Locus 4360

Sequence ID 3R_DroMel_CAF1
Location 11,487,138 – 11,487,232
Length 94
Max. P 0.983553
window7129 window7130

overview

Window 9

Location 11,487,138 – 11,487,232
Length 94
Sequences 6
Columns 104
Reading direction forward
Mean pairwise identity 73.96
Mean single sequence MFE -34.80
Consensus MFE -15.44
Energy contribution -15.73
Covariance contribution 0.29
Combinations/Pair 1.21
Mean z-score -2.32
Structure conservation index 0.44
SVM decision value 1.46
SVM RNA-class probability 0.955740
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11487138 94 + 27905053
UACGGCCAACUGCAGUGUGGAAUGUGGGCUAAAAGAGGCGAACGCCU-ACCC----AUGGCAGG--GAAAUGGCC-AAGGUGGGCG--UAGUUGAGAGUUGGCU
...((((((((.(((............(((......)))..((((((-(((.----.((((...--......)))-).))))))))--)..)))..)))))))) ( -36.30)
>DroSec_CAF1 21351 88 + 1
UACGGCCAACUGCAGUGUGGAAUGUGGGCUAAAA--------CGCCU-ACCC----AUGGCAGGGCGAAAUGGCC-AAGGUGGGCG--UAGUUUAGAGUUGGCU
...(((((((((((........)))...((((((--------(((((-(((.----.((((...........)))-).))))))))--)..))))))))))))) ( -35.70)
>DroSim_CAF1 21461 96 + 1
UACGGCCAACUGCAGUGUGGAAUGUGGGCUAAAACAGGCCAACGCCU-ACCC----AUGGCAGGGGGAAAUGGCC-AAGGUGGGCG--UAGUUGAGAGUUGGCU
...((((((((.(((..(((..(((........)))..)))((((((-(((.----.((((...........)))-).))))))))--)..)))..)))))))) ( -40.30)
>DroEre_CAF1 24671 72 + 1
UACGGCCAACUGCAGUGUGGAAUGUGGGCCAAAACCGGC-----------------------------AAUGGCC-AAGGUGGGCG--UAGUUGAGAGUUGGCU
...(((((((((((........)))..(((...((((((-----------------------------....)))-..))).))).--........)))))))) ( -24.80)
>DroYak_CAF1 18635 94 + 1
UACGGCCAACUGCAGUGUGGAAUGUGGGCCAAAACGGGCGAACGCCU-ACCC----AUGGCGGG--GAAAUGGCC-AAGGUGGACG--UAGUUGAGAGCUGGCU
..(((((((((((.............(((((....((((....))))-.(((----.....)))--....)))))-..(.....))--))))))...))))... ( -32.20)
>DroAna_CAF1 109053 92 + 1
UACGGCCAGCUGCAGCGUGGAAUGUAGGCCAAAAAGGAGCACUCCCGAACCCCCAGAUGGUUGG---------CUGGAGGUUGGAGGCUGGC---UGGCUGGCU
..((((((((..((((..(((.(((...((.....)).))).)))(.((((.((((........---------)))).)))).)..))))))---))))))... ( -39.50)
>consensus
UACGGCCAACUGCAGUGUGGAAUGUGGGCCAAAACAGGC_AACGCCU_ACCC____AUGGCAGG__GAAAUGGCC_AAGGUGGGCG__UAGUUGAGAGUUGGCU
...(((((((((((........))).(((((............(((............))).........))))).....................)))))))) (-15.44 = -15.73 +   0.29)

alignment

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secondary structure

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dotplot

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Window 0

Location 11,487,138 – 11,487,232
Length 94
Sequences 6
Columns 104
Reading direction reverse
Mean pairwise identity 73.96
Mean single sequence MFE -28.55
Consensus MFE -12.36
Energy contribution -13.67
Covariance contribution 1.31
Combinations/Pair 1.35
Mean z-score -2.56
Structure conservation index 0.43
SVM decision value 1.95
SVM RNA-class probability 0.983553
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11487138 94 - 27905053
AGCCAACUCUCAACUA--CGCCCACCUU-GGCCAUUUC--CCUGCCAU----GGGU-AGGCGUUCGCCUCUUUUAGCCCACAUUCCACACUGCAGUUGGCCGUA
.(((((((.......(--((((.(((((-(((......--...)))).----))))-.)))))..((........))................))))))).... ( -27.80)
>DroSec_CAF1 21351 88 - 1
AGCCAACUCUAAACUA--CGCCCACCUU-GGCCAUUUCGCCCUGCCAU----GGGU-AGGCG--------UUUUAGCCCACAUUCCACACUGCAGUUGGCCGUA
.((((((((((((..(--((((.(((((-(((...........)))).----))))-.))))--------)))))).................))))))).... ( -28.02)
>DroSim_CAF1 21461 96 - 1
AGCCAACUCUCAACUA--CGCCCACCUU-GGCCAUUUCCCCCUGCCAU----GGGU-AGGCGUUGGCCUGUUUUAGCCCACAUUCCACACUGCAGUUGGCCGUA
.(((((((.......(--((((.(((((-(((...........)))).----))))-.))))).(((........)))...............))))))).... ( -30.60)
>DroEre_CAF1 24671 72 - 1
AGCCAACUCUCAACUA--CGCCCACCUU-GGCCAUU-----------------------------GCCGGUUUUGGCCCACAUUCCACACUGCAGUUGGCCGUA
.((((((.........--.(((......-)))...(-----------------------------((.(((..(((........))).)))))))))))).... ( -17.40)
>DroYak_CAF1 18635 94 - 1
AGCCAGCUCUCAACUA--CGUCCACCUU-GGCCAUUUC--CCCGCCAU----GGGU-AGGCGUUCGCCCGUUUUGGCCCACAUUCCACACUGCAGUUGGCCGUA
.(((((((.......(--((((.(((((-(((......--...)))).----))))-.)))))..(((......)))................))))))).... ( -28.50)
>DroAna_CAF1 109053 92 - 1
AGCCAGCCA---GCCAGCCUCCAACCUCCAG---------CCAACCAUCUGGGGGUUCGGGAGUGCUCCUUUUUGGCCUACAUUCCACGCUGCAGCUGGCCGUA
.((((((((---((.(((((((.((((((((---------........))))))))...)))).)))......(((........))).))))..)))))).... ( -39.00)
>consensus
AGCCAACUCUCAACUA__CGCCCACCUU_GGCCAUUUC__CCUGCCAU____GGGU_AGGCGUU_GCCCGUUUUAGCCCACAUUCCACACUGCAGUUGGCCGUA
.(((((((...........(((.......)))....................((((..(((....))).......))))..............))))))).... (-12.36 = -13.67 +   1.31)

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 11:27:15 2006