Locus 9311

Sequence ID 3R_DroMel_CAF1
Location 24,778,966 – 24,779,078
Length 112
Max. P 0.979713
window14884 window14885

overview

Window 4

Location 24,778,966 – 24,779,078
Length 112
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 74.37
Mean single sequence MFE -28.18
Consensus MFE -13.40
Energy contribution -13.80
Covariance contribution 0.40
Combinations/Pair 1.18
Mean z-score -1.76
Structure conservation index 0.48
SVM decision value 0.14
SVM RNA-class probability 0.603506
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24778966 112 + 27905053
GCGGGCCAAAAGGGGU----AAAUUGGUAGAAAGUUGGCAGACAUCCUUGAAUUUCCAUGCAAUUUUGGUAUUCCUUUUUUUCAUUUCACACCAGG----UUUUCCCUUUGGCAAAGAUU
....((((((.((((.----...(((((.(((((((....)))......((((..(((........))).))))..........))))..))))).----...))))))))))....... ( -26.90)
>DroSec_CAF1 10070 101 + 1
GCGGGCCAAAAGGGGUAAGUAAAUUGGCAGAAAGUUGGCAGACUUCCUUGAAUUUGGAUGCAAUU---------------UUCACUUCACACCUAC----UUUUCCUUUUGGCUGAGAUU
...((((((((((((.(((((...(((..((((((((.((....(((........))))))))))---------------)))...)))....)))----))))))))))))))...... ( -30.50)
>DroSim_CAF1 5446 101 + 1
GCGGGCCAAAAGGGGUAAGUAAAUUGGCAGAAAGUUGGCAGACUUCCUUGAAUUUGGAUGCAAUU---------------UUCACUUCACACCUAC----UUUUCCUUUUGGCUGAGUUU
...((((((((((((.(((((...(((..((((((((.((....(((........))))))))))---------------)))...)))....)))----))))))))))))))...... ( -30.50)
>DroEre_CAF1 19044 95 + 1
GCGGGCCAAAAGGGGU----AAAUUUGGAGAAAGUUGGCAGACGUCCUUGAAUUUGCAUGGAA---------------------AUUCCUGCACUCCUUCUUUUCCAUUUGGCUGAGAUU
...(((((((.((((.----......((((......(((....)))........((((.((..---------------------...)))))))))).....)))).)))))))...... ( -25.90)
>DroYak_CAF1 10624 107 + 1
UCGAGCCAAAAGGGUU----AAAUUGGCAGAAAGUUGGCAGAGUUCCCUGAAUUUCCAUGCAU---------UUCUUAUUUUCAUUUUAUACCUGCUUUUUUUUCCUUUUGGCUAAGAUU
...(((((((((((..----(((..(((((...(((((..((((((...))))))))).))..---------....(((.........))).)))))..))).)))))))))))...... ( -27.10)
>consensus
GCGGGCCAAAAGGGGU____AAAUUGGCAGAAAGUUGGCAGACUUCCUUGAAUUUGCAUGCAAUU_______________UUCACUUCACACCUAC____UUUUCCUUUUGGCUGAGAUU
...(((((((((((.........(..((.....))..)(((......))).....................................................)))))))))))...... (-13.40 = -13.80 +   0.40)

alignment

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secondary structure

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dotplot

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Window 5

Location 24,778,966 – 24,779,078
Length 112
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 74.37
Mean single sequence MFE -24.88
Consensus MFE -15.52
Energy contribution -16.60
Covariance contribution 1.08
Combinations/Pair 1.18
Mean z-score -2.11
Structure conservation index 0.62
SVM decision value 1.84
SVM RNA-class probability 0.979713
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24778966 112 - 27905053
AAUCUUUGCCAAAGGGAAAA----CCUGGUGUGAAAUGAAAAAAAGGAAUACCAAAAUUGCAUGGAAAUUCAAGGAUGUCUGCCAACUUUCUACCAAUUU----ACCCCUUUUGGCCCGC
.......(((((((((....----..((((((................))))))((((((..((((((.....((....))......)))))).))))))----...))))))))).... ( -24.89)
>DroSec_CAF1 10070 101 - 1
AAUCUCAGCCAAAAGGAAAA----GUAGGUGUGAAGUGAA---------------AAUUGCAUCCAAAUUCAAGGAAGUCUGCCAACUUUCUGCCAAUUUACUUACCCCUUUUGGCCCGC
.......(((((((((..((----(((((((..(......---------------..)..))))........(((((((......))))))).......)))))...))))))))).... ( -27.30)
>DroSim_CAF1 5446 101 - 1
AAACUCAGCCAAAAGGAAAA----GUAGGUGUGAAGUGAA---------------AAUUGCAUCCAAAUUCAAGGAAGUCUGCCAACUUUCUGCCAAUUUACUUACCCCUUUUGGCCCGC
.......(((((((((..((----(((((((..(......---------------..)..))))........(((((((......))))))).......)))))...))))))))).... ( -27.30)
>DroEre_CAF1 19044 95 - 1
AAUCUCAGCCAAAUGGAAAAGAAGGAGUGCAGGAAU---------------------UUCCAUGCAAAUUCAAGGACGUCUGCCAACUUUCUCCAAAUUU----ACCCCUUUUGGCCCGC
.......((((((.((.(((...((((.(((((...---------------------.(((.((......)).)))..))))).......))))...)))----.))...)))))).... ( -22.10)
>DroYak_CAF1 10624 107 - 1
AAUCUUAGCCAAAAGGAAAAAAAAGCAGGUAUAAAAUGAAAAUAAGAA---------AUGCAUGGAAAUUCAGGGAACUCUGCCAACUUUCUGCCAAUUU----AACCCUUUUGGCUCGA
......((((((((((........((((((((...((....)).....---------)))).(((.....((((....))))))).....))))......----...))))))))))... ( -22.83)
>consensus
AAUCUCAGCCAAAAGGAAAA____GCAGGUGUGAAAUGAA_______________AAUUGCAUGCAAAUUCAAGGAAGUCUGCCAACUUUCUGCCAAUUU____ACCCCUUUUGGCCCGC
.......(((((((((...........(((((((.......................))))))).(((((..(((((((......)))))))...))))).......))))))))).... (-15.52 = -16.60 +   1.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:31:17 2006