Locus 6057

Sequence ID 2R_DroMel_CAF1
Location 19,061,586 – 19,061,704
Length 118
Max. P 0.779271
window9705 window9706

overview

Window 5

Location 19,061,586 – 19,061,682
Length 96
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 70.38
Mean single sequence MFE -25.08
Consensus MFE -9.13
Energy contribution -9.60
Covariance contribution 0.48
Combinations/Pair 1.50
Mean z-score -1.82
Structure conservation index 0.36
SVM decision value 0.03
SVM RNA-class probability 0.546546
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19061586 96 + 20766785
UACAGUUGCCCCAAA--U-CG------CAGAAAUUUUCAUUUUUCUUUGCACAAGAGGAAAAAGGGAAAGCCCAAUGAUUAGCCAACUAA---UUGGGCUGUAACCUG
....((((((((...--.-..------..((.....)).(((((((((......))))))))))))..((((((((...(((....))))---))))))))))))... ( -25.50)
>DroSec_CAF1 4101 96 + 1
UACAGUUGCCCCAAA--U-CG------CAGAGAUUUCUAUUUUUCUUUGCACCAGCAGAAAAAGGGAAAGCCCAAUGAUUAGCCAACCAA---UUGGGCUGAGUCCUG
...............--.-.(------((((((..........))))))).............((((.((((((((.............)---)))))))...)))). ( -25.72)
>DroSim_CAF1 3989 95 + 1
UACAGUUGCCCCAAA--U-CG------CAGAGAUUUAUAUU-UUCUUUGCACCAGCAGAAAAAGGGAAAGCCCAAUGAUUAGCCAACCAA---UUGGGCUGUGUCCUG
...............--.-.(------((((((........-.))))))).............((((.((((((((.............)---)))))))...)))). ( -25.82)
>DroEre_CAF1 3943 96 + 1
UACAGUUGCCCCAAU--U-CG------UGGGUAUUUCCAUUUUUCCUAGCCACAACCAAAACAGGGAAACCCCAAUGAUUAGCCAACCAA---UCGGGCUGCGUCCUG
....((.((((....--.-.(------(((.((.............)).))))..........(((....)))...((((........))---)))))).))...... ( -20.02)
>DroYak_CAF1 4272 95 + 1
UACAGUUGCCCCAAU--U-CA------AGGGAAUUUCCAUUUUUCUUGGCC-CAACCAAAACUUGGAAACCCCAAUGAUUAGCCAACCAA---UUGGGCUAUGUGCUG
((((...((((.(((--(-..------.(((..((((((......((((..-...))))....)))))).)))..((......))...))---))))))..))))... ( -22.00)
>DroAna_CAF1 3638 96 + 1
UACAGUUGUCACAACAAUGGAUGGAAAUGGGU-UUUUCACACUUUCCGGCC-----------GGGCAAGCCCCAAAAAGGAAGUGACUAAACUUUGGGGCAUGUCCUU
....(((((....)))))((.((((((((((.-...)).)).)))))).))-----------(((((.(((((((......(((......)))))))))).))))).. ( -31.40)
>consensus
UACAGUUGCCCCAAA__U_CG______CAGAAAUUUCCAUUUUUCUUUGCACCAGCAGAAAAAGGGAAACCCCAAUGAUUAGCCAACCAA___UUGGGCUGUGUCCUG
............................(((((........)))))................((((..(((((((..................)))))))...)))). ( -9.13 =  -9.60 +   0.48)

alignment

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secondary structure

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dotplot

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Window 6

Location 19,061,609 – 19,061,704
Length 95
Sequences 6
Columns 98
Reading direction forward
Mean pairwise identity 72.20
Mean single sequence MFE -23.56
Consensus MFE -11.77
Energy contribution -12.19
Covariance contribution 0.42
Combinations/Pair 1.45
Mean z-score -1.74
Structure conservation index 0.50
SVM decision value 0.55
SVM RNA-class probability 0.779271
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19061609 95 + 20766785
AUUUUCAUUUUUCUUUGCACAAGAGGAAAAAGGGAAAGCCCAAUGAUUAGCCAACUAA---UUGGGCUGUAACCUGGUCGCACUUUUCAAGGACAUUC
...........((((((...(((.(((...(((...((((((((...(((....))))---)))))))....)))..)).).)))..))))))..... ( -23.40)
>DroSec_CAF1 4124 95 + 1
AUUUCUAUUUUUCUUUGCACCAGCAGAAAAAGGGAAAGCCCAAUGAUUAGCCAACCAA---UUGGGCUGAGUCCUGGUCGCACUCUCCAAGGACAUUC
..((((.(((((((..((....))))))))).))))((((((((.............)---)))))))..(((((((.........)).))))).... ( -28.22)
>DroSim_CAF1 4012 94 + 1
AUUUAUAUU-UUCUUUGCACCAGCAGAAAAAGGGAAAGCCCAAUGAUUAGCCAACCAA---UUGGGCUGUGUCCUGGUCGCACUCUCCAAGGACAUUC
.(((...((-((.(((((....))))).)))).)))((((((((.............)---)))))))(((((((((.........)).))))))).. ( -26.22)
>DroEre_CAF1 3966 95 + 1
AUUUCCAUUUUUCCUAGCCACAACCAAAACAGGGAAACCCCAAUGAUUAGCCAACCAA---UCGGGCUGCGUCCUGGUCCCACUUUUCAAGGACGUUC
...............((((............(((....)))..(((((........))---)))))))(((((((..............))))))).. ( -21.04)
>DroYak_CAF1 4295 94 + 1
AUUUCCAUUUUUCUUGGCC-CAACCAAAACUUGGAAACCCCAAUGAUUAGCCAACCAA---UUGGGCUAUGUGCUGGUCCCACUUUUCAAGGACGUUC
.............((((..-...))))..((((((((.......(((((((((.((..---..))....)).)))))))....))))))))....... ( -17.90)
>DroAna_CAF1 3670 84 + 1
-UUUUCACACUUUCCGGCC-----------GGGCAAGCCCCAAAAAGGAAGUGACUAAACUUUGGGGCAUGUCCUUGACCAGUGUUUGAUGGAC--UC
-.....(((((....(((.-----------(((((.(((((((......(((......)))))))))).)))))..).))))))).........--.. ( -24.60)
>consensus
AUUUCCAUUUUUCUUUGCACCAGCAGAAAAAGGGAAACCCCAAUGAUUAGCCAACCAA___UUGGGCUGUGUCCUGGUCCCACUUUUCAAGGACAUUC
..........((((((..............))))))(((((((..................)))))))(((((((((.........))).)))))).. (-11.77 = -12.19 +   0.42)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:01:30 2006