Locus 2859

Sequence ID 3R_DroMel_CAF1
Location 7,679,494 – 7,679,632
Length 138
Max. P 0.999884
window4618 window4619 window4620

overview

Window 8

Location 7,679,494 – 7,679,600
Length 106
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 78.26
Mean single sequence MFE -25.32
Consensus MFE -14.30
Energy contribution -15.78
Covariance contribution 1.48
Combinations/Pair 1.32
Mean z-score -2.10
Structure conservation index 0.56
SVM decision value 0.95
SVM RNA-class probability 0.888521
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7679494 106 - 27905053
-GUACGUAUAUUGUUUGUAUGAAAAUGCAAAUAUAU-------------UAUACAGUUAGCACAUGGUGCGCAAAAAGUAGUUUAAAUGUCGUCUGUGGUUGAACUACAUCUGCGUUAAA
-....(((((.(((((((((....)))))))))...-------------))))).....((((...))))(((....(((((((((....(....)...)))))))))...)))...... ( -27.20)
>DroSec_CAF1 29432 103 - 1
-GUA--UAUAGUGU-UGCAUGAAAGUGCAAAUAUAU-------------UAUACAGUUAGCACAUGGUGCGCAAAAAGUAGUUUAAAUGUCGUCUGUGGUUGAACUACAUCUGCGUUAAA
-(((--((((...(-(((((....))))))...)).-------------))))).....((((...))))(((....(((((((((....(....)...)))))))))...)))...... ( -25.90)
>DroSim_CAF1 29440 104 - 1
-GUA--UAUAGUGUUUGCAUGAAAAUGCAAAUAUAU-------------UAUACAUUUAGCACAUGGUGCGCAAAAAGUAGUUUAAAUGUCGUCUGUGGUUGAACUACAUCUGCGUUAAA
-(((--((..((((((((((....))))))))))..-------------))))).....((((...))))(((....(((((((((....(....)...)))))))))...)))...... ( -30.30)
>DroYak_CAF1 29571 114 - 1
-AUC-----AGUGUUUGCAUGAAUUUGGAAAAAUAUACAUACUCGUAUAUAUAAAGUUAGCACAUGGUGCGCAAAAAGUAGUUUAAAUGUCGUCUGUGGUUGAACUACAUGUGCGUUAAA
-(((-----((((((.((......((....))((((((......)))))).....)).))))).))))(((((....(((((((((....(....)...)))))))))...))))).... ( -25.00)
>DroAna_CAF1 32211 96 - 1
AGUA--CACA-UAUUUGC---AAAUUGCAAGUAAAU------------------CGUUAGUGCAUGUUGUGCAAAAAGCUGUUUAAAUGUCAUCUCUGUCCGCACUACAACUGUGUUAAA
...(--((((-(((((((---.....)))))))...------------------.((.(((((.......((.....)).........(.((....)).).)))))))...))))).... ( -18.20)
>consensus
_GUA__UAUAGUGUUUGCAUGAAAAUGCAAAUAUAU_____________UAUACAGUUAGCACAUGGUGCGCAAAAAGUAGUUUAAAUGUCGUCUGUGGUUGAACUACAUCUGCGUUAAA
..........((((((((((....)))))))))).........................((((...))))(((....(((((((((....((....)).)))))))))...)))...... (-14.30 = -15.78 +   1.48)

alignment

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secondary structure

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dotplot

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Window 9

Location 7,679,534 – 7,679,632
Length 98
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 69.51
Mean single sequence MFE -18.94
Consensus MFE -4.88
Energy contribution -6.52
Covariance contribution 1.64
Combinations/Pair 1.07
Mean z-score -2.19
Structure conservation index 0.26
SVM decision value 1.30
SVM RNA-class probability 0.939192
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7679534 98 + 27905053
UACUUUUUGCGCACCAUGUGCUAACUGUAUA-------------AUAUAUUUGCAUUUUCAUACAAACAAUAUACGUAC-AUAU--------AUGUAGGUCGCAAUAGUUUUAAAGCUUU
.(((..(((((.(((.(((((.....)))))-------------............................((((((.-...)--------))))))))))))).)))........... ( -17.20)
>DroSec_CAF1 29472 89 + 1
UACUUUUUGCGCACCAUGUGCUAACUGUAUA-------------AUAUAUUUGCACUUUCAUGCA-ACACUAUA--UAC-ACAC--------A------UCGCAAUAGUUUUAAAGCUUU
.(((..(((((....(((((.....((((((-------------......(((((......))))-).....))--)))-))))--------)------)))))).)))........... ( -15.80)
>DroSim_CAF1 29480 96 + 1
UACUUUUUGCGCACCAUGUGCUAAAUGUAUA-------------AUAUAUUUGCAUUUUCAUGCAAACACUAUA--UAC-ACAC--------AUAUAGGUCGCAAUAGUUUUAAAGCUUU
.(((..(((((.((((((((.....((((((-------------.....(((((((....))))))).....))--)))-)..)--------)))).)))))))).)))........... ( -22.90)
>DroYak_CAF1 29611 104 + 1
UACUUUUUGCGCACCAUGUGCUAACUUUAUAUAUACGAGUAUGUAUAUUUUUCCAAAUUCAUGCAAACACU-----GAU-A--U--------AUGUAGGUCGCAAUAGUUUUAAAGCUUU
.(((..(((((.(((..((....))..((((((((..(((.(((((((((....))))..)))))...)))-----..)-)--)--------))))))))))))).)))........... ( -18.40)
>DroAna_CAF1 32251 94 + 1
AGCUUUUUGCACAACAUGCACUAACG------------------AUUUACUUGCAAUUU---GCAAAUA-UGUG--UACUACACAGCGUUGUCUACAAAUAGCAG--CUAUUGAAGCUUU
.(((.((((.(((((..((.......------------------......((((.....---))))...-((((--.....)))))))))))...)))).)))((--((.....)))).. ( -20.40)
>consensus
UACUUUUUGCGCACCAUGUGCUAACUGUAUA_____________AUAUAUUUGCAAUUUCAUGCAAACACUAUA__UAC_ACAC________AUAUAGGUCGCAAUAGUUUUAAAGCUUU
......((((((((...))))............................((((((......))))))..................................))))............... ( -4.88 =  -6.52 +   1.64)

alignment

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secondary structure

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dotplot

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Window 0

Location 7,679,534 – 7,679,632
Length 98
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 69.51
Mean single sequence MFE -24.97
Consensus MFE -12.39
Energy contribution -13.43
Covariance contribution 1.04
Combinations/Pair 1.35
Mean z-score -3.45
Structure conservation index 0.50
SVM decision value 4.38
SVM RNA-class probability 0.999884
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7679534 98 - 27905053
AAAGCUUUAAAACUAUUGCGACCUACAU--------AUAU-GUACGUAUAUUGUUUGUAUGAAAAUGCAAAUAUAU-------------UAUACAGUUAGCACAUGGUGCGCAAAAAGUA
...(((((.......((((((((((((.--------...)-))).(((((.(((((((((....)))))))))...-------------)))))...........))).)))))))))). ( -24.61)
>DroSec_CAF1 29472 89 - 1
AAAGCUUUAAAACUAUUGCGA------U--------GUGU-GUA--UAUAGUGU-UGCAUGAAAGUGCAAAUAUAU-------------UAUACAGUUAGCACAUGGUGCGCAAAAAGUA
...(((((...((((((((..------(--------((((-(.(--((((...(-(((((....)))))).)))))-------------))))))....))).)))))......))))). ( -25.40)
>DroSim_CAF1 29480 96 - 1
AAAGCUUUAAAACUAUUGCGACCUAUAU--------GUGU-GUA--UAUAGUGUUUGCAUGAAAAUGCAAAUAUAU-------------UAUACAUUUAGCACAUGGUGCGCAAAAAGUA
...(((((.......(((((..((((.(--------((((-(((--((..((((((((((....))))))))))..-------------)))))))...))).))))..)))))))))). ( -31.41)
>DroYak_CAF1 29611 104 - 1
AAAGCUUUAAAACUAUUGCGACCUACAU--------A--U-AUC-----AGUGUUUGCAUGAAUUUGGAAAAAUAUACAUACUCGUAUAUAUAAAGUUAGCACAUGGUGCGCAAAAAGUA
...(((((.......((((((((.((((--------.--.-...-----.)))).(((.(((.((((.....((((((......)))))).)))).))))))...))).)))))))))). ( -17.61)
>DroAna_CAF1 32251 94 - 1
AAAGCUUCAAUAG--CUGCUAUUUGUAGACAACGCUGUGUAGUA--CACA-UAUUUGC---AAAUUGCAAGUAAAU------------------CGUUAGUGCAUGUUGUGCAAAAAGCU
..((((.....))--))(((.((((((((((.(((((((.....--))).-(((((((---.....)))))))...------------------....))))..)))).)))))).))). ( -25.80)
>consensus
AAAGCUUUAAAACUAUUGCGACCUACAU________GUGU_GUA__UAUAGUGUUUGCAUGAAAAUGCAAAUAUAU_____________UAUACAGUUAGCACAUGGUGCGCAAAAAGUA
...(((((.......((((...............................((((((((((....)))))))))).........................((((...))))))))))))). (-12.39 = -13.43 +   1.04)

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 10:46:26 2006