Locus 3799

Sequence ID 2L_DroMel_CAF1
Location 11,103,664 – 11,103,805
Length 141
Max. P 0.998594
window5989 window5990 window5991 window5992

overview

Window 9

Location 11,103,664 – 11,103,766
Length 102
Sequences 5
Columns 102
Reading direction forward
Mean pairwise identity 85.94
Mean single sequence MFE -27.04
Consensus MFE -20.10
Energy contribution -19.62
Covariance contribution -0.48
Combinations/Pair 1.21
Mean z-score -1.85
Structure conservation index 0.74
SVM decision value 0.46
SVM RNA-class probability 0.743299
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11103664 102 + 22407834
GGAACACACGGAAUGUUUUGGAAGUUCCUUAGUUUGUUAUAGCAUUGCAGGGGAUAAGUGCGGAUCUACGAAAUACUAUCCCCUACAAGGCUUUAUUUAAUG
(((((...((((....))))...)))))...(((...((.(((.(((.((((((((.(((((......))...))))))))))).))).))).))...))). ( -27.90)
>DroSec_CAF1 6891 98 + 1
AGGACACACGGAAAGUUUUGGAAGUUCCUUAGUCUGUUAUAGCAUUGAAGGGGAUAAGUGAAGGUAUACGAAAUACUAUCCCCUACAAGGCUU----UAAUG
.((((....((((..((...))..))))...))))((((.(((.(((.((((((((.(((..(.....)....))))))))))).))).))).----)))). ( -27.20)
>DroSim_CAF1 7149 98 + 1
AGGACACACGGAAAGUUUUGGAAGUUCCUUAGUCUGUUAUAGCAUUGCAGGGGAUAAGUGAAGGUGUACGAAAUACUAUCCCCUACAAGGCUU----UAAUG
.((((....((((..((...))..))))...))))((((.(((.(((.((((((((.(((..(.....)....))))))))))).))).))).----)))). ( -27.20)
>DroEre_CAF1 7028 98 + 1
GGGACACAGCGAAAUUUUUCGAAAUUCCUUAGUCUAAUACAGCAAUGCAGGGGGUAGGUGUAGGUCUACGAAAUAUUAUCCCCUACAAGGCUU----UAAUG
((((.....((((....))))....))))........((.(((..((.(((((((((.((((....)))).....))))))))).))..))).----))... ( -25.10)
>DroYak_CAF1 6767 98 + 1
GGGACACACAGAAAGUUUUGAGAGUUCCUUAGUCUAAUACAGCAAUGCAGGGGAUAGGUGUAGGUCUGCGAAAUAUUAUCCCCUACAAGGCUU----UAAAG
(((((.(.((((....)))).).))))).........((.(((..((.(((((((((.((((....)))).....))))))))).))..))).----))... ( -27.80)
>consensus
GGGACACACGGAAAGUUUUGGAAGUUCCUUAGUCUGUUAUAGCAUUGCAGGGGAUAAGUGAAGGUCUACGAAAUACUAUCCCCUACAAGGCUU____UAAUG
.((((....((((..((...))..))))...)))).....(((.(((.(((((((.((((..(.....)....))))))))))).))).))).......... (-20.10 = -19.62 +  -0.48)

alignment

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secondary structure

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dotplot

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Window 0

Location 11,103,664 – 11,103,766
Length 102
Sequences 5
Columns 102
Reading direction reverse
Mean pairwise identity 85.94
Mean single sequence MFE -25.16
Consensus MFE -21.99
Energy contribution -22.95
Covariance contribution 0.96
Combinations/Pair 1.09
Mean z-score -2.83
Structure conservation index 0.87
SVM decision value 3.15
SVM RNA-class probability 0.998594
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11103664 102 - 22407834
CAUUAAAUAAAGCCUUGUAGGGGAUAGUAUUUCGUAGAUCCGCACUUAUCCCCUGCAAUGCUAUAACAAACUAAGGAACUUCCAAAACAUUCCGUGUGUUCC
..........(((.(((((((((((((.....((......))...))))))))))))).)))............(((((..................))))) ( -26.67)
>DroSec_CAF1 6891 98 - 1
CAUUA----AAGCCUUGUAGGGGAUAGUAUUUCGUAUACCUUCACUUAUCCCCUUCAAUGCUAUAACAGACUAAGGAACUUCCAAAACUUUCCGUGUGUCCU
..(((----.(((.(((.((((((((((((.....)))).......)))))))).))).))).)))..(((...((((...........))))....))).. ( -23.51)
>DroSim_CAF1 7149 98 - 1
CAUUA----AAGCCUUGUAGGGGAUAGUAUUUCGUACACCUUCACUUAUCCCCUGCAAUGCUAUAACAGACUAAGGAACUUCCAAAACUUUCCGUGUGUCCU
..(((----.(((.((((((((((((((...............)).)))))))))))).))).)))..(((...((((...........))))....))).. ( -27.26)
>DroEre_CAF1 7028 98 - 1
CAUUA----AAGCCUUGUAGGGGAUAAUAUUUCGUAGACCUACACCUACCCCCUGCAUUGCUGUAUUAGACUAAGGAAUUUCGAAAAAUUUCGCUGUGUCCC
.....----.(((..((((((((..........((((........))))))))))))..)))......(((...(((((((....))))))).....))).. ( -24.50)
>DroYak_CAF1 6767 98 - 1
CUUUA----AAGCCUUGUAGGGGAUAAUAUUUCGCAGACCUACACCUAUCCCCUGCAUUGCUGUAUUAGACUAAGGAACUCUCAAAACUUUCUGUGUGUCCC
.....----.(((..(((((((((((....................)))))))))))..)))......(((..(((((..........)))))....))).. ( -23.85)
>consensus
CAUUA____AAGCCUUGUAGGGGAUAGUAUUUCGUAGACCUACACUUAUCCCCUGCAAUGCUAUAACAGACUAAGGAACUUCCAAAACUUUCCGUGUGUCCC
..........(((.(((((((((((((..................))))))))))))).)))......(((...((((...........))))....))).. (-21.99 = -22.95 +   0.96)

alignment

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secondary structure

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dotplot

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Window 1

Location 11,103,686 – 11,103,805
Length 119
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 86.36
Mean single sequence MFE -27.92
Consensus MFE -19.12
Energy contribution -19.32
Covariance contribution 0.20
Combinations/Pair 1.16
Mean z-score -1.99
Structure conservation index 0.68
SVM decision value 0.28
SVM RNA-class probability 0.667694
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11103686 119 + 22407834
AGUUCCUUAGUUUGUUAUAGCAUUGCAGGGGAUAAGUGCGGAUCUACGAAAUACUAUCCCCUACAAGGCUUUAUUUAAUGACCAAGGCAUAUAAAACGACACAGAUUGAAAUUCUCAGA
......(((((((((((.(((.(((.((((((((.(((((......))...))))))))))).))).))).))(((((((.(....)))).)))).....))))))))).......... ( -27.50)
>DroSec_CAF1 6913 115 + 1
AGUUCCUUAGUCUGUUAUAGCAUUGAAGGGGAUAAGUGAAGGUAUACGAAAUACUAUCCCCUACAAGGCUU----UAAUGACCAAAGCAUAUAAAACGACACAGAUUGAAAUACGCAGA
.((...(((((((((.......(((.((((((((.(((..(.....)....))))))))))).))).((((----(.......)))))............)))))))))...))..... ( -28.20)
>DroSim_CAF1 7171 115 + 1
AGUUCCUUAGUCUGUUAUAGCAUUGCAGGGGAUAAGUGAAGGUGUACGAAAUACUAUCCCCUACAAGGCUU----UAAUGACCAAAGCAUAUAAAACGACACAGAUUGAAAUACGCAGA
.((...(((((((((.......(((.((((((((.(((..(.....)....))))))))))).))).((((----(.......)))))............)))))))))...))..... ( -28.20)
>DroEre_CAF1 7050 115 + 1
AAUUCCUUAGUCUAAUACAGCAAUGCAGGGGGUAGGUGUAGGUCUACGAAAUAUUAUCCCCUACAAGGCUU----UAAUGACCAAGACAAAUUAAACGACACAGACUGAAAUACGCAAG
......(((((((.....(((..((.(((((((((.((((....)))).....))))))))).))..)))(----((((...........))))).......)))))))....(....) ( -26.50)
>DroYak_CAF1 6789 115 + 1
AGUUCCUUAGUCUAAUACAGCAAUGCAGGGGAUAGGUGUAGGUCUGCGAAAUAUUAUCCCCUACAAGGCUU----UAAAGACCAAGGCAAUCAAAACGACACAAUUUGAAAUACGCAAG
....((((.((((..((.(((..((.(((((((((.((((....)))).....))))))))).))..))).----)).)))).))))...(((((.........)))))....(....) ( -29.20)
>consensus
AGUUCCUUAGUCUGUUAUAGCAUUGCAGGGGAUAAGUGAAGGUCUACGAAAUACUAUCCCCUACAAGGCUU____UAAUGACCAAGGCAUAUAAAACGACACAGAUUGAAAUACGCAGA
....((((.(((......(((.(((.(((((((.((((..(.....)....))))))))))).))).))).........))).))))................................ (-19.12 = -19.32 +   0.20)

alignment

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secondary structure

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dotplot

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Window 2

Location 11,103,686 – 11,103,805
Length 119
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 86.36
Mean single sequence MFE -31.52
Consensus MFE -26.69
Energy contribution -27.69
Covariance contribution 1.00
Combinations/Pair 1.08
Mean z-score -2.76
Structure conservation index 0.85
SVM decision value 2.83
SVM RNA-class probability 0.997285
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11103686 119 - 22407834
UCUGAGAAUUUCAAUCUGUGUCGUUUUAUAUGCCUUGGUCAUUAAAUAAAGCCUUGUAGGGGAUAGUAUUUCGUAGAUCCGCACUUAUCCCCUGCAAUGCUAUAACAAACUAAGGAACU
....(((((..((.....))..))))).....(((((((.......((.(((.(((((((((((((.....((......))...))))))))))))).))).))....))))))).... ( -29.80)
>DroSec_CAF1 6913 115 - 1
UCUGCGUAUUUCAAUCUGUGUCGUUUUAUAUGCUUUGGUCAUUA----AAGCCUUGUAGGGGAUAGUAUUUCGUAUACCUUCACUUAUCCCCUUCAAUGCUAUAACAGACUAAGGAACU
...((((((........))).)))........((((((((.(((----.(((.(((.((((((((((((.....)))).......)))))))).))).))).)))..)))))))).... ( -29.01)
>DroSim_CAF1 7171 115 - 1
UCUGCGUAUUUCAAUCUGUGUCGUUUUAUAUGCUUUGGUCAUUA----AAGCCUUGUAGGGGAUAGUAUUUCGUACACCUUCACUUAUCCCCUGCAAUGCUAUAACAGACUAAGGAACU
...((((((........))).)))........((((((((.(((----.(((.((((((((((((((...............)).)))))))))))).))).)))..)))))))).... ( -32.76)
>DroEre_CAF1 7050 115 - 1
CUUGCGUAUUUCAGUCUGUGUCGUUUAAUUUGUCUUGGUCAUUA----AAGCCUUGUAGGGGAUAAUAUUUCGUAGACCUACACCUACCCCCUGCAUUGCUGUAUUAGACUAAGGAAUU
...((((((........))).)))........((((((((..((----.(((..((((((((..........((((........))))))))))))..))).))...)))))))).... ( -29.70)
>DroYak_CAF1 6789 115 - 1
CUUGCGUAUUUCAAAUUGUGUCGUUUUGAUUGCCUUGGUCUUUA----AAGCCUUGUAGGGGAUAAUAUUUCGCAGACCUACACCUAUCCCCUGCAUUGCUGUAUUAGACUAAGGAACU
..........(((((.........)))))...(((((((((...----.(((..(((((((((((....................)))))))))))..))).....))))))))).... ( -36.35)
>consensus
UCUGCGUAUUUCAAUCUGUGUCGUUUUAUAUGCCUUGGUCAUUA____AAGCCUUGUAGGGGAUAGUAUUUCGUAGACCUACACUUAUCCCCUGCAAUGCUAUAACAGACUAAGGAACU
................................((((((((.........(((.(((((((((((((..................))))))))))))).)))......)))))))).... (-26.69 = -27.69 +   1.00)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:01:45 2006