Locus 3297

Sequence ID 3L_DroMel_CAF1
Location 9,677,471 – 9,677,606
Length 135
Max. P 0.956650
window5128 window5129 window5130

overview

Window 8

Location 9,677,471 – 9,677,574
Length 103
Sequences 6
Columns 109
Reading direction forward
Mean pairwise identity 75.11
Mean single sequence MFE -42.35
Consensus MFE -20.53
Energy contribution -22.95
Covariance contribution 2.42
Combinations/Pair 1.11
Mean z-score -2.04
Structure conservation index 0.48
SVM decision value 0.82
SVM RNA-class probability 0.859842
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9677471 103 + 23771897
GAGGGAGCCGCUGGUGUCUCCUCCGGCUGUCCAGCAGCCG------AGGCUCCCUCGUCGGAGCCGGAUUUCUGCAUCCUGGCCAAUGCAAAAAUCAAAGGAUAUUGGC
(((((((((...((.....))..((((((.....))))))------.)))))))))(((((..((.(((((.(((((........))))).)))))...))...))))) ( -47.00)
>DroPse_CAF1 76736 109 + 1
GCCUGCUGUGACGGCGGCUCCUCUGGCUGGGCGGAUGCCGCCCCAGCAGCUGCCUCGUCGGAGCUUCCUUUUUGCAUCCUCGCAGAUGCACAAAUCGAUUUGCAUUGUG
((..(((.(((((((((((......(((((((((...))).)))))))))))))..)))).))).((..(((((((((......)))))).)))..))...))...... ( -43.40)
>DroSim_CAF1 76685 103 + 1
GAGGGAGCCGCUGGCGUCUCCUCAGGCUGGCCAGCAGCCG------AAGCUCCCUCGUCGGAGCCGGAUUUCUGCAUCCUGCCCAAUGCACAAAUCAAAGGAUAUUGGU
((((((((.((((((((((....))))..)))))).....------..))))))))((.(((..(((....)))..))).))((((((..(........)..)))))). ( -39.40)
>DroEre_CAF1 73585 103 + 1
GAGGGAGCCGCUGGCGUCUCCUCCGGCUGGCCAGCAGCCG------AGGCUCCCUCAUCGGAGCCAGAUUUCUGCAUCCUGGCCAAUGCACAAAUCAACACAAAUUGGC
((((((((((((((.(....).)))))((((.....))))------.)))))))))...(((..(((....)))..)))..((((((................)))))) ( -43.79)
>DroYak_CAF1 73796 103 + 1
GAGGAAGCAGCUGGCGUCUCCUCCGUCUGGCCAGCAGCCG------AGGCUCCUUCAUCGGAGCCCGAUUUCUGCAUCCUGGCCAAUGCACAAAUCAACGCAAAUUGCA
(((((.((.....))...))))).((.((((((((((.((------.((((((......))))))))....))))....))))))..))..........((.....)). ( -37.10)
>DroPer_CAF1 75715 109 + 1
GCCUGCUGUGACGGCGGCUCCUCUGGCUGGGCGGAUGCCGCCCCAGCAGCUGCCUCGUCGGAGCUUCCUUUUUGCAUCCUCGCAGAUGCACAAAUCGAUUUGCAUUGUG
((..(((.(((((((((((......(((((((((...))).)))))))))))))..)))).))).((..(((((((((......)))))).)))..))...))...... ( -43.40)
>consensus
GAGGGAGCCGCUGGCGUCUCCUCCGGCUGGCCAGCAGCCG______AAGCUCCCUCGUCGGAGCCGGAUUUCUGCAUCCUGGCCAAUGCACAAAUCAAAGCAAAUUGGC
(((((.((.......)).))))).(((((.....)))))........((((((......)))))).(((((.(((((........))))).)))))............. (-20.53 = -22.95 +   2.42)

alignment

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secondary structure

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dotplot

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Window 9

Location 9,677,471 – 9,677,574
Length 103
Sequences 6
Columns 109
Reading direction reverse
Mean pairwise identity 75.11
Mean single sequence MFE -44.53
Consensus MFE -24.07
Energy contribution -26.27
Covariance contribution 2.20
Combinations/Pair 1.14
Mean z-score -2.16
Structure conservation index 0.54
SVM decision value 1.47
SVM RNA-class probability 0.956650
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9677471 103 - 23771897
GCCAAUAUCCUUUGAUUUUUGCAUUGGCCAGGAUGCAGAAAUCCGGCUCCGACGAGGGAGCCU------CGGCUGCUGGACAGCCGGAGGAGACACCAGCGGCUCCCUC
(((((......))((((((((((((......)))))))))))).)))......(((((((((.------((((((.....)))))((.(....).)).).))))))))) ( -48.30)
>DroPse_CAF1 76736 109 - 1
CACAAUGCAAAUCGAUUUGUGCAUCUGCGAGGAUGCAAAAAGGAAGCUCCGACGAGGCAGCUGCUGGGGCGGCAUCCGCCCAGCCAGAGGAGCCGCCGUCACAGCAGGC
.....(((...(((.(((.(((((((....))))))).)))((.....))..))).))).((((((.((((((.(((...........)))))))))....)))))).. ( -44.00)
>DroSim_CAF1 76685 103 - 1
ACCAAUAUCCUUUGAUUUGUGCAUUGGGCAGGAUGCAGAAAUCCGGCUCCGACGAGGGAGCUU------CGGCUGCUGGCCAGCCUGAGGAGACGCCAGCGGCUCCCUC
.............(((((.((((((......)))))).))))).((((((......)))))).------.((((((((((...((...))....))))))))))..... ( -40.00)
>DroEre_CAF1 73585 103 - 1
GCCAAUUUGUGUUGAUUUGUGCAUUGGCCAGGAUGCAGAAAUCUGGCUCCGAUGAGGGAGCCU------CGGCUGCUGGCCAGCCGGAGGAGACGCCAGCGGCUCCCUC
((((.........(((((.((((((......)))))).)))))))))......(((((((((.------((((((.....)))))((.(....).)).).))))))))) ( -48.10)
>DroYak_CAF1 73796 103 - 1
UGCAAUUUGCGUUGAUUUGUGCAUUGGCCAGGAUGCAGAAAUCGGGCUCCGAUGAAGGAGCCU------CGGCUGCUGGCCAGACGGAGGAGACGCCAGCUGCUUCCUC
.(((.((.(((((..(((((...(((((((....((((...(((((((((......)))))).------)))))))))))))))))))...))))).)).)))...... ( -42.80)
>DroPer_CAF1 75715 109 - 1
CACAAUGCAAAUCGAUUUGUGCAUCUGCGAGGAUGCAAAAAGGAAGCUCCGACGAGGCAGCUGCUGGGGCGGCAUCCGCCCAGCCAGAGGAGCCGCCGUCACAGCAGGC
.....(((...(((.(((.(((((((....))))))).)))((.....))..))).))).((((((.((((((.(((...........)))))))))....)))))).. ( -44.00)
>consensus
CCCAAUAUACAUUGAUUUGUGCAUUGGCCAGGAUGCAGAAAUCAGGCUCCGACGAGGGAGCCU______CGGCUGCUGGCCAGCCGGAGGAGACGCCAGCGGCUCCCUC
.............(((((.((((((......)))))).))))).((((((......))))))........(((.((((((...((...))....)))))).)))..... (-24.07 = -26.27 +   2.20)

alignment

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secondary structure

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dotplot

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Window 0

Location 9,677,502 – 9,677,606
Length 104
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 76.33
Mean single sequence MFE -31.07
Consensus MFE -18.63
Energy contribution -18.93
Covariance contribution 0.31
Combinations/Pair 1.18
Mean z-score -1.66
Structure conservation index 0.60
SVM decision value 0.63
SVM RNA-class probability 0.805861
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9677502 104 - 23771897
ACUACGAGCAACGAAACAAUCAAUCAAUA-AUGGCCAAUAUCCUUUGAUUUUUGCAUUGGCCAGGAUGCAGAAAUCCGGCUCCGACGAGGGAGCCU------CGGCUGCUG
......((((.(((...............-.(((((((((((....)))......))))))))((((......))))((((((......)))))))------))..)))). ( -34.00)
>DroPse_CAF1 76767 105 - 1
A----UAGCAACCGAAAAAUCAAUCAAUA--UGCACAAUGCAAAUCGAUUUGUGCAUCUGCGAGGAUGCAAAAAGGAAGCUCCGACGAGGCAGCUGCUGGGGCGGCAUCCG
.----..(((...((....)).......(--(((((((...........)))))))).)))..((((((.....((.((((((.....)).)))).))......)))))). ( -30.20)
>DroSim_CAF1 76716 104 - 1
ACUACGAGCAACGAAACAAUAAAUCAAUA-AUGACCAAUAUCCUUUGAUUUGUGCAUUGGGCAGGAUGCAGAAAUCCGGCUCCGACGAGGGAGCUU------CGGCUGCUG
......((((.((((..............-................(((((.((((((......)))))).)))))..(((((......)))))))------))..)))). ( -28.30)
>DroEre_CAF1 73616 105 - 1
GCCAAGAGAAACGAAACAAUCAAUCAAUAAAUGGCCAAUUUGUGUUGAUUUGUGCAUUGGCCAGGAUGCAGAAAUCUGGCUCCGAUGAGGGAGCCU------CGGCUGCUG
(((............................(((((((..((..(......)..)))))))))((((......))))((((((......)))))).------.)))..... ( -31.80)
>DroYak_CAF1 73827 104 - 1
GCCAAGAGAAACGAAACAAUCAAUCAAUA-AUGUGCAAUUUGCGUUGAUUUGUGCAUUGGCCAGGAUGCAGAAAUCGGGCUCCGAUGAAGGAGCCU------CGGCUGCUG
(((.........................(-((((.......)))))(((((.((((((......)))))).)))))(((((((......)))))))------.)))..... ( -31.90)
>DroPer_CAF1 75746 105 - 1
A----UAGCAACCGAAAAAUCAAUCAAUA--UGCACAAUGCAAAUCGAUUUGUGCAUCUGCGAGGAUGCAAAAAGGAAGCUCCGACGAGGCAGCUGCUGGGGCGGCAUCCG
.----..(((...((....)).......(--(((((((...........)))))))).)))..((((((.....((.((((((.....)).)))).))......)))))). ( -30.20)
>consensus
AC_A_GAGCAACGAAACAAUCAAUCAAUA_AUGCCCAAUAUACAUUGAUUUGUGCAUUGGCCAGGAUGCAGAAAUCAGGCUCCGACGAGGGAGCCU______CGGCUGCUG
..............................................(((((.((((((......)))))).))))).((((((......))))))................ (-18.63 = -18.93 +   0.31)

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 10:54:14 2006