Locus 1067

Sequence ID X_DroMel_CAF1
Location 3,117,973 – 3,118,107
Length 134
Max. P 0.950588
window1733 window1734 window1735

overview

Window 3

Location 3,117,973 – 3,118,073
Length 100
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 80.57
Mean single sequence MFE -21.13
Consensus MFE -17.05
Energy contribution -17.05
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.28
Structure conservation index 0.81
SVM decision value 0.27
SVM RNA-class probability 0.663068
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3117973 100 + 22224390
-------------CACAGUUAUCCA-------CGAUACAAGUCGCAGCUGUUAAUGCAAGGCUAGUCAUGUGCUUCGAUUUAUCGACAGCAUUUCUAUUUGUACUUUUGCCACAAAAUAU
-------------.((((((.....-------((((....)))).))))))........(((.(((((.(((((((((....)))).))))).......)).)))...)))......... ( -20.10)
>DroPse_CAF1 96927 89 + 1
ACC----------CGCAG---------------------ACUCGCAGCUGCUAAUGCAAGGCUAGUCAUGUGCUUCGAUUUAUCGACAGCAUUUCUAUUUGUACUCUUGCCACAAAAUAU
...----------.((((---------------------(((.((...(((....)))..)).))))..(((((((((....)))).)))))...............))).......... ( -21.20)
>DroSim_CAF1 77260 109 + 1
ACA----CACACACACAGAUAUCCA-------CGAUACAAGUCGCAGCUGUUAAUGCAAGGCUAGUCAUGUGCUUCGAUUUAUCGACAGCAUUUCUAUUUGUACUUUUGCCACAAAAUAU
...----.......(((((((....-------.(((...((((...((.......))..)))).)))..(((((((((....)))).)))))...))))))).................. ( -18.60)
>DroEre_CAF1 77781 100 + 1
-------------CACAGAUAUCCA-------CGAUACAAGUCGCAGCUGUUAAUGCAAGGCUAGUCAUGUGCUUCGAUUUAUCGAAAGCAUUUCUAUUUGUACUUUUGCCACAAAAUAU
-------------.(((((((....-------.(((...((((...((.......))..)))).)))..(((((((((....))).))))))...))))))).................. ( -18.60)
>DroAna_CAF1 95350 120 + 1
AGAUACAUAUACUCAGAUAUAUCUAGAUACUUGAAUACAAGUCGCAGCUGUUAAUGCAAGGCUAGUCAUGUGCUUCGAUUUAUCGACAGCAUUUCUAUUUGUACUUUUGCCGCAAAAUAU
(((((.((........)).)))))....(((((....))))).((.((.......))..(((.(((((.(((((((((....)))).))))).......)).)))...)))))....... ( -22.60)
>DroPer_CAF1 99487 89 + 1
ACC----------CGCAG---------------------ACUAGCAGCUGCUAAUGCAAGGCUAGUCAUGUGCUUCGAUUUAUCGACAGCAUUUCUAUUUGUACUCUUGCCACAAAAUAU
...----------.((((---------------------((((((...(((....)))..)))))))..(((((((((....)))).)))))...............))).......... ( -25.70)
>consensus
AC___________CACAGAUAUCCA_______CGAUACAAGUCGCAGCUGUUAAUGCAAGGCUAGUCAUGUGCUUCGAUUUAUCGACAGCAUUUCUAUUUGUACUUUUGCCACAAAAUAU
...........................................(((........)))..(((.(((((.(((((((((....)))).))))).......)).)))...)))......... (-17.05 = -17.05 +   0.00) 

alignment

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secondary structure

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dotplot

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Window 4

Location 3,117,993 – 3,118,107
Length 114
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 91.47
Mean single sequence MFE -30.16
Consensus MFE -27.18
Energy contribution -27.85
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -1.79
Structure conservation index 0.90
SVM decision value 1.40
SVM RNA-class probability 0.950588
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3117993 114 + 22224390
GUCGCAGCUGUUAAUGCAAGGCUAGUCAUGUGCUUCGAUUUAUCGACAGCAUUUCUAUUUGUACUUUUGCCACAAAAUAUUUACACAAUUGACAGCUGCUUCUGUUCAGUGCCC------
...(((((((((((((((((..(((....(((((((((....)))).)))))..))))))))..(((((...)))))..........))))))))))))...............------ ( -30.20)
>DroPse_CAF1 96936 120 + 1
CUCGCAGCUGCUAAUGCAAGGCUAGUCAUGUGCUUCGAUUUAUCGACAGCAUUUCUAUUUGUACUCUUGCCACAAAAUAUUUACACAACUGACAGCUGCUUCUGUUCGGUGCUGGGUGCU
..(.(((((((....))).(((.(((((.(((((((((....)))).))))).......)).)))...)))................((((((((......))).))))))))).).... ( -28.40)
>DroEre_CAF1 77801 114 + 1
GUCGCAGCUGUUAAUGCAAGGCUAGUCAUGUGCUUCGAUUUAUCGAAAGCAUUUCUAUUUGUACUUUUGCCACAAAAUAUUUACACAAUUGACAGCUGCUUCUGCUCAGUGCCC------
...(((((((((((((((((..(((....(((((((((....))).))))))..))))))))..(((((...)))))..........))))))))))))....((.....))..------ ( -30.80)
>DroYak_CAF1 81586 114 + 1
GUCGCAGCUGUUAAUGCAAGGCUAGUCAUGUGCUUCGAUUUAUCGACAGCAUUUCUAUUUGUACUUUUGCCACAAAAUAUUUACACAAUUGACAGCUGCUUCUGUUCAGUGCCC------
...(((((((((((((((((..(((....(((((((((....)))).)))))..))))))))..(((((...)))))..........))))))))))))...............------ ( -30.20)
>DroAna_CAF1 95390 120 + 1
GUCGCAGCUGUUAAUGCAAGGCUAGUCAUGUGCUUCGAUUUAUCGACAGCAUUUCUAUUUGUACUUUUGCCGCAAAAUAUUUACACAAUUGACAGCUGCUUCUUUUCAGUACAGUGGAGU
...((((((((((((((..(((.(((((.(((((((((....)))).))))).......)).)))...))))))..............)))))))))))....(((((......))))). ( -31.53)
>DroPer_CAF1 99496 120 + 1
CUAGCAGCUGCUAAUGCAAGGCUAGUCAUGUGCUUCGAUUUAUCGACAGCAUUUCUAUUUGUACUCUUGCCACAAAAUAUUUACACAACUGACAGCUGCUUCUGUUCGGUGCUGGGUGCU
(((((...(((....)))..)))))....(((((((((....)))).)))))........((((((..((.................((((((((......))).))))))).)))))). ( -29.82)
>consensus
GUCGCAGCUGUUAAUGCAAGGCUAGUCAUGUGCUUCGAUUUAUCGACAGCAUUUCUAUUUGUACUUUUGCCACAAAAUAUUUACACAAUUGACAGCUGCUUCUGUUCAGUGCCC______
...((((((((((((....(((.(((((.(((((((((....)))).))))).......)).)))...)))................))))))))))))..................... (-27.18 = -27.85 +   0.67) 

alignment

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secondary structure

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dotplot

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Window 5

Location 3,117,993 – 3,118,107
Length 114
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 91.47
Mean single sequence MFE -29.20
Consensus MFE -27.39
Energy contribution -26.95
Covariance contribution -0.44
Combinations/Pair 1.07
Mean z-score -1.37
Structure conservation index 0.94
SVM decision value 1.10
SVM RNA-class probability 0.915701
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3117993 114 - 22224390
------GGGCACUGAACAGAAGCAGCUGUCAAUUGUGUAAAUAUUUUGUGGCAAAAGUACAAAUAGAAAUGCUGUCGAUAAAUCGAAGCACAUGACUAGCCUUGCAUUAACAGCUGCGAC
------...............((((((((.....((((((....((((((.(....)))))))......((((.((((....))))))))...........))))))..))))))))... ( -27.50)
>DroPse_CAF1 96936 120 - 1
AGCACCCAGCACCGAACAGAAGCAGCUGUCAGUUGUGUAAAUAUUUUGUGGCAAGAGUACAAAUAGAAAUGCUGUCGAUAAAUCGAAGCACAUGACUAGCCUUGCAUUAGCAGCUGCGAG
.((.....))...........((((((((.(((..(((......((((((.(....))))))).......(((.((((....))))))))))..))).((...))....))))))))... ( -31.40)
>DroEre_CAF1 77801 114 - 1
------GGGCACUGAGCAGAAGCAGCUGUCAAUUGUGUAAAUAUUUUGUGGCAAAAGUACAAAUAGAAAUGCUUUCGAUAAAUCGAAGCACAUGACUAGCCUUGCAUUAACAGCUGCGAC
------..((.....))....((((((((.....((((((....((((((.(....)))))))......(((((.(((....))))))))...........))))))..))))))))... ( -28.50)
>DroYak_CAF1 81586 114 - 1
------GGGCACUGAACAGAAGCAGCUGUCAAUUGUGUAAAUAUUUUGUGGCAAAAGUACAAAUAGAAAUGCUGUCGAUAAAUCGAAGCACAUGACUAGCCUUGCAUUAACAGCUGCGAC
------...............((((((((.....((((((....((((((.(....)))))))......((((.((((....))))))))...........))))))..))))))))... ( -27.50)
>DroAna_CAF1 95390 120 - 1
ACUCCACUGUACUGAAAAGAAGCAGCUGUCAAUUGUGUAAAUAUUUUGCGGCAAAAGUACAAAUAGAAAUGCUGUCGAUAAAUCGAAGCACAUGACUAGCCUUGCAUUAACAGCUGCGAC
...........((....))..((((((((.....((((((.((((((((.......))).)))))....((((.((((....))))))))...........))))))..))))))))... ( -28.20)
>DroPer_CAF1 99496 120 - 1
AGCACCCAGCACCGAACAGAAGCAGCUGUCAGUUGUGUAAAUAUUUUGUGGCAAGAGUACAAAUAGAAAUGCUGUCGAUAAAUCGAAGCACAUGACUAGCCUUGCAUUAGCAGCUGCUAG
.((.....))..........(((((((((.(((..(((......((((((.(....))))))).......(((.((((....))))))))))..))).((...))....))))))))).. ( -32.10)
>consensus
______CGGCACUGAACAGAAGCAGCUGUCAAUUGUGUAAAUAUUUUGUGGCAAAAGUACAAAUAGAAAUGCUGUCGAUAAAUCGAAGCACAUGACUAGCCUUGCAUUAACAGCUGCGAC
.....................((((((((.....((((((.((((((......))))))..........((((.((((....))))))))...........))))))..))))))))... (-27.39 = -26.95 +  -0.44) 

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 10:00:49 2006