Locus 3044

Sequence ID 2L_DroMel_CAF1
Location 8,683,776 – 8,683,898
Length 122
Max. P 0.978281
window4844 window4845 window4846

overview

Window 4

Location 8,683,776 – 8,683,879
Length 103
Sequences 5
Columns 108
Reading direction forward
Mean pairwise identity 86.30
Mean single sequence MFE -29.60
Consensus MFE -27.38
Energy contribution -27.38
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.80
Structure conservation index 0.92
SVM decision value 1.35
SVM RNA-class probability 0.944747
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8683776 103 + 22407834
CAAAUACUUA---AAAAAA-AUGCUUUCGCAUU-CUCCCCGACGGGGAAUUGAACCCCGGUCUCCCGCGUGACAGGCGGGGAUACUAACCACUAUACUAUCGAGGACG
..........---.....(-((((....)))))-.(((.((((((((.......)))))(((.(((((.......))))))))................))).))).. ( -30.50)
>DroPse_CAF1 3309 101 + 1
AUAA-AAUA-UAAAAAGAA-----AUCUACAUUCCUCCCCGACGGGGAAUUGAACCCCGGUCUCCCGCGUGACAGGCGGGGAUACUAACCACUAUACUAUCGAGGAUU
....-....-.........-----........(((((.....(((((.......)))))(((.(((((.......))))))))..................))))).. ( -28.30)
>DroSec_CAF1 3400 107 + 1
CAUAUAUGUACGAAAAAAAUGUGCUUUCACAUU-CUCCCCGACGGGGAAUUGAACCCCGGUCUCCCGCGUGACAGGCGGGGAUACUAACCACUAUACUAUCGAGGAUG
.......(((((.......))))).....((((-(((.....(((((.......)))))(((.(((((.......))))))))..................))))))) ( -31.00)
>DroSim_CAF1 2342 106 + 1
CAUAUAUGUACGAAAAAAA-ACGCUUUCACAUU-CUCCCCGACGGGGAAUUGAACCCCGGUCUCCCGCGUGACAGGCGGGGAUACUAACCACUAUACUAUCGAGGAUG
...........((((....-....)))).((((-(((.....(((((.......)))))(((.(((((.......))))))))..................))))))) ( -29.90)
>DroPer_CAF1 2243 102 + 1
AUAAAAAUA-UAAAAAGAA-----GUUUACAUUCCUCCCCGACGGGGAAUUGAACCCCGGUCUCCCGCGUGACAGGCGGGGAUACUAACCACUAUACUAUCGAGGAUU
.........-.........-----........(((((.....(((((.......)))))(((.(((((.......))))))))..................))))).. ( -28.30)
>consensus
CAAAUAAUUACAAAAAAAA___GCUUUCACAUU_CUCCCCGACGGGGAAUUGAACCCCGGUCUCCCGCGUGACAGGCGGGGAUACUAACCACUAUACUAUCGAGGAUG
...................................(((.((((((((.......)))))(((.(((((.......))))))))................))).))).. (-27.38 = -27.38 +   0.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 8,683,776 – 8,683,879
Length 103
Sequences 5
Columns 108
Reading direction reverse
Mean pairwise identity 86.30
Mean single sequence MFE -35.62
Consensus MFE -29.98
Energy contribution -29.98
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.23
Structure conservation index 0.84
SVM decision value 1.81
SVM RNA-class probability 0.978281
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8683776 103 - 22407834
CGUCCUCGAUAGUAUAGUGGUUAGUAUCCCCGCCUGUCACGCGGGAGACCGGGGUUCAAUUCCCCGUCGGGGAG-AAUGCGAAAGCAU-UUUUUU---UAAGUAUUUG
..((((((((........((((......(((((.......))))).))))((((.......))))))))))))(-(((((....))))-))....---.......... ( -38.20)
>DroPse_CAF1 3309 101 - 1
AAUCCUCGAUAGUAUAGUGGUUAGUAUCCCCGCCUGUCACGCGGGAGACCGGGGUUCAAUUCCCCGUCGGGGAGGAAUGUAGAU-----UUCUUUUUA-UAUU-UUAU
..((((((((........((((......(((((.......))))).))))((((.......))))))))))))((((((((((.-----.....))))-))))-)).. ( -35.60)
>DroSec_CAF1 3400 107 - 1
CAUCCUCGAUAGUAUAGUGGUUAGUAUCCCCGCCUGUCACGCGGGAGACCGGGGUUCAAUUCCCCGUCGGGGAG-AAUGUGAAAGCACAUUUUUUUCGUACAUAUAUG
.......(((((....((((.........)))))))))....((....))((((.......))))((((..(((-((((((....)))))))))..)).))....... ( -35.70)
>DroSim_CAF1 2342 106 - 1
CAUCCUCGAUAGUAUAGUGGUUAGUAUCCCCGCCUGUCACGCGGGAGACCGGGGUUCAAUUCCCCGUCGGGGAG-AAUGUGAAAGCGU-UUUUUUUCGUACAUAUAUG
..((((((((........((((......(((((.......))))).))))((((.......))))))))))))(-(((((....))))-))................. ( -34.60)
>DroPer_CAF1 2243 102 - 1
AAUCCUCGAUAGUAUAGUGGUUAGUAUCCCCGCCUGUCACGCGGGAGACCGGGGUUCAAUUCCCCGUCGGGGAGGAAUGUAAAC-----UUCUUUUUA-UAUUUUUAU
..((((((((........((((......(((((.......))))).))))((((.......))))))))))))((((((((((.-----.....))))-))))))... ( -34.00)
>consensus
CAUCCUCGAUAGUAUAGUGGUUAGUAUCCCCGCCUGUCACGCGGGAGACCGGGGUUCAAUUCCCCGUCGGGGAG_AAUGUGAAAGC___UUUUUUUCAUAAAUAUUUG
..((((((((........((((......(((((.......))))).))))((((.......))))))))))))................................... (-29.98 = -29.98 +   0.00)

alignment

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secondary structure

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dotplot

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Window 6

Location 8,683,800 – 8,683,898
Length 98
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 79.62
Mean single sequence MFE -31.80
Consensus MFE -27.33
Energy contribution -27.33
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.20
Structure conservation index 0.86
SVM decision value 0.32
SVM RNA-class probability 0.686862
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8683800 98 + 22407834
GCAUU-CUCCCCGACGGGGAAUUGAACCCCGGUCUCCCGCGUGACAGGCGGGGAUACUAACCACUAUACUAUCGAGGACGUUGAUACUUUUGAGUCAAA---------------------
.....-.(((.((((((((.......)))))(((.(((((.......))))))))................))).)))..(((((.(....).))))).--------------------- ( -29.90)
>DroPse_CAF1 3330 120 + 1
ACAUUCCUCCCCGACGGGGAAUUGAACCCCGGUCUCCCGCGUGACAGGCGGGGAUACUAACCACUAUACUAUCGAGGAUUUUCUUCUUCUGCCGUCAAACUGCUAUUUUACCACUAUACU
...........((.((((..((((.....))))..))))))((((.((((((((((.((.......)).))))((((.....)))).))))))))))....................... ( -29.20)
>DroEre_CAF1 3581 98 + 1
ACAUU-CUCCCCGACGGGGAAUUGAACCCCGGUCUCCCGCGUGACAGGCGGGGAUACUAACCACUAUACUAUCGAGGACGGUGAACGAGGGAACUCAAA---------------------
.(((.-.(((.((((((((.......)))))(((.(((((.......))))))))................))).)))..)))...(((....)))...--------------------- ( -36.40)
>DroYak_CAF1 2381 98 + 1
ACAUU-CUCCCCGACGGGGAAUUGAACCCCGGUCUCCCGCGUGACAGGCGGGGAUACUAACCACUAUACUAUCGAGGACGGUGGACGACCUUAGUCAAA---------------------
.(((.-.(((.((((((((.......)))))(((.(((((.......))))))))................))).)))..)))(((.......)))...--------------------- ( -34.40)
>DroAna_CAF1 2137 98 + 1
ACAUU-CUCCCCGACGGGGAAUUGAACCCCGGUCUCCCGCGUGACAGGCGGGGAUACUAACCACUAUACUAUCGAGGACGGUGAUGGACGAGCGCCUAU---------------------
.(((.-.(((.((((((((.......)))))(((.(((((.......))))))))................))).)))..)))..((.(....)))...--------------------- ( -32.10)
>DroPer_CAF1 2265 120 + 1
ACAUUCCUCCCCGACGGGGAAUUGAACCCCGGUCUCCCGCGUGACAGGCGGGGAUACUAACCACUAUACUAUCGAGGAUUUGCUUCUUCUGCCGUCAAACUGCUAUUUUACCACUAUACU
............(((((((.......))))(((.((((((.......))))))....................(((((......))))).))))))........................ ( -28.80)
>consensus
ACAUU_CUCCCCGACGGGGAAUUGAACCCCGGUCUCCCGCGUGACAGGCGGGGAUACUAACCACUAUACUAUCGAGGACGGUGAUCGACUGCAGUCAAA_____________________
.......(((.((((((((.......)))))(((.(((((.......))))))))................))).))).......................................... (-27.33 = -27.33 +  -0.00)

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 10:42:58 2006