Locus 3505

Sequence ID 2R_DroMel_CAF1
Location 11,742,881 – 11,743,001
Length 120
Max. P 0.851207
window5711 window5712

overview

Window 1

Location 11,742,881 – 11,743,001
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 76.72
Mean single sequence MFE -41.23
Consensus MFE -21.69
Energy contribution -23.42
Covariance contribution 1.73
Combinations/Pair 1.35
Mean z-score -1.98
Structure conservation index 0.53
SVM decision value 0.68
SVM RNA-class probability 0.820028
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11742881 120 + 20766785
UCUUUACAGUACUUUGAAGCUGCCAUGGUCUCGAAGACUUGUGAUCCCGAAAUGACCGUCACGGAGGAUCGGAUAGCAUCCACAGCCAAGUACUUUGGUCCCAGUUGCAAGGCUGGUCCU
...(((((((.((((((..((.....))..)))))))).)))))..(((..((....))..)))(((((.((((...)))).(((((..(((..(((....))).)))..)))))))))) ( -34.10)
>DroVir_CAF1 12518 120 + 1
CUUUUGCAGUAUUUCGAGUCAGCCUUGGUCGCCAAGUCCUGCAAUCCUGAGAUUACUUUAACUGAGGAUCGAAUUGCUGCCUCUGCUAGGUUUUUUGGACCCAGCUGCAAGGCGGGUCCC
.....((((((.((((((.(((.(((((...)))))..))))..((((.((..........)).))))))))).))))))................((((((.(((....))))))))). ( -41.20)
>DroPse_CAF1 5462 120 + 1
AAUUUGCAGUAUUUUGAAGCCGCUUUGGUUUCCAAGACAUGCGAUCCAGAGCUGACGGUCACAGAGGAUCGGAUAGCGGCCUCGUCGAGAUACUUUGGGCCCAGCUGCAAGGCUGGUCCC
.......((((((((((.((((((((((...))))...((.((((((....(((.......))).)))))).))))))))....))))))))))..(((.((((((....)))))).))) ( -47.40)
>DroWil_CAF1 34094 120 + 1
UUUUUUUAGUACUUUGAAGCCACCAUGGUGGCCAAGUCAUGUGAUCCAGAGAUUAGUUUAACUGAAGAUCGCAUUGCUGCCUCAGCGAAAUUCUUUGGACCAAGUUGCAAGGCUGGUCCU
..............(((.(((((....)))))....)))((((((((((..(......)..)))..)))))))((((((...))))))........((((((.(((....))))))))). ( -34.70)
>DroMoj_CAF1 23218 119 + 1
C-UUUGCAGUACUUCGAGUCAACCUUGGUAGCAAAGUCCUGCAAUCCAGAUAUUACAUUAACUGAAGACCGCAUUGCGGCUUCAGCGAGGUAUUUUGGACCCAGCUGCAAAGCUGGUCCU
.-.....(((((((((........((((..(((......)))...))))............((((((.((((...)))))))))))))))))))..(((((.((((....))))))))). ( -42.60)
>DroPer_CAF1 5679 120 + 1
ACUUUGCAGUAUUUUGAAGCCGCUUUGGUUUCCAAGACAUGCGAUCCAGAGCUGACGGUCACAGAGGAUCGGAUAGCGGCCUCGUCGAGAUACUUUGGGCCCAGCUGCAAGGCUGGUCCC
.......((((((((((.((((((((((...))))...((.((((((....(((.......))).)))))).))))))))....))))))))))..(((.((((((....)))))).))) ( -47.40)
>consensus
ACUUUGCAGUACUUUGAAGCCGCCUUGGUCGCCAAGACAUGCGAUCCAGAGAUGACGGUAACUGAGGAUCGGAUAGCGGCCUCAGCGAGAUACUUUGGACCCAGCUGCAAGGCUGGUCCC
.......(((((((((..((((((((((...))))).....((((((..................))))))....))))).....)))))))))..(((((.((((....))))))))). (-21.69 = -23.42 +   1.73)

alignment

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secondary structure

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dotplot

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Window 2

Location 11,742,881 – 11,743,001
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 76.72
Mean single sequence MFE -39.62
Consensus MFE -20.27
Energy contribution -21.75
Covariance contribution 1.48
Combinations/Pair 1.29
Mean z-score -2.08
Structure conservation index 0.51
SVM decision value 0.79
SVM RNA-class probability 0.851207
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11742881 120 - 20766785
AGGACCAGCCUUGCAACUGGGACCAAAGUACUUGGCUGUGGAUGCUAUCCGAUCCUCCGUGACGGUCAUUUCGGGAUCACAAGUCUUCGAGACCAUGGCAGCUUCAAAGUACUGUAAAGA
.((.((((........))))..))..(((((((((((((((((...))))((((((..(((.....)))...))))))....(((.....)))....))))))...)))))))....... ( -35.70)
>DroVir_CAF1 12518 120 - 1
GGGACCCGCCUUGCAGCUGGGUCCAAAAAACCUAGCAGAGGCAGCAAUUCGAUCCUCAGUUAAAGUAAUCUCAGGAUUGCAGGACUUGGCGACCAAGGCUGACUCGAAAUACUGCAAAAG
.......(((((...(((((((.......))))))).))))).(((.(((((...(((((....((((((....))))))....(((((...)))))))))).)))))....)))..... ( -39.90)
>DroPse_CAF1 5462 120 - 1
GGGACCAGCCUUGCAGCUGGGCCCAAAGUAUCUCGACGAGGCCGCUAUCCGAUCCUCUGUGACCGUCAGCUCUGGAUCGCAUGUCUUGGAAACCAAAGCGGCUUCAAAAUACUGCAAAUU
(((.(((((......))))).)))..(((((......(((((((((...((((((.(((.......)))....))))))......((((...)))))))))))))...)))))....... ( -43.10)
>DroWil_CAF1 34094 120 - 1
AGGACCAGCCUUGCAACUUGGUCCAAAGAAUUUCGCUGAGGCAGCAAUGCGAUCUUCAGUUAAACUAAUCUCUGGAUCACAUGACUUGGCCACCAUGGUGGCUUCAAAGUACUAAAAAAA
.(((((((.........)))))))..........((((...)))).(((.(((((..((..........))..))))).))).((((((((((....))))))...)))).......... ( -32.80)
>DroMoj_CAF1 23218 119 - 1
AGGACCAGCUUUGCAGCUGGGUCCAAAAUACCUCGCUGAAGCCGCAAUGCGGUCUUCAGUUAAUGUAAUAUCUGGAUUGCAGGACUUUGCUACCAAGGUUGACUCGAAGUACUGCAAA-G
.(((((((((....)))).)))))....(((...(((((((((((...)))).)))))))....))).........((((((.((((((..((....)).....)))))).)))))).-. ( -43.10)
>DroPer_CAF1 5679 120 - 1
GGGACCAGCCUUGCAGCUGGGCCCAAAGUAUCUCGACGAGGCCGCUAUCCGAUCCUCUGUGACCGUCAGCUCUGGAUCGCAUGUCUUGGAAACCAAAGCGGCUUCAAAAUACUGCAAAGU
(((.(((((......))))).)))..(((((......(((((((((...((((((.(((.......)))....))))))......((((...)))))))))))))...)))))....... ( -43.10)
>consensus
AGGACCAGCCUUGCAGCUGGGUCCAAAGUACCUCGCUGAGGCCGCAAUCCGAUCCUCAGUGAAAGUAAUCUCUGGAUCGCAUGACUUGGAAACCAAGGCGGCUUCAAAAUACUGCAAAAA
.((.(((((......)))))..)).............((((((((.....(((((...(((.....)))....)))))......(((((...)))))))))))))............... (-20.27 = -21.75 +   1.48)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:57:10 2006