Locus 3084

Sequence ID 2R_DroMel_CAF1
Location 10,550,021 – 10,550,247
Length 226
Max. P 0.993374
window5092 window5093 window5094 window5095

overview

Window 2

Location 10,550,021 – 10,550,127
Length 106
Sequences 3
Columns 108
Reading direction forward
Mean pairwise identity 82.37
Mean single sequence MFE -18.37
Consensus MFE -17.19
Energy contribution -16.97
Covariance contribution -0.22
Combinations/Pair 1.05
Mean z-score -0.73
Structure conservation index 0.94
SVM decision value 0.57
SVM RNA-class probability 0.785996
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10550021 106 + 20766785
AGUUGUCAAUGCUUUUAUAUACCUAUGUAGAUUGCCCUAAUGCUGAUUAGGUCGACGACAUAUAAACACACACUCAUGGGCAUAAAAUAUACAAAUGUACAUAUG--U
.((((((...((.(((((((....)))))))..))((((((....))))))..))))))............((..(((..(((...........)))..)))..)--) ( -20.30)
>DroSim_CAF1 39604 94 + 1
AGUUGUCAAUGCUUUUAUAUACCUAUGUAGAUUGCCCUAAUGCUGAUUAGGUCGACGACAUAUAGACACACACUCAUGGGCAUAAAAUAUAC--------------AU
.((((((...((.(((((((....)))))))..))((((((....))))))..)))))).................................--------------.. ( -17.30)
>DroEre_CAF1 44269 94 + 1
AGUUGUCAAUGCUUUUAUGUAGCUAUGUAGAUUGCCCUAAUGCUGAUUAGGUCGACGACAUAUAGACAAACACACAUGCUCGUA---UAUACA-----------AUAC
.((((((...((.(((((((....)))))))..))((((((....))))))..))))))(((((((((........)).)).))---)))...-----------.... ( -17.50)
>consensus
AGUUGUCAAUGCUUUUAUAUACCUAUGUAGAUUGCCCUAAUGCUGAUUAGGUCGACGACAUAUAGACACACACUCAUGGGCAUAAAAUAUACA_____________AU
.((((((...((.(((((((....)))))))..))((((((....))))))..))))))................................................. (-17.19 = -16.97 +  -0.22)

alignment

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secondary structure

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Window 3

Location 10,550,051 – 10,550,167
Length 116
Sequences 3
Columns 118
Reading direction reverse
Mean pairwise identity 82.75
Mean single sequence MFE -29.30
Consensus MFE -20.25
Energy contribution -20.48
Covariance contribution 0.23
Combinations/Pair 1.12
Mean z-score -1.65
Structure conservation index 0.69
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10550051 116 - 20766785
UUCGAUACCAAAUUGAGCGGCCUACUCACUCGGGGUAUACA--CAUAUGUACAUUUGUAUAUUUUAUGCCCAUGAGUGUGUGUUUAUAUGUCGUCGACCUAAUCAGCAUUAGGGCAAU
.(((((..((...(((((.....((.(((((((((((((..--...((((((....))))))..))))))).)))))).)))))))..))..)))))((((((....))))))..... ( -35.20)
>DroSim_CAF1 39634 104 - 1
UUCGAUACCAAAUUGAGCGGCCUACUCAUUUGGGGUAUAUAU--------------GUAUAUUUUAUGCCCAUGAGUGUGUGUCUAUAUGUCGUCGACCUAAUCAGCAUUAGGGCAAU
.(((((..((...((..((.(.(((((((...(((((((...--------------........)))))))))))))).)))..))..))..)))))((((((....))))))..... ( -27.40)
>DroEre_CAF1 44299 104 - 1
UUCGAUACCAAAUUGAGCGGCCUACUCACACGGGGUAUACGUAU-----------UGUAUA---UACGAGCAUGUGUGUUUGUCUAUAUGUCGUCGACCUAAUCAGCAUUAGGGCAAU
.(((((..(.......(((...(((((.....)))))..)))..-----------.(((((---.(((((((....))))))).))))))..)))))((((((....))))))..... ( -25.30)
>consensus
UUCGAUACCAAAUUGAGCGGCCUACUCACUCGGGGUAUACAU_____________UGUAUAUUUUAUGCCCAUGAGUGUGUGUCUAUAUGUCGUCGACCUAAUCAGCAUUAGGGCAAU
.(((((..((.((.((......(((.(((((((((((((.........................))))))).)))))).))))).)).))..)))))((((((....))))))..... (-20.25 = -20.48 +   0.23)

alignment

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secondary structure

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Window 4

Location 10,550,091 – 10,550,207
Length 116
Sequences 3
Columns 118
Reading direction reverse
Mean pairwise identity 82.75
Mean single sequence MFE -30.87
Consensus MFE -22.73
Energy contribution -22.84
Covariance contribution 0.12
Combinations/Pair 1.10
Mean z-score -2.21
Structure conservation index 0.74
SVM decision value 0.89
SVM RNA-class probability 0.876305
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10550091 116 - 20766785
AUUAGCAUUAAAAUGUUUUAGGAAAAACGACCGGGCCACGUUCGAUACCAAAUUGAGCGGCCUACUCACUCGGGGUAUACA--CAUAUGUACAUUUGUAUAUUUUAUGCCCAUGAGUG
.............((((((....))))))...(((((..(((((((.....))))))))))))...(((((((((((((..--...((((((....))))))..))))))).)))))) ( -35.70)
>DroSim_CAF1 39674 104 - 1
AUUAGCAUUAAAAUGUCUUAGGAAAAACGACCGGGCCACGUUCGAUACCAAAUUGAGCGGCCUACUCAUUUGGGGUAUAUAU--------------GUAUAUUUUAUGCCCAUGAGUG
....((((....))))....((........))(((((..(((((((.....))))))))))))((((((...(((((((...--------------........))))))))))))). ( -28.60)
>DroEre_CAF1 44339 104 - 1
AUUAGCAUUAAAAUGUCUUAGGAAAAACGAGCGGGCCACGUUCGAUACCAAAUUGAGCGGCCUACUCACACGGGGUAUACGUAU-----------UGUAUA---UACGAGCAUGUGUG
....((((....))))............(((..((((..(((((((.....)))))))))))..)))(((((..((...(((((-----------.....)---)))).)).))))). ( -28.30)
>consensus
AUUAGCAUUAAAAUGUCUUAGGAAAAACGACCGGGCCACGUUCGAUACCAAAUUGAGCGGCCUACUCACUCGGGGUAUACAU_____________UGUAUAUUUUAUGCCCAUGAGUG
....((((....))))................(((((..(((((((.....))))))))))))...(((((((((((((.........................))))))).)))))) (-22.73 = -22.84 +   0.12)

alignment

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secondary structure

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dotplot

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Window 5

Location 10,550,127 – 10,550,247
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.00
Mean single sequence MFE -36.13
Consensus MFE -33.26
Energy contribution -33.10
Covariance contribution -0.16
Combinations/Pair 1.09
Mean z-score -1.84
Structure conservation index 0.92
SVM decision value 2.39
SVM RNA-class probability 0.993374
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10550127 120 - 20766785
GCCCACACCUAGGCUAAAGUAGGUCUACAGCUUGCGGCUCAUUAGCAUUAAAAUGUUUUAGGAAAAACGACCGGGCCACGUUCGAUACCAAAUUGAGCGGCCUACUCACUCGGGGUAUAC
((((.....(((((....((((((.....))))))(((((...(((((....)))))...((........))))))).((((((((.....)))))))))))))........)))).... ( -36.52)
>DroSec_CAF1 47915 120 - 1
GCCCACACCUAGGCUAAAGUAGGUCUACAGCUUGCGGCUCAUUAGCAUUAAAAUGUCUUAGGAAAAACGACCGGGCCACGUUCGAUACCAAAUUGAGCGGCCUACUCACUCGGUAUAUAU
(((......(((((....((((((.....))))))(((((....((((....))))....((........))))))).((((((((.....))))))))))))).......)))...... ( -32.62)
>DroSim_CAF1 39698 120 - 1
GCCCACACCUAGGCUAAAGUAGGUCUACAGCUUGCGGCUCAUUAGCAUUAAAAUGUCUUAGGAAAAACGACCGGGCCACGUUCGAUACCAAAUUGAGCGGCCUACUCAUUUGGGGUAUAU
((((.....(((((....((((((.....))))))(((((....((((....))))....((........))))))).((((((((.....)))))))))))))........)))).... ( -36.02)
>DroEre_CAF1 44363 120 - 1
GCCCACACCUAGGCCAAAGUAGGUCUACAGCUUGCGGCUCAUUAGCAUUAAAAUGUCUUAGGAAAAACGAGCGGGCCACGUUCGAUACCAAAUUGAGCGGCCUACUCACACGGGGUAUAC
((((...((((((.((..((((((.....)))))).(((....))).......)).))))))......(((..((((..(((((((.....)))))))))))..))).....)))).... ( -41.40)
>DroYak_CAF1 44536 120 - 1
GCCCACACCUAGGCCAAAGUAGGUCUACAGCUUGCGGCUCAUUAGCAUUAAAAUGUCUUAGGAAAAACGACCGGGCCACGUUCGAUACCAAAUUGAACAGCCUACUCACUCGGGGUAUAU
((((...((((((.((..((((((.....)))))).(((....))).......)).))))))......((..((((...(((((((.....))))))).))))..)).....)))).... ( -34.10)
>consensus
GCCCACACCUAGGCUAAAGUAGGUCUACAGCUUGCGGCUCAUUAGCAUUAAAAUGUCUUAGGAAAAACGACCGGGCCACGUUCGAUACCAAAUUGAGCGGCCUACUCACUCGGGGUAUAU
.(((...((((((.((..((((((.....)))))).(((....))).......)).))))))......((..(((((..(((((((.....))))))))))))..))....)))...... (-33.26 = -33.10 +  -0.16)

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 10:47:11 2006