Locus 6724

Sequence ID 2L_DroMel_CAF1
Location 18,779,654 – 18,779,793
Length 139
Max. P 0.852647
window10735 window10736

overview

Window 5

Location 18,779,654 – 18,779,764
Length 110
Sequences 5
Columns 110
Reading direction reverse
Mean pairwise identity 83.76
Mean single sequence MFE -29.37
Consensus MFE -21.54
Energy contribution -21.90
Covariance contribution 0.36
Combinations/Pair 1.04
Mean z-score -2.03
Structure conservation index 0.73
SVM decision value 0.79
SVM RNA-class probability 0.852647
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18779654 110 - 22407834
AGGUUGAAUUUUGGGGGAAAAUUCAAGAGAGGUGGGAAAUUCAAGGCGGGUGGUGGUUGUGAAAAAGCCCACUGAGCUAACGAAGCCACAAUCCCCAAACCAAAAGCCGA
.((((....((((((((....(((....)))((((....(((..(((.(((((.(.((......)).))))))..)))...))).))))..)))))))).....)))).. ( -33.60)
>DroSec_CAF1 42630 96 - 1
AGGUUGAAUUUUGGGGGAAAAUUCAAGGGAGGUG--------------GGUGCUGGUUGUGAAAAAGCCCACUGAGCUAACGAAGCCACAAUCCCCAAACCAAAAGCCGA
.((((....((((((((....(((...((.((((--------------(((...............)))))))...))...))).......)))))))).....)))).. ( -27.96)
>DroSim_CAF1 41311 96 - 1
AGGUUGAAUUUUGGGGGAAAAUUCAAGAGAGGUG--------------GGUGCGGGUUGUGAAAAAGCCCACUGAGCUAACGAAGCCACAAUCCCCAUACCAAAAGCCAA
.((((........(((((...(((....)))(((--------------(....(((((.......))))).((...(....).))))))..)))))........)))).. ( -27.59)
>DroEre_CAF1 43490 96 - 1
AGGUUGAAUUUGGGGGAAAAAUUCUUAGG-------------AGGG-GUGUGCUGGUUGUGAAAAAGCCCACUGAGCUAACGAAGCCACAAUCCCCAAACCAAAAGCCGA
.((((...((((((((........((((.-------------..((-((.(((.....))).....)))).))))(((.....))).....)))))))).....)))).. ( -26.20)
>DroYak_CAF1 43655 108 - 1
AGGUUGAAUUUGGGGGAAAAAUUCAGAGGGAGUGGGAAAUUCAAGG-GGGUGCUGGUUGUGAA-AAGCCCACUGAGCUAUCGAAGCCACAAUCCCCAAACCAAAAGCCGA
.((((((((((.......))))))...((((((.....))))..((-((((..(((((.(((.-.(((.......))).))).)))))..))))))...))...)))).. ( -31.50)
>consensus
AGGUUGAAUUUUGGGGGAAAAUUCAAGGGAGGUG________A_GG_GGGUGCUGGUUGUGAAAAAGCCCACUGAGCUAACGAAGCCACAAUCCCCAAACCAAAAGCCGA
.((((....((((((((................................(((..((((.......)))))))((.(((.....)))))...)))))))).....)))).. (-21.54 = -21.90 +   0.36)

alignment

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secondary structure

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dotplot

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Window 6

Location 18,779,694 – 18,779,793
Length 99
Sequences 6
Columns 99
Reading direction forward
Mean pairwise identity 75.60
Mean single sequence MFE -14.09
Consensus MFE -9.12
Energy contribution -9.57
Covariance contribution 0.45
Combinations/Pair 1.11
Mean z-score -1.12
Structure conservation index 0.65
SVM decision value -0.05
SVM RNA-class probability 0.509168
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18779694 99 + 22407834
GGGCUUUUUCACAACCACCACCCGCCUUGAAUUUCCCACCUCUCUUGAAUUUUCCCCCAAAAUUCAACCUGCGUCUGUUCCAAAGCGUGCGCAAUAAGC
(((....((((................))))...))).......(((((((((.....)))))))))..(((((.(((......))).)))))...... ( -17.09)
>DroSec_CAF1 42670 85 + 1
GGGCUUUUUCACAACCAGCACC--------------CACCUCCCUUGAAUUUUCCCCCAAAAUUCAACCUGCGUCUGUUCCAAAGCGUGCGCAAUAAGC
(((((...........))).))--------------........(((((((((.....)))))))))..(((((.(((......))).)))))...... ( -15.50)
>DroSim_CAF1 41351 85 + 1
GGGCUUUUUCACAACCCGCACC--------------CACCUCUCUUGAAUUUUCCCCCAAAAUUCAACCUGCGUCUGUUCCAAAGCGUGCGCAAUAAGC
(((...........)))((...--------------........(((((((((.....)))))))))..(((((.(((......))).)))))....)) ( -16.70)
>DroEre_CAF1 43530 85 + 1
GGGCUUUUUCACAACCAGCACAC-CCCU-------------CCUAAGAAUUUUUCCCCCAAAUUCAACCUGCGUCUGUUCCAAAGCGUGCGCAAUAAGC
(((((...........)))....-....-------------.....((((((.......))))))..))(((((.(((......))).)))))...... ( -12.90)
>DroYak_CAF1 43695 97 + 1
GGGCUU-UUCACAACCAGCACCC-CCUUGAAUUUCCCACUCCCUCUGAAUUUUUCCCCCAAAUUCAACCUGCGUCUGUUCCAAAGCUUGCGCAAUAAGC
(((...-((((............-...))))...)))........(((((((.......)))))))...(((((..((......))..)))))...... ( -15.46)
>DroPer_CAF1 53430 80 + 1
GGGCUUU-UCUC---------UC-CCUU--------CCUCUCUCUCGCUUCCCCCCCCCAGCACCCACCGACGUCUGUUCCAAAGCGUGCGCAAUAAGC
(((....-....---------.)-))..--------..........(((..........))).......(.(((.(((......))).))))....... (  -6.90)
>consensus
GGGCUUUUUCACAACCAGCACCC_CCUU________CACCUCCCUUGAAUUUUCCCCCAAAAUUCAACCUGCGUCUGUUCCAAAGCGUGCGCAAUAAGC
..((((........................................((((((.......))))))....(((((.(((......))).)))))..)))) ( -9.12 =  -9.57 +   0.45)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:18:27 2006