Input and runtime details for job 5344133 (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 5344133 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:28:43 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:36:11 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 02:15:51 CET 2018
	Post-Processing Finished		@ Sat Feb 17 02:15:58 CET 2018
	Job Completed		@ Sat Feb 17 02:16:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5344133&toolName=CopraRNA ( 30 days expiry )

Description of the job

RybB

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
62	0.003256	0.1843	b1243	oppA	-14.22	0.042360	208 -- 232	1 -- 21	oligopeptide ABC transporter periplasmic binding protein	_____________207_______________________233\n_____________\|_________________________\|\n5'-UGU...GACCA______CC_________UU___A__AGCUG...UCA-3'\n______________ACAUCA__AAGAGAAGU__AGU_GC\n______________\|\|\|\|\|\|__\|\|\|\|:\|\|\|:__\|\|\|_\|\|\n______________UGUAGU__UUCUUUUCG__UCA_CG\n3'-UUU...ACCCC______________________C__-5'\n_____________\|________________________\|\n_____________22_______________________1\n	218 -- 224	7 -- 13	-18.9529 kcal/mol	3.22094 kcal/mol	1.51103 kcal/mol	207 233@LB@ \| \|@LB@5'-UGU...GACCA CC UU A AGCUG...UCA-3'@LB@ ACAUCA AAGAGAAGU AGU GC@LB@ \|\|\|\|\|\| \|\|\|\|:\|\|\|: \|\|\| \|\|@LB@ UGUAGU UUCUUUUCG UCA CG@LB@3'-UUU...ACCCC C -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -14.22 kcal/mol@LB@Hybridization Energy -18.9529 kcal/mol@LB@Unfolding Energy - mRNA 3.22094 kcal/mol@LB@Unfolding Energy - sRNA 1.51103 kcal/mol@LB@@LB@Position - mRNA 208 -- 232@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 218 -- 224@LB@Position Seed - sRNA 7 -- 13@LB@
17	0.0006839	0.1243	b1247	oppF	-10.96	0.191014	264 -- 288	1 -- 22	oligopeptide ABC transporter ATPase	_____________263________________________289\n_____________\|__________________________\|\n5'-GCG...ACUUU__A________U____AAAC______UCUGG...CGC-3'\n______________GA_AUCAAAGA__GGC____AGUGGU\n______________\|\|_\|\|\|\|\|\|\|\|__:\|\|____\|\|\|\|\|:\n______________CU_UAGUUUCU__UCG____UCACCG\n3'-UUU...UACCC__G________UU_____________-5'\n_____________\|_________________________\|\n_____________23________________________1\n	268 -- 274	12 -- 18	-19.2479 kcal/mol	6.74487 kcal/mol	1.54023 kcal/mol	263 289@LB@ \| \|@LB@5'-GCG...ACUUU A U AAAC UCUGG...CGC-3'@LB@ GA AUCAAAGA GGC AGUGGU@LB@ \|\| \|\|\|\|\|\|\|\| :\|\| \|\|\|\|\|:@LB@ CU UAGUUUCU UCG UCACCG@LB@3'-UUU...UACCC G UU -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -10.96 kcal/mol@LB@Hybridization Energy -19.2479 kcal/mol@LB@Unfolding Energy - mRNA 6.74487 kcal/mol@LB@Unfolding Energy - sRNA 1.54023 kcal/mol@LB@@LB@Position - mRNA 264 -- 288@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 12 -- 18@LB@
93	0.00579	0.2147	b1256	ompW	-13.14	0.073154	206 -- 220	1 -- 16	outer membrane protein W	_____________205______________221\n_____________\|________________\|\n5'-GAC...AUGAA____UU__________GGCUU...CUG-3'\n______________AAAG__AA_CAGUGGC\n______________\|\|\|\|__\|\|_\|\|\|\|\|\|\|\n______________UUUC__UU_GUCACCG\n3'-UUU...UGUAG____UU__C_______-5'\n_____________\|_______________\|\n_____________17______________1\n	214 -- 220	1 -- 7	-16.0357 kcal/mol	1.55126 kcal/mol	1.34555 kcal/mol	205 221@LB@ \| \|@LB@5'-GAC...AUGAA UU GGCUU...CUG-3'@LB@ AAAG AA CAGUGGC@LB@ \|\|\|\| \|\| \|\|\|\|\|\|\|@LB@ UUUC UU GUCACCG@LB@3'-UUU...UGUAG UU C -5'@LB@ \| \|@LB@ 17 1@LB@@LB@@LB@Energy -13.14 kcal/mol@LB@Hybridization Energy -16.0357 kcal/mol@LB@Unfolding Energy - mRNA 1.55126 kcal/mol@LB@Unfolding Energy - sRNA 1.34555 kcal/mol@LB@@LB@Position - mRNA 206 -- 220@LB@Position - sRNA 1 -- 16@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 1 -- 7@LB@
179	0.01303	0.2504	b1276	acnA	-14.81	0.030801	184 -- 199	7 -- 22	aconitate hydratase 1; aconitase A	_____________183______________200\n_____________\|________________\|\n5'-CUU...ACCCU_U______________UAUGU...GCG-3'\n______________G_CAUUAAGGAGGAGC\n______________\|_\|\|\|:\|\|:\|\|::\|\|\|\n______________C_GUAGUUUCUUUUCG\n3'-UUU...UACCC_U______________UCACCG-5'\n_____________\|________________\|\n_____________23_______________6\n	193 -- 199	7 -- 13	-17.7225 kcal/mol	2.31939 kcal/mol	0.590875 kcal/mol	183 200@LB@ \| \|@LB@5'-CUU...ACCCU U UAUGU...GCG-3'@LB@ G CAUUAAGGAGGAGC@LB@ \| \|\|\|:\|\|:\|\|::\|\|\|@LB@ C GUAGUUUCUUUUCG@LB@3'-UUU...UACCC U UCACCG-5'@LB@ \| \|@LB@ 23 6@LB@@LB@@LB@Energy -14.81 kcal/mol@LB@Hybridization Energy -17.7225 kcal/mol@LB@Unfolding Energy - mRNA 2.31939 kcal/mol@LB@Unfolding Energy - sRNA 0.590875 kcal/mol@LB@@LB@Position - mRNA 184 -- 199@LB@Position - sRNA 7 -- 22@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 7 -- 13@LB@
100	0.006296	0.2188	b1321	ycjX	-13.69	0.055797	38 -- 45	18 -- 25	DUF463 family protein puatative P-loop NTPase	_____________37_______46\n_____________\|________\|\n5'-UGA...UAGUA________AGGUC...CAG-3'\n______________GGGGACAU\n______________\|\|\|\|\|\|\|\|\n______________CCCCUGUA\n3'-UUU...UUUUA________GUUUC...CCG-5'\n_____________\|________\|\n_____________26_______17\n	39 -- 45	18 -- 24	-15.5505 kcal/mol	1.21152 kcal/mol	0.65218 kcal/mol	37 46@LB@ \| \|@LB@5'-UGA...UAGUA AGGUC...CAG-3'@LB@ GGGGACAU@LB@ \|\|\|\|\|\|\|\|@LB@ CCCCUGUA@LB@3'-UUU...UUUUA GUUUC...CCG-5'@LB@ \| \|@LB@ 26 17@LB@@LB@@LB@Energy -13.69 kcal/mol@LB@Hybridization Energy -15.5505 kcal/mol@LB@Unfolding Energy - mRNA 1.21152 kcal/mol@LB@Unfolding Energy - sRNA 0.65218 kcal/mol@LB@@LB@Position - mRNA 38 -- 45@LB@Position - sRNA 18 -- 25@LB@Position Seed - mRNA 39 -- 45@LB@Position Seed - sRNA 18 -- 24@LB@
187	0.01374	0.2529	b1344	ttcA	-15.51	0.020761	46 -- 73	1 -- 29	tRNA s(2)C32 thioltransferase iron sulfur cluster protein	_____________45_____________________________74\n_____________\|______________________________\|\n5'-GCU...CAGCC____________G___CUGC_____A____GUAUG...UCA-3'\n______________AAAUGGGG_CAU_AAA_____GCAG_UGGU\n______________\|\|\|\|\|\|\|\|_\|\|\|_\|\|\|_____\|\|\|\|_\|\|\|:\n______________UUUACCCC_GUA_UUU_____CGUC_ACCG\n3'-UUU...GGUGU________U___G___CUUUU_________-5'\n_____________\|_____________________________\|\n_____________30____________________________1\n	47 -- 53	22 -- 28	-26.0543 kcal/mol	8.02666 kcal/mol	2.51907 kcal/mol	45 74@LB@ \| \|@LB@5'-GCU...CAGCC G CUGC A GUAUG...UCA-3'@LB@ AAAUGGGG CAU AAA GCAG UGGU@LB@ \|\|\|\|\|\|\|\| \|\|\| \|\|\| \|\|\|\| \|\|\|:@LB@ UUUACCCC GUA UUU CGUC ACCG@LB@3'-UUU...GGUGU U G CUUUU -5'@LB@ \| \|@LB@ 30 1@LB@@LB@@LB@Energy -15.51 kcal/mol@LB@Hybridization Energy -26.0543 kcal/mol@LB@Unfolding Energy - mRNA 8.02666 kcal/mol@LB@Unfolding Energy - sRNA 2.51907 kcal/mol@LB@@LB@Position - mRNA 46 -- 73@LB@Position - sRNA 1 -- 29@LB@Position Seed - mRNA 47 -- 53@LB@Position Seed - sRNA 22 -- 28@LB@
135	0.009724	0.2504	b1387	paaZ	-12.57	0.095542	174 -- 198	5 -- 30	oxepin-CoA hydrolase and 3-oxo-5 6-dehydrosuberyl-CoA semialdehyde dehydrogenase	_____________173_________________________199\n_____________\|___________________________\|\n5'-UAA...CAACA______U_AA_____U___________CGAUG...AAG-3'\n______________GAAAUG_G__ACAUC___GGAGAGUAG\n______________:\|\|\|\|\|_\|__\|\|\|\|\|___\|:\|:\|\|:\|\|\n______________UUUUAC_C__UGUAG___CUUUUCGUC\n3'-UUU...AGGUG________CC_____UUU_________ACCG-5'\n_____________\|___________________________\|\n_____________31__________________________4\n	192 -- 198	5 -- 11	-19.0129 kcal/mol	3.93627 kcal/mol	2.50278 kcal/mol	173 199@LB@ \| \|@LB@5'-UAA...CAACA U AA U CGAUG...AAG-3'@LB@ GAAAUG G ACAUC GGAGAGUAG@LB@ :\|\|\|\|\| \| \|\|\|\|\| \|:\|:\|\|:\|\|@LB@ UUUUAC C UGUAG CUUUUCGUC@LB@3'-UUU...AGGUG CC UUU ACCG-5'@LB@ \| \|@LB@ 31 4@LB@@LB@@LB@Energy -12.57 kcal/mol@LB@Hybridization Energy -19.0129 kcal/mol@LB@Unfolding Energy - mRNA 3.93627 kcal/mol@LB@Unfolding Energy - sRNA 2.50278 kcal/mol@LB@@LB@Position - mRNA 174 -- 198@LB@Position - sRNA 5 -- 30@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 5 -- 11@LB@
134	0.009704	0.2504	b1444	patD	-10.55	0.224369	279 -- 297	10 -- 25	gamma-aminobutyraldehyde dehydrogenase	_____________278_________________298\n_____________\|___________________\|\n5'-UCG...CAACG_________UUACU_____UUG-3'\n______________GGGGACGUU_____GGAAA\n______________\|\|\|\|\|\|:\|:_____:\|\|\|\|\n______________CCCCUGUAG_____UCUUU\n3'-UUU...UUUUA_________UU________UCGUC...CCG-5'\n_____________\|___________________\|\n_____________26__________________9\n	281 -- 287	17 -- 23	-18.1658 kcal/mol	6.94606 kcal/mol	0.670388 kcal/mol	278 298@LB@ \| \|@LB@5'-UCG...CAACG UUACU UUG-3'@LB@ GGGGACGUU GGAAA@LB@ \|\|\|\|\|\|:\|: :\|\|\|\|@LB@ CCCCUGUAG UCUUU@LB@3'-UUU...UUUUA UU UCGUC...CCG-5'@LB@ \| \|@LB@ 26 9@LB@@LB@@LB@Energy -10.55 kcal/mol@LB@Hybridization Energy -18.1658 kcal/mol@LB@Unfolding Energy - mRNA 6.94606 kcal/mol@LB@Unfolding Energy - sRNA 0.670388 kcal/mol@LB@@LB@Position - mRNA 279 -- 297@LB@Position - sRNA 10 -- 25@LB@Position Seed - mRNA 281 -- 287@LB@Position Seed - sRNA 17 -- 23@LB@
63	0.003337	0.1851	b1453	ansP	-14.01	0.047364	263 -- 293	1 -- 34	L-asparagine transporter	_____________262_________________________________294\n_____________\|___________________________________\|\n5'-GUC...AAUGC________A__________C_________AUG___AAUCGCC-3'\n______________CCACGAAG_GGGG_UAUCA____AAAGCG___GGC\n______________\|\|\|\|:\|\|:_\|\|\|\|_:\|\|\|\|____\|\|\|\|\|:___\|\|\|\n______________GGUGUUUU_CCCC_GUAGU____UUUCGU___CCG\n3'-UUU...CCCGA________A____U_____UUCU______CA____-5'\n_____________\|__________________________________\|\n_____________35_________________________________1\n	263 -- 269	28 -- 34	-31.7064 kcal/mol	13.4305 kcal/mol	4.26884 kcal/mol	262 294@LB@ \| \|@LB@5'-GUC...AAUGC A C AUG AAUCGCC-3'@LB@ CCACGAAG GGGG UAUCA AAAGCG GGC@LB@ \|\|\|\|:\|\|: \|\|\|\| :\|\|\|\| \|\|\|\|\|: \|\|\|@LB@ GGUGUUUU CCCC GUAGU UUUCGU CCG@LB@3'-UUU...CCCGA A U UUCU CA -5'@LB@ \| \|@LB@ 35 1@LB@@LB@@LB@Energy -14.01 kcal/mol@LB@Hybridization Energy -31.7064 kcal/mol@LB@Unfolding Energy - mRNA 13.4305 kcal/mol@LB@Unfolding Energy - sRNA 4.26884 kcal/mol@LB@@LB@Position - mRNA 263 -- 293@LB@Position - sRNA 1 -- 34@LB@Position Seed - mRNA 263 -- 269@LB@Position Seed - sRNA 28 -- 34@LB@
80	0.004856	0.213	b1478	adhP	-8.37	0.463200	263 -- 276	48 -- 59	ethanol-active dehydrogenase/acetaldehyde-active reductase	_____________262____________277\n_____________\|______________\|\n5'-GCA...CGCUC_______CA_____AAGCC...GUU-3'\n______________ACUGAAA__UGGCG\n______________\|\|:\|\|\|\|__\|\|\|\|\|\n______________UGGCUUU__ACCGC\n3'-UUU...GAACU______________CCCAA...CCG-5'\n_____________\|______________\|\n_____________60_____________47\n	263 -- 269	53 -- 59	-14.4135 kcal/mol	2.08604 kcal/mol	3.96136 kcal/mol	262 277@LB@ \| \|@LB@5'-GCA...CGCUC CA AAGCC...GUU-3'@LB@ ACUGAAA UGGCG@LB@ \|\|:\|\|\|\| \|\|\|\|\|@LB@ UGGCUUU ACCGC@LB@3'-UUU...GAACU CCCAA...CCG-5'@LB@ \| \|@LB@ 60 47@LB@@LB@@LB@Energy -8.37 kcal/mol@LB@Hybridization Energy -14.4135 kcal/mol@LB@Unfolding Energy - mRNA 2.08604 kcal/mol@LB@Unfolding Energy - sRNA 3.96136 kcal/mol@LB@@LB@Position - mRNA 263 -- 276@LB@Position - sRNA 48 -- 59@LB@Position Seed - mRNA 263 -- 269@LB@Position Seed - sRNA 53 -- 59@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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