Input and runtime details for job 6756176 (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 6756176 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:58 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:23:17 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:01:55 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:02:03 CET 2018
	Job Completed		@ Fri Feb 16 20:02:30 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6756176&toolName=CopraRNA ( 30 days expiry )

Description of the job

DsrA

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
166	0.01873	0.3614	b0473	htpG	-6.61	0.137913	119 -- 133	26 -- 39	protein refolding molecular co-chaperone Hsp90 Hsp70-dependent; heat-shock protein; ATPase	_____________118_____________134\n_____________\|_______________\|\n5'-UCA...GCUCU_________UU____UCCCU...GUG-3'\n______________CGCUUGAAA__AUUC\n______________\|:\|\|\|:\|\|\|__\|\|\|\|\n______________GUGAAUUUU__UAAG\n3'-UUU...UCUUC_________U_____CAAUG...CAA-5'\n_____________\|_______________\|\n_____________40______________25\n	121 -- 127	31 -- 37	-10.0825 kcal/mol	1.82368 kcal/mol	1.64668 kcal/mol	118 134@LB@ \| \|@LB@5'-UCA...GCUCU UU UCCCU...GUG-3'@LB@ CGCUUGAAA AUUC@LB@ \|:\|\|\|:\|\|\| \|\|\|\|@LB@ GUGAAUUUU UAAG@LB@3'-UUU...UCUUC U CAAUG...CAA-5'@LB@ \| \|@LB@ 40 25@LB@@LB@@LB@Energy -6.61 kcal/mol@LB@Hybridization Energy -10.0825 kcal/mol@LB@Unfolding Energy - mRNA 1.82368 kcal/mol@LB@Unfolding Energy - sRNA 1.64668 kcal/mol@LB@@LB@Position - mRNA 119 -- 133@LB@Position - sRNA 26 -- 39@LB@Position Seed - mRNA 121 -- 127@LB@Position Seed - sRNA 31 -- 37@LB@
199	0.02405	0.3893	b2412	zipA	-4.86	0.342002	121 -- 136	25 -- 40	FtsZ stabilizer	_____________120______________137\n_____________\|________________\|\n5'-CAG...CACUU__________UAA___GCAAA...CUU-3'\n______________GCACUUGAGG___UCG\n______________\|\|\|\|\|\|:\|::___\|\|\|\n______________CGUGAAUUUU___AGC\n3'-UUU...UUCUU__________UUA___AAUGU...CAA-5'\n_____________\|________________\|\n_____________41_______________24\n	124 -- 130	31 -- 37	-13.2366 kcal/mol	6.7246 kcal/mol	1.64821 kcal/mol	120 137@LB@ \| \|@LB@5'-CAG...CACUU UAA GCAAA...CUU-3'@LB@ GCACUUGAGG UCG@LB@ \|\|\|\|\|\|:\|:: \|\|\|@LB@ CGUGAAUUUU AGC@LB@3'-UUU...UUCUU UUA AAUGU...CAA-5'@LB@ \| \|@LB@ 41 24@LB@@LB@@LB@Energy -4.86 kcal/mol@LB@Hybridization Energy -13.2366 kcal/mol@LB@Unfolding Energy - mRNA 6.7246 kcal/mol@LB@Unfolding Energy - sRNA 1.64821 kcal/mol@LB@@LB@Position - mRNA 121 -- 136@LB@Position - sRNA 25 -- 40@LB@Position Seed - mRNA 124 -- 130@LB@Position Seed - sRNA 31 -- 37@LB@
54	0.002706	0.1597	b0200	gmhB	-8.11	0.056337	123 -- 141	35 -- 53	D D-heptose 1 7-bisphosphate phosphatase	_____________122_________________142\n_____________\|___________________\|\n5'-AAA...AUCAG_____U____A________UCUUG...ACG-3'\n______________GUUUA_GCGA_GAGCACUU\n______________\|:\|\|\|_\|\|:\|_:\|\|\|\|\|\|\|\n______________CGAAU_CGUU_UUCGUGAA\n3'-UUU...UUGAA_____U____C________UUUUU...CAA-5'\n_____________\|___________________\|\n_____________54__________________34\n	135 -- 141	35 -- 41	-19.8402 kcal/mol	5.62708 kcal/mol	6.10399 kcal/mol	122 142@LB@ \| \|@LB@5'-AAA...AUCAG U A UCUUG...ACG-3'@LB@ GUUUA GCGA GAGCACUU@LB@ \|:\|\|\| \|\|:\| :\|\|\|\|\|\|\|@LB@ CGAAU CGUU UUCGUGAA@LB@3'-UUU...UUGAA U C UUUUU...CAA-5'@LB@ \| \|@LB@ 54 34@LB@@LB@@LB@Energy -8.11 kcal/mol@LB@Hybridization Energy -19.8402 kcal/mol@LB@Unfolding Energy - mRNA 5.62708 kcal/mol@LB@Unfolding Energy - sRNA 6.10399 kcal/mol@LB@@LB@Position - mRNA 123 -- 141@LB@Position - sRNA 35 -- 53@LB@Position Seed - mRNA 135 -- 141@LB@Position Seed - sRNA 35 -- 41@LB@
99	0.007347	0.239	b4348	hsdS	-4.18	0.460078	133 -- 139	70 -- 76	specificity determinant for hsdM and hsdR	_____________132_____140\n_____________\|_______\|\n5'-CUG...GUGAA_______CGAGC...UAA-3'\n______________CUGGGGG\n______________\|\|\|:\|\|\|\n______________GACUCCC\n3'-UUU...GCUGG_______CCAGC...CAA-5'\n_____________\|_______\|\n_____________77______69\n	133 -- 139	70 -- 76	-10.3039 kcal/mol	2.51492 kcal/mol	3.60488 kcal/mol	132 140@LB@ \| \|@LB@5'-CUG...GUGAA CGAGC...UAA-3'@LB@ CUGGGGG@LB@ \|\|\|:\|\|\|@LB@ GACUCCC@LB@3'-UUU...GCUGG CCAGC...CAA-5'@LB@ \| \|@LB@ 77 69@LB@@LB@@LB@Energy -4.18 kcal/mol@LB@Hybridization Energy -10.3039 kcal/mol@LB@Unfolding Energy - mRNA 2.51492 kcal/mol@LB@Unfolding Energy - sRNA 3.60488 kcal/mol@LB@@LB@Position - mRNA 133 -- 139@LB@Position - sRNA 70 -- 76@LB@Position Seed - mRNA 133 -- 139@LB@Position Seed - sRNA 70 -- 76@LB@
160	0.01746	0.3504	b4542	yohO	-11.65	0.004993	133 -- 150	23 -- 41	putative membrane protein	_____________132_________________151\n_____________\|___________________\|\n5'-UCG...CACUC_________U_________AACAA...GUG-3'\n______________GGCAUUUAA__GAUUCGUU\n______________:\|\|\|:\|\|\|\|__:\|\|\|\|\|\|\|\n______________UCGUGAAUU__UUAAGCAA\n3'-UUU...GUUCU_________UU________UGUGG...CAA-5'\n_____________\|___________________\|\n_____________42__________________22\n	144 -- 150	23 -- 29	-16.4387 kcal/mol	3.13759 kcal/mol	1.64896 kcal/mol	132 151@LB@ \| \|@LB@5'-UCG...CACUC U AACAA...GUG-3'@LB@ GGCAUUUAA GAUUCGUU@LB@ :\|\|\|:\|\|\|\| :\|\|\|\|\|\|\|@LB@ UCGUGAAUU UUAAGCAA@LB@3'-UUU...GUUCU UU UGUGG...CAA-5'@LB@ \| \|@LB@ 42 22@LB@@LB@@LB@Energy -11.65 kcal/mol@LB@Hybridization Energy -16.4387 kcal/mol@LB@Unfolding Energy - mRNA 3.13759 kcal/mol@LB@Unfolding Energy - sRNA 1.64896 kcal/mol@LB@@LB@Position - mRNA 133 -- 150@LB@Position - sRNA 23 -- 41@LB@Position Seed - mRNA 144 -- 150@LB@Position Seed - sRNA 23 -- 29@LB@
168	0.01885	0.3614	b1792	yeaO	-5.97	0.195997	133 -- 142	25 -- 34	DUF488 family protein	_____________132________143\n_____________\|__________\|\n5'-UGU...AGACA__________CUAAU...CCG-3'\n______________AAGAAAUUCG\n______________\|\|:\|\|\|\|\|\|\|\n______________UUUUUUAAGC\n3'-UUU...GUGAA__________AAUGU...CAA-5'\n_____________\|__________\|\n_____________35_________24\n	136 -- 142	25 -- 31	-8.43117 kcal/mol	1.28773 kcal/mol	1.16883 kcal/mol	132 143@LB@ \| \|@LB@5'-UGU...AGACA CUAAU...CCG-3'@LB@ AAGAAAUUCG@LB@ \|\|:\|\|\|\|\|\|\|@LB@ UUUUUUAAGC@LB@3'-UUU...GUGAA AAUGU...CAA-5'@LB@ \| \|@LB@ 35 24@LB@@LB@@LB@Energy -5.97 kcal/mol@LB@Hybridization Energy -8.43117 kcal/mol@LB@Unfolding Energy - mRNA 1.28773 kcal/mol@LB@Unfolding Energy - sRNA 1.16883 kcal/mol@LB@@LB@Position - mRNA 133 -- 142@LB@Position - sRNA 25 -- 34@LB@Position Seed - mRNA 136 -- 142@LB@Position Seed - sRNA 25 -- 31@LB@
106	0.009044	0.2693	b3360	pabA	-9.65	0.020637	134 -- 165	7 -- 41	aminodeoxychorismate synthase subunit II	_____________133_________________________________166\n_____________\|___________________________________\|\n5'-GCG...UAUUU____AAGUGGUAAG___AA________________GUAAA...CGU-3'\n______________AGCA___________CG____GCCGGGGAAUCUGA\n______________\|\|\|\|___________\|\|____:\|\|:\|\|:\|\|\|\|\|\|\|\n______________UCGU___________GC____UGGUCCUUUAGACU\n3'-UUU...GUUCU____GAAUUUUUUAA__AAUG______________ACACAA-5'\n_____________\|___________________________________\|\n_____________42__________________________________6\n	156 -- 162	10 -- 16	-26.3396 kcal/mol	7.46958 kcal/mol	9.22092 kcal/mol	133 166@LB@ \| \|@LB@5'-GCG...UAUUU AAGUGGUAAG AA GUAAA...CGU-3'@LB@ AGCA CG GCCGGGGAAUCUGA@LB@ \|\|\|\| \|\| :\|\|:\|\|:\|\|\|\|\|\|\|@LB@ UCGU GC UGGUCCUUUAGACU@LB@3'-UUU...GUUCU GAAUUUUUUAA AAUG ACACAA-5'@LB@ \| \|@LB@ 42 6@LB@@LB@@LB@Energy -9.65 kcal/mol@LB@Hybridization Energy -26.3396 kcal/mol@LB@Unfolding Energy - mRNA 7.46958 kcal/mol@LB@Unfolding Energy - sRNA 9.22092 kcal/mol@LB@@LB@Position - mRNA 134 -- 165@LB@Position - sRNA 7 -- 41@LB@Position Seed - mRNA 156 -- 162@LB@Position Seed - sRNA 10 -- 16@LB@
86	0.005829	0.217	b2399	yfeD	-9.44	0.023742	136 -- 182	13 -- 56	DUF1323 family putative DNA-binding protein	_____________135______________________________________________183\n_____________\|________________________________________________\|\n5'-UGA...ACAUC_______CU________G_A___UC____________ACGC_______UUCGC...GGA-3'\n______________CUUGCUU__GCGGGAAG_G_UUA__GGAUU_GUUACA____UUAGGGA\n______________\|\|\|\|\|\|\|__\|\|::\|\|\|\|_:_\|\|\|__::\|\|\|_\|\|\|\|\|\|____::\|\|\|:\|\n______________GAACGAA__CGUUCUUC_U_AAU__UUUAA_CAAUGU____GGUCCUU\n3'-UUU...ACUUU_______UU________G_G___UU_____G_________________UAGAC...CAA-5'\n_____________\|________________________________________________\|\n_____________57_______________________________________________12\n	146 -- 152	40 -- 46	-35.8501 kcal/mol	12.5789 kcal/mol	13.8302 kcal/mol	135 183@LB@ \| \|@LB@5'-UGA...ACAUC CU G A UC ACGC UUCGC...GGA-3'@LB@ CUUGCUU GCGGGAAG G UUA GGAUU GUUACA UUAGGGA@LB@ \|\|\|\|\|\|\| \|\|::\|\|\|\| : \|\|\| ::\|\|\| \|\|\|\|\|\| ::\|\|\|:\|@LB@ GAACGAA CGUUCUUC U AAU UUUAA CAAUGU GGUCCUU@LB@3'-UUU...ACUUU UU G G UU G UAGAC...CAA-5'@LB@ \| \|@LB@ 57 12@LB@@LB@@LB@Energy -9.44 kcal/mol@LB@Hybridization Energy -35.8501 kcal/mol@LB@Unfolding Energy - mRNA 12.5789 kcal/mol@LB@Unfolding Energy - sRNA 13.8302 kcal/mol@LB@@LB@Position - mRNA 136 -- 182@LB@Position - sRNA 13 -- 56@LB@Position Seed - mRNA 146 -- 152@LB@Position Seed - sRNA 40 -- 46@LB@
125	0.01132	0.2916	b4152	frdC	-8.74	0.037729	137 -- 154	25 -- 41	fumarate reductase (anaerobic) membrane anchor subunit	_____________136________________155\n_____________\|__________________\|\n5'-AGA...AGCAG____AAG___________AAAGA...CGG-3'\n______________GGCA___UAGAAAGUUCG\n______________:\|\|\|___\|\|:\|\|\|:\|\|\|\|\n______________UCGU___AUUUUUUAAGC\n3'-UUU...GUUCU____GA____________AAUGU...CAA-5'\n_____________\|__________________\|\n_____________42_________________24\n	148 -- 154	25 -- 31	-13.3883 kcal/mol	3.00162 kcal/mol	1.64839 kcal/mol	136 155@LB@ \| \|@LB@5'-AGA...AGCAG AAG AAAGA...CGG-3'@LB@ GGCA UAGAAAGUUCG@LB@ :\|\|\| \|\|:\|\|\|:\|\|\|\|@LB@ UCGU AUUUUUUAAGC@LB@3'-UUU...GUUCU GA AAUGU...CAA-5'@LB@ \| \|@LB@ 42 24@LB@@LB@@LB@Energy -8.74 kcal/mol@LB@Hybridization Energy -13.3883 kcal/mol@LB@Unfolding Energy - mRNA 3.00162 kcal/mol@LB@Unfolding Energy - sRNA 1.64839 kcal/mol@LB@@LB@Position - mRNA 137 -- 154@LB@Position - sRNA 25 -- 41@LB@Position Seed - mRNA 148 -- 154@LB@Position Seed - sRNA 25 -- 31@LB@
126	0.01159	0.2964	b3693	dgoK	-8.44	0.045823	138 -- 160	34 -- 54	2-oxo-3-deoxygalactonate kinase	_____________137_____________________161\n_____________\|_______________________\|\n5'-CAG...GGCGA___GGCA_______C________CCAUG...CAG-3'\n______________UGC____GAGCAGG_GGCGCUUA\n______________\|\|\|____:\|\|\|\|:\|_:\|\|:\|\|\|\|\n______________ACG____UUCGUUC_UCGUGAAU\n3'-UUU...UUUGA___AA_________U________UUUUU...CAA-5'\n_____________\|_______________________\|\n_____________55______________________33\n	154 -- 160	34 -- 40	-23.026 kcal/mol	8.41527 kcal/mol	6.17478 kcal/mol	137 161@LB@ \| \|@LB@5'-CAG...GGCGA GGCA C CCAUG...CAG-3'@LB@ UGC GAGCAGG GGCGCUUA@LB@ \|\|\| :\|\|\|\|:\| :\|\|:\|\|\|\|@LB@ ACG UUCGUUC UCGUGAAU@LB@3'-UUU...UUUGA AA U UUUUU...CAA-5'@LB@ \| \|@LB@ 55 33@LB@@LB@@LB@Energy -8.44 kcal/mol@LB@Hybridization Energy -23.026 kcal/mol@LB@Unfolding Energy - mRNA 8.41527 kcal/mol@LB@Unfolding Energy - sRNA 6.17478 kcal/mol@LB@@LB@Position - mRNA 138 -- 160@LB@Position - sRNA 34 -- 54@LB@Position Seed - mRNA 154 -- 160@LB@Position Seed - sRNA 34 -- 40@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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