Locus 5519

Sequence ID	X_DroMel_CAF1
Location	14,285,539 – 14,285,686
Length	147
Max. P	0.781721

overview

Window 5

Location	14,285,539 – 14,285,646
Length	107
Sequences	4
Columns	110
Reading direction	forward
Mean pairwise identity	94.93
Mean single sequence MFE	-31.35
Consensus MFE	-27.59
Energy contribution	-27.65
Covariance contribution	0.06
Combinations/Pair	1.04
Mean z-score	-1.81
Structure conservation index	0.88
SVM decision value	0.56
SVM RNA-class probability	0.781721
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14285539 107 + 22224390
AGAAGGAAAACCGCCGACACACGCCGCACCACGCCACGCCCACCUAUCCAGCCGCCCACUUUCUUUUGGGCGAGUGGCAG---CCAUUUGGCAGUACAUAACUUUCACUA
.(((((.....((.((.....)).))....(((((((((...........))((((((........)))))).))))).(---((....))).))......))))).... ( -30.00)
>DroSec_CAF1 25897 107 + 1
AGAAGGAAAACCGCCGACACACGCCGCACCACGCCACGCCCACCUGUCCAGCCGCCCACUUUCUUUUGGGCGAGUGGCAG---CCAUUCGGCAGUACAUAACUUUCACUA
.(((((...((.(((((....((..((.....))..)).....(((.(((..((((((........))))))..))))))---....))))).))......))))).... ( -31.40)
>DroSim_CAF1 29200 110 + 1
AGAAGGAAAACCGCCGACACACGCCGCACCACGCCACGCCCACCUAUCCAGCCGCCCACUUUCUUUUGGGCGAGUGGCAGCCGCCAUUCGGCAGUACAUAACUUUCACUA
.(((((...((.(((((.....((.((.....(((((((...........))((((((........)))))).))))).)).))...))))).))......))))).... ( -32.70)
>DroEre_CAF1 27708 106 + 1
AGCAGGAAAACCGCCGACACAUGCCGCGCCAUGCCACGCCCACCUAACCAGCCGCCCACUUUCUU-UGGGCGAGUGGCAG---CCAUUCGGCAGUACAUAACUUUCACUA
.((.((....))(((((....((((((((........)).............((((((.......-)))))).)))))).---....))))).))............... ( -31.30)
>consensus
AGAAGGAAAACCGCCGACACACGCCGCACCACGCCACGCCCACCUAUCCAGCCGCCCACUUUCUUUUGGGCGAGUGGCAG___CCAUUCGGCAGUACAUAACUUUCACUA
.(((((...((.(((((.....(......)..(((((((...........))((((((........)))))).))))).........))))).))......))))).... (-27.59 = -27.65 +   0.06)

alignment

secondary structure

dotplot

Window 6

Location	14,285,569 – 14,285,686
Length	117
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	90.86
Mean single sequence MFE	-30.94
Consensus MFE	-25.39
Energy contribution	-27.02
Covariance contribution	1.63
Combinations/Pair	1.04
Mean z-score	-1.53
Structure conservation index	0.82
SVM decision value	0.51
SVM RNA-class probability	0.763050
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14285569 117 + 22224390
ACGCCACGCCCACCUAUCCAGCCGCCCACUUUCUUUUGGGCGAGUGGCAG---CCAUUUGGCAGUACAUAACUUUCACUAACCUUUAGCGGCGUUUUCAGCCAAGAGAGCACAUUACCGU
..(((((((...........))((((((........)))))).))))).(---((....))).(((.....(((((.(((.....))).(((.......)))..))))).....)))... ( -33.50)
>DroSec_CAF1 25927 117 + 1
ACGCCACGCCCACCUGUCCAGCCGCCCACUUUCUUUUGGGCGAGUGGCAG---CCAUUCGGCAGUACAUAACUUUCACUAACCUUUAGCGGCGUUUUCAGCCAAGAGAGCACAUUACCGU
..(((((((...........))((((((........)))))).))))).(---((....))).(((.....(((((.(((.....))).(((.......)))..))))).....)))... ( -33.20)
>DroSim_CAF1 29230 120 + 1
ACGCCACGCCCACCUAUCCAGCCGCCCACUUUCUUUUGGGCGAGUGGCAGCCGCCAUUCGGCAGUACAUAACUUUCACUAACCUUUAGCGGCGUUUUCAGCCAAGAGAGCACAUUACCGU
..(((.(.............((((((((........)))))(((((((....))))))))))(((.....)))..............).)))((((((......)))))).......... ( -36.80)
>DroEre_CAF1 27738 116 + 1
AUGCCACGCCCACCUAACCAGCCGCCCACUUUCUU-UGGGCGAGUGGCAG---CCAUUCGGCAGUACAUAACUUUCACUAACCUUUAGCGGCGUUUUCAGCCAAGAGAGCACAUUACCGU
.((((((((...........))((((((.......-)))))).))))))(---((....))).(((.....(((((.(((.....))).(((.......)))..))))).....)))... ( -33.60)
>DroYak_CAF1 29560 99 + 1
AUGCCACGCCCACCUAUCCAGCCGCCCACUUUCUU---------------------UUCGGCAGUGCAUAACUUUCACUAACCUUUAGCGGCGUUUUCAGCCAAGAGAGCACAUUACCGU
..(((.(.............((((...........---------------------..))))((((.(.....).))))........).)))((((((......)))))).......... ( -17.62)
>consensus
ACGCCACGCCCACCUAUCCAGCCGCCCACUUUCUUUUGGGCGAGUGGCAG___CCAUUCGGCAGUACAUAACUUUCACUAACCUUUAGCGGCGUUUUCAGCCAAGAGAGCACAUUACCGU
..(((.(.............((((((((........)))))((((((......)))))))))(((.....)))..............).)))((((((......)))))).......... (-25.39 = -27.02 +   1.63)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:49:56 2006