Input and runtime details for job 5774122 (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 5774122 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:30:38 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:16:08 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 23:32:42 CET 2018
	Post-Processing Finished		@ Fri Feb 16 23:32:50 CET 2018
	Job Completed		@ Fri Feb 16 23:33:10 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5774122&toolName=CopraRNA ( 30 days expiry )

Description of the job

FsrA

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_000964 Bacillus subtilis subsp. subtilis str. 168

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	Additional homologs
127	0.01117	0.2883	bsu05980	tatAY	-16.78	0.012784	171 -- 194	21 -- 43	Sec-independent protein translocase protein TatAy		_____________170______________________195\n_____________\|________________________\|\n5'-CCG...AGGAA___GA________AAA__A_____CCAAA...ACA-3'\n______________AUC__AUAGAGGG___GG_GGAGC\n______________\|\|\|__\|\|\|\|\|\|\|\|___\|\|_\|\|\|:\|\n______________UAG__UAUCUCCC___CC_CCUUG\n3'-UUU...AGAAC___AC________CAA________UCUCU...AUA-5'\n_____________\|________________________\|\n_____________44_______________________20\n	177 -- 183	31 -- 37	-24.2003 kcal/mol	4.65314 kcal/mol	2.76238 kcal/mol	170 195@LB@ \| \|@LB@5'-CCG...AGGAA GA AAA A CCAAA...ACA-3'@LB@ AUC AUAGAGGG GG GGAGC@LB@ \|\|\| \|\|\|\|\|\|\|\| \|\| \|\|\|:\|@LB@ UAG UAUCUCCC CC CCUUG@LB@3'-UUU...AGAAC AC CAA UCUCU...AUA-5'@LB@ \| \|@LB@ 44 20@LB@@LB@@LB@Energy -16.78 kcal/mol@LB@Hybridization Energy -24.2003 kcal/mol@LB@Unfolding Energy - mRNA 4.65314 kcal/mol@LB@Unfolding Energy - sRNA 2.76238 kcal/mol@LB@@LB@Position - mRNA 171 -- 194@LB@Position - sRNA 21 -- 43@LB@Position Seed - mRNA 177 -- 183@LB@Position Seed - sRNA 31 -- 37@LB@
103	0.008788	0.2778	bsu06070	ydiP	-8.66	0.321247	183 -- 194	27 -- 44	BsuMI modification methylase subunit YdiP	bsu20250	_____________182________________195\n_____________\|__________________\|\n5'-GGA...AAAAA__________________AUAUC...UGG-3'\n______________GAUUUGA______GGUUG\n______________\|\|\|:\|\|\|______\|\|\|\|\|\n______________CUAGACU______CCAAC\n3'-UUU...UAGAA_______AUCUCC_____CCCUU...AUA-5'\n_____________\|__________________\|\n_____________45_________________26\n	183 -- 189	38 -- 44	-12.3729 kcal/mol	2.73997 kcal/mol	0.971452 kcal/mol	182 195@LB@ \| \|@LB@5'-GGA...AAAAA AUAUC...UGG-3'@LB@ GAUUUGA GGUUG@LB@ \|\|\|:\|\|\| \|\|\|\|\|@LB@ CUAGACU CCAAC@LB@3'-UUU...UAGAA AUCUCC CCCUU...AUA-5'@LB@ \| \|@LB@ 45 26@LB@@LB@@LB@Energy -8.66 kcal/mol@LB@Hybridization Energy -12.3729 kcal/mol@LB@Unfolding Energy - mRNA 2.73997 kcal/mol@LB@Unfolding Energy - sRNA 0.971452 kcal/mol@LB@@LB@Position - mRNA 183 -- 194@LB@Position - sRNA 27 -- 44@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 38 -- 44@LB@
102	0.008773	0.2778	bsu06170	ydjE	-10.58	0.175640	264 -- 284	30 -- 50	sugar kinase YdjE		_____________263___________________285\n_____________\|_____________________\|\n5'-GGG...AUGUU__CG_______A_____A___CGCCA...AAA-3'\n______________GA__UUGAUUU_AUGGA_GGG\n______________\|\|__\|\|\|\|\|:\|_\|\|:\|\|_\|\|\|\n______________CU__AACUAGA_UAUCU_CCC\n3'-UUU...AAAGC__AG_______C_____C___AACCC...AUA-5'\n_____________\|_____________________\|\n_____________51____________________29\n	268 -- 274	40 -- 46	-17.5575 kcal/mol	6.00068 kcal/mol	0.974272 kcal/mol	263 285@LB@ \| \|@LB@5'-GGG...AUGUU CG A A CGCCA...AAA-3'@LB@ GA UUGAUUU AUGGA GGG@LB@ \|\| \|\|\|\|\|:\| \|\|:\|\| \|\|\|@LB@ CU AACUAGA UAUCU CCC@LB@3'-UUU...AAAGC AG C C AACCC...AUA-5'@LB@ \| \|@LB@ 51 29@LB@@LB@@LB@Energy -10.58 kcal/mol@LB@Hybridization Energy -17.5575 kcal/mol@LB@Unfolding Energy - mRNA 6.00068 kcal/mol@LB@Unfolding Energy - sRNA 0.974272 kcal/mol@LB@@LB@Position - mRNA 264 -- 284@LB@Position - sRNA 30 -- 50@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 40 -- 46@LB@
89	0.00694	0.2588	bsu06230	iolT	-9.37	0.260314	174 -- 193	31 -- 49	major myo-inositol transporter IolT		_____________173__________________194\n_____________\|____________________\|\n5'-AAA...UACGC_______AAAA__CU_____AAACA...AUG-3'\n______________AUUUUGA____GA__GGGGG\n______________\|\|:\|\|\|\|____\|\|__\|:\|\|\|\n______________UAGAACU____CU__CUCCC\n3'-UUU...AAGCC_______AGA___AU_____CAACC...AUA-5'\n_____________\|____________________\|\n_____________50___________________30\n	174 -- 180	43 -- 49	-14.1903 kcal/mol	3.84886 kcal/mol	0.970571 kcal/mol	173 194@LB@ \| \|@LB@5'-AAA...UACGC AAAA CU AAACA...AUG-3'@LB@ AUUUUGA GA GGGGG@LB@ \|\|:\|\|\|\| \|\| \|:\|\|\|@LB@ UAGAACU CU CUCCC@LB@3'-UUU...AAGCC AGA AU CAACC...AUA-5'@LB@ \| \|@LB@ 50 30@LB@@LB@@LB@Energy -9.37 kcal/mol@LB@Hybridization Energy -14.1903 kcal/mol@LB@Unfolding Energy - mRNA 3.84886 kcal/mol@LB@Unfolding Energy - sRNA 0.970571 kcal/mol@LB@@LB@Position - mRNA 174 -- 193@LB@Position - sRNA 31 -- 49@LB@Position Seed - mRNA 174 -- 180@LB@Position Seed - sRNA 43 -- 49@LB@
81	0.005945	0.2448	bsu06390	yebD	-16.11	0.017881	267 -- 291	30 -- 53	Evidence 5: No homology to any previously reported sequences		_____________266_______________________292\n_____________\|_________________________\|\n5'-UUU...UGCUC_____A___U___AA__A_______AACAG...UUG-3'\n______________UCGGA_UUU_AUC__GG_AGAGGGG\n______________\|\|\|\|\|_:\|\|_\|\|\|__\|:_\|\|\|\|\|\|\|\n______________AGCCU_GAA_UAG__CU_UCUCCCC\n3'-UUU...AAAAA_____A___C___A___A_______AACCC...AUA-5'\n_____________\|_________________________\|\n_____________54________________________29\n	285 -- 291	30 -- 36	-22.0812 kcal/mol	4.98677 kcal/mol	0.985344 kcal/mol	266 292@LB@ \| \|@LB@5'-UUU...UGCUC A U AA A AACAG...UUG-3'@LB@ UCGGA UUU AUC GG AGAGGGG@LB@ \|\|\|\|\| :\|\| \|\|\| \|: \|\|\|\|\|\|\|@LB@ AGCCU GAA UAG CU UCUCCCC@LB@3'-UUU...AAAAA A C A A AACCC...AUA-5'@LB@ \| \|@LB@ 54 29@LB@@LB@@LB@Energy -16.11 kcal/mol@LB@Hybridization Energy -22.0812 kcal/mol@LB@Unfolding Energy - mRNA 4.98677 kcal/mol@LB@Unfolding Energy - sRNA 0.985344 kcal/mol@LB@@LB@Position - mRNA 267 -- 291@LB@Position - sRNA 30 -- 53@LB@Position Seed - mRNA 285 -- 291@LB@Position Seed - sRNA 30 -- 36@LB@
61	0.003607	0.1972	bsu06860	yezE	-12.02	0.104394	226 -- 262	26 -- 52	TetR family transcriptional regulator		_____________225___________________________________263\n_____________\|_____________________________________\|\n5'-AGG...UGAUA___CG____U___UCACAGGGC________UUU____AGAGU...UGC-3'\n______________CGG__CUUG_UCU_________GAUAGAGG___UUGG\n______________\|\|\|__\|\|\|\|_\|\|\|_________\|\|\|\|\|\|\|\|___\|\|\|\|\n______________GCC__GAAC_AGA_________CUAUCUCC___AACC\n3'-UUU...AAAAA___UA____U____________________CC_____CCUUG...AUA-5'\n_____________\|_____________________________________\|\n_____________53____________________________________25\n	249 -- 255	32 -- 38	-24.4528 kcal/mol	11.4473 kcal/mol	0.980817 kcal/mol	225 263@LB@ \| \|@LB@5'-AGG...UGAUA CG U UCACAGGGC UUU AGAGU...UGC-3'@LB@ CGG CUUG UCU GAUAGAGG UUGG@LB@ \|\|\| \|\|\|\| \|\|\| \|\|\|\|\|\|\|\| \|\|\|\|@LB@ GCC GAAC AGA CUAUCUCC AACC@LB@3'-UUU...AAAAA UA U CC CCUUG...AUA-5'@LB@ \| \|@LB@ 53 25@LB@@LB@@LB@Energy -12.02 kcal/mol@LB@Hybridization Energy -24.4528 kcal/mol@LB@Unfolding Energy - mRNA 11.4473 kcal/mol@LB@Unfolding Energy - sRNA 0.980817 kcal/mol@LB@@LB@Position - mRNA 226 -- 262@LB@Position - sRNA 26 -- 52@LB@Position Seed - mRNA 249 -- 255@LB@Position Seed - sRNA 32 -- 38@LB@
53	0.002724	0.1697	bsu06970	yesO	-13.13	0.067695	188 -- 199	26 -- 36	ABC transporter substrate-binding protein		_____________187__________200\n_____________\|____________\|\n5'-CGA...AUUAA_______A____UUUGA...UUA-3'\n______________AGGGGGG_UUGG\n______________\|\|:\|\|\|\|_\|\|\|\|\n______________UCUCCCC_AACC\n3'-UUU...GACUA____________CCUUG...AUA-5'\n_____________\|____________\|\n_____________37___________25\n	188 -- 194	30 -- 36	-17.5942 kcal/mol	4.33325 kcal/mol	0.135623 kcal/mol	187 200@LB@ \| \|@LB@5'-CGA...AUUAA A UUUGA...UUA-3'@LB@ AGGGGGG UUGG@LB@ \|\|:\|\|\|\| \|\|\|\|@LB@ UCUCCCC AACC@LB@3'-UUU...GACUA CCUUG...AUA-5'@LB@ \| \|@LB@ 37 25@LB@@LB@@LB@Energy -13.13 kcal/mol@LB@Hybridization Energy -17.5942 kcal/mol@LB@Unfolding Energy - mRNA 4.33325 kcal/mol@LB@Unfolding Energy - sRNA 0.135623 kcal/mol@LB@@LB@Position - mRNA 188 -- 199@LB@Position - sRNA 26 -- 36@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 30 -- 36@LB@
22	0.0004167	0.06318	bsu07570	yflS	-5.44	0.672400	163 -- 208	8 -- 27	malate transporter YflS		_____________162____________________________________________209\n_____________\|______________________________________________\|\n5'-AUG...GAAAA_____U____AAACAAGUAUAUAG___GAGACCUAUUUA_______AGAAA...CUC-3'\n______________GGGGA_CGGA______________GAG____________UGGCUUC\n______________\|\|\|\|\|_\|:\|\|______________\|\|\|____________\|:\|\|\|\|\|\n______________CCCCU_GUCU______________CUC____________AUCGAAG\n3'-UUU...CCCAA_____U________________________________________AGAGAUA-5'\n_____________\|______________________________________________\|\n_____________28_____________________________________________7\n	202 -- 208	8 -- 14	-21.2785 kcal/mol	9.2406 kcal/mol	6.59627 kcal/mol	162 209@LB@ \| \|@LB@5'-AUG...GAAAA U AAACAAGUAUAUAG GAGACCUAUUUA AGAAA...CUC-3'@LB@ GGGGA CGGA GAG UGGCUUC@LB@ \|\|\|\|\| \|:\|\| \|\|\| \|:\|\|\|\|\|@LB@ CCCCU GUCU CUC AUCGAAG@LB@3'-UUU...CCCAA U AGAGAUA-5'@LB@ \| \|@LB@ 28 7@LB@@LB@@LB@Energy -5.44 kcal/mol@LB@Hybridization Energy -21.2785 kcal/mol@LB@Unfolding Energy - mRNA 9.2406 kcal/mol@LB@Unfolding Energy - sRNA 6.59627 kcal/mol@LB@@LB@Position - mRNA 163 -- 208@LB@Position - sRNA 8 -- 27@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 8 -- 14@LB@
149	0.01325	0.2966	bsu07610	citM	-7.43	0.445360	149 -- 162	15 -- 27	Mg(2+)/citrate complex secondary transporter		_____________148____________163\n_____________\|______________\|\n5'-AUU...AAAAA_______A______AAAAA...UUG-3'\n______________GGGGAGU_AGGGAG\n______________\|\|\|\|\|::_\|\|:\|\|\|\n______________CCCCUUG_UCUCUC\n3'-UUU...CCCAA______________AUCGA...AUA-5'\n_____________\|______________\|\n_____________28_____________14\n	149 -- 155	21 -- 27	-17.4184 kcal/mol	3.9771 kcal/mol	6.01129 kcal/mol	148 163@LB@ \| \|@LB@5'-AUU...AAAAA A AAAAA...UUG-3'@LB@ GGGGAGU AGGGAG@LB@ \|\|\|\|\|:: \|\|:\|\|\|@LB@ CCCCUUG UCUCUC@LB@3'-UUU...CCCAA AUCGA...AUA-5'@LB@ \| \|@LB@ 28 14@LB@@LB@@LB@Energy -7.43 kcal/mol@LB@Hybridization Energy -17.4184 kcal/mol@LB@Unfolding Energy - mRNA 3.9771 kcal/mol@LB@Unfolding Energy - sRNA 6.01129 kcal/mol@LB@@LB@Position - mRNA 149 -- 162@LB@Position - sRNA 15 -- 27@LB@Position Seed - mRNA 149 -- 155@LB@Position Seed - sRNA 21 -- 27@LB@
9	8.212e-05	0.03044	bsu07800	treP	-22.21	0.000470	182 -- 210	21 -- 52	PTS system-trehalose-specific transporter subunit EIIBC		_____________181____________________________________211\n_____________\|______________________________________\|\n5'-UUA...AAAAA_____AC__________________GGCAUG_______UGAAC...UUG-3'\n______________CGGAU___________GGAGGGGUU______GGGGAAC\n______________\|\|\|\|\|___________:\|\|\|\|\|\|\|\|______\|\|\|\|\|\|\|\n______________GCCUA___________UCUCCCCAA______CCCCUUG\n3'-UUU...AAAAA_____GAACUAGACUA______________________UCUCU...AUA-5'\n_____________\|______________________________________\|\n_____________53_____________________________________20\n	204 -- 210	21 -- 27	-29.9746 kcal/mol	4.99416 kcal/mol	2.77037 kcal/mol	181 211@LB@ \| \|@LB@5'-UUA...AAAAA AC GGCAUG UGAAC...UUG-3'@LB@ CGGAU GGAGGGGUU GGGGAAC@LB@ \|\|\|\|\| :\|\|\|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ GCCUA UCUCCCCAA CCCCUUG@LB@3'-UUU...AAAAA GAACUAGACUA UCUCU...AUA-5'@LB@ \| \|@LB@ 53 20@LB@@LB@@LB@Energy -22.21 kcal/mol@LB@Hybridization Energy -29.9746 kcal/mol@LB@Unfolding Energy - mRNA 4.99416 kcal/mol@LB@Unfolding Energy - sRNA 2.77037 kcal/mol@LB@@LB@Position - mRNA 182 -- 210@LB@Position - sRNA 21 -- 52@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 21 -- 27@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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