Locus 6677

Sequence ID 3R_DroMel_CAF1
Location 17,560,919 – 17,561,062
Length 143
Max. P 0.999986
window10856 window10857 window10858

overview

Window 6

Location 17,560,919 – 17,561,024
Length 105
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.55
Mean single sequence MFE -27.44
Consensus MFE -20.38
Energy contribution -21.30
Covariance contribution 0.92
Combinations/Pair 1.07
Mean z-score -1.64
Structure conservation index 0.74
SVM decision value 0.09
SVM RNA-class probability 0.578042
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17560919 105 - 27905053
CAAAUCCACUAGGAUCUACAUGGAAAUCGCAUUCAUAGUUGAGUGUUUCUGGUUGCAUCGAAUAUUUAUAUAAGCAAUUUCUU--------UCGG-------UUUUUGCAUUUGAAAUUC
((((...((((((((((....)))....(((((((....))))))))))))))(((((((((....................)--------))))-------....))))))))...... ( -17.45)
>DroSec_CAF1 80 113 - 1
CAAAGCAGCCAGGAUCUACAUGGAAAUCGCAUUCAUAGUUGAGUGUUUCUGGCUGCAUCGAAUAUUUAUACAAGGAAUUUCUUCGGCUUUUUCCA-------AUUUUGCAUUUGAAAUUC
....(((((((((((((....)))....(((((((....)))))))))))))))))..................(((((((....((........-------.....))....))))))) ( -32.12)
>DroSim_CAF1 80 113 - 1
CAAAGCCGCCAGGAUCUACAUGGAAAUCGCAUUCAUAGUUGAGUGUUUCUGGCUGCAUCGAAUAUUUAUACAAGGAAUUUCUUCGGGUUUUUCGA-------UUUUUGCAUUUGAAACUC
....((.((((((((((....)))....(((((((....)))))))))))))).)).((((((..........((((..((....))..))))..-------.......))))))..... ( -29.01)
>DroEre_CAF1 1369 120 - 1
CAAAGCCGCCAGGAUCUACAUGGAAAUCGCAUUCAUAGUUGAGUGUUUCUGGCUGCAUCGAAUAUUUAUACAAGGAAUUUCUUUUGGUUUUUCGUUUCUUGCUUUUUGCAUUUGAAAUCC
....((.((((((((((....)))....(((((((....)))))))))))))).)).................((((..((....))..))))(((((.(((.....)))...))))).. ( -29.10)
>DroYak_CAF1 1291 113 - 1
CAAAGCCGCCAGGAUCUACAUGGAAAUCGCAUUCAUAGUUGAGUGUUUCUGGCUGCAUCGAAUAUUUAUACAAGGAAUUUCUUCGGGUUUUUCGG-------UUUUUGCAUUUGAAAUUC
....((.((((((((((....)))....(((((((....)))))))))))))).)).((((((..........((((..((....))..)))).(-------(....))))))))..... ( -29.50)
>consensus
CAAAGCCGCCAGGAUCUACAUGGAAAUCGCAUUCAUAGUUGAGUGUUUCUGGCUGCAUCGAAUAUUUAUACAAGGAAUUUCUUCGGGUUUUUCGA_______UUUUUGCAUUUGAAAUUC
((((((.((((((((((....)))....(((((((....)))))))))))))).)).................((((..((....))..)))).................))))...... (-20.38 = -21.30 +   0.92)

alignment

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secondary structure

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dotplot

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Window 7

Location 17,560,944 – 17,561,062
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.47
Mean single sequence MFE -25.06
Consensus MFE -22.10
Energy contribution -22.42
Covariance contribution 0.32
Combinations/Pair 1.09
Mean z-score -1.43
Structure conservation index 0.88
SVM decision value 0.83
SVM RNA-class probability 0.860930
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17560944 118 + 27905053
AAAUUGCUUAUAUAAAUAUUCGAUGCAACCAGAAACACUCAACUAUGAAUGCGAUUUCCAUGUAGAUCCUAGUGGAUUUGGCACGUGCGCCAAACGAACUAUAUAAUAAAUUUGC--AAA
.......................(((((...((((((.(((....))).))...)))).((((((.(((....)))((((((......))))))....)))))).......))))--).. ( -19.70)
>DroSec_CAF1 113 120 + 1
AAAUUCCUUGUAUAAAUAUUCGAUGCAGCCAGAAACACUCAACUAUGAAUGCGAUUUCCAUGUAGAUCCUGGCUGCUUUGGCACGUGCGCCAAACAAACUAUACAAUAAAUUUGCGAAAA
(((((..(((((((..........((((((((...((.(((....))).)).(((((......)))))))))))))((((((......)))))).....)))))))..)))))....... ( -31.60)
>DroSim_CAF1 113 120 + 1
AAAUUCCUUGUAUAAAUAUUCGAUGCAGCCAGAAACACUCAACUAUGAAUGCGAUUUCCAUGUAGAUCCUGGCGGCUUUGGCACGUGCGCCAAACAAACUAUACAAUAAAUUUGCGAAAA
(((((..(((((((..........((.(((((...((.(((....))).)).(((((......)))))))))).))((((((......)))))).....)))))))..)))))....... ( -27.00)
>DroEre_CAF1 1409 117 + 1
AAAUUCCUUGUAUAAAUAUUCGAUGCAGCCAGAAACACUCAACUAUGAAUGCGAUUUCCAUGUAGAUCCUGGCGGCUUUGGCACGUGCGCCA-ACAAACUACACAAUAAGUUUGC--AAA
........................((.(((((...((.(((....))).)).(((((......)))))))))).)).(((((......))))-)((((((........)))))).--... ( -23.50)
>DroYak_CAF1 1324 117 + 1
AAAUUCCUUGUAUAAAUAUUCGAUGCAGCCAGAAACACUCAACUAUGAAUGCGAUUUCCAUGUAGAUCCUGGCGGCUUUGGCACGUGCGCCA-ACAAACUACACAAUAAGUUUGC--AAA
........................((.(((((...((.(((....))).)).(((((......)))))))))).)).(((((......))))-)((((((........)))))).--... ( -23.50)
>consensus
AAAUUCCUUGUAUAAAUAUUCGAUGCAGCCAGAAACACUCAACUAUGAAUGCGAUUUCCAUGUAGAUCCUGGCGGCUUUGGCACGUGCGCCAAACAAACUAUACAAUAAAUUUGC__AAA
(((((..(((((((..........((.(((((...((.(((....))).)).(((((......)))))))))).))((((((......)))))).....)))))))..)))))....... (-22.10 = -22.42 +   0.32)

alignment

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secondary structure

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dotplot

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Window 8

Location 17,560,944 – 17,561,062
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.47
Mean single sequence MFE -35.70
Consensus MFE -34.42
Energy contribution -34.42
Covariance contribution 0.00
Combinations/Pair 1.11
Mean z-score -2.95
Structure conservation index 0.96
SVM decision value 5.42
SVM RNA-class probability 0.999986
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17560944 118 - 27905053
UUU--GCAAAUUUAUUAUAUAGUUCGUUUGGCGCACGUGCCAAAUCCACUAGGAUCUACAUGGAAAUCGCAUUCAUAGUUGAGUGUUUCUGGUUGCAUCGAAUAUUUAUAUAAGCAAUUU
.((--((.......(((((((((((((((((((....)))))))...((((((((((....)))....(((((((....)))))))))))))).....)))))...)))))))))))... ( -28.11)
>DroSec_CAF1 113 120 - 1
UUUUCGCAAAUUUAUUGUAUAGUUUGUUUGGCGCACGUGCCAAAGCAGCCAGGAUCUACAUGGAAAUCGCAUUCAUAGUUGAGUGUUUCUGGCUGCAUCGAAUAUUUAUACAAGGAAUUU
.......((((((.(((((((((((((((((((....)))))))(((((((((((((....)))....(((((((....)))))))))))))))))..)))))...))))))).)))))) ( -42.80)
>DroSim_CAF1 113 120 - 1
UUUUCGCAAAUUUAUUGUAUAGUUUGUUUGGCGCACGUGCCAAAGCCGCCAGGAUCUACAUGGAAAUCGCAUUCAUAGUUGAGUGUUUCUGGCUGCAUCGAAUAUUUAUACAAGGAAUUU
.......((((((.(((((((((((((((((((....)))))))((.((((((((((....)))....(((((((....)))))))))))))).))..)))))...))))))).)))))) ( -38.20)
>DroEre_CAF1 1409 117 - 1
UUU--GCAAACUUAUUGUGUAGUUUGU-UGGCGCACGUGCCAAAGCCGCCAGGAUCUACAUGGAAAUCGCAUUCAUAGUUGAGUGUUUCUGGCUGCAUCGAAUAUUUAUACAAGGAAUUU
...--.........(((((((((((((-(((((....)))))).((.((((((((((....)))....(((((((....)))))))))))))).))..)))))...)))))))....... ( -34.70)
>DroYak_CAF1 1324 117 - 1
UUU--GCAAACUUAUUGUGUAGUUUGU-UGGCGCACGUGCCAAAGCCGCCAGGAUCUACAUGGAAAUCGCAUUCAUAGUUGAGUGUUUCUGGCUGCAUCGAAUAUUUAUACAAGGAAUUU
...--.........(((((((((((((-(((((....)))))).((.((((((((((....)))....(((((((....)))))))))))))).))..)))))...)))))))....... ( -34.70)
>consensus
UUU__GCAAAUUUAUUGUAUAGUUUGUUUGGCGCACGUGCCAAAGCCGCCAGGAUCUACAUGGAAAUCGCAUUCAUAGUUGAGUGUUUCUGGCUGCAUCGAAUAUUUAUACAAGGAAUUU
.......((((((.(((((((((((((((((((....)))))))((.((((((((((....)))....(((((((....)))))))))))))).))..)))))...))))))).)))))) (-34.42 = -34.42 +   0.00)

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 12:27:22 2006