Locus 535

Sequence ID 2L_DroMel_CAF1
Location 1,673,428 – 1,673,643
Length 215
Max. P 0.696673
window853 window854 window855

overview

Window 3

Location 1,673,428 – 1,673,530
Length 102
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 77.01
Mean single sequence MFE -19.80
Consensus MFE -12.56
Energy contribution -13.12
Covariance contribution 0.56
Combinations/Pair 1.09
Mean z-score -1.62
Structure conservation index 0.63
SVM decision value 0.26
SVM RNA-class probability 0.659178
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1673428 102 + 22407834
-----------ACACAUCAUUGUGGGCUGCAGCAGCAGCAGCAGCAACCCCGAACGAGAUUCAUUAAAAA-------AAUGUUGGGAAUAUAAAAAAUUGUUUUCCAUACGCAUUAAUGC
-----------.((((....)))).(((((.((....)).))))).........................-------(((((..((((.((((....)))).))))....)))))..... ( -22.20)
>DroSim_CAF1 799 95 + 1
------AACUCACACA---UCGUGGGCUGCAG---------CAGCAACCCCGAACGAGAUUCAUUAAAAA-------AAUGUUGGGAAUAUAAAAAAUUGUUUUCCAUACGCAUUAAUGC
------..(((.....---(((.(((.(((..---------..))).))))))..)))............-------(((((..((((.((((....)))).))))....)))))..... ( -20.50)
>DroYak_CAF1 819 108 + 1
ACACACAACACACACA---UCCUUUGCUGCAG---------CAGCAACCCCGAACGAGAUUCAUUAACAAAAAAUGAAAUGCUCGGAACAUAAAAAAUUGUUUUCCAUACGCAUUAAUGC
................---....((((((...---------))))))........(((.((((((.......))))))...)))((((.((((....)))).))))....(((....))) ( -16.70)
>consensus
______AAC_CACACA___UCGUGGGCUGCAG_________CAGCAACCCCGAACGAGAUUCAUUAAAAA_______AAUGUUGGGAAUAUAAAAAAUUGUUUUCCAUACGCAUUAAUGC
...................(((.(((.(((.............))).))))))........................(((((..((((.((((....)))).))))....)))))..... (-12.56 = -13.12 +   0.56)

alignment

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secondary structure

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dotplot

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Window 4

Location 1,673,457 – 1,673,564
Length 107
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 85.26
Mean single sequence MFE -25.25
Consensus MFE -19.37
Energy contribution -19.04
Covariance contribution -0.33
Combinations/Pair 1.14
Mean z-score -2.01
Structure conservation index 0.77
SVM decision value 0.34
SVM RNA-class probability 0.696673
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1673457 107 - 22407834
UCCGUAACCACGUU------UACUUUACUUACGCAUUGCUGCAUUAAUGCGUAUGGAAAACAAUUUUUUAUAUUCCCAACAUU-------UUUUUAAUGAAUCUCGUUCGGGGUUGCUGC
...((((((..(((------(.((.....(((((((((......))))))))).)).)))).............((.(((...-------.(((....)))....))).))))))))... ( -22.50)
>DroSim_CAF1 822 104 - 1
UCCUUAACCGCGUU--------CUUUACUUACGCAUUGCUGCAUUAAUGCGUAUGGAAAACAAUUUUUUAUAUUCCCAACAUU-------UUUUUAAUGAAUCUCGUUCGGGGUUGCUG-
....(((((.((..--------(......(((((((((......))))))))).((((..............))))...((((-------.....))))......)..)).)))))...- ( -19.94)
>DroYak_CAF1 848 119 - 1
UCCGCGAUCACGUUGUUACGUUCUUUACUUACGCAUUGCUGCAUUAAUGCGUAUGGAAAACAAUUUUUUAUGUUCCGAGCAUUUCAUUUUUUGUUAAUGAAUCUCGUUCGGGGUUGCUG-
...((((((..((((((...((((.....(((((((((......))))))))).))))))))))..........((((((..((((((.......))))))....))))))))))))..- ( -33.30)
>consensus
UCCGUAACCACGUU______U_CUUUACUUACGCAUUGCUGCAUUAAUGCGUAUGGAAAACAAUUUUUUAUAUUCCCAACAUU_______UUUUUAAUGAAUCUCGUUCGGGGUUGCUG_
...((((((.((.................(((((((((......))))))))).((((..............))))................................)).))))))... (-19.37 = -19.04 +  -0.33)

alignment

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secondary structure

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dotplot

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Window 5

Location 1,673,530 – 1,673,643
Length 113
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 90.96
Mean single sequence MFE -32.05
Consensus MFE -26.16
Energy contribution -25.41
Covariance contribution -0.75
Combinations/Pair 1.17
Mean z-score -1.51
Structure conservation index 0.82
SVM decision value 0.11
SVM RNA-class probability 0.589809
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1673530 113 + 22407834
AGCAAUGCGUAAGUAAAGUA------AACGUGGUUACGGAAUGGGAAAGUGUGGUGGCCAGACUUGGUUAUG-ACUAUAAAGCCAUGUGGCAUAACAUGGGGUAGUCCUCCUUGGGAUUU
.....(((....)))..(((------(......))))(((((((..((((.(((...))).))))..))))(-(((((....((((((......)))))).)))))).)))......... ( -28.40)
>DroSec_CAF1 5 111 + 1
AGCAAUGCGUAAGUAAAG--------AACGCGGUUAAGGAAUGGGAAGGUGUGGUGGCCAGACUUGGUUAUG-ACUAUAAAGCCAUGUGGCAUAACAUGGGGUAGUCCUCCUUGGGAUUU
.....(((((........--------.))))).(((((((((((..((((.(((...))).))))..))))(-(((((....((((((......)))))).)))))).)))))))..... ( -31.80)
>DroSim_CAF1 894 111 + 1
AGCAAUGCGUAAGUAAAG--------AACGCGGUUAAGGAAUGGGGAGGUGUGGUGGCCAGACUUGGUUAUG-ACUAUAAAGCCAUGUGGCAUAACAUGGGGUAGUCCUCCUUGGGAUUU
.....(((((........--------.)))))..........((((((.....((((((......))))))(-(((((....((((((......)))))).))))))))))))....... ( -31.70)
>DroYak_CAF1 927 120 + 1
AGCAAUGCGUAAGUAAAGAACGUAACAACGUGAUCGCGGAAUGGGAAAGUGUGGUGGCCAGACUUGGCUAUGGACUAUAAAGCCAUGUGGAAUAACAUGGGGUAGUCCUUCUUGGGAUUU
.....(((....)))....((((....))))((((.((((((((..((((.(((...))).))))..))))(((((((....((((((......)))))).))))))).)).)).)))). ( -36.30)
>consensus
AGCAAUGCGUAAGUAAAG________AACGCGGUUAAGGAAUGGGAAAGUGUGGUGGCCAGACUUGGUUAUG_ACUAUAAAGCCAUGUGGCAUAACAUGGGGUAGUCCUCCUUGGGAUUU
.....(((((.................))))).(((((((((((..((((.(((...))).))))..))))(.(((((....((((((......)))))).))))).))))))))..... (-26.16 = -25.41 +  -0.75)

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 09:38:34 2006