Locus 125

Sequence ID X_DroMel_CAF1
Location 515,831 – 516,187
Length 356
Max. P 0.993733
window166 window167 window168 window169 window170

overview

Window 6

Location 515,831 – 515,933
Length 102
Sequences 3
Columns 102
Reading direction forward
Mean pairwise identity 92.00
Mean single sequence MFE -27.42
Consensus MFE -23.40
Energy contribution -22.96
Covariance contribution -0.44
Combinations/Pair 1.10
Mean z-score -1.92
Structure conservation index 0.85
SVM decision value 0.11
SVM RNA-class probability 0.587689
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 515831 102 + 22224390
GGGGGCUGUGUUCUUGAGUCAAAGACUGAGGUGAAAGGCAGGCAACGCAAAGAAAAGAAAAGAAAGCACGGCGGAGCCAAAAAAUUGUAAAGCGGCCUGAGC
..(((((((...(((.((((...)))).))).........(((..(((......................)))..))).............))))))).... ( -24.85)
>DroSec_CAF1 2002 96 + 1
GG-GGCUGUGCUCUUGAGUCAAAGACUGAGGUGAAAGGCAGCCAAGGCAAAGAA-----AAGAACGCACGGCGGAGCCAAAAAAUUGUAAAGCGGCCCGAGC
.(-((((((.(.(((.((((...)))).))).)...(((.(((...((......-----......))..)))...))).............))))))).... ( -30.00)
>DroSim_CAF1 1996 96 + 1
GG-GGCUGUGCUCUUGAGUCAAAGACUGAGGUGAAAGGCAGGCAAGGCAAAGAA-----AGGAACGCACGGCGGAGCCAAAAAAUUGUAAAGCGGCCCGAGC
.(-((((((.(.(((.((((...)))).))).)...(((..((...((......-----......))...))...))).............))))))).... ( -27.40)
>consensus
GG_GGCUGUGCUCUUGAGUCAAAGACUGAGGUGAAAGGCAGGCAAGGCAAAGAA_____AAGAACGCACGGCGGAGCCAAAAAAUUGUAAAGCGGCCCGAGC
....(((((((.(((.((((...)))).)))......((.......)).................)))))))((.(((...............))))).... (-23.40 = -22.96 +  -0.44) 

alignment

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secondary structure

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Window 7

Location 515,933 – 516,034
Length 101
Sequences 3
Columns 101
Reading direction reverse
Mean pairwise identity 92.59
Mean single sequence MFE -36.50
Consensus MFE -32.79
Energy contribution -33.23
Covariance contribution 0.45
Combinations/Pair 1.03
Mean z-score -2.56
Structure conservation index 0.90
SVM decision value 1.24
SVM RNA-class probability 0.934681
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 515933 101 - 22224390
GGGGUGAGUCGGUGGGUCCAAGGAAAUGCACACUAAUUACUCCUUGGCACUGCCAAGUUGGCUGGGGGAGUGGAAGGUCCUUUCUUCUUUUCCGCUCCUCU
.((.(((.(.((..(..((((((((((........)))..)))))))..)..)).).))).))((((((((((((((..........)))))))))))))) ( -38.10)
>DroSec_CAF1 2098 95 - 1
GGG------CGCUGUGUCCAAGGAAAUGCACACUAAUUACUCCUUGGCACUGCCAAGUUGGCUGGGGGUGUGGAAAGUCCUUUCUUCUUUUCCGCUCCUCU
.((------((..(((.((((((((((........)))..)))))))))))))).........(((((.((((((((..........)))))))).))))) ( -33.30)
>DroSim_CAF1 2092 95 - 1
GGG------CUCUGUGUCCAAGGAAAUGCACACUAAUUACUCCUUGGCACUGCCAAGUUGGCUGGGGGAGUGGAAAGUCCUUUCUUCUUUUCCGCUCCUCU
.((------(...(((.((((((((((........)))..)))))))))).))).........((((((((((((((..........)))))))))))))) ( -38.10)
>consensus
GGG______CGCUGUGUCCAAGGAAAUGCACACUAAUUACUCCUUGGCACUGCCAAGUUGGCUGGGGGAGUGGAAAGUCCUUUCUUCUUUUCCGCUCCUCU
.............(((.((((((((((........)))..)))))))))).(((.....))).((((((((((((((..........)))))))))))))) (-32.79 = -33.23 +   0.45) 

alignment

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secondary structure

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dotplot

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Window 8

Location 516,034 – 516,154
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 88.82
Mean single sequence MFE -32.20
Consensus MFE -25.99
Energy contribution -27.68
Covariance contribution 1.69
Combinations/Pair 1.03
Mean z-score -2.43
Structure conservation index 0.81
SVM decision value 2.03
SVM RNA-class probability 0.986118
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 516034 120 + 22224390
CCCCCCACCCACCCUAUCCCCUUGCUGCGUGUGUUUGUGCAACAUUUGCUUUUCCACUUCGUUUGCGACAAUCAAAUGUAACAAAGGAGCGAAAAAAGGUUGCACAAAAAAGUGGGAAAA
...(((((.(((.(............).)))..((((((((((.(((((((((......((((((.......))))))......))))))))).....))))))))))...))))).... ( -32.50)
>DroSec_CAF1 2193 114 + 1
CCUCCCACC------AUCCCCUUGCUGCGUGUGUUUGUGCAACAUUUGCUUUUCCACUUCGUUUGCGACAAUCAAAUGUAACAAAGGAGCGAAAAAAGGUUGCACAAAAAAGUGGGAAAA
..(((((((------(..(.(.....).)..))((((((((((.(((((((((......((((((.......))))))......))))))))).....))))))))))...))))))... ( -33.30)
>DroSim_CAF1 2187 114 + 1
CCUCCCACC------AUCCCCUUGCUGCGUGUGUUUGUGCAACAUUUGCUUUUCCACUUCGUUUGCGACAAUCAAAUGUAACAAAGGAGCGAAAAAAGGUUGCACAAAAAAGUGGGAAAA
..(((((((------(..(.(.....).)..))((((((((((.(((((((((......((((((.......))))))......))))))))).....))))))))))...))))))... ( -33.30)
>DroEre_CAF1 1988 98 + 1
---------------------UUGCUGCGUGUGUUUGUGCAACAUUUGCUUUUCCACUUCGUUUGCGACAAUCAAAUGUAACAAAGGAGCGAAAAAAGGUUGCACAAAAAGU-GCGGAAA
---------------------...((((((...((((((((((.(((((((((......((((((.......))))))......))))))))).....))))))))))..))-))))... ( -30.10)
>DroYak_CAF1 2032 113 + 1
CCCCCCACC------CCCCCCUUGCUGCGUGUGUUUGUGCAACAUUUGCUUUUCCACUUCGUUUGCGACAAUCAAAUGUAACAAAGGAGCGAAAAAAGGGUGCACAAAAAAG-CGGGGAA
..((((...------...(((((....(((.(.(((((...(((((((.((.((((.......)).)).)).))))))).))))).).)))....))))).((........)-))))).. ( -31.80)
>consensus
CCCCCCACC______AUCCCCUUGCUGCGUGUGUUUGUGCAACAUUUGCUUUUCCACUUCGUUUGCGACAAUCAAAUGUAACAAAGGAGCGAAAAAAGGUUGCACAAAAAAGUGGGAAAA
..((((((...............((.....)).((((((((((.(((((((((......((((((.......))))))......))))))))).....))))))))))...))))))... (-25.99 = -27.68 +   1.69) 

alignment

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secondary structure

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dotplot

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Window 9

Location 516,034 – 516,154
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 88.82
Mean single sequence MFE -37.24
Consensus MFE -29.23
Energy contribution -31.28
Covariance contribution 2.05
Combinations/Pair 1.08
Mean z-score -2.94
Structure conservation index 0.78
SVM decision value 2.42
SVM RNA-class probability 0.993733
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 516034 120 - 22224390
UUUUCCCACUUUUUUGUGCAACCUUUUUUCGCUCCUUUGUUACAUUUGAUUGUCGCAAACGAAGUGGAAAAGCAAAUGUUGCACAAACACACGCAGCAAGGGGAUAGGGUGGGUGGGGGG
.(..((((((..((((((((((.(((((((((((.(((((.(((......))).))))).).)))))))))).....))))))))))..(((.(............).)))))))))..) ( -40.80)
>DroSec_CAF1 2193 114 - 1
UUUUCCCACUUUUUUGUGCAACCUUUUUUCGCUCCUUUGUUACAUUUGAUUGUCGCAAACGAAGUGGAAAAGCAAAUGUUGCACAAACACACGCAGCAAGGGGAU------GGUGGGAGG
..(((((((...((((((((((.(((((((((((.(((((.(((......))).))))).).)))))))))).....))))))))))((..(.(.....).)..)------)))))))). ( -39.20)
>DroSim_CAF1 2187 114 - 1
UUUUCCCACUUUUUUGUGCAACCUUUUUUCGCUCCUUUGUUACAUUUGAUUGUCGCAAACGAAGUGGAAAAGCAAAUGUUGCACAAACACACGCAGCAAGGGGAU------GGUGGGAGG
..(((((((...((((((((((.(((((((((((.(((((.(((......))).))))).).)))))))))).....))))))))))((..(.(.....).)..)------)))))))). ( -39.20)
>DroEre_CAF1 1988 98 - 1
UUUCCGC-ACUUUUUGUGCAACCUUUUUUCGCUCCUUUGUUACAUUUGAUUGUCGCAAACGAAGUGGAAAAGCAAAUGUUGCACAAACACACGCAGCAA---------------------
.....((-....((((((((((.(((((((((((.(((((.(((......))).))))).).)))))))))).....)))))))))).....)).....--------------------- ( -28.20)
>DroYak_CAF1 2032 113 - 1
UUCCCCG-CUUUUUUGUGCACCCUUUUUUCGCUCCUUUGUUACAUUUGAUUGUCGCAAACGAAGUGGAAAAGCAAAUGUUGCACAAACACACGCAGCAAGGGGGG------GGUGGGGGG
.((((((-(((((.......((((((((((((((.(((((.(((......))).))))).).))))))))).....((((((..........)))))))))))))------)))))))). ( -38.81)
>consensus
UUUUCCCACUUUUUUGUGCAACCUUUUUUCGCUCCUUUGUUACAUUUGAUUGUCGCAAACGAAGUGGAAAAGCAAAUGUUGCACAAACACACGCAGCAAGGGGAU______GGUGGGAGG
..((((((((..((((((((((.(((((((((((.(((((.(((......))).))))).).)))))))))).....))))))))))....(.(.....).).........)))))))). (-29.23 = -31.28 +   2.05) 

alignment

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secondary structure

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dotplot

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Window 0

Location 516,074 – 516,187
Length 113
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.16
Mean single sequence MFE -24.26
Consensus MFE -17.83
Energy contribution -17.83
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.07
Structure conservation index 0.73
SVM decision value 0.53
SVM RNA-class probability 0.772327
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 516074 113 - 22224390
-------UCCUCUUCCUUGCACUUCCCCAUCUCAGCUUUGUUUUCCCACUUUUUUGUGCAACCUUUUUUCGCUCCUUUGUUACAUUUGAUUGUCGCAAACGAAGUGGAAAAGCAAAUGUU
-------..........................(((((((((((.((((((((((((((((.(.......((......)).......).))).)))))).))))))).)))))))).))) ( -23.14)
>DroSec_CAF1 2227 120 - 1
CGCUGUAUCCUCUUCCUUGCACUUCCCCAUCUCAGCUUUGUUUUCCCACUUUUUUGUGCAACCUUUUUUCGCUCCUUUGUUACAUUUGAUUGUCGCAAACGAAGUGGAAAAGCAAAUGUU
.((((...........................))))((((((((.((((((((((((((((.(.......((......)).......).))).)))))).))))))).)))))))).... ( -25.17)
>DroSim_CAF1 2221 120 - 1
CGCUGUAUCCUCUUCCUUGCACUUCCCCAUCUCAGCUUUGUUUUCCCACUUUUUUGUGCAACCUUUUUUCGCUCCUUUGUUACAUUUGAUUGUCGCAAACGAAGUGGAAAAGCAAAUGUU
.((((...........................))))((((((((.((((((((((((((((.(.......((......)).......).))).)))))).))))))).)))))))).... ( -25.17)
>DroEre_CAF1 2007 119 - 1
CGCCUUAUCCUGUUCCCUGCACUUCCCCAUCUGGGCUUUGUUUCCGC-ACUUUUUGUGCAACCUUUUUUCGCUCCUUUGUUACAUUUGAUUGUCGCAAACGAAGUGGAAAAGCAAAUGUU
.................(((.....(((....)))..........((-((.....)))).....((((((((((.(((((.(((......))).))))).).))))))))))))...... ( -26.60)
>DroYak_CAF1 2066 119 - 1
CGCCUUAUCCUGCUCCCCGCACCUCCCCGCCUCGCCUUUGUUCCCCG-CUUUUUUGUGCACCCUUUUUUCGCUCCUUUGUUACAUUUGAUUGUCGCAAACGAAGUGGAAAAGCAAAUGUU
.((.......(((.....))).......))...((.(((((.....(-(........)).....((((((((((.(((((.(((......))).))))).).)))))))))))))).)). ( -21.24)
>consensus
CGCCGUAUCCUCUUCCUUGCACUUCCCCAUCUCAGCUUUGUUUUCCCACUUUUUUGUGCAACCUUUUUUCGCUCCUUUGUUACAUUUGAUUGUCGCAAACGAAGUGGAAAAGCAAAUGUU
..................((((.................................))))....(((((((((((.(((((.(((......))).))))).).))))))))))........ (-17.83 = -17.83 +   0.00) 

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:34:57 2006