Locus 1939

Sequence ID 3L_DroMel_CAF1
Location 5,394,400 – 5,394,560
Length 160
Max. P 0.845330
window3028 window3029

overview

Window 8

Location 5,394,400 – 5,394,520
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 94.72
Mean single sequence MFE -28.44
Consensus MFE -23.70
Energy contribution -24.96
Covariance contribution 1.25
Combinations/Pair 1.00
Mean z-score -2.25
Structure conservation index 0.83
SVM decision value 0.77
SVM RNA-class probability 0.845330
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5394400 120 - 23771897
AGCAAUGCCCAUCUCACUCCCCAUCCCACAUGAGCAGCCAGACGAAAGUCAUUCGGUGCCCUUUUCGAUGGCACCCAUUAAAUCCCCUCAACUCCUGUCUGAUGCACUCCAUUGAUGGAA
........(((((........((((..(((.(((......(((....)))....((((((.........))))))................))).)))..)))).........))))).. ( -30.83)
>DroSec_CAF1 43390 120 - 1
AGCAAUGCCCAUCUCACUCCCCAUCUCACAUGAGCAGCCAGACGAAAGUCAUUCGGUGCCCCUUUGGAUGACACCCAUUAAAUCCCCUCAACUCCUGUCUGAUGCACUCCAUUGAUGGAA
........(((((........((((..(((.(((......(((....)))....(((((((....))..).))))................))).)))..)))).........))))).. ( -25.93)
>DroSim_CAF1 43049 119 - 1
AGCAAUGCCCAUCUCACUC-CCAUCUCACAUGAGCAGCCAGACGAAAGUCAUUCGGUGCCCCUUUGGAUGGCACCCAGUAAAUCCCCUCAACUCCUGUCUGAUGCACUCCAUUGAUGGAA
........(((((......-.((((..(((.(((......(((....)))(((.((((((((...))..)))))).)))............))).)))..)))).........))))).. ( -31.99)
>DroYak_CAF1 43096 120 - 1
AGCAAUGCCCAUCUCACUUUACAGCUCACAUGAGCAGCCAGACGAAAGUCAUUCAGUGCCCCUUUCGAUGCCACCCAUUAAAUCCCCUCAACUCCUGACUGAUGCACUCCAUUGAUGGAA
........(((((..........((((....)))).....(((....)))....(((((.......((((.....))))..(((...(((.....)))..)))))))).....))))).. ( -25.00)
>consensus
AGCAAUGCCCAUCUCACUCCCCAUCUCACAUGAGCAGCCAGACGAAAGUCAUUCGGUGCCCCUUUCGAUGGCACCCAUUAAAUCCCCUCAACUCCUGUCUGAUGCACUCCAUUGAUGGAA
........(((((........((((..(((.(((......(((....)))....((((((.........))))))................))).)))..)))).........))))).. (-23.70 = -24.96 +   1.25)

alignment

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secondary structure

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dotplot

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Window 9

Location 5,394,440 – 5,394,560
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 94.31
Mean single sequence MFE -32.35
Consensus MFE -26.99
Energy contribution -28.43
Covariance contribution 1.44
Combinations/Pair 1.06
Mean z-score -1.56
Structure conservation index 0.83
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5394440 120 + 23771897
UAAUGGGUGCCAUCGAAAAGGGCACCGAAUGACUUUCGUCUGGCUGCUCAUGUGGGAUGGGGAGUGAGAUGGGCAUUGCUAAACAAAUUUGCACUCGAGUAAAUUAAAAACAAACAACAA
(((((((((((.........))))))........(((((((.(((.(((((.....))))).))).)))))))))))).......(((((((......)))))))............... ( -34.30)
>DroSec_CAF1 43430 120 + 1
UAAUGGGUGUCAUCCAAAGGGGCACCGAAUGACUUUCGUCUGGCUGCUCAUGUGAGAUGGGGAGUGAGAUGGGCAUUGCUAAACAAAUUUGCUUUCGAGUAAAUUAAAAACAAACAACAA
(((((((((((.((....))))))))........(((((((.(((.(((((.....))))).))).)))))))))))).......((((((((....))))))))............... ( -32.70)
>DroSim_CAF1 43089 119 + 1
UACUGGGUGCCAUCCAAAGGGGCACCGAAUGACUUUCGUCUGGCUGCUCAUGUGAGAUGG-GAGUGAGAUGGGCAUUGCUAAACAAAUUUGCUUUCGAGUAAAUUAAAAACAAACAACAA
.....((((((.((....)))))))).((((....((((((.(((.(((((.....))))-)))).)))))).))))........((((((((....))))))))............... ( -32.10)
>DroYak_CAF1 43136 120 + 1
UAAUGGGUGGCAUCGAAAGGGGCACUGAAUGACUUUCGUCUGGCUGCUCAUGUGAGCUGUAAAGUGAGAUGGGCAUUGCUAAACAAAUUUGCUUUCGAGUAAAUUAAAAACAAACAACAA
.....((((.(.((....))).))))(((.....)))((.(((((((((((.(..(((....))).).)))))))..)))).)).((((((((....))))))))............... ( -30.30)
>consensus
UAAUGGGUGCCAUCCAAAGGGGCACCGAAUGACUUUCGUCUGGCUGCUCAUGUGAGAUGGGGAGUGAGAUGGGCAUUGCUAAACAAAUUUGCUUUCGAGUAAAUUAAAAACAAACAACAA
(((((((((((.((....))))))))........(((((((.(((.(((((.....))))).))).)))))))))))).......(((((((......)))))))............... (-26.99 = -28.43 +   1.44)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:20:32 2006