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
188	0.08401	0.363	ct_024	N/A	-5.57	0.284242	184 -- 199	20 -- 35	release factor glutamine methyltransferase	_____________183______________200\n_____________\|________________\|\n5'-AGA...GUACA____C________G__CAUGA...AGA-3'\n______________UCGG_AGCUAUUC_GU\n______________\|\|:\|_\|\|\|\|\|\|\|\|_:\|\n______________AGUC_UCGAUAAG_UA\n3'-UUU...AUCUC____U________G__CCGCA...GAA-5'\n_____________\|________________\|\n_____________36_______________19\n	190 -- 196	23 -- 29	-16.0617 kcal/mol	5.57694 kcal/mol	4.91708 kcal/mol	183 200@LB@ \| \|@LB@5'-AGA...GUACA C G CAUGA...AGA-3'@LB@ UCGG AGCUAUUC GU@LB@ \|\|:\| \|\|\|\|\|\|\|\| :\|@LB@ AGUC UCGAUAAG UA@LB@3'-UUU...AUCUC U G CCGCA...GAA-5'@LB@ \| \|@LB@ 36 19@LB@@LB@@LB@Energy -5.57 kcal/mol@LB@Hybridization Energy -16.0617 kcal/mol@LB@Unfolding Energy - mRNA 5.57694 kcal/mol@LB@Unfolding Energy - sRNA 4.91708 kcal/mol@LB@@LB@Position - mRNA 184 -- 199@LB@Position - sRNA 20 -- 35@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 23 -- 29@LB@
184	0.0822	0.363	ct_497	dnaB	-7.07	0.138978	138 -- 179	3 -- 57	replicative DNA helicase	_____________137________________________________________________________180\n_____________\|__________________________________________________________\|\n5'-ACG...AUAUU_____A_____CCU________CCG____G_________UU_________________CAUAA...GUG-3'\n______________CCCCU___UAC___AAC_CUGG____AGA_AGCU__UCC____________UACCAAC\n______________\|\|\|\|\|___\|\|\|___\|\|\|_\|\|:\|____\|\|\|_\|\|\|\|__\|\|\|____________\|\|\|\|\|\|\|\n______________GGGGA___AUG___UUG_GAUC____UCU_UCGA__AGG____________AUGGUUG\n3'-UUU...GAAGG_____CAC___U_____U____UCAG________UA___UACCGCAAUCUU_______AA-5'\n_____________\|__________________________________________________________\|\n_____________58_________________________________________________________2\n	173 -- 179	3 -- 9	-29.7257 kcal/mol	6.10481 kcal/mol	16.5501 kcal/mol	137 180@LB@ \| \|@LB@5'-ACG...AUAUU A CCU CCG G UU CAUAA...GUG-3'@LB@ CCCCU UAC AAC CUGG AGA AGCU UCC UACCAAC@LB@ \|\|\|\|\| \|\|\| \|\|\| \|\|:\| \|\|\| \|\|\|\| \|\|\| \|\|\|\|\|\|\|@LB@ GGGGA AUG UUG GAUC UCU UCGA AGG AUGGUUG@LB@3'-UUU...GAAGG CAC U U UCAG UA UACCGCAAUCUU AA-5'@LB@ \| \|@LB@ 58 2@LB@@LB@@LB@Energy -7.07 kcal/mol@LB@Hybridization Energy -29.7257 kcal/mol@LB@Unfolding Energy - mRNA 6.10481 kcal/mol@LB@Unfolding Energy - sRNA 16.5501 kcal/mol@LB@@LB@Position - mRNA 138 -- 179@LB@Position - sRNA 3 -- 57@LB@Position Seed - mRNA 173 -- 179@LB@Position Seed - sRNA 3 -- 9@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@
127	0.0509	0.3262	ct_808	cafE	-7.80	0.095102	169 -- 204	18 -- 57	ribonuclease E	_____________168_________________________________________205\n_____________\|___________________________________________\|\n5'-GUU...GAGGA_______A______________CAU______ACG_________AAAAC...AAA-3'\n______________CUCCUGU____GAGCGC_AGAG___UUAGGA______CCAUGG\n______________\|:\|\|\|\|\|____:\|:\|:\|_\|\|\|\|___\|:\|\|:\|______\|\|\|\|\|\|\n______________GGGGACA____UUUGUG_UCUC___AGUCUU______GGUACC\n3'-UUU...GAAGG_______CAUG______A_____________CGAUAA______GCAAU...GAA-5'\n_____________\|___________________________________________\|\n_____________58__________________________________________17\n	169 -- 175	51 -- 57	-30.1775 kcal/mol	9.43695 kcal/mol	12.9362 kcal/mol	168 205@LB@ \| \|@LB@5'-GUU...GAGGA A CAU ACG AAAAC...AAA-3'@LB@ CUCCUGU GAGCGC AGAG UUAGGA CCAUGG@LB@ \|:\|\|\|\|\| :\|:\|:\| \|\|\|\| \|:\|\|:\| \|\|\|\|\|\|@LB@ GGGGACA UUUGUG UCUC AGUCUU GGUACC@LB@3'-UUU...GAAGG CAUG A CGAUAA GCAAU...GAA-5'@LB@ \| \|@LB@ 58 17@LB@@LB@@LB@Energy -7.80 kcal/mol@LB@Hybridization Energy -30.1775 kcal/mol@LB@Unfolding Energy - mRNA 9.43695 kcal/mol@LB@Unfolding Energy - sRNA 12.9362 kcal/mol@LB@@LB@Position - mRNA 169 -- 204@LB@Position - sRNA 18 -- 57@LB@Position Seed - mRNA 169 -- 175@LB@Position Seed - sRNA 51 -- 57@LB@
52	0.01886	0.29	ct_784	rnpA	-5.05	0.354130	114 -- 120	80 -- 86	ribonuclease P protein component	_____________113_____121\n_____________\|_______\|\n5'-UCU...CUCGC_______CAAAA...UGA-3'\n______________AUGGCUA\n______________\|:\|\|\|\|\|\n______________UGCCGAU\n3'-UUU...CUCUA_______UGAGG...GAA-5'\n_____________\|_______\|\n_____________87______79\n	114 -- 120	80 -- 86	-8.53572 kcal/mol	2.4168 kcal/mol	1.06449 kcal/mol	113 121@LB@ \| \|@LB@5'-UCU...CUCGC CAAAA...UGA-3'@LB@ AUGGCUA@LB@ \|:\|\|\|\|\|@LB@ UGCCGAU@LB@3'-UUU...CUCUA UGAGG...GAA-5'@LB@ \| \|@LB@ 87 79@LB@@LB@@LB@Energy -5.05 kcal/mol@LB@Hybridization Energy -8.53572 kcal/mol@LB@Unfolding Energy - mRNA 2.4168 kcal/mol@LB@Unfolding Energy - sRNA 1.06449 kcal/mol@LB@@LB@Position - mRNA 114 -- 120@LB@Position - sRNA 80 -- 86@LB@Position Seed - mRNA 114 -- 120@LB@Position Seed - sRNA 80 -- 86@LB@
120	0.04883	0.3262	ct_827	nrdA	-5.19	0.334730	7 -- 13	82 -- 88	ribonucleoside-diphosphate reductase subunit alpha	_____________6_______14\n_____________\|_______\|\n_____5'-UUCUAU_______AUACA...CUU-3'\n______________AUAUGGU\n______________\|\|\|:\|\|:\n______________UAUGCCG\n3'-UUU...GCCUC_______AUUGA...GAA-5'\n_____________\|_______\|\n_____________89______81\n	7 -- 13	82 -- 88	-6.89581 kcal/mol	0.608866 kcal/mol	1.09753 kcal/mol	6 14@LB@ \| \|@LB@ 5'-UUCUAU AUACA...CUU-3'@LB@ AUAUGGU@LB@ \|\|\|:\|\|:@LB@ UAUGCCG@LB@3'-UUU...GCCUC AUUGA...GAA-5'@LB@ \| \|@LB@ 89 81@LB@@LB@@LB@Energy -5.19 kcal/mol@LB@Hybridization Energy -6.89581 kcal/mol@LB@Unfolding Energy - mRNA 0.608866 kcal/mol@LB@Unfolding Energy - sRNA 1.09753 kcal/mol@LB@@LB@Position - mRNA 7 -- 13@LB@Position - sRNA 82 -- 88@LB@Position Seed - mRNA 7 -- 13@LB@Position Seed - sRNA 82 -- 88@LB@
157	0.06639	0.3424	ct_213	rpiA	-7.48	0.112460	245 -- 274	28 -- 57	ribose-5-phosphate isomerase A	_____________244____________________________275\n_____________\|______________________________\|\n5'-GAA...UUUUU____AUCAA_____A_____C_C_______AGUAG...UGU-3'\n______________CCCU_____GCAGA_ACUAG_G_UAGAGGC\n______________\|\|\|:_____:\|\|:\|_\|\|\|\|\|_\|_:\|\|\|:\|\|\n______________GGGG_____UGUUU_UGAUC_C_GUCUUCG\n3'-UUU...GAAGG____ACACA_____G_____U_A_______AUAAG...GAA-5'\n_____________\|______________________________\|\n_____________58_____________________________27\n	268 -- 274	28 -- 34	-25.4315 kcal/mol	5.87242 kcal/mol	12.0748 kcal/mol	244 275@LB@ \| \|@LB@5'-GAA...UUUUU AUCAA A C C AGUAG...UGU-3'@LB@ CCCU GCAGA ACUAG G UAGAGGC@LB@ \|\|\|: :\|\|:\| \|\|\|\|\| \| :\|\|\|:\|\|@LB@ GGGG UGUUU UGAUC C GUCUUCG@LB@3'-UUU...GAAGG ACACA G U A AUAAG...GAA-5'@LB@ \| \|@LB@ 58 27@LB@@LB@@LB@Energy -7.48 kcal/mol@LB@Hybridization Energy -25.4315 kcal/mol@LB@Unfolding Energy - mRNA 5.87242 kcal/mol@LB@Unfolding Energy - sRNA 12.0748 kcal/mol@LB@@LB@Position - mRNA 245 -- 274@LB@Position - sRNA 28 -- 57@LB@Position Seed - mRNA 268 -- 274@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@
169	0.07086	0.3447	ct_615	sigA	-4.07	0.514760	248 -- 272	10 -- 33	RNA polymerase sigma factor	_____________247________________________273\n_____________\|__________________________\|\n5'-GGU...CAAGA_____AAA_____AAGAAA_______GAGUU...AAG-3'\n______________AGAAG____UCCA______GUUAGAA\n______________\|\|\|\|\|____\|\|\|\|______\|\|\|\|\|\|\|\n______________UCUUC____AGGU______CAAUCUU\n3'-UUU...CUCAG_____GAUA____ACCG_________AUGGU...GAA-5'\n_____________\|__________________________\|\n_____________34_________________________9\n	266 -- 272	10 -- 16	-15.5151 kcal/mol	2.85327 kcal/mol	8.5898 kcal/mol	247 273@LB@ \| \|@LB@5'-GGU...CAAGA AAA AAGAAA GAGUU...AAG-3'@LB@ AGAAG UCCA GUUAGAA@LB@ \|\|\|\|\| \|\|\|\| \|\|\|\|\|\|\|@LB@ UCUUC AGGU CAAUCUU@LB@3'-UUU...CUCAG GAUA ACCG AUGGU...GAA-5'@LB@ \| \|@LB@ 34 9@LB@@LB@@LB@Energy -4.07 kcal/mol@LB@Hybridization Energy -15.5151 kcal/mol@LB@Unfolding Energy - mRNA 2.85327 kcal/mol@LB@Unfolding Energy - sRNA 8.5898 kcal/mol@LB@@LB@Position - mRNA 248 -- 272@LB@Position - sRNA 10 -- 33@LB@Position Seed - mRNA 266 -- 272@LB@Position Seed - sRNA 10 -- 16@LB@
110	0.04403	0.3262	ct_742	ygcA	-7.58	0.107160	204 -- 253	23 -- 59	rRNA methyltransferse	_____________203__________________________________________________254\n_____________\|____________________________________________________\|\n5'-AAC...AGUUG________CUAUCGUAAC___________UU___C___UGU___________AUCUC...UUG-3'\n______________CUCUCCUG__________UGUA__AACAU__UGG_GUC___GGAGGCUGUUC\n______________\|:\|:\|\|\|\|__________\|\|\|\|__\|\|\|\|:__\|:\|_\|\|\|___:\|\|:\|\|\|:\|\|\|\n______________GGGGGGAC__________ACAU__UUGUG__AUC_CAG___UCUUCGAUAAG\n3'-UUU...CUGAA______________________GU__________U_________________GUACC...GAA-5'\n_____________\|____________________________________________________\|\n_____________60___________________________________________________22\n	247 -- 253	23 -- 29	-33.6475 kcal/mol	12.386 kcal/mol	13.6844 kcal/mol	203 254@LB@ \| \|@LB@5'-AAC...AGUUG CUAUCGUAAC UU C UGU AUCUC...UUG-3'@LB@ CUCUCCUG UGUA AACAU UGG GUC GGAGGCUGUUC@LB@ \|:\|:\|\|\|\| \|\|\|\| \|\|\|\|: \|:\| \|\|\| :\|\|:\|\|\|:\|\|\|@LB@ GGGGGGAC ACAU UUGUG AUC CAG UCUUCGAUAAG@LB@3'-UUU...CUGAA GU U GUACC...GAA-5'@LB@ \| \|@LB@ 60 22@LB@@LB@@LB@Energy -7.58 kcal/mol@LB@Hybridization Energy -33.6475 kcal/mol@LB@Unfolding Energy - mRNA 12.386 kcal/mol@LB@Unfolding Energy - sRNA 13.6844 kcal/mol@LB@@LB@Position - mRNA 204 -- 253@LB@Position - sRNA 23 -- 59@LB@Position Seed - mRNA 247 -- 253@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)

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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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