Locus 3711

Sequence ID 3R_DroMel_CAF1
Location 10,086,493 – 10,086,613
Length 120
Max. P 0.669261
window5945 window5946

overview

Window 5

Location 10,086,493 – 10,086,613
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 79.50
Mean single sequence MFE -58.13
Consensus MFE -30.44
Energy contribution -32.83
Covariance contribution 2.39
Combinations/Pair 1.26
Mean z-score -2.09
Structure conservation index 0.52
SVM decision value 0.29
SVM RNA-class probability 0.669261
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10086493 120 + 27905053
CGGCCAGUGCCGCCUCCGCCGCACGAGCGGAUUGAGCUGCCUUGGCGGCCAGUUCGUUUUUGACCUGGGAUGCAGCCGCCUCGGCAGCUGCCAUCUGCGAAUCGCUGGCUGCCUUGGCCU
.((((((.((.(((..((.(((..((((((((((.(((((....)))))))))))))))........(((((((((.((....)).)))).))))))))...))..))).)).)))))). ( -61.60)
>DroVir_CAF1 198117 120 + 1
CCGCGAGCGCUGCCUCUGCGGCGCGAGCGGAUUGAGCCGCCCUCUCGGCCAGCUCCUGCUUGACCUGCGUGGCAGCUGCCUCUGCGGCGGCCAUUUGUGCAUCACUGGCAGCCCUCGCCU
..(((((.((((((...((((.((((((((((((.((((......))))))).))).))))).)))))(((((.(((((....))))).)))))............)))))).))))).. ( -61.20)
>DroPse_CAF1 147103 120 + 1
CCGCGAGUGCUGCUUCUGCUGCACGCGCCGACUGCGCCGCUUUCUCGGCCAGCUCUGUCUUCACCUGGGUGGCUGCUGCCUCGGCUGCCGACAUUUGGGCAUCGCUAGCCGCCUUGGCAU
..(((.((((.((....)).)))).))).(((((.((((......))))))).))........((.((((((((((.((....))((((........))))..)).)))))))).))... ( -51.00)
>DroGri_CAF1 175592 120 + 1
CCGCCAGCGCCGCCUCUGCUGCACGAGCCGACUGCGCCGCCCUCUCGGCCAGCUCUGCUUUAACCUGAGAUGCGGCGGCUUCGGCGGCGGCCAUUUGUGCAUCGCUGGCGGCCCUCGCCU
..((.((.((((((..((.(((((((((((.(((((((((((((((((..(((...))).....)))))).).))))))....))))))))...))))))).))..)))))).)).)).. ( -60.40)
>DroMoj_CAF1 176988 120 + 1
CGGCCAGCGCUGCCUCGGCGGCACGUGCCGACUGCGCCGCCCGCUCGGCCAACUGCUGCUUGACCUGUGUGGCAGCUGCCUCUGCGGCGGCCAUUUGCGCAUCGCUGGCGGCCCUCGCCU
..(((((((((((....)))))..(((((((.((.((((((.((..(((...((((..(.........)..))))..)))...)))))))))).))).)))).))))))(((....))). ( -63.60)
>DroPer_CAF1 148304 120 + 1
CCGCGAGUGCUGCUUCUGCUGCACGCGCCGACUGCGCCGCUUUCUCGGCCAGCUCUGUCUUCACCUGGGUGGCUGCUGCCUCGGCUGCCGACAUUUGGGCAUCGCUAGCCGCCUUGGCAU
..(((.((((.((....)).)))).))).(((((.((((......))))))).))........((.((((((((((.((....))((((........))))..)).)))))))).))... ( -51.00)
>consensus
CCGCCAGCGCUGCCUCUGCUGCACGAGCCGACUGCGCCGCCCUCUCGGCCAGCUCUGUCUUGACCUGGGUGGCAGCUGCCUCGGCGGCGGCCAUUUGCGCAUCGCUGGCCGCCCUCGCCU
..((..((((.((....)).))))..((((((((.((((......))))))).))...........(((((((.((.((....)).)).))))))).)))...)).((((.....)))). (-30.44 = -32.83 +   2.39)

alignment

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secondary structure

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dotplot

Postscript

Window 6

Location 10,086,493 – 10,086,613
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 79.50
Mean single sequence MFE -57.97
Consensus MFE -32.82
Energy contribution -32.35
Covariance contribution -0.47
Combinations/Pair 1.35
Mean z-score -1.79
Structure conservation index 0.57
SVM decision value 0.14
SVM RNA-class probability 0.603209
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10086493 120 - 27905053
AGGCCAAGGCAGCCAGCGAUUCGCAGAUGGCAGCUGCCGAGGCGGCUGCAUCCCAGGUCAAAAACGAACUGGCCGCCAAGGCAGCUCAAUCCGCUCGUGCGGCGGAGGCGGCACUGGCCG
.(((((..((.(((.((.(((....))).))(((((((..((((((.......(((.((......)).)))))))))..)))))))...((((((.....))))))))).))..))))). ( -60.51)
>DroVir_CAF1 198117 120 - 1
AGGCGAGGGCUGCCAGUGAUGCACAAAUGGCCGCCGCAGAGGCAGCUGCCACGCAGGUCAAGCAGGAGCUGGCCGAGAGGGCGGCUCAAUCCGCUCGCGCCGCAGAGGCAGCGCUCGCGG
..(((((.((((((.(((.(((.....((((((((.....))).((......)).)))))(((..((((((.((....)).)))))).....))).))).)))...)))))).))))).. ( -62.40)
>DroPse_CAF1 147103 120 - 1
AUGCCAAGGCGGCUAGCGAUGCCCAAAUGUCGGCAGCCGAGGCAGCAGCCACCCAGGUGAAGACAGAGCUGGCCGAGAAAGCGGCGCAGUCGGCGCGUGCAGCAGAAGCAGCACUCGCGG
..(((..((.((((.((..((((........))))((....)).)))))).))..))).......((.(((((((......)))).))))).(((.((((.((....)).)))).))).. ( -48.60)
>DroGri_CAF1 175592 120 - 1
AGGCGAGGGCCGCCAGCGAUGCACAAAUGGCCGCCGCCGAAGCCGCCGCAUCUCAGGUUAAAGCAGAGCUGGCCGAGAGGGCGGCGCAGUCGGCUCGUGCAGCAGAGGCGGCGCUGGCGG
.(((....)))((((((....((....))(((((((((((...((((((.((((.(((...(((...))).)))))))..))))))...)))))((........)))))))))))))).. ( -63.80)
>DroMoj_CAF1 176988 120 - 1
AGGCGAGGGCCGCCAGCGAUGCGCAAAUGGCCGCCGCAGAGGCAGCUGCCACACAGGUCAAGCAGCAGUUGGCCGAGCGGGCGGCGCAGUCGGCACGUGCCGCCGAGGCAGCGCUGGCCG
.(((....)))(((((((.(((((...((((((((.....))).(((((.((....))...)))))....))))).)).((((((((.((....))))))))))...))).))))))).. ( -63.90)
>DroPer_CAF1 148304 120 - 1
AUGCCAAGGCGGCUAGCGAUGCCCAAAUGUCGGCAGCCGAGGCAGCAGCCACCCAGGUGAAGACAGAGCUGGCCGAGAAAGCGGCGCAGUCGGCGCGUGCAGCAGAAGCAGCACUCGCGG
..(((..((.((((.((..((((........))))((....)).)))))).))..))).......((.(((((((......)))).))))).(((.((((.((....)).)))).))).. ( -48.60)
>consensus
AGGCCAAGGCCGCCAGCGAUGCACAAAUGGCCGCCGCCGAGGCAGCUGCCACCCAGGUCAAGAAAGAGCUGGCCGAGAAGGCGGCGCAGUCGGCUCGUGCAGCAGAGGCAGCACUCGCGG
.((((.((....)).((.((......)).))))))((....)).(((((......(((((.........)))))......))))).......(((.((((.((....)).)))).))).. (-32.82 = -32.35 +  -0.47)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:08:06 2006