Locus 4838

Sequence ID 3L_DroMel_CAF1
Location 13,567,549 – 13,567,672
Length 123
Max. P 0.993378
window7630 window7631 window7632

overview

Window 0

Location 13,567,549 – 13,567,652
Length 103
Sequences 3
Columns 103
Reading direction forward
Mean pairwise identity 96.09
Mean single sequence MFE -26.30
Consensus MFE -24.40
Energy contribution -24.40
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -3.51
Structure conservation index 0.93
SVM decision value 1.90
SVM RNA-class probability 0.981997
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13567549 103 + 23771897
CACCAGCAUCCCCCUUUUUUCGCCCACUUCCAUGGGCCCCAGGCCAUAGGAAAUAUGGUCGAACCGAGGCCUAACUCCUUUCACCACUUUUCCCCCAAUGCCA
.....................(((((......)))))....(((....(((((..((((.(((..(((......)))..)))))))..)))))......))). ( -27.90)
>DroSec_CAF1 49114 101 + 1
CACCAGCAUACCCCUU-UUCCGCCCACUUCCAUGGGCCCCAGGCCAUAGGAAAUAUGGUCGAACCGAGGCCUAACUCCUUUCACCACUU-UCCCUCAAUGCCA
.....((((...(((.-....(((((......)))))...))).....(((((..((((.(((..(((......)))..))))))).))-)))....)))).. ( -25.70)
>DroSim_CAF1 35277 101 + 1
CACCAGCAGCCCCCUU-UUCCGCCCACUUCCAUGGGCCCCAGGCCAUAGGAAAUAUGGUCGAACCGAGGCCUAACUCCUUUCACCACUU-UCCCCCAAUGCCA
................-....(((((......)))))....(((....(((((..((((.(((..(((......)))..))))))).))-)))......))). ( -25.30)
>consensus
CACCAGCAUCCCCCUU_UUCCGCCCACUUCCAUGGGCCCCAGGCCAUAGGAAAUAUGGUCGAACCGAGGCCUAACUCCUUUCACCACUU_UCCCCCAAUGCCA
.....................(((((......)))))....(((....(((.(..((((.(((..(((......)))..)))))))..).)))......))). (-24.40 = -24.40 +   0.00)

alignment

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secondary structure

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dotplot

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Window 1

Location 13,567,549 – 13,567,652
Length 103
Sequences 3
Columns 103
Reading direction reverse
Mean pairwise identity 96.09
Mean single sequence MFE -36.00
Consensus MFE -32.49
Energy contribution -32.27
Covariance contribution -0.22
Combinations/Pair 1.04
Mean z-score -2.40
Structure conservation index 0.90
SVM decision value 0.91
SVM RNA-class probability 0.880498
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13567549 103 - 23771897
UGGCAUUGGGGGAAAAGUGGUGAAAGGAGUUAGGCCUCGGUUCGACCAUAUUUCCUAUGGCCUGGGGCCCAUGGAAGUGGGCGAAAAAAGGGGGAUGCUGGUG
.((((((..((((((.((((((((..(((......)))..))).))))).))))))....(((...((((((....))))))......)))..)))))).... ( -37.20)
>DroSec_CAF1 49114 101 - 1
UGGCAUUGAGGGA-AAGUGGUGAAAGGAGUUAGGCCUCGGUUCGACCAUAUUUCCUAUGGCCUGGGGCCCAUGGAAGUGGGCGGAA-AAGGGGUAUGCUGGUG
.(((....(((((-(.((((((((..(((......)))..))).))))).))))))(((.(((...((((((....))))))....-..))).)))))).... ( -35.30)
>DroSim_CAF1 35277 101 - 1
UGGCAUUGGGGGA-AAGUGGUGAAAGGAGUUAGGCCUCGGUUCGACCAUAUUUCCUAUGGCCUGGGGCCCAUGGAAGUGGGCGGAA-AAGGGGGCUGCUGGUG
...(((..(((((-((((((((((..(((......)))..))).))))).))))))..(((((...((((((....))))))....-....))))).)..))) ( -35.50)
>consensus
UGGCAUUGGGGGA_AAGUGGUGAAAGGAGUUAGGCCUCGGUUCGACCAUAUUUCCUAUGGCCUGGGGCCCAUGGAAGUGGGCGGAA_AAGGGGGAUGCUGGUG
.(((....(((((...((((((((..(((......)))..))).)))))..)))))...)))....((((((....))))))..................... (-32.49 = -32.27 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 2

Location 13,567,575 – 13,567,672
Length 97
Sequences 5
Columns 111
Reading direction forward
Mean pairwise identity 89.90
Mean single sequence MFE -19.58
Consensus MFE -16.86
Energy contribution -17.10
Covariance contribution 0.24
Combinations/Pair 1.06
Mean z-score -2.19
Structure conservation index 0.86
SVM decision value 2.39
SVM RNA-class probability 0.993378
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13567575 97 + 23771897
CUUCCAUGGGCCCCAGGCCAUAGGAAAUAUGGUCGAACCGAGGCCUAACUCCUUUCACCACUUUUCCCCCAAUGCCA--------------CUUUCCACUUCCCAUACGAU
.....(((((((...))))...(((((..((((.(((..(((......)))..)))))))..)))))..........--------------............)))..... ( -22.60)
>DroSec_CAF1 49139 96 + 1
CUUCCAUGGGCCCCAGGCCAUAGGAAAUAUGGUCGAACCGAGGCCUAACUCCUUUCACCACUU-UCCCUCAAUGCCA--------------CUUUCCACUUUCCAUACGAU
.....(((((((...))))...(((((..((((.(((..(((......)))..))))))).))-)))..........--------------............)))..... ( -20.00)
>DroSim_CAF1 35302 96 + 1
CUUCCAUGGGCCCCAGGCCAUAGGAAAUAUGGUCGAACCGAGGCCUAACUCCUUUCACCACUU-UCCCCCAAUGCCA--------------CUUUCCACUUUCCAUACGAU
.....(((((((...))))...(((((..((((.(((..(((......)))..))))))).))-)))..........--------------............)))..... ( -20.00)
>DroEre_CAF1 49915 110 + 1
CUUCCAUCGGCCCCAGGCCAUAGGAAAUAUGGUCGAACCGAGGCCUAACUCCUUUUACCACUU-UCCCCCAAUGCCACUGUCCACUUUCCACUUUCCACUUUCCAUACGAU
.....(((((((...))))...(((((..((((.(((..(((......)))..))))))).))-))).........................................))) ( -18.10)
>DroYak_CAF1 51681 96 + 1
CUUCCAAAACCCUCGGGCCAUAGGAAAUAUGGUCGAACCGAGGCCUAACUCCUUUCACCACUU-UCCCCCAAUGCCA--------------CUUUCCACUUUCCAUGCGAU
...............(((....(((((..((((.(((..(((......)))..))))))).))-)))......))).--------------.................... ( -17.20)
>consensus
CUUCCAUGGGCCCCAGGCCAUAGGAAAUAUGGUCGAACCGAGGCCUAACUCCUUUCACCACUU_UCCCCCAAUGCCA______________CUUUCCACUUUCCAUACGAU
.((((...((((...))))...))))...((((.(((..(((......)))..)))))))................................................... (-16.86 = -17.10 +   0.24)

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 11:34:51 2006