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
18	6.719e-05	0.01313	b2935	tktA	-10.85	0.025018	263 -- 275	52 -- 64	transketolase 1 thiamine triphosphate-binding	_____________262___________276\n_____________\|_____________\|\n5'-AAG...CAGAA_____________CACCC...UGG-3'\n______________AGCCAAAUCCGGU\n______________\|\|\|\|\|\|\|\|\|\|\|:\|\n______________UCGGUUUAGGCUA\n3'-AUU...AUAAG_____________AUGCA...AUG-5'\n_____________\|_____________\|\n_____________65____________51\n	269 -- 275	52 -- 58	-21.1603 kcal/mol	4.16811 kcal/mol	6.16128 kcal/mol	262 276@LB@ \| \|@LB@5'-AAG...CAGAA CACCC...UGG-3'@LB@ AGCCAAAUCCGGU@LB@ \|\|\|\|\|\|\|\|\|\|\|:\|@LB@ UCGGUUUAGGCUA@LB@3'-AUU...AUAAG AUGCA...AUG-5'@LB@ \| \|@LB@ 65 51@LB@@LB@@LB@Energy -10.85 kcal/mol@LB@Hybridization Energy -21.1603 kcal/mol@LB@Unfolding Energy - mRNA 4.16811 kcal/mol@LB@Unfolding Energy - sRNA 6.16128 kcal/mol@LB@@LB@Position - mRNA 263 -- 275@LB@Position - sRNA 52 -- 64@LB@Position Seed - mRNA 269 -- 275@LB@Position Seed - sRNA 52 -- 58@LB@
27	0.0002115	0.02687	b2607	trmD	-14.32	0.001383	229 -- 258	48 -- 75	tRNA m(1)G37 methyltransferase SAM-dependent	_____________228____________________________259\n_____________\|______________________________\|\n5'-UCG...GUUUC___________C__G___U_A_________GGGUA...UCC-3'\n______________CUGAAAUGUUC_GC_CAA_U_CCGAUUACG\n______________\|\|:\|\|\|\|:\|\|\|_\|\|_\|\|\|_\|_\|\|\|\|\|\|\|\|\|\n______________GAUUUUAUAAG_CG_GUU_A_GGCUAAUGC\n3'-AUU...CCGCC___________U______U___________ACUUC...AUG-5'\n_____________\|______________________________\|\n_____________76_____________________________47\n	252 -- 258	48 -- 54	-28.476 kcal/mol	6.50272 kcal/mol	7.67232 kcal/mol	228 259@LB@ \| \|@LB@5'-UCG...GUUUC C G U A GGGUA...UCC-3'@LB@ CUGAAAUGUUC GC CAA U CCGAUUACG@LB@ \|\|:\|\|\|\|:\|\|\| \|\| \|\|\| \| \|\|\|\|\|\|\|\|\|@LB@ GAUUUUAUAAG CG GUU A GGCUAAUGC@LB@3'-AUU...CCGCC U U ACUUC...AUG-5'@LB@ \| \|@LB@ 76 47@LB@@LB@@LB@Energy -14.32 kcal/mol@LB@Hybridization Energy -28.476 kcal/mol@LB@Unfolding Energy - mRNA 6.50272 kcal/mol@LB@Unfolding Energy - sRNA 7.67232 kcal/mol@LB@@LB@Position - mRNA 229 -- 258@LB@Position - sRNA 48 -- 75@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 48 -- 54@LB@
56	0.0008344	0.05242	b3651	trmH	-7.19	0.238334	68 -- 84	17 -- 32	tRNA mG18-2'-O-methyltransferase SAM-dependent	_____________67________________85\n_____________\|_________________\|\n5'-CGC...GAAGA_________UC______ACAGC...UUU-3'\n______________GAAAGAUGG__GCGUCU\n______________\|\|\|\|\|\|\|:\|__:\|:\|\|\|\n______________CUUUCUAUC__UGUAGA\n3'-AUU...CCAGA_________U_______AUGGA...AUG-5'\n_____________\|_________________\|\n_____________33________________16\n	70 -- 76	24 -- 30	-18.3937 kcal/mol	6.9506 kcal/mol	4.26839 kcal/mol	67 85@LB@ \| \|@LB@5'-CGC...GAAGA UC ACAGC...UUU-3'@LB@ GAAAGAUGG GCGUCU@LB@ \|\|\|\|\|\|\|:\| :\|:\|\|\|@LB@ CUUUCUAUC UGUAGA@LB@3'-AUU...CCAGA U AUGGA...AUG-5'@LB@ \| \|@LB@ 33 16@LB@@LB@@LB@Energy -7.19 kcal/mol@LB@Hybridization Energy -18.3937 kcal/mol@LB@Unfolding Energy - mRNA 6.9506 kcal/mol@LB@Unfolding Energy - sRNA 4.26839 kcal/mol@LB@@LB@Position - mRNA 68 -- 84@LB@Position - sRNA 17 -- 32@LB@Position Seed - mRNA 70 -- 76@LB@Position Seed - sRNA 24 -- 30@LB@
146	0.005604	0.1342	b1637	tyrS	-10.18	0.040102	30 -- 71	2 -- 50	tyrosyl-tRNA synthetase	_____________29________________________________________________72\n_____________\|_________________________________________________\|\n5'-CAU...UACCA_______AAU___U_CG________U__U____________________AAAAG...CGA-3'\n______________GCGUGAA____GA_G__UGGAAGAU_GA_CGUCUUGC______ACCCUG\n______________:\|\|\|\|\|\|____:\|_\|__\|\|:\|\|\|\|\|_\|\|_\|:\|\|\|\|:\|______\|\|\|\|\|:\n______________UGCACUU____UU_C__ACUUUCUA_CU_GUAGAAUG______UGGGAU\n3'-AUU...GCUAA_______CAUU__C_AG________U__U________GAGACA______G-5'\n_____________\|_________________________________________________\|\n_____________51________________________________________________1\n	30 -- 36	44 -- 50	-35.883 kcal/mol	13.0482 kcal/mol	12.6769 kcal/mol	29 72@LB@ \| \|@LB@5'-CAU...UACCA AAU U CG U U AAAAG...CGA-3'@LB@ GCGUGAA GA G UGGAAGAU GA CGUCUUGC ACCCUG@LB@ :\|\|\|\|\|\| :\| \| \|\|:\|\|\|\|\| \|\| \|:\|\|\|\|:\| \|\|\|\|\|:@LB@ UGCACUU UU C ACUUUCUA CU GUAGAAUG UGGGAU@LB@3'-AUU...GCUAA CAUU C AG U U GAGACA G-5'@LB@ \| \|@LB@ 51 1@LB@@LB@@LB@Energy -10.18 kcal/mol@LB@Hybridization Energy -35.883 kcal/mol@LB@Unfolding Energy - mRNA 13.0482 kcal/mol@LB@Unfolding Energy - sRNA 12.6769 kcal/mol@LB@@LB@Position - mRNA 30 -- 71@LB@Position - sRNA 2 -- 50@LB@Position Seed - mRNA 30 -- 36@LB@Position Seed - sRNA 44 -- 50@LB@
95	0.002686	0.09947	b2419	yfeK	-12.78	0.005552	57 -- 65	1 -- 9	uncharacterized protein	_____________56________66\n_____________\|_________\|\n5'-GUU...CUGCA_________UCUUA...UGG-3'\n______________GUGCCCUAC\n______________\|\|:\|\|\|\|\|\|\n______________CAUGGGAUG\n3'-AUU...GGAGA_________-5'\n_____________\|________\|\n_____________10_______1\n	59 -- 65	1 -- 7	-16.152 kcal/mol	1.26264 kcal/mol	2.12872 kcal/mol	56 66@LB@ \| \|@LB@5'-GUU...CUGCA UCUUA...UGG-3'@LB@ GUGCCCUAC@LB@ \|\|:\|\|\|\|\|\|@LB@ CAUGGGAUG@LB@3'-AUU...GGAGA -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -12.78 kcal/mol@LB@Hybridization Energy -16.152 kcal/mol@LB@Unfolding Energy - mRNA 1.26264 kcal/mol@LB@Unfolding Energy - sRNA 2.12872 kcal/mol@LB@@LB@Position - mRNA 57 -- 65@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 59 -- 65@LB@Position Seed - sRNA 1 -- 7@LB@
178	0.007695	0.1511	b4567	yjjZ	-7.25	0.231371	185 -- 218	2 -- 33	uncharacterized protein	_____________184_________________________________219\n_____________\|___________________________________\|\n5'-CGG...AUCAA_______GAU___AU___G____AA______G___GGCAG...GGA-3'\n______________UGAAAGA___GAA__CAU_UUGC__C_GUAC_CUG\n______________\|\|\|\|\|\|\|___\|\|\|__\|\|\|_\|\|:\|__\|_\|\|\|\|_\|\|:\n______________ACUUUCU___CUU__GUA_AAUG__G_CAUG_GAU\n3'-AUU...UCCAG_______AU_________G____GA_A____G___G-5'\n_____________\|___________________________________\|\n_____________34__________________________________1\n	185 -- 191	27 -- 33	-22.8177 kcal/mol	6.54395 kcal/mol	9.04499 kcal/mol	184 219@LB@ \| \|@LB@5'-CGG...AUCAA GAU AU G AA G GGCAG...GGA-3'@LB@ UGAAAGA GAA CAU UUGC C GUAC CUG@LB@ \|\|\|\|\|\|\| \|\|\| \|\|\| \|\|:\| \| \|\|\|\| \|\|:@LB@ ACUUUCU CUU GUA AAUG G CAUG GAU@LB@3'-AUU...UCCAG AU G GA A G G-5'@LB@ \| \|@LB@ 34 1@LB@@LB@@LB@Energy -7.25 kcal/mol@LB@Hybridization Energy -22.8177 kcal/mol@LB@Unfolding Energy - mRNA 6.54395 kcal/mol@LB@Unfolding Energy - sRNA 9.04499 kcal/mol@LB@@LB@Position - mRNA 185 -- 218@LB@Position - sRNA 2 -- 33@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 27 -- 33@LB@
167	0.00683	0.1439	b0387	yaiI	-9.54	0.061403	53 -- 70	51 -- 65	UPF0178 family protein	_____________52_________________71\n_____________\|__________________\|\n5'-CAC...UGCCG_______UAAAA______UUCUU...CAA-3'\n______________CAGCCAA_____CCGAUU\n______________\|\|\|\|\|\|\|_____\|\|\|\|\|\|\n______________GUCGGUU_____GGCUAA\n3'-AUU...UAUAA_______UA_________UGCAC...AUG-5'\n_____________\|__________________\|\n_____________66_________________50\n	53 -- 59	59 -- 65	-16.8495 kcal/mol	1.14267 kcal/mol	6.18987 kcal/mol	52 71@LB@ \| \|@LB@5'-CAC...UGCCG UAAAA UUCUU...CAA-3'@LB@ CAGCCAA CCGAUU@LB@ \|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ GUCGGUU GGCUAA@LB@3'-AUU...UAUAA UA UGCAC...AUG-5'@LB@ \| \|@LB@ 66 50@LB@@LB@@LB@Energy -9.54 kcal/mol@LB@Hybridization Energy -16.8495 kcal/mol@LB@Unfolding Energy - mRNA 1.14267 kcal/mol@LB@Unfolding Energy - sRNA 6.18987 kcal/mol@LB@@LB@Position - mRNA 53 -- 70@LB@Position - sRNA 51 -- 65@LB@Position Seed - mRNA 53 -- 59@LB@Position Seed - sRNA 59 -- 65@LB@
160	0.006479	0.1413	b0391	yaiE	-12.00	0.010520	148 -- 162	1 -- 15	UPF0345 family protein	_____________147_____________163\n_____________\|_______________\|\n5'-GAU...CCAGC_______GC______AGUGA...GCG-3'\n______________GCCUCUG__CCCUAU\n______________:\|\|\|\|\|\|__\|\|\|\|\|:\n______________UGGAGAC__GGGAUG\n3'-AUU...UAGAA_______AU______-5'\n_____________\|______________\|\n_____________16_____________1\n	148 -- 154	9 -- 15	-21.6181 kcal/mol	3.81195 kcal/mol	5.82808 kcal/mol	147 163@LB@ \| \|@LB@5'-GAU...CCAGC GC AGUGA...GCG-3'@LB@ GCCUCUG CCCUAU@LB@ :\|\|\|\|\|\| \|\|\|\|\|:@LB@ UGGAGAC GGGAUG@LB@3'-AUU...UAGAA AU -5'@LB@ \| \|@LB@ 16 1@LB@@LB@@LB@Energy -12.00 kcal/mol@LB@Hybridization Energy -21.6181 kcal/mol@LB@Unfolding Energy - mRNA 3.81195 kcal/mol@LB@Unfolding Energy - sRNA 5.82808 kcal/mol@LB@@LB@Position - mRNA 148 -- 162@LB@Position - sRNA 1 -- 15@LB@Position Seed - mRNA 148 -- 154@LB@Position Seed - sRNA 9 -- 15@LB@
196	0.008709	0.1558	b2498	upp	-7.14	0.244299	249 -- 259	45 -- 56	uracil phosphoribosyltransferase	_____________248__________260\n_____________\|____________\|\n5'-GGC...UGGGA____________GCAAG...CCG-3'\n______________CUGA_UGCGUGA\n______________\|:\|\|_\|:\|\|\|\|\|\n______________GGCU_AUGCACU\n3'-AUU...GUUUA____A_______UCAUU...AUG-5'\n_____________\|____________\|\n_____________57___________44\n	253 -- 259	45 -- 51	-12.6155 kcal/mol	3.20986 kcal/mol	2.27945 kcal/mol	248 260@LB@ \| \|@LB@5'-GGC...UGGGA GCAAG...CCG-3'@LB@ CUGA UGCGUGA@LB@ \|:\|\| \|:\|\|\|\|\|@LB@ GGCU AUGCACU@LB@3'-AUU...GUUUA A UCAUU...AUG-5'@LB@ \| \|@LB@ 57 44@LB@@LB@@LB@Energy -7.14 kcal/mol@LB@Hybridization Energy -12.6155 kcal/mol@LB@Unfolding Energy - mRNA 3.20986 kcal/mol@LB@Unfolding Energy - sRNA 2.27945 kcal/mol@LB@@LB@Position - mRNA 249 -- 259@LB@Position - sRNA 45 -- 56@LB@Position Seed - mRNA 253 -- 259@LB@Position Seed - sRNA 45 -- 51@LB@
38	0.0004278	0.03766	b3092	uxaC	-12.53	0.006845	206 -- 269	1 -- 57	uronate isomerase	_____________205_________________________________________________________________270\n_____________\|___________________________________________________________________\|\n5'-UUG...AUGAC____U_____AC_____AUUUC______UU_____CC____UUGCCC___G________ACGA____GCAAA...AUU-3'\n______________UCCG_UUAUG__UGAAG________CUG__AGAUA__GAAU______GCC_UCUGUAUC____CUAC\n______________\|\|\|\|_\|\|\|:\|__\|\|\|\|\|________\|\|\|__\|\|\|\|\|__\|\|\|:______:\|\|_\|\|\|\|\|\|:\|____\|\|\|\|\n______________AGGC_AAUGC__ACUUC________GAC__UCUAU__CUUG______UGG_AGACAUGG____GAUG\n3'-AUU...GGUUU____U____________AUUUUCCA___UU___________UAGAA_____________________-5'\n_____________\|__________________________________________________________________\|\n_____________58_________________________________________________________________1\n	255 -- 261	5 -- 11	-36.5836 kcal/mol	11.3711 kcal/mol	12.7026 kcal/mol	205 270@LB@ \| \|@LB@5'-UUG...AUGAC U AC AUUUC UU CC UUGCCC G ACGA GCAAA...AUU-3'@LB@ UCCG UUAUG UGAAG CUG AGAUA GAAU GCC UCUGUAUC CUAC@LB@ \|\|\|\| \|\|\|:\| \|\|\|\|\| \|\|\| \|\|\|\|\| \|\|\|: :\|\| \|\|\|\|\|\|:\| \|\|\|\|@LB@ AGGC AAUGC ACUUC GAC UCUAU CUUG UGG AGACAUGG GAUG@LB@3'-AUU...GGUUU U AUUUUCCA UU UAGAA -5'@LB@ \| \|@LB@ 58 1@LB@@LB@@LB@Energy -12.53 kcal/mol@LB@Hybridization Energy -36.5836 kcal/mol@LB@Unfolding Energy - mRNA 11.3711 kcal/mol@LB@Unfolding Energy - sRNA 12.7026 kcal/mol@LB@@LB@Position - mRNA 206 -- 269@LB@Position - sRNA 1 -- 57@LB@Position Seed - mRNA 255 -- 261@LB@Position Seed - sRNA 5 -- 11@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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