Locus 3915

Sequence ID	3R_DroMel_CAF1
Location	10,659,160 – 10,659,340
Length	180
Max. P	0.882971

overview

Window 0

Location	10,659,160 – 10,659,279
Length	119
Sequences	3
Columns	119
Reading direction	forward
Mean pairwise identity	97.76
Mean single sequence MFE	-38.57
Consensus MFE	-36.39
Energy contribution	-36.50
Covariance contribution	0.11
Combinations/Pair	1.03
Mean z-score	-1.76
Structure conservation index	0.94
SVM decision value	0.31
SVM RNA-class probability	0.681813
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10659160 119 + 27905053
UGUCCUGGCGCCCAAAUUCUACGCUCUGCGGGCUUAUGCAAAUAAGCAACUAAUUAAACUGAUGUAAAUCAGCUGCGUCCUUCGUUUGGGAUCCAGAUGGGGUCCUCAUUUUGGACGCU
....((((..(((((((...((((...((..((((((....))))))............((((....)))))).)))).....)))))))..))))..((.((((.......)))).)) ( -38.20)
>DroSec_CAF1 823 119 + 1
UGUCCUGGCGCCCAAAUUCUCCGCUCUGCGGGCCUAUGCAAAUAAGCAACUAAUUAAACUGAUGUAAAUCAGCUGCGUCCUUCGUUUGGGAUCCGGAUGGGGUCCCCAUUUUGGACGCU
.....(((.((((................)))))))(((......)))..........(((((....)))))..((((((.......(((((((.....)))))))......)))))). ( -37.41)
>DroSim_CAF1 836 119 + 1
UGUCCUGGCGCCCAAAUUCUCCGCUCUGCGGGCUUAUGCAAAUAAGCAACUAAUUAAACUGAUGUAAAUCAGCUGCGUCCUUCGUUUGGGAUCCGGAUGGGGUCCCCAUUUUGGACGCU
.((((.(((((.........((((...))))((((((....))))))...........(((((....)))))..)))))........(((((((.....)))))))......))))... ( -40.10)
>consensus
UGUCCUGGCGCCCAAAUUCUCCGCUCUGCGGGCUUAUGCAAAUAAGCAACUAAUUAAACUGAUGUAAAUCAGCUGCGUCCUUCGUUUGGGAUCCGGAUGGGGUCCCCAUUUUGGACGCU
......((((.(((((...........((((((((((....))))))...........(((((....)))))))))...........(((((((.....)))))))...))))).)))) (-36.39 = -36.50 +   0.11)

alignment

secondary structure

dotplot

Window 1

Location	10,659,160 – 10,659,279
Length	119
Sequences	3
Columns	119
Reading direction	reverse
Mean pairwise identity	97.76
Mean single sequence MFE	-39.23
Consensus MFE	-36.47
Energy contribution	-36.80
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-2.04
Structure conservation index	0.93
SVM decision value	0.61
SVM RNA-class probability	0.799235
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10659160 119 - 27905053
AGCGUCCAAAAUGAGGACCCCAUCUGGAUCCCAAACGAAGGACGCAGCUGAUUUACAUCAGUUUAAUUAGUUGCUUAUUUGCAUAAGCCCGCAGAGCGUAGAAUUUGGGCGCCAGGACA
.(((((((((.((.(((.((.....)).))))).(((......((((((((((.((....))..))))))))))...(((((........))))).)))....)))))))))....... ( -36.90)
>DroSec_CAF1 823 119 - 1
AGCGUCCAAAAUGGGGACCCCAUCCGGAUCCCAAACGAAGGACGCAGCUGAUUUACAUCAGUUUAAUUAGUUGCUUAUUUGCAUAGGCCCGCAGAGCGGAGAAUUUGGGCGCCAGGACA
.((((((((((((((((.((.....)).))))...((((.((.((((((((((.((....))..)))))))))))).)))))))....((((...))))....)))))))))....... ( -40.40)
>DroSim_CAF1 836 119 - 1
AGCGUCCAAAAUGGGGACCCCAUCCGGAUCCCAAACGAAGGACGCAGCUGAUUUACAUCAGUUUAAUUAGUUGCUUAUUUGCAUAAGCCCGCAGAGCGGAGAAUUUGGGCGCCAGGACA
.((((((((((((((((.((.....)).))))...((((.((.((((((((((.((....))..)))))))))))).)))))))....((((...))))....)))))))))....... ( -40.40)
>consensus
AGCGUCCAAAAUGGGGACCCCAUCCGGAUCCCAAACGAAGGACGCAGCUGAUUUACAUCAGUUUAAUUAGUUGCUUAUUUGCAUAAGCCCGCAGAGCGGAGAAUUUGGGCGCCAGGACA
.(((((((((...((((.((.....)).))))...((......((((((((((.((....))..))))))))))...(((((........))))).)).....)))))))))....... (-36.47 = -36.80 +   0.33)

alignment

secondary structure

dotplot

Window 2

Location	10,659,240 – 10,659,340
Length	100
Sequences	3
Columns	100
Reading direction	forward
Mean pairwise identity	96.00
Mean single sequence MFE	-40.13
Consensus MFE	-38.17
Energy contribution	-38.73
Covariance contribution	0.56
Combinations/Pair	1.06
Mean z-score	-2.08
Structure conservation index	0.95
SVM decision value	0.92
SVM RNA-class probability	0.882971
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10659240 100 + 27905053
UUCGUUUGGGAUCCAGAUGGGGUCCUCAUUUUGGACGCUUGGACGCUUGGCCGUGUGACCUUUUGGGCCAGAUCGAACACCUGGUCCAAUCCCAGGCCAU
..((((..((.((((((((((...)))).))))))..))..))))..(((((.((.((....(((((((((.........))))))))))).))))))). ( -39.00)
>DroSec_CAF1 903 100 + 1
UUCGUUUGGGAUCCGGAUGGGGUCCCCAUUUUGGACGCUUGGACGCUUGGCCGUGUGACCUUUUGGGCCAAAUCGAACACCUGGUCCAAAGGCAGGCCAU
..((((..((.((((((((((...)))).))))))..))..))))..(((((...((.(((((.((((((...........)))))))))))))))))). ( -40.70)
>DroSim_CAF1 916 100 + 1
UUCGUUUGGGAUCCGGAUGGGGUCCCCAUUUUGGACGCUUGGACGCUUGGCCGUGUGACCUUUUGGGCCAAAUCGAACACCUGGUCCAAAGGCAGGCCAU
..((((..((.((((((((((...)))).))))))..))..))))..(((((...((.(((((.((((((...........)))))))))))))))))). ( -40.70)
>consensus
UUCGUUUGGGAUCCGGAUGGGGUCCCCAUUUUGGACGCUUGGACGCUUGGCCGUGUGACCUUUUGGGCCAAAUCGAACACCUGGUCCAAAGGCAGGCCAU
..((((..((.((((((((((...)))).))))))..))..))))..(((((.((....(((((((((((...........)))))))))))))))))). (-38.17 = -38.73 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:13:17 2006