Locus 333

Sequence ID 2L_DroMel_CAF1
Location 1,008,432 – 1,008,556
Length 124
Max. P 0.992194
window526 window527 window528

overview

Window 6

Location 1,008,432 – 1,008,527
Length 95
Sequences 5
Columns 108
Reading direction forward
Mean pairwise identity 80.69
Mean single sequence MFE -29.96
Consensus MFE -16.58
Energy contribution -17.86
Covariance contribution 1.28
Combinations/Pair 1.08
Mean z-score -2.03
Structure conservation index 0.55
SVM decision value 0.34
SVM RNA-class probability 0.697469
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1008432 95 + 22407834
UUGCACAU-------------UAACUGUGUGGUUAUUUCACUAGAUAAUUUGCUUUUGGCUUAGAAGCCAGGUCUCUUUGGUGAGACGAAACAAGUGGUUAUUGGCUU
..((.((.-------------(((((.(((..(..((((((((((......(((..(((((....))))))))...))))))))))..).)))...))))).)))).. ( -25.90)
>DroSec_CAF1 120180 108 + 1
UUGCACAUUUCAAGUGUGGCUUAACUGUGUGGUUAUUUCGGUAGAUAUUCUGCUUUUGGCUUAGAAGCCAGGUCUCUUUGGUGAGACGAAACAAUUGGGUGGUGGCUU
...(((((.....)))))(((..((..(.(((((.(((((((((.....))))).((((((....))))))(((((......))))))))).))))).)..))))).. ( -33.10)
>DroSim_CAF1 120754 108 + 1
UUGCACAUUUCAAGUGUGGCUUAAUUGUGUGGUUAUUUUGGUAGAUAUUUUGCAUUUGGCUUAGAAGCCAGGUCUCUUUGGUGAGACGAAACAAUUGGGUGGUGGCUU
...(((((.....)))))(((((((((((..(.(((((....)))))..)..)..((((((....))))))(((((......)))))...))))))))))........ ( -30.20)
>DroEre_CAF1 125310 97 + 1
UUGCACAUUUCAA-UGUGGCUUAACUG--UGGUUAUUUCCAUAGAUAUUUGGCUAAGGGCUU-GGAGCCAGGUCUCUGCGCUGAGACGAAACAAGUGUGA-------U
(..(((.((((..-..((((((..(((--(((......))))))......(((.....))).-.)))))).(((((......)))))))))...)))..)-------. ( -31.70)
>DroYak_CAF1 127308 106 + 1
UUGCACAUUUCAAGUGUGGAUUAACUG--UGGUUAUUUCGCUAGAUAUUUUGCUAUUGGCUUAGGAGCCAGGUCUCUUUGCUGAGACGAAACAAUUGUGUAGUGACUC
(((((((((((....(((((.((((..--..)))).)))))..............((((((....))))))(((((......)))))))))....)))))))...... ( -28.90)
>consensus
UUGCACAUUUCAAGUGUGGCUUAACUGUGUGGUUAUUUCGCUAGAUAUUUUGCUUUUGGCUUAGAAGCCAGGUCUCUUUGGUGAGACGAAACAAUUGGGUAGUGGCUU
...(((((.....)))))...(((((....)))))((((................((((((....))))))(((((......)))))))))................. (-16.58 = -17.86 +   1.28)

alignment

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secondary structure

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dotplot

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Window 7

Location 1,008,432 – 1,008,527
Length 95
Sequences 5
Columns 108
Reading direction reverse
Mean pairwise identity 80.69
Mean single sequence MFE -20.64
Consensus MFE -15.28
Energy contribution -15.68
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -2.37
Structure conservation index 0.74
SVM decision value 1.76
SVM RNA-class probability 0.975719
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1008432 95 - 22407834
AAGCCAAUAACCACUUGUUUCGUCUCACCAAAGAGACCUGGCUUCUAAGCCAAAAGCAAAUUAUCUAGUGAAAUAACCACACAGUUA-------------AUGUGCAA
..((((.((((...((((((.(((((......))))).(((((....))))).))))))........(((.......)))...))))-------------.)).)).. ( -22.80)
>DroSec_CAF1 120180 108 - 1
AAGCCACCACCCAAUUGUUUCGUCUCACCAAAGAGACCUGGCUUCUAAGCCAAAAGCAGAAUAUCUACCGAAAUAACCACACAGUUAAGCCACACUUGAAAUGUGCAA
..............((((((((((((......))))).(((((....))))).................))))))).((((...(((((.....)))))..))))... ( -22.80)
>DroSim_CAF1 120754 108 - 1
AAGCCACCACCCAAUUGUUUCGUCUCACCAAAGAGACCUGGCUUCUAAGCCAAAUGCAAAAUAUCUACCAAAAUAACCACACAAUUAAGCCACACUUGAAAUGUGCAA
..((.................(((((......))))).(((((....)))))...))......................((((.(((((.....)))))..))))... ( -18.00)
>DroEre_CAF1 125310 97 - 1
A-------UCACACUUGUUUCGUCUCAGCGCAGAGACCUGGCUCC-AAGCCCUUAGCCAAAUAUCUAUGGAAAUAACCA--CAGUUAAGCCACA-UUGAAAUGUGCAA
.-------...(((..((((((((((......))))).(((((..-....((.(((........))).))...((((..--..)))))))))..-..))))))))... ( -19.50)
>DroYak_CAF1 127308 106 - 1
GAGUCACUACACAAUUGUUUCGUCUCAGCAAAGAGACCUGGCUCCUAAGCCAAUAGCAAAAUAUCUAGCGAAAUAACCA--CAGUUAAUCCACACUUGAAAUGUGCAA
.........((((.((((((((((((......))))).(((((....))))).................))))))).((--.(((........)))))...))))... ( -20.10)
>consensus
AAGCCACCACCCAAUUGUUUCGUCUCACCAAAGAGACCUGGCUUCUAAGCCAAAAGCAAAAUAUCUACCGAAAUAACCACACAGUUAAGCCACACUUGAAAUGUGCAA
..............((((((((((((......))))).(((((....))))).................)))))))................................ (-15.28 = -15.68 +   0.40)

alignment

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secondary structure

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dotplot

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Window 8

Location 1,008,447 – 1,008,556
Length 109
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 77.23
Mean single sequence MFE -24.98
Consensus MFE -16.52
Energy contribution -17.20
Covariance contribution 0.68
Combinations/Pair 1.05
Mean z-score -2.45
Structure conservation index 0.66
SVM decision value 2.31
SVM RNA-class probability 0.992194
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1008447 109 - 22407834
CGUUCUCACCAGAGACU--------UGGUUUUU---AAGAAAGCCAAUAACCACUUGUUUCGUCUCACCAAAGAGACCUGGCUUCUAAGCCAAAAGCAAAUUAUCUAGUGAAAUAACCAC
.....((((.(((...(--------(((((((.---...)))))))).......((((((.(((((......))))).(((((....))))).))))))....))).))))......... ( -27.80)
>DroSec_CAF1 120208 109 - 1
CGGUCUCACCAGAGACU--------UGGUUUCU---CAGAAAGCCACCACCCAAUUGUUUCGUCUCACCAAAGAGACCUGGCUUCUAAGCCAAAAGCAGAAUAUCUACCGAAAUAACCAC
.((((((....))))))--------((((((..---....))))))........((((((((((((......))))).(((((....))))).................))))))).... ( -28.90)
>DroSim_CAF1 120782 109 - 1
CGAUCUCACCAGAGACU--------UGGUUUUU---CAGAAAGCCACCACCCAAUUGUUUCGUCUCACCAAAGAGACCUGGCUUCUAAGCCAAAUGCAAAAUAUCUACCAAAAUAACCAC
...((((....))))..--------(((((((.---...)))))))........((((...(((((......))))).(((((....)))))...))))..................... ( -22.10)
>DroEre_CAF1 125336 103 - 1
CCAACUCACCAGAGACA--------GCGUUUAUAAUCGGAA-------UCACACUUGUUUCGUCUCAGCGCAGAGACCUGGCUCC-AAGCCCUUAGCCAAAUAUCUAUGGAAAUAACCA-
(((.(((....)))...--------(((((......(((((-------(.......))))))....)))))(((....(((((..-........)))))....))).))).........- ( -19.80)
>DroYak_CAF1 127335 119 - 1
CGAUCUCAGCAGAUGCGUCUCACAUGCGUUUAAAAUCCGAGAGUCACUACACAAUUGUUUCGUCUCAGCAAAGAGACCUGGCUCCUAAGCCAAUAGCAAAAUAUCUAGCGAAAUAACCA-
.((((((.(.((((((((.....)))))))).....).)))).)).........((((((((((((......))))).(((((....))))).................)))))))...- ( -26.30)
>consensus
CGAUCUCACCAGAGACU________UGGUUUAU___CAGAAAGCCACCACCCAAUUGUUUCGUCUCACCAAAGAGACCUGGCUUCUAAGCCAAAAGCAAAAUAUCUACCGAAAUAACCAC
...((((....)))).......................................((((((((((((......))))).(((((....))))).................))))))).... (-16.52 = -17.20 +   0.68)

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 09:33:13 2006