Locus 1907

Sequence ID 3R_DroMel_CAF1
Location 5,432,968 – 5,433,123
Length 155
Max. P 0.999970
window3136 window3137 window3138

overview

Window 6

Location 5,432,968 – 5,433,083
Length 115
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 88.93
Mean single sequence MFE -27.16
Consensus MFE -24.78
Energy contribution -25.38
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -3.39
Structure conservation index 0.91
SVM decision value 4.77
SVM RNA-class probability 0.999948
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5432968 115 + 27905053
AGAUAUUCGCGCCUUUUCACACUACUACUUCUUCUUCUUGU---UCUUCUGGGUUAACGUCAGCGUUAACCCGU-UUGCCAGGCCAAUUACCCCGCCCCAUAAC-CCAGCAUGAAUAUCG
.((((((((.((.............................---......(((((((((....)))))))))((-(.....(((..........)))....)))-...)).)))))))). ( -28.40)
>DroSec_CAF1 19578 118 + 1
AGAUAUUCGCACCUUUUCACACUACCACUUCUUCUUCUUCUUCGUCUUCUGGGUUAACGUCAGCGUUAACCCGU-UUGCCAAGCCAAUUACCCCGCCCCAUAAC-CCAGCAUGAAUAUCG
.((((((((..............................(((.((....((((((((((....)))))))))).-..)).)))...........((........-...)).)))))))). ( -23.30)
>DroSim_CAF1 14609 118 + 1
AGAUAUUCGCGCCUUUUCACACUACCACUUCUUCUUCUUCUUCGUCUUCUGGGUUAACGUCAGCGUUAACCCGU-UUGCCAAGCCAAUUACCCCGCCCCAUAAC-CCAGCAUGAAUAUCG
.((((((((.((......................................(((((((((....)))))))))((-(.....)))....................-...)).)))))))). ( -24.90)
>DroEre_CAF1 20177 104 + 1
AGAUAUUCGCGCCUUUUCACACUACU------------UCUU---CUUCUGGGUUAACGUCAGCGUUAACCCGU-UUGCCAGGCCAAUUACCCCGCCCCAUAACCCCAGCAUGAAUAUCG
.((((((((.((..............------------....---.....(((((((((....)))))))))((-(.....(((..........)))....)))....)).)))))))). ( -28.40)
>DroYak_CAF1 20510 107 + 1
AGAUAUUCGCGCCUUUUCACACUACU------------UCUUCAUCUUCUGGGUUAACGUCAGCGUUAACCCGUUUUGCCAGGCCAAUUACCCCGCCCCAAAAG-CCAGCAUGAAUAUCG
.((((((((.((..............------------............(((((((((....)))))))))(((((....(((..........)))...))))-)..)).)))))))). ( -30.80)
>consensus
AGAUAUUCGCGCCUUUUCACACUACUACUUCUUCUUCUUCUUC_UCUUCUGGGUUAACGUCAGCGUUAACCCGU_UUGCCAGGCCAAUUACCCCGCCCCAUAAC_CCAGCAUGAAUAUCG
.((((((((.((......................................(((((((((....))))))))).........(((..........)))...........)).)))))))). (-24.78 = -25.38 +   0.60)

alignment

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secondary structure

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dotplot

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Window 7

Location 5,432,968 – 5,433,083
Length 115
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 88.93
Mean single sequence MFE -36.38
Consensus MFE -34.96
Energy contribution -34.76
Covariance contribution -0.20
Combinations/Pair 1.07
Mean z-score -3.08
Structure conservation index 0.96
SVM decision value 5.04
SVM RNA-class probability 0.999970
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5432968 115 - 27905053
CGAUAUUCAUGCUGG-GUUAUGGGGCGGGGUAAUUGGCCUGGCAA-ACGGGUUAACGCUGACGUUAACCCAGAAGA---ACAAGAAGAAGAAGUAGUAGUGUGAAAAGGCGCGAAUAUCU
.(((((((.(((((.-.((.....((.((((.....)))).))..-..(((((((((....)))))))))......---..........))..)))))((((......))))))))))). ( -37.90)
>DroSec_CAF1 19578 118 - 1
CGAUAUUCAUGCUGG-GUUAUGGGGCGGGGUAAUUGGCUUGGCAA-ACGGGUUAACGCUGACGUUAACCCAGAAGACGAAGAAGAAGAAGAAGUGGUAGUGUGAAAAGGUGCGAAUAUCU
.(((((((..(((..-.((((...((.((((.....)))).))..-..(((((((((....)))))))))..............................))))...)))..))))))). ( -33.00)
>DroSim_CAF1 14609 118 - 1
CGAUAUUCAUGCUGG-GUUAUGGGGCGGGGUAAUUGGCUUGGCAA-ACGGGUUAACGCUGACGUUAACCCAGAAGACGAAGAAGAAGAAGAAGUGGUAGUGUGAAAAGGCGCGAAUAUCU
.(((((((.(((..(-((((....((...))...)))))..))).-..(((((((((....)))))))))............................((((......))))))))))). ( -35.10)
>DroEre_CAF1 20177 104 - 1
CGAUAUUCAUGCUGGGGUUAUGGGGCGGGGUAAUUGGCCUGGCAA-ACGGGUUAACGCUGACGUUAACCCAGAAG---AAGA------------AGUAGUGUGAAAAGGCGCGAAUAUCU
.(((((((.((((....((((...((.((((.....)))).))..-..(((((((((....))))))))).....---....------------......))))...)))).))))))). ( -37.10)
>DroYak_CAF1 20510 107 - 1
CGAUAUUCAUGCUGG-CUUUUGGGGCGGGGUAAUUGGCCUGGCAAAACGGGUUAACGCUGACGUUAACCCAGAAGAUGAAGA------------AGUAGUGUGAAAAGGCGCGAAUAUCU
.(((((((.((((..-((((....((.((((.....)))).)).....(((((((((....))))))))).......)))).------------))))((((......))))))))))). ( -38.80)
>consensus
CGAUAUUCAUGCUGG_GUUAUGGGGCGGGGUAAUUGGCCUGGCAA_ACGGGUUAACGCUGACGUUAACCCAGAAGA_GAAGAAGAAGAAGAAGUAGUAGUGUGAAAAGGCGCGAAUAUCU
.(((((((.((((....((((...((.((((.....)))).)).....(((((((((....)))))))))..............................))))...)))).))))))). (-34.96 = -34.76 +  -0.20)

alignment

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secondary structure

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dotplot

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Window 8

Location 5,433,008 – 5,433,123
Length 115
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.95
Mean single sequence MFE -40.52
Consensus MFE -38.53
Energy contribution -38.29
Covariance contribution -0.24
Combinations/Pair 1.03
Mean z-score -2.74
Structure conservation index 0.95
SVM decision value 4.72
SVM RNA-class probability 0.999943
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5433008 115 - 27905053
GAAUCAAGCAAUUGUCGAGGCACUUUUAUUCUGUCUUAAGCGAUAUUCAUGCUGG-GUUAUGGGGCGGGGUAAUUGGCCUGGCAA-ACGGGUUAACGCUGACGUUAACCCAGAAGA---A
...((......(((((.((((.(..(((((((((((((((((.......))))..-....)))))))))))))..))))))))))-..(((((((((....))))))))).))...---. ( -40.50)
>DroSec_CAF1 19618 118 - 1
GAAUCAAGCAAUUGUCGAGGCACUUUUAUUCUGUCUUAAGCGAUAUUCAUGCUGG-GUUAUGGGGCGGGGUAAUUGGCUUGGCAA-ACGGGUUAACGCUGACGUUAACCCAGAAGACGAA
...((......((((((((.((...(((((((((((((((((.......))))..-....))))))))))))).)).))))))))-..(((((((((....))))))))).......)). ( -39.70)
>DroSim_CAF1 14649 118 - 1
GAAUCAAGCAAUUGUCGAGGCACUUUUAUUCUGUCUUAAGCGAUAUUCAUGCUGG-GUUAUGGGGCGGGGUAAUUGGCUUGGCAA-ACGGGUUAACGCUGACGUUAACCCAGAAGACGAA
...((......((((((((.((...(((((((((((((((((.......))))..-....))))))))))))).)).))))))))-..(((((((((....))))))))).......)). ( -39.70)
>DroEre_CAF1 20205 116 - 1
GAAUAAAGCAAUUGUCGAGGCACUUUUAUUCUGUCUUAAGCGAUAUUCAUGCUGGGGUUAUGGGGCGGGGUAAUUGGCCUGGCAA-ACGGGUUAACGCUGACGUUAACCCAGAAG---AA
...........(((((.((((.(..(((((((((((((((((.......)))).......)))))))))))))..))))))))))-..(((((((((....))))))))).....---.. ( -40.01)
>DroYak_CAF1 20538 119 - 1
GAAUCAAGCAAUUGUCGAGGCACUUUUAUUCUGUCUUAAGCGAUAUUCAUGCUGG-CUUUUGGGGCGGGGUAAUUGGCCUGGCAAAACGGGUUAACGCUGACGUUAACCCAGAAGAUGAA
..(((......(((((.((((.(..((((((((((((((((.(.........).)-))..)))))))))))))..))))))))))...(((((((((....)))))))))....)))... ( -42.70)
>consensus
GAAUCAAGCAAUUGUCGAGGCACUUUUAUUCUGUCUUAAGCGAUAUUCAUGCUGG_GUUAUGGGGCGGGGUAAUUGGCCUGGCAA_ACGGGUUAACGCUGACGUUAACCCAGAAGA_GAA
...........(((((.((((.(..(((((((((((((((((.......)))).......)))))))))))))..))))))))))...(((((((((....))))))))).......... (-38.53 = -38.29 +  -0.24)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:22:34 2006