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
121	0.004045	0.1176	b1738	chbB	-6.64	0.311906	2 -- 15	34 -- 50	N N'-diacetylchitobiose-specific enzyme IIB component of PTS	_____________1_________________16\n_____________\|_________________\|\n__________5'-A_________________AUAAC...CGG-3'\n______________AUGUGAAG___AGGGUC\n______________\|:\|\|\|\|\|\|___\|:\|\|\|\|\n______________UGCACUUC___UUCCAG\n3'-AUU...GCUAA________AUU______ACUUU...AUG-5'\n_____________\|_________________\|\n_____________51________________33\n	3 -- 9	43 -- 49	-17.276 kcal/mol	2.8636 kcal/mol	7.69543 kcal/mol	1 16@LB@ \| \|@LB@ 5'-A AUAAC...CGG-3'@LB@ AUGUGAAG AGGGUC@LB@ \|:\|\|\|\|\|\| \|:\|\|\|\|@LB@ UGCACUUC UUCCAG@LB@3'-AUU...GCUAA AUU ACUUU...AUG-5'@LB@ \| \|@LB@ 51 33@LB@@LB@@LB@Energy -6.64 kcal/mol@LB@Hybridization Energy -17.276 kcal/mol@LB@Unfolding Energy - mRNA 2.8636 kcal/mol@LB@Unfolding Energy - sRNA 7.69543 kcal/mol@LB@@LB@Position - mRNA 2 -- 15@LB@Position - sRNA 34 -- 50@LB@Position Seed - mRNA 3 -- 9@LB@Position Seed - sRNA 43 -- 49@LB@
151	0.006118	0.1406	b1103	hinT	-6.52	0.328434	216 -- 241	45 -- 70	purine nucleoside phosphoramidase dadA activator protein	_____________215________________________242\n_____________\|__________________________\|\n5'-CAA...AAACU_________A_____AUUCGU_____GAUCC...CGC-3'\n______________AUAUUCAGC_AAAUU______CGUGA\n______________\|\|\|\|\|\|\|\|\|_\|\|\|\|:______\|\|\|\|\|\n______________UAUAAGUCG_UUUAG______GCACU\n3'-AUU...GAUUU_________G_____GCUAAU_____UCAUU...AUG-5'\n_____________\|__________________________\|\n_____________71_________________________44\n	218 -- 224	62 -- 68	-20.3535 kcal/mol	5.67357 kcal/mol	8.1779 kcal/mol	215 242@LB@ \| \|@LB@5'-CAA...AAACU A AUUCGU GAUCC...CGC-3'@LB@ AUAUUCAGC AAAUU CGUGA@LB@ \|\|\|\|\|\|\|\|\| \|\|\|\|: \|\|\|\|\|@LB@ UAUAAGUCG UUUAG GCACU@LB@3'-AUU...GAUUU G GCUAAU UCAUU...AUG-5'@LB@ \| \|@LB@ 71 44@LB@@LB@@LB@Energy -6.52 kcal/mol@LB@Hybridization Energy -20.3535 kcal/mol@LB@Unfolding Energy - mRNA 5.67357 kcal/mol@LB@Unfolding Energy - sRNA 8.1779 kcal/mol@LB@@LB@Position - mRNA 216 -- 241@LB@Position - sRNA 45 -- 70@LB@Position Seed - mRNA 218 -- 224@LB@Position Seed - sRNA 62 -- 68@LB@
187	0.008276	0.1556	b0827	moeA	-6.51	0.330510	82 -- 91	23 -- 32	molybdopterin molybdenumtransferase; molybdopterin biosynthesis protein	_____________81_________92\n_____________\|__________\|\n5'-AUU...AUAUA__________UAUGG...UAC-3'\n______________GAAAGAUGGA\n______________\|\|\|\|\|\|\|:\|\|\n______________CUUUCUAUCU\n3'-AUU...CCAGA__________UGUAG...AUG-5'\n_____________\|__________\|\n_____________33_________22\n	85 -- 91	23 -- 29	-12.1772 kcal/mol	2.37895 kcal/mol	3.23951 kcal/mol	81 92@LB@ \| \|@LB@5'-AUU...AUAUA UAUGG...UAC-3'@LB@ GAAAGAUGGA@LB@ \|\|\|\|\|\|\|:\|\|@LB@ CUUUCUAUCU@LB@3'-AUU...CCAGA UGUAG...AUG-5'@LB@ \| \|@LB@ 33 22@LB@@LB@@LB@Energy -6.51 kcal/mol@LB@Hybridization Energy -12.1772 kcal/mol@LB@Unfolding Energy - mRNA 2.37895 kcal/mol@LB@Unfolding Energy - sRNA 3.23951 kcal/mol@LB@@LB@Position - mRNA 82 -- 91@LB@Position - sRNA 23 -- 32@LB@Position Seed - mRNA 85 -- 91@LB@Position Seed - sRNA 23 -- 29@LB@
109	0.003426	0.1101	b2280	nuoJ	-6.41	0.346318	31 -- 43	48 -- 59	NADH:ubiquinone oxidoreductase membrane subunit J	_____________30____________44\n_____________\|_____________\|\n5'-GAU...GCCAG_________U___AGAAA...UUA-3'\n______________GAUCUGGUU_ACG\n______________:\|\|\|:\|:\|\|_\|\|\|\n______________UUAGGCUAA_UGC\n3'-AUU...UCGGU_____________ACUUC...AUG-5'\n_____________\|_____________\|\n_____________60____________47\n	33 -- 39	51 -- 57	-11.2654 kcal/mol	3.27917 kcal/mol	1.55995 kcal/mol	30 44@LB@ \| \|@LB@5'-GAU...GCCAG U AGAAA...UUA-3'@LB@ GAUCUGGUU ACG@LB@ :\|\|\|:\|:\|\| \|\|\|@LB@ UUAGGCUAA UGC@LB@3'-AUU...UCGGU ACUUC...AUG-5'@LB@ \| \|@LB@ 60 47@LB@@LB@@LB@Energy -6.41 kcal/mol@LB@Hybridization Energy -11.2654 kcal/mol@LB@Unfolding Energy - mRNA 3.27917 kcal/mol@LB@Unfolding Energy - sRNA 1.55995 kcal/mol@LB@@LB@Position - mRNA 31 -- 43@LB@Position - sRNA 48 -- 59@LB@Position Seed - mRNA 33 -- 39@LB@Position Seed - sRNA 51 -- 57@LB@
131	0.004483	0.1204	b2069	yegD	-6.32	0.360285	213 -- 222	48 -- 57	Hsp70 chaperone family protein	_____________212________223\n_____________\|__________\|\n5'-CAC...UUGGU__________GUACA...UGC-3'\n______________UUUGAUUACG\n______________\|::\|\|\|\|\|\|\|\n______________AGGCUAAUGC\n3'-AUU...GGUUU__________ACUUC...AUG-5'\n_____________\|__________\|\n_____________58_________47\n	216 -- 222	48 -- 54	-10.2333 kcal/mol	2.33693 kcal/mol	1.55976 kcal/mol	212 223@LB@ \| \|@LB@5'-CAC...UUGGU GUACA...UGC-3'@LB@ UUUGAUUACG@LB@ \|::\|\|\|\|\|\|\|@LB@ AGGCUAAUGC@LB@3'-AUU...GGUUU ACUUC...AUG-5'@LB@ \| \|@LB@ 58 47@LB@@LB@@LB@Energy -6.32 kcal/mol@LB@Hybridization Energy -10.2333 kcal/mol@LB@Unfolding Energy - mRNA 2.33693 kcal/mol@LB@Unfolding Energy - sRNA 1.55976 kcal/mol@LB@@LB@Position - mRNA 213 -- 222@LB@Position - sRNA 48 -- 57@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 48 -- 54@LB@
200	0.009019	0.1567	b3343	tusB	-6.18	0.382258	145 -- 152	1 -- 8	mnm(5)-s(2)U34-tRNA synthesis 2-thiolation protein	_____________144______153\n_____________\|________\|\n5'-GCU...GCAGA________GCCGC...GCG-3'\n______________UGCCUUAC\n______________\|:\|\|:\|\|\|\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	146 -- 152	1 -- 7	-9.97017 kcal/mol	1.6972 kcal/mol	2.11603 kcal/mol	144 153@LB@ \| \|@LB@5'-GCU...GCAGA GCCGC...GCG-3'@LB@ UGCCUUAC@LB@ \|:\|\|:\|\|\|@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -6.18 kcal/mol@LB@Hybridization Energy -9.97017 kcal/mol@LB@Unfolding Energy - mRNA 1.6972 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 145 -- 152@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 146 -- 152@LB@Position Seed - sRNA 1 -- 7@LB@
98	0.002849	0.1023	b0772	ybhC	-6.17	0.383539	27 -- 33	49 -- 55	acyl-CoA thioesterase lipoprotein	_____________26______34\n_____________\|_______\|\n5'-UCA...CGCCU_______UGCGA...AUC-3'\n______________CGAUUAC\n______________\|\|\|\|\|\|\|\n______________GCUAAUG\n3'-AUU...UUUAG_______CACUU...AUG-5'\n_____________\|_______\|\n_____________56______48\n	27 -- 33	49 -- 55	-7.86935 kcal/mol	1.39337 kcal/mol	0.311712 kcal/mol	26 34@LB@ \| \|@LB@5'-UCA...CGCCU UGCGA...AUC-3'@LB@ CGAUUAC@LB@ \|\|\|\|\|\|\|@LB@ GCUAAUG@LB@3'-AUU...UUUAG CACUU...AUG-5'@LB@ \| \|@LB@ 56 48@LB@@LB@@LB@Energy -6.17 kcal/mol@LB@Hybridization Energy -7.86935 kcal/mol@LB@Unfolding Energy - mRNA 1.39337 kcal/mol@LB@Unfolding Energy - sRNA 0.311712 kcal/mol@LB@@LB@Position - mRNA 27 -- 33@LB@Position - sRNA 49 -- 55@LB@Position Seed - mRNA 27 -- 33@LB@Position Seed - sRNA 49 -- 55@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@
96	0.002764	0.1002	b1034	ycdX	-5.77	0.451964	102 -- 115	32 -- 46	alkaline phosphatase	_____________101_____________116\n_____________\|_______________\|\n5'-GGC...AAAAA_______________CGGGC...AAC-3'\n______________GGGG_AGAGGGUCUG\n______________\|::\|_\|:\|:\|\|\|\|\|\|\n______________CUUC_UUUUCCAGAC\n3'-AUU...AUGCA____A__________UUUCU...AUG-5'\n_____________\|_______________\|\n_____________47______________31\n	109 -- 115	32 -- 38	-16.8058 kcal/mol	3.54072 kcal/mol	7.24668 kcal/mol	101 116@LB@ \| \|@LB@5'-GGC...AAAAA CGGGC...AAC-3'@LB@ GGGG AGAGGGUCUG@LB@ \|::\| \|:\|:\|\|\|\|\|\|@LB@ CUUC UUUUCCAGAC@LB@3'-AUU...AUGCA A UUUCU...AUG-5'@LB@ \| \|@LB@ 47 31@LB@@LB@@LB@Energy -5.77 kcal/mol@LB@Hybridization Energy -16.8058 kcal/mol@LB@Unfolding Energy - mRNA 3.54072 kcal/mol@LB@Unfolding Energy - sRNA 7.24668 kcal/mol@LB@@LB@Position - mRNA 102 -- 115@LB@Position - sRNA 32 -- 46@LB@Position Seed - mRNA 109 -- 115@LB@Position Seed - sRNA 32 -- 38@LB@
156	0.006236	0.1406	b2922	yggE	-5.46	0.507768	199 -- 207	42 -- 50	oxidative stress defense protein	_____________198_______208\n_____________\|_________\|\n5'-GCA...GACUA_________UCAAA...CCG-3'\n______________ACGUGAAGU\n______________\|\|\|\|\|\|\|\|\|\n______________UGCACUUCA\n3'-AUU...GCUAA_________UUUUC...AUG-5'\n_____________\|_________\|\n_____________51________41\n	201 -- 207	42 -- 48	-12.7727 kcal/mol	4.07491 kcal/mol	3.2504 kcal/mol	198 208@LB@ \| \|@LB@5'-GCA...GACUA UCAAA...CCG-3'@LB@ ACGUGAAGU@LB@ \|\|\|\|\|\|\|\|\|@LB@ UGCACUUCA@LB@3'-AUU...GCUAA UUUUC...AUG-5'@LB@ \| \|@LB@ 51 41@LB@@LB@@LB@Energy -5.46 kcal/mol@LB@Hybridization Energy -12.7727 kcal/mol@LB@Unfolding Energy - mRNA 4.07491 kcal/mol@LB@Unfolding Energy - sRNA 3.2504 kcal/mol@LB@@LB@Position - mRNA 199 -- 207@LB@Position - sRNA 42 -- 50@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 42 -- 48@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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