Input and runtime details for job 5882223 (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 5882223 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:39:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 03:02:39 CET 2018
	Post-Processing Finished		@ Sat Feb 17 03:02:47 CET 2018
	Job Completed		@ Sat Feb 17 03:03:15 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5882223&toolName=CopraRNA ( 30 days expiry )

Description of the job

Spot42

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
177	0.007672	0.1511	b2307	hisM	-10.48	0.032509	175 -- 237	1 -- 57	histidine ABC transporter permease	_____________174__________________________________________________________________238\n_____________\|____________________________________________________________________\|\n5'-CUC...GCUAC____UGGG___________________CCUGU___C___________AUGAAUA___GAA___G____UGUGG...CGG-3'\n______________UCCG____UGUGAAG___AGGG_CUGA_____GAU_GAA_AUCUUAC_______CUG___ACC_CUGC\n______________\|\|\|\|____:\|\|\|\|\|\|___\|:\|\|_\|\|\|\|_____\|\|\|_\|\|\|_\|\|\|\|\|\|\|_______\|\|\|___\|\|\|_\|\|:\|\n______________AGGC____GCACUUC___UUCC_GACU_____CUA_CUU_UAGAAUG_______GAC___UGG_GAUG\n3'-AUU...GGUUU____UAAU_______AUU____A____UU______U___G_______GA________A__________-5'\n_____________\|___________________________________________________________________\|\n_____________58__________________________________________________________________1\n	210 -- 216	14 -- 20	-38.5224 kcal/mol	15.358 kcal/mol	12.7026 kcal/mol	174 238@LB@ \| \|@LB@5'-CUC...GCUAC UGGG CCUGU C AUGAAUA GAA G UGUGG...CGG-3'@LB@ UCCG UGUGAAG AGGG CUGA GAU GAA AUCUUAC CUG ACC CUGC@LB@ \|\|\|\| :\|\|\|\|\|\| \|:\|\| \|\|\|\| \|\|\| \|\|\| \|\|\|\|\|\|\| \|\|\| \|\|\| \|\|:\|@LB@ AGGC GCACUUC UUCC GACU CUA CUU UAGAAUG GAC UGG GAUG@LB@3'-AUU...GGUUU UAAU AUU A UU U G GA A -5'@LB@ \| \|@LB@ 58 1@LB@@LB@@LB@Energy -10.48 kcal/mol@LB@Hybridization Energy -38.5224 kcal/mol@LB@Unfolding Energy - mRNA 15.358 kcal/mol@LB@Unfolding Energy - sRNA 12.7026 kcal/mol@LB@@LB@Position - mRNA 175 -- 237@LB@Position - sRNA 1 -- 57@LB@Position Seed - mRNA 210 -- 216@LB@Position Seed - sRNA 14 -- 20@LB@
131	0.004483	0.1204	b2069	yegD	-6.32	0.360285	213 -- 222	48 -- 57	Hsp70 chaperone family protein	_____________212________223\n_____________\|__________\|\n5'-CAC...UUGGU__________GUACA...UGC-3'\n______________UUUGAUUACG\n______________\|::\|\|\|\|\|\|\|\n______________AGGCUAAUGC\n3'-AUU...GGUUU__________ACUUC...AUG-5'\n_____________\|__________\|\n_____________58_________47\n	216 -- 222	48 -- 54	-10.2333 kcal/mol	2.33693 kcal/mol	1.55976 kcal/mol	212 223@LB@ \| \|@LB@5'-CAC...UUGGU GUACA...UGC-3'@LB@ UUUGAUUACG@LB@ \|::\|\|\|\|\|\|\|@LB@ AGGCUAAUGC@LB@3'-AUU...GGUUU ACUUC...AUG-5'@LB@ \| \|@LB@ 58 47@LB@@LB@@LB@Energy -6.32 kcal/mol@LB@Hybridization Energy -10.2333 kcal/mol@LB@Unfolding Energy - mRNA 2.33693 kcal/mol@LB@Unfolding Energy - sRNA 1.55976 kcal/mol@LB@@LB@Position - mRNA 213 -- 222@LB@Position - sRNA 48 -- 57@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 48 -- 54@LB@
105	0.003348	0.1101	b2218	rcsC	-11.03	0.021992	174 -- 214	1 -- 37	hybrid sensory kinase in two-component regulatory system with RcsB and YojN	_____________173_______________________________________215\n_____________\|_________________________________________\|\n5'-AGC...CCAUC____ACCU____C_____U__GCC______AAA________UUCUU...CCG-3'\n______________GGUC____GAGG_GGAGC_UC___CCUUUG___UACCUUGC\n______________\|\|\|\|____:\|\|:_:\|\|:\|_\|\|___\|\|\|:\|\|___\|\|\|\|:\|:\|\n______________CCAG____UUCU_UCUUG_AG___GGAGAC___AUGGGAUG\n3'-AUU...AUUUU____ACU_____A_____U__AAU_________________-5'\n_____________\|________________________________________\|\n_____________38_______________________________________1\n	208 -- 214	1 -- 7	-33.3544 kcal/mol	10.9963 kcal/mol	11.3499 kcal/mol	173 215@LB@ \| \|@LB@5'-AGC...CCAUC ACCU C U GCC AAA UUCUU...CCG-3'@LB@ GGUC GAGG GGAGC UC CCUUUG UACCUUGC@LB@ \|\|\|\| :\|\|: :\|\|:\| \|\| \|\|\|:\|\| \|\|\|\|:\|:\|@LB@ CCAG UUCU UCUUG AG GGAGAC AUGGGAUG@LB@3'-AUU...AUUUU ACU A U AAU -5'@LB@ \| \|@LB@ 38 1@LB@@LB@@LB@Energy -11.03 kcal/mol@LB@Hybridization Energy -33.3544 kcal/mol@LB@Unfolding Energy - mRNA 10.9963 kcal/mol@LB@Unfolding Energy - sRNA 11.3499 kcal/mol@LB@@LB@Position - mRNA 174 -- 214@LB@Position - sRNA 1 -- 37@LB@Position Seed - mRNA 208 -- 214@LB@Position Seed - sRNA 1 -- 7@LB@
108	0.003398	0.1101	b0973	hyaB	-11.40	0.016694	267 -- 275	48 -- 56	hydrogenase 1 large subunit	_____________266_______276\n_____________\|_________\|\n5'-GGU...UCGAC_________CGCAU...GCG-3'\n______________CCGAUUACG\n______________\|\|\|\|\|\|\|\|\|\n______________GGCUAAUGC\n3'-AUU...GUUUA_________ACUUC...AUG-5'\n_____________\|_________\|\n_____________57________47\n	269 -- 275	48 -- 54	-14.3171 kcal/mol	1.33562 kcal/mol	1.55919 kcal/mol	266 276@LB@ \| \|@LB@5'-GGU...UCGAC CGCAU...GCG-3'@LB@ CCGAUUACG@LB@ \|\|\|\|\|\|\|\|\|@LB@ GGCUAAUGC@LB@3'-AUU...GUUUA ACUUC...AUG-5'@LB@ \| \|@LB@ 57 47@LB@@LB@@LB@Energy -11.40 kcal/mol@LB@Hybridization Energy -14.3171 kcal/mol@LB@Unfolding Energy - mRNA 1.33562 kcal/mol@LB@Unfolding Energy - sRNA 1.55919 kcal/mol@LB@@LB@Position - mRNA 267 -- 275@LB@Position - sRNA 48 -- 56@LB@Position Seed - mRNA 269 -- 275@LB@Position Seed - sRNA 48 -- 54@LB@
17	5.719e-05	0.01183	b3675	yidG	-12.05	0.010096	82 -- 130	1 -- 56	inner membrane protein	_____________81_____________________________________________________________131\n_____________\|______________________________________________________________\|\n5'-CGC...UUGCG_________CAAU_A_____CGAUGC__________GG________________________ACCAA...CGU-3'\n______________CUGGUUACG____G_AAAAG______GUCUGAAAGA___________ACCU____GCCCUAC\n______________\|:\|:\|\|\|\|\|____\|_\|\|\|\|\|______\|\|\|\|\|\|\|\|\|\|___________\|\|\|\|____:\|\|\|\|\|\|\n______________GGCUAAUGC____C_UUUUC______CAGACUUUCU___________UGGA____UGGGAUG\n3'-AUU...GUUUA_________ACUU_A_____________________AUCUUGUAGAA____GACA_______-5'\n_____________\|_____________________________________________________________\|\n_____________57____________________________________________________________1\n	124 -- 130	1 -- 7	-38.348 kcal/mol	13.6157 kcal/mol	12.7022 kcal/mol	81 131@LB@ \| \|@LB@5'-CGC...UUGCG CAAU A CGAUGC GG ACCAA...CGU-3'@LB@ CUGGUUACG G AAAAG GUCUGAAAGA ACCU GCCCUAC@LB@ \|:\|:\|\|\|\|\| \| \|\|\|\|\| \|\|\|\|\|\|\|\|\|\| \|\|\|\| :\|\|\|\|\|\|@LB@ GGCUAAUGC C UUUUC CAGACUUUCU UGGA UGGGAUG@LB@3'-AUU...GUUUA ACUU A AUCUUGUAGAA GACA -5'@LB@ \| \|@LB@ 57 1@LB@@LB@@LB@Energy -12.05 kcal/mol@LB@Hybridization Energy -38.348 kcal/mol@LB@Unfolding Energy - mRNA 13.6157 kcal/mol@LB@Unfolding Energy - sRNA 12.7022 kcal/mol@LB@@LB@Position - mRNA 82 -- 130@LB@Position - sRNA 1 -- 56@LB@Position Seed - mRNA 124 -- 130@LB@Position Seed - sRNA 1 -- 7@LB@
113	0.003703	0.1147	b1728	ydjM	-2.69	0.937889	161 -- 167	1 -- 7	inner membrane protein regulated by LexA	_____________160_____168\n_____________\|_______\|\n5'-CGC...UAAAA_______ACUGU...AUA-3'\n______________AUCCUAU\n______________\|:\|\|\|\|:\n______________UGGGAUG\n3'-AUU...AGACA_______-5'\n_____________\|______\|\n_____________8______1\n	161 -- 167	1 -- 7	-7.15055 kcal/mol	2.44298 kcal/mol	2.03949 kcal/mol	160 168@LB@ \| \|@LB@5'-CGC...UAAAA ACUGU...AUA-3'@LB@ AUCCUAU@LB@ \|:\|\|\|\|:@LB@ UGGGAUG@LB@3'-AUU...AGACA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -2.69 kcal/mol@LB@Hybridization Energy -7.15055 kcal/mol@LB@Unfolding Energy - mRNA 2.44298 kcal/mol@LB@Unfolding Energy - sRNA 2.03949 kcal/mol@LB@@LB@Position - mRNA 161 -- 167@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 161 -- 167@LB@Position Seed - sRNA 1 -- 7@LB@
36	0.0003681	0.03584	b1136	icd	-11.32	0.017792	275 -- 286	49 -- 60	isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase	_____________274__________287\n_____________\|____________\|\n5'-GUA...CCUGA____________CCCUU...AAG-3'\n______________AAAUCCGAUUAU\n______________\|\|\|\|\|\|\|\|\|\|\|:\n______________UUUAGGCUAAUG\n3'-AUU...GUCGG____________CACUU...AUG-5'\n_____________\|____________\|\n_____________61___________48\n	280 -- 286	49 -- 55	-13.1162 kcal/mol	1.49253 kcal/mol	0.319946 kcal/mol	274 287@LB@ \| \|@LB@5'-GUA...CCUGA CCCUU...AAG-3'@LB@ AAAUCCGAUUAU@LB@ \|\|\|\|\|\|\|\|\|\|\|:@LB@ UUUAGGCUAAUG@LB@3'-AUU...GUCGG CACUU...AUG-5'@LB@ \| \|@LB@ 61 48@LB@@LB@@LB@Energy -11.32 kcal/mol@LB@Hybridization Energy -13.1162 kcal/mol@LB@Unfolding Energy - mRNA 1.49253 kcal/mol@LB@Unfolding Energy - sRNA 0.319946 kcal/mol@LB@@LB@Position - mRNA 275 -- 286@LB@Position - sRNA 49 -- 60@LB@Position Seed - mRNA 280 -- 286@LB@Position Seed - sRNA 49 -- 55@LB@
29	0.0002348	0.02849	b4015	aceA	-10.12	0.041760	186 -- 214	1 -- 27	isocitrate lyase	_____________185____________________________215\n_____________\|______________________________\|\n5'-UUG...UAACU______________ACA__AAA____G___ACAAC...UGA-3'\n______________AUGGAGCAUCU_GC___UG___ACCC_UAC\n______________\|\|:\|\|:\|\|\|\|\|_:\|___\|\|___\|\|\|\|_\|\|\|\n______________UAUCUUGUAGA_UG___AC___UGGG_AUG\n3'-AUU...CUUUC___________A__GAG__A__________-5'\n_____________\|_____________________________\|\n_____________28____________________________1\n	190 -- 196	17 -- 23	-23.282 kcal/mol	5.13768 kcal/mol	8.046 kcal/mol	185 215@LB@ \| \|@LB@5'-UUG...UAACU ACA AAA G ACAAC...UGA-3'@LB@ AUGGAGCAUCU GC UG ACCC UAC@LB@ \|\|:\|\|:\|\|\|\|\| :\| \|\| \|\|\|\| \|\|\|@LB@ UAUCUUGUAGA UG AC UGGG AUG@LB@3'-AUU...CUUUC A GAG A -5'@LB@ \| \|@LB@ 28 1@LB@@LB@@LB@Energy -10.12 kcal/mol@LB@Hybridization Energy -23.282 kcal/mol@LB@Unfolding Energy - mRNA 5.13768 kcal/mol@LB@Unfolding Energy - sRNA 8.046 kcal/mol@LB@@LB@Position - mRNA 186 -- 214@LB@Position - sRNA 1 -- 27@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 17 -- 23@LB@
83	0.001985	0.08414	b1901	araF	-10.36	0.035498	164 -- 171	1 -- 8	L-arabinose ABC transporter periplasmic binding protein	_____________163______172\n_____________\|________\|\n5'-UCC...GUUUU________ACAAA...AGC-3'\n______________UGCCCUAC\n______________\|:\|\|\|\|\|\|\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	165 -- 171	1 -- 7	-13.292 kcal/mol	0.840759 kcal/mol	2.11603 kcal/mol	163 172@LB@ \| \|@LB@5'-UCC...GUUUU ACAAA...AGC-3'@LB@ UGCCCUAC@LB@ \|:\|\|\|\|\|\|@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -10.36 kcal/mol@LB@Hybridization Energy -13.292 kcal/mol@LB@Unfolding Energy - mRNA 0.840759 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 164 -- 171@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 165 -- 171@LB@Position Seed - sRNA 1 -- 7@LB@
129	0.004413	0.1199	b0062	araA	-8.60	0.109835	267 -- 273	1 -- 7	L-arabinose isomerase	_____________266_____274\n_____________\|_______\|\n5'-CGC...CGGAA_______GUCAG...ACG-3'\n______________ACCCUGC\n______________\|\|\|\|\|:\|\n______________UGGGAUG\n3'-AUU...AGACA_______-5'\n_____________\|______\|\n_____________8______1\n	267 -- 273	1 -- 7	-12.3746 kcal/mol	1.75625 kcal/mol	2.03949 kcal/mol	266 274@LB@ \| \|@LB@5'-CGC...CGGAA GUCAG...ACG-3'@LB@ ACCCUGC@LB@ \|\|\|\|\|:\|@LB@ UGGGAUG@LB@3'-AUU...AGACA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -8.60 kcal/mol@LB@Hybridization Energy -12.3746 kcal/mol@LB@Unfolding Energy - mRNA 1.75625 kcal/mol@LB@Unfolding Energy - sRNA 2.03949 kcal/mol@LB@@LB@Position - mRNA 267 -- 273@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 267 -- 273@LB@Position Seed - sRNA 1 -- 7@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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