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
187	0.009506	0.1776	b1243	oppA	-10.52	0.199375	11 -- 17	40 -- 46	oligopeptide ABC transporter periplasmic binding protein	_____________10______18\n_____________\|_______\|\n5'-UGU...CUCGA_______GACAC...UCA-3'\n______________CAGGGGA\n______________\|\|\|\|\|\|\|\n______________GUCCCCU\n3'-UUU...AGUGA_______AAAGG...GCA-5'\n_____________\|_______\|\n_____________47______39\n	11 -- 17	40 -- 46	-13.6251 kcal/mol	1.75344 kcal/mol	1.35582 kcal/mol	10 18@LB@ \| \|@LB@5'-UGU...CUCGA GACAC...UCA-3'@LB@ CAGGGGA@LB@ \|\|\|\|\|\|\|@LB@ GUCCCCU@LB@3'-UUU...AGUGA AAAGG...GCA-5'@LB@ \| \|@LB@ 47 39@LB@@LB@@LB@Energy -10.52 kcal/mol@LB@Hybridization Energy -13.6251 kcal/mol@LB@Unfolding Energy - mRNA 1.75344 kcal/mol@LB@Unfolding Energy - sRNA 1.35582 kcal/mol@LB@@LB@Position - mRNA 11 -- 17@LB@Position - sRNA 40 -- 46@LB@Position Seed - mRNA 11 -- 17@LB@Position Seed - sRNA 40 -- 46@LB@
27	0.0003358	0.04376	b1784	yeaH	-12.48	0.082239	130 -- 197	41 -- 99	UPF0229 family protein	_____________129___________________________________________________________________198\n_____________\|_____________________________________________________________________\|\n5'-UGU...ACGAC___GAAC______CCUG___A_C_____CAC____GUA_________UGGCAAA___AG___G______CAUAU...CGA-3'\n______________AGC____CGUGGG____AGA_G_GGCAA___AGGC___GCAUACAGU_______UGU__UAC__GGGGG\n______________\|\|\|____\|\|\|\|\|\|____\|\|\|_\|_\|\|\|\|\|___\|\|:\|___:\|\|:\|\|\|\|:_______\|\|\|__:\|\|__:\|\|\|\|\n______________UCG____GCACCC____UCU_C_CCGUU___UCUG___UGUGUGUCG_______ACA__GUG__UCCCC\n_____3'-UUUUUU___GGUA_____________A______________A___________UUAAGCA___AA___AG_____UAAAG...GCA-5'\n_____________\|_____________________________________________________________________\|\n_____________100___________________________________________________________________40\n	170 -- 176	63 -- 69	-48.2653 kcal/mol	18.2122 kcal/mol	17.5731 kcal/mol	129 198@LB@ \| \|@LB@5'-UGU...ACGAC GAAC CCUG A C CAC GUA UGGCAAA AG G CAUAU...CGA-3'@LB@ AGC CGUGGG AGA G GGCAA AGGC GCAUACAGU UGU UAC GGGGG@LB@ \|\|\| \|\|\|\|\|\| \|\|\| \| \|\|\|\|\| \|\|:\| :\|\|:\|\|\|\|: \|\|\| :\|\| :\|\|\|\|@LB@ UCG GCACCC UCU C CCGUU UCUG UGUGUGUCG ACA GUG UCCCC@LB@ 3'-UUUUUU GGUA A A UUAAGCA AA AG UAAAG...GCA-5'@LB@ \| \|@LB@ 100 40@LB@@LB@@LB@Energy -12.48 kcal/mol@LB@Hybridization Energy -48.2653 kcal/mol@LB@Unfolding Energy - mRNA 18.2122 kcal/mol@LB@Unfolding Energy - sRNA 17.5731 kcal/mol@LB@@LB@Position - mRNA 130 -- 197@LB@Position - sRNA 41 -- 99@LB@Position Seed - mRNA 170 -- 176@LB@Position Seed - sRNA 63 -- 69@LB@
32	0.0005139	0.05552	b4070	nrfA	-17.83	0.003136	66 -- 107	41 -- 78	nitrite reductase formate-dependent cytochrome	_____________65_________________________________________108\n_____________\|__________________________________________\|\n5'-UGU...UGAUU______A___UU_______UG___AU_____A___A______CGAGC...CAA-3'\n______________AAAGAC_ACA__CACAGUG__GUU__UUGUU_CAC_UAGGGG\n______________\|\|\|\|\|\|_\|\|\|__\|\|\|\|\|::__:\|\|__\|\|\|\|\|_\|\|\|_:\|\|\|\|\|\n______________UUUCUG_UGU__GUGUCGU__UAA__AACAA_GUG_GUCCCC\n3'-UUU...ACCCG______A_________________GC_____A___A______UAAAG...GCA-5'\n_____________\|__________________________________________\|\n_____________79_________________________________________40\n	78 -- 84	62 -- 68	-32.7887 kcal/mol	10.1881 kcal/mol	4.77302 kcal/mol	65 108@LB@ \| \|@LB@5'-UGU...UGAUU A UU UG AU A A CGAGC...CAA-3'@LB@ AAAGAC ACA CACAGUG GUU UUGUU CAC UAGGGG@LB@ \|\|\|\|\|\| \|\|\| \|\|\|\|\|:: :\|\| \|\|\|\|\| \|\|\| :\|\|\|\|\|@LB@ UUUCUG UGU GUGUCGU UAA AACAA GUG GUCCCC@LB@3'-UUU...ACCCG A GC A A UAAAG...GCA-5'@LB@ \| \|@LB@ 79 40@LB@@LB@@LB@Energy -17.83 kcal/mol@LB@Hybridization Energy -32.7887 kcal/mol@LB@Unfolding Energy - mRNA 10.1881 kcal/mol@LB@Unfolding Energy - sRNA 4.77302 kcal/mol@LB@@LB@Position - mRNA 66 -- 107@LB@Position - sRNA 41 -- 78@LB@Position Seed - mRNA 78 -- 84@LB@Position Seed - sRNA 62 -- 68@LB@
44	0.001243	0.09943	b3064	tsaD	-15.06	0.020167	98 -- 131	41 -- 82	tRNA(ANN) t(6)A37 threonylcarbamoyladenosine modification protein; glycation binding protein	_____________97___________________________________________132\n_____________\|____________________________________________\|\n5'-CAU...UAUAA_________G_______GA________________U________CGAAC...UGA-3'\n______________GGGUGAGGA_UAUACAC__GGC_________UUUC_C_CAGGGG\n______________\|\|\|::\|:\|\|_\|\|:\|\|\|\|__:\|\|_________\|\|\|\|_\|_\|\|\|\|\|\|\n______________CCCGUUUCU_AUGUGUG__UCG_________AAAG_G_GUCCCC\n3'-UUU...CUCUA_________G____________UUAAGCAAC____U_A______UAAAG...GCA-5'\n_____________\|____________________________________________\|\n_____________83___________________________________________40\n	108 -- 114	66 -- 72	-38.4936 kcal/mol	9.4641 kcal/mol	13.9685 kcal/mol	97 132@LB@ \| \|@LB@5'-CAU...UAUAA G GA U CGAAC...UGA-3'@LB@ GGGUGAGGA UAUACAC GGC UUUC C CAGGGG@LB@ \|\|\|::\|:\|\| \|\|:\|\|\|\| :\|\| \|\|\|\| \| \|\|\|\|\|\|@LB@ CCCGUUUCU AUGUGUG UCG AAAG G GUCCCC@LB@3'-UUU...CUCUA G UUAAGCAAC U A UAAAG...GCA-5'@LB@ \| \|@LB@ 83 40@LB@@LB@@LB@Energy -15.06 kcal/mol@LB@Hybridization Energy -38.4936 kcal/mol@LB@Unfolding Energy - mRNA 9.4641 kcal/mol@LB@Unfolding Energy - sRNA 13.9685 kcal/mol@LB@@LB@Position - mRNA 98 -- 131@LB@Position - sRNA 41 -- 82@LB@Position Seed - mRNA 108 -- 114@LB@Position Seed - sRNA 66 -- 72@LB@
57	0.002011	0.1223	b3057	bacA	-16.67	0.007222	149 -- 193	41 -- 71	undecaprenyl pyrophosphate phosphatase	_____________148___________________________________________194\n_____________\|_____________________________________________\|\n5'-UUC...UGGUC_______________GACAAG_GGUACAUUUUAAUA_________UUUAU...UUG-3'\n______________AUACGCAGUAGUUCG______C______________AUUUAGGGG\n______________\|:\|\|:\|\|\|:\|:\|\|\|\|______\|______________\|:\|:\|\|\|\|\|\n______________UGUGUGUCGUUAAGC______G______________UGAGUCCCC\n3'-UUU...UCUGA_______________AACAAA________________________UAAAG...GCA-5'\n_____________\|_____________________________________________\|\n_____________72____________________________________________40\n	187 -- 193	41 -- 47	-30.087 kcal/mol	8.67993 kcal/mol	4.74226 kcal/mol	148 194@LB@ \| \|@LB@5'-UUC...UGGUC GACAAG GGUACAUUUUAAUA UUUAU...UUG-3'@LB@ AUACGCAGUAGUUCG C AUUUAGGGG@LB@ \|:\|\|:\|\|\|:\|:\|\|\|\| \| \|:\|:\|\|\|\|\|@LB@ UGUGUGUCGUUAAGC G UGAGUCCCC@LB@3'-UUU...UCUGA AACAAA UAAAG...GCA-5'@LB@ \| \|@LB@ 72 40@LB@@LB@@LB@Energy -16.67 kcal/mol@LB@Hybridization Energy -30.087 kcal/mol@LB@Unfolding Energy - mRNA 8.67993 kcal/mol@LB@Unfolding Energy - sRNA 4.74226 kcal/mol@LB@@LB@Position - mRNA 149 -- 193@LB@Position - sRNA 41 -- 71@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 41 -- 47@LB@
123	0.005464	0.1553	b3746	ravA	-13.51	0.048673	243 -- 263	41 -- 65	hexameric AAA+ MoxR family ATPase putative molecular chaperone	_____________242_______________________264\n_____________\|_________________________\|\n5'-UGA...GCCUG____________GAAA_________CUUUA...UAU-3'\n______________AGCAGUUCGUUG________AGGGG\n______________\|\|\|\|:\|\|\|\|\|\|\|________\|\|\|\|\|\n______________UCGUUAAGCAAC________UCCCC\n3'-UUU...GUGUG____________AAAGUGAG_____UAAAG...GCA-5'\n_____________\|_________________________\|\n_____________66________________________40\n	248 -- 254	54 -- 60	-25.3509 kcal/mol	7.14336 kcal/mol	4.70281 kcal/mol	242 264@LB@ \| \|@LB@5'-UGA...GCCUG GAAA CUUUA...UAU-3'@LB@ AGCAGUUCGUUG AGGGG@LB@ \|\|\|\|:\|\|\|\|\|\|\| \|\|\|\|\|@LB@ UCGUUAAGCAAC UCCCC@LB@3'-UUU...GUGUG AAAGUGAG UAAAG...GCA-5'@LB@ \| \|@LB@ 66 40@LB@@LB@@LB@Energy -13.51 kcal/mol@LB@Hybridization Energy -25.3509 kcal/mol@LB@Unfolding Energy - mRNA 7.14336 kcal/mol@LB@Unfolding Energy - sRNA 4.70281 kcal/mol@LB@@LB@Position - mRNA 243 -- 263@LB@Position - sRNA 41 -- 65@LB@Position Seed - mRNA 248 -- 254@LB@Position Seed - sRNA 54 -- 60@LB@
166	0.008074	0.1711	b2158	yeiH	-9.26	0.321503	233 -- 257	41 -- 72	UPF0324 family inner membrane protein	_____________232_______________________________258\n_____________\|_________________________________\|\n5'-CAC...CAUCG_____UG_____________________C____UUAGC...GUG-3'\n______________UACAC__UGGCA________UUUUAUUC_GGGG\n______________\|\|\|\|\|__::\|\|\|________\|\|\|:\|:\|\|_\|\|\|\|\n______________AUGUG__GUCGU________AAAGUGAG_CCCC\n3'-UUU...UUCUG_____U______UAAGCAAC________U____UAAAG...GCA-5'\n_____________\|_________________________________\|\n_____________73________________________________40\n	246 -- 252	46 -- 52	-21.8619 kcal/mol	7.84401 kcal/mol	4.75632 kcal/mol	232 258@LB@ \| \|@LB@5'-CAC...CAUCG UG C UUAGC...GUG-3'@LB@ UACAC UGGCA UUUUAUUC GGGG@LB@ \|\|\|\|\| ::\|\|\| \|\|\|:\|:\|\| \|\|\|\|@LB@ AUGUG GUCGU AAAGUGAG CCCC@LB@3'-UUU...UUCUG U UAAGCAAC U UAAAG...GCA-5'@LB@ \| \|@LB@ 73 40@LB@@LB@@LB@Energy -9.26 kcal/mol@LB@Hybridization Energy -21.8619 kcal/mol@LB@Unfolding Energy - mRNA 7.84401 kcal/mol@LB@Unfolding Energy - sRNA 4.75632 kcal/mol@LB@@LB@Position - mRNA 233 -- 257@LB@Position - sRNA 41 -- 72@LB@Position Seed - mRNA 246 -- 252@LB@Position Seed - sRNA 46 -- 52@LB@
186	0.009502	0.1776	b1631	rsxG	-12.74	0.072174	210 -- 253	41 -- 74	SoxR iron-sulfur cluster reduction factor component; putative membrane protein of electron transport complex	_____________209____________________________________________254\n_____________\|______________________________________________\|\n5'-CUG...UGAAA_____CCGAAA________UUA_____G______AUUUG___C___UUCAA...CGA-3'\n______________ACUAU______ACACGGCA___CGUUG___CGCU_____CAG_GGG\n______________\|\|\|\|:______\|\|\|\|:\|\|\|___\|\|\|\|\|___\|:\|\|_____\|\|\|_\|\|\|\n______________UGAUG______UGUGUCGU___GCAAC___GUGA_____GUC_CCC\n3'-UUU...GUUUC___________________UAA_____AAA________________UAAAG...GCA-5'\n_____________\|______________________________________________\|\n_____________75_____________________________________________40\n	222 -- 228	62 -- 68	-28.539 kcal/mol	11.0247 kcal/mol	4.77133 kcal/mol	209 254@LB@ \| \|@LB@5'-CUG...UGAAA CCGAAA UUA G AUUUG C UUCAA...CGA-3'@LB@ ACUAU ACACGGCA CGUUG CGCU CAG GGG@LB@ \|\|\|\|: \|\|\|\|:\|\|\| \|\|\|\|\| \|:\|\| \|\|\| \|\|\|@LB@ UGAUG UGUGUCGU GCAAC GUGA GUC CCC@LB@3'-UUU...GUUUC UAA AAA UAAAG...GCA-5'@LB@ \| \|@LB@ 75 40@LB@@LB@@LB@Energy -12.74 kcal/mol@LB@Hybridization Energy -28.539 kcal/mol@LB@Unfolding Energy - mRNA 11.0247 kcal/mol@LB@Unfolding Energy - sRNA 4.77133 kcal/mol@LB@@LB@Position - mRNA 210 -- 253@LB@Position - sRNA 41 -- 74@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 62 -- 68@LB@
195	0.009901	0.1776	b1098	tmk	-15.44	0.015998	201 -- 230	41 -- 71	thymidylate kinase	_____________200_____________________________231\n_____________\|_______________________________\|\n5'-UAA...AAAAA___________GUAUAUCG______G_____CUGGA...GCG-3'\n______________AUGCGCAGUAA_________UCAUU_AGGGG\n______________\|::\|:\|\|\|:\|\|_________\|\|\|:\|_\|\|\|\|\|\n______________UGUGUGUCGUU_________AGUGA_UCCCC\n3'-UUU...UCUGA___________AAGCAACAA_____G_____UAAAG...GCA-5'\n_____________\|_______________________________\|\n_____________72______________________________40\n	205 -- 211	61 -- 67	-28.5877 kcal/mol	8.40445 kcal/mol	4.74226 kcal/mol	200 231@LB@ \| \|@LB@5'-UAA...AAAAA GUAUAUCG G CUGGA...GCG-3'@LB@ AUGCGCAGUAA UCAUU AGGGG@LB@ \|::\|:\|\|\|:\|\| \|\|\|:\| \|\|\|\|\|@LB@ UGUGUGUCGUU AGUGA UCCCC@LB@3'-UUU...UCUGA AAGCAACAA G UAAAG...GCA-5'@LB@ \| \|@LB@ 72 40@LB@@LB@@LB@Energy -15.44 kcal/mol@LB@Hybridization Energy -28.5877 kcal/mol@LB@Unfolding Energy - mRNA 8.40445 kcal/mol@LB@Unfolding Energy - sRNA 4.74226 kcal/mol@LB@@LB@Position - mRNA 201 -- 230@LB@Position - sRNA 41 -- 71@LB@Position Seed - mRNA 205 -- 211@LB@Position Seed - sRNA 61 -- 67@LB@
16	0.00012	0.02638	b3089	sstT	-15.87	0.012233	203 -- 224	42 -- 75	sodium:serine/threonine symporter	_____________202________________________________225\n_____________\|__________________________________\|\n5'-CAC...AAAAU_________ACG______________________CUAUU...CAU-3'\n______________GACUACGCA______________UUCAC_CGGGG\n______________\|\|\|\|\|\|:\|\|______________\|\|\|\|\|_\|:\|\|\|\n______________CUGAUGUGU______________AAGUG_GUCCC\n3'-UUU...CGUUU_________GUCGUUAAGCAACA_____A_____CUAAA...GCA-5'\n_____________\|__________________________________\|\n_____________76_________________________________41\n	205 -- 211	67 -- 73	-24.6329 kcal/mol	4.00159 kcal/mol	4.76397 kcal/mol	202 225@LB@ \| \|@LB@5'-CAC...AAAAU ACG CUAUU...CAU-3'@LB@ GACUACGCA UUCAC CGGGG@LB@ \|\|\|\|\|\|:\|\| \|\|\|\|\| \|:\|\|\|@LB@ CUGAUGUGU AAGUG GUCCC@LB@3'-UUU...CGUUU GUCGUUAAGCAACA A CUAAA...GCA-5'@LB@ \| \|@LB@ 76 41@LB@@LB@@LB@Energy -15.87 kcal/mol@LB@Hybridization Energy -24.6329 kcal/mol@LB@Unfolding Energy - mRNA 4.00159 kcal/mol@LB@Unfolding Energy - sRNA 4.76397 kcal/mol@LB@@LB@Position - mRNA 203 -- 224@LB@Position - sRNA 42 -- 75@LB@Position Seed - mRNA 205 -- 211@LB@Position Seed - sRNA 67 -- 73@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

Use the following button if you want to resubmit the job with altered input or parameterization:

usability assessment

Please support us by filling this short quality survey for evaluating this

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

Main Menu

Freiburg RNA Tools

Interaction Prediction

Seq-Str Alignment

CRISPR

Sequence Design

Splicing

SNP & Mutation

Classification

Gene set extension

MoDPepInt Server

CPSP-Tools Server

Galaxy-FR

CMV server

Teaching