Locus 9324

Sequence ID 3R_DroMel_CAF1
Location 24,787,107 – 24,787,297
Length 190
Max. P 0.849829
window14913 window14914 window14915 window14916

overview

Window 3

Location 24,787,107 – 24,787,217
Length 110
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 91.29
Mean single sequence MFE -17.64
Consensus MFE -15.47
Energy contribution -15.80
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.27
Structure conservation index 0.88
SVM decision value 0.78
SVM RNA-class probability 0.849829
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24787107 110 - 27905053
AACACAUUCCAUAUCAUUACUGGAGAAGGCCACAAAAAUUUUCUCAAUCCUUAAAUGUGGCAUGCCCCCUCCUAACUC----------ACACACACACCAACAUACAAGGCAGUAACAUC
................(((((((((((((.........)))))))...((((..((((((..((..............----------.....))..)).))))..)))))))))).... ( -15.51)
>DroEre_CAF1 27270 120 - 1
AACACAUUCCAUAUCAUUACUGGAGGAGGCCACAAAAAUUUCCUCAAUCCUUAAAUGUGGCAUGCCCCCUCCUAACUCACGCUCACACACACACACACCAGCACACAAGGCAGUAACAUC
................((((((((((..((((((.....................))))))......)))))............................((.......))))))).... ( -18.70)
>DroYak_CAF1 19214 116 - 1
AACACAUUCCAUAUCAUUACUGGAGGAGGCCACAAAAAUUUCCUCAAUCCUUAAAUGUGGCAUGCCCCCUCCUAACUUACU----CACACACACACACCAGCACACAAGGCAGUAACAUC
................((((((((((..((((((.....................))))))......))))).........----...............((.......))))))).... ( -18.70)
>consensus
AACACAUUCCAUAUCAUUACUGGAGGAGGCCACAAAAAUUUCCUCAAUCCUUAAAUGUGGCAUGCCCCCUCCUAACUCAC_____CACACACACACACCAGCACACAAGGCAGUAACAUC
................((((((((((..((((((.....................))))))......))))).........................((.........)).))))).... (-15.47 = -15.80 +   0.33)

alignment

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secondary structure

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dotplot

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Window 4

Location 24,787,139 – 24,787,257
Length 118
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 97.22
Mean single sequence MFE -29.87
Consensus MFE -30.01
Energy contribution -29.57
Covariance contribution -0.44
Combinations/Pair 1.06
Mean z-score -1.48
Structure conservation index 1.00
SVM decision value 0.27
SVM RNA-class probability 0.661068
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24787139 118 + 27905053
--GAGUUAGGAGGGGGCAUGCCACAUUUAAGGAUUGAGAAAAUUUUUGUGGCCUUCUCCAGUAAUGAUAUGGAAUGUGUUGGAAUUUCAAGAAGUUACUCCAGAUUUCUUUAUUUAUUUA
--(((((.((((((((...((((((....((((((.....))))))))))))..))))).(((((....((((((........))))))....)))))))).)))))............. ( -27.90)
>DroEre_CAF1 27310 120 + 1
GUGAGUUAGGAGGGGGCAUGCCACAUUUAAGGAUUGAGGAAAUUUUUGUGGCCUCCUCCAGUAAUGAUAUGGAAUGUGUUGGAAUUUCAAGAAGUUACUCCAGAUUUCUUUAUUUAUUUA
((((((.(((((((((...((((((....((((((.....))))))))))))..)))))((((((....((((((........))))))....)))))).......)))).))))))... ( -30.90)
>DroYak_CAF1 19250 120 + 1
GUAAGUUAGGAGGGGGCAUGCCACAUUUAAGGAUUGAGGAAAUUUUUGUGGCCUCCUCCAGUAAUGAUAUGGAAUGUGUUGGAAUUUCAAGAAGUUACUCCAGAUUUCUUUAUUUAUUUA
((((((.(((((((((...((((((....((((((.....))))))))))))..)))))((((((....((((((........))))))....)))))).......)))).))))))... ( -30.80)
>consensus
GUGAGUUAGGAGGGGGCAUGCCACAUUUAAGGAUUGAGGAAAUUUUUGUGGCCUCCUCCAGUAAUGAUAUGGAAUGUGUUGGAAUUUCAAGAAGUUACUCCAGAUUUCUUUAUUUAUUUA
..(((((.((((((((...((((((....((((((.....))))))))))))..))))).(((((....((((((........))))))....)))))))).)))))............. (-30.01 = -29.57 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 5

Location 24,787,139 – 24,787,257
Length 118
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 97.22
Mean single sequence MFE -19.57
Consensus MFE -18.59
Energy contribution -18.37
Covariance contribution -0.22
Combinations/Pair 1.04
Mean z-score -1.82
Structure conservation index 0.95
SVM decision value 0.47
SVM RNA-class probability 0.747298
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24787139 118 - 27905053
UAAAUAAAUAAAGAAAUCUGGAGUAACUUCUUGAAAUUCCAACACAUUCCAUAUCAUUACUGGAGAAGGCCACAAAAAUUUUCUCAAUCCUUAAAUGUGGCAUGCCCCCUCCUAACUC--
...................((((...(((((((......))).....((((((....)).))))))))((((((.....................)))))).......))))......-- ( -18.70)
>DroEre_CAF1 27310 120 - 1
UAAAUAAAUAAAGAAAUCUGGAGUAACUUCUUGAAAUUCCAACACAUUCCAUAUCAUUACUGGAGGAGGCCACAAAAAUUUCCUCAAUCCUUAAAUGUGGCAUGCCCCCUCCUAACUCAC
............((....((((((..(.....)..))))))....................(((((..((((((.....................))))))......)))))....)).. ( -19.80)
>DroYak_CAF1 19250 120 - 1
UAAAUAAAUAAAGAAAUCUGGAGUAACUUCUUGAAAUUCCAACACAUUCCAUAUCAUUACUGGAGGAGGCCACAAAAAUUUCCUCAAUCCUUAAAUGUGGCAUGCCCCCUCCUAACUUAC
..........(((.....((((((..(.....)..))))))....................(((((..((((((.....................))))))......)))))...))).. ( -20.20)
>consensus
UAAAUAAAUAAAGAAAUCUGGAGUAACUUCUUGAAAUUCCAACACAUUCCAUAUCAUUACUGGAGGAGGCCACAAAAAUUUCCUCAAUCCUUAAAUGUGGCAUGCCCCCUCCUAACUCAC
...................((((...(((((((......))).....((((((....)).))))))))((((((.....................)))))).......))))........ (-18.59 = -18.37 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 6

Location 24,787,177 – 24,787,297
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 99.44
Mean single sequence MFE -31.77
Consensus MFE -30.90
Energy contribution -30.90
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.78
Structure conservation index 0.97
SVM decision value 0.53
SVM RNA-class probability 0.771014
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24787177 120 + 27905053
AAUUUUUGUGGCCUUCUCCAGUAAUGAUAUGGAAUGUGUUGGAAUUUCAAGAAGUUACUCCAGAUUUCUUUAUUUAUUUAAAUGAGCAGCCAGCGCGAAUGCCACAAAGUCAGGCCCGUA
...(((((((((.(((((((.........))))..(((((((...((((.((((((......))))))((((......))))))))...)))))))))).)))))))))........... ( -33.50)
>DroEre_CAF1 27350 120 + 1
AAUUUUUGUGGCCUCCUCCAGUAAUGAUAUGGAAUGUGUUGGAAUUUCAAGAAGUUACUCCAGAUUUCUUUAUUUAUUUAAAUGAGCAGCCAGCGCGAAUGCCACAAAGUCAGGCCCGUA
...(((((((((....((((.........)))).((((((((...((((.((((((......))))))((((......))))))))...))))))))...)))))))))........... ( -30.90)
>DroYak_CAF1 19290 120 + 1
AAUUUUUGUGGCCUCCUCCAGUAAUGAUAUGGAAUGUGUUGGAAUUUCAAGAAGUUACUCCAGAUUUCUUUAUUUAUUUAAAUGAGCAGCCAGCGCGAAUGCCACAAAGUCAGGCCCGUA
...(((((((((....((((.........)))).((((((((...((((.((((((......))))))((((......))))))))...))))))))...)))))))))........... ( -30.90)
>consensus
AAUUUUUGUGGCCUCCUCCAGUAAUGAUAUGGAAUGUGUUGGAAUUUCAAGAAGUUACUCCAGAUUUCUUUAUUUAUUUAAAUGAGCAGCCAGCGCGAAUGCCACAAAGUCAGGCCCGUA
...(((((((((....((((.........)))).((((((((...((((.((((((......))))))((((......))))))))...))))))))...)))))))))........... (-30.90 = -30.90 +   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 13:31:44 2006