Locus 1201

Sequence ID 2L_DroMel_CAF1
Location 3,238,793 – 3,238,991
Length 198
Max. P 0.999974
window1956 window1957 window1958 window1959 window1960

overview

Window 6

Location 3,238,793 – 3,238,912
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.83
Mean single sequence MFE -34.06
Consensus MFE -28.32
Energy contribution -27.72
Covariance contribution -0.60
Combinations/Pair 1.12
Mean z-score -1.52
Structure conservation index 0.83
SVM decision value 0.55
SVM RNA-class probability 0.779888
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3238793 119 + 22407834
AACAUAGCUGUCGAAUGAAUCGCAAAUCGAGUGAACACAAUACAAGUGGCGGAAUGCAGUUGCGUUUGCAGUCUUGUUUUUUCGCUGAGCCCAACAAUU-UCAAAUCGGAUUCAGCGAGU
((((..((((.(((((((((.(((..(((......(((.......))).)))..))).))).))))))))))..))))..((((((((..((.......-.......))..)))))))). ( -33.34)
>DroSec_CAF1 72989 120 + 1
AACACAGCUGUCGAAUGAAUCGCAAAUCGAGUGAACACAAUACAAGUGGCGGAAUGCAGUUGCGUUUGCAGUCUUGUUUUUUCGCUGAGCCCAACAAUUUUCAAAUCGGAUUCAGCGAGU
((((..((((.(((((((((.(((..(((......(((.......))).)))..))).))).))))))))))..))))..((((((((..((...............))..)))))))). ( -32.46)
>DroSim_CAF1 74680 119 + 1
AACACAGCUGUCGAAUGAAUCGCAAAUCGAGUGAACACAAUACAAGUGGCGGAAUGCAGUUGCGUUUGCAGUCUUGUUUUUUCGCUGAGCCCAACAAUU-UCAAAUCGGAUUCAGCGAGU
((((..((((.(((((((((.(((..(((......(((.......))).)))..))).))).))))))))))..))))..((((((((..((.......-.......))..)))))))). ( -32.54)
>DroEre_CAF1 69934 120 + 1
UACACAGCUGUCGAAUGGCUCGUAAAUCGAGUGAACACAAUACGAGUGGCGGAAUGCAGUUGCGUUUGCAGUCUUGUUUUUUCGCUGAGCUCAACAUUUUUCAAAUCGAAUUCAGCGAGU
......((((((((.(.(((((.....))))).).........(((((((((((.((((((((....)))).).)))..)))))))..)))).............))))...)))).... ( -32.60)
>DroYak_CAF1 68962 120 + 1
CACACAGCUGUCGAAUGCCUCGCAAAUCGAGGGAACACAAUACAAGUGUUGCAAUGCAGUUGCGUUUGCAGUCUUGUUUUUUCGCUGAGUCCAACAAUUUUCAAAUCGGAUUUAGCGAGU
.(((..((((.(((((((((((.....))))(.(((((.......))))).).........)))))))))))..)))...((((((((((((...............)))))))))))). ( -39.36)
>consensus
AACACAGCUGUCGAAUGAAUCGCAAAUCGAGUGAACACAAUACAAGUGGCGGAAUGCAGUUGCGUUUGCAGUCUUGUUUUUUCGCUGAGCCCAACAAUUUUCAAAUCGGAUUCAGCGAGU
.(((..((((.((((((...((((..(((......(((.......))).)))..))).)...))))))))))..)))...(((((((((.((...............)).))))))))). (-28.32 = -27.72 +  -0.60)

alignment

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secondary structure

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dotplot

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Window 7

Location 3,238,793 – 3,238,912
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.83
Mean single sequence MFE -31.23
Consensus MFE -28.00
Energy contribution -27.92
Covariance contribution -0.08
Combinations/Pair 1.06
Mean z-score -1.33
Structure conservation index 0.90
SVM decision value 0.69
SVM RNA-class probability 0.823664
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3238793 119 - 22407834
ACUCGCUGAAUCCGAUUUGA-AAUUGUUGGGCUCAGCGAAAAAACAAGACUGCAAACGCAACUGCAUUCCGCCACUUGUAUUGUGUUCACUCGAUUUGCGAUUCAUUCGACAGCUAUGUU
..(((((((..(((((....-....)))))..)))))))...((((((.(((..(((((((.((((..........)))))))))))...((((............))))))))).)))) ( -32.00)
>DroSec_CAF1 72989 120 - 1
ACUCGCUGAAUCCGAUUUGAAAAUUGUUGGGCUCAGCGAAAAAACAAGACUGCAAACGCAACUGCAUUCCGCCACUUGUAUUGUGUUCACUCGAUUUGCGAUUCAUUCGACAGCUGUGUU
..(((((((..(((((.(....)..)))))..)))))))......((.((.((.(((((((.((((..........))))))))))).........(((((.....))).)))).)).)) ( -31.50)
>DroSim_CAF1 74680 119 - 1
ACUCGCUGAAUCCGAUUUGA-AAUUGUUGGGCUCAGCGAAAAAACAAGACUGCAAACGCAACUGCAUUCCGCCACUUGUAUUGUGUUCACUCGAUUUGCGAUUCAUUCGACAGCUGUGUU
..(((((((..(((((....-....)))))..)))))))......((.((.((.(((((((.((((..........))))))))))).........(((((.....))).)))).)).)) ( -32.10)
>DroEre_CAF1 69934 120 - 1
ACUCGCUGAAUUCGAUUUGAAAAAUGUUGAGCUCAGCGAAAAAACAAGACUGCAAACGCAACUGCAUUCCGCCACUCGUAUUGUGUUCACUCGAUUUACGAGCCAUUCGACAGCUGUGUA
..(((((((.((((((((....)).)))))).)))))))................(((((.(((..........((((((...((......))...))))))........))).))))). ( -29.57)
>DroYak_CAF1 68962 120 - 1
ACUCGCUAAAUCCGAUUUGAAAAUUGUUGGACUCAGCGAAAAAACAAGACUGCAAACGCAACUGCAUUGCAACACUUGUAUUGUGUUCCCUCGAUUUGCGAGGCAUUCGACAGCUGUGUG
..(((((.(.((((((.(....)..)))))).).)))))................(((((.((((..((((((((.......)))))..((((.....)))))))...).))).))))). ( -31.00)
>consensus
ACUCGCUGAAUCCGAUUUGAAAAUUGUUGGGCUCAGCGAAAAAACAAGACUGCAAACGCAACUGCAUUCCGCCACUUGUAUUGUGUUCACUCGAUUUGCGAUUCAUUCGACAGCUGUGUU
..(((((((.((((((.........)))))).)))))))....(((((.(((..(((((((.((((..........)))))))))))...((((............))))))))).))). (-28.00 = -27.92 +  -0.08)

alignment

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secondary structure

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Window 8

Location 3,238,833 – 3,238,951
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.66
Mean single sequence MFE -36.61
Consensus MFE -34.26
Energy contribution -33.82
Covariance contribution -0.44
Combinations/Pair 1.21
Mean z-score -2.24
Structure conservation index 0.94
SVM decision value 3.83
SVM RNA-class probability 0.999643
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3238833 118 + 22407834
UACAAGUGGCGGAAUGCAGUUGCGUUUGCAGUCUUGUUUUUUCGCUGAGCCCAACAAUU-UCAAAUCGGAUUCAGCGAGUUUUUUCGCACUUGCUAAGUA-UUGCAGGUCCUCUGCUUGG
..((((..(.(((.((((((.(((..(((............(((((((..((.......-.......))..)))))))(......))))..))).....)-)))))..))).)..)))). ( -38.54)
>DroSec_CAF1 73029 120 + 1
UACAAGUGGCGGAAUGCAGUUGCGUUUGCAGUCUUGUUUUUUCGCUGAGCCCAACAAUUUUCAAAUCGGAUUCAGCGAGUUUUUUCGCACUUGCUAAGUUUUUGCAGAUACUCCGCUUGG
..(((((((.(...(((((..((....((((((.......((((((((..((...............))..)))))))).......).)).)))...))..)))))....).))))))). ( -36.50)
>DroSim_CAF1 74720 118 + 1
UACAAGUGGCGGAAUGCAGUUGCGUUUGCAGUCUUGUUUUUUCGCUGAGCCCAACAAUU-UCAAAUCGGAUUCAGCGAGUUUUUUCGCACUUGCUAAGUUUUUGCAGGUCCU-CGCUUGG
..(((((((((((((((((......)))))..........((((((((..((.......-.......))..))))))))...))))))((((((.........))))))...-)))))). ( -38.14)
>DroEre_CAF1 69974 120 + 1
UACGAGUGGCGGAAUGCAGUUGCGUUUGCAGUCUUGUUUUUUCGCUGAGCUCAACAUUUUUCAAAUCGAAUUCAGCGAGUUUUUUCGCACUUGCUAAGUUUUUGCGGGUUCUCCACUUGG
..(((((((.(((.(((((..((....((((((.......(((((((((.((...............)).))))))))).......).)).)))...))..)))))..))).))))))). ( -36.40)
>DroYak_CAF1 69002 120 + 1
UACAAGUGUUGCAAUGCAGUUGCGUUUGCAGUCUUGUUUUUUCGCUGAGUCCAACAAUUUUCAAAUCGGAUUUAGCGAGUUUUUUCGCACUUGCUAAGUUUUUGCGGGUUCUCUACGUGG
..(((((((((((((((....))).)))))..........((((((((((((...............)))))))))))).......)))))))........(..((.........))..) ( -33.46)
>consensus
UACAAGUGGCGGAAUGCAGUUGCGUUUGCAGUCUUGUUUUUUCGCUGAGCCCAACAAUUUUCAAAUCGGAUUCAGCGAGUUUUUUCGCACUUGCUAAGUUUUUGCAGGUCCUCCGCUUGG
..(((((((.(((.(((((..((....((((((.......(((((((((.((...............)).))))))))).......).)).)))...))..)))))..))).))))))). (-34.26 = -33.82 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 9

Location 3,238,833 – 3,238,951
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.66
Mean single sequence MFE -34.88
Consensus MFE -31.76
Energy contribution -32.00
Covariance contribution 0.24
Combinations/Pair 1.16
Mean z-score -3.59
Structure conservation index 0.91
SVM decision value 5.11
SVM RNA-class probability 0.999974
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3238833 118 - 22407834
CCAAGCAGAGGACCUGCAA-UACUUAGCAAGUGCGAAAAAACUCGCUGAAUCCGAUUUGA-AAUUGUUGGGCUCAGCGAAAAAACAAGACUGCAAACGCAACUGCAUUCCGCCACUUGUA
....((((.....))))..-......(((((((((.......(((((((..(((((....-....)))))..)))))))........((.((((........)))).)))).))))))). ( -39.40)
>DroSec_CAF1 73029 120 - 1
CCAAGCGGAGUAUCUGCAAAAACUUAGCAAGUGCGAAAAAACUCGCUGAAUCCGAUUUGAAAAUUGUUGGGCUCAGCGAAAAAACAAGACUGCAAACGCAACUGCAUUCCGCCACUUGUA
....((((.....)))).........(((((((((.......(((((((..(((((.(....)..)))))..)))))))........((.((((........)))).)))).))))))). ( -38.70)
>DroSim_CAF1 74720 118 - 1
CCAAGCG-AGGACCUGCAAAAACUUAGCAAGUGCGAAAAAACUCGCUGAAUCCGAUUUGA-AAUUGUUGGGCUCAGCGAAAAAACAAGACUGCAAACGCAACUGCAUUCCGCCACUUGUA
....(((-......))).........(((((((((.......(((((((..(((((....-....)))))..)))))))........((.((((........)))).)))).))))))). ( -35.80)
>DroEre_CAF1 69974 120 - 1
CCAAGUGGAGAACCCGCAAAAACUUAGCAAGUGCGAAAAAACUCGCUGAAUUCGAUUUGAAAAAUGUUGAGCUCAGCGAAAAAACAAGACUGCAAACGCAACUGCAUUCCGCCACUCGUA
....((((.....)))).........((.((((((.......(((((((.((((((((....)).)))))).)))))))........((.((((........)))).)))).)))).)). ( -31.90)
>DroYak_CAF1 69002 120 - 1
CCACGUAGAGAACCCGCAAAAACUUAGCAAGUGCGAAAAAACUCGCUAAAUCCGAUUUGAAAAUUGUUGGACUCAGCGAAAAAACAAGACUGCAAACGCAACUGCAUUGCAACACUUGUA
...(((.(((.............(((((.(((........))).))))).((((((.(....)..))))))))).))).....(((((..(((((..((....)).)))))...))))). ( -28.60)
>consensus
CCAAGCGGAGAACCUGCAAAAACUUAGCAAGUGCGAAAAAACUCGCUGAAUCCGAUUUGAAAAUUGUUGGGCUCAGCGAAAAAACAAGACUGCAAACGCAACUGCAUUCCGCCACUUGUA
....((((.....)))).........(((((((((.......(((((((.((((((.........)))))).)))))))........((.((((........)))).)))).))))))). (-31.76 = -32.00 +   0.24)

alignment

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secondary structure

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dotplot

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Window 0

Location 3,238,873 – 3,238,991
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 86.07
Mean single sequence MFE -27.14
Consensus MFE -21.16
Energy contribution -20.64
Covariance contribution -0.52
Combinations/Pair 1.26
Mean z-score -1.90
Structure conservation index 0.78
SVM decision value 0.73
SVM RNA-class probability 0.835967
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3238873 118 - 22407834
AUCGAACAUAAAAAAGGUGGAAGCCGUUAAACGCCUAAAUCCAAGCAGAGGACCUGCAA-UACUUAGCAAGUGCGAAAAAACUCGCUGAAUCCGAUUUGA-AAUUGUUGGGCUCAGCGAA
.(((.((.......(((((............)))))........((((.....))))..-..........)).)))......(((((((..(((((....-....)))))..))))))). ( -33.30)
>DroSec_CAF1 73069 120 - 1
AUCGAACAUAAAAAAGAUGGAAGCCCUUAAAUGCCUAAAUCCAAGCGGAGUAUCUGCAAAAACUUAGCAAGUGCGAAAAAACUCGCUGAAUCCGAUUUGAAAAUUGUUGGGCUCAGCGAA
.(((.((..........((((.((........)).....)))).((((.....)))).............)).)))......(((((((..(((((.(....)..)))))..))))))). ( -29.40)
>DroSim_CAF1 74760 102 - 1
AUCG----------------AAGCCGUUAAAUGCCUAAAUCCAAGCG-AGGACCUGCAAAAACUUAGCAAGUGCGAAAAAACUCGCUGAAUCCGAUUUGA-AAUUGUUGGGCUCAGCGAA
.(((----------------.....(((((.(((.....(((.....-.)))...))).....))))).....)))......(((((((..(((((....-....)))))..))))))). ( -25.80)
>DroEre_CAF1 70014 120 - 1
AUUGAACAUAAAAAUGCUGGAAGCCGUUAAAUGCCUAAAUCCAAGUGGAGAACCCGCAAAAACUUAGCAAGUGCGAAAAAACUCGCUGAAUUCGAUUUGAAAAAUGUUGAGCUCAGCGAA
..............(((((((((.(((...))).))...)))..((((.....))))........)))).............(((((((.((((((((....)).)))))).))))))). ( -26.10)
>DroYak_CAF1 69042 120 - 1
AUCGAACAUAAAAAAGAUGGAAACCUUUGAAUGCCUAAAUCCACGUAGAGAACCCGCAAAAACUUAGCAAGUGCGAAAAAACUCGCUAAAUCCGAUUUGAAAAUUGUUGGACUCAGCGAA
......(((...((((..(....)))))..)))..........(((.(((.............(((((.(((........))).))))).((((((.(....)..))))))))).))).. ( -21.10)
>consensus
AUCGAACAUAAAAAAGAUGGAAGCCGUUAAAUGCCUAAAUCCAAGCGGAGAACCUGCAAAAACUUAGCAAGUGCGAAAAAACUCGCUGAAUCCGAUUUGAAAAUUGUUGGGCUCAGCGAA
...............................(((..........((((.....))))....(((.....)))))).......(((((((.((((((.........)))))).))))))). (-21.16 = -20.64 +  -0.52)

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 09:56:21 2006