Locus 149

Sequence ID	4_DroMel_CAF1
Location	985,635 – 985,890
Length	255
Max. P	0.966873

overview

Window 6

Location	985,635 – 985,755
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.67
Mean single sequence MFE	-37.03
Consensus MFE	-32.32
Energy contribution	-32.92
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-1.68
Structure conservation index	0.87
SVM decision value	1.32
SVM RNA-class probability	0.941656
Prediction	RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 985635 120 + 1281640
CGCUCCGCUUCCCUGCGGGUAAUCAUGCCACAUCGUCGGGAACUCACUGGCAUGGCGCCAGCUCUUCUCAAUAUUUCCAAUUGCACGGGUGUACAUUGUACACAAGUAAUGCCAAGAGCA
((((((((......)))))....(((((((....((.....))....))))))))))...((((((..((.(((((((........))((((((...))))))))))).))..)))))). ( -36.90)
>DroSec_CAF1 18618 120 + 1
CGCUCCGCUUCCCUGCGGGUAAUCAUGCCACAUCGUCGGGAACUCACUGGCAUGGCGCCCGCUCUCCUCAAUAUUUCCAAUUGCACGGGUGUACAUUGUACACCAGUAAUGCCAAGAGCG
(((((.((......((((((..((((((((....((.....))....)))))))).)))))).................(((((...(((((((...))))))).)))))))...))))) ( -41.30)
>DroSim_CAF1 16262 120 + 1
CGCUCCGCUUCCCUGCGGGUAAUCAUGCCACAUCGUCGGGAACUCACUGGCAUGGCGCCCGCUCUCCUCAAUAUUUCCAAUUGCACGGGUGUACAUUGUACACAAGUAAUGCCAAGAGCG
(((((.((......((((((..((((((((....((.....))....)))))))).)))))).................(((((....((((((...))))))..)))))))...))))) ( -37.70)
>DroEre_CAF1 19462 120 + 1
CGCUCCGCUUCCCUUCGGGUUAUCAUGCCACAUCGUCGGGAACUCACUGGCAUGGCGCCAGCUCUUCUCAAUAUUUCCAAUUGCACGGGUGUACAUUGUACACAAGUAAUGCCCAGAGCA
.((((.(((((((..(((((......)))....))..)))))....(((((.....))))).....................))..((((((((.(((....))))).)))))).)))). ( -35.10)
>DroYak_CAF1 19807 120 + 1
CGCUCCGCUUCUCUGCGGGUUAUCAUGCCACAUCGUCGUGAACUUACUGGCAUUGCGCCAGCUCUUCUCAAUAUUUCCAAUUGCACGGGUGUACAUUGUACACAAGUAAUGCCAAGAGCA
.(((((((......))).....(((((.(.....).)))))......(((((((((.((.((....................))..))((((((...))))))..))))))))).)))). ( -34.15)
>consensus
CGCUCCGCUUCCCUGCGGGUAAUCAUGCCACAUCGUCGGGAACUCACUGGCAUGGCGCCAGCUCUUCUCAAUAUUUCCAAUUGCACGGGUGUACAUUGUACACAAGUAAUGCCAAGAGCA
((((((((......)))))....(((((((....((.....))....))))))))))...(((((...((.(((((((........))((((((...))))))))))).))...))))). (-32.32 = -32.92 +   0.60)

alignment

secondary structure

dotplot

Window 7

Location	985,715 – 985,835
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.33
Mean single sequence MFE	-31.15
Consensus MFE	-25.86
Energy contribution	-26.22
Covariance contribution	0.36
Combinations/Pair	1.13
Mean z-score	-1.96
Structure conservation index	0.83
SVM decision value	1.60
SVM RNA-class probability	0.966873
Prediction	RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 985715 120 - 1281640
CAAGAGCGCCUUUGCUUGGCGCAAAUUUCAAAUACAUUACUAAAACAAUUCAGUUACAACGAGAUACACAACAGGAGAGUUGCUCUUGGCAUUACUUGUGUACAAUGUACACCCGUGCAA
((((((((.((((.((((......(((((...((......)).(((......))).....)))))......)))))))).))))))))((((.....((((((...))))))..)))).. ( -27.40)
>DroSec_CAF1 18698 120 - 1
CAGGAGCGCCUGUGCUGGGGGCAAAUAUCAGAUUCUUUUCUAAAGCAAUUCAGUGUCAACGAGAUACACAACAGGAGAGUCGCUCUUGGCAUUACUGGUGUACAAUGUACACCCGUGCAA
((((((((.((.(.(((..(.........(((......)))...........(((((.....))))).)..))).).)).))))))))((((....(((((((...))))))).)))).. ( -40.20)
>DroSim_CAF1 16342 120 - 1
CAAGAGCGCCUUUGCUUGGCGCAAAUAUCAAAUACAUUACUAAAACAAUUCAGUUACAACGAGAUACACAACAGGAGAGUCGCUCUUGGCAUUACUUGUGUACAAUGUACACCCGUGCAA
((((((((.((((.((((.......((((.........(((.((....)).)))........)))).....)))))))).))))))))((((.....((((((...))))))..)))).. ( -28.33)
>DroEre_CAF1 19542 120 - 1
CAAGAGCGCCUUUGCUUGGCGCAAAUCUCAAAUACAUUACUGAAACAAUUUAGUUAUAACGAGAUACAUAACAGGAGAGUUGCUCUGGGCAUUACUUGUGUACAAUGUACACCCGUGCAA
.....((((...((((..(.((((.((((.........((((((....))))))............(......))))).)))).)..))))......((((((...))))))..)))).. ( -30.80)
>DroYak_CAF1 19887 120 - 1
CAAGAGCGCCUUUGUUUGGCGCAAAUCUCAAAUACAUUAUUAAAACAAUUCAGUUAUAACGAGAUACACAACAGGAGAGUUGCUCUUGGCAUUACUUGUGUACAAUGUACACCCGUGCAA
.....(((((.......)))))..(((((.((((...))))..(((......))).....)))))......((((((.....))))))((((.....((((((...))))))..)))).. ( -29.00)
>consensus
CAAGAGCGCCUUUGCUUGGCGCAAAUAUCAAAUACAUUACUAAAACAAUUCAGUUACAACGAGAUACACAACAGGAGAGUUGCUCUUGGCAUUACUUGUGUACAAUGUACACCCGUGCAA
((((((((.((((.((((......(((((...............................)))))......)))))))).))))))))((((.....((((((...))))))..)))).. (-25.86 = -26.22 +   0.36)

alignment

secondary structure

dotplot

Window 8

Location	985,795 – 985,890
Length	95
Sequences	4
Columns	95
Reading direction	forward
Mean pairwise identity	97.02
Mean single sequence MFE	-25.95
Consensus MFE	-24.81
Energy contribution	-24.62
Covariance contribution	-0.19
Combinations/Pair	1.05
Mean z-score	-1.92
Structure conservation index	0.96
SVM decision value	0.82
SVM RNA-class probability	0.859191
Prediction	RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 985795 95 + 1281640
GUAAUGUAUUUGAAAUUUGCGCCAAGCAAAGGCGCUCUUGACCUUCAAUGUGCAGGGAUACAAUCUGCACUCCGUACAGCAAAACGGAGCUUACC
((((.((..(((((.((.(((((.......)))))....))..))))).(((((((.......)))))))(((((........))))))))))). ( -26.90)
>DroSim_CAF1 16422 95 + 1
GUAAUGUAUUUGAUAUUUGCGCCAAGCAAAGGCGCUCUUGACCUUCAAUGUGCAAGGAUACAAUCUGCACUCCGUACAGCAAAACGGAGCUAACC
(((.((((((........(((((.......))))).((((..(......)..))))))))))...))).((((((........))))))...... ( -25.20)
>DroEre_CAF1 19622 95 + 1
GUAAUGUAUUUGAGAUUUGCGCCAAGCAAAGGCGCUCUUGACCUUCAAUGUGCAAGGAUACAAUCUGCACUCCGUACAGCAAAACGGAGCUAACC
(((.((((((..(((...(((((.......))))))))..)(((((.....).)))))))))...))).((((((........))))))...... ( -26.10)
>DroYak_CAF1 19967 95 + 1
AUAAUGUAUUUGAGAUUUGCGCCAAACAAAGGCGCUCUUGACCUUCAAUGUGCAAGGAUACAAUCUGCACUCCGUACAGCAAAACGGAGCUAACC
....((((((..(((...(((((.......))))))))..)(((((.....).))))))))).......((((((........))))))...... ( -25.60)
>consensus
GUAAUGUAUUUGAGAUUUGCGCCAAGCAAAGGCGCUCUUGACCUUCAAUGUGCAAGGAUACAAUCUGCACUCCGUACAGCAAAACGGAGCUAACC
....((((((........(((((.......))))).((((..(......)..)))))))))).......((((((........))))))...... (-24.81 = -24.62 +  -0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:37:11 2006