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
65	0.02498	0.29	ct_846	N/A	-7.66	0.102535	215 -- 232	42 -- 57		_____________214________________233\n_____________\|__________________\|\n5'-GCG...AUCUU____GAUAA_________AACUC...CUC-3'\n______________CCCC_____GUACAAACA\n______________\|\|\|\|_____\|\|\|\|\|\|\|\|\|\n______________GGGG_____CAUGUUUGU\n3'-UUU...GAAGG____ACA___________GAUCU...GAA-5'\n_____________\|__________________\|\n_____________58_________________41\n	226 -- 232	42 -- 48	-18.5622 kcal/mol	3.08308 kcal/mol	7.81778 kcal/mol	214 233@LB@ \| \|@LB@5'-GCG...AUCUU GAUAA AACUC...CUC-3'@LB@ CCCC GUACAAACA@LB@ \|\|\|\| \|\|\|\|\|\|\|\|\|@LB@ GGGG CAUGUUUGU@LB@3'-UUU...GAAGG ACA GAUCU...GAA-5'@LB@ \| \|@LB@ 58 41@LB@@LB@@LB@Energy -7.66 kcal/mol@LB@Hybridization Energy -18.5622 kcal/mol@LB@Unfolding Energy - mRNA 3.08308 kcal/mol@LB@Unfolding Energy - sRNA 7.81778 kcal/mol@LB@@LB@Position - mRNA 215 -- 232@LB@Position - sRNA 42 -- 57@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 42 -- 48@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@
121	0.04894	0.3262	ct_310	atpE	-7.64	0.103947	27 -- 34	80 -- 87	V-type ATP synthase subunit E	_____________26_______35\n_____________\|________\|\n5'-GCA...CCUUC________CCUUC...UUC-3'\n______________UACGGCUG\n______________\|\|\|\|\|\|\|:\n______________AUGCCGAU\n3'-UUU...CCUCU________UGAGG...GAA-5'\n_____________\|________\|\n_____________88_______79\n	28 -- 34	80 -- 86	-11.9035 kcal/mol	3.17039 kcal/mol	1.09752 kcal/mol	26 35@LB@ \| \|@LB@5'-GCA...CCUUC CCUUC...UUC-3'@LB@ UACGGCUG@LB@ \|\|\|\|\|\|\|:@LB@ AUGCCGAU@LB@3'-UUU...CCUCU UGAGG...GAA-5'@LB@ \| \|@LB@ 88 79@LB@@LB@@LB@Energy -7.64 kcal/mol@LB@Hybridization Energy -11.9035 kcal/mol@LB@Unfolding Energy - mRNA 3.17039 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 27 -- 34@LB@Position - sRNA 80 -- 87@LB@Position Seed - mRNA 28 -- 34@LB@Position Seed - sRNA 80 -- 86@LB@
180	0.07821	0.3571	ct_831	murB	-7.63	0.104376	230 -- 248	17 -- 33	UDP-N-acetylenolpyruvoylglucosamine reductase	_____________229_________________249\n_____________\|___________________\|\n5'-GUU...GUUCA____U_________UAA__CGCUU...UAA-3'\n______________AGAA_CUGUUCCAU___GC\n______________\|\|\|\|_\|\|:\|\|\|\|\|\|___\|\|\n______________UCUU_GAUAAGGUA___CG\n3'-UUU...CUCAG____C_________C____CAAUC...GAA-5'\n_____________\|___________________\|\n_____________34__________________16\n	237 -- 243	20 -- 26	-14.8604 kcal/mol	2.25495 kcal/mol	4.97804 kcal/mol	229 249@LB@ \| \|@LB@5'-GUU...GUUCA U UAA CGCUU...UAA-3'@LB@ AGAA CUGUUCCAU GC@LB@ \|\|\|\| \|\|:\|\|\|\|\|\| \|\|@LB@ UCUU GAUAAGGUA CG@LB@3'-UUU...CUCAG C C CAAUC...GAA-5'@LB@ \| \|@LB@ 34 16@LB@@LB@@LB@Energy -7.63 kcal/mol@LB@Hybridization Energy -14.8604 kcal/mol@LB@Unfolding Energy - mRNA 2.25495 kcal/mol@LB@Unfolding Energy - sRNA 4.97804 kcal/mol@LB@@LB@Position - mRNA 230 -- 248@LB@Position - sRNA 17 -- 33@LB@Position Seed - mRNA 237 -- 243@LB@Position Seed - sRNA 20 -- 26@LB@
91	0.03287	0.2942	ct_674	yscC	-7.61	0.105180	32 -- 46	36 -- 57	type II secretion system protein	_____________31_____________________47\n_____________\|______________________\|\n5'-UGG...ACACA______________G_______AUUUG...CGG-3'\n______________CCCC_______AAA_GCUAGAG\n______________\|\|\|\|_______\|\|\|_:\|\|\|\|\|\|\n______________GGGG_______UUU_UGAUCUC\n3'-UUU...GAAGG____ACACAUG___G_______AGUCU...GAA-5'\n_____________\|______________________\|\n_____________58_____________________35\n	40 -- 46	36 -- 42	-18.3 kcal/mol	2.71277 kcal/mol	7.97448 kcal/mol	31 47@LB@ \| \|@LB@5'-UGG...ACACA G AUUUG...CGG-3'@LB@ CCCC AAA GCUAGAG@LB@ \|\|\|\| \|\|\| :\|\|\|\|\|\|@LB@ GGGG UUU UGAUCUC@LB@3'-UUU...GAAGG ACACAUG G AGUCU...GAA-5'@LB@ \| \|@LB@ 58 35@LB@@LB@@LB@Energy -7.61 kcal/mol@LB@Hybridization Energy -18.3 kcal/mol@LB@Unfolding Energy - mRNA 2.71277 kcal/mol@LB@Unfolding Energy - sRNA 7.97448 kcal/mol@LB@@LB@Position - mRNA 32 -- 46@LB@Position - sRNA 36 -- 57@LB@Position Seed - mRNA 40 -- 46@LB@Position Seed - sRNA 36 -- 42@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@
159	0.06732	0.3424	ct_663	N/A	-7.57	0.107718	228 -- 234	15 -- 21	type III secretion system chaperone	_____________227_____235\n_____________\|_______\|\n5'-UCU...AUUUU_______AUAUG...GCC-3'\n______________GUGGCGU\n______________:\|\|\|\|\|\|\n______________UACCGCA\n3'-UUU...UAAGG_______AUCUU...GAA-5'\n_____________\|_______\|\n_____________22______14\n	228 -- 234	15 -- 21	-10.4333 kcal/mol	1.67755 kcal/mol	1.18845 kcal/mol	227 235@LB@ \| \|@LB@5'-UCU...AUUUU AUAUG...GCC-3'@LB@ GUGGCGU@LB@ :\|\|\|\|\|\|@LB@ UACCGCA@LB@3'-UUU...UAAGG AUCUU...GAA-5'@LB@ \| \|@LB@ 22 14@LB@@LB@@LB@Energy -7.57 kcal/mol@LB@Hybridization Energy -10.4333 kcal/mol@LB@Unfolding Energy - mRNA 1.67755 kcal/mol@LB@Unfolding Energy - sRNA 1.18845 kcal/mol@LB@@LB@Position - mRNA 228 -- 234@LB@Position - sRNA 15 -- 21@LB@Position Seed - mRNA 228 -- 234@LB@Position Seed - sRNA 15 -- 21@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@
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@
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@

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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