Locus 1116

Sequence ID 2R_DroMel_CAF1
Location 4,459,088 – 4,459,282
Length 194
Max. P 0.943562
window1969 window1970 window1971

overview

Window 9

Location 4,459,088 – 4,459,182
Length 94
Sequences 5
Columns 95
Reading direction forward
Mean pairwise identity 93.86
Mean single sequence MFE -36.46
Consensus MFE -29.68
Energy contribution -30.12
Covariance contribution 0.44
Combinations/Pair 1.10
Mean z-score -2.00
Structure conservation index 0.81
SVM decision value 1.34
SVM RNA-class probability 0.943562
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4459088 94 + 20766785
CAGUC-GAAAGAGUGCUGUUGGCCGGCCAAUGGUUAUAUUGGUGGCACGUCACUUGAUCAUUGAGCGGGGGGGUGAGGUGCUUACCCUUCCAGUG
((((.-((..(((((.(((..((((.((((((....))))))))))))).)))))..))))))...(((((((((((...))))))))))).... ( -38.50)
>DroSec_CAF1 6745 93 + 1
CAGUC-GAAAGAGUGCUGUUGGCCGGCCAAUGGUUAUAUUGGUGGCACGUCACUUGAUCAUUGGGCGGG-GGGUGAGGUGCUUACUCUGCCAGUG
((.((-....)).))...(((((((.((((((((((....(((((....))))))))))))))).)).(-(((((((...))))))))))))).. ( -38.00)
>DroSim_CAF1 6814 94 + 1
CAGUC-GAAAGAGUGCUGUUGGCCGGCCAAUGGUUAUAUUGGUGGCACGUCACUUGAUCAUUGGGCGGGGGGGUGAGGUGCUUACCCUGCCAGUG
((.((-....)).))...(((((((.((((((((((....(((((....))))))))))))))).))..((((((((...))))))))))))).. ( -41.00)
>DroEre_CAF1 7223 94 + 1
CAGUCCGAAAGAGUGCUGUUGGCCGGCCAAUGGUUAUAUUGGUGGCACGUCACUUGAUCAUUGGGCGGG-GGGUGAGGAGUGUGCCCUGCCAGUG
((((((....).).))))(((((((.((((((((((....(((((....))))))))))))))).)).(-((((.........)))))))))).. ( -36.10)
>DroYak_CAF1 6645 94 + 1
CAGUCCAAAAGAGUGCUGUUGGCCGGCCAAUGGUUAUAUUGGUGGCACGUCACUUGAUCAUCUAGCGGG-GGGUGAGGAGUUUACCCUGCCAGUG
..........(((((.(((..((((.((((((....))))))))))))).)))))......((.(((((-(.............)))))).)).. ( -28.72)
>consensus
CAGUC_GAAAGAGUGCUGUUGGCCGGCCAAUGGUUAUAUUGGUGGCACGUCACUUGAUCAUUGGGCGGG_GGGUGAGGUGCUUACCCUGCCAGUG
..............((((....(((.((((((((((....(((((....))))))))))))))).)))..(((((((...)))))))...)))). (-29.68 = -30.12 +   0.44)

alignment

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secondary structure

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dotplot

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Window 0

Location 4,459,104 – 4,459,222
Length 118
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 93.03
Mean single sequence MFE -50.86
Consensus MFE -40.90
Energy contribution -42.26
Covariance contribution 1.36
Combinations/Pair 1.03
Mean z-score -1.52
Structure conservation index 0.80
SVM decision value 0.29
SVM RNA-class probability 0.671844
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4459104 118 + 20766785
GUUGGCCGGCCAAUGGUUAUAUUGGUGGCACGUCACUUGAUCAUUGAGCGGGGGGGUGAGGUGCUUACCCUUCCAGUGUGACCCUCGCUCAGCGCUGCGGAAAUCCGUGCAGCUGUGG
(((((....)))))(((((((((((.(((((.((((((..((.......))..)))))).))))).......)))))))))))....(.((((((.((((....)))))).)))).). ( -48.50)
>DroSec_CAF1 6761 117 + 1
GUUGGCCGGCCAAUGGUUAUAUUGGUGGCACGUCACUUGAUCAUUGGGCGGG-GGGUGAGGUGCUUACUCUGCCAGUGUGACCCUCGCGCGGCGCUGCGGAAAUCCGUGCAGCUGUGG
(((((....)))))(((((((((((((((((.((((((..((.......)).-)))))).)))))......))))))))))))....((((((((.((((....)))))).)))))). ( -51.70)
>DroSim_CAF1 6830 118 + 1
GUUGGCCGGCCAAUGGUUAUAUUGGUGGCACGUCACUUGAUCAUUGGGCGGGGGGGUGAGGUGCUUACCCUGCCAGUGUGACCCUCGCGCGGCGCUGCGCAAAUCCGUGCAGCUGUGG
....((((.((((((((((....(((((....))))))))))))))).)((.((((((((...)))))))).)).(((((.....))))))))(((((((......)))))))..... ( -58.00)
>DroEre_CAF1 7240 116 + 1
GUUGGCCGGCCAAUGGUUAUAUUGGUGGCACGUCACUUGAUCAUUGGGCGGG-GGGUGAGGAGUGUGCCCUGCCAGUGUGACCCUCGCGGGGAGCUGCCGAAAUCUG-GCAGCUGUGG
.(((((((.((((((((((....(((((....))))))))))))))).)).(-((((.........)))))))))).....(((.....)))((((((((.....))-)))))).... ( -49.70)
>DroYak_CAF1 6662 117 + 1
GUUGGCCGGCCAAUGGUUAUAUUGGUGGCACGUCACUUGAUCAUCUAGCGGG-GGGUGAGGAGUUUACCCUGCCAGUGUGACCCUCGCGCGGCGCUGCGGAAAUCUGUGCAGCUGUGG
....((((((....(((((((((((..(......((((..((((((......-)))))).)))).....)..)))))))))))...)).))))((((((.(....).))))))..... ( -46.40)
>consensus
GUUGGCCGGCCAAUGGUUAUAUUGGUGGCACGUCACUUGAUCAUUGGGCGGG_GGGUGAGGUGCUUACCCUGCCAGUGUGACCCUCGCGCGGCGCUGCGGAAAUCCGUGCAGCUGUGG
....((((((....(((((((((((((((((.((((((..((.......))..)))))).)))))......))))))))))))...)).))))((((((........))))))..... (-40.90 = -42.26 +   1.36)

alignment

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secondary structure

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dotplot

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Window 1

Location 4,459,182 – 4,459,282
Length 100
Sequences 4
Columns 115
Reading direction forward
Mean pairwise identity 80.76
Mean single sequence MFE -40.40
Consensus MFE -25.99
Energy contribution -26.30
Covariance contribution 0.31
Combinations/Pair 1.18
Mean z-score -1.67
Structure conservation index 0.64
SVM decision value 0.04
SVM RNA-class probability 0.551373
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4459182 100 + 20766785
UGACCCUCGCUCAGCGCUGCGGAAAUCCGUGCAGCUGUGGUGCCGCCGCUGCGCAAUACUUUUGUCACAUGUGGCGCAAAAUUCAAAUGCGG-A--------------UUUUUGA
.............((((..(((....))(((((((.(((....))).)))))))................)..))))(((((((......))-)--------------))))... ( -34.70)
>DroSec_CAF1 6838 114 + 1
UGACCCUCGCGCGGCGCUGCGGAAAUCCGUGCAGCUGUGGUGCUGGCGCUGCGCAAUACUUUUGCCACAUGUGGCGCGAAAUUCAAAUGCGG-AUGCAGACAGACGAAUUUUUCA
........(((((((((.((((....)))).((((......))))))))))))).........((((....))))(.(((((((...(((..-..))).......))))))).). ( -43.00)
>DroSim_CAF1 6908 113 + 1
UGACCCUCGCGCGGCGCUGCGCAAAUCCGUGCAGCUGUGGUGCUGGCGCUGCGCAAUACUUUUGCCACAUGUGGCGCAAAAUUCAAAUGCGG-AUGCAGA-AGACGAAUUUUUCA
........((((((((((((((......))))(((......))))))))))))).........((((....))))(.(((((((...(((..-..)))..-....))))))).). ( -41.40)
>DroEre_CAF1 7317 107 + 1
UGACCCUCGCGGGGAGCUGCCGAAAUCUG-GCAGCUGUGGUGGUGCCGCCUCGCAAUAAUUUUGCCACAUUUGGCGCAAUAUUCAAAGGCGGUCCGCAAGAAG-------UUUCC
...(((.....)))((((((((.....))-))))))...((((.(((((((...((((.((.(((((....))))).))))))...)))))))))))......-------..... ( -42.50)
>consensus
UGACCCUCGCGCGGCGCUGCGGAAAUCCGUGCAGCUGUGGUGCUGCCGCUGCGCAAUACUUUUGCCACAUGUGGCGCAAAAUUCAAAUGCGG_AUGCAGA_AG_____UUUUUCA
....((.((((((((((((((........))))))...((.....))))))))).........((((....)))).............).))....................... (-25.99 = -26.30 +   0.31)

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 09:56:55 2006