Locus 4335

Sequence ID X_DroMel_CAF1
Location 11,405,995 – 11,406,147
Length 152
Max. P 0.975784
window7120 window7121 window7122

overview

Window 0

Location 11,405,995 – 11,406,107
Length 112
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 82.77
Mean single sequence MFE -27.23
Consensus MFE -22.76
Energy contribution -23.10
Covariance contribution 0.34
Combinations/Pair 1.07
Mean z-score -1.55
Structure conservation index 0.84
SVM decision value 0.33
SVM RNA-class probability 0.693069
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11405995 112 + 22224390
CAAAAUAGAAUGAAUGAAUGAAU-----AAAAA-AAUGCAUCCAGU-GGUU-AGCGUAAUGCAUUUGCAAUGCGGAUCGCCUUCGGUGGAAAACCUUAAGGCAGAGACAUGCAAAUGCAA
.......................-----.....-.((((..((...-))..-.))))..((((((((((....(..(((((((.(((.....)))..))))).))..).)))))))))). ( -27.50)
>DroSim_CAF1 155 114 + 1
CAAAAUAGAAUGAAUGAAUGAAU----GAAAAA-AAUGCAUGCAGU-GCUUAAGCGUAAUGCAUUUGCAAUGCGGAUCGCCUUCGGAGGAAAACCUUAAGGCAGAGACAUGCAAAUGCAA
.......................----......-..((((((((..-.(((...((((.(((....))).))))....(((((..((((....))))))))).)))...))))..)))). ( -28.30)
>DroYak_CAF1 148 112 + 1
CA-------AUGAAUGAAUGAGAAAUUGAAGCGCAUCGCAUCCAGUUGGUGUAGCGUAAUGCAUUUGCAAUGCGGAUCGCCUUCGGAGGAGAACCUUAAGCCAGAGACAUGCAAAUGCC-
..-------.....................((((...(((((.....))))).))))...(((((((((..(((...)))((..((..(((...)))...))..))...))))))))).- ( -25.90)
>consensus
CAAAAUAGAAUGAAUGAAUGAAU____GAAAAA_AAUGCAUCCAGU_GGUU_AGCGUAAUGCAUUUGCAAUGCGGAUCGCCUUCGGAGGAAAACCUUAAGGCAGAGACAUGCAAAUGCAA
...................................((((..((....))....))))...(((((((((....(..(((((((..((((....))))))))).))..).))))))))).. (-22.76 = -23.10 +   0.34)

alignment

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secondary structure

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dotplot

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Window 1

Location 11,405,995 – 11,406,107
Length 112
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 82.77
Mean single sequence MFE -27.90
Consensus MFE -23.62
Energy contribution -23.73
Covariance contribution 0.11
Combinations/Pair 1.07
Mean z-score -2.52
Structure conservation index 0.85
SVM decision value 1.76
SVM RNA-class probability 0.975784
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11405995 112 - 22224390
UUGCAUUUGCAUGUCUCUGCCUUAAGGUUUUCCACCGAAGGCGAUCCGCAUUGCAAAUGCAUUACGCU-AACC-ACUGGAUGCAUU-UUUUU-----AUUCAUUCAUUCAUUCUAUUUUG
.(((((((((((((...((((((..(((.....))).))))))....))).)))))))))).......-....-..((((((.((.-.....-----)).)))))).............. ( -28.50)
>DroSim_CAF1 155 114 - 1
UUGCAUUUGCAUGUCUCUGCCUUAAGGUUUUCCUCCGAAGGCGAUCCGCAUUGCAAAUGCAUUACGCUUAAGC-ACUGCAUGCAUU-UUUUUC----AUUCAUUCAUUCAUUCUAUUUUG
.(((((((((((((...((((((.(((....)))...))))))....))).))))))))))..........((-(.....)))...-......----....................... ( -27.50)
>DroYak_CAF1 148 112 - 1
-GGCAUUUGCAUGUCUCUGGCUUAAGGUUCUCCUCCGAAGGCGAUCCGCAUUGCAAAUGCAUUACGCUACACCAACUGGAUGCGAUGCGCUUCAAUUUCUCAUUCAUUCAU-------UG
-.((....))..((((.(((....(((....)))))).))))((..(((((((((...((.....))....((....)).)))))))))..))..................-------.. ( -27.70)
>consensus
UUGCAUUUGCAUGUCUCUGCCUUAAGGUUUUCCUCCGAAGGCGAUCCGCAUUGCAAAUGCAUUACGCU_AACC_ACUGGAUGCAUU_UUUUUC____AUUCAUUCAUUCAUUCUAUUUUG
..((((((((((((...((((((.(((....)))...))))))....))).)))))))))................((((((.((............)).)))))).............. (-23.62 = -23.73 +   0.11)

alignment

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secondary structure

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dotplot

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Window 2

Location 11,406,029 – 11,406,147
Length 118
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 90.20
Mean single sequence MFE -35.47
Consensus MFE -27.53
Energy contribution -27.53
Covariance contribution 0.00
Combinations/Pair 1.06
Mean z-score -2.27
Structure conservation index 0.78
SVM decision value 0.19
SVM RNA-class probability 0.624839
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11406029 118 - 22224390
AUGUGUGUGGUGUCUAUAAAUUGUGAAUUACUCAUGGCAUUUGCAUUUGCAUGUCUCUGCCUUAAGGUUUUCCACCGAAGGCGAUCCGCAUUGCAAAUGCAUUACGCU-AACC-ACUGGA
..(((..((((((.........((((.....)))).(((((((((..(((..(((...(((((..(((.....))).))))))))..))).)))))))))...)))))-)..)-)).... ( -36.60)
>DroSim_CAF1 190 117 - 1
AUGA--GUGGUGUCUAUAAAUUGUGAAUUACUCAUGGCAUUUGCAUUUGCAUGUCUCUGCCUUAAGGUUUUCCUCCGAAGGCGAUCCGCAUUGCAAAUGCAUUACGCUUAAGC-ACUGCA
((((--(((((..(........)...))))))))).(((..(((((((((((((...((((((.(((....)))...))))))....))).))))))))))....((....))-..))). ( -38.10)
>DroYak_CAF1 181 116 - 1
AUGU--GCAGUGUCUAUAAAUUGUGAAUUACUCAUGGCG--GGCAUUUGCAUGUCUCUGGCUUAAGGUUCUCCUCCGAAGGCGAUCCGCAUUGCAAAUGCAUUACGCUACACCAACUGGA
....--.((((...........((((.....))))((((--.((((((((((((...(.((((..((.......))..)))).)...))).)))))))))....))))......)))).. ( -31.70)
>consensus
AUGU__GUGGUGUCUAUAAAUUGUGAAUUACUCAUGGCAUUUGCAUUUGCAUGUCUCUGCCUUAAGGUUUUCCUCCGAAGGCGAUCCGCAUUGCAAAUGCAUUACGCU_AACC_ACUGGA
........(((((.......(..(((.....)))..).....((((((((((((...((((((.(((....)))...))))))....))).)))))))))...)))))...((....)). (-27.53 = -27.53 +   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 11:22:25 2006