Locus 1857

Sequence ID X_DroMel_CAF1
Location 5,128,025 – 5,128,185
Length 160
Max. P 0.991552
window3018 window3019 window3020 window3021

overview

Window 8

Location 5,128,025 – 5,128,145
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 90.83
Mean single sequence MFE -37.62
Consensus MFE -30.82
Energy contribution -33.06
Covariance contribution 2.25
Combinations/Pair 1.00
Mean z-score -1.83
Structure conservation index 0.82
SVM decision value 0.63
SVM RNA-class probability 0.804754
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5128025 120 + 22224390
CACCCACCAUGCCCACAUAGCCGCCCACUUUGGCGCCCAGUCCGCCCGCUGCUCCGUCAGCGGCAGACAAGGACAUCAAGUUGUCCUGUCGCGGCCAGCGAAAGGCAGCAACAAAUUUUA
.........((((......((((((......))))....(.((((((((((......))))))..((((.(((((......))))))))))))).).))....))))............. ( -40.80)
>DroSec_CAF1 4441 120 + 1
CACCCACCACGCCCACUUAGCCGCCCACUUUGGCGCCCAGUCCGCCCGCUGCUCCGUCAGCGGCAGACAUGGACAUCAAGUUGUCCUGUCGCGGCCAGCGAAAGGCAGCAACAAAUUUUA
..........((..(((..((.(((......)))))..)))..))..((((((.(((..((.((.((((.(((((......))))))))))).))..)))...))))))........... ( -41.40)
>DroSim_CAF1 4147 120 + 1
CACCCACCACGCCCAUUUAGCCGCCCACUUUGGCGCCCAGUCCGCCCGCUGCUCCGUCAGCGGCAGACAAGGACAUCAAGUUGUCCUGUCGCGGCCAGCGAAAGGCAGCAACAAAUUUUA
..........(((......((((((......))))....(.((((((((((......))))))..((((.(((((......))))))))))))).).))....))).............. ( -40.10)
>DroYak_CAF1 5118 110 + 1
CACCCUCCACGCCCACUCUGCCGCCCACUCCACCGCCCAGUC----------UCCGUCAGCAGCAGACAAGGACAUCAAGUUGUCCUGUCGCGGCCAGCGAAAGGCAGCAACAAAUUUUA
..........(((..(.(((((((..........((...((.----------.......)).)).((((.(((((......))))))))))))).))).)...))).............. ( -28.20)
>consensus
CACCCACCACGCCCACUUAGCCGCCCACUUUGGCGCCCAGUCCGCCCGCUGCUCCGUCAGCGGCAGACAAGGACAUCAAGUUGUCCUGUCGCGGCCAGCGAAAGGCAGCAACAAAUUUUA
..........(((......(((((.......((((.......)))).((((((.....)))))).((((.(((((......))))))))))))))........))).............. (-30.82 = -33.06 +   2.25)

alignment

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secondary structure

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dotplot

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Window 9

Location 5,128,025 – 5,128,145
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 90.83
Mean single sequence MFE -51.90
Consensus MFE -41.61
Energy contribution -43.55
Covariance contribution 1.94
Combinations/Pair 1.08
Mean z-score -2.10
Structure conservation index 0.80
SVM decision value 0.89
SVM RNA-class probability 0.874426
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5128025 120 - 22224390
UAAAAUUUGUUGCUGCCUUUCGCUGGCCGCGACAGGACAACUUGAUGUCCUUGUCUGCCGCUGACGGAGCAGCGGGCGGACUGGGCGCCAAAGUGGGCGGCUAUGUGGGCAUGGUGGGUG
.....((((((((.(((.......))).))))))))((.(((..((((((..(((((((((((......)))).)))))))(((.((((......)))).)))...)))))))))..)). ( -52.30)
>DroSec_CAF1 4441 120 - 1
UAAAAUUUGUUGCUGCCUUUCGCUGGCCGCGACAGGACAACUUGAUGUCCAUGUCUGCCGCUGACGGAGCAGCGGGCGGACUGGGCGCCAAAGUGGGCGGCUAAGUGGGCGUGGUGGGUG
.....((((((((.(((.......))).))))))))((.(((..(((((((((((((((((((......)))).)))))))(((.((((......)))).))).)))))))))))..)). ( -54.90)
>DroSim_CAF1 4147 120 - 1
UAAAAUUUGUUGCUGCCUUUCGCUGGCCGCGACAGGACAACUUGAUGUCCUUGUCUGCCGCUGACGGAGCAGCGGGCGGACUGGGCGCCAAAGUGGGCGGCUAAAUGGGCGUGGUGGGUG
....(((..(..(.((((...((((.((((..((((....))))..((((..(((((((((((......)))).))))))).))))......)))).)))).....)))))..)..))). ( -53.00)
>DroYak_CAF1 5118 110 - 1
UAAAAUUUGUUGCUGCCUUUCGCUGGCCGCGACAGGACAACUUGAUGUCCUUGUCUGCUGCUGACGGA----------GACUGGGCGGUGGAGUGGGCGGCAGAGUGGGCGUGGAGGGUG
..............(((((((((.(.((((...((((((......))))))..(((((((((.((...----------.(((....)))...)).))))))))))))).)))))))))). ( -47.40)
>consensus
UAAAAUUUGUUGCUGCCUUUCGCUGGCCGCGACAGGACAACUUGAUGUCCUUGUCUGCCGCUGACGGAGCAGCGGGCGGACUGGGCGCCAAAGUGGGCGGCUAAGUGGGCGUGGUGGGUG
.....((((((((.(((.......))).))))))))...((((.((((((..(((((((((((......)))).)))))))(((.((((......)))).)))...))))))...)))). (-41.61 = -43.55 +   1.94)

alignment

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secondary structure

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dotplot

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Window 0

Location 5,128,065 – 5,128,185
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 98.33
Mean single sequence MFE -43.17
Consensus MFE -42.07
Energy contribution -42.40
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -3.45
Structure conservation index 0.97
SVM decision value 2.16
SVM RNA-class probability 0.989380
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5128065 120 + 22224390
UCCGCCCGCUGCUCCGUCAGCGGCAGACAAGGACAUCAAGUUGUCCUGUCGCGGCCAGCGAAAGGCAGCAACAAAUUUUAAAAGUUGCGUCUGCAAUUUUGCUCUUGCCUUAUUUUAUUU
..(((..(((((.(((....)))..((((.(((((......))))))))))))))..))).(((((((((((...........)))))....(((....)))...))))))......... ( -43.40)
>DroSec_CAF1 4481 120 + 1
UCCGCCCGCUGCUCCGUCAGCGGCAGACAUGGACAUCAAGUUGUCCUGUCGCGGCCAGCGAAAGGCAGCAACAAAUUUUAAAAGUUGCGUCUGCAAUUUUGCUCUUGCCUUAUUUUAUUU
..(((..(((((.(((....)))..((((.(((((......))))))))))))))..))).(((((((((((...........)))))....(((....)))...))))))......... ( -43.40)
>DroSim_CAF1 4187 120 + 1
UCCGCCCGCUGCUCCGUCAGCGGCAGACAAGGACAUCAAGUUGUCCUGUCGCGGCCAGCGAAAGGCAGCAACAAAUUUUAAAAGUGGCGUUUGCAAUUUUGCUCUUGCCUUAUUUUAUUU
.......((((((.(((..((.((.((((.(((((......))))))))))).))..)))...)))))).........(((((..((((...(((....)))...))))...)))))... ( -42.70)
>consensus
UCCGCCCGCUGCUCCGUCAGCGGCAGACAAGGACAUCAAGUUGUCCUGUCGCGGCCAGCGAAAGGCAGCAACAAAUUUUAAAAGUUGCGUCUGCAAUUUUGCUCUUGCCUUAUUUUAUUU
..(((..(((((.(((....)))..((((.(((((......))))))))))))))..))).(((((((((((...........)))))....(((....)))...))))))......... (-42.07 = -42.40 +   0.33)

alignment

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secondary structure

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dotplot

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Window 1

Location 5,128,065 – 5,128,185
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 98.33
Mean single sequence MFE -43.27
Consensus MFE -43.27
Energy contribution -43.60
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -3.07
Structure conservation index 1.00
SVM decision value 2.27
SVM RNA-class probability 0.991552
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5128065 120 - 22224390
AAAUAAAAUAAGGCAAGAGCAAAAUUGCAGACGCAACUUUUAAAAUUUGUUGCUGCCUUUCGCUGGCCGCGACAGGACAACUUGAUGUCCUUGUCUGCCGCUGACGGAGCAGCGGGCGGA
.........((((((...(((....)))....(((((...........))))))))))).......(((((((((((((......))))).))))..((((((......)))))))))). ( -44.60)
>DroSec_CAF1 4481 120 - 1
AAAUAAAAUAAGGCAAGAGCAAAAUUGCAGACGCAACUUUUAAAAUUUGUUGCUGCCUUUCGCUGGCCGCGACAGGACAACUUGAUGUCCAUGUCUGCCGCUGACGGAGCAGCGGGCGGA
.........((((((...(((....)))....(((((...........))))))))))).......(((((((((((((......))))).))))..((((((......)))))))))). ( -44.60)
>DroSim_CAF1 4187 120 - 1
AAAUAAAAUAAGGCAAGAGCAAAAUUGCAAACGCCACUUUUAAAAUUUGUUGCUGCCUUUCGCUGGCCGCGACAGGACAACUUGAUGUCCUUGUCUGCCGCUGACGGAGCAGCGGGCGGA
............((((........))))...((((((...........))((((((..((((..(((.(((((((((((......))))).)))).)).)))..)))))))))))))).. ( -40.60)
>consensus
AAAUAAAAUAAGGCAAGAGCAAAAUUGCAGACGCAACUUUUAAAAUUUGUUGCUGCCUUUCGCUGGCCGCGACAGGACAACUUGAUGUCCUUGUCUGCCGCUGACGGAGCAGCGGGCGGA
.........((((((...(((....)))....(((((...........))))))))))).......(((((((((((((......))))).))))..((((((......)))))))))). (-43.27 = -43.60 +   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 10:20:23 2006