Locus 2177

Sequence ID	2L_DroMel_CAF1
Location	5,883,217 – 5,883,442
Length	225
Max. P	0.690080

overview

Window 4

Location	5,883,217 – 5,883,322
Length	105
Sequences	5
Columns	105
Reading direction	forward
Mean pairwise identity	90.95
Mean single sequence MFE	-27.08
Consensus MFE	-19.67
Energy contribution	-20.39
Covariance contribution	0.72
Combinations/Pair	1.10
Mean z-score	-2.06
Structure conservation index	0.73
SVM decision value	0.33
SVM RNA-class probability	0.690080
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5883217 105 + 22407834
CCGUCUAUACUACAUGGGAAAGUCAGUGCCCAUGAAUUCUACUAAGAAAAUAUUUCGUUGGAGCCCAGAACUUAUGGGUAUAGGUUUCUUUAAUAAACUUGGAAA
...((((........((((((.((.((((((((((.((((.(((((((.....))).)))).....)))).)))))))))).)))))))).........)))).. ( -23.53)
>DroSec_CAF1 73159 105 + 1
CCGUCUAUACUACAUGGGAAAGUCAGUGCCCAUGAAUUCCACUAAAAAAAUAUUGUGUUGGGGCACAGAACUUAUGGGUAUGGGUUUCUUUAAUAAACUUGAAAA
...((((((((.((((((....((.((((((........(((............)))...)))))).)).))))))))))))))..................... ( -24.40)
>DroSim_CAF1 74004 105 + 1
CCGUCUAUACUACAUGGGAAAGUCAGUGCCCAUGAAUUCUACUAAGAAAAUAUUGUGUUGGGGCACAGAACUCAUGGGUAUGGGUUUCUUUAAUAAACUUGGAAA
...((((........((((((.(((.(((((((((.((((....))))....((((((....))))))...)))))))))))).)))))).........)))).. ( -30.13)
>DroEre_CAF1 96972 105 + 1
CCGUCUAUACUGCAUGAGAAACCCAGAGCCCAUGAGUUCUACUAAGAAAAUAUUGAGUUGCGGCACAGAAAUGAUGGGUAUGGGUUUCUUUAAUAAACUUGGAAA
...((((........((((((((((..((((((...((((....)))).................((....)))))))).)))))))))).........)))).. ( -28.73)
>DroYak_CAF1 98826 105 + 1
CCGUCUAUACUACAUGAGAAACGCAGUGCCCAUGAAUUCUACUCAGAAAAUAUUAAGUUGGGCCACAGAAAUUAUGGGUAUGGGUUUCUUUAAUAAACUUGGAAA
...((((........(((((((.((.(((((((((.((((.(((((...........)))))....)))).))))))))))).))))))).........)))).. ( -28.63)
>consensus
CCGUCUAUACUACAUGGGAAAGUCAGUGCCCAUGAAUUCUACUAAGAAAAUAUUGAGUUGGGGCACAGAACUUAUGGGUAUGGGUUUCUUUAAUAAACUUGGAAA
...((((........((((((.(((.(((((((((.((((........(((.....))).......)))).)))))))))))).)))))).........)))).. (-19.67 = -20.39 +   0.72)

alignment

secondary structure

dotplot

Window 5

Location	5,883,322 – 5,883,442
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.83
Mean single sequence MFE	-30.81
Consensus MFE	-26.03
Energy contribution	-25.95
Covariance contribution	-0.08
Combinations/Pair	1.07
Mean z-score	-1.35
Structure conservation index	0.84
SVM decision value	0.02
SVM RNA-class probability	0.544855
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5883322 120 - 22407834
CAUAUUGCCCACGCUCCUACUCUCCGUCAAAACAAAUAACUUUUCCAAUGAUUGUAUGGCUUUUACUGCUUUCCAUAUUCCGUGUGGAGUUGCGGAGUUUACUGAGCGCUGUGCGUUGCA
......((.(((((((.....((((((((..((((................)))).)))).......((.((((((((...))))))))..))))))......))))).)).))...... ( -29.49)
>DroSec_CAF1 73264 120 - 1
CAUAUCGCCCACGCUCCUACUCUCCGUCAAAACAAAUAACUUUUCCAAUGAUUGUAUGGCUUUUACUGCUUUCCAUAUUCCGUGUGGAGUUGCGGAGUUUACGGAGCGUUGUGCGUUGCA
.....((((.(((((((((..((((((((..((((................)))).)))).......((.((((((((...))))))))..))))))..)).))))))).).)))..... ( -35.99)
>DroSim_CAF1 74109 120 - 1
CAUAUCGCCCACGCUCCUACUCUCCGUCAAAACAAAUAACUUUUCCAAUGAUUGUAUGUCUUUUACUGCUUUCCAUAUUCCGUGNGGAGUUGCGGAGUUUACGGAGCGUUGUGCGUUGCA
.....((((.(((((((((..((((((......................((..(((.((.....)))))..))...(((((....))))).))))))..)).))))))).).)))..... ( -31.70)
>DroEre_CAF1 97077 120 - 1
CAUAUCGCCCACGCUCCUACGCCCCGUCAAAACAAAUAACUUUUCCAAUGAUUGUAUGGCUUUUACUGCUUUCCAUAUUCCGUGUGGAGUUGCAGAGUUUACUGAGCGCUGUGCGUUGCA
.....(((.(((((((....((((.((((....(((.....)))....)))).)...))).....((((.((((((((...))))))))..))))........))))).)).)))..... ( -29.60)
>DroYak_CAF1 98931 120 - 1
CAUAUUGCCCACGCUCCCACUCUCCGUCAAAACAAAUAACUUUUCCAAUGAUUGUAUGGCUUUUACUGCUUUCCAUAUUCCGUGUGGAGUUGCAGAGUUUACCGAGCGCUGUGCGCUGCA
......((.(((((((.........((((..((((................)))).)))).....((((.((((((((...))))))))..))))........))))).)).))...... ( -27.29)
>consensus
CAUAUCGCCCACGCUCCUACUCUCCGUCAAAACAAAUAACUUUUCCAAUGAUUGUAUGGCUUUUACUGCUUUCCAUAUUCCGUGUGGAGUUGCGGAGUUUACGGAGCGCUGUGCGUUGCA
.....(((.(((((((.........((((..((((................)))).)))).....((((.((((((((...))))))))..))))........))))).)).)))..... (-26.03 = -25.95 +  -0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:21:31 2006