Locus 4154

Sequence ID 3R_DroMel_CAF1
Location 11,322,900 – 11,323,035
Length 135
Max. P 0.602179
window6658 window6659

overview

Window 8

Location 11,322,900 – 11,323,020
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.00
Mean single sequence MFE -31.75
Consensus MFE -26.66
Energy contribution -26.86
Covariance contribution 0.20
Combinations/Pair 1.06
Mean z-score -1.38
Structure conservation index 0.84
SVM decision value 0.03
SVM RNA-class probability 0.548612
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11322900 120 + 27905053
CAGGAUAAUUAAGAAAUUUUUCAGUUCCCGUCUCUGGACCUCACUUUUGUGGCCCUCAUUGGGUCCUUCGGUGGUGCGACUUUCGCUAUCGAAAUAAAUGGAAAUUGAUUGAAUUCCAUU
............(((.((..((((((.((((....(((((((((....))).........))))))((((((((((.......))))))))))....)))).))))))..)).))).... ( -31.30)
>DroSec_CAF1 62107 120 + 1
CAGGAUAAUUAAGAAAUUUUUCAGUUCCCGCCUCUGGACCCCACUUUAGUGGCCCUCAUUGGGUCCUUCGGUGGUGCGACUUUCGCUAUCGAAAUAAAUGGAAAUUGAUUGAAUUCCAUU
..(((...((((..((((((.((.((((((((...(((((((((....))).........))))))...))))).(((.....)))....))).....))))))))..))))..)))... ( -32.50)
>DroSim_CAF1 58389 120 + 1
CAGGAUAAUUAAGAAAUUUUUCAGUUCCCGCCUCUGGACCCCACUUUUGUGGCCCUCAUUGGGUCCUUCGGUGGUGCGACUUUCGCUAUCGAAAUAAAUGGAAAUUGAUUGAAUUCCAUU
..(((...((((..((((((.((.((((((((...(((((((((....))).........))))))...))))).(((.....)))....))).....))))))))..))))..)))... ( -32.80)
>DroEre_CAF1 57415 120 + 1
CAGGAUAAUUAAGAAAUUUUUCAGUUCCCGCCUCUGGACCCCACUUUCCUGGCCCUCGUUGGGUCCUUUGGUGGUGCGACUUUCGCUAUCGAAGUAAAUGGAAAUUGAUUGAAUUCCAUU
..(((...((((..(((((((.(.((((((((...((((((.((.............)).))))))...))))).(((.....)))....))).)....)))))))..))))..)))... ( -32.92)
>DroYak_CAF1 59014 120 + 1
CAGGAUAAUUAAGAAAUUUUUCAGUUCCCGCCUCUGGACCCCACUUUCCUGGCCCUCAUUGGGAACUUUGGUGGUGCGACUUUGGCUAUCGAAAUAAAUGGAAAUUGAUUGAAUUCCAUU
..(((...((((..((((((.(((((((((((...(((........))).))).......))))))(((((((((.........))))))))).....))))))))..))))..)))... ( -29.21)
>consensus
CAGGAUAAUUAAGAAAUUUUUCAGUUCCCGCCUCUGGACCCCACUUUCGUGGCCCUCAUUGGGUCCUUCGGUGGUGCGACUUUCGCUAUCGAAAUAAAUGGAAAUUGAUUGAAUUCCAUU
..(((...((((..((((((((((.........)))))..(((.......(((((.....))))).((((((((((.......)))))))))).....))))))))..))))..)))... (-26.66 = -26.86 +   0.20)

alignment

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secondary structure

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dotplot

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Window 9

Location 11,322,940 – 11,323,035
Length 95
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 84.39
Mean single sequence MFE -34.51
Consensus MFE -27.86
Energy contribution -27.78
Covariance contribution -0.08
Combinations/Pair 1.07
Mean z-score -1.57
Structure conservation index 0.81
SVM decision value 0.14
SVM RNA-class probability 0.602179
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11322940 95 + 27905053
UCACUUUUGUGGCCCUCAUUGGGUCCUUCGGUGGUGCGACUUUCGCUAUCGAAAUAAAUGGAAAUUGAUUGAAUUCCAUUAGGCCAGGAAGGGAA-------------------------
((.(((((.(((((............((((((((((.......))))))))))...(((((((.((....)).))))))).))))).))))))).------------------------- ( -32.50)
>DroSec_CAF1 62147 120 + 1
CCACUUUAGUGGCCCUCAUUGGGUCCUUCGGUGGUGCGACUUUCGCUAUCGAAAUAAAUGGAAAUUGAUUGAAUUCCAUUAGGCCAGGAAGGGAAGCAGGCGAAAUCGAACCAAGCCCAA
((((....))))((((..((((..((((((((((((.......))))))))))...(((((((.((....)).))))))).))))))..)))).....(((.............)))... ( -35.92)
>DroSim_CAF1 58429 120 + 1
CCACUUUUGUGGCCCUCAUUGGGUCCUUCGGUGGUGCGACUUUCGCUAUCGAAAUAAAUGGAAAUUGAUUGAAUUCCAUUAGGCCAGGAAGGAAAGCAGGCGAAAUCGAACCAAGCCAAA
...(((((.(((((............((((((((((.......))))))))))...(((((((.((....)).))))))).))))).)))))......(((.............)))... ( -35.92)
>DroEre_CAF1 57455 115 + 1
CCACUUUCCUGGCCCUCGUUGGGUCCUUUGGUGGUGCGACUUUCGCUAUCGAAGUAAAUGGAAAUUGAUUGAAUUCCAUUAGGCCAGCAUAGGCAGCAGGCGAAAUCGAACCGC-----A
..........(((((.....))))).....(((((.(((.(((((((.........(((((((.((....)).)))))))..(((......)))....)))))))))).)))))-----. ( -38.30)
>DroYak_CAF1 59054 115 + 1
CCACUUUCCUGGCCCUCAUUGGGAACUUUGGUGGUGCGACUUUGGCUAUCGAAAUAAAUGGAAAUUGAUUGAAUUCCAUUAGGCCAGCAAAGGAAGCAGGCGAAAUCGAACCAA-----A
(((((.......(((.....)))......))))).......((((...((((....(((((((.((....)).)))))))..(((.((.......)).)))....)))).))))-----. ( -29.92)
>consensus
CCACUUUCGUGGCCCUCAUUGGGUCCUUCGGUGGUGCGACUUUCGCUAUCGAAAUAAAUGGAAAUUGAUUGAAUUCCAUUAGGCCAGGAAGGGAAGCAGGCGAAAUCGAACCAA_____A
...((((..(((((............((((((((((.......))))))))))...(((((((.((....)).))))))).)))))..))))............................ (-27.86 = -27.78 +  -0.08)

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 11:19:38 2006