Locus 5955

Sequence ID 2R_DroMel_CAF1
Location 18,771,188 – 18,771,304
Length 116
Max. P 0.809775
window9553 window9554

overview

Window 3

Location 18,771,188 – 18,771,284
Length 96
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 80.89
Mean single sequence MFE -25.02
Consensus MFE -21.10
Energy contribution -20.77
Covariance contribution -0.33
Combinations/Pair 1.22
Mean z-score -1.60
Structure conservation index 0.84
SVM decision value 0.64
SVM RNA-class probability 0.809775
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18771188 96 - 20766785
AAAGCGACUUUGCAACAGUUGUAAAAAUGCAGCUAAAUUCAAAUUUGACAUGCAGCAGAGUCCAGAGACUUGCAGCCAAA-GUUGGCGGUGGCGGUG------------------
...((.(((.((((..(((((((....)))))))....(((....)))..))))(((.((((....))))))).((((..-..))))))).))....------------------ ( -27.00)
>DroSec_CAF1 133717 90 - 1
AAAGCGACUUUGCAACAGUUGUAAAAAUCCAGCUAAAUUCAAAUUUGACAUGCAGCAGAGUCCAGAGACUUGCAGCCAAA-GUUGGCG------GUG------------------
...(.((((((((...(((((........)))))....(((....)))......)))))))))........((.((((..-..)))).------)).------------------ ( -21.40)
>DroSim_CAF1 136103 90 - 1
AAAGCGACUUUGCAACAGUUGUAAAAAUGCAGCUAAAUUCAAAUUUGACAUGCAGCAGAGUCCAGAGACUUGCAGCCAAA-GUUGGCG------GUG------------------
...(.((((((((...(((((((....)))))))....(((....)))......)))))))))........((.((((..-..)))).------)).------------------ ( -24.20)
>DroEre_CAF1 135668 84 - 1
AA---GACUUUGCAACAGUUGUAAAAAUGCAGCUAAAUUCAAAUUUGACAUGCAGCAGAGUCG---GACUUGCAGCCCAA-GUUGGCG------GUG------------------
..---((((((((...(((((((....)))))))....(((....)))......)))))))).---.....((.(((...-...))).------)).------------------ ( -23.30)
>DroYak_CAF1 136796 105 - 1
AAAGCGACUUUGCAACAGUUGUAAAAAUGCAGCUAAAUUCAAAUUUGACAUGCAGCAGCGUCC---GACUUGCAGCCGAA-GUUGGCG------GUGGCGAUGAAGUUGGAGGUG
.........(((((..(((((((....)))))))....(((....)))..)))))..((.(((---(((((...((((..-(....).------.))))....)))))))).)). ( -30.00)
>DroAna_CAF1 134008 93 - 1
AAAGAGACUUUGCAACAGUUGUAAAAAUGCAGCUAAAUUCAAAUUUGACAUGCAGCGAAGUCA---GAGUUGCCCGCGGAGGCUGAGG-CUGAGACA------------------
.....((((((((...(((((((....)))))))....(((....)))......)))))))).---..(((((((((....)).).))-)...))).------------------ ( -24.20)
>consensus
AAAGCGACUUUGCAACAGUUGUAAAAAUGCAGCUAAAUUCAAAUUUGACAUGCAGCAGAGUCC___GACUUGCAGCCAAA_GUUGGCG______GUG__________________
.....((((((((...(((((((....)))))))....(((....)))......))))))))............(((((...)))))............................ (-21.10 = -20.77 +  -0.33)

alignment

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secondary structure

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dotplot

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Window 4

Location 18,771,209 – 18,771,304
Length 95
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 80.89
Mean single sequence MFE -22.37
Consensus MFE -16.86
Energy contribution -16.92
Covariance contribution 0.06
Combinations/Pair 1.11
Mean z-score -1.32
Structure conservation index 0.75
SVM decision value 0.23
SVM RNA-class probability 0.643047
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18771209 95 - 20766785
--CAACCGAAG----------------ACUGGGAACUGAAAGCGACUUUGCAACAGUUGUAAAAAUGCAGCUAAAUUCAAAUUUGACAUGCAGCAGAGUCCAGAGACUUGCAG
--...(((...----------------..)))...(((.((((((((((((...(((((((....)))))))....(((....)))......))))))))....).))).))) ( -20.80)
>DroSec_CAF1 133732 95 - 1
--CAACCGAAG----------------ACUGGGAACUGAAAGCGACUUUGCAACAGUUGUAAAAAUCCAGCUAAAUUCAAAUUUGACAUGCAGCAGAGUCCAGAGACUUGCAG
--...(((...----------------..)))...(((.((((((((((((...(((((........)))))....(((....)))......))))))))....).))).))) ( -18.00)
>DroSim_CAF1 136118 95 - 1
--CAACCGAAG----------------ACUGGGAACUGAAAGCGACUUUGCAACAGUUGUAAAAAUGCAGCUAAAUUCAAAUUUGACAUGCAGCAGAGUCCAGAGACUUGCAG
--...(((...----------------..)))...(((.((((((((((((...(((((((....)))))))....(((....)))......))))))))....).))).))) ( -20.80)
>DroEre_CAF1 135683 87 - 1
--GAGCUGGAGC-----------------UGG-AGCUGAA---GACUUUGCAACAGUUGUAAAAAUGCAGCUAAAUUCAAAUUUGACAUGCAGCAGAGUCG---GACUUGCAG
--..((.(((((-----------------...-.)))...---((((((((...(((((((....)))))))....(((....)))......)))))))).---..)).)).. ( -24.20)
>DroYak_CAF1 136829 110 - 1
GAGAGCUGAAGACUGAGCAACUGGGAAACUGGCAACUGAAAGCGACUUUGCAACAGUUGUAAAAAUGCAGCUAAAUUCAAAUUUGACAUGCAGCAGCGUCC---GACUUGCAG
................((((.(.(((..((((((((((...(((....)))..))))))).....((((..(((((....)))))...)))).)))..)))---.).)))).. ( -27.70)
>DroAna_CAF1 134029 84 - 1
--AAGCUCA------------------------AGUUGAAAGAGACUUUGCAACAGUUGUAAAAAUGCAGCUAAAUUCAAAUUUGACAUGCAGCGAAGUCA---GAGUUGCCC
--.(((((.------------------------..((....))((((((((...(((((((....)))))))....(((....)))......)))))))).---))))).... ( -22.70)
>consensus
__CAACCGAAG________________ACUGGGAACUGAAAGCGACUUUGCAACAGUUGUAAAAAUGCAGCUAAAUUCAAAUUUGACAUGCAGCAGAGUCC___GACUUGCAG
...........................................((((((((...(((((((....)))))))....(((....)))......))))))))............. (-16.86 = -16.92 +   0.06)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:58:58 2006