Input and runtime details for job 6860187 (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 6860187 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:33 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:58 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 01:36:19 CET 2018
	Post-Processing Finished		@ Sat Feb 17 01:36:26 CET 2018
	Job Completed		@ Sat Feb 17 01:36:50 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6860187&toolName=CopraRNA ( 30 days expiry )

Description of the job

SgrS

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	Additional homologs
129	0.01414	0.3575	b3579	yiaO	-11.03	0.174508	249 -- 273	50 -- 76	2 3-diketo-L-gulonate-binding periplasmic protein		_____________248_________________________274\n_____________\|___________________________\|\n5'-ACU...CGUCC____________C__UA__________UUGUU...AAA-3'\n______________UGGUUUUAUAUU_AU__UUAGUCGUAU\n______________\|\|:\|\|\|\|\|:\|::_\|\|__\|:\|\|\|\|::\|:\n______________ACUAAAAUGUGG_UA__AGUCAGUGUG\n3'-UUU...CGCCC____________U__UG__________UACUA...UAG-5'\n_____________\|___________________________\|\n_____________77__________________________49\n	132 -- 138	168 -- 174	-19.0823 kcal/mol	5.4875 kcal/mol	5.03533 kcal/mol	248 274@LB@ \| \|@LB@5'-ACU...CGUCC C UA UUGUU...AAA-3'@LB@ UGGUUUUAUAUU AU UUAGUCGUAU@LB@ \|\|:\|\|\|\|\|:\|:: \|\| \|:\|\|\|\|::\|:@LB@ ACUAAAAUGUGG UA AGUCAGUGUG@LB@3'-UUU...CGCCC U UG UACUA...UAG-5'@LB@ \| \|@LB@ 77 49@LB@@LB@@LB@Energy -11.03 kcal/mol@LB@Hybridization Energy -19.0823 kcal/mol@LB@Unfolding Energy - mRNA 5.4875 kcal/mol@LB@Unfolding Energy - sRNA 5.03533 kcal/mol@LB@@LB@Position - mRNA 249 -- 273@LB@Position - sRNA 50 -- 76@LB@Position Seed - mRNA 132 -- 138@LB@Position Seed - sRNA 168 -- 174@LB@
132	0.0143	0.3575	b0147	ligT	-9.89	0.288456	69 -- 117	16 -- 69	2'-5' RNA ligase		_____________68__________________________________118\n_____________\|___________________________________\|\n5'-CCA...AAGUA______GUA_G___GCAGCAA_______C_A____ACAAA...CGG-3'\n______________AUUCAG___A_ACG_______CGGGCAA_G_CGAC\n______________\|:\|\|\|\|___\|_\|\|:_______\|:\|\|\|\|\|_\|_\|:\|\|\n______________UGAGUC___U_UGU_______GUCCGUU_C_GUUG\n3'-UUU...GGUUA______AG__G___ACUAC___________A____AAAGU...UAG-5'\n_____________\|___________________________________\|\n_____________70__________________________________15\n	112 -- 118	155 -- 161	-21.4956 kcal/mol	4.52534 kcal/mol	8.18567 kcal/mol	68 118@LB@ \| \|@LB@5'-CCA...AAGUA GUA G GCAGCAA C A ACAAA...CGG-3'@LB@ AUUCAG A ACG CGGGCAA G CGAC@LB@ \|:\|\|\|\| \| \|\|: \|:\|\|\|\|\| \| \|:\|\|@LB@ UGAGUC U UGU GUCCGUU C GUUG@LB@3'-UUU...GGUUA AG G ACUAC A AAAGU...UAG-5'@LB@ \| \|@LB@ 70 15@LB@@LB@@LB@Energy -9.89 kcal/mol@LB@Hybridization Energy -21.4956 kcal/mol@LB@Unfolding Energy - mRNA 4.52534 kcal/mol@LB@Unfolding Energy - sRNA 8.18567 kcal/mol@LB@@LB@Position - mRNA 69 -- 117@LB@Position - sRNA 16 -- 69@LB@Position Seed - mRNA 112 -- 118@LB@Position Seed - sRNA 155 -- 161@LB@
41	0.003653	0.2912	b2842	kduD	-13.01	0.069205	14 -- 50	128 -- 174	2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase; KDG oxidoreductase; 20-ketosteroid reductase	b4266 b2774	_____________13_______________________________________________51\n_____________\|________________________________________________\|\n5'-CCG...AACGC______U____________________GAG____________G_____CCCGA...CGG-3'\n______________GUCAUA_UGUGAUGCA_______UAAC___CAG____GCGGU_AUCUC\n______________\|\|\|\|:\|_::\|\|\|\|\|\|\|_______:\|\|\|___\|\|\|____\|\|\|\|\|_\|\|\|:\|\n______________CAGUGU_GUACUACGU_______GUUG___GUC____CGCCA_UAGGG\n3'-UUU...UGAGU________________CCGUUCA____AAA___UUAA_____G_____UGACG...UAG-5'\n_____________\|________________________________________________\|\n_____________175______________________________________________127\n	23 -- 29	160 -- 166	-35.8105 kcal/mol	9.71011 kcal/mol	15.5834 kcal/mol	13 51@LB@ \| \|@LB@5'-CCG...AACGC U GAG G CCCGA...CGG-3'@LB@ GUCAUA UGUGAUGCA UAAC CAG GCGGU AUCUC@LB@ \|\|\|\|:\| ::\|\|\|\|\|\|\| :\|\|\| \|\|\| \|\|\|\|\| \|\|\|:\|@LB@ CAGUGU GUACUACGU GUUG GUC CGCCA UAGGG@LB@3'-UUU...UGAGU CCGUUCA AAA UUAA G UGACG...UAG-5'@LB@ \| \|@LB@ 175 127@LB@@LB@@LB@Energy -13.01 kcal/mol@LB@Hybridization Energy -35.8105 kcal/mol@LB@Unfolding Energy - mRNA 9.71011 kcal/mol@LB@Unfolding Energy - sRNA 15.5834 kcal/mol@LB@@LB@Position - mRNA 14 -- 50@LB@Position - sRNA 128 -- 174@LB@Position Seed - mRNA 23 -- 29@LB@Position Seed - sRNA 160 -- 166@LB@
33	0.002591	0.2642	b0331	prpB	-22.44	0.000909	137 -- 159	1 -- 22	2-methylisocitrate lyase		_____________136__________________160\n_____________\|____________________\|\n5'-GUC...AUUGU_____A______________UUUAU...UGG-3'\n______________GGCAC_CCCCUUGCUUUGUC\n______________\|\|\|\|\|_\|\|\|\|\|\|\|\|\|\|::\|\|\n______________CCGUG_GGGGAACGAAGUAG\n3'-UUU...GUACC____________________-5'\n_____________\|___________________\|\n_____________23__________________1\n	153 -- 159	1 -- 7	-33.844 kcal/mol	4.2272 kcal/mol	8.43224 kcal/mol	136 160@LB@ \| \|@LB@5'-GUC...AUUGU A UUUAU...UGG-3'@LB@ GGCAC CCCCUUGCUUUGUC@LB@ \|\|\|\|\| \|\|\|\|\|\|\|\|\|\|::\|\|@LB@ CCGUG GGGGAACGAAGUAG@LB@3'-UUU...GUACC -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -22.44 kcal/mol@LB@Hybridization Energy -33.844 kcal/mol@LB@Unfolding Energy - mRNA 4.2272 kcal/mol@LB@Unfolding Energy - sRNA 8.43224 kcal/mol@LB@@LB@Position - mRNA 137 -- 159@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 153 -- 159@LB@Position Seed - sRNA 1 -- 7@LB@
148	0.01584	0.3602	b1822	rlmA	-10.68	0.203557	148 -- 239	111 -- 186	23S rRNA m(1)G745 methyltransferase SAM-dependent		_____________147___________240\n_____________\|_____________\|\n5'-AAG...GCGUG_____C_______UUGCG...GGU-3'\n______________AUUCG_GUUACAC\n______________\|:\|\|:_\|\|:\|\|\|\|\n______________UGAGU_CAGUGUG\n3'-UUU...GGUUA_____________UACUA...UAG-5'\n_____________\|_____________\|\n_____________187___________110\n	163 -- 169	168 -- 174	-12.5288 kcal/mol	1.89227 kcal/mol	0.283892 kcal/mol	147 240@LB@ \| \|@LB@5'-AAG...GCGUG C UUGCG...GGU-3'@LB@ AUUCG GUUACAC@LB@ \|:\|\|: \|\|:\|\|\|\|@LB@ UGAGU CAGUGUG@LB@3'-UUU...GGUUA UACUA...UAG-5'@LB@ \| \|@LB@ 187 110@LB@@LB@@LB@Energy -10.68 kcal/mol@LB@Hybridization Energy -12.5288 kcal/mol@LB@Unfolding Energy - mRNA 1.89227 kcal/mol@LB@Unfolding Energy - sRNA 0.283892 kcal/mol@LB@@LB@Position - mRNA 148 -- 239@LB@Position - sRNA 111 -- 186@LB@Position Seed - mRNA 163 -- 169@LB@Position Seed - sRNA 168 -- 174@LB@
44	0.003817	0.292	b0967	rlmI	-10.41	0.230051	81 -- 118	128 -- 161	23S rRNA m(5)C1962 methyltransferase SAM-dependent		_____________80_________________________________119\n_____________\|__________________________________\|\n5'-CGU...UGAAC____C___AAACC_______UUAU_CA_______GACAU...AAG-3'\n______________UCGC_CGU_____CAGGCAA____G__GACUUUC\n______________\|\|:\|_\|:\|_____\|\|\|\|\|\|\|____\|__:\|\|\|\|\|\|\n______________AGUG_GUA_____GUCCGUU____C__UUGAAAG\n3'-UUU...GAGUC____U___CUAC_____________AG_______UCUUA...UAG-5'\n_____________\|__________________________________\|\n_____________162________________________________127\n	95 -- 101	145 -- 151	-21.0542 kcal/mol	5.99356 kcal/mol	7.97203 kcal/mol	80 119@LB@ \| \|@LB@5'-CGU...UGAAC C AAACC UUAU CA GACAU...AAG-3'@LB@ UCGC CGU CAGGCAA G GACUUUC@LB@ \|\|:\| \|:\| \|\|\|\|\|\|\| \| :\|\|\|\|\|\|@LB@ AGUG GUA GUCCGUU C UUGAAAG@LB@3'-UUU...GAGUC U CUAC AG UCUUA...UAG-5'@LB@ \| \|@LB@ 162 127@LB@@LB@@LB@Energy -10.41 kcal/mol@LB@Hybridization Energy -21.0542 kcal/mol@LB@Unfolding Energy - mRNA 5.99356 kcal/mol@LB@Unfolding Energy - sRNA 7.97203 kcal/mol@LB@@LB@Position - mRNA 81 -- 118@LB@Position - sRNA 128 -- 161@LB@Position Seed - mRNA 95 -- 101@LB@Position Seed - sRNA 145 -- 151@LB@
16	0.0008966	0.1886	b0807	rlmF	-16.29	0.014793	117 -- 160	51 -- 97	23S rRNA m(6)A1618 methyltransferase SAM-dependent		_____________116_____________________________________________161\n_____________\|_______________________________________________\|\n5'-AUU...UUAAG___U_____AA______A_______________U__A_C________UUAUG...UCC-3'\n______________GUU_UGGGG____UGAU_AACGCAGCCAG_AUA_UU_C_CUGUCGCG\n______________\|\|\|_\|\|\|\|:____\|:\|:_\|\|\|\|\|\|:\|\|\|\|_\|:\|_:\|_\|_\|\|\|\|\|\|\|\|\n______________CAA_ACCCU____AUUG_UUGCGUUGGUC_UGU_GA_G_GACAGCGC\n3'-UUU...AUUAG___C_____GCGA____G___________G___U__A_C________CAUUU...UAG-5'\n_____________\|_______________________________________________\|\n_____________98______________________________________________50\n	154 -- 160	51 -- 57	-44.7843 kcal/mol	10.0752 kcal/mol	25.3667 kcal/mol	116 161@LB@ \| \|@LB@5'-AUU...UUAAG U AA A U A C UUAUG...UCC-3'@LB@ GUU UGGGG UGAU AACGCAGCCAG AUA UU C CUGUCGCG@LB@ \|\|\| \|\|\|\|: \|:\|: \|\|\|\|\|\|:\|\|\|\| \|:\| :\| \| \|\|\|\|\|\|\|\|@LB@ CAA ACCCU AUUG UUGCGUUGGUC UGU GA G GACAGCGC@LB@3'-UUU...AUUAG C GCGA G G U A C CAUUU...UAG-5'@LB@ \| \|@LB@ 98 50@LB@@LB@@LB@Energy -16.29 kcal/mol@LB@Hybridization Energy -44.7843 kcal/mol@LB@Unfolding Energy - mRNA 10.0752 kcal/mol@LB@Unfolding Energy - sRNA 25.3667 kcal/mol@LB@@LB@Position - mRNA 117 -- 160@LB@Position - sRNA 51 -- 97@LB@Position Seed - mRNA 154 -- 160@LB@Position Seed - sRNA 51 -- 57@LB@
186	0.02152	0.3833	b3581	sgbH	-10.17	0.255482	135 -- 158	123 -- 153	3-keto-L-gulonate 6-phosphate decarboxylase		_____________134________159\n_____________\|__________\|\n5'-UUU...UAAGG__________UAUGA...AAG-3'\n______________AG_CACACAU\n______________\|\|_\|\|\|\|\|\|\|\n______________UC_GUGUGUA\n3'-UUU...AUGAG__A_______CUACG...UAG-5'\n_____________\|__________\|\n_____________154________122\n	193 -- 199	166 -- 172	-9.15702 kcal/mol	1.98532 kcal/mol	0.591348 kcal/mol	134 159@LB@ \| \|@LB@5'-UUU...UAAGG UAUGA...AAG-3'@LB@ AG CACACAU@LB@ \|\| \|\|\|\|\|\|\|@LB@ UC GUGUGUA@LB@3'-UUU...AUGAG A CUACG...UAG-5'@LB@ \| \|@LB@ 154 122@LB@@LB@@LB@Energy -10.17 kcal/mol@LB@Hybridization Energy -9.15702 kcal/mol@LB@Unfolding Energy - mRNA 1.98532 kcal/mol@LB@Unfolding Energy - sRNA 0.591348 kcal/mol@LB@@LB@Position - mRNA 135 -- 158@LB@Position - sRNA 123 -- 153@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 166 -- 172@LB@
25	0.002009	0.2633	b0134	panB	-9.88	0.290153	57 -- 67	176 -- 186	3-methyl-2-oxobutanoate hydroxymethyltransferase		_____________56__________68\n_____________\|___________\|\n5'-CAG...AAAGC___________UCCAG...UUG-3'\n______________CACCAGUACUU\n______________\|\|\|\|\|:\|\|\|\|:\n______________GUGGUUAUGAG\n3'-UUU...AAAAU___________UCAGU...UAG-5'\n_____________\|___________\|\n_____________187_________175\n	61 -- 67	176 -- 182	-15.2136 kcal/mol	0.973349 kcal/mol	3.38772 kcal/mol	56 68@LB@ \| \|@LB@5'-CAG...AAAGC UCCAG...UUG-3'@LB@ CACCAGUACUU@LB@ \|\|\|\|\|:\|\|\|\|:@LB@ GUGGUUAUGAG@LB@3'-UUU...AAAAU UCAGU...UAG-5'@LB@ \| \|@LB@ 187 175@LB@@LB@@LB@Energy -9.88 kcal/mol@LB@Hybridization Energy -15.2136 kcal/mol@LB@Unfolding Energy - mRNA 0.973349 kcal/mol@LB@Unfolding Energy - sRNA 3.38772 kcal/mol@LB@@LB@Position - mRNA 57 -- 67@LB@Position - sRNA 176 -- 186@LB@Position Seed - mRNA 61 -- 67@LB@Position Seed - sRNA 176 -- 182@LB@
109	0.01201	0.3575	b1096	pabC	-8.08	0.578936	115 -- 139	144 -- 163	4-amino-4-deoxychorismate lyase component of para-aminobenzoate synthase multienzyme complex		_____________114____________140\n_____________\|______________\|\n5'-GUU...GUGUA_______CG_____GGUGG...ACG-3'\n______________ACUCCUU__GCUUC\n______________\|\|:\|\|:\|__\|\|\|\|\|\n______________UGGGGGA__CGAAG\n3'-UUU...CCCCG_______A______UAG-5'\n_____________\|______________\|\n_____________164____________143\n	29 -- 35	10 -- 16	-15.037 kcal/mol	0.971533 kcal/mol	6.96912 kcal/mol	114 140@LB@ \| \|@LB@5'-GUU...GUGUA CG GGUGG...ACG-3'@LB@ ACUCCUU GCUUC@LB@ \|\|:\|\|:\| \|\|\|\|\|@LB@ UGGGGGA CGAAG@LB@3'-UUU...CCCCG A UAG-5'@LB@ \| \|@LB@ 164 143@LB@@LB@@LB@Energy -8.08 kcal/mol@LB@Hybridization Energy -15.037 kcal/mol@LB@Unfolding Energy - mRNA 0.971533 kcal/mol@LB@Unfolding Energy - sRNA 6.96912 kcal/mol@LB@@LB@Position - mRNA 115 -- 139@LB@Position - sRNA 144 -- 163@LB@Position Seed - mRNA 29 -- 35@LB@Position Seed - sRNA 10 -- 16@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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