Locus 9222

Sequence ID	3R_DroMel_CAF1
Location	24,575,303 – 24,575,470
Length	167
Max. P	0.912671

overview

Window 9

Location	24,575,303 – 24,575,408
Length	105
Sequences	5
Columns	105
Reading direction	forward
Mean pairwise identity	87.81
Mean single sequence MFE	-26.20
Consensus MFE	-20.67
Energy contribution	-20.51
Covariance contribution	-0.16
Combinations/Pair	1.22
Mean z-score	-1.56
Structure conservation index	0.79
SVM decision value	0.22
SVM RNA-class probability	0.637943
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24575303 105 + 27905053
GUAGCCGACAGCUCAUCGAAGUGCAUCCUGCGAAUUGAUUGAGGGCAAGUUAUUUUUCAAUGAACAAUAACUCAGAUAGCUGACCACACAGCUCAUAAAAGUAUA
...(((.....((((((((..(((.....)))..)))).))))))).(((((((.(((...))).))))))).....(((((......)))))............ ( -22.60)
>DroSec_CAF1 73794 105 + 1
GUGGCCGACAGCUCAUCGAAGUGCUUCCUGCGAAUUGAUUGAGGGUUAGUUAUUUUUCAAUGAGCAAUAACUCAGAAAGCUGACCACACAGCUCAUAAAGAUAUA
(((........((((((((..(((.....)))..)))).))))(((((((....((((..((((......))))))))))))))).)))................ ( -26.10)
>DroSim_CAF1 75354 105 + 1
GUGGCCGACAGCUCAUCGAAGUGCAUCCUGCGAAUUGAUUGAGGGUUAGUUAUUUUUCAAUGAACAAUAGCUCAAAUAGCUGACCACACAGCUCAUAAAAGCACA
(((........((((((((..(((.....)))..)))).))))(((((((((((......(((........)))))))))))))).))).(((......)))... ( -27.40)
>DroEre_CAF1 78326 105 + 1
GUGGCCGACAGCUCGUCAAAGUGCAUCCUGCGAGUUGAUUGAGUGUUAGUUAUUUUUCAAUUAACCAUAACUCAGAUAACUGGCCACACAGCUCAGAAAAUCACA
(((((((.((((((((...((......)))))))))).(((((((((((((.......)))))))....)))))).....))))))).................. ( -30.50)
>DroYak_CAF1 75120 105 + 1
GUGGCCGACAGCUCGUCAAAGUGCAUCCUGCGAGUUGAUUGAGGGUUAGUUAUUUUUCAUAUAACCAUAACACAGAUAACUGAGCACACUGCUCAUAAAAAUUUA
(((........((((((((..(((.....)))..)))).))))(((((.............)))))....))).......(((((.....))))).......... ( -24.42)
>consensus
GUGGCCGACAGCUCAUCGAAGUGCAUCCUGCGAAUUGAUUGAGGGUUAGUUAUUUUUCAAUGAACAAUAACUCAGAUAGCUGACCACACAGCUCAUAAAAAUAUA
..(((.(....((((((((..(((.....)))..)))).))))((((((((((((..................))))))))))))...).)))............ (-20.67 = -20.51 +  -0.16)

alignment

secondary structure

dotplot

Window 0

Location	24,575,374 – 24,575,470
Length	96
Sequences	5
Columns	96
Reading direction	forward
Mean pairwise identity	72.77
Mean single sequence MFE	-14.12
Consensus MFE	-1.84
Energy contribution	-2.44
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-1.92
Structure conservation index	0.13
SVM decision value	1.08
SVM RNA-class probability	0.912671
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24575374 96 + 27905053
UCAGAUAGCUGACCACACAGCUCAUAAAAGUAUAACUUUUAGAGCUACAUAAAAAUGUGUAAGAUAUAUUAAACCAAAAGAUGCCAUCAUUACUGA
...(((.((..........((((.((((((.....))))))))))((((((....)))))).....................)).)))........ ( -17.40)
>DroSec_CAF1 73865 91 + 1
UCAGAAAGCUGACCACACAGCUCAUAAAGAUAUA--UUGUAGAGCUACAUGAAAAUGUGUUAGAUAUAUAAU---AAGAAAUGCCAUCAUUACUGA
((((..(((((......))))).......(((((--((....(((.((((....))))))).)))))))...---.................)))) ( -17.80)
>DroSim_CAF1 75425 96 + 1
UCAAAUAGCUGACCACACAGCUCAUAAAAGCACAACUUUUAGAGGAACAUGAAAACGUGUUAGAUAUAUAAAACCAAAAGAGGCCAUCAUUACUGA
......(((((......)))))..((((((.....))))))((((((((((....))))))............((......)))).))........ ( -14.40)
>DroEre_CAF1 78397 85 + 1
UCAGAUAACUGGCCACACAGCUCAGAAAAUCACAACUAUUAG---------CACAAAUGUUAUAAAUAUAAUAAUGAAAACUGCAAUCAUAACU--
...(((..(((((......)).)))................(---------((.....(((((.......)))))......))).)))......-- (  -7.80)
>DroYak_CAF1 75191 87 + 1
ACAGAUAACUGAGCACACUGCUCAUAAAAAUUUAACUAUUAG---------CACAUAUGUUAUAAAUAUAAUAUUAAAAGCUGCAAUCAUAACUAA
...(((...(((((.....)))))...............(((---------(....(((((((....))))))).....))))..)))........ ( -13.20)
>consensus
UCAGAUAGCUGACCACACAGCUCAUAAAAAUAUAACUUUUAGAG__ACAU_AAAAUGUGUUAGAUAUAUAAUACCAAAAGAUGCCAUCAUUACUGA
......(((((......))))).......................................................................... ( -1.84 =  -2.44 +   0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:29:17 2006