Locus 8450

Sequence ID 3L_DroMel_CAF1
Location 22,229,086 – 22,229,208
Length 122
Max. P 0.958681
window13813 window13814 window13815

overview

Window 3

Location 22,229,086 – 22,229,176
Length 90
Sequences 5
Columns 93
Reading direction forward
Mean pairwise identity 89.91
Mean single sequence MFE -21.64
Consensus MFE -17.26
Energy contribution -18.38
Covariance contribution 1.12
Combinations/Pair 1.10
Mean z-score -2.12
Structure conservation index 0.80
SVM decision value 1.43
SVM RNA-class probability 0.952830
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22229086 90 + 23771897
GUUUCUUCGGUUAUUCGAGGGUUGCGUUGUGGCUAAUACUAAACUUUAAGCAUGAUUAAAGUUUAUAUUAAUUAGUGUGUUCAAUGCUU---G
...(((((((....)))))))..((((((..((((((..((((((((((......)))))))))).....)))))).....))))))..---. ( -22.90)
>DroSim_CAF1 6511 93 + 1
GUUUCUUCGGUUAUUCGAGGGUUGCGUUGUGGCUAAUACUAAACUUUAAGCAUGAUUAAAGUUUAUAUUAAUUAGUGUGUUCAAUGCUUGAUG
...(((((((....)))))))..((((((..((((((..((((((((((......)))))))))).....)))))).....))))))...... ( -22.90)
>DroEre_CAF1 6494 90 + 1
GUUUCUUCGGUUAUUCGAGGGCUGCGUUGUGGCUAAUACUAAACUUUAAGCAUGAUUAAAGUUUGUAUUAAUUAGUGUAUUCAAUGCUG---G
...(((((((....)))))))..((((((..((((((((.(((((((((......)))))))))))))))......))...))))))..---. ( -23.90)
>DroYak_CAF1 8162 90 + 1
GUUUCUUCGGUUAUUCGAGGGUUGCGUUGUAGCUAAUACUAAACUUUAAGCAUGAUUAAAGUUUAUAUUAAUUAGUGUAUUCAAUGCUU---G
...(((((((....)))))))..((((((..((((((..((((((((((......)))))))))).....)))))).....))))))..---. ( -24.00)
>DroAna_CAF1 6923 85 + 1
GUUUCUUCGGUUAUUCAAGGGCUGAACUGUGACUAAUACUAAACUU----CACGAUUAAAGUUUAUAUUAAUU-GUGUGUUGAAUGCCU---U
........(((.((((((.(((......))................----(((((((((........))))))-)))).))))))))).---. ( -14.50)
>consensus
GUUUCUUCGGUUAUUCGAGGGUUGCGUUGUGGCUAAUACUAAACUUUAAGCAUGAUUAAAGUUUAUAUUAAUUAGUGUGUUCAAUGCUU___G
...(((((((....)))))))..((((((..((((((..((((((((((......)))))))))).....)))))).....))))))...... (-17.26 = -18.38 +   1.12)

alignment

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secondary structure

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Window 4

Location 22,229,086 – 22,229,176
Length 90
Sequences 5
Columns 93
Reading direction reverse
Mean pairwise identity 89.91
Mean single sequence MFE -13.28
Consensus MFE -9.42
Energy contribution -9.70
Covariance contribution 0.28
Combinations/Pair 1.11
Mean z-score -2.08
Structure conservation index 0.71
SVM decision value 0.25
SVM RNA-class probability 0.653548
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22229086 90 - 23771897
C---AAGCAUUGAACACACUAAUUAAUAUAAACUUUAAUCAUGCUUAAAGUUUAGUAUUAGCCACAACGCAACCCUCGAAUAACCGAAGAAAC
.---..((.(((......(((((.....((((((((((......))))))))))..)))))...))).)).....(((......)))...... ( -13.00)
>DroSim_CAF1 6511 93 - 1
CAUCAAGCAUUGAACACACUAAUUAAUAUAAACUUUAAUCAUGCUUAAAGUUUAGUAUUAGCCACAACGCAACCCUCGAAUAACCGAAGAAAC
..((..((.(((......(((((.....((((((((((......))))))))))..)))))...))).)).....(((......))).))... ( -13.30)
>DroEre_CAF1 6494 90 - 1
C---CAGCAUUGAAUACACUAAUUAAUACAAACUUUAAUCAUGCUUAAAGUUUAGUAUUAGCCACAACGCAGCCCUCGAAUAACCGAAGAAAC
.---..((...............(((((((((((((((......))))))))).))))))((......)).))..(((......)))...... ( -14.40)
>DroYak_CAF1 8162 90 - 1
C---AAGCAUUGAAUACACUAAUUAAUAUAAACUUUAAUCAUGCUUAAAGUUUAGUAUUAGCUACAACGCAACCCUCGAAUAACCGAAGAAAC
.---..((.(((......(((((.....((((((((((......))))))))))..)))))...))).)).....(((......)))...... ( -13.00)
>DroAna_CAF1 6923 85 - 1
A---AGGCAUUCAACACAC-AAUUAAUAUAAACUUUAAUCGUG----AAGUUUAGUAUUAGUCACAGUUCAGCCCUUGAAUAACCGAAGAAAC
.---.(((....(((....-.((((((((((((((((....))----)))))).))))))))....)))..)))................... ( -12.70)
>consensus
C___AAGCAUUGAACACACUAAUUAAUAUAAACUUUAAUCAUGCUUAAAGUUUAGUAUUAGCCACAACGCAACCCUCGAAUAACCGAAGAAAC
......................((((((((((((((((......))))))))).)))))))..............(((......)))...... ( -9.42 =  -9.70 +   0.28)

alignment

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secondary structure

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dotplot

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Window 5

Location 22,229,101 – 22,229,208
Length 107
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 75.03
Mean single sequence MFE -12.75
Consensus MFE -8.26
Energy contribution -8.65
Covariance contribution 0.39
Combinations/Pair 1.12
Mean z-score -1.86
Structure conservation index 0.65
SVM decision value 1.49
SVM RNA-class probability 0.958681
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22229101 107 - 23771897
AAAA--UAAGACAACAACA------AAAACAAAGGAAAAGC---AAGCAUUGAACACACUAAUUAAUAUAAACUUUAAUCAUGCUUAAAGUUUAGUAUUAGCCACAACGCAACCCUCG
....--.............------................---..((.(((......(((((.....((((((((((......))))))))))..)))))...))).))........ ( -11.70)
>DroGri_CAF1 6906 103 - 1
AAACAUCACGACAC--------AACAACACACAGAAUACACUUCA---AUUUAA----CUCAUUAAUAUAAACUUUAAUCGCGUUUAAAGUUGAAUAUUAGUCACAAAGCAAACCCAC
.........(((..--------...........(((.....))).---......----.....((((((.((((((((......))))))))..)))))))))............... ( -12.40)
>DroSim_CAF1 6526 116 - 1
AAAA--UAAGACAACAAAAAAAAAAAAAACAAAGGACAAGCAUCAAGCAUUGAACACACUAAUUAAUAUAAACUUUAAUCAUGCUUAAAGUUUAGUAUUAGCCACAACGCAACCCUCG
....--..........................(((.(((((.....)).)))......(((((.....((((((((((......))))))))))..)))))............))).. ( -13.60)
>DroEre_CAF1 6509 102 - 1
AAAA--UAAGACAA-----------GAUACAAAGGAAAAGC---CAGCAUUGAAUACACUAAUUAAUACAAACUUUAAUCAUGCUUAAAGUUUAGUAUUAGCCACAACGCAGCCCUCG
....--........-----------........((.....)---).((...............(((((((((((((((......))))))))).))))))((......)).))..... ( -14.00)
>DroYak_CAF1 8177 102 - 1
AAAA--UAAGACAA-----------AAAACAAAGGAAAAGC---AAGCAUUGAAUACACUAAUUAAUAUAAACUUUAAUCAUGCUUAAAGUUUAGUAUUAGCUACAACGCAACCCUCG
....--........-----------.......(((......---...................(((((((((((((((......))))))))).))))))((......))...))).. ( -12.10)
>DroAna_CAF1 6938 93 - 1
AAAC------ACAC-----------AAAACAUUUAAAAAAA---AGGCAUUCAACACAC-AAUUAAUAUAAACUUUAAUCGUG----AAGUUUAGUAUUAGUCACAGUUCAGCCCUUG
....------....-----------................---.(((....(((....-.((((((((((((((((....))----)))))).))))))))....)))..))).... ( -12.70)
>consensus
AAAA__UAAGACAA___________AAAACAAAGGAAAAGC___AAGCAUUGAACACACUAAUUAAUAUAAACUUUAAUCAUGCUUAAAGUUUAGUAUUAGCCACAACGCAACCCUCG
..............................................................((((((((((((((((......))))))))).)))))))................. ( -8.26 =  -8.65 +   0.39)

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 13:15:38 2006