Input and runtime details for job 1229462 (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 1229462 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:41 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:59 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:22:57 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:23:04 CET 2018
	Job Completed		@ Fri Feb 16 20:23:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1229462&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicF

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
35	0.003306	0.3101	b0551	quuD	-13.48	0.016718	188 -- 210	3 -- 24	DLP12 prophage; putative antitermination protein	_____________187_____________________211\n_____________\|_______________________\|\n5'-ACU...UUUUU_____GU_________C______UUCAG...GAU-3'\n______________GUGGA__AAGUUGAUG_GUGAUA\n______________:\|::\|__\|\|\|\|\|:\|\|\|_:\|\|\|\|\|\n______________UAUUU__UUCAAUUAC_UACUAU\n3'-UUU...GCCAU_____AU________________CG-5'\n_____________\|_______________________\|\n_____________25______________________2\n	197 -- 203	9 -- 15	-17.2545 kcal/mol	3.66311 kcal/mol	0.108279 kcal/mol	187 211@LB@ \| \|@LB@5'-ACU...UUUUU GU C UUCAG...GAU-3'@LB@ GUGGA AAGUUGAUG GUGAUA@LB@ :\|::\| \|\|\|\|\|:\|\|\| :\|\|\|\|\|@LB@ UAUUU UUCAAUUAC UACUAU@LB@3'-UUU...GCCAU AU CG-5'@LB@ \| \|@LB@ 25 2@LB@@LB@@LB@Energy -13.48 kcal/mol@LB@Hybridization Energy -17.2545 kcal/mol@LB@Unfolding Energy - mRNA 3.66311 kcal/mol@LB@Unfolding Energy - sRNA 0.108279 kcal/mol@LB@@LB@Position - mRNA 188 -- 210@LB@Position - sRNA 3 -- 24@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 9 -- 15@LB@
87	0.01323	0.4992	b1951	rcsA	-11.40	0.049597	149 -- 196	25 -- 65	transcriptional regulator of colanic acid capsular biosynthesis	_____________148______________________________________________197\n_____________\|________________________________________________\|\n5'-GUU...CAUGA_______UUCA______G___AUUAU____ACGCAU_______G____UGCCA...UUG-3'\n______________UGAAAUA____GGUAAG_GGA_____CGUU______UGAGUGA_GGUA\n______________\|\|\|\|\|\|\|____\|\|\|\|\|:_:\|\|_____\|:\|\|______\|\|\|:\|\|\|_\|\|\|\|\n______________ACUUUAU____CCAUUU_UCU_____GUAA______ACUUACU_CCAU\n3'-UUU...GGCCA_______CC________G____________GUCUUU_______G____UAUUU...UCG-5'\n_____________\|________________________________________________\|\n_____________66_______________________________________________24\n	149 -- 155	59 -- 65	-29.5865 kcal/mol	10.9819 kcal/mol	7.2015 kcal/mol	148 197@LB@ \| \|@LB@5'-GUU...CAUGA UUCA G AUUAU ACGCAU G UGCCA...UUG-3'@LB@ UGAAAUA GGUAAG GGA CGUU UGAGUGA GGUA@LB@ \|\|\|\|\|\|\| \|\|\|\|\|: :\|\| \|:\|\| \|\|\|:\|\|\| \|\|\|\|@LB@ ACUUUAU CCAUUU UCU GUAA ACUUACU CCAU@LB@3'-UUU...GGCCA CC G GUCUUU G UAUUU...UCG-5'@LB@ \| \|@LB@ 66 24@LB@@LB@@LB@Energy -11.40 kcal/mol@LB@Hybridization Energy -29.5865 kcal/mol@LB@Unfolding Energy - mRNA 10.9819 kcal/mol@LB@Unfolding Energy - sRNA 7.2015 kcal/mol@LB@@LB@Position - mRNA 149 -- 196@LB@Position - sRNA 25 -- 65@LB@Position Seed - mRNA 149 -- 155@LB@Position Seed - sRNA 59 -- 65@LB@
51	0.006039	0.3887	b3822	recQ	-9.34	0.130811	192 -- 200	50 -- 58	ATP-dependent DNA helicase	_____________191_______201\n_____________\|_________\|\n5'-CGC...CAAUC_________GUGGC...UUA-3'\n______________GGGGUGAAU\n______________\|\|\|\|\|:\|\|:\n______________CCCCAUUUG\n3'-UUU...UUUAU_________UCUGU...UCG-5'\n_____________\|_________\|\n_____________59________49\n	194 -- 200	50 -- 56	-13.8974 kcal/mol	3.8337 kcal/mol	0.72763 kcal/mol	191 201@LB@ \| \|@LB@5'-CGC...CAAUC GUGGC...UUA-3'@LB@ GGGGUGAAU@LB@ \|\|\|\|\|:\|\|:@LB@ CCCCAUUUG@LB@3'-UUU...UUUAU UCUGU...UCG-5'@LB@ \| \|@LB@ 59 49@LB@@LB@@LB@Energy -9.34 kcal/mol@LB@Hybridization Energy -13.8974 kcal/mol@LB@Unfolding Energy - mRNA 3.8337 kcal/mol@LB@Unfolding Energy - sRNA 0.72763 kcal/mol@LB@@LB@Position - mRNA 192 -- 200@LB@Position - sRNA 50 -- 58@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 50 -- 56@LB@
131	0.02082	0.5217	b2038	rfbC	-12.83	0.023839	249 -- 268	2 -- 18	dTDP-4-deoxyrhamnose-3 5-epimerase	_____________248__________________269\n_____________\|____________________\|\n5'-GGG...AGCCA_____AUU____________AGGUU...CAG-3'\n______________AGAGU___UGGUGAUGAUAG\n______________\|:\|\|\|___\|::\|\|\|\|\|\|\|\|\|\n______________UUUCA___AUUACUACUAUC\n3'-UUU...AUUUA____________________G-5'\n_____________\|____________________\|\n_____________19___________________1\n	262 -- 268	2 -- 8	-17.1909 kcal/mol	4.30321 kcal/mol	0.0608678 kcal/mol	248 269@LB@ \| \|@LB@5'-GGG...AGCCA AUU AGGUU...CAG-3'@LB@ AGAGU UGGUGAUGAUAG@LB@ \|:\|\|\| \|::\|\|\|\|\|\|\|\|\|@LB@ UUUCA AUUACUACUAUC@LB@3'-UUU...AUUUA G-5'@LB@ \| \|@LB@ 19 1@LB@@LB@@LB@Energy -12.83 kcal/mol@LB@Hybridization Energy -17.1909 kcal/mol@LB@Unfolding Energy - mRNA 4.30321 kcal/mol@LB@Unfolding Energy - sRNA 0.0608678 kcal/mol@LB@@LB@Position - mRNA 249 -- 268@LB@Position - sRNA 2 -- 18@LB@Position Seed - mRNA 262 -- 268@LB@Position Seed - sRNA 2 -- 8@LB@
89	0.01433	0.5059	b0636	rlmH	-12.18	0.033475	189 -- 207	1 -- 19	23S rRNA m(3)Psi1915 pseudouridine methyltransferase SAM-dependent	_____________188__________________208\n_____________\|____________________\|\n5'-CGG...AACUC___________C________UGCAA...UCG-3'\n______________UGGAGUUAAUG_GUGA_AGC\n______________\|::\|\|\|\|\|\|\|\|_:\|\|\|_\|\|\|\n______________AUUUCAAUUAC_UACU_UCG\n3'-UUU...UAUUU________________A___-5'\n_____________\|___________________\|\n_____________20__________________1\n	193 -- 199	9 -- 15	-16.4949 kcal/mol	4.25175 kcal/mol	0.0638423 kcal/mol	188 208@LB@ \| \|@LB@5'-CGG...AACUC C UGCAA...UCG-3'@LB@ UGGAGUUAAUG GUGA AGC@LB@ \|::\|\|\|\|\|\|\|\| :\|\|\| \|\|\|@LB@ AUUUCAAUUAC UACU UCG@LB@3'-UUU...UAUUU A -5'@LB@ \| \|@LB@ 20 1@LB@@LB@@LB@Energy -12.18 kcal/mol@LB@Hybridization Energy -16.4949 kcal/mol@LB@Unfolding Energy - mRNA 4.25175 kcal/mol@LB@Unfolding Energy - sRNA 0.0638423 kcal/mol@LB@@LB@Position - mRNA 189 -- 207@LB@Position - sRNA 1 -- 19@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 9 -- 15@LB@
129	0.02061	0.5217	b0633	rlpA	-9.57	0.117965	261 -- 273	1 -- 12	septal ring protein suppressor of prc minor lipoprotein	_____________260___________274\n_____________\|_____________\|\n5'-CGG...CAAGC_________C___AACAG...CUG-3'\n______________GAUGAUGGU_AGC\n______________:\|\|\|\|\|\|:\|_\|\|\|\n______________UUACUACUA_UCG\n3'-UUU...UUCAA_____________-5'\n_____________\|____________\|\n_____________13___________1\n	263 -- 269	4 -- 10	-13.3317 kcal/mol	3.7231 kcal/mol	0.0394463 kcal/mol	260 274@LB@ \| \|@LB@5'-CGG...CAAGC C AACAG...CUG-3'@LB@ GAUGAUGGU AGC@LB@ :\|\|\|\|\|\|:\| \|\|\|@LB@ UUACUACUA UCG@LB@3'-UUU...UUCAA -5'@LB@ \| \|@LB@ 13 1@LB@@LB@@LB@Energy -9.57 kcal/mol@LB@Hybridization Energy -13.3317 kcal/mol@LB@Unfolding Energy - mRNA 3.7231 kcal/mol@LB@Unfolding Energy - sRNA 0.0394463 kcal/mol@LB@@LB@Position - mRNA 261 -- 273@LB@Position - sRNA 1 -- 12@LB@Position Seed - mRNA 263 -- 269@LB@Position Seed - sRNA 4 -- 10@LB@
50	0.005695	0.3739	b1086	rluC	-13.13	0.020232	139 -- 168	28 -- 55	23S rRNA pseudouridine(955 2504 2580) synthase	_____________138____________________________169\n_____________\|______________________________\|\n5'-UCC...CAAAA_______UAA____AG_A____________CGAAU...UAC-3'\n______________GUAAAUA___GCAU__A_AAAUGAGUGGCG\n______________\|\|\|\|\|:\|___:\|\|\|__\|_\|\|\|\|\|\|:\|\|:\|\|\n______________CAUUUGU___UGUA__U_UUUACUUACUGC\n3'-UUU...AUCCC_______C______AG_C____________CAUUA...UCG-5'\n_____________\|______________________________\|\n_____________56_____________________________27\n	161 -- 167	29 -- 35	-21.8911 kcal/mol	2.47099 kcal/mol	6.28725 kcal/mol	138 169@LB@ \| \|@LB@5'-UCC...CAAAA UAA AG A CGAAU...UAC-3'@LB@ GUAAAUA GCAU A AAAUGAGUGGCG@LB@ \|\|\|\|\|:\| :\|\|\| \| \|\|\|\|\|\|:\|\|:\|\|@LB@ CAUUUGU UGUA U UUUACUUACUGC@LB@3'-UUU...AUCCC C AG C CAUUA...UCG-5'@LB@ \| \|@LB@ 56 27@LB@@LB@@LB@Energy -13.13 kcal/mol@LB@Hybridization Energy -21.8911 kcal/mol@LB@Unfolding Energy - mRNA 2.47099 kcal/mol@LB@Unfolding Energy - sRNA 6.28725 kcal/mol@LB@@LB@Position - mRNA 139 -- 168@LB@Position - sRNA 28 -- 55@LB@Position Seed - mRNA 161 -- 167@LB@Position Seed - sRNA 29 -- 35@LB@
188	0.03165	0.5492	b3247	rng	-10.28	0.085420	187 -- 220	10 -- 64	ribonuclease G	_____________186_____________________________________________________221\n_____________\|_______________________________________________________\|\n5'-GUU...CGUGA_________A____________________________C_______U________AAACG...CGC-3'\n______________GAAA_AGGG_UAAAC________________AUGACGG___UGAAU___GUUAGU\n______________\|\|\|\|_\|\|\|\|_\|\|\|\|\|________________\|\|\|\|\|\|\|___\|:\|\|\|___\|\|\|\|:\|\n______________CUUU_UCCC_AUUUG________________UACUGCC___AUUUA___CAAUUA\n3'-UUU...GCCAA____A____C_____UCUGUAAGUCUUUACU_______AUU_____UUU______CUACU...UCG-5'\n_____________\|_______________________________________________________\|\n_____________65______________________________________________________9\n	201 -- 207	27 -- 33	-22.7807 kcal/mol	6.16544 kcal/mol	6.33995 kcal/mol	186 221@LB@ \| \|@LB@5'-GUU...CGUGA A C U AAACG...CGC-3'@LB@ GAAA AGGG UAAAC AUGACGG UGAAU GUUAGU@LB@ \|\|\|\| \|\|\|\| \|\|\|\|\| \|\|\|\|\|\|\| \|:\|\|\| \|\|\|\|:\|@LB@ CUUU UCCC AUUUG UACUGCC AUUUA CAAUUA@LB@3'-UUU...GCCAA A C UCUGUAAGUCUUUACU AUU UUU CUACU...UCG-5'@LB@ \| \|@LB@ 65 9@LB@@LB@@LB@Energy -10.28 kcal/mol@LB@Hybridization Energy -22.7807 kcal/mol@LB@Unfolding Energy - mRNA 6.16544 kcal/mol@LB@Unfolding Energy - sRNA 6.33995 kcal/mol@LB@@LB@Position - mRNA 187 -- 220@LB@Position - sRNA 10 -- 64@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 27 -- 33@LB@
147	0.02463	0.526	b2830	rppH	-8.72	0.170707	205 -- 218	1 -- 14	RNA pyrophosphohydrolase	_____________204____________219\n_____________\|______________\|\n5'-UUC...GGUGA_______C______UACCG...GGC-3'\n______________UUGAUGA_GAUGGC\n______________\|\|:\|\|\|\|_\|\|\|:\|\|\n______________AAUUACU_CUAUCG\n3'-UUU...AUUUC_______A______-5'\n_____________\|_____________\|\n_____________15____________1\n	205 -- 211	8 -- 14	-13.7427 kcal/mol	4.97796 kcal/mol	0.0473494 kcal/mol	204 219@LB@ \| \|@LB@5'-UUC...GGUGA C UACCG...GGC-3'@LB@ UUGAUGA GAUGGC@LB@ \|\|:\|\|\|\| \|\|\|:\|\|@LB@ AAUUACU CUAUCG@LB@3'-UUU...AUUUC A -5'@LB@ \| \|@LB@ 15 1@LB@@LB@@LB@Energy -8.72 kcal/mol@LB@Hybridization Energy -13.7427 kcal/mol@LB@Unfolding Energy - mRNA 4.97796 kcal/mol@LB@Unfolding Energy - sRNA 0.0473494 kcal/mol@LB@@LB@Position - mRNA 205 -- 218@LB@Position - sRNA 1 -- 14@LB@Position Seed - mRNA 205 -- 211@LB@Position Seed - sRNA 8 -- 14@LB@
102	0.01618	0.5059	b3306	rpsH	-10.04	0.095208	179 -- 210	1 -- 36	30S ribosomal subunit protein S8	_____________178____________________________________211\n_____________\|______________________________________\|\n5'-AGC...CCAAU_____C________________ACA_______GCAU__AAGAU...AAG-3'\n______________UGAAU_ACGG____GAGUAAAG_____GAUGA____GC\n______________\|\|\|\|\|_\|\|\|\|____:\|:\|\|\|\|\|_____\|\|\|\|\|____\|\|\n______________ACUUA_UGCC____UUUAUUUC_____CUACU____CG\n3'-UUU...UCUUU_____C____AUUA________AAUUA_____AU____-5'\n_____________\|_____________________________________\|\n_____________37____________________________________1\n	190 -- 196	15 -- 21	-20.3749 kcal/mol	4.57112 kcal/mol	5.76239 kcal/mol	178 211@LB@ \| \|@LB@5'-AGC...CCAAU C ACA GCAU AAGAU...AAG-3'@LB@ UGAAU ACGG GAGUAAAG GAUGA GC@LB@ \|\|\|\|\| \|\|\|\| :\|:\|\|\|\|\| \|\|\|\|\| \|\|@LB@ ACUUA UGCC UUUAUUUC CUACU CG@LB@3'-UUU...UCUUU C AUUA AAUUA AU -5'@LB@ \| \|@LB@ 37 1@LB@@LB@@LB@Energy -10.04 kcal/mol@LB@Hybridization Energy -20.3749 kcal/mol@LB@Unfolding Energy - mRNA 4.57112 kcal/mol@LB@Unfolding Energy - sRNA 5.76239 kcal/mol@LB@@LB@Position - mRNA 179 -- 210@LB@Position - sRNA 1 -- 36@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 15 -- 21@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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