Locus 1084

Sequence ID	2L_DroMel_CAF1
Location	2,993,064 – 2,993,224
Length	160
Max. P	0.970882

overview

Window 5

Location	2,993,064 – 2,993,184
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	96.25
Mean single sequence MFE	-43.17
Consensus MFE	-41.08
Energy contribution	-41.57
Covariance contribution	0.50
Combinations/Pair	1.02
Mean z-score	-2.11
Structure conservation index	0.95
SVM decision value	1.27
SVM RNA-class probability	0.938624
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2993064 120 - 22407834
UCCGCAGAUUUGCGGACUAGAUUUGCGUUCUUGCAGCACGAAAUUCGCGCUUUUGGCGCGGGUUUUGAAGUCAAGAAAGGGAAGGCAGUCCGGCCCGCACUUUAUUGCCUCAUUUUGCAC
...(((((..((.((....((..(((.((((((.....((((((((((((.....))))))))))))....)))))).(((..((....))..))))))..))....)).)).))))).. ( -41.90)
>DroSec_CAF1 4835 120 - 1
UCCGCAGAUUUGCGGACUAGAUUUGCGUUCUUGCAGCUCGAAAUUCGCGCAUUUGGCGCGAGUUUUGGAGUCAAGAAAGGGAAGGCAGUCCGGCCCGCACUUUAUUGCCUCAUUUUGCAC
...(((((..((.((....((..(((.((((((..(((((((((((((((.....))))))))))).)))))))))).(((..((....))..))))))..))....)).)).))))).. ( -45.30)
>DroSim_CAF1 4809 120 - 1
UCCGCAGAUUUGCGGACUAGAUUUGCGUUCUUGCAGCUCGAAAUUCGCGCAUUUGGCGCGAGUUUUGGAGUCAAGAAAGGGAAGGCAGUCCGGCCCGCACUUUAUUGCCUCAUUUUGCAC
...(((((..((.((....((..(((.((((((..(((((((((((((((.....))))))))))).)))))))))).(((..((....))..))))))..))....)).)).))))).. ( -45.30)
>DroYak_CAF1 4835 120 - 1
UCCGCAAAUUUGCGGACUAGAUUUGCGUUCUUGCAGCUCGAAAUUCGCGCUUUUGGCGCGGGAUUUUAAGUCAAGAAAGGGAAGGCAGUCCGGCCCACACUUUAUUGCCUCAUUUUGCAC
((((((....)))))).......(((..(((((..(((..((((((((((.....)))).))))))..))))))))((((..(((((((..((......))..)))))))..))))))). ( -40.20)
>consensus
UCCGCAGAUUUGCGGACUAGAUUUGCGUUCUUGCAGCUCGAAAUUCGCGCAUUUGGCGCGAGUUUUGAAGUCAAGAAAGGGAAGGCAGUCCGGCCCGCACUUUAUUGCCUCAUUUUGCAC
((((((....)))))).......(((..(((((..(((((((((((((((.....)))))))))))).))))))))((((..(((((((..((......))..)))))))..))))))). (-41.08 = -41.57 +   0.50)

alignment

secondary structure

dotplot

Window 6

Location	2,993,104 – 2,993,224
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	96.67
Mean single sequence MFE	-31.73
Consensus MFE	-29.55
Energy contribution	-29.55
Covariance contribution	0.00
Combinations/Pair	1.03
Mean z-score	-2.09
Structure conservation index	0.93
SVM decision value	1.02
SVM RNA-class probability	0.901295
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2993104 120 + 22407834
CCUUUCUUGACUUCAAAACCCGCGCCAAAAGCGCGAAUUUCGUGCUGCAAGAACGCAAAUCUAGUCCGCAAAUCUGCGGAAGUGUUGGUACUACCACUUAAUUGUAUUUGUAAUUGUAAU
...((((((.(..((.....(((((.....))))).......))..))))))).((((((.(((((((((....)))))(((((.((....)).))))).)))).))))))......... ( -28.90)
>DroSec_CAF1 4875 120 + 1
CCUUUCUUGACUCCAAAACUCGCGCCAAAUGCGCGAAUUUCGAGCUGCAAGAACGCAAAUCUAGUCCGCAAAUCUGCGGAAGUGUUGGUACUACCACUUAAUUGUAUUUGUAAUUGUAAU
...((((((.(((..(((.((((((.....)))))).))).)))...)))))).((((((.(((((((((....)))))(((((.((....)).))))).)))).))))))......... ( -33.00)
>DroSim_CAF1 4849 120 + 1
CCUUUCUUGACUCCAAAACUCGCGCCAAAUGCGCGAAUUUCGAGCUGCAAGAACGCAAAUCUAGUCCGCAAAUCUGCGGAAGUGUUGGUACUACCACUUAAUUGUAUUUGUAAUUGUAAU
...((((((.(((..(((.((((((.....)))))).))).)))...)))))).((((((.(((((((((....)))))(((((.((....)).))))).)))).))))))......... ( -33.00)
>DroYak_CAF1 4875 120 + 1
CCUUUCUUGACUUAAAAUCCCGCGCCAAAAGCGCGAAUUUCGAGCUGCAAGAACGCAAAUCUAGUCCGCAAAUUUGCGGAAGUGUUGGUACUACCACUUAAUUGUAUUUGUAAUUGUAAU
...((((((.((..((((..(((((.....))))).))))..))...)))))).((((((.(((((((((....)))))(((((.((....)).))))).)))).))))))......... ( -32.00)
>consensus
CCUUUCUUGACUCCAAAACCCGCGCCAAAAGCGCGAAUUUCGAGCUGCAAGAACGCAAAUCUAGUCCGCAAAUCUGCGGAAGUGUUGGUACUACCACUUAAUUGUAUUUGUAAUUGUAAU
...((((((.(((.(((...(((((.....)))))..))).)))...)))))).((((((.(((((((((....)))))(((((.((....)).))))).)))).))))))......... (-29.55 = -29.55 +   0.00)

alignment

secondary structure

dotplot

Window 7

Location	2,993,104 – 2,993,224
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	96.67
Mean single sequence MFE	-36.03
Consensus MFE	-34.71
Energy contribution	-35.02
Covariance contribution	0.31
Combinations/Pair	1.05
Mean z-score	-2.42
Structure conservation index	0.96
SVM decision value	1.67
SVM RNA-class probability	0.970882
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2993104 120 - 22407834
AUUACAAUUACAAAUACAAUUAAGUGGUAGUACCAACACUUCCGCAGAUUUGCGGACUAGAUUUGCGUUCUUGCAGCACGAAAUUCGCGCUUUUGGCGCGGGUUUUGAAGUCAAGAAAGG
..(((.(((((............))))).)))((......(((((......)))))((.((((((((....)))....((((((((((((.....))))))))))))))))).))...)) ( -34.90)
>DroSec_CAF1 4875 120 - 1
AUUACAAUUACAAAUACAAUUAAGUGGUAGUACCAACACUUCCGCAGAUUUGCGGACUAGAUUUGCGUUCUUGCAGCUCGAAAUUCGCGCAUUUGGCGCGAGUUUUGGAGUCAAGAAAGG
..(((.(((((............))))).)))((........((((((((((.....))))))))))((((((..(((((((((((((((.....))))))))))).)))))))))).)) ( -38.00)
>DroSim_CAF1 4849 120 - 1
AUUACAAUUACAAAUACAAUUAAGUGGUAGUACCAACACUUCCGCAGAUUUGCGGACUAGAUUUGCGUUCUUGCAGCUCGAAAUUCGCGCAUUUGGCGCGAGUUUUGGAGUCAAGAAAGG
..(((.(((((............))))).)))((........((((((((((.....))))))))))((((((..(((((((((((((((.....))))))))))).)))))))))).)) ( -38.00)
>DroYak_CAF1 4875 120 - 1
AUUACAAUUACAAAUACAAUUAAGUGGUAGUACCAACACUUCCGCAAAUUUGCGGACUAGAUUUGCGUUCUUGCAGCUCGAAAUUCGCGCUUUUGGCGCGGGAUUUUAAGUCAAGAAAGG
..(((.(((((............))))).)))((........((((((((((.....))))))))))((((((..(((..((((((((((.....)))).))))))..))))))))).)) ( -33.20)
>consensus
AUUACAAUUACAAAUACAAUUAAGUGGUAGUACCAACACUUCCGCAGAUUUGCGGACUAGAUUUGCGUUCUUGCAGCUCGAAAUUCGCGCAUUUGGCGCGAGUUUUGAAGUCAAGAAAGG
..(((.(((((............))))).)))((........((((((((((.....))))))))))((((((..(((((((((((((((.....)))))))))))).))))))))).)) (-34.71 = -35.02 +   0.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:53:08 2006