@ CCCCU UGCAAGCAC@LB@ \|\|\|\|\| \|:\|\|\|:\|\|\|@LB@ GGGGA AUGUUUGUG@LB@3'-UUU...GAAGG CAC AUCUC...GAA-5'@LB@ \| \|@LB@ 58 40@LB@@LB@@LB@Energy -10.66 kcal/mol@LB@Hybridization Energy -19.7128 kcal/mol@LB@Unfolding Energy - mRNA 1.2348 kcal/mol@LB@Unfolding Energy - sRNA 7.82241 kcal/mol@LB@@LB@Position - mRNA 186 -- 200@LB@Position - sRNA 41 -- 57@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 41 -- 47@LB@
87	0.03104	0.29	ct_437	fusA	-5.85	0.250219	118 -- 125	79 -- 86	elongation factor G	_____________117______126\n_____________\|________\|\n5'-AUC...AUCGC________AGCAA...UCU-3'\n______________AUGGCUGA\n______________\|:\|\|\|\|:\|\n______________UGCCGAUU\n3'-UUU...CUCUA________GAGGU...GAA-5'\n_____________\|________\|\n_____________87_______78\n	119 -- 125	79 -- 85	-8.84241 kcal/mol	1.89322 kcal/mol	1.09752 kcal/mol	117 126@LB@ \| \|@LB@5'-AUC...AUCGC AGCAA...UCU-3'@LB@ AUGGCUGA@LB@ \|:\|\|\|\|:\|@LB@ UGCCGAUU@LB@3'-UUU...CUCUA GAGGU...GAA-5'@LB@ \| \|@LB@ 87 78@LB@@LB@@LB@Energy -5.85 kcal/mol@LB@Hybridization Energy -8.84241 kcal/mol@LB@Unfolding Energy - mRNA 1.89322 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 118 -- 125@LB@Position - sRNA 79 -- 86@LB@Position Seed - mRNA 119 -- 125@LB@Position Seed - sRNA 79 -- 85@LB@
44	0.01666	0.29	ct_438	rs7	-6.33	0.200160	214 -- 223	79 -- 88	30S ribosomal protein S7	_____________213________224\n_____________\|__________\|\n5'-GCA...ACGAC__________GAAGA...ACG-3'\n______________AUGCGGCUGA\n______________\|\|:\|\|\|\|\|:\|\n______________UAUGCCGAUU\n3'-UUU...GCCUC__________GAGGU...GAA-5'\n_____________\|__________\|\n_____________89_________78\n	217 -- 223	79 -- 85	-13.0034 kcal/mol	5.57631 kcal/mol	1.09753 kcal/mol	213 224@LB@ \| \|@LB@5'-GCA...ACGAC GAAGA...ACG-3'@LB@ AUGCGGCUGA@LB@ \|\|:\|\|\|\|\|:\|@LB@ UAUGCCGAUU@LB@3'-UUU...GCCUC GAGGU...GAA-5'@LB@ \| \|@LB@ 89 78@LB@@LB@@LB@Energy -6.33 kcal/mol@LB@Hybridization Energy -13.0034 kcal/mol@LB@Unfolding Energy - mRNA 5.57631 kcal/mol@LB@Unfolding Energy - sRNA 1.09753 kcal/mol@LB@@LB@Position - mRNA 214 -- 223@LB@Position - sRNA 79 -- 88@LB@Position Seed - mRNA 217 -- 223@LB@Position Seed - sRNA 79 -- 85@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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