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	Additional homologs
121	0.005439	0.1553	b1640	anmK	-7.89	0.496680	290 -- 297	63 -- 70	anhydro-N-acetylmuramic acid kinase		_____________289______298\n_____________\|________\|\n5'-CCA...CGGGU________UGG-3'\n______________CGCACAGC\n______________\|:\|\|\|\|\|\|\n______________GUGUGUCG\n3'-UUU...CUGAU________UUAAG...GCA-5'\n_____________\|________\|\n_____________71_______62\n	291 -- 297	63 -- 69	-13.0848 kcal/mol	2.06561 kcal/mol	3.13161 kcal/mol	289 298@LB@ \| \|@LB@5'-CCA...CGGGU UGG-3'@LB@ CGCACAGC@LB@ \|:\|\|\|\|\|\|@LB@ GUGUGUCG@LB@3'-UUU...CUGAU UUAAG...GCA-5'@LB@ \| \|@LB@ 71 62@LB@@LB@@LB@Energy -7.89 kcal/mol@LB@Hybridization Energy -13.0848 kcal/mol@LB@Unfolding Energy - mRNA 2.06561 kcal/mol@LB@Unfolding Energy - sRNA 3.13161 kcal/mol@LB@@LB@Position - mRNA 290 -- 297@LB@Position - sRNA 63 -- 70@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 63 -- 69@LB@
122	0.005462	0.1553	b3143	yraI	-10.36	0.212908	69 -- 81	40 -- 51	putative periplasmic pilin chaperone	b0939 b4316 b0531	_____________68____________82\n_____________\|_____________\|\n5'-GGA...AGAAA____CC_______AGCAG...UGA-3'\n______________UCAC__CAGGGGA\n______________\|\|\|\|__\|\|\|\|\|\|\|\n______________AGUG__GUCCCCU\n3'-UUU...AACAA____A________AAAGG...GCA-5'\n_____________\|_____________\|\n_____________52____________39\n	75 -- 81	40 -- 46	-16.6795 kcal/mol	4.56539 kcal/mol	1.76028 kcal/mol	68 82@LB@ \| \|@LB@5'-GGA...AGAAA CC AGCAG...UGA-3'@LB@ UCAC CAGGGGA@LB@ \|\|\|\| \|\|\|\|\|\|\|@LB@ AGUG GUCCCCU@LB@3'-UUU...AACAA A AAAGG...GCA-5'@LB@ \| \|@LB@ 52 39@LB@@LB@@LB@Energy -10.36 kcal/mol@LB@Hybridization Energy -16.6795 kcal/mol@LB@Unfolding Energy - mRNA 4.56539 kcal/mol@LB@Unfolding Energy - sRNA 1.76028 kcal/mol@LB@@LB@Position - mRNA 69 -- 81@LB@Position - sRNA 40 -- 51@LB@Position Seed - mRNA 75 -- 81@LB@Position Seed - sRNA 40 -- 46@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@
124	0.005471	0.1553	b1249	clsA	-8.47	0.418250	164 -- 196	34 -- 71	cardiolipin synthase 1		_____________163____________________________________197\n_____________\|______________________________________\|\n5'-GUC...CGUAA__U____A____G__C_______AAA____________AUCUA...CAG-3'\n______________AC_CAUA_CAAU_CG___UUUCA______GGAUUUCUA\n______________\|\|_\|\|:\|_\|\|\|\|_\|\|___\|\|\|\|\|______\|\|\|\|\|\|\|:\|\n______________UG_GUGU_GUUA_GC___AAAGU______CCUAAAGGU\n3'-UUU...UCUGA__U____C____A__AAC_____GAGUCC_________ACGAA...GCA-5'\n_____________\|______________________________________\|\n_____________72_____________________________________33\n	190 -- 196	34 -- 40	-20.3655 kcal/mol	7.10457 kcal/mol	4.79237 kcal/mol	163 197@LB@ \| \|@LB@5'-GUC...CGUAA U A G C AAA AUCUA...CAG-3'@LB@ AC CAUA CAAU CG UUUCA GGAUUUCUA@LB@ \|\| \|\|:\| \|\|\|\| \|\| \|\|\|\|\| \|\|\|\|\|\|\|:\|@LB@ UG GUGU GUUA GC AAAGU CCUAAAGGU@LB@3'-UUU...UCUGA U C A AAC GAGUCC ACGAA...GCA-5'@LB@ \| \|@LB@ 72 33@LB@@LB@@LB@Energy -8.47 kcal/mol@LB@Hybridization Energy -20.3655 kcal/mol@LB@Unfolding Energy - mRNA 7.10457 kcal/mol@LB@Unfolding Energy - sRNA 4.79237 kcal/mol@LB@@LB@Position - mRNA 164 -- 196@LB@Position - sRNA 34 -- 71@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 34 -- 40@LB@
125	0.005556	0.1564	b3384	trpS	-12.26	0.091693	207 -- 244	40 -- 100	tryptophanyl-tRNA synthetase		_____________206___________________________________________________________245\n_____________\|_____________________________________________________________\|\n5'-ACA...UGACU___________UUUUA__________________________________________U__AUUGA...AUG-3'\n______________AAGCCCAUCGU_____GUGG__________CGCACAGC____________C_CUCAGG_GA\n______________\|\|\|\|\|\|\|\|\|\|\|_____:\|\|\|__________\|:\|\|\|\|\|\|____________\|_\|\|\|\|\|\|_\|\|\n______________UUCGGGUAGCA_____UACC__________GUGUGUCG____________G_GAGUCC_CU\n______3'-UUUUU___________CCCUC____CGUUUCUGAU________UUAAGCAACAAA_U______C__AAAGG...GCA-5'\n_____________\|_____________________________________________________________\|\n_____________101___________________________________________________________39\n	228 -- 234	63 -- 69	-41.2838 kcal/mol	11.4457 kcal/mol	17.5818 kcal/mol	206 245@LB@ \| \|@LB@5'-ACA...UGACU UUUUA U AUUGA...AUG-3'@LB@ AAGCCCAUCGU GUGG CGCACAGC C CUCAGG GA@LB@ \|\|\|\|\|\|\|\|\|\|\| :\|\|\| \|:\|\|\|\|\|\| \| \|\|\|\|\|\| \|\|@LB@ UUCGGGUAGCA UACC GUGUGUCG G GAGUCC CU@LB@ 3'-UUUUU CCCUC CGUUUCUGAU UUAAGCAACAAA U C AAAGG...GCA-5'@LB@ \| \|@LB@ 101 39@LB@@LB@@LB@Energy -12.26 kcal/mol@LB@Hybridization Energy -41.2838 kcal/mol@LB@Unfolding Energy - mRNA 11.4457 kcal/mol@LB@Unfolding Energy - sRNA 17.5818 kcal/mol@LB@@LB@Position - mRNA 207 -- 244@LB@Position - sRNA 40 -- 100@LB@Position Seed - mRNA 228 -- 234@LB@Position Seed - sRNA 63 -- 69@LB@
126	0.00562	0.157	b3017	ftsP	-15.30	0.017476	190 -- 242	38 -- 84	septal ring component that protects the divisome from stress; multicopy suppressor of ftsI(Ts)		_____________189____________________________________________________243\n_____________\|______________________________________________________\|\n5'-GAC...UUUAC____A_____U__GU___U____CGG____CAG________GGCAUC_______GCACU...CGC-3'\n______________AUGG_GCAAA_AU__CAC_CAGU____CGU___UUCAUUCA______GGGGAUU\n______________\|\|\|\|_\|\|\|\|\|_\|:__\|\|\|_\|\|\|:____\|\|\|___\|\|\|\|:\|\|\|______\|\|\|\|\|\|\|\n______________UACC_CGUUU_UG__GUG_GUCG____GCA___AAGUGAGU______CCCCUAA\n3'-UUU...CCCUC__________C__AU___U____UUAA___ACA_____________________AGGUA...GCA-5'\n_____________\|______________________________________________________\|\n_____________85_____________________________________________________37\n	236 -- 242	38 -- 44	-40.4092 kcal/mol	11.1124 kcal/mol	13.9994 kcal/mol	189 243@LB@ \| \|@LB@5'-GAC...UUUAC A U GU U CGG CAG GGCAUC GCACU...CGC-3'@LB@ AUGG GCAAA AU CAC CAGU CGU UUCAUUCA GGGGAUU@LB@ \|\|\|\| \|\|\|\|\| \|: \|\|\| \|\|\|: \|\|\| \|\|\|\|:\|\|\| \|\|\|\|\|\|\|@LB@ UACC CGUUU UG GUG GUCG GCA AAGUGAGU CCCCUAA@LB@3'-UUU...CCCUC C AU U UUAA ACA AGGUA...GCA-5'@LB@ \| \|@LB@ 85 37@LB@@LB@@LB@Energy -15.30 kcal/mol@LB@Hybridization Energy -40.4092 kcal/mol@LB@Unfolding Energy - mRNA 11.1124 kcal/mol@LB@Unfolding Energy - sRNA 13.9994 kcal/mol@LB@@LB@Position - mRNA 190 -- 242@LB@Position - sRNA 38 -- 84@LB@Position Seed - mRNA 236 -- 242@LB@Position Seed - sRNA 38 -- 44@LB@
127	0.005686	0.1575	b1176	minC	-17.54	0.003902	3 -- 40	35 -- 74	inhibitor of FtsZ ring polymerization		_____________2________________________________________41\n_____________\|________________________________________\|\n_________5'-AA_G_____________GG____A__G__A_____U______UAAGC...AAG-3'\n______________A_UACG_ACGGCAAU__GUUG_UU_AC__AGGG_AUUUUU\n______________\|_\|\|\|:_\|\|:\|\|\|\|\|__\|\|\|\|_\|\|_\|\|__\|\|\|\|_\|\|\|\|::\n______________U_AUGU_UGUCGUUA__CAAC_AA_UG__UCCC_UAAAGG\n3'-UUU...GUUUC_G____G________AG____A__G__AG____C______UACGA...GCA-5'\n_____________\|________________________________________\|\n_____________75_______________________________________34\n	10 -- 16	60 -- 66	-29.7113 kcal/mol	7.37167 kcal/mol	4.80541 kcal/mol	2 41@LB@ \| \|@LB@ 5'-AA G GG A G A U UAAGC...AAG-3'@LB@ A UACG ACGGCAAU GUUG UU AC AGGG AUUUUU@LB@ \| \|\|\|: \|\|:\|\|\|\|\| \|\|\|\| \|\| \|\| \|\|\|\| \|\|\|\|::@LB@ U AUGU UGUCGUUA CAAC AA UG UCCC UAAAGG@LB@3'-UUU...GUUUC G G AG A G AG C UACGA...GCA-5'@LB@ \| \|@LB@ 75 34@LB@@LB@@LB@Energy -17.54 kcal/mol@LB@Hybridization Energy -29.7113 kcal/mol@LB@Unfolding Energy - mRNA 7.37167 kcal/mol@LB@Unfolding Energy - sRNA 4.80541 kcal/mol@LB@@LB@Position - mRNA 3 -- 40@LB@Position - sRNA 35 -- 74@LB@Position Seed - mRNA 10 -- 16@LB@Position Seed - sRNA 60 -- 66@LB@
128	0.005802	0.1577	b2889	idi	-10.08	0.237455	129 -- 166	33 -- 74	isopentenyl diphosphate isomerase		_____________128________________________________________167\n_____________\|__________________________________________\|\n5'-CUC...UAAAC_______UU___UAA__A___________UUCAAUUA_____AAUGA...UCG-3'\n______________GCU_CAC__GGU___UC____UUUCACUC________UCUAU\n______________:\|\|_\|\|\|__:\|:___\|\|____\|\|\|\|\|\|\|\|________\|\|:\|\|\n______________UGA_GUG__UCG___AG____AAAGUGAG________AGGUA\n3'-UUU...GUUUC___U___UG___UUA__CAAC________UCCCCUAA_____CGAAU...GCA-5'\n_____________\|__________________________________________\|\n_____________75_________________________________________32\n	147 -- 153	46 -- 52	-18.0124 kcal/mol	3.11816 kcal/mol	4.81602 kcal/mol	128 167@LB@ \| \|@LB@5'-CUC...UAAAC UU UAA A UUCAAUUA AAUGA...UCG-3'@LB@ GCU CAC GGU UC UUUCACUC UCUAU@LB@ :\|\| \|\|\| :\|: \|\| \|\|\|\|\|\|\|\| \|\|:\|\|@LB@ UGA GUG UCG AG AAAGUGAG AGGUA@LB@3'-UUU...GUUUC U UG UUA CAAC UCCCCUAA CGAAU...GCA-5'@LB@ \| \|@LB@ 75 32@LB@@LB@@LB@Energy -10.08 kcal/mol@LB@Hybridization Energy -18.0124 kcal/mol@LB@Unfolding Energy - mRNA 3.11816 kcal/mol@LB@Unfolding Energy - sRNA 4.81602 kcal/mol@LB@@LB@Position - mRNA 129 -- 166@LB@Position - sRNA 33 -- 74@LB@Position Seed - mRNA 147 -- 153@LB@Position Seed - sRNA 46 -- 52@LB@
129	0.005822	0.1577	b0713	ybgL	-14.99	0.021088	226 -- 247	61 -- 83	UPF0271 family protein		_____________225_____________________248\n_____________\|_______________________\|\n5'-GCC...CGAUC_______________________CGCAG...AUG-3'\n______________UGGGCGAAGGCUGCGC_CAGCGA\n______________\|\|\|\|\|:\|\|\|:\|\|:\|:\|_\|\|\|\|:\|\n______________ACCCGUUUCUGAUGUG_GUCGUU\n3'-UUU...CCUCU________________U______AAGCA...GCA-5'\n_____________\|_______________________\|\n_____________84______________________60\n	234 -- 240	69 -- 75	-36.9571 kcal/mol	11.7384 kcal/mol	10.2322 kcal/mol	225 248@LB@ \| \|@LB@5'-GCC...CGAUC CGCAG...AUG-3'@LB@ UGGGCGAAGGCUGCGC CAGCGA@LB@ \|\|\|\|\|:\|\|\|:\|\|:\|:\| \|\|\|\|:\|@LB@ ACCCGUUUCUGAUGUG GUCGUU@LB@3'-UUU...CCUCU U AAGCA...GCA-5'@LB@ \| \|@LB@ 84 60@LB@@LB@@LB@Energy -14.99 kcal/mol@LB@Hybridization Energy -36.9571 kcal/mol@LB@Unfolding Energy - mRNA 11.7384 kcal/mol@LB@Unfolding Energy - sRNA 10.2322 kcal/mol@LB@@LB@Position - mRNA 226 -- 247@LB@Position - sRNA 61 -- 83@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 69 -- 75@LB@
130	0.005881	0.1577	b0965	yccU	-10.68	0.186123	93 -- 125	46 -- 74	putative CoA-binding protein		_____________92________________________________126\n_____________\|_________________________________\|\n5'-UCA...UACUU___A________A__UAU___CCGC________UCAUU...UGA-3'\n______________ACU_ACAUAUAG_CA___UUC____UUUUGCUC\n______________\|\|\|_\|\|\|:\|:\|\|_\|\|___\|\|\|____\|\|\|::\|\|\|\n______________UGA_UGUGUGUC_GU___AAG____AAAGUGAG\n3'-UUU...GUUUC_______________U_____CAAC________UCCCC...GCA-5'\n_____________\|_________________________________\|\n_____________75________________________________45\n	119 -- 125	46 -- 52	-18.0647 kcal/mol	3.65669 kcal/mol	3.72594 kcal/mol	92 126@LB@ \| \|@LB@5'-UCA...UACUU A A UAU CCGC UCAUU...UGA-3'@LB@ ACU ACAUAUAG CA UUC UUUUGCUC@LB@ \|\|\| \|\|\|:\|:\|\| \|\| \|\|\| \|\|\|::\|\|\|@LB@ UGA UGUGUGUC GU AAG AAAGUGAG@LB@3'-UUU...GUUUC U CAAC UCCCC...GCA-5'@LB@ \| \|@LB@ 75 45@LB@@LB@@LB@Energy -10.68 kcal/mol@LB@Hybridization Energy -18.0647 kcal/mol@LB@Unfolding Energy - mRNA 3.65669 kcal/mol@LB@Unfolding Energy - sRNA 3.72594 kcal/mol@LB@@LB@Position - mRNA 93 -- 125@LB@Position - sRNA 46 -- 74@LB@Position Seed - mRNA 119 -- 125@LB@Position Seed - sRNA 46 -- 52@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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