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
92	0.03292	0.2942	ct_558	lipA	-15.60	0.000793	187 -- 244	3 -- 58	lipoyl synthase	_____________186_________________________________________________________245\n_____________\|___________________________________________________________\|\n5'-ACU...AUAUG_______CUAAA_____ACC__U______UCUC_______UAAAAAAUCU______C__CAGAU...AAA-3'\n______________CCCCCUG_____AAAUG___GA_UCAGAA____CUAUUCC___________AUACC_GC\n______________\|\|\|\|\|\|\|_____\|\|\|::___\|\|_\|\|\|\|\|\|____\|\|\|\|\|\|\|___________\|\|\|\|\|_:\|\n______________GGGGGAC_____UUUGU___CU_AGUCUU____GAUAAGG___________UAUGG_UG\n3'-UUU...UGAAG_______ACAUG_____GAU__C______C__________UACCGCAAUCU_____U__AA-5'\n_____________\|___________________________________________________________\|\n_____________59__________________________________________________________2\n	220 -- 226	22 -- 28	-35.9268 kcal/mol	3.77883 kcal/mol	16.5523 kcal/mol	186 245@LB@ \| \|@LB@5'-ACU...AUAUG CUAAA ACC U UCUC UAAAAAAUCU C CAGAU...AAA-3'@LB@ CCCCCUG AAAUG GA UCAGAA CUAUUCC AUACC GC@LB@ \|\|\|\|\|\|\| \|\|\|:: \|\| \|\|\|\|\|\| \|\|\|\|\|\|\| \|\|\|\|\| :\|@LB@ GGGGGAC UUUGU CU AGUCUU GAUAAGG UAUGG UG@LB@3'-UUU...UGAAG ACAUG GAU C C UACCGCAAUCU U AA-5'@LB@ \| \|@LB@ 59 2@LB@@LB@@LB@Energy -15.60 kcal/mol@LB@Hybridization Energy -35.9268 kcal/mol@LB@Unfolding Energy - mRNA 3.77883 kcal/mol@LB@Unfolding Energy - sRNA 16.5523 kcal/mol@LB@@LB@Position - mRNA 187 -- 244@LB@Position - sRNA 3 -- 58@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 22 -- 28@LB@
194	0.08693	0.3657	ct_285	lplA_1	-4.48	0.444512	66 -- 74	27 -- 35	lipoate protein ligase	_____________65________75\n_____________\|_________\|\n5'-CUU...AAUUU_________UUUUU...UUC-3'\n______________UUAGAAGCU\n______________\|:\|\|\|\|\|\|\|\n______________AGUCUUCGA\n3'-UUU...AUCUC_________UAAGG...GAA-5'\n_____________\|_________\|\n_____________36________26\n	68 -- 74	27 -- 33	-10.5389 kcal/mol	1.46011 kcal/mol	4.60001 kcal/mol	65 75@LB@ \| \|@LB@5'-CUU...AAUUU UUUUU...UUC-3'@LB@ UUAGAAGCU@LB@ \|:\|\|\|\|\|\|\|@LB@ AGUCUUCGA@LB@3'-UUU...AUCUC UAAGG...GAA-5'@LB@ \| \|@LB@ 36 26@LB@@LB@@LB@Energy -4.48 kcal/mol@LB@Hybridization Energy -10.5389 kcal/mol@LB@Unfolding Energy - mRNA 1.46011 kcal/mol@LB@Unfolding Energy - sRNA 4.60001 kcal/mol@LB@@LB@Position - mRNA 66 -- 74@LB@Position - sRNA 27 -- 35@LB@Position Seed - mRNA 68 -- 74@LB@Position Seed - sRNA 27 -- 33@LB@
21	0.0049	0.1918	ct_531	lpxA	-7.30	0.123824	16 -- 37	17 -- 34	acyl-[acyl-carrier-protein]--UDP-N- acetylglucosamine O-acyltransferase	_____________15_____________________38\n_____________\|______________________\|\n5'-UUG...GUAUC___A____AAA_______CA__CUGUU...CGC-3'\n______________CAG_AAGC___AUUCCGU__GC\n______________\|\|\|_\|\|\|\|___\|\|\|\|\|:\|__\|\|\n______________GUC_UUCG___UAAGGUA__CG\n3'-UUU...UCUCA________A_________C___CAAUC...GAA-5'\n_____________\|______________________\|\n_____________35_____________________16\n	27 -- 33	20 -- 26	-14.3796 kcal/mol	2.10386 kcal/mol	4.97809 kcal/mol	15 38@LB@ \| \|@LB@5'-UUG...GUAUC A AAA CA CUGUU...CGC-3'@LB@ CAG AAGC AUUCCGU GC@LB@ \|\|\| \|\|\|\| \|\|\|\|\|:\| \|\|@LB@ GUC UUCG UAAGGUA CG@LB@3'-UUU...UCUCA A C CAAUC...GAA-5'@LB@ \| \|@LB@ 35 16@LB@@LB@@LB@Energy -7.30 kcal/mol@LB@Hybridization Energy -14.3796 kcal/mol@LB@Unfolding Energy - mRNA 2.10386 kcal/mol@LB@Unfolding Energy - sRNA 4.97809 kcal/mol@LB@@LB@Position - mRNA 16 -- 37@LB@Position - sRNA 17 -- 34@LB@Position Seed - mRNA 27 -- 33@LB@Position Seed - sRNA 20 -- 26@LB@
147	0.05913	0.3307	ct_243	lpxD	-5.18	0.335797	179 -- 192	18 -- 32	UDP-3-O-acylglucosamine N-acyltransferase	_____________178_____________193\n_____________\|_______________\|\n5'-UCA...CAUGC_______G____A__AGUGC...UCG-3'\n______________GAAGCUA__CCG_GG\n______________\|\|\|\|\|\|\|__\|\|:_\|\|\n______________CUUCGAU__GGU_CC\n3'-UUU...UCAGU_______AA___A__GCAAU...GAA-5'\n_____________\|_______________\|\n_____________33______________17\n	179 -- 185	26 -- 32	-15.005 kcal/mol	4.85774 kcal/mol	4.96566 kcal/mol	178 193@LB@ \| \|@LB@5'-UCA...CAUGC G A AGUGC...UCG-3'@LB@ GAAGCUA CCG GG@LB@ \|\|\|\|\|\|\| \|\|: \|\|@LB@ CUUCGAU GGU CC@LB@3'-UUU...UCAGU AA A GCAAU...GAA-5'@LB@ \| \|@LB@ 33 17@LB@@LB@@LB@Energy -5.18 kcal/mol@LB@Hybridization Energy -15.005 kcal/mol@LB@Unfolding Energy - mRNA 4.85774 kcal/mol@LB@Unfolding Energy - sRNA 4.96566 kcal/mol@LB@@LB@Position - mRNA 179 -- 192@LB@Position - sRNA 18 -- 32@LB@Position Seed - mRNA 179 -- 185@LB@Position Seed - sRNA 26 -- 32@LB@
179	0.07718	0.3544	ct_781	lysS	-5.99	0.234962	194 -- 201	79 -- 86	lysine--tRNA ligase	_____________193______202\n_____________\|________\|\n5'-AAA...AAAGG________UGUCU...AUC-3'\n______________ACGGUUGA\n______________\|\|\|\|:\|:\|\n______________UGCCGAUU\n3'-UUU...CUCUA________GAGGU...GAA-5'\n_____________\|________\|\n_____________87_______78\n	195 -- 201	79 -- 85	-9.06205 kcal/mol	1.97593 kcal/mol	1.09752 kcal/mol	193 202@LB@ \| \|@LB@5'-AAA...AAAGG UGUCU...AUC-3'@LB@ ACGGUUGA@LB@ \|\|\|\|:\|:\|@LB@ UGCCGAUU@LB@3'-UUU...CUCUA GAGGU...GAA-5'@LB@ \| \|@LB@ 87 78@LB@@LB@@LB@Energy -5.99 kcal/mol@LB@Hybridization Energy -9.06205 kcal/mol@LB@Unfolding Energy - mRNA 1.97593 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 194 -- 201@LB@Position - sRNA 79 -- 86@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 79 -- 85@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@
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@
88	0.03104	0.29	ct_766	miaA	-2.38	0.813549	82 -- 88	27 -- 33	tRNA dimethylallyltransferase	_____________81______89\n_____________\|_______\|\n5'-AUA...UAAUG_______UUGUA...UGU-3'\n______________GGAAGCU\n______________:\|\|\|\|\|\|\n______________UCUUCGA\n3'-UUU...CUCAG_______UAAGG...GAA-5'\n_____________\|_______\|\n_____________34______26\n	82 -- 88	27 -- 33	-8.83329 kcal/mol	1.86027 kcal/mol	4.59825 kcal/mol	81 89@LB@ \| \|@LB@5'-AUA...UAAUG UUGUA...UGU-3'@LB@ GGAAGCU@LB@ :\|\|\|\|\|\|@LB@ UCUUCGA@LB@3'-UUU...CUCAG UAAGG...GAA-5'@LB@ \| \|@LB@ 34 26@LB@@LB@@LB@Energy -2.38 kcal/mol@LB@Hybridization Energy -8.83329 kcal/mol@LB@Unfolding Energy - mRNA 1.86027 kcal/mol@LB@Unfolding Energy - sRNA 4.59825 kcal/mol@LB@@LB@Position - mRNA 82 -- 88@LB@Position - sRNA 27 -- 33@LB@Position Seed - mRNA 82 -- 88@LB@Position Seed - sRNA 27 -- 33@LB@
93	0.03342	0.2954	ct_815	mrsA_2	-4.95	0.370159	203 -- 227	23 -- 45	phosphoglucosamine mutase	_____________202_______________________228\n_____________\|_________________________\|\n5'-UAC...GCAAU_____GU__U__G___C________GGAAC...AGG-3'\n______________GACAC__GA_GU_AGA_AGCUAUUC\n______________:\|\|\|\|__\|\|_\|\|_\|\|\|_\|\|\|\|\|\|\|\|\n______________UUGUG__CU_CA_UCU_UCGAUAAG\n3'-UUU...CAUGU_____AU_____G____________GUACC...GAA-5'\n_____________\|_________________________\|\n_____________46________________________22\n	221 -- 227	23 -- 29	-22.8159 kcal/mol	6.25755 kcal/mol	11.6121 kcal/mol	202 228@LB@ \| \|@LB@5'-UAC...GCAAU GU U G C GGAAC...AGG-3'@LB@ GACAC GA GU AGA AGCUAUUC@LB@ :\|\|\|\| \|\| \|\| \|\|\| \|\|\|\|\|\|\|\|@LB@ UUGUG CU CA UCU UCGAUAAG@LB@3'-UUU...CAUGU AU G GUACC...GAA-5'@LB@ \| \|@LB@ 46 22@LB@@LB@@LB@Energy -4.95 kcal/mol@LB@Hybridization Energy -22.8159 kcal/mol@LB@Unfolding Energy - mRNA 6.25755 kcal/mol@LB@Unfolding Energy - sRNA 11.6121 kcal/mol@LB@@LB@Position - mRNA 203 -- 227@LB@Position - sRNA 23 -- 45@LB@Position Seed - mRNA 221 -- 227@LB@Position Seed - sRNA 23 -- 29@LB@
30	0.009028	0.2474	ct_455	murA	-8.03	0.084305	255 -- 264	26 -- 35	UDP-N-acetylglucosamine 1-carboxyvinyltransferase	_____________254________265\n_____________\|__________\|\n5'-AAA...GCGUG__________AAAAU...UAC-3'\n______________UCAGGAGCUA\n______________\|\|\|\|:\|\|\|\|\|\n______________AGUCUUCGAU\n3'-UUU...AUCUC__________AAGGU...GAA-5'\n_____________\|__________\|\n_____________36_________25\n	258 -- 264	26 -- 32	-13.9898 kcal/mol	1.25877 kcal/mol	4.69985 kcal/mol	254 265@LB@ \| \|@LB@5'-AAA...GCGUG AAAAU...UAC-3'@LB@ UCAGGAGCUA@LB@ \|\|\|\|:\|\|\|\|\|@LB@ AGUCUUCGAU@LB@3'-UUU...AUCUC AAGGU...GAA-5'@LB@ \| \|@LB@ 36 25@LB@@LB@@LB@Energy -8.03 kcal/mol@LB@Hybridization Energy -13.9898 kcal/mol@LB@Unfolding Energy - mRNA 1.25877 kcal/mol@LB@Unfolding Energy - sRNA 4.69985 kcal/mol@LB@@LB@Position - mRNA 255 -- 264@LB@Position - sRNA 26 -- 35@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 26 -- 32@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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