Locus 1882

Sequence ID 2R_DroMel_CAF1
Location 7,085,095 – 7,085,218
Length 123
Max. P 0.866171
window3115 window3116 window3117

overview

Window 5

Location 7,085,095 – 7,085,200
Length 105
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 89.81
Mean single sequence MFE -30.44
Consensus MFE -26.77
Energy contribution -27.77
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -1.58
Structure conservation index 0.88
SVM decision value 0.48
SVM RNA-class probability 0.751896
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7085095 105 + 20766785
AGGCGACAUUUGUUAAUGUUCGGU-UUU------------UGCCGGC--AUGGCGGCUCACGUGAGCAUAAAUCAAAGAGAUUAAUCGAACAUGGCUCAAUUGCCAGUUAACAUGGCAAG
.((((((....))).(((((((((-(..------------((((...--..))))((((....))))...((((.....)))))))))))))).)))...((((((.......)))))). ( -31.20)
>DroPse_CAF1 119472 107 + 1
AGGCGACAUUUGUUAAUGUUCGGC-AUU------------UGCCGGUAUAUGGCGGCUCACGUGAGCAUAAAUCAAAGAGAUUAAUCGAACAUGGCUCAAUUGCCAAUGAACAUGGCAAC
.((((((....))).((((((((.-...------------(((((.....)))))((((....))))...((((.....))))..)))))))).)))...((((((.......)))))). ( -29.50)
>DroEre_CAF1 117871 117 + 1
AGGCGACAUUUGUUAAUGUUCGGU-UUUUAUUUUUUUUCUUGCCGGC--AUGGCGGCUCACGUGAGCAUAAAUCAAAGAGAUUAAUCGAACAUGGCUCAAUUGCCAGUUAACAUGGCAAG
.((((((....))).(((((((((-(...((((((((...((((...--..))))((((....)))).......)))))))).)))))))))).)))...((((((.......)))))). ( -34.90)
>DroWil_CAF1 178459 103 + 1
AGGCGACAUUUGUUAAUGUUCGGU-UUU------------UGGC--U--CUGGCGGCUCACGUGAGCAUAAAUCAAAGAGAUUAAUCGAACAUGGCUCAAUUGCAUGCGAACAUGGCAAU
..((..((.(((...(((((((((-(..------------...(--(--((....((((....)))).........))))...))))))))))....))).))((((....))))))... ( -27.32)
>DroAna_CAF1 116786 106 + 1
AGGCGACAUUUGUUAAUGUUCGGUAUUU------------UGCCGGC--AUGGCGGCUCACGUGAGCAUAAAUCAAAGAGAUUAAUCGAACAUGGCUCAAUUGCCAAUGAACAUGGCAAG
.((((((....))).(((((((((....------------((((...--..))))((((....))))...((((.....)))).))))))))).)))...((((((.......)))))). ( -30.20)
>DroPer_CAF1 117193 107 + 1
AGGCGACAUUUGUUAAUGUUCGGC-AUU------------UGCCGGUAUAUGGCGGCUCACGUGAGCAUAAAUCAAAGAGAUUAAUCGAACAUGGCUCAAUUGCCAAUGAACAUGGCAAC
.((((((....))).((((((((.-...------------(((((.....)))))((((....))))...((((.....))))..)))))))).)))...((((((.......)))))). ( -29.50)
>consensus
AGGCGACAUUUGUUAAUGUUCGGU_UUU____________UGCCGGC__AUGGCGGCUCACGUGAGCAUAAAUCAAAGAGAUUAAUCGAACAUGGCUCAAUUGCCAAUGAACAUGGCAAG
.((((((....))).(((((((((................(((((.....)))))((((....))))...((((.....)))).))))))))).)))...((((((.......)))))). (-26.77 = -27.77 +   1.00)

alignment

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secondary structure

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dotplot

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Window 6

Location 7,085,122 – 7,085,218
Length 96
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 81.25
Mean single sequence MFE -27.74
Consensus MFE -20.25
Energy contribution -20.25
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.56
Structure conservation index 0.73
SVM decision value 0.37
SVM RNA-class probability 0.710514
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7085122 96 + 20766785
UGCCGGC--AUGGCGGCUCACGUGAGCAUAAAUCAAAGAGAUUAAUCGAACAUGGCUCAAUUGCCAGUUAACAUGGCAAGCAG--CCC----------------CACCAACCAA-AA
....((.--.(((.(((((...(((((..........((......)).......))))).((((((.......))))))).))--)))----------------))))......-.. ( -25.43)
>DroPse_CAF1 119499 116 + 1
UGCCGGUAUAUGGCGGCUCACGUGAGCAUAAAUCAAAGAGAUUAAUCGAACAUGGCUCAAUUGCCAAUGAACAUGGCAACAAGACCAGGCGGAAGGAGGGAUUGCAGCCGCCAG-GA
..........((((((((..((((..(((.((((.....)))).........((((......)))))))..))))....(((..((...(....)..))..))).)))))))).-.. ( -34.00)
>DroEre_CAF1 117910 98 + 1
UGCCGGC--AUGGCGGCUCACGUGAGCAUAAAUCAAAGAGAUUAAUCGAACAUGGCUCAAUUGCCAGUUAACAUGGCAAGCUGACCCC----------------CACCGACCAA-AA
...(((.--.(((.((.(((.((((((..........((......)).......))))..((((((.......))))))))))).)))----------------))))).....-.. ( -25.03)
>DroYak_CAF1 121802 96 + 1
UGCCGGU--AUGGCGGCUCACGUGAGCAUAAAUCAAAGAGAUUAAUCGAACAUGGCUCAAUUGCCAGUUAACAUGGCAACCAAACUGC----------------CAACAA--AG-AA
.(((...--..))).((((....))))...((((.....))))..((.(((.((((......)))))))....(((((.......)))----------------))....--.)-). ( -24.30)
>DroAna_CAF1 116814 99 + 1
UGCCGGC--AUGGCGGCUCACGUGAGCAUAAAUCAAAGAGAUUAAUCGAACAUGGCUCAAUUGCCAAUGAACAUGGCAAGCAAACCAA----------------AACCGACCAAGGA
(((.(.(--(((.((((((....))))...((((.....))))...))..)))).)....((((((.......)))))))))......----------------..((......)). ( -23.70)
>DroPer_CAF1 117220 116 + 1
UGCCGGUAUAUGGCGGCUCACGUGAGCAUAAAUCAAAGAGAUUAAUCGAACAUGGCUCAAUUGCCAAUGAACAUGGCAACAAGACCAGGCGGAAGGAGGGAUUGCAGCCGCCAG-GA
..........((((((((..((((..(((.((((.....)))).........((((......)))))))..))))....(((..((...(....)..))..))).)))))))).-.. ( -34.00)
>consensus
UGCCGGC__AUGGCGGCUCACGUGAGCAUAAAUCAAAGAGAUUAAUCGAACAUGGCUCAAUUGCCAAUGAACAUGGCAACCAGACCAC________________CACCAACCAA_AA
(((((.....(((((((((....))))..........(((.(((........))))))...))))).......)))))....................................... (-20.25 = -20.25 +   0.00)

alignment

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secondary structure

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dotplot

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Window 7

Location 7,085,122 – 7,085,218
Length 96
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 81.25
Mean single sequence MFE -32.92
Consensus MFE -22.15
Energy contribution -21.90
Covariance contribution -0.25
Combinations/Pair 1.04
Mean z-score -2.32
Structure conservation index 0.67
SVM decision value 0.85
SVM RNA-class probability 0.866171
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7085122 96 - 20766785
UU-UUGGUUGGUG----------------GGG--CUGCUUGCCAUGUUAACUGGCAAUUGAGCCAUGUUCGAUUAAUCUCUUUGAUUUAUGCUCACGUGAGCCGCCAU--GCCGGCA
..-...((((((.----------------.((--(.((((((((.(....)))))...(((((.(((.((((.........))))..))))))))...)))).)))..--)))))). ( -32.30)
>DroPse_CAF1 119499 116 - 1
UC-CUGGCGGCUGCAAUCCCUCCUUCCGCCUGGUCUUGUUGCCAUGUUCAUUGGCAAUUGAGCCAUGUUCGAUUAAUCUCUUUGAUUUAUGCUCACGUGAGCCGCCAUAUACCGGCA
..-.((((((((((((..((...........))..))))(((((.......)))))..(((((.(((.((((.........))))..))))))))....)))))))).......... ( -33.50)
>DroEre_CAF1 117910 98 - 1
UU-UUGGUCGGUG----------------GGGGUCAGCUUGCCAUGUUAACUGGCAAUUGAGCCAUGUUCGAUUAAUCUCUUUGAUUUAUGCUCACGUGAGCCGCCAU--GCCGGCA
..-...(((((((----------------(.(((..((((((((.(....))))))).(((((.(((.((((.........))))..)))))))).))..))).))..--)))))). ( -33.80)
>DroYak_CAF1 121802 96 - 1
UU-CU--UUGUUG----------------GCAGUUUGGUUGCCAUGUUAACUGGCAAUUGAGCCAUGUUCGAUUAAUCUCUUUGAUUUAUGCUCACGUGAGCCGCCAU--ACCGGCA
..-..--.....(----------------((.(((..(((((((.(....))))))))..)))(((((..(...((((.....))))....)..))))).)))(((..--...))). ( -30.70)
>DroAna_CAF1 116814 99 - 1
UCCUUGGUCGGUU----------------UUGGUUUGCUUGCCAUGUUCAUUGGCAAUUGAGCCAUGUUCGAUUAAUCUCUUUGAUUUAUGCUCACGUGAGCCGCCAU--GCCGGCA
......((((((.----------------.(((((..(((((((.......)))))).(((((.(((.((((.........))))..)))))))).)..)))))....--)))))). ( -33.70)
>DroPer_CAF1 117220 116 - 1
UC-CUGGCGGCUGCAAUCCCUCCUUCCGCCUGGUCUUGUUGCCAUGUUCAUUGGCAAUUGAGCCAUGUUCGAUUAAUCUCUUUGAUUUAUGCUCACGUGAGCCGCCAUAUACCGGCA
..-.((((((((((((..((...........))..))))(((((.......)))))..(((((.(((.((((.........))))..))))))))....)))))))).......... ( -33.50)
>consensus
UC_CUGGUCGGUG________________GUGGUCUGCUUGCCAUGUUAACUGGCAAUUGAGCCAUGUUCGAUUAAUCUCUUUGAUUUAUGCUCACGUGAGCCGCCAU__ACCGGCA
.......................................((((..((....((((((((((((...))))))))((((.....))))...((((....)))).))))...)).)))) (-22.15 = -21.90 +  -0.25)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:15:27 2006