Locus 1570

Sequence ID 3R_DroMel_CAF1
Location 4,503,047 – 4,503,207
Length 160
Max. P 0.999931
window2590 window2591 window2592 window2593

overview

Window 0

Location 4,503,047 – 4,503,167
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.67
Mean single sequence MFE -39.83
Consensus MFE -35.76
Energy contribution -37.04
Covariance contribution 1.28
Combinations/Pair 1.11
Mean z-score -1.46
Structure conservation index 0.90
SVM decision value 1.10
SVM RNA-class probability 0.915009
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4503047 120 + 27905053
UCAGUCGCCGGGGGGUCCUGCCUCAAUGUACGCCCAUUUUCUCAACAAGGCGGGCAGGCUGCUGUACGACACCAUCUUGUACCGCACCAACAACCCGGAAACCAUCCUUGUUGAGUGCGA
....((((..(((.((.(.........).)).))).....((((((((((.(((..((.(((.((((((.......)))))).))))).....)))(....)...)))))))))).)))) ( -40.80)
>DroSec_CAF1 3029 120 + 1
UCAGUCGCCGGGGGGUCCUGCCUCAAUGUACGCCCACUUUCUCAACAAGGCGGGCAGGCUGCUGUACGACACCAUCUUGUACCGCACCAACAACCCGGAAACCAUCCUUGUUGAGUGCGA
..(((.(((..((((.....)))).......((((.((((......)))).)))).))).)))((((((.......))))))(((((((((((...(((.....))))))))).))))). ( -43.30)
>DroSim_CAF1 3026 120 + 1
UCAGUCGCCGGGGGGUCCUGCCUCAAUGUACGCCCACUUUCUCAACAAGGCGGGCAGGCUGCUGUACGACACCAUCUUGUACCGCACCAACAACCCGGAAACCAUCCUUGUUGAGUGCGA
..(((.(((..((((.....)))).......((((.((((......)))).)))).))).)))((((((.......))))))(((((((((((...(((.....))))))))).))))). ( -43.30)
>DroEre_CAF1 3026 120 + 1
UCGGUCGCCGGGAGGUCCUGCCUCAAUGUACGCCCACUUCCUCAACAAGGCGGGCAGGCUUCUGUAUGACACAAUCAUGUACCGCACCAACAACCCAGAAACCAUCCUAGUUGAGUGCGA
.(((..(((..((((.....)))).......((((.(((........))).)))).)))..)))(((((.....)))))...(((((((((..................)))).))))). ( -35.57)
>DroYak_CAF1 3039 120 + 1
UCGUUCACCGGGGGGUCCUGCCUCAAUGUACGCCCACUUCCUCAACAAGGCGGGCAGGCUGCUGUACGACACAAUCUUGUACCGCACCAACAAUCCGGAAACCAUCCUAAUUGAGUGCGA
((((.(.((((((((.....))))..(((..((((.(((........))).)))).((.(((.((((((.......)))))).))))).)))..))))....((.......)).).)))) ( -36.20)
>consensus
UCAGUCGCCGGGGGGUCCUGCCUCAAUGUACGCCCACUUUCUCAACAAGGCGGGCAGGCUGCUGUACGACACCAUCUUGUACCGCACCAACAACCCGGAAACCAUCCUUGUUGAGUGCGA
..(((.(((..((((.....)))).......((((.((((......)))).)))).))).)))((((((.......))))))(((((((((((...(((.....))))))))).))))). (-35.76 = -37.04 +   1.28)

alignment

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secondary structure

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dotplot

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Window 1

Location 4,503,047 – 4,503,167
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.67
Mean single sequence MFE -47.54
Consensus MFE -45.38
Energy contribution -45.74
Covariance contribution 0.36
Combinations/Pair 1.10
Mean z-score -1.49
Structure conservation index 0.95
SVM decision value 1.76
SVM RNA-class probability 0.976002
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4503047 120 - 27905053
UCGCACUCAACAAGGAUGGUUUCCGGGUUGUUGGUGCGGUACAAGAUGGUGUCGUACAGCAGCCUGCCCGCCUUGUUGAGAAAAUGGGCGUACAUUGAGGCAGGACCCCCCGGCGACUGA
((((.((((((((((.(((....((((((((((.((((..((......))..)))))))))))))).))))))))))))).....(((.((...(((...))).)))))...)))).... ( -51.20)
>DroSec_CAF1 3029 120 - 1
UCGCACUCAACAAGGAUGGUUUCCGGGUUGUUGGUGCGGUACAAGAUGGUGUCGUACAGCAGCCUGCCCGCCUUGUUGAGAAAGUGGGCGUACAUUGAGGCAGGACCCCCCGGCGACUGA
((((.((((((((((.(((....((((((((((.((((..((......))..)))))))))))))).)))))))))))))...(.(((.((...(((...))).)).)))).)))).... ( -51.80)
>DroSim_CAF1 3026 120 - 1
UCGCACUCAACAAGGAUGGUUUCCGGGUUGUUGGUGCGGUACAAGAUGGUGUCGUACAGCAGCCUGCCCGCCUUGUUGAGAAAGUGGGCGUACAUUGAGGCAGGACCCCCCGGCGACUGA
((((.((((((((((.(((....((((((((((.((((..((......))..)))))))))))))).)))))))))))))...(.(((.((...(((...))).)).)))).)))).... ( -51.80)
>DroEre_CAF1 3026 120 - 1
UCGCACUCAACUAGGAUGGUUUCUGGGUUGUUGGUGCGGUACAUGAUUGUGUCAUACAGAAGCCUGCCCGCCUUGUUGAGGAAGUGGGCGUACAUUGAGGCAGGACCUCCCGGCGACCGA
.(((.((((((.(((..((((((((......(((..((((.....))))..)))..))))))))......))).))))))...)))(((((.....((((.....))))...))).)).. ( -41.20)
>DroYak_CAF1 3039 120 - 1
UCGCACUCAAUUAGGAUGGUUUCCGGAUUGUUGGUGCGGUACAAGAUUGUGUCGUACAGCAGCCUGCCCGCCUUGUUGAGGAAGUGGGCGUACAUUGAGGCAGGACCCCCCGGUGAACGA
((((.((((((.(((..(((....((.((((((.((((..(((....)))..)))))))))))).)))..))).))))))...)))).(((.(((((.((........))))))).))). ( -41.70)
>consensus
UCGCACUCAACAAGGAUGGUUUCCGGGUUGUUGGUGCGGUACAAGAUGGUGUCGUACAGCAGCCUGCCCGCCUUGUUGAGAAAGUGGGCGUACAUUGAGGCAGGACCCCCCGGCGACUGA
((((.((((((((((.(((....((((((((((.((((..((......))..)))))))))))))).))))))))))))).....(((.((...(((...))).)).)))..)))).... (-45.38 = -45.74 +   0.36)

alignment

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secondary structure

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dotplot

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Window 2

Location 4,503,087 – 4,503,207
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.25
Mean single sequence MFE -44.14
Consensus MFE -41.38
Energy contribution -42.34
Covariance contribution 0.96
Combinations/Pair 1.10
Mean z-score -2.60
Structure conservation index 0.94
SVM decision value 4.47
SVM RNA-class probability 0.999904
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4503087 120 + 27905053
CUCAACAAGGCGGGCAGGCUGCUGUACGACACCAUCUUGUACCGCACCAACAACCCGGAAACCAUCCUUGUUGAGUGCGAUCGGGAGGCUUCCUCGGACUUCCGACGCCAUCUUCGCACC
.(((((((((.(((..((.(((.((((((.......)))))).))))).....)))(....)...)))))))))((((((..((..(((....((((....)))).)))..)))))))). ( -47.20)
>DroSec_CAF1 3069 120 + 1
CUCAACAAGGCGGGCAGGCUGCUGUACGACACCAUCUUGUACCGCACCAACAACCCGGAAACCAUCCUUGUUGAGUGCGAUCGGGAGGCUUCCUCGGACUUCCGACGCCACCUGCGCACC
.(((((((((.(((..((.(((.((((((.......)))))).))))).....)))(....)...)))))))))(((((..((((.(((....((((....)))).))).))))))))). ( -49.60)
>DroSim_CAF1 3066 120 + 1
CUCAACAAGGCGGGCAGGCUGCUGUACGACACCAUCUUGUACCGCACCAACAACCCGGAAACCAUCCUUGUUGAGUGCGAUCGGGAGGCUUCCUCGGACUUCCGACGCCACCUGCGCACC
.(((((((((.(((..((.(((.((((((.......)))))).))))).....)))(....)...)))))))))(((((..((((.(((....((((....)))).))).))))))))). ( -49.60)
>DroEre_CAF1 3066 120 + 1
CUCAACAAGGCGGGCAGGCUUCUGUAUGACACAAUCAUGUACCGCACCAACAACCCAGAAACCAUCCUAGUUGAGUGCGAUCGGGAGGCUUCCUCGGACUUUCGACGCCACCUGCGCACU
.(((((.((((((((((....))))((((.....))))...))))............((.....)))).)))))(((((..((((.(((....((((....)))).))).))))))))). ( -34.30)
>DroYak_CAF1 3079 120 + 1
CUCAACAAGGCGGGCAGGCUGCUGUACGACACAAUCUUGUACCGCACCAACAAUCCGGAAACCAUCCUAAUUGAGUGCGAUCGGGAGGCUUCCUCGGACUUCCGACGCCACCUCCGCACU
.........(((((..((((((.((((((.......)))))).)))..........((((.((.(((..((((....))))..))))).))))((((....)))).)))...)))))... ( -40.00)
>consensus
CUCAACAAGGCGGGCAGGCUGCUGUACGACACCAUCUUGUACCGCACCAACAACCCGGAAACCAUCCUUGUUGAGUGCGAUCGGGAGGCUUCCUCGGACUUCCGACGCCACCUGCGCACC
.(((((((((.(((..((.(((.((((((.......)))))).))))).....)))(....)...)))))))))(((((..((((.(((....((((....)))).))).))))))))). (-41.38 = -42.34 +   0.96)

alignment

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secondary structure

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dotplot

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Window 3

Location 4,503,087 – 4,503,207
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.25
Mean single sequence MFE -53.94
Consensus MFE -50.94
Energy contribution -52.02
Covariance contribution 1.08
Combinations/Pair 1.05
Mean z-score -2.63
Structure conservation index 0.94
SVM decision value 4.63
SVM RNA-class probability 0.999931
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4503087 120 - 27905053
GGUGCGAAGAUGGCGUCGGAAGUCCGAGGAAGCCUCCCGAUCGCACUCAACAAGGAUGGUUUCCGGGUUGUUGGUGCGGUACAAGAUGGUGUCGUACAGCAGCCUGCCCGCCUUGUUGAG
.((((((.((.(((.((((....))))....)))))....))))))(((((((((.(((....((((((((((.((((..((......))..)))))))))))))).)))))))))))). ( -57.20)
>DroSec_CAF1 3069 120 - 1
GGUGCGCAGGUGGCGUCGGAAGUCCGAGGAAGCCUCCCGAUCGCACUCAACAAGGAUGGUUUCCGGGUUGUUGGUGCGGUACAAGAUGGUGUCGUACAGCAGCCUGCCCGCCUUGUUGAG
.(((((..((.(((.((((....))))....))).))....)))))(((((((((.(((....((((((((((.((((..((......))..)))))))))))))).)))))))))))). ( -58.70)
>DroSim_CAF1 3066 120 - 1
GGUGCGCAGGUGGCGUCGGAAGUCCGAGGAAGCCUCCCGAUCGCACUCAACAAGGAUGGUUUCCGGGUUGUUGGUGCGGUACAAGAUGGUGUCGUACAGCAGCCUGCCCGCCUUGUUGAG
.(((((..((.(((.((((....))))....))).))....)))))(((((((((.(((....((((((((((.((((..((......))..)))))))))))))).)))))))))))). ( -58.70)
>DroEre_CAF1 3066 120 - 1
AGUGCGCAGGUGGCGUCGAAAGUCCGAGGAAGCCUCCCGAUCGCACUCAACUAGGAUGGUUUCUGGGUUGUUGGUGCGGUACAUGAUUGUGUCAUACAGAAGCCUGCCCGCCUUGUUGAG
.(((((..((.(((.(((......)))....))).))....)))))(((((.(((..((((((((......(((..((((.....))))..)))..))))))))......))).))))). ( -42.70)
>DroYak_CAF1 3079 120 - 1
AGUGCGGAGGUGGCGUCGGAAGUCCGAGGAAGCCUCCCGAUCGCACUCAAUUAGGAUGGUUUCCGGAUUGUUGGUGCGGUACAAGAUUGUGUCGUACAGCAGCCUGCCCGCCUUGUUGAG
.((((((((((..(.((((....)))).)..)))))).....))))(((((.(((..(((....((.((((((.((((..(((....)))..)))))))))))).)))..))).))))). ( -52.40)
>consensus
GGUGCGCAGGUGGCGUCGGAAGUCCGAGGAAGCCUCCCGAUCGCACUCAACAAGGAUGGUUUCCGGGUUGUUGGUGCGGUACAAGAUGGUGUCGUACAGCAGCCUGCCCGCCUUGUUGAG
.(((((..((.(((.((((....))))....))).))....)))))(((((((((.(((....((((((((((.((((..((......))..)))))))))))))).)))))))))))). (-50.94 = -52.02 +   1.08)

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 10:13:48 2006