Locus 910

Sequence ID 2R_DroMel_CAF1
Location 4,054,628 – 4,054,771
Length 143
Max. P 0.982764
window1600 window1601 window1602 window1603

overview

Window 0

Location 4,054,628 – 4,054,731
Length 103
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 90.13
Mean single sequence MFE -26.38
Consensus MFE -22.86
Energy contribution -22.93
Covariance contribution 0.06
Combinations/Pair 1.04
Mean z-score -2.53
Structure conservation index 0.87
SVM decision value 1.92
SVM RNA-class probability 0.982764
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4054628 103 + 20766785
AA-----------------AAAAUAGGAUAAGAUAGCGAUGUAUAAUAUGGAAAUAUAUAUUCGCAUAUUGGCGUGUUUUGACAUUUAUCGGCACGUCCUCCGACAUGCCGGCAAAAUUA
..-----------------((((((.(....((((((((.(((((.(((....)))))))))))).))))..).))))))....(((..(((((.(((....))).)))))..))).... ( -27.20)
>DroSec_CAF1 37308 103 + 1
AA-----------------AAAAUAGCAUAAGAUAGCGAUGUAUAAUAUGGAAAUAUAUAUUCGCAUAUUGGCAUGUUUUGACAUUUAUCGGCACGUCCUCCGACAUGCCGGCAAAAUUA
..-----------------((((((((....((((((((.(((((.(((....)))))))))))).)))).)).))))))....(((..(((((.(((....))).)))))..))).... ( -27.60)
>DroSim_CAF1 43434 103 + 1
AA-----------------AAAAUAGGAUAAGAUAGCGAUGUAUAAUAUGGAAAUAUAUAUUCGCAUAUUGGCAUGUUUUGACAUUUAUCGGCACGUCCUCCGACAUGCCGGCAAAAUUA
..-----------------((((((.(....((((((((.(((((.(((....)))))))))))).))))..).))))))....(((..(((((.(((....))).)))))..))).... ( -25.10)
>DroEre_CAF1 37251 120 + 1
AAAAAUAGGGAAAAUAGGGAAAAUAGGAUAAGAUAGCGCUGUAUAAUAUGAAAAUAUAUAUUCGCAUAUUGGCAUGUUUUGACAUUUAUCGGCACGUCCUCUGACAUGCCGGCAAAAUUA
................(..((((((.(....(((((((..(((((.(((....)))))))).))).))))..).))))))..).(((..(((((.(((....))).)))))..))).... ( -25.60)
>consensus
AA_________________AAAAUAGGAUAAGAUAGCGAUGUAUAAUAUGGAAAUAUAUAUUCGCAUAUUGGCAUGUUUUGACAUUUAUCGGCACGUCCUCCGACAUGCCGGCAAAAUUA
...................................(((((((..((((((..(((((........)))))..))))))...)))))...(((((.(((....))).)))))))....... (-22.86 = -22.93 +   0.06)

alignment

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secondary structure

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dotplot

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Window 1

Location 4,054,628 – 4,054,731
Length 103
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 90.13
Mean single sequence MFE -22.50
Consensus MFE -21.51
Energy contribution -21.32
Covariance contribution -0.19
Combinations/Pair 1.05
Mean z-score -1.94
Structure conservation index 0.96
SVM decision value 1.61
SVM RNA-class probability 0.967581
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4054628 103 - 20766785
UAAUUUUGCCGGCAUGUCGGAGGACGUGCCGAUAAAUGUCAAAACACGCCAAUAUGCGAAUAUAUAUUUCCAUAUUAUACAUCGCUAUCUUAUCCUAUUUU-----------------UU
.......(((((((((((....)))))))))...................((((((.(((.......))))))))).......))................-----------------.. ( -22.10)
>DroSec_CAF1 37308 103 - 1
UAAUUUUGCCGGCAUGUCGGAGGACGUGCCGAUAAAUGUCAAAACAUGCCAAUAUGCGAAUAUAUAUUUCCAUAUUAUACAUCGCUAUCUUAUGCUAUUUU-----------------UU
.......(((((((((((....)))))))))....((((....)))))).((((((.(((.......))))))))).......((........))......-----------------.. ( -23.20)
>DroSim_CAF1 43434 103 - 1
UAAUUUUGCCGGCAUGUCGGAGGACGUGCCGAUAAAUGUCAAAACAUGCCAAUAUGCGAAUAUAUAUUUCCAUAUUAUACAUCGCUAUCUUAUCCUAUUUU-----------------UU
.......((.(((((((.....(((((........)))))...)))))))((((((.(((.......))))))))).......))................-----------------.. ( -22.60)
>DroEre_CAF1 37251 120 - 1
UAAUUUUGCCGGCAUGUCAGAGGACGUGCCGAUAAAUGUCAAAACAUGCCAAUAUGCGAAUAUAUAUUUUCAUAUUAUACAGCGCUAUCUUAUCCUAUUUUCCCUAUUUUCCCUAUUUUU
.......((.(((((((.....(((((........)))))...)))))))((((((.((((....)))).)))))).....))..................................... ( -22.10)
>consensus
UAAUUUUGCCGGCAUGUCGGAGGACGUGCCGAUAAAUGUCAAAACAUGCCAAUAUGCGAAUAUAUAUUUCCAUAUUAUACAUCGCUAUCUUAUCCUAUUUU_________________UU
.......(((((((((((....)))))))))...................((((((.(((.......))))))))).......))................................... (-21.51 = -21.32 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 2

Location 4,054,651 – 4,054,771
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 98.33
Mean single sequence MFE -32.19
Consensus MFE -31.08
Energy contribution -30.89
Covariance contribution -0.19
Combinations/Pair 1.03
Mean z-score -2.54
Structure conservation index 0.97
SVM decision value 1.29
SVM RNA-class probability 0.938401
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4054651 120 + 20766785
GUAUAAUAUGGAAAUAUAUAUUCGCAUAUUGGCGUGUUUUGACAUUUAUCGGCACGUCCUCCGACAUGCCGGCAAAAUUAUUUUCAUGCUAGCCUGCCCCCCAAUACGUUGGCAUGCAAA
(((((.(((....))))))))..((((..(((((((........(((..(((((.(((....))).)))))..)))........)))))))(((.((..........)).)))))))... ( -31.89)
>DroSec_CAF1 37331 120 + 1
GUAUAAUAUGGAAAUAUAUAUUCGCAUAUUGGCAUGUUUUGACAUUUAUCGGCACGUCCUCCGACAUGCCGGCAAAAUUAUUUUCAUGCUAGCCUGCCCCCCAAUACGUUGGCAUGCAAA
(((((.(((....))))))))..((((..(((((((........(((..(((((.(((....))).)))))..)))........)))))))(((.((..........)).)))))))... ( -32.29)
>DroSim_CAF1 43457 120 + 1
GUAUAAUAUGGAAAUAUAUAUUCGCAUAUUGGCAUGUUUUGACAUUUAUCGGCACGUCCUCCGACAUGCCGGCAAAAUUAUUUUCAUGCUAGCCUGCCCCCCAAUACGUUGGCAUGCAAA
(((((.(((....))))))))..((((..(((((((........(((..(((((.(((....))).)))))..)))........)))))))(((.((..........)).)))))))... ( -32.29)
>DroEre_CAF1 37291 120 + 1
GUAUAAUAUGAAAAUAUAUAUUCGCAUAUUGGCAUGUUUUGACAUUUAUCGGCACGUCCUCUGACAUGCCGGCAAAAUUAUUUUCAUGCUAGCCUGCCCUCCAAUACGUUGGCAUGCAAA
....((((((..(((....)))..))))))((((((........(((..(((((.(((....))).)))))..)))........)))))).((.((((..(......)..)))).))... ( -32.29)
>consensus
GUAUAAUAUGGAAAUAUAUAUUCGCAUAUUGGCAUGUUUUGACAUUUAUCGGCACGUCCUCCGACAUGCCGGCAAAAUUAUUUUCAUGCUAGCCUGCCCCCCAAUACGUUGGCAUGCAAA
....((((((......)))))).((((..(((((((........(((..(((((.(((....))).)))))..)))........)))))))(((.((..........)).)))))))... (-31.08 = -30.89 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 3

Location 4,054,651 – 4,054,771
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 98.33
Mean single sequence MFE -36.62
Consensus MFE -36.05
Energy contribution -36.12
Covariance contribution 0.06
Combinations/Pair 1.03
Mean z-score -2.86
Structure conservation index 0.98
SVM decision value 1.60
SVM RNA-class probability 0.966982
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4054651 120 - 20766785
UUUGCAUGCCAACGUAUUGGGGGGCAGGCUAGCAUGAAAAUAAUUUUGCCGGCAUGUCGGAGGACGUGCCGAUAAAUGUCAAAACACGCCAAUAUGCGAAUAUAUAUUUCCAUAUUAUAC
((((((((((..(......)..))).(((..(((.((......)).)))(((((((((....)))))))))................)))...))))))).................... ( -34.80)
>DroSec_CAF1 37331 120 - 1
UUUGCAUGCCAACGUAUUGGGGGGCAGGCUAGCAUGAAAAUAAUUUUGCCGGCAUGUCGGAGGACGUGCCGAUAAAUGUCAAAACAUGCCAAUAUGCGAAUAUAUAUUUCCAUAUUAUAC
...((.((((..(......)..)))).))..(((((........((((.(((((((((....))))))))).))))........))))).((((((.(((.......))))))))).... ( -38.09)
>DroSim_CAF1 43457 120 - 1
UUUGCAUGCCAACGUAUUGGGGGGCAGGCUAGCAUGAAAAUAAUUUUGCCGGCAUGUCGGAGGACGUGCCGAUAAAUGUCAAAACAUGCCAAUAUGCGAAUAUAUAUUUCCAUAUUAUAC
...((.((((..(......)..)))).))..(((((........((((.(((((((((....))))))))).))))........))))).((((((.(((.......))))))))).... ( -38.09)
>DroEre_CAF1 37291 120 - 1
UUUGCAUGCCAACGUAUUGGAGGGCAGGCUAGCAUGAAAAUAAUUUUGCCGGCAUGUCAGAGGACGUGCCGAUAAAUGUCAAAACAUGCCAAUAUGCGAAUAUAUAUUUUCAUAUUAUAC
...((.((((..(......)..)))).))....(((((((((..((((((((((((((....)))))))))....((((....))))........)))))....)))))))))....... ( -35.50)
>consensus
UUUGCAUGCCAACGUAUUGGGGGGCAGGCUAGCAUGAAAAUAAUUUUGCCGGCAUGUCGGAGGACGUGCCGAUAAAUGUCAAAACAUGCCAAUAUGCGAAUAUAUAUUUCCAUAUUAUAC
...((.((((..(......)..)))).))..(((((........((((.(((((((((....))))))))).))))........))))).((((((.(((.......))))))))).... (-36.05 = -36.12 +   0.06)

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 09:51:03 2006