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
121	0.01323	0.3575	b3429	glgA	-14.56	0.033318	190 -- 240	123 -- 176	glycogen synthase	_____________189__________________241\n_____________\|____________________\|\n5'-GUA...AUGCA__________GU________AGAUG...ACG-3'\n______________GGUUUUACAU__AUGUUCAG\n______________\|:\|\|\|\|\|\|\|:__\|\|::\|\|\|\|\n______________CUAAAAUGUG__UAUGAGUC\n3'-UUU...GCCCA__________GU________AGUGU...UAG-5'\n_____________\|____________________\|\n_____________177__________________122\n	219 -- 225	174 -- 180	-15.9439 kcal/mol	3.46677 kcal/mol	4.94566 kcal/mol	189 241@LB@ \| \|@LB@5'-GUA...AUGCA GU AGAUG...ACG-3'@LB@ GGUUUUACAU AUGUUCAG@LB@ \|:\|\|\|\|\|\|\|: \|\|::\|\|\|\|@LB@ CUAAAAUGUG UAUGAGUC@LB@3'-UUU...GCCCA GU AGUGU...UAG-5'@LB@ \| \|@LB@ 177 122@LB@@LB@@LB@Energy -14.56 kcal/mol@LB@Hybridization Energy -15.9439 kcal/mol@LB@Unfolding Energy - mRNA 3.46677 kcal/mol@LB@Unfolding Energy - sRNA 4.94566 kcal/mol@LB@@LB@Position - mRNA 190 -- 240@LB@Position - sRNA 123 -- 176@LB@Position Seed - mRNA 219 -- 225@LB@Position Seed - sRNA 174 -- 180@LB@
122	0.01342	0.3575	b4087	alsA	-13.14	0.065197	11 -- 23	124 -- 136	D-allose ABC transporter ATPase	_____________10___________24\n_____________\|____________\|\n5'-AAU...GGCAA____________GGAUA...UAC-3'\n______________GGUUAUCCCGCU\n______________\|\|\|:\|\|\|\|\|:\|\|\n______________CCAGUAGGGUGA\n3'-UUU...UAACG____________CGUAG...UAG-5'\n_____________\|____________\|\n_____________137__________123\n	16 -- 22	125 -- 131	-19.4238 kcal/mol	3.3353 kcal/mol	6.53419 kcal/mol	10 24@LB@ \| \|@LB@5'-AAU...GGCAA GGAUA...UAC-3'@LB@ GGUUAUCCCGCU@LB@ \|\|\|:\|\|\|\|\|:\|\|@LB@ CCAGUAGGGUGA@LB@3'-UUU...UAACG CGUAG...UAG-5'@LB@ \| \|@LB@ 137 123@LB@@LB@@LB@Energy -13.14 kcal/mol@LB@Hybridization Energy -19.4238 kcal/mol@LB@Unfolding Energy - mRNA 3.3353 kcal/mol@LB@Unfolding Energy - sRNA 6.53419 kcal/mol@LB@@LB@Position - mRNA 11 -- 23@LB@Position - sRNA 124 -- 136@LB@Position Seed - mRNA 16 -- 22@LB@Position Seed - sRNA 125 -- 131@LB@
123	0.01344	0.3575	b2615	nadK	-10.03	0.271821	99 -- 122	57 -- 77	NAD kinase	_____________98____________123\n_____________\|_____________\|\n5'-CUC...CCCAC________AC___ACUGA...AAG-3'\n______________GGCACCCC__UGC\n______________\|\|\|\|\|\|\|\|__\|\|\|\n______________CCGUGGGG__ACG\n3'-UUU...GUACC________GA___AAGUAG-5'\n_____________\|_____________\|\n_____________78____________56\n	245 -- 251	12 -- 18	-21.986 kcal/mol	5.26387 kcal/mol	8.16826 kcal/mol	98 123@LB@ \| \|@LB@5'-CUC...CCCAC AC ACUGA...AAG-3'@LB@ GGCACCCC UGC@LB@ \|\|\|\|\|\|\|\| \|\|\|@LB@ CCGUGGGG ACG@LB@3'-UUU...GUACC GA AAGUAG-5'@LB@ \| \|@LB@ 78 56@LB@@LB@@LB@Energy -10.03 kcal/mol@LB@Hybridization Energy -21.986 kcal/mol@LB@Unfolding Energy - mRNA 5.26387 kcal/mol@LB@Unfolding Energy - sRNA 8.16826 kcal/mol@LB@@LB@Position - mRNA 99 -- 122@LB@Position - sRNA 57 -- 77@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 12 -- 18@LB@
124	0.0136	0.3575	b4065	yjcE	-10.85	0.188871	258 -- 289	125 -- 174	putative cation/proton antiporter	_____________257___________290\n_____________\|_____________\|\n5'-UAU...UGGUC_____U_______CCUUU...UGC-3'\n______________ACUCG_GUCAUGC\n______________\|\|\|\|:_\|\|\|\|::\|\n______________UGAGU_CAGUGUG\n3'-UUU...GGUUA_____________UACUA...UAG-5'\n_____________\|_____________\|\n_____________175___________124\n	267 -- 273	168 -- 174	-13.2629 kcal/mol	3.88311 kcal/mol	0.283892 kcal/mol	257 290@LB@ \| \|@LB@5'-UAU...UGGUC U CCUUU...UGC-3'@LB@ ACUCG GUCAUGC@LB@ \|\|\|\|: \|\|\|\|::\|@LB@ UGAGU CAGUGUG@LB@3'-UUU...GGUUA UACUA...UAG-5'@LB@ \| \|@LB@ 175 124@LB@@LB@@LB@Energy -10.85 kcal/mol@LB@Hybridization Energy -13.2629 kcal/mol@LB@Unfolding Energy - mRNA 3.88311 kcal/mol@LB@Unfolding Energy - sRNA 0.283892 kcal/mol@LB@@LB@Position - mRNA 258 -- 289@LB@Position - sRNA 125 -- 174@LB@Position Seed - mRNA 267 -- 273@LB@Position Seed - sRNA 168 -- 174@LB@
125	0.01377	0.3575	b2827	thyA	-14.98	0.027366	100 -- 109	16 -- 25	thymidylate synthetase	_____________99_____________________110\n_____________\|______________________\|\n5'-CAG...AAACA________A_____________AAAAG...AGA-3'\n______________GUAUUUAG__AC___UGAUGCA\n______________:\|\|:\|:\|\|__\|\|___\|\|\|\|\|\|\|\n______________UAUGAGUC__UG___ACUACGU\n3'-UUU...GUGGU________AG__UGU_______CCGUU...UAG-5'\n_____________\|______________________\|\n_____________26_____________________15\n	220 -- 226	160 -- 166	-15.3976 kcal/mol	3.04146 kcal/mol	4.80633 kcal/mol	99 110@LB@ \| \|@LB@5'-CAG...AAACA A AAAAG...AGA-3'@LB@ GUAUUUAG AC UGAUGCA@LB@ :\|\|:\|:\|\| \|\| \|\|\|\|\|\|\|@LB@ UAUGAGUC UG ACUACGU@LB@3'-UUU...GUGGU AG UGU CCGUU...UAG-5'@LB@ \| \|@LB@ 26 15@LB@@LB@@LB@Energy -14.98 kcal/mol@LB@Hybridization Energy -15.3976 kcal/mol@LB@Unfolding Energy - mRNA 3.04146 kcal/mol@LB@Unfolding Energy - sRNA 4.80633 kcal/mol@LB@@LB@Position - mRNA 100 -- 109@LB@Position - sRNA 16 -- 25@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 160 -- 166@LB@
126	0.01383	0.3575	b1843	yobB	-8.48	0.503741	101 -- 118	168 -- 185	C-N hydrolase family protein	_____________100____________119\n_____________\|______________\|\n5'-CCU...AACUU____AG________UUUCU...CCA-3'\n______________AUAC__AGUUACAC\n______________\|\|\|\|__\|\|\|:\|\|\|\|\n______________UAUG__UCAGUGUG\n3'-UUU...GUGGU____AG________UACUA...UAG-5'\n_____________\|______________\|\n_____________186____________167\n	112 -- 118	168 -- 174	-13.9608 kcal/mol	3.09724 kcal/mol	0.286881 kcal/mol	100 119@LB@ \| \|@LB@5'-CCU...AACUU AG UUUCU...CCA-3'@LB@ AUAC AGUUACAC@LB@ \|\|\|\| \|\|\|:\|\|\|\|@LB@ UAUG UCAGUGUG@LB@3'-UUU...GUGGU AG UACUA...UAG-5'@LB@ \| \|@LB@ 186 167@LB@@LB@@LB@Energy -8.48 kcal/mol@LB@Hybridization Energy -13.9608 kcal/mol@LB@Unfolding Energy - mRNA 3.09724 kcal/mol@LB@Unfolding Energy - sRNA 0.286881 kcal/mol@LB@@LB@Position - mRNA 101 -- 118@LB@Position - sRNA 168 -- 185@LB@Position Seed - mRNA 112 -- 118@LB@Position Seed - sRNA 168 -- 174@LB@
127	0.01385	0.3575	b3832	rmuC	-11.83	0.120260	236 -- 246	193 -- 203	DNA recombination protein	_____________235____________________________________________________________247\n_____________\|______________________________________________________________\|\n5'-AAA...UUGUA________AUUC___UUU_____________GUU__G______AGGC_______AUU_____AUCAU...AGC-3'\n______________CAG_CACA____UAU___GUGCGGGUAAGUU___GC__UCAGG____GUUGUGG___UCUCA\n______________\|\|\|_\|\|\|\|____:\|\|___:\|\|\|:\|\|:\|\|\|\|:___:\|__\|\|\|\|:____:\|\|\|:\|\|___\|\|:\|\|\n______________GUC_GUGU____GUA___UACGUCCGUUCAG___UG__AGUCU____UAACGCC___AGGGU\n3'-UUU...UAUGA___A___________C_______________U____AA________________AGU_____GACGU...UAG-5'\n_____________\|______________________________________________________________\|\n_____________204____________________________________________________________192\n	198 -- 204	135 -- 141	-42.9883 kcal/mol	19.1075 kcal/mol	15.6146 kcal/mol	235 247@LB@ \| \|@LB@5'-AAA...UUGUA AUUC UUU GUU G AGGC AUU AUCAU...AGC-3'@LB@ CAG CACA UAU GUGCGGGUAAGUU GC UCAGG GUUGUGG UCUCA@LB@ \|\|\| \|\|\|\| :\|\| :\|\|\|:\|\|:\|\|\|\|: :\| \|\|\|\|: :\|\|\|:\|\| \|\|:\|\|@LB@ GUC GUGU GUA UACGUCCGUUCAG UG AGUCU UAACGCC AGGGU@LB@3'-UUU...UAUGA A C U AA AGU GACGU...UAG-5'@LB@ \| \|@LB@ 204 192@LB@@LB@@LB@Energy -11.83 kcal/mol@LB@Hybridization Energy -42.9883 kcal/mol@LB@Unfolding Energy - mRNA 19.1075 kcal/mol@LB@Unfolding Energy - sRNA 15.6146 kcal/mol@LB@@LB@Position - mRNA 236 -- 246@LB@Position - sRNA 193 -- 203@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 135 -- 141@LB@
128	0.01397	0.3575	b2440	eutC	-11.59	0.134682	23 -- 48	126 -- 153	ethanolamine ammonia-lyase small subunit (light chain)	_____________22______________________________49\n_____________\|_______________________________\|\n______5'-CCGCU_______G_______________AC______GACCA...ACU-3'\n______________GGGUGAU___ACAUC_AUGCUCA__UAC_CA\n______________\|\|\|\|\|\|\|___\|\|\|:\|_\|\|:\|\|\|\|__:\|\|_\|\|\n______________CCCACUA___UGUGG_UAUGAGU__GUG_GU\n3'-UUU...GACCG_______AAA_____U_______CA___U__ACUAC...UAG-5'\n_____________\|_______________________________\|\n_____________154_____________________________125\n	19 -- 25	175 -- 181	-25.4577 kcal/mol	6.00586 kcal/mol	5.22711 kcal/mol	22 49@LB@ \| \|@LB@ 5'-CCGCU G AC GACCA...ACU-3'@LB@ GGGUGAU ACAUC AUGCUCA UAC CA@LB@ \|\|\|\|\|\|\| \|\|\|:\| \|\|:\|\|\|\| :\|\| \|\|@LB@ CCCACUA UGUGG UAUGAGU GUG GU@LB@3'-UUU...GACCG AAA U CA U ACUAC...UAG-5'@LB@ \| \|@LB@ 154 125@LB@@LB@@LB@Energy -11.59 kcal/mol@LB@Hybridization Energy -25.4577 kcal/mol@LB@Unfolding Energy - mRNA 6.00586 kcal/mol@LB@Unfolding Energy - sRNA 5.22711 kcal/mol@LB@@LB@Position - mRNA 23 -- 48@LB@Position - sRNA 126 -- 153@LB@Position Seed - mRNA 19 -- 25@LB@Position Seed - sRNA 175 -- 181@LB@
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@
130	0.0142	0.3575	b0885	aat	-14.04	0.042507	189 -- 220	112 -- 144	leucyl/phenylalanyl-tRNA-protein transferase	_____________188_______________________________221\n_____________\|_________________________________\|\n5'-CGU...UUUUG________________CU_______________UCGCC...UUA-3'\n______________CGGUCAUGC_____GC__GGU___UCAGCUUUC\n______________\|:\|\|\|\|::\|_____\|\|__\|\|:___\|\|\|:\|\|\|\|\|\n______________GUCAGUGUG_____CG__CCG___AGUUGAAAG\n3'-UUU...UAUGA_________UACUA__U____UUC_________UCUUA...UAG-5'\n_____________\|_________________________________\|\n_____________145_______________________________111\n	214 -- 220	145 -- 151	-24.916 kcal/mol	8.31603 kcal/mol	8.21863 kcal/mol	188 221@LB@ \| \|@LB@5'-CGU...UUUUG CU UCGCC...UUA-3'@LB@ CGGUCAUGC GC GGU UCAGCUUUC@LB@ \|:\|\|\|\|::\| \|\| \|\|: \|\|\|:\|\|\|\|\|@LB@ GUCAGUGUG CG CCG AGUUGAAAG@LB@3'-UUU...UAUGA UACUA U UUC UCUUA...UAG-5'@LB@ \| \|@LB@ 145 111@LB@@LB@@LB@Energy -14.04 kcal/mol@LB@Hybridization Energy -24.916 kcal/mol@LB@Unfolding Energy - mRNA 8.31603 kcal/mol@LB@Unfolding Energy - sRNA 8.21863 kcal/mol@LB@@LB@Position - mRNA 189 -- 220@LB@Position - sRNA 112 -- 144@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 145 -- 151@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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