Locus 65

Sequence ID	3L_DroMel_CAF1
Location	255,353 – 255,526
Length	173
Max. P	0.593986

overview

Window 2

Location	255,353 – 255,461
Length	108
Sequences	5
Columns	112
Reading direction	reverse
Mean pairwise identity	91.42
Mean single sequence MFE	-28.06
Consensus MFE	-22.32
Energy contribution	-22.40
Covariance contribution	0.08
Combinations/Pair	1.05
Mean z-score	-1.45
Structure conservation index	0.80
SVM decision value	0.12
SVM RNA-class probability	0.593986
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 255353 108 - 23771897
GCACCCACAUUCCUUUAAAUCCGCUAGCCCAACCACUCUUAUACGGCUGUUCCACUCAACGCGAAUCCUCUCCGGACGACA--ACA--CAGGAAGGGGUGCCCUGCACACGC
((((((...(((((.......(((.((((...............))))(((......))))))..(((.....))).....--...--.))))).))))))........... ( -26.46)
>DroSec_CAF1 23183 110 - 1
GCACCCACAUUCCUUUAAAUCCGCUAGCCCAACCACUCUUAUACGGCUGUUCCACUCAACGCGAAUACUCUCCGGACGACA--GCAGGAAGGAAAGGGUGCCCUGCACACGC
((((((...(((((.....((((((((((...............))))...........((.((......))))......)--)).)))))))).))))))........... ( -25.46)
>DroSim_CAF1 23649 110 - 1
GCACCCACAUUCCUUUAAAUCCGCUAGCCCAACCACUCUUAUACGGCUGUUCCACUCAACGCGAAUACUCUCCGGACGACA--GCAGGAAGGAAAGGGUGCCCUGCACACGC
((((((...(((((.....((((((((((...............))))...........((.((......))))......)--)).)))))))).))))))........... ( -25.46)
>DroEre_CAF1 23474 105 - 1
GCACCCACAUUCCUCCAAAUUCGCCAGCCUAACCACUCUUAUACGGCUAUUCCACUCAACGCGAAUUCUCUCCGGACGAC-------GAAGGAAGGGGUGCCCUGCACACGC
((((((...(((((...(((((((.((((...............))))............))))))).....((.....)-------).))))).))))))........... ( -26.28)
>DroYak_CAF1 23342 112 - 1
GCACCCACAUUCCUCCAAAUUCGCCAGCCUAACCACUCUUAUACGGCUGUUCCACUCAACGCGAAUUCUCUCCGGACGACCAGGAAGGAAGGAAGGGGUGCCCUGCACACGC
((((((...(((((((.((((((((((((...............)))))...........)))))))...(((((....)).))).)).))))).))))))........... ( -36.66)
>consensus
GCACCCACAUUCCUUUAAAUCCGCUAGCCCAACCACUCUUAUACGGCUGUUCCACUCAACGCGAAUACUCUCCGGACGACA__GCAGGAAGGAAGGGGUGCCCUGCACACGC
((((((...(((((..........(((((...............)))))..........((.((......))))...............))))).))))))........... (-22.32 = -22.40 +   0.08)

alignment

secondary structure

dotplot

Window 3

Location	255,421 – 255,526
Length	105
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	81.88
Mean single sequence MFE	-31.80
Consensus MFE	-20.48
Energy contribution	-18.88
Covariance contribution	-1.60
Combinations/Pair	1.37
Mean z-score	-1.67
Structure conservation index	0.64
SVM decision value	-0.01
SVM RNA-class probability	0.527655
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 255421 105 + 23771897
AAGAGUGGUUGGGCUAGCGGAUUUAAAGGAAUGUGGGUGCUGUGC-CUUUAAGUUAGGACUCCUUGUG-------------ACUCGGGAUACG-AGAGAAGAGGCUGGAUCGCGAGAUAU
....((((((.(((.....((((((((((...((....))....)-)))))))))....(((.((...-------------.((((.....))-)).)).)))))).))))))....... ( -29.80)
>DroSec_CAF1 23253 104 + 1
AAGAGUGGUUGGGCUAGCGGAUUUAAAGGAAUGUGGGUGCUGUGC-CUUUAAGUUAGGACUCCUUGUG-------------AA--GGGAUACGCAGAGCAGCGGCUGGAUCGCAAGUUAU
....((((((.((((..((.((((....)))).))(.((((.(((-(((......)))..(((((...-------------.)--))))...))).)))).))))).))))))....... ( -32.10)
>DroSim_CAF1 23719 104 + 1
AAGAGUGGUUGGGCUAGCGGAUUUAAAGGAAUGUGGGUGCUGUGC-CUUUAAGUUAGGACUCCUUGUG-------------AA--GGGAUACGCAGAGCAGCGGCUGGAUCGCAAGUUAU
....((((((.((((..((.((((....)))).))(.((((.(((-(((......)))..(((((...-------------.)--))))...))).)))).))))).))))))....... ( -32.10)
>DroEre_CAF1 23539 104 + 1
AAGAGUGGUUAGGCUGGCGAAUUUGGAGGAAUGUGGGUGCUGUGC-CUUUAAGUUGGGAUGCGCUAUG-------------GA--GGGACACGCAGACCAGUAGCUAGAUCGCAAGUUAA
....((((((.(((((.(.((((((((((...((....))....)-)))))))))((..((((...((-------------..--....))))))..)).)))))).))))))....... ( -31.60)
>DroYak_CAF1 23414 118 + 1
AAGAGUGGUUAGGCUGGCGAAUUUGGAGGAAUGUGGGUGCUGUGUUCUCUGAGUUAGGAUGCCCUAUGAUAUGAGGGAUACGA--GGGAUACGCACAGCAGUAGCUAGAUCGCAAGUUAU
....((((((.(((((.((.((((....)))).))..(((((((((((((..((.......((((........))))..)).)--))))...)))))))).))))).))))))....... ( -33.40)
>consensus
AAGAGUGGUUGGGCUAGCGGAUUUAAAGGAAUGUGGGUGCUGUGC_CUUUAAGUUAGGACUCCUUGUG_____________AA__GGGAUACGCAGAGCAGCGGCUGGAUCGCAAGUUAU
....((((((.((((.((.((((((((((...((....))....).)))))))))(((....)))...................................)))))).))))))....... (-20.48 = -18.88 +  -1.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:31:26 2006