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
182	0.07944	0.3588	ct_320	nusG	-7.37	0.119406	230 -- 236	81 -- 87	transcription termination/antitermination protein NusG	_____________229_____237\n_____________\|_______\|\n5'-AAC...GUUUU_______CAAGA...UUA-3'\n______________UACGGCU\n______________\|\|\|\|\|\|\|\n______________AUGCCGA\n3'-UUU...CCUCU_______UUGAG...GAA-5'\n_____________\|_______\|\n_____________88______80\n	230 -- 236	81 -- 87	-10.814 kcal/mol	2.34788 kcal/mol	1.09752 kcal/mol	229 237@LB@ \| \|@LB@5'-AAC...GUUUU CAAGA...UUA-3'@LB@ UACGGCU@LB@ \|\|\|\|\|\|\|@LB@ AUGCCGA@LB@3'-UUU...CCUCU UUGAG...GAA-5'@LB@ \| \|@LB@ 88 80@LB@@LB@@LB@Energy -7.37 kcal/mol@LB@Hybridization Energy -10.814 kcal/mol@LB@Unfolding Energy - mRNA 2.34788 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 230 -- 236@LB@Position - sRNA 81 -- 87@LB@Position Seed - mRNA 230 -- 236@LB@Position Seed - sRNA 81 -- 87@LB@
1	6.997e-05	0.03358	ct_198	oppA_3	-8.59	0.062291	189 -- 206	17 -- 33	oligopeptide ABC transporter substrate-binding protein	_____________188________________207\n_____________\|__________________\|\n5'-AAA...UCUAA______C________C__AAGAU...CUC-3'\n______________GGAGGU_AUUCCAUG_GC\n______________:\|\|:\|:_\|\|\|\|\|\|\|\|_\|\|\n______________UCUUCG_UAAGGUAC_CG\n3'-UUU...CUCAG______A___________CAAUC...GAA-5'\n_____________\|__________________\|\n_____________34_________________16\n	197 -- 203	19 -- 25	-19.6111 kcal/mol	6.04348 kcal/mol	4.97804 kcal/mol	188 207@LB@ \| \|@LB@5'-AAA...UCUAA C C AAGAU...CUC-3'@LB@ GGAGGU AUUCCAUG GC@LB@ :\|\|:\|: \|\|\|\|\|\|\|\| \|\|@LB@ UCUUCG UAAGGUAC CG@LB@3'-UUU...CUCAG A CAAUC...GAA-5'@LB@ \| \|@LB@ 34 16@LB@@LB@@LB@Energy -8.59 kcal/mol@LB@Hybridization Energy -19.6111 kcal/mol@LB@Unfolding Energy - mRNA 6.04348 kcal/mol@LB@Unfolding Energy - sRNA 4.97804 kcal/mol@LB@@LB@Position - mRNA 189 -- 206@LB@Position - sRNA 17 -- 33@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 19 -- 25@LB@
63	0.02436	0.29	ct_270	pbp3	-9.04	0.048476	131 -- 156	5 -- 34	penicillin-binding protein	_____________130_____________________________157\n_____________\|_______________________________\|\n5'-UAA...UGUUG____U____U____UCC______________GUAUC...GAG-3'\n______________CAGA_AGCU_UUCU________AGAAUACCA\n______________\|\|\|\|_\|\|\|\|_\|\|\|:________\|\|\|\|\|\|\|\|\|\n______________GUCU_UCGA_AAGG________UCUUAUGGU\n3'-UUU...UCUCA_________U____UACCGCAA_________UGAA-5'\n_____________\|_______________________________\|\n_____________35______________________________4\n	149 -- 155	6 -- 12	-21.654 kcal/mol	4.02029 kcal/mol	8.59194 kcal/mol	130 157@LB@ \| \|@LB@5'-UAA...UGUUG U U UCC GUAUC...GAG-3'@LB@ CAGA AGCU UUCU AGAAUACCA@LB@ \|\|\|\| \|\|\|\| \|\|\|: \|\|\|\|\|\|\|\|\|@LB@ GUCU UCGA AAGG UCUUAUGGU@LB@3'-UUU...UCUCA U UACCGCAA UGAA-5'@LB@ \| \|@LB@ 35 4@LB@@LB@@LB@Energy -9.04 kcal/mol@LB@Hybridization Energy -21.654 kcal/mol@LB@Unfolding Energy - mRNA 4.02029 kcal/mol@LB@Unfolding Energy - sRNA 8.59194 kcal/mol@LB@@LB@Position - mRNA 131 -- 156@LB@Position - sRNA 5 -- 34@LB@Position Seed - mRNA 149 -- 155@LB@Position Seed - sRNA 6 -- 12@LB@
195	0.08712	0.3657	ct_704	pcnB_2	-3.31	0.654425	101 -- 107	28 -- 34	poly A polymerase	_____________100_____108\n_____________\|_______\|\n5'-CAA...UACGG_______CAUCC...UGC-3'\n______________UAGAAGC\n______________:\|\|\|\|\|\|\n______________GUCUUCG\n3'-UUU...UCUCA_______AUAAG...GAA-5'\n_____________\|_______\|\n_____________35______27\n	101 -- 107	28 -- 34	-7.75845 kcal/mol	0.338622 kcal/mol	4.11458 kcal/mol	100 108@LB@ \| \|@LB@5'-CAA...UACGG CAUCC...UGC-3'@LB@ UAGAAGC@LB@ :\|\|\|\|\|\|@LB@ GUCUUCG@LB@3'-UUU...UCUCA AUAAG...GAA-5'@LB@ \| \|@LB@ 35 27@LB@@LB@@LB@Energy -3.31 kcal/mol@LB@Hybridization Energy -7.75845 kcal/mol@LB@Unfolding Energy - mRNA 0.338622 kcal/mol@LB@Unfolding Energy - sRNA 4.11458 kcal/mol@LB@@LB@Position - mRNA 101 -- 107@LB@Position - sRNA 28 -- 34@LB@Position Seed - mRNA 101 -- 107@LB@Position Seed - sRNA 28 -- 34@LB@
64	0.02465	0.29	ct_045	pepA	-6.49	0.184926	191 -- 205	17 -- 33	cytosol aminopeptidase	_____________190_______________206\n_____________\|_________________\|\n5'-UUU...AACAA_________________AUUAC...CUG-3'\n______________AGAGGUUAUU__GUGGU\n______________\|\|\|:\|:\|\|\|\|__:\|\|\|:\n______________UCUUCGAUAA__UACCG\n3'-UUU...CUCAG__________GG_____CAAUC...GAA-5'\n_____________\|_________________\|\n_____________34________________16\n	191 -- 197	27 -- 33	-15.0477 kcal/mol	3.57571 kcal/mol	4.97804 kcal/mol	190 206@LB@ \| \|@LB@5'-UUU...AACAA AUUAC...CUG-3'@LB@ AGAGGUUAUU GUGGU@LB@ \|\|\|:\|:\|\|\|\| :\|\|\|:@LB@ UCUUCGAUAA UACCG@LB@3'-UUU...CUCAG GG CAAUC...GAA-5'@LB@ \| \|@LB@ 34 16@LB@@LB@@LB@Energy -6.49 kcal/mol@LB@Hybridization Energy -15.0477 kcal/mol@LB@Unfolding Energy - mRNA 3.57571 kcal/mol@LB@Unfolding Energy - sRNA 4.97804 kcal/mol@LB@@LB@Position - mRNA 191 -- 205@LB@Position - sRNA 17 -- 33@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 27 -- 33@LB@
191	0.08461	0.363	ct_112	pepF	-2.97	0.715117	121 -- 127	54 -- 60	oligoendopeptidase F	_____________120_____128\n_____________\|_______\|\n5'-UCU...UCUCU_______ACUGG...AAG-3'\n______________UCCCCUU\n______________\|\|\|\|\|::\n______________AGGGGGG\n3'-UUU...ACUGA_______ACACA...GAA-5'\n_____________\|_______\|\n_____________61______53\n	121 -- 127	54 -- 60	-10.8708 kcal/mol	1.46061 kcal/mol	6.44182 kcal/mol	120 128@LB@ \| \|@LB@5'-UCU...UCUCU ACUGG...AAG-3'@LB@ UCCCCUU@LB@ \|\|\|\|\|::@LB@ AGGGGGG@LB@3'-UUU...ACUGA ACACA...GAA-5'@LB@ \| \|@LB@ 61 53@LB@@LB@@LB@Energy -2.97 kcal/mol@LB@Hybridization Energy -10.8708 kcal/mol@LB@Unfolding Energy - mRNA 1.46061 kcal/mol@LB@Unfolding Energy - sRNA 6.44182 kcal/mol@LB@@LB@Position - mRNA 121 -- 127@LB@Position - sRNA 54 -- 60@LB@Position Seed - mRNA 121 -- 127@LB@Position Seed - sRNA 54 -- 60@LB@
29	0.008327	0.236	ct_722	pgm	-9.49	0.037543	218 -- 230	17 -- 29	2 3-bisphosphoglycerate-dependent phosphoglycerate mutase	_____________217___________231\n_____________\|_____________\|\n5'-CUU...AUCUU____CG_______CAAUC...UUC-3'\n______________GCUA__CCAUGGC\n______________\|\|\|\|__\|\|\|\|\|\|\|\n______________CGAU__GGUACCG\n3'-UUU...GUCUU____AA_______CAAUC...GAA-5'\n_____________\|_____________\|\n_____________30____________16\n	224 -- 230	17 -- 23	-17.8075 kcal/mol	3.64492 kcal/mol	4.66832 kcal/mol	217 231@LB@ \| \|@LB@5'-CUU...AUCUU CG CAAUC...UUC-3'@LB@ GCUA CCAUGGC@LB@ \|\|\|\| \|\|\|\|\|\|\|@LB@ CGAU GGUACCG@LB@3'-UUU...GUCUU AA CAAUC...GAA-5'@LB@ \| \|@LB@ 30 16@LB@@LB@@LB@Energy -9.49 kcal/mol@LB@Hybridization Energy -17.8075 kcal/mol@LB@Unfolding Energy - mRNA 3.64492 kcal/mol@LB@Unfolding Energy - sRNA 4.66832 kcal/mol@LB@@LB@Position - mRNA 218 -- 230@LB@Position - sRNA 17 -- 29@LB@Position Seed - mRNA 224 -- 230@LB@Position Seed - sRNA 17 -- 23@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@
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@
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@

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

Use the following button if you want to resubmit the job with altered input or parameterization:

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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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