Locus 1200

Sequence ID 2L_DroMel_CAF1
Location 3,238,307 – 3,238,466
Length 159
Max. P 0.812181
window1954 window1955

overview

Window 4

Location 3,238,307 – 3,238,426
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.24
Mean single sequence MFE -35.04
Consensus MFE -28.98
Energy contribution -29.58
Covariance contribution 0.60
Combinations/Pair 1.06
Mean z-score -1.60
Structure conservation index 0.83
SVM decision value 0.65
SVM RNA-class probability 0.812181
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3238307 119 - 22407834
AAACAACUGGCAUAGAUAAGUGGCGAACUCUGGGUGGCAAUUAGGGAACUAUCGCUGCACCUGCGUCUAGCUA-GCCAAUUAGCGCUGUUUAUGCCCACGCAAUUAACAAGCCUGUUAAC
........((((((((((.((((((......(((..((...(((....)))..))..).))..))))..((((-(....))))))))))))))))).......((((((....)))))). ( -34.50)
>DroSec_CAF1 72483 119 - 1
AAACAACUAGCAUAGAUAAGUGCCGAACGAUGGGUGGCAAUUAGGGAACUAUCGCUGCACCUGCGUACAGCUA-GCCAAUUAGCGCUGUUUAUGCCCACGCAAUUAACAAGCCUGUUAAC
.........(((((((((.((((..(....(((.((((...(((....))).(((.......)))....))))-.))).)..)))))))))))))........((((((....)))))). ( -32.40)
>DroSim_CAF1 74173 119 - 1
AAACAACUAGCAUAGAUAAGUGGCGAACGCUGGGUGGCAAUUAGGGAACUAUCGCUGCACCUGCGUACAGCUA-GCCAAUUAGCGCUGUUUAUGCCCACGCAAUUAACAAGCCUGUUAAC
.........((((((((....((((.((((.(((..((...(((....)))..))..).)).)))).).((((-(....))))))))))))))))........((((((....)))))). ( -35.40)
>DroEre_CAF1 69451 120 - 1
CAACAACUGGCAUAGAUAAGUGGCGAAUGCUGGGUGGCAAUUAGGAAACUAUCGCUGCACCUGCGUCCAGCAAUCCCAAUUAGCGCUGUUUAUGGCCACGCAAUUAACAAGCCUGUUAAC
....(((.(((.....(((.(((.((.(((((((.(((...(((....)))..)))((....)).))))))).))))).)))(((..((.....))..))).........))).)))... ( -36.20)
>DroYak_CAF1 68446 120 - 1
UAACAACUGGCAUAGAUAAGUGCCGAAUGCUGGGUGGCAAUUAGGAAACUAUCGCUGCACCUGCGUCCAGCUAUGCCAAUUAGCGCUGUUUAUGGCCACGCAAUUAACAAGCCUGUUAAC
(((((..((((((......))))))...(((((.(((((..(((....)))..((((.((....)).))))..))))).)))))((((((....((...))....))).))).))))).. ( -36.70)
>consensus
AAACAACUGGCAUAGAUAAGUGGCGAACGCUGGGUGGCAAUUAGGGAACUAUCGCUGCACCUGCGUCCAGCUA_GCCAAUUAGCGCUGUUUAUGCCCACGCAAUUAACAAGCCUGUUAAC
.......(((((((((((.((...(.((((.(((..((...(((....)))..))..).)).)))).).((((.......)))))))))))))).))).....((((((....)))))). (-28.98 = -29.58 +   0.60)

alignment

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secondary structure

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dotplot

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Window 5

Location 3,238,347 – 3,238,466
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 88.28
Mean single sequence MFE -34.32
Consensus MFE -26.96
Energy contribution -27.28
Covariance contribution 0.32
Combinations/Pair 1.14
Mean z-score -1.58
Structure conservation index 0.79
SVM decision value 0.25
SVM RNA-class probability 0.653477
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3238347 119 - 22407834
UUGCUUCGCCUUCCUUUUUUUUUUCGCCCACUUGCUGGUCAAACAACUGGCAUAGAUAAGUGGCGAACUCUGGGUGGCAAUUAGGGAACUAUCGCUGCACCUGCGUCUAGCUA-GCCAAU
..(((.(((.............((((((.((((((((((((......)))).))).)))))))))))....(((..((...(((....)))..))..).)).)))...)))..-...... ( -36.30)
>DroSec_CAF1 72523 114 - 1
UUGCUUCGACUUC-----UUUUUUCGCCCACUUGCUGGUCAAACAACUAGCAUAGAUAAGUGCCGAACGAUGGGUGGCAAUUAGGGAACUAUCGCUGCACCUGCGUACAGCUA-GCCAAU
.............-----.......((((((((((((((......))))))).))....((.....))..)))))(((...(((....)))..((((.((....)).))))..-)))... ( -29.00)
>DroSim_CAF1 74213 114 - 1
UUGCUUCGACUUC-----UUUUUUCGCCCACUUGCUGGUCAAACAACUAGCAUAGAUAAGUGGCGAACGCUGGGUGGCAAUUAGGGAACUAUCGCUGCACCUGCGUACAGCUA-GCCAAU
..(((........-----.....(((((.((((((((((......)))))))......))))))))((((.(((..((...(((....)))..))..).)).))))..)))..-...... ( -37.00)
>DroEre_CAF1 69491 113 - 1
---CUUUUCCUUCUU----UUUUUCGCCCAUUUGUUGGUCCAACAACUGGCAUAGAUAAGUGGCGAAUGCUGGGUGGCAAUUAGGAAACUAUCGCUGCACCUGCGUCCAGCAAUCCCAAU
---............----...((((((.(((((((.(.(((.....))))...)))))))))))))(((((((.(((...(((....)))..)))((....)).)))))))........ ( -35.20)
>DroYak_CAF1 68486 117 - 1
UUGCCUCGCCUUCAU---UUUUUCCGCCCAUUUGCUGGUCUAACAACUGGCAUAGAUAAGUGCCGAAUGCUGGGUGGCAAUUAGGAAACUAUCGCUGCACCUGCGUCCAGCUAUGCCAAU
..((((.((.(((..---.....((((......)).))..........(((((......)))))))).)).))))((((..(((....)))..((((.((....)).))))..))))... ( -34.10)
>consensus
UUGCUUCGCCUUC_U___UUUUUUCGCCCACUUGCUGGUCAAACAACUGGCAUAGAUAAGUGGCGAACGCUGGGUGGCAAUUAGGGAACUAUCGCUGCACCUGCGUCCAGCUA_GCCAAU
..((...................(((((.((((((((((......)))))))......))))))))((((.(((..((...(((....)))..))..).)).))))...))......... (-26.96 = -27.28 +   0.32)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:56:16 2006