Locus 6335

Sequence ID X_DroMel_CAF1
Location 15,991,732 – 15,991,845
Length 113
Max. P 0.802480
window10333 window10334

overview

Window 3

Location 15,991,732 – 15,991,845
Length 113
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 68.61
Mean single sequence MFE -26.52
Consensus MFE -9.84
Energy contribution -11.03
Covariance contribution 1.19
Combinations/Pair 1.26
Mean z-score -2.62
Structure conservation index 0.37
SVM decision value 0.62
SVM RNA-class probability 0.802480
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15991732 113 + 22224390
UUAGUGAACCACCGGGUAUUAGUACUCACACCUGUACUCCCUGCCAACCGAUACCACAUGUA-----GUAUGUACAUAUGUAU--ACGUAUGUACACAGAGAAAAUUCCAUUGGGGACAU
...........((.((((..(((((........)))))...))))..(((((..........-----...((((((((((...--.)))))))))).............))))))).... ( -26.37)
>DroSec_CAF1 59612 100 + 1
U------------------UAGUACUCACACCUGUACUCCCUGCCAGCCGAUACCACAUGUAUGUACAUAUGUACAUAUGUAC--ACGAAUGUACACAGGGAAAAUUCCAUUGGGGACAU
.------------------..((((........))))((((((................((((((((....))))))))((((--(....))))).))))))...((((....))))... ( -27.80)
>DroSim_CAF1 50688 100 + 1
U------------------UAGUACUCACACCUGUACUCCCUGCCAACCGAUACCACAUGUAUGUACAUAUAUACAUAUGUAC--ACGAAUGUACACAGGGAAAAUUCCAUUGGGGACAU
.------------------..((((........))))((((((..............((((((((....)))))))).(((((--(....))))))))))))...((((....))))... ( -25.90)
>DroYak_CAF1 42734 89 + 1
UUAGUACAC---CCGGUAUUAGUACUCACACCUGUACUCU--------CUGUACAGUAUGUA--------------------UGUACAUGUGUACACGGAGGAAAUUCCAUUGGGGACAU
...((...(---(((((....((((..(((.((((((...--------..))))))..))).--------------------.))))..........((((....)))))))))).)).. ( -26.00)
>consensus
U__________________UAGUACUCACACCUGUACUCCCUGCCAACCGAUACCACAUGUA_____AUAUGUACAUAUGUAC__ACGAAUGUACACAGAGAAAAUUCCAUUGGGGACAU
.....................((((........))))((((((......(....)((((....((((((((....))))))))......))))...))))))...((((....))))... ( -9.84 = -11.03 +   1.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 15,991,732 – 15,991,845
Length 113
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 68.61
Mean single sequence MFE -28.43
Consensus MFE -13.66
Energy contribution -15.60
Covariance contribution 1.94
Combinations/Pair 1.14
Mean z-score -1.79
Structure conservation index 0.48
SVM decision value 0.32
SVM RNA-class probability 0.686789
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15991732 113 - 22224390
AUGUCCCCAAUGGAAUUUUCUCUGUGUACAUACGU--AUACAUAUGUACAUAC-----UACAUGUGGUAUCGGUUGGCAGGGAGUACAGGUGUGAGUACUAAUACCCGGUGGUUCACUAA
.((.((((.........(((((((((((((((.(.--...).)))))))((((-----((....))))))......))))))))....(((((........))))).)).))..)).... ( -29.60)
>DroSec_CAF1 59612 100 - 1
AUGUCCCCAAUGGAAUUUUCCCUGUGUACAUUCGU--GUACAUAUGUACAUAUGUACAUACAUGUGGUAUCGGCUGGCAGGGAGUACAGGUGUGAGUACUA------------------A
...(((.....)))....(((((((..((((..((--((((((((....))))))))))..))))(((....))).)))))))((((........))))..------------------. ( -30.00)
>DroSim_CAF1 50688 100 - 1
AUGUCCCCAAUGGAAUUUUCCCUGUGUACAUUCGU--GUACAUAUGUAUAUAUGUACAUACAUGUGGUAUCGGUUGGCAGGGAGUACAGGUGUGAGUACUA------------------A
...(((.....)))....(((((((...((..((.--...(((((((((........)))))))))....))..)))))))))((((........))))..------------------. ( -27.80)
>DroYak_CAF1 42734 89 - 1
AUGUCCCCAAUGGAAUUUCCUCCGUGUACACAUGUACA--------------------UACAUACUGUACAG--------AGAGUACAGGUGUGAGUACUAAUACCGG---GUGUACUAA
.........(((((......)))))((((((..((((.--------------------(((((.((((((..--------...))))))))))).)))).........---))))))... ( -26.30)
>consensus
AUGUCCCCAAUGGAAUUUUCCCUGUGUACAUACGU__AUACAUAUGUACAUAU_____UACAUGUGGUAUCGGUUGGCAGGGAGUACAGGUGUGAGUACUA__________________A
...(((.....))).....((((((((((...(((..((((((((....))))))))....)))..))))......))))))(((((........))))).................... (-13.66 = -15.60 +   1.94)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:11:01 2006