Locus 7273

Sequence ID 3L_DroMel_CAF1
Location 19,474,485 – 19,474,635
Length 150
Max. P 0.944868
window11822 window11823 window11824

overview

Window 2

Location 19,474,485 – 19,474,600
Length 115
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 93.62
Mean single sequence MFE -32.78
Consensus MFE -28.48
Energy contribution -28.76
Covariance contribution 0.28
Combinations/Pair 1.10
Mean z-score -1.53
Structure conservation index 0.87
SVM decision value 1.05
SVM RNA-class probability 0.906070
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19474485 115 + 23771897
AAGUUCAAUUGGUGUGACCUGCCAAUUGGCAUAAAGGAAAAGAUUUCAAAUGGCCGCCAAGUUGGCAAAAUGUUGGCCU-GUGAAA-AGUUUCCGGCGAAAAUGUCGGGAAAAUACG
..((.((((((((.......)))))))))).............(((((...(((((((.....)))........)))).-.)))))-..((((((((......))))))))...... ( -33.30)
>DroSec_CAF1 114461 116 + 1
AAGUUCAAUUGGUGUGACCUGCCAAUUGGCAUAAAGGAAAAGAUUUCAAAUGGCCGCCAAGUUGGCAAAAUGUUGGCCUCGUGGAA-AGUUUCCGGGGAAAAUGUCGGGGAAAUACG
...........((((..((((((....))).....(((((...(((((...(((((((.....)))........))))...)))))-..)))))............)))...)))). ( -31.30)
>DroSim_CAF1 114582 116 + 1
AAGUUCAAUUGGUGUGACCUGCCAAUUGGCAUAAAGGAAAAGAUUUCAAAUAGCCGCCAAGUUGGCAAAAUGUUGGCCUCGCGGAA-AGUUUCCGGGGAAAAUGUCGGGGAAAUACG
...........((((..(((((((((((((.((...(((.....)))...))...))).)))))))...(((((..(((((.(((.-...))))))))..))))).)))...)))). ( -30.50)
>DroEre_CAF1 99944 113 + 1
AAGUUCAAUUGGUGUGACCUGCCAAUUGGCAUAAAGGAAAAGAUUUCGAAUGGCCGCCAAGUUGCCAAAAUGUUGGCCU-GUGGAA-AUUUUCCGGGGAAAAUGCCGGGC--GUACG
..(((((((((((.......)))))))(((((...((((((..(((((...(((((....(((.....)))..))))).-.)))))-.)))))).......)))))))))--..... ( -33.40)
>DroYak_CAF1 152973 114 + 1
AAGUUCAAUUGGUGUGACCUGCCAAUUGGCAUAAAGGAAAAGAUUUCAAAUGGCCGCCAAGUUGGCAAAAUGUUGGCCU-GUGGAAAAGUUUCCGGGAAAAAUGCCGGGC--GUACG
..(((((((((((.......)))))))(((((...(((((...(((((...(((((((.....)))........)))).-.)))))...))))).......)))))))))--..... ( -35.40)
>consensus
AAGUUCAAUUGGUGUGACCUGCCAAUUGGCAUAAAGGAAAAGAUUUCAAAUGGCCGCCAAGUUGGCAAAAUGUUGGCCU_GUGGAA_AGUUUCCGGGGAAAAUGUCGGGCAAAUACG
..((....((((..(..((((((....))).....(((((...(((((...(((((((.....)))........))))...)))))...))))))))....)..))))......)). (-28.48 = -28.76 +   0.28)

alignment

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secondary structure

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dotplot

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Window 3

Location 19,474,485 – 19,474,600
Length 115
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 93.62
Mean single sequence MFE -26.40
Consensus MFE -21.40
Energy contribution -21.04
Covariance contribution -0.36
Combinations/Pair 1.14
Mean z-score -1.65
Structure conservation index 0.81
SVM decision value 0.61
SVM RNA-class probability 0.797830
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19474485 115 - 23771897
CGUAUUUUCCCGACAUUUUCGCCGGAAACU-UUUCAC-AGGCCAACAUUUUGCCAACUUGGCGGCCAUUUGAAAUCUUUUCCUUUAUGCCAAUUGGCAGGUCACACCAAUUGAACUU
...........(((.........(((((..-(((((.-.((((........(((.....)))))))...)))))...)))))....((((....)))).)))............... ( -26.80)
>DroSec_CAF1 114461 116 - 1
CGUAUUUCCCCGACAUUUUCCCCGGAAACU-UUCCACGAGGCCAACAUUUUGCCAACUUGGCGGCCAUUUGAAAUCUUUUCCUUUAUGCCAAUUGGCAGGUCACACCAAUUGAACUU
...........(((.........(((((.(-(((.....((((........(((.....)))))))....))))...)))))....((((....)))).)))............... ( -23.70)
>DroSim_CAF1 114582 116 - 1
CGUAUUUCCCCGACAUUUUCCCCGGAAACU-UUCCGCGAGGCCAACAUUUUGCCAACUUGGCGGCUAUUUGAAAUCUUUUCCUUUAUGCCAAUUGGCAGGUCACACCAAUUGAACUU
...........(((.....(((((((....-.)))).).))........(((((((.((((((.......(((.....))).....))))))))))))))))............... ( -25.30)
>DroEre_CAF1 99944 113 - 1
CGUAC--GCCCGGCAUUUUCCCCGGAAAAU-UUCCAC-AGGCCAACAUUUUGGCAACUUGGCGGCCAUUCGAAAUCUUUUCCUUUAUGCCAAUUGGCAGGUCACACCAAUUGAACUU
.(..(--(((.((.((((((....))))))-..))..-..(((((....))))).....))))..).(((((..............((((....))))((.....))..)))))... ( -29.30)
>DroYak_CAF1 152973 114 - 1
CGUAC--GCCCGGCAUUUUUCCCGGAAACUUUUCCAC-AGGCCAACAUUUUGCCAACUUGGCGGCCAUUUGAAAUCUUUUCCUUUAUGCCAAUUGGCAGGUCACACCAAUUGAACUU
.....--(((.(((((.......(((((..((((...-.((((........(((.....)))))))....))))...)))))...)))))....))).((.....)).......... ( -26.90)
>consensus
CGUAUUUCCCCGACAUUUUCCCCGGAAACU_UUCCAC_AGGCCAACAUUUUGCCAACUUGGCGGCCAUUUGAAAUCUUUUCCUUUAUGCCAAUUGGCAGGUCACACCAAUUGAACUU
...........(((.........(((((...(((.....((((........(((.....)))))))....)))....)))))....((((....)))).)))............... (-21.40 = -21.04 +  -0.36)

alignment

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secondary structure

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dotplot

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Window 4

Location 19,474,524 – 19,474,635
Length 111
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 92.67
Mean single sequence MFE -30.74
Consensus MFE -24.84
Energy contribution -25.04
Covariance contribution 0.20
Combinations/Pair 1.16
Mean z-score -2.01
Structure conservation index 0.81
SVM decision value 1.35
SVM RNA-class probability 0.944868
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19474524 111 + 23771897
AAGAUUUCAAAUGGCCGCCAAGUUGGCAAAAUGUUGGCCU-GUGAAA-AGUUUCCGGCGAAAAUGUCGGGAAAAUACGGUCGUGAAAUGAAAAGUGGAGGCUAUGAAAAGGGC
....(((((..(((((.(((.((..((.....))..))((-(((...-..((((((((......))))))))..)))))...............))).))))))))))..... ( -32.10)
>DroSec_CAF1 114500 112 + 1
AAGAUUUCAAAUGGCCGCCAAGUUGGCAAAAUGUUGGCCUCGUGGAA-AGUUUCCGGGGAAAAUGUCGGGGAAAUACGGUCGUGAAAUGAAAAGUGGAGGCUAUGAAAAGGGC
....(((((..(((((.(((.((..((.....))..)).(((((...-..(..((((........))))..)..)))))...............))).))))))))))..... ( -29.20)
>DroSim_CAF1 114621 112 + 1
AAGAUUUCAAAUAGCCGCCAAGUUGGCAAAAUGUUGGCCUCGCGGAA-AGUUUCCGGGGAAAAUGUCGGGGAAAUACGGUCGCGAAAUGAAAAGUGGAGGCUAUGAAAAGGGC
....(((((..(((((.(((.((..((.....))..)).((((((..-..(..((((........))))..).......)))))).........))).))))))))))..... ( -34.30)
>DroEre_CAF1 99983 109 + 1
AAGAUUUCGAAUGGCCGCCAAGUUGCCAAAAUGUUGGCCU-GUGGAA-AUUUUCCGGGGAAAAUGCCGGGC--GUACGGUUGUGAAAUGAAAAGUGGAGGCUAUGAAAAGGGC
....((((..((((((.(((..(((((((....)))))((-.((((.-....)))).)).....((((...--...))))..........))..))).))))))))))..... ( -29.90)
>DroYak_CAF1 153012 110 + 1
AAGAUUUCAAAUGGCCGCCAAGUUGGCAAAAUGUUGGCCU-GUGGAAAAGUUUCCGGGAAAAAUGCCGGGC--GUACGGUCGUGAAAUGAAAAGUGGAGGCUAUGAAAAGGGC
....(((((.((((((((((.((..((.....))..))..-.))).......(((((........))))).--...)))))))....))))).......(((.(....).))) ( -28.20)
>consensus
AAGAUUUCAAAUGGCCGCCAAGUUGGCAAAAUGUUGGCCU_GUGGAA_AGUUUCCGGGGAAAAUGUCGGGCAAAUACGGUCGUGAAAUGAAAAGUGGAGGCUAUGAAAAGGGC
....(((((..(((((.(((..((..((......(((((..(((......(((((((........)))))))..)))))))).....)).))..))).))))))))))..... (-24.84 = -25.04 +   0.20)

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 12:42:49 2006