Locus 1011

Sequence ID 2R_DroMel_CAF1
Location 4,213,834 – 4,213,994
Length 160
Max. P 0.973380
window1789 window1790 window1791

overview

Window 9

Location 4,213,834 – 4,213,954
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 92.22
Mean single sequence MFE -45.85
Consensus MFE -39.76
Energy contribution -40.20
Covariance contribution 0.44
Combinations/Pair 1.08
Mean z-score -2.48
Structure conservation index 0.87
SVM decision value 1.71
SVM RNA-class probability 0.973380
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4213834 120 + 20766785
GUGUGCCUUUGUGGCGAGUGCCAAGGACUGCAAUAGGAGCACUAAUGUGCUGCCAUACAUGAGGAUCAUGGCCUGCGAUCUGAACUGCGUAAACGAAUUCGAGCAGGUUAUCUUCCUCGC
((((((((...((((....))))))).........(.(((((....))))).))))))..(((((..(((((((((....((((...((....))..)))).)))))))))..))))).. ( -44.30)
>DroSec_CAF1 25492 120 + 1
GUGUGCCUUUGUGGCGAAAGCCAAGGACUGCAAUAGGAGCACCAAUGUGCUGCCCUACAUGAGGAUCAUGGCCUGCGACCUGAACUGCGUAAACGAAUUCGAGCAGGUCAUCUUCCUCAC
.(((.(((...((((....)))))))...))).(((((((((....)))))..))))..((((((..(((((((((....((((...((....))..)))).)))))))))..)))))). ( -48.70)
>DroEre_CAF1 27351 120 + 1
CUGUGCCUUUGUGCUGAAGGCCAAGGAUUGCAAUAGGAGCACCAAUGUGCUGCCCUACAUGAGGAUCAUGGCCUGCGACCUGAACUGCGUUAACGAGUUCGAGCAGGUCAUCGUCCUGGC
.((.((((((.....))))))))......((..(((((((((....)))))..))))....(((((.(((((((((....((((((.((....)))))))).))))))))).))))).)) ( -46.90)
>DroYak_CAF1 28145 120 + 1
GUGUGCCUUUGUGGAGAAGGCCAAGGACUGCAAUAGGAGCACCAAUGUGCUGCCCUACAUGAGGAUCAUGGCCUGCGAUCUGAACUGCGUCAACGAAUUCCAGCAGGUCAUCUUCCUCAC
.((.((((((.....))))))))..........(((((((((....)))))..))))..((((((..(((((((((.....(((...((....))..)))..)))))))))..)))))). ( -43.50)
>consensus
GUGUGCCUUUGUGGCGAAGGCCAAGGACUGCAAUAGGAGCACCAAUGUGCUGCCCUACAUGAGGAUCAUGGCCUGCGACCUGAACUGCGUAAACGAAUUCGAGCAGGUCAUCUUCCUCAC
.(((.(((...((((....)))))))...)))...(((((((....))))).)).....((((((..(((((((((....((((...((....))..)))).)))))))))..)))))). (-39.76 = -40.20 +   0.44) 

alignment

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secondary structure

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dotplot

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Window 0

Location 4,213,834 – 4,213,954
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 92.22
Mean single sequence MFE -42.38
Consensus MFE -35.71
Energy contribution -36.65
Covariance contribution 0.94
Combinations/Pair 1.05
Mean z-score -1.96
Structure conservation index 0.84
SVM decision value 0.85
SVM RNA-class probability 0.866857
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4213834 120 - 20766785
GCGAGGAAGAUAACCUGCUCGAAUUCGUUUACGCAGUUCAGAUCGCAGGCCAUGAUCCUCAUGUAUGGCAGCACAUUAGUGCUCCUAUUGCAGUCCUUGGCACUCGCCACAAAGGCACAC
..(((((..((..((((((((((((((....)).))))).))..)))))..))..))))).((((.((.(((((....)))))))...))))(((((((((....))))...))).)).. ( -40.90)
>DroSec_CAF1 25492 120 - 1
GUGAGGAAGAUGACCUGCUCGAAUUCGUUUACGCAGUUCAGGUCGCAGGCCAUGAUCCUCAUGUAGGGCAGCACAUUGGUGCUCCUAUUGCAGUCCUUGGCUUUCGCCACAAAGGCACAC
(((((((..(((.((((((((((((((....)).))))).))..))))).)))..)))))))((((((.(((((....))))))))..))).(((((((((....))))...))).)).. ( -44.40)
>DroEre_CAF1 27351 120 - 1
GCCAGGACGAUGACCUGCUCGAACUCGUUAACGCAGUUCAGGUCGCAGGCCAUGAUCCUCAUGUAGGGCAGCACAUUGGUGCUCCUAUUGCAAUCCUUGGCCUUCAGCACAAAGGCACAG
(((........(((((....(((((((....)).))))))))))((((((((.(((.....(((((((.(((((....))))))))..)))))))..))))))...)).....))).... ( -41.90)
>DroYak_CAF1 28145 120 - 1
GUGAGGAAGAUGACCUGCUGGAAUUCGUUGACGCAGUUCAGAUCGCAGGCCAUGAUCCUCAUGUAGGGCAGCACAUUGGUGCUCCUAUUGCAGUCCUUGGCCUUCUCCACAAAGGCACAC
(((((((..(((.(((((..(((((((....)).))))).....))))).)))..)))))))((((((.(((((....))))))))..)))......(((((((.......))))).)). ( -42.30)
>consensus
GCGAGGAAGAUGACCUGCUCGAAUUCGUUUACGCAGUUCAGAUCGCAGGCCAUGAUCCUCAUGUAGGGCAGCACAUUGGUGCUCCUAUUGCAGUCCUUGGCCUUCGCCACAAAGGCACAC
..(((((..(((.(((((..(((((((....)).))))).....))))).)))..))))).(((((((.(((((....))))))))..)))).....(((((((.......))))).)). (-35.71 = -36.65 +   0.94) 

alignment

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secondary structure

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dotplot

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Window 1

Location 4,213,874 – 4,213,994
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 90.56
Mean single sequence MFE -38.80
Consensus MFE -31.58
Energy contribution -32.45
Covariance contribution 0.87
Combinations/Pair 1.09
Mean z-score -1.58
Structure conservation index 0.81
SVM decision value 0.24
SVM RNA-class probability 0.648867
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4213874 120 + 20766785
ACUAAUGUGCUGCCAUACAUGAGGAUCAUGGCCUGCGAUCUGAACUGCGUAAACGAAUUCGAGCAGGUUAUCUUCCUCGCUCUGUUCAUGGGUCUGUGCUACGAGAUACUUGUUCUGCUG
......(..(.(((..(((((((((..(((((((((....((((...((....))..)))).)))))))))..))))))...))).....)))..)..).(((((...)))))....... ( -32.90)
>DroSec_CAF1 25532 120 + 1
ACCAAUGUGCUGCCCUACAUGAGGAUCAUGGCCUGCGACCUGAACUGCGUAAACGAAUUCGAGCAGGUCAUCUUCCUCACUCUGUUCAUGGGUCUCUGCUACGAGAUACUUGUUCUGCUG
...........((((.(((((((((..(((((((((....((((...((....))..)))).)))))))))..))))))...)))....))))....((.(((((...)))))...)).. ( -37.60)
>DroEre_CAF1 27391 120 + 1
ACCAAUGUGCUGCCCUACAUGAGGAUCAUGGCCUGCGACCUGAACUGCGUUAACGAGUUCGAGCAGGUCAUCGUCCUGGCACUCUUCAUGGCUCUCUGCUAUGGGAUACUUGUGCUGCUG
....(((((......))))).(((((.(((((((((....((((((.((....)))))))).))))))))).)))))((((((((.((((((.....))))))))).....))))).... ( -45.30)
>DroYak_CAF1 28185 120 + 1
ACCAAUGUGCUGCCCUACAUGAGGAUCAUGGCCUGCGAUCUGAACUGCGUCAACGAAUUCCAGCAGGUCAUCUUCCUCACAUUGUUCAUGGCCCUCUGCUAUGAGAUAUUUGUGCUGCUG
........((.((.......(((((..(((((((((.....(((...((....))..)))..)))))))))..)))))(((...((((((((.....)))))))).....))))).)).. ( -39.40)
>consensus
ACCAAUGUGCUGCCCUACAUGAGGAUCAUGGCCUGCGACCUGAACUGCGUAAACGAAUUCGAGCAGGUCAUCUUCCUCACACUGUUCAUGGCUCUCUGCUACGAGAUACUUGUGCUGCUG
...........((...(((((((((..(((((((((....((((...((....))..)))).)))))))))..)))))).....((((((((.....)))))))).....)))...)).. (-31.58 = -32.45 +   0.87) 

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 09:54:05 2006