Input and runtime details for job 6793193 (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 6793193 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:27:03 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:32 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:26:02 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:26:10 CET 2018
	Job Completed		@ Fri Feb 16 21:26:45 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6793193&toolName=CopraRNA ( 30 days expiry )

Description of the job

RprA

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
1	5.015e-10	1.765e-06	b0680	glnS	-23.71	0.000006	155 -- 198	34 -- 77	glutamyl-tRNA synthetase	_____________154___________________________________________199\n_____________\|_____________________________________________\|\n5'-UGC...CUUAU_____C______C__U__A________A_____U_A___A_____CGAUG...CGC-3'\n______________AAGAU_AUACGC_GU_AU_CGUUGUUU_CGCUU_G_GGA__UCCA\n______________\|\|\|\|:_\|:\|\|:\|_\|:_\|\|_\|\|\|\|\|\|\|\|_\|:\|\|:_\|_\|\|\|__\|\|\|\|\n______________UUCUG_UGUGUG_CG_UA_GCAACAAA_GUGAG_C_CCU__AGGU\n3'-UUU...CCCGU_____A______U__U__A______________U_C___AA____ACGAA...GCA-5'\n_____________\|_____________________________________________\|\n_____________78____________________________________________33\n	175 -- 181	51 -- 57	-34.8912 kcal/mol	6.37021 kcal/mol	4.81601 kcal/mol	154 199@LB@ \| \|@LB@5'-UGC...CUUAU C C U A A U A A CGAUG...CGC-3'@LB@ AAGAU AUACGC GU AU CGUUGUUU CGCUU G GGA UCCA@LB@ \|\|\|\|: \|:\|\|:\| \|: \|\| \|\|\|\|\|\|\|\| \|:\|\|: \| \|\|\| \|\|\|\|@LB@ UUCUG UGUGUG CG UA GCAACAAA GUGAG C CCU AGGU@LB@3'-UUU...CCCGU A U U A U C AA ACGAA...GCA-5'@LB@ \| \|@LB@ 78 33@LB@@LB@@LB@Energy -23.71 kcal/mol@LB@Hybridization Energy -34.8912 kcal/mol@LB@Unfolding Energy - mRNA 6.37021 kcal/mol@LB@Unfolding Energy - sRNA 4.81601 kcal/mol@LB@@LB@Position - mRNA 155 -- 198@LB@Position - sRNA 34 -- 77@LB@Position Seed - mRNA 175 -- 181@LB@Position Seed - sRNA 51 -- 57@LB@
2	1.464e-07	0.0002576	b2741	rpoS	-16.90	0.006155	67 -- 107	33 -- 71	RNA polymerase sigma S (sigma 38) factor	_____________66______________________________________________108\n_____________\|_______________________________________________\|\n5'-CGG...GUUCA______UU___UUUUGAA______________A_______AA_____AAACC...AGG-3'\n______________ACACGC__GCA_______AUUCGUU_____AC__AGGGGA__UCCGU\n______________\|\|\|\|:\|__\|\|\|_______\|\|\|\|\|\|\|_____\|\|__\|\|\|\|\|\|__\|\|\|:\|\n______________UGUGUG__CGU_______UAAGCAA_____UG__UCCCCU__AGGUA\n3'-UUU...UCUGA______U__________________CAAAG__AG______AA_____CGAAU...GCA-5'\n_____________\|_______________________________________________\|\n_____________72______________________________________________32\n	85 -- 91	55 -- 61	-29.972 kcal/mol	8.28292 kcal/mol	4.7924 kcal/mol	66 108@LB@ \| \|@LB@5'-CGG...GUUCA UU UUUUGAA A AA AAACC...AGG-3'@LB@ ACACGC GCA AUUCGUU AC AGGGGA UCCGU@LB@ \|\|\|\|:\| \|\|\| \|\|\|\|\|\|\| \|\| \|\|\|\|\|\| \|\|\|:\|@LB@ UGUGUG CGU UAAGCAA UG UCCCCU AGGUA@LB@3'-UUU...UCUGA U CAAAG AG AA CGAAU...GCA-5'@LB@ \| \|@LB@ 72 32@LB@@LB@@LB@Energy -16.90 kcal/mol@LB@Hybridization Energy -29.972 kcal/mol@LB@Unfolding Energy - mRNA 8.28292 kcal/mol@LB@Unfolding Energy - sRNA 4.7924 kcal/mol@LB@@LB@Position - mRNA 67 -- 107@LB@Position - sRNA 33 -- 71@LB@Position Seed - mRNA 85 -- 91@LB@Position Seed - sRNA 55 -- 61@LB@
3	3.356e-06	0.003937	b3724	phoU	-15.84	0.012477	157 -- 192	43 -- 78	negative regulator of PhoR/PhoB two-component regulator	_____________156____________________________________193\n_____________\|______________________________________\|\n5'-ACC...AAACA______________C_________ACGG__G_______AGUGC...AGC-3'\n______________GAAGACUACAU_CA_CGG_UCGUU____UU_AUUCAGG\n______________:\|\|\|\|\|\|\|\|\|:_\|\|_\|::_\|\|\|\|\|____\|\|_\|:\|\|\|\|\|\n______________UUUCUGAUGUG_GU_GUU_AGCAA____AA_UGAGUCC\n3'-UUU...ACCCG___________U__C___A_____CA____G_______CCUAA...GCA-5'\n_____________\|______________________________________\|\n_____________79_____________________________________42\n	186 -- 192	43 -- 49	-29.823 kcal/mol	9.63349 kcal/mol	4.35315 kcal/mol	156 193@LB@ \| \|@LB@5'-ACC...AAACA C ACGG G AGUGC...AGC-3'@LB@ GAAGACUACAU CA CGG UCGUU UU AUUCAGG@LB@ :\|\|\|\|\|\|\|\|\|: \|\| \|:: \|\|\|\|\| \|\| \|:\|\|\|\|\|@LB@ UUUCUGAUGUG GU GUU AGCAA AA UGAGUCC@LB@3'-UUU...ACCCG U C A CA G CCUAA...GCA-5'@LB@ \| \|@LB@ 79 42@LB@@LB@@LB@Energy -15.84 kcal/mol@LB@Hybridization Energy -29.823 kcal/mol@LB@Unfolding Energy - mRNA 9.63349 kcal/mol@LB@Unfolding Energy - sRNA 4.35315 kcal/mol@LB@@LB@Position - mRNA 157 -- 192@LB@Position - sRNA 43 -- 78@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 43 -- 49@LB@
4	8.9e-06	0.006694	b3281	aroE	-13.87	0.039990	230 -- 259	45 -- 75	dehydroshikimate reductase NAD(P)-binding	_____________229_____________________________260\n_____________\|_______________________________\|\n5'-UUU...AAUCC___A__C________A___CCA_________UCAGC...AUG-3'\n______________GAU_GC_CACAGCAA_UCG____UUCAUUCA\n______________\|\|:_:\|_\|\|\|\|\|\|\|\|_\|\|\|____\|\|\|\|:\|\|\|\n______________CUG_UG_GUGUCGUU_AGC____AAGUGAGU\n3'-UUU...CGUUU___A__U________A___AACA________CCCCU...GCA-5'\n_____________\|_______________________________\|\n_____________76______________________________44\n	253 -- 259	45 -- 51	-26.2723 kcal/mol	8.66309 kcal/mol	3.74078 kcal/mol	229 260@LB@ \| \|@LB@5'-UUU...AAUCC A C A CCA UCAGC...AUG-3'@LB@ GAU GC CACAGCAA UCG UUCAUUCA@LB@ \|\|: :\| \|\|\|\|\|\|\|\| \|\|\| \|\|\|\|:\|\|\|@LB@ CUG UG GUGUCGUU AGC AAGUGAGU@LB@3'-UUU...CGUUU A U A AACA CCCCU...GCA-5'@LB@ \| \|@LB@ 76 44@LB@@LB@@LB@Energy -13.87 kcal/mol@LB@Hybridization Energy -26.2723 kcal/mol@LB@Unfolding Energy - mRNA 8.66309 kcal/mol@LB@Unfolding Energy - sRNA 3.74078 kcal/mol@LB@@LB@Position - mRNA 230 -- 259@LB@Position - sRNA 45 -- 75@LB@Position Seed - mRNA 253 -- 259@LB@Position Seed - sRNA 45 -- 51@LB@
5	9.512e-06	0.006694	b4006	purH	-17.40	0.004319	188 -- 204	31 -- 46	IMP cyclohydrolase and phosphoribosylaminoimidazolecarboxamide formyltransferase	_____________187_______________205\n_____________\|_________________\|\n5'-GUA...AAAUC__________A______AACAA...AGC-3'\n______________CAGGGGAUUU_CCAUGC\n______________\|\|\|\|\|\|\|\|\|\|_\|\|\|\|\|\|\n______________GUCCCCUAAA_GGUACG\n3'-UUU...AGUGA_________________AAUAU...GCA-5'\n_____________\|_________________\|\n_____________47________________30\n	191 -- 197	37 -- 43	-27.6893 kcal/mol	6.33421 kcal/mol	3.95768 kcal/mol	187 205@LB@ \| \|@LB@5'-GUA...AAAUC A AACAA...AGC-3'@LB@ CAGGGGAUUU CCAUGC@LB@ \|\|\|\|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ GUCCCCUAAA GGUACG@LB@3'-UUU...AGUGA AAUAU...GCA-5'@LB@ \| \|@LB@ 47 30@LB@@LB@@LB@Energy -17.40 kcal/mol@LB@Hybridization Energy -27.6893 kcal/mol@LB@Unfolding Energy - mRNA 6.33421 kcal/mol@LB@Unfolding Energy - sRNA 3.95768 kcal/mol@LB@@LB@Position - mRNA 188 -- 204@LB@Position - sRNA 31 -- 46@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 37 -- 43@LB@
6	1.32e-05	0.00774	b0475	hemH	-21.46	0.000115	123 -- 162	34 -- 75	ferrochelatase	_____________122__________________________________________163\n_____________\|____________________________________________\|\n5'-CGG...GAUUU___CU_U__________A___CUUC________CU_________CUACA...GCG-3'\n______________GAC__C_CACAGCAAUU_GUU____UUC_CUCA_____UUUCCG\n______________\|\|\|__\|_\|\|\|\|\|\|\|\|\|\|_\|\|\|____\|\|\|_\|\|\|\|_____\|\|\|\|\|:\n______________CUG__G_GUGUCGUUAA_CAA____AAG_GAGU_____AAAGGU\n3'-UUU...CGUUU___AU_U__________G___CA_____U____CCCCU______ACGAA...GCA-5'\n_____________\|____________________________________________\|\n_____________76___________________________________________33\n	133 -- 139	59 -- 65	-29.8744 kcal/mol	3.60304 kcal/mol	4.816 kcal/mol	122 163@LB@ \| \|@LB@5'-CGG...GAUUU CU U A CUUC CU CUACA...GCG-3'@LB@ GAC C CACAGCAAUU GUU UUC CUCA UUUCCG@LB@ \|\|\| \| \|\|\|\|\|\|\|\|\|\| \|\|\| \|\|\| \|\|\|\| \|\|\|\|\|:@LB@ CUG G GUGUCGUUAA CAA AAG GAGU AAAGGU@LB@3'-UUU...CGUUU AU U G CA U CCCCU ACGAA...GCA-5'@LB@ \| \|@LB@ 76 33@LB@@LB@@LB@Energy -21.46 kcal/mol@LB@Hybridization Energy -29.8744 kcal/mol@LB@Unfolding Energy - mRNA 3.60304 kcal/mol@LB@Unfolding Energy - sRNA 4.816 kcal/mol@LB@@LB@Position - mRNA 123 -- 162@LB@Position - sRNA 34 -- 75@LB@Position Seed - mRNA 133 -- 139@LB@Position Seed - sRNA 59 -- 65@LB@
7	1.819e-05	0.009142	b1849	purT	-22.68	0.000026	168 -- 199	33 -- 74	phosphoribosylglycinamide formyltransferase 2	_____________167________________________________________200\n_____________\|__________________________________________\|\n5'-UUU...UUUAU________________AA__________________A_____UAUGA...GUC-3'\n______________ACUGCGCGCGG_AAUU___________UCAGGGGAU_UUCGU\n______________\|\|\|:\|:\|:\|:\|_\|\|\|\|___________\|\|\|\|\|\|\|\|\|_\|:\|:\|\n______________UGAUGUGUGUC_UUAA___________AGUCCCCUA_AGGUA\n3'-UUU...GUUUC___________G____GCAACAAAGUG_________A_____CGAAU...GCA-5'\n_____________\|__________________________________________\|\n_____________75_________________________________________32\n	187 -- 193	39 -- 45	-34.2979 kcal/mol	6.80622 kcal/mol	4.81602 kcal/mol	167 200@LB@ \| \|@LB@5'-UUU...UUUAU AA A UAUGA...GUC-3'@LB@ ACUGCGCGCGG AAUU UCAGGGGAU UUCGU@LB@ \|\|\|:\|:\|:\|:\| \|\|\|\| \|\|\|\|\|\|\|\|\| \|:\|:\|@LB@ UGAUGUGUGUC UUAA AGUCCCCUA AGGUA@LB@3'-UUU...GUUUC G GCAACAAAGUG A CGAAU...GCA-5'@LB@ \| \|@LB@ 75 32@LB@@LB@@LB@Energy -22.68 kcal/mol@LB@Hybridization Energy -34.2979 kcal/mol@LB@Unfolding Energy - mRNA 6.80622 kcal/mol@LB@Unfolding Energy - sRNA 4.81602 kcal/mol@LB@@LB@Position - mRNA 168 -- 199@LB@Position - sRNA 33 -- 74@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 39 -- 45@LB@
8	3.984e-05	0.01752	b2752	cysD	-11.53	0.128779	103 -- 132	45 -- 74	sulfate adenylyltransferase subunit 2	_____________102____________________________133\n_____________\|______________________________\|\n5'-GCC...AAGGA_____U___UC_____G__AA_________UUCUC...UCU-3'\n______________ACUAC_CAU__UAAUU_GU__UUUCAUUCG\n______________\|\|\|\|\|_\|\|:__:\|\|\|\|_\|\|__\|\|\|\|\|:\|\|:\n______________UGAUG_GUG__GUUAA_CA__AAAGUGAGU\n3'-UUU...GUUUC_____U___UC_____G__AC_________CCCCU...GCA-5'\n_____________\|______________________________\|\n_____________75_____________________________44\n	126 -- 132	45 -- 51	-20.8412 kcal/mol	5.57115 kcal/mol	3.74056 kcal/mol	102 133@LB@ \| \|@LB@5'-GCC...AAGGA U UC G AA UUCUC...UCU-3'@LB@ ACUAC CAU UAAUU GU UUUCAUUCG@LB@ \|\|\|\|\| \|\|: :\|\|\|\| \|\| \|\|\|\|\|:\|\|:@LB@ UGAUG GUG GUUAA CA AAAGUGAGU@LB@3'-UUU...GUUUC U UC G AC CCCCU...GCA-5'@LB@ \| \|@LB@ 75 44@LB@@LB@@LB@Energy -11.53 kcal/mol@LB@Hybridization Energy -20.8412 kcal/mol@LB@Unfolding Energy - mRNA 5.57115 kcal/mol@LB@Unfolding Energy - sRNA 3.74056 kcal/mol@LB@@LB@Position - mRNA 103 -- 132@LB@Position - sRNA 45 -- 74@LB@Position Seed - mRNA 126 -- 132@LB@Position Seed - sRNA 45 -- 51@LB@
9	4.743e-05	0.01855	b1204	pth	-17.38	0.004387	162 -- 190	43 -- 74	peptidyl-tRNA hydrolase	_____________161_______________________________191\n_____________\|_________________________________\|\n5'-UGG...AGUAA________________A_____ACA________ACAAA...AGC-3'\n______________ACUACGCGC__CAGUU___UGU___CACUCAGG\n______________\|\|\|\|\|:\|:\|__\|\|:\|\|___\|\|\|___\|\|\|\|\|\|\|\|\n______________UGAUGUGUG__GUUAA___ACA___GUGAGUCC\n3'-UUU...GUUUC_________UC_____GCA___AA_________CCUAA...GCA-5'\n_____________\|_________________________________\|\n_____________75________________________________42\n	184 -- 190	43 -- 49	-27.969 kcal/mol	6.24318 kcal/mol	4.35222 kcal/mol	161 191@LB@ \| \|@LB@5'-UGG...AGUAA A ACA ACAAA...AGC-3'@LB@ ACUACGCGC CAGUU UGU CACUCAGG@LB@ \|\|\|\|\|:\|:\| \|\|:\|\| \|\|\| \|\|\|\|\|\|\|\|@LB@ UGAUGUGUG GUUAA ACA GUGAGUCC@LB@3'-UUU...GUUUC UC GCA AA CCUAA...GCA-5'@LB@ \| \|@LB@ 75 42@LB@@LB@@LB@Energy -17.38 kcal/mol@LB@Hybridization Energy -27.969 kcal/mol@LB@Unfolding Energy - mRNA 6.24318 kcal/mol@LB@Unfolding Energy - sRNA 4.35222 kcal/mol@LB@@LB@Position - mRNA 162 -- 190@LB@Position - sRNA 43 -- 74@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 43 -- 49@LB@
10	6.564e-05	0.0231	b3458	livK	-17.14	0.005196	153 -- 196	35 -- 71	leucine transporter subunit	_____________152____________________________________________197\n_____________\|______________________________________________\|\n5'-UGU...UGUUA______AAAAACAA_____CACAACA______GAAU__________GACUA...CGA-3'\n______________ACACAU________AGCAA_________UCAC____GGGGAUUUUU\n______________\|\|\|\|\|:________\|\|\|\|\|_________\|\|\|\|____\|\|\|\|\|\|\|\|::\n______________UGUGUG________UCGUU_________AGUG____CCCCUAAAGG\n3'-UUU...UCUGA___________________AAGCAACAA____AGU___________UACGA...GCA-5'\n_____________\|______________________________________________\|\n_____________72_____________________________________________34\n	190 -- 196	35 -- 41	-26.3585 kcal/mol	4.43917 kcal/mol	4.78171 kcal/mol	152 197@LB@ \| \|@LB@5'-UGU...UGUUA AAAAACAA CACAACA GAAU GACUA...CGA-3'@LB@ ACACAU AGCAA UCAC GGGGAUUUUU@LB@ \|\|\|\|\|: \|\|\|\|\| \|\|\|\| \|\|\|\|\|\|\|\|::@LB@ UGUGUG UCGUU AGUG CCCCUAAAGG@LB@3'-UUU...UCUGA AAGCAACAA AGU UACGA...GCA-5'@LB@ \| \|@LB@ 72 34@LB@@LB@@LB@Energy -17.14 kcal/mol@LB@Hybridization Energy -26.3585 kcal/mol@LB@Unfolding Energy - mRNA 4.43917 kcal/mol@LB@Unfolding Energy - sRNA 4.78171 kcal/mol@LB@@LB@Position - mRNA 153 -- 196@LB@Position - sRNA 35 -- 71@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 35 -- 41@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)

Job resubmission

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service.

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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