Locus 1840

Sequence ID 2L_DroMel_CAF1
Location 5,080,964 – 5,081,152
Length 188
Max. P 0.679576
window2957 window2958

overview

Window 7

Location 5,080,964 – 5,081,058
Length 94
Sequences 4
Columns 94
Reading direction forward
Mean pairwise identity 89.55
Mean single sequence MFE -30.67
Consensus MFE -22.41
Energy contribution -24.22
Covariance contribution 1.81
Combinations/Pair 1.04
Mean z-score -1.56
Structure conservation index 0.73
SVM decision value 0.01
SVM RNA-class probability 0.540189
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5080964 94 + 22407834
GCGAUGCAGAGGUGGAGAAGUGGGUGGCUUGGGCAGGGGCAGCAACACUAUGCUUAAAUAUGCAGUUGCAUGUGCGGCAAGACCCCAGAAGAGG
..........((.((...((((.((.((((......)))).))..)))).((((...((((((....))))))..))))...))))........ ( -23.30)
>DroSec_CAF1 10451 91 + 1
GGUAGGCAGGGGUGCAGAAGUGGGUGGCUGGGGCAGUGGCAGC---ACUCUGCUUAAAUAUGCAGUUGCAUGUGCGGCAAGACCCCAGAAGAGG
........((((((((((.(((.((.((((...)))).))..)---)))))))...........(((((....)))))...)))))........ ( -32.80)
>DroSim_CAF1 12666 91 + 1
GGUAGCCAGGGGUGCAGAAGUGGGUGGCUGGGGCAGGGGCAGC---ACUCUGCUUAAAUAUGCAGUUGCAUGUGCGGCAAGACCCCAGAAGAGG
.(((.(....).)))....(.((((.((((((((((((.....---.))))))))..((((((....)))))).))))...)))))........ ( -32.30)
>DroYak_CAF1 11793 91 + 1
GGGAUGCGGAUGUGCAGAAGUGGGUGGCUUGGGCAGGGGCAAC---ACUCUGCUUAAAUAUGCAGUUGCAUGUGCAGCAGGAACCCAGAAGAGG
(((.((((.((((((((...((.(((..((((((((((.....---.)))))))))).))).)).)))))))).).)))....)))........ ( -34.30)
>consensus
GGGAGGCAGAGGUGCAGAAGUGGGUGGCUGGGGCAGGGGCAGC___ACUCUGCUUAAAUAUGCAGUUGCAUGUGCGGCAAGACCCCAGAAGAGG
........(((((.......((.(((..((((((((((.........)))))))))).))).))(((((....)))))...)))))........ (-22.41 = -24.22 +   1.81)

alignment

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secondary structure

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dotplot

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Window 8

Location 5,081,058 – 5,081,152
Length 94
Sequences 5
Columns 108
Reading direction forward
Mean pairwise identity 77.24
Mean single sequence MFE -20.37
Consensus MFE -9.36
Energy contribution -9.96
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -1.93
Structure conservation index 0.46
SVM decision value 0.30
SVM RNA-class probability 0.679576
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5081058 94 + 22407834
CAAACUUCAGUGG-CGCUCACUGGAGUGCCCUUUUUAGGGCAUGUCAGG--CCAUCAAUAAUACAUUUGAUAAC-----------AAGAAAACGUAAAAAAUAUAUUU
...(((((((((.-....)))))))))(((((....)))))...((..(--..(((((........)))))..)-----------..))................... ( -23.40)
>DroPse_CAF1 15338 99 + 1
AGAACUUCAGCUGCUGCACACAGGAGUGGCCCAU--C------GUCGGGAAUCAUCAAUAAUAAAUUUAAA-AAAGCGGCAAAUGAAAAUAACACAAAAAGGAAAUUC
.....((((..((((((.(((....))).(((..--.------...)))......................-...))))))..))))..................... ( -20.10)
>DroSec_CAF1 10542 92 + 1
CAAACUUCAGUGG-CGCUCACUGGAGUGCCCUUU--CAGCCAUGUCAGG--CCAUCAAUAAUACAAUUGCUAAC-----------AAGGAAACGUAAAAAAUAUAUUU
........((.((-(((((....)))))))))..--..(((......))--).........(((..(((....)-----------))(....))))............ ( -18.50)
>DroSim_CAF1 12757 92 + 1
CAAACUUCAGUGG-CGCUCACUGGAGUGCCCUUU--CAGCCAUGUCAGC--CCAUCAAUAAUACAUUUGCUAAC-----------AAGGAAACGUAAAAAAUAUAUUU
........((.((-(((((....)))))))))..--...((.(((.(((--.................))).))-----------).))................... ( -17.73)
>DroYak_CAF1 11884 92 + 1
CAAACUUCAGUGG-CGCUCACUGGAGUGCCCUUU--CAGCCAUGUCAGG--CCAUCAAUAAUACAUUUGAUAAC-----------AAGGAGACGUAAAAAAUAAAUUU
....((((((.((-(((((....)))))))))..--..(((......))--).(((((........)))))...-----------..))))................. ( -22.10)
>consensus
CAAACUUCAGUGG_CGCUCACUGGAGUGCCCUUU__CAGCCAUGUCAGG__CCAUCAAUAAUACAUUUGAUAAC___________AAGGAAACGUAAAAAAUAUAUUU
...(((((((((......)))))))))................................................................................. ( -9.36 =  -9.96 +   0.60)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:12:34 2006