Locus 8313

Sequence ID X_DroMel_CAF1
Location 20,663,911 – 20,664,085
Length 174
Max. P 0.962162
window13653 window13654

overview

Window 3

Location 20,663,911 – 20,664,022
Length 111
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 92.05
Mean single sequence MFE -33.02
Consensus MFE -27.47
Energy contribution -28.55
Covariance contribution 1.08
Combinations/Pair 1.06
Mean z-score -1.91
Structure conservation index 0.83
SVM decision value 1.54
SVM RNA-class probability 0.962162
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20663911 111 - 22224390
-------AACGGAAACGGGCCAAGUCUCGACGAAAAUCCAUUUCCAUGUGCUUUGGA-CUCGUUGUGGGAUUGCCUGCAAUUGUGCGGGAAAAAGGAAAACAGAAGCAUAAAAUCAAAU
-------...(((((.(((....((....)).....))).))))).((((((((...-(((((((..((....))..)).....))))).....(.....).))))))))......... ( -26.50)
>DroSec_CAF1 65587 111 - 1
-------AGCGGAAACGGGCCAAGUCUCGACGAGAAUCCAUUUCCAUGUGCUUUGGA-CUCCCUGUGGGAUUGCCUGCAAUUGUGCGGGGAAAAAGAAAACAGAAGCAUAAAAUCAAAU
-------.(((((((.(((.....((((...)))).))).))))).(((.((((...-.((((((((.(((((....))))).)))))))).))))...)))...))............ ( -34.00)
>DroSim_CAF1 43045 111 - 1
-------AGCGGAAACGGGCCAAGUCUCGACGAGAAUCCAUUUCCAUGUGCUUUGGA-CUCCCUGUGUGAUUGCCUGCAAUUGUGCGGGGAAAAAGAAAACAGAAGCAUAAAAUCAAAU
-------.(((((((.(((.....((((...)))).))).))))).(((.((((...-.((((((((..((((....))))..)))))))).))))...)))...))............ ( -34.80)
>DroEre_CAF1 61177 112 - 1
-------AACGGAAACGGGCCAAGUCUCGACGAGAAUCCAUUUCCAUGUGCUUGGGGUCUGCCUGUGGGAUUGCCUGCAAUUGUGCGGGGAAAAAGAAAACAGAAGCAUAAAAUCAAAU
-------...(((((.(((.....((((...)))).))).))))).(((((((..(.(((.((((((.(((((....))))).)))))).....)))...)..)))))))......... ( -32.50)
>DroYak_CAF1 62502 119 - 1
AAACGGAAACGGAAACGGGCCAAGUCUCGACGAGAAUCCAUUUCCAUGUGCCUGGGAGCUCCCCGUGGGAUUGCCUGCAAUUGUGCGGGGAUAAAGAAAACAGAAGCAUAAAAUCAAAU
....(((((((....))((.....((((...))))..)).))))).((((((((....(((((((((.(((((....))))).))))))))....)....)))..)))))......... ( -37.30)
>consensus
_______AACGGAAACGGGCCAAGUCUCGACGAGAAUCCAUUUCCAUGUGCUUUGGA_CUCCCUGUGGGAUUGCCUGCAAUUGUGCGGGGAAAAAGAAAACAGAAGCAUAAAAUCAAAU
..........(((((.(((.....((((...)))).))).))))).((((((((.....((((((((.(((((....))))).))))))))...........))))))))......... (-27.47 = -28.55 +   1.08)

alignment

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secondary structure

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dotplot

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Window 4

Location 20,663,989 – 20,664,085
Length 96
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 83.93
Mean single sequence MFE -28.32
Consensus MFE -17.38
Energy contribution -17.62
Covariance contribution 0.24
Combinations/Pair 1.06
Mean z-score -1.87
Structure conservation index 0.61
SVM decision value -0.03
SVM RNA-class probability 0.517956
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20663989 96 - 22224390
AAGUACAUCAUGA-GGGAAGUACCC-AC-AAUCCAAAUA--------UGGCCAAGAUGGCGGUGGUUAGCAGGA------------AACGGAAACGGGCCAAGUCUCGACGAAAAUCCA
..((.((((.((.-(((.....)))-.)-).........--------..(((.....))))))).......((.------------..((....))..))........))......... ( -20.60)
>DroSec_CAF1 65665 97 - 1
AAGUACAUCAAGAAGAGAAGUACCC-AC-AAUCCAAAUA--------UGGCCAAGAUGGCGAUGGUUGGCAGGA------------AGCGGAAACGGGCCAAGUCUCGACGAGAAUCCA
.......((..(..((((....(((-.(-...((((.((--------(.(((.....))).))).))))...).------------...(....)))).....))))..)..))..... ( -24.40)
>DroSim_CAF1 43123 97 - 1
AAGUACAUCAAGAAGGGAAGUACCC-UC-AAUCCAAAUA--------UGGCCAAGAUGGCGAUGGUUGGCAGGA------------AGCGGAAACGGGCCAAGUCUCGACGAGAAUCCA
...........((.(((.....)))-))-...((((.((--------(.(((.....))).))).))))..(((------------..((....)).......((((...)))).))). ( -24.80)
>DroEre_CAF1 61256 106 - 1
AAGUACAUCAAGA-GGGGAAUACCCCCCAAAAGCAAAUAUGGCGAGAUGGCCAAGAUGGCGAUGGUUGGCAGGA------------AACGGAAACGGGCCAAGUCUCGACGAGAAUCCA
..((.((((....-((((......))))...........((((......)))).)))).(((.(.(((((.(..------------..)(....)..))))).).)))))......... ( -33.40)
>DroYak_CAF1 62581 109 - 1
AAGUACUUGAAGA-GGGAAGUAUCC-CCAAAUCCAAGCA--------UGGCCAAGAUGGCUAUGGUUGGCAGGAAACUGAAACGGAAACGGAAACGGGCCAAGUCUCGACGAGAAUCCA
.....((((..((-((((....)))-).....((((.((--------(((((.....))))))).))))(((....)))....((...((....))..)).....))..))))...... ( -38.40)
>consensus
AAGUACAUCAAGA_GGGAAGUACCC_AC_AAUCCAAAUA________UGGCCAAGAUGGCGAUGGUUGGCAGGA____________AACGGAAACGGGCCAAGUCUCGACGAGAAUCCA
...............(((.............................(((((......((........))..................((....)))))))..((((...)))).))). (-17.38 = -17.62 +   0.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:00:55 2006