Locus 4875

Sequence ID 3R_DroMel_CAF1
Location 12,819,883 – 12,820,077
Length 194
Max. P 0.973890
window7981 window7982 window7983 window7984

overview

Window 1

Location 12,819,883 – 12,819,997
Length 114
Sequences 3
Columns 114
Reading direction forward
Mean pairwise identity 95.91
Mean single sequence MFE -32.63
Consensus MFE -28.81
Energy contribution -28.70
Covariance contribution -0.11
Combinations/Pair 1.06
Mean z-score -1.87
Structure conservation index 0.88
SVM decision value 0.08
SVM RNA-class probability 0.574780
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12819883 114 + 27905053
UUUAACCGUCCGCUGGAUUAUCAGCGCUGCCCUCGCUGCCCUGCAGUCGUCGAUUGCACCUACAGUGCUAUGCAAGUAAAUAUGCAUAUGGUUAUUGCCAUGUACGUAUAUAAA
..........(((((......))))).(((...(((((...(((((((...)))))))....)))))....))).....(((((.(((((((....))))))).)))))..... ( -31.90)
>DroSim_CAF1 197496 114 + 1
UUUAACCGUCCGCUGGAUUAUCAGCGCUGCCCUCGCUGCCCUGCAGUCGUCGAUUGCACCUACAGUGCUAUGCAAGUAAAUAUGCACAUGGUUAUUUCCAUGUACGUAUAUAAA
..........(((((......))))).(((...(((((...(((((((...)))))))....)))))....))).....(((((.((((((......)))))).)))))..... ( -32.20)
>DroYak_CAF1 195750 113 + 1
UUUAACCGUCCGCUGGAUUAUCAGCGCUGCCCUCGGUGCCCUGCAGUCGUCGAUUGCACCUACAGUGCUAUGCAAGUAUAUAUACAUAUGG-UAUUGCCAUGUGCGUAUAUAAA
..........(((((........((((((....))))))..(((((((...)))))))....))))).........((((((..(((((((-.....)))))))..)))))).. ( -33.80)
>consensus
UUUAACCGUCCGCUGGAUUAUCAGCGCUGCCCUCGCUGCCCUGCAGUCGUCGAUUGCACCUACAGUGCUAUGCAAGUAAAUAUGCAUAUGGUUAUUGCCAUGUACGUAUAUAAA
..........(((((......))))).(((...(((((...(((((((...)))))))....)))))....))).....((((((((((((......))))))..))))))... (-28.81 = -28.70 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 2

Location 12,819,923 – 12,820,037
Length 114
Sequences 3
Columns 114
Reading direction forward
Mean pairwise identity 92.40
Mean single sequence MFE -34.50
Consensus MFE -31.87
Energy contribution -31.10
Covariance contribution -0.77
Combinations/Pair 1.13
Mean z-score -2.78
Structure conservation index 0.92
SVM decision value 1.72
SVM RNA-class probability 0.973890
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12819923 114 + 27905053
CUGCAGUCGUCGAUUGCACCUACAGUGCUAUGCAAGUAAAUAUGCAUAUGGUUAUUGCCAUGUACGUAUAUAAAUUUGCAAUUGUAUGACGAUGGACACGCACAAACCUAGUGA
.(((.(((((((...((((.....))))..(((((((..(((((((((((((....)))))))..))))))..)))))))......)))))))(....))))............ ( -33.10)
>DroSim_CAF1 197536 114 + 1
CUGCAGUCGUCGAUUGCACCUACAGUGCUAUGCAAGUAAAUAUGCACAUGGUUAUUUCCAUGUACGUAUAUAAAUUUGCAAUCGUAUGGCGAUGGACACGCACAAGCCUAGUGA
.(((((((...)))))))......((((..(((((((..((((((((((((......))))))..))))))..)))))))((((.....))))......))))........... ( -34.80)
>DroYak_CAF1 195790 113 + 1
CUGCAGUCGUCGAUUGCACCUACAGUGCUAUGCAAGUAUAUAUACAUAUGG-UAUUGCCAUGUGCGUAUAUAAAUAUGCAAUCGUAUGACGAUGGACAUGCAUGAGCCUAGUGA
.(((((((...)))))))..(((((.(((((((...((((((..(((((((-.....)))))))..))))))...((((.((((.....)))).).))))))).))))).))). ( -35.60)
>consensus
CUGCAGUCGUCGAUUGCACCUACAGUGCUAUGCAAGUAAAUAUGCAUAUGGUUAUUGCCAUGUACGUAUAUAAAUUUGCAAUCGUAUGACGAUGGACACGCACAAGCCUAGUGA
(((..((((((((((((((.....))))...((((((..((((((((((((......))))))..))))))..))))))))))).)))))..))).(((...........))). (-31.87 = -31.10 +  -0.77)

alignment

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secondary structure

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dotplot

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Window 3

Location 12,819,923 – 12,820,037
Length 114
Sequences 3
Columns 114
Reading direction reverse
Mean pairwise identity 92.40
Mean single sequence MFE -30.13
Consensus MFE -24.63
Energy contribution -24.30
Covariance contribution -0.33
Combinations/Pair 1.10
Mean z-score -2.03
Structure conservation index 0.82
SVM decision value 0.00
SVM RNA-class probability 0.535045
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12819923 114 - 27905053
UCACUAGGUUUGUGCGUGUCCAUCGUCAUACAAUUGCAAAUUUAUAUACGUACAUGGCAAUAACCAUAUGCAUAUUUACUUGCAUAGCACUGUAGGUGCAAUCGACGACUGCAG
.(((.......)))..(((...(((((.......(((((.(..((((..(((.((((......)))).)))))))..).)))))..((((.....))))....)))))..))). ( -25.10)
>DroSim_CAF1 197536 114 - 1
UCACUAGGCUUGUGCGUGUCCAUCGCCAUACGAUUGCAAAUUUAUAUACGUACAUGGAAAUAACCAUGUGCAUAUUUACUUGCAUAGCACUGUAGGUGCAAUCGACGACUGCAG
.......((.((((.(((.....)))))))(((((((............((((((((......))))))))......(((((((......))))))))))))))......)).. ( -34.50)
>DroYak_CAF1 195790 113 - 1
UCACUAGGCUCAUGCAUGUCCAUCGUCAUACGAUUGCAUAUUUAUAUACGCACAUGGCAAUA-CCAUAUGUAUAUAUACUUGCAUAGCACUGUAGGUGCAAUCGACGACUGCAG
.......((....)).(((...(((((....(((((((....((((((..((.((((.....-)))).))..))))))((((((......))))))))))))))))))..))). ( -30.80)
>consensus
UCACUAGGCUUGUGCGUGUCCAUCGUCAUACGAUUGCAAAUUUAUAUACGUACAUGGCAAUAACCAUAUGCAUAUUUACUUGCAUAGCACUGUAGGUGCAAUCGACGACUGCAG
............((((.(((..(((.....)((((((............(((.((((......)))).)))......(((((((......))))))))))))))).))))))). (-24.63 = -24.30 +  -0.33)

alignment

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secondary structure

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dotplot

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Window 4

Location 12,819,961 – 12,820,077
Length 116
Sequences 3
Columns 116
Reading direction forward
Mean pairwise identity 91.38
Mean single sequence MFE -25.05
Consensus MFE -21.71
Energy contribution -21.17
Covariance contribution -0.55
Combinations/Pair 1.14
Mean z-score -1.92
Structure conservation index 0.87
SVM decision value 0.24
SVM RNA-class probability 0.648195
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12819961 116 + 27905053
AAUAUGCAUAUGGUUAUUGCCAUGUACGUAUAUAAAUUUGCAAUUGUAUGACGAUGGACACGCACAAACCUAGUGAGAAUUAAUCUAGUGCAUUAAAGCAAUUUUUACAAUAAUAA
.(((((.(((((((....))))))).))))).((((.((((...(((((...(((.......(((.......))).......)))..))))).....))))..))))......... ( -22.14)
>DroSim_CAF1 197574 116 + 1
AAUAUGCACAUGGUUAUUUCCAUGUACGUAUAUAAAUUUGCAAUCGUAUGGCGAUGGACACGCACAAGCCUAGUGAGAAUUAAUCUAGUGCAUUAAAGCAAUUUUUACAAAAAUAA
.(((((.((((((......)))))).))))).((((.((((.((((.....))))......((((.((..((((....))))..)).))))......))))..))))......... ( -26.90)
>DroYak_CAF1 195828 115 + 1
UAUAUACAUAUGG-UAUUGCCAUGUGCGUAUAUAAAUAUGCAAUCGUAUGACGAUGGACAUGCAUGAGCCUAGUGAGAAUUAAUCUAGUGCAUUAUAGCAAUUUUUACAAUAAUAA
((((..(((((((-.....)))))))..))))....((((((((((.....)))).....))))))......(((((((((...(((........))).)))))))))........ ( -26.10)
>consensus
AAUAUGCAUAUGGUUAUUGCCAUGUACGUAUAUAAAUUUGCAAUCGUAUGACGAUGGACACGCACAAGCCUAGUGAGAAUUAAUCUAGUGCAUUAAAGCAAUUUUUACAAUAAUAA
.((((((((((((......))))))..)))))).....(((.((((.....))))......((((.((..((((....))))..)).))))......)))................ (-21.71 = -21.17 +  -0.55)

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 11:40:59 2006