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
82	0.02927	0.29	ct_342	rs21	-5.39	0.307662	118 -- 125	14 -- 21	30S ribosomal protein S21	_____________117______126\n_____________\|________\|\n5'-UUA...UAAAA________ACAAU...AGU-3'\n______________GUGGUGUU\n______________:\|\|\|:\|\|\|\n______________UACCGCAA\n3'-UUU...UAAGG________UCUUA...GAA-5'\n_____________\|________\|\n_____________22_______13\n	119 -- 125	14 -- 20	-8.72589 kcal/mol	2.15057 kcal/mol	1.18847 kcal/mol	117 126@LB@ \| \|@LB@5'-UUA...UAAAA ACAAU...AGU-3'@LB@ GUGGUGUU@LB@ :\|\|\|:\|\|\|@LB@ UACCGCAA@LB@3'-UUU...UAAGG UCUUA...GAA-5'@LB@ \| \|@LB@ 22 13@LB@@LB@@LB@Energy -5.39 kcal/mol@LB@Hybridization Energy -8.72589 kcal/mol@LB@Unfolding Energy - mRNA 2.15057 kcal/mol@LB@Unfolding Energy - sRNA 1.18847 kcal/mol@LB@@LB@Position - mRNA 118 -- 125@LB@Position - sRNA 14 -- 21@LB@Position Seed - mRNA 119 -- 125@LB@Position Seed - sRNA 14 -- 20@LB@
135	0.05472	0.3262	ct_283	N/A	-6.89	0.152000	262 -- 284	14 -- 35		_____________261______________________285\n_____________\|________________________\|\n5'-UAC...GUUUA_____CU________GC_______UGUUU...UUG-3'\n______________UCGGA__AGUUA_UC__UGGCGUU\n______________\|\|:\|\|__\|\|:\|\|_\|\|__\|\|\|\|\|\|\|\n______________AGUCU__UCGAU_AG__ACCGCAA\n3'-UUU...AUCUC____________A__GU_______UCUUA...GAA-5'\n_____________\|________________________\|\n_____________36_______________________13\n	278 -- 284	14 -- 20	-19.9844 kcal/mol	4.64246 kcal/mol	8.44936 kcal/mol	261 285@LB@ \| \|@LB@5'-UAC...GUUUA CU GC UGUUU...UUG-3'@LB@ UCGGA AGUUA UC UGGCGUU@LB@ \|\|:\|\| \|\|:\|\| \|\| \|\|\|\|\|\|\|@LB@ AGUCU UCGAU AG ACCGCAA@LB@3'-UUU...AUCUC A GU UCUUA...GAA-5'@LB@ \| \|@LB@ 36 13@LB@@LB@@LB@Energy -6.89 kcal/mol@LB@Hybridization Energy -19.9844 kcal/mol@LB@Unfolding Energy - mRNA 4.64246 kcal/mol@LB@Unfolding Energy - sRNA 8.44936 kcal/mol@LB@@LB@Position - mRNA 262 -- 284@LB@Position - sRNA 14 -- 35@LB@Position Seed - mRNA 278 -- 284@LB@Position Seed - sRNA 14 -- 20@LB@
183	0.08019	0.3602	ct_648	N/A	-7.31	0.122948	212 -- 231	14 -- 34		_____________211___________________232\n_____________\|_____________________\|\n5'-ACU...GUAAG________UAAG_________UAUGU...UUA-3'\n______________UAGAAGCU_____AUGGUGUU\n______________:\|\|\|\|\|\|\|_____\|\|\|\|:\|\|\|\n______________GUCUUCGA_____UACCGCAA\n3'-UUU...UCUCA________UAAGG________UCUUA...GAA-5'\n_____________\|_____________________\|\n_____________35____________________13\n	225 -- 231	14 -- 20	-20.6397 kcal/mol	4.879 kcal/mol	8.44924 kcal/mol	211 232@LB@ \| \|@LB@5'-ACU...GUAAG UAAG UAUGU...UUA-3'@LB@ UAGAAGCU AUGGUGUU@LB@ :\|\|\|\|\|\|\| \|\|\|\|:\|\|\|@LB@ GUCUUCGA UACCGCAA@LB@3'-UUU...UCUCA UAAGG UCUUA...GAA-5'@LB@ \| \|@LB@ 35 13@LB@@LB@@LB@Energy -7.31 kcal/mol@LB@Hybridization Energy -20.6397 kcal/mol@LB@Unfolding Energy - mRNA 4.879 kcal/mol@LB@Unfolding Energy - sRNA 8.44924 kcal/mol@LB@@LB@Position - mRNA 212 -- 231@LB@Position - sRNA 14 -- 34@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 14 -- 20@LB@
33	0.01042	0.2518	ct_780	N/A	-7.85	0.092931	30 -- 50	15 -- 34		_____________29____________________51\n_____________\|_____________________\|\n5'-UGU...AAAAA___C____GAA_G________GUCAA...UCA-3'\n______________CAG_AAGU___U_CAUGGCGU\n______________\|\|\|_\|\|\|:___\|_\|\|\|\|\|\|\|\|\n______________GUC_UUCG___A_GUACCGCA\n3'-UUU...UCUCA________AUA_G________AUCUU...GAA-5'\n_____________\|_____________________\|\n_____________35____________________14\n	44 -- 50	15 -- 21	-20.7959 kcal/mol	4.71518 kcal/mol	8.23265 kcal/mol	29 51@LB@ \| \|@LB@5'-UGU...AAAAA C GAA G GUCAA...UCA-3'@LB@ CAG AAGU U CAUGGCGU@LB@ \|\|\| \|\|\|: \| \|\|\|\|\|\|\|\|@LB@ GUC UUCG A GUACCGCA@LB@3'-UUU...UCUCA AUA G AUCUU...GAA-5'@LB@ \| \|@LB@ 35 14@LB@@LB@@LB@Energy -7.85 kcal/mol@LB@Hybridization Energy -20.7959 kcal/mol@LB@Unfolding Energy - mRNA 4.71518 kcal/mol@LB@Unfolding Energy - sRNA 8.23265 kcal/mol@LB@@LB@Position - mRNA 30 -- 50@LB@Position - sRNA 15 -- 34@LB@Position Seed - mRNA 44 -- 50@LB@Position Seed - sRNA 15 -- 21@LB@
126	0.05087	0.3262	ct_474	N/A	-6.92	0.149609	150 -- 156	15 -- 21		_____________149_____157\n_____________\|_______\|\n5'-AAA...ACGAA_______GUAUA...UAU-3'\n______________GUGGCGU\n______________:\|\|\|\|\|\|\n______________UACCGCA\n3'-UUU...UAAGG_______AUCUU...GAA-5'\n_____________\|_______\|\n_____________22______14\n	150 -- 156	15 -- 21	-10.3963 kcal/mol	2.28336 kcal/mol	1.18845 kcal/mol	149 157@LB@ \| \|@LB@5'-AAA...ACGAA GUAUA...UAU-3'@LB@ GUGGCGU@LB@ :\|\|\|\|\|\|@LB@ UACCGCA@LB@3'-UUU...UAAGG AUCUU...GAA-5'@LB@ \| \|@LB@ 22 14@LB@@LB@@LB@Energy -6.92 kcal/mol@LB@Hybridization Energy -10.3963 kcal/mol@LB@Unfolding Energy - mRNA 2.28336 kcal/mol@LB@Unfolding Energy - sRNA 1.18845 kcal/mol@LB@@LB@Position - mRNA 150 -- 156@LB@Position - sRNA 15 -- 21@LB@Position Seed - mRNA 150 -- 156@LB@Position Seed - sRNA 15 -- 21@LB@
159	0.06732	0.3424	ct_663	N/A	-7.57	0.107718	228 -- 234	15 -- 21	type III secretion system chaperone	_____________227_____235\n_____________\|_______\|\n5'-UCU...AUUUU_______AUAUG...GCC-3'\n______________GUGGCGU\n______________:\|\|\|\|\|\|\n______________UACCGCA\n3'-UUU...UAAGG_______AUCUU...GAA-5'\n_____________\|_______\|\n_____________22______14\n	228 -- 234	15 -- 21	-10.4333 kcal/mol	1.67755 kcal/mol	1.18845 kcal/mol	227 235@LB@ \| \|@LB@5'-UCU...AUUUU AUAUG...GCC-3'@LB@ GUGGCGU@LB@ :\|\|\|\|\|\|@LB@ UACCGCA@LB@3'-UUU...UAAGG AUCUU...GAA-5'@LB@ \| \|@LB@ 22 14@LB@@LB@@LB@Energy -7.57 kcal/mol@LB@Hybridization Energy -10.4333 kcal/mol@LB@Unfolding Energy - mRNA 1.67755 kcal/mol@LB@Unfolding Energy - sRNA 1.18845 kcal/mol@LB@@LB@Position - mRNA 228 -- 234@LB@Position - sRNA 15 -- 21@LB@Position Seed - mRNA 228 -- 234@LB@Position Seed - sRNA 15 -- 21@LB@
16	0.003859	0.1836	ct_666	N/A	-9.59	0.035525	190 -- 206	16 -- 33		_____________189________________207\n_____________\|__________________\|\n5'-GAU...AAAAG_____G____________AGCGG...AAA-3'\n______________AGAGG_UA_UCUAUGGCG\n______________\|\|\|:\|_\|\|_\|\|:\|\|\|\|\|\|\n______________UCUUC_AU_AGGUACCGC\n3'-UUU...CUCAG_____G__A_________AAUCU...GAA-5'\n_____________\|__________________\|\n_____________34_________________15\n	200 -- 206	16 -- 22	-21.7302 kcal/mol	4.22495 kcal/mol	7.91433 kcal/mol	189 207@LB@ \| \|@LB@5'-GAU...AAAAG G AGCGG...AAA-3'@LB@ AGAGG UA UCUAUGGCG@LB@ \|\|\|:\| \|\| \|\|:\|\|\|\|\|\|@LB@ UCUUC AU AGGUACCGC@LB@3'-UUU...CUCAG G A AAUCU...GAA-5'@LB@ \| \|@LB@ 34 15@LB@@LB@@LB@Energy -9.59 kcal/mol@LB@Hybridization Energy -21.7302 kcal/mol@LB@Unfolding Energy - mRNA 4.22495 kcal/mol@LB@Unfolding Energy - sRNA 7.91433 kcal/mol@LB@@LB@Position - mRNA 190 -- 206@LB@Position - sRNA 16 -- 33@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 16 -- 22@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@
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@
8	0.0008373	0.07962	ct_066	N/A	-11.14	0.014316	190 -- 205	17 -- 33		_____________189_______________206\n_____________\|_________________\|\n5'-UUU...CACUA_________________UACGG...GUU-3'\n______________AGGAGCUAUUC_AUGGC\n______________\|\|:\|\|\|\|\|\|\|\|_\|\|\|\|\|\n______________UCUUCGAUAAG_UACCG\n3'-UUU...CUCAG___________G_____CAAUC...GAA-5'\n_____________\|_________________\|\n_____________34________________16\n	194 -- 200	23 -- 29	-22.6652 kcal/mol	6.55112 kcal/mol	4.97804 kcal/mol	189 206@LB@ \| \|@LB@5'-UUU...CACUA UACGG...GUU-3'@LB@ AGGAGCUAUUC AUGGC@LB@ \|\|:\|\|\|\|\|\|\|\| \|\|\|\|\|@LB@ UCUUCGAUAAG UACCG@LB@3'-UUU...CUCAG G CAAUC...GAA-5'@LB@ \| \|@LB@ 34 16@LB@@LB@@LB@Energy -11.14 kcal/mol@LB@Hybridization Energy -22.6652 kcal/mol@LB@Unfolding Energy - mRNA 6.55112 kcal/mol@LB@Unfolding Energy - sRNA 4.97804 kcal/mol@LB@@LB@Position - mRNA 190 -- 205@LB@Position - sRNA 17 -- 33@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 23 -- 29@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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