Locus 4292

Sequence ID 2R_DroMel_CAF1
Location 14,103,228 – 14,103,353
Length 125
Max. P 0.837357
window6888 window6889 window6890

overview

Window 8

Location 14,103,228 – 14,103,322
Length 94
Sequences 5
Columns 100
Reading direction forward
Mean pairwise identity 92.32
Mean single sequence MFE -36.96
Consensus MFE -29.26
Energy contribution -29.30
Covariance contribution 0.04
Combinations/Pair 1.04
Mean z-score -1.79
Structure conservation index 0.79
SVM decision value 0.71
SVM RNA-class probability 0.829922
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14103228 94 + 20766785
GACAGUCGGUAGAAAGUGCCGCCGGCGGCACCGUUAAAAUAAUGAGCUGCAACAGCGGCACUGUGAUUUGUUGUUGCCGUGGCCGUU------GUCGUUG
(((((.((((....((((((((..(((((..(((((...))))).)))))....))))))))(..((.....))..)....))))))------))).... ( -37.60)
>DroSec_CAF1 12305 94 + 1
GACAGUCGGUAGAAAGUGCCGCCGGCGGCACCGUUAAAAUAAUGAGCUGCAACAGCGGCACUGUGAUUUGUUGUUGCCGUGGCCGUU------GCCGUUG
..(((.((((((...(.(((((.(((((((.(((((...))))).(((((....)))))............))))))))))))).))------))))))) ( -36.30)
>DroSim_CAF1 25577 100 + 1
GACAGUCGGUAGAAAGUGCCGCCGGCGGCACCGUUAAAAUAAUGAGCUGCAACAGCGGCACUGUGAUUUGUUGUUGCCGUGGCCGUUGCCGUUGCCGUUG
(.(((.((((((...(.(((((.(((((((.(((((...))))).(((((....)))))............))))))))))))).))))))))).).... ( -37.10)
>DroEre_CAF1 7480 94 + 1
GACAGUCGGUAGAAAGUGCCGCCGGCGGCACCGUUAAAAUAAUGAGCUGCAACAGCGGAACUGUGAUUUGUUGUUGCCAUUGC------CGUUGCCGUUG
..(((.((((.((..((((((....))))))..)).....((((.((.(((((((((((.......)))))))))))....))------))))))))))) ( -33.00)
>DroYak_CAF1 23191 100 + 1
GACAGUCGGUAGAAAGUGCCGCCGGCGGCACCGUUAAAAUAAUGAGCUGCAACAGCGGCACUGUGAUUUGUUGUUGCCGCUGCCGUUGCUGUUGCCGUUG
((((((((((((..((((((((..(((((..(((((...))))).)))))....))))))))(..((.....))..)..))))))..))))))....... ( -40.80)
>consensus
GACAGUCGGUAGAAAGUGCCGCCGGCGGCACCGUUAAAAUAAUGAGCUGCAACAGCGGCACUGUGAUUUGUUGUUGCCGUGGCCGUU___GUUGCCGUUG
..(((.((((....((((((((..(((((..(((((...))))).)))))....))))))))(..((.....))..)................))))))) (-29.26 = -29.30 +   0.04)

alignment

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secondary structure

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dotplot

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Window 9

Location 14,103,228 – 14,103,322
Length 94
Sequences 5
Columns 100
Reading direction reverse
Mean pairwise identity 92.32
Mean single sequence MFE -30.89
Consensus MFE -24.08
Energy contribution -24.48
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.90
Structure conservation index 0.78
SVM decision value 0.74
SVM RNA-class probability 0.837357
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14103228 94 - 20766785
CAACGAC------AACGGCCACGGCAACAACAAAUCACAGUGCCGCUGUUGCAGCUCAUUAUUUUAACGGUGCCGCCGGCGGCACUUUCUACCGACUGUC
....(((------(.(((....(....)..........((((((((((..(((.(.............).)))...)))))))))).....)))..)))) ( -28.42)
>DroSec_CAF1 12305 94 - 1
CAACGGC------AACGGCCACGGCAACAACAAAUCACAGUGCCGCUGUUGCAGCUCAUUAUUUUAACGGUGCCGCCGGCGGCACUUUCUACCGACUGUC
...((((------((((((...((((..............))))))))))))................(((((((....)))))))......))...... ( -29.44)
>DroSim_CAF1 25577 100 - 1
CAACGGCAACGGCAACGGCCACGGCAACAACAAAUCACAGUGCCGCUGUUGCAGCUCAUUAUUUUAACGGUGCCGCCGGCGGCACUUUCUACCGACUGUC
...(((.....((((((((...((((..............))))))))))))................(((((((....))))))).....)))...... ( -32.04)
>DroEre_CAF1 7480 94 - 1
CAACGGCAACG------GCAAUGGCAACAACAAAUCACAGUUCCGCUGUUGCAGCUCAUUAUUUUAACGGUGCCGCCGGCGGCACUUUCUACCGACUGUC
...((((((((------((..((....))((........))...))))))))................(((((((....)))))))......))...... ( -27.80)
>DroYak_CAF1 23191 100 - 1
CAACGGCAACAGCAACGGCAGCGGCAACAACAAAUCACAGUGCCGCUGUUGCAGCUCAUUAUUUUAACGGUGCCGCCGGCGGCACUUUCUACCGACUGUC
...(((....(((..(((((((((((..............)))))))))))..)))............(((((((....))))))).....)))...... ( -36.74)
>consensus
CAACGGCAAC___AACGGCCACGGCAACAACAAAUCACAGUGCCGCUGUUGCAGCUCAUUAUUUUAACGGUGCCGCCGGCGGCACUUUCUACCGACUGUC
...(((...........((....)).............((((((((((..(((.(.............).)))...)))))))))).....)))...... (-24.08 = -24.48 +   0.40)

alignment

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secondary structure

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dotplot

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Window 0

Location 14,103,261 – 14,103,353
Length 92
Sequences 5
Columns 98
Reading direction reverse
Mean pairwise identity 91.55
Mean single sequence MFE -22.13
Consensus MFE -15.92
Energy contribution -16.72
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -2.22
Structure conservation index 0.72
SVM decision value 0.32
SVM RNA-class probability 0.687264
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14103261 92 - 20766785
AAAAGGAAAACUGAAAACCGAAAGCGGUACACAACGAC------AACGGCCACGGCAACAACAAAUCACAGUGCCGCUGUUGCAGCUCAUUAUUUUAA
...........(((....(((.((((((((....((..------..))((....))..............)))))))).)))....)))......... ( -19.00)
>DroSec_CAF1 12338 92 - 1
AAAAGGAAAACUGAAAACCGAAAGCGGUACACAACGGC------AACGGCCACGGCAACAACAAAUCACAGUGCCGCUGUUGCAGCUCAUUAUUUUAA
...........(((....(((.((((((((....((..------..))((....))..............)))))))).)))....)))......... ( -22.80)
>DroSim_CAF1 25610 98 - 1
AAAAGGAAAACUGAAAACCGAAAGCGGUACACAACGGCAACGGCAACGGCCACGGCAACAACAAAUCACAGUGCCGCUGUUGCAGCUCAUUAUUUUAA
...........(((....(((.((((((((.....(((..((....)))))..(....)...........)))))))).)))....)))......... ( -25.80)
>DroEre_CAF1 7513 92 - 1
AAAAGGAAAACUGAAAAUCGAAAGCGGUACACAACGGCAACG------GCAAUGGCAACAACAAAUCACAGUUCCGCUGUUGCAGCUCAUUAUUUUAA
...........(((....(((.(((((.((....((....))------....((....))..........)).))))).)))....)))......... ( -17.80)
>DroYak_CAF1 23224 98 - 1
AAAAGGAAAACUGAAAAUCGAAAGCGGUACACAACGGCAACAGCAACGGCAGCGGCAACAACAAAUCACAGUGCCGCUGUUGCAGCUCAUUAUUUUAA
...........(((((.......((.((.....)).))...(((..(((((((((((..............)))))))))))..))).....))))). ( -25.24)
>consensus
AAAAGGAAAACUGAAAACCGAAAGCGGUACACAACGGCAAC___AACGGCCACGGCAACAACAAAUCACAGUGCCGCUGUUGCAGCUCAUUAUUUUAA
...........(((....(((.((((((((.....(((..........)))..(....)...........)))))))).)))....)))......... (-15.92 = -16.72 +   0.80)

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 11:16:22 2006