Locus 1855

Sequence ID 3R_DroMel_CAF1
Location 5,326,323 – 5,326,501
Length 178
Max. P 0.784026
window3049 window3050 window3051

overview

Window 9

Location 5,326,323 – 5,326,439
Length 116
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 89.83
Mean single sequence MFE -24.90
Consensus MFE -24.10
Energy contribution -24.43
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.32
Structure conservation index 0.97
SVM decision value 0.35
SVM RNA-class probability 0.701744
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5326323 116 - 27905053
GCACUUCAUGUUUCAAGGGAGUGCAUUAAAUGCACAGCAAUUAUGUUUAAAUAAUUUAUUAUGUGUAUUAAUUACGAGCCGCGCGCUCUCGCUCGAUACAGUUUCAUUUUCA----UCAU
(((((((..........)))))))....((((((((..((((((......)))))).....)))))))).....(((((...........))))).................----.... ( -25.10)
>DroSim_CAF1 31899 114 - 1
GCACUUCAUGUUUCAAGGGAGUGCAUUAAAUGCACAGCAAUUAUGUUUAAAUAAUUUAUUAUGUGUAUUAAUUACGAGCUGCGCGC--UCGCUCGAUACAGUUUCAUUUUCA----UCAU
(((((((..........)))))))....((((((((..((((((......)))))).....)))))))).....(((((.....))--))).....................----.... ( -25.90)
>DroYak_CAF1 31479 112 - 1
GCACUUCAUGUUCCAAGGGAGUGCAUUAAAGGCACAGCAAUUAUGUUUAAAUAAUUUAUUAUGUGUAUUAAUUUCGAGCCGC--------GCUCGAUACAGUUUCAUUUUCCAUUUGCAU
(((((((..........)))))))(((((..(((((..((((((......)))))).....))))).))))).((((((...--------))))))........................ ( -23.70)
>consensus
GCACUUCAUGUUUCAAGGGAGUGCAUUAAAUGCACAGCAAUUAUGUUUAAAUAAUUUAUUAUGUGUAUUAAUUACGAGCCGCGCGC__UCGCUCGAUACAGUUUCAUUUUCA____UCAU
(((((((..........)))))))....((((((((..((((((......)))))).....)))))))).....(((((...........)))))......................... (-24.10 = -24.43 +   0.33)

alignment

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secondary structure

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dotplot

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Window 0

Location 5,326,359 – 5,326,461
Length 102
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 83.63
Mean single sequence MFE -27.87
Consensus MFE -23.29
Energy contribution -23.40
Covariance contribution 0.11
Combinations/Pair 1.04
Mean z-score -1.80
Structure conservation index 0.84
SVM decision value 0.57
SVM RNA-class probability 0.784026
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5326359 102 - 27905053
GUUCACGGACUGCCGGGCAU------------------GUGCACUUCAUGUUUCAAGGGAGUGCAUUAAAUGCACAGCAAUUAUGUUUAAAUAAUUUAUUAUGUGUAUUAAUUACGAGCC
.....(((....)))(((..------------------(((((((((..........)))))))))..((((((((..((((((......)))))).....))))))))........))) ( -27.70)
>DroSim_CAF1 31933 102 - 1
GUUCACGGACUGGCGGGCAU------------------GUGCACUUCAUGUUUCAAGGGAGUGCAUUAAAUGCACAGCAAUUAUGUUUAAAUAAUUUAUUAUGUGUAUUAAUUACGAGCU
((((................------------------(((((((((..........)))))))))..((((((((..((((((......)))))).....))))))))......)))). ( -24.60)
>DroYak_CAF1 31511 120 - 1
GUUCAGGGACUGCAAUGCAUGUACAUGUGCAUAUGCAUAUGCACUUCAUGUUCCAAGGGAGUGCAUUAAAGGCACAGCAAUUAUGUUUAAAUAAUUUAUUAUGUGUAUUAAUUUCGAGCC
((((.(..(.((((((((((......)))))).)))).(((((((((..........))))))))).....(((((..((((((......)))))).....))))).....)..))))). ( -31.30)
>consensus
GUUCACGGACUGCCGGGCAU__________________GUGCACUUCAUGUUUCAAGGGAGUGCAUUAAAUGCACAGCAAUUAUGUUUAAAUAAUUUAUUAUGUGUAUUAAUUACGAGCC
((((..................................(((((((((..........)))))))))..((((((((..((((((......)))))).....))))))))......)))). (-23.29 = -23.40 +   0.11)

alignment

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secondary structure

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dotplot

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Window 1

Location 5,326,399 – 5,326,501
Length 102
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 83.04
Mean single sequence MFE -30.29
Consensus MFE -22.99
Energy contribution -23.00
Covariance contribution 0.01
Combinations/Pair 1.12
Mean z-score -1.57
Structure conservation index 0.76
SVM decision value -0.01
SVM RNA-class probability 0.528477
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5326399 102 - 27905053
AGAGGCCAAGCCUGUAGAUAACAAUGAACUGGAAUAAGUUGUUCACGGACUGCCGGGCAU------------------GUGCACUUCAUGUUUCAAGGGAGUGCAUUAAAUGCACAGCAA
...(((..((.((((..(((((...............)))))..)))).)))))..((((------------------(((((((((..........)))))))))...))))....... ( -27.86)
>DroSim_CAF1 31973 102 - 1
AGAGGCCAAGCCUGUAGAUAACAAUGAACUGGAAUAAGAUGUUCACGGACUGGCGGGCAU------------------GUGCACUUCAUGUUUCAAGGGAGUGCAUUAAAUGCACAGCAA
....((((..(((((.....))).(((((...........))))).))..))))..((((------------------(((((((((..........)))))))))...))))....... ( -28.10)
>DroYak_CAF1 31551 120 - 1
AGAGGCCAAGCCUGCAGAUAACAAUGAACUGGAGUAAGAUGUUCAGGGACUGCAAUGCAUGUACAUGUGCAUAUGCAUAUGCACUUCAUGUUCCAAGGGAGUGCAUUAAAGGCACAGCAA
....((...((((((((....(..(((((...........)))))..).)))).((((((((.(....).))))))))(((((((((..........)))))))))...))))...)).. ( -34.90)
>consensus
AGAGGCCAAGCCUGUAGAUAACAAUGAACUGGAAUAAGAUGUUCACGGACUGCCGGGCAU__________________GUGCACUUCAUGUUUCAAGGGAGUGCAUUAAAUGCACAGCAA
....((...((((((((....(..(((((...........)))))..).)))).))))....................(((((((((..........)))))))))..........)).. (-22.99 = -23.00 +   0.01)

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 10:21:11 2006