Locus 5533

Sequence ID	2R_DroMel_CAF1
Location	17,668,074 – 17,668,308
Length	234
Max. P	0.552107

overview

Window 0

Location	17,668,074 – 17,668,190
Length	116
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	97.19
Mean single sequence MFE	-38.85
Consensus MFE	-34.46
Energy contribution	-34.27
Covariance contribution	-0.19
Combinations/Pair	1.03
Mean z-score	-1.73
Structure conservation index	0.89
SVM decision value	0.04
SVM RNA-class probability	0.552107
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17668074 116 - 20766785
AUGCCGUACAUAUAGAAGGCGCUCGUAUAUAUAUCUUCGAUGUGGCCUAUCUACCAUGCGCCUACAUAUCGCAGU----GUGUGUGCGAGUGAGUGUGUCUACUACUGGCAAGUCCGCAU
.(((((((....((((...((((((((((((((.((.(((((((((.(((.....))).)))...)))))).)))----)))))))))))))......)))).))).))))......... ( -37.90)
>DroSec_CAF1 21491 116 - 1
AUGCCGUACAUAUAGAAGGCGCUCGUAUAUAUAUCUUCGAUGUGGCCUAUCUACCGUGCGCCUACAUAUCGCAGU----GUGUGUGCGAGUGAGUGUGUCUACUACUGGCAAGUCCGCAU
.(((((((....((((...((((((((((((((.((.(((((((((.(((.....))).)))...)))))).)))----)))))))))))))......)))).))).))))......... ( -38.20)
>DroEre_CAF1 21904 118 - 1
AUGCCGUACAUAUAGCAGGCGCUCGUAUAUAUAUCUUCGAUGUGGCCUAUCUACCGUGCGCCUACAUAUCGCAGU--GUGUGUGUGCGAGUGAGUGUGUCUACUACUGGCAAGUCCGCAU
.(((((((......(((..(((((((((((((((((.(((((((((.(((.....))).)))...)))))).)).--)))))))))))))))..)))......))).))))......... ( -41.80)
>DroYak_CAF1 33633 120 - 1
AUGCCGUACAUAUAGAAGGCGCUCGUAUAUAUAUCUUCGAUGUGGCCUAUCUACCGUGCGCCUACAUAUCGCAGUAUGUGUGUGUGCGAGUGAGUGUGUCUACUACUGGCAAGUCCGCAU
.(((((((....((((...(((((((((((((((((.(((((((((.(((.....))).)))...)))))).))...)))))))))))))))......)))).))).))))......... ( -37.50)
>consensus
AUGCCGUACAUAUAGAAGGCGCUCGUAUAUAUAUCUUCGAUGUGGCCUAUCUACCGUGCGCCUACAUAUCGCAGU____GUGUGUGCGAGUGAGUGUGUCUACUACUGGCAAGUCCGCAU
.(((((((.(((((.....(((((((((((((..((.(((((((((.(((.....))).)))...)))))).)).....)))))))))))))..))))).)))....))))......... (-34.46 = -34.27 +  -0.19)

alignment

secondary structure

dotplot

Window 1

Location	17,668,190 – 17,668,308
Length	118
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	85.51
Mean single sequence MFE	-29.05
Consensus MFE	-27.70
Energy contribution	-27.95
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-1.14
Structure conservation index	0.95
SVM decision value	-0.03
SVM RNA-class probability	0.517058
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17668190 118 - 20766785
ACGU--GAUCCGUGUGAUUCCUGAACUUCUUGAGCACCCCACUUGGUGGCUUUAUCACGGGGCAGCUUGAGAGUUGUUACCUUUUGUUGCCACAAACUUUUUGAGUUAUUUUUCCCGUGC
..(.--.(((.....)))..)..........(((((((......))).))))...(((((((((((..(((.((....)))))..))))))...(((((...))))).......))))). ( -28.80)
>DroSec_CAF1 21607 97 - 1
-----------------------AACUUCUUGACCACCCCACUUGGUGGCUUUAUCACGGGGCAGCUUGAGAGUUGUUACCUUUUGUUGCCACAAACUUUUUGAGUUAUUUUUCCCGUGC
-----------------------..........(((((......)))))......(((((((((((..(((.((....)))))..))))))...(((((...))))).......))))). ( -29.10)
>DroEre_CAF1 22022 115 - 1
G-----AACCAAUGUGCUAUCCGAACUUCUUGACCACCCCACUUGGUGGCUUUAUCACGGGGCAGCUUGAGAGUUGUUACCUUUUGUUGCCACAAACUUUUUGAGUUAUUUUUCCCGUGC
.-----...........................(((((......)))))......(((((((((((..(((.((....)))))..))))))...(((((...))))).......))))). ( -29.10)
>DroYak_CAF1 33753 120 - 1
GUGUGUAAUCUGUGUAAUUCCUGAACUUCUUGACCACCCCACGCGGUGGCUUUAUCACGGGGCAGCUUGAGAGUUGUUACCUUUUGUUGCCACAAACUUUUUGAGUUAUUUUUCCCGUGC
.................................(((((......)))))......(((((((((((..(((.((....)))))..))))))...(((((...))))).......))))). ( -29.20)
>consensus
G_____AAUC_GUGUGAUUCCUGAACUUCUUGACCACCCCACUUGGUGGCUUUAUCACGGGGCAGCUUGAGAGUUGUUACCUUUUGUUGCCACAAACUUUUUGAGUUAUUUUUCCCGUGC
.................................(((((......)))))......(((((((((((..(((.((....)))))..))))))...(((((...))))).......))))). (-27.70 = -27.95 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:48:09 2006