Locus 5858

Sequence ID 2L_DroMel_CAF1
Location 16,580,690 – 16,580,871
Length 181
Max. P 0.997784
window9296 window9297 window9298 window9299

overview

Window 6

Location 16,580,690 – 16,580,807
Length 117
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 93.36
Mean single sequence MFE -31.26
Consensus MFE -28.86
Energy contribution -30.14
Covariance contribution 1.28
Combinations/Pair 1.09
Mean z-score -1.72
Structure conservation index 0.92
SVM decision value 2.25
SVM RNA-class probability 0.991159
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16580690 117 + 22407834
AGUUGAUGGCAGUGGUUUGGUCGAAAAAGAGCUCAUUCCUGCUCAAGGUAUUUUCGACAAUGACAAUAA-AAAAAUUGCUGGCUCUAAAGUUGAGCCGGACUAAAAAUAAAGUUUGGC
....((.(.(((..((((.((((((((.((((........))))......))))))))...........-..))))..))).))).........((((((((........)))))))) ( -31.24)
>DroSec_CAF1 35946 117 + 1
AGUUGGUGGCAGUGGUUCGGUCAGAAAGGAGCUCAUUCCUGCUCAAGGUAUUUUCGACAAUGACAAUAA-AAAAAUUGCUGGCUCUAAAGUUGAGCCGGACUAAAAAUAAAGUUUGGC
..((((.(.(((..(((..((((.....((((........))))..((.....)).....)))).....-...)))..))).).))))......((((((((........)))))))) ( -29.10)
>DroSim_CAF1 33896 117 + 1
AGUUGGUGGCAGUGGUUCGGUCAGAAAGGAGCUCAUUCCUGCUCAAGGUAUUUUCGACAAUGACAAUAA-AAAAAUUGCUGGCUCUAAAGUUGAGCCGGACUAAAAAUAAAGUUUGGC
..((((.(.(((..(((..((((.....((((........))))..((.....)).....)))).....-...)))..))).).))))......((((((((........)))))))) ( -29.10)
>DroEre_CAF1 34754 118 + 1
AGUUGGGGGCAGUGGUUUGGUAGAAAAGGAGCUCAUUCUUGCUCAAGGUAUUUUCGACAAUGAUAAUAAGAAAAAUUGCUGGCUCCAGAGUUAAGCCGGACUAAAAAUAAAGUUUGGC
..((((((.(((..((((.((.(((((.((((........))))......))))).))..............))))..))).))))))......((((((((........)))))))) ( -35.66)
>DroYak_CAF1 35026 116 + 1
AGUUGG-GGCAGUGGCUUGGUAGAAAAGGAGCUCAUUCUUGCUCAAGGUAUUUUCGACAAUGUCAAUAA-AAAAAUUGCUGGCUCUACAGUUAAGCCGGACUAAAAAUAAAGUUUGGC
.((.((-(.((((((((((...(((((.((((........))))......)))))..))).)))(((..-....))))))).))).))......((((((((........)))))))) ( -31.20)
>consensus
AGUUGGUGGCAGUGGUUUGGUCGAAAAGGAGCUCAUUCCUGCUCAAGGUAUUUUCGACAAUGACAAUAA_AAAAAUUGCUGGCUCUAAAGUUGAGCCGGACUAAAAAUAAAGUUUGGC
..((((.(.(((..((((.((((((((.((((........))))......))))))))..............))))..))).).))))......((((((((........)))))))) (-28.86 = -30.14 +   1.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 16,580,730 – 16,580,836
Length 106
Sequences 5
Columns 107
Reading direction forward
Mean pairwise identity 95.39
Mean single sequence MFE -24.11
Consensus MFE -19.86
Energy contribution -20.26
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.49
Structure conservation index 0.82
SVM decision value 0.19
SVM RNA-class probability 0.627102
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16580730 106 + 22407834
GCUCAAGGUAUUUUCGACAAUGACAAUAA-AAAAAUUGCUGGCUCUAAAGUUGAGCCGGACUAAAAAUAAAGUUUGGCCUUGUCAGCUUUAAGUUAAUCCACGAAAG
...........(((((.......((((..-....)))).(((((.(((((((((((((((((........))))))))....)))))))))))))).....))))). ( -25.60)
>DroSec_CAF1 35986 106 + 1
GCUCAAGGUAUUUUCGACAAUGACAAUAA-AAAAAUUGCUGGCUCUAAAGUUGAGCCGGACUAAAAAUAAAGUUUGGCCUUGUCAGCUUUAAGUUAAUCCACGAAAG
...........(((((.......((((..-....)))).(((((.(((((((((((((((((........))))))))....)))))))))))))).....))))). ( -25.60)
>DroSim_CAF1 33936 106 + 1
GCUCAAGGUAUUUUCGACAAUGACAAUAA-AAAAAUUGCUGGCUCUAAAGUUGAGCCGGACUAAAAAUAAAGUUUGGCCUUGUCAGCUUUAAGUUAAUCCACGAAAG
...........(((((.......((((..-....)))).(((((.(((((((((((((((((........))))))))....)))))))))))))).....))))). ( -25.60)
>DroEre_CAF1 34794 107 + 1
GCUCAAGGUAUUUUCGACAAUGAUAAUAAGAAAAAUUGCUGGCUCCAGAGUUAAGCCGGACUAAAAAUAAAGUUUGGCCUUGUCAGCUUUAAGUUAAUCCAGAGAAG
.(((..(((.(((((..............)))))...((((((....(((....((((((((........))))))))))))))))).........)))..)))... ( -22.04)
>DroYak_CAF1 35065 106 + 1
GCUCAAGGUAUUUUCGACAAUGUCAAUAA-AAAAAUUGCUGGCUCUACAGUUAAGCCGGACUAAAAAUAAAGUUUGGCCUUGUCAGCUUUAAGUUUAUCCAGGGAAG
.(((..(((......(((...))).....-.......((((......))))...)))(((.((((..(((((((.(((...))))))))))..))))))).)))... ( -21.70)
>consensus
GCUCAAGGUAUUUUCGACAAUGACAAUAA_AAAAAUUGCUGGCUCUAAAGUUGAGCCGGACUAAAAAUAAAGUUUGGCCUUGUCAGCUUUAAGUUAAUCCACGAAAG
(((((((((........((((.............))))(((((((.......))))))).................))))))..))).................... (-19.86 = -20.26 +   0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 16,580,767 – 16,580,871
Length 104
Sequences 4
Columns 104
Reading direction forward
Mean pairwise identity 82.04
Mean single sequence MFE -26.42
Consensus MFE -20.85
Energy contribution -21.85
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -3.05
Structure conservation index 0.79
SVM decision value 2.93
SVM RNA-class probability 0.997784
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16580767 104 + 22407834
CUGGCUCUAAAGUUGAGCCGGACUAAAAAUAAAGUUUGGCCUUGUCAGCUUUAAGUUAAUCCACGAAAGAUGGGAAUAUAUGUAUAUAUAGAAGGAGAGAAAAG
.(((((.(((((((((((((((((........))))))))....)))))))))))))).(((((....).)))).............................. ( -26.90)
>DroSec_CAF1 36023 102 + 1
CUGGCUCUAAAGUUGAGCCGGACUAAAAAUAAAGUUUGGCCUUGUCAGCUUUAAGUUAAUCCACGAAAGAUGGGAAUAUAU--AUACAUAGAGUGAGAGAAAAG
((.(((((((((((((((((((((........))))))))....)))))))))......(((((....).)))).......--.......)))).))....... ( -31.10)
>DroSim_CAF1 33973 102 + 1
CUGGCUCUAAAGUUGAGCCGGACUAAAAAUAAAGUUUGGCCUUGUCAGCUUUAAGUUAAUCCACGAAAGAUGGGAAUAUAU--AUACAUAGAGUGAGAGAAAAG
((.(((((((((((((((((((((........))))))))....)))))))))......(((((....).)))).......--.......)))).))....... ( -31.10)
>DroYak_CAF1 35102 78 + 1
CUGGCUCUACAGUUAAGCCGGACUAAAAAUAAAGUUUGGCCUUGUCAGCUUUAAGUUUAUCCAGGGAAGAGAGGAACU--------------------------
((..((((.(......((((((((........))))))))((((..(((.....)))....))))).)))).))....-------------------------- ( -16.60)
>consensus
CUGGCUCUAAAGUUGAGCCGGACUAAAAAUAAAGUUUGGCCUUGUCAGCUUUAAGUUAAUCCACGAAAGAUGGGAAUAUAU__AUACAUAGAGUGAGAGAAAAG
.(((((.(((((((((((((((((........))))))))....)))))))))))))).(((.(....)...)))............................. (-20.85 = -21.85 +   1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 16,580,767 – 16,580,871
Length 104
Sequences 4
Columns 104
Reading direction reverse
Mean pairwise identity 82.04
Mean single sequence MFE -16.12
Consensus MFE -16.14
Energy contribution -16.20
Covariance contribution 0.06
Combinations/Pair 1.05
Mean z-score -1.09
Structure conservation index 1.00
SVM decision value 0.81
SVM RNA-class probability 0.857601
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16580767 104 - 22407834
CUUUUCUCUCCUUCUAUAUAUACAUAUAUUCCCAUCUUUCGUGGAUUAACUUAAAGCUGACAAGGCCAAACUUUAUUUUUAGUCCGGCUCAACUUUAGAGCCAG
..........................................(((((((..(((((.((.......))..)))))...)))))))(((((.......))))).. ( -17.20)
>DroSec_CAF1 36023 102 - 1
CUUUUCUCUCACUCUAUGUAU--AUAUAUUCCCAUCUUUCGUGGAUUAACUUAAAGCUGACAAGGCCAAACUUUAUUUUUAGUCCGGCUCAACUUUAGAGCCAG
.....................--...................(((((((..(((((.((.......))..)))))...)))))))(((((.......))))).. ( -17.20)
>DroSim_CAF1 33973 102 - 1
CUUUUCUCUCACUCUAUGUAU--AUAUAUUCCCAUCUUUCGUGGAUUAACUUAAAGCUGACAAGGCCAAACUUUAUUUUUAGUCCGGCUCAACUUUAGAGCCAG
.....................--...................(((((((..(((((.((.......))..)))))...)))))))(((((.......))))).. ( -17.20)
>DroYak_CAF1 35102 78 - 1
--------------------------AGUUCCUCUCUUCCCUGGAUAAACUUAAAGCUGACAAGGCCAAACUUUAUUUUUAGUCCGGCUUAACUGUAGAGCCAG
--------------------------................(((((((..(((((.((.......))..)))))..))).))))(((((.......))))).. ( -12.90)
>consensus
CUUUUCUCUCACUCUAUGUAU__AUAUAUUCCCAUCUUUCGUGGAUUAACUUAAAGCUGACAAGGCCAAACUUUAUUUUUAGUCCGGCUCAACUUUAGAGCCAG
..........................................(((((((..(((((.((.......))..)))))...)))))))(((((.......))))).. (-16.14 = -16.20 +   0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:54:48 2006