Locus 1955

Sequence ID 3L_DroMel_CAF1
Location 5,409,507 – 5,409,641
Length 134
Max. P 0.839086
window3059 window3060

overview

Window 9

Location 5,409,507 – 5,409,611
Length 104
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 79.45
Mean single sequence MFE -27.38
Consensus MFE -23.48
Energy contribution -23.65
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -1.48
Structure conservation index 0.86
SVM decision value 0.74
SVM RNA-class probability 0.839086
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5409507 104 + 23771897
UCCG-UUUCCA---------UCUCUCUUUAUCCACAGUCUCGCCAAUGAUUUGGGUGCCGAAUCAACUUGUUGGCGCCCCAUCCGGCACAGAUGUAACCAUCGAUUGCCACACG
....-......---------..............(((((..(((...(((..(((((((((.........))))))))).))).)))...((((....)))))))))....... ( -27.50)
>DroVir_CAF1 28018 98 + 1
UCUG----------------CCCCGCGCUUUAUUCAGUCUCGCCAAUGAUUUGGGUGCCGAAUCAACUUGUUGGCGCGCCAGCUGGCACAGAUGUAACCAUCGAUUGCCACACC
...(----------------(..((((((......)))...(((((((((((((...)))))))).....))))))))...))(((((..((((....))))...))))).... ( -28.30)
>DroGri_CAF1 55957 103 + 1
ACUUCGCUU-----------CGCGUCUCUUCAAAUAGUCUCGCCAAUGAUUUGGGUGCCGAAUCAACUUGUUGGCGCGCCAGCUGGCACAGAUGUAACCAUCGAUUGCCACACC
.....(((.-----------((((...((......))...)(((((((((((((...)))))))).....))))))))..)))(((((..((((....))))...))))).... ( -29.70)
>DroYak_CAF1 4617 113 + 1
UCCG-UUUCCCUCUCUUAUUCCCCUCUCUAUCCACAGUCUCGCCAAUGAUUUGGGUGCCGAAUCAACUUGUUGGCGCUCCAUCCGGCACAGAUGUAACCAUCGAUUGCCACACG
....-.............................(((((..(((...(((..(((((((((.........))))))))).))).)))...((((....)))))))))....... ( -24.50)
>DroMoj_CAF1 27474 99 + 1
UCUC-CAUU-----------CACCUCUCU---UGCAGUCUCGCCCAUGAUUUGGGUGCCGAAUCAACUUGUUGGCGCGCCAGCUGGCACAGAUGUAACCAUCGAUUGCCACACC
....-....-----------.........---.((((((..(((..((((((((...))))))))....(((((....))))).)))...((((....))))))))))...... ( -29.30)
>DroAna_CAF1 20069 91 + 1
UUCA-UUUCAA----------------------ACAGUUUCGCCAAUGAUUUGGGUGCCGAAUCAACUUGUUGGCGCCCCAUCCGGCACAGAUGUAACCAUCGAUUGCCACACG
....-......----------------------..............(((..(((((((((.........))))))))).))).((((..((((....))))...))))..... ( -25.00)
>consensus
UCCG_UUUC___________CCCCUCUCU_U_CACAGUCUCGCCAAUGAUUUGGGUGCCGAAUCAACUUGUUGGCGCGCCAGCCGGCACAGAUGUAACCAUCGAUUGCCACACC
........................................((((((((((((((...)))))))).....))))))........((((..((((....))))...))))..... (-23.48 = -23.65 +   0.17)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 5,409,531 – 5,409,641
Length 110
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 85.49
Mean single sequence MFE -34.38
Consensus MFE -29.35
Energy contribution -28.93
Covariance contribution -0.42
Combinations/Pair 1.09
Mean z-score -1.53
Structure conservation index 0.85
SVM decision value 0.10
SVM RNA-class probability 0.582211
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5409531 110 + 23771897
CAGUCUCGCCAAUGAUUUGGGUGCCGAAUCAACUUGUUGGCGCCCCAUCCGGCACAGAUGUAACCAUCGAUUGCCACACGGAGGCGCAUCCCAAGUGAGUCUACUC-GGA-U--------
.((.(((.....((((((((...))))))))(((((...(((((((....((((..((((....))))...))))....)).)))))....)))))))).))....-...-.-------- ( -39.40)
>DroVir_CAF1 28036 112 + 1
CAGUCUCGCCAAUGAUUUGGGUGCCGAAUCAACUUGUUGGCGCGCCAGCUGGCACAGAUGUAACCAUCGAUUGCCACACCGAGGCUCAUCCCAAGUGAGUUUUUCAUUCAUU--------
.(((((((....((((((((...))))))))....(((((....)))))(((((..((((....))))...)))))...))))))).......(((((((.....)))))))-------- ( -35.40)
>DroGri_CAF1 55980 109 + 1
UAGUCUCGCCAAUGAUUUGGGUGCCGAAUCAACUUGUUGGCGCGCCAGCUGGCACAGAUGUAACCAUCGAUUGCCACACCGAGGCGCAUCCCAAGUAAGCUUUUCAUA---U--------
.......((.....(((((((.(((((.........)))))(((((.(.(((((..((((....))))...)))))...)..)))))..)))))))..))........---.-------- ( -34.40)
>DroWil_CAF1 73871 118 + 1
CAGUCUCUCCCAUGAUUUGGGUACCGAAUCAACUUGUUGGUGCUCCAGCUGGCACAGAUGUAACCAUCGAUUGCCACACCGAGGCACAUCCCAAGUAAGUUCUUUA-CAC-UUUUCUCUC
..(((((.....((((((((...))))))))....(((((....)))))(((((..((((....))))...)))))....))))).........(((((...))))-)..-......... ( -30.70)
>DroMoj_CAF1 27493 112 + 1
CAGUCUCGCCCAUGAUUUGGGUGCCGAAUCAACUUGUUGGCGCGCCAGCUGGCACAGAUGUAACCAUCGAUUGCCACACCGAGGCCCAUCCCAAGUGAGUUUUUCUCCCACU--------
..((((((....((((((((...))))))))....(((((....)))))(((((..((((....))))...)))))...)))))).........(.(((.....))).)...-------- ( -33.40)
>DroAna_CAF1 20080 117 + 1
CAGUUUCGCCAAUGAUUUGGGUGCCGAAUCAACUUGUUGGCGCCCCAUCCGGCACAGAUGUAACCAUCGAUUGCCACACGGAGGCACAUCCCAAGUGAGUUUUCCCUAGA-U-UUUCAU-
.......(((........(((((((((.........)))))))))..(((((((..((((....))))...))))....)))))).........(((((...((....))-.-.)))))- ( -33.00)
>consensus
CAGUCUCGCCAAUGAUUUGGGUGCCGAAUCAACUUGUUGGCGCGCCAGCUGGCACAGAUGUAACCAUCGAUUGCCACACCGAGGCACAUCCCAAGUGAGUUUUUCAUACA_U________
..(((((..........((((((((((.........))))))).)))...((((..((((....))))...)))).....)))))................................... (-29.35 = -28.93 +  -0.42)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:21:01 2006