Locus 6975

Sequence ID 2L_DroMel_CAF1
Location 19,380,336 – 19,380,506
Length 170
Max. P 0.928078
window11124 window11125 window11126 window11127 window11128

overview

Window 4

Location 19,380,336 – 19,380,430
Length 94
Sequences 4
Columns 96
Reading direction forward
Mean pairwise identity 76.67
Mean single sequence MFE -34.86
Consensus MFE -18.66
Energy contribution -21.10
Covariance contribution 2.44
Combinations/Pair 1.20
Mean z-score -2.38
Structure conservation index 0.54
SVM decision value 1.19
SVM RNA-class probability 0.928078
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19380336 94 + 22407834
UGCCAAACUGAGAGUUAAAGGCGGCAUUG-CUGCCGAAGUUGGUGGCGGCAUUGCUGC-CGAAGUUGGUGGCGGCAUUGCUGCCGAAGUUGGAGGC
.(((.(((.....)))...(((((((.((-((((((.......(((((((...)))))-)).......)))))))).))))))).........))) ( -44.44)
>DroSim_CAF1 14200 94 + 1
UGCCAAACUGAGAGUUGAAGGCGGCAUUG-CUGCCGAAGUUGGAGGCGGUGUUGCUGC-CGAAGUUGGUGGCGGCAUUGCUGCCGAAGGUGGAGGC
.(((..(((..........((((((...)-)))))....((((.(((((((((((..(-((....)))..))))))))))).)))).)))...))) ( -42.70)
>DroWil_CAF1 24311 88 + 1
UGCCGAAUUGAGAGCCAA-------AUUGACUACCGAA-UUGACUGCCGAAUUGCUGAUUGACUUUAAAGGCAGAGUUGGUGCCGAAAUUAGAGGC
.(((.((((..(.(((((-------.(((.....))).-....(((((.((...(.....)...))...)))))..)))))..)..))))...))) ( -18.60)
>DroYak_CAF1 14424 94 + 1
UGCCGAGCUGAGAGUUGAAGGCGGCAUUG-CUACCGAAGUUGGAGGCGGUAUUACUGC-CAAAGUUGGAGGCGACAUUGCUGCCAAAAGUGGAGGC
.(((.(((.....)))...((((((((((-((.((((..((...(((((.....))))-)))..)))).)))))...))))))).........))) ( -33.70)
>consensus
UGCCAAACUGAGAGUUAAAGGCGGCAUUG_CUACCGAAGUUGGAGGCGGUAUUGCUGC_CGAAGUUGGAGGCGGCAUUGCUGCCGAAAGUGGAGGC
.(((.(((.....)))...((((((((((.(((((((..(((...((((.....)))).)))..))))))))))...))))))).........))) (-18.66 = -21.10 +   2.44)

alignment

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secondary structure

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dotplot

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Window 5

Location 19,380,336 – 19,380,430
Length 94
Sequences 4
Columns 96
Reading direction reverse
Mean pairwise identity 76.67
Mean single sequence MFE -25.57
Consensus MFE -13.11
Energy contribution -13.93
Covariance contribution 0.81
Combinations/Pair 1.31
Mean z-score -2.30
Structure conservation index 0.51
SVM decision value 0.70
SVM RNA-class probability 0.826681
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19380336 94 - 22407834
GCCUCCAACUUCGGCAGCAAUGCCGCCACCAACUUCG-GCAGCAAUGCCGCCACCAACUUCGGCAG-CAAUGCCGCCUUUAACUCUCAGUUUGGCA
(((...((((..(((.(((.(((.(((.........)-)).))).))).)))........(((((.-...)))))............)))).))). ( -33.90)
>DroSim_CAF1 14200 94 - 1
GCCUCCACCUUCGGCAGCAAUGCCGCCACCAACUUCG-GCAGCAACACCGCCUCCAACUUCGGCAG-CAAUGCCGCCUUCAACUCUCAGUUUGGCA
............((((....))))((((..((((..(-(..((......))..)).....(((((.-...)))))............)))))))). ( -27.70)
>DroWil_CAF1 24311 88 - 1
GCCUCUAAUUUCGGCACCAACUCUGCCUUUAAAGUCAAUCAGCAAUUCGGCAGUCAA-UUCGGUAGUCAAU-------UUGGCUCUCAAUUCGGCA
(((.........((((.......))))......((......)).....))).(((((-((.((.((((...-------..)))))).)))).))). ( -17.50)
>DroYak_CAF1 14424 94 - 1
GCCUCCACUUUUGGCAGCAAUGUCGCCUCCAACUUUG-GCAGUAAUACCGCCUCCAACUUCGGUAG-CAAUGCCGCCUUCAACUCUCAGCUCGGCA
(((.........(((.(((.(((..((.........(-((.(.....).))).........))..)-)).))).))).....(.....)...))). ( -23.17)
>consensus
GCCUCCAACUUCGGCAGCAAUGCCGCCACCAACUUCG_GCAGCAAUACCGCCUCCAACUUCGGCAG_CAAUGCCGCCUUCAACUCUCAGUUCGGCA
(((........(((((....)))))...................................(((((.....))))).................))). (-13.11 = -13.93 +   0.81)

alignment

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secondary structure

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dotplot

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Window 6

Location 19,380,364 – 19,380,470
Length 106
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 57.19
Mean single sequence MFE -35.83
Consensus MFE -9.62
Energy contribution -9.73
Covariance contribution 0.11
Combinations/Pair 1.45
Mean z-score -2.45
Structure conservation index 0.27
SVM decision value 0.66
SVM RNA-class probability 0.814318
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19380364 106 + 22407834
G-CUGCCGAAGUUGGUGGCGGCAUUGCUGC-CGAAGUUGGUGGCGGCAUUGCUGCCGAAGUUGGAGGCAGCAUUGCUGCCAAAGGUGGAGGCGGCAUUCGAUCCGUAA
(-(((((........((((((((.((((((-(........(((((((...)))))))........))))))).))))))))........))))))............. ( -54.58)
>DroSec_CAF1 13995 86 + 1
---------------------CAUUGCUGC-CGAAGUUGGAGGCGGUAUUGCUGCCGAAGUUCGUGGCGGCAUUGCUGCCAAAGGUGGAGGCGGCAUUCGAUCCGUAG
---------------------...((((((-(..(.((...(((((((.((((((((.......)))))))).)))))))..)).)...)))))))............ ( -38.30)
>DroSim_CAF1 14228 82 + 1
G-CUGCCGAAGUUGGAGGCGGUGUUGCUGC-CGAAGUUGGUGGCGGCAUUGCUGCCGAAGGUGGAGGCGGC------------------------AUUCGAUCCGUAG
(-(((((....((((.(((((((((((..(-((....)))..))))))))))).)))).......))))))------------------------............. ( -40.10)
>DroEre_CAF1 14139 82 + 1
G-CUA------------------------C-CGAAGUUCGAGGCGGCAUUGCUGCCAAAGUUGCUGGCGGCAUUGCUGCCAAAGGAGGAGGCGGCAUUCGAUCCGUAG
(-(..------------------------(-(....(((..(((((((.((((((((.......)))))))).)))))))...)))...))..))............. ( -36.20)
>DroWil_CAF1 24332 83 + 1
GACUACCGAA-UUGACUGCCGAAUUGCUGAUUGACUUUAAAGGCAGAGUUGGUGCCGAAAUUAGAGGCAGACUGGCCCCCA------------------------UAG
..........-....(((((.((((.(.(((..(((((......)))))..)).).).))))...)))))...........------------------------... ( -16.70)
>DroYak_CAF1 14452 82 + 1
G-CUACCGAAGUUGGAGGCGGUAUUACUGC-CAAAGUUGGAGGCGACAUUGCUGCCAAAAGUGGAGGCGGCAUUCG------------------------AUCCGUAG
.-((((..........(((((.....))))-)......(((..(((...(((((((.........))))))).)))------------------------.))))))) ( -29.10)
>consensus
G_CUACCGAA_UUGG_GGCGGCAUUGCUGC_CGAAGUUGGAGGCGGCAUUGCUGCCGAAGUUGGAGGCGGCAUUGCUGCCA______________AUUCGAUCCGUAG
...................................((((....))))..(((((((.........))))))).................................... ( -9.62 =  -9.73 +   0.11)

alignment

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secondary structure

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dotplot

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Window 7

Location 19,380,391 – 19,380,506
Length 115
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 68.91
Mean single sequence MFE -40.70
Consensus MFE -20.49
Energy contribution -21.17
Covariance contribution 0.67
Combinations/Pair 1.43
Mean z-score -1.50
Structure conservation index 0.50
SVM decision value 0.20
SVM RNA-class probability 0.632826
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19380391 115 + 22407834
GCCGAAGUUGGUGGCGGCAUUGCUGCCGAAGUUGGAGGCAGCAUUGCUGCCAAAGGUGGAGGCGGCAUUCGAUCCGUAAGUCAAACGGCUGCUGGCAACUGGCUGAACCAGCUGU
((((.(((((.((((((((.(((((((.........))))))).))))))))....(((..((((........))))...)))..)))))..))))....(((((...))))).. ( -50.80)
>DroSec_CAF1 14002 115 + 1
GCCGAAGUUGGAGGCGGUAUUGCUGCCGAAGUUCGUGGCGGCAUUGCUGCCAAAGGUGGAGGCGGCAUUCGAUCCGUAGGUUAAACGGCUGCUGGCAACUGGCUGAACCAGUUGU
((((...((((..((((...(((((((........(((((((...)))))))........)))))))......))))...)))).)))).....((((((((.....)))))))) ( -48.69)
>DroSim_CAF1 14255 91 + 1
GCCGAAGUUGGUGGCGGCAUUGCUGCCGAAGGUGGAGGCGGC------------------------AUUCGAUCCGUAGGUUAAACGGCUGCUGGCAACUGGCUGAACCAGCUGU
.....(((((.(((((((..(((((((.........))))))------------------------).......(((.......)))))))))).)))))(((((...))))).. ( -35.00)
>DroEre_CAF1 14143 114 + 1
-CCGAAGUUCGAGGCGGCAUUGCUGCCAAAGUUGCUGGCGGCAUUGCUGCCAAAGGAGGAGGCGGCAUUCGAUCCGUAGGUUAAGCGGCUGCUGGCAGCUGGCUGAAUCAGUUGU
-.........((..((((...(((((((.(((((((.((((...(((((((.........)))))))......))))......)))))))..)))))))..))))..))...... ( -48.80)
>DroYak_CAF1 14479 91 + 1
GCCAAAGUUGGAGGCGACAUUGCUGCCAAAAGUGGAGGCGGCAUUCG------------------------AUCCGUAGGUCAAACGGCUGCUGGCAACUGGCUGAACCAGCUGU
((((.....(((..(((...(((((((.........))))))).)))------------------------.)))((((.((....))))))))))....(((((...))))).. ( -32.30)
>DroMoj_CAF1 19319 88 + 1
GUUGACCUUAAAGGCGGAGUUGGUGCCGAAGCUGGAGCCGGUCUUCG------------------------AGCCGUAGGUGAAGCUAGCCGAG---GGCUGCUGGACGAUCUGU
(((.((((....((((((((((((.(((....))).))))).)))).------------------------.)))..))))..(((.((((...---))))))).)))....... ( -28.60)
>consensus
GCCGAAGUUGGAGGCGGCAUUGCUGCCGAAGUUGGAGGCGGCAUUGC___________________AUUCGAUCCGUAGGUUAAACGGCUGCUGGCAACUGGCUGAACCAGCUGU
((((..((((..((((((...((((((.........))))))................................(((.......)))))))))..))))))))............ (-20.49 = -21.17 +   0.67)

alignment

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secondary structure

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dotplot

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Window 8

Location 19,380,391 – 19,380,506
Length 115
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 68.91
Mean single sequence MFE -31.48
Consensus MFE -16.32
Energy contribution -17.80
Covariance contribution 1.48
Combinations/Pair 1.33
Mean z-score -1.40
Structure conservation index 0.52
SVM decision value 0.03
SVM RNA-class probability 0.549123
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19380391 115 - 22407834
ACAGCUGGUUCAGCCAGUUGCCAGCAGCCGUUUGACUUACGGAUCGAAUGCCGCCUCCACCUUUGGCAGCAAUGCUGCCUCCAACUUCGGCAGCAAUGCCGCCACCAACUUCGGC
.(((((((.....)))))))......((((.(((......(((.((.....))..))).....((((.(((.(((((((.........))))))).))).)))).)))...)))) ( -43.40)
>DroSec_CAF1 14002 115 - 1
ACAACUGGUUCAGCCAGUUGCCAGCAGCCGUUUAACCUACGGAUCGAAUGCCGCCUCCACCUUUGGCAGCAAUGCCGCCACGAACUUCGGCAGCAAUACCGCCUCCAACUUCGGC
.(((((((.....)))))))......((((.........(((......(((.(((.........))).))).(((.(((.........))).)))...)))..........)))) ( -34.71)
>DroSim_CAF1 14255 91 - 1
ACAGCUGGUUCAGCCAGUUGCCAGCAGCCGUUUAACCUACGGAUCGAAU------------------------GCCGCCUCCACCUUCGGCAGCAAUGCCGCCACCAACUUCGGC
.(((((((.....))))))).......((((.......)))).......------------------------((((..........(((((....)))))..........)))) ( -28.35)
>DroEre_CAF1 14143 114 - 1
ACAACUGAUUCAGCCAGCUGCCAGCAGCCGCUUAACCUACGGAUCGAAUGCCGCCUCCUCCUUUGGCAGCAAUGCCGCCAGCAACUUUGGCAGCAAUGCCGCCUCGAACUUCGG-
....((((((((((..((((....)))).)))........(((.((.....))..)))......(((.(((.(((.(((((.....))))).))).))).)))..)))..))))- ( -33.40)
>DroYak_CAF1 14479 91 - 1
ACAGCUGGUUCAGCCAGUUGCCAGCAGCCGUUUGACCUACGGAU------------------------CGAAUGCCGCCUCCACUUUUGGCAGCAAUGUCGCCUCCAACUUUGGC
.(((((((.....)))))))...((.(.(((((((.(....).)------------------------)))))).)(((.........))).))......(((.........))) ( -27.60)
>DroMoj_CAF1 19319 88 - 1
ACAGAUCGUCCAGCAGCC---CUCGGCUAGCUUCACCUACGGCU------------------------CGAAGACCGGCUCCAGCUUCGGCACCAACUCCGCCUUUAAGGUCAAC
...((((((..(((((((---...)))).)))..))....((((------------------------((.....))).....((....)).........))).....))))... ( -21.40)
>consensus
ACAGCUGGUUCAGCCAGUUGCCAGCAGCCGUUUAACCUACGGAUCGAAU___________________GCAAUGCCGCCUCCAACUUCGGCAGCAAUGCCGCCUCCAACUUCGGC
.(((((((.....)))))))......((((.........(((......(((((..........)))))......)))..........(((((....)))))..........)))) (-16.32 = -17.80 +   1.48)

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 12:24:23 2006