Input and runtime details for job 1654565 (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 1654565 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:23:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:24:05 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:25:53 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:26:01 CET 2018
	Job Completed		@ Fri Feb 16 22:26:34 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1654565&toolName=CopraRNA ( 30 days expiry )

Description of the job

FnrS

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
154	0.005979	0.1368	b4136	dsbD	-7.81	0.321864	41 -- 58	35 -- 56	thiol:disulfide interchange protein and activator of DsbC		_____________40______________________59\n_____________\|_______________________\|\n5'-UGC...UUACU___A___________________AAGAA...CGG-3'\n______________GGG_AGGUAAG_C____UGGAGC\n______________:\|\|_\|:\|\|\|\|\|_\|____\|\|\|\|\|\|\n______________UCC_UUCAUUC_G____ACCUCG\n3'-UUU...UUUUU___________U_UUAU______CGUUG...ACG-5'\n_____________\|_______________________\|\n_____________57______________________34\n	45 -- 51	47 -- 53	-17.7247 kcal/mol	5.71782 kcal/mol	4.15888 kcal/mol	40 59@LB@ \| \|@LB@5'-UGC...UUACU A AAGAA...CGG-3'@LB@ GGG AGGUAAG C UGGAGC@LB@ :\|\| \|:\|\|\|\|\| \| \|\|\|\|\|\|@LB@ UCC UUCAUUC G ACCUCG@LB@3'-UUU...UUUUU U UUAU CGUUG...ACG-5'@LB@ \| \|@LB@ 57 34@LB@@LB@@LB@Energy -7.81 kcal/mol@LB@Hybridization Energy -17.7247 kcal/mol@LB@Unfolding Energy - mRNA 5.71782 kcal/mol@LB@Unfolding Energy - sRNA 4.15888 kcal/mol@LB@@LB@Position - mRNA 41 -- 58@LB@Position - sRNA 35 -- 56@LB@Position Seed - mRNA 45 -- 51@LB@Position Seed - sRNA 47 -- 53@LB@
99	0.003254	0.1114	b2839	lysR	-9.43	0.148712	276 -- 282	1 -- 7	transcriptional activator of lysA; autorepressor		_____________275_____283\n_____________\|_______\|\n5'-GGC...CGGCA_______UACAC...CAA-3'\n______________CACCUGC\n______________\|\|\|\|\|\|\|\n______________GUGGACG\n3'-UUU...CGUAA_______-5'\n_____________\|______\|\n_____________8______1\n	276 -- 282	1 -- 7	-13.2779 kcal/mol	1.51062 kcal/mol	2.34039 kcal/mol	275 283@LB@ \| \|@LB@5'-GGC...CGGCA UACAC...CAA-3'@LB@ CACCUGC@LB@ \|\|\|\|\|\|\|@LB@ GUGGACG@LB@3'-UUU...CGUAA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -9.43 kcal/mol@LB@Hybridization Energy -13.2779 kcal/mol@LB@Unfolding Energy - mRNA 1.51062 kcal/mol@LB@Unfolding Energy - sRNA 2.34039 kcal/mol@LB@@LB@Position - mRNA 276 -- 282@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 1 -- 7@LB@
130	0.00465	0.126	b2916	argP	-9.43	0.148863	238 -- 266	47 -- 73	transcriptional regulator for arginine transport and DNA replication genes; replication initiation inhibitor		_____________237___________________________267\n_____________\|_____________________________\|\n5'-GGC...ACUGG__________ACG____C_____UU____CGCGC...CAG-3'\n______________AUGCGGUGAU___UGAA_GAGGA__UGAG\n______________\|\|\|\|:\|\|:\|\|___::\|\|_:\|\|\|\|__\|:\|\|\n______________UACGUCAUUA___GUUU_UUCCU__AUUC\n3'-UUU...CACGA__________A______U_____UC____UGUUA...ACG-5'\n_____________\|_____________________________\|\n_____________74____________________________46\n	240 -- 246	65 -- 71	-19.9139 kcal/mol	5.97985 kcal/mol	4.50495 kcal/mol	237 267@LB@ \| \|@LB@5'-GGC...ACUGG ACG C UU CGCGC...CAG-3'@LB@ AUGCGGUGAU UGAA GAGGA UGAG@LB@ \|\|\|\|:\|\|:\|\| ::\|\| :\|\|\|\| \|:\|\|@LB@ UACGUCAUUA GUUU UUCCU AUUC@LB@3'-UUU...CACGA A U UC UGUUA...ACG-5'@LB@ \| \|@LB@ 74 46@LB@@LB@@LB@Energy -9.43 kcal/mol@LB@Hybridization Energy -19.9139 kcal/mol@LB@Unfolding Energy - mRNA 5.97985 kcal/mol@LB@Unfolding Energy - sRNA 4.50495 kcal/mol@LB@@LB@Position - mRNA 238 -- 266@LB@Position - sRNA 47 -- 73@LB@Position Seed - mRNA 240 -- 246@LB@Position Seed - sRNA 65 -- 71@LB@
4	1.28e-06	0.001128	b0884	infA	-17.67	0.000535	178 -- 264	1 -- 71	translation initiation factor IF-1		_____________177_______________________________________________________________________________________265\n_____________\|_________________________________________________________________________________________\|\n5'-UUU...UUACG________ACCCC______UUAGAUGGCCAA_____________U__AA_____G__A___________AA______CUAA____A___UCCGC...CUG-3'\n______________GUAGUGAU_____AGAGGA____________AG_AAGACAAUAU_GA__UGCAA_GU_CCGUU_CUUGA__CGUUGC____UACC_UGU\n______________\|:\|\|\|:\|\|_____\|:\|\|\|\|____________\|\|_\|\|\|\|\|\|\|\|\|\|_\|\|__:\|\|\|\|_\|:_\|\|:\|:_\|\|\|\|\|__\|\|\|\|\|\|____:\|\|\|_\|\|:\n______________CGUCAUUA_____UUUCCU____________UC_UUCUGUUAUA_CU__GCGUU_CG_GGUAG_GAACU__GCAACG____GUGG_ACG\n3'-UUU...CGAUA________AGUUU____________________A__________C__C______G________C_____________UAA_________-5'\n_____________\|________________________________________________________________________________________\|\n_____________72_______________________________________________________________________________________1\n	214 -- 220	40 -- 46	-55.7119 kcal/mol	17.4656 kcal/mol	20.5786 kcal/mol	177 265@LB@ \| \|@LB@5'-UUU...UUACG ACCCC UUAGAUGGCCAA U AA G A AA CUAA A UCCGC...CUG-3'@LB@ GUAGUGAU AGAGGA AG AAGACAAUAU GA UGCAA GU CCGUU CUUGA CGUUGC UACC UGU@LB@ \|:\|\|\|:\|\| \|:\|\|\|\| \|\| \|\|\|\|\|\|\|\|\|\| \|\| :\|\|\|\| \|: \|\|:\|: \|\|\|\|\| \|\|\|\|\|\| :\|\|\| \|\|:@LB@ CGUCAUUA UUUCCU UC UUCUGUUAUA CU GCGUU CG GGUAG GAACU GCAACG GUGG ACG@LB@3'-UUU...CGAUA AGUUU A C C G C UAA -5'@LB@ \| \|@LB@ 72 1@LB@@LB@@LB@Energy -17.67 kcal/mol@LB@Hybridization Energy -55.7119 kcal/mol@LB@Unfolding Energy - mRNA 17.4656 kcal/mol@LB@Unfolding Energy - sRNA 20.5786 kcal/mol@LB@@LB@Position - mRNA 178 -- 264@LB@Position - sRNA 1 -- 71@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 40 -- 46@LB@
28	0.0001471	0.01851	b0997	torA	-9.78	0.123932	184 -- 203	41 -- 60	trimethylamine N-oxide (TMAO) reductase I catalytic subunit	b3551 b1872	_____________183__________________204\n_____________\|____________________\|\n5'-UAC...GCGAU__________A__A______AACAA...CGC-3'\n______________AAGAAGGAAG_AA_AUAAUG\n______________\|\|:\|\|\|\|\|\|\|_\|\|_\|:\|\|\|:\n______________UUUUUCCUUC_UU_UGUUAU\n3'-UUU...UAAGU__________A__C______ACCUC...ACG-5'\n_____________\|____________________\|\n_____________61___________________40\n	187 -- 193	51 -- 57	-13.1224 kcal/mol	1.37417 kcal/mol	1.96633 kcal/mol	183 204@LB@ \| \|@LB@5'-UAC...GCGAU A A AACAA...CGC-3'@LB@ AAGAAGGAAG AA AUAAUG@LB@ \|\|:\|\|\|\|\|\|\| \|\| \|:\|\|\|:@LB@ UUUUUCCUUC UU UGUUAU@LB@3'-UUU...UAAGU A C ACCUC...ACG-5'@LB@ \| \|@LB@ 61 40@LB@@LB@@LB@Energy -9.78 kcal/mol@LB@Hybridization Energy -13.1224 kcal/mol@LB@Unfolding Energy - mRNA 1.37417 kcal/mol@LB@Unfolding Energy - sRNA 1.96633 kcal/mol@LB@@LB@Position - mRNA 184 -- 203@LB@Position - sRNA 41 -- 60@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 51 -- 57@LB@
145	0.00562	0.1365	b2532	trmJ	-9.44	0.148020	215 -- 233	68 -- 84	tRNA mC32 mU32 2'-O-methyltransferase SAM-dependent		_____________214_________________234\n_____________\|___________________\|\n5'-CGU...AAUAU__G__________G__G__ACGUC...UGU-3'\n______________UC_AAUUGUGCUG_UG_AG\n______________\|\|_\|\|\|\|\|\|\|\|\|:_\|\|_\|\|\n______________AG_UUAACACGAU_AC_UC\n3'-UUU...UGCUU________________G__AUUAA...ACG-5'\n_____________\|___________________\|\n_____________85__________________67\n	221 -- 227	73 -- 79	-16.7979 kcal/mol	3.71432 kcal/mol	3.64047 kcal/mol	214 234@LB@ \| \|@LB@5'-CGU...AAUAU G G G ACGUC...UGU-3'@LB@ UC AAUUGUGCUG UG AG@LB@ \|\| \|\|\|\|\|\|\|\|\|: \|\| \|\|@LB@ AG UUAACACGAU AC UC@LB@3'-UUU...UGCUU G AUUAA...ACG-5'@LB@ \| \|@LB@ 85 67@LB@@LB@@LB@Energy -9.44 kcal/mol@LB@Hybridization Energy -16.7979 kcal/mol@LB@Unfolding Energy - mRNA 3.71432 kcal/mol@LB@Unfolding Energy - sRNA 3.64047 kcal/mol@LB@@LB@Position - mRNA 215 -- 233@LB@Position - sRNA 68 -- 84@LB@Position Seed - mRNA 221 -- 227@LB@Position Seed - sRNA 73 -- 79@LB@
141	0.005411	0.1351	b3260	dusB	-10.20	0.098848	236 -- 254	20 -- 38	tRNA-dihydrouridine synthase B		_____________235_________________255\n_____________\|___________________\|\n5'-ACU...CGCCU__U____________G___GGCAU...GAG-3'\n______________GA_CGCAGCGCCCAU_GCU\n______________\|\|_\|\|\|\|:\|\|\|\|\|\|\|_\|\|\|\n______________CU_GCGUUGCGGGUA_CGA\n3'-UUU...UAUAC__C____________G___ACUGC...ACG-5'\n_____________\|___________________\|\n_____________39__________________19\n	244 -- 250	24 -- 30	-30.8965 kcal/mol	8.5282 kcal/mol	12.1733 kcal/mol	235 255@LB@ \| \|@LB@5'-ACU...CGCCU U G GGCAU...GAG-3'@LB@ GA CGCAGCGCCCAU GCU@LB@ \|\| \|\|\|\|:\|\|\|\|\|\|\| \|\|\|@LB@ CU GCGUUGCGGGUA CGA@LB@3'-UUU...UAUAC C G ACUGC...ACG-5'@LB@ \| \|@LB@ 39 19@LB@@LB@@LB@Energy -10.20 kcal/mol@LB@Hybridization Energy -30.8965 kcal/mol@LB@Unfolding Energy - mRNA 8.5282 kcal/mol@LB@Unfolding Energy - sRNA 12.1733 kcal/mol@LB@@LB@Position - mRNA 236 -- 254@LB@Position - sRNA 20 -- 38@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 24 -- 30@LB@
108	0.003432	0.1114	b3159	yhbV	-7.84	0.318675	148 -- 178	4 -- 39	U32 peptidase family protein		_____________147___________________________________179\n_____________\|_____________________________________\|\n5'-GUG...CCGAA__CA_____A_______U_____________A_____GUAAA...AUC-3'\n______________GG__CGCAA___CCA_C_CUUGGCG___CAU_UCACC\n______________\|\|__\|\|\|\|\|___\|\|\|_\|_\|\|\|\|:\|\|___\|\|\|_\|\|\|\|\|\n______________CC__GCGUU___GGU_G_GAACUGC___GUA_AGUGG\n3'-UUU...UUAUA__UC_____GCG___A_C_______AAC_________ACG-5'\n_____________\|_____________________________________\|\n_____________40____________________________________3\n	163 -- 169	15 -- 21	-29.1995 kcal/mol	6.07879 kcal/mol	15.29 kcal/mol	147 179@LB@ \| \|@LB@5'-GUG...CCGAA CA A U A GUAAA...AUC-3'@LB@ GG CGCAA CCA C CUUGGCG CAU UCACC@LB@ \|\| \|\|\|\|\| \|\|\| \| \|\|\|\|:\|\| \|\|\| \|\|\|\|\|@LB@ CC GCGUU GGU G GAACUGC GUA AGUGG@LB@3'-UUU...UUAUA UC GCG A C AAC ACG-5'@LB@ \| \|@LB@ 40 3@LB@@LB@@LB@Energy -7.84 kcal/mol@LB@Hybridization Energy -29.1995 kcal/mol@LB@Unfolding Energy - mRNA 6.07879 kcal/mol@LB@Unfolding Energy - sRNA 15.29 kcal/mol@LB@@LB@Position - mRNA 148 -- 178@LB@Position - sRNA 4 -- 39@LB@Position Seed - mRNA 163 -- 169@LB@Position Seed - sRNA 15 -- 21@LB@
77	0.00185	0.08273	b2325	yfcL	-11.04	0.061434	190 -- 213	35 -- 57	uncharacterized protein		_____________189______________________214\n_____________\|________________________\|\n5'-AAC...ACAAU______AG________CGC_____UUGAA...GCC-3'\n______________GAGGAA__AAGAUGAU___GGAGU\n______________:\|\|\|\|\|__\|\|\|\|::\|\|___\|\|\|\|:\n______________UUCCUU__UUCUGUUA___CCUCG\n3'-UUU...GUUUU______CA________UA______CGUUG...ACG-5'\n_____________\|________________________\|\n_____________58_______________________34\n	199 -- 205	42 -- 48	-19.5886 kcal/mol	4.3321 kcal/mol	4.1846 kcal/mol	189 214@LB@ \| \|@LB@5'-AAC...ACAAU AG CGC UUGAA...GCC-3'@LB@ GAGGAA AAGAUGAU GGAGU@LB@ :\|\|\|\|\| \|\|\|\|::\|\| \|\|\|\|:@LB@ UUCCUU UUCUGUUA CCUCG@LB@3'-UUU...GUUUU CA UA CGUUG...ACG-5'@LB@ \| \|@LB@ 58 34@LB@@LB@@LB@Energy -11.04 kcal/mol@LB@Hybridization Energy -19.5886 kcal/mol@LB@Unfolding Energy - mRNA 4.3321 kcal/mol@LB@Unfolding Energy - sRNA 4.1846 kcal/mol@LB@@LB@Position - mRNA 190 -- 213@LB@Position - sRNA 35 -- 57@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 42 -- 48@LB@
137	0.005185	0.1333	b2256	arnD	-10.61	0.078275	62 -- 106	20 -- 56	undecaprenyl phosphate-alpha-L-ara4FN deformylase		_____________61____________________________________________107\n_____________\|_____________________________________________\|\n5'-UUC...AUAUC____C____A___UC___AACC____AUCC__________C____GCCUG...AGG-3'\n______________AGGA_GUAG_GCA__GUA____GAGC____GCAAUGCCCA_CGCU\n______________\|\|\|\|_\|\|\|:_:\|\|__:\|\|____\|\|\|\|____\|\|\|\|:\|\|\|\|\|_\|\|\|\|\n______________UCCU_CAUU_UGU__UAU____CUCG____CGUUGCGGGU_GCGA\n3'-UUU...UUUUU____U____C________AC____________________A____ACUGC...ACG-5'\n_____________\|_____________________________________________\|\n_____________57____________________________________________19\n	95 -- 101	25 -- 31	-37.0072 kcal/mol	12.6417 kcal/mol	13.7538 kcal/mol	61 107@LB@ \| \|@LB@5'-UUC...AUAUC C A UC AACC AUCC C GCCUG...AGG-3'@LB@ AGGA GUAG GCA GUA GAGC GCAAUGCCCA CGCU@LB@ \|\|\|\| \|\|\|: :\|\| :\|\| \|\|\|\| \|\|\|\|:\|\|\|\|\| \|\|\|\|@LB@ UCCU CAUU UGU UAU CUCG CGUUGCGGGU GCGA@LB@3'-UUU...UUUUU U C AC A ACUGC...ACG-5'@LB@ \| \|@LB@ 57 19@LB@@LB@@LB@Energy -10.61 kcal/mol@LB@Hybridization Energy -37.0072 kcal/mol@LB@Unfolding Energy - mRNA 12.6417 kcal/mol@LB@Unfolding Energy - sRNA 13.7538 kcal/mol@LB@@LB@Position - mRNA 62 -- 106@LB@Position - sRNA 20 -- 56@LB@Position Seed - mRNA 95 -- 101@LB@Position Seed - sRNA 25 -- 31@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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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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