Locus 1055

Sequence ID 2R_DroMel_CAF1
Location 4,319,970 – 4,320,079
Length 109
Max. P 0.917766
window1863 window1864

overview

Window 3

Location 4,319,970 – 4,320,079
Length 109
Sequences 5
Columns 110
Reading direction forward
Mean pairwise identity 77.35
Mean single sequence MFE -21.69
Consensus MFE -9.43
Energy contribution -11.89
Covariance contribution 2.46
Combinations/Pair 1.15
Mean z-score -2.08
Structure conservation index 0.43
SVM decision value 0.69
SVM RNA-class probability 0.824818
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4319970 109 + 20766785
UUUGGUGUUAGUAAUAAAACCCAUGCU-CACACAUAAAAAGCACUUAAGCUUUGUUUUUUGUUGUUUUUUUUUUUUUUUGUCAGCUUAAGCAAAGUGCAAGUGUGUGUAU
....((((.((((..........))))-.)))).......((((((..(((((((((...((((.................))))..)))))))))..))))))...... ( -25.03)
>DroSec_CAF1 75014 91 + 1
UUUGGUGUUAGUAAUAAAACCCCUGCU-CACACAUAAAAUGCACUUAAGCUUUGUUGUU------------------UUUGCAGCUUAAGCAAAGUGAAAGUGUGUGUAU
...(((.(((....))).)))......-.(((((((.....(((((..((((.(((((.------------------...)))))..)))).)))))....))))))).. ( -25.30)
>DroSim_CAF1 78614 92 + 1
UUUGGUGUUAGUAAUAAAACCCCUGCU-CACACAUAAAAAGCACUUAGGCUUUGUUGUUU-----------------UUUGCAGCUUAAGCAAAGUGAAAGUGUGUGUAU
...(((.(((....))).)))......-.(((((((.....(((((..((((.(((((..-----------------...)))))..)))).)))))....))))))).. ( -26.10)
>DroEre_CAF1 74155 90 + 1
UUUGGUGUUAGUAAUAAAACCCAUGUUUUGCUCAUAAAAAGCACUUAAGCCUUGUU---U-----------------UUUGCAGCUUAAGCUAAGUGAAAGCGUACAUAU
...(((.(((....))).))).((((((((((.......))).(((((((..(((.---.-----------------...)))))))))).......)))))))...... ( -17.60)
>DroYak_CAF1 76488 87 + 1
--UGGUGUUAGUAAUAAAUUCCACGCU-UACACAUAAAAAGCACUUAACUCUUUUU---U-----------------UGUUCAGCUUACGCAAAAUGAAAGUGCAUAUAA
--..((((.(((............)))-.)))).......((((((...((...((---(-----------------(((.........)))))).))))))))...... ( -14.40)
>consensus
UUUGGUGUUAGUAAUAAAACCCAUGCU_CACACAUAAAAAGCACUUAAGCUUUGUU_UUU_________________UUUGCAGCUUAAGCAAAGUGAAAGUGUGUGUAU
...(((.(((....))).)))...................((((((..((((((((................................))))))))..))))))...... ( -9.43 = -11.89 +   2.46)

alignment

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secondary structure

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dotplot

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Window 4

Location 4,319,970 – 4,320,079
Length 109
Sequences 5
Columns 110
Reading direction reverse
Mean pairwise identity 77.35
Mean single sequence MFE -18.50
Consensus MFE -11.79
Energy contribution -11.63
Covariance contribution -0.16
Combinations/Pair 1.30
Mean z-score -1.98
Structure conservation index 0.64
SVM decision value 1.12
SVM RNA-class probability 0.917766
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4319970 109 - 20766785
AUACACACACUUGCACUUUGCUUAAGCUGACAAAAAAAAAAAAAAACAACAAAAAACAAAGCUUAAGUGCUUUUUAUGUGUG-AGCAUGGGUUUUAUUACUAACACCAAA
...((((((...(((((.....((((((...............................)))))))))))......))))))-....((((((........))).))).. ( -20.48)
>DroSec_CAF1 75014 91 - 1
AUACACACACUUUCACUUUGCUUAAGCUGCAAA------------------AACAACAAAGCUUAAGUGCAUUUUAUGUGUG-AGCAGGGGUUUUAUUACUAACACCAAA
.....(((((.........(((((((((.....------------------........))))))))).........)))))-....((.(((........))).))... ( -20.09)
>DroSim_CAF1 78614 92 - 1
AUACACACACUUUCACUUUGCUUAAGCUGCAAA-----------------AAACAACAAAGCCUAAGUGCUUUUUAUGUGUG-AGCAGGGGUUUUAUUACUAACACCAAA
...((((((.......(((((.......)))))-----------------.......(((((......)))))...))))))-....((.(((........))).))... ( -17.50)
>DroEre_CAF1 74155 90 - 1
AUAUGUACGCUUUCACUUAGCUUAAGCUGCAAA-----------------A---AACAAGGCUUAAGUGCUUUUUAUGAGCAAAACAUGGGUUUUAUUACUAACACCAAA
.(((((..((((.......(((((((((.....-----------------.---.....))))))))).........))))...)))))(((.(((....))).)))... ( -19.09)
>DroYak_CAF1 76488 87 - 1
UUAUAUGCACUUUCAUUUUGCGUAAGCUGAACA-----------------A---AAAAAGAGUUAAGUGCUUUUUAUGUGUA-AGCGUGGAAUUUAUUACUAACACCA--
...((((((.........)))))).(((..(((-----------------.---..(((((((.....)))))))...))).-)))(((..............)))..-- ( -15.34)
>consensus
AUACACACACUUUCACUUUGCUUAAGCUGCAAA_________________AAA_AACAAAGCUUAAGUGCUUUUUAUGUGUG_AGCAUGGGUUUUAUUACUAACACCAAA
...((((((..........(((((((((...............................)))))))))........))))))......(((((........))).))... (-11.79 = -11.63 +  -0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:55:16 2006