Locus 8733

Sequence ID 3R_DroMel_CAF1
Location 23,318,830 – 23,318,972
Length 142
Max. P 0.999534
window14024 window14025 window14026 window14027 window14028 window14029

overview

Window 4

Location 23,318,830 – 23,318,920
Length 90
Sequences 5
Columns 90
Reading direction forward
Mean pairwise identity 94.78
Mean single sequence MFE -31.66
Consensus MFE -29.34
Energy contribution -29.38
Covariance contribution 0.04
Combinations/Pair 1.04
Mean z-score -2.25
Structure conservation index 0.93
SVM decision value 3.69
SVM RNA-class probability 0.999534
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23318830 90 + 27905053
AAUGUUGACCAAUAUUUCAGCUAGGCUCCUUAGUUGCCGAUGACUGGAUUGGUUUCGGAUCCUUGCUUUGGGAUCCGGCGUCCGAUGUCC
.(((((((((((...((((((..(((.........)))...).)))))))))).(((((((((......)))))))))....)))))).. ( -28.70)
>DroSec_CAF1 116303 90 + 1
AAUGUUGACCAAUAUUUCAGCUAGGCUCCUUAGUUGCCGGUGACUGGAUUGGUUUCGGAUCCUUGCUUUGGGAUCCGGCGUCCGAAGUCC
.((((.(((((((....((((((((...))))))))(((....).))))))))).((((((((......))))))))))))......... ( -30.20)
>DroSim_CAF1 120559 90 + 1
AAUGUUGACCAAUAUUUCAGCUAGGCUCCUUAGUUGCCGGUGACUGGAUUGGUCUCGGAUCCUUGCUUUGGGAUCCGGCGUCCGAAGUCC
.((((.(((((((....((((((((...))))))))(((....).))))))))).((((((((......))))))))))))......... ( -32.70)
>DroEre_CAF1 122550 90 + 1
AAUGUUGACCAAUAUUUCAGCUAGGCUCCUUAGUUGCCGGUGACUGGAUUGGUUUCGGAUCCUUGCCUUGGGAUCCGGAGUCGGGAGUCG
...(((((........)))))..(((((((......(((....).))...(..((((((((((......))))))))))..)))))))). ( -36.50)
>DroYak_CAF1 127519 90 + 1
AAUGUUGACCAAUAUUUCAGCUAGGCUCCUUAGUUGCCGGUGACUGGAUUGGUUUCGGAUCCUUGCCUUGGGAUCCGGAUUCCGUAUUCC
......(((((((....((((((((...))))))))(((....).)))))))))(((((((((......)))))))))............ ( -30.20)
>consensus
AAUGUUGACCAAUAUUUCAGCUAGGCUCCUUAGUUGCCGGUGACUGGAUUGGUUUCGGAUCCUUGCUUUGGGAUCCGGCGUCCGAAGUCC
......(((((((....((((((((...))))))))((((...)))))))))))(((((((((......)))))))))............ (-29.34 = -29.38 +   0.04)

alignment

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secondary structure

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Window 5

Location 23,318,830 – 23,318,920
Length 90
Sequences 5
Columns 90
Reading direction reverse
Mean pairwise identity 94.78
Mean single sequence MFE -23.36
Consensus MFE -22.02
Energy contribution -22.02
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.31
Structure conservation index 0.94
SVM decision value 0.98
SVM RNA-class probability 0.893899
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23318830 90 - 27905053
GGACAUCGGACGCCGGAUCCCAAAGCAAGGAUCCGAAACCAAUCCAGUCAUCGGCAACUAAGGAGCCUAGCUGAAAUAUUGGUCAACAUU
.(((...((....(((((((........)))))))...))....((((....(((.........)))..))))........)))...... ( -22.50)
>DroSec_CAF1 116303 90 - 1
GGACUUCGGACGCCGGAUCCCAAAGCAAGGAUCCGAAACCAAUCCAGUCACCGGCAACUAAGGAGCCUAGCUGAAAUAUUGGUCAACAUU
((.(....)...))((((((........))))))...((((((.((((....(((.........)))..))))....))))))....... ( -22.80)
>DroSim_CAF1 120559 90 - 1
GGACUUCGGACGCCGGAUCCCAAAGCAAGGAUCCGAGACCAAUCCAGUCACCGGCAACUAAGGAGCCUAGCUGAAAUAUUGGUCAACAUU
((.(....)...))((((((........))))))..(((((((.((((....(((.........)))..))))....)))))))...... ( -27.20)
>DroEre_CAF1 122550 90 - 1
CGACUCCCGACUCCGGAUCCCAAGGCAAGGAUCCGAAACCAAUCCAGUCACCGGCAACUAAGGAGCCUAGCUGAAAUAUUGGUCAACAUU
.............(((((((........)))))))..((((((.((((....(((.........)))..))))....))))))....... ( -22.00)
>DroYak_CAF1 127519 90 - 1
GGAAUACGGAAUCCGGAUCCCAAGGCAAGGAUCCGAAACCAAUCCAGUCACCGGCAACUAAGGAGCCUAGCUGAAAUAUUGGUCAACAUU
(((........)))((((((........))))))...((((((.((((....(((.........)))..))))....))))))....... ( -22.30)
>consensus
GGACUUCGGACGCCGGAUCCCAAAGCAAGGAUCCGAAACCAAUCCAGUCACCGGCAACUAAGGAGCCUAGCUGAAAUAUUGGUCAACAUU
.............(((((((........)))))))..((((((.((((....(((.........)))..))))....))))))....... (-22.02 = -22.02 +  -0.00)

alignment

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secondary structure

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Window 6

Location 23,318,844 – 23,318,947
Length 103
Sequences 5
Columns 116
Reading direction forward
Mean pairwise identity 90.48
Mean single sequence MFE -46.72
Consensus MFE -34.86
Energy contribution -35.54
Covariance contribution 0.68
Combinations/Pair 1.03
Mean z-score -3.28
Structure conservation index 0.75
SVM decision value 1.94
SVM RNA-class probability 0.983252
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23318844 103 + 27905053
UUUCAGCUAGGCUCCUUAGUUGCCGAUGACUGGAUUGGUUUCGGAUCCUUGCUUUGGGAUCCGGCGUCCGAUGUCC-------------GGAGUCCCUUCCAUCCGGAUUGCCAUA
...((((((((...))))))))........((((((((..(((((((((......)))))))))...)))))((((-------------(((..........)))))))..))).. ( -37.30)
>DroSec_CAF1 116317 110 + 1
UUUCAGCUAGGCUCCUUAGUUGCCGGUGACUGGAUUGGUUUCGGAUCCUUGCUUUGGGAUCCGGCGUCCGAAGUCCGGAGUC------CGGAGUCCCUUCCAUCCGGAUUGCCAUA
...((((((((...))))))))..(((..(((((((((..(((((((((......)))))))))...)))..))))))((((------((((..........)))))))))))... ( -45.40)
>DroSim_CAF1 120573 110 + 1
UUUCAGCUAGGCUCCUUAGUUGCCGGUGACUGGAUUGGUCUCGGAUCCUUGCUUUGGGAUCCGGCGUCCGAAGUCCGGAGUC------CGGAGUCCCUUCCAUCCGGAUUGCCAUA
...((((((((...))))))))..(((..(((((((((.((((((((((......))))))))).).)))..))))))((((------((((..........)))))))))))... ( -46.70)
>DroEre_CAF1 122564 116 + 1
UUUCAGCUAGGCUCCUUAGUUGCCGGUGACUGGAUUGGUUUCGGAUCCUUGCCUUGGGAUCCGGAGUCGGGAGUCGGGAGUCGGGAGUCGGAGUCCCUUCCAUCCGGAUUGCCAUA
...((((((((...))))))))..((..(((((((((..((((((((((......))))))))))..))((((..((((.((.(....).)).)))))))))))))).)..))... ( -52.00)
>DroYak_CAF1 127533 110 + 1
UUUCAGCUAGGCUCCUUAGUUGCCGGUGACUGGAUUGGUUUCGGAUCCUUGCCUUGGGAUCCGGAUUCCGUAUUCCGGAGUC------CAGAGACCCUUCCAUCCGGAUUGCCAUA
...((((((((...))))))))((((....((((..(((((((((((((......)))))))((((((((.....)))))))------).))))))..)))).))))......... ( -52.20)
>consensus
UUUCAGCUAGGCUCCUUAGUUGCCGGUGACUGGAUUGGUUUCGGAUCCUUGCUUUGGGAUCCGGCGUCCGAAGUCCGGAGUC______CGGAGUCCCUUCCAUCCGGAUUGCCAUA
...((((((((...))))))))..((((((((((((((..(((((((((......)))))))))...))))..................((((....)))).))))).)))))... (-34.86 = -35.54 +   0.68)

alignment

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secondary structure

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Window 7

Location 23,318,844 – 23,318,947
Length 103
Sequences 5
Columns 116
Reading direction reverse
Mean pairwise identity 90.48
Mean single sequence MFE -36.98
Consensus MFE -29.18
Energy contribution -30.18
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.04
Structure conservation index 0.79
SVM decision value 1.19
SVM RNA-class probability 0.927775
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23318844 103 - 27905053
UAUGGCAAUCCGGAUGGAAGGGACUCC-------------GGACAUCGGACGCCGGAUCCCAAAGCAAGGAUCCGAAACCAAUCCAGUCAUCGGCAACUAAGGAGCCUAGCUGAAA
...(((..(((.(((((...(((.(((-------------(.....))))...(((((((........))))))).......)))..)))))(....)...))))))......... ( -33.30)
>DroSec_CAF1 116317 110 - 1
UAUGGCAAUCCGGAUGGAAGGGACUCCG------GACUCCGGACUUCGGACGCCGGAUCCCAAAGCAAGGAUCCGAAACCAAUCCAGUCACCGGCAACUAAGGAGCCUAGCUGAAA
...(((..(((((.((((.((((.((((------(..((((.....))))..))))))))).......((........))..))))....))(....)...))))))......... ( -37.20)
>DroSim_CAF1 120573 110 - 1
UAUGGCAAUCCGGAUGGAAGGGACUCCG------GACUCCGGACUUCGGACGCCGGAUCCCAAAGCAAGGAUCCGAGACCAAUCCAGUCACCGGCAACUAAGGAGCCUAGCUGAAA
...(((..(((((.((((..((.(((.(------(..((((.....))))..))((((((........))))))))).))..))))....))(....)...))))))......... ( -38.60)
>DroEre_CAF1 122564 116 - 1
UAUGGCAAUCCGGAUGGAAGGGACUCCGACUCCCGACUCCCGACUCCCGACUCCGGAUCCCAAGGCAAGGAUCCGAAACCAAUCCAGUCACCGGCAACUAAGGAGCCUAGCUGAAA
...(((..(((((((((..((((.((.(....).)).))))............(((((((........)))))))...)).)))).......(....)...))))))......... ( -34.60)
>DroYak_CAF1 127533 110 - 1
UAUGGCAAUCCGGAUGGAAGGGUCUCUG------GACUCCGGAAUACGGAAUCCGGAUCCCAAGGCAAGGAUCCGAAACCAAUCCAGUCACCGGCAACUAAGGAGCCUAGCUGAAA
...(((..(((((.((((..(((.((.(------((.((((.....)))).)))((((((........)))))))).)))..))))....))(....)...))))))......... ( -41.20)
>consensus
UAUGGCAAUCCGGAUGGAAGGGACUCCG______GACUCCGGACUUCGGACGCCGGAUCCCAAAGCAAGGAUCCGAAACCAAUCCAGUCACCGGCAACUAAGGAGCCUAGCUGAAA
...(((..((((..((((..((...............((((.....))))...(((((((........)))))))...))..))))..)...(....)...))))))......... (-29.18 = -30.18 +   1.00)

alignment

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secondary structure

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Window 8

Location 23,318,880 – 23,318,972
Length 92
Sequences 5
Columns 105
Reading direction forward
Mean pairwise identity 84.11
Mean single sequence MFE -39.45
Consensus MFE -23.06
Energy contribution -24.46
Covariance contribution 1.40
Combinations/Pair 1.00
Mean z-score -2.23
Structure conservation index 0.58
SVM decision value 0.22
SVM RNA-class probability 0.638256
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23318880 92 + 27905053
GGUUUCGGAUCCUUGCUUUGGGAUCCGGCGUCCGAUGUCC-------------GGAGUCCCUUCCAUCCGGAUUGCCAUAAAUUAUGAGAAGGCGAGUGGAGGAG
((....(((((((......)))))))(((.((((.....)-------------)))))))).(((.((((..(((((..............))))).))))))). ( -33.54)
>DroSec_CAF1 116353 99 + 1
GGUUUCGGAUCCUUGCUUUGGGAUCCGGCGUCCGAAGUCCGGAGUC------CGGAGUCCCUUCCAUCCGGAUUGCCAUAAAUUAUGAGAAGGCGUGUGGAGGAG
....(((((((((......)))))))))(.((((.((((((((...------.((((....)))).))))))))(((..............)))...)))).).. ( -36.84)
>DroSim_CAF1 120609 99 + 1
GGUCUCGGAUCCUUGCUUUGGGAUCCGGCGUCCGAAGUCCGGAGUC------CGGAGUCCCUUCCAUCCGGAUUGCCAUAAAUUAUGAGAAGGCGAGUGGAGGAG
((.((((((((((......)))))))((..((((.....))))..)------).))).))..(((.((((..(((((..............))))).))))))). ( -39.24)
>DroEre_CAF1 122600 104 + 1
GGUUUCGGAUCCUUGCCUUGGGAUCCGGAGUCGGGAGUCGGGAGUCGGGAGUCGGAGUCCCUUCCAUCCGGAUUGCCAUAAAUUAUGAGGAGGCAAGU-GGGGUG
(..((((((((((......))))))))))..).((((..((((.((.(....).)).))))))))((((.(.(((((..............))))).)-.)))). ( -42.84)
>DroYak_CAF1 127569 94 + 1
GGUUUCGGAUCCUUGCCUUGGGAUCCGGAUUCCGUAUUCCGGAGUC------CAGAGACCCUUCCAUCCGGAUUGCCAUAAAUUAUGAGGAGU----G-GGAGUG
(((((((((((((......)))))))((((((((.....)))))))------).))))))(((((((((.((((......))))....))).)----)-)))).. ( -44.80)
>consensus
GGUUUCGGAUCCUUGCUUUGGGAUCCGGCGUCCGAAGUCCGGAGUC______CGGAGUCCCUUCCAUCCGGAUUGCCAUAAAUUAUGAGAAGGCGAGUGGAGGAG
(((.(((((((((......))))))))).......((((((((..........((((....)))).)))))))))))............................ (-23.06 = -24.46 +   1.40)

alignment

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secondary structure

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dotplot

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Window 9

Location 23,318,880 – 23,318,972
Length 92
Sequences 5
Columns 105
Reading direction reverse
Mean pairwise identity 84.11
Mean single sequence MFE -31.01
Consensus MFE -19.34
Energy contribution -20.58
Covariance contribution 1.24
Combinations/Pair 1.05
Mean z-score -2.08
Structure conservation index 0.62
SVM decision value 0.28
SVM RNA-class probability 0.664710
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23318880 92 - 27905053
CUCCUCCACUCGCCUUCUCAUAAUUUAUGGCAAUCCGGAUGGAAGGGACUCC-------------GGACAUCGGACGCCGGAUCCCAAAGCAAGGAUCCGAAACC
....(((....(((..............)))..((((((.(.......))))-------------)))....)))...(((((((........)))))))..... ( -27.64)
>DroSec_CAF1 116353 99 - 1
CUCCUCCACACGCCUUCUCAUAAUUUAUGGCAAUCCGGAUGGAAGGGACUCCG------GACUCCGGACUUCGGACGCCGGAUCCCAAAGCAAGGAUCCGAAACC
.(((((((..((..((.(((((...))))).))..))..)))).((((.((((------(..((((.....))))..))))))))).......)))......... ( -32.70)
>DroSim_CAF1 120609 99 - 1
CUCCUCCACUCGCCUUCUCAUAAUUUAUGGCAAUCCGGAUGGAAGGGACUCCG------GACUCCGGACUUCGGACGCCGGAUCCCAAAGCAAGGAUCCGAGACC
.(((((((..((..((.(((((...))))).))..))..)))).((((.((((------(..((((.....))))..))))))))).......)))......... ( -33.50)
>DroEre_CAF1 122600 104 - 1
CACCCC-ACUUGCCUCCUCAUAAUUUAUGGCAAUCCGGAUGGAAGGGACUCCGACUCCCGACUCCCGACUCCCGACUCCGGAUCCCAAGGCAAGGAUCCGAAACC
......-.(((((((............(((..(((((((.(((.((((.((.(....).)).))))...)))....))))))).))))))))))........... ( -31.50)
>DroYak_CAF1 127569 94 - 1
CACUCC-C----ACUCCUCAUAAUUUAUGGCAAUCCGGAUGGAAGGGUCUCUG------GACUCCGGAAUACGGAAUCCGGAUCCCAAGGCAAGGAUCCGAAACC
..((.(-(----(.((((((((...)))))......)))))).))(((.((.(------((.((((.....)))).)))((((((........)))))))).))) ( -29.70)
>consensus
CUCCUCCACUCGCCUUCUCAUAAUUUAUGGCAAUCCGGAUGGAAGGGACUCCG______GACUCCGGACUUCGGACGCCGGAUCCCAAAGCAAGGAUCCGAAACC
...........(((..............)))..((((((((((......)))).........))))))..........(((((((........)))))))..... (-19.34 = -20.58 +   1.24)

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 13:18:26 2006