Locus 2376

Sequence ID 3R_DroMel_CAF1
Location 6,736,771 – 6,737,006
Length 235
Max. P 0.977808
window3832 window3833 window3834 window3835

overview

Window 2

Location 6,736,771 – 6,736,891
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 96.11
Mean single sequence MFE -30.30
Consensus MFE -30.02
Energy contribution -29.80
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -1.64
Structure conservation index 0.99
SVM decision value 0.52
SVM RNA-class probability 0.767411
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6736771 120 - 27905053
AAUCAAAAGUGUUUCGCCAUCGAGGCGUAGCACACAUUUAUGCAUAAAUUGUAUUUACAUUUCUAUAUCCAGCCAGAAAAAAGUGGCAUAUCGCCGCGCAAUGUCCGCUGCUUGUUGCAC
........(((((.((((.....)))).))))).......((((.....(((....))).....(((..((((..((.....(((((.....)))))......)).))))..))))))). ( -30.40)
>DroSec_CAF1 1689 120 - 1
AAUCAAAAGUGUUUCGCCAUCGAGGCGUAGCACACAUUUAUGCAUAAAUUGUAUUUACAUUCCUAUAUCCAGCCAGAAAAAAGUGGCAUAUCGCCGCGCUUUGUCCGCUGCUUGUUGCAC
........(((((.((((.....)))).))))).......((((.....(((....))).....(((..((((....(((..(((((.....)))))..)))....))))..))))))). ( -30.80)
>DroSim_CAF1 5964 119 - 1
AAUCAAAAGUGUUUCGCCAUCGAGGCGUAGCACACAAUUAUGCAUAAAUUGUAUUUACAUUUCUAUAUCCAGUCAGAA-AAAGUGGCUUAUCGCCGCGCAAUGUCCGCUGCUUGUUGCAC
........(((((.((((.....)))).))))).((((...(((...(((((.......(((((..........))))-)..(((((.....))))))))))......)))..))))... ( -29.70)
>consensus
AAUCAAAAGUGUUUCGCCAUCGAGGCGUAGCACACAUUUAUGCAUAAAUUGUAUUUACAUUUCUAUAUCCAGCCAGAAAAAAGUGGCAUAUCGCCGCGCAAUGUCCGCUGCUUGUUGCAC
........(((((.((((.....)))).))))).......((((.....(((....))).....(((..((((..((.....(((((.....)))))......)).))))..))))))). (-30.02 = -29.80 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 3

Location 6,736,851 – 6,736,966
Length 115
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 82.40
Mean single sequence MFE -30.03
Consensus MFE -18.10
Energy contribution -19.10
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.16
Structure conservation index 0.60
SVM decision value 0.07
SVM RNA-class probability 0.570352
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6736851 115 + 27905053
UAAAUGUGUGCUACGCCUCGAUGGCGAAACACUUUUGAUUUACAACACUGUGUGCAAAAAGUAUUCG-----CAUUGCCAUGCCCAUGCUUUUUGCUCAGAUCUUUCAAUUUCAAUGUCA
((((.((((....((((.....))))..)))).))))..........(((...(((((((((((..(-----(((....))))..))))))))))).))).................... ( -30.60)
>DroSec_CAF1 1769 102 + 1
UAAAUGUGUGCUACGCCUCGAUGGCGAAACACUUUUGAUUUACAACACUGUGUGCAAAAAGUAUUCGGAUGGCAUGGCAAUGCCA--A----------------UGACAUUUCAAUGUCA
((((.((((....((((.....))))..)))).))))..........(((.((((.....)))).))).((((((....))))))--.----------------((((((....)))))) ( -29.00)
>DroSim_CAF1 6043 118 + 1
UAAUUGUGUGCUACGCCUCGAUGGCGAAACACUUUUGAUUUACAACACUGUGUGCAAAAAGUAUUCGGAUGGCAUGGCAAUGCCC--GCUUUUUGCUCAGAUCUUUCGAUUUCAAUGUCA
(((..((((....((((.....))))..))))..)))..........(((...(((((((((........(((((....))))).--))))))))).))).......(((......))). ( -30.50)
>consensus
UAAAUGUGUGCUACGCCUCGAUGGCGAAACACUUUUGAUUUACAACACUGUGUGCAAAAAGUAUUCGGAUGGCAUGGCAAUGCCC__GCUUUUUGCUCAGAUCUUUCAAUUUCAAUGUCA
.....((((....((((.....))))..))))..((((.........(((.((((.....)))).)))..(((((....)))))...........................))))..... (-18.10 = -19.10 +   1.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 6,736,851 – 6,736,966
Length 115
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 82.40
Mean single sequence MFE -32.67
Consensus MFE -22.90
Energy contribution -23.57
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.92
Structure conservation index 0.70
SVM decision value 1.80
SVM RNA-class probability 0.977808
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6736851 115 - 27905053
UGACAUUGAAAUUGAAAGAUCUGAGCAAAAAGCAUGGGCAUGGCAAUG-----CGAAUACUUUUUGCACACAGUGUUGUAAAUCAAAAGUGUUUCGCCAUCGAGGCGUAGCACACAUUUA
.(((((((..(((....)))....((((((((.((..((((....)))-----)..)).))))))))...)))))))...........(((((.((((.....)))).)))))....... ( -34.60)
>DroSec_CAF1 1769 102 - 1
UGACAUUGAAAUGUCA----------------U--UGGCAUUGCCAUGCCAUCCGAAUACUUUUUGCACACAGUGUUGUAAAUCAAAAGUGUUUCGCCAUCGAGGCGUAGCACACAUUUA
((((((....))))))----------------.--((((((....))))))...........((((((........))))))......(((((.((((.....)))).)))))....... ( -27.00)
>DroSim_CAF1 6043 118 - 1
UGACAUUGAAAUCGAAAGAUCUGAGCAAAAAGC--GGGCAUUGCCAUGCCAUCCGAAUACUUUUUGCACACAGUGUUGUAAAUCAAAAGUGUUUCGCCAUCGAGGCGUAGCACACAAUUA
.(((((((..(((....)))....(((((((((--((((((....))))...)))....))))))))...)))))))...........(((((.((((.....)))).)))))....... ( -36.40)
>consensus
UGACAUUGAAAUCGAAAGAUCUGAGCAAAAAGC__GGGCAUUGCCAUGCCAUCCGAAUACUUUUUGCACACAGUGUUGUAAAUCAAAAGUGUUUCGCCAUCGAGGCGUAGCACACAUUUA
.(((((((............................(((((....)))))...((((.....))))....)))))))...........(((((.((((.....)))).)))))....... (-22.90 = -23.57 +   0.67)

alignment

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secondary structure

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dotplot

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Window 5

Location 6,736,891 – 6,737,006
Length 115
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 81.84
Mean single sequence MFE -27.50
Consensus MFE -16.30
Energy contribution -17.63
Covariance contribution 1.33
Combinations/Pair 1.00
Mean z-score -2.50
Structure conservation index 0.59
SVM decision value 0.53
SVM RNA-class probability 0.769623
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6736891 115 - 27905053
AUAAGCUGCAAAAAUGCAAUAUUUUUUUUCGCUACCAAAAUGACAUUGAAAUUGAAAGAUCUGAGCAAAAAGCAUGGGCAUGGCAAUG-----CGAAUACUUUUUGCACACAGUGUUGUA
......((((....)))).....................(..((((((..(((....)))....((((((((.((..((((....)))-----)..)).))))))))...))))))..). ( -25.40)
>DroSec_CAF1 1809 101 - 1
AUAAGCUGCAAAAAUGCAAUAUUU-UUUGCGCUACCAAAAUGACAUUGAAAUGUCA----------------U--UGGCAUUGCCAUGCCAUCCGAAUACUUUUUGCACACAGUGUUGUA
...(((.(((((((........))-)))))))).....((((((((....))))))----------------)--)(((((....))))).....((((((..........))))))... ( -24.20)
>DroSim_CAF1 6083 118 - 1
AUAAGCUGCAAAAAUGCAAUAUUUUUUUGCGCUACCAAAAUGACAUUGAAAUCGAAAGAUCUGAGCAAAAAGC--GGGCAUUGCCAUGCCAUCCGAAUACUUUUUGCACACAGUGUUGUA
...(((.(((((((.........))))))))))......(..((((((..(((....)))....(((((((((--((((((....))))...)))....))))))))...))))))..). ( -32.90)
>consensus
AUAAGCUGCAAAAAUGCAAUAUUUUUUUGCGCUACCAAAAUGACAUUGAAAUCGAAAGAUCUGAGCAAAAAGC__GGGCAUUGCCAUGCCAUCCGAAUACUUUUUGCACACAGUGUUGUA
...(((.(((((((.........))))))))))......(..((((((............................(((((....)))))...((((.....))))....))))))..). (-16.30 = -17.63 +   1.33)

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 10:33:49 2006