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
32	0.001499	0.1635	b0661	miaB	-12.88	0.082685	213 -- 250	6 -- 36	tRNA-i(6)A37 methylthiotransferase		_____________212____________________________________251\n_____________\|______________________________________\|\n5'-CGC...AAAAA_______UU_AAACC_____C_______U___C_____CGAUU...AAC-3'\n______________CUCCAUA__A_____UGGGG_UGUCAGA_GAA_GAGUA\n______________\|\|\|\|\|:\|__\|_____\|\|\|\|\|_::\|\|\|:\|_\|\|\|_:\|\|:\|\n______________GAGGUGU__U_____ACCCC_GUAGUUU_CUU_UUCGU\n3'-UUU...UACCC_______UU___________U_________________CACCG-5'\n_____________\|______________________________________\|\n_____________37_____________________________________5\n	234 -- 240	14 -- 20	-26.1374 kcal/mol	6.57825 kcal/mol	6.67617 kcal/mol	212 251@LB@ \| \|@LB@5'-CGC...AAAAA UU AAACC C U C CGAUU...AAC-3'@LB@ CUCCAUA A UGGGG UGUCAGA GAA GAGUA@LB@ \|\|\|\|\|:\| \| \|\|\|\|\| ::\|\|\|:\| \|\|\| :\|\|:\|@LB@ GAGGUGU U ACCCC GUAGUUU CUU UUCGU@LB@3'-UUU...UACCC UU U CACCG-5'@LB@ \| \|@LB@ 37 5@LB@@LB@@LB@Energy -12.88 kcal/mol@LB@Hybridization Energy -26.1374 kcal/mol@LB@Unfolding Energy - mRNA 6.57825 kcal/mol@LB@Unfolding Energy - sRNA 6.67617 kcal/mol@LB@@LB@Position - mRNA 213 -- 250@LB@Position - sRNA 6 -- 36@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 14 -- 20@LB@
51	0.00253	0.1729	b0699	ybfA	-18.06	0.004001	182 -- 204	2 -- 32	DUF2517 family protein		_____________181_____________________________205\n_____________\|_______________________________\|\n5'-AUG...UAGAU_______________________________AACUC...GGA-3'\n______________ACAAAA_GGGG______GAGAAAAGUA_UGG\n______________\|\|\|\|\|\|_\|\|\|\|______:\|\|\|\|\|\|\|:\|_\|\|\|\n______________UGUUUU_CCCC______UUCUUUUCGU_ACC\n3'-UUU...CGAGG______A____UGUAGU__________C___G-5'\n_____________\|_______________________________\|\n_____________33______________________________1\n	195 -- 201	6 -- 12	-23.7835 kcal/mol	3.18782 kcal/mol	2.53929 kcal/mol	181 205@LB@ \| \|@LB@5'-AUG...UAGAU AACUC...GGA-3'@LB@ ACAAAA GGGG GAGAAAAGUA UGG@LB@ \|\|\|\|\|\| \|\|\|\| :\|\|\|\|\|\|\|:\| \|\|\|@LB@ UGUUUU CCCC UUCUUUUCGU ACC@LB@3'-UUU...CGAGG A UGUAGU C G-5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -18.06 kcal/mol@LB@Hybridization Energy -23.7835 kcal/mol@LB@Unfolding Energy - mRNA 3.18782 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 182 -- 204@LB@Position - sRNA 2 -- 32@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 6 -- 12@LB@
97	0.005972	0.2161	b0768	ybhD	-15.34	0.022873	51 -- 78	6 -- 32	putative DNA-binding transcriptional regulator	b2409	_____________50___________________________79\n_____________\|____________________________\|\n5'-CAG...UUAUU____U____UU__________C______UCUCU...CAU-3'\n______________GCGA_AUGG__ACAUUAAGGG_AAAGCA\n______________:\|:\|_\|\|\|\|__\|\|\|\|:\|\|:\|:_\|\|\|\|\|\|\n______________UGUU_UACC__UGUAGUUUCU_UUUCGU\n3'-UUU...CGAGG____U____CC_________________CACCG-5'\n_____________\|____________________________\|\n_____________33___________________________5\n	64 -- 70	13 -- 19	-24.2506 kcal/mol	6.37495 kcal/mol	2.53457 kcal/mol	50 79@LB@ \| \|@LB@5'-CAG...UUAUU U UU C UCUCU...CAU-3'@LB@ GCGA AUGG ACAUUAAGGG AAAGCA@LB@ :\|:\| \|\|\|\| \|\|\|\|:\|\|:\|: \|\|\|\|\|\|@LB@ UGUU UACC UGUAGUUUCU UUUCGU@LB@3'-UUU...CGAGG U CC CACCG-5'@LB@ \| \|@LB@ 33 5@LB@@LB@@LB@Energy -15.34 kcal/mol@LB@Hybridization Energy -24.2506 kcal/mol@LB@Unfolding Energy - mRNA 6.37495 kcal/mol@LB@Unfolding Energy - sRNA 2.53457 kcal/mol@LB@@LB@Position - mRNA 51 -- 78@LB@Position - sRNA 6 -- 32@LB@Position Seed - mRNA 64 -- 70@LB@Position Seed - sRNA 13 -- 19@LB@
110	0.007401	0.2348	b0784	moaD	-14.78	0.031320	178 -- 203	3 -- 25	molybdopterin synthase small subunit		_____________177________________________204\n_____________\|__________________________\|\n5'-GCA...AAGUC___U___U______U________A__AUUAA...AGC-3'\n______________GGG_GAC_UUAAGG_GGAAGCGG_UG\n______________\|\|\|_\|\|\|_\|:\|\|:\|_::\|\|\|\|:\|_\|\|\n______________CCC_CUG_AGUUUC_UUUUCGUC_AC\n3'-UUU...UUUUA_______U__________________CG-5'\n_____________\|__________________________\|\n_____________26_________________________2\n	194 -- 200	5 -- 11	-23.9822 kcal/mol	6.68375 kcal/mol	2.5166 kcal/mol	177 204@LB@ \| \|@LB@5'-GCA...AAGUC U U U A AUUAA...AGC-3'@LB@ GGG GAC UUAAGG GGAAGCGG UG@LB@ \|\|\| \|\|\| \|:\|\|:\| ::\|\|\|\|:\| \|\|@LB@ CCC CUG AGUUUC UUUUCGUC AC@LB@3'-UUU...UUUUA U CG-5'@LB@ \| \|@LB@ 26 2@LB@@LB@@LB@Energy -14.78 kcal/mol@LB@Hybridization Energy -23.9822 kcal/mol@LB@Unfolding Energy - mRNA 6.68375 kcal/mol@LB@Unfolding Energy - sRNA 2.5166 kcal/mol@LB@@LB@Position - mRNA 178 -- 203@LB@Position - sRNA 3 -- 25@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 5 -- 11@LB@
36	0.001784	0.1648	b0785	moaE	-14.28	0.040953	241 -- 264	1 -- 21	molybdopterin synthase large subunit		_____________240______________________265\n_____________\|________________________\|\n5'-AGA...GUUCA____A___________CCC_____UGGCG...CCU-3'\n______________GCGU_GGAGAAGAGUA___GUGGC\n______________:\|:\|_::\|\|\|\|:\|\|:\|___\|\|\|\|\|\n______________UGUA_UUUCUUUUCGU___CACCG\n3'-UUU...ACCCC____G___________________-5'\n_____________\|_______________________\|\n_____________22______________________1\n	250 -- 256	6 -- 12	-21.7367 kcal/mol	5.94077 kcal/mol	1.51103 kcal/mol	240 265@LB@ \| \|@LB@5'-AGA...GUUCA A CCC UGGCG...CCU-3'@LB@ GCGU GGAGAAGAGUA GUGGC@LB@ :\|:\| ::\|\|\|\|:\|\|:\| \|\|\|\|\|@LB@ UGUA UUUCUUUUCGU CACCG@LB@3'-UUU...ACCCC G -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -14.28 kcal/mol@LB@Hybridization Energy -21.7367 kcal/mol@LB@Unfolding Energy - mRNA 5.94077 kcal/mol@LB@Unfolding Energy - sRNA 1.51103 kcal/mol@LB@@LB@Position - mRNA 241 -- 264@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 250 -- 256@LB@Position Seed - sRNA 6 -- 12@LB@
138	0.0102	0.2504	b0830	gsiB	-12.88	0.082739	282 -- 298	1 -- 16	glutathione ABC transporter periplasmic binding protein		_____________281_______________299\n_____________\|_________________\|\n5'-GGC...CUGCC_____UGU_________GG-3'\n______________AAAGA___GGUGGUGGC\n______________\|\|\|\|\|___:\|::\|\|\|\|\|\n______________UUUCU___UCGUCACCG\n3'-UUU...UGUAG_____UU__________-5'\n_____________\|________________\|\n_____________17_______________1\n	292 -- 298	1 -- 7	-17.0557 kcal/mol	2.82856 kcal/mol	1.34555 kcal/mol	281 299@LB@ \| \|@LB@5'-GGC...CUGCC UGU GG-3'@LB@ AAAGA GGUGGUGGC@LB@ \|\|\|\|\| :\|::\|\|\|\|\|@LB@ UUUCU UCGUCACCG@LB@3'-UUU...UGUAG UU -5'@LB@ \| \|@LB@ 17 1@LB@@LB@@LB@Energy -12.88 kcal/mol@LB@Hybridization Energy -17.0557 kcal/mol@LB@Unfolding Energy - mRNA 2.82856 kcal/mol@LB@Unfolding Energy - sRNA 1.34555 kcal/mol@LB@@LB@Position - mRNA 282 -- 298@LB@Position - sRNA 1 -- 16@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 1 -- 7@LB@
196	0.01416	0.2529	b0870	ltaE	-12.27	0.109556	23 -- 39	7 -- 23	L-allo-threonine aldolase PLP-dependent		_____________22________________40\n_____________\|_________________\|\n5'-GUC...GUGGU__U__C___________UAGCC...ACC-3'\n______________GG_CG_CAAAGAAGAGU\n______________\|\|_\|:_\|\|\|\|\|\|\|:\|\|:\n______________CC_GU_GUUUCUUUUCG\n3'-UUU...UUACC__U__A___________UCACCG-5'\n_____________\|_________________\|\n_____________24________________6\n	33 -- 39	7 -- 13	-15.8177 kcal/mol	2.94498 kcal/mol	0.599063 kcal/mol	22 40@LB@ \| \|@LB@5'-GUC...GUGGU U C UAGCC...ACC-3'@LB@ GG CG CAAAGAAGAGU@LB@ \|\| \|: \|\|\|\|\|\|\|:\|\|:@LB@ CC GU GUUUCUUUUCG@LB@3'-UUU...UUACC U A UCACCG-5'@LB@ \| \|@LB@ 24 6@LB@@LB@@LB@Energy -12.27 kcal/mol@LB@Hybridization Energy -15.8177 kcal/mol@LB@Unfolding Energy - mRNA 2.94498 kcal/mol@LB@Unfolding Energy - sRNA 0.599063 kcal/mol@LB@@LB@Position - mRNA 23 -- 39@LB@Position - sRNA 7 -- 23@LB@Position Seed - mRNA 33 -- 39@LB@Position Seed - sRNA 7 -- 13@LB@
28	0.001242	0.1512	b0879	macB	-8.34	0.466885	135 -- 159	1 -- 22	macrolide ABC transporter peremase/ATPase		_____________134_________________________160\n_____________\|___________________________\|\n5'-AAU...GUUGA__U_________GCUU___________GAUGA...CGG-3'\n______________GA_UGUCAAAGG____GAAGC_G_GGC\n______________\|\|_::\|\|\|\|\|\|:____:\|\|\|\|_\|_\|\|\|\n______________CU_GUAGUUUCU____UUUCG_C_CCG\n3'-UUU...UACCC_____________________U_A___-5'\n_____________\|__________________________\|\n_____________23_________________________1\n	140 -- 146	12 -- 18	-17.2972 kcal/mol	7.41924 kcal/mol	1.54023 kcal/mol	134 160@LB@ \| \|@LB@5'-AAU...GUUGA U GCUU GAUGA...CGG-3'@LB@ GA UGUCAAAGG GAAGC G GGC@LB@ \|\| ::\|\|\|\|\|\|: :\|\|\|\| \| \|\|\|@LB@ CU GUAGUUUCU UUUCG C CCG@LB@3'-UUU...UACCC U A -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -8.34 kcal/mol@LB@Hybridization Energy -17.2972 kcal/mol@LB@Unfolding Energy - mRNA 7.41924 kcal/mol@LB@Unfolding Energy - sRNA 1.54023 kcal/mol@LB@@LB@Position - mRNA 135 -- 159@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 140 -- 146@LB@Position Seed - sRNA 12 -- 18@LB@
52	0.002562	0.1729	b0881	clpS	-16.21	0.013666	11 -- 25	5 -- 25	regulatory protein for ClpA substrate specificity		_____________10____________________26\n_____________\|_____________________\|\n5'-GCA...UGACA_____________________GUAUG...UCA-3'\n______________GGGGACA______AGGGGCAG\n______________\|\|\|\|\|\|\|______\|:::\|\|\|\|\n______________CCCCUGU______UUUUCGUC\n3'-UUU...UUUUA_______AGUUUC________ACCG-5'\n_____________\|_____________________\|\n_____________26____________________4\n	19 -- 25	5 -- 11	-21.27 kcal/mol	2.56205 kcal/mol	2.50017 kcal/mol	10 26@LB@ \| \|@LB@5'-GCA...UGACA GUAUG...UCA-3'@LB@ GGGGACA AGGGGCAG@LB@ \|\|\|\|\|\|\| \|:::\|\|\|\|@LB@ CCCCUGU UUUUCGUC@LB@3'-UUU...UUUUA AGUUUC ACCG-5'@LB@ \| \|@LB@ 26 4@LB@@LB@@LB@Energy -16.21 kcal/mol@LB@Hybridization Energy -21.27 kcal/mol@LB@Unfolding Energy - mRNA 2.56205 kcal/mol@LB@Unfolding Energy - sRNA 2.50017 kcal/mol@LB@@LB@Position - mRNA 11 -- 25@LB@Position - sRNA 5 -- 25@LB@Position Seed - mRNA 19 -- 25@LB@Position Seed - sRNA 5 -- 11@LB@
164	0.01206	0.2504	b0882	clpA	-9.12	0.369525	95 -- 107	48 -- 60	ATPase and specificity subunit of ClpA-ClpP ATP-dependent serine protease chaperone activity		_____________94____________108\n_____________\|_____________\|\n5'-UUU...GCAGA____A________AUGGU...CGC-3'\n______________AACC_AAGUGGCG\n______________\|\|\|\|_\|\|:\|\|\|\|\|\n______________UUGG_UUUACCGC\n3'-UUU...GGAAC____C________CCCAA...CCG-5'\n_____________\|_____________\|\n_____________61____________47\n	101 -- 107	48 -- 54	-16.8445 kcal/mol	3.76103 kcal/mol	3.96136 kcal/mol	94 108@LB@ \| \|@LB@5'-UUU...GCAGA A AUGGU...CGC-3'@LB@ AACC AAGUGGCG@LB@ \|\|\|\| \|\|:\|\|\|\|\|@LB@ UUGG UUUACCGC@LB@3'-UUU...GGAAC C CCCAA...CCG-5'@LB@ \| \|@LB@ 61 47@LB@@LB@@LB@Energy -9.12 kcal/mol@LB@Hybridization Energy -16.8445 kcal/mol@LB@Unfolding Energy - mRNA 3.76103 kcal/mol@LB@Unfolding Energy - sRNA 3.96136 kcal/mol@LB@@LB@Position - mRNA 95 -- 107@LB@Position - sRNA 48 -- 60@LB@Position Seed - mRNA 101 -- 107@LB@Position Seed - sRNA 48 -- 54@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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