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
168	0.008282	0.1723	b3822	recQ	-12.50	0.081546	124 -- 155	43 -- 77	ATP-dependent DNA helicase	_____________123___________________________________156\n_____________\|_____________________________________\|\n5'-CGC...UCUCA_______AAA____U_______C_________G____CGCUG...UUA-3'\n______________GAGACUA___GCAU_GCAGUUU______UCGC_CAGG\n______________:\|\|\|\|\|\|___:\|\|:_\|\|\|:\|\|:______\|\|:\|_\|\|\|\|\n______________UUCUGAU___UGUG_CGUUAAG______AGUG_GUCC\n3'-UUU...CCCGU_______G______U_______CAACAA____A____CCUAA...GCA-5'\n_____________\|_____________________________________\|\n_____________78____________________________________42\n	139 -- 145	58 -- 64	-25.7534 kcal/mol	8.90299 kcal/mol	4.3531 kcal/mol	123 156@LB@ \| \|@LB@5'-CGC...UCUCA AAA U C G CGCUG...UUA-3'@LB@ GAGACUA GCAU GCAGUUU UCGC CAGG@LB@ :\|\|\|\|\|\| :\|\|: \|\|\|:\|\|: \|\|:\| \|\|\|\|@LB@ UUCUGAU UGUG CGUUAAG AGUG GUCC@LB@3'-UUU...CCCGU G U CAACAA A CCUAA...GCA-5'@LB@ \| \|@LB@ 78 42@LB@@LB@@LB@Energy -12.50 kcal/mol@LB@Hybridization Energy -25.7534 kcal/mol@LB@Unfolding Energy - mRNA 8.90299 kcal/mol@LB@Unfolding Energy - sRNA 4.3531 kcal/mol@LB@@LB@Position - mRNA 124 -- 155@LB@Position - sRNA 43 -- 77@LB@Position Seed - mRNA 139 -- 145@LB@Position Seed - sRNA 58 -- 64@LB@
142	0.006549	0.1605	b3902	rhaD	-9.93	0.251242	192 -- 218	44 -- 69	rhamnulose-1-phosphate aldolase	_____________191_________________________219\n_____________\|___________________________\|\n5'-AGA...CAGGA______AACAUGCAAAACA________UCCUG...UGA-3'\n______________ACACAG_____________UUACUCAG\n______________\|\|\|\|\|\|_____________\|:\|\|\|\|\|\|\n______________UGUGUC_____________AGUGAGUC\n3'-UUU...UGAUG______GUUAAGCAACAA_________CCCUA...GCA-5'\n_____________\|___________________________\|\n_____________70__________________________43\n	212 -- 218	44 -- 50	-16.231 kcal/mol	2.20309 kcal/mol	4.09554 kcal/mol	191 219@LB@ \| \|@LB@5'-AGA...CAGGA AACAUGCAAAACA UCCUG...UGA-3'@LB@ ACACAG UUACUCAG@LB@ \|\|\|\|\|\| \|:\|\|\|\|\|\|@LB@ UGUGUC AGUGAGUC@LB@3'-UUU...UGAUG GUUAAGCAACAA CCCUA...GCA-5'@LB@ \| \|@LB@ 70 43@LB@@LB@@LB@Energy -9.93 kcal/mol@LB@Hybridization Energy -16.231 kcal/mol@LB@Unfolding Energy - mRNA 2.20309 kcal/mol@LB@Unfolding Energy - sRNA 4.09554 kcal/mol@LB@@LB@Position - mRNA 192 -- 218@LB@Position - sRNA 44 -- 69@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 44 -- 50@LB@
85	0.003677	0.1509	b0813	rhtA	-9.71	0.273689	106 -- 123	34 -- 46	threonine and homoserine efflux system	_____________105________________124\n_____________\|__________________\|\n5'-CAG...CAAAA_______AAAUU______ACAAA...CAC-3'\n______________CGGGGGA_____UUUUCA\n______________\|:\|\|\|\|\|_____\|\|\|:\|\|\n______________GUCCCCU_____AAAGGU\n3'-UUU...AGUGA__________________ACGAA...GCA-5'\n_____________\|__________________\|\n_____________47_________________33\n	106 -- 112	40 -- 46	-14.6812 kcal/mol	3.4305 kcal/mol	1.54427 kcal/mol	105 124@LB@ \| \|@LB@5'-CAG...CAAAA AAAUU ACAAA...CAC-3'@LB@ CGGGGGA UUUUCA@LB@ \|:\|\|\|\|\| \|\|\|:\|\|@LB@ GUCCCCU AAAGGU@LB@3'-UUU...AGUGA ACGAA...GCA-5'@LB@ \| \|@LB@ 47 33@LB@@LB@@LB@Energy -9.71 kcal/mol@LB@Hybridization Energy -14.6812 kcal/mol@LB@Unfolding Energy - mRNA 3.4305 kcal/mol@LB@Unfolding Energy - sRNA 1.54427 kcal/mol@LB@@LB@Position - mRNA 106 -- 123@LB@Position - sRNA 34 -- 46@LB@Position Seed - mRNA 106 -- 112@LB@Position Seed - sRNA 40 -- 46@LB@
114	0.005004	0.1545	b0025	ribF	-11.63	0.123109	210 -- 237	43 -- 71	bifunctional riboflavin kinase/FAD synthetase	_____________209___________________________238\n_____________\|_____________________________\|\n5'-UGG...AGCUG__________UACAUAAUC____GC____CCCCG...GCG-3'\n______________AUACGCGGCA__________UCA__CAGG\n______________\|:\|\|:\|:\|\|\|__________\|\|\|__\|\|\|\|\n______________UGUGUGUCGU__________AGU__GUCC\n3'-UUU...UCUGA__________UAAGCAACAA___GA____CCUAA...GCA-5'\n_____________\|_____________________________\|\n_____________72____________________________42\n	213 -- 219	62 -- 68	-21.1915 kcal/mol	5.23887 kcal/mol	4.32409 kcal/mol	209 238@LB@ \| \|@LB@5'-UGG...AGCUG UACAUAAUC GC CCCCG...GCG-3'@LB@ AUACGCGGCA UCA CAGG@LB@ \|:\|\|:\|:\|\|\| \|\|\| \|\|\|\|@LB@ UGUGUGUCGU AGU GUCC@LB@3'-UUU...UCUGA UAAGCAACAA GA CCUAA...GCA-5'@LB@ \| \|@LB@ 72 42@LB@@LB@@LB@Energy -11.63 kcal/mol@LB@Hybridization Energy -21.1915 kcal/mol@LB@Unfolding Energy - mRNA 5.23887 kcal/mol@LB@Unfolding Energy - sRNA 4.32409 kcal/mol@LB@@LB@Position - mRNA 210 -- 237@LB@Position - sRNA 43 -- 71@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 62 -- 68@LB@
88	0.003962	0.1538	b3084	rlmG	-11.78	0.115170	185 -- 197	40 -- 51	23S rRNA m(2)G1835 methyltransferase SAM-dependent	_____________184___________198\n_____________\|_____________\|\n5'-UGU...UUUUA_________A___CCGAU...AAU-3'\n______________UCAUUCAGG_GGG\n______________\|\|\|:\|\|\|\|\|_\|\|:\n______________AGUGAGUCC_CCU\n3'-UUU...AACAA_____________AAAGG...GCA-5'\n_____________\|_____________\|\n_____________52____________39\n	187 -- 193	43 -- 49	-16.9089 kcal/mol	3.37488 kcal/mol	1.76028 kcal/mol	184 198@LB@ \| \|@LB@5'-UGU...UUUUA A CCGAU...AAU-3'@LB@ UCAUUCAGG GGG@LB@ \|\|\|:\|\|\|\|\| \|\|:@LB@ AGUGAGUCC CCU@LB@3'-UUU...AACAA AAAGG...GCA-5'@LB@ \| \|@LB@ 52 39@LB@@LB@@LB@Energy -11.78 kcal/mol@LB@Hybridization Energy -16.9089 kcal/mol@LB@Unfolding Energy - mRNA 3.37488 kcal/mol@LB@Unfolding Energy - sRNA 1.76028 kcal/mol@LB@@LB@Position - mRNA 185 -- 197@LB@Position - sRNA 40 -- 51@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 43 -- 49@LB@
108	0.004771	0.1538	b2594	rluD	-7.24	0.588975	189 -- 206	62 -- 78	23S rRNA pseudouridine(1911 1915 1917) synthase	_____________188________________207\n_____________\|__________________\|\n5'-CCC...ACGAA____C_G___________CAACG...GUU-3'\n______________GAAG_A_UAUAUAUGGCA\n______________:\|\|\|_\|_\|\|:\|:\|::\|\|\|\n______________UUUC_U_AUGUGUGUCGU\n3'-UUU...ACCCG______G___________UAAGC...GCA-5'\n_____________\|__________________\|\n_____________79_________________61\n	200 -- 206	62 -- 68	-13.9289 kcal/mol	3.43926 kcal/mol	3.2555 kcal/mol	188 207@LB@ \| \|@LB@5'-CCC...ACGAA C G CAACG...GUU-3'@LB@ GAAG A UAUAUAUGGCA@LB@ :\|\|\| \| \|\|:\|:\|::\|\|\|@LB@ UUUC U AUGUGUGUCGU@LB@3'-UUU...ACCCG G UAAGC...GCA-5'@LB@ \| \|@LB@ 79 61@LB@@LB@@LB@Energy -7.24 kcal/mol@LB@Hybridization Energy -13.9289 kcal/mol@LB@Unfolding Energy - mRNA 3.43926 kcal/mol@LB@Unfolding Energy - sRNA 3.2555 kcal/mol@LB@@LB@Position - mRNA 189 -- 206@LB@Position - sRNA 62 -- 78@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 62 -- 68@LB@
58	0.002015	0.1223	b0189	rof	-8.06	0.473679	29 -- 61	40 -- 71	modulator of Rho-dependent transcription termination	_____________28_________________________________62\n_____________\|__________________________________\|\n5'-AGG...AGUUA_______A_____A__CG_AAA________C___GACUU...GCG-3'\n______________AUACGCA_GCGGU_CG__G___UCGC_CAG_GGA\n______________\|:\|\|:\|\|_\|\|::\|_\|\|__\|___\|\|:\|_\|\|\|_\|\|\|\n______________UGUGUGU_CGUUA_GC__C___AGUG_GUC_CCU\n3'-UUU...UCUGA_____________A__AA_AA_____A___C___AAAGG...GCA-5'\n_____________\|__________________________________\|\n_____________72_________________________________39\n	29 -- 35	65 -- 71	-25.5885 kcal/mol	12.7864 kcal/mol	4.74818 kcal/mol	28 62@LB@ \| \|@LB@5'-AGG...AGUUA A A CG AAA C GACUU...GCG-3'@LB@ AUACGCA GCGGU CG G UCGC CAG GGA@LB@ \|:\|\|:\|\| \|\|::\| \|\| \| \|\|:\| \|\|\| \|\|\|@LB@ UGUGUGU CGUUA GC C AGUG GUC CCU@LB@3'-UUU...UCUGA A AA AA A C AAAGG...GCA-5'@LB@ \| \|@LB@ 72 39@LB@@LB@@LB@Energy -8.06 kcal/mol@LB@Hybridization Energy -25.5885 kcal/mol@LB@Unfolding Energy - mRNA 12.7864 kcal/mol@LB@Unfolding Energy - sRNA 4.74818 kcal/mol@LB@@LB@Position - mRNA 29 -- 61@LB@Position - sRNA 40 -- 71@LB@Position Seed - mRNA 29 -- 35@LB@Position Seed - sRNA 65 -- 71@LB@
170	0.008354	0.1723	b3294	rplQ	-12.86	0.068031	178 -- 204	31 -- 54	50S ribosomal subunit protein L17	_____________177_________________________205\n_____________\|___________________________\|\n5'-UAU...UUAAG________G__AA____AAGG______GCCAU...UCA-3'\n______________GUUUUACU_AG__GGAU____UCAUGC\n______________\|\|\|\|:\|\|\|_\|\|__\|\|\|\|____:\|\|\|\|\|\n______________CAAAGUGA_UC__CCUA____GGUACG\n3'-UUU...AGCAA________G__C_____AA________AAUAU...GCA-5'\n_____________\|___________________________\|\n_____________55__________________________30\n	179 -- 185	47 -- 53	-21.6424 kcal/mol	4.376 kcal/mol	4.40484 kcal/mol	177 205@LB@ \| \|@LB@5'-UAU...UUAAG G AA AAGG GCCAU...UCA-3'@LB@ GUUUUACU AG GGAU UCAUGC@LB@ \|\|\|\|:\|\|\| \|\| \|\|\|\| :\|\|\|\|\|@LB@ CAAAGUGA UC CCUA GGUACG@LB@3'-UUU...AGCAA G C AA AAUAU...GCA-5'@LB@ \| \|@LB@ 55 30@LB@@LB@@LB@Energy -12.86 kcal/mol@LB@Hybridization Energy -21.6424 kcal/mol@LB@Unfolding Energy - mRNA 4.376 kcal/mol@LB@Unfolding Energy - sRNA 4.40484 kcal/mol@LB@@LB@Position - mRNA 178 -- 204@LB@Position - sRNA 31 -- 54@LB@Position Seed - mRNA 179 -- 185@LB@Position Seed - sRNA 47 -- 53@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@
162	0.007731	0.1668	b4202	rpsR	-9.58	0.287294	60 -- 77	62 -- 76	30S ribosomal subunit protein S18	_____________59_________________78\n_____________\|__________________\|\n5'-CGG...AAACC____CAU___U_______UAACG...UCA-3'\n______________AGGC___UAC_CACAGUA\n______________\|\|:\|___\|\|\|_\|\|\|\|\|:\|\n______________UCUG___AUG_GUGUCGU\n3'-UUU...CCGUU__________U_______UAAGC...GCA-5'\n_____________\|__________________\|\n_____________77_________________61\n	71 -- 77	62 -- 68	-14.2281 kcal/mol	1.39912 kcal/mol	3.25371 kcal/mol	59 78@LB@ \| \|@LB@5'-CGG...AAACC CAU U UAACG...UCA-3'@LB@ AGGC UAC CACAGUA@LB@ \|\|:\| \|\|\| \|\|\|\|\|:\|@LB@ UCUG AUG GUGUCGU@LB@3'-UUU...CCGUU U UAAGC...GCA-5'@LB@ \| \|@LB@ 77 61@LB@@LB@@LB@Energy -9.58 kcal/mol@LB@Hybridization Energy -14.2281 kcal/mol@LB@Unfolding Energy - mRNA 1.39912 kcal/mol@LB@Unfolding Energy - sRNA 3.25371 kcal/mol@LB@@LB@Position - mRNA 60 -- 77@LB@Position - sRNA 62 -- 76@LB@Position Seed - mRNA 71 -- 77@LB@Position Seed - sRNA 62 -- 68@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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