Locus 4499

Sequence ID	3L_DroMel_CAF1
Location	12,988,813 – 12,988,933
Length	120
Max. P	0.927991

overview

Window 6

Location	12,988,813 – 12,988,933
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	92.64
Mean single sequence MFE	-36.15
Consensus MFE	-32.58
Energy contribution	-33.08
Covariance contribution	0.50
Combinations/Pair	1.12
Mean z-score	-1.43
Structure conservation index	0.90
SVM decision value	0.20
SVM RNA-class probability	0.629210
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12988813 120 + 23771897
CUGCAUCGAGCAGUGCGGGAAUUCCCAAAUAUUUCUCGGCCGUUGUAAAGGCCAAAUCGUUGUUCUCAUAGAUAUCGUCUGCUUUAAGUCGGUCGAAAUCUAUAAGAUCCGGCCGAAAGU
((((.....))))...(((....))).....((((..((((........)))).....((((.(((.((((((.(((.((((.....).))).))).)))))).)))..)))).)))).. ( -36.30)
>DroSim_CAF1 115773 120 + 1
CUGCAUCGAGCAGUGCAGGAAUUCCCAAAUAUUUCUCGGCCGUUGUAAAGGCCAAAUCGUUGUUCUCAUAGAUAUCGUCUGCUUUAAGUCGGUCAAAGUCUAUAAGGUCAGGCCGAAAGU
((((((......)))))).................(((((((((.....)))........((..((.((((((((((.((......)).))))....)))))).))..)))))))).... ( -30.30)
>DroEre_CAF1 112148 120 + 1
CUGCAUCGAGCAGUGCUGGAAUUCCCAAGUAUUUCUCGGCCGUUGUAAAGGCCAAAUCAUUGUUCUCAUAGAUAUCGUCCGCCUUCAGUCGGUCGAAAUCUAUGAGGUCCGGCCGAAAGU
((((.....)))).((((((.................((((........))))..........((((((((((.(((.(((.(....).))).))).))))))))))))))))(....). ( -44.10)
>DroYak_CAF1 110938 120 + 1
CUGCAUCAAGCAGUGCGGGUAUUCCCAAGUAUUUCUCGGCCGUUGUAAAGGCCAAAUCAUUGUUCUCAUAAAUAUCGUCUGCCCUCAGUCGGUCGAAGUCUAUGAGGUCCGGCCGAAAGU
((((.....))))...(((....))).........((((((((((.......)))........(((((((.((.(((.((((.....).))).))).)).)))))))..))))))).... ( -33.90)
>consensus
CUGCAUCGAGCAGUGCGGGAAUUCCCAAAUAUUUCUCGGCCGUUGUAAAGGCCAAAUCAUUGUUCUCAUAGAUAUCGUCUGCCUUAAGUCGGUCGAAAUCUAUAAGGUCCGGCCGAAAGU
((((((......)))))).................(((((((((.....)))...........((((((((((.(((.((((.....).))).))).))))))))))...)))))).... (-32.58 = -33.08 +   0.50)

alignment

secondary structure

dotplot

Window 7

Location	12,988,813 – 12,988,933
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	92.64
Mean single sequence MFE	-37.33
Consensus MFE	-33.05
Energy contribution	-33.30
Covariance contribution	0.25
Combinations/Pair	1.12
Mean z-score	-2.00
Structure conservation index	0.89
SVM decision value	1.19
SVM RNA-class probability	0.927991
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12988813 120 - 23771897
ACUUUCGGCCGGAUCUUAUAGAUUUCGACCGACUUAAAGCAGACGAUAUCUAUGAGAACAACGAUUUGGCCUUUACAACGGCCGAGAAAUAUUUGGGAAUUCCCGCACUGCUCGAUGCAG
..(((((((((..((((((((((.(((.(.(........).).))).))))))))))........(((.......)))))))))))).......(((....)))...((((.....)))) ( -38.90)
>DroSim_CAF1 115773 120 - 1
ACUUUCGGCCUGACCUUAUAGACUUUGACCGACUUAAAGCAGACGAUAUCUAUGAGAACAACGAUUUGGCCUUUACAACGGCCGAGAAAUAUUUGGGAAUUCCUGCACUGCUCGAUGCAG
..((((((((....((((((((..(((.(.(........).).)))..)))))))).........(((.......))).)))))))).......(((....)))...((((.....)))) ( -29.00)
>DroEre_CAF1 112148 120 - 1
ACUUUCGGCCGGACCUCAUAGAUUUCGACCGACUGAAGGCGGACGAUAUCUAUGAGAACAAUGAUUUGGCCUUUACAACGGCCGAGAAAUACUUGGGAAUUCCAGCACUGCUCGAUGCAG
..(((((((((...(((((((((.(((.(((.(.....)))).))).)))))))))..(((....)))..........))))))))).....((((.....))))..((((.....)))) ( -43.20)
>DroYak_CAF1 110938 120 - 1
ACUUUCGGCCGGACCUCAUAGACUUCGACCGACUGAGGGCAGACGAUAUUUAUGAGAACAAUGAUUUGGCCUUUACAACGGCCGAGAAAUACUUGGGAAUACCCGCACUGCUUGAUGCAG
..(((((((((...((((((((..(((.((......)).....)))..))))))))..(((....)))..........))))))))).......(((....)))...((((.....)))) ( -38.20)
>consensus
ACUUUCGGCCGGACCUCAUAGACUUCGACCGACUGAAAGCAGACGAUAUCUAUGAGAACAACGAUUUGGCCUUUACAACGGCCGAGAAAUACUUGGGAAUUCCCGCACUGCUCGAUGCAG
..(((((((((...(((((((((.(((.(.(.(.....)).).))).)))))))))..(((....)))..........))))))))).......(((....)))...((((.....)))) (-33.05 = -33.30 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:25:02 2006