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
170	0.03041	0.5559	b1629	rsxC	-10.04	0.103937	197 -- 215	64 -- 83	SoxR iron-sulfur cluster reduction factor component; putative membrane-associated NADH oxidoreductase of electron transport complex	_____________196__________________216\n_____________\|____________________\|\n5'-UCA...UGGAA___CAU_____A________UCUGC...CCC-3'\n______________CAC____GCUU_AGUUAUUC\n______________\|\|\|____\|\|\|\|_\|\|\|\|\|\|\|\|\n______________GUG____CGAA_UCAAUAAG\n3'-CGC...UUCAA___CAAC____A________CUCAA...AAG-5'\n_____________\|____________________\|\n_____________84___________________63\n	209 -- 215	64 -- 70	-13.7112 kcal/mol	3.10702 kcal/mol	0.560651 kcal/mol	196 216@LB@ \| \|@LB@5'-UCA...UGGAA CAU A UCUGC...CCC-3'@LB@ CAC GCUU AGUUAUUC@LB@ \|\|\| \|\|\|\| \|\|\|\|\|\|\|\|@LB@ GUG CGAA UCAAUAAG@LB@3'-CGC...UUCAA CAAC A CUCAA...AAG-5'@LB@ \| \|@LB@ 84 63@LB@@LB@@LB@Energy -10.04 kcal/mol@LB@Hybridization Energy -13.7112 kcal/mol@LB@Unfolding Energy - mRNA 3.10702 kcal/mol@LB@Unfolding Energy - sRNA 0.560651 kcal/mol@LB@@LB@Position - mRNA 197 -- 215@LB@Position - sRNA 64 -- 83@LB@Position Seed - mRNA 209 -- 215@LB@Position Seed - sRNA 64 -- 70@LB@
128	0.02183	0.5385	b0874	ybjE	-9.13	0.148469	198 -- 230	59 -- 85	putative transporter	_____________197_______________________________231\n_____________\|_________________________________\|\n5'-GGG...GGGUU________UUCUG____GUUAAUC____U____CCCCU...UAA-3'\n______________UUCAUGUU_____GGCU_______AUUC_GGUU\n______________\|\|\|\|:\|\|\|_____\|\|\|\|_______\|\|\|\|_:\|\|\|\n______________AAGUGCAA_____CCGA_______UAAG_UCAA\n3'-CGC...UUUUC_________________AAUCAA_____C____CUCUU...AAG-5'\n_____________\|_________________________________\|\n_____________86________________________________58\n	199 -- 205	78 -- 84	-15.801 kcal/mol	4.95896 kcal/mol	1.70749 kcal/mol	197 231@LB@ \| \|@LB@5'-GGG...GGGUU UUCUG GUUAAUC U CCCCU...UAA-3'@LB@ UUCAUGUU GGCU AUUC GGUU@LB@ \|\|\|\|:\|\|\| \|\|\|\| \|\|\|\| :\|\|\|@LB@ AAGUGCAA CCGA UAAG UCAA@LB@3'-CGC...UUUUC AAUCAA C CUCUU...AAG-5'@LB@ \| \|@LB@ 86 58@LB@@LB@@LB@Energy -9.13 kcal/mol@LB@Hybridization Energy -15.801 kcal/mol@LB@Unfolding Energy - mRNA 4.95896 kcal/mol@LB@Unfolding Energy - sRNA 1.70749 kcal/mol@LB@@LB@Position - mRNA 198 -- 230@LB@Position - sRNA 59 -- 85@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 78 -- 84@LB@
87	0.01529	0.5385	b3636	rpmG	-10.80	0.076825	199 -- 224	53 -- 84	50S ribosomal subunit protein L33	_____________198______________________________225\n_____________\|________________________________\|\n5'-CAC...AUAAA___________AA__G________________AUCAA...AAC-3'\n______________UCA___UGGCU__AG_UAUUCG___UGAGAAA\n______________\|\|\|___\|\|\|\|\|__\|\|_\|\|\|\|\|\|___\|\|\|\|\|\|\|\n______________AGU___ACCGA__UC_AUAAGC___ACUCUUU\n3'-CGC...UUUCA___GCA_____AA__A______UCA_______GAGAG...AAG-5'\n_____________\|________________________________\|\n_____________85_______________________________52\n	218 -- 224	53 -- 59	-20.7518 kcal/mol	5.65772 kcal/mol	4.29409 kcal/mol	198 225@LB@ \| \|@LB@5'-CAC...AUAAA AA G AUCAA...AAC-3'@LB@ UCA UGGCU AG UAUUCG UGAGAAA@LB@ \|\|\| \|\|\|\|\| \|\| \|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ AGU ACCGA UC AUAAGC ACUCUUU@LB@3'-CGC...UUUCA GCA AA A UCA GAGAG...AAG-5'@LB@ \| \|@LB@ 85 52@LB@@LB@@LB@Energy -10.80 kcal/mol@LB@Hybridization Energy -20.7518 kcal/mol@LB@Unfolding Energy - mRNA 5.65772 kcal/mol@LB@Unfolding Energy - sRNA 4.29409 kcal/mol@LB@@LB@Position - mRNA 199 -- 224@LB@Position - sRNA 53 -- 84@LB@Position Seed - mRNA 218 -- 224@LB@Position Seed - sRNA 53 -- 59@LB@
107	0.01867	0.5385	b1478	adhP	-13.80	0.022588	200 -- 222	62 -- 83	ethanol-active dehydrogenase/acetaldehyde-active reductase	_____________199_____________________223\n_____________\|_______________________\|\n5'-GCA...GGAAC____AA____GC_______A___AGGAU...GUU-3'\n______________UAUG__GGCU__AGUUGUU_CGA\n______________:\|:\|__\|\|\|\|__\|\|\|\|:\|\|_\|\|\|\n______________GUGC__CCGA__UCAAUAA_GCU\n3'-CGC...UUCAA____AA____AA___________CAACU...AAG-5'\n_____________\|_______________________\|\n_____________84______________________61\n	212 -- 218	65 -- 71	-18.0685 kcal/mol	2.64248 kcal/mol	1.62352 kcal/mol	199 223@LB@ \| \|@LB@5'-GCA...GGAAC AA GC A AGGAU...GUU-3'@LB@ UAUG GGCU AGUUGUU CGA@LB@ :\|:\| \|\|\|\| \|\|\|\|:\|\| \|\|\|@LB@ GUGC CCGA UCAAUAA GCU@LB@3'-CGC...UUCAA AA AA CAACU...AAG-5'@LB@ \| \|@LB@ 84 61@LB@@LB@@LB@Energy -13.80 kcal/mol@LB@Hybridization Energy -18.0685 kcal/mol@LB@Unfolding Energy - mRNA 2.64248 kcal/mol@LB@Unfolding Energy - sRNA 1.62352 kcal/mol@LB@@LB@Position - mRNA 200 -- 222@LB@Position - sRNA 62 -- 83@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 65 -- 71@LB@
109	0.0187	0.5385	b2616	recN	-10.46	0.088138	200 -- 208	75 -- 83	recombination and repair protein	_____________199_______209\n_____________\|_________\|\n5'-UGA...ACGAC_________ACAAC...CGG-3'\n______________UAUGUUGGC\n______________:\|:\|\|\|\|\|\|\n______________GUGCAACCG\n3'-CGC...UUCAA_________AAAUC...AAG-5'\n_____________\|_________\|\n_____________84________74\n	202 -- 208	75 -- 81	-13.4657 kcal/mol	2.51607 kcal/mol	0.492259 kcal/mol	199 209@LB@ \| \|@LB@5'-UGA...ACGAC ACAAC...CGG-3'@LB@ UAUGUUGGC@LB@ :\|:\|\|\|\|\|\|@LB@ GUGCAACCG@LB@3'-CGC...UUCAA AAAUC...AAG-5'@LB@ \| \|@LB@ 84 74@LB@@LB@@LB@Energy -10.46 kcal/mol@LB@Hybridization Energy -13.4657 kcal/mol@LB@Unfolding Energy - mRNA 2.51607 kcal/mol@LB@Unfolding Energy - sRNA 0.492259 kcal/mol@LB@@LB@Position - mRNA 200 -- 208@LB@Position - sRNA 75 -- 83@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 75 -- 81@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@
80	0.01445	0.5385	b4257	yjgN	-10.51	0.086376	202 -- 215	65 -- 78	DUF898 family inner membrane protein	_____________201____________216\n_____________\|______________\|\n5'-UUA...UUUUA_____CA_______AAUGA...UGU-3'\n______________UGGCU__AGUUAUU\n______________\|\|\|\|\|__\|\|\|\|\|\|\|\n______________ACCGA__UCAAUAA\n3'-CGC...GUGCA_____AA_______GCUCA...AAG-5'\n_____________\|______________\|\n_____________79_____________64\n	209 -- 215	65 -- 71	-13.5706 kcal/mol	2.80573 kcal/mol	0.256929 kcal/mol	201 216@LB@ \| \|@LB@5'-UUA...UUUUA CA AAUGA...UGU-3'@LB@ UGGCU AGUUAUU@LB@ \|\|\|\|\| \|\|\|\|\|\|\|@LB@ ACCGA UCAAUAA@LB@3'-CGC...GUGCA AA GCUCA...AAG-5'@LB@ \| \|@LB@ 79 64@LB@@LB@@LB@Energy -10.51 kcal/mol@LB@Hybridization Energy -13.5706 kcal/mol@LB@Unfolding Energy - mRNA 2.80573 kcal/mol@LB@Unfolding Energy - sRNA 0.256929 kcal/mol@LB@@LB@Position - mRNA 202 -- 215@LB@Position - sRNA 65 -- 78@LB@Position Seed - mRNA 209 -- 215@LB@Position Seed - sRNA 65 -- 71@LB@
81	0.01462	0.5385	b3296	rpsD	-10.19	0.098165	202 -- 218	60 -- 78	30S ribosomal subunit protein S4	_____________201_________________219\n_____________\|___________________\|\n5'-AAG...GAAAA____A____A_________CCUAA...AAA-3'\n______________UGGC___AG_UAUUUGGGU\n______________\|\|\|\|___\|\|_\|\|\|\|:\|:\|\|\n______________ACCG___UC_AUAAGCUCA\n3'-CGC...GUGCA____AAA__A_________ACUCU...AAG-5'\n_____________\|___________________\|\n_____________79__________________59\n	212 -- 218	60 -- 66	-14.6837 kcal/mol	3.69927 kcal/mol	0.797083 kcal/mol	201 219@LB@ \| \|@LB@5'-AAG...GAAAA A A CCUAA...AAA-3'@LB@ UGGC AG UAUUUGGGU@LB@ \|\|\|\| \|\| \|\|\|\|:\|:\|\|@LB@ ACCG UC AUAAGCUCA@LB@3'-CGC...GUGCA AAA A ACUCU...AAG-5'@LB@ \| \|@LB@ 79 59@LB@@LB@@LB@Energy -10.19 kcal/mol@LB@Hybridization Energy -14.6837 kcal/mol@LB@Unfolding Energy - mRNA 3.69927 kcal/mol@LB@Unfolding Energy - sRNA 0.797083 kcal/mol@LB@@LB@Position - mRNA 202 -- 218@LB@Position - sRNA 60 -- 78@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 60 -- 66@LB@
88	0.01545	0.5385	b3009	yghB	-9.13	0.148475	202 -- 216	61 -- 78	general envelope maintenance protein; DedA family inner membrane protein; putative multidrug efflux transporter	_____________201________________217\n_____________\|__________________\|\n5'-UCU...GUCCA_______________A__AUAUC...UUG-3'\n______________UGGCU___GUUAUUC_AG\n______________\|\|\|\|\|___\|\|\|\|\|\|\|_\|\|\n______________ACCGA___CAAUAAG_UC\n3'-CGC...GUGCA_____AAU_______C__AACUC...AAG-5'\n_____________\|__________________\|\n_____________79_________________60\n	207 -- 213	64 -- 70	-14.1767 kcal/mol	4.24529 kcal/mol	0.796888 kcal/mol	201 217@LB@ \| \|@LB@5'-UCU...GUCCA A AUAUC...UUG-3'@LB@ UGGCU GUUAUUC AG@LB@ \|\|\|\|\| \|\|\|\|\|\|\| \|\|@LB@ ACCGA CAAUAAG UC@LB@3'-CGC...GUGCA AAU C AACUC...AAG-5'@LB@ \| \|@LB@ 79 60@LB@@LB@@LB@Energy -9.13 kcal/mol@LB@Hybridization Energy -14.1767 kcal/mol@LB@Unfolding Energy - mRNA 4.24529 kcal/mol@LB@Unfolding Energy - sRNA 0.796888 kcal/mol@LB@@LB@Position - mRNA 202 -- 216@LB@Position - sRNA 61 -- 78@LB@Position Seed - mRNA 207 -- 213@LB@Position Seed - sRNA 64 -- 70@LB@
34	0.00612	0.5385	b1837	yebW	-12.39	0.040382	203 -- 226	63 -- 86	uncharacterized protein	_____________202______________________227\n_____________\|________________________\|\n5'-ACC...GAAAU_______C____ACUUU_______CUACC...UGA-3'\n______________GUUCGCG_UGGU_____UUGUUUG\n______________\|\|\|\|:\|\|_\|\|\|:_____\|\|:\|\|:\|\n______________CAAGUGC_ACCG_____AAUAAGC\n3'-CGC...GUUUU_______A____AAAUC_______UCAAC...AAG-5'\n_____________\|________________________\|\n_____________87_______________________62\n	220 -- 226	63 -- 69	-18.9836 kcal/mol	4.90011 kcal/mol	1.69827 kcal/mol	202 227@LB@ \| \|@LB@5'-ACC...GAAAU C ACUUU CUACC...UGA-3'@LB@ GUUCGCG UGGU UUGUUUG@LB@ \|\|\|\|:\|\| \|\|\|: \|\|:\|\|:\|@LB@ CAAGUGC ACCG AAUAAGC@LB@3'-CGC...GUUUU A AAAUC UCAAC...AAG-5'@LB@ \| \|@LB@ 87 62@LB@@LB@@LB@Energy -12.39 kcal/mol@LB@Hybridization Energy -18.9836 kcal/mol@LB@Unfolding Energy - mRNA 4.90011 kcal/mol@LB@Unfolding Energy - sRNA 1.69827 kcal/mol@LB@@LB@Position - mRNA 203 -- 226@LB@Position - sRNA 63 -- 86@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 63 -- 69@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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