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	Additional homologs
121	0.008566	0.2484	b3466	yhhL	-13.33	0.066537	119 -- 150	1 -- 32	DUF1145 family protein		_____________118_________________________________151\n_____________\|___________________________________\|\n5'-GUU...UUCCA_____C___UCAUU_____________________GGGUC...UUA-3'\n______________GCAAA_UGG_____ACAUC_GGGAAAA__AGUGGC\n______________:\|\|\|\|_\|\|\|_____\|\|\|\|\|_::\|\|\|\|\|__\|\|\|\|\|\|\n______________UGUUU_ACC_____UGUAG_UUCUUUU__UCACCG\n3'-UUU...CGAGG_____U___CC________U_______CG______-5'\n_____________\|__________________________________\|\n_____________33_________________________________1\n	138 -- 144	9 -- 15	-23.4834 kcal/mol	7.61069 kcal/mol	2.53929 kcal/mol	118 151@LB@ \| \|@LB@5'-GUU...UUCCA C UCAUU GGGUC...UUA-3'@LB@ GCAAA UGG ACAUC GGGAAAA AGUGGC@LB@ :\|\|\|\| \|\|\| \|\|\|\|\| ::\|\|\|\|\| \|\|\|\|\|\|@LB@ UGUUU ACC UGUAG UUCUUUU UCACCG@LB@3'-UUU...CGAGG U CC U CG -5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -13.33 kcal/mol@LB@Hybridization Energy -23.4834 kcal/mol@LB@Unfolding Energy - mRNA 7.61069 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 119 -- 150@LB@Position - sRNA 1 -- 32@LB@Position Seed - mRNA 138 -- 144@LB@Position Seed - sRNA 9 -- 15@LB@
122	0.008886	0.2491	b4366	bglJ	-14.76	0.031763	19 -- 32	15 -- 29	bgl operon transcriptional activator		_____________18______________33\n_____________\|_______________\|\n5'-CUG...GUAAA_______________CCAGA...GUA-3'\n______________GGAUGGGG_CAUCAA\n______________::\|\|\|\|\|\|_\|\|\|\|\|\|\n______________UUUACCCC_GUAGUU\n3'-UUU...GGUGU________U______UCUUU...CCG-5'\n_____________\|_______________\|\n_____________30______________14\n	20 -- 26	22 -- 28	-19.2746 kcal/mol	3.84044 kcal/mol	0.677927 kcal/mol	18 33@LB@ \| \|@LB@5'-CUG...GUAAA CCAGA...GUA-3'@LB@ GGAUGGGG CAUCAA@LB@ ::\|\|\|\|\|\| \|\|\|\|\|\|@LB@ UUUACCCC GUAGUU@LB@3'-UUU...GGUGU U UCUUU...CCG-5'@LB@ \| \|@LB@ 30 14@LB@@LB@@LB@Energy -14.76 kcal/mol@LB@Hybridization Energy -19.2746 kcal/mol@LB@Unfolding Energy - mRNA 3.84044 kcal/mol@LB@Unfolding Energy - sRNA 0.677927 kcal/mol@LB@@LB@Position - mRNA 19 -- 32@LB@Position - sRNA 15 -- 29@LB@Position Seed - mRNA 20 -- 26@LB@Position Seed - sRNA 22 -- 28@LB@
123	0.008923	0.2491	b3243	aaeR	-15.21	0.024673	72 -- 99	1 -- 34	transcriptional regulator for aaeXAB operon		_____________71_________________________________100\n_____________\|__________________________________\|\n5'-AAC...UGUCG________AA__________________C_____GAGAG...UCA-3'\n______________CCGCAGAG___GGGCAU____GGAAAGC_G_GGC\n______________\|\|:\|\|:\|:___\|\|:\|\|\|____\|:\|\|\|\|\|_\|_\|\|\|\n______________GGUGUUUU___CCUGUA____CUUUUCG_C_CCG\n3'-UUU...CCCGA________ACC______GUUU_______U_A___-5'\n_____________\|_________________________________\|\n_____________35________________________________1\n	88 -- 94	7 -- 13	-28.4227 kcal/mol	8.94529 kcal/mol	4.26884 kcal/mol	71 100@LB@ \| \|@LB@5'-AAC...UGUCG AA C GAGAG...UCA-3'@LB@ CCGCAGAG GGGCAU GGAAAGC G GGC@LB@ \|\|:\|\|:\|: \|\|:\|\|\| \|:\|\|\|\|\| \| \|\|\|@LB@ GGUGUUUU CCUGUA CUUUUCG C CCG@LB@3'-UUU...CCCGA ACC GUUU U A -5'@LB@ \| \|@LB@ 35 1@LB@@LB@@LB@Energy -15.21 kcal/mol@LB@Hybridization Energy -28.4227 kcal/mol@LB@Unfolding Energy - mRNA 8.94529 kcal/mol@LB@Unfolding Energy - sRNA 4.26884 kcal/mol@LB@@LB@Position - mRNA 72 -- 99@LB@Position - sRNA 1 -- 34@LB@Position Seed - mRNA 88 -- 94@LB@Position Seed - sRNA 7 -- 13@LB@
124	0.008958	0.2491	b0124	gcd	-13.85	0.051383	179 -- 193	48 -- 62	glucose dehydrogenase		_____________178_____________194\n_____________\|_______________\|\n5'-UAA...AUUAA_______________UCUCU...GGC-3'\n______________UGAAUUGAAAUGGUG\n______________\|\|\|\|::\|\|\|\|\|\|\|:\|\n______________ACUUGGCUUUACCGC\n3'-UUU...UUGGA_______________CCCAA...CCG-5'\n_____________\|_______________\|\n_____________63______________47\n	187 -- 193	48 -- 54	-20.4838 kcal/mol	2.67361 kcal/mol	3.96136 kcal/mol	178 194@LB@ \| \|@LB@5'-UAA...AUUAA UCUCU...GGC-3'@LB@ UGAAUUGAAAUGGUG@LB@ \|\|\|\|::\|\|\|\|\|\|\|:\|@LB@ ACUUGGCUUUACCGC@LB@3'-UUU...UUGGA CCCAA...CCG-5'@LB@ \| \|@LB@ 63 47@LB@@LB@@LB@Energy -13.85 kcal/mol@LB@Hybridization Energy -20.4838 kcal/mol@LB@Unfolding Energy - mRNA 2.67361 kcal/mol@LB@Unfolding Energy - sRNA 3.96136 kcal/mol@LB@@LB@Position - mRNA 179 -- 193@LB@Position - sRNA 48 -- 62@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 48 -- 54@LB@
125	0.009022	0.2491	b0658	ybeX	-16.01	0.015431	14 -- 34	5 -- 21	putative ion transport		_____________13____________________35\n_____________\|_____________________\|\n5'-UUA...CGAUC__________UGAC_______AAGAA...ACC-3'\n______________ACAUCGAAGA____GAAGCAG\n______________\|\|\|\|\|:\|\|\|\|____:\|\|\|\|\|\|\n______________UGUAGUUUCU____UUUCGUC\n3'-UUU...ACCCC_____________________ACCG-5'\n_____________\|_____________________\|\n_____________22____________________4\n	28 -- 34	5 -- 11	-20.2475 kcal/mol	2.73159 kcal/mol	1.5073 kcal/mol	13 35@LB@ \| \|@LB@5'-UUA...CGAUC UGAC AAGAA...ACC-3'@LB@ ACAUCGAAGA GAAGCAG@LB@ \|\|\|\|\|:\|\|\|\| :\|\|\|\|\|\|@LB@ UGUAGUUUCU UUUCGUC@LB@3'-UUU...ACCCC ACCG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -16.01 kcal/mol@LB@Hybridization Energy -20.2475 kcal/mol@LB@Unfolding Energy - mRNA 2.73159 kcal/mol@LB@Unfolding Energy - sRNA 1.5073 kcal/mol@LB@@LB@Position - mRNA 14 -- 34@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 28 -- 34@LB@Position Seed - sRNA 5 -- 11@LB@
126	0.009112	0.2491	b0299	insF1	-12.99	0.078544	136 -- 158	1 -- 32	IS3 transposase B	b0372 b0541 b1026 b2089 b3558	_____________135______________________________159\n_____________\|________________________________\|\n5'-ACU...AGCUG______C_________________________UAUCC...GUC-3'\n______________GCAGAA__GGGAU______GAAGAGC__UGGC\n______________:\|\|:\|\|__\|\|\|\|:______\|\|\|:\|\|\|__\|\|\|\|\n______________UGUUUU__CCCUG______CUUUUCG__ACCG\n3'-UUU...CGAGG______AC_____UAGUUU_______UC____-5'\n_____________\|_______________________________\|\n_____________33______________________________1\n	148 -- 154	7 -- 13	-22.7833 kcal/mol	7.25293 kcal/mol	2.53929 kcal/mol	135 159@LB@ \| \|@LB@5'-ACU...AGCUG C UAUCC...GUC-3'@LB@ GCAGAA GGGAU GAAGAGC UGGC@LB@ :\|\|:\|\| \|\|\|\|: \|\|\|:\|\|\| \|\|\|\|@LB@ UGUUUU CCCUG CUUUUCG ACCG@LB@3'-UUU...CGAGG AC UAGUUU UC -5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -12.99 kcal/mol@LB@Hybridization Energy -22.7833 kcal/mol@LB@Unfolding Energy - mRNA 7.25293 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 136 -- 158@LB@Position - sRNA 1 -- 32@LB@Position Seed - mRNA 148 -- 154@LB@Position Seed - sRNA 7 -- 13@LB@
127	0.009277	0.2491	b2781	mazG	-12.70	0.090074	53 -- 69	8 -- 24	nucleoside triphosphate pyrophosphohydrolase		_____________52________________70\n_____________\|_________________\|\n5'-UGA...CAAGA__A___A__________AACAG...CGC-3'\n______________GG_GCA_CGAAGAAAGG\n______________\|\|_:\|\|_\|:\|\|\|\|\|\|:\|\n______________CC_UGU_GUUUCUUUUC\n3'-UUU...UUUAC__C___A__________GUCACCG-5'\n_____________\|_________________\|\n_____________25________________7\n	63 -- 69	8 -- 14	-16.258 kcal/mol	2.86814 kcal/mol	0.688982 kcal/mol	52 70@LB@ \| \|@LB@5'-UGA...CAAGA A A AACAG...CGC-3'@LB@ GG GCA CGAAGAAAGG@LB@ \|\| :\|\| \|:\|\|\|\|\|\|:\|@LB@ CC UGU GUUUCUUUUC@LB@3'-UUU...UUUAC C A GUCACCG-5'@LB@ \| \|@LB@ 25 7@LB@@LB@@LB@Energy -12.70 kcal/mol@LB@Hybridization Energy -16.258 kcal/mol@LB@Unfolding Energy - mRNA 2.86814 kcal/mol@LB@Unfolding Energy - sRNA 0.688982 kcal/mol@LB@@LB@Position - mRNA 53 -- 69@LB@Position - sRNA 8 -- 24@LB@Position Seed - mRNA 63 -- 69@LB@Position Seed - sRNA 8 -- 14@LB@
128	0.00928	0.2491	b0491	fetB	-12.70	0.090276	178 -- 195	1 -- 17	iron export ABC transporter permease; peroxide resistance protein		_____________177________________196\n_____________\|__________________\|\n5'-GCC...CAUGC________U____GAA__ACGCU...AGA-3'\n______________CGGAGAAA_GCAG___GC\n______________\|::\|\|\|\|\|_\|\|\|\|___\|\|\n______________GUUUCUUU_CGUC___CG\n3'-UUU...CUGUA________U____AC___-5'\n_____________\|_________________\|\n_____________18________________1\n	179 -- 185	10 -- 16	-17.1669 kcal/mol	3.03232 kcal/mol	1.43853 kcal/mol	177 196@LB@ \| \|@LB@5'-GCC...CAUGC U GAA ACGCU...AGA-3'@LB@ CGGAGAAA GCAG GC@LB@ \|::\|\|\|\|\| \|\|\|\| \|\|@LB@ GUUUCUUU CGUC CG@LB@3'-UUU...CUGUA U AC -5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -12.70 kcal/mol@LB@Hybridization Energy -17.1669 kcal/mol@LB@Unfolding Energy - mRNA 3.03232 kcal/mol@LB@Unfolding Energy - sRNA 1.43853 kcal/mol@LB@@LB@Position - mRNA 178 -- 195@LB@Position - sRNA 1 -- 17@LB@Position Seed - mRNA 179 -- 185@LB@Position Seed - sRNA 10 -- 16@LB@
129	0.009293	0.2491	b0428	cyoE	-12.51	0.098557	18 -- 26	1 -- 9	protoheme IX farnesyltransferase		_____________17________27\n_____________\|_________\|\n5'-GGA...GCAAU_________ACAGG...GCA-3'\n______________GGCAGUGGU\n______________:\|\|\|\|\|\|\|:\n______________UCGUCACCG\n3'-UUU...UCUUU_________-5'\n_____________\|________\|\n_____________10_______1\n	20 -- 26	1 -- 7	-15.8954 kcal/mol	2.13019 kcal/mol	1.2588 kcal/mol	17 27@LB@ \| \|@LB@5'-GGA...GCAAU ACAGG...GCA-3'@LB@ GGCAGUGGU@LB@ :\|\|\|\|\|\|\|:@LB@ UCGUCACCG@LB@3'-UUU...UCUUU -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -12.51 kcal/mol@LB@Hybridization Energy -15.8954 kcal/mol@LB@Unfolding Energy - mRNA 2.13019 kcal/mol@LB@Unfolding Energy - sRNA 1.2588 kcal/mol@LB@@LB@Position - mRNA 18 -- 26@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 20 -- 26@LB@Position Seed - sRNA 1 -- 7@LB@
130	0.009344	0.2491	b2840	ygeA	-9.74	0.301486	266 -- 295	2 -- 29	Asp/Glu_racemase family protein		_____________265____________________________296\n_____________\|______________________________\|\n5'-AAA...UUGAU_____AA_________C__C___UU_____GCUUC-3'\n______________AAAUG__GGCAUUAAA_AG_GGC__GGUGG\n______________\|\|\|\|\|__\|:\|\|\|:\|\|\|_\|:_:\|\|__:\|\|\|\|\n______________UUUAC__CUGUAGUUU_UU_UCG__UCACC\n3'-UUU...GGUGU_____CC_________C__U__________G-5'\n_____________\|______________________________\|\n_____________30_____________________________1\n	275 -- 281	14 -- 20	-20.8158 kcal/mol	8.56062 kcal/mol	2.51906 kcal/mol	265 296@LB@ \| \|@LB@5'-AAA...UUGAU AA C C UU GCUUC-3'@LB@ AAAUG GGCAUUAAA AG GGC GGUGG@LB@ \|\|\|\|\| \|:\|\|\|:\|\|\| \|: :\|\| :\|\|\|\|@LB@ UUUAC CUGUAGUUU UU UCG UCACC@LB@3'-UUU...GGUGU CC C U G-5'@LB@ \| \|@LB@ 30 1@LB@@LB@@LB@Energy -9.74 kcal/mol@LB@Hybridization Energy -20.8158 kcal/mol@LB@Unfolding Energy - mRNA 8.56062 kcal/mol@LB@Unfolding Energy - sRNA 2.51906 kcal/mol@LB@@LB@Position - mRNA 266 -- 295@LB@Position - sRNA 2 -- 29@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 14 -- 20@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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