Locus 868

Sequence ID X_DroMel_CAF1
Location 2,446,815 – 2,446,947
Length 132
Max. P 0.905250
window1407 window1408 window1409

overview

Window 7

Location 2,446,815 – 2,446,913
Length 98
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 81.94
Mean single sequence MFE -45.77
Consensus MFE -34.71
Energy contribution -35.93
Covariance contribution 1.23
Combinations/Pair 1.07
Mean z-score -2.09
Structure conservation index 0.76
SVM decision value 0.92
SVM RNA-class probability 0.882941
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2446815 98 + 22224390
UUUACUCGGCGGACUGCUCUGUGCAAUCCAGUUGUCCAU---UUGCCCUAAUCGAAGGGGA-UGGGCCAACCGUUUGCAUGGCC-CCUUUUGUAACUGCCGGC-----------------
.....((((((((.(((.....))).)))(((((.....---...((((......))))..-.((((((..........)))))-)......)))))))))).----------------- ( -33.40)
>DroSec_CAF1 7616 120 + 1
UUUACUCGGCGGACUGCUCUGUGCGGUCCAGUUGUCCAGUUCUUGCCCUAAUCGCAGGGAUGGGGGCCCACCGUUUGCAUGGCCCCCUUUUGCAACUGGCGGCCUGCACUCGAGGAAACC
....(((((((((((((.....))))))).((((.((((((....((((......))))..(((((((............)))))))......))))))))))..))...))))...... ( -50.20)
>DroSim_CAF1 9838 120 + 1
UUUACUCGGCGGACUGCUCUGUGCGGUCCAGUUGUCCAGUUCUUGCCCUAAUCGAAGGGCUGGGGGCCCACCGUUUGCAUGGCCCCCUUUUGCAACUGGCGGCCUGCACUCGAGGAAACC
....(((((((((((((.....))))))).((((.((((((...(((((......))))).(((((((............)))))))......))))))))))..))...))))...... ( -53.70)
>consensus
UUUACUCGGCGGACUGCUCUGUGCGGUCCAGUUGUCCAGUUCUUGCCCUAAUCGAAGGGAUGGGGGCCCACCGUUUGCAUGGCCCCCUUUUGCAACUGGCGGCCUGCACUCGAGGAAACC
.......((((((((((.....)))))))((((((..........((((......))))..(((((((............)))))))....))))))....)))................ (-34.71 = -35.93 +   1.23)

alignment

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secondary structure

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dotplot

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Window 8

Location 2,446,815 – 2,446,913
Length 98
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 81.94
Mean single sequence MFE -45.70
Consensus MFE -30.42
Energy contribution -33.20
Covariance contribution 2.78
Combinations/Pair 1.03
Mean z-score -2.41
Structure conservation index 0.67
SVM decision value 1.04
SVM RNA-class probability 0.905250
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2446815 98 - 22224390
-----------------GCCGGCAGUUACAAAAGG-GGCCAUGCAAACGGUUGGCCCA-UCCCCUUCGAUUAGGGCAA---AUGGACAACUGGAUUGCACAGAGCAGUCCGCCGAGUAAA
-----------------((((((((((.......(-(((((.((.....)))))))).-..((((......))))...---......))))(((((((.....))))))))))).))... ( -38.10)
>DroSec_CAF1 7616 120 - 1
GGUUUCCUCGAGUGCAGGCCGCCAGUUGCAAAAGGGGGCCAUGCAAACGGUGGGCCCCCAUCCCUGCGAUUAGGGCAAGAACUGGACAACUGGACCGCACAGAGCAGUCCGCCGAGUAAA
((.((.(((..((((.((...((((((((....(((((((.(((.....))))))))))..(((((....))))).........).))))))).)))))).))).)).)).......... ( -47.20)
>DroSim_CAF1 9838 120 - 1
GGUUUCCUCGAGUGCAGGCCGCCAGUUGCAAAAGGGGGCCAUGCAAACGGUGGGCCCCCAGCCCUUCGAUUAGGGCAAGAACUGGACAACUGGACCGCACAGAGCAGUCCGCCGAGUAAA
((.((.(((..((((.((...((((((((....(((((((.(((.....)))))))))).(((((......)))))........).))))))).)))))).))).)).)).......... ( -51.80)
>consensus
GGUUUCCUCGAGUGCAGGCCGCCAGUUGCAAAAGGGGGCCAUGCAAACGGUGGGCCCCCACCCCUUCGAUUAGGGCAAGAACUGGACAACUGGACCGCACAGAGCAGUCCGCCGAGUAAA
................(((..((((((......(((((((.(((.....))))))))))..((((......))))....))))))......((((.((.....)).)))))))....... (-30.42 = -33.20 +   2.78)

alignment

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secondary structure

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dotplot

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Window 9

Location 2,446,854 – 2,446,947
Length 93
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 78.99
Mean single sequence MFE -41.27
Consensus MFE -24.30
Energy contribution -25.50
Covariance contribution 1.20
Combinations/Pair 1.03
Mean z-score -2.21
Structure conservation index 0.59
SVM decision value 0.66
SVM RNA-class probability 0.813495
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2446854 93 + 22224390
--UUGCCCUAAUCGAAGGGGA-UGGGCCAACCGUUUGCAUGGCC-CCUUUUGUAACUGCCGGC---------------------CACAUUUUACUUGUGGC--CACCAUAAGCGAGUGGC
--..((((...((....))..-.))))...((((((((..(((.-............)))(((---------------------((((.......))))))--).......)))))))). ( -34.22)
>DroSec_CAF1 7656 119 + 1
UCUUGCCCUAAUCGCAGGGAUGGGGGCCCACCGUUUGCAUGGCCCCCUUUUGCAACUGGCGGCCUGCACUCGAGGAAACCUGCCCACAUUUCACUUGUGGCCCCACCAUAAACGAGUG-C
....((((((...(((((...(((((((............))))))).)))))...))).)))..(((((((.(....)....(((((.......)))))............))))))-) ( -43.30)
>DroSim_CAF1 9878 117 + 1
UCUUGCCCUAAUCGAAGGGCUGGGGGCCCACCGUUUGCAUGGCCCCCUUUUGCAACUGGCGGCCUGCACUCGAGGAAACCUGCCCACAUUUCACUUGUGGC--CACCAUAAACGAGUG-C
.((.(((((......))))).))(((((..(((.(((((.((...))...))))).))).)))))(((((((.(....).((.(((((.......))))).--)).......))))))-) ( -46.30)
>consensus
UCUUGCCCUAAUCGAAGGGAUGGGGGCCCACCGUUUGCAUGGCCCCCUUUUGCAACUGGCGGCCUGCACUCGAGGAAACCUGCCCACAUUUCACUUGUGGC__CACCAUAAACGAGUG_C
.....((((......)))).((.(((((..(((.(((((.((...))...))))).))).))))).))..................(((((...((((((.....))))))..))))).. (-24.30 = -25.50 +   1.20)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:55:50 2006