Locus 4748

Sequence ID 3R_DroMel_CAF1
Location 12,456,498 – 12,456,633
Length 135
Max. P 0.970634
window7793 window7794 window7795

overview

Window 3

Location 12,456,498 – 12,456,618
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 88.70
Mean single sequence MFE -37.40
Consensus MFE -33.84
Energy contribution -33.40
Covariance contribution -0.44
Combinations/Pair 1.12
Mean z-score -1.39
Structure conservation index 0.90
SVM decision value -0.01
SVM RNA-class probability 0.527685
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12456498 120 + 27905053
GAAUGGAUUGAAUGGACGUGAAGCACCUAUUUCUAGGCCUAGCCACUUUUUUUUCGGUGUACAUGCGUGUGUAUUGGCGAUGCCAGAGCAUAGAUAUGUACAGCAGGCAGGGGAAAUGGG
.........................(((((((((..((((.((.(((........)))(((((((..(((((.(((((...))))).)))))..))))))).))))))...))))))))) ( -38.50)
>DroSim_CAF1 4725 114 + 1
GAAUUGAUUG-----ACGUGAAGCACCUAUUUCUAGGCUUAGCCACUUUU-UUUCGGUGUACAUGCGUGUGUAUUGGCGAUGCCAGAGCAUAGAUAUGUGCAGCAGGCAGGGGAAAUGGG
..........-----..........(((((((((..((((.(((......-....)))(((((((..(((((.(((((...))))).)))))..)))))))...))))...))))))))) ( -35.60)
>DroEre_CAF1 4690 114 + 1
CACUGGAUUG-----ACAUGAAGCAUCUAUUCCUCGGCUUAGCCCCUUUU-UUCCGGUGUACAUGCGUGUGUAUUGGCGAUGCCAGAGCAUAGAUAUGUGCAGCAGGCAGGGGAAGGGGA
..(((..(((-----(...(((.......))).))))..)))((((((((-(((((.((((((((..(((((.(((((...))))).)))))..)))))))).).))..)))))))))). ( -38.10)
>consensus
GAAUGGAUUG_____ACGUGAAGCACCUAUUUCUAGGCUUAGCCACUUUU_UUUCGGUGUACAUGCGUGUGUAUUGGCGAUGCCAGAGCAUAGAUAUGUGCAGCAGGCAGGGGAAAUGGG
.........................(((((((((..((((.(((...........)))(((((((..(((((.(((((...))))).)))))..)))))))...))))...))))))))) (-33.84 = -33.40 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 4

Location 12,456,538 – 12,456,633
Length 95
Sequences 3
Columns 101
Reading direction forward
Mean pairwise identity 90.40
Mean single sequence MFE -31.10
Consensus MFE -26.98
Energy contribution -26.10
Covariance contribution -0.88
Combinations/Pair 1.10
Mean z-score -3.45
Structure conservation index 0.87
SVM decision value 1.66
SVM RNA-class probability 0.970634
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12456538 95 + 27905053
AGCCACUUUUUUUUCGGUGUACAUGCGUGUGUAUUGGCGAUGCCAGAGCAUAGAUAUGUACAGCAGGCAGGGGAAAUGGGAAUGGAA------AAGGGAAA
..((.(((((((((((.((((((((..(((((.(((((...))))).)))))..)))))))).)...((.......)).))).))))------)))))... ( -28.90)
>DroSim_CAF1 4760 100 + 1
AGCCACUUUU-UUUCGGUGUACAUGCGUGUGUAUUGGCGAUGCCAGAGCAUAGAUAUGUGCAGCAGGCAGGGGAAAUGGGAAUGGAAAAGGAAAAGGGAAA
.....(((((-(((((.((((((((..(((((.(((((...))))).)))))..)))))))).)...((.......))...........)))))))))... ( -28.60)
>DroEre_CAF1 4725 100 + 1
AGCCCCUUUU-UUCCGGUGUACAUGCGUGUGUAUUGGCGAUGCCAGAGCAUAGAUAUGUGCAGCAGGCAGGGGAAGGGGAAAUGGAAAAGGGAAAGGAAAA
..((((((((-(((((.((((((((..(((((.(((((...))))).)))))..)))))))).).))..))))))))))...................... ( -35.80)
>consensus
AGCCACUUUU_UUUCGGUGUACAUGCGUGUGUAUUGGCGAUGCCAGAGCAUAGAUAUGUGCAGCAGGCAGGGGAAAUGGGAAUGGAAAAGG_AAAGGGAAA
..(((.((((.(((((.((((((((..(((((.(((((...))))).)))))..)))))))).).)).)).)))).)))...................... (-26.98 = -26.10 +  -0.88)

alignment

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secondary structure

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dotplot

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Window 5

Location 12,456,538 – 12,456,633
Length 95
Sequences 3
Columns 101
Reading direction reverse
Mean pairwise identity 90.40
Mean single sequence MFE -16.03
Consensus MFE -15.90
Energy contribution -14.80
Covariance contribution -1.10
Combinations/Pair 1.20
Mean z-score -1.55
Structure conservation index 0.99
SVM decision value 0.93
SVM RNA-class probability 0.884935
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12456538 95 - 27905053
UUUCCCUU------UUCCAUUCCCAUUUCCCCUGCCUGCUGUACAUAUCUAUGCUCUGGCAUCGCCAAUACACACGCAUGUACACCGAAAAAAAAGUGGCU
........------..(((((....((((...(((.((((((.(((....)))...((((...))))....))).))).)))....))))....))))).. ( -13.90)
>DroSim_CAF1 4760 100 - 1
UUUCCCUUUUCCUUUUCCAUUCCCAUUUCCCCUGCCUGCUGCACAUAUCUAUGCUCUGGCAUCGCCAAUACACACGCAUGUACACCGAAA-AAAAGUGGCU
......................((((((....((((....(((........)))...))))(((....((((......))))...)))..-..)))))).. ( -14.30)
>DroEre_CAF1 4725 100 - 1
UUUUCCUUUCCCUUUUCCAUUUCCCCUUCCCCUGCCUGCUGCACAUAUCUAUGCUCUGGCAUCGCCAAUACACACGCAUGUACACCGGAA-AAAAGGGGCU
........((((((((....((((........((((....(((........)))...)))).......((((......))))....))))-)))))))).. ( -19.90)
>consensus
UUUCCCUUU_CCUUUUCCAUUCCCAUUUCCCCUGCCUGCUGCACAUAUCUAUGCUCUGGCAUCGCCAAUACACACGCAUGUACACCGAAA_AAAAGUGGCU
......................((((((....((((....(((........)))...))))(((....((((......))))...))).....)))))).. (-15.90 = -14.80 +  -1.10)

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 11:37:59 2006