Locus 3235

Sequence ID 2L_DroMel_CAF1
Location 9,293,883 – 9,294,012
Length 129
Max. P 0.882763
window5139 window5140

overview

Window 9

Location 9,293,883 – 9,293,974
Length 91
Sequences 6
Columns 105
Reading direction forward
Mean pairwise identity 78.75
Mean single sequence MFE -24.03
Consensus MFE -14.60
Energy contribution -14.33
Covariance contribution -0.27
Combinations/Pair 1.41
Mean z-score -1.73
Structure conservation index 0.61
SVM decision value 0.48
SVM RNA-class probability 0.751024
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9293883 91 + 22407834
---AAUGAAAUGGUUUAGUGAAGUAUAAUCA-AAAGGCUUGAAGACUGGUAAUGAC----------CUGACACCAUUGCCAGGCUUCACAGACCGGUCGAAUGCC
---..(((..((((((.(((((((....(((-(.....))))...(((((((((..----------.......)))))))))))))))))))))).)))...... ( -29.40)
>DroSec_CAF1 123622 91 + 1
---AAUGAAAUGGUUUAGUAAAGUAUAAUCA-AAAGGCUUGAAGACUGGCAAUGAC----------CUAACACCAUUGUCAUGCUUCACAGACCGGUCGAAUGCC
---..(((..((((((.((.((((((..(((-(.....)))).....(((((((..----------.......))))))))))))).)))))))).)))...... ( -20.20)
>DroSim_CAF1 126331 91 + 1
---AAUGAAAUGGUUUAGUGAAGUAUAAUCA-AAAGGCUUGAAGACUGGCAAUGAC----------CUAACACAAUUGCCAUGCUUCACAGAUCGGUCGAAUGUC
---..(((..((((((.(((((((((..(((-(.....)))).....((((((...----------........))))))))))))))))))))).)))...... ( -24.10)
>DroEre_CAF1 133767 91 + 1
---AAUGAAAUGAUUUAGUGAAGUAUAAUCA-AAAGGCUUGAAGGCUGGCCAUGAC----------CUAACAGCAUUGCCAGGCUUCACAGACAGGUGGAACGCC
---..............(((((((....(((-(.....))))...(((((.(((.(----------......)))).)))))))))))).....((((...)))) ( -22.40)
>DroYak_CAF1 131535 91 + 1
---AAUGAAAUGAUUUAGUGAAGUAUAAUCA-AAAGGCUUGAAGGCUGGCCAUGAC----------CUAGCAGCGUUGCCAGACUUCACAGACAGGUGGAACGCC
---..............(((((((....(((-(.....))))...(((((.(((.(----------......)))).)))))))))))).....((((...)))) ( -21.50)
>DroPer_CAF1 146463 97 + 1
GACGAUGAAAU-----AACG--AUAUAAUCAAAAAGGCCCGAGGGCUGUCAAUGACUCGCUGCAAUCCAGCGACAUUGCCAGACCUCACAGACAGGA-GACCGUU
((((.......-----....--..................((((.(((.(((((..((((((.....))))))))))).))).)))).......(..-..))))) ( -26.60)
>consensus
___AAUGAAAUGGUUUAGUGAAGUAUAAUCA_AAAGGCUUGAAGACUGGCAAUGAC__________CUAACACCAUUGCCAGGCUUCACAGACAGGUCGAACGCC
...................................(((..((((.(((((((((...................))))))))).)))).......(......)))) (-14.60 = -14.33 +  -0.27)

alignment

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secondary structure

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dotplot

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Window 0

Location 9,293,917 – 9,294,012
Length 95
Sequences 6
Columns 105
Reading direction forward
Mean pairwise identity 77.02
Mean single sequence MFE -30.77
Consensus MFE -18.67
Energy contribution -19.39
Covariance contribution 0.73
Combinations/Pair 1.33
Mean z-score -1.84
Structure conservation index 0.61
SVM decision value 0.92
SVM RNA-class probability 0.882763
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9293917 95 + 22407834
UUGAAGACUGGUAAUGAC----------CUGACACCAUUGCCAGGCUUCACAGACCGGUCGAAUGCCAUUGGAUGUGAAACAAUCAGUGUGGCCAGACCUCACUU
.(((((.(((((((((..----------.......))))))))).)))))......((((....(((((..(((........)))...)))))..))))...... ( -33.30)
>DroSec_CAF1 123656 95 + 1
UUGAAGACUGGCAAUGAC----------CUAACACCAUUGUCAUGCUUCACAGACCGGUCGAAUGCCAUUGGAUGUGAAACAAUCAGUGUGGCCAGACCUCACUU
.(((((..((((((((..----------.......))))))))..)))))......((((....(((((..(((........)))...)))))..))))...... ( -29.50)
>DroSim_CAF1 126365 95 + 1
UUGAAGACUGGCAAUGAC----------CUAACACAAUUGCCAUGCUUCACAGAUCGGUCGAAUGUCAUUGGAUGUGAAACAAUCAGUGUGGCCAGACCUCACUU
.(((((..(((((((...----------........)))))))..)))))......((((....(((((..(((........)))...)))))..))))...... ( -27.10)
>DroEre_CAF1 133801 95 + 1
UUGAAGGCUGGCCAUGAC----------CUAACAGCAUUGCCAGGCUUCACAGACAGGUGGAACGCCAUGGGAUGUGAAACAAUCAGUGUGCCCAGACCUCACUU
.(((.((((((((((((.----------......(((((.(((((((((((......)))))..))).)))))))).......))).)).).)))).)))))... ( -28.14)
>DroYak_CAF1 131569 95 + 1
UUGAAGGCUGGCCAUGAC----------CUAGCAGCGUUGCCAGACUUCACAGACAGGUGGAACGCCAUGGGAUGAGAAACAAUCAGUGUGGCCAGAGCCCACUU
.....((((((((((..(----------(((...(((((.(((..((........)).))))))))..)))).(((.......)))..))))))..))))..... ( -30.10)
>DroPer_CAF1 146494 98 + 1
CCGAGGGCUGUCAAUGACUCGCUGCAAUCCAGCGACAUUGCCAGACCUCACAGACAGGA-GACCGUUGUGGCAUAGGGAACAU---GUCUGGCAUCAGCG---CU
...((.((((..((((..((((((.....))))))))))(((((((.((((((.(.(..-..).)))))))....(....)..---)))))))..)))).---)) ( -36.50)
>consensus
UUGAAGACUGGCAAUGAC__________CUAACACCAUUGCCAGGCUUCACAGACAGGUCGAACGCCAUGGGAUGUGAAACAAUCAGUGUGGCCAGACCUCACUU
..((((.(((((((((...................))))))))).))))...............(((((..(((........)))...)))))............ (-18.67 = -19.39 +   0.73)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:47:39 2006