Locus 2400

Sequence ID 2R_DroMel_CAF1
Location 8,639,715 – 8,639,912
Length 197
Max. P 0.971281
window3968 window3969 window3970 window3971

overview

Window 8

Location 8,639,715 – 8,639,832
Length 117
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 87.48
Mean single sequence MFE -34.32
Consensus MFE -25.27
Energy contribution -26.15
Covariance contribution 0.88
Combinations/Pair 1.13
Mean z-score -3.17
Structure conservation index 0.74
SVM decision value 1.67
SVM RNA-class probability 0.971281
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8639715 117 - 20766785
UAAGGAUAAAAUAACUCUGGAAACAAAAGAGUUAGCC---CAAAGUGGAAUGAAGCUUCGAAGGACUUACAUCAUAAAAAUGGUGAGGGCAUCCCAGGGCUCACUAUCACUGGUCUGACA
...((((....((((((((....)...)))))))(((---(...........(((..((....))))).((((((....)))))).))))))))((((.(...........).))))... ( -30.00)
>DroSec_CAF1 19891 117 - 1
UACGGAUAAAAUAACUCUGGAAACAAAAGAGUUAGCC---CAAAGUGGAAUGAAGCUUUAAAGGACCUACAUCAUAAAUAUGGUGAGUCCAUCCCAGGGCUCACUAUCACUGGUCUGGCA
...........((((((((....)...)))))))(((---.(((((........)))))...(((((............(((((((((((......)))))))))))....)))))))). ( -35.49)
>DroSim_CAF1 23568 117 - 1
UACGGAUAAAAUAACUCUGGAAACAAAAGAGUUAGCC---CACAGUGGAAUGAAGCUUCAAAGGACCUACAUCAUAAAAAUGGUGAGUCCAUCCCAGGGCUCACUAUCACUGGUCUGGCA
..(((((....((((((((....)...)))))))...---..(((((((.((.((.((.....)).)).))))......(((((((((((......)))))))))))))))))))))... ( -37.00)
>DroYak_CAF1 19859 120 - 1
CACCGAUAACAUAACUCUGCAAACAGAAGAGUUAGCCAUCUAAAGCGGUAUAAAGCUUCGGGAGACUUACAUCAUGAAAAUGGUGAGUCCAUCCCAGGACCCACUUUCACUCGUCUGGCA
...........(((((((.........)))))))(((.((..((((........))))..))((((...((((((....)))))).((((......))))............))))))). ( -34.80)
>consensus
UACGGAUAAAAUAACUCUGGAAACAAAAGAGUUAGCC___CAAAGUGGAAUGAAGCUUCAAAGGACCUACAUCAUAAAAAUGGUGAGUCCAUCCCAGGGCUCACUAUCACUGGUCUGGCA
...........((((((((....)...)))))))(((.....((((........))))....(((((.....(((....)))((((((((......)))))))).......)))))))). (-25.27 = -26.15 +   0.88)

alignment

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secondary structure

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dotplot

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Window 9

Location 8,639,755 – 8,639,872
Length 117
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 86.78
Mean single sequence MFE -28.06
Consensus MFE -18.31
Energy contribution -16.88
Covariance contribution -1.44
Combinations/Pair 1.22
Mean z-score -2.04
Structure conservation index 0.65
SVM decision value 0.30
SVM RNA-class probability 0.679721
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8639755 117 + 20766785
UUUUUAUGAUGUAAGUCCUUCGAAGCUUCAUUCCACUUUG---GGCUAACUCUUUUGUUUCCAGAGUUAUUUUAUCCUUAAUGAGUUUCAUAGUGGCAUUAUCUACUCUGUGGGACUACU
..........(((.(((((.(((((((.((((..((((((---((..(((......)))))))))))............))))))))))..(((((......)))))..).)))))))). ( -26.24)
>DroSec_CAF1 19931 117 + 1
UAUUUAUGAUGUAGGUCCUUUAAAGCUUCAUUCCACUUUG---GGCUAACUCUUUUGUUUCCAGAGUUAUUUUAUCCGUAAUGAGUUUCAUAGUGACAUUAUUUACUCUGUGGGACUACU
...((((((((.((((........)))))))...((((((---((..(((......))))))))))).........)))))..(((..(((((.(..........).)))))..)))... ( -22.50)
>DroSim_CAF1 23608 117 + 1
UUUUUAUGAUGUAGGUCCUUUGAAGCUUCAUUCCACUGUG---GGCUAACUCUUUUGUUUCCAGAGUUAUUUUAUCCGUAAUGUGUUUCAUAGUGACAUUAUUUACUCUGUGGGACUACU
..........(((((((((.((((((..((((.(...(((---((.(((((((.........))))))).)))))..).)))).)))))).)).)))........((.....)).)))). ( -23.90)
>DroYak_CAF1 19899 120 + 1
UUUUCAUGAUGUAAGUCUCCCGAAGCUUUAUACCGCUUUAGAUGGCUAACUCUUCUGUUUGCAGAGUUAUGUUAUCGGUGAUGAGUUGCAUUGUGGCAUUCUCCACCCUGUGGGACUACU
...(((..((((((.(((((((((((........))))).(((((((((((((.(.....).))))))).)))))))).)).)).))))))..)))...((.((((...))))))..... ( -39.60)
>consensus
UUUUUAUGAUGUAAGUCCUUCGAAGCUUCAUUCCACUUUG___GGCUAACUCUUUUGUUUCCAGAGUUAUUUUAUCCGUAAUGAGUUUCAUAGUGACAUUAUCUACUCUGUGGGACUACU
..........((.((((((....((((.((........))...))))((((((.........))))))....................((.(((((......))))).)).)))))))). (-18.31 = -16.88 +  -1.44)

alignment

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secondary structure

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dotplot

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Window 0

Location 8,639,755 – 8,639,872
Length 117
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 86.78
Mean single sequence MFE -25.38
Consensus MFE -17.48
Energy contribution -17.79
Covariance contribution 0.31
Combinations/Pair 1.07
Mean z-score -2.48
Structure conservation index 0.69
SVM decision value 0.94
SVM RNA-class probability 0.886356
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8639755 117 - 20766785
AGUAGUCCCACAGAGUAGAUAAUGCCACUAUGAAACUCAUUAAGGAUAAAAUAACUCUGGAAACAAAAGAGUUAGCC---CAAAGUGGAAUGAAGCUUCGAAGGACUUACAUCAUAAAAA
.(((((((..(..(((........((((((((.....)))...((......((((((((....)...)))))))..)---)..)))))......)))..)..)))).))).......... ( -25.34)
>DroSec_CAF1 19931 117 - 1
AGUAGUCCCACAGAGUAAAUAAUGUCACUAUGAAACUCAUUACGGAUAAAAUAACUCUGGAAACAAAAGAGUUAGCC---CAAAGUGGAAUGAAGCUUUAAAGGACCUACAUCAUAAAUA
.((((..((.((((((......((((...(((.....)))....)))).....))))))......((((..(((..(---(.....))..)))..))))...))..)))).......... ( -25.30)
>DroSim_CAF1 23608 117 - 1
AGUAGUCCCACAGAGUAAAUAAUGUCACUAUGAAACACAUUACGGAUAAAAUAACUCUGGAAACAAAAGAGUUAGCC---CACAGUGGAAUGAAGCUUCAAAGGACCUACAUCAUAAAAA
.((((..((.((((((......((((...(((.....)))....)))).....)))))).......(((..(((..(---(.....))..)))..)))....))..)))).......... ( -22.80)
>DroYak_CAF1 19899 120 - 1
AGUAGUCCCACAGGGUGGAGAAUGCCACAAUGCAACUCAUCACCGAUAACAUAACUCUGCAAACAGAAGAGUUAGCCAUCUAAAGCGGUAUAAAGCUUCGGGAGACUUACAUCAUGAAAA
.((((((((....((((..((.(((......)))..))..))))(((....(((((((.........)))))))...)))..((((........)))).))))...)))).......... ( -28.10)
>consensus
AGUAGUCCCACAGAGUAAAUAAUGCCACUAUGAAACUCAUUACGGAUAAAAUAACUCUGGAAACAAAAGAGUUAGCC___CAAAGUGGAAUGAAGCUUCAAAGGACCUACAUCAUAAAAA
.(((((((....((((........((((((((.....)))...........((((((((....)...))))))).........)))))......))))....)))).))).......... (-17.48 = -17.79 +   0.31)

alignment

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secondary structure

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dotplot

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Window 1

Location 8,639,795 – 8,639,912
Length 117
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 88.19
Mean single sequence MFE -27.47
Consensus MFE -22.85
Energy contribution -22.66
Covariance contribution -0.19
Combinations/Pair 1.12
Mean z-score -2.43
Structure conservation index 0.83
SVM decision value 1.66
SVM RNA-class probability 0.970371
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8639795 117 - 20766785
CUCUUAUUAUCGGUUAACUUACCCUGAUCUUUGACUAGAAAGUAGUCCCACAGAGUAGAUAAUGCCACUAUGAAACUCAUUAAGGAUAAAAUAACUCUGGAAACAAAAGAGUUAGCC---
...........(((((((((............(((((.....)))))...((((((........((...(((.....)))...))........)))))).........)))))))))--- ( -24.89)
>DroSec_CAF1 19971 117 - 1
CUCUUAUUAGCGGCUAACUUACCCUGAUCUUUGACUAGAAAGUAGUCCCACAGAGUAAAUAAUGUCACUAUGAAACUCAUUACGGAUAAAAUAACUCUGGAAACAAAAGAGUUAGCC---
...........(((((((((............(((((.....)))))...((((((......((((...(((.....)))....)))).....)))))).........)))))))))--- ( -27.30)
>DroSim_CAF1 23648 117 - 1
CUCUUAUUAUCGGCUAACUUACCCUGAUCUUUGACUAGAAAGUAGUCCCACAGAGUAAAUAAUGUCACUAUGAAACACAUUACGGAUAAAAUAACUCUGGAAACAAAAGAGUUAGCC---
...........(((((((((............(((((.....)))))...((((((......((((...(((.....)))....)))).....)))))).........)))))))))--- ( -26.30)
>DroYak_CAF1 19939 120 - 1
GGUUAAUAAUCGGUUCACUUACUCUGAUCUUUGACUAGGAAGUAGUCCCACAGGGUGGAGAAUGCCACAAUGCAACUCAUCACCGAUAACAUAACUCUGCAAACAGAAGAGUUAGCCAUC
(((((((.((((((.....(((((((......(((((.....)))))...)))))))(((..(((......))).)))...))))))........((((....))))...)))))))... ( -31.40)
>consensus
CUCUUAUUAUCGGCUAACUUACCCUGAUCUUUGACUAGAAAGUAGUCCCACAGAGUAAAUAAUGCCACUAUGAAACUCAUUACGGAUAAAAUAACUCUGGAAACAAAAGAGUUAGCC___
...........(((((((((............(((((.....)))))...((((((........((...(((.....)))...))........)))))).........)))))))))... (-22.85 = -22.66 +  -0.19)

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 10:29:08 2006