Input and runtime details for job 5882223 (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 5882223 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:39:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 03:02:39 CET 2018
	Post-Processing Finished		@ Sat Feb 17 03:02:47 CET 2018
	Job Completed		@ Sat Feb 17 03:03:15 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5882223&toolName=CopraRNA ( 30 days expiry )

Description of the job

Spot42

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
75	0.001328	0.06227	b1748	astC	-8.39	0.124654	121 -- 127	1 -- 7	succinylornithine transaminase PLP-dependent	_____________120_____128\n_____________\|_______\|\n5'-UCA...CACGA_______AAUCU...UGU-3'\n______________ACCCUGC\n______________\|\|\|\|\|:\|\n______________UGGGAUG\n3'-AUU...AGACA_______-5'\n_____________\|______\|\n_____________8______1\n	121 -- 127	1 -- 7	-11.9071 kcal/mol	1.50434 kcal/mol	2.03949 kcal/mol	120 128@LB@ \| \|@LB@5'-UCA...CACGA AAUCU...UGU-3'@LB@ ACCCUGC@LB@ \|\|\|\|\|:\|@LB@ UGGGAUG@LB@3'-AUU...AGACA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -8.39 kcal/mol@LB@Hybridization Energy -11.9071 kcal/mol@LB@Unfolding Energy - mRNA 1.50434 kcal/mol@LB@Unfolding Energy - sRNA 2.03949 kcal/mol@LB@@LB@Position - mRNA 121 -- 127@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 121 -- 127@LB@Position Seed - sRNA 1 -- 7@LB@
101	0.00315	0.1097	b1822	rlmA	-7.85	0.169074	182 -- 190	1 -- 9	23S rRNA m(1)G745 methyltransferase SAM-dependent	_____________181_______191\n_____________\|_________\|\n5'-AAG...CUUUA_________CGGAG...GGU-3'\n______________GUAUCCUGC\n______________\|\|\|:\|\|\|:\|\n______________CAUGGGAUG\n3'-AUU...GGAGA_________-5'\n_____________\|________\|\n_____________10_______1\n	184 -- 190	1 -- 7	-13.1594 kcal/mol	3.20778 kcal/mol	2.12872 kcal/mol	181 191@LB@ \| \|@LB@5'-AAG...CUUUA CGGAG...GGU-3'@LB@ GUAUCCUGC@LB@ \|\|\|:\|\|\|:\|@LB@ CAUGGGAUG@LB@3'-AUU...GGAGA -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -7.85 kcal/mol@LB@Hybridization Energy -13.1594 kcal/mol@LB@Unfolding Energy - mRNA 3.20778 kcal/mol@LB@Unfolding Energy - sRNA 2.12872 kcal/mol@LB@@LB@Position - mRNA 182 -- 190@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 1 -- 7@LB@
83	0.001985	0.08414	b1901	araF	-10.36	0.035498	164 -- 171	1 -- 8	L-arabinose ABC transporter periplasmic binding protein	_____________163______172\n_____________\|________\|\n5'-UCC...GUUUU________ACAAA...AGC-3'\n______________UGCCCUAC\n______________\|:\|\|\|\|\|\|\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	165 -- 171	1 -- 7	-13.292 kcal/mol	0.840759 kcal/mol	2.11603 kcal/mol	163 172@LB@ \| \|@LB@5'-UCC...GUUUU ACAAA...AGC-3'@LB@ UGCCCUAC@LB@ \|:\|\|\|\|\|\|@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -10.36 kcal/mol@LB@Hybridization Energy -13.292 kcal/mol@LB@Unfolding Energy - mRNA 0.840759 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 164 -- 171@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 165 -- 171@LB@Position Seed - sRNA 1 -- 7@LB@
9	1.988e-05	0.007771	b1985	yeeO	-11.51	0.015356	224 -- 255	1 -- 39	putative multdrug exporter MATE family	_____________223_____________________________________256\n_____________\|_______________________________________\|\n5'-GAU...CAAUU______GGCUUU___________________________GCCAG...GCU-3'\n______________AAGGUC_________GAAUAUCU__CCUCUG__CUUUAC\n______________\|\|\|\|\|\|_________\|\|\|:\|\|\|\|__\|\|\|\|\|\|__\|::\|\|\|\n______________UUCCAG_________CUUGUAGA__GGAGAC__GGGAUG\n3'-AUU...UCAUU______ACUUUCUAU________AU______AU______-5'\n_____________\|______________________________________\|\n_____________40_____________________________________1\n	237 -- 243	17 -- 23	-28.0657 kcal/mol	5.21805 kcal/mol	11.3576 kcal/mol	223 256@LB@ \| \|@LB@5'-GAU...CAAUU GGCUUU GCCAG...GCU-3'@LB@ AAGGUC GAAUAUCU CCUCUG CUUUAC@LB@ \|\|\|\|\|\| \|\|\|:\|\|\|\| \|\|\|\|\|\| \|::\|\|\|@LB@ UUCCAG CUUGUAGA GGAGAC GGGAUG@LB@3'-AUU...UCAUU ACUUUCUAU AU AU -5'@LB@ \| \|@LB@ 40 1@LB@@LB@@LB@Energy -11.51 kcal/mol@LB@Hybridization Energy -28.0657 kcal/mol@LB@Unfolding Energy - mRNA 5.21805 kcal/mol@LB@Unfolding Energy - sRNA 11.3576 kcal/mol@LB@@LB@Position - mRNA 224 -- 255@LB@Position - sRNA 1 -- 39@LB@Position Seed - mRNA 237 -- 243@LB@Position Seed - sRNA 17 -- 23@LB@
84	0.002084	0.08729	b2067	yegE	-5.99	0.414041	137 -- 150	1 -- 15	putative diguanylate cyclase	_____________136_____________151\n_____________\|_______________\|\n5'-AGU...GUAAA___________A___AUAAA...CGC-3'\n______________ACUUUUGUACU__GC\n______________\|\|:\|:\|\|\|\|\|:__:\|\n______________UGGAGACAUGG__UG\n3'-AUU...UAGAA___________GA__-5'\n_____________\|______________\|\n_____________16_____________1\n	141 -- 147	5 -- 11	-13.6769 kcal/mol	1.88278 kcal/mol	5.82808 kcal/mol	136 151@LB@ \| \|@LB@5'-AGU...GUAAA A AUAAA...CGC-3'@LB@ ACUUUUGUACU GC@LB@ \|\|:\|:\|\|\|\|\|: :\|@LB@ UGGAGACAUGG UG@LB@3'-AUU...UAGAA GA -5'@LB@ \| \|@LB@ 16 1@LB@@LB@@LB@Energy -5.99 kcal/mol@LB@Hybridization Energy -13.6769 kcal/mol@LB@Unfolding Energy - mRNA 1.88278 kcal/mol@LB@Unfolding Energy - sRNA 5.82808 kcal/mol@LB@@LB@Position - mRNA 137 -- 150@LB@Position - sRNA 1 -- 15@LB@Position Seed - mRNA 141 -- 147@LB@Position Seed - sRNA 5 -- 11@LB@
58	0.000878	0.0531	b2150	mglB	-10.24	0.038484	153 -- 179	1 -- 24	methyl-galactoside transporter subunit	_____________152__________________________180\n_____________\|____________________________\|\n5'-GUA...CCGCC______________AAGCAC________AUAAG...AUA-3'\n______________GAGCAUU_UAUCUC______UACCCUGC\n______________\|\|:\|\|\|:_\|\|:\|\|\|______\|\|\|\|\|\|:\|\n______________CUUGUAG_AUGGAG______AUGGGAUG\n3'-AUU...UCUAU_______A______AC____________-5'\n_____________\|___________________________\|\n_____________25__________________________1\n	173 -- 179	1 -- 7	-24.5136 kcal/mol	6.27388 kcal/mol	8.02158 kcal/mol	152 180@LB@ \| \|@LB@5'-GUA...CCGCC AAGCAC AUAAG...AUA-3'@LB@ GAGCAUU UAUCUC UACCCUGC@LB@ \|\|:\|\|\|: \|\|:\|\|\| \|\|\|\|\|\|:\|@LB@ CUUGUAG AUGGAG AUGGGAUG@LB@3'-AUU...UCUAU A AC -5'@LB@ \| \|@LB@ 25 1@LB@@LB@@LB@Energy -10.24 kcal/mol@LB@Hybridization Energy -24.5136 kcal/mol@LB@Unfolding Energy - mRNA 6.27388 kcal/mol@LB@Unfolding Energy - sRNA 8.02158 kcal/mol@LB@@LB@Position - mRNA 153 -- 179@LB@Position - sRNA 1 -- 24@LB@Position Seed - mRNA 173 -- 179@LB@Position Seed - sRNA 1 -- 7@LB@
105	0.003348	0.1101	b2218	rcsC	-11.03	0.021992	174 -- 214	1 -- 37	hybrid sensory kinase in two-component regulatory system with RcsB and YojN	_____________173_______________________________________215\n_____________\|_________________________________________\|\n5'-AGC...CCAUC____ACCU____C_____U__GCC______AAA________UUCUU...CCG-3'\n______________GGUC____GAGG_GGAGC_UC___CCUUUG___UACCUUGC\n______________\|\|\|\|____:\|\|:_:\|\|:\|_\|\|___\|\|\|:\|\|___\|\|\|\|:\|:\|\n______________CCAG____UUCU_UCUUG_AG___GGAGAC___AUGGGAUG\n3'-AUU...AUUUU____ACU_____A_____U__AAU_________________-5'\n_____________\|________________________________________\|\n_____________38_______________________________________1\n	208 -- 214	1 -- 7	-33.3544 kcal/mol	10.9963 kcal/mol	11.3499 kcal/mol	173 215@LB@ \| \|@LB@5'-AGC...CCAUC ACCU C U GCC AAA UUCUU...CCG-3'@LB@ GGUC GAGG GGAGC UC CCUUUG UACCUUGC@LB@ \|\|\|\| :\|\|: :\|\|:\| \|\| \|\|\|:\|\| \|\|\|\|:\|:\|@LB@ CCAG UUCU UCUUG AG GGAGAC AUGGGAUG@LB@3'-AUU...AUUUU ACU A U AAU -5'@LB@ \| \|@LB@ 38 1@LB@@LB@@LB@Energy -11.03 kcal/mol@LB@Hybridization Energy -33.3544 kcal/mol@LB@Unfolding Energy - mRNA 10.9963 kcal/mol@LB@Unfolding Energy - sRNA 11.3499 kcal/mol@LB@@LB@Position - mRNA 174 -- 214@LB@Position - sRNA 1 -- 37@LB@Position Seed - mRNA 208 -- 214@LB@Position Seed - sRNA 1 -- 7@LB@
177	0.007672	0.1511	b2307	hisM	-10.48	0.032509	175 -- 237	1 -- 57	histidine ABC transporter permease	_____________174__________________________________________________________________238\n_____________\|____________________________________________________________________\|\n5'-CUC...GCUAC____UGGG___________________CCUGU___C___________AUGAAUA___GAA___G____UGUGG...CGG-3'\n______________UCCG____UGUGAAG___AGGG_CUGA_____GAU_GAA_AUCUUAC_______CUG___ACC_CUGC\n______________\|\|\|\|____:\|\|\|\|\|\|___\|:\|\|_\|\|\|\|_____\|\|\|_\|\|\|_\|\|\|\|\|\|\|_______\|\|\|___\|\|\|_\|\|:\|\n______________AGGC____GCACUUC___UUCC_GACU_____CUA_CUU_UAGAAUG_______GAC___UGG_GAUG\n3'-AUU...GGUUU____UAAU_______AUU____A____UU______U___G_______GA________A__________-5'\n_____________\|___________________________________________________________________\|\n_____________58__________________________________________________________________1\n	210 -- 216	14 -- 20	-38.5224 kcal/mol	15.358 kcal/mol	12.7026 kcal/mol	174 238@LB@ \| \|@LB@5'-CUC...GCUAC UGGG CCUGU C AUGAAUA GAA G UGUGG...CGG-3'@LB@ UCCG UGUGAAG AGGG CUGA GAU GAA AUCUUAC CUG ACC CUGC@LB@ \|\|\|\| :\|\|\|\|\|\| \|:\|\| \|\|\|\| \|\|\| \|\|\| \|\|\|\|\|\|\| \|\|\| \|\|\| \|\|:\|@LB@ AGGC GCACUUC UUCC GACU CUA CUU UAGAAUG GAC UGG GAUG@LB@3'-AUU...GGUUU UAAU AUU A UU U G GA A -5'@LB@ \| \|@LB@ 58 1@LB@@LB@@LB@Energy -10.48 kcal/mol@LB@Hybridization Energy -38.5224 kcal/mol@LB@Unfolding Energy - mRNA 15.358 kcal/mol@LB@Unfolding Energy - sRNA 12.7026 kcal/mol@LB@@LB@Position - mRNA 175 -- 237@LB@Position - sRNA 1 -- 57@LB@Position Seed - mRNA 210 -- 216@LB@Position Seed - sRNA 14 -- 20@LB@
114	0.003723	0.1147	b2327	yfcA	-8.38	0.125082	22 -- 29	1 -- 8	TauE/TSUP family inner membrane protein	_____________21_______30\n_____________\|________\|\n5'-CAU...UACGU________CGAUA...GUG-3'\n______________UGCCCUGC\n______________\|:\|\|\|\|:\|\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	23 -- 29	1 -- 7	-12.241 kcal/mol	1.76759 kcal/mol	2.11603 kcal/mol	21 30@LB@ \| \|@LB@5'-CAU...UACGU CGAUA...GUG-3'@LB@ UGCCCUGC@LB@ \|:\|\|\|\|:\|@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -8.38 kcal/mol@LB@Hybridization Energy -12.241 kcal/mol@LB@Unfolding Energy - mRNA 1.76759 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 22 -- 29@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 23 -- 29@LB@Position Seed - sRNA 1 -- 7@LB@
21	0.0001601	0.02641	b2344	fadL	-13.31	0.003531	80 -- 135	1 -- 58	long-chain fatty acid outer membrane transporter	_____________79_________________________________________________________________136\n_____________\|__________________________________________________________________\|\n5'-UCC...AGCUG______CCUA___UCUCGCCACU________UUUCU____________________A_________ACUUC...UUU-3'\n______________GUCCGA____UAC___________GGUCUGA_____AAGAUG________UACCUC_G_ACCCUAC\n______________:\|\|\|\|\|____\|\|\|___________\|\|\|\|\|\|\|_____\|\|\|\|\|:________\|\|\|\|\|\|_\|_\|\|\|\|\|\|\|\n______________UAGGCU____AUG___________CCAGACU_____UUCUAU________AUGGAG_C_UGGGAUG\n3'-AUU...CGGUU______A______CACUUCAUUUU__________________CUUGUAGA______A_A_______-5'\n_____________\|_________________________________________________________________\|\n_____________59________________________________________________________________1\n	129 -- 135	1 -- 7	-38.7471 kcal/mol	12.7593 kcal/mol	12.7027 kcal/mol	79 136@LB@ \| \|@LB@5'-UCC...AGCUG CCUA UCUCGCCACU UUUCU A ACUUC...UUU-3'@LB@ GUCCGA UAC GGUCUGA AAGAUG UACCUC G ACCCUAC@LB@ :\|\|\|\|\| \|\|\| \|\|\|\|\|\|\| \|\|\|\|\|: \|\|\|\|\|\| \| \|\|\|\|\|\|\|@LB@ UAGGCU AUG CCAGACU UUCUAU AUGGAG C UGGGAUG@LB@3'-AUU...CGGUU A CACUUCAUUUU CUUGUAGA A A -5'@LB@ \| \|@LB@ 59 1@LB@@LB@@LB@Energy -13.31 kcal/mol@LB@Hybridization Energy -38.7471 kcal/mol@LB@Unfolding Energy - mRNA 12.7593 kcal/mol@LB@Unfolding Energy - sRNA 12.7027 kcal/mol@LB@@LB@Position - mRNA 80 -- 135@LB@Position - sRNA 1 -- 58@LB@Position Seed - mRNA 129 -- 135@LB@Position Seed - sRNA 1 -- 7@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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