Locus 9298

Sequence ID 3R_DroMel_CAF1
Location 24,771,015 – 24,771,149
Length 134
Max. P 0.879898
window14863 window14864 window14865

overview

Window 3

Location 24,771,015 – 24,771,119
Length 104
Sequences 3
Columns 108
Reading direction forward
Mean pairwise identity 80.66
Mean single sequence MFE -26.60
Consensus MFE -16.88
Energy contribution -17.77
Covariance contribution 0.89
Combinations/Pair 1.04
Mean z-score -2.10
Structure conservation index 0.63
SVM decision value 0.61
SVM RNA-class probability 0.797783
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24771015 104 + 27905053
GAGGGCGAGGGUGCCCUUUGCGGCCCAGAGAAAUUAAUAAGCGUCGCAUUUAUUAGCAGUCAAAUAAAGUGAUCAAAAUGUCACUCAUACGCAACGUAUGCCGC----
(((((((....))))))).(((((...((....)).....((((.((.((((((........))))))(((((......)))))......)).))))..)))))---- ( -29.10)
>DroPse_CAF1 23118 89 + 1
AAGGGCGU-------------------CAGAAAUUAAUAAGCGUCGCAUUUAUUAGCAGUCAAAUAAAGUGAUCAAAAUGUCACUCAUACGCAGCGUGUGCCGCCCGA
..(((((.-------------------((...........((((.((.((((((........))))))(((((......)))))......)).)))).)).))))).. ( -21.80)
>DroPer_CAF1 23420 89 + 1
AAGGGCGU-------------------CAGAAAUUAAUAAGCGUCGCAUUUAUUAGCAGUCAAAUAAAGUGAUCAAAAUGUCACUCAUACGCUGCGUCUGCCGCCCGA
..(((((.-------------------((((...(((((((.......)))))))(((((.......((((((......)))))).....))))).)))).))))).. ( -28.90)
>consensus
AAGGGCGU___________________CAGAAAUUAAUAAGCGUCGCAUUUAUUAGCAGUCAAAUAAAGUGAUCAAAAUGUCACUCAUACGCAGCGUAUGCCGCCCGA
..(((((......................((..((((((((.......))))))))...))......((((((......))))))((((((...)))))).))))).. (-16.88 = -17.77 +   0.89)

alignment

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secondary structure

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dotplot

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Window 4

Location 24,771,015 – 24,771,119
Length 104
Sequences 3
Columns 108
Reading direction reverse
Mean pairwise identity 80.66
Mean single sequence MFE -27.27
Consensus MFE -18.99
Energy contribution -19.43
Covariance contribution 0.45
Combinations/Pair 1.05
Mean z-score -2.06
Structure conservation index 0.70
SVM decision value 0.91
SVM RNA-class probability 0.879898
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24771015 104 - 27905053
----GCGGCAUACGUUGCGUAUGAGUGACAUUUUGAUCACUUUAUUUGACUGCUAAUAAAUGCGACGCUUAUUAAUUUCUCUGGGCCGCAAAGGGCACCCUCGCCCUC
----(((((...((((((((..(((((((.....).))))))((((........)))).))))))))((.............)))))))..(((((......))))). ( -30.82)
>DroPse_CAF1 23118 89 - 1
UCGGGCGGCACACGCUGCGUAUGAGUGACAUUUUGAUCACUUUAUUUGACUGCUAAUAAAUGCGACGCUUAUUAAUUUCUG-------------------ACGCCCUU
..(((((((....)).((((..(((((((.....).))))))........(((........))))))).............-------------------.))))).. ( -22.90)
>DroPer_CAF1 23420 89 - 1
UCGGGCGGCAGACGCAGCGUAUGAGUGACAUUUUGAUCACUUUAUUUGACUGCUAAUAAAUGCGACGCUUAUUAAUUUCUG-------------------ACGCCCUU
..(((((.((((.((((((...(((((((.....).))))))....)).))))((((((..((...))))))))...))))-------------------.))))).. ( -28.10)
>consensus
UCGGGCGGCACACGCUGCGUAUGAGUGACAUUUUGAUCACUUUAUUUGACUGCUAAUAAAUGCGACGCUUAUUAAUUUCUG___________________ACGCCCUU
..(((((((....)).((((..(((((((.....).))))))........(((........))))))).................................))))).. (-18.99 = -19.43 +   0.45)

alignment

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secondary structure

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dotplot

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Window 5

Location 24,771,053 – 24,771,149
Length 96
Sequences 3
Columns 100
Reading direction forward
Mean pairwise identity 94.33
Mean single sequence MFE -26.67
Consensus MFE -23.64
Energy contribution -24.53
Covariance contribution 0.89
Combinations/Pair 1.04
Mean z-score -1.92
Structure conservation index 0.89
SVM decision value 0.23
SVM RNA-class probability 0.643716
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24771053 96 + 27905053
AAGCGUCGCAUUUAUUAGCAGUCAAAUAAAGUGAUCAAAAUGUCACUCAUACGCAACGUAUGCCGC----CAGCUGAUGCUGUGGCAACAGUAAAAUAUU
..((((.((.((((((........))))))(((((......)))))......)).)))).((((((----.(((....)))))))))............. ( -25.50)
>DroPse_CAF1 23137 100 + 1
AAGCGUCGCAUUUAUUAGCAGUCAAAUAAAGUGAUCAAAAUGUCACUCAUACGCAGCGUGUGCCGCCCGACAGCUGAUGCUGUGGCAACGGUAAAAUAUU
....((((((..(((((((.(((......((((((......))))))((((((...))))))......))).))))))).)))))).............. ( -27.70)
>DroPer_CAF1 23439 100 + 1
AAGCGUCGCAUUUAUUAGCAGUCAAAUAAAGUGAUCAAAAUGUCACUCAUACGCUGCGUCUGCCGCCCGACAGCUGAUGCUGUGGCAACGGUAAAAUAUU
....((((((..(((((((.(((......((((((......)))))).....((.((....)).))..))).))))))).)))))).............. ( -26.80)
>consensus
AAGCGUCGCAUUUAUUAGCAGUCAAAUAAAGUGAUCAAAAUGUCACUCAUACGCAGCGUAUGCCGCCCGACAGCUGAUGCUGUGGCAACGGUAAAAUAUU
....((((((..(((((((.(((......((((((......))))))((((((...))))))......))).))))))).)))))).............. (-23.64 = -24.53 +   0.89)

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 13:30:59 2006