Locus 4438

Sequence ID 3R_DroMel_CAF1
Location 11,713,520 – 11,713,650
Length 130
Max. P 0.940410
window7254 window7255 window7256 window7257

overview

Window 4

Location 11,713,520 – 11,713,610
Length 90
Sequences 5
Columns 90
Reading direction forward
Mean pairwise identity 88.62
Mean single sequence MFE -25.60
Consensus MFE -19.35
Energy contribution -19.91
Covariance contribution 0.56
Combinations/Pair 1.05
Mean z-score -1.74
Structure conservation index 0.76
SVM decision value 0.35
SVM RNA-class probability 0.701137
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11713520 90 + 27905053
AUUGUUCUUUUUUAGCUGCCCGUAGUUGUAUAUAUCUUGGCAGCAGCUGGCUCUACAGACAUGUGCCAACAGCCAAGAGCCAACCGGCAA
.....((((.....((((((.(((........)))...)))))).((((....((((....))))....)))).))))(((....))).. ( -24.20)
>DroSec_CAF1 50809 90 + 1
AUUGUUCUUUUUUAGCUGCCCGUGGUUGUAUAUAUCUUGGCAGCAGCUGGCUCUACAGACAUGUGCCAAGAGCCAAGAGCCAAGCGGCAA
..............(((((...(((((.(.....((((((((.((.(((......)))...))))))))))....).))))).))))).. ( -32.40)
>DroSim_CAF1 52483 83 + 1
AUUGUUCUUUUUUAGCUGCCCGUGGUUGUAUAUAUCUUGGCAGCAGCUGGCUCUACAGACAUGUGCCAAGA-------GCCAACUGGCAA
................((((..((((........((((((((.((.(((......)))...))))))))))-------))))...)))). ( -26.30)
>DroEre_CAF1 50733 83 + 1
AUUGUUAUUUUCUAGCUGCCUGUACUUGUAUACAUCUUGGCAGCAGCUGGGUCUACGGACAUGUGCCAAGA-------GCCAACCGCCAA
...........((((((((.(((...((....)).....)))))))))))(((....))).((.((.....-------))))........ ( -22.00)
>DroYak_CAF1 54150 83 + 1
AUUGUUCUUUUUUAGCUGCCUGUAGUUGUAUAUAUCUUGGCAGCAGCUGGGUCUACGGACAUGUGCCAAGA-------GCCAACCGCCAA
...((((((.....((((((.(((........)))...)))))).((...(((....)))....)).))))-------)).......... ( -23.10)
>consensus
AUUGUUCUUUUUUAGCUGCCCGUAGUUGUAUAUAUCUUGGCAGCAGCUGGCUCUACAGACAUGUGCCAAGA_______GCCAACCGGCAA
................((((.((...........((((((((.((.(((......)))...))))))))))...........)).)))). (-19.35 = -19.91 +   0.56)

alignment

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secondary structure

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dotplot

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Window 5

Location 11,713,520 – 11,713,610
Length 90
Sequences 5
Columns 90
Reading direction reverse
Mean pairwise identity 88.62
Mean single sequence MFE -27.20
Consensus MFE -17.62
Energy contribution -18.26
Covariance contribution 0.64
Combinations/Pair 1.05
Mean z-score -2.47
Structure conservation index 0.65
SVM decision value 0.04
SVM RNA-class probability 0.551767
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11713520 90 - 27905053
UUGCCGGUUGGCUCUUGGCUGUUGGCACAUGUCUGUAGAGCCAGCUGCUGCCAAGAUAUAUACAACUACGGGCAGCUAAAAAAGAACAAU
.....((((((((((.((((((....))).)))...))))))))))((((((.((..........))...)))))).............. ( -30.10)
>DroSec_CAF1 50809 90 - 1
UUGCCGCUUGGCUCUUGGCUCUUGGCACAUGUCUGUAGAGCCAGCUGCUGCCAAGAUAUAUACAACCACGGGCAGCUAAAAAAGAACAAU
..(((....)))((((((((((.(((....)))...))))))....((((((..................)))))).....))))..... ( -28.07)
>DroSim_CAF1 52483 83 - 1
UUGCCAGUUGGC-------UCUUGGCACAUGUCUGUAGAGCCAGCUGCUGCCAAGAUAUAUACAACCACGGGCAGCUAAAAAAGAACAAU
.....(((((((-------(((.(((....)))...))))))))))((((((..................)))))).............. ( -29.07)
>DroEre_CAF1 50733 83 - 1
UUGGCGGUUGGC-------UCUUGGCACAUGUCCGUAGACCCAGCUGCUGCCAAGAUGUAUACAAGUACAGGCAGCUAGAAAAUAACAAU
(((..((((((.-------(((((((....).))).))).))))))((((((....(((((....)))))))))))..........))). ( -26.10)
>DroYak_CAF1 54150 83 - 1
UUGGCGGUUGGC-------UCUUGGCACAUGUCCGUAGACCCAGCUGCUGCCAAGAUAUAUACAACUACAGGCAGCUAAAAAAGAACAAU
(((..((((((.-------(((((((....).))).))).))))))((((((..................))))))..........))). ( -22.67)
>consensus
UUGCCGGUUGGC_______UCUUGGCACAUGUCUGUAGAGCCAGCUGCUGCCAAGAUAUAUACAACUACGGGCAGCUAAAAAAGAACAAU
.....(((((((.......(((.(((....)))...))))))))))((((((..................)))))).............. (-17.62 = -18.26 +   0.64)

alignment

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secondary structure

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dotplot

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Window 6

Location 11,713,546 – 11,713,650
Length 104
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 80.88
Mean single sequence MFE -32.80
Consensus MFE -19.90
Energy contribution -19.93
Covariance contribution 0.03
Combinations/Pair 1.23
Mean z-score -2.54
Structure conservation index 0.61
SVM decision value 0.92
SVM RNA-class probability 0.881762
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11713546 104 + 27905053
UGUAUAUAUCUUGGCAGCAGCUGG------CUCUACAGACAUGUGCCAACAGCCAAGAGCCAACCGGCAAUUGCCAAGAAGGAAGCAGCCUUAAAUUGCAGCUAAAAGCC
........(((((((((..(((((------((((...(...(((....))).)..))))))....)))..)))))))))....(((.((........)).)))....... ( -29.80)
>DroSec_CAF1 50835 104 + 1
UGUAUAUAUCUUGGCAGCAGCUGG------CUCUACAGACAUGUGCCAAGAGCCAAGAGCCAAGCGGCAAUUGCCAAGAAGGAAGCAGCCUUAAAUGGCAGCUAAGAGCC
........(((((((.((.(((((------(((((((....)))((.....))..)))))).))).))...(((((..((((......))))...))))))))))))... ( -38.50)
>DroSim_CAF1 52509 97 + 1
UGUAUAUAUCUUGGCAGCAGCUGG------CUCUACAGACAUGUGCCAAGA-------GCCAACUGGCAAUUGCCAAGAAGGAAGCAGCCUUAAAUGGCAGCUAAGAGCC
........(((((((..(((.(((------(((((((....)))....)))-------)))).))).....(((((..((((......))))...))))))))))))... ( -36.00)
>DroEre_CAF1 50759 97 + 1
UGUAUACAUCUUGGCAGCAGCUGG------GUCUACGGACAUGUGCCAAGA-------GCCAACCGCCAAAAGCCAAGAUGGAAGCAGCCUUAAAUGGCAGUUAAGAGCC
(((...(((((((((....((.((------(((....))).((.((.....-------)))).)))).....)))))))))...)))(((......)))........... ( -31.50)
>DroYak_CAF1 54176 97 + 1
UGUAUAUAUCUUGGCAGCAGCUGG------GUCUACGGACAUGUGCCAAGA-------GCCAACCGCCAAUUGCCAACAAGGAAGCAGCCUUAAAUGGCAGCUAAGAGUC
........(((((((.((.(.(((------.(((..((.(....))).)))-------.))).).))....(((((..((((......))))...))))))))))))... ( -29.60)
>DroAna_CAF1 50408 89 + 1
UGCAUAUAUCUUGGCAGCAGCUGCUGGAAUGUCCACGGACAUGUGGC---------------------AAGUGCCAAGAAGGAAGCGCUUUGAAUUGGCAGCCAAGAGCC
........(((((((....((..(....(((((....))))))..))---------------------...((((((.((((.....))))...)))))))))))))... ( -31.40)
>consensus
UGUAUAUAUCUUGGCAGCAGCUGG______CUCUACAGACAUGUGCCAAGA_______GCCAACCGGCAAUUGCCAAGAAGGAAGCAGCCUUAAAUGGCAGCUAAGAGCC
........(((((((.(((.(((............)))...)))...........................(((((..((((......))))...))))))))))))... (-19.90 = -19.93 +   0.03)

alignment

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secondary structure

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dotplot

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Window 7

Location 11,713,546 – 11,713,650
Length 104
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 80.88
Mean single sequence MFE -36.58
Consensus MFE -17.81
Energy contribution -20.23
Covariance contribution 2.42
Combinations/Pair 1.08
Mean z-score -3.43
Structure conservation index 0.49
SVM decision value 1.29
SVM RNA-class probability 0.940410
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11713546 104 - 27905053
GGCUUUUAGCUGCAAUUUAAGGCUGCUUCCUUCUUGGCAAUUGCCGGUUGGCUCUUGGCUGUUGGCACAUGUCUGUAGAG------CCAGCUGCUGCCAAGAUAUAUACA
((.....(((.((........)).))).)).((((((((...((.((((((((((.((((((....))).)))...))))------))))))))))))))))........ ( -38.40)
>DroSec_CAF1 50835 104 - 1
GGCUCUUAGCUGCCAUUUAAGGCUGCUUCCUUCUUGGCAAUUGCCGCUUGGCUCUUGGCUCUUGGCACAUGUCUGUAGAG------CCAGCUGCUGCCAAGAUAUAUACA
((.....(((.(((......))).))).)).((((((((...((.(((.((((((.(((...........)))...))))------))))).))))))))))........ ( -38.80)
>DroSim_CAF1 52509 97 - 1
GGCUCUUAGCUGCCAUUUAAGGCUGCUUCCUUCUUGGCAAUUGCCAGUUGGC-------UCUUGGCACAUGUCUGUAGAG------CCAGCUGCUGCCAAGAUAUAUACA
((.....(((.(((......))).))).)).((((((((...((.(((((((-------(((.(((....)))...))))------))))))))))))))))........ ( -41.80)
>DroEre_CAF1 50759 97 - 1
GGCUCUUAACUGCCAUUUAAGGCUGCUUCCAUCUUGGCUUUUGGCGGUUGGC-------UCUUGGCACAUGUCCGUAGAC------CCAGCUGCUGCCAAGAUGUAUACA
(((........)))...............(((((((((....(((((((((.-------(((((((....).))).))).------))))))))))))))))))...... ( -37.90)
>DroYak_CAF1 54176 97 - 1
GACUCUUAGCUGCCAUUUAAGGCUGCUUCCUUGUUGGCAAUUGGCGGUUGGC-------UCUUGGCACAUGUCCGUAGAC------CCAGCUGCUGCCAAGAUAUAUACA
...((((.(((((((..(((((......))))).)))))...(((((((((.-------(((((((....).))).))).------))))))))))).))))........ ( -34.80)
>DroAna_CAF1 50408 89 - 1
GGCUCUUGGCUGCCAAUUCAAAGCGCUUCCUUCUUGGCACUU---------------------GCCACAUGUCCGUGGACAUUCCAGCAGCUGCUGCCAAGAUAUAUGCA
(((........)))..........((.....((((((((.((---------------------((...(((((....)))))....))))....)))))))).....)). ( -27.80)
>consensus
GGCUCUUAGCUGCCAUUUAAGGCUGCUUCCUUCUUGGCAAUUGCCGGUUGGC_______UCUUGGCACAUGUCCGUAGAC______CCAGCUGCUGCCAAGAUAUAUACA
.......(((.(((......))).)))....((((((((.....(((((((............(((....))).............))))))).))))))))........ (-17.81 = -20.23 +   2.42)

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 11:29:18 2006