Locus 4140

Sequence ID 3R_DroMel_CAF1
Location 11,293,382 – 11,293,477
Length 95
Max. P 0.601263
window6632 window6633

overview

Window 2

Location 11,293,382 – 11,293,477
Length 95
Sequences 5
Columns 110
Reading direction forward
Mean pairwise identity 85.12
Mean single sequence MFE -23.60
Consensus MFE -16.36
Energy contribution -16.36
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.76
Structure conservation index 0.69
SVM decision value 0.14
SVM RNA-class probability 0.601263
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11293382 95 + 27905053
UCUGUUAUUGUUAUUGUU---------------AUUGCUCUGGCUGUGCAUUUGAAUGCACAUCGAUUUGGCGGCCAGCAGGCUCUAAAUUAUUAAUUCCAUAAUAUCUA
..((((((.((((...((---------------(..(((((((((((((((....)))).((......))))))))))..)))..))).....))))...)))))).... ( -22.20)
>DroSec_CAF1 28129 95 + 1
UCUGUUAUUCUUAUUUUU---------------AUUGCUCUGGCUGUGCAUUUGGAUGCAAAUCGAUUUGGCGGCCAGCAGGCUCUAAAUUAUUAAUUCCAUAAUAUCUA
..((..(((..((..(((---------------(..(((((((((((.((..(.(((....))).)..))))))))))..)))..)))).))..)))..))......... ( -22.30)
>DroSim_CAF1 28816 95 + 1
UCUGUAAUUGUUAUUGUU---------------AUUGCUCUGGCUGUGCAUUUGGAUGCAAAUCGAUUUGGCGGCCAGCAGGCUUUAAAUUAUUAAUUCCAUAAUAUCUA
..((.(((((.((...((---------------(..(((((((((((.((..(.(((....))).)..))))))))))..)))..)))..)).))))).))......... ( -23.50)
>DroEre_CAF1 27282 101 + 1
UCUGUUAUUAUUAUUGUUAUUGUG---------AUUGCUCUGGCUGUGCAUUUUGAUGCAAAUCGUUUUGGCGGCCAGCGGGCUCUAAAUUAUGAGUUCCAUAAUCUAAA
..................((((((---------......((((((((.((...((((....))))...)))))))))).((((((........))))))))))))..... ( -25.50)
>DroYak_CAF1 27779 110 + 1
UCUGUGAUUGUUAUUGUUAUUGUUAUUGCUGUUAUUGCUCUGGCUGUGCAUUUUGAUGCAAAUCGUUUUGGCGGCCAGCAGGCUCUGAAUUAUUAGUUCCAUAAUCCAUA
..((.((((((...............(((((...(((((..(((..(((((....)))))....)))..))))).)))))((..((((....))))..)))))))))).. ( -24.50)
>consensus
UCUGUUAUUGUUAUUGUU_______________AUUGCUCUGGCUGUGCAUUUGGAUGCAAAUCGAUUUGGCGGCCAGCAGGCUCUAAAUUAUUAAUUCCAUAAUAUCUA
....................................(((((((((((((((....))))....(.....)))))))))..)))........................... (-16.36 = -16.36 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 11,293,382 – 11,293,477
Length 95
Sequences 5
Columns 110
Reading direction reverse
Mean pairwise identity 85.12
Mean single sequence MFE -18.08
Consensus MFE -13.66
Energy contribution -13.66
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.54
Structure conservation index 0.76
SVM decision value -0.00
SVM RNA-class probability 0.533167
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11293382 95 - 27905053
UAGAUAUUAUGGAAUUAAUAAUUUAGAGCCUGCUGGCCGCCAAAUCGAUGUGCAUUCAAAUGCACAGCCAGAGCAAU---------------AACAAUAACAAUAACAGA
(((((((((......)))).)))))..((...(((((((......)).(((((((....)))))))))))).))...---------------.................. ( -19.30)
>DroSec_CAF1 28129 95 - 1
UAGAUAUUAUGGAAUUAAUAAUUUAGAGCCUGCUGGCCGCCAAAUCGAUUUGCAUCCAAAUGCACAGCCAGAGCAAU---------------AAAAAUAAGAAUAACAGA
....(((((......))))).((((..((...(((((((......))...(((((....)))))..))))).))..)---------------)))............... ( -15.30)
>DroSim_CAF1 28816 95 - 1
UAGAUAUUAUGGAAUUAAUAAUUUAAAGCCUGCUGGCCGCCAAAUCGAUUUGCAUCCAAAUGCACAGCCAGAGCAAU---------------AACAAUAACAAUUACAGA
(((((((((......)))).)))))..((...(((((((......))...(((((....)))))..))))).))...---------------.................. ( -14.50)
>DroEre_CAF1 27282 101 - 1
UUUAGAUUAUGGAACUCAUAAUUUAGAGCCCGCUGGCCGCCAAAACGAUUUGCAUCAAAAUGCACAGCCAGAGCAAU---------CACAAUAACAAUAAUAAUAACAGA
(((((((((((.....)))))))))))((...(((((((......))...(((((....)))))..))))).))...---------........................ ( -21.50)
>DroYak_CAF1 27779 110 - 1
UAUGGAUUAUGGAACUAAUAAUUCAGAGCCUGCUGGCCGCCAAAACGAUUUGCAUCAAAAUGCACAGCCAGAGCAAUAACAGCAAUAACAAUAACAAUAACAAUCACAGA
..((((((((.......))))))))....((((((((((......))...(((((....)))))..))))).((.......)).......................))). ( -19.80)
>consensus
UAGAUAUUAUGGAAUUAAUAAUUUAGAGCCUGCUGGCCGCCAAAUCGAUUUGCAUCCAAAUGCACAGCCAGAGCAAU_______________AACAAUAACAAUAACAGA
...........................((...(((((((......))...(((((....)))))..))))).)).................................... (-13.66 = -13.66 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:19:13 2006