Locus 8666

Sequence ID 3L_DroMel_CAF1
Location 22,483,215 – 22,483,360
Length 145
Max. P 0.834166
window14201 window14202 window14203

overview

Window 1

Location 22,483,215 – 22,483,330
Length 115
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 76.38
Mean single sequence MFE -21.89
Consensus MFE -9.26
Energy contribution -9.59
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.16
Structure conservation index 0.42
SVM decision value 0.35
SVM RNA-class probability 0.698866
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22483215 115 + 23771897
AUAUUUGCGGUUAAACGCACCAAAAACAAACCGCAAAAGUAAAUCAUAUCCAGAGCAGGCAUUG-----GACAUGGCCAAGCAUCCGAGGCAAAGAAUUUCUCUUGCCUCACCCGACCGU
...(((((((((................)))))))))......((((.(((((.(....).)))-----)).))))..........(((((((((.....)).))))))).......... ( -29.49)
>DroVir_CAF1 680 91 + 1
AUAUUUGCGGUUAAACGCACCAAAAACAAACCGCAAAAGUAAAUCAUACCCAAAGUAGACACCG-----AGCAUG--------------GCCAAGAAUUUCUCUGUGCUU----------
...(((((((((................)))))))))..........................(-----((((((--------------(...((.....))))))))))---------- ( -16.99)
>DroPse_CAF1 13968 95 + 1
AUAUUUGCGGUUAAACGCACCAAAAACAAACCGCACAAGUAAAUCAUAUCCAGAGUAGACAUCG-----GACAUG--------------CCAAGGAAUUUCCUUUGCUCUACUC------
.....(((((((................))))))).................(((((((((..(-----((.((.--------------(....).)).)))..)).)))))))------ ( -21.49)
>DroYak_CAF1 769 115 + 1
AUAUUUGCGGUUAAACGCACCAAAAACAAACCGCAAAAGUAAAUCAUAUCCAAAACAGACAUUG-----GACACGGCCAAGCAUCCAAGGCAAGGAAUUUCUCUUGCCUCACCCGACCGU
...(((((((((................)))))))))...........(((((........)))-----)).((((...........((((((((......)))))))).......)))) ( -26.26)
>DroMoj_CAF1 545 96 + 1
AUAUUUGCGGUUAAACGCACCAAAAACAAACCGCAAAAGUAAAUCAUACCCAAAGUAGACACCGGACCGGACAUG--------------GCCAAGAAUUUCUCUCGACUU----------
...(((((((((................)))))))))...............((((.((....((.(((....))--------------)))..((.....)))).))))---------- ( -15.59)
>DroPer_CAF1 13944 95 + 1
AUAUUUGCGGUUAAACGCACCAAAAACAAACCGCACAAGUAAAUCAUAUCCAGAGUAGACAUCG-----GACAUG--------------CCAAGGAAUUUCCUUUGCUCUACUC------
.....(((((((................))))))).................(((((((((..(-----((.((.--------------(....).)).)))..)).)))))))------ ( -21.49)
>consensus
AUAUUUGCGGUUAAACGCACCAAAAACAAACCGCAAAAGUAAAUCAUAUCCAAAGUAGACAUCG_____GACAUG______________GCAAAGAAUUUCUCUUGCCUUAC_C______
...(((((((((................)))))))))................................................................................... ( -9.26 =  -9.59 +   0.33)

alignment

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secondary structure

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dotplot

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Window 2

Location 22,483,215 – 22,483,330
Length 115
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 76.38
Mean single sequence MFE -30.93
Consensus MFE -14.31
Energy contribution -14.18
Covariance contribution -0.13
Combinations/Pair 1.36
Mean z-score -2.18
Structure conservation index 0.46
SVM decision value 0.73
SVM RNA-class probability 0.834166
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22483215 115 - 23771897
ACGGUCGGGUGAGGCAAGAGAAAUUCUUUGCCUCGGAUGCUUGGCCAUGUC-----CAAUGCCUGCUCUGGAUAUGAUUUACUUUUGCGGUUUGUUUUUGGUGCGUUUAACCGCAAAUAU
..((((((((((((((.(((.....)))))))))....))))))))(((((-----((..(....)..)))))))........((((((((((((.......)))...)))))))))... ( -40.30)
>DroVir_CAF1 680 91 - 1
----------AAGCACAGAGAAAUUCUUGGC--------------CAUGCU-----CGGUGUCUACUUUGGGUAUGAUUUACUUUUGCGGUUUGUUUUUGGUGCGUUUAACCGCAAAUAU
----------..((...(((.....))).))--------------((((((-----(((........))))))))).......((((((((((((.......)))...)))))))))... ( -23.20)
>DroPse_CAF1 13968 95 - 1
------GAGUAGAGCAAAGGAAAUUCCUUGG--------------CAUGUC-----CGAUGUCUACUCUGGAUAUGAUUUACUUGUGCGGUUUGUUUUUGGUGCGUUUAACCGCAAAUAU
------(((((((((.((((.....)))).)--------------)(((((-----((..(....)..)))))))..))))))).((((((((((.......)))...)))))))..... ( -27.80)
>DroYak_CAF1 769 115 - 1
ACGGUCGGGUGAGGCAAGAGAAAUUCCUUGCCUUGGAUGCUUGGCCGUGUC-----CAAUGUCUGUUUUGGAUAUGAUUUACUUUUGCGGUUUGUUUUUGGUGCGUUUAACCGCAAAUAU
((((((((((((((((((.(.....)))))))))....))))))))))(((-----(((........))))))..........((((((((((((.......)))...)))))))))... ( -42.20)
>DroMoj_CAF1 545 96 - 1
----------AAGUCGAGAGAAAUUCUUGGC--------------CAUGUCCGGUCCGGUGUCUACUUUGGGUAUGAUUUACUUUUGCGGUUUGUUUUUGGUGCGUUUAACCGCAAAUAU
----------..((((((((...))))))))--------------(((..((((...(((....)))))))..))).......((((((((((((.......)))...)))))))))... ( -24.30)
>DroPer_CAF1 13944 95 - 1
------GAGUAGAGCAAAGGAAAUUCCUUGG--------------CAUGUC-----CGAUGUCUACUCUGGAUAUGAUUUACUUGUGCGGUUUGUUUUUGGUGCGUUUAACCGCAAAUAU
------(((((((((.((((.....)))).)--------------)(((((-----((..(....)..)))))))..))))))).((((((((((.......)))...)))))))..... ( -27.80)
>consensus
______G_GUAAGGCAAGAGAAAUUCCUUGC______________CAUGUC_____CGAUGUCUACUCUGGAUAUGAUUUACUUUUGCGGUUUGUUUUUGGUGCGUUUAACCGCAAAUAU
.......((((((...((((.....))))................((((((...................)))))).))))))((((((((((((.......)))...)))))))))... (-14.31 = -14.18 +  -0.13)

alignment

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secondary structure

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dotplot

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Window 3

Location 22,483,255 – 22,483,360
Length 105
Sequences 3
Columns 110
Reading direction reverse
Mean pairwise identity 85.23
Mean single sequence MFE -33.57
Consensus MFE -26.27
Energy contribution -27.50
Covariance contribution 1.23
Combinations/Pair 1.19
Mean z-score -1.82
Structure conservation index 0.78
SVM decision value 0.16
SVM RNA-class probability 0.611207
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22483255 105 - 23771897
UCUAAUAUUUUUGCCUACA-----AAUGCCGGACGACGGUCGGGUGAGGCAAGAGAAAUUCUUUGCCUCGGAUGCUUGGCCAUGUCCAAUGCCUGCUCUGGAUAUGAUUU
............(((....-----...(((.(((....))).)))((((((.(((.....)))))))))........)))((((((((..(....)..)))))))).... ( -34.60)
>DroEre_CAF1 844 108 - 1
UCUAAU-UUUUUGCCUACGAGUUGAGUUCCGGACGACUUUUGGGGGCGGCAAGAGAAAUUCCUUGCCUCGGAUGCUUGGCCACGUCC-AUGUCUGUUUUAGAUAUGAUUU
(((((.-......((((.((((((.........)))))).))))(((((((((.(.....)))))))..(((((........)))))-..)))....)))))........ ( -29.30)
>DroYak_CAF1 809 105 - 1
UCUAAUAUUUUUGCCUUCA-----AGUUCCGGACGACGGUCGGGUGAGGCAAGAGAAAUUCCUUGCCUUGGAUGCUUGGCCGUGUCCAAUGUCUGUUUUGGAUAUGAUUU
...................-----......((((.((((((((((((((((((.(.....)))))))))....)))))))))))))).((((((.....))))))..... ( -36.80)
>consensus
UCUAAUAUUUUUGCCUACA_____AGUUCCGGACGACGGUCGGGUGAGGCAAGAGAAAUUCCUUGCCUCGGAUGCUUGGCCAUGUCCAAUGUCUGUUUUGGAUAUGAUUU
............(((............(((.(((....))).)))((((((((.(.....)))))))))........)))(((((((((........))))))))).... (-26.27 = -27.50 +   1.23)

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 13:21:47 2006