Locus 5490

Sequence ID X_DroMel_CAF1
Location 14,258,072 – 14,258,208
Length 136
Max. P 0.999101
window8903 window8904 window8905 window8906

overview

Window 3

Location 14,258,072 – 14,258,191
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 85.18
Mean single sequence MFE -40.78
Consensus MFE -28.26
Energy contribution -30.94
Covariance contribution 2.68
Combinations/Pair 1.03
Mean z-score -3.08
Structure conservation index 0.69
SVM decision value 1.83
SVM RNA-class probability 0.979233
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14258072 119 + 22224390
UGUGUAGAGCAGGGUAGCCGGCUUUCGAUCGGCUCCAAAUUGCCACUCGUUGUAA-AGUGGCAAUUAACGCCACAUGACGCUGUCAACAAAUGGCCCUGGCUAGGCAUUACACACCCACA
(((((((.....((.(((((((....).)))))))).((((((((((........-))))))))))...(((...((((...)))).....((((....))))))).)))))))...... ( -42.10)
>DroPse_CAF1 1778 90 + 1
------------------------UCGAUCGGCUCCAAAUUGCCACUCGUUGUAA-AGUGGCAAUUAACGCCACAUGACGCUGUCAACAAAUGGCGGCGCCUCCCC-----ACCCCCCUA
------------------------......(((....((((((((((........-))))))))))...)))......((((((((.....)))))))).......-----......... ( -29.00)
>DroSim_CAF1 2473 119 + 1
UGUGUAGAGCAGGGUAGCCGGCUUUCGAUCGGCUCCAAAUUGCCACUCGUUGUAA-AGUGGCAAUUAACGCCACAUGACGCUGUCAACAAAUGGCCCUGGCUAGGCAUUACACACCCACA
(((((((.....((.(((((((....).)))))))).((((((((((........-))))))))))...(((...((((...)))).....((((....))))))).)))))))...... ( -42.10)
>DroEre_CAF1 2538 119 + 1
UGUGUAGAGCAGGGGAGCCGGCUUUCGAUCGGCUCCAAAUUGCCACUCGUUGUAA-AGUGGCAAUUAACGCCACAUGACGCUGUCAACAAAUGGCCCUGGCUAGGCAUUACACACCCACA
(((((((......(((((((((....).)))))))).((((((((((........-))))))))))...(((...((((...)))).....((((....))))))).)))))))...... ( -45.90)
>DroYak_CAF1 2498 120 + 1
UGUGUAUAGCAGGGGAGCUGGUUUUCGAUCGGCUCCAAAUUGCCACUCGUUGUAAAAGUGGCAAUUAACGCCACAUGACGCUGUCAACAAUUGGCCCUGGCUAGGCAUUACACACCCACA
(((((((((((((((((((((((...)))))))))).....((((...(((((....(((((.......))))).((((...)))))))))))))))).)))).....))))))...... ( -44.80)
>consensus
UGUGUAGAGCAGGGGAGCCGGCUUUCGAUCGGCUCCAAAUUGCCACUCGUUGUAA_AGUGGCAAUUAACGCCACAUGACGCUGUCAACAAAUGGCCCUGGCUAGGCAUUACACACCCACA
(((((((.((.....((((((.........(((....((((((((((.........))))))))))...))).......(((((......))))).))))))..)).)))))))...... (-28.26 = -30.94 +   2.68)

alignment

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secondary structure

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dotplot

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Window 4

Location 14,258,072 – 14,258,191
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 85.18
Mean single sequence MFE -43.20
Consensus MFE -29.87
Energy contribution -32.46
Covariance contribution 2.59
Combinations/Pair 1.03
Mean z-score -2.52
Structure conservation index 0.69
SVM decision value 1.14
SVM RNA-class probability 0.920853
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14258072 119 - 22224390
UGUGGGUGUGUAAUGCCUAGCCAGGGCCAUUUGUUGACAGCGUCAUGUGGCGUUAAUUGCCACU-UUACAACGAGUGGCAAUUUGGAGCCGAUCGAAAGCCGGCUACCCUGCUCUACACA
.((((((((...))))).(((.(((((((.........((((((....))))))((((((((((-(......))))))))))))))(((((..(....).))))).)))))))...))). ( -45.40)
>DroPse_CAF1 1778 90 - 1
UAGGGGGGU-----GGGGAGGCGCCGCCAUUUGUUGACAGCGUCAUGUGGCGUUAAUUGCCACU-UUACAACGAGUGGCAAUUUGGAGCCGAUCGA------------------------
.........-----.((..(((.(((((((....((((...)))).)))))...((((((((((-(......))))))))))).)).)))..))..------------------------ ( -34.40)
>DroSim_CAF1 2473 119 - 1
UGUGGGUGUGUAAUGCCUAGCCAGGGCCAUUUGUUGACAGCGUCAUGUGGCGUUAAUUGCCACU-UUACAACGAGUGGCAAUUUGGAGCCGAUCGAAAGCCGGCUACCCUGCUCUACACA
.((((((((...))))).(((.(((((((.........((((((....))))))((((((((((-(......))))))))))))))(((((..(....).))))).)))))))...))). ( -45.40)
>DroEre_CAF1 2538 119 - 1
UGUGGGUGUGUAAUGCCUAGCCAGGGCCAUUUGUUGACAGCGUCAUGUGGCGUUAAUUGCCACU-UUACAACGAGUGGCAAUUUGGAGCCGAUCGAAAGCCGGCUCCCCUGCUCUACACA
.((((((((...))))).(((.((((((((((((((((...)))..((((((.....)))))).-....)))))))))).....(((((((..(....).)))))))))))))...))). ( -50.10)
>DroYak_CAF1 2498 120 - 1
UGUGGGUGUGUAAUGCCUAGCCAGGGCCAAUUGUUGACAGCGUCAUGUGGCGUUAAUUGCCACUUUUACAACGAGUGGCAAUUUGGAGCCGAUCGAAAACCAGCUCCCCUGCUAUACACA
.((((((((...)))))((((.(((((((.....((((...))))..))))...(((((((((((.......))))))))))).(((((.(.........).))))))))))))..))). ( -40.70)
>consensus
UGUGGGUGUGUAAUGCCUAGCCAGGGCCAUUUGUUGACAGCGUCAUGUGGCGUUAAUUGCCACU_UUACAACGAGUGGCAAUUUGGAGCCGAUCGAAAGCCGGCUACCCUGCUCUACACA
.......(((((..((....((((.(((((((((((((...)))..((((((.....))))))......))))))))))...))))(((((.........))))).....))..))))). (-29.87 = -32.46 +   2.59)

alignment

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secondary structure

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Window 5

Location 14,258,112 – 14,258,208
Length 96
Sequences 3
Columns 113
Reading direction forward
Mean pairwise identity 74.22
Mean single sequence MFE -22.80
Consensus MFE -18.49
Energy contribution -17.60
Covariance contribution -0.89
Combinations/Pair 1.11
Mean z-score -2.09
Structure conservation index 0.81
SVM decision value 3.37
SVM RNA-class probability 0.999101
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14258112 96 + 22224390
UGCCACUCGUUGUAAAGUGGCAAUUAACGCCACAUGACGCUGUCAACAAAUGGCCCUGGCUAGGCAUUACACACCCACAUUCACAUUCA-----------------CAUCUCC
((((.....((((...(((((.......))))).((((...)))))))).((((....)))))))).......................-----------------....... ( -22.30)
>DroPse_CAF1 1794 108 + 1
UGCCACUCGUUGUAAAGUGGCAAUUAACGCCACAUGACGCUGUCAACAAAUGGCGGCGCCUCCCC-----ACCCCCCUAACCCCAGCCACCUACCCGCAUUCUACAUAUGUAC
(((((((........))))))).........(((((.((((((((.....)))))))).......-----...............((.........))........))))).. ( -23.80)
>DroSim_CAF1 2513 96 + 1
UGCCACUCGUUGUAAAGUGGCAAUUAACGCCACAUGACGCUGUCAACAAAUGGCCCUGGCUAGGCAUUACACACCCACACCCACAUUCA-----------------UAUCGCC
((((.....((((...(((((.......))))).((((...)))))))).((((....)))))))).......................-----------------....... ( -22.30)
>consensus
UGCCACUCGUUGUAAAGUGGCAAUUAACGCCACAUGACGCUGUCAACAAAUGGCCCUGGCUAGGCAUUACACACCCACAACCACAUUCA_________________UAUCUCC
.((((....((((...(((((.......))))).((((...)))))))).))))((......))................................................. (-18.49 = -17.60 +  -0.89)

alignment

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secondary structure

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dotplot

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Window 6

Location 14,258,112 – 14,258,208
Length 96
Sequences 3
Columns 113
Reading direction reverse
Mean pairwise identity 74.22
Mean single sequence MFE -31.33
Consensus MFE -25.95
Energy contribution -25.07
Covariance contribution -0.89
Combinations/Pair 1.10
Mean z-score -0.95
Structure conservation index 0.83
SVM decision value 0.54
SVM RNA-class probability 0.775663
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14258112 96 - 22224390
GGAGAUG-----------------UGAAUGUGAAUGUGGGUGUGUAAUGCCUAGCCAGGGCCAUUUGUUGACAGCGUCAUGUGGCGUUAAUUGCCACUUUACAACGAGUGGCA
.......-----------------............(((((((...)))))))......(((((((((((((...)))..((((((.....)))))).....)))))))))). ( -28.20)
>DroPse_CAF1 1794 108 - 1
GUACAUAUGUAGAAUGCGGGUAGGUGGCUGGGGUUAGGGGGGU-----GGGGAGGCGCCGCCAUUUGUUGACAGCGUCAUGUGGCGUUAAUUGCCACUUUACAACGAGUGGCA
.(((....))).(((.(.(((.....))).).))).....(((-----(......))))(((((((((((((...)))..((((((.....)))))).....)))))))))). ( -33.80)
>DroSim_CAF1 2513 96 - 1
GGCGAUA-----------------UGAAUGUGGGUGUGGGUGUGUAAUGCCUAGCCAGGGCCAUUUGUUGACAGCGUCAUGUGGCGUUAAUUGCCACUUUACAACGAGUGGCA
.......-----------------........(((.(((((((...))))))))))...(((((((((((((...)))..((((((.....)))))).....)))))))))). ( -32.00)
>consensus
GGAGAUA_________________UGAAUGUGGAUGUGGGUGUGUAAUGCCUAGCCAGGGCCAUUUGUUGACAGCGUCAUGUGGCGUUAAUUGCCACUUUACAACGAGUGGCA
.................................................((......))(((((((((((((...)))..((((((.....)))))).....)))))))))). (-25.95 = -25.07 +  -0.89)

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 11:49:11 2006