Locus 8596

Sequence ID 3L_DroMel_CAF1
Location 22,384,853 – 22,384,973
Length 120
Max. P 0.940488
window14081 window14082 window14083 window14084

overview

Window 1

Location 22,384,853 – 22,384,954
Length 101
Sequences 5
Columns 101
Reading direction forward
Mean pairwise identity 88.81
Mean single sequence MFE -30.44
Consensus MFE -21.16
Energy contribution -20.92
Covariance contribution -0.24
Combinations/Pair 1.13
Mean z-score -2.49
Structure conservation index 0.70
SVM decision value 0.62
SVM RNA-class probability 0.801260
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22384853 101 + 23771897
CAACAGUAACUCUUUCUUGCAGUCUUCAUAAAUUUAAUUUUUACAUGCGGCCCAAUGUCAGUGCCCUUGGUUUUGGGCCUUCCCAAGCCGCGUCUGGGCCA
..................(((........................)))((((((((((..........(((((.(((....)))))))))))).)))))). ( -22.36)
>DroSec_CAF1 35970 101 + 1
CGACCGUAACUCUUUCUUGCAGUCUUCAUAAAUUUCAUUUUUUCAUGCGGUCCAAUGUCAGUGCCCUUGGUUUUGGGCCUUCCCAACCCGCGCCUGGGCCA
.(((((((.........((.(((........))).))........)))))))........(.((((..(((.(((((....))))).....))).))))). ( -23.33)
>DroSim_CAF1 51554 101 + 1
CGACCGUAACUCUUUCUUGCAGUCUUCAUAAAUUUCAUUUUUACAUGCGGCCCAAUGUCAGUGCCCUUGGUUUUGGGCCUUCCCAACCCGCGCCUGGGCCA
.(((.((((.......)))).)))........................((((((......((((....(((..((((....))))))).)))).)))))). ( -25.70)
>DroEre_CAF1 52293 101 + 1
CGACCGUAAUUCUUUCUUGCGGUCUUCAUAAAUUCCGUUUUUACAUGCGGCCCAGUGUCAGUGGCCUUGGCUUUGGGCCUGCCCAACACGUCUCUGGGCCA
.((((((((.......))))))))........................(((((((.(...(((((....)).(((((....))))))))..).))))))). ( -39.90)
>DroYak_CAF1 52529 101 + 1
CGACCGUAAUUCUUUCUUGCGGUCUUCAUAAAUUUAAUUUUUACAUGUGGCCCAGUGUCAGGGCCCUUGGCUUUGGGCCUUGCCAGAACAUCUCUGGGCCA
.((((((((.......)))))))).......................((((((((((.((((((((........)))))))).))........)))))))) ( -40.90)
>consensus
CGACCGUAACUCUUUCUUGCAGUCUUCAUAAAUUUCAUUUUUACAUGCGGCCCAAUGUCAGUGCCCUUGGUUUUGGGCCUUCCCAACCCGCGUCUGGGCCA
.(((.((((.......)))).)))........................(((((((.(((((.....))))).)))))))..((((.........))))... (-21.16 = -20.92 +  -0.24)

alignment

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secondary structure

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dotplot

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Window 2

Location 22,384,853 – 22,384,954
Length 101
Sequences 5
Columns 101
Reading direction reverse
Mean pairwise identity 88.81
Mean single sequence MFE -30.48
Consensus MFE -23.26
Energy contribution -23.90
Covariance contribution 0.64
Combinations/Pair 1.13
Mean z-score -1.91
Structure conservation index 0.76
SVM decision value 0.67
SVM RNA-class probability 0.818467
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22384853 101 - 23771897
UGGCCCAGACGCGGCUUGGGAAGGCCCAAAACCAAGGGCACUGACAUUGGGCCGCAUGUAAAAAUUAAAUUUAUGAAGACUGCAAGAAAGAGUUACUGUUG
.....(((..((((((..(..((((((........)))).))....)..))))))......................((((.(......))))).)))... ( -27.70)
>DroSec_CAF1 35970 101 - 1
UGGCCCAGGCGCGGGUUGGGAAGGCCCAAAACCAAGGGCACUGACAUUGGACCGCAUGAAAAAAUGAAAUUUAUGAAGACUGCAAGAAAGAGUUACGGUCG
.(((((......))))).(..((((((........)))).))..)....(((((((((((.........))))))..((((.(......))))).))))). ( -26.90)
>DroSim_CAF1 51554 101 - 1
UGGCCCAGGCGCGGGUUGGGAAGGCCCAAAACCAAGGGCACUGACAUUGGGCCGCAUGUAAAAAUGAAAUUUAUGAAGACUGCAAGAAAGAGUUACGGUCG
.((((..(((.(((((..(....((((........)))).)..)).))).)))(((.((....((((...))))....))))).............)))). ( -30.20)
>DroEre_CAF1 52293 101 - 1
UGGCCCAGAGACGUGUUGGGCAGGCCCAAAGCCAAGGCCACUGACACUGGGCCGCAUGUAAAAACGGAAUUUAUGAAGACCGCAAGAAAGAAUUACGGUCG
.(((((((.(.(((((((((....))))).((....))))).).).)))))))........................(((((.((.......)).))))). ( -33.00)
>DroYak_CAF1 52529 101 - 1
UGGCCCAGAGAUGUUCUGGCAAGGCCCAAAGCCAAGGGCCCUGACACUGGGCCACAUGUAAAAAUUAAAUUUAUGAAGACCGCAAGAAAGAAUUACGGUCG
((((((((((.....))..((.(((((........))))).))...))))))))((((.............))))..(((((.((.......)).))))). ( -34.62)
>consensus
UGGCCCAGACGCGGGUUGGGAAGGCCCAAAACCAAGGGCACUGACAUUGGGCCGCAUGUAAAAAUGAAAUUUAUGAAGACUGCAAGAAAGAGUUACGGUCG
.(((((((......(((((....((((........)))).))))).)))))))........................(((((.((.......)).))))). (-23.26 = -23.90 +   0.64)

alignment

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secondary structure

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dotplot

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Window 3

Location 22,384,883 – 22,384,973
Length 90
Sequences 5
Columns 90
Reading direction forward
Mean pairwise identity 88.33
Mean single sequence MFE -27.74
Consensus MFE -20.66
Energy contribution -19.78
Covariance contribution -0.88
Combinations/Pair 1.19
Mean z-score -1.90
Structure conservation index 0.74
SVM decision value 0.51
SVM RNA-class probability 0.763676
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22384883 90 + 23771897
AAUUUAAUUUUUACAUGCGGCCCAAUGUCAGUGCCCUUGGUUUUGGGCCUUCCCAAGCCGCGUCUGGGCCAACUGGACCAACCAAAUAUG
................(((((.....(..((.((((........))))))..)...)))))(((..(.....)..)))............ ( -24.70)
>DroSec_CAF1 36000 90 + 1
AAUUUCAUUUUUUCAUGCGGUCCAAUGUCAGUGCCCUUGGUUUUGGGCCUUCCCAACCCGCGCCUGGGCCAACUGGACCAACCAAAUAUG
..................((((((..((..(.((((..(((.(((((....))))).....))).))))).))))))))........... ( -24.50)
>DroSim_CAF1 51584 90 + 1
AAUUUCAUUUUUACAUGCGGCCCAAUGUCAGUGCCCUUGGUUUUGGGCCUUCCCAACCCGCGCCUGGGCCAACUGGACCAACCAAAUAUG
.............((((.((((((......((((....(((..((((....))))))).)))).))))))...(((.....)))..)))) ( -23.00)
>DroEre_CAF1 52323 90 + 1
AAUUCCGUUUUUACAUGCGGCCCAGUGUCAGUGGCCUUGGCUUUGGGCCUGCCCAACACGUCUCUGGGCCAACUGGACCGUCCAAAUAUG
...(((((........))(((((((.(...(((((....)).(((((....))))))))..).)))))))....)))............. ( -32.00)
>DroYak_CAF1 52559 90 + 1
AAUUUAAUUUUUACAUGUGGCCCAGUGUCAGGGCCCUUGGCUUUGGGCCUUGCCAGAACAUCUCUGGGCCAACUGGACCGUCCAAAUAUG
.............((((((((((((((.((((((((........)))))))).))........)))))))...(((.....))).))))) ( -34.50)
>consensus
AAUUUCAUUUUUACAUGCGGCCCAAUGUCAGUGCCCUUGGUUUUGGGCCUUCCCAACCCGCGUCUGGGCCAACUGGACCAACCAAAUAUG
.............((((.(((((((.(((((.....))))).)))))))...............(((.((....)).)))......)))) (-20.66 = -19.78 +  -0.88)

alignment

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secondary structure

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dotplot

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Window 4

Location 22,384,883 – 22,384,973
Length 90
Sequences 5
Columns 90
Reading direction reverse
Mean pairwise identity 88.33
Mean single sequence MFE -30.56
Consensus MFE -24.42
Energy contribution -24.26
Covariance contribution -0.16
Combinations/Pair 1.15
Mean z-score -2.08
Structure conservation index 0.80
SVM decision value 1.31
SVM RNA-class probability 0.940488
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22384883 90 - 23771897
CAUAUUUGGUUGGUCCAGUUGGCCCAGACGCGGCUUGGGAAGGCCCAAAACCAAGGGCACUGACAUUGGGCCGCAUGUAAAAAUUAAAUU
...((((((((((.((....)).))....((((((..(..((((((........)))).))....)..)))))).......)))))))). ( -31.30)
>DroSec_CAF1 36000 90 - 1
CAUAUUUGGUUGGUCCAGUUGGCCCAGGCGCGGGUUGGGAAGGCCCAAAACCAAGGGCACUGACAUUGGACCGCAUGAAAAAAUGAAAUU
....(((.(((((((((((.(((((......))))).(..((((((........)))).))..)))))))))).)).))).......... ( -29.90)
>DroSim_CAF1 51584 90 - 1
CAUAUUUGGUUGGUCCAGUUGGCCCAGGCGCGGGUUGGGAAGGCCCAAAACCAAGGGCACUGACAUUGGGCCGCAUGUAAAAAUGAAAUU
(((.(((((((((((((((.(((((......))))).(..((((((........)))).))..)))))))))).)).)))).)))..... ( -28.60)
>DroEre_CAF1 52323 90 - 1
CAUAUUUGGACGGUCCAGUUGGCCCAGAGACGUGUUGGGCAGGCCCAAAGCCAAGGCCACUGACACUGGGCCGCAUGUAAAAACGGAAUU
..(((...(.(((((((((.(((((((.......)))))).((((.........)))).....)))))))))))..)))........... ( -31.90)
>DroYak_CAF1 52559 90 - 1
CAUAUUUGGACGGUCCAGUUGGCCCAGAGAUGUUCUGGCAAGGCCCAAAGCCAAGGGCCCUGACACUGGGCCACAUGUAAAAAUUAAAUU
..(((.((...((((((((.(..((((((...))))))((.(((((........))))).)).))))))))).)).)))........... ( -31.10)
>consensus
CAUAUUUGGUUGGUCCAGUUGGCCCAGACGCGGGUUGGGAAGGCCCAAAACCAAGGGCACUGACAUUGGGCCGCAUGUAAAAAUGAAAUU
...........((((((((.(.(((((.......))))).((((((........)))).))..))))))))).................. (-24.42 = -24.26 +  -0.16)

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 13:19:55 2006