Locus 2821

Sequence ID X_DroMel_CAF1
Location 7,548,808 – 7,548,910
Length 102
Max. P 0.993500
window4631 window4632

overview

Window 1

Location 7,548,808 – 7,548,910
Length 102
Sequences 4
Columns 116
Reading direction forward
Mean pairwise identity 81.33
Mean single sequence MFE -25.68
Consensus MFE -17.01
Energy contribution -16.82
Covariance contribution -0.19
Combinations/Pair 1.05
Mean z-score -1.97
Structure conservation index 0.66
SVM decision value 0.68
SVM RNA-class probability 0.819316
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7548808 102 + 22224390
CCUCCC-----CACCCAUUACCCCAACCCCC-UUUCAACACACACUC----ACACA----CACACACCGCGCUCGUGUGUAGAUUUGUGUGCGCAUGUAAGGGUAACAGGCCAACG
......-----..((..((((((..((....-......((((((.((----(((((----(.............)))))).))..)))))).....))..))))))..))...... ( -21.58)
>DroSec_CAF1 41485 110 + 1
AGCGCG-----CACCCAUUACCCCAACUCCC-UUUCCAAACACACUCCUCUGCACAGCGGCACACACCGCGCACGUGUGUAGAUUUGUGUGCGCAUGUAAGGGUAACAGGCCAACG
......-----..........((.....(((-((......(((((...((((((((((((......)))).....))))))))...))))).......))))).....))...... ( -29.82)
>DroEre_CAF1 52625 95 + 1
CCUCCC-----CGCCCAUUGCCCCAACCCCCGUCUCCACAAA------------CA----CACACACCACGCUCGUGUGUAGAUUUGUGUGUGCAUGUAAGGGUAACAGGCCAACG
......-----.(((..((((((..((....))....(((..------------((----(((((((.((((....)))).)...))))))))..)))..))))))..)))..... ( -26.50)
>DroYak_CAF1 42441 101 + 1
CCUCCCCUACCCACCCAUUACCCCAACCCCC-UCUCCACACACA----------CA----CACACACCACGCUCGUGUGUAGAUUUGUGUGUGCAUGUAAGGGUAACAGGCCAACG
.............((..((((((..((....-....((((((((----------..----(((((((.......)))))).)...))))))))...))..))))))..))...... ( -24.80)
>consensus
CCUCCC_____CACCCAUUACCCCAACCCCC_UCUCCACACACA__________CA____CACACACCACGCUCGUGUGUAGAUUUGUGUGCGCAUGUAAGGGUAACAGGCCAACG
.............((..((((((..((..................................((((((.......))))))......(((....)))))..))))))..))...... (-17.01 = -16.82 +  -0.19)

alignment

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secondary structure

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dotplot

Postscript

Window 2

Location 7,548,808 – 7,548,910
Length 102
Sequences 4
Columns 116
Reading direction reverse
Mean pairwise identity 81.33
Mean single sequence MFE -41.00
Consensus MFE -29.66
Energy contribution -30.73
Covariance contribution 1.06
Combinations/Pair 1.07
Mean z-score -2.74
Structure conservation index 0.72
SVM decision value 2.40
SVM RNA-class probability 0.993500
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7548808 102 - 22224390
CGUUGGCCUGUUACCCUUACAUGCGCACACAAAUCUACACACGAGCGCGGUGUGUG----UGUGU----GAGUGUGUGUUGAAA-GGGGGUUGGGGUAAUGGGUG-----GGGAGG
..((.((((((((((((.((..((((((((..((.((((((((.......))))))----)).))----..)))))))).....-....)).)))))))))))).-----)).... ( -40.80)
>DroSec_CAF1 41485 110 - 1
CGUUGGCCUGUUACCCUUACAUGCGCACACAAAUCUACACACGUGCGCGGUGUGUGCCGCUGUGCAGAGGAGUGUGUUUGGAAA-GGGAGUUGGGGUAAUGGGUG-----CGCGCU
(((..((((((((((((.((....((((((...(((.((((((.((((.....)))))).)))).)))...))))))((....)-)...)).)))))))))))).-----.))).. ( -43.20)
>DroEre_CAF1 52625 95 - 1
CGUUGGCCUGUUACCCUUACAUGCACACACAAAUCUACACACGAGCGUGGUGUGUG----UG------------UUUGUGGAGACGGGGGUUGGGGCAAUGGGCG-----GGGAGG
(((((.(((...(((((((((.(((((((((...((((.(....).))))))))))----))------------).)))(....))))))).))).)))))....-----...... ( -38.40)
>DroYak_CAF1 42441 101 - 1
CGUUGGCCUGUUACCCUUACAUGCACACACAAAUCUACACACGAGCGUGGUGUGUG----UG----------UGUGUGUGGAGA-GGGGGUUGGGGUAAUGGGUGGGUAGGGGAGG
..((.((((((((((((((((((((((((((...((((.(....).))))..))))----))----------))))))))....-.......)))))))))))).))......... ( -41.60)
>consensus
CGUUGGCCUGUUACCCUUACAUGCACACACAAAUCUACACACGAGCGCGGUGUGUG____UG__________UGUGUGUGGAAA_GGGGGUUGGGGUAAUGGGUG_____GGGAGG
.....((((((((((((.((.(.((((((((....(((((((.......)))))))................)))))))).).......)).))))))))))))............ (-29.66 = -30.73 +   1.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:44:23 2006