Locus 7608

Sequence ID 3R_DroMel_CAF1
Location 20,404,208 – 20,404,391
Length 183
Max. P 0.999889
window12273 window12274 window12275 window12276

overview

Window 3

Location 20,404,208 – 20,404,316
Length 108
Sequences 5
Columns 109
Reading direction reverse
Mean pairwise identity 95.02
Mean single sequence MFE -31.33
Consensus MFE -25.98
Energy contribution -26.38
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.93
Structure conservation index 0.83
SVM decision value 1.33
SVM RNA-class probability 0.942675
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20404208 108 - 27905053
ACGGAACCGAAUGGAUCGGAUCUUCGAAGAGGGUUGCUGCACCCCAUUAAAAGAAACUGCAUGCGGCAACCCACAGUUAAGUAUGUAAUUUUCUGCCAUC-CAUAUGCA
.((....)).((((((.((......((((((((((((((((....................)))))))))))(((........)))..)))))..)))))-)))..... ( -30.65)
>DroSec_CAF1 26783 108 - 1
ACGGAACCGAAUGGAUCGGAUCUUCGAAGAGGGUUGCUGCACCCCAUUAUAAGAAACUGCAUGCGGCAACCCACAGUUAAGUAUGUAAUUUUCUGCCAUC-CAUAUGCA
.((....)).((((((.((......((((((((((((((((....................)))))))))))(((........)))..)))))..)))))-)))..... ( -30.65)
>DroSim_CAF1 29784 108 - 1
ACGGAACCGAAUGGAUCGGAUCUUCGAAGAGGGUUGCUGCACCCCAUUAAAAGAAACUGCAUGCGGCAACCCACAGUUAAGUAUGCAAUUUUCUGCCAUC-CAUAUGCA
.((....)).((((((.((...........(((((((((((....................))))))))))).(((..((........))..))))))))-)))..... ( -30.25)
>DroEre_CAF1 26388 109 - 1
ACGGAACCGAAUGGAUCGGAUCUUCCGGGAGGGUUGCUGCAACCCAUUAUAAGAAACUGCAUGCGGCAACCCACAGUUAAGUAUGUAAUUUUCUGCCAUCCCAUAUGCA
..((((((((.....))))...))))(((((((((((((((....................))))))))))).(((..((........))..)))...))))....... ( -35.05)
>DroYak_CAF1 30578 108 - 1
ACGGAACCGAAUGAAUCGGAUCUUCCGGCAGGGUAGCUGCAAUCCAUUAUAAGAAACUGCAUGCGGCAACCCACAGUUAAGUAUGUAAUUUUCUGCCAUC-CAUAUGCA
..(((.((((.....)))).......((((((((.((((((....................)))))).))))(((........))).......)))).))-)....... ( -30.05)
>consensus
ACGGAACCGAAUGGAUCGGAUCUUCGAAGAGGGUUGCUGCACCCCAUUAUAAGAAACUGCAUGCGGCAACCCACAGUUAAGUAUGUAAUUUUCUGCCAUC_CAUAUGCA
..(((.((((.....)))).))).......(((((((((((....................)))))))))))........((((((................)))))). (-25.98 = -26.38 +   0.40)

alignment

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secondary structure

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dotplot

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Window 4

Location 20,404,243 – 20,404,354
Length 111
Sequences 5
Columns 111
Reading direction forward
Mean pairwise identity 94.23
Mean single sequence MFE -33.18
Consensus MFE -28.92
Energy contribution -29.72
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -2.02
Structure conservation index 0.87
SVM decision value 2.33
SVM RNA-class probability 0.992496
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20404243 111 + 27905053
UGGGUUGCCGCAUGCAGUUUCUUUUAAUGGGGUGCAGCAACCCUCUUCGAAGAUCCGAUCCAUUCGGUUCCGUUUCGAUACGAUUGCUUUUUCCACGCGAAAAACUCAUUU
.(((((((.((((.(.(((......))).).)))).)))))))...((((((..((((.....)))).....)))))).....((((.........))))........... ( -32.20)
>DroSec_CAF1 26818 111 + 1
UGGGUUGCCGCAUGCAGUUUCUUAUAAUGGGGUGCAGCAACCCUCUUCGAAGAUCCGAUCCAUUCGGUUCCGUUUCGAUACGAUUGCUUUUUCCACGCGGAAAACUCAUUU
.(((((((.((((.(.(((......))).).)))).)))))))...((((((..((((.....)))).....))))))......((..((((((....))))))..))... ( -35.60)
>DroSim_CAF1 29819 111 + 1
UGGGUUGCCGCAUGCAGUUUCUUUUAAUGGGGUGCAGCAACCCUCUUCGAAGAUCCGAUCCAUUCGGUUCCGUUUCGAUACGAUUGCUUUUUCCACGCGGAAAACUCAUUU
.(((((((.((((.(.(((......))).).)))).)))))))...((((((..((((.....)))).....))))))......((..((((((....))))))..))... ( -35.60)
>DroEre_CAF1 26424 111 + 1
UGGGUUGCCGCAUGCAGUUUCUUAUAAUGGGUUGCAGCAACCCUCCCGGAAGAUCCGAUCCAUUCGGUUCCGUUUCGAUACGAUUGCUUUUUCCACACGGAAAACUCAUUU
.(((((((.(((.((.(((......)))..))))).)))))))(((.((((((..(((((...((((.......))))...)))))..))))))....))).......... ( -33.50)
>DroYak_CAF1 30613 111 + 1
UGGGUUGCCGCAUGCAGUUUCUUAUAAUGGAUUGCAGCUACCCUGCCGGAAGAUCCGAUUCAUUCGGUUCCGUUUCGAUACGACUGCUUUUUCCCCACGGAAAACUCAUUU
((((((.......((((((......((((((..((((.....))))(....)..((((.....)))).)))))).......))))))...((((....))))))))))... ( -29.02)
>consensus
UGGGUUGCCGCAUGCAGUUUCUUAUAAUGGGGUGCAGCAACCCUCUUCGAAGAUCCGAUCCAUUCGGUUCCGUUUCGAUACGAUUGCUUUUUCCACGCGGAAAACUCAUUU
.(((((((.((((.(.(((......))).).)))).)))))))........((.((((.....)))).))(((......)))..((..((((((....))))))..))... (-28.92 = -29.72 +   0.80)

alignment

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secondary structure

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dotplot

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Window 5

Location 20,404,243 – 20,404,354
Length 111
Sequences 5
Columns 111
Reading direction reverse
Mean pairwise identity 94.23
Mean single sequence MFE -34.81
Consensus MFE -32.73
Energy contribution -32.93
Covariance contribution 0.20
Combinations/Pair 1.07
Mean z-score -2.47
Structure conservation index 0.94
SVM decision value 4.40
SVM RNA-class probability 0.999889
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20404243 111 - 27905053
AAAUGAGUUUUUCGCGUGGAAAAAGCAAUCGUAUCGAAACGGAACCGAAUGGAUCGGAUCUUCGAAGAGGGUUGCUGCACCCCAUUAAAAGAAACUGCAUGCGGCAACCCA
...((..((((((....))))))..)).((...((((...(((.((((.....)))).))))))).))(((((((((((....................))))))))))). ( -33.05)
>DroSec_CAF1 26818 111 - 1
AAAUGAGUUUUCCGCGUGGAAAAAGCAAUCGUAUCGAAACGGAACCGAAUGGAUCGGAUCUUCGAAGAGGGUUGCUGCACCCCAUUAUAAGAAACUGCAUGCGGCAACCCA
...((..((((((....))))))..)).((...((((...(((.((((.....)))).))))))).))(((((((((((....................))))))))))). ( -35.95)
>DroSim_CAF1 29819 111 - 1
AAAUGAGUUUUCCGCGUGGAAAAAGCAAUCGUAUCGAAACGGAACCGAAUGGAUCGGAUCUUCGAAGAGGGUUGCUGCACCCCAUUAAAAGAAACUGCAUGCGGCAACCCA
...((..((((((....))))))..)).((...((((...(((.((((.....)))).))))))).))(((((((((((....................))))))))))). ( -35.95)
>DroEre_CAF1 26424 111 - 1
AAAUGAGUUUUCCGUGUGGAAAAAGCAAUCGUAUCGAAACGGAACCGAAUGGAUCGGAUCUUCCGGGAGGGUUGCUGCAACCCAUUAUAAGAAACUGCAUGCGGCAACCCA
...((..((((((....))))))..))............(((((((((.....))))...)))))...(((((((((((....................))))))))))). ( -36.15)
>DroYak_CAF1 30613 111 - 1
AAAUGAGUUUUCCGUGGGGAAAAAGCAGUCGUAUCGAAACGGAACCGAAUGAAUCGGAUCUUCCGGCAGGGUAGCUGCAAUCCAUUAUAAGAAACUGCAUGCGGCAACCCA
...((..((((((....))))))..))(((((......))((((((((.....))))...))))))).((((.((((((....................)))))).)))). ( -32.95)
>consensus
AAAUGAGUUUUCCGCGUGGAAAAAGCAAUCGUAUCGAAACGGAACCGAAUGGAUCGGAUCUUCGAAGAGGGUUGCUGCACCCCAUUAUAAGAAACUGCAUGCGGCAACCCA
...((..((((((....))))))..))......((((...(((.((((.....)))).)))))))...(((((((((((....................))))))))))). (-32.73 = -32.93 +   0.20)

alignment

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secondary structure

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dotplot

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Window 6

Location 20,404,276 – 20,404,391
Length 115
Sequences 5
Columns 116
Reading direction reverse
Mean pairwise identity 95.15
Mean single sequence MFE -25.84
Consensus MFE -23.36
Energy contribution -23.40
Covariance contribution 0.04
Combinations/Pair 1.08
Mean z-score -1.32
Structure conservation index 0.90
SVM decision value 0.67
SVM RNA-class probability 0.818020
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20404276 115 - 27905053
CAAUAGAAAUGUAAAUAGGA-AAUUUUAAUAAUGAUUGAAAUGAGUUUUUCGCGUGGAAAAAGCAAUCGUAUCGAAACGGAACCGAAUGGAUCGGAUCUUCGAAGAGGGUUGCUGC
........(((..((.....-.((((((((....))))))))......))..)))......(((((((.(.((((...(((.((((.....)))).)))))))..).))))))).. ( -24.60)
>DroSec_CAF1 26851 115 - 1
CAAUAGAAAUGUAAAUAGGA-AAUUUUAAUAAUGAUUGAAAUGAGUUUUCCGCGUGGAAAAAGCAAUCGUAUCGAAACGGAACCGAAUGGAUCGGAUCUUCGAAGAGGGUUGCUGC
..(((....)))........-.((((((((....))))))))...((((((....))))))(((((((.(.((((...(((.((((.....)))).)))))))..).))))))).. ( -26.50)
>DroSim_CAF1 29852 115 - 1
CAAUAGAAAUGUAAAUAGGA-AAUUUUAAUAAUGAUUGAAAUGAGUUUUCCGCGUGGAAAAAGCAAUCGUAUCGAAACGGAACCGAAUGGAUCGGAUCUUCGAAGAGGGUUGCUGC
..(((....)))........-.((((((((....))))))))...((((((....))))))(((((((.(.((((...(((.((((.....)))).)))))))..).))))))).. ( -26.50)
>DroEre_CAF1 26457 116 - 1
CAAUAGAAAUGUAAAUAGGAAAAUUUUAAUAAUGAUUGAAAUGAGUUUUCCGUGUGGAAAAAGCAAUCGUAUCGAAACGGAACCGAAUGGAUCGGAUCUUCCGGGAGGGUUGCUGC
..(((....))).....(((((((((................)))))))))..........(((((((...((....(((((((((.....))))...))))).)).))))))).. ( -25.69)
>DroYak_CAF1 30646 115 - 1
CAAUAGAAAUGUAAAUAGCA-AAUUUUAAUAAUGAUUGAAAUGAGUUUUCCGUGGGGAAAAAGCAGUCGUAUCGAAACGGAACCGAAUGAAUCGGAUCUUCCGGCAGGGUAGCUGC
..(((....)))...((((.-..(((..(((.((((((.......((((((....))))))..)))))))))..)))(((((((((.....))))...)))))........)))). ( -25.90)
>consensus
CAAUAGAAAUGUAAAUAGGA_AAUUUUAAUAAUGAUUGAAAUGAGUUUUCCGCGUGGAAAAAGCAAUCGUAUCGAAACGGAACCGAAUGGAUCGGAUCUUCGAAGAGGGUUGCUGC
..(((....)))..........((((((((....))))))))...((((((....))))))(((((((.(.((((...(((.((((.....)))).)))))))..).))))))).. (-23.36 = -23.40 +   0.04)

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 12:50:03 2006