Locus 5574

Sequence ID X_DroMel_CAF1
Location 14,404,595 – 14,404,820
Length 225
Max. P 0.987005
window9044 window9045 window9046

overview

Window 4

Location 14,404,595 – 14,404,697
Length 102
Sequences 4
Columns 104
Reading direction reverse
Mean pairwise identity 77.12
Mean single sequence MFE -29.78
Consensus MFE -15.90
Energy contribution -16.21
Covariance contribution 0.31
Combinations/Pair 1.17
Mean z-score -2.81
Structure conservation index 0.53
SVM decision value 2.06
SVM RNA-class probability 0.987005
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14404595 102 - 22224390
AUUUCAUUUGCAUGCCGCGCGCAAAGGCAGCGGCGCUGAAAGAAGAAGAACAAGCGGACGGUGUGGA-GCG-GAGCGGUAGCGGCAAAAAGAAAUUAAACACAA
(((((.(((((.((((((.(((....(((.((.((((...............))))..)).)))...-)))-..))))))...)))))..)))))......... ( -31.56)
>DroSec_CAF1 114602 102 - 1
AUUUCAUUUGCAUGCCGCGCGCAAAGGCAGCGCCGCUGGAAGAAGAAGCAGAAGCGGACGGUGUGGA-GCG-GAGCGGUAGCGGCAAAAAGAAAUUAAACACAA
(((((.(((((.((((((.(((....(((.(((((((...............))))).)).)))...-)))-..))))))...)))))..)))))......... ( -35.26)
>DroYak_CAF1 114236 82 - 1
AUUUCAUUUGCAUGCCGCGUGCAAAGGCAGCGGCGGUAGAAGAAGA------AGCG----------------GAGCGGUAGCGGCAAAAAGAAAUUAAACACAA
.((((.(((((.((((((.(((....)))))))))))))).)))).------.((.----------------..((....)).))................... ( -24.30)
>DroAna_CAF1 180746 98 - 1
AUUUCAUUUGCAUGCCGCGCGCAAAGUCAGCAGAGGCAGAGGCAGA------GGCAGAGACUGUGGCAGCAACAGUAGUGGCAGCAAAAAGAAAUUAAACACAA
(((((.(((((.((((((((.((.((((.((....((....))...------.))...)))).)))).((....)).)))))))))))..)))))......... ( -28.00)
>consensus
AUUUCAUUUGCAUGCCGCGCGCAAAGGCAGCGGCGCUAGAAGAAGA______AGCGGACGGUGUGGA_GCG_GAGCGGUAGCGGCAAAAAGAAAUUAAACACAA
(((((.(((((.((((((((((....)).))..((((...............))))..................))))))...)))))..)))))......... (-15.90 = -16.21 +   0.31)

alignment

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secondary structure

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dotplot

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Window 5

Location 14,404,664 – 14,404,760
Length 96
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 85.07
Mean single sequence MFE -38.88
Consensus MFE -27.29
Energy contribution -27.48
Covariance contribution 0.20
Combinations/Pair 1.14
Mean z-score -2.34
Structure conservation index 0.70
SVM decision value -0.05
SVM RNA-class probability 0.509933
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14404664 96 + 22224390
CCGCUGCCUUUGCGCGCGGCAUGCAAAUGAAAUGUCAUAAAAAUUGCAACUCGGCAGC----------------GGCA-CGGGCAGCGACGUCAAUGUUGCAGCUGCCACUAU
((((((((..(((.....)))(((((((((....)))).....)))))....))))))----------------))..-..((((((..((.......))..))))))..... ( -36.50)
>DroSec_CAF1 114671 96 + 1
GCGCUGCCUUUGCGCGCGGCAUGCAAAUGAAAUGUCAUAAAAAUUGCAACUCGGCAGC----------------GGCA-CGGGCAGCGACGUCAAUGUUGCAGCUGCCACUAU
.((((((((.(((.((((((((.........)))))........(((......)))))----------------))))-.))))))))........((.((....)).))... ( -34.60)
>DroEre_CAF1 99932 96 + 1
CCGCCGCCUUUGCGCGCGGCAUGCAAAUGAAAUGUCAUAAAAAUUGCAACUCGGCAGC----------------GGCA-AGGGCAGCGACGUCAAUGUUGCAGCUGCCACUGU
(((((((....))).))))..(((((((((....)))).....)))))....((((((----------------.((.-...)).((((((....)))))).))))))..... ( -35.20)
>DroYak_CAF1 114285 102 + 1
CCGCUGCCUUUGCACGCGGCAUGCAAAUGAAAUGUCAUAAAAAUUGCAACUCGGCAGCGGCA----------GCGGCA-CGGGCAGCGACGUCAAUGUUGCAGCUGCCACUGU
((((((((.((((.((.(...(((((((((....)))).....))))).).)))))).))))----------))))..-..((((((..((.......))..))))))..... ( -41.80)
>DroAna_CAF1 180811 103 + 1
CUGCUGACUUUGCGCGCGGCAUGCAAAUGAAAUGUCAUAAAAAUUGCAGCUCGGCAGGGAGG----------GGGGCAGCGGGCAGCGGCAUCAAUGUUGCAGCUGCCACUAU
(((((..((((.(((.((((.(((((((((....)))).....))))))).)))).).))))----------..)))))..((((((.(((.......))).))))))..... ( -40.80)
>DroPer_CAF1 125997 109 + 1
CUGCUGCCUUUGCGCGUGGCAUGCAAAUGAAAUGUCAUAAAAAUUGCAACUCUGCUGCGACGCUGCCGUGCUGCAACG-CUGGCAGCGGCGUCAAUGUUGCAGCUGCCGC---
..((.((....))))((((((.((..((((....))))......((((((..((..(((.((((((((.((......)-))))))))).)))))..))))))))))))))--- ( -44.40)
>consensus
CCGCUGCCUUUGCGCGCGGCAUGCAAAUGAAAUGUCAUAAAAAUUGCAACUCGGCAGC________________GGCA_CGGGCAGCGACGUCAAUGUUGCAGCUGCCACUAU
..(((((........))))).(((((((((....)))).....)))))....((((((.................((.....)).((((((....)))))).))))))..... (-27.29 = -27.48 +   0.20)

alignment

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secondary structure

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dotplot

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Window 6

Location 14,404,722 – 14,404,820
Length 98
Sequences 4
Columns 104
Reading direction forward
Mean pairwise identity 72.23
Mean single sequence MFE -28.30
Consensus MFE -16.61
Energy contribution -18.18
Covariance contribution 1.56
Combinations/Pair 1.05
Mean z-score -1.86
Structure conservation index 0.59
SVM decision value 1.08
SVM RNA-class probability 0.912502
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14404722 98 + 22224390
-GGCACGGGCAGCGACGUCAAUGUUGCAGCUGCCACUAUCGCAGCACUGAGAGAAAAGUGC-CAAGCAAA--GGGAUUUUAAGUCA-GCUAUGCAAGUGUGAU-
-.((((.((((((((((....)))))).(((((.......))))).............)))-)..(((.(--(.(((.....))).-.)).)))..))))...- ( -31.10)
>DroSec_CAF1 114729 103 + 1
-GGCACGGGCAGCGACGUCAAUGUUGCAGCUGCCACUAUCGCAGCACUGAGAGAAAAGUGCACAAGUAAAAAGUAAUUAGAAAUCGAGCGCUAAAAACUAAAUU
-(((...((((((..((.......))..))))))......((.(((((........))))).........((....)).........)))))............ ( -24.70)
>DroEre_CAF1 99990 85 + 1
-GGCAAGGGCAGCGACGUCAAUGUUGCAGCUGCCACUGUCGCAGCACUGAGAGAAAAGCAG---CGCAAG--U---UGCAAGUUC--ACGCA---AGUU-----
-((((..((((((..((.......))..))))))..))))............(((..((((---(....)--)---)))...)))--((...---.)).----- ( -31.40)
>DroYak_CAF1 114348 97 + 1
CGGCACGGGCAGCGACGUCAAUGUUGCAGCUGCCACUGUCGCUGCACUAAGAAAAAAGCAC---AGCAAA--AGCAUCUAAAGCU--ACGCAGAAAGUUAAAUU
(((((..((((((..((.......))..))))))..)))))((((............((..---.))...--(((.......)))--..))))........... ( -26.00)
>consensus
_GGCACGGGCAGCGACGUCAAUGUUGCAGCUGCCACUAUCGCAGCACUGAGAGAAAAGCAC___AGCAAA__GG_AUUUAAAGUC__ACGCAGAAAGUUAAAU_
.((((..((((((..((.......))..))))))..))))((.(((((........)))))....))..................................... (-16.61 = -18.18 +   1.56)

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 11:51:15 2006