Input and runtime details for job 6038639 (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 6038639 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:35:57 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:19:35 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:35:30 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:35:37 CET 2018
	Job Completed		@ Fri Feb 16 21:35:51 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6038639&toolName=CopraRNA ( 30 days expiry )

Description of the job

IhtA

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_000117 Chlamydia trachomatis D/UW-3/CX

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
37	0.01294	0.2859	ct_591	sdhB	-7.06	0.139804	161 -- 176	18 -- 34	succinate dehydrogenase iron sulfur subunit	_____________160_______________177\n_____________\|_________________\|\n5'-AAA...AUUUA_____________UG__AAAUA...GGG-3'\n______________UAGAGGC_GUUCC__GG\n______________:\|\|\|:\|\|_:\|\|\|\|__\|\|\n______________GUCUUCG_UAAGG__CC\n3'-UUU...UCUCA_______A_____UA__GCAAU...GAA-5'\n_____________\|_________________\|\n_____________35________________17\n	161 -- 167	28 -- 34	-17.8156 kcal/mol	5.77845 kcal/mol	4.97803 kcal/mol	160 177@LB@ \| \|@LB@5'-AAA...AUUUA UG AAAUA...GGG-3'@LB@ UAGAGGC GUUCC GG@LB@ :\|\|\|:\|\| :\|\|\|\| \|\|@LB@ GUCUUCG UAAGG CC@LB@3'-UUU...UCUCA A UA GCAAU...GAA-5'@LB@ \| \|@LB@ 35 17@LB@@LB@@LB@Energy -7.06 kcal/mol@LB@Hybridization Energy -17.8156 kcal/mol@LB@Unfolding Energy - mRNA 5.77845 kcal/mol@LB@Unfolding Energy - sRNA 4.97803 kcal/mol@LB@@LB@Position - mRNA 161 -- 176@LB@Position - sRNA 18 -- 34@LB@Position Seed - mRNA 161 -- 167@LB@Position Seed - sRNA 28 -- 34@LB@
186	0.08332	0.363	ct_811	plsX	-5.83	0.252304	163 -- 171	79 -- 87	phosphate acyltransferase	_____________162_______172\n_____________\|_________\|\n5'-GGC...GUUAU_________GAAGU...AAC-3'\n______________UACGGUUGA\n______________\|\|\|\|\|:\|:\|\n______________AUGCCGAUU\n3'-UUU...CCUCU_________GAGGU...GAA-5'\n_____________\|_________\|\n_____________88________78\n	165 -- 171	79 -- 85	-10.158 kcal/mol	3.22704 kcal/mol	1.09752 kcal/mol	162 172@LB@ \| \|@LB@5'-GGC...GUUAU GAAGU...AAC-3'@LB@ UACGGUUGA@LB@ \|\|\|\|\|:\|:\|@LB@ AUGCCGAUU@LB@3'-UUU...CCUCU GAGGU...GAA-5'@LB@ \| \|@LB@ 88 78@LB@@LB@@LB@Energy -5.83 kcal/mol@LB@Hybridization Energy -10.158 kcal/mol@LB@Unfolding Energy - mRNA 3.22704 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 163 -- 171@LB@Position - sRNA 79 -- 87@LB@Position Seed - mRNA 165 -- 171@LB@Position Seed - sRNA 79 -- 85@LB@
11	0.002752	0.1836	ct_015	phoH	-12.12	0.007844	167 -- 186	33 -- 60	ATPase	_____________166__________________________187\n_____________\|____________________________\|\n5'-CCA...CUAUC_____________________U______UUUAG...UAA-3'\n______________UCCCCCUU________ACACU_GAGUCA\n______________\|\|\|\|\|\|:\|________\|\|\|\|\|_\|\|\|\|\|\|\n______________AGGGGGGA________UGUGA_CUCAGU\n3'-UUU...ACUGA________CACAUGUU_____U______CUUCG...GAA-5'\n_____________\|____________________________\|\n_____________61___________________________32\n	168 -- 174	53 -- 59	-26.4608 kcal/mol	2.95889 kcal/mol	11.3851 kcal/mol	166 187@LB@ \| \|@LB@5'-CCA...CUAUC U UUUAG...UAA-3'@LB@ UCCCCCUU ACACU GAGUCA@LB@ \|\|\|\|\|\|:\| \|\|\|\|\| \|\|\|\|\|\|@LB@ AGGGGGGA UGUGA CUCAGU@LB@3'-UUU...ACUGA CACAUGUU U CUUCG...GAA-5'@LB@ \| \|@LB@ 61 32@LB@@LB@@LB@Energy -12.12 kcal/mol@LB@Hybridization Energy -26.4608 kcal/mol@LB@Unfolding Energy - mRNA 2.95889 kcal/mol@LB@Unfolding Energy - sRNA 11.3851 kcal/mol@LB@@LB@Position - mRNA 167 -- 186@LB@Position - sRNA 33 -- 60@LB@Position Seed - mRNA 168 -- 174@LB@Position Seed - sRNA 53 -- 59@LB@
70	0.02698	0.29	ct_381	artJ	-6.76	0.162330	168 -- 194	31 -- 57	arginine ABC transporter substrate-binding protein ArtJ	_____________167__________________________195\n_____________\|____________________________\|\n5'-AUU...UAUAG______CC__UA__C_____________GUGAG...GUG-3'\n______________UCCCUG__GU__GA_CAUU_GAGUCGGA\n______________:\|\|\|\|\|__\|\|__:\|_\|\|:\|_\|\|\|\|\|:\|\|\n______________GGGGAC__CA__UU_GUGA_CUCAGUCU\n3'-UUU...GAAGG______A___UG__U____U________UCGAU...GAA-5'\n_____________\|____________________________\|\n_____________58___________________________30\n	188 -- 194	31 -- 37	-25.975 kcal/mol	9.18513 kcal/mol	10.0297 kcal/mol	167 195@LB@ \| \|@LB@5'-AUU...UAUAG CC UA C GUGAG...GUG-3'@LB@ UCCCUG GU GA CAUU GAGUCGGA@LB@ :\|\|\|\|\| \|\| :\| \|\|:\| \|\|\|\|\|:\|\|@LB@ GGGGAC CA UU GUGA CUCAGUCU@LB@3'-UUU...GAAGG A UG U U UCGAU...GAA-5'@LB@ \| \|@LB@ 58 30@LB@@LB@@LB@Energy -6.76 kcal/mol@LB@Hybridization Energy -25.975 kcal/mol@LB@Unfolding Energy - mRNA 9.18513 kcal/mol@LB@Unfolding Energy - sRNA 10.0297 kcal/mol@LB@@LB@Position - mRNA 168 -- 194@LB@Position - sRNA 31 -- 57@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 31 -- 37@LB@
127	0.0509	0.3262	ct_808	cafE	-7.80	0.095102	169 -- 204	18 -- 57	ribonuclease E	_____________168_________________________________________205\n_____________\|___________________________________________\|\n5'-GUU...GAGGA_______A______________CAU______ACG_________AAAAC...AAA-3'\n______________CUCCUGU____GAGCGC_AGAG___UUAGGA______CCAUGG\n______________\|:\|\|\|\|\|____:\|:\|:\|_\|\|\|\|___\|:\|\|:\|______\|\|\|\|\|\|\n______________GGGGACA____UUUGUG_UCUC___AGUCUU______GGUACC\n3'-UUU...GAAGG_______CAUG______A_____________CGAUAA______GCAAU...GAA-5'\n_____________\|___________________________________________\|\n_____________58__________________________________________17\n	169 -- 175	51 -- 57	-30.1775 kcal/mol	9.43695 kcal/mol	12.9362 kcal/mol	168 205@LB@ \| \|@LB@5'-GUU...GAGGA A CAU ACG AAAAC...AAA-3'@LB@ CUCCUGU GAGCGC AGAG UUAGGA CCAUGG@LB@ \|:\|\|\|\|\| :\|:\|:\| \|\|\|\| \|:\|\|:\| \|\|\|\|\|\|@LB@ GGGGACA UUUGUG UCUC AGUCUU GGUACC@LB@3'-UUU...GAAGG CAUG A CGAUAA GCAAU...GAA-5'@LB@ \| \|@LB@ 58 17@LB@@LB@@LB@Energy -7.80 kcal/mol@LB@Hybridization Energy -30.1775 kcal/mol@LB@Unfolding Energy - mRNA 9.43695 kcal/mol@LB@Unfolding Energy - sRNA 12.9362 kcal/mol@LB@@LB@Position - mRNA 169 -- 204@LB@Position - sRNA 18 -- 57@LB@Position Seed - mRNA 169 -- 175@LB@Position Seed - sRNA 51 -- 57@LB@
149	0.06369	0.3424	ct_124	accC	-5.62	0.277702	171 -- 193	17 -- 31	acetyl-CoA carboxylase biotin carboxylase subunit	_____________170_____________________194\n_____________\|_______________________\|\n5'-CUC...GUUCU____________AUAGUUAA___UUAGU...UGG-3'\n______________AAGUUAUUCCGU________GGC\n______________\|\|\|:\|\|\|\|\|\|:\|________\|\|\|\n______________UUCGAUAAGGUA________CCG\n3'-UUU...CAGUC_______________________CAAUC...GAA-5'\n_____________\|_______________________\|\n_____________32______________________16\n	176 -- 182	20 -- 26	-15.1557 kcal/mol	4.67447 kcal/mol	4.86101 kcal/mol	170 194@LB@ \| \|@LB@5'-CUC...GUUCU AUAGUUAA UUAGU...UGG-3'@LB@ AAGUUAUUCCGU GGC@LB@ \|\|\|:\|\|\|\|\|\|:\| \|\|\|@LB@ UUCGAUAAGGUA CCG@LB@3'-UUU...CAGUC CAAUC...GAA-5'@LB@ \| \|@LB@ 32 16@LB@@LB@@LB@Energy -5.62 kcal/mol@LB@Hybridization Energy -15.1557 kcal/mol@LB@Unfolding Energy - mRNA 4.67447 kcal/mol@LB@Unfolding Energy - sRNA 4.86101 kcal/mol@LB@@LB@Position - mRNA 171 -- 193@LB@Position - sRNA 17 -- 31@LB@Position Seed - mRNA 176 -- 182@LB@Position Seed - sRNA 20 -- 26@LB@
89	0.03269	0.2942	ct_269	murE	-8.94	0.051230	172 -- 183	46 -- 57	UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2 6-diaminopimelate ligase	_____________171__________184\n_____________\|____________\|\n5'-AUC...UGAAG____________UGUCU...UUG-3'\n______________CCCUUGUGUGCG\n______________\|\|\|:\|\|\|\|\|:\|:\n______________GGGGACACAUGU\n3'-UUU...GAAGG____________UUGUG...GAA-5'\n_____________\|____________\|\n_____________58___________45\n	176 -- 182	47 -- 53	-19.7508 kcal/mol	3.51628 kcal/mol	7.29173 kcal/mol	171 184@LB@ \| \|@LB@5'-AUC...UGAAG UGUCU...UUG-3'@LB@ CCCUUGUGUGCG@LB@ \|\|\|:\|\|\|\|\|:\|:@LB@ GGGGACACAUGU@LB@3'-UUU...GAAGG UUGUG...GAA-5'@LB@ \| \|@LB@ 58 45@LB@@LB@@LB@Energy -8.94 kcal/mol@LB@Hybridization Energy -19.7508 kcal/mol@LB@Unfolding Energy - mRNA 3.51628 kcal/mol@LB@Unfolding Energy - sRNA 7.29173 kcal/mol@LB@@LB@Position - mRNA 172 -- 183@LB@Position - sRNA 46 -- 57@LB@Position Seed - mRNA 176 -- 182@LB@Position Seed - sRNA 47 -- 53@LB@
75	0.02725	0.29	ct_536	dnaQ_2	-6.54	0.180881	173 -- 186	18 -- 31	DNA polymerase III subunit epsilon	_____________172____________187\n_____________\|______________\|\n5'-AGA...GAUUU_____U________AGAAC...GGU-3'\n______________GAGCU_UUUUAUGG\n______________:\|\|\|\|_\|\|::\|\|\|\|\n______________UUCGA_AAGGUACC\n3'-UUU...CAGUC_____U________GCAAU...GAA-5'\n_____________\|______________\|\n_____________32_____________17\n	180 -- 186	18 -- 24	-14.3298 kcal/mol	2.92947 kcal/mol	4.86077 kcal/mol	172 187@LB@ \| \|@LB@5'-AGA...GAUUU U AGAAC...GGU-3'@LB@ GAGCU UUUUAUGG@LB@ :\|\|\|\| \|\|::\|\|\|\|@LB@ UUCGA AAGGUACC@LB@3'-UUU...CAGUC U GCAAU...GAA-5'@LB@ \| \|@LB@ 32 17@LB@@LB@@LB@Energy -6.54 kcal/mol@LB@Hybridization Energy -14.3298 kcal/mol@LB@Unfolding Energy - mRNA 2.92947 kcal/mol@LB@Unfolding Energy - sRNA 4.86077 kcal/mol@LB@@LB@Position - mRNA 173 -- 186@LB@Position - sRNA 18 -- 31@LB@Position Seed - mRNA 180 -- 186@LB@Position Seed - sRNA 18 -- 24@LB@
137	0.05536	0.3262	ct_389	N/A	-5.69	0.269629	175 -- 181	80 -- 86		_____________174_____182\n_____________\|_______\|\n5'-GUU...AUAAC_______UCUCA...GCC-3'\n______________GCGGCUG\n______________:\|\|\|\|\|:\n______________UGCCGAU\n3'-UUU...CUCUA_______UGAGG...GAA-5'\n_____________\|_______\|\n_____________87______79\n	175 -- 181	80 -- 86	-10.4159 kcal/mol	3.66497 kcal/mol	1.06449 kcal/mol	174 182@LB@ \| \|@LB@5'-GUU...AUAAC UCUCA...GCC-3'@LB@ GCGGCUG@LB@ :\|\|\|\|\|:@LB@ UGCCGAU@LB@3'-UUU...CUCUA UGAGG...GAA-5'@LB@ \| \|@LB@ 87 79@LB@@LB@@LB@Energy -5.69 kcal/mol@LB@Hybridization Energy -10.4159 kcal/mol@LB@Unfolding Energy - mRNA 3.66497 kcal/mol@LB@Unfolding Energy - sRNA 1.06449 kcal/mol@LB@@LB@Position - mRNA 175 -- 181@LB@Position - sRNA 80 -- 86@LB@Position Seed - mRNA 175 -- 181@LB@Position Seed - sRNA 80 -- 86@LB@
25	0.00654	0.2093	ct_672	N/A	-9.75	0.032384	176 -- 205	17 -- 33	type III secretion system protein	_____________175____________________________206\n_____________\|______________________________\|\n5'-AUC...GUAGA_______CAUAUAUAAGGU___C_______AGUUG...CUG-3'\n______________AGAAGCU____________AUU_CCAUGGC\n______________\|\|\|\|\|\|\|____________\|\|\|_\|\|\|\|\|\|\|\n______________UCUUCGA____________UAA_GGUACCG\n3'-UUU...CUCAG______________________________CAAUC...GAA-5'\n_____________\|______________________________\|\n_____________34_____________________________16\n	199 -- 205	17 -- 23	-19.3096 kcal/mol	4.57941 kcal/mol	4.97804 kcal/mol	175 206@LB@ \| \|@LB@5'-AUC...GUAGA CAUAUAUAAGGU C AGUUG...CUG-3'@LB@ AGAAGCU AUU CCAUGGC@LB@ \|\|\|\|\|\|\| \|\|\| \|\|\|\|\|\|\|@LB@ UCUUCGA UAA GGUACCG@LB@3'-UUU...CUCAG CAAUC...GAA-5'@LB@ \| \|@LB@ 34 16@LB@@LB@@LB@Energy -9.75 kcal/mol@LB@Hybridization Energy -19.3096 kcal/mol@LB@Unfolding Energy - mRNA 4.57941 kcal/mol@LB@Unfolding Energy - sRNA 4.97804 kcal/mol@LB@@LB@Position - mRNA 176 -- 205@LB@Position - sRNA 17 -- 33@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 17 -- 23@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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