Locus 232

Sequence ID 3L_DroMel_CAF1
Location 635,866 – 635,966
Length 100
Max. P 0.999880
window344 window345

overview

Window 4

Location 635,866 – 635,966
Length 100
Sequences 4
Columns 106
Reading direction forward
Mean pairwise identity 64.83
Mean single sequence MFE -26.59
Consensus MFE -11.10
Energy contribution -13.48
Covariance contribution 2.37
Combinations/Pair 1.13
Mean z-score -3.54
Structure conservation index 0.42
SVM decision value 2.62
SVM RNA-class probability 0.995786
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 635866 100 + 23771897
ACUAAAACUAAAUUCCCCGACUUUCAAGGAGAGCUAUAAUUAUUAGCUUUAAGAUUGAAGCUCUCUUUUAUGCCCGGAAUUAGGUUCUAGUG------UUUCCCAA
((((.((((.((((((.........((((((((((.(((((...........))))).)))))))))).......)))))).)))).)))).------........ ( -26.09)
>DroSec_CAF1 3202 83 + 1
ACUAAAACCAAAUUCCUAGACUUUCAAGGAGAGCUAUC-------------AGAUU--AGCUCUCUUCUAUGCCCGGAAUUUGGUUCUAGUG--------UCCCAA
((((.(((((((((((..(.(.....((((((((((..-------------....)--)))))))))....))..))))))))))).)))).--------...... ( -31.80)
>DroEre_CAF1 6010 104 + 1
GCUAAAACCAAAUUCAUCAGCAUUAAAGGAGAG-CAUCA-GAUGCAUUUCAAGUUCGAAGCUCUUUUUUAUGCCUAGAAUUAGGUUCUAAGGUGGUAGCAUCCCAG
((((..(((..........((((.(((((((((-(.((.-.((.........))..)).)))))))))))))).((((((...)))))).)))..))))....... ( -29.90)
>DroYak_CAF1 3401 87 + 1
GCUUAAACCAAAUUCUUGCACUUUUAAGGAUAGCCAUCA-GAU------------------UCCCUUUUAUGCAUAGAAUUAGGUUCUAAGAUGGUAGUGGCCCAA
.((((((((.((((((((((.....((((..........-...------------------..))))...)))).)))))).)))).))))..(((....)))... ( -18.56)
>consensus
ACUAAAACCAAAUUCCUCGACUUUCAAGGAGAGCCAUCA_GAU________AGAUU__AGCUCUCUUUUAUGCCCAGAAUUAGGUUCUAAGG______U_UCCCAA
((((.((((.((((((.........(((((((((.........................))))))))).......)))))).)))).))))............... (-11.10 = -13.48 +   2.37)

alignment

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secondary structure

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dotplot

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Window 5

Location 635,866 – 635,966
Length 100
Sequences 4
Columns 106
Reading direction reverse
Mean pairwise identity 64.83
Mean single sequence MFE -28.33
Consensus MFE -15.19
Energy contribution -15.75
Covariance contribution 0.56
Combinations/Pair 1.31
Mean z-score -3.53
Structure conservation index 0.54
SVM decision value 4.36
SVM RNA-class probability 0.999880
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 635866 100 - 23771897
UUGGGAAA------CACUAGAACCUAAUUCCGGGCAUAAAAGAGAGCUUCAAUCUUAAAGCUAAUAAUUAUAGCUCUCCUUGAAAGUCGGGGAAUUUAGUUUUAGU
...(....------)((((((((..((((((.(((...((.(((((((..(((.............)))..))))))).))....)))..))))))..)))))))) ( -26.72)
>DroSec_CAF1 3202 83 - 1
UUGGGA--------CACUAGAACCAAAUUCCGGGCAUAGAAGAGAGCU--AAUCU-------------GAUAGCUCUCCUUGAAAGUCUAGGAAUUUGGUUUUAGU
......--------.((((((((((((((((((((...((.(((((((--(....-------------..)))))))).))....)))).)))))))))))))))) ( -37.60)
>DroEre_CAF1 6010 104 - 1
CUGGGAUGCUACCACCUUAGAACCUAAUUCUAGGCAUAAAAAAGAGCUUCGAACUUGAAAUGCAUC-UGAUG-CUCUCCUUUAAUGCUGAUGAAUUUGGUUUUAGC
.(((.......)))..((((((((.(((((..((((((((..(((((.(((....((.....))..-))).)-))))..))).)))))...))))).)))))))). ( -27.90)
>DroYak_CAF1 3401 87 - 1
UUGGGCCACUACCAUCUUAGAACCUAAUUCUAUGCAUAAAAGGGA------------------AUC-UGAUGGCUAUCCUUAAAAGUGCAAGAAUUUGGUUUAAGC
.(((.......))).((((((.((.((((((.(((((..((((((------------------..(-....)..).)))))....))))))))))).)))))))). ( -21.10)
>consensus
UUGGGA_A______CACUAGAACCUAAUUCCAGGCAUAAAAGAGAGCU__AAUCU________AUC_UGAUAGCUCUCCUUGAAAGUCGAGGAAUUUGGUUUUAGC
................((((((((.((((((.(((...((.(((((((.......................))))))).))....)))..)))))).)))))))). (-15.19 = -15.75 +   0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:36:58 2006