Locus 5784

Sequence ID	3R_DroMel_CAF1
Location	15,080,439 – 15,080,572
Length	133
Max. P	0.926962

overview

Window 9

Location	15,080,439 – 15,080,542
Length	103
Sequences	4
Columns	103
Reading direction	forward
Mean pairwise identity	87.54
Mean single sequence MFE	-23.05
Consensus MFE	-16.69
Energy contribution	-17.25
Covariance contribution	0.56
Combinations/Pair	1.15
Mean z-score	-2.09
Structure conservation index	0.72
SVM decision value	0.70
SVM RNA-class probability	0.826323
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15080439 103 + 27905053
CAAUGUUUUUGGAAAUGUGCAAAUGUAUUUUAUUAAUUGGCACCUGUUCUUAAACUGGUUAGCUUCCAGAGGCUAAGCCAUAAAUAUUUACUUCAUUGACCUC
(((((.(((.((((..((((.(((...........))).))))...)))).))).((((((((((....))))).))))).............)))))..... ( -20.60)
>DroSec_CAF1 5370 103 + 1
CAAUGUUUCUGGAAAUGCAAAAAUGUAUUUUAUUAAUUGGCACCUGUUCCUAAACGGGUUAGCUUCCAUAGGCUUAGCCAUAAAUAUUUACUUUAUUGACCUC
(((((......((((((((....))))))))......(((((((((((....))))))).((((......))))..)))).............)))))..... ( -22.60)
>DroSim_CAF1 3280 103 + 1
CAAUGUUUCUGUAAAUGCAGAAAUGUAUUUUAUUAAUUGGCACCUGUUCCCAAACUGGUUAGCUCCCAUGGGCUAAGCCAUAAAUAUUUACUUUAUUGACCUC
((((((((((((....))))))))(((...((((...(((((((.(((....))).)))((((((....)))))).))))..))))..)))...))))..... ( -26.20)
>DroEre_CAF1 5162 102 + 1
CACUGUUUCUAGAGGCGUAGAAAUUCAAUUUAUUAAUUGGCACCUGUUCUGAAACUGGUUAGCUUUCAUAGGCU-AGCCAUAAAUAUUUAUUUUAUUGACCUC
....(((((.(.(((.((.......(((((....))))))).))).)...)))))((((((((((....)))))-)))))....................... ( -22.81)
>consensus
CAAUGUUUCUGGAAAUGCAGAAAUGUAUUUUAUUAAUUGGCACCUGUUCCUAAACUGGUUAGCUUCCAUAGGCUAAGCCAUAAAUAUUUACUUUAUUGACCUC
(((((((((((......)))))).(((...((((...(((((((.(((....))).)))((((((....)))))).))))..))))..)))..)))))..... (-16.69 = -17.25 +   0.56)

alignment

secondary structure

dotplot

Window 0

Location	15,080,462 – 15,080,572
Length	110
Sequences	4
Columns	110
Reading direction	forward
Mean pairwise identity	91.97
Mean single sequence MFE	-25.76
Consensus MFE	-20.30
Energy contribution	-20.93
Covariance contribution	0.63
Combinations/Pair	1.03
Mean z-score	-1.90
Structure conservation index	0.79
SVM decision value	0.43
SVM RNA-class probability	0.733039
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15080462 110 + 27905053
UGUAUUUUAUUAAUUGGCACCUGUUCUUAAACUGGUUAGCUUCCAGAGGCUAAGCCAUAAAUAUUUACUUCAUUGACCUCCCGUUGGCCAACAUCCCAUGGAGCUUCCAG
.(((...((((...(((((((.(((....))).)))((((((....)))))).))))..))))..))).........((((...(((........))).))))....... ( -23.40)
>DroSec_CAF1 5393 110 + 1
UGUAUUUUAUUAAUUGGCACCUGUUCCUAAACGGGUUAGCUUCCAUAGGCUUAGCCAUAAAUAUUUACUUUAUUGACCUCCCGUUGGCCAACAUCCCAUGGAGCUUCCAG
.(((...((((...(((((((((((....))))))).((((......))))..))))..))))..))).........((((...(((........))).))))....... ( -24.30)
>DroSim_CAF1 3303 110 + 1
UGUAUUUUAUUAAUUGGCACCUGUUCCCAAACUGGUUAGCUCCCAUGGGCUAAGCCAUAAAUAUUUACUUUAUUGACCUCCCGUUGGCCAACAUCCCAUGGAGCUUCCAG
.............((((.........)))).((((..((((((.(((((....((((...........................))))......))))))))))).)))) ( -27.43)
>DroEre_CAF1 5185 109 + 1
UUCAAUUUAUUAAUUGGCACCUGUUCUGAAACUGGUUAGCUUUCAUAGGCU-AGCCAUAAAUAUUUAUUUUAUUGACCUCCCGUUGGCCAACGUGCCAUGGAGCUUCCAU
..............((((((............((((((((((....)))))-)))))...............(((.((.......)).))).))))))(((.....))). ( -27.90)
>consensus
UGUAUUUUAUUAAUUGGCACCUGUUCCUAAACUGGUUAGCUUCCAUAGGCUAAGCCAUAAAUAUUUACUUUAUUGACCUCCCGUUGGCCAACAUCCCAUGGAGCUUCCAG
.(((...((((...(((((((.(((....))).)))((((((....)))))).))))..))))..))).........((((...(((........))).))))....... (-20.30 = -20.93 +   0.63)

alignment

secondary structure

dotplot

Window 1

Location	15,080,462 – 15,080,572
Length	110
Sequences	4
Columns	110
Reading direction	reverse
Mean pairwise identity	91.97
Mean single sequence MFE	-29.73
Consensus MFE	-25.55
Energy contribution	-26.05
Covariance contribution	0.50
Combinations/Pair	1.09
Mean z-score	-2.08
Structure conservation index	0.86
SVM decision value	1.18
SVM RNA-class probability	0.926962
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15080462 110 - 27905053
CUGGAAGCUCCAUGGGAUGUUGGCCAACGGGAGGUCAAUGAAGUAAAUAUUUAUGGCUUAGCCUCUGGAAGCUAACCAGUUUAAGAACAGGUGCCAAUUAAUAAAAUACA
.(((.(((((((.(((..(((((((.......))))))).((((...........))))..))).))).)))).(((.(((....))).))).))).............. ( -25.70)
>DroSec_CAF1 5393 110 - 1
CUGGAAGCUCCAUGGGAUGUUGGCCAACGGGAGGUCAAUAAAGUAAAUAUUUAUGGCUAAGCCUAUGGAAGCUAACCCGUUUAGGAACAGGUGCCAAUUAAUAAAAUACA
.(((.(((((((((((...((((((..(....)....(((((.......))))))))))).))))))).)))).(((.(((....))).))).))).............. ( -31.00)
>DroSim_CAF1 3303 110 - 1
CUGGAAGCUCCAUGGGAUGUUGGCCAACGGGAGGUCAAUAAAGUAAAUAUUUAUGGCUUAGCCCAUGGGAGCUAACCAGUUUGGGAACAGGUGCCAAUUAAUAAAAUACA
((((.(((((((((((.((((((((.......))))))))((((...........))))..))))).))))))..)))).((((.(.....).))))............. ( -34.20)
>DroEre_CAF1 5185 109 - 1
AUGGAAGCUCCAUGGCACGUUGGCCAACGGGAGGUCAAUAAAAUAAAUAUUUAUGGCU-AGCCUAUGAAAGCUAACCAGUUUCAGAACAGGUGCCAAUUAAUAAAUUGAA
.(((.....)))(((((((((((((.......)))))))..............(((.(-(((........)))).)))............)))))).............. ( -28.00)
>consensus
CUGGAAGCUCCAUGGGAUGUUGGCCAACGGGAGGUCAAUAAAGUAAAUAUUUAUGGCUUAGCCUAUGGAAGCUAACCAGUUUAAGAACAGGUGCCAAUUAAUAAAAUACA
.(((.(((((((((((.((((((((.......))))))))..((((....)))).......))))))).)))).(((.(((....))).))).))).............. (-25.55 = -26.05 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:04:44 2006