Locus 931

Sequence ID 3R_DroMel_CAF1
Location 3,118,094 – 3,118,257
Length 163
Max. P 0.924127
window1472 window1473 window1474

overview

Window 2

Location 3,118,094 – 3,118,196
Length 102
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 81.27
Mean single sequence MFE -32.37
Consensus MFE -25.10
Energy contribution -24.88
Covariance contribution -0.22
Combinations/Pair 1.10
Mean z-score -1.28
Structure conservation index 0.78
SVM decision value 0.13
SVM RNA-class probability 0.598034
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3118094 102 - 27905053
CAACAACUAAAUGCAACAACUCAAUUGCCUUUGCAGGUCACUUUCUGGAUGACAAUCGUCUGGAGCAUCACGCGGUUACCGGACAAGGUGAGUUGAUGGUUG------------------
...((((((.......((((((....(((((....(((.(((.((..((((.....))))..))((.....))))).)))....))))))))))).))))))------------------ ( -28.70)
>DroPse_CAF1 5346 120 - 1
AGUCCAAGUAAUGUUACAACUCAAUUGCCAUUGCAGGUCACUUUCUGGAUGACAAUCGUCUGGAGCAUCAUGCGGUGGCCGGACAAGGUGAGUUACAUGUGGCAGCAUCUGUUAAGACAG
.((((..((((((...(((.....))).)))))).(((((((.((..((((.....))))..))((.....))))))))))))).(((((.((((....))))..))))).......... ( -38.10)
>DroSim_CAF1 11050 102 - 1
CAACAACUAAAUGCAACAACUCAAUUGCCUUUGCAGGUCACUUUCUGGAUGACAAUCGUCUGGAGCAUCAUGCGGUUACCGGACAAGGUGAGUUGAUGGUUG------------------
...((((((.......((((((....(((((....(((.(((.((..((((.....))))..))((.....))))).)))....))))))))))).))))))------------------ ( -29.00)
>DroPer_CAF1 5341 120 - 1
AGUCCAAGAAAUGUUACAACUCAAUUGCCAUUGCAGGUCACUUUCUGGAUGACAAUCGUCUGGAGCAUCAUGCGGUGGCCGGACAAGGUGAGUUACAUGUGGCAGCAUCUGUUGAGACAG
.((((((((..(((((((......(..((.((((.(((((((.((..((((.....))))..))((.....))))))))).).)))))..)......)))))))...)))..)).))).. ( -40.60)
>DroEre_CAF1 5506 102 - 1
CAACAACUAAAGGCAACAACUCAAUUGCUCUUGCAGGUCACUUUCUGGAUGACAAUCGUCUGGAGCAUCACGCGGUUACCGGACAAGGUGAGUUGAUGGGUG------------------
.............((.(((((((.....((((((.(((.(((.((..((((.....))))..))((.....))))).))).).)))))))))))).))....------------------ ( -28.50)
>DroYak_CAF1 9306 104 - 1
UAACAACUAAAUGCAACAACUCAAUUGCUUUUGCAGGUCACUUUCUGGAUGACAAUCGUCUGGAGCAUCACGCGGUUACCGGACAAGGUGAGUUGAUGGGUG---GA-------------
..........((.((.(((((((..(((....)))(((.(((.((..((((.....))))..))((.....))))).)))........))))))).)).)).---..------------- ( -29.30)
>consensus
CAACAACUAAAUGCAACAACUCAAUUGCCUUUGCAGGUCACUUUCUGGAUGACAAUCGUCUGGAGCAUCACGCGGUUACCGGACAAGGUGAGUUGAUGGUUG__________________
.............((.((((((....(((.((((.(((.(((.((..((((.....))))..))((.....))))).))).).)))))))))))).))...................... (-25.10 = -24.88 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 3

Location 3,118,156 – 3,118,257
Length 101
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 81.40
Mean single sequence MFE -42.88
Consensus MFE -29.45
Energy contribution -29.32
Covariance contribution -0.13
Combinations/Pair 1.20
Mean z-score -2.85
Structure conservation index 0.69
SVM decision value 1.16
SVM RNA-class probability 0.924127
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3118156 101 + 27905053
UGACCUGCAAAGGCAAUUGAGUUGUUGCAUUUAGUUGUUGUGUGUCAGCGGAG--------------UGGCG----CCACGGCUUGGGGCAGCA-UUAGUGCUGCCCCACGGUUGUCCAU
((((.((((...((((((((((......)))))))))))))).))))..((((--------------((...----.)))((((((((((((((-....)))))))))).)))).))).. ( -42.10)
>DroSec_CAF1 5804 101 + 1
UGACCUGCAAAGGCAAUUGAGUUGUUGCAUUUAGUUGUUGUGUGUCAGCGUAG--------------UGGCG----CCACGGCUUGGGGCAGCA-UUAGUGCUGCCCCACGGUUGUCCAU
((((.((((...((((((((((......)))))))))))))).))))((((..--------------..)))----).((((((((((((((((-....)))))))))).)))))).... ( -42.30)
>DroSim_CAF1 11112 101 + 1
UGACCUGCAAAGGCAAUUGAGUUGUUGCAUUUAGUUGUUGUGUGUCAGCGUAG--------------UGGCG----CCACGGCUUGGGGCAGCA-UUAGUGCUGCCCCACGGUUGUCCAU
((((.((((...((((((((((......)))))))))))))).))))((((..--------------..)))----).((((((((((((((((-....)))))))))).)))))).... ( -42.30)
>DroPer_CAF1 5421 119 + 1
UGACCUGCAAUGGCAAUUGAGUUGUAACAUUUCUUGGACUUGCGACUUGAGACUCGCGACGAGCGAGUUGUGUAUGUCA-GCCGUGUGGCGCCGUCUAAUGCUGCCCCAUGGUUGUCCAU
.(((.((((.......(..((((((((((.....))...))))))))..)(((((((.....))))))).)))).)))(-((((((.(((((........)).))).)))))))...... ( -41.60)
>DroEre_CAF1 5568 107 + 1
UGACCUGCAAGAGCAAUUGAGUUGUUGCCUUUAGUUGUUGUGUGUCAGCGCAG--------UGGCAGUGGCG----CCACGGCUUGGGGCAGCA-UUAGUGCUGCCCCACGGUUGUCCAU
..........(..((((((((((((((((....((..((((((....))))))--------..))...))))----..))))))((((((((((-....))))))))))))))))..).. ( -47.80)
>DroYak_CAF1 9370 101 + 1
UGACCUGCAAAAGCAAUUGAGUUGUUGCAUUUAGUUGUUAUAUGUCAGCGCAG--------------UGGCG----CCACGGCUUGGGGCAGCA-UUGGUGCUGCCCCACGGUUGUCCAU
....((((....(((((......))))).....((((........))))))))--------------(((..----..((((((((((((((((-....)))))))))).))))))))). ( -41.20)
>consensus
UGACCUGCAAAGGCAAUUGAGUUGUUGCAUUUAGUUGUUGUGUGUCAGCGCAG______________UGGCG____CCACGGCUUGGGGCAGCA_UUAGUGCUGCCCCACGGUUGUCCAU
.((((.((....(((((......))))).....((((........))))....................)).............((((((((((.....)))))))))).))))...... (-29.45 = -29.32 +  -0.13)

alignment

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secondary structure

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dotplot

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Window 4

Location 3,118,156 – 3,118,257
Length 101
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 81.40
Mean single sequence MFE -33.55
Consensus MFE -22.28
Energy contribution -22.95
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.52
Structure conservation index 0.66
SVM decision value 0.92
SVM RNA-class probability 0.882140
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3118156 101 - 27905053
AUGGACAACCGUGGGGCAGCACUAA-UGCUGCCCCAAGCCGUGG----CGCCA--------------CUCCGCUGACACACAACAACUAAAUGCAACAACUCAAUUGCCUUUGCAGGUCA
((((....))))(((((((((....-)))))))))..(((((((----((...--------------...)))).))..............(((((...(......)...)))))))).. ( -31.60)
>DroSec_CAF1 5804 101 - 1
AUGGACAACCGUGGGGCAGCACUAA-UGCUGCCCCAAGCCGUGG----CGCCA--------------CUACGCUGACACACAACAACUAAAUGCAACAACUCAAUUGCCUUUGCAGGUCA
((((....))))(((((((((....-)))))))))..(((((((----((...--------------...)))).))..............(((((...(......)...)))))))).. ( -32.00)
>DroSim_CAF1 11112 101 - 1
AUGGACAACCGUGGGGCAGCACUAA-UGCUGCCCCAAGCCGUGG----CGCCA--------------CUACGCUGACACACAACAACUAAAUGCAACAACUCAAUUGCCUUUGCAGGUCA
((((....))))(((((((((....-)))))))))..(((((((----((...--------------...)))).))..............(((((...(......)...)))))))).. ( -32.00)
>DroPer_CAF1 5421 119 - 1
AUGGACAACCAUGGGGCAGCAUUAGACGGCGCCACACGGC-UGACAUACACAACUCGCUCGUCGCGAGUCUCAAGUCGCAAGUCCAAGAAAUGUUACAACUCAAUUGCCAUUGCAGGUCA
.(((((..((.((.(((.((........))))).)).)).-.(((.......((((((.....)))))).....)))....))))).((..(((.....(......).....)))..)). ( -30.10)
>DroEre_CAF1 5568 107 - 1
AUGGACAACCGUGGGGCAGCACUAA-UGCUGCCCCAAGCCGUGG----CGCCACUGCCA--------CUGCGCUGACACACAACAACUAAAGGCAACAACUCAAUUGCUCUUGCAGGUCA
((((....))))(((((((((....-)))))))))..((.((((----((....)))))--------).))...(((..............(....).......((((....))))))). ( -40.60)
>DroYak_CAF1 9370 101 - 1
AUGGACAACCGUGGGGCAGCACCAA-UGCUGCCCCAAGCCGUGG----CGCCA--------------CUGCGCUGACAUAUAACAACUAAAUGCAACAACUCAAUUGCUUUUGCAGGUCA
...(((.....((((((((((....-)))))))))).((.((((----(((..--------------..))))).))...............((((........))))....))..))). ( -35.00)
>consensus
AUGGACAACCGUGGGGCAGCACUAA_UGCUGCCCCAAGCCGUGG____CGCCA______________CUACGCUGACACACAACAACUAAAUGCAACAACUCAAUUGCCUUUGCAGGUCA
...(((.....((((((((((.....))))))))))....................................................................((((....))))))). (-22.28 = -22.95 +   0.67)

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 09:55:41 2006