Locus 6088

Sequence ID 2R_DroMel_CAF1
Location 19,159,818 – 19,159,912
Length 94
Max. P 0.987221
window9754 window9755

overview

Window 4

Location 19,159,818 – 19,159,912
Length 94
Sequences 4
Columns 118
Reading direction forward
Mean pairwise identity 76.37
Mean single sequence MFE -25.98
Consensus MFE -14.19
Energy contribution -14.12
Covariance contribution -0.06
Combinations/Pair 1.14
Mean z-score -2.66
Structure conservation index 0.55
SVM decision value 2.07
SVM RNA-class probability 0.987221
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19159818 94 + 20766785
UACAGUGGCAACCAGUUUAAUUGAACGCACUCCAACUGGUUUUUGCU-UUGGCAGAUUCAUAAUGUUGAAA-----------------UCU------GCCUAAAUUCAGGUUUUACUU
...((..(.((((((((....((....))....)))))))).)..))-..((((((((((......)).))-----------------)))------))).................. ( -24.90)
>DroSec_CAF1 43581 95 + 1
UUCAGUGGCAACCAGUUUGAUUGAACGCACUCUAACUGGUUUUUGUUUUUGGCAGAUUCAUUAAGUUGAAA-----------------UCU------GCUUAAAUUCAGGUUUUACUU
...(((((.((((((((.((.((....)).)).))))))))((((..(((((((((((((......)).))-----------------)))------)).))))..))))..))))). ( -25.30)
>DroSim_CAF1 44626 95 + 1
UUCAGUGGCAACCAGUUUGAUUGAACGCACUCUAACUGGUUUUUGUUUUUGGCAGAUUCAUAAAGUUGAAA-----------------UCU------GCCUAAAUUCAGGUUUUUGUU
..(((..((((((((((.((.((....)).)).)))))))).(((..(((((((((((((......)).))-----------------)))------))).)))..)))))..))).. ( -28.30)
>DroYak_CAF1 50501 114 + 1
UUCAUUAGCAACCAGUUUGAUUGAACGCACUCUAACUGGUUUAUGCCUAUGG----UUCAUUGAGUUCAGAAGGCAAUAAGUAUUUUUUUUGCCACAGCGAUAAUUCAGGUUUCACUU
.((((..((((((((((.((.((....)).)).)))))))...)))..))))----....(((((((..(..(((((.(((....))).)))))....)...)))))))......... ( -25.40)
>consensus
UUCAGUGGCAACCAGUUUGAUUGAACGCACUCUAACUGGUUUUUGCUUUUGGCAGAUUCAUAAAGUUGAAA_________________UCU______GCCUAAAUUCAGGUUUUACUU
..(((.(((((((((((.((.((....)).)).)))))))...)))).))).....((((......))))................................................ (-14.19 = -14.12 +  -0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 19,159,818 – 19,159,912
Length 94
Sequences 4
Columns 118
Reading direction reverse
Mean pairwise identity 76.37
Mean single sequence MFE -22.85
Consensus MFE -10.56
Energy contribution -10.38
Covariance contribution -0.19
Combinations/Pair 1.08
Mean z-score -2.66
Structure conservation index 0.46
SVM decision value 0.94
SVM RNA-class probability 0.885710
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19159818 94 - 20766785
AAGUAAAACCUGAAUUUAGGC------AGA-----------------UUUCAACAUUAUGAAUCUGCCAA-AGCAAAAACCAGUUGGAGUGCGUUCAAUUAAACUGGUUGCCACUGUA
.(((..............(((------(((-----------------((.((......))))))))))..-.(((...(((((((..(((.......))).)))))))))).)))... ( -24.20)
>DroSec_CAF1 43581 95 - 1
AAGUAAAACCUGAAUUUAAGC------AGA-----------------UUUCAACUUAAUGAAUCUGCCAAAAACAAAAACCAGUUAGAGUGCGUUCAAUCAAACUGGUUGCCACUGAA
.(((...............((------(((-----------------((.((......)))))))))..........((((((((.((.((....)).)).))))))))...)))... ( -20.10)
>DroSim_CAF1 44626 95 - 1
AACAAAAACCUGAAUUUAGGC------AGA-----------------UUUCAACUUUAUGAAUCUGCCAAAAACAAAAACCAGUUAGAGUGCGUUCAAUCAAACUGGUUGCCACUGAA
..................(((------(((-----------------((.((......)))))))))).........((((((((.((.((....)).)).))))))))......... ( -23.60)
>DroYak_CAF1 50501 114 - 1
AAGUGAAACCUGAAUUAUCGCUGUGGCAAAAAAAAUACUUAUUGCCUUCUGAACUCAAUGAA----CCAUAGGCAUAAACCAGUUAGAGUGCGUUCAAUCAAACUGGUUGCUAAUGAA
.(((((...........)))))..(((((.((......)).)))))................----.(((.((((...(((((((.((.((....)).)).))))))))))).))).. ( -23.50)
>consensus
AAGUAAAACCUGAAUUUAGGC______AGA_________________UUUCAACUUAAUGAAUCUGCCAAAAACAAAAACCAGUUAGAGUGCGUUCAAUCAAACUGGUUGCCACUGAA
.............................................................................((((((((.((.((....)).)).))))))))......... (-10.56 = -10.38 +  -0.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:02:29 2006