Locus 3574

Sequence ID 3R_DroMel_CAF1
Location 9,672,467 – 9,672,610
Length 143
Max. P 0.789747
window5746 window5747 window5748

overview

Window 6

Location 9,672,467 – 9,672,586
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 78.44
Mean single sequence MFE -31.66
Consensus MFE -20.68
Energy contribution -23.38
Covariance contribution 2.70
Combinations/Pair 1.15
Mean z-score -1.73
Structure conservation index 0.65
SVM decision value 0.46
SVM RNA-class probability 0.746320
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9672467 119 + 27905053
UGUUUUGCGAGCACCUCGAAUUUGGCAUUCUUUCAUCGGGAGUAUUUCAAAUUCUCUGGACUCGAAUUAGAAUUCGUUUAUGGGCUGUUGCCUCAUAAAGGAAUGGUGGUGCUUA-AUUU
........(((((((.(((((((((.((.((((.....)))).)).)))))))).................((((.(((((((((....))).)))))).)))).).))))))).-.... ( -36.70)
>DroSec_CAF1 64171 120 + 1
UGUUUUGCGAGCACCUCGAAUUUGGCAUUCUUUCAUCGGGAGUAUUUCAAAUUCUCUGGACUCGAAUUGGAAUUCGUUUAUGGGCUGUUGCCUCAUAAAGGAAUGGUGGUGCCUAAAUUU
..........(((((.(((((((((.((.((((.....)))).)).)))))))).................((((.(((((((((....))).)))))).)))).).)))))........ ( -33.80)
>DroSim_CAF1 67103 120 + 1
UGUUUUGCGAGCACCUCGAAUUUGGCAUUCUUUCAUCGGGAGUAUUUCAAAUUCUCUGGACUCGAAUUGGAAUUCGUUUAUGGGCUGUUGCCUCAUAAAGGAAUGGUGGUGCUUAAAUUU
........(((((((.(((((((((.((.((((.....)))).)).)))))))).................((((.(((((((((....))).)))))).)))).).)))))))...... ( -36.70)
>DroEre_CAF1 65298 92 + 1
UGUUUGGCGAGCCCCUCGGACUUGGCAGUCUUUCACCAGGAGUAUUUCGAAUUCUCUGGAUU-----------UCGAAUA-----------------CAAGAAUGCUGUUGCUUAAAUAU
(((((((((((((....)).)))((((.((((((.....))(((((.((((.((....)).)-----------)))))))-----------------))))).))))...)).)))))). ( -21.00)
>DroYak_CAF1 69166 103 + 1
UGUUUGGCGAGCACCUCGAAUUUGGCAUUCCUUCACCGGGAGUAUUUCAGAUUCGCUGGACUCGAAGGAGAAUUCAUUUA-----------------UAGGAUUGGUGGUGCUUAAAUUU
........(((((((..((((((((.((((((.....))))))...))))))))(((...(((....)))(((((.....-----------------..)))))))))))))))...... ( -30.10)
>consensus
UGUUUUGCGAGCACCUCGAAUUUGGCAUUCUUUCAUCGGGAGUAUUUCAAAUUCUCUGGACUCGAAUUAGAAUUCGUUUAUGGGCUGUUGCCUCAUAAAGGAAUGGUGGUGCUUAAAUUU
........(((((((..((((((((.((((((.....))))))...)))))))).................((((.(((((((((....))).)))))).))))...)))))))...... (-20.68 = -23.38 +   2.70)

alignment

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secondary structure

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dotplot

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Window 7

Location 9,672,467 – 9,672,586
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 78.44
Mean single sequence MFE -25.10
Consensus MFE -13.08
Energy contribution -15.86
Covariance contribution 2.78
Combinations/Pair 1.13
Mean z-score -2.04
Structure conservation index 0.52
SVM decision value 0.58
SVM RNA-class probability 0.789747
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9672467 119 - 27905053
AAAU-UAAGCACCACCAUUCCUUUAUGAGGCAACAGCCCAUAAACGAAUUCUAAUUCGAGUCCAGAGAAUUUGAAAUACUCCCGAUGAAAGAAUGCCAAAUUCGAGGUGCUCGCAAAACA
....-..((((((........((((((.(((....)))))))))((((((...((((..(((..(((.((.....)).)))..)))....))))....)))))).))))))......... ( -29.60)
>DroSec_CAF1 64171 120 - 1
AAAUUUAGGCACCACCAUUCCUUUAUGAGGCAACAGCCCAUAAACGAAUUCCAAUUCGAGUCCAGAGAAUUUGAAAUACUCCCGAUGAAAGAAUGCCAAAUUCGAGGUGCUCGCAAAACA
.......((((((........((((((.(((....)))))))))((((((...((((..(((..(((.((.....)).)))..)))....))))....)))))).))))))......... ( -29.60)
>DroSim_CAF1 67103 120 - 1
AAAUUUAAGCACCACCAUUCCUUUAUGAGGCAACAGCCCAUAAACGAAUUCCAAUUCGAGUCCAGAGAAUUUGAAAUACUCCCGAUGAAAGAAUGCCAAAUUCGAGGUGCUCGCAAAACA
.......((((((........((((((.(((....)))))))))((((((...((((..(((..(((.((.....)).)))..)))....))))....)))))).))))))......... ( -29.60)
>DroEre_CAF1 65298 92 - 1
AUAUUUAAGCAACAGCAUUCUUG-----------------UAUUCGA-----------AAUCCAGAGAAUUCGAAAUACUCCUGGUGAAAGACUGCCAAGUCCGAGGGGCUCGCCAAACA
........((...(((......(-----------------(((((((-----------(.((....)).)))).)))))((((.(.....((((....))))).))))))).))...... ( -17.50)
>DroYak_CAF1 69166 103 - 1
AAAUUUAAGCACCACCAAUCCUA-----------------UAAAUGAAUUCUCCUUCGAGUCCAGCGAAUCUGAAAUACUCCCGGUGAAGGAAUGCCAAAUUCGAGGUGCUCGCCAAACA
.......((((((..........-----------------........(((.((...((((.(((.....)))....))))..)).))).((((.....))))..))))))......... ( -19.20)
>consensus
AAAUUUAAGCACCACCAUUCCUUUAUGAGGCAACAGCCCAUAAACGAAUUCCAAUUCGAGUCCAGAGAAUUUGAAAUACUCCCGAUGAAAGAAUGCCAAAUUCGAGGUGCUCGCAAAACA
.......((((((...((((.((((((.(((....))))))))).)))).................(((((((..((.((.........)).))..)))))))..))))))......... (-13.08 = -15.86 +   2.78)

alignment

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secondary structure

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dotplot

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Window 8

Location 9,672,507 – 9,672,610
Length 103
Sequences 3
Columns 104
Reading direction reverse
Mean pairwise identity 96.79
Mean single sequence MFE -17.33
Consensus MFE -15.07
Energy contribution -15.40
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.88
Structure conservation index 0.87
SVM decision value -0.03
SVM RNA-class probability 0.517881
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9672507 103 - 27905053
UAAUUACAAUAAUUUGAGUACAAUAAAU-UAAGCACCACCAUUCCUUUAUGAGGCAACAGCCCAUAAACGAAUUCUAAUUCGAGUCCAGAGAAUUUGAAAUACU
......(((....)))((((........-............(((.((((((.(((....))))))))).)))(((.(((((.........))))).))).)))) ( -16.20)
>DroSec_CAF1 64211 104 - 1
UAAUUACAACAAUUUGAGUACAAUAAAUUUAGGCACCACCAUUCCUUUAUGAGGCAACAGCCCAUAAACGAAUUCCAAUUCGAGUCCAGAGAAUUUGAAAUACU
...........((((((((............((.....))((((.((((((.(((....))))))))).))))....))))))))................... ( -17.20)
>DroSim_CAF1 67143 104 - 1
UAAUUACAACAAUUUGAGUUCAAUAAAUUUAAGCACCACCAUUCCUUUAUGAGGCAACAGCCCAUAAACGAAUUCCAAUUCGAGUCCAGAGAAUUUGAAAUACU
............((..(((((........................((((((.(((....)))))))))(((((....)))))........)))))..))..... ( -18.60)
>consensus
UAAUUACAACAAUUUGAGUACAAUAAAUUUAAGCACCACCAUUCCUUUAUGAGGCAACAGCCCAUAAACGAAUUCCAAUUCGAGUCCAGAGAAUUUGAAAUACU
................((((.....................(((.((((((.(((....))))))))).)))(((.(((((.........))))).))).)))) (-15.07 = -15.40 +   0.33)

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 11:04:40 2006