Locus 1013

Sequence ID 2L_DroMel_CAF1
Location 2,898,526 – 2,898,712
Length 186
Max. P 0.999960
window1624 window1625 window1626

overview

Window 4

Location 2,898,526 – 2,898,645
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.64
Mean single sequence MFE -35.62
Consensus MFE -33.02
Energy contribution -33.74
Covariance contribution 0.72
Combinations/Pair 1.06
Mean z-score -3.33
Structure conservation index 0.93
SVM decision value 4.90
SVM RNA-class probability 0.999960
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2898526 119 - 22407834
GGGAAAUUCCUAAUUGAAA-AGGGUUAGUUCAUUUCUAUUAGCCCAAAUGUCCUGCGUGUUAUGAUUAUUCCGGGAAUAAUAAUGGAGUAAGUUAUGAUGAUUGCCAGAAUUUCCCACAA
(((((((((..........-.((((((((........)))))))).........(((.(((((((((((((((..........)))))).)))))))))...)))..))))))))).... ( -35.70)
>DroSec_CAF1 17121 119 - 1
GGGAAAUUCCUAAUUGAAA-AGGGUUAGUGCAUUUCUAUUAGCCCAAAUGUCCUGCGUGUUAUGAUUAUUCCGGGAAUAAUAAUGGAGUAAGUUAUGAUGAUUGCCAGAAUUUCCCACAA
(((((((((..........-.(((((((((......))))))))).........(((.(((((((((((((((..........)))))).)))))))))...)))..))))))))).... ( -36.30)
>DroSim_CAF1 17495 117 - 1
GGGAAAUUCCUAAUUGAAA-AGGGUUAGUGCAUUUCUAUUAGCCCAAAUGUCCUGCGUGUUAUGAUUAUUCCGGGAAUAAUAAUGGAGUAAGUUAUGAUGAUUGCCAGAAUUUCCCAC--
(((((((((..........-.(((((((((......))))))))).........(((.(((((((((((((((..........)))))).)))))))))...)))..)))))))))..-- ( -36.30)
>DroEre_CAF1 17480 119 - 1
GGGAAAUUCCCAAUUGAAA-AAGGCUAGUGCAUUUGUAUUAGCCCAAAUGUCCUGCGUGUUAUGAUUAUUCCGGGAAUAAUAAUGGAGUAAGUUAUGAUGAUUGCCAGAAUUUCCCACAA
(((((((((.(((((....-..(((((((((....)))))))))..............(((((((((((((((..........)))))).))))))))))))))...))))))))).... ( -38.70)
>DroYak_CAF1 17653 120 - 1
GGGAAAUUCCUAAUUGAAAGAAGGCUAGAGCAUUUCUACUAACCCAAAUGUCCUGCGUGUUAUGAUUAUUCCGGGAAUAAUAAUGGAGUAAGUUAUGAUGAUUGCCCGAAUUUCCCACAA
(((((((((....((....)).((((((..(((((..........)))))..)))...(((((((((((((((..........)))))).)))))))))....))).))))))))).... ( -31.10)
>consensus
GGGAAAUUCCUAAUUGAAA_AGGGUUAGUGCAUUUCUAUUAGCCCAAAUGUCCUGCGUGUUAUGAUUAUUCCGGGAAUAAUAAUGGAGUAAGUUAUGAUGAUUGCCAGAAUUUCCCACAA
(((((((((............(((((((((......))))))))).........(((.(((((((((((((((..........)))))).)))))))))...)))..))))))))).... (-33.02 = -33.74 +   0.72)

alignment

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secondary structure

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dotplot

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Window 5

Location 2,898,566 – 2,898,684
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 88.80
Mean single sequence MFE -27.30
Consensus MFE -21.42
Energy contribution -21.66
Covariance contribution 0.24
Combinations/Pair 1.14
Mean z-score -1.82
Structure conservation index 0.78
SVM decision value 0.72
SVM RNA-class probability 0.831137
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2898566 118 - 22407834
CCAAACAUUUAUUAUUCGC-UAGAAAUCAUUGAAAAUACUGGGAAAUUCCUAAUUGAAA-AGGGUUAGUUCAUUUCUAUUAGCCCAAAUGUCCUGCGUGUUAUGAUUAUUCCGGGAAUAA
...........((((((.(-..((((((((....((((((((((..(((......))).-.((((((((........)))))))).....))))).))))))))))..)))..))))))) ( -25.60)
>DroSec_CAF1 17161 115 - 1
CCAAAAA---AUUAUUCGC-CAGAAGUCAUUGAAAAUACUGGGAAAUUCCUAAUUGAAA-AGGGUUAGUGCAUUUCUAUUAGCCCAAAUGUCCUGCGUGUUAUGAUUAUUCCGGGAAUAA
.......---.((((((.(-(.((((((((....((((((((((..(((......))).-.(((((((((......))))))))).....))))).))))))))))..))).)))))))) ( -27.90)
>DroSim_CAF1 17533 115 - 1
CCAAAUA---AUUAUUCGC-UAGAAGUCAUUGAAAAUACUGGGAAAUUCCUAAUUGAAA-AGGGUUAGUGCAUUUCUAUUAGCCCAAAUGUCCUGCGUGUUAUGAUUAUUCCGGGAAUAA
.......---.((((((.(-..((((((((....((((((((((..(((......))).-.(((((((((......))))))))).....))))).))))))))))..)))..))))))) ( -26.50)
>DroEre_CAF1 17520 116 - 1
CUAACUG---AUUGUUCUCACAACAGUCAUUUGGAAUACUGGGAAAUUCCCAAUUGAAA-AAGGCUAGUGCAUUUGUAUUAGCCCAAAUGUCCUGCGUGUUAUGAUUAUUCCGGGAAUAA
.......---.(((((((((((.(((.((((((......((((.....)))).......-..(((((((((....)))))))))))))))..)))..)))...((....)).)))))))) ( -32.90)
>DroYak_CAF1 17693 116 - 1
UCAAAUG---AUUAUUCAC-CAAUGGUCAUUGAAAAUACUGGGAAAUUCCUAAUUGAAAGAAGGCUAGAGCAUUUCUACUAACCCAAAUGUCCUGCGUGUUAUGAUUAUUCCGGGAAUAA
.......---.((((((.(-((((((((((....(((((((((.....))))...........((.((..(((((..........)))))..))))))))))))))))))..)))))))) ( -23.60)
>consensus
CCAAAUA___AUUAUUCGC_CAGAAGUCAUUGAAAAUACUGGGAAAUUCCUAAUUGAAA_AGGGUUAGUGCAUUUCUAUUAGCCCAAAUGUCCUGCGUGUUAUGAUUAUUCCGGGAAUAA
...........((((((.(.....((((((....((((((((((..(((......)))...(((((((((......))))))))).....))))).))))))))))).....).)))))) (-21.42 = -21.66 +   0.24)

alignment

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secondary structure

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dotplot

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Window 6

Location 2,898,606 – 2,898,712
Length 106
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 75.07
Mean single sequence MFE -22.12
Consensus MFE -2.55
Energy contribution -1.95
Covariance contribution -0.60
Combinations/Pair 1.50
Mean z-score -1.56
Structure conservation index 0.12
SVM decision value 0.41
SVM RNA-class probability 0.723279
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2898606 106 + 22407834
AAUAGAAAUGAACUAACCCU-UUUCAAUUAGGAAUUUCCCAGUAUUUUCAAUGAUUUCUA-GCGAAUAAUAAAUGUUUGGUAGGAA------------AAACAGUGCGCAAUUAGCAAAC
....((((...(((......-((((.....))))......)))..)))).....((((((-.((((((.....)))))).))))))------------......(((.......)))... ( -15.30)
>DroSec_CAF1 17201 103 + 1
AAUAGAAAUGCACUAACCCU-UUUCAAUUAGGAAUUUCCCAGUAUUUUCAAUGACUUCUG-GCGAAUAAU---UUUUUGGUAGGAG------------AAACAGUGCACAAUCAGCAAAC
....((..((((((...(((-........)))......................((((((-.((((....---..)))).))))))------------....))))))...))....... ( -20.30)
>DroSim_CAF1 17573 103 + 1
AAUAGAAAUGCACUAACCCU-UUUCAAUUAGGAAUUUCCCAGUAUUUUCAAUGACUUCUA-GCGAAUAAU---UAUUUGGUAGGAG------------AAACAGUGCAAAAUCAGCAAAC
........((((((...(((-........)))......................((((((-.(((((...---.))))).))))))------------....))))))............ ( -20.90)
>DroEre_CAF1 17560 116 + 1
AAUACAAAUGCACUAGCCUU-UUUCAAUUGGGAAUUUCCCAGUAUUCCAAAUGACUGUUGUGAGAACAAU---CAGUUAGUGGGAAUUUGAAUUGGGAAAACUGUGCACCAUCAGCACAC
........(((((...(((.-.((((((((((.....))))))(((((...((((((((((....)))).---))))))...))))).))))..)))......)))))............ ( -36.70)
>DroYak_CAF1 17733 93 + 1
AGUAGAAAUGCUCUAGCCUUCUUUCAAUUAGGAAUUUCCCAGUAUUUUCAAUGACCAUUG-GUGAAUAAU---CAUUUGAUGGGAAUUU-----------------------CAGCCUAC
.(((((((((((......(((((......)))))......)))))))..(((..((((..-((((....)---)).)..))))..))).-----------------------....)))) ( -17.40)
>consensus
AAUAGAAAUGCACUAACCCU_UUUCAAUUAGGAAUUUCCCAGUAUUUUCAAUGACUUCUG_GCGAAUAAU___UAUUUGGUAGGAA____________AAACAGUGCACAAUCAGCAAAC
........(((((..........(((.((.(((((........))))).)))))((.(((.................))).))....................)))))............ ( -2.55 =  -1.95 +  -0.60)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:51:03 2006