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
36	0.01184	0.2704	ct_030	gmk	-11.03	0.015227	49 -- 70	6 -- 34	guanylate kinase	_____________48____________________________71\n_____________\|_____________________________\|\n5'-AUA...UGAUG_____________________________CCGAG...CAC-3'\n______________CGGAAGCU___UCAUG____UAGAGUACC\n______________\|:\|\|\|\|\|\|___:\|\|\|\|____\|\|\|\|:\|\|\|\|\n______________GUCUUCGA___GGUAC____AUCUUAUGG\n3'-UUU...UCUCA________UAA_____CGCA_________UUGAA-5'\n_____________\|_____________________________\|\n_____________35____________________________5\n	64 -- 70	6 -- 12	-24.3478 kcal/mol	4.72233 kcal/mol	8.59183 kcal/mol	48 71@LB@ \| \|@LB@5'-AUA...UGAUG CCGAG...CAC-3'@LB@ CGGAAGCU UCAUG UAGAGUACC@LB@ \|:\|\|\|\|\|\| :\|\|\|\| \|\|\|\|:\|\|\|\|@LB@ GUCUUCGA GGUAC AUCUUAUGG@LB@3'-UUU...UCUCA UAA CGCA UUGAA-5'@LB@ \| \|@LB@ 35 5@LB@@LB@@LB@Energy -11.03 kcal/mol@LB@Hybridization Energy -24.3478 kcal/mol@LB@Unfolding Energy - mRNA 4.72233 kcal/mol@LB@Unfolding Energy - sRNA 8.59183 kcal/mol@LB@@LB@Position - mRNA 49 -- 70@LB@Position - sRNA 6 -- 34@LB@Position Seed - mRNA 64 -- 70@LB@Position Seed - sRNA 6 -- 12@LB@
148	0.06134	0.3407	ct_434	ygbB	-10.66	0.019089	186 -- 200	41 -- 57	2-C-methyl-D-erythritol 2 4-cyclodiphosphate synthase	_____________185_______________201\n_____________\|_________________\|\n5'-GGU...CCUGU_____U___________AUGAC...AUC-3'\n______________CCCCU___UGCAAGCAC\n______________\|\|\|\|\|___\|:\|\|\|:\|\|\|\n______________GGGGA___AUGUUUGUG\n3'-UUU...GAAGG_____CAC_________AUCUC...GAA-5'\n_____________\|_________________\|\n_____________58________________40\n	194 -- 200	41 -- 47	-19.7128 kcal/mol	1.2348 kcal/mol	7.82241 kcal/mol	185 201@LB@ \| \|@LB@5'-GGU...CCUGU U AUGAC...AUC-3'@LB@ CCCCU UGCAAGCAC@LB@ \|\|\|\|\| \|:\|\|\|:\|\|\|@LB@ GGGGA AUGUUUGUG@LB@3'-UUU...GAAGG CAC AUCUC...GAA-5'@LB@ \| \|@LB@ 58 40@LB@@LB@@LB@Energy -10.66 kcal/mol@LB@Hybridization Energy -19.7128 kcal/mol@LB@Unfolding Energy - mRNA 1.2348 kcal/mol@LB@Unfolding Energy - sRNA 7.82241 kcal/mol@LB@@LB@Position - mRNA 186 -- 200@LB@Position - sRNA 41 -- 57@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 41 -- 47@LB@
13	0.003406	0.1836	ct_744	N/A	-10.55	0.020316	225 -- 240	17 -- 33		_____________224_______________241\n_____________\|_________________\|\n5'-AAA...UCUCU_________________UUCUG...AAU-3'\n______________GGAAGCUGUU_CAUGGU\n______________:\|\|\|\|\|\|:\|\|_\|\|\|\|\|:\n______________UCUUCGAUAA_GUACCG\n3'-UUU...CUCAG__________G______CAAUC...GAA-5'\n_____________\|_________________\|\n_____________34________________16\n	225 -- 231	27 -- 33	-21.2225 kcal/mol	5.69382 kcal/mol	4.97804 kcal/mol	224 241@LB@ \| \|@LB@5'-AAA...UCUCU UUCUG...AAU-3'@LB@ GGAAGCUGUU CAUGGU@LB@ :\|\|\|\|\|\|:\|\| \|\|\|\|\|:@LB@ UCUUCGAUAA GUACCG@LB@3'-UUU...CUCAG G CAAUC...GAA-5'@LB@ \| \|@LB@ 34 16@LB@@LB@@LB@Energy -10.55 kcal/mol@LB@Hybridization Energy -21.2225 kcal/mol@LB@Unfolding Energy - mRNA 5.69382 kcal/mol@LB@Unfolding Energy - sRNA 4.97804 kcal/mol@LB@@LB@Position - mRNA 225 -- 240@LB@Position - sRNA 17 -- 33@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 27 -- 33@LB@
14	0.003406	0.1836	ct_744	N/A	-10.55	0.020316	225 -- 240	17 -- 33		_____________224_______________241\n_____________\|_________________\|\n5'-AAA...UCUCU_________________UUCUG...AAU-3'\n______________GGAAGCUGUU_CAUGGU\n______________:\|\|\|\|\|\|:\|\|_\|\|\|\|\|:\n______________UCUUCGAUAA_GUACCG\n3'-UUU...CUCAG__________G______CAAUC...GAA-5'\n_____________\|_________________\|\n_____________34________________16\n	225 -- 231	27 -- 33	-21.2225 kcal/mol	5.69382 kcal/mol	4.97804 kcal/mol	224 241@LB@ \| \|@LB@5'-AAA...UCUCU UUCUG...AAU-3'@LB@ GGAAGCUGUU CAUGGU@LB@ :\|\|\|\|\|\|:\|\| \|\|\|\|\|:@LB@ UCUUCGAUAA GUACCG@LB@3'-UUU...CUCAG G CAAUC...GAA-5'@LB@ \| \|@LB@ 34 16@LB@@LB@@LB@Energy -10.55 kcal/mol@LB@Hybridization Energy -21.2225 kcal/mol@LB@Unfolding Energy - mRNA 5.69382 kcal/mol@LB@Unfolding Energy - sRNA 4.97804 kcal/mol@LB@@LB@Position - mRNA 225 -- 240@LB@Position - sRNA 17 -- 33@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 27 -- 33@LB@
50	0.01829	0.29	ct_588	rbsU	-10.49	0.021035	31 -- 46	21 -- 34	serine phosphatase RsbU	_____________30_______________47\n_____________\|________________\|\n5'-GUC...GGGUC________CU______AGAUU...UCC-3'\n______________CAGAAGCU__AUUCCA\n______________\|\|\|\|\|\|\|\|__\|\|\|\|\|\|\n______________GUCUUCGA__UAAGGU\n3'-UUU...UCUCA________________ACCGC...GAA-5'\n_____________\|________________\|\n_____________35_______________20\n	32 -- 38	27 -- 33	-17.905 kcal/mol	2.68182 kcal/mol	4.73132 kcal/mol	30 47@LB@ \| \|@LB@5'-GUC...GGGUC CU AGAUU...UCC-3'@LB@ CAGAAGCU AUUCCA@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ GUCUUCGA UAAGGU@LB@3'-UUU...UCUCA ACCGC...GAA-5'@LB@ \| \|@LB@ 35 20@LB@@LB@@LB@Energy -10.49 kcal/mol@LB@Hybridization Energy -17.905 kcal/mol@LB@Unfolding Energy - mRNA 2.68182 kcal/mol@LB@Unfolding Energy - sRNA 4.73132 kcal/mol@LB@@LB@Position - mRNA 31 -- 46@LB@Position - sRNA 21 -- 34@LB@Position Seed - mRNA 32 -- 38@LB@Position Seed - sRNA 27 -- 33@LB@
3	0.0003482	0.07439	ct_023	prfA	-10.22	0.024627	158 -- 204	18 -- 56	peptide chain release factor	_____________157_____________________________________________205\n_____________\|_______________________________________________\|\n5'-GAA...CUGGU______UAG_G____________AAAGG______AAGUCG_______AAAUA...CGC-3'\n______________CUUUGU___A_AGAUACUAGAGU_____CAGAAG______UUCAUGG\n______________\|::\|\|\|___\|_\|:\|:\|\|\|\|\|\|\|\|_____\|\|\|\|\|\|______\|:\|\|\|\|\|\n______________GGGACA___U_UUUGUGAUCUCA_____GUCUUC______AGGUACC\n3'-UUU...AAGGG______CA__G_______________________GAUA_________GCAAU...GAA-5'\n_____________\|_______________________________________________\|\n_____________57______________________________________________17\n	198 -- 204	18 -- 24	-35.7937 kcal/mol	12.6341 kcal/mol	12.9359 kcal/mol	157 205@LB@ \| \|@LB@5'-GAA...CUGGU UAG G AAAGG AAGUCG AAAUA...CGC-3'@LB@ CUUUGU A AGAUACUAGAGU CAGAAG UUCAUGG@LB@ \|::\|\|\| \| \|:\|:\|\|\|\|\|\|\|\| \|\|\|\|\|\| \|:\|\|\|\|\|@LB@ GGGACA U UUUGUGAUCUCA GUCUUC AGGUACC@LB@3'-UUU...AAGGG CA G GAUA GCAAU...GAA-5'@LB@ \| \|@LB@ 57 17@LB@@LB@@LB@Energy -10.22 kcal/mol@LB@Hybridization Energy -35.7937 kcal/mol@LB@Unfolding Energy - mRNA 12.6341 kcal/mol@LB@Unfolding Energy - sRNA 12.9359 kcal/mol@LB@@LB@Position - mRNA 158 -- 204@LB@Position - sRNA 18 -- 56@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 18 -- 24@LB@
53	0.01942	0.29	ct_580	N/A	-10.14	0.025883	244 -- 280	22 -- 57	S-adenosylmethionine/S-adenosylhomocysteine transporter	_____________243___________________________________281\n_____________\|_____________________________________\|\n5'-GUU...ACAAA___G_____U_____C___UU__GACAU_________CUUAA...CUU-3'\n______________CCU_UGUGU_UAAAC_CUG__GU_____GGCUAUUUU\n______________\|\|:_\|\|\|\|\|_:\|\|\|\|_\|\|:__\|\|_____:\|\|\|\|\|\|::\n______________GGG_ACACA_GUUUG_GAU__CA_____UCGAUAAGG\n3'-UUU...GAAGG___G_____U_____U___CU__GUCU__________UACCG...GAA-5'\n_____________\|_____________________________________\|\n_____________58____________________________________21\n	273 -- 279	23 -- 29	-28.6785 kcal/mol	5.85369 kcal/mol	12.6861 kcal/mol	243 281@LB@ \| \|@LB@5'-GUU...ACAAA G U C UU GACAU CUUAA...CUU-3'@LB@ CCU UGUGU UAAAC CUG GU GGCUAUUUU@LB@ \|\|: \|\|\|\|\| :\|\|\|\| \|\|: \|\| :\|\|\|\|\|\|::@LB@ GGG ACACA GUUUG GAU CA UCGAUAAGG@LB@3'-UUU...GAAGG G U U CU GUCU UACCG...GAA-5'@LB@ \| \|@LB@ 58 21@LB@@LB@@LB@Energy -10.14 kcal/mol@LB@Hybridization Energy -28.6785 kcal/mol@LB@Unfolding Energy - mRNA 5.85369 kcal/mol@LB@Unfolding Energy - sRNA 12.6861 kcal/mol@LB@@LB@Position - mRNA 244 -- 280@LB@Position - sRNA 22 -- 57@LB@Position Seed - mRNA 273 -- 279@LB@Position Seed - sRNA 23 -- 29@LB@
45	0.01671	0.29	ct_469	N/A	-9.81	0.031394	4 -- 20	17 -- 35		_____________3___________________21\n_____________\|___________________\|\n________5'-AUU___________________AACCU...UCU-3'\n______________UCAGAAGCU_UUUC_UGGU\n______________\|\|\|\|\|\|\|\|\|_\|\|:\|_\|\|\|:\n______________AGUCUUCGA_AAGG_ACCG\n3'-UUU...AUCUC_________U____U____CAAUC...GAA-5'\n_____________\|___________________\|\n_____________36__________________16\n	6 -- 12	27 -- 33	-19.4129 kcal/mol	4.62874 kcal/mol	4.9781 kcal/mol	3 21@LB@ \| \|@LB@ 5'-AUU AACCU...UCU-3'@LB@ UCAGAAGCU UUUC UGGU@LB@ \|\|\|\|\|\|\|\|\| \|\|:\| \|\|\|:@LB@ AGUCUUCGA AAGG ACCG@LB@3'-UUU...AUCUC U U CAAUC...GAA-5'@LB@ \| \|@LB@ 36 16@LB@@LB@@LB@Energy -9.81 kcal/mol@LB@Hybridization Energy -19.4129 kcal/mol@LB@Unfolding Energy - mRNA 4.62874 kcal/mol@LB@Unfolding Energy - sRNA 4.9781 kcal/mol@LB@@LB@Position - mRNA 4 -- 20@LB@Position - sRNA 17 -- 35@LB@Position Seed - mRNA 6 -- 12@LB@Position Seed - sRNA 27 -- 33@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@
43	0.01649	0.29	ct_590	N/A	-9.68	0.033714	159 -- 170	17 -- 28		_____________158__________171\n_____________\|____________\|\n5'-AGU...CAAUU____________AAAGG...UCA-3'\n______________UUAUUCCAUGGU\n______________:\|\|\|\|\|\|\|\|\|\|:\n______________GAUAAGGUACCG\n3'-UUU...UCUUC____________CAAUC...GAA-5'\n_____________\|____________\|\n_____________29___________16\n	164 -- 170	17 -- 23	-16.2126 kcal/mol	1.90936 kcal/mol	4.62088 kcal/mol	158 171@LB@ \| \|@LB@5'-AGU...CAAUU AAAGG...UCA-3'@LB@ UUAUUCCAUGGU@LB@ :\|\|\|\|\|\|\|\|\|\|:@LB@ GAUAAGGUACCG@LB@3'-UUU...UCUUC CAAUC...GAA-5'@LB@ \| \|@LB@ 29 16@LB@@LB@@LB@Energy -9.68 kcal/mol@LB@Hybridization Energy -16.2126 kcal/mol@LB@Unfolding Energy - mRNA 1.90936 kcal/mol@LB@Unfolding Energy - sRNA 4.62088 kcal/mol@LB@@LB@Position - mRNA 159 -- 170@LB@Position - sRNA 17 -- 28@LB@Position Seed - mRNA 164 -- 170@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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