Locus 7369

Sequence ID 2L_DroMel_CAF1
Location 20,524,249 – 20,524,375
Length 126
Max. P 0.999992
window11833 window11834 window11835 window11836

overview

Window 3

Location 20,524,249 – 20,524,349
Length 100
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 90.17
Mean single sequence MFE -24.57
Consensus MFE -22.25
Energy contribution -22.28
Covariance contribution 0.03
Combinations/Pair 1.04
Mean z-score -1.44
Structure conservation index 0.91
SVM decision value 0.61
SVM RNA-class probability 0.799103
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20524249 100 + 22407834
UUUUUCCUU-U-------------------GCCUUUGAGAUUUGCGUGUUUCGCUUAAUGAAGAAGACAAAUAAUCGCGCAAUUAAAGCCUUUUAGCUUUAAGCGCGAGUAAAUAAUUGC
.......((-(-------------------(.((((...(((.(((.....)))..)))...)))).))))...((((((..(((((((......)))))))))))))............ ( -23.80)
>DroSim_CAF1 46618 100 + 1
CUUUUCCUU-U-------------------GCCUUUGAGAUUUGCGUGUUUCGCUUAAUGAAGAAGACAAAUAAUCGCGCAAUUAAAGCCUUUUAGCUUUAAGCGCGAGUAAAUAAUUGC
.......((-(-------------------(.((((...(((.(((.....)))..)))...)))).))))...((((((..(((((((......)))))))))))))............ ( -23.80)
>DroEre_CAF1 38740 112 + 1
CUUUUCCUU-UU-------CCUUUGCCUUCGCCUUUGAGAUUUGCGUGUUUCGCCUAAUGAAGAAGACAAAUAAUCGUGCAAUUAAAGCCUUUUAGCUUUAAGCGCGAGUAAAUAAUUGC
.........-..-------..((((((((((....((((((......)))))).....)))))...........((((((..(((((((......))))))))))))))))))....... ( -22.80)
>DroYak_CAF1 40903 100 + 1
CUUUUCCUU-U-------------------GCCUUUGAGAUUUGCGUGUUUCGCUUAAUGAAGAAGACAAAUAAUCGCGCAAUUAAAGCCUUUUAGCUUUAAGCGCGAGUAAAUAAUUGC
.......((-(-------------------(.((((...(((.(((.....)))..)))...)))).))))...((((((..(((((((......)))))))))))))............ ( -23.80)
>DroAna_CAF1 38493 101 + 1
CUUUUCCUUUU-------------------GCCUUUGAGAUUUGCGUGUUUCGCUUAAUGAAGAAGACAAAUAAUCGCGCAAUUAAAGCCUUUUAGCUUUAAGCGCGAGUAAAUAAUUGC
........(((-------------------(.((((...(((.(((.....)))..)))...)))).))))...((((((..(((((((......)))))))))))))............ ( -23.90)
>DroPer_CAF1 88185 119 + 1
CUUUUCCUU-GUGCUGGUGCCUUUGCCUUUGCCUUUGAGAUUUGCGUGUUUCGCUUAAUGAAGAAGACAAAUAAUCGCGCAAUUAAAGCCUUUUAGCUUUAAGCGCAAGUAAAUAAUUGC
..(((.(((-(((((.((((..(((..((((.((((...(((.(((.....)))..)))...)))).)))))))..))))...((((((......)))))))))))))).)))....... ( -29.30)
>consensus
CUUUUCCUU_U___________________GCCUUUGAGAUUUGCGUGUUUCGCUUAAUGAAGAAGACAAAUAAUCGCGCAAUUAAAGCCUUUUAGCUUUAAGCGCGAGUAAAUAAUUGC
.......................................((((((((.(((..(.....)..))).))......((((((..(((((((......)))))))))))))))))))...... (-22.25 = -22.28 +   0.03)

alignment

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secondary structure

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Window 4

Location 20,524,249 – 20,524,349
Length 100
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 90.17
Mean single sequence MFE -25.89
Consensus MFE -20.83
Energy contribution -20.86
Covariance contribution 0.03
Combinations/Pair 1.05
Mean z-score -2.52
Structure conservation index 0.80
SVM decision value 0.52
SVM RNA-class probability 0.767822
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20524249 100 - 22407834
GCAAUUAUUUACUCGCGCUUAAAGCUAAAAGGCUUUAAUUGCGCGAUUAUUUGUCUUCUUCAUUAAGCGAAACACGCAAAUCUCAAAGGC-------------------A-AAGGAAAAA
............((((((((((((((....))))))))..))))))...((((((((.........(((.....)))........)))))-------------------)-))....... ( -25.93)
>DroSim_CAF1 46618 100 - 1
GCAAUUAUUUACUCGCGCUUAAAGCUAAAAGGCUUUAAUUGCGCGAUUAUUUGUCUUCUUCAUUAAGCGAAACACGCAAAUCUCAAAGGC-------------------A-AAGGAAAAG
............((((((((((((((....))))))))..))))))...((((((((.........(((.....)))........)))))-------------------)-))....... ( -25.93)
>DroEre_CAF1 38740 112 - 1
GCAAUUAUUUACUCGCGCUUAAAGCUAAAAGGCUUUAAUUGCACGAUUAUUUGUCUUCUUCAUUAGGCGAAACACGCAAAUCUCAAAGGCGAAGGCAAAGG-------AA-AAGGAAAAG
((..........(((.((((((((((....))))))))..)).)))...(((((((........)))))))....)).....((....((....))....)-------).-......... ( -24.60)
>DroYak_CAF1 40903 100 - 1
GCAAUUAUUUACUCGCGCUUAAAGCUAAAAGGCUUUAAUUGCGCGAUUAUUUGUCUUCUUCAUUAAGCGAAACACGCAAAUCUCAAAGGC-------------------A-AAGGAAAAG
............((((((((((((((....))))))))..))))))...((((((((.........(((.....)))........)))))-------------------)-))....... ( -25.93)
>DroAna_CAF1 38493 101 - 1
GCAAUUAUUUACUCGCGCUUAAAGCUAAAAGGCUUUAAUUGCGCGAUUAUUUGUCUUCUUCAUUAAGCGAAACACGCAAAUCUCAAAGGC-------------------AAAAGGAAAAG
............((((((((((((((....))))))))..))))))...((((((((.........(((.....)))........)))))-------------------)))........ ( -25.93)
>DroPer_CAF1 88185 119 - 1
GCAAUUAUUUACUUGCGCUUAAAGCUAAAAGGCUUUAAUUGCGCGAUUAUUUGUCUUCUUCAUUAAGCGAAACACGCAAAUCUCAAAGGCAAAGGCAAAGGCACCAGCAC-AAGGAAAAG
((..........((((((((((((((....))))))))..))))))...((((((((.........(((.....)))........)))))))).))....((....))..-......... ( -27.03)
>consensus
GCAAUUAUUUACUCGCGCUUAAAGCUAAAAGGCUUUAAUUGCGCGAUUAUUUGUCUUCUUCAUUAAGCGAAACACGCAAAUCUCAAAGGC___________________A_AAGGAAAAG
............((((((((((((((....))))))))..))))))......(((((.........(((.....)))........))))).............................. (-20.83 = -20.86 +   0.03)

alignment

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secondary structure

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Window 5

Location 20,524,269 – 20,524,375
Length 106
Sequences 6
Columns 106
Reading direction forward
Mean pairwise identity 97.99
Mean single sequence MFE -32.25
Consensus MFE -31.97
Energy contribution -31.75
Covariance contribution -0.22
Combinations/Pair 1.07
Mean z-score -3.34
Structure conservation index 0.99
SVM decision value 5.67
SVM RNA-class probability 0.999992
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20524269 106 + 22407834
UUUGCGUGUUUCGCUUAAUGAAGAAGACAAAUAAUCGCGCAAUUAAAGCCUUUUAGCUUUAAGCGCGAGUAAAUAAUUGCUGUGAGUGCAGAAACGAACGCACGCA
..(((((((((((.....................((((((..(((((((......)))))))))))))...........((((....))))...)))).))))))) ( -32.70)
>DroSec_CAF1 45696 106 + 1
UUUGCGUGUUUCGCUUAAUGAAGAAGACAAAUAAUCGCGCAAUUAAAGCCUUUUAGCUUUAAGCGCGAGUAAAUAAUUGCUGUGAGUGCAGAAACGAACGCACGCA
..(((((((((((.....................((((((..(((((((......)))))))))))))...........((((....))))...)))).))))))) ( -32.70)
>DroSim_CAF1 46638 106 + 1
UUUGCGUGUUUCGCUUAAUGAAGAAGACAAAUAAUCGCGCAAUUAAAGCCUUUUAGCUUUAAGCGCGAGUAAAUAAUUGCUGUGAGUGCAGAAACGAACGCACGCA
..(((((((((((.....................((((((..(((((((......)))))))))))))...........((((....))))...)))).))))))) ( -32.70)
>DroYak_CAF1 40923 105 + 1
UUUGCGUGUUUCGCUUAAUGAAGAAGACAAAUAAUCGCGCAAUUAAAGCCUUUUAGCUUUAAGCGCGAGUAAAUAAUUGCUGUGAGUGCAGAA-CGAACACACGCA
..(((((((((((.....................((((((..(((((((......)))))))))))))...........((((....))))..-)))).))))))) ( -32.70)
>DroAna_CAF1 38514 106 + 1
UUUGCGUGUUUCGCUUAAUGAAGAAGACAAAUAAUCGCGCAAUUAAAGCCUUUUAGCUUUAAGCGCGAGUAAAUAAUUGCUGUGAGUGCAGAAACGAACACACGCA
..(((((((((((.....................((((((..(((((((......)))))))))))))...........((((....))))...)))).))))))) ( -32.70)
>DroPer_CAF1 88224 105 + 1
UUUGCGUGUUUCGCUUAAUGAAGAAGACAAAUAAUCGCGCAAUUAAAGCCUUUUAGCUUUAAGCGCAAGUAAAUAAUUGCUGUGAGUGCAGAA-CGAGAACACGCA
..(((((((((((((((...................((((..(((((((......))))))))))).(((((....))))).)))))).....-...))))))))) ( -30.00)
>consensus
UUUGCGUGUUUCGCUUAAUGAAGAAGACAAAUAAUCGCGCAAUUAAAGCCUUUUAGCUUUAAGCGCGAGUAAAUAAUUGCUGUGAGUGCAGAAACGAACACACGCA
..(((((((((((.....................((((((..(((((((......)))))))))))))...........((((....))))...)))).))))))) (-31.97 = -31.75 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 6

Location 20,524,269 – 20,524,375
Length 106
Sequences 6
Columns 106
Reading direction reverse
Mean pairwise identity 97.99
Mean single sequence MFE -34.23
Consensus MFE -30.92
Energy contribution -31.12
Covariance contribution 0.19
Combinations/Pair 1.03
Mean z-score -4.72
Structure conservation index 0.90
SVM decision value 4.34
SVM RNA-class probability 0.999876
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20524269 106 - 22407834
UGCGUGCGUUCGUUUCUGCACUCACAGCAAUUAUUUACUCGCGCUUAAAGCUAAAAGGCUUUAAUUGCGCGAUUAUUUGUCUUCUUCAUUAAGCGAAACACGCAAA
((((((..(((((((.(((.......)))..((..((.((((((((((((((....))))))))..)))))).))..))...........))))))).)))))).. ( -34.00)
>DroSec_CAF1 45696 106 - 1
UGCGUGCGUUCGUUUCUGCACUCACAGCAAUUAUUUACUCGCGCUUAAAGCUAAAAGGCUUUAAUUGCGCGAUUAUUUGUCUUCUUCAUUAAGCGAAACACGCAAA
((((((..(((((((.(((.......)))..((..((.((((((((((((((....))))))))..)))))).))..))...........))))))).)))))).. ( -34.00)
>DroSim_CAF1 46638 106 - 1
UGCGUGCGUUCGUUUCUGCACUCACAGCAAUUAUUUACUCGCGCUUAAAGCUAAAAGGCUUUAAUUGCGCGAUUAUUUGUCUUCUUCAUUAAGCGAAACACGCAAA
((((((..(((((((.(((.......)))..((..((.((((((((((((((....))))))))..)))))).))..))...........))))))).)))))).. ( -34.00)
>DroYak_CAF1 40923 105 - 1
UGCGUGUGUUCG-UUCUGCACUCACAGCAAUUAUUUACUCGCGCUUAAAGCUAAAAGGCUUUAAUUGCGCGAUUAUUUGUCUUCUUCAUUAAGCGAAACACGCAAA
(((((((.((((-((.(((.......)))..((..((.((((((((((((((....))))))))..)))))).))..))............))))))))))))).. ( -34.90)
>DroAna_CAF1 38514 106 - 1
UGCGUGUGUUCGUUUCUGCACUCACAGCAAUUAUUUACUCGCGCUUAAAGCUAAAAGGCUUUAAUUGCGCGAUUAUUUGUCUUCUUCAUUAAGCGAAACACGCAAA
(((((((.(((((((.(((.......)))..((..((.((((((((((((((....))))))))..)))))).))..))...........)))))))))))))).. ( -35.70)
>DroPer_CAF1 88224 105 - 1
UGCGUGUUCUCG-UUCUGCACUCACAGCAAUUAUUUACUUGCGCUUAAAGCUAAAAGGCUUUAAUUGCGCGAUUAUUUGUCUUCUUCAUUAAGCGAAACACGCAAA
((((((((.(((-((.(((.......)))..((..((.((((((((((((((....))))))))..)))))).))..))............))))))))))))).. ( -32.80)
>consensus
UGCGUGCGUUCGUUUCUGCACUCACAGCAAUUAUUUACUCGCGCUUAAAGCUAAAAGGCUUUAAUUGCGCGAUUAUUUGUCUUCUUCAUUAAGCGAAACACGCAAA
((((((...((((((.(((.......)))..((..((.((((((((((((((....))))))))..)))))).))..))...........))))))..)))))).. (-30.92 = -31.12 +   0.19)

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 12:35:01 2006