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
53	0.01942	0.29	ct_580	N/A	-10.14	0.025883	244 -- 280	22 -- 57	S-adenosylmethionine/S-adenosylhomocysteine transporter	_____________243___________________________________281\n_____________\|_____________________________________\|\n5'-GUU...ACAAA___G_____U_____C___UU__GACAU_________CUUAA...CUU-3'\n______________CCU_UGUGU_UAAAC_CUG__GU_____GGCUAUUUU\n______________\|\|:_\|\|\|\|\|_:\|\|\|\|_\|\|:__\|\|_____:\|\|\|\|\|\|::\n______________GGG_ACACA_GUUUG_GAU__CA_____UCGAUAAGG\n3'-UUU...GAAGG___G_____U_____U___CU__GUCU__________UACCG...GAA-5'\n_____________\|_____________________________________\|\n_____________58____________________________________21\n	273 -- 279	23 -- 29	-28.6785 kcal/mol	5.85369 kcal/mol	12.6861 kcal/mol	243 281@LB@ \| \|@LB@5'-GUU...ACAAA G U C UU GACAU CUUAA...CUU-3'@LB@ CCU UGUGU UAAAC CUG GU GGCUAUUUU@LB@ \|\|: \|\|\|\|\| :\|\|\|\| \|\|: \|\| :\|\|\|\|\|\|::@LB@ GGG ACACA GUUUG GAU CA UCGAUAAGG@LB@3'-UUU...GAAGG G U U CU GUCU UACCG...GAA-5'@LB@ \| \|@LB@ 58 21@LB@@LB@@LB@Energy -10.14 kcal/mol@LB@Hybridization Energy -28.6785 kcal/mol@LB@Unfolding Energy - mRNA 5.85369 kcal/mol@LB@Unfolding Energy - sRNA 12.6861 kcal/mol@LB@@LB@Position - mRNA 244 -- 280@LB@Position - sRNA 22 -- 57@LB@Position Seed - mRNA 273 -- 279@LB@Position Seed - sRNA 23 -- 29@LB@
50	0.01829	0.29	ct_588	rbsU	-10.49	0.021035	31 -- 46	21 -- 34	serine phosphatase RsbU	_____________30_______________47\n_____________\|________________\|\n5'-GUC...GGGUC________CU______AGAUU...UCC-3'\n______________CAGAAGCU__AUUCCA\n______________\|\|\|\|\|\|\|\|__\|\|\|\|\|\|\n______________GUCUUCGA__UAAGGU\n3'-UUU...UCUCA________________ACCGC...GAA-5'\n_____________\|________________\|\n_____________35_______________20\n	32 -- 38	27 -- 33	-17.905 kcal/mol	2.68182 kcal/mol	4.73132 kcal/mol	30 47@LB@ \| \|@LB@5'-GUC...GGGUC CU AGAUU...UCC-3'@LB@ CAGAAGCU AUUCCA@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ GUCUUCGA UAAGGU@LB@3'-UUU...UCUCA ACCGC...GAA-5'@LB@ \| \|@LB@ 35 20@LB@@LB@@LB@Energy -10.49 kcal/mol@LB@Hybridization Energy -17.905 kcal/mol@LB@Unfolding Energy - mRNA 2.68182 kcal/mol@LB@Unfolding Energy - sRNA 4.73132 kcal/mol@LB@@LB@Position - mRNA 31 -- 46@LB@Position - sRNA 21 -- 34@LB@Position Seed - mRNA 32 -- 38@LB@Position Seed - sRNA 27 -- 33@LB@
153	0.06453	0.3424	ct_729	serS	-6.28	0.205305	1 -- 23	3 -- 33	serine--tRNA ligase	______________1______________________________24\n______________\|______________________________\|\n___________5'-____C_G_____U__________________CCUCA...UGG-3'\n______________AGAA_C_AUUCC_UG________AUGCCAAC\n______________\|\|\|\|_\|_\|\|\|\|\|_\|\|________\|\|:\|\|\|\|\|\n______________UCUU_G_UAAGG_AC________UAUGGUUG\n3'-UUU...CUCAG____C_A_____U__CGCAAUCU________AA-5'\n_____________\|_______________________________\|\n_____________34______________________________2\n	17 -- 23	3 -- 9	-16.9997 kcal/mol	2.1318 kcal/mol	8.59196 kcal/mol	1 24@LB@ \| \|@LB@ 5'- C G U CCUCA...UGG-3'@LB@ AGAA C AUUCC UG AUGCCAAC@LB@ \|\|\|\| \| \|\|\|\|\| \|\| \|\|:\|\|\|\|\|@LB@ UCUU G UAAGG AC UAUGGUUG@LB@3'-UUU...CUCAG C A U CGCAAUCU AA-5'@LB@ \| \|@LB@ 34 2@LB@@LB@@LB@Energy -6.28 kcal/mol@LB@Hybridization Energy -16.9997 kcal/mol@LB@Unfolding Energy - mRNA 2.1318 kcal/mol@LB@Unfolding Energy - sRNA 8.59196 kcal/mol@LB@@LB@Position - mRNA 1 -- 23@LB@Position - sRNA 3 -- 33@LB@Position Seed - mRNA 17 -- 23@LB@Position Seed - sRNA 3 -- 9@LB@
10	0.001873	0.154	ct_367	aroL	-15.55	0.000817	132 -- 208	3 -- 59	shikimate kinase	_____________131_______________________________________________________________________________209\n_____________\|_________________________________________________________________________________\|\n5'-UGU...ACAAA_______CUGUAACACACA___________________UUCCA__________AUUGCA___C____CACUAC________GUUCG...UGC-3'\n______________CCCUCCU____________GUGUAUAAAUA__AGAGUU______UAUUUCGUG______GCG__AGA______AUGCCAAC\n______________\|\|\|:\|\|\|____________\|\|\|\|\|:\|\|\|:\|__\|\|\|\|\|:______\|\|\|\|:\|:\|\|______\|\|\|__\|\|\|______\|\|:\|\|\|\|\|\n______________GGGGGGA____________CACAUGUUUGU__UCUCAG______AUAAGGUAC______CGC__UCU______UAUGGUUG\n3'-UUU...CUGAA______________________________GA______UCUUCG__________________AA_________________AA-5'\n_____________\|_________________________________________________________________________________\|\n_____________60________________________________________________________________________________2\n	202 -- 208	3 -- 9	-46.252 kcal/mol	13.1534 kcal/mol	17.5467 kcal/mol	131 209@LB@ \| \|@LB@5'-UGU...ACAAA CUGUAACACACA UUCCA AUUGCA C CACUAC GUUCG...UGC-3'@LB@ CCCUCCU GUGUAUAAAUA AGAGUU UAUUUCGUG GCG AGA AUGCCAAC@LB@ \|\|\|:\|\|\| \|\|\|\|\|:\|\|\|:\| \|\|\|\|\|: \|\|\|\|:\|:\|\| \|\|\| \|\|\| \|\|:\|\|\|\|\|@LB@ GGGGGGA CACAUGUUUGU UCUCAG AUAAGGUAC CGC UCU UAUGGUUG@LB@3'-UUU...CUGAA GA UCUUCG AA AA-5'@LB@ \| \|@LB@ 60 2@LB@@LB@@LB@Energy -15.55 kcal/mol@LB@Hybridization Energy -46.252 kcal/mol@LB@Unfolding Energy - mRNA 13.1534 kcal/mol@LB@Unfolding Energy - sRNA 17.5467 kcal/mol@LB@@LB@Position - mRNA 132 -- 208@LB@Position - sRNA 3 -- 59@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 3 -- 9@LB@
4	0.0004436	0.07439	ct_864	xerD	-16.31	0.000480	24 -- 38	17 -- 31	site-specific tyrosine recombinase XerD	_____________23______________39\n_____________\|_______________\|\n5'-CAU...AUGGA_______________ACCUU...AUU-3'\n______________GAGCUAUUCCAUGGU\n______________:\|\|\|\|\|\|\|\|\|\|\|\|\|:\n______________UUCGAUAAGGUACCG\n3'-UUU...CAGUC_______________CAAUC...GAA-5'\n_____________\|_______________\|\n_____________32______________16\n	32 -- 38	17 -- 23	-24.2689 kcal/mol	3.09995 kcal/mol	4.86101 kcal/mol	23 39@LB@ \| \|@LB@5'-CAU...AUGGA ACCUU...AUU-3'@LB@ GAGCUAUUCCAUGGU@LB@ :\|\|\|\|\|\|\|\|\|\|\|\|\|:@LB@ UUCGAUAAGGUACCG@LB@3'-UUU...CAGUC CAAUC...GAA-5'@LB@ \| \|@LB@ 32 16@LB@@LB@@LB@Energy -16.31 kcal/mol@LB@Hybridization Energy -24.2689 kcal/mol@LB@Unfolding Energy - mRNA 3.09995 kcal/mol@LB@Unfolding Energy - sRNA 4.86101 kcal/mol@LB@@LB@Position - mRNA 24 -- 38@LB@Position - sRNA 17 -- 31@LB@Position Seed - mRNA 32 -- 38@LB@Position Seed - sRNA 17 -- 23@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@
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@
136	0.05474	0.3262	ct_592	sdhA	-7.43	0.115894	38 -- 56	18 -- 34	succinate dehydrogenase flavoprotein subunit	_____________37__________________57\n_____________\|___________________\|\n5'-UCU...UGUUA___CU_____UU_______GUUUA...UGU-3'\n______________UAG__GCUGU__UCCAUGG\n______________:\|\|__\|\|\|:\|__\|\|\|\|\|\|\|\n______________GUC__CGAUA__AGGUACC\n3'-UUU...UCUCA___UU______________GCAAU...GAA-5'\n_____________\|___________________\|\n_____________35__________________17\n	50 -- 56	18 -- 24	-18.2308 kcal/mol	5.82664 kcal/mol	4.97803 kcal/mol	37 57@LB@ \| \|@LB@5'-UCU...UGUUA CU UU GUUUA...UGU-3'@LB@ UAG GCUGU UCCAUGG@LB@ :\|\| \|\|\|:\| \|\|\|\|\|\|\|@LB@ GUC CGAUA AGGUACC@LB@3'-UUU...UCUCA UU GCAAU...GAA-5'@LB@ \| \|@LB@ 35 17@LB@@LB@@LB@Energy -7.43 kcal/mol@LB@Hybridization Energy -18.2308 kcal/mol@LB@Unfolding Energy - mRNA 5.82664 kcal/mol@LB@Unfolding Energy - sRNA 4.97803 kcal/mol@LB@@LB@Position - mRNA 38 -- 56@LB@Position - sRNA 18 -- 34@LB@Position Seed - mRNA 50 -- 56@LB@Position Seed - sRNA 18 -- 24@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@
80	0.02888	0.29	ct_821	sucC	-7.97	0.087313	257 -- 264	53 -- 60	succinyl-CoA ligase subunit beta	_____________256______265\n_____________\|________\|\n5'-UCG...CCUAU________AUCAC...CAG-3'\n______________UCCCCCCU\n______________\|\|\|\|\|\|\|\|\n______________AGGGGGGA\n3'-UUU...ACUGA________CACAU...GAA-5'\n_____________\|________\|\n_____________61_______52\n	258 -- 264	53 -- 59	-16.0066 kcal/mol	1.58949 kcal/mol	6.45136 kcal/mol	256 265@LB@ \| \|@LB@5'-UCG...CCUAU AUCAC...CAG-3'@LB@ UCCCCCCU@LB@ \|\|\|\|\|\|\|\|@LB@ AGGGGGGA@LB@3'-UUU...ACUGA CACAU...GAA-5'@LB@ \| \|@LB@ 61 52@LB@@LB@@LB@Energy -7.97 kcal/mol@LB@Hybridization Energy -16.0066 kcal/mol@LB@Unfolding Energy - mRNA 1.58949 kcal/mol@LB@Unfolding Energy - sRNA 6.45136 kcal/mol@LB@@LB@Position - mRNA 257 -- 264@LB@Position - sRNA 53 -- 60@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 53 -- 59@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)

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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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