Locus 6613

Sequence ID 3R_DroMel_CAF1
Location 17,408,380 – 17,408,575
Length 195
Max. P 0.998632
window10764 window10765 window10766

overview

Window 4

Location 17,408,380 – 17,408,500
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.66
Mean single sequence MFE -23.52
Consensus MFE -20.44
Energy contribution -20.88
Covariance contribution 0.44
Combinations/Pair 1.05
Mean z-score -1.26
Structure conservation index 0.87
SVM decision value 0.11
SVM RNA-class probability 0.587408
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17408380 120 + 27905053
ACGUAUCAUACACUUAAGAUGACUAAGCCAACUUAGUAGAACCGACUAAACCCUCAAAACUUUUGCCGCUUCAAAAACGGUUAGGUCUUGAACUAAAGAUGUGCCAAGCUGAAGUGGAAA
.((..((...(((....).))((((((....)))))).))..)).....................((((((((.....(((.(.(((((......))))).))))....))))))))... ( -23.70)
>DroSec_CAF1 12423 118 + 1
ACGUAUGAUACACUUAAGAUGACUAAGUCAACUUAGUAGAACCGCCUAAACCCUCAAAACUUUAGCCACUUCAAAAACGGUUAAGUCUUGAACUAAAGAU--GCCAAGCUGAAGUGGAAA
.....(((.....(((((.((((...)))).)))))(((......))).....))).........((((((((.....(((...(((((......)))))--)))....))))))))... ( -22.90)
>DroSim_CAF1 9712 118 + 1
ACGUAUGAUACACUUAAGAUGACUAAGUCAACUUAGUUGAACCGCCUAAACCCUCAAAACUUUAGCCACUUCAAAAACGGUUAGGUCUUGAACUAAAGAU--GCCAAGCUGAAGUGGAAA
..........((.(((((.((((...)))).))))).))..........................((((((((.....(((...(((((......)))))--)))....))))))))... ( -24.00)
>DroEre_CAF1 11198 118 + 1
AACUAUGUUACACUUAAGAUGACUAAGUCCACUUAGUAGACCCGCCUAAACCCACAAAACUUUAGCCACUUCAAAAACGAUUGGGUCUUGAACUAAAGAU--GCCAAGCUGAAGUGGAAA
.....................((((((....))))))............................((((((((.......(((((((((......)))))--.))))..))))))))... ( -23.50)
>DroYak_CAF1 9515 118 + 1
AUAUAUGUUACGUUCAAGAUGACUAAGUCCACUUAGUAGAACCGCAUAAGCCCACAAAACUUUAGCCACUUGAAAAACGUUUAGGUCUUGAACUAAAGAU--GCCAAGCUAAAGUGGAAA
...(((((...((((......((((((....)))))).)))).)))))..........((((((((..((((((.....))))))((((......)))).--.....))))))))..... ( -23.50)
>consensus
ACGUAUGAUACACUUAAGAUGACUAAGUCAACUUAGUAGAACCGCCUAAACCCUCAAAACUUUAGCCACUUCAAAAACGGUUAGGUCUUGAACUAAAGAU__GCCAAGCUGAAGUGGAAA
.....................((((((....))))))............................((((((((.....(((...(((((......)))))..)))....))))))))... (-20.44 = -20.88 +   0.44)

alignment

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secondary structure

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dotplot

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Window 5

Location 17,408,420 – 17,408,540
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.19
Mean single sequence MFE -31.76
Consensus MFE -25.38
Energy contribution -26.42
Covariance contribution 1.04
Combinations/Pair 1.03
Mean z-score -1.65
Structure conservation index 0.80
SVM decision value 0.37
SVM RNA-class probability 0.710779
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17408420 120 + 27905053
ACCGACUAAACCCUCAAAACUUUUGCCGCUUCAAAAACGGUUAGGUCUUGAACUAAAGAUGUGCCAAGCUGAAGUGGAAACACGGCGGCUGAUGAUGACGCGAUAAGGGGAAAGGAAAGG
...........(((.....((((((.(((.(((.....(((.(.(((((......))))).)))).(((((..(((....)))..))))).....))).))).))))))...)))..... ( -35.40)
>DroSec_CAF1 12463 118 + 1
ACCGCCUAAACCCUCAAAACUUUAGCCACUUCAAAAACGGUUAAGUCUUGAACUAAAGAU--GCCAAGCUGAAGUGGAAACACGGUGGCUGAUGAUGACGCGAUAAGGGGAAAAGAAAGG
.((.(((...((.(((.....(((((((((.......(((((..(((((......)))))--....)))))..(((....))))))))))))...))).).)...))))).......... ( -32.50)
>DroSim_CAF1 9752 118 + 1
ACCGCCUAAACCCUCAAAACUUUAGCCACUUCAAAAACGGUUAGGUCUUGAACUAAAGAU--GCCAAGCUGAAGUGGAAACACGGCGGCUGAUGAUGACGCGAUAAGGGGAAAGGAAAGG
.((.(((...((((.......((((((.((.......(((((.((((((......)))..--))).)))))..(((....))))).))))))((......))...))))...)))...)) ( -32.80)
>DroEre_CAF1 11238 118 + 1
CCCGCCUAAACCCACAAAACUUUAGCCACUUCAAAAACGAUUGGGUCUUGAACUAAAGAU--GCCAAGCUGAAGUGGAAACACGGCGGCUGAUGAUGACGCGAUAAGGGGAAAGGAAAGG
.((.(((...(((........((((((.............(((((((((......)))))--.))))(((...(((....))))))))))))((......))....)))...)))...)) ( -32.70)
>DroYak_CAF1 9555 118 + 1
ACCGCAUAAGCCCACAAAACUUUAGCCACUUGAAAAACGUUUAGGUCUUGAACUAAAGAU--GCCAAGCUAAAGUGGAAACACGGCGGCUGAUGAUGACGCGAUAAGGGGAAAGGAAAGG
.((.(((.((((..(.....((((((..((((((.....))))))((((......)))).--.....))))))(((....))))..)))).)))....(.(.....).)....))..... ( -25.40)
>consensus
ACCGCCUAAACCCUCAAAACUUUAGCCACUUCAAAAACGGUUAGGUCUUGAACUAAAGAU__GCCAAGCUGAAGUGGAAACACGGCGGCUGAUGAUGACGCGAUAAGGGGAAAGGAAAGG
.((.(((...(((........((((((...........(((...(((((......)))))..)))..(((...(((....))))))))))))((......))....)))...)))...)) (-25.38 = -26.42 +   1.04)

alignment

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secondary structure

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dotplot

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Window 6

Location 17,408,460 – 17,408,575
Length 115
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 95.67
Mean single sequence MFE -34.64
Consensus MFE -31.18
Energy contribution -31.26
Covariance contribution 0.08
Combinations/Pair 1.04
Mean z-score -2.26
Structure conservation index 0.90
SVM decision value 3.17
SVM RNA-class probability 0.998632
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17408460 115 + 27905053
UUAGGUCUUGAACUAAAGAUGUGCCAAGCUGAAGUGGAAACACGGCGGCUGAUGAUGACGCGAUAAGGGGAAAGGAAAGGGCCAGGCCAAAGCGAAACUGGCUCGGCUCGGCUGG
..(.(((((......))))).)(((.(((((..(((....)))..)))))............................(((((..((((.........))))..))))))))... ( -39.20)
>DroSec_CAF1 12503 108 + 1
UUAAGUCUUGAACUAAAGAU--GCCAAGCUGAAGUGGAAACACGGUGGCUGAUGAUGACGCGAUAAGGGGAAAAGAAAGGGCCAGGCCAAAGCGAAACUGGCUC-----GGCUGG
....(((((......)))))--(((.(((((..(((....)))..)))))............................(((((((............)))))))-----)))... ( -32.80)
>DroSim_CAF1 9792 108 + 1
UUAGGUCUUGAACUAAAGAU--GCCAAGCUGAAGUGGAAACACGGCGGCUGAUGAUGACGCGAUAAGGGGAAAGGAAAGGGCCAGGCCAAAGCGAAACUGGCUC-----GGCUGG
....(((((......)))))--(((.(((((..(((....)))..)))))............................(((((((............)))))))-----)))... ( -34.90)
>DroEre_CAF1 11278 108 + 1
UUGGGUCUUGAACUAAAGAU--GCCAAGCUGAAGUGGAAACACGGCGGCUGAUGAUGACGCGAUAAGGGGAAAGGAAAGGGCCAGGCCAAAGCGAAACUGGCUC-----GGCUGG
....(((((......)))))--(((.(((((..(((....)))..)))))............................(((((((............)))))))-----)))... ( -34.90)
>DroYak_CAF1 9595 108 + 1
UUAGGUCUUGAACUAAAGAU--GCCAAGCUAAAGUGGAAACACGGCGGCUGAUGAUGACGCGAUAAGGGGAAAGGAAAGGGCCAGGCCAAAGCGAAACUGGCUC-----GGCUGG
....(((((......)))))--(((.((((...(((....)))...))))............................(((((((............)))))))-----)))... ( -31.40)
>consensus
UUAGGUCUUGAACUAAAGAU__GCCAAGCUGAAGUGGAAACACGGCGGCUGAUGAUGACGCGAUAAGGGGAAAGGAAAGGGCCAGGCCAAAGCGAAACUGGCUC_____GGCUGG
....(((((......)))))..(((.(((((..(((....)))..)))))............................(((((((............))))))).....)))... (-31.18 = -31.26 +   0.08)

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 12:25:53 2006