Locus 2316

Sequence ID 2R_DroMel_CAF1
Location 8,522,574 – 8,522,713
Length 139
Max. P 0.969573
window3813 window3814 window3815

overview

Window 3

Location 8,522,574 – 8,522,676
Length 102
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 84.21
Mean single sequence MFE -33.73
Consensus MFE -30.03
Energy contribution -30.03
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.36
Structure conservation index 0.89
SVM decision value 1.64
SVM RNA-class probability 0.969573
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8522574 102 + 20766785
GCC-CGAUACCCGAU---ACCCGAU--------------ACACACUCACGUUCCUCAUCGGGGCGAUAAAAUUUUAACGAUUUUGCGCCGCUUUGAGCGAGCGUGUCAGGCAUAAAGAUA
(((-.(((((.((..---...))..--------------..........((((((((..(.((((.(((((((.....))))))))))).)..)))).))))))))).)))......... ( -33.90)
>DroSim_CAF1 908 98 + 1
GCCCCGAUACCCGAU---AC-------------------ACACACUCACGUUCCUCAUCGGGGCGAUAAAAUUUUAACGAUUUUGCGCCGCUUUGAGCGAGCGUGUCAGGCAUAAAGAUA
(((.((.....))..---..-------------------.......(((((((((((..(.((((.(((((((.....))))))))))).)..)))).)))))))...)))......... ( -32.60)
>DroYak_CAF1 906 119 + 1
GCC-AGAUACCCGACCCGACCCGAUAUACUCGUACACACACUCACUCACGUUCCUCAGCGGGGCGAUAAAAUUUUAACGAUUUUGCGCCGCUUUGAGCGAGCGUGUCAGGCAUAAAGAUA
(((-.................(((.....)))..............((((((((((((.(.((((.(((((((.....))))))))))).).))))).)))))))...)))......... ( -34.70)
>consensus
GCC_CGAUACCCGAU___ACCCGAU______________ACACACUCACGUUCCUCAUCGGGGCGAUAAAAUUUUAACGAUUUUGCGCCGCUUUGAGCGAGCGUGUCAGGCAUAAAGAUA
(((..(.....)..................................(((((((((((..(.((((.(((((((.....))))))))))).)..)))).)))))))...)))......... (-30.03 = -30.03 +   0.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 8,522,574 – 8,522,676
Length 102
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 84.21
Mean single sequence MFE -36.77
Consensus MFE -25.49
Energy contribution -25.83
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.81
Structure conservation index 0.69
SVM decision value -0.00
SVM RNA-class probability 0.533417
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8522574 102 - 20766785
UAUCUUUAUGCCUGACACGCUCGCUCAAAGCGGCGCAAAAUCGUUAAAAUUUUAUCGCCCCGAUGAGGAACGUGAGUGUGU--------------AUCGGGU---AUCGGGUAUCG-GGC
...((..((((((((..(((.(((.....)))))).......................(((((((....((....))...)--------------)))))).---.))))))))..-)). ( -33.80)
>DroSim_CAF1 908 98 - 1
UAUCUUUAUGCCUGACACGCUCGCUCAAAGCGGCGCAAAAUCGUUAAAAUUUUAUCGCCCCGAUGAGGAACGUGAGUGUGU-------------------GU---AUCGGGUAUCGGGGC
..(((..((((((((.((((.((((((....((((.(((((.......)))))..))))((.....))....)))))).))-------------------))---.))))))))..))). ( -34.70)
>DroYak_CAF1 906 119 - 1
UAUCUUUAUGCCUGACACGCUCGCUCAAAGCGGCGCAAAAUCGUUAAAAUUUUAUCGCCCCGCUGAGGAACGUGAGUGAGUGUGUGUACGAGUAUAUCGGGUCGGGUCGGGUAUCU-GGC
...((..((((((((((((((((((((.(((((.(((((((.......)))))...)).)))))........))))))))))).....(((.(......).))).)))))))))..-)). ( -41.80)
>consensus
UAUCUUUAUGCCUGACACGCUCGCUCAAAGCGGCGCAAAAUCGUUAAAAUUUUAUCGCCCCGAUGAGGAACGUGAGUGUGU______________AUCGGGU___AUCGGGUAUCG_GGC
.......(((((((((((((((((.......((((.(((((.......)))))..))))((.....))...)))))))))..........................))))))))...... (-25.49 = -25.83 +   0.33)

alignment

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secondary structure

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dotplot

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Window 5

Location 8,522,596 – 8,522,713
Length 117
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 97.20
Mean single sequence MFE -30.17
Consensus MFE -29.80
Energy contribution -29.80
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.21
Structure conservation index 0.99
SVM decision value 1.38
SVM RNA-class probability 0.948397
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8522596 117 + 20766785
CACACUCACGUUCCUCAUCGGGGCGAUAAAAUUUUAACGAUUUUGCGCCGCUUUGAGCGAGCGUGUCAGGCAUAAAGAUACAAAACAAUACUUGGGCAUAUA---UAAACAAAAGCAAAC
......(((((((((((..(.((((.(((((((.....))))))))))).)..)))).)))))))....((...(((((........)).)))..)).....---............... ( -30.00)
>DroSim_CAF1 926 117 + 1
CACACUCACGUUCCUCAUCGGGGCGAUAAAAUUUUAACGAUUUUGCGCCGCUUUGAGCGAGCGUGUCAGGCAUAAAGAUACAAAACAAUACUUGGGCAUAUA---UAAACAAAAGCAAAC
......(((((((((((..(.((((.(((((((.....))))))))))).)..)))).)))))))....((...(((((........)).)))..)).....---............... ( -30.00)
>DroYak_CAF1 945 120 + 1
CUCACUCACGUUCCUCAGCGGGGCGAUAAAAUUUUAACGAUUUUGCGCCGCUUUGAGCGAGCGUGUCAGGCAUAAAGAUACAAAACAAUACUUGGGCAUAUACAAUAAACAAAAGCAAAC
......((((((((((((.(.((((.(((((((.....))))))))))).).))))).)))))))....((...(((((........)).)))..))....................... ( -30.50)
>consensus
CACACUCACGUUCCUCAUCGGGGCGAUAAAAUUUUAACGAUUUUGCGCCGCUUUGAGCGAGCGUGUCAGGCAUAAAGAUACAAAACAAUACUUGGGCAUAUA___UAAACAAAAGCAAAC
......(((((((((((..(.((((.(((((((.....))))))))))).)..)))).)))))))....((...(((((........)).)))..))....................... (-29.80 = -29.80 +   0.00)

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 10:26:40 2006