Input and runtime details for job 3429477 (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 3429477 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:26:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:01 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:15:20 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:15:27 CET 2018
	Job Completed		@ Fri Feb 16 20:15:52 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3429477&toolName=CopraRNA ( 30 days expiry )

Description of the job

OxyS

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
186	0.03285	0.5559	b1003	yccJ	-7.53	0.270746	41 -- 54	75 -- 88	uncharacterized protein	_____________40_____________55\n_____________\|______________\|\n5'-CCU...UUCAC_________GC___ACGCC...GGU-3'\n______________AGGUUCGCG__GGU\n______________\|:\|\|\|\|:\|\|__\|\|:\n______________UUCAAGUGC__CCG\n3'-CGC...GCGUU_________AA___AAAUC...AAG-5'\n_____________\|______________\|\n_____________89_____________74\n	43 -- 49	80 -- 86	-16.6206 kcal/mol	8.57413 kcal/mol	0.515884 kcal/mol	40 55@LB@ \| \|@LB@5'-CCU...UUCAC GC ACGCC...GGU-3'@LB@ AGGUUCGCG GGU@LB@ \|:\|\|\|\|:\|\| \|\|:@LB@ UUCAAGUGC CCG@LB@3'-CGC...GCGUU AA AAAUC...AAG-5'@LB@ \| \|@LB@ 89 74@LB@@LB@@LB@Energy -7.53 kcal/mol@LB@Hybridization Energy -16.6206 kcal/mol@LB@Unfolding Energy - mRNA 8.57413 kcal/mol@LB@Unfolding Energy - sRNA 0.515884 kcal/mol@LB@@LB@Position - mRNA 41 -- 54@LB@Position - sRNA 75 -- 88@LB@Position Seed - mRNA 43 -- 49@LB@Position Seed - sRNA 80 -- 86@LB@
90	0.01553	0.5385	b1043	csgC	-15.92	0.009464	100 -- 115	69 -- 84	curli assembly protein	_____________99_______________116\n_____________\|________________\|\n5'-GUG...GUGAC___G____________AACAA...UUA-3'\n______________UCA_GUUGGCUUUGGU\n______________\|\|\|_\|\|\|\|\|\|\|\|\|:\|\|\n______________AGU_CAACCGAAAUCA\n3'-CGC...UUUCA___G____________AUAAG...AAG-5'\n_____________\|________________\|\n_____________85_______________68\n	109 -- 115	69 -- 75	-23.6243 kcal/mol	7.14442 kcal/mol	0.563592 kcal/mol	99 116@LB@ \| \|@LB@5'-GUG...GUGAC G AACAA...UUA-3'@LB@ UCA GUUGGCUUUGGU@LB@ \|\|\| \|\|\|\|\|\|\|\|\|:\|\|@LB@ AGU CAACCGAAAUCA@LB@3'-CGC...UUUCA G AUAAG...AAG-5'@LB@ \| \|@LB@ 85 68@LB@@LB@@LB@Energy -15.92 kcal/mol@LB@Hybridization Energy -23.6243 kcal/mol@LB@Unfolding Energy - mRNA 7.14442 kcal/mol@LB@Unfolding Energy - sRNA 0.563592 kcal/mol@LB@@LB@Position - mRNA 100 -- 115@LB@Position - sRNA 69 -- 84@LB@Position Seed - mRNA 109 -- 115@LB@Position Seed - sRNA 69 -- 75@LB@
200	0.03481	0.5559	b1058	yceO	-9.40	0.133707	85 -- 100	70 -- 85	uncharacterized protein	_____________84_______________101\n_____________\|________________\|\n5'-CCU...UUAAA_______CA_______GGGAA...GAU-3'\n______________UUUGCGU__GUUUUAG\n______________\|\|::\|\|\|__\|:\|\|\|\|\|\n______________AAGUGCA__CGAAAUC\n3'-CGC...UUUUC_______AC_______AAUAA...AAG-5'\n_____________\|________________\|\n_____________86_______________69\n	94 -- 100	70 -- 76	-11.7699 kcal/mol	1.79867 kcal/mol	0.567379 kcal/mol	84 101@LB@ \| \|@LB@5'-CCU...UUAAA CA GGGAA...GAU-3'@LB@ UUUGCGU GUUUUAG@LB@ \|\|::\|\|\| \|:\|\|\|\|\|@LB@ AAGUGCA CGAAAUC@LB@3'-CGC...UUUUC AC AAUAA...AAG-5'@LB@ \| \|@LB@ 86 69@LB@@LB@@LB@Energy -9.40 kcal/mol@LB@Hybridization Energy -11.7699 kcal/mol@LB@Unfolding Energy - mRNA 1.79867 kcal/mol@LB@Unfolding Energy - sRNA 0.567379 kcal/mol@LB@@LB@Position - mRNA 85 -- 100@LB@Position - sRNA 70 -- 85@LB@Position Seed - mRNA 94 -- 100@LB@Position Seed - sRNA 70 -- 76@LB@
72	0.0135	0.5385	b1117	lolD	-8.66	0.177865	184 -- 202	66 -- 83	outer membrane-specific lipoprotein transporter subunit	_____________183_________________203\n_____________\|___________________\|\n5'-GCU...CAACC___UGA_______C_____GAAUA...GCG-3'\n______________CGC___GGCUUUA_GUUAU\n______________\|:\|___\|\|\|\|\|\|\|_\|\|\|\|\|\n______________GUG___CCGAAAU_CAAUA\n3'-CGC...UUCAA___CAA_____________AGCUC...AAG-5'\n_____________\|___________________\|\n_____________84__________________65\n	190 -- 196	71 -- 77	-15.2298 kcal/mol	6.00943 kcal/mol	0.556032 kcal/mol	183 203@LB@ \| \|@LB@5'-GCU...CAACC UGA C GAAUA...GCG-3'@LB@ CGC GGCUUUA GUUAU@LB@ \|:\| \|\|\|\|\|\|\| \|\|\|\|\|@LB@ GUG CCGAAAU CAAUA@LB@3'-CGC...UUCAA CAA AGCUC...AAG-5'@LB@ \| \|@LB@ 84 65@LB@@LB@@LB@Energy -8.66 kcal/mol@LB@Hybridization Energy -15.2298 kcal/mol@LB@Unfolding Energy - mRNA 6.00943 kcal/mol@LB@Unfolding Energy - sRNA 0.556032 kcal/mol@LB@@LB@Position - mRNA 184 -- 202@LB@Position - sRNA 66 -- 83@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 71 -- 77@LB@
142	0.02338	0.5385	b1126	potA	-10.56	0.084569	277 -- 295	14 -- 34	spermidine/putrescine ABC transporter ATPase	_____________276___________________296\n_____________\|_____________________\|\n5'-CAA...CAAAU_______U_____________CAUUC-3'\n______________GCUUUGA_GGU__AAAGAGGU\n______________:\|\|\|::\|_\|\|\|__\|\|\|\|\|\|\|\|\n______________UGAAGUU_CCA__UUUCUCCA\n3'-CGC...GUCAC_______C___AU________CGGCG...AAG-5'\n_____________\|_____________________\|\n_____________35____________________13\n	289 -- 295	14 -- 20	-18.1028 kcal/mol	4.21038 kcal/mol	3.33169 kcal/mol	276 296@LB@ \| \|@LB@5'-CAA...CAAAU U CAUUC-3'@LB@ GCUUUGA GGU AAAGAGGU@LB@ :\|\|\|::\| \|\|\| \|\|\|\|\|\|\|\|@LB@ UGAAGUU CCA UUUCUCCA@LB@3'-CGC...GUCAC C AU CGGCG...AAG-5'@LB@ \| \|@LB@ 35 13@LB@@LB@@LB@Energy -10.56 kcal/mol@LB@Hybridization Energy -18.1028 kcal/mol@LB@Unfolding Energy - mRNA 4.21038 kcal/mol@LB@Unfolding Energy - sRNA 3.33169 kcal/mol@LB@@LB@Position - mRNA 277 -- 295@LB@Position - sRNA 14 -- 34@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 14 -- 20@LB@
116	0.01945	0.5385	b1175	minD	-9.10	0.150484	222 -- 240	13 -- 34	inhibitor of FtsZ ring polymerization; chromosome-membrane tethering protein; membrane ATPase of the MinCDEE system	_____________221____________________241\n_____________\|______________________\|\n5'-CUG...UUGUU__________C___________UUGGU...AAA-3'\n______________ACUUC__GGG__AAAGGGGGUG\n______________\|\|\|\|\|__\|\|\|__\|\|\|:\|:\|\|\|\|\n______________UGAAG__CCC__UUUUCUCCAC\n3'-CGC...GUCAC_____UU___AA__________GGCGA...AAG-5'\n_____________\|______________________\|\n_____________35_____________________12\n	234 -- 240	13 -- 19	-19.7427 kcal/mol	7.311 kcal/mol	3.33198 kcal/mol	221 241@LB@ \| \|@LB@5'-CUG...UUGUU C UUGGU...AAA-3'@LB@ ACUUC GGG AAAGGGGGUG@LB@ \|\|\|\|\| \|\|\| \|\|\|:\|:\|\|\|\|@LB@ UGAAG CCC UUUUCUCCAC@LB@3'-CGC...GUCAC UU AA GGCGA...AAG-5'@LB@ \| \|@LB@ 35 12@LB@@LB@@LB@Energy -9.10 kcal/mol@LB@Hybridization Energy -19.7427 kcal/mol@LB@Unfolding Energy - mRNA 7.311 kcal/mol@LB@Unfolding Energy - sRNA 3.33198 kcal/mol@LB@@LB@Position - mRNA 222 -- 240@LB@Position - sRNA 13 -- 34@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 13 -- 19@LB@
117	0.01966	0.5385	b1203	ychF	-10.24	0.095997	26 -- 41	73 -- 87	catalase inhibitor protein; ATPase K+-dependent ribosome-associated	_____________25_______________42\n_____________\|________________\|\n5'-GAA...AAUGU_______A_A______GACCA...CAU-3'\n______________GGUUUAC_G_UGGCUU\n______________:\|\|\|:\|\|_\|_\|\|\|\|\|\|\n______________UCAAGUG_C_ACCGAA\n3'-CGC...CGUUU_________A______AUCAA...AAG-5'\n_____________\|________________\|\n_____________88_______________72\n	26 -- 32	81 -- 87	-15.1856 kcal/mol	4.42747 kcal/mol	0.51474 kcal/mol	25 42@LB@ \| \|@LB@5'-GAA...AAUGU A A GACCA...CAU-3'@LB@ GGUUUAC G UGGCUU@LB@ :\|\|\|:\|\| \| \|\|\|\|\|\|@LB@ UCAAGUG C ACCGAA@LB@3'-CGC...CGUUU A AUCAA...AAG-5'@LB@ \| \|@LB@ 88 72@LB@@LB@@LB@Energy -10.24 kcal/mol@LB@Hybridization Energy -15.1856 kcal/mol@LB@Unfolding Energy - mRNA 4.42747 kcal/mol@LB@Unfolding Energy - sRNA 0.51474 kcal/mol@LB@@LB@Position - mRNA 26 -- 41@LB@Position - sRNA 73 -- 87@LB@Position Seed - mRNA 26 -- 32@LB@Position Seed - sRNA 81 -- 87@LB@
11	0.002269	0.5385	b1205	ychH	-11.36	0.061344	181 -- 195	75 -- 90	DUF2583 family putative inner membrane protein	_____________180______________196\n_____________\|________________\|\n5'-CAA...ACCCA___________GA___GACAU...UAC-3'\n______________GAAAGUUC_CG__GGU\n______________:\|\|\|\|\|\|\|_\|\|__\|\|:\n______________UUUUCAAG_GC__CCG\n3'-CGC...AGGCG________U__AA___AAAUC...AAG-5'\n_____________\|________________\|\n_____________91_______________74\n	182 -- 188	83 -- 89	-14.0006 kcal/mol	2.12575 kcal/mol	0.517251 kcal/mol	180 196@LB@ \| \|@LB@5'-CAA...ACCCA GA GACAU...UAC-3'@LB@ GAAAGUUC CG GGU@LB@ :\|\|\|\|\|\|\| \|\| \|\|:@LB@ UUUUCAAG GC CCG@LB@3'-CGC...AGGCG U AA AAAUC...AAG-5'@LB@ \| \|@LB@ 91 74@LB@@LB@@LB@Energy -11.36 kcal/mol@LB@Hybridization Energy -14.0006 kcal/mol@LB@Unfolding Energy - mRNA 2.12575 kcal/mol@LB@Unfolding Energy - sRNA 0.517251 kcal/mol@LB@@LB@Position - mRNA 181 -- 195@LB@Position - sRNA 75 -- 90@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 83 -- 89@LB@
108	0.0187	0.5385	b1210	hemA	-9.14	0.148366	174 -- 184	75 -- 84	glutamyl tRNA reductase	_____________173_________185\n_____________\|___________\|\n5'-CCU...CCCUA__A________AUUAU...ACA-3'\n______________UC_ACGUUGGU\n______________\|\|_\|\|\|\|\|\|\|:\n______________AG_UGCAACCG\n3'-CGC...UUUCA___________AAAUC...AAG-5'\n_____________\|___________\|\n_____________85__________74\n	178 -- 184	75 -- 81	-12.935 kcal/mol	3.29275 kcal/mol	0.505918 kcal/mol	173 185@LB@ \| \|@LB@5'-CCU...CCCUA A AUUAU...ACA-3'@LB@ UC ACGUUGGU@LB@ \|\| \|\|\|\|\|\|\|:@LB@ AG UGCAACCG@LB@3'-CGC...UUUCA AAAUC...AAG-5'@LB@ \| \|@LB@ 85 74@LB@@LB@@LB@Energy -9.14 kcal/mol@LB@Hybridization Energy -12.935 kcal/mol@LB@Unfolding Energy - mRNA 3.29275 kcal/mol@LB@Unfolding Energy - sRNA 0.505918 kcal/mol@LB@@LB@Position - mRNA 174 -- 184@LB@Position - sRNA 75 -- 84@LB@Position Seed - mRNA 178 -- 184@LB@Position Seed - sRNA 75 -- 81@LB@
55	0.01095	0.5385	b1220	ychO	-5.56	0.517016	132 -- 175	64 -- 91	putative invasin	_____________131__________________________________________176\n_____________\|____________________________________________\|\n5'-UCA...UACGA________GCCAGUAAU____AUUCUUUAA____A_____U___AUUAU...CAA-3'\n______________CAAAAGUU_________CGUU_________GGCU_UGGUU_UUC\n______________\|\|\|\|\|\|\|\|_________\|\|\|\|_________\|\|\|\|_\|:\|\|\|_\|\|\|\n______________GUUUUCAA_________GCAA_________CCGA_AUCAA_AAG\n3'-CGC...UAGGC________GU________________________A_____U___CUCAA...AAG-5'\n_____________\|____________________________________________\|\n_____________92___________________________________________63\n	133 -- 139	84 -- 90	-16.5622 kcal/mol	8.12255 kcal/mol	2.88465 kcal/mol	131 176@LB@ \| \|@LB@5'-UCA...UACGA GCCAGUAAU AUUCUUUAA A U AUUAU...CAA-3'@LB@ CAAAAGUU CGUU GGCU UGGUU UUC@LB@ \|\|\|\|\|\|\|\| \|\|\|\| \|\|\|\| \|:\|\|\| \|\|\|@LB@ GUUUUCAA GCAA CCGA AUCAA AAG@LB@3'-CGC...UAGGC GU A U CUCAA...AAG-5'@LB@ \| \|@LB@ 92 63@LB@@LB@@LB@Energy -5.56 kcal/mol@LB@Hybridization Energy -16.5622 kcal/mol@LB@Unfolding Energy - mRNA 8.12255 kcal/mol@LB@Unfolding Energy - sRNA 2.88465 kcal/mol@LB@@LB@Position - mRNA 132 -- 175@LB@Position - sRNA 64 -- 91@LB@Position Seed - mRNA 133 -- 139@LB@Position Seed - sRNA 84 -- 90@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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