Locus 4489

Sequence ID 2R_DroMel_CAF1
Location 14,761,637 – 14,761,797
Length 160
Max. P 0.982499
window7176 window7177 window7178 window7179

overview

Window 6

Location 14,761,637 – 14,761,757
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 87.57
Mean single sequence MFE -23.61
Consensus MFE -19.71
Energy contribution -19.71
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.72
Structure conservation index 0.83
SVM decision value 1.20
SVM RNA-class probability 0.930145
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14761637 120 + 20766785
UGAAAAGCUAUAAACACGAUAACCAGGCCUACGUCUGUCCACCCUUAACCCAUAACCCUUAACCCUCUCUCUCUCUCUCUCUCAUUCGAAAGCAAGGGUUAUGGUUAUGAACACCCGAUG
................((.....(((((....))))).............(((((((..(((((((..((.((..............)).))..))))))).)))))))......))... ( -24.34)
>DroSim_CAF1 2070 114 + 1
UGAAAAGCUAUAAACACGAUAUCCAGGCCUACGUCUGUCCACCCUUAACCCAUAACCCUUAACCCUCUCUCUCUCUUUA------UCGAAAGCAAGGGUUAUGGUUAUGAACACCCGAUG
................((.....(((((....))))).............(((((((..(((((((..((.((......------..)).))..))))))).)))))))......))... ( -25.60)
>DroYak_CAF1 3398 102 + 1
UGAAAAGCUAUAAACACGAUAUCCAGGCCUACGUCUGUCCACCCUUAACCCAUAACCCUUAACCCUCUCUCUCUC------------------AUGGGUUAUGGUUAUGAACACCCAAUG
.......................(((((....))))).............(((((((..((((((..........------------------..)))))).)))))))........... ( -20.90)
>consensus
UGAAAAGCUAUAAACACGAUAUCCAGGCCUACGUCUGUCCACCCUUAACCCAUAACCCUUAACCCUCUCUCUCUCU_U_______UCGAAAGCAAGGGUUAUGGUUAUGAACACCCGAUG
.......................(((((....))))).............(((((((..((((((..............................)))))).)))))))........... (-19.71 = -19.71 +   0.00)

alignment

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secondary structure

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dotplot

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Window 7

Location 14,761,637 – 14,761,757
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 87.57
Mean single sequence MFE -32.57
Consensus MFE -28.09
Energy contribution -29.87
Covariance contribution 1.78
Combinations/Pair 1.03
Mean z-score -1.64
Structure conservation index 0.86
SVM decision value 0.10
SVM RNA-class probability 0.585442
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14761637 120 - 20766785
CAUCGGGUGUUCAUAACCAUAACCCUUGCUUUCGAAUGAGAGAGAGAGAGAGAGAGGGUUAAGGGUUAUGGGUUAAGGGUGGACAGACGUAGGCCUGGUUAUCGUGUUUAUAGCUUUUCA
((((....(..(((((((.((((((((.(((((...(....)...)))))...))))))))..)))))))..)....))))((.((..((((((.((.....)).))))))..))..)). ( -35.30)
>DroSim_CAF1 2070 114 - 1
CAUCGGGUGUUCAUAACCAUAACCCUUGCUUUCGA------UAAAGAGAGAGAGAGGGUUAAGGGUUAUGGGUUAAGGGUGGACAGACGUAGGCCUGGAUAUCGUGUUUAUAGCUUUUCA
((((....(..(((((((.((((((((.(((((..------....)))))...))))))))..)))))))..)....))))((.((..((((((.((.....)).))))))..))..)). ( -36.00)
>DroYak_CAF1 3398 102 - 1
CAUUGGGUGUUCAUAACCAUAACCCAU------------------GAGAGAGAGAGGGUUAAGGGUUAUGGGUUAAGGGUGGACAGACGUAGGCCUGGAUAUCGUGUUUAUAGCUUUUCA
.....(((((((....(((((((((.(------------------((...........))).))))))))).....((((..((....))..)))))))))))................. ( -26.40)
>consensus
CAUCGGGUGUUCAUAACCAUAACCCUUGCUUUCGA_______A_AGAGAGAGAGAGGGUUAAGGGUUAUGGGUUAAGGGUGGACAGACGUAGGCCUGGAUAUCGUGUUUAUAGCUUUUCA
((((....(..(((((((.((((((((.(((((..............))))).))))))))..)))))))..)....))))((.((..((((((.((.....)).))))))..))..)). (-28.09 = -29.87 +   1.78)

alignment

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secondary structure

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dotplot

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Window 8

Location 14,761,677 – 14,761,797
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 88.14
Mean single sequence MFE -29.18
Consensus MFE -25.81
Energy contribution -25.81
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -4.82
Structure conservation index 0.88
SVM decision value 1.48
SVM RNA-class probability 0.957902
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14761677 120 + 20766785
ACCCUUAACCCAUAACCCUUAACCCUCUCUCUCUCUCUCUCUCAUUCGAAAGCAAGGGUUAUGGUUAUGAACACCCGAUGUGUGGGUUAACCAAAAGGCAUUUUCAAUAAAUACCAAUUA
....(((((((((((((..(((((((..((.((..............)).))..))))))).))))))..((((.....)))))))))))......((.((((.....)))).))..... ( -29.64)
>DroSim_CAF1 2110 114 + 1
ACCCUUAACCCAUAACCCUUAACCCUCUCUCUCUCUUUA------UCGAAAGCAAGGGUUAUGGUUAUGAACACCCGAUGUGUGGGUUAACCAAAAGGCAUUUUCAAUAAAUACCAAUUA
....(((((((((((((..(((((((..((.((......------..)).))..))))))).))))))..((((.....)))))))))))......((.((((.....)))).))..... ( -30.90)
>DroYak_CAF1 3438 102 + 1
ACCCUUAACCCAUAACCCUUAACCCUCUCUCUCUC------------------AUGGGUUAUGGUUAUGAACACCCAAUGUGUGGGUUAACCAAAAGGCAUUUUCAAUAAAUACCAAUUA
....(((((((((((((..((((((..........------------------..)))))).))))))..((((.....)))))))))))......((.((((.....)))).))..... ( -27.00)
>consensus
ACCCUUAACCCAUAACCCUUAACCCUCUCUCUCUCU_U_______UCGAAAGCAAGGGUUAUGGUUAUGAACACCCGAUGUGUGGGUUAACCAAAAGGCAUUUUCAAUAAAUACCAAUUA
....(((((((((((((..((((((..............................)))))).))))))..((((.....)))))))))))......((.((((.....)))).))..... (-25.81 = -25.81 +   0.00)

alignment

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secondary structure

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dotplot

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Window 9

Location 14,761,677 – 14,761,797
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 88.14
Mean single sequence MFE -37.93
Consensus MFE -34.14
Energy contribution -36.14
Covariance contribution 2.00
Combinations/Pair 1.00
Mean z-score -4.15
Structure conservation index 0.90
SVM decision value 1.92
SVM RNA-class probability 0.982499
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14761677 120 - 20766785
UAAUUGGUAUUUAUUGAAAAUGCCUUUUGGUUAACCCACACAUCGGGUGUUCAUAACCAUAACCCUUGCUUUCGAAUGAGAGAGAGAGAGAGAGAGGGUUAAGGGUUAUGGGUUAAGGGU
(((..(((((((.....)))))))..))).(((((((((((.....))))..((((((.((((((((.(((((...(....)...)))))...))))))))..))))))))))))).... ( -41.00)
>DroSim_CAF1 2110 114 - 1
UAAUUGGUAUUUAUUGAAAAUGCCUUUUGGUUAACCCACACAUCGGGUGUUCAUAACCAUAACCCUUGCUUUCGA------UAAAGAGAGAGAGAGGGUUAAGGGUUAUGGGUUAAGGGU
(((..(((((((.....)))))))..))).(((((((((((.....))))..((((((.((((((((.(((((..------....)))))...))))))))..))))))))))))).... ( -41.70)
>DroYak_CAF1 3438 102 - 1
UAAUUGGUAUUUAUUGAAAAUGCCUUUUGGUUAACCCACACAUUGGGUGUUCAUAACCAUAACCCAU------------------GAGAGAGAGAGGGUUAAGGGUUAUGGGUUAAGGGU
(((..(((((((.....)))))))..))).(((((((((((.....))))..((((((.((((((..------------------..........))))))..))))))))))))).... ( -31.10)
>consensus
UAAUUGGUAUUUAUUGAAAAUGCCUUUUGGUUAACCCACACAUCGGGUGUUCAUAACCAUAACCCUUGCUUUCGA_______A_AGAGAGAGAGAGGGUUAAGGGUUAUGGGUUAAGGGU
(((..(((((((.....)))))))..))).(((((((((((.....))))..((((((.((((((((.(((((..............))))).))))))))..))))))))))))).... (-34.14 = -36.14 +   2.00)

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 11:21:00 2006