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
181	0.007802	0.1516	b1797	yeaR	-7.07	0.254063	142 -- 149	2 -- 9	DUF1971 family protein nitrate-inducible	_____________141______150\n_____________\|________\|\n5'-UGC...CAGGC________AAACG...AAG-3'\n______________GUACCCUG\n______________\|\|\|\|\|\|\|:\n______________CAUGGGAU\n3'-AUU...GGAGA________G-5'\n_____________\|________\|\n_____________10_______1\n	143 -- 149	2 -- 8	-12.2602 kcal/mol	3.09143 kcal/mol	2.12684 kcal/mol	141 150@LB@ \| \|@LB@5'-UGC...CAGGC AAACG...AAG-3'@LB@ GUACCCUG@LB@ \|\|\|\|\|\|\|:@LB@ CAUGGGAU@LB@3'-AUU...GGAGA G-5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -7.07 kcal/mol@LB@Hybridization Energy -12.2602 kcal/mol@LB@Unfolding Energy - mRNA 3.09143 kcal/mol@LB@Unfolding Energy - sRNA 2.12684 kcal/mol@LB@@LB@Position - mRNA 142 -- 149@LB@Position - sRNA 2 -- 9@LB@Position Seed - mRNA 143 -- 149@LB@Position Seed - sRNA 2 -- 8@LB@
9	1.988e-05	0.007771	b1985	yeeO	-11.51	0.015356	224 -- 255	1 -- 39	putative multdrug exporter MATE family	_____________223_____________________________________256\n_____________\|_______________________________________\|\n5'-GAU...CAAUU______GGCUUU___________________________GCCAG...GCU-3'\n______________AAGGUC_________GAAUAUCU__CCUCUG__CUUUAC\n______________\|\|\|\|\|\|_________\|\|\|:\|\|\|\|__\|\|\|\|\|\|__\|::\|\|\|\n______________UUCCAG_________CUUGUAGA__GGAGAC__GGGAUG\n3'-AUU...UCAUU______ACUUUCUAU________AU______AU______-5'\n_____________\|______________________________________\|\n_____________40_____________________________________1\n	237 -- 243	17 -- 23	-28.0657 kcal/mol	5.21805 kcal/mol	11.3576 kcal/mol	223 256@LB@ \| \|@LB@5'-GAU...CAAUU GGCUUU GCCAG...GCU-3'@LB@ AAGGUC GAAUAUCU CCUCUG CUUUAC@LB@ \|\|\|\|\|\| \|\|\|:\|\|\|\| \|\|\|\|\|\| \|::\|\|\|@LB@ UUCCAG CUUGUAGA GGAGAC GGGAUG@LB@3'-AUU...UCAUU ACUUUCUAU AU AU -5'@LB@ \| \|@LB@ 40 1@LB@@LB@@LB@Energy -11.51 kcal/mol@LB@Hybridization Energy -28.0657 kcal/mol@LB@Unfolding Energy - mRNA 5.21805 kcal/mol@LB@Unfolding Energy - sRNA 11.3576 kcal/mol@LB@@LB@Position - mRNA 224 -- 255@LB@Position - sRNA 1 -- 39@LB@Position Seed - mRNA 237 -- 243@LB@Position Seed - sRNA 17 -- 23@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@
84	0.002084	0.08729	b2067	yegE	-5.99	0.414041	137 -- 150	1 -- 15	putative diguanylate cyclase	_____________136_____________151\n_____________\|_______________\|\n5'-AGU...GUAAA___________A___AUAAA...CGC-3'\n______________ACUUUUGUACU__GC\n______________\|\|:\|:\|\|\|\|\|:__:\|\n______________UGGAGACAUGG__UG\n3'-AUU...UAGAA___________GA__-5'\n_____________\|______________\|\n_____________16_____________1\n	141 -- 147	5 -- 11	-13.6769 kcal/mol	1.88278 kcal/mol	5.82808 kcal/mol	136 151@LB@ \| \|@LB@5'-AGU...GUAAA A AUAAA...CGC-3'@LB@ ACUUUUGUACU GC@LB@ \|\|:\|:\|\|\|\|\|: :\|@LB@ UGGAGACAUGG UG@LB@3'-AUU...UAGAA GA -5'@LB@ \| \|@LB@ 16 1@LB@@LB@@LB@Energy -5.99 kcal/mol@LB@Hybridization Energy -13.6769 kcal/mol@LB@Unfolding Energy - mRNA 1.88278 kcal/mol@LB@Unfolding Energy - sRNA 5.82808 kcal/mol@LB@@LB@Position - mRNA 137 -- 150@LB@Position - sRNA 1 -- 15@LB@Position Seed - mRNA 141 -- 147@LB@Position Seed - sRNA 5 -- 11@LB@
11	3.674e-05	0.01134	b2099	yegU	-10.44	0.033453	166 -- 229	3 -- 59	ADP-ribosylglycohydrolase family protein	_____________165_________________________________________________________________230\n_____________\|___________________________________________________________________\|\n5'-GUG...UCGAU____G____AU____U___CAC______AAGUUAAA_____AC________AU______G_______UUAUG...CAC-3'\n______________GAUC_CGAU__UGCG_UGA___AAGGGG________UGAAA___AGAACGU____UCUC_GUGCUCU\n______________:\|\|\|_\|\|\|\|__\|:\|\|_\|\|\|___\|\|::\|\|________\|\|\|\|\|___\|\|\|\|\|:\|____:\|\|\|_\|\|:\|:\|\|\n______________UUAG_GCUA__AUGC_ACU___UUUUCC________ACUUU___UCUUGUA____GGAG_CAUGGGA\n3'-AUU...UCGGU___________________UCA______AG___________CUA_______GAAU____A_______UG-5'\n_____________\|___________________________________________________________________\|\n_____________60__________________________________________________________________2\n	223 -- 229	3 -- 9	-36.2809 kcal/mol	13.1575 kcal/mol	12.7026 kcal/mol	165 230@LB@ \| \|@LB@5'-GUG...UCGAU G AU U CAC AAGUUAAA AC AU G UUAUG...CAC-3'@LB@ GAUC CGAU UGCG UGA AAGGGG UGAAA AGAACGU UCUC GUGCUCU@LB@ :\|\|\| \|\|\|\| \|:\|\| \|\|\| \|\|::\|\| \|\|\|\|\| \|\|\|\|\|:\| :\|\|\| \|\|:\|:\|\|@LB@ UUAG GCUA AUGC ACU UUUUCC ACUUU UCUUGUA GGAG CAUGGGA@LB@3'-AUU...UCGGU UCA AG CUA GAAU A UG-5'@LB@ \| \|@LB@ 60 2@LB@@LB@@LB@Energy -10.44 kcal/mol@LB@Hybridization Energy -36.2809 kcal/mol@LB@Unfolding Energy - mRNA 13.1575 kcal/mol@LB@Unfolding Energy - sRNA 12.7026 kcal/mol@LB@@LB@Position - mRNA 166 -- 229@LB@Position - sRNA 3 -- 59@LB@Position Seed - mRNA 223 -- 229@LB@Position Seed - sRNA 3 -- 9@LB@
114	0.003723	0.1147	b2327	yfcA	-8.38	0.125082	22 -- 29	1 -- 8	TauE/TSUP family inner membrane protein	_____________21_______30\n_____________\|________\|\n5'-CAU...UACGU________CGAUA...GUG-3'\n______________UGCCCUGC\n______________\|:\|\|\|\|:\|\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	23 -- 29	1 -- 7	-12.241 kcal/mol	1.76759 kcal/mol	2.11603 kcal/mol	21 30@LB@ \| \|@LB@5'-CAU...UACGU CGAUA...GUG-3'@LB@ UGCCCUGC@LB@ \|:\|\|\|\|:\|@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -8.38 kcal/mol@LB@Hybridization Energy -12.241 kcal/mol@LB@Unfolding Energy - mRNA 1.76759 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 22 -- 29@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 23 -- 29@LB@Position Seed - sRNA 1 -- 7@LB@
172	0.007198	0.1466	b2395	yfeA	-7.88	0.166321	272 -- 292	49 -- 69	putative diguanylate cyclase	_____________271____________________293\n_____________\|______________________\|\n5'-ACC...GUACU__________UC____UU____UUCGCCAC-3'\n______________UAUUCAGCUA___CCG__UUAU\n______________\|\|\|\|\|\|\|\|:\|___\|\|\|__\|\|\|:\n______________AUAAGUCGGU___GGC__AAUG\n3'-AUU...AUUUU__________UUA___U_____CACUU...AUG-5'\n_____________\|______________________\|\n_____________70_____________________48\n	275 -- 281	60 -- 66	-16.2546 kcal/mol	2.18624 kcal/mol	6.21499 kcal/mol	271 293@LB@ \| \|@LB@5'-ACC...GUACU UC UU UUCGCCAC-3'@LB@ UAUUCAGCUA CCG UUAU@LB@ \|\|\|\|\|\|\|\|:\| \|\|\| \|\|\|:@LB@ AUAAGUCGGU GGC AAUG@LB@3'-AUU...AUUUU UUA U CACUU...AUG-5'@LB@ \| \|@LB@ 70 48@LB@@LB@@LB@Energy -7.88 kcal/mol@LB@Hybridization Energy -16.2546 kcal/mol@LB@Unfolding Energy - mRNA 2.18624 kcal/mol@LB@Unfolding Energy - sRNA 6.21499 kcal/mol@LB@@LB@Position - mRNA 272 -- 292@LB@Position - sRNA 49 -- 69@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 60 -- 66@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@
192	0.008619	0.1558	b2561	yfhH	-12.96	0.004772	194 -- 222	4 -- 32	putative DNA-binding transcriptional regulator	_____________193____________________________223\n_____________\|______________________________\|\n5'-CCU...GCGAG________U_____G_______________GUCAG...GCC-3'\n______________GAAAGAUA_GAACG_CUUACUUC_GUAUCC\n______________\|\|\|\|\|\|\|\|_\|\|\|\|:_\|\|\|\|\|:\|\|_\|\|\|:\|\|\n______________CUUUCUAU_CUUGU_GAAUGGAG_CAUGGG\n3'-AUU...CCAGA______________A________A______AUG-5'\n_____________\|______________________________\|\n_____________33_____________________________3\n	195 -- 201	25 -- 31	-31.2741 kcal/mol	9.51226 kcal/mol	8.82263 kcal/mol	193 223@LB@ \| \|@LB@5'-CCU...GCGAG U G GUCAG...GCC-3'@LB@ GAAAGAUA GAACG CUUACUUC GUAUCC@LB@ \|\|\|\|\|\|\|\| \|\|\|\|: \|\|\|\|\|:\|\| \|\|\|:\|\|@LB@ CUUUCUAU CUUGU GAAUGGAG CAUGGG@LB@3'-AUU...CCAGA A A AUG-5'@LB@ \| \|@LB@ 33 3@LB@@LB@@LB@Energy -12.96 kcal/mol@LB@Hybridization Energy -31.2741 kcal/mol@LB@Unfolding Energy - mRNA 9.51226 kcal/mol@LB@Unfolding Energy - sRNA 8.82263 kcal/mol@LB@@LB@Position - mRNA 194 -- 222@LB@Position - sRNA 4 -- 32@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 25 -- 31@LB@
139	0.005017	0.127	b2603	yfiR	-11.92	0.011246	223 -- 243	1 -- 19	putative periplasmic inhibitor of YfiN activity	_____________222___________________244\n_____________\|_____________________\|\n5'-GUA...ACUGU___________AUUC______UGACG...GUA-3'\n______________UCUUACUUCUG____UCCUGC\n______________\|\|\|\|\|\|:\|\|\|\|____:\|\|\|:\|\n______________AGAAUGGAGAC____GGGAUG\n3'-AUU...CUUGU___________AU________-5'\n_____________\|____________________\|\n_____________20___________________1\n	227 -- 233	9 -- 15	-21.8705 kcal/mol	2.00959 kcal/mol	7.96751 kcal/mol	222 244@LB@ \| \|@LB@5'-GUA...ACUGU AUUC UGACG...GUA-3'@LB@ UCUUACUUCUG UCCUGC@LB@ \|\|\|\|\|\|:\|\|\|\| :\|\|\|:\|@LB@ AGAAUGGAGAC GGGAUG@LB@3'-AUU...CUUGU AU -5'@LB@ \| \|@LB@ 20 1@LB@@LB@@LB@Energy -11.92 kcal/mol@LB@Hybridization Energy -21.8705 kcal/mol@LB@Unfolding Energy - mRNA 2.00959 kcal/mol@LB@Unfolding Energy - sRNA 7.96751 kcal/mol@LB@@LB@Position - mRNA 223 -- 243@LB@Position - sRNA 1 -- 19@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 9 -- 15@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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