Locus 2467

Sequence ID 3L_DroMel_CAF1
Location 6,971,148 – 6,971,325
Length 177
Max. P 0.992664
window3804 window3805 window3806

overview

Window 4

Location 6,971,148 – 6,971,265
Length 117
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 84.97
Mean single sequence MFE -40.27
Consensus MFE -27.47
Energy contribution -28.11
Covariance contribution 0.64
Combinations/Pair 1.17
Mean z-score -1.72
Structure conservation index 0.68
SVM decision value 0.04
SVM RNA-class probability 0.556070
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6971148 117 + 23771897
UAGGCAAAACAUUUUUCU-CAGUGUCUGAGACGCAGGC--CGGCUUCGGAGUUGGAAAAAAAAUGGCCAGACAAACACAUCGCCGGCCAAAUGGAUGCACAGGCAUGCCGGCGAAGGCAG
..(((....(((((.(((-(((...))))))....(((--((((...((.(((........)))..)).((........)))))))))))))).((((....))))))).((....)).. ( -38.90)
>DroSec_CAF1 40094 106 + 1
-----------UUUUUCU-CAGUGUCUGAGGCGCAGGC--CGGCUUCGGAGCCGGGAAAAAAAUGGCCAGACAAACACAUCGCCGGCCAAAUGGAUGCACAGGCAUGCCGGCGAAGGCAG
-----------(((((((-(.((.((((((((......--..)))))))))).))))))))....(((.(.....)...((((((((.......((((....)))))))))))).))).. ( -40.81)
>DroSim_CAF1 40855 106 + 1
-----------UUUUUCU-CAGUGUCUGAGGCGGAGGC--CGGCUUCGGAGCCGGGAAAAAAAUGGCCAGACAAACACAUCGCCGGCCAAAUGGAUGCACAGGCAUGCCGGCGAAGGCAG
-----------(((((((-(.((.((((((((.(....--).)))))))))).))))))))....(((.(.....)...((((((((.......((((....)))))))))))).))).. ( -42.11)
>DroEre_CAF1 41136 118 + 1
CAGGUUGAUCAUUUCUCU-CAGUGUCUUUGGCGGAGGCUCUGGCUCUGGAGCCGGGAA-AAAAUAUCCAGACAAACACAUCGCCGGCCAAAUGGAUGCACAGGCAUGCCGGCGAAGGCAG
..((..((.....))..)-)..((((((((.(((..((.(((((((((..(((((((.-....................)).)))))....)))).)).)))))...))).)))))))). ( -37.60)
>DroYak_CAF1 42235 118 + 1
CAAGCAGAUAUUUUUUUUCCAGUGUCUUGGGCGGAGGC--UGGCUUUGGAGGCGGAAAAAAAAUGUCCAGACAAACACAUCGGCGGCCAAAUGGAUGCACAGGCAUGCCGGCGAAGGCAG
...((.((((((((((((((.((.(((..(((......--..)))..))).))))))))))))))))..........(.(((.((((.......((((....)))))))).))).))).. ( -41.91)
>consensus
_A_G___A___UUUUUCU_CAGUGUCUGAGGCGGAGGC__CGGCUUCGGAGCCGGGAAAAAAAUGGCCAGACAAACACAUCGCCGGCCAAAUGGAUGCACAGGCAUGCCGGCGAAGGCAG
......................((((((...(((((.(...).)))))..((((.........))))))))))....(.((((((((.......((((....)))))))))))).).... (-27.47 = -28.11 +   0.64)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 6,971,185 – 6,971,297
Length 112
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.22
Mean single sequence MFE -39.99
Consensus MFE -34.79
Energy contribution -34.87
Covariance contribution 0.08
Combinations/Pair 1.10
Mean z-score -2.10
Structure conservation index 0.87
SVM decision value 2.34
SVM RNA-class probability 0.992664
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6971185 112 + 23771897
CGGCUUCGGAGUUGGAAAAAAAAUGGCCAGACAAACACAUCGCCGGCCAAAUGGAUGCACAGGCAUGCCGGCGAAGGCAGUUCAAGUGCACAUGGCCAACAUGAGCUGCGAU--------
.((((......((....)).....)))).........(.((((((((.......((((....)))))))))))).)((((((((.((((.....))..)).))))))))...-------- ( -38.81)
>DroSec_CAF1 40120 112 + 1
CGGCUUCGGAGCCGGGAAAAAAAUGGCCAGACAAACACAUCGCCGGCCAAAUGGAUGCACAGGCAUGCCGGCGAAGGCAGUUCAAGUGCACAUGGCCAACAUGAGCUGCGAU--------
(((((....))))).......................(.((((((((.......((((....)))))))))))).)((((((((.((((.....))..)).))))))))...-------- ( -39.91)
>DroSim_CAF1 40881 112 + 1
CGGCUUCGGAGCCGGGAAAAAAAUGGCCAGACAAACACAUCGCCGGCCAAAUGGAUGCACAGGCAUGCCGGCGAAGGCAGUUCAAGUGCACAUGGCCAACAUGAGCUGCGAG--------
(((((....))))).......................(.((((((((.......((((....)))))))))))).)((((((((.((((.....))..)).))))))))...-------- ( -39.91)
>DroEre_CAF1 41175 119 + 1
UGGCUCUGGAGCCGGGAA-AAAAUAUCCAGACAAACACAUCGCCGGCCAAAUGGAUGCACAGGCAUGCCGGCGAAGGCAGUUCAAGUGCACAUGGCCAACAUGAGCUGCGAUUCUGCGAU
.((((....)))).....-.....(((((((......(.((((((((.......((((....)))))))))))).)((((((((.((((.....))..)).))))))))...)))).))) ( -43.51)
>DroYak_CAF1 42273 120 + 1
UGGCUUUGGAGGCGGAAAAAAAAUGUCCAGACAAACACAUCGGCGGCCAAAUGGAUGCACAGGCAUGCCGGCGAAGGCAGUUCAAGUGCACAUAGGCAACAUGAGCUGCAAUUCUGCGAU
...........((((((......(((....)))....(.(((.((((.......((((....)))))))).))).)((((((((..(((......)))...))))))))..))))))... ( -37.81)
>consensus
CGGCUUCGGAGCCGGGAAAAAAAUGGCCAGACAAACACAUCGCCGGCCAAAUGGAUGCACAGGCAUGCCGGCGAAGGCAGUUCAAGUGCACAUGGCCAACAUGAGCUGCGAU________
(((((....))))).......................(.((((((((.......((((....)))))))))))).)((((((((.((((.....))..)).))))))))........... (-34.79 = -34.87 +   0.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 6,971,225 – 6,971,325
Length 100
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 83.58
Mean single sequence MFE -37.41
Consensus MFE -28.01
Energy contribution -28.41
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.52
Structure conservation index 0.75
SVM decision value -0.03
SVM RNA-class probability 0.520389
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6971225 100 + 23771897
CGCCGGCCAAAUGGAUGCACAGGCAUGCCGGCGAAGGCAGUUCAAGUGCACAUGGCCAACAUGAGCUGCGAU--------GCU--------GCGAUGCUGU----GAUGCUGCUUGAAUA
(((((((.......((((....))))))))))).((((((((((...(((((((.....))))(((......--------)))--------....)))..)----)).)))))))..... ( -37.61)
>DroSec_CAF1 40160 92 + 1
CGCCGGCCAAAUGGAUGCACAGGCAUGCCGGCGAAGGCAGUUCAAGUGCACAUGGCCAACAUGAGCUGCGAU------------------------GCUGU----GAUGCUGCUUGAAUA
(((((((.......((((....)))))))))))......(((((((((((((((.....))))(((......------------------------)))..----..))).)))))))). ( -34.61)
>DroSim_CAF1 40921 96 + 1
CGCCGGCCAAAUGGAUGCACAGGCAUGCCGGCGAAGGCAGUUCAAGUGCACAUGGCCAACAUGAGCUGCGAG------------------------CUUCUAGAGAAUGCUGCUUGAAUA
(((((((.......((((....)))))))))))......((((((((((.((((.....)))).))....((------------------------((((....))).))))))))))). ( -35.31)
>DroEre_CAF1 41214 108 + 1
CGCCGGCCAAAUGGAUGCACAGGCAUGCCGGCGAAGGCAGUUCAAGUGCACAUGGCCAACAUGAGCUGCGAUUCUGCGAUGCU--------GCGAUGCUGU----GAUGCUGCUUGAAUA
(((((((.......((((....))))))))))).((((((((((...(((((((.....))))(((((((....))))..)))--------....)))..)----)).)))))))..... ( -38.81)
>DroYak_CAF1 42313 116 + 1
CGGCGGCCAAAUGGAUGCACAGGCAUGCCGGCGAAGGCAGUUCAAGUGCACAUAGGCAACAUGAGCUGCAAUUCUGCGAUGCUGCGAGGCUGCGAUGCUGU----GAUGCUGCUUGAAUA
((((((((...((......))))).)))))((....)).((((((((((((((((.((.(...(((((((....))))..)))(((....)))).))))))----).))).)))))))). ( -40.70)
>consensus
CGCCGGCCAAAUGGAUGCACAGGCAUGCCGGCGAAGGCAGUUCAAGUGCACAUGGCCAACAUGAGCUGCGAU________GCU________GCGAUGCUGU____GAUGCUGCUUGAAUA
(((((((.......((((....)))))))))))...((((((((.((((.....))..)).))))))))................................................... (-28.01 = -28.41 +   0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:33:02 2006