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
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@
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@
67	0.02533	0.29	ct_395	grpE	-6.02	0.231793	191 -- 203	19 -- 33	stress response protein GrpE	_____________190_____________204\n_____________\|_______________\|\n5'-CCU...CGCUA_______________ACAGA...UAA-3'\n______________AGGAGCUAU__CAUG\n______________\|\|:\|\|\|\|\|\|__\|\|\|\|\n______________UCUUCGAUA__GUAC\n3'-UUU...CUCAG_________AG____CGCAA...GAA-5'\n_____________\|_______________\|\n_____________34______________18\n	192 -- 198	26 -- 32	-14.6636 kcal/mol	3.66894 kcal/mol	4.97702 kcal/mol	190 204@LB@ \| \|@LB@5'-CCU...CGCUA ACAGA...UAA-3'@LB@ AGGAGCUAU CAUG@LB@ \|\|:\|\|\|\|\|\| \|\|\|\|@LB@ UCUUCGAUA GUAC@LB@3'-UUU...CUCAG AG CGCAA...GAA-5'@LB@ \| \|@LB@ 34 18@LB@@LB@@LB@Energy -6.02 kcal/mol@LB@Hybridization Energy -14.6636 kcal/mol@LB@Unfolding Energy - mRNA 3.66894 kcal/mol@LB@Unfolding Energy - sRNA 4.97702 kcal/mol@LB@@LB@Position - mRNA 191 -- 203@LB@Position - sRNA 19 -- 33@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 26 -- 32@LB@
26	0.006621	0.2093	ct_267	ihfA	-8.59	0.062448	193 -- 205	17 -- 31	DNA-binding protein HU	_____________192_____________206\n_____________\|_______________\|\n5'-UAA...GCAAC_______________AACGA...AUA-3'\n______________AAGCUA__CCAUGGC\n______________\|\|\|\|\|\|__\|\|\|\|\|\|\|\n______________UUCGAU__GGUACCG\n3'-UUU...CAGUC______AA_______CAAUC...GAA-5'\n_____________\|_______________\|\n_____________32______________16\n	199 -- 205	17 -- 23	-17.4173 kcal/mol	3.97125 kcal/mol	4.86101 kcal/mol	192 206@LB@ \| \|@LB@5'-UAA...GCAAC AACGA...AUA-3'@LB@ AAGCUA CCAUGGC@LB@ \|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ UUCGAU GGUACCG@LB@3'-UUU...CAGUC AA CAAUC...GAA-5'@LB@ \| \|@LB@ 32 16@LB@@LB@@LB@Energy -8.59 kcal/mol@LB@Hybridization Energy -17.4173 kcal/mol@LB@Unfolding Energy - mRNA 3.97125 kcal/mol@LB@Unfolding Energy - sRNA 4.86101 kcal/mol@LB@@LB@Position - mRNA 193 -- 205@LB@Position - sRNA 17 -- 31@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 17 -- 23@LB@
161	0.06753	0.3424	ct_656	N/A	-5.22	0.330968	193 -- 236	21 -- 57		_____________192_____________________________________________237\n_____________\|_______________________________________________\|\n5'-AUG...GGGAG_________________GCAAUUCAUAGC_______U________G_AACCA...UGA-3'\n______________UCUCU_UGUAUGGACAC____________GAGUCAG___CUGUUC_A\n______________:\|:\|\|_\|\|\|\|:::\|\|\|\|____________\|\|\|\|\|\|\|___\|\|:\|\|\|_\|\n______________GGGGA_ACAUGUUUGUG____________CUCAGUC___GAUAAG_U\n3'-UUU...GAAGG_____C___________AU_________________UUC______G_ACCGC...GAA-5'\n_____________\|_______________________________________________\|\n_____________58______________________________________________20\n	221 -- 227	32 -- 38	-30.4155 kcal/mol	12.5085 kcal/mol	12.6912 kcal/mol	192 237@LB@ \| \|@LB@5'-AUG...GGGAG GCAAUUCAUAGC U G AACCA...UGA-3'@LB@ UCUCU UGUAUGGACAC GAGUCAG CUGUUC A@LB@ :\|:\|\| \|\|\|\|:::\|\|\|\| \|\|\|\|\|\|\| \|\|:\|\|\| \|@LB@ GGGGA ACAUGUUUGUG CUCAGUC GAUAAG U@LB@3'-UUU...GAAGG C AU UUC G ACCGC...GAA-5'@LB@ \| \|@LB@ 58 20@LB@@LB@@LB@Energy -5.22 kcal/mol@LB@Hybridization Energy -30.4155 kcal/mol@LB@Unfolding Energy - mRNA 12.5085 kcal/mol@LB@Unfolding Energy - sRNA 12.6912 kcal/mol@LB@@LB@Position - mRNA 193 -- 236@LB@Position - sRNA 21 -- 57@LB@Position Seed - mRNA 221 -- 227@LB@Position Seed - sRNA 32 -- 38@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@
160	0.06752	0.3424	ct_324	N/A	-4.86	0.383763	195 -- 205	17 -- 27		_____________194_________206\n_____________\|___________\|\n5'-ACA...GUAGA__GG_______CAAAG...UGC-3'\n______________UA__CCAUGGU\n______________\|\|__\|\|\|\|\|\|:\n______________AU__GGUACCG\n3'-UUU...CUUCG__AA_______CAAUC...GAA-5'\n_____________\|___________\|\n_____________28__________16\n	199 -- 205	17 -- 23	-11.7516 kcal/mol	2.4023 kcal/mol	4.49196 kcal/mol	194 206@LB@ \| \|@LB@5'-ACA...GUAGA GG CAAAG...UGC-3'@LB@ UA CCAUGGU@LB@ \|\| \|\|\|\|\|\|:@LB@ AU GGUACCG@LB@3'-UUU...CUUCG AA CAAUC...GAA-5'@LB@ \| \|@LB@ 28 16@LB@@LB@@LB@Energy -4.86 kcal/mol@LB@Hybridization Energy -11.7516 kcal/mol@LB@Unfolding Energy - mRNA 2.4023 kcal/mol@LB@Unfolding Energy - sRNA 4.49196 kcal/mol@LB@@LB@Position - mRNA 195 -- 205@LB@Position - sRNA 17 -- 27@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 17 -- 23@LB@
5	0.0004969	0.07439	ct_056	N/A	-17.69	0.000175	196 -- 255	6 -- 56		_____________195________________________________________________________________256\n_____________\|__________________________________________________________________\|\n5'-GUG...AGGAU_____AU__________CCCU__C______UUACGUAAACAGACAU_______A____________UUCCU...AAG-3'\n______________CCCUG______GACACU____UC_GAAGCU________________UUCC_UG__GUUAGAAUACC\n______________\|\|\|\|\|______:\|\|\|\|\|____\|\|_\|\|\|\|\|\|________________\|\|\|\|_\|\|__\|\|\|\|\|\|\|\|\|\|\|\n______________GGGAC______UUGUGA____AG_CUUCGA________________AAGG_AC__CAAUCUUAUGG\n3'-UUU...AAGGG_____ACAUGU______UCUC__U______U___________________U__CG___________UUGAA-5'\n_____________\|__________________________________________________________________\|\n_____________57_________________________________________________________________5\n	249 -- 255	6 -- 12	-39.697 kcal/mol	5.45688 kcal/mol	16.5497 kcal/mol	195 256@LB@ \| \|@LB@5'-GUG...AGGAU AU CCCU C UUACGUAAACAGACAU A UUCCU...AAG-3'@LB@ CCCUG GACACU UC GAAGCU UUCC UG GUUAGAAUACC@LB@ \|\|\|\|\| :\|\|\|\|\| \|\| \|\|\|\|\|\| \|\|\|\| \|\| \|\|\|\|\|\|\|\|\|\|\|@LB@ GGGAC UUGUGA AG CUUCGA AAGG AC CAAUCUUAUGG@LB@3'-UUU...AAGGG ACAUGU UCUC U U U CG UUGAA-5'@LB@ \| \|@LB@ 57 5@LB@@LB@@LB@Energy -17.69 kcal/mol@LB@Hybridization Energy -39.697 kcal/mol@LB@Unfolding Energy - mRNA 5.45688 kcal/mol@LB@Unfolding Energy - sRNA 16.5497 kcal/mol@LB@@LB@Position - mRNA 196 -- 255@LB@Position - sRNA 6 -- 56@LB@Position Seed - mRNA 249 -- 255@LB@Position Seed - sRNA 6 -- 12@LB@
131	0.05291	0.3262	ct_842	pnp	-7.97	0.086989	198 -- 205	17 -- 24	polyribonucleotide nucleotidyltransferase	_____________197______206\n_____________\|________\|\n5'-UGA...ACAAC________UUUUG...UCA-3'\n______________UCCAUGGC\n______________\|\|\|\|\|\|\|\|\n______________AGGUACCG\n3'-UUU...CGAUA________CAAUC...GAA-5'\n_____________\|________\|\n_____________25_______16\n	199 -- 205	17 -- 23	-14.0999 kcal/mol	1.64992 kcal/mol	4.47615 kcal/mol	197 206@LB@ \| \|@LB@5'-UGA...ACAAC UUUUG...UCA-3'@LB@ UCCAUGGC@LB@ \|\|\|\|\|\|\|\|@LB@ AGGUACCG@LB@3'-UUU...CGAUA CAAUC...GAA-5'@LB@ \| \|@LB@ 25 16@LB@@LB@@LB@Energy -7.97 kcal/mol@LB@Hybridization Energy -14.0999 kcal/mol@LB@Unfolding Energy - mRNA 1.64992 kcal/mol@LB@Unfolding Energy - sRNA 4.47615 kcal/mol@LB@@LB@Position - mRNA 198 -- 205@LB@Position - sRNA 17 -- 24@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 17 -- 23@LB@
78	0.0282	0.29	ct_131	N/A	-9.30	0.042003	199 -- 219	17 -- 35		_____________198___________________220\n_____________\|_____________________\|\n5'-GAG...UGAAU___U_____GUUC________AUAAA...AAU-3'\n______________UCA_GAAGC____UCCAUGGU\n______________\|\|\|_\|\|\|\|\|____\|\|\|\|\|\|\|:\n______________AGU_CUUCG____AGGUACCG\n3'-UUU...AUCUC_________AUA_________CAAUC...GAA-5'\n_____________\|_____________________\|\n_____________36____________________16\n	213 -- 219	17 -- 23	-20.9121 kcal/mol	6.63751 kcal/mol	4.9781 kcal/mol	198 220@LB@ \| \|@LB@5'-GAG...UGAAU U GUUC AUAAA...AAU-3'@LB@ UCA GAAGC UCCAUGGU@LB@ \|\|\| \|\|\|\|\| \|\|\|\|\|\|\|:@LB@ AGU CUUCG AGGUACCG@LB@3'-UUU...AUCUC AUA CAAUC...GAA-5'@LB@ \| \|@LB@ 36 16@LB@@LB@@LB@Energy -9.30 kcal/mol@LB@Hybridization Energy -20.9121 kcal/mol@LB@Unfolding Energy - mRNA 6.63751 kcal/mol@LB@Unfolding Energy - sRNA 4.9781 kcal/mol@LB@@LB@Position - mRNA 199 -- 219@LB@Position - sRNA 17 -- 35@LB@Position Seed - mRNA 213 -- 219@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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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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