Locus 5404

Sequence ID 2R_DroMel_CAF1
Location 17,449,852 – 17,449,951
Length 99
Max. P 0.990231
window8620 window8621

overview

Window 0

Location 17,449,852 – 17,449,951
Length 99
Sequences 5
Columns 107
Reading direction forward
Mean pairwise identity 81.17
Mean single sequence MFE -28.24
Consensus MFE -19.40
Energy contribution -20.44
Covariance contribution 1.04
Combinations/Pair 1.17
Mean z-score -2.79
Structure conservation index 0.69
SVM decision value 2.20
SVM RNA-class probability 0.990231
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17449852 99 + 20766785
-GGGUCCUUGGGAAAUGCAACUGCAAGUGC-------AAAUGCAGCUUGCGCAAUAAAUGCGUUCAUUUAACAUGAAAUGCAAGUCGCAAGCUGCAAGUAUUGAAAU
-...(((...)))(((((...(((....))-------)..(((((((((((.......(((((((((.....))).))))))...))))))))))).)))))..... ( -30.80)
>DroVir_CAF1 185880 89 + 1
---------G--AGCUGCACCGCAAAGUUCAGCAAGGAAACGCAGCUCG---UAUAAAUGCGUUCAUUUAACACGAAAUGCAACUUAAGGGCUCGAA----UCAAAU
---------(--((((((...)).(((((......(....)(((..(((---(.((((((....))))))..))))..))))))))...)))))...----...... ( -21.30)
>DroSim_CAF1 169473 99 + 1
-GGGUCCUUGGGAAAUGCAACUGCAAGUGC-------AAAUGCAGCUUGUGCAAUAAAUGCGUUCAUUUAACAUGAAAUGCAAGUCGCAAGCUGCAAGUAUUGAAAU
-...(((...)))(((((...(((....))-------)..(((((((((((.......(((((((((.....))).))))))...))))))))))).)))))..... ( -28.90)
>DroEre_CAF1 163369 100 + 1
UGGAUCCUUGGGAAAUGCAACUGCAAGUGC-------AAAUGCAGCUUGCGCAAUAAAUGCGUUCAUUUAACAUGAAAUGCAAGUCGCAAGCUGCAAGUAUUGAAAU
....(((...)))(((((...(((....))-------)..(((((((((((.......(((((((((.....))).))))))...))))))))))).)))))..... ( -30.90)
>DroYak_CAF1 149747 100 + 1
UGGUUCCUUGGGAAAUGCAACUGCAAGUGC-------AAAUGCAGCUUGUGCAAUAAAUGCGUUCAUUUAACAUGAAAUGCAAGUUGCAAGCUGCAAGUAUUGAAAU
...(((....)))(((((...(((....))-------)..(((((((..((((((...(((((((((.....))).)))))).))))))))))))).)))))..... ( -29.30)
>consensus
_GGGUCCUUGGGAAAUGCAACUGCAAGUGC_______AAAUGCAGCUUGCGCAAUAAAUGCGUUCAUUUAACAUGAAAUGCAAGUCGCAAGCUGCAAGUAUUGAAAU
...............(((....)))...............(((((((((((.......(((((((((.....))).))))))...)))))))))))........... (-19.40 = -20.44 +   1.04)

alignment

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secondary structure

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dotplot

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Window 1

Location 17,449,852 – 17,449,951
Length 99
Sequences 5
Columns 107
Reading direction reverse
Mean pairwise identity 81.17
Mean single sequence MFE -26.18
Consensus MFE -17.48
Energy contribution -18.12
Covariance contribution 0.64
Combinations/Pair 1.17
Mean z-score -2.78
Structure conservation index 0.67
SVM decision value 2.12
SVM RNA-class probability 0.988452
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17449852 99 - 20766785
AUUUCAAUACUUGCAGCUUGCGACUUGCAUUUCAUGUUAAAUGAACGCAUUUAUUGCGCAAGCUGCAUUU-------GCACUUGCAGUUGCAUUUCCCAAGGACCC-
.........((((.((((((((...(((..(((((.....))))).))).......))))))))(((.((-------((....)))).)))......)))).....- ( -29.10)
>DroVir_CAF1 185880 89 - 1
AUUUGA----UUCGAGCCCUUAAGUUGCAUUUCGUGUUAAAUGAACGCAUUUAUA---CGAGCUGCGUUUCCUUGCUGAACUUUGCGGUGCAGCU--C---------
......----............((((((...((((((.(((((....))))))))---)))((((((.(((......)))...))))))))))))--.--------- ( -22.40)
>DroSim_CAF1 169473 99 - 1
AUUUCAAUACUUGCAGCUUGCGACUUGCAUUUCAUGUUAAAUGAACGCAUUUAUUGCACAAGCUGCAUUU-------GCACUUGCAGUUGCAUUUCCCAAGGACCC-
.........((((.....(((((((.(((.(((((.....))))).(((.....((((.....))))..)-------))...)))))))))).....)))).....- ( -24.90)
>DroEre_CAF1 163369 100 - 1
AUUUCAAUACUUGCAGCUUGCGACUUGCAUUUCAUGUUAAAUGAACGCAUUUAUUGCGCAAGCUGCAUUU-------GCACUUGCAGUUGCAUUUCCCAAGGAUCCA
.........((((.((((((((...(((..(((((.....))))).))).......))))))))(((.((-------((....)))).)))......))))...... ( -29.10)
>DroYak_CAF1 149747 100 - 1
AUUUCAAUACUUGCAGCUUGCAACUUGCAUUUCAUGUUAAAUGAACGCAUUUAUUGCACAAGCUGCAUUU-------GCACUUGCAGUUGCAUUUCCCAAGGAACCA
....((((...((((((((((((..(((..(((((.....))))).)))....)))))..)))))))..(-------((....)))))))...((((...))))... ( -25.40)
>consensus
AUUUCAAUACUUGCAGCUUGCGACUUGCAUUUCAUGUUAAAUGAACGCAUUUAUUGCACAAGCUGCAUUU_______GCACUUGCAGUUGCAUUUCCCAAGGACCC_
...........((((((((((((..(((..(((((.....))))).)))....))))..))))))))..........(((........)))................ (-17.48 = -18.12 +   0.64)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:43:57 2006