Input and runtime details for job 3429477 (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 3429477 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:26:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:01 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:15:20 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:15:27 CET 2018
	Job Completed		@ Fri Feb 16 20:15:52 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3429477&toolName=CopraRNA ( 30 days expiry )

Description of the job

OxyS

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_000913 Escherichia coli str. K-12 substr. MG1655

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
140	0.02329	0.5385	b3026	qseC	-7.47	0.277092	174 -- 202	52 -- 78	quorum sensing sensory histidine kinase in two-component regulatory system with QseB	_____________173___________________________203\n_____________\|_____________________________\|\n5'-AAA...GUGCA____A_______CA_AUU__G________GAAAU...GGA-3'\n______________UGGU_UUGGUUA__C___AG_UGAGAAAU\n______________\|\|\|:_\|\|:\|\|\|\|__\|___\|\|_\|\|\|\|\|\|\|:\n______________ACCG_AAUCAAU__G___UC_ACUCUUUG\n3'-CGC...GUGCA____A_______AA_C____A________AGAGC...AAG-5'\n_____________\|_____________________________\|\n_____________79____________________________51\n	196 -- 202	52 -- 58	-18.6962 kcal/mol	6.8409 kcal/mol	4.38944 kcal/mol	173 203@LB@ \| \|@LB@5'-AAA...GUGCA A CA AUU G GAAAU...GGA-3'@LB@ UGGU UUGGUUA C AG UGAGAAAU@LB@ \|\|\|: \|\|:\|\|\|\| \| \|\| \|\|\|\|\|\|\|:@LB@ ACCG AAUCAAU G UC ACUCUUUG@LB@3'-CGC...GUGCA A AA C A AGAGC...AAG-5'@LB@ \| \|@LB@ 79 51@LB@@LB@@LB@Energy -7.47 kcal/mol@LB@Hybridization Energy -18.6962 kcal/mol@LB@Unfolding Energy - mRNA 6.8409 kcal/mol@LB@Unfolding Energy - sRNA 4.38944 kcal/mol@LB@@LB@Position - mRNA 174 -- 202@LB@Position - sRNA 52 -- 78@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 52 -- 58@LB@
141	0.02331	0.5385	b1844	exoX	-7.22	0.302733	200 -- 217	62 -- 83	exodeoxyribonuclease 10; DNA exonuclease X	_____________199_____________________218\n_____________\|_______________________\|\n5'-UUA...CAUGC_______C__A____________UACAG...UGA-3'\n______________CAUGUUG_GC_UUA_____UCGA\n______________\|\|:\|\|\|\|_\|\|_\|\|\|_____\|\|\|\|\n______________GUGCAAC_CG_AAU_____AGCU\n3'-CGC...UUCAA__________A___CAAUA____CAACU...AAG-5'\n_____________\|_______________________\|\n_____________84______________________61\n	200 -- 206	77 -- 83	-13.618 kcal/mol	4.77882 kcal/mol	1.62352 kcal/mol	199 218@LB@ \| \|@LB@5'-UUA...CAUGC C A UACAG...UGA-3'@LB@ CAUGUUG GC UUA UCGA@LB@ \|\|:\|\|\|\| \|\| \|\|\| \|\|\|\|@LB@ GUGCAAC CG AAU AGCU@LB@3'-CGC...UUCAA A CAAUA CAACU...AAG-5'@LB@ \| \|@LB@ 84 61@LB@@LB@@LB@Energy -7.22 kcal/mol@LB@Hybridization Energy -13.618 kcal/mol@LB@Unfolding Energy - mRNA 4.77882 kcal/mol@LB@Unfolding Energy - sRNA 1.62352 kcal/mol@LB@@LB@Position - mRNA 200 -- 217@LB@Position - sRNA 62 -- 83@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 77 -- 83@LB@
142	0.02338	0.5385	b1126	potA	-10.56	0.084569	277 -- 295	14 -- 34	spermidine/putrescine ABC transporter ATPase	_____________276___________________296\n_____________\|_____________________\|\n5'-CAA...CAAAU_______U_____________CAUUC-3'\n______________GCUUUGA_GGU__AAAGAGGU\n______________:\|\|\|::\|_\|\|\|__\|\|\|\|\|\|\|\|\n______________UGAAGUU_CCA__UUUCUCCA\n3'-CGC...GUCAC_______C___AU________CGGCG...AAG-5'\n_____________\|_____________________\|\n_____________35____________________13\n	289 -- 295	14 -- 20	-18.1028 kcal/mol	4.21038 kcal/mol	3.33169 kcal/mol	276 296@LB@ \| \|@LB@5'-CAA...CAAAU U CAUUC-3'@LB@ GCUUUGA GGU AAAGAGGU@LB@ :\|\|\|::\| \|\|\| \|\|\|\|\|\|\|\|@LB@ UGAAGUU CCA UUUCUCCA@LB@3'-CGC...GUCAC C AU CGGCG...AAG-5'@LB@ \| \|@LB@ 35 13@LB@@LB@@LB@Energy -10.56 kcal/mol@LB@Hybridization Energy -18.1028 kcal/mol@LB@Unfolding Energy - mRNA 4.21038 kcal/mol@LB@Unfolding Energy - sRNA 3.33169 kcal/mol@LB@@LB@Position - mRNA 277 -- 295@LB@Position - sRNA 14 -- 34@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 14 -- 20@LB@
143	0.02402	0.5467	b4029	yjbH	-10.20	0.097639	107 -- 117	75 -- 85	DUF940 family extracellular polysaccharide protein	_____________106_________118\n_____________\|___________\|\n5'-GCG...CAUUA___________CUCGC...AUU-3'\n______________UUUAUGUUGGC\n______________\|\|:\|:\|\|\|\|\|\|\n______________AAGUGCAACCG\n3'-CGC...UUUUC___________AAAUC...AAG-5'\n_____________\|___________\|\n_____________86__________74\n	111 -- 117	75 -- 81	-14.6823 kcal/mol	3.97178 kcal/mol	0.509769 kcal/mol	106 118@LB@ \| \|@LB@5'-GCG...CAUUA CUCGC...AUU-3'@LB@ UUUAUGUUGGC@LB@ \|\|:\|:\|\|\|\|\|\|@LB@ AAGUGCAACCG@LB@3'-CGC...UUUUC AAAUC...AAG-5'@LB@ \| \|@LB@ 86 74@LB@@LB@@LB@Energy -10.20 kcal/mol@LB@Hybridization Energy -14.6823 kcal/mol@LB@Unfolding Energy - mRNA 3.97178 kcal/mol@LB@Unfolding Energy - sRNA 0.509769 kcal/mol@LB@@LB@Position - mRNA 107 -- 117@LB@Position - sRNA 75 -- 85@LB@Position Seed - mRNA 111 -- 117@LB@Position Seed - sRNA 75 -- 81@LB@
144	0.02429	0.5467	b3156	yhbS	-10.71	0.079718	207 -- 222	50 -- 67	GNAT family putative N-acetyltransferase	_____________206________________223\n_____________\|__________________\|\n5'-CCG...UGCUA__________________CCAUU...AUC-3'\n______________AUUCGAGU__AGAAAUUC\n______________\|\|\|\|\|\|\|\|__\|\|\|\|\|:\|\|\n______________UAAGCUCA__UCUUUGAG\n3'-CGC...AUCAA________AC________AGCUU...AAG-5'\n_____________\|__________________\|\n_____________68_________________49\n	216 -- 222	50 -- 56	-17.6544 kcal/mol	2.73618 kcal/mol	4.21029 kcal/mol	206 223@LB@ \| \|@LB@5'-CCG...UGCUA CCAUU...AUC-3'@LB@ AUUCGAGU AGAAAUUC@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|:\|\|@LB@ UAAGCUCA UCUUUGAG@LB@3'-CGC...AUCAA AC AGCUU...AAG-5'@LB@ \| \|@LB@ 68 49@LB@@LB@@LB@Energy -10.71 kcal/mol@LB@Hybridization Energy -17.6544 kcal/mol@LB@Unfolding Energy - mRNA 2.73618 kcal/mol@LB@Unfolding Energy - sRNA 4.21029 kcal/mol@LB@@LB@Position - mRNA 207 -- 222@LB@Position - sRNA 50 -- 67@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 50 -- 56@LB@
145	0.02443	0.5467	b2569	lepA	-12.53	0.038132	5 -- 17	71 -- 85	back-translocating elongation factor EF4 GTPase	_____________4_______________18\n_____________\|_______________\|\n_______5'-UGAU_______________UUGCA...ACC-3'\n______________UUCAC__UGGCUUUG\n______________\|\|\|\|\|__\|\|\|\|\|\|\|:\n______________AAGUG__ACCGAAAU\n3'-CGC...UUUUC_____CA________CAAUA...AAG-5'\n_____________\|_______________\|\n_____________86______________70\n	11 -- 17	71 -- 77	-14.3569 kcal/mol	1.27074 kcal/mol	0.560731 kcal/mol	4 18@LB@ \| \|@LB@ 5'-UGAU UUGCA...ACC-3'@LB@ UUCAC UGGCUUUG@LB@ \|\|\|\|\| \|\|\|\|\|\|\|:@LB@ AAGUG ACCGAAAU@LB@3'-CGC...UUUUC CA CAAUA...AAG-5'@LB@ \| \|@LB@ 86 70@LB@@LB@@LB@Energy -12.53 kcal/mol@LB@Hybridization Energy -14.3569 kcal/mol@LB@Unfolding Energy - mRNA 1.27074 kcal/mol@LB@Unfolding Energy - sRNA 0.560731 kcal/mol@LB@@LB@Position - mRNA 5 -- 17@LB@Position - sRNA 71 -- 85@LB@Position Seed - mRNA 11 -- 17@LB@Position Seed - sRNA 71 -- 77@LB@
146	0.0246	0.5467	b2813	mltA	-8.67	0.177423	203 -- 222	69 -- 90	membrane-bound lytic murein transglycosylase A	_____________202____________________223\n_____________\|______________________\|\n5'-UGC...ACAAU_____G_________G_AA___ACCUU...AAG-3'\n______________GAAAG___ACGUUGG_U__AGU\n______________:\|\|\|\|___\|\|\|\|\|\|\|_\|__\|\|\|\n______________UUUUC___UGCAACC_A__UCA\n3'-CGC...AGGCG_____AAG_______G_AA___AUAAG...AAG-5'\n_____________\|______________________\|\n_____________91_____________________68\n	209 -- 215	76 -- 82	-14.1188 kcal/mol	4.87564 kcal/mol	0.572281 kcal/mol	202 223@LB@ \| \|@LB@5'-UGC...ACAAU G G AA ACCUU...AAG-3'@LB@ GAAAG ACGUUGG U AGU@LB@ :\|\|\|\| \|\|\|\|\|\|\| \| \|\|\|@LB@ UUUUC UGCAACC A UCA@LB@3'-CGC...AGGCG AAG G AA AUAAG...AAG-5'@LB@ \| \|@LB@ 91 68@LB@@LB@@LB@Energy -8.67 kcal/mol@LB@Hybridization Energy -14.1188 kcal/mol@LB@Unfolding Energy - mRNA 4.87564 kcal/mol@LB@Unfolding Energy - sRNA 0.572281 kcal/mol@LB@@LB@Position - mRNA 203 -- 222@LB@Position - sRNA 69 -- 90@LB@Position Seed - mRNA 209 -- 215@LB@Position Seed - sRNA 76 -- 82@LB@
147	0.02477	0.5467	b3259	prmA	-10.37	0.091190	111 -- 125	72 -- 88	methyltransferase for 50S ribosomal subunit protein L11	_____________110_______________126\n_____________\|_________________\|\n5'-GCC...CUACU_________________CCUGG...AGG-3'\n______________AAGUUUGC__UGGCUUU\n______________\|\|\|\|\|::\|__\|\|\|\|\|\|\|\n______________UUCAAGUG__ACCGAAA\n3'-CGC...GCGUU________CA_______UCAAU...AAG-5'\n_____________\|_________________\|\n_____________89________________71\n	119 -- 125	72 -- 78	-14.8408 kcal/mol	3.95141 kcal/mol	0.517175 kcal/mol	110 126@LB@ \| \|@LB@5'-GCC...CUACU CCUGG...AGG-3'@LB@ AAGUUUGC UGGCUUU@LB@ \|\|\|\|\|::\| \|\|\|\|\|\|\|@LB@ UUCAAGUG ACCGAAA@LB@3'-CGC...GCGUU CA UCAAU...AAG-5'@LB@ \| \|@LB@ 89 71@LB@@LB@@LB@Energy -10.37 kcal/mol@LB@Hybridization Energy -14.8408 kcal/mol@LB@Unfolding Energy - mRNA 3.95141 kcal/mol@LB@Unfolding Energy - sRNA 0.517175 kcal/mol@LB@@LB@Position - mRNA 111 -- 125@LB@Position - sRNA 72 -- 88@LB@Position Seed - mRNA 119 -- 125@LB@Position Seed - sRNA 72 -- 78@LB@
148	0.0249	0.5467	b2131	osmF	-10.26	0.095288	236 -- 244	75 -- 83	putative ABC transporter periplasmic binding protein	_____________235_______245\n_____________\|_________\|\n5'-AGG...CUGGU_________AGCCG...UCG-3'\n______________UAUGUUGGC\n______________:\|:\|\|\|\|\|\|\n______________GUGCAACCG\n3'-CGC...UUCAA_________AAAUC...AAG-5'\n_____________\|_________\|\n_____________84________74\n	238 -- 244	75 -- 81	-12.6611 kcal/mol	1.90691 kcal/mol	0.492259 kcal/mol	235 245@LB@ \| \|@LB@5'-AGG...CUGGU AGCCG...UCG-3'@LB@ UAUGUUGGC@LB@ :\|:\|\|\|\|\|\|@LB@ GUGCAACCG@LB@3'-CGC...UUCAA AAAUC...AAG-5'@LB@ \| \|@LB@ 84 74@LB@@LB@@LB@Energy -10.26 kcal/mol@LB@Hybridization Energy -12.6611 kcal/mol@LB@Unfolding Energy - mRNA 1.90691 kcal/mol@LB@Unfolding Energy - sRNA 0.492259 kcal/mol@LB@@LB@Position - mRNA 236 -- 244@LB@Position - sRNA 75 -- 83@LB@Position Seed - mRNA 238 -- 244@LB@Position Seed - sRNA 75 -- 81@LB@
149	0.0249	0.5467	b0737	tolQ	-11.44	0.059241	123 -- 143	57 -- 77	membrane spanning protein in TolA-TolQ-TolR complex	_____________122___________________144\n_____________\|_____________________\|\n5'-GCA...GCAGA____C__________C_____CCCAC...CCA-3'\n______________GGUU_UGGUUGUUUG_GUUGA\n______________\|\|:\|_\|:\|\|\|:\|\|:\|_\|\|\|\|\|\n______________CCGA_AUCAAUAAGC_CAACU\n3'-CGC...UGCAA____A__________U_____CUUUG...AAG-5'\n_____________\|_____________________\|\n_____________78____________________56\n	130 -- 136	64 -- 70	-20.7122 kcal/mol	8.05008 kcal/mol	1.21841 kcal/mol	122 144@LB@ \| \|@LB@5'-GCA...GCAGA C C CCCAC...CCA-3'@LB@ GGUU UGGUUGUUUG GUUGA@LB@ \|\|:\| \|:\|\|\|:\|\|:\| \|\|\|\|\|@LB@ CCGA AUCAAUAAGC CAACU@LB@3'-CGC...UGCAA A U CUUUG...AAG-5'@LB@ \| \|@LB@ 78 56@LB@@LB@@LB@Energy -11.44 kcal/mol@LB@Hybridization Energy -20.7122 kcal/mol@LB@Unfolding Energy - mRNA 8.05008 kcal/mol@LB@Unfolding Energy - sRNA 1.21841 kcal/mol@LB@@LB@Position - mRNA 123 -- 143@LB@Position - sRNA 57 -- 77@LB@Position Seed - mRNA 130 -- 136@LB@Position Seed - sRNA 64 -- 70@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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