Locus 4152

Sequence ID 3R_DroMel_CAF1
Location 11,321,720 – 11,321,949
Length 229
Max. P 0.997994
window6652 window6653 window6654 window6655 window6656

overview

Window 2

Location 11,321,720 – 11,321,840
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.33
Mean single sequence MFE -25.36
Consensus MFE -20.78
Energy contribution -20.66
Covariance contribution -0.12
Combinations/Pair 1.07
Mean z-score -2.45
Structure conservation index 0.82
SVM decision value 1.75
SVM RNA-class probability 0.975267
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11321720 120 + 27905053
GGAUUGGCGGUUCAAAUAAAUAAUGAAAACAAAGGGCGCAUAAAUAUUUGAAGAUCGCAAACCGAAUGAACCGAAACGACUUACGAAAGUAGGUGGGAAACAAGUGAAUUGAAAAUUAUU
.((((.((((((((..(((((((((....(....)...)))...))))))....(((.....))).))))))....(.((((((....)))))).).......)).)))).......... ( -24.40)
>DroSec_CAF1 60944 120 + 1
GGAUUGGCGGUUCAAAUAAAUAAUGAAAACAAAGGGCGCAUAAAUAUUUGAAGAUCGCAAACCGAGCGAACCGAAACGACUUACGAAAGUAGGUGGGAAACAAGUGAAUUGAAAAUUAUU
.((((.((((((((((((....(((....(....)...)))...)))))))...((((.......)))))))....(.((((((....)))))).).......)).)))).......... ( -25.70)
>DroSim_CAF1 57189 120 + 1
GGAUUGGCGGUUCAAAUAAAUAAUGAAAACAAAGGGCGCAUAAAUAUUUGAAGAUCGCAAACCGAGCGAACCGAAACGACUUACGAAAGUAGGUGGGAAACAAGUGAAUUGAAAAUUAUU
.((((.((((((((((((....(((....(....)...)))...)))))))...((((.......)))))))....(.((((((....)))))).).......)).)))).......... ( -25.70)
>DroEre_CAF1 56207 120 + 1
GGAUUCGCGAGUCAAAUAAAUAAUGAAAACAAAGGGCGCAUAAAUAUUUGAAGAUCGCAAGCCGAAUGAACCGAAACGGCUUACGAAAGUAGGUGGGAAACAAGUGAAUUGAAAAUUAUU
.(((((((((.(((((((....(((....(....)...)))...)))))))...))))..................(.((((((....)))))).).........))))).......... ( -25.90)
>DroYak_CAF1 57723 120 + 1
GGAUUCGCGGGUCAAAUAAAUAAUGAAAACAAAGGGCGCAUAAAUAUUUGAAGAUCGCAAAGCGAAUGAAUCGAAACGACUUACGAAAGUAGGUGGGAAACAAGUGAAUUGAAAAUUAUU
.(((((((((.(((((((....(((....(....)...)))...)))))))...))))....(((.....)))...(.((((((....)))))).).........))))).......... ( -25.10)
>consensus
GGAUUGGCGGUUCAAAUAAAUAAUGAAAACAAAGGGCGCAUAAAUAUUUGAAGAUCGCAAACCGAAUGAACCGAAACGACUUACGAAAGUAGGUGGGAAACAAGUGAAUUGAAAAUUAUU
((....((((.(((((((....(((....(....)...)))...)))))))...))))...)).............(.((((((....)))))).)....(((.....)))......... (-20.78 = -20.66 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 3

Location 11,321,760 – 11,321,880
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 97.33
Mean single sequence MFE -29.50
Consensus MFE -26.36
Energy contribution -25.56
Covariance contribution -0.80
Combinations/Pair 1.12
Mean z-score -2.45
Structure conservation index 0.89
SVM decision value 2.98
SVM RNA-class probability 0.997994
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11321760 120 + 27905053
UAAAUAUUUGAAGAUCGCAAACCGAAUGAACCGAAACGACUUACGAAAGUAGGUGGGAAACAAGUGAAUUGAAAAUUAUUUCCAAUUCGUUUGCUUUUCUCAUUAUAAUUGAGGCGCAAA
......((((......((((((..............(.((((((....)))))).).........(((((((((....))).))))))))))))...(((((.......)))))..)))) ( -26.40)
>DroSec_CAF1 60984 120 + 1
UAAAUAUUUGAAGAUCGCAAACCGAGCGAACCGAAACGACUUACGAAAGUAGGUGGGAAACAAGUGAAUUGAAAAUUAUUUCCAAUUCGUUUGCUUUUCUCAUUAUAAUUGAGGCGCAAA
...............(((.....((((((((.....(.((((((....)))))).).........(((((((((....))).))))))))))))))..((((.......))))))).... ( -30.60)
>DroSim_CAF1 57229 120 + 1
UAAAUAUUUGAAGAUCGCAAACCGAGCGAACCGAAACGACUUACGAAAGUAGGUGGGAAACAAGUGAAUUGAAAAUUAUUUCCAAUUCGUUUGCUUUUCUCAUUAUAAUUGAGGCGCAAA
...............(((.....((((((((.....(.((((((....)))))).).........(((((((((....))).))))))))))))))..((((.......))))))).... ( -30.60)
>DroEre_CAF1 56247 120 + 1
UAAAUAUUUGAAGAUCGCAAGCCGAAUGAACCGAAACGGCUUACGAAAGUAGGUGGGAAACAAGUGAAUUGAAAAUUAUUUCCAAUUCGUUUGCUUUUCUCAUUAUAAUUGAGGCGCAAA
................((..(((...............((((((....))))))((((((((((((((((((((....))).)))))))))))..))))))...........)))))... ( -27.90)
>DroYak_CAF1 57763 120 + 1
UAAAUAUUUGAAGAUCGCAAAGCGAAUGAAUCGAAACGACUUACGAAAGUAGGUGGGAAACAAGUGAAUUGAAAAUUAUUUCCAUUUCGUUUGCUUUUCUCAUUAUAAUUGAGGCGCAAA
...............(((((((((((((((..(((((.((((((....)))))).)....(((.....))).......))))...)))))))))))).((((.......))))))).... ( -32.00)
>consensus
UAAAUAUUUGAAGAUCGCAAACCGAAUGAACCGAAACGACUUACGAAAGUAGGUGGGAAACAAGUGAAUUGAAAAUUAUUUCCAAUUCGUUUGCUUUUCUCAUUAUAAUUGAGGCGCAAA
...............((((((.((((((((..(((((.((((((....)))))).)....(((.....))).......))))...)))))))).))).((((.......))))))).... (-26.36 = -25.56 +  -0.80)

alignment

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secondary structure

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Window 4

Location 11,321,760 – 11,321,880
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.33
Mean single sequence MFE -23.96
Consensus MFE -22.74
Energy contribution -22.86
Covariance contribution 0.12
Combinations/Pair 1.07
Mean z-score -1.54
Structure conservation index 0.95
SVM decision value 1.51
SVM RNA-class probability 0.960080
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11321760 120 - 27905053
UUUGCGCCUCAAUUAUAAUGAGAAAAGCAAACGAAUUGGAAAUAAUUUUCAAUUCACUUGUUUCCCACCUACUUUCGUAAGUCGUUUCGGUUCAUUCGGUUUGCGAUCUUCAAAUAUUUA
(((((..((((.......))))....))))).(((((((((.....)))))))))...................((((((..((............))..)))))).............. ( -23.00)
>DroSec_CAF1 60984 120 - 1
UUUGCGCCUCAAUUAUAAUGAGAAAAGCAAACGAAUUGGAAAUAAUUUUCAAUUCACUUGUUUCCCACCUACUUUCGUAAGUCGUUUCGGUUCGCUCGGUUUGCGAUCUUCAAAUAUUUA
(((((..((((.......))))....))))).(((((((((.....)))))))))...................((((((..((...((...))..))..)))))).............. ( -23.30)
>DroSim_CAF1 57229 120 - 1
UUUGCGCCUCAAUUAUAAUGAGAAAAGCAAACGAAUUGGAAAUAAUUUUCAAUUCACUUGUUUCCCACCUACUUUCGUAAGUCGUUUCGGUUCGCUCGGUUUGCGAUCUUCAAAUAUUUA
(((((..((((.......))))....))))).(((((((((.....)))))))))...................((((((..((...((...))..))..)))))).............. ( -23.30)
>DroEre_CAF1 56247 120 - 1
UUUGCGCCUCAAUUAUAAUGAGAAAAGCAAACGAAUUGGAAAUAAUUUUCAAUUCACUUGUUUCCCACCUACUUUCGUAAGCCGUUUCGGUUCAUUCGGCUUGCGAUCUUCAAAUAUUUA
(((((..((((.......))))....))))).(((((((((.....)))))))))...................((((((((((............)))))))))).............. ( -29.70)
>DroYak_CAF1 57763 120 - 1
UUUGCGCCUCAAUUAUAAUGAGAAAAGCAAACGAAAUGGAAAUAAUUUUCAAUUCACUUGUUUCCCACCUACUUUCGUAAGUCGUUUCGAUUCAUUCGCUUUGCGAUCUUCAAAUAUUUA
.((((..((((.......)))).(((((((((((...((((((((............))))))))....(((....)))..)))))).((.....))))))))))).............. ( -20.50)
>consensus
UUUGCGCCUCAAUUAUAAUGAGAAAAGCAAACGAAUUGGAAAUAAUUUUCAAUUCACUUGUUUCCCACCUACUUUCGUAAGUCGUUUCGGUUCAUUCGGUUUGCGAUCUUCAAAUAUUUA
(((((..((((.......))))....))))).(((((((((.....)))))))))...................((((((((((............)))))))))).............. (-22.74 = -22.86 +   0.12)

alignment

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secondary structure

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Window 5

Location 11,321,800 – 11,321,912
Length 112
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 93.71
Mean single sequence MFE -27.02
Consensus MFE -23.32
Energy contribution -24.12
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -1.94
Structure conservation index 0.86
SVM decision value 2.05
SVM RNA-class probability 0.986627
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11321800 112 - 27905053
AGGA------GAUACCGAUUCCGAGAUGCAGGGGCAACUUUGCGCCUCAAUUAUAAUGAGAAAAGCAAACGAAUUGGAAAUAAUUUUCAAUUCACUUGUUUCCCACCUACUUUCGUAA
.(((------((((........(((.(((((((....))))))).)))......................(((((((((.....)))))))))...)))))))............... ( -29.20)
>DroSec_CAF1 61024 112 - 1
AGGA------GAUACCGAUUCCGCGAUGCAGGGGCAACUUUGCGCCUCAAUUAUAAUGAGAAAAGCAAACGAAUUGGAAAUAAUUUUCAAUUCACUUGUUUCCCACCUACUUUCGUAA
.(((------((((........((...((((((....))))))..((((.......))))....))....(((((((((.....)))))))))...)))))))............... ( -29.20)
>DroSim_CAF1 57269 112 - 1
AGGA------GAUACCGAUUCCGCGAUGCAGGGGCAACUUUGCGCCUCAAUUAUAAUGAGAAAAGCAAACGAAUUGGAAAUAAUUUUCAAUUCACUUGUUUCCCACCUACUUUCGUAA
.(((------((((........((...((((((....))))))..((((.......))))....))....(((((((((.....)))))))))...)))))))............... ( -29.20)
>DroEre_CAF1 56287 118 - 1
UGCCGAUUCCGAUUCCGAUUCCCAGUUGCAGGGGCAACUUUGCGCCUCAAUUAUAAUGAGAAAAGCAAACGAAUUGGAAAUAAUUUUCAAUUCACUUGUUUCCCACCUACUUUCGUAA
...............(((.....(((((.(((.(((....))).)))))))).......(..((((((..(((((((((.....)))))))))..))))))..)........)))... ( -23.90)
>DroYak_CAF1 57803 109 - 1
A---------GACACCGAUUCCGAGAUGCAGGGGCAACUUUGCGCCUCAAUUAUAAUGAGAAAAGCAAACGAAAUGGAAAUAAUUUUCAAUUCACUUGUUUCCCACCUACUUUCGUAA
.---------.....(((....(((.(((((((....))))))).)))...........(..((((((..(((.(((((.....))))).)))..))))))..)........)))... ( -23.60)
>consensus
AGGA______GAUACCGAUUCCGAGAUGCAGGGGCAACUUUGCGCCUCAAUUAUAAUGAGAAAAGCAAACGAAUUGGAAAUAAUUUUCAAUUCACUUGUUUCCCACCUACUUUCGUAA
...............(((....(((.(((((((....))))))).)))...........(..((((((..(((((((((.....)))))))))..))))))..)........)))... (-23.32 = -24.12 +   0.80)

alignment

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secondary structure

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dotplot

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Window 6

Location 11,321,840 – 11,321,949
Length 109
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 88.11
Mean single sequence MFE -33.40
Consensus MFE -26.96
Energy contribution -27.32
Covariance contribution 0.36
Combinations/Pair 1.11
Mean z-score -1.66
Structure conservation index 0.81
SVM decision value 0.53
SVM RNA-class probability 0.772378
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11321840 109 - 27905053
CAGCAGUCGAAGGGGAUACCAGCUGGGUAACCGGAGG---AGGA------GAUACCGAUUCCGAGAUGCAGGGGCAACUUUGCGCCUCAAUUAUAAUGAGAAAAGCAAACGAAUUGGA
...((((((..((.....)).(((((....))((((.---.((.------....))..))))(((.(((((((....))))))).)))...............)))...)).)))).. ( -32.40)
>DroSec_CAF1 61064 112 - 1
CAGCAGUCGACGGGGAUACCAGCUGGGGAACCGGAGGAGGAGGA------GAUACCGAUUCCGCGAUGCAGGGGCAACUUUGCGCCUCAAUUAUAAUGAGAAAAGCAAACGAAUUGGA
..((.((((.(((.....))..((((....)))).((((..((.------....))..)))))))))((((((....))))))..((((.......))))....))............ ( -33.30)
>DroSim_CAF1 57309 112 - 1
CAGCAGUCGAAGGGGAUACCAGCUGGGGAACCGGAGGAGGAGGA------GAUACCGAUUCCGCGAUGCAGGGGCAACUUUGCGCCUCAAUUAUAAUGAGAAAAGCAAACGAAUUGGA
...((((((..((.....))..((((....)))).((((..((.------....))..))))((...((((((....))))))..((((.......))))....))...)).)))).. ( -33.20)
>DroEre_CAF1 56327 115 - 1
C---AGUCGAAGGGGAAACAGGCCGAGGAACCGGAGGAGAUGCCGAUUCCGAUUCCGAUUCCCAGUUGCAGGGGCAACUUUGCGCCUCAAUUAUAAUGAGAAAAGCAAACGAAUUGGA
(---(((((...(((((...((....((((.(((........))).))))....))..))))).(((((((((....))))))..((((.......))))...)))...)).)))).. ( -35.10)
>DroYak_CAF1 57843 109 - 1
CAGCAGUCGAAGGGGAAACUGGCUGAGGAACCGGAGGAGGA---------GACACCGAUUCCGAGAUGCAGGGGCAACUUUGCGCCUCAAUUAUAAUGAGAAAAGCAAACGAAAUGGA
((....(((...((....)).(((..((((.(((....(..---------..).))).))))(((.(((((((....))))))).)))...............)))...)))..)).. ( -33.00)
>consensus
CAGCAGUCGAAGGGGAUACCAGCUGGGGAACCGGAGGAGGAGGA______GAUACCGAUUCCGAGAUGCAGGGGCAACUUUGCGCCUCAAUUAUAAUGAGAAAAGCAAACGAAUUGGA
.....(((....((....))..((((....))))................))).(((((((......((((((....))))))((((((.......))))....))....))))))). (-26.96 = -27.32 +   0.36)

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 11:19:35 2006