Locus 4599

Sequence ID 2L_DroMel_CAF1
Location 13,173,505 – 13,173,641
Length 136
Max. P 0.935718
window7255 window7256 window7257

overview

Window 5

Location 13,173,505 – 13,173,601
Length 96
Sequences 6
Columns 96
Reading direction forward
Mean pairwise identity 84.44
Mean single sequence MFE -33.70
Consensus MFE -22.57
Energy contribution -22.63
Covariance contribution 0.06
Combinations/Pair 1.27
Mean z-score -3.10
Structure conservation index 0.67
SVM decision value 0.39
SVM RNA-class probability 0.715553
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13173505 96 + 22407834
CCCUCCUCGGUGCUGCCCGGAGCAGUGGCAUCGCCCACUGCUCCGCCGUUUAACGCAGCAAUUGUUUCAUCUGCUGCCAUUUGUACAUUAUUGGCA
.((......((((....(((((((((((......))))))))))).........((((((..((...))..)))))).....))))......)).. ( -35.90)
>DroSec_CAF1 22268 96 + 1
CCCUCCUCGGUGAUGCCCGGAGCUGUGGCAUCGCCCACUGCUCCGCCGUUUAACGCAGCAAUUGUUUCAUCUGCUGCCAUUUGUACAUUAUUGGCA
......(((((((((..((((((.((((......)))).)))))).........((((((..((...))..))))))........))))))))).. ( -32.60)
>DroSim_CAF1 14631 96 + 1
CCCUCCUCGCUGAGGCCCGGAGCUGUGGCAUCGCCCACUGCUCCGCCGUUUAACGCAGCAAUUGUUUCAUCUGCUGCCAUUUGUACAUUAUUGGCA
........((..((((..(((((.((((......)))).)))))))).......((((((..((...))..)))))).............)..)). ( -33.50)
>DroEre_CAF1 14803 96 + 1
CCCUCUUCGGUGCUUCCCGGAGCUGUGGCAUCUCCCACUGCUCCGCCGUUCAACGCAGCAAUUGUUUCAUCUGCUGCCAUUUGUACAUUAGUGGCA
.((.((...((((....((((((.((((......)))).)))))).........((((((..((...))..)))))).....))))...)).)).. ( -33.70)
>DroWil_CAF1 78192 96 + 1
CCGUUUGCCUGGCCAGCUGGGGCGACAGCAUCGCCUACAUCGCCACCAUUCAAUGCGGCUAUCGUCUCAUCGGUGGCCAUUUGUAUUGUAUUGGCA
.....((((((((......((((((.....)))))).....)))).....((((((((((((((......))))))))....))))))....)))) ( -35.30)
>DroYak_CAF1 22738 96 + 1
CCCUCCUCGUUGCUUCCCGGAGCUGCGGCAUCUCCCACAGCUCCGCCGUUCAACGCAGCAAUUGUUUCAUCUGCUGCCAUUUGUACAUUAUUGGCA
.((.....((((.....((((((((.((......)).)))))))).....))))((((((..((...))..))))))...............)).. ( -31.20)
>consensus
CCCUCCUCGGUGCUGCCCGGAGCUGUGGCAUCGCCCACUGCUCCGCCGUUCAACGCAGCAAUUGUUUCAUCUGCUGCCAUUUGUACAUUAUUGGCA
...........(((...((((((.((((......)))).))))))..((.(((.((((((..((...))..))))))...))).))......))). (-22.57 = -22.63 +   0.06)

alignment

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secondary structure

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Window 6

Location 13,173,505 – 13,173,601
Length 96
Sequences 6
Columns 96
Reading direction reverse
Mean pairwise identity 84.44
Mean single sequence MFE -36.03
Consensus MFE -25.55
Energy contribution -25.80
Covariance contribution 0.25
Combinations/Pair 1.30
Mean z-score -2.73
Structure conservation index 0.71
SVM decision value 0.37
SVM RNA-class probability 0.707612
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13173505 96 - 22407834
UGCCAAUAAUGUACAAAUGGCAGCAGAUGAAACAAUUGCUGCGUUAAACGGCGGAGCAGUGGGCGAUGCCACUGCUCCGGGCAGCACCGAGGAGGG
((((...............(((((((.((...)).))))))).........(((((((((((......)))))))))))))))...((.....)). ( -40.90)
>DroSec_CAF1 22268 96 - 1
UGCCAAUAAUGUACAAAUGGCAGCAGAUGAAACAAUUGCUGCGUUAAACGGCGGAGCAGUGGGCGAUGCCACAGCUCCGGGCAUCACCGAGGAGGG
((((...............(((((((.((...)).))))))).........((((((.((((......)))).))))))))))...((.....)). ( -35.40)
>DroSim_CAF1 14631 96 - 1
UGCCAAUAAUGUACAAAUGGCAGCAGAUGAAACAAUUGCUGCGUUAAACGGCGGAGCAGUGGGCGAUGCCACAGCUCCGGGCCUCAGCGAGGAGGG
.(((...............(((((((.((...)).)))))))(.....))))(((((.((((......)))).)))))...((((......)))). ( -35.20)
>DroEre_CAF1 14803 96 - 1
UGCCACUAAUGUACAAAUGGCAGCAGAUGAAACAAUUGCUGCGUUGAACGGCGGAGCAGUGGGAGAUGCCACAGCUCCGGGAAGCACCGAAGAGGG
(((..((..(((.(((...(((((((.((...)).))))))).))).))).((((((.((((......)))).))))))))..)))((.....)). ( -33.80)
>DroWil_CAF1 78192 96 - 1
UGCCAAUACAAUACAAAUGGCCACCGAUGAGACGAUAGCCGCAUUGAAUGGUGGCGAUGUAGGCGAUGCUGUCGCCCCAGCUGGCCAGGCAAACGG
((((.......((((..(.(((((((..((..((.....))..))...))))))).)))))(((.(.((((......))))).))).))))..... ( -31.90)
>DroYak_CAF1 22738 96 - 1
UGCCAAUAAUGUACAAAUGGCAGCAGAUGAAACAAUUGCUGCGUUGAACGGCGGAGCUGUGGGAGAUGCCGCAGCUCCGGGAAGCAACGAGGAGGG
..((...............(((((((.((...)).)))))))((((.....(((((((((((......))))))))))).....)))).....)). ( -39.00)
>consensus
UGCCAAUAAUGUACAAAUGGCAGCAGAUGAAACAAUUGCUGCGUUAAACGGCGGAGCAGUGGGCGAUGCCACAGCUCCGGGCAGCACCGAGGAGGG
((((...............(((((((.((...)).))))))).........((((((.((((......)))).))))))))))............. (-25.55 = -25.80 +   0.25)

alignment

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secondary structure

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Window 7

Location 13,173,521 – 13,173,641
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 77.17
Mean single sequence MFE -46.15
Consensus MFE -21.73
Energy contribution -22.40
Covariance contribution 0.67
Combinations/Pair 1.36
Mean z-score -2.49
Structure conservation index 0.47
SVM decision value 1.25
SVM RNA-class probability 0.935718
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13173521 120 + 22407834
CCGGAGCAGUGGCAUCGCCCACUGCUCCGCCGUUUAACGCAGCAAUUGUUUCAUCUGCUGCCAUUUGUACAUUAUUGGCAGCUGCGUCGCCGCCCAUUGACAUGGGUUCGCCGAAGCUAU
..((((((((((......))))))))))((.((.....)).))....(((((....(((((((............))))))).(((.....((((((....)))))).))).)))))... ( -48.70)
>DroVir_CAF1 17874 120 + 1
GGGGCGCUGCAGCAUCCCCAACUGCGCCGCCAUUCAGUGCCGCAAUUGUCUCAUCCGUGGACAUCUGCACAUUGUUGGCGGCAGCAUCGCCGCCCAGUGACAUGGGCUCCCCAAACCCAU
((((((.(((.(((........)))(((((((..(((((..(((..((((.((....))))))..))).))))).))))))).))).))))(((((......)))))...))........ ( -55.60)
>DroPse_CAF1 44479 120 + 1
CUGGGGCCGCUGCAUCGCCCACGGCAGCACCAUUUAAGGCCGCAAUGGUCUCAUCGGCGGCCAUCUGUACAUUAUGGGCGGCGGCAUCACCGCCCAAAGACAUGGGCUCUCCAAAACUAU
.(((((..(((((..((((((.((.....))......((((((.(((....)))..))))))............)))))))))))......(((((......))))).)))))....... ( -48.40)
>DroGri_CAF1 46289 120 + 1
GUGGCGCCGCAGCGUCUCCAACGGCUCCGCCAUUUAGCGCCGCAAUUGUCUCGUCCGUUGCCAUCUGCACAUUGUUGGCGGCCGCAUCGCCGCCCAGCGACAUCGGCUCUCCAAAACCAU
((((.((((............)))).)))).....((.((((....((((......((.((.....))))...(((((((((......)))).))))))))).)))).)).......... ( -38.30)
>DroWil_CAF1 78208 120 + 1
CUGGGGCGACAGCAUCGCCUACAUCGCCACCAUUCAAUGCGGCUAUCGUCUCAUCGGUGGCCAUUUGUAUUGUAUUGGCAGCGGCAUCGCCGCCCAAAGACAUUGGCUGACCAAAACCAU
.((((((((.....)))))......(((((((..((((((((((((((......))))))))....))))))...)))..(((((...)))))..........))))...)))....... ( -43.80)
>DroMoj_CAF1 59984 120 + 1
GCGGCGCAGCAGCAUCGCCAACGGCAGCUCCAUUCAGUGCUGCAAUUGUCUCCUCCGUGGCCAUUUGCACAUUAUUGGCAGCUGCAUCCCCGCCCAGCGACAUGGGCUCCCCGAAUCCGU
(((..((....))..)))..((((((((((((...((((.(((((..(((........)))...)))))))))..))).))))))......(((((......)))))..........))) ( -42.10)
>consensus
CUGGCGCAGCAGCAUCGCCAACGGCACCGCCAUUCAAUGCCGCAAUUGUCUCAUCCGUGGCCAUCUGCACAUUAUUGGCAGCGGCAUCGCCGCCCAGAGACAUGGGCUCCCCAAAACCAU
.(((.(((((.((...((.....)).............(((((.............)))))................)).)))))......(((((......)))))...)))....... (-21.73 = -22.40 +   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 11:22:10 2006