Input and runtime details for job 6860187 (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 6860187 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:33 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:58 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 01:36:19 CET 2018
	Post-Processing Finished		@ Sat Feb 17 01:36:26 CET 2018
	Job Completed		@ Sat Feb 17 01:36:50 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6860187&toolName=CopraRNA ( 30 days expiry )

Description of the job

SgrS

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
101	0.01097	0.3575	b1882	cheY	-8.64	0.475467	226 -- 255	72 -- 99	chemotaxis regulator transmitting signal to flagellar motor component	_____________225_______________256\n_____________\|_________________\|\n5'-GCG...AGGCG_______GGA_______GCAAA...UUG-3'\n______________GGGGCAU___CCCUUGC\n______________\|\|\|\|\|\|:___\|\|\|\|\|\|\|\n______________CCCCGUG___GGGAACG\n3'-UUU...GCGUA_______G_________AAGUAG-5'\n_____________\|_________________\|\n_____________100_______________71\n	38 -- 44	7 -- 13	-25.3164 kcal/mol	8.48869 kcal/mol	10.1447 kcal/mol	225 256@LB@ \| \|@LB@5'-GCG...AGGCG GGA GCAAA...UUG-3'@LB@ GGGGCAU CCCUUGC@LB@ \|\|\|\|\|\|: \|\|\|\|\|\|\|@LB@ CCCCGUG GGGAACG@LB@3'-UUU...GCGUA G AAGUAG-5'@LB@ \| \|@LB@ 100 71@LB@@LB@@LB@Energy -8.64 kcal/mol@LB@Hybridization Energy -25.3164 kcal/mol@LB@Unfolding Energy - mRNA 8.48869 kcal/mol@LB@Unfolding Energy - sRNA 10.1447 kcal/mol@LB@@LB@Position - mRNA 226 -- 255@LB@Position - sRNA 72 -- 99@LB@Position Seed - mRNA 38 -- 44@LB@Position Seed - sRNA 7 -- 13@LB@
7	0.0005448	0.1842	b1912	pgsA	-14.68	0.031521	247 -- 274	111 -- 134	phosphatidylglycerophosphate synthetase	_____________246__________________________275\n_____________\|____________________________\|\n5'-GUC...CAUCC_________UCUU_______________UCUGC...UUG-3'\n______________UUAUCCCAU____UGUAUUGGUCUUUUA\n______________\|:\|\|\|\|\|\|:____\|\|:\|\|::\|\|\|:\|\|:\|\n______________AGUAGGGUG____ACGUAGUCAGGAAGU\n3'-UUU...ACGCC____________________________UCGUA...UAG-5'\n_____________\|____________________________\|\n_____________135__________________________110\n	268 -- 274	111 -- 117	-27.9222 kcal/mol	1.79949 kcal/mol	14.1586 kcal/mol	246 275@LB@ \| \|@LB@5'-GUC...CAUCC UCUU UCUGC...UUG-3'@LB@ UUAUCCCAU UGUAUUGGUCUUUUA@LB@ \|:\|\|\|\|\|\|: \|\|:\|\|::\|\|\|:\|\|:\|@LB@ AGUAGGGUG ACGUAGUCAGGAAGU@LB@3'-UUU...ACGCC UCGUA...UAG-5'@LB@ \| \|@LB@ 135 110@LB@@LB@@LB@Energy -14.68 kcal/mol@LB@Hybridization Energy -27.9222 kcal/mol@LB@Unfolding Energy - mRNA 1.79949 kcal/mol@LB@Unfolding Energy - sRNA 14.1586 kcal/mol@LB@@LB@Position - mRNA 247 -- 274@LB@Position - sRNA 111 -- 134@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 111 -- 117@LB@
161	0.01797	0.3749	b1921	fliZ	-13.03	0.068461	73 -- 137	125 -- 204	RpoS antagonist; putative regulator of FliA activity	_____________72__________________________________________138\n_____________\|___________________________________________\|\n5'-UGC...GAGGU_______AU______G___C_G___________GC________UAUUA...AUC-3'\n______________CGGG_GA_____CGC_GGU_A_UCAGUUACACA_____CAGGC\n______________\|\|\|\|_\|\|_____\|:\|_::\|_\|_\|\|\|\|\|:\|\|\|\|\|_____\|\|\|\|\|\n______________GCCC_CU_____GUG_UUA_U_AGUCAGUGUGU_____GUCCG\n3'-UUU...CGACC____A__AAAAU___G_____G___________ACUAC_____UUCAG...UAG-5'\n_____________\|___________________________________________\|\n_____________205_________________________________________124\n	105 -- 111	167 -- 173	-36.0631 kcal/mol	8.93512 kcal/mol	13.9606 kcal/mol	72 138@LB@ \| \|@LB@5'-UGC...GAGGU AU G C G GC UAUUA...AUC-3'@LB@ CGGG GA CGC GGU A UCAGUUACACA CAGGC@LB@ \|\|\|\| \|\| \|:\| ::\| \| \|\|\|\|\|:\|\|\|\|\| \|\|\|\|\|@LB@ GCCC CU GUG UUA U AGUCAGUGUGU GUCCG@LB@3'-UUU...CGACC A AAAAU G G ACUAC UUCAG...UAG-5'@LB@ \| \|@LB@ 205 124@LB@@LB@@LB@Energy -13.03 kcal/mol@LB@Hybridization Energy -36.0631 kcal/mol@LB@Unfolding Energy - mRNA 8.93512 kcal/mol@LB@Unfolding Energy - sRNA 13.9606 kcal/mol@LB@@LB@Position - mRNA 73 -- 137@LB@Position - sRNA 125 -- 204@LB@Position Seed - mRNA 105 -- 111@LB@Position Seed - sRNA 167 -- 173@LB@
84	0.009006	0.3575	b1924	fliD	-8.51	0.498321	24 -- 43	139 -- 158	flagellar filament capping protein	_____________23_____________44\n_____________\|______________\|\n5'-CGU...UAAAA____C_________UUUUU...UUU-3'\n______________CAAC_UUUAGAAUU\n______________\|\|\|\|_\|\|:\|\|\|\|\|\|\n______________GUUG_AAGUCUUAA\n3'-UUU...GUUCA____A_________CGCCA...UAG-5'\n_____________\|______________\|\n_____________159____________138\n	37 -- 43	139 -- 145	-11.0468 kcal/mol	1.39956 kcal/mol	1.83266 kcal/mol	23 44@LB@ \| \|@LB@5'-CGU...UAAAA C UUUUU...UUU-3'@LB@ CAAC UUUAGAAUU@LB@ \|\|\|\| \|\|:\|\|\|\|\|\|@LB@ GUUG AAGUCUUAA@LB@3'-UUU...GUUCA A CGCCA...UAG-5'@LB@ \| \|@LB@ 159 138@LB@@LB@@LB@Energy -8.51 kcal/mol@LB@Hybridization Energy -11.0468 kcal/mol@LB@Unfolding Energy - mRNA 1.39956 kcal/mol@LB@Unfolding Energy - sRNA 1.83266 kcal/mol@LB@@LB@Position - mRNA 24 -- 43@LB@Position - sRNA 139 -- 158@LB@Position Seed - mRNA 37 -- 43@LB@Position Seed - sRNA 139 -- 145@LB@
67	0.006568	0.3261	b1927	amyA	-8.95	0.423898	77 -- 95	58 -- 76	cytoplasmic alpha-amylase	_____________76_____________________96\n_____________\|______________________\|\n5'-UUA...GAAAC__G_______GU___C______AAAAU...AUA-3'\n______________UG_UCGGUCA__CAU_GGUGCA\n______________\|:_\|\|:\|\|\|\|__\|\|\|_\|:\|\|\|\|\n______________AU_AGUCAGU__GUA_CUACGU\n3'-UUU...UGGUU__G_______GU__________CCGUU...UAG-5'\n_____________\|______________________\|\n_____________77_____________________57\n	35 -- 41	171 -- 177	-21.7732 kcal/mol	10.1812 kcal/mol	4.80336 kcal/mol	76 96@LB@ \| \|@LB@5'-UUA...GAAAC G GU C AAAAU...AUA-3'@LB@ UG UCGGUCA CAU GGUGCA@LB@ \|: \|\|:\|\|\|\| \|\|\| \|:\|\|\|\|@LB@ AU AGUCAGU GUA CUACGU@LB@3'-UUU...UGGUU G GU CCGUU...UAG-5'@LB@ \| \|@LB@ 77 57@LB@@LB@@LB@Energy -8.95 kcal/mol@LB@Hybridization Energy -21.7732 kcal/mol@LB@Unfolding Energy - mRNA 10.1812 kcal/mol@LB@Unfolding Energy - sRNA 4.80336 kcal/mol@LB@@LB@Position - mRNA 77 -- 95@LB@Position - sRNA 58 -- 76@LB@Position Seed - mRNA 35 -- 41@LB@Position Seed - sRNA 171 -- 177@LB@
96	0.01055	0.3575	b1953	yodD	-11.39	0.147949	264 -- 273	196 -- 205	uncharacterized protein	_____________263_____274\n_____________\|_______\|\n5'-CCA...UUCAC_______GUUUU...AAG-3'\n______________CUUCAUC\n______________\|\|\|\|\|\|\|\n______________GAAGUAG\n3'-UUU...GGAAC_______-5'\n_____________\|______\|\n_____________206____196\n	33 -- 39	1 -- 7	-8.82286 kcal/mol	0.690587 kcal/mol	0.701705 kcal/mol	263 274@LB@ \| \|@LB@5'-CCA...UUCAC GUUUU...AAG-3'@LB@ CUUCAUC@LB@ \|\|\|\|\|\|\|@LB@ GAAGUAG@LB@3'-UUU...GGAAC -5'@LB@ \| \|@LB@ 206 196@LB@@LB@@LB@Energy -11.39 kcal/mol@LB@Hybridization Energy -8.82286 kcal/mol@LB@Unfolding Energy - mRNA 0.690587 kcal/mol@LB@Unfolding Energy - sRNA 0.701705 kcal/mol@LB@@LB@Position - mRNA 264 -- 273@LB@Position - sRNA 196 -- 205@LB@Position Seed - mRNA 33 -- 39@LB@Position Seed - sRNA 1 -- 7@LB@
59	0.005693	0.3247	b1959	yedA	-9.74	0.306961	258 -- 278	1 -- 22	amino acid exporter for phenylalanine threonine	_____________257_______279\n_____________\|_________\|\n5'-UCA...UGAUA_________CAGGU...GCU-3'\n______________CUUGCUUCA\n______________\|\|\|\|\|\|\|\|\|\n______________GAACGAAGU\n3'-UUU...UGGGG_________AG-5'\n_____________\|_________\|\n_____________23________0\n	90 -- 96	3 -- 9	-13.1616 kcal/mol	3.16944 kcal/mol	1.03153 kcal/mol	257 279@LB@ \| \|@LB@5'-UCA...UGAUA CAGGU...GCU-3'@LB@ CUUGCUUCA@LB@ \|\|\|\|\|\|\|\|\|@LB@ GAACGAAGU@LB@3'-UUU...UGGGG AG-5'@LB@ \| \|@LB@ 23 0@LB@@LB@@LB@Energy -9.74 kcal/mol@LB@Hybridization Energy -13.1616 kcal/mol@LB@Unfolding Energy - mRNA 3.16944 kcal/mol@LB@Unfolding Energy - sRNA 1.03153 kcal/mol@LB@@LB@Position - mRNA 258 -- 278@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 90 -- 96@LB@Position Seed - sRNA 3 -- 9@LB@
113	0.01268	0.3575	b2066	udk	-9.33	0.364673	240 -- 253	17 -- 31	uridine/cytidine kinase	_____________239________________254\n_____________\|__________________\|\n5'-CGC...UUCGU_________C__AA____CAGGU...GUG-3'\n______________CGCCCCCUU_CU__CAUC\n______________\|:\|\|\|\|\|\|\|_\|\|__\|\|\|\|\n______________GUGGGGGAA_GA__GUAG\n3'-UUU...ACCCC_________C__A_____-5'\n_____________\|_________________\|\n_____________32________________17\n	161 -- 167	9 -- 15	-20.5437 kcal/mol	3.26859 kcal/mol	7.16879 kcal/mol	239 254@LB@ \| \|@LB@5'-CGC...UUCGU C AA CAGGU...GUG-3'@LB@ CGCCCCCUU CU CAUC@LB@ \|:\|\|\|\|\|\|\| \|\| \|\|\|\|@LB@ GUGGGGGAA GA GUAG@LB@3'-UUU...ACCCC C A -5'@LB@ \| \|@LB@ 32 17@LB@@LB@@LB@Energy -9.33 kcal/mol@LB@Hybridization Energy -20.5437 kcal/mol@LB@Unfolding Energy - mRNA 3.26859 kcal/mol@LB@Unfolding Energy - sRNA 7.16879 kcal/mol@LB@@LB@Position - mRNA 240 -- 253@LB@Position - sRNA 17 -- 31@LB@Position Seed - mRNA 161 -- 167@LB@Position Seed - sRNA 9 -- 15@LB@
4	0.0001068	0.08442	b2069	yegD	-18.64	0.004982	22 -- 145	51 -- 187	Hsp70 chaperone family protein	_____________21_________________146\n_____________\|__________________\|\n5'-CAC...ACAUC__________A_______CGCUU...UGC-3'\n______________GCAUCUCCUU__UUCAUC\n______________\|\|\|:\|:\|\|\|\|__\|\|\|\|\|\|\n______________CGUGGGGGAA__AAGUAG\n3'-UUU...UACCC__________CG______-5'\n_____________\|_________________\|\n_____________188_______________51\n	72 -- 78	9 -- 15	-21.4418 kcal/mol	1.05479 kcal/mol	7.2533 kcal/mol	21 146@LB@ \| \|@LB@5'-CAC...ACAUC A CGCUU...UGC-3'@LB@ GCAUCUCCUU UUCAUC@LB@ \|\|\|:\|:\|\|\|\| \|\|\|\|\|\|@LB@ CGUGGGGGAA AAGUAG@LB@3'-UUU...UACCC CG -5'@LB@ \| \|@LB@ 188 51@LB@@LB@@LB@Energy -18.64 kcal/mol@LB@Hybridization Energy -21.4418 kcal/mol@LB@Unfolding Energy - mRNA 1.05479 kcal/mol@LB@Unfolding Energy - sRNA 7.2533 kcal/mol@LB@@LB@Position - mRNA 22 -- 145@LB@Position - sRNA 51 -- 187@LB@Position Seed - mRNA 72 -- 78@LB@Position Seed - sRNA 9 -- 15@LB@
57	0.00565	0.3247	b2081	yegQ	-17.30	0.009213	136 -- 160	1 -- 21	putative peptidase	_____________135_______________________161\n_____________\|_________________________\|\n5'-AUU...AAGUG_______U_____AACC________AGGUG...GUU-3'\n______________GGGGCAC_CCCCU____GCUUCAUC\n______________\|\|\|\|\|\|\|_\|\|\|\|\|____\|\|\|\|\|\|\|\|\n______________CCCCGUG_GGGGA____CGAAGUAG\n3'-UUU...GCGUA_____________A___________-5'\n_____________\|________________________\|\n_____________22_______________________1\n	154 -- 160	1 -- 7	-36.7075 kcal/mol	11.7869 kcal/mol	10.2895 kcal/mol	135 161@LB@ \| \|@LB@5'-AUU...AAGUG U AACC AGGUG...GUU-3'@LB@ GGGGCAC CCCCU GCUUCAUC@LB@ \|\|\|\|\|\|\| \|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ CCCCGUG GGGGA CGAAGUAG@LB@3'-UUU...GCGUA A -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -17.30 kcal/mol@LB@Hybridization Energy -36.7075 kcal/mol@LB@Unfolding Energy - mRNA 11.7869 kcal/mol@LB@Unfolding Energy - sRNA 10.2895 kcal/mol@LB@@LB@Position - mRNA 136 -- 160@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 154 -- 160@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)

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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