Locus 2835

Sequence ID	2R_DroMel_CAF1
Location	9,832,877 – 9,833,057
Length	180
Max. P	0.749970

overview

Window 6

Location	9,832,877 – 9,832,983
Length	106
Sequences	5
Columns	118
Reading direction	forward
Mean pairwise identity	89.52
Mean single sequence MFE	-35.78
Consensus MFE	-26.92
Energy contribution	-27.52
Covariance contribution	0.60
Combinations/Pair	1.06
Mean z-score	-1.85
Structure conservation index	0.75
SVM decision value	0.47
SVM RNA-class probability	0.749970
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9832877 106 + 20766785
AAUGGUAAUGGGCCAACUGGGUAAUGGAUAGAAGCAGAAGGUAAUGGCUAUA------------CCUAGUGGGCAGUUUCCAAUGGGCUUGACGAAGGUCGUCGCUGUCCAUUCUUCU
..(((.(((..(((.((((((((.(((.((...((.....))..)).)))))------------)))))).))).))).)))((((((.(((((.....)))))..))))))...... ( -35.00)
>DroSec_CAF1 70337 106 + 1
AAUGGUAAUGGGCCAACUGGGUAAUGGAUAGAAGCAGAAGGUAAUGGCUAUG------------GCUAGUGGGCAGUUUCCAAUGGGCUUGACGAAGGUCGUCGCUGUCCAUUCUUCU
..((((.....))))...(((.(((((((((((((....((...((.((((.------------....)))).))....)).....))))((((.....)))).))))))))).))). ( -32.00)
>DroSim_CAF1 72164 100 + 1
AAUGGUAAUGGGCCAACUGGGUAAUGGAUAGAAGCAGAAGGUAAUG------------------GCUAGUGGGCAGUUUCCAAUGGGCUUGACGAAGGUCGUCGCUGUCCAUUCUUCU
..((((.....))))...(((.(((((((((..((..........(------------------(((..((((.....))))...)))).(((....)))))..))))))))).))). ( -31.10)
>DroEre_CAF1 75343 112 + 1
AAUGGUAAUGGGCCAACUGUGUAAUGGAUAGAAGUAGAGGGUAAUGGCUAUGG------CUCUGGCCAGUGGGCAGUUGCCAAUGGGCUUGACGAAGGUCGUCGCUGUCCAUUCUUCU
..((((.....)))).......(((((((((((((....((((((.(((.(((------(....))))...))).)))))).....))))((((.....)))).)))))))))..... ( -40.80)
>DroYak_CAF1 72714 118 + 1
AAUGGUAAUGGGCCAACUGGGUAAUGGAUAGAAGUAGAAGGUAAUGGCUAUGGCUAUGGCUAUGGCUAGUGGGCUGUUUCCAAUGGGCUUGACGAAGGUCGUCGCUGUCCAUUCUUCU
..((((.....))))...(((.(((((((((((((....((.(((((((.(((((((....)))))))...))))))).)).....))))((((.....)))).))))))))).))). ( -40.00)
>consensus
AAUGGUAAUGGGCCAACUGGGUAAUGGAUAGAAGCAGAAGGUAAUGGCUAUG____________GCUAGUGGGCAGUUUCCAAUGGGCUUGACGAAGGUCGUCGCUGUCCAUUCUUCU
..((((.....))))...(((.(((((((((((((....(((....)))................(((.((((.....)))).)))))))((((.....)))).))))))))).))). (-26.92 = -27.52 +   0.60)

alignment

secondary structure

dotplot

Window 7

Location	9,832,943 – 9,833,057
Length	114
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	91.78
Mean single sequence MFE	-23.19
Consensus MFE	-19.72
Energy contribution	-20.75
Covariance contribution	1.03
Combinations/Pair	1.04
Mean z-score	-1.49
Structure conservation index	0.85
SVM decision value	-0.05
SVM RNA-class probability	0.507060
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9832943 114 - 20766785
AAAUCUU------UACAUAUAUAACCAAAAUAUUUUUCUUUAGAAAUCUGCGCAUUCAUCUAAAGCAAAGAAGAGACUGAAGAAGAAUGGACAGCGACGACCUUCGUCAAGCCCAUUGGA
.......------...........((((..(((((((((((((...(((..((...........)).....)))..)))))))))))))......((((.....)))).......)))). ( -23.20)
>DroSec_CAF1 70403 114 - 1
AAAUCUU------UACAUCUAUAACCAAAAUAUUUUUCUUUAGAAAUCUGCGCAUUCAUCUAAAGCAAAGAAGAGGCUGAAGAAGAAUGGACAGCGACGACCUUCGUCAAGCCCAUUGGA
.......------...........((((..(((((((((((((...(((..((...........)).....)))..)))))))))))))......((((.....)))).......)))). ( -24.30)
>DroSim_CAF1 72224 114 - 1
AAAUCUU------UACAUCUAUAACCAAAAUAUUUUUCUUUAGAAAUCUGCGCAUUCAUCUAAAGCAAAGAAGAGGCUGAAGAAGAAUGGACAGCGACGACCUUCGUCAAGCCCAUUGGA
.......------...........((((..(((((((((((((...(((..((...........)).....)))..)))))))))))))......((((.....)))).......)))). ( -24.30)
>DroEre_CAF1 75415 114 - 1
AAAUCUU------UACAUCUAUAACCAAAAUAUUUUUCUUUAGAAAUCUGCGCAUUCAUCUAAAGCAAAGAAGAGGCUGAAGAAGAAUGGACAGCGACGACCUUCGUCAAGCCCAUUGGC
.......------...........((((..(((((((((((((...(((..((...........)).....)))..)))))))))))))......((((.....)))).......)))). ( -23.60)
>DroYak_CAF1 72792 114 - 1
AAAUCUU------UACAUCUAUAACCAAAAUAUUUUUCUUUAGAAAUCUGCGCAUUCAUCUAAAGCAAAGAAGAGGCUGAAGAAGAAUGGACAGCGACGACCUUCGUCAAGCCCAUUGGA
.......------...........((((..(((((((((((((...(((..((...........)).....)))..)))))))))))))......((((.....)))).......)))). ( -24.30)
>DroAna_CAF1 70155 112 - 1
AAGUCUUUUUUGUUACAUCCAAAGCCAAAAUAUUUUUCUUUAGAAAUCUGCGCAUUCAUCUAAAGCAAAGAAGAGGCUGAAG---AAUAUACAGCAACGACCUUCGUCAGA-----AGAC
..(((.((.((((....((...((((......((((((((((((..............))))))).)))))...))))...)---)....)))).)).)))((((....))-----)).. ( -19.44)
>consensus
AAAUCUU______UACAUCUAUAACCAAAAUAUUUUUCUUUAGAAAUCUGCGCAUUCAUCUAAAGCAAAGAAGAGGCUGAAGAAGAAUGGACAGCGACGACCUUCGUCAAGCCCAUUGGA
........................((((..(((((((((((((...(((..((...........)).....)))..)))))))))))))......((((.....)))).......)))). (-19.72 = -20.75 +   1.03)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:40:40 2006