Locus 296

Sequence ID 2L_DroMel_CAF1
Location 843,643 – 843,820
Length 177
Max. P 0.999518
window471 window472 window473 window474 window475 window476

overview

Window 1

Location 843,643 – 843,759
Length 116
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 85.82
Mean single sequence MFE -32.67
Consensus MFE -20.03
Energy contribution -20.63
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -2.62
Structure conservation index 0.61
SVM decision value 0.46
SVM RNA-class probability 0.744298
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 843643 116 + 22407834
AUUAUUGGCUUGUUAUUAAUUAUAAAUGGGAUAACUGAAAUUACCAGUUGAAAGUUGGCAAUUACAUAUG-AGGCAAUUAAUUACCCAGCGCCCACUGUACUUGCGAGUGGGCUCCA
.....(((..................((((.((((((.......))))))..(((((.(...........-.).))))).....))))..(((((((((....)).))))))).))) ( -27.80)
>DroSec_CAF1 9060 116 + 1
AUUAUUGGCUUGUUCUUAAUUACAAAUGGGAUAACUGACAAUACCAGUUGAAAGUUGGCAAUUACAUAGA-AGGCAAUUAAUUAGCCAGCGCCCACUGUACUUGCGAGUGGGCUCCA
......((((..(((.(((.((((..((((.((((((.......))))))...(((((((((((......-.......))))).)))))).)))).)))).))).)))..))))... ( -33.42)
>DroSim_CAF1 9716 116 + 1
AUUAUUGGCUUGUUCUUAAUUAUAAAUGGGAUAACUGACAUUACCAGUUGAAAGUUGGCAAUUACAUAGA-AGGCAAUUAAUUAGCCAGCGCCCACUGUACUUGCGAGUGGGCUCCA
......((((..(((.(((.((((..((((.((((((.......))))))...(((((((((((......-.......))))).)))))).)))).)))).))).)))..))))... ( -31.52)
>DroEre_CAF1 8612 101 + 1
AUUAAUGGCUUGUCUUUAACUAUAAAUUAGAUAACUGAAAUUACCAGUUGCGAGUCGACAAUU----------------AAUUACCCAGCGCCCACUGUACUUGCGAGUGGGCUCCA
.....((((((((......(((.....)))..(((((.......)))))))))))))......----------------...........(((((((((....)).))))))).... ( -25.90)
>DroYak_CAF1 7884 117 + 1
AUUAUUGGCUUGUUCUUAAUUGUAAAUUGGCUAACUGAAAUUACCAGUUGCAAGUUGACAAUUACUUGGCUGGGCAUUUAAUUGCCCAGCGCCCACUGUACUUGCGAGUGGGCUCCA
.....(((........(((((((.((((.((.(((((.......))))))).)))).)))))))....((((((((......))))))))(((((((((....)).))))))).))) ( -44.70)
>consensus
AUUAUUGGCUUGUUCUUAAUUAUAAAUGGGAUAACUGAAAUUACCAGUUGAAAGUUGGCAAUUACAUAGA_AGGCAAUUAAUUACCCAGCGCCCACUGUACUUGCGAGUGGGCUCCA
.....(((.......................((((((.......))))))...(((((...........................)))))(((((((((....)).))))))).))) (-20.03 = -20.63 +   0.60)

alignment

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secondary structure

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Window 2

Location 843,643 – 843,759
Length 116
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 85.82
Mean single sequence MFE -31.97
Consensus MFE -23.45
Energy contribution -23.64
Covariance contribution 0.19
Combinations/Pair 1.11
Mean z-score -2.94
Structure conservation index 0.73
SVM decision value 1.95
SVM RNA-class probability 0.983624
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 843643 116 - 22407834
UGGAGCCCACUCGCAAGUACAGUGGGCGCUGGGUAAUUAAUUGCCU-CAUAUGUAAUUGCCAACUUUCAACUGGUAAUUUCAGUUAUCCCAUUUAUAAUUAAUAACAAGCCAAUAAU
(((.((((((((....)...)))))))..((((....((((((...-.......((((((((.........)))))))).)))))).))))..................)))..... ( -29.50)
>DroSec_CAF1 9060 116 - 1
UGGAGCCCACUCGCAAGUACAGUGGGCGCUGGCUAAUUAAUUGCCU-UCUAUGUAAUUGCCAACUUUCAACUGGUAUUGUCAGUUAUCCCAUUUGUAAUUAAGAACAAGCCAAUAAU
....((((((((....)...)))))))..(((((..((((((((..-.....(((((((.(((...((....))..))).))))))).......)))))))).....)))))..... ( -31.54)
>DroSim_CAF1 9716 116 - 1
UGGAGCCCACUCGCAAGUACAGUGGGCGCUGGCUAAUUAAUUGCCU-UCUAUGUAAUUGCCAACUUUCAACUGGUAAUGUCAGUUAUCCCAUUUAUAAUUAAGAACAAGCCAAUAAU
.(((((((((((....)...)))))))((((((........(((..-.....)))(((((((.........)))))))))))))..)))............................ ( -28.30)
>DroEre_CAF1 8612 101 - 1
UGGAGCCCACUCGCAAGUACAGUGGGCGCUGGGUAAUU----------------AAUUGUCGACUCGCAACUGGUAAUUUCAGUUAUCUAAUUUAUAGUUAAAGACAAGCCAUUAAU
....((((((((....)...)))))))(((..((..((----------------((((((.((.....((((((.....))))))......)).))))))))..)).)))....... ( -27.00)
>DroYak_CAF1 7884 117 - 1
UGGAGCCCACUCGCAAGUACAGUGGGCGCUGGGCAAUUAAAUGCCCAGCCAAGUAAUUGUCAACUUGCAACUGGUAAUUUCAGUUAGCCAAUUUACAAUUAAGAACAAGCCAAUAAU
(((.((((((((....)...)))))))((((((((......))))))))....(((((((......((((((((.....)))))).))......)))))))........)))..... ( -43.50)
>consensus
UGGAGCCCACUCGCAAGUACAGUGGGCGCUGGGUAAUUAAUUGCCU_UCUAUGUAAUUGCCAACUUUCAACUGGUAAUUUCAGUUAUCCCAUUUAUAAUUAAGAACAAGCCAAUAAU
....((((((((....)...)))))))(((.((((((((..((......))..)))))))).......((((((.....))))))......................)))....... (-23.45 = -23.64 +   0.19)

alignment

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secondary structure

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Window 3

Location 843,683 – 843,786
Length 103
Sequences 5
Columns 108
Reading direction forward
Mean pairwise identity 78.78
Mean single sequence MFE -28.89
Consensus MFE -17.67
Energy contribution -18.27
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -1.84
Structure conservation index 0.61
SVM decision value 0.46
SVM RNA-class probability 0.743344
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 843683 103 + 22407834
UUACCAGUUGAAAGUUGGCAAUUACAUAUG-AGGCAAUUAAUUACCCAGCGCCCACUGUACUUGCGAGUGGGCUCCACAAAUAUUGGGCGAGUG----UUUGUUUGGC
...((((......(((((.(((((......-.......)))))..)))))(((((((((....)).)))))))...(((((((((.....))))----))))))))). ( -26.32)
>DroSec_CAF1 9100 92 + 1
AUACCAGUUGAAAGUUGGCAAUUACAUAGA-AGGCAAUUAAUUAGCCAGCGCCCACUGUACUUGCGAGUGGGCUCCACAAAUAU---------------UUGUUUGGC
...((((..(((.(((((((((((......-.......))))).))))))(((((((((....)).)))))))..........)---------------))..)))). ( -26.52)
>DroSim_CAF1 9756 92 + 1
UUACCAGUUGAAAGUUGGCAAUUACAUAGA-AGGCAAUUAAUUAGCCAGCGCCCACUGUACUUGCGAGUGGGCUCCACAAAUAU---------------UUGUUUGGC
...((((..(((.(((((((((((......-.......))))).))))))(((((((((....)).)))))))..........)---------------))..)))). ( -26.52)
>DroEre_CAF1 8652 92 + 1
UUACCAGUUGCGAGUCGACAAUU----------------AAUUACCCAGCGCCCACUGUACUUGCGAGUGGGCUCCACAAAUAUUAGGUGAAUGUCUCUCUGUUUGGC
...((((..(((((..((((...----------------...........(((((((((....)).)))))))..(((.........)))..)))).))).)))))). ( -24.00)
>DroYak_CAF1 7924 108 + 1
UUACCAGUUGCAAGUUGACAAUUACUUGGCUGGGCAUUUAAUUGCCCAGCGCCCACUGUACUUGCGAGUGGGCUCCACAAAUAUUGGCUGAAUAUCUGUUUGUUUGGC
....((((..(((((........)))))((((((((......))))))))(((((((((....)).))))))).........))))((..((((......))))..)) ( -41.10)
>consensus
UUACCAGUUGAAAGUUGGCAAUUACAUAGA_AGGCAAUUAAUUACCCAGCGCCCACUGUACUUGCGAGUGGGCUCCACAAAUAUU_G__GA_U_____UUUGUUUGGC
...((((......(((((...........................)))))(((((((((....)).)))))))..............................)))). (-17.67 = -18.27 +   0.60)

alignment

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secondary structure

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Window 4

Location 843,683 – 843,786
Length 103
Sequences 5
Columns 108
Reading direction reverse
Mean pairwise identity 78.78
Mean single sequence MFE -29.62
Consensus MFE -21.03
Energy contribution -21.22
Covariance contribution 0.19
Combinations/Pair 1.12
Mean z-score -2.64
Structure conservation index 0.71
SVM decision value 2.49
SVM RNA-class probability 0.994537
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 843683 103 - 22407834
GCCAAACAAA----CACUCGCCCAAUAUUUGUGGAGCCCACUCGCAAGUACAGUGGGCGCUGGGUAAUUAAUUGCCU-CAUAUGUAAUUGCCAACUUUCAACUGGUAA
((((......----((..((((((.((((((((.((....))))))))))...)))))).))((((((((..((...-))....))))))))..........)))).. ( -29.20)
>DroSec_CAF1 9100 92 - 1
GCCAAACAA---------------AUAUUUGUGGAGCCCACUCGCAAGUACAGUGGGCGCUGGCUAAUUAAUUGCCU-UCUAUGUAAUUGCCAACUUUCAACUGGUAU
((((.((((---------------....))))(((((((((((....)...)))))))..((((.....((((((..-.....))))))))))...)))...)))).. ( -24.90)
>DroSim_CAF1 9756 92 - 1
GCCAAACAA---------------AUAUUUGUGGAGCCCACUCGCAAGUACAGUGGGCGCUGGCUAAUUAAUUGCCU-UCUAUGUAAUUGCCAACUUUCAACUGGUAA
((((.((((---------------....))))(((((((((((....)...)))))))..((((.....((((((..-.....))))))))))...)))...)))).. ( -24.90)
>DroEre_CAF1 8652 92 - 1
GCCAAACAGAGAGACAUUCACCUAAUAUUUGUGGAGCCCACUCGCAAGUACAGUGGGCGCUGGGUAAUU----------------AAUUGUCGACUCGCAACUGGUAA
((((....(((.(((((((((.........)))))((((((((....)...)))))))...........----------------...))))..))).....)))).. ( -27.60)
>DroYak_CAF1 7924 108 - 1
GCCAAACAAACAGAUAUUCAGCCAAUAUUUGUGGAGCCCACUCGCAAGUACAGUGGGCGCUGGGCAAUUAAAUGCCCAGCCAAGUAAUUGUCAACUUGCAACUGGUAA
((((.....(((((((((.....)))))))))...((((((((....)...)))))))((((((((......))))))))(((((........)))))....)))).. ( -41.50)
>consensus
GCCAAACAAA_____A_UC__C_AAUAUUUGUGGAGCCCACUCGCAAGUACAGUGGGCGCUGGGUAAUUAAUUGCCU_UCUAUGUAAUUGCCAACUUUCAACUGGUAA
((((............................((.((((((((....)...))))))).)).((((((((..((......))..))))))))..........)))).. (-21.03 = -21.22 +   0.19)

alignment

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secondary structure

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dotplot

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Window 5

Location 843,722 – 843,820
Length 98
Sequences 5
Columns 102
Reading direction forward
Mean pairwise identity 87.86
Mean single sequence MFE -25.76
Consensus MFE -22.10
Energy contribution -22.10
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.33
Structure conservation index 0.86
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 843722 98 + 22407834
AUUACCCAGCGCCCACUGUACUUGCGAGUGGGCUCCACAAAUAUUGGGCGAGUG----UUUGUUUGGCAAAUAGAUGAAAAUUGCCGCUAACUUUGAUUUGG
.......((((((((((((....)).))))))).............(((((...----((..((((.....))))..))..))))))))............. ( -28.20)
>DroSec_CAF1 9139 87 + 1
AUUAGCCAGCGCCCACUGUACUUGCGAGUGGGCUCCACAAAUAU---------------UUGUUUGGCAAAUAGAUGAAAAUUGCCGCUAACUUUGAUUUGG
.(((((..(((((((((((....)).)))))))....((..(((---------------(((.....))))))..))......)).)))))........... ( -25.00)
>DroSim_CAF1 9795 87 + 1
AUUAGCCAGCGCCCACUGUACUUGCGAGUGGGCUCCACAAAUAU---------------UUGUUUGGCAAAUAGAUGAAAAUUGCCGCUAACUUUGAUUUGG
.(((((..(((((((((((....)).)))))))....((..(((---------------(((.....))))))..))......)).)))))........... ( -25.00)
>DroEre_CAF1 8676 102 + 1
AUUACCCAGCGCCCACUGUACUUGCGAGUGGGCUCCACAAAUAUUAGGUGAAUGUCUCUCUGUUUGGCAAAUAAAUGAAAAUUGCCGCUAACUUUGAUUUGG
..........(((((((((....)).)))))))....(((((...((((((((........))))(((((...........)))))....))))..))))). ( -23.50)
>DroYak_CAF1 7964 102 + 1
AUUGCCCAGCGCCCACUGUACUUGCGAGUGGGCUCCACAAAUAUUGGCUGAAUAUCUGUUUGUUUGGCAAAUAAAUGAAAAUUGCCGCUAACUUUGAUUUGG
.....((((.(((((((((....)).)))))))....((((..(((((.(((((......)))))(((((...........)))))))))).))))..)))) ( -27.10)
>consensus
AUUACCCAGCGCCCACUGUACUUGCGAGUGGGCUCCACAAAUAUU_G__GA_U_____UUUGUUUGGCAAAUAGAUGAAAAUUGCCGCUAACUUUGAUUUGG
.......((((((((((((....)).)))))))................................(((((...........))))))))............. (-22.10 = -22.10 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 6

Location 843,722 – 843,820
Length 98
Sequences 5
Columns 102
Reading direction reverse
Mean pairwise identity 87.86
Mean single sequence MFE -29.38
Consensus MFE -25.18
Energy contribution -25.18
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -3.16
Structure conservation index 0.86
SVM decision value 3.68
SVM RNA-class probability 0.999518
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 843722 98 - 22407834
CCAAAUCAAAGUUAGCGGCAAUUUUCAUCUAUUUGCCAAACAAA----CACUCGCCCAAUAUUUGUGGAGCCCACUCGCAAGUACAGUGGGCGCUGGGUAAU
.........(.((((((((((...........))))).......----.....(((((.((((((((.((....))))))))))...)))))))))).)... ( -29.00)
>DroSec_CAF1 9139 87 - 1
CCAAAUCAAAGUUAGCGGCAAUUUUCAUCUAUUUGCCAAACAA---------------AUAUUUGUGGAGCCCACUCGCAAGUACAGUGGGCGCUGGCUAAU
.........((((((((((((...........)))))......---------------...........((((((((....)...))))))))))))))... ( -29.90)
>DroSim_CAF1 9795 87 - 1
CCAAAUCAAAGUUAGCGGCAAUUUUCAUCUAUUUGCCAAACAA---------------AUAUUUGUGGAGCCCACUCGCAAGUACAGUGGGCGCUGGCUAAU
.........((((((((((((...........)))))......---------------...........((((((((....)...))))))))))))))... ( -29.90)
>DroEre_CAF1 8676 102 - 1
CCAAAUCAAAGUUAGCGGCAAUUUUCAUUUAUUUGCCAAACAGAGAGACAUUCACCUAAUAUUUGUGGAGCCCACUCGCAAGUACAGUGGGCGCUGGGUAAU
.........(.((((((((((...........)))))..(((((.((........))....)))))...((((((((....)...)))))))))))).)... ( -27.50)
>DroYak_CAF1 7964 102 - 1
CCAAAUCAAAGUUAGCGGCAAUUUUCAUUUAUUUGCCAAACAAACAGAUAUUCAGCCAAUAUUUGUGGAGCCCACUCGCAAGUACAGUGGGCGCUGGGCAAU
..........(((((((((((...........)))))......(((((((((.....)))))))))...((((((((....)...)))))))))).)))... ( -30.60)
>consensus
CCAAAUCAAAGUUAGCGGCAAUUUUCAUCUAUUUGCCAAACAAA_____A_UC__C_AAUAUUUGUGGAGCCCACUCGCAAGUACAGUGGGCGCUGGGUAAU
...........((((((((((...........)))))................................((((((((....)...))))))))))))..... (-25.18 = -25.18 +  -0.00)

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 09:32:23 2006