Locus 3425

Sequence ID	3L_DroMel_CAF1
Location	10,052,619 – 10,052,723
Length	104
Max. P	0.975419

overview

Window 3

Location	10,052,619 – 10,052,723
Length	104
Sequences	5
Columns	114
Reading direction	forward
Mean pairwise identity	79.21
Mean single sequence MFE	-28.58
Consensus MFE	-21.70
Energy contribution	-22.02
Covariance contribution	0.32
Combinations/Pair	1.10
Mean z-score	-1.45
Structure conservation index	0.76
SVM decision value	0.26
SVM RNA-class probability	0.658728
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10052619 104 + 23771897
----------UGUAUUGAAUUGAAUUAUUUUUAACUUGAAUAUGUAUUUAAGGCCAUCUACACGGUUGAAUACGGAACUUCGAUGUUGCCGUGAAACAUCGCUAGAUGGCGCUA
----------........................(((((((....)))))))((((((((..((((....((((((((......))).)))))....)))).)))))))).... ( -27.20)
>DroSec_CAF1 97383 114 + 1
UGUGCUCAAUUUUCUUGAAUUGAAUUAUCUUUAACUUGUAAAGGUAUUUAAGGCCAUCUACACGGUUGAACACGGAACUUCGCUGUUGCCGUGAAACAUCGCUAGAUGGCGCUU
...(((((((((....)))))))..((((((((.....))))))))......((((((((..((((....((((((((......))).)))))....)))).)))))))))).. ( -34.80)
>DroSim_CAF1 107365 114 + 1
UGUGCUCAUUUAUCUUGAAUUGAAUUACCUUUAACCUGUAAAGGUAUUUAAGGCCAUCUACACGGUUGAACACGGAACUUCGCUGUUGCCGUGAAACAUCGCUAGAUGGCGCUU
...((........((((((......((((((((.....))))))))))))))((((((((..((((....((((((((......))).)))))....)))).)))))))))).. ( -35.40)
>DroEre_CAF1 101883 107 + 1
UUUCCUUUCUUAUCUGCAAUUGAAUUAAAUUGAGUUUGAACGG-------UGGCCACCUACACGGUUGAAUAAGGAACUUCCGUGUUGCCGUGAAACACCGCUAGAUGGCGCUU
...((.(((....((.(((((......)))))))...))).))-------..((((.(((((((((..((((.((.....)).)))))))))).........))).)))).... ( -24.80)
>DroYak_CAF1 102362 114 + 1
UUUCCGUUUUUAUUUUUAAUUGAAUUAUCUUGAACUUGAAUAGGUAUUUGAGGCCACCUAUACGGUUGAACAAGGAACUUGUGUGUUGCCAUGAAACACCGCUAGAUGGCGCAU
..................................((..(((....)))..))((((.(((..((((....((.(((((......))).)).))....)))).))).)))).... ( -20.70)
>consensus
UGUCCUCAUUUAUCUUGAAUUGAAUUAUCUUUAACUUGAAAAGGUAUUUAAGGCCAUCUACACGGUUGAACACGGAACUUCGCUGUUGCCGUGAAACAUCGCUAGAUGGCGCUU
....................................................((((((((..((((....((((((((......))).)))))....)))).)))))))).... (-21.70 = -22.02 +   0.32)

alignment

secondary structure

dotplot

Window 4

Location	10,052,619 – 10,052,723
Length	104
Sequences	5
Columns	114
Reading direction	reverse
Mean pairwise identity	79.21
Mean single sequence MFE	-27.74
Consensus MFE	-20.46
Energy contribution	-21.02
Covariance contribution	0.56
Combinations/Pair	1.05
Mean z-score	-2.25
Structure conservation index	0.74
SVM decision value	1.75
SVM RNA-class probability	0.975419
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10052619 104 - 23771897
UAGCGCCAUCUAGCGAUGUUUCACGGCAACAUCGAAGUUCCGUAUUCAACCGUGUAGAUGGCCUUAAAUACAUAUUCAAGUUAAAAAUAAUUCAAUUCAAUACA----------
.((.(((((((((((.((..(.((((.(((......))))))))..))..))).))))))))))........................................---------- ( -21.10)
>DroSec_CAF1 97383 114 - 1
AAGCGCCAUCUAGCGAUGUUUCACGGCAACAGCGAAGUUCCGUGUUCAACCGUGUAGAUGGCCUUAAAUACCUUUACAAGUUAAAGAUAAUUCAAUUCAAGAAAAUUGAGCACA
..(((((((((((((.((...(((((.(((......))))))))..))..))).)))))))).........(((((.....))))).....((((((......))))))))... ( -30.60)
>DroSim_CAF1 107365 114 - 1
AAGCGCCAUCUAGCGAUGUUUCACGGCAACAGCGAAGUUCCGUGUUCAACCGUGUAGAUGGCCUUAAAUACCUUUACAGGUUAAAGGUAAUUCAAUUCAAGAUAAAUGAGCACA
..(((((((((((((.((...(((((.(((......))))))))..))..))).))))))))......((((((((.....))))))))....................))... ( -34.30)
>DroEre_CAF1 101883 107 - 1
AAGCGCCAUCUAGCGGUGUUUCACGGCAACACGGAAGUUCCUUAUUCAACCGUGUAGGUGGCCA-------CCGUUCAAACUCAAUUUAAUUCAAUUGCAGAUAAGAAAGGAAA
..(.(((((((.((.(((...))).)).((((((..(.........)..)))))))))))))).-------((.(((...(((((((......))))).))....))).))... ( -28.40)
>DroYak_CAF1 102362 114 - 1
AUGCGCCAUCUAGCGGUGUUUCAUGGCAACACACAAGUUCCUUGUUCAACCGUAUAGGUGGCCUCAAAUACCUAUUCAAGUUCAAGAUAAUUCAAUUAAAAAUAAAAACGGAAA
....(((((((((((((....((.((.(((......))))).))....))))).)))))))).................................................... ( -24.30)
>consensus
AAGCGCCAUCUAGCGAUGUUUCACGGCAACACCGAAGUUCCGUGUUCAACCGUGUAGAUGGCCUUAAAUACCUAUUCAAGUUAAAGAUAAUUCAAUUCAAGAUAAAAAAGCAAA
....(((((((((((......(((((.(((......))))))))......))).)))))))).................................................... (-20.46 = -21.02 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:57:52 2006