Locus 2638

Sequence ID 3L_DroMel_CAF1
Location 7,264,308 – 7,264,401
Length 93
Max. P 0.999974
window4139 window4140

overview

Window 9

Location 7,264,308 – 7,264,401
Length 93
Sequences 4
Columns 93
Reading direction forward
Mean pairwise identity 69.71
Mean single sequence MFE -17.20
Consensus MFE -12.59
Energy contribution -12.77
Covariance contribution 0.19
Combinations/Pair 1.30
Mean z-score -3.00
Structure conservation index 0.73
SVM decision value 5.11
SVM RNA-class probability 0.999974
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7264308 93 + 23771897
UUACUACUGUAAGGUAUACUGUAAAAGAAUUUUUAAAAUAUAUCAAACACUUUAAAUUUCUCUCAGUGUCCUCCCACUCCCAGAGGACACUGG
((((....))))((((((...(((((....)))))...))))))...................((((((((((.........)))))))))). ( -22.40)
>DroSim_CAF1 21238 81 + 1
U--CUACU------UAU----UCAAAAAAUAUUUAAAAUAUAUCAUAUACUUCAAAUUUCUCUCAGUGUUCUCCCACUCCCAGAGGACACUGG
.--.....------...----..........................................((((((((((.........)))))))))). ( -14.00)
>DroEre_CAF1 20919 82 + 1
A--AUACU------UGU---GAAAAAAAAUGUUUAUAACAGAGCAAUCACUUCAAAUUUCGCUCGGUGCACUCCCACUCCCAGGGGACACUGG
.--.....------.((---((((.....(((.....)))((....))........)))))).(((((...((((........))))))))). ( -16.50)
>DroYak_CAF1 21986 74 + 1
A--AUAUU------UA----GUAAAG-AAUUCUUUAAAUAUCCUAAUCGCUGCCACUUUCUCUCGGUGUCCUCCCAC------AGGACACUGG
.--.....------..----.(((((-....)))))...........................(((((((((.....------))))))))). ( -15.90)
>consensus
A__AUACU______UAU___GUAAAAAAAUUUUUAAAAUAUAUCAAACACUUCAAAUUUCUCUCAGUGUCCUCCCACUCCCAGAGGACACUGG
...............................................................((((((((((.........)))))))))). (-12.59 = -12.77 +   0.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 7,264,308 – 7,264,401
Length 93
Sequences 4
Columns 93
Reading direction reverse
Mean pairwise identity 69.71
Mean single sequence MFE -19.85
Consensus MFE -10.04
Energy contribution -11.60
Covariance contribution 1.56
Combinations/Pair 1.09
Mean z-score -1.71
Structure conservation index 0.51
SVM decision value 0.20
SVM RNA-class probability 0.632581
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7264308 93 - 23771897
CCAGUGUCCUCUGGGAGUGGGAGGACACUGAGAGAAAUUUAAAGUGUUUGAUAUAUUUUAAAAAUUCUUUUACAGUAUACCUUACAGUAGUAA
.(((((((((((.......)))))))))))((((((.((((((((((.....))))))))))..))))))(((.(((.....))).))).... ( -28.60)
>DroSim_CAF1 21238 81 - 1
CCAGUGUCCUCUGGGAGUGGGAGAACACUGAGAGAAAUUUGAAGUAUAUGAUAUAUUUUAAAUAUUUUUUGA----AUA------AGUAG--A
.((((((.((((.......)))).))))))((((((((((((((((((...)))))))))))).))))))..----...------.....--. ( -20.00)
>DroEre_CAF1 20919 82 - 1
CCAGUGUCCCCUGGGAGUGGGAGUGCACCGAGCGAAAUUUGAAGUGAUUGCUCUGUUAUAAACAUUUUUUUUC---ACA------AGUAU--U
((((......))))..(((..((......((((((.((.....))..))))))(((.....)))....))..)---)).------.....--. ( -15.60)
>DroYak_CAF1 21986 74 - 1
CCAGUGUCCU------GUGGGAGGACACCGAGAGAAAGUGGCAGCGAUUAGGAUAUUUAAAGAAUU-CUUUAC----UA------AAUAU--U
((((((((((------.....)))))))(....)....)))..........(((((((((((....-)))...----))------)))))--) ( -15.20)
>consensus
CCAGUGUCCUCUGGGAGUGGGAGGACACCGAGAGAAAUUUGAAGUGAUUGAUAUAUUUUAAAAAUUUUUUUAC___AUA______AGUAG__A
.(((((((((((.......)))))))))))............................................................... (-10.04 = -11.60 +   1.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:38:15 2006