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
65	0.02498	0.29	ct_846	N/A	-7.66	0.102535	215 -- 232	42 -- 57		_____________214________________233\n_____________\|__________________\|\n5'-GCG...AUCUU____GAUAA_________AACUC...CUC-3'\n______________CCCC_____GUACAAACA\n______________\|\|\|\|_____\|\|\|\|\|\|\|\|\|\n______________GGGG_____CAUGUUUGU\n3'-UUU...GAAGG____ACA___________GAUCU...GAA-5'\n_____________\|__________________\|\n_____________58_________________41\n	226 -- 232	42 -- 48	-18.5622 kcal/mol	3.08308 kcal/mol	7.81778 kcal/mol	214 233@LB@ \| \|@LB@5'-GCG...AUCUU GAUAA AACUC...CUC-3'@LB@ CCCC GUACAAACA@LB@ \|\|\|\| \|\|\|\|\|\|\|\|\|@LB@ GGGG CAUGUUUGU@LB@3'-UUU...GAAGG ACA GAUCU...GAA-5'@LB@ \| \|@LB@ 58 41@LB@@LB@@LB@Energy -7.66 kcal/mol@LB@Hybridization Energy -18.5622 kcal/mol@LB@Unfolding Energy - mRNA 3.08308 kcal/mol@LB@Unfolding Energy - sRNA 7.81778 kcal/mol@LB@@LB@Position - mRNA 215 -- 232@LB@Position - sRNA 42 -- 57@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 42 -- 48@LB@
114	0.04665	0.3262	ct_848	N/A	-8.83	0.054442	279 -- 286	79 -- 86		_____________278______287\n_____________\|________\|\n5'-CAA...CUGCA________UGAGA...CAC-3'\n______________ACGGCUGA\n______________\|\|\|\|\|\|:\|\n______________UGCCGAUU\n3'-UUU...CUCUA________GAGGU...GAA-5'\n_____________\|________\|\n_____________87_______78\n	280 -- 286	79 -- 85	-11.4013 kcal/mol	1.46996 kcal/mol	1.09752 kcal/mol	278 287@LB@ \| \|@LB@5'-CAA...CUGCA UGAGA...CAC-3'@LB@ ACGGCUGA@LB@ \|\|\|\|\|\|:\|@LB@ UGCCGAUU@LB@3'-UUU...CUCUA GAGGU...GAA-5'@LB@ \| \|@LB@ 87 78@LB@@LB@@LB@Energy -8.83 kcal/mol@LB@Hybridization Energy -11.4013 kcal/mol@LB@Unfolding Energy - mRNA 1.46996 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 279 -- 286@LB@Position - sRNA 79 -- 86@LB@Position Seed - mRNA 280 -- 286@LB@Position Seed - sRNA 79 -- 85@LB@
197	0.08765	0.3657	ct_851	map	-5.60	0.279866	107 -- 113	81 -- 87	methionine aminopeptidase	_____________106_____114\n_____________\|_______\|\n5'-GCU...CUUUC_______UUCAA...AAC-3'\n______________UACGGCU\n______________\|\|\|\|\|\|\|\n______________AUGCCGA\n3'-UUU...CCUCU_______UUGAG...GAA-5'\n_____________\|_______\|\n_____________88______80\n	107 -- 113	81 -- 87	-10.6361 kcal/mol	3.93565 kcal/mol	1.09752 kcal/mol	106 114@LB@ \| \|@LB@5'-GCU...CUUUC UUCAA...AAC-3'@LB@ UACGGCU@LB@ \|\|\|\|\|\|\|@LB@ AUGCCGA@LB@3'-UUU...CCUCU UUGAG...GAA-5'@LB@ \| \|@LB@ 88 80@LB@@LB@@LB@Energy -5.60 kcal/mol@LB@Hybridization Energy -10.6361 kcal/mol@LB@Unfolding Energy - mRNA 3.93565 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 107 -- 113@LB@Position - sRNA 81 -- 87@LB@Position Seed - mRNA 107 -- 113@LB@Position Seed - sRNA 81 -- 87@LB@
27	0.007389	0.2199	ct_855	fumC	-7.16	0.132975	201 -- 207	82 -- 88	fumarate hydratase	_____________200_____208\n_____________\|_______\|\n5'-AUA...AGCAU_______AAGAG...GUA-3'\n______________AUGCGGC\n______________\|\|:\|\|\|\|\n______________UAUGCCG\n3'-UUU...GCCUC_______AUUGA...GAA-5'\n_____________\|_______\|\n_____________89______81\n	201 -- 207	82 -- 88	-10.3037 kcal/mol	2.04792 kcal/mol	1.09753 kcal/mol	200 208@LB@ \| \|@LB@5'-AUA...AGCAU AAGAG...GUA-3'@LB@ AUGCGGC@LB@ \|\|:\|\|\|\|@LB@ UAUGCCG@LB@3'-UUU...GCCUC AUUGA...GAA-5'@LB@ \| \|@LB@ 89 81@LB@@LB@@LB@Energy -7.16 kcal/mol@LB@Hybridization Energy -10.3037 kcal/mol@LB@Unfolding Energy - mRNA 2.04792 kcal/mol@LB@Unfolding Energy - sRNA 1.09753 kcal/mol@LB@@LB@Position - mRNA 201 -- 207@LB@Position - sRNA 82 -- 88@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 82 -- 88@LB@
165	0.06872	0.3424	ct_859	lytB	-7.21	0.129268	10 -- 22	19 -- 31	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	_____________9_____________23\n_____________\|_____________\|\n5'-UCG...UAUAA___________A_UAUCU...CUA-3'\n______________AGGCUAUUCCG_G\n______________\|:\|\|\|\|\|\|\|\|:_\|\n______________UUCGAUAAGGU_C\n3'-UUU...CAGUC___________A_CGCAA...GAA-5'\n_____________\|_____________\|\n_____________32____________18\n	14 -- 20	21 -- 27	-14.969 kcal/mol	2.89565 kcal/mol	4.85984 kcal/mol	9 23@LB@ \| \|@LB@5'-UCG...UAUAA A UAUCU...CUA-3'@LB@ AGGCUAUUCCG G@LB@ \|:\|\|\|\|\|\|\|\|: \|@LB@ UUCGAUAAGGU C@LB@3'-UUU...CAGUC A CGCAA...GAA-5'@LB@ \| \|@LB@ 32 18@LB@@LB@@LB@Energy -7.21 kcal/mol@LB@Hybridization Energy -14.969 kcal/mol@LB@Unfolding Energy - mRNA 2.89565 kcal/mol@LB@Unfolding Energy - sRNA 4.85984 kcal/mol@LB@@LB@Position - mRNA 10 -- 22@LB@Position - sRNA 19 -- 31@LB@Position Seed - mRNA 14 -- 20@LB@Position Seed - sRNA 21 -- 27@LB@
104	0.03845	0.3036	ct_860	N/A	-5.72	0.265250	231 -- 258	29 -- 56	type III secretion system translocator CopD2	_____________230__________________________259\n_____________\|____________________________\|\n5'-AGU...CACUA____CAU________A___CAA______AGCAG...CCA-3'\n______________CCUU___UACAAACA_UAG___CAGGAG\n______________\|\|:\|___\|\|\|\|\|\|\|\|_\|\|\|___\|\|\|:\|\|\n______________GGGA___AUGUUUGU_AUC___GUCUUC\n3'-UUU...AAGGG____CAC________G___UCA______GAUAA...GAA-5'\n_____________\|____________________________\|\n_____________57___________________________28\n	239 -- 245	42 -- 48	-21.1219 kcal/mol	3.33524 kcal/mol	12.064 kcal/mol	230 259@LB@ \| \|@LB@5'-AGU...CACUA CAU A CAA AGCAG...CCA-3'@LB@ CCUU UACAAACA UAG CAGGAG@LB@ \|\|:\| \|\|\|\|\|\|\|\| \|\|\| \|\|\|:\|\|@LB@ GGGA AUGUUUGU AUC GUCUUC@LB@3'-UUU...AAGGG CAC G UCA GAUAA...GAA-5'@LB@ \| \|@LB@ 57 28@LB@@LB@@LB@Energy -5.72 kcal/mol@LB@Hybridization Energy -21.1219 kcal/mol@LB@Unfolding Energy - mRNA 3.33524 kcal/mol@LB@Unfolding Energy - sRNA 12.064 kcal/mol@LB@@LB@Position - mRNA 231 -- 258@LB@Position - sRNA 29 -- 56@LB@Position Seed - mRNA 239 -- 245@LB@Position Seed - sRNA 42 -- 48@LB@
48	0.01795	0.29	ct_863	N/A	-9.34	0.040980	222 -- 242	40 -- 60		_____________221___________________243\n_____________\|_____________________\|\n5'-AAU...CCCUU______G_ACCG_________UCUCU...UUC-3'\n______________UCCUCC_U____ACAAACGCU\n______________\|\|\|:\|\|_\|____\|\|\|\|\|\|:\|\|\n______________AGGGGG_A____UGUUUGUGA\n3'-UUU...ACUGA______G_CACA_________UCUCA...GAA-5'\n_____________\|_____________________\|\n_____________61____________________39\n	235 -- 241	41 -- 47	-20.8327 kcal/mol	1.69613 kcal/mol	9.79654 kcal/mol	221 243@LB@ \| \|@LB@5'-AAU...CCCUU G ACCG UCUCU...UUC-3'@LB@ UCCUCC U ACAAACGCU@LB@ \|\|\|:\|\| \| \|\|\|\|\|\|:\|\|@LB@ AGGGGG A UGUUUGUGA@LB@3'-UUU...ACUGA G CACA UCUCA...GAA-5'@LB@ \| \|@LB@ 61 39@LB@@LB@@LB@Energy -9.34 kcal/mol@LB@Hybridization Energy -20.8327 kcal/mol@LB@Unfolding Energy - mRNA 1.69613 kcal/mol@LB@Unfolding Energy - sRNA 9.79654 kcal/mol@LB@@LB@Position - mRNA 222 -- 242@LB@Position - sRNA 40 -- 60@LB@Position Seed - mRNA 235 -- 241@LB@Position Seed - sRNA 41 -- 47@LB@
4	0.0004436	0.07439	ct_864	xerD	-16.31	0.000480	24 -- 38	17 -- 31	site-specific tyrosine recombinase XerD	_____________23______________39\n_____________\|_______________\|\n5'-CAU...AUGGA_______________ACCUU...AUU-3'\n______________GAGCUAUUCCAUGGU\n______________:\|\|\|\|\|\|\|\|\|\|\|\|\|:\n______________UUCGAUAAGGUACCG\n3'-UUU...CAGUC_______________CAAUC...GAA-5'\n_____________\|_______________\|\n_____________32______________16\n	32 -- 38	17 -- 23	-24.2689 kcal/mol	3.09995 kcal/mol	4.86101 kcal/mol	23 39@LB@ \| \|@LB@5'-CAU...AUGGA ACCUU...AUU-3'@LB@ GAGCUAUUCCAUGGU@LB@ :\|\|\|\|\|\|\|\|\|\|\|\|\|:@LB@ UUCGAUAAGGUACCG@LB@3'-UUU...CAGUC CAAUC...GAA-5'@LB@ \| \|@LB@ 32 16@LB@@LB@@LB@Energy -16.31 kcal/mol@LB@Hybridization Energy -24.2689 kcal/mol@LB@Unfolding Energy - mRNA 3.09995 kcal/mol@LB@Unfolding Energy - sRNA 4.86101 kcal/mol@LB@@LB@Position - mRNA 24 -- 38@LB@Position - sRNA 17 -- 31@LB@Position Seed - mRNA 32 -- 38@LB@Position Seed - sRNA 17 -- 23@LB@
129	0.0523	0.3262	ct_872	pmpH	-6.76	0.162049	85 -- 103	18 -- 34	outer membrane protein PmpH	_____________84__________________104\n_____________\|___________________\|\n5'-AGA...CAAUA_______A___GG______AAGAU...AUG-3'\n______________UAGAAGU_UAU__CCAUGG\n______________:\|\|\|\|\|:_\|\|\|__\|\|\|\|\|\|\n______________GUCUUCG_AUA__GGUACC\n3'-UUU...UCUCA___________A_______GCAAU...GAA-5'\n_____________\|___________________\|\n_____________35__________________17\n	85 -- 91	28 -- 34	-16.9306 kcal/mol	5.18888 kcal/mol	4.97803 kcal/mol	84 104@LB@ \| \|@LB@5'-AGA...CAAUA A GG AAGAU...AUG-3'@LB@ UAGAAGU UAU CCAUGG@LB@ :\|\|\|\|\|: \|\|\| \|\|\|\|\|\|@LB@ GUCUUCG AUA GGUACC@LB@3'-UUU...UCUCA A GCAAU...GAA-5'@LB@ \| \|@LB@ 35 17@LB@@LB@@LB@Energy -6.76 kcal/mol@LB@Hybridization Energy -16.9306 kcal/mol@LB@Unfolding Energy - mRNA 5.18888 kcal/mol@LB@Unfolding Energy - sRNA 4.97803 kcal/mol@LB@@LB@Position - mRNA 85 -- 103@LB@Position - sRNA 18 -- 34@LB@Position Seed - mRNA 85 -- 91@LB@Position Seed - sRNA 28 -- 34@LB@
100	0.03658	0.3007	ct_875	N/A	-4.31	0.472369	272 -- 278	28 -- 34		_____________271_____279\n_____________\|_______\|\n5'-GGG...AAUCG_______CAAAA...AUA-3'\n______________CAGAAGU\n______________\|\|\|\|\|\|:\n______________GUCUUCG\n3'-UUU...UCUCA_______AUAAG...GAA-5'\n_____________\|_______\|\n_____________35______27\n	272 -- 278	28 -- 34	-8.98313 kcal/mol	0.5541 kcal/mol	4.11458 kcal/mol	271 279@LB@ \| \|@LB@5'-GGG...AAUCG CAAAA...AUA-3'@LB@ CAGAAGU@LB@ \|\|\|\|\|\|:@LB@ GUCUUCG@LB@3'-UUU...UCUCA AUAAG...GAA-5'@LB@ \| \|@LB@ 35 27@LB@@LB@@LB@Energy -4.31 kcal/mol@LB@Hybridization Energy -8.98313 kcal/mol@LB@Unfolding Energy - mRNA 0.5541 kcal/mol@LB@Unfolding Energy - sRNA 4.11458 kcal/mol@LB@@LB@Position - mRNA 272 -- 278@LB@Position - sRNA 28 -- 34@LB@Position Seed - mRNA 272 -- 278@LB@Position Seed - sRNA 28 -- 34@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)

Job resubmission

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service.

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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